From lorenzo.paulatto at impmc.upmc.fr Sat Oct 1 11:54:41 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Sat, 01 Oct 2011 11:54:41 +0200 Subject: [Pw_forum] GADGET and PWSCF In-Reply-To: <4E8633D2.7070608@nc.rr.com> References: <4E8633D2.7070608@nc.rr.com> Message-ID: In data 30 settembre 2011 alle ore 23:25:38, Alex Shearer ha scritto: > The geometries of adsorption are often non-trivial; in papers dealing > with similar systems, a tool known as GADGET is often used for geometry > optimizations (see reference below). It seems that this tool, written in > python, is designed to work in conjunction with VASP itself. Dear Alex, QE includes several optimization methods, one based on the BFGS algorithm and a few based on damped dynamics. On the otehr hand, I could not get a very clear description of what GADGET is supposed to do and it is not publicly available. All I could guess for mthe paper you cite, is that it runs VASP repeatedly and uses the DIIS algorithm to optimize the configuration. In fact from some reference I could find online it appers that DIIS is just a variant of the BFGS method, slightly more efficient in some cases but slightly less in others. My opinion is that just doing a geometry optimization with QE using the default setting is probably pretty much the same as doing a VASP+GADGET optimization, although I cannot be 100% sure. best regards -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From charlie.eppes0113 at gmail.com Sat Oct 1 14:37:05 2011 From: charlie.eppes0113 at gmail.com (Charlie Eppes) Date: Sat, 1 Oct 2011 15:37:05 +0300 Subject: [Pw_forum] images and pools Message-ID: Hello all, I was wondering, in a system administrating point of view, how far is varying the number of images and pools can affect the speed, efficiency, and the results of execution?! I understand the basic concepts of them, but how dependent on the specific input and purpose are they?? can we look to them as pure system and network variables or are they highly dependent on the specific task?? do they affect the answer?? thank you in advance.. any further reading is highly appreciated... Charlie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111001/0cf1e2bc/attachment.htm From ambesh.espresso at gmail.com Sun Oct 2 13:08:53 2011 From: ambesh.espresso at gmail.com (ambesh dixit) Date: Sun, 2 Oct 2011 16:38:53 +0530 Subject: [Pw_forum] CuO bulk Error during compilation Message-ID: Dear all, I tried to compile bulk CuO SCF calculation using following input file, which i built......... &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/espresso/espresso-4.3.2/tmpCuO/' , pseudo_dir = '/home/espresso/espresso-4.3.2/pseudo/' , prefix = 'CuO' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 12, celldm(1) = 5.137, celldm(2) = 0.91356823, celldm(3) = 0.66731555, celldm(4) = -0.165839393, nat = 8, ntyp = 2, ecutwfc = 35 , ecutrho = 240.0 , nbnd = 50, occupations = 'smearing' , degauss = 0.01 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = 0.50, starting_magnetization(2) = -0.50, / &ELECTRONS conv_thr = 1.0d-6 , mixing_mode = 'plain' , mixing_beta = 0.3 , mixing_fixed_ns = 0, / ATOMIC_SPECIES Cu1 63.546 Cu.pbe-paw_kj.UPF Cu2 63.546 Cu.pbe-paw_kj.UPF O1 15.99940 O.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal Cu1 0.250000000 0.250000000 0.000000000 Cu2 0.750000000 0.750000000 0.000000000 Cu2 0.750000000 0.250000000 0.500000000 Cu1 0.250000000 0.750000000 0.500000000 O1 0.000000000 0.419999987 0.250000000 O1 0.000000000 0.580000043 0.750000000 O1 0.500000000 0.919999957 0.250000000 O1 0.500000000 0.080000013 0.750000000 K_POINTS automatic 4 4 4 0 0 0 After running pw.x i got following error............ Warning: card O1 15.9994 O.PBE-RRKJUS.UPF ignored %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_cards : error # 5 species O1 in ATOMIC_POSITIONS is nonexistent %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I dont understand why, evenwhen i visualize using VESTA or xcrysden, there is no problem in getting right monoclinic structure. Kindly suggest where is problem. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111002/46cf0120/attachment.htm From flux_ray12 at 163.com Sun Oct 2 13:42:28 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Sun, 2 Oct 2011 19:42:28 +0800 (CST) Subject: [Pw_forum] CuO bulk Error during compilation In-Reply-To: References: Message-ID: <3bb1dcda.6c5c.132c4713efc.Coremail.flux_ray12@163.com> Since you defined there are 2 types of elements, but in ATOMIC_POSITIONS, you defined 3 kinds, i.e., Cu1, Cu2 and O1. You have at least 2 choices. 1, remove the number behind elements' symble and combined Cu1 and Cu2 as one element, Cu; 2, change the parameter ntyp from 2 to 3. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-02 19:08:53,"ambesh dixit" wrote: Dear all, I tried to compile bulk CuO SCF calculation using following input file, which i built......... &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/espresso/espresso-4.3.2/tmpCuO/' , pseudo_dir = '/home/espresso/espresso-4.3.2/pseudo/' , prefix = 'CuO' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 12, celldm(1) = 5.137, celldm(2) = 0.91356823, celldm(3) = 0.66731555, celldm(4) = -0.165839393, nat = 8, ntyp = 2, ecutwfc = 35 , ecutrho = 240.0 , nbnd = 50, occupations = 'smearing' , degauss = 0.01 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = 0.50, starting_magnetization(2) = -0.50, / &ELECTRONS conv_thr = 1.0d-6 , mixing_mode = 'plain' , mixing_beta = 0.3 , mixing_fixed_ns = 0, / ATOMIC_SPECIES Cu1 63.546 Cu.pbe-paw_kj.UPF Cu2 63.546 Cu.pbe-paw_kj.UPF O1 15.99940 O.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal Cu1 0.250000000 0.250000000 0.000000000 Cu2 0.750000000 0.750000000 0.000000000 Cu2 0.750000000 0.250000000 0.500000000 Cu1 0.250000000 0.750000000 0.500000000 O1 0.000000000 0.419999987 0.250000000 O1 0.000000000 0.580000043 0.750000000 O1 0.500000000 0.919999957 0.250000000 O1 0.500000000 0.080000013 0.750000000 K_POINTS automatic 4 4 4 0 0 0 After running pw.x i got following error............ Warning: card O1 15.9994 O.PBE-RRKJUS.UPF ignored %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_cards : error # 5 species O1 in ATOMIC_POSITIONS is nonexistent %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I dont understand why, evenwhen i visualize using VESTA or xcrysden, there is no problem in getting right monoclinic structure. Kindly suggest where is problem. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111002/2d4bf0dd/attachment.htm From Michael at ihpc.a-star.edu.sg Sun Oct 2 13:45:00 2011 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Sun, 2 Oct 2011 19:45:00 +0800 Subject: [Pw_forum] CuO bulk Error during compilation In-Reply-To: References: Message-ID: <155ADEEB-E51C-4D2E-87BD-9E9FEC338547@ihpc.a-star.edu.sg> Hi, Please be polite and sign your message with your name and affiliation. I see one problem that you have ntyp=2 when it should be 3 since you have 3 things in ATOMIC_SPECIES. Mike Sullivan Institute of High Performance Computing, Singapore michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ On 02-Oct-2011, at 7:08 PM, ambesh dixit wrote: > Dear all, > > I tried to compile bulk CuO SCF calculation using following input file, which i built......... > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/espresso/espresso-4.3.2/tmpCuO/' , > pseudo_dir = '/home/espresso/espresso-4.3.2/pseudo/' , > prefix = 'CuO' , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 12, > celldm(1) = 5.137, > celldm(2) = 0.91356823, > celldm(3) = 0.66731555, > celldm(4) = -0.165839393, > nat = 8, > ntyp = 2, > ecutwfc = 35 , > ecutrho = 240.0 , > nbnd = 50, > occupations = 'smearing' , > degauss = 0.01 , > smearing = 'gaussian' , > nspin = 2 , > starting_magnetization(1) = 0.50, > starting_magnetization(2) = -0.50, > > / > &ELECTRONS > conv_thr = 1.0d-6 , > mixing_mode = 'plain' , > mixing_beta = 0.3 , > mixing_fixed_ns = 0, > / > ATOMIC_SPECIES > Cu1 63.546 Cu.pbe-paw_kj.UPF > Cu2 63.546 Cu.pbe-paw_kj.UPF > O1 15.99940 O.pbe-rrkjus.UPF > > ATOMIC_POSITIONS crystal > Cu1 0.250000000 0.250000000 0.000000000 > Cu2 0.750000000 0.750000000 0.000000000 > Cu2 0.750000000 0.250000000 0.500000000 > Cu1 0.250000000 0.750000000 0.500000000 > O1 0.000000000 0.419999987 0.250000000 > O1 0.000000000 0.580000043 0.750000000 > O1 0.500000000 0.919999957 0.250000000 > O1 0.500000000 0.080000013 0.750000000 > > K_POINTS automatic > 4 4 4 0 0 0 > > After running pw.x i got following error............ > > Warning: card O1 15.9994 O.PBE-RRKJUS.UPF ignored > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_cards : error # 5 > species O1 in ATOMIC_POSITIONS is nonexistent > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > I dont understand why, evenwhen i visualize using VESTA or xcrysden, there is no problem in getting right monoclinic structure. Kindly suggest where is problem. > > > > Thanks > > > "1991-2011 - Creating Growth, Enhancing Lives. Commemorating A*STAR's 20 Years of Science, Technology and Research in Singapore." IHPC Values :: Impact :: Honesty :: Performance :: Co-operation This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From parishok at gmail.com Sun Oct 2 17:25:19 2011 From: parishok at gmail.com (pari shok) Date: Sun, 2 Oct 2011 11:25:19 -0400 Subject: [Pw_forum] A Question about ILDOS on different planes Message-ID: Dear All, Hi. I got obsessed with finding LDOS on parallel planes of a structure and I am trying to find a way to get some results. In the last attempt, I calculated ILDOS on the plane denoted by: e1(1) = 1, e1(2) = 0, e1(3) = 0, e2(1) = 0, e2(2) = 1, e2(3) = 0, e3(1) = 0, e3(2) = 0, e3(3) = 0, in the hope that I get the ILDOS on the plane at the bottom of the structure, and the other time with: e1(1) = 1, e1(2) = 0, e1(3) = 0, e2(1) = 0, e2(2) = 1, e2(3) = 0, e3(1) = 0, e3(2) = 0, e3(3) = 0.5, for getting ILDOS on the plane in the middle of the structure. However, to my surprise, the results are just the same for the same range of the energy. I was wondering whether the post possessing is working properly or I made a mistake. I really appreciate your help and suggestion. P. Shok PhD candidate at UMD. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111002/bc310c19/attachment-0001.htm From gabriele.sclauzero at epfl.ch Mon Oct 3 10:05:41 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Mon, 3 Oct 2011 10:05:41 +0200 Subject: [Pw_forum] A Question about ILDOS on different planes In-Reply-To: References: Message-ID: Dear P. Shok, Il giorno 02/ott/2011, alle ore 17.25, pari shok ha scritto: > Dear All, > Hi. > I got obsessed Obsessed? OMG, take it easier! > with finding LDOS on parallel planes of a structure and I am trying to find a way to get some results. > In the last attempt, I calculated ILDOS on the plane denoted by: First, do you want to compute LDOS and visualize it on a plane or integrate it on a slice of the unit cell? ILDOS is usually referring to LDOS integrated over an ENERGY range, but in your last email you were confusing the space and energy integrals... > e1(1) = 1, > e1(2) = 0, > e1(3) = 0, > e2(1) = 0, > e2(2) = 1, > e2(3) = 0, > e3(1) = 0, > e3(2) = 0, > e3(3) = 0, > in the hope that I get the ILDOS on the plane at the bottom of the structure, and the other time with: > e1(1) = 1, > e1(2) = 0, > e1(3) = 0, > e2(1) = 0, > e2(2) = 1, > e2(3) = 0, > e3(1) = 0, > e3(2) = 0, > e3(3) = 0.5, > for getting ILDOS on the plane in the middle of the structure. You should first understand carefully what the e1,e2,e3 variables are and what units they use. Moreover, you forgot to specify x0, didn't you? Please have a look here: http://www.quantum-espresso.org/input-syntax/INPUT_PP.html#id4264978 The vectors and x0 are in alat units (this means cartesian coordinates, NOT crystal coordinates)! Is your cell cubic or tetragonal? Then, what did you specify for x0? I would strongly suggest you to run and understand example05 before going on. > However, to my surprise, the results are just the same for the same range of the energy. Of course, if you have used iflag=2 (which I can just guess, since you did not report the complete input), then e3 is not used (you have to define a portion of plane, how many vectors do you need, once you have given the origin x0?). HTH GS > I was wondering whether the post possessing is working properly or I made a mistake. > I really appreciate your help and suggestion. > P. Shok > PhD candidate at UMD. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111003/55836ce8/attachment.htm From giannozz at democritos.it Tue Oct 4 08:42:42 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 4 Oct 2011 08:42:42 +0200 Subject: [Pw_forum] images and pools In-Reply-To: References: Message-ID: <691A82BD-FD0D-4F7F-9A37-B0688E9811A3@democritos.it> On Oct 1, 2011, at 14:37 , Charlie Eppes wrote: > I was wondering, in a system administrating point of view, how far > is varying the number of images and pools can affect the speed, > efficiency, and the results of execution?! I understand the basic > concepts of them, but how dependent on the specific input and > purpose are they?? can we look to them as pure system and network > variables or are they highly dependent on the specific task?? I am not sure I understand your question, but as a rule, the effectiveness of all kinds of parallelization depends quite a bit on both the available hardware/ software and on the specific calculation > do they affect the answer?? the final result? of course they don't (apart from small unavoidable numerical differences) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Oct 4 09:11:44 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 04 Oct 2011 09:11:44 +0200 Subject: [Pw_forum] projwfc.x error In-Reply-To: <1675BB3F3586E9459BBC8B9812C3532020C7997A85@EXPO20.exchange.mit.edu> References: <1675BB3F3586E9459BBC8B9812C3532020C7997A85@EXPO20.exchange.mit.edu> Message-ID: <1317712304.7838.1.camel@fe12lx.fisica.uniud.it> On Wed, 2011-09-28 at 23:04 -0400, Zhiting Tian wrote: > from d_matrix_so : error # 19 > D_S (j=1/2) for this symmetry operation is not unitary please provide an example with all needed data to be reproduced, or file a bug report on qe-forge.org P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From ashishespresso at gmail.com Tue Oct 4 11:43:00 2011 From: ashishespresso at gmail.com (Ashish Kumar) Date: Tue, 4 Oct 2011 15:13:00 +0530 Subject: [Pw_forum] problem in vc-relax Message-ID: Hello to all, I have tried for the vc-relax of Mo2C hexagonal system, job is not done properly it come out in between and the atomic positions what I have given in the input file and what I am getting in the out file is different. (i) Why the crystal positions changes. what I think that the nature of the atomic postions must be retained. In Input file ATOMIC_POSITIONS (alat) C 0.00 0.00 0.00 Mo 0.3333333 0.666666 0.25 Mo 0.6666666 0.333333 0.75 In out file we get CELL_PARAMETERS (alat= 5.67296009) 0.946518633 0.001215132 -0.004855406 -0.474470641 0.819090796 -0.000958606 0.009278926 0.007480907 1.741942673 ATOMIC_POSITIONS (alat) C 0.156590059 0.041446237 -0.212516996 Mo 0.157761886 0.589915381 0.269109338 Mo 0.636664528 0.321113609 1.041609035 (ii) why cell_parameter changes in the out file . (I think that for hexagonal system it must be what given in the input file) my input file &control calculation='vc-relax' restart_mode='from_scratch', pseudo_dir = '/home/ashish/softwares/espresso/pseudo/', outdir='/home/ashish/dft/espresso_mo2c/test1/tmp_espresso/' prefix='mo2c' tprnfor = .true., tstress = .true. / &system ibrav=4, celldm(1) =5.672960087 , celldm(3)=1.573617588 , nat=3, ntyp=2, nspin = 1, starting_magnetization(1)=0.7, ecutwfc = 24.0, ecutrho = 288.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.02 / &electrons diagonalization='cg' conv_thr = 1.0e-8 mixing_beta = 0.7 / &ions ion_dynamics='bfgs' / &cell cell_dynamics='bfgs' / ATOMIC_SPECIES {crystal} C 12.01 C.pw91-van_ak.UPF Mo 95.94 Mo.pw91-n-van.UPF ATOMIC_POSITIONS C 0.0 0.0 0.0 Mo 1/3 2/3 1/4 Mo 2/3 1/3 3/4 K_POINTS automatic 4 4 4 0 0 0 can any one help me. What is the mistake (in my input file or else) with best wishes Ashish -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111004/dddf99a9/attachment.htm From menendezmanuel at uniovi.es Tue Oct 4 12:01:36 2011 From: menendezmanuel at uniovi.es (jose manuel menendez montes) Date: Tue, 04 Oct 2011 12:01:36 +0200 Subject: [Pw_forum] problem with ibrav = -12 Message-ID: <1317722496.9651.107.camel@cloro.quimica.uniovi.es> Dear All, Has anyone used the new setting for the P monoclinic Bravais lattice (ibrav=-12)? Using 4.3.2 version or the svn latest one everything goes smooth but when it comes to analyse the crystal vectors, it turns out to work out a completely different thing from what it is said in the manual (INPUT_PW.html). The relevant part of the output is pasted below: celldm(1)= 7.982458 celldm(2)= 1.638821 celldm(3)= 1.861446 celldm(4)= 0.000000 celldm(5)= -0.167251 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of alat) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( 0.000000 1.638821 0.000000 ) a(3) = ( -0.311328 0.000000 1.835226 ) According to the manual: "Alternate choice (ibrav=-12) uses b as unique axis: v1 = (a,0,0), v2 = (0,b,0), v3 = (a*sin(beta),0,c*cos(beta)) where beta is the angle between axis a and c". That is, a and b are correct but c is not. Instead of (a*sin(beta),0,c*cos(beta)), we are geting (c*cos(beta),0,c*sin(beta)). Am I doing anything wrong? Any help would be very much appreciated. ------------------------------------------------------------------------ J.M. Menendez Universidad de Oviedo (Spain) Departamento de Quimica Fisica y Analitica http://www.malta-consolider.com From degironc at sissa.it Tue Oct 4 14:29:04 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 04 Oct 2011 14:29:04 +0200 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: Message-ID: <4E8AFC10.7030800@sissa.it> If you know where the atoms and the cell should be, then you do not need vc-relax (not even relax)... but the code apparently disagrees with your thoughts. trying to figure out why is probably going to increase your understanding. have you visualized the initial and final configuration by XCrysDen or other visualization tool? is it what you think ? stefano On 10/04/2011 11:43 AM, Ashish Kumar wrote: > Hello to all, > > I have tried for the vc-relax of Mo2C hexagonal system, job is not done > properly it come out in between and the atomic positions > > what I have given in the input file and what I am getting in the out file is > different. > (i) Why the crystal positions changes. what I think that the nature of the > atomic postions must be retained. > > In Input file > ATOMIC_POSITIONS (alat) > C 0.00 0.00 0.00 > Mo 0.3333333 0.666666 0.25 > Mo 0.6666666 0.333333 0.75 > > > > In out file we get > > CELL_PARAMETERS (alat= 5.67296009) > 0.946518633 0.001215132 -0.004855406 > -0.474470641 0.819090796 -0.000958606 > 0.009278926 0.007480907 1.741942673 > > ATOMIC_POSITIONS (alat) > C 0.156590059 0.041446237 -0.212516996 > Mo 0.157761886 0.589915381 0.269109338 > Mo 0.636664528 0.321113609 1.041609035 > > > > > (ii) why cell_parameter changes in the out file . (I think that for > hexagonal system it must be what given in the input file) > > > my input file > > &control > calculation='vc-relax' > restart_mode='from_scratch', > pseudo_dir = '/home/ashish/softwares/espresso/pseudo/', > outdir='/home/ashish/dft/espresso_mo2c/test1/tmp_espresso/' > prefix='mo2c' > tprnfor = .true., > tstress = .true. > / > &system > ibrav=4, celldm(1) =5.672960087 , celldm(3)=1.573617588 , nat=3, ntyp=2, > nspin = 1, starting_magnetization(1)=0.7, > ecutwfc = 24.0, ecutrho = 288.0, > occupations='smearing', smearing='methfessel-paxton', degauss=0.02 > / > &electrons > diagonalization='cg' > conv_thr = 1.0e-8 > mixing_beta = 0.7 > / > &ions > ion_dynamics='bfgs' > / > &cell > cell_dynamics='bfgs' > / > ATOMIC_SPECIES {crystal} > C 12.01 C.pw91-van_ak.UPF > Mo 95.94 Mo.pw91-n-van.UPF > ATOMIC_POSITIONS > C 0.0 0.0 0.0 > Mo 1/3 2/3 1/4 > Mo 2/3 1/3 3/4 > > K_POINTS automatic > 4 4 4 0 0 0 > > > can any one help me. What is the mistake (in my input file or else) > > > with best wishes > Ashish > > > > _______________________________________________ > 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/20111004/43dac65c/attachment.htm From arvifis at gmail.com Tue Oct 4 14:34:31 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Tue, 4 Oct 2011 09:34:31 -0300 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: Message-ID: Hi Ashish Kumar, if you don't know: vc-relax means variable-cell relax. So, you're doing this kind of calculation, where the default is relax all cell parameters ( axis, angles, position). You can choose which parameters are fixed or which parameters are relaxed, please read the QE manual, the section &CELL , the variable "cell_dofree" Best. PhD stud Arles V. Gil Rebaza IFLP - Argentina 2011/10/4 Ashish Kumar > Hello to all, > > I have tried for the vc-relax of Mo2C hexagonal system, job is not done > properly it come out in between and the atomic positions > > what I have given in the input file and what I am getting in the out file > is different. > (i) Why the crystal positions changes. what I think that the nature of the > atomic postions must be retained. > > In Input file > ATOMIC_POSITIONS (alat) > C 0.00 0.00 0.00 > Mo 0.3333333 0.666666 0.25 > Mo 0.6666666 0.333333 0.75 > > > > In out file we get > > CELL_PARAMETERS (alat= 5.67296009) > 0.946518633 0.001215132 -0.004855406 > -0.474470641 0.819090796 -0.000958606 > 0.009278926 0.007480907 1.741942673 > > ATOMIC_POSITIONS (alat) > C 0.156590059 0.041446237 -0.212516996 > Mo 0.157761886 0.589915381 0.269109338 > Mo 0.636664528 0.321113609 1.041609035 > > > > > (ii) why cell_parameter changes in the out file . (I think that for > hexagonal system it must be what given in the input file) > > > my input file > > &control > calculation='vc-relax' > restart_mode='from_scratch', > pseudo_dir = '/home/ashish/softwares/espresso/pseudo/', > outdir='/home/ashish/dft/espresso_mo2c/test1/tmp_espresso/' > prefix='mo2c' > tprnfor = .true., > tstress = .true. > / > &system > ibrav=4, celldm(1) =5.672960087 , celldm(3)=1.573617588 , nat=3, > ntyp=2, > nspin = 1, starting_magnetization(1)=0.7, > ecutwfc = 24.0, ecutrho = 288.0, > occupations='smearing', smearing='methfessel-paxton', degauss=0.02 > / > &electrons > diagonalization='cg' > conv_thr = 1.0e-8 > mixing_beta = 0.7 > / > &ions > ion_dynamics='bfgs' > / > &cell > cell_dynamics='bfgs' > / > ATOMIC_SPECIES {crystal} > C 12.01 C.pw91-van_ak.UPF > Mo 95.94 Mo.pw91-n-van.UPF > ATOMIC_POSITIONS > C 0.0 0.0 0.0 > Mo 1/3 2/3 1/4 > Mo 2/3 1/3 3/4 > > K_POINTS automatic > 4 4 4 0 0 0 > > > can any one help me. What is the mistake (in my input file or else) > > > with best wishes > Ashish > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111004/0c55a1f4/attachment.htm From giannozz at democritos.it Tue Oct 4 15:53:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 04 Oct 2011 15:53:33 +0200 Subject: [Pw_forum] problem with ibrav = -12 In-Reply-To: <1317722496.9651.107.camel@cloro.quimica.uniovi.es> References: <1317722496.9651.107.camel@cloro.quimica.uniovi.es> Message-ID: <1317736413.14029.4.camel@fe12lx.fisica.uniud.it> On Tue, 2011-10-04 at 12:01 +0200, jose manuel menendez montes wrote: > According to the manual: "Alternate choice (ibrav=-12) uses b as unique > axis: v1 = (a,0,0), v2 = (0,b,0), v3 = (a*sin(beta),0,c*cos(beta)) > where beta is the angle between axis a and c". That is, a and b are > correct but c is not. Instead of (a*sin(beta),0,c*cos(beta)), we are > getting (c*cos(beta),0,c*sin(beta)). Am I doing anything wrong? you did nothing wrong. I think that the manual is wrong: v3 = (c*sin(beta),0,c*cos(beta)) Thank you for remarking this P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From Michael.Mehl at nrl.navy.mil Tue Oct 4 15:55:12 2011 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Tue, 04 Oct 2011 09:55:12 -0400 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: Message-ID: <4E8B1040.50905@nrl.navy.mil> On 10/04/2011 05:43 AM, Ashish Kumar wrote: > Hello to all, > > I have tried for the vc-relax of Mo2C hexagonal system, job is not done > properly it come out in between and the atomic positions > > what I have given in the input file and what I am getting in the out > file is different. > (i) Why the crystal positions changes. what I think that the nature of > the atomic postions must be retained. > > In Input file > ATOMIC_POSITIONS (alat) > C 0.00 0.00 0.00 > Mo 0.3333333 0.666666 0.25 > Mo 0.6666666 0.333333 0.75 > alat tells the program that the coordinates are Cartesian positions. You want "crystal" here. -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From zhiting at MIT.EDU Tue Oct 4 16:19:35 2011 From: zhiting at MIT.EDU (Zhiting Tian) Date: Tue, 4 Oct 2011 10:19:35 -0400 Subject: [Pw_forum] projwfc.x error In-Reply-To: <1317712304.7838.1.camel@fe12lx.fisica.uniud.it> References: <1675BB3F3586E9459BBC8B9812C3532020C7997A85@EXPO20.exchange.mit.edu>, <1317712304.7838.1.camel@fe12lx.fisica.uniud.it> Message-ID: <1675BB3F3586E9459BBC8B9812C3532020C7997AB0@EXPO20.exchange.mit.edu> Sorry that I was using espresso-4.2. When I use a newer version, it works now. ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi [giannozz at democritos.it] Sent: Tuesday, October 04, 2011 3:11 AM To: PWSCF Forum Subject: Re: [Pw_forum] projwfc.x error On Wed, 2011-09-28 at 23:04 -0400, Zhiting Tian wrote: > from d_matrix_so : error # 19 > D_S (j=1/2) for this symmetry operation is not unitary please provide an example with all needed data to be reproduced, or file a bug report on qe-forge.org P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From vkarthik at MIT.EDU Tue Oct 4 18:11:11 2011 From: vkarthik at MIT.EDU (vkarthik) Date: Tue, 04 Oct 2011 12:11:11 -0400 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: Message-ID: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> ATOMIC_POSITIONS {crystal} C 0.00 0.00 0.00 Mo 0.3333333 0.666666 0.25 Mo 0.6666666 0.333333 0.75 This will work for hexagonal system. Quoting "Arles V. Gil Rebaza" : > Hi Ashish Kumar, if you don't know: vc-relax means variable-cell relax. So, > you're doing this kind of calculation, where the default is relax all cell > parameters ( axis, angles, position). You can choose which parameters are > fixed or which parameters are relaxed, please read the QE manual, the > section &CELL , the variable "cell_dofree" > > Best. > > PhD stud Arles V. Gil Rebaza > IFLP - Argentina > > 2011/10/4 Ashish Kumar > >> Hello to all, >> >> I have tried for the vc-relax of Mo2C hexagonal system, job is not done >> properly it come out in between and the atomic positions >> >> what I have given in the input file and what I am getting in the out file >> is different. >> (i) Why the crystal positions changes. what I think that the nature of the >> atomic postions must be retained. >> >> In Input file >> ATOMIC_POSITIONS (alat) >> C 0.00 0.00 0.00 >> Mo 0.3333333 0.666666 0.25 >> Mo 0.6666666 0.333333 0.75 >> >> >> >> In out file we get >> >> CELL_PARAMETERS (alat= 5.67296009) >> 0.946518633 0.001215132 -0.004855406 >> -0.474470641 0.819090796 -0.000958606 >> 0.009278926 0.007480907 1.741942673 >> >> ATOMIC_POSITIONS (alat) >> C 0.156590059 0.041446237 -0.212516996 >> Mo 0.157761886 0.589915381 0.269109338 >> Mo 0.636664528 0.321113609 1.041609035 >> >> >> >> >> (ii) why cell_parameter changes in the out file . (I think that for >> hexagonal system it must be what given in the input file) >> >> >> my input file >> >> &control >> calculation='vc-relax' >> restart_mode='from_scratch', >> pseudo_dir = '/home/ashish/softwares/espresso/pseudo/', >> outdir='/home/ashish/dft/espresso_mo2c/test1/tmp_espresso/' >> prefix='mo2c' >> tprnfor = .true., >> tstress = .true. >> / >> &system >> ibrav=4, celldm(1) =5.672960087 , celldm(3)=1.573617588 , nat=3, >> ntyp=2, >> nspin = 1, starting_magnetization(1)=0.7, >> ecutwfc = 24.0, ecutrho = 288.0, >> occupations='smearing', smearing='methfessel-paxton', degauss=0.02 >> / >> &electrons >> diagonalization='cg' >> conv_thr = 1.0e-8 >> mixing_beta = 0.7 >> / >> &ions >> ion_dynamics='bfgs' >> / >> &cell >> cell_dynamics='bfgs' >> / >> ATOMIC_SPECIES {crystal} >> C 12.01 C.pw91-van_ak.UPF >> Mo 95.94 Mo.pw91-n-van.UPF >> ATOMIC_POSITIONS >> C 0.0 0.0 0.0 >> Mo 1/3 2/3 1/4 >> Mo 2/3 1/3 3/4 >> >> K_POINTS automatic >> 4 4 4 0 0 0 >> >> >> can any one help me. What is the mistake (in my input file or else) >> >> >> with best wishes >> Ashish >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ###---------> Arles V. <---------### > From agkvashnin at gmail.com Tue Oct 4 21:34:26 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Tue, 4 Oct 2011 12:34:26 -0700 Subject: [Pw_forum] problem in vc-relax In-Reply-To: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> References: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> Message-ID: Dear QE users, I have some trouble with obtaining energy of atomic hydrogen using LDA pseudopotentials. When I ran my calculations I have the following error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from calbec : error # 1 size mismatch %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% But when I try to use GGA pseudos I haven't got this error, and calculation done successfully Has anyone known what's problem? input file attached. Thanks for any advice -- Sincerely yours *Alexander G. Kvashnin* -------------------------------------------------------------------------------------------------------------------------------- Second year of master degree study Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111004/a641cd36/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: input_H.opt Type: application/octet-stream Size: 890 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111004/a641cd36/attachment.obj From giannozz at democritos.it Tue Oct 4 22:21:43 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 4 Oct 2011 22:21:43 +0200 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> Message-ID: On Oct 4, 2011, at 21:34 , Alexander G. Kvashnin wrote: > from calbec : error # 1 > size mismatch > Has anyone known what's problem? input file attached. it works for me. What version of QE are you using? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From agkvashnin at gmail.com Tue Oct 4 22:23:06 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Tue, 4 Oct 2011 13:23:06 -0700 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> Message-ID: I'm using QE 4.2.1. 4.1.3 and 4.3 also didn't work On 4 October 2011 13:21, Paolo Giannozzi wrote: > > On Oct 4, 2011, at 21:34 , Alexander G. Kvashnin wrote: > > > from calbec : error # 1 > > size mismatch > > > Has anyone known what's problem? input file attached. > > it works for me. What version of QE are you using? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely yours *Alexander G. Kvashnin* -------------------------------------------------------------------------------------------------------------------------------- Second year of master degree study Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111004/86afdf8b/attachment.htm From giannozz at democritos.it Tue Oct 4 22:27:24 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 4 Oct 2011 22:27:24 +0200 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> Message-ID: On Oct 4, 2011, at 22:23 , Alexander G. Kvashnin wrote: > I'm using QE 4.2.1. > 4.1.3 and 4.3 also didn't work go into tests/ and run "./check-pw.x.j lattice-ibrav*in". Does it work? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From agkvashnin at gmail.com Tue Oct 4 23:03:35 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Tue, 4 Oct 2011 14:03:35 -0700 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> Message-ID: Yes, I check that, it works On 4 October 2011 13:27, Paolo Giannozzi wrote: > > On Oct 4, 2011, at 22:23 , Alexander G. Kvashnin wrote: > > > I'm using QE 4.2.1. > > 4.1.3 and 4.3 also didn't work > > go into tests/ and run "./check-pw.x.j lattice-ibrav*in". > Does it work? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely yours *Alexander G. Kvashnin* -------------------------------------------------------------------------------------------------------------------------------- Second year of master degree study Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111004/ede7dfcb/attachment-0001.htm From germaneau at gucas.ac.cn Wed Oct 5 14:45:54 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Wed, 05 Oct 2011 08:45:54 -0400 Subject: [Pw_forum] Issue with phonon calculation on supercell. Message-ID: <4E8C5182.9060008@gucas.ac.cn> Dear all, I'm attempting to compute phonon at gamma point of a 2x2x2 crystal structure but I get the error bellow : *.....* Atomic displacements: There are 192 irreducible representations Representation 1 1 modes - To be done Representation 2 1 modes - To be done *....* Representation 191 1 modes - To be done Representation 192 1 modes - To be done Alpha used in Ewald sum = 2.8000 PHONON : 51m 2.98s CPU 51m13.49s WALL Electric Fields Calculation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from calbec : error # 1 size mismatch %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Signal 15 received. Signal 15 received. Signal 15 received. Signal 15 received. Signal 15 received. Signal 15 received. Signal 15 received. Signal 15 received. Signal 15 received. Signal 15 received. Signal 15 received. Signal 15 received. Signal 15 received. Here is my input phonons &inputph tr2_ph=1.0d-14, prefix='S007__086_B4N4.vcrelax.vcrelax_2x2x2', epsil=.true., amass(1)=10.811000, amass(2)=14.006700, outdir='./SCF_PH', fildyn='S007__086_B4N4.vcrelax.vcrelax_2x2x2.dynG', / 0.0 0.0 0.0 What sounds weird to me is that I don't have any problem when I perform the same calculation on the unit cell, I mean the 1x1x1 structure. Before running ph.x I do a regular scf calculation at gamma point only which ends normally: K_POINTS automatic 1 1 1 0 0 0 I generate my supercell from the optimized unit cell and do not optimized it again due to time consuming. I don't have much experience in phonon calculations so any hits are welcome. Thank you, ?ric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111005/c2c5a07f/attachment.htm From g0800703 at nus.edu.sg Wed Oct 5 05:22:13 2011 From: g0800703 at nus.edu.sg (He Jinghui) Date: Wed, 05 Oct 2011 11:22:13 +0800 Subject: [Pw_forum] nspin=1 in NEB calculation Message-ID: <4E8BCD65.9090300@nus.edu.sg> Dear QE users: I was wondering once i set nspin=1, do i have to settot_magnetization? In my calculation, i was going to perform a geometry relaxation on a cluster model. Then I will search the transition state by the NEB calculation. The system is of even number of electrons. The transition state probably involve free radical. So I want to switch on the spin, then let the system determine the spin in SCF cycle. When I set nspin=1, the pw.x program require me the tot_magnetization. Since I just move from siesta to QE, the former only need to set spin_polarized true. So I was a little confused about the setting in QE. How could I do? Thanks for your help in advance. regards Jinghui From flux_ray12 at 163.com Wed Oct 5 07:41:57 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Wed, 5 Oct 2011 13:41:57 +0800 (CST) Subject: [Pw_forum] Can we obtain anharmonic vibration energy from s3.x? Message-ID: <5517cb25.21ce.132d29a436f.Coremail.flux_ray12@163.com> Dear QE developer and users: I am using ph.x and QHA to calculate thermodynamics properties of some compositions and their solid-solutions. However, for some materials and their solid-solution, the results shows agaist to the thermodynamics "general sense", for example, DeltaG,Delta Gibbs Free Energy, lower than ideal solution at low temperature but higher at high temperature. But in "general sense", the ideal solution line cannot be overcome, that means if one solution's DeltaG was once lower than ideal solution's, then ideal solution line should be its limitation even at very high temperature. Therefore, I want to check whether this phenomenon was due to anharmonic effect or not. I have known that we can calculate anharmonic dynamic matrix for specified q-point by s3.x code, but I also want to know whether we can gather the anharmonic dynamic matrics to form IFC and anharmonic-phDOS. Moreover, if we can obtain IFC and phDOS for anharmonic case, is it possible to calculate Fvib from them? Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111005/19689af9/attachment.htm From giannozz at democritos.it Wed Oct 5 08:18:40 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 5 Oct 2011 08:18:40 +0200 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> Message-ID: <05A5A450-40D2-4BF9-8FC7-A9F22DE1D4EC@democritos.it> On Oct 4, 2011, at 23:03 , Alexander G. Kvashnin wrote: > Yes, I check that, it works it is the same as your case (H atom with local pseudopotential). Are you by any chance compiling with g95? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From science35 at gmail.com Wed Oct 5 09:06:24 2011 From: science35 at gmail.com (patriot pershing) Date: Wed, 5 Oct 2011 09:06:24 +0200 Subject: [Pw_forum] how to calculate magnetic moment on each atoms Message-ID: dear any one: i have performed scf calculations for Ferromagnetic (FM) and anti-ferromagnetic (AFM) state of C doped ZnO and i would known how to calculate the magnetic moment on each atoms in my supercell as well as electronic charge density for the spin up and down best regards -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111005/e05f3adb/attachment.htm From cyrille.barreteau at cea.fr Wed Oct 5 09:37:30 2011 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Wed, 5 Oct 2011 09:37:30 +0200 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__how_to_calculate_magnetic_mom?= =?iso-8859-1?q?ent_on_each_atoms?= References: Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE31731@DIODON.extra.cea.fr> You can use projwfc.x to obtain a lowdin projection onto atomic like wavefunctions of the electronic density. You will obtain both local integrated quantities (local charges and moments) and local density of states on each atom and orbital. cyrille ================================================= Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Bat. 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================== -------- Message d'origine-------- De: pw_forum-bounces at pwscf.org de la part de patriot pershing Date: mer. 05/10/2011 09:06 ?: Pw_forum at pwscf.org Objet : [Pw_forum] how to calculate magnetic moment on each atoms dear any one: i have performed scf calculations for Ferromagnetic (FM) and anti-ferromagnetic (AFM) state of C doped ZnO and i would known how to calculate the magnetic moment on each atoms in my supercell as well as electronic charge density for the spin up and down best regards -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 3179 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111005/85bc4928/attachment-0001.bin From lmartinsamos at gmail.com Wed Oct 5 10:33:09 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 5 Oct 2011 10:33:09 +0200 Subject: [Pw_forum] server maintenance Message-ID: Dear all, this afternoon there will be probably some connection problems with the Quantum ESPRESSO web page due to server maintenance. thank you for your comprehension Layla -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111005/93e4798f/attachment.htm From fratesi at mater.unimib.it Wed Oct 5 10:37:39 2011 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Wed, 5 Oct 2011 10:37:39 +0200 (CEST) Subject: [Pw_forum] nspin=1 in NEB calculation In-Reply-To: <4E8BCD65.9090300@nus.edu.sg> References: <4E8BCD65.9090300@nus.edu.sg> Message-ID: Dear Jinghui, > I was wondering once i set nspin=1, do i have to settot_magnetization? do you mean "nspin=2"? This is indeed the option for a spin-polarized (collinear) calculation, see Doc/INPUT_PW.txt In that case, yes, you have to specify the starting magnetization of the system (there are a number of ways, again have a look to Doc/INPUT_PW.txt). And yes, the default is different from SIESTA where -forbid me, I'm not experienced of that code- imposing "spin_polarized true" implies by default a ferromagnetic starting point. HTH, Guido PS As for NEB, keep in mind that if the magnetization of your system is crucially depending on coordinates (as an example, if your transition state is magnetic but the initial and final states are not), then you might have some difficulty in imposing the true magnetized state for some image in the path, because the starting charge density might be extrapolated from previous steps where the system is not magnetic. In that case, you could either continue the calculation but restarting from atomic charges, or replace that charge from one of a separate, controlled SCF calculation. -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From arvifis at gmail.com Wed Oct 5 13:41:34 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Wed, 5 Oct 2011 08:41:34 -0300 Subject: [Pw_forum] how to calculate magnetic moment on each atoms In-Reply-To: References: Message-ID: Hi Patriot, if you want to get the magnetic moment per atom just add the variable "report = 1" in &SYSTEM, please read the QE manual. Best PhD stud Arles V. Gil Rebaza IFLP - Argentina 2011/10/5 patriot pershing > dear any one: > i have performed scf calculations for Ferromagnetic (FM) and > anti-ferromagnetic (AFM) state of C doped ZnO and i would known how to > calculate the magnetic moment on each atoms in my supercell as well as > electronic charge density for the spin up and down > best regards > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111005/faead63a/attachment.htm From marc.blanchard at impmc.upmc.fr Wed Oct 5 16:10:05 2011 From: marc.blanchard at impmc.upmc.fr (Marc Blanchard) Date: Wed, 5 Oct 2011 16:10:05 +0200 Subject: [Pw_forum] Open postdoctoral position in computational molecular modelling for geochemical applications Message-ID: <374CBEC5-56D9-4124-84E5-A28108A81676@impmc.upmc.fr> A 2 years postdoctoral position is available at the IMPMC laboratory (Paris, France). The proposing group is one of the world-leading groups in the field of the theoretical determination of isotopic properties of a system from ab initio calculation of the vibrational density of states. The method has been successfully applied to solids (e.g. Blanchard et al. 2009). The post-doctoral fellowship will be mainly devoted to the development of this method to liquid phases. This work will be conducted within a collaborative project involving mineralogists and physicists, which aims at improving our understanding of the crystal-chemistry of iron- bearing minerals and of the geochemistry of minor and trace metal pollutants at solid-solution interfaces. Applicants should have a strong background in quantum molecular computer simulations (computer codes employed in this project are based on density functional theory). Knowledge in geosciences will be greatly appreciated. See attachment for further information. ___________________________ Dr Marc Blanchard Equipe de Min?ralogie Environnementale Institut de Min?ralogie et de Physique des Milieux Consens?s (IMPMC) Tour 23 - Couloir 23/24 - 4e ?tage - Bureau 23 Case courrier 115 4 place Jussieu 75252 Paris Cedex 05 Tel: +33 (0)1 44 27 98 22 Fax: +33 (0)1 44 27 37 85 http://www-int.impmc.upmc.fr/~blanchard -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc_ANR_CrIMin.pdf Type: application/pdf Size: 96149 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111005/10fb8c0b/attachment-0001.pdf From landaulev at 163.com Wed Oct 5 17:38:41 2011 From: landaulev at 163.com (jinxi) Date: Wed, 5 Oct 2011 23:38:41 +0800 (CST) Subject: [Pw_forum] molecule raman tensor calculation meet error Message-ID: <172a808.2f3a.132d4bc9743.Coremail.landaulev@163.com> Dear all: I try to calculate the raman tensors of pyridine molecule: phonons of py at Gamma &inputph tr2_ph=1.0d-14, prefix='py', epsil=.true., trans=.true., lraman=.true., elop=.true., amass(1)=12.01, amass(2)=14.007, amass(3)=1.0079, outdir='./stor', fildyn='py.dynG', fildrho='py.drho', / 0.0 0.0 0.0 Then the output file gives the error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from io_pattern : error # 1 wrong iflag %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Is there anything wrong with my input? Many thanks! best wishes jinxi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111005/a831d531/attachment.htm From landaulev at 163.com Wed Oct 5 17:27:32 2011 From: landaulev at 163.com (jinxi) Date: Wed, 5 Oct 2011 23:27:32 +0800 (CST) Subject: [Pw_forum] molecule raman tensor calculation meet error Message-ID: Dear all: I try to calculate the raman tensors of pyridine molecule: phonons of py at Gamma &inputph tr2_ph=1.0d-14, prefix='py', epsil=.true., trans=.true., lraman=.true., elop=.true., amass(1)=12.01, amass(2)=14.007, amass(3)=1.0079, outdir='./stor', fildyn='py.dynG', fildrho='py.drho', / 0.0 0.0 0.0 Then the output file gives the error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from io_pattern : error # 1 wrong iflag %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Is there anything wrong with my input? Many thanks! best wishes jinxi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111005/1cf092c4/attachment.htm From parishok at gmail.com Wed Oct 5 18:28:59 2011 From: parishok at gmail.com (pari shok) Date: Wed, 5 Oct 2011 12:28:59 -0400 Subject: [Pw_forum] A Question about ILDOS on different planes Message-ID: Dear Gabriel, Thank you very much for your answer. The original problem that I need to solve is getting the local density of states on different planes of the structure. As you know, QE calculates 3D-DOS of the structure and I need to convert it to quasi-2D-DOS, somehow. This is what is done by "Takahiro Yamasaki et al.", in "Geometric and electronic structures of SiO2/Si(001)? interfaces"; they divided the unit cell into 1.0 a.u. (50.529 ?) thick slices parallel to the interface, and specify each slice as a local region, and then define a local density of states for each region. I need to do the same thing for my structure, and I was wondering if (and how)I can get it with QE. I know ILDOS is the integration in a range of energy. What I wanted to do was finding ILDOS on planes (I don't know how) for a very small fraction of energy each time to get them all in a wide range of energies to have a rough estimate of LDOS on the parallel planes. My structure is hexagonal with vacuum in z direction. I got all the x0(i)=0 (I thought I didn't need to change the origin given by x0(i), while I change e3) and iflag=2. I need to get 2D-DOS for further calculation, thus I don't need to visualize, just the data. A couple of months ago, I thought that I might have got LDOS on planes by summing the partial projected DOS of all atoms at the interface (which I guess it was silly). If you (or anybody) could give me hints, I would really appreciate. Yours P Shock PhD candidate UMD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111005/063db707/attachment.htm From agkvashnin at gmail.com Wed Oct 5 20:57:01 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Wed, 5 Oct 2011 11:57:01 -0700 Subject: [Pw_forum] problem in vc-relax In-Reply-To: <05A5A450-40D2-4BF9-8FC7-A9F22DE1D4EC@democritos.it> References: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> <05A5A450-40D2-4BF9-8FC7-A9F22DE1D4EC@democritos.it> Message-ID: I compiled it with gfortran, and also did it with g95, but I also have this error On 4 October 2011 23:18, Paolo Giannozzi wrote: > > On Oct 4, 2011, at 23:03 , Alexander G. Kvashnin wrote: > > > Yes, I check that, it works > > it is the same as your case (H atom with local pseudopotential). > Are you by any chance compiling with g95? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely yours *Alexander G. Kvashnin* -------------------------------------------------------------------------------------------------------------------------------- Second year of master degree study Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111005/47f03a18/attachment.htm From giannozz at democritos.it Wed Oct 5 23:01:05 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 5 Oct 2011 23:01:05 +0200 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> <05A5A450-40D2-4BF9-8FC7-A9F22DE1D4EC@democritos.it> Message-ID: On Oct 5, 2011, at 20:57 , Alexander G. Kvashnin wrote: > I compiled it with gfortran, and also did it with g95, but I also > have this error all I can say is that the problem you observe is in some way related to the case of zero nonlocal projectors, but 1) it works for me (and everybody else, I guess) 2) if it works on the tests, it should work in all other cases P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Oct 5 23:03:17 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 5 Oct 2011 23:03:17 +0200 Subject: [Pw_forum] molecule raman tensor calculation meet error In-Reply-To: References: Message-ID: On Oct 5, 2011, at 17:27 , jinxi wrote: > from io_pattern : error # 1 > wrong iflag this should be a problem of v.4.3, fixed in v.4.3.1 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From gabriele.sclauzero at epfl.ch Thu Oct 6 09:09:34 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Thu, 6 Oct 2011 09:09:34 +0200 Subject: [Pw_forum] A Question about ILDOS on different planes In-Reply-To: References: Message-ID: <1C1DBCF8-188C-440A-80C3-D7DF0D7388C5@epfl.ch> Il giorno 05/ott/2011, alle ore 18.28, pari shok ha scritto: > Dear Gabriel, > Thank you very much for your answer. > The original problem that I need to solve is getting the local density of states on different planes of the structure. As you know, QE calculates 3D-DOS of the structure and I need to convert it to quasi-2D-DOS, somehow. What is "quasi-2D-DOS"? Could you please make an effort to define better the quantity that you want to plot? > This is what is done by "Takahiro Yamasaki et al.", in "Geometric and electronic structures of SiO2/Si(001)? interfaces"; they divided the unit cell into 1.0 a.u. (50.529 ?) thick slices parallel to the interface, and specify each slice as a local region, and then define a local density of states for each region. > I need to do the same thing for my structure, and I was wondering if (and how)I can get it with QE. Again, so how do they define that? Sorry, I'm not going to read that paper to understand what you need... > I know ILDOS is the integration in a range of energy. > What I wanted to do was finding ILDOS on planes (I don't know how) for a very small fraction of energy each time to get them all in a wide range of energies to have a rough estimate of LDOS on the parallel planes. > My structure is hexagonal with vacuum in z direction. I got all the x0(i)=0 (I thought I didn't need to change the origin given by x0(i), while I change e3) and iflag=2. Please read CAREFULLY the INPUT_PP documentation and example01, as I suggested in my previous email. Since you want a 2D plot you need to use iflag=2 (as you do), so the e3 vector will NOT be used. Instead, you'll definitely need to change x0 if you want to plot the ILDOS on different planes. Suppose your planes are normal to the z axis. Then e1 and e2 need to be chosen according to the size and shape of the basal plane of your unit cell (you could take the first and second unit vectors of the hexagonal cell, see INPUT_PW), while z will run from (0,0,0) to (0,0,celldm(3)), for instance. > I need to get 2D-DOS for further calculation, thus I don't need to visualize, just the data. > A couple of months ago, I thought that I might have got LDOS on planes by summing the partial projected DOS of all atoms at the interface (which I guess it was silly). PDOS != LDOS > If you (or anybody) could give me hints, I would really appreciate. I did, now I hope you make your best to understand and go on by yourself. GS > Yours > P Shock > PhD candidate UMD _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111006/3ca8fdb5/attachment-0001.htm From fratesi at mater.unimib.it Thu Oct 6 10:01:57 2011 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Thu, 6 Oct 2011 10:01:57 +0200 (CEST) Subject: [Pw_forum] A Question about ILDOS on different planes In-Reply-To: References: Message-ID: Dear P. Shok, > What I wanted to do was finding ILDOS on planes (I don't know how) for a > very small fraction of energy each time to get them all in a wide range of > energies to have a rough estimate of LDOS on the parallel planes. If what you want to get is f(E)=\int_{vol}dr LDOS(r,E) , where vol=the volume of your choice, then have a look to example16; http://www.democritos.it/pipermail/pw_forum/2011-May/020530.html HTH, GF -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From ambesh.espresso at gmail.com Thu Oct 6 10:31:21 2011 From: ambesh.espresso at gmail.com (ambesh dixit) Date: Thu, 6 Oct 2011 01:31:21 -0700 Subject: [Pw_forum] Pw_forum Digest, Vol 52, Issue 3 In-Reply-To: References: Message-ID: Dear All Thnx for CuO help, it worked. Kind Regards Ambesh Dixit On Sun, Oct 2, 2011 at 8:25 AM, wrote: > 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. CuO bulk Error during compilation (ambesh dixit) > 2. Re: CuO bulk Error during compilation (GAO Zhe) > 3. Re: CuO bulk Error during compilation (Michael Sullivan) > 4. A Question about ILDOS on different planes (pari shok) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 2 Oct 2011 16:38:53 +0530 > From: ambesh dixit > Subject: [Pw_forum] CuO bulk Error during compilation > To: pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I tried to compile bulk CuO SCF calculation using following input file, > which i built......... > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/espresso/espresso-4.3.2/tmpCuO/' , > pseudo_dir = '/home/espresso/espresso-4.3.2/pseudo/' , > prefix = 'CuO' , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 12, > celldm(1) = 5.137, > celldm(2) = 0.91356823, > celldm(3) = 0.66731555, > celldm(4) = -0.165839393, > nat = 8, > ntyp = 2, > ecutwfc = 35 , > ecutrho = 240.0 , > nbnd = 50, > occupations = 'smearing' , > degauss = 0.01 , > smearing = 'gaussian' , > nspin = 2 , > starting_magnetization(1) = 0.50, > starting_magnetization(2) = -0.50, > > / > &ELECTRONS > conv_thr = 1.0d-6 , > mixing_mode = 'plain' , > mixing_beta = 0.3 , > mixing_fixed_ns = 0, > / > ATOMIC_SPECIES > Cu1 63.546 Cu.pbe-paw_kj.UPF > Cu2 63.546 Cu.pbe-paw_kj.UPF > O1 15.99940 O.pbe-rrkjus.UPF > > ATOMIC_POSITIONS crystal > Cu1 0.250000000 0.250000000 0.000000000 > Cu2 0.750000000 0.750000000 0.000000000 > Cu2 0.750000000 0.250000000 0.500000000 > Cu1 0.250000000 0.750000000 0.500000000 > O1 0.000000000 0.419999987 0.250000000 > O1 0.000000000 0.580000043 0.750000000 > O1 0.500000000 0.919999957 0.250000000 > O1 0.500000000 0.080000013 0.750000000 > > K_POINTS automatic > 4 4 4 0 0 0 > > After running pw.x i got following error............ > > Warning: card O1 15.9994 O.PBE-RRKJUS.UPF ignored > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_cards : error # 5 > species O1 in ATOMIC_POSITIONS is nonexistent > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > I dont understand why, evenwhen i visualize using VESTA or xcrysden, there > is no problem in getting right monoclinic structure. Kindly suggest where > is > problem. > > > > Thanks > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20111002/46cf0120/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Sun, 2 Oct 2011 19:42:28 +0800 (CST) > From: "GAO Zhe" > Subject: Re: [Pw_forum] CuO bulk Error during compilation > To: "PWSCF Forum" > Message-ID: <3bb1dcda.6c5c.132c4713efc.Coremail.flux_ray12 at 163.com> > Content-Type: text/plain; charset="gbk" > > Since you defined there are 2 types of elements, but in ATOMIC_POSITIONS, > you defined 3 kinds, i.e., Cu1, Cu2 and O1. > You have at least 2 choices. 1, remove the number behind elements' symble > and combined Cu1 and Cu2 as one element, Cu; 2, change the parameter ntyp > from 2 to 3. > > > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > > At 2011-10-02 19:08:53,"ambesh dixit" wrote: > Dear all, > > I tried to compile bulk CuO SCF calculation using following input file, > which i built......... > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/espresso/espresso-4.3.2/tmpCuO/' , > pseudo_dir = '/home/espresso/espresso-4.3.2/pseudo/' , > prefix = 'CuO' , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 12, > celldm(1) = 5.137, > celldm(2) = 0.91356823, > celldm(3) = 0.66731555, > celldm(4) = -0.165839393, > nat = 8, > ntyp = 2, > ecutwfc = 35 , > ecutrho = 240.0 , > nbnd = 50, > occupations = 'smearing' , > degauss = 0.01 , > smearing = 'gaussian' , > nspin = 2 , > starting_magnetization(1) = 0.50, > starting_magnetization(2) = -0.50, > > / > &ELECTRONS > conv_thr = 1.0d-6 , > mixing_mode = 'plain' , > mixing_beta = 0.3 , > mixing_fixed_ns = 0, > / > ATOMIC_SPECIES > Cu1 63.546 Cu.pbe-paw_kj.UPF > Cu2 63.546 Cu.pbe-paw_kj.UPF > O1 15.99940 O.pbe-rrkjus.UPF > > ATOMIC_POSITIONS crystal > Cu1 0.250000000 0.250000000 0.000000000 > Cu2 0.750000000 0.750000000 0.000000000 > Cu2 0.750000000 0.250000000 0.500000000 > Cu1 0.250000000 0.750000000 0.500000000 > O1 0.000000000 0.419999987 0.250000000 > O1 0.000000000 0.580000043 0.750000000 > O1 0.500000000 0.919999957 0.250000000 > O1 0.500000000 0.080000013 0.750000000 > > K_POINTS automatic > 4 4 4 0 0 0 > > After running pw.x i got following error............ > > Warning: card O1 15.9994 O.PBE-RRKJUS.UPF ignored > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_cards : error # 5 > species O1 in ATOMIC_POSITIONS is nonexistent > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > I dont understand why, evenwhen i visualize using VESTA or xcrysden, there > is no problem in getting right monoclinic structure. Kindly suggest where is > problem. > > > > Thanks > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20111002/2d4bf0dd/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Sun, 2 Oct 2011 19:45:00 +0800 > From: Michael Sullivan > Subject: Re: [Pw_forum] CuO bulk Error during compilation > To: PWSCF Forum > Message-ID: <155ADEEB-E51C-4D2E-87BD-9E9FEC338547 at ihpc.a-star.edu.sg> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > Please be polite and sign your message with your name and affiliation. > > I see one problem that you have ntyp=2 when it should be 3 since you have 3 > things in ATOMIC_SPECIES. > > Mike Sullivan > Institute of High Performance Computing, Singapore > michael at ihpc.a-star.edu.sg > http://www.sullivan.sg/ > > On 02-Oct-2011, at 7:08 PM, ambesh dixit wrote: > > > Dear all, > > > > I tried to compile bulk CuO SCF calculation using following input file, > which i built......... > > > > &CONTROL > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > outdir = '/home/espresso/espresso-4.3.2/tmpCuO/' , > > pseudo_dir = '/home/espresso/espresso-4.3.2/pseudo/' , > > prefix = 'CuO' , > > tstress = .true. , > > tprnfor = .true. , > > / > > &SYSTEM > > ibrav = 12, > > celldm(1) = 5.137, > > celldm(2) = 0.91356823, > > celldm(3) = 0.66731555, > > celldm(4) = -0.165839393, > > nat = 8, > > ntyp = 2, > > ecutwfc = 35 , > > ecutrho = 240.0 , > > nbnd = 50, > > occupations = 'smearing' , > > degauss = 0.01 , > > smearing = 'gaussian' , > > nspin = 2 , > > starting_magnetization(1) = 0.50, > > starting_magnetization(2) = -0.50, > > > > / > > &ELECTRONS > > conv_thr = 1.0d-6 , > > mixing_mode = 'plain' , > > mixing_beta = 0.3 , > > mixing_fixed_ns = 0, > > / > > ATOMIC_SPECIES > > Cu1 63.546 Cu.pbe-paw_kj.UPF > > Cu2 63.546 Cu.pbe-paw_kj.UPF > > O1 15.99940 O.pbe-rrkjus.UPF > > > > ATOMIC_POSITIONS crystal > > Cu1 0.250000000 0.250000000 0.000000000 > > Cu2 0.750000000 0.750000000 0.000000000 > > Cu2 0.750000000 0.250000000 0.500000000 > > Cu1 0.250000000 0.750000000 0.500000000 > > O1 0.000000000 0.419999987 0.250000000 > > O1 0.000000000 0.580000043 0.750000000 > > O1 0.500000000 0.919999957 0.250000000 > > O1 0.500000000 0.080000013 0.750000000 > > > > K_POINTS automatic > > 4 4 4 0 0 0 > > > > After running pw.x i got following error............ > > > > Warning: card O1 15.9994 O.PBE-RRKJUS.UPF ignored > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from read_cards : error # 5 > > species O1 in ATOMIC_POSITIONS is nonexistent > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > stopping ... > > > > > > I dont understand why, evenwhen i visualize using VESTA or xcrysden, > there is no problem in getting right monoclinic structure. Kindly suggest > where is problem. > > > > > > > > Thanks > > > > > > > > > "1991-2011 - Creating Growth, Enhancing Lives. Commemorating A*STAR's 20 > Years of Science, Technology and Research in Singapore." > > IHPC Values :: Impact :: Honesty :: Performance :: > Co-operation > This email is confidential and may be privileged. If you are not the > intended recipient, please delete it and notify us immediately. Please do > not copy or use it for any purpose, or disclose its contents to any other > person. Thank you. > > > ------------------------------ > > Message: 4 > Date: Sun, 2 Oct 2011 11:25:19 -0400 > From: pari shok > Subject: [Pw_forum] A Question about ILDOS on different planes > To: pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > Hi. > I got obsessed with finding LDOS on parallel planes of a structure and I am > trying to find a way to get some results. > In the last attempt, I calculated ILDOS on the plane denoted by: > e1(1) = 1, > e1(2) = 0, > e1(3) = 0, > e2(1) = 0, > e2(2) = 1, > e2(3) = 0, > e3(1) = 0, > e3(2) = 0, > e3(3) = 0, > in the hope that I get the ILDOS on the plane at the bottom of the > structure, and the other time with: > e1(1) = 1, > e1(2) = 0, > e1(3) = 0, > e2(1) = 0, > e2(2) = 1, > e2(3) = 0, > e3(1) = 0, > e3(2) = 0, > e3(3) = 0.5, > for getting ILDOS on the plane in the middle of the structure. > However, to my surprise, the results are just the same for the same range > of > the energy. > I was wondering whether the post possessing is working properly or I made a > mistake. > I really appreciate your help and suggestion. > P. Shok > PhD candidate at UMD. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20111002/bc310c19/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 52, Issue 3 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111006/508cb2bd/attachment-0001.htm From g0800703 at nus.edu.sg Thu Oct 6 11:27:36 2011 From: g0800703 at nus.edu.sg (He Jinghui) Date: Thu, 06 Oct 2011 17:27:36 +0800 Subject: [Pw_forum] nspin=1 in NEB calculation In-Reply-To: References: Message-ID: <4E8D7488.8060901@nus.edu.sg> Dear Guido and others: Thanks for your kind reply. I have read the manual and still a little bit confused. Please point out if i have a wrong understanding. Does "tot_magnetization" parameter is only for induce starting magnetization, which allowed pw.x to determine during SCF cycles, or it is used to freeze the value during whole calculation? Is this parameter of the same function with: constrained_magnetization='total' together with fixed_magnetization(i), i=1,3 if i used nspin=0, in output file there is still rho_up and rho_down, does this mean the spin-DFT has already been considered even nspin=0? In my case, I want to perform a cluster calculation with even electrons. But the cluster may be at triplet state or singlet one. I just want to switch on the spin-DFT, and let the program determine which one is the ground state and obtained the stable geometry. So want should I set? Thank you all so much for your help! best regards He jinghui Department of Chemistry, NUS, singapore in may > Dear Jinghui, > >> I was wondering once i set nspin=1, do i have to settot_magnetization? > do you mean "nspin=2"? This is indeed the option for a spin-polarized > (collinear) calculation, see Doc/INPUT_PW.txt > > In that case, yes, you have to specify the starting magnetization of the > system (there are a number of ways, again have a look to > Doc/INPUT_PW.txt). And yes, the default is different from SIESTA where > -forbid me, I'm not experienced of that code- imposing "spin_polarized > true" implies by default a ferromagnetic starting point. > > HTH, > Guido > > PS As for NEB, keep in mind that if the magnetization of your system is > crucially depending on coordinates (as an example, if your transition > state is magnetic but the initial and final states are not), then you > might have some difficulty in imposing the true magnetized state for some > image in the path, because the starting charge density might be > extrapolated from previous steps where the system is not magnetic. In that > case, you could either continue the calculation but restarting from atomic > charges, or replace that charge from one of a separate, controlled SCF > calculation. > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111006/dcdf8c48/attachment.htm From fratesi at mater.unimib.it Thu Oct 6 12:19:31 2011 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Thu, 6 Oct 2011 12:19:31 +0200 (CEST) Subject: [Pw_forum] nspin=1 in NEB calculation In-Reply-To: <4E8D7488.8060901@nus.edu.sg> References: <4E8D7488.8060901@nus.edu.sg> Message-ID: > Does "tot_magnetization" parameter is only for induce starting magnetization, > which allowed pw.x to determine during SCF cycles, or it is used to freeze > the value during whole calculation? To induce a starting magnetization, and let the code optimize the energy and find if the ground state is actually spin-polarized, use "starting_magnetization(i)". Have a look to example01, especially the Ni case. Compare with the Cu one. Try adding the same parameters defining the starting magnetization in Cu as you can find for Ni, and see what happens. > if i used nspin=0, in output file there is still rho_up and rho_down, does > this mean the spin-DFT has already been considered even nspin=0? nspin can take values 1,2,4. What would be the meaning of nspin=0? Please have a better look to the documentation eg Doc/INPUT_PW.txt > In my case, I want to perform a cluster calculation with even electrons. But > the cluster may be at triplet state or singlet one. I just want to switch on > the spin-DFT, and let the program determine which one is the ground state and > obtained the stable geometry. So want should I set? see above regards, Guido From jenaparadies at googlemail.com Thu Oct 6 12:46:01 2011 From: jenaparadies at googlemail.com (Lars Matthes) Date: Thu, 6 Oct 2011 10:46:01 +0000 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> <05A5A450-40D2-4BF9-8FC7-A9F22DE1D4EC@democritos.it> Message-ID: I followed the discussion quite a while, hoping somebody knows the solution to this problem. I'm using QE 4.3.2 and due to the structure of our cluster I had no other choice than compiling the program with gfortran as well. During the calculations the same problem in the "calbec" routine occured. On another cluster where I compiled QE with the xlf compiler the error disappeared. Therefore, I think it is a problem related to the gfortran compiler. Any further ideas how to overcome the problem? 