From akohlmey at cmm.chem.upenn.edu Fri Aug 1 01:15:56 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 31 Jul 2008 19:15:56 -0400 (EDT) Subject: [Pw_forum] vc-relax with constraint In-Reply-To: <22ae3ca40807311037p46c8be46wd4bafbf041c9ede4@mail.gmail.com> References: <22ae3ca40807311037p46c8be46wd4bafbf041c9ede4@mail.gmail.com> Message-ID: On Thu, 31 Jul 2008, alan chen wrote: AC> Dear PWSCF users, AC> I want to calcuate LAO strained on STO. Therefore the lattice constant AC> of LAO in x and y direction is fixed to be the lattice constant of STO. AC> However I want to 'vc-relax' LAO to get the lattice constant in z direction. AC> In PWSCF can we relax the cell in one direction while fixing the lengths of AC> cell in the other two directions? search for the "cell_dofree" variable in the input file documentation. please always RTFM before asking these kind of things. cheers, axel. AC> Thank you. AC> AC> Hanghui Chen AC> Department of Physics AC> Yale University AC> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at democritos.it Fri Aug 1 08:27:59 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 1 Aug 2008 08:27:59 +0200 Subject: [Pw_forum] vc-relax with constraint In-Reply-To: References: <22ae3ca40807311037p46c8be46wd4bafbf041c9ede4@mail.gmail.com> Message-ID: On Aug 1, 2008, at 1:15 , Axel Kohlmeyer wrote: > AC> I want to calcuate LAO strained on STO. Therefore the > lattice constant > AC> of LAO in x and y direction is fixed to be the lattice constant > of STO. > AC> However I want to 'vc-relax' LAO to get the lattice constant in > z direction. > AC> In PWSCF can we relax the cell in one direction while fixing > the lengths of > AC> cell in the other two directions? > > search for the "cell_dofree" variable in the input file documentation. ..and check if it is really implemented: I am not sure it is in the most recent bfgs algorithm Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 1 09:06:27 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 1 Aug 2008 09:06:27 +0200 Subject: [Pw_forum] GGA underestimates lattice constant in BaO In-Reply-To: <39790.210.212.8.60.1216792727.squirrel@webmail.iitg.ac.in> References: <39790.210.212.8.60.1216792727.squirrel@webmail.iitg.ac.in> Message-ID: <573C6D11-4F73-4B0B-A134-BFF6B7A3DA26@democritos.it> On Jul 23, 2008, at 7:58 , Munima Bora Sahariah wrote: > For last couple of days I have been trying to find the equilibrium > lattice > constant of BaO with GGA (pw91) and has found that my calculated > value > underestimates the experimental one by 1.3% (GGA = 10.301 a.u., EXP = > 10.431 a.u.). Surprizingly, while trying with LDA, I obtained a value > which is closer to the experimental one as compared to GGA (LDA = > 10.324 > a.u.) [...] > While doing a search on the web, I found one paper (Phys. Rev. B 71, > 085203) where GGA and LDA results for lattice constant of BaO have > been > listed. In this paper calculations were done in CASTEP. Here the > LDA value > underestimates the experimental lattice constant while the GGA > (pw91) value > improves the situation and is closer to the experimental one. try different pseudopotentials if you can: this might be one of those cases in which the results are more sensitive than desired to the quality of pseudopotentials (in particular of Ba). Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From meisam_a84 at yahoo.com Fri Aug 1 09:10:37 2008 From: meisam_a84 at yahoo.com (meisam aghtar) Date: Fri, 1 Aug 2008 00:10:37 -0700 (PDT) Subject: [Pw_forum] (no subject) Message-ID: <937581.67322.qm@web30607.mail.mud.yahoo.com> Dear all ? ?I want to relax a system containing hydrogenated nanotube. The BFGS method was used But after some cycles it didn?t converge anymore. I changed some parameters such as Kpoint,con-thr , mixing method , mixing-beta ,ecutrho, etc but it didn?t work. What?should I do? ? Thank you. ? M.aghtar Msc student, physics department of Kashan university? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080801/b2e919ad/attachment.htm From baroni at sissa.it Fri Aug 1 09:21:36 2008 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 1 Aug 2008 09:21:36 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <937581.67322.qm@web30607.mail.mud.yahoo.com> References: <937581.67322.qm@web30607.mail.mud.yahoo.com> Message-ID: <25EB47FE-C2FB-4518-9317-6E15D597B45D@sissa.it> On Aug 1, 2008, at 9:10 AM, meisam aghtar wrote: > Dear all > > I want to relax a system containing hydrogenated nanotube. The BFGS > method was used > But after some cycles it didn?t converge anymore. I changed some > parameters such as Kpoint,con-thr , mixing method , mixing- > beta ,ecutrho, etc but it didn?t work. What should I do? provide some information on what you actually did (input file) and what you agtually got (sample of the output file) also, a short description of the content of your post in the subject field of the mail, as well as a more intellegible affiliation would be appreciated SB > > Thank you. > > M.aghtar > Msc student, physics department of Kashan university > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080801/bace274c/attachment.htm From meisam_a84 at yahoo.com Fri Aug 1 10:03:22 2008 From: meisam_a84 at yahoo.com (meisam aghtar) Date: Fri, 1 Aug 2008 01:03:22 -0700 (PDT) Subject: [Pw_forum] convergence of relaxation caculation Message-ID: <805307.4651.qm@web30607.mail.mud.yahoo.com> Dear Stefano I didn?t change any parameters and they are in default mode. I used automatic meshing BZ,1*1*8.also I have not fixed any position. in output , after 5 scf cycles the system doesn?t converge. I think if I ?disrupt the position it would converge but I don?t know how I could make this system converge. ? ? Thanks for your attention. ? M.aghtar Msc student, physics department of Kashan university? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080801/380a491a/attachment.htm From hande at newton.physics.metu.edu.tr Fri Aug 1 10:08:47 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Fri, 1 Aug 2008 11:08:47 +0300 (EEST) Subject: [Pw_forum] convergence of relaxation caculation In-Reply-To: <805307.4651.qm@web30607.mail.mud.yahoo.com> Message-ID: Dear Meisam, You would still need to provide input and output because "doesn't converge" means very little out of context. We need to see what that means. Besides, 5 scf cycles is not very many cycles. Is it possible that you mean atomic steps? Even so, it's still acceptable. Hande On Fri, 1 Aug 2008, meisam aghtar wrote: > Dear Stefano I didn?t change any parameters and they are in default mode. I used automatic meshing BZ,1*1*8.also I have not fixed any position. in output , after 5 scf cycles the system doesn?t converge. I think if I ?disrupt the position it would converge but I don?t know how I could make this system converge. ? ? Thanks for your attention. ? M.aghtar Msc student, physics department of Kashan university? -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From meisam_a84 at yahoo.com Fri Aug 1 10:27:15 2008 From: meisam_a84 at yahoo.com (meisam aghtar) Date: Fri, 1 Aug 2008 01:27:15 -0700 (PDT) Subject: [Pw_forum] convergence of relaxation caculation Message-ID: <398735.25108.qm@web30601.mail.mud.yahoo.com> ?&SYSTEM ?????????????????????? ibrav = 4, ?????????????????? celldm(1) = 32, ?????????????????? celldm(3) = 0.251568464, ???????????????????????? nat = 80, ? ??????????????????????ntyp = 2, ???????????????????? ecutwfc = 36 , ???????????????????? ecutrho = 400 , ??????????????????????? ?/ ?&ELECTRONS ?/ ?&IONS ?/ ATOMIC_SPECIES ??? C?? 12.01070? C.pz-vbc.UPF ??? H??? 1.00794? H.vbc.UPF ATOMIC_POSITIONS angstrom C???? 3.91443516? 0.00000000? -1.42000000 C???? 3.16684457? 2.30084726? -1.42000000 C???? 1.20962699? 3.72284906? -1.42000000 C???? -1.209626993.72284906? -1.42000000 C???? -3.166844572.30084726? -1.42000000 C???? -3.914435160.00000000? -1.42000000 C???? -3.16684457-2.30084726-1.42000000 C???? -1.20962699-3.72284906-1.42000000 C???? 1.20962699? -3.72284906-1.42000000 C???? 3.16684457? -2.30084726-1.42000000 C???? 3.72284906? 1.20962699? -0.71000000 C???? 2.30084726? 3.16684457? -0.71000000 C???? 0.00000000? 3.91443516? -0.71000000 C???? -2.300847263.16684457? -0.71000000 C???? -3.722849061.20962699? -0.71000000 C???? -3.72284906-1.20962699-0.71000000 C???? -2.30084726-3.16684457-0.71000000 C???? 0.00000000? -3.91443516-0.71000000 C???? 2.30084726? -3.16684457-0.71000000 C???? 3.72284906? -1.20962699-0.71000000 C???? 3.72284906? 1.20962699? 0.71000000 C???? 2.30084726? 3.16684457? 0.71000000 C???? 0.00000000? 3.91443516? 0.71000000 C???? -2.300847263.16684457? 0.71000000 C???? -3.722849061.20962699? 0.71000000 C???? -3.72284906-1.209626990.71000000 C???? -2.30084726-3.166844570.71000000 C???? 0.00000000? -3.914435160.71000000 C???? 2.30084726? -3.166844570.71000000 C???? 3.72284906? -1.209626990.71000000 C???? 3.91443516? 0.00000000? 1.42000000 C???? 3.16684457? 2.30084726? 1.42000000 C???? 1.20962699? 3.72284906? 1.42000000 C???? -1.209626993.72284906? 1.42000000 C???? -3.166844572.30084726? 1.42000000 C???? -3.914435160.00000000? 1.42000000 C???? -3.16684457-2.300847261.42000000 C???? -1.20962699-3.722849061.42000000 C???? 1.20962699? -3.722849061.42000000 C???? 3.16684457? -2.300847261.42000000 H???? 2.82443516? 0.00000000? -1.42000000 H???? 2.28501604? 1.66016133? -1.42000000 H???? 0.87279846? 2.68619746? -1.42000000 H???? -0.872798462.68619746? -1.42000000 H???? -2.285016041.66016133? -1.42000000 H???? -2.824435160.00000000? -1.42000000 H???? -2.28501604-1.66016133-1.42000000 H???? -0.87279846-2.68619746-1.42000000 H???? 0.87279846? -2.68619746-1.42000000 H???? 2.28501604? -1.66016133-1.42000000 H???? 2.68619746? 0.87279846? -0.71000000 H???? 1.66016133? 2.28501604? -0.71000000 H???? 0.00000000? 2.82443516? -0.71000000 H???? -1.660161332.28501604? -0.71000000 H???? -2.686197460.87279846? -0.71000000 H???? -2.68619746-0.87279846-0.71000000 H???? -1.66016133-2.28501604-0.71000000 H???? 0.00000000? -2.82443516-0.71000000 H???? 1.66016133? -2.28501604-0.71000000 H???? 2.68619746? -0.87279846-0.71000000 H???? 2.68619746? 0.87279846? 0.71000000 H???? 1.66016133? 2.28501604? 0.71000000 H???? 0.00000000? 2.82443516? 0.71000000 H???? -1.660161332.28501604? 0.71000000 H???? -2.686197460.87279846? 0.71000000 H???? -2.68619746-0.872798460.71000000 H???? -1.66016133-2.285016040.71000000 H???? 0.00000000? -2.824435160.71000000 H???? 1.66016133? -2.285016040.71000000 H???? 2.68619746? -0.872798460.71000000 H???? 2.82443516? 0.00000000? 1.42000000 H???? 2.28501604? 1.66016133? 1.42000000 H???? 0.87279846? 2.68619746? 1.42000000 H???? -0.872798462.68619746? 1.42000000 H???? -2.285016041.66016133? 1.42000000 H???? -2.824435160.00000000? 1.42000000 H???? -2.28501604-1.660161331.42000000 H???? -0.87279846-2.686197461.42000000 H???? 0.87279846? -2.686197461.42000000 H???? 2.28501604? -1.660161331.42000000 ??? K_POINTS automatic ? 1 1 8?? 0 0 1 output: ... Total force =???? 0.764727???? Total SCF correction =???? 0.001974 ???? entering subroutine stress ... ????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=? -46.33 ? -0.00030189? ?0.00000000?? 0.00000000??????? -44.41????? 0.00????? 0.00 ?? 0.00000000? -0.00020564?? 0.00000000????????? 0.00??? -30.25????? 0.00 ?? 0.00000000?? 0.00000000? -0.00043733????????? 0.00????? 0.00??? -64.33 ???? number of scf cycles??? =?? 5 ???? number of bfgs steps??? =?? 4 ???? energy old????????????? =??? -492.3117315584 Ry ???? energy new????????????? =??? -493.0294336293 Ry ???? CASE: energy_new < energy_old ???? new trust radius??????? =?????? 0.8000000000 bohr ???? new conv_thr??????????? =??? ???0.0000010000 Ry ... ???? iteration # 89???? ecut=??? 36.00 Ry???? beta=0.70 ???? Davidson diagonalization with overlap ???? ethr =? 4.42E-08,? avg # of iterations =? 1.5 ???? total cpu time spent up to now is? 17055.30 secs ???? total energy????????????? =? -493.53120359 Ry ???? Harris-Foulkes estimate?? =? -493.53121645 Ry ???? estimated scf accuracy??? To: PWSCF Forum Sent: Friday, August 1, 2008 12:38:47 PM Subject: Re: [Pw_forum] convergence of relaxation caculation Dear Meisam, You would still need to provide input and output because "doesn't converge" means very little out of context. We need to see what that means. Besides, 5 scf cycles is not very many cycles. Is it possible that you mean atomic steps? Even so, it's still acceptable. Hande On Fri, 1 Aug 2008, meisam aghtar wrote: > Dear Stefano I didn?t change any parameters and they are in default mode. I used automatic meshing BZ,1*1*8.also I have not fixed any position. in output , after 5 scf cycles the system doesn?t converge. I think if I ?disrupt the position it would converge but I don?t know how I could make this system converge. ? ? Thanks for your attention. ? M.aghtar Msc student, physics department of Kashan university? -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande _______________________________________________ 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/20080801/e03b3edf/attachment-0001.htm From giannozz at democritos.it Fri Aug 1 10:37:16 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 01 Aug 2008 10:37:16 +0200 Subject: [Pw_forum] convergence of relaxation caculation In-Reply-To: <805307.4651.qm@web30607.mail.mud.yahoo.com> References: <805307.4651.qm@web30607.mail.mud.yahoo.com> Message-ID: <4892CB3C.80504@democritos.it> meisam aghtar wrote: > I didn?t change any parameters and they are in default mode. really? in your earlier post, you mentioned that > I changed some parameters such as Kpoint,con-thr , mixing method , > mixing-beta ,ecutrho, etc but it didn?t work. anyway: > What should I do? you should read the following section: http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_(PWscf)#self-consistency_is_slow_or_does_not_converge in particular the second paragraph, since it looks to me very likely that your system can become metallic in some steps of the calculation, so without a small broadening it will never converge Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From hande at newton.physics.metu.edu.tr Fri Aug 1 10:51:31 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Fri, 1 Aug 2008 11:51:31 +0300 (EEST) Subject: [Pw_forum] convergence of relaxation caculation In-Reply-To: <398735.25108.qm@web30601.mail.mud.yahoo.com> Message-ID: Dear Meisam, I still don't have a clear idea of how exactly the system fails to converge but since you've hit about 100 electronic steps, it looks to me like a typical case of charge sloshing with oscillating energies. This happens a lot when one or more dimensions of your simulation cell is much larger than the others. Try adding smearing, which sometimes tends to stabilize the convergence (I don't really know why but maybe because it introduces empty states which act as more degrees of freedom the system can explore?) and which is something you should do anyway because you have no idea whether this system would be a metal or not. As an aside, carbon nanotubes have been widely studied as hydrogen storage materials and by themselves they are not that great. You usually need some metal such as Ti. As a second aside I'd be really surprised if this system held together with that many hydrogens on the inner sides of a NT. Hope this helps. Hande On Fri, 1 Aug 2008, meisam aghtar wrote: > ?&SYSTEM ?????????????????????? ibrav = 4, ?????????????????? celldm(1) = 32, ?????????????????? celldm(3) = 0.251568464, ???????????????????????? nat = 80, ? ??????????????????????ntyp = 2, ???????????????????? ecutwfc = 36 , ???????????????????? ecutrho = 400 , ??????????????????????? ?/ ?&ELECTRONS ?/ ?&IONS ?/ ATOMIC_SPECIES ??? C?? 12.01070? C.pz-vbc.UPF ??? H??? 1.00794? H.vbc.UPF ATOMIC_POSITIONS angstrom C???? 3.91443516? 0.00000000? -1.42000000 C???? 3.16684457? 2.30084726? -1.42000000 C???? 1.20962699? 3.72284906? -1.42000000 C???? -1.209626993.72284906? -1.42000000 C???? -3.166844572.30084726? -1.42000000 C???? -3.914435160.00000000? -1.42000000 C???? -3.16684457-2.30084726-1.42000000 C???? -1.20962699-3.72284906-1.42000000 C???? 1.20962699? -3.72284906-1.42000000 C???? 3.16684457? -2.30084726-1.42000000 C???? 3.72284906? 1.20962699? -0.71000000 C???? 2.30084726? 3.16684457? -0.71000000 C???? 0.00000000? 3.91443516? -0.71000000 C???? -2.300847263.16684457? -0.71000000 C???? -3.722849061.20962699? -0.71000000 C???? -3.72284906-1.20962699-0.71000000 C???? -2.30084726-3.16684457-0.71000000 C???? 0.00000000? -3.91443516-0.71000000 C???? 2.30084726? -3.16684457-0.71000000 C???? 3.72284906? -1.20962699-0.71000000 C???? 3.72284906? 1.20962699? 0.71000000 C???? 2.30084726? 3.16684457? 0.71000000 C???? 0.00000000? 3.91443516? 0.71000000 C???? -2.300847263.16684457? 0.71000000 C???? -3.722849061.20962699? 0.71000000 C???? -3.72284906-1.209626990.71000000 C???? -2.30084726-3.166844570.71000000 C???? 0.00000000? -3.914435160.71000000 C???? 2.30084726? -3.166844570.71000000 C???? 3.72284906? -1.209626990.71000000 C???? 3.91443516? 0.00000000? 1.42000000 C???? 3.16684457? 2.30084726? 1.42000000 C???? 1.20962699? 3.72284906? 1.42000000 C???? -1.209626993.72284906? 1.42000000 C???? -3.166844572.30084726? 1.42000000 C???? -3.914435160.00000000? 1.42000000 C???? -3.16684457-2.300847261.42000000 C???? -1.20962699-3.722849061.42000000 C???? 1.20962699? -3.722849061.42000000 C???? 3.16684457? -2.300847261.42000000 H???? 2.82443516? 0.00000000? -1.42000000 H???? 2.28501604? 1.66016133? -1.42000000 H???? 0.87279846? 2.68619746? -1.42000000 H???? -0.872798462.68619746? -1.42000000 H???? -2.285016041.66016133? -1.42000000 H???? -2.824435160.00000000? -1.42000000 H???? -2.28501604-1.66016133-1.42000000 H???? -0.87279846-2.68619746-1.42000000 H???? 0.87279846? -2.68619746-1.42000000 H???? 2.28501604? -1.66016133-1.42000000 H???? 2.68619746? 0.87279846? -0.71000000 H???? 1.66016133? 2.28501604? -0.71000000 H???? 0.00000000? 2.82443516? -0.71000000 H???? -1.660161332.28501604? -0.71000000 H???? -2.686197460.87279846? -0.71000000 H???? -2.68619746-0.87279846-0.71000000 H???? -1.66016133-2.28501604-0.71000000 H???? 0.00000000? -2.82443516-0.71000000 H???? 1.66016133? -2.28501604-0.71000000 H???? 2.68619746? -0.87279846-0.71000000 H???? 2.68619746? 0.87279846? 0.71000000 H???? 1.66016133? 2.28501604? 0.71000000 H???? 0.00000000? 2.82443516? 0.71000000 H???? -1.660161332.28501604? 0.71000000 H???? -2.686197460.87279846? 0.71000000 H???? -2.68619746-0.872798460.71000000 H???? -1.66016133-2.285016040.71000000 H???? 0.00000000? -2.824435160.71000000 H???? 1.66016133? -2.285016040.71000000 H???? 2.68619746? -0.872798460.71000000 H???? 2.82443516? 0.00000000? 1.42000000 H???? 2.28501604? 1.66016133? 1.42000000 H???? 0.87279846? 2.68619746? 1.42000000 H???? -0.872798462.68619746? 1.42000000 H???? -2.285016041.66016133? 1.42000000 H???? -2.824435160.00000000? 1.42000000 H???? -2.28501604-1.660161331.42000000 H???? -0.87279846-2.686197461.42000000 H???? 0.87279846? -2.686197461.42000000 H???? 2.28501604? -1.660161331.42000000 ??? K_POINTS automatic ? 1 1 8?? 0 0 1 output: ... Total force =???? 0.764727???? Total SCF correction =???? 0.001974 ???? entering subroutine stress ... ????????? total?? stress? (Ry/bohr**3)?????????????????? (kbar)???? P=? -46.33 ? -0.00030189? ?0.00000000?? 0.00000000??????? -44.41????? 0.00????? 0.00 ?? 0.00000000? -0.00020564?? 0.00000000????????? 0.00??? -30.25????? 0.00 ?? 0.00000000?? 0.00000000? -0.00043733????????? 0.00????? 0.00??? -64.33 ???? number of scf cycles??? =?? 5 ???? number of bfgs steps??? =?? 4 ???? energy old????????????? =??? -492.3117315584 Ry ???? energy new????????????? =??? -493.0294336293 Ry ???? CASE: energy_new < energy_old ???? new trust radius??????? =?????? 0.8000000000 bohr ???? new conv_thr??????????? =??? ???0.0000010000 Ry ... ???? iteration # 89???? ecut=??? 36.00 Ry???? beta=0.70 ???? Davidson diagonalization with overlap ???? ethr =? 4.42E-08,? avg # of iterations =? 1.5 ???? total cpu time spent up to now is? 17055.30 secs ???? total energy????????????? =? -493.53120359 Ry ???? Harris-Foulkes estimate?? =? -493.53121645 Ry ???? estimated scf accuracy??? To: PWSCF Forum Sent: Friday, August 1, 2008 12:38:47 PM Subject: Re: [Pw_forum] convergence of relaxation caculation Dear Meisam, You would still need to provide input and output because "doesn't converge" means very little out of context. We need to see what that means. Besides, 5 scf cycles is not very many cycles. Is it possible that you mean atomic steps? Even so, it's still acceptable. Hande On Fri, 1 Aug 2008, meisam aghtar wrote: > Dear Stefano I didn?t change any parameters and they are in default mode. I used automatic meshing BZ,1*1*8.also I have not fixed any position. in output , after 5 scf cycles the system doesn?t converge. I think if I ?disrupt the position it would converge but I don?t know how I could make this system converge. ? ? Thanks for your attention. ? M.aghtar Msc student, physics department of Kashan university? -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From munima at iitg.ernet.in Fri Aug 1 12:19:16 2008 From: munima at iitg.ernet.in (Munima Bora Sahariah) Date: Fri, 1 Aug 2008 15:49:16 +0530 (IST) Subject: [Pw_forum] GGA underestimates lattice constant in BaO In-Reply-To: <573C6D11-4F73-4B0B-A134-BFF6B7A3DA26@democritos.it> References: <39790.210.212.8.60.1216792727.squirrel@webmail.iitg.ac.in> <573C6D11-4F73-4B0B-A134-BFF6B7A3DA26@democritos.it> Message-ID: <48413.125.20.8.170.1217585956.squirrel@webmail.iitg.ac.in> Dear Paolo Thanks for your reply. In fact I tried GGA(PBE) also. In this case the lattice parameter is better than GGA(pw91) (PBE = 10.313 a.u.) but is still less than that of LDA. If I generate new pseudopotentials for Ba, primarily which parameters would you suggest me to tune in order to improve the quality? regards munima > > On Jul 23, 2008, at 7:58 , Munima Bora Sahariah wrote: > >> For last couple of days I have been trying to find the equilibrium >> lattice >> constant of BaO with GGA (pw91) and has found that my calculated >> value >> underestimates the experimental one by 1.3% (GGA = 10.301 a.u., EXP = >> 10.431 a.u.). Surprizingly, while trying with LDA, I obtained a value >> which is closer to the experimental one as compared to GGA (LDA = >> 10.324 >> a.u.) [...] >> While doing a search on the web, I found one paper (Phys. Rev. B 71, >> 085203) where GGA and LDA results for lattice constant of BaO have >> been >> listed. In this paper calculations were done in CASTEP. Here the >> LDA value >> underestimates the experimental lattice constant while the GGA >> (pw91) value >> improves the situation and is closer to the experimental one. > > try different pseudopotentials if you can: this might be one of those > cases > in which the results are more sensitive than desired to the quality of > pseudopotentials (in particular of Ba). > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > Dr. Munima B. Sahariah PI, DST Fast Track Project IASST, Guwahati Assam, INDIA ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ac.in From hande at newton.physics.metu.edu.tr Fri Aug 1 12:29:23 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Fri, 1 Aug 2008 13:29:23 +0300 (EEST) Subject: [Pw_forum] GGA underestimates lattice constant in BaO In-Reply-To: <573C6D11-4F73-4B0B-A134-BFF6B7A3DA26@democritos.it> Message-ID: Dear Munima, I also ran into the exact same problem just yesterday using the PBE pseudopotential from the web site. The lattice constant that you quote is almost identical to the one I obtained. Inspired by your post, I calculated the lattice constant for BaS to compare to the result in the paper you quote and it matches better (almost the same as the experimental value). I don't know if this is supposed to make us feel better. I also thought of generating a new pseudopotential but as far as I know, the generator cannot include two orbitals of the same l even though they might be from different shells. Thus we couldn't include 5s and 6s orbitals simultaneously. Am I right? I would also appreciate thoughts on what we could do or pseudopotentials that have been converted from other codes if there are any lying around. Thank you very much. Best, Hande On Fri, 1 Aug 2008, Paolo Giannozzi wrote: > > On Jul 23, 2008, at 7:58 , Munima Bora Sahariah wrote: > > > For last couple of days I have been trying to find the equilibrium > > lattice > > constant of BaO with GGA (pw91) and has found that my calculated > > value > > underestimates the experimental one by 1.3% (GGA = 10.301 a.u., EXP = > > 10.431 a.u.). Surprizingly, while trying with LDA, I obtained a value > > which is closer to the experimental one as compared to GGA (LDA = > > 10.324 > > a.u.) [...] > > While doing a search on the web, I found one paper (Phys. Rev. B 71, > > 085203) where GGA and LDA results for lattice constant of BaO have > > been > > listed. In this paper calculations were done in CASTEP. Here the > > LDA value > > underestimates the experimental lattice constant while the GGA > > (pw91) value > > improves the situation and is closer to the experimental one. > > try different pseudopotentials if you can: this might be one of those > cases > in which the results are more sensitive than desired to the quality of > pseudopotentials (in particular of Ba). > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From iphyboy at hotmail.com Fri Aug 1 13:36:39 2008 From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=) Date: Fri, 1 Aug 2008 19:36:39 +0800 Subject: [Pw_forum] electron-interaction at any given q-point Message-ID: Dear all: I want to calculate the electron phonon interaction of any given q-point, but as far as I know,the phonon code can only the q-point in a q-grid. so, can anyone give me some suggestion on how to do this ? Thanks very much ! Wenmei Ming _________________________________________________________________ ?????MSN?????????? http://im.live.cn/click/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080801/d420f86c/attachment.htm From iphyboy at hotmail.com Fri Aug 1 13:40:08 2008 From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=) Date: Fri, 1 Aug 2008 19:40:08 +0800 Subject: [Pw_forum] electron-interaction in a given q point Message-ID: Dear all: Sorry, just now I did not express myself clearly. I want to calculate the electron phonon interaction of any given q-point,but as far as I know,the phonon code can only calculate the electron phonon interaction of the q-point in a q-grid. so, can anyone give me some suggestion on how to do this ? Thanks very much ! Wenmei Ming _________________________________________________________________ ???MSN??????????????????? http://mobile.msn.com.cn/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080801/9eba484d/attachment.htm From giannozz at democritos.it Fri Aug 1 15:06:01 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 1 Aug 2008 15:06:01 +0200 Subject: [Pw_forum] electron-interaction in a given q point In-Reply-To: References: Message-ID: On Aug 1, 2008, at 13:40 , ??? wrote: > I want to calculate the electron phonon interaction of any given q- > point, > but as far as I know,the phonon code can only calculate the > electron phonon > interaction of the q-point in a q-grid. > so, can anyone give me some suggestion on how to do this ? it was possible in older versions (I think < 3) of the code. You can try to install an old version, or to replace the new electron-phonon code with the old one (it should be quite straightforward) Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From akohlmey at cmm.chem.upenn.edu Fri Aug 1 16:05:48 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 1 Aug 2008 10:05:48 -0400 (EDT) Subject: [Pw_forum] convergence of relaxation caculation In-Reply-To: <398735.25108.qm@web30601.mail.mud.yahoo.com> References: <398735.25108.qm@web30601.mail.mud.yahoo.com> Message-ID: On Fri, 1 Aug 2008, meisam aghtar wrote: dear meisam, please note, that you are using norm-conserving pseudopotentials yet wavefunction and density cutoff parameters as if it were ultra-soft potentials. this means your wavefunction cutoff is too small and your density cutoff too large (no gain from going higher than 4x ecutwfc). did you make any tests of those pseudopotentials? e.g. on a small graphene sheet or a benzene/naphtaline molecule?? cheers, axel. MA> ?&SYSTEM ?????????????????????? ibrav = 4, ?????????????????? celldm(1) = 32, ?????????????????? celldm(3) = 0.251568464, ???????????????????????? nat = 80, ? ??????????????????????ntyp = 2, ???????????????????? ecutwfc = 36 , ???????????????????? ecutrho = 400 , ??????????????????????? [...] ??? C?? 12.01070? C.pz-vbc.UPF ??? H??? 1.00794? H.vbc.UPF -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From amosleffler at sbcglobal.net Sat Aug 2 02:07:15 2008 From: amosleffler at sbcglobal.net (Amos Leffler) Date: Fri, 1 Aug 2008 17:07:15 -0700 Subject: [Pw_forum] Electron-phonon calculations in Examples 02 and 07. Message-ID: <505EFF5EBC8A45B2A91AC31BDD1EFBB1@leffler2> Dear Forum, On May 12 Dong Hee Lim reported a problem with Example 02 when running espresso-4.0.1. Paolo G. asked for more details but I have not seen any since then. I am reporting a similar problem with some of the output. These were run using espresso-4.0.1 in serial mode using a fortran g95 fortran compiler. /home/amos/Desktop/espresso-4.0.1/examples/example02 env LD_LIBRARY_PATH=/opt/intel/mkl/10.0.3.020/lib/em64t ./run_example This example shows how to use pw.x and ph.x to calculate phonon frequencies at Gamma and X for Si and C in the diamond structure and for fcc-Ni executables directory: /home/amos/Desktop/espresso-4.0.1/bin pseudo directory: /home/amos/Desktop/espresso-4.0.1/pseudo temporary directory /home/amos/tmp checking that needed directories and files exist... done running pw.x as : /home/amos/Desktop/espresso-4.0.1/bin/pw.x running ph.x as : /home/amos/Desktop/espresso-4.0.1/bin/ph.x cleaning /home/amos/tmp... done running the scf calculation... done running the phonon calculation at Gamma... done running the nscf calculation at X for a single mode... done running the phonon calculation at X for a single mode ... STOP 2 Error condition encountered during test: exit status = 2 Aborting Example 07 This gives the same sort of sequence through running pw.x, ph.x, q2r.x, matdyn.x. It then goes through: cleaning /home/amos/tmp. running the scf calculation with dense k-point grid... done running the scf calculation... done running the el-ph calculation... STOP 2 Error condtion encountered during test: exit status = 2 Aborting Both examples stop in the same portion of the run_example and probably have the same cause. Some other examples complete properly but I have not tested all of them Amos Leffler. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080801/67473f14/attachment.htm From iphyboy at hotmail.com Sat Aug 2 19:03:25 2008 From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=) Date: Sun, 3 Aug 2008 01:03:25 +0800 Subject: [Pw_forum] spin-polarized calculation in optimizing lattice Message-ID: Dear all: I have a very step-in question: when optimizing the lattice,should the magnetism calculation be included ? or just the none spin-polarized calculation is OK ? I think that for a solid possessing magnetism the magnetism calculation should be used to obtain the relaxed lattice in optimizing lattice. am I right? Any suggestion is greatly appreciated . Thanks very much ! Wenmei Ming _________________________________________________________________ ??????????????? http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AA&Form=MEVHAA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080803/e91a0664/attachment.htm From giannozz at democritos.it Sat Aug 2 21:55:55 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 2 Aug 2008 20:55:55 +0100 Subject: [Pw_forum] Electron-phonon calculations in Examples 02 and 07. In-Reply-To: <505EFF5EBC8A45B2A91AC31BDD1EFBB1@leffler2> References: <505EFF5EBC8A45B2A91AC31BDD1EFBB1@leffler2> Message-ID: <200808022155.55964.giannozz@democritos.it> On Saturday 02 August 2008 02:07, Amos Leffler wrote: > On May 12 Dong Hee Lim reported a problem with Example 02 when > running espresso-4.0.1. Paolo G. asked for more details but I have not > seen any since then. I am reporting a similar problem with some of the > output. These were run using espresso-4.0.1 in serial mode using a fortran > g95 fortran compiler [...]. > running the phonon calculation at X for a single mode ... STOP 2 ...and? -- Paolo Giannozzi, Democritos and Udine University From eyvaz_isaev at yahoo.com Sun Aug 3 01:49:10 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 2 Aug 2008 16:49:10 -0700 (PDT) Subject: [Pw_forum] spin-polarized calculation in optimizing lattice Message-ID: <744019.54021.qm@web65702.mail.ac4.yahoo.com> Dear Wenmei, Yes, of course, if you have a magnetic system, you should carry out spin-polarized calculations. But, as magnetic calculations are twice expensive, you can first try relax nonmagnetic system and then turn on magnetism using basis vectors and atomic positions you obtained. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: ??? To: pw_forum at pwscf.org Sent: Saturday, August 2, 2008 7:03:25 PM Subject: [Pw_forum] spin-polarized calculation in optimizing lattice Dear all: I have a very step-in question: when optimizing the lattice,should the magnetism calculation be included ? or just the none spin-polarized calculation is OK ? I think that for a solid possessing magnetism the magnetism calculation should be used to obtain the relaxed lattice in optimizing lattice. am I right? Any suggestion is greatly appreciated . Thanks very much ! Wenmei Ming ________________________________ ????? Windows Live Messenger ???????? ????? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080802/e7275d58/attachment.htm From padmaja_patnaik at yahoo.co.uk Sun Aug 3 04:27:33 2008 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Sun, 3 Aug 2008 02:27:33 +0000 (GMT) Subject: [Pw_forum] (no subject) Message-ID: <770827.79828.qm@web25405.mail.ukl.yahoo.com> Dear all I have doubt in calculating magnetic moment.? Found few communications on this topic but no where a clear answer is found. If i want to find out the magnetic moment of an atom in a system, how am i going to get it. After doing the pdos calculations the *.pdos.out file is obtined which contains the Lowdin charges. For example say the following is the portion of the Lowdin charges obtained. Lowdin Charges: Atom # 5: total charge = 4.5686, s, p, d, f = 0.2749 0.8321 3.4616 spin up = 2.9945, s, p, d, f = 0.1449 0.4269 2.4227 spin down = 1.5742, s, p, d, f = 0.1300 0.4052 1.0390 polarization = 1.4203, s, p, d, f = 0.0149 0.0217 1.3837 How do i get the magnetic moment for the atom 5 from this? The total magnetization is reflected in the *.scf.out file. Is there any formula regarding this? Please advise. Thanks in advance regards Padmaja Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India __________________________________________________________ Not happy with your email address?. Get the one you really want - millions of new email addresses available now at Yahoo! http://uk.docs.yahoo.com/ymail/new.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080803/3ef68bda/attachment.htm From mansourehp at gmail.com Sun Aug 3 04:32:43 2008 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Sun, 3 Aug 2008 06:02:43 +0330 Subject: [Pw_forum] dos and pdos Message-ID: Dear all I otain dos and odos plots a bit lower than zero.how can I correct them.dose it correct with increasing k points or k mesh.I chose 6 6 3 for k points.if I use 18 18 9 it migth be better? good luck Mansoureh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080803/d95b98df/attachment.htm From sauluck at iitk.ac.in Sun Aug 3 09:52:51 2008 From: sauluck at iitk.ac.in (Sushil Auluck) Date: Sun, 03 Aug 2008 13:22:51 +0530 Subject: [Pw_forum] (no subject) In-Reply-To: <770827.79828.qm@web25405.mail.ukl.yahoo.com> References: <770827.79828.qm@web25405.mail.ukl.yahoo.com> Message-ID: <489563D3.7080803@iitk.ac.in> hi, the output which you have given has the answer to your question. magnetic moment is polarisation. and it is coming from the d electrons. the equations are (for number of electrons) N_total = N_up + N_down Moment = N_up - N_down (or down - up ) s.auluck -- ....................................................................... Prof. Sushil Auluck Phone:+91-512-6797092/6148 Department of Physics +91-512-6798177(Home) Indian Institute of Technology Cell :+91-9305548667 Kanpur 208016 (UP) Fax :+91-512-6790914 India E-mail:sauluck at iitk.ac.in ...............................................:sauluck at gmail.com http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html ....................................................................... From lfhuang at theory.issp.ac.cn Sun Aug 3 10:31:31 2008 From: lfhuang at theory.issp.ac.cn (L.F.Huang) Date: Sun, 3 Aug 2008 16:31:31 +0800 (CST) Subject: [Pw_forum] dos and pdos Message-ID: <32823.210.73.17.131.1217752291.squirrel@210.73.16.4> Dear Mansoureh Pashangpour: Could you tell us what is your system? I have encountered your problem ago when I calculating phonon dispersions of graphene and graphite. And I finally solve it with painfull testings. Besides k points grid, maybe there are some other parameters you should pay attention to: ecutwfc; ecutrho: maybe above ten times of ecutwfc; conv_thr: 1d*-12 maybe good enouph for pw.x; tr2_ph: in some cases, especially surface and layered systems, even 1d*-18 may be necessary; FFT grid: you can try to increase nr1 nr2 nr3 to see what will happen; ZAR: you can take 'simple' or 'crystal' in the input file of q2r.x and matdyn.x.; Beside these personal comments, I would like to thank prof. Dal Corsov for his brief guide for me on these problems in Shanghai China in July! ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== From hande at newton.physics.metu.edu.tr Sun Aug 3 11:19:24 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Sun, 3 Aug 2008 12:19:24 +0300 (EEST) Subject: [Pw_forum] dos and pdos In-Reply-To: Message-ID: Dear Mansoureh, It might be due to your smearing scheme. Try Marzari-Vanderbilt or Gaussian. Best, Hande On Sun, 3 Aug 2008, Mansoureh Pashangpour wrote: > Dear all > I otain dos and odos plots a bit lower than zero.how can I correct them.dose > it correct with increasing k points or k mesh.I chose 6 6 3 for k points.if > I use 18 18 9 it migth be better? > good luck > Mansoureh > -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From prasenjit.jnc at gmail.com Sun Aug 3 11:57:38 2008 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Sun, 3 Aug 2008 11:57:38 +0200 Subject: [Pw_forum] dos and pdos In-Reply-To: References: Message-ID: <627e0ffa0808030257x229992fct3768a2e48664533d@mail.gmail.com> try using Gaussian smearing..............most probably ur using Mathfessel-Paxton smearing. Prasenjit. 2008/8/3 Hande Ustunel > Dear Mansoureh, > > It might be due to your smearing scheme. Try Marzari-Vanderbilt or > Gaussian. > > Best, > Hande > > On Sun, 3 Aug 2008, Mansoureh Pashangpour wrote: > > > Dear all > > I otain dos and odos plots a bit lower than zero.how can I correct > them.dose > > it correct with increasing k points or k mesh.I chose 6 6 3 for k > points.if > > I use 18 18 9 it migth be better > > good luck > > Mansoureh > > > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080803/5eef434f/attachment.htm From giannozz at democritos.it Sun Aug 3 21:52:54 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 3 Aug 2008 21:52:54 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <770827.79828.qm@web25405.mail.ukl.yahoo.com> References: <770827.79828.qm@web25405.mail.ukl.yahoo.com> Message-ID: <200808032152.55476.giannozz@democritos.it> On Sunday 03 August 2008 04:27, Padmaja Patnaik wrote: > I have doubt in calculating magnetic moment.? Found few communications > on this topic but no where a clear answer is found. If i want to find out > the magnetic moment of an atom in a system, how am i going to get it. a clear answer has been given many times on this forum: there is no such thing as "the magnetic moment of an atom in a system". You can define such a quantity by using appropriate projections onto atomic or atomic-like wavefunctions or partition of the charge into domains, but the results will depend upon the choice of the procedure > Lowdin Charges: > Atom # 5: total charge = 4.5686, s, p, d, f = 0.2749 0.8321 3.4616 > spin up = 2.9945, s, p, d, f = 0.1449 0.4269 2.4227 > spin down = 1.5742, s, p, d, f = 0.1300 0.4052 1.0390 > polarization = 1.4203, s, p, d, f = 0.0149 0.0217 1.3837 > > How do i get the magnetic moment for the atom 5 from this? hint: polarization = spin up - spin down. Of course if you are looking for orbital contributions as well things are much more complicated Paolo -- Paolo Giannozzi, Democritos and Udine University From chenhanghuipwscf at gmail.com Mon Aug 4 05:04:34 2008 From: chenhanghuipwscf at gmail.com (alan chen) Date: Sun, 3 Aug 2008 23:04:34 -0400 Subject: [Pw_forum] Finite electric field calculation Message-ID: <22ae3ca40808032004m72d1a19ey20c9bdd8ef1e080b@mail.gmail.com> Dear PWSCF users, I have two questions about finite electric field calculation based on Berry phase. First, I have found in the source code that the formula to calcuate the polarization in the presence of finite electric field is different in Version 4.0 from in Version 3.2. A couple of factors like sqrt(2) and alat are added in the new version. I just want to make sure that if I use ultrasoft psedupotential and turn on finite electric field, does the latest version (4.0) of PWSCF calculate the polarization and atomic force correctly? No offense intended. Second, is there a range of electric field in which the Berry phase method works? In the example31 the electric field is 0.001 a.u. I want to calculate some properties under the electric field as large as 0.01 a.u. In principle I think the method works for any value of electric field but in practice any restriction on the maximum of electric field? Thank you very much. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080803/b928b068/attachment.htm From marzari at MIT.EDU Mon Aug 4 07:34:23 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Mon, 04 Aug 2008 13:34:23 +0800 Subject: [Pw_forum] Finite electric field calculation In-Reply-To: <22ae3ca40808032004m72d1a19ey20c9bdd8ef1e080b@mail.gmail.com> References: <22ae3ca40808032004m72d1a19ey20c9bdd8ef1e080b@mail.gmail.com> Message-ID: <489694DF.4090709@mit.edu> Dear Hanghui, Paolo Umari might be better suited to answer the first question - he has fixed a few things lately, mostly to allow fields in arbitrary directions (I think). On the second one, I might be more helpful - as the electric field increases, or the k-point sampling becomes finer, the system will fall into a "runaway" solution, and not converge. This is the computational counterpart of the fact that in a periodic system in an electric field the energy is strictly unbound from below (that's where you "run away" - an inescapable fall into the abyss that silently awaits). The ground states of the electric enthalpy are interpreted as the metastable solutions corresponding to a physical system in which you adiabatically turn on a field, and whose actual lifetimes can be much longer that any experiment would be. Details in abundance in the 2002 (?) PRLs of Umari/Pasquarello and of Souza/Iniguez/Vanderbilt, plus I believe later PRBs from the same groups. nicola alan chen wrote: > Dear PWSCF users, > I have two questions about finite electric field calculation based > on Berry phase. > First, I have found in the source code that the formula to calcuate > the polarization in the presence of finite electric field is different > in Version 4.0 from in Version 3.2. A couple of factors like sqrt(2) and > alat are added in the new version. I just want to make sure that if I > use ultrasoft psedupotential and turn on finite electric field, does the > latest version (4.0) of PWSCF calculate the polarization and atomic > force correctly? No offense intended. > Second, is there a range of electric field in which the Berry phase > method works? In the example31 the electric field is 0.001 a.u. I want > to calculate some properties under the electric field as large as 0.01 > a.u. In principle I think the method works for any value of electric > field but in practice any restriction on the maximum of electric field? > Thank you very much. > > Hanghui Chen > Department of Physics > Yale University > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From degironc at sissa.it Mon Aug 4 09:59:36 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 04 Aug 2008 09:59:36 +0200 Subject: [Pw_forum] Electron-phonon calculations in Examples 02 and 07. In-Reply-To: <505EFF5EBC8A45B2A91AC31BDD1EFBB1@leffler2> References: <505EFF5EBC8A45B2A91AC31BDD1EFBB1@leffler2> Message-ID: <4896B6E8.8090000@sissa.it> Dear Amos Leffler, what you are showing us is the error found by the script, which says that ...there was an error. have you verified the content of the several output files that are created by the codes in the result directory? they might be more informative and you may discover that you not even need our help... best regards, stefano Amos Leffler wrote: > Dear Forum, > On May 12 Dong Hee Lim reported a problem with Example 02 when > running espresso-4.0.1. Paolo G. asked for more details but I have > not seen any since then. I am reporting a similar problem with some > of the output. These were run using espresso-4.0.1 in serial mode > using a fortran g95 fortran compiler. > > /home/amos/Desktop/espresso-4.0.1/examples/example02 > env LD_LIBRARY_PATH=/opt/intel/mkl/10.0.3.020/lib/em64t ./run_example > > This example shows how to use pw.x and ph.x to calculate phonon > frequencies at Gamma and X for Si and C > in the diamond structure and for fcc-Ni > > executables directory: /home/amos/Desktop/espresso-4.0.1/bin > pseudo directory: /home/amos/Desktop/espresso-4.0.1/pseudo > temporary directory /home/amos/tmp > > checking that needed directories and files exist... done > > running pw.x as : /home/amos/Desktop/espresso-4.0.1/bin/pw.x > running ph.x as : /home/amos/Desktop/espresso-4.0.1/bin/ph.x > > cleaning /home/amos/tmp... done > running the scf calculation... done > running the phonon calculation at Gamma... done > running the nscf calculation at X for a single mode... done > running the phonon calculation at X for a single mode ... STOP 2 > Error condition encountered during test: exit status = 2 > Aborting > > Example 07 > > This gives the same sort of sequence through running pw.x, ph.x, > q2r.x, matdyn.x. It then goes through: cleaning /home/amos/tmp. > > running the scf calculation with dense k-point grid... done > running the scf calculation... done > running the el-ph calculation... STOP 2 > Error condtion encountered during test: exit status = 2 > Aborting > > Both examples stop in the same portion of the run_example and probably > have the same cause. Some other examples complete properly but I have > not tested all of them > > > Amos Leffler. > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From degironc at sissa.it Mon Aug 4 10:39:26 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 04 Aug 2008 10:39:26 +0200 Subject: [Pw_forum] optimization of any structure In-Reply-To: <627e0ffa0807300057kd2d4bbfx84a9df40fa727727@mail.gmail.com> References: <20080730062814.2100.qmail@f4mail-235-220.rediffmail.com> <627e0ffa0807300057kd2d4bbfx84a9df40fa727727@mail.gmail.com> Message-ID: <4896C03E.9000502@sissa.it> Dar Sathya, Starting from version 4.0 there is an additional option for the vc-relaxation that may be worth trying. Just specify cell_dymanics='bfgs' in the &CELL namelist (and ion_dymanics='bfgs' in &IONS) and the optimization will be done with a quasi-newton bfgs algorithm. It has been recently implemented, report to the list in case of problems best regards, stefano PS: as already noticed by others etot_conv_thr = 1.0E-10 and forc_conv_thr = 1.0D-10 are extremely tight thresholds ... Start using the default values and then modify them to get your own feeling on what is a good threshold for your system... Prasenjit Ghosh wrote: > Dear Sathya, > > I have no experience in using 'vc-relax'.......so I can't help you out > on this. Either you wait for other people's comments or you can search > the pw forum mailing list. There were discussions regarding this > earlier in this forum. I said its tricky because you need to choose > different parameters correctly to reach the minima quickly and > correctly. What I would suggest is to play around with different > parameters for some small system and understand how they affects the > calculation. Later you can go for production run. > > Prasenjit. > > 2008/7/30 sathya subramanyan > > > > Dear Dr. Prasenjit, > Thank you so much for your reply and the link. > I'm doing the vc-relax calculation but it has > been running for more than 36 hours.Is this why you have mentioned > that vc-relax is tricky ? I have attached the I/P file for > reference and if you could please take a look at it. > I'm also trying the manual relaxation and will > let you know the status of my results. > > INPUT FILE FOR VC-RELAX > > &CONTROL > calculation = "vc-relax" , > restart_mode = 'from_scratch' , > outdir='/home/413107002/tmp/' , > pseudo_dir = '/home/413107002/espresso-4.0.1/pseudo' , > nstep = 1000 , > etot_conv_thr = 1.0E-10 , > forc_conv_thr = 1.0D-10 , > dt = 150 , > / > &SYSTEM > ibrav = 6 , > celldm(1)=7.373 , > celldm(3)=1.065, > nat = 5 , > ntyp = 3 , > ecutwfc = 30.0, > ecutrho = 300.0 , > occupations = 'fixed' , > degauss = 0.00 , > / > &ELECTRONS > conv_thr = 1.0d-10 , > diagonalization = 'david' , > / > &IONS > ion_dynamics = 'damp' > / > &CELL > cell_dynamics = 'damp-w' , > > / > ATOMIC_SPECIES > Pb 207.2 Pb.vdb.UPF > Ti 47.867 Ti.vdb.UPF > O 15.9994 O.vdb.UPF > ATOMIC_POSITIONS > Pb 0.000 0.000 0.000 > Ti 0.500 0.500 0.538 > O 0.500 0.000 0.612 > O 0.000 0.500 0.612 > O 0.500 0.500 0.117 > K_POINTS {automatic} > 4 4 4 1 1 1 > > Thanking you, > > SATHYA SHEELA.S > Grad. Student > Department of Physics > National Institute of Technology > Tiruchirapalli - 620015 > India > > HP > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > +39 3807528672 (M) > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From umari at democritos.it Mon Aug 4 10:43:16 2008 From: umari at democritos.it (umari at democritos.it) Date: Mon, 04 Aug 2008 10:43:16 +0200 Subject: [Pw_forum] finite electric field calculation (Paolo Umari) Message-ID: <20080804104316.kot6tnzqckgw800o@mail.democritos.it> Dear Alan, > I have two questions about finite electric field calculation based on > Berry phase. > First, I have found in the source code that the formula to calcuate the > polarization in the presence of finite electric field is different in > Version 4.0 from in Version 3.2. A couple of factors like sqrt(2) and alat > are added in the new version. I just want to make sure that if I use > ultrasoft psedupotential and turn on finite electric field, does the latest > version (4.0) of PWSCF calculate the polarization and atomic force > correctly? No offense intended. In the version 3.2 the electric field intensity was erroneously divided by a factor of sqrt(2.), at the same time the reported polarization was multiplied by the same factor. Note that sqrt(2) is the value of the electronic charge in Rydberg atomic units (in Hartree atomic units this value is 1.) Note also that in the linear limit this error doesn't cause any change in the calculated polarizabilitis. Moreover, the version 4.0 has other improvents with respect to the 3.2: -better treatment of the quantum of polarization -it works also for non-orthorombic cells -parallel also for gdir=1, and gdir=2 -faster -atomic forces are correctly calculated also for US pseudopotentials I suggest you to see also the new cvs version, which permits to treat electric fields on arbitrary Cartesian directions and reports the polarization also on Cartesian coordinates. You can find some documentation in the exemple 31. > Second, is there a range of electric field in which the Berry phase > method works? In the example31 the electric field is 0.001 a.u. I want to > calculate some properties under the electric field as large as 0.01 a.u. In > principle I think the method works for any value of electric field but in > practice any restriction on the maximum of electric field? Above a certain maximum value of the electric field, which depends on the system and on the number of k-points in the string, the electric enthalpy functional can no longer be minimized. Based on my experience, usually elctric fields of 0.01 a.u. can be reached. Note that , depending on the studied system, non-linear effects can become important. Best regards, Paolo Umari DEMOCRITOS ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From degironc at sissa.it Mon Aug 4 13:00:12 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 04 Aug 2008 13:00:12 +0200 Subject: [Pw_forum] Small U for Co in ZnO for LDA+U In-Reply-To: <65c086de0807030422h78aea2a2qca3dd83493bf6ce4@mail.gmail.com> References: <414899242.31069@mail.sdu.edu.cn> <486C7CD8.5050802@mit.edu> <65c086de0807030422h78aea2a2qca3dd83493bf6ce4@mail.gmail.com> Message-ID: <4896E13C.7040000@sissa.it> Dear all, the occupation matrix for the LDA+U calculations is computed starting from the atomic wavefuncitons which are ASSUMED to be normalized... Unfortunately a number of pseudopotentials (especially US ones) that have been generated in the past did not enforce the normalization of the atomic wavefunctions. This went mostly unnoticed because this properties is not really needed in most situations were atomic wfc are used by pw.x... but it is important in LDA+U and the of use these pseudopotentials in LDA+U calculation results in "strange" occupations which are basically wrong... (other projection options like "ortho-atomic", or "norm-atomic", approximately orthogonalize the atomic wave-fuctions but this is done in a way that 1) is crystal dependent 2) makes technically more involved the calculation of forces and stress that are therefore disabled). To put an end to this problem in the CVS version (unfortunately not in 4.0 nor in 4.0.1) normalization of atomic wavefunctions is tested and enforced upon pseudopotential reading. If you experience stange unexpected behaviors using LDA+U please make sure to use the CVS version and report any problem that may still persist. Hope this helps, best regards, Stefano de Gironcoli Nektarios Lathiotakis wrote > Hi all, > > the option 'atomic' is the default and maybe that should change? I > dont know. It created > me a lot of trouble however. I confirm Shu-jun numbers (2.6 > occupations)... I get the same. > I think we used the same functional and consequently potentials for > Zn, O, Co (PBE functional). > > Shu-jun, did you use the same pseudo for Co in ZnO and SnO2? > > With the 'atomic' option in this case , U_Co=0.5 is enough to push all > Co-d states into the valence. The rule I found is that the U_Co with > option > 'atomic' has the same effect as 8*U with option 'ortho-atomic' on the > Co-d projected DOS. > > So the self consistent value of Shu-jun correspond to U=2.5eV with > ortho-atomic. Of course this applies to > the position of Co-d occupied bands. Dont know about other properties. > I will have to > repeat calculations with 'ortho-atomic' or 'norm-atomic' option. > > Thanks for the discussion > Nektarios > > On Thu, Jul 3, 2008 at 10:16 AM, Nicola Marzari > wrote: > > > > > Dear Shu-jun, All, > > > I get very nervous about using U with non-normalized occupations. Even > if U can have some amount of pseudopotential dependency, using it > with unnormalized projectors really messes up any meaningful > discussion > of occupation values and U values. > > And of course referees would go nuts at seeing that a U=0.3eV is > relevant - the reason is that that number doesn't really make sense. > > To me, it's an option ("atomic") that should be removed altogether > from > the code - others might have other opinions, but if we leave it as it > stands, we risk creating an enormous amount of headaches down the > line. > > nicola > > > > > ??? Shu-jun Hu wrote: > > Dear All, > > > > I would post my comments on the topic of LDA+U calculation of > small U_Co. > > > > (1) The self-consistently calculated U_Co is indeed sensitive to > the oxidation > > state of Co. In Co-doped ZnO DMS, the value is about 0.31 eV, a > very "small" > > number. However, in Co-doped SnO2, we got a "reasonable" value > of 3.7 eV. > > U_projection_type is specified as the default (atomic) in both > cases during the > > calculation of U_Co. > > > > (2) The calculated band structure is much sensitive to the value > of U_Co and > > U_Co=0.31 eV does have a significant effect with respect to U=0. > U_Co=0.31 eV can > > well fit the experimental results (APL 84 4233 (2004), and also > J. Appl. Phys. 103 > > 07D130 (2008)), where the occupied Co:3d majority state are deep > in the valence > > band rather than in the gap. If U_Co=2 to 5 eV is implemented, > Nektarios is right: > > a Co-d projected DOS far deep into the valence (completely non > sense). > > > > (3) The occupation is larger than 1 but not less than 1 in the > "atomic" case. A > > piece of output file is listed in the end. > > > > Best wishes. > > > > > -- > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu > http://quasiamore.mit.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > -------------------------------------------------------------------- > Dr. Nektarios N. Lathiotakis > -------------------------------------------------------------------- > Theoretical and Physical Chemistry Institute > National Hellenic Research Foundation > Vass. Constantinou 48, GR-11635, > Athens, Greece > -------------------------------------------------------------------- > Tel: +30 210 7273805 FAX: +30 210 7273794 > Inst. secretary: +30 210 7273792, +30 210 7273795 > -------------------------------------------------------------------- > Web: http:www.eie.gr/nhrf/institutes/tpci/cvs/cv-lathiotakis-en.html > > -------------------------------------------------------------------- > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From bipulrr at gmail.com Mon Aug 4 13:09:33 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Mon, 4 Aug 2008 16:39:33 +0530 Subject: [Pw_forum] cvs version of espresso Message-ID: <3a749910808040409o4457107br1c3963bbaf184c1c@mail.gmail.com> Hello pwscf user, I want to ask how to get and install the cvs version of espresso. I want to install in my laptop with ifort and mkl libraries and also in aix sp5 parallel machines. regards Bipul -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080804/d9c6cba0/attachment.htm From Giovanni.Cantele at na.infn.it Mon Aug 4 13:17:22 2008 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Mon, 04 Aug 2008 13:17:22 +0200 Subject: [Pw_forum] cvs version of espresso In-Reply-To: <3a749910808040409o4457107br1c3963bbaf184c1c@mail.gmail.com> References: <3a749910808040409o4457107br1c3963bbaf184c1c@mail.gmail.com> Message-ID: <4896E542.1010902@na.infn.it> Bipul Rakshit wrote: > Hello pwscf user, > I want to ask how to get and install the cvs version of espresso. I > want to install in my laptop with ifort and mkl libraries and also in > aix sp5 parallel machines. > regards > Bipul how to get: http://www.quantum-espresso.org/wiki/index.php/Developer_Manual#Using_CVS how to install: http://www.quantum-espresso.org/wiki/index.php/Installation how to install using ifort + mkl: http://www.quantum-espresso.org/wiki/index.php/Installation#Linux_PCs_with_Intel_compiler_.28ifort.2C_formerly_ifc.29 http://www.quantum-espresso.org/wiki/index.php/Installation#Linux_PCs_with_MKL_libraries IBM AIX: http://www.quantum-espresso.org/wiki/index.php/Installation#IBM_AIX hope this helps, giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From bipulrr at gmail.com Mon Aug 4 14:09:19 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Mon, 4 Aug 2008 17:39:19 +0530 Subject: [Pw_forum] cvs version of espresso In-Reply-To: <4896E542.1010902@na.infn.it> References: <3a749910808040409o4457107br1c3963bbaf184c1c@mail.gmail.com> <4896E542.1010902@na.infn.it> Message-ID: <3a749910808040509x3c845d7cnbea157714f26e69f@mail.gmail.com> Dear Giovanni, Thanks for the kind reply. This means the cvs version is only available to ictp or sissa users. Am i write?? But how a general user can get the cvs version of espresso? Or it is not possible. Bcoz it asks for the user name and password. On Mon, Aug 4, 2008 at 4:47 PM, Giovanni Cantele < Giovanni.Cantele at na.infn.it> wrote: > Bipul Rakshit wrote: > > Hello pwscf user, > > I want to ask how to get and install the cvs version of espresso. I > > want to install in my laptop with ifort and mkl libraries and also in > > aix sp5 parallel machines. > > regards > > Bipul > how to get: > http://www.quantum-espresso.org/wiki/index.php/Developer_Manual#Using_CVS > > how to install: > http://www.quantum-espresso.org/wiki/index.php/Installation > > how to install using ifort + mkl: > > http://www.quantum-espresso.org/wiki/index.php/Installation#Linux_PCs_with_Intel_compiler_.28ifort.2C_formerly_ifc.29 > > http://www.quantum-espresso.org/wiki/index.php/Installation#Linux_PCs_with_MKL_libraries > > IBM AIX: > http://www.quantum-espresso.org/wiki/index.php/Installation#IBM_AIX > > hope this helps, > giovanni > > -- > > > > Dr. Giovanni Cantele > Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario di Monte S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 > Fax: +39 081 676346 > E-mail: giovanni.cantele at cnr.it > giovanni.cantele at na.infn.it > Web: http://people.na.infn.it/~cantele > Research Group: http://www.nanomat.unina.it > > _______________________________________________ > 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/20080804/bf0dcce6/attachment-0001.htm From Giovanni.Cantele at na.infn.it Mon Aug 4 14:21:01 2008 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Mon, 04 Aug 2008 14:21:01 +0200 Subject: [Pw_forum] cvs version of espresso In-Reply-To: <3a749910808040509x3c845d7cnbea157714f26e69f@mail.gmail.com> References: <3a749910808040409o4457107br1c3963bbaf184c1c@mail.gmail.com> <4896E542.1010902@na.infn.it> <3a749910808040509x3c845d7cnbea157714f26e69f@mail.gmail.com> Message-ID: <4896F42D.3030906@na.infn.it> Bipul Rakshit wrote: > Dear Giovanni, > Thanks for the kind reply. This means the cvs version is only > available to ictp or sissa users. Am i write?? actually not. From the first link below: Anonymous CVS You have to define the environment variables CVS_RSH and CVSROOT. For csh/tcsh, use setenv CVS_RSH ssh setenv CVSROOT :pserver:cvsanon at democritos.sissa.it:/home/cvs For sh/ksh/bash, use export CVS_RSH=ssh export CVSROOT=:pserver:cvsanon at democritos.sissa.it:/home/cvs Then: cvs login and enter password: /cvsanon/ So, define the two environment variables CVS_RSH and CVSROOT Then, after "cvs login" it should ask just the password, that is "cvsanon" If you want to get the code for the first time, enter "cvs co espresso" If you already have a previous version, you can update it by entering the directory where you stored the cvs distribution and then "cvs update -dP" > But how a general user can get the cvs version of espresso? Or it is > not possible. Bcoz it asks for the user name and password. So, getting the cvs version is open to any user! giovanni > > > > On Mon, Aug 4, 2008 at 4:47 PM, Giovanni Cantele > > wrote: > > Bipul Rakshit wrote: > > Hello pwscf user, > > I want to ask how to get and install the cvs version of espresso. I > > want to install in my laptop with ifort and mkl libraries and > also in > > aix sp5 parallel machines. > > regards > > Bipul > how to get: > http://www.quantum-espresso.org/wiki/index.php/Developer_Manual#Using_CVS > > how to install: > http://www.quantum-espresso.org/wiki/index.php/Installation > > how to install using ifort + mkl: > http://www.quantum-espresso.org/wiki/index.php/Installation#Linux_PCs_with_Intel_compiler_.28ifort.2C_formerly_ifc.29 > http://www.quantum-espresso.org/wiki/index.php/Installation#Linux_PCs_with_MKL_libraries > > IBM AIX: > http://www.quantum-espresso.org/wiki/index.php/Installation#IBM_AIX > > hope this helps, > giovanni > > -- > > > > Dr. Giovanni Cantele > Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario di Monte S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 > Fax: +39 081 676346 > E-mail: giovanni.cantele at cnr.it > giovanni.cantele at na.infn.it > > Web: http://people.na.infn.it/~cantele > > Research Group: http://www.nanomat.unina.it > > > _______________________________________________ > 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 > -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From eyvaz_isaev at yahoo.com Mon Aug 4 14:30:53 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 4 Aug 2008 05:30:53 -0700 (PDT) Subject: [Pw_forum] cvs version of espresso Message-ID: <207358.39532.qm@web65706.mail.ac4.yahoo.com> Hi, No, any user can download the CVS version. You were not carefull reading the web-page mentioned by Giovanni, as there is: cvs login and enter password: cvsanon Before you should enter 2 lines (see the page) depending on shell you use (bash or csh). Of course, you should have installed CVS. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: Bipul Rakshit To: Giovanni.Cantele at na.infn.it; PWSCF Forum Sent: Monday, August 4, 2008 2:09:19 PM Subject: Re: [Pw_forum] cvs version of espresso Dear Giovanni, Thanks for the kind reply. This means the cvs version is only available to ictp or sissa users. Am i write?? But how a general user can get the cvs version of espresso? Or it is not possible. Bcoz it asks for the user name and password. On Mon, Aug 4, 2008 at 4:47 PM, Giovanni Cantele wrote: Bipul Rakshit wrote: > Hello pwscf user, > I want to ask how to get and install the cvs version of espresso. I > want to install in my laptop with ifort and mkl libraries and also in > aix sp5 parallel machines. > regards > Bipul how to get: http://www.quantum-espresso.org/wiki/index.php/Developer_Manual#Using_CVS how to install: http://www.quantum-espresso.org/wiki/index.php/Installation how to install using ifort + mkl: http://www.quantum-espresso.org/wiki/index.php/Installation#Linux_PCs_with_Intel_compiler_.28ifort.2C_formerly_ifc.29 http://www.quantum-espresso.org/wiki/index.php/Installation#Linux_PCs_with_MKL_libraries IBM AIX: http://www.quantum-espresso.org/wiki/index.php/Installation#IBM_AIX hope this helps, giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it _______________________________________________ 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/20080804/eb2babc6/attachment.htm From amosleffler at sbcglobal.net Mon Aug 4 21:50:32 2008 From: amosleffler at sbcglobal.net (Amos Leffler) Date: Mon, 4 Aug 2008 12:50:32 -0700 Subject: [Pw_forum] Electron-phonon calculations in Examples 02 and 07. Message-ID: <1993ADE75E6C46C2BDF2CD79B3360EB8@leffler2> Dear Stefano, In Example02 I compared the reference file to the results file outputs as below: reference results si.phX.out 23065 16206 si.phXsingle.out 25830 22505 At the end of the results file in each case was the message "from broyden file factorization error". Using grep in the PH directory I found matches for broyden noted in the dynmat.x, matdyn.x, ph.x, and q2r.x binary files. All of the remaining listed files were either exactly or close to the same length. This agrees with the error message. The problem is that I don't know where the problem is in the PH directory. Is there any way to debug the directory? Nothing is said in the user_guide. I did note in the phq_readin.f90 file line 154 it is possible to reset lnscf to true but I am not sure what this will tell me. Your comments would be appreciated. Amos Leffler unaffiliated Stefano de Gironcoli wrote: Dear Amos Leffler, what you are showing us is the error found by the script, which says that ...there was an error. have you verified the content of the several output files that are created by the codes in the result directory? they might be more informative and you may discover that you not even need our help... best regards, stefano Amos Leffler wrote: Dear Forum, On May 12 Dong Hee Lim reported a problem with Example 02 when running espresso-4.0.1. Paolo G. asked for more details but I have not seen any since then. I am reporting a similar problem with some of the output. These were run using espresso-4.0.1 in serial mode using a fortran g95 fortran compiler. /home/amos/Desktop/espresso-4.0.1/examples/example02 env LD_LIBRARY_PATH=/opt/intel/mkl/10.0.3.020/lib/em64t ./run_example This example shows how to use pw.x and ph.x to calculate phonon frequencies at Gamma and X for Si and C in the diamond structure and for fcc-Ni executables directory: /home/amos/Desktop/espresso-4.0.1/bin pseudo directory: /home/amos/Desktop/espresso-4.0.1/pseudo temporary directory /home/amos/tmp checking that needed directories and files exist... done running pw.x as : /home/amos/Desktop/espresso-4.0.1/bin/pw.x running ph.x as : /home/amos/Desktop/espresso-4.0.1/bin/ph.x cleaning /home/amos/tmp... done running the scf calculation... done running the phonon calculation at Gamma... done running the nscf calculation at X for a single mode... done running the phonon calculation at X for a single mode ... STOP 2 Error condition encountered during test: exit status = 2 Aborting Example 07 This gives the same sort of sequence through running pw.x, ph.x, q2r.x, matdyn.x. It then goes through: cleaning /home/amos/tmp. running the scf calculation with dense k-point grid... done running the scf calculation... done running the el-ph calculation... STOP 2 Error condtion encountered during test: exit status = 2 Aborting Both examples stop in the same portion of the run_example and probably have the same cause. Some other examples complete properly but I have not tested all of them Amos Leffler. unaffiliated -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080804/f062df3a/attachment.htm From akohlmey at cmm.chem.upenn.edu Mon Aug 4 22:52:52 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Mon, 4 Aug 2008 16:52:52 -0400 (EDT) Subject: [Pw_forum] Electron-phonon calculations in Examples 02 and 07. In-Reply-To: <1993ADE75E6C46C2BDF2CD79B3360EB8@leffler2> References: <1993ADE75E6C46C2BDF2CD79B3360EB8@leffler2> Message-ID: On Mon, 4 Aug 2008, Amos Leffler wrote: AL> Dear Stefano, amos, AL> In Example02 I compared the reference file to the results file outputs as below: AL> reference results AL> si.phX.out 23065 16206 AL> si.phXsingle.out 25830 22505 what is this? the size of the files? this still doesn't say anything about _what_ went wrong. wouldn't it make much more sense to show _where_ they are different? you say you are running a serial compile using g95 on an x86_64 platform, right? so i ran a check on my machine (x86_64, intel xeon 5150 dual core, fedora core 6). using the QE-4.0.1 source from www.pwscf.org and the last g95 release version (0.91!, Feb 27 2008). compiled using the defaults as found by FC=g95 F90=g95 ./configure which picks up intel MKL (10.0.1.014 on my machine), and the result is that i can _not_ reproduce your crash report. example02 runs just fine and so does example07. do you by any chance use a g95 compiler with 64bit integers? or a non-release version? the next option would be a problem in BLAS/LAPACK from MKL (since you have a different version than i have, but that is rather unlikely). can you run all the checks in the "tests" subdirectory successfully? please also try to disable all native language support or locale settings via exporting LC_ALL=C beyond that, you have to provide more details about the platform you are running on and the components that you are using and what else _exactly_ you are doing. right now, it looks as if something you use or how you use it is broken but not the QE code itself (at least not for those specific examples). AL> At the end of the results file in each case was the message "from AL> broyden file factorization error". Using grep in the PH directory I AL> found matches for broyden noted in the dynmat.x, matdyn.x, ph.x, and AL> q2r.x binary files. this is not the problem, but the code leading up to it may give a hint. AL> All of the remaining listed files were either exactly or AL> close to the same length. This agrees with the error AL> message. The problem is that I don't know where the problem AL> is in the PH directory. Is there any way to debug the the only way to find this is to run under a debugger and single step through the code from the last know to work location. as long as nobody else can reproduce your problem, you are on your own with that... AL> directory? Nothing is said in the user_guide. I did note in AL> the phq_readin.f90 file line 154 it is possible to reset AL> lnscf to true but I am not sure what this will tell me. Your AL> comments would be appreciated. please explain what that is supposed to achieve? how would this specific flag be relate to your problem? there are a large number of defaults that you can set differently, but that cannot be the problem. cheers, axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From meisam_a84 at yahoo.com Tue Aug 5 13:52:37 2008 From: meisam_a84 at yahoo.com (meisam aghtar) Date: Tue, 5 Aug 2008 04:52:37 -0700 (PDT) Subject: [Pw_forum] relaxation Message-ID: <205879.5043.qm@web30605.mail.mud.yahoo.com> Dear Paolo and Hande At first I appreciate you for your help. You were right the system was relaxed with a small broadening. I thought that this system is semiconductor like many other hydrogenated nanotubes , but it was metallic with a high density of bands near Fermi surface. Another problem is that I?m not sure that I could use BFGS in relaxing this system because achieving the lowest energy is more important than remaining the symmetries of the system. Should I use damp method or MD? Would you please introduce me papers containing these relaxation methods about when and how these methods are used? ? Thanks ? M.aghtar Msc student, physics department of Kashan university. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080805/ea53ce69/attachment.htm From mansourehp at gmail.com Wed Aug 6 07:34:06 2008 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Wed, 6 Aug 2008 09:04:06 +0330 Subject: [Pw_forum] dos for FeO Message-ID: Dear all my question is about FeO dos plot.when I found total dos for FeO in Cococcinoni papers ,it was different with his FeO example in VLab lectures(2006).when I obtained FeO's dos plot ,it was similar FeO example in VLab(2006).I like to know why are they different and how can I find correct dos? Thanks Mansoureh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080806/273d387c/attachment.htm From bipulrr at gmail.com Wed Aug 6 14:37:44 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Wed, 6 Aug 2008 18:07:44 +0530 Subject: [Pw_forum] fermi level Message-ID: <3a749910808060537g1cda5a49r9c26e35d6c9d818e@mail.gmail.com> Hello Pwscf user, Generally in bands structure and DOS calculation, when we plot the graphs, the fermi level is not set at zero. so my query is where we able to see the fermi level (in output files), so that i able to plot the band structure and the DOS with fermi level set at zero. thanks Bipul Phd. student -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080806/febcfb64/attachment.htm From degironc at sissa.it Wed Aug 6 14:44:43 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 06 Aug 2008 14:44:43 +0200 Subject: [Pw_forum] fermi level In-Reply-To: <3a749910808060537g1cda5a49r9c26e35d6c9d818e@mail.gmail.com> References: <3a749910808060537g1cda5a49r9c26e35d6c9d818e@mail.gmail.com> Message-ID: <48999CBB.7090608@sissa.it> Fermi energy is written in output whenever it is calculated, that is in any scf calculations for metals. stefano Bipul Rakshit wrote: > Hello Pwscf user, > Generally in bands structure and DOS calculation, when we plot the > graphs, the fermi level is not set at zero. so my query is where we > able to see the fermi level (in output files), so that i able to plot > the band structure and the DOS with fermi level set at zero. > > thanks > Bipul > Phd. student > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mgkrishn at ncsu.edu Wed Aug 6 19:10:44 2008 From: mgkrishn at ncsu.edu (mgkrishn at ncsu.edu) Date: Wed, 6 Aug 2008 13:10:44 -0400 (EDT) Subject: [Pw_forum] fermi level In-Reply-To: <48999CBB.7090608@sissa.it> References: <3a749910808060537g1cda5a49r9c26e35d6c9d818e@mail.gmail.com> <48999CBB.7090608@sissa.it> Message-ID: <1165.24.5.121.8.1218042644.squirrel@webmail.ncsu.edu> you can also get it from tmp folder .save/K00001/eigenval.xml > Fermi energy is written in output whenever it is calculated, that is in > any scf calculations for metals. > stefano > > Bipul Rakshit wrote: >> Hello Pwscf user, >> Generally in bands structure and DOS calculation, when we plot the >> graphs, the fermi level is not set at zero. so my query is where we >> able to see the fermi level (in output files), so that i able to plot >> the band structure and the DOS with fermi level set at zero. >> >> thanks >> Bipul >> Phd. student >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 raamesh123 at rediffmail.com Thu Aug 7 04:35:39 2008 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 7 Aug 2008 02:35:39 -0000 Subject: [Pw_forum] fhi2upf.f90 Message-ID: <20080807023539.30154.qmail@f5mail-237-237.rediffmail.com> Dear all i want to convert the pseudopotential from abinit form to pwscf form. i used the executable fhi2upf.x. it asked (wavefunction 1,2,3 and 4) label and occupancy print '("Wavefunction # ",i1,": label, occupancy > ",$)', i read (5,*) els(i), oc(i) nns (i) = 0 lchi(i) = i-1 rcut(i) = 0.0d0 rcutus(i)= 0.0d0 epseu(i) = 0.0d0 i compared with the available UPF format and it should be nl and occupancy but how to feed it??????? with regards K. Ramesh Kumar Research scholar Department of physics IIT Madras Chennai-600036 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080807/81e05019/attachment.htm From munima at iitg.ernet.in Thu Aug 7 05:59:24 2008 From: munima at iitg.ernet.in (Munima Bora Sahariah) Date: Thu, 7 Aug 2008 09:29:24 +0530 (IST) Subject: [Pw_forum] fhi2upf.f90 In-Reply-To: <20080807023539.30154.qmail@f5mail-237-237.rediffmail.com> References: <20080807023539.30154.qmail@f5mail-237-237.rediffmail.com> Message-ID: <59272.172.16.48.134.1218081564.squirrel@webmail.iitg.ac.in> Dear Ramesh yesterday I tried the same fhi2upf.x for Ba pseudopotential. Below is the input. Input file > 56-Ba.GGA.fhi read_fhi: assuming abinit format Pseudopotential with NLCC successfully read DFT read from abinit file: * DFT > pbe Wavefunction # 1: label, occupancy > 6S, 2 Wavefunction # 2: label, occupancy > 5P, 6 Wavefunction # 3: label, occupancy > 5S, 2 Wavefunction # 4: label, occupancy > 4P, 6 Pseudopotential successfully converted Output PP file in UPF format : 56-Ba.GGA.fhi.UPF thanks munima > > > Dear all > > i want to convert the pseudopotential from abinit form to pwscf form. i > used the executable fhi2upf.x. it asked (wavefunction 1,2,3 and 4) label > and occupancy > > print '("Wavefunction # ",i1,": label, occupancy > ",$)', i > read (5,*) els(i), oc(i) > nns (i) = 0 > lchi(i) = i-1 > rcut(i) = 0.0d0 > rcutus(i)= 0.0d0 > epseu(i) = 0.0d0 > > i compared with the available UPF format and it should be nl and occupancy > but how to feed it??????? > > with regards > K. Ramesh Kumar > Research scholar > Department of physics > IIT Madras > Chennai-600036_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > Dr. Munima B. Sahariah PI, DST Fast Track Project IASST, Guwahati Assam, INDIA ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ac.in From munima at iitg.ernet.in Thu Aug 7 06:31:16 2008 From: munima at iitg.ernet.in (Munima Bora Sahariah) Date: Thu, 7 Aug 2008 10:01:16 +0530 (IST) Subject: [Pw_forum] GGA underestimates lattice constant in BaO In-Reply-To: References: <573C6D11-4F73-4B0B-A134-BFF6B7A3DA26@democritos.it> Message-ID: <39262.172.16.48.134.1218083476.squirrel@webmail.iitg.ac.in> Dear Dr. Toffoli thanks for putting your comments and interest in this matter. The pbe pseudopotential that I took from pwscf already has 5S, 5P, 5D, 6S and 6P orbitals included. I am not sure whether inclusion of more orbitals (4P at least) would make any difference. We can give it a try. yesterday I tried with Ba and O GGA pseudopotentials taken from ABINIT. they are norm conserving ones. I found the lattice constant for BaO too much overestimated. I will let you know if I find some more information. regards munima > Dear Munima, > > I also ran into the exact same problem just yesterday using the PBE > pseudopotential from the web site. The lattice constant that you quote is > almost identical to the one I obtained. Inspired by your post, I > calculated > the lattice constant for BaS to compare to the result in the paper you > quote and it matches better (almost the same as the experimental value). I > don't know if this is supposed to make us feel better. > > I also thought of generating a new pseudopotential but as far as I know, > the generator cannot include two orbitals of the same l even though they > might be from different shells. Thus we couldn't include 5s and 6s > orbitals > simultaneously. Am I right? >I would also appreciate thoughts on what we > could do or pseudopotentials that have been converted from other codes if > there are any lying around. > > Thank you very much. > > Best, > Hande > > On Fri, 1 Aug 2008, Paolo Giannozzi wrote: > >> >> On Jul 23, 2008, at 7:58 , Munima Bora Sahariah wrote: >> >> > For last couple of days I have been trying to find the equilibrium >> > lattice >> > constant of BaO with GGA (pw91) and has found that my calculated >> > value >> > underestimates the experimental one by 1.3% (GGA = 10.301 a.u., EXP = >> > 10.431 a.u.). Surprizingly, while trying with LDA, I obtained a value >> > which is closer to the experimental one as compared to GGA (LDA = >> > 10.324 >> > a.u.) [...] >> > While doing a search on the web, I found one paper (Phys. Rev. B 71, >> > 085203) where GGA and LDA results for lattice constant of BaO have >> > been >> > listed. In this paper calculations were done in CASTEP. Here the >> > LDA value >> > underestimates the experimental lattice constant while the GGA >> > (pw91) value >> > improves the situation and is closer to the experimental one. >> >> try different pseudopotentials if you can: this might be one of those >> cases >> in which the results are more sensitive than desired to the quality of >> pseudopotentials (in particular of Ba). >> >> Paolo >> --- >> Paolo Giannozzi, Dept of Physics, University of Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ac.in From bipulrr at gmail.com Thu Aug 7 08:40:27 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 7 Aug 2008 08:40:27 +0200 Subject: [Pw_forum] About band structure. Message-ID: <3a749910808062340q73e9420elfcfea1fc0110115d@mail.gmail.com> Hello PWscf users, I have a question about the band structure. 1. I have plotted the band structure of ScSb. There i found that in that post script file it draw the band very near the fermi level (-12.0:3.0) only. But if I want the bands range say -20:20, what and where I have to change? 2. I have given the K-points as used in Si calculation in examples, in my ScSb file. It works well. But I am also using SIESTA, where we mention the k-points as below BandLinesScale pi/a %block BandLines # These are comments 1 0.000 0.000 0.000 \Gamma # Begin at Gamma 25 2.000 0.000 0.000 X # 25 points from Gamma to X 10 2.000 1.000 0.000 W # 10 points from X to W 15 1.000 1.000 1.000 L # 15 points from W to L 20 0.000 0.000 0.000 \Gamma # 20 points from L to Gamma 25 1.500 1.500 1.500 K # 25 points from Gamma to K %endblock BandLines the first column after* %block BandLines* shows the number of points between the given k-points (like 25 points between Gamma and X). In this way we dont have to mention all the k-points and we get a smooth graph. But in pwscf I have to mention all the k-points in order to get a smooth graph as in the example of Si. So my question is, is there any way so that we have to mention only the points at the zone boundary, and rest of the points it will take automatically? -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080807/62f43f65/attachment.htm From bipulrr at gmail.com Thu Aug 7 09:36:15 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 7 Aug 2008 09:36:15 +0200 Subject: [Pw_forum] About band structure. Message-ID: <3a749910808070036q44f58b45id9c107339cc3c495@mail.gmail.com> Hello PWscf users, I have a question about the band structure. 1. I have plotted the band structure of ScSb. There i found that in that post script file it draw the band very near the fermi level (-12.0:3.0) only. But if I want the bands range say -20:20, what and where I have to change? 2. I have given the K-points as used in Si calculation in examples, in my ScSb file. It works well. But I am also using SIESTA, where we mention the k-points as below BandLinesScale pi/a %block BandLines # These are comments 1 0.000 0.000 0.000 \Gamma # Begin at Gamma 25 2.000 0.000 0.000 X # 25 points from Gamma to X 10 2.000 1.000 0.000 W # 10 points from X to W 15 1.000 1.000 1.000 L # 15 points from W to L 20 0.000 0.000 0.000 \Gamma # 20 points from L to Gamma 25 1.500 1.500 1.500 K # 25 points from Gamma to K %endblock BandLines the first column after* %block BandLines* shows the number of points between the given k-points (like 25 points between Gamma and X). In this way we dont have to mention all the k-points and we get a smooth graph. But in pwscf I have to mention all the k-points in order to get a smooth graph as in the example of Si. So my question is, is there any way so that we have to mention only the points at the zone boundary, and rest of the points it will take automatically? -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080807/25da98fd/attachment.htm From degironc at sissa.it Thu Aug 7 09:45:02 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 07 Aug 2008 09:45:02 +0200 Subject: [Pw_forum] About band structure. In-Reply-To: <3a749910808062340q73e9420elfcfea1fc0110115d@mail.gmail.com> References: <3a749910808062340q73e9420elfcfea1fc0110115d@mail.gmail.com> Message-ID: <489AA7FE.8080202@sissa.it> 1.) change the plotting range given in input to your plotting routine 2.) write a 5-10 line fortran_code/bash_script /awk/java/whathever_you_are_familiar_with that makes this trivial task for you and feed the resulting data to pw.x best regards, Stefano Bipul Rakshit wrote: > Hello PWscf users, > I have a question about the band structure. > 1. I have plotted the band structure of ScSb. There i found that in > that post script file it draw the band very near the fermi level > (-12.0:3.0) only. But if I want the bands range say -20:20, what and > where I have to change? > > 2. I have given the K-points as used in Si calculation in examples, in > my ScSb file. It works well. But I am also using SIESTA, where we > mention the k-points as below > > BandLinesScale pi/a > %block BandLines # These are comments > 1 0.000 0.000 0.000 \Gamma # Begin at Gamma > 25 2.000 0.000 0.000 X # 25 points from Gamma to X > 10 2.000 1.000 0.000 W # 10 points from X to W > 15 1.000 1.000 1.000 L # 15 points from W to L > 20 0.000 0.000 0.000 \Gamma # 20 points from L to Gamma > 25 1.500 1.500 1.500 K # 25 points from Gamma to K > %endblock BandLines > > the first column after* %block BandLines* shows the number of points > between the given k-points (like 25 points between Gamma and X). In > this way we dont have to mention all the k-points and we get a smooth > graph. But in pwscf I have to mention all the k-points in order to get > a smooth graph as in the example of Si. > So my question is, is there any way so that we have to mention only > the points at the zone boundary, and rest of the points it will take > automatically? > > -- > Bipul Rakshit > PhD Student, > Barkatullah University, > Bhopal 462026, > MP, India > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From bipulrr at gmail.com Thu Aug 7 10:35:23 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 7 Aug 2008 10:35:23 +0200 Subject: [Pw_forum] About band structure. In-Reply-To: <489AA7FE.8080202@sissa.it> References: <3a749910808062340q73e9420elfcfea1fc0110115d@mail.gmail.com> <489AA7FE.8080202@sissa.it> Message-ID: <3a749910808070135g5143e3bbqa90885d2cea329c3@mail.gmail.com> Hello Stefano, I am trying to make to programme, which able to generate the k-points automatically along given two points. But from where I get some hint to do this? And what is */awk/java/whathever_you_are_familiar_with* ? thanks On Thu, Aug 7, 2008 at 9:45 AM, Stefano de Gironcoli wrote: > 1.) change the plotting range given in input to your plotting routine > 2.) write a 5-10 line fortran_code/bash_script > /awk/java/whathever_you_are_familiar_with that makes this trivial task > for you and feed the resulting data to pw.x > best regards, > Stefano > > > Bipul Rakshit wrote: > > Hello PWscf users, > > I have a question about the band structure. > > 1. I have plotted the band structure of ScSb. There i found that in > > that post script file it draw the band very near the fermi level > > (-12.0:3.0) only. But if I want the bands range say -20:20, what and > > where I have to change? > > > > 2. I have given the K-points as used in Si calculation in examples, in > > my ScSb file. It works well. But I am also using SIESTA, where we > > mention the k-points as below > > > > BandLinesScale pi/a > > %block BandLines # These are comments > > 1 0.000 0.000 0.000 \Gamma # Begin at Gamma > > 25 2.000 0.000 0.000 X # 25 points from Gamma to X > > 10 2.000 1.000 0.000 W # 10 points from X to W > > 15 1.000 1.000 1.000 L # 15 points from W to L > > 20 0.000 0.000 0.000 \Gamma # 20 points from L to Gamma > > 25 1.500 1.500 1.500 K # 25 points from Gamma to K > > %endblock BandLines > > > > the first column after* %block BandLines* shows the number of points > > between the given k-points (like 25 points between Gamma and X). In > > this way we dont have to mention all the k-points and we get a smooth > > graph. But in pwscf I have to mention all the k-points in order to get > > a smooth graph as in the example of Si. > > So my question is, is there any way so that we have to mention only > > the points at the zone boundary, and rest of the points it will take > > automatically? > > > > -- > > Bipul Rakshit > > PhD Student, > > Barkatullah University, > > Bhopal 462026, > > MP, India > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080807/cf8ade65/attachment.htm From lanhaiping at gmail.com Thu Aug 7 11:03:01 2008 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 7 Aug 2008 17:03:01 +0800 Subject: [Pw_forum] About band structure. In-Reply-To: <3a749910808070135g5143e3bbqa90885d2cea329c3@mail.gmail.com> References: <3a749910808062340q73e9420elfcfea1fc0110115d@mail.gmail.com> <489AA7FE.8080202@sissa.it> <3a749910808070135g5143e3bbqa90885d2cea329c3@mail.gmail.com> Message-ID: let me give you a example in python def kptline(kpt1,kpt2,nkpt): kptlist=zeros([3,nkpt+1]) dkpt=(kpt2-kpt1)/(nkpt) for i in range(nkpt+1): kptlist[:,i]=kpt1+i*dkpt then the kptlist is what you want .. On Thu, Aug 7, 2008 at 4:35 PM, Bipul Rakshit wrote: > Hello Stefano, > I am trying to make to programme, which able to generate the k-points > automatically along given two points. But from where I get some hint to do > this? > And what is */awk/java/whathever_you_are_familiar_with* ? > > thanks > > > > On Thu, Aug 7, 2008 at 9:45 AM, Stefano de Gironcoli wrote: > >> 1.) change the plotting range given in input to your plotting routine >> 2.) write a 5-10 line fortran_code/bash_script >> /awk/java/whathever_you_are_familiar_with that makes this trivial task >> for you and feed the resulting data to pw.x >> best regards, >> Stefano >> >> >> Bipul Rakshit wrote: >> > Hello PWscf users, >> > I have a question about the band structure. >> > 1. I have plotted the band structure of ScSb. There i found that in >> > that post script file it draw the band very near the fermi level >> > (-12.0:3.0) only. But if I want the bands range say -20:20, what and >> > where I have to change? >> > >> > 2. I have given the K-points as used in Si calculation in examples, in >> > my ScSb file. It works well. But I am also using SIESTA, where we >> > mention the k-points as below >> > >> > BandLinesScale pi/a >> > %block BandLines # These are comments >> > 1 0.000 0.000 0.000 \Gamma # Begin at Gamma >> > 25 2.000 0.000 0.000 X # 25 points from Gamma to X >> > 10 2.000 1.000 0.000 W # 10 points from X to W >> > 15 1.000 1.000 1.000 L # 15 points from W to L >> > 20 0.000 0.000 0.000 \Gamma # 20 points from L to Gamma >> > 25 1.500 1.500 1.500 K # 25 points from Gamma to K >> > %endblock BandLines >> > >> > the first column after* %block BandLines* shows the number of points >> > between the given k-points (like 25 points between Gamma and X). In >> > this way we dont have to mention all the k-points and we get a smooth >> > graph. But in pwscf I have to mention all the k-points in order to get >> > a smooth graph as in the example of Si. >> > So my question is, is there any way so that we have to mention only >> > the points at the zone boundary, and rest of the points it will take >> > automatically? >> > >> > -- >> > Bipul Rakshit >> > PhD Student, >> > Barkatullah University, >> > Bhopal 462026, >> > MP, India >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Bipul Rakshit > PhD Student, > Barkatullah University, > Bhopal 462026, > MP, India > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080807/5799242d/attachment-0001.htm From marcel at physik.tu-berlin.de Thu Aug 7 11:02:37 2008 From: marcel at physik.tu-berlin.de (Marcel Mohr) Date: Thu, 7 Aug 2008 11:02:37 +0200 (CEST) Subject: [Pw_forum] About band structure. In-Reply-To: <3a749910808070135g5143e3bbqa90885d2cea329c3@mail.gmail.com> References: <3a749910808062340q73e9420elfcfea1fc0110115d@mail.gmail.com> <489AA7FE.8080202@sissa.it> <3a749910808070135g5143e3bbqa90885d2cea329c3@mail.gmail.com> Message-ID: On Thu, 7 Aug 2008, Bipul Rakshit wrote: > And what is /awk/java/whathever_you_are_familiar_with ? I am afraid I can't help you there. I do also not know what /awk/java/whatever_I_am_familar_with is, but do know a little python, In the attachment is a skript, that calculates the k-points along several endpoints ("points"), with "fineness", the number of k-points in between. Cheers Marcel > > thanks > > > On Thu, Aug 7, 2008 at 9:45 AM, Stefano de Gironcoli wrote: > 1.) change the plotting range given in input to your plotting routine > 2.) write a 5-10 line fortran_code/bash_script > /awk/java/whathever_you_are_familiar_with that makes this trivial task > for you and feed the resulting data to pw.x > best regards, > ?Stefano > > > Bipul Rakshit wrote: > > Hello PWscf users, > > I have a question about the band structure. > > 1. ?I have plotted the band structure of ScSb. There i found that in > > that post script file it draw the band very near the fermi level > > (-12.0:3.0) only. But if I want the bands range say -20:20, what and > > where I have to change? > > > > 2. I have given the K-points as used in Si calculation in examples, in > > my ScSb file. It works well. But I am also using SIESTA, where we > > mention the k-points as below > > > > ? ? BandLinesScale ?pi/a > > ? ? ?%block BandLines ? ? ? ? ? ? ? ? ?# These are comments > > ? ? ? 1 ?0.000 ?0.000 ?0.000 ?\Gamma ? # Begin at Gamma > > ? ? ?25 ?2.000 ?0.000 ?0.000 ? ? X ? ? # 25 points from Gamma to X > > ? ? ?10 ?2.000 ?1.000 ?0.000 ? ? W ? ? # 10 points from X to W > > ? ? ?15 ?1.000 ?1.000 ?1.000 ? ? L ? ? # 15 points from W to L > > ? ? ?20 ?0.000 ?0.000 ?0.000 ?\Gamma ? # 20 points from L to Gamma > > ? ? ?25 ?1.500 ?1.500 ?1.500 ? ? K ? ? # 25 points from Gamma to K > > ? ? ?%endblock BandLines > > > > the first column after* %block BandLines* shows the number of points > > between the given k-points (like 25 points between Gamma and X). In > > this way we dont have to mention all the k-points and we get a smooth > > graph. But in pwscf I have to mention all the k-points in order to get > > a smooth graph as in the example of Si. > > So my question is, is there any way so that we have to mention only > > the points at the zone boundary, and rest of the points it will take > > automatically? > > > > -- > > Bipul Rakshit > > PhD Student, > > Barkatullah University, > > Bhopal 462026, > > MP, India > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Bipul Rakshit > PhD Student, > Barkatullah University, > Bhopal 462026, > MP, India > > -------------- next part -------------- # This program produces a list of q-points needed for anadbb. The total amount of q-points is written. # It connects the points with steps between. The first entry of fineness governs the steps between the 1st # and 2nd entry of points. from Numeric import array, Float import sys points=array([ [0,0,0] , [0.5,0.5,0.0] , [1 , 0 ,0]]) fineness=array([99,57])#,15,29,15,29,29,29]) counter=0 # check of fineness contains points-1 entries if fineness.shape[0] != (points.shape[0]-1): print ("Die Anzahl der Schritte und K-Punte stimmt nicht ueberein") sys.exit() #produce q-points for i in range(points.shape[0]-1): divisor=float(fineness[i]) for j in range(int(divisor)): jfloat=float(j) punkt=points[i]+jfloat/divisor*(points[i+1]-points[i]) print "\t %5.5f \t %5.5f \t %5.5f \t 1.0" % (punkt[0],punkt[1],punkt[2]) counter=counter+1 #last point print "\t %5.5f \t %5.5f \t %5.5f \t 1.0" % (points[i+1][0],points[i+1][1],points[i+1][2]) #print number of qpoints print counter+1 From marzari at MIT.EDU Thu Aug 7 11:26:23 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 07 Aug 2008 17:26:23 +0800 Subject: [Pw_forum] About band structure. In-Reply-To: References: <3a749910808062340q73e9420elfcfea1fc0110115d@mail.gmail.com> <489AA7FE.8080202@sissa.it> <3a749910808070135g5143e3bbqa90885d2cea329c3@mail.gmail.com> Message-ID: <489ABFBF.2060103@mit.edu> Dear Bipul, > On Thu, 7 Aug 2008, Bipul Rakshit wrote: > >> And what is /awk/java/whathever_you_are_familiar_with ? keep in mind that google is perfect for these questions. You ask, it answers. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From hande at newton.physics.metu.edu.tr Thu Aug 7 11:31:46 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Thu, 7 Aug 2008 12:31:46 +0300 (EEST) Subject: [Pw_forum] About band structure. In-Reply-To: Message-ID: > > And what is /awk/java/whathever_you_are_familiar_with ? I believe what Stefano meant is just take any known computer language (which fortran, awk, bash, java each are) or any other one you are already using and write a simple code that generates a given number of points between two arbitrary points in space. I would suggest octave or matlab if you are unfamiliar with coding. Maybe something like this : function ks=get_points(point1,point2,nks) kx = [linspace(point1(1),point2(1),nks)]'; ky = [linspace(point1(2),point2(2),nks)]'; kz = [linspace(point1(3),point2(3),nks)]'; ks=[ kx ky kz ones(nks,1)]; endfunction Just copy this into a file called get_points.m, start octave (you should already have this, assuming you are using linux), type something like get_points([0 0 0], [1 0 0], 25) and copy and paste the result in your input. You have to repeat this for each pair of points. Make sure you don't repeat the same point (say K) twice because plotband really hates that. Also beware that I put in the weights in the above script assuming that you are running an nscf or a bands calculation where it doesn't matter what you have for weights. If you are running anything else it does. Hope this helps. Hande -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From bipulrr at gmail.com Thu Aug 7 11:52:31 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 7 Aug 2008 11:52:31 +0200 Subject: [Pw_forum] About band structure. In-Reply-To: References: <3a749910808062340q73e9420elfcfea1fc0110115d@mail.gmail.com> <489AA7FE.8080202@sissa.it> <3a749910808070135g5143e3bbqa90885d2cea329c3@mail.gmail.com> Message-ID: <3a749910808070252lea4438aj5a45d4c64e29606e@mail.gmail.com> Hello Marcel, Thanks for the help. But can you tell me how it works? On Thu, Aug 7, 2008 at 11:02 AM, Marcel Mohr wrote: > On Thu, 7 Aug 2008, Bipul Rakshit wrote: > > And what is /awk/java/whathever_you_are_familiar_with ? >> > > I am afraid I can't help you there. > I do also not know what /awk/java/whatever_I_am_familar_with is, > but do know a little python, > In the attachment is a skript, that calculates the k-points along several > endpoints ("points"), with "fineness", the number of k-points in between. > > Cheers Marcel > > > > > >> thanks >> >> >> On Thu, Aug 7, 2008 at 9:45 AM, Stefano de Gironcoli >> wrote: >> 1.) change the plotting range given in input to your plotting routine >> 2.) write a 5-10 line fortran_code/bash_script >> /awk/java/whathever_you_are_familiar_with that makes this trivial >> task >> for you and feed the resulting data to pw.x >> best regards, >> Stefano >> >> >> Bipul Rakshit wrote: >> > Hello PWscf users, >> > I have a question about the band structure. >> > 1. I have plotted the band structure of ScSb. There i found that in >> > that post script file it draw the band very near the fermi level >> > (-12.0:3.0) only. But if I want the bands range say -20:20, what and >> > where I have to change? >> > >> > 2. I have given the K-points as used in Si calculation in examples, in >> > my ScSb file. It works well. But I am also using SIESTA, where we >> > mention the k-points as below >> > >> > BandLinesScale pi/a >> > %block BandLines # These are comments >> > 1 0.000 0.000 0.000 \Gamma # Begin at Gamma >> > 25 2.000 0.000 0.000 X # 25 points from Gamma to X >> > 10 2.000 1.000 0.000 W # 10 points from X to W >> > 15 1.000 1.000 1.000 L # 15 points from W to L >> > 20 0.000 0.000 0.000 \Gamma # 20 points from L to Gamma >> > 25 1.500 1.500 1.500 K # 25 points from Gamma to K >> > %endblock BandLines >> > >> > the first column after* %block BandLines* shows the number of points >> > between the given k-points (like 25 points between Gamma and X). In >> > this way we dont have to mention all the k-points and we get a smooth >> > graph. But in pwscf I have to mention all the k-points in order to get >> > a smooth graph as in the example of Si. >> > So my question is, is there any way so that we have to mention only >> > the points at the zone boundary, and rest of the points it will take >> > automatically? >> > >> > -- >> > Bipul Rakshit >> > PhD Student, >> > Barkatullah University, >> > Bhopal 462026, >> > MP, India >> > ------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> -- >> Bipul Rakshit >> PhD Student, >> Barkatullah University, >> Bhopal 462026, >> MP, India >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080807/0f519bee/attachment.htm From marcel at physik.tu-berlin.de Thu Aug 7 11:59:08 2008 From: marcel at physik.tu-berlin.de (Marcel Mohr) Date: Thu, 7 Aug 2008 11:59:08 +0200 (CEST) Subject: [Pw_forum] About band structure. In-Reply-To: <3a749910808070252lea4438aj5a45d4c64e29606e@mail.gmail.com> References: <3a749910808062340q73e9420elfcfea1fc0110115d@mail.gmail.com> <489AA7FE.8080202@sissa.it> <3a749910808070135g5143e3bbqa90885d2cea329c3@mail.gmail.com> <3a749910808070252lea4438aj5a45d4c64e29606e@mail.gmail.com> Message-ID: python ________________________________________________________________________ Marcel Mohr Institut f?r Festk?rperphysik, TU Berlin marcel(at)physik.tu-berlin.de Sekr. EW 5-4 TEL: +49-30-314 24442 Hardenbergstr. 36 FAX: +49-30-314 27705 10623 Berlin On Thu, 7 Aug 2008, Bipul Rakshit wrote: > Hello Marcel, > Thanks for the help. But can you tell me how it works? > > On Thu, Aug 7, 2008 at 11:02 AM, Marcel Mohr wrote: > On Thu, 7 Aug 2008, Bipul Rakshit wrote: > > And what is /awk/java/whathever_you_are_familiar_with ? > > > I am afraid I can't help you there. > I do also not know what /awk/java/whatever_I_am_familar_with is, > but do know a little python, > In the attachment is a skript, that calculates the k-points along several endpoints ("points"), with "fineness", the > number of k-points in between. > > Cheers Marcel > > > > > > thanks > > > On Thu, Aug 7, 2008 at 9:45 AM, Stefano de Gironcoli wrote: > ? ? ?1.) change the plotting range given in input to your plotting routine > ? ? ?2.) write a 5-10 line fortran_code/bash_script > ? ? ?/awk/java/whathever_you_are_familiar_with that makes this trivial task > ? ? ?for you and feed the resulting data to pw.x > ? ? ?best regards, > ? ? ??Stefano > > > Bipul Rakshit wrote: > > Hello PWscf users, > > I have a question about the band structure. > > 1. ?I have plotted the band structure of ScSb. There i found that in > > that post script file it draw the band very near the fermi level > > (-12.0:3.0) only. But if I want the bands range say -20:20, what and > > where I have to change? > > > > 2. I have given the K-points as used in Si calculation in examples, in > > my ScSb file. It works well. But I am also using SIESTA, where we > > mention the k-points as below > > > > ? ? BandLinesScale ?pi/a > > ? ? ?%block BandLines ? ? ? ? ? ? ? ? ?# These are comments > > ? ? ? 1 ?0.000 ?0.000 ?0.000 ?\Gamma ? # Begin at Gamma > > ? ? ?25 ?2.000 ?0.000 ?0.000 ? ? X ? ? # 25 points from Gamma to X > > ? ? ?10 ?2.000 ?1.000 ?0.000 ? ? W ? ? # 10 points from X to W > > ? ? ?15 ?1.000 ?1.000 ?1.000 ? ? L ? ? # 15 points from W to L > > ? ? ?20 ?0.000 ?0.000 ?0.000 ?\Gamma ? # 20 points from L to Gamma > > ? ? ?25 ?1.500 ?1.500 ?1.500 ? ? K ? ? # 25 points from Gamma to K > > ? ? ?%endblock BandLines > > > > the first column after* %block BandLines* shows the number of points > > between the given k-points (like 25 points between Gamma and X). In > > this way we dont have to mention all the k-points and we get a smooth > > graph. But in pwscf I have to mention all the k-points in order to get > > a smooth graph as in the example of Si. > > So my question is, is there any way so that we have to mention only > > the points at the zone boundary, and rest of the points it will take > > automatically? > > > > -- > > Bipul Rakshit > > PhD Student, > > Barkatullah University, > > Bhopal 462026, > > MP, India > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Bipul Rakshit > PhD Student, > Barkatullah University, > Bhopal 462026, > MP, India > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Bipul Rakshit > PhD Student, > Barkatullah University, > Bhopal 462026, > MP, India > > From raamesh123 at rediffmail.com Thu Aug 7 13:11:48 2008 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 7 Aug 2008 11:11:48 -0000 Subject: [Pw_forum] fhi2upf.f90 Message-ID: <20080807111148.16006.qmail@f5mail-237-215.rediffmail.com> Dear Munima thanks for ur help. i have followed ur suggestions and it created the pp.UPF but i have one more question it didnt take "l" value correctly.... Rcut and E pseu everything is (zero) different from the available upf files..... i have copied the information and given below... nl pn l occ Rcut Rcut US E pseu 3S 0 0 2.00 0.00000000000 0.00000000000 0.00000000000 3P 0 1 6.00 0.00000000000 0.00000000000 0.00000000000 4S 0 2 2.00 0.00000000000 0.00000000000 0.00000000000 3D 0 3 5.00 0.00000000000 0.00000000000 0.00000000000 is there something wrong ????????? thanks again On Thu, 07 Aug 2008 Munima Bora Sahariah wrote : >Dear Ramesh > >yesterday I tried the same fhi2upf.x for Ba pseudopotential. Below is the >input. > >Input file > 56-Ba.GGA.fhi >read_fhi: assuming abinit format >Pseudopotential with NLCC successfully read >DFT read from abinit file: * >DFT > pbe >Wavefunction # 1: label, occupancy > 6S, 2 >Wavefunction # 2: label, occupancy > 5P, 6 >Wavefunction # 3: label, occupancy > 5S, 2 >Wavefunction # 4: label, occupancy > 4P, 6 >Pseudopotential successfully converted >Output PP file in UPF format : 56-Ba.GGA.fhi.UPF > >thanks > >munima > > > > > > > > > > Dear all > > > > i want to convert the pseudopotential from abinit form to pwscf form. i > > used the executable fhi2upf.x. it asked (wavefunction 1,2,3 and 4) label > > and occupancy > > > > print '("Wavefunction # ",i1,": label, occupancy > ",$)', i > > read (5,*) els(i), oc(i) > > nns (i) = 0 > > lchi(i) = i-1 > > rcut(i) = 0.0d0 > > rcutus(i)= 0.0d0 > > epseu(i) = 0.0d0 > > > > i compared with the available UPF format and it should be nl and occupancy > > but how to feed it??????? > > > > with regards > > K. Ramesh Kumar > > Research scholar > > Department of physics > > IIT Madras > > Chennai-600036_______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > >Dr. Munima B. Sahariah >PI, DST Fast Track Project >IASST, Guwahati >Assam, INDIA > > >----------------------------------------------------------------------------------- >This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. >http://www.iitg.ac.in With regards K. Ramesh Kumar Research Scholar Department of Physics IIT-Madras Chennai-600 036 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080807/38056fdb/attachment.htm From hande at newton.physics.metu.edu.tr Thu Aug 7 13:37:33 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Thu, 7 Aug 2008 14:37:33 +0300 (EEST) Subject: [Pw_forum] GGA underestimates lattice constant in BaO In-Reply-To: <39262.172.16.48.134.1218083476.squirrel@webmail.iitg.ac.in> Message-ID: Dear Munima, I have in fact come across a study that claims that Ba 4d states would make a difference : JAP 100, 086103 (2006) Best wishes, Hande -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From giannozz at democritos.it Thu Aug 7 14:55:16 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 7 Aug 2008 14:55:16 +0200 Subject: [Pw_forum] fhi2upf.f90 In-Reply-To: <20080807111148.16006.qmail@f5mail-237-215.rediffmail.com> References: <20080807111148.16006.qmail@f5mail-237-215.rediffmail.com> Message-ID: <200808071455.17350.giannozz@democritos.it> On Thursday 07 August 2008 13:11, ramesh kumar wrote: > Rcut and E pseu everything is (zero) different from the available > upf files [...] > nl pn l occ Rcut Rcut US E pseu > 3S 0 0 2.00 0.00000000000 0.00000000000 0.00000000000 > 3P 0 1 6.00 0.00000000000 0.00000000000 0.00000000000 > 4S 0 2 2.00 0.00000000000 0.00000000000 0.00000000000 > 3D 0 3 5.00 0.00000000000 0.00000000000 0.00000000000 > > is there something wrong ????????? nothing is wrong. A converter can convert data from one format into another, but it cannot invent data that is not available. The FHI format does not contain, to the best of my knowledge, information on either matching radii or pseudization energies. In any case, these are not actually used by quantum-espresso. They are useful only if you want to generate the pseudopotentials Paolo -- Paolo Giannozzi, Democritos and Udine University From bipulrr at gmail.com Fri Aug 8 07:14:47 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Fri, 8 Aug 2008 07:14:47 +0200 Subject: [Pw_forum] About band structure. In-Reply-To: References: Message-ID: <3a749910808072214seaa6357v4b6da4c010693317@mail.gmail.com> Dear Hande, Thanks for helping me. It really works and really solves my problem. Just one thing to ask is that, while plotting the bands structure, it generates file.xmgr file. The x-axis are the k-points. But my question is the k-points are three no. (e.g. like 0.5 0.5 0.5), but it convert it in a single number. Can you please tell me the formula, with which it convert? Its a very basic question. And sorry for asking that. regards On Thu, Aug 7, 2008 at 11:31 AM, Hande Ustunel < hande at newton.physics.metu.edu.tr> wrote: > > > And what is /awk/java/whathever_you_are_familiar_with ? > > I believe what Stefano meant is just take any known computer language > (which fortran, awk, bash, java each are) or any other one you are already > using and write a simple code that generates a given number of points > between two arbitrary points in space. I would suggest octave or matlab if > you are unfamiliar with coding. Maybe something like this : > > function ks=get_points(point1,point2,nks) > > kx = [linspace(point1(1),point2(1),nks)]'; > ky = [linspace(point1(2),point2(2),nks)]'; > kz = [linspace(point1(3),point2(3),nks)]'; > > > ks=[ kx ky kz ones(nks,1)]; > > endfunction > > Just copy this into a file called get_points.m, start octave (you should > already have this, assuming you are using linux), type something like > get_points([0 0 0], [1 0 0], 25) and copy and paste the result in your > input. You have to repeat this for each pair of points. Make sure you don't > repeat the same point (say K) twice because plotband really hates > that. Also beware that I put in the weights in the above script assuming > that you are running an nscf or a bands calculation where it doesn't matter > what you have for weights. If you are running anything else it does. > > Hope this helps. > Hande > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080808/b75f16b3/attachment.htm From hande at newton.physics.metu.edu.tr Fri Aug 8 08:52:43 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Fri, 8 Aug 2008 09:52:43 +0300 (EEST) Subject: [Pw_forum] About band structure. In-Reply-To: <3a749910808072214seaa6357v4b6da4c010693317@mail.gmail.com> Message-ID: Dear Bipul, > Thanks for helping me. It really works and really solves my problem. Just Glad it works for you. > one thing to ask is that, while plotting the bands structure, it generates > file.xmgr file. The x-axis are the k-points. But my question is the k-points > are three no. (e.g. like 0.5 0.5 0.5), but it convert it in a single number. I'm not exactly sure what you are asking but I'll assume that you are asking how a three-component vector can be represented by a single point on a plot. Here a good textbook on solid state is what you should be consulting. What we call the "band structure" is really a complicated four-dimensional plot : three axes kx, ky, kz and the energy values corresponding to each of these points. Since it is impossible to draw such a plot, this scheme has been devised where you pick some high-symmetry kpoints in the BZ and draw the band structures along lines that are drawn between these points. You can then represent this on a two-dimensional plot. Luckily all the interestin things happen between these points. These points are usually chosen at the edges of the BZ (or sometimes halfway) and are usually labeled with capital Latin letters (except Gamma) like X, J, M, J' so on and so forth. So for a cubic lattice, Gamma corresponds to (0,0,0), X corresponds to (pi/a,0,0) etc. Each of the points you see on the xmgr plot then corresponds to a point along one of these lines. This is a very basic topic so you should be able to read it in any of the core textbooks such as Kittel or Ashcroft and Mermin. There's a section on this also in R. Martin's electronic structure book. Best, Hande -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From miguel.martinez at ehu.es Fri Aug 8 11:28:26 2008 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Fri, 8 Aug 2008 11:28:26 +0200 Subject: [Pw_forum] Silent Calculations Message-ID: <20080808112826.0a0b24c2@ehu.es> Dear everybody, I've been running into a few issues as of late, when running some calculations, it seems the calculations have stalled for a pretty long period of time. The one that troubles me less, taking into account that it's pretty expensive, is an electron-phonon calculation. This is a pretty large system (20 atoms in the primitive cell) and computing the phonons at gamma took ages (well two days using 4 processors). It would be great if some output were written just to remind you the code is still working, maybe something related to convergence. But I find somewhat disturbing that no line was written since the electron phonon calculation began. My other issue is a very similar stalling in a Raman calculation. No, it's not the same structure. Here, I lack from experience, since this is the first Raman calculation I've done outside the examples. Self-consistent input is: &control calculation='scf' restart_mode='from_scratch', prefix='sih4', tstress = .true. tprnfor = .true. pseudo_dir = '/home/wmbmacam/pseudo/', outdir='/scratch/wmbmacam/fdd2-raman/' / &system ibrav= 10, celldm(1) = 12.65898481, celldm(2) = 1.07100858, celldm(3) = 0.621208699, nat=10, ntyp= 2, ecutwfc = 55.0 nr1= 72, nr2= 72, nr3= 72 / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Si 28.0855 Si.pbe-rrkj.UPF H 1.0079 H.pbe-vbc.UPF ATOMIC_POSITIONS {crystal} Si 0.614368447799 0.385631552201 0.614368447799 Si 0.864368447799 0.635631552201 0.864368447799 H 0.442372877617 0.836174882136 0.364427192728 H 0.364427192728 0.357025047520 0.442372877617 H 0.892974952480 0.885572807272 0.413825117864 H 0.413825117864 0.807627122383 0.892974952480 H 0.378768583324 0.338682246661 0.003482898532 H 0.003482898532 0.279066271483 0.378768583324 H 0.970933728517 0.246517101468 0.911317753339 H 0.911317753339 0.871231416676 0.970933728517 K_POINTS {automatic} 12 12 12 1 1 1 The phonon input is: phonons of Sih4 at Gamma &inputph tr2_ph=1.0d-16, prefix='sih4', epsil=.true., trans=.true., lraman=.true., elop=.true., amass(1)=28.0855, amass(2)=1.00794, outdir='/scratch/wmbmacam/fdd2-raman/', fildyn='sih4.dynG', fildrho='sih4.drho', / 0.0 0.0 0.0 The calculations stalled right after the effective charges calculations. After that, it spent 24 hours without writing anything (it needed 10 hours to compute the effective charges). No convergence, no threshold, no crashes, no nothing. Is this behaviour normal? Or are my compiled binaries just telling me I should stop bothering them in August? Finally, I just wanted to note that the amasses in example 15 are seemingly wrong. While the masses in the scf run are fine, the ones used in the phonon calculations correspond to GaAs instead of AlAs. Regards, Miguel -- ---------------------------------------- Miguel Mart?nez Canales Dto. F?sica de la Materia Condensada UPV/EHU Facultad de Ciencia y Tecnolog?a Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5326 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From eyvaz_isaev at yahoo.com Fri Aug 8 12:24:12 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 8 Aug 2008 03:24:12 -0700 (PDT) Subject: [Pw_forum] Silent Calculations In-Reply-To: <20080808112826.0a0b24c2@ehu.es> Message-ID: <380115.52704.qm@web65707.mail.ac4.yahoo.com> Dear Miguel, It might be I am wrong, but I am not sure phonons and shifted k-points are compatible. At least, I never did it (i.e. used only unshifted k-vectors). As concerns your joke about August, well, it is pretty good. And add September, October, November, etc. This one recalled me a famous math problem ... Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 8/8/08, Miguel Mart?nez wrote: > From: Miguel Mart?nez > Subject: [Pw_forum] Silent Calculations > To: "PWscf Forum" > Date: Friday, August 8, 2008, 1:28 PM > Dear everybody, > > I've been running into a few issues as of late, when > running some > calculations, it seems the calculations have stalled for a > pretty long > period of time. > > The one that troubles me less, taking into account that > it's pretty > expensive, is an electron-phonon calculation. This is a > pretty large > system (20 atoms in the primitive cell) and computing the > phonons at > gamma took ages (well two days using 4 processors). It > would be great > if some output were written just to remind you the code is > still > working, maybe something related to convergence. But I find > somewhat > disturbing that no line was written since the electron > phonon > calculation began. > > My other issue is a very similar stalling in a Raman > calculation. No, > it's not the same structure. Here, I lack from > experience, since this > is the first Raman calculation I've done outside the > examples. > > Self-consistent input is: > &control > calculation='scf' > restart_mode='from_scratch', > prefix='sih4', > tstress = .true. > tprnfor = .true. > pseudo_dir = '/home/wmbmacam/pseudo/', > outdir='/scratch/wmbmacam/fdd2-raman/' > / > &system > ibrav= 10, celldm(1) = 12.65898481, celldm(2) = > 1.07100858, > celldm(3) = 0.621208699, nat=10, ntyp= 2, > ecutwfc = 55.0 > nr1= 72, nr2= 72, nr3= 72 > / > &electrons > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Si 28.0855 Si.pbe-rrkj.UPF > H 1.0079 H.pbe-vbc.UPF > ATOMIC_POSITIONS {crystal} > Si 0.614368447799 0.385631552201 0.614368447799 > Si 0.864368447799 0.635631552201 0.864368447799 > H 0.442372877617 0.836174882136 0.364427192728 > H 0.364427192728 0.357025047520 0.442372877617 > H 0.892974952480 0.885572807272 0.413825117864 > H 0.413825117864 0.807627122383 0.892974952480 > H 0.378768583324 0.338682246661 0.003482898532 > H 0.003482898532 0.279066271483 0.378768583324 > H 0.970933728517 0.246517101468 0.911317753339 > H 0.911317753339 0.871231416676 0.970933728517 > K_POINTS {automatic} > 12 12 12 1 1 1 > > > The phonon input is: > > phonons of Sih4 at Gamma > &inputph > tr2_ph=1.0d-16, > prefix='sih4', > epsil=.true., > trans=.true., > lraman=.true., > elop=.true., > amass(1)=28.0855, > amass(2)=1.00794, > outdir='/scratch/wmbmacam/fdd2-raman/', > fildyn='sih4.dynG', > fildrho='sih4.drho', > / > 0.0 0.0 0.0 > > > The calculations stalled right after the effective charges > calculations. > After that, it spent 24 hours without writing anything (it > needed 10 > hours to compute the effective charges). No convergence, no > threshold, > no crashes, no nothing. > > Is this behaviour normal? Or are my compiled binaries just > telling me I > should stop bothering them in August? > > Finally, I just wanted to note that the amasses in example > 15 are > seemingly wrong. While the masses in the scf run are fine, > the ones > used in the phonon calculations correspond to GaAs instead > of AlAs. > > Regards, > > Miguel > > -- > ---------------------------------------- > Miguel Mart?nez Canales > Dto. F?sica de la Materia Condensada > UPV/EHU > Facultad de Ciencia y Tecnolog?a > Apdo. 644 > 48080 Bilbao (Spain) > Fax: +34 94 601 3500 > Tlf: +34 94 601 5326 > ---------------------------------------- > > "If you have an apple and I have an apple and > we exchange these apples then you and I will > still each have one apple. But if you have an > idea and I have an idea and we exchange these > ideas, then each of us will have two ideas." > > George Bernard Shaw > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From lataprem29 at gmail.com Fri Aug 8 12:39:25 2008 From: lataprem29 at gmail.com (premlata pandit) Date: Fri, 8 Aug 2008 16:09:25 +0530 Subject: [Pw_forum] problem releated to calculating elastic constants Message-ID: <6f289440808080339i2a19ca11k775eb8ed55565477@mail.gmail.com> hello the experimental lattice constant of Li2S is 10.7867 a.u. and my calculated equlibrium lattice constant is 10.375 a.u. by using LDA pseudopotential in pwscf calculation. can i use this lattice canstant to calculating elastic constants? -- Premlata Pandit Bhopal (MP) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080808/3b0ecbaf/attachment.htm From lataprem29 at gmail.com Fri Aug 8 12:55:49 2008 From: lataprem29 at gmail.com (premlata pandit) Date: Fri, 8 Aug 2008 16:25:49 +0530 Subject: [Pw_forum] elastic constant calculation Message-ID: <6f289440808080355m13cb11e2ha77ac9a33bf196e6@mail.gmail.com> hello How to calculate elastic constant? -- Premlata Pandit Ph.d. student Barkatullah university Bhopal (MP) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080808/ed7ee9e8/attachment.htm From hande at newton.physics.metu.edu.tr Fri Aug 8 12:57:24 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Fri, 8 Aug 2008 13:57:24 +0300 (EEST) Subject: [Pw_forum] problem releated to calculating elastic constants In-Reply-To: <6f289440808080339i2a19ca11k775eb8ed55565477@mail.gmail.com> Message-ID: Dear Premlata, It's normal for LDA to underestimate the lattice but in your case the error is about 4%. I would start to get nervous. One usually aims at 1 or at most 2 percent. I suggest you try other pseudopotentials and/or try to make sure that you are getting good fits for your Ecut, Nk, smearing (if necessary) parameters. By a "good curve" I mean one which is not too bumpy. Best, Hande On Fri, 8 Aug 2008, premlata pandit wrote: > hello > the experimental lattice constant of Li2S is 10.7867 a.u. > and my calculated equlibrium lattice constant is 10.375 a.u. by using LDA > pseudopotential in pwscf calculation. > can i use this lattice canstant to calculating elastic constants? > > -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From eyvaz_isaev at yahoo.com Fri Aug 8 12:58:52 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 8 Aug 2008 03:58:52 -0700 (PDT) Subject: [Pw_forum] problem releated to calculating elastic constants In-Reply-To: <6f289440808080339i2a19ca11k775eb8ed55565477@mail.gmail.com> Message-ID: <890443.39142.qm@web65714.mail.ac4.yahoo.com> Dear Premlata, --- On Fri, 8/8/08, premlata pandit wrote: > the experimental lattice constant of Li2S is 10.7867 a.u. > and my calculated equlibrium lattice constant is 10.375 > a.u. by using LDA pseudopotential in pwscf calculation. > can i use this lattice canstant to calculating elastic > constants? > The difference is around 4%, so, you can use it. Even you can use any lattice parameter for this purpose, the main question is what you expect. If you like compare with experiment, most likely calculated elastic constants will be larger than experimental ones. Commonly accepted practice is the use of experimental lattice parameter. But, for sure, you have to test pseudopotentials you apply. Bests, Eyvaz. > -- > Premlata Pandit > Bhopal (MP) ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From miguel.martinez at ehu.es Fri Aug 8 13:03:53 2008 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Fri, 8 Aug 2008 13:03:53 +0200 Subject: [Pw_forum] Silent Calculations In-Reply-To: <380115.52704.qm@web65707.mail.ac4.yahoo.com> References: <20080808112826.0a0b24c2@ehu.es> <380115.52704.qm@web65707.mail.ac4.yahoo.com> Message-ID: <20080808130353.0c37f993@ehu.es> Dear Eyvaz, Thanks for your answer. The only times I use unshifted grids are for electron-phonon calculations and for hexagonal (trigonal) lattices. So far, shifted meshes in phonons have worked fine for me, and they are used extensively in the examples that run ph.x (02, 14, 15 and 24 at least). Maybe npool isn't supported in raman calculations, but the code doesn't complain. I don't know. On Fri, 8 Aug 2008 03:24:12 -0700 (PDT) Eyvaz Isaev wrote: > Dear Miguel, > > It might be I am wrong, but I am not sure phonons and shifted > k-points are compatible. At least, I never did it (i.e. used only > unshifted k-vectors). > > As concerns your joke about August, well, it is pretty good. And add > September, October, November, etc. This one recalled me a famous math > problem ... > > Bests, > Eyvaz. -- ---------------------------------------- Miguel Mart?nez Canales Dto. F?sica de la Materia Condensada UPV/EHU Facultad de Ciencia y Tecnolog?a Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5326 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From eyvaz_isaev at yahoo.com Fri Aug 8 13:08:08 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 8 Aug 2008 04:08:08 -0700 (PDT) Subject: [Pw_forum] elastic constant calculation In-Reply-To: <6f289440808080355m13cb11e2ha77ac9a33bf196e6@mail.gmail.com> Message-ID: <296495.67175.qm@web65708.mail.ac4.yahoo.com> > How to calculate elastic constant? You should start with this question. Please have a look at papers Mehl MJ. Phys Rev B 1993;47:2493, and our just published paper on Pt-Sc alloys: Intermetallics 16 (2008) 982?986. Actually, there are tonns of papers devoted to calculation of elastic constants. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 8/8/08, premlata pandit wrote: > From: premlata pandit > Subject: [Pw_forum] elastic constant calculation > To: pw_forum at pwscf.org > Date: Friday, August 8, 2008, 2:55 PM > hello > How to calculate elastic constant? > -- > Premlata Pandit > Ph.d. student > Barkatullah university > Bhopal (MP) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From baroni at sissa.it Fri Aug 8 13:51:39 2008 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 8 Aug 2008 13:51:39 +0200 Subject: [Pw_forum] problem releated to calculating elastic constants In-Reply-To: References: Message-ID: non-linear core corrections to XC energies may be an issue here - you may want to chack cheers - SB On Aug 8, 2008, at 12:57 PM, Hande Ustunel wrote: > Dear Premlata, > > It's normal for LDA to underestimate the lattice but in your case > the error > is about 4%. I would start to get nervous. One usually aims at 1 or > at most > 2 percent. I suggest you try other pseudopotentials and/or try to > make sure > that you are getting good fits for your Ecut, Nk, smearing (if > necessary) > parameters. By a "good curve" I mean one which is not too bumpy. > > Best, > Hande > > On Fri, 8 Aug 2008, premlata pandit wrote: > >> hello >> the experimental lattice constant of Li2S is 10.7867 a.u. >> and my calculated equlibrium lattice constant is 10.375 a.u. by >> using LDA >> pseudopotential in pwscf calculation. >> can i use this lattice canstant to calculating elastic constants? >> >> > > > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080808/afb1994d/attachment.htm From subhra at iitg.ernet.in Fri Aug 8 12:49:55 2008 From: subhra at iitg.ernet.in (Subhradip Ghosh) Date: Fri, 8 Aug 2008 16:19:55 +0530 (IST) Subject: [Pw_forum] Silent Calculations In-Reply-To: <380115.52704.qm@web65707.mail.ac4.yahoo.com> References: <380115.52704.qm@web65707.mail.ac4.yahoo.com> Message-ID: <57955.172.16.48.18.1218192595.squirrel@webmail.iitg.ernet.in> Dear Eyvaz, It would be nice if you explain why phonons and shifted k-mesh are incompatible. Hiowever, I have used shifted k-mesh for phonon calculations and didn't find anything unusual for the systems I tried so far. Regards, Subhradip > Dear Miguel, > > It might be I am wrong, but I am not sure phonons and shifted k-points are > compatible. > At least, I never did it (i.e. used only unshifted k-vectors). > > As concerns your joke about August, well, it is pretty good. And add > September, October, November, etc. > This one recalled me a famous math problem ... > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Fri, 8/8/08, Miguel Mart?nez wrote: > >> From: Miguel Mart?nez >> Subject: [Pw_forum] Silent Calculations >> To: "PWscf Forum" >> Date: Friday, August 8, 2008, 1:28 PM >> Dear everybody, >> >> I've been running into a few issues as of late, when >> running some >> calculations, it seems the calculations have stalled for a >> pretty long >> period of time. >> >> The one that troubles me less, taking into account that >> it's pretty >> expensive, is an electron-phonon calculation. This is a >> pretty large >> system (20 atoms in the primitive cell) and computing the >> phonons at >> gamma took ages (well two days using 4 processors). It >> would be great >> if some output were written just to remind you the code is >> still >> working, maybe something related to convergence. But I find >> somewhat >> disturbing that no line was written since the electron >> phonon >> calculation began. >> >> My other issue is a very similar stalling in a Raman >> calculation. No, >> it's not the same structure. Here, I lack from >> experience, since this >> is the first Raman calculation I've done outside the >> examples. >> >> Self-consistent input is: >> &control >> calculation='scf' >> restart_mode='from_scratch', >> prefix='sih4', >> tstress = .true. >> tprnfor = .true. >> pseudo_dir = '/home/wmbmacam/pseudo/', >> outdir='/scratch/wmbmacam/fdd2-raman/' >> / >> &system >> ibrav= 10, celldm(1) = 12.65898481, celldm(2) = >> 1.07100858, >> celldm(3) = 0.621208699, nat=10, ntyp= 2, >> ecutwfc = 55.0 >> nr1= 72, nr2= 72, nr3= 72 >> / >> &electrons >> conv_thr = 1.0d-8 >> mixing_beta = 0.7 >> / >> ATOMIC_SPECIES >> Si 28.0855 Si.pbe-rrkj.UPF >> H 1.0079 H.pbe-vbc.UPF >> ATOMIC_POSITIONS {crystal} >> Si 0.614368447799 0.385631552201 0.614368447799 >> Si 0.864368447799 0.635631552201 0.864368447799 >> H 0.442372877617 0.836174882136 0.364427192728 >> H 0.364427192728 0.357025047520 0.442372877617 >> H 0.892974952480 0.885572807272 0.413825117864 >> H 0.413825117864 0.807627122383 0.892974952480 >> H 0.378768583324 0.338682246661 0.003482898532 >> H 0.003482898532 0.279066271483 0.378768583324 >> H 0.970933728517 0.246517101468 0.911317753339 >> H 0.911317753339 0.871231416676 0.970933728517 >> K_POINTS {automatic} >> 12 12 12 1 1 1 >> >> >> The phonon input is: >> >> phonons of Sih4 at Gamma >> &inputph >> tr2_ph=1.0d-16, >> prefix='sih4', >> epsil=.true., >> trans=.true., >> lraman=.true., >> elop=.true., >> amass(1)=28.0855, >> amass(2)=1.00794, >> outdir='/scratch/wmbmacam/fdd2-raman/', >> fildyn='sih4.dynG', >> fildrho='sih4.drho', >> / >> 0.0 0.0 0.0 >> >> >> The calculations stalled right after the effective charges >> calculations. >> After that, it spent 24 hours without writing anything (it >> needed 10 >> hours to compute the effective charges). No convergence, no >> threshold, >> no crashes, no nothing. >> >> Is this behaviour normal? Or are my compiled binaries just >> telling me I >> should stop bothering them in August? >> >> Finally, I just wanted to note that the amasses in example >> 15 are >> seemingly wrong. While the masses in the scf run are fine, >> the ones >> used in the phonon calculations correspond to GaAs instead >> of AlAs. >> >> Regards, >> >> Miguel >> >> -- >> ---------------------------------------- >> Miguel Mart?nez Canales >> Dto. F?sica de la Materia Condensada >> UPV/EHU >> Facultad de Ciencia y Tecnolog?a >> Apdo. 644 >> 48080 Bilbao (Spain) >> Fax: +34 94 601 3500 >> Tlf: +34 94 601 5326 >> ---------------------------------------- >> >> "If you have an apple and I have an apple and >> we exchange these apples then you and I will >> still each have one apple. But if you have an >> idea and I have an idea and we exchange these >> ideas, then each of us will have two ideas." >> >> George Bernard Shaw >> >> _______________________________________________ >> 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 > > ************************************************************************ Dr. Subhradip Ghosh Assistant Professor Department of Physics Indian Institute of Technology Guwahati,Assam-781039 India E-mail:subhra at iitg.ernet.in Phone: +91 361 2582717(O) +91 361 2584717(R) Fax: +91 361 2582749 (Physics) +91 361 2690762 (General) ************************************************************************ From huang87 at purdue.edu Fri Aug 8 15:10:19 2008 From: huang87 at purdue.edu (Zhen Huang) Date: Fri, 8 Aug 2008 09:10:19 -0400 Subject: [Pw_forum] Phonon dos and dispersion calculation problem. Message-ID: <1218201019.489c45bb76cea@webmail.purdue.edu> Dear friends, I am running a single-wall carbon nanotube case (5,0). The result of phdos shows Max |d(i,j)-d*(j,i)|/|d(i,j)|: 210.0909% Max |d(i,j)-d*(j,i)| = 0.062230 Max |d(i,j)-d*(j,i)|/|d(i,j)|: 266.6923% Max |d(i,j)-d*(j,i)| = 0.062230 Max |d(i,j)-d*(j,i)|/|d(i,j)|: 253.1387% Max |d(i,j)-d*(j,i)| = 0.062230 Max |d(i,j)-d*(j,i)|/|d(i,j)|: 233.9506% Max |d(i,j)-d*(j,i)| = 0.062230 Max |d(i,j)-d*(j,i)|/|d(i,j)|: 208.3492% Max |d(i,j)-d*(j,i)| = 0.062230 Max |d(i,j)-d*(j,i)|/|d(i,j)|: 213.2651% Max |d(i,j)-d*(j,i)| = 0.062230 Max |d(i,j)-d*(j,i)|/|d(i,j)|: 256.8845% Max |d(i,j)-d*(j,i)| = 0.062230 Does any one know what is wrong with it? On the other hand, I used C.pz-rrkjus.UPF for PP. It works well with graphite and give reasonable dispersion. However, there are several negative value in nanotube results. I use 1,1,40 in relax calculation and nq=1,1,32 for ph.x calculation. --------------- Zhen Huang Ph.D. Student Nanoscale Transport Research Group School of Mechanical Engineering Purdue University Tel: 765 426 9302 From degironc at sissa.it Fri Aug 8 17:02:17 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 08 Aug 2008 17:02:17 +0200 Subject: [Pw_forum] Phonon dos and dispersion calculation problem. In-Reply-To: <1218201019.489c45bb76cea@webmail.purdue.edu> References: <1218201019.489c45bb76cea@webmail.purdue.edu> Message-ID: <489C5FF9.6060006@sissa.it> this message means that the dynamical matrix is not hermitian as it should... it may be due to poor self-consistent convergence in the phonon calculation this may also be the reason for the negative (imaginary) frequencies you get. try to tighten the tr2_ph threshold. stefano Zhen Huang wrote: > Dear friends, > > I am running a single-wall carbon nanotube case (5,0). The result of phdos shows > Max |d(i,j)-d*(j,i)|/|d(i,j)|: 210.0909% > Max |d(i,j)-d*(j,i)| = 0.062230 > Max |d(i,j)-d*(j,i)|/|d(i,j)|: 266.6923% > Max |d(i,j)-d*(j,i)| = 0.062230 > Max |d(i,j)-d*(j,i)|/|d(i,j)|: 253.1387% > Max |d(i,j)-d*(j,i)| = 0.062230 > Max |d(i,j)-d*(j,i)|/|d(i,j)|: 233.9506% > Max |d(i,j)-d*(j,i)| = 0.062230 > Max |d(i,j)-d*(j,i)|/|d(i,j)|: 208.3492% > Max |d(i,j)-d*(j,i)| = 0.062230 > Max |d(i,j)-d*(j,i)|/|d(i,j)|: 213.2651% > Max |d(i,j)-d*(j,i)| = 0.062230 > Max |d(i,j)-d*(j,i)|/|d(i,j)|: 256.8845% > Max |d(i,j)-d*(j,i)| = 0.062230 > > Does any one know what is wrong with it? > > On the other hand, I used C.pz-rrkjus.UPF for PP. It works well with graphite > and give reasonable dispersion. However, there are several negative value in > nanotube results. I use 1,1,40 in relax calculation and nq=1,1,32 for ph.x > calculation. > > --------------- > Zhen Huang > Ph.D. Student > Nanoscale Transport Research Group > School of Mechanical Engineering > Purdue University > Tel: 765 426 9302 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From degironc at sissa.it Fri Aug 8 17:03:53 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 08 Aug 2008 17:03:53 +0200 Subject: [Pw_forum] Silent Calculations In-Reply-To: <57955.172.16.48.18.1218192595.squirrel@webmail.iitg.ernet.in> References: <380115.52704.qm@web65707.mail.ac4.yahoo.com> <57955.172.16.48.18.1218192595.squirrel@webmail.iitg.ernet.in> Message-ID: <489C6059.9050104@sissa.it> there should be no incompatibility between shifted grids and phonon calculations. stefano Subhradip Ghosh wrote: > Dear Eyvaz, > > It would be nice if you explain why phonons and shifted k-mesh are > incompatible. Hiowever, I have used shifted k-mesh for phonon calculations > and didn't find anything unusual for the systems I tried so far. > > Regards, > > Subhradip > > > > >> Dear Miguel, >> >> It might be I am wrong, but I am not sure phonons and shifted k-points are >> compatible. >> At least, I never did it (i.e. used only unshifted k-vectors). >> >> As concerns your joke about August, well, it is pretty good. And add >> September, October, November, etc. >> This one recalled me a famous math problem ... >> >> Bests, >> Eyvaz. >> >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >> Russia, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >> Sweden >> Condensed Matter Theory Group, Uppsala University, Sweden >> Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> --- On Fri, 8/8/08, Miguel Mart?nez wrote: >> >> >>> From: Miguel Mart?nez >>> Subject: [Pw_forum] Silent Calculations >>> To: "PWscf Forum" >>> Date: Friday, August 8, 2008, 1:28 PM >>> Dear everybody, >>> >>> I've been running into a few issues as of late, when >>> running some >>> calculations, it seems the calculations have stalled for a >>> pretty long >>> period of time. >>> >>> The one that troubles me less, taking into account that >>> it's pretty >>> expensive, is an electron-phonon calculation. This is a >>> pretty large >>> system (20 atoms in the primitive cell) and computing the >>> phonons at >>> gamma took ages (well two days using 4 processors). It >>> would be great >>> if some output were written just to remind you the code is >>> still >>> working, maybe something related to convergence. But I find >>> somewhat >>> disturbing that no line was written since the electron >>> phonon >>> calculation began. >>> >>> My other issue is a very similar stalling in a Raman >>> calculation. No, >>> it's not the same structure. Here, I lack from >>> experience, since this >>> is the first Raman calculation I've done outside the >>> examples. >>> >>> Self-consistent input is: >>> &control >>> calculation='scf' >>> restart_mode='from_scratch', >>> prefix='sih4', >>> tstress = .true. >>> tprnfor = .true. >>> pseudo_dir = '/home/wmbmacam/pseudo/', >>> outdir='/scratch/wmbmacam/fdd2-raman/' >>> / >>> &system >>> ibrav= 10, celldm(1) = 12.65898481, celldm(2) = >>> 1.07100858, >>> celldm(3) = 0.621208699, nat=10, ntyp= 2, >>> ecutwfc = 55.0 >>> nr1= 72, nr2= 72, nr3= 72 >>> / >>> &electrons >>> conv_thr = 1.0d-8 >>> mixing_beta = 0.7 >>> / >>> ATOMIC_SPECIES >>> Si 28.0855 Si.pbe-rrkj.UPF >>> H 1.0079 H.pbe-vbc.UPF >>> ATOMIC_POSITIONS {crystal} >>> Si 0.614368447799 0.385631552201 0.614368447799 >>> Si 0.864368447799 0.635631552201 0.864368447799 >>> H 0.442372877617 0.836174882136 0.364427192728 >>> H 0.364427192728 0.357025047520 0.442372877617 >>> H 0.892974952480 0.885572807272 0.413825117864 >>> H 0.413825117864 0.807627122383 0.892974952480 >>> H 0.378768583324 0.338682246661 0.003482898532 >>> H 0.003482898532 0.279066271483 0.378768583324 >>> H 0.970933728517 0.246517101468 0.911317753339 >>> H 0.911317753339 0.871231416676 0.970933728517 >>> K_POINTS {automatic} >>> 12 12 12 1 1 1 >>> >>> >>> The phonon input is: >>> >>> phonons of Sih4 at Gamma >>> &inputph >>> tr2_ph=1.0d-16, >>> prefix='sih4', >>> epsil=.true., >>> trans=.true., >>> lraman=.true., >>> elop=.true., >>> amass(1)=28.0855, >>> amass(2)=1.00794, >>> outdir='/scratch/wmbmacam/fdd2-raman/', >>> fildyn='sih4.dynG', >>> fildrho='sih4.drho', >>> / >>> 0.0 0.0 0.0 >>> >>> >>> The calculations stalled right after the effective charges >>> calculations. >>> After that, it spent 24 hours without writing anything (it >>> needed 10 >>> hours to compute the effective charges). No convergence, no >>> threshold, >>> no crashes, no nothing. >>> >>> Is this behaviour normal? Or are my compiled binaries just >>> telling me I >>> should stop bothering them in August? >>> >>> Finally, I just wanted to note that the amasses in example >>> 15 are >>> seemingly wrong. While the masses in the scf run are fine, >>> the ones >>> used in the phonon calculations correspond to GaAs instead >>> of AlAs. >>> >>> Regards, >>> >>> Miguel >>> >>> -- >>> ---------------------------------------- >>> Miguel Mart?nez Canales >>> Dto. F?sica de la Materia Condensada >>> UPV/EHU >>> Facultad de Ciencia y Tecnolog?a >>> Apdo. 644 >>> 48080 Bilbao (Spain) >>> Fax: +34 94 601 3500 >>> Tlf: +34 94 601 5326 >>> ---------------------------------------- >>> >>> "If you have an apple and I have an apple and >>> we exchange these apples then you and I will >>> still each have one apple. But if you have an >>> idea and I have an idea and we exchange these >>> ideas, then each of us will have two ideas." >>> >>> George Bernard Shaw >>> >>> _______________________________________________ >>> 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 >> >> >> > > > ************************************************************************ > Dr. Subhradip Ghosh > Assistant Professor > Department of Physics > Indian Institute of Technology > Guwahati,Assam-781039 > India > E-mail:subhra at iitg.ernet.in > Phone: +91 361 2582717(O) > +91 361 2584717(R) > Fax: +91 361 2582749 (Physics) > +91 361 2690762 (General) > ************************************************************************ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sks.jnc at gmail.com Fri Aug 8 18:41:53 2008 From: sks.jnc at gmail.com (S. K. S.) Date: Fri, 8 Aug 2008 22:11:53 +0530 Subject: [Pw_forum] Silent Calculations In-Reply-To: <20080808112826.0a0b24c2@ehu.es> References: <20080808112826.0a0b24c2@ehu.es> Message-ID: Dear Miguel, Yes, you are right. The linear response calculation needs much time even for calculating phonons at Gamma point. Only for Gamma point phonon one can use "Frozen phonon" method because it is much faster. The calculations can be got stalled for many reasons. You have not mentioned whether at last (I mean staying in the silence mode for few weeks) your jobs properly (without any error) get over or not??? If yes, then it can be due to the problem in your parallel computer - may be out of 16 processors some particular processor was down for some time. If the answer of the above question is no, then the memory of your computer is not sufficient enough to tackle a large system with lot of atoms because it needs large memory and as well as generates a huge tmp file. All input parameters (deguass, la2F, filedvscf ......) also should be given correctly for electron-phonon calculation. regards, SKS JNCASR Bangalore On 8/8/08, Miguel Mart?nez wrote: > > Dear everybody, > > I've been running into a few issues as of late, when running some > calculations, it seems the calculations have stalled for a pretty long > period of time. > > The one that troubles me less, taking into account that it's pretty > expensive, is an electron-phonon calculation. This is a pretty large > system (20 atoms in the primitive cell) and computing the phonons at > gamma took ages (well two days using 4 processors). It would be great > if some output were written just to remind you the code is still > working, maybe something related to convergence. But I find somewhat > disturbing that no line was written since the electron phonon > calculation began. > > My other issue is a very similar stalling in a Raman calculation. No, > it's not the same structure. Here, I lack from experience, since this > is the first Raman calculation I've done outside the examples. > > Self-consistent input is: > &control > calculation='scf' > restart_mode='from_scratch', > prefix='sih4', > tstress = .true. > tprnfor = .true. > pseudo_dir = '/home/wmbmacam/pseudo/', > outdir='/scratch/wmbmacam/fdd2-raman/' > / > &system > ibrav= 10, celldm(1) = 12.65898481, celldm(2) = 1.07100858, > celldm(3) = 0.621208699, nat=10, ntyp= 2, > ecutwfc = 55.0 > nr1= 72, nr2= 72, nr3= 72 > / > &electrons > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Si 28.0855 Si.pbe-rrkj.UPF > H 1.0079 H.pbe-vbc.UPF > ATOMIC_POSITIONS {crystal} > Si 0.614368447799 0.385631552201 0.614368447799 > Si 0.864368447799 0.635631552201 0.864368447799 > H 0.442372877617 0.836174882136 0.364427192728 > H 0.364427192728 0.357025047520 0.442372877617 > H 0.892974952480 0.885572807272 0.413825117864 > H 0.413825117864 0.807627122383 0.892974952480 > H 0.378768583324 0.338682246661 0.003482898532 > H 0.003482898532 0.279066271483 0.378768583324 > H 0.970933728517 0.246517101468 0.911317753339 > H 0.911317753339 0.871231416676 0.970933728517 > K_POINTS {automatic} > 12 12 12 1 1 1 > > > The phonon input is: > > phonons of Sih4 at Gamma > &inputph > tr2_ph=1.0d-16, > prefix='sih4', > epsil=.true., > trans=.true., > lraman=.true., > elop=.true., > amass(1)=28.0855, > amass(2)=1.00794, > outdir='/scratch/wmbmacam/fdd2-raman/', > fildyn='sih4.dynG', > fildrho='sih4.drho', > / > 0.0 0.0 0.0 > > > The calculations stalled right after the effective charges calculations. > After that, it spent 24 hours without writing anything (it needed 10 > hours to compute the effective charges). No convergence, no threshold, > no crashes, no nothing. > > Is this behaviour normal? Or are my compiled binaries just telling me I > should stop bothering them in August? > > Finally, I just wanted to note that the amasses in example 15 are > seemingly wrong. While the masses in the scf run are fine, the ones > used in the phonon calculations correspond to GaAs instead of AlAs. > > Regards, > > Miguel > > -- > ---------------------------------------- > Miguel Mart?nez Canales > Dto. F?sica de la Materia Condensada > UPV/EHU > Facultad de Ciencia y Tecnolog?a > Apdo. 644 > 48080 Bilbao (Spain) > Fax: +34 94 601 3500 > Tlf: +34 94 601 5326 > ---------------------------------------- > > "If you have an apple and I have an apple and > we exchange these apples then you and I will > still each have one apple. But if you have an > idea and I have an idea and we exchange these > ideas, then each of us will have two ideas." > > George Bernard Shaw > > _______________________________________________ > 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/20080808/77a0fabe/attachment.htm From baroni at sissa.it Fri Aug 8 19:44:53 2008 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 8 Aug 2008 19:44:53 +0200 Subject: [Pw_forum] Silent Calculations In-Reply-To: References: <20080808112826.0a0b24c2@ehu.es> Message-ID: <702C2A96-602D-41D9-BEFF-1B39BE3120FA@sissa.it> On Aug 8, 2008, at 6:41 PM, S. K. S. wrote: > > > Dear Miguel, > > Yes, you are right. The linear response calculation needs > much time even for calculating phonons at Gamma point. > Only for Gamma point phonon one > can use "Frozen > phonon" method because > it is much faster. I beg to differ ... SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080808/cff00530/attachment.htm From giannozz at democritos.it Fri Aug 8 22:20:29 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 8 Aug 2008 22:20:29 +0200 Subject: [Pw_forum] Silent Calculations In-Reply-To: <20080808112826.0a0b24c2@ehu.es> References: <20080808112826.0a0b24c2@ehu.es> Message-ID: <6DCD0D38-302A-494B-8A30-3B6ACB66D0EE@democritos.it> On Aug 8, 2008, at 11:28 , Miguel Mart?nez wrote: > The calculations stalled right after the effective charges > calculations. > After that, it spent 24 hours without writing anything (it needed 10 > hours to compute the effective charges). No convergence, no threshold, > no crashes, no nothing. > > Is this behaviour normal? it depends. It seems to me unlikely that the code will spend so much time without doing nothing, but it is not impossible. You need an idea of how much time a calculation requires. Typically you should start with a smaller system, or with a minimal k-point grid, to get such an idea. Note that the phonon code is not yet well optimized in some cases and for large cells, so it may require some tuning work. If you are running in parallel, consider that the code can "hang" if something goes wrong on any process, sometimes in very subtle ways > Or are my compiled binaries just telling me I > should stop bothering them in August? this is also very likely > Finally, I just wanted to note that the amasses in example 15 are were (fixed in the cvs version) > seemingly wrong. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 8 22:22:53 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 8 Aug 2008 22:22:53 +0200 Subject: [Pw_forum] Silent Calculations In-Reply-To: References: <20080808112826.0a0b24c2@ehu.es> Message-ID: <6CD1AE3D-87E0-4FA0-A884-39B4D0492355@democritos.it> On Aug 8, 2008, at 18:41 , S. K. S. wrote: > Only for Gamma point phonon one can use "Frozen > phonon" method because it is much faster. not true in general. Each linear-response calculation costs approx. as much as a self-consistent one, and you need at least as many scf calculations as linear-response calculations Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From marzari at MIT.EDU Sat Aug 9 05:08:55 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 09 Aug 2008 10:08:55 +0700 Subject: [Pw_forum] Silent Calculations In-Reply-To: <489C6059.9050104@sissa.it> References: <380115.52704.qm@web65707.mail.ac4.yahoo.com> <57955.172.16.48.18.1218192595.squirrel@webmail.iitg.ernet.in> <489C6059.9050104@sissa.it> Message-ID: <489D0A47.4090603@mit.edu> Stefano de Gironcoli wrote: > there should be no incompatibility between shifted grids and phonon > calculations. > stefano Stefano, all, let us know if this is still relevant: the phonons are usually calculated on a regular q-mesh that includes gamma (I think because of how qtor is written, although nothing would stop anyone from modifying it to work with a generic q mesh). Then, if the q-mesh is unshifted, and the k-mesh is shifted, the cost of the calculation can increase, because all the psi at k+q are needed, but k+q is not a point in the k-mesh list, unless the k-mesh (shifted) is fine enough and appropriately chosen so that all the k+q are in there. nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From sks.jnc at gmail.com Sat Aug 9 08:30:13 2008 From: sks.jnc at gmail.com (S. K. S.) Date: Sat, 9 Aug 2008 12:00:13 +0530 Subject: [Pw_forum] Silent Calculations In-Reply-To: <6CD1AE3D-87E0-4FA0-A884-39B4D0492355@democritos.it> References: <20080808112826.0a0b24c2@ehu.es> <6CD1AE3D-87E0-4FA0-A884-39B4D0492355@democritos.it> Message-ID: On Sat, Aug 9, 2008 at 1:52 AM, Paolo Giannozzi wrote: > Only for Gamma point phonon one can use "Frozen > phonon" method because it is much faster. not true in general. Each linear-response calculation costs approx. as much as a self-consistent one, and you need at least as many scf calculations as linear-response calculations. Dear Sir, I agree with you that for small system each linear-response calculation costs approx. as much as a self-consistent one, and we need at least as many scf calculations as linear-response calculations. However, IN CASE OF very large system (say about 64 atoms per unit cell), I found that a single representation takes too much computer time compared to a single scf run. Moreover, in some cluster which have multiple cpu for each node and in some quad or octa core computer, always phonon paralization is much slower than manual scf paralization (I mean manually divide your all scf calculations in different processors). In case of Frozen phonon method, one can also accomplish the same goal by using less memory and disk space. However, for non-zone center phonon Linear response is the best way. There is still a scope in PWSCF to make Phonon calculation much faster by implementing the representation number parallization. regards, SKS JNCASR BANGALORE On Sat, Aug 9, 2008 at 1:52 AM, Paolo Giannozzi wrote: > > On Aug 8, 2008, at 18:41 , S. K. S. wrote: > > > Only for Gamma point phonon one can use "Frozen > > phonon" method because it is much faster. > > not true in general. Each linear-response calculation > costs approx. as much as a self-consistent one, and > you need at least as many scf calculations as > linear-response calculations > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of 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/20080809/b3409ab5/attachment.htm From miguel.martinez at ehu.es Sat Aug 9 12:51:14 2008 From: miguel.martinez at ehu.es (Miguel =?UTF-8?B?TWFydMOtbmV6?