From trambui at u.boisestate.edu Wed Feb 1 00:13:01 2012 From: trambui at u.boisestate.edu (Tram Bui) Date: Tue, 31 Jan 2012 16:13:01 -0700 Subject: [Pw_forum] Ultrasoft Pseudopotential of Eu In-Reply-To: References: <4DB852D2.4070809@materials.ox.ac.uk> Message-ID: Dear Nicola, Hanghui and Trinh, I'm sorry for interupting but I've been trying to find someone who have had experiences with generating an ultrasoft pseudopotential for QE, and I saw your email back and forth so I just want to give it a shot to ask you couple of questions. Please accept my apology for any inconvenience. By the way, I've tried to generate an US PP for Cs and have not get much luck with it. To be honest I really don't have any background on PP, so it was really tough for me to be able to understand what each variable means and how to determine them (even though I have read the PP generation notes for QE users, and several papers or information online about PP). So would you spare me some time and give me some guidance on how to build a meaningful input file for PP generation? For Cs (Z=55), I want to include the 5s, 5p and 6s state for my valence and below is the input file I have build so far (it is not running correctly though). However, there are several things that I'm still unclear about. &input title='Cs', zed=55.0, prefix='Cs', iswitch=3, rel=1, dft='PBE', config='[Kr] 4d10 5s2 5p6 6s1 ', till this part, I understand that is to run the all-electron (AE) calculation rlderiv=4.20, (here I'm not quite sure how one can come up with the value for rlderiv, in this case I used the radius at most outpeak, 6s, from the AE wfc plot), so is it a right approach to obtain rlderiv? and what effect does it have on pseudizing the wfc process? is this the same as the cut of radius? eminld=-8.0, emaxld=3.0, deld=0.01d0, nld=3, For this value, I assume that I want to include 3 energy state, 5s 5p 6s, so I need to have 3 number of logarithmic derivative. is that correct? / &inputp lloc=0, here, from the ld1-input.txt, i know the lloc has to be equal to the last lls # in the card list below (in this case =0), but what does it mean by the "local chanel"? (what is a local chanel?) if I have lloc=0 here, does it mean that my local chanel is the 5s ? pseudotype=3, rho0=0.01, file_pseudopw='Cs.uspp-tb.UPF' / 4 6S 1 0 1.00 0.00 4.20 4.50 6S 1 0 0.00 1.00 4.00 4.50 5P 2 1 6.00 0.00 1.60 1.60 5S 1 0 2.00 0.00 1.40 1.40 For the wfc configuration above, - what does it indicate when one have difference (or the same) rcuts for norm-conversing and US PP? - when rcuts of US and NC are difference, why do one need two energies/channel? - In the case of when the second row is needed when rcuts are different, based on what one can determine the value for the "ener" (energy used to pseudize correspoding state)? I only know what it ener is zero for bound state, but most of the examples i looked at, everyone was using a nonzero value when they have another row for the same wfc( e.g. 6s in this case), does it mean the second row is the unbound state? I'm really sorry for the long email and the color code i used if that is bothering you. I'm doing this all alone without any help of any expert around here. So things are very confusing to me especially when it comes to quantum physics in which I have very limited understanding. I really appreciate any input you have for me. Best Regards, Tram Bui On Wed, Apr 27, 2011 at 12:48 PM, Vo, Trinh (388C) wrote: > Dear Nicola, > > I am working on generating pseudo potentials for a few elements of > Lanthanides too, but so far I am not successful yet (it is still bad). I > appreciate if you could share with me your parameter input. > > Thank you very much in advance, > > Trinh > > > On 4/27/11 10:30 AM, "Nicola Marzari" > wrote: > > > On 4/27/11 5:45 PM, hanghui chen wrote: > >> Dear PWscf community, > >> I am wondering if any one has succeeded in generating the > >> ultrasoft pseudopotential of Eu, using uspp-736. Now in the literature, > >> for most of the work that involves Eu, the calculation is done with VASP > >> where the pseudopotential is provided in its own library. > >> Thank you very much indeed. > >> > >> Hanghui Chen > >> Department of Physics, > >> Yale University > > > > > > Dear Hanghui, > > > > we have a test one normconserving, with f electrons in the valence, and > > an ultrasoft one, with f electrons in the core. This is part of a > > project developing and testing lanthanides pseudos, to be released later > > on, but if you want to give them a try, I can send them to you (would > > be great to have some test feedback). > > > > nicola > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- 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/20120131/1c210c3f/attachment.htm From konda.physics at gmail.com Wed Feb 1 07:31:54 2012 From: konda.physics at gmail.com (Kondaiah Samudrala) Date: Wed, 1 Feb 2012 12:01:54 +0530 Subject: [Pw_forum] Regarding Vdw interactions Message-ID: Dear all, I have confusion on implementation of grimme (london = .true.) in DFT. Is it valid only for ground state or at high pressures also???? Please give clarification for me to do High pressure structral transitions using grimme correction to PBE is how much valid????? I expect favorable reply Thanks in advance with regards S.Appalakondaiah Research scholar University of Hyderabad Hyderabad India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120201/65e30309/attachment-0001.htm From pdunne2 at gmail.com Wed Feb 1 14:20:56 2012 From: pdunne2 at gmail.com (Peter Dunne) Date: Wed, 1 Feb 2012 14:20:56 +0100 Subject: [Pw_forum] xsf to pwscf input In-Reply-To: <1327663704.3895.19.camel@catalyst.ijs.si> References: <1327663704.3895.19.camel@catalyst.ijs.si> Message-ID: Here is a slightly modified version to deal with supercells. It also includes two sed lines to replace Z values for Zn and O, change as is needed Payam. Best regards, Peter. --- Peter Dunne IFW Dresden, On 27 January 2012 12:28, Tone Kokalj wrote: > On Wed, 2012-01-25 at 18:54 -0600, Payam Norouzzadeh wrote: > > Hello QE users > > Is there any way,software,.. to convert xsf file formats(readable by > > Xcrysden) to input file for PWSCF( just crystal structure and atom > > coordinates)? > > I noticed I have a shell script that does the job. Regards, Tone > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120201/a7b308a2/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: xsf2pwi.sh Type: application/x-sh Size: 1239 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120201/a7b308a2/attachment.sh From pandey.bramha at gmail.com Wed Feb 1 17:24:52 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Wed, 1 Feb 2012 21:54:52 +0530 Subject: [Pw_forum] problem to convert Cv (R) to Cv(in J/mol.K) Message-ID: Hi..Dear QE users I have a problem to calculate the Cv value in J/mol.K from Cv(R gas constant). At 300K, the value of Cv is 0.0000002506 . I multiplied 0.0000002506 by 3NR(3*2*8.314) which comes 1.25*10^-5 which was very less compare to experimental Cv value. Please someone help me. Thanks in advanced for your kind help. -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120201/46a1da82/attachment.htm From giannozz at democritos.it Wed Feb 1 18:42:09 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 01 Feb 2012 18:42:09 +0100 Subject: [Pw_forum] BEC from DFPT In-Reply-To: References: Message-ID: <1328118129.16216.9.camel@fe12lx.fisica.uniud.it> On Tue, 2012-01-31 at 13:27 +0400, ?????? ???????? wrote: > I am trying to calculate Born effective charges from DFTP for the > spin-polarized system. However, these systems must be treated as > metallic (scf-calculation with occupations='smearing'). > The problem is that ph.x complains about my calculation, > but the system has an insulator behavior. in that case, if you comment out the check, it should work. There are various ways to specify occupation numbers in spin-polarized systems, if you know the final answer. Not sure which ones are accepted by the phonon codde P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From elie.moujaes at hotmail.co.uk Wed Feb 1 21:57:06 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Wed, 1 Feb 2012 20:57:06 +0000 Subject: [Pw_forum] error when restarting ph.x in the parallel computing mode Message-ID: I was running some phonon calculations in the parallel mode and then the network system crashed due to heavy rain and when I restarted the calculations and added recover=.true. , the calculations stopped with the following error: forrtl: severe (24): end-of-file during read, unit 40, file /home/emoujaes/GB60/Results-GB60/GrBo60ph.a2Fsave Image PC Routine Line Source ph.x 00000000009B103A Unknown Unknown Unknown ph.x 00000000009AFBB5 Unknown Unknown Unknown ph.x 00000000009302CA Unknown Unknown Unknown ph.x 00000000008D9B19 Unknown Unknown Unknown ph.x 00000000008D9406 Unknown Unknown Unknown ph.x 00000000008FF1B5 Unknown Unknown Unknown ph.x 000000000041A0CF elphsum_ 412 elphon.f90 ph.x 0000000000406450 MAIN__ 134 phonon.f90 ph.x 0000000000406282 Unknown Unknown Unknown libc.so.6 00000033C301D994 Unknown Unknown Unknown ph.x 00000000004061A9 Unknown Unknown Unknown what could be a source of such an error? Thank you all Elie MoujaesUniversity of NottinghamBG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120201/65ce627d/attachment.htm From hqzhou at nju.edu.cn Thu Feb 2 03:28:50 2012 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Thu, 2 Feb 2012 10:28:50 +0800 Subject: [Pw_forum] Requesting for structural details References: Message-ID: <11557AB51D13443499E36513E58C7AEE@solarflare> You just need to pick up a math textbook of high school. Given a vector a = (ax, ay, az), |a| = sqrt(ax^2+ay^2+az^2). For the angle between two vectors, you need to know their dot product, cos(angle) = a dot b /(|a||b|), where a dot b = ax*bx + ay*by + az*bz. Hope you know which two lattice vectors correspond to which angle. zhou huiqun @earth sciences, nanjing university, china ----- Original Message ----- From: Kondaiah Samudrala To: pw_forum at pwscf.org Sent: Sunday, January 29, 2012 4:31 AM Subject: [Pw_forum] Requesting for structural details Dear All, I am working on layered type material which crystallizes in rhombohedral structure with space group 166 ( ibrav =5). In the i/p file for VC-Relax, i used the lattice parameters and angle as celldm(1)=7.4870 and celldm(4)=0.586005. In the first step of the of the o/p file shows the basis vectors as 0.454970 -0.262677 0.850884 0.000000 0.525354 0.850884 -0.4504970 -0.262677 0.850884 After completing the VC-Relax i got the basis vectors as CELL-PARAMETERS ( alat=7.4870) 0.441119855 -0.254680667 0.78874941 0.00000000 0.509361335 0.78874941 -0.441119855 -0.254680667 0.78874941 with this o/p values, how can i calculate lattice vector and angle for my material ( For orthorhombic and tetragonal structures i calculated lattice parametrs successfully but i am not able to do this structure ). i am requesting your favorable reply. with regards S.Appalakondaiah PhD Scholar University of Hyderabad Hyderabad 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/20120202/858e442d/attachment.htm From yukihiro_okuno at fujifilm.co.jp Thu Feb 2 07:47:33 2012 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Thu, 2 Feb 2012 15:47:33 +0900 Subject: [Pw_forum] Excited State Gradients in TDDFT Message-ID: Dear PWSCF users and developers. I want to know the possibility of excited state gradients in TDDFT implemented in Quantum Espresso. Can the PWSCF calculate the excited state gradients (Force of atoms in excited state ) by PWSCF, or are there plan to develop the excited state gradient calculation ? The implementation of TDDFT in PWSCf uses lanczos method and does not explicitly calculate the excited energy, and is it difficult to extend to calculate force in this formalism ? Sincerely, Yukihiro Okuno. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120202/2be0cb70/attachment-0001.htm From pandey.bramha at gmail.com Thu Feb 2 11:40:38 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Thu, 2 Feb 2012 16:10:38 +0530 Subject: [Pw_forum] problem to convert Cv (R) to Cv(in J/mol.K) In-Reply-To: References: Message-ID: Sorry to disturbing all of you. ?But Really i need your's help to understand the the following results. Here i am attaching some more information which is obtained through the F_QHA.X code. # Zero vibration energy:????? 0.0000000005? (Ry/cell) # Phonon DOS norm????? :????? 0.000000????? ! 3N for check purpose, N number of atoms in the unit cell # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by 3N modes), S in k_B # #?? T???????? E_internal??????? F_vibration????????? Specific heat (C_v)?????? Entropy ############################################################################################################ ??? 5.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000000 ????? 0.0000000000 ?? 10.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000000 ????? 0.0000000000 ?? 15.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000001 ????? 0.0000000000 ?? 20.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000002 ????? 0.0000000001 ?? 25.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000004 ????? 0.0000000001 ?? 30.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000010 ????? 0.0000000002 ?? 35.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000020 ????? 0.0000000005 ?? 40.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000036 ????? 0.0000000008 ?? 45.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000059 ????? 0.0000000014 ?? 50.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000090 ????? 0.0000000021 ?? 55.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000128 ????? 0.0000000032 ?? 60.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000172 ????? 0.0000000045 ?? 65.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000223 ????? 0.0000000060 ?? 70.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000278 ????? 0.0000000079 ?? 75.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000338 ????? 0.0000000100 ?? 80.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000402 ????? 0.0000000124 ?? 85.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000468 ????? 0.0000000150 ?? 90.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000537 ????? 0.0000000179 ?? 95.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000607 ????? 0.0000000210 Now sir question remain same how i will get the Cv value in J/Mol.K from R.? Your valuable help is needed to me. On Wed, Feb 1, 2012 at 9:54 PM, bramha pandey wrote: > > > Hi..Dear? QE users > > I have a problem to calculate the Cv value in J/mol.K from Cv(R gas constant). At 300K, the value of Cv is? 0.0000002506 . I multiplied? 0.0000002506? by 3NR(3*2*8.314) which comes 1.25*10^-5 which was very less compare to experimental Cv value. > > Please someone help me. > Thanks in advanced for your kind help. > -- > 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 -- 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 degironc at sissa.it Thu Feb 2 12:46:56 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 02 Feb 2012 12:46:56 +0100 Subject: [Pw_forum] =?utf-8?q?problem_to_convert_Cv_=28R=29_to_Cv=28in_J/m?= =?utf-8?b?b2wuSyk=?= In-Reply-To: References: Message-ID: Dear Bramha Prasad Pandey, the question rather seams to me how is it that your phonon DOS normalization is zero... this means that the code thinks your system has zero atoms. stefano On 02.02.2012 11:40, bramha pandey wrote: > Sorry to disturbing all of you. > ?But Really i need your's help to understand the the following > results. Here i am attaching some more information which is obtained > through the F_QHA.X code. > > # Zero vibration energy:????? 0.0000000005? (Ry/cell) > # Phonon DOS norm????? :????? 0.000000????? ! 3N for check purpose, N > number of atoms in the unit cell > # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by > 3N > modes), S in k_B > # > #?? T???????? E_internal??????? F_vibration????????? Specific heat > (C_v)?????? Entropy > > ############################################################################################################ > ??? 5.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000000 > ????? 0.0000000000 > ?? 10.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000000 > ????? 0.0000000000 > ?? 15.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000001 > ????? 0.0000000000 > ?? 20.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000002 > ????? 0.0000000001 > ?? 25.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000004 > ????? 0.0000000001 > ?? 30.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000010 > ????? 0.0000000002 > ?? 35.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000020 > ????? 0.0000000005 > ?? 40.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000036 > ????? 0.0000000008 > ?? 45.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000059 > ????? 0.0000000014 > ?? 50.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000090 > ????? 0.0000000021 > ?? 55.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000128 > ????? 0.0000000032 > ?? 60.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000172 > ????? 0.0000000045 > ?? 65.00????? 0.0000000005????? 0.0000000005?????????? 0.0000000223 > ????? 0.0000000060 > ?? 70.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000278 > ????? 0.0000000079 > ?? 75.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000338 > ????? 0.0000000100 > ?? 80.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000402 > ????? 0.0000000124 > ?? 85.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000468 > ????? 0.0000000150 > ?? 90.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000537 > ????? 0.0000000179 > ?? 95.00????? 0.0000000006????? 0.0000000005?????????? 0.0000000607 > ????? 0.0000000210 > > Now sir question remain same how i will get the Cv value in J/Mol.K > from R.? > > Your valuable help is needed to me. > > On Wed, Feb 1, 2012 at 9:54 PM, bramha pandey > wrote: >> >> >> Hi..Dear? QE users >> >> I have a problem to calculate the Cv value in J/mol.K from Cv(R gas >> constant). At 300K, the value of Cv is? 0.0000002506 . I multiplied? >> 0.0000002506? by 3NR(3*2*8.314) which comes 1.25*10^-5 which was very >> less compare to experimental Cv value. >> >> Please someone help me. >> Thanks in advanced for your kind help. >> -- >> 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 pandey.bramha at gmail.com Thu Feb 2 13:40:42 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Thu, 2 Feb 2012 18:10:42 +0530 Subject: [Pw_forum] problem to convert Cv (R) to Cv(in J/mol.K) In-Reply-To: References: Message-ID: Dear Stefano de Gironcoli Sir... First thanks to you for your kind response. When i plot the graph between Cv(R) and T(K) it was showing the good shape of the Cv vs Tempertaure which was generaly known but difference is that the scalling of Cv(R) is from 1*10^-7 to 7*10^-7. is it the problem of sacaling or something else. Here i am attaching the input file for pw.x and ph.x. pw.x input File. &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/' , pseudo_dir = '/' , prefix = 'aln' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 2, celldm(1) = 8.97, nat = 2, ntyp = 2, ecutwfc = 28 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / ATOMIC_SPECIES Al 26.98000 Al.pz-vbc.UPF N 14.01000 N.pz-vbc.UPF ATOMIC_POSITIONS alat Al 0.000000000 0.000000000 0.000000000 N 0.250000000 0.250000000 0.250000000 K_POINTS automatic 6 6 6 0 0 0 ph.x input file:: phonons at 444 &INPUTPH outdir = '/' , prefix = 'aln' , fildyn = 'dyn' , ldisp = .true., trans = .true., nq1=4, nq2=4, nq3=4, epsil = .false., amass(1) = 26.98000, amass(2) = 14.01000, iverbosity = 0 , tr2_ph = 1.0d-14 , / If the code has read my system has Zero atoms then how can i get rid of this problem. Your help in any form is appreciated. On Thu, Feb 2, 2012 at 5:16 PM, Stefano de Gironcoli wrote: > Dear Bramha Prasad Pandey, > the question rather seams to me how is it that your phonon DOS > normalization is zero... > this means that the code thinks your system has zero atoms. > stefano > > > On 02.02.2012 11:40, bramha pandey wrote: > > Sorry to disturbing all of you. > > But Really i need your's help to understand the the following > > results. Here i am attaching some more information which is obtained > > through the F_QHA.X code. > > > > # Zero vibration energy: 0.0000000005 (Ry/cell) > > # Phonon DOS norm : 0.000000 ! 3N for check purpose, N > > number of atoms in the unit cell > > # T in K, F_vib in Ry/cell, C_v in R (the universal gas constant by > > 3N > > modes), S in k_B > > # > > # T E_internal F_vibration Specific heat > > (C_v) Entropy > > > > > ############################################################################################################ > > 5.00 0.0000000005 0.0000000005 0.0000000000 > > 0.0000000000 > > 10.00 0.0000000005 0.0000000005 0.0000000000 > > 0.0000000000 > > 15.00 0.0000000005 0.0000000005 0.0000000001 > > 0.0000000000 > > 20.00 0.0000000005 0.0000000005 0.0000000002 > > 0.0000000001 > > 25.00 0.0000000005 0.0000000005 0.0000000004 > > 0.0000000001 > > 30.00 0.0000000005 0.0000000005 0.0000000010 > > 0.0000000002 > > 35.00 0.0000000005 0.0000000005 0.0000000020 > > 0.0000000005 > > 40.00 0.0000000005 0.0000000005 0.0000000036 > > 0.0000000008 > > 45.00 0.0000000005 0.0000000005 0.0000000059 > > 0.0000000014 > > 50.00 0.0000000005 0.0000000005 0.0000000090 > > 0.0000000021 > > 55.00 0.0000000005 0.0000000005 0.0000000128 > > 0.0000000032 > > 60.00 0.0000000005 0.0000000005 0.0000000172 > > 0.0000000045 > > 65.00 0.0000000005 0.0000000005 0.0000000223 > > 0.0000000060 > > 70.00 0.0000000006 0.0000000005 0.0000000278 > > 0.0000000079 > > 75.00 0.0000000006 0.0000000005 0.0000000338 > > 0.0000000100 > > 80.00 0.0000000006 0.0000000005 0.0000000402 > > 0.0000000124 > > 85.00 0.0000000006 0.0000000005 0.0000000468 > > 0.0000000150 > > 90.00 0.0000000006 0.0000000005 0.0000000537 > > 0.0000000179 > > 95.00 0.0000000006 0.0000000005 0.0000000607 > > 0.0000000210 > > > > Now sir question remain same how i will get the Cv value in J/Mol.K > > from R.? > > > > Your valuable help is needed to me. > > > > On Wed, Feb 1, 2012 at 9:54 PM, bramha pandey > > wrote: > >> > >> > >> Hi..Dear QE users > >> > >> I have a problem to calculate the Cv value in J/mol.K from Cv(R gas > >> constant). At 300K, the value of Cv is 0.0000002506 . I multiplied > >> 0.0000002506 by 3NR(3*2*8.314) which comes 1.25*10^-5 which was very > >> less compare to experimental Cv value. > >> > >> Please someone help me. > >> Thanks in advanced for your kind help. > >> -- > >> 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120202/7ee18eff/attachment-0001.htm From giuseppe.mattioli at ism.cnr.it Thu Feb 2 16:46:59 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 2 Feb 2012 16:46:59 +0100 Subject: [Pw_forum] compile GIPAW on aix Message-ID: <201202021646.59608.giuseppe.mattioli@ism.cnr.it> Dear all I'm trying to compile the XSPECTRA code (4.3.2 version) on a power/AIX machine (sp.sp6 at cineca.it) where everything else goes generally fine. When the compiler tries to compile the GIPAW directory, it stops complaining something that seems likely to be an "AIX related" issue (make -C src make: Not a recognized flag: C) that I am not able to solve. cd install ; make -f plugins_makefile gipaw make: 1254-053 Command "$(dummy-variable)" expands to empty string. if test ! -d ../GIPAW; then (gzip -dc ../archive/qe-gipaw-latest.tar.gz | (cd ../ ; tar -xvf -)) ; (cd ../ ; ln -s qe-gipaw* GIPAW) ; fi touch uncompress-gipaw cd ../GIPAW ; ./configure --with-qe-source=/gpfs/scratch/userexternal/gmattiol/4.3.2 checking for /gpfs/scratch/userexternal/gmattiol/4.3.2/make.sys... yes checking for /gpfs/scratch/userexternal/gmattiol/4.3.2/Modules/version.f90... yes checking quantum-Espresso version... 4.3.2 configure: creating ./config.status config.status: creating makedeps.sh config.status: creating src/Makefile config.status: executing default commands sed: illegal option -- i Usage: sed [-n] [-u] Script [File ...] sed [-n] [-u] [-e Script] ... [-f Script_file] ... [File ...] sed: illegal option -- i Usage: sed [-n] [-u] Script [File ...] sed [-n] [-u] [-e Script] ... [-f Script_file] ... [File ...] touch ./configure-gipaw if test -d ../GIPAW; then cd ../GIPAW; make all; cd ../bin; ln -fs ../GIPAW/bin/gipaw.x . ; fi Building ce-gipaw... make -C src make: Not a recognized flag: C usage: make [-einqrst] [-k|-S] [-d[A|adg[1|2]mstv]] [-D variable] [-f makefile] [-j [jobs]] [variable=value ...] [target ...] make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 2. Stop. Can you provide any advice? Yours Giuseppe -- ******************************************************** - 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 ism.cnr.it Thu Feb 2 17:05:34 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 2 Feb 2012 17:05:34 +0100 Subject: [Pw_forum] compile GIPAW on aix In-Reply-To: <20120202165246.Horde._5TrZx8V4mxPKrFOXtFmBHA@webmail.sissa.it> References: <201202021646.59608.giuseppe.mattioli@ism.cnr.it> <20120202165246.Horde._5TrZx8V4mxPKrFOXtFmBHA@webmail.sissa.it> Message-ID: <201202021705.35302.giuseppe.mattioli@ism.cnr.it> ciao Emine It seems to work... Thanks G. On Thursday 02 February 2012 16:52:46 you wrote: > ciao Giuseppe, > try loading the available modules at sp6 first, i usually load make and > sed. hope it helps > emine kucukbenli > > Quoting Giuseppe Mattioli : > > Dear all > > I'm trying to compile the XSPECTRA code (4.3.2 version) on a > > power/AIX machine (sp.sp6 at cineca.it) > > where everything else goes generally fine. > > When the compiler tries to compile the GIPAW directory, it stops > > complaining something that seems > > likely to be an "AIX related" issue (make -C src make: Not a > > recognized flag: C) that I am not able > > to solve. > > > > cd install ; make -f plugins_makefile gipaw > > make: 1254-053 Command "$(dummy-variable)" expands to empty string. > > > > if test ! -d ../GIPAW; then (gzip -dc > > ../archive/qe-gipaw-latest.tar.gz | (cd ../ ; > > tar -xvf -)) ; (cd ../ ; ln -s qe-gipaw* GIPAW) ; fi > > touch uncompress-gipaw > > cd ../GIPAW ; ./configure > > --with-qe-source=/gpfs/scratch/userexternal/gmattiol/4.3.2 > > checking for /gpfs/scratch/userexternal/gmattiol/4.3.2/make.sys... yes > > checking for > > /gpfs/scratch/userexternal/gmattiol/4.3.2/Modules/version.f90... yes > > checking quantum-Espresso version... 4.3.2 > > configure: creating ./config.status > > config.status: creating makedeps.sh > > config.status: creating src/Makefile > > config.status: executing default commands > > sed: illegal option -- i > > Usage: sed [-n] [-u] Script [File ...] > > sed [-n] [-u] [-e Script] ... [-f Script_file] ... [File ...] > > sed: illegal option -- i > > Usage: sed [-n] [-u] Script [File ...] > > sed [-n] [-u] [-e Script] ... [-f Script_file] ... [File ...] > > touch ./configure-gipaw > > if test -d ../GIPAW; then cd ../GIPAW; make all; cd ../bin; > > ln -fs ../GIPAW/bin/gipaw.x . ; > > fi > > Building ce-gipaw... > > make -C src > > make: Not a recognized flag: C > > usage: make [-einqrst] [-k|-S] [-d[A|adg[1|2]mstv]] [-D variable] > > [-f makefile] [-j [jobs]] > > [variable=value ...] [target ...] > > make: 1254-004 The error code from the last command is 2. > > > > > > Stop. > > make: 1254-004 The error code from the last command is 2. > > > > > > Stop. > > make: 1254-004 The error code from the last command is 2. > > > > > > Stop. > > > > > > Can you provide any advice? > > > > Yours > > > > Giuseppe > > > > -- > > ******************************************************** > > - 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 -- ******************************************************** - 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 akohlmey at gmail.com Thu Feb 2 17:06:05 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Thu, 2 Feb 2012 11:06:05 -0500 Subject: [Pw_forum] compile GIPAW on aix In-Reply-To: <201202021646.59608.giuseppe.mattioli@ism.cnr.it> References: <201202021646.59608.giuseppe.mattioli@ism.cnr.it> Message-ID: On Thu, Feb 2, 2012 at 10:46 AM, Giuseppe Mattioli wrote: > > Dear all > I'm trying to compile the XSPECTRA code (4.3.2 version) on a power/AIX machine (sp.sp6 at cineca.it) > where everything else goes generally fine. > When the compiler tries to compile the GIPAW directory, it stops complaining something that seems > likely to be an "AIX related" issue (make -C src make: Not a recognized flag: C) that I am not able > to solve. > > ? ? ? ?cd install ; make ?-f plugins_makefile gipaw > make: 1254-053 Command "$(dummy-variable)" expands to empty string. > > ? ? ? ?if test ! -d ../GIPAW; then ?(gzip -dc ../archive/qe-gipaw-latest.tar.gz | (cd ../ ; > tar -xvf -)) ; ?(cd ../ ; ln -s qe-gipaw* GIPAW) ; fi > ? ? ? ?touch uncompress-gipaw > ? ? ? ?cd ../GIPAW ; ?./configure --with-qe-source=/gpfs/scratch/userexternal/gmattiol/4.3.2 > checking for /gpfs/scratch/userexternal/gmattiol/4.3.2/make.sys... yes > checking for /gpfs/scratch/userexternal/gmattiol/4.3.2/Modules/version.f90... yes > checking quantum-Espresso version... 4.3.2 > configure: creating ./config.status > config.status: creating makedeps.sh > config.status: creating src/Makefile > config.status: executing default commands > sed: illegal option -- i > Usage: ?sed [-n] [-u] Script [File ...] > ? ? ? ?sed [-n] [-u] [-e Script] ... [-f Script_file] ... [File ...] > sed: illegal option -- i > Usage: ?sed [-n] [-u] Script [File ...] > ? ? ? ?sed [-n] [-u] [-e Script] ... [-f Script_file] ... [File ...] > ? ? ? ?touch ./configure-gipaw > ? ? ? ?if test -d ../GIPAW; then ?cd ../GIPAW; make all; cd ../bin; ln -fs ../GIPAW/bin/gipaw.x . ; > fi > Building ce-gipaw... > ? ? ? ?make -C src > make: Not a recognized flag: C > usage: make [-einqrst] [-k|-S] [-d[A|adg[1|2]mstv]] [-D variable] [-f makefile] [-j [jobs]] > [variable=value ...] [target ...] > make: 1254-004 The error code from the last command is 2. > > > Stop. > make: 1254-004 The error code from the last command is 2. > > > Stop. > make: 1254-004 The error code from the last command is 2. > > > Stop. > > > Can you provide any advice? neither the "make" nor the "sed" program are compatible with what QE expects. try using/installing their GNU counterparts instead. axel. > > Yours > > Giuseppe > > -- > ******************************************************** > - 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 -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From Ari.P.Seitsonen at iki.fi Thu Feb 2 17:10:14 2012 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Thu, 2 Feb 2012 17:10:14 +0100 (CET) Subject: [Pw_forum] compile GIPAW on aix In-Reply-To: <201202021646.59608.giuseppe.mattioli@ism.cnr.it> References: <201202021646.59608.giuseppe.mattioli@ism.cnr.it> Message-ID: Dear Giuseppe, Adding to Axel's answer: # ibm01 (~) : which sed # /opt/freeware/bin/sed # ibm01 (~) : whereis sed # sed: /usr/bin/sed The former one, provided at least on some IBM AIX PowerX systems, contains the version of make/sed/etc employing the GNU-like syntax, the latter one are defaults from the AIX and have often different options. You can check if the /opt/freeware exists on your machine and put it in your variable PATH before the /usr/bin/ or /bin/. Just my experience... Greetings from Zurich, 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 Thu, 2 Feb 2012, Giuseppe Mattioli wrote: > > Dear all > I'm trying to compile the XSPECTRA code (4.3.2 version) on a power/AIX machine (sp.sp6 at cineca.it) > where everything else goes generally fine. > When the compiler tries to compile the GIPAW directory, it stops complaining something that seems > likely to be an "AIX related" issue (make -C src make: Not a recognized flag: C) that I am not able > to solve. > > cd install ; make -f plugins_makefile gipaw > make: 1254-053 Command "$(dummy-variable)" expands to empty string. > > if test ! -d ../GIPAW; then (gzip -dc ../archive/qe-gipaw-latest.tar.gz | (cd ../ ; > tar -xvf -)) ; (cd ../ ; ln -s qe-gipaw* GIPAW) ; fi > touch uncompress-gipaw > cd ../GIPAW ; ./configure --with-qe-source=/gpfs/scratch/userexternal/gmattiol/4.3.2 > checking for /gpfs/scratch/userexternal/gmattiol/4.3.2/make.sys... yes > checking for /gpfs/scratch/userexternal/gmattiol/4.3.2/Modules/version.f90... yes > checking quantum-Espresso version... 4.3.2 > configure: creating ./config.status > config.status: creating makedeps.sh > config.status: creating src/Makefile > config.status: executing default commands > sed: illegal option -- i > Usage: sed [-n] [-u] Script [File ...] > sed [-n] [-u] [-e Script] ... [-f Script_file] ... [File ...] > sed: illegal option -- i > Usage: sed [-n] [-u] Script [File ...] > sed [-n] [-u] [-e Script] ... [-f Script_file] ... [File ...] > touch ./configure-gipaw > if test -d ../GIPAW; then cd ../GIPAW; make all; cd ../bin; ln -fs ../GIPAW/bin/gipaw.x . ; > fi > Building ce-gipaw... > make -C src > make: Not a recognized flag: C > usage: make [-einqrst] [-k|-S] [-d[A|adg[1|2]mstv]] [-D variable] [-f makefile] [-j [jobs]] > [variable=value ...] [target ...] > make: 1254-004 The error code from the last command is 2. > > > Stop. > make: 1254-004 The error code from the last command is 2. > > > Stop. > make: 1254-004 The error code from the last command is 2. > > > Stop. > > > Can you provide any advice? > > Yours > > Giuseppe > > -- > ******************************************************** > - 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 giuseppe.mattioli at ism.cnr.it Thu Feb 2 17:12:52 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 2 Feb 2012 17:12:52 +0100 Subject: [Pw_forum] compile GIPAW on aix In-Reply-To: References: <201202021646.59608.giuseppe.mattioli@ism.cnr.it> Message-ID: <201202021712.52901.giuseppe.mattioli@ism.cnr.it> Thanks to all for the ultrafast answers! G. On Thursday 02 February 2012 17:10:14 Ari P Seitsonen wrote: > Dear Giuseppe, > > Adding to Axel's answer: > > # ibm01 (~) : which sed > # /opt/freeware/bin/sed > # ibm01 (~) : whereis sed > # sed: /usr/bin/sed > > The former one, provided at least on some IBM AIX PowerX systems, contains > the version of make/sed/etc employing the GNU-like syntax, the latter one > are defaults from the AIX and have often different options. You can check > if the /opt/freeware exists on your machine and put it in your > variable PATH before the /usr/bin/ or /bin/. > > Just my experience... > > Greetings from Zurich, > > 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 Thu, 2 Feb 2012, Giuseppe Mattioli wrote: > > Dear all > > I'm trying to compile the XSPECTRA code (4.3.2 version) on a power/AIX > > machine (sp.sp6 at cineca.it) where everything else goes generally fine. > > When the compiler tries to compile the GIPAW directory, it stops > > complaining something that seems likely to be an "AIX related" issue > > (make -C src make: Not a recognized flag: C) that I am not able to solve. > > > > cd install ; make -f plugins_makefile gipaw > > make: 1254-053 Command "$(dummy-variable)" expands to empty string. > > > > if test ! -d ../GIPAW; then (gzip -dc > > ../archive/qe-gipaw-latest.tar.gz | (cd ../ ; tar -xvf -)) ; (cd ../ ; > > ln -s qe-gipaw* GIPAW) ; fi > > touch uncompress-gipaw > > cd ../GIPAW ; ./configure > > --with-qe-source=/gpfs/scratch/userexternal/gmattiol/4.3.2 checking for > > /gpfs/scratch/userexternal/gmattiol/4.3.2/make.sys... yes checking for > > /gpfs/scratch/userexternal/gmattiol/4.3.2/Modules/version.f90... yes > > checking quantum-Espresso version... 4.3.2 > > configure: creating ./config.status > > config.status: creating makedeps.sh > > config.status: creating src/Makefile > > config.status: executing default commands > > sed: illegal option -- i > > Usage: sed [-n] [-u] Script [File ...] > > sed [-n] [-u] [-e Script] ... [-f Script_file] ... [File ...] > > sed: illegal option -- i > > Usage: sed [-n] [-u] Script [File ...] > > sed [-n] [-u] [-e Script] ... [-f Script_file] ... [File ...] > > touch ./configure-gipaw > > if test -d ../GIPAW; then cd ../GIPAW; make all; cd ../bin; ln > > -fs ../GIPAW/bin/gipaw.x . ; fi > > Building ce-gipaw... > > make -C src > > make: Not a recognized flag: C > > usage: make [-einqrst] [-k|-S] [-d[A|adg[1|2]mstv]] [-D variable] [-f > > makefile] [-j [jobs]] [variable=value ...] [target ...] > > make: 1254-004 The error code from the last command is 2. > > > > > > Stop. > > make: 1254-004 The error code from the last command is 2. > > > > > > Stop. > > make: 1254-004 The error code from the last command is 2. > > > > > > Stop. > > > > > > Can you provide any advice? > > > > Yours > > > > Giuseppe > > > > -- > > ******************************************************** > > - 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 -- ******************************************************** - 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 vv0210 at gmail.com Thu Feb 2 20:48:53 2012 From: vv0210 at gmail.com (Vikas Varshney) Date: Thu, 2 Feb 2012 14:48:53 -0500 Subject: [Pw_forum] Some questions on Electron Phonon Calculations. Message-ID: Dear Users, I am willing to run electron-phonon calculations for my Ni system of interest and have few queries to clarify and questions as well. I will highly appreciate your answers towards better understanding of the el-ph calculations. Based on Al example, I have gathered that after scf-relaxation (for dense k points), the el-ph calculations is performed this way. 1. Estimate # of q points (based on provided nqs) 2. For each q point, calculate the dynamical matrix 2a) First estimate # of irreducible representations (which are the branches in phonon dispersion curve) for that q 2b) For each irreducible representation, run the convergence test 3. Once 2a) and 2b) are done, diagonalize the dynamical matrix. 4. Calculate the frequencies (n) for that q. 5. Calculate lambda (q,n) and gamma (q,n) with 10 different gaussian broadening (0.005 to 0.05) 6. Proceed to step 2 for next q. Please guide if my understanding is wrong. The queries I have are follows *A. What is gamma (q,n) in point 5 which shows in elph output file as follows. * lambda( 2)= 0.0841 gamma= 72.85 GHz lambda( 3)= 0.0306 gamma= 97.74 GHz ** *B. The lambda and gamma are calculated for 10 different gaussian broadening values. This value is irrespective of what is used in scf.fit calculations prior to elph calculations. How should we interpret these 10 values? How should one decide which gaussian broadening is appropriate? * Now coming to my problem of interest. I am planning to calculate cummulative lambda for single layer of Ni atoms. So, I start by relaxing a bulk Ni crystal, cut out a fcc plane from (relaxed crystal) that with 4 atoms and create a supercell (with empty vaccum space). Now, I run scf calculation with dense grid (24,24,8) followed by second scf run with (8,8,2) grid. Then I run my elph-calculation. Here is the input file for elph. &INPUTPH outdir = './' , prefix = '1slab' , fildyn = '1slab.dyn' , fildvscf = '1slab' , ldisp = .true., tr2_ph=1.0d-10, nq1 = 8 , nq2 = 8 , nq3 = 2 , alpha_mix(1) = 0.4 , epsil = .false., elph = .true., fpol = .false. , recover = .false. , amass(1) = 58.69340 , iverbosity = 1 , / *I have two more questions for this particular system. * *1. For q=(0,0,0) convergence is achieved successfully. However, I see 2 negative frequencies. Similarly for q=(0,0,-0.12), I see one neg frequency. Does that mean that* * a) My atoms are not fully relaxed. * * b) My SCF grid is not dense enough?* * c) erho, ecut values are not big enough? I used erhowfc of 55 and erhocut of 550?* ** *Please guide.* ** *2. For the next q point, I do not get convergence acheived in 100 (default) interations for certain polarization. This is what I get at the end* ** iter # 89 total cpu time : 8505.8 secs av.it.: 34.3 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.439E+23 iter # 90 total cpu time : 8648.0 secs av.it.: 36.0 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.592E+23 iter # 91 total cpu time : 8790.0 secs av.it.: 35.9 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.195E+25 iter # 92 total cpu time : 8931.3 secs av.it.: 35.7 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.199E+25 iter # 93 total cpu time : 9079.5 secs av.it.: 37.7 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.197E+25 iter # 94 total cpu time : 9230.5 secs av.it.: 38.4 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.295E+27 iter # 95 total cpu time : 9382.6 secs av.it.: 38.7 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.426E+26 iter # 96 total cpu time : 9538.3 secs av.it.: 39.8 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.130E+27 iter # 97 total cpu time : 9697.1 secs av.it.: 40.4 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.182E+29 iter # 98 total cpu time : 9855.5 secs av.it.: 40.4 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.216E+28 iter # 99 total cpu time : 10019.0 secs av.it.: 41.8 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.732E+28 iter # 100 total cpu time : 10183.3 secs av.it.: 42.0 thresh= 0.100E-01 alpha_mix = 0.400 |ddv_scf|^2 = 0.123E+31 End of self-consistent calculation No convergence has been achieved *It can be seen that |ddv_scf|^2 is exponentially increasing instead of decreasing. What could be the possible reason behind it? * Any help will be highly appreaciated. Thanks in advance and best Regards, Vikas Computational Reasearcher, Wright Patterson Air Force Base, Dayton OH. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120202/ed91a999/attachment.htm From chengyu.young at gmail.com Thu Feb 2 22:20:39 2012 From: chengyu.young at gmail.com (chengyu yang) Date: Thu, 2 Feb 2012 16:20:39 -0500 Subject: [Pw_forum] how to calculate the total energy under load ? Message-ID: Dear everyone, I have a question: Can Quantum Espresso calculate the movement of atoms under load? Or can it at least calculate the total energy of the system under load? Which package should I employ? Thank you. Best regards. Chengyu Yang MMAE,University of Central Florida -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120202/7bdb74a5/attachment.htm From berbermohamed at yahoo.fr Thu Feb 2 22:29:02 2012 From: berbermohamed at yahoo.fr (berber mo) Date: Thu, 2 Feb 2012 21:29:02 +0000 (GMT) Subject: [Pw_forum] volume optimization Message-ID: <1328218142.43580.YahooMailNeo@web171407.mail.ir2.yahoo.com> I work on wien2k 8 and i have problem with volume optimization . I would like to know in detail how to optimize the volume a =15.95 u.a ? ? ? ? ? ? ? b = 19.53 u.a?????????????????????????? c =15.95 u.a alpha=90 ???????????????? ? beta =90 ??????????????????????????????? ?? gamma =144.73 ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120202/43eb9cc8/attachment.htm From cwandtj at gmail.com Thu Feb 2 23:32:56 2012 From: cwandtj at gmail.com (Chan-Woo Lee) Date: Thu, 2 Feb 2012 17:32:56 -0500 Subject: [Pw_forum] GGA+U: Sensitivity of occupation matrix Message-ID: <00ec01cce1fa$9d44b0e0$d7ce12a0$@gmail.com> Dear QE developers and users: This is kind of follow-up question of my previous post: http://www.democritos.it/pipermail/pw_forum/2011-December/022823.html I found that current Ce psp has some critical problems (for both CeO2 and Ce2O3) and tried to modify the psp. In doing so, I found Ce psp from Prof. Fabris ( http://www.democritos.it/~fabris/Ce4_ps_f1d1-pbe-rc1.0.uspp.UPF ) and tried it with current O psp. The Ce psp is ultrasoft and the O psp is RRKJ. Both use PBE functionals. In working with the psp, I found interesting results. I tried two cases: 1) SCF without any atomic relaxation 2) RELAX. I use QE 4.3.2 and Effective U is chosen as 5.0. Initial structures are adopted from http://prb.aps.org/abstract/PRB/v75/i4/e045121 . As relax from case 2) doesn't do much, final structures from two cases are identical. While the structures are identical, occupation of f orbitals are different and DOS are also not the same. For 1) case, occupation is almost 1.0 (~0.9) at single orbital state which is desirable, I think. Also, DOS shows that there is no partially filled f states near Fermi level which is the case for conventional DFT. So, Ce2O3 is predicted to be insulating. For 2) case, occupations are somewhat even: 0.23, 0.26, 0.29, and 0.12.. Also, electronic structure doesn't change that much and there is still partially filled f states. Same atomic structures but totally difference electronic structures. While I tried to understand and explain this to myself, I can't find any good answers for this. I am currently testing "starting_ns_eigenvalue" and "mixing_fixed_ns" to see forcing certain occupations will be helpful or not.. but I am not sure. Any comments or suggestions.??? ------- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120202/e36bb9b4/attachment-0001.htm From ndzsau at yahoo.co.uk Fri Feb 3 05:03:09 2012 From: ndzsau at yahoo.co.uk (Nguyen Doan Sau) Date: Fri, 3 Feb 2012 04:03:09 +0000 Subject: [Pw_forum] need help on calculation... Message-ID: Dear Q.E users, I am currently carrying a structural relaxation of the crystal structure of a new oxide compound. There are two new oxides: one I solved its crystal structure by single crystal X-ray diffraction data and the other is iso-structural to the first. As I have not been successful in obtaining the crystals of the later, I have to use the powder X-ray diffraction data for solving its crystal structure. I got its unit cell parameter by peak indexing, using the atomic coordinations of the crystal structure of the first as its initial atomic coordinations for refinement. Okay, I can do the refinement. It went well for the heavy metal atoms but not for light metal atoms like Li and anion like O (you may suggest using neutron diffraction for these light atoms. Actually, I talked to my boss about it but we are unable to have it done before next year. :) Therefore, I think of another solution: first, obtaining the atomic coordination of the heavy metal atoms by the refinement; second, structural relax of the lighter atom (Lithium, oxygen) to obtain their reasonable atomic coordination and bonds to the heavier atoms. So far, everything have been going well except for that the relaxation is time-consuming as the relax involved 204 atoms in the unit cells of volume of 2750 Ang^3. I use a desktop equipped with Xeon 2.66 GHz and 8 GB RAM. The time needed for an average iteration is 1 week. I guess it may take me more than 3 months to have it done properly or just nothing. :) Therefore, I would ask for a favor. Is there any way for me to submit my calculation to a strong computing facility. I would have it done in less than 2 weeks. I could not give my input here publicly but I can send input file personally to who kindly want to help. Thanks,Sau NguyenDepartment of ChemistryUniversity of Houston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120203/c6a1f8de/attachment.htm From mohnish.iitk at gmail.com Fri Feb 3 06:49:53 2012 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Fri, 3 Feb 2012 11:19:53 +0530 Subject: [Pw_forum] volume optimization In-Reply-To: <1328218142.43580.YahooMailNeo@web171407.mail.ir2.yahoo.com> References: <1328218142.43580.YahooMailNeo@web171407.mail.ir2.yahoo.com> Message-ID: On Fri, Feb 3, 2012 at 2:59 AM, berber mo wrote: > I work on wien2k 8 and i have problem with volume optimization . > I would like to know in detail how to optimize the volume > a =15.95 u.a b = 19.53 u.a c =15.95 > u.a > alpha=90 ? beta =90 ? gamma > =144.73 ? > The information you provided is very less. As far as I can understand this is the input that you want to give and then see the optimized structure with optimized volume and atomic coordinates. since your alpha and beta are equal as well "a" and "c" so I will suggest you to reorient (rotate the unit cell around x-axis by Pi/2 ) the cell such that your "b" becomes "c" and "gamma" will become "alpha." So in the new unit cell you will have (just check it carefully, I may be slightly wrong) a =15.95 A? b =15.95 A? c =19.53 A? alpha=144.73 ? beta =90 ? gamma =90 ? With this cell you can use the option ibrav = 5 ( celldm4 = cos(alpha) ). And next time you post on this forum please sign in your affiliation. > > _______________________________________________ > 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/20120203/1b3c62f5/attachment.htm From giannozz at democritos.it Fri Feb 3 08:32:21 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 3 Feb 2012 08:32:21 +0100 Subject: [Pw_forum] volume optimization In-Reply-To: References: <1328218142.43580.YahooMailNeo@web171407.mail.ir2.yahoo.com> Message-ID: <1BFED35D-6555-47FB-B3B7-B36B1BF1D0DE@democritos.it> On Feb 3, 2012, at 6:49 , mohnish pandey wrote: > a =15.95 A? b =15.95 A? > c =19.53 A? > alpha=144.73 ? beta =90 ? > gamma =90 ? > With this cell you can use the option ibrav = 5 ( celldm4 = cos > (alpha) ). ibrav=5 is trigonal; this looks like monoclinic P (ibrav=12 or -12, detailed description in file INPUT_PW.