2011/10/5 Paolo Giannozzi > > On Oct 5, 2011, at 20:57 , Alexander G. Kvashnin wrote: > > > I compiled it with gfortran, and also did it with g95, but I also > > have this error > > all I can say is that the problem you observe is in some way related > to the > case of zero nonlocal projectors, but > 1) it works for me (and everybody else, I guess) > 2) if it works on the tests, it should work in all other cases > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Lars Matthes Institut f?r Festk?rpertheorie und -optik Friedrich-Schiller-Universit?t Jena Max-Wien-Platz 1 07743 Jena Germany Phone: +49.3641.947163 Mail: Lars.Matthes at uni-jena.de -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111006/29b3e8a2/attachment.htm From valemar at cab.cnea.gov.ar Thu Oct 6 16:03:01 2011 From: valemar at cab.cnea.gov.ar (valemar at cab.cnea.gov.ar) Date: Thu, 6 Oct 2011 11:03:01 -0300 (ART) Subject: [Pw_forum] problems with Fluor pseudopotentials Message-ID: <1117.200.0.233.52.1317909781.squirrel@mail.cab.cnea.gov.ar> Dear all I've problems with the adsorption of a AlF3 molecule on Cu(100). The relaxation calculation never end. I 've doubts about if the pseudopotential of Fluorine is correct. I proved with a simple test system like fluorine bulk and calculate the cell parameter. The structure of bulk fluorine used in the calculation is a cubic Pm-3n (223) spacial group with 8 atoms in the 2a y 6d positions. The lattice parameter experimental data is 6,67 A but mi result is around 4,23 A. I proved with higher ecutrho and both pseudopotential present in http://www.quantum-espresso.org/pseudo.php and the result is the same; around 4 A. Has anyone work with these pseudopotential for Fluorine? These is some problem in yours calculations? My input file is: &control prefix='fluor', outdir='./output' pseudo_dir = '/home/valeria/QE_4.3.2/espresso-4.3.2/pseudo' calculation = 'scf' tprnfor = .TRUE. tstress = .TRUE. / &system ibrav= 1, celldm(1) = 12.00, nat= 8, ntyp= 1, ecutwfc = 30 ecutrho = 400 occupations = 'smearing' smearing = 'mv' degauss = 0.02 / &electrons conv_thr = 1.D-5 / &ions / ATOMIC_SPECIES F 18.9984 F.pbe-n-van_ak.UPF ATOMIC_POSITIONS crystal F 0.000000000 0.000000000 0.000000000 F 0.500000000 0.500000000 0.500000000 F 0.250000000 0.500000000 0.000000000 F 0.750000000 0.500000000 0.000000000 F 0.000000000 0.250000000 0.500000000 F 0.000000000 0.750000000 0.500000000 F 0.500000000 0.000000000 0.250000000 F 0.500000000 0.000000000 0.750000000 K_POINTS automatic 6 6 6 1 1 1 Thank you in advance Valeria Martin DAEE-Bariloche Atomic Center-CNEA From giannozz at democritos.it Thu Oct 6 17:33:37 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 6 Oct 2011 17:33:37 +0200 Subject: [Pw_forum] problem in vc-relax In-Reply-To: References: <20111004121111.rwgsan6dwswcwgwc@webmail.mit.edu> <05A5A450-40D2-4BF9-8FC7-A9F22DE1D4EC@democritos.it> Message-ID: On Oct 6, 2011, at 12:46 , Lars Matthes wrote: > I think it is a problem related to the gfortran compiler. > Any further ideas how to overcome the problem? try to print the dimensions of the various arrays passed to "calbec", using the "size" intrinsic and this is easy). Then try to print the dimensions of the same array in the calling routine (less easy: it is called in several places). Then try to reproduce the problem in a smaller test program (not easy) and file a bug report in the gcc bugzilla. Gfortran developers can be very quick in fixing bugs. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Oct 6 18:54:36 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 6 Oct 2011 18:54:36 +0200 Subject: [Pw_forum] problems with Fluor pseudopotentials In-Reply-To: <1117.200.0.233.52.1317909781.squirrel@mail.cab.cnea.gov.ar> References: <1117.200.0.233.52.1317909781.squirrel@mail.cab.cnea.gov.ar> Message-ID: <6AC82414-FC5F-4D74-A93C-3EB2A70EFB80@democritos.it> On Oct 6, 2011, at 16:03 , valemar at cab.cnea.gov.ar wrote: > I 've doubts about if the pseudopotential of Fluorine is correct. > I proved with a simple test system like fluorine bulk a simpler test is the HF or F2 molecule. There are data for F in atomic_doc/pseudo_library: you can try to use those to generate a new F pseudopotential. Please let us now which pseudopotentials exactly you think are bad P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From germaneau at gucas.ac.cn Fri Oct 7 17:40:33 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Fri, 07 Oct 2011 11:40:33 -0400 Subject: [Pw_forum] Issue with phonon calculation on supercell. In-Reply-To: <517774101.05937@gscas.net.cn> References: <517774101.05937@gscas.net.cn> Message-ID: <4E8F1D71.2090405@gucas.ac.cn> Dear all, Can someone tell me the meaning of the error from calbec : error # 1 size mismatch when running ph.x. Thank you, ?ric. On 10/05/2011 08:45 AM, ?ric Germaneau wrote: > Dear all, > > I'm attempting to compute phonon at gamma point of a 2x2x2 crystal > structure but I get the error bellow : > > *.....* > Atomic displacements: > There are 192 irreducible representations > > Representation 1 1 modes - To be done > > Representation 2 1 modes - To be done > *....* > Representation 191 1 modes - To be done > > Representation 192 1 modes - To be done > > > Alpha used in Ewald sum = 2.8000 > PHONON : 51m 2.98s CPU 51m13.49s WALL > > > Electric Fields Calculation > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from calbec : error # 1 > size mismatch > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > > Here is my input > > phonons > &inputph > tr2_ph=1.0d-14, > prefix='S007__086_B4N4.vcrelax.vcrelax_2x2x2', > epsil=.true., > amass(1)=10.811000, > amass(2)=14.006700, > outdir='./SCF_PH', > fildyn='S007__086_B4N4.vcrelax.vcrelax_2x2x2.dynG', > / > 0.0 0.0 0.0 > > What sounds weird to me is that I don't have any problem when I > perform the same calculation on the unit cell, I mean the 1x1x1 structure. > Before running ph.x I do a regular scf calculation at gamma point only > which ends normally: > > K_POINTS automatic > 1 1 1 0 0 0 > > I generate my supercell from the optimized unit cell and do not > optimized it again due to time consuming. > I don't have much experience in phonon calculations so any hits are > welcome. > Thank you, > > ?ric. > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > /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 -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111007/890e21b5/attachment-0001.htm From physics.skgupta at gmail.com Fri Oct 7 05:49:36 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Fri, 7 Oct 2011 09:19:36 +0530 Subject: [Pw_forum] Issue with phonon calculation on supercell. In-Reply-To: <4E8F1D71.2090405@gucas.ac.cn> References: <517774101.05937@gscas.net.cn> <4E8F1D71.2090405@gucas.ac.cn> Message-ID: Dear ?ric Germaneau Please follow the recent link of "problem in vc-relax", there is something same problem (If i understood correctly), Prof. Paolo Giannozzi suggested that, this is Gfortran problem. Thanks Sanjeev 2011/10/7 ?ric Germaneau > Dear all, > > Can someone tell me the meaning of the error > > from calbec : error # 1 > size mismatch > > when running ph.x. > > Thank you, > > ?ric. > > > On 10/05/2011 08:45 AM, ?ric Germaneau wrote: > > Dear all, > > I'm attempting to compute phonon at gamma point of a 2x2x2 crystal > structure but I get the error bellow : > > *.....* > Atomic displacements: > There are 192 irreducible representations > > Representation 1 1 modes - To be done > > Representation 2 1 modes - To be done > *....* > Representation 191 1 modes - To be done > > Representation 192 1 modes - To be done > > > Alpha used in Ewald sum = 2.8000 > PHONON : 51m 2.98s CPU 51m13.49s WALL > > > Electric Fields Calculation > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from calbec : error # 1 > size mismatch > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > Signal 15 received. > > Here is my input > > phonons > &inputph > tr2_ph=1.0d-14, > prefix='S007__086_B4N4.vcrelax.vcrelax_2x2x2', > epsil=.true., > amass(1)=10.811000, > amass(2)=14.006700, > outdir='./SCF_PH', > fildyn='S007__086_B4N4.vcrelax.vcrelax_2x2x2.dynG', > / > 0.0 0.0 0.0 > > What sounds weird to me is that I don't have any problem when I perform the > same calculation on the unit cell, I mean the 1x1x1 structure. > Before running ph.x I do a regular scf calculation at gamma point only > which ends normally: > > K_POINTS automatic > 1 1 1 0 0 0 > > I generate my supercell from the optimized unit cell and do not optimized > it again due to time consuming. > I don't have much experience in phonon calculations so any hits are > welcome. > Thank you, > > ?ric. > > -- > * Be the change you wish to see in the world > * ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > * 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 listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > -- > * Be the change you wish to see in the world > * ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > * 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 > > -- *Dr. Sanjeev Kumar Gupta* *Post Doctoral Fellow, (Ministry of New and Renewable Energy) Department of Physics, Bhavnagar University, Bhavnagar-364 022 Gujarat, India* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111007/78fa3f8e/attachment.htm From germaneau at gucas.ac.cn Fri Oct 7 18:18:48 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Fri, 07 Oct 2011 12:18:48 -0400 Subject: [Pw_forum] Issue with phonon calculation on supercell. In-Reply-To: <517957891.02419@gscas.net.cn> References: <517774101.05937@gscas.net.cn> <4E8F1D71.2090405@gucas.ac.cn> <517957891.02419@gscas.net.cn> Message-ID: <4E8F2668.7060303@gucas.ac.cn> Dear Sanjeev, Thank you for noticed it. I've just ask to the administrator the compile it with ifort. We'll see. ?ric. On 10/06/2011 11:49 PM, Sanjeev Gupta wrote: > Dear ?ric Germaneau > > Please follow the recent link of "problem in vc-relax", there is > something same problem (If i understood correctly), Prof. Paolo > Giannozzi suggested that, this is Gfortran problem. > > Thanks > > Sanjeev > > > 2011/10/7 ?ric Germaneau > > > Dear all, > > Can someone tell me the meaning of the error > > from calbec : error # 1 > size mismatch > > when running ph.x. > > Thank you, > > ?ric. > > > On 10/05/2011 08:45 AM, ?ric Germaneau wrote: >> Dear all, >> >> I'm attempting to compute phonon at gamma point of a 2x2x2 >> crystal structure but I get the error bellow : >> >> *.....* >> Atomic displacements: >> There are 192 irreducible representations >> >> Representation 1 1 modes - To be done >> >> Representation 2 1 modes - To be done >> *....* >> Representation 191 1 modes - To be done >> >> Representation 192 1 modes - To be done >> >> >> Alpha used in Ewald sum = 2.8000 >> PHONON : 51m 2.98s CPU 51m13.49s WALL >> >> >> Electric Fields Calculation >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from calbec : error # 1 >> size mismatch >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> stopping ... >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> Signal 15 received. >> >> Here is my input >> >> phonons >> &inputph >> tr2_ph=1.0d-14, >> prefix='S007__086_B4N4.vcrelax.vcrelax_2x2x2', >> epsil=.true., >> amass(1)=10.811000, >> amass(2)=14.006700, >> outdir='./SCF_PH', >> fildyn='S007__086_B4N4.vcrelax.vcrelax_2x2x2.dynG', >> / >> 0.0 0.0 0.0 >> >> What sounds weird to me is that I don't have any problem when I >> perform the same calculation on the unit cell, I mean the 1x1x1 >> structure. >> Before running ph.x I do a regular scf calculation at gamma point >> only which ends normally: >> >> K_POINTS automatic >> 1 1 1 0 0 0 >> >> I generate my supercell from the optimized unit cell and do not >> optimized it again due to time consuming. >> I don't have much experience in phonon calculations so any hits >> are welcome. >> Thank you, >> >> ?ric. >> >> -- >> /Be the change you wish to see in the world >> / --- Mahatma Gandhi --- >> >> Dr. ?ric Germaneau >> >> >> Graduate University of Chinese Academy of Sciences >> College of Physical Sciences >> Yuquan Road 19A >> Beijing 100049 >> China >> >> /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 > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > /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 > > > > > -- > *Dr. Sanjeev Kumar Gupta* > *Post Doctoral Fellow, > /(Ministry of New and Renewable Energy/) > Department of Physics, > Bhavnagar University, Bhavnagar-364 022 > Gujarat, India* > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111007/96b8dc21/attachment-0001.htm From hasanx at gmail.com Fri Oct 7 11:15:40 2011 From: hasanx at gmail.com (HASAN SAHIN) Date: Fri, 7 Oct 2011 12:15:40 +0300 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes Message-ID: Dear all, When I calculate phonon spectra of my structure I see that all the modes (including acoustics) are both Raman and Infrared active. Being both R+IR active of all modes seems unphysical. Did anyone experience this type of error ? -- *SINCERELY ########################################## Hasan Sahin Bilkent University National Nanotechnology Research Center http://www.bilkent.edu.tr/~shasan/ http://www.researcherid.com/rid/G-4747-2010 ##########################################* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111007/a4ddb865/attachment.htm From giannozz at democritos.it Fri Oct 7 13:41:48 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 07 Oct 2011 13:41:48 +0200 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes In-Reply-To: References: Message-ID: <1317987708.23944.1.camel@fe12lx.fisica.uniud.it> On Fri, 2011-10-07 at 12:15 +0300, HASAN SAHIN wrote: > all the modes (including acoustics) are both Raman and > Infrared active. Being both R+IR active of all modes > seems unphysical. if there is no symmetry, all modes are both Raman- and IR-active P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri Oct 7 13:52:48 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 07 Oct 2011 13:52:48 +0200 Subject: [Pw_forum] problem in xspectra calculations In-Reply-To: <1317214742.49087.YahooMailClassic@web95706.mail.in.yahoo.com> References: <1317214742.49087.YahooMailClassic@web95706.mail.in.yahoo.com> Message-ID: <1317988368.23944.5.camel@fe12lx.fisica.uniud.it> On Wed, 2011-09-28 at 18:29 +0530, Niharika Joshi wrote: > 'Could not find the element C in the table of K edge energies!' it should be a compiler weirdness. Try to replace in xspectra.f90 e_1s=mygetK(upf(xiabs)%psd)) with e_1s=mygetK(trim(adjustl(upf(xiabs)%psd))) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From hasanx at gmail.com Fri Oct 7 14:54:16 2011 From: hasanx at gmail.com (HASAN SAHIN) Date: Fri, 7 Oct 2011 15:54:16 +0300 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes Message-ID: The following result is obtained by single calculation at gamma point: Mode symmetry, C_3v (3m) point group: omega( 1 - 2) = -7.7 [cm-1] --> E L_3 I+R omega( 3 - 3) = -2.7 [cm-1] --> A_1 L_1 I+R omega( 4 - 5) = 99.4 [cm-1] --> E L_3 I+R omega( 6 - 7) = 134.5 [cm-1] --> E L_3 I+R omega( 8 - 8) = 413.2 [cm-1] --> A_1 L_1 I+R omega( 9 - 10) = 756.0 [cm-1] --> E L_3 I+R omega( 11 - 11) = 852.2 [cm-1] --> A_1 L_1 I+R omega( 12 - 12) = 1058.3 [cm-1] --> A_1 L_1 I+R According to this, my system has a symmetry. -- *SINCERELY ########################################## Hasan Sahin Bilkent University National Nanotechnology Research Center http://www.bilkent.edu.tr/~shasan/ http://www.researcherid.com/rid/G-4747-2010 ##########################################* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111007/9cac5e4d/attachment.htm From giannozz at democritos.it Fri Oct 7 15:35:13 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 07 Oct 2011 15:35:13 +0200 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes In-Reply-To: References: Message-ID: <1317994513.23944.28.camel@fe12lx.fisica.uniud.it> On Fri, 2011-10-07 at 15:54 +0300, HASAN SAHIN wrote: > According to this, my system has a symmetry. it has no inversion symmetry. If I remember correctly, in systems having inversion symmetry, modes are either IR- or Raman-active but not both. Do you have any evidence that some of the modes indicated as active are not? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From hasanx at gmail.com Fri Oct 7 16:06:49 2011 From: hasanx at gmail.com (HASAN SAHIN) Date: Fri, 7 Oct 2011 17:06:49 +0300 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes Message-ID: >* According to this, my system has a symmetry. * it has no inversion symmetry. If I remember correctly, in systems having inversion symmetry, modes are either IR- or Raman-active but not both. Do you have any evidence that some of the modes indicated as active are not? There is no any experimental data on this structure, however I know some structures (having C_3v symmetry) with seperated R and IR peaks. Actually, being R (or IR) active of acoustic modes arouses suspicion about calculation. -- *SINCERELY ########################################## Hasan Sahin Bilkent University National Nanotechnology Research Center http://www.bilkent.edu.tr/~shasan/ http://www.researcherid.com/rid/G-4747-2010 ##########################################* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111007/b4551bbc/attachment.htm From ma at nano.ku.dk Fri Oct 7 15:58:21 2011 From: ma at nano.ku.dk (Martin Andersson) Date: Fri, 07 Oct 2011 15:58:21 +0200 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes In-Reply-To: <1317994513.23944.28.camel@fe12lx.fisica.uniud.it> References: <1317994513.23944.28.camel@fe12lx.fisica.uniud.it> Message-ID: <4E8F057D.7070807@nano.ku.dk> In C3v symmetry the A1 and E modes are both IR and Raman active. The A2 modes are inactive in both techniques. See e.g. http://www.webqc.org/printable-symmetrypointgroup-ct-c3v.html x,y,z are IR active, and x2+y2,xy,etc are Raman active Cheers, Martin Andersson, university of Copenhagen On 10/7/2011 3:35 PM, Paolo Giannozzi wrote: > On Fri, 2011-10-07 at 15:54 +0300, HASAN SAHIN wrote: > >> According to this, my system has a symmetry. > it has no inversion symmetry. If I remember correctly, in systems > having inversion symmetry, modes are either IR- or Raman-active > but not both. Do you have any evidence that some of the modes > indicated as active are not? > > P. From baroni at sissa.it Fri Oct 7 16:33:18 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 7 Oct 2011 16:33:18 +0200 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes In-Reply-To: References: Message-ID: <264783C2-A278-4421-B9BE-6C0374348416@sissa.it> Dear Hasan, > Actually, being R (or IR) active of acoustic modes arouses suspicion about calculation. I do not know how the IR/Raman character of lattice vibrations is assigned in QE (Andrea Dal Corso may want to comment on this). All I can say is that symmetry analysis alone can only say if a mode *may* be Raman. IR active or not, *NOT* if it actually is. (i.e. it can only say which modes are inactive, not which ones are active). The resulting intensity may be exceedingly small (or even rigorously vanishing) for dynamical reasons that have nothing to do with symmetry. For instance, zone-center acoustic modes are inactive because of translational symmetry, which can hardly be detected by point-symmetry arguments. This is the case even for finite systems. Take any polar molecule (H2O, CO, ...) as an example. A rigid translation of the molecule (the 3 independent such modes) has zero frequency and is IR and Raman inactive. I do not believe that such inactivity can be predicted by any rotational symmetry arguments ... In any event, I think that if the code is incorrect, it should be easy to demonstrate. Just take the table of characters of the symmetry group of the system you are interested in, and assign the IR/Raman activity of each mode by yourself. It should not be difficult to do, and it is very instructive to do once in one's life, if you have never done it. If it turns out that the activities reported by QE are incorrect (either because the symmetry group is incorrectly assigned, or because the activity for a given group are incorrectly predicted), please revert to us with a detailed report. Enjoy! Stefano B --- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111007/c25638bc/attachment.htm From dalcorso at sissa.it Fri Oct 7 16:41:42 2011 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Fri, 07 Oct 2011 16:41:42 +0200 Subject: [Pw_forum] Problem with Raman and Infrared Active Modes In-Reply-To: <264783C2-A278-4421-B9BE-6C0374348416@sissa.it> References: <264783C2-A278-4421-B9BE-6C0374348416@sissa.it> Message-ID: <1317998502.32672.17.camel@ulisse.cm.sissa.it> On Fri, 2011-10-07 at 16:33 +0200, Stefano Baroni wrote: > Dear Hasan, > > > > Actually, being R (or IR) active of acoustic modes arouses > > suspicion about calculation. > > > I do not know how the IR/Raman character of lattice vibrations is > assigned in QE (Andrea Dal Corso may want to comment on this). All I > can say is that symmetry analysis alone can only say if a mode *may* > be Raman. IR active or not, *NOT* if it actually is. (i.e. it can only > say which modes are inactive, not which ones are active). The > resulting intensity may be exceedingly small (or even rigorously > vanishing) for dynamical reasons that have nothing to do with > symmetry. For instance, zone-center acoustic modes are inactive > because of translational symmetry, which can hardly be detected by > point-symmetry arguments. This is the case even for finite systems. > Take any polar molecule (H2O, CO, ...) as an example. A rigid > translation of the molecule (the 3 independent such modes) has zero > frequency and is IR and Raman inactive. I do not believe that such > inactivity can be predicted by any rotational symmetry arguments ... > > > In any event, I think that if the code is incorrect, it should be easy > to demonstrate. Just take the table of characters of the symmetry > group of the system you are interested in, and assign the IR/Raman > activity of each mode by yourself. It should not be difficult to do, > and it is very instructive to do once in one's life, if you have never > done it. If it turns out that the activities reported by QE are > incorrect (either because the symmetry group is incorrectly assigned, > or because the activity for a given group are incorrectly predicted), > please revert to us with a detailed report. > This is actually what the code does. It puts a label close to the irreducible representation. The label is taken from the tables of characters for irreducible representation (if x,y, or z are basis functions for the representation it puts IR, if xy, or xz, ecc. are basis functions it puts R, if it has basis of both types it puts R+IR). HTH Andrea > > Enjoy! > Stefano B > > --- > 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 > > > _______________________________________________ > 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 Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it From natalia at npavlenko.com Fri Oct 7 18:19:33 2011 From: natalia at npavlenko.com (Natalia Pavlenko) Date: Fri, 7 Oct 2011 09:19:33 -0700 (PDT) Subject: [Pw_forum] problems with pp.x for parallel processing Message-ID: <1318004373.79142.YahooMailClassic@web5708.biz.mail.ne1.yahoo.com> Dear users, I am trying to calculate charge density plots using pp.x for 8 parallel processors. The scf and nscf calculations are successfully finished. With pp.x, I receive the following warning after the CRASH: ------------------------- task # 0 from local_dos : error # 1 problems with xk_pool ------------------------- In my case, the variable npool=2, which is set in the job script file. In the subroutine local_dos, I have found the following commands: ------------from local_dos--------------------- IF (npool>1) THEN CALL xk_pool( kpoint, nkstot, kpoint_pool, which_pool ) IF (kpoint_pool<1 .or. kpoint_pool> nks) & CALL errore('local_dos','problems with xk_pool',1) i_am_the_pool=(my_pool_id==which_pool) ELSE i_am_the_pool=.true. kpoint_pool=kpoint ENDIF ------------------ How to set up kpoint_pool in this case? In my structure, the k-points are automatically defined: K_POINTS automatic I would be grateful for any advices. Regards, Natalia Pavlenko ------------------------------- Dr. Natalia Pavlenko Institute for Condensed Matter Physics, Lviv, Ukraine Tel.: +38-0322-707401 Fax: +38-0322-761158 From mashiatalaaii at gmail.com Fri Oct 7 18:48:44 2011 From: mashiatalaaii at gmail.com (mashiat alaaii) Date: Fri, 7 Oct 2011 12:48:44 -0400 Subject: [Pw_forum] input and output of average.x Message-ID: Dear All, Hi and thank you for your help in advance. I was wondering if the input and output of average.x are described somewhere. I really didn't figure out how to write the input and output from the code. I really appreciate your help. M. Alaaii -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111007/94d76cb6/attachment.htm From giannozz at democritos.it Fri Oct 7 18:50:52 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 7 Oct 2011 18:50:52 +0200 Subject: [Pw_forum] input and output of average.x In-Reply-To: References: Message-ID: On Oct 7, 2011, at 18:48 , mashiat alaaii wrote: > I was wondering if the input and output of average.x are described > somewhere. simple codes that do not seem to have separate documentation are documented (sort of) in the header of the fortran file. See the header of PP/average.f90 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Oct 7 19:40:28 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 7 Oct 2011 19:40:28 +0200 Subject: [Pw_forum] problems with pp.x for parallel processing In-Reply-To: <1318004373.79142.YahooMailClassic@web5708.biz.mail.ne1.yahoo.com> References: <1318004373.79142.YahooMailClassic@web5708.biz.mail.ne1.yahoo.com> Message-ID: <49AB6842-F196-40EA-B1C9-EA62DA5BC78F@democritos.it> On Oct 7, 2011, at 18:19 , Natalia Pavlenko wrote: > I am trying to calculate charge density plots using pp.x for 8 > parallel > processors. The scf and nscf calculations are successfully finished. > With pp.x, I receive the following warning after the CRASH: you didn't try to run on a diferent number of pools from the one used in the nscf calculation? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From natalia at npavlenko.com Fri Oct 7 20:09:04 2011 From: natalia at npavlenko.com (Natalia Pavlenko) Date: Fri, 7 Oct 2011 11:09:04 -0700 (PDT) Subject: [Pw_forum] problems with pp.x for parallel processing In-Reply-To: <49AB6842-F196-40EA-B1C9-EA62DA5BC78F@democritos.it> Message-ID: <1318010944.42561.YahooMailClassic@web5708.biz.mail.ne1.yahoo.com> I tried two different possibilities: first, I used the same number of pools ("-npool 2") in nscf and in pp.x. In this case I received the message: ------------- from local_dos : error # 1 problems with xk_pool ------------------ Second, I tried to run pp.x without setting the option npool (just pp.x < case_rho.in > case_rho.out), in this case I get the following message after the crash: ------------------ from postproc : error # 1 pw.x run with a different number of pools. Use wf_collect=.true. ------------------- Best regards, N. Pavlenko Dr. Natalia Pavlenko Institute for Condensed Matter Physics, Lviv, Ukraine Tel.: +38-0322-707401 Fax: +38-0322-761158 --- On Fri, 10/7/11, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: Re: [Pw_forum] problems with pp.x for parallel processing > To: "PWSCF Forum" > Date: Friday, October 7, 2011, 10:40 AM > > On Oct 7, 2011, at 18:19 , Natalia Pavlenko wrote: > > > I am trying to calculate charge density plots using > pp.x for 8 > > parallel > > processors. The scf and nscf calculations are > successfully finished. > > With pp.x, I receive the following warning after the > CRASH: > > you didn't try to run on a diferent number of pools from > the one > used in the nscf calculation? > > P. > --- > Paolo Giannozzi, Dept of > Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From hannes at 2horns.com Fri Oct 7 20:01:11 2011 From: hannes at 2horns.com (Hans Horn) Date: Fri, 07 Oct 2011 11:01:11 -0700 Subject: [Pw_forum] working neb example Message-ID: <4E8F3E67.7090201@2horns.com> Folks, could someone pls post a working (simple yet non-trivial) neb example with output. Thx a lot.! H. From crma at sissa.it Fri Oct 7 21:01:41 2011 From: crma at sissa.it (Changru Ma) Date: Fri, 7 Oct 2011 21:01:41 +0200 Subject: [Pw_forum] working neb example In-Reply-To: <4E8F3E67.7090201@2horns.com> References: <4E8F3E67.7090201@2horns.com> Message-ID: Hi, Please have a look at example 17. HTH, Changru On 7 Oct, 2011, at 20:01, Hans Horn wrote: > Folks, > > could someone pls post a working (simple yet non-trivial) neb example > with output. > Thx a lot.! > > H. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111007/b0e8e953/attachment.htm From flux_ray12 at 163.com Fri Oct 7 21:23:40 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Sat, 8 Oct 2011 03:23:40 +0800 (CST) Subject: [Pw_forum] problems with pp.x for parallel processing In-Reply-To: <1318010944.42561.YahooMailClassic@web5708.biz.mail.ne1.yahoo.com> References: <1318010944.42561.YahooMailClassic@web5708.biz.mail.ne1.yahoo.com> Message-ID: <36b06087.ab81.132dfd747f4.Coremail.flux_ray12@163.com> In my opinion, the easiest way to solve this problem is to add wf_collect=.t. in nscf calculation "input" file, then use pp.x output without parallelism. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-08 02:09:04,"Natalia Pavlenko" wrote: >I tried two different possibilities: first, I used the same number of pools ("-npool 2") in nscf and in pp.x. In this case I received the message: >------------- >from local_dos : error # 1 > problems with xk_pool >------------------ >Second, I tried to run pp.x without setting the option npool >(just pp.x < case_rho.in > case_rho.out), in this case I get the following message after the crash: >------------------ >from postproc : error # 1 >pw.x run with a different number of pools. Use wf_collect=.true. >------------------- > >Best regards, N. Pavlenko >Dr. Natalia Pavlenko >Institute for Condensed Matter Physics, >Lviv, Ukraine > >Tel.: +38-0322-707401 >Fax: +38-0322-761158 > > > >--- On Fri, 10/7/11, Paolo Giannozzi wrote: > >> From: Paolo Giannozzi >> Subject: Re: [Pw_forum] problems with pp.x for parallel processing >> To: "PWSCF Forum" >> Date: Friday, October 7, 2011, 10:40 AM >> >> On Oct 7, 2011, at 18:19 , Natalia Pavlenko wrote: >> >> > I am trying to calculate charge density plots using >> pp.x for 8 >> > parallel >> > processors. The scf and nscf calculations are >> successfully finished. >> > With pp.x, I receive the following warning after the >> CRASH: >> >> you didn't try to run on a diferent number of pools from >> the one >> used in the nscf calculation? >> >> P. >> --- >> Paolo Giannozzi, Dept of >> Chemistry&Physics&Environment, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> _______________________________________________ >> 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/20111008/27dba665/attachment-0001.htm From maxradin at umich.edu Fri Oct 7 21:30:07 2011 From: maxradin at umich.edu (maxradin at umich.edu) Date: Fri, 07 Oct 2011 15:30:07 -0400 Subject: [Pw_forum] xspectra - spin polarization and core-hole delocalization Message-ID: <1dae22025b69e7e0d3454748addae4da@umich.edu> Hi, I have two questions regarding XAS calculations. 1. For a system whose ground state is non-magnetic, should the core-hole SCF calculation be spin-polarized? My understanding is that the excited state must be non-magnetic to conserve spin. Thus I would expect that the non-spin-polarized calculation is more physical, even though in my case it is higher in energy than the spin-polarized calculation. 2. From what I've read in the literature, in some systems core-holes are delocalized over two neighboring symmetry equivalent sites. Has anyone tried modeling this situation with xspectra? I could imagine that one might use a half core-hole PP at both sites instead of a full core-hole at one site. Thanks in advance. Max Radin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111007/93b6c445/attachment.htm From natalia at npavlenko.com Fri Oct 7 22:29:06 2011 From: natalia at npavlenko.com (Natalia Pavlenko) Date: Fri, 7 Oct 2011 13:29:06 -0700 (PDT) Subject: [Pw_forum] problems with pp.x for parallel processing In-Reply-To: <36b06087.ab81.132dfd747f4.Coremail.flux_ray12@163.com> Message-ID: <1318019346.19139.YahooMailClassic@web5711.biz.mail.ne1.yahoo.com> It does not work, unfortunately. -------------------------------------------- Dr. Natalia Pavlenko Institute for Condensed Matter Physics, Lviv, Ukraine Tel.: +38-0322-707401 Fax: +38-0322-761158 --- On Fri, 10/7/11, GAO Zhe wrote: From: GAO Zhe Subject: Re: [Pw_forum] problems with pp.x for parallel processing To: "PWSCF Forum" Date: Friday, October 7, 2011, 12:23 PM In my opinion, the easiest way to solve this problem is to add wf_collect=.t. in nscf calculation "input" file, then use pp.x output without parallelism. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At?2011-10-08?02:09:04,"Natalia?Pavlenko"??wrote: >I?tried?two?different?possibilities:?first,?I?used?the?same?number?of?pools?("-npool?2")?in?nscf?and?in?pp.x.?In?this?case?I?received?the?message: >------------- >from?local_dos?:?error?#?????????1 >?????problems?with?xk_pool >------------------ >Second,?I?tried?to?run?pp.x?without?setting?the?option?npool >(just?pp.x??case_rho.out),?in?this?case?I?get?the?following?message?after?the?crash: >------------------ >from?postproc?:?error?#?????????1 >pw.x?run?with?a?different?number?of?pools.?Use?wf_collect=.true. >------------------- > >Best?regards,?N.?Pavlenko >Dr.?Natalia?Pavlenko >Institute?for?Condensed?Matter?Physics, >Lviv,?Ukraine > >Tel.:?+38-0322-707401 >Fax:?+38-0322-761158 > > > >---?On?Fri,?10/7/11,?Paolo?Giannozzi??wrote: > >>?From:?Paolo?Giannozzi? >>?Subject:?Re:?[Pw_forum]?problems?with?pp.x?for?parallel?processing >>?To:?"PWSCF?Forum"? >>?Date:?Friday,?October?7,?2011,?10:40?AM >>? >>?On?Oct?7,?2011,?at?18:19?,?Natalia?Pavlenko?wrote: >>? >>?>?I?am?trying?to?calculate?charge?density?plots?using >>?pp.x?for?8?? >>?>?parallel >>?>?processors.?The?scf?and?nscf?calculations?are >>?successfully?finished. >>?>?With?pp.x,?I?receive?the?following?warning?after?the >>?CRASH: >>? >>?you?didn't?try?to?run?on?a?diferent?number?of?pools?from >>?the?one >>?used?in?the?nscf?calculation? >>? >>?P. >>?--- >>?Paolo?Giannozzi,?Dept?of >>?Chemistry&Physics&Environment, >>?Univ.?Udine,?via?delle?Scienze?208,?33100?Udine,?Italy >>?Phone?+39-0432-558216,?fax?+39-0432-558222 >>? >>? >>? >>? >>?_______________________________________________ >>?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 -----Inline Attachment Follows----- _______________________________________________ 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/20111007/96f061c7/attachment.htm From giannozz at democritos.it Fri Oct 7 22:32:44 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 7 Oct 2011 22:32:44 +0200 Subject: [Pw_forum] problems with pp.x for parallel processing In-Reply-To: <1318019346.19139.YahooMailClassic@web5711.biz.mail.ne1.yahoo.com> References: <1318019346.19139.YahooMailClassic@web5711.biz.mail.ne1.yahoo.com> Message-ID: On Oct 7, 2011, at 22:29 , Natalia Pavlenko wrote: > It does not work, unfortunately. please provide an example that can be run in a reasonable amount of time P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From science35 at gmail.com Sat Oct 8 08:42:22 2011 From: science35 at gmail.com (patriot pershing) Date: Sat, 8 Oct 2011 08:42:22 +0200 Subject: [Pw_forum] how to calculate magnetic moment on each atoms In-Reply-To: References: Message-ID: thank you very much -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111008/02521879/attachment.htm From science35 at gmail.com Sat Oct 8 08:43:42 2011 From: science35 at gmail.com (patriot pershing) Date: Sat, 8 Oct 2011 08:43:42 +0200 Subject: [Pw_forum] RE : how to calculate magnetic moment on each atoms Message-ID: thank you very much 2011/10/5 BARRETEAU Cyrille > > You can use projwfc.x to obtain a lowdin projection onto atomic like > wavefunctions of the electronic density. > You will obtain both local integrated quantities (local charges and > moments) and local density of > states on each atom and orbital. > > cyrille > > ================================================= > Cyrille Barreteau phone : +33 (0)1 69 08 29 51 > CEA Saclay fax : +33 (0)1 69 08 84 46 > IRAMIS, SPCSI, Bat. 462 email cyrille.barreteau at cea.fr > 91191 Gif sur Yvette Cedex > FRANCE > ~~~~~~~~~~~~~~~~~~~~~~~~ > Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ > ================================================== > > > > -------- Message d'origine-------- > De: pw_forum-bounces at pwscf.org de la part de patriot pershing > Date: mer. 05/10/2011 09:06 > ?: Pw_forum at pwscf.org > Objet : [Pw_forum] how to calculate magnetic moment on each atoms > > dear any one: > i have performed scf calculations for Ferromagnetic (FM) and > anti-ferromagnetic (AFM) state of C doped ZnO and i would known how to > calculate the magnetic moment on each atoms in my supercell as well as > electronic charge density for the spin up and down > best regards > > > _______________________________________________ > 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/20111008/c47e4452/attachment.htm From natalia at npavlenko.com Sat Oct 8 10:54:07 2011 From: natalia at npavlenko.com (Natalia Pavlenko) Date: Sat, 8 Oct 2011 01:54:07 -0700 (PDT) Subject: [Pw_forum] problems with pp.x for parallel processing Message-ID: <1318064047.8778.YahooMailClassic@web5703.biz.mail.ne1.yahoo.com> Dear Paolo, In attachment I am sending 3 job scripts for a simple SrTiO3 layered structure which can be calculated pretty fast: (1)scf, (2)nscf and (3) pp.x for evaluation of charge density contours. The scf and nscf calculations are performed without any problem, but pp.x is crashed with the same warning: from local_dos : error # 1 problems with xk_pool I would be grateful for your assistance. With best regards, Natalia ----------------------------------------- Dr. Natalia Pavlenko Institute for Condensed Matter Physics, Lviv, Ukraine Tel.: +38-0322-707401 Fax: +38-0322-761158 --- On Fri, 10/7/11, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: Re: [Pw_forum] problems with pp.x for parallel processing > To: "PWSCF Forum" > Date: Friday, October 7, 2011, 1:32 PM > > On Oct 7, 2011, at 22:29 , Natalia Pavlenko wrote: > > > It does not work, unfortunately. > > please provide an example that can be run in a reasonable > amount of time > > P. > --- > Paolo Giannozzi, Dept of > Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- A non-text attachment was scrubbed... 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Name: 0job_rho Type: application/octet-stream Size: 2500 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111008/0f7330ed/attachment-0002.obj From mariammalmir86 at gmail.com Sat Oct 8 11:45:12 2011 From: mariammalmir86 at gmail.com (mariam malmir) Date: Sat, 8 Oct 2011 13:15:12 +0330 Subject: [Pw_forum] problem Message-ID: i doped one atom on carbon nanotube in few positions. how understand which position is good? thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111008/04c8fb6e/attachment.htm From cyrille.barreteau at cea.fr Sat Oct 8 11:55:31 2011 From: cyrille.barreteau at cea.fr (BARRETEAU Cyrille) Date: Sat, 8 Oct 2011 11:55:31 +0200 Subject: [Pw_forum] =?iso-8859-1?q?RE=A0=3A__problem?= References: Message-ID: <18E4AC9C2FAC504E994A6759DE5ABE8DE31765@DIODON.extra.cea.fr> Could you be more precise and sign your post!! Cyrille ================================================= Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, Bat. 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ ================================================== -------- Message d'origine-------- De: pw_forum-bounces at pwscf.org de la part de mariam malmir Date: sam. 08/10/2011 11:45 ?: pw_forum at pwscf.org Objet : [Pw_forum] problem i doped one atom on carbon nanotube in few positions. how understand which position is good? thanks -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 2684 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111008/0b60d733/attachment.bin From arvifis at gmail.com Sat Oct 8 15:29:23 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Sat, 8 Oct 2011 10:29:23 -0300 Subject: [Pw_forum] problem In-Reply-To: References: Message-ID: Hi mariam, a possible criteria to choose a good position is using the position with minimal total energy. please provide you affiliation PhD stud Arles V. Gil Rebaza IFLP - Argentine 2011/10/8 mariam malmir > i doped one atom on carbon nanotube in few positions. > how understand which position is good? > thanks > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111008/381206a8/attachment.htm From giannozz at democritos.it Sat Oct 8 22:07:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 8 Oct 2011 22:07:46 +0200 Subject: [Pw_forum] problems with pp.x for parallel processing In-Reply-To: <1318064047.8778.YahooMailClassic@web5703.biz.mail.ne1.yahoo.com> References: <1318064047.8778.YahooMailClassic@web5703.biz.mail.ne1.yahoo.com> Message-ID: There is definitely some problem with k-point parallelization (-npool option) in pp.x. However, it worked for me if the "wf_collect" option is used and pp.x is launched without k-point parallelization P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From yaldachem at gmail.com Sun Oct 9 00:31:19 2011 From: yaldachem at gmail.com (yaldaa kh) Date: Sun, 9 Oct 2011 02:01:19 +0330 Subject: [Pw_forum] problem with 4.2.1 version Message-ID: Dear all Beforehand, i did calculation for NO molecule in gas phase by pw.x version 4.0 , now tried to repeat my calculation by 4.2.1 version with the same input file but emerged problem and stopped calculation with this message: ------------------------------------------------------------------------------------------------------- Bad data for namelist object starting_magnetization namelist read: misplaced= sign bad data for namelist object starting_magnetization stop 2 ---------------------------------------------------------------------------------------------------------- &CONTROL calculation = "scf", title = " ", prefix = "nag1", pseudo_dir = "/home/f/espresso-4.0/pseudo", outdir = "/home/f/tmp", / &SYSTEM ibrav = 1, celldm(1) = 25, nat = 2, ntyp = 2, ecutwfc = 60, ecutrho = 400, nosym = .true., nspin = 2 , starting_magnetization(1)= 0.5, multiplicity= 2 , / &ELECTRONS conv_thr = 1.D-7, mixing_beta = 0.7D0, / &IONS / ATOMIC_SPECIES N 1.00 N.pbe-rrkjus.UPF O 1.00 O.pbe-rrkjus.UPF ATOMIC_POSITIONS N 0.0 0.0 0.0 0 0 0 O 0.0 0.0 0.088483035 K_POINTS {automatic} 1 1 1 0 0 0 thank you in advance yaldaa k chemistry teacher dehkhoda highschool hendijan From muirs at onid.orst.edu Sun Oct 9 01:12:40 2011 From: muirs at onid.orst.edu (Sean Muir) Date: Sat, 8 Oct 2011 16:12:40 -0700 Subject: [Pw_forum] Compile error when using Cygwin and gfortran 4.7 Message-ID: Hello Folks, I am band new to quantum espresso and have been trying to get it compiled on my Windows system using Cygwin. I have successfully ran ./configure. During the make pw process I ran into this error. I searched the archives with no luck. The message seems to indicate it is a compiler error and not with quantum espresso. The manual section 2.7 mentions that the compiler is probably buggy and says *'Try to lower the optimization level, or to remove optimization just for the routine that has problems. If it doesn't work, or if you experience weird problems at run time, try to install patches for your version of the compiler'* How would I go about lowering the optimization level? I am using the latest gfortran 4.7 for cygwin, might it help to go back to some previous version? Any help would be appreciated, Sean Oregon State University ( cd SRC; make ) make[3]: Entering directory `/home/smuir/QESource/ espresso-4.3/lapack-3.2/SRC' gfortran -O3 -g -c dlarrv.f -o dlarrv.o dlarrv.f: In function `dlarrv': dlarrv.f:895:0: error: insn does not satisfy its constraints: (insn 2435 54 2436 47 (set (mem/c:SI (plus:SI (reg/f:SI 7 sp) (const_int 108 [0x6c])) [0 S4 A32]) (reg/v/f:SI 15 st(7) [orig:827 indexw ] [827])) dlarrv.f:1 50 {*movsi_internal} (nil)) dlarrv.f:895:0: internal compiler error: in reload_cse_simplify_operands, at postreload.c:403 Please submit a full bug report, with preprocessed source if appropriate. See for instructions. make[3]: *** [dlarrv.o] Error 1 make[3]: Leaving directory `/home/smuir/QESource/espresso-4.3/lapack-3.2/SRC' make[2]: *** [lapacklib] Error 2 make[2]: Leaving directory `/home/smuir/QESource/espresso-4.3/lapack-3.2' make[1]: *** [liblapack_internal] Error 2 make[1]: Leaving directory `/home/smuir/QESource/espresso-4.3/extlibs' make: *** [liblapack] Error 2 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111008/777f29b7/attachment.htm From mashiatalaaii at gmail.com Sun Oct 9 02:30:40 2011 From: mashiatalaaii at gmail.com (mashiat alaaii) Date: Sat, 8 Oct 2011 20:30:40 -0400 Subject: [Pw_forum] input and output of average.x Message-ID: Dear Dr, Giannozi, The output pf "average.x" provides a three-column quantity. I was wondering which quantity is averaged. Actually, I want to get the psi of the structure on different planes and get the planar average of this psi. I was wondering whether I can get the planar average of psi with this program. If positive what the filename should be. Thank you very much. M Alaaii -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111008/6a5d58c5/attachment.htm From mariammalmir86 at gmail.com Sun Oct 9 07:34:37 2011 From: mariammalmir86 at gmail.com (mariam malmir) Date: Sun, 9 Oct 2011 09:04:37 +0330 Subject: [Pw_forum] Pw_forum Digest, Vol 52, Issue 17 In-Reply-To: References: Message-ID: On Sat, Oct 8, 2011 at 11:37 PM, wrote: > 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. Re: problems with pp.x for parallel processing (Natalia Pavlenko) > 2. problem (mariam malmir) > 3. RE?: problem (BARRETEAU Cyrille) > 4. Re: problem (Arles V. Gil Rebaza) > 5. Re: problems with pp.x for parallel processing (Paolo Giannozzi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 8 Oct 2011 01:54:07 -0700 (PDT) > From: Natalia Pavlenko > Subject: Re: [Pw_forum] problems with pp.x for parallel processing > To: PWSCF Forum > Cc: Paolo Giannozzi > Message-ID: > <1318064047.8778.YahooMailClassic at web5703.biz.mail.ne1.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Dear Paolo, > > In attachment I am sending 3 job scripts for a simple SrTiO3 layered > structure which can be calculated pretty fast: (1)scf, (2)nscf and > (3) pp.x for evaluation of charge density contours. The scf and nscf > calculations are performed without any problem, but pp.x is crashed with the > same warning: > > from local_dos : error # 1 > problems with xk_pool > > I would be grateful for your assistance. > With best regards, Natalia > ----------------------------------------- > Dr. Natalia Pavlenko > Institute for Condensed Matter Physics, > Lviv, Ukraine > > Tel.: +38-0322-707401 > Fax: +38-0322-761158 > > > > --- On Fri, 10/7/11, Paolo Giannozzi wrote: > > > From: Paolo Giannozzi > > Subject: Re: [Pw_forum] problems with pp.x for parallel processing > > To: "PWSCF Forum" > > Date: Friday, October 7, 2011, 1:32 PM > > > > On Oct 7, 2011, at 22:29 , Natalia Pavlenko wrote: > > > > > It does not work, unfortunately. > > > > please provide an example that can be run in a reasonable > > amount of time > > > > P. > > --- > > Paolo Giannozzi, Dept of > > Chemistry&Physics&Environment, > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: 0job > Type: application/octet-stream > Size: 3353 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20111008/0f7330ed/attachment-0003.obj > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: 0job_nscf > Type: application/octet-stream > Size: 3407 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20111008/0f7330ed/attachment-0004.obj > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: 0job_rho > Type: application/octet-stream > Size: 2500 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20111008/0f7330ed/attachment-0005.obj > > ------------------------------ > > Message: 2 > Date: Sat, 8 Oct 2011 13:15:12 +0330 > From: mariam malmir > Subject: [Pw_forum] problem > To: pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > i doped one atom on carbon nanotube in few positions. > how understand which position is good? > thanks > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20111008/04c8fb6e/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Sat, 8 Oct 2011 11:55:31 +0200 > From: "BARRETEAU Cyrille" > Subject: [Pw_forum] RE?: problem > To: "PWSCF Forum" > Message-ID: > <18E4AC9C2FAC504E994A6759DE5ABE8DE31765 at DIODON.extra.cea.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Could you be more precise and sign your post!! > > Cyrille > > ================================================= > Cyrille Barreteau phone : +33 (0)1 69 08 29 51 > CEA Saclay fax : +33 (0)1 69 08 84 46 > IRAMIS, SPCSI, Bat. 462 email cyrille.barreteau at cea.fr > 91191 Gif sur Yvette Cedex > FRANCE > ~~~~~~~~~~~~~~~~~~~~~~~~ > Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/ > ================================================== > > > > -------- Message d'origine-------- > De: pw_forum-bounces at pwscf.org de la part de mariam malmir > Date: sam. 08/10/2011 11:45 > ?: pw_forum at pwscf.org > Objet : [Pw_forum] problem > > i doped one atom on carbon nanotube in few positions. > how understand which position is good? > thanks > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: not available > Type: application/ms-tnef > Size: 2684 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20111008/0b60d733/attachment-0001.bin > > ------------------------------ > > Message: 4 > Date: Sat, 8 Oct 2011 10:29:23 -0300 > From: "Arles V. Gil Rebaza" > Subject: Re: [Pw_forum] problem > To: PWSCF Forum > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi mariam, a possible criteria to choose a good position is using the > position with minimal total energy. > > please provide you affiliation > > PhD stud Arles V. Gil Rebaza > IFLP - Argentine > > 2011/10/8 mariam malmir > > > i doped one atom on carbon nanotube in few positions. > > how understand which position is good? > > thanks > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > ###---------> Arles V. <---------### > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20111008/381206a8/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Sat, 8 Oct 2011 22:07:46 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] problems with pp.x for parallel processing > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; format=flowed > > There is definitely some problem with k-point parallelization > (-npool option) in pp.x. However, it worked for me if the > "wf_collect" option is used and pp.x is launched without > k-point parallelization > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 52, Issue 17 > **************************************** > Hi,i study(8,0) carbon nanotube and it's DOS plot show it is a metal?what the problem i did vc-relax whith DEGAUSS 0.01 and 0.003 but dos plot was metal? what is role of pseudopotentials in this problem?i use c.pz-rrkjus.upf -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111009/b12270b1/attachment-0001.htm From natalia at npavlenko.com Sun Oct 9 07:54:41 2011 From: natalia at npavlenko.com (Natalia Pavlenko) Date: Sat, 8 Oct 2011 22:54:41 -0700 (PDT) Subject: [Pw_forum] problems with pp.x for parallel processing In-Reply-To: Message-ID: <1318139681.56443.YahooMailClassic@web5710.biz.mail.ne1.yahoo.com> I know that pp.x works well without k-parallelization, but for this I need to recalculate nscf with wf_collect which takes pretty much time and more memory sources. Best, Natalia Dr. Natalia Pavlenko Institute for Condensed Matter Physics, Lviv, Ukraine Tel.: +38-0322-707401 Fax: +38-0322-761158 --- On Sat, 10/8/11, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: Re: [Pw_forum] problems with pp.x for parallel processing > To: "PWSCF Forum" > Date: Saturday, October 8, 2011, 1:07 PM > There is definitely some problem with > k-point parallelization > (-npool option) in pp.x. However, it worked for me if the > "wf_collect" option is used and pp.x is launched without > k-point parallelization > > P. > --- > Paolo Giannozzi, Dept of > Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From flux_ray12 at 163.com Sun Oct 9 14:47:18 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Sun, 9 Oct 2011 20:47:18 +0800 (CST) Subject: [Pw_forum] Is it possible to calculate free energy of graphite at specified temperature? Message-ID: <6fb8ef28.fc34.132e8b91c2a.Coremail.flux_ray12@163.com> Dear QE developer and users: I am using QE 4.3.2 to calculate phonon and thermaldynamis properties of materials. These days, I need to find the Gibbs (or Helmholtz) Free energy of carbon. Thus, I compared diamond and graphite phases at 0K. As a result, graphite provides lower energy per carbon atom (about 0.3eV/atom lower than of diamond). However, the phonon dispersion result shows that the imaginary frequency occurred at Gamma, H, A and K, so it is impossible by using QHA to find the vibrational free energy at specified temperature. The graphite model I used is: ibrav = 0 , celldm(1) = 1.889725989 , CELL_PARAMETERS 2.130421558318710 -1.229999460182690 0.000000000000000 0.000000000000000 2.459998920365380 0.000000000000000 0.000000000000000 0.000000000000000 6.800000000000000 ATOMIC_POSITIONS crystal C 0.0000000000000000 0.0000000000000000 0.2500000000000000 C 0.0000000000000000 0.0000000000000000 0.7500000000000000 C 0.3333333333333330 0.6666666666666669 0.2500000000000000 C -0.3333333333333330 -0.6666666666666669 0.7500000000000000 Is there any other methods or models can calculate the free energy of graphite at specified temperature? Any suggestion will be welcome. Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111009/62e49347/attachment.htm From bdslipun at gmail.com Sun Oct 9 14:52:02 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 9 Oct 2011 18:22:02 +0530 Subject: [Pw_forum] Is it possible to calculate free energy of graphite at specified temperature? In-Reply-To: <6fb8ef28.fc34.132e8b91c2a.Coremail.flux_ray12@163.com> References: <6fb8ef28.fc34.132e8b91c2a.Coremail.flux_ray12@163.com> Message-ID: no because it is not valid for negative frequncy in phonon spectrum 2011/10/9 GAO Zhe > Dear QE developer and users: > I am using QE 4.3.2 to calculate phonon and thermaldynamis properties of > materials. These days, I need to find the Gibbs (or Helmholtz) Free energy > of carbon. Thus, I compared diamond and graphite phases at 0K. As a result, > graphite provides lower energy per carbon atom (about 0.3eV/atom lower than > of diamond). > However, the phonon dispersion result shows that the imaginary frequency > occurred at Gamma, H, A and K, so it is impossible by using QHA to find the > vibrational free energy at specified temperature. > The graphite model I used is: > *ibrav = 0 , > celldm(1) = 1.889725989 , > CELL_PARAMETERS > 2.130421558318710 -1.229999460182690 0.000000000000000 > 0.000000000000000 2.459998920365380 0.000000000000000 > 0.000000000000000 0.000000000000000 6.800000000000000 > ATOMIC_POSITIONS crystal > C 0.0000000000000000 0.0000000000000000 0.2500000000000000 > C 0.0000000000000000 0.0000000000000000 0.7500000000000000 > C 0.3333333333333330 0.6666666666666669 0.2500000000000000 > C -0.3333333333333330 -0.6666666666666669 0.7500000000000000* > Is there any other methods or models can calculate the free energy of > graphite at specified temperature? > Any suggestion will be welcome. > Thanks. > > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > > > _______________________________________________ > 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/20111009/40c5d362/attachment.htm From yaldachem at gmail.com Sun Oct 9 20:53:38 2011 From: yaldachem at gmail.com (yaldaa kh) Date: Sun, 9 Oct 2011 22:23:38 +0330 Subject: [Pw_forum] problem in calculation by 4.2.1 version Message-ID: Dear all Beforehand, i did calculation about NO molecule in gas phase by pw.x version 4.0 , when tried to repeat my calculation by 4.2.1 version with the same input file, it emerged problem and stopped calculation with this message: ------------------------------------------------------------------------------------------------------- Bad data for namelist object starting_magnetization namelist read: misplaced= sign bad data for namelist object starting_magnetization stop 2 ---------------------------------------------------------------------------------------------------------- the input file is : &CONTROL calculation = "scf", title = " ", prefix = "nag1", pseudo_dir = "/home/f/espresso-4.0/pseudo", outdir = "/home/f/tmp", / &SYSTEM ibrav = 1, celldm(1) = 25, nat = 2, ntyp = 2, ecutwfc = 60, ecutrho = 400, nosym = .true., nspin = 2 , starting_magnetization(1)= 0.5, multiplicity= 2 , / &ELECTRONS conv_thr = 1.D-7, mixing_beta = 0.7D0, / &IONS / ATOMIC_SPECIES N 1.00 N.pbe-rrkjus.UPF O 1.00 O.pbe-rrkjus.UPF ATOMIC_POSITIONS N 0.0 0.0 0.0 0 0 0 O 0.0 0.0 0.088483035 K_POINTS {automatic} 1 1 1 0 0 0 why this problem is happend ? thank you in advance yaldaa k chemistry teacher dehkhoda highschool hendijan From Trinh.Vo at jpl.nasa.gov Mon Oct 10 02:07:50 2011 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Sun, 9 Oct 2011 17:07:50 -0700 Subject: [Pw_forum] species list in "set_hubbard_l.f90" and "tabd.f90" Message-ID: Dear AlL, I checked the list of species in 2 files "set_hubbard_l.f90" and "tabd.f90." The list does not contain transition atoms and La with configuration of d^1. Is there any reason why those species are not included? Thank you, Trinh Vo Computing group JPL/CalTech -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111009/cad1b9c8/attachment.htm From ptao10b at imr.ac.cn Mon Oct 10 04:50:02 2011 From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=) Date: Mon, 10 Oct 2011 10:50:02 +0800 (CST) Subject: [Pw_forum] How to obtain the viberating modes from the file *.dyn? Message-ID: <431129.29369.132ebbca9ef.Coremail.ptao10b@imr.ac.cn> Dear all, I want to visualise the viberating modes at random k point. And I know the dynamic matrixes are written in the file *.dyn while I cannot understand it. Could someone give me an approach to solve the problem? Thank you very much! best reagards, Plato Tao From murty.iitd at gmail.com Mon Oct 10 05:57:02 2011 From: murty.iitd at gmail.com (PLN Murty) Date: Mon, 10 Oct 2011 09:27:02 +0530 Subject: [Pw_forum] (no subject) Message-ID: Dear sir, Shall I know what is Pw_forum mailing list submissions. I have received this mail three times. PLN Murty, IIT Delhi. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111010/3f64d711/attachment.htm From flux_ray12 at 163.com Mon Oct 10 06:37:38 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Mon, 10 Oct 2011 12:37:38 +0800 (CST) Subject: [Pw_forum] Is it possible to calculate free energy of graphite at specified temperature? In-Reply-To: References: <6fb8ef28.fc34.132e8b91c2a.Coremail.flux_ray12@163.com> Message-ID: <40ba7cab.100b0.132ec1f2d69.Coremail.flux_ray12@163.com> Thank you for your kindly reply. Well, normally, if we found imaginary frequency in phonon dispersion, it indicates that this structure is not stable or, at least, unstable at 0K. Therefore, the vibrational free energy becomes unmeaningful because of the imaginary value. However, as we know, graphite is stable phase in a wild temperature range, including 0K. And when we discuss about formation free energy of carbide at specified temperature, graphite is used as reference pure material instead of diamond. This means that the free energy of graphite really exists. Therefore, I wondered whether there are some methods, for example, improving the graphite model, can deal with this problem and calculate vibrational free energy of graphite. Or, whether it is possible that we canneglect the vibration including z-direction and only consider vibration in xy-plane. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-09 20:52:02,"bhabya sahoo" wrote: no because it is not valid for negative frequncy in phonon spectrum 2011/10/9 GAO Zhe Dear QE developer and users: I am using QE 4.3.2 to calculate phonon and thermaldynamis properties of materials. These days, I need to find the Gibbs (or Helmholtz) Free energy of carbon. Thus, I compared diamond and graphite phases at 0K. As a result, graphite provides lower energy per carbon atom (about 0.3eV/atom lower than of diamond). However, the phonon dispersion result shows that the imaginary frequency occurred at Gamma, H, A and K, so it is impossible by using QHA to find the vibrational free energy at specified temperature. The graphite model I used is: ibrav = 0 , celldm(1) = 1.889725989 , CELL_PARAMETERS 2.130421558318710 -1.229999460182690 0.000000000000000 0.000000000000000 2.459998920365380 0.000000000000000 0.000000000000000 0.000000000000000 6.800000000000000 ATOMIC_POSITIONS crystal C 0.0000000000000000 0.0000000000000000 0.2500000000000000 C 0.0000000000000000 0.0000000000000000 0.7500000000000000 C 0.3333333333333330 0.6666666666666669 0.2500000000000000 C -0.3333333333333330 -0.6666666666666669 0.7500000000000000 Is there any other methods or models can calculate the free energy of graphite at specified temperature? Any suggestion will be welcome. Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea _______________________________________________ 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/20111010/4bc0b240/attachment-0001.htm From germaneau at gucas.ac.cn Mon Oct 10 19:05:44 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Mon, 10 Oct 2011 13:05:44 -0400 Subject: [Pw_forum] Is it possible to calculate free energy of graphite at specified temperature? In-Reply-To: <518220858.30290@gscas.net.cn> References: <6fb8ef28.fc34.132e8b91c2a.Coremail.flux_ray12@163.com> <518220858.30290@gscas.net.cn> Message-ID: <4E9325E8.5000107@gucas.ac.cn> Hey Gao, Well, I have a naive question/reply. Why do you get imaginary frequencies? I'd be very surprised of graphite instability at 0K ... Is you structure relaxed enough? This structure has been so much studied, have you ever read such graphite properties before? May experts can tell us more about it. ?ric. On 10/10/2011 12:37 AM, GAO Zhe wrote: > Thank you for your kindly reply. > Well, normally, if we found imaginary frequency in phonon dispersion, > it indicates that this structure is not stable or, at least, unstable > at 0K. Therefore, the vibrational free energy becomes unmeaningful > because of the imaginary value. > However, as we know, graphite is stable phase in a wild temperature > range, including 0K. And when we discuss about formation free energy > of carbide at specified temperature, graphite is used as reference > pure material instead of diamond. This means that the free energy of > graphite really exists. > Therefore, I wondered whether there are some methods, for example, > improving the graphite model, can deal with this problem and calculate > vibrational free energy of graphite. Or, whether it is possible that > we can neglect the vibration including z-direction and only consider > vibration in xy-plane. > > -- > GAO Zhe > CMC Lab, MSE , SNU, Seoul, S.Korea > > At 2011-10-09 20:52:02,"bhabya sahoo" wrote: > > no because it is not valid for negative frequncy in phonon spectrum > > > 2011/10/9 GAO Zhe > > > Dear QE developer and users: > I am using QE 4.3.2 to calculate phonon and thermaldynamis > properties of materials. These days, I need to find the Gibbs > (or Helmholtz) Free energy of carbon. Thus, I compared diamond > and graphite phases at 0K. As a result, graphite provides > lower energy per carbon atom (about 0.3eV/atom lower than of > diamond). > However, the phonon dispersion result shows that the imaginary > frequency occurred at Gamma, H, A and K, so it is impossible > by using QHA to find the vibrational free energy at specified > temperature. > The graphite model I used is: > /ibrav = 0 , > celldm(1) = 1.889725989 , > CELL_PARAMETERS > 2.130421558318710 -1.229999460182690 > 0.000000000000000 > 0.000000000000000 2.459998920365380 > 0.000000000000000 > 0.000000000000000 0.000000000000000 > 6.800000000000000 > ATOMIC_POSITIONS crystal > C 0.0000000000000000 0.0000000000000000 0.2500000000000000 > C 0.0000000000000000 0.0000000000000000 0.7500000000000000 > C 0.3333333333333330 0.6666666666666669 0.2500000000000000 > C -0.3333333333333330 -0.6666666666666669 > 0.7500000000000000/ > Is there any other methods or models can calculate the free > energy of graphite at specified temperature? > Any suggestion will be welcome. > Thanks. > > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > > > _______________________________________________ > 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 -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111010/cb306e70/attachment.htm From flux_ray12 at 163.com Mon Oct 10 07:47:43 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Mon, 10 Oct 2011 13:47:43 +0800 (CST) Subject: [Pw_forum] Is it possible to calculate free energy of graphite at specified temperature? In-Reply-To: <4E9325E8.5000107@gucas.ac.cn> References: <4E9325E8.5000107@gucas.ac.cn> <6fb8ef28.fc34.132e8b91c2a.Coremail.flux_ray12@163.com> <518220858.30290@gscas.net.cn> Message-ID: <4c56c9c3.10ca1.132ec5f562b.Coremail.flux_ray12@163.com> Dear Eric, Thank you very much for your reply. I haven't calculated graphite, and when I tried to calculate it, I was in dormitory, at where I cannot download any paper...... After reading your suggestion, I searched a paper publised at Solid State Communications 131, 141-152, it clearly showed that the phonon dispersion of graphite is stable. I think I may use too small cut-off and k-points due to my poor performance of laptop~ I will try it, again, for a better relaxation and result. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-11 01:05:44,"?ric Germaneau" wrote: Hey Gao, Well, I have a naive question/reply. Why do you get imaginary frequencies? I'd be very surprised of graphite instability at 0K ... Is you structure relaxed enough? This structure has been so much studied, have you ever read such graphite properties before? May experts can tell us more about it. ?ric. On 10/10/2011 12:37 AM, GAO Zhe wrote: Thank you for your kindly reply. Well, normally, if we found imaginary frequency in phonon dispersion, it indicates that this structure is not stable or, at least, unstable at 0K. Therefore, the vibrational free energy becomes unmeaningful because of the imaginary value. However, as we know, graphite is stable phase in a wild temperature range, including 0K. And when we discuss about formation free energy of carbide at specified temperature, graphite is used as reference pure material instead of diamond. This means that the free energy of graphite really exists. Therefore, I wondered whether there are some methods, for example, improving the graphite model, can deal with this problem and calculate vibrational free energy of graphite. Or, whether it is possible that we canneglect the vibration including z-direction and only consider vibration in xy-plane. -- GAO Zhe CMC Lab, MSE , SNU, Seoul, S.Korea At 2011-10-09 20:52:02,"bhabya sahoo" wrote: no because it is not valid for negative frequncy in phonon spectrum 2011/10/9 GAO Zhe Dear QE developer and users: I am using QE 4.3.2 to calculate phonon and thermaldynamis properties of materials. These days, I need to find the Gibbs (or Helmholtz) Free energy of carbon. Thus, I compared diamond and graphite phases at 0K. As a result, graphite provides lower energy per carbon atom (about 0.3eV/atom lower than of diamond). However, the phonon dispersion result shows that the imaginary frequency occurred at Gamma, H, A and K, so it is impossible by using QHA to find the vibrational free energy at specified temperature. The graphite model I used is: ibrav = 0 , celldm(1) = 1.889725989 , CELL_PARAMETERS 2.130421558318710 -1.229999460182690 0.000000000000000 0.000000000000000 2.459998920365380 0.000000000000000 0.000000000000000 0.000000000000000 6.800000000000000 ATOMIC_POSITIONS crystal C 0.0000000000000000 0.0000000000000000 0.2500000000000000 C 0.0000000000000000 0.0000000000000000 0.7500000000000000 C 0.3333333333333330 0.6666666666666669 0.2500000000000000 C -0.3333333333333330 -0.6666666666666669 0.7500000000000000 Is there any other methods or models can calculate the free energy of graphite at specified temperature? Any suggestion will be welcome. Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea _______________________________________________ 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.orghttp://www.democritos.it/mailman/listinfo/pw_forum -- Be the change you wish to see in the world ? Mahatma Gandhi ? Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China 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/20111010/c2241d00/attachment-0001.htm From germaneau at gucas.ac.cn Mon Oct 10 20:11:58 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Mon, 10 Oct 2011 14:11:58 -0400 Subject: [Pw_forum] Is it possible to calculate free energy of graphite at specified temperature? In-Reply-To: <518224228.26356@test1.gucas.ac.cn> References: <4E9325E8.5000107@gucas.ac.cn> <6fb8ef28.fc34.132e8b91c2a.Coremail.flux_ray12@163.com> <518220858.30290@gscas.net.cn> <518224228.26356@test1.gucas.ac.cn> Message-ID: <4E93356E.9090206@gucas.ac.cn> Laptop?! That's my me the point ... Also usually people use a supercell to compute phonon. On 10/10/2011 01:47 AM, GAO Zhe wrote: > Dear Eric, > Thank you very much for your reply. > I haven't calculated graphite, and when I tried to calculate it, I was > in dormitory, at where I cannot download any paper...... > After reading your suggestion, I searched a paper publised at Solid > State Communications 131, 141-152, it clearly showed that the phonon > dispersion of graphite is stable. > I think I may use too small cut-off and k-points due to my poor > performance of laptop~ I will try it, again, for a better relaxation > and result. > > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-10-11 01:05:44,"?ric Germaneau" wrote: > > Hey Gao, > > Well, I have a naive question/reply. > > Why do you get imaginary frequencies? > > I'd be very surprised of graphite instability at 0K ... > Is you structure relaxed enough? > > This structure has been so much studied, have you ever read such > graphite properties before? > > May experts can tell us more about it. > > ?ric. > > On 10/10/2011 12:37 AM, GAO Zhe wrote: >> Thank you for your kindly reply. >> Well, normally, if we found imaginary frequency in phonon >> dispersion, it indicates that this structure is not stable or, at >> least, unstable at 0K. Therefore, the vibrational free energy >> becomes unmeaningful because of the imaginary value. >> However, as we know, graphite is stable phase in a wild >> temperature range, including 0K. And when we discuss about >> formation free energy of carbide at specified temperature, >> graphite is used as reference pure material instead of diamond. >> This means that the free energy of graphite really exists. >> Therefore, I wondered whether there are some methods, for >> example, improving the graphite model, can deal with this problem >> and calculate vibrational free energy of graphite. Or, whether it >> is possible that we can neglect the vibration including >> z-direction and only consider vibration in xy-plane. >> >> -- >> GAO Zhe >> CMC Lab, MSE , SNU, Seoul, S.Korea >> >> At 2011-10-09 20:52:02,"bhabya sahoo" wrote: >> >> no because it is not valid for negative frequncy in phonon >> spectrum >> >> >> 2011/10/9 GAO Zhe > > >> >> Dear QE developer and users: >> I am using QE 4.3.2 to calculate phonon and >> thermaldynamis properties of materials. These days, I >> need to find the Gibbs (or Helmholtz) Free energy of >> carbon. Thus, I compared diamond and graphite phases at >> 0K. As a result, graphite provides lower energy per >> carbon atom (about 0.3eV/atom lower than of diamond). >> However, the phonon dispersion result shows that the >> imaginary frequency occurred at Gamma, H, A and K, so it >> is impossible by using QHA to find the vibrational free >> energy at specified temperature. >> The graphite model I used is: >> /ibrav = 0 , >> celldm(1) = 1.889725989 , >> CELL_PARAMETERS >> 2.130421558318710 -1.229999460182690 >> 0.000000000000000 >> 0.000000000000000 2.459998920365380 >> 0.000000000000000 >> 0.000000000000000 0.000000000000000 >> 6.800000000000000 >> ATOMIC_POSITIONS crystal >> C 0.0000000000000000 0.0000000000000000 >> 0.2500000000000000 >> C 0.0000000000000000 0.0000000000000000 >> 0.7500000000000000 >> C 0.3333333333333330 0.6666666666666669 >> 0.2500000000000000 >> C -0.3333333333333330 -0.6666666666666669 >> 0.7500000000000000/ >> Is there any other methods or models can calculate the >> free energy of graphite at specified temperature? >> Any suggestion will be welcome. >> Thanks. >> >> -- >> GAO Zhe >> CMC Lab, MSE, SNU, Seoul, S.Korea >> >> >> >> _______________________________________________ >> 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 > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > /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 -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111010/deeb0a5d/attachment.htm From giannozz at democritos.it Mon Oct 10 08:30:52 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Oct 2011 08:30:52 +0200 Subject: [Pw_forum] Is it possible to calculate free energy of graphite at specified temperature? In-Reply-To: <4E93356E.9090206@gucas.ac.cn> References: <4E9325E8.5000107@gucas.ac.cn> <6fb8ef28.fc34.132e8b91c2a.Coremail.flux_ray12@163.com> <518220858.30290@gscas.net.cn> <518224228.26356@test1.gucas.ac.cn> <4E93356E.9090206@gucas.ac.cn> Message-ID: On Oct 10, 2011, at 20:11 , ?ric Germaneau wrote: > Also usually people use a supercell to compute phonon. people using linear response do not need any supercell P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Oct 10 08:34:51 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Oct 2011 08:34:51 +0200 Subject: [Pw_forum] problem in calculation by 4.2.1 version In-Reply-To: References: Message-ID: <85CA9C2E-DC66-47C3-ABE1-19F78E345653@democritos.it> On Oct 9, 2011, at 20:53 , yaldaa kh wrote: > Bad data for namelist object starting_magnetization > namelist read: misplaced= sign the error message says everything > starting_magnetization(1)= 0.5, > multiplicity= 2 you shouldn't use both. Actually you should use "tot_magnetization" instead in this case P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From gabriele.sclauzero at epfl.ch Mon Oct 10 08:49:14 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Mon, 10 Oct 2011 08:49:14 +0200 Subject: [Pw_forum] input and output of average.x In-Reply-To: References: Message-ID: <1ECA9FE1-4E8E-4DAC-900E-5DE4D33D74C8@epfl.ch> Il giorno 09/ott/2011, alle ore 02.30, mashiat alaaii ha scritto: > Dear Dr, Giannozi, I'm not Paolo GiannoZZi but I can try to reply anyway... > The output pf "average.x" provides a three-column quantity. Yes, you are right. The planar averages are on the second column, while the third reports the macroscopic average. (maybe this information should be added to the header of the source file as well). > I was wondering which quantity is averaged. The one that you have requested with your input, i.e. weight(1)*filename(1)+weight(2)*filename(2)+...+weight(nfile)*filename(nfile) > Actually, I want to get the psi of the structure on different planes and get the planar average of this psi. I was wondering whether I can get the planar average of psi with this program. Yes, of course. Since usually you get |psi|^2 from pp.x, that's what you can average, unless you change the code. > If positive what the filename should be. This only you can tell! You should first extract the 3D-FFT data of the corresponding wave function on a file (using pp.x) and then use average.x on that file. HTH GS > Thank you very much. > M Alaaii > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111010/9b6235ff/attachment-0001.htm From germaneau at gucas.ac.cn Mon Oct 10 20:55:20 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Mon, 10 Oct 2011 14:55:20 -0400 Subject: [Pw_forum] Issue with phonon calculation on supercell. In-Reply-To: <517959689.14509@test1.gucas.ac.cn> References: <517774101.05937@gscas.net.cn> <4E8F1D71.2090405@gucas.ac.cn> <517957891.02419@gscas.net.cn> <517959689.14509@test1.gucas.ac.cn> Message-ID: <4E933F98.40702@gucas.ac.cn> Dear all, After recompiling QE 4.3.2 with ifort 9.1 and mkl 8.1.1 I got an other error : from davcio : error # 99 error while writing to file This looks so weird to me. Thank you, ?ric. On 10/07/2011 12:18 PM, ?ric Germaneau wrote: > Dear Sanjeev, > > Thank you for noticed it. > I've just ask to the administrator the compile it with ifort. > We'll see. > > ?ric. > > On 10/06/2011 11:49 PM, Sanjeev Gupta wrote: >> Dear ?ric Germaneau >> >> Please follow the recent link of "problem in vc-relax", there is >> something same problem (If i understood correctly), Prof. Paolo >> Giannozzi suggested that, this is Gfortran problem. >> >> Thanks >> >> Sanjeev >> >> >> 2011/10/7 ?ric Germaneau > > >> >> Dear all, >> >> Can someone tell me the meaning of the error >> >> from calbec : error # 1 >> size mismatch >> >> when running ph.x. >> >> Thank you, >> >> ?ric. >> >> >> On 10/05/2011 08:45 AM, ?ric Germaneau wrote: >>> Dear all, >>> >>> I'm attempting to compute phonon at gamma point of a 2x2x2 >>> crystal structure but I get the error bellow : >>> >>> *.....* >>> Atomic displacements: >>> There are 192 irreducible representations >>> >>> Representation 1 1 modes - To be done >>> >>> Representation 2 1 modes - To be done >>> *....* >>> Representation 191 1 modes - To be done >>> >>> Representation 192 1 modes - To be done >>> >>> >>> Alpha used in Ewald sum = 2.8000 >>> PHONON : 51m 2.98s CPU 51m13.49s WALL >>> >>> >>> Electric Fields Calculation >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> from calbec : error # 1 >>> size mismatch >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> >>> stopping ... >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> Signal 15 received. >>> >>> Here is my input >>> >>> phonons >>> &inputph >>> tr2_ph=1.0d-14, >>> prefix='S007__086_B4N4.vcrelax.vcrelax_2x2x2', >>> epsil=.true., >>> amass(1)=10.811000, >>> amass(2)=14.006700, >>> outdir='./SCF_PH', >>> fildyn='S007__086_B4N4.vcrelax.vcrelax_2x2x2.dynG', >>> / >>> 0.0 0.0 0.0 >>> >>> What sounds weird to me is that I don't have any problem when I >>> perform the same calculation on the unit cell, I mean the 1x1x1 >>> structure. >>> Before running ph.x I do a regular scf calculation at gamma >>> point only which ends normally: >>> >>> K_POINTS automatic >>> 1 1 1 0 0 0 >>> >>> I generate my supercell from the optimized unit cell and do not >>> optimized it again due to time consuming. >>> I don't have much experience in phonon calculations so any hits >>> are welcome. >>> Thank you, >>> >>> ?ric. >>> >>> -- >>> /Be the change you wish to see in the world >>> / --- Mahatma Gandhi --- >>> >>> Dr. ?ric Germaneau >>> >>> >>> Graduate University of Chinese Academy of Sciences >>> College of Physical Sciences >>> Yuquan Road 19A >>> Beijing 100049 >>> China >>> >>> /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 >> >> -- >> /Be the change you wish to see in the world >> / --- Mahatma Gandhi --- >> >> Dr. ?ric Germaneau >> >> >> Graduate University of Chinese Academy of Sciences >> College of Physical Sciences >> Yuquan Road 19A >> Beijing 100049 >> China >> >> /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 >> >> >> >> >> -- >> *Dr. Sanjeev Kumar Gupta* >> *Post Doctoral Fellow, >> /(Ministry of New and Renewable Energy/) >> Department of Physics, >> Bhavnagar University, Bhavnagar-364 022 >> Gujarat, India* >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > /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 -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111010/13539010/attachment.htm From flux_ray12 at 163.com Mon Oct 10 09:05:37 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Mon, 10 Oct 2011 15:05:37 +0800 (CST) Subject: [Pw_forum] Is it possible to calculate free energy of graphite at specified temperature? In-Reply-To: References: <4E9325E8.5000107@gucas.ac.cn> <6fb8ef28.fc34.132e8b91c2a.Coremail.flux_ray12@163.com> <518220858.30290@gscas.net.cn> <518224228.26356@test1.gucas.ac.cn> <4E93356E.9090206@gucas.ac.cn> Message-ID: <5ffedda4.1218d.132eca6a7be.Coremail.flux_ray12@163.com> Dear Prof. Giannozzi: Thank you very much for your attention on my question. I still have a problem about graphite phonon. I saw a lot of persons calculated that, including prof. Marzari. However, all of their calculations were based on xy-plane, i.e., Gamma-M-K-Gamma q-path, even one of papers mentioned about calculating IFC through nk1*nk2, 2-dimensional MP grid. Therefore, I am wondering that, if I calculate IFC in 2D, does QHA work on this 2D-IFC? -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea ? 2011-10-10 14:30:52?"Paolo Giannozzi" ??? > >On Oct 10, 2011, at 20:11 , ?ric Germaneau wrote: > >> Also usually people use a supercell to compute phonon. > >people using linear response do not need any supercell > >P. >--- >Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > >_______________________________________________ >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/20111010/1f24e7b2/attachment-0001.htm From giannozz at democritos.it Mon Oct 10 09:21:59 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Oct 2011 09:21:59 +0200 Subject: [Pw_forum] Compile error when using Cygwin and gfortran 4.7 In-Reply-To: References: Message-ID: <1318231319.29598.9.camel@fe12lx.fisica.uniud.it> On Sat, 2011-10-08 at 16:12 -0700, Sean Muir wrote: > I am using the latest gfortran 4.7 for cygwin, might it help to go > back to some previous version? unlikely, but you may give it a try: maybe your 4.7 version is more unstable than usual, since it doesn't even compile lapack. To lower optimization, use -O2 or -O instead of -O3. In any event, please do what it is recommanded: > Please submit a full bug report, Gfortran developers are usually quick in fixing bug. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Mon Oct 10 09:34:24 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Oct 2011 09:34:24 +0200 Subject: [Pw_forum] problems with pp.x for parallel processing In-Reply-To: <1318139681.56443.YahooMailClassic@web5710.biz.mail.ne1.yahoo.com> References: <1318139681.56443.YahooMailClassic@web5710.biz.mail.ne1.yahoo.com> Message-ID: <1318232064.29598.16.camel@fe12lx.fisica.uniud.it> On Sat, 2011-10-08 at 22:54 -0700, Natalia Pavlenko wrote: > I know that pp.x works well without k-parallelization I had understood the opposite from one of your previous messages > but for this I need to recalculate nscf with wf_collect > which takes pretty much time and more memory sources. if you run the nscf calcul;ation with npool*nproc_pool processors, you may actually run the postprocessing on nproc_pool processors with npool=1. You have to remove the following lines from postproc.f90: IF (nproc /= nproc_file .and. .not. twfcollect .and. needwf) & CALL errore('postproc',& 'pw.x run with a different number of processors. Use wf_collect=.true.',1) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From pc229 at kent.ac.uk Mon Oct 10 11:37:46 2011 From: pc229 at kent.ac.uk (pieremanuele canepa) Date: Mon, 10 Oct 2011 10:37:46 +0100 Subject: [Pw_forum] some suggestions regarding the DFT-D module Message-ID: Dear all, (P. Giannozzi) Yesterday, I was playing with the London dispersion DFT-D implemented in QE (PWscf) by Barone and coworkers. I realised that PWscf does print a set of ******* whenever the C6 constant, associated to one species, is larger that 999 (i.e. atom with Z larger than 49). Looking at the printing line in module mm_dispersion.f90 in Modules the number of correct digits is printed changing F7.3 (in ----> line, see below) to F8.3 or F9.3/ ] WRITE ( stdout ,'( /, 5X, "-------------------------------------" , & & /, 5X, "Parameters for Dispersion Correction:" , & & /, 5X, "-------------------------------------" , & & /, 5X, " atom VdW radius C_6 " , / )' ) DO ata = 1 , ntyp ! ----> WRITE (stdout , '( 8X, A3 , 6X , F7.3 , 8X , F9.3 )' ) & atom_label ( ata ) , R_vdw ( ata ) , C6_i ( ata ) ! END DO I guess it would be also nice printing the composed Cij just below. Eventually I was wondering why PWscf doesn't print the dispersion magnitude on the final energy? It would be nice to see it somewhere. Thanks, Piero -- *Please consider the environment before printing this e-mail.* ** Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229 at kent.ac.uk mobile: +44 (0) 772-9756456 ----------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111010/1d86cdf7/attachment.htm From mariammalmir86 at gmail.com Mon Oct 10 13:42:57 2011 From: mariammalmir86 at gmail.com (mariam malmir) Date: Mon, 10 Oct 2011 15:12:57 +0330 Subject: [Pw_forum] problem Message-ID: Hi, i study (8,0) carbon nanotube whose DOS show metal nano tube that it is wrong. i want to know what is the problem? what is the probable wrong? thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111010/3bc6c245/attachment.htm From mariammalmir86 at gmail.com Mon Oct 10 13:44:21 2011 From: mariammalmir86 at gmail.com (mariam malmir) Date: Mon, 10 Oct 2011 04:44:21 -0700 Subject: [Pw_forum] mariam malmir wants to chat Message-ID: ----------------------------------------------------------------------- mariam malmir wants to stay in better touch using some of Google's coolest new products. If you already have Gmail or Google Talk, visit: http://mail.google.com/mail/b-b16d1788c9-ead9569711-polJH4ZO1_Whh1qVbbyMx9hmztY You'll need to click this link to be able to chat with mariam malmir. To get Gmail - a free email account from Google with over 2,800 megabytes of storage - and chat with mariam malmir, visit: http://mail.google.com/mail/a-b16d1788c9-ead9569711-polJH4ZO1_Whh1qVbbyMx9hmztY Gmail offers: - Instant messaging right inside Gmail - Powerful spam protection - Built-in search for finding your messages and a helpful way of organizing emails into "conversations" - No pop-up ads or untargeted banners - just text ads and related information that are relevant to the content of your messages All this, and its yours for free. But wait, there's more! By opening a Gmail account, you also get access to Google Talk, Google's instant messaging service: http://www.google.com/talk/ Google Talk offers: - Web-based chat that you can use anywhere, without a download - A contact list that's synchronized with your Gmail account - Free, high quality PC-to-PC voice calls when you download the Google Talk client We're working hard to add new features and make improvements, so we might also ask for your comments and suggestions periodically. We appreciate your help in making our products even better! Thanks, The Google Team To learn more about Gmail and Google Talk, visit: http://mail.google.com/mail/help/about.html http://www.google.com/talk/about.html (If clicking the URLs in this message does not work, copy and paste them into the address bar of your browser). From giannozz at democritos.it Mon Oct 10 13:53:21 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 10 Oct 2011 13:53:21 +0200 Subject: [Pw_forum] some suggestions regarding the DFT-D module In-Reply-To: References: Message-ID: <1318247601.31351.5.camel@fe12lx.fisica.uniud.it> On Mon, 2011-10-10 at 10:37 +0100, pieremanuele canepa wrote: > Looking at the printing line in module mm_dispersion.f90 in Modules > the number of correct digits is printed changing F7.3 (in ----> line, > see below) to F8.3 or F9.3/ fixed > I guess it would be also nice printing the composed Cij just below. > Eventually I was wondering why PWscf doesn't print the dispersion > magnitude on the final energy? It would be nice to see it somewhere. can you translate this into fortran 90? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From pc229 at kent.ac.uk Mon Oct 10 14:24:53 2011 From: pc229 at kent.ac.uk (P.Canepa) Date: Mon, 10 Oct 2011 13:24:53 +0100 Subject: [Pw_forum] some suggestions regarding the DFT-D module In-Reply-To: <1318247601.31351.5.camel@fe12lx.fisica.uniud.it> References: , <1318247601.31351.5.camel@fe12lx.fisica.uniud.it> Message-ID: <42054E10C02CD44D81EF510077A30A075D27ABC848@MAPI.ad.kent.ac.uk> I'll do it -:) -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229 at kent.ac.uk mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi [giannozz at democritos.it] Sent: Monday, October 10, 2011 12:53 PM To: PWSCF Forum Subject: Re: [Pw_forum] some suggestions regarding the DFT-D module On Mon, 2011-10-10 at 10:37 +0100, pieremanuele canepa wrote: > Looking at the printing line in module mm_dispersion.f90 in Modules > the number of correct digits is printed changing F7.3 (in ----> line, > see below) to F8.3 or F9.3/ fixed > I guess it would be also nice printing the composed Cij just below. > Eventually I was wondering why PWscf doesn't print the dispersion > magnitude on the final energy? It would be nice to see it somewhere. can you translate this into fortran 90? P. -- Paolo Giannozzi, IOM-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 Mon Oct 10 14:15:19 2011 From: pc229 at kent.ac.uk (P.Canepa) Date: Mon, 10 Oct 2011 13:15:19 +0100 Subject: [Pw_forum] some suggestions regarding the DFT-D module In-Reply-To: <1318247601.31351.5.camel@fe12lx.fisica.uniud.it> References: , <1318247601.31351.5.camel@fe12lx.fisica.uniud.it> Message-ID: <42054E10C02CD44D81EF510077A30A075D27ABC847@MAPI.ad.kent.ac.uk> I will :) -- Please consider the environment before printing this e-mail. Pieremanuele Canepa Room 104 Functional Material Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom e-mail: pc229 at kent.ac.uk mobile: +44 (0) 7772-9756456 ----------------------------------------------------------- ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi [giannozz at democritos.it] Sent: Monday, October 10, 2011 12:53 PM To: PWSCF Forum Subject: Re: [Pw_forum] some suggestions regarding the DFT-D module On Mon, 2011-10-10 at 10:37 +0100, pieremanuele canepa wrote: > Looking at the printing line in module mm_dispersion.f90 in Modules > the number of correct digits is printed changing F7.3 (in ----> line, > see below) to F8.3 or F9.3/ fixed > I guess it would be also nice printing the composed Cij just below. > Eventually I was wondering why PWscf doesn't print the dispersion > magnitude on the final energy? It would be nice to see it somewhere. can you translate this into fortran 90? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From heatherjkulik at gmail.com Mon Oct 10 23:10:25 2011 From: heatherjkulik at gmail.com (Heather Kulik) Date: Mon, 10 Oct 2011 14:10:25 -0700 Subject: [Pw_forum] species list in "set_hubbard_l.f90" and "tabd.f90" In-Reply-To: References: Message-ID: Hi Trinh, I think the list of elements in tabd and set_hubbard_l are not meant to be complete. Matteo and others who update the code tend to omit the nearly full and nearly empty d^x and f^x elements and they tend to not have lanthanides/actinides. It's straightforward to modify those files yourself and add more elements. It's an inconvenience, but I don't think the absence of La from the two Hubbard files is particularly intentional. Heather On Sun, Oct 9, 2011 at 5:07 PM, Vo, Trinh (388C) wrote: > Dear AlL, > > I checked the list of species in 2 files "set_hubbard_l.f90" and > "tabd.f90." The list does not contain transition atoms and La with > configuration of d^1. Is there any reason why those species are not > included? > > Thank you, > > Trinh Vo > > Computing group > JPL/CalTech > > > _______________________________________________ > 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/20111010/c8b78823/attachment.htm From Trinh.Vo at jpl.nasa.gov Tue Oct 11 00:53:46 2011 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Mon, 10 Oct 2011 15:53:46 -0700 Subject: [Pw_forum] species list in "set_hubbard_l.f90" and "tabd.f90" In-Reply-To: Message-ID: Hi Heather, Thanks for clarification. Yes, I added some missing species that I need. Since it was accidentally that those transition metals with configuration d^1 ( and La, Ac) are missing from the list, I am not sure if there is some reason, so I asked for to verify. Trinh From: Heather Kulik > Reply-To: PWSCF Forum > Date: Mon, 10 Oct 2011 14:10:25 -0700 To: PWSCF Forum > Subject: Re: [Pw_forum] species list in "set_hubbard_l.f90" and "tabd.f90" Hi Trinh, I think the list of elements in tabd and set_hubbard_l are not meant to be complete. Matteo and others who update the code tend to omit the nearly full and nearly empty d^x and f^x elements and they tend to not have lanthanides/actinides. It's straightforward to modify those files yourself and add more elements. It's an inconvenience, but I don't think the absence of La from the two Hubbard files is particularly intentional. Heather On Sun, Oct 9, 2011 at 5:07 PM, Vo, Trinh (388C) > wrote: Dear AlL, I checked the list of species in 2 files "set_hubbard_l.f90" and "tabd.f90." The list does not contain transition atoms and La with configuration of d^1. Is there any reason why those species are not included? Thank you, Trinh Vo Computing group JPL/CalTech _______________________________________________ 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/20111010/3fa655aa/attachment-0001.htm From chenhanghuipwscf at gmail.com Tue Oct 11 05:40:32 2011 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Mon, 10 Oct 2011 23:40:32 -0400 Subject: [Pw_forum] charge ordered state Message-ID: To PWscf community, I have a general question. I want to calculate a charge ordered state of nickelates. I specify two types of Ni atoms and relax the structure. It turns out that since the starting potential is from atoms, the two types of Ni have the same initial guess of charge density (correct me if I am wrong on this) and after relaxation, the two types of Ni have almost the same charge density (all the symmetries are intentionally broken). I wonder whether there is a way to give different charge density initial guess on the two types of Ni atoms in QE? 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/20111010/d5b7f560/attachment.htm From pankaj.espresso at gmail.com Tue Oct 11 07:45:00 2011 From: pankaj.espresso at gmail.com (Pankaj Pankaj) Date: Tue, 11 Oct 2011 11:15:00 +0530 Subject: [Pw_forum] Phonon Cal for Pnam Space group Message-ID: Dear Espresso Users, I am struggling to calculte the phonon spectrum of crystall symmetry with Pnma having point group symmetry mmm (D2h) in quantum espresso, which usually disregard this symmetry point. I noticed this in my Pnma SCF and Bands calculations. Thank you in advance. Kind Regards Pankaj Pankaj Researcher @ AU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/dbcfc577/attachment.htm From mulwawinfred at gmail.com Tue Oct 11 08:27:59 2011 From: mulwawinfred at gmail.com (Winfred Mulwa) Date: Tue, 11 Oct 2011 09:27:59 +0300 Subject: [Pw_forum] inputfile of magnesium Hydride Message-ID: Dear all, I am trying to create an input file of magnesium Hydride, but after visualizing the cell in xcrysden, i am not getting the correct image. Can any one give me the correct input file. Mulwa Winfred. M Phil Student, Computational Material Science Group, Chepkoilel University College Eldoret, Kenya. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/4613e30a/attachment.htm From giannozz at democritos.it Tue Oct 11 09:57:15 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 11 Oct 2011 09:57:15 +0200 Subject: [Pw_forum] Phonon Cal for Pnam Space group In-Reply-To: References: Message-ID: <55EDD6A0-8AC2-4ECA-BD0C-DA370B542474@democritos.it> On Oct 11, 2011, at 7:45 , Pankaj Pankaj wrote: > I am struggling to calculate the phonon spectrum of crystall > symmetry with Pnma having point group symmetry mmm (D2h) > in quantum espresso, which usually disregard this symmetry point what do you mean by "disregard"? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Oct 11 10:02:22 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 11 Oct 2011 10:02:22 +0200 Subject: [Pw_forum] charge ordered state In-Reply-To: References: Message-ID: <56638186-BB39-48AB-AA25-ED0396201F62@democritos.it> On Oct 11, 2011, at 5:40 , hanghui chen wrote: > I have a general question. I want to calculate a charge > ordered state of nickelates. I am afraid that the general answer is "DFT is very bad at this" > I wonder if there is a way to give different charge density initial > guess on the two types of Ni atoms in QE? you may use two different Ni pseudopotential files that are the same except for the atomic charge density (field PP_RHOATOM) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From psavita at crlindia.com Tue Oct 11 10:22:27 2011 From: psavita at crlindia.com (psavita) Date: Tue, 11 Oct 2011 13:52:27 +0530 Subject: [Pw_forum] ELF error with version 4.3 In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/bae0d8f0/attachment.htm From joshiniharika20 at yahoo.in Tue Oct 11 11:31:33 2011 From: joshiniharika20 at yahoo.in (Niharika Joshi) Date: Tue, 11 Oct 2011 15:01:33 +0530 (IST) Subject: [Pw_forum] problem in xspectra calculations Message-ID: <1318325493.18035.YahooMailClassic@web95715.mail.in.yahoo.com> Hello Paolo Sir, Thank you for your reply. I tried running the xanes calculation after making the change in xspectra.f90. But it is still giving me the same message 'Could not find the element? C in the table of K edge energies!' at the end and leaving the output file incomplete. For some reason, the condition for 'if-loop' in mygetK.f90 is not getting satisfied and thus it is not getting executed. I wrote the variables sym and seuilK_tab(6) . For both variables it writes 'C' but does not enter the if-loop. -Niharika Joshi (project student, IISER Pune) ? --- On Fri, 7/10/11, Paolo Giannozzi wrote: From: Paolo Giannozzi Subject: Re: [Pw_forum] problem in xspectra calculations To: "PWSCF Forum" Date: Friday, 7 October, 2011, 11:52 AM On Wed, 2011-09-28 at 18:29 +0530, Niharika Joshi wrote: > 'Could not find the element? C in the table of K edge energies!' it should be a compiler weirdness. Try to replace in xspectra.f90 ? e_1s=mygetK(upf(xiabs)%psd)) with ? e_1s=mygetK(trim(adjustl(upf(xiabs)%psd))) P. -- Paolo Giannozzi, IOM-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/20111011/24fd70c8/attachment.htm From bdslipun at gmail.com Tue Oct 11 12:50:47 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 11 Oct 2011 16:20:47 +0530 Subject: [Pw_forum] compilation QHA code Message-ID: when i compile QHA the error gives gfortan -O3 -c tetra.f make: gfortan: Command not found make: *** [tetra.o] Error 127 gfortran -O3 -c Debye.f90 Debye.f90:144.8: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer Debye.f90:144.11: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Start expression in DO loop at (1) must be integer Debye.f90:144.24: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: End expression in DO loop at (1) must be integer Debye.f90:144.31: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Step expression in DO loop at (1) must be integer Debye.f90:177.4: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer Debye.f90:177.7: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Start expression in DO loop at (1) must be integer Debye.f90:177.16: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: End expression in DO loop at (1) must be integer Debye.f90:177.24: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Step expression in DO loop at (1) must be integer gfortran -O3 -c Debye_T.f gfortran -O3 -c debye3.f gfortran -O3 -c cheval.f gfortran -O3 -c d1mach.f gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o fortran -FR -c Mean_square_displacement.f90 make: fortran: Command not found make: *** [Mean_square_displacement.o] Error 127 ln: creating symbolic link `tetra.x': File exists ln: creating symbolic link `phonon_dos.x': File exists ln: creating symbolic link `Debye.x': File exists ln: creating symbolic link `Atom_projected_properties.x': File exists ln: creating symbolic link `F_QHA.x': File exists ln: creating symbolic link `Ghost_DOS.x': File exists ln: creating symbolic link `Partial_phonon_DOS.x': File exists ln: creating symbolic link `Mean_square_displacement.x': File exists ln: creating symbolic link `atom_info.x': File exists bds at Planck:~/bhabya/espresso-4.3/QHA$ what should i do b d sahoo reserch scholar barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/525688cd/attachment.htm From baroni at sissa.it Tue Oct 11 13:14:13 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 11 Oct 2011 13:14:13 +0200 Subject: [Pw_forum] compilation QHA code In-Reply-To: References: Message-ID: <9C1E1DD8-26BA-4A25-98A6-16F9217B73A1@sissa.it> 1) use a different compiler OR 2) modify the code, so as to feed the DO loop with integer indeces SB On Oct 11, 2011, at 12:50 PM, bhabya sahoo wrote: > when i compile QHA the error gives > > > > > > gfortan -O3 -c tetra.f > make: gfortan: Command not found > make: *** [tetra.o] Error 127 > gfortran -O3 -c Debye.f90 > Debye.f90:144.8: > > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: Loop variable at (1) must be integer > Debye.f90:144.11: > > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: Start expression in DO loop at (1) must be integer > Debye.f90:144.24: > > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: End expression in DO loop at (1) must be integer > Debye.f90:144.31: > > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: Step expression in DO loop at (1) must be integer > Debye.f90:177.4: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: Loop variable at (1) must be integer > Debye.f90:177.7: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: Start expression in DO loop at (1) must be integer > Debye.f90:177.16: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: End expression in DO loop at (1) must be integer > Debye.f90:177.24: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: Step expression in DO loop at (1) must be integer > gfortran -O3 -c Debye_T.f > gfortran -O3 -c debye3.f > gfortran -O3 -c cheval.f > gfortran -O3 -c d1mach.f > gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o > fortran -FR -c Mean_square_displacement.f90 > make: fortran: Command not found > make: *** [Mean_square_displacement.o] Error 127 > ln: creating symbolic link `tetra.x': File exists > ln: creating symbolic link `phonon_dos.x': File exists > ln: creating symbolic link `Debye.x': File exists > ln: creating symbolic link `Atom_projected_properties.x': File exists > ln: creating symbolic link `F_QHA.x': File exists > ln: creating symbolic link `Ghost_DOS.x': File exists > ln: creating symbolic link `Partial_phonon_DOS.x': File exists > ln: creating symbolic link `Mean_square_displacement.x': File exists > ln: creating symbolic link `atom_info.x': File exists > bds at Planck:~/bhabya/espresso-4.3/QHA$ > > > > what should i do > > > > b d sahoo reserch scholar > barc > mumbai > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/32b9da96/attachment-0001.htm From flux_ray12 at 163.com Tue Oct 11 13:57:40 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Tue, 11 Oct 2011 19:57:40 +0800 (CST) Subject: [Pw_forum] compilation QHA code In-Reply-To: References: Message-ID: <35547298.ebc9.132f2d8646e.Coremail.flux_ray12@163.com> You problem came from here: fortran -FR -c Mean_square_displacement.f90 make: fortran: Command not found Check carefully for each "makefile" and make sure that all of the compiler name is cerect. Moreover, it is suggeted to use ifort or other fortran compiler rather than gfortran for QHA, since gfortran does not support un-integer as step-length in loop. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-11 18:50:47,"bhabya sahoo" wrote: when i compile QHA the error gives gfortan -O3 -c tetra.f make: gfortan: Command not found make: *** [tetra.o] Error 127 gfortran -O3 -c Debye.f90 Debye.f90:144.8: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer Debye.f90:144.11: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Start expression in DO loop at (1) must be integer Debye.f90:144.24: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: End expression in DO loop at (1) must be integer Debye.f90:144.31: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Step expression in DO loop at (1) must be integer Debye.f90:177.4: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer Debye.f90:177.7: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Start expression in DO loop at (1) must be integer Debye.f90:177.16: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: End expression in DO loop at (1) must be integer Debye.f90:177.24: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Step expression in DO loop at (1) must be integer gfortran -O3 -c Debye_T.f gfortran -O3 -c debye3.f gfortran -O3 -c cheval.f gfortran -O3 -c d1mach.f gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o fortran -FR -c Mean_square_displacement.f90 make: fortran: Command not found make: *** [Mean_square_displacement.o] Error 127 ln: creating symbolic link `tetra.x': File exists ln: creating symbolic link `phonon_dos.x': File exists ln: creating symbolic link `Debye.x': File exists ln: creating symbolic link `Atom_projected_properties.x': File exists ln: creating symbolic link `F_QHA.x': File exists ln: creating symbolic link `Ghost_DOS.x': File exists ln: creating symbolic link `Partial_phonon_DOS.x': File exists ln: creating symbolic link `Mean_square_displacement.x': File exists ln: creating symbolic link `atom_info.x': File exists bds at Planck:~/bhabya/espresso-4.3/QHA$ what should i do b d sahoo reserch scholar barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/a7df13dc/attachment.htm From bdslipun at gmail.com Tue Oct 11 14:08:28 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 11 Oct 2011 17:38:28 +0530 Subject: [Pw_forum] (no subject) Message-ID: where should i get iforttran how can i install it -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/37884eea/attachment.htm From matteo.calandra at impmc.jussieu.fr Tue Oct 11 14:25:34 2011 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Tue, 11 Oct 2011 14:25:34 +0200 Subject: [Pw_forum] problem in xspectra calculations In-Reply-To: References: Message-ID: <4E9435BE.8050507@impmc.jussieu.fr> > Message: 4 > Date: Tue, 11 Oct 2011 15:01:33 +0530 (IST) > From: Niharika Joshi > Subject: Re: [Pw_forum] problem in xspectra calculations > To: PWSCF Forum > Message-ID: > <1318325493.18035.YahooMailClassic at web95715.mail.in.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Paolo Sir, > Thank you for your reply. > I tried running the xanes calculation after making the change in xspectra.f90. But it is still giving me the same message 'Could not find the element? C in the table of K edge energies!' at the end and leaving the output file incomplete. > For some reason, the condition for 'if-loop' in mygetK.f90 is not getting satisfied and thus it is not getting executed. I wrote the variables sym and seuilK_tab(6) . For both variables it writes 'C' but does not enter the if-loop. > -Niharika Joshi > (project student, IISER Pune) Dear Niharita, which compiler/Machine are you using ? It seems it treats in a strange way string variables. Moreover, are you using the pseudo of the example for Carbon or another one ? You can try the following two options: 1) in ligne 66 in mygetK.f90 change line if(sym.eq.seuilK_tab(i)%name) then in if(sym.eq.trim(adjustl(seuilK_tab(i)%name))) then 2) if it doesn't work, then replace in xspectra.f90 all the lines with (two lines) of e_1s=mygetK(upf(xiabs)%psd) with the actual value of the Carbon K-edge energy, namely with e_1s=284.2 All the best, M. -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Mineralogie et de Physique des Milieux Condenses de Paris Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From swapnil.chandratre at gmail.com Tue Oct 11 18:47:43 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Tue, 11 Oct 2011 12:47:43 -0400 Subject: [Pw_forum] Piezoelectric Response Message-ID: Hi, I want to understand the concept of piezoelectricity in Espresso, I have some doubts, Is it necessary that in order to observe the phenomenon in direct manner (ie application of strain to get polarization), i need to create vaccum in the direction of polarization? or i can work with periordic systems, and observe polarization.? With respect to the same, if i want to see the effect of field on length dimension of input geometry, I have to proceed with applying vaccum in that direction.? Is my understanding of the approach incorrect ? can anyone help me understand it better. -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/23fad8d7/attachment.htm From giannozz at democritos.it Tue Oct 11 19:22:07 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 11 Oct 2011 19:22:07 +0200 Subject: [Pw_forum] compilation QHA code In-Reply-To: References: Message-ID: On Oct 11, 2011, at 12:50 , bhabya sahoo wrote: > what should i do try looking at error messages: it helps > gfortan -O3 -c tetra.f > make: gfortan: Command not found you misspelled "gfortran" > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: Loop variable at (1) must be integer this is a warning: you can ignore it > fortran -FR -c Mean_square_displacement.f90 > make: fortran: Command not found you misspelled "gfortran" once again --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Oct 11 19:23:23 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 11 Oct 2011 19:23:23 +0200 Subject: [Pw_forum] ELF error with version 4.3 In-Reply-To: References: Message-ID: <5BA23118-203C-40D4-9C72-07CDCA390E92@democritos.it> On Oct 11, 2011, at 10:22 , psavita wrote: > from invfft : error # 1 > inconsistent descriptor for Dense fft this should not happen. Did you by any chance tried to use elf with two FFT grids (ecutrho /= 4*ecutwfc)? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From dorabman at gmail.com Tue Oct 11 19:31:13 2011 From: dorabman at gmail.com (Hua Bao) Date: Tue, 11 Oct 2011 13:31:13 -0400 Subject: [Pw_forum] electron-phonon coupling tutorial Message-ID: Dear QE users, I am learning to use QE to calculate e-ph coupling. I have followed the tutorial and also performed calculation in example07 (QE4.3.1). However, there is very limited information about the input and output of the related module (dynmax, q2r, and lambda, etc). It is not even easy to understand the output format. I am wondering if there is any good documentation, so that I can at least make an connection between the output data of QE and the quantities such as a^2F, g, gamma, etc. Thanks, Hua Bao -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/1ba0d1eb/attachment.htm From baroni at sissa.it Tue Oct 11 21:57:23 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 11 Oct 2011 21:57:23 +0200 Subject: [Pw_forum] Piezoelectric Response In-Reply-To: References: Message-ID: Dear Swapnil, piezoelectricity is a bulk property. No supercells are needed. See e.g.: R.M. Martin, PRB 5, 1607 (1972), http://link.aps.org/doi/10.1103/PhysRevB.5.1607 S. de Gironcoli et al., Phys. Rev. Lett. 62, 2853?2856 (1989), http://link.aps.org/doi/10.1103/PhysRevLett.62.2853 Regards, SB , On Oct 11, 2011, at 6:47 PM, swapnil chandratre wrote: > Hi, > > I want to understand the concept of piezoelectricity in Espresso, I have some doubts, > > Is it necessary that in order to observe the phenomenon in direct manner (ie application of strain to get polarization), i need to create vaccum in the direction of polarization? or i can work with periordic systems, and observe polarization.? > > With respect to the same, if i want to see the effect of field on length dimension of input geometry, I have to proceed with applying vaccum in that direction.? > > Is my understanding of the approach incorrect ? can anyone help me understand it better. > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/39bbaec6/attachment-0001.htm From swapnil.chandratre at gmail.com Tue Oct 11 23:00:32 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Tue, 11 Oct 2011 17:00:32 -0400 Subject: [Pw_forum] Piezoelectric Response In-Reply-To: References: Message-ID: so if i have a 2-D system, say BN sheet, i have to model layers with more vaccum space in between them to extract the response ? On Tue, Oct 11, 2011 at 3:57 PM, Stefano Baroni wrote: > Dear Swapnil, > > piezoelectricity is a bulk property. No supercells are needed. > See e.g.: > R.M. Martin, PRB 5, 1607 (1972), > http://link.aps.org/doi/10.1103/PhysRevB.5.1607 > S. de Gironcoli et al., Phys. Rev. Lett. 62, 2853?2856 (1989), > http://link.aps.org/doi/10.1103/PhysRevLett.62.2853 > > Regards, SB > > , > On Oct 11, 2011, at 6:47 PM, swapnil chandratre wrote: > > Hi, > > I want to understand the concept of piezoelectricity in Espresso, I have > some doubts, > > Is it necessary that in order to observe the phenomenon in direct manner > (ie application of strain to get polarization), i need to create vaccum in > the direction of polarization? or i can work with periordic systems, and > observe polarization.? > > With respect to the same, if i want to see the effect of field on length > dimension of input geometry, I have to proceed with applying vaccum in that > direction.? > > Is my understanding of the approach incorrect ? can anyone help me > understand it better. > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > _______________________________________________ > 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 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/76631efa/attachment.htm From njuxuyuehua at gmail.com Wed Oct 12 04:53:33 2011 From: njuxuyuehua at gmail.com (xu yuehua) Date: Wed, 12 Oct 2011 10:53:33 +0800 Subject: [Pw_forum] which criterion does not meet during relax progresss Message-ID: Hi, all I relaxed a system, my relaxation criterion is etot_conv_thr=1.D-5 forc_conv_thr=1.D-4, and conv_thr = 1.D-8 , and in my output file, i see the force_conv_thr is met, and the conv_thr seems also met. for in the last relaxation step, the printed information is : *! total energy = -551.13047812 Ry Harris-Foulkes estimate = -551.13047807 Ry estimated scf accuracy < 2.4E-11 Ry The total energy is the sum of the following terms: one-electron contribution = -2144.14675345 Ry hartree contribution = 1097.77738769 Ry xc contribution = -134.85772630 Ry ewald contribution = 630.09661393 Ry convergence has been achieved in 9 iterations Forces acting on atoms (Ry/au): atom 1 type 2 force = 0.00006652 0.00001074 0.00001717 atom 2 type 1 force = -0.00001149 -0.00003650 0.00002296 atom 3 type 1 force = 0.00002092 0.00003527 0.00001095 atom 4 type 2 force = -0.00006106 -0.00005036 0.00002893 atom 5 type 1 force = 0.00012199 -0.00005785 -0.00011993 atom 6 type 1 force = -0.00005472 0.00002358 0.00009707 atom 7 type 2 force = 0.00003025 0.00003532 0.00004727 atom 8 type 1 force = 0.00001390 0.00009541 0.00000283 atom 9 type 1 force = -0.00007213 -0.00012498 -0.00005854 atom 10 type 2 force = -0.00000989 -0.00001883 -0.00002476 atom 11 type 1 force = 0.00002862 -0.00010630 0.00001950 atom 12 type 1 force = 0.00000813 0.00006367 -0.00002737 atom 13 type 2 force = -0.00010953 0.00005997 0.00012796 atom 14 type 1 force = 0.00012468 0.00004819 0.00006199 atom 15 type 1 force = -0.00003227 -0.00002568 -0.00012529 atom 16 type 2 force = 0.00000131 0.00002155 0.00006799 atom 17 type 1 force = 0.00002056 0.00002091 0.00006192 atom 18 type 1 force = -0.00004895 -0.00000474 -0.00012101 atom 19 type 2 force = -0.00000208 -0.00000446 0.00003292 atom 20 type 1 force = -0.00003014 0.00001046 0.00005040 atom 21 type 1 force = -0.00000665 0.00000012 -0.00002565 atom 22 type 2 force = 0.00004366 0.00001375 -0.00003139 atom 23 type 1 force = 0.00001038 0.00000199 -0.00004611 atom 24 type 1 force = 0.00000001 -0.00002044 0.00003004 atom 25 type 2 force = -0.00000668 -0.00002989 0.00007813 atom 26 type 1 force = 0.00003097 -0.00004437 0.00003757 atom 27 type 1 force = 0.00001552 0.00000595 -0.00005710 atom 28 type 2 force = 0.00001236 0.00004340 0.00012950 atom 29 type 1 force = -0.00002372 0.00002505 -0.00007569 atom 30 type 1 force = 0.00003122 0.00000291 0.00000276 atom 31 type 2 force = -0.00001390 -0.00010264 -0.00009180 atom 32 type 1 force = 0.00004590 0.00003207 0.00003011 atom 33 type 1 force = -0.00002671 0.00005738 -0.00001122 atom 34 type 2 force = -0.00001380 -0.00001243 -0.00005321 atom 35 type 1 force = -0.00002033 0.00001199 0.00006508 atom 36 type 1 force = 0.00001161 -0.00000439 -0.00003033 atom 37 type 2 force = -0.00008127 0.00002129 0.00005130 atom 38 type 1 force = -0.00004667 -0.00008260 -0.00004117 atom 39 type 1 force = 0.00000793 0.00013767 -0.00000675 atom 40 type 2 force = 0.00001123 -0.00004604 0.00006549 atom 41 type 1 force = 0.00003825 0.00001125 -0.00000180 atom 42 type 1 force = -0.00005610 0.00001922 -0.00008202 atom 43 type 2 force = -0.00001184 0.00000509 -0.00002456 atom 44 type 1 force = -0.00005112 -0.00001419 0.00000597 atom 45 type 1 force = 0.00009312 -0.00000567 -0.00002162 atom 46 type 2 force = -0.00002442 -0.00003492 0.00009560 atom 47 type 1 force = -0.00005855 0.00002530 -0.00010962 atom 48 type 1 force = 0.00008502 -0.00001219 -0.00005446 Total force = 0.000643 Total SCF correction = 0.000037* ** *entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= -1.92 -0.00001798 0.00000011 0.00000000 -2.64 0.02 0.00 0.00000011 -0.00001708 0.00000001 0.02 -2.51 0.00 0.00000000 0.00000001 -0.00000407 0.00 0.00 -0.60 The maximum number of steps has been reached. End of BFGS Geometry Optimization* Ie. the code saying *The maximum number of steps has been reached.* the relaxation is not convergence. I am puzzled the etot_conv_thr does not meet ?? The etot_conv_thr is not high, and the nstep is already 200. try a lower etot_conv_thr? i wish someone could have a look at the output. Thanks a lot ! -- Yuehua Xu Group of Computational Condensed Matter Physics, National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, P. R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/e88609be/attachment.htm From germaneau at gucas.ac.cn Wed Oct 12 17:43:44 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Wed, 12 Oct 2011 11:43:44 -0400 Subject: [Pw_forum] iotk error Message-ID: <4E95B5B0.3000700@gucas.ac.cn> Dear all, I recently got the error bellow when running band calculation (calculation = 'band' and pw.x) : /# FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_end (iotk_scan.f90:241) # CVS Revision: 1.23 # foundl # ERROR IN: iotk_close_read (iotk_files.f90:746) # CVS Revision: 1.20/ Note that scf calculation goes well. Does anyone knows what does that mean? I use the release 4.3.2 built with gfortran. Thank you, ?ric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111012/6e013a19/attachment.htm From germaneau at gucas.ac.cn Wed Oct 12 17:48:04 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Wed, 12 Oct 2011 11:48:04 -0400 Subject: [Pw_forum] which criterion does not meet during relax progresss In-Reply-To: <518386492.03850@test1.gucas.ac.cn> References: <518386492.03850@test1.gucas.ac.cn> Message-ID: <4E95B6B4.1070307@gucas.ac.cn> Hey Yuehua, I think that means the program was not able to optimized the structure with the parameter you provided. Try to reduce etot_conv_thr or to increase the maximum number of steps by setting nstep. Hope it helps, ?ric. On 10/11/2011 10:53 PM, xu yuehua wrote: > Hi, all > I relaxed a system, my relaxation criterion is > etot_conv_thr=1.D-5 > forc_conv_thr=1.D-4, > and conv_thr = 1.D-8 , > and in my output file, i see the force_conv_thr is met, and the > conv_thr seems also met. > for in the last relaxation step, the printed information is : > > /! total energy = -551.13047812 Ry > Harris-Foulkes estimate = -551.13047807 Ry > estimated scf accuracy < 2.4E-11 Ry > > The total energy is the sum of the following terms: > > one-electron contribution = -2144.14675345 Ry > hartree contribution = 1097.77738769 Ry > xc contribution = -134.85772630 Ry > ewald contribution = 630.09661393 Ry > > convergence has been achieved in 9 iterations > > Forces acting on atoms (Ry/au): > > atom 1 type 2 force = 0.00006652 0.00001074 0.00001717 > atom 2 type 1 force = -0.00001149 -0.00003650 0.00002296 > atom 3 type 1 force = 0.00002092 0.00003527 0.00001095 > atom 4 type 2 force = -0.00006106 -0.00005036 0.00002893 > atom 5 type 1 force = 0.00012199 -0.00005785 -0.00011993 > atom 6 type 1 force = -0.00005472 0.00002358 0.00009707 > atom 7 type 2 force = 0.00003025 0.00003532 0.00004727 > atom 8 type 1 force = 0.00001390 0.00009541 0.00000283 > atom 9 type 1 force = -0.00007213 -0.00012498 -0.00005854 > atom 10 type 2 force = -0.00000989 -0.00001883 -0.00002476 > atom 11 type 1 force = 0.00002862 -0.00010630 0.00001950 > atom 12 type 1 force = 0.00000813 0.00006367 -0.00002737 > atom 13 type 2 force = -0.00010953 0.00005997 0.00012796 > atom 14 type 1 force = 0.00012468 0.00004819 0.00006199 > atom 15 type 1 force = -0.00003227 -0.00002568 -0.00012529 > atom 16 type 2 force = 0.00000131 0.00002155 0.00006799 > atom 17 type 1 force = 0.00002056 0.00002091 0.00006192 > atom 18 type 1 force = -0.00004895 -0.00000474 -0.00012101 > atom 19 type 2 force = -0.00000208 -0.00000446 0.00003292 > atom 20 type 1 force = -0.00003014 0.00001046 0.00005040 > atom 21 type 1 force = -0.00000665 0.00000012 -0.00002565 > atom 22 type 2 force = 0.00004366 0.00001375 -0.00003139 > atom 23 type 1 force = 0.00001038 0.00000199 -0.00004611 > atom 24 type 1 force = 0.00000001 -0.00002044 0.00003004 > atom 25 type 2 force = -0.00000668 -0.00002989 0.00007813 > atom 26 type 1 force = 0.00003097 -0.00004437 0.00003757 > atom 27 type 1 force = 0.00001552 0.00000595 -0.00005710 > atom 28 type 2 force = 0.00001236 0.00004340 0.00012950 > atom 29 type 1 force = -0.00002372 0.00002505 -0.00007569 > atom 30 type 1 force = 0.00003122 0.00000291 0.00000276 > atom 31 type 2 force = -0.00001390 -0.00010264 -0.00009180 > atom 32 type 1 force = 0.00004590 0.00003207 0.00003011 > atom 33 type 1 force = -0.00002671 0.00005738 -0.00001122 > atom 34 type 2 force = -0.00001380 -0.00001243 -0.00005321 > atom 35 type 1 force = -0.00002033 0.00001199 0.00006508 > atom 36 type 1 force = 0.00001161 -0.00000439 -0.00003033 > atom 37 type 2 force = -0.00008127 0.00002129 0.00005130 > atom 38 type 1 force = -0.00004667 -0.00008260 -0.00004117 > atom 39 type 1 force = 0.00000793 0.00013767 -0.00000675 > atom 40 type 2 force = 0.00001123 -0.00004604 0.00006549 > atom 41 type 1 force = 0.00003825 0.00001125 -0.00000180 > atom 42 type 1 force = -0.00005610 0.00001922 -0.00008202 > atom 43 type 2 force = -0.00001184 0.00000509 -0.00002456 > atom 44 type 1 force = -0.00005112 -0.00001419 0.00000597 > atom 45 type 1 force = 0.00009312 -0.00000567 -0.00002162 > atom 46 type 2 force = -0.00002442 -0.00003492 0.00009560 > atom 47 type 1 force = -0.00005855 0.00002530 -0.00010962 > atom 48 type 1 force = 0.00008502 -0.00001219 -0.00005446 > > Total force = 0.000643 Total SCF correction = 0.000037/ > // > /entering subroutine stress ... > > total stress (Ry/bohr**3) (kbar) > P= -1.92 > -0.00001798 0.00000011 0.00000000 -2.64 0.02 0.00 > 0.00000011 -0.00001708 0.00000001 0.02 -2.51 0.00 > 0.00000000 0.00000001 -0.00000407 0.00 0.00 -0.60 > > > The maximum number of steps has been reached. > > End of BFGS Geometry Optimization/ > Ie. the code saying /The maximum number of steps has been reached./ > the relaxation is not convergence. I am puzzled the etot_conv_thr > does not meet ?? The etot_conv_thr is not high, and the nstep is > already 200. try a lower etot_conv_thr? > i wish someone could have a look at the output. Thanks a lot ! > > -- > Yuehua Xu > Group of Computational Condensed Matter Physics, > National Laboratory of Solid State Microstructures and Department of > Physics, > Nanjing University, > Nanjing 210093, > P. R. China > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111012/1678daaa/attachment-0001.htm From bdslipun at gmail.com Wed Oct 12 06:32:53 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 12 Oct 2011 10:02:53 +0530 Subject: [Pw_forum] compilation problem Message-ID: ****** input tetrahedra for BZ-integration ****** 6 3 12 0.000000 0.000000 0.000000 0.750000 0.750000 0.000000 1.000000 0.500000 0.000000 0.500000 0.500000 0.500000 1.000000 0.000000 0.000000 1.000000 0.250000 0.250000 ****** input tetrahedra for BZ-integration ****** ********************** generate_tetra ********************* NT0= 3 NTETMX= 1728 0.0000 0.7500 1.0000 0.5000 0.0000 0.7500 0.5000 0.5000 0.0000 0.0000 0.0000 0.5000 1.0000 1.0000 1.0000 1.0000 volume of tetrahedron = 0.03125 0.0000 1.0000 1.0000 1.0000 0.0000 0.5000 0.0000 0.2500 0.0000 0.0000 0.0000 0.2500 1.0000 1.0000 1.0000 1.0000 volume of tetrahedron = 0.02083 0.0000 1.0000 0.5000 1.0000 0.0000 0.5000 0.5000 0.2500 0.0000 0.0000 0.5000 0.2500 1.0000 1.0000 1.0000 1.0000 volume of tetrahedron = 0.03125 total volume of BZ is = 0.0833 omg48= 24.0000 ****************** end of generate_tetra ****************** Recalculating omega(q) from C(R) Cannot match namelist object name alas444 STOP 2 head: cannot open `frequency' for reading: No such file or directory head: cannot open `frequency' for reading: No such file or directory (standard_in) 1: syntax error At line 27 of file Partial_phonon_DOS.f90 (unit = 5, file = 'stdin') Fortran runtime error: Bad integer for item 1 in list input ./run_Phonon_DOS.sh: line 204: frequency: No such file or directory At line 6 of file atom_info.f90 (unit = 5, file = 'stdin') Fortran runtime error: Bad integer for item 1 in list input At line 58 of file Atom_projected_properties.f90 (unit = 9, file = 'projected.DOS') Fortran runtime error: End of file At line 66 of file Mean_square_displacement.f90 (unit = 5, file = 'stdin') Fortran runtime error: End of file mv: cannot stat `Displacements': No such file or directory At line 6 of file atom_info.f90 (unit = 5, file = 'stdin') Fortran runtime error: Bad integer for item 1 in list input At line 58 of file Atom_projected_properties.f90 (unit = 9, file = 'projected.DOS') Fortran runtime error: End of file At line 66 of file Mean_square_displacement.f90 (unit = 5, file = 'stdin') Fortran runtime error: End of file mv: cannot stat `Displacements': No such file or directory At line 75 of file Debye.f90 (unit = 10, file = 'PHDOS.out') Fortran runtime error: End of file At line 92 of file F_QHA.f90 (unit = 1, file = 'PHDOS.out') Fortran runtime error: End of file Phonon DOS and Quasiharmonic calculations have finished. Now you can analyse these data using Gnuplot or xmgrace Enjoy! bds at Planck:~/bhabya/espresso-4.3/QHA/Examples/AlAs$ i want to compile the QHA code the error looks like what should i do -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/bd3d52e7/attachment.htm From giannozz at democritos.it Wed Oct 12 07:51:11 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 Oct 2011 07:51:11 +0200 Subject: [Pw_forum] compilation problem In-Reply-To: References: Message-ID: <459D6378-DBA5-418A-B341-94C90D2D5CCD@democritos.it> On Oct 12, 2011, at 6:32 , bhabya sahoo wrote: > i want to compile the QHA code the error looks like what should i do the relevant error is the first one: > Recalculating omega(q) from C(R) > Cannot match namelist object name alas444 > STOP 2 and you should understand why P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From germaneau at gucas.ac.cn Wed Oct 12 20:11:00 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Wed, 12 Oct 2011 14:11:00 -0400 Subject: [Pw_forum] Issue with phonon calculation on supercell. In-Reply-To: <518228367.28104@test1.gucas.ac.cn> References: <517774101.05937@gscas.net.cn> <4E8F1D71.2090405@gucas.ac.cn> <517957891.02419@gscas.net.cn> <517959689.14509@test1.gucas.ac.cn> <518228367.28104@test1.gucas.ac.cn> Message-ID: <4E95D834.6080403@gucas.ac.cn> Dear all, This seems to be solved by our system administrator. He just made some space on the storage server. ?ric. On 10/10/2011 02:55 PM, ?ric Germaneau wrote: > Dear all, > > After recompiling QE 4.3.2 with ifort 9.1 and mkl 8.1.1 I got an other > error : > > from davcio : error # 99 > error while writing to file > > This looks so weird to me. > Thank you, > > ?ric. > > On 10/07/2011 12:18 PM, ?ric Germaneau wrote: >> Dear Sanjeev, >> >> Thank you for noticed it. >> I've just ask to the administrator the compile it with ifort. >> We'll see. >> >> ?ric. >> >> On 10/06/2011 11:49 PM, Sanjeev Gupta wrote: >>> Dear ?ric Germaneau >>> >>> Please follow the recent link of "problem in vc-relax", there is >>> something same problem (If i understood correctly), Prof. Paolo >>> Giannozzi suggested that, this is Gfortran problem. >>> >>> Thanks >>> >>> Sanjeev >>> >>> >>> 2011/10/7 ?ric Germaneau >> > >>> >>> Dear all, >>> >>> Can someone tell me the meaning of the error >>> >>> from calbec : error # 1 >>> size mismatch >>> >>> when running ph.x. >>> >>> Thank you, >>> >>> ?ric. >>> >>> >>> On 10/05/2011 08:45 AM, ?ric Germaneau wrote: >>>> Dear all, >>>> >>>> I'm attempting to compute phonon at gamma point of a 2x2x2 >>>> crystal structure but I get the error bellow : >>>> >>>> *.....