=) Date: Sat, 9 Aug 2008 12:51:14 +0200 Subject: [Pw_forum] Silent Calculations In-Reply-To: <6DCD0D38-302A-494B-8A30-3B6ACB66D0EE@democritos.it> References: <20080808112826.0a0b24c2@ehu.es> <6DCD0D38-302A-494B-8A30-3B6ACB66D0EE@democritos.it> Message-ID: <20080809125114.69d229a3@ehu.es> Thank you everybody for all your answers. I never thought using a shifted grid would have an effect in the time needed for computing phonons! I'll try and see whether this effects my calculations or not. You'll be glad to hear that after decreasing the K_POINT mesh to 10 10 10 and tr2_ph to 1.0d-14 the code seems to be working as well as ever, although it's taking longer than expected. Regards, Miguel On Fri, 8 Aug 2008 22:20:29 +0200 Paolo Giannozzi wrote: > > it depends. It seems to me unlikely that the code will spend so much > time without doing nothing, but it is not impossible. You need an idea > of how much time a calculation requires. Typically you should start > with a smaller system, or with a minimal k-point grid, to get such an > idea. Note that the phonon code is not yet well optimized in some > cases and for large cells, so it may require some tuning work. > > If you are running in parallel, consider that the code can "hang" if > something goes wrong on any process, sometimes in very subtle ways > > > Or are my compiled binaries just telling me I > > should stop bothering them in August? > > this is also very likely > > > Finally, I just wanted to note that the amasses in example 15 are > > were (fixed in the cvs version) > > > seemingly wrong. > > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ---------------------------------------- Miguel Mart?nez Canales Dto. F?sica de la Materia Condensada UPV/EHU Facultad de Ciencia y Tecnolog?a Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5326 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From ali_jalaukhan at yahoo.com Sat Aug 9 21:31:37 2008 From: ali_jalaukhan at yahoo.com (ali jalaukhan) Date: Sat, 9 Aug 2008 12:31:37 -0700 (PDT) Subject: [Pw_forum] force Message-ID: <651218.94963.qm@web110014.mail.gq1.yahoo.com> Dear All I want to know about the suitable value for force-convergence threshold .Is .002 0r 0.003(Ryd/a.u) appropriate or not ? thanks Ali jalaukhan karbala university,Iraq From akohlmey at cmm.chem.upenn.edu Sat Aug 9 21:51:26 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 9 Aug 2008 15:51:26 -0400 (EDT) Subject: [Pw_forum] force In-Reply-To: <651218.94963.qm@web110014.mail.gq1.yahoo.com> References: <651218.94963.qm@web110014.mail.gq1.yahoo.com> Message-ID: On Sat, 9 Aug 2008, ali jalaukhan wrote: AJ> Dear All dear ali, AJ> I want to know about the suitable value for force-convergence AJ> threshold .Is .002 0r 0.003(Ryd/a.u) appropriate or not ? sorry, but this question is as easy to answer as whether blue or green is a suitable color for a car. as you can see from the many, many discussions in the mailing archives, the answer always depends on the kind of accuracy you expect from your calculation and how accurate your electron strucuture calculation is, and many other tiny details. if you want absolute answers, you have to change fields to philosophy or religious studies... cheers, axel. AJ> thanks AJ> Ali jalaukhan AJ> karbala university,Iraq AJ> AJ> AJ> AJ> AJ> AJ> _______________________________________________ AJ> Pw_forum mailing list AJ> Pw_forum at pwscf.org AJ> http://www.democritos.it/mailman/listinfo/pw_forum AJ> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From j.antonio.montoya at gmail.com Sun Aug 10 01:22:05 2008 From: j.antonio.montoya at gmail.com (j.antonio.montoya at gmail.com) Date: Sat, 9 Aug 2008 23:22:05 +0000 Subject: [Pw_forum] force Message-ID: <1380168523-1218324191-cardhu_decombobulator_blackberry.rim.net-1120839450-@bxe114.bisx.prod.on.blackberry> Dear Ali, In general you should try to stay above 0.00001. Therefore, the two values that you mentioned are both reasonable values for forc_conv_thr. Javier J. A. Montoya Geophysical Laboratory Washington, DC USA ------Original Message------ From: ali jalaukhan Sender: pw_forum-bounces at pwscf.org To: Pw_forum at pwscf.org ReplyTo: ali_jalaukhan at yahoo.com ReplyTo: PWSCF Forum Sent: Aug 9, 2008 3:31 PM Subject: [Pw_forum] force Dear All I want to know about the suitable value for force-convergence threshold .Is .002 0r 0.003(Ryd/a.u) appropriate or not ? thanks Ali jalaukhan karbala university,Iraq _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum Sent via BlackBerry by AT&T From bnrj.rudra at yahoo.com Sun Aug 10 09:40:19 2008 From: bnrj.rudra at yahoo.com (Rudra Banerjee) Date: Sun, 10 Aug 2008 13:10:19 +0530 (IST) Subject: [Pw_forum] help in using cputimer.c Message-ID: <734483.38745.qm@web94104.mail.in2.yahoo.com> dear friends, i am trying to call the PW function cputime.c in one of my f90 code as t0cpu(1) = scnds() t0wall(1) = cclock() but due to my horrible knowledge, i dont know what is to be put in the INTERFACE block to make an explicit interface. will anybody plz help me? -- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu..org/philosophy/no-word-attachments.html Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/ From baroni at sissa.it Sun Aug 10 11:19:01 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 10 Aug 2008 11:19:01 +0200 Subject: [Pw_forum] Silent Calculations In-Reply-To: References: <20080808112826.0a0b24c2@ehu.es> <6CD1AE3D-87E0-4FA0-A884-39B4D0492355@democritos.it> Message-ID: Dear S.K.S., dear all: I maintain that if a linear-response calculation takes longer than an ordinary SCF calculation for a same system, this can only be due to the fact that the implementation of LRT is not as optimized as that of SCF. This may well be the case for codes in Quantum Espresso, at least for some systems, but it has NOT to be so by necessity. If it continues to be so it is that too many people have misconceptions about LRT and/or have not the time/fiber/keennes to improve upon existing implementations. Nothing wrong with this state of affairs, given the fact that SCF calculations have a much larger scope of application. It would be worse if SCF were less optimized than LRT. This being said, I believe that general and apodictic statements such as those made by SKS should be substantiated by more solid arguments than episodic experience. Once again, nothing wrong in reporting about one's own episodic experience, provided it is reported as such, and not as an absolute truth. Cheers, Stefano On Aug 9, 2008, at 8:30 AM, S. K. S. wrote: > > > > On Sat, Aug 9, 2008 at 1:52 AM, Paolo Giannozzi > wrote: > > Only for Gamma point phonon one can use "Frozen > > phonon" method because it is much faster. > > not true in general. Each linear-response calculation > costs approx. as much as a self-consistent one, and > you need at least as many scf calculations as > linear-response calculations. > > Dear Sir, > I agree with you that for small system each > linear-response calculation > costs approx. as much as a self-consistent one, and > we need at least as many scf calculations as > linear-response calculations. > > However, IN CASE OF very large system (say about 64 atoms per unit > cell), > I found that a single representation takes too much computer time > compared to a single scf run. > > Moreover, in some cluster which have multiple cpu > for each node and in some quad or octa core computer, always > phonon paralization is much slower than manual > scf paralization (I mean manually divide your all scf > calculations in > different processors). In case of Frozen phonon method, one can > also accomplish the same goal by using less memory and > disk space. > However, for non-zone center phonon Linear response is the best way. > There is still a scope in PWSCF to make Phonon calculation much faster > by implementing the representation number parallization. > > regards, > SKS > JNCASR > BANGALORE > > > On Sat, Aug 9, 2008 at 1:52 AM, Paolo Giannozzi > wrote: > > On Aug 8, 2008, at 18:41 , S. K. S. wrote: > > > Only for Gamma point phonon one can use "Frozen > > phonon" method because it is much faster. > > not true in general. Each linear-response calculation > costs approx. as much as a self-consistent one, and > you need at least as many scf calculations as > linear-response calculations > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080810/31e065d6/attachment.htm From giannozz at democritos.it Sun Aug 10 11:19:04 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 10 Aug 2008 11:19:04 +0200 Subject: [Pw_forum] help in using cputimer.c In-Reply-To: <734483.38745.qm@web94104.mail.in2.yahoo.com> References: <734483.38745.qm@web94104.mail.in2.yahoo.com> Message-ID: <3732732B-8120-46D1-B07B-634F0FEDD62C@democritos.it> On Aug 10, 2008, at 9:40 , Rudra Banerjee wrote: > i am trying to call the PW function cputime.c in one of my f90 code as > t0cpu(1) = scnds() > t0wall(1) = cclock() > [...] i dont know what is to be put in the INTERFACE block to make an > explicit interface. you do not need an explicit interface: those are C routines that can be directly called by linking clib/clib.a, or simply clib/cptimer.o . You just need to define them as double precision functions in the calling program (see Modules/clocks.f90) Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From baroni at sissa.it Sun Aug 10 11:54:44 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 10 Aug 2008 11:54:44 +0200 Subject: [Pw_forum] force In-Reply-To: <651218.94963.qm@web110014.mail.gq1.yahoo.com> References: <651218.94963.qm@web110014.mail.gq1.yahoo.com> Message-ID: Dear Ali, first of all, let me rejoice for receiving scientific correspondence from such a troubled part of the world, and let me express the wish that having the state of mind to ask serious scientific questions is a promise of peace. Coming to your question. The correct answer is a very frequent one in science: "it depends". Let me explain what I mean by this. I suppose you want to know the force threshold below which an energy minimization should be stopped. Let us ask ourself, first, what enegry minimizations are meant for. If they are meant to find equilibrium geometries, then the first thing you should ask is to which precision you want to know the interatomic distances. This only you can say (it depends on the accuracy the data are known experimentally, or the further use you may want to make of these calculated data). Then, you have to ask what maximum error in the force is compatible with the error that you judge tolerable in the distances. The answer depends on the stiffness of the material (or, technically, on the magnitude of the interatomic force constants), that you have to know (explicitly or implicitly), at least as an order of magnitude. If you do not have the faintest idea of how stiff the material is, the rule of thumb is: form an idea by yourself, and do not rely on "internet rumors". An inexpensive way of forming your own ideas is to do some computer experiment. Do a calculation with some force threshold. Repeat the same calculation with a threshold ten times as small. How much do the atomic positions change? Repeat the same game for different thresholds and for different, but related, systems. You will soon see what is best in your specific case. Little by little, you will develop your own rules of thumb. If they are good, they will not be general. You will see that the same threshold would apply for the majority of cases, but you will also discover exceptions. Many people here would suggest that a threshold in between 0.1 and 1 mRy/au is adequate in many circumstances, but this suggestion will never surrogate your own experience. Hope this helps a little bit. Salam aleykum - Stefano Baroni On Aug 9, 2008, at 9:31 PM, ali jalaukhan wrote: > Dear All > I want to know about the suitable value for force-convergence > threshold .Is .002 0r 0.003(Ryd/a.u) appropriate or not ? > thanks > Ali jalaukhan > karbala university,Iraq > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080810/4c60a719/attachment-0001.htm From sks.jnc at gmail.com Mon Aug 11 05:42:28 2008 From: sks.jnc at gmail.com (S. K. S.) Date: Mon, 11 Aug 2008 09:12:28 +0530 Subject: [Pw_forum] Silent Calculations In-Reply-To: References: <20080808112826.0a0b24c2@ehu.es> <6CD1AE3D-87E0-4FA0-A884-39B4D0492355@democritos.it> Message-ID: Dear Sir, Sorry, for my statements. I did not want to report them as an absolute truth. My comments was only based on the Quantum esspresso code. In other packages, the LRT can be more efficient. I have not checked them yet. Anyway, I would like to thank Prof. Baroni for his excellent reply which will really help to clear people's misconceptions about LRT regards SKS JNCASR BANGALORE -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080811/815d1fbc/attachment.htm From wangqj1 at 126.com Mon Aug 11 11:38:10 2008 From: wangqj1 at 126.com (wangqj1) Date: Mon, 11 Aug 2008 17:38:10 +0800 (CST) Subject: [Pw_forum] how to visual the lattice consistant use xcrysden ? Message-ID: <15814685.210521218447490377.JavaMail.coremail@bj126app27.126.com> Dear xcrysden users I want to know the detailed process of installing the xcrysden in my PC. Because after I installed the xcrysden ,I use it to see the structure of a out.file ,I found that the modules(AdvGeom and Properties) of xrysden can not use . Anybody who gives usefull help will be appreciated . qjwang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080811/7a390dc6/attachment.htm From iphyboy at hotmail.com Mon Aug 11 18:28:09 2008 From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=) Date: Tue, 12 Aug 2008 00:28:09 +0800 Subject: [Pw_forum] second energy parameter setting in RRKJ USPP Message-ID: Dear all: I want to generate my own RRKJ type ultrasoft pseudopotential with atomic code in PWSCF, I encountered a very confusing situation: when I chose -0.20Ry as the second energy used to pseudize the 5s orbit, the ld1.x always complains : ================================================= from gener_pseudo : error # 1 too many nodes ================================================= however if I change the energy to be -0.50Ry, the corresponding complain disappeared. How should I choose these energy parameters to generate a good pseudopotential and how should I have a correct understanding of these parameters? Thanks very much . Wenmei My &inputp file is also listed as : 64D 3 2 10 0.00 1.00 2.004D 3 2 0 -0.20 1.00 2.005S 1 0 2 0.00 2.00 2.505S 1 0 0 -0.50 2.00 2.505P 2 1 3 0.00 2.66 2.985P 2 1 0 -0.20 2.66 2.98 _________________________________________________________________ ??????????????? http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AA&Form=MEVHAA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080812/db86c347/attachment.htm From hande at newton.physics.metu.edu.tr Mon Aug 11 18:36:23 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Mon, 11 Aug 2008 19:36:23 +0300 (EEST) Subject: [Pw_forum] second energy parameter setting in RRKJ USPP In-Reply-To: Message-ID: Dear Wenmei, I usually look at the output of the all-electron calculation and choose an energy close to the ae orbital energy. Once I manage to generate the pseudopotential I go as far away as possible from that reference without upsetting the code. Hope this helps... Hande On Tue, 12 Aug 2008, [gb2312] ?????? wrote: > > Dear all: > > I want to generate my own RRKJ type ultrasoft pseudopotential with atomic code in PWSCF, > I encountered a very confusing situation: > > when I chose -0.20Ry as the second energy used to pseudize the 5s orbit, the ld1.x always complains : > ================================================= > from gener_pseudo : error # 1 too many nodes > ================================================= > however if I change the energy to be -0.50Ry, the corresponding complain disappeared. > > How should I choose these energy parameters to generate a good pseudopotential and how should I have a > correct understanding of these parameters? > > Thanks very much . > > Wenmei > > My &inputp file is also listed as : > > 64D 3 2 10 0.00 1.00 2.004D 3 2 0 -0.20 1.00 2.005S 1 0 2 0.00 2.00 2.505S 1 0 0 -0.50 2.00 2.505P 2 1 3 0.00 2.66 2.985P 2 1 0 -0.20 2.66 2.98 > > > > > > _________________________________________________________________ > ?????????????????????????????? > http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AA&Form=MEVHAA -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From baroni at sissa.it Mon Aug 11 21:42:18 2008 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 11 Aug 2008 21:42:18 +0200 Subject: [Pw_forum] second energy parameter setting in RRKJ USPP In-Reply-To: References: Message-ID: <08D4B86F-2978-452F-A5AE-AEECA19E271C@sissa.it> Dear Wenmei: besides the very sound suggestion by Hande, I would also recommend that you take a glance at any (possibly, old) textbook in elementary quantum mechanics. Why old? Because modern texts often given elementary stuff for granted, which usually it is not. Coming to the specific issue that you raise. The number of nodes in the solution of a 1D Schroedinger equation depends on the energy parameter. The lower the energy, the fewer the nodes. Of course, for an arbitrary energy parameter the resulting wavefunction is not normalizable, that is why it has to be discarded, but for very special, discrete, values, and energy is quantized. It is interesting to understand "intuitively" how quantization of energy comes about. As you rise the energy from any given value, the outer node moves out furthhr and futher from the origin, but the number of nodes stays constant if you do not change the energy too much. If the energy is raised too much, a further node will appear. For some critical value of the energy, the "extra" node will be at infinity: that's when an energy eigenvalue is crossed. I do not expect that, if you have never heard about similar arguments, you will understand mine, which have been stated rather sloppily. Actually, if you decide to study this matter in a serious book, your ability to understand my "sloppy arguments" will be a check of your actual understanding of the serious arguments expounded in the book. Hope this helps, a bit Stefano On Aug 11, 2008, at 6:36 PM, Hande Ustunel wrote: > Dear Wenmei, > > I usually look at the output of the all-electron calculation and > choose an > energy close to the ae orbital energy. Once I manage to generate the > pseudopotential I go as far away as possible from that reference > without > upsetting the code. > > Hope this helps... > Hande > > On Tue, 12 Aug 2008, [gb2312] ?????? wrote: > >> >> Dear all: >> >> I want to generate my own RRKJ type ultrasoft pseudopotential >> with atomic code in PWSCF, >> I encountered a very confusing situation: >> >> when I chose -0.20Ry as the second energy used to pseudize the 5s >> orbit, the ld1.x always complains : >> ================================================= >> from gener_pseudo : error # 1 too many nodes >> ================================================= >> however if I change the energy to be -0.50Ry, the corresponding >> complain disappeared. >> >> How should I choose these energy parameters to generate a good >> pseudopotential and how should I have a >> correct understanding of these parameters? >> >> Thanks very much . >> >> Wenmei >> >> My &inputp file is also listed as : >> >> 64D 3 2 10 0.00 1.00 2.004D 3 2 0 -0.20 1.00 >> 2.005S 1 0 2 0.00 2.00 2.505S 1 0 0 -0.50 2.00 >> 2.505P 2 1 3 0.00 2.66 2.985P 2 1 0 -0.20 2.66 >> 2.98 >> >> >> >> >> >> _________________________________________________________________ >> ?????????????????????????????? >> http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AA&Form=MEVHAA > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From prasenjit.jnc at gmail.com Mon Aug 11 22:43:55 2008 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Mon, 11 Aug 2008 22:43:55 +0200 Subject: [Pw_forum] second energy parameter setting in RRKJ USPP In-Reply-To: <08D4B86F-2978-452F-A5AE-AEECA19E271C@sissa.it> References: <08D4B86F-2978-452F-A5AE-AEECA19E271C@sissa.it> Message-ID: <627e0ffa0808111343k62e6bdaah5cd46c4c8a8f3e7e@mail.gmail.com> Dear Stefano, Thanks for the nice explanation. Can you please suggest some "old" quantum mechanics books or some other reading materials where they deal with such issues? With regards, Prasenjit. 2008/8/11 Stefano Baroni > Dear Wenmei: > > besides the very sound suggestion by Hande, I would also recommend > that you take a glance at any (possibly, old) textbook in elementary > quantum mechanics. Why old? Because modern texts often given > elementary stuff for granted, which usually it is not. > > Coming to the specific issue that you raise. The number of nodes in > the solution of a 1D Schroedinger equation depends on the energy > parameter. The lower the energy, the fewer the nodes. Of course, for > an arbitrary energy parameter the resulting wavefunction is not > normalizable, that is why it has to be discarded, but for very > special, discrete, values, and energy is quantized. It is interesting > to understand "intuitively" how quantization of energy comes about. As > you rise the energy from any given value, the outer node moves out > furthhr and futher from the origin, but the number of nodes stays > constant if you do not change the energy too much. If the energy is > raised too much, a further node will appear. For some critical value > of the energy, the "extra" node will be at infinity: that's when an > energy eigenvalue is crossed. > > I do not expect that, if you have never heard about similar > arguments, you will understand mine, which have been stated rather > sloppily. Actually, if you decide to study this matter in a serious > book, your ability to understand my "sloppy arguments" will be a check > of your actual understanding of the serious arguments expounded in the > book. > > Hope this helps, a bit > Stefano > > On Aug 11, 2008, at 6:36 PM, Hande Ustunel wrote: > > > Dear Wenmei, > > > > I usually look at the output of the all-electron calculation and > > choose an > > energy close to the ae orbital energy. Once I manage to generate the > > pseudopotential I go as far away as possible from that reference > > without > > upsetting the code. > > > > Hope this helps... > > Hande > > > > On Tue, 12 Aug 2008, [gb2312] ??? wrote: > > > >> > >> Dear all: > >> > >> I want to generate my own RRKJ type ultrasoft pseudopotential > >> with atomic code in PWSCF, > >> I encountered a very confusing situation: > >> > >> when I chose -0.20Ry as the second energy used to pseudize the 5s > >> orbit, the ld1.x always complains : > >> ================================================= > >> from gener_pseudo : error # 1 too many nodes > >> ================================================= > >> however if I change the energy to be -0.50Ry, the corresponding > >> complain disappeared. > >> > >> How should I choose these energy parameters to generate a good > >> pseudopotential and how should I have a > >> correct understanding of these parameters? > >> > >> Thanks very much . > >> > >> Wenmei > >> > >> My &inputp file is also listed as : > >> > >> 64D 3 2 10 0.00 1.00 2.004D 3 2 0 -0.20 1.00 > >> 2.005S 1 0 2 0.00 2.00 2.505S 1 0 0 -0.50 2.00 > >> 2.505P 2 1 3 0.00 2.66 2.985P 2 1 0 -0.20 2.66 > >> 2.98 > >> > >> > >> > >> > >> > >> _________________________________________________________________ > >> ??????????????? > >> > http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AA&Form=MEVHAA > > > > -- > > Hande Toffoli > > Department of Physics > > Office 439 > > Middle East Technical University > > Ankara 06531, Turkey > > Tel : +90 312 210 3264 > > http://www.physics.metu.edu.tr/~hande > > > > _______________________________________________ > > 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 > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080811/f89e6ba4/attachment-0001.htm From naylin.nll at gmail.com Tue Aug 12 03:14:55 2008 From: naylin.nll at gmail.com (Nay Lin) Date: Tue, 12 Aug 2008 09:14:55 +0800 Subject: [Pw_forum] How to produce supercells with plane and line defects Message-ID: <619d39dc0808111814v5ec523f2j3000c2f3e02740bc@mail.gmail.com> Dear PWScf users, I want to know how to produce the supercells with plane and line defects. Is there some downloadable tools to construct from the CIF file downloaded from crystal structure databases. thanks Lin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080812/2aa82092/attachment.htm From iphyboy at hotmail.com Tue Aug 12 05:05:36 2008 From: iphyboy at hotmail.com (=?utf-8?Q?=E6=98=8E=E6=96=87=E7=BE=8E?=) Date: Tue, 12 Aug 2008 11:05:36 +0800 Subject: [Pw_forum] second energy parameter setting in RRKJ USPP In-Reply-To: <08D4B86F-2978-452F-A5AE-AEECA19E271C@sissa.it> References: <08D4B86F-2978-452F-A5AE-AEECA19E271C@sissa.it> Message-ID: Dear Prof. Stefano Baroni and Prof. Hande Toffoli: Thanks for all your helpful suggestion.I understand your useful comments. Best regards. Wenmei> From: baroni at sissa.it> To: pw_forum at pwscf.org> Date: Mon, 11 Aug 2008 21:42:18 +0200> Subject: Re: [Pw_forum] second energy parameter setting in RRKJ USPP> > Dear Wenmei:> > besides the very sound suggestion by Hande, I would also recommend > that you take a glance at any (possibly, old) textbook in elementary > quantum mechanics. Why old? Because modern texts often given > elementary stuff for granted, which usually it is not.> > Coming to the specific issue that you raise. The number of nodes in > the solution of a 1D Schroedinger equation depends on the energy > parameter. The lower the energy, the fewer the nodes. Of course, for > an arbitrary energy parameter the resulting wavefunction is not > normalizable, that is why it has to be discarded, but for very > special, discrete, values, and energy is quantized. It is interesting > to understand "intuitively" how quantization of energy comes about. As > you rise the energy from any given value, the outer node moves out > furthhr and futher from the origin, but the number of nodes stays > constant if you do not change the energy too much. If the energy is > raised too much, a further node will appear. For some critical value > of the energy, the "extra" node will be at infinity: that's when an > energy eigenvalue is crossed.> > I do not expect that, if you have never heard about similar > arguments, you will understand mine, which have been stated rather > sloppily. Actually, if you decide to study this matter in a serious > book, your ability to understand my "sloppy arguments" will be a check > of your actual understanding of the serious arguments expounded in the > book.> > Hope this helps, a bit> Stefano> > On Aug 11, 2008, at 6:36 PM, Hande Ustunel wrote:> > > Dear Wenmei,> >> > I usually look at the output of the all-electron calculation and > > choose an> > energy close to the ae orbital energy. Once I manage to generate the> > pseudopotential I go as far away as possible from that reference > > without> > upsetting the code.> >> > Hope this helps...> > Hande> >> > On Tue, 12 Aug 2008, [gb2312] ?????? wrote:> >> >>> >> Dear all:> >>> >> I want to generate my own RRKJ type ultrasoft pseudopotential > >> with atomic code in PWSCF,> >> I encountered a very confusing situation:> >>> >> when I chose -0.20Ry as the second energy used to pseudize the 5s > >> orbit, the ld1.x always complains :> >> =================================================> >> from gener_pseudo : error # 1 too many nodes> >> =================================================> >> however if I change the energy to be -0.50Ry, the corresponding > >> complain disappeared.> >>> >> How should I choose these energy parameters to generate a good > >> pseudopotential and how should I have a> >> correct understanding of these parameters?> >>> >> Thanks very much .> >>> >> Wenmei> >>> >> My &inputp file is also listed as :> >>> >> 64D 3 2 10 0.00 1.00 2.004D 3 2 0 -0.20 1.00 > >> 2.005S 1 0 2 0.00 2.00 2.505S 1 0 0 -0.50 2.00 > >> 2.505P 2 1 3 0.00 2.66 2.985P 2 1 0 -0.20 2.66 > >> 2.98> >>> >>> >>> >>> >>> >> _________________________________________________________________> >> ??????????????????????????????> >> http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AA&Form=MEVHAA> >> > -- > > Hande Toffoli> > Department of Physics> > Office 439> > Middle East Technical University> > Ankara 06531, Turkey> > Tel : +90 312 210 3264> > http://www.physics.metu.edu.tr/~hande> >> > _______________________________________________> > 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 _________________________________________________________________ ???MSN??????????????????? http://mobile.msn.com.cn/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080812/82cee97e/attachment.htm From baroni at sissa.it Tue Aug 12 08:33:55 2008 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 12 Aug 2008 08:33:55 +0200 Subject: [Pw_forum] second energy parameter setting in RRKJ USPP In-Reply-To: <627e0ffa0808111343k62e6bdaah5cd46c4c8a8f3e7e@mail.gmail.com> References: <08D4B86F-2978-452F-A5AE-AEECA19E271C@sissa.it> <627e0ffa0808111343k62e6bdaah5cd46c4c8a8f3e7e@mail.gmail.com> Message-ID: I am too old too remember, and too lazy to search in the library ... ;-) Actually, the matter is probably treated in "old" math phys books, such as Courant & Hilbert or Morse & Feshbach. The chapter where this is dealt with is on Sturm Liouville theory (http://en.wikipedia.org/wiki/Sturm-Liouville_theory ). You do not need to dig very much in math. All I know I learnt why I wrote a solver for the 1D Schroedinger equation, which is the ancestor of the solvers presently included in the QE distribution ... ("practice is the Mother of learning") Cheers - SB On Aug 11, 2008, at 10:43 PM, Prasenjit Ghosh wrote: > Dear Stefano, > > Thanks for the nice explanation. > Can you please suggest some "old" quantum mechanics books or some > other reading materials where they deal with such issues? > > With regards, > Prasenjit. > > 2008/8/11 Stefano Baroni > Dear Wenmei: > > besides the very sound suggestion by Hande, I would also recommend > that you take a glance at any (possibly, old) textbook in elementary > quantum mechanics. Why old? Because modern texts often given > elementary stuff for granted, which usually it is not. > > Coming to the specific issue that you raise. The number of nodes in > the solution of a 1D Schroedinger equation depends on the energy > parameter. The lower the energy, the fewer the nodes. Of course, for > an arbitrary energy parameter the resulting wavefunction is not > normalizable, that is why it has to be discarded, but for very > special, discrete, values, and energy is quantized. It is interesting > to understand "intuitively" how quantization of energy comes about. As > you rise the energy from any given value, the outer node moves out > furthhr and futher from the origin, but the number of nodes stays > constant if you do not change the energy too much. If the energy is > raised too much, a further node will appear. For some critical value > of the energy, the "extra" node will be at infinity: that's when an > energy eigenvalue is crossed. > > I do not expect that, if you have never heard about similar > arguments, you will understand mine, which have been stated rather > sloppily. Actually, if you decide to study this matter in a serious > book, your ability to understand my "sloppy arguments" will be a check > of your actual understanding of the serious arguments expounded in the > book. > > Hope this helps, a bit > Stefano > > On Aug 11, 2008, at 6:36 PM, Hande Ustunel wrote: > > > Dear Wenmei, > > > > I usually look at the output of the all-electron calculation and > > choose an > > energy close to the ae orbital energy. Once I manage to generate the > > pseudopotential I go as far away as possible from that reference > > without > > upsetting the code. > > > > Hope this helps... > > Hande > > > > On Tue, 12 Aug 2008, [gb2312] ??? wrote: > > > >> > >> Dear all: > >> > >> I want to generate my own RRKJ type ultrasoft pseudopotential > >> with atomic code in PWSCF, > >> I encountered a very confusing situation: > >> > >> when I chose -0.20Ry as the second energy used to pseudize the 5s > >> orbit, the ld1.x always complains : > >> ================================================= > >> from gener_pseudo : error # 1 too many nodes > >> ================================================= > >> however if I change the energy to be -0.50Ry, the corresponding > >> complain disappeared. > >> > >> How should I choose these energy parameters to generate a good > >> pseudopotential and how should I have a > >> correct understanding of these parameters? > >> > >> Thanks very much . > >> > >> Wenmei > >> > >> My &inputp file is also listed as : > >> > >> 64D 3 2 10 0.00 1.00 2.004D 3 2 0 -0.20 1.00 > >> 2.005S 1 0 2 0.00 2.00 2.505S 1 0 0 -0.50 2.00 > >> 2.505P 2 1 3 0.00 2.66 2.985P 2 1 0 -0.20 2.66 > >> 2.98 > >> > >> > >> > >> > >> > >> _________________________________________________________________ > >> ??????????????? > >> http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AA&Form=MEVHAA > > > > -- > > Hande Toffoli > > Department of Physics > > Office 439 > > Middle East Technical University > > Ankara 06531, Turkey > > Tel : +90 312 210 3264 > > http://www.physics.metu.edu.tr/~hande > > > > _______________________________________________ > > 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 > > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > +39 3807528672 (M) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080812/7e5229fb/attachment-0001.htm From tone.kokalj at ijs.si Tue Aug 12 09:36:29 2008 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 12 Aug 2008 09:36:29 +0200 Subject: [Pw_forum] how to visual the lattice consistant use xcrysden ? In-Reply-To: <15814685.210521218447490377.JavaMail.coremail@bj126app27.126.com> References: <15814685.210521218447490377.JavaMail.coremail@bj126app27.126.com> Message-ID: <1218526589.4716.12.camel@walk.ijs.si> On Mon, 2008-08-11 at 17:38 +0800, wangqj1 wrote: > > > Dear xcrysden users > I want to know the detailed process of installing the xcrysden > in my PC. > Because after I installed the xcrysden ,I use it to see the > structure of a out.file ,I found that the modules(AdvGeom and > Properties) of xrysden can not use . Which is what you should see: the AdvGeom & Properties menus should be disabled (they are only active when working with the www.crystal.unito.it program). Apparently, you installed it correctly. Regards, Tone PS: if you want to visualize isosurfaces/contours (e.g. charge density), you will use: Tools->Data Grid menu. -- Tone Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) From iphyboy at hotmail.com Tue Aug 12 12:10:45 2008 From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=) Date: Tue, 12 Aug 2008 18:10:45 +0800 Subject: [Pw_forum] local pseudopotential part construction Message-ID: Dear all: Recently, I have been studying pseudopotential theory. As many papers point out : the pseudopotential is general non-local and uaually can be written as a locaol potential and some l-dependent projectors.Also I knew that in principle the local potential can be arbitarily chosen. But I am very confused how the local potential is chosen in practice,e.g.in realastic DFT code implementation.Can someone recommend some papers concerning the construction scheme of local potential to me ? Thanks very much. Wenmei _________________________________________________________________ ??????????????? http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AA&Form=MEVHAA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080812/2f39efa3/attachment.htm From mansourehp at gmail.com Tue Aug 12 15:59:06 2008 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Tue, 12 Aug 2008 17:29:06 +0330 Subject: [Pw_forum] DOS with gnuplot Message-ID: Dear all My question might be not related to PWscf code,but one can help me solve my problem.It's related to DOS plotting with gnuplot.how can I shift x=0(origin) to Fermi energy with gnuplot?(how can one perform a shift in x axis with gnuplot)? I look forward to hearing from you good luck Mansoureh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080812/cb76300e/attachment.htm From eyvaz_isaev at yahoo.com Tue Aug 12 16:08:22 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 12 Aug 2008 07:08:22 -0700 (PDT) Subject: [Pw_forum] DOS with gnuplot In-Reply-To: Message-ID: <889330.19409.qm@web65701.mail.ac4.yahoo.com> Yes, quite easily. let us take ef as 10(eV) ef=10 set yzeroaxis plot [a:b] [:] "DOS.file" u ($1-ef):2 w l lw 2 Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 8/12/08, Mansoureh Pashangpour wrote: > From: Mansoureh Pashangpour > Subject: [Pw_forum] DOS with gnuplot > To: Pw_forum at pwscf.org > Date: Tuesday, August 12, 2008, 5:59 PM > Dear all > My question might be not related to PWscf code,but one can > help me solve my > problem.It's related to DOS plotting with gnuplot.how > can I shift > x=0(origin) to Fermi energy with gnuplot?(how can one > perform a shift in x > axis with gnuplot)? > I look forward to hearing from you > good luck > Mansoureh > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From mansourehp at gmail.com Tue Aug 12 16:16:57 2008 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Tue, 12 Aug 2008 17:46:57 +0330 Subject: [Pw_forum] DOS with gnuplot In-Reply-To: <889330.19409.qm@web65701.mail.ac4.yahoo.com> References: <889330.19409.qm@web65701.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz thanks alot.It works and solved my problem. bye Mansoureh On Tue, Aug 12, 2008 at 5:38 PM, Eyvaz Isaev wrote: > Yes, quite easily. > let us take ef as 10(eV) > > ef=10 > set yzeroaxis > > plot [a:b] [:] "DOS.file" u ($1-ef):2 w l lw 2 > > Bests, > Eyvaz. > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Tue, 8/12/08, Mansoureh Pashangpour wrote: > > > From: Mansoureh Pashangpour > > Subject: [Pw_forum] DOS with gnuplot > > To: Pw_forum at pwscf.org > > Date: Tuesday, August 12, 2008, 5:59 PM > > Dear all > > My question might be not related to PWscf code,but one can > > help me solve my > > problem.It's related to DOS plotting with gnuplot.how > > can I shift > > x=0(origin) to Fermi energy with gnuplot?(how can one > > perform a shift in x > > axis with gnuplot)? > > I look forward to hearing from you > > good luck > > Mansoureh > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080812/c2b2c4d0/attachment.htm From sauluck at iitk.ac.in Tue Aug 12 17:35:25 2008 From: sauluck at iitk.ac.in (Sushil Auluck) Date: Tue, 12 Aug 2008 21:05:25 +0530 (IST) Subject: [Pw_forum] DOS with gnuplot In-Reply-To: References: Message-ID: <1178.172.24.120.49.1218555325.squirrel@newwebmail.iitk.ac.in> hi, here is an excellent reference/guide to gnuplot. http://t16web.lanl.gov/Kawano/gnuplot/index-e.html s.auluck > Dear all > My question might be not related to PWscf code,but one can help me solve > my > problem.It's related to DOS plotting with gnuplot.how can I shift > x=0(origin) to Fermi energy with gnuplot?(how can one perform a shift in x > axis with gnuplot)? > I look forward to hearing from you > good luck > Mansoureh > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ....................................................................... Prof. Sushil Auluck Phone:+91-512-6797092/6148 Department of Physics +91-512-6798177(Home) Indian Institute of Technology Cell :+91-9305548667 Kanpur 208016 (UP) Fax :+91-512-6790914 India E-mail:sauluck at iitk.ac.in ...............................................:sauluck at gmail.com http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html ....................................................................... ~ From gaoguoying at gmail.com Wed Aug 13 03:47:20 2008 From: gaoguoying at gmail.com (Guoying Gao) Date: Wed, 13 Aug 2008 09:47:20 +0800 Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf' Message-ID: <6234c0c60808121847l1932096eif55c3ac554873126@mail.gmail.com> Dear PW users, I performed a electronic band structure calculation with "m-p" smearing using Quantum-ESPRESSO code. At the end of 'scf and 'nscf' calculations, both gave Fermi energy. However, they are not the same. some parameters in the input file: scf: k-mesh grids 10*10*10 (282kpoints in *.scf.out file) nscf: we give 121 kpoints along high symmetry direction What I want to know is: why the two Fermi energy is different, if we want to plot energy band structure which Fermi energy should we use, why? Any suggestions will be welcomed. Best wishes! Guoying National Lab of Superhard Materials Jilin Univ. P.R.China From mansourehp at gmail.com Wed Aug 13 06:20:19 2008 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Wed, 13 Aug 2008 07:50:19 +0330 Subject: [Pw_forum] plot with gnuplot Message-ID: Dear all I am using gnuplot to plot DOS plots,but when I make its output as a postscript file and then use it to make its pdf and send it to word.doc ,its resolution decreases.Does anyone a good sugesstion to solve this problem? good luck Mansoureh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080813/bcb6fb60/attachment.htm From hande at newton.physics.metu.edu.tr Wed Aug 13 07:34:46 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Wed, 13 Aug 2008 08:34:46 +0300 (EEST) Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf' In-Reply-To: <6234c0c60808121847l1932096eif55c3ac554873126@mail.gmail.com> Message-ID: Dear Guoying, > scf: k-mesh grids 10*10*10 (282kpoints in > *.scf.out file) > nscf: we give 121 kpoints along high symmetry direction > In order to find the Fermi energy, the code performs an integration in k-space and this integration is of course numerically performed over the kpoints you provide. In the nscf run, you provide a highly heterogeneous set of kpoints so the Fermi energy you get is not the same as the scf solution where the BZ is sampled more evenly (and also more densely in your case). As a result, you should trust the scf result. Best, Hande -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From lawrence_lee_lee at yahoo.com.hk Wed Aug 13 08:58:33 2008 From: lawrence_lee_lee at yahoo.com.hk (Lawrence Lee) Date: Wed, 13 Aug 2008 14:58:33 +0800 Subject: [Pw_forum] plot with gnuplot In-Reply-To: References: Message-ID: <1218610713.17008.7.camel@scg11> Dear Mansoureh, A better way to put the graphs into WORD is to first convert the eps file into png (or other format like jpg. Personally I prefer png for its small file size and lossless compression). To do this, if you are Windows user, Photoshop will work fine. If you use Linux, GIMP can also perform this conversion easily. If you would like to use commands, you may install Imagemagick. Then type, for example, convert -density 300 input.eps output.png 300 is the width resolution in dpi. If you omit this, you turn out to have a low resolution png like what you saw before. On Wed, 2008-08-13 at 07:50 +0330, Mansoureh Pashangpour wrote: > Dear all > I am using gnuplot to plot DOS plots,but when I make its output as a > postscript file and then use it to make its pdf and send it to > word.doc ,its resolution decreases.Does anyone a good sugesstion to > solve this problem? > good luck > Mansoureh > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- S.H. Lee M.Phil Physics Division The CUHK Graduate School _______________________________________ ?x?????? - Yahoo! Messenger ???????]?????W?????????????????????????o???????????W?r???????????????????f???????????? http://messenger.yahoo.com.hk From gaoguoying at gmail.com Wed Aug 13 09:18:34 2008 From: gaoguoying at gmail.com (Guoying Gao) Date: Wed, 13 Aug 2008 15:18:34 +0800 Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf' In-Reply-To: References: <6234c0c60808121847l1932096eif55c3ac554873126@mail.gmail.com> Message-ID: <6234c0c60808130018w15eeab88tef3a25d545004ec8@mail.gmail.com> Dear Hande, Thanks for your answer. I have got it. Regards! Guoying From wangxinquan at tju.edu.cn Wed Aug 13 10:26:57 2008 From: wangxinquan at tju.edu.cn (wangxinquan) Date: Wed, 13 Aug 2008 16:26:57 +0800 Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'(XQ Wang) References: <418611239.09594@tju.edu.cn> Message-ID: <418616042.21309@tju.edu.cn> >>Dear Guoying >> >> scf: k-mesh grids 10*10*10 (282kpoints in >> *.scf.out file) >> nscf: we give 121 kpoints along high symmetry direction >> >> >>In order to find the Fermi energy, the code performs an integration in >>k-space and this integration is of course numerically performed over the >>kpoints you provide. In the nscf run, you provide a highly heterogeneous >>set of kpoints so the Fermi energy you get is not the same as the scf >>solution where the BZ is sampled more evenly (and also more densely in your >>case). As a result, you should trust the scf result. Dear Guoying, In my opinion, you should use the nscf results if you want to calculate the band structure. According to the example 08 of espresso-4.0.1, the calculation of DOS for Ni follows three steps:1. pw.x (scf);2.pw.x(nscf);3.dos.x(dos). The calculation of nscf modifies the wavefunctions obtained by scf calculations. You will see that the k-points were identified manually in scf while they were automatically selected in nscf. So the Fermi energy used in band structure calculation should be the result from nscf. I'm not sure that the above suggestions are absolutely right. It's just my limited experience. You'd better investigate the README file in the example 08 by yourself. Hope this help. Cheers, XQ Wang ===================================== X.Q. Wang wangxinquan at tju.edu.cn School of Chemical Engineering and Technology Tianjin University 92 Weijin Road, Tianjin, P. R. China tel:86-22-27890268, fax: 86-22-27892301 ===================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080813/6b323abe/attachment.htm From prasenjit.jnc at gmail.com Wed Aug 13 13:53:49 2008 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Wed, 13 Aug 2008 13:53:49 +0200 Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'(XQ Wang) In-Reply-To: <418616042.21309@tju.edu.cn> References: <418611239.09594@tju.edu.cn> <418616042.21309@tju.edu.cn> Message-ID: <627e0ffa0808130453r5bc627e8w16a1a1ec11db4ba4@mail.gmail.com> Dear Wang, In principle both the scf & nscf should give exactly the same value of Fermi energy if your calculations are converged w.r.t. the k-point sampling (since evaluation of Fermi energy involves numerical integration in k-space). The fact that that the two procedures give different energies suggest that the k-point mesh is not converged. Since these are numerical integrations, the more the no of k-points the more accurate is the value of the integral. Therefore for Guoying's case, the value of Fermi energy obtained from scf is more accurate than that from nscf as suggested by Hande. If the difference in Fermi energy is quite large, what I would suggest is to increase the no. of k-points in the nscf cal. & redo it. With regards, Prasenjit. 2008/8/13 wangxinquan > >>Dear Guoying > >> > >> scf: k-mesh grids 10*10*10 (282kpoints in > >> *.scf.out file) > > >> nscf: we give 121 kpoints along high symmetry direction > >> > >> > >>In order to find the Fermi energy, the code performs an integration in > >>k-space and this integration is of course numerically performed over the > >>kpoints you provide. In the nscf run, you provide a highly heterogeneous > >>set of kpoints so the Fermi energy you get is not the same as the scf > > >>solution where the BZ is sampled more evenly (and also more densely in your > >>case). As a result, you should trust the scf result. > > Dear Guoying, > > In my opinion, you should use the nscf results if you want to calculate > the band > structure. According to the example 08 of espresso-4.0.1, the calculation > of DOS for Ni follows three steps:1. pw.x (scf);2.pw.x(nscf);3.dos.x(dos). > The calculation > of nscf modifies the wavefunctions obtained by scf calculations. You will > see > that the k-points were identified manually in scf while they were > automatically selected in > nscf. So the Fermi energy used in band structure calculation should be the > result from nscf. > I'm not sure that the above suggestions are absolutely right. It's just > my limited experience. > You'd better investigate the README file in the example 08 by yourself. > Hope this help. > > Cheers, > XQ Wang > > > ===================================== > > X.Q. Wang > > wangxinquan at tju.edu.cn > > School of Chemical Engineering and Technology > > Tianjin University > > 92 Weijin Road, Tianjin, P. R. China > > tel:86-22-27890268, fax: 86-22-27892301 > > ===================================== > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080813/18219ab0/attachment.htm From hande at newton.physics.metu.edu.tr Wed Aug 13 14:22:16 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Wed, 13 Aug 2008 15:22:16 +0300 (EEST) Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'(XQ Wang) In-Reply-To: <627e0ffa0808130453r5bc627e8w16a1a1ec11db4ba4@mail.gmail.com> Message-ID: Dear Prasenjit, > If the difference in Fermi energy is quite large, what I would suggest is to > increase the no. of k-points in the nscf cal. & redo it. The fact that Guoying's nscf calculation was conducted along high symmetry points suggests that it was to be followed by a band structure run. In that case, it is not necessary to try to obtain a "good" Fermi energy from the nscf run other than convince oneself since this is not the point here. Besides, I don't think increasing the number of kpoints along these high symmetry directions would mean much because since you would still have a severely heterogeneous sampling. It should just sufficient to just draw the band structure from nscf along with the Fermi energy from the scf calculation. But you would be absolutely right if what we were trying to do here was to, say, increase resolution in a DOS plot. On a separate note, I suggest that you try bands rather than nscf if you are trying to draw a band structure since nscf worries about symmetries and creates extra points whereas bands just does the ones you ask it to do. Best, Hande -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From lanhaiping at gmail.com Wed Aug 13 18:09:50 2008 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 14 Aug 2008 00:09:50 +0800 Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'(XQ Wang) In-Reply-To: References: <627e0ffa0808130453r5bc627e8w16a1a1ec11db4ba4@mail.gmail.com> Message-ID: dear hande, i do wonder a point about fermi energy. when we draw a bands along high symmetry points, which values of fermi energy we should do align with ? the situation of 'nscf' calculation with large BZ sampling ,or just the 'bands' calculation along the high symmetry points ? Bests, On Wed, Aug 13, 2008 at 8:22 PM, Hande Ustunel < hande at newton.physics.metu.edu.tr> wrote: > Dear Prasenjit, > > > If the difference in Fermi energy is quite large, what I would suggest is > to > > increase the no. of k-points in the nscf cal. & redo it. > > The fact that Guoying's nscf calculation was conducted along high symmetry > points suggests that it was to be followed by a band structure run. In that > case, it is not necessary to try to obtain a "good" Fermi energy from the > nscf run other than convince oneself since this is not the point > here. Besides, I don't think increasing the number of kpoints along these > high symmetry directions would mean much because since you would still have > a severely heterogeneous sampling. It should just sufficient to just draw > the band structure from nscf along with the Fermi energy from the scf > calculation. But you would be absolutely right if what we were trying to do > here was to, say, increase resolution in a DOS plot. > > On a separate note, I suggest that you try bands rather than nscf if you > are trying to draw a band structure since nscf worries about symmetries and > creates extra points whereas bands just does the ones you ask it to do. > > Best, > Hande > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080814/834663b0/attachment-0001.htm From Steven.Kirk at hv.se Wed Aug 13 17:10:02 2008 From: Steven.Kirk at hv.se (Steven Kirk) Date: Wed, 13 Aug 2008 17:10:02 +0200 Subject: [Pw_forum] Wavefunction format documentation for PWSCF version 3.0 Message-ID: <48A2F94A.6090807@hv.se> Hello, I have some old simulation results produced using PWSCF v3.0, specifically old input files, .wfc and .chdens files. I need to be able to extract the wavefunction information in order to calculate the Bohm quantum potential. Is there any documentation for the .wfc file format other than the source code itself? If so, where can I find it? Regards, Steve Kirk -- Dr. Steven R. Kirk Dept. of Technology, Mathematics & Computer Science (P)+46 520 223215 University West (F)+46 520 223299 Trollhattan 461 86 SWEDEN http://beacon.webhop.org From degironc at sissa.it Wed Aug 13 18:24:20 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 13 Aug 2008 18:24:20 +0200 Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'(XQ Wang) In-Reply-To: References: <627e0ffa0808130453r5bc627e8w16a1a1ec11db4ba4@mail.gmail.com> Message-ID: <48A30AB4.9060703@sissa.it> Dear Haiping, the ONLY Fermi energy that is meaningful is the one corresponding to a scf calculation... which is calculated consistently with the corresponding charge density. All nscf or band calculations are performed on grids which might give non-regular sampling of the BZ... you should not use the corresponding fermi energy . stefano lan haiping wrote: > dear hande, > i do wonder a point about fermi energy. > when we draw a bands along high symmetry points, which > values of fermi energy we should do align with ? the situation of > 'nscf' calculation with large BZ sampling ,or just > the 'bands' calculation along the high symmetry points ? > Bests, > > On Wed, Aug 13, 2008 at 8:22 PM, Hande Ustunel > > wrote: > > Dear Prasenjit, > > > If the difference in Fermi energy is quite large, what I would > suggest is to > > increase the no. of k-points in the nscf cal. & redo it. > > The fact that Guoying's nscf calculation was conducted along high > symmetry > points suggests that it was to be followed by a band structure > run. In that > case, it is not necessary to try to obtain a "good" Fermi energy > from the > nscf run other than convince oneself since this is not the point > here. Besides, I don't think increasing the number of kpoints > along these > high symmetry directions would mean much because since you would > still have > a severely heterogeneous sampling. It should just sufficient to > just draw > the band structure from nscf along with the Fermi energy from the scf > calculation. But you would be absolutely right if what we were > trying to do > here was to, say, increase resolution in a DOS plot. > > On a separate note, I suggest that you try bands rather than nscf > if you > are trying to draw a band structure since nscf worries about > symmetries and > creates extra points whereas bands just does the ones you ask it > to do. > > Best, > Hande > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com , hplan at pku.edu.cn > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From chenhanghuipwscf at gmail.com Wed Aug 13 20:46:15 2008 From: chenhanghuipwscf at gmail.com (alan chen) Date: Wed, 13 Aug 2008 14:46:15 -0400 Subject: [Pw_forum] vc-relax in the presence of finite electric field Message-ID: <22ae3ca40808131146v1fa739a5kb890c9e5be459d0@mail.gmail.com> Dear PWSCF users, I have done a calculation of LaAlO3 recently, using 'vc-relax' with the contraints that only z-direction is relaxed and x,y directions are fixed, and in the presence of finite electric field (based on Berry Phase method). The input file is attached at the end. However I am very confused with the results. The equilibrium lattice constant in z direction is c=0.95*a (a is the lattice constant in x and y direction). The final ionic polarization is 72.03 a.u. and electronic polarization is 4.50 a.u. Then I use the equilibrium unit cell (c=0.95*a) and just 'relax' the atoms in the presence of the same electric field. I obtain: ionic polarization is 75.13 a.u. and electronic polarization is 1.36 a.u. Even more confusing is that if I use the equilibrium unit cell (c=0.95*a) and put the atom in the ideal position (i.e. no ionic polarization), the reference ionic polarization is 73.24 a.u. Shall I trust the 'vc-relax' calculation in the presence of finite electric field? Thank you very much. Input file reads: &CONTROL calculation='vc-relax' wf_collect=.true. pseudo_dir = './psp' outdir='/scratch' wfcdir='/scratch' prefix='sLAO-vc' tprnfor = .true. tstress = .true. disk_io='low' verbosity='high' dt=80.D0 lelfield=.true. gdir=3 nppstr=16 nberrycyc=1 / &SYSTEM ibrav= 6 celldm(1) = 7.27 celldm(3) = 0.9506 nat= 5 ntyp= 3 ecutwfc = 30.0 ecutrho = 180.0 occupations='fixed' nosym=.true. /&ELECTRONS diagonalization='david' mixing_beta = 0.7D0 diago_david_ndim = 4 startingwfc='random' startingpot='atomic' efield=0.00348 conv_thr = 1.0d-9 / &IONS ion_dynamics = 'damp' phase_space = 'full' pot_extrapolation = 'second_order' wfc_extrapolation = 'second_order' / &CELL cell_dynamics = 'damp-w' cell_dofree = 'z' / ATOMIC_SPECIES La 138.91 057-La-ca-nsp-hanghui.uspp.format.UPF Al 26.98 013-Al-ca--hanghui.uspp.format.UPF O 16.00 008-O-ca--vgrp.uspp.format.UPF ATOMIC_POSITIONS crystal La 0.00 0.00 0.00 Al 0.50 0.50 0.50 O 0.50 0.50 0.00 O 0.00 0.50 0.50 O 0.50 0.00 0.50 K_POINTS crystal 256 (The k points are omitted here) Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080813/3f303cc7/attachment.htm From peterwiney at gmail.com Wed Aug 13 23:22:39 2008 From: peterwiney at gmail.com (Peter Winey) Date: Wed, 13 Aug 2008 17:22:39 -0400 Subject: [Pw_forum] npwx in pwscf v.4.0 Message-ID: Dear all, I just noticed that in pwscf v4.0, some information, such as nbnd and npwx etc, are no longer printed out in the pw.x output file, even when I used "verbosity= high". I am particular interested in knowing "npwx". Is there a quick way of getting it or do I have to go back to version 3.2.x? Thanks in advance! -Peter ******************************************** Peter Winey, Ph.D., DuPont peterwiney at gmail.com ******************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080813/a4e502da/attachment.htm From chenhanghuipwscf at gmail.com Wed Aug 13 23:33:56 2008 From: chenhanghuipwscf at gmail.com (alan chen) Date: Wed, 13 Aug 2008 17:33:56 -0400 Subject: [Pw_forum] IOTK library Message-ID: <22ae3ca40808131433m52802a3do94106d27509387fe@mail.gmail.com> Dear PWSCF users, I have encountered this problem many times and I checked the archive but I still did not get how to fix the problem. Some of my jobs are killed by the following errors: ######################################################################################################################## # FROM IOTK LIBRARY, VERSION 1.1.0development # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_getline (iotk_scan.spp:812) # CVS Revision: 1.7 # iostat=-1 # ERROR IN: iotk_scan_tag (iotk_scan.spp:516) # CVS Revision: 1.7 # ERROR IN: iotk_scan (iotk_scan.spp:710) # CVS Revision: 1.7 # ERROR IN: iotk_scan_end (iotk_scan.spp:211) # CVS Revision: 1.7 # foundl # ERROR IN: iotk_close_read (iotk_files.spp:589) # CVS Revision: 1.3 ######################################################################################################################## Paolo suggested a quick fix: change Q_REAL in Q_REAL_SPACE in Modules/xml_io_base.f90 (thanks to Giovanni Bussi). Does that mean: replace Q_REAL_SPACE by Q_REAL? Could any one provide more specific procedures to fix the bug? Thank you very much. Hanghui Chen Department of Physics, Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080813/d86fccae/attachment.htm From eyvaz_isaev at yahoo.com Wed Aug 13 23:59:35 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 13 Aug 2008 14:59:35 -0700 (PDT) Subject: [Pw_forum] npwx in pwscf v.4.0 In-Reply-To: Message-ID: <19927.7114.qm@web65706.mail.ac4.yahoo.com> Dear Peter, nbnd now is printed as "number of Kohn-Sham states", as concerns npwx, it is worth looking at "Kohn-Sham Wavefunctions" right after k-points, where the firts number is npwx, the second one, again, is nbnd. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 8/14/08, Peter Winey wrote: > From: Peter Winey > Subject: [Pw_forum] npwx in pwscf v.4.0 > To: pw_forum at pwscf.org > Date: Thursday, August 14, 2008, 1:22 AM > Dear all, > > I just noticed that in pwscf v4.0, some information, such > as nbnd and npwx > etc, > are no longer printed out in the pw.x output file, even > when I used > "verbosity= high". > > I am particular interested in knowing "npwx". Is > there a quick way of > getting it or > do I have to go back to version 3.2.x? > > Thanks in advance! > > -Peter > > ******************************************** > Peter Winey, Ph.D., DuPont > peterwiney at gmail.com > ******************************************** > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From peterwiney at gmail.com Thu Aug 14 00:18:50 2008 From: peterwiney at gmail.com (Peter Winey) Date: Wed, 13 Aug 2008 18:18:50 -0400 Subject: [Pw_forum] npwx in pwscf v.4.0 In-Reply-To: <19927.7114.qm@web65706.mail.ac4.yahoo.com> References: <19927.7114.qm@web65706.mail.ac4.yahoo.com> Message-ID: Got it. Thanks a lot for the quick reply! -Peter On 8/13/08, Eyvaz Isaev wrote: > > Dear Peter, > > nbnd now is printed as "number of Kohn-Sham states", > as concerns npwx, it is worth looking at > "Kohn-Sham Wavefunctions" right after k-points, where the firts number is > npwx, the second one, again, is nbnd. > > Bests, > Eyvaz. > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080813/75f96538/attachment.htm From sauluck at iitk.ac.in Thu Aug 14 06:04:12 2008 From: sauluck at iitk.ac.in (Sushil Auluck) Date: Thu, 14 Aug 2008 09:34:12 +0530 Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'(XQ Wang) In-Reply-To: References: <627e0ffa0808130453r5bc627e8w16a1a1ec11db4ba4@mail.gmail.com> Message-ID: <48A3AEBC.9030908@iitk.ac.in> hi, as emphasized many times on this forum the correct fermi is the one calculated with a k-mesh that is spread over the whole brilluoin zone ...NOT the one that comes out of a band structure calculation which is from a k-mesh that is along symmetry directions. s.auluck -- ....................................................................... Prof. Sushil Auluck Phone:+91-512-6797092/6148 Department of Physics +91-512-6798177(Home) Indian Institute of Technology Cell :+91-9305548667 Kanpur 208016 (UP) Fax :+91-512-6790914 India E-mail:sauluck at iitk.ac.in ...............................................:sauluck at gmail.com http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html ....................................................................... From wangxinquan at tju.edu.cn Thu Aug 14 08:39:51 2008 From: wangxinquan at tju.edu.cn (wangxinquan) Date: Thu, 14 Aug 2008 14:39:51 +0800 Subject: [Pw_forum] Fermi energy in 'scf' and 'nscf'(XQ Wang) References: <418643850.28397@tju.edu.cn> Message-ID: <418696018.06565@tju.edu.cn> >Dear Wang, Dear Prasenjit, > >In principle both the scf & nscf should give exactly the same value of Fermi >energy if your calculations are converged w.r.t. the k-point sampling >(since evaluation of Fermi energy involves numerical integration in >k-space).The fact that that the two procedures give different energies >suggest that the k-point mesh is not converged. Since these are numerical >integrations, the more the no of k-points the more accurate is the value of >the integral. Therefore for Guoying's case, the value of Fermi energy >obtained from scf is more accurate than that from nscf as suggested by >Hande. > >If the difference in Fermi energy is quite large, what I would suggest is to >increase the no. of k-points in the nscf cal. & redo it. As I'm a newbie in this field, the basic concept of quantum mechanics and condensed matter physics(DFT, the Bloch theory and plane wave) are rather abstract for me, following contents may have some misunderstanding of your suggestions. From only1xiaoyuan at 163.com Thu Aug 14 08:40:30 2008 From: only1xiaoyuan at 163.com (only1xiaoyuan) Date: Thu, 14 Aug 2008 14:40:30 +0800 (CST) Subject: [Pw_forum] how to generate gipaw-pseudopotentials Message-ID: <1937552.801371218696030251.JavaMail.coremail@bj163app97.163.com> Dear all, I am about to calculate g tensor of EPR using GIPAW,as I know it need a gipaw-pseudopotential,but I do not know how to generate gipaw-pseudopotentials.Is there some examples? Thank you for your attention! Yuan Wang School of Chemical Eng. & Techn., Tianjin Univ. E-mail: only1xiaoyuan at tju.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080814/4603e75b/attachment.htm From hande at newton.physics.metu.edu.tr Thu Aug 14 09:14:20 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Thu, 14 Aug 2008 10:14:20 +0300 (EEST) Subject: [Pw_forum] how to generate gipaw-pseudopotentials In-Reply-To: <1937552.801371218696030251.JavaMail.coremail@bj163app97.163.com> Message-ID: > Dear all, > I am about to calculate g tensor of EPR using GIPAW,as I know it need a > gipaw-pseudopotential,but I do not know how to generate > gipaw-pseudopotentials.Is there some examples? Take a look into ~/espresso-4.x/atomic_doc/paw_library The README explains what the subdirectories contain. Best, Hande -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From ari.p.seitsonen at iki.fi Thu Aug 14 10:48:53 2008 From: ari.p.seitsonen at iki.fi (Ari P Seitsonen) Date: Thu, 14 Aug 2008 10:48:53 +0200 (CEST) Subject: [Pw_forum] how to generate gipaw-pseudopotentials In-Reply-To: <1937552.801371218696030251.JavaMail.coremail@bj163app97.163.com> References: <1937552.801371218696030251.JavaMail.coremail@bj163app97.163.com> Message-ID: Dear Yuan, There is a very short introduction at the second half of http://www.impmc.jussieu.fr/~software/gipaw/instructions.html If you need further help please let us know. Greetings, apsi PS Please notice that GIPAW != PAW; the former is used for the calculation of magnetic properties (plus X-ray spectroscopies in Quantum Espresso) whereas the latter is a completely self-consistent scheme. The magnetic properties have not been implemented into the PAW scheme yet On Thu, 14 Aug 2008, only1xiaoyuan wrote: > Dear all, > I am about to calculate g tensor of EPR using GIPAW,as I know it need a gipaw-pseudopotential,but I do not know how to generate gipaw-pseudopotentials.Is there some examples? > Thank you for your attention! > > Yuan Wang > School of Chemical Eng. & Techn., Tianjin Univ. > E-mail: only1xiaoyuan at tju.edu.cn > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ IMPMC, CNRS & Universit? Pierre et Marie Curie Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 From vegalew at hotmail.com Thu Aug 14 18:51:24 2008 From: vegalew at hotmail.com (vega) Date: Fri, 15 Aug 2008 00:51:24 +0800 Subject: [Pw_forum] fermi level In-Reply-To: <3a749910808060537g1cda5a49r9c26e35d6c9d818e@mail.gmail.com> <48999CBB.7090608@sissa.it> References: <3a749910808060537g1cda5a49r9c26e35d6c9d818e@mail.gmail.com> <48999CBB.7090608@sissa.it> Message-ID: Dear all, > Fermi energy is written in output whenever it is calculated, that is in > any scf calculations for metals. How about the case for semi-conductors like TiO2? When calculations for TiO2 was achieved, I can't find any information about Fermi energy in my output file. could anyone can help me. vega ============================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China From jlz101 at unlserve.unl.edu Thu Aug 14 19:35:11 2008 From: jlz101 at unlserve.unl.edu (J. D. Burton) Date: Thu, 14 Aug 2008 12:35:11 -0500 Subject: [Pw_forum] fermi level In-Reply-To: References: <3a749910808060537g1cda5a49r9c26e35d6c9d818e@mail.gmail.com> <48999CBB.7090608@sissa.it> Message-ID: <001c01c8fe34$1a27a760$4e76f620$@unl.edu> Dear vega, The "Fermi energy" is the highest occupied energy, and for an insulator this is the valence band maximum. Just plot the DOS or the bands and look for the gap and your "Fermi energy" is at the bottom of the gap. Alternatively, for insulators make sure you have occupations='fixed' and search your scf output file for "highest occupied" or "lowest unoccupied". If these are not listed you would need to run an nscf calc *using a k-point grid that samples the complete BZ (usually the same as your scf calc, or more dense if you want)* with an increased nbnd (larger than the number of valence electrons) so that some conduction band levels are also calculated. Cheers, J. D. ************************************ J. D. Burton, Ph.D. jlz101 at unlserve.unl.edu University of Nebraska Lincoln Physics and Astronomy Office Ph. (402) 472 2499 213C Ferguson Hall ************************************ "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of vega Sent: Thursday, August 14, 2008 11:51 AM To: PWSCF Forum Subject: Re: [Pw_forum] fermi level Dear all, > Fermi energy is written in output whenever it is calculated, that is in > any scf calculations for metals. How about the case for semi-conductors like TiO2? When calculations for TiO2 was achieved, I can't find any information about Fermi energy in my output file. could anyone can help me. vega ============================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Thu Aug 14 20:35:46 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 14 Aug 2008 11:35:46 -0700 (PDT) Subject: [Pw_forum] fermi level In-Reply-To: Message-ID: <713212.19693.qm@web65712.mail.ac4.yahoo.com> Dear Vega, > How about the case for semi-conductors like TiO2? When > calculations for TiO2 was achieved, I can't find any > information about Fermi energy in my output file. Let me resend you my reply to almost the same question of Padmaja Patnaik. Please see below. Bests, Eyvaz. --- On Thu, 7/8/08, Eyvaz Isaev wrote: From: Eyvaz Isaev Subject: Re: [Pw_forum] doubt in occupations:2 To: "Padmaja Patnaik" Date: Thursday, 7 August, 2008, 4:52 AM Dear Padmaja, I have repeated your calculations and do not see any problem with them. First of all I have to note that THERE IS NO FERMI LEVEL FOR SEMICONDUCTORS AND INSULATORS. Why, please read a textbook, say Kittel, Ashcroft&Mermin, etc. For them we can consider only the top of the valence bands and the bottom of the conductivity bands. As the Fermi level is defined as \int_{e_min}^{e_F}n(E)dE=N, where e_F is the Fermi level, n(E) is the DOS and N is the number of valence electrons, it does not matter where you put the Fermi level in the band gap. Because the DOS for E>E_{top valence level} (but E4*ecutwf, even skip this keyword. b) Use more k-points for the DOS calculations. Bests, Eyvaz. -- On Tue, 8/5/08, Padmaja Patnaik wrote: > From: Padmaja Patnaik > Subject: Re: [Pw_forum] doubt in occupations:2 > To: eyvaz_isaev at yahoo.com > Date: Tuesday, August 5, 2008, 6:16 PM > Dear Sir > Hope you remember our communication regarding the > occupations and Fermi energy. > I am here sending you the input and output file for > DOS plotting of SiC. Please have a look. The scf > calculations doesn't give Fermi energy. Am i doing > anything wrong again? > Secondly, when plot the DOS, usually we take the Fermi > energy as zero of the energy axis. So when i make > Fermi energy as zero(by subtracting the Fermi energy > from dos.out file, from the energy values of the > plot) then the valence band maximum is not at zero > but is less than zero. Why is this happening? > Attaching here both scf and dos files. > > Regards > Padmaja Patnaik > > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 8/14/08, vega wrote: > From: vega > Subject: Re: [Pw_forum] fermi level > To: "PWSCF Forum" > Date: Thursday, August 14, 2008, 8:51 PM > Dear all, > > > Fermi energy is written in output whenever it is > calculated, that is in any scf calculations for metals. > > How about the case for semi-conductors like TiO2? When > calculations for TiO2 was achieved, I can't find any > information about Fermi energy in my output file. > > could anyone can help me. > > vega > > ============================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical > Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, > China > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From wangxinquan at tju.edu.cn Fri Aug 15 02:51:46 2008 From: wangxinquan at tju.edu.cn (wangxinquan) Date: Fri, 15 Aug 2008 08:51:46 +0800 Subject: [Pw_forum] fermi level (XQ Wang) References: <418737016.29674@tju.edu.cn> Message-ID: <418761527.16612@tju.edu.cn> >Dear all, Dear vega, > Fermi energy is written in output whenever it is calculated, that is in > any scf calculations for metals. >How about the case for semi-conductors like TiO2? When calculations for TiO2 >was achieved, I can't find any information about Fermi energy in my output >file. You could search the key words "the Fermi energy is" in your output file. It mostly lies above the "total energy" term of the last BFGS convergence. Best regards, XQ Wang ===================================== X.Q. Wang wangxinquan at tju.edu.cn School of Chemical Engineering and Technology Tianjin University 92 Weijin Road, Tianjin, P. R. China tel:86-22-27890268, fax: 86-22-27892301 ===================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080815/0f4f6cfe/attachment.htm From only1xiaoyuan at 163.com Fri Aug 15 04:31:53 2008 From: only1xiaoyuan at 163.com (only1xiaoyuan) Date: Fri, 15 Aug 2008 10:31:53 +0800 (CST) Subject: [Pw_forum] how to generate gipaw-peseudopotentials(Yuan Wang) In-Reply-To: References: Message-ID: <6315462.124891218767513852.JavaMail.coremail@bj163app115.163.com> Dear Seitsonen, >Dear Yuan, > > There is a very short introduction at the second half of > >http://www.impmc.jussieu.fr/~software/gipaw/instructions.html > > If you need further help please let us know. > > Greetings, > > apsi > >PS Please notice that GIPAW != PAW; the former is used for the > calculation of magnetic properties (plus X-ray spectroscopies in Quantum > Espresso) whereas the latter is a completely self-consistent scheme. The > magnetic properties have not been implemented into the PAW scheme yet Thank you very much for your prompt reply,it is useful for me to reconstruct the wave function. Thanks again and best regards. Yuan Wang School of Chemical Eng. & Techn., Tianjin Univ. E-mail: only1xiaoyuan at 163.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080815/1ef2488e/attachment.htm From sauluck at iitk.ac.in Fri Aug 15 07:46:57 2008 From: sauluck at iitk.ac.in (Sushil Auluck) Date: Fri, 15 Aug 2008 11:16:57 +0530 (IST) Subject: [Pw_forum] fermi level In-Reply-To: References: <3a749910808060537g1cda5a49r9c26e35d6c9d818e@mail.gmail.com> <48999CBB.7090608@sissa.it> Message-ID: <41942.122.162.198.24.1218779217.squirrel@newwebmail.iitk.ac.in> hi, in semiconductors/insulators the fermi energy can be placed at the top of the valance bands OR bottom of the conduction bands OR if you like anywere inside the gap. if mass of holes = mass of electrons then the fermi level could be placed in the middle of the gap. s.auluck > Dear all, > >> Fermi energy is written in output whenever it is calculated, that is in >> any scf calculations for metals. > > How about the case for semi-conductors like TiO2? When calculations for > TiO2 > was achieved, I can't find any information about Fermi energy in my output > file. > > could anyone can help me. > > vega > > ============================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ....................................................................... Prof. Sushil Auluck Phone:+91-512-6797092/6148 Department of Physics +91-512-6798177(Home) Indian Institute of Technology Cell :+91-9305548667 Kanpur 208016 (UP) Fax :+91-512-6790914 India E-mail:sauluck at iitk.ac.in ...............................................:sauluck at gmail.com http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html ....................................................................... ~ From lanhaiping at gmail.com Fri Aug 15 09:20:14 2008 From: lanhaiping at gmail.com (lan haiping) Date: Fri, 15 Aug 2008 15:20:14 +0800 Subject: [Pw_forum] fermi level (XQ Wang) In-Reply-To: <418761527.16612@tju.edu.cn> References: <418737016.29674@tju.edu.cn> <418761527.16612@tju.edu.cn> Message-ID: No, it depends on smearing scheme used in the calculation! 2008/8/15 wangxinquan > >Dear all, > Dear vega, > > Fermi energy is written in output whenever it is calculated, that is in > > any scf calculations for metals. > > > >How about the case for semi-conductors like TiO2? When calculations for TiO2 > > >was achieved, I can't find any information about Fermi energy in my output > >file. > You could search the key words "the Fermi energy is" in your output > file. It > mostly lies above the "total energy" term of the last BFGS convergence. > > Best regards, > XQ Wang > > ===================================== > > X.Q. Wang > > wangxinquan at tju.edu.cn > > School of Chemical Engineering and Technology > > Tianjin University > > 92 Weijin Road, Tianjin, P. R. China > > tel:86-22-27890268, fax: 86-22-27892301 > > ===================================== > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080815/a8aeca9b/attachment.htm From wangxinquan at tju.edu.cn Fri Aug 15 11:47:19 2008 From: wangxinquan at tju.edu.cn (wangxinquan) Date: Fri, 15 Aug 2008 17:47:19 +0800 Subject: [Pw_forum] fermi level (XQ Wang) References: <418781673.17787@tju.edu.cn> Message-ID: <418793662.32505@tju.edu.cn> Dear Eyvaz, >1. Scf calculations do not give the Fermi level, because you use fixed occupations used by default for semiconductors (insulators). I.e. if nothing specified as occupations, >your system is considered as a semiconductor >(insulator). In this case the number of bands treated is exactly half of the number of valence electrons, i.e. 4 in your case. Do you mean that the occupations of electrons were constrained during iterations? To my limited experiences, the occupations should be changed by setting the "starting_ns_eigenvalue" parameters (lda+u calculation) and the occupation matrix will be tuned through the iterations process. I'm sorry for that I confused "electron density" with "occupation". In my opinion, both concepts describe the probabilty of electrons locating at lattic site. The "electron density" which is derived from wavefunctions belongs to quantum mechanics field, while "occupation" belongs to condensed matter physics field with respect to band structure.The electron density should be changed but the occupation of bands should be fixed in scf calculation. right? The electron states(eigenvalue of the density matrix) which construct the band structures will not be occupated entirely. For insulator, the valence band is full while the conduct band is empty. In the output file of scf I have no idea what the "fermi energy" results are. Does it not mean the "real" fermi energy? E.J.Yoffa and D.Adler (Phy. Rev. B, 12, 2260) have talked about the calculation of fermi energy for Mott insulator. I'm afraid the definition of fermi energy were misunderstood. My brain doesn't work. Any help to remove my understanding to fermi energy will be deeply appreciated. Best regards, XQ Wang ===================================== X.Q. Wang wangxinquan at tju.edu.cn School of Chemical Engineeringand and Technology Tianjin University 92 Weijin Road, Tianjin, P. R. China tel:86-22-27890268, fax: 86-22-27892301 ===================================== From only1xiaoyuan at 163.com Fri Aug 15 11:41:22 2008 From: only1xiaoyuan at 163.com (only1xiaoyuan) Date: Fri, 15 Aug 2008 17:41:22 +0800 (CST) Subject: [Pw_forum] about davcio error Message-ID: <24754315.398471218793282423.JavaMail.coremail@bj163app64.163.com> Dear all, I am about to calculate g tensor of EPR using GIPAW,but there are some questions .Could anyone tell me what means the following error message: ---------------------------------- from davcio : error # 14 error while reading from file ----------------------------------- is it due to lda+U in scf calculation? Thank you for your attention! Yuan Wang School of Chemical Eng. & Techn., Tianjin Univ. E-mail: only1xiaoyuan at 163.