*) 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 fabris at democritos.it Fri Feb 3 09:50:09 2012 From: fabris at democritos.it (Stefano Fabris) Date: Fri, 3 Feb 2012 09:50:09 +0100 Subject: [Pw_forum] GGA+U: Sensitivity of occupation matrix In-Reply-To: <00ec01cce1fa$9d44b0e0$d7ce12a0$@gmail.com> References: <00ec01cce1fa$9d44b0e0$d7ce12a0$@gmail.com> Message-ID: <5C3C8695-2C71-40E6-BBD1-46F780ECCA0C@democritos.it> Dear Chan-Woo Lee, if I understand correctly your mail, you are experiencing a common problem in DFT+U calculations. The issue is related to the existence of several local minima of the electronic solution present for the SAME crystal structure. One example of this for the case of FeO is provided in DFT+U example of the QE distribution (example 25 if I remember correctly). In that case, you can reach two electronic self-consistent solutions: one in which one electron is distributed over three d orbitals with almost equal occupancy, the other (with lower energy) in which the electron occupies only one d orbital. The calculation converges to one or the other depending on the initial values of the occupations. See the effect of starting_ns_eigenvalue In my experience, the case of cerium oxides is even more delicate (and more frustrating the more you move towards complex crystal structures), but the way out is the same. Always carefully check the final occupancies, and in case of fractional occupations, play with starting_ns_eigenvalue and try to reach a lower energy solution with interger occupations on the localized orbitals entering the U term. Hope this helps. Stefano On Feb 2, 2012, at 11:32 PM, Chan-Woo Lee wrote: > Dear QE developers and users: > > This is kind of follow-up question of my previous post: http://www.democritos.it/pipermail/pw_forum/2011-December/022823.html > > I found that current Ce psp has some critical problems (for both CeO2 and Ce2O3) and tried to modify the psp. In doing so, I found Ce psp from Prof. Fabris (http://www.democritos.it/~fabris/Ce4_ps_f1d1-pbe-rc1.0.uspp.UPF ) and tried it with current O psp. The Ce psp is ultrasoft and the O psp is RRKJ. Both use PBE functionals. > > In working with the psp, I found interesting results. I tried two cases: 1) SCF without any atomic relaxation 2) RELAX. I use QE 4.3.2 and Effective U is chosen as 5.0. Initial structures are adopted from http://prb.aps.org/abstract/PRB/v75/i4/e045121 . As relax from case 2) doesn?t do much, final structures from two cases are identical. > > While the structures are identical, occupation of f orbitals are different and DOS are also not the same. For 1) case, occupation is almost 1.0 (~0.9) at single orbital state which is desirable, I think. Also, DOS shows that there is no partially filled f states near Fermi level which is the case for conventional DFT. So, Ce2O3 is predicted to be insulating. For 2) case, occupations are somewhat even: 0.23, 0.26, 0.29, and 0.12.. Also, electronic structure doesn?t change that much and there is still partially filled f states. Same atomic structures but totally difference electronic structures? > > While I tried to understand and explain this to myself, I can?t find any good answers for this. I am currently testing ?starting_ns_eigenvalue? and ?mixing_fixed_ns? to see forcing certain occupations will be helpful or not.. but I am not sure. > > Any comments or suggestions???? > > ------- > Chan-Woo Lee, Ph.D. > Postdoctoral Research Associate > > Department of Chemistry > University of Pennsylvania > 231 South 34th Street > Philadelphia, PA 19104-6323 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Fabris CNR-IOM DEMOCRITOS Simulation Center and SISSA - Scuola Internazionale Superiore di Studi Avanzati tel: @SISSA +39 040 3787-872 @Elettra: +39 040 3758-735 email: fabris at sissa.it http://people.sissa.it/~fabris --- From giannozz at democritos.it Fri Feb 3 10:09:28 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 03 Feb 2012 10:09:28 +0100 Subject: [Pw_forum] how to calculate the total energy under load ? In-Reply-To: References: Message-ID: <1328260168.32678.2.camel@fe12lx.fisica.uniud.it> On Thu, 2012-02-02 at 16:20 -0500, chengyu yang wrote: > Can Quantum Espresso calculate the movement of atoms under load? "under load" ? what do you mean: under an external strain? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri Feb 3 10:29:07 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 03 Feb 2012 10:29:07 +0100 Subject: [Pw_forum] error when restarting ph.x in the parallel computing mode In-Reply-To: References: Message-ID: <1328261347.6797.6.camel@fe12lx.fisica.uniud.it> On Wed, 2012-02-01 at 20:57 +0000, Elie M wrote: > what could be a source of such an error? it is explained in the error message: one of the files, /home/emoujaes/GB60/Results-GB60/GrBo60ph.a2Fsave is either corrupted or incomplete. Restarting from an interrupted calculation doesn't always work, because files are not always properly saved. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From akohlmey at gmail.com Fri Feb 3 14:37:11 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Fri, 3 Feb 2012 08:37:11 -0500 Subject: [Pw_forum] need help on calculation... In-Reply-To: References: Message-ID: On Thu, Feb 2, 2012 at 11:03 PM, Nguyen Doan Sau wrote: > Dear Q.E users, > > I am currently carrying a structural relaxation of the crystal structure of > a new oxide compound. There are two new oxides: one I solved its crystal > structure by single crystal X-ray diffraction data and the other is > iso-structural to the first. As I have not been?successful in obtaining the > crystals of the later, I have to use the powder X-ray diffraction data for > solving its crystal structure. I got its unit cell parameter by peak > indexing, using the atomic coordinations of the crystal structure of the > first as its initial atomic coordinations for refinement. > > Okay, I can do the refinement. It went well for the heavy metal atoms but > not for light metal atoms like Li and anion like O (you may suggest using > neutron diffraction for these light atoms. Actually, I talked to my boss > about it but we are unable to have it done before next year. :) Therefore, I > think of another solution: first, obtaining the atomic coordination of the > heavy metal atoms by the refinement; second, structural relax of the lighter > atom (Lithium, oxygen) to obtain their reasonable atomic coordination and > bonds to the heavier atoms. > > ?So far, everything have been going well except for that the relaxation is > time-consuming as the relax involved 204 atoms in the unit cells of volume > of 2750 Ang^3. I use a desktop?equipped?with ?Xeon 2.66 GHz and 8 GB RAM. > The time needed for an average?iteration?is 1 week. I guess it may take me > more than 3 months to have it done properly or just nothing. :) > > Therefore, I would ask for a favor. Is there any way for me to submit my > calculation to a strong computing facility. I would have it done in less > than 2 weeks. I could not give my input here publicly but I can send input > file personally to who kindly want to help. computer time costs money and is always scarce. as a member of the US research community, however, you can apply for access to an NSF funded supercomputer via XSEDE http://xsede.org/ to expedite the process, please have your adviser contact your local XSEDE campus champion, who already has some discretionary computer time for purposes of getting researchers on XSEDE machines. check out: https://www.xsede.org/web/guest/current-champions cheers, axel. > > Thanks, > Sau Nguyen > Department of Chemistry > University of Houston > > > > > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From bdslipun at gmail.com Fri Feb 3 18:39:55 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Fri, 3 Feb 2012 23:09:55 +0530 Subject: [Pw_forum] optimisation Message-ID: i have a question regarding optimisation if i optimise a large system(no of atoms more ) is optimised for 4*4*4 grid kpoints can its optimised lattice parameter and internal coordinates valid for dense grid of kpoints if not shall i start with dense kpoints but it will requird more time how it can be tacklled bhabya reserch scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120203/e63e21a6/attachment.htm From xgz at ornl.gov Fri Feb 3 20:28:39 2012 From: xgz at ornl.gov (Xiaoguang Zhang) Date: Fri, 03 Feb 2012 14:28:39 -0500 Subject: [Pw_forum] segmentation fault in local.f90 line 228 PWCOND version 4.3.2 Message-ID: <4F2C3567.6050700@ornl.gov> pwcond.x crashes when it is trying to access vppot(1,2161,1,1) while calculating the eigenvalues for the left lead. I inserted a print statement in local.f90 and verified that this is the element that caused the crash. After inserting these lines: *** 213,218 **** --- 213,220 ---- ! ! set and solve the eigenvalue equation for each slab ! + print *, nrz,nrx*nry,npol + print *, vppot(1,2161,1,1) DO WHILE(kin.LE.kfin) amat=(0.d0,0.d0) the program crashed at the print statement with the last output 20 2916 1 which are nrz, nrx*nry, npol. There is no reason for it to crash. Full error message below: ../../espresso-4.3.2/bin/pwcond.x < Alwirebig.cond.in > Alwirebig.cond.out forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source pwcond.x 0000000000432BEF local_1_ 228 local.f90 pwcond.x 000000000042FAA9 local_ 71 local.f90 pwcond.x 00000000004161FC do_cond_ 421 do_cond.f90 pwcond.x 000000000041130C MAIN__ 20 condmain.f90 pwcond.x 0000000000403922 Unknown Unknown Unknown libc.so.6 0000002A9580F4CB Unknown Unknown Unknown pwcond.x 000000000040386A Unknown Unknown Unknown From giannozz at democritos.it Fri Feb 3 20:56:08 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 3 Feb 2012 20:56:08 +0100 Subject: [Pw_forum] segmentation fault in local.f90 line 228 PWCOND version 4.3.2 In-Reply-To: <4F2C3567.6050700@ornl.gov> References: <4F2C3567.6050700@ornl.gov> Message-ID: On Feb 3, 2012, at 20:28 , Xiaoguang Zhang wrote: > There is no reason for it to crash if it is really so, problem solved: it is the compiler. Before saying that, try to recompile PWCOND with debugging flags (-g -fpe0 -CB for ifort), or to run it with "valgrind", to verify if there are out-of-bounds errors. 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 Feb 3 20:58:19 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 3 Feb 2012 20:58:19 +0100 Subject: [Pw_forum] optimisation In-Reply-To: References: Message-ID: <23731BA8-8B42-416C-9D1F-FC54A06ACECB@democritos.it> It is hard to decipher what you mean. As a rule: you can spare some time by optimizing with reduced k-points grid and cutoff, increase them later 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 Feb 3 21:04:18 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 3 Feb 2012 21:04:18 +0100 Subject: [Pw_forum] Some questions on Electron Phonon Calculations. In-Reply-To: References: Message-ID: <1BEDD8EA-4B01-41F3-B2D6-E117C16DB293@democritos.it> On Feb 2, 2012, at 20:48 , Vikas Varshney wrote: > For the next q point, I do not get convergence try first of all to reduce alpha_mix 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 baroni at sissa.it Fri Feb 3 21:18:43 2012 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 3 Feb 2012 21:18:43 +0100 Subject: [Pw_forum] Excited State Gradients in TDDFT In-Reply-To: References: Message-ID: <498D9CEC-3A8F-4286-96BB-58BC25C5FE8D@sissa.it> On Feb 2, 2012, at 7:47 AM, yukihiro_okuno at fujifilm.co.jp wrote: > Dear PWSCF users and developers. > > I want to know the possibility of excited state gradients in TDDFT implemented in > > Quantum Espresso. > > Can the PWSCF calculate the excited state gradients (Force of atoms in excited state ) > pwscf does not implement any excited-state features (tddft energies, gradient or other). The QE distribution does contain some specialized codes that perform some of these calculations (turbo_tddft implements the Liouville-Lanczos approach to TDDFT, whereas GWL is an implementation of the GW method particularly suitable for large systems) > > by PWSCF, or are there plan to develop the excited state gradient calculation ? > > The implementation of TDDFT in PWSCf uses lanczos method and does not > > explicitly calculate the excited energy, and is it difficult to extend to > > calculate force in this formalism ? > the present implementation of tddft is particularly suited for the calculation of the entire spectrum of large systems, whereas excited-state energy gradients would require the calculation of individual eigenpairs of the Liouvillian. That should not be difficult to implement, but it is not considered to be a priority at this time. Should anybody be interested in implementing this feature, we in Trieste would be delighted to help. 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/20120203/b64e4e94/attachment-0001.htm From payam.norouzzadeh at gmail.com Sat Feb 4 06:34:19 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Sat, 4 Feb 2012 09:04:19 +0330 Subject: [Pw_forum] No plane waves Message-ID: Dear QE users I tried to relax my system by vc_relax and it was working well. Near to end of run (based on force and energy criteria) it crashed with producing this error: from n_plane_waves : error # 1 No plane waves found: running on too many processors? I can't understand it.Anyone has idea about this error? How can I resolve it? Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120204/31208ebd/attachment.htm From yccheng.nju at gmail.com Sat Feb 4 09:51:38 2012 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Sat, 4 Feb 2012 11:51:38 +0300 Subject: [Pw_forum] BEC from DFPT In-Reply-To: References: Message-ID: If the system is insulator, WHY it must be treated as metallic? Would you please tell us the REASON? I think you can try occupations='fixed' to get the Born effective charge for your system. 2012/1/31 ?????? ???????? > Dear all, > I am trying to calculate Born effective charges from DFTP for the > spin-polarized system. However, these systems must be treated as metallic > (scf-calculation with occupations='smearing'). > The problem is that ph.x complains about my calculation, but the system > has an insulator behavior. > Are there any methods to solve this problem? > > Sincerely, > Sergey Nikolaev > Department of theoretical physics and applied mathematics > Ural Federal University > Yekaterinburg, Russia > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120204/cf4b3050/attachment.htm From giannozz at democritos.it Sat Feb 4 10:16:01 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 4 Feb 2012 10:16:01 +0100 Subject: [Pw_forum] No plane waves In-Reply-To: References: Message-ID: On Feb 4, 2012, at 6:34 , Payam Norouzzadeh wrote: > Near to end of run (based on force and energy criteria) > it crashed with producing this error: > from n_plane_waves : error # 1 > No plane waves found: running on too many processors? has it happened in the last scf cycle, after convergence was reached? is a rather curos case, indicating however that you were running in parallel on a too large number of processes 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 Feb 4 10:23:25 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 4 Feb 2012 10:23:25 +0100 Subject: [Pw_forum] No plane waves In-Reply-To: References: Message-ID: On Feb 4, 2012, at 10:16 , Paolo Giannozzi wrote: > has it happened in the last scf cycle, after convergence was > reached? is a rather curos case I meant "curious 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 giannozz at democritos.it Sat Feb 4 10:30:43 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 4 Feb 2012 10:30:43 +0100 Subject: [Pw_forum] BEC from DFPT In-Reply-To: References: Message-ID: <49EA9740-3E76-4EE5-9451-3D7BEECE4803@democritos.it> On Feb 4, 2012, at 9:51 , ??? wrote: > If the system is insulator, WHY it must be treated as metallic? > Would you please tell us the REASON? because it is the only way to guarantee a smooth and safe convergence to the ground state in a spin-polarized system, if you do not want to constrain the final magnetization. > I think you can try occupations='fixed' to get the Born effective > charge for your system. Not sure: the scf code may complain. It is one of the many checks that are there to prevent a bad usage of the code. 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 elie.moujaes at hotmail.co.uk Sun Feb 5 02:37:56 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Sun, 5 Feb 2012 01:37:56 +0000 Subject: [Pw_forum] Problem with parallel execution Message-ID: Dear all, I am running a parallel execution (pw.x) on a SLURM LINUX interface and once I run the command sbatch filename.srm, the calculation starts running and then stops with the follwing error: "mpiexec_veredas5: cannot connect to local mpd (/tmp/mpd2.console_sushil); possible causes: 1. no mpd is running on this host 2. an mpd is running but was started without a "console" (-n option) In case 1, you can start an mpd on this host with: mpd & and you will be able to run jobs just on this host. For more details on starting mpds on a set of hosts, see the MPICH2 Installation Guide." I saw a previous message posted in 2009 about this error. I followed what prof. andrea did: I created a file elie.mpd.hosts and included one line in it (localhosts) then ran the coomad mpdboot -f ~/elie.mpd.hosts and run sbatch command again but in 3 seconds time, it stops with the same error. can anyone help.. N.B: veredas 5 is the node at which I am executing the command but whatever node I try on , I get the same error Elie MoujaesUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120205/ac4eb61e/attachment.htm From akohlmey at gmail.com Sun Feb 5 04:05:08 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Sat, 4 Feb 2012 22:05:08 -0500 Subject: [Pw_forum] Problem with parallel execution In-Reply-To: References: Message-ID: On Sat, Feb 4, 2012 at 8:37 PM, Elie M wrote: > Dear all, > > I am running a parallel execution (pw.x) on a SLURM LINUX interface and once > I run the command sbatch filename.srm, the calculation starts running and > then stops with the follwing error: > > "mpiexec_veredas5: cannot connect to local mpd this is a local system setup issue and has nothing to do with quantum espresso. i would recommend to talk to your local system administrator or somebody else that has experience running in parallel on your local machine. failing that, you may try to get help on the MPICH mailing list and/or study the MPICH2 documentation very carefully and first try running a small (trivial) MPI test program. once you figured out how to make that work, it should be straightforward to get Q-E to run. cheers, axel. > > ?(/tmp/mpd2.console_sushil); possible causes: > > ??1. no mpd is running on this host > > ?2. an mpd is running but was started without a "console" (-n option) > > ?In case 1, you can start an mpd on this host with: > > ? ??mpd & > > ?and you will be able to run jobs just on this host. > > ?For more details on starting mpds on a set of hosts, see > > ?the MPICH2 Installation Guide." > > > I saw a previous message posted in 2009 about this error. I followed what > prof. andrea did: I created a file elie.mpd.hosts and included one line in > it (localhosts) then ran the coomad mpdboot -f ~/elie.mpd.hosts and run > sbatch command again but in 3 seconds time, it stops with the same error. > can anyone help.. > > > N.B: veredas 5 is the node at which I am executing the command but whatever > node I try on , I get the same error > > > Elie Moujaes > > University of Nottingham > > NG7 2RD > > UK > > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From vranjan at ncsu.edu Sun Feb 5 07:16:17 2012 From: vranjan at ncsu.edu (Vivek Ranjan) Date: Sun, 5 Feb 2012 01:16:17 -0500 Subject: [Pw_forum] low frequency dielectric constant Message-ID: Hello, Wonder if it is already coded in PWSCF to calculate: frequency dependent dielctric constant (low frequency dynamical ones) static dielectric constant mode effective charges -- Regards, Vivek Ranjan NC State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120205/aa61951f/attachment.htm From giannozz at democritos.it Sun Feb 5 11:19:13 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 5 Feb 2012 11:19:13 +0100 Subject: [Pw_forum] No plane waves In-Reply-To: References: Message-ID: <7CE354ED-512E-4365-92C4-421B85C856DB@democritos.it> On Feb 4, 2012, at 22:55 , Payam Norouzzadeh wrote: > I have attached the last lines of output if you are running in parallel, there is no guarantee that the last lines of output are really the last lines of output. The number of plane waves per processor is kept constant during a variable-cell optimization, except for the last step when the number of plane waves is recalculated. The number of plane waves per processor is printed at the beginning, in the section G-vector sticks info -------------------- sticks: dense smooth PW G-vecs: dense smooth PW 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 payam.norouzzadeh at gmail.com Sun Feb 5 17:22:51 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Sun, 5 Feb 2012 19:52:51 +0330 Subject: [Pw_forum] Fwd: No plane waves In-Reply-To: References: <7CE354ED-512E-4365-92C4-421B85C856DB@democritos.it> Message-ID: ---------- Forwarded message ---------- From: Payam Norouzzadeh Date: Sun, Feb 5, 2012 at 7:33 PM Subject: Re: [Pw_forum] No plane waves To: Paolo Giannozzi Dear Prof.Giannozzi Does it mean that I don't need to restart the job because it is happening in the last step? Even when I submit a job with last atom coordinates and lattice vectors I obtained from previous runs but in the "from_scratch" mode the same error is produced "No plane wave....".Do I need to increase the cutoff energy? Thank you. Best regards,Payam Norouzzadeh On Sun, Feb 5, 2012 at 1:49 PM, Paolo Giannozzi wrote: > > On Feb 4, 2012, at 22:55 , Payam Norouzzadeh wrote: > > I have attached the last lines of output >> > > if you are running in parallel, there is no guarantee that > the last lines of output are really the last lines of output. > > The number of plane waves per processor is kept constant > during a variable-cell optimization, except for the last step > when the number of plane waves is recalculated. The number > of plane waves per processor is printed at the beginning, in > the section > G-vector sticks info > -------------------- > sticks: dense smooth PW G-vecs: dense smooth PW > > > 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 > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120205/0f484d06/attachment.htm From giannozz at democritos.it Sun Feb 5 17:57:04 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 5 Feb 2012 17:57:04 +0100 Subject: [Pw_forum] No plane waves In-Reply-To: References: <7CE354ED-512E-4365-92C4-421B85C856DB@democritos.it> Message-ID: <77821F02-A50A-4A91-B9C6-C98BBAE8DA2B@democritos.it> On Feb 5, 2012, at 17:03 , Payam Norouzzadeh wrote: > Does it mean that I don't need to restart the job because > it is happening in the last step? very likely. Look at the energy, forces and pressure, and decide. > Even when I submit a job with last atom coordinates and lattice > vectors > I obtained from previous runs but in the "from_scratch" mode the same > error is produced "No plane wave....". Do I need to increase the > cutoff energy? most likely, you need to reduce the number of processors on which you are running (unless there is some other reason, which I won't believe unless I see it) 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 salazar at physics.utoronto.ca Mon Feb 6 07:56:39 2012 From: salazar at physics.utoronto.ca (Cuauhtemoc Salazar) Date: Mon, 6 Feb 2012 01:56:39 -0500 Subject: [Pw_forum] Hartree Fock Message-ID: <3F4E0CA6-8CDA-46C3-8495-274E8E58815C@physics.utoronto.ca> Hello Dear developers/users of Quantum Expresso, I would like to know if I can use Quantum Expresso to perform an "old-fashion" Hartree?Fock calculation of the ground state of a periodic crystal (I am interested in graphene). Would it be sufficient to use the Hartree-Fock and Hybrid functionals described in Section 5.1.0.6 of http://www.quantum-espresso.org/user_guide/node26.html#SECTION00061060000000000000 ? Actually I would be interested in *all electron* Hartree-Fock calculations. Best regards, Salazar -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120206/77f07cc3/attachment.htm From yukihiro_okuno at fujifilm.co.jp Mon Feb 6 09:50:44 2012 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Mon, 6 Feb 2012 17:50:44 +0900 Subject: [Pw_forum] Excited State Gradients in TDDFT In-Reply-To: <498D9CEC-3A8F-4286-96BB-58BC25C5FE8D@sissa.it> Message-ID: Dear Prof. Baroni. Thank you very much for your response. I'm very glad. >>by PWSCF, or are there plan to develop the excited state gradient calculation ? >>The implementation of TDDFT in PWSCf uses lanczos method and does not >>explicitly calculate the excited energy, and is it difficult to extend to >>calculate force in this formalism ? >the present implementation of tddft is particularly suited for the calculation of the entire spectrum of large systems, whereas excited-state energy gradients would require the calculation of individual eigenpairs >of the Liouvillian. That should not be difficult to implement, but it is not considered to be a priority at this time. Should anybody be interested in implementing this feature, we in Trieste would be delighted to help. Thank you for your advice. You mean if we diagonalize the Liouvillean operator by usual method instead of using Lanczos chain, and get eigenvalue and eigenvectors, we can get excited-state gradient ? Are there already formalism to calculate the excited energy gradient within occupied state only method ? Usual Casida's matrix, the dimension of the Matrix is \Omega_{i_j, k_q} where, i and j are occupied and unoccupied state (k and q are also occupied and unoccupied state pair), and the dimension is (2*Nc*Nv) * (2* Nc * Nv) where Nc and Nv is the number of the unoccupied and occupied states. But your Liouvillean matrix dimension is (2*Nv) * (2 *Nv), and it is very small than the usual Casida's one. It seems very attractive to perform the large molecule, because the possibilities to calculate the large molecule's excited state energy gradient is very important quantities in photochemistry. Sincerely, Yukihiro Okuno. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120206/e28a3505/attachment.htm From baroni at sissa.it Mon Feb 6 10:38:46 2012 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 6 Feb 2012 10:38:46 +0100 Subject: [Pw_forum] Hartree Fock In-Reply-To: <3F4E0CA6-8CDA-46C3-8495-274E8E58815C@physics.utoronto.ca> References: <3F4E0CA6-8CDA-46C3-8495-274E8E58815C@physics.utoronto.ca> Message-ID: <8638016C-8F5F-4FFD-BC86-EA7288902C96@sissa.it> On Feb 6, 2012, at 7:56 AM, Cuauhtemoc Salazar wrote: > Hello Dear developers/users of Quantum Expresso, > > I would like to know if I can use Quantum Expresso to perform an "old-fashion" Hartree?Fock calculation of the ground state of a periodic crystal (I am interested in graphene). not sure what an "old fashion" HS calculations is, but I would say so ... > Would it be sufficient to use the Hartree-Fock and Hybrid functionals described in Section 5.1.0.6 of > http://www.quantum-espresso.org/user_guide/node26.html#SECTION00061060000000000000 ? so I presume ... > Actually I would be interested in *all electron* Hartree-Fock calculations. no way, I am afraid, unless you are ready to use basis sets of zillions of plane waves ... 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/20120206/86b424b3/attachment.htm From Silvia.Bahmann at physik.tu-freiberg.de Mon Feb 6 12:04:25 2012 From: Silvia.Bahmann at physik.tu-freiberg.de (Silvia Bahmann) Date: Mon, 6 Feb 2012 12:04:25 +0100 Subject: [Pw_forum] Corrupting "input_tmp.in" when starting jobs at once Message-ID: <201202061204.25934.Silvia.Bahmann@physik.tu-freiberg.de> Hi everyone, I'm starting many pw.x calculations with the inputfiles located in the same directory using a script. Since the original inputfile is converted to "input_tmp.in", I encounter the problem, that the resulting input is corrupted. This is happening, because several jobs want to write "input_tmp.in" simultaneously. Is there any way to suppress the "loop way" of writing "input_tmp.in" and read directly from the given inputfile? Thanks for your help! Best regards, Silvia Silvia Bahmann Institute for Theoretical Physics TU Bergakademie Freiberg, Germany From lmartinsamos at gmail.com Mon Feb 6 13:26:18 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 6 Feb 2012 13:26:18 +0100 Subject: [Pw_forum] Corrupting "input_tmp.in" when starting jobs at once In-Reply-To: <201202061204.25934.Silvia.Bahmann@physik.tu-freiberg.de> References: <201202061204.25934.Silvia.Bahmann@physik.tu-freiberg.de> Message-ID: Dear Silvia, we moved to this intermediate input_tmp.in for preparing pw to the automatic detection of xml input format. There is no simple way to overcome this step. One of the think you can do is to run on different directories. Do you need help for modifying the scritps? best Layla 2012/2/6 Silvia Bahmann > > Hi everyone, > > I'm starting many pw.x calculations with the inputfiles located in the same > directory using a script. > > Since the original inputfile is converted to "input_tmp.in", I encounter > the > problem, that the resulting input is corrupted. This is happening, because > several jobs want to write "input_tmp.in" simultaneously. > > Is there any way to suppress the "loop way" of writing "input_tmp.in" and > read > directly from the given inputfile? > > Thanks for your help! > > Best regards, Silvia > > > Silvia Bahmann > Institute for Theoretical Physics > TU Bergakademie Freiberg, Germany > _______________________________________________ > 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/20120206/08fd9001/attachment.htm From giannozz at democritos.it Mon Feb 6 13:47:46 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 6 Feb 2012 13:47:46 +0100 Subject: [Pw_forum] Corrupting "input_tmp.in" when starting jobs at once In-Reply-To: References: <201202061204.25934.Silvia.Bahmann@physik.tu-freiberg.de> Message-ID: On Feb 6, 2012, at 13:26 , Layla Martin-Samos wrote: > Dear Silvia, we moved to this intermediate input_tmp.in for > preparing pw > to the automatic detection of xml input format. There is no simple way > to overcome this step. there are a few possibilities to prevent overwriting by other processes: - add a unique identifier, e.g. the process ID, to the file name; - add a random number to the file name; - rename the file to input_tmp_N.in, with N= smallest number such that no input_tmp_N.in is detected; but none is trivial to implement in a portable and safe way. I don't think however that the input file is copied to input_tmp.in, when it is read using the -in option (as opposed to " < file"). So everything should work if the -in (or -inp, or -input) option is used. Paolo --- 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 lmartinsamos at gmail.com Mon Feb 6 13:58:02 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 6 Feb 2012 13:58:02 +0100 Subject: [Pw_forum] Corrupting "input_tmp.in" when starting jobs at once In-Reply-To: References: <201202061204.25934.Silvia.Bahmann@physik.tu-freiberg.de> Message-ID: Dear all independetly of the way one runs pw whatever input is copied inside input_tmp.in and then the test for xml is done there. this is something that we can change in the future, it will just make open_input_file a little more complex. bests Layla 2012/2/6 Paolo Giannozzi > > On Feb 6, 2012, at 13:26 , Layla Martin-Samos wrote: > > Dear Silvia, we moved to this intermediate input_tmp.in for preparing pw >> to the automatic detection of xml input format. There is no simple way >> to overcome this step. >> > > there are a few possibilities to prevent overwriting by other processes: > - add a unique identifier, e.g. the process ID, to the file name; > - add a random number to the file name; > - rename the file to input_tmp_N.in, with N= smallest number such that > no input_tmp_N.in is detected; > but none is trivial to implement in a portable and safe way. > > I don't think however that the input file is copied to input_tmp.in, when > it is read using the -in option (as opposed to " < file"). So everything > should work if the -in (or -inp, or -input) option is used. > > Paolo > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120206/a9b8c1ea/attachment-0001.htm From Silvia.Bahmann at physik.tu-freiberg.de Mon Feb 6 14:02:40 2012 From: Silvia.Bahmann at physik.tu-freiberg.de (Silvia Bahmann) Date: Mon, 6 Feb 2012 14:02:40 +0100 Subject: [Pw_forum] Corrupting "input_tmp.in" when starting jobs at once In-Reply-To: References: <201202061204.25934.Silvia.Bahmann@physik.tu-freiberg.de> Message-ID: <201202061402.40325.Silvia.Bahmann@physik.tu-freiberg.de> When using the following line in the jobfile "input_tmp.in" also is generated and possibly read?! mpirun -np 8 pw.x -in test.in > test.out Silvia On Monday 06 February 2012 13:47:46 Paolo Giannozzi wrote: > On Feb 6, 2012, at 13:26 , Layla Martin-Samos wrote: > > Dear Silvia, we moved to this intermediate input_tmp.in for > > preparing pw > > to the automatic detection of xml input format. There is no simple way > > to overcome this step. > > there are a few possibilities to prevent overwriting by other processes: > - add a unique identifier, e.g. the process ID, to the file name; > - add a random number to the file name; > - rename the file to input_tmp_N.in, with N= smallest number such that > no input_tmp_N.in is detected; > but none is trivial to implement in a portable and safe way. > > I don't think however that the input file is copied to input_tmp.in, > when > it is read using the -in option (as opposed to " < file"). So everything > should work if the -in (or -inp, or -input) option is used. > > Paolo > --- > 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 lmartinsamos at gmail.com Mon Feb 6 14:04:46 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 6 Feb 2012 14:04:46 +0100 Subject: [Pw_forum] Corrupting "input_tmp.in" when starting jobs at once In-Reply-To: <201202061402.40325.Silvia.Bahmann@physik.tu-freiberg.de> References: <201202061204.25934.Silvia.Bahmann@physik.tu-freiberg.de> <201202061402.40325.Silvia.Bahmann@physik.tu-freiberg.de> Message-ID: yes allways!!! even with -in -inp .... open_input_file first dump to input_tmp.in. bests Layla 2012/2/6 Silvia Bahmann > > When using the following line in the jobfile "input_tmp.in" also is > generated > and possibly read?! > mpirun -np 8 pw.x -in test.in > test.out > > Silvia > > On Monday 06 February 2012 13:47:46 Paolo Giannozzi wrote: > > On Feb 6, 2012, at 13:26 , Layla Martin-Samos wrote: > > > Dear Silvia, we moved to this intermediate input_tmp.in for > > > preparing pw > > > to the automatic detection of xml input format. There is no simple way > > > to overcome this step. > > > > there are a few possibilities to prevent overwriting by other processes: > > - add a unique identifier, e.g. the process ID, to the file name; > > - add a random number to the file name; > > - rename the file to input_tmp_N.in, with N= smallest number such that > > no input_tmp_N.in is detected; > > but none is trivial to implement in a portable and safe way. > > > > I don't think however that the input file is copied to input_tmp.in, > > when > > it is read using the -in option (as opposed to " < file"). So everything > > should work if the -in (or -inp, or -input) option is used. > > > > Paolo > > --- > > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120206/67749de9/attachment.htm From akohlmey at gmail.com Mon Feb 6 15:10:55 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 6 Feb 2012 09:10:55 -0500 Subject: [Pw_forum] Hartree Fock In-Reply-To: <3F4E0CA6-8CDA-46C3-8495-274E8E58815C@physics.utoronto.ca> References: <3F4E0CA6-8CDA-46C3-8495-274E8E58815C@physics.utoronto.ca> Message-ID: On Mon, Feb 6, 2012 at 1:56 AM, Cuauhtemoc Salazar wrote: > Hello Dear developers/users of Quantum Expresso, > > I would like to know if I can use Quantum Expresso to perform an > ?"old-fashion" ?Hartree?Fock calculation of the ground state of a periodic > crystal (I am interested in graphene). > > Would it be sufficient to use the Hartree-Fock and Hybrid functionals > described in Section?5.1.0.6 ?of > http://www.quantum-espresso.org/user_guide/node26.html#SECTION00061060000000000000?? > > Actually I would be interested in *all electron*?Hartree-Fock calculations. why don't you try an "old-fashioned" hartree-fock code then? why try to squeeze a camel through the eye of a needle? axel. > > Best regards, > Salazar > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From jafernandes at ua.pt Mon Feb 6 15:38:15 2012 From: jafernandes at ua.pt (=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes) Date: Mon, 06 Feb 2012 14:38:15 +0000 Subject: [Pw_forum] pseudopotentials for C, H, O and Cl Message-ID: Hello I need to perform a structure optimization for a molecule containing C,H, O and Cl. I could not find a pseudopotential common to this four elements. How can I proceed? Best regards Jos? Fernandes Departamento de Quimica Universidade de Aveiro 3810-193 Aveiro Portugal Tel: +351234370720 Fax: +351234370084 From giuseppe.mattioli at ism.cnr.it Mon Feb 6 16:03:28 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Mon, 6 Feb 2012 16:03:28 +0100 Subject: [Pw_forum] pseudopotentials for C, H, O and Cl In-Reply-To: References: Message-ID: <20120206160328.7e21staso4s0cso4@webmail.sic.rm.cnr.it> Dear Jos? First, have a better look... http://qe-forge.org/projects/pslibrary/ http://www.quantum-espresso.org/pseudo.php HTH Giuseppe Giuseppe Mattioli Quoting Jos? Alberto Pires Fernandes : > Hello > > I need to perform a structure optimization for a molecule > containing C,H, O and Cl. > I could not find a pseudopotential common to this four > elements. How can I proceed? > > Best regards > > > > Jos? Fernandes > Departamento de Quimica > Universidade de Aveiro > 3810-193 Aveiro > Portugal > Tel: +351234370720 > Fax: +351234370084 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From m.abbasnejad at gmail.com Mon Feb 6 17:38:33 2012 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Mon, 6 Feb 2012 20:08:33 +0330 Subject: [Pw_forum] Regarding anatase structure Message-ID: Dear users, I have a question regarding the anatase TiO2 structure, space group 141 (* I41/amd*). There are two ways of representing this structure, using the group Wyckoff positions for "origin choice 1" or using them for the "origin choice 2". 1- I was wondering which of these origin is being used in QE? As I have read though it, in "origin choice 1", Ti atoms are occupying *"4a" * sites and O atoms occupying *"8e"* sites, while in "origin choice 2", Ti atoms are in *"4b" *sites and the O atoms in *"8e" *sites. 2- Would you please tell me whether the occupying sites are true or not? Thanks in advance. Mohaddeseh --------------------------------------------------------- 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/20120206/f1d16824/attachment.htm From roccad at gmail.com Mon Feb 6 20:20:09 2012 From: roccad at gmail.com (dario rocca) Date: Mon, 6 Feb 2012 11:20:09 -0800 Subject: [Pw_forum] Excited State Gradients in TDDFT In-Reply-To: References: <498D9CEC-3A8F-4286-96BB-58BC25C5FE8D@sissa.it> Message-ID: Dear Yukihiro > You mean if we diagonalize the Liouvillean operator by usual method > instead of using Lanczos chain, and get > > eigenvalue and eigenvectors, we can get excited-state gradient ? > There are not "usual methods" to get eigenvalues and eigenvectors for TDDFT because the eigenvalue problem is non-Hermitian. I have been lately working on this type of eigenvalue problems in order to diagonalize the Liouvillian in the TDDFT formalism without empty states (J. Chem. Phys. 136, 034111 (2012)). This new method seems very promising but at this stage it still needs an efficient preconditioner to become more practical. > > Are there already formalism to calculate the excited energy gradient > within occupied state only method ? > I think that a necessary ingredient for the calculation of gradients is the diagonalization of the Liouvillian. Once this is done I think that the formalism used for the Casida's equations can be extended to the TDDFT without empty states. > > Usual Casida's matrix, the dimension of the Matrix is \Omega_{i_j, k_q} > where, i and j are occupied and unoccupied state (k and q are also occupied > and unoccupied state pair), > > and the dimension is (2*Nc*Nv) * (2* Nc * Nv) where Nc and Nv is the > number of the unoccupied and occupied states. > > But your Liouvillean matrix dimension is (2*Nv) * (2 *Nv), and it is very > small than the usual Casida's one. > The dimension of the Liouvillian is actually (2*Nv*Npw)*(2*Nv*Npw). This dimension is basically the same as that of Casida's equation when Nc is the total number of conduction states. The advantage of the Liouvillian approach is not exactly in the matrix dimension but I would say that some of the advantages are: -The matrix is big but never built explicitly and its application to a vector involve a number of orbitals that is equal to the number of occupied states (it scales better than Casida's equations, that involve a number of orbitals equal to Nc) -The convergence of the spectra with the number of empty states in never an issue (even at high energy or when there is a strong dependence of the spectrum at low energy on the states at higher energy) -The use of plane-waves avoids the convergence problems with respect to the basis set typical of the localized basis sets Dario Rocca -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120206/984a3ae0/attachment-0001.htm From jafernandes at ua.pt Mon Feb 6 23:56:01 2012 From: jafernandes at ua.pt (=?iso-8859-1?Q?Jos=E9?= Alberto Pires Fernandes) Date: Mon, 06 Feb 2012 22:56:01 +0000 Subject: [Pw_forum] pseudopotentials for C, H, O and Cl (Giuseppe Mattioli) Message-ID: Hello Giuseppe Please considere that in http://www.quantum-espresso.org/pseudo.php the only pseudopotentials available for Cl are Cl.blyp-mt.UPF Cl.pw91-mt.UPF Cl.pz-bhs.UPF Cl.pbe-n-van.UPF From these pseudopotentials I could find similar for C and O: C.blyp.mt.UPF and O.blyp.mt.UPF but no one in common for hydrogen. Jos? Fernandes Departamento de Quimica Universidade de Aveiro 3810-193 Aveiro Portugal Tel: +351234370720 Fax: +351234370084 From cwandtj at gmail.com Tue Feb 7 00:03:24 2012 From: cwandtj at gmail.com (Chan-Woo Lee) Date: Mon, 6 Feb 2012 18:03:24 -0500 Subject: [Pw_forum] pseudopotentials for C, H, O and Cl (Giuseppe Mattioli) In-Reply-To: References: Message-ID: <004501cce523$87e3efa0$97abcee0$@gmail.com> Dear Jose: You may find H psp from OPIUM website: http://opium.sourceforge.net/ . At left below of the page, there are links for LDA and GGA psp library. We have GGA psp for H, C and O. While there is no Cl psp, you can mix Cl.pbe-n-van.UPF with these psp from the library. Hope this is helpful... Chan-Woo ------- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Jose Alberto Pires Fernandes Sent: Monday, February 06, 2012 5:56 PM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] pseudopotentials for C, H, O and Cl (Giuseppe Mattioli) Hello Giuseppe Please considere that in http://www.quantum-espresso.org/pseudo.php the only pseudopotentials available for Cl are Cl.blyp-mt.UPF Cl.pw91-mt.UPF Cl.pz-bhs.UPF Cl.pbe-n-van.UPF From these pseudopotentials I could find similar for C and O: C.blyp.mt.UPF and O.blyp.mt.UPF but no one in common for hydrogen. Jos? Fernandes Departamento de Quimica Universidade de Aveiro 3810-193 Aveiro Portugal Tel: +351234370720 Fax: +351234370084 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From nicola.marzari at epfl.ch Tue Feb 7 00:04:17 2012 From: nicola.marzari at epfl.ch (Nicola Marzari) Date: Tue, 07 Feb 2012 00:04:17 +0100 Subject: [Pw_forum] pseudopotentials for C, H, O and Cl (Giuseppe Mattioli) In-Reply-To: References: Message-ID: <4F305C71.8060308@epfl.ch> Dear Jose Fernandes, the key issue is that the pseudopotentials should all be generated with the same exchange-correlation functional - and there are actually two different H pseudopotentials available generated with BLYP. So basically for Cl/C/O molecule you can do a BLYP calculation (or a LDA calculation, or a PBE calculation, or a PW91 calculation). For a given exchange correlation functional, there are different technologies to generate the pseudopotential, and maybe this confused the matter. They are named in "field 4" of the UPF convention - have a look at this http://www.quantum-espresso.org/wiki/index.php/Naming_convention_for_the_pseudopotential and maybe do some reading on these different techniques. nicola On 06/02/2012 23:56, Jos? Alberto Pires Fernandes wrote: > Hello Giuseppe > > Please considere that in > http://www.quantum-espresso.org/pseudo.php > > the only pseudopotentials available for Cl are > > Cl.blyp-mt.UPF > Cl.pw91-mt.UPF > Cl.pz-bhs.UPF > Cl.pbe-n-van.UPF > > From these pseudopotentials I could find similar for C > and O: > > C.blyp.mt.UPF > > and > > O.blyp.mt.UPF > > but no one in common for hydrogen. > > > Jos? Fernandes > Departamento de Quimica > Universidade de Aveiro > 3810-193 Aveiro > Portugal > Tel: +351234370720 > Fax: +351234370084 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ---------------------------------------------------------------------- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL From akohlmey at gmail.com Tue Feb 7 00:05:35 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 6 Feb 2012 18:05:35 -0500 Subject: [Pw_forum] pseudopotentials for C, H, O and Cl (Giuseppe Mattioli) In-Reply-To: References: Message-ID: 2012/2/6 Jos? Alberto Pires Fernandes : > Hello Giuseppe > > Please considere that in > http://www.quantum-espresso.org/pseudo.php > > the only pseudopotentials available for Cl are > > Cl.blyp-mt.UPF > Cl.pw91-mt.UPF > Cl.pz-bhs.UPF > Cl.pbe-n-van.UPF > > ?From these pseudopotentials I could find similar for C > and O: > > C.blyp.mt.UPF > > and > > O.blyp.mt.UPF > > but no one in common for hydrogen. H.blyp-vbc.UPF is consistent with the "mt" potentials, since it is a norm-conserving potential as well. axel. > > > Jos? Fernandes > Departamento de Quimica > Universidade de Aveiro > 3810-193 Aveiro > Portugal > Tel: +351234370720 > Fax: +351234370084 > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From giacsport at libero.it Tue Feb 7 09:38:38 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Tue, 7 Feb 2012 09:38:38 +0100 (CET) Subject: [Pw_forum] scalability of the code Message-ID: <10273511.18814901328603918224.JavaMail.root@wmail39> Dear All, I have maybe a silly question. I would like to know which is the highest number of processors used and reported for running PWscf code. Are there data or reports on the scalability of the code (well) above 1000 processors? I know of course that performances change according to the machine used, but also a qualitative answer would be sufficient. I am reading here and there how to improve the scalability of the code for example in machine like IBM Blue Gene. We are indeed interested in installing the code in a massively parallel machine, but before doing it we would like to have more information. Thanks in advance, Giacomo ----- Giacomo GIORGI, PhD. Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan E-mail: giacomo at tcl.t.u-tokyo.ac.jp From giannozz at democritos.it Tue Feb 7 10:57:14 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 07 Feb 2012 10:57:14 +0100 Subject: [Pw_forum] scalability of the code In-Reply-To: <10273511.18814901328603918224.JavaMail.root@wmail39> References: <10273511.18814901328603918224.JavaMail.root@wmail39> Message-ID: <1328608634.18193.41.camel@fe12lx.fisica.uniud.it> On Tue, 2012-02-07 at 09:38 +0100, giacsport at libero.it wrote: > I would like to know which is the highest number of processors > used and reported for running PWscf code. I have seen a test run on 65536 processors (cores, I mean). Unfortunately I do not find any longer a test on a 8000-atom system recently done: I guess it was also run on more than just a few processors. > Are there data or reports on the scalability of the code (well) > above 1000 processors? there is something in the Benchmark section of the new web site ( http://testwp.qe-forge.it/wordpress-3.1.4/?page_id=44 ). More data will (maybe) come (subject to my allergy to both benchmarks and wordpress, and to everybody's allergy to documentation) > We are indeed interested in installing the code in a massively parallel > machine, but before doing it we would like to have more information. QE has been installed (with little effort) on several BlueGene machines. It works (i.e. it has ben used for real scientific purposes and has produced published results in at least one case I am aware of). You have to be careful with I/O, which can become easily a limiting factor. You may need to use all available parallelization levels, in particular OpenMP, to satisfy the machine owners who, for sure, wants you to run on a number of cores vastly exceeding what you actually need P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From gabriele.sclauzero at epfl.ch Tue Feb 7 11:25:08 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 7 Feb 2012 11:25:08 +0100 Subject: [Pw_forum] scalability of the code In-Reply-To: <1328608634.18193.41.camel@fe12lx.fisica.uniud.it> References: <10273511.18814901328603918224.JavaMail.root@wmail39> <1328608634.18193.41.camel@fe12lx.fisica.uniud.it> Message-ID: <6BCBEFD7-7AEF-45D7-8354-23CAE00765D3@epfl.ch> I've been using QE on BG/P for several months and I'm pretty happy with that, thanks to the effort of Carlo Cavazzoni, Paolo, and others. As Paolo mentioned here below, it is worth running on BG only if you have a big system in hands (~1000 atoms), because the sysadmins will ask you to run on at least 2048 cores to show that the machine was really worth the lots of money it costed :D ... no, actually also because that's the smallest piece of machine that can be connected in the torus topology (peculiarity of the BG network). I agree with Paolo about I/O, it becomes very expensive because usually there are only little I/O nodes compared to number of computing nodes. I use io_level='low', which should be safe enough because BG/P nodes crash very rarely (at least on the machine I use) and they have a very good diagnostic system that helps admins to foresee possible node failures. Since you will compute systems with many electrons you will definitely need to compile with scalapack support and use the -ndiag option to pw.x. The OpenMP parallelization is useful only if the code stops complaining that there are not enough plane waves. In my experience, before that number of processors is reached, the MPI parallelization gives much better performances than the OpenMP one, probably because there are still several parts of the code that have not been "threaded" so far. HTH GS Il giorno 07/feb/2012, alle ore 10.57, Paolo Giannozzi ha scritto: >> We are indeed interested in installing the code in a massively parallel >> machine, but before doing it we would like to have more information. > > QE has been installed (with little effort) on several BlueGene machines. > It works (i.e. it has ben used for real scientific purposes and has > produced published results in at least one case I am aware of). You > have to be careful with I/O, which can become easily a limiting factor. > You may need to use all available parallelization levels, in particular > OpenMP, to satisfy the machine owners who, for sure, wants you to run > on a number of cores vastly exceeding what you actually need > > 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 ? 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/20120207/49899410/attachment.htm From giacsport at libero.it Tue Feb 7 11:46:26 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Tue, 7 Feb 2012 11:46:26 +0100 (CET) Subject: [Pw_forum] R: Re: scalability of the code Message-ID: <25664628.18915711328611586577.JavaMail.root@wmail39> Very useful information. Grazie Paolo, G >----Messaggio originale---- >Da: giannozz at democritos.it >Data: 07/02/2012 10.57 >A: "giacsport at libero.it" >Cc: >Ogg: Re: [Pw_forum] scalability of the code > >On Tue, 2012-02-07 at 09:38 +0100, giacsport at libero.it wrote: > >> I would like to know which is the highest number of processors >> used and reported for running PWscf code. > >I have seen a test run on 65536 processors (cores, I mean). >Unfortunately I do not find any longer a test on a 8000-atom >system recently done: I guess it was also run on more than >just a few processors. > >> Are there data or reports on the scalability of the code (well) >> above 1000 processors? > >there is something in the Benchmark section of the new web site >( http://testwp.qe-forge.it/wordpress-3.1.4/?page_id=44 ). >More data will (maybe) come (subject to my allergy to both benchmarks >and wordpress, and to everybody's allergy to documentation) > >> We are indeed interested in installing the code in a massively parallel >> machine, but before doing it we would like to have more information. > >QE has been installed (with little effort) on several BlueGene machines. >It works (i.e. it has ben used for real scientific purposes and has >produced published results in at least one case I am aware of). You >have to be careful with I/O, which can become easily a limiting factor. >You may need to use all available parallelization levels, in particular >OpenMP, to satisfy the machine owners who, for sure, wants you to run >on a number of cores vastly exceeding what you actually need > >P. >-- >Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > From giannozz at democritos.it Tue Feb 7 12:04:55 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 07 Feb 2012 12:04:55 +0100 Subject: [Pw_forum] scalability of the code In-Reply-To: <6BCBEFD7-7AEF-45D7-8354-23CAE00765D3@epfl.ch> References: <10273511.18814901328603918224.JavaMail.root@wmail39> <1328608634.18193.41.camel@fe12lx.fisica.uniud.it> <6BCBEFD7-7AEF-45D7-8354-23CAE00765D3@epfl.ch> Message-ID: <1328612695.19467.7.camel@fe12lx.fisica.uniud.it> On Tue, 2012-02-07 at 11:25 +0100, Gabriele Sclauzero wrote: > The OpenMP parallelization is useful only if the code stops > complaining that there are not enough plane waves. In my experience, > before that number of processors is reached, the MPI parallelization > gives much better performances than the OpenMP one, probably because > there are still several parts of the code that have not been "threaded" so far. I guess you are referring to PWscf. I have been working with the Car-Parrinello code instead, which shows good OpenMP scalability. In any case, things are (slowly) improving for OpenMP parallelization in all codes. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Tue Feb 7 12:15:29 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 07 Feb 2012 12:15:29 +0100 Subject: [Pw_forum] low frequency dielectric constant In-Reply-To: References: Message-ID: <1328613329.19467.20.camel@fe12lx.fisica.uniud.it> On Sun, 2012-02-05 at 01:16 -0500, Vivek Ranjan wrote: > Wonder if it is already coded in PWSCF to calculate: > frequency dependent dielctric constant (low frequency dynamical ones) > static dielectric constant > mode effective charges not directly, but everything should be easily calculated from calculated quantities (dielectric tensor \espilon_\infty, dynamical matrix, atomic effective charges) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giuseppe.mattioli at ism.cnr.it Tue Feb 7 12:25:33 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Tue, 7 Feb 2012 12:25:33 +0100 Subject: [Pw_forum] pseudopotentials for C, H, O and Cl (Giuseppe Mattioli) In-Reply-To: References: Message-ID: <20120207122533.dfq8wpsksok8k48s@webmail.sic.rm.cnr.it> Dear Jos? Only a final remark: H.pbe-rrkjus.UPF H.pbe-van_ak.UPF H.pbe-van_bm.UPF O.pbe-van_ak.UPF O.pbe-rrkjus.UPF O.pbe-van_bm.UPF C.pbe-van_ak.UPF C.pbe-van_bm.UPF C.pbe-rrkjus.UPF Cl.pbe-n-van.UPF A combination of the above (ultrasoft) PPs may be the right one... However, there is plenty of pseudopotentials in the new library: http://qe-forge.org/projects/pslibrary/ The above ones are in the online library since... ages ago! So they may be considered as "tested", even if nothing is really tested until you really use it. HTH Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting Axel Kohlmeyer : > 2012/2/6 Jos? Alberto Pires Fernandes : >> Hello Giuseppe >> >> Please considere that in >> http://www.quantum-espresso.org/pseudo.php >> >> the only pseudopotentials available for Cl are >> >> Cl.blyp-mt.UPF >> Cl.pw91-mt.UPF >> Cl.pz-bhs.UPF >> Cl.pbe-n-van.UPF >> >> ?From these pseudopotentials I could find similar for C >> and O: >> >> C.blyp.mt.UPF >> >> and >> >> O.blyp.mt.UPF >> >> but no one in common for hydrogen. > > H.blyp-vbc.UPF > > is consistent with the "mt" potentials, > since it is a norm-conserving potential as well. > > > axel. > >> >> >> Jos? Fernandes >> Departamento de Quimica >> Universidade de Aveiro >> 3810-193 Aveiro >> Portugal >> Tel: +351234370720 >> Fax: +351234370084 >> _______________________________________________ >> 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 > > College of Science and Technology > Temple University, Philadelphia PA, USA. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From xgz at ornl.gov Tue Feb 7 17:17:09 2012 From: xgz at ornl.gov (Xiaoguang Zhang) Date: Tue, 07 Feb 2012 11:17:09 -0500 Subject: [Pw_forum] segmentation fault in local.f90 line 228 PWCOND version 4.3.2 In-Reply-To: <4F2C3567.6050700@ornl.gov> References: <4F2C3567.6050700@ornl.gov> Message-ID: <4F314E85.1040701@ornl.gov> Finally got the code to flag the array bound problem: Subscript #2 of the array VPPOTL has value 2161 which is greater than the upper bound of 1600 but I checked, nrx=54, nry=54, and nrx*nry=2916 so I don't understand why the upper bound is only 1600 On 02/03/2012 02:28 PM, Xiaoguang Zhang wrote: > pwcond.x crashes when it is trying to access vppot(1,2161,1,1) while > calculating the eigenvalues for the left lead. I inserted a print > statement in local.f90 and verified that this is the element that caused > the crash. After inserting these lines: > *** 213,218 **** > --- 213,220 ---- > ! > ! set and solve the eigenvalue equation for each slab > ! > + print *, nrz,nrx*nry,npol > + print *, vppot(1,2161,1,1) > DO WHILE(kin.LE.kfin) > > amat=(0.d0,0.d0) > the program crashed at the print statement with the last output > 20 2916 1 > which are nrz, nrx*nry, npol. There is no reason for it to crash. > > Full error message below: > ../../espresso-4.3.2/bin/pwcond.x< Alwirebig.cond.in> Alwirebig.cond.out > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line > Source > pwcond.x 0000000000432BEF local_1_ 228 > local.f90 > pwcond.x 000000000042FAA9 local_ 71 > local.f90 > pwcond.x 00000000004161FC do_cond_ 421 > do_cond.f90 > pwcond.x 000000000041130C MAIN__ 20 > condmain.f90 > pwcond.x 0000000000403922 Unknown Unknown Unknown > libc.so.6 0000002A9580F4CB Unknown Unknown Unknown > pwcond.x 000000000040386A Unknown Unknown Unknown > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Tue Feb 7 17:40:57 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 7 Feb 2012 17:40:57 +0100 Subject: [Pw_forum] segmentation fault in local.f90 line 228 PWCOND version 4.3.2 In-Reply-To: <4F314E85.1040701@ornl.gov> References: <4F2C3567.6050700@ornl.gov> <4F314E85.1040701@ornl.gov> Message-ID: <91A07DC5-B844-42E8-969F-303EDCE21C62@democritos.it> On Feb 7, 2012, at 17:17 , Xiaoguang Zhang wrote: > Finally got the code to flag the array bound problem: > Subscript #2 of the array VPPOTL has value 2161 which is greater than > the upper bound of 1600 > > but I checked, nrx=54, nry=54, and nrx*nry=2916 so I don't understand > why the upper bound is only 1600 very funny. Have you tried the same job - on a different number of processors / serially ? - on a different machine / compiler ? - with the latest development version ? If it is a real bug, some problem (not necessarily of the same kind) should show up in other machines as well. Irreproducible errors are very often compiler 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 xgz at ornl.gov Tue Feb 7 20:34:18 2012 From: xgz at ornl.gov (Xiaoguang Zhang) Date: Tue, 07 Feb 2012 14:34:18 -0500 Subject: [Pw_forum] segmentation fault in local.f90 line 228 PWCOND version 4.3.2 In-Reply-To: <91A07DC5-B844-42E8-969F-303EDCE21C62@democritos.it> References: <4F2C3567.6050700@ornl.gov> <4F314E85.1040701@ornl.gov> <91A07DC5-B844-42E8-969F-303EDCE21C62@democritos.it> Message-ID: <4F317CBA.3070605@ornl.gov> The problem was caused by different ecutwfc in lead and scattering regions. Changing the ecutwfc to the same number for both input files fixed the problem. On 02/07/2012 11:40 AM, Paolo Giannozzi wrote: > > On Feb 7, 2012, at 17:17 , Xiaoguang Zhang wrote: > >> Finally got the code to flag the array bound problem: >> Subscript #2 of the array VPPOTL has value 2161 which is greater than >> the upper bound of 1600 >> >> but I checked, nrx=54, nry=54, and nrx*nry=2916 so I don't understand >> why the upper bound is only 1600 > > very funny. Have you tried the same job > - on a different number of processors / serially ? > - on a different machine / compiler ? > - with the latest development version ? > If it is a real bug, some problem (not necessarily of the same > kind) should show up in other machines as well. Irreproducible > errors are very often compiler 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 avallabh at purdue.edu Wed Feb 8 04:00:47 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Tue, 7 Feb 2012 22:00:47 -0500 (EST) Subject: [Pw_forum] Identifying the phonon mode from eigen vector In-Reply-To: <2094271753.341055.1328668818919.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <1264536952.341128.1328670047559.JavaMail.root@mailhub016.itcs.purdue.edu> Dear users and developers, I am trying to understand how the atoms will be displaced for each of the six phonon modes in graphene at various q's from the eigen vectors. At gamma point (0,0,0), the eigen vectors are symmetric with the real part being of the same sign for acoustic modes and of opposite signs for optical modes with zero imaginary part for all of them. But for a different q like the one showed below, I can tell which are long, transv and out of plane (z) modes, but i want to know if it is possible to distinguish optical and acoustic modes (assuming frequencies and dispersion curves are not known). On a relevant note, i read some previous archives of 2009 discussing the possibility of identifying the frequencies by it's branch, not just from lowest to highest, i was wondering if that is possible at all without looking at the eigen vectors at each q. Diagonalizing the dynamical matrix q = ( 0.000000000 0.384900179 0.000000000 ) ************************************************************************** omega( 1) = 8.644497 [THz] = 288.349368 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 -0.111751 0.698190 ) ( 0.000000 0.000000 0.000000 0.000000 -0.707137 0.000000 ) omega( 2) = 16.684631 [THz] = 556.539398 [cm-1] ( 0.369888 0.602593 0.000000 0.000000 0.000000 0.000000 ) ( -0.687258 0.166557 0.000000 0.000000 0.000000 0.000000 ) omega( 3) = 23.786354 [THz] = 793.427359 [cm-1] ( 0.000000 0.000000 0.000000 0.000000 -0.111760 0.698249 ) ( 0.000000 0.000000 0.000000 0.000000 0.707077 0.000000 ) omega( 4) = 29.776017 [THz] = 993.221002 [cm-1] ( 0.000000 0.000000 0.667916 0.231960 0.000000 0.000000 ) ( 0.000000 0.000000 0.111765 0.698277 0.000000 0.000000 ) omega( 5) = 42.320122 [THz] = 1411.647329 [cm-1] ( -0.312873 0.634172 0.000000 0.000000 0.000000 0.000000 ) ( 0.507076 0.492758 0.000000 0.000000 0.000000 0.000000 ) omega( 6) = 45.622781 [THz] = 1521.812160 [cm-1] ( 0.000000 0.000000 0.668026 0.231999 0.000000 0.000000 ) ( 0.000000 0.000000 -0.111746 -0.698162 0.000000 0.000000 ) ************************************************************************** Thanks Ajit From flux_ray12 at 163.com Wed Feb 8 08:18:40 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Wed, 8 Feb 2012 15:18:40 +0800 (CST) Subject: [Pw_forum] The iotk error occurrd in ph.x Message-ID: <7e04438c.23c6b.1355bd4156d.Coremail.flux_ray12@163.com> Dear QE developer and users I am using an old cluster for calculation, where mpich2 1.2.1 was compiled by gortran 4.1.2 in Fedora 7 x86_64. The pw.x calculations were fine, but when I was executing ph.x, the iotk error occurred (no matter multi-nodes or single-core, this error occurred as soon as the input file read by ph.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 As I known, such a problem is due to the bug of compiler, i.e., gfortran 4.1.2. However, since I just have the normal user authority in this cluster, I cannot upgrade gfortran or install other fortran compiler. Even mpich2 was installed in /usr, so I cannot re-compile it. In such a case, do I have to give up the phonon calculaitons in this cluster ? -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120208/37513e5d/attachment.htm From henod2001 at yahoo.com Wed Feb 8 11:14:00 2012 From: henod2001 at yahoo.com (henry odhiambo) Date: Wed, 8 Feb 2012 02:14:00 -0800 (PST) Subject: [Pw_forum] Pseudopotentials Message-ID: <1328696040.11803.YahooMailClassic@web121001.mail.ne1.yahoo.com> Hello everyone, Kindly,? could someone, please, share with me GGA and Hybrid pseudopotentials and Green's functions for Te, Sb and Ge. I would highly appreciate. Regards, Henry O. Otunga -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120208/f5311421/attachment.htm From baroni at sissa.it Wed Feb 8 11:21:45 2012 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 8 Feb 2012 11:21:45 +0100 Subject: [Pw_forum] Identifying the phonon mode from eigen vector In-Reply-To: <1264536952.341128.1328670047559.JavaMail.root@mailhub016.itcs.purdue.edu> References: <1264536952.341128.1328670047559.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: On Feb 8, 2012, at 4:00 AM, Ajit Vallabhaneni wrote: > > Dear users and developers, > > I am trying to understand how the atoms will be displaced for each of the six phonon modes in graphene at various q's from the eigen vectors. At gamma point (0,0,0), the eigen vectors are symmetric with the real part being of the same sign for acoustic modes and of opposite signs for optical modes with zero imaginary part for all of them. But for a different q like the one showed below, I can tell which are long, transv and out of plane (z) modes, but i want to know if it is possible to distinguish optical and acoustic modes (assuming frequencies and dispersion curves are not known). Dear Ajit, In general, the distinction between acoustic and optical modes is conventional. "acoustic modes" are all those whose frequency is continuously connected with the three zone-center zero modes whose eigen-displacements correspond to a rigid translation of the entire crystal. All the others are, by convention, "optic modes". There is no rigorous way of telling which is which in the most general crystal structure at the most general q-point in the Brillouin zone. If asked to bet, I would say that modes whose displacements in the unit cell are "more parallel" would have a more "optic character" than those whose displacements are "anti-parallel", but again this statement is not rigorous, nor entirely meaningful either ... > On a relevant note, i read some previous archives of 2009 discussing the possibility of identifying the frequencies by it's branch, not just from lowest to highest, i was wondering if that is possible at all without looking at the eigen vectors at each q. As said, the only meaningful statement can be made on the branch to which a mode belongs. If the frequency of the branch vanishes at q=0, then the entore branch is (conventionally) acoustic, otherwise it is deemed to be optic ... Hope this helps ... 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/20120208/5dbe87a5/attachment.htm From lmartinsamos at gmail.com Wed Feb 8 11:27:14 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 8 Feb 2012 11:27:14 +0100 Subject: [Pw_forum] Pseudopotentials In-Reply-To: <1328696040.11803.YahooMailClassic@web121001.mail.ne1.yahoo.com> References: <1328696040.11803.YahooMailClassic@web121001.mail.ne1.yahoo.com> Message-ID: Dear Henry, if with "hybrid" you mean with a fraction of exact exchange. There are no pseudos with EXX fraction. I saw some calcuations made with pseudo potentials built with OEP approximation, simil Hartree-Fock. If you think that with exx the semicore could play a role, you need to include the semicore in your calculations. bests Layla 2012/2/8 henry odhiambo > Hello everyone, > > Kindly, could someone, please, share with me GGA and Hybrid > pseudopotentials and Green's functions for Te, Sb and Ge. I would highly > appreciate. > > Regards, > Henry O. Otunga > > > _______________________________________________ > 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/20120208/53d77ec3/attachment.htm From mari.ijas at aalto.fi Wed Feb 8 12:04:00 2012 From: mari.ijas at aalto.fi (=?iso-8859-1?Q?Ij=E4s_Mari?=) Date: Wed, 8 Feb 2012 11:04:00 +0000 Subject: [Pw_forum] Segfault in ph.x (QE 4.3.2, 4.3.1) Message-ID: Dear everyone, I'm trying to calculate the vibrational modes for diamond. I have compiled QE using gfortran and gcc, and pw.x runs just fine. When running ph.x, however, the execution stops with a segmentation fault (in my system, all information I get is: [1]+ Segmentation fault: 11 ../espresso-4.3.1/bin/ph.x < ph_diamond.in > ph_diamond.out). In the output file, the last lines are: Atomic displacements: There are 2 irreducible representations Representation 1 3 modes -A_1g G_1 G_1+ To be done Representation 2 3 modes -A_1g G_1 G_1+ To be done This is similar in both 4.3.1 and 4.3.2. I tried to search the archives but didn't find other reports matching this problem. I'm attaching the input files for my scf and ph calculation, if they happen to be of any help. Please let me know if any other information is required. Best wishes, Mari Ij?s Department of Applied Physics Aalto University School of Science -------------- next part -------------- A non-text attachment was scrubbed... Name: ph_diamond.in Type: application/octet-stream Size: 342 bytes Desc: ph_diamond.in Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120208/98dcd41b/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: scf_diamond.in Type: application/octet-stream Size: 1169 bytes Desc: scf_diamond.in Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120208/98dcd41b/attachment-0001.obj From Lorenzo.Paulatto at impmc.upmc.fr Wed Feb 8 14:34:08 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 08 Feb 2012 14:34:08 +0100 Subject: [Pw_forum] Segfault in ph.x (QE 4.3.2, 4.3.1) In-Reply-To: References: Message-ID: On Wed, 08 Feb 2012 12:04:00 +0100, Ij?s Mari wrote: > Atomic displacements: > There are 2 irreducible representations > > Representation 1 3 modes -A_1g G_1 G_1+ To be done > > Representation 2 3 modes -A_1g G_1 G_1+ To be done Dear Ij?s, the cutoff you are using is extremely high, are you sure you're not just running out of memory? Have you tried running with lower cutoffs and got the some error? Anyway, gfortran often miscompiles the phonon code, which version are you using? 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 akohlmey at gmail.com Wed Feb 8 15:12:02 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Wed, 8 Feb 2012 09:12:02 -0500 Subject: [Pw_forum] The iotk error occurrd in ph.x In-Reply-To: <7e04438c.23c6b.1355bd4156d.Coremail.flux_ray12@163.com> References: <7e04438c.23c6b.1355bd4156d.Coremail.flux_ray12@163.com> Message-ID: 2012/2/8 GAO Zhe : > Dear QE developer and users > I am using an old cluster for calculation, where mpich2 1.2.1 was compiled > by gortran 4.1.2 in Fedora 7 x86_64. > The pw.x calculations were fine, but when I was executing ph.x, the iotk > error occurred (no matter multi-nodes or single-core, this error occurred as > soon as the input file read by ph.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 > As I known, such a problem is due to the bug of compiler, i.e., gfortran > 4.1.2. However, since I just have the normal user authority in this cluster, > I cannot upgrade gfortran or install other fortran compiler. Even mpich2 was > installed in /usr, so I cannot re-compile it. yes, you can compile and install both the GCC compilers (including gfortran) and the MPI library without superuser privilege and override the system defaults. it just takes some effort and requires reading of the corresponding documentation. i have done both many times on very different machines without having root access. axel. > In such a case, do I have to give up the phonon calculaitons in this cluster > ? > > -- > GAO Zhe > CMC Lab, Materials Science & Engineering Department, > Seoul National University, South Korea > > > > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From flux_ray12 at 163.com Wed Feb 8 18:00:48 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 9 Feb 2012 01:00:48 +0800 (CST) Subject: [Pw_forum] The iotk error occurrd in ph.x In-Reply-To: References: <7e04438c.23c6b.1355bd4156d.Coremail.flux_ray12@163.com> Message-ID: <478dabf1.e.1355de90a7a.Coremail.flux_ray12@163.com> Dear Axel, thank you very much. I will try ifort+mpich2 in my own directory, hoping it works and the newest ifort 12 can work in Fedora 7. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-08 22:12:02,"Axel Kohlmeyer" wrote: >2012/2/8 GAO Zhe : >> Dear QE developer and users >> I am using an old cluster for calculation, where mpich2 1.2.1 was compiled >> by gortran 4.1.2 in Fedora 7 x86_64. >> The pw.x calculations were fine, but when I was executing ph.x, the iotk >> error occurred (no matter multi-nodes or single-core, this error occurred as >> soon as the input file read by ph.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 >> As I known, such a problem is due to the bug of compiler, i.e., gfortran >> 4.1.2. However, since I just have the normal user authority in this cluster, >> I cannot upgrade gfortran or install other fortran compiler. Even mpich2 was >> installed in /usr, so I cannot re-compile it. > >yes, you can compile and install both the GCC compilers >(including gfortran) and the MPI library without superuser >privilege and override the system defaults. it just takes >some effort and requires reading of the corresponding >documentation. i have done both many times on very >different machines without having root access. > >axel. > > >> In such a case, do I have to give up the phonon calculaitons in this cluster >> ? >> >> -- >> GAO Zhe >> CMC Lab, Materials Science & Engineering Department, >> Seoul National University, South Korea >> >> >> >> >> _______________________________________________ >> 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 > >College of Science and Technology >Temple University, Philadelphia PA, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/d413b127/attachment.htm From samolyuk at gmail.com Wed Feb 8 19:28:23 2012 From: samolyuk at gmail.com (German Samolyuk) Date: Wed, 8 Feb 2012 13:28:23 -0500 Subject: [Pw_forum] pwscf: constrained total magnetic moment In-Reply-To: References: <8A46AB04-62AB-4586-93AF-FEED76E4A0A6@epfl.ch> Message-ID: Dear Gabriele, I do two Fermi level fixed magnetic moment calculation. There is print in subroutine electrons.f90 version 4.2.1 in line 462 WRITE( stdout, 9072 ) bfield(3), and bfield(3) is determined as (ef_up-ef_dn)/2. I gives some estimation for for "equivalent" magnetic field. I understand that this is very rough estimate. The question was how to recalulcate it to Tesla. As I understand, it should be (ef_up-ef_dn)/(2mu_B). Thanks, German ORNL On Fri, Jan 6, 2012 at 3:26 AM, Gabriele Sclauzero wrote: > Dear German, > > ? ?In my previous answer I actually didn't get the point of your question. > Now I think I've understood better your concern, but some points of your > message still look obscure to me. > > Il giorno 05/gen/2012, alle ore 19.41, German Samolyuk ha scritto: > > Dear Gabriele, > > Thank you for your answer. > I use version 4.2.1 and the input I used works for this version. For > the 4.3.2 vesion the input should be as you mentioned > tot_magnetization = some_number;. The results obtained with both > version are the same. > > > What results? Do you mean the same energy? Total magnetization? Both? > > > The output from 4.2.1 version has value of "corresponding" magnetic > field which according to text is defined as (e_f_up-e_f_dn)/2 in > Rydbergs. > > > Which text? Where did you find this definition? What is the "corresponding" > magnetic field? > > My question was if there is any way to estimate corresponding external > magnetic field? > > > If you use the constrained magnetization method, the external magnetic field > should vanish as you reach the ground state with the target magnetization > (see the form of the penalty functional here below). This may not happen if > your value of lambda is too small, because it needs to be large enough to > make energetically favored the state with the target symmetry.?I don't think > you should attach any physical importance to a nonzero?constraining > field.?This said, things can be tricky, because if you increase lambda the > charge density might become nearly impossible to??converge. If this happens, > you should try to decrease mixing_beta and/or make a chain of several runs > where you "restart" from the previous charge density by progressively > increasing lambda. > > If you use the other method in version 4.3.2, there shouldn't be any > external magnetic field. > > HTH > > GS > > > Thank you, > > German > > > On Thu, Jan 5, 2012 at 5:50 AM, Gabriele Sclauzero > wrote: > > Dear German, > > > ? ? have you checked the manuals? In the input description of PWscf I've > > found: > > > ? ? ? ? ? ? ? ? ? ?'total': > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? total magnetization is constrained by > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? adding a penalty functional to the total energy: > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? LAMBDA * SUM_{i} ( magnetization(i) - > > fixed_magnetization(i) )**2 > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? where the sum over i runs over the three > > components of > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? the magnetization. Lambda is a real number (see > > below). > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? Noncolinear case only. Use "tot_magnetization" > > for LSDA > > > I think that, in order to fix the total magnetization in LSDA calculations > > (nspin=2), you should simply set the tot_magnetization parameter > > (two-Fermi-energies method) and not specify the constrained_magnetization > > keyword. Which version of QE are you using? > > > > HTH > > > GS > > > > Il giorno 03/gen/2012, alle ore 20.10, German Samolyuk ha scritto: > > > Dear all, > > > I do self-consistent calculation of supercell with 135 Fe atoms with > > constrained magnetization. > > > nspin = 2, > > fixed_magnetization(3) = 360.0, > > constrained_magnetization = 'total' , > > > The output value of magnetic field: > > > ??Magnetic field ???????????= ??0.0785401 Ry > > > > In order to make a rough estimation of corresponding magnetic field in > > Tesla I should divide this value by mu_B and difference between > > total magnetic moments of system with constrain and without it? > > > Thank you > > > German Samolyuk > > Oak Rigde National Laboratory > > _______________________________________________ > > 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 > > > > > ? Gabriele Sclauzero,?EPFL SB ITP CSEA > ?? PH H2 462, Station 3,?CH-1015 Lausanne > > > > > > > From samolyuk at gmail.com Wed Feb 8 19:39:59 2012 From: samolyuk at gmail.com (German Samolyuk) Date: Wed, 8 Feb 2012 13:39:59 -0500 Subject: [Pw_forum] Uranium pseudopotenial Message-ID: Dear quantum espresso users, How I can add 6s state in the basis of Uranum pseudopotential? I could not find any example for two channels with the same L and different principal number, Thank you German Samolyuk, ORNL, USA the input I used to build pspot: &input title='U', zed=92., rel=1, iswitch=3, config='[Rn] 5f3.0 6d1.0 7s1.0', dft='PBE' rlderiv=2.80, eminld=-14.0, emaxld=4.0, deld=0.01, nld=4, / &inputp lloc=0, pseudotype=3, file_pseudopw='U.pbe-rrkjus.UPF', nlcc=.true., rcore=1.1, author='GDS', / 7 5F 4 3 3.00 0.0 1.060 1.600 5F 4 3 0.00 -.2 1.060 1.600 6P 2 1 6.00 0.0 1.300 1.700 6P 2 1 0.00 -.2 1.300 1.700 6D 3 2 1.00 0.0 2.400 2.600 6D 3 2 0.00 -.2 2.400 2.600 7S 1 0 1.00 0.0 3.500 3.500 From dorabman at gmail.com Wed Feb 8 22:56:48 2012 From: dorabman at gmail.com (Hua Bao) Date: Wed, 8 Feb 2012 16:56:48 -0500 Subject: [Pw_forum] The output of d3x Message-ID: Dear All, I am working on the anharmonic force constant calculation following example 14. Since there is not much description of the output format (let me know if I am wrong), I have to guess what the parameters are. Based on Debernardi's thesis and the discussions, I guess the code calculates C(0,q,-q), but this quantity is also a function of p, p', p'', which are the components of atomic displacements. I have read the code a little bit. The d3 matrix is stored in the quantity phi, which is a function of atom index and direction index( i guess?). However, I could not understand the output format as follows modo: 1 1 1 -0.138777878078E-15 0.000000000000E+00 -0.832667268469E-16 0.000000000000E+00 -0.277555756156E-16 0.000000000000E+00 -0.416333634234E-16 0.000000000000E+00 0.832667268469E-16 0.000000000000E+00 0.383064069101E+00 0.000000000000E+00 -0.111022302463E-15 0.000000000000E+00 0.383064069101E+00 0.000000000000E+00 -0.277555756156E-16 0.000000000000E+0 I cannot understand "modo" and (1,1). I suspect (1 1) means atom index, but there are p, p', p''. Which two (1,1) stands for? Also, in the README file. It shows something like C_{x,y,z} (0,0,0|1,1,1). I can understand (0,0,0) are the three q-points, but what does this 1,1,1 stands for? It does not look like phonon branch index or atom index. I have been struggling on this for quite some time. I really appreciate if anyone can help me to clarify this issue. Thanks, Hua -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120208/8af9892f/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Wed Feb 8 23:48:29 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 08 Feb 2012 23:48:29 +0100 Subject: [Pw_forum] The output of d3x In-Reply-To: References: Message-ID: Dear Hua Bao, you can understand the meaning of the several fields from the loop that actually writes those files, in write_d3dyn.f90: do i = 1, 3 * nat if (wrmode (i) ) then write (iudyn, '(/,12x,"modo:",i5,/)') i nc = (i - 1) / 3 + 1 kcar = i - 3 * (nc - 1) do na = 1, nat do nb = 1, nat write (iudyn, '(2i3)') na, nb do icar = 1, 3 write (iudyn, '(3e24.12)') (phi (kcar, icar, jcar, nc, na, nb) & , jcar = 1, 3) enddo enddo enddo endif enddo phi has 6 indexes that correspond to the modes (cartesian index + atomic index) of the 3 phonons involved in the process. I.e. phi(1,2,3, 5,6,7) corresponds to (atom5_x, atom6_y, atom7_z) Keep in mind that when doing a calculation with d3.x at q the first phonon corresponds to the Gamma point, the second to -q and the third to q. More specifically, inside the file, the index that follows "modo:" is the mode for Gamma (modo is just italian for mode), it is composite cartesian+atom, ie. 1=atom1_x, 2=atom1_y, 3=atom1_z, 4=atom2_x, ... Then, the 2 isolated integers ("1 1" in your examples) are the indexes of the atoms for the second and third mode. Finally, the 3x3 matrix of *complex* numbers follows. Every *two* lines the second cartesian index increments by one. While the the third index increases by one every couple of numbers (each are the real and imaginary part of one element). Yes, the second one has the real part in a line and the imaginary in the next... It sounds a bit complicated, but it is only complicated to explain in text. If you study the code for a few minutes it should be clear. bests On Wed, 08 Feb 2012 22:56:48 +0100, Hua Bao wrote: > Dear All, > > I am working on the anharmonic force constant calculation following > example > 14. > Since there is not much description of the output format (let me know if > I > am wrong), I have to guess what the parameters are. > > Based on Debernardi's thesis and the discussions, > I guess the code calculates C(0,q,-q), but this quantity is also a > function of p, p', p'', which are the components of atomic displacements. > > I have read the code a little bit. The d3 matrix is stored in the > quantity > phi, which is a function of atom index and direction index( i guess?). > > However, I could not understand the output format as follows > > modo: 1 > > 1 1 > -0.138777878078E-15 0.000000000000E+00 -0.832667268469E-16 > 0.000000000000E+00 -0.277555756156E-16 0.000000000000E+00 > -0.416333634234E-16 0.000000000000E+00 0.832667268469E-16 > 0.000000000000E+00 0.383064069101E+00 0.000000000000E+00 > -0.111022302463E-15 0.000000000000E+00 0.383064069101E+00 > 0.000000000000E+00 -0.277555756156E-16 0.000000000000E+0 > > I cannot understand "modo" and (1,1). > I suspect (1 1) means atom index, but there are p, p', p''. Which two > (1,1) > stands for? > > Also, in the README file. It shows something like C_{x,y,z} > (0,0,0|1,1,1). > I can understand (0,0,0) are the three q-points, but what does this 1,1,1 > stands for? It does not look like phonon branch index or atom index. > > I have been struggling on this for quite some time. I really appreciate > if > anyone can help me to clarify this issue. > > Thanks, > Hua -- 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 samolyuk at gmail.com Wed Feb 8 23:58:51 2012 From: samolyuk at gmail.com (German Samolyuk) Date: Wed, 8 Feb 2012 17:58:51 -0500 Subject: [Pw_forum] large system parallel execution problem Message-ID: Dear QE users and developers, I'm trying to optimize structure of super cell containing 433 magnetic Fe atoms on Cray xt4 machine. The program runs electronic structure self consistency and calculate forces but stops at first structure optimization step. Do you know possible reason. It works for smaller systems. I've attached archive with input and output files together with pbatch I used Thank you German Samolyuk ORNL, USA -------------- next part -------------- A non-text attachment was scrubbed... Name: 111.tar.gz Type: application/x-gzip Size: 93666 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120208/4dfa2796/attachment-0001.bin From magda.birowska at gmail.com Thu Feb 9 14:14:20 2012 From: magda.birowska at gmail.com (Magdalena Birowska) Date: Thu, 9 Feb 2012 14:14:20 +0100 Subject: [Pw_forum] LDA+U+non-collinear magnetism Message-ID: Dear users; Does LDA+U work with non-collinear magnetism? best regards Magdalena Birowska -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/43712426/attachment.htm From asmogunov at gmail.com Thu Feb 9 14:30:34 2012 From: asmogunov at gmail.com (Alex Smogunov) Date: Thu, 9 Feb 2012 14:30:34 +0100 Subject: [Pw_forum] LDA+U+non-collinear magnetism In-Reply-To: References: Message-ID: Dear Magdalena. It is coming very soon, this week hopefully. It should also work with SOC and will include separately U, J, and other parameters to calculate Coulomb matrix elements. regards, Alexander 2012/2/9 Magdalena Birowska > Dear users; > > Does LDA+U work with non-collinear magnetism? > > best regards > Magdalena Birowska > > _______________________________________________ > 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/20120209/3cbc55fa/attachment.htm From baroni at sissa.it Thu Feb 9 14:47:01 2012 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 9 Feb 2012 14:47:01 +0100 Subject: [Pw_forum] Identifying the phonon mode from eigen vector In-Reply-To: References: <1264536952.341128.1328670047559.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: > > If asked to bet, I would say that modes whose displacements in the unit cell are "more parallel" would have a more "optic character" Of, course, I meant "acoustic character". Sorry for the misunderstanding. SB From flux_ray12 at 163.com Thu Feb 9 15:15:18 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 9 Feb 2012 22:15:18 +0800 (CST) Subject: [Pw_forum] Calculation stopped at the beginning of ph.x process Message-ID: <3810e16f.16410.1356277e16a.Coremail.flux_ray12@163.com> Dear QE developer and users: At first, I want to say thanks to Alex Kohlmeyer, who made me realized I still can run the calculation by normal user access. I compiled pw.x and ph.x, again, by mpich2 1.4.1p1 which was compiled by PGI fortran 9.0 (trial version). The pw.x calculation among 12 nodes (24 cores) was very nice. But when I run the ph.x, the calculation stopped at the initial step. The terminate displayed as: mpirun -machinefile nodes -np 24 ${KKK}/ph.x -npool 3 -in ${KKK}/binary.ph.in > ${KKK}/binary.ph.out application called MPI_Abort(MPI_COMM_WORLD, 0) - process 2 ......... application called MPI_Abort(MPI_COMM_WORLD, 0) - process 23 And I checked the output file, binary.ph.out, it did not show the information about process stopping: Parallel version (MPI), running on 24 processors K-points division: npool = 3 R & G space division: proc/pool = 8 Ultrasoft (Vanderbilt) Pseudopotentials Info: using nr1, nr2, nr3 values from input Info: using nr1s, nr2s, nr3s values from input Message from routine read_ions : PP will be read from ./ Parallelization info -------------------- sticks: dense smooth PW G-vecs: dense smooth PW Min 253 253 72 8611 8611 1298 Max 254 254 73 8614 8614 1301 Sum 2025 2025 577 68891 68891 10395 Dynamical matrices for ( 3, 3, 3,) uniform grid of q-points ( 4q-points): N xq(1) xq(2) xq(3) 1 0.000000000 0.000000000 0.000000000 2 0.000000000 0.000000000 0.333333333 3 0.000000000 0.333333333 0.333333333 4 0.333333333 0.333333333 0.333333333 Calculation of q = 0.0000000 0.0000000 0.0000000 rank 3 in job 73 node01_35097 caused collective abort of all ranks exit status of rank 3: killed by signal 9 .......... rank 22 in job 73 node01_35097 caused collective abort of all ranks exit status of rank 22: killed by signal 9 Why did this problem occurred? I ran the same input file in my own computer, with mpich2 1.4.1p1 and ifort 12. It worked well at least up to the "break point". Is this problem caused by the fortran compilor PGI 9.0? Looking forward to any suggestion. Thanks a lot. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/fc8426d2/attachment.htm From pandey.bramha at gmail.com Thu Feb 9 15:49:27 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Thu, 9 Feb 2012 20:19:27 +0530 Subject: [Pw_forum] How we can give Temperature to equilibrium system (T=o) Message-ID: Dear QE users... i want to know how we can introduce the temperature in our equilibrium system(i.e after running scf with proper setting of lattice parameter, ecut and k point, we get ground state total energy(T=0) in scf run). As i read somewhere that SCF will gives the minimum total energy at T=0, because in DFT there is no term of temperature. May be i am wrong but can we introduce temperature by changing the any parameter in input file of pw.x. Actualy i want to generate the phonon by the thermal excitation in my input file by increasing the temperature of my system or any other means by which i can generate phonon for thermo-dynamical property calculation of the system. Any type of help will be appreciable . -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/213c50cb/attachment.htm From flux_ray12 at 163.com Thu Feb 9 15:54:35 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 9 Feb 2012 22:54:35 +0800 (CST) Subject: [Pw_forum] How we can give Temperature to equilibrium system (T=o) In-Reply-To: References: Message-ID: <4ff9a4.16ac2.135629bdb9d.Coremail.flux_ray12@163.com> You can obtain thermodynamics properties at finite temperature by calculating phonon (ph.x) and treating phonon through QHA method. If temperature was high, you may need an-harmonic calculation by d3.x -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-09 22:49:27,"bramha pandey" wrote: Dear QE users... i want to know how we can introduce the temperature in our equilibrium system(i.e after running scf with proper setting of lattice parameter, ecut and k point, we get ground state total energy(T=0) in scf run). As i read somewhere that SCF will gives the minimum total energy at T=0, because in DFT there is no term of temperature. May be i am wrong but can we introduce temperature by changing the any parameter in input file of pw.x. Actualy i want to generate the phonon by the thermal excitation in my input file by increasing the temperature of my system or any other means by which i can generate phonon for thermo-dynamical property calculation of the system. Any type of help will be appreciable . -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/84ba8dc9/attachment.htm From giannozz at democritos.it Thu Feb 9 16:08:39 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 09 Feb 2012 16:08:39 +0100 Subject: [Pw_forum] Calculation stopped at the beginning of ph.x process In-Reply-To: <3810e16f.16410.1356277e16a.Coremail.flux_ray12@163.com> References: <3810e16f.16410.1356277e16a.Coremail.flux_ray12@163.com> Message-ID: <1328800119.29169.4.camel@fe12lx.fisica.uniud.it> On Thu, 2012-02-09 at 22:15 +0800, GAO Zhe wrote: > I ran the same input file in my own computer, with mpich2 1.4.1p1 > and ifort 12. It worked well at least up to the "break point". > Is this problem caused by the fortran compilor PGI 9.0? likely so. Try to run with debug flags; if it is not a compiler bug you should get some more info P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From gabriele.sclauzero at epfl.ch Thu Feb 9 16:21:40 2012 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Thu, 9 Feb 2012 16:21:40 +0100 Subject: [Pw_forum] Fwd: Uranium pseudopotenial References: Message-ID: Or maybe it has been implemented only recently... indeed, just today I've found some examples of ld1 input files where semicore states have the same L as valence states. Check the ps_library input files (see http://qe-forge.org/projects/pslibrary/)... GS Inizio messaggio inoltrato: > Da: Gabriele Sclauzero > Data: 09 febbraio 2012 10.54.08 GMT+01.00 > A: German Samolyuk > Oggetto: Re: [Pw_forum] Uranium pseudopotenial > > Dear German, > >> How I can add 6s state in the basis of Uranum pseudopotential? >> I could not find any example for two channels with the same L and >> different principal number, > > that's simply because this possibility is not implemented in ld1.x. > Maybe other codes can do this, you could try to search on the forum archives for some related information, I remember that there were discussions about that in the past. > > > HTH > > > GS > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > ? 