* >>>> Atomic displacements: >>>> There are 192 irreducible representations >>>> >>>> Representation 1 1 modes - To be done >>>> >>>> Representation 2 1 modes - To be done >>>> *....* >>>> Representation 191 1 modes - To be done >>>> >>>> Representation 192 1 modes - To be done >>>> >>>> >>>> Alpha used in Ewald sum = 2.8000 >>>> PHONON : 51m 2.98s CPU 51m13.49s WALL >>>> >>>> >>>> Electric Fields Calculation >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> from calbec : error # 1 >>>> size mismatch >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> >>>> stopping ... >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> Signal 15 received. >>>> >>>> Here is my input >>>> >>>> phonons >>>> &inputph >>>> tr2_ph=1.0d-14, >>>> prefix='S007__086_B4N4.vcrelax.vcrelax_2x2x2', >>>> epsil=.true., >>>> amass(1)=10.811000, >>>> amass(2)=14.006700, >>>> outdir='./SCF_PH', >>>> fildyn='S007__086_B4N4.vcrelax.vcrelax_2x2x2.dynG', >>>> / >>>> 0.0 0.0 0.0 >>>> >>>> What sounds weird to me is that I don't have any problem when I >>>> perform the same calculation on the unit cell, I mean the 1x1x1 >>>> structure. >>>> Before running ph.x I do a regular scf calculation at gamma >>>> point only which ends normally: >>>> >>>> K_POINTS automatic >>>> 1 1 1 0 0 0 >>>> >>>> I generate my supercell from the optimized unit cell and do not >>>> optimized it again due to time consuming. >>>> I don't have much experience in phonon calculations so any hits >>>> are welcome. >>>> Thank you, >>>> >>>> ?ric. >>>> >>>> -- >>>> /Be the change you wish to see in the world >>>> / --- Mahatma Gandhi --- >>>> >>>> Dr. ?ric Germaneau >>>> >>>> >>>> Graduate University of Chinese Academy of Sciences >>>> College of Physical Sciences >>>> Yuquan Road 19A >>>> Beijing 100049 >>>> China >>>> >>>> /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 >>> >>> -- >>> /Be the change you wish to see in the world >>> / --- Mahatma Gandhi --- >>> >>> Dr. ?ric Germaneau >>> >>> >>> Graduate University of Chinese Academy of Sciences >>> College of Physical Sciences >>> Yuquan Road 19A >>> Beijing 100049 >>> China >>> >>> /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 >>> >>> >>> >>> >>> -- >>> *Dr. Sanjeev Kumar Gupta* >>> *Post Doctoral Fellow, >>> /(Ministry of New and Renewable Energy/) >>> Department of Physics, >>> Bhavnagar University, Bhavnagar-364 022 >>> Gujarat, India* >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> /Be the change you wish to see in the world >> / --- Mahatma Gandhi --- >> >> Dr. ?ric Germaneau >> >> >> Graduate University of Chinese Academy of Sciences >> College of Physical Sciences >> Yuquan Road 19A >> Beijing 100049 >> China >> >> /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 > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > /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 -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111012/8d156a3c/attachment-0001.htm From giannozz at democritos.it Wed Oct 12 08:14:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 Oct 2011 08:14:33 +0200 Subject: [Pw_forum] iotk error In-Reply-To: <4E95B5B0.3000700@gucas.ac.cn> References: <4E95B5B0.3000700@gucas.ac.cn> Message-ID: <06E24DEB-9AA2-4DF0-9595-7F926AC9CD8C@democritos.it> On Oct 12, 2011, at 17:43 , ?ric Germaneau wrote: > I recently got the error bellow when running band calculation > [...] Does anyone knows what does that mean? it means (with 99.99% probability) that your compiler is buggy > P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Oct 12 08:16:42 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 Oct 2011 08:16:42 +0200 Subject: [Pw_forum] which criterion does not meet during relax progresss In-Reply-To: References: Message-ID: <4623DA00-D560-46C4-83B2-AA7A205D9CC6@democritos.it> On Oct 12, 2011, at 4:53 , xu yuehua wrote: > I relaxed a system, my relaxation criterion is > etot_conv_thr=1.D-5 this is a quite strict crterion. It means that the energy (in Ry) should not change by more than 1.D-5 between successive iterations P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From germaneau at gucas.ac.cn Wed Oct 12 20:18:06 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Wed, 12 Oct 2011 14:18:06 -0400 Subject: [Pw_forum] iotk error In-Reply-To: <518389511.05633@test1.gucas.ac.cn> References: <518389511.05633@test1.gucas.ac.cn> Message-ID: <4E95D9DE.6020601@gucas.ac.cn> Dear all, After some investigations it seems to me that this issue has something to do with reading the 'outdir' directory. I make a directory call SCF, then preform a scf calculation by setting outdir to SCF. Then for the band calculation, I also set outdir to SCF, but it's like the program can not read its contents. On the other hand it works find on my desktop, so that may be a cluster configuration issue. Is it possible nodes can't get access to directories created by the head? Thank you, ?ric. On 10/12/2011 11:43 AM, ?ric Germaneau wrote: > Dear all, > > I recently got the error bellow when running band calculation > (calculation = 'band' and pw.x) : > > /# FROM IOTK LIBRARY, VERSION 1.2.0 > # UNRECOVERABLE ERROR (ierr=1) > # ERROR IN: iotk_scan_end (iotk_scan.f90:241) > # CVS Revision: 1.23 > # foundl > # ERROR IN: iotk_close_read (iotk_files.f90:746) > # CVS Revision: 1.20/ > > Note that scf calculation goes well. > Does anyone knows what does that mean? > I use the release 4.3.2 built with gfortran. > > Thank you, > > ?ric. > > > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > /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 -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111012/93a74f80/attachment.htm From germaneau at gucas.ac.cn Wed Oct 12 20:21:34 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Wed, 12 Oct 2011 14:21:34 -0400 Subject: [Pw_forum] iotk error In-Reply-To: <518398613.21635@gscas.net.cn> References: <4E95B5B0.3000700@gucas.ac.cn> <518398613.21635@gscas.net.cn> Message-ID: <4E95DAAE.9030302@gucas.ac.cn> Dear Professor Giannozzi, Thank you for your reply. I'll try with ifort then. Best, ?ric. On 10/12/2011 02:14 AM, Paolo Giannozzi wrote: > On Oct 12, 2011, at 17:43 , ?ric Germaneau wrote: > >> I recently got the error bellow when running band calculation >> [...] Does anyone knows what does that mean? > it means (with 99.99% probability) that your compiler is buggy > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111012/739a7941/attachment.htm From bdslipun at gmail.com Wed Oct 12 08:50:53 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 12 Oct 2011 12:20:53 +0530 Subject: [Pw_forum] compilation Qha Message-ID: i donot understand because that force constant matrix file is there in my directory -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/ab45b1a9/attachment.htm From bdslipun at gmail.com Wed Oct 12 11:37:56 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 12 Oct 2011 15:07:56 +0530 Subject: [Pw_forum] (no subject) Message-ID: can the QHA code be run on gfortrtan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/7120c4b5/attachment.htm From bdslipun at gmail.com Wed Oct 12 11:40:09 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 12 Oct 2011 15:10:09 +0530 Subject: [Pw_forum] compilation Message-ID: can the QHA code be run on gfortran compiler -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/91e2fb17/attachment.htm From pankaj.espresso at gmail.com Wed Oct 12 11:41:21 2011 From: pankaj.espresso at gmail.com (Pankaj Pankaj) Date: Wed, 12 Oct 2011 15:11:21 +0530 Subject: [Pw_forum] Phonon calculation for Pnma structure Message-ID: On Tue, Oct 11, 2011 at 4:44 PM, wrote: > 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. Re: Phonon Cal for Pnam Space group (Paolo Giannozzi) > 2. Re: charge ordered state (Paolo Giannozzi) > 3. ELF error with version 4.3 (psavita) > 4. Re: problem in xspectra calculations (Niharika Joshi) > 5. compilation QHA code (bhabya sahoo) > 6. Re: compilation QHA code (Stefano Baroni) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Oct 2011 09:57:15 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Phonon Cal for Pnam Space group > To: PWSCF Forum > Message-ID: <55EDD6A0-8AC2-4ECA-BD0C-DA370B542474 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Oct 11, 2011, at 7:45 , Pankaj Pankaj wrote: > > > I am struggling to calculate the phonon spectrum of crystall > > symmetry with Pnma having point group symmetry mmm (D2h) > > in quantum espresso, which usually disregard this symmetry point > > what do you mean by "disregard"? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > Hello Paolo, I mean ............... When i do SCF calculation for Pnma structure, do not see all symmetries present in system and find only 2 symmetries, which is not the case for Pnma. Also message displays symmetries with points 0.5 0.5 0.5 ignored.................So i dont understand with this message, and only 2 symmetries, calculations are correct or not......................and getting less symmetry points is a real problem with my calculation or something else. Please let me know where is problem, > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 11 Oct 2011 10:02:22 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] charge ordered state > To: PWSCF Forum > Message-ID: <56638186-BB39-48AB-AA25-ED0396201F62 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Oct 11, 2011, at 5:40 , hanghui chen wrote: > > > I have a general question. I want to calculate a charge > > ordered state of nickelates. > > I am afraid that the general answer is "DFT is very bad at this" > > > I wonder if there is a way to give different charge density initial > > guess on the two types of Ni atoms in QE? > > you may use two different Ni pseudopotential files that are > the same except for the atomic charge density (field > PP_RHOATOM) > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > ------------------------------ > > Message: 3 > Date: Tue, 11 Oct 2011 13:52:27 +0530 > From: psavita > Subject: [Pw_forum] ELF error with version 4.3 > To: pw_forum at pwscf.org > Message-ID: > < > OF8E6AF5D0.4BA58AC6-ON65257926.002E0031-65257926.002E003C at crlindia.com> > > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20111011/bae0d8f0/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Tue, 11 Oct 2011 15:01:33 +0530 (IST) > From: Niharika Joshi > Subject: Re: [Pw_forum] problem in xspectra calculations > To: PWSCF Forum > Message-ID: > <1318325493.18035.YahooMailClassic at web95715.mail.in.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Paolo Sir, > Thank you for your reply. > I tried running the xanes calculation after making the change in > xspectra.f90. But it is still giving me the same message 'Could not find the > element? C in the table of K edge energies!' at the end and leaving the > output file incomplete. > For some reason, the condition for 'if-loop' in mygetK.f90 is not getting > satisfied and thus it is not getting executed. I wrote the variables sym and > seuilK_tab(6) . For both variables it writes 'C' but does not enter the > if-loop. > -Niharika Joshi > (project student, IISER Pune) > > ? > --- On Fri, 7/10/11, Paolo Giannozzi wrote: > > From: Paolo Giannozzi > > Subject: Re: [Pw_forum] problem in xspectra calculations > To: "PWSCF Forum" > Date: Friday, 7 October, 2011, 11:52 AM > > On Wed, 2011-09-28 at 18:29 +0530, Niharika Joshi wrote: > > > 'Could not find the element? C in the table of K edge energies!' > > it should be a compiler weirdness. Try to replace in xspectra.f90 > ? e_1s=mygetK(upf(xiabs)%psd)) > with > ? e_1s=mygetK(trim(adjustl(upf(xiabs)%psd))) > P. > -- > Paolo Giannozzi, IOM-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/20111011/24fd70c8/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Tue, 11 Oct 2011 16:20:47 +0530 > From: bhabya sahoo > Subject: [Pw_forum] compilation QHA code > To: PWSCF Forum > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > when i compile QHA the error gives > > > > > > gfortan -O3 -c tetra.f > make: gfortan: Command not found > make: *** [tetra.o] Error 127 > gfortran -O3 -c Debye.f90 > Debye.f90:144.8: > > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: Loop variable at (1) must be integer > Debye.f90:144.11: > > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: Start expression in DO loop at (1) must be > integer > Debye.f90:144.24: > > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: End expression in DO loop at (1) must be integer > Debye.f90:144.31: > > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: Step expression in DO loop at (1) must be integer > Debye.f90:177.4: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: Loop variable at (1) must be integer > Debye.f90:177.7: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: Start expression in DO loop at (1) must be > integer > Debye.f90:177.16: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: End expression in DO loop at (1) must be integer > Debye.f90:177.24: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: Step expression in DO loop at (1) must be integer > gfortran -O3 -c Debye_T.f > gfortran -O3 -c debye3.f > gfortran -O3 -c cheval.f > gfortran -O3 -c d1mach.f > gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o > fortran -FR -c Mean_square_displacement.f90 > make: fortran: Command not found > make: *** [Mean_square_displacement.o] Error 127 > ln: creating symbolic link `tetra.x': File exists > ln: creating symbolic link `phonon_dos.x': File exists > ln: creating symbolic link `Debye.x': File exists > ln: creating symbolic link `Atom_projected_properties.x': File exists > ln: creating symbolic link `F_QHA.x': File exists > ln: creating symbolic link `Ghost_DOS.x': File exists > ln: creating symbolic link `Partial_phonon_DOS.x': File exists > ln: creating symbolic link `Mean_square_displacement.x': File exists > ln: creating symbolic link `atom_info.x': File exists > bds at Planck:~/bhabya/espresso-4.3/QHA$ > > > > what should i do > > > > b d sahoo reserch scholar > barc > mumbai > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20111011/525688cd/attachment-0001.htm > > ------------------------------ > > Message: 6 > Date: Tue, 11 Oct 2011 13:14:13 +0200 > From: Stefano Baroni > Subject: Re: [Pw_forum] compilation QHA code > To: PWSCF Forum > Message-ID: <9C1E1DD8-26BA-4A25-98A6-16F9217B73A1 at sissa.it> > Content-Type: text/plain; charset="iso-8859-1" > > 1) use a different compiler > OR > 2) modify the code, so as to feed the DO loop with integer indeces > SB > > On Oct 11, 2011, at 12:50 PM, bhabya sahoo wrote: > > > when i compile QHA the error gives > > > > > > > > > > > > gfortan -O3 -c tetra.f > > make: gfortan: Command not found > > make: *** [tetra.o] Error 127 > > gfortran -O3 -c Debye.f90 > > Debye.f90:144.8: > > > > do T = T_low_start, T_low, T_low_delta > > 1 > > Warning: Deleted feature: Loop variable at (1) must be integer > > Debye.f90:144.11: > > > > do T = T_low_start, T_low, T_low_delta > > 1 > > Warning: Deleted feature: Start expression in DO loop at (1) must be > integer > > Debye.f90:144.24: > > > > do T = T_low_start, T_low, T_low_delta > > 1 > > Warning: Deleted feature: End expression in DO loop at (1) must be > integer > > Debye.f90:144.31: > > > > do T = T_low_start, T_low, T_low_delta > > 1 > > Warning: Deleted feature: Step expression in DO loop at (1) must be > integer > > Debye.f90:177.4: > > > > do T = T_low+5, T_high, T_high_delta > > 1 > > Warning: Deleted feature: Loop variable at (1) must be integer > > Debye.f90:177.7: > > > > do T = T_low+5, T_high, T_high_delta > > 1 > > Warning: Deleted feature: Start expression in DO loop at (1) must be > integer > > Debye.f90:177.16: > > > > do T = T_low+5, T_high, T_high_delta > > 1 > > Warning: Deleted feature: End expression in DO loop at (1) must be > integer > > Debye.f90:177.24: > > > > do T = T_low+5, T_high, T_high_delta > > 1 > > Warning: Deleted feature: Step expression in DO loop at (1) must be > integer > > gfortran -O3 -c Debye_T.f > > gfortran -O3 -c debye3.f > > gfortran -O3 -c cheval.f > > gfortran -O3 -c d1mach.f > > gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o > > fortran -FR -c Mean_square_displacement.f90 > > make: fortran: Command not found > > make: *** [Mean_square_displacement.o] Error 127 > > ln: creating symbolic link `tetra.x': File exists > > ln: creating symbolic link `phonon_dos.x': File exists > > ln: creating symbolic link `Debye.x': File exists > > ln: creating symbolic link `Atom_projected_properties.x': File exists > > ln: creating symbolic link `F_QHA.x': File exists > > ln: creating symbolic link `Ghost_DOS.x': File exists > > ln: creating symbolic link `Partial_phonon_DOS.x': File exists > > ln: creating symbolic link `Mean_square_displacement.x': File exists > > ln: creating symbolic link `atom_info.x': File exists > > bds at Planck:~/bhabya/espresso-4.3/QHA$ > > > > > > > > what should i do > > > > > > > > b d sahoo reserch scholar > > barc > > mumbai > > _______________________________________________ > > 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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20111011/32b9da96/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 52, Issue 27 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/5d6b594f/attachment-0001.htm From bdslipun at gmail.com Wed Oct 12 12:25:54 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 12 Oct 2011 15:55:54 +0530 Subject: [Pw_forum] compilation in QHA Message-ID: gfortran -O3 -c tetra.f gfortran -O3 -c k_brillouin.f gfortran -O3 -c generate_tetra.f gfortran -O3 -c det3.f gfortran -O3 -c det4.f gfortran -static -o tetra.x tetra.o k_brillouin.o generate_tetra.o det3.o det4.o gfortran -O3 -c phonon_dos.f gfortran -O3 -c Tetrahedra.f gfortran -O3 -c Integration.f Integration.f:111.72: * 13X,"g_y",13X,"g_z")') 1 Warning: Extension: Tab character in format at (1) gfortran -static phonon_dos.o k_brillouin.o generate_tetra.o det3.o det4.o Tetrahedra.o Integration.o -o phonon_dos.x gfortran -O3 -c Debye.f90 Debye.f90:144.8: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer Debye.f90:144.11: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Start expression in DO loop at (1) must be integer Debye.f90:144.24: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: End expression in DO loop at (1) must be integer Debye.f90:144.31: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Step expression in DO loop at (1) must be integer Debye.f90:177.4: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer Debye.f90:177.7: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Start expression in DO loop at (1) must be integer Debye.f90:177.16: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: End expression in DO loop at (1) must be integer Debye.f90:177.24: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Step expression in DO loop at (1) must be integer gfortran -O3 -c Debye_T.f gfortran -O3 -c debye3.f gfortran -O3 -c cheval.f gfortran -O3 -c d1mach.f gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o gfortran -FR -c Mean_square_displacement.f90 Mean_square_displacement.f90:162.7: do T=T_start,T_end,T_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer gfortran -static -o Mean_square_displacement.x Mean_square_displacement.o gfortran -FR -c Atom_projected_properties.f90 Atom_projected_properties.f90:180.7: do T=T_start, T_end, T_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer Atom_projected_properties.f90:180.9: do T=T_start, T_end, T_delta 1 Warning: Deleted feature: Start expression in DO loop at (1) must be integer Atom_projected_properties.f90:180.17: do T=T_start, T_end, T_delta 1 Warning: Deleted feature: End expression in DO loop at (1) must be integer Atom_projected_properties.f90:180.24: do T=T_start, T_end, T_delta 1 Warning: Deleted feature: Step expression in DO loop at (1) must be integer gfortran -static -o Atom_projected_properties.x Atom_projected_properties.o gfortran -FR -c F_QHA.f90 F_QHA.f90:134.7: do T=T_start,T_end,T_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer gfortran -static -o F_QHA.x F_QHA.o gfortran -FR -c Ghost_DOS.f90 gfortran -static -o Ghost_DOS.x Ghost_DOS.o gfortran -FR -c Partial_phonon_DOS.f90 gfortran -static -o Partial_phonon_DOS.x Partial_phonon_DOS.o gfortran -FR -c atom_info.f90 gfortran -static -o atom_info.x atom_info.o ln: creating symbolic link `tetra.x': File exists ln: creating symbolic link `phonon_dos.x': File exists ln: creating symbolic link `Debye.x': File exists ln: creating symbolic link `Atom_projected_properties.x': File exists ln: creating symbolic link `F_QHA.x': File exists ln: creating symbolic link `Ghost_DOS.x': File exists ln: creating symbolic link `Partial_phonon_DOS.x': File exists ln: creating symbolic link `Mean_square_displacement.x': File exists ln: creating symbolic link `atom_info.x': File exists when i want to confuger QHA code warning comes with gfortran compiler i have no ifort so how i shall remove thoes warnings is it ok because example files are not running the error looks like this ./run_Phonon_DOS.sh ****** input tetrahedra for BZ-integration ****** 6 3 12 0.000000 0.000000 0.000000 0.750000 0.750000 0.000000 1.000000 0.500000 0.000000 0.500000 0.500000 0.500000 1.000000 0.000000 0.000000 1.000000 0.250000 0.250000 ****** input tetrahedra for BZ-integration ****** ********************** generate_tetra ********************* NT0= 3 NTETMX= 1728 0.0000 0.7500 1.0000 0.5000 0.0000 0.7500 0.5000 0.5000 0.0000 0.0000 0.0000 0.5000 1.0000 1.0000 1.0000 1.0000 volume of tetrahedron = 0.03125 0.0000 1.0000 1.0000 1.0000 0.0000 0.5000 0.0000 0.2500 0.0000 0.0000 0.0000 0.2500 1.0000 1.0000 1.0000 1.0000 volume of tetrahedron = 0.02083 0.0000 1.0000 0.5000 1.0000 0.0000 0.5000 0.5000 0.2500 0.0000 0.0000 0.5000 0.2500 1.0000 1.0000 1.0000 1.0000 volume of tetrahedron = 0.03125 total volume of BZ is = 0.0833 omg48= 24.0000 ****************** end of generate_tetra ****************** Recalculating omega(q) from C(R) Cannot match namelist object name alas444.fc STOP 2 head: cannot open `frequency' for reading: No such file or directory head: cannot open `frequency' for reading: No such file or directory (standard_in) 1: syntax error At line 27 of file Partial_phonon_DOS.f90 (unit = 5, file = 'stdin') Fortran runtime error: Bad integer for item 1 in list input ./run_Phonon_DOS.sh: line 204: frequency: No such file or directory At line 6 of file atom_info.f90 (unit = 5, file = 'stdin') Fortran runtime error: Bad integer for item 1 in list input At line 58 of file Atom_projected_properties.f90 (unit = 9, file = 'projected.DOS') Fortran runtime error: End of file At line 66 of file Mean_square_displacement.f90 (unit = 5, file = 'stdin') Fortran runtime error: End of file mv: cannot stat `Displacements': No such file or directory At line 6 of file atom_info.f90 (unit = 5, file = 'stdin') Fortran runtime error: Bad integer for item 1 in list input At line 58 of file Atom_projected_properties.f90 (unit = 9, file = 'projected.DOS') Fortran runtime error: End of file At line 66 of file Mean_square_displacement.f90 (unit = 5, file = 'stdin') Fortran runtime error: End of file mv: cannot stat `Displacements': No such file or directory At line 75 of file Debye.f90 (unit = 10, file = 'PHDOS.out') Fortran runtime error: End of file At line 92 of file F_QHA.f90 (unit = 1, file = 'PHDOS.out') Fortran runtime error: End of file Phonon DOS and Quasiharmonic calculations have finished. Now you can analyse these data using Gnuplot or xmgrace Enjoy! b d sahoo barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/55d2df33/attachment.htm From pascal.boulet at univ-provence.fr Wed Oct 12 12:43:46 2011 From: pascal.boulet at univ-provence.fr (pascal boulet) Date: Wed, 12 Oct 2011 12:43:46 +0200 Subject: [Pw_forum] general question on openMP Message-ID: <4E956F62.6000300@univ-provence.fr> Dear all, I am not familiar with the openMP parallelization. I would like to know in what circumstances openMP is worth being used? Same question for MPI+openMP. Thank you for your help. Best regards Pascal From ali.allam2 at hotmail.com Wed Oct 12 16:09:07 2011 From: ali.allam2 at hotmail.com (Ali ALLAM) Date: Wed, 12 Oct 2011 16:09:07 +0200 Subject: [Pw_forum] Problem - Message-ID: Dear all I am ali allam , a PhD student I work on the software Quantum Espresso 4.3.2 After optimization of the structure, I want to calculate the nscf My 'input' file, is : CONTROL calculation = 'nscf' prefix = '', pseudo_dir = '', outdir = '', / &SYSTEM ibrav = 0, celldm(1) = 1.d0, nat = 44, ntyp = 2, nspin = 1, ecutwfc = 30.d0, ecutrho = 300.0, nbnd = 190, occupations = 'tetrahedra', / &ELECTRONS conv_thr = 1.d-8, mixing_beta = 0.1d0, diagonalization = 'cg', / ATOMIC_SPECIES ...... ...... K_POINTS {automatic} 12 12 4 1 1 1 ATOMIC_POSITIONS (crystal) ...... ..... CELL_PARAMETERS ... ... ... The problem, is that in the output file, i have these remarks Band Structure Calculation CG style diagonalization c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 6 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 6 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged I think that my input file is good, but i don't know from where the problem comes Thank you for helping me, to resolve this problem I am wainting for your reply Thanks BEST regards Ali -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/60e1b511/attachment.htm From zhiting at MIT.EDU Wed Oct 12 16:51:02 2011 From: zhiting at MIT.EDU (Zhiting Tian) Date: Wed, 12 Oct 2011 10:51:02 -0400 Subject: [Pw_forum] Problem - In-Reply-To: References: Message-ID: <1675BB3F3586E9459BBC8B9812C3532020C7997ACA@EXPO20.exchange.mit.edu> I have met this problem before.Try to change "tetrahedra? to see whether it helps. Zhiting ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of Ali ALLAM [ali.allam2 at hotmail.com] Sent: Wednesday, October 12, 2011 10:09 AM To: pw_forum at pwscf.org Subject: [Pw_forum] Problem - Dear all I am ali allam , a PhD student I work on the software Quantum Espresso 4.3.2 After optimization of the structure, I want to calculate the nscf My 'input' file, is : CONTROL calculation = 'nscf' prefix = '', pseudo_dir = '', outdir = '', / &SYSTEM ibrav = 0, celldm(1) = 1.d0, nat = 44, ntyp = 2, nspin = 1, ecutwfc = 30.d0, ecutrho = 300.0, nbnd = 190, occupations = 'tetrahedra', / &ELECTRONS conv_thr = 1.d-8, mixing_beta = 0.1d0, diagonalization = 'cg', / ATOMIC_SPECIES ...... ...... K_POINTS {automatic} 12 12 4 1 1 1 ATOMIC_POSITIONS (crystal) ...... ..... CELL_PARAMETERS ... ... ... The problem, is that in the output file, i have these remarks Band Structure Calculation CG style diagonalization c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 6 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 6 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged I think that my input file is good, but i don't know from where the problem comes Thank you for helping me, to resolve this problem I am wainting for your reply Thanks BEST regards Ali From faccin.giovani at gmail.com Wed Oct 12 16:59:04 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Wed, 12 Oct 2011 10:59:04 -0400 Subject: [Pw_forum] general question on openMP In-Reply-To: <4E956F62.6000300@univ-provence.fr> References: <4E956F62.6000300@univ-provence.fr> Message-ID: Dear Pascal, I've been playing with both for some time. From the point of view of efficiency, it seens to me that mpi is at the moment better paralellized, which means you get a faster calculation with the same number of processors. However there's a big drawback in pure mpi: each process has it's own memory requirements, which means you might get in a situation where your total number of processors is limited by the memory available in the supercomputer node. In this situation, OpenMP is nice; running a job with 1 processor and with 8 under OpenMP increases the memory requirements much less than with MPI, which in practice allows you to run with more processors. I believe that the hybrid scheme is preferable when you have a computer architecture that demands it. For example, a cluster of networked PCs, each node containing 8 cores, without shared memory. In this case, you could spawn a mpi process for each node, and run them with openmp to use the cores without overloading the memory. If on the other hand you are using a supercomputer with shared memory, then you can simply go for pure MPI if the machine can handle it. Regards Giovani M. Faccin UFMS / Brazil 2011/10/12 pascal boulet > Dear all, > > > I am not familiar with the openMP parallelization. I would like to know > in what circumstances openMP is worth being used? Same question for > MPI+openMP. > > Thank you for your help. > Best regards > Pascal > _______________________________________________ > 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/20111012/0d8159b3/attachment.htm From giannozz at democritos.it Wed Oct 12 17:03:28 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 Oct 2011 17:03:28 +0200 Subject: [Pw_forum] general question on openMP In-Reply-To: <4E956F62.6000300@univ-provence.fr> References: <4E956F62.6000300@univ-provence.fr> Message-ID: <1318431808.1949.84.camel@fe12lx.fisica.uniud.it> On Wed, 2011-10-12 at 12:43 +0200, pascal boulet wrote: > I am not familiar with the openMP parallelization. I would > like to know in what circumstances openMP is worth being used? > Same question for MPI+openMP. Right now, OpenMP alone is seldom faster than MPI, but MPI+OpenMP is very useful for large calculations on machines like IBM BlueGene P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Wed Oct 12 17:04:56 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 Oct 2011 17:04:56 +0200 Subject: [Pw_forum] Problem - In-Reply-To: <1675BB3F3586E9459BBC8B9812C3532020C7997ACA@EXPO20.exchange.mit.edu> References: <1675BB3F3586E9459BBC8B9812C3532020C7997ACA@EXPO20.exchange.mit.edu> Message-ID: <1318431896.1949.87.camel@fe12lx.fisica.uniud.it> On Wed, 2011-10-12 at 10:51 -0400, Zhiting Tian wrote: > I have met this problem before.Try to change "tetrahedra? > to see whether it helps. it is not necessarily a problem, and it is unrelated to the usage of tetrahedra. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Wed Oct 12 17:07:26 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 Oct 2011 17:07:26 +0200 Subject: [Pw_forum] compilation in QHA In-Reply-To: References: Message-ID: <1318432046.1949.91.camel@fe12lx.fisica.uniud.it> On Wed, 2011-10-12 at 15:55 +0530, bhabya sahoo wrote: > when i want to confuger QHA code warning comes with gfortran compiler these warnings are harmless and completely unrelated to the error: > Cannot match namelist object name alas444.fc which means that an incorrect syntax was used in input -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Wed Oct 12 17:09:23 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 Oct 2011 17:09:23 +0200 Subject: [Pw_forum] Phonon calculation for Pnma structure In-Reply-To: References: Message-ID: <1318432163.1949.94.camel@fe12lx.fisica.uniud.it> On Wed, 2011-10-12 at 15:11 +0530, Pankaj Pankaj wrote: > When i do SCF calculation for Pnma structure, do not see all > symmetries present in system and find only 2 symmetries, which is not > the case for Pnma. Also message displays symmetries with points 0.5 > 0.5 0.5 ignored.................So i dont understand with this > message, and only 2 symmetries, calculations are correct or > not......................and getting less symmetry points is a real > problem with my calculation or something else. > > Please let me know where is problem, the problem is that you, like everybody else, didn't bother looking into the user guide: http://www.quantum-espresso.org/user_guide/node52.html#SECTION0001210190000000000000 -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Wed Oct 12 17:41:00 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 12 Oct 2011 17:41:00 +0200 Subject: [Pw_forum] electron-phonon coupling tutorial In-Reply-To: References: Message-ID: <1318434060.1949.123.camel@fe12lx.fisica.uniud.it> On Tue, 2011-10-11 at 13:31 -0400, Hua Bao wrote: > However, there is very limited information about the input and output > of the related module (dynmax, q2r, and lambda, etc). It is not even > easy to understand the output format. input is documented as usual in INPUT_PH.* . Output should be quite self-explanatory. Attached, a few notes on the calculated quantities. > I am wondering if there is any good documentation there is no good documentation and there will never be any, because everybody wants documentation but nobody wants to write it. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy -------------- next part -------------- A non-text attachment was scrubbed... Name: e-ph.pdf Type: application/pdf Size: 45083 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111012/c4cff9ce/attachment-0001.pdf From Lorenzo.Paulatto at impmc.upmc.fr Wed Oct 12 18:05:40 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 12 Oct 2011 18:05:40 +0200 Subject: [Pw_forum] iotk error In-Reply-To: <4E95B5B0.3000700@gucas.ac.cn> References: <4E95B5B0.3000700@gucas.ac.cn> Message-ID: On Wed, 12 Oct 2011 17:43:44 +0200, ?ric Germaneau wrote: > I recently got the error bellow when running band calculation > (calculation = 'band' and pw.x) : > > /# FROM IOTK LIBRARY, VERSION 1.2.0 This error can also be caused by a band calculation when restart_mode='restart'; see the bug tracker for details (http://qe-forge.org/tracker/?atid=133&group_id=10&func=browse). If this is your case, the simpler solution is to remove restart_mode from the band calculation input bests -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From stewart at cnf.cornell.edu Wed Oct 12 19:33:05 2011 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Wed, 12 Oct 2011 13:33:05 -0400 Subject: [Pw_forum] Upcoming PASI Workshop "Computational Materials Science for Energy Generation and Conversion" Message-ID: <4E95CF51.9060301@cnf.cornell.edu> Hi everyone, I am organizing a Pan American Advanced Studies Institute (PASI) on Computational Materials Science for Energy Conversion and Generation in Santiago, Chile from January 9-20, 2012. This workshop focuses on training young researchers (graduate students and post-docs) on simulation techniques with energy research applications. As part of the workshop, we will provide lectures on density functional theory and calculations using Quantum Espresso. I have provided a full call below for those interested. The registration deadline is coming up soon on Oct. 21, 2011 and there a limited number of spots. *We will be providing travel support for participants.* Please note that due to the terms of the NSF grant, the participants must be researchers working in North or South America. Feel free to contact me if you have any questions. I hope to see some of you in Santiago this winter! Best regards, Derek *Computational Materials Science for Energy Conversion and Generation* *Pan-American Advanced Studies Institute* *January 9-20, 2012* *Santiago, Chile -- Pontifica Universidad Catolica de Chile* *http://www.cnf.cornell.edu/cnf_pasi2012.html* *Registration Deadline: Oct. 21, 2011* *Travel funding available for participants* *_Overview_* This workshop will provide young researchers (graduate students and post-docs) from across the Americas with lectures and hands-on tutorials on computational material science for energy applications.Participants will also give presentations on their own research and work together in collaborative teams on challenge projects.This two week workshop provides a unique opportunity to develop international connections and collaborations. *_Energy Topics include:_* Thermoelectrics (electronic and thermal transport), Battery Design Optimization , Structure Searches for New Materials, Piezoelectric Energy Harvesting, Nanophotonics for Solar Energy Applications, Catalysis Design *_Code Tutorials in:_ *Density functional theory (Quantum Espresso, Siesta, OpenMX), Molecular dynamics (LAMMPS), Photonics (MEEP, MPB), Multiphysics (Elmer), and more *_Registration Info:_ *The registration procedure is available on the PASI website.All qualifying participants will receive travel and expenses support to attend the workshop.*Applicants must be doing research in a country in North or South America.*** There are limited spots so please apply early. Registration Deadline: October 21, 2011 *Questions?*:Please contact the workshop organizers Derek Stewart (derek.stewart at cornell.edu ) or Richard Hennig (rhennig at cornell.edu ) *Funding:* This workshop is made possible through generous support from the National Science Foundation, U.S. Department of Energy, the Office of Naval Research Global (ONRG), the International Center for Materials Research (ICMR), and the National Nanotechnology Infrastructure Network (NNIN). -- ################################ Derek Stewart, Ph. D. Senior Research Associate ** New Webpage ** http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/2e3ea3ad/attachment-0001.htm From ivan.girotto at ichec.ie Wed Oct 12 20:01:26 2011 From: ivan.girotto at ichec.ie (Ivan Girotto) Date: Wed, 12 Oct 2011 19:01:26 +0100 Subject: [Pw_forum] PW for hybrid CPU/GPU systems Message-ID: <4E95D5F6.4040600@ichec.ie> Dear PW user, this message is for who of you have any interest to know more about PWscf calculation on hybrid CPU/GPU system. Tomorrow morning from 11:10 a.m. CEST my colleague Filippo Spiga will introduce basic concepts with a detailed analysis of the performance, at the Advanced School of Parallel Computing at CINECA (Italy). The lesson can be followed live in streaming from the link: http://www.cineca.it/page/advanced-school-parallel-computing. A discussion can follow on the QE-GPU forum. Please apologize the use of this mailing list for the announcement but I reckon some of you might be interested to this topic even though they are not subscribed to the QE-GPU forum. Enjoy GPU computing, Ivan -- Ivan Girotto - ivan.girotto at ichec.ie ICHEC - Computational Group - http://www.ichec.ie - GPU Team Leader - http://gpgpu.ichec.ie/ The Tower - 7th floor Trinity Technology& Enterprise Campus Grand Canal Quay - Dublin 2 - Ireland +353-1-5241608 ex. 32 (ph) / +353-1-7645845 (fax) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/b6a930c0/attachment.htm From baroni at sissa.it Wed Oct 12 20:18:53 2011 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 12 Oct 2011 20:18:53 +0200 Subject: [Pw_forum] PW for hybrid CPU/GPU systems In-Reply-To: <4E95D5F6.4040600@ichec.ie> References: <4E95D5F6.4040600@ichec.ie> Message-ID: You are most welcome, Ivan. Thanks for letting us know. Stefano On Oct 12, 2011, at 8:01 PM, Ivan Girotto wrote: > Dear PW user, > > this message is for who of you have any interest to know more about PWscf calculation on hybrid CPU/GPU system. > > Tomorrow morning from 11:10 a.m. CEST my colleague Filippo Spiga will introduce basic concepts with a detailed analysis of the performance, at the Advanced School of Parallel Computing at CINECA (Italy). The lesson can be followed live in streaming from the link: http://www.cineca.it/page/advanced-school-parallel-computing. A discussion can follow on the QE-GPU forum. > > Please apologize the use of this mailing list for the announcement but I reckon some of you might be interested to this topic even though they are not subscribed to the QE-GPU forum. > > Enjoy GPU computing, > > Ivan > -- > > Ivan Girotto - ivan.girotto at ichec.ie > ICHEC - Computational Group - http://www.ichec.ie > - GPU Team Leader - http://gpgpu.ichec.ie/ > The Tower - 7th floor > Trinity Technology & Enterprise Campus > Grand Canal Quay - Dublin 2 - Ireland > > +353-1-5241608 ex. 32 (ph) / +353-1-7645845 (fax) > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/c86ef2df/attachment.htm From ptao10b at imr.ac.cn Thu Oct 13 02:20:20 2011 From: ptao10b at imr.ac.cn (=?utf-8?B?6Zm26bmP?=) Date: Thu, 13 Oct 2011 08:20:20 +0800 (CST) Subject: [Pw_forum] Problem - In-Reply-To: <1318431896.1949.87.camel@fe12lx.fisica.uniud.it> References: <1318431896.1949.87.camel@fe12lx.fisica.uniud.it> <1675BB3F3586E9459BBC8B9812C3532020C7997ACA@EXPO20.exchange.mit.edu> Message-ID: <1882bd3.53910.132faa6afc8.Coremail.ptao10b@imr.ac.cn> Does that mean we can ignore it and continue our calculation? > Re: [Pw_forum] Problem - > > On Wed, 2011-10-12 at 10:51 -0400, Zhiting Tian wrote: > > > I have met this problem before.Try to change "tetrahedra? > > to see whether it helps. > > it is not necessarily a problem, and it is unrelated to the > usage of tetrahedra. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From germaneau at gucas.ac.cn Thu Oct 13 18:05:02 2011 From: germaneau at gucas.ac.cn (=?UTF-8?B?w4lyaWMgR2VybWFuZWF1?=) Date: Thu, 13 Oct 2011 12:05:02 -0400 Subject: [Pw_forum] iotk error In-Reply-To: <518434037.23363@test1.gucas.ac.cn> References: <4E95B5B0.3000700@gucas.ac.cn> <518434037.23363@test1.gucas.ac.cn> Message-ID: <4E970C2E.8070308@gucas.ac.cn> Dear Professor Paulatto, Thank you for your reply but this is to the case. When I execute the pp.x (or band calculation) with *ifort* *10.1* _on several nodes_ it says /pp.x: error while loading shared libraries: libmpi.so.3.2: cannot open shared object file: No such file or directory/ whereas /ldd pp.x/ gives /libmpi.so.3.2 => /opt/intel/impi/3.1/lib64/libmpi.so.3.2 (0x00002ba86f2c6000)/ But when I run it on the head node only I get /from postproc : error # 1 reading inputpp namelist/ and /from read_rho_xml : error # 1 cannot open ./SCF/vc-relax_tetragonal.save/charge-density.dat file for reading/ For some reasons the contents of SCF directory is not accessible, I do a chmod -R ugo+xwr ./SCF. This is differently with this machine since it works well on my desktop (with gfortran 4.4.4). I'll figure out. Thank you, ?ric. On 10/12/2011 12:05 PM, Lorenzo Paulatto wrote: > On Wed, 12 Oct 2011 17:43:44 +0200, ?ric Germaneau > wrote: >> I recently got the error bellow when running band calculation >> (calculation = 'band' and pw.x) : >> >> /# FROM IOTK LIBRARY, VERSION 1.2.0 > This error can also be caused by a band calculation when > restart_mode='restart'; see the bug tracker for details > (http://qe-forge.org/tracker/?atid=133&group_id=10&func=browse). > > If this is your case, the simpler solution is to remove restart_mode from > the band calculation input > > bests > > -- /Be the change you wish to see in the world / ? Mahatma Gandhi ? Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111013/f115f310/attachment.htm From rcdong at gmail.com Thu Oct 13 06:55:13 2011 From: rcdong at gmail.com (Richard Dong) Date: Wed, 12 Oct 2011 21:55:13 -0700 Subject: [Pw_forum] Questions about band calculation Message-ID: Dear QE users, I am a PhD student who is new to QE. I got some questions when I did some simple test calculations on material OsO2. First, my input file for "scf" calculation is: &CONTROL calculation='scf' restart_mode='from_scratch', pseudo_dir='/espresso-4.3.2/pseudo/', outdir='./', prefix='OsO2' / &SYSTEM ibrav=6, celldm(1)=8.52551, celldm(3)=0.70731, nat=6, ntyp=2, nbnd=26, ecutwfc=30.0,ecutrho=300 occupations='smearing',smearing='marzari-vanderbilt', degauss=0.05 / &ELECTRONS diagonalization='david' mixing_beta=0.5, / ATOMIC_SPECIES Os 190.23 Os.pw91-n-van.UPF O 15.9994 O.pw91-van_ak.UPF ATOMIC_POSITIONS crystal Os 0.0 0.0 0.0 Os 0.5 0.5 0.5 O 0.3 0.3 0.0 O -0.3 -0.3 0.0 O 0.8 0.2 0.5 O -0.8 -0.2 -0.5 K_POINTS automatic 6 6 8 0 0 0 Then I did the "bands" calculation which just replaced the calculation="bands" and set the K_POINTS path. Finally I runned bands.x and plotbands.x to get the band structures. I actually got two strange flat bands in Os 5d bands (plot is attached below). Does anyone know the reason that can cause this kind of flat bands? Another question is about the spin-orbital coupling. If I further add spin-orbital coupling to my calculation, I am wondering if I have to use the full-relativistic pseudopoentials? If this is the case, is there any tested version I can get or I have to generate by myself, since there is no full-relativistic PPs on the QE website. Thank you very much in advance. Best regards, Ruanchen Dong -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111012/3e89c016/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: OsO2.pdf Type: application/pdf Size: 19109 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111012/3e89c016/attachment-0001.pdf From psavita at crlindia.com Thu Oct 13 07:27:35 2011 From: psavita at crlindia.com (psavita) Date: Thu, 13 Oct 2011 10:57:35 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 52, Issue 28 In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111013/66ab7c6d/attachment.htm From joshiniharika20 at yahoo.in Thu Oct 13 09:19:56 2011 From: joshiniharika20 at yahoo.in (Niharika Joshi) Date: Thu, 13 Oct 2011 12:49:56 +0530 (IST) Subject: [Pw_forum] problem in xspectra calculations Message-ID: <1318490396.27680.YahooMailClassic@web95709.mail.in.yahoo.com> Thank you Matteo sir for your reply. Replacing the 'if' statement didn't work. I'm using a 64-bit machine with composerxe-2011.4.191 compiler. And yes, I'm using pseudo of the example for carbon. -Niharika Joshi (project student,IISER Pune) --- On Tue, 11/10/11, Matteo Calandra wrote: From: Matteo Calandra Subject: [Pw_forum] problem in xspectra calculations To: pw_forum at pwscf.org Date: Tuesday, 11 October, 2011, 12:25 PM > Message: 4 > Date: Tue, 11 Oct 2011 15:01:33 +0530 (IST) > From: Niharika Joshi > Subject: Re: [Pw_forum] problem in xspectra calculations > To: PWSCF Forum > Message-ID: > ??? <1318325493.18035.YahooMailClassic at web95715.mail.in.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Paolo Sir, > Thank you for your reply. > I tried running the xanes calculation after making the change in xspectra.f90. But it is still giving me the same message 'Could not find the element? C in the table of K edge energies!' at the end and leaving the output file incomplete. > For some reason, the condition for 'if-loop' in mygetK.f90 is not getting satisfied and thus it is not getting executed. I wrote the variables sym and seuilK_tab(6) . For both variables it writes 'C' but does not enter the if-loop. > -Niharika Joshi > (project student, IISER Pune) Dear Niharita, ???which compiler/Machine are you using ? It seems it treats in a strange way string variables. Moreover, are you using the pseudo of the example for Carbon or another one ? You can try the following two options: 1) in ligne 66 in mygetK.f90 change line if(sym.eq.seuilK_tab(i)%name) then in if(sym.eq.trim(adjustl(seuilK_tab(i)%name))) then 2) if it doesn't work, then replace in xspectra.f90 all the lines with (two lines) of e_1s=mygetK(upf(xiabs)%psd) with the actual value of the Carbon K-edge energy, namely with e_1s=284.2 All the best, M. -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Mineralogie et de Physique des Milieux Condenses de Paris Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16? ? ???Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra _______________________________________________ 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/20111013/93882d13/attachment.htm From mourad_fsm at yahoo.fr Thu Oct 13 12:50:54 2011 From: mourad_fsm at yahoo.fr (debbichi mourad) Date: Thu, 13 Oct 2011 11:50:54 +0100 (BST) Subject: [Pw_forum] error band structure of ZnO In-Reply-To: <1318495761.665.YahooMailNeo@web29503.mail.ird.yahoo.com> References: <1318495761.665.YahooMailNeo@web29503.mail.ird.yahoo.com> Message-ID: <1318503054.33306.YahooMailNeo@web29513.mail.ird.yahoo.com> Dear QE users, I am a new user of QE.? when I went to test the band structure calculation on material ZnO (ibrav=4) with this input file ,I got error band structue (flatt band dispersion). ?calculation='bands' ??? pseudo_dir = '$PSEUDO_DIR/', ??? outdir='$TMP_DIR/', ??? prefix='ZnO' ?/ ?&system ? ibrav = 4, nbnd =18, ?????????????????? celldm(1) = 6.213, ?????????????????? celldm(3) = 1.610, ???????????????????????? nat = 4, ??????????????????????? ntyp = 2, ???????????????????? ecutwfc = 40, ???????????????????? ecutrho = 240 , ??? occupations ='smearing', smearing ='methfessel-paxton', degauss = 0.05, ?/ ?&electrons ???????????????? mixing_mode = 'plain' , ???????????????? mixing_beta = 0.7 , ???????????? diagonalization = 'david' , ??????????? conv_thr = 1.0d-8, ?/ ATOMIC_SPECIES ?Zn?? 65.39200? Zn.pbe-van.UPF ? O?? 16.00000? O.pbe-rrkjus.UPF ATOMIC_POSITIONS ?? Zn????? 0.666666667??? 0.333333333??? 0.000000000 ?? Zn????? 0.333333333??? 0.666666667??? 0.500000000 ??? O????? 0.666666667??? 0.333333333??? 0.380000000 ?? O????? 0.333333333??? 0.666666667??? 0.880000000 K_POINTS 9 ?? 0.0000000000???? 0.0000000000???? 0.0000000000??? 1 ?? 0.5000000000???? 0.0000000000???? 0.5000000000??? 2 ?? 0.5000000000???? 0.0000000000???? 0.0000000000??? 3 ?? 0.3333333333???? 0.3333333333???? 0.5000000000??? 4 ?? 0.0000000000???? 0.0000000000???? 0.5000000000??? 5 ?? 0.0000000000???? 0.0000000000???? 0.0000000000??? 6 ?? 0.0000000000???? 0.5000000000???? 0.5000000000??? 7 ? 0.3333333333??? 0.3333333333???? 0.0000000000???? 8 ?? 0.3333333333???? 0.6666666667??? 0.5000000000??? 9 thanks for help ?? DEBBICHI Mourad Unit? de Recherche Physique des Solides,99/UR/13-19, D?partement de Physique, Facult? des Science de Monastir, Avenue de l'Environnement 5019, Monastir Tunisie. t?l:+21697487042 mourad_fsm at yahoo.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111013/940fb15a/attachment.htm From 1009ukumar at gmail.com Thu Oct 13 13:46:37 2011 From: 1009ukumar at gmail.com (Sonu Kumar) Date: Thu, 13 Oct 2011 17:16:37 +0530 Subject: [Pw_forum] GPU enabled QE for 64 bit architecture ? Message-ID: Is GPU enabled QE for 64 bit arch. available? If yes, can anyone tell me the link to it. Is it possible to download without using svn command. Unfortunately, i am not able to update my OS, so unable to install "svn" command. Also, where is the link to QE-GPU forum? QE main site seems not to have this information? Thanks in advance Regards Sonu Phd student, IITD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111013/d2cbdf8a/attachment.htm From gkucukdalyan at gmail.com Thu Oct 13 17:01:16 2011 From: gkucukdalyan at gmail.com (Gulcin Kucukdalyan) Date: Thu, 13 Oct 2011 11:01:16 -0400 Subject: [Pw_forum] Graphene input file Message-ID: Hi All, I am pretty new to Quantum Espresso, and would like to know how can i create an input file for graphene to calculate its Density of State and band structures from the scratch? Thanks, Rosegarden -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111013/c8dbbabd/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Thu Oct 13 17:13:02 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 13 Oct 2011 17:13:02 +0200 Subject: [Pw_forum] Graphene input file In-Reply-To: References: Message-ID: Dear Gulcin, there are many pages of manuals, examples and tutorials devoted to Quantum-ESPRESSO calculations, please take some time to browse the official web site and the documentation included with the packages and have a look at the examples. If there is anyone experienced in QE in your laboratory and/or institution I would suggest you contact him/her for help. best regards On Thu, 13 Oct 2011 17:01:16 +0200, Gulcin Kucukdalyan wrote: > Hi All, > > I am pretty new to Quantum Espresso, and would like to know how can i > create > an input file for graphene to calculate its Density of State and band > structures from the scratch? > > Thanks, > > Rosegarden -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From mashiatalaaii at gmail.com Thu Oct 13 18:57:48 2011 From: mashiatalaaii at gmail.com (mashiat alaaii) Date: Thu, 13 Oct 2011 12:57:48 -0400 Subject: [Pw_forum] input and output of average.x Message-ID: Dear Gabriele, Thank you very much for your help and answer. Please let me ask you the last question in this regard. This is the input that I use for getting psi^2 on parallel planes: &INPUTPP prefix = A' , outdir = '' , filplot = 'Apsi' , plot_num = 7, kpoint=1, kband=200, / &PLOT nfile = 1 , filepp(1) = 'A', weight(1) = 1.0, fileout = 'Apsi.dat' iflag = 2 , output_format = 2 , e1(1) = 1, e1(2) = 0, e1(3) = 0, e2(1) = 0, e2(2) = 1, e2(3) = 0, x0(1) = 1, x0(2) = 1, x0(3) = 1, nx = 100 , ny = 100 , / I thought by changing the x0(3) from zero to highest value of structure in z direction, I could get psi^2 on parallel planes. I use the following input for average.x: 1 Apsi 1 1000 3 3 however when I change x0(3), the output of average remains the same. Does it make sense? If positive, how could I get psi^2 on planes? Thank you very much for your help; I really really appreciate it. M Alaaii -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111013/6b118eb4/attachment.htm From germaneau at gucas.ac.cn Fri Oct 14 12:26:22 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Fri, 14 Oct 2011 06:26:22 -0400 Subject: [Pw_forum] GPU enabled QE for 64 bit architecture ? In-Reply-To: <518504852.09284@gscas.net.cn> References: <518504852.09284@gscas.net.cn> Message-ID: <4E980E4E.1000007@gucas.ac.cn> On 10/13/2011 07:46 AM, Sonu Kumar wrote: > Is GPU enabled QE for 64 bit arch. available? yes it is. > > If yes, can anyone tell me the link to it. Is it possible to download > without > using svn command. Unfortunately, i am not able to update my OS, so > unable to > install "svn" command. I don't know, I just used this commend : svn checkout svn://scm.qe-forge.org/scmrepos/svn/q-e/branches/espresso-PRACE > > Also, where is the link to QE-GPU forum? QE main site seems not to > have this information? http://qe-forge.org/mail/?group_id=10 and http://qeforge.qe-forge.org/mailman/listinfo/q-e-gpgpu > Thanks in advance welcome. ?ric. > > Regards > Sonu > Phd student, IITD > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111014/7b1bec13/attachment-0001.htm From m.abbasnejad at gmail.com Fri Oct 14 04:30:54 2011 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Fri, 14 Oct 2011 11:30:54 +0900 Subject: [Pw_forum] dist.x utility Message-ID: Dear users, Hi, I am trying to use ?dist.x? utility. I have provided the input file according to the header of pwtools/dist.f. However, when I run the utility it gives me such an error: ?forrtl: severe (59): list-directed I/O syntax error, unit 1, file /home/mohaddeseh/test Image PC Routine Line Source dist.x 00000000005014C6 Unknown Unknown Unknown dist.x 0000000000500458 Unknown Unknown Unknown dist.x 00000000004C8C4E Unknown Unknown Unknown dist.x 000000000048D769 Unknown Unknown Unknown dist.x 000000000048D056 Unknown Unknown Unknown dist.x 00000000004AC647 Unknown Unknown Unknown dist.x 0000000000403F02 MAIN__ 50 dist.f dist.x 0000000000403D96 Unknown Unknown Unknown libc.so.6 00000038A621E576 Unknown Unknown Unknown dist.x 0000000000403CA9 Unknown Unknown Unknown ? which I think it might be related to the input file. The provided input file is: nat=2, ibrav=0, celldm(1) =10.26 CELL_PARAMETERS (alat) -0.500000000 0.000000000 0.500000000 0.000000000 0.500000000 0.500000000 -0.500000000 0.500000000 0.000000000 ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 I will be thankful if any one helps me. Thanks in advance. Yours truly, Mohaddeseh Abbasnejad, --------------------------------------------------------- Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +98 917 731 7514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111014/7b11673b/attachment.htm From gabriele.sclauzero at epfl.ch Fri Oct 14 10:09:42 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Fri, 14 Oct 2011 10:09:42 +0200 Subject: [Pw_forum] input and output of average.x In-Reply-To: References: Message-ID: <38772E6E-F7DD-40AE-ACF9-85B86676E56F@epfl.ch> Dear M Alaii, Il giorno 13/ott/2011, alle ore 18.57, mashiat alaaii ha scritto: > Dear Gabriele, > Thank you very much for your help and answer. > Please let me ask you the last question in this regard. OK, I'll give you my last reply. > This is the input that I use for getting psi^2 on parallel planes: > &INPUTPP > prefix = A' , > outdir = '' , > filplot = 'Apsi' , > plot_num = 7, > kpoint=1, > kband=200, > / > &PLOT > nfile = 1 , > filepp(1) = 'A', > weight(1) = 1.0, > fileout = 'Apsi.dat' > iflag = 2 , > output_format = 2 , > e1(1) = 1, > e1(2) = 0, > e1(3) = 0, > e2(1) = 0, > e2(2) = 1, > e2(3) = 0, > x0(1) = 1, > x0(2) = 1, > x0(3) = 1, > nx = 100 , > ny = 100 , > / > > I thought by changing the x0(3) from zero to highest value of structure in z direction, I could get psi^2 on parallel planes. This input file has some mistakes in the file names. Notably, filplot should be equal to filepp(1). > I use the following input for average.x: I don't understand why you should use both the &plot namelist and the average program. First you should understand WHAT you really want (and I'm a bit surprised that you haven't yet): 2D plots on a plane (using pp.x including &plot in the input) OR averages over those planes? In both cases you start from the 3D quantity, given by pp.x using the &inputpp namelist. Please read CAREFULLY Doc/INPUT_PP.txt. > 1 > Apsi > 1 > 1000 > 3 > 3 > > however when I change x0(3), the output of average remains the same. Does it make sense? It's not clear what you are looking at! Of course, if you run pp.x changing x0, but then you look at the output of average.x (which reads filplot only, a file that does not change by modifying &plot), you will get always the same result. > If positive, how could I get psi^2 on planes? Specify appropriate values of x0 and e2. You should be able to find out by yourself which ones. You don't need to use average.x unless you want the averages over those planes. GS > Thank you very much for your help; I really really appreciate it. > > M Alaaii > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111014/22b7989b/attachment.htm From giannozz at democritos.it Fri Oct 14 14:05:36 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 14 Oct 2011 14:05:36 +0200 Subject: [Pw_forum] dist.x utility In-Reply-To: References: Message-ID: <1318593936.7854.10.camel@fe12lx.fisica.uniud.it> On Fri, 2011-10-14 at 11:30 +0900, mohaddeseh abbasnejad wrote: > The provided input file is wrong: ! first line contains nat, ibrav, celldm(1-6) > nat=2, ibrav=0, celldm(1) =10.26 read(1,*) nat, ibrav, celldm so you need 2 0 10.26 0.0 0.0 0.0 0.0 0. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri Oct 14 14:21:03 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 14 Oct 2011 14:21:03 +0200 Subject: [Pw_forum] iotk error In-Reply-To: <4E970C2E.8070308@gucas.ac.cn> References: <4E95B5B0.3000700@gucas.ac.cn> <518434037.23363@test1.gucas.ac.cn> <4E970C2E.8070308@gucas.ac.cn> Message-ID: <1318594863.7854.19.camel@fe12lx.fisica.uniud.it> On Thu, 2011-10-13 at 12:05 -0400, ?ric Germaneau wrote: > When I execute the pp.x (or band calculation) with ifort 10.1 on > several nodes it says > pp.x: error while loading shared libraries: libmpi.so.3.2: > cannot open shared object file: No such file or directory http://www.quantum-espresso.org/user_guide/node52.html#SECTION000121010000000000000 > But when I run it on the head node only I get > from postproc : error # 1 > reading inputpp namelist either there is an error in namelist inputpp, or the code doesn't read it, for reasons explained in in the above link at point 11.1.0.3, or here: http://www.quantum-espresso.org/user_guide/node19.html > from read_rho_xml : error # 1 > cannot > open ./SCF/vc-relax_tetragonal.save/charge-density.dat file > for reading the file it is not there P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri Oct 14 14:24:12 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 14 Oct 2011 14:24:12 +0200 Subject: [Pw_forum] problem in xspectra calculations In-Reply-To: <1318490396.27680.YahooMailClassic@web95709.mail.in.yahoo.com> References: <1318490396.27680.YahooMailClassic@web95709.mail.in.yahoo.com> Message-ID: <1318595052.7854.23.camel@fe12lx.fisica.uniud.it> On Thu, 2011-10-13 at 12:49 +0530, Niharika Joshi wrote: > Replacing the 'if' statement didn't work. are sure? really? -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri Oct 14 14:43:55 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 14 Oct 2011 14:43:55 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 52, Issue 28 In-Reply-To: References: Message-ID: <1318596235.7854.35.camel@fe12lx.fisica.uniud.it> On Thu, 2011-10-13 at 10:57 +0530, psavita wrote: > Hello Paulo, "Paolo" > In fact I have been using USPP hence ecutrho = 6*ecutwfc. the implementation of elf with USPP is incomplete (and it has always been) > The thing is, the same choice is used while running pp.x > in the older version (4.2) and there is no error. new versions contain new bugs as well. The elf code is prime target for new bugs, since nobody seems to know and to care about it P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From songsongfc at yahoo.com.cn Fri Oct 14 15:03:48 2011 From: songsongfc at yahoo.com.cn (=?utf-8?B?5LmL546LIOaUueeOiw==?=) Date: Fri, 14 Oct 2011 21:03:48 +0800 (CST) Subject: [Pw_forum] Zn NC_PP from qe-forge Message-ID: <1318597428.4394.YahooMailClassic@web15804.mail.cnb.yahoo.com> Hi, ? Recently,I generate Zn NC-PP using the PP library from qe-forge project. I want to generate Zn.pz-nc.UPF using ld1.x. My Zn.-nc.in is followed: ?&input ?? title='Zn', ?? zed=30., ?? rel=0, ?? config='[Ar] 4s2.0 4p0.0 3d10.0', ?? iswitch=3, ?? dft='PZ' ?/ ?&inputp ?? pseudotype=2, ?? file_pseudopw='Zn.pz-nc.UPF', ?? author='TM', ?? lloc=0, ?? nlcc=.true., ?? tm=.true. ?/ 3 4P? 2? 1? 0.00? 0.00? 2.30? 2.30? 0.0 3D? 3? 2 10.00? 0.00? 2.30? 2.30? 0.0 4S? 1? 0? 2.00? 0.00? 2.30? 2.30? 0.0 And I calculate ZnO vc-relax using Zn.pz-nc.UPF and O.pz-mt.UPF, the theory is a=6.223 c/a=1.614, after calculating vc-relax is a=6.191 c/a=1.614 with ecutwfc=62Ry. However, No matter how I try to calculate,the phonon frequency is negative The scf and ph file is followed: &CONTROL ???????????????? calculation = 'scf' , ??????????????? restart_mode = 'from_scratch' , ????????????????????? outdir = '/root/ZnO/915-phonon' , ????????????????? pseudo_dir = '/root/pseudopotential' , ????????????????????? prefix = 'ZnO' , ?????????????? etot_conv_thr = 1.0D-5 , ?????????????? forc_conv_thr = 1.0D-4 , ???????????????????? tstress = .true. , ???????????????????? tprnfor = .true. , ?/ ?&SYSTEM ?????????????????????? ibrav = 4, ?????????????????? celldm(1) = 6.191, ?????????????????? celldm(3) = 1.614, ???????????????????????? nat = 4, ??????????????????????? ntyp = 2, ???????????????????? ecutwfc = 62 , ?/ ?&ELECTRONS ??????????????????? conv_thr = 1.0d-10 , ???????????????? mixing_mode = 'plain' , ???????????????? mixing_beta = 0.6 , ???????????? diagonalization = 'david' , ?/ ATOMIC_SPECIES ?? Zn?? 65.40900? Zn.pz-nc.UPF ??? O?? 15.99940? O.pz-mt.UPF ATOMIC_POSITIONS crystal Zn?????? 0.333333333?? 0.666666667? -0.000036499?? 1 1 1 Zn?????? 0.666666667?? 0.333333333?? 0.499963501?? 1 1 1 O??????? 0.333333333?? 0.666666667?? 0.379036499?? 1 1 1 O??????? 0.666666667?? 0.333333333?? 0.879036499?? 1 1 1 K_POINTS automatic ? 4 4 4?? 1 1 1 phonons of ZnO??????????????????????????????????????? ?&INPUTPH ????????????????????? outdir = '/root/ZnO/915-phonon' , ????????????????????? prefix = 'ZnO' , ????????????????????? fildyn = 'ZnO_IR.dyn' , ??????????????????? fildvscf = 'ZnO.dv' , ?????????????????????? ldisp = .true., ???????????????????????? nq1 = 4 , ???????????????????????? nq2 = 4 , ???????????????????????? nq3 = 4 , ?????????????????????? epsil = .false., ??????????????????????? elph = .false., ??????????????????????? fpol = .false. , ???????????????????? recover = .false. , ??????????????????? amass(1) = 65.4090, ??????????????????? amass(2) = 15.9994, ????????????????????? tr2_ph = 1.0d-12 , ?/ Best Regards Yun Song,Kang Department Physical Science and Technology of Inner Mongolia University. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111014/447d8632/attachment-0001.htm From giuseppe.mattioli at mlib.ism.cnr.it Fri Oct 14 15:12:51 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 14 Oct 2011 15:12:51 +0200 Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <1318597428.4394.YahooMailClassic@web15804.mail.cnb.yahoo.com> References: <1318597428.4394.YahooMailClassic@web15804.mail.cnb.yahoo.com> Message-ID: <201110141512.52211.giuseppe.mattioli@mlib.ism.cnr.it> Dear Yun Song A 62Ry cutoff could be quite poor both in the case of your NC Zn (it contains a quite deep 3d shell) and for your NC O. You should reach concergence with respect to the wf cutoff before attempting to perform phonon calculations. HTH Giuseppe On Friday 14 October 2011 15:03:48 ?? ?? wrote: > Hi, > ? Recently,I generate Zn NC-PP using the PP library from qe-forge project. > I want to generate Zn.pz-nc.UPF using ld1.x. > My Zn.-nc.in is followed: > ?&input > ?? title='Zn', > ?? zed=30., > ?? rel=0, > ?? config='[Ar] 4s2.0 4p0.0 3d10.0', > ?? iswitch=3, > ?? dft='PZ' > ?/ > ?&inputp > ?? pseudotype=2, > ?? file_pseudopw='Zn.pz-nc.UPF', > ?? author='TM', > ?? lloc=0, > ?? nlcc=.true., > ?? tm=.true. > ?/ > 3 > 4P? 2? 1? 0.00? 0.00? 2.30? 2.30? 0.0 > 3D? 3? 2 10.00? 0.00? 2.30? 2.30? 0.0 > 4S? 1? 0? 2.00? 0.00? 2.30? 2.30? 