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080815/875ea131/attachment.htm From eyvaz_isaev at yahoo.com Fri Aug 15 15:30:33 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 15 Aug 2008 06:30:33 -0700 (PDT) Subject: [Pw_forum] fermi level (XQ Wang) In-Reply-To: <418793662.32505@tju.edu.cn> Message-ID: <700819.16091.qm@web65704.mail.ac4.yahoo.com> Dear Wang, Now I am confused with the questions you post. --- On Fri, 8/15/08, wangxinquan wrote: > Do you mean that the occupations of electrons were > constrained during iterations? No. > To my limited experiences, the occupations should be > changed by setting the "starting_ns_eigenvalue" parameters > (lda+u calculation) and the occupation matrix will be > tuned through the iterations process. I am not so experienced in the LDA+U calculations, but the idea that an occupation number should be defined self-consistently, is correct. > > I'm sorry for that I confused "electron density" with > "occupation". In my opinion, both concepts describe > the probabilty of electrons locating at lattic site. This is a WRONG conception, electrons are delocalized in the unit cell and you (and anybody) can not locate an electron on a lattice site. Besides, electron density is a square of a wavefunction \Psi(r), but occupation number is a consequence of quantum statistics. > The "electron density" which is derived from > wavefunctions belongs to quantum > mechanics field, while "occupation" > belongs to condensed matter physics field with respect to > band structure.The electron density > should be changed but the occupation of bands should be > fixed in scf calculation. right? No, this is not true for metals. Only for semiconductors (insulators) valence bands are kept fully occupied, i.e. 2 electrons per band according to Pauli principle. > > The electron states(eigenvalue of the density matrix) which > construct the band structures will not > be occupated entirely. Probably I missed something, but eigenvalues are solutions of (T+V_H+V_XC+V_ext)\Psi=E\Psi The second part of your suggestion is misleading completely. In this case where you put electrons? > For insulator, the valence band is full while the conduct band is empty. Correct. > In the output file of scf I have no idea what the > "fermi energy" results are. Does it not mean the > "real" fermi energy? By definition: the Fermi energy is an energy which separates the valence (occupied) electrons from the conductivity (unoccupied) electrons. In our DFT calculations there is no "real" Fermi energy (E_F), only the one for which \int_{E_min}^{E_F)N(E)dE = N is fulfilled (N(E) is the DOS, N is total number of valence electrons). > E.J.Yoffa and D.Adler (Phy. Rev. B, 12, 2260) have > talked about the calculation of fermi energy for > Mott insulator. I'm afraid the definition of fermi > energy were misunderstood. > At least, from Abstract of the paper it is clear that what they did does not contradict to what we discussed before. > My brain doesn't work. It should work. Please read again Kittel's or Ashcroft-Mermin's or Ricahrd Martin's o Harrison's or Zyman's, etc. etc etc texbooks. Bests, Eyvaz. >Any help to remove my > understanding to fermi energy will be deeply appreciated. > > Best regards, > XQ Wang > ===================================== > X.Q. Wang > wangxinquan at tju.edu.cn > School of Chemical Engineeringand and Technology > Tianjin University > 92 Weijin Road, Tianjin, P. R. China > tel:86-22-27890268, fax: 86-22-27892301 > ===================================== > > > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From baroni at sissa.it Fri Aug 15 15:30:59 2008 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 15 Aug 2008 15:30:59 +0200 Subject: [Pw_forum] fermi level (XQ Wang) In-Reply-To: <418793662.32505@tju.edu.cn> References: <418781673.17787@tju.edu.cn> <418793662.32505@tju.edu.cn> Message-ID: <6052CB46-4FA5-4B6C-AF6A-85AAFAACAB23@sissa.it> OK. Let me try to throw my own 5 cents into the discussion. Let me start with some very general, very elementary statements, and I will comment later on some of the statements made by others. The concept of Fermi energy is a very simple one and is best explained thinking of a system of non-interacting electrons (of which Fermi liquids are generalizations I will not comment on). 1) The eigenstates of the Hamiltonian of a system of non-interacting electrons can ALWAYS be chosen as antisymmetrized products ("Slater deteminants") of one-particle wavefunctions ("molecular orbitals" in quantum chemistry, "Bloch states" in solid-state physics) which are eigenfunctions of a one-electron Hamiltonian. Pay attention to the conceptually simple, trivial, but often overlooked, difference between the many-body Hamiltonian (with its-own eigenfunctions and eigenstates) and the one-particle Hamiltonian. The many-body energy is simply the sum of the one-electron energies of all the molecular orbitals whose product is the many-body eigenstate. 2) The antisymmetric nature of the many-body wavefunctions is such that, if you construct a product of a set of functions where two of them are equal, the result will vanish. This is the PAULI PRINCIPLE. No two electrons can occupy the same one-electron state. 3) Because of (2), the lowest possible many-body energy (ground state) is the sum of the lowest N one-particle energy eigenvalues (N being the number of electrons). The highest occupied one-electron energy level is the difference between the ground state energy of the system with N electrons and that with N-1 electrons (ionization potential). The lowest unoccupied energy is the difference between the ground states with N+1 and N electrons (electron affinity). 4) For any finite system (as well as for insulating infinite ones) the electron affinity is different from the ionization potential. For (infinite) metals, they coincide and the define the Fermi energy: by definition, the energy necessary to add or to remove an electron from the system (in classical thermodynamics this same quantity is called the chemical potential). For insulators, it is not that the Fermi energy "does not exist". Only, it is ill-defined it the zero- temperature limit (it can be assumed to take any value between the electron affinity and the ionization potential). At any finite temperature, thermodynamic considerations remove this indeterminacy. On Aug 15, 2008, at 11:47 AM, wangxinquan wrote: > Dear Eyvaz, > >> 1. Scf calculations do not give the Fermi level, because you use >> fixed occupations used by default for semiconductors (insulators). >> I.e. if nothing specified as occupations, >your system is >> considered as a semiconductor >> (insulator). In this case the number of bands treated is exactly >> half of the number of valence electrons, i.e. 4 in your case. > Do you mean that the occupations of electrons were constrained > during iterations? To my limited experiences, > the occupations should be changed by setting the > "starting_ns_eigenvalue" parameters (lda+u calculation) and > the occupation matrix will be tuned through the iterations process. the electron occupations are usually fixed following the "filling principle": states with lower energies are filled first. in an insulator, this is easily done because the number of filled states is independent of the wavevector in the Brilloion zone. in metals, this is more tricky because the number of occupied states will depend on the key point, and in order to sort out this dependence one has to know in advance the electronic structure (i.e. the sequence of energy levels) at ALL the k points in the Brillouin zone > I'm sorry for that I confused "electron density" with "occupation". > In my opinion, both > concepts describe the probabilty of electrons locating at lattic site. I am sorry but your opinion is wrong. The "occupation" does not refer to the probability of finding an electron at any particular lattice site, but rather in any of the molecular orbitals (which, being generally delocalized, cannot be attached at any specific lattice site). > The "electron density" > which is derived from wavefunctions belongs to quantum mechanics > field, while "occupation" > belongs to condensed matter physics field with respect to band > structure. I do not quite see the difference between "belonging to quantum bechanics" as opposed to "belonging to condensed matter", but for the fact that you may have learnt one concept in one textbook and another in a different book. As a rule of thumb, what you learn tends to be rather useless up the time when you can forget where/when you learnt it and you can pretend that the concepts you are using are YOURS ... > The electron density > should be changed but the occupation of bands should be fixed in scf > calculation. right? if so you like to think, this is not wrong ... (which indicates that you could have seen by yourself why your previous statement is wrong) > The electron states(eigenvalue of the density matrix) what a mess, here! electron states, if ever, may be eigenSTATES of a quantum operator, not eigenVALUES. it is true that for independent electrons the "electron states" (i.e. the eigensSTATES of the one- particle Hamiltonian) are also eigenstates of the one-particle density matrix, but the viceversa is not true. Being an eigenstate of the density matrix is not a sufficient condition for being a legitamate "electron state" (in the sense of being an eigenstate of the Hamiltonian). this is so because the density matrix is a projector, whose eigenvalues (0 and 1) are highly degenerate ... > which construct the band structures will not > be occupated entirely. For insulator, the valence band is full while > the conduct band is empty. > In the output file of scf I have no idea what the "fermi energy" > results are. Does it not mean the > "real" fermi energy? E.J.Yoffa and D.Adler (Phy. Rev. B, 12, 2260) > have talked about the calculation > of fermi energy for Mott insulator. I'm afraid the definition of > fermi energy were misunderstood. if you mean misunderstood by you, this is quite probable. > My brain doesn't work. take it easy. you are probably one of the many victims of the modern tendency to study advanced (at times, very advanced) topics without having properly understood the fundamentals. as trivial as these fundamentals may be, it takes time to master them. I am sure it is not your fault. > Any help to remove my understanding to fermi energy will be deeply > appreciated. hope I did help, a little bit - stay tuned Stefano B --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080815/ab8d125a/attachment-0001.htm From calderin at physics.queensu.ca Fri Aug 15 16:10:50 2008 From: calderin at physics.queensu.ca (Lazaro Calderin) Date: Fri, 15 Aug 2008 16:10:50 +0200 Subject: [Pw_forum] fermi level (XQ Wang) In-Reply-To: <200808151747195847506@tju.edu.cn> References: <418781673.17787@tju.edu.cn> <200808151747195847506@tju.edu.cn> Message-ID: <1218809451.2783.148.camel@wolfe> Dear XQ Wang, > My brain doesn't work. Any help to remove my understanding to fermi energy will be deeply appreciated. May be mine neither ;-) ... but this is my understanding of the Fermi energy .. which could be wrong of course. Usually the Fermi energy is introduced in the context of the free electron (gas) and nearly free electron models and it is defined as the highest occupied electron state at T=0K. Based on those models some electronic properties are calculated at non-zero T and what should be called the chemical potential is often still called Fermi energy. The chemical potential (\mu) is that number that constrains the integral over the energy (E) of the Fermi-Dirac distribution (f) at a given temperature (T) times the density of states (n), to be equal to the number of electron (N) in the system. That is: \int_{-\infty}^\infty n(E) f(E,T,\mu) dE = N (1) The chemical potential goes to the Fermi energy as the temperature approaches 0K. But also, for metals the chemical potential usually equals the Fermi energy at non-zero temperature because there are abundant unoccupied states just above and all the way from the Fermi energy up. I guess that is why we still call Fermi energy to the chemical potential. In semiconductors there are no empty states just above the highest occupied one (top of the valence band). Therefore at non-zero temperature the chemical potential is displaced to energies higher than the top of the valence band, taking values usually in the energy gap and therefore it can not be equal to the energy of any allowed electron state. As for metals, we often call Fermi energy to what should be called chemical potential. But while for metal it is fine to interchange the terms chemical potential and Fermi energy, for semiconductors it is not. I think it would be better to keep the definition of Fermi energy separated from the definition of chemical potential. If we stick to the definition of the Fermi energy as the energy of the highest occupied electron state at T=0K then there is a Fermi energy in semiconductors, that is the top of the valence band, and a chemical potential somewhere in the gap depending on the temperature. If the Fermi energy is defined as a value of the energy that divides occupied and empty states (as in Ashcroft & Mermin I think) then any value in the gap could be taken as a Fermi energy. Hope this helps, Lazaro -- =============================================================== Lazaro Calderin Department of Physics, Queen's University, Kingston, ON, Canada E-mail: calderin at physics.queensu.ca From vegalew at hotmail.com Fri Aug 15 21:14:15 2008 From: vegalew at hotmail.com (vega) Date: Sat, 16 Aug 2008 03:14:15 +0800 Subject: [Pw_forum] fermi level In-Reply-To: <3a749910808060537g1cda5a49r9c26e35d6c9d818e@mail.gmail.com><48999CBB.7090608@sissa.it> References: <3a749910808060537g1cda5a49r9c26e35d6c9d818e@mail.gmail.com><48999CBB.7090608@sissa.it> Message-ID: Dear all, thank you for all your help about fermi level. Now I'm more clear about it. vega -------------------------------------------------- From: "vega" Sent: Friday, August 15, 2008 12:51 AM To: "PWSCF Forum" Subject: Re: [Pw_forum] fermi level > Dear all, > >> Fermi energy is written in output whenever it is calculated, that is in >> any scf calculations for metals. > > How about the case for semi-conductors like TiO2? When calculations for > TiO2 > was achieved, I can't find any information about Fermi energy in my output > file. > > could anyone can help me. > > vega > > ============================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From amosleffler at sbcglobal.net Sat Aug 16 01:28:05 2008 From: amosleffler at sbcglobal.net (Amos Leffler) Date: Fri, 15 Aug 2008 16:28:05 -0700 Subject: [Pw_forum] Problems with Espresso-4.0.1 Message-ID: <4E54785C55974076B4B9E570066C6C14@leffler2> Dear Forum, I have been trying to get the espresso-4.0.1 to run totally for a while. I have been using g95_x86_64 compiler and mkl 10.0.3.020 library in serial mode. The program compiles without errors but only some of the examples run properly. Example01 runs but example02 and example03 will not. In both cases the error is in the phonon routines with the output: running the phonon calculation at X... STOP 2 Error condition encountered during test: exit status = 2 . The difficulty I have is to find where the error is occuring in the program. Is there bad input from pw.x or is it somewhere in ph.x? Is there any way to debug the program or is there a flow sheet available? Both pw.x and ph.x are large directories with many files and unless you know the organization of the program finding errors is very difficult. The Users Guide does not seem to have information of this sort or references to where it could be found. Any help would be most appreciated. Amos Leffler Unaffiliated -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080815/3823553a/attachment.htm From mansourehp at gmail.com Sat Aug 16 06:45:26 2008 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Sat, 16 Aug 2008 08:15:26 +0330 Subject: [Pw_forum] impurity Message-ID: Dear all I am going to calculate affect of adding impurities to a system.I know I must consider a supercell for this propose but I don't know how and where I should add an impurity?How can I have different percent of impurities in a system? please let me know its answer. good luck Mansoureh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080816/c8304ef5/attachment.htm From wangxinquan at tju.edu.cn Sat Aug 16 09:57:06 2008 From: wangxinquan at tju.edu.cn (wangxinquan) Date: Sat, 16 Aug 2008 15:57:06 +0800 Subject: [Pw_forum] fermi level(XQ Wang) References: <418807137.05238@tju.edu.cn> Message-ID: <418873451.26062@tju.edu.cn> Dear Stefano, Eyvaz and Lazaro, I deeply appreciate your kindly help. I must be cautious in understanding the fundamental concepts of quantum mechanics indeed. I need spend more time to master them as Stefano suggested. Although they are rather abstract for me, I hope I can apprehend their physical essence. wrote by Stefano B: >1) The eigenstates of the Hamiltonian of a system of non-interacting >electrons can ALWAYS be chosen as antisymmetrized products ("Slater >deteminants") of one-particle wavefunctions ("molecular orbitals" in >quantum chemistry, "Bloch states" in solid-state physics) which are >eigenfunctions of a one-electron Hamiltonian. Pay attention to the >conceptually simple, trivial, but often overlooked, difference between >the many-body Hamiltonian (with its-own eigenfunctions and >eigenstates) and the one-particle Hamiltonian. The many-body energy is >simply the sum of the one-electron energies of all the molecular >orbitals whose product is the many-body eigenstate. > >2) The antisymmetric nature of the many-body wavefunctions is such >that, if you construct a product of a set of functions where two of >them are equal, the result will vanish. This is the PAULI PRINCIPLE. >No two electrons can occupy the same one-electron state. > >3) Because of (2), the lowest possible many-body energy (ground state) >is the sum of the lowest N one-particle energy eigenvalues (N being >the number of electrons). The highest occupied one-electron energy >level is the difference between the ground state energy of the system >with N electrons and that with N-1 electrons (ionization potential). >The lowest unoccupied energy is the difference between the ground >states with N+1 and N electrons (electron affinity). The occupation of electrons depends on the sequence of their energies. >4) For any finite system (as well as for insulating infinite ones) the >electron affinity is different from the ionization potential. For >(infinite) metals, they coincide and the define the Fermi energy: by >definition, the energy necessary to add or to remove an electron from >the system (in classical thermodynamics this same quantity is called >the chemical potential). For insulators, it is not that the Fermi >energy "does not exist". Only, it is ill-defined it the zero- >temperature limit (it can be assumed to take any value between the >electron affinity and the ionization potential). At any finite >temperature, thermodynamic considerations remove this indeterminacy. I need more time to understand these comments. >> The electron states(eigenvalue of the density matrix) >what a mess, here! electron states, if ever, may be eigenSTATES of a >quantum operator, not eigenVALUES. it is true that for independent >electrons the "electron states" (i.e. the eigensSTATES of the one- >particle Hamiltonian) are also eigenstates of the one-particle density >matrix, but the viceversa is not true. Being an eigenstate of the >density matrix is not a sufficient condition for being a legitamate >"electron state" (in the sense of being an eigenstate of the >Hamiltonian). this is so because the density matrix is a projector, >whose eigenvalues (0 and 1) are highly degenerate ... I'm sorry for my terrible opinion. eigenSTATE should be the eigenvector of matrix (quantum operator) and eigenVALUE should be the mean value of quantum operator. I have read some quantum mechanics textbooks as Eyvaz suggested (C.KITTEL), unfortunately I fail to make a connection between the book and application. >> My brain doesn't work. >take it easy. you are probably one of the many victims of the modern >tendency to study advanced (at times, very advanced) topics without >having properly understood the fundamentals. as trivial as these >fundamentals may be, it takes time to master them. I am sure it is not >your fault. In fact the chemical process is my interesting and the physical analysis are the most powerful and essential idea to get a deep insight into the mechanism of reactions. Honest to myself, the output information( local relaxtion, electron state around fermi level and redox energy) are important to me. However the results largely depends on the input which can only be setted exactly by a systematic understanding of the quantum mechanic theory. (To what extent of the knowledge should I achieve in quantum mechanics field is another problem which has confused me for a long time...) Thanks again to Stefano for giving me confidence. I will try my best. wrote by Lazaro: >... ... ... >I think it would be better to keep the definition of Fermi energy >separated from the definition of chemical potential. If we stick to the >definition of the Fermi energy as the energy of the highest occupied >electron state at T=0K then there is a Fermi energy in semiconductors, >that is the top of the valence band, and a chemical potential somewhere >in the gap depending on the temperature. If the Fermi energy is defined >as a value of the energy that divides occupied and empty states (as in >Ashcroft & Mermin I think) then any value in the gap could be taken as a >Fermi energy. I found that it is the clearest explanation of fermi energy. I deeply agree with you. At last I deeply appreciate all your kindly helps once more. Best regards, XQ Wang ===================================== X.Q. Wang wangxinquan at tju.edu.cn School of Chemical Engineering and Technology Tianjin University 92 Weijin Road, Tianjin, P. R. China tel:86-22-27890268, fax: 86-22-27892301 ===================================== -------------- next part -------------- An HTML attachment was scrubbed... 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Name: not available Type: image/gif Size: 1662 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20080816/7edc1fff/attachment.gif From baroni at sissa.it Sat Aug 16 10:30:12 2008 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 16 Aug 2008 10:30:12 +0200 Subject: [Pw_forum] impurity In-Reply-To: References: Message-ID: <08CD2717-8C05-49F2-B99C-B4BF03CE2294@sissa.it> On Aug 16, 2008, at 6:45 AM, Mansoureh Pashangpour wrote: > Dear all > I am going to calculate affect of adding impurities to a system.I > know I must consider a supercell for this propose but I don't know > how and where I should add an impurity? how could WE know, if you don't? it depends on stability issues (you may want to look for the minimum-energy geometry), if you think that the system you are interested in has had enough time to relax to the most stable configuration, or on the details of the preparation process, if you suspect that the system is trapped in one metastable confiuration > How can I have different percent of impurities in a system? how about considering different supercells with a different numbers of "stranger" atoms? > please let me know its answer. > good luck all the same to you > Mansoureh how about your affiliation? Cheers - SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080816/18cb2ee8/attachment-0001.htm From szs_naghavi at yahoo.com Sat Aug 16 18:53:51 2008 From: szs_naghavi at yahoo.com (zahra sadat naghavi) Date: Sat, 16 Aug 2008 09:53:51 -0700 (PDT) Subject: [Pw_forum] error Message-ID: <854705.56502.qm@web63003.mail.re1.yahoo.com> dear all ! what is this error in ph.x? ?? from phq_readin : error #???????? 1 ???? cannot start from pw.x data file using Gamma-point tricks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080816/bb6e409b/attachment.htm From eyvaz_isaev at yahoo.com Sat Aug 16 22:20:47 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 16 Aug 2008 13:20:47 -0700 (PDT) Subject: [Pw_forum] error In-Reply-To: <854705.56502.qm@web63003.mail.re1.yahoo.com> Message-ID: <634017.18336.qm@web65715.mail.ac4.yahoo.com> Hi, It is clear from the message that you use only Gamma point technique for SCF, and then try calculate phonons. Instead of "K_POINTS Gamma" you can use "K_POINTS automatic" and dividing numbers with shifts. This allows you to avoid the message you obtained, even you use 1 1 1 0 0 0 which gives only Gamma point again, Please provide your affiliation as it is accepted in this forum by default. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Sat, 8/16/08, zahra sadat naghavi wrote: > From: zahra sadat naghavi > Subject: [Pw_forum] error > To: Pw_forum at pwscf.org > Date: Saturday, August 16, 2008, 8:53 PM > dear all ! > what is this error in ph.x? > ?? from phq_readin : error #???????? 1 > ???? cannot start from pw.x data file using Gamma-point > tricks > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Sun Aug 17 14:29:12 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 17 Aug 2008 05:29:12 -0700 (PDT) Subject: [Pw_forum] fermi level(XQ Wang) In-Reply-To: <418873451.26062@tju.edu.cn> Message-ID: <861756.27595.qm@web65713.mail.ac4.yahoo.com> Dear Wang, ? >I'm sorry for?my terrible opinion. eigenSTATE should be the >eigenvector of matrix (quantum operator) and eigenVALUE should >be the mean value of quantum operator.?I have read some >quantum mechanics textbooks as Eyvaz suggested (C.KITTEL), >unfortunately I fail to?make a connection between the book >and?application.?? ? >>?My?brain?doesn't?work. Wait, wait, Kittel is a solid state textbook, but not quantum mechanics one. If you like you can read QM textbooks like Landau&Lifshits (volume 3, Quantum Mechanics), Shiff, Messia, Cohen-Tannondji etc. There is a textbook by Flugge with QM problems and their solutions. So, paper and pen are your good friends. Bests, Eyvaz. ? ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080817/5e171b56/attachment.htm From lshulenburger at ciw.edu Mon Aug 18 21:36:38 2008 From: lshulenburger at ciw.edu (lshulenburger at ciw.edu) Date: Mon, 18 Aug 2008 15:36:38 -0400 (EDT) Subject: [Pw_forum] pw2casino difficulty Message-ID: <52030.10.1.20.105.1219088198.squirrel@mail.ciw.edu> Hello, I am having difficulty with the version of pw2casino that is included in the 4.0.1 distribution of quantum espresso. Whenever I attempt to run this utility I get an error message from each node stating: Atom 01 not found And then the program exits. Looking at the source I see that at line 284 of pw2casino.f90 the program is attempting to write out information about the atoms used in the calculation. I do not need this information, so I simply commented out the next five lines: ! DO na = 1, nat ! nt = ityp(na) ! at_num = atomic_number(TRIM(atm(nt))) ! WRITE(io,'(i6,3f20.14)') at_num, (alat*tau(j,na),j=1,3) ! ENDDO and the utility runs without issue. I am not particularly familiar with the code base of pwscf and as such am not sure whether this is a trivial problem to fix or even whether it is due to some error in the way I am using the code. Has anyone else experienced this issue? Luke Shulenburger (lshulenburger at ciw.edu) From eyvaz_isaev at yahoo.com Mon Aug 18 23:09:06 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 18 Aug 2008 14:09:06 -0700 (PDT) Subject: [Pw_forum] Update Bibliography In-Reply-To: <6052CB46-4FA5-4B6C-AF6A-85AAFAACAB23@sissa.it> Message-ID: <86246.907.qm@web65707.mail.ac4.yahoo.com> Dear users, I suggest it is a good idea to update the Bibliography section on the website http://www.quantum-espresso.org/wiki/index.php/Bibliography adding your papers published where you used QuantumEspresso code. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From gaoguoying at gmail.com Tue Aug 19 08:16:23 2008 From: gaoguoying at gmail.com (Guoying Gao) Date: Tue, 19 Aug 2008 14:16:23 +0800 Subject: [Pw_forum] pseudopotential for lithium Message-ID: <6234c0c60808182316u7fba241dt1724afde9a6e2b43@mail.gmail.com> Dear PW users, I want to study the properties of lithium under high presssure (about 200 GPa), we all know that the effect of 1s2 electron states cann't be neglected at the monment. So we should consider 1s2 as the valence electron. However, there is no such pseudopotential for lithium in the pwscf website. In addition, it is very difficult to generate this pseudopotential . So is there anyone has the pseudopotential for lithium with 1s2 and 2s1 as valence electrons. Any suggestions or hints will be appreciated. Best wishes! Guoying Nab of Superhard Materials Jilin Univ. P.R.China From gaoguoying at gmail.com Tue Aug 19 08:30:07 2008 From: gaoguoying at gmail.com (Guoying Gao) Date: Tue, 19 Aug 2008 14:30:07 +0800 Subject: [Pw_forum] question on Nonlinear core correction Message-ID: <6234c0c60808182330u5a24ce35u8f9e45b4d6162c09@mail.gmail.com> Dear everyone, I searched "Nonclear core correction" in pw forum and found that the core correction is more important for atoms with few valence electrons. So my question is what is "Nonlinear core correction", why it is more important for atoms with few valence electrons? Any interapretation or suggestion will be welcomed. Regards! Guoying Nab of Superhard Materials Jilin Univ. P.R.China From baroni at sissa.it Tue Aug 19 09:16:42 2008 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 19 Aug 2008 09:16:42 +0200 Subject: [Pw_forum] question on Nonlinear core correction In-Reply-To: <6234c0c60808182330u5a24ce35u8f9e45b4d6162c09@mail.gmail.com> References: <6234c0c60808182330u5a24ce35u8f9e45b4d6162c09@mail.gmail.com> Message-ID: Dear Guoying: Google is your friend. Typing "non linear core correction" in google you would get you several relevant links. The most important one is the sixth, which points to the original paper by Steven Louie (never mind the title: the non linear core correction is important for non-magnetic materials as well) http://prola.aps.org/abstract/PRB/v26/i4/p1738_1 Have a nice reading. SB On Aug 19, 2008, at 8:30 AM, Guoying Gao wrote: > Dear everyone, > > I searched "Nonclear core correction" in pw forum and found > that the core correction is more important for atoms with few valence > electrons. So my question is what is "Nonlinear core correction", why > it is more important for atoms with few valence electrons? Any > interapretation or suggestion will be welcomed. > > Regards! > > Guoying > Nab of Superhard Materials > Jilin Univ. > P.R.China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://www.sissa.it/~baroni / [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080819/b5742ead/attachment.htm From wangqj1 at 126.com Tue Aug 19 15:30:19 2008 From: wangqj1 at 126.com (wangqj1) Date: Tue, 19 Aug 2008 21:30:19 +0800 (CST) Subject: [Pw_forum] The resulte of optimizing the ZnO lattice constant use vc-relax Message-ID: <32273636.262091219152619079.JavaMail.coremail@bj126app52.126.com> Dear pwscf users I run vc-relax to optimize the lattice constant of ZnO unit cell,my input file and out file as follows: &CONTROL title = ZnOVC , calculation = 'vc-relax' , restart_mode = 'from_scratch' , pseudo_dir = '/root/espresso-3.2.3/pseudo/' , prefix = ZnO , etot_conv_thr = 1.D-5 , nstep = 100 , tstress = .true. , tprnfor = .true. , dt = 100 , tefield = .false. , / &SYSTEM ibrav = 4, celldm(1) = 6.14161, celldm(3) = 1.6022, nat = 4, ntyp = 2, ecutwfc = 40 , ecutrho = 300 , nosym = .true. , nbnd = 25, occupations = 'smearing' , degauss = 0.002 , smearing = 'methfessel-paxton' , lda_plus_u = .false. , / &ELECTRONS conv_thr = 1.D-8 , startingpot = 'atomic' , startingwfc = 'atomic' , mixing_mode = 'plain' , mixing_beta = 0.6 , diagonalization = 'david' , diago_full_acc = .true. , / &IONS ion_dynamics = 'damp' , / &CELL cell_dynamics = 'damp-w' , / ATOMIC_SPECIES Zn 65.00000 Zn.pz-van_ak.UPF O 16.00000 O.pz-rrkjus.UPF ATOMIC_POSITIONS crystal Zn 0.333333333 0.666666667 0.000000000 1 1 1 O 0.333333333 0.666666667 0.381700000 1 1 1 Zn 0.666666667 0.333333333 0.500000000 1 1 1 O 0.666666667 0.333333300 0.881700000 1 1 1 K_POINTS automatic 4 4 4 0 0 0 -------------------------------------------------------------------------------- Program PWSCF v.3.2.2 starts ... Today is 18Aug2008 at 23: 7:36 Ultrasoft (Vanderbilt) Pseudopotentials Current dimensions of program pwscf are: ntypx = 10 npk = 40000 lmax = 3 nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 Title: ZnOVC bravais-lattice index = 4 lattice parameter (a_0) = 6.1416 a.u. unit-cell volume = 321.4357 (a.u.)^3 number of atoms/cell = 4 number of atomic types = 2 kinetic-energy cutoff = 40.0000 Ry charge density cutoff = 300.0000 Ry convergence threshold = 1.0E-08 beta = 0.6000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE (1434) nstep = 100 celldm(1)= 6.141610 celldm(2)= 0.000000 celldm(3)= 1.602200 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( -0.500000 0.866025 0.000000 ) a(3) = ( 0.000000 0.000000 1.602200 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.000000 0.577350 0.000000 ) b(2) = ( 0.000000 1.154701 0.000000 ) b(3) = ( 0.000000 0.000000 0.624142 ) ....... ....... outfile: Final estimate of lattice vectors (input alat units) 1.011331020 0.000000000 0.000000000 -0.505665507 0.875838356 0.000000001 0.000000000 -0.000000002 1.627761723 final unit-cell volume = 334.0064 (a.u.)^3 input alat = 6.1416 (a.u.) CELL_PARAMETERS (alat) 1.011331020 0.000000000 0.000000000 -0.505665507 0.875838356 0.000000001 0.000000000 -0.000000002 1.627761723 ATOMIC_POSITIONS (crystal) Zn 0.333333347 0.666666677 0.000438189 O 0.333333356 0.666666677 0.380132292 Zn 0.666666690 0.333333345 0.500438960 O 0.666666695 0.333333331 0.880132483 from the outfile I can see the c/a=1.627761723 and from the final unit-cell volume =334.0064 (a.u.)^3,I can compute the a=6.189678(Bohr)=3.2754(A)?From the value of caculating ,we can see that the c/a and a are both bigger than the experiment , I don't konw whether the result is right or wrong . Anybody who know about the question and give me the useful advice will be appreciated . Sincerely -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080819/6758972c/attachment-0001.htm From paulatto at sissa.it Tue Aug 19 16:16:22 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 19 Aug 2008 16:16:22 +0200 (CEST) Subject: [Pw_forum] local pseudopotential part construction In-Reply-To: References: Message-ID: <24051.147.122.5.216.1219155382.squirrel@webmail.sissa.it> On Mar, Agosto 12, 2008 12:10, ?????? wrote: > Can someone recommend some papers concerning the > construction scheme of local potential to me ? Dear Wenmei, there are many possible recipes for constructing the local part. Have a look at the ld1 documentation to see which are actually implemented in our code. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From eyvaz_isaev at yahoo.com Tue Aug 19 16:20:39 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 19 Aug 2008 07:20:39 -0700 (PDT) Subject: [Pw_forum] The resulte of optimizing the ZnO lattice constant use vc-relax In-Reply-To: <32273636.262091219152619079.JavaMail.coremail@bj126app52.126.com> Message-ID: <92016.18794.qm@web65707.mail.ac4.yahoo.com> Dear user, Please keep in mind that results of your calcultions might be different of experiment and other calculations due to many reasons. The main question is how much. As concerns your results, they seem to be good, "a" parameter is just 1.1% elongated (3.287Ang against 3.25Ang), and c/a=1.627761723/1.011331020 = 1.6095 in quite good agreement with experimental. > useful advice will be appreciated And we will appreciate if you provide your affiliation. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Tue, 8/19/08, wangqj1 wrote: > From: wangqj1 > Subject: [Pw_forum] The resulte of optimizing the ZnO lattice constant use vc-relax > To: "pw_forum" > Date: Tuesday, August 19, 2008, 5:30 PM > Dear pwscf users > I run vc-relax to optimize the lattice constant of > ZnO unit cell,my input file and out file as follows: > > &CONTROL > title = ZnOVC , > calculation = 'vc-relax' , > restart_mode = 'from_scratch' , > pseudo_dir = > '/root/espresso-3.2.3/pseudo/' , > prefix = ZnO , > etot_conv_thr = 1.D-5 , > nstep = 100 , > tstress = .true. , > tprnfor = .true. , > dt = 100 , > tefield = .false. , > / > &SYSTEM > ibrav = 4, > celldm(1) = 6.14161, > celldm(3) = 1.6022, > nat = 4, > ntyp = 2, > ecutwfc = 40 , > ecutrho = 300 , > nosym = .true. , > nbnd = 25, > occupations = 'smearing' , > degauss = 0.002 , > smearing = 'methfessel-paxton' > , > lda_plus_u = .false. , > / > &ELECTRONS > conv_thr = 1.D-8 , > startingpot = 'atomic' , > startingwfc = 'atomic' , > mixing_mode = 'plain' , > mixing_beta = 0.6 , > diagonalization = 'david' , > diago_full_acc = .true. , > / > &IONS > ion_dynamics = 'damp' , > / > &CELL > cell_dynamics = 'damp-w' , > / > ATOMIC_SPECIES > Zn 65.00000 Zn.pz-van_ak.UPF > O 16.00000 O.pz-rrkjus.UPF > ATOMIC_POSITIONS crystal > Zn 0.333333333 0.666666667 0.000000000 1 > 1 1 > O 0.333333333 0.666666667 0.381700000 1 > 1 1 > Zn 0.666666667 0.333333333 0.500000000 1 > 1 1 > O 0.666666667 0.333333300 0.881700000 1 > 1 1 > K_POINTS automatic > 4 4 4 0 0 0 > > -------------------------------------------------------------------------------- > Program PWSCF v.3.2.2 starts ... > Today is 18Aug2008 at 23: 7:36 > Ultrasoft (Vanderbilt) Pseudopotentials > Current dimensions of program pwscf are: > ntypx = 10 npk = 40000 lmax = 3 > nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 > Title: > ZnOVC > > > bravais-lattice index = 4 > lattice parameter (a_0) = 6.1416 a.u. > unit-cell volume = 321.4357 (a.u.)^3 > number of atoms/cell = 4 > number of atomic types = 2 > kinetic-energy cutoff = 40.0000 Ry > charge density cutoff = 300.0000 Ry > convergence threshold = 1.0E-08 > beta = 0.6000 > number of iterations used = 8 plain > mixing > Exchange-correlation = SLA PW PBE PBE (1434) > nstep = 100 > celldm(1)= 6.141610 celldm(2)= 0.000000 > celldm(3)= 1.602200 > celldm(4)= 0.000000 celldm(5)= 0.000000 > celldm(6)= 0.000000 > crystal axes: (cart. coord. in units of a_0) > a(1) = ( 1.000000 0.000000 0.000000 ) > a(2) = ( -0.500000 0.866025 0.000000 ) > a(3) = ( 0.000000 0.000000 1.602200 ) > reciprocal axes: (cart. coord. in units 2 pi/a_0) > b(1) = ( 1.000000 0.577350 0.000000 ) > b(2) = ( 0.000000 1.154701 0.000000 ) > b(3) = ( 0.000000 0.000000 0.624142 ) > > ....... > ....... > outfile: > > Final estimate of lattice vectors (input alat units) > 1.011331020 0.000000000 0.000000000 > -0.505665507 0.875838356 0.000000001 > 0.000000000 -0.000000002 1.627761723 > final unit-cell volume = 334.0064 (a.u.)^3 > input alat = 6.1416 (a.u.) > CELL_PARAMETERS (alat) > 1.011331020 0.000000000 0.000000000 > -0.505665507 0.875838356 0.000000001 > 0.000000000 -0.000000002 1.627761723 > ATOMIC_POSITIONS (crystal) > Zn 0.333333347 0.666666677 0.000438189 > O 0.333333356 0.666666677 0.380132292 > Zn 0.666666690 0.333333345 0.500438960 > O 0.666666695 0.333333331 0.880132483 > > from the outfile I can see the c/a=1.627761723 and from the > final unit-cell volume =334.0064 (a.u.)^3,I can compute the > a=6.189678(Bohr)=3.2754(A)?From the value of caculating > ,we can see that the c/a and a are both bigger than the > experiment , I don't konw whether the result is right or > wrong . > > Anybody who know about the question and give me the useful > advice will be appreciated . > > Sincerely > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From lfhuang at theory.issp.ac.cn Wed Aug 20 06:21:49 2008 From: lfhuang at theory.issp.ac.cn (L.F.Huang) Date: Wed, 20 Aug 2008 12:21:49 +0800 (CST) Subject: [Pw_forum] question on Nonlinear core correction Message-ID: <34542.210.73.17.131.1219206109.squirrel@210.73.16.4> Dear Guoying Gao In addition to prof. Baroni's advice, I recommend you read the notes written by prof. Paolo Giannozzi named "Notes on Pseudopotential generation" and all the reference papers he has given(including PRB v26,1738), which may help you grasp some details of the PSEUDOPOTENTIAL. PS: The notes can be find in the atomic_doc/pseudo-gen.tex in the espresso package. Best Wishes! Yours Sincerely ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== From acicek at akdeniz.edu.tr Wed Aug 20 10:22:47 2008 From: acicek at akdeniz.edu.tr (Ahmet Cicek) Date: Wed, 20 Aug 2008 11:22:47 +0300 Subject: [Pw_forum] Site Occupancy In-Reply-To: <3c4d36390808200121u6b2aff3ew36c427d723371ca2@mail.gmail.com> References: <3c4d36390808200121u6b2aff3ew36c427d723371ca2@mail.gmail.com> Message-ID: <3c4d36390808200122w48db700ax7289fcc719380617@mail.gmail.com> ---------- Forwarded message ---------- From: Ahmet Cicek Date: Wed, Aug 20, 2008 at 11:21 AM Subject: [Pw_forum] Site Occupancy To: PWSCF Forum Hi, I am trying to obtain the band structure of Ammonium Hexafluorosilicate-(NH_4)_2SiF_6-where the space group is Fm3m, location and occupancies* of the base atoms are: atom position occupancy ------------------------------------------------------------------------ Si (0,0,0) 1 F (0.2011,0,0) 1 N (0.25,0.25,0.25) 1 H (0.168,0.168,0.269) 1/3 When the structure is contructed via symmetry operations, the number of the H atoms are three times the actual value. Could you please help me in how to use the knowledge of "occupancy" of the H atoms so that the band structure calculation gives results corresponding to the physical structure? Thank you. *http://rruff.geo.arizona.edu/AMS/result.php?mineral=cryptohalite -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080820/e37a6b82/attachment.htm From eyvaz_isaev at yahoo.com Wed Aug 20 12:19:04 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 20 Aug 2008 03:19:04 -0700 (PDT) Subject: [Pw_forum] Site Occupancy In-Reply-To: <3c4d36390808200122w48db700ax7289fcc719380617@mail.gmail.com> Message-ID: <349809.30936.qm@web65703.mail.ac4.yahoo.com> Dear Ahmet, Pseudopotential and most of Full-Potential programs can not deal with fractional site occupation. The only way for this purpose is the use of programs within Coherent-Potential-Approximation. But, actually, I am not sure it will work in your case, as you have to mix "empty sphere" and H to get fully occupied site. If you ("randomly") remove some H atoms you will get correct stoichiometry, though each H site is fully occupied. Please also provide your affiliation. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 8/20/08, Ahmet Cicek wrote: > From: Ahmet Cicek > Subject: [Pw_forum] Site Occupancy > To: "PWSCF Forum" > Date: Wednesday, August 20, 2008, 12:22 PM > ---------- Forwarded message ---------- > From: Ahmet Cicek > Date: Wed, Aug 20, 2008 at 11:21 AM > Subject: [Pw_forum] Site Occupancy > To: PWSCF Forum > > > Hi, > > I am trying to obtain the band structure of Ammonium > Hexafluorosilicate-(NH_4)_2SiF_6-where the space group is > Fm3m, location and > occupancies* of the base atoms are: > > atom position occupancy > ------------------------------------------------------------------------ > Si (0,0,0) 1 > F (0.2011,0,0) 1 > N (0.25,0.25,0.25) 1 > H (0.168,0.168,0.269) 1/3 > > When the structure is contructed via symmetry operations, > the number of the > H atoms are three times the actual value. Could you please > help me in how to > use the knowledge of "occupancy" of the H atoms > so that the band structure > calculation gives results corresponding to the physical > structure? > Thank you. > > > *http://rruff.geo.arizona.edu/AMS/result.php?mineral=cryptohalite > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From calderin at physics.queensu.ca Wed Aug 20 12:30:11 2008 From: calderin at physics.queensu.ca (Lazaro Calderin) Date: Wed, 20 Aug 2008 12:30:11 +0200 Subject: [Pw_forum] Site Occupancy In-Reply-To: <3c4d36390808200122w48db700ax7289fcc719380617@mail.gmail.com> References: <3c4d36390808200121u6b2aff3ew36c427d723371ca2@mail.gmail.com> <3c4d36390808200122w48db700ax7289fcc719380617@mail.gmail.com> Message-ID: <1219228211.2892.23.camel@wolfe> Hi Ahmet, > > I am trying to obtain the band structure of Ammonium > Hexafluorosilicate-(NH_4)_2SiF_6-where the space group is Fm3m, > location and occupancies* of the base atoms are: > > atom position occupancy > ------------------------------------------------------------------------ > Si (0,0,0) 1 > F (0.2011,0,0) 1 > N (0.25,0.25,0.25) 1 > H (0.168,0.168,0.269) 1/3 > > When the structure is contructed via symmetry operations, the number > of the H atoms are three times the actual value. Could you please help > me in how to use the knowledge of "occupancy" of the H atoms so that > the band structure calculation gives results corresponding to the > physical structure? Occupancies are usually not a direct input for electronic structure calculations. To simulate the occupancies one just reduces the number of atom in the structure by hand, I mean deleting those atoms that are not supposed to be there. Sometimes it is obvious what sites should be occupied or empty, for example when H ions are very close to each other. However if it is not the case then you should generate all the non-equivalent possibilities of having 1/3 of the H positions empty and fully relaxed them under the same computational conditions to find the most stable configuration(s). Lazaro -- ============================================================= Lazaro Calderin Department of Physics Queen's University, Kingston, Ontario, Canada E-mails: calderin at physics.queensu.ca From d.kasinathan at ifw-dresden.de Wed Aug 20 14:42:31 2008 From: d.kasinathan at ifw-dresden.de (Deepa Kasinathan) Date: Wed, 20 Aug 2008 14:42:31 +0200 (CEST) Subject: [Pw_forum] Restarting ph.x in version 4.0.1 In-Reply-To: Message-ID: Hello, I run ph.x using Version 2.1.5, and the CPU time limit is exceeded before all the phonon frequencies are calculated. When I restart this calculation, the program recognizes that and continues with the phonon modes that were not yet calculated. I do the same thing with Version 4.0.1, but every time the program starts to calculate from the first phonon mode. Is there a new flag that needs to be added to the input file in the new version so as to not redo the phonon modes that are already converged ? I appreciate any help regarding this problem. Regards, Deepa Deepa Kasinathan Max Planck Institute for Chemical Physics of Solids Noethnitzer Strasse 40, D-01187 Dresden, Germany. Phone: +49 351 4646 4424. From eyvaz_isaev at yahoo.com Wed Aug 20 15:32:46 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 20 Aug 2008 06:32:46 -0700 (PDT) Subject: [Pw_forum] Restarting ph.x in version 4.0.1 In-Reply-To: Message-ID: <52702.58717.qm@web65714.mail.ac4.yahoo.com> Dear Deepa, You can try adding "recover=.true." to your *.ph.in, but it requires saved temporary files. If this does not fix your problem (one reason is you use parallel environment and temporary files are deleted right after your job stopped or crashed) let me know and I can send you modified files. Bests Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 8/20/08, Deepa Kasinathan wrote: > From: Deepa Kasinathan > Subject: [Pw_forum] Restarting ph.x in version 4.0.1 > To: pw_forum at pwscf.org > Date: Wednesday, August 20, 2008, 4:42 PM > Hello, > > I run ph.x using Version 2.1.5, and the CPU time limit > is exceeded > before all the phonon frequencies are calculated. When I > restart this > calculation, the program recognizes that and continues with > the phonon > modes that were not yet calculated. > > I do the same thing with Version 4.0.1, but every time > the program > starts to calculate from the first phonon mode. Is there a > new flag that > needs to be added to the input file in the new version so > as to not > redo the phonon modes that are already converged ? > > I appreciate any help regarding this problem. > > Regards, > Deepa > > Deepa Kasinathan > Max Planck Institute for Chemical Physics of Solids > Noethnitzer Strasse 40, D-01187 Dresden, Germany. > Phone: +49 351 4646 4424. > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From prasenjit.jnc at gmail.com Wed Aug 20 15:21:16 2008 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Wed, 20 Aug 2008 15:21:16 +0200 Subject: [Pw_forum] Restarting ph.x in version 4.0.1 In-Reply-To: References: Message-ID: <627e0ffa0808200621x4978ccc1rbfa38d8c25adb79f@mail.gmail.com> Dear Deepa, You should use set the "recover" flag to .true. to restart the phonon cal. Prasenjit. 2008/8/20 Deepa Kasinathan > Hello, > > I run ph.x using Version 2.1.5, and the CPU time limit is exceeded > before all the phonon frequencies are calculated. When I restart this > calculation, the program recognizes that and continues with the phonon > modes that were not yet calculated. > > I do the same thing with Version 4.0.1, but every time the program > starts to calculate from the first phonon mode. Is there a new flag that > needs to be added to the input file in the new version so as to not > redo the phonon modes that are already converged ? > > I appreciate any help regarding this problem. > > Regards, > Deepa > > Deepa Kasinathan > Max Planck Institute for Chemical Physics of Solids > Noethnitzer Strasse 40, D-01187 Dresden, Germany. > Phone: +49 351 4646 4424. > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- PRASENJIT GHOSH, POST-DOC, ROOM NO: 265, MAIN BUILDING, CM SECTION, ICTP, STRADA COSTERIA 11, TRIESTE, 34104, ITALY PHONE: +39 040 2240 369 (O) +39 3807528672 (M) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080820/ac3941ea/attachment.htm From stewart at cnf.cornell.edu Wed Aug 20 16:39:06 2008 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Wed, 20 Aug 2008 10:39:06 -0400 Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos Message-ID: <20080820143906.3325.qmail@mail.spidergraphics.com> Hi everyone, I am looking at the density of states of graphene and I have run into a problem with the projwfc program. When I plot out the total density of states for the system and compare this to the sum of the partial density of states found in the pdos_tot file, I find that the sum of the partial DOS is missing some large peaks at energies above the Fermi energy. The total DOS from the projwfc run matches the total DOS generated using dos.x and the tetrahedra technique. The bands responsible for these missing peaks also show up in the band plot. I have tried using both methfessel-paxton and marzari-vanderbilt smearing (degauss 0.01) but this does not have any effect on the problem. I thought that perhaps the projection onto the atomic orbitals was missing a significant portion of the charge, however my spilling parameter is fairly low 0.0116. This is comparable to the spilling parameter found in example08 for nickel 0.0115 where the total and partial dos match reasonable well (although slightly shifted in energy in the reference data). I would appreciate any thoughts as to why I am missing these DOS peaks in the partial dos. Are there difficulties in projecting plane waves to orbitals for conduction bands? Has anyone else run into this problem? For the details of my calculation, I am using C.pz-rrkjus.UPF, ecutwfc=45, ecutrho=450, k-grid for self-consistent calculation (64x64x1), k-grid for non-scf for dos (96x96x1), number of bands=20 and working with espresso 4.0.1. Thanks, Derek ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From jlz101 at unlserve.unl.edu Wed Aug 20 17:09:51 2008 From: jlz101 at unlserve.unl.edu (J. D. Burton) Date: Wed, 20 Aug 2008 10:09:51 -0500 Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos In-Reply-To: <20080820143906.3325.qmail@mail.spidergraphics.com> References: <20080820143906.3325.qmail@mail.spidergraphics.com> Message-ID: <002901c902d6$cb32f0e0$6198d2a0$@unl.edu> Derek, Why would you need to calculate more than 8 bands? (1 s-state + 3 p-states) x 2 C atoms per unit cell = 8 bands, and half of them are doubly-occupied. By setting nbnd = 20 (10 per atom in the unit cell) you get all the way up into d-like-bands, and your pseudopotential file doesn't contain atomic d-wavefunctions of carbon. That would explain why the sum of your projected dos doesn't match your total density, i.e. the extra peaks are d-bands. Cheers, J. D. ************************************ J. D. Burton, Ph.D. jlz101 at unlserve.unl.edu University of Nebraska Lincoln Physics and Astronomy Office Ph. (402) 472 2499 213C Ferguson Hall ************************************ "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of stewart at cnf.cornell.edu Sent: Wednesday, August 20, 2008 9:39 AM To: pw_forum at pwscf.org Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos Hi everyone, I am looking at the density of states of graphene and I have run into a problem with the projwfc program. When I plot out the total density of states for the system and compare this to the sum of the partial density of states found in the pdos_tot file, I find that the sum of the partial DOS is missing some large peaks at energies above the Fermi energy. The total DOS from the projwfc run matches the total DOS generated using dos.x and the tetrahedra technique. The bands responsible for these missing peaks also show up in the band plot. I have tried using both methfessel-paxton and marzari-vanderbilt smearing (degauss 0.01) but this does not have any effect on the problem. I thought that perhaps the projection onto the atomic orbitals was missing a significant portion of the charge, however my spilling parameter is fairly low 0.0116. This is comparable to the spilling parameter found in example08 for nickel 0.0115 where the total and partial dos match reasonable well (although slightly shifted in energy in the reference data). I would appreciate any thoughts as to why I am missing these DOS peaks in the partial dos. Are there difficulties in projecting plane waves to orbitals for conduction bands? Has anyone else run into this problem? For the details of my calculation, I am using C.pz-rrkjus.UPF, ecutwfc=45, ecutrho=450, k-grid for self-consistent calculation (64x64x1), k-grid for non-scf for dos (96x96x1), number of bands=20 and working with espresso 4.0.1. Thanks, Derek ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From stewart at cnf.cornell.edu Wed Aug 20 17:42:54 2008 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Wed, 20 Aug 2008 11:42:54 -0400 Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos In-Reply-To: <002901c902d6$cb32f0e0$6198d2a0$@unl.edu> References: <20080820143906.3325.qmail@mail.spidergraphics.com> <002901c902d6$cb32f0e0$6198d2a0$@unl.edu> Message-ID: <20080820154254.9057.qmail@mail.spidergraphics.com> Hi J. D., Thanks for your comment! I am currently working on a project where it would be helpful to know the orbital character of the higher energy dos peaks. I know that they will have little effect on the self-consistent calculation. You raise an important point that I perhaps missed with the projwfc implementation. If projwfc can only map back to the orbitals provided in the pseudopotential (2s 2p), then this will limit its usefulness for determining the orbital character of higher energy conduction bands. Thanks, Derek J. D. Burton writes: > Derek, > > Why would you need to calculate more than 8 bands? (1 s-state + 3 p-states) > x 2 C atoms per unit cell = 8 bands, and half of them are doubly-occupied. > By setting nbnd = 20 (10 per atom in the unit cell) you get all the way up > into d-like-bands, and your pseudopotential file doesn't contain atomic > d-wavefunctions of carbon. That would explain why the sum of your projected > dos doesn't match your total density, i.e. the extra peaks are d-bands. > > Cheers, > J. D. > > ************************************ > J. D. Burton, Ph.D. > jlz101 at unlserve.unl.edu > University of Nebraska Lincoln > Physics and Astronomy > Office Ph. (402) 472 2499 > 213C Ferguson Hall > ************************************ > "The job of a scientist is to generate wrong ideas as fast as possible." > -- Murray Gell-Mann > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of stewart at cnf.cornell.edu > Sent: Wednesday, August 20, 2008 9:39 AM > To: pw_forum at pwscf.org > Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos > > Hi everyone, > > I am looking at the density of states of graphene and I have run into a > problem with the projwfc program. When I plot out the total density of > states for the system and compare this to the sum of the partial density of > states found in the pdos_tot file, I find that the sum of the partial DOS is > > missing some large peaks at energies above the Fermi energy. The total DOS > from the projwfc run matches the total DOS generated using dos.x and the > tetrahedra technique. The bands responsible for these missing peaks also > show up in the band plot. I have tried using both methfessel-paxton and > marzari-vanderbilt smearing (degauss 0.01) but this does not have any effect > > on the problem. > > I thought that perhaps the projection onto the atomic orbitals was missing a > > significant portion of the charge, however my spilling parameter is fairly > low 0.0116. This is comparable to the spilling parameter found in example08 > > for nickel 0.0115 where the total and partial dos match reasonable well > (although slightly shifted in energy in the reference data). > > I would appreciate any thoughts as to why I am missing these DOS peaks in > the partial dos. Are there difficulties in projecting plane waves to > orbitals for conduction bands? Has anyone else run into this problem? > > For the details of my calculation, I am using C.pz-rrkjus.UPF, ecutwfc=45, > ecutrho=450, k-grid for self-consistent calculation (64x64x1), k-grid for > non-scf for dos (96x96x1), number of bands=20 and working with espresso > 4.0.1. > > Thanks, > > Derek > > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > http://www.people.cornell.edu/pages/das248/ > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > _______________________________________________ > 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 > ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From calderin at physics.queensu.ca Wed Aug 20 18:28:47 2008 From: calderin at physics.queensu.ca (Lazaro Calderin) Date: Wed, 20 Aug 2008 18:28:47 +0200 Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos In-Reply-To: <20080820154254.9057.qmail@mail.spidergraphics.com> References: <20080820143906.3325.qmail@mail.spidergraphics.com> <002901c902d6$cb32f0e0$6198d2a0$@unl.edu> <20080820154254.9057.qmail@mail.spidergraphics.com> Message-ID: <1219249727.2892.53.camel@wolfe> Hi Derek, > You raise an important point that I perhaps missed with the projwfc > implementation. If projwfc can only map back to the orbitals provided in > the pseudopotential (2s 2p), then this will limit its usefulness for > determining the orbital character of higher energy conduction bands. What about regenerating the pseudopotential with the same configuration for the s and p channels as the original and including a d-channel ? You could then use projwfc to get projection on the d-orbitals. Bye, Lazaro -- ============================================================= Lazaro Calderin Department of Physics Queen's University, Kingston, Ontario, Canada E-mails: calderin at physics.queensu.ca From jlz101 at unlserve.unl.edu Wed Aug 20 18:34:16 2008 From: jlz101 at unlserve.unl.edu (J. D. Burton) Date: Wed, 20 Aug 2008 11:34:16 -0500 Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos In-Reply-To: <20080820154254.9057.qmail@mail.spidergraphics.com> References: <20080820143906.3325.qmail@mail.spidergraphics.com> <002901c902d6$cb32f0e0$6198d2a0$@unl.edu> <20080820154254.9057.qmail@mail.spidergraphics.com> Message-ID: <003b01c902e2$964ddf00$c2e99d00$@unl.edu> Hi Derek, Interesting, though it shouldn't be that difficult to just take the pseudopotential (PSP) as it is and use the ld1.x program (comes with the espresso package) and calculate other atomic pseudowavefunctions that you can then project onto. You can then include these in your PSP file. I suppose if you're really ambitious, you could alter the projwfc program to not use the atomic functions in the PSP file, but instead use different localized functions in a file that you provide (for example, you could try Wannier functions). I know that you can do this with the lda+u feature, like setting U_projection_type to 'file'. See the INPUT_PW.txt file for details on that. Cheers, J. D. ************************************ J. D. Burton, Ph.D. jlz101 at unlserve.unl.edu University of Nebraska Lincoln Physics and Astronomy Office Ph. (402) 472 2499 213C Ferguson Hall ************************************ "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of stewart at cnf.cornell.edu Sent: Wednesday, August 20, 2008 10:43 AM To: PWSCF Forum Subject: Re: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos Hi J. D., Thanks for your comment! I am currently working on a project where it would be helpful to know the orbital character of the higher energy dos peaks. I know that they will have little effect on the self-consistent calculation. You raise an important point that I perhaps missed with the projwfc implementation. If projwfc can only map back to the orbitals provided in the pseudopotential (2s 2p), then this will limit its usefulness for determining the orbital character of higher energy conduction bands. Thanks, Derek J. D. Burton writes: > Derek, > > Why would you need to calculate more than 8 bands? (1 s-state + 3 p-states) > x 2 C atoms per unit cell = 8 bands, and half of them are doubly-occupied. > By setting nbnd = 20 (10 per atom in the unit cell) you get all the way up > into d-like-bands, and your pseudopotential file doesn't contain atomic > d-wavefunctions of carbon. That would explain why the sum of your projected > dos doesn't match your total density, i.e. the extra peaks are d-bands. > > Cheers, > J. D. > > ************************************ > J. D. Burton, Ph.D. > jlz101 at unlserve.unl.edu > University of Nebraska Lincoln > Physics and Astronomy > Office Ph. (402) 472 2499 > 213C Ferguson Hall > ************************************ > "The job of a scientist is to generate wrong ideas as fast as possible." > -- Murray Gell-Mann > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of stewart at cnf.cornell.edu > Sent: Wednesday, August 20, 2008 9:39 AM > To: pw_forum at pwscf.org > Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos > > Hi everyone, > > I am looking at the density of states of graphene and I have run into a > problem with the projwfc program. When I plot out the total density of > states for the system and compare this to the sum of the partial density of > states found in the pdos_tot file, I find that the sum of the partial DOS is > > missing some large peaks at energies above the Fermi energy. The total DOS > from the projwfc run matches the total DOS generated using dos.x and the > tetrahedra technique. The bands responsible for these missing peaks also > show up in the band plot. I have tried using both methfessel-paxton and > marzari-vanderbilt smearing (degauss 0.01) but this does not have any effect > > on the problem. > > I thought that perhaps the projection onto the atomic orbitals was missing a > > significant portion of the charge, however my spilling parameter is fairly > low 0.0116. This is comparable to the spilling parameter found in example08 > > for nickel 0.0115 where the total and partial dos match reasonable well > (although slightly shifted in energy in the reference data). > > I would appreciate any thoughts as to why I am missing these DOS peaks in > the partial dos. Are there difficulties in projecting plane waves to > orbitals for conduction bands? Has anyone else run into this problem? > > For the details of my calculation, I am using C.pz-rrkjus.UPF, ecutwfc=45, > ecutrho=450, k-grid for self-consistent calculation (64x64x1), k-grid for > non-scf for dos (96x96x1), number of bands=20 and working with espresso > 4.0.1. > > Thanks, > > Derek > > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > http://www.people.cornell.edu/pages/das248/ > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > _______________________________________________ > 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 > ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From stewart at cnf.cornell.edu Wed Aug 20 19:38:40 2008 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Wed, 20 Aug 2008 13:38:40 -0400 Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos In-Reply-To: <003b01c902e2$964ddf00$c2e99d00$@unl.edu> References: <20080820143906.3325.qmail@mail.spidergraphics.com> <002901c902d6$cb32f0e0$6198d2a0$@unl.edu> <20080820154254.9057.qmail@mail.spidergraphics.com> <003b01c902e2$964ddf00$c2e99d00$@unl.edu> Message-ID: <20080820173840.19932.qmail@mail.spidergraphics.com> Hi J. D. and Lazaro, Thanks for your suggestions. After my last email, I actually started down the route of adding more orbitals to the C pseudopotential by taking the original format and switching the 3d line to 3D 3 2 0.00 0.15 1.30 1.30 before it had a -2.00 to neglect this band. I'll try it out and see how much it affects my total density of states and see if it catches the missing bands. Using Wannier functions sounds interesting. I'll look into that possibility as well. Best regards, Derek J. D. Burton writes: > Hi Derek, > > Interesting, though it shouldn't be that difficult to just take the > pseudopotential (PSP) as it is and use the ld1.x program (comes with the > espresso package) and calculate other atomic pseudowavefunctions that you > can then project onto. You can then include these in your PSP file. > I suppose if you're really ambitious, you could alter the projwfc program to > not use the atomic functions in the PSP file, but instead use different > localized functions in a file that you provide (for example, you could try > Wannier functions). I know that you can do this with the lda+u feature, like > setting U_projection_type to 'file'. See the INPUT_PW.txt file for details > on that. > > Cheers, > J. D. > > > ************************************ > J. D. Burton, Ph.D. > jlz101 at unlserve.unl.edu > University of Nebraska Lincoln > Physics and Astronomy > Office Ph. (402) 472 2499 > 213C Ferguson Hall > ************************************ > "The job of a scientist is to generate wrong ideas as fast as possible." > -- Murray Gell-Mann > > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of stewart at cnf.cornell.edu > Sent: Wednesday, August 20, 2008 10:43 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos > > Hi J. D., > > Thanks for your comment! I am currently working on a project where it would > > be helpful to know the orbital character of the higher energy dos peaks. I > know that they will have little effect on the self-consistent calculation. > > You raise an important point that I perhaps missed with the projwfc > implementation. If projwfc can only map back to the orbitals provided in > the pseudopotential (2s 2p), then this will limit its usefulness for > determining the orbital character of higher energy conduction bands. > > Thanks, > > Derek > > > J. D. Burton writes: > >> Derek, >> >> Why would you need to calculate more than 8 bands? (1 s-state + 3 > p-states) >> x 2 C atoms per unit cell = 8 bands, and half of them are doubly-occupied. >> By setting nbnd = 20 (10 per atom in the unit cell) you get all the way up >> into d-like-bands, and your pseudopotential file doesn't contain atomic >> d-wavefunctions of carbon. That would explain why the sum of your > projected >> dos doesn't match your total density, i.e. the extra peaks are d-bands. >> >> Cheers, >> J. D. >> >> ************************************ >> J. D. Burton, Ph.D. >> jlz101 at unlserve.unl.edu >> University of Nebraska Lincoln >> Physics and Astronomy >> Office Ph. (402) 472 2499 >> 213C Ferguson Hall >> ************************************ >> "The job of a scientist is to generate wrong ideas as fast as possible." >> -- Murray Gell-Mann >> >> -----Original Message----- >> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On >> Behalf Of stewart at cnf.cornell.edu >> Sent: Wednesday, August 20, 2008 9:39 AM >> To: pw_forum at pwscf.org >> Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos >> >> Hi everyone, >> >> I am looking at the density of states of graphene and I have run into a >> problem with the projwfc program. When I plot out the total density of >> states for the system and compare this to the sum of the partial density > of >> states found in the pdos_tot file, I find that the sum of the partial DOS > is >> >> missing some large peaks at energies above the Fermi energy. The total > DOS >> from the projwfc run matches the total DOS generated using dos.x and the >> tetrahedra technique. The bands responsible for these missing peaks also >> show up in the band plot. I have tried using both methfessel-paxton and >> marzari-vanderbilt smearing (degauss 0.01) but this does not have any > effect >> >> on the problem. >> >> I thought that perhaps the projection onto the atomic orbitals was missing > a >> >> significant portion of the charge, however my spilling parameter is fairly > >> low 0.0116. This is comparable to the spilling parameter found in > example08 >> >> for nickel 0.0115 where the total and partial dos match reasonable well >> (although slightly shifted in energy in the reference data). >> >> I would appreciate any thoughts as to why I am missing these DOS peaks in >> the partial dos. Are there difficulties in projecting plane waves to >> orbitals for conduction bands? Has anyone else run into this problem? >> >> For the details of my calculation, I am using C.pz-rrkjus.UPF, ecutwfc=45, > >> ecutrho=450, k-grid for self-consistent calculation (64x64x1), k-grid for >> non-scf for dos (96x96x1), number of bands=20 and working with espresso >> 4.0.1. >> >> Thanks, >> >> Derek >> >> >> ################################ >> Derek Stewart, Ph. D. >> Scientific Computation Associate >> http://www.people.cornell.edu/pages/das248/ >> 250 Duffield Hall >> Cornell Nanoscale Facility (CNF) >> Ithaca, NY 14853 >> stewart (at) cnf.cornell.edu >> (607) 255-2856 >> _______________________________________________ >> 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 >> > > > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > http://www.people.cornell.edu/pages/das248/ > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > _______________________________________________ > 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 > ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From giannozz at democritos.it Wed Aug 20 20:54:28 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 20 Aug 2008 20:54:28 +0200 Subject: [Pw_forum] IOTK library In-Reply-To: <22ae3ca40808131433m52802a3do94106d27509387fe@mail.gmail.com> References: <22ae3ca40808131433m52802a3do94106d27509387fe@mail.gmail.com> Message-ID: <791E8D00-8203-47D4-830D-B1DC7B09E726@democritos.it> On Aug 13, 2008, at 23:33 , alan chen wrote: > Paolo suggested a quick fix: change Q_REAL in Q_REAL_SPACE in > Modules/xml_io_base.f90 (thanks to Giovanni Bussi). > Does that mean: replace Q_REAL_SPACE by Q_REAL? no, it means the opposite: replace Q_REAL with Q_REAL_SPACE --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Aug 20 21:01:53 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 20 Aug 2008 21:01:53 +0200 Subject: [Pw_forum] Wavefunction format documentation for PWSCF version 3.0 In-Reply-To: <48A2F94A.6090807@hv.se> References: <48A2F94A.6090807@hv.se> Message-ID: On Aug 13, 2008, at 17:10 , Steven Kirk wrote: > I have some old simulation results produced using PWSCF v3.0, > specifically old input files, .wfc and .chdens files. I need to be > able > to extract the wavefunction information in order to calculate the Bohm > quantum potential. Is there any documentation for the .wfc file format > other than the source code itself? no, but old .wfc files should be still readable, since their format hasn't really changed and it is still used during execution; but you have a chance to read them only on machines with the same representation of floating-point numbers, on the same number of processors and pools, etc. etc., of the machine that produced the original data Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Aug 20 21:05:42 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 20 Aug 2008 21:05:42 +0200 Subject: [Pw_forum] Problems with Espresso-4.0.1 In-Reply-To: <4E54785C55974076B4B9E570066C6C14@leffler2> References: <4E54785C55974076B4B9E570066C6C14@leffler2> Message-ID: <99145A24-0A21-41B3-A376-7DAB4D2247B6@democritos.it> On Aug 16, 2008, at 1:28 , Amos Leffler wrote: > I have been trying to get the espresso-4.0.1 to run totally for a > while. > I have been using g95_x86_64 compiler and mkl 10.0.3.020 library didn't somebody tell you not to use g95 with default 64-bit integer? --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Aug 20 21:11:05 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 20 Aug 2008 21:11:05 +0200 Subject: [Pw_forum] about davcio error In-Reply-To: <24754315.398471218793282423.JavaMail.coremail@bj163app64.163.com> References: <24754315.398471218793282423.JavaMail.coremail@bj163app64.163.com> Message-ID: <06B067E8-D705-4BD7-B1DA-F7E33B02CEFB@democritos.it> On Aug 15, 2008, at 11:41 , only1xiaoyuan wrote: > I am about to calculate g tensor of EPR using GIPAW, > but there are some questions .Could anyone tell me > what means the following error message: > ---------------------------------- > from davcio : error # 14 > error while reading from file > ----------------------------------- it means that there was an error while reading from file (opened as fortran unit 14) > is it due to lda+U in scf calculation? please try a calculation without U and answer by yourself Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Aug 20 21:15:51 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 20 Aug 2008 21:15:51 +0200 Subject: [Pw_forum] pw2casino difficulty In-Reply-To: <52030.10.1.20.105.1219088198.squirrel@mail.ciw.edu> References: <52030.10.1.20.105.1219088198.squirrel@mail.ciw.edu> Message-ID: On Aug 18, 2008, at 21:36 , lshulenburger at ciw.edu wrote: > I am having difficulty with the version of pw2casino that is > included in > the 4.0.1 distribution of quantum espresso. Whenever I attempt to run > this utility I get an error message from each node stating: > > Atom 01 not found > > And then the program exits. Looking at the source I see that at > line 284 > of pw2casino.f90 the program is attempting to write out information > about > the atoms used in the calculation. I do not need this information, > so I > simply commented out the next five lines: > > ! DO na = 1, nat > ! nt = ityp(na) > ! at_num = atomic_number(TRIM(atm(nt))) na = atom number nt = atom type atm(nt) = atom name TRIM(atm(nt)) = atom name without trailing spaces atomic_number(TRIM(atm(nt))) = atomic number for atom of a given name For some reason, the atom name is "01" and function atomic_number complains P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From lshulenburger at ciw.edu Wed Aug 20 21:43:58 2008 From: lshulenburger at ciw.edu (lshulenburger at ciw.edu) Date: Wed, 20 Aug 2008 15:43:58 -0400 (EDT) Subject: [Pw_forum] pw2casino difficulty In-Reply-To: References: <52030.10.1.20.105.1219088198.squirrel@mail.ciw.edu> Message-ID: <52809.10.1.20.105.1219261438.squirrel@mail.ciw.edu> >> so I >> simply commented out the next five lines: >> >> ! DO na = 1, nat >> ! nt = ityp(na) >> ! at_num = atomic_number(TRIM(atm(nt))) > > na = atom number > nt = atom type > atm(nt) = atom name > TRIM(atm(nt)) = atom name without trailing spaces > atomic_number(TRIM(atm(nt))) = atomic number for atom of a given name > > For some reason, the atom name is "01" and function atomic_number > complains > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 Thanks, This leads me to one mistake I have made and a question. When I wrote the error message Atom 01 not found I should have written Atom O1 not found. The calculation I was working on is for antiferromagnetic FeO and I used as species labels O1, Fe1 and Fe2. Looking at the atomic_number function I can't tell i fit can handle these labels (which I believe are necessary on Fe to break the spin degeneracy). However I notice that oxygen is listed in the table of atomic symbols as ' O' does this mean that I need to somehow include a space in my species label? Luke Shulenburger (lshulenburger at ciw.edu) Geophysical Laboratory Carnegie Institute of Washington From bipulrr at gmail.com Thu Aug 21 08:31:49 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Thu, 21 Aug 2008 12:01:49 +0530 Subject: [Pw_forum] about PDOS Message-ID: <3a749910808202331j4c2896e0t571a30e0c9042657@mail.gmail.com> Hello pwscf users, I am doing electronic calculation on ScSb. I am using *Sb.pw91-n-van.UPF* pp for Sb, which contains 4d, 5s and 5p orbitals. But when i draw the PDOS with projwfc.x command, then it gives 1d, 2s and 3p orbitals file not 4d, 5s and 5p. I unable to understand why it is doing so? Is 1d~4d 2s~5s and 3p~5p according to the programme???? thanks -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080821/b187641d/attachment.htm From giannozz at democritos.it Thu Aug 21 11:48:28 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 21 Aug 2008 11:48:28 +0200 Subject: [Pw_forum] pw2casino difficulty In-Reply-To: <52809.10.1.20.105.1219261438.squirrel@mail.ciw.edu> References: <52030.10.1.20.105.1219088198.squirrel@mail.ciw.edu> <52809.10.1.20.105.1219261438.squirrel@mail.ciw.edu> Message-ID: <48AD39EC.9020708@democritos.it> lshulenburger at ciw.edu wrote: > I should have written Atom O1 not found. The calculation I was working on > is for antiferromagnetic FeO and I used as species labels O1, Fe1 and Fe2. > Looking at the atomic_number function I can't tell if it can handle these > labels (which I believe are necessary on Fe to break the spin degeneracy). > However I notice that oxygen is listed in the table of atomic symbols as > ' O' does this mean that I need to somehow include a space in my species > label? Fe1, Fe2, Fe1million are fine, since only the first two letters are used by function atomic_number. There is however a problem for all one-letter elements: B C F H K I N O P S V W Y. For the time being, just use O as species label instead of O1 (you can change it in the data.xml file). Not sure specifying sn atomic symbol as ' O1' will work. Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Aug 21 11:50:54 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 21 Aug 2008 11:50:54 +0200 Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos In-Reply-To: <20080820154254.9057.qmail@mail.spidergraphics.com> References: <20080820143906.3325.qmail@mail.spidergraphics.com> <002901c902d6$cb32f0e0$6198d2a0$@unl.edu> <20080820154254.9057.qmail@mail.spidergraphics.com> Message-ID: <48AD3A7E.3050101@democritos.it> stewart at cnf.cornell.edu wrote: > You raise an important point that I perhaps missed with the projwfc > implementation. If projwfc can only map back to the orbitals provided in > the pseudopotential (2s 2p), then this will limit its usefulness for > determining the orbital character of higher energy conduction bands. projwfc uses only atomic (pseudo-)orbitals contained in the pseudopotential file(s). Maybe this should be explicitly stated somewhere Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From eyvaz_isaev at yahoo.com Thu Aug 21 12:15:34 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 21 Aug 2008 03:15:34 -0700 (PDT) Subject: [Pw_forum] about PDOS In-Reply-To: <3a749910808202331j4c2896e0t571a30e0c9042657@mail.gmail.com> Message-ID: <107774.18357.qm@web65711.mail.ac4.yahoo.com> Dear Bipul, > Is 1d~4d, 2s~5s, and 3p~5p according to the programme???? Yes, it is. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 8/21/08, Bipul Rakshit wrote: > From: Bipul Rakshit > Subject: [Pw_forum] about PDOS > To: "PWSCF Forum" > Date: Thursday, August 21, 2008, 10:31 AM > Hello pwscf users, > I am doing electronic calculation on ScSb. I am using > *Sb.pw91-n-van.UPF* > pp for Sb, which contains 4d, 5s and 5p orbitals. But when > i draw the PDOS > with projwfc.x command, then it gives 1d, 2s and 3p > orbitals file not 4d, 5s > and 5p. I unable to understand why it is doing so? > Is 1d~4d > 2s~5s > and 3p~5p > according to the programme???? > > thanks > > -- > Bipul Rakshit > PhD Student, > Barkatullah University, > Bhopal 462026, > MP, India > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From baroni at sissa.it Thu Aug 21 12:20:50 2008 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 21 Aug 2008 12:20:50 +0200 Subject: [Pw_forum] about PDOS In-Reply-To: <107774.18357.qm@web65711.mail.ac4.yahoo.com> References: <107774.18357.qm@web65711.mail.ac4.yahoo.com> Message-ID: <540E8763-E7DA-4A67-8482-C116DCCDDB87@sissa.it> On Aug 21, 2008, at 12:15 PM, Eyvaz Isaev wrote: > Dear Bipul, > >> Is 1d~4d, 2s~5s, and 3p~5p according to the programme???? > > Yes, it is. as well as as according to the convention universally accepted in the atomic spectroscopy community SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080821/bdf7e9df/attachment.htm From zhaohscas at yahoo.com.cn Thu Aug 21 15:37:52 2008 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Thu, 21 Aug 2008 21:37:52 +0800 Subject: [Pw_forum] The corresponding electronic state of the band gap. Message-ID: <105724792.20080821213752@yahoo.com.cn> Dear all, I now doing some study on BaHfO_3 with uspp scheme. The states Ba 5s2 5p6 6s2, Hf 5d2 6s2 and O 2s2 2p4 were treated as valence states. I also found that following paper has done some researches on BaHfO_3: http://dx.doi.org/10.1016/j.physleta.2008.04.015 In th abstract of the above paper, the authors said: ----------------- Band structures show that BaHfO3 is a direct band gap between the occupied O 2p and unoccupied Hf d states. ----------------- I just want to know how to decide the O 2p and Hf 5d as the the occupied and the unoccupied states corresponding to the band gap? In detail, in the above computation, the p states are comes from Ba and O simultaneously, so why can they only said the O 2p? Sincerely yours, -- Hongsheng Zhao Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences GnuPG DSA: 0xD108493 2008-8-21 __________________________________________________ ????????????????????????????? http://cn.mail.yahoo.com From giannozz at democritos.it Thu Aug 21 18:20:00 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 21 Aug 2008 18:20:00 +0200 Subject: [Pw_forum] The corresponding electronic state of the band gap. In-Reply-To: <105724792.20080821213752@yahoo.com.cn> References: <105724792.20080821213752@yahoo.com.cn> Message-ID: <48AD95B0.8000408@democritos.it> Hongsheng Zhao wrote: > In the abstract of the above paper, the authors said: > > ----------------- > Band structures show that BaHfO3 is a direct band gap between the occupied O 2p and unoccupied Hf d states. > ----------------- > > I just want to know how to decide the O 2p and Hf 5d as the the occupied and the unoccupied states corresponding to the band gap? > In detail, in the above computation, the p states are comes from Ba and O simultaneously, so why can they only said the O 2p? the above statement just means that the top of the valence band is mainly composed of O 2p states, while the bottom of the conduction band is mainly composed of Hf 5d states. You can easily check if this is true using code 'projwfc.x'. Disclaimed: I am not sure I understood what you mean, and I know nothing about BaHfO3 Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Aug 21 21:12:32 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 21 Aug 2008 21:12:32 +0200 Subject: [Pw_forum] pseudopotential for lithium In-Reply-To: <6234c0c60808182316u7fba241dt1724afde9a6e2b43@mail.gmail.com> References: <6234c0c60808182316u7fba241dt1724afde9a6e2b43@mail.gmail.com> Message-ID: On Aug 19, 2008, at 8:16 , Guoying Gao wrote: > I want to study the properties of lithium under high presssure > (about 200 GPa), we all know that the effect of 1s2 electron states > cann't be neglected at the monment. So we should consider 1s2 as the > valence electron. However, there is no such pseudopotential for > lithium in the pwscf website. now there are, courtesy of Axel Kohlmeyer, but beware: the ultrasoft ones are known to yield strange results in phonon calculations (they were removed some time ago for this reason), while norm-conserving ones will require a very high cutoff P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From adrainzhou at yahoo.com.cn Fri Aug 22 01:52:12 2008 From: adrainzhou at yahoo.com.cn (Adrain Zhou) Date: Fri, 22 Aug 2008 07:52:12 +0800 (CST) Subject: [Pw_forum] Hybrid functional calcualtion! Message-ID: <368292.41418.qm@web15806.mail.cnb.yahoo.com> Dear all, I am trying to run hybrid functional test. When I changed the number of nqx1,nqx2 and nqx3. The error information is "k + q is not an S*k " and stopped. I checked the readme file in the Exx_example. It says that the vaule of nqx1,nqx2 and nqx3 must be compatible with the k-points used (that is k+q must be equivalent to some other k in the k-points list).Can anybody please explain more on this sentence to me? Many thanks! Regards, Adrian ___________________________________________________________ ???????????? http://cn.mail.yahoo.com/ From wangqj1 at 126.com Fri Aug 22 09:13:34 2008 From: wangqj1 at 126.com (wangqj1) Date: Fri, 22 Aug 2008 15:13:34 +0800 (CST) Subject: [Pw_forum] Lattice constant optimize Message-ID: <6591402.425911219389214287.JavaMail.coremail@bj126app104.126.com> Dear pwscf users I want to optimize the lattice constant of ZnO use VC-relax,should I set the X-Iforce,Y-iforce,Z-iforce to 0 or 1 ? In my opinion ,I think they should be set to 0. does it right ? besides ,I want to know the reliability of this method .What's the criterion to know whether the derived lattice constant (a ,c/a)is right or not ? Any useful advice will be appreciated . Sincerely wangqj -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080822/3ae3eb83/attachment.htm From pysdw at bath.ac.uk Fri Aug 22 10:35:25 2008 From: pysdw at bath.ac.uk (pysdw at bath.ac.uk) Date: Fri, 22 Aug 2008 09:35:25 +0100 Subject: [Pw_forum] phcg in espresso-4.0.1 Message-ID: <000601c90432$08324d40$f2a9268a@campus.bath.ac.uk> Dear developers, I've been using pw, phcg, dynmat to calculate Raman intensities of some simple molecules in espresso-3.2.3 and have just moved to espresso-4.0.1; am using either a single linux PC (1GB) or, for parallel, a E5462 Supermicro cluster (128 cores total, 2 GB/core). Both code versions were compiled on both machines with recent versions (>9.0.0) of the Intel FC. In 3.2.3, all appears fine (code completes, results look credible) but, in 4.0.1, phcg generates a SIGSEGV error in the first calculation after the point 'Starting calculation of Raman coefficients' on both machines. I've read the forum messages - changing stack limits does not solve this. Have not experienced any other such crashes in 4.0.1 so far. My question is whether I am safe to stick to espresso 3.2.3 for this work? It seems the simplest solution. I've browsed the change log and didn't see any reason why not, but your comments would be appreciated. Since the forum suggests it's a compiler problem, I haven't posted my input files, but I will be happy to post them if anyone does want them. best regards, Daniel Wolverson Department of Physics University of Bath Bath BA2 7AY UK From giannozz at democritos.it Fri Aug 22 13:19:57 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 22 Aug 2008 13:19:57 +0200 Subject: [Pw_forum] phcg in espresso-4.0.1 In-Reply-To: <000601c90432$08324d40$f2a9268a@campus.bath.ac.uk> References: <000601c90432$08324d40$f2a9268a@campus.bath.ac.uk> Message-ID: On Aug 22, 2008, at 10:35 , wrote: > My question is whether I am safe to stick to espresso 3.2.3 for > this work? > It seems the simplest solution. I've browsed the change log and > didn't see > any reason why not, but your comments would be appreciated. I do not think much has changed since 3.2.3 in the Raman part. Serious bugs are usually reported in Doc/BUGS. I don't see any. > Since the forum suggests it's a compiler problem well...it's not that all SIGSEGV are compiler bugs, but they are so often that I have stopped to worry about such error, unless it is reproduced on a different machine (is it?). The same applies to all MPI errors, by the way. Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From degironc at sissa.it Fri Aug 22 13:26:34 2008 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 22 Aug 2008 13:26:34 +0200 Subject: [Pw_forum] Hybrid functional calcualtion! In-Reply-To: <368292.41418.qm@web15806.mail.cnb.yahoo.com> References: <368292.41418.qm@web15806.mail.cnb.yahoo.com> Message-ID: <48AEA26A.703@sissa.it> what is needed is that ,if nk1,nk2,nk3 are the parameters defining the k-point regular grid, then nk1/nqx1 nk2/nqx2 and nk3/nqx3 must all be whole integer numbers. stefano Adrain Zhou wrote: > Dear all, > > I am trying to run hybrid functional test. When I > changed the number of nqx1,nqx2 and nqx3. The error > information is "k + q is not an S*k " and stopped. I > checked the readme file in the Exx_example. It says > that the vaule of nqx1,nqx2 and nqx3 must be > compatible with the k-points used (that is k+q must be > equivalent to some other k in the k-points list).Can > anybody please explain more on this sentence to me? > Many thanks! > > Regards, > Adrian > > > ___________________________________________________________ > ???????????? > http://cn.mail.yahoo.com/ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From eyvaz_isaev at yahoo.com Fri Aug 22 13:27:13 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 22 Aug 2008 04:27:13 -0700 (PDT) Subject: [Pw_forum] Lattice constant optimize In-Reply-To: <6591402.425911219389214287.JavaMail.coremail@bj126app104.126.com> Message-ID: <147943.96198.qm@web65716.mail.ac4.yahoo.com> Dear wangqj (sounds strange, right?) --- On Fri, 8/22/08, wangqj1 wrote: > Dear pwscf users > I want to optimize the lattice constant of ZnO use > VC-relax,should I set the X-Iforce,Y-iforce,Z-iforce to 0 > or 1 ? In my opinion ,I think they should be set > to 0. does it right ? No, it is not correct. If you mean like "Atom X Y Z 1 0 0", it means move atom in X direction, but keep fixed Y and Z coordinates. Besides I do not remember keywords like X-Iforce etc., you can not fix forces, they are calculated self-consistently. For the ground (equilibrium) state, of course, they should be around zero (sometime forces are zeroes due to symmetry reasons). If you just specify atomic position "X Y Z", so, atoms are allowed to relax their positions along X, Y, Z directions. > besides, I want to know the reliability of > this method. What's the criterion to know whether the > derived lattice constant (a ,c/a)is right or not ? Sorry, this one is your own responsibility to decide whether you got good parameters. See von Barth paper Physica Scripta. Vol. T109, 9?39, 2004 to understand basics of the DFT. Compare with experiment and previous calculations and analyze why you got different parameters. More general, trial and fail method is very good. > Any useful advice will be appreciated . > And we will appreciate providing your affiliation. And your own name. Bests, Eyvaz. > Sincerely > > > wangqj_______________________________________________ ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com From wangqj1 at 126.com Fri Aug 22 16:12:18 2008 From: wangqj1 at 126.com (wangqj1) Date: Fri, 22 Aug 2008 22:12:18 +0800 (CST) Subject: [Pw_forum] The difference between vc-relax and relax . Message-ID: <4243396.532351219414338723.JavaMail.coremail@bj126app27.126.com> Dear all Could someone tell me the difference between vc-relax and relax ? What are the functions of them . In what conditions to use them ? Thank you very much for your help and your comments! With kind regards qjwang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080822/932cb8b3/attachment.htm From jlz101 at unlserve.unl.edu Fri Aug 22 16:25:49 2008 From: jlz101 at unlserve.unl.edu (J. D. Burton) Date: Fri, 22 Aug 2008 09:25:49 -0500 Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos In-Reply-To: <20080820173840.19932.qmail@mail.spidergraphics.com> References: <20080820143906.3325.qmail@mail.spidergraphics.com> <002901c902d6$cb32f0e0$6198d2a0$@unl.edu> <20080820154254.9057.qmail@mail.spidergraphics.com> <003b01c902e2$964ddf00$c2e99d00$@unl.edu> <20080820173840.19932.qmail@mail.spidergraphics.com> Message-ID: <002801c90462$f9c6a0e0$ed53e2a0$@unl.edu> Derek, You should also include 3S and 3P channels, since their corresponding atomic pseudowfcs will each contain one radial node, whereas your 2S and 2P atomic pseudowfcs do not (or at least should not) contain any. Cheers, J. D. ************************************ J. D. Burton, Ph.D. jlz101 at unlserve.unl.edu University of Nebraska Lincoln Physics and Astronomy Office Ph. (402) 472 2499 213C Ferguson Hall ************************************ "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of stewart at cnf.cornell.edu Sent: Wednesday, August 20, 2008 12:39 PM To: PWSCF Forum Subject: Re: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos Hi J. D. and Lazaro, Thanks for your suggestions. After my last email, I actually started down the route of adding more orbitals to the C pseudopotential by taking the original format and switching the 3d line to 3D 3 2 0.00 0.15 1.30 1.30 before it had a -2.00 to neglect this band. I'll try it out and see how much it affects my total density of states and see if it catches the missing bands. Using Wannier functions sounds interesting. I'll look into that possibility as well. Best regards, Derek J. D. Burton writes: > Hi Derek, > > Interesting, though it shouldn't be that difficult to just take the > pseudopotential (PSP) as it is and use the ld1.x program (comes with the > espresso package) and calculate other atomic pseudowavefunctions that you > can then project onto. You can then include these in your PSP file. > I suppose if you're really ambitious, you could alter the projwfc program to > not use the atomic functions in the PSP file, but instead use different > localized functions in a file that you provide (for example, you could try > Wannier functions). I know that you can do this with the lda+u feature, like > setting U_projection_type to 'file'. See the INPUT_PW.txt file for details > on that. > > Cheers, > J. D. > > > ************************************ > J. D. Burton, Ph.D. > jlz101 at unlserve.unl.edu > University of Nebraska Lincoln > Physics and Astronomy > Office Ph. (402) 472 2499 > 213C Ferguson Hall > ************************************ > "The job of a scientist is to generate wrong ideas as fast as possible." > -- Murray Gell-Mann > > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of stewart at cnf.cornell.edu > Sent: Wednesday, August 20, 2008 10:43 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos > > Hi J. D., > > Thanks for your comment! I am currently working on a project where it would > > be helpful to know the orbital character of the higher energy dos peaks. I > know that they will have little effect on the self-consistent calculation. > > You raise an important point that I perhaps missed with the projwfc > implementation. If projwfc can only map back to the orbitals provided in > the pseudopotential (2s 2p), then this will limit its usefulness for > determining the orbital character of higher energy conduction bands. > > Thanks, > > Derek > > > J. D. Burton writes: > >> Derek, >> >> Why would you need to calculate more than 8 bands? (1 s-state + 3 > p-states) >> x 2 C atoms per unit cell = 8 bands, and half of them are doubly-occupied. >> By setting nbnd = 20 (10 per atom in the unit cell) you get all the way up >> into d-like-bands, and your pseudopotential file doesn't contain atomic >> d-wavefunctions of carbon. That would explain why the sum of your > projected >> dos doesn't match your total density, i.e. the extra peaks are d-bands. >> >> Cheers, >> J. D. >> >> ************************************ >> J. D. Burton, Ph.D. >> jlz101 at unlserve.unl.edu >> University of Nebraska Lincoln >> Physics and Astronomy >> Office Ph. (402) 472 2499 >> 213C Ferguson Hall >> ************************************ >> "The job of a scientist is to generate wrong ideas as fast as possible." >> -- Murray Gell-Mann >> >> -----Original Message----- >> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On >> Behalf Of stewart at cnf.cornell.edu >> Sent: Wednesday, August 20, 2008 9:39 AM >> To: pw_forum at pwscf.org >> Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos >> >> Hi everyone, >> >> I am looking at the density of states of graphene and I have run into a >> problem with the projwfc program. When I plot out the total density of >> states for the system and compare this to the sum of the partial density > of >> states found in the pdos_tot file, I find that the sum of the partial DOS > is >> >> missing some large peaks at energies above the Fermi energy. The total > DOS >> from the projwfc run matches the total DOS generated using dos.x and the >> tetrahedra technique. The bands responsible for these missing peaks also >> show up in the band plot. I have tried using both methfessel-paxton and >> marzari-vanderbilt smearing (degauss 0.01) but this does not have any > effect >> >> on the problem. >> >> I thought that perhaps the projection onto the atomic orbitals was missing > a >> >> significant portion of the charge, however my spilling parameter is fairly > >> low 0.0116. This is comparable to the spilling parameter found in > example08 >> >> for nickel 0.0115 where the total and partial dos match reasonable well >> (although slightly shifted in energy in the reference data). >> >> I would appreciate any thoughts as to why I am missing these DOS peaks in >> the partial dos. Are there difficulties in projecting plane waves to >> orbitals for conduction bands? Has anyone else run into this problem? >> >> For the details of my calculation, I am using C.pz-rrkjus.UPF, ecutwfc=45, > >> ecutrho=450, k-grid for self-consistent calculation (64x64x1), k-grid for >> non-scf for dos (96x96x1), number of bands=20 and working with espresso >> 4.0.1. >> >> Thanks, >> >> Derek >> >> >> ################################ >> Derek Stewart, Ph. D. >> Scientific Computation Associate >> http://www.people.cornell.edu/pages/das248/ >> 250 Duffield Hall >> Cornell Nanoscale Facility (CNF) >> Ithaca, NY 14853 >> stewart (at) cnf.cornell.edu >> (607) 255-2856 >> _______________________________________________ >> 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 >> > > > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > http://www.people.cornell.edu/pages/das248/ > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > _______________________________________________ > 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 > ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From stewart at cnf.cornell.edu Fri Aug 22 16:34:22 2008 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Fri, 22 Aug 2008 10:34:22 -0400 Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos In-Reply-To: <002801c90462$f9c6a0e0$ed53e2a0$@unl.edu> References: <20080820143906.3325.qmail@mail.spidergraphics.com> <002901c902d6$cb32f0e0$6198d2a0$@unl.edu> <20080820154254.9057.qmail@mail.spidergraphics.com> <003b01c902e2$964ddf00$c2e99d00$@unl.edu> <20080820173840.19932.qmail@mail.spidergraphics.com> <002801c90462$f9c6a0e0$ed53e2a0$@unl.edu> Message-ID: <20080822143422.22017.qmail@mail.spidergraphics.com> Hi J. D., Thanks for the suggestion. However, after looking into this route in some detail and consulting with Andrea Dal Corso, it looks like it will be difficult to implement the higher energy states into the pseudopotential with the atomic code. In order to do this you need to go to an ionic configuration and this could probably cause more problems then benefits. For now, I will probably try to complement with my current calculations with some DOS analysis using a different approach. Best regards, Derek J. D. Burton writes: > Derek, > > You should also include 3S and 3P channels, since their corresponding atomic > pseudowfcs will each contain one radial node, whereas your 2S and 2P atomic > pseudowfcs do not (or at least should not) contain any. > > Cheers, > J. D. > > ************************************ > J. D. Burton, Ph.D. > jlz101 at unlserve.unl.edu > University of Nebraska Lincoln > Physics and Astronomy > Office Ph. (402) 472 2499 > 213C Ferguson Hall > ************************************ > "The job of a scientist is to generate wrong ideas as fast as possible." > -- Murray Gell-Mann > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of stewart at cnf.cornell.edu > Sent: Wednesday, August 20, 2008 12:39 PM > To: PWSCF Forum > Subject: Re: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos > > Hi J. D. and Lazaro, > > Thanks for your suggestions. After my last email, I actually started down > the route of adding more orbitals to the C pseudopotential by taking the > original format and switching the 3d line to > > 3D 3 2 0.00 0.15 1.30 1.30 > > before it had a -2.00 to neglect this band. I'll try it out and see how > much it affects my total density of states and see if it catches the missing > > bands. > > Using Wannier functions sounds interesting. I'll look into that possibility > > as well. > > Best regards, > > Derek > > > J. D. Burton writes: > >> Hi Derek, >> >> Interesting, though it shouldn't be that difficult to just take the >> pseudopotential (PSP) as it is and use the ld1.x program (comes with the >> espresso package) and calculate other atomic pseudowavefunctions that you >> can then project onto. You can then include these in your PSP file. >> I suppose if you're really ambitious, you could alter the projwfc program > to >> not use the atomic functions in the PSP file, but instead use different >> localized functions in a file that you provide (for example, you could try >> Wannier functions). I know that you can do this with the lda+u feature, > like >> setting U_projection_type to 'file'. See the INPUT_PW.txt file for details >> on that. >> >> Cheers, >> J. D. >> >> >> ************************************ >> J. D. Burton, Ph.D. >> jlz101 at unlserve.unl.edu >> University of Nebraska Lincoln >> Physics and Astronomy >> Office Ph. (402) 472 2499 >> 213C Ferguson Hall >> ************************************ >> "The job of a scientist is to generate wrong ideas as fast as possible." >> -- Murray Gell-Mann >> >> >> -----Original Message----- >> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On >> Behalf Of stewart at cnf.cornell.edu >> Sent: Wednesday, August 20, 2008 10:43 AM >> To: PWSCF Forum >> Subject: Re: [Pw_forum] projwfc problem: sum of pdos doesn't match total > dos >> >> Hi J. D., >> >> Thanks for your comment! I am currently working on a project where it > would >> >> be helpful to know the orbital character of the higher energy dos peaks. > I >> know that they will have little effect on the self-consistent calculation. > >> >> You raise an important point that I perhaps missed with the projwfc >> implementation. If projwfc can only map back to the orbitals provided in >> the pseudopotential (2s 2p), then this will limit its usefulness for >> determining the orbital character of higher energy conduction bands. >> >> Thanks, >> >> Derek >> >> >> J. D. Burton writes: >> >>> Derek, >>> >>> Why would you need to calculate more than 8 bands? (1 s-state + 3 >> p-states) >>> x 2 C atoms per unit cell = 8 bands, and half of them are > doubly-occupied. >>> By setting nbnd = 20 (10 per atom in the unit cell) you get all the way > up >>> into d-like-bands, and your pseudopotential file doesn't contain atomic >>> d-wavefunctions of carbon. That would explain why the sum of your >> projected >>> dos doesn't match your total density, i.e. the extra peaks are d-bands. >>> >>> Cheers, >>> J. D. >>> >>> ************************************ >>> J. D. Burton, Ph.D. >>> jlz101 at unlserve.unl.edu >>> University of Nebraska Lincoln >>> Physics and Astronomy >>> Office Ph. (402) 472 2499 >>> 213C Ferguson Hall >>> ************************************ >>> "The job of a scientist is to generate wrong ideas as fast as possible." >>> -- Murray Gell-Mann >>> >>> -----Original Message----- >>> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On >>> Behalf Of stewart at cnf.cornell.edu >>> Sent: Wednesday, August 20, 2008 9:39 AM >>> To: pw_forum at pwscf.org >>> Subject: [Pw_forum] projwfc problem: sum of pdos doesn't match total dos > >>> >>> Hi everyone, >>> >>> I am looking at the density of states of graphene and I have run into a >>> problem with the projwfc program. When I plot out the total density of >>> states for the system and compare this to the sum of the partial density >> of >>> states found in the pdos_tot file, I find that the sum of the partial DOS >> is >>> >>> missing some large peaks at energies above the Fermi energy. The total >> DOS >>> from the projwfc run matches the total DOS generated using dos.x and the >>> tetrahedra technique. The bands responsible for these missing peaks also > >>> show up in the band plot. I have tried using both methfessel-paxton and >>> marzari-vanderbilt smearing (degauss 0.01) but this does not have any >> effect >>> >>> on the problem. >>> >>> I thought that perhaps the projection onto the atomic orbitals was > missing >> a >>> >>> significant portion of the charge, however my spilling parameter is > fairly >> >>> low 0.0116. This is comparable to the spilling parameter found in >> example08 >>> >>> for nickel 0.0115 where the total and partial dos match reasonable well >>> (although slightly shifted in energy in the reference data). >>> >>> I would appreciate any thoughts as to why I am missing these DOS peaks in > >>> the partial dos. Are there difficulties in projecting plane waves to >>> orbitals for conduction bands? Has anyone else run into this problem? >>> >>> For the details of my calculation, I am using C.pz-rrkjus.UPF, > ecutwfc=45, >> >>> ecutrho=450, k-grid for self-consistent calculation (64x64x1), k-grid for > >>> non-scf for dos (96x96x1), number of bands=20 and working with espresso >>> 4.0.1. >>> >>> Thanks, >>> >>> Derek >>> >>> >>> ################################ >>> Derek Stewart, Ph. D. >>> Scientific Computation Associate >>> http://www.people.cornell.edu/pages/das248/ >>> 250 Duffield Hall >>> Cornell Nanoscale Facility (CNF) >>> Ithaca, NY 14853 >>> stewart (at) cnf.cornell.edu >>> (607) 255-2856 >>> _______________________________________________ >>> 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 >>> >> >> >> >> ################################ >> Derek Stewart, Ph. D. >> Scientific Computation Associate >> http://www.people.cornell.edu/pages/das248/ >> 250 Duffield Hall >> Cornell Nanoscale Facility (CNF) >> Ithaca, NY 14853 >> stewart (at) cnf.cornell.edu >> (607) 255-2856 >> _______________________________________________ >> 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 >> > > > > ################################ > Derek Stewart, Ph. D. > Scientific Computation Associate > http://www.people.cornell.edu/pages/das248/ > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > _______________________________________________ > 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 > ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From j.antonio.montoya at gmail.com Fri Aug 22 16:41:30 2008 From: j.antonio.montoya at gmail.com (Javier Antonio Montoya) Date: Fri, 22 Aug 2008 10:41:30 -0400 Subject: [Pw_forum] The difference between vc-relax and relax . In-Reply-To: <4243396.532351219414338723.JavaMail.coremail@bj126app27.126.com> References: <4243396.532351219414338723.JavaMail.coremail@bj126app27.126.com> Message-ID: <993c5eba0808220741ya0423d5ud7c9b41c50f8a21a@mail.gmail.com> Dear Qjwang On Fri, Aug 22, 2008 at 10:12 AM, wangqj1 wrote: > > > Dear all > Could someone tell me the difference between vc-relax and relax ? > What are the functions of them . In what conditions to use them ? > > PLEASE READ THE DOCUMENTATION, it is in espresso-whateverversion/Doc/INPUT_PW Both can relax the ionic positions until each and every ion feel zero forces (Actually is not zero but a minimum force that you define inside &control) "vc" in vc-relax stands for variable cell, which means that the cell is also relaxed towards a target pressure (read &cell in the documentation) > Thank you very much for your help and your comments! > You a re welcome . > > With kind regards > > qjwang > That is not enough please always provide your affiliation. Sincerely, Javier. -- Javier A. Montoya Geophysical Laboratory Carnegie Institution of Washington 5251 Broad Branch Rd. NW Washington, DC 20015 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080822/b378f631/attachment.htm From eyvaz_isaev at yahoo.com Fri Aug 22 16:58:49 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 22 Aug 2008 07:58:49 -0700 (PDT) Subject: [Pw_forum] The difference between vc-relax and relax . In-Reply-To: <4243396.532351219414338723.JavaMail.coremail@bj126app27.126.com> Message-ID: <378093.1628.qm@web65711.mail.ac4.yahoo.com> Dear user wangqj1, --- On Fri, 8/22/08, wangqj1 wrote: > Could someone tell me the difference between vc-relax > and relax? What are the functions of them . In what > conditions to use them ? > Shortly: relax - only relax atomic positions and keep the cell volume and shape; vc-relax - In addition relaxed atomic positions you can also change the cell volume (keep the form), or relax everything, i.e. volume, shape, atomic positions. > > qjwang_______________________________________________ Why you do not like add your affiliation? It seems, I asked you about this one in my both previous mails. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From shrek_826 at yahoo.com.cn Sat Aug 23 03:40:46 2008 From: shrek_826 at yahoo.com.cn (Fan Yang) Date: Sat, 23 Aug 2008 09:40:46 +0800 (CST) Subject: [Pw_forum] question about example 22 Message-ID: <874844.60383.qm@web15302.mail.cnb.yahoo.com> Dear everyone, I have a small question about?the example22, which shows how to use pw.x to calculate the total energy of fcc-Pt with a fully relativistic US-PP which includes spin-orbit effects. Why does the atomic mass should be?set as 79.90 in pt.scf.in and 58.69 in pt4.in, rather than 195.08??And? why does they using different atomic mass when applying the same US-PP? I think?it?may be?the reason of using relativistic US-PP, am I right? If so, once I using PtrelPBE.RRKJ3.UPF, how should I set the atomic mass? Best Regards, ???? ? ====================================== Fan Yang PH.D Candidate?in Electrochemistry????????????????????? College of Chemistry and Molecular Science??????????? Wuhan University,430072,Hubei Province,China? E-mail:shrek_826 at yahoo.com.cn ====================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080823/46b1cf30/attachment.htm From dalcorso at sissa.it Sat Aug 23 06:56:24 2008 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Sat, 23 Aug 2008 06:56:24 +0200 Subject: [Pw_forum] question about example 22 Message-ID: <20080823065624.x9ilhcjpc4kkgkgw@webmail.sissa.it> Thank you for reporting this. Actually in example22 the atomic masses are not used so they are not properly set. However you are right, the numbers in the example may cause some confusion. Best Regards Andrea Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Beirut 2/4 Fax. 0039-040-3787528 34014 Trieste (Italy) e-mail: dalcorso at sissa.it Dear everyone, I have a small question about the example22, which shows how to use pw.x to calculate the total energy of fcc-Pt with a fully relativistic US-PP which includes spin-orbit effects. Why does the atomic mass should be set as 79.90 in pt.scf.in and 58.69 in pt4.in, rather than 195.08? And why does they using different atomic mass when applying the same US-PP? I think it may be the reason of using relativistic US-PP, am I right? If so, once I using PtrelPBE.RRKJ3.UPF, how should I set the atomic mass? Best Regards, ====================================== Fan Yang PH.D Candidate in Electrochemistry College of Chemistry and Molecular Science Wuhan University,430072,Hubei Province,China E-mail:shrek_826 at yahoo.com.cn ====================================== ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From munima at iitg.ernet.in Sat Aug 23 07:23:20 2008 From: munima at iitg.ernet.in (Munima Bora Sahariah) Date: Sat, 23 Aug 2008 10:53:20 +0530 (IST) Subject: [Pw_forum] output of fildrho Message-ID: <52952.172.16.48.134.1219469000.squirrel@webmail.iitg.ac.in> Dear friends, Could anyone please help me out in reading the output fildrho files? What exactly are the five columns in each of the output files for three cartesian directions? regards munima Dr. Munima B. Sahariah PI, DST Fast Track Project IASST, Guwahati Assam, INDIA ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ac.in From penghua8503 at 163.com Sat Aug 23 10:31:21 2008 From: penghua8503 at 163.com (penghua) Date: Sat, 23 Aug 2008 16:31:21 +0800 (CST) Subject: [Pw_forum] awin in average.x Message-ID: <9001135.136871219480281038.JavaMail.coremail@bj163app43.163.com> Hello everyone, I used averge.x to calculate the planer planar average (pav) and macroscopic average (mav) of the resulting quantity of a supercell, but I didn?t understand the meaning of the 'awin' in the input file. What is the use of it? Besides when I changed the value of awin, I got different mav curve, so how should I set the value of awin. Any help will be appreciated. penghua shandong university penghua8503 at 163.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080823/01f51d1b/attachment.htm From hande at newton.physics.metu.edu.tr Sat Aug 23 11:13:26 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Sat, 23 Aug 2008 12:13:26 +0300 (EEST) Subject: [Pw_forum] awin in average.x In-Reply-To: <9001135.136871219480281038.JavaMail.coremail@bj163app43.163.com> Message-ID: Dear penghua, awin is the width of the window(=interval) around each point over which you average the planar average to get the macroscopic average. That is to say, it should correspond to something like, in Latex-ish math, f_{mav}(x)=\int_{-awin/2}^{awin/2} f_{pav}(x-x') dx' where f is your quantity of choice (density, potential etc). Hope this helps. Best, Hande On Sat, 23 Aug 2008, penghua wrote: > > > Hello everyone, > > I used averge.x to calculate the planer planar average (pav) and macroscopic average (mav) of the resulting quantity of a supercell, but I didn??t understand the meaning of the 'awin' in the input file. What is the use of it? Besides when I changed the value of awin, I got different mav curve, so how should I set the value of awin. > > Any help will be appreciated. > > > > penghua > > shandong university > > penghua8503 at 163.com > > -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From penghua8503 at 163.com Sat Aug 23 11:54:30 2008 From: penghua8503 at 163.com (penghua) Date: Sat, 23 Aug 2008 17:54:30 +0800 (CST) Subject: [Pw_forum] awin in average.x In-Reply-To: References: Message-ID: <3932443.158691219485270524.JavaMail.coremail@bj163app43.163.com> Thanks Hande for your answer, but I am still confuse with how to get the value of awin?should I try a lot of data, and then select one? Thanks penghua shandong university P.R.China ?2008-08-23?"Hande Ustunel" ??? >Dear penghua, > >awin is the width of the window(=interval) around each point over which you >average the planar average to get the macroscopic average. That is to say, >it should correspond to something like, in Latex-ish math, > > f_{mav}(x)=\int_{-awin/2}^{awin/2} f_{pav}(x-x') dx' > >where f is your quantity of choice (density, potential etc). > >Hope this helps. >Best, >Hande > >On Sat, 23 Aug 2008, penghua wrote: > >> >> >> Hello everyone, >> >> I used averge.x to calculate the planer planar average (pav) and macroscopic average (mav) of the resulting quantity of a supercell, but I didn??t understand the meaning of the 'awin' in the input file. What is the use of it? Besides when I changed the value of awin, I got different mav curve, so how should I set the value of awin. >> >> Any help will be appreciated. >> >> >> >> penghua >> >> shandong university >> >> penghua8503 at 163.com >> >> > >-- >Hande Toffoli >Department of Physics >Office 439 >Middle East Technical University >Ankara 06531, Turkey >Tel : +90 312 210 3264 >http://www.physics.metu.edu.tr/~hande > >_______________________________________________ >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/20080823/9b1506f6/attachment.htm From hande at newton.physics.metu.edu.tr Sat Aug 23 12:08:28 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Sat, 23 Aug 2008 13:08:28 +0300 (EEST) Subject: [Pw_forum] awin in average.x In-Reply-To: <3932443.158691219485270524.JavaMail.coremail@bj163app43.163.com> Message-ID: That depends on what you want to do. If you want to calculate, say, band offsets, for which you would be interested in macroscopically averaged bulk potential, it would be the spacing between crystal planes, assuming they are evenly spaced in the direction you are interested in. See, for instance, Phys. Rev. B 48, 17607 - 17610 (1993), and other publications by the authors for a good explanation. Best, Hande On Sat, 23 Aug 2008, penghua wrote: > > > Thanks Hande for your answer, but I am still confuse with how to get the value of awin???should I try a lot of data, and then select one? > > Thanks > > penghua > > shandong university > > P.R.China > > > > > > ???2008-08-23???"Hande Ustunel" ????????? > >Dear penghua, > > > >awin is the width of the window(=interval) around each point over which you > >average the planar average to get the macroscopic average. That is to say, > >it should correspond to something like, in Latex-ish math, > > > > f_{mav}(x)=\int_{-awin/2}^{awin/2} f_{pav}(x-x') dx' > > > >where f is your quantity of choice (density, potential etc). > > > >Hope this helps. > >Best, > >Hande > > > >On Sat, 23 Aug 2008, penghua wrote: > > > >> > >> > >> Hello everyone, > >> > >> I used averge.x to calculate the planer planar average (pav) and macroscopic average (mav) of the resulting quantity of a supercell, but I didn????t understand the meaning of the 'awin' in the input file. What is the use of it? Besides when I changed the value of awin, I got different mav curve, so how should I set the value of awin. > >> > >> Any help will be appreciated. > >> > >> > >> > >> penghua > >> > >> shandong university > >> > >> penghua8503 at 163.com > >> > >> > > > >-- > >Hande Toffoli > >Department of Physics > >Office 439 > >Middle East Technical University > >Ankara 06531, Turkey > >Tel : +90 312 210 3264 > >http://www.physics.metu.edu.tr/~hande > > > >_______________________________________________ > >Pw_forum mailing list > >Pw_forum at pwscf.org > >http://www.democritos.it/mailman/listinfo/pw_forum > -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From kazempoor2000 at yahoo.com Sat Aug 23 12:48:02 2008 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Sat, 23 Aug 2008 03:48:02 -0700 (PDT) Subject: [Pw_forum] spin orbit Message-ID: <563416.13752.qm@web33108.mail.mud.yahoo.com> Dear All first,I want to see the importance of spin-orbit interaction in compound MnAs nanowire(~1 nm). This is because that we know that the reduction of coordination number from bulk to nanscale lead to higher value for magnetic moment ,also increasion of anisotropy. How and by when(see which parameter like energy , magnetic moment) ,can I understand that in my nanostructure system , the addition of spin-orbit has substantially effect in results or not? As you know, in nanostructures the edge atoms play essential role in cohesive energy.moreover if we have magnetic atoms in the edge of nanomaterial,the anisotropy axis (hard and easy) are alternatively varied from when nonmagnetic atom sit on the edge. How can I calculate the easy and hard axis of MnAs nanowire by highlighting the edge atoms contribution?(which kpoint and thereshold are enough for obtaining correct results)? thanks Ali Kazempour Isfahan University of technology, Isfahan,Iran From mansourehp at gmail.com Sun Aug 24 10:11:12 2008 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Sun, 24 Aug 2008 11:41:12 +0330 Subject: [Pw_forum] impurity Message-ID: Dear all do you know which kind of impurity I can add to Mg(OH)2 or Ni(OH)2 good luck mansoureh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080824/96c7029f/attachment.html From cyrille.barreteau at cea.fr Mon Aug 25 09:03:47 2008 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Mon, 25 Aug 2008 09:03:47 +0200 Subject: [Pw_forum] spin orbit In-Reply-To: <563416.13752.qm@web33108.mail.mud.yahoo.com> References: <563416.13752.qm@web33108.mail.mud.yahoo.com> Message-ID: <48B25953.7010700@cea.fr> Dear Ali This is a rather general question that you are asking here. Dimensionality is indeed playing a crucial role in magnetic properties and particularly in magnetic anisotropy. To be able to isolate the role of edge atoms, for instance, in the magnetic anisotropy energy one should be able to decompose the total energy as the sum over the various atomic sites. I know that it has been done in FLAPW like the FLEUR code (see PRB 73, 104427 (2006)) but I doubt that it has been implemented in PWscf (correct me if I'm wrong..). It is also quite commonly done in tight-binding schemes but with the usual limitations of TB.. best wishes cyrille -- ================================================================== Cyrille Barreteau | phone : +33 (0)1 69 08 29 51 CEA Saclay | fax : +33 (0)1 69 08 84 46 DSM/IRAMIS/SPCSI | email cyrille.barreteau at cea.fr Batiment 462 | 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ http://iramis.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html ================================================================== ali kazempoor wrote: >Dear All >first,I want to see the importance of spin-orbit interaction in compound MnAs nanowire(~1 nm). This is because that we know that the reduction of coordination number from bulk to nanscale lead to higher value for magnetic moment ,also increasion of anisotropy. How and by when(see which parameter like energy , magnetic moment) ,can I understand that in my nanostructure system , the addition of spin-orbit has substantially effect in results or not? >As you know, in nanostructures the edge atoms play essential role in cohesive energy.moreover if we have magnetic atoms in the edge of nanomaterial,the anisotropy axis (hard and easy) are alternatively varied from when nonmagnetic atom sit on the edge. >How can I calculate the easy and hard axis of MnAs nanowire by highlighting the edge atoms contribution?(which kpoint and thereshold are enough for obtaining correct results)? >thanks >Ali Kazempour >Isfahan University of technology, Isfahan,Iran > > > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From asafis at yahoo.com.br Mon Aug 25 15:48:18 2008 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Mon, 25 Aug 2008 06:48:18 -0700 (PDT) Subject: [Pw_forum] Pseudopotential GGA Co with spin orbit Message-ID: <734375.29830.qm@web52306.mail.re2.yahoo.com> Hello everyone. I need a pseudopotencial GGA with spin orbit for the Co. If someone can help me, thank you very much. ?????????????????????????????? Sincerely, Alvaro A. S. Santos Universidade Federal Fluminense - RJ - Brazil Novos endere?os, o Yahoo! que voc? conhece. Crie um email novo com a sua cara @ymail.com ou @rocketmail.com. http://br.new.mail.yahoo.com/addresses -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080825/63663318/attachment.htm From chenhanghuipwscf at gmail.com Tue Aug 26 00:23:52 2008 From: chenhanghuipwscf at gmail.com (alan chen) Date: Mon, 25 Aug 2008 18:23:52 -0400 Subject: [Pw_forum] lelfield and lberry Message-ID: <22ae3ca40808251523p65af6329o28a6717d8996fdd7@mail.gmail.com> Dear PWSCF users, I am now running a calculation of strained STO and try to calculate its spontaneous polarization based on Berry phase method. I try two different ways: 1) run a self-consistent calculation turning on lelfield=.true. and set efield=0.0 2) first run a self-consistent calculation and then run a non-self-consistent calculation turning on lberry=.true. Are these two method equivalent? When I try these two methods on the same system, method 1) works well but method 2) fails because "probably because G_par is NOT a reciprocal lattice vector". I notice that (in the version 4.0) in the two subroutines bp_c_phase.f90 and c_phase_field.f90 the definition of gpar are different by a factor DBLE(nppstr)/DBLE(nppstr-1). But I think these two gpar should be the same thing? I just want to ask whether the option lberry is fully tested and compatible with 'lelfield = .true.'. Thank you very much for your help. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080825/bff942d5/attachment.htm From eariel99 at gmail.com Tue Aug 26 00:42:21 2008 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Mon, 25 Aug 2008 18:42:21 -0400 Subject: [Pw_forum] poor k-points convergence, ghost states ? Message-ID: Hi, I am trying to reproduce a paper on AgSbTe. I am having problems to obtain convergence against the number of k-points. With a supercell of 8 atoms, I do not have convergence with 26x26x26 Monkhorst-Pack mesh. I think that this is a quite dense mesh and I should have obtained convergence much before. My student is also having troble to complete the band calculations. I am using BHS pseudopotentials for Sb and Te, and US for Ag. I suspect that I have ghost states. Is there other possible reasonable cause? Thanks -- Eduardo Menendez University of Chile -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080825/450c947d/attachment.htm From lfhuang at theory.issp.ac.cn Tue Aug 26 04:03:22 2008 From: lfhuang at theory.issp.ac.cn (L.F.Huang) Date: Tue, 26 Aug 2008 10:03:22 +0800 (CST) Subject: [Pw_forum] about one "fatal error" Message-ID: <32812.210.73.17.131.1219716202.squirrel@210.73.16.4> Hello everyone: I am calculating graphene supercell with one vacancy impurity, whose size is 4*4*1. It is an magnetic system whose magnetization is 0.8 bohr magneton. And there are 31 atoms and 93 representations with one mode for each. At first, ph.x is executing well, however, when the 23th representation is being done, there comes out some strange thing: ********************************************************************** FATAL ERROR on MPI node 3 (ganode054): GM send to MPI node 10 (??? [00:60:dd:49:08:2a]) failed: status 18 (target node was unreachable) check the target host, mapping or cables Small/Ctrl message completion error! forrtl: error (76): IOT trap signal FATAL ERROR on MPI node 9 (ganode057): GM send to MPI node 10 (??? [00:60:dd:49:08:2a]) failed: status 18 (target node was unreachable) check the target host, mapping or cables Small/Ctrl message completion error! forrtl: error (76): IOT trap signal ********************************************************************** AND: PWSCF version: QE3.2.3 K_point grid: 10*10*1 with 52*2(the 2 is due to magneticity) reduced k_points Number of nodes: -np 8 Does anyone knows what is the reason of this error? and How can I do to solve it? I would like appreciate any advice very much!!! Yours Sincerely Huang ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== From wangqj1 at 126.com Tue Aug 26 04:22:37 2008 From: wangqj1 at 126.com (wangqj1) Date: Tue, 26 Aug 2008 10:22:37 +0800 (CST) Subject: [Pw_forum] about charge density Message-ID: <24990374.62621219717357353.JavaMail.coremail@bj126app81.126.com> Dear all When I plot the 2D charge density of ZnO (1 0 0) with pp.x,but I don't know how to set the parameter of the vectors : e1(1) =?, e1(2)=? e1(3) = ?, e2(1) =?, e2(2)=?, e2(3) = ?, Could somebody who know it tell me the answer? Your advice will be appreciated . qianjin wang e-mail: wangqj1 at 126.com Xiangtan university Xiangtan, Hunan Province, China. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080826/e917efe7/attachment.htm From zhaohscas at yahoo.com.cn Tue Aug 26 05:32:59 2008 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Tue, 26 Aug 2008 11:32:59 +0800 Subject: [Pw_forum] about charge density In-Reply-To: <24990374.62621219717357353.JavaMail.coremail@bj126app81.126.com> References: <24990374.62621219717357353.JavaMail.coremail@bj126app81.126.com> Message-ID: <1428636857.20080826113259@yahoo.com.cn> On Tuesday, August 26, 2008 at 10:22, wangqj1 at 126.com wrote: > > Dear all > When I plot the 2D charge density of ZnO (1 0 0) with > pp.x,but I don't know how to set the parameter of the vectors : > e1(1) =?, e1(2)=? e1(3) = ?, > e2(1) =?, e2(2)=?, e2(3) = ?, > Could somebody who know it tell me the answer? They're two span vectors of your plane on which you want to present the 2D charge density, this job can use the pwgui to accomplish, it is very convenient and also have some descriptions of the span vectors you mentioned above in the pwgui's help. Sincerely yours, -- Hongsheng Zhao Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences GnuPG DSA: 0xD108493 2008-8-26 __________________________________________________ ??????????????? http://cn.mail.yahoo.com From only1xiaoyuan at 163.com Tue Aug 26 08:45:04 2008 From: only1xiaoyuan at 163.com (only1xiaoyuan) Date: Tue, 26 Aug 2008 14:45:04 +0800 (CST) Subject: [Pw_forum] about grid_gather error Message-ID: <32116416.81331219733104802.JavaMail.coremail@bj163app114.163.com> Dear all, I am about to calculate g tensor of EPR using GIPAW,but there are some questions .Could anyone tell me what means the following error message: ---------------------------------- from grid_gather : error # 152000 f_out too small ---------------------------------- I find some information from the fft_base.f90: ---------------------------------------------------------------------------- info = SIZE( f_out ) - displs( nproc_pool - 1 ) - recvcount( nproc_pool - 1 ) ! IF( info < 0 ) & CALL errore( ' grid_gather ', ' f_out too small ', -info ) ---------------------------------------------------------------------------- how can I do? Thank you! Yuan Wang School of Chemical Eng. & Techn., Tianjin Univ. E-mail: only1xiaoyuan at 163.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080826/d5c242eb/attachment.htm From ari.p.seitsonen at iki.fi Tue Aug 26 09:12:25 2008 From: ari.p.seitsonen at iki.fi (Ari P Seitsonen) Date: Tue, 26 Aug 2008 09:12:25 +0200 (CEST) Subject: [Pw_forum] about grid_gather error In-Reply-To: <32116416.81331219733104802.JavaMail.coremail@bj163app114.163.com> References: <32116416.81331219733104802.JavaMail.coremail@bj163app114.163.com> Message-ID: Dear Yuan, Could you please provide some information about - your system (input) - how you started the program (how many pools etc) - which version of the code are you using (v4.0.1, recent checkout from the CVS server, ...?) Then we might be able to help you more. This looks like if you have asked for too many pools or so. Greetings, apsi On Tue, 26 Aug 2008, only1xiaoyuan wrote: > Dear all, > > I am about to calculate g tensor of EPR using GIPAW,but there are some questions .Could anyone tell me what means the following error message: > ---------------------------------- > from grid_gather : error # 152000 > f_out too small > ---------------------------------- > > I find some information from the fft_base.f90: > ---------------------------------------------------------------------------- > info = SIZE( f_out ) - displs( nproc_pool - 1 ) - recvcount( nproc_pool - 1 ) > ! > IF( info < 0 ) & > CALL errore( ' grid_gather ', ' f_out too small ', -info ) > ---------------------------------------------------------------------------- > > how can I do? > > Thank you! > > Yuan Wang > School of Chemical Eng. & Techn., Tianjin Univ. > E-mail: only1xiaoyuan at 163.com > > > > -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ IMPMC, CNRS & Universit? Pierre et Marie Curie Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820 From zhaohscas at yahoo.com.cn Tue Aug 26 13:17:02 2008 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Tue, 26 Aug 2008 19:17:02 +0800 Subject: [Pw_forum] Why uspp Hf has the p state weights in pdos analysis? Message-ID: <1651551635.20080826191702@yahoo.com.cn> Dear users, I use the Hf 5d2 6s2 in the uspp scheme for my research, in the pdos analysis of my results, I can also find the Hf's p state weights in pdos analysis. Why does this happen? Sincerely yours, PS The attachment is the snapshot of the p state of Hf. -- Hongsheng Zhao Xinjiang Technical Institute of Physics and Chemistry Chinese Academy of Sciences GnuPG DSA: 0xD108493 2008-8-26 -------------- next part -------------- A non-text attachment was scrubbed... Name: hf_p_state.png Type: image/png Size: 3981 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20080826/a9b14318/attachment.png From paulatto at sissa.it Tue Aug 26 13:34:51 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 26 Aug 2008 13:34:51 +0200 (CEST) Subject: [Pw_forum] Why uspp Hf has the p state weights in pdos analysis? In-Reply-To: <1651551635.20080826191702@yahoo.com.cn> References: <1651551635.20080826191702@yahoo.com.cn> Message-ID: <12951.147.122.5.216.1219750491.squirrel@webmail.sissa.it> On Mar, Agosto 26, 2008 13:17, Hongsheng Zhao wrote: > I use the Hf 5d2 6s2 in the uspp scheme for my research, in the pdos > analysis of my results, I can also find the Hf's p state weights in pdos > analysis. Why does this happen? Dear Hongsheng Zhao, in order to make a good pseudopotential it is normally necessary to include at least one projector (semi-local potential) per angular momentum. Even if the 6p state is empty in isolated Hf you cannot exclude a priori that it will not play any role in a chemical environment. We should have more detail on the pseudopotential itself to give you more insight; but whomever have generated the pseudo has probably inserted a projector for the 6p state, or used it to generate the local potential. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From stewart at cnf.cornell.edu Tue Aug 26 14:32:52 2008 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Tue, 26 Aug 2008 08:32:52 -0400 Subject: [Pw_forum] =?utf-8?q?about_one_=22fatal_error=22?= In-Reply-To: <32812.210.73.17.131.1219716202.squirrel@210.73.16.4> References: <32812.210.73.17.131.1219716202.squirrel@210.73.16.4> Message-ID: <20080826123252.99698.qmail@mail.spidergraphics.com> Dear L. F. Huang, I don't think that this is a Quantum Espresso error. It looks like your calculation was working well and then node 10 on your cluster failed or lost communication with the rest of the network. Are you still able to log into node 10? Best regards, Derek L.F.Huang writes: > Hello everyone: > I am calculating graphene supercell with one vacancy impurity, whose size > is 4*4*1. It is an magnetic system whose magnetization is 0.8 bohr magneton. > And there are 31 atoms and 93 representations with one mode for each. At > first, ph.x is executing well, however, when the 23th representation is being > done, there comes out some strange thing: > ********************************************************************** > FATAL ERROR on MPI node 3 (ganode054): GM send to MPI node 10 (??? > [00:60:dd:49:08:2a]) failed: status 18 (target node was unreachable) check > the target host, mapping or cables > Small/Ctrl message completion error! > forrtl: error (76): IOT trap signal > FATAL ERROR on MPI node 9 (ganode057): GM send to MPI node 10 (??? > [00:60:dd:49:08:2a]) failed: status 18 (target node was unreachable) check > the target host, mapping or cables > Small/Ctrl message completion error! > forrtl: error (76): IOT trap signal > ********************************************************************** > AND: > PWSCF version: QE3.2.3 > K_point grid: 10*10*1 with 52*2(the 2 is due to magneticity) reduced k_points > Number of nodes: -np 8 > > Does anyone knows what is the reason of this error? and How can I do to > solve it? > I would like appreciate any advice very much!!! > > Yours Sincerely > Huang > > ====================================================================== > L.F.Huang(?????) lfhuang at theory.issp.ac.cn > ====================================================================== > Add: Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591464-328(office) > Fax: 86-551-5591434 > Web: http://theory.issp.ac.cn (website of our theory group) > http://www.issp.ac.cn (website of our institute) > ====================================================================== > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ################################ Derek Stewart, Ph. D. Scientific Computation Associate http://www.people.cornell.edu/pages/das248/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From umari at democritos.it Tue Aug 26 16:25:19 2008 From: umari at democritos.it (umari at democritos.it) Date: Tue, 26 Aug 2008 16:25:19 +0200 Subject: [Pw_forum] lelfield and lberry (P Umari) Message-ID: <20080826162519.55ttzl8w0w84ksc4@mail.democritos.it> Dear Chen, > I am now running a calculation of strained STO and try to calculate > its spontaneous polarization based on Berry phase method. I try two > different ways: > 1) run a self-consistent calculation turning on lelfield=.true. and set > efield=0.0 > 2) first run a self-consistent calculation and then run a > non-self-consistent calculation turning on lberry=.true. > Are these two method equivalent? When I try these two methods on the same > system, method 1) works well but method 2) fails because "probably because > G_par is NOT a reciprocal lattice vector". I think this is due to the fact that the berry's phase calculation (option lberry=.true.) is working on parallel machines only for the gdir =3 option. The Berry's phase polarization is also calculated through the electric field routines which are working in parallel for any choice of the gdir parameter. For the gdir = 3 case or for calculations on serial machines the two methods are expected to give the same polarization differences. Best regards, Paolo Umari, DEMOCRITOS ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From anna.ferrari at unito.it Tue Aug 26 19:31:17 2008 From: anna.ferrari at unito.it (Anna Maria Ferrari) Date: Tue, 26 Aug 2008 18:31:17 +0100 Subject: [Pw_forum] (no subject) Message-ID: <006901c907a1$8f7bbcb0$2376c082@desdemona> dear all i have two questions 1) using the pp program to plot a property what are the units of the e1 vector? 2) how to perform a DOS projected on different atoms? (partial DOS) thanks all anna *********************************** Anna Maria Ferrari Dipartimento Chimica IFM Universit? di Torino via P. Giuria 5 10125 Torino ITALY phone ++39 +11 6707563 fax ++39 +11 670 7855 *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080826/422303ee/attachment-0001.htm From paulatto at sissa.it Tue Aug 26 18:47:57 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 26 Aug 2008 18:47:57 +0200 (CEST) Subject: [Pw_forum] (no subject) In-Reply-To: <006901c907a1$8f7bbcb0$2376c082@desdemona> References: <006901c907a1$8f7bbcb0$2376c082@desdemona> Message-ID: <10459.147.122.5.216.1219769277.squirrel@webmail.sissa.it> Dear Anna, On Mar, Agosto 26, 2008 19:31, Anna Maria Ferrari wrote: > 1) using the pp program to plot a property > what are the units of the e1 vector? it is expressed in units of "alat" which usually is the celldm(1) parameter of you input > 2) how to perform a DOS projected on different atoms? (partial DOS) The program projwfc.x which is included in QE can do it... actually it computes pdos for all valence orbitals of all atoms in you system. See Doc/INPUT_PROJWFC.html for details; it should be straightforward to use (I'm assuming you are already familiar with normal dos calculations). cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From lfhuang at theory.issp.ac.cn Wed Aug 27 03:38:08 2008 From: lfhuang at theory.issp.ac.cn (L.F.Huang) Date: Wed, 27 Aug 2008 09:38:08 +0800 (CST) Subject: [Pw_forum] Pw_forum Digest, Vol 14, Issue 46 In-Reply-To: References: Message-ID: <32789.210.73.17.131.1219801088.squirrel@210.73.16.4> Deaar Stewart: Thank you for your advice and your question! And I am sorry for that I have made a mistake: When I found calculation on 8 nodes is not fast enouph for me, I changed up to 12 nodes, keeping in mind I was using 8 nodes(Ah, so forgetful!). The number of reduced k points(52) can not be divided by 12, but 8 or 13. And when I changed it to 13 nodes, It works well. It may be clear now that the error is due to the communication failure as you said. Thanks for your kind heart! Best Wishes! Yours Sincerely Huang > Date: Tue, 26 Aug 2008 08:32:52 -0400 > From: stewart at cnf.cornell.edu > Subject: Re: [Pw_forum] about one "fatal error" > To: PWSCF Forum > Message-ID: <20080826123252.99698.qmail at mail.spidergraphics.com> > Content-Type: text/plain; charset="utf-8"; format=flowed > > Dear L. F. Huang, > > I don't think that this is a Quantum Espresso error. It looks like your > calculation was working well and then node 10 on your cluster failed or > lost communication with the rest of the network. Are you still able to > log into node 10? > > Best regards, > > Derek > > > > L.F.Huang writes: > >> Hello everyone: >> I am calculating graphene supercell with one vacancy impurity, whose >> size >> is 4*4*1. It is an magnetic system whose magnetization is 0.8 bohr >> magneton. And there are 31 atoms and 93 representations with one mode >> for each. At first, ph.x is executing well, however, when the 23th >> representation is being done, there comes out some strange thing: >> ********************************************************************** >> FATAL ERROR on MPI node 3 (ganode054): GM send to MPI node 10 (??? >> [00:60:dd:49:08:2a]) failed: status 18 (target node was unreachable) >> check the target host, mapping or cables >> Small/Ctrl message completion error! >> forrtl: error (76): IOT trap signal >> FATAL ERROR on MPI node 9 (ganode057): GM send to MPI node 10 (??? >> [00:60:dd:49:08:2a]) failed: status 18 (target node was unreachable) >> check the target host, mapping or cables >> Small/Ctrl message completion error! >> forrtl: error (76): IOT trap signal >> ********************************************************************** >> AND: >> PWSCF version: QE3.2.3 >> K_point grid: 10*10*1 with 52*2(the 2 is due to magneticity) reduced >> k_points Number of nodes: -np 8 >> >> Does anyone knows what is the reason of this error? and How can I do >> to solve it? >> I would like appreciate any advice very much!!! >> >> Yours Sincerely >> Huang >> >> ====================================================================== >> L.F.Huang(?????) lfhuang at theory.issp.ac.cn >> ====================================================================== >> Add: Research Laboratory for Computational Materials Sciences, >> Instutue of Solid State Physics,the Chinese Academy of Sciences, >> P.O.Box 1129, Hefei 230031, P.R.China >> Tel: 86-551-5591464-328(office) >> Fax: 86-551-5591434 >> Web: http://theory.issp.ac.cn (website of our theory group) >> http://www.issp.ac.cn (website of our institute) >> ====================================================================== From bipulrr at gmail.com Wed Aug 27 11:37:38 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Wed, 27 Aug 2008 11:37:38 +0200 Subject: [Pw_forum] Phonon calculation at high pressure Message-ID: <3a749910808270237u14c8900bv85f415dd8c4e9d2a@mail.gmail.com> Dear PWscf users, I am doing phonon calculation for ScAs in B1(NaCl) and B2 (CsCl) structure. For B1 structure, all the phonon modes comes +ve in the entire brillouin zone. For B2 structure, I first get the minimum energy by running relax and then scf. and then I step over to phonon calculation, as in B1 structure. But for B2 structure I am getting many -ve frequencies. Although ScAs (B2) structure is stable at some high pressure, so do i have to set some pressure in the system and then I have to do the phonon calculation? In simple words, how can i do the phonon calculation for ScAs (B2) structure which is structure at high pressure? -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080827/7f3987ce/attachment.htm From raamesh123 at rediffmail.com Wed Aug 27 11:32:29 2008 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 27 Aug 2008 09:32:29 -0000 Subject: [Pw_forum] NiMnSb calculations Message-ID: <20080827093229.27260.qmail@f5mail-237-217.rediffmail.com> Dear all and Dr. Alberto Debernardi i am learning band structure for half metallic ferromagnets. To start with i am trying to do for NiMnSb (debernardi etal Volume 23, Issues 6-8, 15 December 2003, Pages 743-746). i used the same pseudo potential and k_points grid but i am not able to reproduce the band structure. the problems i faced 1. fluctuations in the convergence (despite 20% increase of the # of bands) 2. all the bands are concentrated within 5 ev which is different from the Dr. Alberto paper. 3. i got half-metallic gap of ~ 1.2 ev i dont know whether i am going in the right direction. Here with i am giving the input file plz correct me if i had committed blunders in the input file. &control calculation='scf' restart_mode='from_scratch', pseudo_dir = '/usr/local/espresso-3.2.3/pseudo/', outdir='/home/mmm-lab/tmp/' prefix='nimnsb-example' / &system ibrav=2, celldm(1) =10.77, nat=3, ntyp=3, nspin = 2, ecutwfc = 35.0, ecutrho = 560.0, nelec=22, tot_magnetization=4, occupations='smearing', smearing='methfessel-paxton', degauss=0.02 / &electrons diagonalization='david' conv_thr = 1.0e-6 mixing_beta = 0.7 / ATOMIC_SPECIES Ni 58.69 Ni_ps.uspp.UPF Mn 54.93 Mn_KB_LDA.uspp.UPF Sb 121.76 Sb.pz-bhs.UPF ATOMIC_POSITIONS Mn 0.25 0.25 0.25 Ni 0.0 0.0 0.0 Sb 0.75 0.75 0.75 K_POINTS {automatic} 8 8 1 0 0 0 With regards K. Ramesh Kumar Research Scholar Department of Physics IIT-Madras Chennai-600 036 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080827/995893d5/attachment.htm From iphyboy at hotmail.com Wed Aug 27 12:00:20 2008 From: iphyboy at hotmail.com (=?gb2312?B?w/fOxMPA?=) Date: Wed, 27 Aug 2008 18:00:20 +0800 Subject: [Pw_forum] fluctuations in bands of phonon linewidth Message-ID: Dear all: I am trying to calculate the electron phonon interaction. For comparison, the same parameters are used as those in an old PRB paper 57 11276 (1998),also the same type pseudopotential constructed from the same scheme was implemented. Confusingly, I can get exactly the same phonon dispersion bands as in the PRB paper, but the bands of phonon linewidth reaulted from electron phonon interaction take on some fluctuations, not as smooth as in the PRB paper.Also , for testing, norm conversing pseudopotentials based on RRKJ and TM schemes are also used, but the similar fluctuations still exist. Any suggestion is greatly appreciated.Best wishes Wenmei Ming my input files are given as followings and also the phonon-related results are attached ahove in PDF format========================================================= 1) densier k-points calculation &control calculation='scf' restart_mode='from_scratch', prefix='al', pseudo_dir = '/home/phymwm/PWSCF/espresso-3.2.3/pseudo/', outdir='./' / &system ibrav= 2, celldm(1) =7.5, nat= 1, ntyp= 1, ecutwfc =40.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.0226, la2F = .true., / &electrons conv_thr = 1.0d-9 mixing_beta = 0.7 /ATOMIC_SPECIES Al 26.98 Al.pz-vbc.UPFATOMIC_POSITIONS Al 0.00 0.00 0.00K_POINTS {automatic} 32 32 32 0 0 0 2) less densier k points calculation &control calculation='scf' restart_mode='from_scratch', prefix='al', pseudo_dir = '/home/phymwm/PWSCF/espresso-3.2.3/pseudo/', outdir='./' / &system ibrav= 2, celldm(1) =7.5, nat= 1, ntyp= 1, ecutwfc =40.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.0226 / &electrons conv_thr = 1.0d-9 mixing_beta = 0.7 /ATOMIC_SPECIES Al 26.98 Al.pz-vbc.UPFATOMIC_POSITIONS Al 0.00 0.00 0.00K_POINTS {automatic} 16 16 16 0 0 0 3) phonon scf calculation Electron-phonon coefficients for Al &inputph tr2_ph=1.0d-16, prefix='al', alpha_mix(1)=0.6, fildvscf='aldv', amass(1)=26.98, outdir='./', fildyn='al.dyn', elph=.true., trans=.true., ldisp=.true. nq1=8, nq2=8, nq3=8 /~ ?MSN??????????????? ???????? _________________________________________________________________ MSN ???????????????????? http://cn.msn.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080827/93a75bbe/attachment.htm From peressi at ts.infn.it Wed Aug 27 12:14:27 2008 From: peressi at ts.infn.it (Maria Peressi) Date: Wed, 27 Aug 2008 12:14:27 +0200 Subject: [Pw_forum] NiMnSb calculations In-Reply-To: <20080827093229.27260.qmail@f5mail-237-217.rediffmail.com> References: <20080827093229.27260.qmail@f5mail-237-217.rediffmail.com> Message-ID: <70cf43df67db929f2fc957fe630120ce@ts.infn.it> Dear dr. K. Ramesh Kumar, since in your input file I read nelec=22, I suppose you are using different pseudopotentials: we used for instance 15 valence electrons for Mn (3s and 3p in valence - see the cited paper), therefore we have much more electrons and hence more bands than you have; this could explain at least why your bands "are concentrated within 5 ev". Regards Maria Peressi On Aug 27, 2008, at 11:32 AM, ramesh kumar wrote: > > > Dear all and? Dr. Alberto Debernardi > > i am learning band structure for half metallic ferromagnets. To start > with i am trying to do for NiMnSb (debernardi etal Volume 23, Issues > 6-8, 15 December 2003, Pages 743-746). i used the same pseudo > potential and k_points grid but i am not able to reproduce the band > structure. > > the problems i faced > > 1. fluctuations in the convergence (despite 20%? increase of the # of > bands) > 2. all the bands are concentrated within 5 ev which is different from > the Dr. Alberto paper. > > 3. i got half-metallic gap of ~ 1.2 ev > > i dont know whether i am going in the right direction. > > Here with i am giving the input file plz correct me if i had > committed blunders in the input file. > &control > ? ? calculation='scf' > ? ? restart_mode='from_scratch', > ? ? pseudo_dir = '/usr/local/espresso-3.2.3/pseudo/', > ? ? outdir='/home/mmm-lab/tmp/' > ? ? prefix='nimnsb-example' > ? ? > / > &system > ? ? ibrav=2, celldm(1) =10.77, nat=3, ntyp=3, > ? ? nspin = 2, ecutwfc = 35.0, ecutrho = 560.0, nelec=22, > tot_magnetization=4, > ? ? occupations='smearing', smearing='methfessel-paxton', degauss=0.02 > / > &electrons > ? ? diagonalization='david' > ? ? conv_thr = 1.0e-6 > ? ? mixing_beta = 0.7 > / > ATOMIC_SPECIES > Ni 58.69? Ni_ps.uspp.UPF > Mn 54.93? Mn_KB_LDA.uspp.UPF > Sb 121.76 Sb.pz-bhs.UPF > > ATOMIC_POSITIONS > Mn 0.25 0.25 0.25 > Ni 0.0 0.0 0.0 > Sb 0.75 0.75 0.75 > K_POINTS {automatic} > 8 8 1 0 0 0 > > With regards > > K. Ramesh?Kumar > Research Scholar > Department of?Physics > IIT-Madras > Chennai-600 036 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > Maria Peressi Department of Theoretical Physics University of Trieste Strada Costiera 11 I-34014 Trieste tel. +39 040 2240242 fax. +39 040 224601 From thefarsky at hotmail.com Wed Aug 27 12:57:04 2008 From: thefarsky at hotmail.com (wangqiang) Date: Wed, 27 Aug 2008 18:57:04 +0800 Subject: [Pw_forum] Pw_forum Digest In-Reply-To: References: Message-ID: hello everyone ,i am a beginner for pwscf. how can I perform a band_FS calculation. i cannot find any doc in the pwscf directory.thanks. _________________________________________________________________ ???MSN??????????????????? http://mobile.msn.com.cn/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080827/39d81713/attachment.htm From eyvaz_isaev at yahoo.com Wed Aug 27 14:07:48 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 27 Aug 2008 05:07:48 -0700 (PDT) Subject: [Pw_forum] Phonon calculation at high pressure In-Reply-To: <3a749910808270237u14c8900bv85f415dd8c4e9d2a@mail.gmail.com> Message-ID: <163996.59723.qm@web65706.mail.ac4.yahoo.com> Dear Bipul, --- On Wed, 8/27/08, Bipul Rakshit wrote: > > But for B2 structure I am getting many -ve frequencies. > Although ScAs (B2) structure is stable at some high > pressure, so do i have to set some pressure > in the system and then I have to do the phonon > calculation? Yes, this is the correct way. Just set up tstress=.true. and tprnfor=.true. in order to monitor what is pressure in your high pressure ScAs phase. > > In simple words, how can i do the phonon calculation for ScAs (B2) structure which is structure at high pressure? > In simple words, decrease the lattice parameter and see what say above mentioned keywords about pressure, then continue your phonon calculations. Bests, Eyvaz. > > -- > Bipul Rakshit > PhD Student, > Barkatullah University, > Bhopal 462026, > MP, India > _______________________________________________ ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Wed Aug 27 14:16:25 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 27 Aug 2008 05:16:25 -0700 (PDT) Subject: [Pw_forum] bands_FS In-Reply-To: Message-ID: <66998.46464.qm@web65710.mail.ac4.yahoo.com> Hi, It seemed this is explained in example08. Please have look at /examples08/run_example file. More questions, please contact me. Well, it might be useful adding some words about this setup somewhere, say in PWINPUT Please do not forget providing your affiliation. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 8/27/08, wangqiang wrote: > From: wangqiang > Subject: [Pw_forum] Pw_forum Digest > To: pw_forum at pwscf.org > Date: Wednesday, August 27, 2008, 2:57 PM > hello everyone ,i am a beginner for pwscf. how can I perform > a band_FS calculation. i cannot find any doc in the pwscf > directory.thanks. > _________________________________________________________________ > ???MSN??????????????????? > http://mobile.msn.com.cn/_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From bipulrr at gmail.com Wed Aug 27 14:24:26 2008 From: bipulrr at gmail.com (Bipul Rakshit) Date: Wed, 27 Aug 2008 14:24:26 +0200 Subject: [Pw_forum] Phonon calculation at high pressure In-Reply-To: <163996.59723.qm@web65706.mail.ac4.yahoo.com> References: <3a749910808270237u14c8900bv85f415dd8c4e9d2a@mail.gmail.com> <163996.59723.qm@web65706.mail.ac4.yahoo.com> Message-ID: <3a749910808270524r63e40ca2kcbe704251b0b250c@mail.gmail.com> Hello Eyvaz Isaev, Thanks for your kind attention and your reply. Just one doubt, you said *"decrease the lattice parameter"*, means keeping in scf (or relax run ) from the initial ScAs (B1) structure or considering ScAs (B2) structure? regards On Wed, Aug 27, 2008 at 2:07 PM, Eyvaz Isaev wrote: > Dear Bipul, > > --- On Wed, 8/27/08, Bipul Rakshit wrote: > > > > > But for B2 structure I am getting many -ve frequencies. > > Although ScAs (B2) structure is stable at some high > > pressure, so do i have to set some pressure > > in the system and then I have to do the phonon > > calculation? > > Yes, this is the correct way. Just set up tstress=.true. and tprnfor=.true. > in order to monitor what is pressure in your high pressure ScAs phase. > > > > > In simple words, how can i do the phonon calculation for ScAs (B2) > structure which is structure at high pressure? > > > > In simple words, decrease the lattice parameter and see what say above > mentioned keywords about pressure, then continue your phonon calculations. > > Bests, > Eyvaz. > > > > -- > > Bipul Rakshit > > PhD Student, > > Barkatullah University, > > Bhopal 462026, > > MP, India > > _______________________________________________ > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > 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 > -- Bipul Rakshit PhD Student, Barkatullah University, Bhopal 462026, MP, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080827/85fc01c6/attachment.htm From anna.ferrari at unito.it Wed Aug 27 17:06:37 2008 From: anna.ferrari at unito.it (Anna Maria Ferrari) Date: Wed, 27 Aug 2008 16:06:37 +0100 Subject: [Pw_forum] (no subject) Message-ID: <00bd01c90856$82e40100$2376c082@desdemona> dear all I started a relax calculation that crashed now I hopefully found the error my question is how can i restart the calculation without repeating the scf? (sorry for the naive question but i am new with pw) with many thanks anna *********************************** Anna Maria Ferrari Dipartimento Chimica IFM Universit? di Torino via P. Giuria 5 10125 Torino ITALY phone ++39 +11 6707563 fax ++39 +11 670 7855 *********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080827/84b912c7/attachment.htm From eyvaz_isaev at yahoo.com Wed Aug 27 20:59:11 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 27 Aug 2008 11:59:11 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: <00bd01c90856$82e40100$2376c082@desdemona> Message-ID: <428979.52072.qm@web65704.mail.ac4.yahoo.com> Dear Anna, If you do not like restart with the SCF calculations, the best way is its skipping. So, just comment (with #) or delete all scf-lines and relaunch your script. restart_mode='restart' is for interrupted jobs or if self-consitence solution was not found for a given number of iterations (electron_maxstep=100 by default). Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 8/27/08, Anna Maria Ferrari wrote: > From: Anna Maria Ferrari > Subject: [Pw_forum] (no subject) > To: pw_forum at pwscf.org > Date: Wednesday, August 27, 2008, 7:06 PM > dear all > > I started a relax calculation that crashed > now I hopefully found the error > > my question is > how can i restart the calculation without repeating the > scf? > > (sorry for the naive question but i am new with pw) > with many thanks > > anna > > *********************************** > Anna Maria Ferrari > Dipartimento Chimica IFM > Universit? di Torino > via P. Giuria 5 > 10125 Torino ITALY > > phone ++39 +11 6707563 > fax ++39 +11 670 7855 > *********************************** > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From chenhanghuipwscf at gmail.com Thu Aug 28 03:52:19 2008 From: chenhanghuipwscf at gmail.com (alan chen) Date: Wed, 27 Aug 2008 21:52:19 -0400 Subject: [Pw_forum] vc-relax Message-ID: <22ae3ca40808271852p36374a0evcda506434f22bdad@mail.gmail.com> Dear PWSCF users, I try to relax the z-axis of STO while its x- and y-axis are fixed (i.e. relax STO under strain). I use 'vc-relax' and cell_dofree=z. The ion-dynamics is 'damp' and cell_dynamics is 'damp-w'. However I found that this 'Wentzcovitch Damped Dynamics' always does 50 iterations and stops. But the strain along the z direction is not necessarily the smallest after 50 iterations. Usually the z-strain is smallest after some iterations (for example 30 iterations) then it goes up. I want to ask why the code does not pick up the value of lattice constant of z direction which minimizes the strain in the z direction but just picks up the final value of lattice constant after 50 iterations? Thank you very much. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080827/c85ad287/attachment.htm From mansourehp at gmail.com Thu Aug 28 07:32:18 2008 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Thu, 28 Aug 2008 10:02:18 +0430 Subject: [Pw_forum] cg in molecular dynamics Message-ID: Dear all I am performing a MD simulation with QE for a strongly correlated system with 90 atoms.when I test this system with 10 atoms It works fast but for 90 atoms it works slowly.how can I increase its speed? how can I leave this message: cg_sub: missed minimum, case 1, iteration 21 Thanks in advance for your help and attention good luck Mansoureh Pashangpour -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080828/9676d095/attachment.htm From thefarsky at hotmail.com Thu Aug 28 08:43:55 2008 From: thefarsky at hotmail.com (wangqiang) Date: Thu, 28 Aug 2008 14:43:55 +0800 Subject: [Pw_forum] Pw_forum Digest, Vol 14, Issue 49 In-Reply-To: References: Message-ID: I guess you don't need so strick condition for minimize the energy. Wang. material department of Kriss. > Message: 4> Date: Wed, 27 Aug 2008 21:52:19 -0400> From: "alan chen" > Subject: [Pw_forum] vc-relax> To: pw_forum at pwscf.org> Message-ID:> <22ae3ca40808271852p36374a0evcda506434f22bdad at mail.gmail.com>> Content-Type: text/plain; charset="iso-8859-1"> > Dear PWSCF users,> I try to relax the z-axis of STO while its x- and y-axis are fixed (i.e.> relax STO under strain). I use 'vc-relax' and cell_dofree=z. The> ion-dynamics is 'damp' and cell_dynamics is 'damp-w'. However I found that> this 'Wentzcovitch Damped Dynamics' always does 50 iterations and stops. But> the strain along the z direction is not necessarily the smallest after 50> iterations. Usually the z-strain is smallest after some iterations (for> example 30 iterations) then it goes up.> I want to ask why the code does not pick up the value of lattice> constant of z direction which minimizes the strain in the z direction but> just picks up the final value of lattice constant after 50 iterations?> Thank you very much.> > Hanghui Chen> Department of Physics> Yale University _________________________________________________________________ ??????????????? http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AA&Form=MEVHAA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080828/fb421b4a/attachment.htm From paulatto at sissa.it Thu Aug 28 09:51:50 2008 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 28 Aug 2008 09:51:50 +0200 (CEST) Subject: [Pw_forum] vc-relax In-Reply-To: <22ae3ca40808271852p36374a0evcda506434f22bdad@mail.gmail.com> References: <22ae3ca40808271852p36374a0evcda506434f22bdad@mail.gmail.com> Message-ID: <17890.82.50.174.28.1219909910.squirrel@webmail.sissa.it> On Gio, Agosto 28, 2008 03:52, alan chen wrote: > always does 50 iterations and stops. Dear Hanghui Chen, if I remember correctly 50 is the default maximum number of iterations, so it stops because it reaches the limit. > Usually the z-strain is smallest after some iterations (for > example 30 iterations) then it goes up. I've never really used damp dynamics, from some simple runs I've got the feeling that it may be a bit tricky to set the damping parameters correctly; you could provide us some further details, so some expert can check them. > Thank you very much. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From vegalew at hotmail.com Thu Aug 28 10:28:28 2008 From: vegalew at hotmail.com (vega) Date: Thu, 28 Aug 2008 16:28:28 +0800 Subject: [Pw_forum] something strange in rutile and anatase calculation Message-ID: Dear all, It is known that the rutile is more stable than anatase in thermodynamics. Surprisingly, when I did the vc-relax calculation by QE, I found the calculated energy of anatase lower than rutile. Both vc-relax calculation for rutile and anatase onverged in 6 scf cycles and 3 bfgs steps, giving the final enthalpy = -362.7585836890 Ry for rutile and -725.5447425835 Ry for antase. So the average energy of [TiO2] unit is -181.3792918445 Ry for rutile and -181.386185645875 Ry for anatase. It looks like anatase is more stable than rutile. Do you think it was quite strange? To make the calculation both for anatase and rutile comparable, I used the same ecutwfc=40 Ry and ecutwfc=400 Ry, and a quite dense k-point mesh for both case, 4x4x7 for rutile and 5x5x2 for anatase. for better understanding in my calculation, please read the input file below, for anatase case, &CONTROL title = 'Anatase lattice' , calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/hjfeng/vega/TiO2/Anatase/lattice/vctest/tmp/' , wfcdir = '/tmp/' , pseudo_dir = '/home/hjfeng/vega/espresso-4.0/pseudo/' , prefix = 'Anatase lattice' , disk_io = 'none' , nstep = 1000 , / &SYSTEM ibrav = 6, celldm(1) = 7.1356, celldm(3) = 2.5122, nat = 12, ntyp = 2, ecutwfc = 40 , ecutrho = 400 , / &ELECTRONS / &IONS ion_dynamics = 'bfgs' , / &CELL cell_dynamics = 'bfgs' , / ATOMIC_SPECIES Ti 47.86700 Ti.pw91-sp-van_ak.UPF O 15.99940 O.pw91-van_ak.UPF ATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 Ti 0.000000000 0.500000000 0.250000000 Ti 0.500000000 0.000000000 0.750000000 O 0.000000000 0.500000000 0.042000000 O 0.000000000 0.000000000 0.208000000 O 0.500000000 0.500000000 0.292000000 O 0.000000000 0.500000000 0.458000000 O 0.500000000 0.000000000 0.542000000 O 0.500000000 0.500000000 0.708000000 O 0.000000000 0.000000000 0.792000000 O 0.500000000 1.000000000 0.958000000 K_POINTS automatic 5 5 2 1 1 1 for rutile case, &CONTROL title = Rutile_lattice , calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/vega32/TiO2/rutile/lattice/vcrelax/tmp' , wfcdir = '/tmp/' , pseudo_dir = '/home/vega32/espresso-4.0.1/pseudo/' , prefix = 'Anatase lattice' , disk_io = 'none' , nstep = 1000 , / &SYSTEM ibrav = 6, celldm(1) = 8.6814, celldm(3) = 0.6441, nat = 6, ntyp = 2, ecutwfc = 40 , ecutrho = 400 , / &ELECTRONS / &IONS ion_dynamics = 'bfgs' , / &CELL cell_dynamics = 'bfgs' , / ATOMIC_SPECIES O 15.99940 O.pw91-van_ak.UPF Ti 47.90000 Ti.pw91-sp-van_ak.UPF ATOMIC_POSITIONS crystal O 0.304800000 0.304800000 0.000000000 O 0.695200000 0.695200000 0.000000000 O 0.195200000 0.804800000 0.500000000 O 0.804800000 0.195200000 0.500000000 Ti 0.500000000 0.500000000 0.500000000 Ti 0.000000000 0.000000000 0.000000000 K_POINTS automatic 4 4 7 1 1 1 vega ============================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080828/03907394/attachment.htm From marzari at MIT.EDU Thu Aug 28 13:01:04 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 28 Aug 2008 14:01:04 +0300 Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: References: Message-ID: <48B68570.3030804@mit.edu> vega wrote: > Dear all, > > It is known that the rutile is more stable than anatase in > thermodynamics. Surprisingly, when I did the vc-relax calculation by > QE, I found the calculated energy of anatase lower than rutile. Both > vc-relax calculation for rutile and anatase onverged in 6 scf cycles and > 3 bfgs steps, giving the final enthalpy = -362.7585836890 Ry for rutile > and -725.5447425835 Ry for antase. So the average energy of [TiO2] unit > is -181.3792918445 Ry for rutile and -181.386185645875 Ry for anatase. > It looks like anatase is more stable than rutile. Do you think it was > quite strange? Dear Vega, your results are probably correct. It's a known failure of LDA and GGA to stabilize anatase more than rutile. nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From vegalew at hotmail.com Thu Aug 28 14:21:13 2008 From: vegalew at hotmail.com (vega) Date: Thu, 28 Aug 2008 20:21:13 +0800 Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: References: Message-ID: Thanks for the help from Nicola and Charles. vega From: vega Sent: Thursday, August 28, 2008 4:28 PM To: PWSCF Subject: [Pw_forum] something strange in rutile and anatase calculation Dear all, It is known that the rutile is more stable than anatase in thermodynamics. Surprisingly, when I did the vc-relax calculation by QE, I found the calculated energy of anatase lower than rutile. Both vc-relax calculation for rutile and anatase onverged in 6 scf cycles and 3 bfgs steps, giving the final enthalpy = -362.7585836890 Ry for rutile and -725.5447425835 Ry for antase. So the average energy of [TiO2] unit is -181.3792918445 Ry for rutile and -181.386185645875 Ry for anatase. It looks like anatase is more stable than rutile. Do you think it was quite strange? To make the calculation both for anatase and rutile comparable, I used the same ecutwfc=40 Ry and ecutwfc=400 Ry, and a quite dense k-point mesh for both case, 4x4x7 for rutile and 5x5x2 for anatase. for better understanding in my calculation, please read the input file below, for anatase case, &CONTROL title = 'Anatase lattice' , calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/hjfeng/vega/TiO2/Anatase/lattice/vctest/tmp/' , wfcdir = '/tmp/' , pseudo_dir = '/home/hjfeng/vega/espresso-4.0/pseudo/' , prefix = 'Anatase lattice' , disk_io = 'none' , nstep = 1000 , / &SYSTEM ibrav = 6, celldm(1) = 7.1356, celldm(3) = 2.5122, nat = 12, ntyp = 2, ecutwfc = 40 , ecutrho = 400 , / &ELECTRONS / &IONS ion_dynamics = 'bfgs' , / &CELL cell_dynamics = 'bfgs' , / ATOMIC_SPECIES Ti 47.86700 Ti.pw91-sp-van_ak.UPF O 15.99940 O.pw91-van_ak.UPF ATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 Ti 0.000000000 0.500000000 0.250000000 Ti 0.500000000 0.000000000 0.750000000 O 0.000000000 0.500000000 0.042000000 O 0.000000000 0.000000000 0.208000000 O 0.500000000 0.500000000 0.292000000 O 0.000000000 0.500000000 0.458000000 O 0.500000000 0.000000000 0.542000000 O 0.500000000 0.500000000 0.708000000 O 0.000000000 0.000000000 0.792000000 O 0.500000000 1.000000000 0.958000000 K_POINTS automatic 5 5 2 1 1 1 for rutile case, &CONTROL title = Rutile_lattice , calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/vega32/TiO2/rutile/lattice/vcrelax/tmp' , wfcdir = '/tmp/' , pseudo_dir = '/home/vega32/espresso-4.0.1/pseudo/' , prefix = 'Anatase lattice' , disk_io = 'none' , nstep = 1000 , / &SYSTEM ibrav = 6, celldm(1) = 8.6814, celldm(3) = 0.6441, nat = 6, ntyp = 2, ecutwfc = 40 , ecutrho = 400 , / &ELECTRONS / &IONS ion_dynamics = 'bfgs' , / &CELL cell_dynamics = 'bfgs' , / ATOMIC_SPECIES O 15.99940 O.pw91-van_ak.UPF Ti 47.90000 Ti.pw91-sp-van_ak.UPF ATOMIC_POSITIONS crystal O 0.304800000 0.304800000 0.000000000 O 0.695200000 0.695200000 0.000000000 O 0.195200000 0.804800000 0.500000000 O 0.804800000 0.195200000 0.500000000 Ti 0.500000000 0.500000000 0.500000000 Ti 0.000000000 0.000000000 0.000000000 K_POINTS automatic 4 4 7 1 1 1 vega ============================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China -------------------------------------------------------------------------------- _______________________________________________ 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/20080828/70e722d7/attachment-0001.htm From eyvaz_isaev at yahoo.com Thu Aug 28 14:58:44 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 28 Aug 2008 05:58:44 -0700 (PDT) Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: <48B68570.3030804@mit.edu> Message-ID: <351789.59954.qm@web65716.mail.ac4.yahoo.com> Hi, One more suggestion. As far as I know the same situation is for \alpha and \omega phases of Ti, as well as HCP and DHCP phases of FeH. But free energy calculations have shown than \alpha-Ti and DHCP FeH are stabilized due to the phonon contribution. For FeH you can see: Eyvaz I. Isaev et al., Dynamical stability of Fe-H in the Earth's mantle and core regions, Proceedings of the National Academy of Sciences of the USA (PNAS), 104 (22), 29 May 2007, 9168. PNAS Special Issue "Geophysics". So, you can try follow this way, if you like. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 8/28/08, Nicola Marzari wrote: > From: Nicola Marzari > Subject: Re: [Pw_forum] something strange in rutile and anatase calculation > To: "PWSCF Forum" > Date: Thursday, August 28, 2008, 3:01 PM > vega wrote: > > Dear all, > > > > It is known that the rutile is more stable than > anatase in > > thermodynamics. Surprisingly, when I did the vc-relax > calculation by > > QE, I found the calculated energy of anatase lower > than rutile. Both > > vc-relax calculation for rutile and anatase onverged > in 6 scf cycles and > > 3 bfgs steps, giving the final enthalpy = > -362.7585836890 Ry for rutile > > and -725.5447425835 Ry for antase. So the average > energy of [TiO2] unit > > is -181.3792918445 Ry for rutile and -181.386185645875 > Ry for anatase. > > It looks like anatase is more stable than rutile. Do > you think it was > > quite strange? > > > Dear Vega, > > your results are probably correct. It's a known failure > of LDA and GGA > to stabilize anatase more than rutile. > > nicola > > -- > --------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials Science and > Engineering > 13-5066 MIT 77 Massachusetts Avenue Cambridge MA > 02139-4307 USA > tel 617.4522758 fax 2586534 marzari at mit.edu > http://quasiamore.mit.edu > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Thu Aug 28 15:06:37 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 28 Aug 2008 15:06:37 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <00bd01c90856$82e40100$2376c082@desdemona> References: <00bd01c90856$82e40100$2376c082@desdemona> Message-ID: On Aug 27, 2008, at 17:06 , Anna Maria Ferrari wrote: > I started a relax calculation that crashed > now I hopefully found the error > > my question is > how can i restart the calculation without repeating the scf? it depends a lot on what you did and how, whether you have final or intermediate data, and how lucky you are. The simplest thing to do is to get the last (or the best) available atomic positions and start from there P. --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From vegalew at hotmail.com Thu Aug 28 15:08:50 2008 From: vegalew at hotmail.com (vega) Date: Thu, 28 Aug 2008 21:08:50 +0800 Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: <351789.59954.qm@web65716.mail.ac4.yahoo.com> References: <351789.59954.qm@web65716.mail.ac4.yahoo.com> Message-ID: Thank you for Prof. Eyvaz Isaev's hints I'll read the excellent article as your suggestion. It's really nice of you. vega -------------------------------------------------- From: "Eyvaz Isaev" Sent: Thursday, August 28, 2008 8:58 PM To: "PWSCF Forum" Subject: Re: [Pw_forum] something strange in rutile and anatase calculation > Hi, > > One more suggestion. > As far as I know the same situation is for \alpha and \omega phases of Ti, > as well as HCP and DHCP phases of FeH. But free energy calculations have > shown than \alpha-Ti and DHCP FeH are stabilized due to the phonon > contribution. > For FeH you can see: Eyvaz I. Isaev et al., Dynamical stability of Fe-H in > the Earth's mantle and core regions, Proceedings of the National Academy > of Sciences of the USA (PNAS), 104 (22), 29 May 2007, 9168. PNAS Special > Issue "Geophysics". > > So, you can try follow this way, if you like. > > Bests, > Eyvaz. > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Thu, 8/28/08, Nicola Marzari wrote: > >> From: Nicola Marzari >> Subject: Re: [Pw_forum] something strange in rutile and anatase >> calculation >> To: "PWSCF Forum" >> Date: Thursday, August 28, 2008, 3:01 PM >> vega wrote: >> > Dear all, >> > >> > It is known that the rutile is more stable than >> anatase in >> > thermodynamics. Surprisingly, when I did the vc-relax >> calculation by >> > QE, I found the calculated energy of anatase lower >> than rutile. Both >> > vc-relax calculation for rutile and anatase onverged >> in 6 scf cycles and >> > 3 bfgs steps, giving the final enthalpy = >> -362.7585836890 Ry for rutile >> > and -725.5447425835 Ry for antase. So the average >> energy of [TiO2] unit >> > is -181.3792918445 Ry for rutile and -181.386185645875 >> Ry for anatase. >> > It looks like anatase is more stable than rutile. Do >> you think it was >> > quite strange? >> >> >> Dear Vega, >> >> your results are probably correct. It's a known failure >> of LDA and GGA >> to stabilize anatase more than rutile. >> >> nicola >> >> -- >> --------------------------------------------------------------------- >> Prof Nicola Marzari Department of Materials Science and >> Engineering >> 13-5066 MIT 77 Massachusetts Avenue Cambridge MA >> 02139-4307 USA >> tel 617.4522758 fax 2586534 marzari at mit.edu >> http://quasiamore.mit.edu >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Thu Aug 28 15:14:23 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 28 Aug 2008 15:14:23 +0200 Subject: [Pw_forum] vc-relax In-Reply-To: <22ae3ca40808271852p36374a0evcda506434f22bdad@mail.gmail.com> References: <22ae3ca40808271852p36374a0evcda506434f22bdad@mail.gmail.com> Message-ID: <15F67103-BCE3-45EA-BCCC-DDA507D832F0@democritos.it> On Aug 28, 2008, at 3:52 , alan chen wrote: > I try to relax the z-axis of STO while its x- and y-axis are fixed > (i.e. relax STO under strain). I use 'vc-relax' and cell_dofree=z. > The ion-dynamics is 'damp' and cell_dynamics is 'damp-w'. However I > found that this 'Wentzcovitch Damped Dynamics' always does 50 > iterations and stops. But the strain along the z direction is not > necessarily the smallest after 50 iterations. Usually the z-strain > is smallest after some iterations (for example 30 iterations) then > it goes up. this behavior is quite typical for damped dynamics that are not "damped" enough, I think Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eyvaz_isaev at yahoo.com Thu Aug 28 15:25:12 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 28 Aug 2008 06:25:12 -0700 (PDT) Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: Message-ID: <184207.91247.qm@web65701.mail.ac4.yahoo.com> Dear Vega, Please be not so official. I add (automatically) my affiliation due to our accepted Netetiquette. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 8/28/08, vega wrote: > From: vega > Subject: Re: [Pw_forum] something strange in rutile and anatase calculation > To: eyvaz_isaev at yahoo.com, "PWSCF Forum" > Date: Thursday, August 28, 2008, 5:08 PM > Thank you for Prof. Eyvaz Isaev's hints > I'll read the excellent article as your suggestion. > It's really nice of you. > > vega > > -------------------------------------------------- > From: "Eyvaz Isaev" > Sent: Thursday, August 28, 2008 8:58 PM > To: "PWSCF Forum" > Subject: Re: [Pw_forum] something strange in rutile and > anatase calculation > > > Hi, > > > > One more suggestion. > > As far as I know the same situation is for \alpha > and \omega phases of Ti, > > as well as HCP and DHCP phases of FeH. But free energy > calculations have > > shown than \alpha-Ti and DHCP FeH are stabilized > due to the phonon > > contribution. > > For FeH you can see: Eyvaz I. Isaev et al., Dynamical > stability of Fe-H in > > the Earth's mantle and core regions, Proceedings > of the National Academy > > of Sciences of the USA (PNAS), 104 (22), 29 May 2007, > 9168. PNAS Special > > Issue "Geophysics". > > > > So, you can try follow this way, if you like. > > > > Bests, > > Eyvaz. > > > > > > > ------------------------------------------------------------------- > > Prof. Eyvaz Isaev, > > Theoretical Physics Department, Moscow State Institute > of Steel & Alloys, > > Russia, > > Department of Physics, Chemistry, and Biology (IFM), > Linkoping University, > > Sweden > > Condensed Matter Theory Group, Uppsala University, > Sweden > > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > > > > > > --- On Thu, 8/28/08, Nicola Marzari > wrote: > > > >> From: Nicola Marzari > >> Subject: Re: [Pw_forum] something strange in > rutile and anatase > >> calculation > >> To: "PWSCF Forum" > > >> Date: Thursday, August 28, 2008, 3:01 PM > >> vega wrote: > >> > Dear all, > >> > > >> > It is known that the rutile is more stable > than > >> anatase in > >> > thermodynamics. Surprisingly, when I did the > vc-relax > >> calculation by > >> > QE, I found the calculated energy of anatase > lower > >> than rutile. Both > >> > vc-relax calculation for rutile and anatase > onverged > >> in 6 scf cycles and > >> > 3 bfgs steps, giving the final enthalpy = > >> -362.7585836890 Ry for rutile > >> > and -725.5447425835 Ry for antase. So the > average > >> energy of [TiO2] unit > >> > is -181.3792918445 Ry for rutile and > -181.386185645875 > >> Ry for anatase. > >> > It looks like anatase is more stable than > rutile. Do > >> you think it was > >> > quite strange? > >> > >> > >> Dear Vega, > >> > >> your results are probably correct. It's a > known failure > >> of LDA and GGA > >> to stabilize anatase more than rutile. > >> > >> nicola > >> > >> -- > >> > --------------------------------------------------------------------- > >> Prof Nicola Marzari Department of Materials > Science and > >> Engineering > >> 13-5066 MIT 77 Massachusetts Avenue > Cambridge MA > >> 02139-4307 USA > >> tel 617.4522758 fax 2586534 marzari at mit.edu > >> http://quasiamore.mit.edu > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > _______________________________________________ > > 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 vegalew at hotmail.com Thu Aug 28 16:05:05 2008 From: vegalew at hotmail.com (vega) Date: Thu, 28 Aug 2008 22:05:05 +0800 Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: <184207.91247.qm@web65701.mail.ac4.yahoo.com> References: <184207.91247.qm@web65701.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz, I have read your PNAS paper just now. I'm very interesting about the phase transition mentioned in your paper. But because of lack of experience in your scopes, I'm not very clear about the detail of the calculations of phase transitions. In the second paragraph of Results and Discussion section, you said 'According to our free-energy calculations, there exist two phase transitions in the FeH system...'. How did you simulated the two phase transitions? How could you calculate the Volume as a function of Pressure as shown in Fig. 2? The line in Fig. 2 went quite smoothly, so you may not plot it point by point. How could you get the line? thank you for reading vega -------------------------------------------------- From: "Eyvaz Isaev" Sent: Thursday, August 28, 2008 9:25 PM To: "PWSCF Forum" Subject: Re: [Pw_forum] something strange in rutile and anatase calculation > Dear Vega, > > Please be not so official. I add (automatically) my affiliation due to our > accepted Netetiquette. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Thu, 8/28/08, vega wrote: > >> From: vega >> Subject: Re: [Pw_forum] something strange in rutile and anatase >> calculation >> To: eyvaz_isaev at yahoo.com, "PWSCF Forum" >> Date: Thursday, August 28, 2008, 5:08 PM >> Thank you for Prof. Eyvaz Isaev's hints >> I'll read the excellent article as your suggestion. >> It's really nice of you. >> >> vega >> >> -------------------------------------------------- >> From: "Eyvaz Isaev" >> Sent: Thursday, August 28, 2008 8:58 PM >> To: "PWSCF Forum" >> Subject: Re: [Pw_forum] something strange in rutile and >> anatase calculation >> >> > Hi, >> > >> > One more suggestion. >> > As far as I know the same situation is for \alpha >> and \omega phases of Ti, >> > as well as HCP and DHCP phases of FeH. But free energy >> calculations have >> > shown than \alpha-Ti and DHCP FeH are stabilized >> due to the phonon >> > contribution. >> > For FeH you can see: Eyvaz I. Isaev et al., Dynamical >> stability of Fe-H in >> > the Earth's mantle and core regions, Proceedings >> of the National Academy >> > of Sciences of the USA (PNAS), 104 (22), 29 May 2007, >> 9168. PNAS Special >> > Issue "Geophysics". >> > >> > So, you can try follow this way, if you like. >> > >> > Bests, >> > Eyvaz. >> > >> > >> > >> ------------------------------------------------------------------- >> > Prof. Eyvaz Isaev, >> > Theoretical Physics Department, Moscow State Institute >> of Steel & Alloys, >> > Russia, >> > Department of Physics, Chemistry, and Biology (IFM), >> Linkoping University, >> > Sweden >> > Condensed Matter Theory Group, Uppsala University, >> Sweden >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, >> eyvaz_isaev at yahoo.com >> > >> > >> > --- On Thu, 8/28/08, Nicola Marzari >> wrote: >> > >> >> From: Nicola Marzari >> >> Subject: Re: [Pw_forum] something strange in >> rutile and anatase >> >> calculation >> >> To: "PWSCF Forum" >> >> >> Date: Thursday, August 28, 2008, 3:01 PM >> >> vega wrote: >> >> > Dear all, >> >> > >> >> > It is known that the rutile is more stable >> than >> >> anatase in >> >> > thermodynamics. Surprisingly, when I did the >> vc-relax >> >> calculation by >> >> > QE, I found the calculated energy of anatase >> lower >> >> than rutile. Both >> >> > vc-relax calculation for rutile and anatase >> onverged >> >> in 6 scf cycles and >> >> > 3 bfgs steps, giving the final enthalpy = >> >> -362.7585836890 Ry for rutile >> >> > and -725.5447425835 Ry for antase. So the >> average >> >> energy of [TiO2] unit >> >> > is -181.3792918445 Ry for rutile and >> -181.386185645875 >> >> Ry for anatase. >> >> > It looks like anatase is more stable than >> rutile. Do >> >> you think it was >> >> > quite strange? >> >> >> >> >> >> Dear Vega, >> >> >> >> your results are probably correct. It's a >> known failure >> >> of LDA and GGA >> >> to stabilize anatase more than rutile. >> >> >> >> nicola >> >> >> >> -- >> >> >> --------------------------------------------------------------------- >> >> Prof Nicola Marzari Department of Materials >> Science and >> >> Engineering >> >> 13-5066 MIT 77 Massachusetts Avenue >> Cambridge MA >> >> 02139-4307 USA >> >> tel 617.4522758 fax 2586534 marzari at mit.edu >> >> http://quasiamore.mit.edu >> >> _______________________________________________ >> >> Pw_forum mailing list >> >> Pw_forum at pwscf.org >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Thu Aug 28 16:31:14 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 28 Aug 2008 16:31:14 +0200 Subject: [Pw_forum] about one "fatal error" In-Reply-To: <32812.210.73.17.131.1219716202.squirrel@210.73.16.4> References: <32812.210.73.17.131.1219716202.squirrel@210.73.16.4> Message-ID: <85F846C2-18ED-4C9D-ABE1-5EEF371A6503@democritos.it> On Aug 26, 2008, at 4:03 , L.F.Huang wrote: > I am calculating graphene supercell with one vacancy impurity, > whose size > is 4*4*1. It is an magnetic system whose magnetization is 0.8 bohr > magneton. > And there are 31 atoms and 93 representations with one mode for > each. At > first, ph.x is executing well, however, when the 23th > representation is being > done, there comes out some strange thing: > ********************************************************************** > FATAL ERROR on MPI node 3 (ganode054): GM send to MPI node 10 (??? > [00:60:dd:49:08:2a]) failed: status 18 (target node was > unreachable) check > the target host, mapping or cables > Small/Ctrl message completion error! > forrtl: error (76): IOT trap signal > [...] > Does anyone knows what is the reason of this error? of course, nobody knows, but somebody might argue that it looks like a problem in node 10 rather than in q-e. Any evidence that the problem is really on the q-e side (i.e. the problem, or some problem, is reproducible on a different machine)? Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From thefarsky at hotmail.com Fri Aug 29 04:25:35 2008 From: thefarsky at hotmail.com (wangqiang) Date: Fri, 29 Aug 2008 10:25:35 +0800 Subject: [Pw_forum] U calculation. Message-ID: hi, everyone. i read about the U calculation in Vlab's lecture. but i am not so clear. could anyone discrib it in more detail? Lee chungnam univerisity. _________________________________________________________________ ??????????????? http://cnweb.search.live.com/video/results.aspx?q=%E5%8F%AF%E7%88%B1%E7%8C%AB%E5%92%AA&Form=MEVHAA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080829/3239c7b5/attachment-0001.htm From marzari at MIT.EDU Fri Aug 29 07:40:41 2008 From: marzari at MIT.EDU (Nicola Marzari) Date: Fri, 29 Aug 2008 08:40:41 +0300 Subject: [Pw_forum] U calculation. In-Reply-To: References: Message-ID: <48B78BD9.4050404@mit.edu> wangqiang wrote: > hi, everyone. i read about the U calculation in Vlab's lecture. but i am > not so clear. could anyone discrib it in more detail? > Lee > chungnam univerisity. have a look at Matteo Cococcioni thesis, from http://www.sissa.it/cm/phd.php . nicola -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From lfhuang at theory.issp.ac.cn Fri Aug 29 08:13:40 2008 From: lfhuang at theory.issp.ac.cn (L.F.Huang) Date: Fri, 29 Aug 2008 14:13:40 +0800 (CST) Subject: [Pw_forum] about one "fatal error" In-Reply-To: References: Message-ID: <32829.210.73.17.131.1219990420.squirrel@210.73.16.4> Dear prof. Giannozzi Thank you very much for your kind attention. I am afraid that I can only have the access to the machine of "SGI origin3900". But the problem seems solved, as I have mentioned before, when I change to 13 nodes that can divide the 52 reduced k points. And my calculation goes on well with 13 nodes. Then, that may tell me the error belongs to the machine, or "communication" as Derek has mentioned before. Best Wishes! Yours Sincerely! L.F.Huang > Date: Thu, 28 Aug 2008 16:31:14 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] about one "fatal error" > To: PWSCF Forum > Message-ID: <85F846C2-18ED-4C9D-ABE1-5EEF371A6503 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Aug 26, 2008, at 4:03 , L.F.Huang wrote: > >> I am calculating graphene supercell with one vacancy impurity, >> whose size >> is 4*4*1. It is an magnetic system whose magnetization is 0.8 bohr >> magneton. >> And there are 31 atoms and 93 representations with one mode for >> each. At >> first, ph.x is executing well, however, when the 23th >> representation is being >> done, there comes out some strange thing: >> ********************************************************************** >> FATAL ERROR on MPI node 3 (ganode054): GM send to MPI node 10 (??? >> [00:60:dd:49:08:2a]) failed: status 18 (target node was >> unreachable) check >> the target host, mapping or cables >> Small/Ctrl message completion error! >> forrtl: error (76): IOT trap signal >> [...] >> Does anyone knows what is the reason of this error? > > of course, nobody knows, but somebody might argue that it looks like a > problem in node 10 rather than in q-e. Any evidence that the problem is > really on the q-e side (i.e. the problem, or some problem, is > reproducible > on a different machine)? > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 ====================================================================== L.F.Huang(???) lfhuang at theory.issp.ac.cn ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-328(office) Fax: 86-551-5591434 Web: http://theory.issp.ac.cn (website of our theory group) http://www.issp.ac.cn (website of our institute) ====================================================================== From giannozz at democritos.it Fri Aug 29 09:53:26 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 29 Aug 2008 09:53:26 +0200 Subject: [Pw_forum] output of fildrho In-Reply-To: <52952.172.16.48.134.1219469000.squirrel@webmail.iitg.ac.in> References: <52952.172.16.48.134.1219469000.squirrel@webmail.iitg.ac.in> Message-ID: <48B7AAF6.8020605@democritos.it> Munima Bora Sahariah wrote: > Could anyone please help me out in reading the output fildrho files? have a look at the header of PH/punch_plot_e.f90 and PH/punch_plot_e.f90 The output files should be readable by pp.x, in the second step (see the description of the input, INPUT_PP.*) Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From anna.ferrari at unito.it Fri Aug 29 13:18:19 2008 From: anna.ferrari at unito.it (anna.ferrari at unito.it) Date: Fri, 29 Aug 2008 13:18:19 +0200 (CEST) Subject: [Pw_forum] relax Message-ID: <10093.87.9.170.15.1220008699.squirrel@mail.unito.it> hi all!!! i'm doing a relax cac?lculation the program stops in this way: first order charge density extrapolation Check: negative starting charge= -0.017665 negative rho (up, down): 0.375E-01 0.000E+00 first order wave-functions extrapolation IOS = 28 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 12 i/o error in davcio %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% the error in the diagonalization is connected with the negative charge? what can i do to avoid this error? thanks again anna From anna.ferrari at unito.it Fri Aug 29 13:29:29 2008 From: anna.ferrari at unito.it (anna.ferrari at unito.it) Date: Fri, 29 Aug 2008 13:29:29 +0200 (CEST) Subject: [Pw_forum] (no subject) In-Reply-To: References: <00bd01c90856$82e40100$2376c082@desdemona> Message-ID: <10118.87.9.170.15.1220009369.squirrel@mail.unito.it> ok i understand i wonder if I select a restart mode and i change something in the input (threshold or something else) these new information are read from the input file or everything is read from teh scratch files of the previous run? thanks again anna > > > ------------------ Messaggio originale ------------------- > Oggetto: Re: [Pw_forum] (no subject) > Da: "Paolo Giannozzi" > Data: Gio, 28 Agosto 2008, 3:06 pm > A: "PWSCF Forum" > ---------------------------------------------------------- > > > On Aug 27, 2008, at 17:06 , Anna Maria Ferrari wrote: > >> I started a relax calculation that crashed >> now I hopefully found the error >> >> my question is >> how can i restart the calculation without repeating the >> scf? > > > it depends a lot on what you did and how, whether you have > final > or intermediate data, and how lucky you are. The simplest > thing to > do is to get the last (or the best) available atomic > positions and start > from there > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From eyvaz_isaev at yahoo.com Fri Aug 29 14:52:34 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 29 Aug 2008 05:52:34 -0700 (PDT) Subject: [Pw_forum] relax In-Reply-To: <10093.87.9.170.15.1220008699.squirrel@mail.unito.it> Message-ID: <769998.95919.qm@web65706.mail.ac4.yahoo.com> Dear Anna, --- On Fri, 8/29/08, anna.ferrari at unito.it wrote: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from davcio : error # 12 > i/o error in davcio > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > the error in the diagonalization is connected with the > negative charge? This one is really very Frequently Asked Question. Please have look at the UserGude (Troubleshooting section). I do not think it is connected to small negative charge, rather it might be connected to the structure you study. If you are absolutely sure your structure is correct then add diagonalization='cg' line into your script. > what can i do to avoid this error? see before. > thanks again Thanks providing your affiliation. > anna > > ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Fri Aug 29 15:00:34 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 29 Aug 2008 06:00:34 -0700 (PDT) Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: Message-ID: <796688.9134.qm@web65704.mail.ac4.yahoo.com> Dear Vega, As you can see we considered three FeH phases (FCC, HCP, and DHCP) and plotted their free energies including phonon contribution with respect to the unit cell volume. On the left side (under pressure) first DHCP has the lowest energy, then hcp, and finally, FCC phase is the lowest in energy. So, we stated, there are DHCP --> HCP and HCP --> FCC phase transitons Hope this helps. Bests, Eyvaz ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Thu, 8/28/08, vega wrote: > From: vega > Subject: Re: [Pw_forum] something strange in rutile and anatase calculation > To: eyvaz_isaev at yahoo.com, "PWSCF Forum" > Date: Thursday, August 28, 2008, 6:05 PM > Dear Eyvaz, > > I have read your PNAS paper just now. I'm very > interesting about the phase > transition mentioned in your paper. But because of lack of > experience in > your scopes, I'm not very clear about the detail of the > calculations of > phase transitions. > In the second paragraph of Results and Discussion section, > you said > 'According to > our free-energy calculations, there exist two phase > transitions in the FeH > system...'. How did you simulated the two phase > transitions? How could you > calculate the Volume as a function of Pressure as shown in > Fig. 2? The line > in Fig. 2 went quite smoothly, so you may not plot it point > by point. How > could you get the line? > > thank you for reading > > vega > > > -------------------------------------------------- > From: "Eyvaz Isaev" > Sent: Thursday, August 28, 2008 9:25 PM > To: "PWSCF Forum" > Subject: Re: [Pw_forum] something strange in rutile and > anatase calculation > > > Dear Vega, > > > > Please be not so official. I add (automatically) my > affiliation due to our > > accepted Netetiquette. > > > > Bests, > > Eyvaz. > > > > > ------------------------------------------------------------------- > > Prof. Eyvaz Isaev, > > Theoretical Physics Department, Moscow State Institute > of Steel & Alloys, > > Russia, > > Department of Physics, Chemistry, and Biology (IFM), > Linkoping University, > > Sweden > > Condensed Matter Theory Group, Uppsala University, > Sweden > > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > > > > > > --- On Thu, 8/28/08, vega > wrote: > > > >> From: vega > >> Subject: Re: [Pw_forum] something strange in > rutile and anatase > >> calculation > >> To: eyvaz_isaev at yahoo.com, "PWSCF Forum" > > >> Date: Thursday, August 28, 2008, 5:08 PM > >> Thank you for Prof. Eyvaz Isaev's hints > >> I'll read the excellent article as your > suggestion. > >> It's really nice of you. > >> > >> vega > >> > >> -------------------------------------------------- > >> From: "Eyvaz Isaev" > > >> Sent: Thursday, August 28, 2008 8:58 PM > >> To: "PWSCF Forum" > > >> Subject: Re: [Pw_forum] something strange in > rutile and > >> anatase calculation > >> > >> > Hi, > >> > > >> > One more suggestion. > >> > As far as I know the same situation is for > \alpha > >> and \omega phases of Ti, > >> > as well as HCP and DHCP phases of FeH. But > free energy > >> calculations have > >> > shown than \alpha-Ti and DHCP FeH are > stabilized > >> due to the phonon > >> > contribution. > >> > For FeH you can see: Eyvaz I. Isaev et al., > Dynamical > >> stability of Fe-H in > >> > the Earth's mantle and core regions, > Proceedings > >> of the National Academy > >> > of Sciences of the USA (PNAS), 104 (22), 29 > May 2007, > >> 9168. PNAS Special > >> > Issue "Geophysics". > >> > > >> > So, you can try follow this way, if you like. > >> > > >> > Bests, > >> > Eyvaz. > >> > > >> > > >> > > >> > ------------------------------------------------------------------- > >> > Prof. Eyvaz Isaev, > >> > Theoretical Physics Department, Moscow State > Institute > >> of Steel & Alloys, > >> > Russia, > >> > Department of Physics, Chemistry, and Biology > (IFM), > >> Linkoping University, > >> > Sweden > >> > Condensed Matter Theory Group, Uppsala > University, > >> Sweden > >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > >> eyvaz_isaev at yahoo.com > >> > > >> > > >> > --- On Thu, 8/28/08, Nicola Marzari > >> wrote: > >> > > >> >> From: Nicola Marzari > > >> >> Subject: Re: [Pw_forum] something strange > in > >> rutile and anatase > >> >> calculation > >> >> To: "PWSCF Forum" > >> > >> >> Date: Thursday, August 28, 2008, 3:01 PM > >> >> vega wrote: > >> >> > Dear all, > >> >> > > >> >> > It is known that the rutile is more > stable > >> than > >> >> anatase in > >> >> > thermodynamics. Surprisingly, when I > did the > >> vc-relax > >> >> calculation by > >> >> > QE, I found the calculated energy of > anatase > >> lower > >> >> than rutile. Both > >> >> > vc-relax calculation for rutile and > anatase > >> onverged > >> >> in 6 scf cycles and > >> >> > 3 bfgs steps, giving the final > enthalpy = > >> >> -362.7585836890 Ry for rutile > >> >> > and -725.5447425835 Ry for antase. > So the > >> average > >> >> energy of [TiO2] unit > >> >> > is -181.3792918445 Ry for rutile and > >> -181.386185645875 > >> >> Ry for anatase. > >> >> > It looks like anatase is more stable > than > >> rutile. Do > >> >> you think it was > >> >> > quite strange? > >> >> > >> >> > >> >> Dear Vega, > >> >> > >> >> your results are probably correct. > It's a > >> known failure > >> >> of LDA and GGA > >> >> to stabilize anatase more than rutile. > >> >> > >> >> nicola > >> >> > >> >> -- > >> >> > >> > --------------------------------------------------------------------- > >> >> Prof Nicola Marzari Department of > Materials > >> Science and > >> >> Engineering > >> >> 13-5066 MIT 77 Massachusetts Avenue > >> Cambridge MA > >> >> 02139-4307 USA > >> >> tel 617.4522758 fax 2586534 > marzari at mit.edu > >> >> http://quasiamore.mit.edu > >> >> > _______________________________________________ > >> >> Pw_forum mailing list > >> >> Pw_forum at pwscf.org > >> >> > http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> > > >> > > >> > > _______________________________________________ > >> > Pw_forum mailing list > >> > Pw_forum at pwscf.org > >> > > http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Fri Aug 29 15:09:55 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 29 Aug 2008 15:09:55 +0200 Subject: [Pw_forum] relax In-Reply-To: <10093.87.9.170.15.1220008699.squirrel@mail.unito.it> References: <10093.87.9.170.15.1220008699.squirrel@mail.unito.it> Message-ID: On Aug 29, 2008, at 13:18 , anna.ferrari at unito.it wrote: > from davcio : error # 12 > i/o error in davcio > > the error in the diagonalization is connected with the negative > charge? there is no error in the diagonalization. The error is in I/O and means that the code encountered an unexpected condition, in which it tried to read data from a nonexistent or empty or corrupted file, or to read data in an incompatible format. It may happen especially if you are trying to restart from a previous run. > what can i do to avoid this error? there shouldn't be any such error if you do things properly (and if the disks of your machine work properly) Paolo --- Paolo Giannozzi, Dept of Physics, University of Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From vegalew at hotmail.com Fri Aug 29 15:22:27 2008 From: vegalew at hotmail.com (vega) Date: Fri, 29 Aug 2008 21:22:27 +0800 Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: <796688.9134.qm@web65704.mail.ac4.yahoo.com> References: <796688.9134.qm@web65704.mail.ac4.yahoo.com> Message-ID: Dear sir, thank you for your so kindly explanation. I also have some questions about your article. > As you can see we considered three FeH phases (FCC, HCP, and DHCP) and > plotted their free energies including phonon contribution with respect to > the unit cell volume. How could you get the relationship between the free energy and volume? Do you mean that you changed the cell volume sequentially and make a scf calculation to gain the free energies for the certain volume? the cell volume was grown bit by bit as your will, then the scf calculation did accordingly? and how could you get the volume as a function of pressure as fig.2 shown? what kind of QE calculation could deal with it? vega -------------------------------------------------- From: "Eyvaz Isaev" Sent: Friday, August 29, 2008 9:00 PM To: "PWSCF Forum" Subject: Re: [Pw_forum] something strange in rutile and anatase calculation > Dear Vega, > > On the left side (under pressure) first DHCP has the lowest energy, then > hcp, and finally, FCC phase is the lowest in energy. So, we stated, there > are DHCP --> HCP and HCP --> FCC phase transitons > > Hope this helps. > > Bests, > Eyvaz > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Thu, 8/28/08, vega wrote: > >> From: vega >> Subject: Re: [Pw_forum] something strange in rutile and anatase >> calculation >> To: eyvaz_isaev at yahoo.com, "PWSCF Forum" >> Date: Thursday, August 28, 2008, 6:05 PM >> Dear Eyvaz, >> >> I have read your PNAS paper just now. I'm very >> interesting about the phase >> transition mentioned in your paper. But because of lack of >> experience in >> your scopes, I'm not very clear about the detail of the >> calculations of >> phase transitions. >> In the second paragraph of Results and Discussion section, >> you said >> 'According to >> our free-energy calculations, there exist two phase >> transitions in the FeH >> system...'. How did you simulated the two phase >> transitions? How could you >> calculate the Volume as a function of Pressure as shown in >> Fig. 2? The line >> in Fig. 2 went quite smoothly, so you may not plot it point >> by point. How >> could you get the line? >> >> thank you for reading >> >> vega >> >> >> -------------------------------------------------- >> From: "Eyvaz Isaev" >> Sent: Thursday, August 28, 2008 9:25 PM >> To: "PWSCF Forum" >> Subject: Re: [Pw_forum] something strange in rutile and >> anatase calculation >> >> > Dear Vega, >> > >> > Please be not so official. I add (automatically) my >> affiliation due to our >> > accepted Netetiquette. >> > >> > Bests, >> > Eyvaz. >> > >> > >> ------------------------------------------------------------------- >> > Prof. Eyvaz Isaev, >> > Theoretical Physics Department, Moscow State Institute >> of Steel & Alloys, >> > Russia, >> > Department of Physics, Chemistry, and Biology (IFM), >> Linkoping University, >> > Sweden >> > Condensed Matter Theory Group, Uppsala University, >> Sweden >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, >> eyvaz_isaev at yahoo.com >> > >> > >> > --- On Thu, 8/28/08, vega >> wrote: >> > >> >> From: vega >> >> Subject: Re: [Pw_forum] something strange in >> rutile and anatase >> >> calculation >> >> To: eyvaz_isaev at yahoo.com, "PWSCF Forum" >> >> >> Date: Thursday, August 28, 2008, 5:08 PM >> >> Thank you for Prof. Eyvaz Isaev's hints >> >> I'll read the excellent article as your >> suggestion. >> >> It's really nice of you. >> >> >> >> vega >> >> >> >> -------------------------------------------------- >> >> From: "Eyvaz Isaev" >> >> >> Sent: Thursday, August 28, 2008 8:58 PM >> >> To: "PWSCF Forum" >> >> >> Subject: Re: [Pw_forum] something strange in >> rutile and >> >> anatase calculation >> >> >> >> > Hi, >> >> > >> >> > One more suggestion. >> >> > As far as I know the same situation is for >> \alpha >> >> and \omega phases of Ti, >> >> > as well as HCP and DHCP phases of FeH. But >> free energy >> >> calculations have >> >> > shown than \alpha-Ti and DHCP FeH are >> stabilized >> >> due to the phonon >> >> > contribution. >> >> > For FeH you can see: Eyvaz I. Isaev et al., >> Dynamical >> >> stability of Fe-H in >> >> > the Earth's mantle and core regions, >> Proceedings >> >> of the National Academy >> >> > of Sciences of the USA (PNAS), 104 (22), 29 >> May 2007, >> >> 9168. PNAS Special >> >> > Issue "Geophysics". >> >> > >> >> > So, you can try follow this way, if you like. >> >> > >> >> > Bests, >> >> > Eyvaz. >> >> > >> >> > >> >> > >> >> >> ------------------------------------------------------------------- >> >> > Prof. Eyvaz Isaev, >> >> > Theoretical Physics Department, Moscow State >> Institute >> >> of Steel & Alloys, >> >> > Russia, >> >> > Department of Physics, Chemistry, and Biology >> (IFM), >> >> Linkoping University, >> >> > Sweden >> >> > Condensed Matter Theory Group, Uppsala >> University, >> >> Sweden >> >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, >> >> eyvaz_isaev at yahoo.com >> >> > >> >> > >> >> > --- On Thu, 8/28/08, Nicola Marzari >> >> wrote: >> >> > >> >> >> From: Nicola Marzari >> >> >> >> Subject: Re: [Pw_forum] something strange >> in >> >> rutile and anatase >> >> >> calculation >> >> >> To: "PWSCF Forum" >> >> >> >> >> Date: Thursday, August 28, 2008, 3:01 PM >> >> >> vega wrote: >> >> >> > Dear all, >> >> >> > >> >> >> > It is known that the rutile is more >> stable >> >> than >> >> >> anatase in >> >> >> > thermodynamics. Surprisingly, when I >> did the >> >> vc-relax >> >> >> calculation by >> >> >> > QE, I found the calculated energy of >> anatase >> >> lower >> >> >> than rutile. Both >> >> >> > vc-relax calculation for rutile and >> anatase >> >> onverged >> >> >> in 6 scf cycles and >> >> >> > 3 bfgs steps, giving the final >> enthalpy = >> >> >> -362.7585836890 Ry for rutile >> >> >> > and -725.5447425835 Ry for antase. >> So the >> >> average >> >> >> energy of [TiO2] unit >> >> >> > is -181.3792918445 Ry for rutile and >> >> -181.386185645875 >> >> >> Ry for anatase. >> >> >> > It looks like anatase is more stable >> than >> >> rutile. Do >> >> >> you think it was >> >> >> > quite strange? >> >> >> >> >> >> >> >> >> Dear Vega, >> >> >> >> >> >> your results are probably correct. >> It's a >> >> known failure >> >> >> of LDA and GGA >> >> >> to stabilize anatase more than rutile. >> >> >> >> >> >> nicola >> >> >> >> >> >> -- >> >> >> >> >> >> --------------------------------------------------------------------- >> >> >> Prof Nicola Marzari Department of >> Materials >> >> Science and >> >> >> Engineering >> >> >> 13-5066 MIT 77 Massachusetts Avenue >> >> Cambridge MA >> >> >> 02139-4307 USA >> >> >> tel 617.4522758 fax 2586534 >> marzari at mit.edu >> >> >> http://quasiamore.mit.edu >> >> >> >> _______________________________________________ >> >> >> Pw_forum mailing list >> >> >> Pw_forum at pwscf.org >> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > >> >> > >> >> > >> >> > >> _______________________________________________ >> >> > Pw_forum mailing list >> >> > Pw_forum at pwscf.org >> >> > >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > >> >> _______________________________________________ >> >> Pw_forum mailing list >> >> Pw_forum at pwscf.org >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From anna.ferrari at unito.it Fri Aug 29 15:24:21 2008 From: anna.ferrari at unito.it (anna.ferrari at unito.it) Date: Fri, 29 Aug 2008 15:24:21 +0200 (CEST) Subject: [Pw_forum] relax In-Reply-To: <769998.95919.qm@web65706.mail.ac4.yahoo.com> References: <10093.87.9.170.15.1220008699.squirrel@mail.unito.it> <769998.95919.qm@web65706.mail.ac4.yahoo.com> Message-ID: <10290.87.9.170.15.1220016261.squirrel@mail.unito.it> the starting geometry has been alredy optimized with another code at the third step i got an increased energy and afterwards the run crashed.. can i simply change diagonalization='cg' and restart the calculation? > > > ------------------ Messaggio originale ------------------- > Oggetto: Re: [Pw_forum] relax > Da: "Eyvaz Isaev" > Data: Ven, 29 Agosto 2008, 2:52 pm > A: "PWSCF Forum" > ---------------------------------------------------------- > > Dear Anna, > > --- On Fri, 8/29/08, anna.ferrari at unito.it > wrote: > >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from davcio : error # 12 >> i/o error in davcio >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> the error in the diagonalization is connected with the >> negative charge? > > This one is really very Frequently Asked Question. Please > have look at the UserGude (Troubleshooting section). > > I do not think it is connected to small negative charge, > rather it might be connected to the structure you study. > If you are absolutely sure your structure is correct then > add diagonalization='cg' line into your script. > >> what can i do to avoid this error? > > see before. > >> thanks again > > Thanks providing your affiliation. > >> anna >> >> > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of > Steel & Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), > Linkoping University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > >> _______________________________________________ >> 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 anna.ferrari at unito.it Fri Aug 29 15:28:27 2008 From: anna.ferrari at unito.it (anna.ferrari at unito.it) Date: Fri, 29 Aug 2008 15:28:27 +0200 (CEST) Subject: [Pw_forum] (no subject) Message-ID: <10311.87.9.170.15.1220016507.squirrel@mail.unito.it> dear all what is the difference bewteen the two pseudo Ti.pw91-sp-van_ak.UPF and Ti.pw91-nsp-van_ak.UPF i see a different occupatrion in the header but i do not know what does it imply thanks again anna From hande at newton.physics.metu.edu.tr Fri Aug 29 15:38:44 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Fri, 29 Aug 2008 16:38:44 +0300 (EEST) Subject: [Pw_forum] (no subject) In-Reply-To: <10311.87.9.170.15.1220016507.squirrel@mail.unito.it> Message-ID: Dear Anna, Different occupations signify that the reference configurations with respect to which the pseudopotentials were generated were taken differently. If you would like to know more about what this means I suggest you read the documentation that comes with the generation code. The other difference is that the one that's called nsp has nonlinear core corrections while the other one doesn't. Best, Hande -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From eyvaz_isaev at yahoo.com Fri Aug 29 15:51:03 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 29 Aug 2008 06:51:03 -0700 (PDT) Subject: [Pw_forum] relax In-Reply-To: <10290.87.9.170.15.1220016261.squirrel@mail.unito.it> Message-ID: <394707.69406.qm@web65715.mail.ac4.yahoo.com> > can i simply change diagonalization='cg' and > restart the calculation? Yes, you can, of course. bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 8/29/08, anna.ferrari at unito.it wrote: > From: anna.ferrari at unito.it > Subject: Re: [Pw_forum] relax > To: eyvaz_isaev at yahoo.com, pw_forum at pwscf.org > Date: Friday, August 29, 2008, 5:24 PM > the starting geometry has been alredy optimized with > another code > at the third step i got an increased energy and afterwards > the run crashed.. > > can i simply change diagonalization='cg' and > restart the > calculation? > > > > > > > > ------------------ Messaggio originale > ------------------- > > Oggetto: Re: [Pw_forum] relax > > Da: "Eyvaz Isaev" > > > Data: Ven, 29 Agosto 2008, 2:52 pm > > A: "PWSCF Forum" > > > > ---------------------------------------------------------- > > > > Dear Anna, > > > > --- On Fri, 8/29/08, anna.ferrari at unito.it > > wrote: > > > >> > >> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >> from davcio : error # 12 > >> i/o error in davcio > >> > >> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >> > >> the error in the diagonalization is connected with > the > >> negative charge? > > > > This one is really very Frequently Asked Question. > Please > > have look at the UserGude (Troubleshooting section). > > > > I do not think it is connected to small negative > charge, > > rather it might be connected to the structure you > study. > > If you are absolutely sure your structure is correct > then > > add diagonalization='cg' line into your > script. > > > >> what can i do to avoid this error? > > > > see before. > > > >> thanks again > > > > Thanks providing your affiliation. > > > >> anna > >> > >> > > > > > ------------------------------------------------------------------- > > Prof. Eyvaz Isaev, > > Theoretical Physics Department, Moscow State Institute > of > > Steel & Alloys, Russia, > > Department of Physics, Chemistry, and Biology (IFM), > > Linkoping University, Sweden > > Condensed Matter Theory Group, Uppsala University, > Sweden > > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > > eyvaz_isaev at yahoo.com > > > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From anna.ferrari at unito.it Fri Aug 29 15:55:33 2008 From: anna.ferrari at unito.it (anna.ferrari at unito.it) Date: Fri, 29 Aug 2008 15:55:33 +0200 (CEST) Subject: [Pw_forum] (no subject) In-Reply-To: References: <10311.87.9.170.15.1220016507.squirrel@mail.unito.it> Message-ID: <10349.87.9.170.15.1220018133.squirrel@mail.unito.it> thank you i think you are right i should read more... but for the immediate i need to choose one of them and i do not know if they preform similarly or not. Maybe you can help me on this point... anna > > > ------------------ Messaggio originale ------------------- > Oggetto: Re: [Pw_forum] (no subject) > Da: "Hande Ustunel" > > Data: Ven, 29 Agosto 2008, 3:38 pm > A: "PWSCF Forum" > ---------------------------------------------------------- > > Dear Anna, > > Different occupations signify that the reference > configurations with > respect to which the pseudopotentials were generated were > taken > differently. If you would like to know more about what > this means I suggest > you read the documentation that comes with the generation > code. > > The other difference is that the one that's called nsp has > nonlinear core > corrections while the other one doesn't. > > Best, > Hande > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From anna.ferrari at unito.it Fri Aug 29 15:57:55 2008 From: anna.ferrari at unito.it (anna.ferrari at unito.it) Date: Fri, 29 Aug 2008 15:57:55 +0200 (CEST) Subject: [Pw_forum] relax In-Reply-To: References: <10093.87.9.170.15.1220008699.squirrel@mail.unito.it> Message-ID: <10362.87.9.170.15.1220018275.squirrel@mail.unito.it> you are right i exeed the disk space on one of the nodes I used I checked just now sorry... bye anna > > > ------------------ Messaggio originale ------------------- > Oggetto: Re: [Pw_forum] relax > Da: "Paolo Giannozzi" > Data: Ven, 29 Agosto 2008, 3:09 pm > A: "PWSCF Forum" > ---------------------------------------------------------- > > > On Aug 29, 2008, at 13:18 , anna.ferrari at unito.it wrote: > >> from davcio : error # 12 >> i/o error in davcio >> >> the error in the diagonalization is connected with the >> negative >> charge? > > there is no error in the diagonalization. The error is in > I/O and > means that > the code encountered an unexpected condition, in which it > tried to read > data from a nonexistent or empty or corrupted file, or to > read data > in an > incompatible format. It may happen especially if you are > trying to > restart > from a previous run. > >> what can i do to avoid this error? > > there shouldn't be any such error if you do things > properly (and if > the disks > of your machine work properly) > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From eyvaz_isaev at yahoo.com Fri Aug 29 15:59:58 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 29 Aug 2008 06:59:58 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: <10311.87.9.170.15.1220016507.squirrel@mail.unito.it> Message-ID: <143360.79840.qm@web65712.mail.ac4.yahoo.com> >what is the difference bewteen the two pseudo > Ti.pw91-sp-van_ak.UPF and Ti.pw91-nsp-van_ak.UPF sp- semi-core s and p electrons are considered as valence ones n- in addition, non-linear core correction is included. van- Vanderbilt type ultrasoft pseudopotetial ak- thanks Axel Kohlmeyer. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 8/29/08, anna.ferrari at unito.it wrote: > From: anna.ferrari at unito.it > Subject: [Pw_forum] (no subject) > To: pw_forum at pwscf.org > Date: Friday, August 29, 2008, 5:28 PM > dear all > what is the difference bewteen the two pseudo > > > Ti.pw91-sp-van_ak.UPF > and > Ti.pw91-nsp-van_ak.UPF > > i see a different occupatrion in the header but i do not > know what does it imply > > > thanks again > anna > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From anna.ferrari at unito.it Fri Aug 29 16:07:27 2008 From: anna.ferrari at unito.it (anna.ferrari at unito.it) Date: Fri, 29 Aug 2008 16:07:27 +0200 (CEST) Subject: [Pw_forum] (no subject) In-Reply-To: <143360.79840.qm@web65712.mail.ac4.yahoo.com> References: <10311.87.9.170.15.1220016507.squirrel@mail.unito.it> <143360.79840.qm@web65712.mail.ac4.yahoo.com> Message-ID: <10412.87.9.170.15.1220018847.squirrel@mail.unito.it> so this combination is accetable? O 15.9994 O.pw91-van_ak.UPF CU 63.54 Cu.pw91-n-van_ak.UPF TI 47.90 Ti.pw91-nsp-van.UPF ???? > > > ------------------ Messaggio originale ------------------- > Oggetto: Re: [Pw_forum] (no subject) > Da: "Eyvaz Isaev" > Data: Ven, 29 Agosto 2008, 3:59 pm > A: "PWSCF Forum" > ---------------------------------------------------------- > >>what is the difference bewteen the two pseudo >> Ti.pw91-sp-van_ak.UPF and Ti.pw91-nsp-van_ak.UPF > > sp- semi-core s and p electrons are considered as valence > ones > > n- in addition, non-linear core correction is included. > > van- Vanderbilt type ultrasoft pseudopotetial > > ak- thanks Axel Kohlmeyer. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of > Steel & Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), > Linkoping University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > > > --- On Fri, 8/29/08, anna.ferrari at unito.it > wrote: > >> From: anna.ferrari at unito.it >> Subject: [Pw_forum] (no subject) >> To: pw_forum at pwscf.org >> Date: Friday, August 29, 2008, 5:28 PM >> dear all >> what is the difference bewteen the two pseudo >> >> >> Ti.pw91-sp-van_ak.UPF >> and >> Ti.pw91-nsp-van_ak.UPF >> >> i see a different occupatrion in the header but i do not >> know what does it imply >> >> >> thanks again >> anna >> _______________________________________________ >> 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 anna.ferrari at unito.it Fri Aug 29 16:07:49 2008 From: anna.ferrari at unito.it (anna.ferrari at unito.it) Date: Fri, 29 Aug 2008 16:07:49 +0200 (CEST) Subject: [Pw_forum] (pseudo) In-Reply-To: <143360.79840.qm@web65712.mail.ac4.yahoo.com> References: <10311.87.9.170.15.1220016507.squirrel@mail.unito.it> <143360.79840.qm@web65712.mail.ac4.yahoo.com> Message-ID: <10417.87.9.170.15.1220018869.squirrel@mail.unito.it> > > > ------------------ Messaggio originale ------------------- > Oggetto: Re: [Pw_forum] (no subject) > Da: "Eyvaz Isaev" > Data: Ven, 29 Agosto 2008, 3:59 pm > A: "PWSCF Forum" > ---------------------------------------------------------- > >>what is the difference bewteen the two pseudo >> Ti.pw91-sp-van_ak.UPF and Ti.pw91-nsp-van_ak.UPF > > sp- semi-core s and p electrons are considered as valence > ones > > n- in addition, non-linear core correction is included. > > van- Vanderbilt type ultrasoft pseudopotetial > > ak- thanks Axel Kohlmeyer. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of > Steel & Alloys, Russia, > Department of Physics, Chemistry, and Biology (IFM), > Linkoping University, Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > > > --- On Fri, 8/29/08, anna.ferrari at unito.it > wrote: > >> From: anna.ferrari at unito.it >> Subject: [Pw_forum] (no subject) >> To: pw_forum at pwscf.org >> Date: Friday, August 29, 2008, 5:28 PM >> dear all >> what is the difference bewteen the two pseudo >> >> >> Ti.pw91-sp-van_ak.UPF >> and >> Ti.pw91-nsp-van_ak.UPF >> >> i see a different occupatrion in the header but i do not >> know what does it imply >> >> >> thanks again >> anna >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From eyvaz_isaev at yahoo.com Fri Aug 29 16:10:39 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 29 Aug 2008 07:10:39 -0700 (PDT) Subject: [Pw_forum] relax In-Reply-To: Message-ID: <275480.57423.qm@web65703.mail.ac4.yahoo.com> Thanks, Stefano, actually I have mixed up the davcio error message with "pw.x stops with error in cdiaghg or rdiaghg". Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 8/29/08, Paolo Giannozzi wrote: > From: Paolo Giannozzi > Subject: Re: [Pw_forum] relax > To: "PWSCF Forum" > Date: Friday, August 29, 2008, 5:09 PM > On Aug 29, 2008, at 13:18 , anna.ferrari at unito.it wrote: > > > from davcio : error # 12 > > i/o error in davcio > > > > the error in the diagonalization is connected with > the negative > > charge? > > there is no error in the diagonalization. The error is in > I/O and > means that > the code encountered an unexpected condition, in which it > tried to read > data from a nonexistent or empty or corrupted file, or to > read data > in an > incompatible format. It may happen especially if you are > trying to > restart > from a previous run. > > > what can i do to avoid this error? > > there shouldn't be any such error if you do things > properly (and if > the disks > of your machine work properly) > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From hande at newton.physics.metu.edu.tr Fri Aug 29 16:11:45 2008 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Fri, 29 Aug 2008 17:11:45 +0300 (EEST) Subject: [Pw_forum] (no subject) In-Reply-To: <10349.87.9.170.15.1220018133.squirrel@mail.unito.it> Message-ID: Dear Anna, The usual preliminary work that you should do before going into production runs is to try to reproduce some experimental/previously published theoretical results using the pseudopotentials you are interested in and trying to see which one does better. The data you could reproduce includes (but is definitely not limited to) bulk moduli, lattice constants, band structures, phonon mode frequencies, properties of compounds etc. For bare Ti, you might be hard-pressed to find data so perhaps something like TiO or TiO2 properties would make your life easier. Best, Hande -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From giannozz at democritos.it Fri Aug 29 16:39:52 2008 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 29 Aug 2008 16:39:52 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <10412.87.9.170.15.1220018847.squirrel@mail.unito.it> References: <10311.87.9.170.15.1220016507.squirrel@mail.unito.it> <143360.79840.qm@web65712.mail.ac4.yahoo.com> <10412.87.9.170.15.1220018847.squirrel@mail.unito.it> Message-ID: <48B80A38.8090707@democritos.it> anna.ferrari at unito.it wrote: > so this combination is accetable? > > O 15.9994 O.pw91-van_ak.UPF > CU 63.54 Cu.pw91-n-van_ak.UPF > TI 47.90 Ti.pw91-nsp-van.UPF > > ???? pseudopotentials of different kinds - but not of different functionals - can be mixed, so in this respect any "combination" is acceptable. Whether it will fit your needs, it depends (in particular, it depends upon what your needs are!). In principle this choice should be fine, within the accuracy of the chosen exchange-correlation functional, but in practise you should always perform a few checks on simple systems for which independent data is available Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From eyvaz_isaev at yahoo.com Fri Aug 29 16:45:22 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 29 Aug 2008 07:45:22 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: <10412.87.9.170.15.1220018847.squirrel@mail.unito.it> Message-ID: <300034.16831.qm@web65705.mail.ac4.yahoo.com> --- On Fri, 8/29/08, anna.ferrari at unito.it wrote: > so this combination is accetable? > > O 15.9994 O.pw91-van_ak.UPF > CU 63.54 Cu.pw91-n-van_ak.UPF > TI 47.90 Ti.pw91-nsp-van.UPF > ???? > The combination is acceptable from the point of view that you will not receive a message like "DFT's are incompatible". But no one can guarantee that final results will be OK. As Hande said you should do some simple tests using these PsPs before studying of a complex system. As you have Oxygen in your system, it seems, it might be more complicated (like strongly correlated systems). Bests, Eyvaz. > > > > > > > ------------------ Messaggio originale > ------------------- > > Oggetto: Re: [Pw_forum] (no subject) > > Da: "Eyvaz Isaev" > > > Data: Ven, 29 Agosto 2008, 3:59 pm > > A: "PWSCF Forum" > > > > ---------------------------------------------------------- > > > >>what is the difference bewteen the two pseudo > >> Ti.pw91-sp-van_ak.UPF and Ti.pw91-nsp-van_ak.UPF > > > > sp- semi-core s and p electrons are considered as > valence > > ones > > > > n- in addition, non-linear core correction is > included. > > > > van- Vanderbilt type ultrasoft pseudopotetial > > > > ak- thanks Axel Kohlmeyer. > > > > Bests, > > Eyvaz. > > > > > ------------------------------------------------------------------- > > Prof. Eyvaz Isaev, > > Theoretical Physics Department, Moscow State Institute > of > > Steel & Alloys, Russia, > > Department of Physics, Chemistry, and Biology (IFM), > > Linkoping University, Sweden > > Condensed Matter Theory Group, Uppsala University, > Sweden > > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > > eyvaz_isaev at yahoo.com > > > > > > --- On Fri, 8/29/08, anna.ferrari at unito.it > > wrote: > > > >> From: anna.ferrari at unito.it > > >> Subject: [Pw_forum] (no subject) > >> To: pw_forum at pwscf.org > >> Date: Friday, August 29, 2008, 5:28 PM > >> dear all > >> what is the difference bewteen the two pseudo > >> > >> > >> Ti.pw91-sp-van_ak.UPF > >> and > >> Ti.pw91-nsp-van_ak.UPF > >> > >> i see a different occupatrion in the header but i > do not > >> know what does it imply > >> > >> > >> thanks again > >> anna > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Fri Aug 29 17:23:30 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 29 Aug 2008 08:23:30 -0700 (PDT) Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: Message-ID: <602117.48404.qm@web65705.mail.ac4.yahoo.com> Dear Vega, --- On Fri, 8/29/08, vega wrote: > How could you get the relationship between the free > energy and volume? Do you mean that you changed the > cell volume sequentially and make a scf > calculation to gain the free energies for the certain > volume? the cell volume was grown bit by bit as > your will, then the scf calculation did accordingly? > We calculated total energy and phonons (then free energy) for a given set of volumes. > and how could you get the volume as a function of > pressure as fig.2 shown? > what kind of QE calculation could deal with it? > If you set up tstress=.true. you can find what is a stress (and pressure) in your system. Again, for a given set of the unit cell volumes. Sometime only a SCF calculation is enough, but sometime, especially for non-cubic systems, you can fix pressure and relax your system. Bests, Eyvaz. > vega > > -------------------------------------------------- > From: "Eyvaz Isaev" > Sent: Friday, August 29, 2008 9:00 PM > To: "PWSCF Forum" > Subject: Re: [Pw_forum] something strange in rutile and > anatase calculation > > > Dear Vega, > > > > > On the left side (under pressure) first DHCP has the > lowest energy, then > > hcp, and finally, FCC phase is the lowest in energy. > So, we stated, there > > are DHCP --> HCP and HCP --> FCC phase > transitons > > > > Hope this helps. > > > > Bests, > > Eyvaz > > > > > ------------------------------------------------------------------- > > Prof. Eyvaz Isaev, > > Theoretical Physics Department, Moscow State Institute > of Steel & Alloys, > > Russia, > > Department of Physics, Chemistry, and Biology (IFM), > Linkoping University, > > Sweden > > Condensed Matter Theory Group, Uppsala University, > Sweden > > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > eyvaz_isaev at yahoo.com > > > > > > --- On Thu, 8/28/08, vega > wrote: > > > >> From: vega > >> Subject: Re: [Pw_forum] something strange in > rutile and anatase > >> calculation > >> To: eyvaz_isaev at yahoo.com, "PWSCF Forum" > > >> Date: Thursday, August 28, 2008, 6:05 PM > >> Dear Eyvaz, > >> > >> I have read your PNAS paper just now. I'm very > >> interesting about the phase > >> transition mentioned in your paper. But because of > lack of > >> experience in > >> your scopes, I'm not very clear about the > detail of the > >> calculations of > >> phase transitions. > >> In the second paragraph of Results and Discussion > section, > >> you said > >> 'According to > >> our free-energy calculations, there exist two > phase > >> transitions in the FeH > >> system...'. How did you simulated the two > phase > >> transitions? How could you > >> calculate the Volume as a function of Pressure as > shown in > >> Fig. 2? The line > >> in Fig. 2 went quite smoothly, so you may not plot > it point > >> by point. How > >> could you get the line? > >> > >> thank you for reading > >> > >> vega > >> > >> > >> -------------------------------------------------- > >> From: "Eyvaz Isaev" > > >> Sent: Thursday, August 28, 2008 9:25 PM > >> To: "PWSCF Forum" > > >> Subject: Re: [Pw_forum] something strange in > rutile and > >> anatase calculation > >> > >> > Dear Vega, > >> > > >> > Please be not so official. I add > (automatically) my > >> affiliation due to our > >> > accepted Netetiquette. > >> > > >> > Bests, > >> > Eyvaz. > >> > > >> > > >> > ------------------------------------------------------------------- > >> > Prof. Eyvaz Isaev, > >> > Theoretical Physics Department, Moscow State > Institute > >> of Steel & Alloys, > >> > Russia, > >> > Department of Physics, Chemistry, and Biology > (IFM), > >> Linkoping University, > >> > Sweden > >> > Condensed Matter Theory Group, Uppsala > University, > >> Sweden > >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, > >> eyvaz_isaev at yahoo.com > >> > > >> > > >> > --- On Thu, 8/28/08, vega > > >> wrote: > >> > > >> >> From: vega > >> >> Subject: Re: [Pw_forum] something strange > in > >> rutile and anatase > >> >> calculation > >> >> To: eyvaz_isaev at yahoo.com, "PWSCF > Forum" > >> > >> >> Date: Thursday, August 28, 2008, 5:08 PM > >> >> Thank you for Prof. Eyvaz Isaev's > hints > >> >> I'll read the excellent article as > your > >> suggestion. > >> >> It's really nice of you. > >> >> > >> >> vega > >> >> > >> >> > -------------------------------------------------- > >> >> From: "Eyvaz Isaev" > >> > >> >> Sent: Thursday, August 28, 2008 8:58 PM > >> >> To: "PWSCF Forum" > >> > >> >> Subject: Re: [Pw_forum] something strange > in > >> rutile and > >> >> anatase calculation > >> >> > >> >> > Hi, > >> >> > > >> >> > One more suggestion. > >> >> > As far as I know the same situation > is for > >> \alpha > >> >> and \omega phases of Ti, > >> >> > as well as HCP and DHCP phases of > FeH. But > >> free energy > >> >> calculations have > >> >> > shown than \alpha-Ti and DHCP > FeH are > >> stabilized > >> >> due to the phonon > >> >> > contribution. > >> >> > For FeH you can see: Eyvaz I. Isaev > et al., > >> Dynamical > >> >> stability of Fe-H in > >> >> > the Earth's mantle and core > regions, > >> Proceedings > >> >> of the National Academy > >> >> > of Sciences of the USA (PNAS), 104 > (22), 29 > >> May 2007, > >> >> 9168. PNAS Special > >> >> > Issue "Geophysics". > >> >> > > >> >> > So, you can try follow this way, if > you like. > >> >> > > >> >> > Bests, > >> >> > Eyvaz. > >> >> > > >> >> > > >> >> > > >> >> > >> > ------------------------------------------------------------------- > >> >> > Prof. Eyvaz Isaev, > >> >> > Theoretical Physics Department, > Moscow State > >> Institute > >> >> of Steel & Alloys, > >> >> > Russia, > >> >> > Department of Physics, Chemistry, > and Biology > >> (IFM), > >> >> Linkoping University, > >> >> > Sweden > >> >> > Condensed Matter Theory Group, > Uppsala > >> University, > >> >> Sweden > >> >> > Eyvaz.Isaev at fysik.uu.se, > isaev at ifm.liu.se, > >> >> eyvaz_isaev at yahoo.com > >> >> > > >> >> > > >> >> > --- On Thu, 8/28/08, Nicola Marzari > >> >> wrote: > >> >> > > >> >> >> From: Nicola Marzari > >> > >> >> >> Subject: Re: [Pw_forum] > something strange > >> in > >> >> rutile and anatase > >> >> >> calculation > >> >> >> To: "PWSCF Forum" > >> >> > >> >> >> Date: Thursday, August 28, 2008, > 3:01 PM > >> >> >> vega wrote: > >> >> >> > Dear all, > >> >> >> > > >> >> >> > It is known that the rutile > is more > >> stable > >> >> than > >> >> >> anatase in > >> >> >> > thermodynamics. > Surprisingly, when I > >> did the > >> >> vc-relax > >> >> >> calculation by > >> >> >> > QE, I found the calculated > energy of > >> anatase > >> >> lower > >> >> >> than rutile. Both > >> >> >> > vc-relax calculation for > rutile and > >> anatase > >> >> onverged > >> >> >> in 6 scf cycles and > >> >> >> > 3 bfgs steps, giving the > final > >> enthalpy = > >> >> >> -362.7585836890 Ry for rutile > >> >> >> > and -725.5447425835 Ry for > antase. > >> So the > >> >> average > >> >> >> energy of [TiO2] unit > >> >> >> > is -181.3792918445 Ry for > rutile and > >> >> -181.386185645875 > >> >> >> Ry for anatase. > >> >> >> > It looks like anatase is > more stable > >> than > >> >> rutile. Do > >> >> >> you think it was > >> >> >> > quite strange? > >> >> >> > >> >> >> > >> >> >> Dear Vega, > >> >> >> > >> >> >> your results are probably > correct. > >> It's a > >> >> known failure > >> >> >> of LDA and GGA > >> >> >> to stabilize anatase more than > rutile. > >> >> >> > >> >> >> nicola > >> >> >> > >> >> >> -- > >> >> >> > >> >> > >> > --------------------------------------------------------------------- > >> >> >> Prof Nicola Marzari Department > of > >> Materials > >> >> Science and > >> >> >> Engineering > >> >> >> 13-5066 MIT 77 Massachusetts > Avenue > >> >> Cambridge MA > >> >> >> 02139-4307 USA > >> >> >> tel 617.4522758 fax 2586534 > >> marzari at mit.edu > >> >> >> http://quasiamore.mit.edu > >> >> >> > >> _______________________________________________ > >> >> >> Pw_forum mailing list > >> >> >> Pw_forum at pwscf.org > >> >> >> > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> >> > > >> >> > > >> >> > > >> >> > > >> _______________________________________________ > >> >> > Pw_forum mailing list > >> >> > Pw_forum at pwscf.org > >> >> > > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> >> > > >> >> > _______________________________________________ > >> >> Pw_forum mailing list > >> >> Pw_forum at pwscf.org > >> >> > http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> > > >> > > >> > > _______________________________________________ > >> > Pw_forum mailing list > >> > Pw_forum at pwscf.org > >> > > http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > _______________________________________________ > > 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 vegalew at hotmail.com Fri Aug 29 17:26:36 2008 From: vegalew at hotmail.com (vega) Date: Fri, 29 Aug 2008 23:26:36 +0800 Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: <602117.48404.qm@web65705.mail.ac4.yahoo.com> References: <602117.48404.qm@web65705.mail.ac4.yahoo.com> Message-ID: Dear sir, thank you for your time. Now I'm more clear about the matter. best wishes, vega ================================================================================= Vega Lew (weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China -------------------------------------------------- From: "Eyvaz Isaev" Sent: Friday, August 29, 2008 11:23 PM To: "PWSCF Forum" Subject: Re: [Pw_forum] something strange in rutile and anatase calculation > Dear Vega, > > --- On Fri, 8/29/08, vega wrote: > >> How could you get the relationship between the free >> energy and volume? Do you mean that you changed the >> cell volume sequentially and make a scf >> calculation to gain the free energies for the certain >> volume? the cell volume was grown bit by bit as >> your will, then the scf calculation did accordingly? >> > > We calculated total energy and phonons (then free energy) for a given set > of volumes. > >> and how could you get the volume as a function of > pressure as fig.2 >> shown? >> what kind of QE calculation could deal with it? >> > If you set up tstress=.true. you can find what is a stress (and pressure) > in your system. Again, for a given set of the unit cell volumes. Sometime > only a SCF calculation is enough, but sometime, especially for non-cubic > systems, you can fix pressure and relax your system. > > Bests, > Eyvaz. > >> vega >> >> -------------------------------------------------- >> From: "Eyvaz Isaev" >> Sent: Friday, August 29, 2008 9:00 PM >> To: "PWSCF Forum" >> Subject: Re: [Pw_forum] something strange in rutile and >> anatase calculation >> >> > Dear Vega, >> > >> >> > On the left side (under pressure) first DHCP has the >> lowest energy, then >> > hcp, and finally, FCC phase is the lowest in energy. >> So, we stated, there >> > are DHCP --> HCP and HCP --> FCC phase >> transitons >> > >> > Hope this helps. >> > >> > Bests, >> > Eyvaz >> > >> > >> ------------------------------------------------------------------- >> > Prof. Eyvaz Isaev, >> > Theoretical Physics Department, Moscow State Institute >> of Steel & Alloys, >> > Russia, >> > Department of Physics, Chemistry, and Biology (IFM), >> Linkoping University, >> > Sweden >> > Condensed Matter Theory Group, Uppsala University, >> Sweden >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, >> eyvaz_isaev at yahoo.com >> > >> > >> > --- On Thu, 8/28/08, vega >> wrote: >> > >> >> From: vega >> >> Subject: Re: [Pw_forum] something strange in >> rutile and anatase >> >> calculation >> >> To: eyvaz_isaev at yahoo.com, "PWSCF Forum" >> >> >> Date: Thursday, August 28, 2008, 6:05 PM >> >> Dear Eyvaz, >> >> >> >> I have read your PNAS paper just now. I'm very >> >> interesting about the phase >> >> transition mentioned in your paper. But because of >> lack of >> >> experience in >> >> your scopes, I'm not very clear about the >> detail of the >> >> calculations of >> >> phase transitions. >> >> In the second paragraph of Results and Discussion >> section, >> >> you said >> >> 'According to >> >> our free-energy calculations, there exist two >> phase >> >> transitions in the FeH >> >> system...'. How did you simulated the two >> phase >> >> transitions? How could you >> >> calculate the Volume as a function of Pressure as >> shown in >> >> Fig. 2? The line >> >> in Fig. 2 went quite smoothly, so you may not plot >> it point >> >> by point. How >> >> could you get the line? >> >> >> >> thank you for reading >> >> >> >> vega >> >> >> >> >> >> -------------------------------------------------- >> >> From: "Eyvaz Isaev" >> >> >> Sent: Thursday, August 28, 2008 9:25 PM >> >> To: "PWSCF Forum" >> >> >> Subject: Re: [Pw_forum] something strange in >> rutile and >> >> anatase calculation >> >> >> >> > Dear Vega, >> >> > >> >> > Please be not so official. I add >> (automatically) my >> >> affiliation due to our >> >> > accepted Netetiquette. >> >> > >> >> > Bests, >> >> > Eyvaz. >> >> > >> >> > >> >> >> ------------------------------------------------------------------- >> >> > Prof. Eyvaz Isaev, >> >> > Theoretical Physics Department, Moscow State >> Institute >> >> of Steel & Alloys, >> >> > Russia, >> >> > Department of Physics, Chemistry, and Biology >> (IFM), >> >> Linkoping University, >> >> > Sweden >> >> > Condensed Matter Theory Group, Uppsala >> University, >> >> Sweden >> >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, >> >> eyvaz_isaev at yahoo.com >> >> > >> >> > >> >> > --- On Thu, 8/28/08, vega >> >> >> wrote: >> >> > >> >> >> From: vega >> >> >> Subject: Re: [Pw_forum] something strange >> in >> >> rutile and anatase >> >> >> calculation >> >> >> To: eyvaz_isaev at yahoo.com, "PWSCF >> Forum" >> >> >> >> >> Date: Thursday, August 28, 2008, 5:08 PM >> >> >> Thank you for Prof. Eyvaz Isaev's >> hints >> >> >> I'll read the excellent article as >> your >> >> suggestion. >> >> >> It's really nice of you. >> >> >> >> >> >> vega >> >> >> >> >> >> >> -------------------------------------------------- >> >> >> From: "Eyvaz Isaev" >> >> >> >> >> Sent: Thursday, August 28, 2008 8:58 PM >> >> >> To: "PWSCF Forum" >> >> >> >> >> Subject: Re: [Pw_forum] something strange >> in >> >> rutile and >> >> >> anatase calculation >> >> >> >> >> >> > Hi, >> >> >> > >> >> >> > One more suggestion. >> >> >> > As far as I know the same situation >> is for >> >> \alpha >> >> >> and \omega phases of Ti, >> >> >> > as well as HCP and DHCP phases of >> FeH. But >> >> free energy >> >> >> calculations have >> >> >> > shown than \alpha-Ti and DHCP >> FeH are >> >> stabilized >> >> >> due to the phonon >> >> >> > contribution. >> >> >> > For FeH you can see: Eyvaz I. Isaev >> et al., >> >> Dynamical >> >> >> stability of Fe-H in >> >> >> > the Earth's mantle and core >> regions, >> >> Proceedings >> >> >> of the National Academy >> >> >> > of Sciences of the USA (PNAS), 104 >> (22), 29 >> >> May 2007, >> >> >> 9168. PNAS Special >> >> >> > Issue "Geophysics". >> >> >> > >> >> >> > So, you can try follow this way, if >> you like. >> >> >> > >> >> >> > Bests, >> >> >> > Eyvaz. >> >> >> > >> >> >> > >> >> >> > >> >> >> >> >> >> ------------------------------------------------------------------- >> >> >> > Prof. Eyvaz Isaev, >> >> >> > Theoretical Physics Department, >> Moscow State >> >> Institute >> >> >> of Steel & Alloys, >> >> >> > Russia, >> >> >> > Department of Physics, Chemistry, >> and Biology >> >> (IFM), >> >> >> Linkoping University, >> >> >> > Sweden >> >> >> > Condensed Matter Theory Group, >> Uppsala >> >> University, >> >> >> Sweden >> >> >> > Eyvaz.Isaev at fysik.uu.se, >> isaev at ifm.liu.se, >> >> >> eyvaz_isaev at yahoo.com >> >> >> > >> >> >> > >> >> >> > --- On Thu, 8/28/08, Nicola Marzari >> >> >> wrote: >> >> >> > >> >> >> >> From: Nicola Marzari >> >> >> >> >> >> Subject: Re: [Pw_forum] >> something strange >> >> in >> >> >> rutile and anatase >> >> >> >> calculation >> >> >> >> To: "PWSCF Forum" >> >> >> >> >> >> >> Date: Thursday, August 28, 2008, >> 3:01 PM >> >> >> >> vega wrote: >> >> >> >> > Dear all, >> >> >> >> > >> >> >> >> > It is known that the rutile >> is more >> >> stable >> >> >> than >> >> >> >> anatase in >> >> >> >> > thermodynamics. >> Surprisingly, when I >> >> did the >> >> >> vc-relax >> >> >> >> calculation by >> >> >> >> > QE, I found the calculated >> energy of >> >> anatase >> >> >> lower >> >> >> >> than rutile. Both >> >> >> >> > vc-relax calculation for >> rutile and >> >> anatase >> >> >> onverged >> >> >> >> in 6 scf cycles and >> >> >> >> > 3 bfgs steps, giving the >> final >> >> enthalpy = >> >> >> >> -362.7585836890 Ry for rutile >> >> >> >> > and -725.5447425835 Ry for >> antase. >> >> So the >> >> >> average >> >> >> >> energy of [TiO2] unit >> >> >> >> > is -181.3792918445 Ry for >> rutile and >> >> >> -181.386185645875 >> >> >> >> Ry for anatase. >> >> >> >> > It looks like anatase is >> more stable >> >> than >> >> >> rutile. Do >> >> >> >> you think it was >> >> >> >> > quite strange? >> >> >> >> >> >> >> >> >> >> >> >> Dear Vega, >> >> >> >> >> >> >> >> your results are probably >> correct. >> >> It's a >> >> >> known failure >> >> >> >> of LDA and GGA >> >> >> >> to stabilize anatase more than >> rutile. >> >> >> >> >> >> >> >> nicola >> >> >> >> >> >> >> >> -- >> >> >> >> >> >> >> >> >> >> --------------------------------------------------------------------- >> >> >> >> Prof Nicola Marzari Department >> of >> >> Materials >> >> >> Science and >> >> >> >> Engineering >> >> >> >> 13-5066 MIT 77 Massachusetts >> Avenue >> >> >> Cambridge MA >> >> >> >> 02139-4307 USA >> >> >> >> tel 617.4522758 fax 2586534 >> >> marzari at mit.edu >> >> >> >> http://quasiamore.mit.edu >> >> >> >> >> >> _______________________________________________ >> >> >> >> Pw_forum mailing list >> >> >> >> Pw_forum at pwscf.org >> >> >> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> _______________________________________________ >> >> >> > Pw_forum mailing list >> >> >> > Pw_forum at pwscf.org >> >> >> > >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> > >> >> >> >> _______________________________________________ >> >> >> Pw_forum mailing list >> >> >> Pw_forum at pwscf.org >> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > >> >> > >> >> > >> >> > >> _______________________________________________ >> >> > Pw_forum mailing list >> >> > Pw_forum at pwscf.org >> >> > >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > >> >> _______________________________________________ >> >> Pw_forum mailing list >> >> Pw_forum at pwscf.org >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From willykohn at gmail.com Fri Aug 29 20:02:56 2008 From: willykohn at gmail.com (willy kohn) Date: Fri, 29 Aug 2008 14:02:56 -0400 Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: References: Message-ID: <8a1b6d820808291102n4c099becwdf7cebf717e545b3@mail.gmail.com> Hi, Vega: A recent result (Jpn. J. Appl. Phys. 39 (2000) L847) showed that different pseudopotential leaded to different conclusions. Best, Wei On Thu, Aug 28, 2008 at 4:28 AM, vega wrote: > Dear all, > > It is known that the rutile is more stable than anatase in thermodynamics. > Surprisingly, when I did the vc-relax calculation by QE, I found > the calculated energy of anatase lower than rutile. Both vc-relax > calculation for rutile and anatase onverged in 6 scf cycles and 3 bfgs > steps, giving the final enthalpy = -362.7585836890 Ry for rutile and > -725.5447425835 Ry for antase. So the average energy of [TiO2] unit > is -181.3792918445 Ry for rutile and -181.386185645875 Ry for anatase. It > looks like anatase is more stable than rutile. Do you think it was quite > strange? > > To make the calculation both for anatase and rutile comparable, I used the > same ecutwfc=40 Ry and ecutwfc=400 Ry, and a quite dense k-point mesh for > both case, 4x4x7 for rutile and 5x5x2 for anatase. > > for better understanding in my calculation, please read the input file > below, > for anatase case, > &CONTROL > title = 'Anatase lattice' , > calculation = 'vc-relax' , > restart_mode = 'from_scratch' , > outdir = > '/home/hjfeng/vega/TiO2/Anatase/lattice/vctest/tmp/' , > wfcdir = '/tmp/' , > pseudo_dir = '/home/hjfeng/vega/espresso-4.0/pseudo/' , > prefix = 'Anatase lattice' , > disk_io = 'none' , > nstep = 1000 , > / > &SYSTEM > ibrav = 6, > celldm(1) = 7.1356, > celldm(3) = 2.5122, > nat = 12, > ntyp = 2, > ecutwfc = 40 , > ecutrho = 400 , > / > &ELECTRONS > > / > &IONS > ion_dynamics = 'bfgs' , > / > &CELL > cell_dynamics = 'bfgs' , > / > ATOMIC_SPECIES > Ti 47.86700 Ti.pw91-sp-van_ak.UPF > O 15.99940 O.pw91-van_ak.UPF > ATOMIC_POSITIONS crystal > Ti 0.000000000 0.000000000 0.000000000 > Ti 0.500000000 0.500000000 0.500000000 > Ti 0.000000000 0.500000000 0.250000000 > Ti 0.500000000 0.000000000 0.750000000 > O 0.000000000 0.500000000 0.042000000 > O 0.000000000 0.000000000 0.208000000 > O 0.500000000 0.500000000 0.292000000 > O 0.000000000 0.500000000 0.458000000 > O 0.500000000 0.000000000 0.542000000 > O 0.500000000 0.500000000 0.708000000 > O 0.000000000 0.000000000 0.792000000 > O 0.500000000 1.000000000 0.958000000 > K_POINTS automatic > 5 5 2 1 1 1 > > for rutile case, > > &CONTROL > title = Rutile_lattice , > calculation = 'vc-relax' , > restart_mode = 'from_scratch' , > outdir = > '/home/vega32/TiO2/rutile/lattice/vcrelax/tmp' , > wfcdir = '/tmp/' , > pseudo_dir = '/home/vega32/espresso-4.0.1/pseudo/' , > prefix = 'Anatase lattice' , > disk_io = 'none' , > nstep = 1000 , > / > &SYSTEM > ibrav = 6, > celldm(1) = 8.6814, > celldm(3) = 0.6441, > nat = 6, > ntyp = 2, > ecutwfc = 40 , > ecutrho = 400 , > / > &ELECTRONS > > / > &IONS > ion_dynamics = 'bfgs' , > / > &CELL > cell_dynamics = 'bfgs' , > / > ATOMIC_SPECIES > O 15.99940 O.pw91-van_ak.UPF > Ti 47.90000 Ti.pw91-sp-van_ak.UPF > ATOMIC_POSITIONS crystal > O 0.304800000 0.304800000 0.000000000 > O 0.695200000 0.695200000 0.000000000 > O 0.195200000 0.804800000 0.500000000 > O 0.804800000 0.195200000 0.500000000 > Ti 0.500000000 0.500000000 0.500000000 > Ti 0.000000000 0.000000000 0.000000000 > K_POINTS automatic > 4 4 7 1 1 1 > > vega > > ============================================================== > Vega Lew ( weijia liu) > PH.D Candidate in Chemical Engineering > State Key Laboratory of Materials-oriented Chemical Engineering > College of Chemistry and Chemical Engineering > Nanjing University of Technology, 210009, Nanjing, Jiangsu, China > > _______________________________________________ > 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/20080829/5a31d55d/attachment.htm From manoj at phys.ufl.edu Fri Aug 29 23:04:48 2008 From: manoj at phys.ufl.edu (Manoj Srivastava) Date: Fri, 29 Aug 2008 17:04:48 -0400 (EDT) Subject: [Pw_forum] question about complex band code Message-ID: Dear Alexander and PWSCF users, I have a question about the subroutine PWCOND of PWSCF, which calculates complex bands. We are solving the generalized eigen value problem, A X=exp(ikd) B X, where A and B and are required matrices. After the problem is solved the information about k, which is complex eigen value is stored in band.re , band.im and band.co files, and as the name suggests they are purely real, purely imaginary and complex eigenvalues, respectively. Generally, for each fixed energy we get few k's either real or imaginary or both. My question is about calculation of this complex eigen value. Total no. of k we get from solving above GEP should be equal to the number of basis used to describe A or B. I believe the information of k is contained in kval(:) array defined in the compbs_2 subroutine of PWCOND. When I print it out, I do get total number of k's which are same as the total number of basis vectors. This is not the case with bands.re, bands.im or bands.co files. For each energy value they have arbitrary number of k's, why is it so? What makes it throw some k values that it gets from 'kval'? I think, I am missing something when the code goes from 'kval(:)' to bands.re, bands.im and bands.co files. Does someone have any idea how does the code go from kval(:) to write bands.re, bands.im or bands.co files? Regards, Manoj Srivastava, Physics Graduate Student, University of Florida, Gainesville, FL 32601 USA From eyvaz_isaev at yahoo.com Sat Aug 30 01:14:36 2008 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 29 Aug 2008 16:14:36 -0700 (PDT) Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: <8a1b6d820808291102n4c099becwdf7cebf717e545b3@mail.gmail.com> Message-ID: <23814.73215.qm@web65703.mail.ac4.yahoo.com> Dear Wei, Thanks a lot for bringing the paper to our attention. I have read the paper and have 2 comments. 1. They used only norm-conserving pseudopotentials constructed by means of different methods. 2. They used only LDA, but not GGA. As it is well known (hopefully I am not wrong here) LDA fails for the ground state of Fe. In contrast to this, GGA does a good job for Fe. So, it will be very good if Vega can calculate the total energies for the rutile and anatase phases in odrer to study whether their energy position is dependent on the choice of exchange-correlation functional. It might also be that there is a transferability problem for these PsPs (I can not prove this, just suggestion). It is my pleasure that they also mentioned that including of phonon contribution might be important. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Fri, 8/29/08, willy kohn wrote: > From: willy kohn > Subject: Re: [Pw_forum] something strange in rutile and anatase calculation > To: "PWSCF Forum" > Date: Friday, August 29, 2008, 10:02 PM > Hi, Vega: > > A recent result (Jpn. J. Appl. Phys. 39 (2000) L847) showed > that different > pseudopotential leaded to different conclusions. > > Best, > > Wei > > On Thu, Aug 28, 2008 at 4:28 AM, vega > wrote: > > > Dear all, > > > > It is known that the rutile is more stable than > anatase in thermodynamics. > > Surprisingly, when I did the vc-relax calculation by > QE, I found > > the calculated energy of anatase lower than rutile. > Both vc-relax > > calculation for rutile and anatase onverged in 6 scf > cycles and 3 bfgs > > steps, giving the final enthalpy = -362.7585836890 Ry > for rutile and > > -725.5447425835 Ry for antase. So the average energy > of [TiO2] unit > > is -181.3792918445 Ry for rutile and -181.386185645875 > Ry for anatase. It > > looks like anatase is more stable than rutile. Do you > think it was quite > > strange? > > > > To make the calculation both for anatase and rutile > comparable, I used the > > same ecutwfc=40 Ry and ecutwfc=400 Ry, and a quite > dense k-point mesh for > > both case, 4x4x7 for rutile and 5x5x2 for anatase. > > > > for better understanding in my calculation, please > read the input file > > below, > > for anatase case, > > &CONTROL > > title = 'Anatase > lattice' , > > calculation = 'vc-relax' , > > restart_mode = 'from_scratch' > , > > outdir = > > > '/home/hjfeng/vega/TiO2/Anatase/lattice/vctest/tmp/' > , > > wfcdir = '/tmp/' , > > pseudo_dir = > '/home/hjfeng/vega/espresso-4.0/pseudo/' , > > prefix = 'Anatase > lattice' , > > disk_io = 'none' , > > nstep = 1000 , > > / > > &SYSTEM > > ibrav = 6, > > celldm(1) = 7.1356, > > celldm(3) = 2.5122, > > nat = 12, > > ntyp = 2, > > ecutwfc = 40 , > > ecutrho = 400 , > > / > > &ELECTRONS > > > > / > > &IONS > > ion_dynamics = 'bfgs' , > > / > > &CELL > > cell_dynamics = 'bfgs' , > > / > > ATOMIC_SPECIES > > Ti 47.86700 Ti.pw91-sp-van_ak.UPF > > O 15.99940 O.pw91-van_ak.UPF > > ATOMIC_POSITIONS crystal > > Ti 0.000000000 0.000000000 0.000000000 > > Ti 0.500000000 0.500000000 0.500000000 > > Ti 0.000000000 0.500000000 0.250000000 > > Ti 0.500000000 0.000000000 0.750000000 > > O 0.000000000 0.500000000 0.042000000 > > O 0.000000000 0.000000000 0.208000000 > > O 0.500000000 0.500000000 0.292000000 > > O 0.000000000 0.500000000 0.458000000 > > O 0.500000000 0.000000000 0.542000000 > > O 0.500000000 0.500000000 0.708000000 > > O 0.000000000 0.000000000 0.792000000 > > O 0.500000000 1.000000000 0.958000000 > > K_POINTS automatic > > 5 5 2 1 1 1 > > > > for rutile case, > > > > &CONTROL > > title = Rutile_lattice , > > calculation = 'vc-relax' , > > restart_mode = 'from_scratch' > , > > outdir = > > '/home/vega32/TiO2/rutile/lattice/vcrelax/tmp' > , > > wfcdir = '/tmp/' , > > pseudo_dir = > '/home/vega32/espresso-4.0.1/pseudo/' , > > prefix = 'Anatase > lattice' , > > disk_io = 'none' , > > nstep = 1000 , > > / > > &SYSTEM > > ibrav = 6, > > celldm(1) = 8.6814, > > celldm(3) = 0.6441, > > nat = 6, > > ntyp = 2, > > ecutwfc = 40 , > > ecutrho = 400 , > > / > > &ELECTRONS > > > > / > > &IONS > > ion_dynamics = 'bfgs' , > > / > > &CELL > > cell_dynamics = 'bfgs' , > > / > > ATOMIC_SPECIES > > O 15.99940 O.pw91-van_ak.UPF > > Ti 47.90000 Ti.pw91-sp-van_ak.UPF > > ATOMIC_POSITIONS crystal > > O 0.304800000 0.304800000 0.000000000 > > O 0.695200000 0.695200000 0.000000000 > > O 0.195200000 0.804800000 0.500000000 > > O 0.804800000 0.195200000 0.500000000 > > Ti 0.500000000 0.500000000 0.500000000 > > Ti 0.000000000 0.000000000 0.000000000 > > K_POINTS automatic > > 4 4 7 1 1 1 > > > > vega > > > > > ============================================================== > > Vega Lew ( weijia liu) > > PH.D Candidate in Chemical Engineering > > State Key Laboratory of Materials-oriented Chemical > Engineering > > College of Chemistry and Chemical Engineering > > Nanjing University of Technology, 210009, Nanjing, > Jiangsu, China > > > > _______________________________________________ > > 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 vegalew at hotmail.com Sat Aug 30 02:39:54 2008 From: vegalew at hotmail.com (vega) Date: Sat, 30 Aug 2008 08:39:54 +0800 Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: <23814.73215.qm@web65703.mail.ac4.yahoo.com> References: <23814.73215.qm@web65703.mail.ac4.yahoo.com> Message-ID: Dear sir, Thank you for getting back to me. > > I have read the paper and have 2 comments. I used to think the paper was written by you. Why did you need to read it again? > 2. They used only LDA, but not GGA. As it is well known (hopefully I am > not wrong here) LDA fails for the ground state of Fe. In contrast to this, > GGA does a good job for Fe. But I found the sentence like this, 'The generalized gradient approximation in the Perdew- Burke-Ernzerhof parametrization was chosen to treat the exchange-correlation effects.' in the Methods section. I was rather confused. > So, it will be very good if Vega can calculate the total energies for the > rutile and anatase phases in odrer to study whether their energy position > is dependent on the choice of exchange-correlation functional. I used to do a little test against this. The results suggested that the GGA overestimate the lattice parameters a little with 1% and LDA underestimate the lattice parameters for both case. I didn't pay a lot attentions on energy position calculated by LDA. I'll check it as soon as possible. But to my best knowledge, there were many reports suggested that the calculated anatase stability was better than rutile. For example, J. Chem. Phys. 126, 154703 (2007) said 'No matter which Hamiltonian or method is used, the results on relative stability of both phases suggest that the anatase is more stable than the rutile phase of TiO2.'. Same conclusion also was mentioned in Phys. Rev. B 2002, 65 (22) and Phys. Rev. B 2007, 76 et al. > It might also be that there is a transferability problem for these PsPs (I > can not prove this, just suggestion). Because I'm a beginner for QE. I though pseudopotentials is quite transferable and we could use the same pseudopotentials for any mater containing the same kind of element. For instance, we could use the same pseudopotentials for hcp Ti, TiN, rutile, brookite, anatase and other polymorphs under high pressure, such as Fluorite,Baddeleyite et al. But now, I think I'm probably wrong. Could you tell me the difference between the Ti pseudopotentials for hcp-Ti and TiN or many polymorphs of TiO2? And I also wonder how to judge whether the pseudopotentials is suitable for certain calculation? to calculate the lattice parameters and compare the results with the experimental data? Is that enough? > It is my pleasure that they also mentioned that including of phonon > contribution might be important. I would like to calculate the phonon contribution. But I have few knowledge about it. I'll learn to do that if necessary. vega ================================================================================= Vega Lew (weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China -------------------------------------------------- From: "Eyvaz Isaev" Sent: Saturday, August 30, 2008 7:14 AM To: "PWSCF Forum" Subject: Re: [Pw_forum] something strange in rutile and anatase calculation > Dear Wei, > > Thanks a lot for bringing the paper to our attention. > > I have read the paper and have 2 comments. > > 1. They used only norm-conserving pseudopotentials constructed by means of > different methods. > > 2. They used only LDA, but not GGA. As it is well known (hopefully I am > not wrong here) LDA fails for the ground state of Fe. In contrast to this, > GGA does a good job for Fe. > > So, it will be very good if Vega can calculate the total energies for the > rutile and anatase phases in odrer to study whether their energy position > is dependent on the choice of exchange-correlation functional. > > It might also be that there is a transferability problem for these PsPs (I > can not prove this, just suggestion). > > It is my pleasure that they also mentioned that including of phonon > contribution might be important. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Condensed Matter Theory Group, Uppsala University, Sweden > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > --- On Fri, 8/29/08, willy kohn wrote: > >> From: willy kohn >> Subject: Re: [Pw_forum] something strange in rutile and anatase >> calculation >> To: "PWSCF Forum" >> Date: Friday, August 29, 2008, 10:02 PM >> Hi, Vega: >> >> A recent result (Jpn. J. Appl. Phys. 39 (2000) L847) showed >> that different >> pseudopotential leaded to different conclusions. >> >> Best, >> >> Wei >> >> On Thu, Aug 28, 2008 at 4:28 AM, vega >> wrote: >> >> > Dear all, >> > >> > It is known that the rutile is more stable than >> anatase in thermodynamics. >> > Surprisingly, when I did the vc-relax calculation by >> QE, I found >> > the calculated energy of anatase lower than rutile. >> Both vc-relax >> > calculation for rutile and anatase onverged in 6 scf >> cycles and 3 bfgs >> > steps, giving the final enthalpy = -362.7585836890 Ry >> for rutile and >> > -725.5447425835 Ry for antase. So the average energy >> of [TiO2] unit >> > is -181.3792918445 Ry for rutile and -181.386185645875 >> Ry for anatase. It >> > looks like anatase is more stable than rutile. Do you >> think it was quite >> > strange? >> > >> > To make the calculation both for anatase and rutile >> comparable, I used the >> > same ecutwfc=40 Ry and ecutwfc=400 Ry, and a quite >> dense k-point mesh for >> > both case, 4x4x7 for rutile and 5x5x2 for anatase. >> > >> > for better understanding in my calculation, please >> read the input file >> > below, >> > for anatase case, >> > &CONTROL >> > title = 'Anatase >> lattice' , >> > calculation = 'vc-relax' , >> > restart_mode = 'from_scratch' >> , >> > outdir = >> > >> '/home/hjfeng/vega/TiO2/Anatase/lattice/vctest/tmp/' >> , >> > wfcdir = '/tmp/' , >> > pseudo_dir = >> '/home/hjfeng/vega/espresso-4.0/pseudo/' , >> > prefix = 'Anatase >> lattice' , >> > disk_io = 'none' , >> > nstep = 1000 , >> > / >> > &SYSTEM >> > ibrav = 6, >> > celldm(1) = 7.1356, >> > celldm(3) = 2.5122, >> > nat = 12, >> > ntyp = 2, >> > ecutwfc = 40 , >> > ecutrho = 400 , >> > / >> > &ELECTRONS >> > >> > / >> > &IONS >> > ion_dynamics = 'bfgs' , >> > / >> > &CELL >> > cell_dynamics = 'bfgs' , >> > / >> > ATOMIC_SPECIES >> > Ti 47.86700 Ti.pw91-sp-van_ak.UPF >> > O 15.99940 O.pw91-van_ak.UPF >> > ATOMIC_POSITIONS crystal >> > Ti 0.000000000 0.000000000 0.000000000 >> > Ti 0.500000000 0.500000000 0.500000000 >> > Ti 0.000000000 0.500000000 0.250000000 >> > Ti 0.500000000 0.000000000 0.750000000 >> > O 0.000000000 0.500000000 0.042000000 >> > O 0.000000000 0.000000000 0.208000000 >> > O 0.500000000 0.500000000 0.292000000 >> > O 0.000000000 0.500000000 0.458000000 >> > O 0.500000000 0.000000000 0.542000000 >> > O 0.500000000 0.500000000 0.708000000 >> > O 0.000000000 0.000000000 0.792000000 >> > O 0.500000000 1.000000000 0.958000000 >> > K_POINTS automatic >> > 5 5 2 1 1 1 >> > >> > for rutile case, >> > >> > &CONTROL >> > title = Rutile_lattice , >> > calculation = 'vc-relax' , >> > restart_mode = 'from_scratch' >> , >> > outdir = >> > '/home/vega32/TiO2/rutile/lattice/vcrelax/tmp' >> , >> > wfcdir = '/tmp/' , >> > pseudo_dir = >> '/home/vega32/espresso-4.0.1/pseudo/' , >> > prefix = 'Anatase >> lattice' , >> > disk_io = 'none' , >> > nstep = 1000 , >> > / >> > &SYSTEM >> > ibrav = 6, >> > celldm(1) = 8.6814, >> > celldm(3) = 0.6441, >> > nat = 6, >> > ntyp = 2, >> > ecutwfc = 40 , >> > ecutrho = 400 , >> > / >> > &ELECTRONS >> > >> > / >> > &IONS >> > ion_dynamics = 'bfgs' , >> > / >> > &CELL >> > cell_dynamics = 'bfgs' , >> > / >> > ATOMIC_SPECIES >> > O 15.99940 O.pw91-van_ak.UPF >> > Ti 47.90000 Ti.pw91-sp-van_ak.UPF >> > ATOMIC_POSITIONS crystal >> > O 0.304800000 0.304800000 0.000000000 >> > O 0.695200000 0.695200000 0.000000000 >> > O 0.195200000 0.804800000 0.500000000 >> > O 0.804800000 0.195200000 0.500000000 >> > Ti 0.500000000 0.500000000 0.500000000 >> > Ti 0.000000000 0.000000000 0.000000000 >> > K_POINTS automatic >> > 4 4 7 1 1 1 >> > >> > vega >> > >> > >> ============================================================== >> > Vega Lew ( weijia liu) >> > PH.D Candidate in Chemical Engineering >> > State Key Laboratory of Materials-oriented Chemical >> Engineering >> > College of Chemistry and Chemical Engineering >> > Nanjing University of Technology, 210009, Nanjing, >> Jiangsu, China >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> > >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From vegalew at hotmail.com Sat Aug 30 02:49:15 2008 From: vegalew at hotmail.com (vega) Date: Sat, 30 Aug 2008 08:49:15 +0800 Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: <8a1b6d820808291102n4c099becwdf7cebf717e545b3@mail.gmail.com> References: <8a1b6d820808291102n4c099becwdf7cebf717e545b3@mail.gmail.com> Message-ID: >A recent result (Jpn. J. Appl. Phys. 39 (2000) L847) showed that different pseudopotential leaded to different conclusions. thank you for your information. I have no subscription for this japanese journal. Please sent it to vegalew at gmail.com if you like me to read it. I am rather curious to know about it. vega ================================================================================= Vega Lew (weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China From: willy kohn Sent: Saturday, August 30, 2008 2:02 AM To: PWSCF Forum Subject: Re: [Pw_forum] something strange in rutile and anatase calculation Hi, Vega: A recent result (Jpn. J. Appl. Phys. 39 (2000) L847) showed that different pseudopotential leaded to different conclusions. Best, Wei On Thu, Aug 28, 2008 at 4:28 AM, vega wrote: Dear all, It is known that the rutile is more stable than anatase in thermodynamics. Surprisingly, when I did the vc-relax calculation by QE, I found the calculated energy of anatase lower than rutile. Both vc-relax calculation for rutile and anatase onverged in 6 scf cycles and 3 bfgs steps, giving the final enthalpy = -362.7585836890 Ry for rutile and -725.5447425835 Ry for antase. So the average energy of [TiO2] unit is -181.3792918445 Ry for rutile and -181.386185645875 Ry for anatase. It looks like anatase is more stable than rutile. Do you think it was quite strange? To make the calculation both for anatase and rutile comparable, I used the same ecutwfc=40 Ry and ecutwfc=400 Ry, and a quite dense k-point mesh for both case, 4x4x7 for rutile and 5x5x2 for anatase. for better understanding in my calculation, please read the input file below, for anatase case, &CONTROL title = 'Anatase lattice' , calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/hjfeng/vega/TiO2/Anatase/lattice/vctest/tmp/' , wfcdir = '/tmp/' , pseudo_dir = '/home/hjfeng/vega/espresso-4.0/pseudo/' , prefix = 'Anatase lattice' , disk_io = 'none' , nstep = 1000 , / &SYSTEM ibrav = 6, celldm(1) = 7.1356, celldm(3) = 2.5122, nat = 12, ntyp = 2, ecutwfc = 40 , ecutrho = 400 , / &ELECTRONS / &IONS ion_dynamics = 'bfgs' , / &CELL cell_dynamics = 'bfgs' , / ATOMIC_SPECIES Ti 47.86700 Ti.pw91-sp-van_ak.UPF O 15.99940 O.pw91-van_ak.UPF ATOMIC_POSITIONS crystal Ti 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.500000000 Ti 0.000000000 0.500000000 0.250000000 Ti 0.500000000 0.000000000 0.750000000 O 0.000000000 0.500000000 0.042000000 O 0.000000000 0.000000000 0.208000000 O 0.500000000 0.500000000 0.292000000 O 0.000000000 0.500000000 0.458000000 O 0.500000000 0.000000000 0.542000000 O 0.500000000 0.500000000 0.708000000 O 0.000000000 0.000000000 0.792000000 O 0.500000000 1.000000000 0.958000000 K_POINTS automatic 5 5 2 1 1 1 for rutile case, &CONTROL title = Rutile_lattice , calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/vega32/TiO2/rutile/lattice/vcrelax/tmp' , wfcdir = '/tmp/' , pseudo_dir = '/home/vega32/espresso-4.0.1/pseudo/' , prefix = 'Anatase lattice' , disk_io = 'none' , nstep = 1000 , / &SYSTEM ibrav = 6, celldm(1) = 8.6814, celldm(3) = 0.6441, nat = 6, ntyp = 2, ecutwfc = 40 , ecutrho = 400 , / &ELECTRONS / &IONS ion_dynamics = 'bfgs' , / &CELL cell_dynamics = 'bfgs' , / ATOMIC_SPECIES O 15.99940 O.pw91-van_ak.UPF Ti 47.90000 Ti.pw91-sp-van_ak.UPF ATOMIC_POSITIONS crystal O 0.304800000 0.304800000 0.000000000 O 0.695200000 0.695200000 0.000000000 O 0.195200000 0.804800000 0.500000000 O 0.804800000 0.195200000 0.500000000 Ti 0.500000000 0.500000000 0.500000000 Ti 0.000000000 0.000000000 0.000000000 K_POINTS automatic 4 4 7 1 1 1 vega ============================================================== Vega Lew ( weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------------------------------------------------------------------------- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080830/69f0da72/attachment.htm From wangqj1 at 126.com Sat Aug 30 09:08:45 2008 From: wangqj1 at 126.com (wangqj1) Date: Sat, 30 Aug 2008 15:08:45 +0800 (CST) Subject: [Pw_forum] how to extract the eigenval with bands.x Message-ID: <18807211.381491220080125786.JavaMail.coremail@bj126app103.126.com> Dear all After I used bands.x to extact the eigenval of spined-caculated,I don't know the result is how to derived ? Does it the average of up-eigenval and down-eigenval ? Any advice will be appreciated . sincerely wjwang Xiangtan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080830/3e00b952/attachment.htm From vegalew at hotmail.com Sun Aug 31 05:51:09 2008 From: vegalew at hotmail.com (vega) Date: Sun, 31 Aug 2008 11:51:09 +0800 Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: <617203.17308.qm@web65709.mail.ac4.yahoo.com> References: <617203.17308.qm@web65709.mail.ac4.yahoo.com> Message-ID: > A famous example is Li which PsP was removed from PWSCF website. I met the > same problem with K and Cs using my own pseudopotentials. Li PsP is still on the website,http://www.quantum-espresso.org/pseudo/1.3/html/Li.html. Name: Lithium Symbol: Li Atomic number: 3 Atomic configuration: [He] 2s1 Atomic mass: 6.914 (2) Available pseudopotentials: Li.pz-n-vbc.UPF (details) Perdew-Zunger (LDA) exch-corr nonlinear core-correction Von Barth-Car (direct fit) Li.pbe-n-van.UPF (details) Perdew-Burke-Ernzerhof (PBE) exch-corr nonlinear core-correction Vanderbilt ultrasoft Li.pw91-n-van.UPF (details) Perdew-Wang 91 gradient-corrected functional nonlinear core-correction Vanderbilt ultrasoft vega ================================================================================= Vega Lew (weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China -------------------------------------------------- From: "Eyvaz Isaev" Sent: Sunday, August 31, 2008 4:19 AM To: "vega" Subject: Re: [Pw_forum] something strange in rutile and anatase calculation > --- On Sat, 8/30/08, vega wrote: > >> thank you for replying > > Welcome. > >> >> >But as far as I know sometime PsPs (not for Ti, in >> general) fail with phonon calculations. >> >> Do you think there is a certain PsPs that could >calculate the lattice >> parameters and bulk modulus correctly >but only fail with phonon >> calculations. > > >> If you find a certain PsPs fail with phonon calculations >> what will you do next? how to adjust it? >> > In this case you have to generate a new PsP, if you like to deal with > phonons. Otherwise, use what you have and what you prefer. > > Bests, > Eyvaz. > P.S. This is not a problem of the QE code. Several times I heard complains > about PAW potentials for VASP. > >> vega >> >> >> ================================================================================= >> Vega Lew (weijia liu) >> PH.D Candidate in Chemical Engineering >> State Key Laboratory of Materials-oriented Chemical >> Engineering >> College of Chemistry and Chemical Engineering >> Nanjing University of Technology, 210009, Nanjing, Jiangsu, >> China >> >> -------------------------------------------------- >> From: "Eyvaz Isaev" >> Sent: Sunday, August 31, 2008 12:15 AM >> To: "vega" >> Subject: Re: [Pw_forum] something strange in rutile and >> anatase calculation >> >> > Dear Vega, >> > >> > --- On Sat, 8/30/08, vega >> wrote: >> > >> >> > I have read the paper and have 2 comments. >> >> >> >> I used to think the paper was written by you. Why >> > did you need to read >> >> it again? >> > >> > As I replied to Willy Kohn's mail, I meant reading >> the paper from >> > Jpn.J.Appl.Phys. Lett., he recommended, but not my own >> paper from PNAS. >> > So, there will be no confusing. All what I said >> concerned only the paper >> > and PsPs used in JpnJApplPhys. >> > >> > If you have done lots of calculations with the Ti >> pseudopotential you used >> > and got reliable results, well, it looks like to be >> transferable. The >> > transferability means that you can put a bare ionic >> atom (with its PsP) >> > into different environment, but its scattering >> properties should be the >> > same as for a real atom. >> > A transferable PsP for a given atom (say Ti) should >> work in most cases (as >> > in your case, if you got results comparable with >> experiments and >> > independent methods). The way you supposed (lattice >> parameters and bulk >> > modulus for known phases and compounds) is correct to >> check a PsP >> > transferability. But as far as I know sometime PsPs >> (not for Ti, in >> > general) fail with phonon calculations. >> > >> > As references you cited support your calculations you >> can belive your own >> > results. >> > >> > Hopefully I replied briefly all questions you posted >> in this mail. >> > >> > Bests, >> > Eyvaz. >> > >> > >> >> > 2. They used only LDA, but not GGA. As it is >> well >> >> known (hopefully I am >> >> > not wrong here) LDA fails for the ground >> state of Fe. >> >> In contrast to this, >> >> > GGA does a good job for Fe. >> >> >> >> But I found the sentence like this, 'The >> generalized >> >> gradient approximation >> >> in the Perdew- >> >> Burke-Ernzerhof parametrization was chosen to >> treat the >> >> exchange-correlation >> >> effects.' in the Methods section. I was rather >> >> confused. >> >> >> >> > So, it will be very good if Vega can >> calculate the >> >> total energies for the >> >> > rutile and anatase phases in odrer to study >> whether >> >> their energy position >> >> > is dependent on the choice of >> exchange-correlation >> >> functional. >> >> >> >> I used to do a little test against this. The >> results >> >> suggested that the GGA >> >> overestimate the lattice parameters a little with >> 1% and >> >> LDA underestimate >> >> the lattice parameters for both case. I didn't >> pay a >> >> lot attentions on >> >> energy position calculated by LDA. I'll check >> it as >> >> soon as possible. But to >> >> my best knowledge, there were many reports >> suggested that >> >> the calculated >> >> anatase stability was better than rutile. For >> example, J. >> >> Chem. Phys. 126, >> >> 154703 (2007) said 'No matter which >> Hamiltonian or >> >> method is used, the >> >> results on relative stability of both phases >> suggest that >> >> the anatase is >> >> more stable than the rutile phase of TiO2.'. >> Same >> >> conclusion also was >> >> mentioned in Phys. Rev. B 2002, 65 (22) and Phys. >> Rev. B >> >> 2007, 76 et al. >> >> >> >> > It might also be that there is a >> transferability >> >> problem for these PsPs (I >> >> > can not prove this, just suggestion). >> >> >> >> Because I'm a beginner for QE. I though >> >> pseudopotentials is quite >> >> transferable and we could use the same >> pseudopotentials for >> >> any mater >> >> containing the same kind of element. For instance, >> we could >> >> use the same >> >> pseudopotentials for hcp Ti, TiN, rutile, >> brookite, anatase >> >> and other >> >> polymorphs under high pressure, such as >> >> Fluorite,Baddeleyite et al. But now, >> >> I think I'm probably wrong. Could you tell me >> the >> >> difference between the Ti >> >> pseudopotentials for hcp-Ti and TiN or many >> polymorphs of >> >> TiO2? And I also >> >> wonder how to judge whether the pseudopotentials >> is >> >> suitable for certain >> >> calculation? to calculate the lattice parameters >> and >> >> compare the results >> >> with the experimental data? Is that enough? >> >> >> >> > It is my pleasure that they also mentioned >> that >> >> including of phonon >> >> > contribution might be important. >> >> I would like to calculate the phonon contribution. >> But I >> >> have few knowledge >> >> about it. I'll learn to do that if necessary. >> >> >> >> vega >> >> >> >> >> >> >> ================================================================================= >> >> Vega Lew (weijia liu) >> >> PH.D Candidate in Chemical Engineering >> >> State Key Laboratory of Materials-oriented >> Chemical >> >> Engineering >> >> College of Chemistry and Chemical Engineering >> >> Nanjing University of Technology, 210009, Nanjing, >> Jiangsu, >> >> China >> >> >> >> -------------------------------------------------- >> >> From: "Eyvaz Isaev" >> >> >> Sent: Saturday, August 30, 2008 7:14 AM >> >> To: "PWSCF Forum" >> >> >> Subject: Re: [Pw_forum] something strange in >> rutile and >> >> anatase calculation >> >> >> >> > Dear Wei, >> >> > >> >> > Thanks a lot for bringing the paper to our >> attention. >> >> > >> >> > I have read the paper and have 2 comments. >> >> > >> >> > 1. They used only norm-conserving >> pseudopotentials >> >> constructed by means of >> >> > different methods. >> >> > >> >> > 2. They used only LDA, but not GGA. As it is >> well >> >> known (hopefully I am >> >> > not wrong here) LDA fails for the ground >> state of Fe. >> >> In contrast to this, >> >> > GGA does a good job for Fe. >> >> > >> >> > So, it will be very good if Vega can >> calculate the >> >> total energies for the >> >> > rutile and anatase phases in odrer to study >> whether >> >> their energy position >> >> > is dependent on the choice of >> exchange-correlation >> >> functional. >> >> > >> >> > It might also be that there is a >> transferability >> >> problem for these PsPs (I >> >> > can not prove this, just suggestion). >> >> > >> >> > It is my pleasure that they also mentioned >> that >> >> including of phonon >> >> > contribution might be important. >> >> > >> >> > Bests, >> >> > Eyvaz. >> >> > >> >> > >> >> >> ------------------------------------------------------------------- >> >> > Prof. Eyvaz Isaev, >> >> > Theoretical Physics Department, Moscow State >> Institute >> >> of Steel & Alloys, >> >> > Russia, >> >> > Department of Physics, Chemistry, and Biology >> (IFM), >> >> Linkoping University, >> >> > Sweden >> >> > Condensed Matter Theory Group, Uppsala >> University, >> >> Sweden >> >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, >> >> eyvaz_isaev at yahoo.com >> >> > >> >> > >> >> > --- On Fri, 8/29/08, willy kohn >> >> wrote: >> >> > >> >> >> From: willy kohn >> >> >> >> Subject: Re: [Pw_forum] something strange >> in >> >> rutile and anatase >> >> >> calculation >> >> >> To: "PWSCF Forum" >> >> >> >> >> Date: Friday, August 29, 2008, 10:02 PM >> >> >> Hi, Vega: >> >> >> >> >> >> A recent result (Jpn. J. Appl. Phys. 39 >> (2000) >> >> L847) showed >> >> >> that different >> >> >> pseudopotential leaded to different >> conclusions. >> >> >> >> >> >> Best, >> >> >> >> >> >> Wei >> >> >> >> >> >> On Thu, Aug 28, 2008 at 4:28 AM, vega >> >> >> wrote: >> >> >> >> >> >> > Dear all, >> >> >> > >> >> >> > It is known that the rutile is more >> stable >> >> than >> >> >> anatase in thermodynamics. >> >> >> > Surprisingly, when I did the >> vc-relax >> >> calculation by >> >> >> QE, I found >> >> >> > the calculated energy of anatase >> lower than >> >> rutile. >> >> >> Both vc-relax >> >> >> > calculation for rutile and anatase >> onverged >> >> in 6 scf >> >> >> cycles and 3 bfgs >> >> >> > steps, giving the final enthalpy = >> >> -362.7585836890 Ry >> >> >> for rutile and >> >> >> > -725.5447425835 Ry for antase. So >> the average >> >> energy >> >> >> of [TiO2] unit >> >> >> > is -181.3792918445 Ry for rutile and >> >> -181.386185645875 >> >> >> Ry for anatase. It >> >> >> > looks like anatase is more stable >> than >> >> rutile. Do you >> >> >> think it was quite >> >> >> > strange? >> >> >> > >> >> >> > To make the calculation both for >> anatase and >> >> rutile >> >> >> comparable, I used the >> >> >> > same ecutwfc=40 Ry and ecutwfc=400 >> Ry, and a >> >> quite >> >> >> dense k-point mesh for >> >> >> > both case, 4x4x7 for rutile and >> 5x5x2 for >> >> anatase. >> >> >> > >> >> >> > for better understanding in my >> calculation, >> >> please >> >> >> read the input file >> >> >> > below, >> >> >> > for anatase case, >> >> >> > &CONTROL >> >> >> > title = >> 'Anatase >> >> >> lattice' , >> >> >> > calculation = >> >> 'vc-relax' , >> >> >> > restart_mode = >> >> 'from_scratch' >> >> >> , >> >> >> > outdir = >> >> >> > >> >> >> >> >> >> '/home/hjfeng/vega/TiO2/Anatase/lattice/vctest/tmp/' >> >> >> , >> >> >> > wfcdir = >> >> '/tmp/' , >> >> >> > pseudo_dir = >> >> >> >> '/home/hjfeng/vega/espresso-4.0/pseudo/' , >> >> >> > prefix = >> 'Anatase >> >> >> lattice' , >> >> >> > disk_io = >> 'none' >> >> , >> >> >> > nstep = 1000 >> , >> >> >> > / >> >> >> > &SYSTEM >> >> >> > ibrav = 6, >> >> >> > celldm(1) = >> 7.1356, >> >> >> > celldm(3) = >> 2.5122, >> >> >> > nat = 12, >> >> >> > ntyp = 2, >> >> >> > ecutwfc = 40 , >> >> >> > ecutrho = 400 , >> >> >> > / >> >> >> > &ELECTRONS >> >> >> > >> >> >> > / >> >> >> > &IONS >> >> >> > ion_dynamics = >> 'bfgs' >> >> , >> >> >> > / >> >> >> > &CELL >> >> >> > cell_dynamics = >> 'bfgs' >> >> , >> >> >> > / >> >> >> > ATOMIC_SPECIES >> >> >> > Ti 47.86700 >> Ti.pw91-sp-van_ak.UPF >> >> >> > O 15.99940 O.pw91-van_ak.UPF >> >> >> > ATOMIC_POSITIONS crystal >> >> >> > Ti 0.000000000 >> 0.000000000 >> >> 0.000000000 >> >> >> > Ti 0.500000000 >> 0.500000000 >> >> 0.500000000 >> >> >> > Ti 0.000000000 >> 0.500000000 >> >> 0.250000000 >> >> >> > Ti 0.500000000 >> 0.000000000 >> >> 0.750000000 >> >> >> > O 0.000000000 >> 0.500000000 >> >> 0.042000000 >> >> >> > O 0.000000000 >> 0.000000000 >> >> 0.208000000 >> >> >> > O 0.500000000 >> 0.500000000 >> >> 0.292000000 >> >> >> > O 0.000000000 >> 0.500000000 >> >> 0.458000000 >> >> >> > O 0.500000000 >> 0.000000000 >> >> 0.542000000 >> >> >> > O 0.500000000 >> 0.500000000 >> >> 0.708000000 >> >> >> > O 0.000000000 >> 0.000000000 >> >> 0.792000000 >> >> >> > O 0.500000000 >> 1.000000000 >> >> 0.958000000 >> >> >> > K_POINTS automatic >> >> >> > 5 5 2 1 1 1 >> >> >> > >> >> >> > for rutile case, >> >> >> > >> >> >> > &CONTROL >> >> >> > title = >> Rutile_lattice >> >> , >> >> >> > calculation = >> >> 'vc-relax' , >> >> >> > restart_mode = >> >> 'from_scratch' >> >> >> , >> >> >> > outdir = >> >> >> > >> >> >> '/home/vega32/TiO2/rutile/lattice/vcrelax/tmp' >> >> >> , >> >> >> > wfcdir = >> >> '/tmp/' , >> >> >> > pseudo_dir = >> >> >> >> '/home/vega32/espresso-4.0.1/pseudo/' , >> >> >> > prefix = >> 'Anatase >> >> >> lattice' , >> >> >> > disk_io = >> 'none' >> >> , >> >> >> > nstep = 1000 >> , >> >> >> > / >> >> >> > &SYSTEM >> >> >> > ibrav = 6, >> >> >> > celldm(1) = >> 8.6814, >> >> >> > celldm(3) = >> 0.6441, >> >> >> > nat = 6, >> >> >> > ntyp = 2, >> >> >> > ecutwfc = 40 , >> >> >> > ecutrho = 400 , >> >> >> > / >> >> >> > &ELECTRONS >> >> >> > >> >> >> > / >> >> >> > &IONS >> >> >> > ion_dynamics = >> 'bfgs' >> >> , >> >> >> > / >> >> >> > &CELL >> >> >> > cell_dynamics = >> 'bfgs' >> >> , >> >> >> > / >> >> >> > ATOMIC_SPECIES >> >> >> > O 15.99940 O.pw91-van_ak.UPF >> >> >> > Ti 47.90000 >> Ti.pw91-sp-van_ak.UPF >> >> >> > ATOMIC_POSITIONS crystal >> >> >> > O 0.304800000 >> 0.304800000 >> >> 0.000000000 >> >> >> > O 0.695200000 >> 0.695200000 >> >> 0.000000000 >> >> >> > O 0.195200000 >> 0.804800000 >> >> 0.500000000 >> >> >> > O 0.804800000 >> 0.195200000 >> >> 0.500000000 >> >> >> > Ti 0.500000000 >> 0.500000000 >> >> 0.500000000 >> >> >> > Ti 0.000000000 >> 0.000000000 >> >> 0.000000000 >> >> >> > K_POINTS automatic >> >> >> > 4 4 7 1 1 1 >> >> >> > >> >> >> > vega >> >> >> > >> >> >> > >> >> >> >> >> >> ============================================================== >> >> >> > Vega Lew ( weijia liu) >> >> >> > PH.D Candidate in Chemical >> Engineering >> >> >> > State Key Laboratory of >> Materials-oriented >> >> Chemical >> >> >> Engineering >> >> >> > College of Chemistry and Chemical >> Engineering >> >> >> > Nanjing University of Technology, >> 210009, >> >> Nanjing, >> >> >> Jiangsu, China >> >> >> > >> >> >> > >> >> _______________________________________________ >> >> >> > Pw_forum mailing list >> >> >> > Pw_forum at pwscf.org >> >> >> > >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> > >> >> >> > >> >> >> >> _______________________________________________ >> >> >> Pw_forum mailing list >> >> >> Pw_forum at pwscf.org >> >> >> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > >> >> > >> >> > >> >> > >> _______________________________________________ >> >> > Pw_forum mailing list >> >> > Pw_forum at pwscf.org >> >> > >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > >> > >> > >> > >> > > > > > From limkr at umich.edu Sun Aug 31 06:17:28 2008 From: limkr at umich.edu (Dong-Hee Lim) Date: Sun, 31 Aug 2008 00:17:28 -0400 Subject: [Pw_forum] Unit of charge density Message-ID: <20080831001728.21066rzbnuvn37cw@web.mail.umich.edu> Dear All I was just wondering what unit of charge density is used in Quantum Espresso and Xcrysden viewer. After I calculate a SCF calculation, I got a charge density result using the following inputs. Xcrysden shows the charge density result with a legend saying "Scale delta n(r)". I would appreciate if you let me know how I understand the unit of charge density. ----------------------------- &inputpp prefix = 'input_file' outdir = '/file_location/, filplot = 'input_file_charge' plot_num= 0 / &plot iflag = 3 output_format = 5 fileout = 'input_file.dat' / ------------------------------------- Thank you, Donghee -- Dong-Hee Lim, Ph.D. candidate Dept. of Civil and Environmental Engineering University of Michigan From akohlmey at cmm.chem.upenn.edu Sun Aug 31 07:54:45 2008 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sun, 31 Aug 2008 01:54:45 -0400 (EDT) Subject: [Pw_forum] something strange in rutile and anatase calculation In-Reply-To: References: <617203.17308.qm@web65709.mail.ac4.yahoo.com> Message-ID: On Sun, 31 Aug 2008, vega wrote: VL> > A famous example is Li which PsP was removed from PWSCF website. I met the VL> > same problem with K and Cs using my own pseudopotentials. VL> VL> Li PsP is still on the VL> website,http://www.quantum-espresso.org/pseudo/1.3/html/Li.html. no. this was with reference to vanderbilt type lithium semi-core potentials. they are actually back on www.pwscf.org due to popular demand. those actually seem to work for phonons, provided one uses wavefunction cutoffs in the neighborhood of 200ry. getting a converged stress tensor is equally crazy, i needed 300ry for a test system recently... for the ultra-soft ones, phonons do not seem to work at all, and there are some hints that this may be true for other "tricky" elements in combination with the vanderbilt scheme. on the other hand, geometries and MD are working fine with reasonable cutoffs (85-90ry for norm conserving and 30ry for ultrasoft with density cutoff ~300ry). this is what they were created for and tested against. as you can see, testing applicability of pseudopotentials to the problem at hand is a good practice and should never be underestimated. blindly trusting existing pseudopotentials without knowing what they were used and parametrized for can easily lead to the large errors... cheers, axel. VL> Name: Lithium VL> Symbol: Li VL> Atomic number: 3 VL> Atomic configuration: [He] 2s1 VL> Atomic mass: 6.914 (2) VL> VL> Available pseudopotentials: VL> VL> Li.pz-n-vbc.UPF (details) VL> VL> Perdew-Zunger (LDA) exch-corr VL> nonlinear core-correction VL> Von Barth-Car (direct fit) VL> VL> Li.pbe-n-van.UPF (details) VL> VL> Perdew-Burke-Ernzerhof (PBE) exch-corr VL> nonlinear core-correction VL> Vanderbilt ultrasoft VL> VL> Li.pw91-n-van.UPF (details) VL> VL> Perdew-Wang 91 gradient-corrected functional VL> nonlinear core-correction VL> Vanderbilt ultrasoft VL> VL> vega VL> VL> ================================================================================= VL> Vega Lew (weijia liu) VL> PH.D Candidate in Chemical Engineering VL> State Key Laboratory of Materials-oriented Chemical Engineering VL> College of Chemistry and Chemical Engineering VL> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China VL> VL> -------------------------------------------------- VL> From: "Eyvaz Isaev" VL> Sent: Sunday, August 31, 2008 4:19 AM VL> To: "vega" VL> Subject: Re: [Pw_forum] something strange in rutile and anatase calculation VL> VL> > --- On Sat, 8/30/08, vega wrote: VL> > VL> >> thank you for replying VL> > VL> > Welcome. VL> > VL> >> VL> >> >But as far as I know sometime PsPs (not for Ti, in VL> >> general) fail with phonon calculations. VL> >> VL> >> Do you think there is a certain PsPs that could >calculate the lattice VL> >> parameters and bulk modulus correctly >but only fail with phonon VL> >> calculations. VL> > VL> VL> > VL> >> If you find a certain PsPs fail with phonon calculations VL> >> what will you do next? how to adjust it? VL> >> VL> > In this case you have to generate a new PsP, if you like to deal with VL> > phonons. Otherwise, use what you have and what you prefer. VL> > VL> > Bests, VL> > Eyvaz. VL> > P.S. This is not a problem of the QE code. Several times I heard complains VL> > about PAW potentials for VASP. VL> > VL> >> vega VL> >> VL> >> VL> >> ================================================================================= VL> >> Vega Lew (weijia liu) VL> >> PH.D Candidate in Chemical Engineering VL> >> State Key Laboratory of Materials-oriented Chemical VL> >> Engineering VL> >> College of Chemistry and Chemical Engineering VL> >> Nanjing University of Technology, 210009, Nanjing, Jiangsu, VL> >> China VL> >> VL> >> -------------------------------------------------- VL> >> From: "Eyvaz Isaev" VL> >> Sent: Sunday, August 31, 2008 12:15 AM VL> >> To: "vega" VL> >> Subject: Re: [Pw_forum] something strange in rutile and VL> >> anatase calculation VL> >> VL> >> > Dear Vega, VL> >> > VL> >> > --- On Sat, 8/30/08, vega VL> >> wrote: VL> >> > VL> >> >> > I have read the paper and have 2 comments. VL> >> >> VL> >> >> I used to think the paper was written by you. Why VL> >> > did you need to read VL> >> >> it again? VL> >> > VL> >> > As I replied to Willy Kohn's mail, I meant reading VL> >> the paper from VL> >> > Jpn.J.Appl.Phys. Lett., he recommended, but not my own VL> >> paper from PNAS. VL> >> > So, there will be no confusing. All what I said VL> >> concerned only the paper VL> >> > and PsPs used in JpnJApplPhys. VL> >> > VL> >> > If you have done lots of calculations with the Ti VL> >> pseudopotential you used VL> >> > and got reliable results, well, it looks like to be VL> >> transferable. The VL> >> > transferability means that you can put a bare ionic VL> >> atom (with its PsP) VL> >> > into different environment, but its scattering VL> >> properties should be the VL> >> > same as for a real atom. VL> >> > A transferable PsP for a given atom (say Ti) should VL> >> work in most cases (as VL> >> > in your case, if you got results comparable with VL> >> experiments and VL> >> > independent methods). The way you supposed (lattice VL> >> parameters and bulk VL> >> > modulus for known phases and compounds) is correct to VL> >> check a PsP VL> >> > transferability. But as far as I know sometime PsPs VL> >> (not for Ti, in VL> >> > general) fail with phonon calculations. VL> >> > VL> >> > As references you cited support your calculations you VL> >> can belive your own VL> >> > results. VL> >> > VL> >> > Hopefully I replied briefly all questions you posted VL> >> in this mail. VL> >> > VL> >> > Bests, VL> >> > Eyvaz. VL> >> > VL> >> > VL> >> >> > 2. They used only LDA, but not GGA. As it is VL> >> well VL> >> >> known (hopefully I am VL> >> >> > not wrong here) LDA fails for the ground VL> >> state of Fe. VL> >> >> In contrast to this, VL> >> >> > GGA does a good job for Fe. VL> >> >> VL> >> >> But I found the sentence like this, 'The VL> >> generalized VL> >> >> gradient approximation VL> >> >> in the Perdew- VL> >> >> Burke-Ernzerhof parametrization was chosen to VL> >> treat the VL> >> >> exchange-correlation VL> >> >> effects.' in the Methods section. I was rather VL> >> >> confused. VL> >> >> VL> >> >> > So, it will be very good if Vega can VL> >> calculate the VL> >> >> total energies for the VL> >> >> > rutile and anatase phases in odrer to study VL> >> whether VL> >> >> their energy position VL> >> >> > is dependent on the choice of VL> >> exchange-correlation VL> >> >> functional. VL> >> >> VL> >> >> I used to do a little test against this. The VL> >> results VL> >> >> suggested that the GGA VL> >> >> overestimate the lattice parameters a little with VL> >> 1% and VL> >> >> LDA underestimate VL> >> >> the lattice parameters for both case. I didn't VL> >> pay a VL> >> >> lot attentions on VL> >> >> energy position calculated by LDA. I'll check VL> >> it as VL> >> >> soon as possible. But to VL> >> >> my best knowledge, there were many reports VL> >> suggested that VL> >> >> the calculated VL> >> >> anatase stability was better than rutile. For VL> >> example, J. VL> >> >> Chem. Phys. 126, VL> >> >> 154703 (2007) said 'No matter which VL> >> Hamiltonian or VL> >> >> method is used, the VL> >> >> results on relative stability of both phases VL> >> suggest that VL> >> >> the anatase is VL> >> >> more stable than the rutile phase of TiO2.'. VL> >> Same VL> >> >> conclusion also was VL> >> >> mentioned in Phys. Rev. B 2002, 65 (22) and Phys. VL> >> Rev. B VL> >> >> 2007, 76 et al. VL> >> >> VL> >> >> > It might also be that there is a VL> >> transferability VL> >> >> problem for these PsPs (I VL> >> >> > can not prove this, just suggestion). VL> >> >> VL> >> >> Because I'm a beginner for QE. I though VL> >> >> pseudopotentials is quite VL> >> >> transferable and we could use the same VL> >> pseudopotentials for VL> >> >> any mater VL> >> >> containing the same kind of element. For instance, VL> >> we could VL> >> >> use the same VL> >> >> pseudopotentials for hcp Ti, TiN, rutile, VL> >> brookite, anatase VL> >> >> and other VL> >> >> polymorphs under high pressure, such as VL> >> >> Fluorite,Baddeleyite et al. But now, VL> >> >> I think I'm probably wrong. Could you tell me VL> >> the VL> >> >> difference between the Ti VL> >> >> pseudopotentials for hcp-Ti and TiN or many VL> >> polymorphs of VL> >> >> TiO2? And I also VL> >> >> wonder how to judge whether the pseudopotentials VL> >> is VL> >> >> suitable for certain VL> >> >> calculation? to calculate the lattice parameters VL> >> and VL> >> >> compare the results VL> >> >> with the experimental data? Is that enough? VL> >> >> VL> >> >> > It is my pleasure that they also mentioned VL> >> that VL> >> >> including of phonon VL> >> >> > contribution might be important. VL> >> >> I would like to calculate the phonon contribution. VL> >> But I VL> >> >> have few knowledge VL> >> >> about it. I'll learn to do that if necessary. VL> >> >> VL> >> >> vega VL> >> >> VL> >> >> VL> >> >> VL> >> ================================================================================= VL> >> >> Vega Lew (weijia liu) VL> >> >> PH.D Candidate in Chemical Engineering VL> >> >> State Key Laboratory of Materials-oriented VL> >> Chemical VL> >> >> Engineering VL> >> >> College of Chemistry and Chemical Engineering VL> >> >> Nanjing University of Technology, 210009, Nanjing, VL> >> Jiangsu, VL> >> >> China VL> >> >> VL> >> >> -------------------------------------------------- VL> >> >> From: "Eyvaz Isaev" VL> >> VL> >> >> Sent: Saturday, August 30, 2008 7:14 AM VL> >> >> To: "PWSCF Forum" VL> >> VL> >> >> Subject: Re: [Pw_forum] something strange in VL> >> rutile and VL> >> >> anatase calculation VL> >> >> VL> >> >> > Dear Wei, VL> >> >> > VL> >> >> > Thanks a lot for bringing the paper to our VL> >> attention. VL> >> >> > VL> >> >> > I have read the paper and have 2 comments. VL> >> >> > VL> >> >> > 1. They used only norm-conserving VL> >> pseudopotentials VL> >> >> constructed by means of VL> >> >> > different methods. VL> >> >> > VL> >> >> > 2. They used only LDA, but not GGA. As it is VL> >> well VL> >> >> known (hopefully I am VL> >> >> > not wrong here) LDA fails for the ground VL> >> state of Fe. VL> >> >> In contrast to this, VL> >> >> > GGA does a good job for Fe. VL> >> >> > VL> >> >> > So, it will be very good if Vega can VL> >> calculate the VL> >> >> total energies for the VL> >> >> > rutile and anatase phases in odrer to study VL> >> whether VL> >> >> their energy position VL> >> >> > is dependent on the choice of VL> >> exchange-correlation VL> >> >> functional. VL> >> >> > VL> >> >> > It might also be that there is a VL> >> transferability VL> >> >> problem for these PsPs (I VL> >> >> > can not prove this, just suggestion). VL> >> >> > VL> >> >> > It is my pleasure that they also mentioned VL> >> that VL> >> >> including of phonon VL> >> >> > contribution might be important. VL> >> >> > VL> >> >> > Bests, VL> >> >> > Eyvaz. VL> >> >> > VL> >> >> > VL> >> >> VL> >> ------------------------------------------------------------------- VL> >> >> > Prof. Eyvaz Isaev, VL> >> >> > Theoretical Physics Department, Moscow State VL> >> Institute VL> >> >> of Steel & Alloys, VL> >> >> > Russia, VL> >> >> > Department of Physics, Chemistry, and Biology VL> >> (IFM), VL> >> >> Linkoping University, VL> >> >> > Sweden VL> >> >> > Condensed Matter Theory Group, Uppsala VL> >> University, VL> >> >> Sweden VL> >> >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, VL> >> >> eyvaz_isaev at yahoo.com VL> >> >> > VL> >> >> > VL> >> >> > --- On Fri, 8/29/08, willy kohn VL> >> >> wrote: VL> >> >> > VL> >> >> >> From: willy kohn VL> >> VL> >> >> >> Subject: Re: [Pw_forum] something strange VL> >> in VL> >> >> rutile and anatase VL> >> >> >> calculation VL> >> >> >> To: "PWSCF Forum" VL> >> >> VL> >> >> >> Date: Friday, August 29, 2008, 10:02 PM VL> >> >> >> Hi, Vega: VL> >> >> >> VL> >> >> >> A recent result (Jpn. J. Appl. Phys. 39 VL> >> (2000) VL> >> >> L847) showed VL> >> >> >> that different VL> >> >> >> pseudopotential leaded to different VL> >> conclusions. VL> >> >> >> VL> >> >> >> Best, VL> >> >> >> VL> >> >> >> Wei VL> >> >> >> VL> >> >> >> On Thu, Aug 28, 2008 at 4:28 AM, vega VL> >> >> >> wrote: VL> >> >> >> VL> >> >> >> > Dear all, VL> >> >> >> > VL> >> >> >> > It is known that the rutile is more VL> >> stable VL> >> >> than VL> >> >> >> anatase in thermodynamics. VL> >> >> >> > Surprisingly, when I did the VL> >> vc-relax VL> >> >> calculation by VL> >> >> >> QE, I found VL> >> >> >> > the calculated energy of anatase VL> >> lower than VL> >> >> rutile. VL> >> >> >> Both vc-relax VL> >> >> >> > calculation for rutile and anatase VL> >> onverged VL> >> >> in 6 scf VL> >> >> >> cycles and 3 bfgs VL> >> >> >> > steps, giving the final enthalpy = VL> >> >> -362.7585836890 Ry VL> >> >> >> for rutile and VL> >> >> >> > -725.5447425835 Ry for antase. So VL> >> the average VL> >> >> energy VL> >> >> >> of [TiO2] unit VL> >> >> >> > is -181.3792918445 Ry for rutile and VL> >> >> -181.386185645875 VL> >> >> >> Ry for anatase. It VL> >> >> >> > looks like anatase is more stable VL> >> than VL> >> >> rutile. Do you VL> >> >> >> think it was quite VL> >> >> >> > strange? VL> >> >> >> > VL> >> >> >> > To make the calculation both for VL> >> anatase and VL> >> >> rutile VL> >> >> >> comparable, I used the VL> >> >> >> > same ecutwfc=40 Ry and ecutwfc=400 VL> >> Ry, and a VL> >> >> quite VL> >> >> >> dense k-point mesh for VL> >> >> >> > both case, 4x4x7 for rutile and VL> >> 5x5x2 for VL> >> >> anatase. VL> >> >> >> > VL> >> >> >> > for better understanding in my VL> >> calculation, VL> >> >> please VL> >> >> >> read the input file VL> >> >> >> > below, VL> >> >> >> > for anatase case, VL> >> >> >> > &CONTROL VL> >> >> >> > title = VL> >> 'Anatase VL> >> >> >> lattice' , VL> >> >> >> > calculation = VL> >> >> 'vc-relax' , VL> >> >> >> > restart_mode = VL> >> >> 'from_scratch' VL> >> >> >> , VL> >> >> >> > outdir = VL> >> >> >> > VL> >> >> >> VL> >> >> VL> >> '/home/hjfeng/vega/TiO2/Anatase/lattice/vctest/tmp/' VL> >> >> >> , VL> >> >> >> > wfcdir = VL> >> >> '/tmp/' , VL> >> >> >> > pseudo_dir = VL> >> >> >> VL> >> '/home/hjfeng/vega/espresso-4.0/pseudo/' , VL> >> >> >> > prefix = VL> >> 'Anatase VL> >> >> >> lattice' , VL> >> >> >> > disk_io = VL> >> 'none' VL> >> >> , VL> >> >> >> > nstep = 1000 VL> >> , VL> >> >> >> > / VL> >> >> >> > &SYSTEM VL> >> >> >> > ibrav = 6, VL> >> >> >> > celldm(1) = VL> >> 7.1356, VL> >> >> >> > celldm(3) = VL> >> 2.5122, VL> >> >> >> > nat = 12, VL> >> >> >> > ntyp = 2, VL> >> >> >> > ecutwfc = 40 , VL> >> >> >> > ecutrho = 400 , VL> >> >> >> > / VL> >> >> >> > &ELECTRONS VL> >> >> >> > VL> >> >> >> > / VL> >> >> >> > &IONS VL> >> >> >> > ion_dynamics = VL> >> 'bfgs' VL> >> >> , VL> >> >> >> > / VL> >> >> >> > &CELL VL> >> >> >> > cell_dynamics = VL> >> 'bfgs' VL> >> >> , VL> >> >> >> > / VL> >> >> >> > ATOMIC_SPECIES VL> >> >> >> > Ti 47.86700 VL> >> Ti.pw91-sp-van_ak.UPF VL> >> >> >> > O 15.99940 O.pw91-van_ak.UPF VL> >> >> >> > ATOMIC_POSITIONS crystal VL> >> >> >> > Ti 0.000000000 VL> >> 0.000000000 VL> >> >> 0.000000000 VL> >> >> >> > Ti 0.500000000 VL> >> 0.500000000 VL> >> >> 0.500000000 VL> >> >> >> > Ti 0.000000000 VL> >> 0.500000000 VL> >> >> 0.250000000 VL> >> >> >> > Ti 0.500000000 VL> >> 0.000000000 VL> >> >> 0.750000000 VL> >> >> >> > O 0.000000000 VL> >> 0.500000000 VL> >> >> 0.042000000 VL> >> >> >> > O 0.000000000 VL> >> 0.000000000 VL> >> >> 0.208000000 VL> >> >> >> > O 0.500000000 VL> >> 0.500000000 VL> >> >> 0.292000000 VL> >> >> >> > O 0.000000000 VL> >> 0.500000000 VL> >> >> 0.458000000 VL> >> >> >> > O 0.500000000 VL> >> 0.000000000 VL> >> >> 0.542000000 VL> >> >> >> > O 0.500000000 VL> >> 0.500000000 VL> >> >> 0.708000000 VL> >> >> >> > O 0.000000000 VL> >> 0.000000000 VL> >> >> 0.792000000 VL> >> >> >> > O 0.500000000 VL> >> 1.000000000 VL> >> >> 0.958000000 VL> >> >> >> > K_POINTS automatic VL> >> >> >> > 5 5 2 1 1 1 VL> >> >> >> > VL> >> >> >> > for rutile case, VL> >> >> >> > VL> >> >> >> > &CONTROL VL> >> >> >> > title = VL> >> Rutile_lattice VL> >> >> , VL> >> >> >> > calculation = VL> >> >> 'vc-relax' , VL> >> >> >> > restart_mode = VL> >> >> 'from_scratch' VL> >> >> >> , VL> >> >> >> > outdir = VL> >> >> >> > VL> >> >> VL> >> '/home/vega32/TiO2/rutile/lattice/vcrelax/tmp' VL> >> >> >> , VL> >> >> >> > wfcdir = VL> >> >> '/tmp/' , VL> >> >> >> > pseudo_dir = VL> >> >> >> VL> >> '/home/vega32/espresso-4.0.1/pseudo/' , VL> >> >> >> > prefix = VL> >> 'Anatase VL> >> >> >> lattice' , VL> >> >> >> > disk_io = VL> >> 'none' VL> >> >> , VL> >> >> >> > nstep = 1000 VL> >> , VL> >> >> >> > / VL> >> >> >> > &SYSTEM VL> >> >> >> > ibrav = 6, VL> >> >> >> > celldm(1) = VL> >> 8.6814, VL> >> >> >> > celldm(3) = VL> >> 0.6441, VL> >> >> >> > nat = 6, VL> >> >> >> > ntyp = 2, VL> >> >> >> > ecutwfc = 40 , VL> >> >> >> > ecutrho = 400 , VL> >> >> >> > / VL> >> >> >> > &ELECTRONS VL> >> >> >> > VL> >> >> >> > / VL> >> >> >> > &IONS VL> >> >> >> > ion_dynamics = VL> >> 'bfgs' VL> >> >> , VL> >> >> >> > / VL> >> >> >> > &CELL VL> >> >> >> > cell_dynamics = VL> >> 'bfgs' VL> >> >> , VL> >> >> >> > / VL> >> >> >> > ATOMIC_SPECIES VL> >> >> >> > O 15.99940 O.pw91-van_ak.UPF VL> >> >> >> > Ti 47.90000 VL> >> Ti.pw91-sp-van_ak.UPF VL> >> >> >> > ATOMIC_POSITIONS crystal VL> >> >> >> > O 0.304800000 VL> >> 0.304800000 VL> >> >> 0.000000000 VL> >> >> >> > O 0.695200000 VL> >> 0.695200000 VL> >> >> 0.000000000 VL> >> >> >> > O 0.195200000 VL> >> 0.804800000 VL> >> >> 0.500000000 VL> >> >> >> > O 0.804800000 VL> >> 0.195200000 VL> >> >> 0.500000000 VL> >> >> >> > Ti 0.500000000 VL> >> 0.500000000 VL> >> >> 0.500000000 VL> >> >> >> > Ti 0.000000000 VL> >> 0.000000000 VL> >> >> 0.000000000 VL> >> >> >> > K_POINTS automatic VL> >> >> >> > 4 4 7 1 1 1 VL> >> >> >> > VL> >> >> >> > vega VL> >> >> >> > VL> >> >> >> > VL> >> >> >> VL> >> >> VL> >> ============================================================== VL> >> >> >> > Vega Lew ( weijia liu) VL> >> >> >> > PH.D Candidate in Chemical VL> >> Engineering VL> >> >> >> > State Key Laboratory of VL> >> Materials-oriented VL> >> >> Chemical VL> >> >> >> Engineering VL> >> >> >> > College of Chemistry and Chemical VL> >> Engineering VL> >> >> >> > Nanjing University of Technology, VL> >> 210009, VL> >> >> Nanjing, VL> >> >> >> Jiangsu, China VL> >> >> >> > VL> >> >> >> > VL> >> >> _______________________________________________ VL> >> >> >> > Pw_forum mailing list VL> >> >> >> > Pw_forum at pwscf.org VL> >> >> >> > VL> >> >> http://www.democritos.it/mailman/listinfo/pw_forum VL> >> >> >> > VL> >> >> >> > VL> >> >> >> VL> >> _______________________________________________ VL> >> >> >> Pw_forum mailing list VL> >> >> >> Pw_forum at pwscf.org VL> >> >> >> VL> >> http://www.democritos.it/mailman/listinfo/pw_forum VL> >> >> > VL> >> >> > VL> >> >> > VL> >> >> > VL> >> _______________________________________________ VL> >> >> > Pw_forum mailing list VL> >> >> > Pw_forum at pwscf.org VL> >> >> > VL> >> http://www.democritos.it/mailman/listinfo/pw_forum VL> >> >> > VL> >> > VL> >> > VL> >> > VL> >> > VL> > VL> > VL> > VL> > VL> _______________________________________________ VL> Pw_forum mailing list VL> Pw_forum at pwscf.org VL> http://www.democritos.it/mailman/listinfo/pw_forum VL> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From kazempoor2000 at yahoo.com Sun Aug 31 09:18:32 2008 From: kazempoor2000 at yahoo.com (ali kazempoor) Date: Sun, 31 Aug 2008 00:18:32 -0700 (PDT) Subject: [Pw_forum] anisotropy energy Message-ID: <623864.91698.qm@web33104.mail.mud.yahoo.com> Dear all For obtaining correct results for MAE(magnetic anisotropy energy), at first we must relax atomic positions. Does This relaxation must be done by a pseudopotential that? include the spin-orbit effect or ?without spin -orbit in pseudopotential? After? obtaining the optimum atomic position , for obtaining the accurate MAE , which?Kpoint mesh is suitable( high K mesh or as perviuos step(relaxation)? common K mesh)? ?And what is suitable for thereshold of energy? thanks a lot Ali Kazempour, Dept. Of . Phys. .Isfahan university of technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080831/33045c92/attachment.htm From anna.ferrari at unito.it Sun Aug 31 11:26:49 2008 From: anna.ferrari at unito.it (anna.ferrari at unito.it) Date: Sun, 31 Aug 2008 11:26:49 +0200 (CEST) Subject: [Pw_forum] (no subject) Message-ID: <10064.87.14.218.240.1220174809.squirrel@mail.unito.it> dear all i have two questions: 1)in restart_mode restart is done from wavefunction or from density? therefore which are the files that should be provided? 2) what is ecutrho exactly and what happens if a value is not provided? thanks anna From vegalew at hotmail.com Sun Aug 31 12:46:53 2008 From: vegalew at hotmail.com (vega) Date: Sun, 31 Aug 2008 18:46:53 +0800 Subject: [Pw_forum] (no subject) In-Reply-To: <10064.87.14.218.240.1220174809.squirrel@mail.unito.it> References: <10064.87.14.218.240.1220174809.squirrel@mail.unito.it> Message-ID: > 2) what is ecutrho exactly and what happens if a value is > not provided? It might use ecutrho=4xecutwfc by default. ================================================================================= Vega Lew (weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China -------------------------------------------------- From: Sent: Sunday, August 31, 2008 5:26 PM To: Subject: [Pw_forum] (no subject) > dear all > i have two questions: > > > 1)in restart_mode > restart is done from wavefunction or from density? > therefore which are the files that should be provided? > > thanks > anna > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From vegalew at hotmail.com Sun Aug 31 12:55:00 2008 From: vegalew at hotmail.com (vega) Date: Sun, 31 Aug 2008 18:55:00 +0800 Subject: [Pw_forum] anisotropy energy In-Reply-To: <623864.91698.qm@web33104.mail.mud.yahoo.com> References: <623864.91698.qm@web33104.mail.mud.yahoo.com> Message-ID: >After obtaining the optimum atomic position , for obtaining the accurate MAE , which Kpoint mesh is suitable( high K >mesh or as perviuos step(relaxation) common K mesh)? I think you should try different K mesh and see whether the results convergenced. for example if 4x4x2 and 2x2x1 give the similar results with 1%~2% errors (maybe 5%) you may use 2x2x1 for simpleness. Also the k point mesh should compromise with the hardware. >And what is suitable for thereshold of energy? I think the default value is suitable for many purposes. see archive for more detail. Prof.Baroni have lectured us many times for this. vega ================================================================================= Vega Lew (weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China From: ali kazempoor Sent: Sunday, August 31, 2008 3:18 PM To: pw_forum at pwscf.org Subject: [Pw_forum] anisotropy energy Dear all For obtaining correct results for MAE(magnetic anisotropy energy), at first we must relax atomic positions. Does This relaxation must be done by a pseudopotential that include the spin-orbit effect or without spin -orbit in pseudopotential? After obtaining the optimum atomic position , for obtaining the accurate MAE , which Kpoint mesh is suitable( high K mesh or as perviuos step(relaxation) common K mesh)? And what is suitable for thereshold of energy? thanks a lot Ali Kazempour, Dept. Of . Phys. .Isfahan university of technology -------------------------------------------------------------------------------- _______________________________________________ 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/20080831/04d1923e/attachment.htm From vegalew at hotmail.com Sun Aug 31 13:22:01 2008 From: vegalew at hotmail.com (vega) Date: Sun, 31 Aug 2008 19:22:01 +0800 Subject: [Pw_forum] The scf calculation is not converged Message-ID: Dear all, First I relaxed a multi-layer structure, something like rutile 110 oriented ultra-thin film illustrated in Phys. Rev. B 2004, 70 (3) (http://prola.aps.org/abstract/PRB/v70/i3/e035419). I want to calculate the binding energy between different layers. So I divided the slab into two parts, up and down. The dimension of the box was remaining the same as the whole relaxed layer slab. the only difference was the number of atoms in the box. some box missing upper part of slab and some down. And then I did a scf calculation for each one. But some scf calculations can't be converged even in 1000 cycles. Also many other scf calculation can be converged in about 30 cycles. How could I deal with the convergence problem? thank you for reading vega ================================================================================= Vega Lew (weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20080831/b46fd09e/attachment.htm From bogus@does.not.exist.com Sun Aug 24 10:11:18 2008 From: bogus@does.not.exist.com () Date: Sun, 24 Aug 2008 08:11:18 -0000 Subject: No subject Message-ID: epsil (default=.false.) - if .true. in a q=0 calculation for a non metal the macroscopic dielectric constant of the system is computed. Do not set epsil to .true. if you have a metallic system or q/=0: the code will complain and stop So, if you like to exclude the electric field contribution in semiconductors (insulators) just consider them as a metallic system. But later you will find an inconsistency between phonons you calculated and experimental data as the electric field leads to splitting of LO-TO modes in semiconductors. > I am new to pwscf Welcome! Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com --- On Wed, 9/3/08, Ravi Maranganti wrote: > From: Ravi Maranganti > Subject: [Pw_forum] How to calculate real space inter-atomic force constants excluding the contribution due to macroscopic electric field > To: pw_forum at pwscf.org > Date: Wednesday, September 3, 2008, 10:05 PM > Hello All > How should i calculate the real space interatomic force > constants with > the contribution due to the macroscopic electric field > being excluded. > According to Giannozzi et al (Ab initio calculation of > phonons in > semiconductors, Phys Rev B, v. 43, p.7231), the > contribution to the > dynamical matrix in polar materials can be written as a > combination of an > analytical term and a non-analytical term (at low > k-vectors). The > non-analytical term involves the Born effective charges and > the dielectric > constant. so, should i subtract this term from the > dynamical matrix at all > k-vectors (or only at certain k-vectors?) and then use > q2r.x to obtain the > real space force constants? Also, should i *not* specify > .epsil. = true? I > am new to pwscf so please bear with me...thanks! > > Ravi Maranganti, > PhD Candidate, Mechanical Engg Dept, > Univ of Houston, TX > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From bogus@does.not.exist.com Sun Aug 24 10:11:18 2008 From: bogus@does.not.exist.com () Date: Sun, 24 Aug 2008 08:11:18 -0000 Subject: No subject Message-ID: calculation is quite low. I think it maybe not up to snuff. For better understanding with my problem, I'll tell more about my = software, hardware and simulation model. Simulation model: my system was a slab model for a certain metal oxide = surface with 3 irregular k points. The pseudopotential was Ultrasoft (Vanderbilt) Pseudopotentials. Hardware: there are two Xeon single core CPUs and 2G physical memory for = each node. The network=20 is infiniband with 10G band width.=20 Software: My fortran and C compile was intel 10.0.015 version. MKL is = l_mkl_p_10.0.3.020.tgz. FFTW is fftw-2.1.5.tar.gz. MPI is mpich2-1.0.7.tar.gz. All of above was = stored at NSF location. My QE was compiled in a NFS location. and the outdir was also on the = NFS. wfcdir was on local disk, /tmp/ folder. In order to reduce the IO, I also set the disk_io = =3D 'none'. Could you tell me what make my CPUs run in a such low efficiency style? = Is there any hints to improve the=20 performance of the parallel efficiency? Do you think 10G infiniband is good enough for 39 nodes? Do you think = it's not necessary to put so much file on NFS localtion? Could tell me which folders must be on a NFS location = so that all the nodes can load and=20 write? =20 I also noticed that the pw.x reported 129.6 Mb memory was required. But = actually, I found the virtual memory was used. Do you think the pw.x underestimate greatly for the memory?=20 thank you for reading. any hints on my problem will be deeply appreciated. vega =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D Vega Lew (weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China ------=_NextPart_000_0008_01C91ABB.63A1E290 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear all,
 
I just finished a relax = calculation for 120=20 atoms. After calculation was done, the outputfile reported as=20 follows,
 
    Program=20 PWSCF     v.4.0.1  starts=20 ...
     Today is 16Sep2008 at 19:14:42 =
 
     Parallel = version=20 (MPI)
 
     Number of = processors in=20 use:      78
     = K-points=20 division:     npool    =20 =3D    3
     R & G space=20 division:  proc/pool =3D   26
 
     For = Norm-Conserving or=20 Ultrasoft (Vanderbilt) Pseudopotentials or PAW
................................
     per-process = dynamical=20 memory:   129.6 Mb
................................
 
    =20 PWSCF        = :    =20 0d   14h46m CPU = time,       =20 2d   18h 4m wall time
 
    =20 init_run     :    91.49s=20 CPU
     electrons    : 47137.56s = CPU=20 (      27 calls,1745.836 s=20 avg)
     update_pot   :   = 187.80s=20 CPU (      26 calls,   7.223 s=20 avg)
     = forces      =20 :  4492.20s CPU (      27 calls, 166.378 s = avg)
 
     Called by=20 init_run:
     = wfcinit     =20 :    23.68s CPU
    =20 potinit      :     3.15s=20 CPU
 
     Called by=20 electrons:
     = c_bands      :=20 23198.29s CPU (     258 calls,  89.916 s=20 avg)
     sum_band     : = 11159.67s=20 CPU (     258 calls,  43.255 s=20 avg)
     v_of_rho     = :  =20 167.39s CPU (     280 calls,   0.598 s=20 avg)
    =20 newd         : 13679.79s CPU=20 (     280 calls,  48.856 s=20 avg)
     mix_rho     =20 :    30.14s CPU (     258 = calls,  =20 0.117 s avg)
 
     Called by=20 c_bands:
     init_us_2   =20 :    48.95s CPU (     517 = calls,  =20 0.095 s avg)
     = cegterg      :=20 23038.94s CPU (     258 calls,  89.298 s=20 avg)
 
     Called by=20 *egterg:
    =20 h_psi        :  8629.82s CPU=20 (    1459 calls,   5.915 s=20 avg)
     = s_psi       =20 :  2230.78s CPU (    1459 calls,   1.529 s = avg)
     = g_psi       =20 :    34.68s CPU (    1200 = calls,   0.029=20 s avg)
     cdiaghg      = : =20 5929.74s CPU (    1427 calls,   4.155 s=20 avg)
 
     Called by=20 h_psi:
     add_vuspsi   :  = 2209.17s CPU=20 (    1459 calls,   1.514 s avg)
 
     General=20 routines
     = calbec      =20 :  2904.12s CPU (    1744 calls,   1.665 s = avg)
     = cft3s       =20 :  4337.89s CPU (  950068 calls,   0.005 s=20 avg)
     interpolate  :    = 34.87s=20 CPU (     538 calls,   0.065 s=20 avg)
 
     Parallel=20 routines
     fft_scatter  :   = 538.83s CPU=20 (  950068 calls,   0.001 s avg)
 
From the reported information, we can = see that the=20 efficiency of my calculation is quite low.
I think it maybe not up to = snuff.
For better understanding with my = problem, I'll tell=20 more about my software, hardware and simulation model.
 
Simulation model: my system was a slab = model for=20 a certain metal oxide surface with 3 irregular k = points.
The pseudopotential was Ultrasoft = (Vanderbilt)=20 Pseudopotentials.
 
Hardware: there are two Xeon single = core CPUs=20 and 2G physical memory for each node. The network
is infiniband with 10G band width. =
 
Software: My fortran and C compile was = intel=20 10.0.015 version. MKL is l_mkl_p_10.0.3.020.tgz.
FFTW is fftw-2.1.5.tar.gz. MPI is=20 mpich2-1.0.7.tar.gz. All of = above was stored=20 at NSF location.
My QE was compiled in a NFS location. = and the=20 outdir was also on the NFS. wfcdir was on local
disk, /tmp/ folder. In order = to reduce=20 the IO, I also set the disk_io =3D 'none'.
 
Could you tell me what make = my CPUs run in a=20 such low efficiency style? Is there any hints to improve the =
performance of the parallel=20 efficiency?
 
Do you think 10G infiniband is good = enough for 39=20 nodes? Do you think it's not necessary to put so much file
on NFS = localtion?  Could tell me=20 which folders must be on a NFS location so that all the nodes can = load=20 and 
write?  
 
I also noticed that the pw.x reported = 129.6 Mb=20 memory was required. But actually, I found the virtual memory = was
used. Do you think the pw.x = underestimate greatly=20 for the memory?
 
thank you for reading.
 
any hints on my problem will be deeply=20 appreciated.
 
vega
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D
Vega=20 Lew (weijia liu)
PH.D Candidate in Chemical Engineering
State Key=20 Laboratory of Materials-oriented Chemical Engineering
College of = Chemistry=20 and Chemical Engineering
Nanjing University of Technology, 210009, = Nanjing,=20 Jiangsu, China
------=_NextPart_000_0008_01C91ABB.63A1E290-- From bogus@does.not.exist.com Sun Aug 24 10:11:18 2008 From: bogus@does.not.exist.com () Date: Sun, 24 Aug 2008 08:11:18 -0000 Subject: No subject Message-ID: could you tell me which dir should be added to the LD_LIBRARY_PATH, or which flags should be added after the QE configure command? thank you vega ================================================================================= Vega Lew (weijia liu) PH.D Candidate in Chemical Engineering State Key Laboratory of Materials-oriented Chemical Engineering College of Chemistry and Chemical Engineering Nanjing University of Technology, 210009, Nanjing, Jiangsu, China -------------------------------------------------- From: "Serge Nakhmanson" Sent: Tuesday, September 30, 2008 7:48 AM To: "PWSCF Forum" Subject: [Pw_forum] Compiling with intel fortran, MKL and MKL FFT wrappers > Dear All, > > Here's a question to those of you who succeeded doing the Subj. > > Here's how MKL distribution looks like on my cluster: > > serafina {1323} > pwd > /usr/local/intel/mkl/10.0.4.023/interfaces > serafina {1324} > ls > blas95 fftw2xc fftw2x_cdft fftw2xf fftw3xc fftw3xf lapack95 > serafina {1325} > > > We (me and our sysadmin) compiled all versions of the MKL FFT > wrappers, but we assumed that the parallel one (fftw2x_cdft) > is the one to be used when compiling Espresso. > > However, linking with that one produces a bunch of undefined > references in {espresso}/clib/fft_stick.c. > > When, instead, we link with fftw2xc (which is serial), everything > compiles and works just fine. > > My question is: is the latter (serial) library really the > one intended to be used with Espresso, or is it the parallel > one that should work but fails due to some function renaming > in the latest MKL version? Or is there something else that > could be wrong? > > Just in case, here are a few informative lines from our make.sys: > > DFLAGS = -D__INTEL -D__FFTW -D__MPI -D__PARA > IFLAGS > = -I../include -I/usr/local/intel/mkl/10.0.4.023/include/fftw > BLAS_LIBS > = -L/usr/local/intel/mkl/10.0.4.023/lib/em64t -lmkl_intel_lp64 > -lmkl_sequential -lmkl_core > LAPACK_LIBS > = -L/usr/local/intel/mkl/10.0.4.023/lib/em64t -lmkl_intel_lp64 > -lmkl_sequential -lmkl_core > #FFT_LIBS > = -L/usr/local/intel/mkl/10.0.4.023/lib/64 -lfftw2x_cdft_DOUBLE > FFT_LIBS = -L/usr/local/intel/mkl/10.0.4.023/lib/64 -lfftw2xc_intel > > > THX, > > Serge > > > -- > ********************************************************* > Serge M. Nakhmanson phone: (630) 252-5205 > Assistant Scientist fax: (630) 252-4798 > MSD-212, Rm. C-224 > Argonne National Laboratory > 9700 S. Cass Ave. > Argonne, IL 60439 > ********************************************************* > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From bogus@does.not.exist.com Sun Aug 24 10:11:18 2008 From: bogus@does.not.exist.com () Date: Sun, 24 Aug 2008 08:11:18 -0000 Subject: No subject Message-ID: Archives=2C I learned ultrasoft PPs may not be desirable for ELF analysi= s due to small amount of electron density loss from augmentation charges=2E So=2C I am wondering whether or not using USPPs is a safe choice for direct space analysis associated= with spin polarization density=2E Best regards=2CSang-Hwan Kim (postdoc) Department of Chemistry University of Houston 136 Fleming Building Houston=2C TX 77204-5003 --Boundary_(ID_He1tyKgEBEwteNaTLSMGHw) Content-type: text/html; charset=utf-8 Content-transfer-encoding: quoted-printable Content-disposition: inline =3Cmeta 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m=3Aval=3D=22Cambria Math=22/=3E =3Cm=3AbrkBin m=3Aval=3D=22before=22/=3E =3Cm=3AbrkBinSub m=3Aval=3D=22=26=2345=3B-=22/=3E =3Cm=3AsmallFrac m=3Aval=3D=22off=22/=3E =3Cm=3AdispDef/=3E =3Cm=3AlMargin m=3Aval=3D=220=22/=3E =3Cm=3ArMargin m=3Aval=3D=220=22/=3E =3Cm=3AdefJc m=3Aval=3D=22centerGroup=22/=3E =3Cm=3AwrapIndent m=3Aval=3D=221440=22/=3E =3Cm=3AintLim m=3Aval=3D=22subSup=22/=3E =3Cm=3AnaryLim m=3Aval=3D=22undOvr=22/=3E =3C/m=3AmathPr=3E=3C/w=3AWordDocument=3E =3C/xml=3E=3C!=5Bendif=5D--=3E=3C!--=5Bif gte mso 9=5D=3E=3Cxml=3E =3Cw=3ALatentStyles DefLockedState=3D=22false=22 DefUnhideWhenUsed=3D=22= true=22 DefSemiHidden=3D=22true=22 DefQFormat=3D=22false=22 DefPriority=3D=229= 9=22 LatentStyleCount=3D=22267=22=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=220=22 SemiHidden= =3D=22false=22 UnhideWhenUsed=3D=22false=22 QFormat=3D=22true=22 Name=3D=22Normal=22= /=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=229=22 SemiHidden= =3D=22false=22 UnhideWhenUsed=3D=22false=22 QFormat=3D=22true=22 Name=3D=22heading 1= =22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=229=22 QFormat=3D= =22true=22 Name=3D=22heading 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=229=22 QFormat=3D= =22true=22 Name=3D=22heading 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=229=22 QFormat=3D= =22true=22 Name=3D=22heading 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=229=22 QFormat=3D= =22true=22 Name=3D=22heading 5=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=229=22 QFormat=3D= =22true=22 Name=3D=22heading 6=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=229=22 QFormat=3D= =22true=22 Name=3D=22heading 7=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=229=22 QFormat=3D= =22true=22 Name=3D=22heading 8=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=229=22 QFormat=3D= =22true=22 Name=3D=22heading 9=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2239=22 Name=3D=22= toc 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2239=22 Name=3D=22= toc 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2239=22 Name=3D=22= toc 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2239=22 Name=3D=22= toc 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2239=22 Name=3D=22= toc 5=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2239=22 Name=3D=22= toc 6=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2239=22 Name=3D=22= toc 7=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2239=22 Name=3D=22= toc 8=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2239=22 Name=3D=22= toc 9=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2235=22 QFormat=3D= =22true=22 Name=3D=22caption=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2210=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 QFormat=3D=22true=22 Name=3D=22Title=22/= =3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=221=22 Name=3D=22= Default Paragraph Font=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2211=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 QFormat=3D=22true=22 Name=3D=22Subtitle=22= /=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2222=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 QFormat=3D=22true=22 Name=3D=22Strong=22= /=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2220=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 QFormat=3D=22true=22 Name=3D=22Emphasis=22= /=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2259=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Table Grid=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 UnhideWhenUsed=3D=22false=22 = Name=3D=22Placeholder Text=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=221=22 SemiHidden= =3D=22false=22 UnhideWhenUsed=3D=22false=22 QFormat=3D=22true=22 Name=3D=22No Spacin= g=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2260=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Shading=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2261=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light List=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2262=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Grid=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2263=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Shading 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2264=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Shading 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2265=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium List 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2266=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium List 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2267=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2268=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2269=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2270=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Dark List=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2271=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful Shading=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2272=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful List=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2273=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful Grid=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2260=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Shading Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2261=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light List Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2262=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Grid Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2263=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Shading 1 Accent 1=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2264=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Shading 2 Accent 1=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2265=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium List 1 Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 UnhideWhenUsed=3D=22false=22 = Name=3D=22Revision=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2234=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 QFormat=3D=22true=22 Name=3D=22List Para= graph=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2229=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 QFormat=3D=22true=22 Name=3D=22Quote=22/= =3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2230=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 QFormat=3D=22true=22 Name=3D=22Intense Q= uote=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2266=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium List 2 Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2267=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 1 Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2268=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 2 Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2269=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 3 Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2270=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Dark List Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2271=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful Shading Accent 1=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2272=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful List Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2273=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful Grid Accent 1=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2260=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Shading Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2261=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light List Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2262=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Grid Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2263=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Shading 1 Accent 2=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2264=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Shading 2 Accent 2=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2265=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium List 1 Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2266=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium List 2 Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2267=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 1 Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2268=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 2 Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2269=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 3 Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2270=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Dark List Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2271=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful Shading Accent 2=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2272=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful List Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2273=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful Grid Accent 2=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2260=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Shading Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2261=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light List Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2262=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Grid Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2263=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Shading 1 Accent 3=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2264=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Shading 2 Accent 3=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2265=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium List 1 Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2266=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium List 2 Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2267=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 1 Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2268=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 2 Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2269=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 3 Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2270=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Dark List Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2271=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful Shading Accent 3=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2272=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful List Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2273=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful Grid Accent 3=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2260=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Shading Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2261=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light List Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2262=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Grid Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2263=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Shading 1 Accent 4=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2264=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Shading 2 Accent 4=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2265=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium List 1 Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2266=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium List 2 Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2267=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 1 Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2268=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 2 Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2269=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Medium Grid 3 Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2270=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Dark List Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2271=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful Shading Accent 4=22/=3E= =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2272=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful List Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2273=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Colorful Grid Accent 4=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2260=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light Shading Accent 5=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2261=22 SemiHidde= n=3D=22false=22 UnhideWhenUsed=3D=22false=22 Name=3D=22Light List Accent 5=22/=3E =3Cw=3ALsdException Locked=3D=22false=22 Priority=3D=2262=22 SemiHidde= 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mso-hansi-font-family=3ACalibri=3B mso-hansi-theme-font=3Aminor-latin=3B=7D =3C/style=3E =3C!=5Bendif=5D--=3E =3Cp class=3D=22MsoNormal=22=3E=3Cspan style=3D=22=22=3EDear users and developers=2C=3Co=3Ap=3E=3C/o=3Ap=3E=3C/span=3E=3C/p=3E =3Cp class=3D=22MsoNormal=22=3E=3Cspan style=3D=22=22=3EFrom the Pw=5Ffo= rum Archives=2C I learned ultrasoft PPs may not be desirable for ELF analysi= s due to small amount of electron density loss from augmentation charges=2E=3Co=3Ap=3E=3C= /o=3Ap=3E=3C/span=3E=3C/p=3E =3Cp class=3D=22MsoNormal=22=3E=3Cspan style=3D=22=22=3ESo=2C I am wonde= ring whether or not using USPPs is a safe choice for direct space analysis associated= with spin polarization density=2E=3C/span=3E=3C/p=3E=3Cp class=3D=22MsoNormal=22=3E= =3Cbr=3E=3Cspan style=3D=22=22=3E=3C/span=3E=3C/p=3E=3Cp class=3D=22MsoN= ormal=22=3E=3Cspan style=3D=22=22=3EBest regards=2C=3C/span=3E=3C/p=3E=3C= p class=3D=22MsoNormal=22=3E=3Cspan style=3D=22=22=3ESang-Hwan Kim (post= doc)=3Cbr=3E=3C/span=3E=3C/p=3E=3Cp class=3D=22MsoNormal=22=3E=3C/p=3E=3C= BR=3E=3CBR=3EDepartment of Chemistry=3Cbr=3EUniversity of Houston=3Cbr=3E= 136 Fleming Building=3Cbr=3EHouston=2C TX 77204-5003=3C/BR=3E=3C/BR=3E --Boundary_(ID_He1tyKgEBEwteNaTLSMGHw)--