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/20120209/79d3a2e1/attachment.htm From giannozz at democritos.it Thu Feb 9 16:32:38 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 09 Feb 2012 16:32:38 +0100 Subject: [Pw_forum] large system parallel execution problem In-Reply-To: References: Message-ID: <1328801558.29169.13.camel@fe12lx.fisica.uniud.it> On Wed, 2012-02-08 at 17:58 -0500, German Samolyuk wrote: > The program runs electronic structure self consistency and calculate forces > but stops at first structure optimization step. Do you know possible reason. since "OOM killer terminated this process", you should discover who OOM killer is (hint: Out Of Memory?) For a better parallelization, you should run with -npool 8 P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From bdslipun at gmail.com Thu Feb 9 18:21:21 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Thu, 9 Feb 2012 22:51:21 +0530 Subject: [Pw_forum] optimisation Message-ID: i have a question about the optimisation 1. for optimising the internal coordinates and lattice parameter i have used 4*4*4 kpoint grid it converged in 10 steps and i get the lattice parameters and internal parameters at equilibrium but when i incresed the kpoint mesh to 8*8*8 then the forces on atoms are large so my equilibrium parametes changes so how can i start whether i should use higher kpoint mesh from start of my calculation? sahu b mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/c3e965c5/attachment.htm From samolyuk at gmail.com Thu Feb 9 19:17:17 2012 From: samolyuk at gmail.com (German Samolyuk) Date: Thu, 9 Feb 2012 13:17:17 -0500 Subject: [Pw_forum] large system parallel execution problem In-Reply-To: <1328801558.29169.13.camel@fe12lx.fisica.uniud.it> References: <1328801558.29169.13.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Paolo, Thank you. About -npool 8: I have problems with memory for this task. As I understand k-points parallelisation does not distribute memory but will take processors from r,k-parallelisation, these two distribute memory, and effectively it will increase memory I'll need to run the task. Did I understand it wrong? German On Thu, Feb 9, 2012 at 10:32 AM, Paolo Giannozzi wrote: > On Wed, 2012-02-08 at 17:58 -0500, German Samolyuk wrote: > >> The program runs electronic structure self consistency and calculate forces >> but stops at first structure optimization step. Do you know possible reason. > > since "OOM killer terminated this process", you should discover who OOM > killer is (hint: Out Of Memory?) > > For a better parallelization, you should run with -npool 8 > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > From samolyuk at gmail.com Thu Feb 9 19:21:37 2012 From: samolyuk at gmail.com (German Samolyuk) Date: Thu, 9 Feb 2012 13:21:37 -0500 Subject: [Pw_forum] Uranium pseudopotenial In-Reply-To: References: Message-ID: Dear Gabriele, Thank you. The Fe.pbe-spn-rrkjus.in is what I'm looking for. German On Thu, Feb 9, 2012 at 10:21 AM, Gabriele Sclauzero wrote: > > Or maybe it has been implemented only recently... indeed, just today I've > found some examples of ld1 input files > where semicore states have the same L as valence states. Check > the?ps_library input files (see?http://qe-forge.org/projects/pslibrary/)... > > GS > > Inizio messaggio inoltrato: > > Da: Gabriele Sclauzero > Data: 09 febbraio 2012 10.54.08 GMT+01.00 > A: German Samolyuk > Oggetto: Re: [Pw_forum] Uranium pseudopotenial > > Dear German, > > How I can add 6s state in the basis of Uranum pseudopotential? > I could not find any example for two channels with the same L and > different principal number, > > > ? ?that's simply because this possibility is not implemented in ld1.x. > Maybe other codes can do this, you could try to search on the forum archives > for some related information, I remember that there were discussions about > that in the past. > > > HTH > > > GS > > > ? Gabriele Sclauzero,?EPFL SB ITP CSEA > ?? PH H2 462, Station 3,?CH-1015 Lausanne > > > > > > > > > > ? Gabriele Sclauzero,?EPFL SB ITP CSEA > ?? PH H2 462, Station 3,?CH-1015 Lausanne > > > > > > > From giannozz at democritos.it Thu Feb 9 19:23:41 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 9 Feb 2012 19:23:41 +0100 Subject: [Pw_forum] large system parallel execution problem In-Reply-To: References: <1328801558.29169.13.camel@fe12lx.fisica.uniud.it> Message-ID: <2B67AED9-49A0-4D47-A92E-811993DF04E4@democritos.it> On Feb 9, 2012, at 19:17 , German Samolyuk wrote: > I have problems with memory for this task. As I understand k-points > parallelisation does not distribute memory [...] Did I understand > it wrong? no, you understood well. It seems to me strange, however, that so much memory is needed. Your job is big but not horribly big. 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 shelaa at stanford.edu Thu Feb 9 22:06:20 2012 From: shelaa at stanford.edu (Shela Aboud) Date: Thu, 9 Feb 2012 13:06:20 -0800 (PST) Subject: [Pw_forum] Your message to Pw_forum awaits moderator approval In-Reply-To: <604674346.415233.1328821497033.JavaMail.root@zm07.stanford.edu> Message-ID: <1582360339.417813.1328821580779.JavaMail.root@zm07.stanford.edu> Dear Moderator, I sent this post to the forum with the wrong email list and I wanted to let you know that I have registered as a a member. Best, Shela pw_forum-bounces at pwscf.org 12:25 PM (38 minutes ago) to me Your mail to 'Pw_forum' with the subject Follow up on thread: [Pw_forum] unitary matrix u Is being held until the list moderator can review it for approval. The reason it is being held: Post by non-member to a members-only list Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://www.democritos.it/mailman/confirm/pw_forum/55c3cd2dfa905219c7eb97452e37bd4392a0f28f -- Shela Aboud Sr. Research Associate 367 Panama St. GES 077A Stanford University Stanford, CA 94305-2220 shela.aboud at stanford.edu (650) 721-2276 From saboud at gmail.com Thu Feb 9 21:25:55 2012 From: saboud at gmail.com (Shela Aboud) Date: Thu, 9 Feb 2012 12:25:55 -0800 Subject: [Pw_forum] Follow up on thread: unitary matrix u Message-ID: I have searched the Pw_forum but was not able to find a response to a previous post. I am including the portion of the original post that I am curious about below. I have the same question. After running my electron-phonon calculations some of my q-points (G-M in graphene) have only a "-1" for each of the real x,y,z-components of one atom and zero everywhere else as written under "modes" in the electron-phonon output file. I assumed "modes" corresponded to the phonon eigenvectors, but this would imply 6 optical modes at some q values which is not correct (although along different symmetry lines it looks like the correct format for eigenvectors). Thank you, Shela Part of original Post: Date: Thu, 14 May 2009 12:05:53 -0400 Subject: [Pw_forum] unitary matrix u Message-ID: <2C1C44865AA64068BE6465660B5DEA6E at ece.ncsu.edu> ".....there is always only one nonzero component. For instance, the first eigenvector is (-1,0,0,0,0,0). Obviously, all six eigenvectors are orthonormal, which is how it's supposed to be. But here is what bothers me. For acoustic phonon modes, the unit cell moves as a whole, i.e. both atoms must move with the same phase. So I expect to see something like (1/sqrt(2),0,0, 1/sqrt(2),0,0), instead of (-1,0,0,0,0,0). For optical branches on the other hand, two atoms have the opposite phase (the center of mass of the unit cell does not move), so I would expect to see something like (1/sqrt(2),0,0, -1/sqrt(2),0,0). My understanding is this: if every eigenvector has only one nonzero component, it means that in each mode, one atom is not moving at all! Maybe, I misunderstood the meaning of components of the matrix u? " -- Shela Aboud CEES Sr. Research Scientist 367 Panama St. GES 077A Stanford University Stanford, CA 94305-2220 shela.aboud at stanford.edu (650) 721-2276 From dt378 at bath.ac.uk Thu Feb 9 14:00:16 2012 From: dt378 at bath.ac.uk (dt378 at bath.ac.uk) Date: Thu, 09 Feb 2012 13:00:16 +0000 Subject: [Pw_forum] write a xsf file using pwi2xsf.sh Message-ID: <20120209130016.Horde.jc27N1Lxr25PM8Ngxg6DcSA@webmail.bath.ac.uk> I have just started to use Espresso so I apologise if my question is a bit silly. I would like to convert my input file in a xsf format but I can't. This is the error it punch out: " chpc-aw7:zns davidetiana$ ~/espresso-4.3.2/pwtools/pwi2xsf.sh zns1.in At line 426 of file pwi2xsf.f Fortran runtime error: End of file " where am I wrong? Thank a lot this is my input: " &control calculation='scf', title='Molecule1', wf_collect=.true., outdir='./', etot_conv_thr=1.0d-4, forc_conv_thr=1.0d-3, pseudo_dir='/Users/davidetiana/espresso-4.3.2/pseudo', / &system ibrav=6, celldm(1)=15.0 celldm(3)=9.66 nat=23, ntyp=6, tot_charge=0.0, ecutwfc=25.0, ecutrho=200.0, nosym=.false., nosym_evc=.false., london=.true., london_s6=0.75, london_rcut=200, / &electrons electron_maxstep=80, conv_thr=1.0d-6, mixing_mode='plain', mixing_beta=0.7, mixing_ndim=8, mixing_fixed_ns=0, diagonalization='david', / ATOMIC_SPECIES H 1.01 H.pbe-van_ak.UPF C 12.0 C.pbe-van_ak.UPF N 14.01 N.pbe-van_ak.UPF Na 22.99 Na.pbe-sp-van_ak.UPF S 32.07 S.pbe-van_bm.UPF Zn 65.39 Zn.pbe-sp-van_ak.UPF ATOMIC_POSITIONS {crystal} C 0.448640 0.000000 0.327710 C 0.551360 0.000000 0.327710 C 0.602730 0.000000 0.189640 C 0.397270 0.000000 0.189640 C 0.551190 0.000000 0.051810 C 0.448810 0.000000 0.051810 H 0.559910 0.164660 0.636860 H 0.440090 0.164660 0.636860 H 0.500000 0.163500 0.798940 H 0.678730 0.000000 0.189520 H 0.321270 0.000000 0.189520 N 0.500000 0.139320 0.690820 Na 0.274970 0.000000 0.68946 Na 0.725030 0.000000 0.68946 S 0.610260 0.000000 -0.11137 S 0.389740 0.000000 -0.11137 S 0.390650 0.000000 0.49147 S 0.609350 0.000000 0.49147 Zn 0.500000 0.000000 0.69076 H 0.440090 -0.164660 0.63686 H 0.559910 -0.164660 0.63686 H 0.500000 -0.163500 0.79894 N 0.500000 -0.139320 0.69082 K_POINTS {automatic} 4 4 4 0 0 0 From giannozz at democritos.it Thu Feb 9 23:08:55 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 9 Feb 2012 23:08:55 +0100 Subject: [Pw_forum] Follow up on thread: unitary matrix u In-Reply-To: References: Message-ID: <23DFFD4E-B480-4D08-A47A-157F4A44EA9F@democritos.it> On Feb 9, 2012, at 21:25 , Shela Aboud wrote: > some of my q-points (G-M in graphene) have only a "-1" for each > of the real x,y,z-components of one atom and zero everywhere > else as written under "modes" in the electron-phonon output file. written where exactly? from your description and the mentioned e-mail, these look like the irreps, i.e. the displacement patterns used to perform the calculation. Phonon displacements are calculated at the end and look like phonons. 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 suza.rri at gmail.com Fri Feb 10 00:32:04 2012 From: suza.rri at gmail.com (Suza W) Date: Fri, 10 Feb 2012 00:32:04 +0100 Subject: [Pw_forum] orthogonality of phonon eigenvectors? In-Reply-To: References: <1325776554.5202.3.camel@fe12lx.fisica.uniud.it> Message-ID: Dear All , > > >> > IIRC the phonon code, and all other auxiliary codes, always print >> > displacement patterns, not phonon eigenvectors >> >> Not always. In case of a homo-atomic system, the phonon eigen-vectots > (v) > can directly be presented as atomic displacements (u) . However, for a > hetero- > atomic system, it is not so straight-forward. We need some more > algebra, because > > u = v / sqrt (M) and SUM_i ( u_i . u_i . M_i ) = constant . > > After that one can obtain correct atomic displacement from the > eigen-vectors in case of a > hetero-atomic system. > For example, after the above algebra, we get, these well-arranged eigen displacements ( 0.0 0.0 2.30182985E-05 ) ( 0.0 0.0 1.65666412E-03 ) ( 0.0 0.0 -1.75258026E-04 ) ( 0.0 0.0 -3.12875743E-03 ) ( 0.0 0.0 -1.75258026E-04 ) ( 0.0 2.30182985E-05 0.0 ) ( 0.0 1.65666412E-03 0.0 ) ( 0.0 -1.75258026E-04 0.0 ) ( 0.0 -3.12875743E-03 0.0 ) ( 0.0 -1.75258026E-04 0.0 ) ( 2.30182985E-05 0.0 0.0 ) ( 1.65666412E-03 0.0 0.0 ) ( -1.75258026E-04 0.0 0.0 ) ( -3.12875743E-03 0.0 0.0 ) ( -1.75258026E-04 0.0 0.0 ) ,whereas the initial eigen-vectors that QE code prints directly (which is indeed messy) after diagonalising the dynamical matrix were omega( 1) = 2.395159 [THz] = 79.894433 [cm-1] ( 0.004885 0.000000 0.000925 0.000000 0.000021 0.000000 ) ( 0.453433 0.000000 0.085812 0.000000 0.001953 0.000000 ) ( -0.869153 0.000000 -0.008829 0.000000 -0.000201 0.000000 ) ( -0.046653 0.000000 -0.164486 0.000000 -0.000201 0.000000 ) ( -0.046653 0.000000 -0.008829 0.000000 -0.003743 0.000000 ) omega( 2) = 2.395159 [THz] = 79.894433 [cm-1] ( 0.000050 0.000000 -0.000153 0.000000 -0.004969 0.000000 ) ( 0.004666 0.000000 -0.014157 0.000000 -0.461245 0.000000 ) ( -0.008943 0.000000 0.001457 0.000000 0.047457 0.000000 ) ( -0.000480 0.000000 0.027136 0.000000 0.047457 0.000000 ) ( -0.000480 0.000000 0.001457 0.000000 0.884127 0.000000 ) omega( 3) = 2.395159 [THz] = 79.894433 [cm-1] ( -0.000923 0.000000 0.004883 0.000000 -0.000159 0.000000 ) ( -0.085707 0.000000 0.453217 0.000000 -0.014777 0.000000 ) ( 0.164285 0.000000 -0.046631 0.000000 0.001520 0.000000 ) ( 0.008818 0.000000 -0.868738 0.000000 0.001520 0.000000 ) ( 0.008818 0.000000 -0.046631 0.000000 0.028326 0.000000 ) Thanking you all, Yours sincerely, Suza > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120210/024c6645/attachment.htm From ma at nano.ku.dk Fri Feb 10 10:09:24 2012 From: ma at nano.ku.dk (Martin Andersson) Date: Fri, 10 Feb 2012 10:09:24 +0100 Subject: [Pw_forum] rgen: error 4, too many r-vectors Message-ID: <4F34DEC4.70800@nano.ku.dk> Hi, I am performing pw.x calculations including empirical london dispersion. I was investigating how my results vary as a function of the cutoff for the dispersion interaction, and got the following message for very short cutoffs: from rgen : error # 2 too many r-vectors with PBE and london_s6=0.75. If I use revpbe and s6=1.25 the error number is 4 but otherwise the same. Any thoughts on why I get this error? Regards, Martin Andersson University of Copenhagen From giannozz at democritos.it Fri Feb 10 14:07:10 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 10 Feb 2012 14:07:10 +0100 Subject: [Pw_forum] orthogonality of phonon eigenvectors? In-Reply-To: References: <1325776554.5202.3.camel@fe12lx.fisica.uniud.it> Message-ID: On Feb 10, 2012, at 24:32 , Suza W wrote: > For example, after the above algebra, we get, these well- > arranged eigen displacements > [...] > ,whereas the initial eigen-vectors that QE code prints directly > (which is indeed messy) if you have degenerate eigenvalues, any linear combination of eigenvectors in the degenerate subspace is a solution. What you get from numerical diagonalization depends upon the phase of the moon. 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 flux_ray12 at 163.com Fri Feb 10 14:46:49 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 10 Feb 2012 21:46:49 +0800 (CST) Subject: [Pw_forum] Calculation stopped at the beginning of ph.x process In-Reply-To: <1328800119.29169.4.camel@fe12lx.fisica.uniud.it> References: <1328800119.29169.4.camel@fe12lx.fisica.uniud.it> <3810e16f.16410.1356277e16a.Coremail.flux_ray12@163.com> Message-ID: <595499f1.27c9a.13567842c4e.Coremail.flux_ray12@163.com> Dear Prof. Giannozzi, thank you very much. Now I solve that problem. Actually, I tried ifort 12 and falled, again, but the some information provided, as: from diropn : error # 21 Then I downloaded the old version, QE 4.2.1 (previous one was QE 4.3.2), and compiled it by ifort 12. Up to now, the parallel running of ph.x is fine. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-09 23:08:39,"Paolo Giannozzi" wrote: >On Thu, 2012-02-09 at 22:15 +0800, GAO Zhe wrote: > >> I ran the same input file in my own computer, with mpich2 1.4.1p1 >> and ifort 12. It worked well at least up to the "break point". >> Is this problem caused by the fortran compilor PGI 9.0? > >likely so. Try to run with debug flags; if it is not a compiler >bug you should get some more info > >P. > >-- >Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120210/5018d750/attachment.htm From tone.kokalj at ijs.si Fri Feb 10 16:37:05 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 10 Feb 2012 16:37:05 +0100 Subject: [Pw_forum] write a xsf file using pwi2xsf.sh In-Reply-To: <20120209130016.Horde.jc27N1Lxr25PM8Ngxg6DcSA@webmail.bath.ac.uk> References: <20120209130016.Horde.jc27N1Lxr25PM8Ngxg6DcSA@webmail.bath.ac.uk> Message-ID: <1328888225.3796.14.camel@catalyst.ijs.si> On Thu, 2012-02-09 at 13:00 +0000, dt378 at bath.ac.uk wrote: > I have just started to use Espresso so I apologise if my question is a > bit silly. > I would like to convert my input file in a xsf format but I can't. > > This is the error it punch out: > " > chpc-aw7:zns davidetiana$ ~/espresso-4.3.2/pwtools/pwi2xsf.sh zns1.in > At line 426 of file pwi2xsf.f > Fortran runtime error: End of file You compiled the pwi2xsf.f with new version of gfortran (e.g. gfortran-4.6), right? It does not compile properly. The code was adopted in the "failing" part. I attach the corrected pwi2xsf.f file. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- A non-text attachment was scrubbed... Name: pwi2xsf.f Type: text/x-fortran Size: 15781 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120210/9068d21d/attachment.bin From pandey.bramha at gmail.com Fri Feb 10 17:08:14 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Fri, 10 Feb 2012 21:38:14 +0530 Subject: [Pw_forum] How we can give Temperature to equilibrium system (T=o) In-Reply-To: <4ff9a4.16ac2.135629bdb9d.Coremail.flux_ray12@163.com> References: <4ff9a4.16ac2.135629bdb9d.Coremail.flux_ray12@163.com> Message-ID: Dear GAO Zhe and QE users...Thanks alot for your quick reply. I have calculated the phonon DOS value and by fqha.x utility which is given in PH/fqha.x. I have calculated the free energy F(T) at different temperature. The normalised phonon 3*N=6.00011 getting which is right.(i am taking 2 atoms in unit cell as FCC in zincblende structure). the Desprsion relation of frequency and PHDOS graph was also seems right. But realy i want to calculate Specific heat (C_v), Entropy. so for that i was tried for QHA package which was given in QE, but it is not giving the accurate value and very less value i was getting in order of 10^-7 of Cv. Here i an attaching the PHDOS.out file please see it. Sir please help me in this regard how can i calculate the Cv value and other thermodynamical parameters. I am heartily appreciated any help regarding this problem. 2012/2/9 GAO Zhe > You can obtain thermodynamics properties at finite temperature by > calculating phonon (ph.x) and treating phonon through QHA method. If > temperature was high, you may need an-harmonic calculation by d3.x > > -- > GAO Zhe > CMC Lab, Materials Science & Engineering Department, > Seoul National University, South Korea > > > At 2012-02-09 22:49:27,"bramha pandey" wrote: > > > Dear QE users... > > i want to know how we can introduce the temperature in our equilibrium > system(i.e after running scf with proper setting of lattice parameter, ecut > and k point, we get ground state total energy(T=0) in scf run). > > As i read somewhere that SCF will gives the minimum total energy at T=0, > because in DFT there is no term of temperature. > May be i am wrong but can we introduce temperature by changing the any > parameter in input file of pw.x. Actualy i want to generate the phonon by > the thermal excitation in my input file by increasing the temperature of > my system or any other means by which i can generate phonon for > thermo-dynamical property calculation of the system. > > Any type of help will be appreciable . > > > -- > 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 > > > > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120210/a1317450/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: PHDOS.out Type: application/octet-stream Size: 22649 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120210/a1317450/attachment-0001.obj From kiprono.kiptiemoi at polito.it Fri Feb 10 18:45:09 2012 From: kiprono.kiptiemoi at polito.it (KORIR KIPRONOH) Date: Fri, 10 Feb 2012 18:45:09 +0100 Subject: [Pw_forum] correct volume for effective charge calculation for supercell Message-ID: Dear QE users, I evaluate the effective charge for ZnO nanostructure using the linear response approach but I'm a bit apprehensive about the results. I have my nanostructure in a supercell(also there is a vacuum in the supercell) so i'm assuming this volume was used in evaluation of this parameter. If that is the case then how do I introduce the correct volume of the nanostructure? Your comments & insights would be highly appreciated. PhD student Politecnico di Torino ....... Korir From mdulski at us.edu.pl Fri Feb 10 19:10:28 2012 From: mdulski at us.edu.pl (mateusz dulski) Date: Fri, 10 Feb 2012 19:10:28 +0100 Subject: [Pw_forum] mixture Message-ID: <000601cce81f$4529cfa0$6501a8c0@polpress88ef18> I would ask if it is possible to calculate different crystal structure when based on the crystalographical data we get two or more atoms in one position i.e mixture position? Mateusz -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120210/a61bb7f3/attachment.htm From kiprono.kiptiemoi at polito.it Sat Feb 11 08:08:34 2012 From: kiprono.kiptiemoi at polito.it (KORIR KIPRONOH) Date: Sat, 11 Feb 2012 08:08:34 +0100 Subject: [Pw_forum] correct volume for effective charge calculation for supercell In-Reply-To: References: Message-ID: Hello Emine & QE users, Thanks for your comments. I'm still seeking more clarification on the same subject, born effective charge is a product of "cell volume" with derivative of the polarization with respect to atomic displacement at zero macroscopic field........so I thought there is dependence on volume?, also the vacuum used is sufficient to ensure there no interaction with its replicas. On 10 February 2012 22:03, KORIR KIPRONOH wrote: > > > Emine Kucukbenli wrote: > >>Ciao Korir >>Do you mean the born effective charges, z*? >>if so there shouldnt be any volume dependence as far as i know. >>..unless the periodic images are interacting strongly, which would mean >>you would need to use more vacuum in between. >>ciao, >>emine kucukbenli >> >>-------- Original Message -------- >>Subject: [Pw_forum] correct volume for effective charge calculation for >>supercell >>Date: 10.02.2012 18:45 >> From: KORIR KIPRONOH >>To: pw_forum at pwscf.org >> >>Dear QE users, >> >>I ?evaluate the effective charge for ZnO nanostructure using the >>linear response approach but I'm a bit apprehensive about the results. >>I have my nanostructure in a supercell(also there is a vacuum in the >>supercell) so i'm assuming this volume was used in evaluation of this >>parameter. If that is the case then how do I introduce the correct >>volume of the nanostructure? >>Your comments & insights would be highly appreciated. >> >> >>PhD student >>Politecnico di Torino >>....... >>Korir >>_______________________________________________ >>Pw_forum mailing list >>Pw_forum at pwscf.org >>http://www.democritos.it/mailman/listinfo/pw_forum >> PhD student Politecnico Di Torino .......... Korir From giannozz at democritos.it Sat Feb 11 12:27:16 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 11 Feb 2012 12:27:16 +0100 Subject: [Pw_forum] correct volume for effective charge calculation for supercell In-Reply-To: References: Message-ID: On Feb 11, 2012, at 8:08 , KORIR KIPRONOH wrote: > I'm still seeking more clarification on the same subject, born > effective > charge is a product of "cell volume" with derivative of the > polarization > with respect to atomic displacement at zero macroscopic > field........so > I thought there is dependence on volume? I am not sure I understand what you mean. If you have a finite object (or simply, a molecule) in a supercell, yes, the effective charges decrease as the volume of the supercell increases. This is normal: the dipole does not depend upon the volume of the supercell (if it is large enough), the dipole per unit volume does. 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 filippo.spiga at ichec.ie Sat Feb 11 15:41:44 2012 From: filippo.spiga at ichec.ie (Filippo Spiga) Date: Sat, 11 Feb 2012 15:41:44 +0100 Subject: [Pw_forum] Call of GPU benchmark inputs for PWSCF Message-ID: <501C03F8-4B6B-474C-A3F5-0B74AD568C23@ichec.ie> Dear all, the GPU porting of PWSCF carried in the past months is going to hit an important milestone: the GPU Technology Conference in San Jose (USA). For that date, we would like to deliver the full package and finally merge the GPU branch into the main code. What it is really important in a project like this is a detailed and a 365-degree assessment of the performance, taking into account as many different scenario (read as many different type of input/calculation) as possible. In the next (missing) two months we are going to finalize some important piece of code and run tests. A lot of tests. As much tests as we can. The purpose of this email is to collect from users new benchmark inputs that reflect real scientific challenges. We are looking to new input for serial and parallel calculations, small or big (not very big... let's say "medium") systems, gamma or k-point, with or without magnetization, with or without exact-exchange, etc... What we are especially looking for "special" inputs. I mean, inputs that are able to intensively stress some specific (and well localized) part of the code. Do not hesitate to contact me. I look forward to receiving new test cases! At the end it will be a pleasure to officially acknowledge all the people that will contribute. Regards, Filippo -- Mr. Filippo SPIGA, Computational Scientist, Irish Centre for High-End Computing (ICHEC) - www.ichec.ie The Tower - Trinity Technology & Enterprise Campus Grand Canal Quay - Dublin 2 - Ireland Tel: +353-1-5241608 ex. 40 ~ Mob: +353-85-816-8710 website: http://filippospiga.me ~ skype: filippo.spiga ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert From 1009ukumar at gmail.com Sat Feb 11 19:21:36 2012 From: 1009ukumar at gmail.com (Sonu Kumar) Date: Sat, 11 Feb 2012 23:51:36 +0530 Subject: [Pw_forum] orthogonality of phonon eigenvectors? In-Reply-To: References: <1325776554.5202.3.camel@fe12lx.fisica.uniud.it> Message-ID: On Fri, Feb 10, 2012 at 6:37 PM, Paolo Giannozzi wrote: > > On Feb 10, 2012, at 24:32 , Suza W wrote: > > > For example, after the above algebra, we get, these well- > > arranged eigen displacements > > [...] > > ,whereas the initial eigen-vectors that QE code prints directly > > (which is indeed messy) > > if you have degenerate eigenvalues, any linear combination of > eigenvectors > in the degenerate subspace is a solution. What you get from numerical > diagonalization depends upon the phase of the moon. > > Dear Prof. Paolo Giannozzi and ALL QE users, If i use "dynmat.x", and use q=0,0,0 point (gamma), i get corrected eigen values and eigen vectors. It seems to me that ASR is applied to eigen vectors, because they are different (more or less) from eigen vectors obtained from conventional "phonon.x" output. Is it so ? However this difference could affect properties depending upon eigen vectors or eigen displacements. Am i right ? One Basic question: since eigen values and eigen vectors are related to eech other through eigen values equation, Ax-\{Lamda}Ix=O. So, if x is changing(corrected) after using dynmax.x (imposing ASR), then why not eigen values are corrected ? or is there any linear combination of eigen vectors is used in the procedure of ASR so as to get the same eigenvalue \Lamda. with kind regards, SK ========================================== Sonu Kumar Phd Student,Physics Department Indian Institute of Technology ,Delhi-110016, India web:-http://www.iitd.ac.in/ ========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120211/2615c88e/attachment.htm From natalia at npavlenko.com Sun Feb 12 10:52:24 2012 From: natalia at npavlenko.com (Natalia Pavlenko) Date: Sun, 12 Feb 2012 01:52:24 -0800 (PST) Subject: [Pw_forum] local basis for projected DOS Message-ID: <1329040344.50233.YahooMailNeo@web5716.biz.mail.ne1.yahoo.com> Dear users, is it possible to calculate the projected orbital density of states in a rotated local basis that is obtained by a rotation of the basis axes defined by ibrav? ? Thanks, N.Pavlenko Dr. Natalia Pavlenko Institute of Physics, University of Augsburg Germany -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120212/5a5d0ede/attachment.htm From suza.rri at gmail.com Sun Feb 12 12:35:18 2012 From: suza.rri at gmail.com (Suza W) Date: Sun, 12 Feb 2012 12:35:18 +0100 Subject: [Pw_forum] orthogonality of phonon eigenvectors? In-Reply-To: References: <1325776554.5202.3.camel@fe12lx.fisica.uniud.it> Message-ID: > > if you have degenerate eigenvalues, any linear combination of > eigenvectors > > in the degenerate subspace is a solution. What you get from numerical > > diagonalization depends upon the phase of the moon. > > Yes Prof. Giannozzi, in principle, it is true. Nevertheless, in practice, phonon code in ABINIT always renders these well-arranged eigen displacements without depending much on the phase of the moon. ( 0.0 0.0 2.30182985E-05 ) ( 0.0 0.0 1.65666412E-03 ) ( 0.0 0.0 -1.75258026E-04 ) ( 0.0 0.0 -3.12875743E-03 ) ( 0.0 0.0 -1.75258026E-04 ) ( 0.0 2.30182985E-05 0.0 ) ( 0.0 1.65666412E-03 0.0 ) ( 0.0 -1.75258026E-04 0.0 ) ( 0.0 -3.12875743E-03 0.0 ) ( 0.0 -1.75258026E-04 0.0 ) ( 2.30182985E-05 0.0 0.0 ) ( 1.65666412E-03 0.0 0.0 ) ( -1.75258026E-04 0.0 0.0 ) ( -3.12875743E-03 0.0 0.0 ) ( -1.75258026E-04 0.0 0.0 ) Thanks and Regards, Suza -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120212/fae7f151/attachment.htm From 1009ukumar at gmail.com Sun Feb 12 17:38:27 2012 From: 1009ukumar at gmail.com (Sonu Kumar) Date: Sun, 12 Feb 2012 22:08:27 +0530 Subject: [Pw_forum] orthogonality of phonon eigenvectors? In-Reply-To: References: <1325776554.5202.3.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Suza, On Sun, Feb 12, 2012 at 5:05 PM, Suza W wrote: > > >> > if you have degenerate eigenvalues, any linear combination of >> eigenvectors >> > in the degenerate subspace is a solution. What you get from numerical >> > diagonalization depends upon the phase of the moon. >> >> Yes Prof. Giannozzi, in principle, it is true. > Nevertheless, in practice, phonon code in ABINIT > always renders these well-arranged eigen displacements > without depending much on the phase of the moon. > > > ( 0.0 0.0 2.30182985E-05 ) > ( 0.0 0.0 1.65666412E-03 ) > ( 0.0 0.0 -1.75258026E-04 ) > ( 0.0 0.0 -3.12875743E-03 ) > ( 0.0 0.0 -1.75258026E-04 ) > > ( 0.0 2.30182985E-05 0.0 ) > ( 0.0 1.65666412E-03 0.0 ) > ( 0.0 -1.75258026E-04 0.0 ) > ( 0.0 -3.12875743E-03 0.0 ) > ( 0.0 -1.75258026E-04 0.0 ) > > ( 2.30182985E-05 0.0 0.0 ) > ( 1.65666412E-03 0.0 0.0 ) > ( -1.75258026E-04 0.0 0.0 ) > ( -3.12875743E-03 0.0 0.0 ) > ( -1.75258026E-04 0.0 0.0 ) > > I think, after applying ASR i.e. using dynmat.x, you can obtain these well arranged eigen vectors. Although no so sure. regards, Sonu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120212/7a33102e/attachment.htm From giannozz at democritos.it Sun Feb 12 19:01:57 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 12 Feb 2012 19:01:57 +0100 Subject: [Pw_forum] orthogonality of phonon eigenvectors? In-Reply-To: References: <1325776554.5202.3.camel@fe12lx.fisica.uniud.it> Message-ID: <922CEC0B-1B44-4696-8E50-A5CEFA421FB9@democritos.it> On Feb 11, 2012, at 19:21 , Sonu Kumar wrote: > It seems to me that ASR is applied to eigen vectors no, it is applied to force constants > However this difference could affect properties depending upon > eigen vectors or eigen displacements. Am i right ? usually, no: the ASR changes only marginally the eigenvectors and the eigendisplacements. The main consequence of ASR is that zero-frequency acoustic modes have zero frequency. 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 fratesi at mater.unimib.it Mon Feb 13 15:30:47 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Mon, 13 Feb 2012 15:30:47 +0100 Subject: [Pw_forum] local basis for projected DOS In-Reply-To: <1329040344.50233.YahooMailNeo@web5716.biz.mail.ne1.yahoo.com> References: <1329040344.50233.YahooMailNeo@web5716.biz.mail.ne1.yahoo.com> Message-ID: <4F391E97.5040709@mater.unimib.it> Dear Natalia, I'm not aware of an automated way, but you can rotate the projections in the basis you want, provided you have a matrix defining the basis transformation and the full projection matrix (squared moduli are commonly written in output). The latter matrix is written by projwfc.x in outdir, the file is named atomic_proj.xml. For each atomic state phi_i, you will find the projections for all n in the field "ATMWFC.i". Then you can conveniently find eigenvalues and kp-weights in the same xml file to reconstruct the PDOS. HTH, Guido Il 02/12/2012 10:52 AM, Natalia Pavlenko ha scritto: > Dear users, > > is it possible to calculate the projected orbital density of states in a > rotated local basis > that is obtained by a rotation of the basis axes defined by ibrav? > > Thanks, N.Pavlenko > > Dr. Natalia Pavlenko > Institute of Physics, University of Augsburg > Germany > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From elie.moujaes at hotmail.co.uk Mon Feb 13 16:36:55 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 13 Feb 2012 15:36:55 +0000 Subject: [Pw_forum] phonon calculations in a spercell of 100 atoms Message-ID: Dear all, I have two questions: (1) I am running phonon calculations on a system of 100 atoms and only at the Gamma point! It is really taking a lot of time. It is running in the parallel computing mode with a total of 16 processors on 2 nodes and still is going slow. Is there a way to speed up things? and is there a way to do the whole phonon dispersion in lesser time? (2) If only the phonon frequencies at the Gamma point were calculated , I was wondering what kind of information about the system can one get? Thanks Elie MoukeasUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120213/f77dea3f/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Mon Feb 13 16:41:04 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 13 Feb 2012 16:41:04 +0100 Subject: [Pw_forum] phonon calculations in a spercell of 100 atoms In-Reply-To: References: Message-ID: On Mon, 13 Feb 2012 16:36:55 +0100, Elie M wrote: > Dear all, > I have two questions: > (1) I am running phonon calculations on a system of 100 atoms and only > at the Gamma point! It is really taking a lot of time. It is running in > the parallel computing mode with a total of 16 processors on 2 nodes and > still is going slow. Is there a way to speed up things? and is there a > way to do the whole phonon dispersion in lesser time? Do not use a supercell? Seriously, phonon calculations are expensive, with many atoms they are extremely expensive. If you only need the phonons at the gamma point, it may be faster to get them by finite displacement, doing 3*nat pw.x ground state calculations. > (2) If only the phonon frequencies at the Gamma point were calculated , > I was wondering what kind of information about the system can one get? > Thanks If the supercell is large enough, all the information you need. 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 elie.moujaes at hotmail.co.uk Mon Feb 13 17:24:50 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 13 Feb 2012 16:24:50 +0000 Subject: [Pw_forum] phonon calculations in a spercell of 100 atoms In-Reply-To: References: , Message-ID: Thanks for your reply. Any reference to the finite displacement method for phonon calculations using QE? Thanks again Elie > To: pw_forum at pwscf.org > Date: Mon, 13 Feb 2012 16:41:04 +0100 > From: Lorenzo.Paulatto at impmc.upmc.fr > Subject: Re: [Pw_forum] phonon calculations in a spercell of 100 atoms > > On Mon, 13 Feb 2012 16:36:55 +0100, Elie M > wrote: > > Dear all, > > I have two questions: > > (1) I am running phonon calculations on a system of 100 atoms and only > > at the Gamma point! It is really taking a lot of time. It is running in > > the parallel computing mode with a total of 16 processors on 2 nodes and > > still is going slow. Is there a way to speed up things? and is there a > > way to do the whole phonon dispersion in lesser time? > > Do not use a supercell? Seriously, phonon calculations are expensive, with > many atoms they are extremely expensive. If you only need the phonons at > the gamma point, it may be faster to get them by finite displacement, > doing 3*nat pw.x ground state calculations. > > > (2) If only the phonon frequencies at the Gamma point were calculated , > > I was wondering what kind of information about the system can one get? > > Thanks > > If the supercell is large enough, all the information you need. > > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120213/4605945a/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Mon Feb 13 17:32:30 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 13 Feb 2012 17:32:30 +0100 Subject: [Pw_forum] phonon calculations in a spercell of 100 atoms In-Reply-To: References: Message-ID: On Mon, 13 Feb 2012 17:24:50 +0100, Elie M wrote: > Thanks for your reply. Any reference to the finite displacement method > for phonon calculations using QE? None that I know, but it is relatively straightforward. The first result I got googling "real space force constant" is , check page 5. 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 elie.moujaes at hotmail.co.uk Mon Feb 13 17:48:38 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Mon, 13 Feb 2012 16:48:38 +0000 Subject: [Pw_forum] phonon calculations in a spercell of 100 atoms In-Reply-To: <1D7CF111-85FD-47F7-B8B8-566F75DD82FC@epfl.ch> References: , , <1D7CF111-85FD-47F7-B8B8-566F75DD82FC@epfl.ch> Message-ID: Dear Gabrielle and Lorenzo, Thanks very much for the links. I will be having a look at them. Regards Elie From: gabriele.sclauzero at epfl.ch Subject: Re: [Pw_forum] phonon calculations in a spercell of 100 atoms Date: Mon, 13 Feb 2012 17:41:13 +0100 To: elie.moujaes at hotmail.co.uk Dear Elie, you might want to have a look at Dario Alf?'s webpagehttp://www.homepages.ucl.ac.uk/~ucfbdxa/phon/He has a code that should do what you need. HTH GS Il giorno 13/feb/2012, alle ore 17.24, Elie M ha scritto:Thanks for your reply. Any reference to the finite displacement method for phonon calculations using QE? Thanks again Elie > To: pw_forum at pwscf.org > Date: Mon, 13 Feb 2012 16:41:04 +0100 > From: Lorenzo.Paulatto at impmc.upmc.fr > Subject: Re: [Pw_forum] phonon calculations in a spercell of 100 atoms > > On Mon, 13 Feb 2012 16:36:55 +0100, Elie M > wrote: > > Dear all, > > I have two questions: > > (1) I am running phonon calculations on a system of 100 atoms and only > > at the Gamma point! It is really taking a lot of time. It is running in > > the parallel computing mode with a total of 16 processors on 2 nodes and > > still is going slow. Is there a way to speed up things? and is there a > > way to do the whole phonon dispersion in lesser time? > > Do not use a supercell? Seriously, phonon calculations are expensive, with > many atoms they are extremely expensive. If you only need the phonons at > the gamma point, it may be faster to get them by finite displacement, > doing 3*nat pw.x ground state calculations. > > > (2) If only the phonon frequencies at the Gamma point were calculated , > > I was wondering what kind of information about the system can one get? > > Thanks > > If the supercell is large enough, all the information you need. > > bests > > > -- > Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 begin_of_the_skype_highlighting +33 (0)1 44275 084 end_of_the_skype_highlighting / 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 _______________________________________________ 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/20120213/f37b5ed1/attachment-0001.htm From giannozz at democritos.it Mon Feb 13 21:45:09 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 13 Feb 2012 21:45:09 +0100 Subject: [Pw_forum] phonon calculations in a spercell of 100 atoms In-Reply-To: References: Message-ID: <9D5DE73F-5BE0-4FD4-AD0D-774DC08EC0D1@democritos.it> On Feb 13, 2012, at 16:41 , Lorenzo Paulatto wrote: > If you only need the phonons at the gamma point, it may be faster > to get them by finite displacement, doing 3*nat pw.x ground state > calculations. faster? not sure, and not by much anyway. A phonon calculation at q=0 also requires 3*nat self-consistent linear-response calculations. Each such calculation has a computational cost comparable to that of a self-consistency. Usually one needs to perform two finite-difference calculations with opposite displacements in order to get good numerical accuracy, by the way. Or at least, this is the way I would do it. For q=0 phonons, using k=0 only for the Brillouiin zone sampling, and norm-conserving PP, there is the simplified version of the phonon code that is definitely faster and takes (relatively) little 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 calderin at physics.queensu.ca Mon Feb 13 21:50:43 2012 From: calderin at physics.queensu.ca (Lazaro Calderin) Date: Mon, 13 Feb 2012 15:50:43 -0500 Subject: [Pw_forum] Quantum Espresso Workshop (Jun 25 - Jun 29 /2012, Penn State Univ., PA, USA) Message-ID: Hello everyone ! This is just to let you know about an upcoming workshop on Quantum Espresso !! You can find more info at the url: http://rcc.its.psu.edu/education/workshops/pages/quantum_espresso_2012/ I hope to welcome you in Pennsylvania for the QE 2012 Workshop ! All the best, Lazaro == Lazaro Calderin Research Computing and Cyberinfrastructure Materials Simulation Center Penn State University 814.865.1134 From joshiniharika20 at yahoo.in Tue Feb 14 08:18:13 2012 From: joshiniharika20 at yahoo.in (Niharika Joshi) Date: Tue, 14 Feb 2012 12:48:13 +0530 (IST) Subject: [Pw_forum] k-resolved DOS Message-ID: <1329203893.37663.YahooMailNeo@web95702.mail.in.yahoo.com> Hello, I was trying out the example 08 (quantum espresso 4.3.2) where k-resolved DOS for Ni is calculated. I plotted the k-resolved DOS for Ni (d orbital) at just one k-point and then the total DOS. The DOS at one k-point are coming higher than the total DOS, which should be the other way round. Can anyone explain this? Thanking in advance. -Niharika Joshi (Project student, Indian Institute of Science Education and Research, Pune, India) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120214/36bb4b61/attachment.htm From fratesi at mater.unimib.it Tue Feb 14 10:45:20 2012 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Tue, 14 Feb 2012 10:45:20 +0100 Subject: [Pw_forum] k-resolved DOS In-Reply-To: <1329203893.37663.YahooMailNeo@web95702.mail.in.yahoo.com> References: <1329203893.37663.YahooMailNeo@web95702.mail.in.yahoo.com> Message-ID: <4F3A2D30.6080503@mater.unimib.it> Dear Niharika, Il 02/14/2012 08:18 AM, Niharika Joshi ha scritto: > Hello, > I was trying out the example 08 (quantum espresso 4.3.2) where > k-resolved DOS for Ni is calculated. > I plotted the k-resolved DOS for Ni (d orbital) at just one k-point and > then the total DOS. > The DOS at one k-point are coming higher than the total DOS, which > should be the other way round. No, there's no such requirement. The k-resolved DOS does not include the k-point weight, which is set here to unity: see Doc/INPUT_PROJWFC. Best, Guido > Can anyone explain this? > Thanking in advance. > -Niharika Joshi > (Project student, Indian Institute of Science Education and Research, > Pune, India) > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From federico at clustering.com.ar Tue Feb 14 15:59:48 2012 From: federico at clustering.com.ar (Federico Vadell) Date: Tue, 14 Feb 2012 11:59:48 -0300 Subject: [Pw_forum] Configure script problem Message-ID: Dear all, I m having trouble with the configure script since it does not seem to find the mkl libs. Im using espresso-PRACE and intel composer XE 2011 sp1. Ive tried this line: ./configure --enable-openmp --enable-cuda LIBDIRS="/opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64/" --prefix=/opt/espresso-PRACE where /opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64 has libaux_ia32_gfortran.a libmkl_core.a libmkl_p4n.so libaux_ia32_gnu.a libmkl_core.so libmkl_pgi_thread.a libaux_ia32_intel.a libmkl_def.so libmkl_pgi_thread.so libaux_intel64_gfortran.a libmkl_gf_ilp64.a libmkl_rt.so libaux_intel64_gnu.a libmkl_gf_ilp64.so libmkl_scalapack_ilp64.a libaux_intel64_intel.a libmkl_gf_lp64.a libmkl_scalapack_ilp64.so libmkl_avx.so libmkl_gf_lp64.so libmkl_scalapack_lp64.a libmkl_blacs_ilp64.a libmkl_gnu_thread.a libmkl_scalapack_lp64.so libmkl_blacs_intelmpi_ilp64.a libmkl_gnu_thread.so libmkl_sequential.a libmkl_blacs_intelmpi_ilp64.so libmkl_intel_ilp64.a libmkl_sequential.so libmkl_blacs_intelmpi_lp64.a libmkl_intel_ilp64.so libmkl_solver_ilp64.a libmkl_blacs_intelmpi_lp64.so libmkl_intel_lp64.a libmkl_solver_ilp64_sequential.a libmkl_blacs_lp64.a libmkl_intel_lp64.so libmkl_solver_lp64.a libmkl_blacs_openmpi_ilp64.a libmkl_intel_sp2dp.a libmkl_solver_lp64_sequential.a libmkl_blacs_openmpi_lp64.a libmkl_intel_sp2dp.so libmkl_vml_avx.so libmkl_blacs_sgimpt_ilp64.a libmkl_intel_thread.a libmkl_vml_def.so libmkl_blacs_sgimpt_lp64.a libmkl_intel_thread.so libmkl_vml_mc2.so libmkl_blas95_ilp64.a libmkl_lapack95_ilp64.a libmkl_vml_mc3.so libmkl_blas95_lp64.a libmkl_lapack95_lp64.a libmkl_vml_mc.so libmkl_cdft_core.a libmkl_mc3.so libmkl_vml_p4n.so libmkl_cdft_core.so libmkl_mc.so locale These are the last lines of the configure: The following libraries have been found: BLAS_LIBS=/opt/espresso-PRACE/phiGEMM/lib/libphigemm.a -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core LAPACK_LIBS= FFT_LIBS= If anyone can help i'd be gratefull Federico.- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120214/b377fe6d/attachment.htm From akohlmey at gmail.com Tue Feb 14 16:25:10 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 14 Feb 2012 10:25:10 -0500 Subject: [Pw_forum] Configure script problem In-Reply-To: References: Message-ID: On Tue, Feb 14, 2012 at 9:59 AM, Federico Vadell wrote: > Dear all, > > I m having trouble with the configure script since it does not seem to find > the mkl libs. Im using espresso-PRACE and intel composer XE 2011 sp1. Ive > tried this line: > > ./configure? --enable-openmp --enable-cuda > LIBDIRS="/opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64/" > --prefix=/opt/espresso-PRACE > > where /opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64 has > > libaux_ia32_gfortran.a????????? libmkl_core.a??????????? libmkl_p4n.so > libaux_ia32_gnu.a?????????????? libmkl_core.so?????????? libmkl_pgi_thread.a > libaux_ia32_intel.a???????????? libmkl_def.so > libmkl_pgi_thread.so > libaux_intel64_gfortran.a?????? libmkl_gf_ilp64.a??????? libmkl_rt.so > libaux_intel64_gnu.a??????????? libmkl_gf_ilp64.so > libmkl_scalapack_ilp64.a > libaux_intel64_intel.a????????? libmkl_gf_lp64.a > libmkl_scalapack_ilp64.so > libmkl_avx.so?????????????????? libmkl_gf_lp64.so > libmkl_scalapack_lp64.a > libmkl_blacs_ilp64.a??????????? libmkl_gnu_thread.a > libmkl_scalapack_lp64.so > libmkl_blacs_intelmpi_ilp64.a?? libmkl_gnu_thread.so???? libmkl_sequential.a > libmkl_blacs_intelmpi_ilp64.so? libmkl_intel_ilp64.a > libmkl_sequential.so > libmkl_blacs_intelmpi_lp64.a??? libmkl_intel_ilp64.so > libmkl_solver_ilp64.a > libmkl_blacs_intelmpi_lp64.so?? libmkl_intel_lp64.a > libmkl_solver_ilp64_sequential.a > libmkl_blacs_lp64.a???????????? libmkl_intel_lp64.so > libmkl_solver_lp64.a > libmkl_blacs_openmpi_ilp64.a??? libmkl_intel_sp2dp.a > libmkl_solver_lp64_sequential.a > libmkl_blacs_openmpi_lp64.a???? libmkl_intel_sp2dp.so??? libmkl_vml_avx.so > libmkl_blacs_sgimpt_ilp64.a???? libmkl_intel_thread.a??? libmkl_vml_def.so > libmkl_blacs_sgimpt_lp64.a????? libmkl_intel_thread.so?? libmkl_vml_mc2.so > libmkl_blas95_ilp64.a?????????? libmkl_lapack95_ilp64.a? libmkl_vml_mc3.so > libmkl_blas95_lp64.a??????????? libmkl_lapack95_lp64.a?? libmkl_vml_mc.so > libmkl_cdft_core.a????????????? libmkl_mc3.so??????????? libmkl_vml_p4n.so > libmkl_cdft_core.so???????????? libmkl_mc.so???????????? locale > > These are the last lines of the configure: > > The following libraries have been found: > ? BLAS_LIBS=/opt/espresso-PRACE/phiGEMM/lib/libphigemm.a > -lmkl_intel_lp64? -lmkl_intel_thread -lmkl_core > ? LAPACK_LIBS= > ? FFT_LIBS= > > If anyone can help i'd be gratefull why do you think there is a problem? it looks to me as if MKL *was* found. axel. > > Federico.- > > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From joshiniharika20 at yahoo.in Tue Feb 14 16:40:45 2012 From: joshiniharika20 at yahoo.in (Niharika Joshi) Date: Tue, 14 Feb 2012 21:10:45 +0530 (IST) Subject: [Pw_forum] k-resolved DOS Message-ID: <1329234045.91827.YahooMailNeo@web95706.mail.in.yahoo.com> Thank you very much for your help. -Niharika Joshi (Project student, Indian Institute of Science Education and Research, Pune, Indian) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120214/d9a7fdb2/attachment.htm From giannozz at democritos.it Tue Feb 14 17:09:32 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 14 Feb 2012 17:09:32 +0100 Subject: [Pw_forum] mixture In-Reply-To: <000601cce81f$4529cfa0$6501a8c0@polpress88ef18> References: <000601cce81f$4529cfa0$6501a8c0@polpress88ef18> Message-ID: <1329235772.21531.8.camel@fe12lx.fisica.uniud.it> On Fri, 2012-02-10 at 19:10 +0100, mateusz dulski wrote: > I would ask if it is possible to calculate different crystal structure > when based on the crystalographical data we get two or more atoms in > one position i.e mixture position? you can use an average pseudo-potential (Virtual Crystal Approximation: see upftools/virtual.f90 ). Or you can set up a supercell. Or you can choose a specific atomic arrangement. What is more appropriate depends upon the system and what you want to calculate P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From federico at clustering.com.ar Tue Feb 14 17:11:59 2012 From: federico at clustering.com.ar (Federico Vadell) Date: Tue, 14 Feb 2012 13:11:59 -0300 Subject: [Pw_forum] Configure script problem In-Reply-To: Message-ID: <1c72c2a245a483c097fe981b3c23fcbc@webmail.clustering.com.ar> Im sorry, i was wrong. The mkl liraries were found, but it did not seem to find the LAPACK and FFTW libs. However I carried on with the compilation, ended without error, the only thing i noticed was the following line in the output of the configure script: checking for library containing dspev... none required I believe dspev is a lapack function, but since it said it was not required I moved on to the examples. I tried example01 in /path/to/espresso/examples/example01 The out put was [root at cuda_1 example01]# ./run_example /opt/espresso-PRACE/examples/example01 : starting This example shows how to use pw.x to calculate the total energy and the band structure of four simple systems: Si, Al, Cu, Ni. executables directory: /opt/espresso-PRACE/bin pseudo directory: /opt/espresso-PRACE/pseudo temporary directory: /root/tmp checking that needed directories and files exist... done running pw.x as: /opt/espresso-PRACE/bin/pw.x running bands.x as: /opt/espresso-PRACE/bin/bands.x cleaning /root/tmp... done running the scf calculation for Si...2 Error condition encountered during test: exit status = 2 Aborting I checked the .out file of the example and found this error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cdiaghg : error # 21 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... Thanks for your answer, Federico.- ----------------mensaje original----------------- De: "Axel Kohlmeyer" akohlmey at gmail.com Para: "Federico Vadell" federico at clustering.com.ar CC: pw_forum at pwscf.org Fecha: Tue, 14 Feb 2012 10:25:10 -0500 ------------------------------------------------- > On Tue, Feb 14, 2012 at 9:59 AM, Federico Vadell > federico at clustering.com.ar wrote: >> Dear all, >> >> I m having trouble with the configure script since it does not seem to find >> the mkl libs. Im using espresso-PRACE and intel composer XE 2011 sp1. Ive >> tried this line: >> >> ./configure? --enable-openmp --enable-cuda >> LIBDIRS="/opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64/" >> --prefix=/opt/espresso-PRACE >> >> where /opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64 has >> >> libaux_ia32_gfortran.a????????? libmkl_core.a??????????? >> libmkl_p4n.so >> libaux_ia32_gnu.a?????????????? libmkl_core.so?????????? >> libmkl_pgi_thread.a >> libaux_ia32_intel.a???????????? libmkl_def.so >> libmkl_pgi_thread.so >> libaux_intel64_gfortran.a?????? libmkl_gf_ilp64.a??????? >> libmkl_rt.so >> libaux_intel64_gnu.a??????????? libmkl_gf_ilp64.so >> libmkl_scalapack_ilp64.a >> libaux_intel64_intel.a????????? libmkl_gf_lp64.a >> libmkl_scalapack_ilp64.so >> libmkl_avx.so?????????????????? libmkl_gf_lp64.so >> libmkl_scalapack_lp64.a >> libmkl_blacs_ilp64.a??????????? libmkl_gnu_thread.a >> libmkl_scalapack_lp64.so >> libmkl_blacs_intelmpi_ilp64.a?? libmkl_gnu_thread.so???? >> libmkl_sequential.a >> libmkl_blacs_intelmpi_ilp64.so? libmkl_intel_ilp64.a >> libmkl_sequential.so >> libmkl_blacs_intelmpi_lp64.a??? libmkl_intel_ilp64.so >> libmkl_solver_ilp64.a >> libmkl_blacs_intelmpi_lp64.so?? libmkl_intel_lp64.a >> libmkl_solver_ilp64_sequential.a >> libmkl_blacs_lp64.a???????????? libmkl_intel_lp64.so >> libmkl_solver_lp64.a >> libmkl_blacs_openmpi_ilp64.a??? libmkl_intel_sp2dp.a >> libmkl_solver_lp64_sequential.a >> libmkl_blacs_openmpi_lp64.a???? libmkl_intel_sp2dp.so??? >> libmkl_vml_avx.so >> libmkl_blacs_sgimpt_ilp64.a???? libmkl_intel_thread.a??? >> libmkl_vml_def.so >> libmkl_blacs_sgimpt_lp64.a????? libmkl_intel_thread.so?? >> libmkl_vml_mc2.so >> libmkl_blas95_ilp64.a?????????? libmkl_lapack95_ilp64.a? >> libmkl_vml_mc3.so >> libmkl_blas95_lp64.a??????????? libmkl_lapack95_lp64.a?? >> libmkl_vml_mc.so >> libmkl_cdft_core.a????????????? libmkl_mc3.so??????????? >> libmkl_vml_p4n.so >> libmkl_cdft_core.so???????????? libmkl_mc.so???????????? locale >> >> These are the last lines of the configure: >> >> The following libraries have been found: >> ? BLAS_LIBS=/opt/espresso-PRACE/phiGEMM/lib/libphigemm.a >> -lmkl_intel_lp64? -lmkl_intel_thread -lmkl_core >> ? LAPACK_LIBS= >> ? FFT_LIBS= >> >> If anyone can help i'd be gratefull > > why do you think there is a problem? > it looks to me as if MKL *was* found. > > axel. > > >> >> Federico.- >> >> >> _______________________________________________ >> 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 > > College of Science and Technology > Temple University, Philadelphia PA, USA. > > From akohlmey at gmail.com Tue Feb 14 19:09:54 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 14 Feb 2012 13:09:54 -0500 Subject: [Pw_forum] Configure script problem In-Reply-To: <1c72c2a245a483c097fe981b3c23fcbc@webmail.clustering.com.ar> References: <1c72c2a245a483c097fe981b3c23fcbc@webmail.clustering.com.ar> Message-ID: On Tue, Feb 14, 2012 at 11:11 AM, Federico Vadell wrote: > ?Im sorry, i was wrong. The mkl liraries were found, but it did not seem to > find the LAPACK and FFTW libs. However I carried on with the compilation, > ended without error, the only thing i noticed was the following line in the > output of the configure script: > > checking for library containing dspev... none required yes, because MKL contains *both* BLAS and LAPACK in one command line. no reason to repeat it, right? > I believe dspev is a lapack function, but since it said it was not required > I moved on to the examples. > I tried example01 in /path/to/espresso/examples/example01 > The out put was > ?[root at cuda_1 example01]# ./run_example arrrrggggghhhh!!!! you are compiling and running a user level application as root??? that is baaaaadd! nobody should do anything as root unless there is no other way. far too easy to mess up a machine and destroy lot of hard work. > /opt/espresso-PRACE/examples/example01 : starting > > This example shows how to use pw.x to calculate the total energy and > the band structure of four simple systems: Si, Al, Cu, Ni. > > ?executables directory: /opt/espresso-PRACE/bin > ?pseudo directory: /opt/espresso-PRACE/pseudo > ?temporary directory: /root/tmp > ?checking that needed directories and files exist... done > > ?running pw.x as: /opt/espresso-PRACE/bin/pw.x > ?running bands.x as: /opt/espresso-PRACE/bin/bands.x > > ?cleaning /root/tmp... done > ?running the scf calculation for Si...2 > Error condition encountered during test: exit status = 2 > Aborting > > I checked the .out file of the example and found this error: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > ?from cdiaghg : error # 21 > ?diagonalization (ZHEGV*) failed > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > ?stopping ... there are selection of possible reasons, miscompiled code due to bad compilers or overoptimization, a problem with the library, memory corruption... i would search the mailing list archive for similar error messages and see what the outcome was. axel. > > Thanks for your answer, > > Federico.- > > ----------------mensaje original----------------- > De: "Axel Kohlmeyer" akohlmey at gmail.com > Para: "Federico Vadell" federico at clustering.com.ar > CC: pw_forum at pwscf.org > Fecha: Tue, 14 Feb 2012 10:25:10 -0500 > ------------------------------------------------- > > >> On Tue, Feb 14, 2012 at 9:59 AM, Federico Vadell >> federico at clustering.com.ar wrote: >>> Dear all, >>> >>> I m having trouble with the configure script since it does not seem to > find >>> the mkl libs. Im using espresso-PRACE and intel composer XE 2011 sp1. Ive >>> tried this line: >>> >>> ./configure? --enable-openmp --enable-cuda >>> LIBDIRS="/opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64/" >>> --prefix=/opt/espresso-PRACE >>> >>> where /opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64 has >>> >>> libaux_ia32_gfortran.a????????? libmkl_core.a >>> libmkl_p4n.so >>> libaux_ia32_gnu.a?????????????? libmkl_core.so >>> libmkl_pgi_thread.a >>> libaux_ia32_intel.a???????????? libmkl_def.so >>> libmkl_pgi_thread.so >>> libaux_intel64_gfortran.a?????? libmkl_gf_ilp64.a >>> libmkl_rt.so >>> libaux_intel64_gnu.a??????????? libmkl_gf_ilp64.so >>> libmkl_scalapack_ilp64.a >>> libaux_intel64_intel.a????????? libmkl_gf_lp64.a >>> libmkl_scalapack_ilp64.so >>> libmkl_avx.so?????????????????? libmkl_gf_lp64.so >>> libmkl_scalapack_lp64.a >>> libmkl_blacs_ilp64.a??????????? libmkl_gnu_thread.a >>> libmkl_scalapack_lp64.so >>> libmkl_blacs_intelmpi_ilp64.a?? libmkl_gnu_thread.so >>> libmkl_sequential.a >>> libmkl_blacs_intelmpi_ilp64.so? libmkl_intel_ilp64.a >>> libmkl_sequential.so >>> libmkl_blacs_intelmpi_lp64.a??? libmkl_intel_ilp64.so >>> libmkl_solver_ilp64.a >>> libmkl_blacs_intelmpi_lp64.so?? libmkl_intel_lp64.a >>> libmkl_solver_ilp64_sequential.a >>> libmkl_blacs_lp64.a???????????? libmkl_intel_lp64.so >>> libmkl_solver_lp64.a >>> libmkl_blacs_openmpi_ilp64.a??? libmkl_intel_sp2dp.a >>> libmkl_solver_lp64_sequential.a >>> libmkl_blacs_openmpi_lp64.a???? libmkl_intel_sp2dp.so >>> libmkl_vml_avx.so >>> libmkl_blacs_sgimpt_ilp64.a???? libmkl_intel_thread.a >>> libmkl_vml_def.so >>> libmkl_blacs_sgimpt_lp64.a????? libmkl_intel_thread.so >>> libmkl_vml_mc2.so >>> libmkl_blas95_ilp64.a?????????? libmkl_lapack95_ilp64.a >>> libmkl_vml_mc3.so >>> libmkl_blas95_lp64.a??????????? libmkl_lapack95_lp64.a >>> libmkl_vml_mc.so >>> libmkl_cdft_core.a????????????? libmkl_mc3.so >>> libmkl_vml_p4n.so >>> libmkl_cdft_core.so???????????? libmkl_mc.so???????????? locale >>> >>> These are the last lines of the configure: >>> >>> The following libraries have been found: >>> ? BLAS_LIBS=/opt/espresso-PRACE/phiGEMM/lib/libphigemm.a >>> -lmkl_intel_lp64? -lmkl_intel_thread -lmkl_core >>> ? LAPACK_LIBS= >>> ? FFT_LIBS= >>> >>> If anyone can help i'd be gratefull >> >> why do you think there is a problem? >> it looks to me as if MKL *was* found. >> >> axel. >> >> >>> >>> Federico.- >>> >>> >>> _______________________________________________ >>> 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 >> >> College of Science and Technology >> Temple University, Philadelphia PA, USA. >> >> > > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From glawe at mpi-halle.mpg.de Tue Feb 14 18:29:41 2012 From: glawe at mpi-halle.mpg.de (Henning Glawe) Date: Tue, 14 Feb 2012 18:29:41 +0100 Subject: [Pw_forum] Bug in fhi2upf.x? Message-ID: <20120214172941.GE8885@ford.simpsons.bogus> Moin, I converted some FHI LDA pseudopotentials to UPF using fhi2upf.x. The results from pw.x were quite strange when using these UPFs, so I dug a bit into the code. The FHI LDA pseudopotentials use the Perdew-Wang 92 LDA XC functional (which, as far as I remember, is the density XC part of the PW91 GGA functional). fhi2upf.x has a hard-coded special case for this, and writes 'PW' in the resulting UPF files. pw.x interprets this as pw density correlation, without any density exchange, which leads to the strange results I observed. Adding slater exchange to the UPF file solves this issue, so the fhi2upf code should actually write 'SLA PW', not just 'PW' as functional into the UPF. Related to this, there seems to be some inconsistencies in espresso-4.3.2/Modules/funct.f90: 1) Comment about PW91 GGA functional short form (line 85): ! "pw91" = "pw +ggx+ggc" = PW91 (aka GGA) 2) Transformation of PW91 short form to individual fields (line 419): ! special case : PW91 = GGX + GGC else if ('PW91'.EQ. TRIM(dftout) ) then call set_dft_value (iexch,1) !Default HG: slater exchange call set_dft_value (icorr,1) !Default HG: Perdew-Zunger correlation call set_dft_value (igcx, 2) call set_dft_value (igcc, 2) call set_dft_value (inlc,0) !Default dft_defined = .true. ! HG: so basically PZ LDA plus gradient corrections 3) Backwards transformation (functional components to short name) (line 901): else if (iexch_==1.and.icorr_==4.and.igcx_==2.and.igcc_==2) then shortname_ = 'PW91' ! HG: now it is slater exchange, but perdew-wang correlation So the main consistency problem is in the documentation (1), which misses the density exchange part of the functional, and which may have caused the bug in fhi2upf.x -- Mit freundlichen Gr??en Henning Glawe Max-Planck-Institut f?r Mikrostrukturphysik Weinberg 2, 06120 Halle (Saale), Germany http://www.mpi-halle.de/~theory Phone: +49-345-5582-613 Fax: +49-345-5511223 Email: glawe at mpi-halle.de From payam.norouzzadeh at gmail.com Tue Feb 14 22:04:20 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Tue, 14 Feb 2012 15:04:20 -0600 Subject: [Pw_forum] Orthorhombic structure of Gallium Message-ID: Hello Q.E users Gallium has an orthorhombic crystal structure but I don't know what number for ibrav is related to it. There are several numbers for orthorhombic structures. Could someone give me a clue to resolve the problem? Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120214/a5a08091/attachment.htm From rcjhawk at gmail.com Wed Feb 15 01:21:54 2012 From: rcjhawk at gmail.com (Michael Mehl) Date: Tue, 14 Feb 2012 19:21:54 -0500 Subject: [Pw_forum] Orthorhombic structure of Gallium In-Reply-To: References: Message-ID: <4F3AFAA2.9000007@gmail.com> It's base-centered orthorhombic, so that would be #9 http://cst-www.nrl.navy.mil/lattice/struk/a11.html Generally "A", "B", or "C" in the space group's International Symbol denotes a base-centered system, be it monoclinic or orthorhombic. On 02/14/2012 04:04 PM, Payam Norouzzadeh wrote: > Hello Q.E users > > Gallium has an orthorhombic crystal structure but I don't know what > number for ibrav is related to it. > There are several numbers for orthorhombic structures. Could someone > give me a clue to resolve the problem? > > Best regards,Payam Norouzzadeh > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Mike Mehl Naval Research Laboratory Washington DC USA From payam.norouzzadeh at gmail.com Wed Feb 15 01:49:43 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Tue, 14 Feb 2012 18:49:43 -0600 Subject: [Pw_forum] Orthorhombic structure of Gallium In-Reply-To: <4F3AFAA2.9000007@gmail.com> References: <4F3AFAA2.9000007@gmail.com> Message-ID: Thank you Prof.Mehl. In the following paper it is said that the structure is faced center (Fig 1): Ab initio calculations of structural and electronic properties of gallium solid-state phases, PHYSICAL REVIEW B VOLUME 52, NUMBER 14 1 OCTOBER 1995-II and that's why I've confused. Best regards,Payam Norouzzadeh On Tue, Feb 14, 2012 at 6:21 PM, Michael Mehl wrote: > It's base-centered orthorhombic, so that would be #9 > > http://cst-www.nrl.navy.mil/**lattice/struk/a11.html > > Generally "A", "B", or "C" in the space group's International Symbol > denotes a base-centered system, be it monoclinic or orthorhombic. > > > On 02/14/2012 04:04 PM, Payam Norouzzadeh wrote: > >> Hello Q.E users >> >> Gallium has an orthorhombic crystal structure but I don't know what >> number for ibrav is related to it. >> There are several numbers for orthorhombic structures. Could someone give >> me a clue to resolve the problem? >> >> Best regards,Payam Norouzzadeh >> >> >> ______________________________**_________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/**mailman/listinfo/pw_forum >> > > > -- > > Mike Mehl > Naval Research Laboratory > Washington DC USA > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120214/008ca2f4/attachment.htm From wxpurw at wm.edu Wed Feb 15 04:36:52 2012 From: wxpurw at wm.edu (Wirawan Purwanto) Date: Tue, 14 Feb 2012 22:36:52 -0500 Subject: [Pw_forum] Issues running PWscf with long path names In-Reply-To: References: Message-ID: (This is a re-send; I thought I already joined this forum before sending.) Hi, I found a trouble while running PWscf with long path names (e.g. wfcdir, or outdir), which I will explain below. I suffered the problem when running PWscf compiled with Intel Fortran (11 or 12, does not matter). I thought first that the problem was in the Intel Fortran itself, but it is not. Cf here: http://software.intel.com/en-us/forums/showthread.php?t=103025 The root cause was the logic used in copying the input content in subroutine open_input_file_x() (file: Modules/open_close_input_file.f90). In official version 4.3.2 this correspond to lines 104-107 (some more lines printed below for context--it's the do while ...enddo block): ! ! copy file ! IF ( ierr == 0 ) THEN lfound=.true. dummy="" do while (TRIM(dummy).ne."MAGICALME") ! LINE 104 read(unit_loc,fmt='(A256)',END=10) dummy ! LINE 105 write(stdtmp,*) trim(dummy) ! LINE 106 enddo ! LINE 107 Two problems I noted here: 1) the write statement with no formatting is troublesome: it adds a white space at the beginning of each line. This manifests in the following symptom. One of my &CONTROL fields contain this line: outdir = '/mnt/lustre/wirawan0/BIGFILES.runtime/.qe-HACK-MnO/AFM2/rh.1x1x1/qe/Opium-GFRG/vol12.98' , and PWscf, running this input, complains not being able to create subdir: '/mnt/lustre/wirawan0/BIGFILES.runtime/.qe-HACK-MnO/AFM2/rh.1x1x1/qe/O pium-GFRG/vol12.98' (notice stray whitespace between "O" and "pium"). Why is this? Because Intel Fortran library prepends a whitespace at each line of temporary input file (input_tmp.in), and happily truncates the output line to 80 characters per line. Doing so, it continues the output in the next line (with an extra whitespace prepended *again*). Long story short, what you should have used for line 106 in the code above is: write(stdtmp,'(A)') trim(dummy) It would not prepend any whitespace, and it would not truncate the output line every 80 characters. 2) In PWscf, path strings (such as outdir above) have a maximum length of 256 characters. However, format width in line 105 above could prevent all 256 characters to be read properly. To avoid this potential problem, the fmt width above should be greater than 256. '(A512)' would be a safe bet (and set length of `dummy' string to 512 as well). Otherwise there can be unexpected problem with input line truncation. The following suggestions err on safe side: 3) If "-input" parameter argument is used, there is no need for input file copying. Why is it still copied anyway? 4) Also, the name of the temporary file should probably be other than " input_tmp.in". It is better to use randomized filename (e.g. C function tmpnam or mkstemp) or make this file in "wfcdir" rather than current directory. This practice will get rid of possible race conditions or unintended overwriting of user's file by the same name. Thanks, -- Wirawan Purwanto Research Scientist College of William and Mary Physics Department Williamsburg, VA 23187 -- Wirawan Purwanto Research Scientist College of William and Mary Physics Department Williamsburg, VA 23187 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120214/a4ea8f6c/attachment.htm From lmartinsamos at gmail.com Wed Feb 15 08:47:34 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 15 Feb 2012 08:47:34 +0100 Subject: [Pw_forum] Issues running PWscf with long path names In-Reply-To: References: Message-ID: Dear Wiriwan, thank you for your notification and suggestions. I have changed the dim of lines to 512. with -input the input file was already not dumped (in the svn version). best regards Layla 2012/2/15 Wirawan Purwanto > (This is a re-send; I thought I already joined this forum before sending.) > > Hi, > > I found a trouble while running PWscf with long path names (e.g. wfcdir, > or outdir), which I will explain below. I suffered the problem when running > PWscf compiled with Intel Fortran (11 or 12, does not matter). I thought > first that the problem was in the Intel Fortran itself, but it is not. Cf > here: > > http://software.intel.com/en-us/forums/showthread.php?t=103025 > > The root cause was the logic used in copying the input content in > subroutine open_input_file_x() (file: Modules/open_close_input_file.f90). > In official version 4.3.2 this correspond to lines 104-107 (some more lines > printed below for context--it's the do while ...enddo block): > > ! > ! copy file > ! > IF ( ierr == 0 ) THEN > lfound=.true. > dummy="" > do while (TRIM(dummy).ne."MAGICALME") ! LINE 104 > read(unit_loc,fmt='(A256)',END=10) dummy ! LINE 105 > write(stdtmp,*) trim(dummy) ! LINE 106 > enddo ! LINE 107 > > > > Two problems I noted here: > > 1) the write statement with no formatting is troublesome: it adds a white > space at the beginning of each line. This manifests in the following > symptom. One of my &CONTROL fields contain this line: > > outdir = > '/mnt/lustre/wirawan0/BIGFILES.runtime/.qe-HACK-MnO/AFM2/rh.1x1x1/qe/Opium-GFRG/vol12.98' > , > > and PWscf, running this input, complains not being able to create subdir: > > '/mnt/lustre/wirawan0/BIGFILES.runtime/.qe-HACK-MnO/AFM2/rh.1x1x1/qe/O > pium-GFRG/vol12.98' > > (notice stray whitespace between "O" and "pium"). Why is this? Because > Intel Fortran library prepends a whitespace at each line of temporary input > file (input_tmp.in), and happily truncates the output line to 80 > characters per line. Doing so, it continues the output in the next line > (with an extra whitespace prepended *again*). > > Long story short, what you should have used for line 106 in the code above > is: > > write(stdtmp,'(A)') trim(dummy) > > It would not prepend any whitespace, and it would not truncate the output > line every 80 characters. > > > 2) In PWscf, path strings (such as outdir above) have a maximum length of > 256 characters. However, format width in line 105 above could prevent all > 256 characters to be read properly. To avoid this potential problem, the > fmt width above should be greater than 256. '(A512)' would be a safe bet > (and set length of `dummy' string to 512 as well). Otherwise there can be > unexpected problem with input line truncation. > > > The following suggestions err on safe side: > > 3) If "-input" parameter argument is used, there is no need for input file > copying. Why is it still copied anyway? > > 4) Also, the name of the temporary file should probably be other than " > input_tmp.in". It is better to use randomized filename (e.g. C function > tmpnam or mkstemp) or make this file in "wfcdir" rather than current > directory. This practice will get rid of possible race conditions or > unintended overwriting of user's file by the same name. > > Thanks, > -- > Wirawan Purwanto > Research Scientist > College of William and Mary > Physics Department > Williamsburg, VA 23187 > > > > > -- > Wirawan Purwanto > Research Scientist > College of William and Mary > Physics Department > Williamsburg, VA 23187 > > _______________________________________________ > 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/20120215/0c94a6a5/attachment-0001.htm From Trinh.Vo at jpl.nasa.gov Wed Feb 15 08:37:12 2012 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Tue, 14 Feb 2012 23:37:12 -0800 Subject: [Pw_forum] How to generatie all kpoints for the case ibrav=0 Message-ID: Dear All, I run a scf calculation for a system, which is base center orthorhombic, (space group #36). In the output file, I obtained a list of kpoits in irreducible BZ. For ibrav > 0, I can use "kpoint.x" to generate the whole kpoint list in the BZ. For the case ibrav=0, is there a way that I can obtain something similar? Thank you very much, Trinh Vo Computing group JPL/CalTech -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120214/52124b04/attachment.htm From giannozz at democritos.it Wed Feb 15 09:33:21 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 15 Feb 2012 09:33:21 +0100 Subject: [Pw_forum] Issues running PWscf with long path names In-Reply-To: References: Message-ID: <1329294801.29057.6.camel@fe12lx.fisica.uniud.it> On Tue, 2012-02-14 at 22:36 -0500, Wirawan Purwanto wrote: > 4) Also, the name of the temporary file should probably be other than "input_tmp.in". > It is better to use randomized filename (e.g. C function tmpnam or mkstemp) or make > this file in "wfcdir" rather than current directory. the latter is not possible because tmpdir and wfcdir are not known before the input is read. For the former, see: http://www.democritos.it/pipermail/pw_forum/2012-February/023220.html The copying of an existing file has been meanwhile removed: see http://qe-forge.org/scm/viewvc.php/trunk/espresso/Modules/open_close_input_file.f90?root=q-e&view=log Thank you for your contribution P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Wed Feb 15 10:27:20 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 15 Feb 2012 10:27:20 +0100 Subject: [Pw_forum] Serious PW91 bug (Was: Bug in fhi2upf.x?) In-Reply-To: <20120214172941.GE8885@ford.simpsons.bogus> References: <20120214172941.GE8885@ford.simpsons.bogus> Message-ID: <1329298040.29057.22.camel@fe12lx.fisica.uniud.it> On Tue, 2012-02-14 at 18:29 +0100, Henning Glawe wrote: > fhi2upf.x has a hard-coded special case for this, and writes 'PW' in the > resulting UPF files. fixed. Ok, this is a problem that occurred only in an exotic case, and was quite easy to spot ... > ! special case : PW91 = GGX + GGC > else if ('PW91'.EQ. TRIM(dftout) ) then > call set_dft_value (iexch,1) !Default HG: slater exchange > call set_dft_value (icorr,1) !Default ... while this is WRONG, affects all PW91 calculations since v.4.3, and may easily go unnoticed. The correct line is call set_dft_value (icorr,4) Thank you for reporting this. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From lmartinsamos at gmail.com Wed Feb 15 10:49:34 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 15 Feb 2012 10:49:34 +0100 Subject: [Pw_forum] How to generatie all kpoints for the case ibrav=0 In-Reply-To: References: Message-ID: Dear Trinh, ibrav=0 mean no sym, or you use the automatic way of defining the kpoint grid K_POINTS automatic nkx nky nkz shiftx shifty shiftz or if you can just write by hand a uniform kpoint grid (Monkhorst-Pack), as following: integer :: ikz, iky, ikx, nk real :: weight real :: shiftx, shifty, shiftz read(*,*) nkx, nky, nkz, shiftx, shifty, shiftz nk=nkx*nky*nkz weight=1.0/real(nk) write(*,*) nk do ikz=1,nkz do iky=1,nky do ikx=1,nkx write(*,"(4f15.9)") (real(ikx)-real(1.0)+shiftx)/real(nkx), (real(iky)-real(1.0)+shifty)/real(nky), & (real(ikz)-real(1.0)+shiftz)/real(nkz), weight enddo enddo enddo the program uses crystal coordinates. So from the output in the pwscf input file you should write K_POINTS crystal ....... bests Layla 2012/2/15 Vo, Trinh (388C) > Dear All, > > I run a scf calculation for a system, which is base center orthorhombic, > (space group #36). In the output file, I obtained a list of kpoits in > irreducible BZ. For ibrav > 0, I can use "kpoint.x" to generate the whole > kpoint list in the BZ. For the case ibrav=0, is there a way that I can > obtain something similar? > > Thank you very much, > > 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/20120215/30aa5b66/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Wed Feb 15 11:23:15 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 15 Feb 2012 11:23:15 +0100 Subject: [Pw_forum] How to generatie all kpoints for the case ibrav=0 In-Reply-To: References: Message-ID: On Wed, 15 Feb 2012 08:37:12 +0100, Vo, Trinh (388C) wrote: > I run a scf calculation for a system, which is base center orthorhombic, > (space group #36). In the output file, I obtained a list of kpoits in > irreducible BZ. For ibrav > 0, I can use "kpoint.x" to generate the > whole kpoint list in the BZ. For the case ibrav=0, is there a way that > I can obtain something similar? You can set-up a "fake" calculation for the system with nosym=.true. and noinv=.true. and run it for just a few seconds until the list of k-points is printed. Then stop the calculation, copy and paste. You may need to set verbosity='high' if the number of k-points is very large. 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 giuseppe.mattioli at ism.cnr.it Wed Feb 15 15:19:32 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Wed, 15 Feb 2012 15:19:32 +0100 Subject: [Pw_forum] constrained MD with cp.x Message-ID: <201202151519.32236.giuseppe.mattioli@ism.cnr.it> Dear all does anybody knows where I can find documentation (richer than INPUT_CP.txt) and/or a tutorial and input examples to perform constrained MD simulations with the cp code? Thanks in advance Giuseppe -- ******************************************************** - 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 payam.norouzzadeh at gmail.com Wed Feb 15 16:17:14 2012 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Wed, 15 Feb 2012 09:17:14 -0600 Subject: [Pw_forum] Orthorhombic structure of Gallium In-Reply-To: <4F3BBEA0.7080705@nrl.navy.mil> References: <4F3AFAA2.9000007@gmail.com> <4F3BBEA0.7080705@nrl.navy.mil> Message-ID: Dear Prof.Mehl It seems that the authors made a mistake. Thank you for your help. Best regards,Payam Norouzzadeh On Wed, Feb 15, 2012 at 8:18 AM, Michael Mehl wrote: > Well, they say it's in space group Cmca, which is a base-centered > orthorhombic structure. A face-centered orthorhombic structure would be > something like Fmmm. If you take a look at the space group tables for Cmca > (#64) and Fmmm (#69), you'll see a the difference right at the top of the > page. > > > On 02/14/2012 07:49 PM, Payam Norouzzadeh wrote: > >> Thank you Prof.Mehl. >> In the following paper it is said that the structure is faced center (Fig >> 1): >> >> Ab initio calculations of structural and electronic properties of gallium >> solid-state phases, PHYSICAL REVIEW B VOLUME 52, NUMBER 14 1 OCTOBER 1995-II >> >> and that's why I've confused. >> Best regards,Payam Norouzzadeh >> >> >> >> >> >> ______________________________**_________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/**mailman/listinfo/pw_forum >> > > > > -- > Michael J. Mehl > Head, Center for Computational Materials Science > Naval Research Laboratory Code 6390 > Washington DC > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120215/ec9b13c0/attachment.htm From xgz at ornl.gov Wed Feb 15 16:30:27 2012 From: xgz at ornl.gov (Xiaoguang Zhang) Date: Wed, 15 Feb 2012 10:30:27 -0500 Subject: [Pw_forum] Jellium calculation? In-Reply-To: <1329294801.29057.6.camel@fe12lx.fisica.uniud.it> References: <1329294801.29057.6.camel@fe12lx.fisica.uniud.it> Message-ID: <4F3BCF93.7030508@ornl.gov> What is the best way to set up a jellium calculation? I need to use a jellium that mimics Al but do not want to do real Al. Thanks, Xiaoguang From shelaa at stanford.edu Wed Feb 15 23:43:48 2012 From: shelaa at stanford.edu (Shela Aboud) Date: Wed, 15 Feb 2012 14:43:48 -0800 (PST) Subject: [Pw_forum] electron-phonon unity mode output In-Reply-To: <1328546391.1076738.1329345506681.JavaMail.root@zm07.stanford.edu> Message-ID: <1537279626.1087034.1329345828734.JavaMail.root@zm07.stanford.edu> After running the electron-phonon calculation there are a series of modes that are printed in the output file. For some of the phonon vectors the pattern of the modes look like the expected displacements but for other modes is gives a series of zeros with a -1 cycled through the different (x,y,z) coordinates. For example for a simulation with a 2 atom basis one of the modes look like the following: Representation 1 1 mode ?A_1 D_1 S_1 ? mode #1 (0.00000 0.00000) (0.00000 0.00000) (-1.00000 0.00000) (0.00000 0.00000) (0.00000 0.00000) (0.00000 0.00000) (0.00000 0.00000) the rest of the 6 modes are identical with the "-1" cycled through each of the real (x,y,z) components of atom 1 and atom 2. Does someone know what this means? I ran across a similar post on the forum but there was no reply. Thanks, Shela From Trinh.Vo at jpl.nasa.gov Thu Feb 16 00:16:34 2012 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Wed, 15 Feb 2012 15:16:34 -0800 Subject: [Pw_forum] How to generatie all kpoints for the case ibrav=0 In-Reply-To: Message-ID: Thank you very much, Layla. Trinh From: Layla Martin-Samos > Date: Wed, 15 Feb 2012 01:49:34 -0800 To: JPL > Cc: PWSCF Forum > Subject: Re: [Pw_forum] How to generatie all kpoints for the case ibrav=0 Dear Trinh, ibrav=0 mean no sym, or you use the automatic way of defining the kpoint grid K_POINTS automatic nkx nky nkz shiftx shifty shiftz or if you can just write by hand a uniform kpoint grid (Monkhorst-Pack), as following: integer :: ikz, iky, ikx, nk real :: weight real :: shiftx, shifty, shiftz read(*,*) nkx, nky, nkz, shiftx, shifty, shiftz nk=nkx*nky*nkz weight=1.0/real(nk) write(*,*) nk do ikz=1,nkz do iky=1,nky do ikx=1,nkx write(*,"(4f15.9)") (real(ikx)-real(1.0)+shiftx)/real(nkx), (real(iky)-real(1.0)+shifty)/real(nky), & (real(ikz)-real(1.0)+shiftz)/real(nkz), weight enddo enddo enddo the program uses crystal coordinates. So from the output in the pwscf input file you should write K_POINTS crystal ....... bests Layla 2012/2/15 Vo, Trinh (388C) > Dear All, I run a scf calculation for a system, which is base center orthorhombic, (space group #36). In the output file, I obtained a list of kpoits in irreducible BZ. For ibrav > 0, I can use "kpoint.x" to generate the whole kpoint list in the BZ. For the case ibrav=0, is there a way that I can obtain something similar? Thank you very much, 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/20120215/973a522b/attachment-0001.htm From Trinh.Vo at jpl.nasa.gov Thu Feb 16 00:17:44 2012 From: Trinh.Vo at jpl.nasa.gov (Vo, Trinh (388C)) Date: Wed, 15 Feb 2012 15:17:44 -0800 Subject: [Pw_forum] How to generatie all kpoints for the case ibrav=0 In-Reply-To: Message-ID: Dear Paulatto, Thank you very much, Best, Trinh On 2/15/12 2:23 AM, "Lorenzo Paulatto" wrote: >On Wed, 15 Feb 2012 08:37:12 +0100, Vo, Trinh (388C) > wrote: >> I run a scf calculation for a system, which is base center >>orthorhombic, >> (space group #36). In the output file, I obtained a list of kpoits >>in >> irreducible BZ. For ibrav > 0, I can use "kpoint.x" to generate the >> whole kpoint list in the BZ. For the case ibrav=0, is there a way that >> >> I can obtain something similar? > > >You can set-up a "fake" calculation for the system with nosym=.true. and >noinv=.true. and run it for just a few seconds until the list of k-points > >is printed. Then stop the calculation, copy and paste. You may need to >set verbosity='high' if the number of k-points is very large. > >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 From tribhuwan.physics at gmail.com Thu Feb 16 07:08:16 2012 From: tribhuwan.physics at gmail.com (Tribhuwan Pandey) Date: Thu, 16 Feb 2012 11:38:16 +0530 Subject: [Pw_forum] Scf calculation help Message-ID: Hi all , I am doing scf calculation for silicon on 2*2*2 supercell,but pw.x code showing me following error %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from check_atoms : error # 1 atoms # 1 and # 4 overlap! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Am generating supercell in crystal maker.I have tried different combination of supercell but each time i am getting the same error. for the error quoted above my atomic position are as follows ATOMIC_POSITIONS Si 0.000000 0.000000 0.000000 Si 0.500000 0.000000 0.000000 Si 0.000000 0.500000 0.000000 Si 0.500000 0.500000 0.000000 Si 0.000000 0.000000 0.500000 Si 0.500000 0.000000 0.500000 Si 0.000000 0.500000 0.500000 Si 0.500000 0.500000 0.500000 Si 0.125000 0.125000 0.125000 Si 0.625000 0.125000 0.125000 Si 0.125000 0.625000 0.125000 Si 0.625000 0.625000 0.125000 Si 0.125000 0.125000 0.625000 Si 0.625000 0.125000 0.625000 Si 0.125000 0.625000 0.625000 Si 0.625000 0.625000 0.625000 K_POINTS {automatic} 4 4 4 0 0 0 I am newbie to quantum espresso .i have no idea how to fix it . Can any one help me in this regard. thanking you Warm Regards Tribhuwan pandey IISc Bangalore * * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120216/14e4351f/attachment.htm From xrhino at gmail.com Thu Feb 16 07:33:48 2012 From: xrhino at gmail.com (YY) Date: Thu, 16 Feb 2012 01:33:48 -0500 Subject: [Pw_forum] TAGS for simulate annealing Message-ID: Dear all, I am trying to simulate the annealing process using pw.x. I set ion_temperature, tempw, delta_t, nraise in the IONS namelist. As my understanding, temperature at the N-step should be T(N) = tempw - delta_t * N / nraise. But after a short test, I find Ekin + Etot is a constant. The temperature fluctuated, and will never go to zero. I want to know are there any other tags I can use to simulate the annealing process. At the end, I attached my input file. Thanks for your help, Yuyang A postdoc at Rensselaer Polytechnic Institute, Troy, NY, USA INPUT FILE &control calculation='md' restart_mode='from_scratch' pseudo_dir = './' outdir='./tmp' prefix='mdtest' wf_collect=.true. nstep=1250 / &system ibrav= 0, celldm(1)=1.8897197 nat= 63, ntyp= 4 ecutwfc =25, ecutrho=150 occupations='smearing', smearing='gaussian', degauss=0.0072 / &electrons / &ions ion_temperature = 'reduce-T' tempw = 500 delta_t = 2 nraise = 5 / CELL_PARAMETERS cubic 10.8441000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 10.2440000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 20.0000000000000000 ... K_POINTS {gamma} From pandey.bramha at gmail.com Thu Feb 16 08:16:30 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Wed, 15 Feb 2012 23:16:30 -0800 Subject: [Pw_forum] Scf calculation help In-Reply-To: References: Message-ID: On Wed, Feb 15, 2012 at 10:08 PM, Tribhuwan Pandey < tribhuwan.physics at gmail.com> wrote: > Hi all , > > I am doing scf calculation for silicon on 2*2*2 supercell,but > pw.x code showing me following error > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 0 > from check_atoms : error # 1 > atoms # 1 and # 4 overlap! > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Am generating supercell in crystal maker. Plz Can i know how you are make it by crystal maker? > I have tried different combination of supercell but each time i am getting > the same error. > for the error quoted above my atomic position are as follows > > ATOMIC_POSITIONS > Si 0.000000 0.000000 0.000000 > Si 0.500000 0.000000 0.000000 > Si 0.000000 0.500000 0.000000 > Si 0.500000 0.500000 0.000000 > Si 0.000000 0.000000 0.500000 > Si 0.500000 0.000000 0.500000 > Si 0.000000 0.500000 0.500000 > Si 0.500000 0.500000 0.500000 > Si 0.125000 0.125000 0.125000 > Si 0.625000 0.125000 0.125000 > Si 0.125000 0.625000 0.125000 > Si 0.625000 0.625000 0.125000 > Si 0.125000 0.125000 0.625000 > Si 0.625000 0.125000 0.625000 > Si 0.125000 0.625000 0.625000 > Si 0.625000 0.625000 0.625000 > K_POINTS {automatic} > 4 4 4 0 0 0 > > > I am newbie to quantum espresso .i have no idea how to fix it . > You can try it with ibrav=0, by the same atomic coordinates. > Can any one help me in this regard. > > thanking you > > > Warm Regards > Tribhuwan pandey > > IISc Bangalore > > * > > * > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120215/7f470d83/attachment.htm From moronaphtaly84 at gmail.com Thu Feb 16 10:10:09 2012 From: moronaphtaly84 at gmail.com (naphtaly moro) Date: Thu, 16 Feb 2012 11:10:09 +0200 Subject: [Pw_forum] Scf calculation help Message-ID: Dear Pandey, A good place to start is for example a unitcell of 8 atom with ibrav=1. ATOMIC_POSITIONS Si 0.000 0.000 0.000 Si 0.500 0.500 0.000 Si 0.500 0.000 0.500 Si 0.000 0.500 0.500 Si 0.250 0.250 0.250 Si 0.750 0.750 0.250 Si 0.750 0.250 0.750 Si 0.250 0.750 0.750 The you can either use pen and paper to expand it to 2x2x2 supercell or if you dont want to do that, you can just used other softwares like VESTA or GDIS to make your self. I have never come acorss the same errors as you have when doing calculations on the Si. To use GDIS you need to save the sttructure in Fractional coordinates. Kind Regards ============================================== OUMA, Cecil Naphtaly Moro PhD. Student Physics Department, University of Pretoria, South Africa Private bag X20 Hatfield Pretoria 0028 Office 5-61, NW-1 Building Cell: +27 721385182 ============================================== "Clouds are not spheres, mountains are not cones, coastlines are not circles,and bark is not smooth, nor does lightning travel in a straight line." - Benoit Mandelbrot * The more progress physical sciences make, the more they tend to enter the domain of mathematics, which is a kind of centre to which they all converge. We may even judge the degree of perfection to which a science has arrived by the facility with which it may be submitted to calculation. Quoted in E Mailly, **Eulogy on Quetelet 1874 * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120216/caf527d8/attachment.htm From Alexandre.Lebon at univ-brest.fr Thu Feb 16 10:01:11 2012 From: Alexandre.Lebon at univ-brest.fr (Alexandre Lebon) Date: Thu, 16 Feb 2012 10:01:11 +0100 Subject: [Pw_forum] reading data with q2r.x Message-ID: <20120216100111.20725gse9uzwd1p3@webmailperso.univ-brest.fr> Dear all, I am trying to construct the phonon dispersion of a fcc material using px.x and ph.x and finnaly q2r.x and matdyn.x I get an output in .xml format au.dyn4.xml. This is unfortunately not readable for q2r.x. I guess the problem is at the level of ph.x How can I avoid to produce .xml output from ph.x? This is actually not documented in the INPUT_PH.html page. Thanks in advance for any hints Alexandre -- Alexandre Lebon, Ma?tre de Conf?rences 28 ?me section CNU tel: (00 33) 02 98 01 64 84 fax: (00 33) 02 98 01 64 39 Laboratoire de Magn?tisme de Bretagne, EA 4522, CNRS 6, avenue Le Gorgeu B?timent G 125 29285 Brest Cedex From Lorenzo.Paulatto at impmc.upmc.fr Thu Feb 16 11:06:00 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 16 Feb 2012 11:06:00 +0100 Subject: [Pw_forum] reading data with q2r.x In-Reply-To: <20120216100111.20725gse9uzwd1p3@webmailperso.univ-brest.fr> References: <20120216100111.20725gse9uzwd1p3@webmailperso.univ-brest.fr> Message-ID: On Thu, 16 Feb 2012 10:01:11 +0100, Alexandre Lebon wrote: > How can I avoid to produce .xml output from ph.x? This is > actually not documented in the INPUT_PH.html page. Dear Alexandre, in principle, the file is written in XML format only if fildyn ends with ".xml", or if you are doing a non-collinear calculation. If you are not in one of these case, please report the exact version of the code you are using, so we can check if there is a bug. 