From njuxuyuehua at gmail.com Sun Mar 1 07:45:15 2009 From: njuxuyuehua at gmail.com (xu yuehua) Date: Sun, 1 Mar 2009 14:45:15 +0800 Subject: [Pw_forum] the dynmaical matrix are like "***********" when the phonons calculation at gama Message-ID: hello all : i am facing unkonwn problem when i calculated the phonons at gama: the dynamical matrix file wrote: ................ Dynamical Matrix in cartesian axes q = ( 0.000000000 0.000000000 0.000000000 ) 1 1 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 1 2 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 1 3 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 1 4 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 1 5 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 1 6 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 1 7 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 1 8 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 1 9 ************ 0.00000000 ************ 0.00000000 ************ 0.00000000 ....... my phone input file : phonons at Gamma &inputph tr2_ph=1.0d-15, prefix='scf_two_b_type', epsil=.true., amass(1)=1.0, amass(2)=15.999, outdir='/disk2/xxx/xxx/espresso-3.2.3/tmp', fildyn='fourringwater.dynG', / 0.0 0.0 0.0 and my scf input file is :&CONTROL calculation = "scf", prefix = "scf_two_b_type" pseudo_dir = "/disk2/xxx/xxx/espresso-3.2.3/pseudo", outdir = "/disk2/jdong/xyh/espresso-3.2.3/tmp", / &SYSTEM ibrav = 4, a=20,b=20,c=5.60,cosab=-0.5,cosac=0,cosbc=0, nat = 24, ntyp = 2, ecutwfc =35 , ecutrho =420 / &ELECTRONS conv_thr = 1.D-9, mixing_beta = 0.2D0, / ATOMIC_SPECIES H 1.0 H.pbe-rrkjus.UPF O 15.999 O.pbe-rrkjus.UPF ATOMIC_POSITIONS { crystal } H 0.040592899 -0.047115761 0.485459003 H 0.114704004 -0.001940711 0.646569902 H 0.077728017 0.073838408 0.485209132 H 0.068286628 0.133313508 0.646050213 H -0.040592899 0.047115761 0.485459003 H -0.114704004 0.001940711 0.646569902 H -0.077728017 -0.073838408 0.485209132 H -0.068286628 -0.133313508 0.646050213 H 0.087725644 0.047173264 0.985851842 H 0.116757198 0.001980553 1.146554001 H -0.003964894 0.073814692 0.985604262 H 0.065042531 0.133450775 1.145919070 H -0.087725644 -0.047173264 0.985851842 H -0.116757198 -0.001980553 1.146554001 H 0.003964894 -0.073814692 0.985604262 H -0.065042531 -0.133450775 1.145919070 O 0.095295444 -0.003121003 0.483499312 O 0.058352838 0.111476844 0.483127474 O -0.095295444 0.003121003 0.483499312 O -0.058352838 -0.111476844 0.483127474 O 0.098444160 0.003183717 0.983638903 O 0.053053024 0.111436979 0.983231173 O -0.098444160 -0.003183717 0.983638903 O -0.053053024 -0.111436979 0.983231173 K_POINTS {automatic} 1 1 12 0 0 0 and my relax out file wrote: convergence has been achieved Forces acting on atoms (Ry/au): atom 1 type 1 force = -0.00000712 -0.00004363 0.00001631 atom 2 type 1 force = 0.00004994 0.00001718 -0.00006583 atom 3 type 1 force = 0.00001729 -0.00001573 0.00002699 atom 4 type 1 force = -0.00000656 0.00003062 0.00005285 atom 5 type 1 force = 0.00000712 0.00004363 0.00001631 atom 6 type 1 force = -0.00004994 -0.00001718 -0.00006583 atom 7 type 1 force = -0.00001729 0.00001573 0.00002699 atom 8 type 1 force = 0.00000656 -0.00003062 0.00005285 atom 9 type 1 force = -0.00000156 -0.00006167 -0.00005767 atom 10 type 1 force = 0.00001092 0.00004788 -0.00001249 atom 11 type 1 force = 0.00005214 -0.00008085 -0.00005460 atom 12 type 1 force = -0.00002474 -0.00007499 0.00003358 atom 13 type 1 force = 0.00000156 0.00006167 -0.00005767 atom 14 type 1 force = -0.00001092 -0.00004788 -0.00001249 atom 15 type 1 force = -0.00005214 0.00008085 -0.00005460 atom 16 type 1 force = 0.00002474 0.00007499 0.00003358 atom 17 type 2 force = 0.00001005 0.00004653 0.00008656 atom 18 type 2 force = 0.00001760 -0.00007784 0.00003639 atom 19 type 2 force = -0.00001005 -0.00004653 0.00008656 atom 20 type 2 force = -0.00001760 0.00007784 0.00003639 atom 21 type 2 force = 0.00002956 -0.00007076 -0.00004942 atom 22 type 2 force = -0.00000699 0.00005606 -0.00001264 atom 23 type 2 force = -0.00002956 0.00007076 -0.00004942 atom 24 type 2 force = 0.00000699 -0.00005606 -0.00001264 Total force = 0.000382 Total SCF correction = 0.000010 entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= -0.40 -0.00000194 0.00000001 0.00000000 -0.29 0.00 0.00 0.00000001 -0.00000179 0.00000000 0.00 -0.26 0.00 0.00000000 0.00000000 -0.00000434 0.00 0.00 -0.64 bfgs converged in 47 scf cycles and 45 bfgs steps End of BFGS Geometry Optimization Final energy = -274.4689566789 Ry so i think the problem is not caused by the structure relaxation. but where is the problem? i can find it . i need your help. thank you if you could give me some hints about the problem! cheers ~ the -- Xu Yuehua physics Department of Nanjing university China From quantumdft at gmail.com Sun Mar 1 09:19:06 2009 From: quantumdft at gmail.com (vega lew) Date: Sun, 1 Mar 2009 16:19:06 +0800 Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 surfaces Message-ID: <412f6c680903010019g61513ecdq9f886b8fa133ad68@mail.gmail.com> Dear all, I am planning to calculate the Oxygen vacancy properties of TiO2 surfaces. The calculation for the ideal surfaces are quite normal and the results are in line with the one that literature reported. But, when I tried to calculate the anatase 101 surface with an Oxygen vacancy (O2c was removed directly from the stoichiometric Anatase 101as described in J. Phys. Chem. C 2007, 111, 16397-16404, I encounter the problem of convergence for SCF cycle. I tried to add 20% more empty band to the system the problem still laid in. How could I overcome the problem? my input file was attached at the bottom of the mail thank you for reading. Any hints will be appreciated. vega &CONTROL title = 'Anatase 101 1x3' , calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/tmp/' , wfcdir = '/tmp/' , pseudo_dir = '/home/vega/espresso-4.0/pseudo/' , prefix = 'Anatase 101 1x3' , disk_io = 'none' , nstep = 1000 , / &SYSTEM ibrav = 8, celldm(1) =19.3269, celldm(2) = 1.1094, celldm(3) = 1.7450, nat = 71, ntyp = 2, nosym = .true. , ecutwfc = 30, ecutrho = 300, / &ELECTRONS / &IONS ion_dynamics = 'bfgs' , / ATOMIC_SPECIES Ti 47.86700 Ti.pw91-sp-van_ak.UPF O 15.99940 O.pw91-van_ak.UPF ATOMIC_POSITIONS crystal Ti 0.79001 0.05515 0.04075 0 0 0 Ti 0.92677 0.05515 0.23765 1 1 1 Ti 0.29001 0.22181 0.04075 0 0 0 Ti 0.42677 0.22181 0.23765 1 1 1 Ti 0.57420 0.22181 0.08998 0 0 0 Ti 0.71096 0.22181 0.28687 1 1 1 Ti 0.07420 0.05515 0.08998 0 0 0 Ti 0.21096 0.05515 0.28687 1 1 1 O 0.61134 0.05515 0.08150 0 0 0 O 0.74810 0.05515 0.27840 1 1 1 O 0.11134 0.22181 0.08150 0 0 0 O 0.24810 0.22181 0.27840 1 1 1 O 0.39553 0.22181 0.13073 0 0 0 O 0.53229 0.22181 0.32763 1 1 1 O 0.89553 0.05515 0.13073 0 0 0 O 0.03229 0.05515 0.32763 1 1 1 O 0.25286 0.05515 0.04922 0 0 0 O 0.38962 0.05515 0.24612 1 1 1 O 0.75286 0.22181 0.04922 0 0 0 O 0.88962 0.22181 0.24612 1 1 1 O 0.46867 0.22181 0.00000 0 0 0 O 0.60543 0.22181 0.19690 1 1 1 O 0.96867 0.05515 0.00000 0 0 0 O 0.10543 0.05515 0.19690 1 1 1 Ti 0.79001 0.38848 0.04075 0 0 0 Ti 0.92677 0.38848 0.23765 1 1 1 Ti 0.29001 0.55515 0.04075 0 0 0 Ti 0.42677 0.55515 0.23765 1 1 1 Ti 0.57420 0.55515 0.08998 0 0 0 Ti 0.71096 0.55515 0.28687 1 1 1 Ti 0.07420 0.38848 0.08998 0 0 0 Ti 0.21096 0.38848 0.28687 1 1 1 O 0.61134 0.38848 0.08150 0 0 0 O 0.74810 0.38848 0.27840 1 1 1 O 0.11134 0.55515 0.08150 0 0 0 O 0.24810 0.55515 0.27840 1 1 1 O 0.39553 0.55515 0.13073 0 0 0 #O 0.53229 0.55515 0.32763 1 1 1 O 0.89553 0.38848 0.13073 0 0 0 O 0.03229 0.38848 0.32763 1 1 1 O 0.25286 0.38848 0.04922 0 0 0 O 0.38962 0.38848 0.24612 1 1 1 O 0.75286 0.55515 0.04922 0 0 0 O 0.88962 0.55515 0.24612 1 1 1 O 0.46867 0.55515 0.00000 0 0 0 O 0.60543 0.55515 0.19690 1 1 1 O 0.96867 0.38848 0.00000 0 0 0 O 0.10543 0.38848 0.19690 1 1 1 Ti 0.79001 0.72181 0.04075 0 0 0 Ti 0.92677 0.72181 0.23765 1 1 1 Ti 0.29001 0.88848 0.04075 0 0 0 Ti 0.42677 0.88848 0.23765 1 1 1 Ti 0.57420 0.88848 0.08998 0 0 0 Ti 0.71096 0.88848 0.28687 1 1 1 Ti 0.07420 0.72181 0.08998 0 0 0 Ti 0.21096 0.72181 0.28687 1 1 1 O 0.61134 0.72181 0.08150 0 0 0 O 0.74810 0.72181 0.27840 1 1 1 O 0.11134 0.88848 0.08150 0 0 0 O 0.24810 0.88848 0.27840 1 1 1 O 0.39553 0.88848 0.13073 0 0 0 O 0.53229 0.88848 0.32763 1 1 1 O 0.89553 0.72181 0.13073 0 0 0 O 0.03229 0.72181 0.32763 1 1 1 O 0.25286 0.72181 0.04922 0 0 0 O 0.38962 0.72181 0.24612 1 1 1 O 0.75286 0.88848 0.04922 0 0 0 O 0.88962 0.88848 0.24612 1 1 1 O 0.46867 0.88848 0.00000 0 0 0 O 0.60543 0.88848 0.19690 1 1 1 O 0.96867 0.72181 0.00000 0 0 0 O 0.10543 0.72181 0.19690 1 1 1 K_POINTS gamma -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090301/3b648290/attachment.htm From ari.p.seitsonen at iki.fi Sun Mar 1 10:08:11 2009 From: ari.p.seitsonen at iki.fi (Ari Paavo Seitsonen) Date: Sun, 1 Mar 2009 10:08:11 +0100 (CET) Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 surfaces In-Reply-To: <412f6c680903010019g61513ecdq9f886b8fa133ad68@mail.gmail.com> References: <412f6c680903010019g61513ecdq9f886b8fa133ad68@mail.gmail.com> Message-ID: Dear Vega, Just my guesses and suggestions: One could try mixing of the density, like &electrons mixing_beta = 0.7 / (or a value even smaller than 0.7, or some other parametres for the mixing) since with a defect you might now have defect levels in the band gap, leading to a more difficult a convergence. Eventually one could also switch on the broadening of the occupation numbers, eventually switching it off for the physical/production jobs, but just to check if the problem in convergence comes due to this. And in the original paper the authors discuss spin-polarisation, one might test also this (nspin = 2), with different initial magnetisations [starting_magnetization(xx) = ...] for the atoms surrounding the defect. Greetings, apsi On Sun, 1 Mar 2009, vega lew wrote: > Dear all, > > I am planning to calculate the Oxygen vacancy properties of TiO2 surfaces. > The calculation for the ideal surfaces are quite normal and the results are > in line with the one that literature reported. But, when I tried to > calculate the anatase 101 surface with an Oxygen vacancy (O2c was removed > directly from the stoichiometric Anatase 101as described in J. Phys. Chem. C > 2007, 111, 16397-16404, I encounter the problem of convergence for SCF > cycle. I tried to add 20% more empty band to the system the problem still > laid in. How could I overcome the problem? > > my input file was attached at the bottom of the mail > > thank you for reading. Any hints will be appreciated. > > vega > ... > > &SYSTEM > ibrav = 8, > celldm(1) =19.3269, > celldm(2) = 1.1094, > celldm(3) = 1.7450, > nat = 71, > ntyp = 2, > nosym = .true., > ecutwfc = 30, > ecutrho = 300, > / > > &ELECTRONS > > / > > &IONS > ion_dynamics = 'bfgs', > / > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ IMPMC, CNRS & Universit? Pierre et Marie Curie Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 From quantumdft at gmail.com Sun Mar 1 12:44:20 2009 From: quantumdft at gmail.com (vega lew) Date: Sun, 1 Mar 2009 19:44:20 +0800 Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 surfaces In-Reply-To: References: <412f6c680903010019g61513ecdq9f886b8fa133ad68@mail.gmail.com> Message-ID: <412f6c680903010344x6bbe9104ld31da568076bc3a0@mail.gmail.com> Dear APSI thank you for you suggestions to me. I will try it ASAP. vega On Sun, Mar 1, 2009 at 5:08 PM, Ari Paavo Seitsonen wrote: > > Dear Vega, > > Just my guesses and suggestions: One could try mixing of the density, like > > &electrons > mixing_beta = 0.7 > / > > (or a value even smaller than 0.7, or some other parametres for the mixing) > since with a defect you might now have defect levels in the band gap, > leading to a more difficult a convergence. Eventually one could also switch > on the broadening of the occupation numbers, eventually switching it off for > the physical/production jobs, but just to check if the problem in > convergence comes due to this. > > And in the original paper the authors discuss spin-polarisation, one might > test also this (nspin = 2), with different initial magnetisations > [starting_magnetization(xx) = ...] for the atoms surrounding the defect. > > Greetings, > > apsi > > > On Sun, 1 Mar 2009, vega lew wrote: > > Dear all, >> >> I am planning to calculate the Oxygen vacancy properties of TiO2 surfaces. >> The calculation for the ideal surfaces are quite normal and the results >> are >> in line with the one that literature reported. But, when I tried to >> calculate the anatase 101 surface with an Oxygen vacancy (O2c was removed >> directly from the stoichiometric Anatase 101as described in J. Phys. Chem. >> C >> 2007, 111, 16397-16404, I encounter the problem of convergence for SCF >> cycle. I tried to add 20% more empty band to the system the problem still >> laid in. How could I overcome the problem? >> >> my input file was attached at the bottom of the mail >> >> thank you for reading. Any hints will be appreciated. >> >> vega >> >> > ... > > > >> &SYSTEM >> ibrav = 8, >> celldm(1) =19.3269, >> celldm(2) = 1.1094, >> celldm(3) = 1.7450, >> nat = 71, >> ntyp = 2, >> nosym = .true., >> ecutwfc = 30, >> ecutrho = 300, >> / >> >> &ELECTRONS >> >> / >> >> &IONS >> ion_dynamics = 'bfgs', >> / >> >> > -- > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > IMPMC, CNRS & Universit? Pierre et Marie Curie > Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090301/30d4dd5c/attachment-0001.htm From quantumdft at gmail.com Sun Mar 1 13:09:06 2009 From: quantumdft at gmail.com (vega lew) Date: Sun, 1 Mar 2009 20:09:06 +0800 Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 surfaces In-Reply-To: <412f6c680903010344x6bbe9104ld31da568076bc3a0@mail.gmail.com> References: <412f6c680903010019g61513ecdq9f886b8fa133ad68@mail.gmail.com> <412f6c680903010344x6bbe9104ld31da568076bc3a0@mail.gmail.com> Message-ID: <412f6c680903010409x68898db2k3c07be9871b767a9@mail.gmail.com> Dear friend, I found there is few supporting materials decribing what the exact meaning for mixing_beta. do you think the following paragraph from the manual of Materials Studio is suitable for this parameters? ------------------------------------------------ SCF tab Electronic minimizer: Specify the electronic minimization method to be used for the SCF calculation. Two options are available, Density Mixing and All Bands/EDFT. Tip. The Density Mixing option is recommended, particularly for variable occupancy calculations. The All Bands/EDFT method is usually slower and requires more memory. However, the EDFT scheme is recommended for metallic systems where converging electronic structure using Density Mixing option proves problematic. Charge: Specify the amplitude for charge density mixing (i.e., the amplitude of the output charge density to mix with the input charge density to obtain input for the next iteration). Note. This option is enabled only if the Density Mixing minimization method is selected. Spin: Specify the amplitude for spin density mixing, i.e. the amplitude of the output spin density to mix with the input spin density to obtain input for the next iteration. Note. This option in enabled only for spin-polarized calculations using the Density Mixing minimization method. ------------------------------------------------- Shoul I consider the mixing_mode option in PWSCF is equal to Density Mixing option in MS, and value of mixing_bate in PWSCF is equal to the one of Charge in MS? Do you think I should swich on the boardening by 'occupations', 'degauss' and 'smearing' command in PWSCF? I also found no detail description for this three options. do you think the following text suitable for the three command in PWSCF? ----------------------------- SCF tab Smearing: Specify the broadening to be applied to the electronic occupation. Note. This option is enabled only for variable occupancy calculations. ----------------------------- If the answer is no, could you please give me some suggestion to understanding the command and make a better use of it. thank you so much for reading best wishes, vega On Sun, Mar 1, 2009 at 7:44 PM, vega lew wrote: > Dear APSI > > thank you for you suggestions to me. > > I will try it ASAP. > > vega > > On Sun, Mar 1, 2009 at 5:08 PM, Ari Paavo Seitsonen < > ari.p.seitsonen at iki.fi> wrote: > >> >> Dear Vega, >> >> Just my guesses and suggestions: One could try mixing of the density, >> like >> >> &electrons >> mixing_beta = 0.7 >> / >> >> (or a value even smaller than 0.7, or some other parametres for the >> mixing) since with a defect you might now have defect levels in the band >> gap, leading to a more difficult a convergence. Eventually one could also >> switch on the broadening of the occupation numbers, eventually switching it >> off for the physical/production jobs, but just to check if the problem in >> convergence comes due to this. >> >> And in the original paper the authors discuss spin-polarisation, one >> might test also this (nspin = 2), with different initial magnetisations >> [starting_magnetization(xx) = ...] for the atoms surrounding the defect. >> >> Greetings, >> >> apsi >> >> >> On Sun, 1 Mar 2009, vega lew wrote: >> >> Dear all, >>> >>> I am planning to calculate the Oxygen vacancy properties of TiO2 >>> surfaces. >>> The calculation for the ideal surfaces are quite normal and the results >>> are >>> in line with the one that literature reported. But, when I tried to >>> calculate the anatase 101 surface with an Oxygen vacancy (O2c was removed >>> directly from the stoichiometric Anatase 101as described in J. Phys. >>> Chem. C >>> 2007, 111, 16397-16404, I encounter the problem of convergence for SCF >>> cycle. I tried to add 20% more empty band to the system the problem >>> still >>> laid in. How could I overcome the problem? >>> >>> my input file was attached at the bottom of the mail >>> >>> thank you for reading. Any hints will be appreciated. >>> >>> vega >>> >>> >> ... >> >> >> >>> &SYSTEM >>> ibrav = 8, >>> celldm(1) =19.3269, >>> celldm(2) = 1.1094, >>> celldm(3) = 1.7450, >>> nat = 71, >>> ntyp = 2, >>> nosym = .true., >>> ecutwfc = 30, >>> ecutrho = 300, >>> / >>> >>> &ELECTRONS >>> >>> / >>> >>> &IONS >>> ion_dynamics = 'bfgs', >>> / >>> >>> >> -- >> >> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- >> Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ >> IMPMC, CNRS & Universit? Pierre et Marie Curie >> Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ****************************************************************************************************************** > > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090301/159807f2/attachment.htm From lanhaiping at gmail.com Sun Mar 1 13:20:58 2009 From: lanhaiping at gmail.com (lan haiping) Date: Sun, 1 Mar 2009 20:20:58 +0800 Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 surfaces In-Reply-To: <412f6c680903010409x68898db2k3c07be9871b767a9@mail.gmail.com> References: <412f6c680903010019g61513ecdq9f886b8fa133ad68@mail.gmail.com> <412f6c680903010344x6bbe9104ld31da568076bc3a0@mail.gmail.com> <412f6c680903010409x68898db2k3c07be9871b767a9@mail.gmail.com> Message-ID: Hi, Weijia, In fact, you can have a look at mix_rho.f90 for detailed agorithms used in QE package for density mixing scheme . The scheme is just modified Broyden's method for charge density mixing , please see D.D. Johnson PRB 38, 12807 (1988). regards, On Sun, Mar 1, 2009 at 8:09 PM, vega lew wrote: > Dear friend, > > I found there is few supporting materials decribing what the exact meaning > for mixing_beta. do you think the following paragraph from the manual of > Materials Studio is suitable for this parameters? > > ------------------------------------------------ > > Electronic minimizer: Specify the electronic minimization method to be > used for the SCF calculation. Two options are available, Density Mixingand All > Bands/EDFT. > > Tip. The Density Mixing option is recommended, particularly for variable > occupancy calculations. The All Bands/EDFT method is usually slower and > requires more memory. However, the EDFT scheme is recommended for metallic > systems where converging electronic structure using Density Mixing option > proves problematic. > > Charge: Specify the amplitude for charge density mixing (i.e., the > amplitude of the output charge density to mix with the input charge density > to obtain input for the next iteration). > > Note. This option is enabled only if the Density Mixing minimization > method is selected. > > Spin: Specify the amplitude for spin density mixing, i.e. the amplitude of > the output spin density to mix with the input spin density to obtain input > for the next iteration. > > Note. This option in enabled only for spin-polarized calculations using > the Density Mixing minimization method. > > ------------------------------------------------- > > Shoul I consider the mixing_mode option in PWSCF is equal to Density > Mixing option in MS, and value of mixing_bate in PWSCF is equal to the one > of Charge in MS? > > Do you think I should swich on the boardening by 'occupations', 'degauss' > and 'smearing' command in PWSCF? > > I also found no detail description for this three options. > > do you think the following text suitable for the three command in PWSCF? > > ----------------------------- > > Smearing: Specify the broadening to be applied to the electronic > occupation. > > Note. This option is enabled only for variable occupancy calculations. > > ----------------------------- > > If the answer is no, could you please give me some suggestion to > understanding the command and make a better use of it. > > thank you so much for reading > > > best wishes, > > vega > > > > On Sun, Mar 1, 2009 at 7:44 PM, vega lew wrote: > >> Dear APSI >> >> thank you for you suggestions to me. >> >> I will try it ASAP. >> >> vega >> >> On Sun, Mar 1, 2009 at 5:08 PM, Ari Paavo Seitsonen < >> ari.p.seitsonen at iki.fi> wrote: >> >>> >>> Dear Vega, >>> >>> Just my guesses and suggestions: One could try mixing of the density, >>> like >>> >>> &electrons >>> mixing_beta = 0.7 >>> / >>> >>> (or a value even smaller than 0.7, or some other parametres for the >>> mixing) since with a defect you might now have defect levels in the band >>> gap, leading to a more difficult a convergence. Eventually one could also >>> switch on the broadening of the occupation numbers, eventually switching it >>> off for the physical/production jobs, but just to check if the problem in >>> convergence comes due to this. >>> >>> And in the original paper the authors discuss spin-polarisation, one >>> might test also this (nspin = 2), with different initial magnetisations >>> [starting_magnetization(xx) = ...] for the atoms surrounding the defect. >>> >>> Greetings, >>> >>> apsi >>> >>> >>> On Sun, 1 Mar 2009, vega lew wrote: >>> >>> Dear all, >>>> >>>> I am planning to calculate the Oxygen vacancy properties of TiO2 >>>> surfaces. >>>> The calculation for the ideal surfaces are quite normal and the results >>>> are >>>> in line with the one that literature reported. But, when I tried to >>>> calculate the anatase 101 surface with an Oxygen vacancy (O2c was >>>> removed >>>> directly from the stoichiometric Anatase 101as described in J. Phys. >>>> Chem. C >>>> 2007, 111, 16397-16404, I encounter the problem of convergence for SCF >>>> cycle. I tried to add 20% more empty band to the system the problem >>>> still >>>> laid in. How could I overcome the problem? >>>> >>>> my input file was attached at the bottom of the mail >>>> >>>> thank you for reading. Any hints will be appreciated. >>>> >>>> vega >>>> >>>> >>> ... >>> >>> >>> >>>> &SYSTEM >>>> ibrav = 8, >>>> celldm(1) =19.3269, >>>> celldm(2) = 1.1094, >>>> celldm(3) = 1.7450, >>>> nat = 71, >>>> ntyp = 2, >>>> nosym = .true., >>>> ecutwfc = 30, >>>> ecutrho = 300, >>>> / >>>> >>>> &ELECTRONS >>>> >>>> / >>>> >>>> &IONS >>>> ion_dynamics = 'bfgs', >>>> / >>>> >>>> >>> -- >>> >>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- >>> Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ >>> IMPMC, CNRS & Universit? Pierre et Marie Curie >>> Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> >> ================================================================================== >> Vega Lew ( weijia liu) >> PH.D Candidate in Chemical Engineering >> State Key Laboratory of Materials-oriented Chemical Engineering >> College of Chemistry and Chemical Engineering >> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China >> >> ****************************************************************************************************************** >> Email: vegalew at gmail.com >> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, >> Nanjing, Jiangsu, China >> ****************************************************************************************************************** >> >> > > > > -- > > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ****************************************************************************************************************** > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090301/be25898f/attachment-0001.htm From eyvaz_isaev at yahoo.com Sun Mar 1 14:17:08 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 1 Mar 2009 05:17:08 -0800 (PST) Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 surfaces In-Reply-To: <412f6c680903010019g61513ecdq9f886b8fa133ad68@mail.gmail.com> Message-ID: <10147.52984.qm@web65708.mail.ac4.yahoo.com> Dear Vega, It was explained many times in the case of surface calculations (you introduced a defect also) you should consider your system as metallic due to induced states (by dangling bonds or defects). So, make your system metallic turning on occupations="smearing" and related keywords. Of course, the use of mixing_mode='local-TF' and mixing_beta=0.1 is preferable in your calculations as your system is highly inhomogeneous. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sun, 3/1/09, vega lew wrote: > From: vega lew > Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 surfaces > To: "PWSCF Forum" > Date: Sunday, March 1, 2009, 11:19 AM > Dear all, > > I am planning to calculate the Oxygen vacancy properties of > TiO2 surfaces. > The calculation for the ideal surfaces are quite normal and > the results are > in line with the one that literature reported. But, when I > tried to > calculate the anatase 101 surface with an Oxygen vacancy > (O2c was removed > directly from the stoichiometric Anatase 101as described in > J. Phys. Chem. C > 2007, 111, 16397-16404, I encounter the problem of > convergence for SCF > cycle. I tried to add 20% more empty band to the system > the problem still > laid in. How could I overcome the problem? > > my input file was attached at the bottom of the mail > > thank you for reading. Any hints will be appreciated. > > vega > > > > &CONTROL > > title = 'Anatase 101 1x3' > , > calculation = 'relax' > , > restart_mode = 'from_scratch' > , > outdir = '/tmp/' , > wfcdir = '/tmp/' > , > pseudo_dir = > '/home/vega/espresso-4.0/pseudo/' , > prefix = 'Anatase 101 1x3' > , > disk_io = 'none' > , > nstep = 1000 > , > / > > &SYSTEM > > ibrav = > 8, > celldm(1) =19.3269, > celldm(2) = 1.1094, > celldm(3) = 1.7450, > nat = > 71, > ntyp = > 2, > nosym = .true. > , > ecutwfc = 30, > ecutrho = 300, > / > > &ELECTRONS > > > > / > > &IONS > > ion_dynamics = 'bfgs' > , > / > > ATOMIC_SPECIES > > Ti 47.86700 > Ti.pw91-sp-van_ak.UPF > O 15.99940 > O.pw91-van_ak.UPF > ATOMIC_POSITIONS > crystal > Ti 0.79001 0.05515 0.04075 0 0 0 > Ti 0.92677 0.05515 0.23765 1 1 1 > Ti 0.29001 0.22181 0.04075 0 0 0 > Ti 0.42677 0.22181 0.23765 1 1 1 > Ti 0.57420 0.22181 0.08998 0 0 0 > Ti 0.71096 0.22181 0.28687 1 1 1 > Ti 0.07420 0.05515 0.08998 0 0 0 > Ti 0.21096 0.05515 0.28687 1 1 1 > O 0.61134 0.05515 0.08150 0 0 0 > O 0.74810 0.05515 0.27840 1 1 1 > O 0.11134 0.22181 0.08150 0 0 0 > O 0.24810 0.22181 0.27840 1 1 1 > O 0.39553 0.22181 0.13073 0 0 0 > O 0.53229 0.22181 0.32763 1 1 1 > O 0.89553 0.05515 0.13073 0 0 0 > O 0.03229 0.05515 0.32763 1 1 1 > O 0.25286 0.05515 0.04922 0 0 0 > O 0.38962 0.05515 0.24612 1 1 1 > O 0.75286 0.22181 0.04922 0 0 0 > O 0.88962 0.22181 0.24612 1 1 1 > O 0.46867 0.22181 0.00000 0 0 0 > O 0.60543 0.22181 0.19690 1 1 1 > O 0.96867 0.05515 0.00000 0 0 0 > O 0.10543 0.05515 0.19690 1 1 1 > Ti 0.79001 0.38848 0.04075 0 0 0 > Ti 0.92677 0.38848 0.23765 1 1 1 > Ti 0.29001 0.55515 0.04075 0 0 0 > Ti 0.42677 0.55515 0.23765 1 1 1 > Ti 0.57420 0.55515 0.08998 0 0 0 > Ti 0.71096 0.55515 0.28687 1 1 1 > Ti 0.07420 0.38848 0.08998 0 0 0 > Ti 0.21096 0.38848 0.28687 1 1 1 > O 0.61134 0.38848 0.08150 0 0 0 > O 0.74810 0.38848 0.27840 1 1 1 > O 0.11134 0.55515 0.08150 0 0 0 > O 0.24810 0.55515 0.27840 1 1 1 > O 0.39553 0.55515 0.13073 0 0 0 > #O 0.53229 0.55515 0.32763 1 1 1 > O 0.89553 0.38848 0.13073 0 0 0 > O 0.03229 0.38848 0.32763 1 1 1 > O 0.25286 0.38848 0.04922 0 0 0 > O 0.38962 0.38848 0.24612 1 1 1 > O 0.75286 0.55515 0.04922 0 0 0 > O 0.88962 0.55515 0.24612 1 1 1 > O 0.46867 0.55515 0.00000 0 0 0 > O 0.60543 0.55515 0.19690 1 1 1 > O 0.96867 0.38848 0.00000 0 0 0 > O 0.10543 0.38848 0.19690 1 1 1 > Ti 0.79001 0.72181 0.04075 0 0 0 > Ti 0.92677 0.72181 0.23765 1 1 1 > Ti 0.29001 0.88848 0.04075 0 0 0 > Ti 0.42677 0.88848 0.23765 1 1 1 > Ti 0.57420 0.88848 0.08998 0 0 0 > Ti 0.71096 0.88848 0.28687 1 1 1 > Ti 0.07420 0.72181 0.08998 0 0 0 > Ti 0.21096 0.72181 0.28687 1 1 1 > O 0.61134 0.72181 0.08150 0 0 0 > O 0.74810 0.72181 0.27840 1 1 1 > O 0.11134 0.88848 0.08150 0 0 0 > O 0.24810 0.88848 0.27840 1 1 1 > O 0.39553 0.88848 0.13073 0 0 0 > O 0.53229 0.88848 0.32763 1 1 1 > O 0.89553 0.72181 0.13073 0 0 0 > O 0.03229 0.72181 0.32763 1 1 1 > O 0.25286 0.72181 0.04922 0 0 0 > O 0.38962 0.72181 0.24612 1 1 1 > O 0.75286 0.88848 0.04922 0 0 0 > O 0.88962 0.88848 0.24612 1 1 1 > O 0.46867 0.88848 0.00000 0 0 0 > O 0.60543 0.88848 0.19690 1 1 1 > O 0.96867 0.72181 0.00000 0 0 0 > O 0.10543 0.72181 0.19690 1 1 1 > K_POINTS gamma > > -- > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical > Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, > China > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan > Road 5#, Nanjing, > Jiangsu, China > ****************************************************************************************************************** > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From quantumdft at gmail.com Sun Mar 1 14:31:20 2009 From: quantumdft at gmail.com (vega lew) Date: Sun, 1 Mar 2009 21:31:20 +0800 Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 surfaces In-Reply-To: References: <412f6c680903010019g61513ecdq9f886b8fa133ad68@mail.gmail.com> <412f6c680903010344x6bbe9104ld31da568076bc3a0@mail.gmail.com> <412f6c680903010409x68898db2k3c07be9871b767a9@mail.gmail.com> Message-ID: <412f6c680903010531j6a589dc1ta51bba405617e384@mail.gmail.com> Dear, haiping I'll check it, thank you for your help. would you please add to QQ group which is composed of many PWSCF users or similar code, such as CASTEP, VASP or DACAPO. The No. is 35451926. We could discuss the code or the scientific problem more convenient with PH. D. student in Chinese. thank you again vega On Sun, Mar 1, 2009 at 8:20 PM, lan haiping wrote: > Hi, Weijia, > In fact, you can have a look at mix_rho.f90 for detailed agorithms used > in QE package for density mixing scheme . > The scheme is just modified Broyden's method for charge density mixing > , please see D.D. Johnson PRB 38, 12807 (1988). > > > regards, > > > > On Sun, Mar 1, 2009 at 8:09 PM, vega lew wrote: > >> Dear friend, >> >> I found there is few supporting materials decribing what the exact meaning >> for mixing_beta. do you think the following paragraph from the manual of >> Materials Studio is suitable for this parameters? >> >> ------------------------------------------------ >> >> Electronic minimizer: Specify the electronic minimization method to be >> used for the SCF calculation. Two options are available, Density Mixingand All >> Bands/EDFT. >> >> Tip. The Density Mixing option is recommended, particularly for variable >> occupancy calculations. The All Bands/EDFT method is usually slower and >> requires more memory. However, the EDFT scheme is recommended for metallic >> systems where converging electronic structure using Density Mixing option >> proves problematic. >> >> Charge: Specify the amplitude for charge density mixing (i.e., the >> amplitude of the output charge density to mix with the input charge density >> to obtain input for the next iteration). >> >> Note. This option is enabled only if the Density Mixing minimization >> method is selected. >> >> Spin: Specify the amplitude for spin density mixing, i.e. the amplitude >> of the output spin density to mix with the input spin density to obtain >> input for the next iteration. >> >> Note. This option in enabled only for spin-polarized calculations using >> the Density Mixing minimization method. >> >> ------------------------------------------------- >> >> Shoul I consider the mixing_mode option in PWSCF is equal to Density >> Mixing option in MS, and value of mixing_bate in PWSCF is equal to the >> one of Charge in MS? >> >> Do you think I should swich on the boardening by 'occupations', 'degauss' >> and 'smearing' command in PWSCF? >> >> I also found no detail description for this three options. >> >> do you think the following text suitable for the three command in PWSCF? >> >> ----------------------------- >> >> Smearing: Specify the broadening to be applied to the electronic >> occupation. >> >> Note. This option is enabled only for variable occupancy calculations. >> >> ----------------------------- >> >> If the answer is no, could you please give me some suggestion to >> understanding the command and make a better use of it. >> >> thank you so much for reading >> >> >> best wishes, >> >> vega >> >> >> >> On Sun, Mar 1, 2009 at 7:44 PM, vega lew wrote: >> >>> Dear APSI >>> >>> thank you for you suggestions to me. >>> >>> I will try it ASAP. >>> >>> vega >>> >>> On Sun, Mar 1, 2009 at 5:08 PM, Ari Paavo Seitsonen < >>> ari.p.seitsonen at iki.fi> wrote: >>> >>>> >>>> Dear Vega, >>>> >>>> Just my guesses and suggestions: One could try mixing of the density, >>>> like >>>> >>>> &electrons >>>> mixing_beta = 0.7 >>>> / >>>> >>>> (or a value even smaller than 0.7, or some other parametres for the >>>> mixing) since with a defect you might now have defect levels in the band >>>> gap, leading to a more difficult a convergence. Eventually one could also >>>> switch on the broadening of the occupation numbers, eventually switching it >>>> off for the physical/production jobs, but just to check if the problem in >>>> convergence comes due to this. >>>> >>>> And in the original paper the authors discuss spin-polarisation, one >>>> might test also this (nspin = 2), with different initial magnetisations >>>> [starting_magnetization(xx) = ...] for the atoms surrounding the defect. >>>> >>>> Greetings, >>>> >>>> apsi >>>> >>>> >>>> On Sun, 1 Mar 2009, vega lew wrote: >>>> >>>> Dear all, >>>>> >>>>> I am planning to calculate the Oxygen vacancy properties of TiO2 >>>>> surfaces. >>>>> The calculation for the ideal surfaces are quite normal and the results >>>>> are >>>>> in line with the one that literature reported. But, when I tried to >>>>> calculate the anatase 101 surface with an Oxygen vacancy (O2c was >>>>> removed >>>>> directly from the stoichiometric Anatase 101as described in J. Phys. >>>>> Chem. C >>>>> 2007, 111, 16397-16404, I encounter the problem of convergence for SCF >>>>> cycle. I tried to add 20% more empty band to the system the problem >>>>> still >>>>> laid in. How could I overcome the problem? >>>>> >>>>> my input file was attached at the bottom of the mail >>>>> >>>>> thank you for reading. Any hints will be appreciated. >>>>> >>>>> vega >>>>> >>>>> >>>> ... >>>> >>>> >>>> >>>>> &SYSTEM >>>>> ibrav = 8, >>>>> celldm(1) =19.3269, >>>>> celldm(2) = 1.1094, >>>>> celldm(3) = 1.7450, >>>>> nat = 71, >>>>> ntyp = 2, >>>>> nosym = .true., >>>>> ecutwfc = 30, >>>>> ecutrho = 300, >>>>> / >>>>> >>>>> &ELECTRONS >>>>> >>>>> / >>>>> >>>>> &IONS >>>>> ion_dynamics = 'bfgs', >>>>> / >>>>> >>>>> >>>> -- >>>> >>>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- >>>> Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ >>>> IMPMC, CNRS & Universit? Pierre et Marie Curie >>>> Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>> >>> >>> -- >>> >>> ================================================================================== >>> Vega Lew ( weijia liu) >>> PH.D Candidate in Chemical Engineering >>> State Key Laboratory of Materials-oriented Chemical Engineering >>> College of Chemistry and Chemical Engineering >>> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China >>> >>> ****************************************************************************************************************** >>> Email: vegalew at gmail.com >>> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, >>> Nanjing, Jiangsu, China >>> ****************************************************************************************************************** >>> >>> >> >> >> >> -- >> >> ================================================================================== >> Vega Lew ( weijia liu) >> PH.D Candidate in Chemical Engineering >> State Key Laboratory of Materials-oriented Chemical Engineering >> College of Chemistry and Chemical Engineering >> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China >> >> ****************************************************************************************************************** >> Email: vegalew at gmail.com >> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, >> Nanjing, Jiangsu, China >> ****************************************************************************************************************** >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090301/8255cfa4/attachment-0001.htm From quantumdft at gmail.com Sun Mar 1 14:52:46 2009 From: quantumdft at gmail.com (vega lew) Date: Sun, 1 Mar 2009 21:52:46 +0800 Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 surfaces In-Reply-To: <10147.52984.qm@web65708.mail.ac4.yahoo.com> References: <412f6c680903010019g61513ecdq9f886b8fa133ad68@mail.gmail.com> <10147.52984.qm@web65708.mail.ac4.yahoo.com> Message-ID: <412f6c680903010552n7a4ef9cejaca074d614106ba8@mail.gmail.com> Dear sir, I apologize for my pool understanding of your mails concerning my problems of convergence for SCF. Because I am not strong enough with the theory background, I am not sensitive with what you said before. Now, you tell me how to overcome the problems so detail. I think I really benefit from your mail this time. By the way, my understanding on quantum mechanism or quantum chemistry is not good enough. My purpose is to use the code to solve the problem and make better understanding with the materials we focus on. Do you think the theory background is really important for all the users of scientific code, even for researchers in chemical engineering or applied physics? thank you for your time. vega On Sun, Mar 1, 2009 at 9:17 PM, Eyvaz Isaev wrote: > Dear Vega, > > It was explained many times in the case of surface calculations (you > introduced a defect also) you should consider your system as metallic due to > induced states (by dangling bonds or defects). > So, make your system metallic turning on occupations="smearing" and related > keywords. > > Of course, the use of mixing_mode='local-TF' and mixing_beta=0.1 is > preferable in your calculations as your system is highly inhomogeneous. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Sun, 3/1/09, vega lew wrote: > > > From: vega lew > > Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 > surfaces > > To: "PWSCF Forum" > > Date: Sunday, March 1, 2009, 11:19 AM > > Dear all, > > > > I am planning to calculate the Oxygen vacancy properties of > > TiO2 surfaces. > > The calculation for the ideal surfaces are quite normal and > > the results are > > in line with the one that literature reported. But, when I > > tried to > > calculate the anatase 101 surface with an Oxygen vacancy > > (O2c was removed > > directly from the stoichiometric Anatase 101as described in > > J. Phys. Chem. C > > 2007, 111, 16397-16404, I encounter the problem of > > convergence for SCF > > cycle. I tried to add 20% more empty band to the system > > the problem still > > laid in. How could I overcome the problem? > > > > my input file was attached at the bottom of the mail > > > > thank you for reading. Any hints will be appreciated. > > > > vega > > > > > > > > &CONTROL > > > > title = 'Anatase 101 1x3' > > , > > calculation = 'relax' > > , > > restart_mode = 'from_scratch' > > , > > outdir = '/tmp/' , > > wfcdir = '/tmp/' > > , > > pseudo_dir = > > '/home/vega/espresso-4.0/pseudo/' , > > prefix = 'Anatase 101 1x3' > > , > > disk_io = 'none' > > , > > nstep = 1000 > > , > > / > > > > &SYSTEM > > > > ibrav = > > 8, > > celldm(1) =19.3269, > > celldm(2) = 1.1094, > > celldm(3) = 1.7450, > > nat = > > 71, > > ntyp = > > 2, > > nosym = .true. > > , > > ecutwfc = 30, > > ecutrho = 300, > > / > > > > &ELECTRONS > > > > > > > > / > > > > &IONS > > > > ion_dynamics = 'bfgs' > > , > > / > > > > ATOMIC_SPECIES > > > > Ti 47.86700 > > Ti.pw91-sp-van_ak.UPF > > O 15.99940 > > O.pw91-van_ak.UPF > > ATOMIC_POSITIONS > > crystal > > Ti 0.79001 0.05515 0.04075 0 0 0 > > Ti 0.92677 0.05515 0.23765 1 1 1 > > Ti 0.29001 0.22181 0.04075 0 0 0 > > Ti 0.42677 0.22181 0.23765 1 1 1 > > Ti 0.57420 0.22181 0.08998 0 0 0 > > Ti 0.71096 0.22181 0.28687 1 1 1 > > Ti 0.07420 0.05515 0.08998 0 0 0 > > Ti 0.21096 0.05515 0.28687 1 1 1 > > O 0.61134 0.05515 0.08150 0 0 0 > > O 0.74810 0.05515 0.27840 1 1 1 > > O 0.11134 0.22181 0.08150 0 0 0 > > O 0.24810 0.22181 0.27840 1 1 1 > > O 0.39553 0.22181 0.13073 0 0 0 > > O 0.53229 0.22181 0.32763 1 1 1 > > O 0.89553 0.05515 0.13073 0 0 0 > > O 0.03229 0.05515 0.32763 1 1 1 > > O 0.25286 0.05515 0.04922 0 0 0 > > O 0.38962 0.05515 0.24612 1 1 1 > > O 0.75286 0.22181 0.04922 0 0 0 > > O 0.88962 0.22181 0.24612 1 1 1 > > O 0.46867 0.22181 0.00000 0 0 0 > > O 0.60543 0.22181 0.19690 1 1 1 > > O 0.96867 0.05515 0.00000 0 0 0 > > O 0.10543 0.05515 0.19690 1 1 1 > > Ti 0.79001 0.38848 0.04075 0 0 0 > > Ti 0.92677 0.38848 0.23765 1 1 1 > > Ti 0.29001 0.55515 0.04075 0 0 0 > > Ti 0.42677 0.55515 0.23765 1 1 1 > > Ti 0.57420 0.55515 0.08998 0 0 0 > > Ti 0.71096 0.55515 0.28687 1 1 1 > > Ti 0.07420 0.38848 0.08998 0 0 0 > > Ti 0.21096 0.38848 0.28687 1 1 1 > > O 0.61134 0.38848 0.08150 0 0 0 > > O 0.74810 0.38848 0.27840 1 1 1 > > O 0.11134 0.55515 0.08150 0 0 0 > > O 0.24810 0.55515 0.27840 1 1 1 > > O 0.39553 0.55515 0.13073 0 0 0 > > #O 0.53229 0.55515 0.32763 1 1 1 > > O 0.89553 0.38848 0.13073 0 0 0 > > O 0.03229 0.38848 0.32763 1 1 1 > > O 0.25286 0.38848 0.04922 0 0 0 > > O 0.38962 0.38848 0.24612 1 1 1 > > O 0.75286 0.55515 0.04922 0 0 0 > > O 0.88962 0.55515 0.24612 1 1 1 > > O 0.46867 0.55515 0.00000 0 0 0 > > O 0.60543 0.55515 0.19690 1 1 1 > > O 0.96867 0.38848 0.00000 0 0 0 > > O 0.10543 0.38848 0.19690 1 1 1 > > Ti 0.79001 0.72181 0.04075 0 0 0 > > Ti 0.92677 0.72181 0.23765 1 1 1 > > Ti 0.29001 0.88848 0.04075 0 0 0 > > Ti 0.42677 0.88848 0.23765 1 1 1 > > Ti 0.57420 0.88848 0.08998 0 0 0 > > Ti 0.71096 0.88848 0.28687 1 1 1 > > Ti 0.07420 0.72181 0.08998 0 0 0 > > Ti 0.21096 0.72181 0.28687 1 1 1 > > O 0.61134 0.72181 0.08150 0 0 0 > > O 0.74810 0.72181 0.27840 1 1 1 > > O 0.11134 0.88848 0.08150 0 0 0 > > O 0.24810 0.88848 0.27840 1 1 1 > > O 0.39553 0.88848 0.13073 0 0 0 > > O 0.53229 0.88848 0.32763 1 1 1 > > O 0.89553 0.72181 0.13073 0 0 0 > > O 0.03229 0.72181 0.32763 1 1 1 > > O 0.25286 0.72181 0.04922 0 0 0 > > O 0.38962 0.72181 0.24612 1 1 1 > > O 0.75286 0.88848 0.04922 0 0 0 > > O 0.88962 0.88848 0.24612 1 1 1 > > O 0.46867 0.88848 0.00000 0 0 0 > > O 0.60543 0.88848 0.19690 1 1 1 > > O 0.96867 0.72181 0.00000 0 0 0 > > O 0.10543 0.72181 0.19690 1 1 1 > > K_POINTS gamma > > > > -- > > > ================================================================================== > > Vega Lew ( weijia liu) > > PH.D Candidate in Chemical Engineering > > State Key Laboratory of Materials-oriented Chemical > > Engineering > > College of Chemistry and Chemical Engineering > > Nanjing University of Technology, 210009, Nanjing, Jiangsu, > > China > > > ****************************************************************************************************************** > > Email: vegalew at gmail.com > > Office: Room A705, Technical Innovation Building, Xinmofan > > Road 5#, Nanjing, > > Jiangsu, China > > > ****************************************************************************************************************** > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090301/0318bb09/attachment.htm From akohlmey at cmm.chem.upenn.edu Sun Mar 1 18:20:20 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 1 Mar 2009 12:20:20 -0500 (EST) Subject: [Pw_forum] converge problem in calculating the vacancy on TiO2 surfaces In-Reply-To: <412f6c680903010552n7a4ef9cejaca074d614106ba8@mail.gmail.com> References: <412f6c680903010019g61513ecdq9f886b8fa133ad68@mail.gmail.com> <10147.52984.qm@web65708.mail.ac4.yahoo.com> <412f6c680903010552n7a4ef9cejaca074d614106ba8@mail.gmail.com> Message-ID: On Sun, 1 Mar 2009, vega lew wrote: VL> Dear sir, VL> VL> I apologize for my pool understanding of your mails concerning my problems VL> of convergence for SCF. VL> VL> Because I am not strong enough with the theory background, I am not VL> sensitive with what you said before. Now, you tell me how to overcome the VL> problems so detail. I think I really benefit from your mail this time. ok. here we go. writing something like that paragraph below is like waving a red in front of a bull (and people that know me in person know that i can do a pretty good impersonation of that when i'm angry). sensitive minds, please hit delete right now. VL> By the way, my understanding on quantum mechanism or quantum chemistry is VL> not good enough. My purpose is to use the code to solve the problem and make VL> better understanding with the materials we focus on. Do you think the theory VL> background is really important for all the users of scientific code, even VL> for researchers in chemical engineering or applied physics? please read this paragraph again, hit yourself on the head three times with a hard item and then answer it yourself. YES!!!!!!!!! if you go to your local do-it-yourself store, you'll see tons of powertools for every purpose. have you seen what these powertools can do in the hand of somebody without sufficient understanding of how they work?? do you know how many accidents (severed fingers, punctured hands, etc.) happen because of that, every year? there _is_ no "just using" of tools. without sufficient knowledge you can get lucky and get it right, but how often? mind you, you don't have to become that much of an expert so you could write your own software or develop new algorithms, but you also have to keep the "garbage-in garbage-out" principle in mind. you have to have at least the ability to tell whether your results are gold or cow dung, and for that - sorry there ain't no escape from the blues - you will have to learn the fundamentals. or to give another example: what good would a pocket calculator be to you, if you don't know the difference between adding and multiplying? ...and for that matter, asking questions on a mailing list is no replacement for working (not reading) through textbooks and building your experience. the mailing list should be used _after_ there is no more help to be found in the textbook, not before. looks like i managed to stay reasonably calm this way. enjoy your "cigar", axel. VL> VL> thank you for your time. VL> VL> vega VL> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From eyvaz_isaev at yahoo.com Sun Mar 1 20:38:18 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 1 Mar 2009 11:38:18 -0800 (PST) Subject: [Pw_forum] the dynmaical matrix are like "***********" when the phonons calculation at gama In-Reply-To: Message-ID: <930232.49838.qm@web65702.mail.ac4.yahoo.com> Hi, As the dynamical matrix is written in the fixed format (like 3(2F12,8, 2x)), and you have large components (say, larger than 999.99999999, or -99.99999999 ), then it can not be printed properly. In my opinion, such kind components will be quite unusual. I have no experience in calculation of H2O properties, but I would recommend the use of thr2_ph=1.d-18, at least, use different thr2_ph and see what happens. If you are really interested in these values then change the format in line 32, write_dyn_on_file.f90 (in /PH, of course), say, to f16.8, then recompile ph.x, and enjoy seeing these values. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sun, 3/1/09, xu yuehua wrote: > From: xu yuehua > Subject: [Pw_forum] the dynmaical matrix are like "***********" when the phonons calculation at gama > To: "PWSCF Forum" > Date: Sunday, March 1, 2009, 9:45 AM > hello all : > > > i am facing unkonwn problem when i calculated the phonons > at gama: > > the dynamical matrix file wrote: > ................ > Dynamical Matrix in cartesian axes > > q = ( 0.000000000 0.000000000 0.000000000 ) > > 1 1 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > 1 2 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > 1 3 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > 1 4 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > 1 5 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > 1 6 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > 1 7 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > 1 8 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > 1 9 > ************ 0.00000000 ************ 0.00000000 > ************ 0.00000000 > ....... > > my phone input file : > phonons at Gamma > &inputph > tr2_ph=1.0d-15, > prefix='scf_two_b_type', > epsil=.true., > amass(1)=1.0, > amass(2)=15.999, > outdir='/disk2/xxx/xxx/espresso-3.2.3/tmp', > fildyn='fourringwater.dynG', > / > 0.0 0.0 0.0 > > > and my scf input file is :&CONTROL > calculation = "scf", > prefix = "scf_two_b_type" > pseudo_dir = > "/disk2/xxx/xxx/espresso-3.2.3/pseudo", > outdir = > "/disk2/jdong/xyh/espresso-3.2.3/tmp", > / > &SYSTEM > ibrav = 4, > a=20,b=20,c=5.60,cosab=-0.5,cosac=0,cosbc=0, > nat = 24, > ntyp = 2, > ecutwfc =35 , > ecutrho =420 > / > &ELECTRONS > conv_thr = 1.D-9, > mixing_beta = 0.2D0, > / > ATOMIC_SPECIES > H 1.0 H.pbe-rrkjus.UPF > O 15.999 O.pbe-rrkjus.UPF > ATOMIC_POSITIONS { crystal } > H 0.040592899 -0.047115761 0.485459003 > H 0.114704004 -0.001940711 0.646569902 > H 0.077728017 0.073838408 0.485209132 > H 0.068286628 0.133313508 0.646050213 > H -0.040592899 0.047115761 0.485459003 > H -0.114704004 0.001940711 0.646569902 > H -0.077728017 -0.073838408 0.485209132 > H -0.068286628 -0.133313508 0.646050213 > H 0.087725644 0.047173264 0.985851842 > H 0.116757198 0.001980553 1.146554001 > H -0.003964894 0.073814692 0.985604262 > H 0.065042531 0.133450775 1.145919070 > H -0.087725644 -0.047173264 0.985851842 > H -0.116757198 -0.001980553 1.146554001 > H 0.003964894 -0.073814692 0.985604262 > H -0.065042531 -0.133450775 1.145919070 > O 0.095295444 -0.003121003 0.483499312 > O 0.058352838 0.111476844 0.483127474 > O -0.095295444 0.003121003 0.483499312 > O -0.058352838 -0.111476844 0.483127474 > O 0.098444160 0.003183717 0.983638903 > O 0.053053024 0.111436979 0.983231173 > O -0.098444160 -0.003183717 0.983638903 > O -0.053053024 -0.111436979 0.983231173 > > > > > > > > K_POINTS {automatic} > 1 1 12 0 0 0 > > > and my relax out file wrote: > > > convergence has been achieved > > Forces acting on atoms (Ry/au): > > atom 1 type 1 force = -0.00000712 > -0.00004363 0.00001631 > atom 2 type 1 force = 0.00004994 > 0.00001718 -0.00006583 > atom 3 type 1 force = 0.00001729 > -0.00001573 0.00002699 > atom 4 type 1 force = -0.00000656 > 0.00003062 0.00005285 > atom 5 type 1 force = 0.00000712 > 0.00004363 0.00001631 > atom 6 type 1 force = -0.00004994 > -0.00001718 -0.00006583 > atom 7 type 1 force = -0.00001729 > 0.00001573 0.00002699 > atom 8 type 1 force = 0.00000656 > -0.00003062 0.00005285 > atom 9 type 1 force = -0.00000156 > -0.00006167 -0.00005767 > atom 10 type 1 force = 0.00001092 > 0.00004788 -0.00001249 > atom 11 type 1 force = 0.00005214 > -0.00008085 -0.00005460 > atom 12 type 1 force = -0.00002474 > -0.00007499 0.00003358 > atom 13 type 1 force = 0.00000156 > 0.00006167 -0.00005767 > atom 14 type 1 force = -0.00001092 > -0.00004788 -0.00001249 > atom 15 type 1 force = -0.00005214 > 0.00008085 -0.00005460 > atom 16 type 1 force = 0.00002474 > 0.00007499 0.00003358 > atom 17 type 2 force = 0.00001005 > 0.00004653 0.00008656 > atom 18 type 2 force = 0.00001760 > -0.00007784 0.00003639 > atom 19 type 2 force = -0.00001005 > -0.00004653 0.00008656 > atom 20 type 2 force = -0.00001760 > 0.00007784 0.00003639 > atom 21 type 2 force = 0.00002956 > -0.00007076 -0.00004942 > atom 22 type 2 force = -0.00000699 > 0.00005606 -0.00001264 > atom 23 type 2 force = -0.00002956 > 0.00007076 -0.00004942 > atom 24 type 2 force = 0.00000699 > -0.00005606 -0.00001264 > > Total force = 0.000382 Total SCF correction = > 0.000010 > > > entering subroutine stress ... > > total stress (Ry/bohr**3) > (kbar) P= -0.40 > -0.00000194 0.00000001 0.00000000 -0.29 > 0.00 0.00 > 0.00000001 -0.00000179 0.00000000 0.00 > -0.26 0.00 > 0.00000000 0.00000000 -0.00000434 0.00 > 0.00 -0.64 > > > bfgs converged in 47 scf cycles and 45 bfgs steps > > End of BFGS Geometry Optimization > > Final energy = -274.4689566789 Ry > > > so i think the problem is not caused by the structure > relaxation. > but where is the problem? i can find it . i need your help. > thank you if you could give me some hints about the > problem! > > > cheers > > > > > > > > > > > ~ > > > > > > the > -- > Xu Yuehua > physics Department of Nanjing university > China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From r95222066 at ntu.edu.tw Mon Mar 2 08:00:57 2009 From: r95222066 at ntu.edu.tw (r95222066 at ntu.edu.tw) Date: Mon, 02 Mar 2009 15:00:57 +0800 Subject: [Pw_forum] Hi!I would like to cease the acception of Pwscf forum message Message-ID: <20090302150057.5g45l1x0hgcc8s44@wmail1.cc.ntu.edu.tw> Hi, I am graduated from the college since last year. So, I would like to ask if I can cease to accept the PWscf forum message form the Internet. I think there are no useful to me at all, because I am not use PWscf anymore. I always have to spend a lot of time to delete the message form my mail box, it really bother me more. Thanks a lot! Your sincerely User From giannozz at democritos.it Mon Mar 2 08:38:55 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 02 Mar 2009 08:38:55 +0100 Subject: [Pw_forum] Hi!I would like to cease the acception of Pwscf forum message In-Reply-To: <20090302150057.5g45l1x0hgcc8s44@wmail1.cc.ntu.edu.tw> References: <20090302150057.5g45l1x0hgcc8s44@wmail1.cc.ntu.edu.tw> Message-ID: <49AB8D0F.9010705@democritos.it> r95222066 at ntu.edu.tw wrote: > I always have to spend a lot of time to delete the > message form my mail box spend 30 more second to unsubscribe: http://www.democritos.it/mailman/listinfo/pw_forum -- Paolo Giannozzi, Democritos and University of Udine, Italy From hqzhou at nju.edu.cn Mon Mar 2 12:05:06 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 2 Mar 2009 19:05:06 +0800 Subject: [Pw_forum] Use of pool References: <21B74D1AD49648479BDC1ABD309ED183@solarflare> <49A3FAE8.5020603@ncsu.edu> Message-ID: Liping, Of course, my tests were made on 8 CPU cores. Huiqun Zhou @Nanjing University, China ----- Original Message ----- From: "Liping Yu" To: "PWSCF Forum" Sent: Tuesday, February 24, 2009 9:49 PM Subject: Re: [Pw_forum] Use of pool > Dear Huiqun, > > If your results are based on the same number of processes for different > npools, they make sense to me. To my understanding, the almost linear > time scaling of using npool means that the computer time is almost > linear to npool (and also the total number of procs) only when we fix > the number of the processors at each pool. > > Please correct me if I am wrong. Thanks! > > Liping Yu > Department of Physics > NC State University, USA > > > Huiqun Zhou wrote: >> Dear list users: >> >> I happened to test duration times of calculating the system I'm >> investigating against number of pools used. There are totally >> 36 k points. But the results surprised me quite a lot. >> >> no pool: 6m21.02s CPU time, 6m45.88s wall time >> 2 pools: 7m19.39s CPU time, 7m38.99s wall time >> 4 pools: 11m59.09s CPU time, 12m14.66s wall time >> 8 pools: 21m28.77s CPU time, 21m38.71s wall time >> >> The machine I'm using is an AMD box with 2 quad core shanghai. >> >> Is my understanding of usage of pool wrong? >> >> Huiqun Zhou >> @Nanjing University, China >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From zah7903 at gmail.com Mon Mar 2 12:26:30 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Mon, 2 Mar 2009 19:26:30 +0800 Subject: [Pw_forum] "charge is wrong" error Message-ID: Hi all, I am new to pwscf and encounter the following error: WARNING: integrated charge= 95.80354228, expected= 96.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from electrons : error # 1 charge is wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... My input file is: ---------------------------------------------------------------------------------------------------- &control calculation = 'relax' restart_mode='from_scratch', prefix='oxy-rh-100', pseudo_dir = '.', outdir='.' verbosity='high' / &system ibrav= 6, celldm(1) = 7.340, celldm(3) = 8, nat= 11, ntyp= 2, ecutwfc = 40.0, ecutrho = 300.0, occupations='smearing', smearing='mp', degauss=0.02 / &electrons diagonalization='cg' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / &IONS bfgs_ndim = 3, pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES Rh 102.90550 Rh.pbe-rrkjus.UPF O 15.9994 O.pbe-rrkjus.UPF ATOMIC_POSITIONS {bohr} Rh 0.000 0.000 0.000 0 0 0 Rh 3.670 3.670 0.000 0 0 0 Rh 3.670 0.000 3.670 0 0 0 Rh 0.000 3.670 3.670 0 0 0 Rh 0.000 0.000 7.340 1 1 1 Rh 3.670 3.670 7.340 1 1 1 Rh 3.670 0.000 11.010 1 1 1 Rh 0.000 3.670 11.010 1 1 1 Rh 0.000 0.000 14.680 1 1 1 Rh 3.670 3.670 14.680 1 1 1 O 3.670 3.670 18.480 1 1 1 K_POINTS automatic 6 6 1 0 0 0 ---------------------------------------------------------------------------------------------------- Could someone kindly give a clue of what's wrong? Thank you very much! Best Zhang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090302/8ef2d7d6/attachment.htm From eyvaz_isaev at yahoo.com Mon Mar 2 12:59:39 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 2 Mar 2009 03:59:39 -0800 (PST) Subject: [Pw_forum] "charge is wrong" error In-Reply-To: Message-ID: <489385.43980.qm@web65713.mail.ac4.yahoo.com> Hi, The use of nbnd=(Number, larger than "number of Kohn-Sham states =N") might be a clue. I.e. add more 4-6 bands to this number. Please provide your affiliation, too. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Mon, 3/2/09, Aihua Zhang wrote: > From: Aihua Zhang > Subject: [Pw_forum] "charge is wrong" error > To: pw_forum at pwscf.org > Date: Monday, March 2, 2009, 2:26 PM > Hi all, > > I am new to pwscf and encounter the following error: > > WARNING: integrated charge= 95.80354228, expected= > 96.00000000 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from electrons : error # 1 > charge is wrong > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > My input file is: > > ---------------------------------------------------------------------------------------------------- > &control > calculation = 'relax' > restart_mode='from_scratch', > prefix='oxy-rh-100', > pseudo_dir = '.', > outdir='.' > verbosity='high' > / > &system > ibrav= 6, celldm(1) = 7.340, celldm(3) = 8, nat= 11, > ntyp= 2, > ecutwfc = 40.0, > ecutrho = 300.0, > occupations='smearing', smearing='mp', > degauss=0.02 > / > &electrons > diagonalization='cg' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > &IONS > bfgs_ndim = 3, > pot_extrapolation = "second_order", > wfc_extrapolation = "second_order", > / > ATOMIC_SPECIES > Rh 102.90550 Rh.pbe-rrkjus.UPF > O 15.9994 O.pbe-rrkjus.UPF > ATOMIC_POSITIONS {bohr} > Rh 0.000 0.000 0.000 0 0 0 > Rh 3.670 3.670 0.000 0 0 0 > Rh 3.670 0.000 3.670 0 0 0 > Rh 0.000 3.670 3.670 0 0 0 > Rh 0.000 0.000 7.340 1 1 1 > Rh 3.670 3.670 7.340 1 1 1 > Rh 3.670 0.000 11.010 1 1 1 > Rh 0.000 3.670 11.010 1 1 1 > Rh 0.000 0.000 14.680 1 1 1 > Rh 3.670 3.670 14.680 1 1 1 > O 3.670 3.670 18.480 1 1 1 > K_POINTS automatic > 6 6 1 0 0 0 > ---------------------------------------------------------------------------------------------------- > > Could someone kindly give a clue of what's wrong? Thank > you very much! > > Best > > Zhang > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Mon Mar 2 13:05:39 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 02 Mar 2009 13:05:39 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: Message-ID: <49ABCB93.2050304@democritos.it> Aihua Zhang wrote: > I am new to pwscf and encounter the following error: when? if it happens after the first optimization step, try to remove all this stuff: > bfgs_ndim = 3, > pot_extrapolation = "second_order", > wfc_extrapolation = "second_order", If not, please provide an input and and an output Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Mon Mar 2 13:06:41 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 02 Mar 2009 13:06:41 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: <49ABCB93.2050304@democritos.it> References: <49ABCB93.2050304@democritos.it> Message-ID: <49ABCBD1.6030400@democritos.it> Paolo Giannozzi wrote: > If not, please provide an input and and an output actually an output is sufficient, since the input was already in your message P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From zah7903 at gmail.com Mon Mar 2 14:06:44 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Mon, 2 Mar 2009 21:06:44 +0800 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: <49ABCBD1.6030400@democritos.it> References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> Message-ID: Dear Eyvaz and Paolo, Thanks for the prompt suggestions. I'll check if it works soon. My affiliation should be in the below signature now. :) Best Zhang On Mon, Mar 2, 2009 at 8:06 PM, Paolo Giannozzi wrote: > Paolo Giannozzi wrote: > > > If not, please provide an input and and an output > > actually an output is sufficient, since the input was > already in your message > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090302/07c31cb1/attachment.htm From zah7903 at gmail.com Mon Mar 2 14:49:53 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Mon, 2 Mar 2009 21:49:53 +0800 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> Message-ID: Unfortunately, the problem seems not due to insufficient number of bands. The number of total electrons is 96 and I increased nbnd to 78, and the error still occurs. As it occurs during the first step of SCF, I don't think the tags in &ions have an effect. Here is the output file. Please have a kind look. Thanks. ------------------------------------------------------------------------------------------ Program PWSCF v.4.0.4 starts ... Today is 2Mar2009 at 21:26:47 Parallel version (MPI) Number of processors in use: 8 R & G space division: proc/pool = 8 For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW Current dimensions of program pwscf are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Iterative solution of the eigenvalue problem a parallel distributed memory algorithm will be used, eigenstates matrixes will be distributed block like on ortho sub-group = 2* 2 procs Planes per process (thick) : nr3 =324 npp = 41 ncplane = 2025 Planes per process (smooth): nr3s=240 npps= 30 ncplanes= 900 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 41 161 34713 30 85 13519 27 2217 2 41 161 34699 30 85 13533 25 2211 3 41 161 34695 30 86 13506 27 2217 4 41 162 34702 30 85 13511 27 2219 5 40 161 34695 30 85 13501 27 2219 6 40 161 34695 30 85 13497 27 2215 7 40 161 34693 30 85 13503 27 2217 8 40 161 34695 30 85 13499 26 2210 tot 324 1289 277587 240 681 108069 213 17725 bravais-lattice index = 6 lattice parameter (a_0) = 7.3400 a.u. unit-cell volume = 3163.5752 (a.u.)^3 number of atoms/cell = 11 number of atomic types = 2 number of electrons = 96.00 number of Kohn-Sham states= 78 kinetic-energy cutoff = 40.0000 Ry charge density cutoff = 300.0000 Ry convergence threshold = 1.0E-08 mixing beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE (1434) nstep = 50 celldm(1)= 7.340000 celldm(2)= 0.000000 celldm(3)= 8.000000 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( 0.000000 1.000000 0.000000 ) a(3) = ( 0.000000 0.000000 8.000000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.000000 0.000000 0.000000 ) b(2) = ( 0.000000 1.000000 0.000000 ) b(3) = ( 0.000000 0.000000 0.125000 ) PseudoPot. # 1 for Rh read from file Rh.pbe-rrkjus.UPF Pseudo is Ultrasoft, Zval = 9.0 Generated by new atomic code, or converted to UPF format Using radial grid of 1191 points, 3 beta functions with: l(1) = 1 l(2) = 2 l(3) = 2 Q(r) pseudized with 0 coefficients PseudoPot. # 2 for O read from file O.pbe-rrkjus.UPF Pseudo is Ultrasoft, Zval = 6.0 Generated by new atomic code, or converted to UPF format Using radial grid of 1269 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 0 coefficients atomic species valence mass pseudopotential Rh 9.00 102.90550 Rh( 1.00) O 6.00 15.99940 O ( 1.00) 8 Sym.Ops. (no inversion) s frac. trans. isym = 1 identity cryst. s( 1) = ( 1 0 0 ) ( 0 1 0 ) ( 0 0 1 ) cart. s( 1) = ( 1.0000000 0.0000000 0.0000000 ) ( 0.0000000 1.0000000 0.0000000 ) ( 0.0000000 0.0000000 1.0000000 ) isym = 2 180 deg rotation - cart. axis [0,0,1] cryst. s( 2) = ( -1 0 0 ) ( 0 -1 0 ) ( 0 0 1 ) cart. s( 2) = ( -1.0000000 0.0000000 0.0000000 ) ( 0.0000000 -1.0000000 0.0000000 ) ( 0.0000000 0.0000000 1.0000000 ) isym = 3 90 deg rotation - cart. axis [0,0,-1] cryst. s( 3) = ( 0 -1 0 ) ( 1 0 0 ) ( 0 0 1 ) cart. s( 3) = ( 0.0000000 1.0000000 0.0000000 ) ( -1.0000000 0.0000000 0.0000000 ) ( 0.0000000 0.0000000 1.0000000 ) isym = 4 90 deg rotation - cart. axis [0,0,1] cryst. s( 4) = ( 0 1 0 ) ( -1 0 0 ) ( 0 0 1 ) cart. s( 4) = ( 0.0000000 -1.0000000 0.0000000 ) ( 1.0000000 0.0000000 0.0000000 ) ( 0.0000000 0.0000000 1.0000000 ) isym = 5 inv. 180 deg rotation - cart. axis [0,1,0] cryst. s( 5) = ( 1 0 0 ) ( 0 -1 0 ) ( 0 0 1 ) cart. s( 5) = ( 1.0000000 0.0000000 0.0000000 ) ( 0.0000000 -1.0000000 0.0000000 ) ( 0.0000000 0.0000000 1.0000000 ) isym = 6 inv. 180 deg rotation - cart. axis [1,0,0] cryst. s( 6) = ( -1 0 0 ) ( 0 1 0 ) ( 0 0 1 ) cart. s( 6) = ( -1.0000000 0.0000000 0.0000000 ) ( 0.0000000 1.0000000 0.0000000 ) ( 0.0000000 0.0000000 1.0000000 ) isym = 7 inv. 180 deg rotation - cart. axis [1,1,0] cryst. s( 7) = ( 0 -1 0 ) ( -1 0 0 ) ( 0 0 1 ) cart. s( 7) = ( 0.0000000 -1.0000000 0.0000000 ) ( -1.0000000 0.0000000 0.0000000 ) ( 0.0000000 0.0000000 1.0000000 ) isym = 8 inv. 180 deg rotation - cart. axis [1,-1,0] cryst. s( 8) = ( 0 1 0 ) ( 1 0 0 ) ( 0 0 1 ) cart. s( 8) = ( 0.0000000 1.0000000 0.0000000 ) ( 1.0000000 0.0000000 0.0000000 ) ( 0.0000000 0.0000000 1.0000000 ) point group C_4v (4mm) there are 5 classes the character table: E 2C4 C2 2s_v 2s_d A_1 1.00 1.00 1.00 1.00 1.00 A_2 1.00 1.00 1.00 -1.00 -1.00 B_1 1.00 -1.00 1.00 1.00 -1.00 B_2 1.00 -1.00 1.00 -1.00 1.00 E 2.00 0.00 -2.00 0.00 0.00 the symmetry operations in each class: E 1 C2 2 2C4 3 4 2s_v 5 6 2s_d 7 8 Cartesian axes site n. atom positions (a_0 units) 1 Rh tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) 2 Rh tau( 2) = ( 0.5000000 0.5000000 0.0000000 ) 3 Rh tau( 3) = ( 0.5000000 0.0000000 0.5000000 ) 4 Rh tau( 4) = ( 0.0000000 0.5000000 0.5000000 ) 5 Rh tau( 5) = ( 0.0000000 0.0000000 1.0000000 ) 6 Rh tau( 6) = ( 0.5000000 0.5000000 1.0000000 ) 7 Rh tau( 7) = ( 0.5000000 0.0000000 1.5000000 ) 8 Rh tau( 8) = ( 0.0000000 0.5000000 1.5000000 ) 9 Rh tau( 9) = ( 0.0000000 0.0000000 2.0000000 ) 10 Rh tau( 10) = ( 0.5000000 0.5000000 2.0000000 ) 11 O tau( 11) = ( 0.5000000 0.5000000 2.5177112 ) Crystallographic axes site n. atom positions (cryst. coord.) 1 Rh tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) 2 Rh tau( 2) = ( 0.5000000 0.5000000 0.0000000 ) 3 Rh tau( 3) = ( 0.5000000 0.0000000 0.0625000 ) 4 Rh tau( 4) = ( 0.0000000 0.5000000 0.0625000 ) 5 Rh tau( 5) = ( 0.0000000 0.0000000 0.1250000 ) 6 Rh tau( 6) = ( 0.5000000 0.5000000 0.1250000 ) 7 Rh tau( 7) = ( 0.5000000 0.0000000 0.1875000 ) 8 Rh tau( 8) = ( 0.0000000 0.5000000 0.1875000 ) 9 Rh tau( 9) = ( 0.0000000 0.0000000 0.2500000 ) 10 Rh tau( 10) = ( 0.5000000 0.5000000 0.2500000 ) 11 O tau( 11) = ( 0.5000000 0.5000000 0.3147139 ) number of k points= 10 gaussian broad. (Ry)= 0.0200 ngauss = 1 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0555556 k( 2) = ( 0.0000000 0.1666667 0.0000000), wk = 0.2222222 k( 3) = ( 0.0000000 0.3333333 0.0000000), wk = 0.2222222 k( 4) = ( 0.0000000 -0.5000000 0.0000000), wk = 0.1111111 k( 5) = ( 0.1666667 0.1666667 0.0000000), wk = 0.2222222 k( 6) = ( 0.1666667 0.3333333 0.0000000), wk = 0.4444444 k( 7) = ( 0.1666667 -0.5000000 0.0000000), wk = 0.2222222 k( 8) = ( 0.3333333 0.3333333 0.0000000), wk = 0.2222222 k( 9) = ( 0.3333333 -0.5000000 0.0000000), wk = 0.2222222 k( 10) = ( -0.5000000 -0.5000000 0.0000000), wk = 0.0555556 cryst. coord. k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0555556 k( 2) = ( 0.0000000 0.1666667 0.0000000), wk = 0.2222222 k( 3) = ( 0.0000000 0.3333333 0.0000000), wk = 0.2222222 k( 4) = ( 0.0000000 -0.5000000 0.0000000), wk = 0.1111111 k( 5) = ( 0.1666667 0.1666667 0.0000000), wk = 0.2222222 k( 6) = ( 0.1666667 0.3333333 0.0000000), wk = 0.4444444 k( 7) = ( 0.1666667 -0.5000000 0.0000000), wk = 0.2222222 k( 8) = ( 0.3333333 0.3333333 0.0000000), wk = 0.2222222 k( 9) = ( 0.3333333 -0.5000000 0.0000000), wk = 0.2222222 k( 10) = ( -0.5000000 -0.5000000 0.0000000), wk = 0.0555556 G cutoff = 409.4055 ( 277587 G-vectors) FFT grid: ( 45, 45,324) G cutoff = 218.3496 ( 108069 G-vectors) smooth grid: ( 30, 30,240) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 2.04 Mb ( 1714, 78) NL pseudopotentials 3.61 Mb ( 1714, 138) Each V/rho on FFT grid 1.27 Mb ( 83025) Each G-vector array 0.26 Mb ( 34713) G-vector shells 0.03 Mb ( 4389) Largest temporary arrays est. size (Mb) dimensions Each subspace H/S matrix 0.09 Mb ( 78, 78) Each matrix 0.16 Mb ( 138, 78) Arrays for rho mixing 10.13 Mb ( 83025, 8) Initial potential from superposition of free atoms starting charge 95.99298, renormalised to 96.00000 negative rho (up, down): 0.422E-04 0.000E+00 Starting wfc are 64 atomic + 14 random wfc total cpu time spent up to now is 7.86 secs per-process dynamical memory: 64.3 Mb Self-consistent Calculation iteration # 1 ecut= 40.00 Ry beta=0.70 CG style diagonalization ethr = 1.00E-02, avg # of iterations = 4.3 negative rho (up, down): 0.222E-04 0.000E+00 total cpu time spent up to now is 126.56 secs WARNING: integrated charge= 95.75373487, expected= 96.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from electrons : error # 1 charge is wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ------------------------------------------------------------------------------------------ Best Zhang On Mon, Mar 2, 2009 at 9:06 PM, Aihua Zhang wrote: > Dear Eyvaz and Paolo, > > Thanks for the prompt suggestions. I'll check if it works soon. > My affiliation should be in the below signature now. :) > > Best > > Zhang > > > On Mon, Mar 2, 2009 at 8:06 PM, Paolo Giannozzi wrote: > >> Paolo Giannozzi wrote: >> >> > If not, please provide an input and and an output >> >> actually an output is sufficient, since the input was >> already in your message >> >> P. >> -- >> Paolo Giannozzi, Democritos and University of Udine, Italy >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > ------------------------------------------------------------------ > Research Fellow, > Dept. of Physics, National Univ. of Singapore > 10 Kent Ridge Crescent, Singapore, 119260 > Tel: +65 6516 7844 > ------------------------------------------------------------------ > > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090302/991f8887/attachment-0001.htm From sclauzer at sissa.it Mon Mar 2 15:31:17 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 02 Mar 2009 15:31:17 +0100 Subject: [Pw_forum] Restart calculation of LSDA In-Reply-To: <22ae3ca40902271907r18018d55v89f4782a0d7bc34d@mail.gmail.com> References: <22ae3ca40902271907r18018d55v89f4782a0d7bc34d@mail.gmail.com> Message-ID: <49ABEDB5.3070602@sissa.it> hanghui chen wrote: > However if I run a spin-polarized calculation (LSDA), I find > that a system could be paramagnetic at "high temperature" and > ferromagnetic at 'low temperature'. That's plausible, since the magnetization is more hard to converge wrt to smearing than the total energy. The former is much more sensitive to the details of the band structure around the Fermi energy (and hence on the value used for the BROADENING parameter) than the latter. If you're sure that the ground state of your relaxed system will be ferro, why don't you try to constrain the total magnetization (search for constrained_magnetization in Doc/INPUT_PW.txt) and then relax the constrain at the end (though not sure that this last step can be done actually...). Another, more simple, solution would be to start from_scratch the "small temperature" run using the atomic positions from the previous run at "high temperature". GS > > Hanghui Chen > Department of Physics > Yale University > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From vormar at gmail.com Mon Mar 2 17:42:48 2009 From: vormar at gmail.com (Marci) Date: Mon, 2 Mar 2009 17:42:48 +0100 Subject: [Pw_forum] wrong record length Message-ID: <34ad5960903020842h5f7edffncbf9d253d18035d9@mail.gmail.com> Dear All, I faced a strange error. I've made a parallel scf calculation with a quite big sytem and after that I've tried to use a postprocess program called epsilon.x. The first calculation went well, however epsilon.x crashed saying: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from diropn : error # 3 wrong record length %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The input file seems OK, I used wfcollect = .true. in the scf calculation and set the same prefix and outdir directory in the postprocess input file. I searched the archive and the source code of espresso and it seems to me that this problem is related to this specific cluster ( http://www.nersc.gov/nusers/systems/bassi ) where I use quantum-espresso. The source code (eg. /PW/diropn.f90 ) says: ! ! the unit for record length is unfortunately machine-dependent ! unf_recl = DIRECT_IO_FACTOR * recl if (unf_recl <= 0) call errore ('diropn', 'wrong record length', 3) Maybe my problem is related to the value of DIRECT_IO_FACTOR? I forgot to mention, I'm using espresso4.0. My question is, why does this happen only with using a postprocess code and how can I cure it? On the top of this, I succeeded in running epsilon.x on a similar but smaller system at my home cluster but it's says USPPs are not implemented. As I would like to perform only a 'jdos' calculation, which doesn't need wavefunctions at all, what if I simply comment out the corresponding part of epsilon.f90? If someone could help me I can send the input files in private. Thanks in advance. Yours, Marton ----------------------------------------------------- M\'arton V\"or\"os, physicist student Department of Atomic Physics Budapest University of Technology and Economics (BUTE) Budafoki ut 8., H-1111, Budapest, Hungary vormar_at_gmail_dot_com, vm776_at_hszk_dot_bme_dot_hu ----------------------------------------------------- From akohlmey at cmm.chem.upenn.edu Mon Mar 2 18:18:15 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 2 Mar 2009 12:18:15 -0500 (EST) Subject: [Pw_forum] wrong record length In-Reply-To: <34ad5960903020842h5f7edffncbf9d253d18035d9@mail.gmail.com> References: <34ad5960903020842h5f7edffncbf9d253d18035d9@mail.gmail.com> Message-ID: On Mon, 2 Mar 2009, Marci wrote: MV> Dear All, MV> MV> I faced a strange error. I've made a parallel scf calculation with a MV> quite big sytem and after that I've tried to use a postprocess program MV> called epsilon.x. The first calculation went well, however epsilon.x MV> crashed saying: MV> MV> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MV> task # 0 MV> from diropn : error # 3 MV> wrong record length MV> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MV> MV> The input file seems OK, I used wfcollect = .true. in the scf MV> calculation and set the same prefix and outdir directory in the MV> postprocess input file. I searched the archive and the source code of MV> espresso and it seems to me that this problem is related to this MV> specific cluster ( http://www.nersc.gov/nusers/systems/bassi ) where I MV> use quantum-espresso. The source code (eg. /PW/diropn.f90 ) says: marton, are you trying to run the postprocessing on your local machine or on the IBM machine? MV> ! MV> ! the unit for record length is unfortunately machine-dependent MV> ! MV> unf_recl = DIRECT_IO_FACTOR * recl MV> if (unf_recl <= 0) call errore ('diropn', 'wrong record length', 3) MV> MV> Maybe my problem is related to the value of DIRECT_IO_FACTOR? I forgot MV> to mention, I'm using espresso4.0. My question is, why does this MV> happen only with using a postprocess code and how can I cure it? that depends on what is causing this. it could just be that you have an integer overflow, due to the size of your system, or it could be that you try to read unformatted data on a different endian machine. i would suggest you insert a print statment into the code that prints out the values of DIRECT_IO_FACTOR and recl as well as unf_recl and then get back to use with the information about the architectures and these numbers (ideally also for the smaller test, where it worked). thanks, axel. MV> On the top of this, I succeeded in running epsilon.x on a similar but MV> smaller system at my home cluster but it's says USPPs are not MV> implemented. As I would like to perform only a 'jdos' calculation, MV> which doesn't need wavefunctions at all, what if I simply comment out MV> the corresponding part of epsilon.f90? MV> MV> If someone could help me I can send the input files in private. MV> MV> Thanks in advance. MV> Yours, MV> Marton MV> MV> ----------------------------------------------------- MV> M\'arton V\"or\"os, physicist student MV> Department of Atomic Physics MV> Budapest University of Technology and Economics (BUTE) MV> Budafoki ut 8., H-1111, Budapest, Hungary MV> vormar_at_gmail_dot_com, vm776_at_hszk_dot_bme_dot_hu MV> ----------------------------------------------------- MV> _______________________________________________ MV> Pw_forum mailing list MV> Pw_forum at pwscf.org MV> http://www.democritos.it/mailman/listinfo/pw_forum MV> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From w2agz at pacbell.net Mon Mar 2 19:09:09 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Mon, 2 Mar 2009 10:09:09 -0800 Subject: [Pw_forum] LDA+U & Phonons Message-ID: <001001c99b61$fc2cfeb0$f486fc10$@net> To All in QE-Land: Is there available, or under development, or planned, anywhere out there a version of phonon.f90 and its supporting routines that accommodates the output of an LDA+U scf calculation? Cheers, -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090302/a24676aa/attachment.htm From vormar at gmail.com Mon Mar 2 21:05:14 2009 From: vormar at gmail.com (Marci) Date: Mon, 2 Mar 2009 21:05:14 +0100 Subject: [Pw_forum] wrong record length In-Reply-To: References: <34ad5960903020842h5f7edffncbf9d253d18035d9@mail.gmail.com> Message-ID: <34ad5960903021205j77f7a279j205cbfd6cbd906a1@mail.gmail.com> Hi Axel, > marton, > > are you trying to run the postprocessing on your local > machine or on the IBM machine? on the IBM machine. I had bad experiences with postprocessing on a different machine because of using the iotk package, converting binary files to text files and back is quite time consuming... (and I hate ssh-ing gygabites of files) > that depends on what is causing this. it could just be that you > have an integer overflow, due to the size of your system, or it > could be that you try to read unformatted data on a different > endian machine. i would suggest you insert a print statment into > the code that prints out the values of DIRECT_IO_FACTOR and recl > as well as unf_recl and then get back to use with the information > about the architectures and these numbers (ideally also for the > smaller test, where it worked). Unfortunately, the espresso I'm using on BASSI was not compiled by myself, and now I'm scared of compiling mine because I'm not sure that it will be able to read the binary that was made with an espresso probably compiled with different compilers and/or compiler options. Yeah, I know... I should have compiled my own version of quantum espresso before making serious calculations to avoid these situtations. So... I made some changes in diropn.f90 in espresso4.0/PW and compiled my own version of espresso (with this I get the same error) to print the values below in the case of the big run, honestly I do not really know much about this cluster, but I'm sure I'm using compiler xl fortran version 11.1.0.3 and library essl 4.2.0.3. recl: 415578000 DIRECT_IO_FACTOR: 8 unf_recl: -970343296 On my home cluster, I used a parallelized espresso-4.0.3 on system "Intel Xeon E5410 @ 2.33Ghz, 16 GB RAM" with ifort 10.1.015, intel mkl libraries 10.0.1.014 and openmpi-1.2.6 and with a smaller but similar system (same pseudos, same cutoff, only gamma point), as I said there is no "wrong record length" error and I got the following values: recl: 97079200 DIRECT_IO_FACTOR: 8 unf_recl: 776633600 If I'm right... 415578000*8 = 3324624000 which is bigger than the largest value of a signed 32 bit integer, maybe that causes the problem? Thanks for your help, Marton From lex at phys.ufl.edu Mon Mar 2 21:50:47 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Mon, 02 Mar 2009 15:50:47 -0500 Subject: [Pw_forum] wrong record length In-Reply-To: <34ad5960903021205j77f7a279j205cbfd6cbd906a1@mail.gmail.com> References: <34ad5960903020842h5f7edffncbf9d253d18035d9@mail.gmail.com> <34ad5960903021205j77f7a279j205cbfd6cbd906a1@mail.gmail.com> Message-ID: <49AC46A7.1030606@phys.ufl.edu> Hi Marton, Just in case you didn't run across this page: http://www.nersc.gov/nusers/systems/bassi/programming.php Cheers, Lex Kemper Department of Physics University of Florida Marci wrote: > Hi Axel, > >> marton, >> >> are you trying to run the postprocessing on your local >> machine or on the IBM machine? > > on the IBM machine. I had bad experiences with postprocessing on a > different machine because of using the iotk package, converting binary > files to text files and back is quite time consuming... (and I hate > ssh-ing gygabites of files) > >> that depends on what is causing this. it could just be that you >> have an integer overflow, due to the size of your system, or it >> could be that you try to read unformatted data on a different >> endian machine. i would suggest you insert a print statment into >> the code that prints out the values of DIRECT_IO_FACTOR and recl >> as well as unf_recl and then get back to use with the information >> about the architectures and these numbers (ideally also for the >> smaller test, where it worked). > > Unfortunately, the espresso I'm using on BASSI was not compiled by > myself, and now I'm scared of compiling mine because I'm not sure that > it will be able to read the binary that was made with an espresso > probably compiled with different compilers and/or compiler options. > Yeah, I know... I should have compiled my own version of quantum > espresso before making serious calculations to avoid these > situtations. > > So... I made some changes in diropn.f90 in espresso4.0/PW and compiled > my own version of espresso (with this I get the same error) to print > the values below in the case of the big run, honestly I do not really > know much about this cluster, but I'm sure I'm using compiler xl > fortran version 11.1.0.3 and library essl 4.2.0.3. > > recl: 415578000 > DIRECT_IO_FACTOR: 8 > unf_recl: -970343296 > > On my home cluster, I used a parallelized espresso-4.0.3 on system > "Intel Xeon E5410 @ 2.33Ghz, 16 GB RAM" with ifort 10.1.015, intel mkl > libraries 10.0.1.014 and openmpi-1.2.6 and with a smaller but similar > system (same pseudos, same cutoff, only gamma point), as I said there > is no "wrong record length" error and I got the following values: > > recl: 97079200 > DIRECT_IO_FACTOR: 8 > unf_recl: 776633600 > > If I'm right... 415578000*8 = 3324624000 which is bigger than the > largest value of a signed 32 bit integer, maybe that causes the > problem? > > Thanks for your help, > Marton > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From akohlmey at cmm.chem.upenn.edu Mon Mar 2 22:10:16 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 2 Mar 2009 16:10:16 -0500 (EST) Subject: [Pw_forum] wrong record length In-Reply-To: <34ad5960903021205j77f7a279j205cbfd6cbd906a1@mail.gmail.com> References: <34ad5960903020842h5f7edffncbf9d253d18035d9@mail.gmail.com> <34ad5960903021205j77f7a279j205cbfd6cbd906a1@mail.gmail.com> Message-ID: On Mon, 2 Mar 2009, Marci wrote: MV> Hi Axel, MV> MV> > marton, MV> > MV> > are you trying to run the postprocessing on your local MV> > machine or on the IBM machine? MV> MV> on the IBM machine. I had bad experiences with postprocessing on a MV> different machine because of using the iotk package, converting binary MV> files to text files and back is quite time consuming... (and I hate MV> ssh-ing gygabites of files) just checking. actually, there are ways to make fortran read IEEE-754 compliant binary floating point numbers on different endian hardware, but i never checked whether iotk can handle this as well. [...] MV> Unfortunately, the espresso I'm using on BASSI was not compiled by MV> myself, and now I'm scared of compiling mine because I'm not sure that MV> it will be able to read the binary that was made with an espresso MV> probably compiled with different compilers and/or compiler options. there is a big difference between linux and non-linux machines. on linux there is a zoo of compilers and math libraries and there are all kinds of subtle compatibility issues. on AIX or other "commercial" platforms, this is generally less of an issue, only that it is not as easy to replace one compiler by another, in case the system provided compiler is broken. MV> Yeah, I know... I should have compiled my own version of quantum MV> espresso before making serious calculations to avoid these MV> situtations. MV> MV> So... I made some changes in diropn.f90 in espresso4.0/PW and compiled MV> my own version of espresso (with this I get the same error) to print MV> the values below in the case of the big run, honestly I do not really MV> know much about this cluster, but I'm sure I'm using compiler xl MV> fortran version 11.1.0.3 and library essl 4.2.0.3. that is fine. MV> MV> recl: 415578000 MV> DIRECT_IO_FACTOR: 8 MV> unf_recl: -970343296 bingo! this is your problem. 8x415578000 is larger than 2^31, so unf_recl defined as integer*4 will overflow. MV> On my home cluster, I used a parallelized espresso-4.0.3 on system MV> "Intel Xeon E5410 @ 2.33Ghz, 16 GB RAM" with ifort 10.1.015, intel mkl MV> libraries 10.0.1.014 and openmpi-1.2.6 and with a smaller but similar MV> system (same pseudos, same cutoff, only gamma point), as I said there MV> is no "wrong record length" error and I got the following values: MV> MV> recl: 97079200 MV> DIRECT_IO_FACTOR: 8 MV> unf_recl: 776633600 MV> MV> If I'm right... 415578000*8 = 3324624000 which is bigger than the MV> largest value of a signed 32 bit integer, maybe that causes the MV> problem? exactly. the interesting question is now, how to work around this problem. you could try and declare unf_recl as integer*8 and try to recompile. perhaps, even just removing the test for negative unf_recl might work, but i doubt it. good luck, axel. MV> Thanks for your help, MV> Marton MV> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From afloris at physik.fu-berlin.de Mon Mar 2 23:06:53 2009 From: afloris at physik.fu-berlin.de (Andrea Floris) Date: Mon, 2 Mar 2009 23:06:53 +0100 (CET) Subject: [Pw_forum] LDA+U & Phonons Message-ID: Dear Paul, the LDA+U + phonons has been implemented, in a version not yet publicly available. Simmetries and parallelization are still not there, but the implementation was extensively tested, and tests on calculated phonon dispersions against the experiments are currently being performed, on several materials. After, I hope-guess that the LDA+U in the linear response will be available, cheers, Andrea --------------- Dr. Andrea Floris Institut fuer Theoretische Physik Freie Universitaet Berlin Arnimallee 14 D-14195 Berlin Germany Tel +49-30-838-53029 Fax +49-30-838-55258 e-mail: andrea.floris at fu-berlin.de To All in QE-Land: Is there available, or under development, or planned, anywhere out there a version of phonon.f90 and its supporting routines that accommodates the output of an LDA+U scf calculation? Cheers, -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com From w2agz at pacbell.net Tue Mar 3 00:22:22 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Mon, 2 Mar 2009 15:22:22 -0800 Subject: [Pw_forum] LDA+U & Phonons In-Reply-To: References: Message-ID: <003801c99b8d$bdaaef40$3900cdc0$@net> Dear Andrea, Thanks for your quick response. Any idea when a version might be available on the O-sesame CVS repository? Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Andrea Floris Sent: Monday, March 02, 2009 2:07 PM To: PWSCF_forum Subject: Re: [Pw_forum] LDA+U & Phonons Dear Paul, the LDA+U + phonons has been implemented, in a version not yet publicly available. Simmetries and parallelization are still not there, but the implementation was extensively tested, and tests on calculated phonon dispersions against the experiments are currently being performed, on several materials. After, I hope-guess that the LDA+U in the linear response will be available, cheers, Andrea --------------- Dr. Andrea Floris Institut fuer Theoretische Physik Freie Universitaet Berlin Arnimallee 14 D-14195 Berlin Germany Tel +49-30-838-53029 Fax +49-30-838-55258 e-mail: andrea.floris at fu-berlin.de To All in QE-Land: Is there available, or under development, or planned, anywhere out there a version of phonon.f90 and its supporting routines that accommodates the output of an LDA+U scf calculation? Cheers, -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From baris.malcioglu at gmail.com Tue Mar 3 09:54:22 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Tue, 3 Mar 2009 09:54:22 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> Message-ID: Dear Zhang, Did you try increasing ecutrho? (you can start with smt. like 400 Ry. in your case). In my experience this kind of errors might also result from US PPs having "slightly exotic" projectors. Sometimes the above trick helps. Best, Baris SISSA On Mon, Mar 2, 2009 at 2:49 PM, Aihua Zhang wrote: > Unfortunately, the problem seems not due to insufficient number of bands. > The number of total electrons is 96 and I increased nbnd to 78, and the > error still occurs. As it occurs during the first step of SCF, I don't think > the tags in &ions have an effect. Here is the output file. Please have a > kind look. Thanks. > > ------------------------------------------------------------------------------------------ > > ???? Program PWSCF???? v.4.0.4? starts ... > ???? Today is? 2Mar2009 at 21:26:47 > > ???? Parallel version (MPI) > > ???? Number of processors in use:?????? 8 > ???? R & G space division:? proc/pool =??? 8 > > ???? For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or PAW > > ???? Current dimensions of program pwscf are: > ???? Max number of different atomic species (ntypx) = 10 > ???? Max number of k-points (npk) =? 40000 > ???? Max angular momentum in pseudopotentials (lmaxx) =? 3 > > ???? Iterative solution of the eigenvalue problem > > ???? a parallel distributed memory algorithm will be used, > ???? eigenstates matrixes will be distributed block like on > ???? ortho sub-group =??? 2*?? 2 procs > > > ???? Planes per process (thick) : nr3 =324 npp =? 41 ncplane = 2025 > ???? Planes per process (smooth): nr3s=240 npps=? 30 ncplanes=? 900 > > ???? Proc/? planes cols???? G??? planes cols??? G????? columns? G > ???? Pool?????? (dense grid)?????? (smooth grid)????? (wavefct grid) > ?????? 1???? 41??? 161??? 34713?? 30???? 85??? 13519???? 27???? 2217 > ?????? 2???? 41??? 161??? 34699?? 30???? 85??? 13533???? 25???? 2211 > ?????? 3???? 41??? 161??? 34695?? 30???? 86??? 13506???? 27???? 2217 > ?????? 4???? 41??? 162??? 34702?? 30???? 85??? 13511???? 27???? 2219 > ?????? 5???? 40??? 161??? 34695?? 30???? 85??? 13501???? 27???? 2219 > ?????? 6???? 40??? 161??? 34695?? 30???? 85??? 13497???? 27???? 2215 > ?????? 7???? 40??? 161??? 34693?? 30???? 85??? 13503???? 27???? 2217 > ?????? 8???? 40??? 161??? 34695?? 30???? 85??? 13499???? 26???? 2210 > ???? tot??? 324?? 1289?? 277587? 240??? 681?? 108069??? 213??? 17725 > > > > ???? bravais-lattice index???? =??????????? 6 > ???? lattice parameter (a_0)?? =?????? 7.3400? a.u. > ???? unit-cell volume????????? =??? 3163.5752 (a.u.)^3 > ???? number of atoms/cell????? =?????????? 11 > ???? number of atomic types??? =??????????? 2 > ???? number of electrons?????? =??????? 96.00 > ???? number of Kohn-Sham states=?????????? 78 > ???? kinetic-energy cutoff???? =????? 40.0000? Ry > ???? charge density cutoff???? =???? 300.0000? Ry > ???? convergence threshold???? =????? 1.0E-08 > ???? mixing beta?????????????? =?????? 0.7000 > ???? number of iterations used =??????????? 8? plain???? mixing > ???? Exchange-correlation????? =? SLA? PW?? PBE? PBE (1434) > ???? nstep???????????????????? =?????????? 50 > > > ???? celldm(1)=?? 7.340000? celldm(2)=?? 0.000000? celldm(3)=?? 8.000000 > ???? celldm(4)=?? 0.000000? celldm(5)=?? 0.000000? celldm(6)=?? 0.000000 > > ???? crystal axes: (cart. coord. in units of a_0) > ?????????????? a(1) = (? 1.000000? 0.000000? 0.000000 ) > ?????????????? a(2) = (? 0.000000? 1.000000? 0.000000 ) > ?????????????? a(3) = (? 0.000000? 0.000000? 8.000000 ) > > ???? reciprocal axes: (cart. coord. in units 2 pi/a_0) > ?????????????? b(1) = (? 1.000000? 0.000000? 0.000000 ) > ?????????????? b(2) = (? 0.000000? 1.000000? 0.000000 ) > ?????????????? b(3) = (? 0.000000? 0.000000? 0.125000 ) > > > ???? PseudoPot. # 1 for Rh read from file Rh.pbe-rrkjus.UPF > ???? Pseudo is Ultrasoft, Zval =? 9.0 > ???? Generated by new atomic code, or converted to UPF format > ???? Using radial grid of 1191 points,? 3 beta functions with: > ??????????????? l(1) =?? 1 > ??????????????? l(2) =?? 2 > ??????????????? l(3) =?? 2 > ???? Q(r) pseudized with 0 coefficients > > > ???? PseudoPot. # 2 for O? read from file O.pbe-rrkjus.UPF > ???? Pseudo is Ultrasoft, Zval =? 6.0 > ???? Generated by new atomic code, or converted to UPF format > ???? Using radial grid of 1269 points,? 4 beta functions with: > ??????????????? l(1) =?? 0 > ??????????????? l(2) =?? 0 > ??????????????? l(3) =?? 1 > ??????????????? l(4) =?? 1 > ???? Q(r) pseudized with 0 coefficients > > > ???? atomic species?? valence??? mass???? pseudopotential > ??????? Rh???????????? 9.00?? 102.90550???? Rh( 1.00) > ??????? O????????????? 6.00??? 15.99940???? O ( 1.00) > > ????? 8 Sym.Ops. (no inversion) > > ??????????????????????????????????? s??????????????????????? frac. trans. > > ????? isym =? 1???? identity > > ?cryst.?? s( 1) = (???? 1????????? 0????????? 0????? ) > ????????????????? (???? 0????????? 1????????? 0????? ) > ????????????????? (???? 0????????? 0????????? 1????? ) > > ?cart.??? s( 1) = (? 1.0000000? 0.0000000? 0.0000000 ) > ????????????????? (? 0.0000000? 1.0000000? 0.0000000 ) > ????????????????? (? 0.0000000? 0.0000000? 1.0000000 ) > > > ????? isym =? 2???? 180 deg rotation - cart. axis [0,0,1] > > ?cryst.?? s( 2) = (??? -1????????? 0????????? 0????? ) > ????????????????? (???? 0???????? -1????????? 0????? ) > ????????????????? (???? 0????????? 0????????? 1????? ) > > ?cart.??? s( 2) = ( -1.0000000? 0.0000000? 0.0000000 ) > ????????????????? (? 0.0000000 -1.0000000? 0.0000000 ) > ????????????????? (? 0.0000000? 0.0000000? 1.0000000 ) > > > ????? isym =? 3????? 90 deg rotation - cart. axis [0,0,-1] > > ?cryst.?? s( 3) = (???? 0???????? -1????????? 0????? ) > ????????????????? (???? 1????????? 0????????? 0????? ) > ????????????????? (???? 0????????? 0????????? 1????? ) > > ?cart.??? s( 3) = (? 0.0000000? 1.0000000? 0.0000000 ) > ????????????????? ( -1.0000000? 0.0000000? 0.0000000 ) > ????????????????? (? 0.0000000? 0.0000000? 1.0000000 ) > > > ????? isym =? 4????? 90 deg rotation - cart. axis [0,0,1] > > ?cryst.?? s( 4) = (???? 0????????? 1????????? 0????? ) > ????????????????? (??? -1????????? 0????????? 0????? ) > ????????????????? (???? 0????????? 0????????? 1????? ) > > ?cart.??? s( 4) = (? 0.0000000 -1.0000000? 0.0000000 ) > ????????????????? (? 1.0000000? 0.0000000? 0.0000000 ) > ????????????????? (? 0.0000000? 0.0000000? 1.0000000 ) > > > ????? isym =? 5???? inv. 180 deg rotation - cart. axis [0,1,0] > > ?cryst.?? s( 5) = (???? 1????????? 0????????? 0????? ) > ????????????????? (???? 0???????? -1????????? 0????? ) > ????????????????? (???? 0????????? 0????????? 1????? ) > > ?cart.??? s( 5) = (? 1.0000000? 0.0000000? 0.0000000 ) > ????????????????? (? 0.0000000 -1.0000000? 0.0000000 ) > ????????????????? (? 0.0000000? 0.0000000? 1.0000000 ) > > > ????? isym =? 6???? inv. 180 deg rotation - cart. axis [1,0,0] > > ?cryst.?? s( 6) = (??? -1????????? 0????????? 0????? ) > ????????????????? (???? 0????????? 1????????? 0????? ) > ????????????????? (???? 0????????? 0????????? 1????? ) > > ?cart.??? s( 6) = ( -1.0000000? 0.0000000? 0.0000000 ) > ????????????????? (? 0.0000000? 1.0000000? 0.0000000 ) > ????????????????? (? 0.0000000? 0.0000000? 1.0000000 ) > > > ????? isym =? 7???? inv. 180 deg rotation - cart. axis [1,1,0] > > ?cryst.?? s( 7) = (???? 0???????? -1????????? 0????? ) > ????????????????? (??? -1????????? 0????????? 0????? ) > ????????????????? (???? 0????????? 0????????? 1????? ) > > ?cart.??? s( 7) = (? 0.0000000 -1.0000000? 0.0000000 ) > ????????????????? ( -1.0000000? 0.0000000? 0.0000000 ) > ????????????????? (? 0.0000000? 0.0000000? 1.0000000 ) > > > ????? isym =? 8???? inv. 180 deg rotation - cart. axis [1,-1,0] > > ?cryst.?? s( 8) = (???? 0????????? 1????????? 0????? ) > ????????????????? (???? 1????????? 0????????? 0????? ) > ????????????????? (???? 0????????? 0????????? 1????? ) > > ?cart.??? s( 8) = (? 0.0000000? 1.0000000? 0.0000000 ) > ????????????????? (? 1.0000000? 0.0000000? 0.0000000 ) > ????????????????? (? 0.0000000? 0.0000000? 1.0000000 ) > > > ???? point group C_4v (4mm) > ???? there are? 5 classes > ???? the character table: > > ?????? E???? 2C4?? C2??? 2s_v? 2s_d > A_1??? 1.00? 1.00? 1.00? 1.00? 1.00 > A_2??? 1.00? 1.00? 1.00 -1.00 -1.00 > B_1??? 1.00 -1.00? 1.00? 1.00 -1.00 > B_2??? 1.00 -1.00? 1.00 -1.00? 1.00 > E????? 2.00? 0.00 -2.00? 0.00? 0.00 > > ???? the symmetry operations in each class: > ???? E??????? 1 > ???? C2?????? 2 > ???? 2C4????? 3??? 4 > ???? 2s_v???? 5??? 6 > ???? 2s_d???? 7??? 8 > > ?? Cartesian axes > > ???? site n.???? atom????????????????? positions (a_0 units) > ???????? 1?????????? Rh? tau(? 1) = (?? 0.0000000?? 0.0000000?? 0.0000000? ) > ???????? 2?????????? Rh? tau(? 2) = (?? 0.5000000?? 0.5000000?? 0.0000000? ) > ???????? 3?????????? Rh? tau(? 3) = (?? 0.5000000?? 0.0000000?? 0.5000000? ) > ???????? 4?????????? Rh? tau(? 4) = (?? 0.0000000?? 0.5000000?? 0.5000000? ) > ???????? 5?????????? Rh? tau(? 5) = (?? 0.0000000?? 0.0000000?? 1.0000000? ) > ???????? 6?????????? Rh? tau(? 6) = (?? 0.5000000?? 0.5000000?? 1.0000000? ) > ???????? 7?????????? Rh? tau(? 7) = (?? 0.5000000?? 0.0000000?? 1.5000000? ) > ???????? 8?????????? Rh? tau(? 8) = (?? 0.0000000?? 0.5000000?? 1.5000000? ) > ???????? 9?????????? Rh? tau(? 9) = (?? 0.0000000?? 0.0000000?? 2.0000000? ) > ??????? 10?????????? Rh? tau( 10) = (?? 0.5000000?? 0.5000000?? 2.0000000? ) > ??????? 11?????????? O?? tau( 11) = (?? 0.5000000?? 0.5000000?? 2.5177112? ) > > ?? Crystallographic axes > > ???? site n.???? atom????????????????? positions (cryst. coord.) > ???????? 1?????????? Rh? tau(? 1) = (? 0.0000000? 0.0000000? 0.0000000? ) > ???????? 2?????????? Rh? tau(? 2) = (? 0.5000000? 0.5000000? 0.0000000? ) > ???????? 3?????????? Rh? tau(? 3) = (? 0.5000000? 0.0000000? 0.0625000? ) > ???????? 4?????????? Rh? tau(? 4) = (? 0.0000000? 0.5000000? 0.0625000? ) > ???????? 5?????????? Rh? tau(? 5) = (? 0.0000000? 0.0000000? 0.1250000? ) > ???????? 6?????????? Rh? tau(? 6) = (? 0.5000000? 0.5000000? 0.1250000? ) > ???????? 7?????????? Rh? tau(? 7) = (? 0.5000000? 0.0000000? 0.1875000? ) > ???????? 8?????????? Rh? tau(? 8) = (? 0.0000000? 0.5000000? 0.1875000? ) > ???????? 9?????????? Rh? tau(? 9) = (? 0.0000000? 0.0000000? 0.2500000? ) > ??????? 10?????????? Rh? tau( 10) = (? 0.5000000? 0.5000000? 0.2500000? ) > ??????? 11?????????? O?? tau( 11) = (? 0.5000000? 0.5000000? 0.3147139? ) > > ???? number of k points=?? 10? gaussian broad. (Ry)=? 0.0200???? ngauss = > 1 > ?????????????????????? cart. coord. in units 2pi/a_0 > ??????? k(??? 1) = (?? 0.0000000?? 0.0000000?? 0.0000000), wk =?? 0.0555556 > ??????? k(??? 2) = (?? 0.0000000?? 0.1666667?? 0.0000000), wk =?? 0.2222222 > ??????? k(??? 3) = (?? 0.0000000?? 0.3333333?? 0.0000000), wk =?? 0.2222222 > ??????? k(??? 4) = (?? 0.0000000? -0.5000000?? 0.0000000), wk =?? 0.1111111 > ??????? k(??? 5) = (?? 0.1666667?? 0.1666667?? 0.0000000), wk =?? 0.2222222 > ??????? k(??? 6) = (?? 0.1666667?? 0.3333333?? 0.0000000), wk =?? 0.4444444 > ??????? k(??? 7) = (?? 0.1666667? -0.5000000?? 0.0000000), wk =?? 0.2222222 > ??????? k(??? 8) = (?? 0.3333333?? 0.3333333?? 0.0000000), wk =?? 0.2222222 > ??????? k(??? 9) = (?? 0.3333333? -0.5000000?? 0.0000000), wk =?? 0.2222222 > ??????? k(?? 10) = (? -0.5000000? -0.5000000?? 0.0000000), wk =?? 0.0555556 > > ?????????????????????? cryst. coord. > ??????? k(??? 1) = (?? 0.0000000?? 0.0000000?? 0.0000000), wk =?? 0.0555556 > ??????? k(??? 2) = (?? 0.0000000?? 0.1666667?? 0.0000000), wk =?? 0.2222222 > ??????? k(??? 3) = (?? 0.0000000?? 0.3333333?? 0.0000000), wk =?? 0.2222222 > ??????? k(??? 4) = (?? 0.0000000? -0.5000000?? 0.0000000), wk =?? 0.1111111 > ??????? k(??? 5) = (?? 0.1666667?? 0.1666667?? 0.0000000), wk =?? 0.2222222 > ??????? k(??? 6) = (?? 0.1666667?? 0.3333333?? 0.0000000), wk =?? 0.4444444 > ??????? k(??? 7) = (?? 0.1666667? -0.5000000?? 0.0000000), wk =?? 0.2222222 > ??????? k(??? 8) = (?? 0.3333333?? 0.3333333?? 0.0000000), wk =?? 0.2222222 > ??????? k(??? 9) = (?? 0.3333333? -0.5000000?? 0.0000000), wk =?? 0.2222222 > ??????? k(?? 10) = (? -0.5000000? -0.5000000?? 0.0000000), wk =?? 0.0555556 > > ???? G cutoff =? 409.4055? ( 277587 G-vectors)???? FFT grid: ( 45, 45,324) > ???? G cutoff =? 218.3496? ( 108069 G-vectors)? smooth grid: ( 30, 30,240) > > ???? Largest allocated arrays???? est. size (Mb)???? dimensions > ??????? Kohn-Sham Wavefunctions???????? 2.04 Mb???? (?? 1714,? 78) > ??????? NL pseudopotentials???????????? 3.61 Mb???? (?? 1714, 138) > ??????? Each V/rho on FFT grid????????? 1.27 Mb???? (? 83025) > ??????? Each G-vector array???????????? 0.26 Mb???? (? 34713) > ??????? G-vector shells???????????????? 0.03 Mb???? (?? 4389) > ???? Largest temporary arrays???? est. size (Mb)???? dimensions > ??????? Each subspace H/S matrix??????? 0.09 Mb???? (???? 78,? 78) > ??????? Each matrix????? 0.16 Mb???? (??? 138,? 78) > ??????? Arrays for rho mixing????????? 10.13 Mb???? (? 83025,?? 8) > > ???? Initial potential from superposition of free atoms > > ???? starting charge?? 95.99298, renormalised to?? 96.00000 > > ???? negative rho (up, down):? 0.422E-04 0.000E+00 > ???? Starting wfc are?? 64 atomic +?? 14 random wfc > > ???? total cpu time spent up to now is????? 7.86 secs > > ???? per-process dynamical memory:??? 64.3 Mb > > ???? Self-consistent Calculation > > ???? iteration #? 1???? ecut=??? 40.00 Ry???? beta=0.70 > ???? CG style diagonalization > ???? ethr =? 1.00E-02,? avg # of iterations =? 4.3 > > ???? negative rho (up, down):? 0.222E-04 0.000E+00 > > ???? total cpu time spent up to now is??? 126.56 secs > > ???? WARNING: integrated charge=??? 95.75373487, expected=??? 96.00000000 > > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > ???? from electrons : error #???????? 1 > ???? charge is wrong > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > ???? stopping ... > > ------------------------------------------------------------------------------------------ > > > Best > > Zhang > > On Mon, Mar 2, 2009 at 9:06 PM, Aihua Zhang wrote: >> >> Dear Eyvaz and Paolo, >> >> Thanks for the prompt suggestions. I'll check if it works soon. >> My affiliation should be in the below signature now. :) >> >> Best >> >> Zhang >> >> On Mon, Mar 2, 2009 at 8:06 PM, Paolo Giannozzi >> wrote: >>> >>> Paolo Giannozzi wrote: >>> >>> > If not, please provide an input and and an output >>> >>> actually an output is sufficient, since the input was >>> already in your message >>> >>> P. >>> -- >>> Paolo Giannozzi, Democritos and University of Udine, Italy >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> -- >> ------------------------------------------------------------------ >> Research Fellow, >> Dept. of Physics, National Univ. of Singapore >> 10 Kent Ridge Crescent, Singapore, 119260 >> Tel: +65 6516 7844 >> ------------------------------------------------------------------ >> > > > > -- > ------------------------------------------------------------------ > Research Fellow, > Dept. of Physics, National Univ. of Singapore > 10 Kent Ridge Crescent, Singapore, 119260 > Tel: +65 6516 7844 > ------------------------------------------------------------------ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at democritos.it Tue Mar 3 10:15:26 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 03 Mar 2009 10:15:26 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> Message-ID: <49ACF52E.60500@democritos.it> O. Baris Malcioglu wrote: > Did you try increasing ecutrho? (you can start with smt. like 400 Ry. > in your case). > > In my experience this kind of errors might also result from US PPs > having "slightly exotic" projectors. Sometimes the above trick helps. it doesn't; there is something else here. It works on my PC but invariably crashes on 8 processors (also for the CVS version). Anyway: one should use mixing_mode='local-TF', a smaller mixing_beta (0.3 or so: the system has slab geometry), diagonalization='david' (faster than 'cg') P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 3 10:23:07 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 03 Mar 2009 10:23:07 +0100 Subject: [Pw_forum] wrong record length In-Reply-To: References: <34ad5960903020842h5f7edffncbf9d253d18035d9@mail.gmail.com> <34ad5960903021205j77f7a279j205cbfd6cbd906a1@mail.gmail.com> Message-ID: <49ACF6FB.3010207@democritos.it> Axel Kohlmeyer wrote: > the interesting question is now, how to work around this problem. > you could try and declare unf_recl as integer*8 and try to recompile. once upon a time there were limitations on the maximum length of direct access records on some machines. I remember I modified the two routines that open and read/write in such a way that each record was split into more records with the maximum allowed length. Anyway, for very big jobs, integers that don't fit into 32 bits will show up somewhere else, so the ultimate solution is to compile with default 64-bit integers, I guess Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From zah7903 at gmail.com Tue Mar 3 10:24:43 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Tue, 3 Mar 2009 17:24:43 +0800 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: <49ACF52E.60500@democritos.it> References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> <49ACF52E.60500@democritos.it> Message-ID: With david, the code crashes with another error. Since the program crashes in the middle the first scf iteration, the mixing setting should not be relevant. Am I right? Zhang On Tue, Mar 3, 2009 at 5:15 PM, Paolo Giannozzi wrote: > O. Baris Malcioglu wrote: > > > Did you try increasing ecutrho? (you can start with smt. like 400 Ry. > > in your case). > > > > In my experience this kind of errors might also result from US PPs > > having "slightly exotic" projectors. Sometimes the above trick helps. > > it doesn't; there is something else here. It works on my PC but > invariably crashes on 8 processors (also for the CVS version). > Anyway: one should use mixing_mode='local-TF', a smaller mixing_beta > (0.3 or so: the system has slab geometry), diagonalization='david' > (faster than 'cg') > - Show quoted text - > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090303/cc7c8a2c/attachment-0001.htm From giannozz at democritos.it Tue Mar 3 10:26:22 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 03 Mar 2009 10:26:22 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> <49ACF52E.60500@democritos.it> Message-ID: <49ACF7BE.1040406@democritos.it> Aihua Zhang wrote: > With david, the code crashes with another error. Since the program > crashes in the middle the first scf iteration, the mixing setting should > not be relevant. run it serially P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From mjfmartins at ice.ufjf.br Tue Mar 3 11:05:30 2009 From: mjfmartins at ice.ufjf.br (=?ISO-8859-1?Q?MATEUS_JOS=C9_FERNANDES_MARTINS?=) Date: Tue, 3 Mar 2009 07:05:30 -0300 Subject: [Pw_forum] Error in ph.x calculation. Message-ID: <85d7d5fd0903030205m4c16a3ffy97c1f09918a89c25@mail.gmail.com> Hello everyone, my ph.x calculation was interrupted. In your restart, your output show the error # 1, the file write the following message: from broyden : error # 1 factorization What does this error, and fix it? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090303/65d95b8f/attachment.htm From paulatto at sissa.it Tue Mar 3 11:27:58 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 03 Mar 2009 11:27:58 +0100 Subject: [Pw_forum] Error in ph.x calculation. In-Reply-To: <85d7d5fd0903030205m4c16a3ffy97c1f09918a89c25@mail.gmail.com> References: <85d7d5fd0903030205m4c16a3ffy97c1f09918a89c25@mail.gmail.com> Message-ID: On Tue, 03 Mar 2009 11:05:30 +0100, MATEUS JOS?? FERNANDES MARTINS wrote: > What does this error, and fix it? Dear Mateus, we have no supernatural powers, you should try and provide as much information as possible about your job if you want to receive a meaningful reply. You problem may be related to the restart or not. Without the full input of the pw and ph calculation, and the full output of both there is little more to say. Please see http://www.celiojunior.com.br/comofazerperguntas.htm for details. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From toashagupta at gmail.com Tue Mar 3 12:42:30 2009 From: toashagupta at gmail.com (Asha gupta) Date: Tue, 3 Mar 2009 17:12:30 +0530 Subject: [Pw_forum] Fwd: In-Reply-To: <49826.203.200.55.101.1236081338.squirrel@sscu.iisc.ernet.in> References: <49826.203.200.55.101.1236081338.squirrel@sscu.iisc.ernet.in> Message-ID: Hi all, I am new to this forum. Recently, started DFT calculations. I have two similar input files a sshown below: FIRST ONE &control calculation='vc-relax', pseudo_dir = '/home/waghmare/asha/pseudo/', outdir='/home/waghmare/asha/CeFeO/tmp/', tstress = .true. tprnfor = .true. prefix='CeFeO' / &system ibrav=0, nat= 23, ntyp=3, ecutwfc = 30.0, ecutrho = 180.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.003, nbnd=110, / &electrons conv_thr = 1.0e-6, mixing_beta = 0.1, / &ions / &cell cell_dynamics = 'damp-pr' , / ATOMIC_SPECIES Fe 55.85 fe_lda_sc.UPF Ce 140.116 Ce_lda_sc.UPF O 16.00 O.pz-rrkjus.UPF CELL_PARAMETERS 10.22 0.00 0.00 0.00 10.22 0.00 0.00 0.00 20.44 ATOMIC_POSITIONS (crystal) Ce 0.000 0.000 0.000 Ce 0.000 0.000 0.500 Ce 0.000 0.500 0.250 Ce 0.000 0.500 0.750 Ce 0.500 0.000 0.250 Ce 0.500 0.000 0.750 Fe 0.500 0.500 0.500 Ce 0.500 0.500 0.000 O 0.250 0.250 0.150 O 0.250 0.250 0.625 O 0.250 -0.250 0.125 O 0.250 0.250 -0.125 O 0.250 0.250 -0.625 O -0.250 0.250 0.125 O -0.250 0.250 0.625 O -0.250 -0.250 0.125 O -0.250 -0.250 0.625 O -0.250 0.250 -0.125 O -0.250 0.250 -0.625 O 0.250 -0.250 -0.125 O 0.250 -0.250 -0.625 O -0.250 -0.250 -0.125 O -0.250 -0.250 -0.625 K_POINTS {automatic} 4 4 4 0 0 0 SECOND ONE &control calculation='vc-relax', pseudo_dir = '/home/waghmare/asha/pseudo/', outdir='/home/waghmare/asha/CeMnO/tmp/', tstress = .true. tprnfor = .true. prefix='CeMnO' / &system ibrav=0, nat= 23, ntyp=3, ecutwfc = 30.0, ecutrho = 180.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.003, nbnd=110, / &electrons conv_thr = 1.0e-6, mixing_beta = 0.1, / &ions / &cell cell_dynamics = 'damp-pr' , / ATOMIC_SPECIES Mn 54.94 Mn.pbe-sp-van.UPF Ce 140.116 Ce_lda_sc.UPF O 16.00 O.pz-rrkjus.UPF CELL_PARAMETERS 10.22 0.00 0.00 0.00 10.22 0.00 0.00 0.00 20.44 ATOMIC_POSITIONS (crystal) Ce 0.000 0.000 0.000 Ce 0.000 0.000 0.500 Ce 0.000 0.500 0.250 Ce 0.000 0.500 0.750 Ce 0.500 0.000 0.250 Ce 0.500 0.000 0.750 Mn 0.500 0.500 0.500 Ce 0.500 0.500 0.000 O 0.250 0.250 0.150 O 0.250 0.250 0.625 O 0.250 -0.250 0.125 O 0.250 0.250 -0.125 O 0.250 0.250 -0.625 O -0.250 0.250 0.125 O -0.250 0.250 0.625 O -0.250 -0.250 0.125 O -0.250 -0.250 0.625 O -0.250 0.250 -0.125 O -0.250 0.250 -0.625 O 0.250 -0.250 -0.125 O 0.250 -0.250 -0.625 O -0.250 -0.250 -0.125 O -0.250 -0.250 -0.625 K_POINTS {automatic} 4 4 4 0 0 0 My problem is while the first one is running properly the second one is showing an error message like %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from readpp : error # 2 inconsistent DFT read %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I am totally at loss. Is there some problem with pseudopotential file?? Please help thanks in advance Asha -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090303/1c6bfa46/attachment.htm From panda.deng.pan at gmail.com Tue Mar 3 13:01:42 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Tue, 3 Mar 2009 20:01:42 +0800 Subject: [Pw_forum] Fwd: In-Reply-To: References: <49826.203.200.55.101.1236081338.squirrel@sscu.iisc.ernet.in> Message-ID: Hi Asha, > ATOMIC_SPECIES > Mn 54.94?? Mn.pbe-sp-van.UPF > Ce 140.116??Ce_lda_sc.UPF > O??16.00????O.pz-rrkjus.UPF > > Is there some problem with pseudopotential file?? yes.You must have the same pseudopotential file.Like they are all pbe or pw or others. From Giovanni.Cantele at na.infn.it Tue Mar 3 12:58:12 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Tue, 03 Mar 2009 12:58:12 +0100 Subject: [Pw_forum] Fwd: inconsistent DFT read In-Reply-To: References: <49826.203.200.55.101.1236081338.squirrel@sscu.iisc.ernet.in> Message-ID: <49AD1B54.7090105@na.infn.it> Asha gupta wrote: > Hi all, > I am new to this forum. Recently, started DFT calculations. I have two > similar input files a sshown below: > > > FIRST ONE > &control > calculation='vc-relax', > pseudo_dir = '/home/waghmare/asha/pseudo/', > outdir='/home/waghmare/asha/CeFeO/tmp/', > tstress = .true. > tprnfor = .true. > prefix='CeFeO' > / > &system > ibrav=0, > nat= 23, > ntyp=3, > ecutwfc = 30.0, > ecutrho = 180.0, > occupations='smearing', > smearing='methfessel-paxton', > degauss=0.003, > nbnd=110, > / > &electrons > conv_thr = 1.0e-6, > mixing_beta = 0.1, > / > &ions > / > &cell > cell_dynamics = 'damp-pr' , > / > ATOMIC_SPECIES > Fe 55.85 fe_lda_sc.UPF > Ce 140.116 Ce_lda_sc.UPF > O 16.00 O.pz-rrkjus.UPF > CELL_PARAMETERS > 10.22 0.00 0.00 > 0.00 10.22 0.00 > 0.00 0.00 20.44 > > ATOMIC_POSITIONS (crystal) > Ce 0.000 0.000 0.000 > Ce 0.000 0.000 0.500 > Ce 0.000 0.500 0.250 > Ce 0.000 0.500 0.750 > Ce 0.500 0.000 0.250 > Ce 0.500 0.000 0.750 > Fe 0.500 0.500 0.500 > Ce 0.500 0.500 0.000 > O 0.250 0.250 0.150 > O 0.250 0.250 0.625 > O 0.250 -0.250 0.125 > O 0.250 0.250 -0.125 > O 0.250 0.250 -0.625 > O -0.250 0.250 0.125 > O -0.250 0.250 0.625 > O -0.250 -0.250 0.125 > O -0.250 -0.250 0.625 > O -0.250 0.250 -0.125 > O -0.250 0.250 -0.625 > O 0.250 -0.250 -0.125 > O 0.250 -0.250 -0.625 > O -0.250 -0.250 -0.125 > O -0.250 -0.250 -0.625 > K_POINTS {automatic} > 4 4 4 0 0 0 > > > SECOND ONE > > &control > calculation='vc-relax', > pseudo_dir = '/home/waghmare/asha/pseudo/', > outdir='/home/waghmare/asha/CeMnO/tmp/', > tstress = .true. > tprnfor = .true. > prefix='CeMnO' > / > &system > ibrav=0, > nat= 23, > ntyp=3, > ecutwfc = 30.0, > ecutrho = 180.0, > occupations='smearing', > smearing='methfessel-paxton', > degauss=0.003, > nbnd=110, > / > &electrons > conv_thr = 1.0e-6, > mixing_beta = 0.1, > / > &ions > / > &cell > cell_dynamics = 'damp-pr' , > / > ATOMIC_SPECIES > Mn 54.94 Mn.pbe-sp-van.UPF > Ce 140.116 Ce_lda_sc.UPF > O 16.00 O.pz-rrkjus.UPF > > CELL_PARAMETERS > 10.22 0.00 0.00 > 0.00 10.22 0.00 > 0.00 0.00 20.44 > > ATOMIC_POSITIONS (crystal) > Ce 0.000 0.000 0.000 > Ce 0.000 0.000 0.500 > Ce 0.000 0.500 0.250 > Ce 0.000 0.500 0.750 > Ce 0.500 0.000 0.250 > Ce 0.500 0.000 0.750 > Mn 0.500 0.500 0.500 > Ce 0.500 0.500 0.000 > O 0.250 0.250 0.150 > O 0.250 0.250 0.625 > O 0.250 -0.250 0.125 > O 0.250 0.250 -0.125 > O 0.250 0.250 -0.625 > O -0.250 0.250 0.125 > O -0.250 0.250 0.625 > O -0.250 -0.250 0.125 > O -0.250 -0.250 0.625 > O -0.250 0.250 -0.125 > O -0.250 0.250 -0.625 > O 0.250 -0.250 -0.125 > O 0.250 -0.250 -0.625 > O -0.250 -0.250 -0.125 > O -0.250 -0.250 -0.625 > K_POINTS {automatic} > 4 4 4 0 0 0 > > My problem is while the first one is running properly the second one is > showing an error message like > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 0 > from readpp : error # 2 > inconsistent DFT read > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The error is related to the different kind of pseudopotentials used in the second run (some LDA, some GGA). The code prevents you from doing that, you can overcome this by commenting the corrsponding lines in the source code. A good practice is searching both the forum archive and the QE wiki. This is one of the questions discussed several times in the forum. In this case you may have a look here: http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_(PWscf)#pw.x_stops_with_.27inconsistent_DFT.27_error or here: http://www.democritos.it/pipermail/pw_forum/2009-January/011162.html (link to links!) giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From zah7903 at gmail.com Tue Mar 3 10:19:22 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Tue, 3 Mar 2009 17:19:22 +0800 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> Message-ID: Dear Baris, Thank you! Yes, I tried but it doesn't work. I tried also different smearing method, different smearing width, spin-polarization, and many others. In the end, I find a more bizarre thing. It works with only bottom layer of Rh (2 atoms), bottom 2 layers (4 atoms), 3 layers and 4 layers, and finally crashes for 5 layers (10 atoms). Now I suspect that something is wrong with the computing environment settings. What a hard computing life. Best, Zhang On Tue, Mar 3, 2009 at 4:54 PM, O. Baris Malcioglu < baris.malcioglu at gmail.com> wrote: > Dear Zhang, > > Did you try increasing ecutrho? (you can start with smt. like 400 Ry. > in your case). > > In my experience this kind of errors might also result from US PPs > having "slightly exotic" projectors. Sometimes the above trick helps. > > Best, > Baris > SISSA > - Show quoted text - > > On Mon, Mar 2, 2009 at 2:49 PM, Aihua Zhang wrote: > > Unfortunately, the problem seems not due to insufficient number of bands. > > The number of total electrons is 96 and I increased nbnd to 78, and the > > error still occurs. As it occurs during the first step of SCF, I don't > think > > the tags in &ions have an effect. Here is the output file. Please have a > > kind look. Thanks. > > > > > ------------------------------------------------------------------------------------------ > > > > Program PWSCF v.4.0.4 starts ... > > Today is 2Mar2009 at 21:26:47 > > > > Parallel version (MPI) > > > > Number of processors in use: 8 > > R & G space division: proc/pool = 8 > > > > For Norm-Conserving or Ultrasoft (Vanderbilt) Pseudopotentials or > PAW > > > > Current dimensions of program pwscf are: > > Max number of different atomic species (ntypx) = 10 > > Max number of k-points (npk) = 40000 > > Max angular momentum in pseudopotentials (lmaxx) = 3 > > > > Iterative solution of the eigenvalue problem > > > > a parallel distributed memory algorithm will be used, > > eigenstates matrixes will be distributed block like on > > ortho sub-group = 2* 2 procs > > > > > > Planes per process (thick) : nr3 =324 npp = 41 ncplane = 2025 > > Planes per process (smooth): nr3s=240 npps= 30 ncplanes= 900 > > > > Proc/ planes cols G planes cols G columns G > > Pool (dense grid) (smooth grid) (wavefct grid) > > 1 41 161 34713 30 85 13519 27 2217 > > 2 41 161 34699 30 85 13533 25 2211 > > 3 41 161 34695 30 86 13506 27 2217 > > 4 41 162 34702 30 85 13511 27 2219 > > 5 40 161 34695 30 85 13501 27 2219 > > 6 40 161 34695 30 85 13497 27 2215 > > 7 40 161 34693 30 85 13503 27 2217 > > 8 40 161 34695 30 85 13499 26 2210 > > tot 324 1289 277587 240 681 108069 213 17725 > > > > > > > > bravais-lattice index = 6 > > lattice parameter (a_0) = 7.3400 a.u. > > unit-cell volume = 3163.5752 (a.u.)^3 > > number of atoms/cell = 11 > > number of atomic types = 2 > > number of electrons = 96.00 > > number of Kohn-Sham states= 78 > > kinetic-energy cutoff = 40.0000 Ry > > charge density cutoff = 300.0000 Ry > > convergence threshold = 1.0E-08 > > mixing beta = 0.7000 > > number of iterations used = 8 plain mixing > > Exchange-correlation = SLA PW PBE PBE (1434) > > nstep = 50 > > > > > > celldm(1)= 7.340000 celldm(2)= 0.000000 celldm(3)= 8.000000 > > celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 > > > > crystal axes: (cart. coord. in units of a_0) > > a(1) = ( 1.000000 0.000000 0.000000 ) > > a(2) = ( 0.000000 1.000000 0.000000 ) > > a(3) = ( 0.000000 0.000000 8.000000 ) > > > > reciprocal axes: (cart. coord. in units 2 pi/a_0) > > b(1) = ( 1.000000 0.000000 0.000000 ) > > b(2) = ( 0.000000 1.000000 0.000000 ) > > b(3) = ( 0.000000 0.000000 0.125000 ) > > > > > > PseudoPot. # 1 for Rh read from file Rh.pbe-rrkjus.UPF > > Pseudo is Ultrasoft, Zval = 9.0 > > Generated by new atomic code, or converted to UPF format > > Using radial grid of 1191 points, 3 beta functions with: > > l(1) = 1 > > l(2) = 2 > > l(3) = 2 > > Q(r) pseudized with 0 coefficients > > > > > > PseudoPot. # 2 for O read from file O.pbe-rrkjus.UPF > > Pseudo is Ultrasoft, Zval = 6.0 > > Generated by new atomic code, or converted to UPF format > > Using radial grid of 1269 points, 4 beta functions with: > > l(1) = 0 > > l(2) = 0 > > l(3) = 1 > > l(4) = 1 > > Q(r) pseudized with 0 coefficients > > > > > > atomic species valence mass pseudopotential > > Rh 9.00 102.90550 Rh( 1.00) > > O 6.00 15.99940 O ( 1.00) > > > > 8 Sym.Ops. (no inversion) > > > > s frac. trans. > > > > isym = 1 identity > > > > cryst. s( 1) = ( 1 0 0 ) > > ( 0 1 0 ) > > ( 0 0 1 ) > > > > cart. s( 1) = ( 1.0000000 0.0000000 0.0000000 ) > > ( 0.0000000 1.0000000 0.0000000 ) > > ( 0.0000000 0.0000000 1.0000000 ) > > > > > > isym = 2 180 deg rotation - cart. axis [0,0,1] > > > > cryst. s( 2) = ( -1 0 0 ) > > ( 0 -1 0 ) > > ( 0 0 1 ) > > > > cart. s( 2) = ( -1.0000000 0.0000000 0.0000000 ) > > ( 0.0000000 -1.0000000 0.0000000 ) > > ( 0.0000000 0.0000000 1.0000000 ) > > > > > > isym = 3 90 deg rotation - cart. axis [0,0,-1] > > > > cryst. s( 3) = ( 0 -1 0 ) > > ( 1 0 0 ) > > ( 0 0 1 ) > > > > cart. s( 3) = ( 0.0000000 1.0000000 0.0000000 ) > > ( -1.0000000 0.0000000 0.0000000 ) > > ( 0.0000000 0.0000000 1.0000000 ) > > > > > > isym = 4 90 deg rotation - cart. axis [0,0,1] > > > > cryst. s( 4) = ( 0 1 0 ) > > ( -1 0 0 ) > > ( 0 0 1 ) > > > > cart. s( 4) = ( 0.0000000 -1.0000000 0.0000000 ) > > ( 1.0000000 0.0000000 0.0000000 ) > > ( 0.0000000 0.0000000 1.0000000 ) > > > > > > isym = 5 inv. 180 deg rotation - cart. axis [0,1,0] > > > > cryst. s( 5) = ( 1 0 0 ) > > ( 0 -1 0 ) > > ( 0 0 1 ) > > > > cart. s( 5) = ( 1.0000000 0.0000000 0.0000000 ) > > ( 0.0000000 -1.0000000 0.0000000 ) > > ( 0.0000000 0.0000000 1.0000000 ) > > > > > > isym = 6 inv. 180 deg rotation - cart. axis [1,0,0] > > > > cryst. s( 6) = ( -1 0 0 ) > > ( 0 1 0 ) > > ( 0 0 1 ) > > > > cart. s( 6) = ( -1.0000000 0.0000000 0.0000000 ) > > ( 0.0000000 1.0000000 0.0000000 ) > > ( 0.0000000 0.0000000 1.0000000 ) > > > > > > isym = 7 inv. 180 deg rotation - cart. axis [1,1,0] > > > > cryst. s( 7) = ( 0 -1 0 ) > > ( -1 0 0 ) > > ( 0 0 1 ) > > > > cart. s( 7) = ( 0.0000000 -1.0000000 0.0000000 ) > > ( -1.0000000 0.0000000 0.0000000 ) > > ( 0.0000000 0.0000000 1.0000000 ) > > > > > > isym = 8 inv. 180 deg rotation - cart. axis [1,-1,0] > > > > cryst. s( 8) = ( 0 1 0 ) > > ( 1 0 0 ) > > ( 0 0 1 ) > > > > cart. s( 8) = ( 0.0000000 1.0000000 0.0000000 ) > > ( 1.0000000 0.0000000 0.0000000 ) > > ( 0.0000000 0.0000000 1.0000000 ) > > > > > > point group C_4v (4mm) > > there are 5 classes > > the character table: > > > > E 2C4 C2 2s_v 2s_d > > A_1 1.00 1.00 1.00 1.00 1.00 > > A_2 1.00 1.00 1.00 -1.00 -1.00 > > B_1 1.00 -1.00 1.00 1.00 -1.00 > > B_2 1.00 -1.00 1.00 -1.00 1.00 > > E 2.00 0.00 -2.00 0.00 0.00 > > > > the symmetry operations in each class: > > E 1 > > C2 2 > > 2C4 3 4 > > 2s_v 5 6 > > 2s_d 7 8 > > > > Cartesian axes > > > > site n. atom positions (a_0 units) > > 1 Rh tau( 1) = ( 0.0000000 0.0000000 > 0.0000000 ) > > 2 Rh tau( 2) = ( 0.5000000 0.5000000 > 0.0000000 ) > > 3 Rh tau( 3) = ( 0.5000000 0.0000000 > 0.5000000 ) > > 4 Rh tau( 4) = ( 0.0000000 0.5000000 > 0.5000000 ) > > 5 Rh tau( 5) = ( 0.0000000 0.0000000 > 1.0000000 ) > > 6 Rh tau( 6) = ( 0.5000000 0.5000000 > 1.0000000 ) > > 7 Rh tau( 7) = ( 0.5000000 0.0000000 > 1.5000000 ) > > 8 Rh tau( 8) = ( 0.0000000 0.5000000 > 1.5000000 ) > > 9 Rh tau( 9) = ( 0.0000000 0.0000000 > 2.0000000 ) > > 10 Rh tau( 10) = ( 0.5000000 0.5000000 > 2.0000000 ) > > 11 O tau( 11) = ( 0.5000000 0.5000000 > 2.5177112 ) > > > > Crystallographic axes > > > > site n. atom positions (cryst. coord.) > > 1 Rh tau( 1) = ( 0.0000000 0.0000000 0.0000000 ) > > 2 Rh tau( 2) = ( 0.5000000 0.5000000 0.0000000 ) > > 3 Rh tau( 3) = ( 0.5000000 0.0000000 0.0625000 ) > > 4 Rh tau( 4) = ( 0.0000000 0.5000000 0.0625000 ) > > 5 Rh tau( 5) = ( 0.0000000 0.0000000 0.1250000 ) > > 6 Rh tau( 6) = ( 0.5000000 0.5000000 0.1250000 ) > > 7 Rh tau( 7) = ( 0.5000000 0.0000000 0.1875000 ) > > 8 Rh tau( 8) = ( 0.0000000 0.5000000 0.1875000 ) > > 9 Rh tau( 9) = ( 0.0000000 0.0000000 0.2500000 ) > > 10 Rh tau( 10) = ( 0.5000000 0.5000000 0.2500000 ) > > 11 O tau( 11) = ( 0.5000000 0.5000000 0.3147139 ) > > > > number of k points= 10 gaussian broad. (Ry)= 0.0200 ngauss = > > 1 > > cart. coord. in units 2pi/a_0 > > k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = > 0.0555556 > > k( 2) = ( 0.0000000 0.1666667 0.0000000), wk = > 0.2222222 > > k( 3) = ( 0.0000000 0.3333333 0.0000000), wk = > 0.2222222 > > k( 4) = ( 0.0000000 -0.5000000 0.0000000), wk = > 0.1111111 > > k( 5) = ( 0.1666667 0.1666667 0.0000000), wk = > 0.2222222 > > k( 6) = ( 0.1666667 0.3333333 0.0000000), wk = > 0.4444444 > > k( 7) = ( 0.1666667 -0.5000000 0.0000000), wk = > 0.2222222 > > k( 8) = ( 0.3333333 0.3333333 0.0000000), wk = > 0.2222222 > > k( 9) = ( 0.3333333 -0.5000000 0.0000000), wk = > 0.2222222 > > k( 10) = ( -0.5000000 -0.5000000 0.0000000), wk = > 0.0555556 > > > > cryst. coord. > > k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = > 0.0555556 > > k( 2) = ( 0.0000000 0.1666667 0.0000000), wk = > 0.2222222 > > k( 3) = ( 0.0000000 0.3333333 0.0000000), wk = > 0.2222222 > > k( 4) = ( 0.0000000 -0.5000000 0.0000000), wk = > 0.1111111 > > k( 5) = ( 0.1666667 0.1666667 0.0000000), wk = > 0.2222222 > > k( 6) = ( 0.1666667 0.3333333 0.0000000), wk = > 0.4444444 > > k( 7) = ( 0.1666667 -0.5000000 0.0000000), wk = > 0.2222222 > > k( 8) = ( 0.3333333 0.3333333 0.0000000), wk = > 0.2222222 > > k( 9) = ( 0.3333333 -0.5000000 0.0000000), wk = > 0.2222222 > > k( 10) = ( -0.5000000 -0.5000000 0.0000000), wk = > 0.0555556 > > > > G cutoff = 409.4055 ( 277587 G-vectors) FFT grid: ( 45, > 45,324) > > G cutoff = 218.3496 ( 108069 G-vectors) smooth grid: ( 30, > 30,240) > > > > Largest allocated arrays est. size (Mb) dimensions > > Kohn-Sham Wavefunctions 2.04 Mb ( 1714, 78) > > NL pseudopotentials 3.61 Mb ( 1714, 138) > > Each V/rho on FFT grid 1.27 Mb ( 83025) > > Each G-vector array 0.26 Mb ( 34713) > > G-vector shells 0.03 Mb ( 4389) > > Largest temporary arrays est. size (Mb) dimensions > > Each subspace H/S matrix 0.09 Mb ( 78, 78) > > Each matrix 0.16 Mb ( 138, 78) > > Arrays for rho mixing 10.13 Mb ( 83025, 8) > > > > Initial potential from superposition of free atoms > > > > starting charge 95.99298, renormalised to 96.00000 > > > > negative rho (up, down): 0.422E-04 0.000E+00 > > Starting wfc are 64 atomic + 14 random wfc > > > > total cpu time spent up to now is 7.86 secs > > > > per-process dynamical memory: 64.3 Mb > > > > Self-consistent Calculation > > > > iteration # 1 ecut= 40.00 Ry beta=0.70 > > CG style diagonalization > > ethr = 1.00E-02, avg # of iterations = 4.3 > > > > negative rho (up, down): 0.222E-04 0.000E+00 > > > > total cpu time spent up to now is 126.56 secs > > > > WARNING: integrated charge= 95.75373487, expected= 96.00000000 > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from electrons : error # 1 > > charge is wrong > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > > > > ------------------------------------------------------------------------------------------ > > > > > > Best > > > > Zhang > > > > On Mon, Mar 2, 2009 at 9:06 PM, Aihua Zhang wrote: > >> > >> Dear Eyvaz and Paolo, > >> > >> Thanks for the prompt suggestions. I'll check if it works soon. > >> My affiliation should be in the below signature now. :) > >> > >> Best > >> > >> Zhang > >> > >> On Mon, Mar 2, 2009 at 8:06 PM, Paolo Giannozzi > > >> wrote: > >>> > >>> Paolo Giannozzi wrote: > >>> > >>> > If not, please provide an input and and an output > >>> > >>> actually an output is sufficient, since the input was > >>> already in your message > >>> > >>> P. > >>> -- > >>> Paolo Giannozzi, Democritos and University of Udine, Italy > >>> _______________________________________________ > >>> Pw_forum mailing list > >>> Pw_forum at pwscf.org > >>> http://www.democritos.it/mailman/listinfo/pw_forum > >> > >> > >> > >> -- > >> ------------------------------------------------------------------ > >> Research Fellow, > >> Dept. of Physics, National Univ. of Singapore > >> 10 Kent Ridge Crescent, Singapore, 119260 > >> Tel: +65 6516 7844 > >> ------------------------------------------------------------------ > >> > > > > > > > > -- > > ------------------------------------------------------------------ > > Research Fellow, > > Dept. of Physics, National Univ. of Singapore > > 10 Kent Ridge Crescent, Singapore, 119260 > > Tel: +65 6516 7844 > > ------------------------------------------------------------------ > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090303/a7682c6a/attachment-0001.htm From njuxuyuehua at gmail.com Tue Mar 3 13:28:05 2009 From: njuxuyuehua at gmail.com (xu yuehua) Date: Tue, 3 Mar 2009 20:28:05 +0800 Subject: [Pw_forum] the dynmaical matrix are like "***********" when the phonons calculation at gama In-Reply-To: <930232.49838.qm@web65702.mail.ac4.yahoo.com> References: <930232.49838.qm@web65702.mail.ac4.yahoo.com> Message-ID: hi : thank Eyvaz Isaev for your hints. but unfortunately, the problem seems more complicated when i use different thr2_ph,from1.d-16 to 1.d-18 the out file wrote: PHONON : 51m46.02s CPU time, 51m50.38s wall time Alpha used in Ewald sum = 2.8000 Electric Fields Calculation iter # 1 total cpu time : 3827.9 secs av.it.: 5.2 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.130E-01 kpoint 1 ibnd 33 solve_e: root not converged NaN kpoint 1 ibnd 33 solve_e: root not converged NaN kpoint 1 ibnd 33 solve_e: root not converged NaN kpoint 2 ibnd 33 solve_e: root not converged NaN kpoint 2 ibnd 33 solve_e: root not converged NaN kpoint 2 ibnd 33 solve_e: root not converged NaN kpoint 3 ibnd 33 solve_e: root not converged NaN kpoint 3 ibnd 33 solve_e: root not converged NaN kpoint 3 ibnd 33 solve_e: root not converged NaN kpoint 4 ibnd 33 solve_e: root not converged NaN kpoint 4 ibnd 33 solve_e: root not converged NaN kpoint 4 ibnd 33 solve_e: root not converged NaN kpoint 5 ibnd 33 solve_e: root not converged NaN kpoint 5 ibnd 33 solve_e: root not converged NaN kpoint 5 ibnd 33 solve_e: root not converged NaN kpoint 6 ibnd 33 solve_e: root not converged NaN kpoint 6 ibnd 33 solve_e: root not converged NaN kpoint 6 ibnd 33 solve_e: root not converged NaN kpoint 7 ibnd 33 solve_e: root not converged NaN kpoint 7 ibnd 33 solve_e: root not converged NaN kpoint 7 ibnd 33 solve_e: root not converged NaN so i think the thr2_ph=1.d-15 is ok,not so tight to cause not converged. but my problem still exists: the ******** in Dynamical Matrix is unphysical. for it causes that the phonons at G is : Mode symmetry, C_2 (2) point group: omega( 1 - 1) = ************ [cm-1] --> B omega( 2 - 2) = ************ [cm-1] --> A omega( 3 - 3) = ************ [cm-1] --> A omega( 4 - 4) = ************ [cm-1] --> ? omega( 4 - 4) = ************ [cm-1] --> 0A omega( 4 - 4) = ************ [cm-1] --> ? omega( 4 - 4) = ************ [cm-1] --> B omega( 5 - 5) = ************ [cm-1] --> ? omega( 5 - 5) = ************ [cm-1] --> 0A omega( 5 - 5) = ************ [cm-1] --> ? omega( 5 - 5) = ************ [cm-1] --> B omega( 6 - 6) = ************ [cm-1] --> ? omega( 6 - 6) = ************ [cm-1] --> 0A omega( 6 - 6) = ************ [cm-1] --> ? omega( 6 - 6) = ************ [cm-1] --> B it is noted that the first several phonon's frequnecies should not so large,they are shoud around at zero cm-1. when is the problem, i think over it,but no answer. i need your help. my input file you can find below. thank you very much if you could give me some hints! 2009/3/2, Eyvaz Isaev : > Hi, > > As the dynamical matrix is written in the fixed format (like 3(2F12,8, 2x)), > and you have large components (say, larger than 999.99999999, or > -99.99999999 ), then it can not be printed properly. In my opinion, such > kind components will be quite unusual. > I have no experience in calculation of H2O properties, but I would recommend > the use of thr2_ph=1.d-18, at least, use different thr2_ph and see what > happens. > > If you are really interested in these values then change the format in line > 32, write_dyn_on_file.f90 (in /PH, of course), say, to f16.8, then recompile > ph.x, and enjoy seeing these values. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Sun, 3/1/09, xu yuehua wrote: > >> From: xu yuehua >> Subject: [Pw_forum] the dynmaical matrix are like "***********" when the >> phonons calculation at gama >> To: "PWSCF Forum" >> Date: Sunday, March 1, 2009, 9:45 AM >> hello all : >> >> >> i am facing unkonwn problem when i calculated the phonons >> at gama: >> >> the dynamical matrix file wrote: >> ................ >> Dynamical Matrix in cartesian axes >> >> q = ( 0.000000000 0.000000000 0.000000000 ) >> >> 1 1 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 2 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 3 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 4 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 5 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 6 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 7 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 8 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 9 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ....... >> >> my phone input file : >> phonons at Gamma >> &inputph >> tr2_ph=1.0d-15, >> prefix='scf_two_b_type', >> epsil=.true., >> amass(1)=1.0, >> amass(2)=15.999, >> outdir='/disk2/xxx/xxx/espresso-3.2.3/tmp', >> fildyn='fourringwater.dynG', >> / >> 0.0 0.0 0.0 >> >> >> and my scf input file is :&CONTROL >> calculation = "scf", >> prefix = "scf_two_b_type" >> pseudo_dir = >> "/disk2/xxx/xxx/espresso-3.2.3/pseudo", >> outdir = >> "/disk2/jdong/xyh/espresso-3.2.3/tmp", >> / >> &SYSTEM >> ibrav = 4, >> a=20,b=20,c=5.60,cosab=-0.5,cosac=0,cosbc=0, >> nat = 24, >> ntyp = 2, >> ecutwfc =35 , >> ecutrho =420 >> / >> &ELECTRONS >> conv_thr = 1.D-9, >> mixing_beta = 0.2D0, >> / >> ATOMIC_SPECIES >> H 1.0 H.pbe-rrkjus.UPF >> O 15.999 O.pbe-rrkjus.UPF >> ATOMIC_POSITIONS { crystal } >> H 0.040592899 -0.047115761 0.485459003 >> H 0.114704004 -0.001940711 0.646569902 >> H 0.077728017 0.073838408 0.485209132 >> H 0.068286628 0.133313508 0.646050213 >> H -0.040592899 0.047115761 0.485459003 >> H -0.114704004 0.001940711 0.646569902 >> H -0.077728017 -0.073838408 0.485209132 >> H -0.068286628 -0.133313508 0.646050213 >> H 0.087725644 0.047173264 0.985851842 >> H 0.116757198 0.001980553 1.146554001 >> H -0.003964894 0.073814692 0.985604262 >> H 0.065042531 0.133450775 1.145919070 >> H -0.087725644 -0.047173264 0.985851842 >> H -0.116757198 -0.001980553 1.146554001 >> H 0.003964894 -0.073814692 0.985604262 >> H -0.065042531 -0.133450775 1.145919070 >> O 0.095295444 -0.003121003 0.483499312 >> O 0.058352838 0.111476844 0.483127474 >> O -0.095295444 0.003121003 0.483499312 >> O -0.058352838 -0.111476844 0.483127474 >> O 0.098444160 0.003183717 0.983638903 >> O 0.053053024 0.111436979 0.983231173 >> O -0.098444160 -0.003183717 0.983638903 >> O -0.053053024 -0.111436979 0.983231173 >> >> >> >> >> >> >> >> K_POINTS {automatic} >> 1 1 12 0 0 0 >> >> >> and my relax out file wrote: >> >> >> convergence has been achieved >> >> Forces acting on atoms (Ry/au): >> >> atom 1 type 1 force = -0.00000712 >> -0.00004363 0.00001631 >> atom 2 type 1 force = 0.00004994 >> 0.00001718 -0.00006583 >> atom 3 type 1 force = 0.00001729 >> -0.00001573 0.00002699 >> atom 4 type 1 force = -0.00000656 >> 0.00003062 0.00005285 >> atom 5 type 1 force = 0.00000712 >> 0.00004363 0.00001631 >> atom 6 type 1 force = -0.00004994 >> -0.00001718 -0.00006583 >> atom 7 type 1 force = -0.00001729 >> 0.00001573 0.00002699 >> atom 8 type 1 force = 0.00000656 >> -0.00003062 0.00005285 >> atom 9 type 1 force = -0.00000156 >> -0.00006167 -0.00005767 >> atom 10 type 1 force = 0.00001092 >> 0.00004788 -0.00001249 >> atom 11 type 1 force = 0.00005214 >> -0.00008085 -0.00005460 >> atom 12 type 1 force = -0.00002474 >> -0.00007499 0.00003358 >> atom 13 type 1 force = 0.00000156 >> 0.00006167 -0.00005767 >> atom 14 type 1 force = -0.00001092 >> -0.00004788 -0.00001249 >> atom 15 type 1 force = -0.00005214 >> 0.00008085 -0.00005460 >> atom 16 type 1 force = 0.00002474 >> 0.00007499 0.00003358 >> atom 17 type 2 force = 0.00001005 >> 0.00004653 0.00008656 >> atom 18 type 2 force = 0.00001760 >> -0.00007784 0.00003639 >> atom 19 type 2 force = -0.00001005 >> -0.00004653 0.00008656 >> atom 20 type 2 force = -0.00001760 >> 0.00007784 0.00003639 >> atom 21 type 2 force = 0.00002956 >> -0.00007076 -0.00004942 >> atom 22 type 2 force = -0.00000699 >> 0.00005606 -0.00001264 >> atom 23 type 2 force = -0.00002956 >> 0.00007076 -0.00004942 >> atom 24 type 2 force = 0.00000699 >> -0.00005606 -0.00001264 >> >> Total force = 0.000382 Total SCF correction = >> 0.000010 >> >> >> entering subroutine stress ... >> >> total stress (Ry/bohr**3) >> (kbar) P= -0.40 >> -0.00000194 0.00000001 0.00000000 -0.29 >> 0.00 0.00 >> 0.00000001 -0.00000179 0.00000000 0.00 >> -0.26 0.00 >> 0.00000000 0.00000000 -0.00000434 0.00 >> 0.00 -0.64 >> >> >> bfgs converged in 47 scf cycles and 45 bfgs steps >> >> End of BFGS Geometry Optimization >> >> Final energy = -274.4689566789 Ry >> >> >> so i think the problem is not caused by the structure >> relaxation. >> but where is the problem? i can find it . i need your help. >> thank you if you could give me some hints about the >> problem! >> >> >> cheers >> >> >> >> >> >> >> >> >> >> >> ~ >> >> >> >> >> >> the >> -- >> Xu Yuehua >> physics Department of Nanjing university >> China >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Xu Yuehua physics Department of Nanjing university China From sclauzer at sissa.it Tue Mar 3 13:42:39 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 03 Mar 2009 13:42:39 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> Message-ID: <49AD25BF.2030003@sissa.it> I think that CG style diagonalization has not been parallelized like the Davidson one, so these lines at the beginning of your output sound strange to me. > > > > Iterative solution of the eigenvalue problem > > > > a parallel distributed memory algorithm will be used, > > eigenstates matrixes will be distributed block like on > > ortho sub-group = 2* 2 procs > > > > Maybe this is not source of any problem, but you could try to run specifying -ndiag 1 as a flag to the pw.x executable. GS -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From prasenjit.jnc at gmail.com Tue Mar 3 14:12:21 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Tue, 3 Mar 2009 14:12:21 +0100 Subject: [Pw_forum] Fwd: inconsistent DFT read In-Reply-To: <49AD1B54.7090105@na.infn.it> References: <49826.203.200.55.101.1236081338.squirrel@sscu.iisc.ernet.in> <49AD1B54.7090105@na.infn.it> Message-ID: <627e0ffa0903030512oc035738tf10a949ae5599aee@mail.gmail.com> > The error is related to the different kind of pseudopotentials used in > the second run (some LDA, some GGA). The code prevents you from > doing that, you can overcome this by commenting the corrsponding lines > in the source code. > > This is dangerous to do!!!!!..........One shouldn't mix two types of exchange -correlation......Mixing of pseudopotentials are allowed provided they use same exchange correlation functional. -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3891833716 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090303/0da9d919/attachment.htm From prasenjit.jnc at gmail.com Tue Mar 3 14:14:17 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Tue, 3 Mar 2009 14:14:17 +0100 Subject: [Pw_forum] Fwd: In-Reply-To: References: <49826.203.200.55.101.1236081338.squirrel@sscu.iisc.ernet.in> Message-ID: <627e0ffa0903030514l2f6b2e0ah95f364f33681b981@mail.gmail.com> The error is due to mixing of 2 types of exchange correlation functional. the bottomline is to use the same exchange correlation functional ..............u can mix 2 different types of PSP's provided they use same exchange correlation functional. Prasenjit. 2009/3/3 ?? > Hi Asha, > > > ATOMIC_SPECIES > > Mn 54.94 Mn.pbe-sp-van.UPF > > Ce 140.116 Ce_lda_sc.UPF > > O 16.00 O.pz-rrkjus.UPF > > > > > Is there some problem with pseudopotential file?? > > yes.You must have the same pseudopotential file.Like they are all pbe > or pw or others. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3891833716 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090303/81657298/attachment.htm From mjfmartins at ice.ufjf.br Tue Mar 3 14:24:02 2009 From: mjfmartins at ice.ufjf.br (=?ISO-8859-1?Q?MATEUS_JOS=C9_FERNANDES_MARTINS?=) Date: Tue, 3 Mar 2009 10:24:02 -0300 Subject: [Pw_forum] Fwd: In-Reply-To: References: <49826.203.200.55.101.1236081338.squirrel@sscu.iisc.ernet.in> Message-ID: <85d7d5fd0903030524x4d458589rdbe818d05024b552@mail.gmail.com> Yes, you are correct. You file contaim two types of pseudopotentials, gga (pbe) and lda. Try to get pseudopotentials files with same sufixes. 2009/3/3 Asha gupta > Hi all, > I am new to this forum. Recently, started DFT calculations. I have two > similar input files a sshown below: > > > FIRST ONE > &control > calculation='vc-relax', > pseudo_dir = '/home/waghmare/asha/pseudo/', > outdir='/home/waghmare/asha/CeFeO/tmp/', > tstress = .true. > tprnfor = .true. > prefix='CeFeO' > / > &system > ibrav=0, > nat= 23, > ntyp=3, > ecutwfc = 30.0, > ecutrho = 180.0, > occupations='smearing', > smearing='methfessel-paxton', > degauss=0.003, > nbnd=110, > / > &electrons > conv_thr = 1.0e-6, > mixing_beta = 0.1, > / > &ions > / > &cell > cell_dynamics = 'damp-pr' , > / > ATOMIC_SPECIES > Fe 55.85 fe_lda_sc.UPF > Ce 140.116 Ce_lda_sc.UPF > O 16.00 O.pz-rrkjus.UPF > CELL_PARAMETERS > 10.22 0.00 0.00 > 0.00 10.22 0.00 > 0.00 0.00 20.44 > > ATOMIC_POSITIONS (crystal) > Ce 0.000 0.000 0.000 > Ce 0.000 0.000 0.500 > Ce 0.000 0.500 0.250 > Ce 0.000 0.500 0.750 > Ce 0.500 0.000 0.250 > Ce 0.500 0.000 0.750 > Fe 0.500 0.500 0.500 > Ce 0.500 0.500 0.000 > O 0.250 0.250 0.150 > O 0.250 0.250 0.625 > O 0.250 -0.250 0.125 > O 0.250 0.250 -0.125 > O 0.250 0.250 -0.625 > O -0.250 0.250 0.125 > O -0.250 0.250 0.625 > O -0.250 -0.250 0.125 > O -0.250 -0.250 0.625 > O -0.250 0.250 -0.125 > O -0.250 0.250 -0.625 > O 0.250 -0.250 -0.125 > O 0.250 -0.250 -0.625 > O -0.250 -0.250 -0.125 > O -0.250 -0.250 -0.625 > K_POINTS {automatic} > 4 4 4 0 0 0 > > > SECOND ONE > > &control > calculation='vc-relax', > pseudo_dir = '/home/waghmare/asha/pseudo/', > outdir='/home/waghmare/asha/CeMnO/tmp/', > tstress = .true. > tprnfor = .true. > prefix='CeMnO' > / > &system > ibrav=0, > nat= 23, > ntyp=3, > ecutwfc = 30.0, > ecutrho = 180.0, > occupations='smearing', > smearing='methfessel-paxton', > degauss=0.003, > nbnd=110, > / > &electrons > conv_thr = 1.0e-6, > mixing_beta = 0.1, > / > &ions > / > &cell > cell_dynamics = 'damp-pr' , > / > ATOMIC_SPECIES > Mn 54.94 Mn.pbe-sp-van.UPF > Ce 140.116 Ce_lda_sc.UPF > O 16.00 O.pz-rrkjus.UPF > > CELL_PARAMETERS > 10.22 0.00 0.00 > 0.00 10.22 0.00 > 0.00 0.00 20.44 > > ATOMIC_POSITIONS (crystal) > Ce 0.000 0.000 0.000 > Ce 0.000 0.000 0.500 > Ce 0.000 0.500 0.250 > Ce 0.000 0.500 0.750 > Ce 0.500 0.000 0.250 > Ce 0.500 0.000 0.750 > Mn 0.500 0.500 0.500 > Ce 0.500 0.500 0.000 > O 0.250 0.250 0.150 > O 0.250 0.250 0.625 > O 0.250 -0.250 0.125 > O 0.250 0.250 -0.125 > O 0.250 0.250 -0.625 > O -0.250 0.250 0.125 > O -0.250 0.250 0.625 > O -0.250 -0.250 0.125 > O -0.250 -0.250 0.625 > O -0.250 0.250 -0.125 > O -0.250 0.250 -0.625 > O 0.250 -0.250 -0.125 > O 0.250 -0.250 -0.625 > O -0.250 -0.250 -0.125 > O -0.250 -0.250 -0.625 > K_POINTS {automatic} > 4 4 4 0 0 0 > > My problem is while the first one is running properly the second one is > showing an error message like > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 0 > from readpp : error # 2 > inconsistent DFT read > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > I am totally at loss. Is there some problem with pseudopotential file?? > Please help > > thanks in advance > > Asha > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090303/1818b592/attachment-0001.htm From giannozz at democritos.it Tue Mar 3 14:35:04 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 03 Mar 2009 14:35:04 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: <49AD25BF.2030003@sissa.it> References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> <49AD25BF.2030003@sissa.it> Message-ID: <49AD3208.4030308@democritos.it> Gabriele Sclauzero wrote: > I think that CG style diagonalization has not been parallelized > like the Davidson one, so these lines at the beginning > of your output sound strange to me. > >> > a parallel distributed memory algorithm will be used, >> > eigenstates matrixes will be distributed block like on >> > ortho sub-group = 2* 2 procs they aren't strange. This is for "subspace diagonalization", which is not directly used in CG diagonalization, but it is used in i) calculating starting wavefunctions, and ii) rotating wavefunctions before starting a new diagonalization (it is equivalent to first-order perturbation theory and improves quite a bit the subsequent diagonalization). Anyway I verified that the problem with charge is present only in parallel execution, both for CG and Davidson, irrespective whether subspace diagonalization is parallel or not Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 3 14:37:08 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 03 Mar 2009 14:37:08 +0100 Subject: [Pw_forum] the dynmaical matrix are like "***********" when the phonons calculation at gama In-Reply-To: References: <930232.49838.qm@web65702.mail.ac4.yahoo.com> Message-ID: <49AD3284.5090706@democritos.it> xu yuehua wrote: > kpoint 1 ibnd 33 solve_e: root not converged NaN "NaN" doesn't mean "Sodium Nitride" here but "Not a Number". There is something seriously wrong going on here and it is completely useless to go on Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From njuxuyuehua at gmail.com Tue Mar 3 15:11:40 2009 From: njuxuyuehua at gmail.com (xu yuehua) Date: Tue, 3 Mar 2009 22:11:40 +0800 Subject: [Pw_forum] the dynmaical matrix are like "***********" when the phonons calculation at gama In-Reply-To: <49AD3284.5090706@democritos.it> References: <930232.49838.qm@web65702.mail.ac4.yahoo.com> <49AD3284.5090706@democritos.it> Message-ID: my problem is not the "nan" , it has aready sovled, my problem is the original problem : i am facing unkonwn problem when i calculated the phonons at gama: the dynamical matrix file wrote: ................ >> Dynamical Matrix in cartesian axes >> >> q = ( 0.000000000 0.000000000 0.000000000 ) >> >> 1 1 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 2 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 3 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 4 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 5 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 6 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 7 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 8 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> 1 9 >> ************ 0.00000000 ************ 0.00000000 >> ************ 0.00000000 >> ....... >> >> my phone input file : >> phonons at Gamma >> &inputph >> tr2_ph=1.0d-15, >> prefix='scf_two_b_type', >> epsil=.true., >> amass(1)=1.0, >> amass(2)=15.999, >> outdir='/disk2/xxx/xxx/espresso-3.2.3/tmp', >> fildyn='fourringwater.dynG', >> / >> 0.0 0.0 0.0 >> >> >> and my scf input file is :&CONTROL >> calculation = "scf", >> prefix = "scf_two_b_type" >> pseudo_dir = >> "/disk2/xxx/xxx/espresso-3.2.3/pseudo", >> outdir = >> "/disk2/jdong/xyh/espresso-3.2.3/tmp", >> / >> &SYSTEM >> ibrav = 4, >> a=20,b=20,c=5.60,cosab=-0.5,cosac=0,cosbc=0, >> nat = 24, >> ntyp = 2, >> ecutwfc =35 , >> ecutrho =420 >> / >> &ELECTRONS >> conv_thr = 1.D-9, >> mixing_beta = 0.2D0, >> / >> ATOMIC_SPECIES >> H 1.0 H.pbe-rrkjus.UPF >> O 15.999 O.pbe-rrkjus.UPF >> ATOMIC_POSITIONS { crystal } >> H 0.040592899 -0.047115761 0.485459003 >> H 0.114704004 -0.001940711 0.646569902 >> H 0.077728017 0.073838408 0.485209132 >> H 0.068286628 0.133313508 0.646050213 >> H -0.040592899 0.047115761 0.485459003 >> H -0.114704004 0.001940711 0.646569902 >> H -0.077728017 -0.073838408 0.485209132 >> H -0.068286628 -0.133313508 0.646050213 >> H 0.087725644 0.047173264 0.985851842 >> H 0.116757198 0.001980553 1.146554001 >> H -0.003964894 0.073814692 0.985604262 >> H 0.065042531 0.133450775 1.145919070 >> H -0.087725644 -0.047173264 0.985851842 >> H -0.116757198 -0.001980553 1.146554001 >> H 0.003964894 -0.073814692 0.985604262 >> H -0.065042531 -0.133450775 1.145919070 >> O 0.095295444 -0.003121003 0.483499312 >> O 0.058352838 0.111476844 0.483127474 >> O -0.095295444 0.003121003 0.483499312 >> O -0.058352838 -0.111476844 0.483127474 >> O 0.098444160 0.003183717 0.983638903 >> O 0.053053024 0.111436979 0.983231173 >> O -0.098444160 -0.003183717 0.983638903 >> O -0.053053024 -0.111436979 0.983231173 >> >> >> >> >> >> >> >> K_POINTS {automatic} >> 1 1 12 0 0 0 >> >> >> and my relax out file wrote: >> >> >> convergence has been achieved >> >> Forces acting on atoms (Ry/au): >> >> atom 1 type 1 force = -0.00000712 >> -0.00004363 0.00001631 >> atom 2 type 1 force = 0.00004994 >> 0.00001718 -0.00006583 >> atom 3 type 1 force = 0.00001729 >> -0.00001573 0.00002699 >> atom 4 type 1 force = -0.00000656 >> 0.00003062 0.00005285 >> atom 5 type 1 force = 0.00000712 >> 0.00004363 0.00001631 >> atom 6 type 1 force = -0.00004994 >> -0.00001718 -0.00006583 >> atom 7 type 1 force = -0.00001729 >> 0.00001573 0.00002699 >> atom 8 type 1 force = 0.00000656 >> -0.00003062 0.00005285 >> atom 9 type 1 force = -0.00000156 >> -0.00006167 -0.00005767 >> atom 10 type 1 force = 0.00001092 >> 0.00004788 -0.00001249 >> atom 11 type 1 force = 0.00005214 >> -0.00008085 -0.00005460 >> atom 12 type 1 force = -0.00002474 >> -0.00007499 0.00003358 >> atom 13 type 1 force = 0.00000156 >> 0.00006167 -0.00005767 >> atom 14 type 1 force = -0.00001092 >> -0.00004788 -0.00001249 >> atom 15 type 1 force = -0.00005214 >> 0.00008085 -0.00005460 >> atom 16 type 1 force = 0.00002474 >> 0.00007499 0.00003358 >> atom 17 type 2 force = 0.00001005 >> 0.00004653 0.00008656 >> atom 18 type 2 force = 0.00001760 >> -0.00007784 0.00003639 >> atom 19 type 2 force = -0.00001005 >> -0.00004653 0.00008656 >> atom 20 type 2 force = -0.00001760 >> 0.00007784 0.00003639 >> atom 21 type 2 force = 0.00002956 >> -0.00007076 -0.00004942 >> atom 22 type 2 force = -0.00000699 >> 0.00005606 -0.00001264 >> atom 23 type 2 force = -0.00002956 >> 0.00007076 -0.00004942 >> atom 24 type 2 force = 0.00000699 >> -0.00005606 -0.00001264 >> >> Total force = 0.000382 Total SCF correction = >> 0.000010 >> >> >> entering subroutine stress ... >> >> total stress (Ry/bohr**3) >> (kbar) P= -0.40 >> -0.00000194 0.00000001 0.00000000 -0.29 >> 0.00 0.00 >> 0.00000001 -0.00000179 0.00000000 0.00 >> -0.26 0.00 >> 0.00000000 0.00000000 -0.00000434 0.00 >> 0.00 -0.64 >> >> >> bfgs converged in 47 scf cycles and 45 bfgs steps >> >> End of BFGS Geometry Optimization >> >> Final energy = -274.4689566789 Ry >> >> >> so i think the problem is not caused by the structure >> relaxation. >> but where is the problem? i can find it . i need your help. >> thank you if you could give me some hints about the >> problem! >> >> >> cheers >> 2009/3/3, Paolo Giannozzi : > xu yuehua wrote: > >> kpoint 1 ibnd 33 solve_e: root not converged NaN > > "NaN" doesn't mean "Sodium Nitride" here but "Not a Number". > There is something seriously wrong going on here and it is > completely useless to go on > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Xu Yuehua physics Department of Nanjing university China From carlo.nervi at unito.it Tue Mar 3 15:44:12 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 03 Mar 2009 15:44:12 +0100 Subject: [Pw_forum] newbie - installation problem Message-ID: <49AD423C.20402@unito.it> Dear community of quantum-espresso, I am an absolute new user to this software, but it seems very interesting. I downloaded the Q-E-4.04, but I have difficulties in compiling. I do have Intel ifort 10.0 compiler and mkl 9.1.023 libraries running on Linux Gentoo. I managed to compile CPMD, but the ./configure script cannot proper recognize my system and I had to modify the make.sys file (if necessary I can post it). When I type make all, ifort compile all, but it exit with the following message: test -d bin || mkdir bin if test -d iotk ; then \ ( cd iotk ; if test "make" = "" ; then make TLDEPS= lib+util ; \ else make TLDEPS= lib+util ; fi ) ; fi make[1]: Entering directory `/home/nervi/src/Quantum-espresso/espresso-4.1CVS/iotk' cd src ; make lib+util make[2]: Entering directory `/home/nervi/src/Quantum-espresso/espresso-4.1CVS/iotk/src' make loclib_only make[3]: Entering directory `/home/nervi/src/Quantum-espresso/espresso-4.1CVS/iotk/src' make[3]: Nothing to be done for `loclib_only'. make[3]: Leaving directory `/home/nervi/src/Quantum-espresso/espresso-4.1CVS/iotk/src' ifort -i-static -openmp -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a ipo: warning #11041: unresolved iotk_print_kinds_x_ Referenced in /tmp/ipo_ifort86WxDo.o ipo: remark #11001: performing single-file optimizations ipo: remark #11005: generating object file /tmp/ipo_ifort86WxDo.o /tmp/ipo_ifort86WxDo.o: In function `MAIN__': /tmp/ipo_ifort86WxDo.f:(.text+0x31): undefined reference to `iotk_print_kinds_x_' make[2]: *** [iotk_print_kinds.x] Error 1 make[2]: Leaving directory `/home/nervi/src/Quantum-espresso/espresso-4.1CVS/iotk/src' make[1]: *** [lib+util] Error 2 make[1]: Leaving directory `/home/nervi/src/Quantum-espresso/espresso-4.1CVS/iotk' make: *** [libiotk] Error 2 I got similar output if I use the 4.0.4 version. I do not get the iotk_print_kinds.x executable, whereas, apparently, the library libiotk.a is succesfully produced (57 Mb in size...) I would greatly appreciaty any help or suggestion. Thank you, Carlo Nervi -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From paulatto at sissa.it Tue Mar 3 15:59:47 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 03 Mar 2009 15:59:47 +0100 Subject: [Pw_forum] newbie - installation problem In-Reply-To: <49AD423C.20402@unito.it> References: <49AD423C.20402@unito.it> Message-ID: On Tue, 03 Mar 2009 15:44:12 +0100, Carlo Nervi wrote: > When I type make all, ifort compile all, but it exit with the following > message: > ipo: warning #11041: unresolved iotk_print_kinds_x_ > Referenced in /tmp/ipo_ifort86WxDo.o Dear carlo, QE configure script uses the default system archiver (ar) when using ifort compiler instead of intel's own wrapper (xiar); unluckily interprocedural optimization (IPO) does not work with ar. You have two possible solutions: 1. disable IPO (by setting the -noipo in F90FLAGS in file make.sys) 2. use xiar instead of ar (by setting the AR variable to xiar in file make.sys) Personally I don't think IPO gives a substantial performance increase, hence I just disable it most of the time (furthermore it's disabled by default on most ifort versions). cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From carlo.nervi at unito.it Tue Mar 3 16:47:57 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 03 Mar 2009 16:47:57 +0100 Subject: [Pw_forum] newbie - installation problem In-Reply-To: References: <49AD423C.20402@unito.it> Message-ID: <49AD512D.9030300@unito.it> Dear Lorenzo, thank you very much for quick reply. Indeed you perfectly get the problem. I still have some difficulties, (how to correctly set the flags for SMP parallel compilation - no MPI, even though I have MPI installed) but I'm working on them. Indeed I have a 8 CPU SMP linux (no cluster, a simple single dual socket xeon MB). Thank you again, Carlo Lorenzo Paulatto ha scritto: > On Tue, 03 Mar 2009 15:44:12 +0100, Carlo Nervi wrote: >> When I type make all, ifort compile all, but it exit with the following >> message: >> ipo: warning #11041: unresolved iotk_print_kinds_x_ >> Referenced in /tmp/ipo_ifort86WxDo.o > > Dear carlo, > QE configure script uses the default system archiver (ar) when using ifort compiler instead of intel's own wrapper (xiar); unluckily interprocedural optimization (IPO) does not work with ar. > > You have two possible solutions: > 1. disable IPO (by setting the -noipo in F90FLAGS in file make.sys) > 2. use xiar instead of ar (by setting the AR variable to xiar in file make.sys) > > Personally I don't think IPO gives a substantial performance increase, hence I just disable it most of the time (furthermore it's disabled by default on most ifort versions). > > cheers > > -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From jjr19 at uakron.edu Tue Mar 3 17:04:55 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Tue, 3 Mar 2009 08:04:55 -0800 (PST) Subject: [Pw_forum] nimage is larger than the available number of images? Message-ID: <443287.98093.qm@web50911.mail.re2.yahoo.com> I'm trying to do an NEB calculation, and I'm getting a puzzling error: nimage is larger than the available number of images I've set the QE job to use 448 CPUs, and the line to execute the job is mpirun.lsf --gm-copy-env ./pw.x -npool 2 -nimage 7 -in "diffBarr2_7_c18_v10_k4_GaLayers2.in" > "diffBarr2_7_c18_v10_k4_GaLayers2.out" 2> "diffBarr2_7_c18_v10_k4_GaLayers2.err" The apparently relevant part of my input file is &IONS pot_extrapolation = "second_order", wfc_extrapolation = "second_order", num_of_images = 7, opt_scheme = 'broyden' / I don't get it. nimage = num_of_images, so why is there a problem? -------------- next part -------------- A non-text attachment was scrubbed... Name: diffBarr2_7_c18_v10_k4_GaLayers2.in Type: application/octet-stream Size: 21839 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090303/5adb1503/attachment-0001.obj From akohlmey at cmm.chem.upenn.edu Tue Mar 3 17:32:00 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 3 Mar 2009 11:32:00 -0500 (EST) Subject: [Pw_forum] newbie - installation problem In-Reply-To: <49AD512D.9030300@unito.it> References: <49AD423C.20402@unito.it> <49AD512D.9030300@unito.it> Message-ID: On Tue, 3 Mar 2009, Carlo Nervi wrote: CN> Dear Lorenzo, CN> thank you very much for quick reply. CN> Indeed you perfectly get the problem. CN> I still have some difficulties, (how to correctly set the flags for SMP CN> parallel compilation - no MPI, even though I have MPI installed) but I'm CN> working on them. CN> Indeed I have a 8 CPU SMP linux (no cluster, a simple single dual socket CN> xeon MB). you still want to run MPI on it. it is much more efficient in all but a few strange corner cases, and you want to make certain that OpenMP is disabled in that case. axel. CN> CN> Thank you again, CN> Carlo CN> CN> Lorenzo Paulatto ha scritto: CN> > On Tue, 03 Mar 2009 15:44:12 +0100, Carlo Nervi wrote: CN> >> When I type make all, ifort compile all, but it exit with the following CN> >> message: CN> >> ipo: warning #11041: unresolved iotk_print_kinds_x_ CN> >> Referenced in /tmp/ipo_ifort86WxDo.o CN> > CN> > Dear carlo, CN> > QE configure script uses the default system archiver (ar) when using ifort compiler instead of intel's own wrapper (xiar); unluckily interprocedural optimization (IPO) does not work with ar. CN> > CN> > You have two possible solutions: CN> > 1. disable IPO (by setting the -noipo in F90FLAGS in file make.sys) CN> > 2. use xiar instead of ar (by setting the AR variable to xiar in file make.sys) CN> > CN> > Personally I don't think IPO gives a substantial performance increase, hence I just disable it most of the time (furthermore it's disabled by default on most ifort versions). CN> > CN> > cheers CN> > CN> > CN> CN> CN> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Tue Mar 3 18:07:16 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 03 Mar 2009 18:07:16 +0100 Subject: [Pw_forum] newbie - installation problem In-Reply-To: <49AD512D.9030300@unito.it> References: <49AD423C.20402@unito.it> <49AD512D.9030300@unito.it> Message-ID: <49AD63C4.9050604@democritos.it> Carlo Nervi wrote: > I still have some difficulties, (how to correctly set the flags for SMP > parallel compilation - no MPI, even though I have MPI installed) but I'm > working on them. there is no such thing as "SMP parallel compilation" in Q-E, or at least, not yet. If you link multithreading libraries (e.g. MKL, including the FFTW interface to MKL) you can get some speedup, though. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From carlo.nervi at unito.it Tue Mar 3 20:08:03 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 3 Mar 2009 20:08:03 +0100 (CET) Subject: [Pw_forum] newbie - installation problem In-Reply-To: References: <49AD423C.20402@unito.it> <49AD512D.9030300@unito.it> Message-ID: <1095.151.59.234.162.1236107283.squirrel@mail.unito.it> First of all, I would like to thanks everybody replyed to my message. Paolo, yes, I was meaning MKL libraries and parallel compiling using ifort. Of course, I'm trying to get the most efficient code for my platform. Thanks for advices. I'm going to try mpich2 to work... > you still want to run MPI on it. it is much more efficient > in all but a few strange corner cases, and you want to > make > certain that OpenMP is disabled in that case. > > axel. Axel, I've heard opposite opinions on openmp and mpich2. The recent Openmp (i've heard) is now efficient and fast. However, I trust the experience of the developers :-). Thanks, Carlo From akohlmey at cmm.chem.upenn.edu Tue Mar 3 21:22:44 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 3 Mar 2009 15:22:44 -0500 (EST) Subject: [Pw_forum] newbie - installation problem In-Reply-To: <1095.151.59.234.162.1236107283.squirrel@mail.unito.it> References: <49AD423C.20402@unito.it> <49AD512D.9030300@unito.it> <1095.151.59.234.162.1236107283.squirrel@mail.unito.it> Message-ID: On Tue, 3 Mar 2009, Carlo Nervi wrote: CN> Axel, I've heard opposite opinions on openmp and mpich2. do yourself a favor and try to install OpenMPI instead of MPICH2 first. it is performing better, or as well, and _much_ less clumsy to use (at least the way we use it in our group). CN> The recent Openmp (i've heard) is now efficient and fast. yes, the compilers may incur less overhead when using OpenMP, but OpenMP is still only fast, if the directives are programmed well and the code rewritten to make good use of it. last time i checked, there were no OpenMP directives in Q-E, so setting the -openmp flag will have no significant effect. in general, OpenMP is not a good way to multithread a code. running your own thread management with a pool of threads to delegate work to, is _much_ more efficient. the reason OpenMP is so attractive is, that you can add _some_ parallelism to your code with very little effort. just sprinkle a few OpenMP directives at the right places, and you get a moderate speedup. a very good deal for the effort. but that by far cannot cope with the efficiency of the MPI distributed data parallelism that is in plane wave codes like Q-E. ...and by the time you have exploited that parallelism to the maximum, you have so little data left, that OpenMP is not helping much anymore. to give you some numbers. using a different, very well OpenMP parallelised plane wave code, (including OpenMP FFT, and OpenMP BLAS/LAPACK), i managed to get about 80% of the efficiency of the MPI parallelization on a single 2x dual core node, using a sizable input. at running across two of those nodes, the efficiency of OpenMP versus MPI (i.e. running 2 MPI tasks * 4 threads vs. 8 MPI tasks) dropped to 60% and for anything larger there was next no gain, or even a slowdown. as was said before. -ipo is a waste of your time. all it does is make the code run slower, and make you wait longer until it is linked, and even more so, quite often code gets miscompiled because of -ipo. all these "advanced" compiler features (like IPO, PGO, SSE/MMX-vectorization) are working best with small test cases, but for any larger, more complex code, they add overhead about as often as they don't. the compiler doesn't really know which parts of a code are executed a lot and which are not, so it may put a lot of effort into optimizing the wrong parts, and - as i wrote before - aggressive optimization has the high risk of miscompiled (overoptimized) code. CN> However, I trust the experience of the developers :-). you should never do that. as a scientist you are obliged to never take anything for granted and convince yourself. i may just be a "compiler terrorist", trying to sabotage sales for the compiler vendors. ;-) cheers, axel. CN> Thanks, CN> Carlo CN> _______________________________________________ CN> Pw_forum mailing list CN> Pw_forum at pwscf.org CN> http://www.democritos.it/mailman/listinfo/pw_forum CN> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From carlo.nervi at unito.it Tue Mar 3 22:46:48 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 3 Mar 2009 22:46:48 +0100 (CET) Subject: [Pw_forum] newbie - installation problem In-Reply-To: References: <49AD423C.20402@unito.it> <49AD512D.9030300@unito.it><1095.151.59.234.162.1236107283.squirrel@mail.unito.it> Message-ID: <2164.151.59.234.162.1236116808.squirrel@mail.unito.it> Thanks Axel for the very exhaustive explanation. I appreciated it. If I would have the time I would like to try to compare and test OpenMP and Mpich2 on my Linux PC, as well as the million of options of the compilers.... Unfortunately, I have to use my (little) time to compile Q-E and, expecially, to learn it! (I consider myself mainly an experimental inorganic chemist, electrochemist, with the passion of computer and quatum mechanical calculations...) CN> However, I trust the experience of the developers :-). > > you should never do that. as a scientist you are obliged > to never take anything for granted and convince yourself. > i may just be a "compiler terrorist", trying to sabotage > sales for the compiler vendors. ;-) > > cheers, > axel. Good answer. I'm trying to start from the most advanced point that I can afford! ...I hope there is no back-trojan virus in the code :-) Best Regards, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From akohlmey at cmm.chem.upenn.edu Wed Mar 4 03:51:22 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 3 Mar 2009 21:51:22 -0500 Subject: [Pw_forum] Use of pool In-Reply-To: <21B74D1AD49648479BDC1ABD309ED183@solarflare> References: <21B74D1AD49648479BDC1ABD309ED183@solarflare> Message-ID: <7b6913e90903031851p482b7709ob4db1878a17711dc@mail.gmail.com> On Tue, Feb 24, 2009 at 1:45 AM, Huiqun Zhou wrote: > Dear list users: hi all, > I happened to test duration times of calculating the system I'm > investigating against number of pools used. There are totally > 36 k points. But the results surprised me quite a lot. > > no pool: 6m21.02s CPU time, 6m45.88s wall time > 2 pools: 7m19.39s CPU time, 7m38.99s wall time > 4 pools: 11m59.09s CPU time, 12m14.66s wall time > 8 pools: 21m28.77s CPU time, 21m38.71s wall time > > The machine I'm using is an AMD box with 2 quad core shanghai. > > Is my understanding of usage of pool wrong? sorry for replying to an old mail in this thread, but it has the proper times to compare to. the input you sent me, does not seem to be the exactly the same as the one you used for the benchmarks (rather a bit larger). but i reduced the number of k-points to yield 36 and have some numbers here. this is on dual intel quad core E5430 @ 2.66GHz cpus with 8GB DDR2 ram. i also modified the input to set wfcdir to use the local scratch rather than my working directory (as this is on an NFS server) and test with disk_io='high' and 'low'. on a single node (always with 8 MPI tasks) i get: 1node-1pools-high.out: PWSCF : 18m55.62s CPU time, 26m 7.20s wall time 1node-2pools-high.out: PWSCF : 14m46.03s CPU time, 18m 0.26s wall time 1node-4pools-high.out: PWSCF : 14m 5.27s CPU time, 16m44.03s wall time 1node-8pools-high.out: PWSCF : 32m29.71s CPU time, 35m 0.35s wall time 1node-1pools-low.out: PWSCF : 18m36.88s CPU time, 19m24.71s wall time 1node-2pools-low.out: PWSCF : 15m 0.98s CPU time, 15m42.56s wall time 1node-4pools-low.out: PWSCF : 14m 6.97s CPU time, 14m55.57s wall time 1node-8pools-low.out: PWSCF : 31m51.68s CPU time, 32m46.77s wall time so the result is not quite as drastic, but with 8 pools on the node, the machine is suffering. one can also see that disk_io='low' is helping to reduce waiting time (disk_io='high' still writes files into the working directory, which is on slow NFS). so for my machine it looks as if 4 pools is the optimal compromise. to further investigate whether pools or gspace parallelization is more efficient i then started to run the same job across multiple nodes. this uses only 4 cores per node, i.e. the total number of mpi tasks is still 8. 2node-1pools-high.out: PWSCF : 12m 0.88s CPU time, 17m42.01s wall time 2node-2pools-high.out: PWSCF : 8m42.96s CPU time, 11m44.88s wall time 2node-4pools-high.out: PWSCF : 6m26.72s CPU time, 8m54.83s wall time 2node-8pools-high.out: PWSCF : 12m47.61s CPU time, 15m18.67s wall time 2node-1pools-low.out: PWSCF : 10m53.87s CPU time, 11m35.94s wall time 2node-2pools-low.out: PWSCF : 8m37.37s CPU time, 9m23.17s wall time 2node-4pools-low.out: PWSCF : 6m22.87s CPU time, 7m11.22s wall time 2node-8pools-low.out: PWSCF : 13m 7.30s CPU time, 13m57.71s wall time in the next test, i doubled the number of nodes again, but this time kept 4 mpi tasks per node, also i'm only using disk_io='low'. 4node-4pools-low.out: PWSCF : 4m52.92s CPU time, 5m38.90s wall time 4node-8pools-low.out: PWSCF : 4m29.73s CPU time, 5m17.86s wall time interesting, now the striking difference between 4 pools and 8 pools is gone. since i doubled the number of nodes, the memory consumption per mpi task in the 8 pools case should have dropped to a similar level as in the 4 pools case with 2 nodes. to confirm this, lets run the same job with 16 pools: 4node-16pools-low.out: PWSCF : 10m54.57s CPU time, 11m53.59s wall time bingo! the only explanation for this is cache memory. so in this specific case, up to about "half a wavefunction" memory consumption per node, the caching of the cpu is much more effective. so the "more pools is better"-rule has to be augmented by "unless it makes the cpu cache less efficient". since 36 kpoints is wholly divisible by 6 but not by 8, now a test with 6 nodes. 6node-4pools-low.out: PWSCF : 3m41.65s CPU time, 4m25.15s wall time 6node-6pools-low.out: PWSCF : 3m40.12s CPU time, 4m23.33s wall time 6node-8pools-low.out: PWSCF : 3m14.13s CPU time, 3m57.76s wall time 6node-12pools-low.out: PWSCF : 3m37.96s CPU time, 4m25.91s wall time 6node-24pools-low.out: PWSCF : 10m55.18s CPU time, 11m47.87s wall time so 6 pools is more efficient than 4, but 8 even more than 6 or 12, which should lead to a better distribution of the work. so the modified "rule" from above seems to hold. ok, can we get any faster. ~4min walltime for a 21 scf cycle single point run is already pretty good and the serial overhead (and wf_collect=.true.) should kick in. so now with 8 nodes and 32 mpi tasks. 8node-4pools-low.out: PWSCF : 3m22.02s CPU time, 4m 7.06s wall time 8node-8pools-low.out: PWSCF : 3m14.52s CPU time, 3m58.86s wall time 8node-16pools-low.out: PWSCF : 3m36.18s CPU time, 4m24.21s wall time hmmm, not much better, but now for the final test. since we have 36 k-points and we need at least two mpi tasks per pool to get good performance, lets try 18 nodes with 4 mpi tasks each: 18node-9pools-low.out: PWSCF : 1m57.06s CPU time, 3m37.31s wall time 18node-18pools-low.out: PWSCF : 2m 2.62s CPU time, 2m45.51s wall time 18node-36pools-low.out: PWSCF : 2m45.61s CPU time, 3m33.00s wall time not spectacular scaling, but still improving. but it looks like writing the final wavefunction costs about 45 seconds or more, as indicated by the difference between cpu and walltime. at this level, you better not use disk_io='high', as that will put a _severe_ disk load on the machine that is carrying the working directory (particularly bad for NFS servers), the code will generate and continuously rewrite in this case 144 files... and the walltime to cputime ratio quickly rises (a factor of 5 in my case so i stopped the job before the NFS server would die). in summary, it is obviously getting more complicated to define a "rule" of what gives the best performance. some experimentation is always required and sometimes there will be surprises. i have not touched the issue of network speed (all tests were done across a 4xDDR infiniband network). i hope this little benchmark excursion was as interesting and thought provoking for you as it was for me. thanks for everybody that gave their input to this discussion. cheers, axel. p.s.: perhaps at some point it might be interesting to organize a workshop on "post-compilation optimization" for pw.x for different types of jobs and hardware. > Huiqun Zhou > @Nanjing University, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Wed Mar 4 03:59:34 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 3 Mar 2009 21:59:34 -0500 (EST) Subject: [Pw_forum] newbie - installation problem In-Reply-To: <2164.151.59.234.162.1236116808.squirrel@mail.unito.it> References: <49AD423C.20402@unito.it> <49AD512D.9030300@unito.it><1095.151.59.234.162.1236107283.squirrel@mail.unito.it> <2164.151.59.234.162.1236116808.squirrel@mail.unito.it> Message-ID: On Tue, 3 Mar 2009, Carlo Nervi wrote: CN> Thanks Axel for the very exhaustive explanation. CN> I appreciated it. CN> If I would have the time I would like to try to compare CN> and test OpenMP and Mpich2 on my Linux PC, as well as the just to make certain: there are OpenMP and OpenMPI. those are quite different entities. see, http://openmp.org/ and http://www.open-mpi.org/ CN> million of options of the compilers.... CN> Unfortunately, I have to use my (little) time to compile CN> Q-E and, expecially, to learn it! i understand that, but in that case it is particularly important to stick with a conservative choice. axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From hqzhou at nju.edu.cn Wed Mar 4 05:02:17 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 4 Mar 2009 12:02:17 +0800 Subject: [Pw_forum] the dynmaical matrix are like "***********" when thephonons calculation at gama References: <930232.49838.qm@web65702.mail.ac4.yahoo.com><49AD3284.5090706@democritos.it> Message-ID: <7C4D607A6F6740F797A2766A2F7A5823@solarflare> Hi, Yuehua, This is not an answer to your question, but I think if you have no special reason to use espresso 3.2.3, you'd better upgrade to 4.0.4 and try again. Since we are on the same campus and I guess you're using our Altix 4700, if this is true and you're willing to, you can run the command below to get the latest compiled copy from my home: scp -r hqzhou at 210.119.46.90:/disk3/hqzhou/espresso-4.0.4 /your/home Call me at 83686750, I'll let you know my password. Huiqun Zhou @Nanjing University, China ----- Original Message ----- From: "xu yuehua" To: "PWSCF Forum" Sent: Tuesday, March 03, 2009 10:11 PM Subject: Re: [Pw_forum] the dynmaical matrix are like "***********" when thephonons calculation at gama > my problem is not the "nan" , it has aready sovled, > > my problem is the original problem : > i am facing unkonwn problem when i calculated the phonons > at gama: > > the dynamical matrix file wrote: > ................ >>> Dynamical Matrix in cartesian axes >>> >>> q = ( 0.000000000 0.000000000 0.000000000 ) >>> >>> 1 1 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> 1 2 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> 1 3 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> 1 4 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> 1 5 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> 1 6 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> 1 7 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> 1 8 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> 1 9 >>> ************ 0.00000000 ************ 0.00000000 >>> ************ 0.00000000 >>> ....... >>> >>> my phone input file : >>> phonons at Gamma >>> &inputph >>> tr2_ph=1.0d-15, >>> prefix='scf_two_b_type', >>> epsil=.true., >>> amass(1)=1.0, >>> amass(2)=15.999, >>> outdir='/disk2/xxx/xxx/espresso-3.2.3/tmp', >>> fildyn='fourringwater.dynG', >>> / >>> 0.0 0.0 0.0 >>> >>> >>> and my scf input file is :&CONTROL >>> calculation = "scf", >>> prefix = "scf_two_b_type" >>> pseudo_dir = >>> "/disk2/xxx/xxx/espresso-3.2.3/pseudo", >>> outdir = >>> "/disk2/jdong/xyh/espresso-3.2.3/tmp", >>> / >>> &SYSTEM >>> ibrav = 4, >>> a=20,b=20,c=5.60,cosab=-0.5,cosac=0,cosbc=0, >>> nat = 24, >>> ntyp = 2, >>> ecutwfc =35 , >>> ecutrho =420 >>> / >>> &ELECTRONS >>> conv_thr = 1.D-9, >>> mixing_beta = 0.2D0, >>> / >>> ATOMIC_SPECIES >>> H 1.0 H.pbe-rrkjus.UPF >>> O 15.999 O.pbe-rrkjus.UPF >>> ATOMIC_POSITIONS { crystal } >>> H 0.040592899 -0.047115761 0.485459003 >>> H 0.114704004 -0.001940711 0.646569902 >>> H 0.077728017 0.073838408 0.485209132 >>> H 0.068286628 0.133313508 0.646050213 >>> H -0.040592899 0.047115761 0.485459003 >>> H -0.114704004 0.001940711 0.646569902 >>> H -0.077728017 -0.073838408 0.485209132 >>> H -0.068286628 -0.133313508 0.646050213 >>> H 0.087725644 0.047173264 0.985851842 >>> H 0.116757198 0.001980553 1.146554001 >>> H -0.003964894 0.073814692 0.985604262 >>> H 0.065042531 0.133450775 1.145919070 >>> H -0.087725644 -0.047173264 0.985851842 >>> H -0.116757198 -0.001980553 1.146554001 >>> H 0.003964894 -0.073814692 0.985604262 >>> H -0.065042531 -0.133450775 1.145919070 >>> O 0.095295444 -0.003121003 0.483499312 >>> O 0.058352838 0.111476844 0.483127474 >>> O -0.095295444 0.003121003 0.483499312 >>> O -0.058352838 -0.111476844 0.483127474 >>> O 0.098444160 0.003183717 0.983638903 >>> O 0.053053024 0.111436979 0.983231173 >>> O -0.098444160 -0.003183717 0.983638903 >>> O -0.053053024 -0.111436979 0.983231173 >>> >>> >>> >>> >>> >>> >>> >>> K_POINTS {automatic} >>> 1 1 12 0 0 0 >>> >>> >>> and my relax out file wrote: >>> >>> >>> convergence has been achieved >>> >>> Forces acting on atoms (Ry/au): >>> >>> atom 1 type 1 force = -0.00000712 >>> -0.00004363 0.00001631 >>> atom 2 type 1 force = 0.00004994 >>> 0.00001718 -0.00006583 >>> atom 3 type 1 force = 0.00001729 >>> -0.00001573 0.00002699 >>> atom 4 type 1 force = -0.00000656 >>> 0.00003062 0.00005285 >>> atom 5 type 1 force = 0.00000712 >>> 0.00004363 0.00001631 >>> atom 6 type 1 force = -0.00004994 >>> -0.00001718 -0.00006583 >>> atom 7 type 1 force = -0.00001729 >>> 0.00001573 0.00002699 >>> atom 8 type 1 force = 0.00000656 >>> -0.00003062 0.00005285 >>> atom 9 type 1 force = -0.00000156 >>> -0.00006167 -0.00005767 >>> atom 10 type 1 force = 0.00001092 >>> 0.00004788 -0.00001249 >>> atom 11 type 1 force = 0.00005214 >>> -0.00008085 -0.00005460 >>> atom 12 type 1 force = -0.00002474 >>> -0.00007499 0.00003358 >>> atom 13 type 1 force = 0.00000156 >>> 0.00006167 -0.00005767 >>> atom 14 type 1 force = -0.00001092 >>> -0.00004788 -0.00001249 >>> atom 15 type 1 force = -0.00005214 >>> 0.00008085 -0.00005460 >>> atom 16 type 1 force = 0.00002474 >>> 0.00007499 0.00003358 >>> atom 17 type 2 force = 0.00001005 >>> 0.00004653 0.00008656 >>> atom 18 type 2 force = 0.00001760 >>> -0.00007784 0.00003639 >>> atom 19 type 2 force = -0.00001005 >>> -0.00004653 0.00008656 >>> atom 20 type 2 force = -0.00001760 >>> 0.00007784 0.00003639 >>> atom 21 type 2 force = 0.00002956 >>> -0.00007076 -0.00004942 >>> atom 22 type 2 force = -0.00000699 >>> 0.00005606 -0.00001264 >>> atom 23 type 2 force = -0.00002956 >>> 0.00007076 -0.00004942 >>> atom 24 type 2 force = 0.00000699 >>> -0.00005606 -0.00001264 >>> >>> Total force = 0.000382 Total SCF correction = >>> 0.000010 >>> >>> >>> entering subroutine stress ... >>> >>> total stress (Ry/bohr**3) >>> (kbar) P= -0.40 >>> -0.00000194 0.00000001 0.00000000 -0.29 >>> 0.00 0.00 >>> 0.00000001 -0.00000179 0.00000000 0.00 >>> -0.26 0.00 >>> 0.00000000 0.00000000 -0.00000434 0.00 >>> 0.00 -0.64 >>> >>> >>> bfgs converged in 47 scf cycles and 45 bfgs steps >>> >>> End of BFGS Geometry Optimization >>> >>> Final energy = -274.4689566789 Ry >>> >>> >>> so i think the problem is not caused by the structure >>> relaxation. >>> but where is the problem? i can find it . i need your help. >>> thank you if you could give me some hints about the >>> problem! >>> >>> >>> cheers >>> > > > 2009/3/3, Paolo Giannozzi : >> xu yuehua wrote: >> >>> kpoint 1 ibnd 33 solve_e: root not converged NaN >> >> "NaN" doesn't mean "Sodium Nitride" here but "Not a Number". >> There is something seriously wrong going on here and it is >> completely useless to go on >> >> Paolo >> -- >> Paolo Giannozzi, Democritos and University of Udine, Italy >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > -- > Xu Yuehua > physics Department of Nanjing university > China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From lidonglin556 at 163.com Wed Mar 4 07:42:54 2009 From: lidonglin556 at 163.com (lidonglin556) Date: Wed, 4 Mar 2009 14:42:54 +0800 (CST) Subject: [Pw_forum] how to use fqha.x Message-ID: <29857869.964501236148974655.JavaMail.coremail@bj163app41.163.com> hi I want get the thermal properties, but I don't know how to do. Does fqha.x can deal with it? And how to write the input? where can I the code? many thanks ! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090304/329dc5d5/attachment.htm From hqzhou at nju.edu.cn Wed Mar 4 08:30:40 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Wed, 4 Mar 2009 15:30:40 +0800 Subject: [Pw_forum] how to use fqha.x References: <29857869.964501236148974655.JavaMail.coremail@bj163app41.163.com> Message-ID: <8E92A5B11CF244A68F5BE4CD29032638@solarflare> lidonglin556, everything in bin is soft link to the real excutable in relevant directiories, respectively. The clever way to find where the code is is to run ls -l bin you can easily find fqha.x there linked to pwtools/fqha.x, then from there you can find again a fqha.f90. Read the source code patiently, you can figure out how to write input soon. Huiqun Zhou @Nanjing University, China ----- Original Message ----- From: lidonglin556 To: pw_forum at pwscf.org Sent: Wednesday, March 04, 2009 2:42 PM Subject: [Pw_forum] how to use fqha.x hi I want get the thermal properties, but I don't know how to do. Does fqha.x can deal with it? And how to write the input? where can I the code? many thanks ! ------------------------------------------------------------------------------ ????????????????? ------------------------------------------------------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090304/642f38a2/attachment.htm From eyvaz_isaev at yahoo.com Wed Mar 4 10:44:36 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 4 Mar 2009 01:44:36 -0800 (PST) Subject: [Pw_forum] how to use fqha.x In-Reply-To: <29857869.964501236148974655.JavaMail.coremail@bj163app41.163.com> Message-ID: <873692.46216.qm@web65703.mail.ac4.yahoo.com> Dear user, Please provide your personal name and affiliation. I will send you a code wich has much more functionality than fqha.f90 and which should be replaced by this one soon, hopefully. Bests, Eyvaz ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 3/4/09, lidonglin556 wrote: > From: lidonglin556 > Subject: [Pw_forum] how to use fqha.x > To: pw_forum at pwscf.org > Date: Wednesday, March 4, 2009, 9:42 AM > hi > I want get the thermal properties, but I don't know how > to do. Does fqha.x can deal with it? And how to write the > input? where can I the code? > many thanks > !_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From paulatto at sissa.it Wed Mar 4 10:55:03 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 04 Mar 2009 10:55:03 +0100 Subject: [Pw_forum] newbie - installation problem In-Reply-To: References: <49AD423C.20402@unito.it> <49AD512D.9030300@unito.it> <1095.151.59.234.162.1236107283.squirrel@mail.unito.it> Message-ID: On Tue, 03 Mar 2009 21:22:44 +0100, Axel Kohlmeyer wrote: > (like IPO, PGO, SSE/MMX-vectorization) are working best with small > test cases, but for any larger, more complex code, they add > overhead about as often as they don't. the compiler doesn't > really know which parts of a code are executed a lot and which > are not, so it may put a lot of effort into optimizing the > wrong parts, and - as i wrote before - aggressive optimization > has the high risk of miscompiled (overoptimized) code. In this regard, some time ago I tryed to compile QE using PGO and IPO, I spent some time compiling the test code and running some extensive profiling. Then recompiling with aggressive optimization and profiling data. The final code was about 5% faster than the original, but it was numerically less stable (due to over-optimization), hence it took two more iterations to converge than the not-so-optimized code, rending the total speedup exactly zero. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From panda.deng.pan at gmail.com Wed Mar 4 14:20:21 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Wed, 4 Mar 2009 21:20:21 +0800 Subject: [Pw_forum] The Number of iteraions Message-ID: Dear All users, I have a quesion here about how set a given number for a scf run.I have read the Doc and could not find the parameter to define. For a special scf run, and if I just want to run a few iteraion e.g a give number like 10.How can I use the proper parameter to define it. Have a nice day to all. Deng Pan Nanjing Universtity From paulatto at sissa.it Wed Mar 4 14:25:24 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 04 Mar 2009 14:25:24 +0100 Subject: [Pw_forum] The Number of iteraions In-Reply-To: References: Message-ID: On Wed, 04 Mar 2009 14:20:21 +0100, ?????? wrote: > For a special scf run, and if I just want to run a few iteraion e.g > a give number like 10.How can I use the proper parameter to define it. dear Deng Pan, there are two different parameters, one is for electronic iterations, the other for ionic iterations. They are both in the documentation (electron_maxstep and nstep). cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From yanxunwang2008 at gmail.com Wed Mar 4 16:42:10 2009 From: yanxunwang2008 at gmail.com (Xun-Wang Yan) Date: Wed, 4 Mar 2009 23:42:10 +0800 Subject: [Pw_forum] DOS calculation for non collinear magnetic ordering Message-ID: Dear pwscf users, I have calculated the density of states for the noncolinear magnetic CuCrO2, the angle between spin directions of two Cr atoms is 120 degrees. the magnetic moment is about 3 Bohr magnetons per Cr atom, I think the pdosup(E) is different from the pdosdw(E), but the 'pdosup(E)' and 'pdosdw(E)' are just the same in output file-- 120-AFM-12at-tricli.pdos_atm#6(Cr3)_wfc#2(d). # E(eV) ldosup(E) ldosdw(E) pdosup(E) pdosdw(E) pdosup(E) pdosdw(E) pdosup(E) -11.138 0.134E-07 0.134E-07 0.336E-08 0.336E-08 0.787E-16 0.787E-16 0.739E-16 ... -11.128 0.105E-04 0.105E-04 0.263E-05 0.263E-05 0.618E-13 0.618E-13 0.580E-13 ... -11.118 0.138E-03 0.138E-03 0.345E-04 0.345E-04 0.232E-11 0.232E-11 0.105E-11 ... -11.108 0.247E-03 0.247E-03 0.618E-04 0.618E-04 0.585E-08 0.585E-08 0.138E-08 -11.098 0.654E-03 0.654E-03 0.165E-03 0.165E-03 0.405E-06 0.405E-06 0.149E-06 -11.088 0.116E-02 0.116E-02 0.285E-03 0.285E-03 0.648E-06 0.648E-06 0.555E-06 -11.078 0.804E-03 0.804E-03 0.209E-03 0.209E-03 0.385E-06 0.385E-06 0.254E-06 -11.068 0.523E-03 0.523E-03 0.128E-03 0.128E-03 0.653E-06 0.653E-06 0.765E-06 -11.058 0.648E-03 0.648E-03 0.152E-03 0.152E-03 0.115E-05 0.115E-05 0.126E-05 -11.048 0.174E-02 0.174E-02 0.450E-03 0.450E-03 0.676E-05 0.676E-05 0.304E-05 -11.038 0.122E-02 0.122E-02 0.302E-03 0.302E-03 0.373E-05 0.373E-05 0.173E-05 my questions : What do pdosup and pdosdw mean in DOS output file for noncolinear magnetic ordjering? the 'up' means Sz=1/2 ? but the spin direction is vertical to z axes in my unit cell. how to deal with the DOS of noncolinear magnetic structure in version espresso-4.0.1? Any comments are welcome , many thanks in advance. Bests Xun-wang Yan ======================================== Institute of Theoretical Physics, CAS Address: No.55, Zhong-Guan-Cun East Road Beijing, China Email: xwyan at itp.ac.cn yanxunwang2008 at gmail.com =================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090304/46f50f56/attachment.htm From quantumdft at gmail.com Wed Mar 4 16:49:17 2009 From: quantumdft at gmail.com (vega lew) Date: Wed, 4 Mar 2009 23:49:17 +0800 Subject: [Pw_forum] The Number of iteraions In-Reply-To: References: Message-ID: <412f6c680903040749u5ac4a3e5l82265bf993f515c4@mail.gmail.com> Dear friend, see these two parameters, nstep and electron_maxstep, for detail. as far as I know, the default value many suitable for most of situations. for specific purpose you can define it following the manual hope helps vega On Wed, Mar 4, 2009 at 9:25 PM, Lorenzo Paulatto wrote: > On Wed, 04 Mar 2009 14:20:21 +0100, ?????? > wrote: > > For a special scf run, and if I just want to run a few iteraion e.g > > a give number like 10.How can I use the proper parameter to define it. > > > dear Deng Pan, > there are two different parameters, one is for electronic iterations, the > other for ionic iterations. They are both in the documentation > (electron_maxstep and nstep). > > cheers > > > > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090304/9a41198f/attachment.htm From idoldog at gmail.com Wed Mar 4 17:03:50 2009 From: idoldog at gmail.com (idoldog) Date: Thu, 5 Mar 2009 00:03:50 +0800 Subject: [Pw_forum] strange bandstructure Message-ID: <200903050003486719489@gmail.com> Dear PWSCF user, I just finished a bandstructure calculation about semiconductor SrTiO3. I get a strange bandstructure. In order to see clearly, I redraw the graph and mark same bands, which may be wrong, with different colors. Some friends tell me it would be better without lines. Another friends tell me to change the path of markde lines. I want to know that whether these bands are correct and if they are wrong, where my mistakes are and how to solve them. The server blocked my files attched, so please visit graph with colorful lines:http://pic.emuch.net/200903/04/33e7b7b230bfd248104b8ba1ada65361.jpg graph without line:http://pic.emuch.net/200903/04/4a2fdd6cbf9f7d0ce2df725c579e57ea.jpg If you couldn't visit them successfully, mail me. I need your help. all the best. Li Fei 2009-03-04 From lex at phys.ufl.edu Wed Mar 4 17:11:10 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Wed, 04 Mar 2009 11:11:10 -0500 Subject: [Pw_forum] strange bandstructure In-Reply-To: <200903050003486719489@gmail.com> References: <200903050003486719489@gmail.com> Message-ID: <49AEA81E.50209@phys.ufl.edu> Hi idoldog, I presume what you're referring to as 'strange' is the lines jumping from one band to another. This is, as I understand it, the bands.x code not seeing enough overlap between the kpoints to order them properly. There are two ways to fix this: (a) Run with more points per line in k-space (b) If you're only interested in a few bands, fix them by hand. Good luck! Lex Kemper University of Florida idoldog wrote: > Dear PWSCF user, > > I just finished a bandstructure calculation about semiconductor SrTiO3. I get a strange bandstructure. > > In order to see clearly, I redraw the graph and mark same bands, which may be wrong, with different colors. > > Some friends tell me it would be better without lines. Another friends tell me to change the path of markde lines. > > I want to know that whether these bands are correct and if they are wrong, where my mistakes are and how to solve them. > > The server blocked my files attched, so please visit > graph with colorful lines:http://pic.emuch.net/200903/04/33e7b7b230bfd248104b8ba1ada65361.jpg > graph without line:http://pic.emuch.net/200903/04/4a2fdd6cbf9f7d0ce2df725c579e57ea.jpg > > If you couldn't visit them successfully, mail me. > > I need your help. > > all the best. > > Li Fei > 2009-03-04 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sclauzer at sissa.it Wed Mar 4 17:15:49 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 04 Mar 2009 17:15:49 +0100 Subject: [Pw_forum] strange bandstructure In-Reply-To: <200903050003486719489@gmail.com> References: <200903050003486719489@gmail.com> Message-ID: <49AEA935.8020107@sissa.it> idoldog wrote: > Dear PWSCF user, > > I just finished a bandstructure calculation about semiconductor SrTiO3. I get a strange > bandstructure. > > In order to see clearly, I redraw the graph and mark same bands, which may be wrong, > with different colors. > > Some friends tell me it would be better without lines. Another friends tell me to > change the path of markde lines. > > I want to know that whether these bands are correct and if they are wrong, where my > mistakes are and how to solve them. > > The server blocked my files attched, so please visit graph with colorful > lines:http://pic.emuch.net/200903/04/33e7b7b230bfd248104b8ba1ada65361.jpg graph without > line:http://pic.emuch.net/200903/04/4a2fdd6cbf9f7d0ce2df725c579e57ea.jpg From your plots it is not clear where is the problem. How did you produce that plots? From which data (from pw.x output or bands.x?). What's the difference between colored and black lines? Do they come from the same data?... > > If you couldn't visit them successfully, mail me. > > I need your help. Please give more helpful details (and possibly a more "readable" example plot which gives the same problem, if any). Version of espresso used, sequence of (post)-processing steps, sample input file for pw... GS > > all the best. > > Li Fei 2009-03-04 > > _______________________________________________ Pw_forum mailing list > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Wed Mar 4 17:22:22 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 04 Mar 2009 17:22:22 +0100 Subject: [Pw_forum] strange bandstructure In-Reply-To: <49AEA81E.50209@phys.ufl.edu> References: <200903050003486719489@gmail.com> <49AEA81E.50209@phys.ufl.edu> Message-ID: <49AEAABE.7000107@sissa.it> Lex Kemper wrote: > Hi idoldog, > > I presume what you're referring to as 'strange' is the lines jumping > from one band to another. This is, as I understand it, the bands.x code > not seeing enough overlap between the kpoints to order them properly. > There are two ways to fix this: > > (a) Run with more points per line in k-space > (b) If you're only interested in a few bands, fix them by hand. > > Good luck! > > Lex Kemper > University of Florida If there is this kind of problem with bands.x, you can do as Lex correctly suggested, or try to upgrade to the latest espresso versions, which should use a symmetry-based analisys rather than the overlap-based one (eventually enabled with lsym=.TRUE., actually much more computationally expensive... but if you really want nice bands labeled by symmetry that's the price you'll have to pay ;-) HTH GS > > idoldog wrote: >> Dear PWSCF user, >> >> I just finished a bandstructure calculation about semiconductor SrTiO3. I get a strange bandstructure. >> >> In order to see clearly, I redraw the graph and mark same bands, which may be wrong, with different colors. >> >> Some friends tell me it would be better without lines. Another friends tell me to change the path of markde lines. >> >> I want to know that whether these bands are correct and if they are wrong, where my mistakes are and how to solve them. >> >> The server blocked my files attched, so please visit >> graph with colorful lines:http://pic.emuch.net/200903/04/33e7b7b230bfd248104b8ba1ada65361.jpg >> graph without line:http://pic.emuch.net/200903/04/4a2fdd6cbf9f7d0ce2df725c579e57ea.jpg >> >> If you couldn't visit them successfully, mail me. >> >> I need your help. >> >> all the best. >> >> Li Fei >> 2009-03-04 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From marcel at physik.tu-berlin.de Wed Mar 4 17:08:36 2009 From: marcel at physik.tu-berlin.de (Marcel Mohr) Date: Wed, 4 Mar 2009 17:08:36 +0100 (CET) Subject: [Pw_forum] strange bandstructure In-Reply-To: <200903050003486719489@gmail.com> References: <200903050003486719489@gmail.com> Message-ID: Everything fine the crossing comes from your viewer program, it does not know, which points should be connected. Cheers Marcel ________________________________________________________________________ Marcel Mohr Institut f?r Festk?rperphysik, TU Berlin marcel(at)physik.tu-berlin.de Sekr. EW 5-4 TEL: +49-30-314 24442 Hardenbergstr. 36 FAX: +49-30-314 27705 10623 Berlin On Thu, 5 Mar 2009, idoldog wrote: > Dear PWSCF user, > > I just finished a bandstructure calculation about semiconductor SrTiO3. I get a strange bandstructure. > > In order to see clearly, I redraw the graph and mark same bands, which may be wrong, with different colors. > > Some friends tell me it would be better without lines. Another friends tell me to change the path of markde lines. > > I want to know that whether these bands are correct and if they are wrong, where my mistakes are and how to solve them. > > The server blocked my files attched, so please visit > graph with colorful lines:http://pic.emuch.net/200903/04/33e7b7b230bfd248104b8ba1ada65361.jpg > graph without line:http://pic.emuch.net/200903/04/4a2fdd6cbf9f7d0ce2df725c579e57ea.jpg > > If you couldn't visit them successfully, mail me. > > I need your help. > > all the best. > > Li Fei > 2009-03-04 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From sclauzer at sissa.it Wed Mar 4 17:52:27 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 04 Mar 2009 17:52:27 +0100 Subject: [Pw_forum] DOS calculation for non collinear magnetic ordering In-Reply-To: References: Message-ID: <49AEB1CB.2070906@sissa.it> Xun-Wang Yan wrote: > Dear pwscf users, > I have calculated the density of states for the noncolinear magnetic > CuCrO2, the angle between spin directions of two Cr atoms is 120 degrees. How do you know this? How many Cr atoms do you have per unit cell? > the magnetic moment is about 3 Bohr magnetons per Cr atom, I think > the pdosup(E) is different from the pdosdw(E), I think you should be right, if you have a net magnetization along z it would split bands into up and down. > but the 'pdosup(E)' and > 'pdosdw(E)' are just the same in output file-- > 120-AFM-12at-tricli.pdos_atm#6(Cr3)_wfc#2(d). Are these energies here below next to the Fermi energy? Maybe states very low in energy are not affected much by the magnetization (although if you really get 3 bohr/atom I guess they should). > > # E(eV) ldosup(E) ldosdw(E) pdosup(E) pdosdw(E) pdosup(E) > pdosdw(E) pdosup(E) > -11.138 0.134E-07 0.134E-07 0.336E-08 0.336E-08 0.787E-16 > 0.787E-16 0.739E-16 ... > -11.128 0.105E-04 0.105E-04 0.263E-05 0.263E-05 0.618E-13 > 0.618E-13 0.580E-13 ... > -11.118 0.138E-03 0.138E-03 0.345E-04 0.345E-04 0.232E-11 > 0.232E-11 0.105E-11 ... > -11.108 0.247E-03 0.247E-03 0.618E-04 0.618E-04 0.585E-08 > 0.585E-08 0.138E-08 > -11.098 0.654E-03 0.654E-03 0.165E-03 0.165E-03 0.405E-06 > 0.405E-06 0.149E-06 > -11.088 0.116E-02 0.116E-02 0.285E-03 0.285E-03 0.648E-06 > 0.648E-06 0.555E-06 > -11.078 0.804E-03 0.804E-03 0.209E-03 0.209E-03 0.385E-06 > 0.385E-06 0.254E-06 > -11.068 0.523E-03 0.523E-03 0.128E-03 0.128E-03 0.653E-06 > 0.653E-06 0.765E-06 > -11.058 0.648E-03 0.648E-03 0.152E-03 0.152E-03 0.115E-05 > 0.115E-05 0.126E-05 > -11.048 0.174E-02 0.174E-02 0.450E-03 0.450E-03 0.676E-05 > 0.676E-05 0.304E-05 > -11.038 0.122E-02 0.122E-02 0.302E-03 0.302E-03 0.373E-05 > 0.373E-05 0.173E-05 > > my questions : > What do pdosup and pdosdw mean in DOS output file for > noncolinear magnetic ordjering? the 'up' means Sz=1/2 ? but the spin > direction is vertical to z axes in my unit cell. The projwfc.x program projects onto atomic orbitals which in this case (non-colinear, non spin-orbit) are eigenstates of S_z (and of L^2 and L_z, in the atom). > how to deal with the DOS of noncolinear magnetic structure in > version espresso-4.0.1? Please try to plot the non collinear magnetization with pp.x (plot_num=13), in order to verify that there is a local magnetization on the atom. GS > > Any comments are welcome , many thanks in advance. > > Bests > > Xun-wang Yan > ======================================== > Institute of Theoretical Physics, CAS > Address: No.55, Zhong-Guan-Cun East Road > Beijing, China > Email: xwyan at itp.ac.cn > > yanxunwang2008 at gmail.com > =================== > > > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From swblelia at ehu.es Wed Mar 4 17:52:05 2009 From: swblelia at ehu.es (Aritz Leonardo Liceranzu) Date: Wed, 4 Mar 2009 17:52:05 +0100 Subject: [Pw_forum] Re[Psi] and Im[Psi] Message-ID: <20090304175205.l37kvdo3cw0gw808@www.ehu.es> Hi pwscf users, My question is regarding the output of the KS wave-functions. For a tddft problem that I am involved into, I need to numerically integrate the equilibrium KS wavefunctions. For this purpose I would like to obtain for each (k,i) Bloch state a chart containing: Rx,Ry,Rz, Re[psi], Im[psi] I surfed through old emails (like the one below) and I found that this feature is not implemented in PP codes (am I right?). Ab-init produces this kind of output but I am trying to avoid using it (I am loyal to espresso :) ). On the other hand, it shouldn't be very difficult to write a small program that does it, any hints so that I do not have to use ab-init???? Thank you in advance Aritz Lorenzo Paulatto paulatto at sissa.it Sat Feb 23 12:48:15 CET 2008 On Sab, 23 Febbraio 2008 5:42 am, nafise rezaei wrote: >> However, I want to extract and to plot parts of real and imaginary >> wave function. >> Do you know any program to generate wave function? If there is no >> program, I can modify what program to write it? The postprocessing utility pp.x can extract the square modulus of a wavefunction (you choose it by specifying kpoint and band index), plotting real and imaginary parts is not implemented, but you may be able to do it youself. On the other hand, if nobody have felt the need to implement it in the last not so few years there could be a reason. If you tell us what you want to do, instead of how you want to do it, you will probably get some more useful advice. Regards, LP From carlo.nervi at unito.it Wed Mar 4 19:51:27 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Wed, 4 Mar 2009 19:51:27 +0100 (CET) Subject: [Pw_forum] newbie update Message-ID: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> Dear all, finally I succesfully compiled the code using ifort, mkl and mpich2. However, I'm getting odd results, very probably due to wrong settings. I tried to run the example01 with the following settings: OMP_NUM_THREADS=1 mpiexec -n 8 The example is executed, but with a very long time. All 8 CPUs are running between 5 and 20 % of the cpu time. For some reason we are not using all the power.. I tried to run also "mpiexec -envall -n 8" (maybe the OMP_NUM_THREADS is not passed) but i got identical results. Here is the results of the first example in the example01 directory: results/si.scf.david.out Writing output data file silicon.save PWSCF : 0.50s CPU time, 7.27s wall time On the other hand, if I set OMP_NUM_THREADS=8 and do not use mpiexec I got: Writing output data file silicon.save PWSCF : 7.10s CPU time, 1.12s wall time Therefore results/si.scf.david.out takes 1.12s instead of 7.27s, a much more reasonable timing. Anyone could give me an advice? Thank you, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From schmidt at chem.wisc.edu Wed Mar 4 20:00:53 2009 From: schmidt at chem.wisc.edu (JR Schmidt) Date: Wed, 04 Mar 2009 13:00:53 -0600 Subject: [Pw_forum] newbie update In-Reply-To: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> Message-ID: <49AECFE5.3020905@chem.wisc.edu> I had problems with MKL not obeyig OMP_NUM_THREADS. I found it was easier to simply link with the MKL serial (non-threaded) library, since that is what you want anyway. > I tried to run the example01 with the following settings: > > OMP_NUM_THREADS=1 > mpiexec -n 8 > > The example is executed, but with a very long time. All 8 > CPUs are running > -- J.R. Schmidt Assistant Professor of Chemistry Room 8305D Department of Chemistry University of Wisconsin-Madison 1101 University Ave Madison, WI 53706 Phone: (608) 262-2996 Fax: (608) 262-9918 E-mail: schmidt at chem.wisc.edu http://www.chem.wisc.edu/people/profiles/schmidt.php From akohlmey at cmm.chem.upenn.edu Wed Mar 4 20:23:33 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 4 Mar 2009 14:23:33 -0500 (EST) Subject: [Pw_forum] newbie update In-Reply-To: <49AECFE5.3020905@chem.wisc.edu> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> <49AECFE5.3020905@chem.wisc.edu> Message-ID: On Wed, 4 Mar 2009, JR Schmidt wrote: JRS> I had problems with MKL not obeyig OMP_NUM_THREADS. I found it was JRS> easier to simply link with the MKL serial (non-threaded) library, since JRS> that is what you want anyway. yes. but in carlo's case it _does_ work correctly. axel. JRS> > I tried to run the example01 with the following settings: JRS> > JRS> > OMP_NUM_THREADS=1 JRS> > mpiexec -n 8 JRS> > JRS> > The example is executed, but with a very long time. All 8 JRS> > CPUs are running JRS> > JRS> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From jjr19 at uakron.edu Wed Mar 4 20:27:50 2009 From: jjr19 at uakron.edu (J. J. Ramsey) Date: Wed, 4 Mar 2009 11:27:50 -0800 (PST) Subject: [Pw_forum] Fw: nimage is larger than the available number of images? Message-ID: <962556.89470.qm@web50902.mail.re2.yahoo.com> > I don't get it. nimage = num_of_images, so why is there a problem? Ok, I figured out what I did to myself. Unless the first and last images are being optimized (done by setting first_last_opt to .TRUE. in the &IONS namelist), then the number of images available to be parallelized is two less than num_of_images, so if num_of_images = 7, then nimage <= 5. From akohlmey at cmm.chem.upenn.edu Wed Mar 4 20:33:05 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 4 Mar 2009 14:33:05 -0500 (EST) Subject: [Pw_forum] newbie update In-Reply-To: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> Message-ID: On Wed, 4 Mar 2009, Carlo Nervi wrote: CN> Dear all, dear carlo, CN> finally I succesfully compiled the code using ifort, mkl CN> and mpich2. CN> However, I'm getting odd results, very probably due to CN> wrong settings. CN> CN> I tried to run the example01 with the following settings: CN> CN> OMP_NUM_THREADS=1 CN> mpiexec -n 8 CN> CN> The example is executed, but with a very long time. All 8 CN> CPUs are running CN> between 5 and 20 % of the cpu time. For some reason we are CN> not using all the power.. please note, example01 is _very_ small. as a result there is little data to parallelize over and quite a bit of i/o. CN> I tried to run also "mpiexec -envall -n 8" (maybe the CN> OMP_NUM_THREADS is not passed) CN> but i got identical results. CN> Here is the results of the first example in the example01 CN> directory: CN> CN> results/si.scf.david.out CN> CN> Writing output data file silicon.save CN> CN> PWSCF : 0.50s CPU time, 7.27s wall time see. these are _seconds_. unless you run a test that runs _minutes_, there is little use to these numbers. as suggested before, a good test to see if your MPI is working well, are the cp.x inputs in example21. have a look at the readme first. running them with ./run_example 32 should be sufficient. CN> On the other hand, if I set CN> CN> OMP_NUM_THREADS=8 CN> and do not use mpiexec I got: CN> CN> Writing output data file silicon.save CN> CN> PWSCF : 7.10s CPU time, 1.12s wall time CN> CN> Therefore results/si.scf.david.out takes 1.12s instead of CN> 7.27s, a much CN> more reasonable timing. CN> Anyone could give me an advice? this is due to having to create 8x the number of files. see my comments in the (longish) e-mail from last night with benchmarks wrt. to the number of pools to use. it also looks briefly into the impact of file io. with this small a system, the impact is correspondingly larger. cheers, axel. CN> Thank you, CN> Carlo CN> CN> -- CN> ------------------------------------------------------ CN> Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 CN> Fax: +39 011 6707855 - Dipartimento di Chimica IFM CN> via P. Giuria 7, 10125 Torino, Italy CN> http://lem.ch.unito.it/ CN> CN> CN> _______________________________________________ CN> Pw_forum mailing list CN> Pw_forum at pwscf.org CN> http://www.democritos.it/mailman/listinfo/pw_forum CN> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From lex at phys.ufl.edu Wed Mar 4 20:47:27 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Wed, 04 Mar 2009 14:47:27 -0500 Subject: [Pw_forum] newbie update In-Reply-To: References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> <49AECFE5.3020905@chem.wisc.edu> Message-ID: <49AEDACF.70806@phys.ufl.edu> Out of curiosity, what behaviour do you see from MKL that it doesn't obey OMP_NUM_THREADS? I ask, because that's what I'm using, and would like to make sure it's behaving right. Thanks, Lex Kemper University of Florida Axel Kohlmeyer wrote: > On Wed, 4 Mar 2009, JR Schmidt wrote: > > JRS> I had problems with MKL not obeyig OMP_NUM_THREADS. I found it was > JRS> easier to simply link with the MKL serial (non-threaded) library, since > JRS> that is what you want anyway. > > yes. but in carlo's case it _does_ work correctly. > > axel. > > JRS> > I tried to run the example01 with the following settings: > JRS> > > JRS> > OMP_NUM_THREADS=1 > JRS> > mpiexec -n 8 > JRS> > > JRS> > The example is executed, but with a very long time. All 8 > JRS> > CPUs are running > JRS> > > JRS> > From akohlmey at cmm.chem.upenn.edu Wed Mar 4 21:06:37 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 4 Mar 2009 15:06:37 -0500 (EST) Subject: [Pw_forum] newbie update In-Reply-To: <49AEDACF.70806@phys.ufl.edu> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> <49AECFE5.3020905@chem.wisc.edu> <49AEDACF.70806@phys.ufl.edu> Message-ID: On Wed, 4 Mar 2009, Lex Kemper wrote: LK> Out of curiosity, what behaviour do you see from MKL that it doesn't LK> obey OMP_NUM_THREADS? I ask, because that's what I'm using, and would LK> like to make sure it's behaving right. lex, it doubt it is mkl that is to blame, but rather the mpirun script/wrapper not exporting environment variables to all tasks, even on remote nodes. if you have a good sysadmin running your machine her or she will have already set OMP_NUM_THREADS=1 in the default environment. with openmpi, for example, the environment is not exported unless explicitly set it via a flag. linking the sequential version of mkl (see mkl docs for) details, is the solution for paranoid people (like me). cheers, axel. LK> LK> Thanks, LK> LK> Lex Kemper LK> University of Florida LK> LK> Axel Kohlmeyer wrote: LK> > On Wed, 4 Mar 2009, JR Schmidt wrote: LK> > LK> > JRS> I had problems with MKL not obeyig OMP_NUM_THREADS. I found it was LK> > JRS> easier to simply link with the MKL serial (non-threaded) library, since LK> > JRS> that is what you want anyway. LK> > LK> > yes. but in carlo's case it _does_ work correctly. LK> > LK> > axel. LK> > LK> > JRS> > I tried to run the example01 with the following settings: LK> > JRS> > LK> > JRS> > OMP_NUM_THREADS=1 LK> > JRS> > mpiexec -n 8 LK> > JRS> > LK> > JRS> > The example is executed, but with a very long time. All 8 LK> > JRS> > CPUs are running LK> > JRS> > LK> > JRS> LK> > LK> _______________________________________________ LK> Pw_forum mailing list LK> Pw_forum at pwscf.org LK> http://www.democritos.it/mailman/listinfo/pw_forum LK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From schmidt at chem.wisc.edu Wed Mar 4 22:32:48 2009 From: schmidt at chem.wisc.edu (JR Schmidt) Date: Wed, 04 Mar 2009 15:32:48 -0600 Subject: [Pw_forum] newbie update In-Reply-To: <49AEDACF.70806@phys.ufl.edu> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> <49AECFE5.3020905@chem.wisc.edu> <49AEDACF.70806@phys.ufl.edu> Message-ID: <49AEF380.2020604@chem.wisc.edu> > > Out of curiosity, what behaviour do you see from MKL that it doesn't > obey OMP_NUM_THREADS? I ask, because that's what I'm using, and would > like to make sure it's behaving right. > I investigated using ps, which with appropriate options ('ps axms' on Linux, I believe) will dump out info on threads for each process. I was seeing lots of threads created for each QE process, regardless OMP_NUM_THREADS (I set it in my profile, so it should have stuck around when executed by mpirun). I noticed that MKL 10.0 also has MKL_NUM_THREADS as well, which didn't seem to work either. At least this should let you investigate. In either case, linking the serial version solved all my issues. -- J.R. Schmidt Assistant Professor of Chemistry Room 8305D Department of Chemistry University of Wisconsin-Madison 1101 University Ave Madison, WI 53706 Phone: (608) 262-2996 Fax: (608) 262-9918 E-mail: schmidt at chem.wisc.edu http://www.chem.wisc.edu/people/profiles/schmidt.php From lex at phys.ufl.edu Wed Mar 4 23:23:07 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Wed, 04 Mar 2009 17:23:07 -0500 Subject: [Pw_forum] newbie update In-Reply-To: References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> <49AECFE5.3020905@chem.wisc.edu> <49AEDACF.70806@phys.ufl.edu> Message-ID: <49AEFF4B.9020007@phys.ufl.edu> Hey Axel, In my case, exporting OMP_NUM_THREADS from my .bashrc was sufficient. I guess that's not the case everywhere. Thanks! Lex Axel Kohlmeyer wrote: > On Wed, 4 Mar 2009, Lex Kemper wrote: > > LK> Out of curiosity, what behaviour do you see from MKL that it doesn't > LK> obey OMP_NUM_THREADS? I ask, because that's what I'm using, and would > LK> like to make sure it's behaving right. > > lex, > > it doubt it is mkl that is to blame, but rather the mpirun > script/wrapper not exporting environment variables to all tasks, > even on remote nodes. if you have a good sysadmin running your > machine her or she will have already set OMP_NUM_THREADS=1 > in the default environment. > > with openmpi, for example, the environment is not exported > unless explicitly set it via a flag. > > linking the sequential version of mkl (see mkl docs for) > details, is the solution for paranoid people (like me). > > cheers, > axel. > > LK> > LK> Thanks, > LK> > LK> Lex Kemper > LK> University of Florida > LK> > LK> Axel Kohlmeyer wrote: > LK> > On Wed, 4 Mar 2009, JR Schmidt wrote: > LK> > > LK> > JRS> I had problems with MKL not obeyig OMP_NUM_THREADS. I found it was > LK> > JRS> easier to simply link with the MKL serial (non-threaded) library, since > LK> > JRS> that is what you want anyway. > LK> > > LK> > yes. but in carlo's case it _does_ work correctly. > LK> > > LK> > axel. > LK> > > LK> > JRS> > I tried to run the example01 with the following settings: > LK> > JRS> > > LK> > JRS> > OMP_NUM_THREADS=1 > LK> > JRS> > mpiexec -n 8 > LK> > JRS> > > LK> > JRS> > The example is executed, but with a very long time. All 8 > LK> > JRS> > CPUs are running > LK> > JRS> > > LK> > JRS> > LK> > > LK> _______________________________________________ > LK> Pw_forum mailing list > LK> Pw_forum at pwscf.org > LK> http://www.democritos.it/mailman/listinfo/pw_forum > LK> > From akohlmey at cmm.chem.upenn.edu Thu Mar 5 01:03:27 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 4 Mar 2009 19:03:27 -0500 (EST) Subject: [Pw_forum] newbie update In-Reply-To: <49AEFF4B.9020007@phys.ufl.edu> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> <49AECFE5.3020905@chem.wisc.edu> <49AEDACF.70806@phys.ufl.edu> <49AEFF4B.9020007@phys.ufl.edu> Message-ID: On Wed, 4 Mar 2009, Lex Kemper wrote: LK> Hey Axel, LK> LK> In my case, exporting OMP_NUM_THREADS from my .bashrc was sufficient. LK> I guess that's not the case everywhere. right. this happens mostly on batch systems when launching jobs through libtorque (very convenient, but you don't get a login shell) and some ssh setups also do not read .profile. also one has to consider that debian based systems (incl ubuntu), don't use /bin/bash as /bin/sh, but have a version of /bin/ash as /bin/sh and that one only reads .profile (which many bash setups in turn don't) but, of course, not .bashrc. so it is actually a good idea to verify this, like JR did. the case of a not exported environment is nasty, because it will slow down the calculation (if you run 8 mpi tasks on a 2x quad-core node, mkl with spawn 8 threads for each of them), without the telltale sign on the rank0 node of cpu time being multiple times larger than the walltime. cheers, axel. LK> Thanks! LK> LK> Lex LK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From swblelia at ehu.es Thu Mar 5 01:13:01 2009 From: swblelia at ehu.es (Aritz Leonardo Liceranzu) Date: Thu, 5 Mar 2009 01:13:01 +0100 Subject: [Pw_forum] Re[Psi] and Im[Psi] Message-ID: <20090305011301.9o70t60vi88cokk4@www.ehu.es> No hints on what to modify on the code to write the wave-function? :( Thanks again Aritz ----- Forwarded message from swblelia at ehu.es ----- Date: Wed, 4 Mar 2009 17:52:05 +0100 From: Aritz Leonardo Liceranzu Reply-To: PWSCF Forum Subject: [Pw_forum] Re[Psi] and Im[Psi] To: pw_forum at pwscf.org Hi pwscf users, My question is regarding the output of the KS wave-functions. For a tddft problem that I am involved into, I need to numerically integrate the equilibrium KS wavefunctions. For this purpose I would like to obtain for each (k,i) Bloch state a chart containing: Rx,Ry,Rz, Re[psi], Im[psi] I surfed through old emails (like the one below) and I found that this feature is not implemented in PP codes (am I right?). Ab-init produces this kind of output but I am trying to avoid using it (I am loyal to espresso :) ). On the other hand, it shouldn't be very difficult to write a small program that does it, any hints so that I do not have to use ab-init???? Thank you in advance Aritz Lorenzo Paulatto paulatto at sissa.it Sat Feb 23 12:48:15 CET 2008 On Sab, 23 Febbraio 2008 5:42 am, nafise rezaei wrote: >> However, I want to extract and to plot parts of real and imaginary >> wave function. >> Do you know any program to generate wave function? If there is no >> program, I can modify what program to write it? The postprocessing utility pp.x can extract the square modulus of a wavefunction (you choose it by specifying kpoint and band index), plotting real and imaginary parts is not implemented, but you may be able to do it youself. On the other hand, if nobody have felt the need to implement it in the last not so few years there could be a reason. If you tell us what you want to do, instead of how you want to do it, you will probably get some more useful advice. Regards, LP _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ----- End forwarded message ----- From idoldog at gmail.com Thu Mar 5 07:23:55 2009 From: idoldog at gmail.com (idoldog) Date: Thu, 5 Mar 2009 14:23:55 +0800 Subject: [Pw_forum] strange bandstructure References: <200903050003486719489@gmail.com>, <49AEA81E.50209@phys.ufl.edu> Message-ID: <200903051423538432460@gmail.com> dear Lex Kemper, Gabriele Sclauzero, Marcel Mohr, I appreciate your help very much. I will try it follow your suggestions. all best. idoldog 2009.3.5 come from: Lex Kemper send date: 2009-03-05 00:12:31 send to: PWSCF Forum subject:Re: [Pw_forum] strange bandstructure Hi idoldog, I presume what you're referring to as 'strange' is the lines jumping from one band to another. This is, as I understand it, the bands.x code not seeing enough overlap between the kpoints to order them properly. There are two ways to fix this: (a) Run with more points per line in k-space (b) If you're only interested in a few bands, fix them by hand. Good luck! Lex Kemper University of Florida idoldog wrote: > Dear PWSCF user, > > I just finished a bandstructure calculation about semiconductor SrTiO3. I get a strange bandstructure. > > In order to see clearly, I redraw the graph and mark same bands, which may be wrong, with different colors. > > Some friends tell me it would be better without lines. Another friends tell me to change the path of markde lines. > > I want to know that whether these bands are correct and if they are wrong, where my mistakes are and how to solve them. > > The server blocked my files attched, so please visit > graph with colorful lines:http://pic.emuch.net/200903/04/33e7b7b230bfd248104b8ba1ada65361.jpg > graph without line:http://pic.emuch.net/200903/04/4a2fdd6cbf9f7d0ce2df725c579e57ea.jpg > > If you couldn't visit them successfully, mail me. > > I need your help. > > all the best. > > Li Fei > 2009-03-04 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Thu Mar 5 08:11:19 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 5 Mar 2009 08:11:19 +0100 Subject: [Pw_forum] Re[Psi] and Im[Psi] In-Reply-To: <20090304175205.l37kvdo3cw0gw808@www.ehu.es> References: <20090304175205.l37kvdo3cw0gw808@www.ehu.es> Message-ID: <3DD86A63-6157-4DFD-BDF4-27D76A6C9C0D@democritos.it> On Mar 4, 2009, at 17:52 , Aritz Leonardo Liceranzu wrote: > For a tddft problem that I am involved into, I need to numerically > integrate the equilibrium KS wavefunctions. For this purpose I would > like to obtain for each (k,i) Bloch state a chart containing: > > Rx,Ry,Rz, Re[psi], Im[psi] in real or reciprocal space? in the latter case, you could modify the "pw2casino" utility. In the former case, you can get the wavefunctions on the FFT grid by Fourier-transfoming them. The correspondence between points in real space and indices in the FFT grid is explained in the FAQ of the user guide. You might try to modify code "elf.f90", for instance: calculate \psi(r) iinstead of grad\psi(r) P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Thu Mar 5 08:32:03 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Mar 2009 08:32:03 +0100 Subject: [Pw_forum] Fw: nimage is larger than the available number of images? In-Reply-To: <962556.89470.qm@web50902.mail.re2.yahoo.com> References: <962556.89470.qm@web50902.mail.re2.yahoo.com> Message-ID: <49AF7FF3.5010907@sissa.it> J. J. Ramsey wrote: >> I don't get it. nimage = num_of_images, so why is there a problem? > > Ok, I figured out what I did to myself. Well done! ;-) > Unless the first and last images are being > optimized (done by setting first_last_opt to .TRUE. in the &IONS namelist), then the > number of images available to be parallelized is two less than num_of_images, so if > num_of_images = 7, then nimage <= 5. Good that you have shared the piece of information you got by yourself with all the community of users. Thanks! Cheers, GS > > > > > _______________________________________________ Pw_forum mailing list > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From glaweh at physik.fu-berlin.de Thu Mar 5 09:10:08 2009 From: glaweh at physik.fu-berlin.de (Henning Glawe) Date: Thu, 5 Mar 2009 09:10:08 +0100 Subject: [Pw_forum] newbie update In-Reply-To: References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> <49AECFE5.3020905@chem.wisc.edu> <49AEDACF.70806@phys.ufl.edu> <49AEFF4B.9020007@phys.ufl.edu> Message-ID: <20090305081008.GA4740@ruprecht.physik.fu-berlin.de> On Wed, Mar 04, 2009 at 07:03:27PM -0500, Axel Kohlmeyer wrote: > also one has to consider that debian based systems (incl ubuntu), > don't use /bin/bash as /bin/sh, but have a version of /bin/ash as > /bin/sh and that one only reads .profile (which many bash setups > in turn don't) but, of course, not .bashrc. actually, it is only ubuntu doing this by default. even debian lenny has bash as /bin/sh (although, of course, one should never rely on sh==bash, especially on machines running on commercial unix variants). therefore when relying on bash features (such as reading .bashrc), one should explicitely write #!/bin/bash and not #!/bin/sh into the job scripts. in case the queuing system does not call jobscript not directly, but instead forces /bin/sh as an interpreter, set the appropriate job options to use /bin/bash instead (in torque, this is job option '-S'). -- c u henning From mpayami at aeoi.org.ir Thu Mar 5 20:59:13 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Thu, 5 Mar 2009 11:59:13 -0800 Subject: [Pw_forum] parallelization issues Message-ID: Dear ALL, In sec. of "parallelization issues" of UG, is mentioned that: "As a general rule, image parallelization may give good scaling..." Could anybody please explain what exactly it means in terms of say, static linking, using more npools, or so. Bests, Mahmoud Payami Physics Group, AEOI. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090305/ab8dd5f2/attachment.htm From sclauzer at sissa.it Thu Mar 5 09:45:04 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Mar 2009 09:45:04 +0100 Subject: [Pw_forum] parallelization issues In-Reply-To: References: Message-ID: <49AF9110.1020108@sissa.it> Mahmoud Payami wrote: > Dear ALL, > > In sec. of "parallelization issues" of UG, is mentioned that: "As a > general rule, image parallelization may give good scaling..." These is relevant to you only if you are performing NEB calculations. > Could anybody please explain what exactly it means in terms of say, > static linking, using more npools, or so. I think it has nothing to do with static linking and in general with any compilation issue. Once you correctly compiled a parallel version, you're free to chose which kind of parallelization to eploit, depending of your type of system and calculation. If you're doing NEB, then the image parallelization is the more efficients since different images have to "speak" very few one to the other, while if not doing NEB you can still use the other levels of parallelization described in the user guide. They do not scale as well as image parallelization, but still do a good job to speed up your code or let you study very big systems. cheers, GS > > Bests, > Mahmoud Payami > Physics Group, AEOI. > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From degironc at sissa.it Thu Mar 5 09:45:05 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 05 Mar 2009 09:45:05 +0100 Subject: [Pw_forum] parallelization issues In-Reply-To: References: Message-ID: <49AF9111.1070907@sissa.it> It means that since very little communication is needed across different images this parallelization does not suffer much (at all) if the communication network is not very fast... however it does not distribute the memory and I/O ... which may be bad for the efficiency of the calculation as we are learning these days from the discussion going on on pool parallelization (which also is less-communication and more-memory&I/O intensive than R&G parallelization)... My today understanding of this is that one could increase the number of processors using R&G parallelization as far as the network at hand allows to get a good scaling... then one can increase further the number of processors by adding pool parallelization and, in case of NEB calculations, some image parallelization. Hope this helps, Stefano de Gironcoli Mahmoud Payami wrote: > Dear ALL, > > In sec. of "parallelization issues" of UG, is mentioned that: "As a > general rule, image parallelization may give good scaling..." > Could anybody please explain what exactly it means in terms of say, > static linking, using more npools, or so. > > Bests, > Mahmoud Payami > Physics Group, AEOI. > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From yaoyg at hotmail.com Thu Mar 5 09:41:13 2009 From: yaoyg at hotmail.com (yaoyugui) Date: Thu, 5 Mar 2009 16:41:13 +0800 Subject: [Pw_forum] separate the surface state and surface resonance state from the bulk state Message-ID: Dear all, I am simulating the Be(0001) surface through N-layer slab construction. But how can I decompose the calculated bands into surface states and bulk states. From degironc at sissa.it Thu Mar 5 09:57:57 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 05 Mar 2009 09:57:57 +0100 Subject: [Pw_forum] separate the surface state and surface resonance state from the bulk state In-Reply-To: References: Message-ID: <49AF9415.4090308@sissa.it> Dear Wenmei Ming, surface states are, by definition, localized at the surface and, in term of band energy, they are located in gaps of the bulk-projected bund structure. as such you can identify them in the list of eigenvalues and then plot their three dimensional density using (for instance) the post processing tool pp.x (plot_num=7)... resonant surface states are more tricky as they do not correspond to a single state but to an energy window and extend inside your slab ... they can be visualized by looking at the integrated local density of states (ILDOS) plot_num=10 in the energy window of interest. Hope this helps, stefano de Gironcoli -SISSA & DEMOCRITOS yaoyugui wrote: > Dear all, > I am simulating the Be(0001) surface through N-layer slab construction. > But how can I decompose the calculated bands into surface states and > bulk states. > From a few publications concerning DFT calculation of surface structure, > the final bands are showed as surface projected bulk bands, > distinctively pointing out > the surface states and the surface resonance states. > How can I separate the surface state and surface resonance state from > the bulk state > using PWSCF package? or additional codes are required ? > Could anyone give me suggestion? > Thanks a million. > Wenmei Ming > Institue of Physics, > Chinese Academy of Sciences > Beijing 100190 > People's Republic of China > > ------------------------------------------------------------------------ > ????? Windows Live Messenger ???????? ????? > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mpayami at aeoi.org.ir Thu Mar 5 21:33:56 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Thu, 5 Mar 2009 12:33:56 -0800 Subject: [Pw_forum] parallelization issues References: <49AF9111.1070907@sissa.it> Message-ID: <3A8513DD2165470D899DB0E0998C6E1E@ctpm> Dear Gabriele and Stefano, Thank you very much for your explanations. Bests, Mahmoud > It means that since very little communication is needed across different > images this parallelization does not suffer much (at all) if the > communication network is not very fast... however it does not > distribute the memory and I/O ... which may be bad for the efficiency > of the calculation as we are learning these days from the discussion > going on on pool parallelization (which also is less-communication and > more-memory&I/O intensive than R&G parallelization)... > My today understanding of this is that one could increase the number of > processors using R&G parallelization as far as the network at hand > allows to get a good scaling... then one can increase further the number > of processors by adding pool parallelization and, in case of NEB > calculations, some image parallelization. > > Hope this helps, > Stefano de Gironcoli > > Mahmoud Payami wrote: >> Dear ALL, >> >> In sec. of "parallelization issues" of UG, is mentioned that: "As a >> general rule, image parallelization may give good scaling..." >> Could anybody please explain what exactly it means in terms of say, >> static linking, using more npools, or so. >> >> Bests, >> Mahmoud Payami >> Physics Group, AEOI. >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From zah7903 at gmail.com Thu Mar 5 10:13:01 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Thu, 5 Mar 2009 17:13:01 +0800 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: <49AD3208.4030308@democritos.it> References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> <49AD25BF.2030003@sissa.it> <49AD3208.4030308@democritos.it> Message-ID: On Tue, Mar 3, 2009 at 9:35 PM, Paolo Giannozzi wrote: > Gabriele Sclauzero wrote: > > > I think that CG style diagonalization has not been parallelized > > like the Davidson one, so these lines at the beginning > > of your output sound strange to me. > > > >> > a parallel distributed memory algorithm will be used, > >> > eigenstates matrixes will be distributed block like on > >> > ortho sub-group = 2* 2 procs > > they aren't strange. This is for "subspace diagonalization", > which is not directly used in CG diagonalization, but it is > used in i) calculating starting wavefunctions, and ii) rotating > wavefunctions before starting a new diagonalization (it is > equivalent to first-order perturbation theory and improves > quite a bit the subsequent diagonalization). > > Anyway I verified that the problem with charge is present only > in parallel execution, both for CG and Davidson, irrespective > whether subspace diagonalization is parallel or not > Is there any work-around now? Parallel execution is indispensable for large systems. > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > - Show quoted text - > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090305/970d83ac/attachment-0001.htm From baris.malcioglu at gmail.com Thu Mar 5 10:16:28 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Thu, 5 Mar 2009 10:16:28 +0100 Subject: [Pw_forum] Re[Psi] and Im[Psi] In-Reply-To: <20090304175205.l37kvdo3cw0gw808@www.ehu.es> References: <20090304175205.l37kvdo3cw0gw808@www.ehu.es> Message-ID: Dear Aritz, First of all, you must notice that norm of the wavefunctions stored will vary depending on what type of pseudopotential you use (Norm conserving Ultrasoft etc.) The most straightforward in terms of mathematical handling is the norm conserving one. I prefer writing new subroutines rather than modifying old ones, since I have witnessed doing that makes things get really messy after a while. Anyhow, here are some exempts from my personal notes, I hope you find them useful. They are a bit unmaintained, thus as a disclaimer, please report any error in them, so that I end up with better documentation. 1) How to calculate the real space grid points: In this exempt, the aim is to find a set of grid points within a certain distance from an atom. The first step is to start an index rolling on available grid points DO ir = 1, nrxxs nrxxs is explained as ?the total dimension of the smooth grid? in gsmooth (PW/pwcom.f90) . It is the total number of grid points in the smooth grid. ! ! ... three dimensional indexes ! index = index0 + ir - 1 k = index / (nrx1s*nrx2s) index = index - (nrx1s*nrx2s)*k j = index / nrx1s index = index - nrx1s*j i = index ! Index0 is an offset for parallelism issues. It separates the grid into processors and each processor starts processing from this offset. nrx1s and nrx2s and nrx3s are again from gsmooth, and defined as ?maximum dimension of the smooth grid? in the corresponding direction, they are used as the reduced forms of nrXs (X=1,2,3) dividing the grid points among the nodes. In the serial case nrxxs=nrx1s*nrx2s*nrx3s but this might or might not always be true for different parallel cases. index (a temporary integer), nrx1s and nrx2s are all integers, so the divisions above are integer divisions (otherwise the algorithm should return 0 always, look at how the k and the index are calculated consecutively). As a convention, the segmentation of grid points should always start from the 3rd dimension (z). The goal is to achieve an arrangement such that the first 1..nrx1s elements correspond to ith element where j=0 k=0; the second 1..nrx1s element correspond to ith element where j=1 k=0 and etc.. This would make an index of higher rank increase only when the cycles of all the lower ranks are complete. So the k index (third dimension) is the total number of i and j cycles completed (that would be nrx1s*nrx2s number of elements for each cycle). When k times the number of elements per cycle is removed from the index count, the excess only refers to i and j components. Using the same trick to subtract the cycles of i (nrx1s elements each) the j index value is obtained, and removing the number of elements per cycle for each j increment from the index, the index for i is obtained. DO ipol = 1, 3 posi(ipol) = DBLE( i )*inv_nr1s*at(ipol,1) + & DBLE( j )*inv_nr2s*at(ipol,2) + & DBLE( k )*inv_nr3s*at(ipol,3) END DO this might be on a non-orthogonal basis and we should be extra careful in the next step. Here ipol is an index running over the basis vectors (these will be called x y and z directions for further reference) at(ipol,1..3) are the simulation cell base vectors (in real space) divided by alat (lattice parameter), in terms of Cartesian components (second index). nr1s, nr2s and nr3s are the actual number of grid points (where nrxXs are reduced in a node specific way to conserve memory) thus at/nr is the vector increment for the particular direction. Multiplying this with the increment counter in that direction, a first iteration for the position vector is obtained. ! posi(:) = posi(:) - tau_ia(:) ! This line offsets the position such that current atom is at the center. tau_ia is just a rename for the tau from Modules/ions_base.f90 which contains the positions of the atomic cores. ! ... minimum image convenction ! CALL cryst_to_cart( 1, posi, bg, -1 ) ! posi(:) = posi(:) - ANINT( posi(:) ) ! CALL cryst_to_cart( 1, posi, at, 1 ) ! cryst_to_cart is a subroutine responsible for conversions of vectors from cartesian coordinates to crystal coordinates (+1) and viceversa (-1). This part ensures that any distance more than 0.5 crystal unit far is treated according to the closest atomic center, not the one it is further away. It is actually the minimum Brillouin cell for the atom at hand. distsq = posi(1)**2 + posi(2)**2 + posi(3)**2 END DO END DO the distance from the center... 2) How to FFT a given band into real space (most simplistic version, no gamma point tricks, no non-collinear, etc.) psic(nls(igk(:))) = evc(:,ibnd) psic is the buffer where this kind of operations are performed. Usually allocated in the initialization steps, so at most times can be used directly. The igk(:) is the g,k correspondence array, and updated for each k point under consideration. nls(igk(:)) returns the corresponding index value in real space for the corresponding reciprocal space point index value. evc are the wavefunctions. First index is the grid point, second is the band. ! CALL cft3s( psic, nr1s, nr2s, nr3s, nrx1s, nrx2s, nrx3s, 2 ) internal pwscf wrapper for the fft that does the actual transformation. After this, psic will contain the real space wavefunctions with an index formalism for real space grids. Best, Baris Malcioglu SISSA On Wed, Mar 4, 2009 at 5:52 PM, Aritz Leonardo Liceranzu wrote: > Hi pwscf users, > > My question is regarding the output of the KS wave-functions. > > For a tddft problem that I am involved into, I need to numerically > integrate the equilibrium KS wavefunctions. For this purpose I would > like to obtain for each (k,i) Bloch state a chart containing: > > Rx,Ry,Rz, Re[psi], Im[psi] > > I surfed through old emails (like the one below) and I found that this > feature is not implemented in PP codes (am I right?). > > Ab-init produces this kind of output but I am trying to avoid using it > (I am loyal to espresso :) ). On the other hand, it shouldn't be very > difficult to write a small program that does it, any hints so that I > do not have to use ab-init???? > > Thank you in advance > Aritz > > > > > Lorenzo Paulatto paulatto at sissa.it > Sat Feb 23 12:48:15 CET 2008 > > On Sab, 23 Febbraio 2008 5:42 am, nafise rezaei wrote: >>> However, I want to extract and to plot parts of real and imaginary >>> wave function. >>> Do you know any program to generate wave function? If there is no >>> program, I can modify what program to write it? > > The postprocessing utility pp.x can extract the square modulus of a > wavefunction (you choose it by specifying kpoint and band index), plotting > real and imaginary parts is not implemented, but you may be able to do it > youself. > > On the other hand, if nobody have felt the need to implement it in the > last not so few years there could be a reason. If you tell us what you > want to do, instead of how you want to do it, you will probably get some > more useful advice. > > Regards, LP > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From paulatto at sissa.it Thu Mar 5 10:51:43 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 05 Mar 2009 10:51:43 +0100 Subject: [Pw_forum] newbie update In-Reply-To: <49AEF380.2020604@chem.wisc.edu> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> <49AECFE5.3020905@chem.wisc.edu> <49AEDACF.70806@phys.ufl.edu> <49AEF380.2020604@chem.wisc.edu> Message-ID: On Wed, 04 Mar 2009 22:32:48 +0100, JR Schmidt wrote: > (I set it in my profile, so it should have stuck around > when executed by mpirun). You have to export the variable, for it to work. e.g. this works: OMP_NUM_THREAD=1 ./myprogram this works as well: export OMP_NUM_THREAD=1 ./myprogram but this does NOT work: OMP_NUM_THREAD=1 ./myprogram mysteries of bash shell... regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From glaweh at physik.fu-berlin.de Thu Mar 5 10:58:57 2009 From: glaweh at physik.fu-berlin.de (Henning Glawe) Date: Thu, 5 Mar 2009 10:58:57 +0100 Subject: [Pw_forum] newbie update In-Reply-To: References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it> <49AECFE5.3020905@chem.wisc.edu> <49AEDACF.70806@phys.ufl.edu> <49AEF380.2020604@chem.wisc.edu> Message-ID: <20090305095856.GB4740@ruprecht.physik.fu-berlin.de> On Thu, Mar 05, 2009 at 10:51:43AM +0100, Lorenzo Paulatto wrote: > You have to export the variable, for it to work. > e.g. this works: > OMP_NUM_THREAD=1 ./myprogram > > this works as well: > export OMP_NUM_THREAD=1 > ./myprogram > > but this does NOT work: > OMP_NUM_THREAD=1 > ./myprogram > > mysteries of bash shell... general property of shell variables: if you set a variable without exporting it, this variable is set only for this shell, but not for its child processes (such as the pw.x). a child process only "sees" environment variables, which you create with the export command :) -- c u henning From panda.deng.pan at gmail.com Thu Mar 5 11:25:44 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Thu, 5 Mar 2009 18:25:44 +0800 Subject: [Pw_forum] Problem with the Band Structure Calculation Message-ID: Dear All, I was trying to calculate the band structure of the BaNi2As2 which had been calculated in the paper 0809.0499v2 on the arxiv.I could not repeat the same struture.The BaNi2As2 occurs in a body centered tetragonal structure (I4/mmm) with Ba,Ni and As at the positions 2a(0,0,0),4d (0.5,0,0.25)and 4e(0,0,z).Here z equels 0.3476 by the experimental result.The lattice parameters are a=4.112 A and c=11.54 A. Any comment about my input of this system? my input of scf run: &control calculation = 'scf' restart_mode='from_scratch' prefix='BaNiAs', pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/disk2/xgwan/tmp/' / &system ibrav=6, celldm(1)=7.7702, celldm(3)=2.806, nat=10, ntyp=3, ecutwfc = 40.0, ecutrho = 400.0, occupations= 'tetrahedra' / &electrons diagonalization = 'cg' mixing_beta = 0.7 conv_thr = 1.0d-6 / ATOMIC_SPECIES Ba 137.327 Ba.pbe-nsp-van.UPF Ni 58.6934 Ni.pbe-nd-rrkjus.UPF As 74.9216 As.pbe-n-van.UPF ATOMIC_POSITIONS crystal Ba 0.0000 0.0000 0.0000 Ba 0.5000 0.5000 0.5000 Ni 0.0 0.5 0.25 Ni 0.5 0.0 0.75 Ni 0.5 0.0 0.25 Ni 0.0 0.5 0.75 As 0.0000 0.0000 0.3476 As 0.0000 0.0000 0.6524 As 0.5000 0.5000 0.8476 As 0.5000 0.5000 0.1524 K_POINTS {automatic} 8 8 8 0 0 0 And my input of band calculation ,bands.x,plotband.x if helps: input of band calculation &control calculation = 'bands' prefix='BaNiAs', pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/disk2/xgwan/tmp/' wf_collect=.true. / &system ibrav=6, celldm(1)=7.7702, celldm(3)=2.806, nat=10, ntyp=3, ecutwfc = 40.0, ecutrho = 400.0, occupations= 'tetrahedra' / &electrons diagonalization = 'cg' mixing_beta = 0.7 conv_thr = 1.0d-6 / ATOMIC_SPECIES Ba 137.327 Ba.pbe-nsp-van.UPF Ni 58.6934 Ni.pbe-nd-rrkjus.UPF As 74.9216 As.pbe-n-van.UPF ATOMIC_POSITIONS crystal Ba 0.5000 0.5000 0.5000 Ni 0.5000 0.0000 0.2500 Ni 0.0000 0.5000 0.2500 Ni 0.0000 0.5000 0.7500 Ni 0.5000 0.0000 0.7500 As 0.0000 0.0000 0.3476 As 0.0000 0.0000 0.6524 As 0.5000 0.5000 0.8476 As 0.5000 0.5000 0.1524 K_POINTS 31 -0.50 0.50 0.50 1 -0.45 0.45 0.45 2 -0.40 0.40 0.40 3 -0.35 0.35 0.35 4 -0.30 0.30 0.30 5 -0.25 0.25 0.25 6 -0.20 0.20 0.20 7 -0.15 0.15 0.15 8 -0.10 0.10 0.10 9 -0.05 0.05 0.05 10 0.00 0.00 0.00 11 0.00 0.00 0.05 12 0.00 0.00 0.10 13 0.00 0.00 0.15 14 0.00 0.00 0.20 15 0.00 0.00 0.25 16 0.00 0.00 0.30 17 0.00 0.00 0.35 18 0.00 0.00 0.40 19 0.00 0.00 0.45 20 0.00 0.00 0.50 21 0.05 0.05 0.45 22 0.10 0.10 0.40 23 0.15 0.15 0.35 24 0.20 0.20 0.30 25 0.25 0.25 0.25 26 0.20 0.30 0.20 27 0.15 0.35 0.15 28 0.10 0.40 0.10 29 0.05 0.45 0.05 30 0.0 0.50 0.0 31 input of bands.x &inputpp prefix = 'BaNiAs' outdir = '/disk2/xgwan/tmp/' filband = 'bands.dat' / input of plotband.x bands.dat 2 17 bands.xmgr bands.ps 10.5264 1.0 10.5264 With these inputs I could not get the same band structure as the paper did.I am appreciate for any suggustion and comments. Please tell me where I was wrong or which detail I ignored. Have a nice day. Deng Pan Nanjing Unversity From sclauzer at sissa.it Thu Mar 5 11:39:35 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Mar 2009 11:39:35 +0100 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: Message-ID: <49AFABE7.4030603@sissa.it> Are you absolutely sure that the atomic configuration and k-point path are the same as those in the paper? Maybe K_POINTS in the bands calculation needs the 'CRYSTAL' option? GS ?? wrote: > Dear All, > > I was trying to calculate the band structure of the BaNi2As2 which > had been calculated in the paper 0809.0499v2 on the arxiv.I could not > repeat the same struture.The BaNi2As2 occurs in a body centered > tetragonal structure (I4/mmm) with Ba,Ni and As at the positions > 2a(0,0,0),4d (0.5,0,0.25)and 4e(0,0,z).Here z equels 0.3476 by the > experimental result.The lattice parameters are a=4.112 A and c=11.54 > A. > Any comment about my input of this system? > my input of scf run: > > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='BaNiAs', > pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/disk2/xgwan/tmp/' > / > &system > ibrav=6, > celldm(1)=7.7702, > celldm(3)=2.806, > nat=10, > ntyp=3, > ecutwfc = 40.0, > ecutrho = 400.0, > occupations= 'tetrahedra' > / > &electrons > diagonalization = 'cg' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ni 58.6934 Ni.pbe-nd-rrkjus.UPF > As 74.9216 As.pbe-n-van.UPF > ATOMIC_POSITIONS crystal > Ba 0.0000 0.0000 0.0000 > Ba 0.5000 0.5000 0.5000 > Ni 0.0 0.5 0.25 > Ni 0.5 0.0 0.75 > Ni 0.5 0.0 0.25 > Ni 0.0 0.5 0.75 > As 0.0000 0.0000 0.3476 > As 0.0000 0.0000 0.6524 > As 0.5000 0.5000 0.8476 > As 0.5000 0.5000 0.1524 > K_POINTS {automatic} > 8 8 8 0 0 0 > > And my input of band calculation ,bands.x,plotband.x if helps: > input of band calculation > &control > calculation = 'bands' > prefix='BaNiAs', > pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/disk2/xgwan/tmp/' > wf_collect=.true. > / > &system > ibrav=6, > celldm(1)=7.7702, > celldm(3)=2.806, > nat=10, > ntyp=3, > ecutwfc = 40.0, > ecutrho = 400.0, > occupations= 'tetrahedra' > / > &electrons > diagonalization = 'cg' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ni 58.6934 Ni.pbe-nd-rrkjus.UPF > As 74.9216 As.pbe-n-van.UPF > ATOMIC_POSITIONS crystal > Ba 0.5000 0.5000 0.5000 > Ni 0.5000 0.0000 0.2500 > Ni 0.0000 0.5000 0.2500 > Ni 0.0000 0.5000 0.7500 > Ni 0.5000 0.0000 0.7500 > As 0.0000 0.0000 0.3476 > As 0.0000 0.0000 0.6524 > As 0.5000 0.5000 0.8476 > As 0.5000 0.5000 0.1524 > K_POINTS > 31 > -0.50 0.50 0.50 1 > -0.45 0.45 0.45 2 > -0.40 0.40 0.40 3 > -0.35 0.35 0.35 4 > -0.30 0.30 0.30 5 > -0.25 0.25 0.25 6 > -0.20 0.20 0.20 7 > -0.15 0.15 0.15 8 > -0.10 0.10 0.10 9 > -0.05 0.05 0.05 10 > 0.00 0.00 0.00 11 > 0.00 0.00 0.05 12 > 0.00 0.00 0.10 13 > 0.00 0.00 0.15 14 > 0.00 0.00 0.20 15 > 0.00 0.00 0.25 16 > 0.00 0.00 0.30 17 > 0.00 0.00 0.35 18 > 0.00 0.00 0.40 19 > 0.00 0.00 0.45 20 > 0.00 0.00 0.50 21 > 0.05 0.05 0.45 22 > 0.10 0.10 0.40 23 > 0.15 0.15 0.35 24 > 0.20 0.20 0.30 25 > 0.25 0.25 0.25 26 > 0.20 0.30 0.20 27 > 0.15 0.35 0.15 28 > 0.10 0.40 0.10 29 > 0.05 0.45 0.05 30 > 0.0 0.50 0.0 31 > > input of bands.x > &inputpp > prefix = 'BaNiAs' > outdir = '/disk2/xgwan/tmp/' > filband = 'bands.dat' > / > input of plotband.x > bands.dat > 2 17 > bands.xmgr > bands.ps > 10.5264 > 1.0 10.5264 > > With these inputs I could not get the same band structure as the paper > did.I am appreciate for any suggustion and comments. > Please tell me where I was wrong or which detail I ignored. > > Have a nice day. > > Deng Pan > Nanjing Unversity > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From yanxunwang2008 at gmail.com Thu Mar 5 12:24:04 2009 From: yanxunwang2008 at gmail.com (Xun-Wang Yan) Date: Thu, 5 Mar 2009 19:24:04 +0800 Subject: [Pw_forum] DOS calculation for non collinear magnetic ordering In-Reply-To: <49AEB1CB.2070906@sissa.it> References: <49AEB1CB.2070906@sissa.it> Message-ID: Dear Gabriele, Thank you very much for your reply. I want to investigate the electronic and magnetic properties of CuCrO2 , its ground state is non-collinear anti-ferromagnetic ordering. CuCrO2 is delafossite compound with R-3m symmetry, and its structure is stacked by Cu-O-Cr-O-Cu layers one by one. [PRL101 ,067204 Fig1] . In my calculation , unit cell is formed by 12 atoms ,i.e. 3 formula cells. so 3 Cr atoms is in a unit cell. In the whole energy scale the column pdosup(E) and pdosdw(E) are just the same. Maybe the process I calculated the DOS is wrong. 1 'scf' calculation -->2 dos calculation with projwfc.x. In example08 the process is 'scf'-->'nscf'-->dos calculation with 'dos.x'--->projected dos calculation with projwfc.x. I will recalculate DOS according to the steps in example08 In addition I will plot the non collinear magnetization with pp.x according to your suggetion. thanks you again Regards Xun-Wang Yan 2009/3/5 Gabriele Sclauzero > > Xun-Wang Yan wrote: > > Dear pwscf users, > > I have calculated the density of states for the noncolinear magnetic > > CuCrO2, the angle between spin directions of two Cr atoms is 120 > degrees. > > How do you know this? How many Cr atoms do you have per unit cell? > > > the magnetic moment is about 3 Bohr magnetons per Cr atom, I think > > the pdosup(E) is different from the pdosdw(E), > > I think you should be right, if you have a net magnetization along z it > would split bands > into up and down. > > > > but the 'pdosup(E)' and > > 'pdosdw(E)' are just the same in output file-- > > 120-AFM-12at-tricli.pdos_atm#6(Cr3)_wfc#2(d). > > Are these energies here below next to the Fermi energy? Maybe states very > low in energy > are not affected much by the magnetization (although if you really get 3 > bohr/atom I guess > they should). > > > > > # E(eV) ldosup(E) ldosdw(E) pdosup(E) pdosdw(E) pdosup(E) > > pdosdw(E) pdosup(E) > > -11.138 0.134E-07 0.134E-07 0.336E-08 0.336E-08 0.787E-16 > > 0.787E-16 0.739E-16 ... > > -11.128 0.105E-04 0.105E-04 0.263E-05 0.263E-05 0.618E-13 > > 0.618E-13 0.580E-13 ... > > -11.118 0.138E-03 0.138E-03 0.345E-04 0.345E-04 0.232E-11 > > 0.232E-11 0.105E-11 ... > > -11.108 0.247E-03 0.247E-03 0.618E-04 0.618E-04 0.585E-08 > > 0.585E-08 0.138E-08 > > -11.098 0.654E-03 0.654E-03 0.165E-03 0.165E-03 0.405E-06 > > 0.405E-06 0.149E-06 > > -11.088 0.116E-02 0.116E-02 0.285E-03 0.285E-03 0.648E-06 > > 0.648E-06 0.555E-06 > > -11.078 0.804E-03 0.804E-03 0.209E-03 0.209E-03 0.385E-06 > > 0.385E-06 0.254E-06 > > -11.068 0.523E-03 0.523E-03 0.128E-03 0.128E-03 0.653E-06 > > 0.653E-06 0.765E-06 > > -11.058 0.648E-03 0.648E-03 0.152E-03 0.152E-03 0.115E-05 > > 0.115E-05 0.126E-05 > > -11.048 0.174E-02 0.174E-02 0.450E-03 0.450E-03 0.676E-05 > > 0.676E-05 0.304E-05 > > -11.038 0.122E-02 0.122E-02 0.302E-03 0.302E-03 0.373E-05 > > 0.373E-05 0.173E-05 > > > > my questions : > > What do pdosup and pdosdw mean in DOS output file for > > noncolinear magnetic ordjering? the 'up' means Sz=1/2 ? but the spin > > direction is vertical to z axes in my unit cell. > > The projwfc.x program projects onto atomic orbitals which in this case > (non-colinear, non > spin-orbit) are eigenstates of S_z (and of L^2 and L_z, in the atom). > > > how to deal with the DOS of noncolinear magnetic structure in > > version espresso-4.0.1? > > Please try to plot the non collinear magnetization with pp.x (plot_num=13), > in order to > verify that there is a local magnetization on the atom. > > GS > > > > > Any comments are welcome , many thanks in advance. > > > > Bests > > > > Xun-wang Yan > > ======================================== > > Institute of Theoretical Physics, CAS > > Address: No.55, Zhong-Guan-Cun East Road > > Beijing, China > > Email: xwyan at itp.ac.cn > > > > yanxunwang2008 at gmail.com > > =================== > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090305/87feb39a/attachment-0001.htm From carlo.nervi at unito.it Thu Mar 5 13:03:23 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Thu, 5 Mar 2009 13:03:23 +0100 (CET) Subject: [Pw_forum] newbie update In-Reply-To: References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it><49AECFE5.3020905@chem.wisc.edu><49AEDACF.70806@phys.ufl.edu> <49AEF380.2020604@chem.wisc.edu> Message-ID: <50905.151.59.233.4.1236254603.squirrel@mail.unito.it> > but this does NOT work: > OMP_NUM_THREAD=1 > ./myprogram > > mysteries of bash shell... > I think this is due to the fact that bash temporarely set the variables for the single command... Anyway, I did few tests, as suggested by Axel, on 32 water molecule (example 21). I started to play with the version 4.1 and forgot that it is under testing. The following results refers to the version 4.1CVS ... sorry... I did two exacutables, v0 is without -ipo, v1 is compiled with -ipo I do have to try to set the sequential, but in my mkl lib it does not exists any lib-sequential... therefore I'm going to try to use some compiler switches Here are the results (read OMP as OMP_NUM_THREADS and MPI as number of cpu used with mpiexec): The test using OMP=8 and no MPI: v0: CP : 4m 1.98s CPU time, 3m 0.83s wall time v1: CP : 3m49.07s CPU time, 2m57.33s wall time Using OMP=1 and MPI=8 v0: CP : 0m36.43s CPU time, 1m31.59s wall time v1: CP : 0m35.39s CPU time, 1m30.67s wall time There is a clear advantage in using MPI, even though each %CPU (with MPI) is only between 40-50%. In fact the CPU time is almost 1/3 of the wall time. I suspect that Axel is right pointing to the disk I/O. I'm afraid that to increase the performance I should set the RAID 10... OMP=2, MPI=8 v0: CP : 0m46.98s CPU time, 1m36.08s wall time little worse than OMP=1 and MPI=8 OMP=4. MPI=4 v0: CP : 1m25.82s CPU time, 2m 4.96s wall time OMP=8, MPI=8 v0: CP : 1m17.36s CPU time, 2m11.83s wall time Here there is probably some interferences between parallel approaches. I did also a couple of run on 64 water molecules: OMP=1, MPI=8 v0: CP : 3m41.49s CPU time, 7m14.67s wall time OMP=8, no MPI v0: CP : 15m27.18s CPU time, 12m56.67s wall time In this case the ratio CPU time/wall time is slightly better, and in fact the %CPU usage were between 50-60% Furthermore, I did also the tests/check-pw.x.j on the version v1 only: ./check-pw.x.j Checking atom-lsda...passed Checking atom-pbe...discrepancy in number of scf iterations detected Reference: 7, You got: 5 discrepancy in pressure detected Reference: -14.44, You got: -14.48 Checking atom-sigmapbe...discrepancy in pressure detected Reference: -15.02, You got: -15.01 Checking atom...passed Checking berry...passed Checking berry, step 2 ...passed Checking electric0...discrepancy in number of scf iterations detected Reference: 8, You got: 9 Checking electric1...passed Checking electric2...passed Checking eval_infix...passed Checking eval_infix, step 2 ...discrepancy in HOMO detected Reference: -8.4542, You got: -8.4554 discrepancy in LUMO detected Reference: -0.4297, You got: -0.4300 Checking lattice-ibrav0-abc...passed Checking lattice-ibrav0-cell_parameters+a...passed Checking lattice-ibrav0-cell_parameters+celldm...passed Checking lattice-ibrav0-cell_parameters...passed Checking lattice-ibrav1-kauto...passed Checking lattice-ibrav1...passed Checking lattice-ibrav10-kauto...passed Checking lattice-ibrav10...passed Checking lattice-ibrav11-kauto...passed Checking lattice-ibrav11...passed Checking lattice-ibrav12-kauto...passed Checking lattice-ibrav12...passed Checking lattice-ibrav13-kauto...passed Checking lattice-ibrav13...passed Checking lattice-ibrav14-kauto...passed Checking lattice-ibrav14...passed Checking lattice-ibrav2-kauto...passed Checking lattice-ibrav2...passed Checking lattice-ibrav3-kauto...passed Checking lattice-ibrav3...passed Checking lattice-ibrav4-kauto...passed Checking lattice-ibrav4...passed Checking lattice-ibrav5-kauto...passed Checking lattice-ibrav5...passed Checking lattice-ibrav6-kauto...passed Checking lattice-ibrav6...passed Checking lattice-ibrav7-kauto...passed Checking lattice-ibrav7...passed Checking lattice-ibrav8-kauto...passed Checking lattice-ibrav8...passed Checking lattice-ibrav9-kauto...passed Checking lattice-ibrav9...passed Checking lda+U-noU...passed Checking lda+U-user_ns...passed Checking lda+U...passed Checking lsda-cg...passed Checking lsda-mixing_TF...passed Checking lsda-mixing_localTF...passed Checking lsda-mixing_ndim...passed Checking lsda-nelup+neldw...passed Checking lsda-tot_magnetization...passed Checking lsda...passed Checking lsda, step 2 ...passed Checking md-pot_extrap1...passed Checking md-pot_extrap2...passed Checking md-wfc_extrap1...passed Checking md-wfc_extrap2...passed Checking md...passed Checking metaGGA...passed Checking metadyn...passed Checking metal-fermi_dirac...passed Checking metal-gaussian...passed Checking metal-tetrahedra...passed Checking metal-tetrahedra, step 2 ...passed Checking metal...passed Checking metal, step 2 ...passed Checking neb1-H2+H...passed Checking neb2-H2+H-symm...passed Checking neb3-H2+H-asym...passed Checking noncolin-cg...passed Checking noncolin-constrain_angle...passed Checking noncolin-constrain_atomic...discrepancy in total energy detected Reference: -55.690284, You got: -55.690283 discrepancy in number of scf iterations detected Reference: 12, You got: 14 Checking noncolin-constrain_total...discrepancy in total energy detected Reference: -55.544783, You got: -55.544784 discrepancy in number of scf iterations detected Reference: 32, You got: 30 Checking noncolin...discrepancy in pressure detected Reference: 193.22, You got: 193.53 Checking noncolin, step 2 ...passed Checking paw-atom...passed Checking paw-atom_l=2...passed Checking paw-atom_lda...passed Checking paw-atom_spin...discrepancy in total energy detected Reference: -41.264991, You got: -41.265001 discrepancy in number of scf iterations detected Reference: 6, You got: 5 Checking paw-atom_spin_lda...discrepancy in total energy detected Reference: -40.244090, You got: -40.244091 Checking paw-bfgs...discrepancy in number of scf iterations detected Reference: 7, You got: 8 Checking paw-vcbfgs...passed Checking relax-damped...passed Checking relax-el...passed Checking relax...passed Checking relax2-bfgs_ndim3...passed Checking relax2...passed Checking scf-cg...passed Checking scf-disk_io...passed Checking scf-gamma...passed Checking scf-k0...passed Checking scf-kauto...passed Checking scf-mixing_TF...passed Checking scf-mixing_beta...passed Checking scf-mixing_localTF...passed Checking scf-mixing_ndim...passed Checking scf-ncpp...discrepancy in total energy detected Reference: -15.839765, You got: -15.839767 Checking scf-wf_collect...passed Checking scf...passed Checking scf, step 2 ...passed Checking spinorbit...passed Checking spinorbit, step 2 ...passed Checking uspp-cg...passed Checking uspp-mixing_TF...passed Checking uspp-mixing_localTF...passed Checking uspp-mixing_ndim...passed Checking uspp-singlegrid...passed Checking uspp...passed Checking uspp, step 2 ...passed Checking uspp1-coulomb...passed Checking uspp1...passed Checking uspp2...discrepancy in pressure detected Reference: -30.68, You got: -30.69 Checking vc-relax1...passed Checking vc-relax2...passed Total wall time (s) spent in this run: 5274.73 Reference : 720.04 There are few discrepancies, but they seems reasonables.. or not? It's only very long... Carlo P.S.: I hope I did not post a message too much long... ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From lanhaiping at gmail.com Thu Mar 5 13:29:34 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 5 Mar 2009 20:29:34 +0800 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: Message-ID: Why do you set different weight numbers for K-path ? Is there any standing point for this ? On Thu, Mar 5, 2009 at 6:25 PM, ?? wrote: > Dear All, > > I was trying to calculate the band structure of the BaNi2As2 which > had been calculated in the paper 0809.0499v2 on the arxiv.I could not > repeat the same struture.The BaNi2As2 occurs in a body centered > tetragonal structure (I4/mmm) with Ba,Ni and As at the positions > 2a(0,0,0),4d (0.5,0,0.25)and 4e(0,0,z).Here z equels 0.3476 by the > experimental result.The lattice parameters are a=4.112 A and c=11.54 > A. > Any comment about my input of this system? > my input of scf run: > > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='BaNiAs', > pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/disk2/xgwan/tmp/' > / > &system > ibrav=6, > celldm(1)=7.7702, > celldm(3)=2.806, > nat=10, > ntyp=3, > ecutwfc = 40.0, > ecutrho = 400.0, > occupations= 'tetrahedra' > / > &electrons > diagonalization = 'cg' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ni 58.6934 Ni.pbe-nd-rrkjus.UPF > As 74.9216 As.pbe-n-van.UPF > ATOMIC_POSITIONS crystal > Ba 0.0000 0.0000 0.0000 > Ba 0.5000 0.5000 0.5000 > Ni 0.0 0.5 0.25 > Ni 0.5 0.0 0.75 > Ni 0.5 0.0 0.25 > Ni 0.0 0.5 0.75 > As 0.0000 0.0000 0.3476 > As 0.0000 0.0000 0.6524 > As 0.5000 0.5000 0.8476 > As 0.5000 0.5000 0.1524 > K_POINTS {automatic} > 8 8 8 0 0 0 > > And my input of band calculation ,bands.x,plotband.x if helps: > input of band calculation > &control > calculation = 'bands' > prefix='BaNiAs', > pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/disk2/xgwan/tmp/' > wf_collect=.true. > / > &system > ibrav=6, > celldm(1)=7.7702, > celldm(3)=2.806, > nat=10, > ntyp=3, > ecutwfc = 40.0, > ecutrho = 400.0, > occupations= 'tetrahedra' > / > &electrons > diagonalization = 'cg' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ni 58.6934 Ni.pbe-nd-rrkjus.UPF > As 74.9216 As.pbe-n-van.UPF > ATOMIC_POSITIONS crystal > Ba 0.5000 0.5000 0.5000 > Ni 0.5000 0.0000 0.2500 > Ni 0.0000 0.5000 0.2500 > Ni 0.0000 0.5000 0.7500 > Ni 0.5000 0.0000 0.7500 > As 0.0000 0.0000 0.3476 > As 0.0000 0.0000 0.6524 > As 0.5000 0.5000 0.8476 > As 0.5000 0.5000 0.1524 > K_POINTS > 31 > -0.50 0.50 0.50 1 > -0.45 0.45 0.45 2 > -0.40 0.40 0.40 3 > -0.35 0.35 0.35 4 > -0.30 0.30 0.30 5 > -0.25 0.25 0.25 6 > -0.20 0.20 0.20 7 > -0.15 0.15 0.15 8 > -0.10 0.10 0.10 9 > -0.05 0.05 0.05 10 > 0.00 0.00 0.00 11 > 0.00 0.00 0.05 12 > 0.00 0.00 0.10 13 > 0.00 0.00 0.15 14 > 0.00 0.00 0.20 15 > 0.00 0.00 0.25 16 > 0.00 0.00 0.30 17 > 0.00 0.00 0.35 18 > 0.00 0.00 0.40 19 > 0.00 0.00 0.45 20 > 0.00 0.00 0.50 21 > 0.05 0.05 0.45 22 > 0.10 0.10 0.40 23 > 0.15 0.15 0.35 24 > 0.20 0.20 0.30 25 > 0.25 0.25 0.25 26 > 0.20 0.30 0.20 27 > 0.15 0.35 0.15 28 > 0.10 0.40 0.10 29 > 0.05 0.45 0.05 30 > 0.0 0.50 0.0 31 > > input of bands.x > &inputpp > prefix = 'BaNiAs' > outdir = '/disk2/xgwan/tmp/' > filband = 'bands.dat' > / > input of plotband.x > bands.dat > 2 17 > bands.xmgr > bands.ps > 10.5264 > 1.0 10.5264 > > With these inputs I could not get the same band structure as the paper > did.I am appreciate for any suggustion and comments. > Please tell me where I was wrong or which detail I ignored. > > Have a nice day. > > Deng Pan > Nanjing Unversity > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090305/b1b1481d/attachment.htm From paulatto at sissa.it Thu Mar 5 13:31:05 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 05 Mar 2009 13:31:05 +0100 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: Message-ID: On Thu, 05 Mar 2009 13:29:34 +0100, lan haiping wrote: > Why do you set different weight numbers for K-path ? Is there any > standing point for this ? Weights are irrelevant for "bands" calculations. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From lanhaiping at gmail.com Thu Mar 5 13:31:27 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 5 Mar 2009 20:31:27 +0800 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: Message-ID: OK, i just check the INPUT, there is no problem for calculating eigenvalues. On Thu, Mar 5, 2009 at 8:29 PM, lan haiping wrote: > Why do you set different weight numbers for K-path ? Is there any standing > point for this ? > > > > On Thu, Mar 5, 2009 at 6:25 PM, ?? wrote: > >> Dear All, >> >> I was trying to calculate the band structure of the BaNi2As2 which >> had been calculated in the paper 0809.0499v2 on the arxiv.I could not >> repeat the same struture.The BaNi2As2 occurs in a body centered >> tetragonal structure (I4/mmm) with Ba,Ni and As at the positions >> 2a(0,0,0),4d (0.5,0,0.25)and 4e(0,0,z).Here z equels 0.3476 by the >> experimental result.The lattice parameters are a=4.112 A and c=11.54 >> A. >> Any comment about my input of this system? >> my input of scf run: >> >> &control >> calculation = 'scf' >> restart_mode='from_scratch' >> prefix='BaNiAs', >> pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', >> outdir='/disk2/xgwan/tmp/' >> / >> &system >> ibrav=6, >> celldm(1)=7.7702, >> celldm(3)=2.806, >> nat=10, >> ntyp=3, >> ecutwfc = 40.0, >> ecutrho = 400.0, >> occupations= 'tetrahedra' >> / >> &electrons >> diagonalization = 'cg' >> mixing_beta = 0.7 >> conv_thr = 1.0d-6 >> / >> ATOMIC_SPECIES >> Ba 137.327 Ba.pbe-nsp-van.UPF >> Ni 58.6934 Ni.pbe-nd-rrkjus.UPF >> As 74.9216 As.pbe-n-van.UPF >> ATOMIC_POSITIONS crystal >> Ba 0.0000 0.0000 0.0000 >> Ba 0.5000 0.5000 0.5000 >> Ni 0.0 0.5 0.25 >> Ni 0.5 0.0 0.75 >> Ni 0.5 0.0 0.25 >> Ni 0.0 0.5 0.75 >> As 0.0000 0.0000 0.3476 >> As 0.0000 0.0000 0.6524 >> As 0.5000 0.5000 0.8476 >> As 0.5000 0.5000 0.1524 >> K_POINTS {automatic} >> 8 8 8 0 0 0 >> >> And my input of band calculation ,bands.x,plotband.x if helps: >> input of band calculation >> &control >> calculation = 'bands' >> prefix='BaNiAs', >> pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', >> outdir='/disk2/xgwan/tmp/' >> wf_collect=.true. >> / >> &system >> ibrav=6, >> celldm(1)=7.7702, >> celldm(3)=2.806, >> nat=10, >> ntyp=3, >> ecutwfc = 40.0, >> ecutrho = 400.0, >> occupations= 'tetrahedra' >> / >> &electrons >> diagonalization = 'cg' >> mixing_beta = 0.7 >> conv_thr = 1.0d-6 >> / >> ATOMIC_SPECIES >> Ba 137.327 Ba.pbe-nsp-van.UPF >> Ni 58.6934 Ni.pbe-nd-rrkjus.UPF >> As 74.9216 As.pbe-n-van.UPF >> ATOMIC_POSITIONS crystal >> Ba 0.5000 0.5000 0.5000 >> Ni 0.5000 0.0000 0.2500 >> Ni 0.0000 0.5000 0.2500 >> Ni 0.0000 0.5000 0.7500 >> Ni 0.5000 0.0000 0.7500 >> As 0.0000 0.0000 0.3476 >> As 0.0000 0.0000 0.6524 >> As 0.5000 0.5000 0.8476 >> As 0.5000 0.5000 0.1524 >> K_POINTS >> 31 >> -0.50 0.50 0.50 1 >> -0.45 0.45 0.45 2 >> -0.40 0.40 0.40 3 >> -0.35 0.35 0.35 4 >> -0.30 0.30 0.30 5 >> -0.25 0.25 0.25 6 >> -0.20 0.20 0.20 7 >> -0.15 0.15 0.15 8 >> -0.10 0.10 0.10 9 >> -0.05 0.05 0.05 10 >> 0.00 0.00 0.00 11 >> 0.00 0.00 0.05 12 >> 0.00 0.00 0.10 13 >> 0.00 0.00 0.15 14 >> 0.00 0.00 0.20 15 >> 0.00 0.00 0.25 16 >> 0.00 0.00 0.30 17 >> 0.00 0.00 0.35 18 >> 0.00 0.00 0.40 19 >> 0.00 0.00 0.45 20 >> 0.00 0.00 0.50 21 >> 0.05 0.05 0.45 22 >> 0.10 0.10 0.40 23 >> 0.15 0.15 0.35 24 >> 0.20 0.20 0.30 25 >> 0.25 0.25 0.25 26 >> 0.20 0.30 0.20 27 >> 0.15 0.35 0.15 28 >> 0.10 0.40 0.10 29 >> 0.05 0.45 0.05 30 >> 0.0 0.50 0.0 31 >> >> input of bands.x >> &inputpp >> prefix = 'BaNiAs' >> outdir = '/disk2/xgwan/tmp/' >> filband = 'bands.dat' >> / >> input of plotband.x >> bands.dat >> 2 17 >> bands.xmgr >> bands.ps >> 10.5264 >> 1.0 10.5264 >> >> With these inputs I could not get the same band structure as the paper >> did.I am appreciate for any suggustion and comments. >> Please tell me where I was wrong or which detail I ignored. >> >> Have a nice day. >> >> Deng Pan >> Nanjing Unversity >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090305/8c6b9991/attachment-0001.htm From panda.deng.pan at gmail.com Thu Mar 5 13:42:46 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Thu, 5 Mar 2009 20:42:46 +0800 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: <49AFABE7.4030603@sissa.it> References: <49AFABE7.4030603@sissa.it> Message-ID: Dear Gabriele Sclauzero, I have tried the K_POINTS with the option fo 'CRYSTAL'.It is not the problem.With the "CRYSTAL" the band structure seems to far more wrong. From ylli at theory.issp.ac.cn Thu Mar 5 13:25:22 2009 From: ylli at theory.issp.ac.cn (=?utf-8?B?TGkgWUw=?=) Date: Thu, 05 Mar 2009 20:25:22 +0800 Subject: [Pw_forum] =?utf-8?q?Character_energy_band=2E?= Message-ID: <20090305122522.19621.qmail@ms.hfcas.ac.cn> Dear all users, How to plot character energy band using PWSCF code? That is to say, I want to know how to classify the energy bands across Fermi level. For example, when both s-electron of A atom and p-electrons of B atom have contributions to Fermi level, how to distinguish which band is from s-electron of A atom and which band is from the p-electron of B atom. Many thanks. Best regards, Yanling Li Institute of solid states physics, CAS, China. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090305/971c04b7/attachment.htm From sclauzer at sissa.it Thu Mar 5 14:20:47 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Mar 2009 14:20:47 +0100 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: <49AFABE7.4030603@sissa.it> Message-ID: <49AFD1AF.20700@sissa.it> ?? wrote: > Dear Gabriele Sclauzero, > I have tried the K_POINTS with the option fo 'CRYSTAL'.It is not the > problem.With the "CRYSTAL" the band structure seems to far more wrong. Before going on, if you want to use safely espresso you should understand those kind of differences (like those between alat or crystal options). You should judge which of the two options is needed in your case, mine was only a suggestion of a common mistake in BS calculations with pw.x. Your input files do not have anything strange at first glance, but I don't know if they will compute the system you actually have in mind. You have to be sure that you're using the same atomic configuration, same k-point path, but also the same functional and to be converged with respect to the relevant parameters (I suppose they have done it in the paper, if they want to publish it). GS > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From prasenjit.jnc at gmail.com Thu Mar 5 14:16:30 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Thu, 5 Mar 2009 14:16:30 +0100 Subject: [Pw_forum] Character energy band. In-Reply-To: <20090305122522.19621.qmail@ms.hfcas.ac.cn> References: <20090305122522.19621.qmail@ms.hfcas.ac.cn> Message-ID: <627e0ffa0903050516h4d1314b8n7173c1cbab17bf1a@mail.gmail.com> Dear Yanling, You can use projwfc.x post-processing tool in the PP directory which projects the DOS on the wavefunction of each atom. Then you can compare the total DOS with the projected dos and you can tell which band is from which wave function of which atom. Regarding the input file for it, you can find the details in Doc/INPUT_PROJWFC.txt With regards, Prasenjit. 2009/3/5 Li YL > Dear all users, > > How to plot character energy band using PWSCF code? That is to > say, I want to know how to classify the energy bands across Fermi level. For example, > when both *s*-electron of A atom and *p*-electrons of B atom have > contributions to Fermi level, how to distinguish which band is from *s* > -electron of A atom and which band is from the p-electron of B atom. > > Many thanks. > > Best regards, > > Yanling Li > > Institute of solid states physics, CAS, China. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3891833716 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090305/f140cff0/attachment.htm From sclauzer at sissa.it Thu Mar 5 14:30:38 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Mar 2009 14:30:38 +0100 Subject: [Pw_forum] Character energy band. In-Reply-To: <20090305122522.19621.qmail@ms.hfcas.ac.cn> References: <20090305122522.19621.qmail@ms.hfcas.ac.cn> Message-ID: <49AFD3FE.3030700@sissa.it> Li YL wrote: > Dear all users, > > How to plot character energy band using PWSCF code? That is to > say, I want to know how to classify the energy bands across Fermi level. For example, > when both /s/-electron of A atom and /p/-electrons of B atom have > contributions to Fermi > level, how to distinguish which band is from /s/-electron of A atom and which band is from the p-electron of B atom. The projwfc.x postprocessing program is all what you need. If things haven't benn changed much since last time I used it for such kind of study, you have to use an input file like this: &inputpp prefix= "CoatPtwire", outdir= "/local_scratch/sclauzer/tmp/", lsym= .FALSE., filproj= "COatPtwire.proj", / using your values for prefix and filenames. In the filproj file you should find, for each atomic state available in your system, the projection of the atomic states onto all KS states produced by the calculation, indexed by k-point and band (so that you can relate the KS eigenstates to the corresponding eigenvalue from the scf calculation output). HTH GS > > Many thanks. > > Best regards, > > Yanling Li > > Institute of solid states physics, CAS, China. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From panda.deng.pan at gmail.com Thu Mar 5 14:36:29 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Thu, 5 Mar 2009 21:36:29 +0800 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: <49AFD1AF.20700@sissa.it> References: <49AFABE7.4030603@sissa.it> <49AFD1AF.20700@sissa.it> Message-ID: > You have to be sure that you're using the same atomic configuration, same k-point path, thanks for your reply first.I got a question here.The same k-point path means that the k-points in the band calculation are the points which were generated in the scf run. From sclauzer at sissa.it Thu Mar 5 14:44:38 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Mar 2009 14:44:38 +0100 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: <49AFABE7.4030603@sissa.it> <49AFD1AF.20700@sissa.it> Message-ID: <49AFD746.8010200@sissa.it> ?? wrote: >> You have to be sure that you're using the same atomic configuration, same k-point path, > thanks for your reply first.I got a question here.The same k-point > path means that the k-points in the band calculation are the points > which were generated in the scf run. No, I meant the same k-point path used for bands in the paper. If you specified k-points coordinates for bands using the wrong option (e.g. alat instead of crystal), you may not get the k-points that you really want (not always, in some lattices the two options give the same k-points). Use the verbosity='high' in the pw run and you will see the difference (if any). GS > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Thu Mar 5 14:49:21 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Mar 2009 14:49:21 +0100 Subject: [Pw_forum] Character energy band. In-Reply-To: <627e0ffa0903050516h4d1314b8n7173c1cbab17bf1a@mail.gmail.com> References: <20090305122522.19621.qmail@ms.hfcas.ac.cn> <627e0ffa0903050516h4d1314b8n7173c1cbab17bf1a@mail.gmail.com> Message-ID: <49AFD861.70203@sissa.it> Prasenjit Ghosh wrote: > Dear Yanling, > > You can use projwfc.x post-processing tool in the PP directory which > projects the DOS on the wavefunction of each atom. Then you can compare > the total DOS with the projected dos and you can tell which band is from > which wave function of which atom. Regarding the input file for it, you > can find the details in Doc/INPUT_PROJWFC.txt The PDOS can be obtained with lsym=.TRUE. (which is the default), but if you want to know the projection on individual KS states (the PDOS is build up on these, by summing up on k-point and bands with correct weights), you need lsym=.FALSE. cheers, GS > > With regards, > Prasenjit. > > 2009/3/5 Li YL > > > Dear all users, > > How to plot character energy band using PWSCF code? That is to > say, I want to know how to classify the energy bands across Fermi level. For example, > when both /s/-electron of A atom and /p/-electrons of B atom have > contributions to Fermi > level, how to distinguish which band is from /s/-electron of A atom and which band is from the p-electron of B atom. > > Many thanks. > > Best regards, > > Yanling Li > > Institute of solid states physics, CAS, China. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > +39 3891833716 (M) > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From eariel99 at gmail.com Thu Mar 5 15:45:51 2009 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 5 Mar 2009 11:45:51 -0300 Subject: [Pw_forum] band and dos input files in xcrysden Message-ID: Well, I also like the way the tasks are distributed, it is conceptually very clear. I know a different code that saves a DOS file after a band calculation and the newbies come to me with strange peaks in DOS that are caused by a flat band along a line. Calling dos from pw.x or pw from dos.x masks that conceptual clarity. However, we have to be practical and run the frequent calculations as easily as possible. I would prepend a nscf calculation with "standard options" , and give warning in the otput file that non-standard options can be done doing the nscf calculation separately. Also, I would alway make pw.x to write the self-consistent DOS in a file after an scf calculation, no matter how coarse is the k-points grid. I find this useful for checking purposes (e.g. to know if an impurity have levels in the gaps). Also, for simple metals the k-points grid needed to have converged energies and forces also is enough to have a good DOS. Then let the user the choice to do post processing if want a DOS with an occupation scheme different than the SCF. I would put this file in the .save directory and name it prefix.scfdos or something like that. Boris, thank for your script. I will soon test it. Maybe it can be embedded in PWGUI. Best regards Eduardo ---------- Mensaje reenviado ---------- > From: Paolo Giannozzi > To: PWSCF Forum > Date: Thu, 26 Feb 2009 10:34:30 +0100 > Subject: Re: [Pw_forum] band and dos input files in xcrysden > > On Feb 21, 2009, at 17:05 , Eduardo Ariel Menendez Proupin wrote: > > Let me remind how is the process to obtain the DOS. It has three >> calculations >> and 3 input files >> >> pw.x < si.scf.in > si.scf.out # self consistent >> pw.x si.dos.out # non selfconsistent dense k-points mesh >> and a few options >> dos.x si.dos2.out # postprocessing >> > > Hi Eduardo, the issue you raise is a serious one and requires some though. > Right now several standard calculations in q-e are clumsy because they > require separate steps. While I think that it is a good idea to keep > separate > steps separate, I also think that at least the most common calculations > might > be streamlined. I am not convinced that the PWGui is the right tool for > this, > though, at least not in the present form (a tool to produce input data). > The ideal solution would be the usage of a high-level scripting language > like > python to "glue" the various pieces together, but this is highly nontrivial > (at least for me and for 99% of q-e users). > A simpler option could be to collapse some calculations into the same > executable: > for instance > - add a call to dos after a nscf calculation in pw.x, > add a call to bands after a bands calculation in pw.x > or > - prepend a nscf calculation to dos.x, > prepend a band calculation to bands.x > Suggestions are welcome > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090305/e9b64e3d/attachment-0001.htm From panda.deng.pan at gmail.com Thu Mar 5 17:34:24 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Fri, 6 Mar 2009 00:34:24 +0800 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: <49AFD746.8010200@sissa.it> References: <49AFABE7.4030603@sissa.it> <49AFD1AF.20700@sissa.it> <49AFD746.8010200@sissa.it> Message-ID: The structure in paper have the sysmmetry of the space group I4/mmm(139) with Ba 2a(0 0 0) Ni 4d (0.5 0 0.25) As (0 0 0.3476). and my input are: &control calculation = 'scf' restart_mode='from_scratch' prefix='BaNiAs', pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/disk2/xgwan/tmp/' / &system ibrav=6, celldm(1)=7.7702, celldm(3)=2.806, nat=10, ntyp=3, ecutwfc = 40.0, ecutrho = 400.0, occupations= 'tetrahedra' / &electrons diagonalization = 'cg' mixing_beta = 0.7 conv_thr = 1.0d-6 / ATOMIC_SPECIES Ba 137.327 Ba.pbe-nsp-van.UPF Ni 58.6934 Ni.pbe-nd-rrkjus.UPF As 74.9216 As.pbe-n-van.UPF ATOMIC_POSITIONS crystal Ba 0.0000 0.0000 0.0000 Ba 0.5000 0.5000 0.5000 Ni 0.0 0.5 0.25 Ni 0.5 0.0 0.75 Ni 0.5 0.0 0.25 Ni 0.0 0.5 0.75 As 0.0000 0.0000 0.3476 As 0.0000 0.0000 0.6524 As 0.5000 0.5000 0.8476 As 0.5000 0.5000 0.1524 K_POINTS {automatic} 8 8 8 0 0 0 Could you tell the structure I inputed are the same of that is in the paper.I compare with XCryden to Wien2k input of this structure,it seems the same. From sclauzer at sissa.it Thu Mar 5 18:09:42 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 05 Mar 2009 18:09:42 +0100 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: <49AFABE7.4030603@sissa.it> <49AFD1AF.20700@sissa.it> <49AFD746.8010200@sissa.it> Message-ID: <49B00756.4080303@sissa.it> I can't tell you if your structure is the same as that of the paper, I don't know these kind of compounds. You have to ensure that your structure is correct, I can only say that it seems reasonable. Please try to point out clearly where your problem really is, otherwise noone will be able to help you. GS ?? wrote: > The structure in paper have the sysmmetry of the space group > I4/mmm(139) with Ba 2a(0 0 0) Ni 4d (0.5 0 0.25) As (0 0 0.3476). > and my input are: > > > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='BaNiAs', > pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/disk2/xgwan/tmp/' > / > &system > ibrav=6, > celldm(1)=7.7702, > celldm(3)=2.806, > nat=10, > ntyp=3, > ecutwfc = 40.0, > ecutrho = 400.0, > occupations= 'tetrahedra' > / > &electrons > diagonalization = 'cg' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ni 58.6934 Ni.pbe-nd-rrkjus.UPF > As 74.9216 As.pbe-n-van.UPF > ATOMIC_POSITIONS crystal > Ba 0.0000 0.0000 0.0000 > Ba 0.5000 0.5000 0.5000 > Ni 0.0 0.5 0.25 > Ni 0.5 0.0 0.75 > Ni 0.5 0.0 0.25 > Ni 0.0 0.5 0.75 > As 0.0000 0.0000 0.3476 > As 0.0000 0.0000 0.6524 > As 0.5000 0.5000 0.8476 > As 0.5000 0.5000 0.1524 > K_POINTS {automatic} > 8 8 8 0 0 0 > > > Could you tell the structure I inputed are the same of that is in the > paper.I compare with XCryden to Wien2k input of this structure,it > seems the same. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From lanhaiping at gmail.com Thu Mar 5 18:18:51 2009 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 6 Mar 2009 01:18:51 +0800 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: <49AFABE7.4030603@sissa.it> <49AFD1AF.20700@sissa.it> <49AFD746.8010200@sissa.it> Message-ID: Hi, To my knowledge, most of bandstructure works just gave symbols of high symmetry points along k-path. If so, i think the problem is mostly due to inconsistent settings for high symmetry points between you assigned to k-path and that paper's. You can check your K-path with xcrysden->Tools . regards. On Fri, Mar 6, 2009 at 12:34 AM, ?? wrote: > The structure in paper have the sysmmetry of the space group > I4/mmm(139) with Ba 2a(0 0 0) Ni 4d (0.5 0 0.25) As (0 0 0.3476). > and my input are: > > > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='BaNiAs', > pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/disk2/xgwan/tmp/' > / > &system > ibrav=6, > celldm(1)=7.7702, > celldm(3)=2.806, > nat=10, > ntyp=3, > ecutwfc = 40.0, > ecutrho = 400.0, > occupations= 'tetrahedra' > / > &electrons > diagonalization = 'cg' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ni 58.6934 Ni.pbe-nd-rrkjus.UPF > As 74.9216 As.pbe-n-van.UPF > ATOMIC_POSITIONS crystal > Ba 0.0000 0.0000 0.0000 > Ba 0.5000 0.5000 0.5000 > Ni 0.0 0.5 0.25 > Ni 0.5 0.0 0.75 > Ni 0.5 0.0 0.25 > Ni 0.0 0.5 0.75 > As 0.0000 0.0000 0.3476 > As 0.0000 0.0000 0.6524 > As 0.5000 0.5000 0.8476 > As 0.5000 0.5000 0.1524 > K_POINTS {automatic} > 8 8 8 0 0 0 > > > Could you tell the structure I inputed are the same of that is in the > paper.I compare with XCryden to Wien2k input of this structure,it > seems the same. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090306/7b5cd032/attachment.htm From giannozz at democritos.it Thu Mar 5 18:20:08 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 05 Mar 2009 18:20:08 +0100 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: Message-ID: <49B009C8.9070008@democritos.it> ?? wrote: > Any comment about my input of this system? > occupations= 'tetrahedra' tetrahedra should be used if you want to calculate the DOS. Forces calculated with tetrahedra are not very accurate (i.e. they are not exactly equal to the derivative of the energy) > diagonalization = 'cg' Davidson is usually faster > With these inputs I could not get the same band structure > as the paper did then look more carefully at your data and at your output. Note that k-points are by default given in units of 2pi/a (I mean: for all cartesian components, including the c axis) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From swblelia at ehu.es Thu Mar 5 18:29:17 2009 From: swblelia at ehu.es (Aritz Leonardo Liceranzu) Date: Thu, 5 Mar 2009 18:29:17 +0100 Subject: [Pw_forum] Re[Psi] and Im[Psi] Message-ID: <20090305182917.ihsyw4tlcsc0k088@www.ehu.es> Dear Baris Malcioglu, THANK YOU for such a detailed explanation. I am going through it and I am sure that it is going to be very helpful. Cheers, Aritz PD: Paolo, the integrations that I need to perform are in the real space. ----- Forwarded message from baris.malcioglu at gmail.com ----- Date: Thu, 5 Mar 2009 10:16:28 +0100 From: "O. Baris Malcioglu" Reply-To: PWSCF Forum Subject: Re: [Pw_forum] Re[Psi] and Im[Psi] To: PWSCF Forum Dear Aritz, First of all, you must notice that norm of the wavefunctions stored will vary depending on what type of pseudopotential you use (Norm conserving Ultrasoft etc.) The most straightforward in terms of mathematical handling is the norm conserving one. I prefer writing new subroutines rather than modifying old ones, since I have witnessed doing that makes things get really messy after a while. Anyhow, here are some exempts from my personal notes, I hope you find them useful. They are a bit unmaintained, thus as a disclaimer, please report any error in them, so that I end up with better documentation. 1) How to calculate the real space grid points: In this exempt, the aim is to find a set of grid points within a certain distance from an atom. The first step is to start an index rolling on available grid points DO ir = 1, nrxxs nrxxs is explained as ?the total dimension of the smooth grid? in gsmooth (PW/pwcom.f90) . It is the total number of grid points in the smooth grid. ! ! ... three dimensional indexes ! index = index0 + ir - 1 k = index / (nrx1s*nrx2s) index = index - (nrx1s*nrx2s)*k j = index / nrx1s index = index - nrx1s*j i = index ! Index0 is an offset for parallelism issues. It separates the grid into processors and each processor starts processing from this offset. nrx1s and nrx2s and nrx3s are again from gsmooth, and defined as ?maximum dimension of the smooth grid? in the corresponding direction, they are used as the reduced forms of nrXs (X=1,2,3) dividing the grid points among the nodes. In the serial case nrxxs=nrx1s*nrx2s*nrx3s but this might or might not always be true for different parallel cases. index (a temporary integer), nrx1s and nrx2s are all integers, so the divisions above are integer divisions (otherwise the algorithm should return 0 always, look at how the k and the index are calculated consecutively). As a convention, the segmentation of grid points should always start from the 3rd dimension (z). The goal is to achieve an arrangement such that the first 1..nrx1s elements correspond to ith element where j=0 k=0; the second 1..nrx1s element correspond to ith element where j=1 k=0 and etc.. This would make an index of higher rank increase only when the cycles of all the lower ranks are complete. So the k index (third dimension) is the total number of i and j cycles completed (that would be nrx1s*nrx2s number of elements for each cycle). When k times the number of elements per cycle is removed from the index count, the excess only refers to i and j components. Using the same trick to subtract the cycles of i (nrx1s elements each) the j index value is obtained, and removing the number of elements per cycle for each j increment from the index, the index for i is obtained. DO ipol = 1, 3 posi(ipol) = DBLE( i )*inv_nr1s*at(ipol,1) + & DBLE( j )*inv_nr2s*at(ipol,2) + & DBLE( k )*inv_nr3s*at(ipol,3) END DO this might be on a non-orthogonal basis and we should be extra careful in the next step. Here ipol is an index running over the basis vectors (these will be called x y and z directions for further reference) at(ipol,1..3) are the simulation cell base vectors (in real space) divided by alat (lattice parameter), in terms of Cartesian components (second index). nr1s, nr2s and nr3s are the actual number of grid points (where nrxXs are reduced in a node specific way to conserve memory) thus at/nr is the vector increment for the particular direction. Multiplying this with the increment counter in that direction, a first iteration for the position vector is obtained. ! posi(:) = posi(:) - tau_ia(:) ! This line offsets the position such that current atom is at the center. tau_ia is just a rename for the tau from Modules/ions_base.f90 which contains the positions of the atomic cores. ! ... minimum image convenction ! CALL cryst_to_cart( 1, posi, bg, -1 ) ! posi(:) = posi(:) - ANINT( posi(:) ) ! CALL cryst_to_cart( 1, posi, at, 1 ) ! cryst_to_cart is a subroutine responsible for conversions of vectors from cartesian coordinates to crystal coordinates (+1) and viceversa (-1). This part ensures that any distance more than 0.5 crystal unit far is treated according to the closest atomic center, not the one it is further away. It is actually the minimum Brillouin cell for the atom at hand. distsq = posi(1)**2 + posi(2)**2 + posi(3)**2 END DO END DO the distance from the center... 2) How to FFT a given band into real space (most simplistic version, no gamma point tricks, no non-collinear, etc.) psic(nls(igk(:))) = evc(:,ibnd) psic is the buffer where this kind of operations are performed. Usually allocated in the initialization steps, so at most times can be used directly. The igk(:) is the g,k correspondence array, and updated for each k point under consideration. nls(igk(:)) returns the corresponding index value in real space for the corresponding reciprocal space point index value. evc are the wavefunctions. First index is the grid point, second is the band. ! CALL cft3s( psic, nr1s, nr2s, nr3s, nrx1s, nrx2s, nrx3s, 2 ) internal pwscf wrapper for the fft that does the actual transformation. After this, psic will contain the real space wavefunctions with an index formalism for real space grids. Best, Baris Malcioglu SISSA On Wed, Mar 4, 2009 at 5:52 PM, Aritz Leonardo Liceranzu wrote: > Hi pwscf users, > > My question is regarding the output of the KS wave-functions. > > For a tddft problem that I am involved into, I need to numerically > integrate the equilibrium KS wavefunctions. For this purpose I would > like to obtain for each (k,i) Bloch state a chart containing: > > Rx,Ry,Rz, Re[psi], Im[psi] > > I surfed through old emails (like the one below) and I found that this > feature is not implemented in PP codes (am I right?). > > Ab-init produces this kind of output but I am trying to avoid using it > (I am loyal to espresso :) ). On the other hand, it shouldn't be very > difficult to write a small program that does it, any hints so that I > do not have to use ab-init???? > > Thank you in advance > Aritz > > > > > Lorenzo Paulatto paulatto at sissa.it > Sat Feb 23 12:48:15 CET 2008 > > On Sab, 23 Febbraio 2008 5:42 am, nafise rezaei wrote: >>> However, I want to extract and to plot parts of real and imaginary >>> wave function. >>> Do you know any program to generate wave function? If there is no >>> program, I can modify what program to write it? > > The postprocessing utility pp.x can extract the square modulus of a > wavefunction (you choose it by specifying kpoint and band index), plotting > real and imaginary parts is not implemented, but you may be able to do it > youself. > > On the other hand, if nobody have felt the need to implement it in the > last not so few years there could be a reason. If you tell us what you > want to do, instead of how you want to do it, you will probably get some > more useful advice. > > Regards, LP > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ----- End forwarded message ----- From giannozz at democritos.it Thu Mar 5 18:51:30 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 05 Mar 2009 18:51:30 +0100 Subject: [Pw_forum] newbie update In-Reply-To: <50905.151.59.233.4.1236254603.squirrel@mail.unito.it> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it><49AECFE5.3020905@chem.wisc.edu><49AEDACF.70806@phys.ufl.edu> <49AEF380.2020604@chem.wisc.edu> <50905.151.59.233.4.1236254603.squirrel@mail.unito.it> Message-ID: <49B01122.8040105@democritos.it> Carlo Nervi wrote: > Total wall time (s) spent in this run: 5274.73 > Reference : 720.04 > > There are few discrepancies, but they seems reasonables.. > or not? they do. What doesn't seem reasonable to me is 2 1/2 h for a series of tests that take 12 min not on the "ExaFlop Machine", but on a rather standard 3GHz IntelCore2 E6850 (the one I have in front). There is something really strange in your setup. > P.S.: I hope I did not post a message too much long... messages longer tha 40Kb are blocked by the mailing list software, so no, you didn't :-) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From ucanxli at ucl.ac.uk Thu Mar 5 19:28:52 2009 From: ucanxli at ucl.ac.uk (xinzheng li) Date: Thu, 05 Mar 2009 18:28:52 +0000 Subject: [Pw_forum] PBE0 in PWSCF Message-ID: <49B019E4.7050707@ucl.ac.uk> Dear friends, My name is Xinzheng Li. I am a postdoc in University College London. I am using PWSCF to perform some PBE0 calculations for water cluster on metal surface recently. In order to make sure that the PBE0 number I got from PWSCF is correct. I performed a test for the binding energy of a water-dimer in gas phase (total energy of 2 water moleculars minus the total energy of a water dimer) taking the all-electron PBE0 results from Gaussian03 as reference. The converged binding energy from Gaussian03 is around 207 meV. While after PBE0 calculation of PWSCF is performed, I have these lines in the output file: ! total energy = -68.48225787 Ry Harris-Foulkes estimate = -72.38797788 Ry estimated scf accuracy < 0.00000008 Ry The total energy is the sum of the following terms: one-electron contribution = -144.72933450 Ry hartree contribution = 71.54274579 Ry xc contribution = -12.87564636 Ry ewald contribution = 13.67425725 Ry Fock energy 1 = -7.81160613 Ry Fock energy 2 = -7.81177236 Ry Half Fock energy 2 = -3.90588618 Ry I have two questions about this output: 1. Shall I take the '! total energy' as the final total energy, or the 'Harris-Foulkes estimate' as the final total energy? For the comment: 'The total energy is the sum of the following terms', if I sum the numbers below, I don't get either 'Harris-Foulkes estimeate', or '! total energy'. Only if I sum the one-electron contribution, hartree contibution, xc contribution and the ewald contribution, can I get the 'Harris-Foulkes estimate'. Does it mean that I should take 'Harris-Foulkes estimate' as the final energy? If so, what is the meaning of the '! total energy'? 3. If I take Harris-Foulke estimate' as the total energy, the binding energy I get is 184 meV. If I take '! total energy' as total energy, the binding energy is 158 meV. Both of these two number are > 20 meV from the Gaussian all-electron benchmark. What is the expectation for the accuracy of such a value in the PWSCF code compared with all-electron Gaussian (when pseudopotentials, and supercell-size convergence are well-tested)? Thanks a lot for your patiency in advance! Sincere Xinzheng ----------------------------------------------------------------- Dr. Xinzheng Li London Centre for Nanotechnology, University College London 17-19 Gordon Street, London WC1H, 0AH ucanxli at ucl.ac.uk ------------------------------------------------------------------ From lex at phys.ufl.edu Thu Mar 5 20:05:52 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Thu, 05 Mar 2009 14:05:52 -0500 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: <49AFABE7.4030603@sissa.it> <49AFD1AF.20700@sissa.it> <49AFD746.8010200@sissa.it> Message-ID: <49B02290.9000009@phys.ufl.edu> I have a passing familiarity with your system and this problem. Comparing band structure is hard, for a number of reasons. One is an inconsistency in the notation -- for simple tetragonal units cells, for example, there are at least two different notations for the high-symmetry points. Secondly, the primitive units cell for system you're looking at is not simple tetragonal, it's body centered tetragonal. This has a whole different set of symmetry points. Now, you can use k-points from the conventional (tetragonal) unit cell, but the number of bands you get will vary, depending on whether you're using the primitive zone or the conventional one. Good luck, Lex Kemper University of Florida ?? wrote: > The structure in paper have the sysmmetry of the space group > I4/mmm(139) with Ba 2a(0 0 0) Ni 4d (0.5 0 0.25) As (0 0 0.3476). > and my input are: > > > &control > calculation = 'scf' > restart_mode='from_scratch' > prefix='BaNiAs', > pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', > outdir='/disk2/xgwan/tmp/' > / > &system > ibrav=6, > celldm(1)=7.7702, > celldm(3)=2.806, > nat=10, > ntyp=3, > ecutwfc = 40.0, > ecutrho = 400.0, > occupations= 'tetrahedra' > / > &electrons > diagonalization = 'cg' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > ATOMIC_SPECIES > Ba 137.327 Ba.pbe-nsp-van.UPF > Ni 58.6934 Ni.pbe-nd-rrkjus.UPF > As 74.9216 As.pbe-n-van.UPF > ATOMIC_POSITIONS crystal > Ba 0.0000 0.0000 0.0000 > Ba 0.5000 0.5000 0.5000 > Ni 0.0 0.5 0.25 > Ni 0.5 0.0 0.75 > Ni 0.5 0.0 0.25 > Ni 0.0 0.5 0.75 > As 0.0000 0.0000 0.3476 > As 0.0000 0.0000 0.6524 > As 0.5000 0.5000 0.8476 > As 0.5000 0.5000 0.1524 > K_POINTS {automatic} > 8 8 8 0 0 0 > > > Could you tell the structure I inputed are the same of that is in the > paper.I compare with XCryden to Wien2k input of this structure,it > seems the same. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From carlo.nervi at unito.it Thu Mar 5 20:19:56 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Thu, 5 Mar 2009 20:19:56 +0100 (CET) Subject: [Pw_forum] newbie update In-Reply-To: <49B01122.8040105@democritos.it> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it><49AECFE5.3020905@chem.wisc.edu><49AEDACF.70806@phys.ufl.edu> <49AEF380.2020604@chem.wisc.edu><50905.151.59.233.4.1236254603.squirrel@mail.unito.it> <49B01122.8040105@democritos.it> Message-ID: <55383.151.59.233.4.1236280796.squirrel@mail.unito.it> > Carlo Nervi wrote: > >> Total wall time (s) spent in this run: 5274.73 >> Reference : 720.04 >> >> There are few discrepancies, but they seems >> reasonables.. >> or not? > > they do. What doesn't seem reasonable to me is 2 1/2 h for > a series of tests that take 12 min not on the "ExaFlop > Machine", but on a rather standard 3GHz IntelCore2 E6850 > (the one I have in front). There is something really > strange in your setup. This is exactly what I was wondering. During the tests 4 CPUs were running at 10%, while the other four were running at 1-5%. It must be something wrong in my settings, but I cannot figure it out. Anyone could please provide a sort of "semi-standard" make.sys for ifort and mkl with a working mpi? Cheers, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From asafis at yahoo.com.br Thu Mar 5 21:51:48 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Thu, 5 Mar 2009 12:51:48 -0800 (PST) Subject: [Pw_forum] Xcrsyden Message-ID: <341053.5690.qm@web52307.mail.re2.yahoo.com> Hello All. I got to the spin polarization using pp.x, creating a file with extension xsf. However when trying to open in Xcrysden, the system is deformed. How to solve this? ??????????????????????????????????? Sincerely, Alvaro Universidade Federal Fluminense - Niteroi - Rio de Janeiro - Brasil Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090305/3c844521/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu Mar 5 22:12:02 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 5 Mar 2009 16:12:02 -0500 (EST) Subject: [Pw_forum] newbie update In-Reply-To: <55383.151.59.233.4.1236280796.squirrel@mail.unito.it> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it><49AECFE5.3020905@chem.wisc.edu><49AEDACF.70806@phys.ufl.edu> <49AEF380.2020604@chem.wisc.edu><50905.151.59.233.4.1236254603.squirrel@mail.unito.it> <49B01122.8040105@democritos.it> <55383.151.59.233.4.1236280796.squirrel@mail.unito.it> Message-ID: On Thu, 5 Mar 2009, Carlo Nervi wrote: CN> > Carlo Nervi wrote: CN> > CN> >> Total wall time (s) spent in this run: 5274.73 CN> >> Reference : 720.04 CN> >> CN> >> There are few discrepancies, but they seems CN> >> reasonables.. CN> >> or not? CN> > CN> > they do. What doesn't seem reasonable to me is 2 1/2 h for CN> > a series of tests that take 12 min not on the "ExaFlop CN> > Machine", but on a rather standard 3GHz IntelCore2 E6850 CN> > (the one I have in front). There is something really CN> > strange in your setup. CN> CN> This is exactly what I was wondering. During the tests 4 CN> CPUs were running at 10%, while the other four were CN> running at 1-5%. CN> It must be something wrong in my settings, but I cannot CN> figure it out. how much memory does your machine have? what else is running on that machine? CN> Anyone could please provide a sort of "semi-standard" CN> make.sys for ifort and mkl with a working mpi? if you could run the tests, your make.sys should be ok. either you do something really strange that limits the MPI communications (and i cannot imagine what that would be) or there is something else going on that you have not paid attention to. how does the machine behave, if you compile a serial executable? cheers, axel. CN> Cheers, CN> Carlo CN> CN> -- CN> ------------------------------------------------------ CN> Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 CN> Fax: +39 011 6707855 - Dipartimento di Chimica IFM CN> via P. Giuria 7, 10125 Torino, Italy CN> http://lem.ch.unito.it/ CN> CN> CN> _______________________________________________ CN> Pw_forum mailing list CN> Pw_forum at pwscf.org CN> http://www.democritos.it/mailman/listinfo/pw_forum CN> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Fri Mar 6 02:12:56 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 5 Mar 2009 20:12:56 -0500 (EST) Subject: [Pw_forum] newbie update In-Reply-To: <50905.151.59.233.4.1236254603.squirrel@mail.unito.it> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it><49AECFE5.3020905@chem.wisc.edu><49AEDACF.70806@phys.ufl.edu> <49AEF380.2020604@chem.wisc.edu> <50905.151.59.233.4.1236254603.squirrel@mail.unito.it> Message-ID: On Thu, 5 Mar 2009, Carlo Nervi wrote: CN> time is almost 1/3 of the wall time. I suspect that Axel CN> is right pointing to the disk I/O. I'm afraid that to CN> increase the performance I should set the RAID 10... no. this cannot be I/O. this is why i suggested this example. unlike with pw.x in some configurations, there usually is no significant i/o when running cp.x. also you have almost exactly 4x the wall time relative to the cpu time. are you _sure_ you are running on a machine with 8 cores? _and_ is that machine otherwise empty? when running on a local 2x quad-core intel xeon E5430 2.66GHz node, i get 42.30s CPU time, 43,87s wall time. with serial MKL and 8 MPI tasks. CN> OMP=2, MPI=8 CN> v0: CP : 0m46.98s CPU time, 1m36.08s CN> wall time CN> little worse than OMP=1 and MPI=8 there is no point in oversubscribing a node. you rather want to test, whether less than the maximum number of total tasks per node is not giving you a better speedup. cheers, axel. [...] -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From idoldog at gmail.com Fri Mar 6 03:39:47 2009 From: idoldog at gmail.com (idoldog) Date: Fri, 6 Mar 2009 10:39:47 +0800 Subject: [Pw_forum] strange bandstructure References: <200903050003486719489@gmail.com> Message-ID: <200903061039461871612@gmail.com> Dear PWSCF user, with the help of Gabriele Sclauzero and Lex Kemper, i have solved the problem. i share it. i follow the suggestion of Gabriele Sclauzero, and increase the k point from 43 to 85. it works. Thank you again. All best idoldog 2009.3.6 From panda.deng.pan at gmail.com Fri Mar 6 07:35:34 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Fri, 6 Mar 2009 14:35:34 +0800 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: <49B00756.4080303@sissa.it> References: <49AFABE7.4030603@sissa.it> <49AFD1AF.20700@sissa.it> <49AFD746.8010200@sissa.it> <49B00756.4080303@sissa.it> Message-ID: > Please try to point out clearly where your problem really is, otherwise noone will be able A mor specific problem is that did I put it correctly for I4/mmm space group in the strucure of "ibrav=6" and 2a 4d 4e coordinates in ATOM_POSITION with crystal option.Are "ibrav=6" and crystal correct?I though I shuold make sure this problem before checking the k_points. From lex at phys.ufl.edu Fri Mar 6 07:38:07 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Fri, 06 Mar 2009 01:38:07 -0500 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: <49AFABE7.4030603@sissa.it> <49AFD1AF.20700@sissa.it> <49AFD746.8010200@sissa.it> <49B00756.4080303@sissa.it> Message-ID: <49B0C4CF.2060801@phys.ufl.edu> If you plot your structure with XCrySDeN or something else, does it look right? Lex Kemper University of Florida ?? wrote: >> Please try to point out clearly where your problem really is, otherwise noone will be able > > A mor specific problem is that did I put it correctly for I4/mmm space > group in the strucure of "ibrav=6" and 2a 4d 4e coordinates in > ATOM_POSITION with crystal option.Are "ibrav=6" and crystal correct?I > though I shuold make sure this problem before checking the k_points. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From panda.deng.pan at gmail.com Fri Mar 6 08:33:40 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Fri, 6 Mar 2009 15:33:40 +0800 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: <49B0C4CF.2060801@phys.ufl.edu> References: <49AFABE7.4030603@sissa.it> <49AFD1AF.20700@sissa.it> <49AFD746.8010200@sissa.it> <49B00756.4080303@sissa.it> <49B0C4CF.2060801@phys.ufl.edu> Message-ID: Dear Lex, > If you plot your structure with XCrySDeN or something else, does it look > right? > I have done it and compared to the structure which is generated by WIEN2k with the same structure.They all look the same. From sclauzer at sissa.it Fri Mar 6 08:54:40 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 06 Mar 2009 08:54:40 +0100 Subject: [Pw_forum] Xcrsyden In-Reply-To: <341053.5690.qm@web52307.mail.re2.yahoo.com> References: <341053.5690.qm@web52307.mail.re2.yahoo.com> Message-ID: <49B0D6C0.1020201@sissa.it> Dear Alvaro, although many people in this forum are using XCrySDen and Tone is so kind that always answers questions about his program even when posted in the wrong forum, I think that you should ask those questions to the correct mailing list, to which you can subscribe at http://www.democritos.it/mailman/listinfo/xcrysden Cheers GS ?lvaro Alves wrote: > > Hello All. I got to the spin polarization using pp.x, creating a file > with extension xsf. However when trying to open in Xcrysden, the system > is deformed. How to solve this? > > Sincerely, Alvaro > > Universidade Federal Fluminense - Niteroi - Rio de Janeiro - Brasil > > > ------------------------------------------------------------------------ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 > > - Celebridades > > - M?sica > > - Esportes > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From tone.kokalj at ijs.si Fri Mar 6 09:03:20 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 06 Mar 2009 09:03:20 +0100 Subject: [Pw_forum] Xcrsyden In-Reply-To: <341053.5690.qm@web52307.mail.re2.yahoo.com> References: <341053.5690.qm@web52307.mail.re2.yahoo.com> Message-ID: <1236326600.4617.2.camel@walk.ijs.si> On Thu, 2009-03-05 at 12:51 -0800, ?lvaro Alves wrote: > > Hello All. I got to the spin polarization using pp.x, creating a file > with extension xsf. However when trying to open in Xcrysden, the > system is deformed. How to solve this? > How deformed? Without appropriate info (i.e. coressponding input files, etc.) nobody will be able to help. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From giannozz at democritos.it Fri Mar 6 09:04:37 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 06 Mar 2009 09:04:37 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> <49AD25BF.2030003@sissa.it> <49AD3208.4030308@democritos.it> Message-ID: <49B0D915.5090105@democritos.it> Aihua Zhang wrote: > Is there any work-around now? not yet > Parallel execution is indispensable for large systems. the system having a problem is not large P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From baris.malcioglu at gmail.com Fri Mar 6 09:46:11 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Fri, 6 Mar 2009 09:46:11 +0100 Subject: [Pw_forum] Problem with the Band Structure Calculation In-Reply-To: References: <49AFD1AF.20700@sissa.it> <49AFD746.8010200@sissa.it> <49B00756.4080303@sissa.it> <49B0C4CF.2060801@phys.ufl.edu> Message-ID: Dear ??, Just to be sure, did you check if the K-Points are what you expect to see in the -output- file? Baris, SISSA On Fri, Mar 6, 2009 at 8:33 AM, ?? wrote: > Dear Lex, > >> If you plot your structure with XCrySDeN or something else, does it look >> right? >> > > I have done it and compared to the structure which is generated by > WIEN2k with the same structure.They all look the same. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mjfmartins at ice.ufjf.br Fri Mar 6 16:59:40 2009 From: mjfmartins at ice.ufjf.br (=?ISO-8859-1?Q?MATEUS_JOS=C9_FERNANDES_MARTINS?=) Date: Fri, 6 Mar 2009 12:59:40 -0300 Subject: [Pw_forum] Problem with dynamical matrix file. Message-ID: <85d7d5fd0903060759o4f947c06w5e7af5497adfba0d@mail.gmail.com> Hello all, I run a phonon calculation with the nat_todo variable enable. The problem is that when I run the application dynmat.x the following error appears. *Reading Dynamical Matrix from file/home/mateus/trabalhos**/Phonons/file.mat * *%%%%%%%%%%%%%%%%%%%* * from readmat : error # 1* * mismatch in reading file* * %%%%%%%%%%%%%%%%%%%%%%%%%%%%%* * stopping ...* Already checked this file with others who have and he does not present anything different to others.I have not found this error anywhere. What is it? My input file of the dynmat is: *&INPUT* * asr = 'crystal'* * fildyn = '/home/mateus/trabalhos//Phonons/file.mat' ,* * filmol = '/home/mateus/trabalhos//Phonons/file.mol' ,* * amass(1) = 26.98000 ,* * amass(2) = 16.00000 ,*** * &END* *0.0 0.0 0.0* PS: Do not post the file .mat because it is very long (110 atoms). If necessary, then post here. Thank you for the yours attention. Mateus Jos? Fernandes Martins Universidade Federal de Juiz de Fora - Brasil -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090306/8d68f432/attachment.htm From degironc at sissa.it Fri Mar 6 17:29:58 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 06 Mar 2009 17:29:58 +0100 Subject: [Pw_forum] PBE0 in PWSCF In-Reply-To: <49B019E4.7050707@ucl.ac.uk> References: <49B019E4.7050707@ucl.ac.uk> Message-ID: <49B14F86.1040903@sissa.it> I reproduce here the answer I gave privately ... just not to let a thread without reply in the forum... Dear Xinzheng Li, the "total energy" should be the right number to look at... it is actually: one-electron contribution + hartree contribution + xc contribution + ewald contribution - Fock energy 1 + Half Fock energy 2 In the Harris Foulkes estimate the Fock energyes are not properly accounted... I'll correct this information. Thank you for the report. regards, stefano xinzheng li wrote: > Dear friends, > > My name is Xinzheng Li. I am a postdoc in University College London. I > am using PWSCF to perform some PBE0 calculations for water cluster on > metal surface recently. In order to make sure that the PBE0 number I got > from PWSCF is correct. I performed a test for the binding energy of a > water-dimer in gas phase (total energy of 2 water moleculars minus the > total energy of a water dimer) taking the all-electron PBE0 results from > Gaussian03 as reference. The converged binding energy from Gaussian03 > is around 207 meV. While after PBE0 calculation of PWSCF is performed, I > have these lines in the output file: > > ! total energy = -68.48225787 Ry > Harris-Foulkes estimate = -72.38797788 Ry > estimated scf accuracy < 0.00000008 Ry > > The total energy is the sum of the following terms: > > one-electron contribution = -144.72933450 Ry > hartree contribution = 71.54274579 Ry > xc contribution = -12.87564636 Ry > ewald contribution = 13.67425725 Ry > Fock energy 1 = -7.81160613 Ry > Fock energy 2 = -7.81177236 Ry > Half Fock energy 2 = -3.90588618 Ry > > I have two questions about this output: > > 1. Shall I take the '! total energy' as the final total energy, or the > 'Harris-Foulkes estimate' as the final total energy? For the comment: > 'The total energy is the sum of the following terms', if I sum the > numbers below, I don't get either 'Harris-Foulkes estimeate', or '! > total energy'. Only if I sum the one-electron contribution, hartree > contibution, xc contribution and the ewald contribution, can I get the > 'Harris-Foulkes estimate'. Does it mean that I should take > 'Harris-Foulkes estimate' as the final energy? If so, what is the > meaning of the '! total energy'? > > 3. If I take Harris-Foulke estimate' as the total energy, the binding > energy I get is 184 meV. If I take '! total energy' as total energy, the > binding energy is 158 meV. Both of these two number are > 20 meV from > the Gaussian all-electron benchmark. What is the expectation for the > accuracy of such a value in the PWSCF code compared with all-electron > Gaussian (when pseudopotentials, and supercell-size convergence are > well-tested)? > > Thanks a lot for your patiency in advance! > > Sincere > Xinzheng > > > > ----------------------------------------------------------------- > Dr. Xinzheng Li > London Centre for Nanotechnology, University College London > 17-19 Gordon Street, London WC1H, 0AH > ucanxli at ucl.ac.uk > ------------------------------------------------------------------ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From idoldog at gmail.com Fri Mar 6 18:13:29 2009 From: idoldog at gmail.com (idoldog) Date: Sat, 7 Mar 2009 01:13:29 +0800 Subject: [Pw_forum] The top of VB in total DOS differ from one in projection DOS Message-ID: <200903070113276259396@gmail.com> Dear PWSCF user, I do DOS calculations of SrTiO3 using code pw.x, dos.x, projwfc.x, and get a strange DOS. The projection DOS shows that top of valence band consists of La 5p and O 2p. But I find the top of valence band in total DOS is different from the one in projection DOS of La 5p and O 2p. I mark the disagreement using two dotted lines in the first picture. I check the data of the three graph, and plot them in the same picture. There are some negative value points. I mark them in the second picture. In my mind, DOS might mean electron number per eV. I don't know what the negative value mean. I guess that these negative value points result in the disagreement between total DOS and projection DOS. If In a same energy, the point in same projection DOS (such as Ti) is negative value, and the others (La 5p and O 2p for example) are positive value, their sum might be zero or negative value. So the top of VB in total DOS differ from one in projection DOS. All DOS. : http://pic.emuch.net/200903/07/7bb56af4f95135d74607726506ed8ded.jpg negative point in DOS. :http://pic.emuch.net/200903/07/eb8445e98a9516b05b13dc28fd90259c.jpg I want to know where my mistakes are and how to solve them. I'm looking forward to your help. All best. -------------- ?? ????? 2009-3-07 ======================== ???????? ?????????94? ======================= From Giovanni.Cantele at na.infn.it Fri Mar 6 18:15:26 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Fri, 06 Mar 2009 18:15:26 +0100 Subject: [Pw_forum] timing vs QE version vs pools Message-ID: <49B15A2E.8090804@na.infn.it> Dear all, I just finished some timing tests relative to QE, stimulated by recent discussions in this forum. I would like to share these tests, and ask a couple of simple (?) questions. Up to now, even if not supported by systematic tests, my feeling has been that for the kind of runs I'm doing on the kind of cluster(s) I'm using, the following rules hold: i) if using a relatively "small" number of CPUs, pools are rather ineffective, I often realized that using pools actually increased job execution time ii) diagonalization parallelism (-ndiag XX) is ineffective as well iii) version 3.2.3 is "better" than 4.0.4 Bearing in mind that I well understand that this kind of issues are often related to the well known problem arising between the keyboard and the chair, these are my results: - system: graphene, 4x4 unit cell (only C atoms) ibrav = 4 celldm(1) = 18.6 celldm(3) = 1.36250 nat = 32 ntyp = 1 ecutwfc = 30.D0 ecutrho = 180.D0 nosym = .true. FFT grid: ( 80, 80,120) smooth grid: ( 72, 72, 90) - computational resources: cluster with dual-core two-processor nodes each processor is an Intel(R) Xeon(R) CPU 5160 @ 3.00GHz Infiniband connection between nodes compiler: ifort (INTEL) 10.1.012 libraries: mkl 10.0.1.014 My tests concerned all possible combinations of the following parameters: - # k-points: 32 or 64 - QE version: 3.2.3 or 4.0.4 - ndiag: default or 1 (only for 4.0.4) - ncpus: 16 or 32 - npools: 1, 2, 4, 8 (just in few cases 16) -------------------------------------------------------------------- 64 k points npools CPU time wall time -------------------------------------- ncpus: 16 nodes: 4 QE 3.2.3 1 8m49.79s 9m 5.89s 2 9m45.15s 9m59.12s 4 12m59.18s 13m14.34s 8 16m 2.94s 16m44.26s -------------------------------------- ncpus: 16 nodes: 4 QE 4.0.4 1 10m51.52s 11m15.80s 2 10m20.63s 10m43.21s 4 13m21.63s 13m45.10s 8 15m59.51s 16m54.57s 1 9m26.57s 9m41.97s -ndiag 1 2 10m22.68s 10m37.74s 4 13m 6.11s 13m25.57s 8 16m 3.49s 17m 3.31s -------------------------------------- ncpus: 32 nodes: 8 QE 3.2.3 1 15m36.93s 15m42.65s 2 5m30.32s 5m37.54s 4 5m 7.28s 5m14.20s 8 6m54.27s 7m 1.82s 16 9m 6.85s 9m28.26s -------------------------------------- ncpus: 32 nodes: 8 QE 4.0.4 1 17m38.71s 17m57.28s 2 9m 7.36s 9m21.41s 4 5m31.61s 5m43.00s 8 7m 1.58s 7m13.86s 16 9m 3.48s 9m33.50s 1 16m 9.52s 16m18.73s -ndiag 1 2 5m49.49s 5m58.75s 4 5m21.05s 5m29.89s 8 6m50.59s 7m 1.20s 16 8m58.71s 9m29.50s -------------------------------------- -------------------------------------------------------------------- -------------------------------------------------------------------- 32 k points npools CPU time wall time -------------------------------------- ncpus: 16 nodes: 4 QE 3.2.3 1 4m44.63s 4m53.08s 2 5m11.63s 5m19.66s 4 7m 8.90s 7m17.45s 8 8m56.42s 9m18.75s -------------------------------------- ncpus: 16 nodes: 4 QE 4.0.4 1 5m54.59s 6m 8.06s 2 5m46.40s 5m56.81s 4 7m15.19s 7m28.52s 8 8m58.10s 9m26.16s 1 5m 3.20s 5m11.53s -ndiag 1 2 5m13.45s 5m23.68s 4 7m 2.97s 7m14.12s 8 8m55.15s 9m24.76s -------------------------------------- ncpus: 32 nodes: 8 QE 3.2.3 1 3m24.75s 3m28.51s 2 2m34.29s 2m38.63s 4 2m57.55s 3m 2.09s 8 4m14.11s 4m19.09s -------------------------------------- ncpus: 32 nodes: 8 QE 4.0.4 1 4m36.23s 4m46.02s 2 3m14.38s 3m20.97s 4 3m18.11s 3m23.60s 8 4m26.24s 4m32.57s 1 3m31.81s 3m37.10s -ndiag 1 2 2m45.79s 2m50.33s 4 3m 2.72s 3m 7.82s 8 4m18.45s 4m24.00s -------------------------------------- -------------------------------------------------------------------- comments: - using pools is, in this case, effective only if ncpus=32, I attribute this to the fact that the FFT is the true bottleneck, thus one should first satisfy FFT grid parallelization. However, from 16 to 32 nodes FFT parallelization is still effective (maybe due to conflict of cores in the same node if using too large resources on that node for ncpus=16), pool parallelization is effective only with -npool 2 - it seems that QE 3.2.3 always performs a little bit better than 4.0.4, any hint on what (if any) is wrong in what I'm doing? - it seems that -ndiag 1 (serial algorithm for the iterative solution of the eigenvalue problem) always performs a little bit better than the default (code) choice. I attribute this to the fact that only for VERY LARGE number of electrons this may give a difference, is that right? Actually the code "default" would lead to this kind of parallelization also for these runs. Thank a lot for reading this message.... Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From paulatto at sissa.it Fri Mar 6 18:42:37 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 06 Mar 2009 18:42:37 +0100 Subject: [Pw_forum] The top of VB in total DOS differ from one in projection DOS In-Reply-To: <200903070113276259396@gmail.com> References: <200903070113276259396@gmail.com> Message-ID: On Fri, 06 Mar 2009 18:13:29 +0100, idoldog wrote: > I want to know where my mistakes are and how to solve them. In order to compute the DOS, dos.x uses, per default, the same kind of smearing used in the SCF calculation; if it is MV or MP, it can deal some small negative DOS. Conversely, projwfc.x uses, per default, the simple gaussian smearing, which cannot produce negative DOS. Have a check at your input files, and see if you are using the different smearing choices consistently. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Fri Mar 6 21:45:51 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 6 Mar 2009 21:45:51 +0100 Subject: [Pw_forum] timing vs QE version vs pools In-Reply-To: <49B15A2E.8090804@na.infn.it> References: <49B15A2E.8090804@na.infn.it> Message-ID: <760A9B34-7C54-4AF8-B4D1-74A319A3A437@democritos.it> On Mar 6, 2009, at 18:15 , Giovanni Cantele wrote: > - it seems that QE 3.2.3 always performs a little bit better than > 4.0.4, > any hint on what (if any) is wrong in what I'm doing? assuming that the two versions are compiled with the same options and libraries: please check where the difference come from, in the cpu time report at the end of each calculation > > - it seems that -ndiag 1 (serial algorithm for the iterative > solution of > the eigenvalue problem) always performs a little bit better than the > default (code) choice. I attribute this to the fact that only for VERY > LARGE number of electrons this may give a difference, is that right? VERY LARGE maybe not, but you will gain (or lose) very little unless you have let's say several hundreds electronic states P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Mar 6 22:27:57 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 6 Mar 2009 22:27:57 +0100 Subject: [Pw_forum] Problem with dynamical matrix file. In-Reply-To: <85d7d5fd0903060759o4f947c06w5e7af5497adfba0d@mail.gmail.com> References: <85d7d5fd0903060759o4f947c06w5e7af5497adfba0d@mail.gmail.com> Message-ID: On Mar 6, 2009, at 16:59 , MATEUS JOS? FERNANDES MARTINS wrote: > I run a phonon calculation with the nat_todo variable enable. The > problem > is that when I run the application dynmat.x the following error > appears > [...] > from readmat : error # 1 > mismatch in reading file I am not sure that the dynmat.x utility is supposed to work in that case (i.e. when the nat_todo variable is enabled) Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From mjfmartins at ice.ufjf.br Sat Mar 7 03:57:22 2009 From: mjfmartins at ice.ufjf.br (=?ISO-8859-1?Q?MATEUS_JOS=C9_FERNANDES_MARTINS?=) Date: Sat, 7 Mar 2009 07:27:22 +0430 Subject: [Pw_forum] Problem with dynamical matrix file. In-Reply-To: References: <85d7d5fd0903060759o4f947c06w5e7af5497adfba0d@mail.gmail.com> Message-ID: <85d7d5fd0903061857p776fe549hb980030fb24c5b90@mail.gmail.com> Hello Paolo, I suspected that. But I did a test a system with less variable nat_todo enabled. Really, he does not write the frequencies in the output of ph.x, but the output of the frequency dynmat.x writes. Only for this calculation that the error is appearing. Mateus. 2009/3/7 Paolo Giannozzi > > On Mar 6, 2009, at 16:59 , MATEUS JOS? FERNANDES MARTINS wrote: > > > I run a phonon calculation with the nat_todo variable enable. The > > problem > > is that when I run the application dynmat.x the following error > > appears > > [...] > > from readmat : error # 1 > > mismatch in reading file > > I am not sure that the dynmat.x utility is supposed to work in that case > (i.e. when the nat_todo variable is enabled) > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090307/7af4fcfb/attachment.htm From yinwei_li at yahoo.cn Sat Mar 7 04:14:12 2009 From: yinwei_li at yahoo.cn (yinwei_li) Date: Sat, 7 Mar 2009 11:14:12 +0800 Subject: [Pw_forum] A method on defining a based-centered monoclinic cell Message-ID: <200903071114082717592@yahoo.cn> Dear Pwscf users, Recently I found an effective way on input defining a based-centered monoclinic cell. In fact, we could change the setting (ibrav=13) in the flib/latgen.f90 from sen = sqrt( 1.d0 - celldm(4) ** 2 ) a1(1) = 0.5 * celldm(1) a1(3) =-a1(1) * celldm(3) a2(1) = celldm(1) * celldm(2) * celldm(4) a2(2) = celldm(1) * celldm(2) * sen a3(1) = a1(1) a3(3) =-a1(3) to sen = sqrt( 1.d0 - celldm(4) ** 2 ) a1(2) = 0.5 * celldm(1) a1(3) =-0.5 * celldm(2) * celldm(1) a2(2) = 0.5 * celldm(1) a2(3) = 0.5 * celldm(2) * celldm(1) a3(1) = celldm(3) * sen * celldm(1) a3(2) = celldm(3) * celldm(4) * celldm(1) which corresponding with the defining form in the MS. I have tested it and found this way of defining could give us a right structure. For some stuctures which have problems in input defining the cell, I think we could resolve it in the same way "change the defining form in latgen.f90 to a new one which corresponding with that in the MS" Good Luck! Yinwei Li2009- Y03-07 body centered tetragonal sen = sqrt( 1.d0 - celldm(4) ** 2 ) a1(1) = 0.5 * celldm(1) a1(3) =-a1(1) * celldm(3) a2(1) = celldm(1) * celldm(2) * celldm(4) a2(2) = celldm(1) * celldm(2) * sen a3(1) = a1(1) a3(3) =-a1(3) yinwei_li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090307/a904465a/attachment.htm From zxf888 at 163.com Sat Mar 7 05:25:51 2009 From: zxf888 at 163.com (Xiang-Feng Zhou) Date: Sat, 7 Mar 2009 12:25:51 +0800 (CST) Subject: [Pw_forum] question about electron phonon calculation Message-ID: <2903948.92961236399951725.JavaMail.coremail@bj163app62.163.com> When I am running the parallel version of espresso-4.0.4 for electron phonon calculation on a Linux cluster, I get the error message after finishing the Gamma point calculation. task #??????? 13from elphsum : error #???????? 1pools and a2F not implementedI noticed that Paolo said ?electron-phonon (EP) calculations do not work together with k-point parallelization?. Does it mean this error message has nothing to do with the version of quantum-espresso? Or whether there is a method which can improve the efficiency of EP calculation? ?I run the order as follows: nohup mpirun ?np 16 ?machinefile node ~/proc/espresso-4.0.4/bin/ph.x ?npool 16 test.elph.out & Thanks in advance, =============================================== Xiang-Feng ZHOU Ph.D candidate Physics Dept. of Nanjing University National Lab. of Solid State Microstructures China =============================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090307/9ac7257a/attachment.htm From idoldog at gmail.com Sat Mar 7 05:50:37 2009 From: idoldog at gmail.com (idoldog) Date: Sat, 7 Mar 2009 12:50:37 +0800 Subject: [Pw_forum] The top of VB in total DOS differ from one inprojection DOS References: <200903070113276259396@gmail.com>, Message-ID: <200903071250360939281@gmail.com> hi Lorenzo Paulatto, Thank you for your kindly help. I used different smearing. I correct them and try again. ======================== ?? ????? ???????? ?????????94? ======================= 2009-03-07 ------------------------------------------------------------- ????Lorenzo Paulatto ?????2009-03-07 01:43:16 ????PWSCF Forum ??? ???Re: [Pw_forum] The top of VB in total DOS differ from one inprojection DOS On Fri, 06 Mar 2009 18:13:29 +0100, idoldog wrote: > I want to know where my mistakes are and how to solve them. In order to compute the DOS, dos.x uses, per default, the same kind of smearing used in the SCF calculation; if it is MV or MP, it can deal some small negative DOS. Conversely, projwfc.x uses, per default, the simple gaussian smearing, which cannot produce negative DOS. Have a check at your input files, and see if you are using the different smearing choices consistently. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From djaithania at yahoo.fr Sat Mar 7 10:31:24 2009 From: djaithania at yahoo.fr (Djani Ait Aissa Hania) Date: Sat, 7 Mar 2009 09:31:24 +0000 (GMT) Subject: [Pw_forum] Re : Problem with the Band Structure Calculation References: <49AFD1AF.20700@sissa.it> <49AFD746.8010200@sissa.it> <49B00756.4080303@sissa.it> <49B0C4CF.2060801@phys.ufl.edu> Message-ID: <993461.59330.qm@web23901.mail.ird.yahoo.com> I4/mmm?, ?ibrav=7 hania Djani CDTA ________________________________ De : O. Baris Malcioglu ? : PWSCF Forum Envoy? le : Vendredi, 6 Mars 2009, 9h46mn 11s Objet?: Re: [Pw_forum] Problem with the Band Structure Calculation Dear ??, Just to be sure, did you check if the K-Points are what you expect to see in the -output- file? Baris, SISSA On Fri, Mar 6, 2009 at 8:33 AM, ?? wrote: > Dear Lex, > >> If you plot your structure with XCrySDeN or something else, does it look >> right? >> > > I have done it and compared to the structure which is generated by > WIEN2k with the same structure.They all look the same. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090307/bedd8a58/attachment.htm From carlo.nervi at unito.it Sat Mar 7 10:37:57 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Sat, 7 Mar 2009 10:37:57 +0100 (CET) Subject: [Pw_forum] mpi problems Message-ID: <1938.151.59.235.214.1236418677.squirrel@mail.unito.it> Dear All, I localized my problems in compiling to MPI. I installed the latest ifort icc and mkl libraries from Intel, as well as mpich2-v1.0.8 in my Linux Gentoo. Now it is compiling (apparently) correctly, but whenever I try to run mpiexec it fail aith Abort message. I tries also to run tests, setting PARA_PREFIX="" (this should run without mpiexec), but I got strange random errors (see below). I think I'm doing something wrong with MPI, perhaps wrong compiler FLAGS or include directories. BRW, now the single CPU is running at 100%... I would appreciate any suggestions... Thanks, Carlo ./check-pw.x.j Checking atom-lsda...passed Checking atom-pbe...passed Checking atom-sigmapbe...passed Checking atom...passed Checking berry...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -333.717527, You got: discrepancy in number of scf iterations detected Reference: 16, You got: Checking berry, step 2 ...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in polarization detected Reference: 0.29312, You got: Checking electric0...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -62.950448, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 8, You got: Checking electric1...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -62.950448, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 1, You got: Checking electric2...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -63.066086, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 4, You got: Checking eval_infix...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -15.794496, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 5, You got: discrepancy in pressure detected Reference: -30.30, You got: Checking eval_infix, step 2 ...passed Checking lattice-ibrav0-abc...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.232039, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav0-cell_parameters+a...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.232039, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav0-cell_parameters+celldm...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.232039, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav0-cell_parameters...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.232039, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav1-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231646, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav1...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.234237, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav10-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231523, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav10...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.237991, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 5, You got: Checking lattice-ibrav11-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231211, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav11...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231893, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav12-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231430, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav12...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231539, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav13-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231320, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav13...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.232363, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav14-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231424, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav14...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.232039, You got: 0.000000 discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav2-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.234027, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav2...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.327848, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav3-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231902, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav3...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.250115, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav4-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231325, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav4...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.232944, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav5-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231427, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav5...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.236472, You got: discrepancy in number of scf iterations detected Reference: 5, You got: Checking lattice-ibrav6-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231540, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav6...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.232909, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav7-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231175, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav7...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.233682, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav8-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231428, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav8...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231982, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav9-kauto...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.231201, You got: discrepancy in number of scf iterations detected Reference: 4, You got: Checking lattice-ibrav9...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -2.237083, You got: discrepancy in number of scf iterations detected Reference: 5, You got: Checking lda+U-noU...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -174.824658, You got: discrepancy in number of scf iterations detected Reference: 9, You got: Checking lda+U-user_ns...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -174.537417, You got: discrepancy in number of scf iterations detected Reference: 10, You got: Checking lda+U...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 discrepancy in total energy detected Reference: -174.453376, You got: discrepancy in number of scf iterations detected Reference: 15, You got: Checking lsda-cg...passed Checking lsda-mixing_TF...passed Checking lsda-mixing_localTF...passed Checking lsda-mixing_ndim...passed Checking lsda-nelup+neldw...passed Checking lsda-tot_magnetization...passed Checking lsda...passed Checking lsda, step 2 ...passed Checking md-pot_extrap1...1 FAILED with error condition! Input: md-pot_extrap1.in, Output: md-pot_extrap1.out, Reference: md-pot_extrap1.ref Aborting -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From lanhaiping at gmail.com Sat Mar 7 11:31:53 2009 From: lanhaiping at gmail.com (lan haiping) Date: Sat, 7 Mar 2009 18:31:53 +0800 Subject: [Pw_forum] How to change velocities of specified ions ? Message-ID: Dear All, I am intending to examine a structure evolution by certain elastic scattering, such as ion bombs, high spread electrons. Therefore, I need to add some kinetic energies for some ions after some times . I checked the INPUT_CP and found it may meet my intent, and i would like to make clear for some points I donot understand well. Could you please give me some hints or suggestions on this issue ? 1, I think I can simulate the scattering process through changing ions' velocities. The card for velocities : ion_velocities has several options such as "default", "change step", "random", "from_input" and "zero". If I just want to change some ions' states and keep others, which option should I choose ? My first guess is "from_input". It seems that i can get the finnal values of ions for previous simulation , then change these values and specify in the ATOMIC_VELOCITIES. Is it OK for me to simulate this scattering process ? Do I lose some points ? 2, About electron_velocities. For elastic scattering on ions, should i consider the change of electron_velocities ? I am not very clear about this tag, would you please explain which physical process this tag account for ? Regards -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090307/a8b2916a/attachment.htm From carlo.nervi at unito.it Sat Mar 7 12:09:53 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Sat, 07 Mar 2009 12:09:53 +0100 Subject: [Pw_forum] newbie update In-Reply-To: References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it><49AECFE5.3020905@chem.wisc.edu><49AEDACF.70806@phys.ufl.edu> <49AEF380.2020604@chem.wisc.edu><50905.151.59.233.4.1236254603.squirrel@mail.unito.it> <49B01122.8040105@democritos.it> <55383.151.59.233.4.1236280796.squirrel@mail.unito.it> Message-ID: <49B25601.4050407@unito.it> Axel Kohlmeyer ha scritto: > how much memory does your machine have? what else is running on that machine? Yes, I'm sure it is a 8 core machine, I have 8 Gb RAM, and nothing else was running. I'm the owner and root user of this PC: a dual socket quad-core Xeon E5345 @2.33GHz on which I installed Gentoo Linux. I'm using the stable (Gentoo) mpich2-v1.0.3 However, I discovered that if mpich2 has been compiled with threads option (USE="mpe threads" emerge mpich2) I got link error messages while compiling QE with ifort. I guess there are few problems with mpich2. The latest version of mpich2 (1.0.8) is marked unstable under Gentoo. I downloaded the most recent ifort/icc/mkl compilers and libraries from the Intel site.... but I'm still in doubt whether to install all or to keep my gcc-4.1.2 p1.3, ifort 10.0 and mkl 9.1.023. I think the main problem lies in my poor understandings of makefile flags, resulting in linking problems with FFTW3 libraries. Right now I'm playing with make.sys and I got: ../Modules/fft_scalar.o: In function 'fft_scalar_mp_cft_b_': fft_scalar.f90(.text+0xc47): undefined reference to 'dfftw_execute_dft_' ... and many other similar link errors... For example, I'm still not sure if this is correct: DFLAGS = -D__INTEL -D__FFTW3 -D__MPI -D__PARA FFT_LIBS = -L/opt/intel/mkl/9.1.023/lib/em64t -lfftw3xf_intel MPI_LIBS = -L/usr/lib64/ -lmpich Sorry for bothering a lot, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From giannozz at democritos.it Sat Mar 7 14:51:12 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 7 Mar 2009 14:51:12 +0100 Subject: [Pw_forum] newbie update In-Reply-To: <49B25601.4050407@unito.it> References: <1187.151.59.235.134.1236192687.squirrel@mail.unito.it><49AECFE5.3020905@chem.wisc.edu><49AEDACF.70806@phys.ufl.edu> <49AEF380.2020604@chem.wisc.edu><50905.151.59.233.4.1236254603.squirrel@mail.unito.it> <49B01122.8040105@democritos.it> <55383.151.59.233.4.1236280796.squirrel@mail.unito.it> <49B25601.4050407@unito.it> Message-ID: On Mar 7, 2009, at 12:09 , Carlo Nervi wrote: > fft_scalar.f90(.text+0xc47): undefined reference to > 'dfftw_execute_dft_' > > ... and many other similar link errors... > > For example, I'm still not sure if this is correct: > DFLAGS = -D__INTEL -D__FFTW3 -D__MPI -D__PARA > FFT_LIBS = -L/opt/intel/mkl/9.1.023/lib/em64t -lfftw3xf_intel -lfftw3x_intel must be loaded before -lmkl (in your case, -lmkl_em64t). Put it whenever you want, but note that LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $ (MPI_LIBS) ... P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From panda.deng.pan at gmail.com Sat Mar 7 16:02:41 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Sat, 7 Mar 2009 23:02:41 +0800 Subject: [Pw_forum] Band structure Message-ID: Dear all users, I have got a 'flat' band structure.I thought it should be wrong.By 'flat' I meant that some bands of my calculation from one point to another were parallel to the x-axis.The number of parallel bands seems too big. I considered error would happen at 'degauss' value for the smearing option.Any suggest or comment on the value and the 'flat' band stucture would be appriciate. my input &control calculation = 'scf' restart_mode='from_scratch' prefix='BaNiAs', pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/disk2/xgwan/tmp/' / &system ibrav=6, celldm(1)=7.7702, celldm(3)=2.806, nat=10, ntyp=3, ecutwfc = 40.0, ecutrho = 400.0, occupations= 'smearing' degauss = 0.03 smearing = 'marzari-vanderbilt' / &electrons diagonalization= 'cg' mixing_beta = 0.7 conv_thr = 1.0d-6 / ATOMIC_SPECIES Ba 137.327 Ba.pbe-nsp-van.UPF Ni 58.6934 Ni.pbe-nd-rrkjus.UPF As 74.9216 As.pbe-n-van.UPF ATOMIC_POSITIONS crystal Ba 0.0000 0.0000 0.0000 Ba 0.5000 0.5000 0.5000 Ni 0.0 0.5 0.25 Ni 0.5 0.0 0.75 Ni 0.5 0.0 0.25 Ni 0.0 0.5 0.75 As 0.0000 0.0000 0.3476 As 0.0000 0.0000 0.6524 As 0.5000 0.5000 0.8476 As 0.5000 0.5000 0.1524 K_POINTS {automatic} 8 8 8 0 0 0 Thanks for all the help. Deng Pan Nanjing University From carlo.nervi at unito.it Sat Mar 7 16:12:47 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Sat, 7 Mar 2009 16:12:47 +0100 (CET) Subject: [Pw_forum] newbie update Message-ID: <2066.151.59.235.214.1236438767.squirrel@mail.unito.it> > -lfftw3x_intel must be loaded before -lmkl (in your case, -lmkl_em64t). > Put it whenever you want, but note that LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $ (MPI_LIBS) ... > P. > --- > Paolo Giannozzi, Democritos and University of Udine, Italy Thanks Paolo. Indeed I figure out myself by tryal & error method...only a little later.. sorry.. In the "mpi problem" post I describe what I did: new ifort. By the way, the new ifort 11.0.081 / mkl 10.1.1.019 works a little different. The file /opt/intel/mkl/10.1.1.019/lib/em64t/libmkl_lapack.a contains: GROUP (libmkl_intel_lp64.a libmkl_intel_thread.a libmkl_core.a) The file /opt/intel/mkl/10.1.1.019/lib/em64t/libmkl_em64t.a contains: GROUP (libmkl_intel_lp64.a libmkl_intel_thread.a libmkl_core.a) Therefore I used the same order, but substituing libmkl_intel_thread.a with libmkl_sequential In this way I can comple all. Anf the librabries order does not seems to have effects.. But the results are strange. If I use mpiexec the code crash, but if I run without mpiexec now it run at 100% CPU usage, on a single cpu...It looks like a MPI problem (mpi v. 1.0.8) (see the "mpi problem" at http://www.democritos.it/pipermail/pw_forum/2009-March/011906.html) Thanks, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From paulatto at sissa.it Sat Mar 7 16:13:50 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 7 Mar 2009 16:13:50 +0100 (CET) Subject: [Pw_forum] Band structure In-Reply-To: References: Message-ID: <34894.78.12.171.2.1236438830.squirrel@webmail.sissa.it> On Sat, 07 Mar 2009 16:02:41 +0100, ??˜?™? wrote: The number of parallel bands seems too big. Why? How many of them are there?? Ba 137.327 Ba.pbe-nsp-van.UPF This pseudopotential has semi-core states 5S and 5P in valence; times 2 atoms it makes 6 flat bands. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From panda.deng.pan at gmail.com Sat Mar 7 16:29:33 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Sat, 7 Mar 2009 23:29:33 +0800 Subject: [Pw_forum] Band structure In-Reply-To: <34894.78.12.171.2.1236438830.squirrel@webmail.sissa.it> References: <34894.78.12.171.2.1236438830.squirrel@webmail.sissa.it> Message-ID: > Why? How many of them are there?? 12.I just repeat the calculation which have been done yet.In that paper do not have the flat bands. > ?Ba 137.327 Ba.pbe-nsp-van.UPF > > This pseudopotential has semi-core states 5S and 5P in valence; times 2 > atoms it makes 6 flat bands. Is not the matter with smearing at all? From hqzhou at nju.edu.cn Sun Mar 8 05:16:11 2009 From: hqzhou at nju.edu.cn (hqzhou) Date: Sun, 8 Mar 2009 12:16:11 +0800 (CST) Subject: [Pw_forum] question about electron phonon calculation Message-ID: It simply means that using pools in phonon calculation is meaningless. But it may not be the main cause of your error. Dr. Huiqun Zhou @Earth Sciences, Nanjing University, China From ylli at theory.issp.ac.cn Sun Mar 8 11:33:58 2009 From: ylli at theory.issp.ac.cn (=?utf-8?B?TGkgWUw=?=) Date: Sun, 08 Mar 2009 18:33:58 +0800 Subject: [Pw_forum] =?utf-8?q?character_band=2E?= Message-ID: <20090308103358.32526.qmail@ms.hfcas.ac.cn> Dear Prasenjit, Thanks for your help. I've got it. But I don't know the meaning of the third row in results file "case. proj". Can you tell me these? Besides, in case.out file, I noticed atomic orbital is numbered. For example, d orbital is given by quantum number l=2 and m=1,2,3,4,5. You know, d orbitals are often written as dz2, dx2-y2,..... Can you tell me atomic orbitals, such as d and p, are arranged in what order? Best regards, Yanling Li. Institute of solid states physics, CAS, China. >Prasenjit Ghosh wrote: > Dear Yanling, > >> You can use projwfc.x post-processing tool in the PP directory which > >projects the DOS on the wavefunction of each atom. Then you can compare > >the total DOS with the projected dos and you can tell which band is from >> which wave function of which atom. Regarding the input file for it, you > >can find the details in Doc/INPUT_PROJWFC.txt >>The PDOS can be obtained with lsym=.TRUE. (which is the default), but if you want to know >>the projection on individual KS states (the PDOS is build up on these, by summing up on >>k-point and bands with correct weights), you need lsym=.FALSE. >>cheers, >GS > > With regards, > Prasenjit. > Dear Prasenjit, Thanks for your help. I've got it. But I don't know the meaning of the third column in results file "case. proj". Can you tell me these? Besides, in case.out file, I noticed atomic orbital is numbered. For example, d orbital is given by quantum number l=2 and m=1,2,3,4,5. You know, d orbitals are often written as dz2, dx2-y2,..... Can you tell me atomic orbitals, such as d and p, are arranged in what order? Best regards, Yanling Li. Institute of solid states physics, CAS, China. >Prasenjit Ghosh wrote: > Dear Yanling, > >> You can use projwfc.x post-processing tool in the PP directory which > >projects the DOS on the wavefunction of each atom. Then you can compare > >the total DOS with the projected dos and you can tell which band is from >> which wave function of which atom. Regarding the input file for it, you > >can find the details in Doc/INPUT_PROJWFC.txt >>The PDOS can be obtained with lsym=.TRUE. (which is the default), but if you want to know >>the projection on individual KS states (the PDOS is build up on these, by summing up on >>k-point and bands with correct weights), you need lsym=.FALSE. >>cheers, >GS > > With regards, > Prasenjit. > References: Message-ID: <30408376.138521236567204642.JavaMail.coremail@bj163app31.163.com> Dear Huiqun I get it. thanks for your quick response! Best regards =============================================== Xiang-Feng ZHOU Ph.D candidate Physics Dept. of Nanjing University National Lab. of Solid State Microstructures China =============================================== ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090309/d6687d26/attachment.htm From lex at phys.ufl.edu Mon Mar 9 04:36:35 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Sun, 08 Mar 2009 23:36:35 -0400 Subject: [Pw_forum] character band. In-Reply-To: <20090308103550.32744.qmail@ms.hfcas.ac.cn> References: <20090308103550.32744.qmail@ms.hfcas.ac.cn> Message-ID: <49B48EC3.2020406@phys.ufl.edu> Hey Yanling, It's in the projwfc.f90 source file. From there: ! Order of m-components for each l in the output: ! ! 1, cos(phi), sin(phi), cos(2*phi), sin(2*phi), .., cos(l*phi), sin(l*phi) ! ! where phi is the polar angle:x=r cos(theta)cos(phi), y=r cos(theta)sin(phi) ! This is determined in file flib/ylmr2.f90 that calculates spherical harm. ! L=1 : ! 1 pz (m=0) ! 2 px (real combination of m=+/-1 with cosine) ! 3 py (real combination of m=+/-1 with sine) ! L=2 : ! 1 dz2 (m=0) ! 2 dzx (real combination of m=+/-1 with cosine) ! 3 dzy (real combination of m=+/-1 with sine) ! 4 dx2-y2 (real combination of m=+/-2 with cosine) ! 5 dxy (real combination of m=+/-1 with sine) Cheers, Lex Li YL wrote: > Dear Prasenjit, > Thanks for your help. I've got it. But I don't know the meaning of the third column in results file "case. proj". > Can you tell me these? > Besides, > in case.out file, I noticed atomic orbital is numbered. For example, /d/ orbital is > given by quantum number /l/=2 and /m/=1,2,3,4,5. You know, /d/ orbitals > are often written as dz2, dx2-y2,..... Can you tell me atomic orbitals, > such as /d/ and /p,/ are arranged in what order? > > Best regards, > > Yanling Li. > > Institute of solid states physics, CAS, China. > >>Prasenjit Ghosh wrote: >> Dear Yanling, >> >>> You can use projwfc.x post-processing tool in the PP directory which >> >projects the DOS on the wavefunction of each atom. Then you can compare >> >the total DOS with the projected dos and you can tell which band is from >>> which wave function of which atom. Regarding the input file for it, you >> >can find the details in Doc/INPUT_PROJWFC.txt > >>>The PDOS can be obtained with lsym=.TRUE. (which is the default), but if you want to know >>>the projection on individual KS states (the PDOS is build up on these, by summing up on >>>k-point and bands with correct weights), you need lsym=.FALSE. > >>>cheers, > >>GS > >> >> With regards, >> Prasenjit. >> > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From w2agz at pacbell.net Mon Mar 9 06:34:46 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Sun, 8 Mar 2009 22:34:46 -0700 Subject: [Pw_forum] ld1.x & US requires... Message-ID: <00a401c9a078$c224ef90$466eceb0$@net> To All: Recently, like today, I tried constructing a new PP for Fe, favored toward 2+. Problems. Reasons follow at the end of this note. Refer to http://www.democritos.it:8888/O-sesame/rlog?f=O-sesame/atomic/ld1_readin.f90 . The input script to ld1.x is below: &input title='Fe 3d6_4s2', zed=26.0, rel=1, config='[Ar] 3d6.0 4s2.0', iswitch=3, dft='LDA', / &inputp lloc=0, pseudotype=3, file_pseudopw='Fe.pz-3d6_4s2-rrkjus.UPF', author='PMG', / 2 3D 3 2 6.00 0.00 1.60 2.20 4S 1 0 2.00 0.00 2.00 2.20 And on invoking ld1.x, I get the complaint in the subject line. My reading of the O-Sesame log is that this message is more of a complaint, than an showstopper. Using the "new" PP did not seem to give any problem, outside an overall absolute value of ground state energy, on various post-processing measurements, such as those produced by dos.x. BTW, I don't get this agony for a similar PP input for 3d9_4s2. Why did I bother doing this exercise? Simply because dos.x apparently arranges the notation for the projected pdos output according to the sequence of states listed in the PP. For Cu, it is 3d-4s, whereas for Ni, Co, Fe, and Mn, it is the reverse. Sigh, -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090308/cfe4eaed/attachment-0001.htm From w2agz at pacbell.net Mon Mar 9 07:24:39 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Sun, 8 Mar 2009 23:24:39 -0700 Subject: [Pw_forum] March American Physical Society Meeting, 3/15-20 Message-ID: <00b501c9a07f$ba4c1990$2ee44cb0$@net> To all in the QE-Democritos Community: The week after next, the American Physical Society will host its annual General Meeting in Pittsburgh, PA. I would ask those in the Community intending to attend to contact me regarding the tools and support provided by those users of PWscf worldwide critical to their individual and institutional research efforts. You can find me hanging around the Press Room and all the sessions on the iron pnictide superconductors (my talk will be given on Wednesday. Link to http://meetings.aps.org/Meeting/MAR09/Event/97186). We should take this opportunity to make our colleagues and the physics community at large aware of our powerful and self-supporting open access resources for computational research into the physics and chemistry of materials. Look me up on www.w2agz.com and w2agz at pacbell.net , and let me know of recent results you've obtained which might be scientifically newsworthy and I'll help get you connected with appropriate press contacts. Regards, -Paul Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090308/f20cf390/attachment.htm From lidonglin556 at 163.com Mon Mar 9 07:57:05 2009 From: lidonglin556 at 163.com (lidonglin556) Date: Mon, 9 Mar 2009 14:57:05 +0800 (CST) Subject: [Pw_forum] thermo.x Message-ID: <19918256.350651236581825345.JavaMail.coremail@bj163app78.163.com> Hi, When I use the thermo.x of the example( EOS with QHA), but there are some faults, As follow: Hello! Wait a few seconds forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source thermo.x 00000000004070E6 Unknown Unknown Unknown thermo.x 0000000000403C42 Unknown Unknown Unknown thermo.x 0000000000402D5E Unknown Unknown Unknown libc.so.6 00000030F121E32A Unknown Unknown Unknown thermo.x 0000000000402C69 Unknown Unknown Unknown How to correct it? Many thanks! bests Dong-lin Li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090309/1e01df00/attachment.htm From ouuing at gmail.com Mon Mar 9 09:05:06 2009 From: ouuing at gmail.com (liu hanyu) Date: Mon, 9 Mar 2009 16:05:06 +0800 Subject: [Pw_forum] A method on defining a based-centered monoclinic cell In-Reply-To: <200903071114082717592@yahoo.cn> References: <200903071114082717592@yahoo.cn> Message-ID: The solution is very excellent. On Sat, Mar 7, 2009 at 11:14 AM, yinwei_li wrote: > Dear?Pwscf?users, > > ??? Recently I found an effective way on input defining a based-centered > monoclinic cell. > > In fact, we could??change the setting (ibrav=13) in the flib/latgen.f90 from > ?????sen?=?sqrt(?1.d0?-?celldm(4)?**?2?) > ?????a1(1)?=?0.5?*?celldm(1) > ?????a1(3)?=-a1(1)?*?celldm(3) > ?????a2(1)?=?celldm(1)?*?celldm(2)?*?celldm(4) > ?????a2(2)?=?celldm(1)?*?celldm(2)?*?sen > ?????a3(1)?=?a1(1) > ?????a3(3)?=-a1(3) > > to > > ?????sen?=?sqrt(?1.d0?-?celldm(4)?**?2?) > ?????a1(2)?=?0.5?*?celldm(1) > ?????a1(3)?=-0.5?*?celldm(2)?*?celldm(1) > ?????a2(2)?=?0.5?*?celldm(1) > ?????a2(3)?=?0.5?*?celldm(2)?*?celldm(1) > ?????a3(1)?=?celldm(3)?*?sen?*?celldm(1) > ?????a3(2)?=?celldm(3)?*?celldm(4)?*?celldm(1) > > which corresponding with the defining form in the MS. > > I have tested it and found this way of defining could give us a right > structure. > > For some stuctures which have problems in input defining the cell, I think > we could resolve it in the same way > "change the defining form in latgen.f90?to?a new?one which corresponding > with that in the MS" > > Good Luck! > > Yinwei Li2009- > > > Y03-07 body?centered?tetragonal > ________________________________ > ?????sen?=?sqrt(?1.d0?-?celldm(4)?**?2?) > ?????a1(1)?=?0.5?*?celldm(1) > ?????a1(3)?=-a1(1)?*?celldm(3) > ?????a2(1)?=?celldm(1)?*?celldm(2)?*?celldm(4) > ?????a2(2)?=?celldm(1)?*?celldm(2)?*?sen > ?????a3(1)?=?a1(1) > ?????a3(3)?=-a1(3) > yinwei_li > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- Hanyu Liu, Master Student State Key Laboratory of Superhard Materials, Jilin University, China Email: ouuing at email.jlu.edu.cn | ouuing at gmail.com From sclauzer at sissa.it Mon Mar 9 10:04:55 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 09 Mar 2009 10:04:55 +0100 Subject: [Pw_forum] question about electron phonon calculation In-Reply-To: References: Message-ID: <49B4DBB7.7070800@sissa.it> hqzhou wrote: > It simply means that using pools in phonon calculation is meaningless. Why do you say this? Phonon calculations with pools parallelization is implemented and works properly! Why should it be meaningless? The error message report you were refering to: from elphsum : error # 1 pools and a2F not implemented does not come from a phonon calculation (which can be done using pools), but from an electron-phonon coupling calculation, which has not yet been parallelized with pools (while distributed FFT parallelization should be already working). GS > But it may not be the main cause of your error. > > Dr. Huiqun Zhou > @Earth Sciences, Nanjing University, China > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Mon Mar 9 11:46:19 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 9 Mar 2009 11:46:19 +0100 Subject: [Pw_forum] A method on defining a based-centered monoclinic cell In-Reply-To: <200903071114082717592@yahoo.cn> References: <200903071114082717592@yahoo.cn> Message-ID: <7A4435F0-2704-4698-84B1-6F3E3E9E173D@democritos.it> On Mar 7, 2009, at 4:14 , yinwei_li wrote: > In fact, we could change the setting (ibrav=13) in the flib/ > latgen.f90 from > [...] to [...] which corresponding with the defining form in the MS. MS = manuscript? Master of Science? Multiple Sclerosis? > > I have tested it and found this way of defining could give us a > right structure. do you have any evidence that the current code produces an incorrect structure, or that the documentation is incorrect? case ibrav=13 has been corrected more than once and as far as I know it is both correct and consistent with what the documentation says. P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Mon Mar 9 12:19:48 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 9 Mar 2009 12:19:48 +0100 Subject: [Pw_forum] How to change velocities of specified ions ? In-Reply-To: References: Message-ID: <3F62F38B-D7CF-4431-B6D4-A5ACBF1A04F3@democritos.it> On Mar 7, 2009, at 11:31 , lan haiping wrote: > 2, About electron_velocities. For elastic scattering on ions, > should i consider the change of electron_velocities ? > I am not very clear about this tag, would you please explain > which physical process this tag account for ? electron velocities are used in Car-Parrinello simulations and there is no related "physical process": the electron dynamics is fictitious P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Mon Mar 9 12:35:05 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 9 Mar 2009 07:35:05 -0400 Subject: [Pw_forum] thermo.x In-Reply-To: <19918256.350651236581825345.JavaMail.coremail@bj163app78.163.com> References: <19918256.350651236581825345.JavaMail.coremail@bj163app78.163.com> Message-ID: <7b6913e90903090435r7616c4b5te17fa4b465345144@mail.gmail.com> On Mon, Mar 9, 2009 at 2:57 AM, lidonglin556 wrote: > > > Hi, > When I use the thermo.x of the example( EOS with QHA), but there are some > faults, > As follow: > Hello! Wait a few seconds > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line > Source > thermo.x 00000000004070E6 Unknown Unknown Unknown > thermo.x 0000000000403C42 Unknown Unknown Unknown > thermo.x 0000000000402D5E Unknown Unknown Unknown > libc.so.6 00000030F121E32A Unknown Unknown Unknown > thermo.x 0000000000402C69 Unknown Unknown Unknown > How to correct it? how to reproduce? axel. > Many thanks! > bests > Dong-lin Li > > ________________________________ > ????????????????? > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From lanhaiping at gmail.com Mon Mar 9 13:07:54 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 9 Mar 2009 20:07:54 +0800 Subject: [Pw_forum] A method on defining a based-centered monoclinic cell In-Reply-To: <7A4435F0-2704-4698-84B1-6F3E3E9E173D@democritos.it> References: <200903071114082717592@yahoo.cn> <7A4435F0-2704-4698-84B1-6F3E3E9E173D@democritos.it> Message-ID: Hi, Paolo, M$ stands for two possible in my words, one is MicroSoft, the other is Material Studio. I guess that guy should use it for the latter case. On Mon, Mar 9, 2009 at 6:46 PM, Paolo Giannozzi wrote: > > On Mar 7, 2009, at 4:14 , yinwei_li wrote: > > > In fact, we could change the setting (ibrav=13) in the flib/ > > latgen.f90 from > > [...] to [...] which corresponding with the defining form in the MS. > > MS = manuscript? Master of Science? Multiple Sclerosis? > > > > > I have tested it and found this way of defining could give us a > > right structure. > > do you have any evidence that the current code produces an incorrect > structure, or that the documentation is incorrect? case ibrav=13 has > been > corrected more than once and as far as I know it is both correct and > consistent with what the documentation says. > > P. > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090309/c36af57b/attachment.htm From eyvaz_isaev at yahoo.com Mon Mar 9 13:13:43 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 9 Mar 2009 05:13:43 -0700 (PDT) Subject: [Pw_forum] QHA code In-Reply-To: <26982934.68301236561583481.JavaMail.coremail@bj163app95.163.com> Message-ID: <889413.44932.qm@web65713.mail.ac4.yahoo.com> Dear Li, I had problems with Internet on holidays. If I did not send to you the code yet, I will send. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Mon, 3/9/09, lidonglin556 wrote: > From: lidonglin556 > Subject: how to correct it > To: "code" > Date: Monday, March 9, 2009, 4:19 AM > Hi Prof.eyvaz, > Maybe you are very busy during those days, may your > everything is ok! > I really worry about it as not get the code from you, as > a postgraduate I don't want to get confused. So I got > one code (attached file) from internet, is it what you said? > And when I run the example of the Static EOS, that's OK! > But there are some problems when use the EOS with QHA, as > follow: > > Hello! Wait a few seconds > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine > Line Source > thermo.x 00000000004070E6 Unknown > Unknown Unknown > thermo.x 0000000000403C42 Unknown > Unknown Unknown > thermo.x 0000000000402D5E Unknown > Unknown Unknown > libc.so.6 00000030F121E32A Unknown > Unknown Unknown > thermo.x 0000000000402C69 Unknown > Unknown Unknown > So where the problem is and how to correct it? > Many thanks! > Dong-lin Li From ouuing at gmail.com Mon Mar 9 13:29:37 2009 From: ouuing at gmail.com (liu hanyu) Date: Mon, 9 Mar 2009 20:29:37 +0800 Subject: [Pw_forum] A method on defining a based-centered monoclinic cell In-Reply-To: References: <200903071114082717592@yahoo.cn> <7A4435F0-2704-4698-84B1-6F3E3E9E173D@democritos.it> Message-ID: I think that MS is Material Studio. On Mon, Mar 9, 2009 at 8:07 PM, lan haiping wrote: > Hi, Paolo, > M$ stands for two possible in my words, one is > MicroSoft, the other is Material Studio. > I guess that guy should use it for the latter case. > On Mon, Mar 9, 2009 at 6:46 PM, Paolo Giannozzi > wrote: >> >> On Mar 7, 2009, at 4:14 , yinwei_li wrote: >> >> > In fact, we could change the setting (ibrav=13) in the flib/ >> > latgen.f90 from >> > [...] to [...] which corresponding with the defining form in the MS. >> >> MS = manuscript? Master of Science? Multiple Sclerosis? >> >> > >> > I have tested it and found this way of defining could give us a >> > right structure. >> >> do you have any evidence that the current code produces an incorrect >> structure, or that the documentation is incorrect? case ibrav=13 has >> been >> corrected more than once and as far as I know it is both correct and >> consistent with what the documentation says. >> >> P. >> --- >> Paolo Giannozzi, Democritos and University of Udine, Italy >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- Hanyu Liu(???), Master Student State Key Laboratory of Superhard Materials, Jilin University, China Email: ouuing at email.jlu.edu.cn | ouuing at gmail.com From yinwei_li at yahoo.cn Mon Mar 9 13:31:36 2009 From: yinwei_li at yahoo.cn (yinwei_li) Date: Mon, 9 Mar 2009 20:31:36 +0800 Subject: [Pw_forum] A method on defining a based-centered monoclinic cell References: <200903071114082717592@yahoo.cn> Message-ID: <200903092031220473418@yahoo.cn> Sorry, everyone, MS is Materials Studio modeling. In fact, I found many users, as well as me, have problems on the input defining a based-centered monoclinic cell. For example, a c2m structure with a=11.692, b=2.159, c=3.463, beta=103.7, A (0.152 0 0.373 ) B (0.054 0.5 0.976) B (0.745 0.5 0.889) B (0.946 0.5 0.388) As described in the documentation, the input information is: ibrav=13, celldm(1)=22.09468665493776184528, celldm(2)=0.18465617516250427642, celldm(3)=0.29618542593226137529, celldm(4)=-0.236838146065618621, nat=8 ntyp= 2, ... ... ATOMIC_POSITIONS {crystal} A 0.15200 0.15200 0.37300 A 0.84800 0.84800 0.62700 B 0.55400 0.55400 0.97600 B 0.24500 0.24500 -0.11100 B 0.44600 0.44600 0.38800 B 0.44600 0.44600 0.02400 B 0.75500 0.75500 0.11100 B 0.55400 0.55400 0.61200 .... However, this will give us a different structure with that in Materials Studio (MS). I know there is something wrong in my input, because the atomic positions I input are directly obtained from the Materials Studio (MS). Unfortunately, the transformation matrix from the unit cell to the primitive cell is different between the MS and PWSCF, therefore, my input form is not accordance with the PWSCF, but I do not know how to change my input. However, If I change the defining form in the PWSCF to the one used in MS, with my input I will get a correct structure. If some one could get a correct structure of the above parameters with the defining form in the PWSCF, please show me the input file. Thanks! 2009-03-09 *************************************** Yinwei Li ????? PHD State Key Lab of Superhard Materials, Jilin University 2699 Qianjin Str. 130012, Changchun P. R. China ******************************************** ???? Paolo Giannozzi ????? 2009-03-09 18:47:32 ???? PWSCF Forum ??? ??? Re: [Pw_forum] A method on defining a based-centered monoclinic cell On Mar 7, 2009, at 4:14 , yinwei_li wrote: > In fact, we could change the setting (ibrav=13) in the flib/ > latgen.f90 from > [...] to [...] which corresponding with the defining form in the MS. MS = manuscript? Master of Science? Multiple Sclerosis? > > I have tested it and found this way of defining could give us a > right structure. do you have any evidence that the current code produces an incorrect structure, or that the documentation is incorrect? case ibrav=13 has been corrected more than once and as far as I know it is both correct and consistent with what the documentation says. P. --- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum __________ Information from ESET Smart Security, version of virus signature database 3919 (20090309) __________ The message was checked by ESET Smart Security. http://www.eset.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090309/94356537/attachment-0001.htm From zucco at dipteris.unige.it Mon Mar 9 13:17:24 2009 From: zucco at dipteris.unige.it (Marino Vetuschi Zuccolini) Date: Mon, 9 Mar 2009 13:17:24 +0100 Subject: [Pw_forum] timing vs QE version vs pools In-Reply-To: <49B15A2E.8090804@na.infn.it> References: <49B15A2E.8090804@na.infn.it> Message-ID: Dear Giovanni, I'm testing our system with more or less the same configuration. Can you send me the input you used in testing your cluster? Many thanks. m. On 6 Mar 2009, at 18:15, Giovanni Cantele wrote: > Dear all, > > I just finished some timing tests relative to QE, stimulated by recent > discussions in this forum. > I would like to share these tests, and ask a couple of simple (?) > questions. > > Up to now, even if not supported by systematic tests, my feeling has > been that > for the kind of runs I'm doing on the kind of cluster(s) I'm using, > the > following rules hold: > > i) if using a relatively "small" number of CPUs, pools are rather > ineffective, I often realized that > using pools actually increased job execution time > > ii) diagonalization parallelism (-ndiag XX) is ineffective as well > > iii) version 3.2.3 is "better" than 4.0.4 > ... ******************************************************* Marino Vetuschi Zuccolini zucco at dipteris.unige.it Researcher / Geochemist Laboratory of Geochemistry DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy From Giovanni.Cantele at na.infn.it Mon Mar 9 14:33:59 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Mon, 09 Mar 2009 14:33:59 +0100 Subject: [Pw_forum] timing vs QE version vs pools In-Reply-To: References: <49B15A2E.8090804@na.infn.it> Message-ID: <49B51AC7.3060309@na.infn.it> Marino Vetuschi Zuccolini wrote: > Dear Giovanni, > I'm testing our system with more or less the same configuration. Can > you send me the input you used in testing your cluster? > > Many thanks. > > m. > warning: k point list just for testing purposes (I just tried to get those specific numbers of k-points) input: &CONTROL calculation = 'scf' title = 'graphene' restart_mode = 'from_scratch' outdir = '/scratch/Giovanni/bench_graph4x4' prefix = 'C' pseudo_dir = '/home/nm_settings/software/CODES/Quantum-ESPRESSO/pseudo/' / &SYSTEM ibrav = 4 celldm(1) = 18.6 celldm(3) = 1.36250 nat = 32 ntyp = 1 ecutwfc = 30.D0 ecutrho = 180.D0 occupations = 'smearing' smearing = 'mv' degauss = 0.007 nosym = .true. / &ELECTRONS / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF ATOMIC_POSITIONS { Angstrom } C 0.000000000 0.000000000 1.676333520 C 1.230336530 0.710335120 1.676333520 C 18.455047875 2.131005372 1.676333520 C 0.000000005 2.841340492 1.676333520 C 17.224711350 4.262010743 1.676333520 C 18.455047880 4.972345863 1.676333520 C 15.994374825 6.393016115 1.676333520 C 17.224711355 7.103351235 1.676333520 C 2.460673050 0.000000000 1.676333520 C 3.691009580 0.710335120 1.676333520 C 1.230336525 2.131005372 1.676333520 C 2.460673055 2.841340492 1.676333520 C 0.000000000 4.262010743 1.676333520 C 1.230336530 4.972345863 1.676333520 C 18.455047875 6.393016115 1.676333520 C 0.000000005 7.103351235 1.676333520 C 4.921346100 0.000000000 1.676333520 C 6.151682630 0.710335120 1.676333520 C 3.691009575 2.131005372 1.676333520 C 4.921346105 2.841340492 1.676333520 C 2.460673050 4.262010743 1.676333520 C 3.691009580 4.972345863 1.676333520 C 1.230336525 6.393016115 1.676333520 C 2.460673055 7.103351235 1.676333520 C 7.382019150 0.000000000 1.676333520 C 8.612355680 0.710335120 1.676333520 C 6.151682625 2.131005372 1.676333520 C 7.382019155 2.841340492 1.676333520 C 4.921346100 4.262010743 1.676333520 C 6.151682630 4.972345863 1.676333520 C 3.691009575 6.393016115 1.676333520 C 4.921346105 7.103351235 1.676333520 The k-point list follows, these are the two tests (32 kpts and 64 kpts) I did: K_POINTS { crystal } 32 0.0000000 0.0000000 0.0000000 1.00 0.2500000 0.1443376 0.0000000 1.00 0.5000000 0.2886751 0.0000000 1.00 0.7500000 0.4330127 0.0000000 1.00 0.0000000 0.2886751 0.0000000 1.00 0.2500000 0.4330127 0.0000000 1.00 0.5000000 0.5773503 0.0000000 1.00 0.7500000 0.7216878 0.0000000 1.00 0.0000000 0.5773503 0.0000000 1.00 0.2500000 0.7216878 0.0000000 1.00 0.5000000 0.8660254 0.0000000 1.00 0.7500000 1.0103630 0.0000000 1.00 0.0000000 0.8660254 0.0000000 1.00 0.2500000 1.0103630 0.0000000 1.00 0.5000000 1.1547005 0.0000000 1.00 0.7500000 1.2990381 0.0000000 1.00 0.0000000 0.0000000 0.3669725 1.00 0.2500000 0.1443376 0.3669725 1.00 0.5000000 0.2886751 0.3669725 1.00 0.7500000 0.4330127 0.3669725 1.00 0.0000000 0.2886751 0.3669725 1.00 0.2500000 0.4330127 0.3669725 1.00 0.5000000 0.5773503 0.3669725 1.00 0.7500000 0.7216878 0.3669725 1.00 0.0000000 0.5773503 0.3669725 1.00 0.2500000 0.7216878 0.3669725 1.00 0.5000000 0.8660254 0.3669725 1.00 0.7500000 1.0103630 0.3669725 1.00 0.0000000 0.8660254 0.3669725 1.00 0.2500000 1.0103630 0.3669725 1.00 0.5000000 1.1547005 0.3669725 1.00 0.7500000 1.2990381 0.3669725 1.00 K_POINTS { crystal } 64 0.0000000 0.0000000 0.0000000 1.00 0.1250000 0.0721688 0.0000000 1.00 0.2500000 0.1443376 0.0000000 1.00 0.3750000 0.2165064 0.0000000 1.00 0.5000000 0.2886751 0.0000000 1.00 0.6250000 0.3608439 0.0000000 1.00 0.7500000 0.4330127 0.0000000 1.00 0.8750000 0.5051815 0.0000000 1.00 0.0000000 0.1443376 0.0000000 1.00 0.1250000 0.2165064 0.0000000 1.00 0.2500000 0.2886751 0.0000000 1.00 0.3750000 0.3608439 0.0000000 1.00 0.5000000 0.4330127 0.0000000 1.00 0.6250000 0.5051815 0.0000000 1.00 0.7500000 0.5773503 0.0000000 1.00 0.8750000 0.6495191 0.0000000 1.00 0.0000000 0.2886751 0.0000000 1.00 0.1250000 0.3608439 0.0000000 1.00 0.2500000 0.4330127 0.0000000 1.00 0.3750000 0.5051815 0.0000000 1.00 0.5000000 0.5773503 0.0000000 1.00 0.6250000 0.6495191 0.0000000 1.00 0.7500000 0.7216878 0.0000000 1.00 0.8750000 0.7938566 0.0000000 1.00 0.0000000 0.4330127 0.0000000 1.00 0.1250000 0.5051815 0.0000000 1.00 0.2500000 0.5773503 0.0000000 1.00 0.3750000 0.6495191 0.0000000 1.00 0.5000000 0.7216878 0.0000000 1.00 0.6250000 0.7938566 0.0000000 1.00 0.7500000 0.8660254 0.0000000 1.00 0.8750000 0.9381942 0.0000000 1.00 0.0000000 0.5773503 0.0000000 1.00 0.1250000 0.6495191 0.0000000 1.00 0.2500000 0.7216878 0.0000000 1.00 0.3750000 0.7938566 0.0000000 1.00 0.5000000 0.8660254 0.0000000 1.00 0.6250000 0.9381942 0.0000000 1.00 0.7500000 1.0103630 0.0000000 1.00 0.8750000 1.0825318 0.0000000 1.00 0.0000000 0.7216878 0.0000000 1.00 0.1250000 0.7938566 0.0000000 1.00 0.2500000 0.8660254 0.0000000 1.00 0.3750000 0.9381942 0.0000000 1.00 0.5000000 1.0103630 0.0000000 1.00 0.6250000 1.0825318 0.0000000 1.00 0.7500000 1.1547005 0.0000000 1.00 0.8750000 1.2268693 0.0000000 1.00 0.0000000 0.8660254 0.0000000 1.00 0.1250000 0.9381942 0.0000000 1.00 0.2500000 1.0103630 0.0000000 1.00 0.3750000 1.0825318 0.0000000 1.00 0.5000000 1.1547005 0.0000000 1.00 0.6250000 1.2268693 0.0000000 1.00 0.7500000 1.2990381 0.0000000 1.00 0.8750000 1.3712069 0.0000000 1.00 0.0000000 1.0103630 0.0000000 1.00 0.1250000 1.0825318 0.0000000 1.00 0.2500000 1.1547005 0.0000000 1.00 0.3750000 1.2268693 0.0000000 1.00 0.5000000 1.2990381 0.0000000 1.00 0.6250000 1.3712069 0.0000000 1.00 0.7500000 1.4433757 0.0000000 1.00 0.8750000 1.5155445 0.0000000 1.00 Please let me know your the results of your tests, I would be curious to compare with mines. Giovanni > On 6 Mar 2009, at 18:15, Giovanni Cantele wrote: > > >> Dear all, >> >> I just finished some timing tests relative to QE, stimulated by recent >> discussions in this forum. >> I would like to share these tests, and ask a couple of simple (?) >> questions. >> >> Up to now, even if not supported by systematic tests, my feeling has >> been that >> for the kind of runs I'm doing on the kind of cluster(s) I'm using, >> the >> following rules hold: >> >> i) if using a relatively "small" number of CPUs, pools are rather >> ineffective, I often realized that >> using pools actually increased job execution time >> >> ii) diagonalization parallelism (-ndiag XX) is ineffective as well >> >> iii) version 3.2.3 is "better" than 4.0.4 >> >> > > ... > > ******************************************************* > Marino Vetuschi Zuccolini > zucco at dipteris.unige.it > Researcher / Geochemist > Laboratory of Geochemistry > > DIPartimento per lo studio della TErra e delle sue RISorse - > Universit? di Genova > Tel. ++39 010 3538136 Fax. ++39 010 352169 > Corso Europa 26, 16132 - Genova - Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From Giovanni.Cantele at na.infn.it Mon Mar 9 14:51:23 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Mon, 09 Mar 2009 14:51:23 +0100 Subject: [Pw_forum] timing vs QE version vs pools In-Reply-To: <49B51AC7.3060309@na.infn.it> References: <49B15A2E.8090804@na.infn.it> <49B51AC7.3060309@na.infn.it> Message-ID: <49B51EDB.2070605@na.infn.it> Giovanni Cantele wrote: > Marino Vetuschi Zuccolini wrote: > >> Dear Giovanni, >> I'm testing our system with more or less the same configuration. Can >> you send me the input you used in testing your cluster? >> >> Many thanks. >> >> m. >> >> > warning: k point list just for testing purposes (I just tried to get > those specific numbers > of k-points) > > > > Please let me know your the results of your tests, I would be curious to > compare with mines. > > Giovanni > sorry, due to too many blanks in the files, they are badly displayed in the e-mail I sent. I'm resending them again, in attachment, with blanks removed! Sorry for duplicating the message. Giovanni > > > >> On 6 Mar 2009, at 18:15, Giovanni Cantele wrote: >> >> >> >>> Dear all, >>> >>> I just finished some timing tests relative to QE, stimulated by recent >>> discussions in this forum. >>> I would like to share these tests, and ask a couple of simple (?) >>> questions. >>> >>> Up to now, even if not supported by systematic tests, my feeling has >>> been that >>> for the kind of runs I'm doing on the kind of cluster(s) I'm using, >>> the >>> following rules hold: >>> >>> i) if using a relatively "small" number of CPUs, pools are rather >>> ineffective, I often realized that >>> using pools actually increased job execution time >>> >>> ii) diagonalization parallelism (-ndiag XX) is ineffective as well >>> >>> iii) version 3.2.3 is "better" than 4.0.4 >>> >>> >>> >> ... >> >> ******************************************************* >> Marino Vetuschi Zuccolini >> zucco at dipteris.unige.it >> Researcher / Geochemist >> Laboratory of Geochemistry >> >> DIPartimento per lo studio della TErra e delle sue RISorse - >> Universit? di Genova >> Tel. ++39 010 3538136 Fax. ++39 010 352169 >> Corso Europa 26, 16132 - Genova - Italy >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> > > > -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: 1a--graphene_4x4_ecut40_ecutrho320_32kpt.scf.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20090309/55c869f0/attachment-0001.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: 1a--graphene_4x4_ecut40_ecutrho320_64kpt.scf.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20090309/55c869f0/attachment-0001.asc From tone.kokalj at ijs.si Mon Mar 9 14:53:30 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 09 Mar 2009 14:53:30 +0100 Subject: [Pw_forum] A method on defining a based-centered monoclinic cell In-Reply-To: <200903092031220473418@yahoo.cn> References: <200903071114082717592@yahoo.cn> <200903092031220473418@yahoo.cn> Message-ID: <1236606810.20040.10.camel@walk.ijs.si> On Mon, 2009-03-09 at 20:31 +0800, yinwei_li wrote: > Sorry, everyone, MS is Materials Studio modeling. > > In fact, I found many users, as well as me, have problems on the input defining a based-centered monoclinic cell. For example, a c2m structure with > a=11.692, b=2.159, c=3.463, beta=103.7, Notice that above you have an angle beta != 90, whereas in QE(quantum espresso) gamma != 90. Draw corresponding pictures of the two settings of the unit cell and you will undestand what you have to "swap". Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From zah7903 at gmail.com Mon Mar 9 15:02:14 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Mon, 9 Mar 2009 22:02:14 +0800 Subject: [Pw_forum] dipole moment calculation Message-ID: Dear all, I tried a test calculation of the dipole moment of water. The water molecule is put into a 20 a.u. ^3 box. The relevant setting are lelfield = .true. efield = 0.01 In the output file, it reports Electronic Dipole per cell (a.u.) -1.921145549061207 Ionic Dipole per cell (a.u.) 116.1997104738884 How is Electronic Dipole defined here? By looking into the source code, Ionic Dipole is defined as in textbook. I also notice that total energy difference with respect to zero-electric-field system is approximately equal to (Electronic Dipole + Ionic Dipole) * Efield. But Electronic Dipole hardly resembles the experimental dipole of water, which is about 1.85 D. Could anyone explain a bit about these quantities? Thank you!! Zhang -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090309/e0743fab/attachment.htm From Giovanni.Cantele at na.infn.it Mon Mar 9 15:19:38 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Mon, 09 Mar 2009 15:19:38 +0100 Subject: [Pw_forum] dipole moment calculation In-Reply-To: References: Message-ID: <49B5257A.9070902@na.infn.it> Aihua Zhang wrote: > Dear all, > > I tried a test calculation of the dipole moment of water. The water > molecule is put into a 20 a.u. ^3 box. The relevant setting are > > lelfield = .true. > efield = 0.01 > > In the output file, it reports > > Electronic Dipole per cell (a.u.) -1.921145549061207 > Ionic Dipole per cell (a.u.) 116.1997104738884 > > How is Electronic Dipole defined here? By looking into the source > code, Ionic Dipole is defined as in textbook. I also notice that total > energy difference with respect to zero-electric-field system is > approximately equal to (Electronic Dipole + Ionic Dipole) * Efield. > But Electronic Dipole hardly resembles the experimental dipole of > water, which is about 1.85 D. Could anyone explain a bit about these > quantities? Thank you!! > > Zhang > > Hi, I'm not very expert about this, however I tried to reproduce your job. I got: Computed dipoles : electron 0.00000 0.00000 -4.61164 ion 0.00000 0.00000 -3.87896 total 0.00000 0.00000 0.73268 Dipole field [a.u.]: 0.0012 As far as I understand total dipole moment = 0.73268 a.u. = 0.73268 * 25.417463 / 10 Debye = 1.86 Debye. I remember I found strange results in electric field calculations some time ago, and the problem was where the molecule is placed within the unit cell, but I'm not very sure (that was a couple of years ago!). The input I used is in attachment. Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: h2otest.4.scf.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20090309/d9a645aa/attachment.asc From giannozz at democritos.it Mon Mar 9 15:45:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 9 Mar 2009 15:45:10 +0100 Subject: [Pw_forum] ld1.x & US requires... In-Reply-To: <00a401c9a078$c224ef90$466eceb0$@net> References: <00a401c9a078$c224ef90$466eceb0$@net> Message-ID: On Mar 9, 2009, at 6:34 , Paul M. Grant wrote: > Why did I bother doing this exercise? Simply because dos.x > apparently arranges the notation for the projected pdos output > according to the sequence of states listed in the PP. For Cu, it > is 3d-4s, whereas for Ni, Co, Fe, and Mn, it is the reverse. > if this is the problem, you can reverse the positions of 3d and 4s atomic states in the pseudopotential file. Nothing bad should happen. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From zah7903 at gmail.com Mon Mar 9 16:39:56 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Mon, 9 Mar 2009 16:39:56 +0100 Subject: [Pw_forum] dipole moment calculation In-Reply-To: <49B5257A.9070902@na.infn.it> References: <49B5257A.9070902@na.infn.it> Message-ID: Dear Giovanni, Thank you for the reply! I have used lelfield option, and you used telfield. The documentation for telfield (saw_tooth potential) in input_pw.html seems different from README (modern theroy of polarizaiton) in example30. What's the difference between these two methods? You maybe should also pay attention to the units. I found at least in the subroutine related to lelfield they use Rydberge atomic units, that is, the unit for dipole is e/sqrt(2)*bohr_radius. In your arithemetic, the Hartree atomic units is used. Best regards Aihua On Mon, Mar 9, 2009 at 10:19 PM, Giovanni Cantele < Giovanni.Cantele at na.infn.it> wrote: > Aihua Zhang wrote: > >> Dear all, >> >> I tried a test calculation of the dipole moment of water. The water >> molecule is put into a 20 a.u. ^3 box. The relevant setting are >> >> lelfield = .true. >> efield = 0.01 >> >> In the output file, it reports >> >> Electronic Dipole per cell (a.u.) -1.921145549061207 >> Ionic Dipole per cell (a.u.) 116.1997104738884 >> >> How is Electronic Dipole defined here? By looking into the source code, >> Ionic Dipole is defined as in textbook. I also notice that total energy >> difference with respect to zero-electric-field system is approximately equal >> to (Electronic Dipole + Ionic Dipole) * Efield. But Electronic Dipole hardly >> resembles the experimental dipole of water, which is about 1.85 D. Could >> anyone explain a bit about these quantities? Thank you!! >> >> Zhang >> >> >> Hi, > > I'm not very expert about this, however I tried to reproduce your job. I > got: > Computed dipoles : electron 0.00000 > 0.00000 -4.61164 ion 0.00000 0.00000 -3.87896 > total 0.00000 0.00000 0.73268 Dipole field > [a.u.]: 0.0012 > > As far as I understand total dipole moment = 0.73268 a.u. = 0.73268 * > 25.417463 / 10 Debye = 1.86 Debye. > > I remember I found strange results in electric field calculations some time > ago, and the problem was where the > molecule is placed within the unit cell, but I'm not very sure (that was a > couple of years ago!). > The input I used is in attachment. > > Giovanni > > > -- > > > > Dr. Giovanni Cantele > Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario di Monte S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 > Fax: +39 081 676346 > E-mail: giovanni.cantele at cnr.it > giovanni.cantele at na.infn.it > Web: http://people.na.infn.it/~cantele > Research Group: http://www.nanomat.unina.it > > > &CONTROL > calculation='scf' > title='H2Otest' > verbosity='high' > restart_mode='from_scratch' > nstep=100 > iprint=1 > tprnfor=.true. > outdir='./tmp/' > prefix='H2Otest' > disk_io='default' > pseudo_dir='/home/cantele/WORK/CODES/Quantum-ESPRESSO/pseudo' > tefield=.true. > dipfield=.true. > / > &SYSTEM > ibrav=1 > celldm(1) = 20 > nat=3 > ntyp=2 > ecutwfc=30.0 > ecutrho=180.0 > occupations='smearing' > degauss=0.01 > edir=3 > eamp=0.D0 > eopreg=0.1 > emaxpos=0.5 > / > &ELECTRONS > / > ATOMIC_SPECIES > O 15.9994 O.pbe-rrkjus.UPF > H 1.00794 H.pbe-rrkjus.UPF > ATOMIC_POSITIONS { Angstrom } > O 0.0 0.0 0.0 > H 0.77 0.0 0.62 > H -0.77 0.0 0.62 > K_POINTS { gamma } > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090309/89d6df84/attachment.htm From vormar at gmail.com Tue Mar 10 00:03:25 2009 From: vormar at gmail.com (Marci) Date: Tue, 10 Mar 2009 00:03:25 +0100 Subject: [Pw_forum] wrong record length In-Reply-To: <49ACF6FB.3010207@democritos.it> References: <34ad5960903020842h5f7edffncbf9d253d18035d9@mail.gmail.com> <34ad5960903021205j77f7a279j205cbfd6cbd906a1@mail.gmail.com> <49ACF6FB.3010207@democritos.it> Message-ID: <34ad5960903091603u12506823xc3f8c3a750d60002@mail.gmail.com> Dear Axel, Lex and Paolo, Sorry for the late answer. Thanks again for all your help. If someone meets the same problem, here is the solution. Unfortunately the easiest way didn't work (just outcommenting the test for negative unf_recl) and declaring unf_recl as integer*8 didn't help either. However on this specific system with XL fortran compiler adding "-qintsize=8" to FFLAGS solved my problem. Yours, Marton 2009/3/3 Paolo Giannozzi : > Axel Kohlmeyer wrote: > >> the interesting question is now, how to work around this problem. >> you could try and declare unf_recl as integer*8 and try to recompile. > > once upon a time there were limitations on the maximum length of > direct access records on some machines. I remember I modified the > two routines that open and read/write in such a way that each > record was split into more records with the maximum allowed > length. Anyway, for very big jobs, integers that don't fit > into 32 bits will show up somewhere else, so the ultimate > solution is to compile with default 64-bit integers, I guess > > Paolo > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From yinwei_li at yahoo.cn Tue Mar 10 02:19:49 2009 From: yinwei_li at yahoo.cn (yinwei_li) Date: Tue, 10 Mar 2009 09:19:49 +0800 Subject: [Pw_forum] A method on defining a based-centered monoclinic cell References: <200903071114082717592@yahoo.cn>, <200903092031220473418@yahoo.cn> Message-ID: <200903100919466681923@yahoo.cn> > a=11.692, b=2.159, c=3.463, beta=103.7, >Notice that above you have an angle beta != 90, whereas in >QE(quantum espresso) gamma != 90. Draw corresponding pictures of the two >settings of the unit cell and you will undestand what you have to >"swap". I have tested in this case. with the right-hand screw rule, the lattice could be changed to: a=3.463, b=11.692, c=2.159, gamma=103.7, the atomic positions in the unit cell was changed too. however, during the transformation to the primitive cell in the Materials Studio, it will give a same atomic positions and lattice parameters (of the primitive cell) with the old one. therefore, I still could not get a correct structure in this way. Maybe this is because of the Materials Studio, which is not a best tool to generate the input information for PWSCF. So I want to know what tools you use to generate the input information such as atomic positions? 2009-03-10 *************************************** Yinwei Li ????? PHD State Key Lab of Superhard Materials, Jilin University 2699 Qianjin Str. 130012, Changchun P. R. China ******************************************** ???? Tone Kokalj ????? 2009-03-09 21:53:32 ???? PWSCF Forum ??? ??? Re: [Pw_forum] A method on defining a based-centered monoclinic cell On Mon, 2009-03-09 at 20:31 +0800, yinwei_li wrote: > Sorry, everyone, MS is Materials Studio modeling. > > In fact, I found many users, as well as me, have problems on the input defining a based-centered monoclinic cell. For example, a c2m structure with > a=11.692, b=2.159, c=3.463, beta=103.7, Notice that above you have an angle beta != 90, whereas in QE(quantum espresso) gamma != 90. Draw corresponding pictures of the two settings of the unit cell and you will undestand what you have to "swap". Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum __________ Information from ESET Smart Security, version of virus signature database 3922 (20090309) __________ The message was checked by ESET Smart Security. http://www.eset.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090310/feaf4ce1/attachment-0001.htm From jtmullen at ncsu.edu Tue Mar 10 01:34:01 2009 From: jtmullen at ncsu.edu (Jeffrey Mullen) Date: Mon, 09 Mar 2009 20:34:01 -0400 Subject: [Pw_forum] Phonon branch enumeration Message-ID: <49B5B579.9060409@ncsu.edu> Greetings I am testing electron-phonon interaction calculations with graphene and have encountered a problem enumerating the resulting phonon branches. When I run the ph.x calculation at the q(0 0 0), the code calculates 4 representations: Representation # 1 modes # 1 2 Representation # 2 mode # 3 Representation # 3 mode # 4 Representation # 4 modes # 5 6 When the values for omega are calculated, the results are: ************************************************************************** omega( 1) = -1.119851 [THz] = -37.354451 [cm-1] omega( 2) = -1.016557 [THz] = -33.908905 [cm-1] omega( 3) = -1.016557 [THz] = -33.908905 [cm-1] omega( 4) = 25.882237 [THz] = 863.344237 [cm-1] omega( 5) = 40.051667 [THz] = 1335.988701 [cm-1] omega( 6) = 40.051667 [THz] = 1335.988701 [cm-1] ************************************************************************** with the following mode symmetries: Mode symmetry, D_6h(6/mmm) point group: omega( 1 - 1) = -37.4 [cm-1] --> A_2u I omega( 2 - 3) = -33.9 [cm-1] --> E_1u I omega( 4 - 4) = 863.3 [cm-1] --> B_2g omega( 5 - 6) = 1336.0 [cm-1] --> E_2g R My question is one of ordering. How do I extract which omega(##) corresponds to which representation/mode? Thanks Jeff Mullen North Carolina State University From hqzhou at nju.edu.cn Tue Mar 10 08:11:01 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Tue, 10 Mar 2009 15:11:01 +0800 Subject: [Pw_forum] Use of pool References: <21B74D1AD49648479BDC1ABD309ED183@solarflare> <7b6913e90903031851p482b7709ob4db1878a17711dc@mail.gmail.com> Message-ID: <49D90B1336264598A78A78A5D9C1D449@solarflare> Axel and list-users, I'm terribly sorry for my delayed response. I personally want to thank Axel for his thorough investigation, to-the-point analysis and detailed report, every bit of experience will benefit us a lot in our future life in computation. As I said, the test maching I used is an AMD box with 2 way quad core Shanghai (opteron 23xx, 2.3 GHz) , which has only 1 MB L2 cache, the test case may make the CPU cache inefficient more quickly than Intel ones (usually 4-6 MB L2 cache) according to your findings. BTW, the input file I sent you is absolutely the same as I used here. AMD's shanghai and Intel's nehalem, which I have done several tests on both platforms, are much better than their previous processors. It seems Axel needs to connect more powerful machines with his high-end infiniBand network(^o^) Thanks again, Axel! Dr. Huiqun Zhou @Earth Sciences, Nanjing University, China ----- Original Message ----- From: "Axel Kohlmeyer" To: "PWSCF Forum" Sent: Wednesday, March 04, 2009 10:51 AM Subject: Re: [Pw_forum] Use of pool > On Tue, Feb 24, 2009 at 1:45 AM, Huiqun Zhou wrote: >> Dear list users: > > hi all, > >> I happened to test duration times of calculating the system I'm >> investigating against number of pools used. There are totally >> 36 k points. But the results surprised me quite a lot. >> >> no pool: 6m21.02s CPU time, 6m45.88s wall time >> 2 pools: 7m19.39s CPU time, 7m38.99s wall time >> 4 pools: 11m59.09s CPU time, 12m14.66s wall time >> 8 pools: 21m28.77s CPU time, 21m38.71s wall time >> >> The machine I'm using is an AMD box with 2 quad core shanghai. >> >> Is my understanding of usage of pool wrong? > > sorry for replying to an old mail in this thread, but it has the > proper times to compare to. the input you sent me, does not > seem to be the exactly the same as the one you used for the > benchmarks (rather a bit larger). but i reduced the number of > k-points to yield 36 and have some numbers here. > this is on dual intel quad core E5430 @ 2.66GHz cpus with 8GB DDR2 ram. > i also modified the input to set wfcdir to use the local scratch rather > than my > working directory (as this is on an NFS server) and test with > disk_io='high' and 'low'. > on a single node (always with 8 MPI tasks) i get: > > 1node-1pools-high.out: PWSCF : 18m55.62s CPU time, 26m > 7.20s wall time > 1node-2pools-high.out: PWSCF : 14m46.03s CPU time, 18m > 0.26s wall time > 1node-4pools-high.out: PWSCF : 14m 5.27s CPU time, > 16m44.03s wall time > 1node-8pools-high.out: PWSCF : 32m29.71s CPU time, 35m > 0.35s wall time > > 1node-1pools-low.out: PWSCF : 18m36.88s CPU time, > 19m24.71s wall time > 1node-2pools-low.out: PWSCF : 15m 0.98s CPU time, > 15m42.56s wall time > 1node-4pools-low.out: PWSCF : 14m 6.97s CPU time, > 14m55.57s wall time > 1node-8pools-low.out: PWSCF : 31m51.68s CPU time, > 32m46.77s wall time > > so the result is not quite as drastic, but with 8 pools on the node, > the machine is suffering. > one can also see that disk_io='low' is helping to reduce waiting time > (disk_io='high' still > writes files into the working directory, which is on slow NFS). so for > my machine it looks > as if 4 pools is the optimal compromise. to further investigate > whether pools or gspace > parallelization is more efficient i then started to run the same job > across multiple nodes. > this uses only 4 cores per node, i.e. the total number of mpi tasks is > still 8. > > 2node-1pools-high.out: PWSCF : 12m 0.88s CPU time, > 17m42.01s wall time > 2node-2pools-high.out: PWSCF : 8m42.96s CPU time, > 11m44.88s wall time > 2node-4pools-high.out: PWSCF : 6m26.72s CPU time, > 8m54.83s wall time > 2node-8pools-high.out: PWSCF : 12m47.61s CPU time, > 15m18.67s wall time > > 2node-1pools-low.out: PWSCF : 10m53.87s CPU time, > 11m35.94s wall time > 2node-2pools-low.out: PWSCF : 8m37.37s CPU time, > 9m23.17s wall time > 2node-4pools-low.out: PWSCF : 6m22.87s CPU time, > 7m11.22s wall time > 2node-8pools-low.out: PWSCF : 13m 7.30s CPU time, > 13m57.71s wall time > > in the next test, i doubled the number of nodes again, but this time > kept 4 mpi tasks per node, > also i'm only using disk_io='low'. > > 4node-4pools-low.out: PWSCF : 4m52.92s CPU time, > 5m38.90s wall time > 4node-8pools-low.out: PWSCF : 4m29.73s CPU time, > 5m17.86s wall time > > interesting, now the striking difference between 4 pools and 8 pools > is gone. since i > doubled the number of nodes, the memory consumption per mpi task in the 8 > pools > case should have dropped to a similar level as in the 4 pools case with 2 > nodes. > to confirm this, lets run the same job with 16 pools: > > 4node-16pools-low.out: PWSCF : 10m54.57s CPU time, > 11m53.59s wall time > > bingo! the only explanation for this is cache memory. so in this specific > case, > up to about "half a wavefunction" memory consumption per node, the caching > of the cpu is much more effective. so the "more pools is better"-rule has > to be > augmented by "unless it makes the cpu cache less efficient". > > since 36 kpoints is wholly divisible by 6 but not by 8, now a test > with 6 nodes. > > 6node-4pools-low.out: PWSCF : 3m41.65s CPU time, > 4m25.15s wall time > 6node-6pools-low.out: PWSCF : 3m40.12s CPU time, > 4m23.33s wall time > 6node-8pools-low.out: PWSCF : 3m14.13s CPU time, > 3m57.76s wall time > 6node-12pools-low.out: PWSCF : 3m37.96s CPU time, > 4m25.91s wall time > 6node-24pools-low.out: PWSCF : 10m55.18s CPU time, > 11m47.87s wall time > > so 6 pools is more efficient than 4, but 8 even more than 6 or 12, > which should lead to > a better distribution of the work. so the modified "rule" from above > seems to hold. > ok, can we get any faster. ~4min walltime for a 21 scf cycle single > point run is already pretty > good and the serial overhead (and wf_collect=.true.) should kick in. > so now with 8 nodes > and 32 mpi tasks. > > 8node-4pools-low.out: PWSCF : 3m22.02s CPU time, 4m > 7.06s wall time > 8node-8pools-low.out: PWSCF : 3m14.52s CPU time, > 3m58.86s wall time > 8node-16pools-low.out: PWSCF : 3m36.18s CPU time, > 4m24.21s wall time > > hmmm, not much better, but now for the final test. since we have 36 > k-points and > we need at least two mpi tasks per pool to get good performance, lets > try 18 nodes > with 4 mpi tasks each: > > 18node-9pools-low.out: PWSCF : 1m57.06s CPU time, > 3m37.31s wall time > 18node-18pools-low.out: PWSCF : 2m 2.62s CPU time, > 2m45.51s wall time > 18node-36pools-low.out: PWSCF : 2m45.61s CPU time, > 3m33.00s wall time > > not spectacular scaling, but still improving. but it looks like > writing the final wavefunction > costs about 45 seconds or more, as indicated by the difference between > cpu and walltime. > > at this level, you better not use disk_io='high', as that will put a > _severe_ disk load on > the machine that is carrying the working directory (particularly bad > for NFS servers), > the code will generate and continuously rewrite in this case 144 files... > and the walltime to cputime ratio quickly rises (a factor of 5 in my > case so i stopped the > job before the NFS server would die). > > in summary, it is obviously getting more complicated to define a > "rule" of what gives > the best performance. some experimentation is always required and > sometimes there > will be surprises. i have not touched the issue of network speed (all > tests were done > across a 4xDDR infiniband network). > > i hope this little benchmark excursion was as interesting and thought > provoking for you > as it was for me. thanks for everybody that gave their input to this > discussion. > > cheers, > axel. > > p.s.: perhaps at some point it might be interesting to organize a workshop > on > "post-compilation optimization" for pw.x for different types of jobs > and hardware. > >> Huiqun Zhou >> @Nanjing University, China >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From hqzhou at nju.edu.cn Tue Mar 10 08:35:39 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Tue, 10 Mar 2009 15:35:39 +0800 Subject: [Pw_forum] question about electron phonon calculation References: <49B4DBB7.7070800@sissa.it> Message-ID: Gabriele, Sorry for my ignorance of developer's fast tempo. I asked a question about q-point parallization in using ph.x nearly one year ago, and got the following answer: http://www.democritos.it/pipermail/pw_forum/2008-April/008667.html It seems things change faster. Thnaks for the effort. Huiqun Zhou ----- Original Message ----- From: "Gabriele Sclauzero" To: "PWSCF Forum" Sent: Monday, March 09, 2009 5:04 PM Subject: Re: [Pw_forum] question about electron phonon calculation > > hqzhou wrote: >> It simply means that using pools in phonon calculation is meaningless. > > Why do you say this? Phonon calculations with pools parallelization is > implemented and > works properly! Why should it be meaningless? > > The error message report you were refering to: > > from elphsum : error # 1 > > pools and a2F not implemented > > does not come from a phonon calculation (which can be done using pools), > but from an > electron-phonon coupling calculation, which has not yet been parallelized > with pools > (while distributed FFT parallelization should be already working). > > GS > >> But it may not be the main cause of your error. >> >> Dr. Huiqun Zhou >> @Earth Sciences, Nanjing University, China >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Tue Mar 10 08:53:45 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 10 Mar 2009 08:53:45 +0100 Subject: [Pw_forum] question about electron phonon calculation In-Reply-To: References: <49B4DBB7.7070800@sissa.it> Message-ID: <49B61C89.4010402@sissa.it> Huiqun Zhou wrote: > Gabriele, > > Sorry for my ignorance of developer's fast tempo. I asked a question about > q-point parallization in using ph.x nearly one year ago, and got the > following > answer: > > http://www.democritos.it/pipermail/pw_forum/2008-April/008667.html > > It seems things change faster. Thnaks for the effort. OK, wait, there is maybe a misunderstanding here: k-point parallelization (the one which is often refered to as "pools parallelization" and can be enabled by the -npool flag) is different thing from q-point parallelization of phonon dispersion calculations. The former is the analogous to the pools parallelization of total energy calculations with pw.x and is available since long time ago, while the latter has been added only recently to the phonon code. It is available in the 4.1-CVS version and is enabled through the keywords start_q, last_q (see INPUT_PH). GS > > Huiqun Zhou > > > ----- Original Message ----- > From: "Gabriele Sclauzero" > To: "PWSCF Forum" > Sent: Monday, March 09, 2009 5:04 PM > Subject: Re: [Pw_forum] question about electron phonon calculation > > >> hqzhou wrote: >>> It simply means that using pools in phonon calculation is meaningless. >> Why do you say this? Phonon calculations with pools parallelization is >> implemented and >> works properly! Why should it be meaningless? >> >> The error message report you were refering to: >> >> from elphsum : error # 1 >> >> pools and a2F not implemented >> >> does not come from a phonon calculation (which can be done using pools), >> but from an >> electron-phonon coupling calculation, which has not yet been parallelized >> with pools >> (while distributed FFT parallelization should be already working). >> >> GS >> >>> But it may not be the main cause of your error. >>> >>> Dr. Huiqun Zhou >>> @Earth Sciences, Nanjing University, China >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From eminekb at yahoo.com Tue Mar 10 08:57:30 2009 From: eminekb at yahoo.com (e kb) Date: Tue, 10 Mar 2009 00:57:30 -0700 (PDT) Subject: [Pw_forum] Phonon branch enumeration In-Reply-To: <49B5B579.9060409@ncsu.edu> Message-ID: <301039.19318.qm@web34802.mail.mud.yahoo.com> Dear Jeff, I am definitely not an expert on the topic but I'd like to understand your question better. Mode symmetry, D_6h(6/mmm) point group: omega( 1 - 1) = -37.4 [cm-1] --> A_2u I omega( 2 - 3) = -33.9 [cm-1] --> E_1u I omega( 4 - 4) = 863.3 [cm-1] --> B_2g omega( 5 - 6) = 1336.0 [cm-1] --> E_2gSo you have the irr. representations and the values for omega (values are printed with higher precision in the previous part after diagonalization as you reported). What exactly do you want to know more (that you cannot check from a book on group theory) ? Emine Kucukbenli, grad. student, SISSA, Italy. --- On Tue, 3/10/09, Jeffrey Mullen wrote: From: Jeffrey Mullen Subject: [Pw_forum] Phonon branch enumeration To: pw_forum at pwscf.org Date: Tuesday, March 10, 2009, 2:34 AM Greetings I am testing electron-phonon interaction calculations with graphene and have encountered a problem enumerating the resulting phonon branches. When I run the ph.x calculation at the q(0 0 0), the code calculates 4 representations: Representation # 1 modes # 1 2 Representation # 2 mode # 3 Representation # 3 mode # 4 Representation # 4 modes # 5 6 When the values for omega are calculated, the results are: ************************************************************************** omega( 1) = -1.119851 [THz] = -37.354451 [cm-1] omega( 2) = -1.016557 [THz] = -33.908905 [cm-1] omega( 3) = -1.016557 [THz] = -33.908905 [cm-1] omega( 4) = 25.882237 [THz] = 863.344237 [cm-1] omega( 5) = 40.051667 [THz] = 1335.988701 [cm-1] omega( 6) = 40.051667 [THz] = 1335.988701 [cm-1] ************************************************************************** with the following mode symmetries: Mode symmetry, D_6h(6/mmm) point group: omega( 1 - 1) = -37.4 [cm-1] --> A_2u I omega( 2 - 3) = -33.9 [cm-1] --> E_1u I omega( 4 - 4) = 863.3 [cm-1] --> B_2g omega( 5 - 6) = 1336.0 [cm-1] --> E_2g R My question is one of ordering. How do I extract which omega(##) corresponds to which representation/mode? Thanks Jeff Mullen North Carolina State University _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090310/c91b86da/attachment.htm From mjfmartins at ice.ufjf.br Tue Mar 10 11:24:11 2009 From: mjfmartins at ice.ufjf.br (=?ISO-8859-1?Q?MATEUS_JOS=C9_FERNANDES_MARTINS?=) Date: Tue, 10 Mar 2009 07:24:11 -0300 Subject: [Pw_forum] Problem with dynamical matrix file. In-Reply-To: <85d7d5fd0903061857p776fe549hb980030fb24c5b90@mail.gmail.com> References: <85d7d5fd0903060759o4f947c06w5e7af5497adfba0d@mail.gmail.com> <85d7d5fd0903061857p776fe549hb980030fb24c5b90@mail.gmail.com> Message-ID: <85d7d5fd0903100324o2e78eb24k22e264483f17ac12@mail.gmail.com> Hello Paolo, I suspected that. But I did a test with a system less and with variable nat_todo enabled. Really, he does not write the frequencies in the output of ph.x, but the output of the frequency dynmat.x writes. Only for this calculation that the error is appearing. Mateus. > > > 2009/3/7 Paolo Giannozzi > > >> On Mar 6, 2009, at 16:59 , MATEUS JOS? FERNANDES MARTINS wrote: >> >> > I run a phonon calculation with the nat_todo variable enable. The >> > problem >> > is that when I run the application dynmat.x the following error >> > appears >> > [...] >> > from readmat : error # 1 >> > mismatch in reading file >> >> I am not sure that the dynmat.x utility is supposed to work in that case >> (i.e. when the nat_todo variable is enabled) >> >> Paolo >> --- >> Paolo Giannozzi, Democritos and University of Udine, Italy >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090310/89295037/attachment.htm From jtmullen at ncsu.edu Tue Mar 10 12:13:58 2009 From: jtmullen at ncsu.edu (Jeffrey Mullen) Date: Tue, 10 Mar 2009 07:13:58 -0400 Subject: [Pw_forum] Phonon branch enumeration In-Reply-To: <301039.19318.qm@web34802.mail.mud.yahoo.com> References: <301039.19318.qm@web34802.mail.mud.yahoo.com> Message-ID: <49B64B76.3080208@ncsu.edu> Emine, I am interested in extracting the matrix elements of the interaction from elphon.f90, which is simple enough to do, however, the question has come up that we do not know from this portion of the code what the order of the modes are in this array in a general way. For instance, I cannot see (from the code) if omega(2-3) is Representation 1 or Representation 4. Cheers Jeff e kb wrote: > Dear Jeff, > I am definitely not an expert on the topic but I'd like to understand > your question better. > > Mode symmetry, D_6h(6/mmm) point group: > > omega( 1 - 1) = -37.4 [cm-1] --> A_2u I > omega( 2 - 3) = -33.9 [cm-1] --> E_1u I > omega( 4 - 4) = 863.3 [cm-1] --> B_2g > omega( 5 - 6) = 1336.0 [cm-1] --> E_2g > > So you have the irr. representations and the values for omega (values > are printed with higher precision in the previous part after > diagonalization as you reported). What exactly do you want to know > more (that you cannot check from a book on group theory) ? > > Emine Kucukbenli, grad. student, SISSA, Italy. > > --- On *Tue, 3/10/09, Jeffrey Mullen //* wrote: > > From: Jeffrey Mullen > Subject: [Pw_forum] Phonon branch enumeration > To: pw_forum at pwscf.org > Date: Tuesday, March 10, 2009, 2:34 AM > >Greetings > >I am testing electron-phonon interaction calculations with graphene and >have encountered a problem enumerating the resulting phonon branches. >When I run the ph.x calculation at the q(0 0 0), the code calculates 4 >representations: > > Representation # 1 modes # 1 2 > Representation # 2 mode # 3 > Representation # 3 mode # 4 > Representation # 4 modes # 5 6 > > >When the values for omega are calculated, the results are: > > ************************************************************************** > omega( 1) = -1.119851 [THz] = -37.354451 [cm-1] > omega( 2) = -1.016557 [THz] = -33.908905 > [cm-1] > omega( 3) = -1.016557 [THz] = -33.908905 [cm-1] > omega( 4) = 25.882237 [THz] = 863.344237 [cm-1] > omega( 5) = 40.051667 [THz] = 1335.988701 [cm-1] > omega( 6) = 40.051667 [THz] = 1335.988701 [cm-1] > ************************************************************************** > > >with the following mode symmetries: > > Mode symmetry, D_6h(6/mmm) point group: > > omega( 1 - 1) = -37.4 [cm-1] --> A_2u I > omega( 2 - 3) = -33.9 [cm-1] --> E_1u I > omega( 4 - 4) = 863.3 [cm-1] --> B_2g > omega( 5 - 6) = 1336.0 [cm-1] --> E_2g R > > >My question is one of ordering. How do I extract which omega(##) >corresponds to which representation/mode? > >Thanks >Jeff Mullen >North Carolina State > University > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > > >------------------------------------------------------------------------ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at democritos.it Tue Mar 10 12:38:14 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 10 Mar 2009 12:38:14 +0100 Subject: [Pw_forum] Phonon branch enumeration In-Reply-To: <49B64B76.3080208@ncsu.edu> References: <301039.19318.qm@web34802.mail.mud.yahoo.com> <49B64B76.3080208@ncsu.edu> Message-ID: <49B65126.7090205@democritos.it> Jeffrey Mullen wrote: > I cannot see (from the code) if omega(2-3) is Representation 1 > or Representation 4. none of the above: it is a combination of the two P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From dalcorso at sissa.it Tue Mar 10 14:53:27 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Tue, 10 Mar 2009 14:53:27 +0100 Subject: [Pw_forum] Phonon branch enumeration In-Reply-To: <49B64B76.3080208@ncsu.edu> References: <301039.19318.qm@web34802.mail.mud.yahoo.com> <49B64B76.3080208@ncsu.edu> Message-ID: <1236693207.3257.31.camel@dhpc-5-20.sissa.it> On Tue, 2009-03-10 at 07:13 -0400, Jeffrey Mullen wrote: > Emine, > > I am interested in extracting the matrix elements of the interaction > from elphon.f90, which is simple enough to do, however, > the question has come up that we do not know from this portion of the > code what the order of the modes are in this array in a general way. For > instance, I cannot see (from the code) if omega(2-3) is Representation 1 > or Representation 4. > It is an interesting idea. I think it is possible to make the symmetry classification of the displacements patterns with the same routine that makes the symmetry classification of the eigenvectors of the dynamical matrix. Presently, this is not done. You can code this feature yourself or just use iverbosity=1. With this option the code writes the displacement patterns and you can check their symmetry. Andrea > > Cheers > Jeff > > > > e kb wrote: > > > Dear Jeff, > > I am definitely not an expert on the topic but I'd like to understand > > your question better. > > > > Mode symmetry, D_6h(6/mmm) point group: > > > > omega( 1 - 1) = -37.4 [cm-1] --> A_2u I > > omega( 2 - 3) = -33.9 [cm-1] --> E_1u I > > omega( 4 - 4) = 863.3 [cm-1] --> B_2g > > omega( 5 - 6) = 1336.0 [cm-1] --> E_2g > > > > So you have the irr. representations and the values for omega (values > > are printed with higher precision in the previous part after > > diagonalization as you reported). What exactly do you want to know > > more (that you cannot check from a book on group theory) ? > > > > Emine Kucukbenli, grad. student, SISSA, Italy. > > > > --- On *Tue, 3/10/09, Jeffrey Mullen //* wrote: > > > > From: Jeffrey Mullen > > Subject: [Pw_forum] Phonon branch enumeration > > To: pw_forum at pwscf.org > > Date: Tuesday, March 10, 2009, 2:34 AM > > > >Greetings > > > >I am testing electron-phonon interaction calculations with graphene and > >have encountered a problem enumerating the resulting phonon branches. > >When I run the ph.x calculation at the q(0 0 0), the code calculates 4 > >representations: > > > > Representation # 1 modes # 1 2 > > Representation # 2 mode # 3 > > Representation # 3 mode # 4 > > Representation # 4 modes # 5 6 > > > > > >When the values for omega are calculated, the results are: > > > > ************************************************************************** > > omega( 1) = -1.119851 [THz] = -37.354451 [cm-1] > > omega( 2) = -1.016557 [THz] = -33.908905 > > [cm-1] > > omega( 3) = -1.016557 [THz] = -33.908905 [cm-1] > > omega( 4) = 25.882237 [THz] = 863.344237 [cm-1] > > omega( 5) = 40.051667 [THz] = 1335.988701 [cm-1] > > omega( 6) = 40.051667 [THz] = 1335.988701 [cm-1] > > ************************************************************************** > > > > > >with the following mode symmetries: > > > > Mode symmetry, D_6h(6/mmm) point group: > > > > omega( 1 - 1) = -37.4 [cm-1] --> A_2u I > > omega( 2 - 3) = -33.9 [cm-1] --> E_1u I > > omega( 4 - 4) = 863.3 [cm-1] --> B_2g > > omega( 5 - 6) = 1336.0 [cm-1] --> E_2g R > > > > > >My question is one of ordering. How do I extract which omega(##) > >corresponds to which representation/mode? > > > >Thanks > >Jeff Mullen > >North Carolina State > > University > > > >_______________________________________________ > >Pw_forum mailing list > >Pw_forum at pwscf.org > >http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Pw_forum mailing list > >Pw_forum at pwscf.org > >http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From Giovanni.Cantele at na.infn.it Tue Mar 10 15:50:59 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Tue, 10 Mar 2009 15:50:59 +0100 Subject: [Pw_forum] dipole moment calculation In-Reply-To: References: <49B5257A.9070902@na.infn.it> Message-ID: <49B67E53.8010407@na.infn.it> Aihua Zhang wrote: > Dear Giovanni, > > Thank you for the reply! I have used lelfield option, and you used > telfield. The documentation for telfield (saw_tooth potential) in > input_pw.html seems different from README (modern theroy of > polarizaiton) in example30. What's the difference between these two > methods? Dear Aihua, one answer is here: http://www.democritos.it/pipermail/pw_forum/2008-July/009409.html I tried to explore some features of the code in the past, and tried to make some test runs on the H2O molecule. There should be many possibilities, for polarization calculations, within QE. One point is that you can make polarization calculation both without and in presence of an external electric field. If you want just to test the spontaneous polarization, rather than the electric-field induced polarization, you don't need to turn on any electric field. Now, due to the fact that QE contains several executables (pw.x / cp.x) with several options (add a saw-tooth electric potential, Berry phase calculation with or without electric field), one (who, just as me, is not very familiar with those options and related issues) might get confused. What I tried to do is (the convergence of all the reported results has *NOT* been checked): i) pw.x calc. with tefield=.true. (check the spelling, tefield not telfield) this is what I reported in the previous e-mail, the result is here: Computed dipoles : electron 0.00000 0.00000 -4.61164 ion 0.00000 0.00000 -3.87896 total 0.00000 0.00000 0.73268 Please notice that in my input the electric field amplitude is zero. ii) pw.x with lberry=.true. my result is here: P = 0.7479015 (mod 20.0000000) (e/Omega).bohr In this case, I think, you don't need to turn on the lelfield=.true. option, because the dipole moment is computed even if lelfield=.false. iii) cp.x with tefield=.true. In this case that variable assumes a different meaning wrt pw.x, because a homogeneous electric field of amplitude efield is added, and the polarization computed using a Berry phase approach. I tried to run example30 re-adapted to the water molecule and got Elct. dipole 1 -1.572721 Ionic dipole 1 2.343260 the sum is 0.770539, which seems to agree with the pw.x result (with tefield=.true.) of 0.73268. I also tried to put the molecule in the middle (instead of at the corner) of the unit cell, but results were unchanged (Elct. dipole 1 2.838308 Ionic dipole 1 -2.067694, sum: 0.770614) You are maybe right in the fact that the documentation for tefield (saw_tooth potential) in input_pw.html seems different from README (modern theory of polarization) in example30, because example30 uses cp.x whose documentation is in Doc/INPUT_CP. If I well understand, using tefield=.true. within cp.x should be (at least regarding the theoretical framework) the same as using lberry=.true. and lelfield=.true. within pw.x. > You maybe should also pay attention to the units. I found at least in > the subroutine related to lelfield they use Rydberge atomic units, > that is, the unit for dipole is e/sqrt(2)*bohr_radius. In your > arithemetic, the Hartree atomic units is used. Well, I think that Hartree au are assumed for the dipole moment, then they are properly converted to Ry atomic units when needed. Just have a look to compute_dip.f90. The ionic dipole is computed as: DO na=1,nat DO ipol=1,3 dipol_ion(ipol)=dipol_ion(ipol)+zv(ityp(na))*(tau(ipol,na)+x0(ipol))*alat ENDDO ENDDO so distances are in Bohr (tau, x0 in units of celldm(1)=alat, alat in bohr), charges in units of e (zv is tha valence of each pesudo-ion). Same for electrons, because in that case the charge density is accounted for through rrho(ir), which again is in units of e. Then when computing the potential amplitude associated to the electric field/dipole moment (add_efield.f90) you get: ! ! The electric field is assumed in a.u.( 1 a.u. of field changes the ! potential energy of an electron of 1 Hartree in a distance of 1 Bohr. ! The factor 2 converts potential energy to Ry. ! NB: dip is the dipole moment per unit area divided by length and ! multiplied by four pi ! vamp=2.0d0*(eamp-dip)*length*REAL(npoints-ndesc,dp)& /REAL(npoints,dp) where vamp is the potential amplitude, this time in Ry. The only place in which it seems that Ry au are used instead, is pw.x with lberry=.true. and lelfield=.true., because this uses the routines in c_phase_field.f90, where I see, for example: !factor sqrt(2) is the electronic charge in Rydberg units pola_ion=0.d0 DO na=1,nat pola_ion=pola_ion+zv(ityp(na))*tau(gdir,na)*alat*dsqrt(2.d0) END DO I'm grateful to anyone more familiar with those parts of the code pointing out anything (or everything!) wrong in what I wrote here!!! Giovanni > Best regards > > Aihua > > On Mon, Mar 9, 2009 at 10:19 PM, Giovanni Cantele > > wrote: > > Aihua Zhang wrote: > > Dear all, > > I tried a test calculation of the dipole moment of water. The > water molecule is put into a 20 a.u. ^3 box. The relevant > setting are > > lelfield = .true. > efield = 0.01 > > In the output file, it reports > > Electronic Dipole per cell (a.u.) -1.921145549061207 > Ionic Dipole per cell (a.u.) 116.1997104738884 > > How is Electronic Dipole defined here? By looking into the > source code, Ionic Dipole is defined as in textbook. I also > notice that total energy difference with respect to > zero-electric-field system is approximately equal to > (Electronic Dipole + Ionic Dipole) * Efield. But Electronic > Dipole hardly resembles the experimental dipole of water, > which is about 1.85 D. Could anyone explain a bit about these > quantities? Thank you!! > > Zhang > > > Hi, > > I'm not very expert about this, however I tried to reproduce your > job. I got: > Computed dipoles : electron > 0.00000 0.00000 -4.61164 ion 0.00000 > 0.00000 -3.87896 total 0.00000 0.00000 > 0.73268 Dipole field [a.u.]: 0.0012 > > As far as I understand total dipole moment = 0.73268 a.u. = > 0.73268 * 25.417463 / 10 Debye = 1.86 Debye. > > I remember I found strange results in electric field calculations > some time ago, and the problem was where the > molecule is placed within the unit cell, but I'm not very sure > (that was a couple of years ago!). > The input I used is in attachment. > > Giovanni > > > -- > > > > Dr. Giovanni Cantele > Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario di Monte S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 > Fax: +39 081 676346 > E-mail: giovanni.cantele at cnr.it > giovanni.cantele at na.infn.it > Web: http://people.na.infn.it/~cantele > > Research Group: http://www.nanomat.unina.it > > > &CONTROL > calculation='scf' > title='H2Otest' > verbosity='high' > restart_mode='from_scratch' > nstep=100 > iprint=1 > tprnfor=.true. > outdir='./tmp/' > prefix='H2Otest' > disk_io='default' > pseudo_dir='/home/cantele/WORK/CODES/Quantum-ESPRESSO/pseudo' > tefield=.true. > dipfield=.true. > / > &SYSTEM > ibrav=1 > celldm(1) = 20 > nat=3 > ntyp=2 > ecutwfc=30.0 > ecutrho=180.0 > occupations='smearing' > degauss=0.01 > edir=3 > eamp=0.D0 > eopreg=0.1 > emaxpos=0.5 > / > &ELECTRONS > / > ATOMIC_SPECIES > O 15.9994 O.pbe-rrkjus.UPF > H 1.00794 H.pbe-rrkjus.UPF > ATOMIC_POSITIONS { Angstrom } > O 0.0 0.0 0.0 > H 0.77 0.0 0.62 > H -0.77 0.0 0.62 > K_POINTS { gamma } > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > ------------------------------------------------------------------ > Research Fellow, > Dept. of Physics, National Univ. of Singapore > 10 Kent Ridge Crescent, Singapore, 119260 > Tel: +65 6516 7844 > ------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From Giovanni.Cantele at na.infn.it Tue Mar 10 16:47:24 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Tue, 10 Mar 2009 16:47:24 +0100 Subject: [Pw_forum] timing vs QE version vs pools In-Reply-To: <760A9B34-7C54-4AF8-B4D1-74A319A3A437@democritos.it> References: <49B15A2E.8090804@na.infn.it> <760A9B34-7C54-4AF8-B4D1-74A319A3A437@democritos.it> Message-ID: <49B68B8C.40909@na.infn.it> >> - it seems that QE 3.2.3 always performs a little bit better than >> 4.0.4, >> any hint on what (if any) is wrong in what I'm doing? > > assuming that the two versions are compiled with the same options > and libraries: please check where the difference come from, in the > cpu time report at the end of each calculation Let's consider one of the tests, namely 16 cpus, 64 k-points, 1 pool (in the case of 4.0.4 I used -ndiag 1 to get rid of any effect/difference coming from the diagonalization parallelism). These are the relevant (that is, showing the largest differences) results: 3.2.3 time / 4.0.4 time 4.0.4 - 3.2.3 difference total CPU time: 8m49.79s / 9m26.57s 36.78 init_run 44.22s / 42.89s -1.33 electrons 485.50s / 522.73s 37.23 c_bands 426.96s / 464.64s 37.68 cegterg 422.70s / 458.23s 35.53 h_psi 286.17s / 299.63s 13.46 diaghg 59.16s / 64.07s 4.91 cft3s 240.42s / 245.56s 5.14 fft_scatter 142.73s / 124.84s -17.89 so, it seems that the main difference is just in the diagonalization-related routines, right? >> >> - it seems that -ndiag 1 (serial algorithm for the iterative >> solution of >> the eigenvalue problem) always performs a little bit better than the >> default (code) choice. I attribute this to the fact that only for VERY >> LARGE number of electrons this may give a difference, is that right? > > VERY LARGE maybe not, but you will gain (or lose) very little unless > you have let's say several hundreds electronic states I'll make, asap, more tests, if I do lose little it is ok. In the above test, turning "off" parallel diag. gave 9m26.57s CPU time, against 10m51.52s (ortho sub-group = 4* 4 procs), which is 84s faster, namely ~ 10%. btw, in this case using 3.2.3 gave 8m49.79s (see above), which is a further 6% gain. In understand that the gaining with the number of electrons would increase very fast, but if you can imagin just this test running for one day, the difference may become relevant. Can it be due to wrong settings of my cluster? I compiled both 3.2.3 and 4.0.4 using the same compiler (I never changed it since the 1st installation of the machine), libraries, etc. The make.sys is generated in both cases using the configure script of the corresponding version. The only difference is that in one case (3.2.3) I turned on the wannier library (-D__WANLIB) and that a "wrong" line LDFLAGS = static -openmp overwrites the above one LDFLAGS = -i-static -openmp which instead is correctly reported for 4.0.4. thanks, giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From giannozz at democritos.it Tue Mar 10 18:25:09 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 10 Mar 2009 18:25:09 +0100 Subject: [Pw_forum] timing vs QE version vs pools In-Reply-To: <49B68B8C.40909@na.infn.it> References: <49B15A2E.8090804@na.infn.it> <760A9B34-7C54-4AF8-B4D1-74A319A3A437@democritos.it> <49B68B8C.40909@na.infn.it> Message-ID: <49B6A275.5030204@democritos.it> Giovanni Cantele wrote: > Can it be due to wrong settings of my cluster? there is no evidence that anything is wrong in your clusters (or more wrong than in the average cluster). I don't see any reason why the new version should be slower than the old one. I never noticed what you report. Not that I trust benchmarks. Years ago, on a IBM 320h machine, I found a case in which the addition of a single unused variable reproducibly increased the cpu time from 27' to 30'. I have also seen a case in which the same executable, on the same empty machine, had random 10-15% variations in the execution time for no apparent reason. About parallel distributed diagonalization: the optimal number of processors used to be selected at run time, but it was slow and not always accurate. Since it was found that in most cases parallel diagonalization was faster or not worse than the serial one, it was chosen as default. Of course it is impossible to choose defaults that are optimal for everybody. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 10 18:27:12 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 10 Mar 2009 18:27:12 +0100 Subject: [Pw_forum] Problem with dynamical matrix file. In-Reply-To: <85d7d5fd0903100324o2e78eb24k22e264483f17ac12@mail.gmail.com> References: <85d7d5fd0903060759o4f947c06w5e7af5497adfba0d@mail.gmail.com> <85d7d5fd0903061857p776fe549hb980030fb24c5b90@mail.gmail.com> <85d7d5fd0903100324o2e78eb24k22e264483f17ac12@mail.gmail.com> Message-ID: <49B6A2F0.5060809@democritos.it> MATEUS JOS? FERNANDES MARTINS wrote: > But I did a test with a system less and with variable nat_todo enabled. > Really, he does not write the frequencies in the output of ph.x, but the > output of the frequency dynmat.x writes. > Only for this calculation that the error is appearing. then verify what is wrong in this calculation. Print what the code is reading and you will understand what is happening and why, and if there is something that can be done, it will be done Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 10 18:37:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 10 Mar 2009 18:37:10 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49ABCB93.2050304@democritos.it> <49ABCBD1.6030400@democritos.it> <49AD25BF.2030003@sissa.it> <49AD3208.4030308@democritos.it> Message-ID: <49B6A546.7070702@democritos.it> Aihua Zhang wrote: > Is there any work-around now? Parallel execution is indispensable for > large systems. you can follow progress (if any) on this issue here: http://qe-forge.org/tracker/index.php?func=detail&aid=6&group_id=10&atid=133 P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From umari at democritos.it Tue Mar 10 20:28:12 2009 From: umari at democritos.it (umari at democritos.it) Date: Tue, 10 Mar 2009 20:28:12 +0100 Subject: [Pw_forum] dipole moment calculation Message-ID: <20090310202812.vntqrcdig0owooss@mail.democritos.it> Dear Zhang, > I tried a test calculation of the dipole moment of water. The water molecule > is put into a 20 a.u. ^3 box. The relevant setting are > > lelfield = .true. > efield = 0.01 > > In the output file, it reports > > Electronic Dipole per cell (a.u.) -1.921145549061207 > Ionic Dipole per cell (a.u.) 116.1997104738884 > How is Electronic Dipole defined here? By looking into the source code, > Ionic Dipole is defined as in textbook. I also notice that total energy > difference with respect to zero-electric-field system is approximately equal > to (Electronic Dipole + Ionic Dipole) * Efield. But Electronic Dipole hardly > resembles the experimental dipole of water, which is about 1.85 D. Could > anyone explain a bit about these quantities? Thank you!! > > Zhang The option lelfield turns on the calculation of the electronic and ionic dipoles under the presence of an electric field. While the electronic dipole is calculated through the modern theory of the polarization formalism (MTP) which is valid also for periodic systems, the reported ionic dipole is given using the simple textbook formula. This is correct if you want to calculate dipole differences (e.g. after a structural relaxation or after the application of an electric field) but does not give directly the dipole of an isolated molecule. For calculating this, the ionic dipole should be calculated consistently through a MTP-like formalism: e.g. zeta_tot=0.d0 DO na=1,nat zeta_tot=zeta_tot+(0.d0,1.d0)*tau(pdir,na)*tpi*zv(ityp(na)) END DO pola_ion=dimag(log(exp(zeta_tot))) pola_ion=pola_ion*dsqrt(2.d0)/tpiba*dkfact write(stdout,*) " Ionic Dipole per cell (a.u.)",pola_ion Note that Ry atomic units are used and to compare with Hartree atomic units you should divide by a factor sqrt(2) Best regards, Paolo Umari CNR-INFM DEMOCRITOS ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From jtmullen at ncsu.edu Wed Mar 11 03:32:46 2009 From: jtmullen at ncsu.edu (Jeffrey Mullen) Date: Tue, 10 Mar 2009 22:32:46 -0400 Subject: [Pw_forum] Phonon branch enumeration In-Reply-To: <1236693207.3257.31.camel@dhpc-5-20.sissa.it> References: <301039.19318.qm@web34802.mail.mud.yahoo.com> <49B64B76.3080208@ncsu.edu> <1236693207.3257.31.camel@dhpc-5-20.sissa.it> Message-ID: <49B722CE.3010409@ncsu.edu> Thanks for the recommendation. I have performed the calculation with the iverbosity set to 1. It will take me a while to parse it and understand the output, but if I can figure out the relationships, I will attempt to code the ordering into the application. Cheers Jeff Mullen North Carolina State University Dal Corso Andrea wrote: > >It is an interesting idea. I think it is possible to make the >symmetry classification of the displacements patterns with the same >routine that makes the symmetry classification of the eigenvectors >of the dynamical matrix. Presently, this is not done. You can >code this feature yourself or just use iverbosity=1. With this option >the code writes the displacement patterns and you can >check their symmetry. > >Andrea > > > > > >>Cheers >>Jeff >> >> >> >>e kb wrote: >> >> >> >>>Dear Jeff, >>>I am definitely not an expert on the topic but I'd like to understand >>>your question better. >>> >>> Mode symmetry, D_6h(6/mmm) point group: >>> >>> omega( 1 - 1) = -37.4 [cm-1] --> A_2u I >>> omega( 2 - 3) = -33.9 [cm-1] --> E_1u I >>> omega( 4 - 4) = 863.3 [cm-1] --> B_2g >>> omega( 5 - 6) = 1336.0 [cm-1] --> E_2g >>> >>>So you have the irr. representations and the values for omega (values >>>are printed with higher precision in the previous part after >>>diagonalization as you reported). What exactly do you want to know >>>more (that you cannot check from a book on group theory) ? >>> >>>Emine Kucukbenli, grad. student, SISSA, Italy. >>> >>>--- On *Tue, 3/10/09, Jeffrey Mullen //* wrote: >>> >>> From: Jeffrey Mullen >>> Subject: [Pw_forum] Phonon branch enumeration >>> To: pw_forum at pwscf.org >>> Date: Tuesday, March 10, 2009, 2:34 AM >>> >>>Greetings >>> >>>I am testing electron-phonon interaction calculations with graphene and >>>have encountered a problem enumerating the resulting phonon branches. >>>When I run the ph.x calculation at the q(0 0 0), the code calculates 4 >>>representations: >>> >>> Representation # 1 modes # 1 2 >>> Representation # 2 mode # 3 >>> Representation # 3 mode # 4 >>> Representation # 4 modes # 5 6 >>> >>> >>>When the values for omega are calculated, the results are: >>> >>>************************************************************************** >>> omega( 1) = -1.119851 [THz] = -37.354451 [cm-1] >>> omega( 2) = -1.016557 [THz] = -33.908905 >>>[cm-1] >>> omega( 3) = -1.016557 [THz] = -33.908905 [cm-1] >>> omega( 4) = 25.882237 [THz] = 863.344237 [cm-1] >>> omega( 5) = 40.051667 [THz] = 1335.988701 [cm-1] >>> omega( 6) = 40.051667 [THz] = 1335.988701 [cm-1] >>>************************************************************************** >>> >>> >>>with the following mode symmetries: >>> >>> Mode symmetry, D_6h(6/mmm) point group: >>> >>> omega( 1 - 1) = -37.4 [cm-1] --> A_2u I >>> omega( 2 - 3) = -33.9 [cm-1] --> E_1u I >>> omega( 4 - 4) = 863.3 [cm-1] --> B_2g >>> omega( 5 - 6) = 1336.0 [cm-1] --> E_2g R >>> >>> >>>My question is one of ordering. How do I extract which omega(##) >>>corresponds to which representation/mode? >>> >>>Thanks >>>Jeff Mullen >>>North Carolina State >>>University >>> >>>_______________________________________________ >>>Pw_forum mailing list >>>Pw_forum at pwscf.org >>>http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> >>>------------------------------------------------------------------------ >>> >>>_______________________________________________ >>>Pw_forum mailing list >>>Pw_forum at pwscf.org >>>http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> >>> >>_______________________________________________ >>Pw_forum mailing list >>Pw_forum at pwscf.org >>http://www.democritos.it/mailman/listinfo/pw_forum >> >> From yuminqian at gmail.com Wed Mar 11 04:43:47 2009 From: yuminqian at gmail.com (yumin qian) Date: Wed, 11 Mar 2009 11:43:47 +0800 Subject: [Pw_forum] fixed spin moment calculation Message-ID: Dear PWSCF users I am doing calculate on the antiferromagnetic ground state of LiNiO2, I want to plot the energy as a function of fixed spin moment of Ni atom. the following is my in put file for pwscf &system ibrav = 0, nat=16 , ntyp= 4, ecutwfc = 35.0, ecutrho = 200.0, occupations='smearing', smearing='gaussian', degauss=0.02 nspin=2,constrained_magnetization='atomic', starting_magnetization(1)= 0.0, starting_magnetization(2)= 1.8, starting_magnetization(3)=-1.8, starting_magnetization(4)= 0.0, lda_plus_u=.true. Hubbard_U(1)=0.0 Hubbard_U(2)=3.0 Hubbard_U(3)=3.0 Hubbard_U(4)=0.0 / &electrons diagonalization='david', conv_thr = 1.0e-6, mixing_beta = 0.5, / ATOMIC_SPECIES Li *6.914* Li.pbe-n-mt_bw.UPF Ni1 *58.6934* Ni.pbe-n-van.UPF Ni2 *58.6934* Ni.pbe-n-van.UPF O 15.9994 O.pbe-van_bm.UPF and the output file gives ============================================================================== atom number 5 relative position : -0.1652 0.2839 0.5083 charge : 2.373353 magnetization : 1.544423 magnetization/charge: 0.650735 constrained moment : 1.800000 ============================================================================== the output file gives a magnetic moment of 1.5444 ,how should I do to make the calculation converge to the starting_magnetization 1.8 ? I change the starting_magnetization(2) and starting_magnetization(3) from 1.8 to 0.8 , then I will get the E(m) curve. how should I do , does anyone give a suggestion ? -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090311/8c984f2c/attachment.htm From zah7903 at gmail.com Wed Mar 11 05:24:38 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Wed, 11 Mar 2009 12:24:38 +0800 Subject: [Pw_forum] dipole moment calculation In-Reply-To: <20090310202812.vntqrcdig0owooss@mail.democritos.it> References: <20090310202812.vntqrcdig0owooss@mail.democritos.it> Message-ID: Dear Giovanni and Paolo, Thank you very much for kind replies. I have reproduced Giovanni's result with tefield option and with the water molecule at origin. When the molecule is away from origin, weird results are produced. I look through the code in add_efield.f90 and compute_dip.f90. I think I found some possible bugs in them. The first one is not vital. In add_efield.f90, the variable, first, is set to false at the very begin of the subroutine. But this variable is used afterwards with an obvious intention that it should be true for the first time when the subroutine is called. With this small bug, the output of the sawlike potential setup is missing if the varialble, dipfield, is also true. The second possible bug is in compute_dip.f90, where r and r in rho(r) seem dismatch when calculating the electronic dipole. After matching r with rho(r) in the code, the reasonable identical results are obtains, i.e. the calculated dipole and total energy are independent of where the molecule is put in the supercell. I have only limited understanding of MTP. If I understand correctly, it is emphasized that the convectional definition of polarization (P=\int r rho(r) d^3r) is ill-behaved for periodic system and only the change of P is meaningful. So is it a proper way to calculate static dipols with lberry and lelfield? BTW, what is the difference and relationship between lberry and lelfield, both dealing with MTP? Since the tefield approach is rather straighforward to me and produce reasonable result, I would stick to it for the time being. Best regards Aihua On Wed, Mar 11, 2009 at 3:28 AM, wrote: > Dear Zhang, > > > > I tried a test calculation of the dipole moment of water. The water > molecule > > is put into a 20 a.u. ^3 box. The relevant setting are > > > > lelfield = .true. > > efield = 0.01 > > > > In the output file, it reports > > > > Electronic Dipole per cell (a.u.) -1.921145549061207 > > Ionic Dipole per cell (a.u.) 116.1997104738884 > > > How is Electronic Dipole defined here? By looking into the source code, > > Ionic Dipole is defined as in textbook. I also notice that total energy > > difference with respect to zero-electric-field system is approximately > equal > > to (Electronic Dipole + Ionic Dipole) * Efield. But Electronic Dipole > hardly > > resembles the experimental dipole of water, which is about 1.85 D. Could > > anyone explain a bit about these quantities? Thank you!! > > > > Zhang > > > The option lelfield turns on the calculation of the electronic and > ionic dipoles under the presence of an electric field. > While the electronic dipole is calculated through the modern theory of > the polarization formalism (MTP) which is valid also for > periodic systems, the reported ionic dipole is given using the simple > textbook formula. This is correct if you want to calculate dipole > differences (e.g. after a structural relaxation or after the application > of an electric field) but does not give directly the dipole of an > isolated molecule. For calculating this, the ionic dipole should be > calculated consistently through a MTP-like > formalism: > e.g. > > zeta_tot=0.d0 > DO na=1,nat > zeta_tot=zeta_tot+(0.d0,1.d0)*tau(pdir,na)*tpi*zv(ityp(na)) > END DO > pola_ion=dimag(log(exp(zeta_tot))) > pola_ion=pola_ion*dsqrt(2.d0)/tpiba*dkfact > write(stdout,*) " Ionic Dipole per cell (a.u.)",pola_ion > > Note that Ry atomic units are used and to compare with Hartree atomic units > you should divide by a factor sqrt(2) > > Best regards, > > Paolo Umari CNR-INFM DEMOCRITOS > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090311/7dafd2de/attachment.htm From sclauzer at sissa.it Wed Mar 11 09:22:41 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 11 Mar 2009 09:22:41 +0100 Subject: [Pw_forum] fixed spin moment calculation In-Reply-To: References: Message-ID: <49B774D1.5050202@sissa.it> yumin qian wrote: > Dear PWSCF users > I am doing calculate on the antiferromagnetic ground state of > LiNiO2, I want to plot the energy as a function of fixed spin moment of > Ni atom. > the following is my in put file for pwscf > > &system > ibrav = 0, nat=16 , ntyp= 4, > ecutwfc = 35.0, ecutrho = 200.0, > occupations='smearing', smearing='gaussian', degauss=0.02 First of all a word of caution: this value of degauss may not be low enough to converge the magnetization (even if it is more than enough to converge the total energy). Also ecutrho may not be high enough to converge total energy, since you're using US PPs. > nspin=2,constrained_magnetization='atomic', > starting_magnetization(1)= 0.0, > starting_magnetization(2)= 1.8, > starting_magnetization(3)=-1.8, > starting_magnetization(4)= 0.0, > lda_plus_u=.true. > Hubbard_U(1)=0.0 > Hubbard_U(2)=3.0 > Hubbard_U(3)=3.0 > Hubbard_U(4)=0.0 > / > &electrons > diagonalization='david', > conv_thr = 1.0e-6, > mixing_beta = 0.5, > / > ATOMIC_SPECIES > Li *6.914* Li.pbe-n-mt_bw.UPF > Ni1 *58.6934* Ni.pbe-n-van.UPF > Ni2 *58.6934* Ni.pbe-n-van.UPF > O 15.9994 O.pbe-van_bm.UPF > > and the output file gives > > ============================================================================== > atom number 5 relative position : -0.1652 0.2839 0.5083 > charge : 2.373353 > magnetization : 1.544423 > magnetization/charge: 0.650735 > constrained moment : 1.800000 > > ============================================================================== > the output file gives a magnetic moment of 1.5444 ,how should I do to > make the calculation converge to the starting_magnetization 1.8 ? You can increase the lambda parameter which premultiplies the penalty energy added in v_of_rho. In the limit your constraint gets satisfied, the energy should not depend on which lambda you chose, but you may want to verify this. The default should be 1. I think is not enough to force the magnetization on the atom. However, I think that the magnetization of a single atom inside a bulk material or in general when it forms covalent bonds is not a well defined quantity, so I would not care too much of the precise number I get for the magnetization, since it may well change if I change which portion of charge is attributed to which atom (remember that you're using a plane waves code, and PWs do not know anything about atomic orbitals a priori...) HTH GS > > I change the starting_magnetization(2) and starting_magnetization(3) > from 1.8 to 0.8 , then I will get the E(m) curve. how should I do , > does anyone give > a suggestion ? > -- > Sincerely Y. M. Qian > Lab.of Condensed Matter Theory and Materials Computation > Institute of Physics > Chinese Academy of Sciences > Tel: + 8610 8264 9147 > E-Mail:yuminqian at gmail.com > P.O.Box 603 Beijing 100190 > China > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From paulatto at sissa.it Wed Mar 11 09:38:46 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 11 Mar 2009 09:38:46 +0100 Subject: [Pw_forum] dipole moment calculation In-Reply-To: References: <20090310202812.vntqrcdig0owooss@mail.democritos.it> Message-ID: On Wed, 11 Mar 2009 05:24:38 +0100, Aihua Zhang wrote: > The second possible bug is in compute_dip.f90, where r and r in rho(r) > seem dismatch when calculating the electronic dipole. After matching r with > rho(r) in the code, the reasonable identical results are obtains, i.e. > the calculated dipole and total energy are independent of where the molecule > is put in the supercell. Good job Aihua Zhang! Could you please provide more information on this bug, so it can be fixed mainstream? I have long suspected a bug in that part, and I know at least another person who's working on it at the moment, as far as I know with no luck. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From carlo.nervi at unito.it Wed Mar 11 17:02:38 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Wed, 11 Mar 2009 17:02:38 +0100 Subject: [Pw_forum] compiling QE4.1 Message-ID: <49B7E09E.9080800@unito.it> Dear all, I managed to compile QE4.1 with MPI, MKL and (perhaps) with MKL_FFTW3, with better performances, but I'm still getting strange timing results. For examples, the "tests" are finished in twice the time of the reference (1500 s instead of about 700), but the example21 with 32 water molecules is done in 1'25", whereas the 64 water molecules is done in 6'50" Since mpiexec apparently run normally, I suppose QE is correctly compiled with MPI. Now, my question is: how can I be sure that MKL_FFTW3 is used? I cannot understand if the clib/fftw.h should be (or not?) correctly replaced by /opt/intel-10.0/Compiler/11.0/081/mkl/include/fftw/fftw.h I included the dir in make.sys, but the LIBOBJS (containing flib.a and clib.a) are (I suppose) linked before the LIBS, therefore I suppose that the fftw.h used is the clib/fftw.h Thank you, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From giannozz at democritos.it Wed Mar 11 21:06:57 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 11 Mar 2009 21:06:57 +0100 Subject: [Pw_forum] compiling QE4.1 In-Reply-To: <49B7E09E.9080800@unito.it> References: <49B7E09E.9080800@unito.it> Message-ID: <63B4AE1D-6075-4848-A12F-1F68FC8180E2@democritos.it> On Mar 11, 2009, at 17:02 , Carlo Nervi wrote: > I managed to compile QE4.1 you mean: the CVS version ? > Now, my question is: how can I be sure that MKL_FFTW3 is used? -D__FFTW3, link -lfftw3xf_intel or whatever you called it > I cannot understand if the clib/fftw.h should be (or not?) correctly > replaced by /opt/intel-10.0/Compiler/11.0/081/mkl/include/fftw/fftw.h clib/fftw.h is used only by FFTW v.2 P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From carlo.nervi at unito.it Wed Mar 11 22:30:26 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Wed, 11 Mar 2009 22:30:26 +0100 (CET) Subject: [Pw_forum] compiling QE4.1 In-Reply-To: <63B4AE1D-6075-4848-A12F-1F68FC8180E2@democritos.it> References: <49B7E09E.9080800@unito.it> <63B4AE1D-6075-4848-A12F-1F68FC8180E2@democritos.it> Message-ID: <47763.151.59.235.57.1236807026.squirrel@mail.unito.it> >> I managed to compile QE4.1 > > you mean: the CVS version ? Yes, the 4.1CVS version. I know that it is under test. But even though I'm a newbye I would like to contribute to perform some testing because I'm interested in GIPAW for simulation of solid state NMR... As far as I understood only QE and CASTEP, at the moment (ABINIT and other uses PAW), are able to use GIPAW. But maybe I'm wrong because I just entered in this world... >> Now, my question is: how can I be sure that MKL_FFTW3 is >> used? > > -D__FFTW3, link -lfftw3xf_intel or whatever you called it Okay. Thanks. Than I did correctly >> I cannot understand if the clib/fftw.h should be (or >> not?) correctly >> replaced by >> /opt/intel-10.0/Compiler/11.0/081/mkl/include/fftw/fftw.h > > clib/fftw.h is used only by FFTW v.2 > Thank you Paolo, this was one (of many) of my doubts. Therefore my binary is hopefully compiled correctly. But I'm still not convinced that MPI is working 100% as it should be (1500 s for the tests using a 8-core Xeon 5345). By the way, in one of my tests, using ./configure the make.sys wrote FDFLAGS instead of FFLAGS. I was using several switches, like LIBDIR, F90, F77, CC... Cheers, Carlo -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From baroni at sissa.it Thu Mar 12 01:46:12 2009 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 12 Mar 2009 11:46:12 +1100 Subject: [Pw_forum] Phonon branch enumeration In-Reply-To: <49B722CE.3010409@ncsu.edu> References: <301039.19318.qm@web34802.mail.mud.yahoo.com> <49B64B76.3080208@ncsu.edu> <1236693207.3257.31.camel@dhpc-5-20.sissa.it> <49B722CE.3010409@ncsu.edu> Message-ID: On Mar 11, 2009, at 1:32 PM, Jeffrey Mullen wrote: > > Thanks for the recommendation. I have performed the calculation with > the > iverbosity set to 1. It will take me a while to parse it and > understand > the output, but if I can figure out the relationships, I will > attempt to > code the ordering into the application. that would be really great! SB > > > Cheers > Jeff Mullen > North Carolina State University > > > Dal Corso Andrea wrote: > >> >> It is an interesting idea. I think it is possible to make the >> symmetry classification of the displacements patterns with the same >> routine that makes the symmetry classification of the eigenvectors >> of the dynamical matrix. Presently, this is not done. You can >> code this feature yourself or just use iverbosity=1. With this option >> the code writes the displacement patterns and you can >> check their symmetry. >> >> Andrea >> >> >> >> >> >>> Cheers >>> Jeff >>> >>> >>> >>> e kb wrote: >>> >>> >>> >>>> Dear Jeff, >>>> I am definitely not an expert on the topic but I'd like to >>>> understand >>>> your question better. >>>> >>>> Mode symmetry, D_6h(6/mmm) point group: >>>> >>>> omega( 1 - 1) = -37.4 [cm-1] --> A_2u I >>>> omega( 2 - 3) = -33.9 [cm-1] --> E_1u I >>>> omega( 4 - 4) = 863.3 [cm-1] --> B_2g >>>> omega( 5 - 6) = 1336.0 [cm-1] --> E_2g >>>> >>>> So you have the irr. representations and the values for omega >>>> (values >>>> are printed with higher precision in the previous part after >>>> diagonalization as you reported). What exactly do you want to know >>>> more (that you cannot check from a book on group theory) ? >>>> >>>> Emine Kucukbenli, grad. student, SISSA, Italy. >>>> >>>> --- On *Tue, 3/10/09, Jeffrey Mullen //* wrote: >>>> >>>> From: Jeffrey Mullen >>>> Subject: [Pw_forum] Phonon branch enumeration >>>> To: pw_forum at pwscf.org >>>> Date: Tuesday, March 10, 2009, 2:34 AM >>>> >>>> Greetings >>>> >>>> I am testing electron-phonon interaction calculations with >>>> graphene and >>>> have encountered a problem enumerating the resulting phonon >>>> branches. >>>> When I run the ph.x calculation at the q(0 0 0), the code >>>> calculates 4 >>>> representations: >>>> >>>> Representation # 1 modes # 1 2 >>>> Representation # 2 mode # 3 >>>> Representation # 3 mode # 4 >>>> Representation # 4 modes # 5 6 >>>> >>>> >>>> When the values for omega are calculated, the results are: >>>> >>>> ************************************************************************** >>>> omega( 1) = -1.119851 [THz] = -37.354451 [cm-1] >>>> omega( 2) = -1.016557 [THz] = -33.908905 >>>> [cm-1] >>>> omega( 3) = -1.016557 [THz] = -33.908905 [cm-1] >>>> omega( 4) = 25.882237 [THz] = 863.344237 [cm-1] >>>> omega( 5) = 40.051667 [THz] = 1335.988701 [cm-1] >>>> omega( 6) = 40.051667 [THz] = 1335.988701 [cm-1] >>>> ************************************************************************** >>>> >>>> >>>> with the following mode symmetries: >>>> >>>> Mode symmetry, D_6h(6/mmm) point group: >>>> >>>> omega( 1 - 1) = -37.4 [cm-1] --> A_2u I >>>> omega( 2 - 3) = -33.9 [cm-1] --> E_1u I >>>> omega( 4 - 4) = 863.3 [cm-1] --> B_2g >>>> omega( 5 - 6) = 1336.0 [cm-1] --> E_2g R >>>> >>>> >>>> My question is one of ordering. How do I extract which omega(##) >>>> corresponds to which representation/mode? >>>> >>>> Thanks >>>> Jeff Mullen >>>> North Carolina State >>>> University >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090312/66355235/attachment-0001.htm From yuminqian at gmail.com Thu Mar 12 02:36:05 2009 From: yuminqian at gmail.com (yumin qian) Date: Thu, 12 Mar 2009 09:36:05 +0800 Subject: [Pw_forum] fixed spin moment calculation In-Reply-To: <49B774D1.5050202@sissa.it> References: <49B774D1.5050202@sissa.it> Message-ID: thanks for your reply ,I changed the lambda=5.0 and used occupations='tetrahedra' but the magnetization still did not converge to the initial value ,but the total energy converged. I do know what is the problem. 2009/3/11 Gabriele Sclauzero > > > yumin qian wrote: > > Dear PWSCF users > > I am doing calculate on the antiferromagnetic ground state of > > LiNiO2, I want to plot the energy as a function of fixed spin moment of > > Ni atom. > > the following is my in put file for pwscf > > > > &system > > ibrav = 0, nat=16 , ntyp= 4, > > ecutwfc = 35.0, ecutrho = 200.0, > > occupations='smearing', smearing='gaussian', degauss=0.02 > > First of all a word of caution: this value of degauss may not be low enough > to converge > the magnetization (even if it is more than enough to converge the total > energy). Also > ecutrho may not be high enough to converge total energy, since you're using > US PPs. > > > nspin=2,constrained_magnetization='atomic', > > starting_magnetization(1)= 0.0, > > starting_magnetization(2)= 1.8, > > starting_magnetization(3)=-1.8, > > starting_magnetization(4)= 0.0, > > lda_plus_u=.true. > > Hubbard_U(1)=0.0 > > Hubbard_U(2)=3.0 > > Hubbard_U(3)=3.0 > > Hubbard_U(4)=0.0 > > / > > &electrons > > diagonalization='david', > > conv_thr = 1.0e-6, > > mixing_beta = 0.5, > > / > > ATOMIC_SPECIES > > Li *6.914* Li.pbe-n-mt_bw.UPF > > Ni1 *58.6934* Ni.pbe-n-van.UPF > > Ni2 *58.6934* Ni.pbe-n-van.UPF > > O 15.9994 O.pbe-van_bm.UPF > > > > and the output file gives > > > > > ============================================================================== > > atom number 5 relative position : -0.1652 0.2839 0.5083 > > charge : 2.373353 > > magnetization : 1.544423 > > magnetization/charge: 0.650735 > > constrained moment : 1.800000 > > > > > ============================================================================== > > the output file gives a magnetic moment of 1.5444 ,how should I do to > > make the calculation converge to the starting_magnetization 1.8 ? > > You can increase the lambda parameter which premultiplies the penalty > energy added in > v_of_rho. In the limit your constraint gets satisfied, the energy should > not depend on > which lambda you chose, but you may want to verify this. > The default should be 1. I think is not enough to force the magnetization > on the atom. > > However, I think that the magnetization of a single atom inside a bulk > material or in > general when it forms covalent bonds is not a well defined quantity, so I > would not care > too much of the precise number I get for the magnetization, since it may > well change if I > change which portion of charge is attributed to which atom (remember that > you're using a > plane waves code, and PWs do not know anything about atomic orbitals a > priori...) > > HTH > > GS > > > > > I change the starting_magnetization(2) and starting_magnetization(3) > > from 1.8 to 0.8 , then I will get the E(m) curve. how should I do , > > does anyone give > > a suggestion ? > > -- > > Sincerely Y. M. Qian > > Lab.of Condensed Matter Theory and Materials Computation > > Institute of Physics > > Chinese Academy of Sciences > > Tel: + 8610 8264 9147 > > E-Mail:yuminqian at gmail.com E-Mail%3Ayuminqian at gmail.com > > > P.O.Box 603 Beijing 100190 > > China > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090312/2ffce358/attachment.htm From yuminqian at gmail.com Thu Mar 12 02:36:59 2009 From: yuminqian at gmail.com (yumin qian) Date: Thu, 12 Mar 2009 09:36:59 +0800 Subject: [Pw_forum] fixed spin moment calculation In-Reply-To: References: <49B774D1.5050202@sissa.it> Message-ID: thanks for your reply ,I changed the lambda=5.0 and used occupations='tetrahedra' but the magnetization still did not converge to the initial value ,but the total energy converged. I do not know what is the problem. > 2009/3/11 Gabriele Sclauzero > > >> >> yumin qian wrote: >> > Dear PWSCF users >> > I am doing calculate on the antiferromagnetic ground state of >> > LiNiO2, I want to plot the energy as a function of fixed spin moment of >> > Ni atom. >> > the following is my in put file for pwscf >> > >> > &system >> > ibrav = 0, nat=16 , ntyp= 4, >> > ecutwfc = 35.0, ecutrho = 200.0, >> > occupations='smearing', smearing='gaussian', degauss=0.02 >> >> First of all a word of caution: this value of degauss may not be low >> enough to converge >> the magnetization (even if it is more than enough to converge the total >> energy). Also >> ecutrho may not be high enough to converge total energy, since you're >> using US PPs. >> >> > nspin=2,constrained_magnetization='atomic', >> > starting_magnetization(1)= 0.0, >> > starting_magnetization(2)= 1.8, >> > starting_magnetization(3)=-1.8, >> > starting_magnetization(4)= 0.0, >> > lda_plus_u=.true. >> > Hubbard_U(1)=0.0 >> > Hubbard_U(2)=3.0 >> > Hubbard_U(3)=3.0 >> > Hubbard_U(4)=0.0 >> > / >> > &electrons >> > diagonalization='david', >> > conv_thr = 1.0e-6, >> > mixing_beta = 0.5, >> > / >> > ATOMIC_SPECIES >> > Li *6.914* Li.pbe-n-mt_bw.UPF >> > Ni1 *58.6934* Ni.pbe-n-van.UPF >> > Ni2 *58.6934* Ni.pbe-n-van.UPF >> > O 15.9994 O.pbe-van_bm.UPF >> > >> > and the output file gives >> > >> > >> ============================================================================== >> > atom number 5 relative position : -0.1652 0.2839 0.5083 >> > charge : 2.373353 >> > magnetization : 1.544423 >> > magnetization/charge: 0.650735 >> > constrained moment : 1.800000 >> > >> > >> ============================================================================== >> > the output file gives a magnetic moment of 1.5444 ,how should I do to >> > make the calculation converge to the starting_magnetization 1.8 ? >> >> You can increase the lambda parameter which premultiplies the penalty >> energy added in >> v_of_rho. In the limit your constraint gets satisfied, the energy should >> not depend on >> which lambda you chose, but you may want to verify this. >> The default should be 1. I think is not enough to force the magnetization >> on the atom. >> >> However, I think that the magnetization of a single atom inside a bulk >> material or in >> general when it forms covalent bonds is not a well defined quantity, so I >> would not care >> too much of the precise number I get for the magnetization, since it may >> well change if I >> change which portion of charge is attributed to which atom (remember that >> you're using a >> plane waves code, and PWs do not know anything about atomic orbitals a >> priori...) >> >> HTH >> >> GS >> >> > >> > I change the starting_magnetization(2) and starting_magnetization(3) >> > from 1.8 to 0.8 , then I will get the E(m) curve. how should I do , >> > does anyone give >> > a suggestion ? >> > -- >> > Sincerely Y. M. Qian >> > Lab.of Condensed Matter Theory and Materials Computation >> > Institute of Physics >> > Chinese Academy of Sciences >> > Tel: + 8610 8264 9147 >> > E-Mail:yuminqian at gmail.com > E-Mail%3Ayuminqian at gmail.com > >> > P.O.Box 603 Beijing 100190 >> > China >> > >> > >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Sincerely Y. M. Qian > Lab.of Condensed Matter Theory and Materials Computation > Institute of Physics > Chinese Academy of Sciences > Tel: + 8610 8264 9147 > E-Mail:yuminqian at gmail.com > P.O.Box 603 Beijing 100190 > China > > -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090312/492f943e/attachment.htm From w2agz at pacbell.net Thu Mar 12 05:29:37 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Wed, 11 Mar 2009 21:29:37 -0700 Subject: [Pw_forum] ld1.x & US requires... In-Reply-To: References: <00a401c9a078$c224ef90$466eceb0$@net> Message-ID: <000d01c9a2cb$276d5ff0$76481fd0$@net> Something bad did happen... The post-processing dos.x tool got the d-s (or s-d) ordering correctly, but... The LDA+U "starting_ns_eigenvalues" coaxing input does not lead to the "correct" spin configuration. Have a look at the PP header change to Fe.pz.nd.UPF below. Try it out on Example 25 and get back to me. Designing PPs is a black art, as many have pointed out. It would be great if there were a resource that contained some examples of ld1.x input one could play around with. There are, of course, considerable databases...espresso, berlin, opium, Vanderbilt...whatever, but, as far as I could find, none provided a large number of input examples one could play around with. Oh...very strange...the d-s ordering in all Cu PPs I've found, including those I've "designed," is the reverse of all those other TMs in the QE database. I use Cu a lot, including tweaking the "sne's." Is there an additional issue I should I should be aware of? Generated using Andrea Dal Corso code (rrkj3) Author: Andrea Dal Corso Generation date: unknown (reversed s & d order) Info: Fe LDA 3d7 4s1 RRKJ3 US 1 The Pseudo was generated with a Scalar-Relativistic Calculation 1.70000000000E+00 Local Potential cutoff radius nl pn l occ Rcut Rcut US E pseu 4S 1 0 1.00 2.00000000000 2.20000000000 0.00000000000 4S 1 0 0.00 2.00000000000 2.20000000000 0.00000000000 4P 2 1 0.00 2.20000000000 2.30000000000 0.00000000000 4P 2 1 0.00 2.20000000000 2.30000000000 0.00000000000 3D 3 2 7.00 1.60000000000 2.20000000000 0.00000000000 3D 3 2 0.00 1.60000000000 2.20000000000 0.00000000000 0 Version Number Fe Element US Ultrasoft pseudopotential T Nonlinear Core Correction SLA PZ NOGX NOGC PZ Exchange-Correlation functional 8.00000000000 Z valence -41.49093103800 Total energy 0.0000000 0.0000000 Suggested cutoff for wfc and rho 2 Max angular momentum component 957 Number of points in mesh 2 6 Number of Wavefunctions, Number of Projectors Wavefunctions nl l occ 3D 2 7.00 4S 0 1.00 Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Monday, March 09, 2009 7:45 AM To: PWSCF Forum Subject: Re: [Pw_forum] ld1.x & US requires... On Mar 9, 2009, at 6:34 , Paul M. Grant wrote: > Why did I bother doing this exercise? Simply because dos.x > apparently arranges the notation for the projected pdos output > according to the sequence of states listed in the PP. For Cu, it > is 3d-4s, whereas for Ni, Co, Fe, and Mn, it is the reverse. > if this is the problem, you can reverse the positions of 3d and 4s atomic states in the pseudopotential file. Nothing bad should happen. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Thu Mar 12 08:21:07 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 Mar 2009 08:21:07 +0100 Subject: [Pw_forum] ld1.x & US requires... In-Reply-To: <000d01c9a2cb$276d5ff0$76481fd0$@net> References: <00a401c9a078$c224ef90$466eceb0$@net> <000d01c9a2cb$276d5ff0$76481fd0$@net> Message-ID: On Mar 12, 2009, at 5:29 , Paul M. Grant wrote: > as far as I could find, none provided a large number of input examples > one could play around with see atomic_doc/pseudo_library --- Paolo Giannozzi, Democritos and University of Udine, Italy From nazari at iasbs.ac.ir Thu Mar 12 12:17:28 2009 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Thu, 12 Mar 2009 11:17:28 -0000 (UTC) Subject: [Pw_forum] Format data/koint and band energy in nscf calculation/ koint and band energy in bands.dat In-Reply-To: <49B774D1.5050202@sissa.it> References: <49B774D1.5050202@sissa.it> Message-ID: <38907.213.176.122.17.1236856648.squirrel@mail.iasbs.ac.ir> Dear All, I have a question about plotting band structure. The band structure for 48 atoms tio2 surface has many unusall jumps.For resolving this problem at first i have checked all the parameters. The parameters were similar to ones which is reported in articles and also in forum. But when I produce the dat file from ncsf.out file by direct transfer of data from nscf.out to dat file without running bands.x the band structure has normal appearance. Would you please let me know what is the corect format for band.dat file? Regards Fariba Nazari IASBS From sclauzer at sissa.it Thu Mar 12 08:48:57 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 12 Mar 2009 08:48:57 +0100 Subject: [Pw_forum] fixed spin moment calculation In-Reply-To: References: <49B774D1.5050202@sissa.it> Message-ID: <49B8BE69.2010501@sissa.it> Dear Yumin Qian, There's something strange in this output. I think that atom number 5 should be a Ni one, since you were interested in the magnetization of that species, but then, why is the charge around that atom only about 2.5? Ni should have 10 electrons in valence, so I would expect to get a number around 10 for the charge (unless the atom goes in a very ionized state, but that seems highly unprobable to me). Are you sure PPs and all the rest is OK? GS yumin qian wrote: > thanks for your reply ,I changed the lambda=5.0 and used > occupations='tetrahedra' but the magnetization still did not > converge to the initial value ,but the total energy converged. > I do know what is the problem. > ============================================================================== > > atom number 5 relative position : -0.1652 0.2839 0.5083 > > charge : 2.373353 > > magnetization : 1.544423 > > magnetization/charge: 0.650735 > > constrained moment : 1.800000 > > > > > ============================================================================== > > the output file gives a magnetic moment of 1.5444 ,how should I do to > > make the calculation converge to the starting_magnetization 1.8 ? > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Thu Mar 12 08:59:46 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 12 Mar 2009 08:59:46 +0100 Subject: [Pw_forum] Format data/koint and band energy in nscf calculation/ koint and band energy in bands.dat In-Reply-To: <38907.213.176.122.17.1236856648.squirrel@mail.iasbs.ac.ir> References: <49B774D1.5050202@sissa.it> <38907.213.176.122.17.1236856648.squirrel@mail.iasbs.ac.ir> Message-ID: <49B8C0F2.5030404@sissa.it> nazari at iasbs.ac.ir wrote: > > Dear All, > > I have a question about plotting band structure. > > The band structure for 48 atoms tio2 surface has many unusall jumps.For > > resolving this problem at first i have checked all the parameters. The > > parameters were similar to ones which is reported in articles and also in > > forum. But when I produce the dat file from ncsf.out file by direct > > transfer of data from nscf.out to dat file without running bands.x the > > band structure has normal appearance. Would you please let me know what > > is the corect format for band.dat file? Sorry, you're not giving enough information to let anyone understand/solve your problem, so please be more precise in your explanation and give some small and understandable example. What do you exactly mean with 'band.dat' file? What kind of jumps? There has been a similar post (about band structure plotting and "strange jumps") few days ago. Please have first a look at the forum archives and check if the problem is the same (and if it has already been discussed and solved!) GS > > Regards > Fariba Nazari > IASBS > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Thu Mar 12 09:13:35 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 Mar 2009 09:13:35 +0100 Subject: [Pw_forum] compiling QE4.1 In-Reply-To: <47763.151.59.235.57.1236807026.squirrel@mail.unito.it> References: <49B7E09E.9080800@unito.it> <63B4AE1D-6075-4848-A12F-1F68FC8180E2@democritos.it> <47763.151.59.235.57.1236807026.squirrel@mail.unito.it> Message-ID: <49B8C42F.8010302@democritos.it> Carlo Nervi wrote: > But I'm still not convinced that MPI is working 100% as it > should be (1500 s for the tests using a 8-core Xeon 5345). tests are not made for benchmarking, even less for parallel execution: most of them are small and may take more time in parallel than in serial execution. As explained by Axel no less than 36 times, running parallel codes in multicore PCs can be tricky. > By the way, in one of my tests, using ./configure the > make.sys wrote FDFLAGS instead of FFLAGS. I was using > several switches, like LIBDIR, F90, F77, CC... and what should one get from such a vague statement? Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Thu Mar 12 10:00:29 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 12 Mar 2009 10:00:29 +0100 Subject: [Pw_forum] Format data/koint and band energy in nscf calculation/ koint and band energy in bands.dat In-Reply-To: <40215.213.176.122.17.1236859771.squirrel@mail.iasbs.ac.ir> References: <40215.213.176.122.17.1236859771.squirrel@mail.iasbs.ac.ir> Message-ID: <49B8CF2D.5000702@sissa.it> From a quick look to your data and plots, I think that your issue is the same as the one posted about one week ago (have looked at it as I suggested?). The overlap algorithm of bands.x gets in trouble when there are a lot of bands and not enough k-points and in these cases outputs a wrong ordering of the bands. I repeat here the two solutions currently available to this problem: i) increase the number of k-points in the nscf calculation ii) use the symmetry based algorithm of bands.x (lsym=.TRUE.) Regarding the number of columns used to output bands, you're right: pw.x uses 8 columns, while bands.x uses 10, but plotband.x should handle correctly both cases if the number of bands is consistent with what written in the &plot namelist at the beginning of the file containing the bands. Cheers, GS nazari at iasbs.ac.ir wrote: > Dear Gabriele Sclauzero, > > Please find in attachment the more explanation. > > Regards > > Fariba Nazari > Iasbs > > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From paulatto at sissa.it Thu Mar 12 10:50:49 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 12 Mar 2009 10:50:49 +0100 Subject: [Pw_forum] Format data/koint and band energy in nscf calculation/ koint and band energy in bands.dat In-Reply-To: <38907.213.176.122.17.1236856648.squirrel@mail.iasbs.ac.ir> References: <49B774D1.5050202@sissa.it> <38907.213.176.122.17.1236856648.squirrel@mail.iasbs.ac.ir> Message-ID: On Thu, 12 Mar 2009 12:17:28 +0100, wrote: > I have a question about plotting band structure. > The band structure for 48 atoms tio2 surface has many unusall jumps. Depending on the definition of "jump" it may mean that your cutoff is too small, or that your kpoint grid is too coarse. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From yuminqian at gmail.com Thu Mar 12 12:01:42 2009 From: yuminqian at gmail.com (yumin qian) Date: Thu, 12 Mar 2009 19:01:42 +0800 Subject: [Pw_forum] fixed spin moment calculation In-Reply-To: <49B8BE69.2010501@sissa.it> References: <49B774D1.5050202@sissa.it> <49B8BE69.2010501@sissa.it> Message-ID: Sorry for confuse you , After checking the input and output file , I found that I also did a LiVO2 crystal calcualtion with the same problem, the input file I posted is for LiNiO2 and the output file I posted is for LiVO2 , here is the complete input and output file from the same calcualtion &control calculation='scf' restart_mode='from_scratch' , pseudo_dir = '~/software/espresso-4test/pseudo', outdir='outscf' nstep=60 prefix='AFM-type' tstress = .true. tprnfor = .true. wf_collect=.true. / &system ibrav = 0, nat=16 , ntyp= 4, ecutwfc = 35.0, ecutrho = 300.0, occupations='tetrahedra', nspin=2,constrained_magnetization='atomic',lambda=5.0, starting_magnetization(1)= 0.0, starting_magnetization(2)= 1.8, starting_magnetization(3)=-1.8, starting_magnetization(4)= 0.0, lda_plus_u=.true. Hubbard_U(1)=0.0 Hubbard_U(2)=3.0 Hubbard_U(3)=3.0 Hubbard_U(4)=0.0 / &electrons diagonalization='david', conv_thr = 1.0e-7, mixing_beta = 0.5, / ATOMIC_SPECIES Li 6.914 Li.pbe-n-mt_bw.UPF V1 50.9415 V.pbe-n-van.UPF V2 50.9415 V.pbe-n-van.UPF O 15.9994 O.pbe-van_bm.UPF ATOMIC_POSITIONS {crystal} Li 0.0000000000000000 0.0000000000000000 0.0 Li 0.0000000000000000 0.0000000000000000 0.5 Li 0.5000000000000000 0.5000000000000000 0.0 Li 0.5000000000000000 0.5000000000000000 0.5 V1 0.0000000000000000 0.5000000000000000 0.25 V2 0.0000000000000000 0.5000000000000000 0.75 V2 0.5000000000000000 0.0000000000000000 0.25 V1 0.5000000000000000 0.0000000000000000 0.75 O 0.2354848230051515 0.0000000000000000 0.35287967 O 0.2354848230051515 0.0000000000000000 0.85287967 O 0.7354848230051516 0.5000000000000000 0.35287967 O 0.7354848230051516 0.5000000000000000 0.85287967 O 0.7645151769948484 0.0000000000000000 0.14712033 O 0.7645151769948484 0.0000000000000000 0.64712033 O 0.2645151769948484 0.5000000000000000 0.14712033 O 0.2645151769948484 0.5000000000000000 0.64712033 K_POINTS {automatic} 8 8 6 1 1 1 CELL_PARAMETERS (alat) 9.903876 0.000000 0.000000 0.000000 5.622988 0.000000 -6.542514 0.000000 20.135790 the output file gives ============================================================================== atom number 4 relative position : 0.1697 0.2839 1.0166 charge : 0.065485 magnetization : 0.000000 magnetization/charge: 0.000000 constrained moment : 0.000000 ============================================================================== ============================================================================== atom number 5 relative position : -0.1652 0.2839 0.5083 charge : 2.371448 magnetization : 1.554551 magnetization/charge: 0.655528 constrained moment : 1.800000 I also changed lambda from 1 to 5 and the final magnetic moment changed from 1.55 to 1.50 so the parameter lambda seems have no impact on the final magnetic moment, there should be something wrong with my calcualtion but I can't spot this error. 2009/3/12 Gabriele Sclauzero > Dear Yumin Qian, > > There's something strange in this output. I think that atom number 5 > should be a Ni > one, since you were interested in the magnetization of that species, but > then, why is the > charge around that atom only about 2.5? Ni should have 10 electrons in > valence, so I would > expect to get a number around 10 for the charge (unless the atom goes in a > very ionized > state, but that seems highly unprobable to me). > Are you sure PPs and all the rest is OK? > > > GS > > yumin qian wrote: > > thanks for your reply ,I changed the lambda=5.0 and used > > occupations='tetrahedra' but the magnetization still did not > > converge to the initial value ,but the total energy converged. > > I do know what is the problem. > > > ============================================================================== > > > atom number 5 relative position : -0.1652 0.2839 > 0.5083 > > > charge : 2.373353 > > > magnetization : 1.544423 > > > magnetization/charge: 0.650735 > > > constrained moment : 1.800000 > > > > > > > > > ============================================================================== > > > the output file gives a magnetic moment of 1.5444 ,how should I do > to > > > make the calculation converge to the starting_magnetization 1.8 ? > > > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090312/989048e4/attachment-0001.htm From lanhaiping at gmail.com Thu Mar 12 13:35:01 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 12 Mar 2009 20:35:01 +0800 Subject: [Pw_forum] Format data/koint and band energy in nscf calculation/ koint and band energy in bands.dat In-Reply-To: References: <49B774D1.5050202@sissa.it> <38907.213.176.122.17.1236856648.squirrel@mail.iasbs.ac.ir> Message-ID: Another possibility is that the number of bands is not enough to get well converged. On Thu, Mar 12, 2009 at 5:50 PM, Lorenzo Paulatto wrote: > On Thu, 12 Mar 2009 12:17:28 +0100, wrote: > > I have a question about plotting band structure. > > The band structure for 48 atoms tio2 surface has many unusall jumps. > > Depending on the definition of "jump" it may mean that your cutoff is too > small, or that your kpoint grid is too coarse. > > cheers > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090312/efd024fd/attachment.htm From eminekb at yahoo.com Thu Mar 12 13:43:42 2009 From: eminekb at yahoo.com (e kb) Date: Thu, 12 Mar 2009 05:43:42 -0700 (PDT) Subject: [Pw_forum] fixed spin moment calculation In-Reply-To: Message-ID: <673802.207.qm@web34806.mail.mud.yahoo.com> Dear Yumin Qian, You may want to check with another pseudopotential for Oxygen. It might be totally unrelated but I've seen this attached in the details part: Warning: this O psp has been tested in liquid water simulations by Patrick Sit and Nicola Marzari. Results for the diffusion coefficient and pair correlation functions were at odd with those obtained with other ultrasoft or norm-conserving pseudopotentials, and recently published result. Emine Kucukbenli, grad student, SISSA, Italy. --- On Thu, 3/12/09, yumin qian wrote: From: yumin qian Subject: Re: [Pw_forum] fixed spin moment calculation To: "PWSCF Forum" Date: Thursday, March 12, 2009, 1:01 PM Sorry for confuse you ,? After checking the input and output file , I found that I also did ?a LiVO2 crystal calcualtion with the same problem, the input file?I?posted?is for LiNiO2 and the output file I posted??is for LiVO2? , here is the complete input and output file?from the same?calcualtion &control ??? calculation='scf' ??? restart_mode='from_scratch' , ??? pseudo_dir = '~/software/espresso-4test/pseudo', ??? outdir='outscf' ??? nstep=60 ??? prefix='AFM-type' ??? tstress = .true. ??? tprnfor = .true. ??? wf_collect=.true. ?/ ?&system ??? ibrav = 0, nat=16 , ntyp= 4, ??? ecutwfc = 35.0, ecutrho = 300.0, ??? occupations='tetrahedra', ??? nspin=2,constrained_magnetization='atomic',lambda=5.0, starting_magnetization(1)= 0.0, starting_magnetization(2)= 1.8, starting_magnetization(3)=-1.8, starting_magnetization(4)= 0.0, lda_plus_u=.true. Hubbard_U(1)=0.0 Hubbard_U(2)=3.0 Hubbard_U(3)=3.0 Hubbard_U(4)=0.0 ? ?/ ?&electrons ??? diagonalization='david', ??? conv_thr = 1.0e-7, ??? mixing_beta = 0.5, ?/ ? ATOMIC_SPECIES Li??? 6.914????? Li.pbe-n-mt_bw.UPF V1? 50.9415?? V.pbe-n-van.UPF V2? 50.9415?? V.pbe-n-van.UPF O?? 15.9994?? O.pbe-van_bm.UPF ATOMIC_POSITIONS {crystal} Li? 0.0000000000000000? 0.0000000000000000? 0.0 Li? 0.0000000000000000? 0.0000000000000000? 0.5 Li? 0.5000000000000000? 0.5000000000000000? 0.0 Li? 0.5000000000000000? 0.5000000000000000? 0.5 V1? 0.0000000000000000? 0.5000000000000000? 0.25 V2? 0.0000000000000000? 0.5000000000000000? 0.75 V2? 0.5000000000000000? 0.0000000000000000? 0.25 V1? 0.5000000000000000? 0.0000000000000000? 0.75 O?? 0.2354848230051515? 0.0000000000000000? 0.35287967 O?? 0.2354848230051515? 0.0000000000000000? 0.85287967 O?? 0.7354848230051516? 0.5000000000000000? 0.35287967 O?? 0.7354848230051516? 0.5000000000000000? 0.85287967 O?? 0.7645151769948484? 0.0000000000000000? 0.14712033 O?? 0.7645151769948484? 0.0000000000000000? 0.64712033 O?? 0.2645151769948484? 0.5000000000000000? 0.14712033 O?? 0.2645151769948484? 0.5000000000000000? 0.64712033 K_POINTS {automatic} ? 8 8 6? 1 1 1 CELL_PARAMETERS (alat) ??? 9.903876??? 0.000000??? 0.000000 ??? 0.000000??? 5.622988??? 0.000000 ?? -6.542514??? 0.000000?? 20.135790 ? the output file gives ? ?============================================================================== ???? atom number??? 4 relative position :??? 0.1697?? 0.2839?? 1.0166 ???? charge :???? 0.065485 ???? magnetization :????????? 0.000000 ???? magnetization/charge:??? 0.000000 ???? constrained moment :???? 0.000000 ???? ?============================================================================== ???? ?============================================================================== ???? atom number??? 5 relative position :?? -0.1652?? 0.2839?? 0.5083 ???? charge :???? 2.371448 ???? magnetization :????????? 1.554551 ???? magnetization/charge:??? 0.655528 ???? constrained moment :???? 1.800000 ???? ? I also? changed lambda from 1 to 5 and the?? final magnetic moment changed from 1.55 to 1.50 so the?parameter lambda?seems? have no impact on the final magnetic moment, there should be something wrong with my calcualtion but I can't spot this error. ? ? 2009/3/12 Gabriele Sclauzero Dear Yumin Qian, ? ?There's something strange in this output. I think that atom number 5 should be a Ni one, since you were interested in the magnetization of that species, but then, why is the charge around that atom only about 2.5? Ni should have 10 electrons in valence, so I would expect to get a number around 10 for the charge (unless the atom goes in a very ionized state, but that seems highly unprobable to me). Are you sure PPs and all the rest is OK? GS yumin qian wrote: > thanks for your reply ,I ?changed the lambda=5.0 and used > ? ?occupations='tetrahedra' ?but the magnetization still did not > converge to the initial value ,but the total energy converged. > I do know what is the problem. > ? ? ?============================================================================== > ? ? ?> ? ? ?atom number ? ?5 relative position : ? -0.1652 ? 0.2839 ? 0.5083 > ? ? ?> ? ? ?charge : ? ? 2.373353 > ? ? ?> ? ? ?magnetization : ? ? ? ? ?1.544423 > ? ? ?> ? ? ?magnetization/charge: ? ?0.650735 > ? ? ?> ? ? ?constrained moment : ? ? 1.800000 > ? ? ?> > ? ? ?> > ? ? ?============================================================================== > ? ? ?> the output file gives a magnetic moment of 1.5444 ,how should I do to > ? ? ?> make the calculation ?converge to the starting_magnetization 1.8 ? > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student ? ? ? ? ? ? ? ? ?| | c/o: ? SISSA & CNR-INFM Democritos, ? ? ? ? ? ? ?| | ? ? ? ?via Beirut 2-4, 34014 Trieste (Italy) ? ? | | email: sclauzer at sissa.it ? ? ? ? ? ? ? ? ? ? ? ? | | phone: +39 040 3787 511 ? ? ? ? ? ? ? ? ? ? ? ? ?| | skype: gurlonotturno ? ? ? ? ? ? ? ? ? ? ? ? ? ? | o ------------------------------------------------ o _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: ?+ 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 ? Beijing 100190 China _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090312/ee23a50f/attachment.htm From sclauzer at sissa.it Thu Mar 12 14:16:58 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 12 Mar 2009 14:16:58 +0100 Subject: [Pw_forum] fixed spin moment calculation In-Reply-To: References: <49B774D1.5050202@sissa.it> <49B8BE69.2010501@sissa.it> Message-ID: <49B90B4A.5090904@sissa.it> yumin qian wrote: > Sorry for confuse you , After checking the input and output file , I > found that I also did a LiVO2 crystal calcualtion with the same > problem, the input file I posted is for LiNiO2 and the output file I > posted is for LiVO2 , here is the complete input and output file from > the same calcualtion This does not help me to help you... why didn'y you post the full input file from the beginning? > > > ============================================================================== > atom number 5 relative position : -0.1652 0.2839 0.5083 > charge : 2.371448 > magnetization : 1.554551 > magnetization/charge: 0.655528 > constrained moment : 1.800000 > > > I also changed lambda from 1 to 5 and the final magnetic moment > changed from 1.55 to 1.50 It sounds strange to me that it decreases if you increase lambda, should be the opposite. > so the parameter lambda seems have no impact on the final magnetic > moment, there should be something wrong with my calcualtion but I can't > spot this error. Maybe a state with such a high local magnetization (consider that you have only 2.37 "local electrons") is energetically quite unfavored and putting the penalty with this lambda is not enough. You can try to increase more lambda. If it doesn't work, maybe there's some other problem I cannot see. GS -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From w2agz at pacbell.net Thu Mar 12 16:10:06 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Thu, 12 Mar 2009 08:10:06 -0700 Subject: [Pw_forum] ld1.x & US requires... In-Reply-To: References: <00a401c9a078$c224ef90$466eceb0$@net> <000d01c9a2cb$276d5ff0$76481fd0$@net> Message-ID: <005101c9a324$a2c96eb0$e85c4c10$@net> Thanks, Paolo. Actually, I was aware of that library of ld1.x input examples, but what I was actually asking about were there any similar examples for the 3d TMs around somewhere. I should have been more specific. Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Thursday, March 12, 2009 12:21 AM To: PWSCF Forum Subject: Re: [Pw_forum] ld1.x & US requires... On Mar 12, 2009, at 5:29 , Paul M. Grant wrote: > as far as I could find, none provided a large number of input examples > one could play around with see atomic_doc/pseudo_library --- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From pc229 at kent.ac.uk Fri Mar 13 01:23:46 2009 From: pc229 at kent.ac.uk (pc229 at kent.ac.uk) Date: Fri, 13 Mar 2009 00:23:46 GMT Subject: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system Message-ID: Dear PWscf developers,? I am trying to? optimize, on the latest version of the espresso code (v4.0.4 ),? the cell parameter and also the ionic coordinate of hematite.? Initially I treat hematite like an insulator using? the following pseudo-potential :Fe.pbe-sp-van_ak.UPF for? Iron and O.pbe-van_ak.UPF for oxygen (I attached the input at the bottom). To optimize? both atomic coordinates and cell parameters I used bfgs algorithm . As you know hematite is an open-shell system, and you need to define the spin orientation in order to describe it like a ferro-magnetic or anti-ferromagnetic system. I choose the anti-ferromagnetic one, that means? to have? the total magnetization equal to 0 every SCF cycle and absolute magnetization ranging from 11-16 (this highly pseudo potential dependent).?? Anyway, for the first SCF cycle the magnetization carried out is correct, while after the first geometry optimization step hematite starts to lose the spin and the energy? also dancing between two value not allowing the SCF to converge.? So attempting to managed this problem I try to run it like a metal introducing? a methfessel-paxton? smearing. Nothing seems to change, the SCF of the second optimization step doesn't converge as previously. Then I tried to restart my calculation from the first point coordinates and the first SCF step converged, whilst the next no as in the previous cases . This is very strange and get me frustrated ! Then I run the same calculation changing both optimization algorithm to damp for the ionic coordinate and damp-w for the cell. In this way the SCFs after the first optimization cycle seem to converge with the right magnetization and the next as well.? I did also a further trial, because I need to use the bfgs algorithm to optimize my structure. I tried to run the same system on a previous version of espresso (v.2.1.2), and treating it like a metal? (with methfessel-paxton? smering) and using bfgs for ionic coordinate and damp for cell optimization (since bfgs wasn't implemented to optimize the cell parameter in this version) the first SCF? reached the convergence and the following as well.?? How can I solve it ?? I also read in the documents related to PWscf that bfgs? for optimizing cell parameters (vc-relax) is still in a experimental version. Would it be possible that It has some problem with spin polarized systems?? How can I manage this problem? I need desperately to use bfgs to optimize the hematite.? ?? Best Regards, Piero ?&CONTROL ?????????????????????? title = 'opt_bulk_PBE_van3.inp' , ???????????????? calculation = 'vc-relax' , ??????????????? restart_mode = 'from_scratch' , ????????????????? wf_collect = .true. , ????????????????????? outdir = '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_PBE_van/' , ????????????????? pseudo_dir = '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/pseudo/' , ????????????????????? prefix = 'opt_bulk_PBE_van3.inp' , ?/ ?&SYSTEM ?????????????????????? ibrav = 5, ?????????????????? celldm(1) = 11.091428, ?????????????????? celldm(4) = 0.587237106, ???????????????????????? nat = 10, ??????????????????????? ntyp = 3, ???????????????????? ecutwfc = 50 , ?????????????????????? nosym = .true. , ??????????????????????? nbnd = 70, ?????????????????????? nelec = 100, ????????????????? tot_charge = 0.000000, ???????????????? occupations = 'fixed' , ?????????????????????? nspin = 2 , ?? starting_magnetization(1) = 1., ?? starting_magnetization(2) = -1., ?? starting_magnetization(3) = 0., ?????????? tot_magnetization = 0 , ?/ ?&ELECTRONS ?/ ?&IONS ??????????????? ion_dynamics = 'bfgs' , ?/ ?&CELL ?????????????? cell_dynamics = 'bfgs' , ?????????????????????? wmass = 2001.0060 , ???????????????? cell_dofree = 'all' , ?/ ATOMIC_SPECIES ?? Fe?? 55.62000? Fe.pbe-sp-van_ak.UPF? ? Fe1?? 55.62000? Fe.pbe-sp-van_ak.UPF? ??? O?? 15.99000? O.pbe-van_ak.UPF? ATOMIC_POSITIONS crystal? ? Fe?????? 0.144358141?? 0.144342247?? 0.144393006 ? Fe1????? 0.355605889?? 0.355642696?? 0.355656118 ? Fe1????? 0.644394003?? 0.644359012?? 0.644344959 ? Fe?????? 0.855641399?? 0.855655859?? 0.855605070 ? O??????? 0.556470421?? 0.943529173?? 0.250007053 ? O??????? 0.250006034?? 0.556470770?? 0.943529639 ? O??????? 0.943529367?? 0.250006711?? 0.556470944 ? O??????? 0.443532949?? 0.056467967?? 0.749992942 ? O??????? 0.749994148?? 0.443532454?? 0.056467520 ? O??????? 0.056467649?? 0.749993110?? 0.443532750???? K_POINTS automatic? ? 4 4 4?? 0 0 0 --? Pieremanuele Canepa Room 230 School of Physical Science? Ingram Building University of Kent, ?Canterbury, ?Kent, CT2 7NH? United Kingdom Cell: +44-7768685833 ID Skype: pieremanuele ID msn:?pieremanuele83 at hotmail.com -------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/9e16eaf1/attachment.htm From hushujun at mail.sdu.edu.cn Fri Mar 13 01:48:28 2009 From: hushujun at mail.sdu.edu.cn (Dr. Shu-jun Hu) Date: Fri, 13 Mar 2009 08:48:28 +0800 Subject: [Pw_forum] xcrysden+cygwin can't display relax process Message-ID: <436905308.15892@mail.sdu.edu.cn> Dear All, When I use the xcyrsden installed on cygwin to display the relaxing process, it just shows the initio structure (only one slide) rather than the whole process. Since some ions have been fixed in the input file, the new structure after each dynamic step is like: ***************** atom 140 type 1 force = 0.00621763 -0.00424409 -0.00889158 Total force = 0.061794 Total SCF correction = 0.002797 Entering Dynamics: iteration = 27 = 0.99727388 ATOMIC_POSITIONS (angstrom) Zn 0.000000000 0.000000000 0.000000000 0 0 0 Zn 2.815600000 1.625600000 0.000000000 0 0 0 O 0.000000000 0.000000000 1.986200000 0 0 0 ******************* The string '0 0 0' means the position of corresponding ions has been fix. When such strings have been removed from the output file, the whole relax process can be displayed correctly. I suggest removing the 0 0 0 string from the output file or fix the bug of xcrysden. Best Shujun From yuminqian at gmail.com Fri Mar 13 03:03:50 2009 From: yuminqian at gmail.com (yumin qian) Date: Fri, 13 Mar 2009 10:03:50 +0800 Subject: [Pw_forum] fixed spin moment calculation In-Reply-To: <49B90B4A.5090904@sissa.it> References: <49B774D1.5050202@sissa.it> <49B8BE69.2010501@sissa.it> <49B90B4A.5090904@sissa.it> Message-ID: Thanks for your reply , It's very kind of you ,I will try your it again following you suggestion 2009/3/12 Gabriele Sclauzero > > yumin qian wrote: > > Sorry for confuse you , After checking the input and output file , I > > found that I also did a LiVO2 crystal calcualtion with the same > > problem, the input file I posted is for LiNiO2 and the output file I > > posted is for LiVO2 , here is the complete input and output file from > > the same calcualtion > > This does not help me to help you... why didn'y you post the full input > file from the > beginning? > > > > > > > > ============================================================================== > > atom number 5 relative position : -0.1652 0.2839 0.5083 > > charge : 2.371448 > > magnetization : 1.554551 > > magnetization/charge: 0.655528 > > constrained moment : 1.800000 > > > > > > I also changed lambda from 1 to 5 and the final magnetic moment > > changed from 1.55 to 1.50 > > It sounds strange to me that it decreases if you increase lambda, should be > the opposite. > > > so the parameter lambda seems have no impact on the final magnetic > > moment, there should be something wrong with my calcualtion but I can't > > spot this error. > > Maybe a state with such a high local magnetization (consider that you have > only 2.37 > "local electrons") is energetically quite unfavored and putting the penalty > with this > lambda is not enough. > You can try to increase more lambda. If it doesn't work, maybe there's some > other problem > I cannot see. > > GS > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/bc587e39/attachment.htm From yuminqian at gmail.com Fri Mar 13 03:04:27 2009 From: yuminqian at gmail.com (yumin qian) Date: Fri, 13 Mar 2009 10:04:27 +0800 Subject: [Pw_forum] fixed spin moment calculation In-Reply-To: <673802.207.qm@web34806.mail.mud.yahoo.com> References: <673802.207.qm@web34806.mail.mud.yahoo.com> Message-ID: thanks for your reply , It is very kind of you 2009/3/12 e kb > Dear Yumin Qian, > You may want to check with another pseudopotential for Oxygen. It might be > totally unrelated but I've seen this attached in the details part: > > Warning: this O psp has been tested in liquid water simulations by > Patrick Sit and Nicola Marzari. Results for the diffusion coefficient > and pair correlation functions were at odd with those obtained with > other ultrasoft or norm-conserving pseudopotentials, and recently > published result. > > Emine Kucukbenli, grad student, SISSA, Italy. > > --- On *Thu, 3/12/09, yumin qian * wrote: > > From: yumin qian > Subject: Re: [Pw_forum] fixed spin moment calculation > To: "PWSCF Forum" > Date: Thursday, March 12, 2009, 1:01 PM > > > Sorry for confuse you , After checking the input and output file , I > found that I also did a LiVO2 crystal calcualtion with the same problem, > the input file I posted is for LiNiO2 and the output file I posted is for > LiVO2 , here is the complete input and output file from the > same calcualtion > > &control > calculation='scf' > restart_mode='from_scratch' , > pseudo_dir = '~/software/espresso-4test/pseudo', > outdir='outscf' > nstep=60 > prefix='AFM-type' > tstress = .true. > tprnfor = .true. > wf_collect=.true. > / > &system > ibrav = 0, nat=16 , ntyp= 4, > ecutwfc = 35.0, ecutrho = 300.0, > occupations='tetrahedra', > nspin=2,constrained_magnetization='atomic',lambda=5.0, > starting_magnetization(1)= 0.0, > starting_magnetization(2)= 1.8, > starting_magnetization(3)=-1.8, > starting_magnetization(4)= 0.0, > lda_plus_u=.true. > Hubbard_U(1)=0.0 > Hubbard_U(2)=3.0 > Hubbard_U(3)=3.0 > Hubbard_U(4)=0.0 > > / > &electrons > diagonalization='david', > conv_thr = 1.0e-7, > mixing_beta = 0.5, > / > > ATOMIC_SPECIES > Li 6.914 Li.pbe-n-mt_bw.UPF > V1 50.9415 V.pbe-n-van.UPF > V2 50.9415 V.pbe-n-van.UPF > O 15.9994 O.pbe-van_bm.UPF > ATOMIC_POSITIONS {crystal} > Li 0.0000000000000000 0.0000000000000000 0.0 > Li 0.0000000000000000 0.0000000000000000 0.5 > Li 0.5000000000000000 0.5000000000000000 0.0 > Li 0.5000000000000000 0.5000000000000000 0.5 > V1 0.0000000000000000 0.5000000000000000 0.25 > V2 0.0000000000000000 0.5000000000000000 0.75 > V2 0.5000000000000000 0.0000000000000000 0.25 > V1 0.5000000000000000 0.0000000000000000 0.75 > O 0.2354848230051515 0.0000000000000000 0.35287967 > O 0.2354848230051515 0.0000000000000000 0.85287967 > O 0.7354848230051516 0.5000000000000000 0.35287967 > O 0.7354848230051516 0.5000000000000000 0.85287967 > O 0.7645151769948484 0.0000000000000000 0.14712033 > O 0.7645151769948484 0.0000000000000000 0.64712033 > O 0.2645151769948484 0.5000000000000000 0.14712033 > O 0.2645151769948484 0.5000000000000000 0.64712033 > K_POINTS {automatic} > 8 8 6 1 1 1 > CELL_PARAMETERS (alat) > 9.903876 0.000000 0.000000 > 0.000000 5.622988 0.000000 > -6.542514 0.000000 20.135790 > > the output file gives > > > ============================================================================== > atom number 4 relative position : 0.1697 0.2839 1.0166 > charge : 0.065485 > magnetization : 0.000000 > magnetization/charge: 0.000000 > constrained moment : 0.000000 > > > ============================================================================== > > > ============================================================================== > atom number 5 relative position : -0.1652 0.2839 0.5083 > charge : 2.371448 > magnetization : 1.554551 > magnetization/charge: 0.655528 > constrained moment : 1.800000 > > > I also changed lambda from 1 to 5 and the final magnetic moment changed > from 1.55 to 1.50 > so the parameter lambda seems have no impact on the final magnetic moment, > there should be something wrong with my calcualtion but I can't spot this > error. > > > 2009/3/12 Gabriele Sclauzero > >> Dear Yumin Qian, >> >> There's something strange in this output. I think that atom number 5 >> should be a Ni >> one, since you were interested in the magnetization of that species, but >> then, why is the >> charge around that atom only about 2.5? Ni should have 10 electrons in >> valence, so I would >> expect to get a number around 10 for the charge (unless the atom goes in a >> very ionized >> state, but that seems highly unprobable to me). >> Are you sure PPs and all the rest is OK? >> >> >> GS >> >> yumin qian wrote: >> > thanks for your reply ,I changed the lambda=5.0 and used >> > occupations='tetrahedra' but the magnetization still did not >> > converge to the initial value ,but the total energy converged. >> > I do know what is the problem. >> > >> ============================================================================== >> > > atom number 5 relative position : -0.1652 0.2839 >> 0.5083 >> > > charge : 2.373353 >> > > magnetization : 1.544423 >> > > magnetization/charge: 0.650735 >> > > constrained moment : 1.800000 >> > > >> > > >> > >> ============================================================================== >> > > the output file gives a magnetic moment of 1.5444 ,how should I >> do to >> > > make the calculation converge to the starting_magnetization 1.8 >> ? >> > >> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Sincerely Y. M. Qian > Lab.of Condensed Matter Theory and Materials Computation > Institute of Physics > Chinese Academy of Sciences > Tel: + 8610 8264 9147 > E-Mail:yuminqian at gmail.com > P.O.Box 603 Beijing 100190 > China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Sincerely Y. M. Qian Lab.of Condensed Matter Theory and Materials Computation Institute of Physics Chinese Academy of Sciences Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/9b3bbfe0/attachment-0001.htm From lex at phys.ufl.edu Fri Mar 13 08:08:25 2009 From: lex at phys.ufl.edu (Lex Kemper) Date: Fri, 13 Mar 2009 03:08:25 -0400 Subject: [Pw_forum] xcrysden+cygwin can't display relax process In-Reply-To: <436905308.15892@mail.sdu.edu.cn> References: <436905308.15892@mail.sdu.edu.cn> Message-ID: <49BA0669.2090906@phys.ufl.edu> Hello Dr. Hu, XCrysDen uses an awk script to parse the relaxation output file. It doesn't like the 0 0 0 because it searches (as I recall) for lines that have 4 entries. It's relatively easy to change it so it'll search for lines that have 4 OR 7 entries. Cheers, Lex Kemper Department of Physics University of Florida Dr. Shu-jun Hu wrote: > Dear All, > > When I use the xcyrsden installed on cygwin to display the relaxing process, it > just shows the initio structure (only one slide) rather than the whole process. > Since some ions have been fixed in the input file, the new structure after each > dynamic step is like: > > ***************** > atom 140 type 1 force = 0.00621763 -0.00424409 -0.00889158 > > Total force = 0.061794 Total SCF correction = 0.002797 > > Entering Dynamics: iteration = 27 > > = 0.99727388 > > ATOMIC_POSITIONS (angstrom) > Zn 0.000000000 0.000000000 0.000000000 0 0 0 > Zn 2.815600000 1.625600000 0.000000000 0 0 0 > O 0.000000000 0.000000000 1.986200000 0 0 0 > ******************* > > The string '0 0 0' means the position of corresponding ions has been fix. When > such strings have been removed from the output file, the whole relax process can > be displayed correctly. I suggest removing the 0 0 0 string from the output file > or fix the bug of xcrysden. > > Best > > Shujun > > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sclauzer at sissa.it Fri Mar 13 09:00:51 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 13 Mar 2009 09:00:51 +0100 Subject: [Pw_forum] xcrysden+cygwin can't display relax process In-Reply-To: <436905308.15892@mail.sdu.edu.cn> References: <436905308.15892@mail.sdu.edu.cn> Message-ID: <49BA12B3.5070104@sissa.it> Dr. Shu-jun Hu wrote: > Dear All, > > When I use the xcyrsden installed on cygwin to display the relaxing process, it > just shows the initio structure (only one slide) rather than the whole process. > Since some ions have been fixed in the input file, the new structure after each > dynamic step is like: > > ***************** > atom 140 type 1 force = 0.00621763 -0.00424409 -0.00889158 > > Total force = 0.061794 Total SCF correction = 0.002797 > > Entering Dynamics: iteration = 27 > > = 0.99727388 > > ATOMIC_POSITIONS (angstrom) > Zn 0.000000000 0.000000000 0.000000000 0 0 0 > Zn 2.815600000 1.625600000 0.000000000 0 0 0 > O 0.000000000 0.000000000 1.986200000 0 0 0 > ******************* > > The string '0 0 0' means the position of corresponding ions has been fix. When > such strings have been removed from the output file, the whole relax process can > be displayed correctly. I suggest removing the 0 0 0 string from the output file > or fix the bug of xcrysden. Which bug? For me (on Linux...) xcrysden works perfectly in displaying the atomic coordinates of relax calculations. If you have clear evidence that this is a bug (and it has not been solved already in a later release... BTW, you did not mention which version of Xcrysden you're using, I suppose you already tried the last one) and it is reproducible, please send a pw output file that gives the error to the xcrysden mailing list (which is not this one). Removing that string from pw output is not good idea, since the atomic positions on the output can be reused as starting configuration for a successive relaxation in case one is obliged to restart from_scratch for some reason. Cheers GS > > Best > > Shujun > > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From giannozz at democritos.it Fri Mar 13 09:04:08 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Mar 2009 09:04:08 +0100 Subject: [Pw_forum] xcrysden+cygwin can't display relax process In-Reply-To: <436905308.15892@mail.sdu.edu.cn> References: <436905308.15892@mail.sdu.edu.cn> Message-ID: <49BA1378.70701@democritos.it> Dr. Shu-jun Hu wrote: > The string '0 0 0' means the position of corresponding ions has been fix. When > such strings have been removed from the output file, the whole relax process can > be displayed correctly. I suggest removing the 0 0 0 string from the output file > or fix the bug of xcrysden. which version of xcrysden are you using? I think this is fixed in the most recent versions P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From tone.kokalj at ijs.si Fri Mar 13 09:23:13 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 13 Mar 2009 09:23:13 +0100 Subject: [Pw_forum] xcrysden+cygwin can't display relax process In-Reply-To: <49BA1378.70701@democritos.it> References: <436905308.15892@mail.sdu.edu.cn> <49BA1378.70701@democritos.it> Message-ID: <1236932593.7411.25.camel@walk.ijs.si> On Fri, 2009-03-13 at 09:04 +0100, Paolo Giannozzi wrote: > Dr. Shu-jun Hu wrote: > > > The string '0 0 0' means the position of corresponding ions has been fix. When > > such strings have been removed from the output file, the whole relax process can > > be displayed correctly. I suggest removing the 0 0 0 string from the output file > > or fix the bug of xcrysden. > > which version of xcrysden are you using? I think this is fixed > in the most recent versions It is! Regards, Tone PS: If the error still persists in the new versions, follow the guidelines of Gabriele: send the output file. -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From eminekb at yahoo.com Fri Mar 13 09:25:40 2009 From: eminekb at yahoo.com (e kb) Date: Fri, 13 Mar 2009 01:25:40 -0700 (PDT) Subject: [Pw_forum] ld1.x & US requires... Message-ID: <7462.35400.qm@web34808.mail.mud.yahoo.com> Dear Paul, For 3d, I guess you can use the Fe psp input in the paw_library. Try commenting the? PAW tags if you want to have an input sample for ultrasoft to work on.. But, you may as well start using PAW instead. Emine Kucukbenli, PhD student, SISSA, Italy --- On Thu, 3/12/09, Paul M. Grant wrote: From: Paul M. Grant Subject: Re: [Pw_forum] ld1.x & US requires... To: "'PWSCF Forum'" Date: Thursday, March 12, 2009, 5:10 PM Thanks, Paolo. Actually, I was aware of that library of ld1.x input examples, but what I was actually asking about were there any similar examples for the 3d TMs around somewhere. I should have been more specific. Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Thursday, March 12, 2009 12:21 AM To: PWSCF Forum Subject: Re: [Pw_forum] ld1.x & US requires... On Mar 12, 2009, at 5:29 , Paul M. Grant wrote: > as far as I could find, none provided a large number of input examples > one could play around with see atomic_doc/pseudo_library --- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/06408946/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Fri Mar 13 12:21:25 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 13 Mar 2009 12:21:25 +0100 Subject: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system In-Reply-To: References: Message-ID: <200903131221.26257.giuseppe.mattioli@mlib.ism.cnr.it> Dear Piero > ?&ELECTRONS > ?/ The default beta mixing parameter is often too high to fit for many purposes. Try to use the keyword mixing_beta = 0.3 (e.g.) within the &electrons group. > ???????????????? occupations = 'fixed' , This is not a good choice (at least in my experience) when you deal with system in which the magnetization may change. Try to add a gaussian or a cold smearing. Yours Giuseppe On Friday 13 March 2009 01:23:46 pc229 at kent.ac.uk wrote: > Dear PWscf developers,? > I am trying to? optimize, on the latest version of the espresso code > (v4.0.4 ),? the cell parameter and also the ionic coordinate of hematite.? > Initially I treat hematite like an insulator using? the following > pseudo-potential :Fe.pbe-sp-van_ak.UPF for? Iron and O.pbe-van_ak.UPF for > oxygen (I attached the input at the bottom). To optimize? both atomic > coordinates and cell parameters I used bfgs algorithm . As you know > hematite is an open-shell system, and you need to define the spin > orientation in order to describe it like a ferro-magnetic or > anti-ferromagnetic system. I choose the anti-ferromagnetic one, that means? > to have? the total magnetization equal to 0 every SCF cycle and absolute > magnetization ranging from 11-16 (this highly pseudo potential dependent). > Anyway, for the first SCF cycle the magnetization carried out is correct, > while after the first geometry optimization step hematite starts to lose > the spin and the energy? also dancing between two value not allowing the > SCF to converge. So attempting to managed this problem I try to run it like > a metal introducing? a methfessel-paxton? smearing. Nothing seems to > change, the SCF of the second optimization step doesn't converge as > previously. Then I tried to restart my calculation from the first point > coordinates and the first SCF step converged, whilst the next no as in the > previous cases . This is very strange and get me frustrated ! Then I run > the same calculation changing both optimization algorithm to damp for the > ionic coordinate and damp-w for the cell. In this way the SCFs after the > first optimization cycle seem to converge with the right magnetization and > the next as well. I did also a further trial, because I need to use the > bfgs algorithm to optimize my structure. I tried to run the same system on > a previous version of espresso (v.2.1.2), and treating it like a metal? > (with methfessel-paxton? smering) and using bfgs for ionic coordinate and > damp for cell optimization (since bfgs wasn't implemented to optimize the > cell parameter in this version) the first SCF? reached the convergence and > the following as well. How can I solve it ?? I also read in the documents > related to PWscf that bfgs? for optimizing cell parameters (vc-relax) is > still in a experimental version. Would it be possible that It has some > problem with spin polarized systems?? How can I manage this problem? I need > desperately to use bfgs to optimize the hematite. > > ?? > Best Regards, Piero > > > ?&CONTROL > ?????????????????????? title = 'opt_bulk_PBE_van3.inp' , > ???????????????? calculation = 'vc-relax' , > ??????????????? restart_mode = 'from_scratch' , > ????????????????? wf_collect = .true. , > ????????????????????? outdir = > '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_PBE_v >an/' , pseudo_dir = > '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/pseudo/' , > prefix = 'opt_bulk_PBE_van3.inp' , > ?/ > ?&SYSTEM > ?????????????????????? ibrav = 5, > ?????????????????? celldm(1) = 11.091428, > ?????????????????? celldm(4) = 0.587237106, > ???????????????????????? nat = 10, > ??????????????????????? ntyp = 3, > ???????????????????? ecutwfc = 50 , > ?????????????????????? nosym = .true. , > ??????????????????????? nbnd = 70, > ?????????????????????? nelec = 100, > ????????????????? tot_charge = 0.000000, > ???????????????? occupations = 'fixed' , > ?????????????????????? nspin = 2 , > ?? starting_magnetization(1) = 1., > ?? starting_magnetization(2) = -1., > ?? starting_magnetization(3) = 0., > ?????????? tot_magnetization = 0 , > ?/ > ?&ELECTRONS > ?/ > ?&IONS > ??????????????? ion_dynamics = 'bfgs' , > ?/ > ?&CELL > ?????????????? cell_dynamics = 'bfgs' , > ?????????????????????? wmass = 2001.0060 , > ???????????????? cell_dofree = 'all' , > ?/ > ATOMIC_SPECIES > ?? Fe?? 55.62000? Fe.pbe-sp-van_ak.UPF? > ? Fe1?? 55.62000? Fe.pbe-sp-van_ak.UPF? > ??? O?? 15.99000? O.pbe-van_ak.UPF? > ATOMIC_POSITIONS crystal? > ? Fe?????? 0.144358141?? 0.144342247?? 0.144393006 > ? Fe1????? 0.355605889?? 0.355642696?? 0.355656118 > ? Fe1????? 0.644394003?? 0.644359012?? 0.644344959 > ? Fe?????? 0.855641399?? 0.855655859?? 0.855605070 > ? O??????? 0.556470421?? 0.943529173?? 0.250007053 > ? O??????? 0.250006034?? 0.556470770?? 0.943529639 > ? O??????? 0.943529367?? 0.250006711?? 0.556470944 > ? O??????? 0.443532949?? 0.056467967?? 0.749992942 > ? O??????? 0.749994148?? 0.443532454?? 0.056467520 > ? O??????? 0.056467649?? 0.749993110?? 0.443532750???? > K_POINTS automatic? > ? 4 4 4?? 0 0 0 > > > --? > Pieremanuele Canepa > Room 230 > School of Physical Science? > Ingram Building > University of Kent, > ?Canterbury, > ?Kent, CT2 7NH? > United Kingdom > Cell: +44-7768685833 > ID Skype: pieremanuele > ID msn:?pieremanuele83 at hotmail.com > -------------------------------------------------------- -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00016 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/ea4f6c17/attachment-0001.htm From panda.deng.pan at gmail.com Fri Mar 13 13:25:22 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Fri, 13 Mar 2009 20:25:22 +0800 Subject: [Pw_forum] forrtl: severe (59) Message-ID: Dear all users, When I was about to calculate the fermisurface, after it have done a nscf run, it gave the error message like this in the turn of which bands_FS.x should be run: forrtl: severe (59): list-directed I/O syntax error, unit 5, file stdin I have no idea what happened.And my inputs for the bands_FS.x. input_FS 16 23 11.6147 LaFeAsO 10 10 10 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.461340 and another input is the output of the nscf run, here is the input of nscf running. &control calculation = 'nscf' prefix='LaFeAsO', pseudo_dir = '/disk2/xgwan/Quantum-Espresso/espresso-4.0.3/pseudo/', outdir='/disk2/xgwan/tmp/' / &system ibrav=6, celldm(1)=7.6232, celldm(3)=2.1676, nat=8, ntyp=4, ecutwfc = 40.0, ecutrho = 300.0, occupations= 'smearing' degauss = 0.03 smearing = 'marzari-vanderbilt' / &electrons mixing_beta = 0.7 conv_thr = 1.0d-11 / ATOMIC_SPECIES La 57.0 La.pbe-nsp-van.UPF Fe 28.0 Fe.pbe-sp-van.UPF As 33.0 As.pbe-n-van.UPF O 16.0 O.pbe-rrkjus.UPF ATOMIC_POSITIONS {crystal} La 0.25 0.25 0.14134 La 0.75 0.75 0.85866 Fe 0.75 0.25 0.5 Fe 0.25 0.75 0.5 As 0.25 0.25 0.65166 As 0.75 0.75 0.34834 O 0.75 0.25 0.0 O 0.25 0.75 0.0 K_POINTS 1331 0.000000 0.000000 0.000000 1.00 0.000000 0.000000 0.046134 1.00 0.000000 0.000000 0.092268 1.00 0.000000 0.000000 0.138402 1.00 0.000000 0.000000 0.184536 1.00 I omitted others K_points here which is generated by kvecs_FS.x. I am appraciate for any suggest and comment. Have a nice day. Pan Deng Nanjing University From giannozz at democritos.it Fri Mar 13 14:58:07 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Mar 2009 14:58:07 +0100 Subject: [Pw_forum] forrtl: severe (59) In-Reply-To: References: Message-ID: <49BA666F.9060304@democritos.it> ?? wrote: > forrtl: severe (59): list-directed I/O syntax error, unit 5, file stdin > > I have no idea what happened then you better learn how to have an idea: these are trivial problems whose solution can be found more often than not by just searching the net. If you search the above message in the mailing list archive, you will find an explanation of what the message means: "wrong input data read from input" (and, by the way, "forrtl" = "fortran run-time library") P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From pc229 at kent.ac.uk Fri Mar 13 15:07:22 2009 From: pc229 at kent.ac.uk (pc229 at kent.ac.uk) Date: Fri, 13 Mar 2009 14:07:22 GMT Subject: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system In-Reply-To: <200903131221.26257.giuseppe.mattioli@mlib.ism.cnr.it> References: <200903131221.26257.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Thanks for the reply, buT I am still thinking that should be a bug in the optimizer, since? I also tried to run my system like a metal and nothing gonna change. If I change the optimization method I can reach easly the convergence. Cheers, Piero? ----- Original Message ----- From: Giuseppe Mattioli Date: Friday, March 13, 2009 11:21 am Subject: Re: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system To: PWSCF Forum > > Dear Piero > > > ?&ELECTRONS > > ?/ > The default beta mixing parameter is often too high to fit for > many purposes. > Try to use the keyword mixing_beta = 0.3 (e.g.) within the > &electrons group. > > ?> ???????????????? occupations = 'fixed' , > This is not a good choice (at least in my experience) when you > deal with > system in which the magnetization may change. Try to add a > gaussian or a cold > smearing. > > Yours > > Giuseppe > ? > On Friday 13 March 2009 01:23:46 pc229 at kent.ac.uk wrote: > > > Dear PWscf developers,? > > I am trying to? optimize, on the latest version of the > espresso code > > (v4.0.4 ),? the cell parameter and also the ionic coordinate > of hematite.? > > Initially I treat hematite like an insulator using? the following > > pseudo-potential :Fe.pbe-sp-van_ak.UPF for? Iron and O.pbe- > van_ak.UPF for > > oxygen (I attached the input at the bottom). To optimize? both > atomic> coordinates and cell parameters I used bfgs algorithm . > As you know > > hematite is an open-shell system, and you need to define the spin > > orientation in order to describe it like a ferro-magnetic or > > anti-ferromagnetic system. I choose the anti-ferromagnetic > one, that means? > > to have? the total magnetization equal to 0 every SCF cycle > and absolute > > magnetization ranging from 11-16 (this highly pseudo potential > dependent).> Anyway, for the first SCF cycle the magnetization > carried out is correct, > > while after the first geometry optimization step hematite > starts to lose > > the spin and the energy? also dancing between two value not > allowing the > > SCF to converge. So attempting to managed this problem I try > to run it like > > a metal introducing? a methfessel-paxton? smearing. Nothing > seems to > > change, the SCF of the second optimization step doesn't > converge as > > previously. Then I tried to restart my calculation from the > first point > > coordinates and the first SCF step converged, whilst the next > no as in the > > previous cases . This is very strange and get me frustrated ! > Then I run > > the same calculation changing both optimization algorithm to > damp for the > > ionic coordinate and damp-w for the cell. In this way the SCFs > after the > > first optimization cycle seem to converge with the right > magnetization and > > the next as well. I did also a further trial, because I need > to use the > > bfgs algorithm to optimize my structure. I tried to run the > same system on > > a previous version of espresso (v.2.1.2), and treating it like > a metal? > > (with methfessel-paxton? smering) and using bfgs for ionic > coordinate and > > damp for cell optimization (since bfgs wasn't implemented to > optimize the > > cell parameter in this version) the first SCF? reached the > convergence and > > the following as well. How can I solve it ?? I also read in > the documents > > related to PWscf that bfgs? for optimizing cell parameters (vc- > relax) is > > still in a experimental version. Would it be possible that It > has some > > problem with spin polarized systems?? How can I manage this > problem? I need > > desperately to use bfgs to optimize the hematite. > > > > ?? > > Best Regards, Piero > > > > > > ?&CONTROL > > ?????????????????????? title = 'opt_bulk_PBE_van3.inp' , > > ???????????????? calculation = 'vc-relax' , > > ??????????????? restart_mode = 'from_scratch' , > > ????????????????? wf_collect = .true. , > > ????????????????????? outdir = > > > '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_PBE_v>an/' , pseudo_dir = > > > '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/pseudo/' , > > prefix = 'opt_bulk_PBE_van3.inp' , > > ?/ > > ?&SYSTEM > > ?????????????????????? ibrav = 5, > > ?????????????????? celldm(1) = 11.091428, > > ?????????????????? celldm(4) = 0.587237106, > > ???????????????????????? nat = 10, > > ??????????????????????? ntyp = 3, > > ???????????????????? ecutwfc = 50 , > > ?????????????????????? nosym = .true. , > > ??????????????????????? nbnd = 70, > > ?????????????????????? nelec = 100, > > ????????????????? tot_charge = 0.000000, > > ???????????????? occupations = 'fixed' , > > ?????????????????????? nspin = 2 , > > ?? starting_magnetization(1) = 1., > > ?? starting_magnetization(2) = -1., > > ?? starting_magnetization(3) = 0., > > ?????????? tot_magnetization = 0 , > > ?/ > > ?&ELECTRONS > > ?/ > > ?&IONS > > ??????????????? ion_dynamics = 'bfgs' , > > ?/ > > ?&CELL > > ?????????????? cell_dynamics = 'bfgs' , > > ?????????????????????? wmass = 2001.0060 , > > ???????????????? cell_dofree = 'all' , > > ?/ > > ATOMIC_SPECIES > > ?? Fe?? 55.62000? Fe.pbe-sp-van_ak.UPF? > > ? Fe1?? 55.62000? Fe.pbe-sp-van_ak.UPF? > > ??? O?? 15.99000? O.pbe-van_ak.UPF? > > ATOMIC_POSITIONS crystal? > > ? Fe?????? 0.144358141?? 0.144342247?? 0.144393006 > > ? Fe1????? 0.355605889?? 0.355642696?? 0.355656118 > > ? Fe1????? 0.644394003?? 0.644359012?? 0.644344959 > > ? Fe?????? 0.855641399?? 0.855655859?? 0.855605070 > > ? O??????? 0.556470421?? 0.943529173?? 0.250007053 > > ? O??????? 0.250006034?? 0.556470770?? 0.943529639 > > ? O??????? 0.943529367?? 0.250006711?? 0.556470944 > > ? O??????? 0.443532949?? 0.056467967?? 0.749992942 > > ? O??????? 0.749994148?? 0.443532454?? 0.056467520 > > ? O??????? 0.056467649?? 0.749993110?? 0.443532750???? > > K_POINTS automatic? > > ? 4 4 4?? 0 0 0 > > > > > > --? > > Pieremanuele Canepa > > Room 230 > > School of Physical Science? > > Ingram Building > > University of Kent, > > ?Canterbury, > > ?Kent, CT2 7NH? > > United Kingdom > > Cell: +44-7768685833 > > ID Skype: pieremanuele > > ID msn:?pieremanuele83 at hotmail.com > > -------------------------------------------------------- > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > ?? Giuseppe > Mattioli??????????????????????????? > ?? CNR - ISTITUTO DI STRUTTURA DELLA > MATERIA?? > ?? v. Salaria Km 29,300 - C.P. > 10??????????????? > ?? I 00016 - Monterotondo Stazione > (RM)????????? > ?? Tel + 39 06 90672836 - Fax +39 06 > 90672316??? > ?? E-mail: > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/8f287951/attachment-0001.htm From paulatto at sissa.it Fri Mar 13 15:09:42 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 13 Mar 2009 15:09:42 +0100 Subject: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system In-Reply-To: References: <200903131221.26257.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: On Fri, 13 Mar 2009 15:07:22 +0100, wrote: > Thanks for the reply, > buT I am still thinking that should be a bug in the optimizer, since I > also tried to run my system like a metal and nothing gonna change. If I were you, I would try without the "cell_dofree" option, which has not been maintained in awhile, to the point I'm not sure it is working as it should, especially for BFGS. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From giannozz at democritos.it Fri Mar 13 16:15:23 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 Mar 2009 16:15:23 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: Message-ID: <49BA788B.6020405@democritos.it> Aihua Zhang wrote: > from electrons : error # 1 > charge is wrong on which machine (hardware and software) do you get this error? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giuseppe.mattioli at mlib.ism.cnr.it Fri Mar 13 17:16:22 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 13 Mar 2009 17:16:22 +0100 Subject: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system In-Reply-To: References: Message-ID: <200903131716.23326.giuseppe.mattioli@mlib.ism.cnr.it> > If I were you, I would try without the "cell_dofree" option, which has not > been maintained in awhile, to the point I'm not sure it is working as it > should, especially for BFGS. I may have missed it, but if not I suggest including a comprehensive example regarding the use of different vc-relax schemes within the next QE distribution... However I used recently the bfgs (both on the ions and on the cell parameters) method and the cell_dofree option without problems. I still suspect that Piero's problem concerns some "electronic" stuff. export FILE="anat12-vcr-bfgs" export INPFILE=$FILE-2.inp export OUTFILE=$FILE-2.out echo " $FILE" echo " $INPFILE" echo " $OUTFILE" cat > $INPFILE << EOF &control calculation = 'vc-relax' restart_mode='restart', prefix='$FILE', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/', tstress=.true., tprnfor=.true., nstep=200, etot_conv_thr=1.0E-5, forc_conv_thr=1.0D-4, / &system ibrav=6, celldm(1)=7.15262, celldm(3)=2.51360, nat=12, ntyp=2, ecutwfc=25.0, ecutrho=150., occupations='smearing', degauss=0.01, nspin=1, / &electrons mixing_mode='plain' mixing_beta=0.3 conv_thr=1.0d-9 electron_maxstep=200 / &ions ion_dynamics='bfgs' / &cell cell_dynamics='bfgs', press =0.00, cell_dofree='xyz', / ATOMIC_SPECIES Ti 47.900 Ti12_pbe.van.UPF O 15.999 O_pbe.van.UPF ATOMIC_POSITIONS {crystal} Ti 0.0000 0.0000 0.0000 Ti 0.0000 0.5000 0.2500 Ti 0.5000 0.5000 0.5000 Ti 0.5000 1.0000 0.7500 O 0.0000 0.0000 0.2066 O 0.0000 0.0000 -0.2066 O 0.0000 0.5000 0.4566 O 0.0000 0.5000 0.0434 O 0.5000 0.5000 0.7066 O 0.5000 0.5000 0.2934 O 0.5000 1.0000 0.9566 O 0.5000 1.0000 0.5434 K_POINTS {automatic} 4, 4, 2, 0, 0, 0 EOF $PARA_PREFIX $ESPRESSO/pw.x $PARA_POSTFIX < $INPFILE >> $OUTFILE On Friday 13 March 2009 15:09:42 Lorenzo Paulatto wrote: > On Fri, 13 Mar 2009 15:07:22 +0100, wrote: > > Thanks for the reply, > > buT I am still thinking that should be a bug in the optimizer, since I > > also tried to run my system like a metal and nothing gonna change. > > > cheers -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00016 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/5287bdaf/attachment.htm From paulatto at sissa.it Fri Mar 13 17:20:09 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 13 Mar 2009 17:20:09 +0100 Subject: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system In-Reply-To: <200903131716.23326.giuseppe.mattioli@mlib.ism.cnr.it> References: <200903131716.23326.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: On Fri, 13 Mar 2009 17:16:22 +0100, Giuseppe Mattioli wrote: > I still suspect that > Piero's problem concerns some "electronic" stuff. yes, of course, but if the minimization algorithm doesn't work well it can take the system to some weird configuration that have trouble converging... this is only a theory of course. Also disabling charge and potential interpolation may help. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From pc229 at kent.ac.uk Fri Mar 13 19:05:40 2009 From: pc229 at kent.ac.uk (pc229 at kent.ac.uk) Date: Fri, 13 Mar 2009 18:05:40 GMT Subject: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system In-Reply-To: References: <200903131716.23326.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Thanks, the solution to the? problem was cell_dofree, removing it . It's work even if at the second SCF hemaite starts with absolute magnetization equal to 0.47, and after some cycles it's becoming higher 13 34 Bohr mag /cell. It is allright ? ----- Original Message ----- From: Lorenzo Paulatto Date: Friday, March 13, 2009 4:20 pm Subject: Re: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system To: PWSCF Forum > On Fri, 13 Mar 2009 17:16:22 +0100, Giuseppe Mattioli > wrote: > > > I still suspect that > > Piero's problem concerns some "electronic" stuff. > > yes, of course, but if the minimization algorithm doesn't work > well it can take the system to some weird configuration that > have trouble converging... this is only a theory of course. Also > disabling charge and potential interpolation may help. > > cheers > > > > > -- > Lorenzo Paulatto > SISSA? &? DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www:?? http://people.sissa.it/~paulatto/ > > ???? *** save italian brains *** > ?http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/cf9fd721/attachment.htm From pc229 at kent.ac.uk Fri Mar 13 19:08:34 2009 From: pc229 at kent.ac.uk (pc229 at kent.ac.uk) Date: Fri, 13 Mar 2009 18:08:34 GMT Subject: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system In-Reply-To: References: <200903131716.23326.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Thanks, the solution to the? problem was cell_dofree, removing the optimization works fine,? even if at the second SCF hemaite starts with absolute magnetization equal to 0.47, and after some cycles it's becoming higher 13.34 Bohr mag /cell. It is allright ? Thanks Piero ----- Original Message ----- From: pc229 at kent.ac.uk Date: Friday, March 13, 2009 6:05 pm Subject: Re: [Pw_forum] roblem with bfgs algorithm optimizer for spin polarized system To: PWSCF Forum > Thanks, > the solution to the? problem was cell_dofree, removing it . It's > work even if at the second SCF hemaite starts with absolute > magnetization equal to 0.47, and after some cycles it's becoming > higher 13 34 Bohr mag /cell. It is allright ? > > ----- Original Message ----- > From: Lorenzo Paulatto > Date: Friday, March 13, 2009 4:20 pm > Subject: Re: [Pw_forum] roblem with bfgs algorithm optimizer for > spin polarized system > To: PWSCF Forum > > > On Fri, 13 Mar 2009 17:16:22 +0100, Giuseppe Mattioli > > wrote: > > > > > I still suspect that > > > Piero's problem concerns some "electronic" stuff. > > > > yes, of course, but if the minimization algorithm doesn't work > > well it can take the system to some weird configuration that > > have trouble converging... this is only a theory of course. > Also > > disabling charge and potential interpolation may help. > > > > cheers > > > > > > > > > > -- > > Lorenzo Paulatto > > SISSA? &? DEMOCRITOS (Trieste) > > phone: +39 040 3787 511 > > skype: paulatz > > www:?? http://people.sissa.it/~paulatto/ > > > > ???? *** save italian brains *** > > ?http://saveitalianbrains.wordpress.com/ > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090313/14b5fa3e/attachment.htm From zah7903 at gmail.com Sat Mar 14 02:54:24 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Sat, 14 Mar 2009 02:54:24 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: <49BA788B.6020405@democritos.it> References: <49BA788B.6020405@democritos.it> Message-ID: CPU is opteron 850. Compiler is pgf95 8.0-4 64-bit target on x86-64 Linux -tp k8-64. Linked with amcl. QE is 4.0.4. The problem is extremely subtle. It disappears if any one of the following changes is applied: nproc is changed (6 or 10 instead of 8) npool is changed (2 instead of default 1) kpoint is changed (4x4x1 instead of 6x6x1, or shifted by 1 1 1) cutfoff is lowered to 30 Ry one layer of atoms is removed. and the problem is not influenced by different occupations schemes, different number of bands (nbnd). The charge is already incorrect before psymrho. The orbitals are orthogonal after c_bands. Aihua On Fri, Mar 13, 2009 at 4:15 PM, Paolo Giannozzi wrote: > Aihua Zhang wrote: > > > from electrons : error # 1 > > charge is wrong > > on which machine (hardware and software) do you get this error? > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090314/ac1cf600/attachment.htm From zah7903 at gmail.com Sat Mar 14 02:59:19 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Sat, 14 Mar 2009 02:59:19 +0100 Subject: [Pw_forum] dipole moment calculation In-Reply-To: References: <20090310202812.vntqrcdig0owooss@mail.democritos.it> Message-ID: Hi, The snippet of code in compute_dip.f90 I changed is as following ! rijk(ipol) = REAL(i1,dp)*at(ipol,1)*deltax + & ! REAL(j1,dp)*at(ipol,2)*deltay + & ! REAL(k11,dp)*at(ipol,3)*deltaz rijk(ipol) = (REAL(i,dp)-1.d0)*at(ipol,1)*deltax + & (REAL(j,dp)-1.d0)*at(ipol,2)*deltay + & (REAL(k,dp)-1.d0)*at(ipol,3)*deltaz It works in my test of water. Someone who understands the code thoroughly should proof the change. Aihua On Wed, Mar 11, 2009 at 9:38 AM, Lorenzo Paulatto wrote: > On Wed, 11 Mar 2009 05:24:38 +0100, Aihua Zhang wrote: > > The second possible bug is in compute_dip.f90, where r and r in rho(r) > > seem dismatch when calculating the electronic dipole. After matching r > with > > rho(r) in the code, the reasonable identical results are obtains, i.e. > > the calculated dipole and total energy are independent of where the > molecule > > is put in the supercell. > > Good job Aihua Zhang! > Could you please provide more information on this bug, so it can be fixed > mainstream? > I have long suspected a bug in that part, and I know at least another > person who's working on it at the moment, as far as I know with no luck. > > cheers > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090314/6bb87fb1/attachment.htm From sporevoyager at gmail.com Sat Mar 14 06:49:03 2009 From: sporevoyager at gmail.com (shangy) Date: Sat, 14 Mar 2009 13:49:03 +0800 Subject: [Pw_forum] HSE pseudopotentials Message-ID: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com> Dear all: Does anyone has the Si pseudopotentials generated by the screened-exchange hybrid functional of Heyd, Scuseria, and Ernerhof [HSE, J. Chem. Phys. 118, 8207 (2003)]? Can it work well within QE? If anyone has one, would you share it with me? I'm very very thirsty for it. Thanks in advance. Best regards. shangy Graduate unversity of Chinese academy of sciences -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090314/f5b23d3f/attachment.htm From giannozz at democritos.it Sat Mar 14 10:39:49 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 14 Mar 2009 10:39:49 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49BA788B.6020405@democritos.it> Message-ID: On Mar 14, 2009, at 2:54 , Aihua Zhang wrote: > Compiler is pgf95 8.0-4 64-bit target on x86-64 Linux -tp k8-64. ah...I reproduced your problem on a different machine (cray xt4) that also uses PGI; when I tried on my PC that uses Intel fortran, I couldn't reproduce it. > The problem is extremely subtle the more I look at it, the more it looks like a compiler bug. There is a long list of problems with PGI that turned out to be due to compiler bugs. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Sat Mar 14 16:28:03 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 14 Mar 2009 11:28:03 -0400 Subject: [Pw_forum] HSE pseudopotentials In-Reply-To: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com> References: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com> Message-ID: <1237044483.3030.11.camel@zero> On Sat, 2009-03-14 at 13:49 +0800, shangy wrote: > Dear all: > Does anyone has the Si pseudopotentials generated by the > screened-exchange hybrid functional of Heyd, Scuseria, and Ernerhof > [HSE, J. Chem. Phys. 118, 8207 (2003)]? Can it work well within QE? If i don't know of any atomic code yet, that does produce hybrid dft pseudopotentials. people usually use the ones from the underlying regular GGA functional (i.e. PBE) in your case. that being said, i don't see any indication that HSE has yet been implemented directly into Q-E. i understand it is just strongly screened variation of PBE0, so you may be able to implement it yourself. > anyone has one, would you share it with me? I'm very very thirsty for > it. Thanks in advance. the potential wouldn't help you much... see above. you'll have to try something else to quench your thirst. cheers, axel. > Best regards. > > shangy > Graduate unversity of Chinese academy of sciences > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From zah7903 at gmail.com Sun Mar 15 02:16:18 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Sun, 15 Mar 2009 02:16:18 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49BA788B.6020405@democritos.it> Message-ID: I think you are right. It is also possible that it's a problem of acml library. A pwscf binary compiled by pgif90 but linked with mkl works smoothly. Aihua On Sat, Mar 14, 2009 at 10:39 AM, Paolo Giannozzi wrote: > > On Mar 14, 2009, at 2:54 , Aihua Zhang wrote: > > > Compiler is pgf95 8.0-4 64-bit target on x86-64 Linux -tp k8-64. > > ah...I reproduced your problem on a different machine (cray xt4) > that also uses PGI; when I tried on my PC that uses Intel fortran, > I couldn't reproduce it. > > > The problem is extremely subtle > > the more I look at it, the more it looks like a compiler bug. > There is a long list of problems with PGI that turned out > to be due to compiler bugs. > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090315/92f2c34a/attachment.htm From phylyh at nus.edu.sg Sun Mar 15 07:54:37 2009 From: phylyh at nus.edu.sg (Lu Yunhao) Date: Sun, 15 Mar 2009 14:54:37 +0800 Subject: [Pw_forum] error about band calculation with pw.x Message-ID: <000301c9a53a$e7fb44a0$474f8489@nusa0bcf64b485> Dear All I do a band calculation after scf, but the follow error always appear. I search in google, It may come from vc-relax, however I never set that. ........... total cpu time spent up to now is 69.56 secs per-process dynamical memory: 376.6 Mb Band Structure Calculation Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% from pzpotrf : error # 151 problems computing cholesky decomposition %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% stopping ... Best regards Yunhao -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090315/4a65d996/attachment.htm From sporevoyager at gmail.com Sun Mar 15 10:53:34 2009 From: sporevoyager at gmail.com (shangy) Date: Sun, 15 Mar 2009 17:53:34 +0800 Subject: [Pw_forum] HSE pseudopotentials In-Reply-To: <1237044483.3030.11.camel@zero> References: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com> <1237044483.3030.11.camel@zero> Message-ID: <94be399f0903150253o4faf71e1w5710442afeae7b46@mail.gmail.com> Deal Axel: Thanks for your kindly reply. I'm not clear about how to generate HSE pseudopotentials directly or indirectly. The paper [PRB 74 121102(R)] demonstrated that the HSE functonal can enable accurate computations on defects in Si in compariation with tradtiona DFT (i.e. LDA, PW91, PBE). Therefore, I want to reproduce their results within Q-E and hope it could solve my calculation problems. As your comment, the paper said "The HSE functional mixes in a fraction (25%) of exact screened Hartree-Fock exchange as done in the PBE hybird (PBEh) funcitonal. The key difference in the HSE, relative to the PBEh functional, is that the exact exchange term is screened at large distances, effectively giving a hybird functional only at short range and GGA behaivor at long range." Their HSE calculations are carried out using GAUSSIAN. But I have no idea to reproduce their results within Q-E. Would you like to give me some indications on the problem? And would you so kindly to share your Si PBE0 pseudopotential with me if you have one? Thanks for your reply again. Best regards! shangy Graduate unversity of Chinese academy of sciences 2009/3/14 Axel Kohlmeyer > On Sat, 2009-03-14 at 13:49 +0800, shangy wrote: > > Dear all: > > Does anyone has the Si pseudopotentials generated by the > > screened-exchange hybrid functional of Heyd, Scuseria, and Ernerhof > > [HSE, J. Chem. Phys. 118, 8207 (2003)]? Can it work well within QE? If > > i don't know of any atomic code yet, that does produce hybrid > dft pseudopotentials. people usually use the ones from the underlying > regular GGA functional (i.e. PBE) in your case. > > that being said, i don't see any indication that HSE has yet > been implemented directly into Q-E. i understand it is just > strongly screened variation of PBE0, so you may be able to > implement it yourself. > > > anyone has one, would you share it with me? I'm very very thirsty for > > it. Thanks in advance. > > the potential wouldn't help you much... see above. you'll have to > try something else to quench your thirst. > > cheers, > axel. > > > Best regards. > > > > shangy > > Graduate unversity of Chinese academy of sciences > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090315/e1603dcb/attachment.htm From akohlmey at cmm.chem.upenn.edu Sun Mar 15 14:33:24 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 15 Mar 2009 09:33:24 -0400 Subject: [Pw_forum] error about band calculation with pw.x In-Reply-To: <000301c9a53a$e7fb44a0$474f8489@nusa0bcf64b485> References: <000301c9a53a$e7fb44a0$474f8489@nusa0bcf64b485> Message-ID: <1237124004.4146.0.camel@zero> On Sun, 2009-03-15 at 14:54 +0800, Lu Yunhao wrote: > Dear All > > > > I do a band calculation after scf, but the follow error always appear. > I search in google, It may come from vc-relax, however I never set > that. have you found (and tried) this as well? http://www.democritos.it/pipermail/pw_forum/2008-July/009397.html cheers, axel. > > > > ?????????.. > > total cpu time spent up to now is 69.56 secs > > > > per-process dynamical memory: 376.6 Mb > > > > Band Structure Calculation > > Davidson diagonalization with overlap > > c_bands: 1 eigenvalues not converged > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > > from pzpotrf : error # 151 > > problems computing cholesky decomposition > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > > > > stopping ... > > > > > > > > Best regards > > Yunhao > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Sun Mar 15 14:43:57 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 15 Mar 2009 09:43:57 -0400 Subject: [Pw_forum] HSE pseudopotentials In-Reply-To: <94be399f0903150253o4faf71e1w5710442afeae7b46@mail.gmail.com> References: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com> <1237044483.3030.11.camel@zero> <94be399f0903150253o4faf71e1w5710442afeae7b46@mail.gmail.com> Message-ID: <1237124637.4146.10.camel@zero> On Sun, 2009-03-15 at 17:53 +0800, shangy wrote: > Deal Axel: dear shangy, > Thanks for your kindly reply. I'm not clear about how to generate > HSE pseudopotentials directly or indirectly. The paper [PRB 74 please tell what i have to do, so that you actually _do read_ what i wrote. i told you that people use regular (i.e. non-hybrid DFT) pseudopotentials, i.e. in your case a PBE pseudopotential. > 121102(R)] demonstrated that the HSE functonal can enable accurate > computations on defects in Si in compariation with tradtiona DFT (i.e. > LDA, PW91, PBE). Therefore, I want to reproduce their results within > Q-E and hope it could solve my calculation problems. as i wrote, the problem is _not_ the pseudopotential, but rather the fact that HSE as such does not (yet) seem to be implemented in Q-E. > As your comment, the paper said "The HSE functional mixes in a > fraction (25%) of exact screened Hartree-Fock exchange as done in the > PBE hybird (PBEh) funcitonal. The key difference in the HSE, relative > to the PBEh functional, is that the exact exchange term is screened at > large distances, effectively giving a hybird functional only at short > range and GGA behaivor at long range." Their HSE calculations are > carried out using GAUSSIAN. But I have no idea to reproduce their > results within Q-E. Would you like to give me some indications on the i already did. you have to implement it into Q-E. the code does have an (experimental) option to compile in exact exchange and within that framework, PBE0 and B3LYP seem to be available. thus also support for HSE would in principle be possible, but _not_ without programming. > problem? And would you so kindly to share your Si PBE0 > pseudopotential with me if you have one? please try to make sense in what you write. how should i have a PBE0 potential, if i don't know of any code that can generate one?? cheers, axel. > Thanks for your reply again. > Best regards! > > shangy > Graduate unversity of Chinese academy of sciences > > 2009/3/14 Axel Kohlmeyer > On Sat, 2009-03-14 at 13:49 +0800, shangy wrote: > > Dear all: > > Does anyone has the Si pseudopotentials generated by > the > > screened-exchange hybrid functional of Heyd, Scuseria, and > Ernerhof > > [HSE, J. Chem. Phys. 118, 8207 (2003)]? Can it work well > within QE? If > > > i don't know of any atomic code yet, that does produce hybrid > dft pseudopotentials. people usually use the ones from the > underlying > regular GGA functional (i.e. PBE) in your case. > > that being said, i don't see any indication that HSE has yet > been implemented directly into Q-E. i understand it is just > strongly screened variation of PBE0, so you may be able to > implement it yourself. > > > anyone has one, would you share it with me? I'm very very > thirsty for > > it. Thanks in advance. > > > the potential wouldn't help you much... see above. you'll have > to > try something else to quench your thirst. > > cheers, > axel. > > > Best regards. > > > > shangy > > Graduate unversity of Chinese academy of sciences > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of > Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: > 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a > better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Axel Kohlmeyer Center for Molecular Modeling - University of Pennsylvania From zah7903 at gmail.com Sun Mar 15 14:57:45 2009 From: zah7903 at gmail.com (Aihua Zhang) Date: Sun, 15 Mar 2009 21:57:45 +0800 Subject: [Pw_forum] dipole moment calculation In-Reply-To: References: <20090310202812.vntqrcdig0owooss@mail.democritos.it> Message-ID: I realize that it is intrinsically difficult to compute the dipole in a periodic supercell. The position of slab should be appropriately chosen according to the code, and the density should not be divided into periodic images. Aihua On Wed, Mar 11, 2009 at 4:38 PM, Lorenzo Paulatto wrote: > On Wed, 11 Mar 2009 05:24:38 +0100, Aihua Zhang wrote: > > The second possible bug is in compute_dip.f90, where r and r in rho(r) > > seem dismatch when calculating the electronic dipole. After matching r > with > > rho(r) in the code, the reasonable identical results are obtains, i.e. > > the calculated dipole and total energy are independent of where the > molecule > > is put in the supercell. > > Good job Aihua Zhang! > Could you please provide more information on this bug, so it can be fixed > mainstream? > I have long suspected a bug in that part, and I know at least another > person who's working on it at the moment, as far as I know with no luck. > > cheers > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------------------------ Research Fellow, Dept. of Physics, National Univ. of Singapore 10 Kent Ridge Crescent, Singapore, 119260 Tel: +65 6516 7844 ------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090315/93f47e0a/attachment.htm From sporevoyager at gmail.com Sun Mar 15 16:10:22 2009 From: sporevoyager at gmail.com (shangy) Date: Sun, 15 Mar 2009 23:10:22 +0800 Subject: [Pw_forum] HSE pseudopotentials In-Reply-To: <1237124637.4146.10.camel@zero> References: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com> <1237044483.3030.11.camel@zero> <94be399f0903150253o4faf71e1w5710442afeae7b46@mail.gmail.com> <1237124637.4146.10.camel@zero> Message-ID: <94be399f0903150810l3729ebe1r3a99f6083fbd863f@mail.gmail.com> Dear Axel: Thanks for your reply. I always benefit form your commnets, from CPMD to QE. It's the time that I try to degist your reply. Best regards. shangy Graduate unversity of Chinese academy of sciences 2009/3/15 Axel Kohlmeyer > On Sun, 2009-03-15 at 17:53 +0800, shangy wrote: > > Deal Axel: > > dear shangy, > > > Thanks for your kindly reply. I'm not clear about how to generate > > HSE pseudopotentials directly or indirectly. The paper [PRB 74 > > please tell what i have to do, so that you actually _do read_ what > i wrote. i told you that people use regular (i.e. non-hybrid DFT) > pseudopotentials, i.e. in your case a PBE pseudopotential. > > > 121102(R)] demonstrated that the HSE functonal can enable accurate > > computations on defects in Si in compariation with tradtiona DFT (i.e. > > LDA, PW91, PBE). Therefore, I want to reproduce their results within > > Q-E and hope it could solve my calculation problems. > > as i wrote, the problem is _not_ the pseudopotential, but rather > the fact that HSE as such does not (yet) seem to be implemented in Q-E. > > > As your comment, the paper said "The HSE functional mixes in a > > fraction (25%) of exact screened Hartree-Fock exchange as done in the > > PBE hybird (PBEh) funcitonal. The key difference in the HSE, relative > > to the PBEh functional, is that the exact exchange term is screened at > > large distances, effectively giving a hybird functional only at short > > range and GGA behaivor at long range." Their HSE calculations are > > carried out using GAUSSIAN. But I have no idea to reproduce their > > results within Q-E. Would you like to give me some indications on the > > i already did. you have to implement it into Q-E. the code does > have an (experimental) option to compile in exact exchange and > within that framework, PBE0 and B3LYP seem to be available. thus > also support for HSE would in principle be possible, but _not_ > without programming. > > > problem? And would you so kindly to share your Si PBE0 > > pseudopotential with me if you have one? > > please try to make sense in what you write. > how should i have a PBE0 potential, if i don't know of any > code that can generate one?? > > cheers, > axel. > > > > Thanks for your reply again. > > Best regards! > > > > > > 2009/3/14 Axel Kohlmeyer > > On Sat, 2009-03-14 at 13:49 +0800, shangy wrote: > > > Dear all: > > > Does anyone has the Si pseudopotentials generated by > > the > > > screened-exchange hybrid functional of Heyd, Scuseria, and > > Ernerhof > > > [HSE, J. Chem. Phys. 118, 8207 (2003)]? Can it work well > > within QE? If > > > > > > i don't know of any atomic code yet, that does produce hybrid > > dft pseudopotentials. people usually use the ones from the > > underlying > > regular GGA functional (i.e. PBE) in your case. > > > > that being said, i don't see any indication that HSE has yet > > been implemented directly into Q-E. i understand it is just > > strongly screened variation of PBE0, so you may be able to > > implement it yourself. > > > > > anyone has one, would you share it with me? I'm very very > > thirsty for > > > it. Thanks in advance. > > > > > > the potential wouldn't help you much... see above. you'll have > > to > > try something else to quench your thirst. > > > > cheers, > > axel. > > > > > Best regards. > > > > > > shangy > > > Graduate unversity of Chinese academy of sciences > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > ======================================================================= > > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > > http://www.cmm.upenn.edu > > Center for Molecular Modeling -- University of > > Pennsylvania > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > > 19104-6323 > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: > > 1-215-898-5425 > > > ======================================================================= > > If you make something idiot-proof, the universe creates a > > better idiot. > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > -- > Axel Kohlmeyer > Center for Molecular Modeling - University of Pennsylvania > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090315/d0a130ae/attachment-0001.htm From erjunkan at mail.ustc.edu.cn Sun Mar 15 18:16:48 2009 From: erjunkan at mail.ustc.edu.cn (Erjun Kan) Date: Sun, 15 Mar 2009 13:16:48 -0400 Subject: [Pw_forum] pwcond calculations about the transmission in two seperated spin channels Message-ID: <437137472.09605@ustc.edu.cn> Dear all, I want to calculate the transmission of ferromagnetic metal Fe in two spin channels, i.e. spin_up and spin_down seperately. Iofspin= 2 is used for the calculation, but the calculated results show only the total transmission, such as: # E-Ef, T 2.950000 1.000000 2.850000 1.000000 2.750000 1.000000 2.650000 1.000000 2.550000 1.000000 2.450000 1.000000 2.350000 1.000000 2.250000 1.000000 2.150000 1.000000 2.050000 1.000000 1.950000 1.000000 1.850000 1.000000 1.750000 1.000000 1.650000 1.000000 1.550000 1.000000 1.450000 1.000000 So anyone have ideas to handle such problem? Bests, Erjun Kan ============================================================= Erjun Kan Department of Chemistry, North Carolina State University Raleigh, North Carolina, USA E-mail: erjunkan at mail.ustc.edu.cn or ekan at ncsu.edu ============================================================= -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090315/b6afa8e3/attachment.htm From mailtoartee at gmail.com Mon Mar 16 04:43:18 2009 From: mailtoartee at gmail.com (artee sharma) Date: Mon, 16 Mar 2009 09:13:18 +0530 Subject: [Pw_forum] US j -average not yet implemented Message-ID: Dear all, I have an input like shown below: &control calculation='relax', pseudo_dir = '', outdir='', tstress = .true. tprnfor = .true. prefix='' wf_collect= .true. , / &system ibrav=0, nat= 95, ntyp=3, ecutwfc = 30.0, ecutrho = 180.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.003, nbnd=400, / &electrons conv_thr = 1.0e-6, mixing_beta = 0.1, / &ions / ATOMIC_SPECIES Pt 195.09 Ptrel.RRKJ3.UPF Ce 140.116 Ce_lda_sc.UPF O 16.00 O.pz-rrkjus.UPF CELL_PARAMETERS 20.4500 0.0000 0.0000 0.00000 20.4500 0.0000 0.00000 0.0000 20.4500 ATOMIC_POSITIONS (crystal) Ce 0.10000 0.05000 0.02000 Ce 0.25500 0.21000 0.02000 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... O 0.37500 0.61500 0.37500 O 0.62500 0.37500 0.39500 O 0.37500 0.32500 0.37500 K_POINTS {automatic} 4 4 4 0 0 0 But its showing error which says "*US j -average not yet implemented*". What does it mean?? does it has something to do with the pseudo file of Pt (Ptrel.RRKJ3.UPF)?? thanks in advance A K S -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/714b5282/attachment.htm From mansourehp at gmail.com Mon Mar 16 06:03:19 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Mon, 16 Mar 2009 08:33:19 +0330 Subject: [Pw_forum] phonon Message-ID: Dear all In run of the standrard example02 on Si and example06 for phonon calculation I got "Fortran Stop 2", and in the out file I have : Program PHONON v.1.3.0 starts ... Today is 18Oct2003 at 20:46:56 Ultrasoft (Vanderbilt) Pseudopotentials %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from phq_readin : error # 146 reading inputph namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... what does it mean and how can I fix it ? Best wishes, Pashangpour -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/67308a67/attachment.htm From panda.deng.pan at gmail.com Mon Mar 16 06:18:28 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 16 Mar 2009 13:18:28 +0800 Subject: [Pw_forum] phonon In-Reply-To: References: Message-ID: > from phq_readin : error # 146 > reading inputph namelist > something wrong in your input.Without the input of yours can not tell where. From lanhaiping at gmail.com Mon Mar 16 06:27:44 2009 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 16 Mar 2009 13:27:44 +0800 Subject: [Pw_forum] phonon In-Reply-To: References: Message-ID: The output information you gave is so strange! The version of PHONON is outdated too much, so does the time ! So , please update the epsresso package. On Mon, Mar 16, 2009 at 1:03 PM, Mansoureh Pashangpour wrote: > Dear all > > In run of the standrard example02 on Si and example06 for phonon calculation > I got "Fortran Stop 2", > and in the out file I have : > > Program PHONON v.1.3.0 starts ... > Today is 18Oct2003 at 20:46:56 > > Ultrasoft (Vanderbilt) Pseudopotentials > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_readin : error # 146 > reading inputph namelist > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > what does it mean and how can I fix it ? > > Best wishes, > Pashangpour > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/609571e6/attachment.htm From mansourehp at gmail.com Mon Mar 16 06:44:00 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Mon, 16 Mar 2009 09:14:00 +0330 Subject: [Pw_forum] phonon In-Reply-To: References: Message-ID: Dear all Thanks for quick reply. It was fixed. I didn't put phonons of Si at first of inputph. Now I would like to ask another question: how can I obtain and plot phonon band? Thanks Pashangpour On 3/16/09, lan haiping wrote: > > The output information you gave is so strange! > The version of PHONON is outdated too much, > so does the time ! So , please update the epsresso package. > > > On Mon, Mar 16, 2009 at 1:03 PM, Mansoureh Pashangpour < > mansourehp at gmail.com> wrote: > >> Dear all >> >> In run of the standrard example02 on Si and example06 for phonon calculation >> I got "Fortran Stop 2", >> and in the out file I have : >> >> Program PHONON v.1.3.0 starts ... >> Today is 18Oct2003 at 20:46:56 >> >> >> >> Ultrasoft (Vanderbilt) Pseudopotentials >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from phq_readin : error # 146 >> reading inputph namelist >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> stopping ... >> >> what does it mean and how can I fix it ? >> >> Best wishes, >> Pashangpour >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/85ab430b/attachment.htm From eminekb at yahoo.com Mon Mar 16 08:25:20 2009 From: eminekb at yahoo.com (e kb) Date: Mon, 16 Mar 2009 00:25:20 -0700 (PDT) Subject: [Pw_forum] US j -average not yet implemented Message-ID: <667638.6632.qm@web34804.mail.mud.yahoo.com> Dear AKS, If I got it correctly, the code uses the fully relativistic pseudopotential as a scalar rel. one if a non collinear calculation is not asked for. This is done in average_pp.f90 it seems, where you get the error which tells you the problem: j-average is not implemented for ultrasoft pseudopotentials. I might be wrong though, this is just the info that i got by 'grep'ping twice. Cheers, Emine kucukbenli, PhD student, SISSA, Italy. --- On Mon, 3/16/09, artee sharma wrote: From: artee sharma Subject: [Pw_forum] US j -average not yet implemented To: pw_forum at pwscf.org Date: Monday, March 16, 2009, 5:43 AM Dear all, ?I have an input like shown below: ? ?&control ??? calculation='relax', ??? pseudo_dir = '', ??? outdir='', ??? tstress = .true. ??? tprnfor = .true. ??? prefix='' ??? wf_collect= .true. , / ?&system ??? ibrav=0, ??? nat= 95, ??? ntyp=3, ??? ecutwfc = 30.0, ??? ecutrho = 180.0, ??? occupations='smearing', ??? smearing='methfessel-paxton', ??? degauss=0.003, ??? nbnd=400, ?/ ?&electrons ??? conv_thr = 1.0e-6, ??? mixing_beta = 0.1, ?/ ?&ions ?/ ATOMIC_SPECIES Pt 195.09?? Ptrel.RRKJ3.UPF Ce 140.116? Ce_lda_sc.UPF O? 16.00??? O.pz-rrkjus.UPF CELL_PARAMETERS ? 20.4500??? 0.0000??? 0.0000 ? 0.00000?? 20.4500??? 0.0000 ? 0.00000??? 0.0000?? 20.4500 ATOMIC_POSITIONS (crystal) Ce????? 0.10000???? 0.05000???? 0.02000 Ce????? 0.25500???? 0.21000???? 0.02000 ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... O?????? 0.37500???? 0.61500???? 0.37500 O?????? 0.62500???? 0.37500???? 0.39500 O?????? 0.37500???? 0.32500???? 0.37500 K_POINTS {automatic} 4? 4? 4? 0? 0? 0 But its showing error which says "US j -average not yet implemented". What does it mean?? does it has something to do with the pseudo file of Pt (Ptrel.RRKJ3.UPF)?? thanks in advance A K S _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/2a9bfa1e/attachment-0001.htm From cdm_mail at 163.com Mon Mar 16 08:43:21 2009 From: cdm_mail at 163.com (cdm_mail) Date: Mon, 16 Mar 2009 15:43:21 +0800 (CST) Subject: [Pw_forum] help Message-ID: <14389331.476161237189401021.JavaMail.coremail@bj163app48.163.com> Date: Mon, 16 Mar 2009 15:36:14 +0800 From: cdm_mail Subject: [Pw_forum] help to look over To: PWSCF Forum Message-ID: Content-Type: text/plain Dear Giovanni, I'm testing our system with more or less the same configuration. I find that the x (y,z) coordinates of most ions are more larger than the value of crystall lattice( orthorhombic P) . This process is after my car-parrinello dynamics.I think it is something wrong with setting the parameter of electronic minimazation process .So the following part is the setting of the begining test that i have reset again. It is kind of you to help me for correcting the unsuitable parameters and tell me some key points to complete CPMD work. Best wishes. > &CONTROL > calculation='cp' > prefix='silica' > restart_mode='from_scratch' > nstep=100 > iprint=20 > dt=5.0 > ndr=50, ndr=51 > outdir='./tmp/' > pseudo_dir='/home/111/Quantum-ESPRESSO/pseudo/' > etot_conv_thr=1d-5 > ekin_conv_thr=1d-9 > / > &SYSTEM > ibrav=8, > celldm(1) = 18.788, celldm(2) = 0.866, celldm(3) = 1.0972 > nat=72 > ntyp=2 > nbnd=192 > spin=1 > nbr1=20, nbr2=20, nbr3=20 > / > &ELECTRONS > emass=700.,emass_cutoff=5 > ecectron_dynamics='damp' > ecectron_dynamics=damping=0.2 > startingwfc='random' > / > &IONS > ion_dynamics='none' > / > ATOMIC_SPECIES > O 16.00 O.pz-rrkjus.UPF > Si 28.00 Si.vbc.UPF > ATOMIC_POSITIONS { bohr } O 3.5406783 15.0448465 1.4126108 O 3.8071642 15.4043722 11.9216204 O 13.0894146 15.3948822 1.5781510 O 13.2522097 15.1658554 11.9361830 O 8.2785587 7.2548118 1.5474833 O 8.5399103 7.0021067 11.6012125 O 17.9968777 6.9402800 1.2878237 O 17.6457939 7.1132650 11.9548235 O 2.4405613 6.3799176 4.7482071 O 2.6654053 6.3422036 15.0544825 O 12.2024078 6.3211975 4.7142868 O 11.8810415 6.4080858 15.3200722 O 7.1940126 14.4133511 4.9239106 O 7.3077059 14.4793634 15.0265102 O 16.9006786 14.3864670 5.0179539 O 16.6793461 14.4224520 15.3299093 O 4.7042437 11.5882969 8.4145012 O 4.8058362 11.7974415 18.5207825 O 14.0459738 11.6190434 8.4245062 O 14.1501627 11.7520666 18.6828041 O 9.4120684 3.5592277 8.1602020 O 9.4435863 3.4508531 18.8181076 O 18.8548489 3.3799570 8.2510424 O 18.8457680 3.6430509 18.4409237 O 4.6323986 4.9528089 9.3928719 O 4.6253457 5.0198221 19.3735943 O 14.1270161 5.0775709 9.1806593 O 14.2851896 5.0468230 19.6615734 O 9.3298197 13.1670465 9.3121605 O 9.6129112 13.2867460 19.5585632 O 18.7938595 13.0344448 9.2933855 O 18.6957073 13.2711039 19.5695648 O 3.7519393 1.4702886 5.7478361 O 3.7406268 1.3143321 16.1506748 O 13.1751394 1.4241230 5.8916039 O 13.2039194 1.6296371 16.2666016 O 8.5475645 9.7668839 5.8549895 O 8.3606243 9.4664469 16.0193081 O 18.0083542 9.4706783 5.8703651 O 17.8562260 9.4727955 15.9772587 O 2.7527096 10.6110735 2.3466952 O 2.6490324 10.4995565 12.5345230 O 11.8460188 10.5480690 2.2722039 O 11.9239492 10.4055338 12.5277109 O 7.4533672 2.5166929 2.2388670 O 7.3775740 2.1962755 12.8475285 O 16.7454376 2.4293642 2.5411322 O 16.6413174 2.5064237 12.7736511 Si 0.4496534 8.2138128 3.6896179 Si 0.5399753 8.1889200 13.9777460 Si 9.8792067 8.2886143 3.7623391 Si 9.8359041 8.5231533 14.1156855 Si 5.2412066 0.0271945 3.5170169 Si 5.1725807 0.0363324 13.8097649 Si 14.5211735 0.0875002 3.5420916 Si 14.3368998 0.0028480 14.0652027 Si 2.4036527 12.8000431 0.2863795 Si 2.3965807 12.7267065 10.3207769 Si 11.6870117 12.6637812 0.1414142 Si 11.6615248 12.7831507 10.3878822 Si 7.2631865 4.6357923 0.2741336 Si 6.9719872 4.4316664 10.6666307 Si 16.4332924 4.5068045 0.2921807 Si 16.6266994 4.4123287 10.3654356 Si 2.5121100 4.1013050 7.1919127 Si 2.2047310 4.1441984 17.4181461 Si 11.9457951 3.9283929 7.2228098 Si 11.7723646 3.9849200 17.5345020 Si 7.1349611 12.1880169 7.1159267 Si 7.1111145 12.1099644 17.5283604 Si 16.3560925 12.0432882 6.9771399 Si 16.5531750 12.0766220 17.5176411 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/950ab9d9/attachment.htm From sclauzer at sissa.it Mon Mar 16 09:04:00 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 16 Mar 2009 09:04:00 +0100 Subject: [Pw_forum] US j -average not yet implemented In-Reply-To: References: Message-ID: <49BE07F0.1010502@sissa.it> artee sharma wrote: > Dear all, > I have an input like shown below: ... > / > ATOMIC_SPECIES > Pt 195.09 Ptrel.RRKJ3.UPF > Ce 140.116 Ce_lda_sc.UPF > O 16.00 O.pz-rrkjus.UPF This problem was already discussed in a very old post, please see http://www.democritos.it/pipermail/pw_forum/2005-January/001940.html things haven't change much since that time (for this specific issue). > > > But its showing error which says "*US j -average not yet implemented*". > What does it mean?? does it has something to do with the pseudo file of > Pt (Ptrel.RRKJ3.UPF)?? It has, since this pseudopotential has been generated in order to include spin orbit coupling effects (irel=2 in ld1.x input), and it is usually refered as a 'fully-relativistic' (FR-PP). If you want to include spin-orbit effects in your calculations (through PPs) you must specify noncolin= .TRUE. lspinorb= .TRUE. in the system namelist. You should also use FR-PP for the other elements (or at least for the heavy ions). If you're not interested in SO-coupling, you can use scalar-relativistic PP (irel=1) for Pt, which include part of the relativistic effects (but not spin-orbit splittings). Regards GS > > > thanks in advance > A K S > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From sclauzer at sissa.it Mon Mar 16 09:11:51 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 16 Mar 2009 09:11:51 +0100 Subject: [Pw_forum] pwcond calculations about the transmission in two seperated spin channels In-Reply-To: <437137472.09605@ustc.edu.cn> References: <437137472.09605@ustc.edu.cn> Message-ID: <49BE09C7.2070501@sissa.it> Erjun Kan wrote: > Dear all, > > I want to calculate the transmission of ferromagnetic metal Fe in two > spin channels, i.e. spin_up and spin_down seperately. > Iofspin= 2 is used for the calculation, but the calculated results show > only the total transmission, such as: It is the total trasmission (i.e. summed over k_|| points) for the spin channel you selected. It is given in units of _half_ G_0, so from your output I guess you have one channel spin-up (or spin-down?) perfectly transmitted. To have what you call total transmission, you must sum up the spin-up transmission to the spin-down one (which come from two different files obtained as output of two calculations, iofspin=1,2). GS > # E-Ef, T > 2.950000 1.000000 > 2.850000 1.000000 > 2.750000 1.000000 > 2.650000 1.000000 > 2.550000 1.000000 > 2.450000 1.000000 > 2.350000 1.000000 > 2.250000 1.000000 > 2.150000 1.000000 > 2.050000 1.000000 > 1.950000 1.000000 > 1.850000 1.000000 > 1.750000 1.000000 > 1.650000 1.000000 > 1.550000 1.000000 > 1.450000 1.000000 > So anyone have ideas to handle such problem? > > Bests, > Erjun Kan > > ============================================================= > Erjun Kan > Department of Chemistry, North Carolina State University > Raleigh, North Carolina, USA > E-mail: erjunkan at mail.ustc.edu.cn or > ekan at ncsu.edu > ============================================================= > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From eyvaz_isaev at yahoo.com Mon Mar 16 10:28:17 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 16 Mar 2009 02:28:17 -0700 (PDT) Subject: [Pw_forum] phonon In-Reply-To: Message-ID: <716704.97395.qm@web65716.mail.ac4.yahoo.com> Dear Mansoureh, > how can I obtain and plot phonon band? I will send you a set of small programs and scripts. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Mon, 3/16/09, Mansoureh Pashangpour wrote: > From: Mansoureh Pashangpour > Subject: Re: [Pw_forum] phonon > To: "PWSCF Forum" > Date: Monday, March 16, 2009, 8:44 AM > Dear all > Thanks for quick reply. It was fixed. I didn't put > phonons of Si > at first of inputph. Now I would like to ask another > question: how can I > obtain and plot phonon band? > Thanks > Pashangpour > On 3/16/09, lan haiping wrote: > > > > The output information you gave is so strange! > > The version of PHONON is outdated too much, > > so does the time ! So , please update the epsresso > package. > > > > > > On Mon, Mar 16, 2009 at 1:03 PM, Mansoureh Pashangpour > < > > mansourehp at gmail.com> wrote: > > > >> Dear all > >> > >> In run of the standrard example02 on Si and > example06 for phonon calculation > >> I got "Fortran Stop 2", > >> and in the out file I have : > >> > >> Program PHONON v.1.3.0 starts ... > >> Today is 18Oct2003 at 20:46:56 > >> > >> > >> > >> Ultrasoft (Vanderbilt) Pseudopotentials > >> > >> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >> from phq_readin : error # 146 > >> reading inputph namelist > >> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >> > >> > >> stopping ... > >> > >> what does it mean and how can I fix it ? > >> > >> Best wishes, > >> Pashangpour > >> > >> > >> > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > >> > > > > > > -- > > Hai-Ping Lan > > Department of Electronics , > > Peking University , Bejing, 100871 > > lanhaiping at gmail.com, hplan at pku.edu.cn > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From mailtoartee at gmail.com Mon Mar 16 10:36:31 2009 From: mailtoartee at gmail.com (artee sharma) Date: Mon, 16 Mar 2009 15:06:31 +0530 Subject: [Pw_forum] US j -average not yet implemented In-Reply-To: <667638.6632.qm@web34804.mail.mud.yahoo.com> References: <667638.6632.qm@web34804.mail.mud.yahoo.com> Message-ID: Dear Emmine, thanks for your prompt reply. i am new to DFT calculations. Mostly i cud not understand your message. can you please tell me how to rectify it. Do i need to change the pseudopotentail file?? thanks a lot asha On Mon, Mar 16, 2009 at 12:55 PM, e kb wrote: > Dear AKS, > If I got it correctly, the code uses the fully relativistic pseudopotential > as a scalar rel. one if a non collinear calculation is not asked for. This > is done in average_pp.f90 it seems, where you get the error which tells you > the problem: j-average is not implemented for ultrasoft pseudopotentials. I > might be wrong though, this is just the info that i got by 'grep'ping twice. > Cheers, > Emine kucukbenli, PhD student, SISSA, Italy. > > --- On *Mon, 3/16/09, artee sharma * wrote: > > From: artee sharma > Subject: [Pw_forum] US j -average not yet implemented > To: pw_forum at pwscf.org > Date: Monday, March 16, 2009, 5:43 AM > > > Dear all, > I have an input like shown below: > > > &control > calculation='relax', > pseudo_dir = '', > outdir='', > tstress = .true. > tprnfor = .true. > prefix='' > wf_collect= .true. , > / > &system > ibrav=0, > nat= 95, > ntyp=3, > ecutwfc = 30.0, > ecutrho = 180.0, > occupations='smearing', > smearing='methfessel-paxton', > degauss=0.003, > nbnd=400, > / > &electrons > conv_thr = 1.0e-6, > mixing_beta = 0.1, > / > &ions > / > ATOMIC_SPECIES > Pt 195.09 Ptrel.RRKJ3.UPF > Ce 140.116 Ce_lda_sc.UPF > O 16.00 O.pz-rrkjus.UPF > > CELL_PARAMETERS > 20.4500 0.0000 0.0000 > 0.00000 20.4500 0.0000 > 0.00000 0.0000 20.4500 > > ATOMIC_POSITIONS (crystal) > Ce 0.10000 0.05000 0.02000 > Ce 0.25500 0.21000 0.02000 > ... > ... > ... > ... > ... > ... > ... > ... > ... > ... > ... > ... > ... > ... > ... > ... > ... > O 0.37500 0.61500 0.37500 > O 0.62500 0.37500 0.39500 > O 0.37500 0.32500 0.37500 > > K_POINTS {automatic} > 4 4 4 0 0 0 > > > > But its showing error which says "*US j -average not yet implemented*". > What does it mean?? does it has something to do with the pseudo file of Pt > (Ptrel.RRKJ3.UPF)?? > > > thanks in advance > A K S > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/ff8997cc/attachment-0001.htm From panda.deng.pan at gmail.com Mon Mar 16 11:00:38 2009 From: panda.deng.pan at gmail.com (=?GB2312?B?xcu1xw==?=) Date: Mon, 16 Mar 2009 18:00:38 +0800 Subject: [Pw_forum] phonon In-Reply-To: <716704.97395.qm@web65716.mail.ac4.yahoo.com> References: <716704.97395.qm@web65716.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz. >> how can I obtain and plot phonon band? > > I will send you a set of small programs and scripts. > Could you send me too?Thanks. cheers Pan Deng Nanjing University From giannozz at democritos.it Mon Mar 16 12:47:47 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 16 Mar 2009 12:47:47 +0100 Subject: [Pw_forum] "charge is wrong" error In-Reply-To: References: <49BA788B.6020405@democritos.it> Message-ID: <49BE3C63.901@democritos.it> Aihua Zhang wrote: > I think you are right. It is also possible that it's a problem of acml > library. A pwscf binary compiled by pgif90 but linked with mkl works > smoothly. I can confirm that the problem disappears if I link the local copy of blas instead of acml. Thank you anyway for the bug report Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From quantumdft at gmail.com Mon Mar 16 13:28:22 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 16 Mar 2009 20:28:22 +0800 Subject: [Pw_forum] where is the instructions for dynmat.x Message-ID: <412f6c680903160528k761d0967m618d8e1301a0605a@mail.gmail.com> Dear all, I found a lot of executive files in /espresso-4.0.3/bin/ folder. But I can't find instructions for some of them, such as dynmat.x. by the way, is there any tutorial or example to instruct how to plot IR spectrum ? thank you for reading vega -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/5d51581d/attachment.htm From liquan777 at gmail.com Mon Mar 16 13:42:47 2009 From: liquan777 at gmail.com (liquan777) Date: Mon, 16 Mar 2009 20:42:47 +0800 Subject: [Pw_forum] =?utf-8?q?Raman_Intensity_of_mental?= Message-ID: <200903162042446926811@gmail.com> Dear all, I am trying to use PWSCF to study Raman properties of mental. I want to know why PWSCF do not permit to calculate Raman intensity of mental? How can I get the Raman intensities of mental? Any reply will be appreciated. Sincerely, Quan Li National Lab of Superhard Materials, Jilin Univ. 2699, Qianjin Str. Changchun 130012 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/b09af4ec/attachment.htm From pemryan at yahoo.cn Mon Mar 16 13:55:06 2009 From: pemryan at yahoo.cn (Yan) Date: Mon, 16 Mar 2009 20:55:06 +0800 Subject: [Pw_forum] where is the instructions for dynmat.x In-Reply-To: <412f6c680903160528k761d0967m618d8e1301a0605a@mail.gmail.com> References: <412f6c680903160528k761d0967m618d8e1301a0605a@mail.gmail.com> Message-ID: <200903162055.10566.pemryan@yahoo.cn> Hello Vega, I suppose you have read the manual. Besides the files in the folder 'doc', there are some examples in the folder 'examples'. cheers, Yan On 2009/3/16 Monday 20:28:22 vega lew wrote: > I found a lot of executive files in /espresso-4.0.3/bin/ folder. But I > can't find instructions for some of them, such as dynmat.x. > > by the way, is there any tutorial or example to instruct how to plot IR > spectrum ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/963362d7/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Mon Mar 16 14:14:25 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Mon, 16 Mar 2009 14:14:25 +0100 Subject: [Pw_forum] Raman Intensity of mental In-Reply-To: <200903162042446926811@gmail.com> References: <200903162042446926811@gmail.com> Message-ID: <200903161414.26543.giuseppe.mattioli@mlib.ism.cnr.it> Before all, what's "mental"? On Monday 16 March 2009 13:42:47 liquan777 wrote: > Dear all, > > I am trying to use PWSCF to study Raman properties of mental. > > I want to know why PWSCF do not permit to calculate Raman intensity of > mental? > > How can I get the Raman intensities of mental? > > Any reply will be appreciated. > > Sincerely, > > Quan Li > National Lab of Superhard Materials, Jilin Univ. > 2699, Qianjin Str. > Changchun 130012 > China -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00016 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/7696ad60/attachment-0001.htm From sclauzer at sissa.it Mon Mar 16 14:20:32 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 16 Mar 2009 14:20:32 +0100 Subject: [Pw_forum] Raman Intensity of mental In-Reply-To: <200903161414.26543.giuseppe.mattioli@mlib.ism.cnr.it> References: <200903162042446926811@gmail.com> <200903161414.26543.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <49BE5220.1030301@sissa.it> In Italy it's very popular: http://www.mental.it/ :-P GS Giuseppe Mattioli wrote: > Before all, what's "mental"? > > On Monday 16 March 2009 13:42:47 liquan777 wrote: > > > Dear all, > > > > > > I am trying to use PWSCF to study Raman properties of mental. > > > > > > I want to know why PWSCF do not permit to calculate Raman intensity of > > > mental? > > > > > > How can I get the Raman intensities of mental? > > > > > > Any reply will be appreciated. > > > > > > Sincerely, > > > > > > Quan Li > > > National Lab of Superhard Materials, Jilin Univ. > > > 2699, Qianjin Str. > > > Changchun 130012 > > > China > > -- > > ******************************************************** > > - Article premier - Les hommes naissent et demeurent > > libres et ?gaux en droits. Les distinctions sociales > > ne peuvent ?tre fond?es que sur l'utilit? commune > > - Article 2 - Le but de toute association politique > > est la conservation des droits naturels et > > imprescriptibles de l'homme. Ces droits sont la libert?, > > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > > ******************************************************** > > Giuseppe Mattioli > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > > v. Salaria Km 29,300 - C.P. 10 > > I 00016 - Monterotondo Stazione (RM) > > Tel + 39 06 90672836 - Fax +39 06 90672316 > > E-mail: > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From carlo.nervi at unito.it Mon Mar 16 14:29:28 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Mon, 16 Mar 2009 14:29:28 +0100 Subject: [Pw_forum] Installation of PWgui Message-ID: <49BE5438.1000303@unito.it> Dear all, perhaps it's a dumb question, but I cannot run PWgui. The following packages are installed in my linux Gentoo: tcl-8.4.18 tk-8.4.18 itcl-3.3-r1 itk-3.3-r1 iwidgets-4.0.1 If I understood correctly sources should work. However, after typing ./pwgui I got the response below. Any suggestions? Thanks, Carlo ================================================== This is PWgui version: 4.1CVS -------------------------------------------------- PWgui: using the system default "tclsh" interpreter PWGUI : /home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS GUIB engine : /home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS/lib/Guib-0.5 couldn't open "/home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS/images/pwgui-logo.gif": no such file or directory while executing "image create photo logo -format gif \ -file [file join $env(PWGUI) images pwgui-logo.gif]" (file "/home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS/src/pwscf.itcl" line 44) invoked from within "source [file join $env(PWGUI) src pwscf.itcl]" (file "/home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS/pwgui.tcl" line 69) -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From liquan777 at gmail.com Mon Mar 16 14:33:34 2009 From: liquan777 at gmail.com (liquan777) Date: Mon, 16 Mar 2009 21:33:34 +0800 Subject: [Pw_forum] Raman Intensity of mental References: <200903162042446926811@gmail.com>, <200903161414.26543.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <200903162133309898283@gmail.com> Sorry, it is metal 2009-03-16 liquan777 ???????? Giuseppe Mattioli ?????????? 2009-03-16 21:14:15 ???????? PWSCF Forum ?????? ?????? Re: [Pw_forum] Raman Intensity of mental Before all, what's "mental"? On Monday 16 March 2009 13:42:47 liquan777 wrote: > Dear all, > > I am trying to use PWSCF to study Raman properties of mental. > > I want to know why PWSCF do not permit to calculate Raman intensity of > mental? > > How can I get the Raman intensities of mental? > > Any reply will be appreciated. > > Sincerely, > > Quan Li > National Lab of Superhard Materials, Jilin Univ. > 2699, Qianjin Str. > Changchun 130012 > China -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit?commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert? la propri?t? la s?ret?et la r?sistance ?l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00016 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/8fa7e260/attachment.htm From giannozz at democritos.it Mon Mar 16 14:42:40 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 16 Mar 2009 14:42:40 +0100 Subject: [Pw_forum] Raman Intensity of mental In-Reply-To: <200903162042446926811@gmail.com> References: <200903162042446926811@gmail.com> Message-ID: <49BE5750.4040607@democritos.it> liquan777 wrote: > I want to know why PWSCF do not permit to calculate Raman intensity of > mental? for good reasons. Please search the archive of the mailing list for "Raman" and "metal" (not "mental") P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Mon Mar 16 14:57:50 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 16 Mar 2009 14:57:50 +0100 Subject: [Pw_forum] Installation of PWgui In-Reply-To: <49BE5438.1000303@unito.it> References: <49BE5438.1000303@unito.it> Message-ID: <49BE5ADE.8040402@democritos.it> Carlo Nervi wrote: > perhaps it's a dumb question, but I cannot run PWgui running PWgui from cvs requires a different procedure than running it from packaged distributions. Did you follow the instructions? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From tone.kokalj at ijs.si Mon Mar 16 14:58:11 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 16 Mar 2009 14:58:11 +0100 Subject: [Pw_forum] Installation of PWgui In-Reply-To: <49BE5438.1000303@unito.it> References: <49BE5438.1000303@unito.it> Message-ID: <1237211891.18604.12.camel@walk.ijs.si> On Mon, 2009-03-16 at 14:29 +0100, Carlo Nervi wrote: > Dear all, > perhaps it's a dumb question, but I cannot run PWgui. > The following packages are installed in my linux Gentoo: > > tcl-8.4.18 > tk-8.4.18 > itcl-3.3-r1 > itk-3.3-r1 > iwidgets-4.0.1 > > If I understood correctly sources should work. Correct! > However, after typing ./pwgui I got the response below. > Any suggestions? > Thanks, > Carlo > > ================================================== > This is PWgui version: 4.1CVS > -------------------------------------------------- > > > PWgui: using the system default "tclsh" interpreter > > PWGUI : > /home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS > GUIB engine : > /home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS/lib/Guib-0.5 > > couldn't open > "/home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS/images/pwgui-logo.gif": > no such file or directory Which actually means it works, but one image file is missing in tgz. You may fix it as: cd /home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS/images/ ln -s pwgui-logo-small.gif pwgui-logo.gif Thanks for reporting this bug. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From liquan777 at gmail.com Mon Mar 16 15:00:45 2009 From: liquan777 at gmail.com (liquan777) Date: Mon, 16 Mar 2009 22:00:45 +0800 Subject: [Pw_forum] Raman Intensity of metal References: <200903162042446926811@gmail.com>, <49BE5750.4040607@democritos.it> Message-ID: <200903162200433649840@gmail.com> Thank you very much! I'm very sorry for the mistake. Sorry to have encroached your valuable time. With my best regards, Q. Li ???? Paolo Giannozzi ????? 2009-03-16 21:42:48 ???? PWSCF Forum ??? ??? Re: [Pw_forum] Raman Intensity of mental liquan777 wrote: > I want to know why PWSCF do not permit to calculate Raman intensity of > mental? for good reasons. Please search the archive of the mailing list for "Raman" and "metal" (not "mental") P. -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/a89a9204/attachment-0001.htm From carlo.nervi at unito.it Mon Mar 16 15:12:36 2009 From: carlo.nervi at unito.it (Carlo Nervi) Date: Mon, 16 Mar 2009 15:12:36 +0100 Subject: [Pw_forum] Installation of PWgui In-Reply-To: <1237211891.18604.12.camel@walk.ijs.si> References: <49BE5438.1000303@unito.it> <1237211891.18604.12.camel@walk.ijs.si> Message-ID: <49BE5E54.4010908@unito.it> Thank you Tone! It works! I supposed (wrongly) that the pwgui-logo.gif should be created... Carlo Tone Kokalj ha scritto: > On Mon, 2009-03-16 at 14:29 +0100, Carlo Nervi wrote: >> Dear all, >> perhaps it's a dumb question, but I cannot run PWgui. >> The following packages are installed in my linux Gentoo: >> >> tcl-8.4.18 >> tk-8.4.18 >> itcl-3.3-r1 >> itk-3.3-r1 >> iwidgets-4.0.1 >> >> If I understood correctly sources should work. > > Correct! > > > >> However, after typing ./pwgui I got the response below. >> Any suggestions? >> Thanks, >> Carlo >> >> ================================================== >> This is PWgui version: 4.1CVS >> -------------------------------------------------- >> >> >> PWgui: using the system default "tclsh" interpreter >> >> PWGUI : >> /home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS >> GUIB engine : >> /home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS/lib/Guib-0.5 >> >> couldn't open >> "/home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS/images/pwgui-logo.gif": >> no such file or directory > > > Which actually means it works, but one image file is missing in tgz. > > You may fix it as: > > cd /home/nervi/src/Quantum-espresso/espresso-4.1CVS/PWgui-4.1CVS/images/ > ln -s pwgui-logo-small.gif pwgui-logo.gif > > Thanks for reporting this bug. > > Regards, Tone > -- ------------------------------------------------------ Carlo Nervi carlo.nervi at unito.it Tel:+39 011 6707507/8 Fax: +39 011 6707855 - Dipartimento di Chimica IFM via P. Giuria 7, 10125 Torino, Italy http://lem.ch.unito.it/ From quantumdft at gmail.com Mon Mar 16 15:51:24 2009 From: quantumdft at gmail.com (vega lew) Date: Mon, 16 Mar 2009 22:51:24 +0800 Subject: [Pw_forum] where is the instructions for dynmat.x In-Reply-To: <200903162055.10566.pemryan@yahoo.cn> References: <412f6c680903160528k761d0967m618d8e1301a0605a@mail.gmail.com> <200903162055.10566.pemryan@yahoo.cn> Message-ID: <412f6c680903160751t2d4bafddidfba907e1498f223@mail.gmail.com> Dear yan, I have searched the readme file under the /espresso-4.0.3/example/ with the keyword 'dynmat.x'. but nothing found. could you please tell me which example told us how to calculate IR spectrum? thank you vega On Mon, Mar 16, 2009 at 8:55 PM, Yan wrote: > Hello Vega, > > > I suppose you have read the manual. > Besides the files in the folder 'doc', there are some examples in the > folder 'examples'. > > > cheers, > > > Yan > > > On 2009/3/16 Monday 20:28:22 vega lew wrote: > > > > I found a lot of executive files in /espresso-4.0.3/bin/ folder. But I > > can't find instructions for some of them, such as dynmat.x. > > > > by the way, is there any tutorial or example to instruct how to plot IR > > spectrum ? > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/453ec1fc/attachment.htm From akohlmey at cmm.chem.upenn.edu Mon Mar 16 15:58:31 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 16 Mar 2009 10:58:31 -0400 Subject: [Pw_forum] where is the instructions for dynmat.x In-Reply-To: <412f6c680903160751t2d4bafddidfba907e1498f223@mail.gmail.com> References: <412f6c680903160528k761d0967m618d8e1301a0605a@mail.gmail.com> <200903162055.10566.pemryan@yahoo.cn> <412f6c680903160751t2d4bafddidfba907e1498f223@mail.gmail.com> Message-ID: <1237215511.3045.27.camel@zero> On Mon, 2009-03-16 at 22:51 +0800, vega lew wrote: > Dear yan, > > I have searched the readme file under the /espresso-4.0.3/example/ > with the keyword 'dynmat.x'. but nothing found. could you please tell > me which example told us how to calculate IR spectrum? grep is your friend. check out example09 [akohlmey at vitriol examples]$ grep dynmat example*/run_example example09/run_example:DYNMAT_COMMAND=" $BIN_DIR/dynmat.x" example09/run_example:$ECHO " running dynmat.x as: $DYNMAT_COMMAND" other than that. if everything else fails, read the source. i promise that in the case of PH/dynmat.f90 it will be very rewarding. axel. > > thank you > > vega > > > On Mon, Mar 16, 2009 at 8:55 PM, Yan wrote: > Hello Vega, > > > > I suppose you have read the manual. > Besides the files in the folder 'doc', there are some examples > in the folder 'examples'. > > > > cheers, > > > > Yan > > > On 2009/3/16 Monday 20:28:22 vega lew wrote: > > > > > I found a lot of executive files in /espresso-4.0.3/bin/ > folder. But I > > can't find instructions for some of them, such as dynmat.x. > > > > by the way, is there any tutorial or example to instruct how > to plot IR > > spectrum ? > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ****************************************************************************************************************** > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From pemryan at yahoo.cn Mon Mar 16 16:05:57 2009 From: pemryan at yahoo.cn (Yan) Date: Mon, 16 Mar 2009 23:05:57 +0800 Subject: [Pw_forum] where is the instructions for dynmat.x In-Reply-To: <412f6c680903160751t2d4bafddidfba907e1498f223@mail.gmail.com> References: <412f6c680903160528k761d0967m618d8e1301a0605a@mail.gmail.com> <200903162055.10566.pemryan@yahoo.cn> <412f6c680903160751t2d4bafddidfba907e1498f223@mail.gmail.com> Message-ID: <200903162306.01715.pemryan@yahoo.cn> On 2009/03/16 Monday 22:51:24 vega lew wrote: > I have searched the readme file under the /espresso-4.0.3/example/ with the > keyword 'dynmat.x'. but nothing found. bash-3.2$ grep dynmat.x */run_example example09/run_example:DYNMAT_COMMAND=" $BIN_DIR/dynmat.x" example09/run_example:$ECHO " running dynmat.x as: $DYNMAT_COMMAND" "dynmat.x" appears in example09/run_example. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/9fdbb491/attachment.htm From quantumdft at gmail.com Mon Mar 16 17:05:16 2009 From: quantumdft at gmail.com (vega lew) Date: Tue, 17 Mar 2009 00:05:16 +0800 Subject: [Pw_forum] where is the instructions for dynmat.x In-Reply-To: <200903162306.01715.pemryan@yahoo.cn> References: <412f6c680903160528k761d0967m618d8e1301a0605a@mail.gmail.com> <200903162055.10566.pemryan@yahoo.cn> <412f6c680903160751t2d4bafddidfba907e1498f223@mail.gmail.com> <200903162306.01715.pemryan@yahoo.cn> Message-ID: <412f6c680903160905t31c0320egad0382d6e7b08b9a@mail.gmail.com> Thank you for your help I'll check it immediately. vega On Mon, Mar 16, 2009 at 11:05 PM, Yan wrote: > > > On 2009/03/16 Monday 22:51:24 vega lew wrote: > > I have searched the readme file under the /espresso-4.0.3/example/ with > the > > keyword 'dynmat.x'. but nothing found. > > > bash-3.2$ grep dynmat.x */run_example > example09/run_example:DYNMAT_COMMAND=" $BIN_DIR/dynmat.x" > example09/run_example:$ECHO " running dynmat.x as: $DYNMAT_COMMAND" > > "dynmat.x" appears in example09/run_example. > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/97698e39/attachment.htm From cyrille.barreteau at cea.fr Mon Mar 16 17:08:44 2009 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Mon, 16 Mar 2009 17:08:44 +0100 Subject: [Pw_forum] Permanent Research Fellow position in nanomagnetism Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8D9499EB@DIODON.extra.cea.fr> Dear Pwscf users and developers... A permanent Research Fellow position (no teaching duties) is available in the theoretical group of ?Modelisation of Surfaces, Interfaces and Nanostructures? (MSIN) of the laboratory ?Service de Physique et Chimie des Surfaces et Interfaces? (SPCSI) (http://iramis.cea.fr/spcsi/) at CEA-Saclay , France. Please find more details in the attached file and text below Cyrille Barreteau ==================================================================== Permanent Research Fellow position CEA-Saclay, France MAGNETISM AND ELECTRONIC TRANSPORT IN NANOSTRUCURES A permanent Research Fellow position (no teaching duties) is available in the theoretical group of ?Modelisation of Surfaces, Interfaces and Nanostructures? (MSIN) of the laboratory ?Service de Physique et Chimie des Surfaces et Interfaces? (SPCSI) (http://iramis.cea.fr/spcsi/) at CEA-Saclay , France. Profile: We are looking for an expert in the magnetic properties of materials (metals, oxides etc..) at the nanometer scale (clusters, surfaces, interfaces) with a strong expertise in electronic structure calculations (DFT-based and/or TB methods) and willing to apply them to realistic systems. Beyond the strict study of the electronic structure, essential to deal with nanomagnetism, a broader knowledge in spin-polarized electronic transport, magnetic interactions and anisotropy would be an advantage. In addition to electronic structure techniques the candidate should also be open to the use and development of (semi)empirical methods (Heisenberg Hamiltonian, interatomic potentials..) in order to study complex systems containing a large number of atoms. The successful candidate will join the MSIN group and will interact with the members of the group, for example by: ? Implementing new theoretical approaches for the study of nanomagnetism. ? Using ab-initio calculations to extract relevant parameters for model Hamiltonians, ? Developing codes for nanoscale spin polarized electronic transport. The successful candidate will then strengthen the existing research activities of our group and will also collaborate with experimental teams at the CEA on the following topics: ? Spin polarized transport in nanostructures and multilayers. ? Magnetic properties of surfaces and interfaces. ? Magnetic interactions in nanostructures. Background: The applicants should hold a PhD, have a postdoctoral research experience and should have a proven track-record of cutting-edge research (in theoretical condensed-matter physics or a related field), including an ability to interact effectively within a research team involving experimentalists as well as other theoreticians. Interested candidates are expected to send: (1) Full CV (2) List of publications (3) 2 reference letters To Dr C. Barreteau ( cyrille.barreteau at cea.fr ) Informal enquiries are welcome and may be addressed to C. Barreteau. Deadline for application: 1st May 2009. ================================================================== Cyrille Barreteau | phone : +33 (0)1 69 08 29 51 CEA Saclay | fax : +33 (0)1 69 08 84 46 DSM/IRAMIS/SPCSI | email cyrille.barreteau at cea.fr Batiment 462 | 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ http://iramis.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html ================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090316/2fed9cd2/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: job-announcement-en.pdf Type: application/pdf Size: 19480 bytes Desc: job-announcement-en.pdf Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090316/2fed9cd2/attachment-0001.pdf From lijin.phy at gmail.com Tue Mar 17 02:33:38 2009 From: lijin.phy at gmail.com (jin li) Date: Tue, 17 Mar 2009 09:33:38 +0800 Subject: [Pw_forum] How to get the interatomic force constant tensor? Message-ID: <13cffdb60903161833h10694fc6te91bdd571c9e7d7b@mail.gmail.com> Dear all: ?????? Following the example 06, alas444.fc has been got. Would somebody give me some explaination about this file? And customarily, the IFC matrix is [ K11? K12? K13?... K1N ] [ K21? K22? K23 ... K2N ] [ ....???????????????????????...?? ] [ KN1? KN2? KN3 ...KNN] How to transform this?IFC in?this file to the?above form? Best wishes, lijin From eyvaz_isaev at yahoo.com Tue Mar 17 04:10:42 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 16 Mar 2009 20:10:42 -0700 (PDT) Subject: [Pw_forum] How to get the interatomic force constant tensor? In-Reply-To: <13cffdb60903161833h10694fc6te91bdd571c9e7d7b@mail.gmail.com> Message-ID: <211139.33021.qm@web65707.mail.ac4.yahoo.com> Dear Lijin, I have explained this one before in the forume. Please search the forum archive. Please also provide your affiliation. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 3/17/09, jin li wrote: > From: jin li > Subject: [Pw_forum] How to get the interatomic force constant tensor? > To: pw_forum at pwscf.org > Date: Tuesday, March 17, 2009, 4:33 AM > Dear all: > ?????? Following the example 06, alas444.fc has been > got. Would > somebody give me some explaination about this file? And > customarily, > the IFC matrix is > [ K11? K12? K13?... K1N ] > [ K21? K22? K23 ... K2N ] > [ ....???????????????????????...?? > ] > [ KN1? KN2? KN3 ...KNN] > How to transform this?IFC in?this file to the?above > form? > Best wishes, > lijin > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From mansourehp at gmail.com Tue Mar 17 06:02:20 2009 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Tue, 17 Mar 2009 08:32:20 +0330 Subject: [Pw_forum] LDA+U Message-ID: Dear all I would like to obtain phonon frequencies for Cd(OH)2 by LDA+U .But the code didn't work with LDA+U for phonon calculation and I just found the frequencies by LDA. Is there any way to obtain these frequencies by LDA+U? Which physical properties can be obtain by PWscf with LDA+U except DOS and Bandstructure? Thanks Pashangpour -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/5ad115f0/attachment.htm From mailtoartee at gmail.com Tue Mar 17 07:14:13 2009 From: mailtoartee at gmail.com (artee sharma) Date: Tue, 17 Mar 2009 11:44:13 +0530 Subject: [Pw_forum] US j -average not yet implemented In-Reply-To: <49BE07F0.1010502@sissa.it> References: <49BE07F0.1010502@sissa.it> Message-ID: Dear GS, thanks for the suggestion. cheers artee On Mon, Mar 16, 2009 at 1:34 PM, Gabriele Sclauzero wrote: > > > artee sharma wrote: > > Dear all, > > I have an input like shown below: > ... > > > / > > ATOMIC_SPECIES > > Pt 195.09 Ptrel.RRKJ3.UPF > > Ce 140.116 Ce_lda_sc.UPF > > O 16.00 O.pz-rrkjus.UPF > > This problem was already discussed in a very old post, please see > http://www.democritos.it/pipermail/pw_forum/2005-January/001940.html > things haven't change much since that time (for this specific issue). > > > > > > > But its showing error which says "*US j -average not yet implemented*". > > What does it mean?? does it has something to do with the pseudo file of > > Pt (Ptrel.RRKJ3.UPF)?? > > It has, since this pseudopotential has been generated in order to include > spin orbit > coupling effects (irel=2 in ld1.x input), and it is usually refered as a > 'fully-relativistic' (FR-PP). > If you want to include spin-orbit effects in your calculations (through > PPs) you must specify > noncolin= .TRUE. > lspinorb= .TRUE. > in the system namelist. > You should also use FR-PP for the other elements (or at least for the heavy > ions). > If you're not interested in SO-coupling, you can use scalar-relativistic PP > (irel=1) for > Pt, which include part of the relativistic effects (but not spin-orbit > splittings). > > Regards > > GS > > > > > > > thanks in advance > > A K S > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/e4716e51/attachment.htm From mailtoartee at gmail.com Tue Mar 17 07:30:34 2009 From: mailtoartee at gmail.com (artee sharma) Date: Tue, 17 Mar 2009 12:00:34 +0530 Subject: [Pw_forum] ussp files Message-ID: Dear all, Is anybody using pseudopotential files of LDA (USSP) for Mn and Cr?? If possible kindly share. thanks artee -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/c5085de5/attachment.htm From sclauzer at sissa.it Tue Mar 17 08:37:29 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 17 Mar 2009 08:37:29 +0100 Subject: [Pw_forum] LDA+U In-Reply-To: References: Message-ID: <49BF5339.7030502@sissa.it> Mansoureh Pashangpour wrote: > Dear all > I would like to obtain phonon frequencies for Cd(OH)2 by LDA+U .But the > code didn't work with LDA+U for phonon calculation and Please have a look at this recent post by Matteo Cococcioni: http://www.democritos.it/pipermail/pw_forum/2009-January/011367.html > I just found the frequencies by LDA. Is there any way to obtain these > frequencies by LDA+U? In the meantime I think you can still use the old, dear frozen phonon method... > Which physical properties can be obtain by PWscf with LDA+U except DOS > and Bandstructure? Forces and stress should work as well. HTH GS > Thanks > Pashangpour > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From ismotochi at gmail.com Tue Mar 17 09:07:08 2009 From: ismotochi at gmail.com (isaac motochi) Date: Tue, 17 Mar 2009 00:07:08 -0800 Subject: [Pw_forum] surface calculations Message-ID: <9d6ea92e0903170107l3932bd48uc64c70eac6f16ea1@mail.gmail.com> Dear all, I wish to get help in setting up a script that can be used in modeling a diamond (111) surface upto 5bilayers. I will also appreciate the script can be sent to my address ismotochi at gmail.com so that I can view it with xcrysden. regards Motochi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/d9d41d42/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Tue Mar 17 10:47:22 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 17 Mar 2009 10:47:22 +0100 Subject: [Pw_forum] ussp files In-Reply-To: References: Message-ID: <200903171047.22594.giuseppe.mattioli@mlib.ism.cnr.it> Dear Artee. First, please provide always your affiliation. If you need some USPP, try to generate and test it! It is not so difficult and you can learn so much about your working tools. I'm keen (!) on Vanderbilt USPP generation code... You can find it at http://www.physics.rutgers.edu/~dhv/uspp/ Of course, you can also try the analogous QE tool (look at your QE/atomic_doc/ directory). You can use the headers of some available PBE or PW91 pseudo to generate your own LDA one. Yours Giuseppe On Tuesday 17 March 2009 07:30:34 artee sharma wrote: > Dear all, > Is anybody using pseudopotential files of LDA (USSP) for Mn and Cr?? If > possible kindly share. > > thanks > artee -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00016 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/72386960/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Tue Mar 17 10:52:34 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 17 Mar 2009 10:52:34 +0100 Subject: [Pw_forum] surface calculations In-Reply-To: <9d6ea92e0903170107l3932bd48uc64c70eac6f16ea1@mail.gmail.com> References: <9d6ea92e0903170107l3932bd48uc64c70eac6f16ea1@mail.gmail.com> Message-ID: <200903171052.35416.giuseppe.mattioli@mlib.ism.cnr.it> Nothing else? On Tuesday 17 March 2009 09:07:08 isaac motochi wrote: > Dear all, > I wish to get help in setting up a script that can be used in modeling a > diamond (111) surface upto 5bilayers. I will also appreciate the script can > be sent to my address ismotochi at gmail.com so that I can view it with > xcrysden. > > regards > > Motochi -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00016 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/7facedab/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Tue Mar 17 10:54:49 2009 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 17 Mar 2009 10:54:49 +0100 Subject: [Pw_forum] surface calculations In-Reply-To: <200903171052.35416.giuseppe.mattioli@mlib.ism.cnr.it> References: <9d6ea92e0903170107l3932bd48uc64c70eac6f16ea1@mail.gmail.com> <200903171052.35416.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <200903171054.49776.giuseppe.mattioli@mlib.ism.cnr.it> Sorry, anything else? On Tuesday 17 March 2009 10:52:34 Giuseppe Mattioli wrote: > Nothing else? > > On Tuesday 17 March 2009 09:07:08 isaac motochi wrote: > > Dear all, > > I wish to get help in setting up a script that can be used in modeling a > > diamond (111) surface upto 5bilayers. I will also appreciate the script > > can be sent to my address ismotochi at gmail.com so that I can view it with > > xcrysden. > > > > regards > > > > Motochi -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00016 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/136f65d3/attachment-0001.htm From mailtoartee at gmail.com Tue Mar 17 11:46:49 2009 From: mailtoartee at gmail.com (artee sharma) Date: Tue, 17 Mar 2009 16:16:49 +0530 Subject: [Pw_forum] ussp files In-Reply-To: <200903171047.22594.giuseppe.mattioli@mlib.ism.cnr.it> References: <200903171047.22594.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: Dear Giuseppe, thanks for the link. i'll try to generate it. regards artee On Tue, Mar 17, 2009 at 3:17 PM, Giuseppe Mattioli < giuseppe.mattioli at mlib.ism.cnr.it> wrote: > Dear Artee. > > First, please provide always your affiliation. > > If you need some USPP, try to generate and test it! It is not so difficult > and you can learn so much about your working tools. > > I'm keen (!) on Vanderbilt USPP generation code... You can find it at > > http://www.physics.rutgers.edu/~dhv/uspp/ > > Of course, you can also try the analogous QE tool (look at your > QE/atomic_doc/ directory). You can use the headers of some available PBE or > PW91 pseudo to generate your own LDA one. > > Yours > > Giuseppe > > On Tuesday 17 March 2009 07:30:34 artee sharma wrote: > > > Dear all, > > > Is anybody using pseudopotential files of LDA (USSP) for Mn and Cr?? If > > > possible kindly share. > > > > > > thanks > > > artee > > -- > > ******************************************************** > > - Article premier - Les hommes naissent et demeurent > > libres et ?gaux en droits. Les distinctions sociales > > ne peuvent ?tre fond?es que sur l'utilit? commune > > - Article 2 - Le but de toute association politique > > est la conservation des droits naturels et > > imprescriptibles de l'homme. Ces droits sont la libert?, > > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > > ******************************************************** > > Giuseppe Mattioli > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > > v. Salaria Km 29,300 - C.P. 10 > > I 00016 - Monterotondo Stazione (RM) > > Tel + 39 06 90672836 - Fax +39 06 90672316 > > E-mail: > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/6ac1b0ea/attachment.htm From lanhaiping at gmail.com Tue Mar 17 12:19:05 2009 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 17 Mar 2009 19:19:05 +0800 Subject: [Pw_forum] surface calculations In-Reply-To: <200903171054.49776.giuseppe.mattioli@mlib.ism.cnr.it> References: <9d6ea92e0903170107l3932bd48uc64c70eac6f16ea1@mail.gmail.com> <200903171052.35416.giuseppe.mattioli@mlib.ism.cnr.it> <200903171054.49776.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: something like an autotool for data processing or paper writing ? On Tue, Mar 17, 2009 at 5:54 PM, Giuseppe Mattioli < giuseppe.mattioli at mlib.ism.cnr.it> wrote: > Sorry, anything else? > > On Tuesday 17 March 2009 10:52:34 Giuseppe Mattioli wrote: > > > Nothing else? > > > > > > On Tuesday 17 March 2009 09:07:08 isaac motochi wrote: > > > > Dear all, > > > > I wish to get help in setting up a script that can be used in modeling > a > > > > diamond (111) surface upto 5bilayers. I will also appreciate the script > > > > can be sent to my address ismotochi at gmail.com so that I can view it > with > > > > xcrysden. > > > > > > > > regards > > > > > > > > Motochi > > -- > > ******************************************************** > > - Article premier - Les hommes naissent et demeurent > > libres et ?gaux en droits. Les distinctions sociales > > ne peuvent ?tre fond?es que sur l'utilit? commune > > - Article 2 - Le but de toute association politique > > est la conservation des droits naturels et > > imprescriptibles de l'homme. Ces droits sont la libert?, > > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > > ******************************************************** > > Giuseppe Mattioli > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > > v. Salaria Km 29,300 - C.P. 10 > > I 00016 - Monterotondo Stazione (RM) > > Tel + 39 06 90672836 - Fax +39 06 90672316 > > E-mail: > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/6b41685c/attachment.htm From miguel.martinez at ehu.es Tue Mar 17 12:31:58 2009 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Tue, 17 Mar 2009 12:31:58 +0100 Subject: [Pw_forum] surface calculations In-Reply-To: References: <9d6ea92e0903170107l3932bd48uc64c70eac6f16ea1@mail.gmail.com> <200903171052.35416.giuseppe.mattioli@mlib.ism.cnr.it> <200903171054.49776.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <20090317123158.696c6fcc@lcpybm> On Tue, 17 Mar 2009 19:19:05 +0800 lan haiping wrote: > something like an autotool for data processing or paper writing ? Automatic acceptance by Nature referees would also be good. Thank you. -- ---------------------------------------- Miguel Mart?nez Canales Condensed Matter Physics Dpt. UPV/EHU Faculty of Science and Technology Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5326 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From eariel99 at gmail.com Tue Mar 17 14:39:59 2009 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Tue, 17 Mar 2009 09:39:59 -0400 Subject: [Pw_forum] new unit-cell volume in variable cell relaxation Message-ID: Hi, When doing variable cell relaxation it is useful to have the current volume of the variable cell. This is reported in the output when cell_dynamics='damp-w', e.g. in a line as the following new unit-cell volume = 3705.0385 (a.u.)^3 However, when cell_dynamics='bfgs' the cell volume is not reported (pw.x of version 4.0.4 ). I see in the text that bfgs is still experimental. If interesting for debuging the code, I can supply an input case where the relaxation fails . In this case, in the 3rd bfgs step, WARNING: integrated charge= 140.52433035, expected= 288.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from electrons : error # 1 charge is wrong I suspect the bgfs made drastic change and the electronic calculation went crazy. With damped dynamics it works smoothly. Best regards -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/a080586c/attachment.htm From idoldog at gmail.com Tue Mar 17 15:46:09 2009 From: idoldog at gmail.com (idoldog) Date: Tue, 17 Mar 2009 22:46:09 +0800 Subject: [Pw_forum] Error:too many bands are not converged Message-ID: <200903172246026561789@gmail.com> Dear PWSCF users, I have done some structure optimization calculations using ecutwfc=25, ecutrho=200 and mixing_ndim = 16 successfully. But when I increase the parameters ecutwfc=30 and ecut=240 and mixing_ndim=8, I got a lot of "c_bands: 10 eigenvalues not converged" warnings, even "too many bands are not converged" errors. I searched the old pw_forum articles and find little things about this. so I want to know the change of which parameters lead to this problem? hoping your kindly reply. all best -------------- ?? ======================== ???????? ?????????94? Email:lifei.chn at mail.nankai.edu.cn QQ:155192560 MSN:lifei.chn at hotmail.com ======================= 2009-03-17 From sks.jnc at gmail.com Tue Mar 17 15:55:09 2009 From: sks.jnc at gmail.com (S. K. S.) Date: Tue, 17 Mar 2009 20:25:09 +0530 Subject: [Pw_forum] USPP Message-ID: >>>>> Dear Prithwish, during next week, I will add to the pseudopotential library (http://www.pwscf.org/pseudo.htm) the Ce pseudopotential we used to study cerium-oxide. As you know, in general, compounds based on rare earths may display quite intriguing properties and our pseudo has not been tested for systems other than cerias. You can refer to me if you have specific questions, I will be happy to contribute as far as I can. Yours sincerely, Stefano <<<< Dear all, Quite a long time ago, the above message was posted regarding Ce pseudopotential. Is anyone of you having an LDA version of the Ce pseudo which takes f-electron in account? Looking forward to your kind reply. regards, S. K. Saha JNCASR Bangalore 560012 From idoldog at gmail.com Tue Mar 17 15:59:51 2009 From: idoldog at gmail.com (idoldog) Date: Tue, 17 Mar 2009 22:59:51 +0800 Subject: [Pw_forum] Error:too many bands are not converged Message-ID: <200903172259500935628@gmail.com> I alse change the k-point mesh from 6 6 6 to 4 4 4. all best -------------- ?? ======================== ???????? ?????????94? Email:lifei.chn at mail.nankai.edu.cn QQ:155192560 MSN:lifei.chn at hotmail.com ======================= 2009-03-17 From lanhaiping at gmail.com Tue Mar 17 16:05:22 2009 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 17 Mar 2009 23:05:22 +0800 Subject: [Pw_forum] Error:too many bands are not converged In-Reply-To: <200903172259500935628@gmail.com> References: <200903172259500935628@gmail.com> Message-ID: Hi, You may reduce your mixing parameters: mixing_beta or change the scheme of diagonalization. regards 2009/3/17 idoldog > I alse change the k-point mesh from 6 6 6 to 4 4 4. > > all best > > -------------- > ?? > > > > ======================== > > ???????? > > ?????????94? > > Email:lifei.chn at mail.nankai.edu.cn > > QQ:155192560 > > MSN:lifei.chn at hotmail.com > > ======================= > 2009-03-17 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090317/09977679/attachment.htm From idoldog at gmail.com Tue Mar 17 17:58:48 2009 From: idoldog at gmail.com (idoldog) Date: Wed, 18 Mar 2009 00:58:48 +0800 Subject: [Pw_forum] Error:too many bands are not converged References: <200903172259500935628@gmail.com> Message-ID: <200903180058464533358@gmail.com> > You may reduce your mixing parameters: mixing_beta or change the scheme of > diagonalization. i can get a successful calculation using a large mixing_beta=16 but for mixing_beta=8 it failed. i always meet a situation that jobs still run but it didn't output informations and modify the data in out directory (just like endless loops) when i use david diagonalization. that might be caused by poor resources. for cg diagonalization, everything is OK. All best From giannozz at democritos.it Tue Mar 17 18:05:40 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 17 Mar 2009 18:05:40 +0100 Subject: [Pw_forum] new unit-cell volume in variable cell relaxation In-Reply-To: References: Message-ID: <49BFD864.2080604@democritos.it> Eduardo Ariel Menendez Proupin wrote: > However, when cell_dynamics='bfgs' the cell volume is not reported (pw.x > of version 4.0.4 ). it works in the cvs version > I see in the text that bfgs is still experimental. If interesting for > debugging the code, I can supply an input case where the relaxation fails please! P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 17 18:35:25 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 17 Mar 2009 18:35:25 +0100 Subject: [Pw_forum] Error:too many bands are not converged In-Reply-To: <200903180058464533358@gmail.com> References: <200903172259500935628@gmail.com> <200903180058464533358@gmail.com> Message-ID: <49BFDF5D.2000700@democritos.it> idoldog wrote: > i can get a successful calculation using a large mixing_beta=16 but for mixing_beta=8 it failed. really? mixing_beta typically is between 0.1 and 0.7 > i always meet a situation that jobs still run but it didn't output informations > and modify the data in out directory (just like endless loops) when i use david > diagonalization. that might be caused by poor resources. for cg diagonalization, > everything is OK. please provide a test job -- Paolo Giannozzi, Democritos and University of Udine, Italy From lfhuang at theory.issp.ac.cn Wed Mar 18 01:18:54 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Wed, 18 Mar 2009 8:18:54 +0800 Subject: [Pw_forum] =?utf-8?q?any_good_paper_on_=22non-collinear=22_using_?= =?utf-8?q?PWSCF=3F?= Message-ID: <20090318001854.26232.qmail@ms.hfcas.ac.cn> Hi everyone: I am planning to use the "non-collinear" method to stydy the magnetic properties of carbon based systems, and I have searched in some famous magazines for some references, but just find several papers related. Could anyone inform me of some good papers on "non-collinear" (not only on carbon based systems), especially using PWSCF ? I would like to appreciate any kindly hearted help and invaluable information! Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090318/d6def594/attachment.htm From ptanhphys at gmail.com Wed Mar 18 01:29:40 2009 From: ptanhphys at gmail.com (TuanAnh Pham) Date: Wed, 18 Mar 2009 05:29:40 +0500 Subject: [Pw_forum] any good paper on "non-collinear" using PWSCF? In-Reply-To: <20090318001854.26232.qmail@ms.hfcas.ac.cn> References: <20090318001854.26232.qmail@ms.hfcas.ac.cn> Message-ID: Hi, For non-collinear spin polarization in PWscf, you can have a look at paper by Ralph et al, PRB 61, 6145 (2000) and references therein. An original paper about theory of non-collinear in DFT is by Barth et al, J. Phys. C: Solid state phys, 5 1972. Hope this helps, Anh. On Wed, Mar 18, 2009 at 5:18 AM, lfhuang wrote: > Hi everyone: > > I am planning to use the "non-collinear" method to stydy the magnetic > properties of carbon > based systems, and I have searched in some famous magazines for some > references, but just > find several papers related. Could anyone inform me of some good papers on > "non-collinear" > (not only on carbon based systems), especially using PWSCF ? I would like > to appreciate any > kindly hearted help and invaluable information! > Best Wishes! > > Yours Sincerely > > L. F. Huang > > ------ > > ====================================================================== > L.F.Huang(???) lfhuang at theory.issp.ac.cn > ====================================================================== > Add: Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591464-328(office) > Fax: 86-551-5591434 > Web: http://theory.issp.ac.cn> (website of our theory group) > http://www.issp.ac.cn> (website of our > institute) > ====================================================================== > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Tuan Anh Pham Graduate Student University of California, Davis Phone: 530-752-0957 Homepage: http://angstrom.ucdavis.edu/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090318/0bb2f8ac/attachment.htm From yccheng.nju at gmail.com Wed Mar 18 02:07:22 2009 From: yccheng.nju at gmail.com (=?utf-8?B?eWNjaGVuZy5uanU=?=) Date: Wed, 18 Mar 2009 09:07:22 +0800 Subject: [Pw_forum] =?utf-8?q?surface_calculations?= Message-ID: <200903180907200154187@gmail.com> Dear motochi, As far as I know, there is not such a script to model diamond(111) surface in pwscf package. But you can build it by yourself with some other tools. If you have Materials Studio Visualizer, this work is very easy. You can follow the instruction of modeling surface in Materials Studio, and covert the *.cell file for pwscf or some other package (abinit, etc. ) ! I think you can google search some modling tools to build the surface. ------------------ yccheng.nju 2009-03-18 ------------------------------------------------------------- ????isaac motochi ?????2009-03-17 16:13:49 ????Pw_forum ??? ???[Pw_forum] surface calculations Dear all, I wish to get help in setting up a script that can be used in modeling a diamond (111) surface upto 5bilayers. I will also appreciate the script can be sent to my address ismotochi at gmail.com so that I can view it with xcrysden. regards Motochi _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From idoldog at gmail.com Wed Mar 18 04:52:25 2009 From: idoldog at gmail.com (idoldog) Date: Wed, 18 Mar 2009 11:52:25 +0800 Subject: [Pw_forum] Error:too many bands are not converged References: <200903172259500935628@gmail.com>, <200903180058464533358@gmail.com> Message-ID: <200903181152241095118@gmail.com> Dear Paolo Giannozzi and other PWSCF users, I make a mistake by mixing up the parameters mixing_beta and mixing_ndim because i didn't mention mixing_deta while lan haiping did. I take the parameter mixing_ndim for granted. I apologize to you. However, I have solved the problem now. One can get different results by changing the parameters of nbnd, mixing_beta, K-point, ecutrho and ecutwfc, even the method of diago, these don't eradicate the problem. By learning the source code, I find this might a problem of another kind of convergence. All best. ------------------ ?? ======================== ???????? ?????????94? Email:lifei.chn at mail.nankai.edu.cn QQ:155192560 MSN:lifei.chn at hotmail.com ======================= 2009-03-18 ------------------------------------------------------------- ????Paolo Giannozzi ?????2009-03-18 01:35:59 ????PWSCF Forum ??? ???Re: [Pw_forum] Error:too many bands are not converged idoldog wrote: > i can get a successful calculation using a large mixing_beta=16 but for mixing_beta=8 it failed. really? mixing_beta typically is between 0.1 and 0.7 > i always meet a situation that jobs still run but it didn't output informations > and modify the data in out directory (just like endless loops) when i use david > diagonalization. that might be caused by poor resources. for cg diagonalization, > everything is OK. please provide a test job -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From lfhuang at theory.issp.ac.cn Wed Mar 18 05:48:01 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Wed, 18 Mar 2009 12:48:01 +0800 Subject: [Pw_forum] =?utf-8?q?any_good_paper_on_=22non-collinear=22_using_?= =?utf-8?q?PWSCF=3F?= Message-ID: <20090318044801.5992.qmail@ms.hfcas.ac.cn> Dear TuanAnh Pham: Thank you very much for your kindly hearted help! Best Wishes! Yours Sincerely L. F. Huang From Institude of Solid State Physics of Chinese Academy Society > From: TuanAnh Pham > Subject: Re: [Pw_forum] any good paper on "non-collinear" using PWSCF? > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="gb2312" > > Hi, > > For non-collinear spin polarization in PWscf, you can have a look at paper > by > Ralph et al, PRB 61, 6145 (2000) and references therein. An original paper > about > theory of non-collinear in DFT is by Barth et al, J. Phys. C: Solid state > phys, 5 > 1972. > Hope this helps, > Anh. > > On Wed, Mar 18, 2009 at 5:18 AM, lfhuang wrote: > > > Hi everyone: > > > > I am planning to use the "non-collinear" method to stydy the magnetic > > properties of carbon > > based systems, and I have searched in some famous magazines for some > > references, but just > > find several papers related. Could anyone inform me of some good papers on > > "non-collinear" > > (not only on carbon based systems), especially using PWSCF ? I would like > > to appreciate any > > kindly hearted help and invaluable information! > > Best Wishes! > > > > Yours Sincerely > > > > L. F. Huang > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090318/ff0e980d/attachment.htm From sclauzer at sissa.it Wed Mar 18 09:42:55 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 18 Mar 2009 09:42:55 +0100 Subject: [Pw_forum] any good paper on "non-collinear" using PWSCF? In-Reply-To: <20090318001854.26232.qmail@ms.hfcas.ac.cn> References: <20090318001854.26232.qmail@ms.hfcas.ac.cn> Message-ID: <49C0B40F.1070509@sissa.it> If you are also interested in how spin-orbit effects are included in the noncolinear formalism through pseudopotentials, you can read Adriano Mosca Conte's PhD thesis: http://www.sissa.it/cm/thesis/2007/moscaconte.pdf and the related paper: http://www.sissa.it/~dalcorso/publications/PRB-71-115106-2005.pdf Applications of this tecnique to noncolinear magnetism in Pt nanocontacts have been recently published by Smogunov et al.: http://www.nature.com/nnano/journal/v3/n1/abs/nnano.2007.419.html http://link.aps.org/abstract/PRB/v78/e014423 Regards GS lfhuang wrote: > Hi everyone: > > I am planning to use the "non-collinear" method to stydy the magnetic > properties of carbon > based systems, and I have searched in some famous magazines for some > references, but just > find several papers related. Could anyone inform me of some good papers > on "non-collinear" > (not only on carbon based systems), especially using PWSCF ? I would > like to appreciate any > kindly hearted help and invaluable information! > Best Wishes! > > Yours Sincerely > > L. F. Huang > > ------ > > ====================================================================== > L.F.Huang(???) lfhuang at theory.issp.ac.cn > > ====================================================================== > Add: Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591464-328(office) > Fax: 86-551-5591434 > Web: http://theory.issp.ac.cn> (website of our theory group) > http://www.issp.ac.cn> (website of our institute) > ====================================================================== > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From subhra at iitg.ernet.in Wed Mar 18 10:24:32 2009 From: subhra at iitg.ernet.in (Subhradip Ghosh) Date: Wed, 18 Mar 2009 14:54:32 +0530 (IST) Subject: [Pw_forum] Fixed spin moment method & Phonon calculation Message-ID: <32857.202.141.81.5.1237368272.squirrel@webmail.iitg.ernet.in> I am interested in calculating phonn dispersions in a metallic system by fixin g the magnetization. To do that, I had fixed the magnetization to a particular value and tried the phonon calculation. However, it failed apprently because "the constrained magnetization is not implemented in the phonon code". Therefore, my question is: Is phonon calculation not possible by fixing total magnetization with the present QE code? I had searched the archive to find answers but no definite solution was found apart from a comment from Paolo which suggests that "If the magnetization you choose is the ground state one, the two Fermi energies would be the same. In that case, commenting out the check in phq_readin.f90 should work. If you constrain the magnetization to a value that is not the ground state, I have no idea what numbers will come out". Does this mean that a phonon calculation(by commenting out the check in phq_readin) by fixing the magnetization at a value other than the ground state value is not reliable? The answer to this question is important to me because I am interested in doing phonons by fixing total magnetization at values other than the ground state value. Help in this regard would be useful. Subhradip ************************************************************************ Dr. Subhradip Ghosh Assistant Professor Department of Physics Indian Institute of Technology Guwahati,Assam-781039 India E-mail:subhra at iitg.ernet.in Phone: +91 361 2582717(O) +91 361 2584717(R) Fax: +91 361 2582749 (Physics) +91 361 2690762 (General) ************************************************************************ From cdm_mail at 163.com Wed Mar 18 13:18:56 2009 From: cdm_mail at 163.com (cdm_mail) Date: Wed, 18 Mar 2009 20:18:56 +0800 (CST) Subject: [Pw_forum] about 'fnosep' Message-ID: <13897204.803661237378736310.JavaMail.coremail@bj163app138.163.com> Date: WED, 18 Mar 2009 20:18:36 +0800 Subject: 'about the parameter of fnosep' To: PWSCF Forum Message-ID: < cdm_mail at 163.com > Content-Type: text/plain :charset=ISO-8859-1; format=flowed -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090318/fc542bde/attachment.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: about the parameter'fnosep'.txt Url: http://www.democritos.it/pipermail/pw_forum/attachments/20090318/fc542bde/attachment.txt From daijiayu at nudt.edu.cn Thu Mar 19 08:58:12 2009 From: daijiayu at nudt.edu.cn (=?gb2312?B?tPe80e7a?=) Date: Thu, 19 Mar 2009 15:58:12 +0800 Subject: [Pw_forum] finite temperature DFT Message-ID: <437449492.31095@nudt.edu.cn> Dear all, I want to know is there the part of finite temperature DFT decribed by Mermin in PWSCF? If not, where could we add it into the code? Thanks in advance. ------------------------------ Jiayu Dai National University of Defense Technology, P R China From daijiayu at nudt.edu.cn Thu Mar 19 08:52:24 2009 From: daijiayu at nudt.edu.cn (=?gb2312?B?tPe80e7a?=) Date: Thu, 19 Mar 2009 15:52:24 +0800 Subject: [Pw_forum] finite temperature DFT Message-ID: <437449144.30415@nudt.edu.cn> Dear all, I want to know is there the part of finite temperature DFT decribed by Fermin in PWSCF? If not, where could we add it into the code? Thanks in advance. ------------------------------ Jiayu Dai National University of Defense Technology, P R China From lfhuang at theory.issp.ac.cn Thu Mar 19 11:50:10 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Thu, 19 Mar 2009 18:50:10 +0800 Subject: [Pw_forum] =?utf-8?q?any_good_paper_on_=22non-collinear=22_using_?= =?utf-8?q?PWSCF=3F?= Message-ID: <20090319105010.32103.qmail@ms.hfcas.ac.cn> Dear Gabriele Sclauzero: Thank you very much for your help! Best Wishes! Yours Sincerely L. F. Huang > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] any good paper on "non-collinear" using PWSCF? > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=UTF-8; format=flowed > > If you are also interested in how spin-orbit effects are included in the noncolinear > formalism through pseudopotentials, you can read Adriano Mosca Conte's PhD thesis: > http://www.sissa.it/cm/thesis/2007/moscaconte.pdf > > and the related paper: > http://www.sissa.it/~dalcorso/publications/PRB-71-115106-2005.pdf > > Applications of this tecnique to noncolinear magnetism in Pt nanocontacts have been > recently published by Smogunov et al.: > http://www.nature.com/nnano/journal/v3/n1/abs/nnano.2007.419.html > http://link.aps.org/abstract/PRB/v78/e014423 > > Regards > > GS ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090319/370537a0/attachment.htm From lfhuang at theory.issp.ac.cn Thu Mar 19 13:45:52 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Thu, 19 Mar 2009 20:45:52 +0800 Subject: [Pw_forum] =?utf-8?q?any_good_paper_on_=22non-collinear=22_using_?= =?utf-8?q?PWSCF=3F?= Message-ID: <20090319124552.12771.qmail@ms.hfcas.ac.cn> Dear Stefano Fabris: Thank you very much! It's very kind of you! And your is very valuable for me! Best Wishes! Yours Sincerely L. F. Huang > I would also suggest you this application of the non-collinear > formalism: http://link.aps.org/doi/10.1103/PhysRevB.78.014416 > > Regards, > Stefano Fabris > --- > Stefano Fabris > Theory at Elettra Group > CNR-INFM DEMOCRITOS National Simulation Center > c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE > website: www.democritos.it/the-group > email: fabris at democritos.it tel: +39 040 375-8735 fax: -8776 > --- ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090319/1b079ad1/attachment.htm From daijiayu at nudt.edu.cn Thu Mar 19 13:51:27 2009 From: daijiayu at nudt.edu.cn (=?gb2312?B?tPe80e7a?=) Date: Thu, 19 Mar 2009 20:51:27 +0800 Subject: [Pw_forum] finite temperature DFT Message-ID: <437467087.32600@nudt.edu.cn> Dear Stefano, >The Mermin functional is obtained if you fill the electronic states >according to the Fermi-Dirac distribution. use occupations='smearing' >and smearing='fermi-dirac'. Temperature must be converted in rydberg >and passed in the smearing_width variable. > >When using this at high temeperature check carefully that the number >of bands used is sufficient to include all partially occupied >levels... FD distribution decays rather slowly w.r.t its argument. > Thanks for your answer, and it is very helpful. So, you mean the temperature is set to be smearing_width here, all right? And if i want to perform molecule dynamics, i have to use the tempw and the method of thermostat at the same time? Then, the tempw and the smearing_width must be equal. And do we need to consider the chemical potential of the ensemble? Thanks a lot. Jiayu Dai National University of Defense Technology, P R China From ismotochi at gmail.com Thu Mar 19 14:29:28 2009 From: ismotochi at gmail.com (isaac motochi) Date: Thu, 19 Mar 2009 16:29:28 +0300 Subject: [Pw_forum] surface calculations In-Reply-To: <200903180907200154187@gmail.com> References: <200903180907200154187@gmail.com> Message-ID: <9d6ea92e0903190629x2dbc292bj9a400ef0e1348c3a@mail.gmail.com> Thanks to you yccheng.nju for your kind gesture to my question. I appreciate as i begin to use your advise On 3/18/09, yccheng.nju wrote: > Dear motochi, > As far as I know, there is not such a script to model diamond(111) > surface in pwscf package. But you can build it by yourself with some other > tools. > If you have Materials Studio Visualizer, this work is very easy. You > can follow the instruction of modeling surface in Materials Studio, and > covert the *.cell file for pwscf or some other package (abinit, etc. ) ! > I think you can google search some modling tools to build the surface. > > > > ------------------ > yccheng.nju > 2009-03-18 > > ------------------------------------------------------------- > ????isaac motochi > ?????2009-03-17 16:13:49 > ????Pw_forum > ??? > ???[Pw_forum] surface calculations > > Dear all, > I wish to get help in setting up a script that can be used in modeling a > diamond (111) surface upto 5bilayers. I will also appreciate the script can > be sent to my address ismotochi at gmail.com so that I can view it with > xcrysden. > > regards > > Motochi > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From marzari at MIT.EDU Thu Mar 19 14:39:49 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 19 Mar 2009 13:39:49 -0000 Subject: [Pw_forum] finite temperature DFT In-Reply-To: <437467087.32600@nudt.edu.cn> References: <437467087.32600@nudt.edu.cn> Message-ID: <49EB2993.1090308@mit.edu> ??? wrote: > Thanks for your answer, and it is very helpful. > > So, you mean the temperature is set to be smearing_width here, all right? And if > i > want to perform molecule dynamics, i have to use the tempw and the method of > thermostat at the same time? Then, the tempw and the smearing_width must be > equal. > And do we need to consider the chemical potential of the ensemble? > > Thanks a lot. > > Jiayu Dai > National University of Defense Technology, P R China Correct (re tempw). But note that unless you have high temperatures, of thousands of degrees, you will not see much of an effect (at all) in what happens to the electrons. Try it yourself, and see how much e.g. forces on atoms depend on smearing_width. The chemical potential of the electrons is the fermi energy, fixed so that you have system neutrality, or whatever you specify in nelec. The atoms are fixed in number, so you cannot specify their chemical potential - you would do simulations in the NVT or NPT ensemble, both for the ions and the electrons. nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From also at if.ufrj.br Thu Mar 19 19:04:49 2009 From: also at if.ufrj.br (Andre Saraiva) Date: Thu, 19 Mar 2009 15:04:49 -0300 Subject: [Pw_forum] Error in User Guide - ibrav Message-ID: <49C28941.3020700@if.ufrj.br> Dear developers, I have noticed what I believe to be an error in the user guide for PWSCF. In the section "Input Data Description", the basis vectors for the Body Centered Tetragonal Bravais Lattice are strange. I believe the correct expression for v1 would be v1 = (a/2)(-1,1,c/a). Using the expression given in the user guide leads to errors in the crystal structure. The corrected expression seems to work just fine. I don't know if I can change the user guide myself or if it is alowed only for developers. Regards, Andr? Saraiva PhD Student @ Koiller - Capaz Group Universidade Federal do Rio de Janeiro Instituto de F?sica +55 21 25627343 also at if.ufrj.br From positronium at gmail.com Thu Mar 19 20:18:03 2009 From: positronium at gmail.com (Lex Kemper) Date: Thu, 19 Mar 2009 15:18:03 -0400 Subject: [Pw_forum] Error in User Guide - ibrav In-Reply-To: <49C28941.3020700@if.ufrj.br> References: <49C28941.3020700@if.ufrj.br> Message-ID: <49C29A6B.6010904@phys.ufl.edu> Hi Andre, I've used the bct unit vectors and believe the results to be okay. Could you point out specifically what problem you found? Thanks, Lex Kemper Department of Physics and QTP University of Florida Andre Saraiva wrote: > Dear developers, > > I have noticed what I believe to be an error in the user guide for > PWSCF. In the section "Input Data Description", the basis vectors for > the Body Centered Tetragonal Bravais Lattice are strange. I believe the > correct expression for v1 would be > > v1 = (a/2)(-1,1,c/a). > > Using the expression given in the user guide leads to errors in the > crystal structure. The corrected expression seems to work just fine. I > don't know if I can change the user guide myself or if it is alowed only > for developers. > > Regards, > > Andr? Saraiva > PhD Student @ Koiller - Capaz Group > Universidade Federal do Rio de Janeiro > Instituto de F?sica > +55 21 25627343 > also at if.ufrj.br > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Thu Mar 19 20:31:19 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 19 Mar 2009 20:31:19 +0100 Subject: [Pw_forum] Error in User Guide - ibrav In-Reply-To: <49C28941.3020700@if.ufrj.br> References: <49C28941.3020700@if.ufrj.br> Message-ID: <238F86AF-4F2E-4E80-ACBD-505815557743@democritos.it> On Mar 19, 2009, at 19:04 , Andre Saraiva wrote: > the basis vectors for the Body Centered Tetragonal Bravais Lattice > are strange. I believe the correct expression for v1 would be > > v1 = (a/2)(-1,1,c/a) the choice of crystal axis is not unique. What the documentation says is consistent, AFAIK, with what the code does. All axis triplets used by PWscf are right-handed, by the way, while yours is left-handed. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From daijiayu at nudt.edu.cn Fri Mar 20 02:34:21 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Fri, 20 Mar 2009 09:34:21 +0800 Subject: [Pw_forum] finite temperature DFT Message-ID: <437512861.21391@nudt.edu.cn> > Correct (re tempw). But note that unless you have high temperatures, of thousands of degrees, you will not see much of an effect (at all) inwhat happens to the electron > Try it yourself, and see how much e.g. forces on atoms depend onsmearing_width. > > The chemical potential of the electrons is the fermi energy, fixed sthat you have system neutrality, or whatever you specify in nele > The atoms are fixed in number, so you cannot specify their chemical >potential - you would do simulations in the NVT or NPT ensemble, botfor the ions and the electrons. > Thanks, Nicola. I have another problem: how to set the number of bands in the scf or MD calculation? The nbnd parameter is just meaningful in the DOS or the band calculations. Is that the nele parameter? And could you tell me which file incudes the program of ferimi-dirac? Is that weights.f90? Besides, in pwscf, the GGA+U is note performed now, right? Thanks. ------------------------------ Jiayu Dai National University of Defense Technology, P R China From lanhaiping at gmail.com Fri Mar 20 03:19:53 2009 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 20 Mar 2009 10:19:53 +0800 Subject: [Pw_forum] finite temperature DFT In-Reply-To: <437512861.21391@nudt.edu.cn> References: <437512861.21391@nudt.edu.cn> Message-ID: Hi, Jiayu On Fri, Mar 20, 2009 at 9:34 AM, Jiayu Dai wrote: > > > > Correct (re tempw). But note that unless you have high temperatures, of > thousands of degrees, you will not see much of an effect (at all) inwhat > happens > to the electron > > Try it yourself, and see how much e.g. forces on atoms depend > onsmearing_width. > > > > The chemical potential of the electrons is the fermi energy, fixed sthat > you > have system neutrality, or whatever you specify in nele > > The atoms are fixed in number, so you cannot specify their chemical > >potential - you would do simulations in the NVT or NPT ensemble, botfor > the ions > and the electrons. > > > Thanks, Nicola. I have another problem: how to set the number of bands in > the scf > or MD calculation? The nbnd parameter is just meaningful in the DOS or the > band > calculations. Is that the nele parameter? > How do you come to this conclusion ? For some metal systems, we need include many bands to reach convergence. Therefore, what is your point for these systems ? thanks! Regards > And could you tell me which file incudes the program of ferimi-dirac? Is > that > weights.f90? > > Besides, in pwscf, the GGA+U is note performed now, right? > > Thanks. > > > > > ------------------------------ > Jiayu Dai > National University of Defense Technology, P R China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090320/e1a7f10f/attachment.htm From pemryan at yahoo.cn Fri Mar 20 03:40:59 2009 From: pemryan at yahoo.cn (Yan) Date: Fri, 20 Mar 2009 10:40:59 +0800 Subject: [Pw_forum] finite temperature DFT In-Reply-To: <437512861.21391@nudt.edu.cn> References: <437512861.21391@nudt.edu.cn> Message-ID: <200903201041.02084.pemryan@yahoo.cn> On 2009/03/20 Friday 09:34:21 Jiayu Dai wrote: > And could you tell me which file incudes the program of ferimi-dirac? Is > that weights.f90? PW/w*gauss.f90, I guess -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090320/93b840fb/attachment.htm From giannozz at democritos.it Fri Mar 20 09:04:30 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 20 Mar 2009 09:04:30 +0100 Subject: [Pw_forum] finite temperature DFT In-Reply-To: <437512861.21391@nudt.edu.cn> References: <437512861.21391@nudt.edu.cn> Message-ID: <49C34E0E.1020509@democritos.it> Jiayu Dai wrote: > Besides, in pwscf, the GGA+U is note performed now, right? "not" performed? it is P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From also at if.ufrj.br Fri Mar 20 13:02:02 2009 From: also at if.ufrj.br (also at if.ufrj.br) Date: Fri, 20 Mar 2009 09:02:02 -0300 (BRT) Subject: [Pw_forum] Error in User Guide - ibrav In-Reply-To: <49C29A6B.6010904@phys.ufl.edu> References: <49C29A6B.6010904@phys.ufl.edu> Message-ID: <65339.201.53.89.156.1237550522.squirrel@web2.if.ufrj.br> Hi, Lex, When I specify the atomic positions in terms of the crystal basis vectors I get the wrong distribution of atoms (as seen e.g. in xcrysden). But if I consider the basis vectors to be those I have pointed out the configuration is OK. Have you noticed something in this line? Thanks, Andr? Saraiva PhD Student @ Koiller - Capaz Group Universidade Federal do Rio de Janeiro Instituto de F?sica +55 21 25627343 also at if.ufrj.br > Hi Andre, > > I've used the bct unit vectors and believe the results to be okay. Could > you point out specifically what problem you found? > > Thanks, > > Lex Kemper > Department of Physics and QTP > University of Florida > > Andre Saraiva wrote: >> Dear developers, >> >> I have noticed what I believe to be an error in the user guide for >> PWSCF. In the section "Input Data Description", the basis vectors for >> the Body Centered Tetragonal Bravais Lattice are strange. I believe the >> correct expression for v1 would be >> >> v1 = (a/2)(-1,1,c/a). >> >> Using the expression given in the user guide leads to errors in the >> crystal structure. The corrected expression seems to work just fine. I >> don't know if I can change the user guide myself or if it is alowed only >> for developers. >> >> Regards, >> >> Andr? Saraiva >> PhD Student @ Koiller - Capaz Group >> Universidade Federal do Rio de Janeiro >> Instituto de F?sica >> +55 21 25627343 >> also at if.ufrj.br >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > From tone.kokalj at ijs.si Fri Mar 20 13:14:51 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 20 Mar 2009 13:14:51 +0100 Subject: [Pw_forum] Error in User Guide - ibrav In-Reply-To: <65339.201.53.89.156.1237550522.squirrel@web2.if.ufrj.br> References: <49C29A6B.6010904@phys.ufl.edu> <65339.201.53.89.156.1237550522.squirrel@web2.if.ufrj.br> Message-ID: <1237551291.10499.34.camel@walk.ijs.si> On Fri, 2009-03-20 at 09:02 -0300, also at if.ufrj.br wrote: > Hi, Lex, > > When I specify the atomic positions in terms of the crystal basis vectors > I get the wrong distribution of atoms (as seen e.g. in xcrysden). Make sure you are using the latest version of it, because some of the centered lattices have been adospted and old version of xcrysden will not be syncronised with pwscf. > But if I > consider the basis vectors to be those I have pointed out the > configuration is OK. Which? Regards, Tone PS: recently there have been several emails on this forum about the centered lattices, and according to my understanding, the source of trouble is the choice of the lattice vectors, which as pointed out by Paolo yesterday is not unique. If one has data corresponding to the choice that is different to that used in the pwscf, the solution is a pencil + sheet-of-paper: one has to draw the two settings of the crystal axis so as to understand what to "swap". -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From also at if.ufrj.br Fri Mar 20 13:27:45 2009 From: also at if.ufrj.br (also at if.ufrj.br) Date: Fri, 20 Mar 2009 09:27:45 -0300 (BRT) Subject: [Pw_forum] Error in User Guide - ibrav In-Reply-To: <238F86AF-4F2E-4E80-ACBD-505815557743@democritos.it> References: <238F86AF-4F2E-4E80-ACBD-505815557743@democritos.it> Message-ID: <59553.201.53.89.156.1237552065.squirrel@web2.if.ufrj.br> Dear Paolo, The user guide contains the following basis triplet for the BCC structure: bcc body entered cubic ==================== v1 = (a/2)(1,1,1), v2 = (a/2)(-1,1,1), v3 = (a/2)(-1,-1,1). While the for BCT structure this is what is seen: body centered tetragonal (i) ================================ v1 = (a/2)(1,-1,c/a), v2 = (a/2)(1,1,c/a), v3 = (a/2)(-1,-1,c/a). Now, I don't think that these two are consistent with the same convention for the choice of basis. They are not both right-handed. Also, The BCT does not have the same relative internal angle between two basis vectors (their scalar products are different). Third, it doesn't work ;) Please, try to specify the atomic positions inside the cell using the flag {crystal}. Then check the results on xcrysden. Probably you will get a weird configuration. Thanks, Andr? Saraiva > > On Mar 19, 2009, at 19:04 , Andre Saraiva wrote: > >> the basis vectors for the Body Centered Tetragonal Bravais Lattice >> are strange. I believe the correct expression for v1 would be >> >> v1 = (a/2)(-1,1,c/a) > > the choice of crystal axis is not unique. What the documentation says > is consistent, AFAIK, with what the code does. All axis triplets used > by PWscf are right-handed, by the way, while yours is left-handed. > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > > From tone.kokalj at ijs.si Fri Mar 20 13:48:32 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 20 Mar 2009 13:48:32 +0100 Subject: [Pw_forum] Error in User Guide - ibrav In-Reply-To: <59553.201.53.89.156.1237552065.squirrel@web2.if.ufrj.br> References: <238F86AF-4F2E-4E80-ACBD-505815557743@democritos.it> <59553.201.53.89.156.1237552065.squirrel@web2.if.ufrj.br> Message-ID: <1237553312.10499.38.camel@walk.ijs.si> On Fri, 2009-03-20 at 09:27 -0300, also at if.ufrj.br wrote: > Dear Paolo, > > The user guide contains the following basis triplet for the BCC structure: > > bcc body entered cubic > ==================== > v1 = (a/2)(1,1,1), v2 = (a/2)(-1,1,1), v3 = (a/2)(-1,-1,1). > > > While the for BCT structure this is what is seen: > > > body centered tetragonal (i) > ================================ > v1 = (a/2)(1,-1,c/a), v2 = (a/2)(1,1,c/a), v3 = (a/2)(-1,-1,c/a). > > > Now, I don't think that these two are consistent with the same convention > for the choice of basis. They are not both right-handed. Oh, but I think they are right-handed ! > Please, try to specify the atomic positions inside the cell using the flag > {crystal}. Then check the results on xcrysden. Probably you will get a > weird configuration. Would you share the "problematic" input file with some description what should the structure look-like. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From giannozz at democritos.it Fri Mar 20 14:45:55 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 20 Mar 2009 14:45:55 +0100 Subject: [Pw_forum] Error in User Guide - ibrav In-Reply-To: <59553.201.53.89.156.1237552065.squirrel@web2.if.ufrj.br> References: <238F86AF-4F2E-4E80-ACBD-505815557743@democritos.it> <59553.201.53.89.156.1237552065.squirrel@web2.if.ufrj.br> Message-ID: <49C39E13.4000909@democritos.it> also at if.ufrj.br wrote: > The user guide contains the following basis triplet for the BCC structure: > > bcc body entered cubic > ==================== > v1 = (a/2)(1,1,1), v2 = (a/2)(-1,1,1), v3 = (a/2)(-1,-1,1). > > While the for BCT structure this is what is seen: > > body centered tetragonal (i) > ================================ > v1 = (a/2)(1,-1,c/a), v2 = (a/2)(1,1,c/a), v3 = (a/2)(-1,-1,c/a). > > > Now, I don't think that these two are consistent with the same convention > for the choice of basis. there is no such thing as an "official" convention for the choice of basis. The one used in q-e may not be the most commonly used or the most appealing, but it is exactly and exhaustively documented. All errors or inconsistencies are immediately corrected. > They are not both right-handed they are. Try v1\cdot (v2\times v3) if you don't believe your eyes. > Also, The BCT does not have the same relative internal angle between > two basis vectors (their scalar products are different). so what? scalar products are different in your proposed basis as well. > Third, it doesn't work ;) it does, if you do things properly. > Please, try to specify the atomic positions inside the cell using the flag > {crystal}. Then check the results on xcrysden. Probably you will get a > weird configuration. if you specify atomic positions written for a different convention, yes, you get weird results. You can specify your choice of axis, by the way, with card CELL_PARAMETERS. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From amosleffler at gmail.com Fri Mar 20 19:20:26 2009 From: amosleffler at gmail.com (Amos Leffler) Date: Fri, 20 Mar 2009 11:20:26 -0700 Subject: [Pw_forum] Compiling QE 4.0.4 Message-ID: <61b264610903201120v332e2b6at4cf08085c9c9865b@mail.gmail.com> I am trying to compile QE 4.0.4 using openmpi-1.2.9. The program did compile successfully using the internal compilers in OpenSuse 10.2 in single mode. With openmpi-1.2.9 the configuration step went OK and it recognized that openmpi was being used. Using the command: "make all" it encountered the error shown below: Entering directory `/home/amos/Desktop/espresso-4.0.4/Modules' mpif90 -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI I../Modules -I../iotk/src -I../PW -I../PH -c fft_parallel.f90 In file fft_parallel.f90:282 send_cnt, send_displ, MPI_DOUBLE_COMPLEX, f(1), & 1 Error: Symbol 'mpi_double_complex' at (1) has no IMPLICIT type In file fft_parallel.f90:234 CALL MPI_ALLTOALLV( f(1), send_cnt, send_displ, MPI_DOUBLE_COMPLEX, yf(1), 1 Error: Symbol 'mpi_double_complex' at (1) has no IMPLICIT type make[1]: *** [fft_parallel.o] Error 1 make[1]: Leaving directory `/home/amos/Desktop/espresso-4.0.4/Modules' I looked in the file and it states "IMPLICIT none" so that the complaint appears to be correct. I checked the forum files but could find no report of an error in the last five months. Is there an easy fix? Hopefully someone has seen this before. Amos Leffler From nemeth at anl.gov Sat Mar 21 05:15:05 2009 From: nemeth at anl.gov (Karoly Nemeth) Date: Fri, 20 Mar 2009 23:15:05 -0500 (CDT) Subject: [Pw_forum] unit-printing error? In-Reply-To: References: Message-ID: Hi, I became aware of some unit printing errors in PWSCF (v.4.0.4). At least it seems to be case. In one of my calculations I got: crystal axes: (cart. coord. in units of a_0) a(1) = ( 2.556193 0.000000 0.000000 ) a(2) = ( 0.000000 2.556193 0.000000 ) a(3) = ( 0.000000 0.000000 30.000000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 0.391207 0.000000 0.000000 ) b(2) = ( 0.000000 0.391207 0.000000 ) b(3) = ( 0.000000 0.000000 0.033333 ) Obviously, the reciprocal axes is printed in units of 1/a_0, and not in "2 pi/a_0". A few lines below in the output, where k-points are listed I see: number of k points= 260 gaussian broad. (Ry)= 0.0300 ngauss = -1 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0039063 k( 2) = ( 0.0000000 0.0000000 0.0041667), wk = 0.0078125 Comparing reciprocal lattice to the listed k-points, it turns out, that k-point are also listed in units of 1/a_0, and not in "2pi/a_0". This seems to be a unit-printing error, as otherwise everything is consistent. If I remember well, in older versions the unit used to be 1/a_0 . Please let me know if I am right with the above. Thanks: Karoly *********************************************************************** Karoly Nemeth, Ph.D. Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439. Advanced Photon Source Accelerator Physics and Operations Group Building 401, Room B2200 Tel. 630-252-5813 Fax: 630-252-4732 *********************************************************************** From degironc at sissa.it Sat Mar 21 06:34:45 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 21 Mar 2009 06:34:45 +0100 Subject: [Pw_forum] unit-printing error? Message-ID: <20090321063445.gilvjdkr0gowkkw4@webmail.sissa.it> there is no unit printing error. remember that the relationship between direct and reciprocal vectors is a(i)*b(j) = 2pi delta_ij which is what you obtain when you use the printed quantities including the declared units. best regards, stefano de Gironcoli Quoting Karoly Nemeth : > > Hi, > > I became aware of some unit printing errors in PWSCF (v.4.0.4). At least > it seems to be case. > In one of my calculations I got: > > crystal axes: (cart. coord. in units of a_0) > a(1) = ( 2.556193 0.000000 0.000000 ) > a(2) = ( 0.000000 2.556193 0.000000 ) > a(3) = ( 0.000000 0.000000 30.000000 ) > > reciprocal axes: (cart. coord. in units 2 pi/a_0) > b(1) = ( 0.391207 0.000000 0.000000 ) > b(2) = ( 0.000000 0.391207 0.000000 ) > b(3) = ( 0.000000 0.000000 0.033333 ) > > > Obviously, the reciprocal axes is printed in units of 1/a_0, and not in > "2 pi/a_0". A few lines below in the output, where k-points are listed > I see: > > number of k points= 260 gaussian broad. (Ry)= 0.0300 ngauss = > -1 > cart. coord. in units 2pi/a_0 > k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = > 0.0039063 > k( 2) = ( 0.0000000 0.0000000 0.0041667), wk = > 0.0078125 > > Comparing reciprocal lattice to the listed k-points, it turns out, that > k-point are also listed in units of 1/a_0, and not in "2pi/a_0". > > This seems to be a unit-printing error, as otherwise everything is > consistent. If I remember well, in older versions the unit used to be 1/a_0 . > Please let me know if I am right with the above. > Thanks: > > Karoly > > > *********************************************************************** > Karoly Nemeth, Ph.D. > Argonne National Laboratory > 9700 S. Cass Ave. Argonne, IL 60439. > Advanced Photon Source > Accelerator Physics and Operations Group > Building 401, Room B2200 > Tel. 630-252-5813 > Fax: 630-252-4732 > *********************************************************************** > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ ----- End forwarded message ----- ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From mailtoartee at gmail.com Sat Mar 21 07:02:34 2009 From: mailtoartee at gmail.com (artee sharma) Date: Sat, 21 Mar 2009 11:32:34 +0530 Subject: [Pw_forum] SCF correction compared to forces is too large, reduce conv_thr Message-ID: Dear all, I have one query. I am getting "*SCF correction compared to forces is too large, reduce conv_thr*" this kind of message in output file. What I am suppose to do now? Shall i stop the calculation in between and reduce the conv thr, or shall i let it run to completion?? thanks in advance regards artee -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090321/37c7d5b9/attachment.htm From akohlmey at cmm.chem.upenn.edu Sat Mar 21 15:59:36 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 21 Mar 2009 10:59:36 -0400 Subject: [Pw_forum] Compiling QE 4.0.4 In-Reply-To: <61b264610903201120v332e2b6at4cf08085c9c9865b@mail.gmail.com> References: <61b264610903201120v332e2b6at4cf08085c9c9865b@mail.gmail.com> Message-ID: <7b6913e90903210759h11920ae3s23415f0b02ed9fa1@mail.gmail.com> On Fri, Mar 20, 2009 at 2:20 PM, Amos Leffler wrote: > I am trying to compile QE 4.0.4 using openmpi-1.2.9. The > program did compile successfully using the internal compilers in > OpenSuse 10.2 in single mode. With openmpi-1.2.9 the configuration > step went OK and it recognized that openmpi was being used. > Using the command: > "make all" it encountered the error shown below: > > Entering directory `/home/amos/Desktop/espresso-4.0.4/Modules' > mpif90 -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW > -D__USE_INTERNAL_FFTW -D__MPI I../Modules -I../iotk/src -I../PW > -I../PH -c fft_parallel.f90 > In file fft_parallel.f90:282 > > send_cnt, send_displ, MPI_DOUBLE_COMPLEX, f(1), & > 1 > Error: Symbol 'mpi_double_complex' at (1) has no IMPLICIT type > In file fft_parallel.f90:234 > > CALL MPI_ALLTOALLV( f(1), send_cnt, send_displ, MPI_DOUBLE_COMPLEX, yf(1), > 1 > Error: Symbol 'mpi_double_complex' at (1) has no IMPLICIT type > make[1]: *** [fft_parallel.o] Error 1 > make[1]: Leaving directory `/home/amos/Desktop/espresso-4.0.4/Modules' > > I looked in the file and it states "IMPLICIT none" so that the > complaint appears to be correct. I checked the forum files but could > find no report of an error in the last five months. Is there an easy > fix? your mpi installation is messed up. have you tried compiling some simple fortran(!) mpi test programs. MPI_DOUBLE_COMPLEX is defined in the mpif.h header and thus it _is_ explicitly declared. it has nothing to do with Q-E. axel. > Hopefully someone has seen this before. > > Amos Leffler > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From mailtoartee at gmail.com Sat Mar 21 16:53:40 2009 From: mailtoartee at gmail.com (artee sharma) Date: Sat, 21 Mar 2009 21:23:40 +0530 Subject: [Pw_forum] SCF correction compared to forces is too large, reduce conv_thr In-Reply-To: <20090321071624.6xmxu0w34s04888w@webmail.sissa.it> References: <20090321071624.6xmxu0w34s04888w@webmail.sissa.it> Message-ID: Dear Stefano. thanks for reply. my conv_thr in input file is 1.0e-5? i have a large system, takes too much time to convarage, so kept it low. Shall i decrease it by further one order? latest output is showing: Total force = 0.023049 Total SCF correction = 0.002483 so i think my system has not converged yet, force is high. regards artee sharma Department of physics Bhavnagar University India On Sat, Mar 21, 2009 at 11:46 AM, Stefano de Gironcoli wrote: > I think it might be better to stop it. According to the message the forces > you are calculating may be not accurate and any further relaxation based on > them is not likely to improve your geometry. > > However, are you sure your system is not yet relaxed enough ? > What is your conv_thr and your force threshold ? > > stefano de Gironcoli - SISSA & DEMOCRITOS > > PS: don't forget to provide your affiliation > > > > > > Quoting artee sharma : > ** > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090321/3efd7b10/attachment.htm From pemryan at yahoo.cn Sun Mar 22 03:01:49 2009 From: pemryan at yahoo.cn (Yan) Date: Sun, 22 Mar 2009 10:01:49 +0800 Subject: [Pw_forum] =?iso-8859-15?q?SCF_correction_compared_to_forces_is_t?= =?iso-8859-15?q?oo_large=2C_reduce_=09conv=5Fthr?= In-Reply-To: References: <20090321071624.6xmxu0w34s04888w@webmail.sissa.it> Message-ID: <200903221001.52148.pemryan@yahoo.cn> On 2009/03/21 Saturday 23:53:40 artee sharma wrote: > Dear Stefano. > thanks for reply. my conv_thr in input file is 1.0e-5? i have a large 1e-8 or lower should be better for relaxation > system, takes too much time to convarage, so kept it low. Shall i decrease > it by further one order? > latest output is showing: > Total force = 0.023049 Total SCF correction = 0.002483 > so i think my system has not converged yet, force is high. I think so. Since your system is a large one, maybe your should optimize it via common MD before SCF calculation. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090322/470d9a70/attachment.htm From sunyang198498 at gmail.com Sun Mar 22 02:58:46 2009 From: sunyang198498 at gmail.com (=?GB2312?B?y+/R9A==?=) Date: Sat, 21 Mar 2009 20:58:46 -0500 Subject: [Pw_forum] Symmetry problem Message-ID: <98e7a0810903211858u226d3c8cl1ea344b748180725@mail.gmail.com> Dear pw users: Hi, this is Yang. I am bothered by such a problem, described by the following. I have a system with twelve atoms contained in a unit cell: ATOMIC_POSITIONS {angstrom} C 0.000000000 0.000000000 0.000000000 H 0.916999000 -0.568453000 0.000000000 H -0.916999000 -0.568453000 0.000000000 C 0.000000000 0.726399000 1.339974000 F 1.099429000 1.502392000 1.339974000 F -1.099429000 1.502392000 1.339974000 C 0.000000000 -0.075546600 2.636186000 H 0.916999000 -0.643999600 2.636186000 H -0.916999000 -0.643999600 2.636186000 C 0.000000000 0.726399000 3.933239800 F 1.099429000 1.502392000 3.933239800 F -1.099429000 1.502392000 3.933239800 and the crystal parameter I chose is the base-centered orthorhombic, ie, ibrav = 9, celldm(1) = 16.11 celldm(2) = 0.57451 celldm(3) = 0.604393 and I do a cell-variable relaxation. The following is the input file. &control calculation='vc-relax' restart_mode='from_scratch', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' prefix='PVDF' etot_conv_thr=1.0e-6 forc_conv_thr=1.0e-5 nstep=100 / &system ibrav = 9, celldm(1) = 16.22 celldm(2) = 0.57226 celldm(3) = 0.59674 nat = 12 ntyp = 3 nspin = 1 ecutwfc = 25.0, ecutrho = 500.0, occupations='smearing', degauss= 0.01 / &electrons conv_thr = 1.0e-8 mixing_beta = 0.7 / &ions / &cell cell_dynamics='damp-pr', / ATOMIC_SPECIES C 12.00 C.pbe-rrkjus.UPF H 1.00 H.pbe-rrkjus.UPF F 19.00 F.pbe-n-van.UPF ATOMIC_POSITIONS {angstrom} C 0.000000000 0.000000000 0.000000000 H 0.916999000 -0.568453000 0.000000000 H -0.916999000 -0.568453000 0.000000000 C 0.000000000 0.726399000 1.339974000 F 1.099429000 1.502392000 1.339974000 F -1.099429000 1.502392000 1.339974000 C 0.000000000 -0.075546600 2.636186000 H 0.916999000 -0.643999600 2.636186000 H -0.916999000 -0.643999600 2.636186000 C 0.000000000 0.726399000 3.933239800 F 1.099429000 1.502392000 3.933239800 F -1.099429000 1.502392000 3.933239800 K_POINTS (automatic) 4 8 8 0 0 0 However, the relaxation result has different symmetry as far as I am concerned. The cell parameter turns out to be the following: CELL_PARAMETERS (alat) 0.496579626 0.283698921 -0.001038829 -0.496579626 0.283698921 -0.001038829 0.000000000 -0.002166536 0.600253523 ATOMIC_POSITIONS (angstrom) C 0.000000000 -0.119443593 0.057434432 H 0.886464714 -0.767241790 0.054456517 H -0.886464714 -0.767241790 0.054456517 C 0.000000000 0.694343614 1.348971837 F 1.113214016 1.554765512 1.352609452 F -1.113214016 1.554765512 1.352609452 C 0.000000000 -0.129168214 2.634282269 H 0.885856007 -0.777144668 2.632570428 H -0.885856007 -0.777144668 2.632570428 C 0.000000000 0.686823893 3.924824395 F 1.113154270 1.547226828 3.928069069 F -1.113154270 1.547226828 3.928069069 By looking at the CELL_PARAMETER, we see that the crystal loose the symmetry of orthorhombic but simply triclinic. Can we do VC-relax by keeping the previous symmetry? Thank you for any suggestion. :) Yang Sun From pemryan at yahoo.cn Sun Mar 22 03:28:36 2009 From: pemryan at yahoo.cn (Yan) Date: Sun, 22 Mar 2009 10:28:36 +0800 Subject: [Pw_forum] Symmetry problem In-Reply-To: <98e7a0810903211858u226d3c8cl1ea344b748180725@mail.gmail.com> References: <98e7a0810903211858u226d3c8cl1ea344b748180725@mail.gmail.com> Message-ID: <200903221028.37999.pemryan@yahoo.cn> On 2009/03/22 Sunday 09:58:46 ?? wrote: > By looking at the CELL_PARAMETER, we see that the crystal loose the > symmetry of orthorhombic but simply triclinic. > > Can we do VC-relax by keeping the previous symmetry? maybe the variable 'cell_dofree' in namelist 'CELL' is something your are looking for. However, this option is not a robust enough, and it is not recommend to use it. you can try to restart with the cell parameters you got and ignore the divergence of symmetry. >CELL_PARAMETERS (alat) > 0.496579626 0.283698921 -0.001038829 > -0.496579626 0.283698921 -0.001038829 > 0.000000000 -0.002166536 0.600253523 CELL_PARAMETERS (alat) 0.496579626 0.283698921 [0] -0.496579626 0.283698921 [0] 0.000000000 [0] 0.600253523 this is only a suggestion, I didn't try it out, so may be incorrect. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090322/79875e47/attachment.htm From degironc at sissa.it Sun Mar 22 04:02:23 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 22 Mar 2009 04:02:23 +0100 Subject: [Pw_forum] SCF correction compared to forces is too large, reduce conv_thr In-Reply-To: References: <20090321071624.6xmxu0w34s04888w@webmail.sissa.it> Message-ID: <20090322040223.za6n31whcscs4cg4@webmail.sissa.it> dear artee sharma, conv_thr=1.0e-5 is a rather large value, acceptable if you just want the energy but not if you want forces. 1.0e-6 is the default and for relaxations one rather tends to reduce it... Convergence for large systems (especially inhomogeneous metallic ones) may be slow. mixing_mode='local-TF' usually helps in these cases. are you using it ? Even when the first scf convergence is painfully slow the subsequent ones should be better as potential and wfcs are extapolated from previous steps. check that you are indeed using these extrapolations (should however be the default for relaxation, so probably you do). Sometime when a system does not want to converge it's trying to tell you something ... Is it a magnetic or metallic system ? are you using smearing ? are you sure the number of bands and your k-point sampling is accurate enough ? hope this helps, stefano Stefano de Gironcoli - SISSA and DEMOCRITOS Quoting artee sharma : > Dear Stefano. > thanks for reply. my conv_thr in input file is 1.0e-5? i have a large > system, takes too much time to convarage, so kept it low. Shall i decrease > it by further one order? > latest output is showing: > Total force = 0.023049 Total SCF correction = 0.002483 > so i think my system has not converged yet, force is high. > regards > artee sharma > Department of physics > Bhavnagar University > India > > > > > On Sat, Mar 21, 2009 at 11:46 AM, Stefano de Gironcoli > wrote: > >> I think it might be better to stop it. According to the message the forces >> you are calculating may be not accurate and any further relaxation based on >> them is not likely to improve your geometry. >> >> However, are you sure your system is not yet relaxed enough ? >> What is your conv_thr and your force threshold ? >> >> stefano de Gironcoli - SISSA & DEMOCRITOS >> >> PS: don't forget to provide your affiliation >> >> >> >> >> >> Quoting artee sharma : >> ** >> >> >> ---------------------------------------------------------------- >> SISSA Webmail https://webmail.sissa.it/ >> Powered by Horde http://www.horde.org/ >> >> >> > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From degironc at sissa.it Sun Mar 22 04:26:22 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 22 Mar 2009 04:26:22 +0100 Subject: [Pw_forum] Symmetry problem In-Reply-To: <98e7a0810903211858u226d3c8cl1ea344b748180725@mail.gmail.com> References: <98e7a0810903211858u226d3c8cl1ea344b748180725@mail.gmail.com> Message-ID: <20090322042622.euypukdi0ck84k88@webmail.sissa.it> Dear Yang Sun, the variable cell relaxation keeps the symmetry that it finds at the beginning of the run and stops with an error message if (for numerical reasons) some symmetry is lost... so your system WAS NOT base-centered orthorhombic in the first place. The fact that you choose a certain Bravais lattoce does not mean that the crystal has the corresponding symmetry. How many symmetry operations are found in your starting configuration ? Is this number what you expected ? if not, look at your crystal structure with xcrysden or other structure visualizer and see if there is some evident problem. check the number of digits you are providing in your crystal structure... symmetry is checked using a certain (small) tollerance. Are you sure you have been using the same conversion factor from Angstrom (used in the coordinates) and atomic units (used for celldm) ? in your case it is probably more convenient defining the structure using the "a,b,c,cosab, cosbc,cosac" set, where the lengths are given in Angstrom, or use crystal coordinates for the atomic positions regards, stefano Stefano de Girocoli - SISSA and DEMOCRITOS Quoting ?? : > Dear pw users: > > Hi, this is Yang. I am bothered by such a problem, described by the > following. > > I have a system with twelve atoms contained in a unit cell: > > ATOMIC_POSITIONS {angstrom} > C 0.000000000 0.000000000 0.000000000 > H 0.916999000 -0.568453000 0.000000000 > H -0.916999000 -0.568453000 0.000000000 > C 0.000000000 0.726399000 1.339974000 > F 1.099429000 1.502392000 1.339974000 > F -1.099429000 1.502392000 1.339974000 > C 0.000000000 -0.075546600 2.636186000 > H 0.916999000 -0.643999600 2.636186000 > H -0.916999000 -0.643999600 2.636186000 > C 0.000000000 0.726399000 3.933239800 > F 1.099429000 1.502392000 3.933239800 > F -1.099429000 1.502392000 3.933239800 > > and the crystal parameter I chose is the base-centered orthorhombic, ie, > > ibrav = 9, > celldm(1) = 16.11 > celldm(2) = 0.57451 > celldm(3) = 0.604393 > > and I do a cell-variable relaxation. The following is the input file. > > &control > calculation='vc-relax' > restart_mode='from_scratch', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > prefix='PVDF' > etot_conv_thr=1.0e-6 > forc_conv_thr=1.0e-5 > nstep=100 > > / > &system > ibrav = 9, > celldm(1) = 16.22 > celldm(2) = 0.57226 > celldm(3) = 0.59674 > > > nat = 12 > ntyp = 3 > nspin = 1 > ecutwfc = 25.0, > ecutrho = 500.0, > occupations='smearing', > degauss= 0.01 > / > &electrons > conv_thr = 1.0e-8 > mixing_beta = 0.7 > / > &ions > / > &cell > cell_dynamics='damp-pr', > / > ATOMIC_SPECIES > C 12.00 C.pbe-rrkjus.UPF > H 1.00 H.pbe-rrkjus.UPF > F 19.00 F.pbe-n-van.UPF > > ATOMIC_POSITIONS {angstrom} > C 0.000000000 0.000000000 0.000000000 > H 0.916999000 -0.568453000 0.000000000 > H -0.916999000 -0.568453000 0.000000000 > C 0.000000000 0.726399000 1.339974000 > F 1.099429000 1.502392000 1.339974000 > F -1.099429000 1.502392000 1.339974000 > C 0.000000000 -0.075546600 2.636186000 > H 0.916999000 -0.643999600 2.636186000 > H -0.916999000 -0.643999600 2.636186000 > C 0.000000000 0.726399000 3.933239800 > F 1.099429000 1.502392000 3.933239800 > F -1.099429000 1.502392000 3.933239800 > > K_POINTS (automatic) > 4 8 8 0 0 0 > > > However, the relaxation result has different symmetry as far as I am > concerned. > The cell parameter turns out to be the following: > > CELL_PARAMETERS (alat) > 0.496579626 0.283698921 -0.001038829 > -0.496579626 0.283698921 -0.001038829 > 0.000000000 -0.002166536 0.600253523 > > ATOMIC_POSITIONS (angstrom) > C 0.000000000 -0.119443593 0.057434432 > H 0.886464714 -0.767241790 0.054456517 > H -0.886464714 -0.767241790 0.054456517 > C 0.000000000 0.694343614 1.348971837 > F 1.113214016 1.554765512 1.352609452 > F -1.113214016 1.554765512 1.352609452 > C 0.000000000 -0.129168214 2.634282269 > H 0.885856007 -0.777144668 2.632570428 > H -0.885856007 -0.777144668 2.632570428 > C 0.000000000 0.686823893 3.924824395 > F 1.113154270 1.547226828 3.928069069 > F -1.113154270 1.547226828 3.928069069 > > By looking at the CELL_PARAMETER, we see that the crystal loose the > symmetry of > orthorhombic but simply triclinic. > > Can we do VC-relax by keeping the previous symmetry? > > Thank you for any suggestion. :) > > > > Yang Sun > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From sks.jnc at gmail.com Sun Mar 22 07:23:29 2009 From: sks.jnc at gmail.com (S. K. S.) Date: Sun, 22 Mar 2009 11:53:29 +0530 Subject: [Pw_forum] DMFT+LDA Message-ID: Dear all, Recently, in abinit, I have seen some on-going developments on DMFT+LDA. I'm a little curious. Has anyone already started or is going to start the similar kind of developmental work in PWSCF???? regards, S. K. Saha JNCASR Bangalore From dmitry at korotin.name Mon Mar 23 04:04:00 2009 From: dmitry at korotin.name (Dmitry Korotin) Date: Mon, 23 Mar 2009 08:04:00 +0500 Subject: [Pw_forum] DMFT+LDA In-Reply-To: References: Message-ID: <166cd7c60903222004j791a20bbk92b86a0af7a92fff@mail.gmail.com> Dear S.K. Saha, LDA+DMFT project for QE already started and the first working code is released. It strongly depends on QE source (uses QE make.sys files), contains only one example (and minimal documentation). But it works. Official LDA+DMFT for QE project site is http://qe-forge.org/projects/dmft/. You can download files there. 2009/3/22 S. K. S. : > Dear all, > Recently, in abinit, I have seen > some on-going developments ?on DMFT+LDA. > I'm a little curious. Has ?anyone already started ?or is > going to start ?the similar kind of developmental work in PWSCF???? > regards, > S. K. Saha > JNCASR > Bangalore > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best regards, Dmitry Korotin Ph. D. Student, Institute of Metal Physics S. Kovalevskaya, 18 620041 Ekaterinburg GSP-170 Russia From toashagupta at gmail.com Mon Mar 23 04:52:45 2009 From: toashagupta at gmail.com (Asha gupta) Date: Mon, 23 Mar 2009 09:22:45 +0530 Subject: [Pw_forum] SCF correction compared to forces is too large, reduce conv_thr In-Reply-To: <20090322040223.za6n31whcscs4cg4@webmail.sissa.it> References: <20090321071624.6xmxu0w34s04888w@webmail.sissa.it> <20090322040223.za6n31whcscs4cg4@webmail.sissa.it> Message-ID: Dear Stefano, i am using the following: &system: ibrav=0, nat= 98, ntyp=4, ecutwfc = 30.0,ecutrho = 180.0,occupations='smearing', smearing='methfessel-paxton', degauss=0.003,nbnd=500, &electrons: conv_thr = 1.0e-5,mixing_beta = 0.1, K_points sampling: 4 4 4 0 0 0, the system is insulator and non-magnetic for sure. the number of bands are little higher than what is actually required for an insulator. Tha same k points sampling for smaller similar system gave results which tallies well reported data. Shall i stop the calculation or let it run to completion? after compleion, then i can take the new refined data as my input and reduced conv_thr and re-run the calculation again. regards artee department of physics Bhavnagar university india On 3/22/09, Stefano de Gironcoli wrote: > > dear artee sharma, > > conv_thr=1.0e-5 is a rather large value, acceptable if you just want > the energy but not if you want forces. 1.0e-6 is the default and for > relaxations one rather tends to reduce it... > > Convergence for large systems (especially inhomogeneous metallic ones) > may be slow. mixing_mode='local-TF' usually helps in these cases. are > you using it ? > > Even when the first scf convergence is painfully slow the subsequent > ones should be better as potential and wfcs are extapolated from > previous steps. check that you are indeed using these extrapolations > (should however be the default for relaxation, so probably you do). > > Sometime when a system does not want to converge it's trying to tell > you something ... Is it a magnetic or metallic system ? are you using > smearing ? are you sure the number of bands and your k-point sampling > is accurate enough ? > > hope this helps, > stefano > > Stefano de Gironcoli - SISSA and DEMOCRITOS > > > Quoting artee sharma : > > > Dear Stefano. > > thanks for reply. my conv_thr in input file is 1.0e-5? i have a large > > > system, takes too much time to convarage, so kept it low. Shall i > decrease > > it by further one order? > > latest output is showing: > > Total force = 0.023049 Total SCF correction = 0.002483 > > so i think my system has not converged yet, force is high. > > > regards > > artee sharma > > Department of physics > > Bhavnagar University > > India > > > > > > > > > > On Sat, Mar 21, 2009 at 11:46 AM, Stefano de Gironcoli > > wrote: > > > >> I think it might be better to stop it. According to the message the > forces > >> you are calculating may be not accurate and any further relaxation based > on > >> them is not likely to improve your geometry. > >> > >> However, are you sure your system is not yet relaxed enough ? > >> What is your conv_thr and your force threshold ? > >> > >> stefano de Gironcoli - SISSA & DEMOCRITOS > >> > >> PS: don't forget to provide your affiliation > >> > >> > >> > >> > >> > >> Quoting artee sharma : > >> ** > >> > >> > >> ---------------------------------------------------------------- > >> SISSA Webmail https://webmail.sissa.it/ > >> Powered by Horde http://www.horde.org/ > >> > >> > >> > > > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090323/456c6a00/attachment.htm From degironc at sissa.it Mon Mar 23 06:40:49 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 23 Mar 2009 06:40:49 +0100 Subject: [Pw_forum] SCF correction compared to forces is too large, reduce conv_thr In-Reply-To: References: <20090321071624.6xmxu0w34s04888w@webmail.sissa.it> <20090322040223.za6n31whcscs4cg4@webmail.sissa.it> Message-ID: <20090323064049.m8pzcnovkoso4sgo@webmail.sissa.it> ear Asha gupta, if your are sure that the system is an non-magnetic insulator then there is no point in using smearing and include more bands. Your smearing_width looks very small to me, especially with methfessel-paxton which, being non positive definite, could give problems of negative occupations if the k-point sampling is not good enough. If you want to keep the smearing use marzari-vanderbilt ... or even plain gaussian smearing ... for an insulator it should not matter anyway. As I said you may want to try mixing_mode='local-TF'. stefano Quoting Asha gupta : > Dear Stefano, > i am using the following: > &system: ibrav=0, nat= 98, ntyp=4, ecutwfc = 30.0,ecutrho = > 180.0,occupations='smearing', smearing='methfessel-paxton', > degauss=0.003,nbnd=500, > &electrons: conv_thr = 1.0e-5,mixing_beta = 0.1, > K_points sampling: 4 4 4 0 0 0, > the system is insulator and non-magnetic for sure. the number of bands are > little higher than what is actually required for an insulator. Tha same k > points sampling for smaller similar system gave results which tallies well > reported data. > Shall i stop the calculation or let it run to completion? after compleion, > then i can take the new refined data as my input and reduced conv_thr and > re-run the calculation again. > regards > artee > department of physics > Bhavnagar university > india > > On 3/22/09, Stefano de Gironcoli wrote: >> >> dear artee sharma, >> >> conv_thr=1.0e-5 is a rather large value, acceptable if you just want >> the energy but not if you want forces. 1.0e-6 is the default and for >> relaxations one rather tends to reduce it... >> >> Convergence for large systems (especially inhomogeneous metallic ones) >> may be slow. mixing_mode='local-TF' usually helps in these cases. are >> you using it ? >> >> Even when the first scf convergence is painfully slow the subsequent >> ones should be better as potential and wfcs are extapolated from >> previous steps. check that you are indeed using these extrapolations >> (should however be the default for relaxation, so probably you do). >> >> Sometime when a system does not want to converge it's trying to tell >> you something ... Is it a magnetic or metallic system ? are you using >> smearing ? are you sure the number of bands and your k-point sampling >> is accurate enough ? >> >> hope this helps, >> stefano >> >> Stefano de Gironcoli - SISSA and DEMOCRITOS >> >> >> Quoting artee sharma : >> >> > Dear Stefano. >> > thanks for reply. my conv_thr in input file is 1.0e-5? i have a large >> >> > system, takes too much time to convarage, so kept it low. Shall i >> decrease >> > it by further one order? >> > latest output is showing: >> > Total force = 0.023049 Total SCF correction = 0.002483 >> > so i think my system has not converged yet, force is high. >> >> > regards >> > artee sharma >> > Department of physics >> > Bhavnagar University >> > India >> > >> > >> > >> > >> > On Sat, Mar 21, 2009 at 11:46 AM, Stefano de Gironcoli >> > wrote: >> > >> >> I think it might be better to stop it. According to the message the >> forces >> >> you are calculating may be not accurate and any further relaxation based >> on >> >> them is not likely to improve your geometry. >> >> >> >> However, are you sure your system is not yet relaxed enough ? >> >> What is your conv_thr and your force threshold ? >> >> >> >> stefano de Gironcoli - SISSA & DEMOCRITOS >> >> >> >> PS: don't forget to provide your affiliation >> >> >> >> >> >> >> >> >> >> >> >> Quoting artee sharma : >> >> ** >> >> >> >> >> >> ---------------------------------------------------------------- >> >> SISSA Webmail https://webmail.sissa.it/ >> >> Powered by Horde http://www.horde.org/ >> >> >> >> >> >> >> > >> >> >> >> ---------------------------------------------------------------- >> SISSA Webmail https://webmail.sissa.it/ >> Powered by Horde http://www.horde.org/ >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From helen at fh.huji.ac.il Mon Mar 23 12:36:50 2009 From: helen at fh.huji.ac.il (Helen) Date: Mon, 23 Mar 2009 13:36:50 +0200 Subject: [Pw_forum] HSE pseudopotentials + BNL functional References: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com> Message-ID: <006301c9abab$a835b860$cd604084@fh.huji.ac.il> Dear all, I've been working on a functional somewhat similar to the HSE functional, the BNL functional (R. Baer and D. Neuhauser, PRL 94,043002 (2005)) which also has a explicit-exchange component. I have implemented this functional into Quantum-Espresso and the full details can be seen in our paper currently submitted for publication and on the archives: arXive:0903.3830v1. Where should I post the Quantum-Espresso code implemented for the BNL functional? Dr Helen Eisenberg Post-doctoral researcher Fritz Haber Research Center for Molecular Dynamics, The Hebrew University of Jerusalem ----- Original Message ----- From: shangy To: PWSCF Forum Sent: Saturday, March 14, 2009 7:49 AM Subject: [Pw_forum] HSE pseudopotentials Dear all: Does anyone has the Si pseudopotentials generated by the screened-exchange hybrid functional of Heyd, Scuseria, and Ernerhof [HSE, J. Chem. Phys. 118, 8207 (2003)]? Can it work well within QE? If anyone has one, would you share it with me? I'm very very thirsty for it. Thanks in advance. Best regards. shangy Graduate unversity of Chinese academy of sciences ------------------------------------------------------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090323/273d4c05/attachment.htm From degironc at sissa.it Mon Mar 23 16:27:42 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 23 Mar 2009 16:27:42 +0100 Subject: [Pw_forum] HSE pseudopotentials + BNL functional In-Reply-To: <006301c9abab$a835b860$cd604084@fh.huji.ac.il> References: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com> <006301c9abab$a835b860$cd604084@fh.huji.ac.il> Message-ID: <20090323162742.0h0ndw9q3kkwsw8c@webmail.sissa.it> Dear Dr. Eisenberg, If you are willing to share your developments it would be very much appreciated. Are your modifications localized in a few files (like exx.f90 and functionals.f90) ? is the functional implemented in the latest version of Quantum-Espresso ? If the annswers are yes the simplest option to contribute your code would be to send me and/or to Layla Martin-Samos (marsamos at democritos.it) the relevant routines so that we can include them in the cvs repository and then revert to you to check that everything is fine. An input (and an output) using the new feature similar to those in the EXXexample directory could also be useful to keep the feature working when the code is updated. best regards and thank you for your contribution, stefano - Stefano de Gironcoli - SISSA and DEMOCRITOS Quoting Helen : > Dear all, > I've been working on a functional somewhat similar to the HSE > functional, the BNL functional (R. Baer and D. Neuhauser, PRL > 94,043002 (2005)) which also has a explicit-exchange component. I > have implemented this functional into Quantum-Espresso and the full > details can be seen in our paper currently submitted for publication > and on the archives: arXive:0903.3830v1. > Where should I post the Quantum-Espresso code implemented for the > BNL functional? > Dr Helen Eisenberg > Post-doctoral researcher > Fritz Haber Research Center for Molecular Dynamics, > The Hebrew University of Jerusalem > > ----- Original Message ----- > From: shangy > To: PWSCF Forum > Sent: Saturday, March 14, 2009 7:49 AM > Subject: [Pw_forum] HSE pseudopotentials > > > Dear all: > Does anyone has the Si pseudopotentials generated by the > screened-exchange hybrid functional of Heyd, Scuseria, and Ernerhof > [HSE, J. Chem. Phys. 118, 8207 (2003)]? Can it work well within QE? > If anyone has one, would you share it with me? I'm very very thirsty > for it. Thanks in advance. > Best regards. > > shangy > Graduate unversity of Chinese academy of sciences > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From yanxunwang2008 at gmail.com Mon Mar 23 16:53:23 2009 From: yanxunwang2008 at gmail.com (Xun-Wang Yan) Date: Mon, 23 Mar 2009 23:53:23 +0800 Subject: [Pw_forum] electrical polarization calculations for non-collinear magnetism Message-ID: Dear pwscf users, I want to calculate the electrical polarizaiton for CuCrO2 with non-collinear antiferromagnetic ground state.After a 'scf' calculation, I run 'nscf' calculation. the input file is following, ------------- &control calculation = 'nscf' prefix='120-AFM-12at-tricli', pseudo_dir ='/home/xwyan/Pseudo/' outdir='/home/xwyan/tmp-120-0/' lberry=.true. gdir=3 nppstr=8 / &system ibrav=14, celldm(1)=9.73748132, celldm(2)=1.155067564,celldm(3)=1.000000, celldm(4)=-0.144291712,celldm(5)=-0.500000,celldm(6)=0.288583423, nat=12, ntyp=5, ecutwfc=30, ecutrho=300, report=10, occupations='fixed',degauss=0.00, noncolin=.true. starting_magnetization(2)=0.5 angle1(2)=90.0 angle2(2)=0.0 starting_magnetization(3)=0.5 angle1(3)=90.0 angle2(3)=120.0 starting_magnetization(4)=0.5 angle1(4)=90.0 angle2(4)=-120.0 nbnd=87 / &electrons electron_maxstep=300 mixing_beta = 0.3 conv_thr = 1.0d-10 / &electrons electron_maxstep=300 mixing_beta = 0.3 conv_thr = 1.0d-10 / ATOMIC_SPECIES Cu 63.55 Cu.pz-d-rrkjus.UPF Cr1 52.00 Cr.pz-rrkjus-5-1.UPF Cr2 52.00 Cr.pz-rrkjus-5-1.UPF Cr3 52.00 Cr.pz-rrkjus-5-1.UPF O 16.00 O.pz-rrkjus.UPF ATOMIC_POSITIONS {angstrom} Cu 0.000000000 0.000000000 -0.000000127 Cu 2.576425576 0.000000000 1.487499959 Cu 0.000000000 0.000000000 2.975000091 Cr1 0.858807500 2.849329739 1.497499627 Cr2 3.435229613 2.849329739 0.009999479 Cr3 3.435229613 2.849329739 2.985001062 O 2.576426737 1.824279229 1.487500064 O 1.717608630 3.874380147 -0.000000400 O 4.294034914 3.874380249 1.487500064 O 5.152850596 1.824279331 -0.000000400 O 1.717611367 3.874380065 2.975000291 O 0.000003312 1.824279413 2.975000291 K_POINTS {automatic} 1 1 8 0 0 ----------------- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 3 from c_phase : error # 1 Polarization only for insulators and no empty bands %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I look over 'bp_c_phase.f90' , and find that electrical polarization calculation is applicable for nspin=1 and nspin=2. I want to know to how to modify the bp_c_phase.f90 to implement the electrical polarization calculation for non-collinear magnetism. Any comments are welcome , many thanks in advance. regards, Xun-wang Yan ======================================== Institute of Theoretical Physics, CAS Address: No.55, Zhong-Guan-Cun East Road Beijing, China Email: xwyan at itp.ac.cn yanxunwang2008 at gmail.com =================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090323/cb44b9c6/attachment.htm From pc229 at kent.ac.uk Mon Mar 23 20:07:24 2009 From: pc229 at kent.ac.uk (Pieremanuele Canepa) Date: Mon, 23 Mar 2009 19:07:24 +0000 Subject: [Pw_forum] I can't print my bands Message-ID: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> Dear all, I am attempting to figure out how to print out a bands graph of my AFM hematite. Then I prepared the file band.in as explained in /Doc/INPUT_Band and I attached it down here &INPUTPP prefix='band_BLYP', outdir='/home/pc229/backup/ Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', filband='band_BLYP.out', / if try to run it using bands.x I will get in my output file the following error: Program POST-PROC v.4.0.4 starts ... Today is 23Mar2009 at 18:56:50 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from bands : error # 1 The bands code with constrained magnetization has not been tested %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... So, what I am suppose to do ? How can I print my bands?? Thank you, Piero -- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom -------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090323/bf3307f4/attachment.htm From nemeth at anl.gov Mon Mar 23 22:56:03 2009 From: nemeth at anl.gov (Karoly Nemeth) Date: Mon, 23 Mar 2009 16:56:03 -0500 (CDT) Subject: [Pw_forum] unit-printing error? In-Reply-To: References: Message-ID: Hi Stefano, thanks, you are right, the units are correct as they are. Sorry for my misunderstanding! Karoly > Message: 9 > Date: Sat, 21 Mar 2009 06:34:45 +0100 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] unit-printing error? > To: pw_forum at pwscf.org > Message-ID: <20090321063445.gilvjdkr0gowkkw4 at webmail.sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > there is no unit printing error. > remember that the relationship between direct and reciprocal vectors is > a(i)*b(j) = 2pi delta_ij > which is what you obtain when you use the printed quantities including > the declared units. > best regards, > stefano de Gironcoli > >> *********************************************************************** >> Karoly Nemeth, Ph.D. >> Argonne National Laboratory >> 9700 S. Cass Ave. Argonne, IL 60439. >> Advanced Photon Source >> Accelerator Physics and Operations Group >> Building 401, Room B2200 >> Tel. 630-252-5813 >> Fax: 630-252-4732 >> *********************************************************************** From quantumdft at gmail.com Tue Mar 24 04:00:59 2009 From: quantumdft at gmail.com (vega lew) Date: Tue, 24 Mar 2009 11:00:59 +0800 Subject: [Pw_forum] questions about the peseudopotential for potassium titanate Message-ID: <412f6c680903232000w126c7d6ag6079d9c1a64c50d5@mail.gmail.com> Dear all I want the calculate the properties of potassium titanate. And I want to use the pw91 functionals for the whole caculation. But I find the peseudopotential for K is something different with the Ti and O. From the name of pp, we could see functionals for K is different from Ti and O. Do you think I could use K.pz-sp-van.UPFwith the O.pw91-van_ak.UPF and Ti.pw91-sp-van_ak.UPF to describe the potassium titanate. Actually I want to use pw91 functionals for the calculation. How could I deal with the K+? thank you for reading any hints will be deeply appreciated vega -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090324/1969b600/attachment-0001.htm From lanhaiping at gmail.com Tue Mar 24 04:23:59 2009 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 24 Mar 2009 11:23:59 +0800 Subject: [Pw_forum] questions about the peseudopotential for potassium titanate In-Reply-To: <412f6c680903232000w126c7d6ag6079d9c1a64c50d5@mail.gmail.com> References: <412f6c680903232000w126c7d6ag6079d9c1a64c50d5@mail.gmail.com> Message-ID: Hi, Donot you think it is reasonable to use different functionals for a system ? Only if you can give the reasons, i donot think it is a serious work. You can try to build a pw91 pseudopotential referring to that for pz situation,and do a series tests on it. And you can aslo have a look at Professor Vanderbilt's pseudopotential library for a luck. regards, On Tue, Mar 24, 2009 at 11:00 AM, vega lew wrote: > Dear all > > I want the calculate the properties of potassium titanate. And I want to > use the pw91 functionals for the whole caculation. But I find the > peseudopotential for K is something different with the Ti and O. From the > name of pp, we could see functionals for K is different from Ti and O. Do > you think I could use K.pz-sp-van.UPFwith the O.pw91-van_ak.UPF and Ti.pw91-sp-van_ak.UPF to describe the > potassium titanate. Actually I want to use pw91 functionals for the > calculation. How could I deal with the K+? > > thank you for reading > > any hints will be deeply appreciated > > vega > > > -- > > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ****************************************************************************************************************** > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090324/c0a3fa14/attachment.htm From degironc at sissa.it Tue Mar 24 05:05:10 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 24 Mar 2009 05:05:10 +0100 Subject: [Pw_forum] questions about the peseudopotential for potassium titanate In-Reply-To: <412f6c680903232000w126c7d6ag6079d9c1a64c50d5@mail.gmail.com> References: <412f6c680903232000w126c7d6ag6079d9c1a64c50d5@mail.gmail.com> Message-ID: <20090324050510.qygyix00zokc40o0@webmail.sissa.it> Dear Vega, THe pseudo K.pz-sp-van.UPF has been generated with the vanderbilt code. you can likely find the corresponding input in the Vanderbilt website. It should be easy to modify it by replacing the LDA PZ functional with pw91. don't forget to test the new pseudo in some simple system before trusting it. hope this helps, stefano - Stefano de Gironcoli -SISSA and DEMOCRITOS Quoting vega lew : > Dear all > > I want the calculate the properties of potassium titanate. And I want to use > the pw91 functionals for the whole caculation. But I find the > peseudopotential for K is something different with the Ti and O. From the > name of pp, we could see functionals for K is different from Ti and O. Do > you think I could use > K.pz-sp-van.UPFwith > the O.pw91-van_ak.UPF and Ti.pw91-sp-van_ak.UPF to describe the > potassium titanate. Actually I want to use pw91 functionals for the > calculation. How could I deal with the K+? > > thank you for reading > > any hints will be deeply appreciated > > vega > > > -- > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, > Jiangsu, China > ****************************************************************************************************************** > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From positronium at gmail.com Tue Mar 24 05:01:09 2009 From: positronium at gmail.com (Lex Kemper) Date: Tue, 24 Mar 2009 00:01:09 -0400 Subject: [Pw_forum] questions about the peseudopotential for potassium titanate In-Reply-To: References: <412f6c680903232000w126c7d6ag6079d9c1a64c50d5@mail.gmail.com> Message-ID: <49C85B05.5050309@phys.ufl.edu> On a related note, has anyone successfully constructed a PBE pseudopotential for K? I've tried for a while, but I am not having any success thus far. Cheers, Lex Kemper Department of Physics and QTP University of Florida lan haiping wrote: > Hi, > Donot you think it is reasonable to use different functionals for a > system ? Only if you can give the reasons, i donot think it is a > serious work. You can try to build a pw91 pseudopotential referring to > that for pz situation,and do a series tests on it. And you can aslo have > a look at Professor Vanderbilt's pseudopotential library for a luck. > > regards, > > On Tue, Mar 24, 2009 at 11:00 AM, vega lew > wrote: > > Dear all > > I want the calculate the properties of potassium titanate. And I > want to use the pw91 functionals for the whole caculation. But I > find the peseudopotential for K is something different with the Ti > and O. From the name of pp, we could see functionals for K is > different from Ti and O. Do you think I could use K.pz-sp-van.UPF > > with the O.pw91-van_ak.UPF and Ti.pw91-sp-van_ak.UPF to describe the > potassium titanate. Actually I want to use pw91 functionals for the > calculation. How could I deal with the K+? > > thank you for reading > > any hints will be deeply appreciated > > vega > > > -- > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ****************************************************************************************************************** > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com , hplan at pku.edu.cn > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From degironc at sissa.it Tue Mar 24 05:17:47 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 24 Mar 2009 05:17:47 +0100 Subject: [Pw_forum] questions about the peseudopotential for potassium titanate In-Reply-To: <49C85B05.5050309@phys.ufl.edu> References: <412f6c680903232000w126c7d6ag6079d9c1a64c50d5@mail.gmail.com> <49C85B05.5050309@phys.ufl.edu> Message-ID: <20090324051747.b5iegwfmassgkocw@webmail.sissa.it> Dear Lex, have you tried the same recipe I suggested to Vega Lew ? take the lda-pz input in the vanderbilt website and change the functional to pbe ? If this does not work for pbe it is probably not a good idea also for pw91 that should be similar... stefano - Stefano de Girocnoli - SISSA and DEMOCRITOS Quoting Lex Kemper : > On a related note, has anyone successfully constructed a PBE > pseudopotential for K? I've tried for a while, but I am not having any > success thus far. > > Cheers, > > Lex Kemper > Department of Physics and QTP > University of Florida > > lan haiping wrote: >> Hi, >> Donot you think it is reasonable to use different functionals for a >> system ? Only if you can give the reasons, i donot think it is a >> serious work. You can try to build a pw91 pseudopotential referring to >> that for pz situation,and do a series tests on it. And you can aslo have >> a look at Professor Vanderbilt's pseudopotential library for a luck. >> >> regards, >> >> On Tue, Mar 24, 2009 at 11:00 AM, vega lew > > wrote: >> >> Dear all >> >> I want the calculate the properties of potassium titanate. And I >> want to use the pw91 functionals for the whole caculation. But I >> find the peseudopotential for K is something different with the Ti >> and O. From the name of pp, we could see functionals for K is >> different from Ti and O. Do you think I could use K.pz-sp-van.UPF >> >> with the O.pw91-van_ak.UPF and Ti.pw91-sp-van_ak.UPF to describe the >> potassium titanate. Actually I want to use pw91 functionals for the >> calculation. How could I deal with the K+? >> >> thank you for reading >> >> any hints will be deeply appreciated >> >> vega >> >> >> -- >> >> ================================================================================== >> Vega Lew ( weijia liu) >> PH.D Candidate in Chemical Engineering >> State Key Laboratory of Materials-oriented Chemical Engineering >> College of Chemistry and Chemical Engineering >> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China >> >> ****************************************************************************************************************** >> Email: vegalew at gmail.com >> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, >> Nanjing, Jiangsu, China >> >> ****************************************************************************************************************** >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> -- >> Hai-Ping Lan >> Department of Electronics , >> Peking University , Bejing, 100871 >> lanhaiping at gmail.com , hplan at pku.edu.cn >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From sporevoyager at gmail.com Tue Mar 24 06:12:44 2009 From: sporevoyager at gmail.com (shangy) Date: Tue, 24 Mar 2009 13:12:44 +0800 Subject: [Pw_forum] HSE pseudopotentials + BNL functional In-Reply-To: <006301c9abab$a835b860$cd604084@fh.huji.ac.il> References: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com> <006301c9abab$a835b860$cd604084@fh.huji.ac.il> Message-ID: <94be399f0903232212r7012dfecu4e25abe9ef985c6f@mail.gmail.com> Dear Eisenberg: I'm very exciting for your BNL information. Would you like to share your Q-E code implemented with BNL funciontal with me and send it to my box sporevoyager at gmail.com ? I may test the BNL calculation on formation energy of Si-defects and compare the results with HSE results in other work. Thanks in advance. Best regards! shangy Graduate unversity of Chinese academy of sciences 2009/3/23 Helen > Dear all, > I've been working on a functional somewhat similar to the HSE functional, > the BNL functional (R. Baer and D. Neuhauser, PRL 94,043002 (2005)) which > also has a explicit-exchange component. I have implemented this functional > into Quantum-Espresso and the full details can be seen in our paper > currently submitted for publication and on the archives: arXive:0903.3830v1. > > Where should I post the Quantum-Espresso code implemented for the BNL > functional? > Dr Helen Eisenberg > Post-doctoral researcher > Fritz Haber Research Center for Molecular Dynamics, > The Hebrew University of Jerusalem > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090324/80b651dc/attachment.htm From sclauzer at sissa.it Tue Mar 24 08:54:05 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 24 Mar 2009 08:54:05 +0100 Subject: [Pw_forum] I can't print my bands In-Reply-To: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> Message-ID: <49C8919D.8090004@sissa.it> Pieremanuele Canepa wrote: > Dear all, > I am attempting to figure out how to print out a bands graph of my AFM > hematite. > Then I prepared the file band.in as explained in > /Doc/INPUT_Band > and I attached it down here > &INPUTPP > prefix='band_BLYP', > outdir='/home/pc229/backup/ > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > filband='band_BLYP.out', > / > > if try to run it using bands.x I will get in my output file the > following error: > Program POST-PROC v.4.0.4 starts ... > Today is 23Mar2009 at 18:56:50 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from bands : error # 1 > The bands code with constrained magnetization has not been tested > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... You are trying to use bands.x with a feature that has not been tested (as the message says). If you trust what you are doing, you can simply comment the corresponding call to errore subroutine in bands.f90 and recompile. You may want to test it before doing serious calculations. If you simply need it to extract the eigenvalues from a scf/nscf pw.x calculations (using no_overlap=.TRUE.) I think it should be safe, but if you need it to reorder bands or do a symmetry analysis of bands (lsym=.TRUE.) you should be careful and double-check results. Cheers GS > > So, what I am suppose to do ? How can I print my bands?? > Thank you, Piero > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > -------------------------------------------------------- > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From pc229 at kent.ac.uk Tue Mar 24 11:59:38 2009 From: pc229 at kent.ac.uk (Pieremanuele Canepa) Date: Tue, 24 Mar 2009 10:59:38 +0000 Subject: [Pw_forum] I can't print my bands In-Reply-To: <49C8919D.8090004@sissa.it> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <49C8919D.8090004@sissa.it> Message-ID: <8b443ba10903240359k70456d3at4d843238f7b9ab12@mail.gmail.com> I tried to do as you suggested me (removing the call to the subroutine and recompiling), what I get if I try to run it is: Program POST-PROC v.4.0.4 starts ... Today is 24Mar2009 at 10:55:52 It seems that nothing works... Do you have any suggestion? Cheers, Piero On Tue, Mar 24, 2009 at 7:54 AM, Gabriele Sclauzero wrote: > > > Pieremanuele Canepa wrote: > > Dear all, > > I am attempting to figure out how to print out a bands graph of my AFM > > hematite. > > Then I prepared the file band.in as explained in > > /Doc/INPUT_Band > > and I attached it down here > > &INPUTPP > > prefix='band_BLYP', > > outdir='/home/pc229/backup/ > > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > > filband='band_BLYP.out', > > / > > > > if try to run it using bands.x I will get in my output file the > > following error: > > Program POST-PROC v.4.0.4 starts ... > > Today is 23Mar2009 at 18:56:50 > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from bands : error # 1 > > The bands code with constrained magnetization has not been tested > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > You are trying to use bands.x with a feature that has not been tested (as > the message > says). If you trust what you are doing, you can simply comment the > corresponding call to > errore subroutine in bands.f90 and recompile. You may want to test it > before doing serious > calculations. > > If you simply need it to extract the eigenvalues from a scf/nscf pw.x > calculations (using > no_overlap=.TRUE.) I think it should be safe, but if you need it to reorder > bands or do a > symmetry analysis of bands (lsym=.TRUE.) you should be careful and > double-check results. > > Cheers > > GS > > > > > > > So, what I am suppose to do ? How can I print my bands?? > > Thank you, Piero > > > > -- > > Pieremanuele Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > -------------------------------------------------------- > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090324/487ffb0e/attachment.htm From sclauzer at sissa.it Tue Mar 24 12:17:20 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 24 Mar 2009 12:17:20 +0100 Subject: [Pw_forum] I can't print my bands In-Reply-To: <8b443ba10903240359k70456d3at4d843238f7b9ab12@mail.gmail.com> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <49C8919D.8090004@sissa.it> <8b443ba10903240359k70456d3at4d843238f7b9ab12@mail.gmail.com> Message-ID: <49C8C140.1030701@sissa.it> Pieremanuele Canepa wrote: > I tried to do as you suggested me (removing the call to the subroutine > and recompiling), what I get if I try to run it is: > Program POST-PROC v.4.0.4 starts ... > Today is 24Mar2009 at 10:55:52 > It seems that nothing works... Do you have any suggestion? With so little information, none. You should try to explain which kind of system you're studying and post a sample for the pw.x input file. First you can try to understand at which point the program hangs, for instance by adding some write statements in the bands.f90 subroutines (or use a debugger if you are familiar with it). GS > Cheers, Piero > > On Tue, Mar 24, 2009 at 7:54 AM, Gabriele Sclauzero > wrote: > > > > Pieremanuele Canepa wrote: > > Dear all, > > I am attempting to figure out how to print out a bands graph of > my AFM > > hematite. > > Then I prepared the file band.in > as explained in > > /Doc/INPUT_Band > > and I attached it down here > > &INPUTPP > > prefix='band_BLYP', > > outdir='/home/pc229/backup/ > > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > > filband='band_BLYP.out', > > / > > > > if try to run it using bands.x I will get in my output file the > > following error: > > Program POST-PROC v.4.0.4 starts ... > > Today is 23Mar2009 at 18:56:50 > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from bands : error # 1 > > The bands code with constrained magnetization has not been > tested > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > You are trying to use bands.x with a feature that has not been > tested (as the message > says). If you trust what you are doing, you can simply comment the > corresponding call to > errore subroutine in bands.f90 and recompile. You may want to test > it before doing serious > calculations. > > If you simply need it to extract the eigenvalues from a scf/nscf > pw.x calculations (using > no_overlap=.TRUE.) I think it should be safe, but if you need it to > reorder bands or do a > symmetry analysis of bands (lsym=.TRUE.) you should be careful and > double-check results. > > Cheers > > GS > > > > > > > So, what I am suppose to do ? How can I print my bands?? > > Thank you, Piero > > > > -- > > Pieremanuele Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > -------------------------------------------------------- > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it > | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > ----------------------------------------------------------- > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From quantumdft at gmail.com Tue Mar 24 13:03:50 2009 From: quantumdft at gmail.com (vega lew) Date: Tue, 24 Mar 2009 20:03:50 +0800 Subject: [Pw_forum] questions about the peseudopotential for potassium titanate In-Reply-To: <20090324051747.b5iegwfmassgkocw@webmail.sissa.it> References: <412f6c680903232000w126c7d6ag6079d9c1a64c50d5@mail.gmail.com> <49C85B05.5050309@phys.ufl.edu> <20090324051747.b5iegwfmassgkocw@webmail.sissa.it> Message-ID: <412f6c680903240503k49233335k2846a368efdc8b53@mail.gmail.com> Dear all, Thank you for all the help. I'll try the recipe. vega On Tue, Mar 24, 2009 at 12:17 PM, Stefano de Gironcoli wrote: > Dear Lex, > > have you tried the same recipe I suggested to Vega Lew ? > take the lda-pz input in the vanderbilt website and change the > functional to pbe ? > If this does not work for pbe it is probably not a good idea also for > pw91 > that should be similar... > > stefano > - > Stefano de Girocnoli - SISSA and DEMOCRITOS > > > Quoting Lex Kemper : > > > On a related note, has anyone successfully constructed a PBE > > pseudopotential for K? I've tried for a while, but I am not having any > > success thus far. > > > > Cheers, > > > > Lex Kemper > > Department of Physics and QTP > > University of Florida > > > > lan haiping wrote: > >> Hi, > >> Donot you think it is reasonable to use different functionals for a > >> system ? Only if you can give the reasons, i donot think it is a > >> serious work. You can try to build a pw91 pseudopotential referring to > >> that for pz situation,and do a series tests on it. And you can aslo have > >> a look at Professor Vanderbilt's pseudopotential library for a luck. > >> > >> regards, > >> > >> On Tue, Mar 24, 2009 at 11:00 AM, vega lew >> > wrote: > >> > >> Dear all > >> > >> I want the calculate the properties of potassium titanate. And I > >> want to use the pw91 functionals for the whole caculation. But I > >> find the peseudopotential for K is something different with the Ti > >> and O. From the name of pp, we could see functionals for K is > >> different from Ti and O. Do you think I could use K.pz-sp-van.UPF > >> > >> with the O.pw91-van_ak.UPF and Ti.pw91-sp-van_ak.UPF to describe the > >> potassium titanate. Actually I want to use pw91 functionals for the > >> calculation. How could I deal with the K+? > >> > >> thank you for reading > >> > >> any hints will be deeply appreciated > >> > >> vega > >> > >> > >> -- > >> > >> > ================================================================================== > >> Vega Lew ( weijia liu) > >> PH.D Candidate in Chemical Engineering > >> State Key Laboratory of Materials-oriented Chemical Engineering > >> College of Chemistry and Chemical Engineering > >> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > >> > >> > ****************************************************************************************************************** > >> Email: vegalew at gmail.com > >> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > >> Nanjing, Jiangsu, China > >> > >> > ****************************************************************************************************************** > >> > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > >> > >> > >> > >> -- > >> Hai-Ping Lan > >> Department of Electronics , > >> Peking University , Bejing, 100871 > >> lanhaiping at gmail.com , hplan at pku.edu.cn > >> > >> > >> > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090324/73a26572/attachment-0001.htm From pc229 at kent.ac.uk Tue Mar 24 13:46:18 2009 From: pc229 at kent.ac.uk (Pieremanuele Canepa) Date: Tue, 24 Mar 2009 12:46:18 +0000 Subject: [Pw_forum] I can't print my bands In-Reply-To: <49C8C140.1030701@sissa.it> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <49C8919D.8090004@sissa.it> <8b443ba10903240359k70456d3at4d843238f7b9ab12@mail.gmail.com> <49C8C140.1030701@sissa.it> Message-ID: <8b443ba10903240546m48f7d89s96c4af9361f6905f@mail.gmail.com> ok, attached down here you would find my input used for n scf band calculation &CONTROL title = 'band_BLYP' , calculation = 'nscf' , restart_mode = 'from_scratch' , outdir = '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/' , pseudo_dir = '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/pseudo/' , prefix = 'band_BLYP' , / &SYSTEM ibrav = 5, celldm(1) = 10.442958667, celldm(4) = 0.578106099, nat = 10, ntyp = 3, ecutwfc = 50 , nosym = .true. , nbnd = 70, nelec = 100, occupations = 'fixed' , nspin = 2 , starting_magnetization(1) = 1., starting_magnetization(2) = -1., starting_magnetization(3) = 0., tot_magnetization = 0 , / &ELECTRONS conv_thr = 1.0d-9 , mixing_beta = 0.3D0 , / ATOMIC_SPECIES Fe 55.62000 Fe.blyp-sp-van_ak.UPF Fe1 55.62000 Fe.blyp-sp-van_ak.UPF O 15.99000 O.blyp-van_ak.UPF ATOMIC_POSITIONS crystal Fe 0.143406978 0.143407026 0.143407451 Fe1 0.356592136 0.356592626 0.356592564 Fe1 0.643407993 0.643407453 0.643407513 Fe 0.856592415 0.856592381 0.856591956 O 0.559962709 0.940037353 0.250000243 O 0.250000058 0.559962717 0.940037453 O 0.940036820 0.250000238 0.559963093 O 0.440038672 0.059961209 0.750000320 O 0.750000498 0.440038689 0.059961097 O 0.059961722 0.750000309 0.440038308 K_POINTS crystal 41 0.000 0.000 0.000 1 0.050 0.000 0.050 1 0.100 0.000 0.100 1 0.150 0.000 0.150 1 0.200 0.000 0.200 1 0.250 0.000 0.250 1 0.300 0.000 0.300 1 0.350 0.000 0.350 1 0.400 0.000 0.400 1 0.450 0.000 0.450 1 0.500 0.000 0.500 1 0.500 0.050 0.500 1 0.500 0.100 0.500 1 0.500 0.150 0.500 1 0.500 0.200 0.500 1 0.500 0.250 0.500 1 0.500 0.300 0.500 1 0.500 0.350 0.500 1 0.500 0.400 0.500 1 0.500 0.450 0.500 1 0.500 0.500 0.500 1 0.500 0.475 0.525 1 0.500 0.450 0.550 1 0.500 0.425 0.575 1 0.500 0.400 0.600 1 0.500 0.375 0.625 1 0.500 0.350 0.650 1 0.500 0.325 0.675 1 0.500 0.300 0.700 1 0.500 0.275 0.725 1 0.500 0.250 0.750 1 0.450 0.225 0.675 1 0.400 0.200 0.600 1 0.350 0.175 0.525 1 0.300 0.150 0.450 1 0.250 0.125 0.375 1 0.200 0.100 0.300 1 0.150 0.075 0.225 1 0.100 0.050 0.150 1 0.050 0.025 0.075 1 0.000 0.000 0.000 1 Thank you On Tue, Mar 24, 2009 at 11:17 AM, Gabriele Sclauzero wrote: > > Pieremanuele Canepa wrote: > > I tried to do as you suggested me (removing the call to the subroutine > > and recompiling), what I get if I try to run it is: > > Program POST-PROC v.4.0.4 starts ... > > Today is 24Mar2009 at 10:55:52 > > It seems that nothing works... Do you have any suggestion? > > With so little information, none. You should try to explain which kind of > system you're > studying and post a sample for the pw.x input file. > First you can try to understand at which point the program hangs, for > instance by adding > some write statements in the bands.f90 subroutines (or use a debugger if > you are familiar > with it). > > GS > > > > Cheers, Piero > > > > On Tue, Mar 24, 2009 at 7:54 AM, Gabriele Sclauzero > > wrote: > > > > > > > > Pieremanuele Canepa wrote: > > > Dear all, > > > I am attempting to figure out how to print out a bands graph of > > my AFM > > > hematite. > > > Then I prepared the file band.in > > as explained in > > > /Doc/INPUT_Band > > > and I attached it down here > > > &INPUTPP > > > prefix='band_BLYP', > > > outdir='/home/pc229/backup/ > > > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > > > filband='band_BLYP.out', > > > / > > > > > > if try to run it using bands.x I will get in my output file the > > > following error: > > > Program POST-PROC v.4.0.4 starts ... > > > Today is 23Mar2009 at 18:56:50 > > > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > from bands : error # 1 > > > The bands code with constrained magnetization has not been > > tested > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > stopping ... > > > > You are trying to use bands.x with a feature that has not been > > tested (as the message > > says). If you trust what you are doing, you can simply comment the > > corresponding call to > > errore subroutine in bands.f90 and recompile. You may want to test > > it before doing serious > > calculations. > > > > If you simply need it to extract the eigenvalues from a scf/nscf > > pw.x calculations (using > > no_overlap=.TRUE.) I think it should be safe, but if you need it to > > reorder bands or do a > > symmetry analysis of bands (lsym=.TRUE.) you should be careful and > > double-check results. > > > > Cheers > > > > GS > > > > > > > > > > > > So, what I am suppose to do ? How can I print my bands?? > > > Thank you, Piero > > > > > > -- > > > Pieremanuele Canepa > > > Room 230 > > > School of Physical Sciences, Ingram Building, > > > University of Kent, Canterbury, Kent, > > > CT2 7NH > > > United Kingdom > > > -------------------------------------------------------- > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > > > > o ------------------------------------------------ o > > | Gabriele Sclauzero, PhD Student | > > | c/o: SISSA & CNR-INFM Democritos, | > > | via Beirut 2-4, 34014 Trieste (Italy) | > > | email: sclauzer at sissa.it > > | > > | phone: +39 040 3787 511 | > > | skype: gurlonotturno | > > o ------------------------------------------------ o > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > -- > > Pieremanuele Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > ----------------------------------------------------------- > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090324/54351a09/attachment.htm From sclauzer at sissa.it Tue Mar 24 14:57:13 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 24 Mar 2009 14:57:13 +0100 Subject: [Pw_forum] I can't print my bands In-Reply-To: <8b443ba10903240359k70456d3at4d843238f7b9ab12@mail.gmail.com> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <49C8919D.8090004@sissa.it> <8b443ba10903240359k70456d3at4d843238f7b9ab12@mail.gmail.com> Message-ID: <49C8E6B9.2020205@sissa.it> Pieremanuele Canepa wrote: > I tried to do as you suggested me (removing the call to the subroutine > and recompiling), what I get if I try to run it is: > Program POST-PROC v.4.0.4 starts ... > Today is 24Mar2009 at 10:55:52 > It seems that nothing works... Why do you think that nothing works? I think that in the serial version without symmetry analysis this is the only output given by bands.x on stdout. You should find your bands in the filband file. Is it there? GS > Do you have any suggestion? > Cheers, Piero > > On Tue, Mar 24, 2009 at 7:54 AM, Gabriele Sclauzero > wrote: > > > > Pieremanuele Canepa wrote: > > Dear all, > > I am attempting to figure out how to print out a bands graph of > my AFM > > hematite. > > Then I prepared the file band.in > as explained in > > /Doc/INPUT_Band > > and I attached it down here > > &INPUTPP > > prefix='band_BLYP', > > outdir='/home/pc229/backup/ > > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > > filband='band_BLYP.out', > > / > > > > if try to run it using bands.x I will get in my output file the > > following error: > > Program POST-PROC v.4.0.4 starts ... > > Today is 23Mar2009 at 18:56:50 > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from bands : error # 1 > > The bands code with constrained magnetization has not been > tested > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > You are trying to use bands.x with a feature that has not been > tested (as the message > says). If you trust what you are doing, you can simply comment the > corresponding call to > errore subroutine in bands.f90 and recompile. You may want to test > it before doing serious > calculations. > > If you simply need it to extract the eigenvalues from a scf/nscf > pw.x calculations (using > no_overlap=.TRUE.) I think it should be safe, but if you need it to > reorder bands or do a > symmetry analysis of bands (lsym=.TRUE.) you should be careful and > double-check results. > > Cheers > > GS > > > > > > > So, what I am suppose to do ? How can I print my bands?? > > Thank you, Piero > > > > -- > > Pieremanuele Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > -------------------------------------------------------- > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it > | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > ----------------------------------------------------------- > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From daijiayu at nudt.edu.cn Tue Mar 24 15:17:17 2009 From: daijiayu at nudt.edu.cn (Jiayu Dai) Date: Tue, 24 Mar 2009 22:17:17 +0800 Subject: [Pw_forum] I can't print my bands Message-ID: <437904237.05283@nudt.edu.cn> As far as i know, the calculation of spin-polarized with BLYP is not performed in PWSCF in espresso3. I don't know whether it is included now, but you can check the calculation with unpolarization. Cheers. Jiayu > ok, attached down here you would find my input used for n scf band > calculation > &CONTROL > title = 'band_BLYP' , > calculation = 'nscf' , > restart_mode = 'from_scratch' , > outdir = > '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/' > , > pseudo_dir = > '/home/pc229/backup/Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/pseudo/' , > prefix = 'band_BLYP' , > / > &SYSTEM > ibrav = 5, > celldm(1) = 10.442958667, > celldm(4) = 0.578106099, > nat = 10, > ntyp = 3, > ecutwfc = 50 , > nosym = .true. , > nbnd = 70, > nelec = 100, > occupations = 'fixed' , > nspin = 2 , > starting_magnetization(1) = 1., > starting_magnetization(2) = -1., > starting_magnetization(3) = 0., > tot_magnetization = 0 , > / > &ELECTRONS > conv_thr = 1.0d-9 , > mixing_beta = 0.3D0 , > / > ATOMIC_SPECIES > Fe 55.62000 Fe.blyp-sp-van_ak.UPF > Fe1 55.62000 Fe.blyp-sp-van_ak.UPF > O 15.99000 O.blyp-van_ak.UPF > ATOMIC_POSITIONS crystal > Fe 0.143406978 0.143407026 0.143407451 > Fe1 0.356592136 0.356592626 0.356592564 > Fe1 0.643407993 0.643407453 0.643407513 > Fe 0.856592415 0.856592381 0.856591956 > O 0.559962709 0.940037353 0.250000243 > O 0.250000058 0.559962717 0.940037453 > O 0.940036820 0.250000238 0.559963093 > O 0.440038672 0.059961209 0.750000320 > O 0.750000498 0.440038689 0.059961097 > O 0.059961722 0.750000309 0.440038308 > K_POINTS crystal > 41 > 0.000 0.000 0.000 1 > 0.050 0.000 0.050 1 > 0.100 0.000 0.100 1 > 0.150 0.000 0.150 1 > 0.200 0.000 0.200 1 > 0.250 0.000 0.250 1 > 0.300 0.000 0.300 1 > 0.350 0.000 0.350 1 > 0.400 0.000 0.400 1 > 0.450 0.000 0.450 1 > 0.500 0.000 0.500 1 > 0.500 0.050 0.500 1 > 0.500 0.100 0.500 1 > 0.500 0.150 0.500 1 > 0.500 0.200 0.500 1 > 0.500 0.250 0.500 1 > 0.500 0.300 0.500 1 > 0.500 0.350 0.500 1 > 0.500 0.400 0.500 1 > 0.500 0.450 0.500 1 > 0.500 0.500 0.500 1 > 0.500 0.475 0.525 1 > 0.500 0.450 0.550 1 > 0.500 0.425 0.575 1 > 0.500 0.400 0.600 1 > 0.500 0.375 0.625 1 > 0.500 0.350 0.650 1 > 0.500 0.325 0.675 1 > 0.500 0.300 0.700 1 > 0.500 0.275 0.725 1 > 0.500 0.250 0.750 1 > 0.450 0.225 0.675 1 > 0.400 0.200 0.600 1 > 0.350 0.175 0.525 1 > 0.300 0.150 0.450 1 > 0.250 0.125 0.375 1 > 0.200 0.100 0.300 1 > 0.150 0.075 0.225 1 > 0.100 0.050 0.150 1 > 0.050 0.025 0.075 1 > 0.000 0.000 0.000 1 > > Thank you > > > On Tue, Mar 24, 2009 at 11:17 AM, Gabriele Sclauzero wrote: > > > > > Pieremanuele Canepa wrote: > > > I tried to do as you suggested me (removing the call to the subroutine > > > and recompiling), what I get if I try to run it is: > > > Program POST-PROC v.4.0.4 starts ... > > > Today is 24Mar2009 at 10:55:52 > > > It seems that nothing works... Do you have any suggestion? > > > > With so little information, none. You should try to explain which kind of > > system you're > > studying and post a sample for the pw.x input file. > > First you can try to understand at which point the program hangs, for > > instance by adding > > some write statements in the bands.f90 subroutines (or use a debugger if > > you are familiar > > with it). > > > > GS > > > > > > > Cheers, Piero > > > > > > On Tue, Mar 24, 2009 at 7:54 AM, Gabriele Sclauzero > > > wrote: > > > > > > > > > > > > Pieremanuele Canepa wrote: > > > > Dear all, > > > > I am attempting to figure out how to print out a bands graph of > > > my AFM > > > > hematite. > > > > Then I prepared the file band.in > > > as explained in > > > > /Doc/INPUT_Band > > > > and I attached it down here > > > > &INPUTPP > > > > prefix='band_BLYP', > > > > outdir='/home/pc229/backup/ > > > > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > > > > filband='band_BLYP.out', > > > > / > > > > > > > > if try to run it using bands.x I will get in my output file the > > > > following error: > > > > Program POST-PROC v.4.0.4 starts ... > > > > Today is 23Mar2009 at 18:56:50 > > > > > > > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > from bands : error # 1 > > > > The bands code with constrained magnetization has not been > > > tested > > > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > > > stopping ... > > > > > > You are trying to use bands.x with a feature that has not been > > > tested (as the message > > > says). If you trust what you are doing, you can simply comment the > > > corresponding call to > > > errore subroutine in bands.f90 and recompile. You may want to test > > > it before doing serious > > > calculations. > > > > > > If you simply need it to extract the eigenvalues from a scf/nscf > > > pw.x calculations (using > > > no_overlap=.TRUE.) I think it should be safe, but if you need it to > > > reorder bands or do a > > > symmetry analysis of bands (lsym=.TRUE.) you should be careful and > > > double-check results. > > > > > > Cheers > > > > > > GS > > > > > > > > > > > > > > > > > So, what I am suppose to do ? How can I print my bands?? > > > > Thank you, Piero > > > > > > > > -- > > > > Pieremanuele Canepa > > > > Room 230 > > > > School of Physical Sciences, Ingram Building, > > > > University of Kent, Canterbury, Kent, > > > > CT2 7NH > > > > United Kingdom > > > > -------------------------------------------------------- > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > > > > > > > > > o ------------------------------------------------ o > > > | Gabriele Sclauzero, PhD Student | > > > | c/o: SISSA & CNR-INFM Democritos, | > > > | via Beirut 2-4, 34014 Trieste (Italy) | > > > | email: sclauzer at sissa.it > > > | > > > | phone: +39 040 3787 511 | > > > | skype: gurlonotturno | > > > o ------------------------------------------------ o > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > > > > -- > > > Pieremanuele Canepa > > > Room 230 > > > School of Physical Sciences, Ingram Building, > > > University of Kent, Canterbury, Kent, > > > CT2 7NH > > > United Kingdom > > > ----------------------------------------------------------- > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > > > > o ------------------------------------------------ o > > | Gabriele Sclauzero, PhD Student | > > | c/o: SISSA & CNR-INFM Democritos, | > > | via Beirut 2-4, 34014 Trieste (Italy) | > > | email: sclauzer at sissa.it | > > | phone: +39 040 3787 511 | > > | skype: gurlonotturno | > > o ------------------------------------------------ o > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > ----------------------------------------------------------- > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090324/54351a09/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Tue, 24 Mar 2009 14:57:13 +0100 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] I can't print my bands > To: PWSCF Forum > Message-ID: <49C8E6B9.2020205 at sissa.it> > > > Pieremanuele Canepa wrote: > > I tried to do as you suggested me (removing the call to the subroutine > > and recompiling), what I get if I try to run it is: > > Program POST-PROC v.4.0.4 starts ... > > Today is 24Mar2009 at 10:55:52 > > It seems that nothing works... > > Why do you think that nothing works? I think that in the serial version without symmetry > analysis this is the only output given by bands.x on stdout. > You should find your bands in the filband file. Is it there? > > GS > > > Do you have any suggestion? > > Cheers, Piero > > > > On Tue, Mar 24, 2009 at 7:54 AM, Gabriele Sclauzero > > wrote: > > > > > > > > Pieremanuele Canepa wrote: > > > Dear all, > > > I am attempting to figure out how to print out a bands graph of > > my AFM > > > hematite. > > > Then I prepared the file band.in > > as explained in > > > /Doc/INPUT_Band > > > and I attached it down here > > > &INPUTPP > > > prefix='band_BLYP', > > > outdir='/home/pc229/backup/ > > > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > > > filband='band_BLYP.out', > > > / > > > > > > if try to run it using bands.x I will get in my output file the > > > following error: > > > Program POST-PROC v.4.0.4 starts ... > > > Today is 23Mar2009 at 18:56:50 > > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > from bands : error # 1 > > > The bands code with constrained magnetization has not been > > tested > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > stopping ... > > > > You are trying to use bands.x with a feature that has not been > > tested (as the message > > says). If you trust what you are doing, you can simply comment the > > corresponding call to > > errore subroutine in bands.f90 and recompile. You may want to test > > it before doing serious > > calculations. > > > > If you simply need it to extract the eigenvalues from a scf/nscf > > pw.x calculations (using > > no_overlap=.TRUE.) I think it should be safe, but if you need it to > > reorder bands or do a > > symmetry analysis of bands (lsym=.TRUE.) you should be careful and > > double-check results. > > > > Cheers > > > > GS > > > > > > > > > > > > So, what I am suppose to do ? How can I print my bands?? > > > Thank you, Piero > > > ------------------------------ Jiayu Dai National University of Defense Technology, P R China From pc229 at kent.ac.uk Tue Mar 24 16:19:19 2009 From: pc229 at kent.ac.uk (Pieremanuele Canepa) Date: Tue, 24 Mar 2009 15:19:19 +0000 Subject: [Pw_forum] I can't print my bands In-Reply-To: <49C8E6B9.2020205@sissa.it> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <49C8919D.8090004@sissa.it> <8b443ba10903240359k70456d3at4d843238f7b9ab12@mail.gmail.com> <49C8E6B9.2020205@sissa.it> Message-ID: <8b443ba10903240819t3c70096cq1d69874ee79cc146@mail.gmail.com> no there is nothing! This thing is driving me crazy!!! On Tue, Mar 24, 2009 at 1:57 PM, Gabriele Sclauzero wrote: > > > Pieremanuele Canepa wrote: > > I tried to do as you suggested me (removing the call to the subroutine > > and recompiling), what I get if I try to run it is: > > Program POST-PROC v.4.0.4 starts ... > > Today is 24Mar2009 at 10:55:52 > > It seems that nothing works... > > Why do you think that nothing works? I think that in the serial version > without symmetry > analysis this is the only output given by bands.x on stdout. > You should find your bands in the filband file. Is it there? > > GS > > > Do you have any suggestion? > > Cheers, Piero > > > > On Tue, Mar 24, 2009 at 7:54 AM, Gabriele Sclauzero > > wrote: > > > > > > > > Pieremanuele Canepa wrote: > > > Dear all, > > > I am attempting to figure out how to print out a bands graph of > > my AFM > > > hematite. > > > Then I prepared the file band.in > > as explained in > > > /Doc/INPUT_Band > > > and I attached it down here > > > &INPUTPP > > > prefix='band_BLYP', > > > outdir='/home/pc229/backup/ > > > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > > > filband='band_BLYP.out', > > > / > > > > > > if try to run it using bands.x I will get in my output file the > > > following error: > > > Program POST-PROC v.4.0.4 starts ... > > > Today is 23Mar2009 at 18:56:50 > > > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > from bands : error # 1 > > > The bands code with constrained magnetization has not been > > tested > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > stopping ... > > > > You are trying to use bands.x with a feature that has not been > > tested (as the message > > says). If you trust what you are doing, you can simply comment the > > corresponding call to > > errore subroutine in bands.f90 and recompile. You may want to test > > it before doing serious > > calculations. > > > > If you simply need it to extract the eigenvalues from a scf/nscf > > pw.x calculations (using > > no_overlap=.TRUE.) I think it should be safe, but if you need it to > > reorder bands or do a > > symmetry analysis of bands (lsym=.TRUE.) you should be careful and > > double-check results. > > > > Cheers > > > > GS > > > > > > > > > > > > So, what I am suppose to do ? How can I print my bands?? > > > Thank you, Piero > > > > > > -- > > > Pieremanuele Canepa > > > Room 230 > > > School of Physical Sciences, Ingram Building, > > > University of Kent, Canterbury, Kent, > > > CT2 7NH > > > United Kingdom > > > -------------------------------------------------------- > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > > > > o ------------------------------------------------ o > > | Gabriele Sclauzero, PhD Student | > > | c/o: SISSA & CNR-INFM Democritos, | > > | via Beirut 2-4, 34014 Trieste (Italy) | > > | email: sclauzer at sissa.it > > | > > | phone: +39 040 3787 511 | > > | skype: gurlonotturno | > > o ------------------------------------------------ o > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > -- > > Pieremanuele Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > ----------------------------------------------------------- > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090324/9b5244f5/attachment.htm From pc229 at kent.ac.uk Tue Mar 24 16:26:39 2009 From: pc229 at kent.ac.uk (pc229 at kent.ac.uk) Date: Tue, 24 Mar 2009 15:26:39 GMT Subject: [Pw_forum] I can't print my bands In-Reply-To: <49C8E6B9.2020205@sissa.it> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <49C8919D.8090004@sissa.it> <8b443ba10903240359k70456d3at4d843238f7b9ab12@mail.gmail.com> <49C8E6B9.2020205@sissa.it> Message-ID: yes I found them. Thanks a lot ----- Original Message ----- From: Gabriele Sclauzero Date: Tuesday, March 24, 2009 1:57 pm Subject: Re: [Pw_forum] I can't print my bands To: PWSCF Forum > > > Pieremanuele Canepa wrote: > > I tried to do as you suggested me (removing the call to the > subroutine > > and recompiling), what I get if I try to run it is: > >?? Program POST-PROC v.4.0.4? starts ... > >????? Today is 24Mar2009 at 10:55:52 > > It seems that nothing works... > > Why do you think that nothing works? I think that in the serial > version without symmetry > analysis this is the only output given by bands.x on stdout. > You should find your bands in the filband file. Is it there? > > GS > > > Do you have any suggestion? > > Cheers, Piero > > > > On Tue, Mar 24, 2009 at 7:54 AM, Gabriele Sclauzero > > > wrote: > > > > > > > >???? Pieremanuele Canepa wrote: > >????? > Dear all, > >????? > I am attempting? to > figure out how to print out a bands graph of > >???? my AFM > >????? > hematite. > >????? > Then I prepared the file > band.in > >???? as explained in > >????? > /Doc/INPUT_Band > >????? > and I attached it down here > >????? > &INPUTPP > >????? > prefix='band_BLYP', > >????? > outdir='/home/pc229/backup/ > >????? > > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/',>????? > filband='band_BLYP.out', > >????? > / > >????? > > >????? > if try to run it using > bands.x? I will get in my output file the > >????? > following error: > >????? >? Program POST-PROC > v.4.0.4? starts ... > >????? >????? > Today is 23Mar2009 at 18:56:50 > >????? > > >????? > > >????? > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%>????? >????? from bands : error #???????? 1 > >????? >????? > The bands code with constrained magnetization has not been > >???? tested > >????? > > >????? > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%>????? > > >????? >????? > stopping ... > > > >???? You are trying to use bands.x with a > feature that has not been > >???? tested (as the message > >???? says). If you trust what you are > doing, you can simply comment the > >???? corresponding call to > >???? errore subroutine in bands.f90 and > recompile. You may want to test > >???? it before doing serious > >???? calculations. > > > >???? If you simply need it to extract the > eigenvalues from a scf/nscf > >???? pw.x calculations (using > >???? no_overlap=.TRUE.) I think it should > be safe, but if you need it to > >???? reorder bands or do a > >???? symmetry analysis of bands > (lsym=.TRUE.) you should be careful and > >???? double-check results. > > > >???? Cheers > > > >???? GS > > > > > > > >????? > > >????? > So, what I am suppose to do > ?? How can I print my bands?? > >????? > Thank you, Piero > >????? > > >????? > -- > >????? > Pieremanuele Canepa > >????? > Room 230 > >????? > School of Physical Sciences, > Ingram Building, > >????? > University of Kent, > Canterbury, Kent, > >????? > CT2 7NH > >????? > United Kingdom > >????? > ------------------------------- > ------------------------- > >????? > > >????? > > >????? > > >???? --------------------------------------- > --------------------------------- > >????? > > >????? > > _______________________________________________>????? > Pw_forum mailing list > >????? > Pw_forum at pwscf.org > >????? > > http://www.democritos.it/mailman/listinfo/pw_forum> > >???? -- > > > > > >???? o ------------------------------------- > ----------- o > >???? | Gabriele Sclauzero, PhD > Student????????????????? | > >???? | c/o:?? SISSA & CNR-INFM > Democritos,????????????? | > >???? > |??????? via Beirut 2-4, > 34014 Trieste (Italy)???? | > >???? | email: sclauzer at sissa.it > ????????????? > >?????????????? | > >???? | phone: +39 040 3787 > 511????????????????????????? | > >???? | skype: > gurlonotturno???????????????????????????? | > >???? o ------------------------------------- > ----------- o > >???? > _______________________________________________>???? Pw_forum mailing list > >???? Pw_forum at pwscf.org > >???? > http://www.democritos.it/mailman/listinfo/pw_forum> > > > > > > > > -- > > Pieremanuele Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > ----------------------------------------------------------- > > > > > > --------------------------------------------------------------- > --------- > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD > Student????????????????? | > | c/o:?? SISSA & CNR-INFM > Democritos,????????????? | > |??????? via Beirut 2-4, > 34014 Trieste (Italy)???? | > | email: > sclauzer at sissa.it???????????????????????? | > | phone: +39 040 3787 > 511????????????????????????? | > | skype: > gurlonotturno???????????????????????????? | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > --- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090324/4f368dc4/attachment-0001.htm From sclauzer at sissa.it Tue Mar 24 16:29:53 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 24 Mar 2009 16:29:53 +0100 Subject: [Pw_forum] I can't print my bands In-Reply-To: <8b443ba10903240819t3c70096cq1d69874ee79cc146@mail.gmail.com> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <49C8919D.8090004@sissa.it> <8b443ba10903240359k70456d3at4d843238f7b9ab12@mail.gmail.com> <49C8E6B9.2020205@sissa.it> <8b443ba10903240819t3c70096cq1d69874ee79cc146@mail.gmail.com> Message-ID: <49C8FC71.80300@sissa.it> Pieremanuele Canepa wrote: > no there is nothing! This thing is driving me crazy!!! Are you getting crazy for so little? ... Anyway I tried with 4.1-CVS version and it seems to work in parallel (at least gives the bands in filband, I don't know if they've been order correclty), so it should also in a serial calculation. I don't see any reason for it not to be working in 4.0.x. Try the CVS version (you can download a snapshot from www.qe-forge.org or through CVS). GS > > On Tue, Mar 24, 2009 at 1:57 PM, Gabriele Sclauzero > wrote: > > > > Pieremanuele Canepa wrote: > > I tried to do as you suggested me (removing the call to the > subroutine > > and recompiling), what I get if I try to run it is: > > Program POST-PROC v.4.0.4 starts ... > > Today is 24Mar2009 at 10:55:52 > > It seems that nothing works... > > Why do you think that nothing works? I think that in the serial > version without symmetry > analysis this is the only output given by bands.x on stdout. > You should find your bands in the filband file. Is it there? > > GS > > > Do you have any suggestion? > > Cheers, Piero > > > > On Tue, Mar 24, 2009 at 7:54 AM, Gabriele Sclauzero > > > >> wrote: > > > > > > > > Pieremanuele Canepa wrote: > > > Dear all, > > > I am attempting to figure out how to print out a bands > graph of > > my AFM > > > hematite. > > > Then I prepared the file band.in > > > as explained in > > > /Doc/INPUT_Band > > > and I attached it down here > > > &INPUTPP > > > prefix='band_BLYP', > > > outdir='/home/pc229/backup/ > > > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > > > filband='band_BLYP.out', > > > / > > > > > > if try to run it using bands.x I will get in my output > file the > > > following error: > > > Program POST-PROC v.4.0.4 starts ... > > > Today is 23Mar2009 at 18:56:50 > > > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > from bands : error # 1 > > > The bands code with constrained magnetization has not > been > > tested > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > stopping ... > > > > You are trying to use bands.x with a feature that has not been > > tested (as the message > > says). If you trust what you are doing, you can simply > comment the > > corresponding call to > > errore subroutine in bands.f90 and recompile. You may want to > test > > it before doing serious > > calculations. > > > > If you simply need it to extract the eigenvalues from a scf/nscf > > pw.x calculations (using > > no_overlap=.TRUE.) I think it should be safe, but if you need > it to > > reorder bands or do a > > symmetry analysis of bands (lsym=.TRUE.) you should be > careful and > > double-check results. > > > > Cheers > > > > GS > > > > > > > > > > > > So, what I am suppose to do ? How can I print my bands?? > > > Thank you, Piero > > > > > > -- > > > Pieremanuele Canepa > > > Room 230 > > > School of Physical Sciences, Ingram Building, > > > University of Kent, Canterbury, Kent, > > > CT2 7NH > > > United Kingdom > > > -------------------------------------------------------- > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > > > > o ------------------------------------------------ o > > | Gabriele Sclauzero, PhD Student | > > | c/o: SISSA & CNR-INFM Democritos, | > > | via Beirut 2-4, 34014 Trieste (Italy) | > > | email: sclauzer at sissa.it > > > > | > > | phone: +39 040 3787 511 | > > | skype: gurlonotturno | > > o ------------------------------------------------ o > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > -- > > Pieremanuele Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > ----------------------------------------------------------- > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it > | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > ----------------------------------------------------------- > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From akohlmey at cmm.chem.upenn.edu Tue Mar 24 17:12:34 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 24 Mar 2009 12:12:34 -0400 Subject: [Pw_forum] questions about the peseudopotential for potassium titanate In-Reply-To: <20090324050510.qygyix00zokc40o0@webmail.sissa.it> References: <412f6c680903232000w126c7d6ag6079d9c1a64c50d5@mail.gmail.com> <20090324050510.qygyix00zokc40o0@webmail.sissa.it> Message-ID: <1237911154.3113.309.camel@zero> On Tue, 2009-03-24 at 05:05 +0100, Stefano de Gironcoli wrote: > Dear Vega, > > > THe pseudo K.pz-sp-van.UPF has been generated with the vanderbilt > code. you can > likely find the corresponding input in the Vanderbilt website. > It should be easy to modify it by replacing the LDA PZ functional with pw91. stefano, unfortunately, it is not that easy. the vdb atomic code requires a different polynomial fitting procedure for GGAs than for LDA. one has to tweak the input a little bit more and most of the time, also include some additional constraints to avoid unphysical negative densities as a result of the different fitting. once you have one GGA functional, you can usually regenerate all of them with the same parameters, as well as an LDA potential. cheers, axel. > don't forget to test the new pseudo in some simple system before > trusting it. > hope this helps, > stefano > - > Stefano de Gironcoli -SISSA and DEMOCRITOS > > > Quoting vega lew : > > > Dear all > > > > I want the calculate the properties of potassium titanate. And I want to use > > the pw91 functionals for the whole caculation. But I find the > > peseudopotential for K is something different with the Ti and O. From the > > name of pp, we could see functionals for K is different from Ti and O. Do > > you think I could use > > K.pz-sp-van.UPFwith > > the O.pw91-van_ak.UPF and Ti.pw91-sp-van_ak.UPF to describe the > > potassium titanate. Actually I want to use pw91 functionals for the > > calculation. How could I deal with the K+? > > > > thank you for reading > > > > any hints will be deeply appreciated > > > > vega > > > > > > -- > > ================================================================================== > > Vega Lew ( weijia liu) > > PH.D Candidate in Chemical Engineering > > State Key Laboratory of Materials-oriented Chemical Engineering > > College of Chemistry and Chemical Engineering > > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > ****************************************************************************************************************** > > Email: vegalew at gmail.com > > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, > > Jiangsu, China > > ****************************************************************************************************************** > > > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From snd2mra at yahoo.com Tue Mar 24 19:58:21 2009 From: snd2mra at yahoo.com (snd2mra at yahoo.com) Date: Tue, 24 Mar 2009 11:58:21 -0700 (PDT) Subject: [Pw_forum] Compilation Error - Cygwin - PGI 8.0.4 Compilers Message-ID: <950637.19883.qm@web53310.mail.re2.yahoo.com> Hello, I am trying to compile pwscf 4.0.4 in CYGWIN using PGI compilers (Ver. 8.0.4). The Configure script failed and I had to create a 'make.sys' and compilation was successful for iotk, iotk.x and iotk_print_kinds.x, but eventually fails. The error are given below. Could someone please help me out to figure out the problem. I was able to compile and use pwscf in many architectures like ia32-ifort, ia64-ifort, IBM PowerPC 4 - AIX, IBM PowerPC 5 - Linux etc except CYGWIN. Thank you. - Madan ---------------------------------------- Madan Mithra .L.M Dept.of Physics Indian Institute of Science Bangalore - 560 012 INDIA ......................................... e-mail : mit at physics.iisc.ernet.in : snd2mra at yahoo.com Phone : 91-80-22932313 (Lab) : 91-80-22932918 (Hostel-S 46) FAX : (080) 360 2602 ----------------------------------------- -----Configure Script------ ./configure ARCH=cygwin --disable-parallel F90=pgf95 F77=pgf95 CC=pgcc "CPP=pgcc -P" The Error is: checking whether make sets $(MAKE)... yes checking whether Fortran files must be preprocessed... yes checking how to get verbose linking output from pgf95... -v checking for Fortran libraries of pgf95... -libpath:c:\prog\PGI/win32/8.0-4/lib checking for dummy main to link with Fortran libraries... unknown configure: error: linking to Fortran libraries from C fails ------- make.sys ------ .SUFFIXES : .SUFFIXES : .o .c .f .f90 .f90.o: $(CPP) $(CPPFLAGS) $< -o $*.F90 $(F90) $(F90FLAGS) -c $*.F90 -o $*.o .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< DFLAGS = -D__LINUX -D__PGI -D__FFTW -D__USE_INTERNAL_FFTW FDFLAGS = $(DFLAGS) IFLAGS = -I../include -I. -I/C/prog/PGI/win32/8.0-4/include/CC \ -I/C/prog/PGI/win32/8.0-4/include MODFLAGS = -I./ -I../Modules -I../iotk/src \ -I../PW -I../PH F90 = pgf95 CC = pgcc F77 = pgf77 CPP = pgcc -P CPPFLAGS = $(DFLAGS) $(IFLAGS) CFLAGS = -fast $(DFLAGS) $(IFLAGS) $(MODFLAGS) $(FFLAGS) F90FLAGS = -g $(FFLAGS) $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O FFLAGS_NOOPT = -O0 LD = pgf95 LDFLAGS = LD_LIBS = BLAS_LIBS = ../flib/blas.a LAPACK_LIBS = ../flib/lapack.a FFT_LIBS = MPI_LIBS = MASS_LIBS = PGPLOT_LIBS = AR = ar ARFLAGS = ruv ARFLAGS_DYNAMIC= ruv RANLIB = ranlib LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) --------------- Error-------- make[1]: Leaving directory `/d/Comp/p404/Modules' ( cd clib ; if test "make" = "" ; then make - --unix TLDEPS= all ; \ else make - --unix TLDEPS= all ; fi ) make[1]: Entering directory `/d/Comp/p404/clib' pgcc -fast -D__LINUX -D__PGI -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I. -I/C/prog/PGI/win32/8.0-4/include/CC -I/C/prog/PGI/win32/8.0-4/include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -O -c stack.c PGC-F-0206-Can't find include file sys/resource.h (stack.c: 11) PGC/x86 Windows 8.0-4: compilation aborted make[1]: *** [stack.o] Error 2 make[1]: Leaving directory `/d/Comp/p404/clib' make: *** [libs] Error 2 From giannozz at democritos.it Tue Mar 24 21:36:04 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 24 Mar 2009 21:36:04 +0100 Subject: [Pw_forum] Compilation Error - Cygwin - PGI 8.0.4 Compilers In-Reply-To: <950637.19883.qm@web53310.mail.re2.yahoo.com> References: <950637.19883.qm@web53310.mail.re2.yahoo.com> Message-ID: On Mar 24, 2009, at 19:58 , snd2mra at yahoo.com wrote: > checking for dummy main to link with Fortran libraries... unknown > configure: error: linking to Fortran libraries from C fails in the cvs version you may try "configure --disable-check" > PGC-F-0206-Can't find include file sys/resource.h (stack.c: 11) clib/stack.c is used only by the Intel compiler, so you can just comment the routine stack.c P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From meheut at impmc.jussieu.fr Wed Mar 25 03:19:05 2009 From: meheut at impmc.jussieu.fr (merlin meheut) Date: Wed, 25 Mar 2009 03:19:05 +0100 Subject: [Pw_forum] I/O problem with qe 4.0.4 Message-ID: <20090325031905.20615692nloa4mft@www-ext.impmc.jussieu.fr> Dear PWSCF users, I am trying calculating a big structure (72 atoms) with quantum espresso 4.0.4. With qe 3.0, I had no particular problem, but with qe 4.0.4 I have this error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 99 error while writing to file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... This is strange because it happened twice at the same point, approximately half-way to the end of the calculation. It may be related to different problems, such as hardware, but I will be happy if you have any hints to make myself a more precise idea of the problem. In particular, the qe 3.0 is probably in a place more easily accessible on the file system, so it may be related to that. Many thanks, Merlin -- Merlin M?heut professional adress: 595 Charles Young Drive East 3806 Geology Building Los Angeles, California 90095-1597 United States of America tel: 310 825 7934 cell phone: 310 893 4253 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From akohlmey at cmm.chem.upenn.edu Wed Mar 25 03:42:00 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 24 Mar 2009 22:42:00 -0400 Subject: [Pw_forum] I/O problem with qe 4.0.4 In-Reply-To: <20090325031905.20615692nloa4mft@www-ext.impmc.jussieu.fr> References: <20090325031905.20615692nloa4mft@www-ext.impmc.jussieu.fr> Message-ID: <1237948920.3075.2.camel@zero> On Wed, 2009-03-25 at 03:19 +0100, merlin meheut wrote: > Dear PWSCF users, > > I am trying calculating a big structure (72 atoms) with quantum > espresso 4.0.4. With qe 3.0, I had no particular problem, but with qe > 4.0.4 I have this error message: > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from davcio : error # 99 > error while writing to file > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > This is strange because it happened twice at the same point, > approximately half-way to the end of the calculation. > > It may be related to different problems, such as hardware, but I will > be happy if you have any hints to make myself a more precise idea of > the problem. i'd first check if you have enough free disk space on the device that you are writing to and sufficient quota, in case your installation uses quotas. axel. > In particular, the qe 3.0 is probably in a place more easily > accessible on the file system, so it may be related to that. > > Many thanks, > > Merlin > > > -- > Merlin M?heut > professional adress: > 595 Charles Young Drive East > 3806 Geology Building > Los Angeles, California 90095-1597 > United States of America > tel: 310 825 7934 > cell phone: 310 893 4253 > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From yccheng.nju at gmail.com Wed Mar 25 04:02:03 2009 From: yccheng.nju at gmail.com (yccheng.nju) Date: Wed, 25 Mar 2009 11:02:03 +0800 Subject: [Pw_forum] Compilation Error - Cygwin - PGI 8.0.4 Compilers Message-ID: <200903251101582504027@gmail.com> I have successfully compile QE4.4 in cygwin using gfortran compiler. You can use gfortran compiler as an alternative. ------------------ yccheng.nju 2009-03-25 ------------------------------------------------------------- ????snd2mra ?????2009-03-25 03:05:32 ????pw_forum ??? ???[Pw_forum] Compilation Error - Cygwin - PGI 8.0.4 Compilers Hello, I am trying to compile pwscf 4.0.4 in CYGWIN using PGI compilers (Ver. 8.0.4). The Configure script failed and I had to create a 'make.sys' and compilation was successful for iotk, iotk.x and iotk_print_kinds.x, but eventually fails. The error are given below. Could someone please help me out to figure out the problem. I was able to compile and use pwscf in many architectures like ia32-ifort, ia64-ifort, IBM PowerPC 4 - AIX, IBM PowerPC 5 - Linux etc except CYGWIN. Thank you. - Madan ---------------------------------------- Madan Mithra .L.M Dept.of Physics Indian Institute of Science Bangalore - 560 012 INDIA ......................................... e-mail : mit at physics.iisc.ernet.in : snd2mra at yahoo.com Phone : 91-80-22932313 (Lab) : 91-80-22932918 (Hostel-S 46) FAX : (080) 360 2602 ----------------------------------------- -----Configure Script------ ./configure ARCH=cygwin --disable-parallel F90=pgf95 F77=pgf95 CC=pgcc "CPP=pgcc -P" The Error is: checking whether make sets $(MAKE)... yes checking whether Fortran files must be preprocessed... yes checking how to get verbose linking output from pgf95... -v checking for Fortran libraries of pgf95... -libpath:c:\prog\PGI/win32/8.0-4/lib checking for dummy main to link with Fortran libraries... unknown configure: error: linking to Fortran libraries from C fails ------- make.sys ------ .SUFFIXES : .SUFFIXES : .o .c .f .f90 .f90.o: $(CPP) $(CPPFLAGS) $< -o $*.F90 $(F90) $(F90FLAGS) -c $*.F90 -o $*.o .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< DFLAGS = -D__LINUX -D__PGI -D__FFTW -D__USE_INTERNAL_FFTW FDFLAGS = $(DFLAGS) IFLAGS = -I../include -I. -I/C/prog/PGI/win32/8.0-4/include/CC \ -I/C/prog/PGI/win32/8.0-4/include MODFLAGS = -I./ -I../Modules -I../iotk/src \ -I../PW -I../PH F90 = pgf95 CC = pgcc F77 = pgf77 CPP = pgcc -P CPPFLAGS = $(DFLAGS) $(IFLAGS) CFLAGS = -fast $(DFLAGS) $(IFLAGS) $(MODFLAGS) $(FFLAGS) F90FLAGS = -g $(FFLAGS) $(FDFLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O FFLAGS_NOOPT = -O0 LD = pgf95 LDFLAGS = LD_LIBS = BLAS_LIBS = ../flib/blas.a LAPACK_LIBS = ../flib/lapack.a FFT_LIBS = MPI_LIBS = MASS_LIBS = PGPLOT_LIBS = AR = ar ARFLAGS = ruv ARFLAGS_DYNAMIC= ruv RANLIB = ranlib LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(PGPLOT_LIBS) $(LD_LIBS) --------------- Error-------- make[1]: Leaving directory `/d/Comp/p404/Modules' ( cd clib ; if test "make" = "" ; then make - --unix TLDEPS= all ; \ else make - --unix TLDEPS= all ; fi ) make[1]: Entering directory `/d/Comp/p404/clib' pgcc -fast -D__LINUX -D__PGI -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I. -I/C/prog/PGI/win32/8.0-4/include/CC -I/C/prog/PGI/win32/8.0-4/include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -O -c stack.c PGC-F-0206-Can't find include file sys/resource.h (stack.c: 11) PGC/x86 Windows 8.0-4: compilation aborted make[1]: *** [stack.o] Error 2 make[1]: Leaving directory `/d/Comp/p404/clib' make: *** [libs] Error 2 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From ddrsmile at gmail.com Wed Mar 25 04:15:35 2009 From: ddrsmile at gmail.com (DdrSmiLe) Date: Wed, 25 Mar 2009 11:15:35 +0800 Subject: [Pw_forum] DMFT+LDA In-Reply-To: <166cd7c60903222004j791a20bbk92b86a0af7a92fff@mail.gmail.com> References: <166cd7c60903222004j791a20bbk92b86a0af7a92fff@mail.gmail.com> Message-ID: Dear All I am using dmft package recently. I want to konw how to creat wannier_ham.x I could not find this executable anywhere after I compiled dmft. Another problem is I could not compile w90 in espresso-4.1CVS package. It showed that there are something loss in W90 package. Thank you much NTLiu 2009/3/23 Dmitry Korotin > Dear S.K. Saha, > LDA+DMFT project for QE already started and the first working code is > released. It strongly depends on QE source (uses QE make.sys files), > contains only one example (and minimal documentation). But it works. > Official LDA+DMFT for QE project site is > http://qe-forge.org/projects/dmft/. You can download files there. > > 2009/3/22 S. K. S. : > > Dear all, > > Recently, in abinit, I have seen > > some on-going developments on DMFT+LDA. > > I'm a little curious. Has anyone already started or is > > going to start the similar kind of developmental work in PWSCF???? > > regards, > > S. K. Saha > > JNCASR > > Bangalore > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > Best regards, > Dmitry Korotin > > Ph. D. Student, > Institute of Metal Physics > S. Kovalevskaya, 18 > 620041 Ekaterinburg GSP-170 > Russia > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090325/2006659b/attachment.htm From lanhaiping at gmail.com Wed Mar 25 06:05:06 2009 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 25 Mar 2009 13:05:06 +0800 Subject: [Pw_forum] DMFT+LDA In-Reply-To: References: <166cd7c60903222004j791a20bbk92b86a0af7a92fff@mail.gmail.com> Message-ID: Hi, You need wannier90 package, take a look at www.wannier.org, and read README first! Hope help ~ On Wed, Mar 25, 2009 at 11:15 AM, DdrSmiLe wrote: > Dear All > I am using dmft package recently. > I want to konw how to creat wannier_ham.x > I could not find this executable anywhere after I compiled dmft. > > Another problem is I could not compile w90 in espresso-4.1CVS package. > It showed that there are something loss in W90 package. > > Thank you much > > NTLiu > 2009/3/23 Dmitry Korotin > > Dear S.K. Saha, >> LDA+DMFT project for QE already started and the first working code is >> released. It strongly depends on QE source (uses QE make.sys files), >> contains only one example (and minimal documentation). But it works. >> Official LDA+DMFT for QE project site is >> http://qe-forge.org/projects/dmft/. You can download files there. >> >> 2009/3/22 S. K. S. : >> > Dear all, >> > Recently, in abinit, I have seen >> > some on-going developments on DMFT+LDA. >> > I'm a little curious. Has anyone already started or is >> > going to start the similar kind of developmental work in PWSCF???? >> > regards, >> > S. K. Saha >> > JNCASR >> > Bangalore >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> Best regards, >> Dmitry Korotin >> >> Ph. D. Student, >> Institute of Metal Physics >> S. Kovalevskaya, 18 >> 620041 Ekaterinburg GSP-170 >> Russia >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090325/30b761e2/attachment.htm From dmitry at korotin.name Wed Mar 25 09:17:41 2009 From: dmitry at korotin.name (Dmitry Korotin) Date: Wed, 25 Mar 2009 09:17:41 +0100 Subject: [Pw_forum] DMFT+LDA In-Reply-To: References: <166cd7c60903222004j791a20bbk92b86a0af7a92fff@mail.gmail.com> Message-ID: <166cd7c60903250117w40e25c63jd8c89e1bffb25f05@mail.gmail.com> 2009/3/25 DdrSmiLe : > Dear All > I am using dmft package recently. > I want to konw how to creat wannier_ham.x > I?could not find this executable anywhere after I compiled dmft. You need to download CVS version of QE and 'make pp'. > > Another problem is I could not compile w90 in espresso-4.1CVS package. > It showed that there are something loss in W90 package. > > Thank you much > > NTLiu > 2009/3/23 Dmitry Korotin >> >> Dear S.K. Saha, >> LDA+DMFT project for QE already started and the first working code is >> released. It strongly depends on QE source (uses QE make.sys files), >> contains only one example (and minimal documentation). But it works. >> Official LDA+DMFT for QE project site is >> http://qe-forge.org/projects/dmft/. You can download files there. >> >> 2009/3/22 S. K. S. : >> > Dear all, >> > Recently, in abinit, I have seen >> > some on-going developments ?on DMFT+LDA. >> > I'm a little curious. Has ?anyone already started ?or is >> > going to start ?the similar kind of developmental work in PWSCF???? >> > regards, >> > S. K. Saha >> > JNCASR >> > Bangalore >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> Best regards, >> Dmitry Korotin >> >> Ph. D. Student, >> Institute of Metal Physics >> S. Kovalevskaya, 18 >> 620041 Ekaterinburg GSP-170 >> Russia >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ? ?????????, ??????? ??????? Best regards, Dmitry Korotin Ph. D. Student, Institute of Metal Physics S. Kovalevskaya, 18 620041 Ekaterinburg GSP-170 Russia From giannozz at democritos.it Wed Mar 25 10:12:31 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 25 Mar 2009 10:12:31 +0100 Subject: [Pw_forum] DMFT+LDA In-Reply-To: References: <166cd7c60903222004j791a20bbk92b86a0af7a92fff@mail.gmail.com> Message-ID: <49C9F57F.1080308@democritos.it> DdrSmiLe wrote: > Another problem is I could not compile w90 in espresso-4.1CVS package. > It showed that there are something loss in W90 package. use the link "[Download The Nightly CVS Tree Snapshot]" from here: ttp://qe-forge.org/scm/?group_id=10 The CVS package you mention wss an experiment and might not be complete P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From helen at fh.huji.ac.il Wed Mar 25 11:46:50 2009 From: helen at fh.huji.ac.il (Helen) Date: Wed, 25 Mar 2009 12:46:50 +0200 Subject: [Pw_forum] HSE pseudopotentials + BNL functional References: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com><006301c9abab$a835b860$cd604084@fh.huji.ac.il> <20090323162742.0h0ndw9q3kkwsw8c@webmail.sissa.it> Message-ID: <008401c9ad37$00ecb850$cd604084@fh.huji.ac.il> Hi, The changes are localized in PW/exx.f90, flib/functionals.f90, Modules/functionals.f90. I've implemented the changes in version 3.2. I need to check I didn't make changes elsewhere as I implemented this about a year ago, and I don't remember all the details. I set on_double_grid to .false. Also in Modules/input_parameters.f90 I set x_gamma_extrapolation=.false. I can create an example input/output file. I also worked on enabling exx.f90 to give the band-structure for general k-points and not just high symmetry k-points. I did this my giving a very small weight to the desired k-point and also including in the k-point list all the generated k+q k-points. It is a bit of an art though as I put in the k+q k-points by hand and sometimes the exx.f90 generates the symmetry points and sometimes I also need to add these by hand. Also sometimes the symmetry points need to have zero weight and sometimes the very small weight to give corect results. Dr Helen Eisenberg Post-doctoral researcher Fritz Haber Research Center for Molecular Dynamics, The Hebrew University of Jerusalem ----- Original Message ----- From: "Stefano de Gironcoli" To: Sent: Monday, March 23, 2009 5:27 PM Subject: Re: [Pw_forum] HSE pseudopotentials + BNL functional > Dear Dr. Eisenberg, > > If you are willing to share your developments it would be very > much appreciated. > > Are your modifications localized in a few files (like exx.f90 and > functionals.f90) ? is the functional implemented in the latest version > of Quantum-Espresso ? > If the annswers are yes the simplest option to contribute your > code would be to send me and/or to Layla Martin-Samos > (marsamos at democritos.it) the relevant routines so that we can include > them in the cvs repository and then revert to you to check that > everything is fine. > An input (and an output) using the new feature similar to those in > the EXXexample directory could also be useful to keep the feature > working when > the code is updated. > > best regards and thank you for your contribution, > > stefano > - > Stefano de Gironcoli - SISSA and DEMOCRITOS > > > Quoting Helen : > >> Dear all, >> I've been working on a functional somewhat similar to the HSE >> functional, the BNL functional (R. Baer and D. Neuhauser, PRL >> 94,043002 (2005)) which also has a explicit-exchange component. I >> have implemented this functional into Quantum-Espresso and the full >> details can be seen in our paper currently submitted for publication >> and on the archives: arXive:0903.3830v1. >> Where should I post the Quantum-Espresso code implemented for the >> BNL functional? >> Dr Helen Eisenberg >> Post-doctoral researcher >> Fritz Haber Research Center for Molecular Dynamics, >> The Hebrew University of Jerusalem >> >> ----- Original Message ----- >> From: shangy >> To: PWSCF Forum >> Sent: Saturday, March 14, 2009 7:49 AM >> Subject: [Pw_forum] HSE pseudopotentials >> >> >> Dear all: >> Does anyone has the Si pseudopotentials generated by the >> screened-exchange hybrid functional of Heyd, Scuseria, and Ernerhof >> [HSE, J. Chem. Phys. 118, 8207 (2003)]? Can it work well within QE? >> If anyone has one, would you share it with me? I'm very very thirsty >> for it. Thanks in advance. >> Best regards. >> >> shangy >> Graduate unversity of Chinese academy of sciences >> >> >> ------------------------------------------------------------------------------ >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From helen at fh.huji.ac.il Wed Mar 25 11:48:47 2009 From: helen at fh.huji.ac.il (Helen) Date: Wed, 25 Mar 2009 12:48:47 +0200 Subject: [Pw_forum] HSE pseudopotentials + BNL functional References: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com><006301c9abab$a835b860$cd604084@fh.huji.ac.il> <94be399f0903232212r7012dfecu4e25abe9ef985c6f@mail.gmail.com> Message-ID: <009301c9ad37$46694380$cd604084@fh.huji.ac.il> Hi, I'm going to first of all send the code to the Quantum-Espresso team so they can check the changes I've made, and when they OK it, I'll send the code to you, Helen ----- Original Message ----- From: shangy To: PWSCF Forum Sent: Tuesday, March 24, 2009 7:12 AM Subject: Re: [Pw_forum] HSE pseudopotentials + BNL functional Dear Eisenberg: I'm very exciting for your BNL information. Would you like to share your Q-E code implemented with BNL funciontal with me and send it to my box sporevoyager at gmail.com ? I may test the BNL calculation on formation energy of Si-defects and compare the results with HSE results in other work. Thanks in advance. Best regards! shangy Graduate unversity of Chinese academy of sciences 2009/3/23 Helen Dear all, I've been working on a functional somewhat similar to the HSE functional, the BNL functional (R. Baer and D. Neuhauser, PRL 94,043002 (2005)) which also has a explicit-exchange component. I have implemented this functional into Quantum-Espresso and the full details can be seen in our paper currently submitted for publication and on the archives: arXive:0903.3830v1. Where should I post the Quantum-Espresso code implemented for the BNL functional? Dr Helen Eisenberg Post-doctoral researcher Fritz Haber Research Center for Molecular Dynamics, The Hebrew University of Jerusalem ------------------------------------------------------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090325/7436f193/attachment.htm From quantumdft at gmail.com Wed Mar 25 12:30:03 2009 From: quantumdft at gmail.com (vega lew) Date: Wed, 25 Mar 2009 19:30:03 +0800 Subject: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency Message-ID: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> Dear all, Is there someone perform QE on intel I7 platform? Do you think parallelzation QE could benefit from the QPI technology of intel I7 series very much? vega -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090325/4ef57279/attachment.htm From greatnaol at gmail.com Wed Mar 25 12:37:27 2009 From: greatnaol at gmail.com (Naol Regassa) Date: Wed, 25 Mar 2009 14:37:27 +0300 Subject: [Pw_forum] Spacing in band structure Message-ID: <97e4b88e0903250437q7e769d24sadca3a44edd80178@mail.gmail.com> Hello everyone We were drawing band structure for the hexagonal crystal structure along the path ?-M-K-?-A. when I want to make the spacing between M-K narrower and ?-M wider, I increase the number of k-points along ?-M and decrease the k-points from M-K but it didn't work. No matter what density of k-points I made the spacing between the high symmetry points does not vary the way that I want? Is this related with the application that I am using i.e 'Image Magic' What do you advice me then? On the way let me add one question. How can remove the dots on the band structure so that it will be smooth? NB: I am facing the same problem on the phonon dispersion. Naol Addis Ababa University, Materials science programe East Africa (Ethiopia) From akohlmey at cmm.chem.upenn.edu Wed Mar 25 13:45:41 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 25 Mar 2009 08:45:41 -0400 Subject: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency In-Reply-To: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> References: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> Message-ID: <1237985141.5873.6.camel@zero> On Wed, 2009-03-25 at 19:30 +0800, vega lew wrote: > Dear all, > > Is there someone perform QE on intel I7 platform? Do you think > parallelzation QE could benefit from the QPI technology of intel I7 > series very much? the integrated memory controller and parallelization have very little connection directly. please don't "believe" in buzzwords. what _will_ help codes like Q-E in general is the greatly enhanced memory bandwidth, particularly the for larger systems. for smaller systems that mostly fit into the cache, the gains will be much smaller. the floating point unit of those cpus is essentially the same as in the current xeon processors. since the various tests posted on the list here demonstrated that (some of) Q-E's parallelization schemes are very much affected by insufficient memory bandwidth, there will be a gain. however, those CPUs will also have a different cache architecture, which may in turn chew up some of the benefits, particularly for smaller problems. cheers, axel. > > vega > > -- > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ****************************************************************************************************************** > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From sclauzer at sissa.it Wed Mar 25 14:27:11 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 25 Mar 2009 14:27:11 +0100 Subject: [Pw_forum] Spacing in band structure In-Reply-To: <97e4b88e0903250437q7e769d24sadca3a44edd80178@mail.gmail.com> References: <97e4b88e0903250437q7e769d24sadca3a44edd80178@mail.gmail.com> Message-ID: <49CA312F.3070405@sissa.it> Naol Regassa wrote: > Hello everyone > > We were drawing band structure for the hexagonal crystal structure > along the path ?-M-K-?-A. when I want to make the spacing between M-K > narrower and ?-M wider, I increase the number of k-points along ?-M > and decrease the k-points from M-K but it didn't work. No matter what > density of k-points I made the spacing between the high symmetry > points does not vary the way that I want? Is this related with the > application that I am using i.e 'Image Magic' What do you advice me > then? On the way let me add one question. How can remove the dots on > the band structure so that it will be smooth? > NB: I am facing the same problem on the phonon dispersion. Your question is not very clear to me. Are you facing problems with the plotting program you're using (in such case maybe this is not the correct forum) or with pwscf itself? Please try to clearify your questions with some small plots/examples or problematic input output files... It is also a good habit to specify the steps followed to produce the data (to understand what you are actually looking at), the QE version etc etc. GS > > Naol > Addis Ababa University, Materials science programe > East Africa (Ethiopia) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From lfhuang at theory.issp.ac.cn Wed Mar 25 15:30:25 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Wed, 25 Mar 2009 22:30:25 +0800 Subject: [Pw_forum] =?utf-8?q?about_the_path_length_in_NEB_calculations?= Message-ID: <20090325143025.7901.qmail@ms.hfcas.ac.cn> Hello everyone: I wonder why the path length in NEB calculation always increase in the progress of calculations(exemple17 and my own calculations for other systems), even though the path is a straight line with the two end fixed? How is the "path" really defined? I would like to appreciate any guide! Yours Sincerely L.F.Huang ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090325/3b0435e1/attachment.htm From resul at ibu.edu.tr Wed Mar 25 15:38:53 2009 From: resul at ibu.edu.tr (Resul Eryigit) Date: Wed, 25 Mar 2009 16:38:53 +0200 Subject: [Pw_forum] Spacing in band structure In-Reply-To: <97e4b88e0903250437q7e769d24sadca3a44edd80178@mail.gmail.com> References: <97e4b88e0903250437q7e769d24sadca3a44edd80178@mail.gmail.com> Message-ID: <49CA41FD.8060306@ibu.edu.tr> Naol Regassa wrote: > Hello everyone > > We were drawing band structure for the hexagonal crystal structure > along the path ?-M-K-?-A. when I want to make the spacing between M-K > narrower and ?-M wider, I increase the number of k-points along ?-M > and decrease the k-points from M-K but it didn't work. No matter what > density of k-points I made the spacing between the high symmetry > points does not vary the way that I want? Is this related with the > application that I am using i.e 'Image Magic' What do you advice me > then? On the way let me add one question. How can remove the dots on > the band structure so that it will be smooth? > NB: I am facing the same problem on the phonon dispersion. > dear naol.. the distance between two special points is fixed by the geometry of the first brillouin zone and for the hexagonal 1BZ the length of \Gamma-M=1/(sqrt(3) a) and the length of M-K=1/(3 a) where a is the basal lattice constant. you can extract energy values and plot them wrt to k-point number (instead of k-length) to have wider or narrower looking segments, but that would not be meaningful. resul > Naol > Addis Ababa University, Materials science programe > East Africa (Ethiopia) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From quantumdft at gmail.com Wed Mar 25 15:51:19 2009 From: quantumdft at gmail.com (vega lew) Date: Wed, 25 Mar 2009 22:51:19 +0800 Subject: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency In-Reply-To: <1237985141.5873.6.camel@zero> References: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> <1237985141.5873.6.camel@zero> Message-ID: <412f6c680903250751g1b5cf98av8332fc6317677b77@mail.gmail.com> Dear sir, You answer is quite helpful to me. Thank you very much. Actully, the speed of calculation for a large system is more important for us. So I think the bandwidth is the key issue. could I recognize the bandwidth you mentioned as the FSB (Front system bus) of the montherboard and the frequency of memory such as 800MHz or 1066 MHz and so on? thank you for your reply vega On Wed, Mar 25, 2009 at 8:45 PM, Axel Kohlmeyer wrote: > On Wed, 2009-03-25 at 19:30 +0800, vega lew wrote: > > Dear all, > > > > Is there someone perform QE on intel I7 platform? Do you think > > parallelzation QE could benefit from the QPI technology of intel I7 > > series very much? > > the integrated memory controller and parallelization have very > little connection directly. please don't "believe" in buzzwords. > > what _will_ help codes like Q-E in general is the greatly enhanced > memory bandwidth, particularly the for larger systems. for smaller > systems that mostly fit into the cache, the gains will be much smaller. > the floating point unit of those cpus is essentially the same as in > the current xeon processors. > since the various tests posted on the list here demonstrated that > (some of) Q-E's parallelization schemes are very much affected by > insufficient memory bandwidth, there will be a gain. however, those > CPUs will also have a different cache architecture, which may in > turn chew up some of the benefits, particularly for smaller problems. > > cheers, > axel. > > > > > > > vega > > > > -- > > > ================================================================================== > > Vega Lew ( weijia liu) > > PH.D Candidate in Chemical Engineering > > State Key Laboratory of Materials-oriented Chemical Engineering > > College of Chemistry and Chemical Engineering > > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > > ****************************************************************************************************************** > > Email: vegalew at gmail.com > > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > > Nanjing, Jiangsu, China > > > ****************************************************************************************************************** > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090325/b803ada5/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Mar 25 16:22:00 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 25 Mar 2009 11:22:00 -0400 Subject: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency In-Reply-To: <412f6c680903250751g1b5cf98av8332fc6317677b77@mail.gmail.com> References: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> <1237985141.5873.6.camel@zero> <412f6c680903250751g1b5cf98av8332fc6317677b77@mail.gmail.com> Message-ID: <1237994520.5873.20.camel@zero> On Wed, 2009-03-25 at 22:51 +0800, vega lew wrote: > Dear sir, > > You answer is quite helpful to me. Thank you very much. Actully, the > speed of calculation for a large system is more > important for us. So I think the bandwidth is the key issue. > > could I recognize the bandwidth you mentioned as the FSB (Front system > bus) of the montherboard and the frequency of memory such as 800MHz or > 1066 MHz and so on? not really. you can see the bandwidth reliably from running the stream benchmark. those numbers do - of course - exist, but are currently under NDA, so nobody can talk about it until the end of next week, IIRC. from what is public already i can tell you, that the architecture of nehalem EP also requires that you pay great care as to where memory modules are plugged in. good mainboards will have memory slots in multiples of three. by placing memory modules in the wrong slots, you can reduce the bandwidth by a factor of three. ;) as with any new architecture, i would also expect that you'll have expect a significant amount of problems with mainboard, bios, drivers etc. and thus you should make sure that you have staff able to deal with it. axel > thank you for your reply > > vega > > On Wed, Mar 25, 2009 at 8:45 PM, Axel Kohlmeyer > wrote: > On Wed, 2009-03-25 at 19:30 +0800, vega lew wrote: > > Dear all, > > > > Is there someone perform QE on intel I7 platform? Do you > think > > parallelzation QE could benefit from the QPI technology of > intel I7 > > series very much? > > > the integrated memory controller and parallelization have very > little connection directly. please don't "believe" in > buzzwords. > > what _will_ help codes like Q-E in general is the greatly > enhanced > memory bandwidth, particularly the for larger systems. for > smaller > systems that mostly fit into the cache, the gains will be much > smaller. > the floating point unit of those cpus is essentially the same > as in > the current xeon processors. > since the various tests posted on the list here demonstrated > that > (some of) Q-E's parallelization schemes are very much affected > by > insufficient memory bandwidth, there will be a gain. however, > those > CPUs will also have a different cache architecture, which may > in > turn chew up some of the benefits, particularly for smaller > problems. > > cheers, > axel. > > > > > > > vega > > > > -- > > > ================================================================================== > > Vega Lew ( weijia liu) > > PH.D Candidate in Chemical Engineering > > State Key Laboratory of Materials-oriented Chemical > Engineering > > College of Chemistry and Chemical Engineering > > Nanjing University of Technology, 210009, Nanjing, Jiangsu, > China > > > ****************************************************************************************************************** > > Email: vegalew at gmail.com > > Office: Room A705, Technical Innovation Building, Xinmofan > Road 5#, > > Nanjing, Jiangsu, China > > > ****************************************************************************************************************** > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of > Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: > 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a > better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > ================================================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > ****************************************************************************************************************** > Email: vegalew at gmail.com > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > Nanjing, Jiangsu, China > ****************************************************************************************************************** > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Wed Mar 25 16:30:05 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 25 Mar 2009 16:30:05 +0100 Subject: [Pw_forum] about the path length in NEB calculations In-Reply-To: <20090325143025.7901.qmail@ms.hfcas.ac.cn> References: <20090325143025.7901.qmail@ms.hfcas.ac.cn> Message-ID: <49CA4DFD.3020605@democritos.it> lfhuang wrote: > I wonder why the path length in NEB calculation always increase in the > progress of calculations [...] even though the path is a straight > line with the two end fixed? the ends are fixed, the length is not. Typically one starts a NEB calculation with a straight line (in configuration space) and ends with a curved line. Guess which one is shorter? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From baris.malcioglu at gmail.com Wed Mar 25 17:16:19 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Wed, 25 Mar 2009 17:16:19 +0100 Subject: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency In-Reply-To: <1237994520.5873.20.camel@zero> References: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> <1237985141.5873.6.camel@zero> <412f6c680903250751g1b5cf98av8332fc6317677b77@mail.gmail.com> <1237994520.5873.20.camel@zero> Message-ID: On the topic of "new architecture" processors, does anyone remember this: http://www.sciencemag.org/cgi/content/citation/267/5195/175 Actually we had one of those processors back in my old university. An early adopter bought it, and due to infamous Intel PR, never was able to return it. Although it worked perfectly in running OS etc, unlike the Intel claim, the error was not so uncommon at all, the machine was hilarious in calculations. Also, in addition to this, each now and then there are these faulty memories with "walking bits", etc which are prone to "invent" some very interesting "results". Try DDR3 in an unshielded case with bad PSU/ Square wave outlet UPS. Best, Baris On Wed, Mar 25, 2009 at 4:22 PM, Axel Kohlmeyer wrote: > On Wed, 2009-03-25 at 22:51 +0800, vega lew wrote: >> Dear sir, >> >> You answer is quite helpful to me. Thank you very much. Actully, the >> speed of calculation for a large system is more >> important for us. So I think the bandwidth is the key issue. >> >> could I recognize the bandwidth you mentioned as the FSB (Front system >> bus) of the montherboard and the frequency of memory such as 800MHz or >> 1066 MHz and so on? > > not really. you can see the bandwidth reliably from running the > stream benchmark. those numbers do - of course - exist, but are > currently under NDA, so nobody can talk about it until the end > of next week, IIRC. > > from what is public already i can tell you, that the architecture > of nehalem EP also requires that you pay great care as to where > memory modules are plugged in. good mainboards will have memory > slots in multiples of three. by placing memory modules in the wrong > slots, you can reduce the bandwidth by a factor of three. ;) > > as with any new architecture, i would also expect that you'll have > expect a significant amount of problems with mainboard, bios, drivers > etc. and thus you should make sure that you have staff able to deal > with it. > > axel > >> thank you for your reply >> >> vega >> >> On Wed, Mar 25, 2009 at 8:45 PM, Axel Kohlmeyer >> wrote: >> ? ? ? ? On Wed, 2009-03-25 at 19:30 +0800, vega lew wrote: >> ? ? ? ? > Dear all, >> ? ? ? ? > >> ? ? ? ? > Is there someone perform QE on intel I7 platform? Do you >> ? ? ? ? think >> ? ? ? ? > parallelzation QE could benefit from the QPI technology of >> ? ? ? ? intel I7 >> ? ? ? ? > series very much? >> >> >> ? ? ? ? the integrated memory controller and parallelization have very >> ? ? ? ? little connection directly. please don't "believe" in >> ? ? ? ? buzzwords. >> >> ? ? ? ? what _will_ help codes like Q-E in general is the greatly >> ? ? ? ? enhanced >> ? ? ? ? memory bandwidth, particularly the for larger systems. for >> ? ? ? ? smaller >> ? ? ? ? systems that mostly fit into the cache, the gains will be much >> ? ? ? ? smaller. >> ? ? ? ? the floating point unit of those cpus is essentially the same >> ? ? ? ? as in >> ? ? ? ? the current xeon processors. >> ? ? ? ? since the various tests posted on the list here demonstrated >> ? ? ? ? that >> ? ? ? ? (some of) Q-E's parallelization schemes are very much affected >> ? ? ? ? by >> ? ? ? ? insufficient memory bandwidth, there will be a gain. however, >> ? ? ? ? those >> ? ? ? ? CPUs will also have a different cache architecture, which may >> ? ? ? ? in >> ? ? ? ? turn chew up some of the benefits, particularly for smaller >> ? ? ? ? problems. >> >> ? ? ? ? cheers, >> ? ? ? ? ? axel. >> >> >> >> ? ? ? ? > >> ? ? ? ? > vega >> ? ? ? ? > >> ? ? ? ? > -- >> ? ? ? ? > >> ? ? ? ? ================================================================================== >> ? ? ? ? > Vega Lew ( weijia liu) >> ? ? ? ? > PH.D Candidate in Chemical Engineering >> ? ? ? ? > State Key Laboratory of Materials-oriented Chemical >> ? ? ? ? Engineering >> ? ? ? ? > College of Chemistry and Chemical Engineering >> ? ? ? ? > Nanjing University of Technology, 210009, Nanjing, Jiangsu, >> ? ? ? ? China >> ? ? ? ? > >> ? ? ? ? ****************************************************************************************************************** >> ? ? ? ? > Email: vegalew at gmail.com >> ? ? ? ? > Office: Room A705, Technical Innovation Building, Xinmofan >> ? ? ? ? Road 5#, >> ? ? ? ? > Nanjing, Jiangsu, China >> ? ? ? ? > >> ? ? ? ? ****************************************************************************************************************** >> >> ? ? ? ? > _______________________________________________ >> ? ? ? ? > Pw_forum mailing list >> ? ? ? ? > Pw_forum at pwscf.org >> ? ? ? ? > http://www.democritos.it/mailman/listinfo/pw_forum >> >> ? ? ? ? -- >> ? ? ? ? ======================================================================= >> ? ? ? ? Axel Kohlmeyer ? akohlmey at cmm.chem.upenn.edu >> ? ? ? ? http://www.cmm.upenn.edu >> ? ? ? ? ? Center for Molecular Modeling ? -- ? University of >> ? ? ? ? Pennsylvania >> ? ? ? ? Department of Chemistry, 231 S.34th Street, Philadelphia, PA >> ? ? ? ? 19104-6323 >> ? ? ? ? tel: 1-215-898-1582, ?fax: 1-215-573-6233, ?office-tel: >> ? ? ? ? 1-215-898-5425 >> ? ? ? ? ======================================================================= >> ? ? ? ? If you make something idiot-proof, the universe creates a >> ? ? ? ? better idiot. >> >> ? ? ? ? _______________________________________________ >> ? ? ? ? Pw_forum mailing list >> ? ? ? ? Pw_forum at pwscf.org >> ? ? ? ? http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> -- >> ================================================================================== >> Vega Lew ( weijia liu) >> PH.D Candidate in Chemical Engineering >> State Key Laboratory of Materials-oriented Chemical Engineering >> College of Chemistry and Chemical Engineering >> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China >> ****************************************************************************************************************** >> Email: vegalew at gmail.com >> Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, >> Nanjing, Jiangsu, China >> ****************************************************************************************************************** >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer ? akohlmey at cmm.chem.upenn.edu ? http://www.cmm.upenn.edu > ? Center for Molecular Modeling ? -- ? University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, ?fax: 1-215-573-6233, ?office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From marzari at MIT.EDU Wed Mar 25 18:04:57 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 25 Mar 2009 13:04:57 -0400 Subject: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency In-Reply-To: References: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> <1237985141.5873.6.camel@zero> <412f6c680903250751g1b5cf98av8332fc6317677b77@mail.gmail.com> <1237994520.5873.20.camel@zero> Message-ID: <49CA6439.4040001@mit.edu> We have some tests for a 4-core i7 920 @ 2.67GHz under: http://quasiamore.mit.edu/pmwiki/index.php?n=Main.SWTTimings This is a very informal page (so skip most of the stuff, and just look at Machine 4, and the AgI CP tests. These are standard tests we perform, and that are detailed more broadly in http://quasiamore.mit.edu/pmwiki/index.php?n=Main.CP90Timings ). Note that the tests above were done on a remote machine that was poorly ventilated. I think Davide Ceresoli might have some more recent results on a 4-core extreme edition at 3.xx GHz . Davide, could you add those to the wiki ? The Xeons are coming out next week, indeed (2 cpus on the same motherboard). But our impression was that the improved bandwidth made it very much worth going for the i7. nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From quantumdft at gmail.com Wed Mar 25 18:38:18 2009 From: quantumdft at gmail.com (vega lew) Date: Thu, 26 Mar 2009 01:38:18 +0800 Subject: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency In-Reply-To: <1237994520.5873.20.camel@zero> References: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> <1237985141.5873.6.camel@zero> <412f6c680903250751g1b5cf98av8332fc6317677b77@mail.gmail.com> <1237994520.5873.20.camel@zero> Message-ID: <412f6c680903251038of4a5408y8ffa5d5a8712a6fa@mail.gmail.com> Dear sir, Thank you for your reply. I think discussing relationship of QE and hardware is quite helpful. Unfortunately, we don't have specific staff dealing with this matter. My supervisor rarely show me 110,000 yuan (equal to ~$20,000). and tell me he want the calculation environment promoted greatly. So I must play the part of that staff. One year ago, I just finished a small system (8 computers with Q6600 and 8G memory on intel S3000AH board / node ) and conquered the problems as you mentioned, such as motherboard, bios, dual channel memory, OS, etc. I'm quite confident that I could make it this time. This time, our aim is to establish a small DIY server standard platform which could calculate less than 200 atoms effectively using QE/CPMD. Unfortunately, we still have no infiniband or myrinet. So I think a strategy of duo-socket/node (8 cores per node) is more suitable for us. as you just told me, the bandwidth of the memory is key issue for us (we didn't concern about it previously). and could you give some benchmarks of QE/CPMD running on various platforms ( both server standard and PC standard). And is there some suggestion for us to built a small cluster suitable for QE/CPMD with less than $20,000(US dollar). thank you for reading. vega On Wed, Mar 25, 2009 at 11:22 PM, Axel Kohlmeyer < akohlmey at cmm.chem.upenn.edu> wrote: > On Wed, 2009-03-25 at 22:51 +0800, vega lew wrote: > > Dear sir, > > > > You answer is quite helpful to me. Thank you very much. Actully, the > > speed of calculation for a large system is more > > important for us. So I think the bandwidth is the key issue. > > > > could I recognize the bandwidth you mentioned as the FSB (Front system > > bus) of the montherboard and the frequency of memory such as 800MHz or > > 1066 MHz and so on? > > not really. you can see the bandwidth reliably from running the > stream benchmark. those numbers do - of course - exist, but are > currently under NDA, so nobody can talk about it until the end > of next week, IIRC. > > from what is public already i can tell you, that the architecture > of nehalem EP also requires that you pay great care as to where > memory modules are plugged in. good mainboards will have memory > slots in multiples of three. by placing memory modules in the wrong > slots, you can reduce the bandwidth by a factor of three. ;) > > as with any new architecture, i would also expect that you'll have > expect a significant amount of problems with mainboard, bios, drivers > etc. and thus you should make sure that you have staff able to deal > with it. > > axel > > > thank you for your reply > > > > vega > > > > On Wed, Mar 25, 2009 at 8:45 PM, Axel Kohlmeyer > > wrote: > > On Wed, 2009-03-25 at 19:30 +0800, vega lew wrote: > > > Dear all, > > > > > > Is there someone perform QE on intel I7 platform? Do you > > think > > > parallelzation QE could benefit from the QPI technology of > > intel I7 > > > series very much? > > > > > > the integrated memory controller and parallelization have very > > little connection directly. please don't "believe" in > > buzzwords. > > > > what _will_ help codes like Q-E in general is the greatly > > enhanced > > memory bandwidth, particularly the for larger systems. for > > smaller > > systems that mostly fit into the cache, the gains will be much > > smaller. > > the floating point unit of those cpus is essentially the same > > as in > > the current xeon processors. > > since the various tests posted on the list here demonstrated > > that > > (some of) Q-E's parallelization schemes are very much affected > > by > > insufficient memory bandwidth, there will be a gain. however, > > those > > CPUs will also have a different cache architecture, which may > > in > > turn chew up some of the benefits, particularly for smaller > > problems. > > > > cheers, > > axel. > > > > > > > > > > > > vega > > > > > > -- > > > > > > ================================================================================== > > > Vega Lew ( weijia liu) > > > PH.D Candidate in Chemical Engineering > > > State Key Laboratory of Materials-oriented Chemical > > Engineering > > > College of Chemistry and Chemical Engineering > > > Nanjing University of Technology, 210009, Nanjing, Jiangsu, > > China > > > > > > ****************************************************************************************************************** > > > Email: vegalew at gmail.com > > > Office: Room A705, Technical Innovation Building, Xinmofan > > Road 5#, > > > Nanjing, Jiangsu, China > > > > > > ****************************************************************************************************************** > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > > ======================================================================= > > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu > > http://www.cmm.upenn.edu > > Center for Molecular Modeling -- University of > > Pennsylvania > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA > > 19104-6323 > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: > > 1-215-898-5425 > > > ======================================================================= > > If you make something idiot-proof, the universe creates a > > better idiot. > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > > > ================================================================================== > > Vega Lew ( weijia liu) > > PH.D Candidate in Chemical Engineering > > State Key Laboratory of Materials-oriented Chemical Engineering > > College of Chemistry and Chemical Engineering > > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > > ****************************************************************************************************************** > > Email: vegalew at gmail.com > > Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, > > Nanjing, Jiangsu, China > > > ****************************************************************************************************************** > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090326/4a45205e/attachment-0001.htm From quantumdft at gmail.com Wed Mar 25 18:52:29 2009 From: quantumdft at gmail.com (vega lew) Date: Thu, 26 Mar 2009 01:52:29 +0800 Subject: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency In-Reply-To: <49CA6439.4040001@mit.edu> References: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> <1237985141.5873.6.camel@zero> <412f6c680903250751g1b5cf98av8332fc6317677b77@mail.gmail.com> <1237994520.5873.20.camel@zero> <49CA6439.4040001@mit.edu> Message-ID: <412f6c680903251052ucf2247emcd7b4ffd492c145a@mail.gmail.com> Dear sir, thank you for your information. I'll check the benchmark on your website. I'm very glad to hear I7 greatly promote the performance of QE. We will consider it. could you please tell me how much does your computer with I7 tech. cost? vega On Thu, Mar 26, 2009 at 1:04 AM, Nicola Marzari wrote: > > > We have some tests for a 4-core i7 920 @ 2.67GHz under: > > http://quasiamore.mit.edu/pmwiki/index.php?n=Main.SWTTimings > > This is a very informal page (so skip most of the stuff, and just > look at Machine 4, and the AgI CP tests. These are standard > tests we perform, and that are detailed more broadly in > http://quasiamore.mit.edu/pmwiki/index.php?n=Main.CP90Timings ). > > Note that the tests above were done on a remote machine that > was poorly ventilated. > > I think Davide Ceresoli might have some more recent results on > a 4-core extreme edition at 3.xx GHz . Davide, could you > add those to the wiki ? > > The Xeons are coming out next week, indeed (2 cpus on the > same motherboard). > > But our impression was that the improved bandwidth made it very > much worth going for the i7. > > > nicola > > > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ================================================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ****************************************************************************************************************** Email: vegalew at gmail.com Office: Room A705, Technical Innovation Building, Xinmofan Road 5#, Nanjing, Jiangsu, China ****************************************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090326/c1b7be83/attachment.htm From marzari at MIT.EDU Wed Mar 25 20:26:31 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 25 Mar 2009 15:26:31 -0400 Subject: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency In-Reply-To: <412f6c680903251052ucf2247emcd7b4ffd492c145a@mail.gmail.com> References: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> <1237985141.5873.6.camel@zero> <412f6c680903250751g1b5cf98av8332fc6317677b77@mail.gmail.com> <1237994520.5873.20.camel@zero> <49CA6439.4040001@mit.edu> <412f6c680903251052ucf2247emcd7b4ffd492c145a@mail.gmail.com> Message-ID: <49CA8567.4090505@mit.edu> > tell me how much does your computer with I7 tech. cost? www.swt.com nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From degironc at sissa.it Thu Mar 26 07:39:45 2009 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 26 Mar 2009 07:39:45 +0100 Subject: [Pw_forum] HSE pseudopotentials + BNL functional In-Reply-To: <008401c9ad37$00ecb850$cd604084@fh.huji.ac.il> References: <94be399f0903132249t15f7903fmfece4362a5384e5e@mail.gmail.com><006301c9abab$a835b860$cd604084@fh.huji.ac.il> <20090323162742.0h0ndw9q3kkwsw8c@webmail.sissa.it> <008401c9ad37$00ecb850$cd604084@fh.huji.ac.il> Message-ID: <20090326073945.byr2v7rv4cocs00k@webmail.sissa.it> Hi, > The changes are localized in PW/exx.f90, flib/functionals.f90, > Modules/functionals.f90. I've implemented the changes in version 3.2. I need > to check I didn't make changes elsewhere as I implemented this about a year > ago, and I don't remember all the details. I set on_double_grid to .false. > Also in Modules/input_parameters.f90 I set x_gamma_extrapolation=.false. OK, just send your code when you have checked that together with an example to verify it. > I can create an example input/output file. I also worked on enabling exx.f90 > to give the band-structure for general k-points and not just high symmetry > k-points. I did this my giving a very small weight to the desired k-point > and also including in the k-point list all the generated k+q k-points. It is > a bit of an art though as I put in the k+q k-points by hand and sometimes > the exx.f90 generates the symmetry points and sometimes I also need to add > these by hand. Also sometimes the symmetry points need to have zero weight > and sometimes the very small weight to give corect results. this is interesting. calculating band structure is tricky with exx now, indeed. Would you method work also in presence of the divergence or is limited to BNL-like functionals ? best regards, stefano - Stefano de Gironcoli - SISSA and DEMOCRITOS > Dr Helen Eisenberg > Post-doctoral researcher > Fritz Haber Research Center for Molecular Dynamics, > The Hebrew University of Jerusalem > > > ----- Original Message ----- > From: "Stefano de Gironcoli" > To: > Sent: Monday, March 23, 2009 5:27 PM > Subject: Re: [Pw_forum] HSE pseudopotentials + BNL functional > > >> Dear Dr. Eisenberg, >> >> If you are willing to share your developments it would be very >> much appreciated. >> >> Are your modifications localized in a few files (like exx.f90 and >> functionals.f90) ? is the functional implemented in the latest version >> of Quantum-Espresso ? >> If the annswers are yes the simplest option to contribute your >> code would be to send me and/or to Layla Martin-Samos >> (marsamos at democritos.it) the relevant routines so that we can include >> them in the cvs repository and then revert to you to check that >> everything is fine. >> An input (and an output) using the new feature similar to those in >> the EXXexample directory could also be useful to keep the feature >> working when >> the code is updated. >> >> best regards and thank you for your contribution, >> >> stefano >> - >> Stefano de Gironcoli - SISSA and DEMOCRITOS >> >> >> Quoting Helen : >> >>> Dear all, >>> I've been working on a functional somewhat similar to the HSE >>> functional, the BNL functional (R. Baer and D. Neuhauser, PRL >>> 94,043002 (2005)) which also has a explicit-exchange component. I >>> have implemented this functional into Quantum-Espresso and the full >>> details can be seen in our paper currently submitted for publication >>> and on the archives: arXive:0903.3830v1. >>> Where should I post the Quantum-Espresso code implemented for the >>> BNL functional? >>> Dr Helen Eisenberg >>> Post-doctoral researcher >>> Fritz Haber Research Center for Molecular Dynamics, >>> The Hebrew University of Jerusalem >>> >>> ----- Original Message ----- >>> From: shangy >>> To: PWSCF Forum >>> Sent: Saturday, March 14, 2009 7:49 AM >>> Subject: [Pw_forum] HSE pseudopotentials >>> >>> >>> Dear all: >>> Does anyone has the Si pseudopotentials generated by the >>> screened-exchange hybrid functional of Heyd, Scuseria, and Ernerhof >>> [HSE, J. Chem. Phys. 118, 8207 (2003)]? Can it work well within QE? >>> If anyone has one, would you share it with me? I'm very very thirsty >>> for it. Thanks in advance. >>> Best regards. >>> >>> shangy >>> Graduate unversity of Chinese academy of sciences >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> ---------------------------------------------------------------- >> SISSA Webmail https://webmail.sissa.it/ >> Powered by Horde http://www.horde.org/ >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From cyrille.barreteau at cea.fr Thu Mar 26 08:39:22 2009 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Thu, 26 Mar 2009 08:39:22 +0100 Subject: [Pw_forum] about the path length in NEB calculations In-Reply-To: <49CA4DFD.3020605@democritos.it> References: <20090325143025.7901.qmail@ms.hfcas.ac.cn> <49CA4DFD.3020605@democritos.it> Message-ID: <49CB312A.3080901@cea.fr> >the ends are fixed, the length is not. Typically one starts a NEB >calculation with a straight line (in configuration space) and ends >with a curved line. Guess which one is shorter? > > > It depends on the curvature of our space:-) Euclidian or not Euclidian that is the question:-) cyrille -- ================================================================== Cyrille Barreteau | phone : +33 (0)1 69 08 29 51 CEA Saclay | fax : +33 (0)1 69 08 84 46 DSM/IRAMIS/SPCSI | email cyrille.barreteau at cea.fr Batiment 462 | 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ http://iramis.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html ================================================================== From barcaro at ipcf.cnr.it Thu Mar 26 13:16:57 2009 From: barcaro at ipcf.cnr.it (Giovanni Barcaro) Date: Thu, 26 Mar 2009 13:16:57 +0100 Subject: [Pw_forum] Fe PP Message-ID: <49CB7239.7070003@ipcf.cnr.it> Dear PWscf users, has anybody developed a fully relativistic pseudo potential to perform non-collinear spin-orbit calculations on Fe? Thank you very much, Giovanni Barcaro Istituto per i Processi Chimico Fisici (IPCF) Consiglio Nazionale delle Ricerche (CNR) Area della Ricerca di Pisa, Via G. Moruzzi 1, 56124, Pisa, Italy From ihsanas at yahoo.com Thu Mar 26 13:36:14 2009 From: ihsanas at yahoo.com (Ihsan Erikat) Date: Thu, 26 Mar 2009 05:36:14 -0700 (PDT) Subject: [Pw_forum] multiplicity Message-ID: <42937.97163.qm@web52309.mail.re2.yahoo.com> Hi ?I want to make a spin polarization calculations (nspin=2 )for a transition surface (Pt) with molecules? on the surface O2 and CO, how can I set the multiplicity for this system. best regards Ihsan Erikat Physics department -Jordan university -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090326/30689ae6/attachment.htm From G.Autes at open.ac.uk Thu Mar 26 17:31:41 2009 From: G.Autes at open.ac.uk (G.Autes) Date: Thu, 26 Mar 2009 16:31:41 -0000 Subject: [Pw_forum] charge transfer in GaAs from projwfc Message-ID: <2DB62B9891E94943806FE03F1C50DC9907E5074E@SHERWOOD.open.ac.uk> Hi I am trying to calculate the local charge in GaAs. I did a self consistent calculation for bulk GaAs which gave me the correct bands structure (for the valence bands). Then I tried to calculate the local DOS and charge on each atom using projwfc.x. I obtain these Lowdin charges (atom 1 is Ga and 2 is As): > Lowdin Charges: > > Atom # 1: total charge = 2.9724, s = 1.0494, p = 1.9231, > Atom # 2: total charge = 4.9937, s = 1.3894, p = 3.6043, > Spilling Parameter: 0.0042 which are the integer charge of the atoms... But we should expect a charge transfer from Ga to As. D. Sanchez-Portal et al. (Solid State Com. 95 685), using the same method, report a charge transfer of 0.42eV in GaAs. I include my input files. Could you tell me if I'm missing something? Thanks -- Gabriel Autes Open University, Milton-Keynes, UK City University, London, UK ----------------------------------- input file for the scf calculation: &control calculation='scf', outdir='./tmp', prefix='gaas', pseudo_dir='/home/gautes/Progs/espresso-4.0.4/pseudo' / &system ibrav=2, celldm(1)=10.6827, nbnd=8, nat=2, ntyp=2, ecutwfc=40.0d0, occupations='fixed', nspin=1 / &electrons conv_thr=1d-6, mixing_beta=0.7, diagonalization='david' / ATOMIC_SPECIES Ga 69.723 Ga.pz-bhs.UPF As 74.92160 As.pz-bhs.UPF ATOMIC_POSITIONS alat Ga 0.0 0.0 0.0 As 0.25 0.25 0.25 K_POINTS automatic 10 10 10 0 0 0 ---------------------------------------- input file for projwfc.x: &INPUTPP prefix='gaas', outdir='./tmp', Emin=-10.0, Emax= 20.0, DeltaE=0.05, filpdos="gaas", filproj="proj.dat" ngauss=0 / --------------------------------- The Open University is incorporated by Royal Charter (RC 000391), an exempt charity in England & Wales and a charity registered in Scotland (SC 038302). From naylin.nll at gmail.com Thu Mar 26 18:30:00 2009 From: naylin.nll at gmail.com (Nay Lin) Date: Fri, 27 Mar 2009 01:30:00 +0800 Subject: [Pw_forum] TBPW program of Prof. Richard Martin of UIUC Message-ID: <619d39dc0903261030u671062c6t13caa5c1b8776557@mail.gmail.com> Dear all Sorry for out of topic request for help... Is anyone have a compiled version of TBPW code of Prof. Richard Martin of UIUC? If you have pls send me to naylin.nll at gmail.com I am studying coding of DFT calculation and TBPW is simple to start with. regards Lin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090327/5c6ab6de/attachment.htm From giannozz at democritos.it Thu Mar 26 18:36:50 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 26 Mar 2009 18:36:50 +0100 Subject: [Pw_forum] TBPW program of Prof. Richard Martin of UIUC In-Reply-To: <619d39dc0903261030u671062c6t13caa5c1b8776557@mail.gmail.com> References: <619d39dc0903261030u671062c6t13caa5c1b8776557@mail.gmail.com> Message-ID: <49CBBD32.3040700@democritos.it> Nay Lin wrote: > Is anyone have a compiled version of TBPW code of Prof. Richard Martin > of UIUC? If you have pls send me are you sure that a code compiled elsewhere will work on your machine? > I am studying coding of DFT calculation and you study coding on compiled codes? -- Paolo Giannozzi, Democritos and University of Udine, Italy From naromero at gmail.com Thu Mar 26 18:39:04 2009 From: naromero at gmail.com (Nichols A. Romero) Date: Thu, 26 Mar 2009 12:39:04 -0500 Subject: [Pw_forum] TBPW program of Prof. Richard Martin of UIUC In-Reply-To: <619d39dc0903261030u671062c6t13caa5c1b8776557@mail.gmail.com> References: <619d39dc0903261030u671062c6t13caa5c1b8776557@mail.gmail.com> Message-ID: <6ac064b60903261039u91b7dabo232970c418ed361a@mail.gmail.com> Lin, Did you send your question to tbpw at mcc.uiuc.edu? On Thu, Mar 26, 2009 at 12:30 PM, Nay Lin wrote: > Dear all > > Sorry for out of topic request for help... > > Is anyone have a compiled version of TBPW code of Prof. Richard Martin of > UIUC? If you have pls send me to naylin.nll at gmail.com > I am studying coding of DFT calculation and TBPW is simple to start with. > > regards > Lin > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Nichols A. Romero, Ph.D. Argonne Leadership Computing Facility Argonne, IL 60490 (630) 252-3441 (O) (630) 470-0462 (C) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090326/d9c01d27/attachment.htm From giannozz at democritos.it Thu Mar 26 18:48:01 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 26 Mar 2009 18:48:01 +0100 Subject: [Pw_forum] charge transfer in GaAs from projwfc In-Reply-To: <2DB62B9891E94943806FE03F1C50DC9907E5074E@SHERWOOD.open.ac.uk> References: <2DB62B9891E94943806FE03F1C50DC9907E5074E@SHERWOOD.open.ac.uk> Message-ID: <49CBBFD1.1080807@democritos.it> G.Autes wrote: > I obtain these Lowdin charges (atom 1 is Ga and 2 is As): > [..] which are the integer charge of the atoms... > But we should expect a charge transfer from Ga to As. > D. Sanchez-Portal et al. (Solid State Com. 95 685), > using the same method, report a charge transfer of 0.42eV in GaAs. they say they use Mulliken charges, so it is not the same method. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Mar 26 18:52:32 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 26 Mar 2009 18:52:32 +0100 Subject: [Pw_forum] multiplicity In-Reply-To: <42937.97163.qm@web52309.mail.re2.yahoo.com> References: <42937.97163.qm@web52309.mail.re2.yahoo.com> Message-ID: <49CBC0E0.9040809@democritos.it> Ihsan Erikat wrote: > I want to make a spin polarization calculations (nspin=2 )for a > transition surface (Pt) with molecules on the surface O2 and CO, > how can I set the multiplicity for this system. multiplicity = 2S+1, so if you want S=1 you specify multiplicity=3. Please read carefully the instructions: there are many different, and mutually exclusive, ways to specify the magnetization P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From w2agz at pacbell.net Thu Mar 26 19:37:38 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Thu, 26 Mar 2009 11:37:38 -0700 Subject: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency In-Reply-To: <49CA8567.4090505@mit.edu> References: <412f6c680903250430u4353745wf93a03d6079ae29f@mail.gmail.com> <1237985141.5873.6.camel@zero> <412f6c680903250751g1b5cf98av8332fc6317677b77@mail.gmail.com> <1237994520.5873.20.camel@zero> <49CA6439.4040001@mit.edu> <412f6c680903251052ucf2247emcd7b4ffd492c145a@mail.gmail.com> <49CA8567.4090505@mit.edu> Message-ID: <014701c9ae41$f180ff00$d482fd00$@net> Nicola, thanks for pointing out this source. I note most of the swt.com machines are based on SuperMicro MBs. I've had very good experience with this company...they are located here in Fremont in the south SF bay area. I roll most of my own equipment, so you can actually save a little more "self-assembling" your own boxes. Four of my five home workstations use various editions of SuperMicro Xeon MBs...the fifth is my son's PS3, and, yes, it can run QE also...rather slowly on the just the PPE plus only 256 Mbytes, though! Paul M. Grant, PhD Physicist and Science Writer Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Nicola Marzari Sent: Wednesday, March 25, 2009 12:27 PM To: PWSCF Forum Subject: Re: [Pw_forum] Do you think Intel I7 series could improve the parallel efficiency > tell me how much does your computer with I7 tech. cost? www.swt.com nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From w2agz at pacbell.net Thu Mar 26 20:34:19 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Thu, 26 Mar 2009 12:34:19 -0700 Subject: [Pw_forum] Line 325 in bands_FS.f90 Message-ID: <016001c9ae49$dcaada80$96008f80$@net> While running bands_FS.x (espresso-4.0 distro) on the output of an PW nscf non-spin-polarized job, I get the following error: At line 325 of file bands_FS.f90 Fortran runtime error: Bad real number in item 5 of list input This only happens for my LSDA=F runs, spin-polarized are OK. (BTW, the LSDA=F run for Ni in example 08 does work. The only difference is that ex08 deals with only 8 bands and 1 formated line, whilst my task computes 20 taking up 3 formated lines.) Line 325 is in the LSDA=F portion of the code follows a commented-out read command line with explicit formatting. I can't see any problem with the output of my nscf run. Before I start messing around with the bands_FS.f90 source, has anyone else run into this issue (Eyvaz?)? Is it possible there is a "line counting" error in the LSDA=F portion when the band energy listing exceeds one line? Sorry if I've made some stupid blunder. Paul M. Grant, PhD Physicist and Science Writer Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090326/6d182aed/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu Mar 26 21:00:07 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 26 Mar 2009 16:00:07 -0400 Subject: [Pw_forum] Line 325 in bands_FS.f90 In-Reply-To: <016001c9ae49$dcaada80$96008f80$@net> References: <016001c9ae49$dcaada80$96008f80$@net> Message-ID: <1238097607.3704.119.camel@zero> On Thu, 2009-03-26 at 12:34 -0700, Paul M. Grant wrote: > While running bands_FS.x (espresso-4.0 distro) on the output of an PW > nscf non-spin-polarized job, I get the following error: > > At line 325 of file bands_FS.f90 > > Fortran runtime error: Bad real number in item 5 of list input paul, please check your input carefully with hexdump to make sure you have no non-ascii characters in there. with some fonts it is hard to tell. i'm attaching a wrapper script that i use myself, which is little bit easier to read (at least for me, as it emulates the hexdumper display that i was using back in the days when i was hacking 6502 processors which almost broke the 1MHz barrier...). i miss begin able to fix bugs in running programs by replacing goto opcodes with NOPs... ;-) cheers, axel. > > This only happens for my LSDA=F runs, spin-polarized are OK. (BTW, > the LSDA=F run for Ni in example 08 does work. The only difference is > that > > ex08 deals with only 8 bands and 1 formated line, whilst my task > computes 20 taking up 3 formated lines.) Line 325 is in the LSDA=F > portion of the code follows a commented-out read command line with > explicit formatting. I can't see any problem with the output of my > nscf run. Before I start messing around with the bands_FS.f90 source, > has anyone else run into this issue (Eyvaz?)? Is it possible there is > a "line counting" error in the LSDA=F portion when the band energy > listing exceeds one line? Sorry if I've made some stupid blunder. > > Paul M. Grant, PhD > > Physicist and Science Writer > > Principal, W2AGZ Technologies > > Visiting Scholar, Applied Physics, Stanford (2005-2008) > > EPRI Science Fellow (Retired) > > IBM Research Staff Member Emeritus > > w2agz at pacbell.net > > http://www.w2agz.com > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. -------------- next part -------------- A non-text attachment was scrubbed... Name: hexview Type: application/x-shellscript Size: 231 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090326/e2878900/attachment.bin From eyvaz_isaev at yahoo.com Thu Mar 26 21:50:46 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 26 Mar 2009 13:50:46 -0700 (PDT) Subject: [Pw_forum] Line 325 in bands_FS.f90 In-Reply-To: <016001c9ae49$dcaada80$96008f80$@net> Message-ID: <593553.85654.qm@web65705.mail.ac4.yahoo.com> Dear Paul, Thanks reporting the error. I will look at why it happens. Bests, Eyvaz. --- On Thu, 3/26/09, Paul M. Grant wrote: > From: Paul M. Grant > Subject: [Pw_forum] Line 325 in bands_FS.f90 > To: "'PWSCF Forum'" > Date: Thursday, March 26, 2009, 10:34 PM > While running bands_FS.x (espresso-4.0 distro) on the output > of an PW nscf > non-spin-polarized job, I get the following error: > > At line 325 of file bands_FS.f90 > Fortran runtime error: Bad real number in item 5 of list > input > > This only happens for my LSDA=F runs, spin-polarized are > OK. (BTW, the > LSDA=F run for Ni in example 08 does work. The only > difference is that > ex08 deals with only 8 bands and 1 formated line, whilst my > task computes 20 > taking up 3 formated lines.) Line 325 is in the LSDA=F > portion of the code > follows a commented-out read command line with explicit > formatting. I can't > see any problem with the output of my nscf run. Before I > start messing > around with the bands_FS.f90 source, has anyone else run > into this issue > (Eyvaz?)? Is it possible there is a "line > counting" error in the LSDA=F > portion when the band energy listing exceeds one line? > Sorry if I've made > some stupid blunder. > > Paul M. Grant, PhD > Physicist and Science Writer > Principal, W2AGZ Technologies > Visiting Scholar, Applied Physics, Stanford (2005-2008) > EPRI Science Fellow (Retired) > IBM Research Staff Member Emeritus > w2agz at pacbell.net > http://www.w2agz.com > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Thu Mar 26 22:14:31 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 26 Mar 2009 14:14:31 -0700 (PDT) Subject: [Pw_forum] Line 325 in bands_FS.f90 In-Reply-To: <016001c9ae49$dcaada80$96008f80$@net> Message-ID: <620097.49786.qm@web65711.mail.ac4.yahoo.com> Dear Paul, I have just tested the code provided in 4.0.4, but with the output of 3.2. Both, Non-Spin polarized, and Spin-Polarized results worked well for Ni. And you can see from the line 325 that there is no limitation for bands numbers. Nevertheless, I will try the code with 4.0.4 output. By the way, it might be much helpful, if you send me your output file for which you have troubles. Bests, Eyvaz. --- On Thu, 3/26/09, Paul M. Grant wrote: > From: Paul M. Grant > Subject: [Pw_forum] Line 325 in bands_FS.f90 > To: "'PWSCF Forum'" > Date: Thursday, March 26, 2009, 10:34 PMI > While running bands_FS.x (espresso-4.0 distro) on the output > of an PW nscf > non-spin-polarized job, I get the following error: > > At line 325 of file bands_FS.f90 > Fortran runtime error: Bad real number in item 5 of list > input > > This only happens for my LSDA=F runs, spin-polarized are > OK. (BTW, the > LSDA=F run for Ni in example 08 does work. The only > difference is that > ex08 deals with only 8 bands and 1 formated line, whilst my > task computes 20 > taking up 3 formated lines.) Line 325 is in the LSDA=F > portion of the code > follows a commented-out read command line with explicit > formatting. I can't > see any problem with the output of my nscf run. Before I > start messing > around with the bands_FS.f90 source, has anyone else run > into this issue > (Eyvaz?)? Is it possible there is a "line > counting" error in the LSDA=F > portion when the band energy listing exceeds one line? > Sorry if I've made > some stupid blunder. > > Paul M. Grant, PhD > Physicist and Science Writer > Principal, W2AGZ Technologies > Visiting Scholar, Applied Physics, Stanford (2005-2008) > EPRI Science Fellow (Retired) > IBM Research Staff Member Emeritus > w2agz at pacbell.net > http://www.w2agz.com > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From w2agz at pacbell.net Fri Mar 27 00:14:31 2009 From: w2agz at pacbell.net (Paul M. Grant) Date: Thu, 26 Mar 2009 16:14:31 -0700 Subject: [Pw_forum] Line 325 in bands_FS.f90 In-Reply-To: <620097.49786.qm@web65711.mail.ac4.yahoo.com> References: <016001c9ae49$dcaada80$96008f80$@net> <620097.49786.qm@web65711.mail.ac4.yahoo.com> Message-ID: <017b01c9ae68$9f10a5f0$dd31f1d0$@net> Axel and Eyvaz, thanks guys for the quick feedback. Eyvaz, I'll send the files under separate cover...let me do a few more checks first so I don't wind up wasting your time. However, I am simply using standard pw.x nscf output. Perhaps some bad characters slipped in, but I don't see how. Incidentally, a number of post-processing tools like bands_FS.f90 parse the pw.x text output files. I wonder if future releases of PWscf will preserve the present layout. Already I've added a number of personal flags to electrons.f90 to help "grep" out stuff I want, but I don't think any of these are causing the present problem, as they're in the scf output, not nscf. Axel, thanks for the hexdump script. I use the distro supplied tool occasionally, but this is a nice wrapper. It reminds me of very useful byte editors we had in TSO/CMS, and fv.exe, an internal IBM utility we had in the original DOS. You're going to find this hilarious. I downloaded hexview.dat onto my Windoze laptop for a quick look, and then "samba-ed" to my Linux boxes. Of course, the newline rat-tracks were left behind, and the bash interpreter didn't like that "one bit." Regards, -Paul Paul M. Grant, PhD Physicist and Science Writer Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Eyvaz Isaev Sent: Thursday, March 26, 2009 2:15 PM To: PWSCF Forum Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 Dear Paul, I have just tested the code provided in 4.0.4, but with the output of 3.2. Both, Non-Spin polarized, and Spin-Polarized results worked well for Ni. And you can see from the line 325 that there is no limitation for bands numbers. Nevertheless, I will try the code with 4.0.4 output. By the way, it might be much helpful, if you send me your output file for which you have troubles. Bests, Eyvaz. --- On Thu, 3/26/09, Paul M. Grant wrote: > From: Paul M. Grant > Subject: [Pw_forum] Line 325 in bands_FS.f90 > To: "'PWSCF Forum'" > Date: Thursday, March 26, 2009, 10:34 PMI > While running bands_FS.x (espresso-4.0 distro) on the output > of an PW nscf > non-spin-polarized job, I get the following error: > > At line 325 of file bands_FS.f90 > Fortran runtime error: Bad real number in item 5 of list > input > > This only happens for my LSDA=F runs, spin-polarized are > OK. (BTW, the > LSDA=F run for Ni in example 08 does work. The only > difference is that > ex08 deals with only 8 bands and 1 formated line, whilst my > task computes 20 > taking up 3 formated lines.) Line 325 is in the LSDA=F > portion of the code > follows a commented-out read command line with explicit > formatting. I can't > see any problem with the output of my nscf run. Before I > start messing > around with the bands_FS.f90 source, has anyone else run > into this issue > (Eyvaz?)? Is it possible there is a "line > counting" error in the LSDA=F > portion when the band energy listing exceeds one line? > Sorry if I've made > some stupid blunder. > > Paul M. Grant, PhD > Physicist and Science Writer > Principal, W2AGZ Technologies > Visiting Scholar, Applied Physics, Stanford (2005-2008) > EPRI Science Fellow (Retired) > IBM Research Staff Member Emeritus > w2agz at pacbell.net > http://www.w2agz.com > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Fri Mar 27 00:29:37 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 26 Mar 2009 16:29:37 -0700 (PDT) Subject: [Pw_forum] Line 325 in bands_FS.f90 In-Reply-To: <017b01c9ae68$9f10a5f0$dd31f1d0$@net> Message-ID: <347405.96383.qm@web65708.mail.ac4.yahoo.com> Paul, OK, I'll wait for your output file. Anyway, I decided to put a new check for bands number, as one guy put more bands number that allowed (for n_last in input_FS) and then claimed that the code does not work. Bests, Eyvaz. --- On Fri, 3/27/09, Paul M. Grant wrote: > From: Paul M. Grant > Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 > To: eyvaz_isaev at yahoo.com, "'PWSCF Forum'" > Date: Friday, March 27, 2009, 2:14 AM > Axel and Eyvaz, thanks guys for the quick feedback. > > Eyvaz, I'll send the files under separate cover...let > me do a few more > checks first so I don't wind up wasting your time. > However, I am simply > using standard pw.x nscf output. Perhaps some bad > characters slipped in, but > I don't see how. Incidentally, a number of > post-processing tools like > bands_FS.f90 parse the pw.x text output files. I wonder if > future releases > of PWscf will preserve the present layout. Already > I've added a number of > personal flags to electrons.f90 to help "grep" > out stuff I want, but I don't > think any of these are causing the present problem, as > they're in the scf > output, not nscf. > > Axel, thanks for the hexdump script. I use the distro > supplied tool > occasionally, but this is a nice wrapper. It reminds me of > very useful byte > editors we had in TSO/CMS, and fv.exe, an internal IBM > utility we had in the > original DOS. You're going to find this hilarious. I > downloaded > hexview.dat onto my Windoze laptop for a quick look, and > then "samba-ed" to > my Linux boxes. Of course, the newline rat-tracks were > left behind, and the > bash interpreter didn't like that "one bit." > > Regards, -Paul > > > > Paul M. Grant, PhD > Physicist and Science Writer > Principal, W2AGZ Technologies > Visiting Scholar, Applied Physics, Stanford (2005-2008) > EPRI Science Fellow (Retired) > IBM Research Staff Member Emeritus > w2agz at pacbell.net > http://www.w2agz.com > ? > ? > > > -----Original Message----- > From: pw_forum-bounces at pwscf.org > [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of Eyvaz Isaev > Sent: Thursday, March 26, 2009 2:15 PM > To: PWSCF Forum > Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 > > > Dear Paul, > > I have just tested the code provided in 4.0.4, but with the > output of 3.2. > Both, Non-Spin polarized, and Spin-Polarized results worked > well for Ni. > > And you can see from the line 325 that there is no > limitation for bands > numbers. > > Nevertheless, I will try the code with 4.0.4 output. > By the way, it might be much helpful, if you send me your > output file for > which you have troubles. > > Bests, > Eyvaz. > > > --- On Thu, 3/26/09, Paul M. Grant > wrote: > > > From: Paul M. Grant > > Subject: [Pw_forum] Line 325 in bands_FS.f90 > > To: "'PWSCF Forum'" > > > Date: Thursday, March 26, 2009, 10:34 PMI > > While running bands_FS.x (espresso-4.0 distro) on the > output > > of an PW nscf > > non-spin-polarized job, I get the following error: > > > > At line 325 of file bands_FS.f90 > > Fortran runtime error: Bad real number in item 5 of > list > > input > > > > This only happens for my LSDA=F runs, spin-polarized > are > > OK. (BTW, the > > LSDA=F run for Ni in example 08 does work. The only > > difference is that > > ex08 deals with only 8 bands and 1 formated line, > whilst my > > task computes 20 > > taking up 3 formated lines.) Line 325 is in the > LSDA=F > > portion of the code > > follows a commented-out read command line with > explicit > > formatting. I can't > > see any problem with the output of my nscf run. > Before I > > start messing > > around with the bands_FS.f90 source, has anyone else > run > > into this issue > > (Eyvaz?)? Is it possible there is a "line > > counting" error in the LSDA=F > > portion when the band energy listing exceeds one line? > > > Sorry if I've made > > some stupid blunder. > > > > Paul M. Grant, PhD > > Physicist and Science Writer > > Principal, W2AGZ Technologies > > Visiting Scholar, Applied Physics, Stanford > (2005-2008) > > EPRI Science Fellow (Retired) > > IBM Research Staff Member Emeritus > > w2agz at pacbell.net > > http://www.w2agz.com > > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From pc229 at kent.ac.uk Fri Mar 27 00:48:27 2009 From: pc229 at kent.ac.uk (Pieremanuele Canepa) Date: Thu, 26 Mar 2009 23:48:27 +0000 Subject: [Pw_forum] I can't print my bands In-Reply-To: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> Message-ID: <8b443ba10903261648h4513c89ch517b4b6dc31b9ff9@mail.gmail.com> Dear all, nobody know how Can I figure out the band gap once I got the bands calculation with PWscf? Do I need to use the ruler or there is some particular feature allowing me to carry it out ? Many Thanks, Piero On Mon, Mar 23, 2009 at 7:07 PM, Pieremanuele Canepa wrote: > Dear all, > I am attempting to figure out how to print out a bands graph of my AFM > hematite. > Then I prepared the file band.in as explained in /Doc/INPUT_Band > and I attached it down here > &INPUTPP > prefix='band_BLYP', > outdir='/home/pc229/backup/ > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > filband='band_BLYP.out', > / > > if try to run it using bands.x I will get in my output file the following > error: > Program POST-PROC v.4.0.4 starts ... > Today is 23Mar2009 at 18:56:50 > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from bands : error # 1 > The bands code with constrained magnetization has not been tested > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > So, what I am suppose to do ? How can I print my bands?? > Thank you, Piero > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > -------------------------------------------------------- > -- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090326/f2a64fb7/attachment.htm From eyvaz_isaev at yahoo.com Fri Mar 27 01:10:31 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 26 Mar 2009 17:10:31 -0700 (PDT) Subject: [Pw_forum] I can't print my bands In-Reply-To: <8b443ba10903261648h4513c89ch517b4b6dc31b9ff9@mail.gmail.com> Message-ID: <436785.26913.qm@web65708.mail.ac4.yahoo.com> Dear Pieremanuele, First of all, I would recommend you reading some textbooks on Solid State Physics, as you have to know some basics to do such kind calculations. Quite recently I put a reply with a list of textbooks (only authors' name were mentioned) and reading (at least, one) of them is highly appreciated. If you can not understand what is a metal, semicondcutor (insulator), valence bands, conductivity bands, the Fermi level, band gap, density of states, then you will never understand what you are doing. In fact, these special terms are keywords to solve your particular problem with the band gap. I think this way (reading textbooks) is much more fruitful and convinient for you rather than I will tell you how to do it "mechanically" (not quantum-). Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 3/27/09, Pieremanuele Canepa wrote: > From: Pieremanuele Canepa > Subject: Re: [Pw_forum] I can't print my bands > To: pw_forum at pwscf.org > Date: Friday, March 27, 2009, 2:48 AM > Dear all, > nobody know how Can I figure out the band gap once I got > the bands > calculation with PWscf? Do I need to use the ruler or there > is some > particular feature allowing me to carry it out ? > Many Thanks, Piero > > On Mon, Mar 23, 2009 at 7:07 PM, Pieremanuele Canepa > wrote: > > > Dear all, > > I am attempting to figure out how to print out a > bands graph of my AFM > > hematite. > > Then I prepared the file band.in as explained in > /Doc/INPUT_Band > > and I attached it down here > > &INPUTPP > > prefix='band_BLYP', > > outdir='/home/pc229/backup/ > > > Counts/PWscf/Fe2O3_bulk/PWSCF/Fe2O3_bulk/opt_bulk_BLYP/', > > filband='band_BLYP.out', > > / > > > > if try to run it using bands.x I will get in my > output file the following > > error: > > Program POST-PROC v.4.0.4 starts ... > > Today is 23Mar2009 at 18:56:50 > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from bands : error # 1 > > The bands code with constrained magnetization has > not been tested > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > > > So, what I am suppose to do ? How can I print my > bands?? > > Thank you, Piero > > > > -- > > Pieremanuele Canepa > > Room 230 > > School of Physical Sciences, Ingram Building, > > University of Kent, Canterbury, Kent, > > CT2 7NH > > United Kingdom > > > -------------------------------------------------------- > > > > > > -- > Pieremanuele Canepa > Room 230 > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > ----------------------------------------------------------- > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From hqzhou at nju.edu.cn Fri Mar 27 05:28:04 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Fri, 27 Mar 2009 12:28:04 +0800 Subject: [Pw_forum] DMFT+LDA References: <166cd7c60903222004j791a20bbk92b86a0af7a92fff@mail.gmail.com> <49C9F57F.1080308@democritos.it> Message-ID: <6ED8A5CDC5CD43E8877F14E5B96E22F4@solarflare> Paolo, Does the snapshot you indicated the same as the cvs version accessed from SISSA's cvs root? Huiqun @Earth Sciences, Nanjing University, China ----- Original Message ----- From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Wednesday, March 25, 2009 5:12 PM Subject: Re: [Pw_forum] DMFT+LDA > DdrSmiLe wrote: > >> Another problem is I could not compile w90 in espresso-4.1CVS package. >> It showed that there are something loss in W90 package. > > use the link "[Download The Nightly CVS Tree Snapshot]" > from here: ttp://qe-forge.org/scm/?group_id=10 > The CVS package you mention wss an experiment and > might not be complete > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Fri Mar 27 08:27:49 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 27 Mar 2009 08:27:49 +0100 Subject: [Pw_forum] DMFT+LDA In-Reply-To: <6ED8A5CDC5CD43E8877F14E5B96E22F4@solarflare> References: <166cd7c60903222004j791a20bbk92b86a0af7a92fff@mail.gmail.com> <49C9F57F.1080308@democritos.it> <6ED8A5CDC5CD43E8877F14E5B96E22F4@solarflare> Message-ID: <29D387B6-5304-4BA9-B28D-93798DB84E6F@democritos.it> On Mar 27, 2009, at 5:28 , Huiqun Zhou wrote: > Does the snapshot you indicated the same as the cvs version > accessed from SISSA's cvs root? please? --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Mar 27 08:30:13 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 27 Mar 2009 08:30:13 +0100 Subject: [Pw_forum] I can't print my bands In-Reply-To: <8b443ba10903261648h4513c89ch517b4b6dc31b9ff9@mail.gmail.com> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <8b443ba10903261648h4513c89ch517b4b6dc31b9ff9@mail.gmail.com> Message-ID: <75895070-8AD8-4B6F-AE84-5DDD6F47B0B7@democritos.it> On Mar 27, 2009, at 24:48 , Pieremanuele Canepa wrote: > how Can I figure out the band gap once I got the bands calculation > with PWscf? the code prints either the Fermi energy (for metals) or the difference between the lowest unoccupied and highest occupied energy levels --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Mar 27 08:41:57 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 27 Mar 2009 08:41:57 +0100 Subject: [Pw_forum] Line 325 in bands_FS.f90 In-Reply-To: <017b01c9ae68$9f10a5f0$dd31f1d0$@net> References: <016001c9ae49$dcaada80$96008f80$@net> <620097.49786.qm@web65711.mail.ac4.yahoo.com> <017b01c9ae68$9f10a5f0$dd31f1d0$@net> Message-ID: <10536426-C224-4C3E-8616-1BE2DF1EF14B@democritos.it> On Mar 27, 2009, at 24:14 , Paul M. Grant wrote: > Incidentally, a number of post-processing tools like bands_FS.f90 > parse > the pw.x text output files. I wonder if future releases of PWscf > will preserve > the present layout. the layout will not change much, but from time to time there will be small changes and additions. Codes that read the output file should locate keywords and not rely on line counting. The safe way to read data is from the data file, though, not from the output. P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From saqib.javaid at ipcms.u-strasbg.fr Fri Mar 27 15:04:22 2009 From: saqib.javaid at ipcms.u-strasbg.fr (saqib.javaid at ipcms.u-strasbg.fr) Date: Fri, 27 Mar 2009 15:04:22 +0100 Subject: [Pw_forum] utilization of different Ultrasoft pseudopotentials Message-ID: <1238162662.49ccdce6d7322@ipcms.u-strasbg.fr> Dear PWSCF users, I have question regarding utilization of different type of Ultrasoft pseudopotentials. Is it correct to use different type of ultrasoft PS ( like rrkjus and Vanderbilt) for different atoms in a given system??? (e.g. one can use rrkjus PS of Cobalt and Vanderbilt PS of Mn with same XC functionals in a given system) With best regards Saqib JAVAID PhD Student University of Strasbourg Strasbourg, France. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From akohlmey at cmm.chem.upenn.edu Fri Mar 27 16:25:57 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 27 Mar 2009 11:25:57 -0400 Subject: [Pw_forum] utilization of different Ultrasoft pseudopotentials In-Reply-To: <1238162662.49ccdce6d7322@ipcms.u-strasbg.fr> References: <1238162662.49ccdce6d7322@ipcms.u-strasbg.fr> Message-ID: <1238167557.3104.3.camel@zero> On Fri, 2009-03-27 at 15:04 +0100, saqib.javaid at ipcms.u-strasbg.fr wrote: > Dear PWSCF users, > I have question regarding utilization of different type of Ultrasoft > pseudopotentials. Is it correct to use different type of ultrasoft PS ( like > rrkjus and Vanderbilt) for different atoms in a given system??? (e.g. one can > use rrkjus PS of Cobalt and Vanderbilt PS of Mn with same XC functionals in a > given system) yes. check out the FAQ. a. > With best regards > Saqib JAVAID > > PhD Student > University of Strasbourg > Strasbourg, France. > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From sclauzer at sissa.it Fri Mar 27 16:32:08 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 27 Mar 2009 16:32:08 +0100 Subject: [Pw_forum] electrical polarization calculations for non-collinear magnetism In-Reply-To: References: Message-ID: <49CCF178.10403@sissa.it> Xun-Wang Yan wrote: > &system > ibrav=14, > celldm(1)=9.73748132, celldm(2)=1.155067564,celldm(3)=1.000000, > celldm(4)=-0.144291712,celldm(5)=-0.500000,celldm(6)=0.288583423, > nat=12, ntyp=5, > ecutwfc=30, ecutrho=300, > report=10, > occupations='fixed',degauss=0.00, > noncolin=.true. > starting_magnetization(2)=0.5 > angle1(2)=90.0 > angle2(2)=0.0 > starting_magnetization(3)=0.5 > angle1(3)=90.0 > angle2(3)=120.0 > starting_magnetization(4)=0.5 > angle1(4)=90.0 > angle2(4)=-120.0 > nbnd=87 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 3 > from c_phase : error # 1 > Polarization only for insulators and no empty bands > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > I look over 'bp_c_phase.f90' , and find that electrical polarization > calculation is applicable for nspin=1 and nspin=2. I don't know if this calculation is available for noncolinear calculation, but if you pay attention to the error message, what it says is different. You need to deal with an insulator (and you are) and you must compute only nelec bands, i.e. NOT adding extra bands through the nbnd keyword, as you're doing. Retry after removing the nbnd line. GS > I want to know to how to modify the bp_c_phase.f90 to implement the > electrical polarization calculation for non-collinear magnetism. > Any comments are welcome , many thanks in advance. > > regards, > Xun-wang Yan > ======================================== > Institute of Theoretical Physics, CAS > Address: No.55, Zhong-Guan-Cun East Road > Beijing, China > Email: xwyan at itp.ac.cn > > yanxunwang2008 at gmail.com > =================== > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From amosleffler at gmail.com Fri Mar 27 17:21:04 2009 From: amosleffler at gmail.com (Amos Leffler) Date: Fri, 27 Mar 2009 09:21:04 -0700 Subject: [Pw_forum] Compilation of espresso-4.0.4 Message-ID: <61b264610903270921r1e010621q75ec73f7616c10f1@mail.gmail.com> Hi Forum, I have been trying to compile espresso-4.0.4 using LAM/MPI-7.1.4. The latter was correctly installed as noted by the program itself. I was able to configure the espresso program in parallel mode as noted by the output of the configure file. However, when I tried to use the "make all" command it started to compile but stopped in the file "fft_paralled.f90" on line 234 with the message "mpi_double_complex has no implicit type". I have run into the same error with OpenMpi-1.2.9 and Axel K. thought that it was due to problems with the OpenMpi. It should be noted that espresso does compile properly in single mode. Hopefully there is a simple work-around. Amos Leffler From akohlmey at cmm.chem.upenn.edu Fri Mar 27 18:01:20 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 27 Mar 2009 13:01:20 -0400 Subject: [Pw_forum] Compilation of espresso-4.0.4 In-Reply-To: <61b264610903270921r1e010621q75ec73f7616c10f1@mail.gmail.com> References: <61b264610903270921r1e010621q75ec73f7616c10f1@mail.gmail.com> Message-ID: <1238173280.3104.71.camel@zero> On Fri, 2009-03-27 at 09:21 -0700, Amos Leffler wrote: > Hi Forum, > I have been trying to compile espresso-4.0.4 using > LAM/MPI-7.1.4. The latter was correctly installed as noted by the > program itself. I was able to configure the espresso program in amos, that doesn't mean anything. can you compile a simple MPI program written in fortran with it? for example the 'pi' example referred to at one of the LAM/MPI tutorial. > parallel mode as noted by the output of the configure file. However, configure only tests whether a parallel compiler wrapper is installed and whether it can compile, link and run a simple, non-parallel executable. it assumes that it is installed correctly for parallel codes if it works on a minimal serial test. otherwise, you have much bigger problems than getting espresso compiled. > when I tried to use the "make all" command it started to compile but > stopped in the file "fft_paralled.f90" on line 234 with the message > "mpi_double_complex has no implicit type". I have run into the > same error with OpenMpi-1.2.9 and Axel K. thought that it was > due to problems with the OpenMpi. It should be noted that espresso as i was already noting in my previous response, this is not a problem of OpenMPI by itself, but a problem of an incorrect installation. so either you must have a messed up the installation of openmpi, or you have an incompatible or bogus mpif.h file somewhere where it is picked up by the mpi compiler wrapper. Both, OpenMPI and LAM/MPI work fine with espresso, and since you get the same error message with both packages, the latter seems more likely. > does compile properly in single mode. that only confirms that the problem is the MPI installation. > Hopefully there is a simple work-around. the simplest workaround is always to hire somebody, who knows about these things. the symptoms you describe are very obvious to check and sort out, so there should be enough people somewhere close to where you are located to have a look at your machine(s), detect what is messed up and sort it out. as discussed many times with people having compilation problems, these are very difficult to sort out remotely, particularly if there are indications of an inconsistent installation. it is obviously not a defect of quantum espresso by itself, or else you would not be the only person reporting it. there are a lot of people using either openmpi or lam/mpi. depending on how large your deployment is, you could also consider wiping the machine and installing a clean distribution. e.g. fedora has been working for me out of the box (it has suitable packages for openmpi, gfortran, atlas as part of the distribution) since version 6, i.e. since two years ago. i'd assume that others like debian 5, ubuntu 08XX or RHEL/CentOS 5.x work just as well. it only gets nasty, if you have to include support for a specific high-speed interconnect or include program launching through a specific batch system, both of which would require a custom compile. adding support for non-native compilers to openmpi can be done without a recompile, all you need is a suitable symlink to opal_wrapper (or opal_wrapper-64, or /etc/alternatives/mpicc in some distros) and a matching > > Amos Leffler please remember the policy of this forum to include your affiliation. thanks. axel. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From pc229 at kent.ac.uk Fri Mar 27 18:15:56 2009 From: pc229 at kent.ac.uk (Pieremanuele Canepa) Date: Fri, 27 Mar 2009 17:15:56 +0000 Subject: [Pw_forum] I can't print my bands In-Reply-To: <75895070-8AD8-4B6F-AE84-5DDD6F47B0B7@democritos.it> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <8b443ba10903261648h4513c89ch517b4b6dc31b9ff9@mail.gmail.com> <75895070-8AD8-4B6F-AE84-5DDD6F47B0B7@democritos.it> Message-ID: <8b443ba10903271015p38e71811u1c3c69128e785d27@mail.gmail.com> Pwscf also print the highest occupied and the lowest unoccupied band when you treat your system like an insulator using fixed ? because I cannot find those two value at the end of the output! I know, when you deal with a metal PWscf use to print out the Fermi energy! This question is actually very stupid, but I can't find them out ! Thanks On Fri, Mar 27, 2009 at 7:30 AM, Paolo Giannozzi wrote: > > On Mar 27, 2009, at 24:48 , Pieremanuele Canepa wrote: > > > how Can I figure out the band gap once I got the bands calculation > > with PWscf? > > the code prints either the Fermi energy (for metals) or the difference > between the lowest unoccupied and highest occupied energy levels > > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090327/bf2284c4/attachment.htm From baris.malcioglu at gmail.com Fri Mar 27 18:11:49 2009 From: baris.malcioglu at gmail.com (O. Baris Malcioglu) Date: Fri, 27 Mar 2009 18:11:49 +0100 Subject: [Pw_forum] Compilation of espresso-4.0.4 In-Reply-To: <61b264610903270921r1e010621q75ec73f7616c10f1@mail.gmail.com> References: <61b264610903270921r1e010621q75ec73f7616c10f1@mail.gmail.com> Message-ID: Hi Amos, On Fri, Mar 27, 2009 at 5:21 PM, Amos Leffler wrote: > Hi Forum, > ? ? ? ? ? ? ?I have been trying to compile espresso-4.0.4 using > LAM/MPI-7.1.4. ? The latter was correctly installed as noted by the > program itself. Please notice that this might or might not be true, trusting the installation script message in this matter is like asking someone if he/she is a liar or not. The answer is hardly useful. > I was able to configure the espresso program in > parallel mode as noted by the output of the configure file. ?However, > when I tried to use the "make all" command it started to compile but > stopped in the file "fft_paralled.f90" on line 234 with the message > ? "mpi_double_complex has no implicit type". ?I have run into the > same error with OpenMpi-1.2.9 and Axel K. thought that it was > due to problems with the OpenMpi. ?It should be noted that espresso > does compile properly in single mode. > ? ? ? ? ? ? Hopefully there is a simple work-around. I am afraid this still means you have an improperly set up parallel environment. Are you sure the mpif90 is able to define MPI related parameters in programs correctly? check if the mpif.h can be found, you are using the mpif90/f90 pair you intend to use (i.e. other broken installations in your path interfering etc. ) The simple solution is to make sure you clean "everything" from your old attempts to install parellel environment, make sure all the environment variables are set such that the intended compiler you will use is "default", and re-install parellel environment again. If this does not work, another easy way is to blame the distro you are using as broken and install a new one. By the way, I really advise you -not- to use "prepackaged" parallel environments (RPM etc.) . Download, and install yourself. Best, Baris Malcioglu SISSA CM sector > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? Amos Leffler > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From akohlmey at cmm.chem.upenn.edu Fri Mar 27 18:25:58 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 27 Mar 2009 13:25:58 -0400 Subject: [Pw_forum] Compilation of espresso-4.0.4 In-Reply-To: References: <61b264610903270921r1e010621q75ec73f7616c10f1@mail.gmail.com> Message-ID: <1238174758.3104.103.camel@zero> On Fri, 2009-03-27 at 18:11 +0100, O. Baris Malcioglu wrote: > By the way, I really advise you -not- to use "prepackaged" parallel > environments (RPM etc.) . Download, and install yourself. i wholeheartedly disagree with that. there are many more chances to mess up, if you compile yourself, particularly if you have little experience with that, rather than how precompiled packages are set up. it used to be different, but distribution vendors have become very good at providing suitable packages. i know this first hand from fedora and debian. cheers, axel. > > Best, > Baris Malcioglu > > SISSA CM sector > > > > > > > > > Amos Leffler > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Fri Mar 27 18:33:12 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 27 Mar 2009 18:33:12 +0100 Subject: [Pw_forum] I can't print my bands In-Reply-To: <8b443ba10903271015p38e71811u1c3c69128e785d27@mail.gmail.com> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <8b443ba10903261648h4513c89ch517b4b6dc31b9ff9@mail.gmail.com> <75895070-8AD8-4B6F-AE84-5DDD6F47B0B7@democritos.it> <8b443ba10903271015p38e71811u1c3c69128e785d27@mail.gmail.com> Message-ID: <49CD0DD8.1020704@democritos.it> Pieremanuele Canepa wrote: > Pwscf also print the highest occupied and the lowest unoccupied band > when you treat your system like an insulator using fixed ? of course it doesn't: by default, with fixed occupancies one calculates only occupied states. The code could print the highest occupied orbital energy, but this contains zero bits of information, since the zero of the energy is undefined P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From pc229 at kent.ac.uk Fri Mar 27 18:37:43 2009 From: pc229 at kent.ac.uk (pc229 at kent.ac.uk) Date: Fri, 27 Mar 2009 17:37:43 GMT Subject: [Pw_forum] I can't print my bands In-Reply-To: <49CD0DD8.1020704@democritos.it> References: <8b443ba10903231207s7b960b27i78a4312e957b0564@mail.gmail.com> <8b443ba10903261648h4513c89ch517b4b6dc31b9ff9@mail.gmail.com> <75895070-8AD8-4B6F-AE84-5DDD6F47B0B7@democritos.it> <8b443ba10903271015p38e71811u1c3c69128e785d27@mail.gmail.com> <49CD0DD8.1020704@democritos.it> Message-ID: Ok Thank you Paolo. Piero ----- Original Message ----- From: Paolo Giannozzi Date: Friday, March 27, 2009 5:33 pm Subject: Re: [Pw_forum] I can't print my bands To: PWSCF Forum > Pieremanuele Canepa wrote: > > > Pwscf also print the highest occupied? and the lowest > unoccupied band > > when you treat your system like an insulator using fixed ? > > of course it doesn't: by default, with fixed occupancies one > calculates only occupied states. The code could print the > highest occupied orbital energy, but this contains zero bits > of information, since the zero of the energy is undefined > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > --- Pieremanuele Canepa Room 230 School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090327/91504f87/attachment.htm From marcel at physik.tu-berlin.de Fri Mar 27 15:17:57 2009 From: marcel at physik.tu-berlin.de (Marcel Mohr) Date: Fri, 27 Mar 2009 15:17:57 +0100 (CET) Subject: [Pw_forum] utilization of different Ultrasoft pseudopotentials In-Reply-To: <1238162662.49ccdce6d7322@ipcms.u-strasbg.fr> References: <1238162662.49ccdce6d7322@ipcms.u-strasbg.fr> Message-ID: On Fri, 27 Mar 2009, saqib.javaid at ipcms.u-strasbg.fr wrote: > > Dear PWSCF users, > I have question regarding utilization of different type of Ultrasoft > pseudopotentials. Is it correct to use different type of ultrasoft PS ( like > rrkjus and Vanderbilt) for different atoms in a given system??? (e.g. one can > use rrkjus PS of Cobalt and Vanderbilt PS of Mn with same XC functionals in a > given system) There is a similar question from beginning of this month, and the answer I remember is yes, as long as they use the same XC functional (as you stated) However I got a question arising from this, too. Why are rrkj pseudos sometimes called ultrasoft? In the book by Richard Martin the terms "ultra-soft" and "norm-conserving" are opposites, so only Vanderbuilt pseudos or (PAW) are "ultrasoft". However Troullier-Martins and rrkj are norm-conserving and thus I conclude "not" ultrasoft ?! I would greatly acknowledge any comment. Cheers Marcel From akohlmey at cmm.chem.upenn.edu Fri Mar 27 19:20:30 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 27 Mar 2009 14:20:30 -0400 Subject: [Pw_forum] utilization of different Ultrasoft pseudopotentials In-Reply-To: References: <1238162662.49ccdce6d7322@ipcms.u-strasbg.fr> Message-ID: <1238178030.3104.117.camel@zero> On Fri, 2009-03-27 at 15:17 +0100, Marcel Mohr wrote: > On Fri, 27 Mar 2009, saqib.javaid at ipcms.u-strasbg.fr wrote: > > > > > Dear PWSCF users, > > I have question regarding utilization of different type of Ultrasoft > > pseudopotentials. Is it correct to use different type of ultrasoft PS ( like > > rrkjus and Vanderbilt) for different atoms in a given system??? (e.g. one can > > use rrkjus PS of Cobalt and Vanderbilt PS of Mn with same XC functionals in a > > given system) > > There is a similar question from beginning of this month, and the answer I > remember is yes, as long as they use the same XC functional (as you > stated) > > However I got a question arising from this, too. > > Why are rrkj pseudos sometimes called ultrasoft? this was referring to "rrkjus" which are indeed ultrasoft. note the additional "us". axel. > In the book by Richard > Martin the terms "ultra-soft" and "norm-conserving" are opposites, so only > Vanderbuilt pseudos or (PAW) are "ultrasoft". > However Troullier-Martins and rrkj are norm-conserving and thus I > conclude "not" ultrasoft ?! > > I would greatly acknowledge any comment. > > Cheers > Marcel > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From spaul at ncsu.edu Fri Mar 27 20:40:58 2009 From: spaul at ncsu.edu (Sujata Paul) Date: Fri, 27 Mar 2009 15:40:58 -0400 (EDT) Subject: [Pw_forum] PP for Planar average of all |psi|^2 Message-ID: <35489.152.14.74.129.1238182858.squirrel@webmail.ncsu.edu> Hi, I have a molecule adsorbed on metal[Pd-(001)] surface. I was trying to do a Post Processing (pp.x) using "plot_num=9". I used /espresso-4.0.4. I got this error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from punch_plot : error # 1 no longer implemented, see PP/plan_avg.f90 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% So I guessed "plot_num=9" is not implemented in post processing. After I got this error I tried the "plan_avg.x" executable with this input file: ========================================= &inputpp prefix='*', outdir = './' filplot = '*.psi-plan_avg.pot', / ========================================= This produced the output file without any CRASH file in the directory. The output file stops after it wrote the usual header. In the directory there is a "*.psi-plan_avg.pot" file but it was empty. So I don't understand what is wrong? Please help me. -- SUJATA PAUL GRADUATE STUDENT PHYSICS DEPARTMENT NORTH CAROLINA STATE UNIVERSITY USA From snd2mra at yahoo.com Fri Mar 27 21:15:08 2009 From: snd2mra at yahoo.com (snd2mra at yahoo.com) Date: Fri, 27 Mar 2009 13:15:08 -0700 (PDT) Subject: [Pw_forum] Compilation Error - Cygwin - PGI 8.0.4 Compilers Message-ID: <358563.71749.qm@web53308.mail.re2.yahoo.com> Dear Giannozzi, Thanks for the reply. I tried commenting the 'stack.o' in the 'Makefile' present in clib/, without altering the contents of 'make.depend'. Now it proceeds all the way upto compiling 'pw.x', but could not find 'clib.a' and quit with the following error. Any suggestions will greatly be appreciated. Thank you. - Madan ---------------------------------------- Madan Mithra .L.M Senior Research Fellow Dept.of Physics Indian Institute of Science Bangalore - 560 012 INDIA ......................................... e-mail : mit at physics.iisc.ernet.in : snd2mra at yahoo.com Phone : 91-80-22932313 (Lab) : 91-80-22932918 (Hostel-S 46) FAX : (080) 360 2602 ----------------------------------------- ---- Error ----- Appending add_vuspsi_nc.o Appending add_vuspsi.o Appending add_efield.o Appending add_bfield.o Appending a2fmod.o ranlib libpw.a make[1]: *** No rule to make target `../clib/clib.a', needed by `pw.x'. Stop. make[1]: Leaving directory `/d/Comp/p404new/PW' make: *** [pw] Error 2 ---------------------------------- ----- Contents of the Makefile present in clib/ ---------- # Makefile for clib include ../make.sys OBJS = \ # stack.o \ c_mkdir.o \ cptimer.o \ fft_stick.o \ indici.o \ memstat.o \ qsort.o all : clib.a clib.a : $(OBJS) $(AR) $(ARFLAGS) $@ $? $(RANLIB) $@ source : co -l $(OBJS:.o=.c) clean : - rm -f clib.a *.o *.mod *.i core* include make.depend ------------- --- On Wed, 3/25/09, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Compilation Error - Cygwin - PGI 8.0.4 Compilers > To: snd2mra at yahoo.com, "PWSCF Forum" > Date: Wednesday, March 25, 2009, 2:06 AM > On Mar 24, 2009, at 19:58 , snd2mra at yahoo.com wrote: > > > checking for dummy main to link with Fortran > libraries... unknown > > configure: error: linking to Fortran libraries from C > fails > > in the cvs version you may try "configure > --disable-check" > > > PGC-F-0206-Can't find include file sys/resource.h > (stack.c: 11) > > > clib/stack.c is used only by the Intel compiler, so you can > just > comment the routine stack.c > > P. > --- > Paolo Giannozzi, Democritos and University of Udine, Italy From akohlmey at cmm.chem.upenn.edu Fri Mar 27 21:19:24 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 27 Mar 2009 16:19:24 -0400 Subject: [Pw_forum] Compilation Error - Cygwin - PGI 8.0.4 Compilers In-Reply-To: <358563.71749.qm@web53308.mail.re2.yahoo.com> References: <358563.71749.qm@web53308.mail.re2.yahoo.com> Message-ID: <1238185164.7843.1.camel@zero> On Fri, 2009-03-27 at 13:15 -0700, snd2mra at yahoo.com wrote: > Dear Giannozzi, > > Thanks for the reply. I tried commenting the 'stack.o' in the 'Makefile' present in clib/, without altering the contents of 'make.depend'. Now it proceeds all the way upto compiling 'pw.x', but could not find 'clib.a' and quit with the following error. Any suggestions will greatly be appreciated. please read up on makefile syntax. you not only commented out one object but all lines following with a continuation character '\'. try just deleting it. axel. > Thank you. > > - Madan > > ---------------------------------------- > Madan Mithra .L.M > Senior Research Fellow > Dept.of Physics > Indian Institute of Science > Bangalore - 560 012 > INDIA > ......................................... > e-mail : mit at physics.iisc.ernet.in > : snd2mra at yahoo.com > Phone : 91-80-22932313 (Lab) > : 91-80-22932918 (Hostel-S 46) > FAX : (080) 360 2602 > ----------------------------------------- > > > ---- Error ----- > Appending add_vuspsi_nc.o > Appending add_vuspsi.o > Appending add_efield.o > Appending add_bfield.o > Appending a2fmod.o > ranlib libpw.a > make[1]: *** No rule to make target `../clib/clib.a', needed by `pw.x'. Stop. > make[1]: Leaving directory `/d/Comp/p404new/PW' > make: *** [pw] Error 2 > ---------------------------------- > > > ----- Contents of the Makefile present in clib/ ---------- > # Makefile for clib > > include ../make.sys > > OBJS = \ > # stack.o \ > c_mkdir.o \ > cptimer.o \ > fft_stick.o \ > indici.o \ > memstat.o \ > qsort.o > > all : clib.a > > clib.a : $(OBJS) > $(AR) $(ARFLAGS) $@ $? > $(RANLIB) $@ > > source : > co -l $(OBJS:.o=.c) > > clean : > - rm -f clib.a *.o *.mod *.i core* > > include make.depend > ------------- > > > --- On Wed, 3/25/09, Paolo Giannozzi wrote: > > > From: Paolo Giannozzi > > Subject: Re: [Pw_forum] Compilation Error - Cygwin - PGI 8.0.4 Compilers > > To: snd2mra at yahoo.com, "PWSCF Forum" > > Date: Wednesday, March 25, 2009, 2:06 AM > > On Mar 24, 2009, at 19:58 , snd2mra at yahoo.com wrote: > > > > > checking for dummy main to link with Fortran > > libraries... unknown > > > configure: error: linking to Fortran libraries from C > > fails > > > > in the cvs version you may try "configure > > --disable-check" > > > > > PGC-F-0206-Can't find include file sys/resource.h > > (stack.c: 11) > > > > > > clib/stack.c is used only by the Intel compiler, so you can > > just > > comment the routine stack.c > > > > P. > > --- > > Paolo Giannozzi, Democritos and University of Udine, Italy > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Fri Mar 27 21:22:53 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 27 Mar 2009 21:22:53 +0100 Subject: [Pw_forum] Compilation Error - Cygwin - PGI 8.0.4 Compilers In-Reply-To: <358563.71749.qm@web53308.mail.re2.yahoo.com> References: <358563.71749.qm@web53308.mail.re2.yahoo.com> Message-ID: On Mar 27, 2009, at 21:15 , snd2mra at yahoo.com wrote: > Thanks for the reply. I tried commenting the 'stack.o' > in the 'Makefile' present in clib/ bad idea. Replace stack.c with the following. /* Copyright (C) 2007-2008 Quantum-Espressogroup This file is distributed under the terms of the GNU General Public License. See the file `License' in the root directory of the present distribution, or http://www.gnu.org/copyleft/gpl.txt . */ #include "c_defs.h" #include #include #ifdef __INTEL #include void F77_FUNC_(remove_stack_limit,REMOVE_STACK_LIMIT) (void) { struct rlimit rlim = { RLIM_INFINITY, RLIM_INFINITY }; /* Modified according to Cesar Da Silva suggestions */ if ( setrlimit(RLIMIT_STACK, &rlim) == -1 ) { if ( getrlimit(RLIMIT_STACK, &rlim) == 0 ) { rlim.rlim_cur = rlim.rlim_max; if ( setrlimit(RLIMIT_STACK, &rlim) == 0 ) { getrlimit(RLIMIT_STACK, &rlim); } else { perror(" Cannot set stack size to new value"); } } } } #else void F77_FUNC_(remove_stack_limit,REMOVE_STACK_LIMIT) (void) { } #endif --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Mar 27 21:25:10 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 27 Mar 2009 21:25:10 +0100 Subject: [Pw_forum] PP for Planar average of all |psi|^2 In-Reply-To: <35489.152.14.74.129.1238182858.squirrel@webmail.ncsu.edu> References: <35489.152.14.74.129.1238182858.squirrel@webmail.ncsu.edu> Message-ID: <82BF1DE5-1C17-4CB4-BC28-9584142F4509@democritos.it> On Mar 27, 2009, at 20:40 , Sujata Paul wrote: > &inputpp > prefix='*', > outdir = './' > filplot = '*.psi-plan_avg.pot', > / "prefix" and "outdir" must be the same as in the preceding scf or non-scf calculation. Setting prefix to '*" is an extraordinarily bad idea P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From yanxunwang2008 at gmail.com Sat Mar 28 06:25:58 2009 From: yanxunwang2008 at gmail.com (Xun-Wang Yan) Date: Sat, 28 Mar 2009 13:25:58 +0800 Subject: [Pw_forum] electrical polarization calculations for non-collinear magnetism In-Reply-To: <49CCF178.10403@sissa.it> References: <49CCF178.10403@sissa.it> Message-ID: Dear Gabriele Sclauzero, Thanks for your reply, the electric polarization calculation for noncolinear magnetism is not available for espresso-4.0.4 version, which can be found from the code 'bp_c_phase.f90'. For this calculation , the nelec bands(in my calculation,87 bands) should be dealt with. I found the 'nscf' calculation is finished, and next step to calculate electric polarization with berry phase method is not implemented, i.e.the running process stop at the code 'bp_c_phase.f90' . In bp_c_phase.f90, the nspin=1 and nspin=2 cases is supported, there is not noncolin=.true. case. how to modify the bp_c_phase.f90 to include the noncolin=.true. case for electric polarization calculation? your suggestion and comment are expected. Bests Xun-Wang 2009/3/27 Gabriele Sclauzero > > Xun-Wang Yan wrote: > > &system > > ibrav=14, > > celldm(1)=9.73748132, celldm(2)=1.155067564,celldm(3)=1.000000, > > celldm(4)=-0.144291712,celldm(5)=-0.500000,celldm(6)=0.288583423, > > nat=12, ntyp=5, > > ecutwfc=30, ecutrho=300, > > report=10, > > occupations='fixed',degauss=0.00, > > noncolin=.true. > > starting_magnetization(2)=0.5 > > angle1(2)=90.0 > > angle2(2)=0.0 > > starting_magnetization(3)=0.5 > > angle1(3)=90.0 > > angle2(3)=120.0 > > starting_magnetization(4)=0.5 > > angle1(4)=90.0 > > angle2(4)=-120.0 > > nbnd=87 > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > task # 3 > > from c_phase : error # 1 > > Polarization only for insulators and no empty bands > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > I look over 'bp_c_phase.f90' , and find that electrical polarization > > calculation is applicable for nspin=1 and nspin=2. > > I don't know if this calculation is available for noncolinear calculation, > but if you pay > attention to the error message, what it says is different. You need to deal > with an > insulator (and you are) and you must compute only nelec bands, i.e. NOT > adding extra bands > through the nbnd keyword, as you're doing. > Retry after removing the nbnd line. > > GS > > > > I want to know to how to modify the bp_c_phase.f90 to implement the > > electrical polarization calculation for non-collinear magnetism. > > Any comments are welcome , many thanks in advance. > > > > regards, > > Xun-wang Yan > > ======================================== > > Institute of Theoretical Physics, CAS > > Address: No.55, Zhong-Guan-Cun East Road > > Beijing, China > > Email: xwyan at itp.ac.cn > > > > yanxunwang2008 at gmail.com > > =================== > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090328/65ba7b23/attachment.htm From ding.y1ding at gmail.com Sat Mar 28 13:03:03 2009 From: ding.y1ding at gmail.com (ding yi) Date: Sat, 28 Mar 2009 20:03:03 +0800 Subject: [Pw_forum] Pw_forum Digest, Vol 21, Issue 81 In-Reply-To: References: Message-ID: Subject: Re: Line 325 in bands_FS.f90 I think that there is a mistake in the bands_FS.f90. In the bands_FS.f90, line 310," backspace(5) " should be replace by " ! back nlines+1 positions (number of eigenvalues lines plus one blank line) ! do k=1,nlines+1 backspace(5) enddo ! " The bands_FS counts the lines of the spin-polarized calculations, while for the non-spin-polarised case it forgets to counts. Yi Ding, Ph.D Candidate Department of Physics, Tsinghua University Beijing 100084, P.R.China 2009/3/27 : > Send Pw_forum mailing list submissions to > ? ? ? ?pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > ? ? ? ?http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > ? ? ? ?pw_forum-request at pwscf.org > > You can reach the person managing the list at > ? ? ? ?pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > ? 1. Line 325 in bands_FS.f90 (Paul M. Grant) > ? 2. Re: Line 325 in bands_FS.f90 (Axel Kohlmeyer) > ? 3. Re: Line 325 in bands_FS.f90 (Eyvaz Isaev) > ? 4. Re: Line 325 in bands_FS.f90 (Eyvaz Isaev) > ? 5. Re: Line 325 in bands_FS.f90 (Paul M. Grant) > ? 6. Re: Line 325 in bands_FS.f90 (Eyvaz Isaev) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 26 Mar 2009 12:34:19 -0700 > From: "Paul M. Grant" > Subject: [Pw_forum] Line 325 in bands_FS.f90 > To: "'PWSCF Forum'" > Message-ID: <016001c9ae49$dcaada80$96008f80$@net> > Content-Type: text/plain; charset="us-ascii" > > While running bands_FS.x (espresso-4.0 distro) on the output of an PW nscf > non-spin-polarized job, I get the following error: > > At line 325 of file bands_FS.f90 > Fortran runtime error: Bad real number in item 5 of list input > > This only happens for my LSDA=F runs, spin-polarized are OK. ?(BTW, the > LSDA=F run for Ni in example 08 does work. ?The only difference is that > ex08 deals with only 8 bands and 1 formated line, whilst my task computes 20 > taking up 3 formated lines.) ?Line 325 is in the LSDA=F portion of the code > follows a commented-out read command line with explicit formatting. ?I can't > see any problem with the output of my nscf run. ?Before I start messing > around with the bands_FS.f90 source, has anyone else run into this issue > (Eyvaz?)? ?Is it possible there is a "line counting" error in the LSDA=F > portion when the band energy listing exceeds one line? ?Sorry if I've made > some stupid blunder. > > Paul M. Grant, PhD > Physicist and Science Writer > Principal, W2AGZ Technologies > Visiting Scholar, Applied Physics, Stanford (2005-2008) > EPRI Science Fellow (Retired) > IBM Research Staff Member Emeritus > w2agz at pacbell.net > http://www.w2agz.com > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090326/6d182aed/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Thu, 26 Mar 2009 16:00:07 -0400 > From: Axel Kohlmeyer > Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 > To: PWSCF Forum > Message-ID: <1238097607.3704.119.camel at zero> > Content-Type: text/plain; charset="us-ascii" > > On Thu, 2009-03-26 at 12:34 -0700, Paul M. Grant wrote: >> While running bands_FS.x (espresso-4.0 distro) on the output of an PW >> nscf non-spin-polarized job, I get the following error: >> >> At line 325 of file bands_FS.f90 >> >> Fortran runtime error: Bad real number in item 5 of list input > > paul, > > please check your input carefully with hexdump to make > sure you have no non-ascii characters in there. with some > fonts it is hard to tell. i'm attaching a wrapper script that > i use myself, which is little bit easier to read (at least for > me, as it emulates the hexdumper display that i was > using back in the days when i was hacking 6502 processors > which almost broke the 1MHz barrier...). i miss begin able > to fix bugs in running programs by replacing goto opcodes > with NOPs... ;-) > > cheers, > ? axel. > > >> >> This only happens for my LSDA=F runs, spin-polarized are OK. ?(BTW, >> the LSDA=F run for Ni in example 08 does work. ?The only difference is >> that >> >> ex08 deals with only 8 bands and 1 formated line, whilst my task >> computes 20 taking up 3 formated lines.) ?Line 325 is in the LSDA=F >> portion of the code follows a commented-out read command line with >> explicit formatting. ?I can't see any problem with the output of my >> nscf run. ?Before I start messing around with the bands_FS.f90 source, >> has anyone else run into this issue (Eyvaz?)? ?Is it possible there is >> a "line counting" error in the LSDA=F portion when the band energy >> listing exceeds one line? ?Sorry if I've made some stupid blunder. >> >> Paul M. Grant, PhD >> >> Physicist and Science Writer >> >> Principal, W2AGZ Technologies >> >> Visiting Scholar, Applied Physics, Stanford (2005-2008) >> >> EPRI Science Fellow (Retired) >> >> IBM Research Staff Member Emeritus >> >> w2agz at pacbell.net >> >> http://www.w2agz.com >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ======================================================================= > Axel Kohlmeyer ? akohlmey at cmm.chem.upenn.edu ? http://www.cmm.upenn.edu > ? Center for Molecular Modeling ? -- ? University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, ?fax: 1-215-573-6233, ?office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: hexview > Type: application/x-shellscript > Size: 231 bytes > Desc: not available > Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090326/e2878900/attachment-0001.bin > > ------------------------------ > > Message: 3 > Date: Thu, 26 Mar 2009 13:50:46 -0700 (PDT) > From: Eyvaz Isaev > Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 > To: PWSCF Forum > Message-ID: <593553.85654.qm at web65705.mail.ac4.yahoo.com> > Content-Type: text/plain; charset=us-ascii > > > Dear Paul, > > Thanks reporting the error. I will look at why it happens. > > Bests, > Eyvaz. > > > --- On Thu, 3/26/09, Paul M. Grant wrote: > >> From: Paul M. Grant >> Subject: [Pw_forum] Line 325 in bands_FS.f90 >> To: "'PWSCF Forum'" >> Date: Thursday, March 26, 2009, 10:34 PM >> While running bands_FS.x (espresso-4.0 distro) on the output >> of an PW nscf >> non-spin-polarized job, I get the following error: >> >> At line 325 of file bands_FS.f90 >> Fortran runtime error: Bad real number in item 5 of list >> input >> >> This only happens for my LSDA=F runs, spin-polarized are >> OK. ?(BTW, the >> LSDA=F run for Ni in example 08 does work. ?The only >> difference is that >> ex08 deals with only 8 bands and 1 formated line, whilst my >> task computes 20 >> taking up 3 formated lines.) ?Line 325 is in the LSDA=F >> portion of the code >> follows a commented-out read command line with explicit >> formatting. ?I can't >> see any problem with the output of my nscf run. ?Before I >> start messing >> around with the bands_FS.f90 source, has anyone else run >> into this issue >> (Eyvaz?)? ?Is it possible there is a "line >> counting" error in the LSDA=F >> portion when the band energy listing exceeds one line? >> Sorry if I've made >> some stupid blunder. >> >> Paul M. Grant, PhD >> Physicist and Science Writer >> Principal, W2AGZ Technologies >> Visiting Scholar, Applied Physics, Stanford (2005-2008) >> EPRI Science Fellow (Retired) >> IBM Research Staff Member Emeritus >> w2agz at pacbell.net >> http://www.w2agz.com >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 4 > Date: Thu, 26 Mar 2009 14:14:31 -0700 (PDT) > From: Eyvaz Isaev > Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 > To: PWSCF Forum > Message-ID: <620097.49786.qm at web65711.mail.ac4.yahoo.com> > Content-Type: text/plain; charset=us-ascii > > > Dear Paul, > > I have just tested the code provided in 4.0.4, but with the output of 3.2. Both, Non-Spin polarized, and Spin-Polarized results worked well for Ni. > > And you can see from the line 325 that there is no limitation for bands numbers. > > Nevertheless, I will try the code with 4.0.4 output. > By the way, it might be much helpful, if you send me your output file for which you have troubles. > > Bests, > Eyvaz. > > > --- On Thu, 3/26/09, Paul M. Grant wrote: > >> From: Paul M. Grant >> Subject: [Pw_forum] Line 325 in bands_FS.f90 >> To: "'PWSCF Forum'" >> Date: Thursday, March 26, 2009, 10:34 PMI >> While running bands_FS.x (espresso-4.0 distro) on the output >> of an PW nscf >> non-spin-polarized job, I get the following error: >> >> At line 325 of file bands_FS.f90 >> Fortran runtime error: Bad real number in item 5 of list >> input >> >> This only happens for my LSDA=F runs, spin-polarized are >> OK. ?(BTW, the >> LSDA=F run for Ni in example 08 does work. ?The only >> difference is that >> ex08 deals with only 8 bands and 1 formated line, whilst my >> task computes 20 >> taking up 3 formated lines.) ?Line 325 is in the LSDA=F >> portion of the code >> follows a commented-out read command line with explicit >> formatting. ?I can't >> see any problem with the output of my nscf run. ?Before I >> start messing >> around with the bands_FS.f90 source, has anyone else run >> into this issue >> (Eyvaz?)? ?Is it possible there is a "line >> counting" error in the LSDA=F >> portion when the band energy listing exceeds one line? >> Sorry if I've made >> some stupid blunder. >> >> Paul M. Grant, PhD >> Physicist and Science Writer >> Principal, W2AGZ Technologies >> Visiting Scholar, Applied Physics, Stanford (2005-2008) >> EPRI Science Fellow (Retired) >> IBM Research Staff Member Emeritus >> w2agz at pacbell.net >> http://www.w2agz.com >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 5 > Date: Thu, 26 Mar 2009 16:14:31 -0700 > From: "Paul M. Grant" > Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 > To: , ? ?"'PWSCF Forum'" > Message-ID: <017b01c9ae68$9f10a5f0$dd31f1d0$@net> > Content-Type: text/plain; ? ? ? charset="iso-8859-1" > > Axel and Eyvaz, thanks guys for the quick feedback. > > Eyvaz, I'll send the files under separate cover...let me do a few more > checks first so I don't wind up wasting your time. ?However, I am simply > using standard pw.x nscf output. Perhaps some bad characters slipped in, but > I don't see how. Incidentally, a number of post-processing tools like > bands_FS.f90 parse the pw.x text output files. ?I wonder if future releases > of PWscf will preserve the present layout. ?Already I've added a number of > personal flags to electrons.f90 to help "grep" out stuff I want, but I don't > think any of these are causing the present problem, as they're in the scf > output, not nscf. > > Axel, thanks for the hexdump script. I use the distro supplied tool > occasionally, but this is a nice wrapper. ?It reminds me of very useful byte > editors we had in TSO/CMS, and fv.exe, an internal IBM utility we had in the > original DOS. ?You're going to find this hilarious. ?I downloaded > hexview.dat onto my Windoze laptop for a quick look, and then "samba-ed" to > my Linux boxes. ?Of course, the newline rat-tracks were left behind, and the > bash interpreter didn't like that "one bit." > > Regards, -Paul > > > > Paul M. Grant, PhD > Physicist and Science Writer > Principal, W2AGZ Technologies > Visiting Scholar, Applied Physics, Stanford (2005-2008) > EPRI Science Fellow (Retired) > IBM Research Staff Member Emeritus > w2agz at pacbell.net > http://www.w2agz.com > ? > ? > > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of Eyvaz Isaev > Sent: Thursday, March 26, 2009 2:15 PM > To: PWSCF Forum > Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 > > > Dear Paul, > > I have just tested the code provided in 4.0.4, but with the output of 3.2. > Both, Non-Spin polarized, and Spin-Polarized results worked well for Ni. > > And you can see from the line 325 that there is no limitation for bands > numbers. > > Nevertheless, I will try the code with 4.0.4 output. > By the way, it might be much helpful, if you send me your output file for > which you have troubles. > > Bests, > Eyvaz. > > > --- On Thu, 3/26/09, Paul M. Grant wrote: > >> From: Paul M. Grant >> Subject: [Pw_forum] Line 325 in bands_FS.f90 >> To: "'PWSCF Forum'" >> Date: Thursday, March 26, 2009, 10:34 PMI >> While running bands_FS.x (espresso-4.0 distro) on the output >> of an PW nscf >> non-spin-polarized job, I get the following error: >> >> At line 325 of file bands_FS.f90 >> Fortran runtime error: Bad real number in item 5 of list >> input >> >> This only happens for my LSDA=F runs, spin-polarized are >> OK. ?(BTW, the >> LSDA=F run for Ni in example 08 does work. ?The only >> difference is that >> ex08 deals with only 8 bands and 1 formated line, whilst my >> task computes 20 >> taking up 3 formated lines.) ?Line 325 is in the LSDA=F >> portion of the code >> follows a commented-out read command line with explicit >> formatting. ?I can't >> see any problem with the output of my nscf run. ?Before I >> start messing >> around with the bands_FS.f90 source, has anyone else run >> into this issue >> (Eyvaz?)? ?Is it possible there is a "line >> counting" error in the LSDA=F >> portion when the band energy listing exceeds one line? >> Sorry if I've made >> some stupid blunder. >> >> Paul M. Grant, PhD >> Physicist and Science Writer >> Principal, W2AGZ Technologies >> Visiting Scholar, Applied Physics, Stanford (2005-2008) >> EPRI Science Fellow (Retired) >> IBM Research Staff Member Emeritus >> w2agz at pacbell.net >> http://www.w2agz.com >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ------------------------------ > > Message: 6 > Date: Thu, 26 Mar 2009 16:29:37 -0700 (PDT) > From: Eyvaz Isaev > Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 > To: PWSCF Forum > Message-ID: <347405.96383.qm at web65708.mail.ac4.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > > Paul, > > OK, I'll wait for your output file. Anyway, I decided to put a new check for bands number, as one guy put more bands number that allowed (for n_last in ?input_FS) and then claimed that the code does not work. > > Bests, > Eyvaz. > > > > --- On Fri, 3/27/09, Paul M. Grant wrote: > >> From: Paul M. Grant >> Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 >> To: eyvaz_isaev at yahoo.com, "'PWSCF Forum'" >> Date: Friday, March 27, 2009, 2:14 AM >> Axel and Eyvaz, thanks guys for the quick feedback. >> >> Eyvaz, I'll send the files under separate cover...let >> me do a few more >> checks first so I don't wind up wasting your time. >> However, I am simply >> using standard pw.x nscf output. Perhaps some bad >> characters slipped in, but >> I don't see how. Incidentally, a number of >> post-processing tools like >> bands_FS.f90 parse the pw.x text output files. ?I wonder if >> future releases >> of PWscf will preserve the present layout. ?Already >> I've added a number of >> personal flags to electrons.f90 to help "grep" >> out stuff I want, but I don't >> think any of these are causing the present problem, as >> they're in the scf >> output, not nscf. >> >> Axel, thanks for the hexdump script. I use the distro >> supplied tool >> occasionally, but this is a nice wrapper. ?It reminds me of >> very useful byte >> editors we had in TSO/CMS, and fv.exe, an internal IBM >> utility we had in the >> original DOS. ?You're going to find this hilarious. ?I >> downloaded >> hexview.dat onto my Windoze laptop for a quick look, and >> then "samba-ed" to >> my Linux boxes. ?Of course, the newline rat-tracks were >> left behind, and the >> bash interpreter didn't like that "one bit." >> >> Regards, -Paul >> >> >> >> Paul M. Grant, PhD >> Physicist and Science Writer >> Principal, W2AGZ Technologies >> Visiting Scholar, Applied Physics, Stanford (2005-2008) >> EPRI Science Fellow (Retired) >> IBM Research Staff Member Emeritus >> w2agz at pacbell.net >> http://www.w2agz.com >> ? >> ? >> >> >> -----Original Message----- >> From: pw_forum-bounces at pwscf.org >> [mailto:pw_forum-bounces at pwscf.org] On >> Behalf Of Eyvaz Isaev >> Sent: Thursday, March 26, 2009 2:15 PM >> To: PWSCF Forum >> Subject: Re: [Pw_forum] Line 325 in bands_FS.f90 >> >> >> Dear Paul, >> >> I have just tested the code provided in 4.0.4, but with the >> output of 3.2. >> Both, Non-Spin polarized, and Spin-Polarized results worked >> well for Ni. >> >> And you can see from the line 325 that there is no >> limitation for bands >> numbers. >> >> Nevertheless, I will try the code with 4.0.4 output. >> By the way, it might be much helpful, if you send me your >> output file for >> which you have troubles. >> >> Bests, >> Eyvaz. >> >> >> --- On Thu, 3/26/09, Paul M. Grant >> wrote: >> >> > From: Paul M. Grant >> > Subject: [Pw_forum] Line 325 in bands_FS.f90 >> > To: "'PWSCF Forum'" >> >> > Date: Thursday, March 26, 2009, 10:34 PMI >> > While running bands_FS.x (espresso-4.0 distro) on the >> output >> > of an PW nscf >> > non-spin-polarized job, I get the following error: >> > >> > At line 325 of file bands_FS.f90 >> > Fortran runtime error: Bad real number in item 5 of >> list >> > input >> > >> > This only happens for my LSDA=F runs, spin-polarized >> are >> > OK. ?(BTW, the >> > LSDA=F run for Ni in example 08 does work. ?The only >> > difference is that >> > ex08 deals with only 8 bands and 1 formated line, >> whilst my >> > task computes 20 >> > taking up 3 formated lines.) ?Line 325 is in the >> LSDA=F >> > portion of the code >> > follows a commented-out read command line with >> explicit >> > formatting. ?I can't >> > see any problem with the output of my nscf run. >> Before I >> > start messing >> > around with the bands_FS.f90 source, has anyone else >> run >> > into this issue >> > (Eyvaz?)? ?Is it possible there is a "line >> > counting" error in the LSDA=F >> > portion when the band energy listing exceeds one line? >> >> > Sorry if I've made >> > some stupid blunder. >> > >> > Paul M. Grant, PhD >> > Physicist and Science Writer >> > Principal, W2AGZ Technologies >> > Visiting Scholar, Applied Physics, Stanford >> (2005-2008) >> > EPRI Science Fellow (Retired) >> > IBM Research Staff Member Emeritus >> > w2agz at pacbell.net >> > http://www.w2agz.com >> > >> > >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 21, Issue 81 > **************************************** > From mazouz_moulay at yahoo.fr Sat Mar 28 13:37:51 2009 From: mazouz_moulay at yahoo.fr (mazouz moulay) Date: Sat, 28 Mar 2009 12:37:51 +0000 (GMT) Subject: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms Message-ID: <806663.82074.qm@web25507.mail.ukl.yahoo.com> Dear PWscf users, ? I performed a magnetic calculation for CoO in the zinc blende structure using the following input file. ? &control calculation = 'scf' restart_mode='from_scratch', prefix='1', pseudo_dir = '/root/espresso-4.0/pseudo/', outdir='/home/mazouz/coo/tmp/' / &system ibrav= 2, celldm(1)= 8.53 nat= 2, ntyp= 2, ecutwfc =50, report=1, nspin=2 occupations='smearing', smearing='gaussian', degauss=0.02 starting_magnetization(1) = 0.5 starting_magnetization(1) = 0.0 / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Co 58.933 Co.pbe-nd-rrkjus.UPF O 15.999 O.pbe-van_ak.UPF ATOMIC_POSITIONS Co 0.00 0.00 0.00 O 0.25 0.25 0.25 K_POINTS AUTOMATIC 8 8 8 0 0 0 ? I would like to ask you if there is any way to specify the antiferromagnetic case for the same input file ? or must I use an input file of 8 atoms? or... Thank you in advance ? M. Mazouz D?partement de Physique Universit? des Sciences et de la Technologie d'Oran. USTO. Mail: mazouz_moulay at yahoo.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090328/42235ce7/attachment.htm From giannozz at democritos.it Sat Mar 28 14:18:23 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 28 Mar 2009 14:18:23 +0100 Subject: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms In-Reply-To: <806663.82074.qm@web25507.mail.ukl.yahoo.com> References: <806663.82074.qm@web25507.mail.ukl.yahoo.com> Message-ID: <28F0A713-3A0F-4C75-9173-D34B2F1627BF@democritos.it> On Mar 28, 2009, at 13:37 , mazouz moulay wrote: > starting_magnetization(1) = 0.5 > starting_magnetization(1) = 0.0 undecided? --- Paolo Giannozzi, Democritos and University of Udine, Italy From chenweiguang82 at gmail.com Sat Mar 28 14:21:02 2009 From: chenweiguang82 at gmail.com (Weiguang Chen) Date: Sat, 28 Mar 2009 21:21:02 +0800 Subject: [Pw_forum] How to use tools dipole.x, voronoy.x and epsilon.x? Message-ID: <9e6d976a0903280621t34b6ad83k486ec68884e3c82a@mail.gmail.com> Hi, I am a newbie about pwscf. There is a little information about the above three tools, what's the usages for these programs although they are not used frequently? I just what to know how to use for preparing the future possible application. Thanks -- Best Wishes ChenWeiguang ************************************************ # Chen, Weiguang # # Postgraduate, Ph. D # 75 University Road, Physics Buliding # 218 # School of Physics & Engineering # Zhengzhou University # Zhengzhou, Henan 450052 CHINA # # Tel: 86-13203730117; # E-mail:chenweiguang82 at gmail.com; # chenweiguang82 at qq.com #********************************************** From giannozz at democritos.it Sat Mar 28 14:25:52 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 28 Mar 2009 14:25:52 +0100 Subject: [Pw_forum] electrical polarization calculations for non-collinear magnetism In-Reply-To: References: <49CCF178.10403@sissa.it> Message-ID: On Mar 28, 2009, at 6:25 , Xun-Wang Yan wrote: > nspin=1 and nspin=2 cases is supported, there is not > noncolin=.true. case. > how to modify the bp_c_phase.f90 to include the noncolin=.true. > case for electric > polarization calculation? I know nothing about polarization and noncolinear calculations, but basically what you need in a polarization calculation is a sequence of scalar products between electronic states at different k-points. In the case of noncolinear calculations, electronic states are spinors and are expanded into plane waves with both spin-up and spin-down components. Coefficients 1 to npw are for spin-up plane waves, coefficients npwx+1 to npwx+npw are for spin-down plane waves. Scalar products are summed over the two sets. Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Sat Mar 28 14:30:27 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 28 Mar 2009 14:30:27 +0100 Subject: [Pw_forum] How to use tools dipole.x, voronoy.x and epsilon.x? In-Reply-To: <9e6d976a0903280621t34b6ad83k486ec68884e3c82a@mail.gmail.com> References: <9e6d976a0903280621t34b6ad83k486ec68884e3c82a@mail.gmail.com> Message-ID: On Mar 28, 2009, at 14:21 , Weiguang Chen wrote: > I am a newbie about pwscf. There is a little information about the > above three tools, what's the usages for these programs although they > are not used frequently? I just what to know how to use for preparing > the future possible application. epsilon.x => Doc/eps_man.tex voronoy.x : Voronoy polyhedra around atoms, see the header of PP/ voronoy.f90 dipole.x: see the header of PP/dipole.f90 P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From mazouz_moulay at yahoo.fr Sat Mar 28 14:39:01 2009 From: mazouz_moulay at yahoo.fr (mazouz moulay) Date: Sat, 28 Mar 2009 13:39:01 +0000 (GMT) Subject: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms Message-ID: <794389.85938.qm@web25505.mail.ukl.yahoo.com> Sorry It was a typing error > starting_magnetization(1) = 0.5 > starting_magnetization(2) = 0.0 ? I added the second line when i wrote the message ! ? this is my original input file : ? &control calculation = 'scf' restart_mode='from_scratch', prefix='1', pseudo_dir = '/root/espresso-4.0/pseudo/', outdir='/home/mazouz/coo/tmp/' / &system ibrav= 2, celldm(1)= 8.53 nat= 2, ntyp= 2, ecutwfc =50, report=1, nspin=2 occupations='smearing', smearing='gaussian', degauss=0.02 starting_magnetization(1) = 0.5 / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Co 58.933 Co.pbe-nd-rrkjus.UPF O 15.999 O.pbe-van_ak.UPF ATOMIC_POSITIONS Co 0.00 0.00 0.00 O 0.25 0.25 0.25 K_POINTS AUTOMATIC 8 8 8 0 0 0 ? thank you ? ? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090328/483ba5a3/attachment.htm From chenweiguang82 at gmail.com Sat Mar 28 14:42:35 2009 From: chenweiguang82 at gmail.com (Weiguang Chen) Date: Sat, 28 Mar 2009 21:42:35 +0800 Subject: [Pw_forum] How to use tools dipole.x, voronoy.x and epsilon.x? In-Reply-To: References: <9e6d976a0903280621t34b6ad83k486ec68884e3c82a@mail.gmail.com> Message-ID: <9e6d976a0903280642t37b0eb01r5493bd172d994998@mail.gmail.com> Thanks very much.The epsilon.x has a detail guide, could you told to me the input files of the other two programs. I just try to read the source code of these two tools, but too many calls that i can not understand it. Thanks again. On Sat, Mar 28, 2009 at 9:30 PM, Paolo Giannozzi wrote: > > On Mar 28, 2009, at 14:21 , Weiguang Chen wrote: > >> ?I am a newbie about pwscf. There is a little information about the >> above three tools, what's the usages for these programs although they >> are not used frequently? I just what to know how to use for preparing >> the future possible application. > > epsilon.x => Doc/eps_man.tex > voronoy.x : Voronoy polyhedra around atoms, see the header of PP/ > voronoy.f90 > dipole.x: see the header of PP/dipole.f90 > > P. > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best Wishes ChenWeiguang ************************************************ # Chen, Weiguang # # Postgraduate, Ph. D # 75 University Road, Physics Buliding # 218 # School of Physics & Engineering # Zhengzhou University # Zhengzhou, Henan 450052 CHINA # # Tel: 86-13203730117; # E-mail:chenweiguang82 at gmail.com; # chenweiguang82 at qq.com #********************************************** From giannozz at democritos.it Sat Mar 28 15:14:09 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 28 Mar 2009 15:14:09 +0100 Subject: [Pw_forum] How to use tools dipole.x, voronoy.x and epsilon.x? In-Reply-To: <9e6d976a0903280642t37b0eb01r5493bd172d994998@mail.gmail.com> References: <9e6d976a0903280621t34b6ad83k486ec68884e3c82a@mail.gmail.com> <9e6d976a0903280642t37b0eb01r5493bd172d994998@mail.gmail.com> Message-ID: On Mar 28, 2009, at 14:42 , Weiguang Chen wrote: > Thanks very much.The epsilon.x has a detail guide, could you told to > me the input files of the other two programs. I just try to read the > source code of these two tools, but too many calls that i can not > understand it. dipole.x one reads the data file from pw.x, voronoy.x reads the intermediate file produced by pp.x . P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From chenweiguang82 at gmail.com Sat Mar 28 15:23:38 2009 From: chenweiguang82 at gmail.com (Weiguang Chen) Date: Sat, 28 Mar 2009 22:23:38 +0800 Subject: [Pw_forum] How to use tools dipole.x, voronoy.x and epsilon.x? In-Reply-To: References: <9e6d976a0903280621t34b6ad83k486ec68884e3c82a@mail.gmail.com> <9e6d976a0903280642t37b0eb01r5493bd172d994998@mail.gmail.com> Message-ID: <9e6d976a0903280723o26e128b6y66a0f700fb484afb@mail.gmail.com> Thanks, I'll try it On Sat, Mar 28, 2009 at 10:14 PM, Paolo Giannozzi wrote: > > On Mar 28, 2009, at 14:42 , Weiguang Chen wrote: > >> Thanks very much.The epsilon.x has a detail guide, could ?you told to >> me the input files of the other two programs. I just try to read the >> source code of these two tools, but too many calls that i can not >> understand it. > > dipole.x one reads the data file from pw.x, voronoy.x reads the > intermediate > file produced by pp.x . > > P. > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best Wishes ChenWeiguang ************************************************ # Chen, Weiguang # # Postgraduate, Ph. D # 75 University Road, Physics Buliding # 218 # School of Physics & Engineering # Zhengzhou University # Zhengzhou, Henan 450052 CHINA # # Tel: 86-13203730117; # E-mail:chenweiguang82 at gmail.com; # chenweiguang82 at qq.com #********************************************** From asafis at yahoo.com.br Sat Mar 28 19:08:44 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Sat, 28 Mar 2009 11:08:44 -0700 (PDT) Subject: [Pw_forum] HUMO and LUMO Message-ID: <855236.71529.qm@web52312.mail.re2.yahoo.com> Hello users. How to calculate the HUMO and LUMO in molecular systems in PWscf? A. S. Santos Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090328/6a2d6d90/attachment.htm From marzari at MIT.EDU Sat Mar 28 19:23:03 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 28 Mar 2009 14:23:03 -0400 Subject: [Pw_forum] Can you help? (was "Fixed spin moment method & Phonon calculation") In-Reply-To: <42206.202.141.81.5.1238220886.squirrel@webmail.iitg.ernet.in> References: <42206.202.141.81.5.1238220886.squirrel@webmail.iitg.ernet.in> Message-ID: <49CE6B07.6000000@mit.edu> Dear Dr Ghosh, I believe this is the current status - anyone please correct me: 1) you can only do phonons in magnetic systems (metallic or insulating) using a "smearing" option in the SCF calculation - i.e. you cannot fix the magnetization, but take whatever the system wants to be. You of course could try to do a standard SCF calculation imposing whatever magnetization you want, converge that, and restart it with no constraint and just smearing, and hope it remains where it is. 2) the NSCF calculation that follows can have or not have the smearing (better test either). If your system is insulating, it should not matter at all. If it is metallic/half-metallic, differences might arise (I would presume smearing in the NSCF would also be the right choice). 3) if the system is insulating, there is still something to do to fix the effective charges, that at present are not correct. Hence, LO/TO splitting at Gamma would be incorrect - everywhere else would be ok. Subhradip Ghosh wrote: > Dear Nicola, > > A week back I had posted a question in the pw-forum. It is related to the > feasibility of calculating phonons by fixing the magnetization. I had > searched the archive for an answer but couldn't find one. Since I haven't > gotten any reply from the forum, I am taking this liberty of disturbing > you by forwarding the question. Can you please take some time from your > schedule and send me a reply. The question is appended below. > > Regards, > > Subhradip > > ---------------------------- Original Message ---------------------------- > Subject: [Pw_forum] Fixed spin moment method & Phonon calculation > From: "Subhradip Ghosh" > Date: Wed, March 18, 2009 2:54 pm > To: pw_forum at pwscf.org > -------------------------------------------------------------------------- > > I am interested in calculating phonn dispersions in a metallic system by > fixin > g the magnetization. To do that, I had fixed the magnetization to a > particular value and tried the phonon calculation. However, it failed > apprently because "the constrained magnetization is not implemented in the > phonon code". Therefore, my question is: > Is phonon calculation not possible by fixing total magnetization with > the present QE code? > > I had searched the archive to find answers but no definite solution was > found apart from a comment from Paolo which suggests that > > "If the magnetization you choose is the ground state one, the two Fermi > energies would be the same. In that case, commenting out the check in > phq_readin.f90 should work. If you constrain the magnetization to a value > that is not the ground state, I have no idea what numbers will come out". > > Does this mean that a phonon calculation(by commenting out the check in > phq_readin) by fixing the magnetization at a value other than the ground > state value is not reliable? The answer to this question is important to > me because I am interested in doing phonons by fixing total magnetization > at values other than the ground state value. > > Help in this regard would be useful. > > Subhradip > > ************************************************************************ > Dr. Subhradip Ghosh > Assistant Professor > Department of Physics > Indian Institute of Technology > Guwahati,Assam-781039 > India > E-mail:subhra at iitg.ernet.in > Phone: +91 361 2582717(O) > +91 361 2584717(R) > Fax: +91 361 2582749 (Physics) > +91 361 2690762 (General) > ************************************************************************ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From asafis at yahoo.com.br Sat Mar 28 19:42:05 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Sat, 28 Mar 2009 11:42:05 -0700 (PDT) Subject: [Pw_forum] HUMO and LUMO Message-ID: <706862.42659.qm@web52311.mail.re2.yahoo.com> Hello users. How to calculate the HUMO and LUMO in molecular systems in PWscf? Regards, A. S. Santos Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090328/7fc7e279/attachment.htm From akohlmey at cmm.chem.upenn.edu Sat Mar 28 20:14:57 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 28 Mar 2009 15:14:57 -0400 Subject: [Pw_forum] HUMO and LUMO In-Reply-To: <855236.71529.qm@web52312.mail.re2.yahoo.com> References: <855236.71529.qm@web52312.mail.re2.yahoo.com> Message-ID: <1238267697.3087.2.camel@zero> On Sat, 2009-03-28 at 11:08 -0700, ?lvaro Alves wrote: > Hello users. How to calculate the HUMO and LUMO in molecular systems > in PWscf? > A. S. Santos can you please explain where _exactly_ your problem is? apart from the fact that a LUMO in DFT is an entity that needs to be treated with great care altogether, you get them like with any other calculation that uses a diagonalization. cheers, axel. > > ______________________________________________________________________ > Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - > Celebridades - M?sica - Esportes > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From chenhanghuipwscf at gmail.com Sat Mar 28 23:34:46 2009 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Sat, 28 Mar 2009 18:34:46 -0400 Subject: [Pw_forum] stress and mimimun of total energy Message-ID: <22ae3ca40903281534g6e0e9741v30adcdd09858b89d@mail.gmail.com> Dear PWSCF users, I found a very confusing thing when I use the Berry phase method to calculate the polarization. Let us take LaAlO3 as an example. LaAlO3 bulk is cubic. However if I fix the lattice constant in the xy-plane but turn on an electric field along the z-direction (using the Berry phase method), you will find: for different c (the latttice constant along the z direction), the stress along the z direction ( i.e. sigma(3,3) ) is different. I tried a few different c values and for each c value, I relaxed all the atoms in the unit cell and checked the stress (sigma(3,3)). I found within some region, the sigma(3,3) changes the sign. However, within the same region, the total energy of the unit cell is monotonically decreasing. I expect the total energy will behave like a parabolic around the "correct" c value. Does that make sense when we turn on an electric field? The input file of one typical calculation is attached below. Thank you very much. Hanghui Chen Department of Physics, Yale University &CONTROL calculation='relax' wf_collect=.true. pseudo_dir = './psp' outdir='/home1/hc336/scratch' wfcdir='/home1/hc336/scratch' prefix='sLAO-e160-relax-0' tprnfor = .true. tstress = .true. disk_io='low' verbosity='default' dt=80.D0 forc_conv_thr=5.0D-4 lelfield=.true. gdir=3 nppstr=12 nberrycyc=1 / &SYSTEM ibrav= 6 celldm(1) = 7.27 celldm(3) = 0.94428125 nat= 5 ntyp= 3 ecutwfc = 30.0 ecutrho = 180.0 occupations='fixed' nosym=.true. / &ELECTRONS diagonalization='david' mixing_beta = 0.7D0 diago_david_ndim = 4 startingwfc='random' startingpot='atomic' efield=0.0016 conv_thr = 1.0d-9 / &IONS ion_dynamics = 'bfgs' phase_space = 'full' pot_extrapolation = 'second_order' wfc_extrapolation = 'second_order' / &CELL cell_dynamics = 'damp-w' / ATOMIC_SPECIES La 138.91 057-La-ca-nsp-hanghui.uspp.format.UPF Al 26.98 013-Al-ca--hanghui.uspp.format.UPF O 16.00 008-O-ca--vgrp.uspp.format.UPF ATOMIC_POSITIONS crystal La 0.00 0.00 0.00 Al 0.50 0.50 0.50 O 0.50 0.50 0.00 O 0.00 0.50 0.50 O 0.50 0.00 0.50 K_POINTS crystal 192 0 0 0 1 0 0 0.0833333333333333 1 0 0 0.166666666666667 1 0 0 0.25 1 0 0 0.333333333333333 1 0 0 0.416666666666667 1 0 0 0.5 1 0 0 0.583333333333333 1 0 0 0.666666666666667 1 0 0 0.75 1 0 0 0.833333333333333 1 0 0 0.916666666666667 1 0 0.25 0 1 0 0.25 0.0833333333333333 1 0 0.25 0.166666666666667 1 0 0.25 0.25 1 0 0.25 0.333333333333333 1 0 0.25 0.416666666666667 1 0 0.25 0.5 1 0 0.25 0.583333333333333 1 0 0.25 0.666666666666667 1 0 0.25 0.75 1 0 0.25 0.833333333333333 1 0 0.25 0.916666666666667 1 0 0.5 0 1 0 0.5 0.0833333333333333 1 0 0.5 0.166666666666667 1 0 0.5 0.25 1 0 0.5 0.333333333333333 1 0 0.5 0.416666666666667 1 0 0.5 0.5 1 0 0.5 0.583333333333333 1 0 0.5 0.666666666666667 1 0 0.5 0.75 1 0 0.5 0.833333333333333 1 0 0.5 0.916666666666667 1 0 0.75 0 1 0 0.75 0.0833333333333333 1 0 0.75 0.166666666666667 1 0 0.75 0.25 1 0 0.75 0.333333333333333 1 0 0.75 0.416666666666667 1 0 0.75 0.5 1 0 0.75 0.583333333333333 1 0 0.75 0.666666666666667 1 0 0.75 0.75 1 0 0.75 0.833333333333333 1 0 0.75 0.916666666666667 1 0.25 0 0 1 0.25 0 0.0833333333333333 1 0.25 0 0.166666666666667 1 0.25 0 0.25 1 0.25 0 0.333333333333333 1 0.25 0 0.416666666666667 1 0.25 0 0.5 1 0.25 0 0.583333333333333 1 0.25 0 0.666666666666667 1 0.25 0 0.75 1 0.25 0 0.833333333333333 1 0.25 0 0.916666666666667 1 0.25 0.25 0 1 0.25 0.25 0.0833333333333333 1 0.25 0.25 0.166666666666667 1 0.25 0.25 0.25 1 0.25 0.25 0.333333333333333 1 0.25 0.25 0.416666666666667 1 0.25 0.25 0.5 1 0.25 0.25 0.583333333333333 1 0.25 0.25 0.666666666666667 1 0.25 0.25 0.75 1 0.25 0.25 0.833333333333333 1 0.25 0.25 0.916666666666667 1 0.25 0.5 0 1 0.25 0.5 0.0833333333333333 1 0.25 0.5 0.166666666666667 1 0.25 0.5 0.25 1 0.25 0.5 0.333333333333333 1 0.25 0.5 0.416666666666667 1 0.25 0.5 0.5 1 0.25 0.5 0.583333333333333 1 0.25 0.5 0.666666666666667 1 0.25 0.5 0.75 1 0.25 0.5 0.833333333333333 1 0.25 0.5 0.916666666666667 1 0.25 0.75 0 1 0.25 0.75 0.0833333333333333 1 0.25 0.75 0.166666666666667 1 0.25 0.75 0.25 1 0.25 0.75 0.333333333333333 1 0.25 0.75 0.416666666666667 1 0.25 0.75 0.5 1 0.25 0.75 0.583333333333333 1 0.25 0.75 0.666666666666667 1 0.25 0.75 0.75 1 0.25 0.75 0.833333333333333 1 0.25 0.75 0.916666666666667 1 0.5 0 0 1 0.5 0 0.0833333333333333 1 0.5 0 0.166666666666667 1 0.5 0 0.25 1 0.5 0 0.333333333333333 1 0.5 0 0.416666666666667 1 0.5 0 0.5 1 0.5 0 0.583333333333333 1 0.5 0 0.666666666666667 1 0.5 0 0.75 1 0.5 0 0.833333333333333 1 0.5 0 0.916666666666667 1 0.5 0.25 0 1 0.5 0.25 0.0833333333333333 1 0.5 0.25 0.166666666666667 1 0.5 0.25 0.25 1 0.5 0.25 0.333333333333333 1 0.5 0.25 0.416666666666667 1 0.5 0.25 0.5 1 0.5 0.25 0.583333333333333 1 0.5 0.25 0.666666666666667 1 0.5 0.25 0.75 1 0.5 0.25 0.833333333333333 1 0.5 0.25 0.916666666666667 1 0.5 0.5 0 1 0.5 0.5 0.0833333333333333 1 0.5 0.5 0.166666666666667 1 0.5 0.5 0.25 1 0.5 0.5 0.333333333333333 1 0.5 0.5 0.416666666666667 1 0.5 0.5 0.5 1 0.5 0.5 0.583333333333333 1 0.5 0.5 0.666666666666667 1 0.5 0.5 0.75 1 0.5 0.5 0.833333333333333 1 0.5 0.5 0.916666666666667 1 0.5 0.75 0 1 0.5 0.75 0.0833333333333333 1 0.5 0.75 0.166666666666667 1 0.5 0.75 0.25 1 0.5 0.75 0.333333333333333 1 0.5 0.75 0.416666666666667 1 0.5 0.75 0.5 1 0.5 0.75 0.583333333333333 1 0.5 0.75 0.666666666666667 1 0.5 0.75 0.75 1 0.5 0.75 0.833333333333333 1 0.5 0.75 0.916666666666667 1 0.75 0 0 1 0.75 0 0.0833333333333333 1 0.75 0 0.166666666666667 1 0.75 0 0.25 1 0.75 0 0.333333333333333 1 0.75 0 0.416666666666667 1 0.75 0 0.5 1 0.75 0 0.583333333333333 1 0.75 0 0.666666666666667 1 0.75 0 0.75 1 0.75 0 0.833333333333333 1 0.75 0 0.916666666666667 1 0.75 0.25 0 1 0.75 0.25 0.0833333333333333 1 0.75 0.25 0.166666666666667 1 0.75 0.25 0.25 1 0.75 0.25 0.333333333333333 1 0.75 0.25 0.416666666666667 1 0.75 0.25 0.5 1 0.75 0.25 0.583333333333333 1 0.75 0.25 0.666666666666667 1 0.75 0.25 0.75 1 0.75 0.25 0.833333333333333 1 0.75 0.25 0.916666666666667 1 0.75 0.5 0 1 0.75 0.5 0.0833333333333333 1 0.75 0.5 0.166666666666667 1 0.75 0.5 0.25 1 0.75 0.5 0.333333333333333 1 0.75 0.5 0.416666666666667 1 0.75 0.5 0.5 1 0.75 0.5 0.583333333333333 1 0.75 0.5 0.666666666666667 1 0.75 0.5 0.75 1 0.75 0.5 0.833333333333333 1 0.75 0.5 0.916666666666667 1 0.75 0.75 0 1 0.75 0.75 0.0833333333333333 1 0.75 0.75 0.166666666666667 1 0.75 0.75 0.25 1 0.75 0.75 0.333333333333333 1 0.75 0.75 0.416666666666667 1 0.75 0.75 0.5 1 0.75 0.75 0.583333333333333 1 0.75 0.75 0.666666666666667 1 0.75 0.75 0.75 1 0.75 0.75 0.833333333333333 1 0.75 0.75 0.916666666666667 1 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090328/931ca72e/attachment.htm From chenhanghuipwscf at gmail.com Sat Mar 28 23:44:58 2009 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Sat, 28 Mar 2009 18:44:58 -0400 Subject: [Pw_forum] stress and electric field Message-ID: <22ae3ca40903281544x677432e0o7b0300246b7ccae4@mail.gmail.com> Dear PWSCF users, I have a question about the stress when the electric field is turned on. If I turn on a 'sawtooth' potential, the code explicitly warns that "Presently stress not available with electric field". However if I use the Berry phase method to turn on an electric field in the bulk, is the stress calculated correctly? If yes, then why we can calculate stress in the Berry phase method but not with the 'sawtooth' potential? If not, does that mean the stress is not meaningful in the Berry phase method? Thank you very much. Hanghui Chen Department of Physics Yale Unversity -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090328/5d77dcdb/attachment.htm From mazouz_moulay at yahoo.fr Sun Mar 29 01:57:56 2009 From: mazouz_moulay at yahoo.fr (mazouz moulay) Date: Sun, 29 Mar 2009 00:57:56 +0000 (GMT) Subject: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms Message-ID: <706107.89629.qm@web25504.mail.ukl.yahoo.com> Dear PWscf users, ? I performed a magnetic calculation for CoO in the zinc blende structure using this input file: ? &control calculation = 'scf' restart_mode='from_scratch', prefix='1', pseudo_dir = '/root/espresso-4.0/pseudo/', outdir='/home/mazouz/coo/tmp/' / &system ibrav= 2, celldm(1)= 8.53 nat= 2, ntyp= 2, ecutwfc =50, report=1, nspin=2 occupations='smearing', smearing='gaussian', degauss=0.02 starting_magnetization(1) = 0.5 / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Co 58.933 Co.pbe-nd-rrkjus.UPF O 15.999 O.pbe-van_ak.UPF ATOMIC_POSITIONS Co 0.00 0.00 0.00 O 0.25 0.25 0.25 K_POINTS AUTOMATIC 8 8 8 0 0 0 ? I would like to ask you if there is any way to specify the antiferromagnetic case for the same input file ? or must I use an input file of 8 atoms? or... Thank you in advance ? M. Mazouz D?partement de Physique Universit? des Sciences et de la Technologie d'Oran. USTO. Algeria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090329/79c030e0/attachment.htm From hqzhou at nju.edu.cn Sun Mar 29 04:48:27 2009 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Sun, 29 Mar 2009 10:48:27 +0800 Subject: [Pw_forum] DMFT+LDA References: <166cd7c60903222004j791a20bbk92b86a0af7a92fff@mail.gmail.com><49C9F57F.1080308@democritos.it><6ED8A5CDC5CD43E8877F14E5B96E22F4@solarflare> <29D387B6-5304-4BA9-B28D-93798DB84E6F@democritos.it> Message-ID: <862FA7196C6A40378CC59CC52214C7AA@solarflare> Paolo, Soory I might not make the question clearer. I mean, I used to access CVS version from the server indicated in README.cvs. Just want to confirm it's the same with that downloaded from qe-forge.org. Huiqun Zhou ----- Original Message ----- From: "Paolo Giannozzi" To: "PWSCF Forum" Sent: Friday, March 27, 2009 3:27 PM Subject: Re: [Pw_forum] DMFT+LDA > > On Mar 27, 2009, at 5:28 , Huiqun Zhou wrote: > >> Does the snapshot you indicated the same as the cvs version >> accessed from SISSA's cvs root? > > please? > > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From yanxunwang2008 at gmail.com Sun Mar 29 05:21:34 2009 From: yanxunwang2008 at gmail.com (Xun-Wang Yan) Date: Sun, 29 Mar 2009 11:21:34 +0800 Subject: [Pw_forum] electrical polarization calculations for non-collinear magnetism In-Reply-To: References: <49CCF178.10403@sissa.it> Message-ID: Dear Paolo, Thank you for your reply, your comment is very useful to me. I shall have a try to change some part of the code 'bp_c_phase.f90' to include the noncolin=.true. case. Best regards Xun-Wang 2009/3/28 Paolo Giannozzi > > On Mar 28, 2009, at 6:25 , Xun-Wang Yan wrote: > > > nspin=1 and nspin=2 cases is supported, there is not > > noncolin=.true. case. > > how to modify the bp_c_phase.f90 to include the noncolin=.true. > > case for electric > > polarization calculation? > > I know nothing about polarization and noncolinear calculations, but > basically > what you need in a polarization calculation is a sequence of scalar > products > between electronic states at different k-points. In the case of > noncolinear > calculations, electronic states are spinors and are expanded into plane > waves with both spin-up and spin-down components. Coefficients 1 to npw > are for spin-up plane waves, coefficients npwx+1 to npwx+npw are for > spin-down plane waves. Scalar products are summed over the two sets. > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090329/d44033bf/attachment-0001.htm From duchl06 at 163.com Sun Mar 29 08:53:04 2009 From: duchl06 at 163.com (duchl06) Date: Sun, 29 Mar 2009 14:53:04 +0800 (CST) Subject: [Pw_forum] Defining an antiferromagnetic graphene nanoribbon Message-ID: <14507901.146141238309584140.JavaMail.coremail@bj163app41.163.com> dear pwscf users, excuse me! i am chinese student and i want do some calculations on graphene nanoribbon with pwscf, i saw Konstantin Kudin gave an example https://kiev.princeton.edu/misc/rg_07.scf.in on [Pw_forum] (http://www.democritos.it/pipermail/pw_forum/2008-May/008899.html) , but i cannot download it, can anyone email it to me or show it on the [Pw_forum] site or give other examples(input files) of graphene nanoribbon? my email address is duchl06 at 163.com . thank you very much! best regards! du -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090329/f43eb4b9/attachment.htm From giannozz at democritos.it Sun Mar 29 14:09:48 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 29 Mar 2009 14:09:48 +0200 Subject: [Pw_forum] DMFT+LDA In-Reply-To: <862FA7196C6A40378CC59CC52214C7AA@solarflare> References: <166cd7c60903222004j791a20bbk92b86a0af7a92fff@mail.gmail.com><49C9F57F.1080308@democritos.it><6ED8A5CDC5CD43E8877F14E5B96E22F4@solarflare> <29D387B6-5304-4BA9-B28D-93798DB84E6F@democritos.it> <862FA7196C6A40378CC59CC52214C7AA@solarflare> Message-ID: <27FD659E-1100-4F98-B301-F25AC347C048@democritos.it> On Mar 29, 2009, at 4:48 , Huiqun Zhou wrote: > Soory I might not make the question clearer. I mean, I used to access > CVS version from the server indicated in README.cvs. Just want to > confirm it's the same with that downloaded from qe-forge.org. the old cvs repository is still valid but no longer updated since a few weeks. The new cvs repository is the one on qe-forge. P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Sun Mar 29 14:10:47 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 29 Mar 2009 14:10:47 +0200 Subject: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms In-Reply-To: <706107.89629.qm@web25504.mail.ukl.yahoo.com> References: <706107.89629.qm@web25504.mail.ukl.yahoo.com> Message-ID: <10102FFD-82EE-4DE0-907C-30A9C8F7F664@democritos.it> On Mar 29, 2009, at 1:5 > I would like to ask you if there is any way to specify the > antiferromagnetic > case for the same input file ? no > or must I use an input file of 8 atoms? you need to use a supercell P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From lfhuang at theory.issp.ac.cn Sun Mar 29 16:14:48 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Sun, 29 Mar 2009 22:14:48 +0800 Subject: [Pw_forum] =?utf-8?q?a_not_reasonable_initial_path_for_NEB_calcul?= =?utf-8?q?ation?= Message-ID: <20090329141448.31150.qmail@ms.hfcas.ac.cn> Hello everyone: I am calculating the diffusion barrier of atomic H on graphene layer using NEB method. The first_image and last_image correspond to structures with a H atom on top of two nearest C atoms, respectively. However, the interpolated initial path is not reasonable that there are some largely displaced C atoms in the configurations between first and last images, because in realistic case the C atoms will sustain a honeycomb structure when atomic H diffuses on it. I have tried increasing the No. of intermediate images from 0 up to 7, and No. of total images from 5 to 19, also changing the symmetry from ibrav=4 to ibrav=0, but it doesn't make any different at all. In addition, I use the QE-3.2.3 version. Could anyone help me? I'd like to appreciate any good advice! Best Wishes! Yours Sincerely! L. F. Huang ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090329/5078192c/attachment.htm From marzari at MIT.EDU Sun Mar 29 18:09:37 2009 From: marzari at MIT.EDU (Nicola Marzari) Date: Sun, 29 Mar 2009 12:09:37 -0400 Subject: [Pw_forum] contribute to the wiki ! Message-ID: <49CF9D41.9010908@mit.edu> Dear All, a brief comment - you remember JF Kennedy saying "Don't ask what Quantum-ESPRESSO can do for you, but what you can do for Quantum-ESPRESSO" ? The idea here is that if Q-E is indeed an important tool for your work or research, it would be great to contribute something back to the community (btw, this is my own stance, not a Q-E policy !). The simplest form is to contribute to the wiki: http://www.quantum-espresso.org/wiki/index.php/Main_Page You can register by asking Nicola Bonini ( bonini at mit.edu ) to open you an account, and then you can update it - e.g. adding your own papers to the bibliography (this is really an *ethical imperative*, if you use Q-E), or summarizing in a FAQ something that has been asked over and over again in the mailing list. Of course, an even more special way of contributing is to help iron out all bugs in the code, or, even better, contributing new capabilities (an excellent example in the last few days was for some hybrid DFT functional). More complex efforts, linked or not to QE, can even be hosted in the "umbrella" page www.qe-forge.org , that is meant to be a tool for developers of any atomistic code. Thanks ! nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From giannozz at democritos.it Sun Mar 29 19:54:17 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 29 Mar 2009 19:54:17 +0200 Subject: [Pw_forum] a not reasonable initial path for NEB calculation In-Reply-To: <20090329141448.31150.qmail@ms.hfcas.ac.cn> References: <20090329141448.31150.qmail@ms.hfcas.ac.cn> Message-ID: <0363615A-335B-4CCE-A4AB-C87F51BF85F4@democritos.it> On Mar 29, 2009, at 16:14 , lfhuang wrote: > I am calculating the diffusion barrier of atomic H on graphene > layer using NEB method. The first_image and last_image correspond > to structures with a H atom on top of two nearest C atoms, > respectively. However, the interpolated initial path is not > reasonable that there are some largely displaced C atoms in the > configurations between first and last images, because [...] > ...the C atom in the first and the last image were not ordered in the same way. > In addition, I use the QE-3.2.3 version > no longer supported, use it at your own risk. > Could anyone help me? I'd like to appreciate any good advice! > I think xcrysden should be able to visualize the path P. --- Paolo Giannozzi, Democritos and University of Udine, Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090329/c5a255cd/attachment.htm From prasenjit.jnc at gmail.com Sun Mar 29 20:49:09 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Sun, 29 Mar 2009 20:49:09 +0200 Subject: [Pw_forum] a not reasonable initial path for NEB calculation In-Reply-To: <20090329141448.31150.qmail@ms.hfcas.ac.cn> References: <20090329141448.31150.qmail@ms.hfcas.ac.cn> Message-ID: <627e0ffa0903291149i3693c2cdp6f8dc315cae32846@mail.gmail.com> if u have some approximate idea of the path, u can provide the guess path by mentioning the images using the option "intermediate image" in the card ATOMIC_POSITIONS Prasenjit. 2009/3/29 lfhuang > Hello everyone: > > I am calculating the diffusion barrier of atomic H on graphene layer > using NEB method. The > > first_image and last_image correspond to structures with a H atom on top of > two nearest > > C atoms, respectively. However, the interpolated initial path is not > reasonable that there > > are some largely displaced C atoms in the configurations between first and > last images, because > > in realistic case the C atoms will sustain a honeycomb structure when > atomic H diffuses on it. I > > have tried increasing the No. of intermediate images from 0 up to 7, and > No. of total images > > from 5 to 19, also changing the symmetry from ibrav=4 to ibrav=0, but it > doesn't make any > > different at all. > > In addition, I use the QE-3.2.3 version. > > Could anyone help me? I'd like to appreciate any good advice! > > Best Wishes! > > Yours Sincerely! > > L. F. Huang > > ------ > > ====================================================================== > L.F.Huang(???) lfhuang at theory.issp.ac.cn > ====================================================================== > Add: Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591464-328(office) > Fax: 86-551-5591434 > Web: http://theory.issp.ac.cn (website of our theory group) > http://www.issp.ac.cn (website of our institute) > ====================================================================== > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090329/acaafb32/attachment-0001.htm From eyvaz_isaev at yahoo.com Sun Mar 29 23:30:21 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 29 Mar 2009 14:30:21 -0700 (PDT) Subject: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms In-Reply-To: <706107.89629.qm@web25504.mail.ukl.yahoo.com> Message-ID: <47837.4122.qm@web65713.mail.ac4.yahoo.com> Dear Mazouz, > if there is any way to specify the antiferromagnetic case for the same input file? No, there is no way, you should differ antiferromagnetically ordered atoms (i.e. consider them as different atoms with antiparallel magnetic moments). > or must I use an input file of 8 atoms? or... It depends on your computers, you can use 8, 16, even 24 etc, but the best way is the use of 4 atoms tetragonal cell. Hopefully you can manage to set up this one. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sun, 3/29/09, mazouz moulay wrote: > From: mazouz moulay > Subject: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms > To: pw_forum at pwscf.org > Date: Sunday, March 29, 2009, 4:57 AM > Dear PWscf users, > ? > I performed a magnetic calculation for CoO in the zinc > blende structure using this input file: > ? > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='1', > pseudo_dir = '/root/espresso-4.0/pseudo/', > outdir='/home/mazouz/coo/tmp/' > / > &system > ibrav= 2, > celldm(1)= 8.53 > nat= 2, > ntyp= 2, > ecutwfc =50, > report=1, > nspin=2 > occupations='smearing', > smearing='gaussian', degauss=0.02 > starting_magnetization(1) = 0.5 > / > &electrons > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > Co 58.933 Co.pbe-nd-rrkjus.UPF > O 15.999 O.pbe-van_ak.UPF > ATOMIC_POSITIONS > Co 0.00 0.00 0.00 > O 0.25 0.25 0.25 > K_POINTS AUTOMATIC > 8 8 8 0 0 0 > ? > I would like to ask you if there is any way to specify the > antiferromagnetic case for the same input file ? or must I > use an input file of 8 atoms? or... > Thank you in advance > ? > M. Mazouz > D?partement de Physique > Universit? des Sciences et de la Technologie d'Oran. > USTO. > Algeria > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Mon Mar 30 01:38:11 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 29 Mar 2009 16:38:11 -0700 (PDT) Subject: [Pw_forum] bands_FS.f90: Update Message-ID: <148419.71597.qm@web65716.mail.ac4.yahoo.com> Dear users, If you use or plan to use bands_FS.f90 for the Fermi Surface calculations, please update it. The file is attached. Thanks Yi Ding, but I found the mistake with "backspace" before, I have received his e-mail. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com -------------- next part -------------- A non-text attachment was scrubbed... Name: bands_FS.f90 Type: application/octet-stream Size: 9920 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20090329/16c62880/attachment.obj From lfhuang at theory.issp.ac.cn Mon Mar 30 01:53:46 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 30 Mar 2009 7:53:46 +0800 Subject: [Pw_forum] =?utf-8?q?a_not_reasonable_initial_path_for_NEB_calcul?= =?utf-8?q?ation?= Message-ID: <20090329235346.468.qmail@ms.hfcas.ac.cn> Dear Paolo Giannozzi and Prasenjit Ghosh: Thank you for your kind attention! I view the initial path in xcrysden, which should mean this is not related to the QE version (am I right?), And there are some C atoms even displace over several lattice constants or substituted by the H adatom. From other literatures, the H atom should diffuse along the C-C bond, based on which I added 3-7 intermediate images, but that doesn't make any different! Although in the first and last images, as P. Giannozzi mentioned, the C atoms are somewhat distorted by the H adatom, the displacement of them are small (less than 0.5 angstroms, the lattice constant is 2.5). So I want to ask, when you meet this kind of failure of the interpolation for the initial path, what would you do to get an reasonable one? Thanks! Best Wishes! Yours Sincerely L. F. Huang > Date: Sun, 29 Mar 2009 19:54:17 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] a not reasonable initial path for NEB > calculation > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > > On Mar 29, 2009, at 16:14 , lfhuang wrote: > > I am calculating the diffusion barrier of atomic H on graphene > > layer using NEB method. The first_image and last_image correspond > > to structures with a H atom on top of two nearest C atoms, > > respectively. However, the interpolated initial path is not > > reasonable that there are some largely displaced C atoms in the > > configurations between first and last images, because [...] > > > ...the C atom in the first and the last image were not ordered in the > same way. > > In addition, I use the QE-3.2.3 version > > > no longer supported, use it at your own risk. > > Could anyone help me? I'd like to appreciate any good advice! > > > > I think xcrysden should be able to visualize the path > > P. > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > Message: 7 > Date: Sun, 29 Mar 2009 20:49:09 +0200 > From: Prasenjit Ghosh > Subject: Re: [Pw_forum] a not reasonable initial path for NEB > calculation > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="gb2312" > > if u have some approximate idea of the path, u can provide the guess path by > mentioning the images using the option "intermediate image" in the card > ATOMIC_POSITIONS > > Prasenjit. > ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/ce3b84a8/attachment-0001.htm From paulatto at sissa.it Mon Mar 30 08:14:37 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 30 Mar 2009 08:14:37 +0200 (CEST) Subject: [Pw_forum] HUMO and LUMO In-Reply-To: <706862.42659.qm@web52311.mail.re2.yahoo.com> References: <706862.42659.qm@web52311.mail.re2.yahoo.com> Message-ID: <54084.78.12.162.122.1238393677.squirrel@webmail.sissa.it> On Sab, Marzo 28, 2009 20:42, ?lvaro Alves wrote: > Hello users. How to calculate the HUMO and LUMO in molecular systems in > PWscf? Dear Alvaro, the definition of homo and lumo only makes sense under certain conditions; if those conditions are respected pw.x will print homo and lumo energy just before the total energy, e.g. highest occupied, lowest unoccupied level (ev): -7.4325 -6.2947 I think it only happens if occupation is 'fixed' or from' input. If you're using a smearing you can still calculate the home and lumo yourself: if you have only one k-point (gamma) it is not difficult at all. If you have a small smearing the code shall print the fermi enegy instead of homo and lumo: the Fermi energy is -4.0615 ev just after the band energies. Go up to the bands and look where the fermi energy lies, e.g. -20.8969 -10.9562 -10.9562 -5.9557 -0.8632 1.4454 1.4552 1.4553 it's here --^ hence -5.9557 is homo and -0.8632 is lumo (as long as the smearing contribution to energy is ~ zero). If you are not using gamma as the only kpoint; e.g. you system is not isolated, than I don't know how much sense it make to compute homo and lumo (you have a band gap instead), nor how to do it reliably. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From prasenjit.jnc at gmail.com Mon Mar 30 10:42:54 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Mon, 30 Mar 2009 10:42:54 +0200 Subject: [Pw_forum] a not reasonable initial path for NEB calculation In-Reply-To: <20090329235346.468.qmail@ms.hfcas.ac.cn> References: <20090329235346.468.qmail@ms.hfcas.ac.cn> Message-ID: <627e0ffa0903300142r2ad50801s57fd87a5980808f1@mail.gmail.com> Dear Huang, You are the best person to guess the best initial path. What I would suggest is to get an idea as to how the H atom diffuses (either by searching literature or from some chemical insight) and provide the guess path by specifying the intermediate images with the option "intermediate_image". This way the code uses your guess path rather than doing an interpolation. Prasenjit. 2009/3/30 lfhuang > Dear Paolo Giannozzi and Prasenjit Ghosh: > Thank you for your kind attention! > I view the initial path in xcrysden, which should mean this is not related > to the QE version (am I right?), And > there are some C atoms even displace over several lattice constants or > substituted by the H adatom. From other > literatures, the H atom should diffuse along the C-C bond, based on which I > added 3-7 intermediate images, but > that doesn't make any different! > Although in the first and last images, as P. Giannozzi mentioned, the C > atoms are somewhat distorted by the > H adatom, the displacement of them are small (less than 0.5 angstroms, the > lattice constant is 2.5). > So I want to ask, when you meet this kind of failure of the interpolation > for the initial path, what would you > do to get an reasonable one? Thanks! > > Best Wishes! > > Yours Sincerely > L. F. Huang > > > Date: Sun, 29 Mar 2009 19:54:17 +0200 > > From: Paolo Giannozzi > > Subject: Re: [Pw_forum] a not reasonable initial path for NEB > > calculation > > To: PWSCF Forum > > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > > > > > On Mar 29, 2009, at 16:14 , lfhuang wrote: > > > I am calculating the diffusion barrier of atomic H on graphene > > > layer using NEB method. The first_image and last_image correspond > > > to structures with a H atom on top of two nearest C atoms, > > > respectively. However, the interpolated initial path is not > > > reasonable that there are some largely displaced C atoms in the > > > configurations between first and last images, because [...] > > > > > ...the C atom in the first and the last image were not ordered in the > > same way. > > > In addition, I use the QE-3.2.3 version > > > > > no longer supported, use it at your own risk. > > > Could anyone help me? I'd like to appreciate any good advice! > > > > > > > I think xcrysden should be able to visualize the path > > > > P. > > --- > > Paolo Giannozzi, Democritos and University of Udine, Italy > > > Message: 7 > > Date: Sun, 29 Mar 2009 20:49:09 +0200 > > From: Prasenjit Ghosh > > Subject: Re: [Pw_forum] a not reasonable initial path for NEB > > calculation > > To: PWSCF Forum > > Message-ID: > > > > Content-Type: text/plain; charset="gb2312" > > > > if u have some approximate idea of the path, u can provide the guess path > by > > mentioning the images using the option "intermediate image" in the card > > ATOMIC_POSITIONS > > > > Prasenjit. > > > > ------ > ====================================================================== > L.F.Huang(???) lfhuang at theory.issp.ac.cn > ====================================================================== > Add: Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591464-328(office) > Fax: 86-551-5591434 > Web: http://theory.issp.ac.cn> (website of our theory group) > http://www.issp.ac.cn> (website of our > institute) > ====================================================================== > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/e6c72ae8/attachment.htm From lfhuang at theory.issp.ac.cn Mon Mar 30 10:41:42 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 30 Mar 2009 16:41:42 +0800 Subject: [Pw_forum] =?utf-8?q?a_not_reasonable_initial_path_for_NEB_calcul?= =?utf-8?q?ation?= Message-ID: <20090330084142.21894.qmail@ms.hfcas.ac.cn> Dear P. Giannozzi and P. Ghosh: I have solve my problem. I find that the coodinates of H adatom in the first_image and last_image should be type in the same line sequence No., or the interpolated initial path will be greatly distorted. Thank you again for your kind hearts! Yours Sincerely L.F.Huang ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/c151f38e/attachment.htm From paulatto at sissa.it Mon Mar 30 11:35:41 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 30 Mar 2009 11:35:41 +0200 Subject: [Pw_forum] HUMO and LUMO In-Reply-To: <54084.78.12.162.122.1238393677.squirrel@webmail.sissa.it> References: <706862.42659.qm@web52311.mail.re2.yahoo.com> <54084.78.12.162.122.1238393677.squirrel@webmail.sissa.it> Message-ID: On Mon, 30 Mar 2009 08:14:37 +0200, Lorenzo Paulatto wrote: > I think it only happens if occupation is 'fixed' or from' input. Somthing I forgot: if you use fixed occupation you have to specify nbnd to *more* than half the number of electrons; otherwise the code has no way to compute the LUMO! This is likely to improve convergence as well. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From umari at democritos.it Mon Mar 30 10:59:19 2009 From: umari at democritos.it (umari at democritos.it) Date: Mon, 30 Mar 2009 10:59:19 +0200 Subject: [Pw_forum] stress and electric field (paolo umari) Message-ID: <20090330105919.4e5p9vd6o0c4wo08@mail.democritos.it> Dear Hanghui, the present version of pw.x does not support yet the calculation of stress in the presence of an electric field with ultrasoft pseudopotentials, but only with normconserving pseudopotentials > If I turn on a 'sawtooth' potential, the code explicitly warns that > "Presently stress not available with electric field". However if I use the > Berry phase method to turn on an electric field in the bulk, is the stress > calculated correctly? If yes, then why we can calculate stress in the Berry > phase method but not with the 'sawtooth' potential? If not, does that mean > the stress is not meaningful in the Berry phase method? the saw-tooth potential is meaningful only for isolated molecules or slabs. However, for isolated molecules or slabs the notion of stress becomes meaningless, so the correct way is to use the Berry's phase method Best regards, Paolo Umari - Democritos ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From djaithania at yahoo.fr Mon Mar 30 11:21:17 2009 From: djaithania at yahoo.fr (Djani Ait Aissa Hania) Date: Mon, 30 Mar 2009 09:21:17 +0000 (GMT) Subject: [Pw_forum] internal position after relax Message-ID: <182964.86171.qm@web23905.mail.ird.yahoo.com> dear all, after?the relaxationof my structure,?I noticed the position of one oxygens atom along the z-direction became greater than celldm(3) wich is?physically impossible. celldm(3)=2.992 O(0.2981? 0.7355? 2.9597) =>after relax O(0.385...? 0.781...? 3.0147). What could that mean? here?are??input and?output informations. Please don't pay attention to the Warning card in the output, I fix it but?the position of that oxygen is still out off 2.299. ? ?/ ?&system ??? ibrav=9 ??? celldm(1)=10.45, ??? celldm(2)=0.994, ??? celldm(3)=2.992, ??? nat=18 ??? ntyp=3 ??? ecutwfc=35.0 ??? ecutrho=200.0, ?/ ?&electrons ??? conv_thr = 1e-6, ??? mixing_beta=0.7, ?/ ?&ions ?/ ATOMIC_SPECIES ? ? W???? 183.84??? W.pz-bhs.UPF ? Bi??? 208.98??? 083-Bi-ca-d-vgrp_ji.uspp.UPF ? O???? 15.9994?? O.pz-van_ak.UPF ? ATOMIC_POSITIONS alat W??????? 0.000000000?? 0.000000000?? 0.000000000 0 0 0 W??????? 0.000000000?? 0.497000000?? 1.496000000 0 1 1 Bi?????? 0.994700000?? 0.508500000?? 0.515300000 Bi?????? 0.994700000?? 0.485500000?? 2.476700000 Bi?????? 0.994700000?? 0.982500000?? 2.011300000 Bi?????? 0.994700000?? 0.011500000?? 0.980700000 O??????? 0.075300000?? 0.952900000?? 0.323100000 O??????? 0.075300000?? 0.041100000?? 2.668900000 O??????? 0.075300000?? 0.538100000?? 1.819100000 O??????? 0.075300000?? 0.455900000?? 1.172900000 O??????? 0.277100000?? 0.253500000?? 2.243700000 O??????? 0.277100000?? 0.740500000?? 0.748300000 O??????? 0.277100000?? 0.243500000?? 0.747700000 O??????? 0.277100000?? 0.750500000? ?2.244300000 O??????? 0.298100000?? 0.735500000?? 2.959700000 O??????? 0.298100000?? 0.258500000?? 0.032300000 O??????? 0.298100000?? 0.755500000?? 1.463700000 O??????? 0.298100000?? 0.238500000?? 1.528300000 K_POINTS{automatic} ? 6 6 2 1 1 1 ? ???? Program PWSCF???? v.3.2.3? starts ... ?????? Ultrasoft (Vanderbilt) Pseudopotentials ???? Current dimensions of program pwscf are: ???? ntypx = 10?? npk = 40000? lmax =? 3 ???? nchix =? 6? ndmx =? 2000? nbrx = 14? nqfx =? 8 Warning: card K_POINTS{AUTOMATIC} ignored Warning: card?? 6 6 2 1 1 1 ignored ???? gamma-point specific algorithms are used ???? bravais-lattice index???? =??????????? 9 ???? lattice parameter (a_0)?? =????? 10.4500? a.u. ???? unit-cell volume????????? =??? 1696.9414 (a.u.)^3 ???? number of atoms/cell????? =?????????? 18 ???? number of atomic types??? =??????????? 3 ???? kinetic-energy cutoff???? =????? 35.0000? Ry ???? charge density cutoff???? =???? 200.0000? Ry ???? convergence threshold ????=????? 1.0E-06 ???? beta????????????????????? =?????? 0.7000 ???? number of iterations used =??????????? 8? plain???? mixing ???? Exchange-correlation????? =? SLA? PZ?? NOGX NOGC (1100) ???? nstep???????????????????? =?????????? 50 ???? celldm(1)=? 10.450000? celldm(2)=?? 0.994000? celldm(3)=?? 2.992000 ???? celldm(4)=?? 0.000000? celldm(5)=?? 0.000000? celldm(6)=?? 0.000000 ???? crystal axes: (cart. coord. in units of a_0) ?????????????? a(1) = (? 0.500000? 0.497000? 0.000000 )? ?????????????? a(2) = ( -0.500000? 0.497000? 0.000000 )? ?????????????? a(3) = (? 0.000000? 0.000000? 2.992000 )? ???? reciprocal axes: (cart. coord. in units 2 pi/a_0) ?????????????? b(1) = (? 1.000000? 1.006036? 0.000000 )? ?????????????? b(2) = ( -1.000000? 1.006036? 0.000000 )? ?????????????? b(3) = (? 0.000000? 0.000000? 0.334225 )?? ????? ???? 4 Sym.Ops. (no inversion) ??? ???? entering subroutine stress ... ????????? total?? stress? (Ry/bohr**3)? ?????????????????(kbar)???? P=? 219.52 ?? 0.00240206?? 0.00000000?? 0.00000000??????? 353.35????? 0.00????? 0.00 ?? 0.00000000?? 0.00197220?? 0.00000000????????? 0.00??? 290.12????? 0.00 ?? 0.00000000?? 0.00000000?? 0.00010257????????? 0.00????? 0.00???? 15.09 ???? The maximum number of steps has been reached. ???? End of BFGS Geometry Optimization CELL_PARAMETERS (alat) ?? 0.500000000?? 0.497000000?? 0.000000000 ? -0.500000000?? 0.497000000?? 0.000000000 ?? 0.000000000?? 0.000000000?? 2.992000000 ATOMIC_POSITIONS (alat) W??????? 0.000000000?? 0.000000000?? 0.000000000 W??????? 0.000000000?? 0.497000000?? 1.496000000 Bi?????? 0.884736162?? 0.286360920?? 0.513309795 Bi?????? 0.884736162?? 0.707639080?? 2.478690205 Bi?????? 0.884736162?? 1.204639080?? 2.009309795 Bi?????? 0.884736162? -0.210639080?? 0.982690205 O??????? 0.114341213?? 0.998396235?? 0.303938731 O??????? 0.114341213? -0.004396235?? 2.688061269 O??????? 0.114341213?? 0.492603765?? 1.799938731 O??????? 0.114341213?? 0.501396235?? 1.192061269 O ???????0.136327487?? 0.459631702?? 2.459832528 O??????? 0.136327487?? 0.534368298?? 0.532167472 O??????? 0.136327487?? 0.037368298?? 0.963832528 O??????? 0.136327487?? 0.956631702?? 2.028167472 O??????? 0.385241009?? 0.781832443?? 3.014719481 O??????? 0.385241009?? 0.212167557? -0.022719481 O??????? 0.385241009?? 0.709167557?? 1.518719481 O??????? 0.385241009?? 0.284832443?? 1.473280519 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/eedf87be/attachment-0001.htm From paulatto at sissa.it Mon Mar 30 11:28:35 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Mon, 30 Mar 2009 11:28:35 +0200 Subject: [Pw_forum] internal position after relax In-Reply-To: <182964.86171.qm@web23905.mail.ird.yahoo.com> References: <182964.86171.qm@web23905.mail.ird.yahoo.com> Message-ID: On Mon, 30 Mar 2009 11:21:17 +0200, Djani Ait Aissa Hania wrote: > > > dear all, > after the relaxationof my structure, I noticed the position of one > oxygens atom along the z-direction became greater than celldm(3) wich > is physically impossible. Dear Djani, don't worry. Your system is composed of a unit cell, described by three vectors, and a basis, describing the atomic positions. There is no constrain on the basis; as periodic boundary conditions even if you put the atoms outside of the cell some there wil be a periodic replica that's inside. This is all done automatically by the software (mostly in reciprocal space, using structure-factor phases). It is very common to put atoms out of the unit cell (often with negative coordinates!) when doing molecules, a bit les when doing bulk crystal, nevertheless there is nothing wrong with it. If you feel uncomfortable you can scale the atom back into the cell by subtracting celldm(3) to its z-coordinate. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From tone.kokalj at ijs.si Mon Mar 30 11:32:11 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 30 Mar 2009 11:32:11 +0200 Subject: [Pw_forum] internal position after relax In-Reply-To: <182964.86171.qm@web23905.mail.ird.yahoo.com> References: <182964.86171.qm@web23905.mail.ird.yahoo.com> Message-ID: <1238405531.5098.10.camel@walk.ijs.si> On Mon, 2009-03-30 at 09:21 +0000, Djani Ait Aissa Hania wrote: > > dear all, > after the relaxation of my structure, I noticed the position of one > oxygens atom along the z-direction became greater than celldm(3) wich > is physically impossible. > celldm(3)=2.992 > O(0.2981 0.7355 2.9597) =>after relax O(0.385... 0.781... 3.0147). > What could that mean? Nothing, because 3.0147-2.9597=0.0227. There is nothing "physically impossible" here. (i.e. this means that your O atom is at the edge of the cell; initially it was a bit left from the edge and after relaxation it is at the right of the edge) > here are input and output informations. Please don't pay attention to > the Warning card in the output, I fix it but the position of that > oxygen is still out off 2.299. Thsi warning is due to missing whitespace: K_POINTS{automatic} should be K_POINTS {automatic} Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Mon Mar 30 11:33:36 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 30 Mar 2009 11:33:36 +0200 Subject: [Pw_forum] internal position after relax In-Reply-To: <1238405531.5098.10.camel@walk.ijs.si> References: <182964.86171.qm@web23905.mail.ird.yahoo.com> <1238405531.5098.10.camel@walk.ijs.si> Message-ID: <1238405616.5098.12.camel@walk.ijs.si> On Mon, 2009-03-30 at 11:32 +0200, Tone Kokalj wrote: > On Mon, 2009-03-30 at 09:21 +0000, Djani Ait Aissa Hania wrote: > > > > dear all, > > after the relaxation of my structure, I noticed the position of one > > oxygens atom along the z-direction became greater than celldm(3) wich > > is physically impossible. > > celldm(3)=2.992 > > O(0.2981 0.7355 2.9597) =>after relax O(0.385... 0.781... 3.0147). > > What could that mean? > > Nothing, because 3.0147-2.9597=0.0227. There is nothing "physically > impossible" here. Actually I meant: 3.014-2.992 [i.e. celldm(3)] Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From prasenjit.jnc at gmail.com Mon Mar 30 15:38:43 2009 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Mon, 30 Mar 2009 15:38:43 +0200 Subject: [Pw_forum] pseudopotential for Ce Message-ID: <627e0ffa0903300638q7f279301t68e72f6cb66cf6d3@mail.gmail.com> Hi, Does anyone have a PBE based ultrasoft pseudopotential for Ce. I will be highly grateful if he/she can share it with me. With regards, Prasenjit. -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/84378925/attachment.htm From lfhuang at theory.issp.ac.cn Mon Mar 30 15:51:09 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 30 Mar 2009 21:51:09 +0800 Subject: [Pw_forum] =?utf-8?q?about_the_logical_parameter_=22use=5Fmasses?= =?utf-8?q?=22_in_IONS_card?= Message-ID: <20090330135109.26004.qmail@ms.hfcas.ac.cn> Hello pwscf developers: What does the definition of "use_masses" in IONS card (mass-weighted) mean? Whose masses are weighted? Is it the weight between the first_image and the last_image, or just the weight in one configuration according to the masses of all the atoms? When should we turn on "use_masses" to be .true.? I can't find the answers for these questions in "INPUT_PW" and this forum. Could any kind one teach me for these? I'd like to appreciate any help very much! Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/514583b7/attachment.htm From lfhuang at theory.issp.ac.cn Mon Mar 30 15:59:25 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 30 Mar 2009 21:59:25 +0800 Subject: [Pw_forum] =?utf-8?q?=282=29_about_the_logical_parameter_=22use?= =?utf-8?q?=5Fmasses=22_in_IONS_card?= Message-ID: <20090330135925.26838.qmail@ms.hfcas.ac.cn> Any original papers or good papers on the parameter "use_masses" ? thanks! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/e132626c/attachment.htm From abdulrafiu.raji at uct.ac.za Mon Mar 30 15:12:17 2009 From: abdulrafiu.raji at uct.ac.za (Abdulrafiu RAJI) Date: Mon, 30 Mar 2009 15:12:17 +0200 Subject: [Pw_forum] Can't run any example in QE v4.0.4 Message-ID: <49D0E152020000C50019A26B@gwiasmtp.uct.ac.za> Dear users, I have just downloaded QE v4.0.4. After successful compilation on my AMD dual- processor, I tried to run some examples in the code. But each time I do this, the following error messages are reported, and this is case of may examples that I have tried : running cp.x as: mpirun -np 2 /home/araji/Codes/espresso-4.0.5/bin/cp.x cleaning /home/araji/tmp... done running the calculation with fixed ions..../run_example: line 131: mpirun: command not found How do I handle this? I should mention that I have been able to run the examples on earlier versions, v.4.0.3, e.t.c, without any hitch. Thanks for your attention. Abdulrafiu Tunde Raji. Physics Department. University of Cape Town. South Africa. Raji Abdulrafiu Tunde, Department of Physics, University of Cape Town (RW James Bld.),Private Bag X3, Rondebosch 7701, Cape Town. South Africa. Office number : Rm. 522 Cell: +27722668228 Fax: +27216503342 ______________________________________________________________________________________________ UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 4500. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. _____________________________________________________________________________________________________ From fabris at democritos.it Mon Mar 30 16:22:38 2009 From: fabris at democritos.it (Stefano Fabris) Date: Mon, 30 Mar 2009 16:22:38 +0200 Subject: [Pw_forum] pseudopotential for Ce In-Reply-To: <627e0ffa0903300638q7f279301t68e72f6cb66cf6d3@mail.gmail.com> References: <627e0ffa0903300638q7f279301t68e72f6cb66cf6d3@mail.gmail.com> Message-ID: <6E3EA16B-C7C0-48D8-9641-49E46E14FEEF@democritos.it> Dear Prasenjit, you can find at this address (www.democritos.it/~fabris/Ce4_ps_f1d1-pbe-rc1.0.uspp.UPF) a PBE pseudopotential for Ce we have used in our recent studies of ceria. Please note that I have tested the pseudo on the properties of CeO2-based materials only. As you know, in general, compounds based on cerium may display quite intriguing properties (subtle transitions in metallic cerium as an example) and I am not sure how well this pseudo work for systems other than cerias. The pseudo includes semicore states 5s and 5p in valence. You can find more details into the PP files. In my experience, adding more projectors to the f channel made very little difference. Moreover, one of our collaborators experienced with pseudos in ionic configurations (+3.5), which gave very similar results and transferability of the pseudo in the neutral configuration. Hope this help. Do not hesitate to contact me if I can be of any help. Yours sincerely, Stefano > --- Stefano Fabris Theory at Elettra Group CNR-INFM DEMOCRITOS National Simulation Center c/o Sincrotrone Trieste - SS14, Km 163,5 Basovizza, I-34012 TRIESTE website: www.democritos.it/the-group email: fabris at democritos.it tel: +39 040 375-8735 fax: -8776 --- From anavat_ila at yahoo.com Mon Mar 30 16:16:59 2009 From: anavat_ila at yahoo.com (Ali Tavana) Date: Mon, 30 Mar 2009 07:16:59 -0700 (PDT) Subject: [Pw_forum] cannot remap grid on k-point list Message-ID: <212143.36833.qm@web51811.mail.re2.yahoo.com> Dear all, I am sorry to discuss this simple problem here. When I want to calculate the e-ph coupling, after the calculation finishes for the q=(0,0,0) point, for the next q point it cannot perfectly output (or maybe determine!) the modes and in input file I get something like this: ? ? ?? omega( 10 - 10) =??????? 190.8? [cm-1]?? --> B_u ???? omega( 11 - 11) =??????? 197.8? [cm-1]?? -->?? ? ???? omega( 11 - 11) =??????? 197.8? [cm-1]?? --> B_g ???? omega( 11 - 11) =??????? 197.8? [cm-1]?? -->?? ? ???? omega( 11 - 11) =??????? 197.8? [cm-1]?? -->?? 0A_u ???? omega( 12 - 12) =??????? 212.6? [cm-1]?? --> A_u ???? omega( 13 - 13) =??????? 276.6? [cm-1]?? --> B_u ???? omega( 14 - 14) =??????? 280.7? [cm-1]?? -->?? ? ???? omega( 14 - 14) =??????? 280.7? [cm-1]?? --> A_g and then the program stops and gives the error: from lint : error #??????? 38 cannot remap grid on k-point list Stop 2 ---------------------------------------------------------------------- I have tried k meshes as dense as (100 100 25)!!? (for higher meshes!! program stops by the error too many k points) as somebody told me that may be because of not enough dense k mesh (my q mesh is (8,8,2)) but the error still exist! I also tried the new CVS version and nothing changed. I have rechecked the input files more than hundred? time? and? I am sure there is every thing ok. Can any body help me? Thank you very much, Ali Tavana Atomistid Modelling and Design of Materials, University of Leoben, Austria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/9b121603/attachment-0001.htm From sclauzer at sissa.it Mon Mar 30 16:25:47 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 30 Mar 2009 16:25:47 +0200 Subject: [Pw_forum] Can't run any example in QE v4.0.4 In-Reply-To: <49D0E152020000C50019A26B@gwiasmtp.uct.ac.za> References: <49D0E152020000C50019A26B@gwiasmtp.uct.ac.za> Message-ID: <49D0D66B.6070304@sissa.it> Abdulrafiu RAJI wrote: > Dear users, > > I have just downloaded QE v4.0.4. After successful compilation on my AMD dual- processor, I tried to run some examples in the code. But each time I do this, the following error messages are reported, and this is case of may examples that I have tried : > > running cp.x as: mpirun -np 2 /home/araji/Codes/espresso-4.0.5/bin/cp.x > > cleaning /home/araji/tmp... done > running the calculation with fixed ions..../run_example: line 131: mpirun: command not found > > How do I handle this? You have to find out where the mpirun command has been hidden... for sure not in the QE folder :-) Seriously: this is not a QE issue, you have to find out why your parallel environment has not been setup properly. You may simply need to load a module, if you're working on a cluster with modules, or at worst reinstall your parallel implementation ;-) If you want to compile a serial version on a multi-core machine, try ./configure --disable-parallel GS > I should mention that I have been able to run the examples on earlier versions, v.4.0.3, e.t.c, without any hitch. > > Thanks for your attention. > > Abdulrafiu Tunde Raji. Physics Department. University of Cape Town. South Africa. > > > Raji Abdulrafiu Tunde, > Department of Physics, > University of Cape Town (RW James Bld.),Private Bag X3, > Rondebosch 7701, > Cape Town. South Africa. > > Office number : Rm. 522 > Cell: +27722668228 > Fax: +27216503342 > > > ______________________________________________________________________________________________ > > UNIVERSITY OF CAPE TOWN > > This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 4500. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. > > _____________________________________________________________________________________________________ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From Giovanni.Cantele at na.infn.it Mon Mar 30 16:29:14 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Mon, 30 Mar 2009 16:29:14 +0200 Subject: [Pw_forum] Can't run any example in QE v4.0.4 In-Reply-To: <49D0E152020000C50019A26B@gwiasmtp.uct.ac.za> References: <49D0E152020000C50019A26B@gwiasmtp.uct.ac.za> Message-ID: <49D0D73A.1040803@na.infn.it> Abdulrafiu RAJI wrote: > Dear users, > > I have just downloaded QE v4.0.4. After successful compilation on my AMD dual- processor, I tried to run some examples in the code. But each time I do this, the following error messages are reported, and this is case of may examples that I have tried : > > running cp.x as: mpirun -np 2 /home/araji/Codes/espresso-4.0.5/bin/cp.x > > cleaning /home/araji/tmp... done > running the calculation with fixed ions..../run_example: line 131: mpirun: command not found > > How do I handle this? I should mention that I have been able to run the examples on earlier versions, v.4.0.3, e.t.c, without any hitch. > > Thanks for your attention. > > Abdulrafiu Tunde Raji. Physics Department. University of Cape Town. South Africa. > > > Raji Abdulrafiu Tunde, > Department of Physics, > University of Cape Town (RW James Bld.),Private Bag X3, > Rondebosch 7701, > Cape Town. South Africa. The error message tells you that you are trying to run "mpirun SOME_COMMAND" but the mpirun command is not found. the run_example script you find in the different example directories, takes the value of some environment variables from examples/environment_variables . You may see this from the lines (of run_example): # set the needed environment variables . ../environment_variables This is done with the aim of changing the environment_variables file once, to fit your system configuration, and then be able to run all the examples without changing the run_example files one by one! If you open the environment_variables you find: # To run the ESPRESSO programs on a parallel machine, you may have to # add the appropriate commands (poe, mpirun, mpprun...) and/or options # (specifying number of processors, pools...) before and after the # executable's name. ............... # To run on a single processor, you can usually leave them empty. PARA_PREFIX="mpirun -np 2" PARA_POSTFIX= As explained, if your machine does not support a parallel environment (either because it is a single core computer or because the parallel environment was improperly installed or not detected by configure) you should leave both the PARA_PREFIX and PARA_POSTFIX variables empty. Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From giannozz at democritos.it Mon Mar 30 16:40:30 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 30 Mar 2009 16:40:30 +0200 Subject: [Pw_forum] cannot remap grid on k-point list In-Reply-To: <212143.36833.qm@web51811.mail.re2.yahoo.com> References: <212143.36833.qm@web51811.mail.re2.yahoo.com> Message-ID: <49D0D9DE.7080906@democritos.it> Ali Tavana wrote: > I have tried [...] I also tried [...] I have rechecked [...] ...but you haven't searched the mailing list archive for this message, that has been discussed approx. 36000 time; nor have you read the README file in example/example07/ : The dense grid must contain all k and k+q grid points used in the subsequent electron-phonon calculation P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From dalcorso at sissa.it Mon Mar 30 16:52:02 2009 From: dalcorso at sissa.it (Dal Corso Andrea) Date: Mon, 30 Mar 2009 16:52:02 +0200 Subject: [Pw_forum] cannot remap grid on k-point list In-Reply-To: <212143.36833.qm@web51811.mail.re2.yahoo.com> References: <212143.36833.qm@web51811.mail.re2.yahoo.com> Message-ID: <1238424722.3256.20.camel@dhpc-5-20.sissa.it> On Mon, 2009-03-30 at 07:16 -0700, Ali Tavana wrote: > omega( 10 - 10) = 190.8 [cm-1] --> B_u > omega( 11 - 11) = 197.8 [cm-1] --> ? > omega( 11 - 11) = 197.8 [cm-1] --> B_g > omega( 11 - 11) = 197.8 [cm-1] --> ? > omega( 11 - 11) = 197.8 [cm-1] --> 0A_u > omega( 12 - 12) = 212.6 [cm-1] --> A_u > omega( 13 - 13) = 276.6 [cm-1] --> B_u > omega( 14 - 14) = 280.7 [cm-1] --> ? > omega( 14 - 14) = 280.7 [cm-1] --> A_g > This might be a problem of the symmetry analyzer unrelated to the problem of the k points in electron phonon. Please provide an input. Andrea -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it From elandry at andrew.cmu.edu Mon Mar 30 16:59:52 2009 From: elandry at andrew.cmu.edu (Eric Landry) Date: Mon, 30 Mar 2009 10:59:52 -0400 Subject: [Pw_forum] interpretation of the file containing the real space force constants Message-ID: <001b01c9b148$2e9777d0$44390280@eLandry> Dear users, I'm trying to understand the format of the file containing the real space force constants output from the q2r.x program. Here is a selection of the output file for calculation of Si using a (444) grid: 4 4 4 1 1 1 1 1 1 1 2.71632979375E-01 2 1 1 -3.79717062500E-03 3 1 1 3.75093750000E-05 4 1 1 -3.79717062500E-03 1 2 1 9.08752437500E-03 2 2 1 -3.62702500000E-04 3 2 1 3.30887500000E-05 4 2 1 -3.79717062500E-03 1 3 1 4.08761312500E-03 2 3 1 -3.62702500000E-04 3 3 1 3.75093750000E-05 4 3 1 -3.62702500000E-04 ... I believe I understand the lines like "1 1 1 1" occurring above, but what are the three numbers before the value of each force constant (how do these numbers correspond to the atomic displacements?) Also, what are the units given for the force constant? Thanks in advance, Eric Landry, Ph.D. candidate Department of Mechanical Engineering, Carnegie Mellon University From chenhanghuipwscf at gmail.com Mon Mar 30 18:23:51 2009 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Mon, 30 Mar 2009 12:23:51 -0400 Subject: [Pw_forum] stress in the Berry phase method Message-ID: <22ae3ca40903300923u2651de1al767e9173baf2046f@mail.gmail.com> Dear PWSCF users, I just have a quick question: if I use the Berry phase method with ultrasoft pseudopotential, is the stress calculated correctly? Thank you. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/b13853b3/attachment.htm From giannozz at democritos.it Mon Mar 30 18:26:03 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 30 Mar 2009 18:26:03 +0200 Subject: [Pw_forum] interpretation of the file containing the real space force constants In-Reply-To: <001b01c9b148$2e9777d0$44390280@eLandry> References: <001b01c9b148$2e9777d0$44390280@eLandry> Message-ID: <49D0F29B.5030508@democritos.it> Eric Landry wrote: > I'm trying to understand the format of the file containing > the real space force constants output from the q2r.x program why? -- Paolo Giannozzi, Democritos and University of Udine, Italy From elandry at andrew.cmu.edu Mon Mar 30 18:29:04 2009 From: elandry at andrew.cmu.edu (Eric Landry) Date: Mon, 30 Mar 2009 12:29:04 -0400 Subject: [Pw_forum] interpretation of the file containing the real space force constants In-Reply-To: <49D0F29B.5030508@democritos.it> References: <001b01c9b148$2e9777d0$44390280@eLandry> <49D0F29B.5030508@democritos.it> Message-ID: <002301c9b154$a43696e0$44390280@eLandry> Paolo, I'd like to use the force constants as input to a code I wrote that calculates the thermal boundary resistance of semiconductor interfaces. Right now, my code uses interatomic potentials to describe the atomic interactions and I'd like to get away from that. Eric -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Monday, March 30, 2009 12:26 PM To: PWSCF Forum Subject: Re: [Pw_forum] interpretation of the file containing the real space force constants Eric Landry wrote: > I'm trying to understand the format of the file containing the real > space force constants output from the q2r.x program why? -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Mon Mar 30 18:46:16 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 30 Mar 2009 18:46:16 +0200 Subject: [Pw_forum] interpretation of the file containing the real space force constants In-Reply-To: <002301c9b154$a43696e0$44390280@eLandry> References: <001b01c9b148$2e9777d0$44390280@eLandry> <49D0F29B.5030508@democritos.it> <002301c9b154$a43696e0$44390280@eLandry> Message-ID: <49D0F758.7070808@democritos.it> Eric Landry wrote: > I'd like to use the force constants as input to a code I wrote that > calculates the thermal boundary resistance of semiconductor interfaces. ok, that's a sufficient reason to invest a few seconds searching for the answer. The "search" facility of the mailing list is unfortunately rather crappy, but I was sure this had been already answered, first with 0 bits of information (but accurate nonetheless): http://www.democritos.it/pipermail/pw_forum/2006-September/004900.html and then with a finite amount of information: http://www.democritos.it/pipermail/pw_forum/2008-September/010099.html Note that the grid of real-space lattice vectors is by construction, periodic! it should be refolded so that it is centered around R=0. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From elandry at andrew.cmu.edu Mon Mar 30 18:51:08 2009 From: elandry at andrew.cmu.edu (Eric Landry) Date: Mon, 30 Mar 2009 12:51:08 -0400 Subject: [Pw_forum] interpretation of the file containing the real space force constants In-Reply-To: <49D0F758.7070808@democritos.it> References: <001b01c9b148$2e9777d0$44390280@eLandry> <49D0F29B.5030508@democritos.it><002301c9b154$a43696e0$44390280@eLandry> <49D0F758.7070808@democritos.it> Message-ID: <002a01c9b157$b9ad4020$44390280@eLandry> Paolo, Perfect! Thanks a lot. Eric -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Monday, March 30, 2009 12:46 PM To: PWSCF Forum Subject: Re: [Pw_forum] interpretation of the file containing the real space force constants Eric Landry wrote: > I'd like to use the force constants as input to a code I wrote that > calculates the thermal boundary resistance of semiconductor interfaces. ok, that's a sufficient reason to invest a few seconds searching for the answer. The "search" facility of the mailing list is unfortunately rather crappy, but I was sure this had been already answered, first with 0 bits of information (but accurate nonetheless): http://www.democritos.it/pipermail/pw_forum/2006-September/004900.html and then with a finite amount of information: http://www.democritos.it/pipermail/pw_forum/2008-September/010099.html Note that the grid of real-space lattice vectors is by construction, periodic! it should be refolded so that it is centered around R=0. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From piotrek at vega.umcs.lublin.pl Mon Mar 30 18:41:35 2009 From: piotrek at vega.umcs.lublin.pl (piotrek at vega.umcs.lublin.pl) Date: Mon, 30 Mar 2009 18:41:35 +0200 (CEST) Subject: [Pw_forum] starting with espressso Message-ID: <729327fc1863b54c2222648354653d26.squirrel@vega.umcs.lublin.pl> Dear Espresso Users, I am beginner with espresso and I have some preliminary problems. I compiled espresso with all options (make all) and try to run test jobs from tutorial: HANDS-ON TUTORIAL OF QUANTUM-ESPRESSO/PWSCF - Simple examples that is: pw.x si.scf.out ( I changed PSEUDO and OUTPUT dir, and download pseudo.pot. file for Si) program started (looking on processor usage and memeory) but there is no output in si.scf.out I guess I probably forget about something, and consequently there is no output but there are no error messages as well. Thanks for help. Piotrek From baroni at sissa.it Mon Mar 30 19:09:11 2009 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 30 Mar 2009 19:09:11 +0200 Subject: [Pw_forum] introducing QE-forge Message-ID: Hi All! The Quantum ESPRESSO community is growing. We want it to be free, creative, altruistic. Free to develop new applications to enhance the functionalities of QE and to make it interoperable with other scientific software. Creative: new developments will allow to calculate properties and to simulate processes that have been so far unaccessible to computer modeling. Altruistic: we encourage all the users/developers to share their own developments with the entire community, and to submit their scientific software to the feedback of the community. The QE-forge portal is a new service that the members of our community can utilize not only to download the latest releases of the QE distribution and related software, but also (and above all, I would say), to allow everyone to open their QE-related project, to maintain it using state-of-the art repository tools, and to share it with other users/developers. QE-forge provides, through a user-friendly web interface, an integrated development environment, whereby researchers can freely upload, manage and maintain their own software, while retaining a full control over it, including the right of not releasing it. The services so far available include source-code management software (CVS or SVN repository), mailing lists, public forums, bug tracking facilities, download space, and wiki pages for projects documentation. QE-forge is expected to become the main tool by which QUANTUM ESPRESSO end users and external contributors can maintain QE-related projects and make them available to the community. Visit http://qe-forge.org Happy QE-forging! Stefano Baroni --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/3ac22a3d/attachment.htm From giannozz at democritos.it Mon Mar 30 19:16:26 2009 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 30 Mar 2009 19:16:26 +0200 Subject: [Pw_forum] starting with espressso In-Reply-To: <729327fc1863b54c2222648354653d26.squirrel@vega.umcs.lublin.pl> References: <729327fc1863b54c2222648354653d26.squirrel@vega.umcs.lublin.pl> Message-ID: <49D0FE6A.3090103@democritos.it> piotrek at vega.umcs.lublin.pl wrote: > pw.x si.scf.out > [...] no output in si.scf.out 1) if you compiled for parallel execution, try pw.x -inp si.scf.in 2) if you didn't, or if the above doesn't work, your f90 compiler is crappy P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From spaul at ncsu.edu Mon Mar 30 19:45:59 2009 From: spaul at ncsu.edu (sujata Paul) Date: Mon, 30 Mar 2009 13:45:59 -0400 Subject: [Pw_forum] PP for Planar average of all |psi|^2 In-Reply-To: 35489.152.14.74.129.1238182858.squirrel@webmail.ncsu.edu Message-ID: <1238435159.30989.0.camel@archimedes> Dear Dr. Giannozzi, Thanks for your reply. I set the prefix properly from scf to PP calculation. When I wrote you earlier I just wanted to write the namelist and parameters I used for my calculations. Sorry for the inconvenience. So could you please tell me how can I make the post processing work when I want to use plot_num=9? Thanks and Regards Sujata Paul From chenhanghuipwscf at gmail.com Mon Mar 30 22:20:02 2009 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Mon, 30 Mar 2009 16:20:02 -0400 Subject: [Pw_forum] force and stress in the Berry phase method Message-ID: <22ae3ca40903301320v7bc9c60dx475e0fea88211889@mail.gmail.com> Dear PWSCF users, In addition to my previous email, I would like to know: if I use ultrasoft psedopotential, are the forces and stress correctly calculated in the Berry phase method in the latest version 4.0.4? Thank you very much. Hanghui Chen Department of Physics, Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/7a46afbe/attachment.htm From tone.kokalj at ijs.si Mon Mar 30 23:45:26 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 30 Mar 2009 23:45:26 +0200 Subject: [Pw_forum] (2) about the logical parameter "use_masses" in IONS card In-Reply-To: <20090330135925.26838.qmail@ms.hfcas.ac.cn> References: <20090330135925.26838.qmail@ms.hfcas.ac.cn> Message-ID: <1238449526.7902.14.camel@walk.ijs.si> On Mon, 2009-03-30 at 21:59 +0800, lfhuang wrote: > Any original papers or good papers on the parameter "use_masses" ? There is no paper on use_masses (as far as I know). Normaly one does not need to use use_masses. This parameter was added out of experience with some systems for the quick-min NEB minimization (i.e. quick-min is a kind of damped dynamics). If some bond is much stiffer than the others then this bond will prevent using larger ds (=time step). Say for example that you want to break C-H bond of adsorbed C2H2 molecule. The triple CC bond is much stiffer than the others, and in this case one may assign to C atom larger "fictitous" mass compared to other atoms. For example you can assing to C a mass of, say, 1.5 and to H the mass of 1.0. If use_masses aids in faster convergence in a given case, and what is the optional ratio between masses, have to be tested. It is difficult to tell it in advance. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From mazouz_moulay at yahoo.fr Tue Mar 31 01:23:38 2009 From: mazouz_moulay at yahoo.fr (mazouz moulay) Date: Mon, 30 Mar 2009 23:23:38 +0000 (GMT) Subject: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms Message-ID: <125524.27039.qm@web25501.mail.ukl.yahoo.com> Dear Prof. Eyvaz ? For ZB CoO supercell it's ok,I can calculate until 16 atoms, no problem. For the other case (4 atoms tetragonal cell), I will try to set up this file using ./exemple25 of Espresso and some other tutorials. Also, I would like to ask you how your QHA code can be cited ? ? Thank you?? Bests regards Moulay Mazouz D?partement de Physique Universit? des Sciences et de la Technologie d'Oran. USTO. Oran.?Alg?rie http://www.ferhatgroup.com/membres.html ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/e2cb8921/attachment.htm From mazouz_moulay at yahoo.fr Tue Mar 31 01:23:43 2009 From: mazouz_moulay at yahoo.fr (mazouz moulay) Date: Mon, 30 Mar 2009 23:23:43 +0000 (GMT) Subject: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms Message-ID: <204005.75796.qm@web25504.mail.ukl.yahoo.com> Dear Prof. Eyvaz ? For ZB CoO supercell it's ok,I can calculate until 16 atoms, no problem. For the other case (4 atoms tetragonal cell), I will try to set up this file using ./exemple25 of Espresso and some other tutorials. Also, I would like to ask you how your QHA code can be cited ? ? Thank you?? Bests regards Moulay Mazouz D?partement de Physique Universit? des Sciences et de la Technologie d'Oran. USTO. Oran.?Alg?rie http://www.ferhatgroup.com/membres.html ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090330/95624b4e/attachment-0001.htm From baroni at sissa.it Tue Mar 31 06:35:02 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 31 Mar 2009 06:35:02 +0200 Subject: [Pw_forum] force and stress in the Berry phase method In-Reply-To: <22ae3ca40903301320v7bc9c60dx475e0fea88211889@mail.gmail.com> References: <22ae3ca40903301320v7bc9c60dx475e0fea88211889@mail.gmail.com> Message-ID: Dear Hanghui Chen, On Mar 30, 2009, at 10:20 PM, hanghui chen wrote: > Dear PWSCF users, > In addition to my previous email, I would like to know: if I use > ultrasoft psedopotential, are the forces and stress correctly > calculated in the Berry phase method in the latest version 4.0.4? forgive my answering your question in a rather indirect and pedagogical way. this is a question that you could (actually, should) easily answer yourself. just repeat your calculation with (slightly) distorted atomic positions / cell parameters, calculate forces and stresses by finite differences, and compare with the results of the code. this way, you would do yourself and us a favor. yourself, because you would learn not to trust ANY code (not even the best, i.e. QE); us because if the code is supposed to give the right answer and id doesn't, then you will have helped discover a bug ... > Thank you very much. Good luck! Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090331/90571755/attachment.htm From baroni at sissa.it Tue Mar 31 06:38:04 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 31 Mar 2009 06:38:04 +0200 Subject: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms In-Reply-To: <204005.75796.qm@web25504.mail.ukl.yahoo.com> References: <204005.75796.qm@web25504.mail.ukl.yahoo.com> Message-ID: <1BABE4C7-BCD7-49AB-BFC8-F9879B7FE256@sissa.it> On Mar 31, 2009, at 1:23 AM, mazouz moulay wrote: > Dear Prof. Eyvaz > > > Also, I would like to ask you how your QHA code can be cited ? > > I would advise Eyvaz to set up an even rudimentary web page on qe- forge.org and encourage people to cite (at least) that page. regards - Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090331/6854d8de/attachment.htm From lfhuang at theory.issp.ac.cn Tue Mar 31 07:38:00 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 31 Mar 2009 13:38:00 +0800 Subject: [Pw_forum] =?utf-8?q?about_the_quantum_tunneling_of_diffusing_ato?= =?utf-8?q?ms?= Message-ID: <20090331053800.31415.qmail@ms.hfcas.ac.cn> Dear Tone Kokalj: First thank you for your kind attention to my previous poster: "about the logical parameter use_masses in IONS card" Now I have another question: How to calculate the potential barrier for the quantum tunneling of diffusing atoms in PWSCF? Any technical method suggested ? If PWSCF can't calculate this kind of things, where should I get a start to edit the code ? PS: In an excellent paper: P. G. Sundell etc., PRL 92, 155901, the authors found a "symmetrically weighted" method to calculate the "coincidence configuration". Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090331/51db9e80/attachment.htm From baroni at sissa.it Tue Mar 31 08:07:01 2009 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 31 Mar 2009 08:07:01 +0200 Subject: [Pw_forum] about the quantum tunneling of diffusing atoms In-Reply-To: <20090331053800.31415.qmail@ms.hfcas.ac.cn> References: <20090331053800.31415.qmail@ms.hfcas.ac.cn> Message-ID: Dear LF Huang, no code will ever be a substitute of common sense. What you need is simply the potential energy (i.e. "total energy" in the usual DFT parlance) of a system, as a function of the coordinates of the diffusing atom. As simple (or as complicated) as that! Stefano On Mar 31, 2009, at 7:38 AM, lfhuang wrote: > Dear Tone Kokalj: > First thank you for your kind attention to my previous poster: > "about the logical parameter use_masses in IONS > card" Now I have another question: How to calculate the potential > barrier for the quantum tunneling of diffusing > atoms in PWSCF? Any technical method suggested ? If PWSCF can't > calculate this kind of things, where should I > get a start to edit the code ? > PS: In an excellent paper: P. G. Sundell etc., PRL 92, 155901, the > authors found a "symmetrically weighted" method > to calculate the "coincidence configuration". > > Best Wishes! > > Yours Sincerely > L. F. Huang > ------ > ====================================================================== > L.F.Huang(???) lfhuang at theory.issp.ac.cn > ====================================================================== > Add: Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591464-328(office) > Fax: 86-551-5591434 > Web: http://theory.issp.ac.cn> (website of our theory group) > http://www.issp.ac.cn> (website of our institute) > ====================================================================== > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090331/973f7b70/attachment-0001.htm From sclauzer at sissa.it Tue Mar 31 10:35:50 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 31 Mar 2009 10:35:50 +0200 Subject: [Pw_forum] PP for Planar average of all |psi|^2 In-Reply-To: <1238435159.30989.0.camel@archimedes> References: <1238435159.30989.0.camel@archimedes> Message-ID: <49D1D5E6.5090505@sissa.it> sujata Paul wrote: > Dear Dr. Giannozzi, > Thanks for your reply. I set the prefix properly from > scf to PP calculation. When I wrote you earlier I just wanted to write > the namelist and parameters I used for my calculations. Sorry for the > inconvenience. > So could you please tell me how can I make the post processing work when > I want to use plot_num=9? It was written in the error message you posted at the beginning: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from punch_plot : error # 1 no longer implemented, see PP/plan_avg.f90 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% So I guessed "plot_num=9" is not implemented in post processing. You have to use the program plan_avg.x in place of pp.x for this task. Though I never used it, from a glance to the source I guess it should be simple to use: NAMELIST / inputpp / outdir, prefix, filplot You simply need to specify these three strings... GS > > Thanks and Regards > Sujata Paul > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From lfhuang at theory.issp.ac.cn Tue Mar 31 11:04:49 2009 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 31 Mar 2009 17:04:49 +0800 Subject: [Pw_forum] =?utf-8?q?about_the_quantum_tunneling_of_diffusing_ato?= =?utf-8?q?ms?= Message-ID: <20090331090449.469.qmail@ms.hfcas.ac.cn> Dear Prof. Baroni: Thank you for your kind attention! Yes, I totally agree with you. But the coordinates for the "quantum tunneling" are different from that for the adiabatic diffusion, and it seems not easy to find to fulfil the realistic processes. So what I need now is well accepted model to find this kind of coordinates. I have found some papers related to quantum tunneling, but I am still wondering: are there some widely accepted model to find the configurations for quantum tunneling? Could you please introduce me some good papers related or expertise advice? Thank you very much! Best Wishes! Yours Sincerely L. F. Huang > From: Stefano Baroni > > Dear LF Huang, > > no code will ever be a substitute of common sense. What you need is > simply the potential energy (i.e. "total energy" in the usual DFT > parlance) of a system, as a function of the coordinates of the > diffusing atom. As simple (or as complicated) as that! > > Stefano > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale > de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > ------ ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090331/8b95cec9/attachment.htm From eyvaz_isaev at yahoo.com Tue Mar 31 13:57:30 2009 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 31 Mar 2009 04:57:30 -0700 (PDT) Subject: [Pw_forum] QHA in qe-forge In-Reply-To: <1BABE4C7-BCD7-49AB-BFC8-F9879B7FE256@sissa.it> Message-ID: <946461.68100.qm@web65702.mail.ac4.yahoo.com> Hi Stefano, In fact, I have started doing that, thanks. My thanks also go to Paolo he adviced me the same and my apologies not responding immediately to his e-mail. Hopefully I will annonce this soon. Bests, Eyvaz. --- On Tue, 3/31/09, Stefano Baroni wrote: > From: Stefano Baroni > Subject: Re: [Pw_forum] antiferromagnetism in ZB input file with 2 atoms > To: "PWSCF Forum" > Date: Tuesday, March 31, 2009, 8:38 AM > On Mar 31, 2009, at 1:23 AM, mazouz moulay wrote: > > > Dear Prof. Eyvaz > > > > > > Also, I would like to ask you how your QHA code can be > cited ? > > > > > > I would advise Eyvaz to set up an even rudimentary web page > on qe-forge.org and encourage people to cite (at least) that > page. > > regards - Stefano > > --- > Stefano Baroni - SISSA & DEMOCRITOS National > Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 > (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique > est une morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or > PowerPoint attachments > Why? See: > http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From akohlmey at cmm.chem.upenn.edu Tue Mar 31 14:31:17 2009 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 31 Mar 2009 08:31:17 -0400 Subject: [Pw_forum] about the quantum tunneling of diffusing atoms In-Reply-To: References: <20090331053800.31415.qmail@ms.hfcas.ac.cn> Message-ID: <1238502677.5280.325.camel@zero> On Tue, 2009-03-31 at 08:07 +0200, Stefano Baroni wrote: > Dear LF Huang, > > > no code will ever be a substitute of common sense. What you need is > simply the potential energy (i.e. "total energy" in the usual DFT > parlance) of a system, as a function of the coordinates of the > diffusing atom. As simple (or as complicated) as that! please let me add my 2 cents to this. you can go back to a quantum mechanics text book and look up for example the discussions of quantum particle vs. wall cases. the potential doesn't change whether the particle is quantum or classical! what you seem to be looking for is some kind of "barrier crossing probability". now, wrt to that i'd have several concerns: - how accurate is your "classical" barrier potential to begin with? you are doing graphite and hydrogen and use plain DFT. the interaction between a benzene molecule and a hydrogen molecule is a frequently used test case for methods that add dispersion interactions corrections to DFT. hmmm... - is tunneling relevant at all? at T > 0K the carbon atoms move and your barrier will fluctuate, that will affect the crossing probability. similarly, if your hydrogen has enough kinetic energy, tunneling is irrelevant. - what is the correlation length of your system? only if it is long quantum effects of the atom core matter. since you seem to be doing a solid state vacuum system, you should be good on that. after you've made sure that all of the above is not rendering any further studies of the quantum effects pointless, _then_ i would look into path-integral methods (e.g. the works of mark tuckerman and dominik marx) that allow studying probability distributions at finite temperature, albeit mostly in imaginary time. mind you, those calculations are hugely expensive and you may be best off to first make some tests with a classical potential. in fact, i would not be surprised if a suitably chosen classical potential would give you a better representation of the potential barrier than DFT. cheers, axel. > > > Stefano > > On Mar 31, 2009, at 7:38 AM, lfhuang wrote: > > > Dear Tone Kokalj: > > First thank you for your kind attention to my previous poster: > > "about the logical parameter use_masses in IONS > > card" Now I have another question: How to calculate the potential > > barrier for the quantum tunneling of diffusing > > atoms in PWSCF? Any technical method suggested ? If PWSCF can't > > calculate this kind of things, where should I > > get a start to edit the code ? > > PS: In an excellent paper: P. G. Sundell etc., PRL 92, 155901, the > > authors found a "symmetrically weighted" method > > to calculate the "coincidence configuration". > > > > Best Wishes! > > > > Yours Sincerely > > L. F. Huang > > ------ > > ====================================================================== > > L.F.Huang(???) lfhuang at theory.issp.ac.cn > > ====================================================================== > > Add: Research Laboratory for Computational Materials Sciences, > > Instutue of Solid State Physics,the Chinese Academy of Sciences, > > P.O.Box 1129, Hefei 230031, P.R.China > > Tel: 86-551-5591464-328(office) > > Fax: 86-551-5591434 > > Web: http://theory.issp.ac.cn> (website of our theory group) > > http://www.issp.ac.cn> (website of our institute) > > ====================================================================== > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > > La morale est une logique de l'action comme la logique est une morale > de la pens?e - Jean Piaget > > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From cristian.degliesposti at unibo.it Tue Mar 31 14:57:11 2009 From: cristian.degliesposti at unibo.it (Cristian Degli Esposti Boschi) Date: Tue, 31 Mar 2009 14:57:11 +0200 Subject: [Pw_forum] Choice of irreducible representations with ph.x Message-ID: <49D21327.6090106@unibo.it> I would like to perform a phonon calculation at Gamma making a choice of only a selected number of irreducible representations. After a proper scf calculation I use with ph.x with an input file like the following one: Phononic spectrum (1) of CoM (at Gamma) &inputph amass(1)=1.00794, amass(2)=12.011, amass(3)=14.007, amass(4)=15.999, amass(5)=55.845, prefix='CoM', outdir='/scratch/userinfm/cne0fm4a/CoM/results/', iverbosity=1, epsil=.false., fildyn='CoM.dm', nrapp=1, / 0.0 0.0 0.0 1 The problem is that the calculation seems to proceed ignoring the nrapp value and the list of numbers I put in the last line and all the irreps are considered. This happens both for nrapp=1 (one value in the list) or nrapp>1 (nrapp values in the list). pw.x and ph.x are run on the CINECA cluster where there appears to be QE ver. 4.1CVS and I would liketo save cpu time by excluding the undesired irreps. Using the same syntax (nrapp and the list of irreps at the end) to modify the scripts of example02 I successfully select only one of the two irreps for Si with QE ver. 3.2 installed on a desktop pc (reporting the message "Not done in this run"). Might it be a version issue? Thanks a lot for your help and time. -- ___________________________________________________ Cristian Degli Esposti Boschi CNR, CNISM, Unita' di Ricerca di Bologna, c/o Dipartimento di Fisica, Universita' di Bologna viale Berti-Pichat, 6/2, 40127, Bologna, Italia tel. ++39 051 2095114 fax ++39 051 2095113 e-mail: cristian.degliesposti -AT- unibo.it web: http://www.df.unibo.it/fismat/theory ___________________________________________________