0.0 > > > And I calculate ZnO vc-relax using Zn.pz-nc.UPF and O.pz-mt.UPF, > the theory is a=6.223 c/a=1.614, after calculating vc-relax is a=6.191 > c/a=1.614 with ecutwfc=62Ry. > > However, No matter how I try to calculate,the phonon frequency is negative > > The scf and ph file is followed: > &CONTROL > ???????????????? calculation = 'scf' , > ??????????????? restart_mode = 'from_scratch' , > ????????????????????? outdir = '/root/ZnO/915-phonon' , > ????????????????? pseudo_dir = '/root/pseudopotential' , > ????????????????????? prefix = 'ZnO' , > ?????????????? etot_conv_thr = 1.0D-5 , > ?????????????? forc_conv_thr = 1.0D-4 , > ???????????????????? tstress = .true. , > ???????????????????? tprnfor = .true. , > ?/ > ?&SYSTEM > ?????????????????????? ibrav = 4, > ?????????????????? celldm(1) = 6.191, > ?????????????????? celldm(3) = 1.614, > ???????????????????????? nat = 4, > ??????????????????????? ntyp = 2, > ???????????????????? ecutwfc = 62 , > ?/ > ?&ELECTRONS > ??????????????????? conv_thr = 1.0d-10 , > ???????????????? mixing_mode = 'plain' , > ???????????????? mixing_beta = 0.6 , > ???????????? diagonalization = 'david' , > ?/ > ATOMIC_SPECIES > ?? Zn?? 65.40900? Zn.pz-nc.UPF > ??? O?? 15.99940? O.pz-mt.UPF > ATOMIC_POSITIONS crystal > Zn?????? 0.333333333?? 0.666666667? -0.000036499?? 1 1 1 > Zn?????? 0.666666667?? 0.333333333?? 0.499963501?? 1 1 1 > O??????? 0.333333333?? 0.666666667?? 0.379036499?? 1 1 1 > O??????? 0.666666667?? 0.333333333?? 0.879036499?? 1 1 1 > K_POINTS automatic > ? 4 4 4?? 1 1 1 > > > > phonons of ZnO??????????????????????????????????????? > ?&INPUTPH > ????????????????????? outdir = '/root/ZnO/915-phonon' , > ????????????????????? prefix = 'ZnO' , > ????????????????????? fildyn = 'ZnO_IR.dyn' , > ??????????????????? fildvscf = 'ZnO.dv' , > ?????????????????????? ldisp = .true., > ???????????????????????? nq1 = 4 , > ???????????????????????? nq2 = 4 , > ???????????????????????? nq3 = 4 , > ?????????????????????? epsil = .false., > ??????????????????????? elph = .false., > ??????????????????????? fpol = .false. , > ???????????????????? recover = .false. , > ??????????????????? amass(1) = 65.4090, > ??????????????????? amass(2) = 15.9994, > ????????????????????? tr2_ph = 1.0d-12 , > ?/ > > Best > Regards > Yun Song,Kang > > Department Physical Science and Technology of Inner Mongolia University. -- ******************************************************** - 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 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From jen7182 at hotmail.com Fri Oct 14 15:22:46 2011 From: jen7182 at hotmail.com (Jennifer Wohlwend) Date: Fri, 14 Oct 2011 09:22:46 -0400 Subject: [Pw_forum] Cholesky error for SCF calculations after successful relax Message-ID: I'm trying to ultimately perform el-ph calculations for slabs of Pb but am getting stuck at the scf steps. I've already relaxed the structures and are therefore using inputs that should be ok (I've also checked them in xcrysden and they look fine) so I don't think that is the issue (which was the main 'problem' discussed when I searched the forums for the Cholesky error). For the scf calculation with la2F=.true. case I'm getting the error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cdiaghg : error # 268 problems computing cholesky %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% for the scf calculation without la2F=.true. I'm getting the error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from c_bands : error # 1 too many bands are not converged %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% My input file is: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = './' , wfcdir = './' , pseudo_dir = '/lustre/app2/espresso/pseudo/' , prefix = '3slab' , etot_conv_thr = 1.0d-12 , forc_conv_thr = 1.0d-8 , / &SYSTEM ibrav = 14, celldm(1) = 13.04099905, celldm(2) = 1, celldm(3) = 4, celldm(4) = 0, celldm(5) = 0, celldm(6) = -0.5, nat = 12, ntyp = 1, ecutwfc = 55 , ecutrho = 500 , occupations = 'smearing' , degauss = 0.01 , smearing = 'methfessel-paxton' , / &ELECTRONS electron_maxstep = 200, conv_thr = 1.0d-12 , mixing_mode = 'local-TF' , mixing_beta = 0.1 , / ATOMIC_SPECIES Pb 207.20000 Pb.pz-d-van.UPF ATOMIC_POSITIONS alat Pb 0.249963773 0.384871758 0.100000000 0 0 0 Pb 0.750036227 0.384871758 0.100000000 0 0 0 Pb 0.000000000 0.817997392 0.100000000 0 0 0 Pb 0.500072453 0.817997392 0.100000000 0 0 0 Pb 0.000004073 0.240561951 0.496233365 Pb 0.500008600 0.240558309 0.496196360 Pb -0.249977229 0.673545116 0.496173310 Pb 0.250037029 0.673564417 0.496147732 Pb 0.250057067 0.096171478 0.891945156 Pb 0.749980943 0.096139649 0.891930149 Pb 0.000045336 0.529277251 0.891922541 Pb 0.499987964 0.529243108 0.891928512 K_POINTS automatic 8 8 2 0 0 0 the la2F=.true. case is the same except it has la2F=.true. and the K_POINTS are 24 24 8. Thank you in advance for any advice! Jennifer Wohlwend Universal Technology Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111014/9765032a/attachment.htm From pandey.bramha at gmail.com Fri Oct 14 15:50:10 2011 From: pandey.bramha at gmail.com (bramha pandey) Date: Fri, 14 Oct 2011 19:20:10 +0530 Subject: [Pw_forum] input and output of average.x In-Reply-To: <38772E6E-F7DD-40AE-ACF9-85B86676E56F@epfl.ch> References: <38772E6E-F7DD-40AE-ACF9-85B86676E56F@epfl.ch> Message-ID: On 10/14/11, Gabriele Sclauzero wrote: > Dear M Alaii, > > > Il giorno 13/ott/2011, alle ore 18.57, mashiat alaaii ha scritto: >> Dear Gabriele, >> Thank you very much for your help and answer. >> Please let me ask you the last question in this regard. > > OK, I'll give you my last reply. > >> This is the input that I use for getting psi^2 on parallel planes: >> &INPUTPP >> prefix = A' , >> outdir = '' , >> filplot = 'Apsi' , >> plot_num = 7, >> kpoint=1, >> kband=200, >> / >> &PLOT >> nfile = 1 , >> filepp(1) = 'A', >> weight(1) = 1.0, >> fileout = 'Apsi.dat' >> iflag = 2 , >> output_format = 2 , >> e1(1) = 1, >> e1(2) = 0, >> e1(3) = 0, >> e2(1) = 0, >> e2(2) = 1, >> e2(3) = 0, >> x0(1) = 1, >> x0(2) = 1, >> x0(3) = 1, >> nx = 100 , >> ny = 100 , >> / >> >> I thought by changing the x0(3) from zero to highest value of structure in >> z direction, I could get psi^2 on parallel planes. > > This input file has some mistakes in the file names. Notably, filplot should > be equal to filepp(1). > >> I use the following input for average.x: > > I don't understand why you should use both the &plot namelist and the > average program. First you should understand WHAT you really want (and I'm a > bit surprised that you haven't yet): 2D plots on a plane (using pp.x > including &plot in the input) OR averages over those planes? In both cases > you start from the 3D quantity, given by pp.x using the &inputpp namelist. > Please read CAREFULLY Doc/INPUT_PP.txt. > >> 1 >> Apsi >> 1 >> 1000 >> 3 >> 3 >> >> however when I change x0(3), the output of average remains the same. Does >> it make sense? > > It's not clear what you are looking at! Of course, if you run pp.x changing > x0, but then you look at the output of average.x (which reads filplot only, > a file that does not change by modifying &plot), you will get always the > same result. > >> If positive, how could I get psi^2 on planes? > > Specify appropriate values of x0 and e2. You should be able to find out by > yourself which ones. You don't need to use average.x unless you want the > averages over those planes. > > > GS > >> Thank you very much for your help; I really really appreciate it. >> >> M Alaaii >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > > -- Thanks and Regards Bramha Prasad Pandey Assistant Professor (Electronics and Communication Engg) GLA Group of Institutions, Mathura. Ph. No. 08954143009 email id pandey.bramha at gmail.com bpglaitm at yahoo.co.in From joshiniharika20 at yahoo.in Fri Oct 14 16:40:10 2011 From: joshiniharika20 at yahoo.in (Niharika Joshi) Date: Fri, 14 Oct 2011 20:10:10 +0530 (IST) Subject: [Pw_forum] problem in xspectra calculations Message-ID: <1318603210.12662.YahooMailClassic@web95712.mail.in.yahoo.com> Hello, Yes, replacing 'if (sym.eq.seuilK_tab(i)%name) then' by 'if(sym.eq.trim(adjustl(seuilK_tab(i)%name)))' in the mygetK.f90 didn't work. It still writes in the 'Could not find the element? C in the table of K edge energies!' at the end of the output file. -Niharika Joshi (project student, IISER Pune) --- On Fri, 14/10/11, Paolo Giannozzi wrote: From: Paolo Giannozzi Subject: Re: [Pw_forum] problem in xspectra calculations To: "PWSCF Forum" Date: Friday, 14 October, 2011, 12:24 PM On Thu, 2011-10-13 at 12:49 +0530, Niharika Joshi wrote: > Replacing the 'if' statement didn't work. are sure? really? -- Paolo Giannozzi, IOM-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/20111014/a77cc023/attachment-0001.htm From giannozz at democritos.it Fri Oct 14 16:56:23 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 14 Oct 2011 16:56:23 +0200 Subject: [Pw_forum] problem in xspectra calculations In-Reply-To: <1318603210.12662.YahooMailClassic@web95712.mail.in.yahoo.com> References: <1318603210.12662.YahooMailClassic@web95712.mail.in.yahoo.com> Message-ID: On Oct 14, 2011, at 16:40 , Niharika Joshi wrote: > Yes, replacing 'if (sym.eq.seuilK_tab(i)%name) then' > by 'if(sym.eq.trim(adjustl(seuilK_tab(i)%name)))' in > the mygetK.f90 didn't work. > It still writes in the 'Could not find the element C > in the table of K edge energies!' at the end of the output file. where does it write, and why? have you located in the code where the error message is issued? have you tried printing the variables whose value is not what is expected? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From Ari.P.Seitsonen at iki.fi Fri Oct 14 16:46:24 2011 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Fri, 14 Oct 2011 16:46:24 +0200 (CEST) Subject: [Pw_forum] problem in xspectra calculations In-Reply-To: <1318603210.12662.YahooMailClassic@web95712.mail.in.yahoo.com> References: <1318603210.12662.YahooMailClassic@web95712.mail.in.yahoo.com> Message-ID: Dear Niharika Joshi, May I suggest that you'll print both values with something like WRITE ( 0, '( "DEBUG>>", A, "<<" ) sym WRITE ( 0, '( "DEBUG>>", A, "<<" ) trim(adjustl(seuilK_tab(i)%name)) and compare those two lines? Maybe you want to use another channel than 0. Sorry for the simple suggestion, but maybe this will lead to the solution of your problem (and you'll learn how to debug such things :). Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Physikalisch-Chemisches Institut der Universitaet Zuerich Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 On Fri, 14 Oct 2011, Niharika Joshi wrote: > Hello, > Yes, replacing 'if (sym.eq.seuilK_tab(i)%name) then' by > 'if(sym.eq.trim(adjustl(seuilK_tab(i)%name)))' in the mygetK.f90 didn't > work. It still writes in the 'Could not find the element? C in the table of > K edge energies!' at the end of the output file. > -Niharika Joshi > (project student, IISER Pune) > > --- On Fri, 14/10/11, Paolo Giannozzi wrote: > > From: Paolo Giannozzi > Subject: Re: [Pw_forum] problem in xspectra calculations > To: "PWSCF Forum" > Date: Friday, 14 October, 2011, 12:24 PM > > On Thu, 2011-10-13 at 12:49 +0530, Niharika Joshi wrote: > > > Replacing the 'if' statement didn't work. > > are sure? really? > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ma at nano.ku.dk Sat Oct 15 06:55:19 2011 From: ma at nano.ku.dk (Martin Andersson) Date: Sat, 15 Oct 2011 06:55:19 +0200 Subject: [Pw_forum] diffusion constants and refolded positions Message-ID: <4E991237.9010906@nano.ku.dk> Hi, I am currently performing 'md' calculations with pw.x and for visualization purposes I use refold_pos=.true. The question is: Do the calculated diffusion constants take into account this or are they too large when atoms jump from one side of the box to the other? Cheers, Martin Andersson University of Copenhagen From songsongfc at yahoo.com.cn Sat Oct 15 15:29:27 2011 From: songsongfc at yahoo.com.cn (=?utf-8?B?5LmL546LIOaUueeOiw==?=) Date: Sat, 15 Oct 2011 21:29:27 +0800 (CST) Subject: [Pw_forum] Zn NC_PP from qe-forge Message-ID: <1318685367.96779.YahooMailClassic@web15803.mail.cnb.yahoo.com> Dear Giuseppe: I see my output file: bfgs converged in?? 7 scf cycles and?? 4 bfgs steps ???? (criteria: energy < 0.10E-04, force < 0.10E-03, cell < 0.50E+00) the con total energy????????????? =??? -338.60645412 Ry ???? Harris-Foulkes estimate?? =??? -338.60645412 Ry ???? estimated scf accuracy??? ??? ???: Giuseppe Mattioli ??: Re: [Pw_forum] Zn NC_PP from qe-forge ???: "PWSCF Forum" ??: 2011?10?14?,??,??9:12 Dear Yun Song A 62Ry cutoff could be quite poor both in the case of your NC Zn (it contains a quite deep 3d shell) and for your NC O. You should reach concergence with respect to the wf cutoff before attempting to perform phonon calculations. HTH Giuseppe On Friday 14 October 2011 15:03:48 ?? ?? wrote: > Hi, > ? Recently,I generate Zn NC-PP using the PP library from qe-forge project. > I want to generate Zn.pz-nc.UPF using ld1.x. > My Zn.-nc.in is followed: > ?&input > ?? title='Zn', > ?? zed=30., > ?? rel=0, > ?? config='[Ar] 4s2.0 4p0.0 3d10.0', > ?? iswitch=3, > ?? dft='PZ' > ?/ > ?&inputp > ?? pseudotype=2, > ?? file_pseudopw='Zn.pz-nc.UPF', > ?? author='TM', > ?? lloc=0, > ?? nlcc=.true., > ?? tm=.true. > ?/ > 3 > 4P? 2? 1? 0.00? 0.00? 2.30? 2.30? 0.0 > 3D? 3? 2 10.00? 0.00? 2.30? 2.30? 0.0 > 4S? 1? 0? 2.00? 0.00? 2.30? 2.30? 0.0 > > > And I calculate ZnO vc-relax using Zn.pz-nc.UPF and O.pz-mt.UPF, > the theory is a=6.223 c/a=1.614, after calculating vc-relax is a=6.191 > c/a=1.614 with ecutwfc=62Ry. > > However, No matter how I try to calculate,the phonon frequency is negative > > The scf and ph file is followed: > &CONTROL > ???????????????? calculation = 'scf' , > ??????????????? restart_mode = 'from_scratch' , > ????????????????????? outdir = '/root/ZnO/915-phonon' , > ????????????????? pseudo_dir = '/root/pseudopotential' , > ????????????????????? prefix = 'ZnO' , > ?????????????? etot_conv_thr = 1.0D-5 , > ?????????????? forc_conv_thr = 1.0D-4 , > ???????????????????? tstress = .true. , > ???????????????????? tprnfor = .true. , > ?/ > ?&SYSTEM > ?????????????????????? ibrav = 4, > ?????????????????? celldm(1) = 6.191, > ?????????????????? celldm(3) = 1.614, > ???????????????????????? nat = 4, > ??????????????????????? ntyp = 2, > ???????????????????? ecutwfc = 62 , > ?/ > ?&ELECTRONS > ??????????????????? conv_thr = 1.0d-10 , > ???????????????? mixing_mode = 'plain' , > ???????????????? mixing_beta = 0.6 , > ???????????? diagonalization = 'david' , > ?/ > ATOMIC_SPECIES > ?? Zn?? 65.40900? Zn.pz-nc.UPF > ??? O?? 15.99940? O.pz-mt.UPF > ATOMIC_POSITIONS crystal > Zn?????? 0.333333333?? 0.666666667? -0.000036499?? 1 1 1 > Zn?????? 0.666666667?? 0.333333333?? 0.499963501?? 1 1 1 > O??????? 0.333333333?? 0.666666667?? 0.379036499?? 1 1 1 > O??????? 0.666666667?? 0.333333333?? 0.879036499?? 1 1 1 > K_POINTS automatic > ? 4 4 4?? 1 1 1 > > > > phonons of ZnO??????????????????????????????????????? > ?&INPUTPH > ????????????????????? outdir = '/root/ZnO/915-phonon' , > ????????????????????? prefix = 'ZnO' , > ????????????????????? fildyn = 'ZnO_IR.dyn' , > ??????????????????? fildvscf = 'ZnO.dv' , > ?????????????????????? ldisp = .true., > ???????????????????????? nq1 = 4 , > ???????????????????????? nq2 = 4 , > ???????????????????????? nq3 = 4 , > ?????????????????????? epsil = .false., > ??????????????????????? elph = .false., > ??????????????????????? fpol = .false. , > ???????????????????? recover = .false. , > ??????????????????? amass(1) = 65.4090, > ??????????????????? amass(2) = 15.9994, > ????????????????????? tr2_ph = 1.0d-12 , > ?/ > > Best > Regards > Yun Song,Kang > > Department Physical Science and Technology of? Inner Mongolia University. -- ******************************************************** - 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 00015 - 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/20111015/70fcbb83/attachment-0001.htm From tkaloni at gmail.com Sat Oct 15 15:46:45 2011 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Sat, 15 Oct 2011 16:46:45 +0300 Subject: [Pw_forum] Request Message-ID: *Dear QE users, Is the B97-D3 scheme implemented in quantum espresso? Which method would be best **to take into account the van der Waals interaction**? Best, Thaneshwor Kaloni KAUST, Saudi Arabia * ** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111015/eb2a4b33/attachment.htm From giannozz at democritos.it Sat Oct 15 18:16:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 15 Oct 2011 18:16:46 +0200 Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <1318685367.96779.YahooMailClassic@web15803.mail.cnb.yahoo.com> References: <1318685367.96779.YahooMailClassic@web15803.mail.cnb.yahoo.com> Message-ID: <6263BBEC-6A1F-4769-A7AF-CAB27BA4DD9D@democritos.it> On Oct 15, 2011, at 15:29 , ?? ?? wrote: > [...] convergence has been achieved in 8 iterations > [...] bfgs converged in 7 scf cycles and 4 bfgs steps these are the convergence of the self-consistent cycle and of structural optimization, respectively > [...] You should reach convergence with respect to the wf cutoff > before attempting to perform phonon calculations. this is the convergence with respect to the basis set. If you do not know the difference between all these convergences, you must learn it, before attempting any serious calculation P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Oct 15 18:22:57 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 15 Oct 2011 18:22:57 +0200 Subject: [Pw_forum] diffusion constants and refolded positions In-Reply-To: <4E991237.9010906@nano.ku.dk> References: <4E991237.9010906@nano.ku.dk> Message-ID: <32FEB9C8-356C-4B0D-AA2F-61253FC4C2F0@democritos.it> On Oct 15, 2011, at 6:55 , Martin Andersson wrote: > I am currently performing 'md' calculations with pw.x and for > visualization purposes I use refold_pos=.true. > > The question is: Do the calculated diffusion constants take into > account > this or are they too large when atoms jump from one side of the box to > the other? interesting question. I am afraid that the diffusion coefficient will turn out to be wrong, but only (computer) experiments, or a deep look at the code, can give a more reliable answer P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Oct 15 18:24:24 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 15 Oct 2011 18:24:24 +0200 Subject: [Pw_forum] Cholesky error for SCF calculations after successful relax In-Reply-To: References: Message-ID: <65CD0661-E346-4AD8-88D8-CC650BCB1FDA@democritos.it> On Oct 14, 2011, at 15:22 , Jennifer Wohlwend wrote: > conv_thr = 1.0d-12 this is a very strict criterion. It may lead to numerical instabilities towards the end of self-consistency P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Oct 15 18:46:08 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 15 Oct 2011 18:46:08 +0200 Subject: [Pw_forum] Request In-Reply-To: References: Message-ID: <68B30F9A-025D-4FF4-A06F-A93E1E8DC1D4@democritos.it> On Oct 15, 2011, at 15:46 , Thaneshwor Kaloni wrote: > Is the B97-D3 scheme implemented in quantum espresso? exchange-correlation? what is implemented is listed in Modules/funct.f90 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From aouahab at yahoo.fr Sun Oct 16 11:38:42 2011 From: aouahab at yahoo.fr (A.ouahab) Date: Sun, 16 Oct 2011 10:38:42 +0100 (BST) Subject: [Pw_forum] Re : error band structure of ZnO In-Reply-To: <1318503054.33306.YahooMailNeo@web29513.mail.ird.yahoo.com> Message-ID: <1318757922.122.YahooMailClassic@web25703.mail.ukl.yahoo.com> Salam Essaye d'enlever nband=18, et relance les caluls Abdelouahab OUAHAB D?partement des Scienses physiques Universit? de Ouargla Alg?rie --- En date de?: Jeu 13.10.11, debbichi mourad a ?crit?: De: debbichi mourad Objet: [Pw_forum] error band structure of ZnO ?: "pw_forum at pwscf.org" Date: Jeudi 13 octobre 2011, 12h50 Dear QE users, I am a new user of QE.? when I went to test the band structure calculation on material ZnO (ibrav=4) with this input file ,I got error band structue (flatt band dispersion). ?calculation='bands' ??? pseudo_dir = '$PSEUDO_DIR/', ??? outdir='$TMP_DIR/', ??? prefix='ZnO' ?/ ?&system ? ibrav = 4, nbnd =18, ?????????????????? celldm(1) = 6.213, ?????????????????? celldm(3) = 1.610, ???????????????????????? nat = 4, ??????????????????????? ntyp = 2, ???????????????????? ecutwfc = 40, ???????????????????? ecutrho = 240 , ??? occupations ='smearing', smearing ='methfessel-paxton', degauss = 0.05, ?/ ?&electrons ???????????????? mixing_mode = 'plain' , ???????????????? mixing_beta = 0.7 , ???????????? diagonalization = 'david' , ??????????? conv_thr = 1.0d-8, ?/ ATOMIC_SPECIES ?Zn?? 65.39200? Zn.pbe-van.UPF ? O?? 16.00000? O.pbe-rrkjus.UPF ATOMIC_POSITIONS ?? Zn????? 0.666666667??? 0.333333333??? 0.000000000 ?? Zn????? 0.333333333??? 0.666666667??? 0.500000000 ??? O????? 0.666666667??? 0.333333333??? 0.380000000 ?? O????? 0.333333333??? 0.666666667??? 0.880000000 K_POINTS 9 ?? 0.0000000000???? 0.0000000000???? 0.0000000000??? 1 ?? 0.5000000000???? 0.0000000000???? 0.5000000000??? 2 ?? 0.5000000000???? 0.0000000000???? 0.0000000000??? 3 ?? 0.3333333333???? 0.3333333333???? 0.5000000000??? 4 ?? 0.0000000000???? 0.0000000000???? 0.5000000000??? 5 ?? 0.0000000000???? 0.0000000000???? 0.0000000000??? 6 ?? 0.0000000000???? 0.5000000000???? 0.5000000000??? 7 ? 0.3333333333??? 0.3333333333???? 0.0000000000???? 8 ?? 0.3333333333???? 0.6666666667??? 0.5000000000??? 9 thanks for help ?? DEBBICHI Mourad Unit? de Recherche Physique des Solides,99/UR/13-19, D?partement de Physique, Facult? des Science de Monastir, Avenue de l'Environnement 5019, Monastir Tunisie. t?l:+21697487042 mourad_fsm at yahoo.fr -----La pi?ce jointe associ?e suit----- _______________________________________________ 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/20111016/0ac6e6dd/attachment.htm From songsongfc at yahoo.com.cn Sun Oct 16 13:13:42 2011 From: songsongfc at yahoo.com.cn (=?utf-8?B?5LmL546LIOaUueeOiw==?=) Date: Sun, 16 Oct 2011 19:13:42 +0800 (CST) Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <201110141512.52211.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <1318763622.30352.YahooMailClassic@web15808.mail.cnb.yahoo.com> Dear Paolo and Giuseppe: Thanks for your help. It seems to be necessary to learn the mean of concergence. Best Regards Yun Song,Kang Department Physical Science and Technology of Inner Mongolia University. --- 11?10?14????, Giuseppe Mattioli ??? ???: Giuseppe Mattioli ??: Re: [Pw_forum] Zn NC_PP from qe-forge ???: "PWSCF Forum" ??: 2011?10?14?,??,??9:12 Dear Yun Song A 62Ry cutoff could be quite poor both in the case of your NC Zn (it contains a quite deep 3d shell) and for your NC O. You should reach concergence with respect to the wf cutoff before attempting to perform phonon calculations. HTH Giuseppe On Friday 14 October 2011 15:03:48 ?? ?? wrote: > Hi, > ? Recently,I generate Zn NC-PP using the PP library from qe-forge project. > I want to generate Zn.pz-nc.UPF using ld1.x. > My Zn.-nc.in is followed: > ?&input > ?? title='Zn', > ?? zed=30., > ?? rel=0, > ?? config='[Ar] 4s2.0 4p0.0 3d10.0', > ?? iswitch=3, > ?? dft='PZ' > ?/ > ?&inputp > ?? pseudotype=2, > ?? file_pseudopw='Zn.pz-nc.UPF', > ?? author='TM', > ?? lloc=0, > ?? nlcc=.true., > ?? tm=.true. > ?/ > 3 > 4P? 2? 1? 0.00? 0.00? 2.30? 2.30? 0.0 > 3D? 3? 2 10.00? 0.00? 2.30? 2.30? 0.0 > 4S? 1? 0? 2.00? 0.00? 2.30? 2.30? 0.0 > > > And I calculate ZnO vc-relax using Zn.pz-nc.UPF and O.pz-mt.UPF, > the theory is a=6.223 c/a=1.614, after calculating vc-relax is a=6.191 > c/a=1.614 with ecutwfc=62Ry. > > However, No matter how I try to calculate,the phonon frequency is negative > > The scf and ph file is followed: > &CONTROL > ???????????????? calculation = 'scf' , > ??????????????? restart_mode = 'from_scratch' , > ????????????????????? outdir = '/root/ZnO/915-phonon' , > ????????????????? pseudo_dir = '/root/pseudopotential' , > ????????????????????? prefix = 'ZnO' , > ?????????????? etot_conv_thr = 1.0D-5 , > ?????????????? forc_conv_thr = 1.0D-4 , > ???????????????????? tstress = .true. , > ???????????????????? tprnfor = .true. , > ?/ > ?&SYSTEM > ?????????????????????? ibrav = 4, > ?????????????????? celldm(1) = 6.191, > ?????????????????? celldm(3) = 1.614, > ???????????????????????? nat = 4, > ??????????????????????? ntyp = 2, > ???????????????????? ecutwfc = 62 , > ?/ > ?&ELECTRONS > ??????????????????? conv_thr = 1.0d-10 , > ???????????????? mixing_mode = 'plain' , > ???????????????? mixing_beta = 0.6 , > ???????????? diagonalization = 'david' , > ?/ > ATOMIC_SPECIES > ?? Zn?? 65.40900? Zn.pz-nc.UPF > ??? O?? 15.99940? O.pz-mt.UPF > ATOMIC_POSITIONS crystal > Zn?????? 0.333333333?? 0.666666667? -0.000036499?? 1 1 1 > Zn?????? 0.666666667?? 0.333333333?? 0.499963501?? 1 1 1 > O??????? 0.333333333?? 0.666666667?? 0.379036499?? 1 1 1 > O??????? 0.666666667?? 0.333333333?? 0.879036499?? 1 1 1 > K_POINTS automatic > ? 4 4 4?? 1 1 1 > > > > phonons of ZnO??????????????????????????????????????? > ?&INPUTPH > ????????????????????? outdir = '/root/ZnO/915-phonon' , > ????????????????????? prefix = 'ZnO' , > ????????????????????? fildyn = 'ZnO_IR.dyn' , > ??????????????????? fildvscf = 'ZnO.dv' , > ?????????????????????? ldisp = .true., > ???????????????????????? nq1 = 4 , > ???????????????????????? nq2 = 4 , > ???????????????????????? nq3 = 4 , > ?????????????????????? epsil = .false., > ??????????????????????? elph = .false., > ??????????????????????? fpol = .false. , > ???????????????????? recover = .false. , > ??????????????????? amass(1) = 65.4090, > ??????????????????? amass(2) = 15.9994, > ????????????????????? tr2_ph = 1.0d-12 , > ?/ > > Best > Regards > Yun Song,Kang > > Department Physical Science and Technology of? Inner Mongolia University. -- ******************************************************** - 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 00015 - 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/20111016/6ba273c4/attachment-0001.htm From baroni at sissa.it Sun Oct 16 12:33:26 2011 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 16 Oct 2011 12:33:26 +0200 Subject: [Pw_forum] Re : error band structure of ZnO In-Reply-To: <1318757922.122.YahooMailClassic@web25703.mail.ukl.yahoo.com> References: <1318757922.122.YahooMailClassic@web25703.mail.ukl.yahoo.com> Message-ID: De l'anglais, SVP. English, please. Merci - thanks - SB On Oct 16, 2011, at 11:38 AM, A.ouahab wrote: > Salam > > Essaye d'enlever nband=18, et relance les caluls > > Abdelouahab OUAHAB > D?partement des Scienses physiques > Universit? de Ouargla > Alg?rie > > > --- En date de : Jeu 13.10.11, debbichi mourad a ?crit : > > De: debbichi mourad > Objet: [Pw_forum] error band structure of ZnO > ?: "pw_forum at pwscf.org" > Date: Jeudi 13 octobre 2011, 12h50 > > > > Dear QE users, > > I am a new user of QE. when I went to test the band structure calculation on material ZnO (ibrav=4) with this input file ,I got error band structue (flatt band dispersion). > > calculation='bands' > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/', > prefix='ZnO' > / > &system > ibrav = 4, nbnd =18, > celldm(1) = 6.213, > celldm(3) = 1.610, > nat = 4, > ntyp = 2, > ecutwfc = 40, > ecutrho = 240 , > occupations ='smearing', > smearing ='methfessel-paxton', > degauss = 0.05, > / > &electrons > mixing_mode = 'plain' , > mixing_beta = 0.7 , > diagonalization = 'david' , > conv_thr = 1.0d-8, > / > ATOMIC_SPECIES > Zn 65.39200 Zn.pbe-van.UPF > O 16.00000 O.pbe-rrkjus.UPF > ATOMIC_POSITIONS > Zn 0.666666667 0.333333333 0.000000000 > Zn 0.333333333 0.666666667 0.500000000 > O 0.666666667 0.333333333 0.380000000 > O 0.333333333 0.666666667 0.880000000 > K_POINTS > 9 > 0.0000000000 0.0000000000 0.0000000000 1 > 0.5000000000 0.0000000000 0.5000000000 2 > 0.5000000000 0.0000000000 0.0000000000 3 > 0.3333333333 0.3333333333 0.5000000000 4 > 0.0000000000 0.0000000000 0.5000000000 5 > 0.0000000000 0.0000000000 0.0000000000 6 > 0.0000000000 0.5000000000 0.5000000000 7 > 0.3333333333 0.3333333333 0.0000000000 8 > 0.3333333333 0.6666666667 0.5000000000 9 > > thanks for help > > > DEBBICHI Mourad > Unit? de Recherche Physique des Solides,99/UR/13-19, > D?partement de Physique, Facult? des Science de Monastir, > Avenue de l'Environnement 5019, Monastir Tunisie. > t?l:+21697487042 > mourad_fsm at yahoo.fr > > > > -----La pi?ce jointe associ?e suit----- > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111016/123f6b0b/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Sun Oct 16 14:33:20 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Sun, 16 Oct 2011 14:33:20 +0200 Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <1318763622.30352.YahooMailClassic@web15808.mail.cnb.yahoo.com> References: <1318763622.30352.YahooMailClassic@web15808.mail.cnb.yahoo.com> Message-ID: <20111016143320.dwttbmlycgg48so0@webmail.sic.rm.cnr.it> Dear Yung Song What Paolo means is that you should perform a series of calculation (for example on the ZnO cell) by raising the wfc cutoff. When all the parameters (Energy, forces, eigenvalues...) become stable between two calculations with different cutoff, then you have reached convergence with respect to the wfc basis set. How much stable? Well... It depends on your purposes (and on your experience of a given system); calculations are sometimes art more than science...:-) Hope this suggestion helps more than the previous one, but listen to Paolo: do not start production runs unless you've really understood them. Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting ?? ?? : > Dear Paolo and Giuseppe: > Thanks for your help. It seems to be necessary to learn the mean of > concergence. > > Best > Regards > > Yun Song,Kang > > Department Physical Science and Technology of Inner Mongolia University. > > --- 11?10?14????, Giuseppe Mattioli ??? > > ???: Giuseppe Mattioli > ??: Re: [Pw_forum] Zn NC_PP from qe-forge > ???: "PWSCF Forum" > ??: 2011?10?14?,??,??9:12 > > > Dear Yun Song > A 62Ry cutoff could be quite poor both in the case of your NC Zn (it contains > a quite deep 3d shell) and for your NC O. > You should reach concergence with respect to the wf cutoff before attempting > to perform phonon calculations. > HTH > Giuseppe > > > On Friday 14 October 2011 15:03:48 ?? ?? wrote: >> Hi, >> ? Recently,I generate Zn NC-PP using the PP library from qe-forge project. >> I want to generate Zn.pz-nc.UPF using ld1.x. >> My Zn.-nc.in is followed: >> ?&input >> ?? title='Zn', >> ?? zed=30., >> ?? rel=0, >> ?? config='[Ar] 4s2.0 4p0.0 3d10.0', >> ?? iswitch=3, >> ?? dft='PZ' >> ?/ >> ?&inputp >> ?? pseudotype=2, >> ?? file_pseudopw='Zn.pz-nc.UPF', >> ?? author='TM', >> ?? lloc=0, >> ?? nlcc=.true., >> ?? tm=.true. >> ?/ >> 3 >> 4P? 2? 1? 0.00? 0.00? 2.30? 2.30? 0.0 >> 3D? 3? 2 10.00? 0.00? 2.30? 2.30? 0.0 >> 4S? 1? 0? 2.00? 0.00? 2.30? 2.30? 0.0 >> >> >> And I calculate ZnO vc-relax using Zn.pz-nc.UPF and O.pz-mt.UPF, >> the theory is a=6.223 c/a=1.614, after calculating vc-relax is a=6.191 >> c/a=1.614 with ecutwfc=62Ry. >> >> However, No matter how I try to calculate,the phonon frequency is negative >> >> The scf and ph file is followed: >> &CONTROL >> ???????????????? calculation = 'scf' , >> ??????????????? restart_mode = 'from_scratch' , >> ????????????????????? outdir = '/root/ZnO/915-phonon' , >> ????????????????? pseudo_dir = '/root/pseudopotential' , >> ????????????????????? prefix = 'ZnO' , >> ?????????????? etot_conv_thr = 1.0D-5 , >> ?????????????? forc_conv_thr = 1.0D-4 , >> ???????????????????? tstress = .true. , >> ???????????????????? tprnfor = .true. , >> ?/ >> ?&SYSTEM >> ?????????????????????? ibrav = 4, >> ?????????????????? celldm(1) = 6.191, >> ?????????????????? celldm(3) = 1.614, >> ???????????????????????? nat = 4, >> ??????????????????????? ntyp = 2, >> ???????????????????? ecutwfc = 62 , >> ?/ >> ?&ELECTRONS >> ??????????????????? conv_thr = 1.0d-10 , >> ???????????????? mixing_mode = 'plain' , >> ???????????????? mixing_beta = 0.6 , >> ???????????? diagonalization = 'david' , >> ?/ >> ATOMIC_SPECIES >> ?? Zn?? 65.40900? Zn.pz-nc.UPF >> ??? O?? 15.99940? O.pz-mt.UPF >> ATOMIC_POSITIONS crystal >> Zn?????? 0.333333333?? 0.666666667? -0.000036499?? 1 1 1 >> Zn?????? 0.666666667?? 0.333333333?? 0.499963501?? 1 1 1 >> O??????? 0.333333333?? 0.666666667?? 0.379036499?? 1 1 1 >> O??????? 0.666666667?? 0.333333333?? 0.879036499?? 1 1 1 >> K_POINTS automatic >> ? 4 4 4?? 1 1 1 >> >> >> >> phonons of ZnO??????????????????????????????????????? >> ?&INPUTPH >> ????????????????????? outdir = '/root/ZnO/915-phonon' , >> ????????????????????? prefix = 'ZnO' , >> ????????????????????? fildyn = 'ZnO_IR.dyn' , >> ??????????????????? fildvscf = 'ZnO.dv' , >> ?????????????????????? ldisp = .true., >> ???????????????????????? nq1 = 4 , >> ???????????????????????? nq2 = 4 , >> ???????????????????????? nq3 = 4 , >> ?????????????????????? epsil = .false., >> ??????????????????????? elph = .false., >> ??????????????????????? fpol = .false. , >> ???????????????????? recover = .false. , >> ??????????????????? amass(1) = 65.4090, >> ??????????????????? amass(2) = 15.9994, >> ????????????????????? tr2_ph = 1.0d-12 , >> ?/ >> >> Best >> Regards >> Yun Song,Kang >> >> Department Physical Science and Technology of? Inner Mongolia University. > > > > -- > ******************************************************** > - 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 00015 - 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 > From swapnil.chandratre at gmail.com Mon Oct 17 01:21:16 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Sun, 16 Oct 2011 18:21:16 -0500 Subject: [Pw_forum] BN polarization Message-ID: Hi, I am trying to calculate the polarization developed in BN on application of uniform strain. I perform scf and when I implement nscf, i get the following error, can anyone suggest how to rectify this error, I tried couple of other k points grid as well. ================================================= POLARIZATION CALCULATION !!! NOT THOROUGHLY TESTED !!! -------------------------------------------------- error: translated G= -7.9872523452569705E-002 -4.6114422721026151E-002 0.000000000000000 with crystal coordinates 0 -1 0 corresponds to ng= 0 but G(ng)= 2.3840890707246431E-318 0.000000000000000 2.6154902494896244E-316 probably because G_par is NOT a reciprocal lattice vector Possible choices as smallest G_par: i= 1 G= 0.000000000000000 0.000000000000000 0.000000000000000 i= 2 G= 0.000000000000000 0.000000000000000 -0.1666666666666667 -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111016/7b4125e1/attachment-0001.htm From swapnil.chandratre at gmail.com Mon Oct 17 01:22:24 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Sun, 16 Oct 2011 18:22:24 -0500 Subject: [Pw_forum] BN polarization In-Reply-To: References: Message-ID: Should I provide the input script ? On Sun, Oct 16, 2011 at 6:21 PM, swapnil chandratre < swapnil.chandratre at gmail.com> wrote: > Hi, > > I am trying to calculate the polarization developed in BN on application of > uniform strain. I perform scf and when I implement nscf, i get the following > error, can anyone suggest how to rectify this error, I tried couple of other > k points grid as well. > > ================================================= > POLARIZATION CALCULATION > !!! NOT THOROUGHLY TESTED !!! > -------------------------------------------------- > > error: translated G= -7.9872523452569705E-002 -4.6114422721026151E-002 > 0.000000000000000 with crystal coordinates 0 > -1 > 0 corresponds to ng= 0 but G(ng)= > 2.3840890707246431E-318 0.000000000000000 > 2.6154902494896244E-316 > probably because G_par is NOT a reciprocal lattice vector > Possible choices as smallest G_par: > i= 1 G= 0.000000000000000 0.000000000000000 > > 0.000000000000000 > i= 2 G= 0.000000000000000 0.000000000000000 > > -0.1666666666666667 > > > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111016/fe189656/attachment.htm From zhaohscas at yahoo.com.cn Mon Oct 17 05:41:20 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Mon, 17 Oct 2011 11:41:20 +0800 Subject: [Pw_forum] qdel cann't kill the job. Message-ID: <4E9BA3E0.1070108@yahoo.com.cn> Hi all, I use pbs as the queuing management system. Currently, I meet the following strange issue, i.e., the qdel cann't kill the job, for detail, see the following: zhaohongsheng at node32:~> qdel 283 qdel: Server could not connect to MOM 283.node32.nxu.edu.cn zhaohongsheng at node32:~> Could you please give me some hints, many thanks in advance. Regards -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From akohlmey at gmail.com Mon Oct 17 05:56:41 2011 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Sun, 16 Oct 2011 23:56:41 -0400 Subject: [Pw_forum] qdel cann't kill the job. In-Reply-To: <4E9BA3E0.1070108@yahoo.com.cn> References: <4E9BA3E0.1070108@yahoo.com.cn> Message-ID: On Sun, Oct 16, 2011 at 11:41 PM, Hongsheng Zhao wrote: > Hi all, > > I use pbs as the queuing management system. ?Currently, I meet the > following strange issue, i.e., the ? qdel cann't kill the job, for > detail, see the following: > > ?zhaohongsheng at node32:~> qdel 283 > qdel: Server could not connect to MOM 283.node32.nxu.edu.cn > zhaohongsheng at node32:~> > > Could you please give me some hints, many thanks in advance. a) this really is a question for the torque mailing list. b) your node's hostname seems to be misconfigured try using qdel from the login node axel > > Regards > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA. From germaneau at gucas.ac.cn Mon Oct 17 18:03:40 2011 From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=) Date: Mon, 17 Oct 2011 12:03:40 -0400 Subject: [Pw_forum] qdel cann't kill the job. In-Reply-To: <518822213.16139@test1.gucas.ac.cn> References: <4E9BA3E0.1070108@yahoo.com.cn> <518822213.16139@test1.gucas.ac.cn> Message-ID: <4E9C51DC.10601@gucas.ac.cn> login to node32 and kill the process doing a kill -9. On 10/16/2011 11:56 PM, Axel Kohlmeyer wrote: > On Sun, Oct 16, 2011 at 11:41 PM, Hongsheng Zhao wrote: >> Hi all, >> >> I use pbs as the queuing management system. Currently, I meet the >> following strange issue, i.e., the qdel cann't kill the job, for >> detail, see the following: >> >> zhaohongsheng at node32:~> qdel 283 >> qdel: Server could not connect to MOM 283.node32.nxu.edu.cn >> zhaohongsheng at node32:~> >> >> Could you please give me some hints, many thanks in advance. > a) this really is a question for the torque mailing list. > b) your node's hostname seems to be misconfigured > try using qdel from the login node > > axel > > >> Regards >> -- >> Hongsheng Zhao >> School of Physics and Electrical Information Science, >> Ningxia University, Yinchuan 750021, China >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111017/af339781/attachment.htm From giannozz at democritos.it Mon Oct 17 09:34:41 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 17 Oct 2011 09:34:41 +0200 Subject: [Pw_forum] BN polarization In-Reply-To: References: Message-ID: <1318836881.11191.9.camel@fe12lx.fisica.uniud.it> On Sun, 2011-10-16 at 18:21 -0500, swapnil chandratre wrote: > can anyone suggest how to rectify this error format the error messgae and it will look like a suggestion: > translated G= -7.987E-2 -4.6114E-002 0.0 > with crystal coordinates 0 -1 0 > corresponds to ng= 0 but G(ng)= 0.0 0.0 0.0 > probably because G_par is NOT a reciprocal lattice vector > Possible choices as smallest G_par: > i= 1 G= 0.00 0.00 0.00 > i= 2 G= 0.00 0.00 -0.1666666666666667 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From swapnil.chandratre at gmail.com Mon Oct 17 09:40:58 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 17 Oct 2011 02:40:58 -0500 Subject: [Pw_forum] BN polarization In-Reply-To: <1318836881.11191.9.camel@fe12lx.fisica.uniud.it> References: <1318836881.11191.9.camel@fe12lx.fisica.uniud.it> Message-ID: Hi Paolo Does it mean that instead of improving k points, i need to improve geometry , or the unit cell dimensions, etc. Sorry if the question sounds too immature. On Mon, Oct 17, 2011 at 2:34 AM, Paolo Giannozzi wrote: > On Sun, 2011-10-16 at 18:21 -0500, swapnil chandratre wrote: > > > can anyone suggest how to rectify this error > > format the error messgae and it will look like a suggestion: > > > translated G= -7.987E-2 -4.6114E-002 0.0 > > with crystal coordinates 0 -1 0 > > corresponds to ng= 0 but G(ng)= 0.0 0.0 0.0 > > probably because G_par is NOT a reciprocal lattice vector > > Possible choices as smallest G_par: > > i= 1 G= 0.00 0.00 0.00 > > i= 2 G= 0.00 0.00 -0.1666666666666667 > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111017/5906fc56/attachment.htm From ali.allam2 at hotmail.com Mon Oct 17 11:23:09 2011 From: ali.allam2 at hotmail.com (Ali ALLAM) Date: Mon, 17 Oct 2011 11:23:09 +0200 Subject: [Pw_forum] Ali - Problem - nscf - c_bands: eigenvalues not converged In-Reply-To: References: Message-ID: Dear all I am ali allam I work on the software Quantum Espresso 4.3.2 After optimization of the structure, I want to calculate the nscf My 'input' file, is : CONTROL calculation = 'nscf' prefix = '', pseudo_dir = '', outdir = '', / &SYSTEM ibrav = 0, celldm(1) = 1.d0, nat = 44, ntyp = 2, nspin = 1, ecutwfc = 30.d0, ecutrho = 300.0, nbnd = 190, occupations = 'tetrahedra', / &ELECTRONS conv_thr = 1.d-8, mixing_beta = 0.1d0, diagonalization = 'david', / ATOMIC_SPECIES ...... ...... K_POINTS {automatic} 12 12 4 1 1 1 ATOMIC_POSITIONS (crystal) ...... ..... CELL_PARAMETERS ... ... ... The problem, is that in the output file, i have these remarks Band Structure Calculation CG style diagonalization c_bands: 5 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 6 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged c_bands: 6 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 3 eigenvalues not converged I think that my input file is good, but i don't know from where the problem comes Thank you for helping me, to resolve this problem I am wainting for your reply Thanks BEST regards Ali -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111017/9e36b700/attachment.htm From joshiniharika20 at yahoo.in Mon Oct 17 12:51:19 2011 From: joshiniharika20 at yahoo.in (Niharika Joshi) Date: Mon, 17 Oct 2011 16:21:19 +0530 (IST) Subject: [Pw_forum] problem in xspectra calculations Message-ID: <1318848679.10888.YahooMailClassic@web95716.mail.in.yahoo.com> Hello, It writes 'Could not find the element? C in the table of K edge energies!' after the calculations for all the k-points is over. I have attached the output file. Yes, I tried printing the variables 'sym' and seuilK_tab(6)%name. For both sym and seuilK_tab(6)%name it prints 'C'. But it does not print if I write inside the 'if-loop'. -Niharika Joshi (project student, IISER Pune) --- On Fri, 14/10/11, Paolo Giannozzi wrote: From: Paolo Giannozzi Subject: Re: [Pw_forum] problem in xspectra calculations To: "PWSCF Forum" Date: Friday, 14 October, 2011, 2:56 PM On Oct 14, 2011, at 16:40 , Niharika Joshi wrote: > Yes, replacing 'if (sym.eq.seuilK_tab(i)%name) then' > by? 'if(sym.eq.trim(adjustl(seuilK_tab(i)%name)))' in > the mygetK.f90 didn't work. > It still writes in the 'Could not find the element? C > in the table of K edge energies!' at the end of the output file. where does it write, and why? have you located in the code where the error message is issued? have you tried printing the variables whose value is not what is expected? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 _______________________________________________ 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/20111017/71c540a5/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: diamondh.xspectra_nocut.out Type: application/octet-stream Size: 32144 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111017/71c540a5/attachment-0001.obj From bdslipun at gmail.com Mon Oct 17 15:24:47 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Mon, 17 Oct 2011 18:54:47 +0530 Subject: [Pw_forum] QHA CODE COMPILATION Message-ID: I HAVE INSTALLED IFORT BUT WHEN I RUN THE EXAMPLE THE WRRORS COME LIKE THIS ****** input tetrahedra for BZ-integration ****** 6 3 12 0.000000 0.000000 0.000000 0.750000 0.750000 0.000000 1.000000 0.500000 0.000000 0.500000 0.500000 0.500000 1.000000 0.000000 0.000000 1.000000 0.250000 0.250000 ****** input tetrahedra for BZ-integration ****** ********************** generate_tetra ********************* NT0= 3 NTETMX= 1728 0.0000 0.7500 1.0000 0.5000 0.0000 0.7500 0.5000 0.5000 0.0000 0.0000 0.0000 0.5000 1.0000 1.0000 1.0000 1.0000 volume of tetrahedron = 0.03125 0.0000 1.0000 1.0000 1.0000 0.0000 0.5000 0.0000 0.2500 0.0000 0.0000 0.0000 0.2500 1.0000 1.0000 1.0000 1.0000 volume of tetrahedron = 0.02083 0.0000 1.0000 0.5000 1.0000 0.0000 0.5000 0.5000 0.2500 0.0000 0.0000 0.5000 0.2500 1.0000 1.0000 1.0000 1.0000 volume of tetrahedron = 0.03125 total volume of BZ is = 0.0833 omg48= 24.0000 ****************** end of generate_tetra ****************** Recalculating omega(q) from C(R) Cannot match namelist object name ca.fc STOP 2 head: cannot open `frequency' for reading: No such file or directory head: cannot open `frequency' for reading: No such file or directory (standard_in) 1: syntax error forrtl: severe (59): list-directed I/O syntax error, unit 5, file stdin Image PC Routine Line Source Partial_phonon_DO 08097123 Unknown Unknown Unknown Partial_phonon_DO 08095E40 Unknown Unknown Unknown Partial_phonon_DO 08069D6E Unknown Unknown Unknown Partial_phonon_DO 0804AA7C Unknown Unknown Unknown Partial_phonon_DO 0804A37A Unknown Unknown Unknown Partial_phonon_DO 0805AC79 Unknown Unknown Unknown Partial_phonon_DO 08058FE4 Unknown Unknown Unknown Partial_phonon_DO 080483CE Unknown Unknown Unknown Partial_phonon_DO 080482D4 Unknown Unknown Unknown Partial_phonon_DO 080A4F8F Unknown Unknown Unknown Partial_phonon_DO 080481C1 Unknown Unknown Unknown ./run_Phonon_DOS.sh: line 204: frequency: No such file or directory forrtl: severe (59): list-directed I/O syntax error, unit 5, file stdin Image PC Routine Line Source atom_info.x 08095213 Unknown Unknown Unknown atom_info.x 08093F30 Unknown Unknown Unknown atom_info.x 08067E5E Unknown Unknown Unknown atom_info.x 0804A8DC Unknown Unknown Unknown atom_info.x 0804A1DA Unknown Unknown Unknown atom_info.x 0805AAD9 Unknown Unknown Unknown atom_info.x 08058E44 Unknown Unknown Unknown atom_info.x 0804836D Unknown Unknown Unknown atom_info.x 080482D4 Unknown Unknown Unknown atom_info.x 080A317F Unknown Unknown Unknown atom_info.x 080481C1 Unknown Unknown Unknown forrtl: severe (24): end-of-file during read, unit 9, file /home/bds/bhabya/espresso-4.3/QHA/Examples/AlAs/projected.DOS Image PC Routine Line Source Atom_projected_pr 08094463 Unknown Unknown Unknown Atom_projected_pr 08093180 Unknown Unknown Unknown Atom_projected_pr 08065BBE Unknown Unknown Unknown Atom_projected_pr 0804C99C Unknown Unknown Unknown Atom_projected_pr 0804C29A Unknown Unknown Unknown Atom_projected_pr 08058992 Unknown Unknown Unknown Atom_projected_pr 0804846C Unknown Unknown Unknown Atom_projected_pr 080482D4 Unknown Unknown Unknown Atom_projected_pr 080A22CF Unknown Unknown Unknown Atom_projected_pr 080481C1 Unknown Unknown Unknown forrtl: severe (24): end-of-file during read, unit 5, file stdin Image PC Routine Line Source Mean_square_displ 0809AEA3 Unknown Unknown Unknown Mean_square_displ 08099BC0 Unknown Unknown Unknown Mean_square_displ 0806D00E Unknown Unknown Unknown Mean_square_displ 0804B66C Unknown Unknown Unknown Mean_square_displ 0804AF6A Unknown Unknown Unknown Mean_square_displ 0805A7D2 Unknown Unknown Unknown Mean_square_displ 08048432 Unknown Unknown Unknown Mean_square_displ 080482D4 Unknown Unknown Unknown Mean_square_displ 080A8D0F Unknown Unknown Unknown Mean_square_displ 080481C1 Unknown Unknown Unknown mv: cannot stat `Displacements': No such file or directory forrtl: severe (59): list-directed I/O syntax error, unit 5, file stdin Image PC Routine Line Source atom_info.x 08095213 Unknown Unknown Unknown atom_info.x 08093F30 Unknown Unknown Unknown atom_info.x 08067E5E Unknown Unknown Unknown atom_info.x 0804A8DC Unknown Unknown Unknown atom_info.x 0804A1DA Unknown Unknown Unknown atom_info.x 0805AAD9 Unknown Unknown Unknown atom_info.x 08058E44 Unknown Unknown Unknown atom_info.x 0804836D Unknown Unknown Unknown atom_info.x 080482D4 Unknown Unknown Unknown atom_info.x 080A317F Unknown Unknown Unknown atom_info.x 080481C1 Unknown Unknown Unknown forrtl: severe (24): end-of-file during read, unit 9, file /home/bds/bhabya/espresso-4.3/QHA/Examples/AlAs/projected.DOS Image PC Routine Line Source Atom_projected_pr 08094463 Unknown Unknown Unknown Atom_projected_pr 08093180 Unknown Unknown Unknown Atom_projected_pr 08065BBE Unknown Unknown Unknown Atom_projected_pr 0804C99C Unknown Unknown Unknown Atom_projected_pr 0804C29A Unknown Unknown Unknown Atom_projected_pr 08058992 Unknown Unknown Unknown Atom_projected_pr 0804846C Unknown Unknown Unknown Atom_projected_pr 080482D4 Unknown Unknown Unknown Atom_projected_pr 080A22CF Unknown Unknown Unknown Atom_projected_pr 080481C1 Unknown Unknown Unknown forrtl: severe (24): end-of-file during read, unit 5, file stdin Image PC Routine Line Source Mean_square_displ 0809AEA3 Unknown Unknown Unknown Mean_square_displ 08099BC0 Unknown Unknown Unknown Mean_square_displ 0806D00E Unknown Unknown Unknown Mean_square_displ 0804B66C Unknown Unknown Unknown Mean_square_displ 0804AF6A Unknown Unknown Unknown Mean_square_displ 0805A7D2 Unknown Unknown Unknown Mean_square_displ 08048432 Unknown Unknown Unknown Mean_square_displ 080482D4 Unknown Unknown Unknown Mean_square_displ 080A8D0F Unknown Unknown Unknown Mean_square_displ 080481C1 Unknown Unknown Unknown mv: cannot stat `Displacements': No such file or directory forrtl: severe (24): end-of-file during read, unit 10, file /home/bds/bhabya/espresso-4.3/QHA/Examples/AlAs/PHDOS.out Image PC Routine Line Source Debye.x 0809E903 Unknown Unknown Unknown Debye.x 0809D620 Unknown Unknown Unknown Debye.x 08069A8E Unknown Unknown Unknown Debye.x 0804C20C Unknown Unknown Unknown Debye.x 0804BB0A Unknown Unknown Unknown Debye.x 0805B372 Unknown Unknown Unknown Debye.x 080485B3 Unknown Unknown Unknown Debye.x 080482D4 Unknown Unknown Unknown Debye.x 080AC86F Unknown Unknown Unknown Debye.x 080481C1 Unknown Unknown Unknown forrtl: severe (24): end-of-file during read, unit 1, file /home/bds/bhabya/espresso-4.3/QHA/Examples/AlAs/PHDOS.out Image PC Routine Line Source F_QHA.x 0809DB23 Unknown Unknown Unknown F_QHA.x 0809C840 Unknown Unknown Unknown F_QHA.x 0806E7EE Unknown Unknown Unknown F_QHA.x 0804BC5C Unknown Unknown Unknown F_QHA.x 0804B55A Unknown Unknown Unknown F_QHA.x 0805ADC2 Unknown Unknown Unknown F_QHA.x 080484E0 Unknown Unknown Unknown F_QHA.x 080482D4 Unknown Unknown Unknown F_QHA.x 080ABA8F Unknown Unknown Unknown F_QHA.x 080481C1 Unknown Unknown Unknown Phonon DOS and Quasiharmonic calculations have finished. Now you can analyse these data using Gnuplot or xmgrace Enjoy! B D SAHOO BARC MUMBAI -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111017/27e816c8/attachment.htm From s.m.rezaeisani at gmail.com Mon Oct 17 15:46:15 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Mon, 17 Oct 2011 17:16:15 +0330 Subject: [Pw_forum] QHA runtime error Message-ID: Dear all I get error while I'm trying to run an example of QHA package. The same happens for all other examples but I haven't made any change to the files. here is a part of the error: Recalculating omega(q) from C(R) Cannot match namelist object name alas444.fc, At line 616 of file matdyn.f90 Fortran runtime error: No such file or directory head: cannot open `frequency' for reading: No such file or directory head: cannot open `frequency' for reading: No such file or directory (standard_in) 1: parse error I've attached the complete runtime message. Any idea is welcome. Thanks in advance. -- ========================================== Seyed Mojtaba Rezaei Sani Computational Materials Science Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel lab: +98 311 391 3731 Group page: http://cmsgroup.iut.ac.ir/ s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111017/c556bbce/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Error Type: application/octet-stream Size: 10385 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111017/c556bbce/attachment-0001.obj From nandan.tandon at gmail.com Mon Oct 17 17:43:44 2011 From: nandan.tandon at gmail.com (Nandan Tandon) Date: Mon, 17 Oct 2011 11:43:44 -0400 Subject: [Pw_forum] Phonon calculation with hybrids?? Message-ID: Hello, I was wondering whether phonon calculations can be done with hybrid functionals? I think i read somewhere that PAW cannot be used for phonon calculations. But from the what i understand from comments in the phonon.f90, it appears that PAW can actually be used. Any comments would be appreciated. Thanks in advance, Nandan. -- *********************************************************************************************** Nandan Tandon Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA ************************************************************************************************* From jonathan.dubois at gmail.com Mon Oct 17 18:21:27 2011 From: jonathan.dubois at gmail.com (Jonathan DuBois) Date: Mon, 17 Oct 2011 09:21:27 -0700 Subject: [Pw_forum] from expint : error # 1, continued fraction failed Message-ID: I've been attempting to use hse with the espresso 4.3 and pw.x keeps crashing with %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from expint : error # 1 continued fraction failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% any ideas why this might be happening and how I can avoid it? input file is below. &CONTROL calculation = "scf" restart_mode = 'restart' prefix = 'Ca_graphene' pseudo_dir = './' verbosity = high outdir = './' wf_collect = .true. / &SYSTEM input_dft = 'HSE' ibrav = 0 ntyp= 2 nat= 33 nbnd = 138 occupations = 'smearing' smearing = 'gaussian' nosym = .false. degauss = 0.001, ecutwfc = 160.0 / &ELECTRONS diagonalization = 'david' conv_thr = 1.0d-8 startingwfc = 'file' / CELL_PARAMETERS hexagonal 16.18932808 -9.346904673 0.0000000000 16.18932808 9.346904673 0.0000000000 0.00000000 0.000000000 28.345889829 sample output at failure: total cpu time spent up to now is 19953.73 secs total energy = -440.37890917 Ry Harris-Foulkes estimate = -440.37891169 Ry estimated scf accuracy < 0.00000727 Ry iteration # 4 ecut= 160.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.27E-09, avg # of iterations = 2.0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from expint : error # 1 continued fraction failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From gabriele.sclauzero at epfl.ch Mon Oct 17 18:22:40 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Mon, 17 Oct 2011 18:22:40 +0200 Subject: [Pw_forum] Phonon calculation with hybrids?? In-Reply-To: References: Message-ID: <8F0B5AE7-8BE1-48C3-954E-74188EBFC7BD@epfl.ch> Il giorno 17/ott/2011, alle ore 17.43, Nandan Tandon ha scritto: > Hello, > > I was wondering whether phonon calculations can be done with hybrid functionals? > > I think i read somewhere that PAW cannot be used for phonon > calculations. What's the connection between the two? (hybrids <--> PAW) > But from > the what i understand from comments in the phonon.f90, it appears that PAW can > actually be used. I think that phonon with PAW has been implemented and should be available at least in the CVS version, if not in the latest distribution. Here you can find the theory http://prb.aps.org/abstract/PRB/v81/i7/e075123 Phonon with hybrids has not been implemented or is just on the way. Let's wait for a reply by Paolo or Stefano dG. GS > > Any comments would be appreciated. Thanks in advance, > > Nandan. > -- > *********************************************************************************************** > Nandan Tandon > Department of Physics, > Worcester Polytechnic Institute, > 100 Institute Road, > Worcester, MA > ************************************************************************************************* > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111017/b95befef/attachment.htm From giannozz at democritos.it Mon Oct 17 18:48:44 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 17 Oct 2011 18:48:44 +0200 Subject: [Pw_forum] from expint : error # 1, continued fraction failed In-Reply-To: References: Message-ID: <1318870124.14711.4.camel@fe12lx.fisica.uniud.it> On Mon, 2011-10-17 at 09:21 -0700, Jonathan DuBois wrote: > I've been attempting to use hse with the espresso 4.3 > and pw.x keeps crashing with > from expint : error # 1 > continued fraction failed should have been fixed in 4.3.1 and subsequent versions P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From nandan.tandon at gmail.com Mon Oct 17 19:08:17 2011 From: nandan.tandon at gmail.com (Nandan Tandon) Date: Mon, 17 Oct 2011 13:08:17 -0400 Subject: [Pw_forum] Phonon calculation with hybrids?? In-Reply-To: <8F0B5AE7-8BE1-48C3-954E-74188EBFC7BD@epfl.ch> References: <8F0B5AE7-8BE1-48C3-954E-74188EBFC7BD@epfl.ch> Message-ID: Actually, the two were independent statements. For hybrids i found no information regarding implementation in phonon program. I was wondering the same for PAW as well. For PAW i now have the reference. Thank you Gabriele! What is the "CVS" version? Nandan. On Mon, Oct 17, 2011 at 12:22 PM, Gabriele Sclauzero wrote: > > Il giorno 17/ott/2011, alle ore 17.43, Nandan Tandon ha scritto: > > Hello, > > I was wondering whether phonon calculations can be done with hybrid > functionals? > > I think i read somewhere that PAW cannot be used for phonon > calculations. > > What's the connection between the two? (hybrids <--> PAW) > > But from > the what i understand from comments in the phonon.f90, it appears that PAW > can > actually be used. > > I think that phonon with PAW has been implemented and should be available at > least in the CVS version, if not in the latest distribution. > Here you can find the theory > http://prb.aps.org/abstract/PRB/v81/i7/e075123 > Phonon with hybrids has not been implemented or is just on the way. Let's > wait for a reply by Paolo or Stefano dG. > GS > > Any comments would be appreciated. Thanks in advance, > > Nandan. > -- > *********************************************************************************************** > Nandan Tandon > Department of Physics, > Worcester Polytechnic Institute, > 100 Institute Road, > Worcester, MA > ************************************************************************************************* > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > ? Gabriele Sclauzero,?EPFL SB ITP CSEA > ?? PH H2 462, Station 3,?CH-1015 Lausanne > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- *********************************************************************************************** Nandan Tandon Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA ************************************************************************************************* From gabriele.sclauzero at epfl.ch Mon Oct 17 19:17:31 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Mon, 17 Oct 2011 19:17:31 +0200 Subject: [Pw_forum] Phonon calculation with hybrids?? In-Reply-To: References: <8F0B5AE7-8BE1-48C3-954E-74188EBFC7BD@epfl.ch> Message-ID: <7AF758B9-4F35-4C20-B9C9-63D28DF142C7@epfl.ch> Il giorno 17/ott/2011, alle ore 19.08, Nandan Tandon ha scritto: > > > > What is the "CVS" version? Well, I should have said SVN... it's the online repository where developers can submit their changes and where you can find the latest changes to the code. Have a look here http://qe-forge.org/scm/?group_id=10 Cheers Gabriele > > Nandan. > > > On Mon, Oct 17, 2011 at 12:22 PM, Gabriele Sclauzero > wrote: >> >> Il giorno 17/ott/2011, alle ore 17.43, Nandan Tandon ha scritto: >> >> Hello, >> >> I was wondering whether phonon calculations can be done with hybrid >> functionals? >> >> I think i read somewhere that PAW cannot be used for phonon >> calculations. >> >> What's the connection between the two? (hybrids <--> PAW) >> >> But from >> the what i understand from comments in the phonon.f90, it appears that PAW >> can >> actually be used. >> >> I think that phonon with PAW has been implemented and should be available at >> least in the CVS version, if not in the latest distribution. >> Here you can find the theory >> http://prb.aps.org/abstract/PRB/v81/i7/e075123 >> Phonon with hybrids has not been implemented or is just on the way. Let's >> wait for a reply by Paolo or Stefano dG. >> GS >> >> Any comments would be appreciated. Thanks in advance, >> >> Nandan. >> -- >> *********************************************************************************************** >> Nandan Tandon >> Department of Physics, >> Worcester Polytechnic Institute, >> 100 Institute Road, >> Worcester, MA >> ************************************************************************************************* >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> PH H2 462, Station 3, CH-1015 Lausanne >> >> >> >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > > -- > *********************************************************************************************** > Nandan Tandon > Department of Physics, > Worcester Polytechnic Institute, > 100 Institute Road, > Worcester, MA > ************************************************************************************************* > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111017/806c5777/attachment-0001.htm From arvifis at gmail.com Mon Oct 17 20:26:19 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 17 Oct 2011 16:26:19 -0200 Subject: [Pw_forum] qdel cann't kill the job. In-Reply-To: <4E9C51DC.10601@gucas.ac.cn> References: <4E9BA3E0.1070108@yahoo.com.cn> <518822213.16139@test1.gucas.ac.cn> <4E9C51DC.10601@gucas.ac.cn> Message-ID: Hi Hongsheng Zhao, you must be like root and try. >> qdel -p XXXX where XXX is the process number.!! Arles V. Gil Rebaza IFLP - Argentina 2011/10/17 ?ric Germaneau > login to node32 and kill the process doing a kill -9. > > On 10/16/2011 11:56 PM, Axel Kohlmeyer wrote: > > On Sun, Oct 16, 2011 at 11:41 PM, Hongsheng Zhao wrote: > > Hi all, > > I use pbs as the queuing management system. Currently, I meet the > following strange issue, i.e., the qdel cann't kill the job, for > detail, see the following: > > zhaohongsheng at node32:~> qdel 283 > qdel: Server could not connect to MOM 283.node32.nxu.edu.cn > zhaohongsheng at node32:~> > > Could you please give me some hints, many thanks in advance. > > a) this really is a question for the torque mailing list. > b) your node's hostname seems to be misconfigured > try using qdel from the login node > > axel > > > > Regards > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > -- > * Be the change you wish to see in the world > * ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > * 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 > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111017/17c4fe1e/attachment.htm From w2agz at w2agz.com Mon Oct 17 20:48:09 2011 From: w2agz at w2agz.com (W2AGZ) Date: Mon, 17 Oct 2011 11:48:09 -0700 Subject: [Pw_forum] Example07 Message-ID: <978501cc8cfd$52173950$f645abf0$@w2agz.com> To the PWscf Community: Example07 is a tutorial on the use of pw.x and ph.x to calculate the Eliashberg parameters of a simple superconductor, in this case aluminum, whose transition temperature is approximately 1.2 K in bulk under ambient pressure and zero applied magnetic field. Paragraph 1) of the README file contains the rather cryptic comment with respect to the use of a 16 x 16 x 16 MP grid in an scf calculation preparatory to calculating subsequent el-phon coefficients, "Note that the k-point grids used here are NOT dense enough for a serious calculation!!!" In the context of Example07, then, what would, with respect to the size of MP grids, including nq-vectors, basis set size (ecutwfc), and respective convergence thresholds, constitute a "serious calculation?" Has such a calculation of the Eliashberg parameters of aluminum using QE been published (I am aware of Wierzboska's paper on Nb)? Thanks, -Paul Paul Grant W2AGZ Technologies Staff Associate, JPL-NASA www.w2agz.com w2agz at w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111017/2a936a09/attachment.htm From giannozz at democritos.it Mon Oct 17 22:35:13 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 17 Oct 2011 22:35:13 +0200 Subject: [Pw_forum] Example07 In-Reply-To: <978501cc8cfd$52173950$f645abf0$@w2agz.com> References: <978501cc8cfd$52173950$f645abf0$@w2agz.com> Message-ID: <9072CD30-9310-4128-9604-ED5CC34EEA6C@democritos.it> On Oct 17, 2011, at 20:48 , W2AGZ wrote: > Paragraph 1) of the README file contains the rather cryptic comment > with respect to the use of a 16 x 16 x 16 MP grid in an scf > calculation preparatory to calculating subsequent el-phon > coefficients, ?Note that the k-point grids used here are NOT dense > enough for a serious calculation!!!? > I don't see anything cryptic: an example is an example and nobody should expect realistic results from an example. > Has such a calculation of the Eliashberg parameters of aluminum > using QE been published > it has been done (by me: the problem was the behavior of Tc under pressure), but never published, because the result looked quite dull and did not add anything to previous, less sophisticated calculation. It was almost 10 years ago. I used something like a 24x24x24 MP grid (not translated) for the double-delta integration of the electron-phonon coefficients, maybe even 32x32x32. This is by far the most critical parameter. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From germaneau at gucas.ac.cn Tue Oct 18 17:27:02 2011 From: germaneau at gucas.ac.cn (=?UTF-8?B?w4lyaWMgR2VybWFuZWF1?=) Date: Tue, 18 Oct 2011 11:27:02 -0400 Subject: [Pw_forum] iotk error In-Reply-To: <518593314.28421@test1.gucas.ac.cn> References: <4E95B5B0.3000700@gucas.ac.cn> <518434037.23363@test1.gucas.ac.cn> <4E970C2E.8070308@gucas.ac.cn> <518593314.28421@test1.gucas.ac.cn> Message-ID: <4E9D9AC6.5010406@gucas.ac.cn> Dear Professor Giannozzi, thank you for your suggestion. First using "-in" does not help, secondly I'm sure of my input since it works fine on my desktop. Now I get this message /FROM IOTK LIBRARY, VERSION 1.2.0 UNRECOVERABLE ERROR (ierr=1) ERROR IN: iotk_scan_end (iotk_scan.f90:241) CVS Revision: 1.23 foundl ERROR IN: iotk_close_read (iotk_files.f90:746) CVS Revision: 1.20 / What does that means? That happen only on this machine. I can run without in problem a scf calculation but for a band calculation for instance I get the error above. I use gfortran, woth ifort it's even scf calculation fails. That's too bad I can not use this machine. Thank you, ?ric. On 10/14/2011 08:21 AM, Paolo Giannozzi wrote: > On Thu, 2011-10-13 at 12:05 -0400, ?ric Germaneau wrote: > >> When I execute the pp.x (or band calculation) with ifort 10.1 on >> several nodes it says >> pp.x: error while loading shared libraries: libmpi.so.3.2: >> cannot open shared object file: No such file or directory > http://www.quantum-espresso.org/user_guide/node52.html#SECTION000121010000000000000 > >> But when I run it on the head node only I get >> from postproc : error # 1 >> reading inputpp namelist > either there is an error in namelist inputpp, or the code doesn't read > it, for reasons explained in in the above link at point 11.1.0.3, > or here: http://www.quantum-espresso.org/user_guide/node19.html > >> from read_rho_xml : error # 1 >> cannot >> open ./SCF/vc-relax_tetragonal.save/charge-density.dat file >> for reading > the file it is not there > > P. -- /Be the change you wish to see in the world / ? Mahatma Gandhi ? Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China /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/20111018/287eafc5/attachment.htm From zhaohscas at yahoo.com.cn Tue Oct 18 06:20:04 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Tue, 18 Oct 2011 12:20:04 +0800 Subject: [Pw_forum] qdel cann't kill the job. In-Reply-To: References: <4E9BA3E0.1070108@yahoo.com.cn> Message-ID: <4E9CFE74.4050001@yahoo.com.cn> On 10/17/2011 11:56 AM, Axel Kohlmeyer wrote: > On Sun, Oct 16, 2011 at 11:41 PM, Hongsheng Zhao wrote: >> Hi all, >> >> I use pbs as the queuing management system. Currently, I meet the >> following strange issue, i.e., the qdel cann't kill the job, for >> detail, see the following: >> >> zhaohongsheng at node32:~> qdel 283 >> qdel: Server could not connect to MOM 283.node32.nxu.edu.cn >> zhaohongsheng at node32:~> >> >> Could you please give me some hints, many thanks in advance. > > a) this really is a question for the torque mailing list. Thanks a lot for you hints. Do you mean this mailing list: torqueusers at supercluster.org? I've just subscribed to it. Thanks again. Regards > b) your node's hostname seems to be misconfigured > try using qdel from the login node > > axel > > >> >> Regards >> -- >> Hongsheng Zhao >> School of Physics and Electrical Information Science, >> Ningxia University, Yinchuan 750021, China >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From zhaohscas at yahoo.com.cn Tue Oct 18 06:25:58 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Tue, 18 Oct 2011 12:25:58 +0800 Subject: [Pw_forum] qdel cann't kill the job. In-Reply-To: References: <4E9BA3E0.1070108@yahoo.com.cn> <518822213.16139@test1.gucas.ac.cn> <4E9C51DC.10601@gucas.ac.cn> Message-ID: <4E9CFFD6.5060100@yahoo.com.cn> On 10/18/2011 02:26 AM, Arles V. Gil Rebaza wrote: > Hi Hongsheng Zhao, you must be like root and try. > > >> qdel -p XXXX > > where XXX is the process number.!! Thanks a lot, the following command do the trick: node32:~ # qdel -p 283 Another issue, why I must run it as root? Regards > > Arles V. Gil Rebaza > IFLP - Argentina > > 2011/10/17 ?ric Germaneau > > > login to node32 and kill the process doing a kill -9. > > On 10/16/2011 11:56 PM, Axel Kohlmeyer wrote: >> On Sun, Oct 16, 2011 at 11:41 PM, Hongsheng Zhao wrote: >>> Hi all, >>> >>> I use pbs as the queuing management system. Currently, I meet the >>> following strange issue, i.e., the qdel cann't kill the job, for >>> detail, see the following: >>> >>> zhaohongsheng at node32:~> qdel 283 >>> qdel: Server could not connect to MOM283.node32.nxu.edu.cn >>> zhaohongsheng at node32:~> >>> >>> Could you please give me some hints, many thanks in advance. >> a) this really is a question for the torque mailing list. >> b) your node's hostname seems to be misconfigured >> try using qdel from the login node >> >> axel >> >> >>> Regards >>> -- >>> Hongsheng Zhao >>> School of Physics and Electrical Information Science, >>> Ningxia University, Yinchuan 750021, China >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> > > -- > /Be the change you wish to see in the world > / ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > > Graduate University of Chinese Academy of Sciences > College of Physical Sciences > Yuquan Road 19A > Beijing 100049 > China > > /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 > > > > > -- > ###---------> Arles V. <---------### > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From giannozz at democritos.it Tue Oct 18 09:05:59 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 18 Oct 2011 09:05:59 +0200 Subject: [Pw_forum] iotk error In-Reply-To: <4E9D9AC6.5010406@gucas.ac.cn> References: <4E95B5B0.3000700@gucas.ac.cn> <518434037.23363@test1.gucas.ac.cn> <4E970C2E.8070308@gucas.ac.cn> <518593314.28421@test1.gucas.ac.cn> <4E9D9AC6.5010406@gucas.ac.cn> Message-ID: <787CB606-6EA9-4779-A991-5CFDE4606C14@democritos.it> On Oct 18, 2011, at 17:27 , ?ric Germaneau wrote: > > FROM IOTK LIBRARY, VERSION 1.2.0 [..] > What does that means? it means that your compiler is buggy (and this must be the 36000th times I say this) > with ifort it's even scf calculation fails. with recent versions of ifort everything works --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Oct 18 09:23:59 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 18 Oct 2011 09:23:59 +0200 Subject: [Pw_forum] BN polarization In-Reply-To: References: <1318836881.11191.9.camel@fe12lx.fisica.uniud.it> Message-ID: <2A3863D6-418D-4963-8529-6DC446FDF686@democritos.it> On Oct 17, 2011, at 9:40 , swapnil chandratre wrote: > Does it mean that instead of improving k points, i need to > improve geometry, or the unit cell dimensions, etc. it means that you need to improve your understanding of what you are calculating and how P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Oct 18 15:53:04 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 18 Oct 2011 15:53:04 +0200 Subject: [Pw_forum] QHA runtime error In-Reply-To: References: Message-ID: On Oct 17, 2011, at 15:46 , Seyed Mojtaba Rezaei Sani wrote: > Recalculating omega(q) from C(R) > Cannot match namelist object name alas444.fc, in QHA/Examples/Edit_Me, there is a line FC_file='alas444.fc' replace it with FC_file="'alas444.fc'" Alternatively, in the following group of lines: cat >matdyn.init < References: Message-ID: On Oct 17, 2011, at 15:24 , bhabya sahoo wrote: > Recalculating omega(q) from C(R) > Cannot match namelist object name ca.fc see my previous message P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From s.m.rezaeisani at gmail.com Tue Oct 18 17:42:59 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Tue, 18 Oct 2011 19:12:59 +0330 Subject: [Pw_forum] QHA runtime error In-Reply-To: References: Message-ID: Dear Prof. Giannozzi Thank you very much. I must understood that. Yours On Tue, Oct 18, 2011 at 5:23 PM, Paolo Giannozzi wrote: > > On Oct 17, 2011, at 15:46 , Seyed Mojtaba Rezaei Sani wrote: > > > Recalculating omega(q) from C(R) > > Cannot match namelist object name alas444.fc, > > in QHA/Examples/Edit_Me, there is a line > FC_file='alas444.fc' > replace it with > FC_file="'alas444.fc'" > > Alternatively, in the following group of lines: > cat >matdyn.init < &input > amass(1)=26.98, > amass(2)=74.922, > asr='crystal', > flfrc=$FC_file, > flfrq='frequency' > &end > EOF > replace line > flfrc=$FC_file, > with > flfrc='$FC_file', > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ========================================== Seyed Mojtaba Rezaei Sani Computational Materials Science Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel lab: +98 311 391 3731 Group page: http://cmsgroup.iut.ac.ir/ s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111018/f45534e7/attachment.htm From dorabman at gmail.com Tue Oct 18 19:34:29 2011 From: dorabman at gmail.com (Hua Bao) Date: Tue, 18 Oct 2011 13:34:29 -0400 Subject: [Pw_forum] electron-phonon coupling tutorial In-Reply-To: <1318434060.1949.123.camel@fe12lx.fisica.uniud.it> References: <1318434060.1949.123.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Paolo Giannozzi and other QE users, Thanks for the information. It helps a lot. I have one follow up question regarding the e-ph coupling calculation. In the formulation I found on the attached document or the QE website, the quantity gamma or lambda is defined on the Fermi surface, so it is not a function of electron energy. But in some literature, such as this one, http://prb.aps.org/abstract/PRB/v81/i12/e121412 people can calculate the scattering rate as a function of electron energy (see fig 2 or fig 4 in the paper). They claimed that they used Quantum Espresso for the calculation. I am wondering how they can do that and what the formulation is for the scattering rate calculation (for electrons not exactly on the Fermi surface). Thanks, Hua On Wed, Oct 12, 2011 at 11:41 AM, Paolo Giannozzi wrote: > On Tue, 2011-10-11 at 13:31 -0400, Hua Bao wrote: > > > However, there is very limited information about the input and output > > of the related module (dynmax, q2r, and lambda, etc). It is not even > > easy to understand the output format. > > input is documented as usual in INPUT_PH.* . Output should be quite > self-explanatory. Attached, a few notes on the calculated quantities. > > > I am wondering if there is any good documentation > > there is no good documentation and there will never be any, because > everybody wants documentation but nobody wants to write it. > > P. > -- > Paolo Giannozzi, IOM-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/20111018/3e9b47a3/attachment.htm From nicola.marzari at epfl.ch Tue Oct 18 22:45:45 2011 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Tue, 18 Oct 2011 22:45:45 +0200 Subject: [Pw_forum] Example07 In-Reply-To: <9072CD30-9310-4128-9604-ED5CC34EEA6C@democritos.it> References: <978501cc8cfd$52173950$f645abf0$@w2agz.com> <9072CD30-9310-4128-9604-ED5CC34EEA6C@democritos.it> Message-ID: <4E9DE579.5030506@epfl.ch> On 10/17/11 10:35 PM, Paolo Giannozzi wrote: > > On Oct 17, 2011, at 20:48 , W2AGZ wrote: > >> Has such a calculation of the Eliashberg parameters of aluminum >> using QE been published >> > it has been done (by me: the problem was the behavior of Tc under > pressure), but never > published, because the result looked quite dull and did not add > anything to previous, less sophisticated calculation. It was almost > 10 years ago. I used something like a 24x24x24 MP > grid (not translated) for the double-delta integration of the > electron-phonon coefficients, > maybe even 32x32x32. This is by far the most critical parameter. Ciao Paolo, Paul! Interestingly, we also have done it (i.e. Al Tc under isotropic or isochoric strain). We did struggle a lot to get results that were well converged (in isochoric strain you lose a lot of symmetries), but not not even 24x24x24 was enough to get a good convergence of T_c (i.e. changes in broadening would affect Tc very significantly, and we didn't have enough cpu to find the sweet spot of k-points/broadening ). nicola ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From xijunw at gmail.com Tue Oct 18 23:31:32 2011 From: xijunw at gmail.com (Xijun Wang) Date: Tue, 18 Oct 2011 17:31:32 -0400 Subject: [Pw_forum] BFGS ionic relax: maximum number of steps? Message-ID: Hi, Whenever I run a "restart" relaxation of ions, it always terminated after one bfgs iteration, and tells me, The maximum number of steps has been reached. End of BFGS Geometry Optimization Begin final coordinates ... Even I set nstep = 1000 and electron_maxstep = 1000 So, I have to copy all coordinates into a new input to run it "from_scratch", then it will run normally, terminate after a lot of iterations. Anything wrong with my input file? A compilation error? Or it just means that the convergence has been reached? Regards, Xijun Wang The input file: ***************** &CONTROL calculation = 'relax', restart_mode = 'restart', prefix = 'trip', outdir = './' pseudo_dir = '/RQusagers/wangxiju/espresso/pseudo' etot_conv_thr = 1.0E-6 forc_conv_thr = 1.0D-5 tstress = .true. , tprnfor = .true. , nstep = 1000 , dt = 150 / &SYSTEM ibrav = 0, celldm(1) = 19.964957 nat = 64, ntyp = 2, ecutwfc = 25, ecutrho = 300 occupations = 'smearing', smearing = 'cold', degauss = 0.03D0 nspin = 2, tot_magnetization = 2 nbnd = 340 / &ELECTRONS diagonalization = 'cg', electron_maxstep = 1000, conv_thr = 1.D-6 mixing_mode = 'plain', mixing_beta = 0.1D0, mixing_ndim = 16 / &IONS ion_dynamics = 'bfgs', upscale = 100.D0 / CELL_PARAMETERS hexagonal 0.992781869 0.000000000 -0.001946740 0.000000000 0.588596312 0.000000000 -0.254396859 0.000000000 1.117512248 ATOMIC_SPECIES Zr 91.22400 Zr.pbe-nsp-van.UPF N 14.00674 N.pbe-van_bm.UPF ATOMIC_POSITIONS angstrom N 6.239044778 1.554381787 1.967061325 N 1.558801609 1.554381786 9.815800854 ...... -- Dept. of Chem and Biochem, Concordia University 7141 Sherbrooke Ouest, Montreal, QC, Canada (H4B 1R6) Tel: 514-848-2424-#5835 (Lab) TA office: SP175.23 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111018/41b31e43/attachment.htm From songsongfc at yahoo.com.cn Wed Oct 19 13:17:54 2011 From: songsongfc at yahoo.com.cn (=?utf-8?B?5LmL546LIOaUueeOiw==?=) Date: Wed, 19 Oct 2011 19:17:54 +0800 (CST) Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <20111016143320.dwttbmlycgg48so0@webmail.sic.rm.cnr.it> Message-ID: <1319023074.60848.YahooMailClassic@web15803.mail.cnb.yahoo.com> Dear Giuseppe: ? Hi, your adivce is great help for me. I have understood a lot since learning your adivce.I think your means?that the?parameters change relatively small?between different wfc cut off(such as 67 and 60) ,it note stable? Is it right? I will try and follow you and Paolo's advice. Best Regrads. Yun Song,Kang Department Physical Science and Technology of Inner Mongolia University. --- 11?10?16????, giuseppe.mattioli at mlib.ism.cnr.it ??? ???: giuseppe.mattioli at mlib.ism.cnr.it ??: Re: [Pw_forum] Zn NC_PP from qe-forge ???: pw_forum at pwscf.org ??: 2011?10?16?,??,??8:33 Dear Yung Song What Paolo means is that you should perform a series of calculation? (for example on the ZnO cell) by raising the wfc cutoff. When all the? parameters (Energy, forces, eigenvalues...) become stable between two? calculations with different cutoff, then you have reached convergence? with respect to the wfc basis set. How much stable? Well... It depends? on your purposes (and on your experience of a given system);? calculations are sometimes art more than science...:-) Hope this suggestion helps more than the previous one, but listen to? Paolo: do not start production runs unless you've really understood? them. Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting ?? ?? : > Dear Paolo and Giuseppe: > Thanks for your help. It seems to be necessary to learn the mean of??? > concergence. > > Best > Regards > > Yun Song,Kang > > Department Physical Science and Technology of? Inner Mongolia University. > > --- 11?10?14????, Giuseppe Mattioli ??? > > ???: Giuseppe Mattioli > ??: Re: [Pw_forum] Zn NC_PP from qe-forge > ???: "PWSCF Forum" > ??: 2011?10?14?,??,??9:12 > > > Dear Yun Song > A 62Ry cutoff could be quite poor both in the case of your NC Zn (it contains > a quite deep 3d shell) and for your NC O. > You should reach concergence with respect to the wf cutoff before attempting > to perform phonon calculations. > HTH > Giuseppe > > > On Friday 14 October 2011 15:03:48 ?? ?? wrote: >> Hi, >> ? Recently,I generate Zn NC-PP using the PP library from qe-forge project. >> I want to generate Zn.pz-nc.UPF using ld1.x. >> My Zn.-nc.in is followed: >> ?&input >> ?? title='Zn', >> ?? zed=30., >> ?? rel=0, >> ?? config='[Ar] 4s2.0 4p0.0 3d10.0', >> ?? iswitch=3, >> ?? dft='PZ' >> ?/ >> ?&inputp >> ?? pseudotype=2, >> ?? file_pseudopw='Zn.pz-nc.UPF', >> ?? author='TM', >> ?? lloc=0, >> ?? nlcc=.true., >> ?? tm=.true. >> ?/ >> 3 >> 4P? 2? 1? 0.00? 0.00? 2.30? 2.30? 0.0 >> 3D? 3? 2 10.00? 0.00? 2.30? 2.30? 0.0 >> 4S? 1? 0? 2.00? 0.00? 2.30? 2.30? 0.0 >> >> >> And I calculate ZnO vc-relax using Zn.pz-nc.UPF and O.pz-mt.UPF, >> the theory is a=6.223 c/a=1.614, after calculating vc-relax is a=6.191 >> c/a=1.614 with ecutwfc=62Ry. >> >> However, No matter how I try to calculate,the phonon frequency is negative >> >> The scf and ph file is followed: >> &CONTROL >> ???????????????? calculation = 'scf' , >> ??????????????? restart_mode = 'from_scratch' , >> ????????????????????? outdir = '/root/ZnO/915-phonon' , >> ????????????????? pseudo_dir = '/root/pseudopotential' , >> ????????????????????? prefix = 'ZnO' , >> ?????????????? etot_conv_thr = 1.0D-5 , >> ?????????????? forc_conv_thr = 1.0D-4 , >> ???????????????????? tstress = .true. , >> ???????????????????? tprnfor = .true. , >> ?/ >> ?&SYSTEM >> ?????????????????????? ibrav = 4, >> ?????????????????? celldm(1) = 6.191, >> ?????????????????? celldm(3) = 1.614, >> ???????????????????????? nat = 4, >> ??????????????????????? ntyp = 2, >> ???????????????????? ecutwfc = 62 , >> ?/ >> ?&ELECTRONS >> ??????????????????? conv_thr = 1.0d-10 , >> ???????????????? mixing_mode = 'plain' , >> ???????????????? mixing_beta = 0.6 , >> ???????????? diagonalization = 'david' , >> ?/ >> ATOMIC_SPECIES >> ?? Zn?? 65.40900? Zn.pz-nc.UPF >> ??? O?? 15.99940? O.pz-mt.UPF >> ATOMIC_POSITIONS crystal >> Zn?????? 0.333333333?? 0.666666667? -0.000036499?? 1 1 1 >> Zn?????? 0.666666667?? 0.333333333?? 0.499963501?? 1 1 1 >> O??????? 0.333333333?? 0.666666667?? 0.379036499?? 1 1 1 >> O??????? 0.666666667?? 0.333333333?? 0.879036499?? 1 1 1 >> K_POINTS automatic >> ? 4 4 4?? 1 1 1 >> >> >> >> phonons of ZnO??????????????????????????????????????? >> ?&INPUTPH >> ????????????????????? outdir = '/root/ZnO/915-phonon' , >> ????????????????????? prefix = 'ZnO' , >> ????????????????????? fildyn = 'ZnO_IR.dyn' , >> ??????????????????? fildvscf = 'ZnO.dv' , >> ?????????????????????? ldisp = .true., >> ???????????????????????? nq1 = 4 , >> ???????????????????????? nq2 = 4 , >> ???????????????????????? nq3 = 4 , >> ?????????????????????? epsil = .false., >> ??????????????????????? elph = .false., >> ??????????????????????? fpol = .false. , >> ???????????????????? recover = .false. , >> ??????????????????? amass(1) = 65.4090, >> ??????????????????? amass(2) = 15.9994, >> ????????????????????? tr2_ph = 1.0d-12 , >> ?/ >> >> Best >> Regards >> Yun Song,Kang >> >> Department Physical Science and Technology of? Inner Mongolia University. > > > > -- > ******************************************************** > - 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 00015 - 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 > _______________________________________________ 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/20111019/fc6b981f/attachment.htm From flux_ray12 at 163.com Wed Oct 19 13:35:25 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Wed, 19 Oct 2011 19:35:25 +0800 (CST) Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <1319023074.60848.YahooMailClassic@web15803.mail.cnb.yahoo.com> References: <1319023074.60848.YahooMailClassic@web15803.mail.cnb.yahoo.com> Message-ID: <49f17ee6.e101.1331bf6e75f.Coremail.flux_ray12@163.com> If you are not farmiliar with convergence test, then it is so dangerous for your calculations, since your result can not be proved as self-consistents and reliable. This PPT may help you understand convergence test, even though it comes from CASTEP group: http://www.castep.org/CASTEP_talks_07/refson1.pdf -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-19 19:17:54,"?? ??" wrote: Dear Giuseppe: Hi, your adivce is great help for me. I have understood a lot since learning your adivce.I think your means that the parameters change relatively small between different wfc cut off(such as 67 and 60) ,it note stable? Is it right? I will try and follow you and Paolo's advice. Best Regrads. Yun Song,Kang Department Physical Science and Technology of Inner Mongolia University. ---11?10?16????,giuseppe.mattioli at mlib.ism.cnr.it ??? ???:giuseppe.mattioli at mlib.ism.cnr.it ??: Re: [Pw_forum] Zn NC_PP from qe-forge ???:pw_forum at pwscf.org ??: 2011?10?16?,??,??8:33 Dear Yung Song What Paolo means is that you should perform a series of calculation (for example on the ZnO cell) by raising the wfc cutoff. When all the parameters (Energy, forces, eigenvalues...) become stable between two calculations with different cutoff, then you have reached convergence with respect to the wfc basis set. How much stable? Well... It depends on your purposes (and on your experience of a given system); calculations are sometimes art more than science...:-) Hope this suggestion helps more than the previous one, but listen to Paolo: do not start production runs unless you've really understood them. Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting ?? ?? : > Dear Paolo and Giuseppe: > Thanks for your help. It seems to be necessary to learn the mean of > concergence. > > Best > Regards > > Yun Song,Kang > > Department Physical Science and Technology of Inner Mongolia University. > > --- 11?10?14????, Giuseppe Mattioli ??? > > ???: Giuseppe Mattioli > ??: Re: [Pw_forum] Zn NC_PP from qe-forge > ???: "PWSCF Forum" > ??: 2011?10?14?,??,??9:12 > > > Dear Yun Song > A 62Ry cutoff could be quite poor both in the case of your NC Zn (it contains > a quite deep 3d shell) and for your NC O. > You should reach concergence with respect to the wf cutoff before attempting > to perform phonon calculations. > HTH > Giuseppe > > > On Friday 14 October 2011 15:03:48 ?? ?? wrote: >> Hi, >> Recently,I generate Zn NC-PP using the PP library from qe-forge project. >> I want to generate Zn.pz-nc.UPF using ld1.x. >> My Zn.-nc.in is followed: >> &input >> title='Zn', >> zed=30., >> rel=0, >> config='[Ar] 4s2.0 4p0.0 3d10.0', >> iswitch=3, >> dft='PZ' >> / >> &inputp >> pseudotype=2, >> file_pseudopw='Zn.pz-nc.UPF', >> author='TM', >> lloc=0, >> nlcc=.true., >> tm=.true. >> / >> 3 >> 4P 2 1 0.00 0.00 2.30 2.30 0.0 >> 3D 3 2 10.00 0.00 2.30 2.30 0.0 >> 4S 1 0 2.00 0.00 2.30 2.30 0.0 >> >> >> And I calculate ZnO vc-relax using Zn.pz-nc.UPF and O.pz-mt.UPF, >> the theory is a=6.223 c/a=1.614, after calculating vc-relax is a=6.191 >> c/a=1.614 with ecutwfc=62Ry. >> >> However, No matter how I try to calculate,the phonon frequency is negative >> >> The scf and ph file is followed: >> &CONTROL >> calculation = 'scf' , >> restart_mode = 'from_scratch' , >> outdir = '/root/ZnO/915-phonon' , >> pseudo_dir = '/root/pseudopotential' , >> prefix = 'ZnO' , >> etot_conv_thr = 1.0D-5 , >> forc_conv_thr = 1.0D-4 , >> tstress = .true. , >> tprnfor = .true. , >> / >> &SYSTEM >> ibrav = 4, >> celldm(1) = 6.191, >> celldm(3) = 1.614, >> nat = 4, >> ntyp = 2, >> ecutwfc = 62 , >> / >> &ELECTRONS >> conv_thr = 1.0d-10 , >> mixing_mode = 'plain' , >> mixing_beta = 0.6 , >> diagonalization = 'david' , >> / >> ATOMIC_SPECIES >> Zn 65.40900 Zn.pz-nc.UPF >> O 15.99940 O.pz-mt.UPF >> ATOMIC_POSITIONS crystal >> Zn 0.333333333 0.666666667 -0.000036499 1 1 1 >> Zn 0.666666667 0.333333333 0.499963501 1 1 1 >> O 0.333333333 0.666666667 0.379036499 1 1 1 >> O 0.666666667 0.333333333 0.879036499 1 1 1 >> K_POINTS automatic >> 4 4 4 1 1 1 >> >> >> >> phonons of ZnO >> &INPUTPH >> outdir = '/root/ZnO/915-phonon' , >> prefix = 'ZnO' , >> fildyn = 'ZnO_IR.dyn' , >> fildvscf = 'ZnO.dv' , >> ldisp = .true., >> nq1 = 4 , >> nq2 = 4 , >> nq3 = 4 , >> epsil = .false., >> elph = .false., >> fpol = .false. , >> recover = .false. , >> amass(1) = 65.4090, >> amass(2) = 15.9994, >> tr2_ph = 1.0d-12 , >> / >> >> Best >> Regards >> Yun Song,Kang >> >> Department Physical Science and Technology of Inner Mongolia University. > > > > -- > ******************************************************** > - 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 00015 - 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 > _______________________________________________ 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/20111019/576f509f/attachment-0001.htm From giuseppe.mattioli at mlib.ism.cnr.it Wed Oct 19 14:59:02 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Wed, 19 Oct 2011 14:59:02 +0200 Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <49f17ee6.e101.1331bf6e75f.Coremail.flux_ray12@163.com> References: <1319023074.60848.YahooMailClassic@web15803.mail.cnb.yahoo.com> <49f17ee6.e101.1331bf6e75f.Coremail.flux_ray12@163.com> Message-ID: <201110191459.02923.giuseppe.mattioli@mlib.ism.cnr.it> Dear Yung Song I think you've "kind of" understood...:-) For example, only to be sure, you may try to calculate the ZnO lattice parameters at increasing wfc cutoffs (70, 80, 90, 100, ... Ry) and check when they become stable (i.e., converge of lattice parameters reached with respect to the wfc cutoff). This is probably the most important convergence test in your case. Yours Giuseppe On Wednesday 19 October 2011 13:35:25 GAO Zhe wrote: > If you are not farmiliar with convergence test, then it is so dangerous for > your calculations, since your result can not be proved as self-consistents > and reliable. This PPT may help you understand convergence test, even > though it comes from CASTEP group: > http://www.castep.org/CASTEP_talks_07/refson1.pdf > > > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > > At 2011-10-19 19:17:54,"?? ??" wrote: > > Dear Giuseppe: > Hi, your adivce is great help for me. I have understood a lot since > learning your adivce.I think your means that the parameters change > relatively small between different wfc cut off(such as 67 and 60) ,it note > stable? Is it right? I will try and follow you and Paolo's advice. > > Best > Regrads. > Yun Song,Kang > Department Physical Science and Technology of Inner Mongolia University. > > ---11?10?16????,giuseppe.mattioli at mlib.ism.cnr.itm.cnr.it> ??? > > > ???:giuseppe.mattioli at mlib.ism.cnr.it > ??: Re: [Pw_forum] Zn NC_PP from qe-forge > ???:pw_forum at pwscf.org > ??: 2011?10?16?,??,??8:33 > > > > Dear Yung Song > What Paolo means is that you should perform a series of calculation > (for example on the ZnO cell) by raising the wfc cutoff. When all the > parameters (Energy, forces, eigenvalues...) become stable between two > calculations with different cutoff, then you have reached convergence > with respect to the wfc basis set. How much stable? Well... It depends > on your purposes (and on your experience of a given system); > calculations are sometimes art more than science...:-) > Hope this suggestion helps more than the previous one, but listen to > Paolo: do not start production runs unless you've really understood > them. > > Giuseppe > > Giuseppe Mattioli > ISM-CNR > Italy > > Quoting ?? ?? : > > Dear Paolo and Giuseppe: > > Thanks for your help. It seems to be necessary to learn the mean of > > concergence. > > > > Best > > Regards > > > > Yun Song,Kang > > > > Department Physical Science and Technology of Inner Mongolia University. > > > > --- 11?10?14????, Giuseppe Mattioli > > ??? > > > > ???: Giuseppe Mattioli > > ??: Re: [Pw_forum] Zn NC_PP from qe-forge > > ???: "PWSCF Forum" > > ??: 2011?10?14?,??,??9:12 > > > > > > Dear Yun Song > > A 62Ry cutoff could be quite poor both in the case of your NC Zn (it > > contains a quite deep 3d shell) and for your NC O. > > You should reach concergence with respect to the wf cutoff before > > attempting to perform phonon calculations. > > HTH > > Giuseppe > > > > On Friday 14 October 2011 15:03:48 ?? ?? wrote: > >> Hi, > >> Recently,I generate Zn NC-PP using the PP library from qe-forge > >> project. I want to generate Zn.pz-nc.UPF using ld1.x. > >> My Zn.-nc.in is followed: > >> &input > >> title='Zn', > >> zed=30., > >> rel=0, > >> config='[Ar] 4s2.0 4p0.0 3d10.0', > >> iswitch=3, > >> dft='PZ' > >> / > >> &inputp > >> pseudotype=2, > >> file_pseudopw='Zn.pz-nc.UPF', > >> author='TM', > >> lloc=0, > >> nlcc=.true., > >> tm=.true. > >> / > >> 3 > >> 4P 2 1 0.00 0.00 2.30 2.30 0.0 > >> 3D 3 2 10.00 0.00 2.30 2.30 0.0 > >> 4S 1 0 2.00 0.00 2.30 2.30 0.0 > >> > >> > >> And I calculate ZnO vc-relax using Zn.pz-nc.UPF and O.pz-mt.UPF, > >> the theory is a=6.223 c/a=1.614, after calculating vc-relax is a=6.191 > >> c/a=1.614 with ecutwfc=62Ry. > >> > >> However, No matter how I try to calculate,the phonon frequency is > >> negative > >> > >> The scf and ph file is followed: > >> &CONTROL > >> calculation = 'scf' , > >> restart_mode = 'from_scratch' , > >> outdir = '/root/ZnO/915-phonon' , > >> pseudo_dir = '/root/pseudopotential' , > >> prefix = 'ZnO' , > >> etot_conv_thr = 1.0D-5 , > >> forc_conv_thr = 1.0D-4 , > >> tstress = .true. , > >> tprnfor = .true. , > >> / > >> &SYSTEM > >> ibrav = 4, > >> celldm(1) = 6.191, > >> celldm(3) = 1.614, > >> nat = 4, > >> ntyp = 2, > >> ecutwfc = 62 , > >> / > >> &ELECTRONS > >> conv_thr = 1.0d-10 , > >> mixing_mode = 'plain' , > >> mixing_beta = 0.6 , > >> diagonalization = 'david' , > >> / > >> ATOMIC_SPECIES > >> Zn 65.40900 Zn.pz-nc.UPF > >> O 15.99940 O.pz-mt.UPF > >> ATOMIC_POSITIONS crystal > >> Zn 0.333333333 0.666666667 -0.000036499 1 1 1 > >> Zn 0.666666667 0.333333333 0.499963501 1 1 1 > >> O 0.333333333 0.666666667 0.379036499 1 1 1 > >> O 0.666666667 0.333333333 0.879036499 1 1 1 > >> K_POINTS automatic > >> 4 4 4 1 1 1 > >> > >> > >> > >> phonons of ZnO > >> &INPUTPH > >> outdir = '/root/ZnO/915-phonon' , > >> prefix = 'ZnO' , > >> fildyn = 'ZnO_IR.dyn' , > >> fildvscf = 'ZnO.dv' , > >> ldisp = .true., > >> nq1 = 4 , > >> nq2 = 4 , > >> nq3 = 4 , > >> epsil = .false., > >> elph = .false., > >> fpol = .false. , > >> recover = .false. , > >> amass(1) = 65.4090, > >> amass(2) = 15.9994, > >> tr2_ph = 1.0d-12 , > >> / > >> > >> Best > >> Regards > >> Yun Song,Kang > >> > >> Department Physical Science and Technology of Inner Mongolia > >> University. > > > > -- > > ******************************************************** > > - 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 00015 - 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - 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 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From songsongfc at yahoo.com.cn Wed Oct 19 15:17:55 2011 From: songsongfc at yahoo.com.cn (=?utf-8?B?5LmL546LIOaUueeOiw==?=) Date: Wed, 19 Oct 2011 21:17:55 +0800 (CST) Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <49f17ee6.e101.1331bf6e75f.Coremail.flux_ray12@163.com> Message-ID: <1319030275.77724.YahooMailClassic@web15808.mail.cnb.yahoo.com> Dear GAO Zhe: ?? Thank you for providing this paper.I will study carefully. Best Regards Yun Song,Kang Department Physical Science and Technology of Inner Mongolia University. --- 11?10?19????, GAO Zhe ??? ???: GAO Zhe ??: Re: [Pw_forum] Zn NC_PP from qe-forge ???: "PWSCF Forum" ??: 2011?10?19?,??,??7:35 If you are not farmiliar with convergence test, then it is so dangerous for your calculations, since your result can not be proved as self-consistents and reliable. This PPT may help you understand convergence test, even though it comes from CASTEP group: http://www.castep.org/CASTEP_talks_07/refson1.pdf -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-19 19:17:54,"?????"? wrote: Dear Giuseppe: ? Hi, your adivce is great help for me. I have understood a lot since learning your adivce.I think your means?that the?parameters change relatively small?between different wfc cut off(such as 67 and 60) ,it note stable? Is it right? I will try and follow you and Paolo's advice. Best Regrads. Yun Song,Kang Department Physical Science and Technology of Inner Mongolia University. --- 11?10?16????, giuseppe.mattioli at mlib.ism.cnr.it ??? ???: giuseppe.mattioli at mlib.ism.cnr.it ??: Re: [Pw_forum] Zn NC_PP from qe-forge ???: pw_forum at pwscf.org ??: 2011?10?16?,??,??8:33 Dear Yung Song What Paolo means is that you should perform a series of calculation? (for example on the ZnO cell) by raising the wfc cutoff. When all the? parameters (Energy, forces, eigenvalues...) become stable between two? calculations with different cutoff, then you have reached convergence? with respect to the wfc basis set. How much stable? Well... It depends? on your purposes (and on your experience of a given system);? calculations are sometimes art more than science...:-) Hope this suggestion helps more than the previous one, but listen to? Paolo: do not start production runs unless you've really understood? them. Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting ?? ?? : > Dear Paolo and Giuseppe: > Thanks for your help. It seems to be necessary to learn the mean of??? > concergence. > > Best > Regards > > Yun Song,Kang > > Department Physical Science and Technology of? Inner Mongolia University. > > --- 11?10?14????, Giuseppe Mattioli ??? > > ???: Giuseppe Mattioli > ??: Re: [Pw_forum] Zn NC_PP from qe-forge > ???: "PWSCF Forum" > ??: 2011?10?14?,??,??9:12 > > > Dear Yun Song > A 62Ry cutoff could be quite poor both in the case of your NC Zn (it contains > a quite deep 3d shell) and for your NC O. > You should reach concergence with respect to the wf cutoff before attempting > to perform phonon calculations. > HTH > Giuseppe > > > On Friday 14 October 2011 15:03:48 ?? ?? wrote: >> Hi, >> ? Recently,I generate Zn NC-PP using the PP library from qe-forge project. >> I want to generate Zn.pz-nc.UPF using ld1.x. >> My Zn.-nc.in is followed: >> ?&input >> ?? title='Zn', >> ?? zed=30., >> ?? rel=0, >> ?? config='[Ar] 4s2.0 4p0.0 3d10.0', >> ?? iswitch=3, >> ?? dft='PZ' >> ?/ >> ?&inputp >> ?? pseudotype=2, >> ?? file_pseudopw='Zn.pz-nc.UPF', >> ?? author='TM', >> ?? lloc=0, >> ?? nlcc=.true., >> ?? tm=.true. >> ?/ >> 3 >> 4P? 2? 1? 0.00? 0.00? 2.30? 2.30? 0.0 >> 3D? 3? 2 10.00? 0.00? 2.30? 2.30? 0.0 >> 4S? 1? 0? 2.00? 0.00? 2.30? 2.30? 0.0 >> >> >> And I calculate ZnO vc-relax using Zn.pz-nc.UPF and O.pz-mt.UPF, >> the theory is a=6.223 c/a=1.614, after calculating vc-relax is a=6.191 >> c/a=1.614 with ecutwfc=62Ry. >> >> However, No matter how I try to calculate,the phonon frequency is negative >> >> The scf and ph file is followed: >> &CONTROL >> ???????????????? calculation = 'scf' , >> ??????????????? restart_mode = 'from_scratch' , >> ????????????????????? outdir = '/root/ZnO/915-phonon' , >> ????????????????? pseudo_dir = '/root/pseudopotential' , >> ????????????????????? prefix = 'ZnO' , >> ?????????????? etot_conv_thr = 1.0D-5 , >> ?????????????? forc_conv_thr = 1.0D-4 , >> ???????????????????? tstress = .true. , >> ???????????????????? tprnfor = .true. , >> ?/ >> ?&SYSTEM >> ?????????????????????? ibrav = 4, >> ?????????????????? celldm(1) = 6.191, >> ?????????????????? celldm(3) = 1.614, >> ???????????????????????? nat = 4, >> ??????????????????????? ntyp = 2, >> ???????????????????? ecutwfc = 62 , >> ?/ >> ?&ELECTRONS >> ??????????????????? conv_thr = 1.0d-10 , >> ???????????????? mixing_mode = 'plain' , >> ???????????????? mixing_beta = 0.6 , >> ???????????? diagonalization = 'david' , >> ?/ >> ATOMIC_SPECIES >> ?? Zn?? 65.40900? Zn.pz-nc.UPF >> ??? O?? 15.99940? O.pz-mt.UPF >> ATOMIC_POSITIONS crystal >> Zn?????? 0.333333333?? 0.666666667? -0.000036499?? 1 1 1 >> Zn?????? 0.666666667?? 0.333333333?? 0.499963501?? 1 1 1 >> O??????? 0.333333333?? 0.666666667?? 0.379036499?? 1 1 1 >> O??????? 0.666666667?? 0.333333333?? 0.879036499?? 1 1 1 >> K_POINTS automatic >> ? 4 4 4?? 1 1 1 >> >> >> >> phonons of ZnO??????????????????????????????????????? >> ?&INPUTPH >> ????????????????????? outdir = '/root/ZnO/915-phonon' , >> ????????????????????? prefix = 'ZnO' , >> ????????????????????? fildyn = 'ZnO_IR.dyn' , >> ??????????????????? fildvscf = 'ZnO.dv' , >> ?????????????????????? ldisp = .true., >> ???????????????????????? nq1 = 4 , >> ???????????????????????? nq2 = 4 , >> ???????????????????????? nq3 = 4 , >> ?????????????????????? epsil = .false., >> ??????????????????????? elph = .false., >> ??????????????????????? fpol = .false. , >> ???????????????????? recover = .false. , >> ??????????????????? amass(1) = 65.4090, >> ??????????????????? amass(2) = 15.9994, >> ????????????????????? tr2_ph = 1.0d-12 , >> ?/ >> >> Best >> Regards >> Yun Song,Kang >> >> Department Physical Science and Technology of? Inner Mongolia University. > > > > -- > ******************************************************** > - 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 00015 - 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 > _______________________________________________ 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/20111019/98215c71/attachment-0001.htm From songsongfc at yahoo.com.cn Wed Oct 19 15:21:33 2011 From: songsongfc at yahoo.com.cn (=?utf-8?B?5LmL546LIOaUueeOiw==?=) Date: Wed, 19 Oct 2011 21:21:33 +0800 (CST) Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <201110191459.02923.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> Dear Giuseppe: ? Thank you for explaining.I will follow this idea. Yours Yun Song Yun Song,Kang Department Physical Science and Technology of Inner Mongolia University. --- 11?10?19????, Giuseppe Mattioli ??? ???: Giuseppe Mattioli ??: Re: [Pw_forum] Zn NC_PP from qe-forge ???: "PWSCF Forum" ??: 2011?10?19?,??,??8:59 Dear Yung Song I think you've "kind of" understood...:-) For example, only to be sure, you may try to calculate the ZnO lattice parameters at increasing wfc cutoffs (70, 80, 90, 100, ... Ry) and check when they become stable (i.e., converge of lattice parameters reached with respect to the wfc cutoff). This is probably the most important convergence test in your case. Yours Giuseppe On Wednesday 19 October 2011 13:35:25 GAO Zhe wrote: > If you are not farmiliar with convergence test, then it is so dangerous for > your calculations, since your result can not be proved as self-consistents > and reliable. This PPT may help you understand convergence test, even > though it comes from CASTEP group: > http://www.castep.org/CASTEP_talks_07/refson1.pdf > > > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > > At 2011-10-19 19:17:54,"?? ??" wrote: > > Dear Giuseppe: >???Hi, your adivce is great help for me. I have understood a lot since > learning your adivce.I think your means that the parameters change > relatively small between different wfc cut off(such as 67 and 60) ,it note > stable? Is it right? I will try and follow you and Paolo's advice. > > Best > Regrads. > Yun Song,Kang > Department Physical Science and Technology of Inner Mongolia University. > > ---11?10?16????,giuseppe.mattioli at mlib.ism.cnr.itm.cnr.it> ??? > > > ???:giuseppe.mattioli at mlib.ism.cnr.it > ??: Re: [Pw_forum] Zn NC_PP from qe-forge > ???:pw_forum at pwscf.org > ??: 2011?10?16?,??,??8:33 > > > > Dear Yung Song > What Paolo means is that you should perform a series of calculation > (for example on the ZnO cell) by raising the wfc cutoff. When all the > parameters (Energy, forces, eigenvalues...) become stable between two > calculations with different cutoff, then you have reached convergence > with respect to the wfc basis set. How much stable? Well... It depends > on your purposes (and on your experience of a given system); > calculations are sometimes art more than science...:-) > Hope this suggestion helps more than the previous one, but listen to > Paolo: do not start production runs unless you've really understood > them. > > Giuseppe > > Giuseppe Mattioli > ISM-CNR > Italy > > Quoting ?? ?? : > > Dear Paolo and Giuseppe: > > Thanks for your help. It seems to be necessary to learn the mean of > > concergence. > > > > Best > > Regards > > > > Yun Song,Kang > > > > Department Physical Science and Technology of? Inner Mongolia University. > > > > --- 11?10?14????, Giuseppe Mattioli > > ??? > > > > ???: Giuseppe Mattioli > > ??: Re: [Pw_forum] Zn NC_PP from qe-forge > > ???: "PWSCF Forum" > > ??: 2011?10?14?,??,??9:12 > > > > > > Dear Yun Song > > A 62Ry cutoff could be quite poor both in the case of your NC Zn (it > > contains a quite deep 3d shell) and for your NC O. > > You should reach concergence with respect to the wf cutoff before > > attempting to perform phonon calculations. > > HTH > > Giuseppe > > > > On Friday 14 October 2011 15:03:48 ?? ?? wrote: > >> Hi, > >>???Recently,I generate Zn NC-PP using the PP library from qe-forge > >> project. I want to generate Zn.pz-nc.UPF using ld1.x. > >> My Zn.-nc.in is followed: > >>? &input > >>? ? title='Zn', > >>? ? zed=30., > >>? ? rel=0, > >>? ? config='[Ar] 4s2.0 4p0.0 3d10.0', > >>? ? iswitch=3, > >>? ? dft='PZ' > >>? / > >>? &inputp > >>? ? pseudotype=2, > >>? ? file_pseudopw='Zn.pz-nc.UPF', > >>? ? author='TM', > >>? ? lloc=0, > >>? ? nlcc=.true., > >>? ? tm=.true. > >>? / > >> 3 > >> 4P? 2? 1? 0.00? 0.00? 2.30? 2.30? 0.0 > >> 3D? 3? 2 10.00? 0.00? 2.30? 2.30? 0.0 > >> 4S? 1? 0? 2.00? 0.00? 2.30? 2.30? 0.0 > >> > >> > >> And I calculate ZnO vc-relax using Zn.pz-nc.UPF and O.pz-mt.UPF, > >> the theory is a=6.223 c/a=1.614, after calculating vc-relax is a=6.191 > >> c/a=1.614 with ecutwfc=62Ry. > >> > >> However, No matter how I try to calculate,the phonon frequency is > >> negative > >> > >> The scf and ph file is followed: > >> &CONTROL > >>? ? ? ? ? ? ? ? ? calculation = 'scf' , > >>? ? ? ? ? ? ? ???restart_mode = 'from_scratch' , > >>? ? ? ? ? ? ? ? ? ? ???outdir = '/root/ZnO/915-phonon' , > >>? ? ? ? ? ? ? ? ???pseudo_dir = '/root/pseudopotential' , > >>? ? ? ? ? ? ? ? ? ? ???prefix = 'ZnO' , > >>? ? ? ? ? ? ? ? etot_conv_thr = 1.0D-5 , > >>? ? ? ? ? ? ? ? forc_conv_thr = 1.0D-4 , > >>? ? ? ? ? ? ? ? ? ? ? tstress = .true. , > >>? ? ? ? ? ? ? ? ? ? ? tprnfor = .true. , > >>? / > >>? &SYSTEM > >>? ? ? ? ? ? ? ? ? ? ? ? ibrav = 4, > >>? ? ? ? ? ? ? ? ? ? celldm(1) = 6.191, > >>? ? ? ? ? ? ? ? ? ? celldm(3) = 1.614, > >>? ? ? ? ? ? ? ? ? ? ? ? ? nat = 4, > >>? ? ? ? ? ? ? ? ? ? ? ???ntyp = 2, > >>? ? ? ? ? ? ? ? ? ? ? ecutwfc = 62 , > >>? / > >>? &ELECTRONS > >>? ? ? ? ? ? ? ? ? ???conv_thr = 1.0d-10 , > >>? ? ? ? ? ? ? ? ? mixing_mode = 'plain' , > >>? ? ? ? ? ? ? ? ? mixing_beta = 0.6 , > >>? ? ? ? ? ? ? diagonalization = 'david' , > >>? / > >> ATOMIC_SPECIES > >>? ? Zn???65.40900? Zn.pz-nc.UPF > >>? ???O???15.99940? O.pz-mt.UPF > >> ATOMIC_POSITIONS crystal > >> Zn? ? ???0.333333333???0.666666667? -0.000036499???1 1 1 > >> Zn? ? ???0.666666667???0.333333333???0.499963501???1 1 1 > >> O? ? ? ? 0.333333333???0.666666667???0.379036499???1 1 1 > >> O? ? ? ? 0.666666667???0.333333333???0.879036499???1 1 1 > >> K_POINTS automatic > >>???4 4 4???1 1 1 > >> > >> > >> > >> phonons of ZnO > >>? &INPUTPH > >>? ? ? ? ? ? ? ? ? ? ???outdir = '/root/ZnO/915-phonon' , > >>? ? ? ? ? ? ? ? ? ? ???prefix = 'ZnO' , > >>? ? ? ? ? ? ? ? ? ? ???fildyn = 'ZnO_IR.dyn' , > >>? ? ? ? ? ? ? ? ? ???fildvscf = 'ZnO.dv' , > >>? ? ? ? ? ? ? ? ? ? ? ? ldisp = .true., > >>? ? ? ? ? ? ? ? ? ? ? ? ? nq1 = 4 , > >>? ? ? ? ? ? ? ? ? ? ? ? ? nq2 = 4 , > >>? ? ? ? ? ? ? ? ? ? ? ? ? nq3 = 4 , > >>? ? ? ? ? ? ? ? ? ? ? ? epsil = .false., > >>? ? ? ? ? ? ? ? ? ? ? ???elph = .false., > >>? ? ? ? ? ? ? ? ? ? ? ???fpol = .false. , > >>? ? ? ? ? ? ? ? ? ? ? recover = .false. , > >>? ? ? ? ? ? ? ? ? ???amass(1) = 65.4090, > >>? ? ? ? ? ? ? ? ? ???amass(2) = 15.9994, > >>? ? ? ? ? ? ? ? ? ? ???tr2_ph = 1.0d-12 , > >>? / > >> > >> Best > >> Regards > >> Yun Song,Kang > >> > >> Department Physical Science and Technology of? Inner Mongolia > >> University. > > > > -- > > ******************************************************** > > - 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 00015 - 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - 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 00015 - 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/20111019/94dbde00/attachment-0001.htm From songsongfc at yahoo.com.cn Wed Oct 19 15:25:05 2011 From: songsongfc at yahoo.com.cn (=?utf-8?B?5LmL546LIOaUueeOiw==?=) Date: Wed, 19 Oct 2011 21:25:05 +0800 (CST) Subject: [Pw_forum] =?utf-8?b?5Zue5aSN77yaICBBbGkgLSBQcm9ibGVtIC0gbnNjZiAt?= =?utf-8?q?_c=5Fbands=3A_eigenvalues_not_converged?= In-Reply-To: Message-ID: <1319030705.34259.YahooMailClassic@web15804.mail.cnb.yahoo.com> Hi, This maybe not a problem. You can see this link:http://www.democritos.it/pipermail/pw_forum/2010-July/017605.html Yun Song,Kang Department Physical Science and Technology of Inner Mongolia University. --- 11?10?17????, Ali ALLAM ??? ???: Ali ALLAM ??: [Pw_forum] Ali - Problem - nscf - c_bands: eigenvalues not converged ???: pw_forum at pwscf.org ??: 2011?10?17?,??,??5:23 #yiv207724715 .yiv207724715ExternalClass .yiv207724715ecxhmmessage P {padding:0px;} #yiv207724715 .yiv207724715ExternalClass body.yiv207724715ecxhmmessage {font-size:10pt;font-family:Tahoma;} Dear all I am ali allam I work on the software Quantum Espresso 4.3.2 After optimization of the structure, I want to calculate the nscf My 'input' file, is : CONTROL ??? calculation = 'nscf' ??? prefix = '', ??? pseudo_dir = '', ??? outdir = '', ?/ ?&SYSTEM ??? ibrav = 0, ??? celldm(1) = 1.d0, ??? nat = 44, ??? ntyp = 2, ??? nspin = 1, ??? ecutwfc = 30.d0, ??? ecutrho = 300.0, ??? nbnd = 190, ??? occupations = 'tetrahedra', ?/ ?&ELECTRONS ??? conv_thr = 1.d-8, ??? mixing_beta = 0.1d0, ??? diagonalization = 'david', ?/ ATOMIC_SPECIES ...... ...... K_POINTS {automatic} ?12 12 4 1 1 1 ? ?ATOMIC_POSITIONS (crystal) ...... ..... CELL_PARAMETERS ? ... ... ... The problem, is that in the output file, i have these remarks ???????????????????????? Band Structure Calculation ???? CG style diagonalization ???? c_bands:? 5 eigenvalues not converged ???? c_bands:? 1 eigenvalues not converged ???? c_bands:? 6 eigenvalues not converged ???? c_bands:? 2 eigenvalues not converged ???? c_bands:? 3 eigenvalues not converged ???? c_bands:? 6 eigenvalues not converged ???? c_bands:? 2 eigenvalues not converged ???? c_bands:? 3 eigenvalues not converged I think that my input file is good, but i don't know from where the problem comes Thank you for helping me, to resolve this problem I am wainting for your reply Thanks BEST regards Ali -----???????----- _______________________________________________ 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/20111019/2c974279/attachment.htm From mulwawinfred at gmail.com Wed Oct 19 15:40:04 2011 From: mulwawinfred at gmail.com (Winfred Mulwa) Date: Wed, 19 Oct 2011 16:40:04 +0300 Subject: [Pw_forum] MgH2 (input file) Message-ID: Dear all, I have created the above inputfile, and when i visualize it in xcrysden, there is bonding between two magnesium atoms which is not supposed to be the case. I have tried changing the lattice parameters but it doesn't seem to be working. Can any one help? Mulwa Winfred. M Phil Student, Computational Material Science Group, Chepkoilel University College Eldoret, Kenya. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111019/2bbac41c/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: mg.scf.in Type: application/octet-stream Size: 990 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111019/2bbac41c/attachment.obj From Lorenzo.Paulatto at impmc.upmc.fr Wed Oct 19 15:45:34 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 19 Oct 2011 15:45:34 +0200 Subject: [Pw_forum] MgH2 (input file) In-Reply-To: References: Message-ID: On Wed, 19 Oct 2011 15:40:04 +0200, Winfred Mulwa wrote: > in xcrysden,there is bonding between two magnesium Dear Mulwa, in xcrysden the bond is draw when two atoms are closer than a certain threshold; you can change this threshold somewhere in the options. However keep in mind that, whatever xcrysden draws, it does not influence the chemical properties of the material. bests -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From m.abbasnejad at gmail.com Wed Oct 19 18:38:15 2011 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 20 Oct 2011 01:38:15 +0900 Subject: [Pw_forum] charge density Message-ID: Dear QE users, Hi, When I try to plot the charge density for my case, the core regions seem to be empty. I wonder what am I missing during the post processig? Should'nt the pseudo wave functions have tail inside the core regions and consequently, should'nt I expect charge density inside the core regions ? I have used 16*16*16 grid of k-points in scf calculation and part of the input file for plotting is like: &plot nfile = 1 filepp(1) = 'charge' weight(1) = 1.0 iflag = 3 output_format =3 fileout = '110-dens.xsf' e1(1) = 1.0, e1(2)=1.0, e1(3)=0.0, e2(1)=0.0, e2(2)=0.0, e2(3) = 1.0, e3(1)=1.0, e3(2)=-1.0, e3(3)=0.0, x0(1)=0.0, x0(2)=0.0,x0(3)=0.0 nx=72, ny=72, nz=72 / Thanks in advance. Yours, Mohaddeseh --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +98 917 731 7514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111020/6e6aed67/attachment.htm From wparker at anl.gov Wed Oct 19 21:51:27 2011 From: wparker at anl.gov (William Parker) Date: Wed, 19 Oct 2011 14:51:27 -0500 Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> Message-ID: <6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov> Dear Yun Song and interested parties, The possibility of a phonon test case in ZnO piqued my curiosity so I decided to have a go at it. I find a very odd convergence pattern with these two pseudopotentials in this system--the total energy has a damped sinusoidal decay with increasing cutoff: (selecting the maxima and minima at 10 Ry sampling) E_cutoff (Ry) E_total (Ry) 100 -338.741 160 -338.660 210 -338.675 290 -338.665 370 -338.668 400 -338.667 Figure here: https://wiki.alcf.anl.gov/wparker/images/b/b5/ZnO_ecut_convergence_lda_ncpp.png Details here: https://wiki.alcf.anl.gov/wparker/index.php/Zinc_Oxide_Parameter_Convergence I have never encountered this kind of behavior with norm-conserving pseudopotentials before. At worst, I've seen little steps in an otherwise smooth convergence to a value. The eigenvalues at the various k-points don't appear to have any ghost states that come and go with cutoff. Has anyone observed this kind of oscillation in the total energy with increasing plane-wave cutoff before? What gives rise to it? --William ********************************************************* William D. Parker Computational Postdoctoral Fellow fax: (630) 252-4798 MSD-212, Rm. C-215 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 ********************************************************* From gkucukdalyan at gmail.com Wed Oct 19 22:52:52 2011 From: gkucukdalyan at gmail.com (Gulcin Kucukdalyan) Date: Wed, 19 Oct 2011 16:52:52 -0400 Subject: [Pw_forum] Running an input file Message-ID: HI All, Could you please tell me how can i run an input file. It is the second time i am asking this question. Last time i was asked to read tutorials. It is not specified there if i have to prepare a text file or an executable file (run_example) like the ones in the examples. If i have to prepare a text file how can i run it. Thanks, Gulcin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111019/55414729/attachment.htm From swapnil.chandratre at gmail.com Wed Oct 19 23:43:12 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Wed, 19 Oct 2011 16:43:12 -0500 Subject: [Pw_forum] Structure Optimization under Sawtooth potential Message-ID: Hi, I am trying to observe in plane piezoelectric response of a system. As I understand I should apply sawtoooth potential and observe the change in positions of atoms. Are there any examples or tutorials on this ? And is what I am thinking the actual way of approaching the problem ? -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111019/71337c92/attachment-0001.htm From naromero at gmail.com Thu Oct 20 02:47:37 2011 From: naromero at gmail.com (Nichols A. Romero) Date: Wed, 19 Oct 2011 19:47:37 -0500 Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov> References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> <6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov> Message-ID: The behavior here is what I might expect for a real-space DFT code, but V_NL is evaluated in reciprocal space right (we don't have real-space projectors)? Just to double-check. Is charge density cutoff 4 times that planewave cutoff? On Wed, Oct 19, 2011 at 2:51 PM, William Parker wrote: > Dear Yun Song and interested parties, > > The possibility of a phonon test case in ZnO piqued my curiosity so I decided to have a go at it. ?I find a very odd convergence pattern with these two pseudopotentials in this system--the total energy has a damped sinusoidal decay with increasing cutoff: > (selecting the maxima and minima at 10 Ry sampling) > > E_cutoff (Ry) ? E_total (Ry) > 100 ? ? ? ? ? ? -338.741 > 160 ? ? ? ? ? ? -338.660 > 210 ? ? ? ? ? ? -338.675 > 290 ? ? ? ? ? ? -338.665 > 370 ? ? ? ? ? ? -338.668 > 400 ? ? ? ? ? ? -338.667 > > Figure here: https://wiki.alcf.anl.gov/wparker/images/b/b5/ZnO_ecut_convergence_lda_ncpp.png > Details here: https://wiki.alcf.anl.gov/wparker/index.php/Zinc_Oxide_Parameter_Convergence > > I have never encountered this kind of behavior with norm-conserving pseudopotentials before. ?At worst, I've seen little steps in an otherwise smooth convergence to a value. ?The eigenvalues at the various k-points don't appear to have any ghost states that come and go with cutoff. ?Has anyone observed this kind of oscillation in the total energy with increasing plane-wave cutoff before? ?What gives rise to it? > > --William > > ********************************************************* > ?William D. Parker > ?Computational Postdoctoral Fellow ? fax: (630) 252-4798 > ?MSD-212, Rm. C-215 > ?Argonne National Laboratory > ?9700 S. Cass Ave. > ?Argonne, IL 60439 > ********************************************************* > > > > > _______________________________________________ > 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) 447-9793 From ejwalt at wm.edu Thu Oct 20 04:13:08 2011 From: ejwalt at wm.edu (Eric J. Walter) Date: Wed, 19 Oct 2011 22:13:08 -0400 Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> <6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov> Message-ID: <4E9F83B4.10609@wm.edu> Hi, >Just to double-check. Is charge density cutoff 4 times that planewave cutoff? I think that this hits on the issue... The Zn.pz-nc.UPF has a sharp core correction. The FFT/Density grid needs to be increased significantly, here is a plot of from 4x to 20x ecutwfc for the case with and without a core correction in Zn. I think this is the cause of the odd *ecutwfc* shown by William Parker. http://dl.dropbox.com/u/8094696/Znplot.pdf So, in this case, no, the density cutoff needs to be higher: Eric On 10/19/2011 08:47 PM, Nichols A. Romero wrote: > The behavior here is what I might expect for a real-space DFT code, > but V_NL is evaluated in reciprocal space right (we don't have > real-space projectors)? > > Just to double-check. Is charge density cutoff 4 times that planewave cutoff? > > > On Wed, Oct 19, 2011 at 2:51 PM, William Parker wrote: >> Dear Yun Song and interested parties, >> >> The possibility of a phonon test case in ZnO piqued my curiosity so I decided to have a go at it. I find a very odd convergence pattern with these two pseudopotentials in this system--the total energy has a damped sinusoidal decay with increasing cutoff: >> (selecting the maxima and minima at 10 Ry sampling) >> >> E_cutoff (Ry) E_total (Ry) >> 100 -338.741 >> 160 -338.660 >> 210 -338.675 >> 290 -338.665 >> 370 -338.668 >> 400 -338.667 >> >> Figure here: https://wiki.alcf.anl.gov/wparker/images/b/b5/ZnO_ecut_convergence_lda_ncpp.png >> Details here: https://wiki.alcf.anl.gov/wparker/index.php/Zinc_Oxide_Parameter_Convergence >> >> I have never encountered this kind of behavior with norm-conserving pseudopotentials before. At worst, I've seen little steps in an otherwise smooth convergence to a value. The eigenvalues at the various k-points don't appear to have any ghost states that come and go with cutoff. Has anyone observed this kind of oscillation in the total energy with increasing plane-wave cutoff before? What gives rise to it? >> >> --William >> >> ********************************************************* >> William D. Parker >> Computational Postdoctoral Fellow fax: (630) 252-4798 >> MSD-212, Rm. C-215 >> Argonne National Laboratory >> 9700 S. Cass Ave. >> Argonne, IL 60439 >> ********************************************************* >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > From mohnish.iitk at gmail.com Thu Oct 20 04:49:10 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 20 Oct 2011 08:19:10 +0530 Subject: [Pw_forum] Structure Optimization under Sawtooth potential In-Reply-To: References: Message-ID: Dear Swapnil ! In the /espresso/doc.pw.html or text file the details of implementation of sawtooth potential are given. Please take a look at that, On Thu, Oct 20, 2011 at 3:13 AM, swapnil chandratre < swapnil.chandratre at gmail.com> wrote: > Hi, > > I am trying to observe in plane piezoelectric response of a system. As I > understand I should apply sawtoooth potential and observe the change in > positions of atoms. Are there any examples or tutorials on this ? And is > what I am thinking the actual way of approaching the problem ? > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111020/54d84c23/attachment.htm From mohnish.iitk at gmail.com Thu Oct 20 04:53:39 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 20 Oct 2011 08:23:39 +0530 Subject: [Pw_forum] Running an input file In-Reply-To: References: Message-ID: Dear Gulcin ! To run an an input file for example an input file of pw.x you should invoke the command for pw.x. /espresso directory/bin/pw.x abc.scf.out. In this /espresso directory/ is the address to espresso directory, " abc.scf.in" is the name of the QE input file and "abc.scf.out" is the the QE output file. This is the crudest way to run an input file. And next time please mention your affiliation. Hope it helps. On Thu, Oct 20, 2011 at 2:22 AM, Gulcin Kucukdalyan wrote: > HI All, > > Could you please tell me how can i run an input file. It is the second time > i am asking this question. Last time i was asked to read tutorials. It is > not specified there if i have to prepare a text file or an executable file > (run_example) like the ones in the examples. If i have to prepare a text > file how can i run it. > > Thanks, > > Gulcin > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111020/757c12bf/attachment.htm From gkucukdalyan at gmail.com Thu Oct 20 05:21:46 2011 From: gkucukdalyan at gmail.com (Gulcin Kucukdalyan) Date: Wed, 19 Oct 2011 23:21:46 -0400 Subject: [Pw_forum] Running an input file In-Reply-To: References: Message-ID: Dear Mohnish, Thanks a lot for your response. I am trying to prepare an input file for graphene. I just prepared a text file and tried to run it and did not work. I really cannot find detailed explanation about how to prepare an input file. Can you please suggest me any if exist? Gulcin On Oct 19, 2011, at 10:53 PM, mohnish pandey wrote: > Dear Gulcin ! > > To run an an input file for example an input file of pw.x you should invoke the command for pw.x. /espresso directory/bin/pw.x abc.scf.out. In this /espresso directory/ is the address to espresso directory, "abc.scf.in" is the name of the QE input file and "abc.scf.out" is the the QE output file. This is the crudest way to run an input file. And next time please mention your affiliation. Hope it helps. > > On Thu, Oct 20, 2011 at 2:22 AM, Gulcin Kucukdalyan wrote: > HI All, > > Could you please tell me how can i run an input file. It is the second time i am asking this question. Last time i was asked to read tutorials. It is not specified there if i have to prepare a text file or an executable file (run_example) like the ones in the examples. If i have to prepare a text file how can i run it. > > Thanks, > > Gulcin > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > BTech-Mtech, IIT Kanpur > Senior Project Associate, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > > _______________________________________________ > 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/20111019/53b1c14a/attachment.htm From mohnish.iitk at gmail.com Thu Oct 20 08:26:30 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 20 Oct 2011 11:56:30 +0530 Subject: [Pw_forum] Running an input file In-Reply-To: References: Message-ID: Before running the calculation visualizing the structure is extremely important. Try using XCrysden to visualize the structure which you made. And some basic info you will find on MIT-OCW Atomistic material modelling lectures to prepare a QE input file. Below is the link. http://ocw.mit.edu/courses/materials-science-and-engineering/3-320-atomistic-computer-modeling-of-materials-sma-5107-spring-2005/ And please sign your affiliation while writing to this forum so that we know whom we are interacting with. On Thu, Oct 20, 2011 at 8:51 AM, Gulcin Kucukdalyan wrote: > Dear Mohnish, > > Thanks a lot for your response. I am trying to prepare an input file for > graphene. I just prepared a text file and tried to run it and did not work. > I really cannot find detailed explanation about how to prepare an input > file. Can you please suggest me any if exist? > > Gulcin > > On Oct 19, 2011, at 10:53 PM, mohnish pandey > wrote: > > Dear Gulcin ! > > To run an an input file for example an input file of pw.x you should invoke > the command for pw.x. /espresso directory/bin/pw.x > abc.scf.out. In this /espresso directory/ is the address to espresso > directory, "abc.scf.in" is the name of the QE input file and "abc.scf.out" > is the the QE output file. This is the crudest way to run an input file. And > next time please mention your affiliation. Hope it helps. > > On Thu, Oct 20, 2011 at 2:22 AM, Gulcin Kucukdalyan < > gkucukdalyan at gmail.com> wrote: > >> HI All, >> >> Could you please tell me how can i run an input file. It is the second >> time i am asking this question. Last time i was asked to read tutorials. It >> is not specified there if i have to prepare a text file or an executable >> file (run_example) like the ones in the examples. If i have to prepare a >> text file how can i run it. >> >> Thanks, >> >> Gulcin >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > BTech-Mtech, IIT Kanpur > Senior Project Associate, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > > _______________________________________________ > 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 > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111020/b057977d/attachment-0001.htm From kucukben at sissa.it Thu Oct 20 10:58:10 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Thu, 20 Oct 2011 10:58:10 +0200 Subject: [Pw_forum] Running an input file In-Reply-To: References: Message-ID: <20111020105810.Horde.QNV_Qx8V4mxOn_KiEU62M1A@webmail.sissa.it> Merhaba Gulcin, Try running the example input files in the examples directory. You will see that every run_example is nothing but a script that generates the input files (text) and invokes the necessary executable (such as pw.x). you can take a look at run_example, it is not binary. If you suspect you are missing something in the format of input files, just edit one of the input files generated by the run_example to represent your system and calculation. to understand the keywords used take a look at their descriptions. The following is the description of input for pw.x executable: http://www.quantum-espresso.org/input-syntax/INPUT_PW.html You seem to be at the beginning of things, if available, local help would let you advance faster than the mailing list. If you provide your affiliation, your chances of finding someone in your area/institute is higher, cheers emine kucukbenli, phd student, sissa, italy Quoting Gulcin Kucukdalyan : > Dear Mohnish, > > Thanks a lot for your response. I am trying to prepare an input file > for graphene. I just prepared a text file and tried to run it and > did not work. I really cannot find detailed explanation about how to > prepare an input file. Can you please suggest me any if exist? > > Gulcin > > On Oct 19, 2011, at 10:53 PM, mohnish pandey wrote: > >> Dear Gulcin ! >> >> To run an an input file for example an input file of pw.x you >> should invoke the command for pw.x. /espresso directory/bin/pw.x >> abc.scf.out. In this /espresso directory/ is the >> address to espresso directory, "abc.scf.in" is the name of the QE >> input file and "abc.scf.out" is the the QE output file. This is the >> crudest way to run an input file. And next time please mention your >> affiliation. Hope it helps. >> >> On Thu, Oct 20, 2011 at 2:22 AM, Gulcin Kucukdalyan >> wrote: >> HI All, >> >> Could you please tell me how can i run an input file. It is the >> second time i am asking this question. Last time i was asked to >> read tutorials. It is not specified there if i have to prepare a >> text file or an executable file (run_example) like the ones in the >> examples. If i have to prepare a text file how can i run it. >> >> Thanks, >> >> Gulcin >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> -- >> Regards, >> MOHNISH, >> ----------------------------------------------------------------- >> Mohnish Pandey >> BTech-Mtech, IIT Kanpur >> Senior Project Associate, >> Department of Chemical Engineering, >> IIT KANPUR, UP, INDIA >> ----------------------------------------------------------------- >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum From giuseppe.mattioli at mlib.ism.cnr.it Thu Oct 20 12:52:05 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Thu, 20 Oct 2011 12:52:05 +0200 Subject: [Pw_forum] normal modes visualization In-Reply-To: <4E9F83B4.10609@wm.edu> References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> <6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov> <4E9F83B4.10609@wm.edu> Message-ID: <20111020125205.ax8wq549i5ckc4s4@webmail.sic.rm.cnr.it> Dear all Does anybody know if there is any post-processing tool which allows one to visualize normal modes calculated with phonon.x or phcg.x in real space, as, for instance, ion displacement movies to be opened with xcrysden or xmakemol? Thank you in advance Giuseppe Giuseppe Mattioli ISM-CNR Italy From kucukben at sissa.it Thu Oct 20 13:17:29 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Thu, 20 Oct 2011 13:17:29 +0200 Subject: [Pw_forum] normal modes visualization In-Reply-To: <20111020125205.ax8wq549i5ckc4s4@webmail.sic.rm.cnr.it> References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> <6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov> <4E9F83B4.10609@wm.edu> <20111020125205.ax8wq549i5ckc4s4@webmail.sic.rm.cnr.it> Message-ID: <20111020131729.Horde.exHRFR8V4mxOoANJ88A1vSA@webmail.sissa.it> Ciao Giuseppe, Yes there is a small program that does that : dynmat.x Call it like this: $espresso_dir/bin/dynmat.x then feed this one line input (no need for a separate input file) &input fildyn='yourfile' / it produces dynmat.axsf where the normal modes are represented as forces in xcrysden, an animated xsf file, one frame per mode. xcrysden --axsf dynmat.axsf This is how it was working last time i checked, i dont think anything has changed.. emine kucukbenli, phd student, sissa, italy ps: after writing i remembered this: http://people.sissa.it/~degironc/QE-Tutorial/tutorial_phon.htm check the "Phonons at Gamma point" section - last bit. Quoting giuseppe.mattioli at mlib.ism.cnr.it: > Dear all > Does anybody know if there is any post-processing tool which allows > one to visualize normal modes calculated with phonon.x or phcg.x in > real space, as, for instance, ion displacement movies to be opened > with xcrysden or xmakemol? > Thank you in advance > > Giuseppe > > Giuseppe Mattioli > ISM-CNR > Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giuseppe.mattioli at mlib.ism.cnr.it Thu Oct 20 13:41:57 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Thu, 20 Oct 2011 13:41:57 +0200 Subject: [Pw_forum] normal modes visualization In-Reply-To: <20111020131729.Horde.exHRFR8V4mxOoANJ88A1vSA@webmail.sissa.it> References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> <6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov> <4E9F83B4.10609@wm.edu> <20111020125205.ax8wq549i5ckc4s4@webmail.sic.rm.cnr.it> <20111020131729.Horde.exHRFR8V4mxOoANJ88A1vSA@webmail.sissa.it> Message-ID: <20111020134157.jzlck060dccgko8s@webmail.sic.rm.cnr.it> Ciao Emine Thank you very much! I'm going to try... Giuseppe Quoting Emine Kucukbenli : > Ciao Giuseppe, > > Yes there is a small program that does that : dynmat.x > Call it like this: > $espresso_dir/bin/dynmat.x > > then feed this one line input (no need for a separate input file) > &input fildyn='yourfile' / > > it produces dynmat.axsf where the normal modes are represented as > forces in xcrysden, > an animated xsf file, one frame per mode. > > xcrysden --axsf dynmat.axsf > > This is how it was working last time i checked, i dont think anything > has changed.. > emine kucukbenli, phd student, sissa, italy > > ps: after writing i remembered this: > http://people.sissa.it/~degironc/QE-Tutorial/tutorial_phon.htm > check the "Phonons at Gamma point" section - last bit. > > Quoting giuseppe.mattioli at mlib.ism.cnr.it: > >> Dear all >> Does anybody know if there is any post-processing tool which allows >> one to visualize normal modes calculated with phonon.x or phcg.x in >> real space, as, for instance, ion displacement movies to be opened >> with xcrysden or xmakemol? >> Thank you in advance >> >> Giuseppe >> >> Giuseppe Mattioli >> ISM-CNR >> 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 > From giuseppe.mattioli at mlib.ism.cnr.it Thu Oct 20 13:42:59 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Thu, 20 Oct 2011 13:42:59 +0200 Subject: [Pw_forum] normal modes visualization In-Reply-To: <20111020131729.Horde.exHRFR8V4mxOoANJ88A1vSA@webmail.sissa.it> References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> <6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov> <4E9F83B4.10609@wm.edu> <20111020125205.ax8wq549i5ckc4s4@webmail.sic.rm.cnr.it> <20111020131729.Horde.exHRFR8V4mxOoANJ88A1vSA@webmail.sissa.it> Message-ID: <20111020134259.7u9pkgbalcgc4owk@webmail.sic.rm.cnr.it> Ciao Emine Thank you very much! I'm going to try... Giuseppe Quoting Emine Kucukbenli : > Ciao Giuseppe, > > Yes there is a small program that does that : dynmat.x > Call it like this: > $espresso_dir/bin/dynmat.x > > then feed this one line input (no need for a separate input file) > &input fildyn='yourfile' / > > it produces dynmat.axsf where the normal modes are represented as > forces in xcrysden, > an animated xsf file, one frame per mode. > > xcrysden --axsf dynmat.axsf > > This is how it was working last time i checked, i dont think anything > has changed.. > emine kucukbenli, phd student, sissa, italy > > ps: after writing i remembered this: > http://people.sissa.it/~degironc/QE-Tutorial/tutorial_phon.htm > check the "Phonons at Gamma point" section - last bit. > > Quoting giuseppe.mattioli at mlib.ism.cnr.it: > >> Dear all >> Does anybody know if there is any post-processing tool which allows >> one to visualize normal modes calculated with phonon.x or phcg.x in >> real space, as, for instance, ion displacement movies to be opened >> with xcrysden or xmakemol? >> Thank you in advance >> >> Giuseppe >> >> Giuseppe Mattioli >> ISM-CNR >> 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 > From natalia at npavlenko.com Thu Oct 20 15:48:41 2011 From: natalia at npavlenko.com (Natalia Pavlenko) Date: Thu, 20 Oct 2011 06:48:41 -0700 (PDT) Subject: [Pw_forum] problems with pp.x for parallel processing In-Reply-To: <1318232064.29598.16.camel@fe12lx.fisica.uniud.it> Message-ID: <1319118521.67019.YahooMailClassic@web5716.biz.mail.ne1.yahoo.com> Dear Paolo, thank you for your help with pp.x, after removing the lines in postproc.f90 mentioned in your last message, I have recomplied it and now it works well without k-parallelization and with wf_collect=.true. in the scf-input. Best regards, N.Pavlenko ----------------------------------- Dr. Natalia Pavlenko Institute for Condensed Matter Physics, Lviv, Ukraine Tel.: +38-0322-707401 Fax: +38-0322-761158 --- On Mon, 10/10/11, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: Re: [Pw_forum] problems with pp.x for parallel processing > To: "PWSCF Forum" > Date: Monday, October 10, 2011, 12:34 AM > On Sat, 2011-10-08 at 22:54 -0700, > Natalia Pavlenko wrote: > > > I know that pp.x works well without k-parallelization > > I had understood the opposite from one of your previous > messages > > >? but for this I need to recalculate nscf with > wf_collect > > which takes pretty much time and more memory sources. > > if you run the nscf calcul;ation with npool*nproc_pool > processors, > you may actually run the postprocessing on nproc_pool > processors > with npool=1. You have to remove the following lines from > postproc.f90: > IF (nproc /= nproc_file .and. .not. twfcollect .and. > needwf)? & > ? ???CALL errore('postproc',& > ? ???'pw.x run with a different number > of processors. Use > wf_collect=.true.',1) > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, > Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mourad_fsm at yahoo.fr Thu Oct 20 17:31:30 2011 From: mourad_fsm at yahoo.fr (debbichi mourad) Date: Thu, 20 Oct 2011 16:31:30 +0100 (BST) Subject: [Pw_forum] Tr : error band structure of ZnO In-Reply-To: <1318757922.122.YahooMailClassic@web25703.mail.ukl.yahoo.com> References: <1318503054.33306.YahooMailNeo@web29513.mail.ird.yahoo.com> <1318757922.122.YahooMailClassic@web25703.mail.ukl.yahoo.com> Message-ID: <1319124690.48232.YahooMailNeo@web29518.mail.ird.yahoo.com> hi, I have the same problem when I delete nbnd=18. Thanks for help DEBBICHI Mourad Unit?de Recherche Physique desSolides,99/UR/13-19, D?partementde Physique, Facult?des Science deMonastir, Avenue del'Environnement 5019, MonastirTunisie. t?l:+21697487042 mourad_fsm at yahoo.fr ----- Mail transf?r? ----- De?: A.ouahab ??: debbichi mourad ; PWSCF Forum Envoy?le : Dimanche 16 Octobre 2011 10h38 Objet?: Re : [Pw_forum] error band structure of ZnO Salam Essayed'enlevernband=18, etrelancelescaluls AbdelouahabOUAHAB D?partementdesScienses physiques Universit?deOuargla Alg?rie --- En date de?: Jeu 13.10.11, debbichi mourad a ?crit?: >De: debbichi mourad >Objet: [Pw_forum] error band structure of ZnO >?: "pw_forum at pwscf.org" >Date: Jeudi 13 octobre 2011, 12h50 > > > > > > >Dear QE users, > >I am a new user of QE.? when I went to test the band structure calculation on material ZnO (ibrav=4) with this input file ,I got error band structue (flatt band dispersion). > >?calculation='bands' >??? pseudo_dir = '$PSEUDO_DIR/', >??? outdir='$TMP_DIR/', >??? prefix='ZnO' >?/ >?&system >? ibrav = 4, nbnd =18, >?????????????????? celldm(1) = 6.213, >?????????????????? celldm(3) = 1.610, >???????????????????????? nat = 4, >??????????????????????? ntyp = 2, >???????????????????? ecutwfc = 40, >???????????????????? ecutrho = 240 , >??? occupations ='smearing', >smearing ='methfessel-paxton', >degauss = 0.05, >?/ >?&electrons >???????????????? mixing_mode = 'plain' , >???????????????? mixing_beta = 0.7 , >???????????? diagonalization = 'david' , >??????????? conv_thr = 1.0d-8, >?/ >ATOMIC_SPECIES >?Zn?? 65.39200? Zn.pbe-van.UPF >? O?? 16.00000? O.pbe-rrkjus.UPF >ATOMIC_POSITIONS >?? Zn????? 0.666666667??? 0.333333333??? 0.000000000 >?? Zn????? 0.333333333??? 0.666666667??? 0.500000000 >??? O????? 0.666666667??? 0.333333333??? 0.380000000 >?? O????? 0.333333333??? 0.666666667??? 0.880000000 >K_POINTS >9 >?? 0.0000000000???? 0.0000000000???? 0.0000000000??? 1 >?? 0.5000000000???? 0.0000000000???? 0.5000000000??? 2 >?? 0.5000000000???? 0.0000000000???? 0.0000000000??? 3 >?? 0.3333333333???? 0.3333333333???? 0.5000000000??? 4 >?? 0.0000000000???? 0.0000000000???? 0.5000000000??? 5 >?? 0.0000000000???? 0.0000000000???? 0.0000000000??? 6 >?? 0.0000000000???? 0.5000000000???? 0.5000000000??? 7 >? 0.3333333333??? 0.3333333333???? 0.0000000000???? 8 >?? 0.3333333333???? 0.6666666667??? 0.5000000000??? 9 > >thanks for help >?? > > >DEBBICHI Mourad >Unit?de Recherche Physique desSolides,99/UR/13-19, >D?partementde Physique, Facult?des Science deMonastir, >Avenue del'Environnement 5019, MonastirTunisie. >t?l:+21697487042 >mourad_fsm at yahoo.fr > > >-----La pi?cejointeassoci?e suit----- > > >_______________________________________________ >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/20111020/fc3eaa09/attachment-0001.htm From Lorenzo.Paulatto at impmc.upmc.fr Thu Oct 20 17:42:36 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 20 Oct 2011 17:42:36 +0200 Subject: [Pw_forum] error band structure of ZnO In-Reply-To: <1318503054.33306.YahooMailNeo@web29513.mail.ird.yahoo.com> References: <1318495761.665.YahooMailNeo@web29503.mail.ird.yahoo.com> <1318503054.33306.YahooMailNeo@web29513.mail.ird.yahoo.com> Message-ID: On Thu, 13 Oct 2011 12:50:54 +0200, debbichi mourad wrote: > ATOMIC_POSITIONS > Zn 0.666666667 0.333333333 0.000000000 > Zn 0.333333333 0.666666667 0.500000000 > O 0.666666667 0.333333333 0.380000000 > O 0.333333333 0.666666667 0.880000000 This choice of atomic positions seems to be appropriate for "crystal" coordinates (i.e. coordinates as linear combination of the lattice vectors), but you are using "cartesian" coordinates (i.e. x,y,z coordinates using celldm(1) as the unit of measure) which is the default for pw.x. In order to use crystal coordinates you have to specify the keyword "crystal" after ATOMIC_POSITIONS (on the same line). > K_POINTS What I said for the atoms hold for the k point too, and BTW why are you specifying them by hand? Normally automatically generated points are perfectly fine (and way less cumbersome to check). bests -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From giannozz at democritos.it Thu Oct 20 17:49:14 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 20 Oct 2011 17:49:14 +0200 Subject: [Pw_forum] problems with pp.x for parallel processing In-Reply-To: <1319118521.67019.YahooMailClassic@web5716.biz.mail.ne1.yahoo.com> References: <1319118521.67019.YahooMailClassic@web5716.biz.mail.ne1.yahoo.com> Message-ID: <3560DF7F-2B71-477F-B040-E82ED1BC36DA@democritos.it> On Oct 20, 2011, at 15:48 , Natalia Pavlenko wrote: > thank you for your help with pp.x, after removing the > lines in postproc.f90 mentioned in your last message, > I have recomplied it and now it works well without > k-parallelization and with wf_collect=.true. in the scf-input. ...and I am no longer sure what the preblem was, because I have tried again to fix it and cannot reproduce it any longer...P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From wparker at anl.gov Thu Oct 20 18:05:31 2011 From: wparker at anl.gov (William Parker) Date: Thu, 20 Oct 2011 11:05:31 -0500 Subject: [Pw_forum] Zn NC_PP from qe-forge In-Reply-To: <4E9F83B4.10609@wm.edu> References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> <6669DB08-98EE-4E1B-B471-0CC2F167E2DA@anl.gov> <4E9F83B4.10609@wm.edu> Message-ID: <8EC42FD1-AADF-4368-91EB-34008CD7DB1C@anl.gov> Thanks, Eric, for the insight. That core correction can be vicious. Turning up the density cutoff does help. There is still oscillation in the total energy at the 100 micro-Ry (meV) level for density cutoff 16 times the wave function cutoff, but I guess one shouldn't expect too much stability at that level. https://wiki.alcf.anl.gov/wparker/images/6/68/ZnO_ecut_convergence_rho4_10_16_lda_ncpp.png --William On Oct 19, 2011, at 9:13 PM, Eric J. Walter wrote: > > Hi, > >> Just to double-check. Is charge density cutoff 4 times that planewave cutoff? > > I think that this hits on the issue... The Zn.pz-nc.UPF has a sharp > core correction. The FFT/Density grid > needs to be increased significantly, here is a plot of from 4x to 20x > ecutwfc for the case with and without > a core correction in Zn. I think this is the cause of the odd *ecutwfc* > shown by William Parker. > > http://dl.dropbox.com/u/8094696/Znplot.pdf > > So, in this case, no, the density cutoff needs to be higher: > > > Eric > > > > > On 10/19/2011 08:47 PM, Nichols A. Romero wrote: >> The behavior here is what I might expect for a real-space DFT code, >> but V_NL is evaluated in reciprocal space right (we don't have >> real-space projectors)? >> >> Just to double-check. Is charge density cutoff 4 times that planewave cutoff? >> >> >> On Wed, Oct 19, 2011 at 2:51 PM, William Parker wrote: >>> Dear Yun Song and interested parties, >>> >>> The possibility of a phonon test case in ZnO piqued my curiosity so I decided to have a go at it. I find a very odd convergence pattern with these two pseudopotentials in this system--the total energy has a damped sinusoidal decay with increasing cutoff: >>> (selecting the maxima and minima at 10 Ry sampling) >>> >>> E_cutoff (Ry) E_total (Ry) >>> 100 -338.741 >>> 160 -338.660 >>> 210 -338.675 >>> 290 -338.665 >>> 370 -338.668 >>> 400 -338.667 >>> >>> Figure here: https://wiki.alcf.anl.gov/wparker/images/b/b5/ZnO_ecut_convergence_lda_ncpp.png >>> Details here: https://wiki.alcf.anl.gov/wparker/index.php/Zinc_Oxide_Parameter_Convergence >>> >>> I have never encountered this kind of behavior with norm-conserving pseudopotentials before. At worst, I've seen little steps in an otherwise smooth convergence to a value. The eigenvalues at the various k-points don't appear to have any ghost states that come and go with cutoff. Has anyone observed this kind of oscillation in the total energy with increasing plane-wave cutoff before? What gives rise to it? >>> >>> --William >>> >>> ********************************************************* >>> William D. Parker >>> Computational Postdoctoral Fellow fax: (630) 252-4798 >>> MSD-212, Rm. C-215 >>> Argonne National Laboratory >>> 9700 S. Cass Ave. >>> Argonne, IL 60439 >>> ********************************************************* >>> >>> >>> >>> >>> _______________________________________________ >>> 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 ********************************************************* William D. Parker Computational Postdoctoral Fellow fax: (630) 252-4798 MSD-212, Rm. C-215 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 ********************************************************* From gkucukdalyan at gmail.com Thu Oct 20 21:48:23 2011 From: gkucukdalyan at gmail.com (Gulcin Kucukdalyan) Date: Thu, 20 Oct 2011 15:48:23 -0400 Subject: [Pw_forum] Running an input file In-Reply-To: <20111020105810.Horde.QNV_Qx8V4mxOn_KiEU62M1A@webmail.sissa.it> References: <20111020105810.Horde.QNV_Qx8V4mxOn_KiEU62M1A@webmail.sissa.it> Message-ID: Merhaba emine, Thanks a lot for your response. I hope this will help.I am studying at university of Akron, Oh, USA. Gulcin On Oct 20, 2011, at 4:58 AM, Emine Kucukbenli wrote: > > Merhaba Gulcin, > Try running the example input files in the examples directory. > You will see that every run_example is nothing but a script that > generates the input files (text) and > invokes the necessary executable (such as pw.x). > you can take a look at run_example, it is not binary. > > If you suspect you are missing something in the format of input files, > just edit one of the input files generated by the run_example > to represent your system and calculation. > > to understand the keywords used take a look at their descriptions. > The following is the description of input for pw.x executable: > > http://www.quantum-espresso.org/input-syntax/INPUT_PW.html > > You seem to be at the beginning of things, > if available, local help would let you advance faster than the mailing list. > If you provide your affiliation, > your chances of finding someone in your area/institute is higher, > cheers > > emine kucukbenli, phd student, sissa, italy > > Quoting Gulcin Kucukdalyan : > >> Dear Mohnish, >> >> Thanks a lot for your response. I am trying to prepare an input file >> for graphene. I just prepared a text file and tried to run it and >> did not work. I really cannot find detailed explanation about how to >> prepare an input file. Can you please suggest me any if exist? >> >> Gulcin >> >> On Oct 19, 2011, at 10:53 PM, mohnish pandey wrote: >> >>> Dear Gulcin ! >>> >>> To run an an input file for example an input file of pw.x you >>> should invoke the command for pw.x. /espresso directory/bin/pw.x >>> abc.scf.out. In this /espresso directory/ is the >>> address to espresso directory, "abc.scf.in" is the name of the QE >>> input file and "abc.scf.out" is the the QE output file. This is the >>> crudest way to run an input file. And next time please mention your >>> affiliation. Hope it helps. >>> >>> On Thu, Oct 20, 2011 at 2:22 AM, Gulcin Kucukdalyan >>> wrote: >>> HI All, >>> >>> Could you please tell me how can i run an input file. It is the >>> second time i am asking this question. Last time i was asked to >>> read tutorials. It is not specified there if i have to prepare a >>> text file or an executable file (run_example) like the ones in the >>> examples. If i have to prepare a text file how can i run it. >>> >>> Thanks, >>> >>> Gulcin >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> >>> >>> -- >>> Regards, >>> MOHNISH, >>> ----------------------------------------------------------------- >>> Mohnish Pandey >>> BTech-Mtech, IIT Kanpur >>> Senior Project Associate, >>> Department of Chemical Engineering, >>> IIT KANPUR, UP, INDIA >>> ----------------------------------------------------------------- >>> >>> _______________________________________________ >>> 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 hqzhou at nju.edu.cn Fri Oct 21 07:30:57 2011 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Fri, 21 Oct 2011 13:30:57 +0800 Subject: [Pw_forum] Running an input file References: Message-ID: Gulicin, It seems you may be a totally beginner in using LINUX/UNIX OS, too. If it's true, just forget the example script for a moment, and prepare an input file of pwscf, then run $ /bin/pw.x -input your_input_file.inp or if you have access to a parallel computer: $ mpirun -np 4 /bin/pw.x -input your_input_file.inp hope this help you. zhou huiqun @earth sciences, nanjing university, china ----- Original Message ----- From: Gulcin Kucukdalyan To: pw_forum at pwscf.org Sent: Thursday, October 20, 2011 4:52 AM Subject: [Pw_forum] Running an input file HI All, Could you please tell me how can i run an input file. It is the second time i am asking this question. Last time i was asked to read tutorials. It is not specified there if i have to prepare a text file or an executable file (run_example) like the ones in the examples. If i have to prepare a text file how can i run it. Thanks, Gulcin ------------------------------------------------------------------------------ _______________________________________________ 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/20111021/e3b92699/attachment.htm From mohnish.iitk at gmail.com Fri Oct 21 07:50:39 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 21 Oct 2011 11:20:39 +0530 Subject: [Pw_forum] error band structure of ZnO In-Reply-To: References: <1318495761.665.YahooMailNeo@web29503.mail.ird.yahoo.com> <1318503054.33306.YahooMailNeo@web29513.mail.ird.yahoo.com> Message-ID: Dear Dr. Paulatto, The automatically generated k-points may not be in the high symmetry direction in which one may want to plot the band structure. Am I right? On Thu, Oct 20, 2011 at 9:12 PM, Lorenzo Paulatto < Lorenzo.Paulatto at impmc.upmc.fr> wrote: > On Thu, 13 Oct 2011 12:50:54 +0200, debbichi mourad > wrote: > > ATOMIC_POSITIONS > > Zn 0.666666667 0.333333333 0.000000000 > > Zn 0.333333333 0.666666667 0.500000000 > > O 0.666666667 0.333333333 0.380000000 > > O 0.333333333 0.666666667 0.880000000 > > This choice of atomic positions seems to be appropriate for "crystal" > coordinates (i.e. coordinates as linear combination of the lattice > vectors), but you are using "cartesian" coordinates (i.e. x,y,z > coordinates using celldm(1) as the unit of measure) which is the default > for pw.x. > > In order to use crystal coordinates you have to specify the keyword > "crystal" after ATOMIC_POSITIONS (on the same line). > > > > K_POINTS > > What I said for the atoms hold for the k point too, and BTW why are you > specifying them by hand? Normally automatically generated points are > perfectly fine (and way less cumbersome to check). > > bests > > > -- > Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111021/c7f7b0e2/attachment-0001.htm From giannozz at democritos.it Fri Oct 21 09:10:39 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Oct 2011 09:10:39 +0200 Subject: [Pw_forum] error band structure of ZnO In-Reply-To: References: <1318495761.665.YahooMailNeo@web29503.mail.ird.yahoo.com> <1318503054.33306.YahooMailNeo@web29513.mail.ird.yahoo.com> Message-ID: <1319181039.31930.6.camel@fe12lx.fisica.uniud.it> On Fri, 2011-10-21 at 11:20 +0530, mohnish pandey wrote: > The automatically generated k-points may not be in the > high symmetry direction in which one may want to plot > the band structure autimatically generated k-points form a uniform grid in the Brillouin Zone. Typically they aren't suitable for a band structure plot P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From lorenzo.paulatto at impmc.upmc.fr Fri Oct 21 09:16:37 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 21 Oct 2011 09:16:37 +0200 Subject: [Pw_forum] error band structure of ZnO In-Reply-To: References: <1318495761.665.YahooMailNeo@web29503.mail.ird.yahoo.com> <1318503054.33306.YahooMailNeo@web29513.mail.ird.yahoo.com> Message-ID: In data 21 ottobre 2011 alle ore 07:50:39, mohnish pandey ha scritto: > The automatically generated k-points may not be in the high symmetry > direction in which one may want to plot the band structure. Am I right? Indeed, i did not notice it was a band calculation.. yet the points chosen by Debbichi are not forming a typical BZ path either; I guess everybody is free to put his k-points wherever he wishes :-) -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From mourad_fsm at yahoo.fr Fri Oct 21 10:34:14 2011 From: mourad_fsm at yahoo.fr (debbichi mourad) Date: Fri, 21 Oct 2011 09:34:14 +0100 (BST) Subject: [Pw_forum] Tr : Pw_forum Digest, Vol 52, Issue 61 In-Reply-To: References: Message-ID: <1319186054.7951.YahooMailNeo@web29519.mail.ird.yahoo.com> ?Hi, thanks for hepl what are the values k-points ??that? can I use in this case thanks ? DEBBICHI Mourad Unit? de Recherche Physique des Solides,99/UR/13-19, D?partement de Physique, Facult? des Science de Monastir, Avenue de l'Environnement 5019, Monastir Tunisie. t?l:+21697487042 mourad_fsm at yahoo.fr ----- Mail transf?r? ----- De?: "pw_forum-request at pwscf.org" ??: pw_forum at pwscf.org Envoy? le : Vendredi 21 Octobre 2011 8h50 Objet?: Pw_forum Digest, Vol 52, Issue 61 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. Re: error band structure of ZnO (Paolo Giannozzi) ? 2. Re: error band structure of ZnO (Lorenzo Paulatto) ---------------------------------------------------------------------- Message: 1 Date: Fri, 21 Oct 2011 09:10:39 +0200 From: Paolo Giannozzi Subject: Re: [Pw_forum] error band structure of ZnO To: PWSCF Forum Message-ID: <1319181039.31930.6.camel at fe12lx.fisica.uniud.it> Content-Type: text/plain On Fri, 2011-10-21 at 11:20 +0530, mohnish pandey wrote: > The automatically generated k-points may not be in the > high symmetry direction in which one may want to plot > the band structure autimatically generated k-points form a uniform grid in the Brillouin Zone. Typically they aren't suitable for a band structure plot P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy ------------------------------ Message: 2 Date: Fri, 21 Oct 2011 09:16:37 +0200 From: "Lorenzo Paulatto" Subject: Re: [Pw_forum] error band structure of ZnO To: "PWSCF Forum" Message-ID: Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes In data 21 ottobre 2011 alle ore 07:50:39, mohnish pandey? ha scritto: > The automatically generated k-points may not be in the high symmetry > direction in which one may want to plot the band structure. Am I right? Indeed, i did not notice it was a band calculation.. yet the points chosen? by Debbichi are not forming a typical BZ path either; I guess everybody is? free to put his k-points wherever he wishes :-) -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www:? http://www.impmc.upmc.fr/~paulatto/ mail:? 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 ------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum End of Pw_forum Digest, Vol 52, Issue 61 **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111021/caaeb7b1/attachment.htm From mohnish.iitk at gmail.com Fri Oct 21 12:34:48 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 21 Oct 2011 16:04:48 +0530 Subject: [Pw_forum] Tr : Pw_forum Digest, Vol 52, Issue 61 In-Reply-To: <1319186054.7951.YahooMailNeo@web29519.mail.ird.yahoo.com> References: <1319186054.7951.YahooMailNeo@web29519.mail.ird.yahoo.com> Message-ID: Dear Debbichi, The k-point grid for the phonon calculation depends upon the symmetry direction in which you want to plot the band structure. Please see some basic solid state physics book for the same. You will get the better idea. And use fine mesh for better calculation. Information will be available in Marder's solid state physics book, and some basic crystallography books... On Fri, Oct 21, 2011 at 2:04 PM, debbichi mourad wrote: > Hi, > thanks for hepl > what are the values k-points ??that can I use in this case > thanks > > DEBBICHI Mourad > Unit? de Recherche Physique des Solides,99/UR/13-19, > D?partement de Physique, Facult? des Science de Monastir, > Avenue de l'Environnement 5019, Monastir Tunisie. > t?l:+21697487042 > mourad_fsm at yahoo.fr > ----- Mail transf?r? ----- > *De :* "pw_forum-request at pwscf.org" > *? :* pw_forum at pwscf.org > *Envoy? le :* Vendredi 21 Octobre 2011 8h50 > *Objet :* Pw_forum Digest, Vol 52, Issue 61 > > 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. Re: error band structure of ZnO (Paolo Giannozzi) > 2. Re: error band structure of ZnO (Lorenzo Paulatto) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 21 Oct 2011 09:10:39 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] error band structure of ZnO > To: PWSCF Forum > Message-ID: <1319181039.31930.6.camel at fe12lx.fisica.uniud.it> > Content-Type: text/plain > > On Fri, 2011-10-21 at 11:20 +0530, mohnish pandey wrote: > > > > The automatically generated k-points may not be in the > > high symmetry direction in which one may want to plot > > the band structure > > autimatically generated k-points form a uniform grid > in the Brillouin Zone. Typically they aren't suitable > for a band structure plot > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > > > ------------------------------ > > Message: 2 > Date: Fri, 21 Oct 2011 09:16:37 +0200 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] error band structure of ZnO > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 21 ottobre 2011 alle ore 07:50:39, mohnish pandey > ha scritto: > > The automatically generated k-points may not be in the high symmetry > > direction in which one may want to plot the band structure. Am I right? > > > Indeed, i did not notice it was a band calculation.. yet the points chosen > > by Debbichi are not forming a typical BZ path either; I guess everybody is > > free to put his k-points wherever he wishes :-) > > > > -- > Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 52, Issue 61 > **************************************** > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111021/bec384ce/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Fri Oct 21 16:25:08 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 21 Oct 2011 16:25:08 +0200 Subject: [Pw_forum] normal modes visualization In-Reply-To: <20111020131729.Horde.exHRFR8V4mxOoANJ88A1vSA@webmail.sissa.it> References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> <20111020125205.ax8wq549i5ckc4s4@webmail.sic.rm.cnr.it> <20111020131729.Horde.exHRFR8V4mxOoANJ88A1vSA@webmail.sissa.it> Message-ID: <201110211625.09210.giuseppe.mattioli@mlib.ism.cnr.it> Dear Emile (and all) Only one further question. I've run the CH4 example (pw.x, ph.x, and dynmat.x). the dynmat.x calculation produce a series of files. dynmat.axsf contains the previously mentioned forces on ions (there is also a dynmat.mold file which seems to contain normal modes, to be opened with molden; I will give a try...). The standard output of dynmat.x contains a list of CH3 normal modes: # mode [cm-1] [THz] IR 1 0.00 0.0000 0.0000 2 0.00 0.0000 0.0000 3 0.00 0.0000 0.0000 4 0.00 0.0000 0.0000 5 0.00 0.0000 0.0000 6 0.00 0.0000 0.0000 7 1262.12 37.8372 0.3460 8 1263.53 37.8796 0.3438 9 1265.00 37.9235 0.3451 10 1482.79 44.4527 0.0000 11 1483.78 44.4823 0.0000 12 2947.63 88.3671 0.0000 13 3069.30 92.0148 0.4037 14 3070.51 92.0509 0.4045 15 3071.15 92.0701 0.4038 I was wondering how the last column (IR) is related to the infrared dipole matrix or oscillator strenght. The Herzberg bible says indeed that "all four are Raman active but only the two triply degenerate vibrations are infrared active". Thanks again Giuseppe On Thursday 20 October 2011 13:17:29 Emine Kucukbenli wrote: > Ciao Giuseppe, > > Yes there is a small program that does that : dynmat.x > Call it like this: > $espresso_dir/bin/dynmat.x > > then feed this one line input (no need for a separate input file) > &input fildyn='yourfile' / > > it produces dynmat.axsf where the normal modes are represented as > forces in xcrysden, > an animated xsf file, one frame per mode. > > xcrysden --axsf dynmat.axsf > > This is how it was working last time i checked, i dont think anything > has changed.. > emine kucukbenli, phd student, sissa, italy > > ps: after writing i remembered this: > http://people.sissa.it/~degironc/QE-Tutorial/tutorial_phon.htm > check the "Phonons at Gamma point" section - last bit. > > Quoting giuseppe.mattioli at mlib.ism.cnr.it: > > Dear all > > Does anybody know if there is any post-processing tool which allows > > one to visualize normal modes calculated with phonon.x or phcg.x in > > real space, as, for instance, ion displacement movies to be opened > > with xcrysden or xmakemol? > > Thank you in advance > > > > Giuseppe > > > > Giuseppe Mattioli > > ISM-CNR > > 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 -- ******************************************************** - 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 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From giuseppe.mattioli at mlib.ism.cnr.it Fri Oct 21 16:28:28 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 21 Oct 2011 16:28:28 +0200 Subject: [Pw_forum] normal modes visualization In-Reply-To: <201110211625.09210.giuseppe.mattioli@mlib.ism.cnr.it> References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> <20111020131729.Horde.exHRFR8V4mxOoANJ88A1vSA@webmail.sissa.it> <201110211625.09210.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <201110211628.28667.giuseppe.mattioli@mlib.ism.cnr.it> Emine, of course... > On Thursday 20 October 2011 13:17:29 Emine Kucukbenli wrote: > > Ciao Giuseppe, > > > > Yes there is a small program that does that : dynmat.x > > Call it like this: > > $espresso_dir/bin/dynmat.x > > > > then feed this one line input (no need for a separate input file) > > &input fildyn='yourfile' / > > > > it produces dynmat.axsf where the normal modes are represented as > > forces in xcrysden, > > an animated xsf file, one frame per mode. > > > > xcrysden --axsf dynmat.axsf > > > > This is how it was working last time i checked, i dont think anything > > has changed.. > > emine kucukbenli, phd student, sissa, italy > > > > ps: after writing i remembered this: > > http://people.sissa.it/~degironc/QE-Tutorial/tutorial_phon.htm > > check the "Phonons at Gamma point" section - last bit. > > > > Quoting giuseppe.mattioli at mlib.ism.cnr.it: > > > Dear all > > > Does anybody know if there is any post-processing tool which allows > > > one to visualize normal modes calculated with phonon.x or phcg.x in > > > real space, as, for instance, ion displacement movies to be opened > > > with xcrysden or xmakemol? > > > Thank you in advance > > > > > > Giuseppe > > > > > > Giuseppe Mattioli > > > ISM-CNR > > > 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 -- ******************************************************** - 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 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From giannozz at democritos.it Fri Oct 21 16:32:07 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Oct 2011 16:32:07 +0200 Subject: [Pw_forum] normal modes visualization In-Reply-To: <201110211625.09210.giuseppe.mattioli@mlib.ism.cnr.it> References: <1319030493.62265.YahooMailClassic@web15806.mail.cnb.yahoo.com> <20111020125205.ax8wq549i5ckc4s4@webmail.sic.rm.cnr.it> <20111020131729.Horde.exHRFR8V4mxOoANJ88A1vSA@webmail.sissa.it> <201110211625.09210.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: On Oct 21, 2011, at 16:25 , Giuseppe Mattioli wrote: > I was wondering how the last column (IR) is related > to the infrared dipole matrix or oscillator strenght. the last column IS the infrared oscillator strength P. -------------- next part -------------- A non-text attachment was scrubbed... Name: IR-raman.pdf Type: application/pdf Size: 64418 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111021/6317125d/attachment-0001.pdf -------------- next part -------------- --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From michelepisarra at yahoo.it Fri Oct 21 17:19:05 2011 From: michelepisarra at yahoo.it (Michele Pisarra) Date: Fri, 21 Oct 2011 16:19:05 +0100 (BST) Subject: [Pw_forum] WaveFunctions and eigenvectors Message-ID: <1319210345.45857.YahooMailNeo@web27003.mail.ukl.yahoo.com> Hi, Is it possible to obtain the converged wave functions at the end of the SCF calculation? I've seen some precedent post to the forum where the pp.x?postprocessing was suggested, but I?wasn't able to find what I serched for. I need the one electron wave functions?for each k point of the BZ sampling used in the calculation. What I need to do is to calculate some matrix element?of one- and two-electrons operators; in fact I have to do some integrals?so what I need are the basis functions (the plane waves or the corresponding K) and the expansion coefficients.? I suppose that they are stored somewhere, I think the prefix.wfc1 file but I wasn't able to find a file convereter in the post processing folder. Thank you in advance. Best Regards, Michele ? Michele Pisarra, PhD Student, Dipartimento di Fisica, Universit? della Calabria Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111021/8f3fdd5b/attachment.htm From bdslipun at gmail.com Fri Oct 21 17:23:44 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Fri, 21 Oct 2011 20:53:44 +0530 Subject: [Pw_forum] themal conductivity Message-ID: i want to know how can thermal conductivity can be calculated by help of espresso code is there any code which supports this i want to know how optical properties can calculated -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111021/43a7f67b/attachment.htm From giannozz at democritos.it Fri Oct 21 19:31:11 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 21 Oct 2011 19:31:11 +0200 Subject: [Pw_forum] charge density In-Reply-To: References: Message-ID: <16048F48-30CB-4754-AB52-4622BD7F59C4@democritos.it> On Oct 19, 2011, at 18:38 , mohaddeseh abbasnejad wrote: > When I try to plot the charge density for my case, the core regions > seem > to be empty. I wonder what am I missing during the post processing? you are missing nothing. The (pseudo-)charge density inside core regions is very small. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From bdslipun at gmail.com Fri Oct 21 20:09:26 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Fri, 21 Oct 2011 23:39:26 +0530 Subject: [Pw_forum] convergence Message-ID: i have used the espresso file which is given i want to convergence it but it is not converging after many itteration also i have incresed nstep and eletron step to high nothing results the input file is the input file for uspex code where kpoints and positions are written by itself the eroor is that force convergence is not achived the file is given b d sahoo reserch scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111021/a0e5c16d/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: bds.docx Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document Size: 13509 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111021/a0e5c16d/attachment-0001.bin From baroni at sissa.it Fri Oct 21 21:24:56 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 21 Oct 2011 21:24:56 +0200 Subject: [Pw_forum] convergence In-Reply-To: References: Message-ID: <7F346219-4D4A-4C3A-8C7B-2F934B098122@sissa.it> a word file to transmit a QE input? oh my goodness! SB On Oct 21, 2011, at 8:09 PM, bhabya sahoo wrote: > i have used the espresso file which is given > i want to convergence it but it is not converging > after many itteration > also i have incresed nstep and eletron step to high nothing results > > > the input file is the input file for uspex code > where kpoints and positions are written by itself > > > > the eroor is that > force convergence is not achived > > > the file is given > > > > > > > > > > > b d sahoo > reserch scholar > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111021/34933499/attachment.htm From akohlmey at gmail.com Fri Oct 21 21:41:29 2011 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Fri, 21 Oct 2011 15:41:29 -0400 Subject: [Pw_forum] convergence In-Reply-To: <7F346219-4D4A-4C3A-8C7B-2F934B098122@sissa.it> References: <7F346219-4D4A-4C3A-8C7B-2F934B098122@sissa.it> Message-ID: On Fri, Oct 21, 2011 at 3:24 PM, Stefano Baroni wrote: > a word file to transmit a QE input? > oh my goodness! it is the best way to shoot yourself in the foot! this way it is guaranteed that nobody will look at it. ;) ciao, axel. > SB > On Oct 21, 2011, at 8:09 PM, bhabya sahoo wrote: > > i have used the espresso file which is given > i want to convergence it but it is not converging > after many itteration > also i have incresed nstep and eletron step to high nothing results > > the input file is the input file for uspex code > where kpoints and positions are written by itself > > > the eroor is that > force convergence is not achived > > the file is given > > > > > > > > > > b d sahoo > reserch scholar > _______________________________________________ > 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA. From bdslipun at gmail.com Fri Oct 21 21:41:51 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sat, 22 Oct 2011 01:11:51 +0530 Subject: [Pw_forum] convergence In-Reply-To: <7F346219-4D4A-4C3A-8C7B-2F934B098122@sissa.it> References: <7F346219-4D4A-4C3A-8C7B-2F934B098122@sissa.it> Message-ID: no the input is given in the input format produced by pwgui it works and the bfgs optimisation runs but at the end the warning comes to reduce conv-threshold shall there may be some modification to the file [image: Reply] [image: More] So, here is the file qEspresso_options_1: &CONTROL calculation = "relax", restart_mode = "from_scratch", prefix = "pp", pseudo_dir = "./", outdir = "./", wf_collect = false nstep = 35 disk_io = 'none' / &SYSTEM ibrav = 0 nat = 8 ntyp = 1 ecutwfc = 40.D0 nosym = .true. occupations='smearing' degauss=0.02 smearing='marzari-vanderbilt' / &ELECTRONS conv_thr = 5.D-04, mixing_beta=0.5, electron_maxstep = 250 / &IONS ion_dynamics='bfgs' trust_radius_max = 0.2 / ATOMIC_SPECIES C 12. C.pbe-van_bm.upf On Sat, Oct 22, 2011 at 12:54 AM, Stefano Baroni wrote: > a word file to transmit a QE input? > oh my goodness! > SB > On Oct 21, 2011, at 8:09 PM, bhabya sahoo wrote: > > i have used the espresso file which is given > i want to convergence it but it is not converging > after many itteration > also i have incresed nstep and eletron step to high nothing results > > > the input file is the input file for uspex code > where kpoints and positions are written by itself > > > > the eroor is that > force convergence is not achived > > > the file is given > > > > > > > > > > > b d sahoo > reserch scholar > > _______________________________________________ > 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 > > > _______________________________________________ > 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/20111022/fc27a66d/attachment.htm From kucukben at sissa.it Fri Oct 21 23:06:01 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Fri, 21 Oct 2011 23:06:01 +0200 Subject: [Pw_forum] convergence In-Reply-To: References: <7F346219-4D4A-4C3A-8C7B-2F934B098122@sissa.it> Message-ID: <20111021230601.Horde.6LpxTh8V4mxOod65LEwW0WA@webmail.sissa.it> Hello Bhabya Darsan, > but at the end the warning comes to reduce conv-threshold > shall there may be some modification to the file Yes this is exactly the modification you need: Reduce the convergence threshold conv_thr. The force threshold you are using is the default 1d-3 You should not expect precise forces when the energy is calculated almost within the same precision. Also, this issue was previously discussed in the mailing list: http://www.democritos.it/pipermail/pw_forum/2009-March/012104.html cheers emine kucukbenli, phd student, sissa, italy From lapenna.giovanni at gmail.com Fri Oct 21 23:53:04 2011 From: lapenna.giovanni at gmail.com (Giovanni La Penna) Date: Fri, 21 Oct 2011 23:53:04 +0200 Subject: [Pw_forum] charge density In-Reply-To: References: Message-ID: > > Dear QE users, > When I try to plot the charge density for my case, the core regions seem to > be empty. We filled the core with Slater approximation of atomic orbitals in real space. It is mandatory for Bader analysis. See Measuring electron sharing between atoms in first-principle simulations Giovanni La Penna, Sara Furlan and Miquel Sol? DOI: 10.1007/s00214-011-0955-3 Giovanni La Penna (Cnr-Iccom, Italy) From chengyu.young at gmail.com Sat Oct 22 19:25:13 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Sat, 22 Oct 2011 13:25:13 -0400 Subject: [Pw_forum] Binding energy of Cu@CNT Message-ID: Dear every one, I am now trying to calculate the binding energy of Cu at CNT, I used one cu atom per unit cell, which is cnt (6,6). First I optimized the structure of cnt and the cu at cnt structure, then I calculated the total energy of a single cu atom. I make hand calculations after I get all the total energy result. At first I used ultrasoft potential for both cu and cnt, but the result is about -1.6 ev, much different from around -0.1 ev in the literature. Then I changed the potential to PAW potential, for that is what's used in the literature, but it seems that the cu at cnt calculation won't converged and the calculation goes on for a day and a night. I don't know what's the problem, now I am posting my script and hope anybody could give me some advice. There may be some small error that I cannot recognize. Thank you beforehand. Case 1(using uspp): (1) cnt.in &CONTROL calculation = 'relax' restart_mode='from_scratch', tstress = .true. tprnfor = .true. outdir = '/home/student/espresso-4.3.1/tmp/' , pseudo_dir = '/home/student/espresso-4.3.1/pseudo/' , prefix = 'cnt' , / &SYSTEM ibrav = 6,celldm(1) = 21.764541128,celldm(3)=0.213765379 nat = 24,ntyp = 1,ecutwfc = 35 , occupations='smearing', smearing='gaussian', degauss=0.02 / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / &IONS bfgs_ndim = 3, upscale = 100.D0, pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES C 12.01100 C.pz-vbc.UPF ATOMIC_POSITIONS angstrom C 4.085165 -0.000000 -1.231010 C 3.838021 1.399343 -1.231010 C 3.537856 2.042582 0.000000 C 2.624152 3.130877 0.000000 C 2.042582 3.537856 -1.231010 C 0.707144 4.023496 -1.231010 C 0.000000 4.085165 0.000000 C -1.399343 3.838021 0.000000 C -2.042582 3.537856 -1.231010 C -3.130877 2.624152 -1.231010 C -3.537856 2.042582 0.000000 C -4.023496 0.707144 0.000000 C -4.085165 0.000000 -1.231010 C -3.838021 -1.399343 -1.231010 C -3.537856 -2.042582 0.000000 C -2.624152 -3.130877 0.000000 C -2.042582 -3.537856 -1.231010 C -0.707144 -4.023496 -1.231010 C -0.000000 -4.085165 0.000000 C 1.399343 -3.838021 0.000000 C 2.042582 -3.537856 -1.231010 C 3.130877 -2.624152 -1.231010 C 3.537856 -2.042582 0.000000 C 4.023496 -0.707144 0.000000 K_POINTS automatic 1 1 5 0 0 0 (2) cucnt.in &CONTROL calculation = 'relax' restart_mode='from_scratch', tstress = .true. tprnfor = .true. outdir = '/home/student/espresso-4.3.1/tmp/' , pseudo_dir = '/home/student/espresso-4.3.1/pseudo/' , prefix = 'cntcu' , / &SYSTEM ibrav = 6,celldm(1) = 21.764541128,celldm(3)=0.213765379 nat = 25,ntyp = 2,ecutwfc = 35 , occupations='smearing', smearing='gaussian', degauss=0.02 / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / &IONS bfgs_ndim = 3, upscale = 100.D0, pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES C 12.01100 C.pz-vbc.UPF Cu 63.55 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS angstrom C 4.085165 -0.000000 -1.231010 C 3.838021 1.399343 -1.231010 C 3.537856 2.042582 0.000000 C 2.624152 3.130877 0.000000 C 2.042582 3.537856 -1.231010 C 0.707144 4.023496 -1.231010 C 0.000000 4.085165 0.000000 C -1.399343 3.838021 0.000000 C -2.042582 3.537856 -1.231010 C -3.130877 2.624152 -1.231010 C -3.537856 2.042582 0.000000 C -4.023496 0.707144 0.000000 C -4.085165 0.000000 -1.231010 C -3.838021 -1.399343 -1.231010 C -3.537856 -2.042582 0.000000 C -2.624152 -3.130877 0.000000 C -2.042582 -3.537856 -1.231010 C -0.707144 -4.023496 -1.231010 C -0.000000 -4.085165 0.000000 C 1.399343 -3.838021 0.000000 C 2.042582 -3.537856 -1.231010 C 3.130877 -2.624152 -1.231010 C 3.537856 -2.042582 0.000000 C 4.023496 -0.707144 0.000000 Cu 0 0 0 K_POINTS automatic 1 1 5 0 0 0 (3) cu.in &CONTROL calculation='scf', restart_mode='from_scratch', outdir = '/home/student/espresso-4.3.1/tmp/' , pseudo_dir = '/home/student/espresso-4.3.1/pseudo/' , prefix = 'cu' , / &SYSTEM ibrav = 1,celldm(1)= 20, nat = 1,ntyp = 1,ecutwfc = 35 , occupations='smearing', smearing='gaussian', degauss=0.002 nspin = 2, starting_magnetization(1)=0.2 / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.3 , / ATOMIC_SPECIES Cu 63.546 Cu.pz-d-rrkjus.UPF ATOMIC_POSITIONS Cu 0.000000000 0.000000000 0.000000000 K_POINTS GAMMA Case 2:(using PAW potential) (1)cnt.in &CONTROL calculation = 'relax' restart_mode='from_scratch', tstress = .true. tprnfor = .true. outdir = '/home/student/espresso-4.3.1/tmp/' , pseudo_dir = '/home/student/espresso-4.3.1/pseudo/' , prefix = 'cnt' , / &SYSTEM ibrav = 6,celldm(1) = 21.764541128,celldm(3)=0.213765379 nat = 24,ntyp = 1,ecutwfc = 50 , occupations='smearing', smearing='gaussian', degauss=0.02 / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / &IONS bfgs_ndim = 3, upscale = 100.D0, pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES C 12.01100 C.pbe-mt_gipaw.UPF ATOMIC_POSITIONS angstrom C 4.085165 -0.000000 -1.231010 C 3.838021 1.399343 -1.231010 C 3.537856 2.042582 0.000000 C 2.624152 3.130877 0.000000 C 2.042582 3.537856 -1.231010 C 0.707144 4.023496 -1.231010 C 0.000000 4.085165 0.000000 C -1.399343 3.838021 0.000000 C -2.042582 3.537856 -1.231010 C -3.130877 2.624152 -1.231010 C -3.537856 2.042582 0.000000 C -4.023496 0.707144 0.000000 C -4.085165 0.000000 -1.231010 C -3.838021 -1.399343 -1.231010 C -3.537856 -2.042582 0.000000 C -2.624152 -3.130877 0.000000 C -2.042582 -3.537856 -1.231010 C -0.707144 -4.023496 -1.231010 C -0.000000 -4.085165 0.000000 C 1.399343 -3.838021 0.000000 C 2.042582 -3.537856 -1.231010 C 3.130877 -2.624152 -1.231010 C 3.537856 -2.042582 0.000000 C 4.023496 -0.707144 0.000000 K_POINTS automatic 1 1 5 0 0 0 (2) cucnt.in &CONTROL calculation = 'relax' restart_mode='from_scratch', tstress = .true. tprnfor = .true. outdir = '/home/student/espresso-4.3.1/tmp/' , pseudo_dir = '/home/student/espresso-4.3.1/pseudo/' , prefix = 'cntcu' , / &SYSTEM ibrav = 6,celldm(1) = 21.764541128,celldm(3)=0.213765379 nat = 25,ntyp = 2,ecutwfc = 50 , occupations='smearing', smearing='gaussian', degauss=0.02 / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / &IONS bfgs_ndim = 3, upscale = 100.D0, pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES C 12.01100 C.pbe-mt_gipaw.UPF Cu 63.55 Cu.pbe-paw_kj.UPF ATOMIC_POSITIONS angstrom C 4.085165 -0.000000 -1.231010 C 3.838021 1.399343 -1.231010 C 3.537856 2.042582 0.000000 C 2.624152 3.130877 0.000000 C 2.042582 3.537856 -1.231010 C 0.707144 4.023496 -1.231010 C 0.000000 4.085165 0.000000 C -1.399343 3.838021 0.000000 C -2.042582 3.537856 -1.231010 C -3.130877 2.624152 -1.231010 C -3.537856 2.042582 0.000000 C -4.023496 0.707144 0.000000 C -4.085165 0.000000 -1.231010 C -3.838021 -1.399343 -1.231010 C -3.537856 -2.042582 0.000000 C -2.624152 -3.130877 0.000000 C -2.042582 -3.537856 -1.231010 C -0.707144 -4.023496 -1.231010 C -0.000000 -4.085165 0.000000 C 1.399343 -3.838021 0.000000 C 2.042582 -3.537856 -1.231010 C 3.130877 -2.624152 -1.231010 C 3.537856 -2.042582 0.000000 C 4.023496 -0.707144 0.000000 Cu 0 0 0 K_POINTS automatic 1 1 5 0 0 0 (3) cu.in &CONTROL calculation='scf', restart_mode='from_scratch', outdir = '/home/student/espresso-4.3.1/tmp/' , pseudo_dir = '/home/student/espresso-4.3.1/pseudo/' , prefix = 'cu' , / &SYSTEM ibrav = 1,celldm(1)= 20, nat = 1,ntyp = 1,ecutwfc = 50 , occupations='smearing', smearing='gaussian', degauss=0.002 nspin = 2, starting_magnetization(1)=0.2 / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.3 , / ATOMIC_SPECIES Cu 63.546 Cu.pbe-paw_kj.UPF ATOMIC_POSITIONS Cu 0.000000000 0.000000000 0.000000000 K_POINTS GAMMA University of Central Florida MMAE Chengyu Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111022/d762d322/attachment.htm From chengyu.young at gmail.com Sat Oct 22 19:42:52 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Sat, 22 Oct 2011 13:42:52 -0400 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: References: Message-ID: Hi all, It seems that my script for single cu atom is wrong in case 2, cause I got a total energy of -212, which is far away from the usual value. The script for case 1 seems to be more correct, but I don't know how to achieve enough accuracy...... Thank you! Chengyu Yang MMAE, University of Central Florida, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111022/89347324/attachment-0001.htm From chengyu.young at gmail.com Sat Oct 22 20:32:55 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Sat, 22 Oct 2011 14:32:55 -0400 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: References: Message-ID: Sorry i found the total energ for paw potential is about -212, so there's no problem here. I just don't know how to get the enough accuracy as the literature. Or is there any way that can make the converge faster? If the case is a copper chain in a carbon nanotube, should I still set a single cu atom here with large unit cell? Or should I set up a copper chain and do the structure optimization? I am not quite sure because in one unit cell there's only one cu in cnt(6,6) . Thank you for somebody who could clarify this. Best regards. Chengyu Yang MMAE, University of Central Florida, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111022/db055aff/attachment.htm From giannozz at democritos.it Sat Oct 22 21:27:26 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 22 Oct 2011 21:27:26 +0200 Subject: [Pw_forum] WaveFunctions and eigenvectors In-Reply-To: <1319210345.45857.YahooMailNeo@web27003.mail.ukl.yahoo.com> References: <1319210345.45857.YahooMailNeo@web27003.mail.ukl.yahoo.com> Message-ID: On Oct 21, 2011, at 17:19 , Michele Pisarra wrote: > Is it possible to obtain the converged wave functions > at the end of the SCF calculation? of course it is > What I need to do is to calculate some matrix element of > one- and two-electrons operators the simplest way is to modify one of the post-processing codes to do what you need. epsilon.f90 calculates the dipole matrix elements, so it might be a god starting point P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Oct 22 21:31:05 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 22 Oct 2011 21:31:05 +0200 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: References: Message-ID: <1626F662-ECD2-44F6-88F2-511622C479CA@democritos.it> On Oct 22, 2011, at 19:25 , chengyu yang wrote: > At first I used ultrasoft potential for both cu and cnt, > but the result is about -1.6 ev, much different from > around -0.1 ev in the literature. > Then I changed the potential to PAW potential, > for that is what's used in the literature you also changed from LDA to PBE. It's not a minor difference, especially if the bonding is weak. Why don't you try a few simpler systems to start with? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From bdslipun at gmail.com Sun Oct 23 08:42:21 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 23 Oct 2011 12:12:21 +0530 Subject: [Pw_forum] convergence In-Reply-To: <20111021230601.Horde.6LpxTh8V4mxOod65LEwW0WA@webmail.sissa.it> References: <7F346219-4D4A-4C3A-8C7B-2F934B098122@sissa.it> <20111021230601.Horde.6LpxTh8V4mxOod65LEwW0WA@webmail.sissa.it> Message-ID: shall i reduce to force con-thershold to 10^-2 On Sat, Oct 22, 2011 at 2:36 AM, Emine Kucukbenli wrote: > Hello Bhabya Darsan, > > > but at the end the warning comes to reduce conv-threshold > > shall there may be some modification to the file > > Yes this is exactly the modification you need: > Reduce the convergence threshold conv_thr. > The force threshold you are using is the default 1d-3 > You should not expect precise forces when the energy is calculated > almost within > the same precision. > > Also, this issue was previously discussed in the mailing list: > http://www.democritos.it/pipermail/pw_forum/2009-March/012104.html > > cheers > emine kucukbenli, phd student, sissa, 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/20111023/cdc0f3b0/attachment.htm From kucukben at sissa.it Sun Oct 23 10:37:47 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Sun, 23 Oct 2011 10:37:47 +0200 Subject: [Pw_forum] convergence In-Reply-To: References: <7F346219-4D4A-4C3A-8C7B-2F934B098122@sissa.it> <20111021230601.Horde.6LpxTh8V4mxOod65LEwW0WA@webmail.sissa.it> Message-ID: <20111023103747.Horde.iO_CYB8V4mxOo9JbSem1PIA@webmail.sissa.it> Hi Bhabya, Well, I would reduce the conv_thr instead, probably to 1d-6 or smaller.. But in principle you can increase the forc_conv_thr=1d-2 and still get rid of the warning you have and probably of the convergence problem too. It all depends on what you want: =If this is a production run, you want accuracy, reduce conv_thr (try the default 1d-6 or smaller) =If this is a test system, a toy problem for you to learn how to run the code, or get some basic idea on the properties of the system that you have and timings of computation, and if your computational resources are tight, then increase forc_conv_thr. Basically, arrange the parameters of your calculations to match your needs. Perform some small tests when you are in doubt. cheers, emine kucukbenli, phd student, sissa, italy. ps: add your affiliation pls. was it Bhabha Atomic Research Centre, Mumbai? Quoting bhabya sahoo : > shall i reduce to force con-thershold to 10^-2 > > On Sat, Oct 22, 2011 at 2:36 AM, Emine Kucukbenli wrote: > >> Hello Bhabya Darsan, >> >> > but at the end the warning comes to reduce conv-threshold >> > shall there may be some modification to the file >> >> Yes this is exactly the modification you need: >> Reduce the convergence threshold conv_thr. >> The force threshold you are using is the default 1d-3 >> You should not expect precise forces when the energy is calculated >> almost within >> the same precision. >> >> Also, this issue was previously discussed in the mailing list: >> http://www.democritos.it/pipermail/pw_forum/2009-March/012104.html >> >> cheers >> emine kucukbenli, phd student, sissa, italy >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> From bdslipun at gmail.com Sun Oct 23 13:53:15 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 23 Oct 2011 17:23:15 +0530 Subject: [Pw_forum] convergence In-Reply-To: References: <7F346219-4D4A-4C3A-8C7B-2F934B098122@sissa.it> <20111021230601.Horde.6LpxTh8V4mxOod65LEwW0WA@webmail.sissa.it> Message-ID: yes bhaba atomic reserch center ok i have to check the parameter On Sun, Oct 23, 2011 at 12:12 PM, bhabya sahoo wrote: > shall i reduce to force con-thershold to 10^-2 > > > On Sat, Oct 22, 2011 at 2:36 AM, Emine Kucukbenli wrote: > >> Hello Bhabya Darsan, >> >> > but at the end the warning comes to reduce conv-threshold >> > shall there may be some modification to the file >> >> Yes this is exactly the modification you need: >> Reduce the convergence threshold conv_thr. >> The force threshold you are using is the default 1d-3 >> You should not expect precise forces when the energy is calculated >> almost within >> the same precision. >> >> Also, this issue was previously discussed in the mailing list: >> http://www.democritos.it/pipermail/pw_forum/2009-March/012104.html >> >> cheers >> emine kucukbenli, phd student, sissa, 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/20111023/3a89d0ee/attachment.htm From jayashree.pan at jncasr.ac.in Mon Oct 24 08:23:18 2011 From: jayashree.pan at jncasr.ac.in (jayashree.pan at jncasr.ac.in) Date: Mon, 24 Oct 2011 11:53:18 +0530 Subject: [Pw_forum] Partial phonon DOS Message-ID: <1319437398.4ea50456ad427@mercury.jncasr.ac.in> Hi, I am a new Quantum Espresso user. I am doing phonon calculation and I also want to do partial phonon DOS using QE. There are some old posts from Prof.Eyvaz Isaev and Dr. Subhradip Ghosh, where they ware talking about it. Please help me if anyone know how to do it. Thank you. Jayashree -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111024/5dd358f7/attachment.htm From flux_ray12 at 163.com Mon Oct 24 11:20:07 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Mon, 24 Oct 2011 17:20:07 +0800 (CST) Subject: [Pw_forum] Partial phonon DOS In-Reply-To: <1319437398.4ea50456ad427@mercury.jncasr.ac.in> References: <1319437398.4ea50456ad427@mercury.jncasr.ac.in> Message-ID: <4395d61f.12a32.133353ad334.Coremail.flux_ray12@163.com> You can just use QHA in QE after IFCs calculated, then ph-pdos will be obtained directly. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-24 14:23:18,"jayashree.pan at jncasr.ac.in" wrote: Hi, I am a new Quantum Espresso user. I am doing phonon calculation and I also want to do partial phonon DOS using QE. There are some old posts from Prof.Eyvaz Isaev and Dr.Subhradip Ghosh, where they ware talking about it. Please help me if anyone know how to do it. Thank you. Jayashree -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111024/a0faad14/attachment.htm From mariammalmir86 at gmail.com Mon Oct 24 12:53:19 2011 From: mariammalmir86 at gmail.com (mariam malmir) Date: Mon, 24 Oct 2011 14:23:19 +0330 Subject: [Pw_forum] problem Message-ID: Hello I am studying carbon nanotubes doped whith a magnatic atom. this system has been relaxed whit nspin=2 , starting_magnetization(1) = 0.9, and starting_magnetization(2) = 0.8 . is this true? befor doped carbon nanotube system relaxed whit nspin=1 , starting_magnetization(1) = 0.9 is this true? thanks for your advices -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111024/20ee82b6/attachment.htm From chengyu.young at gmail.com Mon Oct 24 20:41:17 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Mon, 24 Oct 2011 14:41:17 -0400 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: <1626F662-ECD2-44F6-88F2-511622C479CA@democritos.it> References: <1626F662-ECD2-44F6-88F2-511622C479CA@democritos.it> Message-ID: Thank you, Dr. Giannozzi . But my question is this: (1) How could I get the correct binding energy? May I use the C.pz-vbc.UPF and Cu.pz-d-rrkjus.UPF potential? Will the choice of potential affect the final result? (2) The literature I am reading used the projector-augmented wave(PAW) potential, and also the electron exchange and correlation is treated by using the Perdew burke Ernzerhof (PBE) formulation of the generalized gradient approximation. In fact I cannot find such potentials in all the pseudo files. (3) It also used conjugate-gradient algorithm to relax the ions, do we have this in our QE, or the algorithm are replaceable? I am sorry to ask, but advice from this forum is important to help. Thank you. Best regards. Chengyu Yang MMAE,University of Central Florida,US 2011/10/22 Paolo Giannozzi > > On Oct 22, 2011, at 19:25 , chengyu yang wrote: > > > At first I used ultrasoft potential for both cu and cnt, > > but the result is about -1.6 ev, much different from > > around -0.1 ev in the literature. > > Then I changed the potential to PAW potential, > > for that is what's used in the literature > > you also changed from LDA to PBE. It's not a minor difference, > especially if the bonding is weak. Why don't you try a few > simpler systems to start with? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > 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/20111024/3661f5e8/attachment.htm From baroni at sissa.it Mon Oct 24 21:26:52 2011 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 24 Oct 2011 21:26:52 +0200 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: References: <1626F662-ECD2-44F6-88F2-511622C479CA@democritos.it> Message-ID: Dear chengyu yang: > I am sorry to ask, but advice from this forum is important to help. Thanks for the appreciation, but remember that no forum is a real substitute for hard work ... Many of the questions that you (as well as many others) ask could be answered by yourself, just trying ... If you try and understand, then you wouldn't need to ask. If you do not understand, in spite of trying hard, then the answers to your legitimate (even more legitimate, after trying hard) questions would be much more instructive for you. Just a suggestion ... SB --- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111024/0de252b3/attachment.htm From chengyu.young at gmail.com Mon Oct 24 21:35:02 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Mon, 24 Oct 2011 15:35:02 -0400 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: References: <1626F662-ECD2-44F6-88F2-511622C479CA@democritos.it> Message-ID: Dear Dr. Baroni, I agree with your opinion, but my problems is that I am a material student, but I am doing research with a lot of physics, and nobody can give me much help but result is required. That's why I feel helpless sometimes. If I know in which direction should I work hard then i certainly would go. Thank you. Chengyu Yang MMAE, University of Central Florida,US 2011/10/24 Stefano Baroni > > Dear chengyu yang: > > I am sorry to ask, but advice from this forum is important to help. > > > Thanks for the appreciation, but remember that no forum is a real > substitute for hard work ... Many of the questions that you (as well as many > others) ask could be answered by yourself, just trying ... If you try and > understand, then you wouldn't need to ask. If you do not understand, in > spite of trying hard, then the answers to your legitimate (even more > legitimate, after trying hard) questions would be much more instructive for > you. > > Just a suggestion ... > > SB > > --- > 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 > > > _______________________________________________ > 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/20111024/6249139b/attachment.htm From carlo.nervi at unito.it Mon Oct 24 22:22:58 2011 From: carlo.nervi at unito.it (Carlo Nervi) Date: Mon, 24 Oct 2011 22:22:58 +0200 (CEST) Subject: [Pw_forum] GIPAW: error in output Message-ID: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it> Hello, I succesfully compiled QE 4.3.2 and the corresponding GIPAW module on a Opteron 6168 linux using gfortran 4.6, acml 5.0.0 and amdlibm 3.0.1. I did the benzene-scf.in job in the GIPAW/examples/benzene-USPP/ directory. The scf energy is the same as the reference output, which is in the same directory (apparently all is okay). I've compiled the gipaw module by the common way 'make gipaw' from the source QE dir. - I hope this was okay... The gipaw calculations proceed, apparently ends normally, but the output contains several NotaNumber (NaN). Anuone have an idea qhat's wrong or could please give some hints how to solve the problem? Thank you, Carlo ... negative rho (up, down): 0.103E-03 0.000E+00 init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333 init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333 init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333 init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333 init_gipaw_1: projectors nearly linearly dependent: ntyp = 1, l/n1/n2 = 0 2 1 0.99622328 init_gipaw_1: projectors nearly linearly dependent: ntyp = 1, l/n1/n2 = 1 2 1 0.99789339 init_paw_1: ntyp= 2 rc= 0.8000 rs= 0.5333 init_paw_1: ntyp= 2 rc= 0.8000 rs= 0.5333 init_gipaw_1: projectors nearly linearly dependent: ntyp = 2, l/n1/n2 = 0 2 1 0.99987400 GIPAW : 4.81s CPU 10.71s WALL Computing the magnetic susceptibility isolve=0 ethr=0.1000E-13 k-point # 1 of 1 pool # 1 ik 1 ibnd 16 linter: root not converged 0.305E+07 ik 1 ibnd 16 linter: root not converged 0.139E+31 ik 1 ibnd 16 linter: root not converged 0.122E+27 End of magnetic susceptibility calculation f-sum rule (1st term): ************** 0.0000 0.0000 0.0000 -29.8546 0.0000 0.0000 0.0000 -29.9120 f-sum rule (2nd term): -0.3248 0.0000 0.0000 0.0000 -0.3248 0.0000 ... Contributions to the NMR chemical shifts: ------------------------------- Core contribution in ppm: Atom 1 C pos: ( 0.000000 0.107679 0.000000) sigma: 200.51 Atom 2 C pos: ( 0.093253 0.053840 0.000000) sigma: 200.51 Atom 3 C pos: ( 0.093253 -0.053840 0.000000) sigma: 200.51 Atom 4 C pos: ( 0.000000 -0.107679 0.000000) sigma: 200.51 Atom 5 C pos: ( -0.093253 -0.053840 0.000000) sigma: 200.51 Atom 6 C pos: ( -0.093253 0.053840 0.000000) sigma: 200.51 Atom 7 H pos: ( 0.000000 0.191523 0.000000) sigma: 0.00 Atom 8 H pos: ( 0.165864 0.095761 0.000000) sigma: 0.00 Atom 9 H pos: ( 0.165864 -0.095761 0.000000) sigma: 0.00 Atom 10 H pos: ( 0.000000 -0.191523 0.000000) sigma: 0.00 Atom 11 H pos: ( -0.165864 -0.095761 0.000000) sigma: 0.00 Atom 12 H pos: ( -0.165864 0.095761 0.000000) sigma: 0.00 Bare contribution in ppm: Atom 1 C pos: ( 0.000000 0.107679 0.000000) sigma: NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN Atom 2 C pos: ( 0.093253 0.053840 0.000000) sigma: NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... Total NMR chemical shifts in ppm: --------------------------------------- Atom 1 C pos: ( 0.000000 0.107679 0.000000) sigma: NaN C 1 anisotropy: NaN eta: 0.0000 C 1 sigma_xx= NaN axis=( NaN NaN 0.000000) C 1 sigma_yy= NaN axis=( NaN NaN 0.000000) C 1 sigma_zz= NaN axis=( 0.000000 0.000000 1.000000) Atom 2 C pos: ( 0.093253 0.053840 0.000000) sigma: NaN C 2 anisotropy: NaN eta: 0.0000 C 2 sigma_xx= NaN axis=( NaN NaN 0.000000) C 2 sigma_yy= NaN axis=( NaN NaN 0.000000) C 2 sigma_zz= NaN axis=( 0.000000 0.000000 1.000000) -- ------------------------------------------------------ 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 dceresoli at gmail.com Tue Oct 25 10:00:29 2011 From: dceresoli at gmail.com (Davide Ceresoli) Date: Tue, 25 Oct 2011 10:00:29 +0200 Subject: [Pw_forum] GIPAW: error in output In-Reply-To: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it> References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it> Message-ID: <4EA66C9D.6060800@gmail.com> Dear Carlo, if I must guess, 90% that it is a problem of the gfortran compiler. I recognize that the situation of fortran compilers and of the floating-point behavior of CPUs is very annoying. I'm using the Intel compiler with MKL and FFTW3 and I've run most calculations of x86_64 CPUs. If I will have time, I'll give a try to gfortran 4.6. Best, Davide On 01/-10/-28163 08:59 PM, Carlo Nervi wrote: > Hello, > I succesfully compiled QE 4.3.2 and the corresponding > GIPAW module on a Opteron 6168 linux using gfortran 4.6, > acml 5.0.0 and amdlibm 3.0.1. > > I did the benzene-scf.in job in the > GIPAW/examples/benzene-USPP/ directory. The scf energy is > the same as the reference output, which is in the same > directory (apparently all is okay). > I've compiled the gipaw module by the common way 'make > gipaw' from the source QE dir. - I hope this was okay... > > The gipaw calculations proceed, apparently ends normally, > but the output contains several NotaNumber (NaN). Anuone > have an idea qhat's wrong or could please give some hints > how to solve the problem? > Thank you, > Carlo > > ... > negative rho (up, down): 0.103E-03 0.000E+00 > init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333 > init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333 > init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333 > init_paw_1: ntyp= 1 rc= 1.4000 rs= 0.9333 > > init_gipaw_1: projectors nearly linearly dependent: > ntyp = 1, l/n1/n2 = 0 2 1 0.99622328 > init_gipaw_1: projectors nearly linearly dependent: > ntyp = 1, l/n1/n2 = 1 2 1 0.99789339 > init_paw_1: ntyp= 2 rc= 0.8000 rs= 0.5333 > init_paw_1: ntyp= 2 rc= 0.8000 rs= 0.5333 > init_gipaw_1: projectors nearly linearly dependent: > ntyp = 2, l/n1/n2 = 0 2 1 0.99987400 > > GIPAW : 4.81s CPU 10.71s WALL > > Computing the magnetic susceptibility isolve=0 > ethr=0.1000E-13 > k-point # 1 of 1 pool # 1 > ik 1 ibnd 16 linter: root not converged 0.305E+07 > ik 1 ibnd 16 linter: root not converged 0.139E+31 > ik 1 ibnd 16 linter: root not converged 0.122E+27 > End of magnetic susceptibility calculation > > f-sum rule (1st term): > ************** 0.0000 0.0000 > 0.0000 -29.8546 0.0000 > 0.0000 0.0000 -29.9120 > > f-sum rule (2nd term): > -0.3248 0.0000 0.0000 > 0.0000 -0.3248 0.0000 > > ... > > Contributions to the NMR chemical shifts: > ------------------------------- > > Core contribution in ppm: > > Atom 1 C pos: ( 0.000000 0.107679 0.000000) > sigma: 200.51 > Atom 2 C pos: ( 0.093253 0.053840 0.000000) > sigma: 200.51 > Atom 3 C pos: ( 0.093253 -0.053840 0.000000) > sigma: 200.51 > Atom 4 C pos: ( 0.000000 -0.107679 0.000000) > sigma: 200.51 > Atom 5 C pos: ( -0.093253 -0.053840 0.000000) > sigma: 200.51 > Atom 6 C pos: ( -0.093253 0.053840 0.000000) > sigma: 200.51 > Atom 7 H pos: ( 0.000000 0.191523 0.000000) > sigma: 0.00 > Atom 8 H pos: ( 0.165864 0.095761 0.000000) > sigma: 0.00 > Atom 9 H pos: ( 0.165864 -0.095761 0.000000) > sigma: 0.00 > Atom 10 H pos: ( 0.000000 -0.191523 0.000000) > sigma: 0.00 > Atom 11 H pos: ( -0.165864 -0.095761 0.000000) > sigma: 0.00 > Atom 12 H pos: ( -0.165864 0.095761 0.000000) > sigma: 0.00 > > Bare contribution in ppm: > > Atom 1 C pos: ( 0.000000 0.107679 0.000000) > sigma: NaN > NaN NaN NaN > NaN NaN NaN > NaN NaN NaN > > Atom 2 C pos: ( 0.093253 0.053840 0.000000) > sigma: NaN > NaN NaN NaN > NaN NaN NaN > NaN NaN NaN > > ... > Total NMR chemical shifts in ppm: > --------------------------------------- > > Atom 1 C pos: ( 0.000000 0.107679 0.000000) > sigma: NaN > C 1 anisotropy: NaN eta: 0.0000 > C 1 sigma_xx= NaN axis=( NaN > NaN 0.000000) > C 1 sigma_yy= NaN axis=( NaN > NaN 0.000000) > C 1 sigma_zz= NaN axis=( 0.000000 > 0.000000 1.000000) > > Atom 2 C pos: ( 0.093253 0.053840 0.000000) > sigma: NaN > C 2 anisotropy: NaN eta: 0.0000 > C 2 sigma_xx= NaN axis=( NaN > NaN 0.000000) > C 2 sigma_yy= NaN axis=( NaN > NaN 0.000000) > C 2 sigma_zz= NaN axis=( 0.000000 > 0.000000 1.000000) > > > From baroni at sissa.it Tue Oct 25 13:30:07 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 25 Oct 2011 13:30:07 +0200 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: References: <1626F662-ECD2-44F6-88F2-511622C479CA@democritos.it> Message-ID: <81B1E720-51E5-41D6-BEBE-931FFD5F966A@sissa.it> I know, I know ... you just need even harder work ... (and advise, of course) SB On Oct 24, 2011, at 9:35 PM, chengyu yang wrote: > Dear Dr. Baroni, > I agree with your opinion, but my problems is that I am a material student, but I am doing research with a lot of physics, and nobody can give me much help but result is required. That's why I feel helpless sometimes. If I know in which direction should I work hard then i certainly would go. > Thank you. > > Chengyu Yang > MMAE, University of Central Florida,US > > > 2011/10/24 Stefano Baroni > > Dear chengyu yang: > >> I am sorry to ask, but advice from this forum is important to help. > > Thanks for the appreciation, but remember that no forum is a real substitute for hard work ... Many of the questions that you (as well as many others) ask could be answered by yourself, just trying ... If you try and understand, then you wouldn't need to ask. If you do not understand, in spite of trying hard, then the answers to your legitimate (even more legitimate, after trying hard) questions would be much more instructive for you. > > Just a suggestion ... > > SB > > --- > 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 > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111025/82ed764e/attachment.htm From ndzsau at yahoo.co.uk Tue Oct 25 17:18:45 2011 From: ndzsau at yahoo.co.uk (Nguyen Doan Sau) Date: Tue, 25 Oct 2011 15:18:45 +0000 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: References: , <1626F662-ECD2-44F6-88F2-511622C479CA@democritos.it>, , , Message-ID: Hi Chengyu Yang,Below is some of my opinion. I am sorry if anyone feel this offensive Not only can you feel helpless in your research. Everyone does have the same feeling when you start doing thing absolutely new to you. Prof. Baroni is absolutely right. This is an only way to get over your helplessness. Trying, reading, doing experiments, thinking critically your results, and after that, discussing your results (after you think critically and prepared your results very carefully) with your postdocs, your advisor? etc and someone else (like one in forum). You only know your direction to go when you spend a lot, I mean a lot of a lot of time of trying reading literature, thinking about your research and doing your experiment. Don?t ever think that research is something you can learn and master for a short time. If it is your career, it?s will be your whole life. Best and lucks, SN U of H Date: Mon, 24 Oct 2011 15:35:02 -0400 From: chengyu.young at gmail.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Binding energy of Cu at CNT Dear Dr. Baroni, I agree with your opinion, but my problems is that I am a material student, but I am doing research with a lot of physics, and nobody can give me much help but result is required. That's why I feel helpless sometimes. If I know in which direction should I work hard then i certainly would go. Thank you. Chengyu Yang MMAE, University of Central Florida,US 2011/10/24 Stefano Baroni Dear chengyu yang: I am sorry to ask, but advice from this forum is important to help. Thanks for the appreciation, but remember that no forum is a real substitute for hard work ... Many of the questions that you (as well as many others) ask could be answered by yourself, just trying ... If you try and understand, then you wouldn't need to ask. If you do not understand, in spite of trying hard, then the answers to your legitimate (even more legitimate, after trying hard) questions would be much more instructive for you. Just a suggestion ... SB --- 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 _______________________________________________ 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/20111025/0fea3078/attachment-0001.htm From chengyu.young at gmail.com Tue Oct 25 17:47:42 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Tue, 25 Oct 2011 11:47:42 -0400 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: References: <1626F662-ECD2-44F6-88F2-511622C479CA@democritos.it> Message-ID: yes it's offensive. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111025/4ebc7707/attachment.htm From carlo.nervi at unito.it Tue Oct 25 18:18:58 2011 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 25 Oct 2011 18:18:58 +0200 Subject: [Pw_forum] GIPAW: error in output In-Reply-To: <4EA66C9D.6060800@gmail.com> References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it> <4EA66C9D.6060800@gmail.com> Message-ID: <4EA6E172.4050302@unito.it> Hello, I tried to compile using the GOTO2 BLAS libs, but I got the same error in gipaw. So I tried to compile all with gfortran 4.4.5, but again I got the same NaN message, with again the following: Computing the magnetic susceptibility isolve=0 ethr=0.1000E-13 k-point # 1 of 1 pool # 1 ik 1 ibnd 16 linter: root not converged 0.651E+09 ik 1 ibnd 16 linter: root not converged 0.261E+30 ik 1 ibnd 16 linter: root not converged 0.362E+30 End of magnetic susceptibility calculation I'm getting frustrated... What is strange is that pw.x compiled with gfortran 4.6.1 is apparently doing very well. This is not the case of gipaw.... 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 Lorenzo.Paulatto at impmc.upmc.fr Tue Oct 25 18:22:32 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 25 Oct 2011 18:22:32 +0200 Subject: [Pw_forum] GIPAW: error in output In-Reply-To: <4EA6E172.4050302@unito.it> References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it> <4EA66C9D.6060800@gmail.com> <4EA6E172.4050302@unito.it> Message-ID: You could try to compile using this option (all together, without spaces): -ffpe-trap=invalid,zero,overflow,underflow,denormal to force the code to crash at the first appearance of NaN, this could help track down the source of the problem. On Tue, 25 Oct 2011 18:18:58 +0200, Carlo Nervi wrote: > Hello, > I tried to compile using the GOTO2 BLAS libs, but I got the same error > in gipaw. > > So I tried to compile all with gfortran 4.4.5, but again I got the same > NaN message, with again the following: > > Computing the magnetic susceptibility isolve=0 > ethr=0.1000E-13 > k-point # 1 of 1 pool # 1 > ik 1 ibnd 16 linter: root not converged 0.651E+09 > ik 1 ibnd 16 linter: root not converged 0.261E+30 > ik 1 ibnd 16 linter: root not converged 0.362E+30 > End of magnetic susceptibility calculation > > I'm getting frustrated... > > What is strange is that pw.x compiled with gfortran 4.6.1 is apparently > doing very well. This is not the case of gipaw.... > > Carlo > -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From carlo.nervi at unito.it Tue Oct 25 18:54:30 2011 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 25 Oct 2011 18:54:30 +0200 Subject: [Pw_forum] GIPAW: error in output In-Reply-To: References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it> <4EA66C9D.6060800@gmail.com> <4EA6E172.4050302@unito.it> Message-ID: <4EA6E9C6.9090102@unito.it> Il 25/10/2011 18.22, Lorenzo Paulatto ha scritto: > You could try to compile using this option (all together, without spaces): > -ffpe-trap=invalid,zero,overflow,underflow,denormal > to force the code to crash at the first appearance of NaN, this could help > track down the source of the problem. Thank you Lorenzo. I did what you suggested and I got many errors like this: [chpc111:47070] Signal: Floating point exception (8) [chpc111:47070] Signal code: Floating point divide-by-zero (3) [chpc111:47070] Failing at address: 0x44e576 [chpc111:47092] [ 0] /lib64/libpthread.so.0(+0x10eb0) [0x2b972490deb0] [chpc111:47092] [ 1] /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(cgsolve_all_+0xff6) [0x44e576] [chpc111:47092] [ 2] /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(greenfunction_+0x1280) [0x44d1a0] [chpc111:47092] [ 3] /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(paramagnetic_correction_aug_+0x1e30) [0x4718f0] [chpc111:47092] [ 4] /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(suscept_crystal_+0x520f) [0x45c02f] [chpc111:47092] [ 5] /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(main+0x1a7) [0x43d227] [chpc111:47092] [ 6] /lib64/libc.so.6(__libc_start_main+0xed) [0x2b9724b3db0d] [chpc111:47092] [ 7] /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x() [0x43d2fd] [chpc111:47092] *** End of error message *** [chpc111:47105] *** Process received signal *** and [chpc111:47076] *** End of error message *** [chpc111:47102] [ 3] /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(paramagnetic_correction_aug_+0x1e30) [0x4718f0] [chpc111:47102] [ 4] /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(suscept_crystal_+0x520f) [0x45c02f] [chpc111:47102] [ 5] /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(main+0x1a7) [0x43d227] [chpc111:47102] [ 6] /lib64/libc.so.6(__libc_start_main+0xed) [0x2ac89299db0d] [chpc111:47102] [ 7] /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x() [0x43d2fd] [chpc111:47102] *** End of error message *** But if I run mpirun -n 1 I got the following: Fortran runtime warning: IEEE 'denormal number' exception not supported. At line 739 of file suscept_crystal.f90 (unit = 99, file = '/tmp/ceresoli/benzene.gipaw_recover') Fortran runtime error: I/O past end of record on unformatted file -------------------------------------------------------------------------- mpirun has exited due to process rank 0 with PID 47850 on node chpc111 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- Any hints? 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 Tue Oct 25 13:30:07 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 25 Oct 2011 13:30:07 +0200 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: References: <1626F662-ECD2-44F6-88F2-511622C479CA@democritos.it> Message-ID: <81B1E720-51E5-41D6-BEBE-931FFD5F966A@sissa.it> I know, I know ... you just need even harder work ... (and advise, of course) SB On Oct 24, 2011, at 9:35 PM, chengyu yang wrote: > Dear Dr. Baroni, > I agree with your opinion, but my problems is that I am a material student, but I am doing research with a lot of physics, and nobody can give me much help but result is required. That's why I feel helpless sometimes. If I know in which direction should I work hard then i certainly would go. > Thank you. > > Chengyu Yang > MMAE, University of Central Florida,US > > > 2011/10/24 Stefano Baroni > > Dear chengyu yang: > >> I am sorry to ask, but advice from this forum is important to help. > > Thanks for the appreciation, but remember that no forum is a real substitute for hard work ... Many of the questions that you (as well as many others) ask could be answered by yourself, just trying ... If you try and understand, then you wouldn't need to ask. If you do not understand, in spite of trying hard, then the answers to your legitimate (even more legitimate, after trying hard) questions would be much more instructive for you. > > Just a suggestion ... > > SB > > --- > 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 > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111025/82ed764e/attachment-0002.htm From Lorenzo.Paulatto at impmc.upmc.fr Tue Oct 25 18:57:41 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 25 Oct 2011 18:57:41 +0200 Subject: [Pw_forum] GIPAW: error in output In-Reply-To: <4EA6E9C6.9090102@unito.it> References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it> <4EA66C9D.6060800@gmail.com> <4EA6E172.4050302@unito.it> <4EA6E9C6.9090102@unito.it> Message-ID: Recent versions of gfortran have a -traceback option that (together with -g, I think) would give you the (almost) exact code line that causes the problem; without that you shoudl still be able to run addr2line -e /wherever/bin/gipaw.x 0x44e576 to get the line of cgsolve_all that triggers a NaN or inf. However, I do not know the gipaw code, maybe Davide can guess something from that. cheers On Tue, 25 Oct 2011 18:54:30 +0200, Carlo Nervi wrote: > Il 25/10/2011 18.22, Lorenzo Paulatto ha scritto: >> You could try to compile using this option (all together, without >> spaces): >> -ffpe-trap=invalid,zero,overflow,underflow,denormal >> to force the code to crash at the first appearance of NaN, this could >> help >> track down the source of the problem. > > Thank you Lorenzo. I did what you suggested and I got many errors like > this: > > [chpc111:47070] Signal: Floating point exception (8) > [chpc111:47070] Signal code: Floating point divide-by-zero (3) > [chpc111:47070] Failing at address: 0x44e576 > [chpc111:47092] [ 0] /lib64/libpthread.so.0(+0x10eb0) [0x2b972490deb0] > [chpc111:47092] [ 1] > /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(cgsolve_all_+0xff6) > [0x44e576] > [chpc111:47092] [ 2] > /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(greenfunction_+0x1280) > [0x44d1a0] > [chpc111:47092] [ 3] > /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(paramagnetic_correction_aug_+0x1e30) > [0x4718f0] > [chpc111:47092] [ 4] > /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(suscept_crystal_+0x520f) > [0x45c02f] > [chpc111:47092] [ 5] > /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(main+0x1a7) > [0x43d227] > [chpc111:47092] [ 6] /lib64/libc.so.6(__libc_start_main+0xed) > [0x2b9724b3db0d] > [chpc111:47092] [ 7] > /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x() [0x43d2fd] > [chpc111:47092] *** End of error message *** > [chpc111:47105] *** Process received signal *** > > and > > [chpc111:47076] *** End of error message *** > [chpc111:47102] [ 3] > /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(paramagnetic_correction_aug_+0x1e30) > [0x4718f0] > [chpc111:47102] [ 4] > /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(suscept_crystal_+0x520f) > [0x45c02f] > [chpc111:47102] [ 5] > /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x(main+0x1a7) > [0x43d227] > [chpc111:47102] [ 6] /lib64/libc.so.6(__libc_start_main+0xed) > [0x2ac89299db0d] > [chpc111:47102] [ 7] > /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x() [0x43d2fd] > [chpc111:47102] *** End of error message *** > > > But if I run mpirun -n 1 I got the following: > > Fortran runtime warning: IEEE 'denormal number' exception not supported. > At line 739 of file suscept_crystal.f90 (unit = 99, file = > '/tmp/ceresoli/benzene.gipaw_recover') > Fortran runtime error: I/O past end of record on unformatted file > -------------------------------------------------------------------------- > mpirun has exited due to process rank 0 with PID 47850 on > node chpc111 exiting without calling "finalize". This may > have caused other processes in the application to be > terminated by signals sent by mpirun (as reported here). > -------------------------------------------------------------------------- > > > Any hints? > Carlo > -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From baroni at sissa.it Tue Oct 25 19:01:15 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 25 Oct 2011 19:01:15 +0200 Subject: [Pw_forum] Binding energy of Cu@CNT In-Reply-To: References: <1626F662-ECD2-44F6-88F2-511622C479CA@democritos.it> Message-ID: Sorry to have started this flame. Actually, I do not feel that anything said in this thread is offensive to anyone. If it was, again: sorry. Let's keep asking questions and feel free to answer politely (as it has always been the case), and frankly (as it has always been the case). Stefano B On Oct 25, 2011, at 5:47 PM, chengyu yang wrote: > yes it's offensive. > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111025/02144716/attachment.htm From carlo.nervi at unito.it Tue Oct 25 19:05:45 2011 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 25 Oct 2011 19:05:45 +0200 Subject: [Pw_forum] GIPAW: error in output In-Reply-To: References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it> <4EA66C9D.6060800@gmail.com> <4EA6E172.4050302@unito.it> <4EA6E9C6.9090102@unito.it> Message-ID: <4EA6EC69.1090000@unito.it> Okay, thanks again. addr2line -e /home/nervi/src/QE432/espresso-4.3.2/GIPAW/src/gipaw.x 0x44e576 /home/nervi/src/QE432/espresso-4.3.2/qe-gipaw-4.3.2/src/cgsolve_all.f90:225 It should be the line with dclamda (see below) - no idea how to furter help the developers ;-) Carlo #ifdef __PARA call mp_sum( a(1:lbnd), intra_pool_comm ) call mp_sum( c(1:lbnd), intra_pool_comm ) #endif lbnd=0 do ibnd = 1, nbnd if (conv (ibnd) .eq.0) then lbnd=lbnd+1 dclambda = CMPLX( - a(lbnd) / c(lbnd), 0.d0,kind=DP) ! ! move to new position ! call zaxpy (ndmx*npol, dclambda, h(1,ibnd), 1, dpsi(1,ibnd), 1) ! ! update to get the gradient ! !g=g+lam call zaxpy (ndmx*npol, dclambda, t(1,lbnd), 1, g(1,ibnd), 1) ! ! save current (now old) h and rho for later use ! call zcopy (ndmx*npol, h(1,ibnd), 1, hold(1,ibnd), 1) rhoold (ibnd) = rho (ibnd) endif enddo -- ------------------------------------------------------ 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 payam.norouzzadeh at gmail.com Tue Oct 25 19:43:43 2011 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Tue, 25 Oct 2011 12:43:43 -0500 Subject: [Pw_forum] Swapping Message-ID: Dear Quantum Espresso Users I think the jobs run slow when they are swapping memory to disk. Is there anything I can do to distribute the memory across more nodes so they don?t have to swap? I want to reduce RAM usage in practice. How it is possible? Thanks in advance. Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111025/e2776dca/attachment.htm From carlo.nervi at unito.it Tue Oct 25 19:52:18 2011 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 25 Oct 2011 19:52:18 +0200 (CEST) Subject: [Pw_forum] Swapping In-Reply-To: References: Message-ID: <56040.130.192.119.45.1319565138.squirrel@mail.unito.it> > Dear Quantum Espresso Users > > I think the jobs run slow when they are swapping memory to > disk. > Is there anything I can do to distribute the memory across > more nodes so > they don???t have to swap? > I want to reduce RAM usage in practice. How it is > possible? It is generally a very bad idea to swap RAM on the HD. Try to reduce the amount of RAM decreasing the size of the problem (i.e. reduce cell dimensions, use lower ecut, etc...) There is also another parameter to be considered, especially in parallel calculations: in namelist &CONTROL disk_io='minimal', or even 'none' see here: http://www.quantum-espresso.org/user_guide/node18.html HTH, Carlo From kissi at uni-mainz.de Tue Oct 25 19:55:55 2011 From: kissi at uni-mainz.de (Kiss, Ioan) Date: Tue, 25 Oct 2011 17:55:55 +0000 Subject: [Pw_forum] USPP pseudopotentials for spin-orbit coupling calculations Message-ID: Dear PWscf forum members and developers, in the future I would like to perform calculations on systems where relativistic effects are not negligible. Although I have generated USPP potentials using the code of Prof. David Vanderbilt's group, after browsing through the forum and checking out some subroutines of PWscf it became clear that potentials based on the Koelling-Harmon scalar relativistic wave equations are not suitable for this puorpose. It seems to me that with the abovementioned code one can not generate fully-relativistic potentials based on the Dirac-Kohn-Sham equations (if I am wrong, please correct me). Now the issue is that by searching around I could not find fully-relativistic pseudopotentials with PBE functional for Bi, Hg, Se and Te. If possible, I would prefer to obtain fully-relativistic USPP potentials for these elements with semicore states treated as valence states, and with Froyen-Louie-Cohen core correction. Is there somewhere a database where such potentials are available and I have overlooked it during my search? If there are no such potentials widely available, can they be easily generated with the ld.x package developed by the group of Prof. Andrea Dal Corso or with other free tools? I would like to thank you for any kind of contructive feedback. Best regards, Janos Kiss. ========================================== Dr. Janos Kiss e-mail: kissi at uni-mainz.de Johannes Gutenberg-Universitaet Institut f. Anorg. u. Analyt. Chemie AK Prof. Dr. Claudia Felser Staudinger Weg 9 / Raum 01-230 55128 Mainz/ Germany Phone: +49-(0)6131-39-22703 Fax: +49-(0)6131-39-26267 Web: http://www.superconductivity.de/ ========================================= From giannozz at democritos.it Tue Oct 25 20:43:41 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 Oct 2011 20:43:41 +0200 Subject: [Pw_forum] GIPAW: error in output In-Reply-To: <4EA6EC69.1090000@unito.it> References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it> <4EA66C9D.6060800@gmail.com> <4EA6E172.4050302@unito.it> <4EA6E9C6.9090102@unito.it> <4EA6EC69.1090000@unito.it> Message-ID: <2F02DA09-12A3-4A51-8BDB-1FA39059FF31@democritos.it> On Oct 25, 2011, at 19:05 , Carlo Nervi wrote: > It should be the line with dclamda (see below) - no idea how to > further > help the developers ;-) > dclambda = CMPLX( - a(lbnd) / c(lbnd), 0.d0,kind=DP) print c(lbnd), check if it is zero; if it is, try to find out where it comes from. Does the same job work on other machines/compilers, by the way? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Oct 25 20:45:06 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 Oct 2011 20:45:06 +0200 Subject: [Pw_forum] Swapping In-Reply-To: <56040.130.192.119.45.1319565138.squirrel@mail.unito.it> References: <56040.130.192.119.45.1319565138.squirrel@mail.unito.it> Message-ID: On Oct 25, 2011, at 19:52 , Carlo Nervi wrote: > in namelist &CONTROL disk_io='minimal', or even 'none' > see here: > http://www.quantum-espresso.org/user_guide/node18.html note that this will actually increase RAM usage, because wavefunctions are not stored to disk but kept in memory P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Oct 25 20:46:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 25 Oct 2011 20:46:33 +0200 Subject: [Pw_forum] USPP pseudopotentials for spin-orbit coupling calculations In-Reply-To: References: Message-ID: <66EB16BC-7787-4D76-8A9C-C8A3FB517B2B@democritos.it> On Oct 25, 2011, at 19:55 , Kiss, Ioan wrote: > If there are no such potentials widely available, can they be > easily generated with the ld.x package generated, yes; easily...not sure P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From dalcorso at sissa.it Tue Oct 25 21:04:49 2011 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Tue, 25 Oct 2011 21:04:49 +0200 Subject: [Pw_forum] USPP pseudopotentials for spin-orbit coupling calculations In-Reply-To: References: Message-ID: <1319569489.2195.1.camel@localhost.localdomain> There are several ld1.x inputs in http://qe-forge.org/projects/pslibrary/ They are still experimental, but you can use them to generate fully relativistic PPs. HTH Andrea On Tue, 2011-10-25 at 17:55 +0000, Kiss, Ioan wrote: > Dear PWscf forum members and developers, > > in the future I would like to perform calculations on systems where relativistic effects > are not negligible. Although I have generated USPP potentials using the code of > Prof. David Vanderbilt's group, after browsing through the forum and checking out some > subroutines of PWscf it became clear that potentials based on the Koelling-Harmon > scalar relativistic wave equations are not suitable for this puorpose. > It seems to me that with the abovementioned code one can not generate fully-relativistic > potentials based on the Dirac-Kohn-Sham equations (if I am wrong, please correct me). > > Now the issue is that by searching around I could not find fully-relativistic pseudopotentials > with PBE functional for Bi, Hg, Se and Te. If possible, I would prefer to obtain fully-relativistic > USPP potentials for these elements with semicore states treated as valence states, and > with Froyen-Louie-Cohen core correction. > Is there somewhere a database where such potentials are available and I have overlooked > it during my search? > If there are no such potentials widely available, can they be easily generated with the ld.x > package developed by the group of Prof. Andrea Dal Corso or with other free tools? > > I would like to thank you for any kind of contructive feedback. > > Best regards, > Janos Kiss. > > > ========================================== > > Dr. Janos Kiss e-mail: kissi at uni-mainz.de > Johannes Gutenberg-Universitaet > Institut f. Anorg. u. Analyt. Chemie > AK Prof. Dr. Claudia Felser > Staudinger Weg 9 / Raum 01-230 > 55128 Mainz/ Germany > Phone: +49-(0)6131-39-22703 > Fax: +49-(0)6131-39-26267 > Web: http://www.superconductivity.de/ > > ========================================= > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From gabriele.sclauzero at epfl.ch Wed Oct 26 09:08:24 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 26 Oct 2011 09:08:24 +0200 Subject: [Pw_forum] Swapping In-Reply-To: References: Message-ID: <6A8DD402-8B04-4A89-BAE9-070DC977FC0E@epfl.ch> Dear Payam, the solution might be simple: increase the number of nodes! The FFT-related quantities will be spread across more nodes, so that the memory per node will decrease (assuming that the number of pools stays the same). It depends however on your system. If you have a very large one in hands (I mean, with a lot of electrons), you need to distribute also the matrix to be diagonalized (in cdiaghg). To achieve this, be sure to compile the scalapack enabled version and to use the -ndiag option properly. If you don't have more nodes, then I'm afraid you'll be forced to reduce the size of your system or PW cutoffs/number of bands. Also, using 'cg' style diagonalization will save some memory, but if this will be effective it depends on your system (about which you don't say a word...). If you need more help please put an effort to be more specific. GS Il giorno 25/ott/2011, alle ore 19.43, Payam Norouzzadeh ha scritto: > Dear Quantum Espresso Users > > I think the jobs run slow when they are swapping memory to disk. > Is there anything I can do to distribute the memory across more nodes so they don?t have to swap? > I want to reduce RAM usage in practice. How it is possible? > > Thanks in advance. > Payam Norouzzadeh > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111026/c911a3d1/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Wed Oct 26 09:52:13 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 26 Oct 2011 09:52:13 +0200 Subject: [Pw_forum] GIPAW: error in output In-Reply-To: <4EA6EC69.1090000@unito.it> References: <54185.130.192.119.45.1319487778.squirrel@mail.unito.it> <4EA66C9D.6060800@gmail.com> <4EA6E172.4050302@unito.it> <4EA6E9C6.9090102@unito.it> <4EA6EC69.1090000@unito.it> Message-ID: In data 25 ottobre 2011 alle ore 19:05:45, Carlo Nervi ha scritto: > It should be the line with dclamda (see below) - no idea how to furter > help the developers ;-) This *could* originate at line 137 where "t" is computed by h_psi (which is really ch_psi_all); t is then used to compute c. In another contest I found cg_solve_all call to ch_psi_all to be extremely easy to get wrong, as it secretly uses a few global variable. The gipaw code uses its own version of ch_psi_all, but how to be sure that is is that one being called an not the one from phonon? In principle the linking order would guarantee it, but better safe then sorry. The two subroutines have the same name, but use different global variables. I would try this, just to be sure: * in GIPAW/ch_psi_all.f90 and GIPAW/greenfunction.f90 change "ch_psi_all" to "ch_psi_all_gipaw" (2 changes for file, 4 total) * recompile * run cheers -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From payam.norouzzadeh at gmail.com Wed Oct 26 18:26:11 2011 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Wed, 26 Oct 2011 11:26:11 -0500 Subject: [Pw_forum] Swapping Message-ID: Thank you Dr.Giannozzi and Dr.Sclauzero for your comments. Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111026/68c28549/attachment.htm From wumindt2 at zju.edu.cn Wed Oct 26 22:36:00 2011 From: wumindt2 at zju.edu.cn (wumindt2) Date: Thu, 27 Oct 2011 04:36:00 +0800 Subject: [Pw_forum] Raman spectra calculatio using QE Message-ID: Dear All, Is there anyone have done Raman spectra using QE? I tried to run the SiH4 example which could be downloaded from the QE website. The process i did is very simple, after scf calculation using the defalt sih4.scf.in file, i ran the sih4.nm.in file using ph.x. But i got an error as " cannot start from pw.x data file using Gamma-point tricks". So what's wrong with my calculation? Thanks for any help! Best regards, Min WU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111027/37850f5b/attachment.htm From scjung at kbsi.re.kr Thu Oct 27 07:06:38 2011 From: scjung at kbsi.re.kr (scjung at kbsi.re.kr) Date: Thu, 27 Oct 2011 14:06:38 +0900 (KST) Subject: [Pw_forum] A problem on GIPAW calculations Message-ID: <809630492.1319691998861.JavaMail.root@mail> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111027/fa02a6b4/attachment.htm From flux_ray12 at 163.com Thu Oct 27 08:29:20 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 27 Oct 2011 14:29:20 +0800 (CST) Subject: [Pw_forum] Raman spectra calculatio using QE In-Reply-To: References: Message-ID: <6d28ee63.787a.13344118cfc.Coremail.flux_ray12@163.com> If you are using K_POINTS gamma in scf but still wanna use ph.x for further calculaiton, why not try changing K_POINTS gamma to: K_POINTS 1 0.0 0.0 0.0 Or, you can using phcg.x as the follower of K_POINTS gamma case. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-27 04:36:00,wumindt2 wrote: Dear All, Is there anyone have done Raman spectra using QE? I tried to run the SiH4 example which could be downloaded from the QE website. The process i did is very simple, after scf calculation using the defalt sih4.scf.in file, i ran the sih4.nm.in file using ph.x. But i got an error as " cannot start from pw.x data file using Gamma-point tricks". So what's wrong with my calculation? Thanks for any help! Best regards, Min WU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111027/aaff2516/attachment.htm From kucukben at sissa.it Thu Oct 27 08:49:50 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Thu, 27 Oct 2011 08:49:50 +0200 Subject: [Pw_forum] A problem on GIPAW calculations In-Reply-To: <809630492.1319691998861.JavaMail.root@mail> References: <809630492.1319691998861.JavaMail.root@mail> Message-ID: <20111027084950.Horde.53xUUB8V4mxOqP8OQiUheEA@webmail.sissa.it> Dear Sung Chul Jung, > A fact that the Li15Si4 system is metallic seems to be related to the > problem but I am not sure. GIPAW for metals is not implemented yet. Would you like to be the one implementing? Contact us :) best, emine kucukbenli, phd student, sissa, italy From eariel99 at gmail.com Thu Oct 27 14:04:34 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 27 Oct 2011 14:04:34 +0200 Subject: [Pw_forum] starting charge 209.99992, renormalised to 240.00000 Message-ID: Hi, I am calculating for fcc C60 I am puzzled by the message starting charge 209.99992, renormalised to 240.00000, th this is with the pseudopotential C.pbe-mt_gipaw.UPF. The difference between 209 and 240 looks a bit too great, it does not depend on the cutoff. in contrast, using with C.pbe-rrkjus.UPF starting charge 239.99684, renormalised to 240.00000 Is this difference of charges a problem? Can this pseudpotential be used for ground state calculations ? -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). Translate from spanish here http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111027/db57b024/attachment.htm From peressi at ts.infn.it Thu Oct 27 14:18:27 2011 From: peressi at ts.infn.it (peressi at ts.infn.it) Date: Thu, 27 Oct 2011 14:18:27 +0200 (CEST) Subject: [Pw_forum] Announcement - PhD IN PHYSICS University of Trieste - a.y. 2011/12 Message-ID: <58508.140.105.31.161.1319717907.squirrel@dftmail.ts.infn.it> Dear all, I'm using this mailing list to circulate this announcement. MP ---------------------------------------------------------------------- The University of Trieste announces public selection procedures for admission to the Doctoral programme in Physics. All details can be found (English version) in: http://www2.units.it/dott/en/?file=DottBandi.inc&cod=2011 (in particular, there is also the Announcement reserved to NON-EU citizens, who are resident outside the EU and have been awarded a degree outside the EU) Deadline for applications: 31.10.2011 (by 12.00pm CET) ---------------------------------------------------------------------- Maria Peressi Department of Physics University of Trieste Strada Costiera 11 I-34151 Trieste tel. +39 040 2240242 fax. +39 040 224601 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From giannozz at democritos.it Thu Oct 27 19:11:37 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 27 Oct 2011 19:11:37 +0200 Subject: [Pw_forum] starting charge 209.99992, renormalised to 240.00000 In-Reply-To: References: Message-ID: <9DA3E484-AC6A-4A6B-B5ED-18CAEDBB2ED9@democritos.it> On Oct 27, 2011, at 14:04 , Eduardo Ariel Menendez Proupin wrote: > I am calculating for fcc C60 I am puzzled by the message > starting charge 209.99992, renormalised to 240.00000 The atomic (pseudo-)charge density that one finds in the pseudopotential file is typically produced during the PP generation procedure, for the reference electronic configuration. Apparently it wasn't the neutral one in your case: 210/60=3.5. It shouldn't be a problem, though, since it is used only to start the scf procedure and for no other purpose. If it is, you can "borrow" the charge density from another PP file (field ), but notice that the radial grid must be exactly the same P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From trambui at u.boisestate.edu Fri Oct 28 00:05:26 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Thu, 27 Oct 2011 16:05:26 -0600 Subject: [Pw_forum] Fermi energy from scf calculation Message-ID: Dear Everyone, I have told that the scf calculation would give out the Fermi energy, Ef, of a material system. I have done some nscf, relax and vc-relax calculations for the same material as well. I was able to obtain the Ef on other calculation but not on the scf calculation. would you give me some information on why it was the case? Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111027/987ad81b/attachment.htm From wumindt2 at zju.edu.cn Fri Oct 28 02:54:38 2011 From: wumindt2 at zju.edu.cn (wumindt2) Date: Fri, 28 Oct 2011 08:54:38 +0800 Subject: [Pw_forum] Raman spectra calculatio using QE Message-ID: Thanks. I ran sih4.scf.in and sih4.nm.in and got the output files. But how can i get the Raman spectra from the output file? Where is the Raman intensity? Min Wu >From: "GAO Zhe" >Reply-To: PWSCF Forum >To: "PWSCF Forum" >Subject: Re: [Pw_forum] Raman spectra calculatio using QE >Date: Thu, 27 Oct 2011 14:29:20 +0800 (CST) > If you are using K_POINTS gamma in scf but still wanna use ph.x for further calculaiton, why not try changing K_POINTS gamma to: K_POINTS 1 0.0 0.0 0.0 Or, you can using phcg.x as the follower of K_POINTS gamma case. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-27 04:36:00,wumindt2 wrote: Dear All, Is there anyone have done Raman spectra using QE? I tried to run the SiH4 example which could be downloaded from the QE website. The process i did is very simple, after scf calculation using the defalt sih4.scf.in file, i ran the sih4.nm.in file using ph.x. But i got an error as " cannot start from pw.x data file using Gamma-point tricks". So what's wrong with my calculation? Thanks for any help! Best regards, Min WU ????????????????????????????! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111028/25ddf165/attachment.htm From mtorabi at uwo.ca Fri Oct 28 02:49:40 2011 From: mtorabi at uwo.ca (Amin Torabi) Date: Thu, 27 Oct 2011 20:49:40 -0400 Subject: [Pw_forum] structure oscillating with vc-md Message-ID: Dear QE users, Will you please do me a favor and take a look at my input file, below. The total energy and force do not converge and keep oscillating... I have tried different dt (between 20-70) and wmass, and still not able to relax the structure Any comment on my the input_cards here (k-point,ecut,pp,conv...?) Many thanks &CONTROL calculation = 'vc-md' pseudo_dir = './' outdir = './' prefix = 'dt20' tstress = .true tprnfor = .true nstep = 100 dt = 20 / &SYSTEM ibrav = 12 celldm(1) = 8.3147 celldm(2) = 1.3 celldm(3) = 1.4772 celldm(4) = -0.260 nat = 16 ntyp = 2 ecutwfc = 85 ecutrho = 1100 input_dft = 'pbesol' nosym = .true / &ELECTRONS conv_thr = 1.0D-9 / &IONS pot_extrapolation='second-order' wfc_extrapolation='second-order' ion_temperature = 'rescaling' tempw = 300 / &CELL press = 0 cell_dynamics = 'w' wmass = 4.2 / ATOMIC_SPECIES B 10.811 B.pbe-n-van.UPF H 1.00794 H.pbe-van_bm.UPF ATOMIC_POSITIONS crystal B 0.005259620 0.145596712 0.040564862 H -0.199830030 0.176142715 0.150841828 H 0.217291388 0.312290957 -0.013967013 H 0.124960907 -0.022012847 0.122883862 B -0.005259620 -0.145596712 -0.040564862 H 0.199830030 -0.176142715 -0.150841828 H -0.217291388 -0.312290957 0.013967013 H -0.124960907 0.022012847 -0.122883862 B 0.494739818 0.354404554 0.540568678 H 0.699828966 0.323861788 0.650847745 H 0.282707973 0.187708799 0.486039576 H 0.375038882 0.522017144 0.622882523 B 0.505260182 0.645595446 0.459431322 H 0.300171034 0.676138212 0.349152255 H 0.717292027 0.812291201 0.513960424 H 0.624961118 0.477982856 0.377117477 K_POINTS automatic 8 8 8 0 0 0 -- Amin Torabi Ph.D. Student Chemistry Department The University *of* Western Ontario London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111027/674c7ac9/attachment.htm From bamideleibrahim at yahoo.com Fri Oct 28 05:29:04 2011 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Thu, 27 Oct 2011 20:29:04 -0700 (PDT) Subject: [Pw_forum] Fermi energy from scf calculation In-Reply-To: References: Message-ID: <1319772544.76253.YahooMailNeo@web39409.mail.mud.yahoo.com> Dear Tram, ? For you to get fermi energy from your scf calculation, you need to set you 'occupation=smearing', and they the type of smearing you want to use follow with 'degauss value'. With all this in place you will get the fermi? energy. Regards, ? Adetunji Bamidele Ibrahim Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. ________________________________ From: Tram Bui To: PWSCF Forum Sent: Thursday, October 27, 2011 11:05 PM Subject: [Pw_forum] Fermi energy from scf calculation Dear Everyone, ???? I have told that the scf calculation would give out the Fermi energy, Ef,?of?a material?system. I have done some nscf, relax and vc-relax calculations for the same material?as well. I was able to obtain the Ef on other calculation but not on the scf calculation. would you give me some information on why it was the case? Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu _______________________________________________ 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/20111027/95044750/attachment-0001.htm From degironc at sissa.it Fri Oct 28 05:52:41 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 28 Oct 2011 05:52:41 +0200 Subject: [Pw_forum] structure oscillating with vc-md In-Reply-To: References: Message-ID: <4EAA2709.9090502@sissa.it> Dear Amin Torabi you are performing a variable-cell MD simulation therefore the enthalpy is not minimized by the Newton equations for atoms+cell are integrated to give you the dynamics around the target pressure (P=0 in your case). to get the relaxation you should use calculation = "vc-relax" and then choose the minimization strategy. the default is bfgs but also damp dynamics is available. check the relevant input variables: ion_dynamics and cell_dynamics. best regards, stefano On 10/28/2011 02:49 AM, Amin Torabi wrote: > Dear QE users, > > Will you please do me a favor and take a look at my input file, below. > The total energy and force do not converge and keep oscillating... > I have tried different dt (between 20-70) and wmass, and still not able to > relax the structure > Any comment on my the input_cards here (k-point,ecut,pp,conv...?) > > Many thanks > > > > &CONTROL > calculation = 'vc-md' > pseudo_dir = './' > outdir = './' > prefix = 'dt20' > tstress = .true > tprnfor = .true > nstep = 100 > dt = 20 > / > &SYSTEM > ibrav = 12 > celldm(1) = 8.3147 > celldm(2) = 1.3 > celldm(3) = 1.4772 > celldm(4) = -0.260 > nat = 16 > ntyp = 2 > ecutwfc = 85 > ecutrho = 1100 > input_dft = 'pbesol' > nosym = .true > / > &ELECTRONS > conv_thr = 1.0D-9 > / > &IONS > pot_extrapolation='second-order' > wfc_extrapolation='second-order' > ion_temperature = 'rescaling' > tempw = 300 > / > &CELL > press = 0 > cell_dynamics = 'w' > wmass = 4.2 > / > ATOMIC_SPECIES > B 10.811 B.pbe-n-van.UPF > H 1.00794 H.pbe-van_bm.UPF > ATOMIC_POSITIONS crystal > B 0.005259620 0.145596712 0.040564862 > H -0.199830030 0.176142715 0.150841828 > H 0.217291388 0.312290957 -0.013967013 > H 0.124960907 -0.022012847 0.122883862 > B -0.005259620 -0.145596712 -0.040564862 > H 0.199830030 -0.176142715 -0.150841828 > H -0.217291388 -0.312290957 0.013967013 > H -0.124960907 0.022012847 -0.122883862 > B 0.494739818 0.354404554 0.540568678 > H 0.699828966 0.323861788 0.650847745 > H 0.282707973 0.187708799 0.486039576 > H 0.375038882 0.522017144 0.622882523 > B 0.505260182 0.645595446 0.459431322 > H 0.300171034 0.676138212 0.349152255 > H 0.717292027 0.812291201 0.513960424 > H 0.624961118 0.477982856 0.377117477 > K_POINTS automatic > 8 8 8 0 0 0 > > > > > _______________________________________________ > 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/20111028/a5f8adec/attachment.htm From giannozz at democritos.it Fri Oct 28 10:13:42 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 28 Oct 2011 10:13:42 +0200 Subject: [Pw_forum] Raman spectra calculatio using QE In-Reply-To: References: Message-ID: <1319789622.4439.5.camel@fe12lx.fisica.uniud.it> On Fri, 2011-10-28 at 08:54 +0800, wumindt2 wrote: > But how can i get the Raman spectra from the output file? > Where is the Raman intensity? example15 -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From michelepisarra at yahoo.it Fri Oct 28 11:31:03 2011 From: michelepisarra at yahoo.it (Michele Pisarra) Date: Fri, 28 Oct 2011 10:31:03 +0100 (BST) Subject: [Pw_forum] QE interface to DP code Message-ID: <1319794263.44379.YahooMailNeo@web27008.mail.ukl.yahoo.com> Hi everyone. Is it possible to use the output obtained with Quantum Espresso as an input for the TDDFT code PW? I know that the input to the DP code is a *.KSS file. I search through the internet and I found that the post processing code pw2gw should do the job, in it right? ?However there are no intruction to prepare the input file and?run this code in the doc directory. Thank you. Best Regards, ? Michele Pisarra, PhD Student, Dipartimento di Fisica, Universit? della Calabria Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111028/b740df25/attachment.htm From baroni at sissa.it Fri Oct 28 12:25:44 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 28 Oct 2011 12:25:44 +0200 Subject: [Pw_forum] QE interface to DP code In-Reply-To: <1319794263.44379.YahooMailNeo@web27008.mail.ukl.yahoo.com> References: <1319794263.44379.YahooMailNeo@web27008.mail.ukl.yahoo.com> Message-ID: <39FFE9D4-BBC2-42BB-808B-5734C7A5FC65@sissa.it> what is "the DP code"? I think that the TDDFT codes distributed with QE are directly interfaced with pw.x See: http://dx.doi.org/10.1016/j.cpc.2011.04.020 SB On Oct 28, 2011, at 11:31 AM, Michele Pisarra wrote: > Hi everyone. > Is it possible to use the output obtained with Quantum Espresso as an input for the TDDFT code PW? > I know that the input to the DP code is a *.KSS file. I search through the internet and I found that the post processing code pw2gw should do the job, in it right? > However there are no intruction to prepare the input file and run this code in the doc directory. > Thank you. > Best Regards, > > Michele Pisarra, PhD Student, > Dipartimento di Fisica, Universit? della Calabria > Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111028/3f6f30ff/attachment.htm From lmartinsamos at gmail.com Fri Oct 28 14:12:06 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Fri, 28 Oct 2011 14:12:06 +0200 Subject: [Pw_forum] QE interface to DP code In-Reply-To: <39FFE9D4-BBC2-42BB-808B-5734C7A5FC65@sissa.it> References: <1319794263.44379.YahooMailNeo@web27008.mail.ukl.yahoo.com> <39FFE9D4-BBC2-42BB-808B-5734C7A5FC65@sissa.it> Message-ID: Dear Michele, if I remember correctly pw2gw.f90 is the interface for the Olivia Pulci's GW code. I am not sure at all that the same interface works for DP (Valerio Olevano's code, also maintained by Francesco Sottile). Maybe you should ask directly to that people. bests Layla 2011/10/28 Stefano Baroni > what is "the DP code"? > I think that the TDDFT codes distributed with QE are directly interfaced > with pw.x > See: http://dx.doi.org/10.1016/j.cpc.2011.04.020 > SB > > On Oct 28, 2011, at 11:31 AM, Michele Pisarra wrote: > > Hi everyone. > Is it possible to use the output obtained with Quantum Espresso as an input > for the TDDFT code PW? > I know that the input to the DP code is a *.KSS file. I search through the > internet and I found that the post processing code pw2gw should do the job, > in it right? > However there are no intruction to prepare the input file and run this > code in the doc directory. > Thank you. > Best Regards, > > Michele Pisarra, PhD Student, > Dipartimento di Fisica, Universit? della Calabria > Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy > _______________________________________________ > 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 > > > _______________________________________________ > 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/20111028/f9eeb8d5/attachment.htm From lmartinsamos at gmail.com Fri Oct 28 17:11:56 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Fri, 28 Oct 2011 17:11:56 +0200 Subject: [Pw_forum] QE interface to DP code In-Reply-To: <1319812668.21612.YahooMailNeo@web27004.mail.ukl.yahoo.com> References: <1319794263.44379.YahooMailNeo@web27008.mail.ukl.yahoo.com> <39FFE9D4-BBC2-42BB-808B-5734C7A5FC65@sissa.it> <1319812668.21612.YahooMailNeo@web27004.mail.ukl.yahoo.com> Message-ID: Dear Michele, there is just a mistake in the allocation. I have attached a version that should avoid the problem. bests Layla 2011/10/28 Michele Pisarra > thank you for the answer > In any case I wasn't able to run the pw2gw.x. > I wasn't able to find an input file to mimic, nor a help file in the > documentation folder. > I run the code with an input file like this one > > &INPUTPP > prefix = 'myprefix' , > outdir = 'mydir', > what = 'gw', > use_gmaps = .FALSE. > / > myprefix and mydir are taken from a previous scf calculation. > I added last two fields after reading the pw2gw.f90, but I'm not > experienced with fortran, so probably I made some mistakes. > I run the code in this way: > espressodir/../PP/pw2gw.x < file.in > file.out > > The program starts running and writes something in some temporary files I > suppose ( fort.15; matrixelements; k.dat; QPLDA) and then stops with the > following error: > "At line 452 of file pw2gw.f90 > Fortran runtime error: Attemtping to allocate already allocated array > 'vec_tab_d2y' " > Thank you > Michele > > *Da:* Layla Martin-Samos > *A:* PWSCF Forum > *Cc:* Michele Pisarra > *Inviato:* Venerd? 28 Ottobre 2011 14:12 > *Oggetto:* Re: [Pw_forum] QE interface to DP code > > Dear Michele, if I remember correctly pw2gw.f90 is the interface for the > Olivia Pulci's GW code. I am not sure at all that the same interface works > for DP (Valerio Olevano's code, also maintained by Francesco Sottile). Maybe > you should ask directly to that people. > > bests > > Layla > > 2011/10/28 Stefano Baroni > > what is "the DP code"? > I think that the TDDFT codes distributed with QE are directly interfaced > with pw.x > See: http://dx.doi.org/10.1016/j.cpc.2011.04.020 > SB > > On Oct 28, 2011, at 11:31 AM, Michele Pisarra wrote: > > Hi everyone. > Is it possible to use the output obtained with Quantum Espresso as an input > for the TDDFT code PW? > I know that the input to the DP code is a *.KSS file. I search through the > internet and I found that the post processing code pw2gw should do the job, > in it right? > However there are no intruction to prepare the input file and run this > code in the doc directory. > Thank you. > Best Regards, > > Michele Pisarra, PhD Student, > Dipartimento di Fisica, Universit? della Calabria > Via P. Bucci, Cubo 31 C VI piano, 87036, Rende (CS), Italy > _______________________________________________ > 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 > > > _______________________________________________ > 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/20111028/18895734/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: pw2gw.f90 Type: text/x-fortran Size: 38074 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111028/18895734/attachment-0001.bin From mtorabi at uwo.ca Fri Oct 28 23:16:27 2011 From: mtorabi at uwo.ca (Amin Torabi) Date: Fri, 28 Oct 2011 17:16:27 -0400 Subject: [Pw_forum] structure oscillating with vc-md In-Reply-To: <4EAA2709.9090502@sissa.it> References: <4EAA2709.9090502@sissa.it> Message-ID: Dear Stefano, I actually was able to relax it using vc-relax; however, I was curious to see what happens with vc-md and vc-cp, mostly because I could set temperature with vc-md and vc-cp and not with vc-relax. Do you think it worth trying with vc-cp? i.e. does vc-cp render more accurate structure, especially if I increase pressure? Thanks in advance! On Thu, Oct 27, 2011 at 11:52 PM, Stefano de Gironcoli wrote: > ** > Dear Amin Torabi > you are performing a variable-cell MD simulation therefore the enthalpy > is not minimized by the Newton equations for atoms+cell are integrated to > give you the dynamics around the target pressure (P=0 in your case). > to get the relaxation you should use calculation = "vc-relax" and then > choose the minimization strategy. > the default is bfgs but also damp dynamics is available. > check the relevant input variables: ion_dynamics and cell_dynamics. > > best regards, > stefano > > > > On 10/28/2011 02:49 AM, Amin Torabi wrote: > > Dear QE users, > > Will you please do me a favor and take a look at my input file, below. > The total energy and force do not converge and keep oscillating... > I have tried different dt (between 20-70) and wmass, and still not able to > relax the structure > Any comment on my the input_cards here (k-point,ecut,pp,conv...?) > > Many thanks > > > > &CONTROL > calculation = 'vc-md' > pseudo_dir = './' > outdir = './' > prefix = 'dt20' > tstress = .true > tprnfor = .true > nstep = 100 > dt = 20 > / > &SYSTEM > ibrav = 12 > celldm(1) = 8.3147 > celldm(2) = 1.3 > celldm(3) = 1.4772 > celldm(4) = -0.260 > nat = 16 > ntyp = 2 > ecutwfc = 85 > ecutrho = 1100 > input_dft = 'pbesol' > nosym = .true > / > &ELECTRONS > conv_thr = 1.0D-9 > / > &IONS > pot_extrapolation='second-order' > wfc_extrapolation='second-order' > ion_temperature = 'rescaling' > tempw = 300 > / > &CELL > press = 0 > cell_dynamics = 'w' > wmass = 4.2 > / > ATOMIC_SPECIES > B 10.811 B.pbe-n-van.UPF > H 1.00794 H.pbe-van_bm.UPF > ATOMIC_POSITIONS crystal > B 0.005259620 0.145596712 0.040564862 > H -0.199830030 0.176142715 0.150841828 > H 0.217291388 0.312290957 -0.013967013 > H 0.124960907 -0.022012847 0.122883862 > B -0.005259620 -0.145596712 -0.040564862 > H 0.199830030 -0.176142715 -0.150841828 > H -0.217291388 -0.312290957 0.013967013 > H -0.124960907 0.022012847 -0.122883862 > B 0.494739818 0.354404554 0.540568678 > H 0.699828966 0.323861788 0.650847745 > H 0.282707973 0.187708799 0.486039576 > H 0.375038882 0.522017144 0.622882523 > B 0.505260182 0.645595446 0.459431322 > H 0.300171034 0.676138212 0.349152255 > H 0.717292027 0.812291201 0.513960424 > H 0.624961118 0.477982856 0.377117477 > K_POINTS automatic > 8 8 8 0 0 0 > > > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Amin Torabi Ph.D. Student Chemistry Department The University *of* Western Ontario London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111028/289446fc/attachment.htm From kalamaillist at gmail.com Sun Oct 30 12:50:54 2011 From: kalamaillist at gmail.com (WF) Date: Sun, 30 Oct 2011 19:50:54 +0800 Subject: [Pw_forum] c_bands: X eigenvalues not converged Message-ID: <000801cc96fa$30f49ef0$92dddcd0$@gmail.com> Hello everyone, I am running a bands calculation based on a scf calculation already done without problem. But after several days the output keeps prompting "c_bands: X eigenvalues not converged", where X = 3~8, and there are already approximately 300 lines of such messages. Is it just in the process or it meets problem and I must kill it? Thanks very much. ------------------------------------------ Wu, F College of Chemistry and Molecular Engineering Peking University ------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111030/0e2a210a/attachment.htm From abmus007 at gmail.com Sun Oct 30 18:52:49 2011 From: abmus007 at gmail.com (Abolore Musari) Date: Sun, 30 Oct 2011 17:52:49 +0000 Subject: [Pw_forum] error in vc-relax In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: Abolore Musari Date: Sun, 30 Oct 2011 06:59:12 +0000 Subject: error in vc-relax To: pw-forum at pwscf.org Dear QE Users, In my vc-relax calculation of my material, l encountered this error: from scale _h: error # Not enough space allocated for radial FFT: try restarting with larger cell_factor. pls l need ur assistance what exactly the input parameter shld l adjust. thanks abmus, Physics dept UNAAB From lorenzo.paulatto at impmc.upmc.fr Sun Oct 30 21:47:55 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Sun, 30 Oct 2011 21:47:55 +0100 Subject: [Pw_forum] error in vc-relax In-Reply-To: References: Message-ID: In data 30 ottobre 2011 alle ore 18:52:49, Abolore Musari ha scritto: > Dear QE Users, In my vc-relax calculation of my material, l > encountered this error: from scale _h: error # Not enough space > allocated for radial FFT: try restarting with larger cell_factor. pls > l need ur assistance what exactly the input parameter shld l adjust. > thanks abmus, Physics dept UNAAB Dear Abolore, just do as the message say: set cell_factor to something larger (check the Doc/INPUT_PW.txt for details), or start with a better guess for the lattice parameter. best regards P.S. there is a message size limit for messages sent to the mailing list but it is high enough that you do not need to use SMS abbreviation. -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From wumindt2 at zju.edu.cn Mon Oct 31 21:40:37 2011 From: wumindt2 at zju.edu.cn (wumindt2) Date: Tue, 01 Nov 2011 04:40:37 +0800 Subject: [Pw_forum] Raman spectra calculation using QE Message-ID: Dear All, I calculated the Raman intensity of quartz and got the result shown below. To plot the Raman spectra, colume [cm-1] should be the x axis, is colume [Raman] exactly the y axis? And what's the meaning of the [depol] colume? By the way, since epsil can only be calculated at q=0, does it mean there is no convergence test of Raman spectra with respect to q point? Thanks for any help! " IR cross sections are in (D/A)^2/amu units Raman cross sections are in A^4/amu units multiply Raman by 0.435857 for Clausius-Mossotti correction # mode [cm-1] [THz] IR Raman depol 1 0.00 0.0000 0.0000 117648.2478 0.0796 2 0.00 0.0000 0.0000 54851.8779 0.0878 3 0.00 0.0000 0.0000 5721.3899 0.1088 4 0.00 0.0000 0.0000 27197.6383 0.0792 5 0.00 0.0000 0.0000 147366.7743 0.0728 6 0.00 0.0000 0.0000 79591.1052 0.0839 7 134.34 4.0273 0.0005 11088.3162 0.6209 8 240.10 7.1981 0.1622 16185.7766 0.1558 9 241.21 7.2313 0.2024 24875.8773 0.1058 10 314.53 9.4293 3.0075 5175.3355 0.2916 11 328.75 9.8557 0.1138 17701.2140 0.6847 12 346.33 10.3827 3.1900 13146.6141 0.1307 13 390.34 11.7020 0.1564 53220.0070 0.0658 14 405.27 12.1496 9.5614 5754.0126 0.2673 15 434.56 13.0277 5.7052 303619.7884 0.0609 16 470.12 14.0938 5.8666 2135.0450 0.5859 17 551.14 16.5227 5.7194 5307.8446 0.7482 18 663.69 19.8969 2.9906 11422.0326 0.7170 19 664.81 19.9304 0.5153 14523.9240 0.4764 20 679.62 20.3742 16.2637 2261.0076 0.2333 21 745.02 22.3351 8.9307 157046.7356 0.1277 22 835.16 25.0373 11.9576 5478.4532 0.6700 23 924.96 27.7294 18.0245 18670.7483 0.2741 24 985.40 29.5415 40.4317 10913.6235 0.3922 25 996.49 29.8738 20.1984 46086.8553 0.5930 26 1052.71 31.5592 13.6824 14469.3320 0.4908 27 1069.38 32.0591 0.0030 39309.3312 0.7484 Min WU University of Saskachewan, Cananda