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 Alexandre.Lebon at univ-brest.fr Thu Feb 16 11:18:13 2012 From: Alexandre.Lebon at univ-brest.fr (Alexandre Lebon) Date: Thu, 16 Feb 2012 11:18:13 +0100 Subject: [Pw_forum] reading data with q2r.x In-Reply-To: References: <20120216100111.20725gse9uzwd1p3@webmailperso.univ-brest.fr> Message-ID: <20120216111813.15601jaa62vs2w9x@webmailperso.univ-brest.fr> Dear Lorenzo I am using a spin orbit calculation without magnetic moment. The version of QE is 4.3.1 Thanks for your early answer Alexandre Lorenzo Paulatto a ?crit?: > On Thu, 16 Feb 2012 10:01:11 +0100, Alexandre Lebon > wrote: >> How can I avoid to produce .xml output from ph.x? This is >> actually not documented in the INPUT_PH.html page. > > > Dear Alexandre, > in principle, the file is written in XML format only if fildyn ends with > ".xml", or if you are doing a non-collinear calculation. If you are not in > one of these case, please report the exact version of the code you are > using, so we can check if there is a bug. > > 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 > -- Alexandre Lebon, Ma?tre de Conf?rences 28 ?me section CNU tel: (00 33) 02 98 01 64 84 fax: (00 33) 02 98 01 64 39 Laboratoire de Magn?tisme de Bretagne, EA 4522, CNRS 6, avenue Le Gorgeu B?timent G 125 29285 Brest Cedex From faccin.giovani at gmail.com Thu Feb 16 12:30:41 2012 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Thu, 16 Feb 2012 07:30:41 -0400 Subject: [Pw_forum] Scf calculation help In-Reply-To: References: Message-ID: Bramha, When asking on the forum, please always send your complete input file. Makes it easier to find what's wrong. My guess is that you wanted the coordinates in crystal units instead of alat units.You can fix it by using ATOMIC_POSITIONS crystal in the input file. Check if it works. Regards Giovani Faccin UFMS / Brazil 2012/2/16 bramha pandey > > > On Wed, Feb 15, 2012 at 10:08 PM, Tribhuwan Pandey < > tribhuwan.physics at gmail.com> wrote: > >> Hi all , >> >> I am doing scf calculation for silicon on 2*2*2 supercell,but >> pw.x code showing me following error >> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> task # 0 >> from check_atoms : error # 1 >> atoms # 1 and # 4 overlap! >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> Am generating supercell in crystal maker. > > Plz Can i know how you are make it by crystal maker? > >> I have tried different combination of supercell but each time i am >> getting the same error. >> for the error quoted above my atomic position are as follows >> >> ATOMIC_POSITIONS >> Si 0.000000 0.000000 0.000000 >> Si 0.500000 0.000000 0.000000 >> Si 0.000000 0.500000 0.000000 >> Si 0.500000 0.500000 0.000000 >> Si 0.000000 0.000000 0.500000 >> Si 0.500000 0.000000 0.500000 >> Si 0.000000 0.500000 0.500000 >> Si 0.500000 0.500000 0.500000 >> Si 0.125000 0.125000 0.125000 >> Si 0.625000 0.125000 0.125000 >> Si 0.125000 0.625000 0.125000 >> Si 0.625000 0.625000 0.125000 >> Si 0.125000 0.125000 0.625000 >> Si 0.625000 0.125000 0.625000 >> Si 0.125000 0.625000 0.625000 >> Si 0.625000 0.625000 0.625000 >> K_POINTS {automatic} >> 4 4 4 0 0 0 >> >> >> I am newbie to quantum espresso .i have no idea how to fix it . >> > You can try it with ibrav=0, by the same atomic coordinates. > >> Can any one help me in this regard. >> >> thanking you >> >> >> Warm Regards >> Tribhuwan pandey >> >> IISc Bangalore >> >> * >> >> * >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Thanks and Regards > Bramha Prasad Pandey > GLA University, Mathura. > 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/20120216/7e5dab5e/attachment.htm From giannozz at democritos.it Thu Feb 16 21:43:51 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 16 Feb 2012 21:43:51 +0100 Subject: [Pw_forum] TAGS for simulate annealing In-Reply-To: References: Message-ID: <39B25FBE-A8CE-43A7-971C-3C523C3FA5A8@democritos.it> On Feb 16, 2012, at 7:33 , YY wrote: > ion_temperature = 'reduce-T' > delta_t = 2 you need delta_t < 0 to reduce the temperature; delta_t > 0 ]has no effect. Not sure this is the smartest choice but it is how it works now 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 Feb 16 21:52:21 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 16 Feb 2012 21:52:21 +0100 Subject: [Pw_forum] electron-phonon unity mode output In-Reply-To: <1537279626.1087034.1329345828734.JavaMail.root@zm07.stanford.edu> References: <1537279626.1087034.1329345828734.JavaMail.root@zm07.stanford.edu> Message-ID: <9CB04E3C-899A-4709-8B9D-EF42977CCD9A@democritos.it> On Feb 15, 2012, at 23:43 , Shela Aboud wrote: > Representation 1 1 mode ?A_1 D_1 S_1 > ? > mode #1 > (0.00000 0.00000) > (0.00000 0.00000) > (-1.00000 0.00000) > (0.00000 0.00000) > (0.00000 0.00000) > (0.00000 0.00000) > (0.00000 0.00000) > > the rest of the 6 modes are identical with the "-1" cycled through > each of the real (x,y,z) components of atom 1 and atom 2. Does > someone know what this means? it means that the 6 irreps used in the calculation are displacement patterns in which only one of the following components is nonzero: - atom 1 along x - atom 1 along y - atom 1 along z - atom 2 along x - atom 2 along y - atom 2 along z The code calculates the linear response to each of the above-mentioned displacements. 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 elie.moujaes at hotmail.co.uk Thu Feb 16 22:59:29 2012 From: elie.moujaes at hotmail.co.uk (Elie M) Date: Thu, 16 Feb 2012 21:59:29 +0000 Subject: [Pw_forum] Hellmann Feynmann forces in QE Message-ID: Hello all, Just a quick question. Is there a way , when doing phonon calculations in QE, to just extract the Hellmann Feynamnn forces exerted on the atoms without going the whole way and compute the phonon frequencies? Thanks Elie MUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120216/f896b6f5/attachment-0001.htm From Lorenzo.Paulatto at impmc.upmc.fr Thu Feb 16 23:01:09 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 16 Feb 2012 23:01:09 +0100 Subject: [Pw_forum] Hellmann Feynmann forces in QE In-Reply-To: References: Message-ID: The Hellmann-Feynman (not sure on the number of n's) forces are printed after the pw.x calculation is tprnfor is set to true On Thu, 16 Feb 2012 22:59:29 +0100, Elie M wrote: > > Hello all, > Just a quick question. Is there a way , when doing phonon calculations > in QE, to just extract the Hellmann Feynamnn forces exerted on the atoms > without going the whole way and compute the phonon frequencies? > Thanks > Elie MUniversity of NottinghamNG7 2RDUK -- 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 xrhino at gmail.com Fri Feb 17 02:31:07 2012 From: xrhino at gmail.com (YY) Date: Thu, 16 Feb 2012 20:31:07 -0500 Subject: [Pw_forum] TAGS for simulate annealing In-Reply-To: <39B25FBE-A8CE-43A7-971C-3C523C3FA5A8@democritos.it> References: <39B25FBE-A8CE-43A7-971C-3C523C3FA5A8@democritos.it> Message-ID: Hi Paolo, Thanks for the reply. While, I try to set delta_t a negative number, and run a test with the following parameters. But it seems it doesn't work. I also attached the temperatures by grep "temperature" from the output file. The results indicate ( 'reduce-T' tag will reduce ionic temperature every "nraise" steps by the (negative) value "delta_t") as written in the manual. I check what Q-E can do from Q-E website, and the conclusion is Q-E didn't implement the function to simulate annealing. Thanks again, Yuyang, postdoc @ RPI, Troy, NY, USA INPUT FILES: nstep=250 ion_temperature = 'reduce-T', tempw = 50, delta_t = -1, nraise = 5 TEMPERATURE: Starting temperature = 50.00 K temperature is controlled by velocity rescaling (reduce-T) temperature = 50.00000000 K temperature = 54.62581151 K temperature = 58.69926774 K temperature = 63.73372568 K temperature = 67.29505957 K temperature = 68.86058283 K temperature = 67.31648743 K temperature = 65.94146522 K temperature = 67.42743943 K temperature = 69.52499054 K 2012/2/16 Paolo Giannozzi : > > On Feb 16, 2012, at 7:33 , YY wrote: > >> ? ion_temperature = 'reduce-T' >> ? delta_t = 2 > > > you need delta_t < 0 to reduce the temperature; delta_t > 0 > ]has no effect. Not sure this is the smartest choice but it > is how it works now > > 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 samadzare at gmail.com Fri Feb 17 04:01:47 2012 From: samadzare at gmail.com (samad zare) Date: Fri, 17 Feb 2012 06:31:47 +0330 Subject: [Pw_forum] lattice parameter ingap Message-ID: hello i want work with pwscf about ingap nanowire but i can not find lattice parameter ingap where and what i can find this lattice parameter thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120217/b1e4b182/attachment.htm From kalamaillist at gmail.com Fri Feb 17 04:35:04 2012 From: kalamaillist at gmail.com (WF) Date: Fri, 17 Feb 2012 11:35:04 +0800 Subject: [Pw_forum] Unit of pp.x charge Message-ID: <002001cced25$255e6d60$701b4820$@gmail.com> Hello everyone, I used pp.x ( plot_num=1) and avg.x to make a 1D charge plot. And then I hope to compare it with atomic core charge, but cannot find the unit of the charge plot in the manual. What is the unit of the charge plot? Thanks very much. ---------------------------------------------------------------------------- ---------- Wu Feng, College of Chemistry and Molecular Engineering, Peking University ---------------------------------------------------------------------------- ---------- From lfhuang at theory.issp.ac.cn Fri Feb 17 05:30:59 2012 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?TGlhbmcgRmVuZyBIdWFuZw==?=) Date: Fri, 17 Feb 2012 12:30:59 +0800 Subject: [Pw_forum] =?utf-8?q?Hellmann_Feynmann_forces_in_QE?= Message-ID: <20120217043059.27312.qmail@ms.hfcas.ac.cn> > Just a quick question. Is there a way , when doing phonon calculations in QE, to just extract the Hellmann Feynamnn forces exerted on the atoms without going the whole way and compute the phonon frequencies? This is the way the frozen-phonon method (or finite-displacement method) follows. ------ ====================================================================== L.F.Huang ?????, Electronic Structure and Phonon Physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591440(office) Fax: 86-551-5591434 ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120217/661c3fb7/attachment.htm From giannozz at democritos.it Fri Feb 17 08:24:21 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Feb 2012 08:24:21 +0100 Subject: [Pw_forum] TAGS for simulate annealing In-Reply-To: References: <39B25FBE-A8CE-43A7-971C-3C523C3FA5A8@democritos.it> Message-ID: <98A4F954-A5AF-43B4-9628-ACB277FE60AD@democritos.it> On Feb 17, 2012, at 2:31 , YY wrote: > it seems it doesn't work look better and you will notice lines like the following: Thermalization: T ( 544.6K) reduced by -2.000 The temperature is free, not fixed, so it may go up and down, but the overall trend will be down. > I check what Q-E can do from Q-E website, and the conclusion is Q-E > didn't implement the function to simulate annealing. There is also the possibility to rescale the temperature by a fixed factor ('rescale-T' and delta_t < 1). If you do not like how these options work, you can easily modify them: "apply_thermostat" routine in PW/dynamics_module.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 bdslipun at gmail.com Fri Feb 17 09:29:21 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Fri, 17 Feb 2012 13:59:21 +0530 Subject: [Pw_forum] band Message-ID: how to colour the bands in electronic band structure in different high symmetry directions -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120217/a5f0dee7/attachment.htm From dalcorso at sissa.it Fri Feb 17 09:43:37 2012 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Fri, 17 Feb 2012 09:43:37 +0100 Subject: [Pw_forum] reading data with q2r.x In-Reply-To: <20120216100111.20725gse9uzwd1p3@webmailperso.univ-brest.fr> References: <20120216100111.20725gse9uzwd1p3@webmailperso.univ-brest.fr> Message-ID: <1329468217.8308.7.camel@ulisse.cm.sissa.it> On Thu, 2012-02-16 at 10:01 +0100, Alexandre Lebon wrote: > Dear all, > > I am trying to construct the phonon dispersion of a fcc > material using px.x and ph.x and finnaly q2r.x and matdyn.x > I get an output in .xml format au.dyn4.xml. This is unfortunately > not readable for q2r.x. I guess the problem is at the level > of ph.x > q2r.x can read .xml files. You just write fildyn='au.dyn.xml' in the input of q2r.x. It seems to work on my PC. Which is the error message in your case? Andrea > How can I avoid to produce .xml output from ph.x? This is > actually not documented in the INPUT_PH.html page. > > > Thanks in advance for any hints > > Alexandre > -- 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 giannozz at democritos.it Fri Feb 17 09:57:46 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 17 Feb 2012 09:57:46 +0100 Subject: [Pw_forum] Unit of pp.x charge In-Reply-To: <002001cced25$255e6d60$701b4820$@gmail.com> References: <002001cced25$255e6d60$701b4820$@gmail.com> Message-ID: <1329469066.28891.5.camel@fe12lx.fisica.uniud.it> On Fri, 2012-02-17 at 11:35 +0800, WF wrote: > cannot find the unit of the charge plot in the manual. > What is the unit of the charge plot? as stated in the top line of the documentation of input: All quantities whose dimensions are not explicitly specified are in RYDBERG ATOMIC UNITS What may not be completely clear is that the charge is "number" charge, i.e. not multiplied by e; potentials are energies, i.e. multiplied by e. So, charge is in (Bohr radii)^{-3} P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giuseppe.mattioli at ism.cnr.it Fri Feb 17 10:56:38 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 17 Feb 2012 10:56:38 +0100 Subject: [Pw_forum] lattice parameter ingap In-Reply-To: References: Message-ID: <201202171056.39357.giuseppe.mattioli@ism.cnr.it> Dear unknown submitter First of all, please sign always your posts to the mailing list and provide your scientific affiliation. (In,Ga)P is an alloy, its lattice parameter(s) depends on composition and could be (i.e., not always "is") somewhere between the InP and GaP lattice parameters. You may find useful information here http://www.semiconductors.co.uk/ HTH Giuseppe On Friday 17 February 2012 04:01:47 samad zare wrote: > hello > i want work with pwscf about ingap nanowire but i can not find lattice > parameter ingap > where and what i can find this lattice parameter > thanks -- ******************************************************** - 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 kalamaillist at gmail.com Fri Feb 17 13:25:12 2012 From: kalamaillist at gmail.com (WF) Date: Fri, 17 Feb 2012 20:25:12 +0800 Subject: [Pw_forum] Unit of pp.x charge In-Reply-To: <1329469066.28891.5.camel@fe12lx.fisica.uniud.it> References: <002001cced25$255e6d60$701b4820$@gmail.com> <1329469066.28891.5.camel@fe12lx.fisica.uniud.it> Message-ID: <000601cced6f$3507d400$9f177c00$@gmail.com> This is stated in pw.x, cp.x and neb.x help documetations, however pp.x manual doesn't say that so I am not sure whether it is still applicable. And due to I made an error in summation of the charge density and volume, I thought it is not (Bohr)-3. Thanks for your help very much. -----Original Message----- From: Paolo Giannozzi [mailto:giannozz at democritos.it] Sent: 2012?2?17? 16:58 To: WF Cc: PWSCF Forum Subject: Re: [Pw_forum] Unit of pp.x charge On Fri, 2012-02-17 at 11:35 +0800, WF wrote: > cannot find the unit of the charge plot in the manual. > What is the unit of the charge plot? as stated in the top line of the documentation of input: All quantities whose dimensions are not explicitly specified are in RYDBERG ATOMIC UNITS What may not be completely clear is that the charge is "number" charge, i.e. not multiplied by e; potentials are energies, i.e. multiplied by e. So, charge is in (Bohr radii)^{-3} P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From thomas.gruber at physik.tu-freiberg.de Fri Feb 17 18:25:42 2012 From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber) Date: Fri, 17 Feb 2012 18:25:42 +0100 Subject: [Pw_forum] convergence problems in phonon calculations Message-ID: <4F3E8D96.1010706@physik.tu-freiberg.de> Dear all, I am doing some phonon calculations and have some convergence problems in the "Self-consistent Calculation" at some q-points and Representations. I noticed that the "|ddv_scf|^2"-value jumps in the second step to a greater value, like in the scf calculation I have done for this phonon calculation. I minimized the jump in the scf calculation, when I use "mixing_mode='TF' ". Is this option also implemented for ph.x? I also tried decreasing the "alpha_mix"-value, it helps but I hope to get better results with mixing_mode (as it does in an scf test calculation). Do I have other options to decrease the cpu time and number of iterations? (a normal convergence takes 10 iterations and not 30 with alpha_mix 0.3) Thanks for help Thomas Gruber Institute for Theoretical Physics TU Bergakademie Freiberg From baroni at sissa.it Sat Feb 18 05:52:12 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 18 Feb 2012 05:52:12 +0100 Subject: [Pw_forum] Hellmann Feynmann forces in QE In-Reply-To: References: Message-ID: Forces are 1st order derivatives of the energy. Phonon frequencies are 2nd order. Of course, you do not need the latter to compute the former. As others have already said, forces are calculated by pw.x, whereas vibrational frequencies are calculated by ph. x. HTH - SB -- Stefano Baroni, Trieste -- swift message written and sent on the go On 16/feb/2012, at 22:59, Elie M wrote: > Hello all, > > Just a quick question. Is there a way , when doing phonon calculations in QE, to just extract the Hellmann Feynamnn forces exerted on the atoms without going the whole way and compute the phonon frequencies? > > Thanks > > Elie M > University of Nottingham > NG7 2RD > UK > _______________________________________________ > 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/20120218/1a45ecce/attachment.htm From giannozz at democritos.it Sat Feb 18 15:23:29 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 18 Feb 2012 15:23:29 +0100 Subject: [Pw_forum] convergence problems in phonon calculations In-Reply-To: <4F3E8D96.1010706@physik.tu-freiberg.de> References: <4F3E8D96.1010706@physik.tu-freiberg.de> Message-ID: On Feb 17, 2012, at 18:25 , Thomas Gruber wrote: > [...] I use "mixing_mode='TF' ". Is this option also implemented > for ph.x? unfortunately not. The self-consistency in the phonon code uses an unsophistcated Anderson (or Broyden, I don't remember) mixing. The algorithm used in the self-consistent code is more sophisticated and has a much better target to be minimized (an estimate on the error on energy). Porting it to the phonon code requires some serious 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 zafartariq2003 at yahoo.com Sat Feb 18 19:58:20 2012 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Sat, 18 Feb 2012 10:58:20 -0800 (PST) Subject: [Pw_forum] T vs volume calculation Message-ID: <1329591500.75576.YahooMailClassic@web65411.mail.ac4.yahoo.com> Dear Quantum Espresso Users I want to calculate volume at different temperatures. Wolud any body guide me by using which calculation(vc md , vc relax or any other) and parameters I can calculate T-V relation. My goal is to calculate coefficient thermal of linear expansion (Alpha). Best regards Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120218/21b5d665/attachment.htm From bahadira at buffalo.edu Mon Feb 20 05:48:09 2012 From: bahadira at buffalo.edu (bahadir) Date: Sun, 19 Feb 2012 23:48:09 -0500 Subject: [Pw_forum] el-phon calculation lambda convergence Message-ID: <4F41D089.4090304@buffalo.edu> hi i am doing electron phonon calculations and Tc. i slowly increase the k-grid and q-grid as must as i can afford and try to converge lambda. i wonder what is the convergence level for lambda value? what should the difference in lambda values be to consider lambda as converged? typical lambda values for degauss 0.005~0.05 below: 1.16890 0.80866 0.72623 0.69491 0.67781 0.66805 0.66393 0.66451 0.66891 0.67648 should i go further increasing grid or is it converged at 6th value 0.66~ thank you Bahadir Altintas,PhD SUNY Buffalo,NY Dept. of Chemistry From baroni at sissa.it Mon Feb 20 06:41:08 2012 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 20 Feb 2012 06:41:08 +0100 Subject: [Pw_forum] T vs volume calculation In-Reply-To: <1329591500.75576.YahooMailClassic@web65411.mail.ac4.yahoo.com> References: <1329591500.75576.YahooMailClassic@web65411.mail.ac4.yahoo.com> Message-ID: <721138C6-E9E1-40D5-B947-9B3F1142CA35@sissa.it> The best option for you may be the quasi-harmonic approximation. You may want to start from here: http://arxiv.org/abs/1112.4977v1 SB -- Stefano Baroni, Trieste -- swift message written and sent on the go On 18/feb/2012, at 19:58, zafar rasheed wrote: > Dear Quantum Espresso Users > > I want to calculate volume at different temperatures. Wolud any body guide me by using which calculation(vc md , vc relax or any other) and parameters I can calculate T-V relation. My goal is to calculate coefficient thermal of linear expansion (Alpha). > > Best regards > > Muhammad Zafar > PhD Scholar > Department of Physics > The Islamia University of Bahawalpur,Pakistan > _______________________________________________ > 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/20120220/98cb1733/attachment.htm From pandey.bramha at gmail.com Mon Feb 20 13:51:05 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Mon, 20 Feb 2012 18:21:05 +0530 Subject: [Pw_forum] Help regarding Cv value using phdos Message-ID: Dear Developers and Usres of QE. Here i am trying to compare the experimental Cv value to calculated (using phdos by ph.x,q2r.x and matdyn.x) Cv, but i am shocked that i am obtaining very large value of Cv and the sum(dos)=5.9782=3*N=3*2 in my system(AlN with 2 atoms per unit cell in fcc structure ) which is very correct. For calculation of Cv, Cv=3*R*integration( D(w)dw (hbar^2w^2/K^2T^2)*exp(x)/(1-exp(x))^2) or 3*R*integration of f(w).where x=hbar*w/K*T. >>experimental Cv approx Cp at 300K=30.239(J/mol.K) >>therotical Cv at 300K=147.4268(J/mol.K). Sir if i will take one degree of freedom then Cv at 300K=147.4268/3=49.1422 which is also not near about 30.239(J/mol.K). I have also plot the graph between Cv/3R vs T/theta which shows good shape which is in litecture but i got y-axis starting from 0 to 5.9104. So should i calculate the phonon dos for lesser value of q point or what should i do for getting correct result. Any kind of help will be appreciable. -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120220/a7bbe120/attachment.htm From kissi at uni-mainz.de Mon Feb 20 17:21:21 2012 From: kissi at uni-mainz.de (Kiss, Ioan) Date: Mon, 20 Feb 2012 16:21:21 +0000 Subject: [Pw_forum] Soft exit signal has no effect (NSCF jobs will be killed by the queuing system) Message-ID: Dear PWSCF users and developers, I have a question regarding the NSCF calculations with Espresso 4.3.2. Namely, is it possible to stop the NSCF calculation in a controlled fashion during a band structure calculation when the code goes over a list of user defined points in the k-space before generating the spaghetti plot? In the computer-center the maximum runtime is only 24 hours, and during such short runtime the NSCF job will not be finished. Thus, the execution of the code will be killed by the queuing system about 10 minutes after the maximum runtime was expired. Due to this the files generated by PWSCF are most often corrupted and I cannot use them to restart the NSCF calculation. I thought that creating the $prefix.EXIT file in the run directory, or in the directory where the binary is located, or defining the maximum runtime with the max_seconds in the input file should properly stop the execution of the code. However, the code does not stop during NSCF calculations independent on the parallel environment (tested on PBS/OpenMPI, LSF/mvapich, loadleveler/IBM poe) no matter where I create the $prefix.EXIT file or what kind of value I define as the max_seconds variable. For the SCF calculations I have tested the soft exit on the same systems and it worked flawlessly, pw.x did properly exit after writing out all files necessary for restart. Therefore, it would be really helpful if someone could tell me what to do to get a similar behavior in case of NSCF calculations as well. I would like to thank you in advance for any helpful comment or idea. 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 Mon Feb 20 17:55:28 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 20 Feb 2012 17:55:28 +0100 Subject: [Pw_forum] Soft exit signal has no effect (NSCF jobs will be killed by the queuing system) In-Reply-To: References: Message-ID: <1329756928.32013.17.camel@fe12lx.fisica.uniud.it> On Mon, 2012-02-20 at 16:21 +0000, Kiss, Ioan wrote: > Namely, is it possible to stop the NSCF calculation in a controlled fashion > during a band structure calculation when the code goes over a list of user > defined points in the k-space before generating the spaghetti plot? it should work. In non-scf calculations, routine "c_bands_nscf" is executed. It is in PW/c_bands.f90, towards the end. Locate the lines: ! ... check is performed only if not interfering with phonon calc. ! IF ( lbands) THEN #ifdef __PARA ! ... beware: with pools, if the number of k-points on different ! ... pools differs, make sure that all processors are still in ! ... the loop on k-points before checking for stop condition ! nkdum = kunit * ( nkstot / kunit / npool ) ! IF (ik .le. nkdum) THEN IF (check_stop_now()) RETURN ENDIF #else IF ( check_stop_now() ) RETURN #endif ENDIF Function check_stop_now() does what its name promises. So if you are performing a 'band" calculation, it should work. If you are performing a 'nscf' calculation, you may need to comment out the if on "lbands" P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From omictronics at yahoo.com Mon Feb 20 18:51:10 2012 From: omictronics at yahoo.com (michael onyeaju) Date: Mon, 20 Feb 2012 09:51:10 -0800 (PST) Subject: [Pw_forum] LATTICE PARAMETER FOR InAs/GaAs QUANTUM DOT Message-ID: <1329760270.50936.YahooMailNeo@web121203.mail.ne1.yahoo.com> Dear Q.E User I am currently working on strained InAs spherical?quantum dot emberded in GaAs substrate but find it difficult to get the number of atom per unit cell (the lattice parameter), please can some one help me out Onyeaju, Michael Department of Physics, Faculty of Science, University of Port Harcourt Phone:+2348068118468 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120220/0d439393/attachment.htm From flux_ray12 at 163.com Mon Feb 20 19:29:50 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Tue, 21 Feb 2012 02:29:50 +0800 (CST) Subject: [Pw_forum] LATTICE PARAMETER FOR InAs/GaAs QUANTUM DOT In-Reply-To: <1329760270.50936.YahooMailNeo@web121203.mail.ne1.yahoo.com> References: <1329760270.50936.YahooMailNeo@web121203.mail.ne1.yahoo.com> Message-ID: <2eeab0eb.4b9.1359c06df92.Coremail.flux_ray12@163.com> You can find structure information here: http://rruff.geo.arizona.edu/AMS/amcsd.php -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-21 01:51:10,"michael onyeaju" wrote: Dear Q.E User I am currently working on strained InAs spherical quantum dot emberded in GaAs substrate but find it difficult to get the number of atom per unit cell (the lattice parameter), please can some one help me out Onyeaju, Michael Department of Physics, Faculty of Science, University of Port Harcourt Phone:+2348068118468 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120221/d167f530/attachment.htm From moronaphtaly84 at gmail.com Tue Feb 21 10:01:14 2012 From: moronaphtaly84 at gmail.com (naphtaly moro) Date: Tue, 21 Feb 2012 11:01:14 +0200 Subject: [Pw_forum] Defect charge transition levels in semiconductors Message-ID: Dear QE users, I am interested in charge transition levels in defect calculations. I have manged to calculate defect formation energies for neutral and charged states but now I want to calculate the caharge transition levels according to methods proposed by C. G. van de Walle in J. Appl. Phys. *95*, 3851 (2004); http://dx.doi.org/10.1063/1.1682673. I have seen form previous works using HSE that this can be done but since hybrids as implemented in Quantum ESPRESSO cannot do band structure calculations yet I wanted to request for assistance on nhow to get the the band gaps using HSE in Quantum ESPRESSO and also the fermi level. I am also aware that there is way of getting the band gap from the KS energy levels which are the outputs of a pw.x scf calculation. looking at the out put file there is this section k =-0.5000-0.5000-0.2500 ( 6120 PWs) bands (ev): -3.6572 -3.6572 -3.6572 -3.6572 -3.6571 -3.6571 -3.6570 -3.6570 -0.2803 -0.2803 -0.2802 -0.2802 -0.2802 -0.2802 -0.2802 -0.2802 3.6306 3.6306 3.6306 3.6306 3.6306 3.6306 3.6307 3.6307 4.8511 4.8511 4.8512 4.8512 4.8514 4.8514 4.8514 4.8514 8.3219 8.3219 8.3219 8.3219 8.3221 8.3221 8.3221 8.3221 9.6199 9.6199 9.6200 9.6200 9.6200 9.6200 9.6200 9.6200 9.9121 9.9121 9.9121 9.9121 9.9121 9.9121 9.9121 9.9121 13.8132 13.8132 13.8133 13.8133 13.8133 13.8133 13.8133 13.8133 are these the KS energy levels in EPRESSO? Kind Regards ============================================== OUMA, Cecil Naphtaly Moro PhD. Student Physics Department, University of Pretoria, South Africa Private bag X20 Hatfield Pretoria 0028 Office 5-61, NW-1 Building Cell: +27 721385182 ============================================== "Clouds are not spheres, mountains are not cones, coastlines are not circles,and bark is not smooth, nor does lightning travel in a straight line." - Benoit Mandelbrot * The more progress physical sciences make, the more they tend to enter the domain of mathematics, which is a kind of centre to which they all converge. We may even judge the degree of perfection to which a science has arrived by the facility with which it may be submitted to calculation. Quoted in E Mailly, **Eulogy on Quetelet 1874 * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120221/2f3eafa4/attachment.htm From mpayami at aeoi.org.ir Tue Feb 21 09:55:53 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Tue, 21 Feb 2012 12:25:53 +0330 Subject: [Pw_forum] Problem using SGE Message-ID: <02CFCA00E0E347EDA8186230497E4EE0@b> Dear QE users, I am using sge for running a parallel job. My "file.qsub" contains the following lines: -- #!/bin/bash # #$ -cwd #$ -j y #$ -S /bin/bash /opt/openmpi/bin/mpirun /opt/qe/bin/pw.x -npool 2 -ndiag 16 < /home/mahmoud/file.in -- Then I use the orte parallel env and use the command: qsub -V -pe orte 32 file.qsub Everything is ok until the first david diagonalization during which the load on some nodes increases the number of processors (that is, the node has totally 8 cores but the load shows at the crash time to be more than 16) , and then those nodes hangup. Any comment is highly appreciated. Best regards, Mahmoud Payami -------------------------------- Mahmoud Payami Physics Group, AEOI, Tehran-Iran Email: mpayami at aeoi.org.ir Phone: +98 (0) 21 82064393 ---------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120221/60732863/attachment.htm From lmartinsamos at gmail.com Tue Feb 21 10:46:20 2012 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Tue, 21 Feb 2012 10:46:20 +0100 Subject: [Pw_forum] Defect charge transition levels in semiconductors In-Reply-To: References: Message-ID: Dear naphtaly yes the output of pw are the KS levels. best regards Layla 2012/2/21 naphtaly moro > Dear QE users, > I am interested in charge transition levels in defect calculations. I have > manged to calculate defect formation energies for neutral and charged > states but now I want to calculate the caharge transition levels according > to methods proposed by C. G. van de Walle in J. Appl. Phys. *95*, 3851 > (2004); http://dx.doi.org/10.1063/1.1682673. > > > I have seen form previous works using HSE that this can be done but since > hybrids as implemented in Quantum ESPRESSO cannot do band structure > calculations yet I wanted to request for assistance on nhow to get the the > band gaps using HSE in Quantum ESPRESSO and also the fermi level. > > I am also aware that there is way of getting the band gap from the KS > energy levels which are the outputs of a pw.x scf calculation. looking at > the out put file there is this section > > k =-0.5000-0.5000-0.2500 ( 6120 PWs) bands (ev): > > -3.6572 -3.6572 -3.6572 -3.6572 -3.6571 -3.6571 -3.6570 -3.6570 > -0.2803 -0.2803 -0.2802 -0.2802 -0.2802 -0.2802 -0.2802 -0.2802 > 3.6306 3.6306 3.6306 3.6306 3.6306 3.6306 3.6307 3.6307 > 4.8511 4.8511 4.8512 4.8512 4.8514 4.8514 4.8514 4.8514 > 8.3219 8.3219 8.3219 8.3219 8.3221 8.3221 8.3221 8.3221 > 9.6199 9.6199 9.6200 9.6200 9.6200 9.6200 9.6200 9.6200 > 9.9121 9.9121 9.9121 9.9121 9.9121 9.9121 9.9121 9.9121 > 13.8132 13.8132 13.8133 13.8133 13.8133 13.8133 13.8133 13.8133 > > are these the KS energy levels in EPRESSO? > > Kind Regards > ============================================== > OUMA, Cecil Naphtaly Moro > PhD. Student > Physics Department, University of Pretoria, South Africa > Private bag X20 > Hatfield > Pretoria > 0028 > Office 5-61, NW-1 Building > Cell: +27 721385182 > ============================================== > "Clouds are not spheres, mountains are not cones, coastlines are not > circles,and bark is not smooth, nor does lightning travel in a straight > line." - Benoit Mandelbrot * > > The more progress physical sciences make, the more they tend to enter the > domain of mathematics, which is a kind of centre to which they all > converge. We may even judge the degree of perfection to which a science has > arrived by the facility with which it may be submitted to calculation. > Quoted in E Mailly, **Eulogy on Quetelet 1874 * > > > _______________________________________________ > 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/20120221/4aea40f9/attachment.htm From yunpengwang at live.com Tue Feb 21 14:46:20 2012 From: yunpengwang at live.com (Yunpeng Wang) Date: Tue, 21 Feb 2012 08:46:20 -0500 Subject: [Pw_forum] about PWCOND In-Reply-To: References: , Message-ID: PWscf authors and users: I want to find answers to the following questions about PWCOND because I am new PWCOND user. 1. Does nonequilibrium Greens function employed in PWCOND? Or, the effective potential in scattering region is self-consistently obtained or from the effective potential from scattering region SCF calculation? In my opinion, effective potential is not self-consistently obtained.2. Is PWCOND applicable to finite-voltage case? In my opinion, it can not. best wishes,Yun-Peng -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120221/78903850/attachment.htm From akohlmey at gmail.com Tue Feb 21 15:59:57 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 21 Feb 2012 09:59:57 -0500 Subject: [Pw_forum] Problem using SGE In-Reply-To: <02CFCA00E0E347EDA8186230497E4EE0@b> References: <02CFCA00E0E347EDA8186230497E4EE0@b> Message-ID: On Tue, Feb 21, 2012 at 3:55 AM, Mahmoud Payami wrote: > Dear QE users, > > I am using sge for running a parallel job. > My "file.qsub" contains the following lines: > -- > #!/bin/bash > # > #$ -cwd > #$ -j y > #$ -S /bin/bash > /opt/openmpi/bin/mpirun /opt/qe/bin/pw.x -npool 2 -ndiag 16 < > /home/mahmoud/file.in > -- > Then I use the orte parallel env and use the command: > qsub -V -pe orte 32 file.qsub > Everything is ok until the first david diagonalization during which the load > on some nodes increases the number of processors (that is,?the node has > totally 8 cores but the load shows at the crash time to be more than 16)?, > and then those nodes hangup. are you sure you're not simply running out of memory and driving the machines to swap until they give up? axel. > Any comment is highly appreciated. > > Best regards, > ????????????????????? Mahmoud Payami > > -------------------------------- > Mahmoud Payami > Physics Group, AEOI, > Tehran-Iran > > Email: mpayami at aeoi.org.ir > Phone: +98 (0) 21 82064393 > ---------------------------------------------- > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From mpayami at aeoi.org.ir Tue Feb 21 16:42:06 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Tue, 21 Feb 2012 19:12:06 +0330 Subject: [Pw_forum] Problem using SGE References: <02CFCA00E0E347EDA8186230497E4EE0@b> Message-ID: Dear Axel, I am happy to hear from you. It is most probable to be so because when I used the "top" command on each of the involved nodes, the memory usage was different for them. How can I use these distributed memories such that the loads are more or less equal? Should I use the fill_up style in sge as round-robin? Bests, mahmoud are you sure you're not simply running out of memory and driving the machines to swap until they give up? axel. > Any comment is highly appreciated. > > Best regards, > Mahmoud Payami > > -------------------------------- > Mahmoud Payami > Physics Group, AEOI, > Tehran-Iran > > Email: mpayami at aeoi.org.ir > Phone: +98 (0) 21 82064393 > ---------------------------------------------- > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From avallabh at purdue.edu Tue Feb 21 18:05:15 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Tue, 21 Feb 2012 12:05:15 -0500 (EST) Subject: [Pw_forum] units of psi in e-ph coupling matrix element Message-ID: <941744808.474811.1329843915516.JavaMail.root@mailhub016.itcs.purdue.edu> Dear users and developers, The e-ph coupling matrix element (g) has the units of 'energy (eV or Ry)' in the literature. But from the expression for calculating the e-ph coupling matrix element, i obtained the unit of 'energy per unit volume' for g assuming the term psi has the unit of 1/sqrt(volume). (since psi^2 ~ probability density from quantum mechanics). I am confused about this. Do i have to multiply it with volume or is psi assumed to be dimensionless? Can someone please correct me where i was wrong? Thanks Ajit From asmogunov at gmail.com Wed Feb 22 14:45:50 2012 From: asmogunov at gmail.com (Alex Smogunov) Date: Wed, 22 Feb 2012 14:45:50 +0100 Subject: [Pw_forum] about PWCOND In-Reply-To: References: Message-ID: Dear Yun-Peng. Le 21 f?vrier 2012 14:46, Yunpeng Wang a ?crit : > PWscf authors and users: > > I want to find answers to the following questions about PWCOND because I > am new PWCOND user. > > 1. Does nonequilibrium Greens function employed in PWCOND? > PWCOND does not use NEGFs it calculates directly the scattering states in real space. > Or, the effective potential in scattering region is self-consistently > obtained or from > the effective potential from scattering region SCF calculation? > It should be run after PW calculations, so it uses the SCF potential of the leads and the scattering region at equilibrium. It is therefore zero bias approach, no finite voltage is implemented yet. best regards, Alexander > In my opinion, effective potential is not self-consistently obtained. > 2. Is PWCOND applicable to finite-voltage case? In my opinion, it can not. > > best wishes, > Yun-Peng > > _______________________________________________ > 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/20120222/bfbe7fa8/attachment.htm From stepanko at gmail.com Wed Feb 22 23:27:16 2012 From: stepanko at gmail.com (stepan) Date: Wed, 22 Feb 2012 16:27:16 -0600 Subject: [Pw_forum] short consultation about pseudopotentials Message-ID: <4F456BC4.5050608@gmail.com> Hello. I am writing to ask for short consultation on pseudopotentials usage in Quantum Espresso. I try to simulate Quart-water surfaces using cp.x. The problem is that I have to specify the pseudopotential in UPF format in the configuration script and I am not very familiar with the topic, so I am afraid that I will use pseudopotentials which are not compatible. So, the part of script where I define them in Quantum Espresso reads: ATOMIC_SPECIES O 16.0d0 O.pbe-van_ak.UPF H 1.0079d0 H.pbe-van_ak.UPF Si 28.0855d0 Si.pbe-n-van.UPF The pseudopotentials are given in files: O.pbe-van_ak.UPF, H.pbe-van_ak.UPF and Si.pbe-n-van.UPF. They seems to be Vanderbilt ultrasoft for the PBE functional, but the last one (Si.pbe-n-van.UPF) has nonlinear core correction property. Since all of them are for PBE functional and ultrasoft they seems to be compatible, but I am not sure about the nonlinear core correction of Si.pbe-n-van.UPF. How do you think, can use them together in calculations? Thank you very much. Stepan From iyad.ne at gmail.com Thu Feb 23 01:53:43 2012 From: iyad.ne at gmail.com (IYAD AL-QASIR) Date: Wed, 22 Feb 2012 19:53:43 -0500 Subject: [Pw_forum] short consultation about pseudopotentials In-Reply-To: <4F456BC4.5050608@gmail.com> References: <4F456BC4.5050608@gmail.com> Message-ID: Hello, Study bulk properties for e.g., SiO2, and see how your results are compared to experimental data and other calculations using different pseudopotentials. Kindest Regards, On Wed, Feb 22, 2012 at 5:27 PM, stepan wrote: > Hello. > > I am writing to ask for short consultation on pseudopotentials usage in > Quantum Espresso. I try to simulate Quart-water surfaces using cp.x. > > The problem is that I have to specify the pseudopotential in UPF format > in the configuration script and I am not very familiar with the topic, > so I am afraid that I will use pseudopotentials which are not > compatible. So, the part of script where I define them in Quantum > Espresso reads: > > ATOMIC_SPECIES > O 16.0d0 O.pbe-van_ak.UPF > H 1.0079d0 H.pbe-van_ak.UPF > Si 28.0855d0 Si.pbe-n-van.UPF > > The pseudopotentials are given in files: O.pbe-van_ak.UPF, > H.pbe-van_ak.UPF and Si.pbe-n-van.UPF. They seems to be Vanderbilt > ultrasoft for the PBE functional, but the last one (Si.pbe-n-van.UPF) > has nonlinear core correction property. Since all of them are for PBE > functional and ultrasoft they seems to be compatible, but I am not sure > about the nonlinear core correction of Si.pbe-n-van.UPF. > > How do you think, can use them together in calculations? > > Thank you very much. > > Stepan > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- _______________________________ IYAD I. AL-QASIR, PhD Research Associate Department of Nuclear Engineering North Carolina State University Campus Box 7909 2500 Stinson Dr. Raleigh, NC 27695-7909 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120222/8edbe8ec/attachment.htm From giacsport at libero.it Thu Feb 23 02:26:15 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 23 Feb 2012 02:26:15 +0100 (CET) Subject: [Pw_forum] ZB ZnO vs WZ ZnO at HSE level Message-ID: <33517568.113551329960375822.JavaMail.defaultUser@defaultHost> Dear All, I have a doubt I am not able to fix by myself. I am doing an "scf" spin polarized calculation for both the ZB and the WZ form of ZnO, at HSE level, with the development version of PWscf. For what regard the pseudo of Zn, I am using one with 2e only in the valence (PRB 81, 125207 (2010)). What I notice is that the DeltaE between the two systems is huge (4.4 Ry), with a macroscopic error on the bandgap of ZB-ZnO. Can this only be ascribed to the small number of electrons in the valence? I here report the two input files for both systems. I moreover think that the downsampling of the Fock exchange operator (q) can not be so much influent. But maybe I am wrong Thanks in advance for any hint you may give me. Best, Giacomo--------------------------------- Giacomo Giorgi Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan E-mail: giacomo at tcl.t.u-tokyo.ac.jp 1) WZ-ZnO &SYSTEM ibrav= 4, celldm(1) =6.140475627, celldm(3)=1.6014648858250753985351141749246, nat= 4, ntyp= 2, ecutwfc =80.0, nbnd = 20,force_symmorphic=.true., nspin=2, tot_magnetization=0, input_dft='hse', nqx1 = 2, nqx2 = 2, nqx3 = 1, x_gamma_extrapolation = .TRUE. / &ELECTRONS diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Zn 65.409 Zn_pz-2_nlcc.cpi.UPF O 15.999 O.pz-mt.UPF ATOMIC_POSITIONS (crystal) Zn 0.33333 0.66667 0.00000 Zn 0.66667 0.33333 0.50000 O 0.33333 0.66667 0.38210 O 0.66667 0.33333 0.88210 K_POINTS (automatic) 8 8 6 0 0 0 for this one I get (and it seems a reasonable result, at least from the gap) highest occupied, lowest unoccupied level (ev): 1.4320 5.2338 total energy = -110.48522966 Ry 2) ZB-ZnO &system ibrav= 2, celldm(1) =8.447075169 nat= 8, ntyp= 2, force_symmorphic=.true., nspin=2, tot_magnetization=0, ecutwfc =80., nbnd = 50, input_dft='hse', nqx1=2, nqx2=2, nqx3=2, x_gamma_extrapolation = .TRUE. / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Zn 65.38 Zn_pz-2_nlcc.cpi.UPF O 15.9994 O.pz-mt.UPF ATOMIC_POSITIONS (crystal) Zn 0.00000 0.00000 0.00000 Zn 0.00000 0.50000 0.50000 Zn 0.50000 0.00000 0.50000 Zn 0.50000 0.50000 0.00000 O 0.25000 0.25000 0.25000 O 0.25000 0.75000 0.75000 O 0.75000 0.75000 0.25000 O 0.75000 0.25000 0.75000 K_POINTS automatic 8 8 8 0 0 0 For this one I get (!!) highest occupied, lowest unoccupied level (ev): 36.4937 31.9513 (!!!) total energy = -200.32746186 Ry -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120223/36a26f43/attachment.htm From builiem1987 at gmail.com Thu Feb 23 04:05:34 2012 From: builiem1987 at gmail.com (=?ISO-8859-1?Q?Thanh_Li=EAm_B=F9i?=) Date: Thu, 23 Feb 2012 10:05:34 +0700 Subject: [Pw_forum] How to appear name of special points on the band structure graph? Message-ID: Dear everybody! I calculate scf and bands for TiO2 rutile, and use plotband.x to plot band structute of rutile. However, in the band structure graph, the name of special points as G, X, Z, A, ... disappears. How to appear the name of special points on the band structure graph? Thank you very much! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120223/b9fd03ff/attachment-0001.htm From ptao10b at imr.ac.cn Thu Feb 23 04:06:02 2012 From: ptao10b at imr.ac.cn (=?GBK?B?zNXF9A==?=) Date: Thu, 23 Feb 2012 11:06:02 +0800 (CST) Subject: [Pw_forum] "Inconsistent nr1, nr2, nr3 read" during e-ph coupling calculation Message-ID: Dear all, When I calculate the e-ph coupling constant with matdyn.x, I happen to meet an error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from readfG : error # 1 inconsistent nr1, nr2, nr3 read %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I'v found that it is the mx /=nrx,(x=1,2,3) in the file matdyn.f90. But I still do not know how to do with the problem. My input files: pb.scf.fit.in(scf and a2f with dense grid) &control calculation='scf' restart_mode='from_scratch', prefix='pb', pseudo_dir = './', outdir=./trat/', tstress=.true. / &system ibrav= 2, celldm(1) =9.02, nat= 1, ntyp= 1, ecutwfc =40.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.05, la2F = .true., / &electrons mixing_beta = 0.7 / ATOMIC_SPECIES Pb 207.2 Pb.pz-bhs.UPF ATOMIC_POSITIONS Pb 0.00 0.00 0.00 K_POINTS {automatic} 32 32 32 0 0 0 ------------------------- pb.scf.in(ordinary scf) &control calculation='scf' restart_mode='from_scratch', prefix='pb', pseudo_dir = './', outdir='./trat/' tstress=.true. / &system ibrav= 2, celldm(1) =9.02, nat= 1, ntyp= 1, ecutwfc =40.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.05, / &electrons mixing_beta = 0.7 / ATOMIC_SPECIES Pb 207.2 Pb.pz-bhs.UPF ATOMIC_POSITIONS Pb 0.00 0.00 0.00 K_POINTS {automatic} 16 16 16 0 0 0 ------------------- pb.elph.in(el-ph calculation) &inputph prefix='pb', fildvscf='pbdv', amass(1)=207.2, outdir='./trat/', fildyn='pb.dyn', elph=.true., trans=.true., ldisp=.true. nq1=8, nq2=8, nq3=8 / -- ------------------------------------------------------------------- PH.D. candidate Peng Tao Magnetism and Magnetic Materials Division National Laboratory for Material Science Institute of Metal Research, Chinese Academy of Sciences Phone +86-024-83978751 ------------------------------------------------------------------- From yunpengwang at live.com Thu Feb 23 06:27:39 2012 From: yunpengwang at live.com (Peter Wang) Date: Thu, 23 Feb 2012 13:27:39 +0800 Subject: [Pw_forum] about PWCOND In-Reply-To: References: Message-ID: Dear Alex: Following the pwcond examples in QE-4.3.2, I calculated the complex bands for 1D aluminum wire and I got the band.re and band.im output files. Because k_x,k_y = 0 is given in input file, so the first column in band.re is the real k_z. But for the first column in band.im, I cannot understand what is the meaning. Any clue? best wishes, Yun-Peng From: Alex Smogunov Sent: Wednesday, February 22, 2012 9:45 PM To: Yunpeng Wang Cc: Forum PWSCF ; alexander.smogunov at cea.fr Subject: Re: [Pw_forum] about PWCOND Dear Yun-Peng. Le 21 f?vrier 2012 14:46, Yunpeng Wang a ?crit : PWscf authors and users: I want to find answers to the following questions about PWCOND because I am new PWCOND user. 1. Does nonequilibrium Greens function employed in PWCOND? PWCOND does not use NEGFs it calculates directly the scattering states in real space. Or, the effective potential in scattering region is self-consistently obtained or from the effective potential from scattering region SCF calculation? It should be run after PW calculations, so it uses the SCF potential of the leads and the scattering region at equilibrium. It is therefore zero bias approach, no finite voltage is implemented yet. best regards, Alexander In my opinion, effective potential is not self-consistently obtained. 2. Is PWCOND applicable to finite-voltage case? In my opinion, it can not. best wishes, Yun-Peng _______________________________________________ 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/20120223/4e358cd3/attachment.htm From giannozz at democritos.it Thu Feb 23 08:52:05 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 23 Feb 2012 08:52:05 +0100 Subject: [Pw_forum] short consultation about pseudopotentials In-Reply-To: <4F456BC4.5050608@gmail.com> References: <4F456BC4.5050608@gmail.com> Message-ID: <1329983525.21699.11.camel@fe12lx.fisica.uniud.it> On Wed, 2012-02-22 at 16:27 -0600, stepan wrote: > Since all of them are for PBE functional and ultrasoft > they seems to be compatible, but I am not sure about > the nonlinear core correction of Si.pbe-n-van.UPF. all pseudopotentials and paw sets are "compatible". Some specialized calculations may not be implemented in all cases, though. Also note the following: the CP code uses for nonlinear core corections the same real-space approach as for the augmentation functions. As a consequence the "box grid" (nr1b, nr2b, nr3b) has to be chosen big enough to accommodate all these quantities. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Thu Feb 23 08:54:43 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 23 Feb 2012 08:54:43 +0100 Subject: [Pw_forum] ZB ZnO vs WZ ZnO at HSE level In-Reply-To: <33517568.113551329960375822.JavaMail.defaultUser@defaultHost> References: <33517568.113551329960375822.JavaMail.defaultUser@defaultHost> Message-ID: <1329983683.21699.14.camel@fe12lx.fisica.uniud.it> On Thu, 2012-02-23 at 02:26 +0100, giacsport at libero.it wrote: > For this one I get (!!) > > highest occupied, lowest unoccupied level (ev): 36.4937 31.9513 > (!!!) have you tried with conventional DFT first? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giacsport at libero.it Thu Feb 23 10:02:46 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Thu, 23 Feb 2012 10:02:46 +0100 (CET) Subject: [Pw_forum] R: Re: ZB ZnO vs WZ ZnO at HSE level Message-ID: <32808269.1664761329987766331.JavaMail.defaultUser@defaultHost> Dear Stefano, thanks....it should be this the key.... It is.... Ibrav=1 (SC) fixes the problem. Thanks a lot! G ----Messaggio originale---- Da: degironc at sissa.it Data: 23/02/2012 9.13 A: "giacsport at libero.it" Ogg: Re: [Pw_forum] ZB ZnO vs WZ ZnO at HSE level with ibrav=2 (fcc) the ZB should have 2 atoms in the unit cell... have you tried to visualize your cell with some graphical tool? stefano On 02/23/2012 02:26 AM, giacsport at libero.it wrote: Dear All, I have a doubt I am not able to fix by myself. I am doing an "scf" spin polarized calculation for both the ZB and the WZ form of ZnO, at HSE level, with the development version of PWscf. For what regard the pseudo of Zn, I am using one with 2e only in the valence (PRB 81, 125207 (2010)). What I notice is that the DeltaE between the two systems is huge (4.4 Ry), with a macroscopic error on the bandgap of ZB-ZnO. Can this only be ascribed to the small number of electrons in the valence? I here report the two input files for both systems. I moreover think that the downsampling of the Fock exchange operator (q) can not be so much influent. But maybe I am wrong Thanks in advance for any hint you may give me. Best, Giacomo--------------------------------- Giacomo Giorgi Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan E-mail: giacomo at tcl.t.u-tokyo.ac.jp 1) WZ-ZnO &amp;SYSTEM ibrav= 4, celldm(1) =6.140475627, celldm(3)=1.6014648858250753985351141749246, nat= 4, ntyp= 2, ecutwfc =80.0, nbnd = 20,force_symmorphic=.true., nspin=2, tot_magnetization=0, input_dft='hse', nqx1 = 2, nqx2 = 2, nqx3 = 1, x_gamma_extrapolation = .TRUE. / &amp;ELECTRONS diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Zn 65.409 Zn_pz-2_nlcc.cpi.UPF O 15.999 O.pz-mt.UPF ATOMIC_POSITIONS (crystal) Zn 0.33333 0.66667 0.00000 Zn 0.66667 0.33333 0.50000 O 0.33333 0.66667 0.38210 O 0.66667 0.33333 0.88210 K_POINTS (automatic) 8 8 6 0 0 0 for this one I get (and it seems a reasonable result, at least from the gap) highest occupied, lowest unoccupied level (ev): 1.4320 5.2338 total energy = -110.48522966 Ry 2) ZB-ZnO &amp;system ibrav= 2, celldm(1) =8.447075169 nat= 8, ntyp= 2, force_symmorphic=.true., nspin=2, tot_magnetization=0, ecutwfc =80., nbnd = 50, input_dft='hse', nqx1=2, nqx2=2, nqx3=2, x_gamma_extrapolation = .TRUE. / &amp;electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Zn 65.38 Zn_pz-2_nlcc.cpi.UPF O 15.9994 O.pz-mt.UPF ATOMIC_POSITIONS (crystal) Zn 0.00000 0.00000 0.00000 Zn 0.00000 0.50000 0.50000 Zn 0.50000 0.00000 0.50000 Zn 0.50000 0.50000 0.00000 O 0.25000 0.25000 0.25000 O 0.25000 0.75000 0.75000 O 0.75000 0.75000 0.25000 O 0.75000 0.25000 0.75000 K_POINTS automatic 8 8 8 0 0 0 For this one I get (!!) highest occupied, lowest unoccupied level (ev): 36.4937 31.9513 (!!!) total energy = -200.32746186 Ry _______________________________________________ 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/20120223/3a4482f7/attachment.htm From hannu.komsa at epfl.ch Thu Feb 23 10:31:26 2012 From: hannu.komsa at epfl.ch (hannu.komsa at epfl.ch) Date: Thu, 23 Feb 2012 10:31:26 +0100 Subject: [Pw_forum] ZB ZnO vs WZ ZnO at HSE level In-Reply-To: References: Message-ID: <20120223103126.15805o1d5oibq0dq@webmail.epfl.ch> Hi It seems to me that: 1. You are using cubic cell of Zinc-blende structure so you should use ibrav=1. 2. You are using LDA PP with hse, which is dangerous. I think PBE PP would be more suitable, but more importantly 3. The last time I checked, NLCC doesn't work correctly with hybrids. It might be a good idea for somebody to add a warning for this. Regards, Hannu-Pekka Komsa University of Helsinki > 2) ZB-ZnO > &system > ibrav= 2, celldm(1) =8.447075169 > nat= 8, ntyp= 2, force_symmorphic=.true., nspin=2, tot_magnetization=0, > ecutwfc =80., nbnd = 50, > input_dft='hse', nqx1=2, nqx2=2, nqx3=2, > x_gamma_extrapolation = .TRUE. > / > &electrons > diagonalization='david' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > Zn 65.38 Zn_pz-2_nlcc.cpi.UPF > O 15.9994 O.pz-mt.UPF > ATOMIC_POSITIONS (crystal) > Zn 0.00000 0.00000 0.00000 > Zn 0.00000 0.50000 0.50000 > Zn 0.50000 0.00000 0.50000 > Zn 0.50000 0.50000 0.00000 > O 0.25000 0.25000 0.25000 > O 0.25000 0.75000 0.75000 > O 0.75000 0.75000 0.25000 > O 0.75000 0.25000 0.75000 > K_POINTS automatic > 8 8 8 0 0 0 > > For this one I get (!!) > > highest occupied, lowest unoccupied level (ev): 36.4937 31.9513 (!!!) > total energy = -200.32746186 Ry From gm030212 at gmail.com Thu Feb 23 12:27:57 2012 From: gm030212 at gmail.com (Fen Hong) Date: Thu, 23 Feb 2012 20:27:57 +0900 Subject: [Pw_forum] phonon calculation problem Message-ID: Dear PWscf users and developers, The frequency calculation is very time-consuming. I read one paper, for example, isocynide molecule, they only calculated partial vibrational spectra instead of full one. Because the difference between frequencies from this two ways is marginal. When isocynide adsorbed on Au(111) surface, the vibration of surface is not considered because gold has quite large atomic mass compared with that of first row atoms. What I want to know is how to calculated particle frequency by fix the position of the surface atoms. I tried ?nat_todo? in *.ph.in, but frequency doesnot show is the out file. Is there someone know how to do particle frequency Thank you Best Regards, Takai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120223/d371afba/attachment.htm From bdslipun at gmail.com Thu Feb 23 13:06:56 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Thu, 23 Feb 2012 17:36:56 +0530 Subject: [Pw_forum] POPULATION OF CHARGE Message-ID: can espresso give the population of charge in in each orbital? b d sahoo reserch scolar mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120223/5179064e/attachment.htm From flux_ray12 at 163.com Thu Feb 23 13:57:31 2012 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 23 Feb 2012 20:57:31 +0800 (CST) Subject: [Pw_forum] POPULATION OF CHARGE In-Reply-To: References: Message-ID: <47b2abd9.f0fc.135aa49b43c.Coremail.flux_ray12@163.com> in the output of projwfc.x, Lowdin Charge -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-23 20:06:56,"bhabya sahoo" wrote: can espresso give the population of charge in in each orbital? b d sahoo reserch scolar mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120223/e72caf4f/attachment.htm From giuseppe.mattioli at ism.cnr.it Thu Feb 23 13:59:59 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 23 Feb 2012 13:59:59 +0100 Subject: [Pw_forum] POPULATION OF CHARGE In-Reply-To: References: Message-ID: <20120223135959.5d7871py00c00oss@webmail.sic.rm.cnr.it> You can use the projwfc program to project Kohn-Sham wavefunction on an atom-centered basis set, and to calculate Lowdin charges, total and for different angular-momentum channels. This information is contained into the standard output. projwfc produces also a lot of other files. Maybe the population of each orbital is contained in one/some of the files... HTH Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting bhabya sahoo : > can espresso give the population of charge in in each orbital? > > > > > > > > > > > > b d sahoo > > reserch scolar > > > mumbai > From divyasrivastava at jncasr.ac.in Thu Feb 23 13:47:47 2012 From: divyasrivastava at jncasr.ac.in (Divya Srivastava) Date: Thu, 23 Feb 2012 18:17:47 +0530 Subject: [Pw_forum] (no subject) Message-ID: <1330001267.4f463573b4988@mercury.jncasr.ac.in> I am getting slightly different shape of the phonon density of states by selecting different K-points and nq's points in ph.x input file. Can any body tell me what is the criteria of selecting k-points and nq's point. Divya Srivastava Research Associate TSU, JNCASR Jakkur, Bangalore-64 Tel: 080-2208-2834 From pandey.bramha at gmail.com Thu Feb 23 19:41:43 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Fri, 24 Feb 2012 00:11:43 +0530 Subject: [Pw_forum] regarding stress in pw.x output file Message-ID: Dear all QE users and developers.. I want to calculate the property of system at T=0 K and at P=0 kbar at starting of my pw.x run. But at the end of run, i obtained force=0 but stress p =-832.77 kbar. I am afraid of this stress value. my input file is given below. &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '.' , pseudo_dir = './' , prefix = 'aln' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 2, celldm(1) = 8.285, nat = 2, ntyp = 2, ecutwfc = 28 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_beta = 0.7 , / ATOMIC_SPECIES Al 26.98000 Al.pz-vbc.UPF N 14.01000 N.pz-vbc.UPF ATOMIC_POSITIONS alat Al 0.000000000 0.000000000 0.000000000 N 0.250000000 0.250000000 0.250000000 K_POINTS automatic 4 4 4 0 0 0 Any type of help is highly appreciated. -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120224/f07a4bc8/attachment-0001.htm From degironc at sissa.it Thu Feb 23 21:15:56 2012 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 23 Feb 2012 21:15:56 +0100 Subject: [Pw_forum] regarding stress in pw.x output file In-Reply-To: References: Message-ID: <4F469E7C.7020704@sissa.it> A norm conserving Nitrogen pseudo-potential is likely to require much more that 28 Ry. have you studied the convergence of your calculated energy and stress with respect to cutoff and k-point sampling ? Stefano de Gironcoli On 02/23/2012 07:41 PM, bramha pandey wrote: > Dear all QE users and developers.. > > I want to calculate the property of system at T=0 K and at P=0 kbar at > starting of my pw.x run. > But at the end of run, i obtained force=0 but stress p =-832.77 kbar. > I am afraid of this stress value. my input file is given below. > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '.' , > pseudo_dir = './' , > prefix = 'aln' , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 2, > celldm(1) = 8.285, > nat = 2, > ntyp = 2, > ecutwfc = 28 , > / > &ELECTRONS > conv_thr = 1.0d-8 , > mixing_beta = 0.7 , > / > ATOMIC_SPECIES > Al 26.98000 Al.pz-vbc.UPF > N 14.01000 N.pz-vbc.UPF > ATOMIC_POSITIONS alat > Al 0.000000000 0.000000000 0.000000000 > N 0.250000000 0.250000000 0.250000000 > K_POINTS automatic > 4 4 4 0 0 0 > > Any type of help is highly appreciated. > > > > > > _______________________________________________ > 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/20120223/9dddd0d2/attachment.htm From giannozz at democritos.it Thu Feb 23 22:52:56 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 23 Feb 2012 22:52:56 +0100 Subject: [Pw_forum] "Inconsistent nr1, nr2, nr3 read" during e-ph coupling calculation In-Reply-To: References: Message-ID: <48FACBEC-51F5-46A6-B06A-8716FC0175F9@democritos.it> On Feb 23, 2012, at 4:06 , ?? wrote: > When I calculate the e-ph coupling constant with matdyn.x, I happen > to meet an error: > > from readfG : error # 1 > inconsistent nr1, nr2, nr3 read it works for me (on the development version) 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 avallabh at purdue.edu Thu Feb 23 23:08:03 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Thu, 23 Feb 2012 17:08:03 -0500 (EST) Subject: [Pw_forum] units of psi in e-ph coupling matrix element In-Reply-To: <724CE535-76C6-413D-944B-CBC16DD1BDDC@democritos.it> Message-ID: <1634524555.483996.1330034883086.JavaMail.root@mailhub016.itcs.purdue.edu> Dr. Paolo, Sorry to bother you again on this. I am familiar with the equation (1) in that file. However, it is still not clear to me how does 'g' has the units of energy (eV or Ry). Is the wave function psi considered unitless ? Thanks Ajit From baroni at sissa.it Fri Feb 24 01:49:21 2012 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 24 Feb 2012 01:49:21 +0100 Subject: [Pw_forum] (no subject) In-Reply-To: <1330001267.4f463573b4988@mercury.jncasr.ac.in> References: <1330001267.4f463573b4988@mercury.jncasr.ac.in> Message-ID: <57A49575-5CB6-4A9E-AFD1-B19F1D479615@sissa.it> Convergence: use as many as necessary to make the difference unimportant for you. SB -- Stefano Baroni, Trieste -- swift message written and sent on the go On 23/feb/2012, at 13:47, Divya Srivastava wrote: > I am getting slightly different shape of the phonon density of states by selecting different K-points and nq's points in ph.x input file. > Can any body tell me what is the criteria of selecting k-points and nq's point. > > Divya Srivastava > Research Associate > TSU, JNCASR > Jakkur, Bangalore-64 > Tel: 080-2208-2834 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From romanog at MIT.EDU Fri Feb 24 03:29:07 2012 From: romanog at MIT.EDU (Giuseppe Romano) Date: Thu, 23 Feb 2012 21:29:07 -0500 Subject: [Pw_forum] phonon lifetimes Message-ID: Dear users, I'm computing the anharmonic scattering time for bulk Silicon. While pw and ph work as expected, d3 crashes. It seems there is some missing parameter. Is "fild0rho" necessary? Below are the scripts. Any help is greatly appreciated. Thanks, Giuseppe *si.pw.in:* &system ibrav=2, celldm(1)=10.20, nat=2, ntyp=1, ecutwfc =16.0 / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Si 28.0855 Si.vbc.UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 K_POINTS 10 0.1250000 0.1250000 0.1250000 1.00 0.1250000 0.1250000 0.3750000 3.00 0.1250000 0.1250000 0.6250000 3.00 0.1250000 0.1250000 0.8750000 3.00 0.1250000 0.3750000 0.3750000 3.00 0.1250000 0.3750000 0.6250000 6.00 0.1250000 0.3750000 0.8750000 6.00 0.1250000 0.6250000 0.6250000 3.00 0.3750000 0.3750000 0.3750000 1.00 0.3750000 0.3750000 0.6250000 3.00 *si.ph.in:* phonons of Si &inputph tr2_ph=1.0d-14, ldisp=.true., nq1=4, nq2=4, nq3=4 amass(1)=28.0855, amass(2)=28.0855, prefix='PH', outdir='tmp/', fildyn='si.dyn', fildrho = 'si.drho', / *si.d3.in:* anharm at the X-point &inputph prefix = 'PH', fildrho = 'si.din', amass(1) = 28.0855, amass(2) = 28.0855, outdir = 'tmp/', fildyn = 'si.anh', / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120223/554b2de0/attachment.htm From giannozz at democritos.it Fri Feb 24 09:02:58 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 24 Feb 2012 09:02:58 +0100 Subject: [Pw_forum] phonon lifetimes In-Reply-To: References: Message-ID: <1330070578.28699.0.camel@fe12lx.fisica.uniud.it> On Thu, 2012-02-23 at 21:29 -0500, Giuseppe Romano wrote: > While pw and ph work as expected, d3 crashes. version? crashes how? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri Feb 24 09:08:13 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 24 Feb 2012 09:08:13 +0100 Subject: [Pw_forum] units of psi in e-ph coupling matrix element In-Reply-To: <1634524555.483996.1330034883086.JavaMail.root@mailhub016.itcs.purdue.edu> References: <1634524555.483996.1330034883086.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <1330070893.28699.5.camel@fe12lx.fisica.uniud.it> On Thu, 2012-02-23 at 17:08 -0500, Ajit Vallabhaneni wrote: > I am familiar with the equation (1) in that file. > However, it is still not clear to me how does 'g' > has the units of energy (eV or Ry). the multiplying factor has the dimension of a length, the matrix element of an energy over a length > Is the wave function psi considered unitless ? no: \int \psi^* \psi dV is adimensional. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Fri Feb 24 09:24:15 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 24 Feb 2012 09:24:15 +0100 Subject: [Pw_forum] phonon calculation problem In-Reply-To: References: Message-ID: <1330071855.28699.8.camel@fe12lx.fisica.uniud.it> On Thu, 2012-02-23 at 20:27 +0900, Fen Hong wrote: > I tried ?nat_todo? in *.ph.in, but frequency > does not show is the out file. use (at your risk) option "ldiag" in conjunction with "nat_todo" P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From Lorenzo.Paulatto at impmc.upmc.fr Fri Feb 24 11:46:38 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 24 Feb 2012 11:46:38 +0100 Subject: [Pw_forum] phonon lifetimes In-Reply-To: References: Message-ID: On Fri, 24 Feb 2012 03:29:07 +0100, Giuseppe Romano wrote: > I'm computing the anharmonic scattering time for bulk Silicon. While pw > and > ph work as expected, d3 crashes. It seems there is some missing > parameter. Is "fild0rho" necessary? Below are the scripts. Dear Giuseppe, there are several things missing in your calculation: 1. perform a pw.x calculation 2. perform a ph.x calculation at Gamma to produce fild0rho, store this file and do not overwrite it 3. another ph.x at the point q you want, this will produce fildrho 4. d3.x calculation with fildrho and fild0rho both set, and of course the point specified at the end of the input file -- notes -- a. step 2 and 3 MUST be done in this orther b. the d3 calculation MUST follow step 4 with no other calculations in between c. the d3.x calculation will corrupt the phonon data (if using nlcc), store a copy of it There is an example somewhere, it is example14 in QE 4.3.2, which pretty much shows the procedure. bests -- 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 Lorenzo.Paulatto at impmc.upmc.fr Fri Feb 24 12:33:01 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 24 Feb 2012 12:33:01 +0100 Subject: [Pw_forum] phonon lifetimes In-Reply-To: References: Message-ID: On Fri, 24 Feb 2012 11:46:38 +0100, Lorenzo Paulatto wrote: > c. the d3.x calculation will corrupt the phonon data (if using nlcc), > store a copy of it Update: I've just fixed this issue in the SVN version (I thought I had fixed it long ago but never did...), another temporary solution is to uncomment ! call drho_cc(-1) in d3toten.f90 at around line 270. However, with this fix, d3 will still corrupt the phonon fildrho file if you terminate it between the two calls to drho_cc bests -- 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 bahadira at buffalo.edu Sat Feb 25 01:47:04 2012 From: bahadira at buffalo.edu (bahadir) Date: Fri, 24 Feb 2012 19:47:04 -0500 Subject: [Pw_forum] small negative stress after optimization Message-ID: <4F482F88.2050506@buffalo.edu> Hi i get a small stress (0.31 KBar) after optimization of my system. I could not be able to exact 0.0KBar for the optimization calculations. I wonder if does it effect on other results such as band structure and especially phonon calculations. Is it possible to get 0.00 KBar stress after optimization? My energy threshold is 10E-14 and force threshold is 10-8. thank you P.S: i tried different ecut and k-grid sampling but, nothing helps, i always get a small negative or positive stress. From baroni at sissa.it Sat Feb 25 09:23:36 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 25 Feb 2012 09:23:36 +0100 Subject: [Pw_forum] small negative stress after optimization In-Reply-To: <4F482F88.2050506@buffalo.edu> References: <4F482F88.2050506@buffalo.edu> Message-ID: On Feb 25, 2012, at 1:47 AM, bahadir wrote: > Hi > > i get a small stress (0.31 KBar) after optimization of my system. I > could not be able to exact 0.0KBar for the optimization calculations. I > wonder if does it effect on other results such as band structure and > especially phonon calculations. the short answer is NO. you can find a convincing explanation by yourself by calculating the volume variation that would correspond to such a small pressure (for this you will need the bulk modulus that you can either compute, or take from experiments, just for the sake of an order-of-magnitude estimate) > Is it possible to get 0.00 KBar stress after optimization? My energy > threshold is 10E-14 and force threshold is 10-8. of course, you will never obtain *exactly zero*. I believe that you can obtain an arbirtrarily small value for the stress, provided you have enough patience, computer time, and passion to obtain something that is not worth the effort ... > thank you you are most welcome. you will be even more welcome in the future if you stick to the current habit in this forum to sign the post you your name and affiliation. 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/20120225/edcd6470/attachment.htm From sohailphysics at yahoo.co.in Sat Feb 25 17:03:43 2012 From: sohailphysics at yahoo.co.in (Sohail Ahmad) Date: Sat, 25 Feb 2012 21:33:43 +0530 (IST) Subject: [Pw_forum] linux Message-ID: <1330185823.24565.YahooMailClassic@web137301.mail.in.yahoo.com> I am using hp laptop (intel core, 4GB RAM,256 GB HD) with dual boot FEDORA 10 My laptop gets off after every 75-80 minutes, probably because of overheating This happens only when i use linux, I can use window even for 10 hrs without such difficulty ? Can any one explain how to resolve the issue, probably there is any option which i dont know ? Thanks in advance ? Sohail Ahmad KIng Khalid University Saudi Arabia ? ? --------------------------------------------------------------------- Sohail Ahmad Abha, Saudi Arabia ? Contact:???+966 (0) 556776986 (M) -------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120225/379fa86c/attachment.htm From pandey.bramha at gmail.com Sat Feb 25 18:01:48 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Sat, 25 Feb 2012 22:31:48 +0530 Subject: [Pw_forum] regarding stress in pw.x output file In-Reply-To: <4F469E7C.7020704@sissa.it> References: <4F469E7C.7020704@sissa.it> Message-ID: Sir, Stefano de Gironcoli Thank you For your kind reply. Yes i have tested my convergence issue but unable to figure out exactly which energy cut off and k point should i select. First i was tried with kpoint=gamma (0 0 0 0 0 0), for fast convergence and i obtained stress(Kbar)=0.24 at 95 Ry of ecut. The number of iteration is 8-9 in every case. Convergence test at kpoint= 0 0 0 0 0 0 (gamma) ecut(Ry) stress(kbar) etot(Ry) 23 -856.12 -22.45678789 28 -816.21 -22.74277097 33 -717.31 -22.99913807 38 -640.04 -23.13068593 43 -538.05 -23.24446298 48 -388.44 -23.36265311 53 -298.19 -23.41743393 58 -228.34 -23.44939498 63 -147.46 -23.48057851 68 -107.24 -23.49317545 73 -81.19 -23.50039187 78 -48.03 -23.50793794 83 -22.26 -23.51292707 88 -10.40 -23.51479400 93 -3.80 -23.51569322 94 -2.96 -23.51578788 95 0.24 -23.51615658 96 0.24 -23.51615658 97 1.44 -23.51628362 98 1.44 -23.51628362 Second with taking kpoint in consideration again the stress was increased at fix ecut=95Ry. And if i decreased or increased the ecut from 95 Ry to 63Ry and 115Ry , the stress value increases and decreased very small respectively . Please see the below which i was mention above in wording. when cosider k point...fix ecut=95 k mess stress(kbar) etot(Ry) 1*1*1 0.24 -23.51615658 2*2*2 -107.01 -24.24731157 3*3*3 -146.30 -24.33808965 4*4*4 -149.74 -24.34988328 5*5*5 -149.91 -24.35200695 6*6*6 -149.97 -24.35245199 8*8*8 -149.85 -24.35256921 10*10*10 -150.01 -24.35257467 when we chnage the ecut 95 to 63::: 8*8*8 -279.21 -24.31814193 when we chnage the ecut= 115Ry::: 8*8*8 -142.60 -24.35372918 Please any suggestion will be appreciable. On Fri, Feb 24, 2012 at 1:45 AM, Stefano de Gironcoli wrote: > ** > A norm conserving Nitrogen pseudo-potential is likely to require much more > that 28 Ry. > have you studied the convergence of your calculated energy and stress with > respect to cutoff and k-point sampling ? > > Stefano de Gironcoli > > On 02/23/2012 07:41 PM, bramha pandey wrote: > > Dear all QE users and developers.. > > I want to calculate the property of system at T=0 K and at P=0 kbar at > starting of my pw.x run. > But at the end of run, i obtained force=0 but stress p =-832.77 kbar. > I am afraid of this stress value. my input file is given below. > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '.' , > pseudo_dir = './' , > prefix = 'aln' , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 2, > celldm(1) = 8.285, > nat = 2, > ntyp = 2, > ecutwfc = 28 , > / > &ELECTRONS > conv_thr = 1.0d-8 , > mixing_beta = 0.7 , > / > ATOMIC_SPECIES > Al 26.98000 Al.pz-vbc.UPF > N 14.01000 N.pz-vbc.UPF > ATOMIC_POSITIONS alat > Al 0.000000000 0.000000000 0.000000000 > N 0.250000000 0.250000000 0.250000000 > K_POINTS automatic > 4 4 4 0 0 0 > > Any type of help is highly appreciated. > > > > > > _______________________________________________ > 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 > > -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120225/2b85bf2a/attachment.htm From akohlmey at gmail.com Sat Feb 25 21:16:16 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Sat, 25 Feb 2012 15:16:16 -0500 Subject: [Pw_forum] linux In-Reply-To: <1330185823.24565.YahooMailClassic@web137301.mail.in.yahoo.com> References: <1330185823.24565.YahooMailClassic@web137301.mail.in.yahoo.com> Message-ID: On Sat, Feb 25, 2012 at 11:03 AM, Sohail Ahmad wrote: > > I am using hp laptop (intel core, 4GB RAM,256 GB HD) with dual boot *FEDORA > 10* > My laptop gets off after every 75-80 minutes, probably because of > overheating > This happens only when i use linux, > I can use window even for 10 hrs without such difficulty > > Can any one explain how to resolve the issue, probably there is any option > which i dont know > please post questions about linux to a linux forum; your chances to get a qualified answer will increase massively. thanks, axel. > > Thanks in advance > > Sohail Ahmad > KIng Khalid University > Saudi Arabia > > > --------------------------------------------------------------------- > > *Sohail Ahmad* > Abha, Saudi Arabia > > Contact: +966 (0) 556776986 (M) > -------------------------------------------------------------------- > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120225/fff28e6d/attachment.htm From makhyoun2 at yahoo.com Sat Feb 25 22:26:48 2012 From: makhyoun2 at yahoo.com (mohamed makhyoun) Date: Sat, 25 Feb 2012 13:26:48 -0800 (PST) Subject: [Pw_forum] compilation error Message-ID: <1330205208.97995.YahooMailClassic@web126005.mail.ne1.yahoo.com> Dear Developers and users: On compiling espresso-4.2.1 and by making " make all " I get the following errors: libpw.a(mix_rho.o): In function `mix_rho': /home/mohamed/espresso-4.2.1/PW/mix_rho.f90:292: undefined reference to `dsytri_' libpw.a(mix_rho.o): In function `approx_screening2': /home/mohamed/espresso-4.2.1/PW/mix_rho.f90:614: undefined reference to `dsytri_' ../Modules/libqemod.a(bfgs_module.o): In function `gdiis_step': /home/mohamed/espresso-4.2.1/Modules/bfgs_module.f90:496: undefined reference to `dsytri_' ../Modules/libqemod.a(path_opt_routines.o): In function `__path_opt_routines_MOD_broyden2': /home/mohamed/espresso-4.2.1/Modules/path_opt_routines.f90:447: undefined reference to `dsytri_' collect2: ld returned 1 exit status make[1]: *** [pw.x] Error 1 make[1]: Leaving directory `/home/mohamed/espresso-4.2.1/PW' make: *** [pw] Error 2 I appreciate any comment and help Best regard Mohamed Makhyoun -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120225/a01df71b/attachment.htm From akohlmey at gmail.com Sat Feb 25 22:44:49 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Sat, 25 Feb 2012 16:44:49 -0500 Subject: [Pw_forum] compilation error In-Reply-To: <1330205208.97995.YahooMailClassic@web126005.mail.ne1.yahoo.com> References: <1330205208.97995.YahooMailClassic@web126005.mail.ne1.yahoo.com> Message-ID: On Sat, Feb 25, 2012 at 4:26 PM, mohamed makhyoun wrote: > Dear Developers and users: > > On compiling espresso-4.2.1 and by making " make all " > > I get the following errors: > > libpw.a(mix_rho.o): In function `mix_rho': > /home/mohamed/espresso-4.2.1/PW/mix_rho.f90:292: undefined reference to > `dsytri_' > libpw.a(mix_rho.o): In function `approx_screening2': > /home/mohamed/espresso-4.2.1/PW/mix_rho.f90:614: undefined reference to > `dsytri_' > ../Modules/libqemod.a(bfgs_module.o): In function `gdiis_step': > /home/mohamed/espresso-4.2.1/Modules/bfgs_module.f90:496: undefined > reference to `dsytri_' > ../Modules/libqemod.a(path_opt_routines.o): In function > `__path_opt_routines_MOD_broyden2': > /home/mohamed/espresso-4.2.1/Modules/path_opt_routines.f90:447: undefined > reference to `dsytri_' > collect2: ld returned 1 exit status > make[1]: *** [pw.x] Error 1 > make[1]: Leaving directory `/home/mohamed/espresso-4.2.1/PW' > make: *** [pw] Error 2 > > > I appreciate any comment and help > DSYTRI is a lapack subroutine. apparently, you are not correctly providing BLAS/LAPACK please note, that you are trying to compile an outdated version. axel. > > Best regard > > Mohamed Makhyoun > > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120225/48648e46/attachment-0001.htm From kazempoor at ph.iut.ac.ir Sun Feb 26 10:56:16 2012 From: kazempoor at ph.iut.ac.ir (kazempoor at ph.iut.ac.ir) Date: Sun, 26 Feb 2012 13:26:16 +0330 (IRST) Subject: [Pw_forum] producing network In-Reply-To: <317cd6b7-b56d-4d5d-a998-4636cdb3be89@mail1.iut.ac.ir> Message-ID: Dear All I want to generate infinite network for a fullerene-like molecule . Can anyone help me how to make unit cell of chain of fullerene? I mean which ibrav and lattice structure is the most suitable and reliable ? Attached you find the xyz structure. Best Ali Kazempour Physics Department, Isfahn University of Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120226/5cf57261/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: mn_convert17526.xyz Type: chemical/x-pdb Size: 10701 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120226/5cf57261/attachment.pdb From bahadira at buffalo.edu Sun Feb 26 20:51:20 2012 From: bahadira at buffalo.edu (bahadir) Date: Sun, 26 Feb 2012 14:51:20 -0500 Subject: [Pw_forum] Bulk modulus under pressure? Message-ID: <4F4A8D38.8000304@buffalo.edu> hi, mayb this is a stupid question but i wonder if is it possible to calculate bulk modulus under different pressures? or is it meaningless. i have seen some articles that gives pressure vs. bulk modulus data. but it confuses me. thanks -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey From henod2001 at yahoo.com Sun Feb 26 21:02:57 2012 From: henod2001 at yahoo.com (henry odhiambo) Date: Sun, 26 Feb 2012 12:02:57 -0800 (PST) Subject: [Pw_forum] Quasi harmonic approximation Message-ID: <1330286577.70512.YahooMailClassic@web121004.mail.ne1.yahoo.com> Hello users, I am looking for a Quantum Espresso?example of a calculation involving the?quasi-harmonic approximation. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120226/1f2aad9f/attachment.htm From baroni at sissa.it Sun Feb 26 21:18:49 2012 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 26 Feb 2012 21:18:49 +0100 Subject: [Pw_forum] Bulk modulus under pressure? In-Reply-To: <4F4A8D38.8000304@buffalo.edu> References: <4F4A8D38.8000304@buffalo.edu> Message-ID: <74FDE756-49D4-414E-B966-2D159BA554C4@sissa.it> Why not? Bulk modulus is just the second derivative of the energy wrt volume (modulo some appropriate definition). Don't be fooled by names. If you are guided by concepts, rather than by names, it should be pretty clear what can be calculated and what cannot. If it's the second derivative of the energy wrt volume that you need, it should be obvious that it can be calculated and how. No matter what the name is. If it is something else, well it depends ... (on concepts, not on names). SB -- Stefano Baroni, Trieste -- swift message written and sent on the go On 26/feb/2012, at 20:51, bahadir wrote: > hi, > mayb this is a stupid question but i wonder if is it possible to > calculate bulk modulus under different pressures? or is it meaningless. > i have seen some articles that gives pressure vs. bulk modulus data. but > it confuses me. > > thanks > > -- > Dr.Bahadir Altintas > > * Dept. of Chemistry > SUNY Buffalo > NY,USA > > * Abant Izzet Baysal University > Dept. of Computer Education > Bolu,Turkey > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giuseppe.mattioli at ism.cnr.it Sun Feb 26 21:22:43 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Sun, 26 Feb 2012 21:22:43 +0100 Subject: [Pw_forum] Bulk modulus under pressure? In-Reply-To: <4F4A8D38.8000304@buffalo.edu> References: <4F4A8D38.8000304@buffalo.edu> Message-ID: <20120226212243.tdm9hbpji80kssgg@webmail.sic.rm.cnr.it> Dear Bahadir The bulk modulus is -V(dP/dV). You may perform several vc-relax calculations with different P targets and construct your P(V) curve. Then you may calculate the derivative of the curve at a given P value. HTH Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting bahadir : > hi, > mayb this is a stupid question but i wonder if is it possible to > calculate bulk modulus under different pressures? or is it meaningless. > i have seen some articles that gives pressure vs. bulk modulus data. but > it confuses me. > > thanks > > -- > Dr.Bahadir Altintas > > * Dept. of Chemistry > SUNY Buffalo > NY,USA > > * Abant Izzet Baysal University > Dept. of Computer Education > Bolu,Turkey > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mpayami at aeoi.org.ir Mon Feb 27 05:32:34 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 27 Feb 2012 08:02:34 +0330 Subject: [Pw_forum] Problem using SGE References: <02CFCA00E0E347EDA8186230497E4EE0@b> Message-ID: <8D0C2962478242DD85437EEFFAC5AF5A@b> I found the solution. m. p. > > Dear Axel, > > I am happy to hear from you. It is most probable to be so because when I > used the "top" command on each of the involved nodes, the memory usage was > different for them. > How can I use these distributed memories such that the loads are more or > less equal? Should I use the fill_up style in sge as round-robin? > Bests, > mahmoud > > are you sure you're not simply running out of memory > and driving the machines to swap until they give up? > > axel. > > >> Any comment is highly appreciated. >> >> Best regards, >> Mahmoud Payami >> >> -------------------------------- >> Mahmoud Payami >> Physics Group, AEOI, >> Tehran-Iran >> >> Email: mpayami at aeoi.org.ir >> Phone: +98 (0) 21 82064393 >> ---------------------------------------------- >> >> _______________________________________________ >> 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 > > College of Science and Technology > Temple University, Philadelphia PA, USA. > _______________________________________________ > 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 avallabh at purdue.edu Mon Feb 27 06:51:25 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Mon, 27 Feb 2012 00:51:25 -0500 (EST) Subject: [Pw_forum] units of psi in e-ph coupling matrix element In-Reply-To: <1330070893.28699.5.camel@fe12lx.fisica.uniud.it> Message-ID: <617486965.490955.1330321885993.JavaMail.root@mailhub016.itcs.purdue.edu> Dr. Paolo, Thanks for your earlier reply. I am trying to find the actual units of "g" now inside the code. In the file elphon.f90, i find this "calculate elphmat(j,i)= for this pertur". what is the exact units of the term dvscf_q in the code? Is it Hartree/Bohr ?( Hartree for energy and Bohr for length) Thanks Ajit From bahadira at buffalo.edu Mon Feb 27 06:58:37 2012 From: bahadira at buffalo.edu (bahadir) Date: Mon, 27 Feb 2012 00:58:37 -0500 Subject: [Pw_forum] Bulk modulus under pressure? In-Reply-To: <74FDE756-49D4-414E-B966-2D159BA554C4@sissa.it> References: <4F4A8D38.8000304@buffalo.edu> <74FDE756-49D4-414E-B966-2D159BA554C4@sissa.it> Message-ID: <4F4B1B8D.1070602@buffalo.edu> thanks for quick, i just tried a quick calculation for my curiosity on this. i just optimized a fcc structure under 100GPa pressure also under 0GPa i calculated bulk modulus for 0GPa system by changing equilibrium celldm(1) in range of -10% and +10% and calculatin energy. and used ev.x for fitting. fiiting curve is an U-shaped plot then i did the same procedure for 100GPa system by calculating energy for the celldm(1) values -10% to +10%. first thing is: alatt vs energy plot is not U-shaped. and if i extend the range from +-10% to +-20% a get an equilibrium energy but obviously it is the same as that of 0GPa's result. that is the point that i am getting confused by. and still curious about, what should i do to calculate a bulk modulus for a system under 100GPa? thank you On 02/26/2012 03:18 PM, Stefano Baroni wrote: > Why not? Bulk modulus is just the second derivative of the energy wrt volume (modulo some appropriate definition). Don't be fooled by names. If you are guided by concepts, rather than by names, it should be pretty clear what can be calculated and what cannot. If it's the second derivative of the energy wrt volume that you need, it should be obvious that it can be calculated and how. No matter what the name is. If it is something else, well it depends ... (on concepts, not on names). SB > > -- > Stefano Baroni, Trieste -- swift message written and sent on the go > > On 26/feb/2012, at 20:51, bahadir wrote: > >> hi, >> mayb this is a stupid question but i wonder if is it possible to >> calculate bulk modulus under different pressures? or is it meaningless. >> i have seen some articles that gives pressure vs. bulk modulus data. but >> it confuses me. >> >> thanks >> >> -- >> Dr.Bahadir Altintas >> >> * Dept. of Chemistry >> SUNY Buffalo >> NY,USA >> >> * Abant Izzet Baysal University >> Dept. of Computer Education >> Bolu,Turkey >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey From moronaphtaly84 at gmail.com Mon Feb 27 07:10:13 2012 From: moronaphtaly84 at gmail.com (naphtaly moro) Date: Mon, 27 Feb 2012 08:10:13 +0200 Subject: [Pw_forum] Quasi harmonic approximation Message-ID: Dear Henry, There are some exmaples in your espresso directory espresso-4.3.2/QHA/Examples Kind Regards ============================================== OUMA, Cecil Naphtaly Moro PhD. Student Physics Department, University of Pretoria, South Africa Private bag X20 Hatfield Pretoria 0028 Office 5-61, NW-1 Building Cell: +27 721385182 ============================================== "Clouds are not spheres, mountains are not cones, coastlines are not circles,and bark is not smooth, nor does lightning travel in a straight line." - Benoit Mandelbrot * The more progress physical sciences make, the more they tend to enter the domain of mathematics, which is a kind of centre to which they all converge. We may even judge the degree of perfection to which a science has arrived by the facility with which it may be submitted to calculation. Quoted in E Mailly, **Eulogy on Quetelet 1874 * On Sun, Feb 26, 2012 at 10:22 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. producing network (kazempoor at ph.iut.ac.ir) > 2. Bulk modulus under pressure? (bahadir) > 3. Quasi harmonic approximation (henry odhiambo) > 4. Re: Bulk modulus under pressure? (Stefano Baroni) > 5. Re: Bulk modulus under pressure? (Giuseppe Mattioli) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 26 Feb 2012 13:26:16 +0330 (IRST) > From: kazempoor at ph.iut.ac.ir > Subject: [Pw_forum] producing network > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="utf-8" > > Dear All > I want to generate infinite network for a fullerene-like molecule . Can > anyone help me how to make unit cell of chain of fullerene? I mean which > ibrav and lattice structure is the most suitable and reliable ? > Attached you find the xyz structure. > Best > > > Ali Kazempour > Physics Department, Isfahn University of Technology > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120226/5cf57261/attachment-0001.htm > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: mn_convert17526.xyz > Type: chemical/x-pdb > Size: 10701 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20120226/5cf57261/attachment-0001.pdb > > ------------------------------ > > Message: 2 > Date: Sun, 26 Feb 2012 14:51:20 -0500 > From: bahadir > Subject: [Pw_forum] Bulk modulus under pressure? > To: pw_forum at pwscf.org > Message-ID: <4F4A8D38.8000304 at buffalo.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > hi, > mayb this is a stupid question but i wonder if is it possible to > calculate bulk modulus under different pressures? or is it meaningless. > i have seen some articles that gives pressure vs. bulk modulus data. but > it confuses me. > > thanks > > -- > Dr.Bahadir Altintas > > * Dept. of Chemistry > SUNY Buffalo > NY,USA > > * Abant Izzet Baysal University > Dept. of Computer Education > Bolu,Turkey > > > > ------------------------------ > > Message: 3 > Date: Sun, 26 Feb 2012 12:02:57 -0800 (PST) > From: henry odhiambo > Subject: [Pw_forum] Quasi harmonic approximation > To: pw_forum at pwscf.org > Message-ID: > <1330286577.70512.YahooMailClassic at web121004.mail.ne1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello users, > I am looking for a Quantum Espresso?example of a calculation involving > the?quasi-harmonic approximation. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120226/1f2aad9f/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Sun, 26 Feb 2012 21:18:49 +0100 > From: Stefano Baroni > Subject: Re: [Pw_forum] Bulk modulus under pressure? > To: bahadir > Cc: "pw_forum at pwscf.org" > Message-ID: <74FDE756-49D4-414E-B966-2D159BA554C4 at sissa.it> > Content-Type: text/plain; charset=us-ascii > > Why not? Bulk modulus is just the second derivative of the energy wrt > volume (modulo some appropriate definition). Don't be fooled by names. If > you are guided by concepts, rather than by names, it should be pretty clear > what can be calculated and what cannot. If it's the second derivative of > the energy wrt volume that you need, it should be obvious that it can be > calculated and how. No matter what the name is. If it is something else, > well it depends ... (on concepts, not on names). SB > > -- > Stefano Baroni, Trieste -- swift message written and sent on the go > > On 26/feb/2012, at 20:51, bahadir wrote: > > > hi, > > mayb this is a stupid question but i wonder if is it possible to > > calculate bulk modulus under different pressures? or is it meaningless. > > i have seen some articles that gives pressure vs. bulk modulus data. but > > it confuses me. > > > > thanks > > > > -- > > Dr.Bahadir Altintas > > > > * Dept. of Chemistry > > SUNY Buffalo > > NY,USA > > > > * Abant Izzet Baysal University > > Dept. of Computer Education > > Bolu,Turkey > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > ------------------------------ > > Message: 5 > Date: Sun, 26 Feb 2012 21:22:43 +0100 > From: Giuseppe Mattioli > Subject: Re: [Pw_forum] Bulk modulus under pressure? > To: pw_forum at pwscf.org > Message-ID: <20120226212243.tdm9hbpji80kssgg at webmail.sic.rm.cnr.it> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > > Dear Bahadir > The bulk modulus is -V(dP/dV). You may perform several vc-relax > calculations with different P targets and construct your P(V) curve. > Then you may calculate the derivative of the curve at a given P value. > HTH > > Giuseppe > > Giuseppe Mattioli > ISM-CNR > Italy > > Quoting bahadir : > > > hi, > > mayb this is a stupid question but i wonder if is it possible to > > calculate bulk modulus under different pressures? or is it meaningless. > > i have seen some articles that gives pressure vs. bulk modulus data. but > > it confuses me. > > > > thanks > > > > -- > > Dr.Bahadir Altintas > > > > * Dept. of Chemistry > > SUNY Buffalo > > NY,USA > > > > * Abant Izzet Baysal University > > Dept. of Computer Education > > Bolu,Turkey > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 56, Issue 45 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120227/fa7db250/attachment-0001.htm From baroni at sissa.it Mon Feb 27 13:24:54 2012 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 27 Feb 2012 13:24:54 +0100 Subject: [Pw_forum] Bulk modulus under pressure? In-Reply-To: <4F4B1B8D.1070602@buffalo.edu> References: <4F4A8D38.8000304@buffalo.edu> <74FDE756-49D4-414E-B966-2D159BA554C4@sissa.it> <4F4B1B8D.1070602@buffalo.edu> Message-ID: Dear Bahdir: > i just tried a quick calculation for my curiosity on this. i just optimized a fcc structure under 100GPa pressure also under 0GPa > i calculated bulk modulus for 0GPa system by changing equilibrium celldm(1) in range of -10% and +10% and calculatin energy. and used ev.x for fitting. fiiting curve is an U-shaped plot +/- 10% may be too large a variation to estimate the second derivative by finite differences, but assuming that you know what you are doing, I would say that the procedure is correct. No surprise that you find a "U-shaped" curve, given that you calculate points on that curve near the minimum (the "bottom of the U") > > then i did the same procedure for 100GPa system by calculating energy for the celldm(1) values -10% to +10%. first thing is: alatt vs energy plot is not U-shaped. why should it? at such a large pressure, you would probably be rather far from the minimum ... > and if i extend the range from +-10% > to +-20% a get an equilibrium energy but obviously it is the same as that of 0GPa's result. > > that is the point that i am getting confused by. > and still curious about, what should i do to calculate a bulk modulus for a system under 100GPa? I maintain that you are probably fooled by names. If you want to calculate the second derivative of the E(V) curve, just do it: the second derivative has well defined value even far from the minimum, where the curve is not "U-shaped". Just do what any text in numerical analysis tells you to do in the chapter on numerical differentiation ... Let's now come to names. Strictly speaking, the bulk modulus is the second derivative of the energy (or free energy) *as a function of volume*. It is therefore a function of volume, not of pressure. Of course, once you have the bulk modulus as a function of volume, B=B(V), you can always use the equation of state, V=V(P), to formally write it as a function of pressure, by a simple change of variable: B(P) "=" B(V(P)). Note the quotation marks that mean: "the bulk modulus at the volume corresponding to the pressure P". I think that some algebraic gymnastics would allow you to obtain this quantity from the second derivative of the enthalpy (which is the appropriate thermodynamical potential that depends on pressure as an independent variable). It all depends on what you need: if you need the second derivative of "A" with respect to "B", then just calculate it, whatever the name of that second derivative is ... HTH - 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/20120227/5d5d19c1/attachment.htm From bahadira at buffalo.edu Mon Feb 27 18:20:04 2012 From: bahadira at buffalo.edu (bahadir) Date: Mon, 27 Feb 2012 12:20:04 -0500 Subject: [Pw_forum] Bulk modulus under pressure? In-Reply-To: References: <4F4A8D38.8000304@buffalo.edu> <74FDE756-49D4-414E-B966-2D159BA554C4@sissa.it> <4F4B1B8D.1070602@buffalo.edu> Message-ID: <4F4BBB44.5030401@buffalo.edu> thank you for the explanation, it is really helpfull bahadir On 02/27/2012 07:24 AM, Stefano Baroni wrote: > Dear Bahdir: > >> i just tried a quick calculation for my curiosity on this. i just >> optimized a fcc structure under 100GPa pressure also under 0GPa >> i calculated bulk modulus for 0GPa system by changing equilibrium >> celldm(1) in range of -10% and +10% and calculatin energy. and used >> ev.x for fitting. fiiting curve is an U-shaped plot > > +/- 10% may be too large a variation to estimate the second derivative > by finite differences, but assuming that you know what you are doing, > I would say that the procedure is correct. No surprise that you find a > "U-shaped" curve, given that you calculate points on that curve near > the minimum (the "bottom of the U") >> >> then i did the same procedure for 100GPa system by calculating energy >> for the celldm(1) values -10% to +10%. first thing is: alatt vs >> energy plot is not U-shaped. > > why should it? at such a large pressure, you would probably be rather > far from the minimum ... > >> and if i extend the range from +-10% >> to +-20% a get an equilibrium energy but obviously it is the same as >> that of 0GPa's result. >> >> that is the point that i am getting confused by. >> and still curious about, what should i do to calculate a bulk modulus >> for a system under 100GPa? > > I maintain that you are probably fooled by names. If you want to > calculate the second derivative of the E(V) curve, just do it: the > second derivative has well defined value even far from the minimum, > where the curve is not "U-shaped". Just do what any text in numerical > analysis tells you to do in the chapter on numerical differentiation ... > > Let's now come to names. Strictly speaking, the bulk modulus is the > second derivative of the energy (or free energy) *as a function of > volume*. It is therefore a function of volume, not of pressure. Of > course, once you have the bulk modulus as a function of volume, > B=B(V), you can always use the equation of state, V=V(P), to formally > write it as a function of pressure, by a simple change of variable: > B(P) "=" B(V(P)). Note the quotation marks that mean: "the bulk > modulus at the volume corresponding to the pressure P". I think that > some algebraic gymnastics would allow you to obtain this quantity from > the second derivative of the enthalpy (which is the appropriate > thermodynamical potential that depends on pressure as an independent > variable). It all depends on what you need: if you need the second > derivative of "A" with respect to "B", then just calculate it, > whatever the name of that second derivative is ... > > HTH - 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 > -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120227/8cea2549/attachment.htm From suza.rri at gmail.com Tue Feb 28 02:19:51 2012 From: suza.rri at gmail.com (Suza W) Date: Tue, 28 Feb 2012 02:19:51 +0100 Subject: [Pw_forum] DC & BEC In-Reply-To: <4ED73CBF.4070903@epfl.ch> References: <4ED73CBF.4070903@epfl.ch> Message-ID: Hello All, As Prof. Marzari mentioned in an earlier post (see below), some of the iterative algorithms used in VASP OR PWSCF may lead to an incorrect ground state. In PWSCF, this can be cured by using startingwfc="atomic+random". How this can be cured in VASP ? This will be indeed a great help if there is a remedy similar to startingwfc also in VASP. I look forward to a helpful answer. Thanks and Regards, Suza W PhD Student Department of Materials Science Bangalore On Thu, Dec 1, 2011 at 9:37 AM, Nicola Marzari wrote: > > slightly puzzling - one thing I recall is that these perovskites > can reach an incorrect ground state where some of the higher > occupied eigenstates have converged to even higher unoccupied > states (this is in principle possible with some of the iterative > algorithms used e.g. in PWSCF or VASP). > > This is typically cured by using startignwfc="atomic+random" - > it looks like this has now become the default in pwscf, but depending on > the version you use it might not have been the case. > > LEt us know, > > nicola > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/980dab36/attachment-0001.htm From akohlmey at gmail.com Tue Feb 28 02:26:51 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Mon, 27 Feb 2012 20:26:51 -0500 Subject: [Pw_forum] DC & BEC In-Reply-To: References: <4ED73CBF.4070903@epfl.ch> Message-ID: On Mon, Feb 27, 2012 at 8:19 PM, Suza W wrote: > ?Hello All, > > ?As Prof. Marzari mentioned in an earlier post (see below), > ?some of the iterative algorithms used in VASP OR PWSCF may > ?lead to an incorrect ground state. In PWSCF, this can be cured by > ?using startingwfc="atomic+random". How this can be cured in VASP ? > ?This will be indeed a great help if there is a remedy similar to > startingwfc > ?also in VASP. > > ?I look forward to a helpful answer. have you considered asking the VASP folks? it is their job to fix VASP, is it not? axel. > > ?Thanks and Regards, > > ?Suza W > ?PhD Student > ?Department of Materials Science > ?Bangalore > > ? On Thu, Dec 1, 2011 at 9:37 AM, Nicola Marzari > wrote: >> >> >> slightly puzzling - one thing I recall is that these perovskites >> can reach an incorrect ground state where some of the higher >> occupied eigenstates have converged to even higher unoccupied >> states (this is in principle possible with some of the iterative >> algorithms used e.g. in PWSCF or VASP). >> >> This is typically cured by using startignwfc="atomic+random" - >> it looks like this has now become the default in pwscf, but depending on >> the version you use it might not have been the case. >> >> LEt us know, >> >> ? ? ? ? ? ? ? ? ? ? ? ?nicola >> > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From bahadira at buffalo.edu Tue Feb 28 02:31:17 2012 From: bahadira at buffalo.edu (bahadir) Date: Mon, 27 Feb 2012 20:31:17 -0500 Subject: [Pw_forum] identifying the phonon bands around fermi level? Message-ID: <4F4C2E65.80003@buffalo.edu> hi, is it possible to get the bands intersecting the fermi level from phonon band structure as in electronic band structure? i don't know too much about phonons and just started to calculate some phonon related properties. thank you -- Dr.Bahadir Altintas * Dept. of Chemistry SUNY Buffalo NY,USA * Abant Izzet Baysal University Dept. of Computer Education Bolu,Turkey From lhuang4 at ncsu.edu Tue Feb 28 07:04:35 2012 From: lhuang4 at ncsu.edu (Liangliang HUANG) Date: Tue, 28 Feb 2012 01:04:35 -0500 Subject: [Pw_forum] successful installation, but segmentation fault Message-ID: Dear PWer, I have a segmentation fault occurred when I am running the examples. The version 4.3.2 has been installed on our own cluster using Intel compiler version 10.1.22 + mpich2 version 1.3a2: $ ./configure MPIF90=mpif90 CC=mpicc $ make all The installation finishes smooth without any error message. However when I tested the example01, I got the following message: running the symmetry analysis for Cu bands...forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source libblas.so.3 00002BA021078234 Unknown Unknown Unknown bands.x 00000000004547A6 find_band_sym_ 383 sym_band.f90 bands.x 000000000044E859 sym_band_ 128 sym_band.f90 bands.x 0000000000406407 MAIN__ 112 bands.f90 bands.x 0000000000406042 Unknown Unknown Unknown libc.so.6 000000363681D994 Unknown Unknown Unknown bands.x 0000000000405F69 Unknown Unknown Unknown It seems to be related with the source code or the compiler. Do you have any hints? Many thanks in advance! Liangliang NC State -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/118bc97c/attachment.htm From bdslipun at gmail.com Tue Feb 28 08:00:28 2012 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 28 Feb 2012 12:30:28 +0530 Subject: [Pw_forum] thermal conductivity Message-ID: how one can calculate the thermal conductivity by the use of boltzmann transport theory using quantum espresso code bcause i have seen some journal papers about this references and suggetions are highly appricieted Bd SAHOO RESERCH SCHOLAR MUMBAI -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/e4078877/attachment.htm From omictronics at yahoo.com Tue Feb 28 11:15:23 2012 From: omictronics at yahoo.com (michael onyeaju) Date: Tue, 28 Feb 2012 02:15:23 -0800 (PST) Subject: [Pw_forum] HOW TO CONFIGURE ESPRESSO IN HPC CLOSTER Message-ID: <1330424123.26539.YahooMailNeo@web121202.mail.ne1.yahoo.com> Dear QE users, I have been having troubles in trying to configure Espresso and Abinit in HPC closters, can any one assist me ?Onyeaju, M.C Department of Physics, Faculty of Science, University of Port Harcourt Phone:+2348068118468 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/bda694f1/attachment.htm From carlo.nervi at unito.it Tue Feb 28 11:33:14 2012 From: carlo.nervi at unito.it (Carlo Nervi) Date: Tue, 28 Feb 2012 11:33:14 +0100 Subject: [Pw_forum] HOW TO CONFIGURE ESPRESSO IN HPC CLOSTER In-Reply-To: <1330424123.26539.YahooMailNeo@web121202.mail.ne1.yahoo.com> References: <1330424123.26539.YahooMailNeo@web121202.mail.ne1.yahoo.com> Message-ID: <4F4CAD6A.2020100@unito.it> Dear Onyeaju, first of all I think you better have a look on the installation manual of Quantum Espresso (if you need help on Abinit, better ask to another community..) and perhaps after some trial-and-errors report a more detailed and specific question. For example machine on which you are going to install, OS, fortran compiler, mpi version, problems and oputput error after attempt in configuration, etc... I guess nobody can help you starting from scratch... I have another suggestion (sorry, I can't refrain myself, it's quite hilarious and I hope you accept the joke): look on google translator for the word "closter"... than we can ask the help of monks.. :-) Cheers, Carlo Il 28/02/2012 11.15, michael onyeaju ha scritto: > Dear QE users, > I have been having troubles in trying to configure Espresso and Abinit > in HPC closters, can any one assist me > Onyeaju, M.C > Department of Physics, > Faculty of Science, > University of Port Harcourt > Phone:+2348068118468 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ------------------------------------------------------------ Prof. Carlo Nervi carlo.nervi at unito.it Tel:+39 0116707507/8 Fax: +39 0116707855 - Dipartimento di Chimica, via P. Giuria 7, 10125 Torino, Italy. http://lem.ch.unito.it/ From pandey.bramha at gmail.com Tue Feb 28 13:42:23 2012 From: pandey.bramha at gmail.com (bramha pandey) Date: Tue, 28 Feb 2012 18:12:23 +0530 Subject: [Pw_forum] Regarding Dielectric constant calculation Message-ID: Dear QE users and developers... I was trying to calculate the static dielectric constant at gamma point. My system is AlN (ZB, fcc, 2 atom per unit cell). PP's are Norm-conversing for Al and N both. As i optimize the system wrt ecut and kpoint mess with 40 Ry and 4*4*4 and at this value by phonon program i obtained dielectric tensor=5.67 approx which is much less than experimental (9.0). But when i take the ecut=18Ry and kpoint=4*4*4, i was able to find the near value of dielectric tensor as 8.57 approx and also the theromodynamic property Cv is coming approx near about experimental value except some variation at lower temperature(up to 100K). My question is that should we perform the phonon calcualtion in unoptimized case i.e we should always put ecut as min for correct calculation of phonon property. At this point i am very much confused. Please any type of comment is highly appreciable. -- Thanks and Regards Bramha Prasad Pandey GLA University, Mathura. INDIA. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/37281cf8/attachment.htm From akohlmey at gmail.com Tue Feb 28 15:22:43 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 28 Feb 2012 09:22:43 -0500 Subject: [Pw_forum] successful installation, but segmentation fault In-Reply-To: References: Message-ID: On Tue, Feb 28, 2012 at 1:04 AM, Liangliang HUANG wrote: > Dear PWer, > > I have a segmentation fault occurred when I am running the examples. > > The version 4.3.2 has been installed on our own cluster using Intel compiler > version 10.1.22 ?+ mpich2 version 1.3a2: > > $?./configure MPIF90=mpif90 CC=mpicc > $ make all > > The installation finishes smooth without any error message. However when I > tested the example01, I got the following message: > > ?running the symmetry analysis for Cu bands...forrtl: severe (174): SIGSEGV, > segmentation fault occurred > Image ? ? ? ? ? ? ?PC ? ? ? ? ? ? ? ?Routine ? ? ? ? ? ?Line ? ? ? ?Source > > libblas.so.3 ? ? ? 00002BA021078234 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown > bands.x ? ? ? ? ? ?00000000004547A6 ?find_band_sym_ ? ? ? ? ? ?383 > ?sym_band.f90 > bands.x ? ? ? ? ? ?000000000044E859 ?sym_band_ ? ? ? ? ? ? ? ? 128 > ?sym_band.f90 > bands.x ? ? ? ? ? ?0000000000406407 ?MAIN__ ? ? ? ? ? ? ? ? ? ?112 > ?bands.f90 > bands.x ? ? ? ? ? ?0000000000406042 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown > libc.so.6 ? ? ? ? ?000000363681D994 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown > bands.x ? ? ? ? ? ?0000000000405F69 ?Unknown ? ? ? ? ? ? ? Unknown ?Unknown > > It seems to be related with the source code or the compiler. Do you have any > hints? check your stack size (ulimit -s) and try increasing it. axel. > Many thanks in advance! > > Liangliang > NC State > > > > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From omictronics at yahoo.com Tue Feb 28 15:26:07 2012 From: omictronics at yahoo.com (michael onyeaju) Date: Tue, 28 Feb 2012 06:26:07 -0800 (PST) Subject: [Pw_forum] PROBLEM RUNNING QE PARALLEL JOB Message-ID: <1330439167.52497.YahooMailNeo@web121204.mail.ne1.yahoo.com> Dear QE USER, I tried running an interactive job?in HPC cluster?using?QE,?but i keep geting this error message: please help ? [login02:25580] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 77 -------------------------------------------------------------------------- It looks like MPI_INIT failed for some reason; your parallel process is likely to abort.? There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems.? This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): ? ompi_mpi_init: orte_init failed ? --> Returned "Not found" (-13) instead of "Success" (0) ? ?Onyeaju, M.C Department of Physics, Faculty of Science, University of Port Harcourt Phone:+2348068118468 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/9e36156e/attachment.htm From lhuang4 at ncsu.edu Tue Feb 28 15:48:14 2012 From: lhuang4 at ncsu.edu (Liangliang HUANG) Date: Tue, 28 Feb 2012 09:48:14 -0500 Subject: [Pw_forum] successful installation, but segmentation fault In-Reply-To: References: Message-ID: Hi Axel, Thanks for that. Unfortunately, I could not change the stack size on the university cluster. I assume the default stack size is 10240KB. My workaround is to use PGI compiler instead. The examples seem to be working. Thanks again! Liangliang CHE at NCSU On Tue, Feb 28, 2012 at 9:22 AM, Axel Kohlmeyer wrote: > On Tue, Feb 28, 2012 at 1:04 AM, Liangliang HUANG > wrote: > > Dear PWer, > > > > I have a segmentation fault occurred when I am running the examples. > > > > The version 4.3.2 has been installed on our own cluster using Intel > compiler > > version 10.1.22 + mpich2 version 1.3a2: > > > > $ ./configure MPIF90=mpif90 CC=mpicc > > $ make all > > > > The installation finishes smooth without any error message. However when > I > > tested the example01, I got the following message: > > > > running the symmetry analysis for Cu bands...forrtl: severe (174): > SIGSEGV, > > segmentation fault occurred > > Image PC Routine Line > Source > > > > libblas.so.3 00002BA021078234 Unknown Unknown > Unknown > > bands.x 00000000004547A6 find_band_sym_ 383 > > sym_band.f90 > > bands.x 000000000044E859 sym_band_ 128 > > sym_band.f90 > > bands.x 0000000000406407 MAIN__ 112 > > bands.f90 > > bands.x 0000000000406042 Unknown Unknown > Unknown > > libc.so.6 000000363681D994 Unknown Unknown > Unknown > > bands.x 0000000000405F69 Unknown Unknown > Unknown > > > > It seems to be related with the source code or the compiler. Do you have > any > > hints? > > check your stack size (ulimit -s) and try increasing it. > > axel. > > > Many thanks in advance! > > > > Liangliang > > NC State > > > > > > > > > > _______________________________________________ > > 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 > > College of Science and Technology > Temple University, Philadelphia PA, USA. > -- Liangliang HUANG Graduate Student Prof. Keith Gubbins Research Group North Carolina State University Dept. of Chemical and Biomolecular Engineering Box 7905 Centennial Campus Engineering Building I 911 Partners Way Raleigh, NC 27695-7905 Office: (919) 513-2051 Cell: (919) 744-6282 Fax: (919) 513-2470 Email: lhuang4 at ncsu.edu Website: http://gubbins.ncsu.edu/users/lhuang4/ Blog: http://qphll.wordpress.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/0b1cd389/attachment-0001.htm From akohlmey at gmail.com Tue Feb 28 17:16:16 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 28 Feb 2012 11:16:16 -0500 Subject: [Pw_forum] successful installation, but segmentation fault In-Reply-To: References: Message-ID: On Tue, Feb 28, 2012 at 9:48 AM, Liangliang HUANG wrote: > Hi Axel, > > Thanks for that. Unfortunately, I could not change the stack size on the > university cluster. I assume the default stack size is 10240KB. you *can* change it. if not, complain to the sysadmins. > My workaround is to use PGI compiler instead. The examples seem to be > working. oh no! PGI is such a horrible compiler. nobody should go this far. if you do have a stack issue with the intel compiler, there is a better workaround. add the flag -heap-arrays 64 at the appropriate place in your make.sys file. axel. > Thanks again! > > Liangliang > CHE at NCSU > > > On Tue, Feb 28, 2012 at 9:22 AM, Axel Kohlmeyer wrote: >> >> On Tue, Feb 28, 2012 at 1:04 AM, Liangliang HUANG >> wrote: >> > Dear PWer, >> > >> > I have a segmentation fault occurred when I am running the examples. >> > >> > The version 4.3.2 has been installed on our own cluster using Intel >> > compiler >> > version 10.1.22 ?+ mpich2 version 1.3a2: >> > >> > $?./configure MPIF90=mpif90 CC=mpicc >> > $ make all >> > >> > The installation finishes smooth without any error message. However when >> > I >> > tested the example01, I got the following message: >> > >> > ?running the symmetry analysis for Cu bands...forrtl: severe (174): >> > SIGSEGV, >> > segmentation fault occurred >> > Image ? ? ? ? ? ? ?PC ? ? ? ? ? ? ? ?Routine ? ? ? ? ? ?Line >> > ?Source >> > >> > libblas.so.3 ? ? ? 00002BA021078234 ?Unknown ? ? ? ? ? ? ? Unknown >> > ?Unknown >> > bands.x ? ? ? ? ? ?00000000004547A6 ?find_band_sym_ ? ? ? ? ? ?383 >> > ?sym_band.f90 >> > bands.x ? ? ? ? ? ?000000000044E859 ?sym_band_ ? ? ? ? ? ? ? ? 128 >> > ?sym_band.f90 >> > bands.x ? ? ? ? ? ?0000000000406407 ?MAIN__ ? ? ? ? ? ? ? ? ? ?112 >> > ?bands.f90 >> > bands.x ? ? ? ? ? ?0000000000406042 ?Unknown ? ? ? ? ? ? ? Unknown >> > ?Unknown >> > libc.so.6 ? ? ? ? ?000000363681D994 ?Unknown ? ? ? ? ? ? ? Unknown >> > ?Unknown >> > bands.x ? ? ? ? ? ?0000000000405F69 ?Unknown ? ? ? ? ? ? ? Unknown >> > ?Unknown >> > >> > It seems to be related with the source code or the compiler. Do you have >> > any >> > hints? >> >> check your stack size (ulimit -s) and try increasing it. >> >> axel. >> >> > Many thanks in advance! >> > >> > Liangliang >> > NC State >> > >> > >> > >> > >> > _______________________________________________ >> > 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 >> >> College of Science and Technology >> Temple University, Philadelphia PA, USA. > > > > > -- > Liangliang HUANG > Graduate Student > Prof. Keith Gubbins Research Group > North Carolina State University > Dept. of Chemical and Biomolecular Engineering > Box 7905 Centennial Campus > Engineering Building I > 911 Partners Way > Raleigh, NC? 27695-7905 > Office: (919) 513-2051 > Cell:? ? (919) 744-6282 > Fax:? ? (919) 513-2470 > Email:? lhuang4 at ncsu.edu > Website: http://gubbins.ncsu.edu/users/lhuang4/ > Blog:?http://qphll.wordpress.com/ > -- Dr. Axel Kohlmeyer akohlmey at gmail.com ?http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA. From b_noori88 at yahoo.com Tue Feb 28 18:23:34 2012 From: b_noori88 at yahoo.com (Banafshe Noori) Date: Tue, 28 Feb 2012 17:23:34 +0000 (GMT) Subject: [Pw_forum] (no subject) Message-ID: <1330449814.10814.YahooMailNeo@web29304.mail.ird.yahoo.com> Hello I work by code espresso, and i want only at two direction of x and z added to my bulk by the code espresso. at dimension of (z) not add to by this code. please guid me. thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/9e280c28/attachment.htm From akohlmey at gmail.com Tue Feb 28 18:56:45 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Tue, 28 Feb 2012 12:56:45 -0500 Subject: [Pw_forum] PROBLEM RUNNING QE PARALLEL JOB In-Reply-To: <1330439167.52497.YahooMailNeo@web121204.mail.ne1.yahoo.com> References: <1330439167.52497.YahooMailNeo@web121204.mail.ne1.yahoo.com> Message-ID: first off, please don't use all capitals in your subject line. in e-mails words written in all caps are considered that same as shouting. ... and i don't think that this is how you want to be experienced. On Tue, Feb 28, 2012 at 9:26 AM, michael onyeaju wrote: > Dear QE USER, > I tried running an interactive job?in HPC cluster?using?QE,?but i keep > geting this error message: > please help > > [login02:25580] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file > runtime/orte_init.c at line 77 > -------------------------------------------------------------------------- > It looks like MPI_INIT failed for some reason; your parallel process is > likely to abort.? There are many reasons that a parallel process can > fail during MPI_INIT; some of which are due to configuration or environment > problems.? This failure appears to be an internal failure; here's some > additional information (which may only be relevant to an Open MPI > developer): > ? ompi_mpi_init: orte_init failed > ? --> Returned "Not found" (-13) instead of "Success" (0) this looks like a completely botched OpenMPI installation. before even trying to compile/install/use quantum espresso, you should first validate that you have a working MPI installation. there are some simple MPI tests and benchmarks. i suggest you get those to work first. cheers, axel. > > ?Onyeaju, M.C > Department of Physics, > Faculty of Science, > University of Port Harcourt > Phone:+2348068118468 > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From somayehfotohi at yahoo.com Tue Feb 28 20:19:04 2012 From: somayehfotohi at yahoo.com (somayeh fotohi) Date: Tue, 28 Feb 2012 11:19:04 -0800 (PST) Subject: [Pw_forum] scf calculation Message-ID: <1330456744.58884.YahooMailClassic@web161403.mail.bf1.yahoo.com> Dear All I run .scf? file. I get the following errors after 23 iterations in output file and running of?.scf?is stopped. ? from c_bands : error #???????? 1 ???? too many bands are not converged I really appreciate if anyone can help me. ? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/304368c0/attachment.htm From cwandtj at gmail.com Tue Feb 28 20:33:58 2012 From: cwandtj at gmail.com (Chan-Woo Lee) Date: Tue, 28 Feb 2012 14:33:58 -0500 Subject: [Pw_forum] scf calculation In-Reply-To: <1330456744.58884.YahooMailClassic@web161403.mail.bf1.yahoo.com> References: <1330456744.58884.YahooMailClassic@web161403.mail.bf1.yahoo.com> Message-ID: <008f01ccf64f$eb7897e0$c269c7a0$@gmail.com> Dear Somayeh: http://www.democritos.it/pipermail/pw_forum/2010-March/016343.html In many cases, goolging brings you to the answers, OK? Chan-Woo ------- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 Phone: 1-215-898-3564 (Office) From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of somayeh fotohi Sent: Tuesday, February 28, 2012 2:19 PM To: pw_forum at pwscf.org Subject: [Pw_forum] scf calculation Dear All I run .scf file. I get the following errors after 23 iterations in output file and running of .scf is stopped. from c_bands : error # 1 too many bands are not converged I really appreciate if anyone can help me. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/ad1c8bb0/attachment.htm From baroni at sissa.it Tue Feb 28 21:43:49 2012 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 28 Feb 2012 21:43:49 +0100 Subject: [Pw_forum] (no subject) In-Reply-To: <1330449814.10814.YahooMailNeo@web29304.mail.ird.yahoo.com> References: <1330449814.10814.YahooMailNeo@web29304.mail.ird.yahoo.com> Message-ID: <5249ECEA-CFA7-407B-9EA3-53D7BB2C43D0@sissa.it> ??? -- Stefano Baroni, Trieste -- swift message written and sent on the go On 28/feb/2012, at 18:23, Banafshe Noori wrote: > Hello > > I work by code espresso, and i want only at two direction of x and z added to my bulk by the code espresso. > > at dimension of (z) not add to by this code. > > please guid me. > > thanks. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120228/cca55f1d/attachment-0001.htm From giacsport at libero.it Wed Feb 29 04:01:45 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Wed, 29 Feb 2012 04:01:45 +0100 (CET) Subject: [Pw_forum] WZ and ZB ZnO Message-ID: <14562907.4042251330484505812.JavaMail.defaultUser@defaultHost> Dear all, regardless the pseudopotentials I use for my optimization and the kpoint sampling, I always obtain that ZB phase of ZnO is (slightly) more stable than WZ. Since I would like to make HSE calculations on such systems I would like to have an already well-ordered (in terms of energy, of course) structures at PBE level. (In my case WZ and ZB look almost degenerate, but always with ZB slightly more stable than WZ) Can anyone help me to refine parameters that allow me to obtain E WZ < E ZB. Here you find the two inputs. Wurtzite ZnO&CONTROL calculation = "scf" pseudo_dir = './' outdir='./', restart_mode="from_scratch", prefix='ZnO_WZ', tprnfor = .true., tstress = .true., wf_collect=.true., / &SYSTEM ibrav= 4, celldm(1) =6.13821, celldm(3)=1.6023951, nat= 4, ntyp= 2, ecutwfc =90.0, nbnd = 80, nspin=2, tot_magnetization=0, / &ELECTRONS diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Zn 65.38 Zn-GGA-pbe.fhi.UPF O 15.9994 O-GGA-pbe.fhi.UPF ATOMIC_POSITIONS (crystal) Zn 0.33333 0.66667 0.00000 Zn 0.66667 0.33333 0.50000 O 0.33333 0.66667 0.38210 O 0.66667 0.33333 0.88210 K_POINTS (automatic) 12 12 9 0 0 0 total energy = -285.55060915 Ry/2 = -142.7753045750 Zincblende ZnO&control calculation = 'scf' restart_mode='from_scratch', prefix='ZnO_ZB', tprnfor = .true., tstress = .true., wf_collect=.true., pseudo_dir='./', outdir='./', / &system ibrav= 1, celldm(1) =8.730534067 nat= 8, ntyp= 2, ecutwfc =90., nbnd = 100, nspin=2, tot_magnetization=0 / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Zn 65.38 Zn-GGA-pbe.fhi.UPF O 15.9994 O-GGA-pbe.fhi.UPF ATOMIC_POSITIONS (crystal) Zn 0.00000 0.00000 0.00000 Zn 0.00000 0.50000 0.50000 Zn 0.50000 0.00000 0.50000 Zn 0.50000 0.50000 0.00000 O 0.25000 0.25000 0.25000 O 0.25000 0.75000 0.75000 O 0.75000 0.75000 0.25000 O 0.75000 0.25000 0.75000 K_POINTS automatic 8 8 8 0 0 0 total energy = -571.10793352 Ry/4 = -142.776983375 Thanks in advance for your help! Very best,Giacomo -- *************************************** Giacomo Giorgi, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: giacomo at tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120229/7100ecb0/attachment.htm From b_noori88 at yahoo.com Wed Feb 29 07:51:26 2012 From: b_noori88 at yahoo.com (Banafshe Noori) Date: Wed, 29 Feb 2012 06:51:26 +0000 (GMT) Subject: [Pw_forum] (no subject) Message-ID: <1330498286.90749.YahooMailNeo@web29306.mail.ird.yahoo.com> Hello I work by espresso code. is it? possible that similar bulksonly in the similar x and y are added to my bulk? please guid me. thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120229/5618a9ed/attachment.htm From giacsport at libero.it Wed Feb 29 07:56:40 2012 From: giacsport at libero.it (giacsport at libero.it) Date: Wed, 29 Feb 2012 07:56:40 +0100 (CET) Subject: [Pw_forum] R: Re: WZ and ZB ZnO Message-ID: <21122816.4050141330498600713.JavaMail.defaultUser@defaultHost> Dear Monish, thanks a lot for the prompt and exhaustive reply. I was wondering that I took an experimental geometry for both WZ and ZB, thus I was thinking that performing a simple "scf" calculation should have reproduce the experimental trend. Thanks a lot!With best regards,Giacomo ----Messaggio originale---- Da: mohnish.iitk at gmail.com Data: 29/02/2012 4.37 A: "giacsport at libero.it" Ogg: Re: [Pw_forum] WZ and ZB ZnO Dear Giacomo, Are you sure that you optimized the structure with "calculation" = "vc-relax" flag? I mean after the optimization the forces and stress should be below the threshold value. And I use PBE ultrasoft pseudopotential and it worked pretty well for me. Below are the inputs attached : By the way the "nspin" flag that you are using needs finite starting magnetization for atleast one species otherwise it wont do the spin polarized calculation. Feel free to ask any further doubt you have. Wurtzite: &control calculation = 'vc-relax', restart_mode='restart', nstep=300 outdir='/home/rajpala/Desktop/zno-wur', pseudo_dir='/home/rajpala/Desktop/zno-wur' prefix='zno', tstress = .true., tprnfor = .true., / &system ibrav= 4, a = 3.25, c = 5.25,nat= 4, ntyp= 2, ecutwfc = 35,ecutrho=280,occupations='smearing',degauss=0.01,smearing='gaussian' / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / &IONS ion_dynamics='bfgs' trust_radius_min=1.D-7 / &CELL cell_dynamics='bfgs' / ATOMIC_SPECIES Zn 65.390 Zn.pbe-van.UPF O 15.099 O.pbe-rrkjus.UPF ATOMIC_POSITIONS (crystal) Zn 0.000000000000 0.0000000000 0.00000000000 Zn 0.333333333333 0.6666666667 0.50000000000 O 0.000000000000 0.0000000000 0.34500000000 O 0.333333333333 0.6666666667 0.84500000000 K_POINTS (automatic) 8 8 6 0 0 0 Final enthalpy = -317.1024506964 Ry = -158.551225348 Ry/formula unit. Zincblende : &control calculation = 'vc-relax' prefix='zno' tstress = .true. tprnfor = .true. outdir="/home/rajpala/Desktop/zno-zincblend-bulk" pseudo_dir="/home/rajpala/Desktop/zno-zincblend-bulk" / &system ibrav= 2, a =4.60,nat= 2, ntyp= 2,ecutwfc = 40,ecutrho =320, occupations='smearing',degauss=0.01,smearing='gaussian' / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / &IONS ion_dynamics='bfgs' / &CELL cell_dynamics='bfgs' / ATOMIC_SPECIES Zn 65.390 Zn.pbe-van.UPF O 15.099 O.pbe-rrkjus.UPF ATOMIC_POSITIONS (crystal) Zn 0.00 0.00 0.00 O 0.25 0.25 0.25 K_POINTS (automatic) 6 6 6 0 0 0 Final enthalpy = -158.5504170143 Ry/formula unit On Wed, Feb 29, 2012 at 8:31 AM, giacsport at libero.it wrote: Dear all, regardless the pseudopotentials I use for my optimization and the kpoint sampling, I always obtain that ZB phase of ZnO is (slightly) more stable than WZ. Since I would like to make HSE calculations on such systems I would like to have an already well-ordered (in terms of energy, of course) structures at PBE level. (In my case WZ and ZB look almost degenerate, but always with ZB slightly more stable than WZ) Can anyone help me to refine parameters that allow me to obtain E WZ < E ZB. Here you find the two inputs. Wurtzite ZnO&CONTROL calculation = "scf" pseudo_dir = './' outdir='./', restart_mode="from_scratch", prefix='ZnO_WZ', tprnfor = .true., tstress = .true., wf_collect=.true., / &SYSTEM ibrav= 4, celldm(1) =6.13821, celldm(3)=1.6023951, nat= 4, ntyp= 2, ecutwfc =90.0, nbnd = 80, nspin=2, tot_magnetization=0, / &ELECTRONS diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Zn 65.38 Zn-GGA-pbe.fhi.UPF O 15.9994 O-GGA-pbe.fhi.UPF ATOMIC_POSITIONS (crystal) Zn 0.33333 0.66667 0.00000 Zn 0.66667 0.33333 0.50000 O 0.33333 0.66667 0.38210 O 0.66667 0.33333 0.88210 K_POINTS (automatic) 12 12 9 0 0 0 total energy = -285.55060915 Ry/2 = -142.7753045750 Zincblende ZnO&control calculation = 'scf' restart_mode='from_scratch', prefix='ZnO_ZB', tprnfor = .true., tstress = .true., wf_collect=.true., pseudo_dir='./', outdir='./', / &system ibrav= 1, celldm(1) =8.730534067 nat= 8, ntyp= 2, ecutwfc =90., nbnd = 100, nspin=2, tot_magnetization=0 / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Zn 65.38 Zn-GGA-pbe.fhi.UPF O 15.9994 O-GGA-pbe.fhi.UPF ATOMIC_POSITIONS (crystal) Zn 0.00000 0.00000 0.00000 Zn 0.00000 0.50000 0.50000 Zn 0.50000 0.00000 0.50000 Zn 0.50000 0.50000 0.00000 O 0.25000 0.25000 0.25000 O 0.25000 0.75000 0.75000 O 0.75000 0.75000 0.25000 O 0.75000 0.25000 0.75000 K_POINTS automatic 8 8 8 0 0 0 total energy = -571.10793352 Ry/4 = -142.776983375 Thanks in advance for your help! Very best,Giacomo -- *************************************** Giacomo Giorgi, Ph.D. Yamashita & Ushiyama Laboratory, Department of Chemical System Engineering, Faculty of Engineering, The University of Tokyo. tel&fax: +81-3-5841-7286 email: giacomo at tcl.t.u-tokyo.ac.jp HP: http://www.tcl.t.u-tokyo.ac.jp/ *************************************** _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish PandeyBTech-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/20120229/310756bb/attachment-0001.htm From baroni at sissa.it Wed Feb 29 08:09:14 2012 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 29 Feb 2012 08:09:14 +0100 Subject: [Pw_forum] (no subject) In-Reply-To: <1330498286.90749.YahooMailNeo@web29306.mail.ird.yahoo.com> References: <1330498286.90749.YahooMailNeo@web29306.mail.ird.yahoo.com> Message-ID: ??? ??? ??? -- Stefano Baroni, Trieste -- swift message written and sent on the go On 29/feb/2012, at 07:51, Banafshe Noori wrote: > Hello > > I work by espresso code. > is it possible that similar bulks only in the similar x and y are added to my bulk? > > > please guid me. > > thanks. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120229/d1d1a611/attachment.htm From mpayami at aeoi.org.ir Wed Feb 29 09:12:40 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 29 Feb 2012 11:42:40 +0330 Subject: [Pw_forum] R&G space division vs K-point division Message-ID: Dear QE users and developers, Is it possible to decouple R & G space division from the K-point division such that they can be asigned arbitrary values? Any comments is highly appreciated. Best regards, Mahmoud Payami -------------------------------- Mahmoud Payami Physics Group Atomic Energy Organization of Iran Tehran-Iran Email: mpayami at aeoi.org.ir Phone: +98 (0) 21 82064393 ---------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120229/e1c5d06b/attachment.htm From gyalcin at sakarya.edu.tr Wed Feb 29 11:06:46 2012 From: gyalcin at sakarya.edu.tr (Battal Gazi =?ISO-8859-9?Q?YAL=C7IN?=) Date: Wed, 29 Feb 2012 12:06:46 +0200 Subject: [Pw_forum] a question about converter FHI_pp to UPF Message-ID: Hello all, I 'm using pwscf code. I want to convert pseudopotantial based on FHI (Fritz-Haber-Institute) to UPF file. But, I don't find clear documents about this problem. Could anybody help me? Thanks Res. As. G Yalcin Sakarya University Physics Department TURKEY ___________________________________________________________________________________________ Bu e-posta, SA? CAWIS WebMail kullan?larak g?nderilmi?tir : http://www.mail.sakarya.edu.tr/ Sakarya ?niversitesi ile ilgili bilgi, haber ve duyurular i?in : http://www.sakarya.edu.tr/ ___________________________________________________________________________________________ From mpayami at aeoi.org.ir Wed Feb 29 11:46:33 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 29 Feb 2012 14:16:33 +0330 Subject: [Pw_forum] a question about converter FHI_pp to UPF References: Message-ID: <03D82F1CB4A2484FB9BF23C393234041@b> Dear Gazi, Look inside upftools folder to find a relevant tool. The comments inside the codes are clear enough. mahmoud -------------------------------- Mahmoud Payami Physics Group Atomic Energy Organization of Iran Tehran-Iran Email: mpayami at aeoi.org.ir Phone: +98 (0) 21 82064393 ---------------------------------------------- Hello all, I 'm using pwscf code. I want to convert pseudopotantial based on FHI (Fritz-Haber-Institute) to UPF file. But, I don't find clear documents about this problem. Could anybody help me? Thanks Res. As. G Yalcin Sakarya University Physics Department TURKEY ___________________________________________________________________________________________ Bu e-posta, SA? CAWIS WebMail kullan?larak g?nderilmi?tir : http://www.mail.sakarya.edu.tr/ Sakarya ?niversitesi ile ilgili bilgi, haber ve duyurular i?in : http://www.sakarya.edu.tr/ ___________________________________________________________________________________________ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Wed Feb 29 11:57:01 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 29 Feb 2012 11:57:01 +0100 Subject: [Pw_forum] a question about converter FHI_pp to UPF In-Reply-To: <03D82F1CB4A2484FB9BF23C393234041@b> References: <03D82F1CB4A2484FB9BF23C393234041@b> Message-ID: <1330513021.17511.5.camel@fe12lx.fisica.uniud.it> On Wed, 2012-02-29 at 14:16 +0330, Mahmoud Payami wrote: > Look inside upftools folder to find a relevant tool. > The comments inside the codes are clear enough. the new version (coming soon) is somewhat clearer. Note that you need to understand the conversion process of a pseudopotential in semi-local form into the non-local form used by all modern plane-wave codes. Clear documentation is not a replacement for clear ideas, nor can it produce the needed information that is not contained in the original file. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Wed Feb 29 12:02:19 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 29 Feb 2012 12:02:19 +0100 Subject: [Pw_forum] R&G space division vs K-point division In-Reply-To: References: Message-ID: <1330513339.17511.11.camel@fe12lx.fisica.uniud.it> On Wed, 2012-02-29 at 11:42 +0330, Mahmoud Payami wrote: ? > Is it possible to decouple R & G space division from the K-point > division such that they can be asigned arbitrary values? not sure what you mean. The parallelization over k-points and over R- and G- space are "decoupled", i.e. you can choose independently how many processors for the latter and how many for the former. There are separate restrictions on both, though. Unless of course you have other restrictions on the total number of processors you can run on (e.g.only powers of 2, as in some machines). P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From zafartariq2003 at yahoo.com Wed Feb 29 13:29:26 2012 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Wed, 29 Feb 2012 04:29:26 -0800 (PST) Subject: [Pw_forum] end of self consistent calculation. No convergence has been achieved Message-ID: <1330518566.12674.YahooMailClassic@web65411.mail.ac4.yahoo.com> Dear QE users, I am trying to perform a phonon calculation on ?a uniform grid of q-points for zinc blend (consists on 8 atoms)structure. First, I did the scf calculation for a 4x4x4 Monkhorst-Pack grid and tried to ?calculate phonons on a uniform (4x4x4) grid via ldisp true,but the program phonon stopped with the error "end of self consistent calculation. No convergence has been achieved" in the representation 2 (mode 2) and not create dyn3 file at alpha_mix from 0.7. When I change alpha_mix from 0.7 to 0.1 same problem occurs at representation 2 (mode 2) and dyn8 file not created. Will any body help me. Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120229/2c844d18/attachment.htm From mpayami at aeoi.org.ir Wed Feb 29 14:30:57 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Wed, 29 Feb 2012 17:00:57 +0330 Subject: [Pw_forum] R&G space division vs K-point division In-Reply-To: <1330513339.17511.11.camel@fe12lx.fisica.uniud.it> References: <1330513339.17511.11.camel@fe12lx.fisica.uniud.it> Message-ID: -------------------------------------------------- Mahmoud Payami Physics Group, AEOI, Tehran-Iran E-mail : mpayami at aeoi.org.ir -------------------------------------------------- -----Original Message----- From: Paolo Giannozzi To: mpayami at aeoi.org.ir Cc: PWSCF Forum Date: Wed, 29 Feb 2012 12:02:19 +0100 Subject: Re: [Pw_forum] R&G space division vs K-point division > On Wed, 2012-02-29 at 11:42 +0330, Mahmoud Payami wrote: > ? > > > Is it possible to decouple R & G space division from the K-point > > division such that they can be asigned arbitrary values? > > not sure what you mean. The parallelization over k-points > and over R- and G- space are "decoupled", i.e. you can > choose independently how many processors for the latter > and how many for the former. There are separate restrictions > on both, though. Unless of course you have other restrictions > on the total number of processors you can run on (e.g.only > powers of 2, as in some machines). > > 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/20120229/02199f38/attachment.htm From mpayami at aeoi.org.ir Wed Feb 29 14:37:01 2012 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Wed, 29 Feb 2012 17:07:01 +0330 Subject: [Pw_forum] R&G space division vs K-point division In-Reply-To: References: <1330513339.17511.11.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Paolo, Thank you very much. Now I got the point. Sorry for somewhat unclear question. Bests, mahmoud > Is it possible to decouple R & G space division from the K-point > division such that they can be asigned arbitrary values? not sure what you mean. The parallelization over k-points and over R- and G- space are "decoupled", i.e. you can choose independently how many processors for the latter and how many for the former. There are separate restrictions on both, though. Unless of course you have other restrictions on the total number of processors you can run on (e.g.only powers of 2, as in some machines). 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/20120229/d8b69223/attachment.htm From hashemifar at cc.iut.ac.ir Wed Feb 29 14:56:31 2012 From: hashemifar at cc.iut.ac.ir (Seyed Javad Hashemifar) Date: Wed, 29 Feb 2012 17:26:31 +0330 Subject: [Pw_forum] Hartree calculations for small molecules Message-ID: Dear Colleagues Foe educational purpose, I am looking for some Hartree calculations on small molecules such as H2. Is it possible to do Hartree calculations with Quantum Espresso, If yes please explain some detail? Moreover, is there any published computational results on hydrogen molecule based on Hartree method. Your kind answers are highly appreciated. S. Javad Hashemifar ====================================== Seyed Javad Hashemifar Department of Physics, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel: +98 311 391 2375 Fax:+98 311 3912376 Email: hashemifar at cc.iut.ac.ir Group Homepage: http://cmsgroup.iut.ac.ir Personal Homepage: http://hashemifar.iut.ac.ir --------------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120229/01db203c/attachment.htm From giuseppe.mattioli at ism.cnr.it Wed Feb 29 15:19:07 2012 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Wed, 29 Feb 2012 15:19:07 +0100 Subject: [Pw_forum] Hartree calculations for small molecules In-Reply-To: References: Message-ID: <201202291519.07187.giuseppe.mattioli@ism.cnr.it> Dear S. Javad Hashemifar If you look into the QE/Modules/funct.f90 file, you may find the labels which are used to enforce the exchange and correlation functionals. You can perform (I suppose) a calculation with no exchange and no correlation by using something like input_dft='nox+noc+nogx+nogc' which should correspond to a dft-based hartree calculation. However, you could face problems (which I am not able to foresee) with pseudopotentials generated by calculations containing exchange and correlation contributions. HTH Giuseppe On Wednesday 29 February 2012 14:56:31 Seyed Javad Hashemifar wrote: > Dear Colleagues > Foe educational purpose, I am looking for some Hartree calculations on > small molecules such as H2. Is it possible to do Hartree calculations with > Quantum Espresso, If yes please explain some detail? > Moreover, is there any published computational results on hydrogen molecule > based on Hartree method. > > Your kind answers are highly appreciated. > S. Javad Hashemifar > > ====================================== > Seyed Javad Hashemifar > Department of Physics, Isfahan University of Technology > 84156-83111 Isfahan, Iran > Tel: +98 311 391 2375 Fax:+98 311 3912376 > Email: hashemifar at cc.iut.ac.ir > Group Homepage: http://cmsgroup.iut.ac.ir > Personal Homepage: http://hashemifar.iut.ac.ir > --------------------------------------------------------------------------- -- ******************************************************** - 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 akohlmey at gmail.com Wed Feb 29 16:12:50 2012 From: akohlmey at gmail.com (Axel Kohlmeyer) Date: Wed, 29 Feb 2012 10:12:50 -0500 Subject: [Pw_forum] (no subject) In-Reply-To: <1330498286.90749.YahooMailNeo@web29306.mail.ird.yahoo.com> References: <1330498286.90749.YahooMailNeo@web29306.mail.ird.yahoo.com> Message-ID: On Wed, Feb 29, 2012 at 1:51 AM, Banafshe Noori wrote: > Hello > > I work by espresso code. > is it? possible that similar bulks only in the similar x and y are added to > my bulk? can you please translate this into plain english? thanks, axel. > > please guid me. > > thanks. > > > _______________________________________________ > 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 College of Science and Technology Temple University, Philadelphia PA, USA. From avallabh at purdue.edu Wed Feb 29 18:14:09 2012 From: avallabh at purdue.edu (Ajit Vallabhaneni) Date: Wed, 29 Feb 2012 12:14:09 -0500 (EST) Subject: [Pw_forum] Units of energy in elphon.f90 Message-ID: <915762053.499920.1330535649977.JavaMail.root@mailhub016.itcs.purdue.edu> Dear users and developers, I am looking for the units of energy in the elphon.f90 file. I believe all the quantities are measured in atomic units ( Hartree for energy). But in the file elphon.f90, i see the following line at the end for units conversion. "gam(nu,isig) = gam(nu,isig)*RytoGHz" The multiplication factor is from Ry to GHz and not Hartree to GHz. So, i am confused about this. I would appreciate if someone could help me in this regard. Thanks Ajit From giannozz at democritos.it Wed Feb 29 18:18:26 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 29 Feb 2012 18:18:26 +0100 Subject: [Pw_forum] Units of energy in elphon.f90 In-Reply-To: <915762053.499920.1330535649977.JavaMail.root@mailhub016.itcs.purdue.edu> References: <915762053.499920.1330535649977.JavaMail.root@mailhub016.itcs.purdue.edu> Message-ID: <1330535906.19716.7.camel@fe12lx.fisica.uniud.it> On Wed, 2012-02-29 at 12:14 -0500, Ajit Vallabhaneni wrote: > I believe all the quantities are measured in atomic units ( Hartree for energy) no, Ry for energy -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Wed Feb 29 18:21:38 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 29 Feb 2012 18:21:38 +0100 Subject: [Pw_forum] end of self consistent calculation. No convergence has been achieved In-Reply-To: <1330518566.12674.YahooMailClassic@web65411.mail.ac4.yahoo.com> References: <1330518566.12674.YahooMailClassic@web65411.mail.ac4.yahoo.com> Message-ID: <1330536098.19716.12.camel@fe12lx.fisica.uniud.it> On Wed, 2012-02-29 at 04:29 -0800, zafar rasheed wrote: > the program phonon stopped with the error "end of > self consistent calculation. No convergence has been > achieved" in the representation 2 there isn't much that can be done, other than reducing further the mixing parameter. The alternative is to find out why convergence is so slow, or ways to improve convergence. Please send messages in plain text P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Wed Feb 29 18:30:41 2012 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 29 Feb 2012 18:30:41 +0100 Subject: [Pw_forum] Hartree calculations for small molecules In-Reply-To: References: Message-ID: <1330536641.19716.17.camel@fe12lx.fisica.uniud.it> On Wed, 2012-02-29 at 17:26 +0330, Seyed Javad Hashemifar wrote: > For educational purpose, I am looking for some Hartree calculations > on small molecules such as H2. not sure QE is the right tool for such a simple problem. Here some simpler tools: http://www.fisica.uniud.it/~giannozz/Corsi/MQ/mq.html P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy