From germaneau at gucas.ac.cn Tue Mar 1 04:55:51 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Mon, 28 Feb 2011 22:55:51 -0500 Subject: [Pw_forum] Bravais lattices & matrix of cell parameters In-Reply-To: <498883713.27999@test1.gucas.ac.cn> References: <4D69D82F.6020003@gucas.ac.cn> <498883713.27999@test1.gucas.ac.cn> Message-ID: <4D6C6E47.5050902@gucas.ac.cn> Well, my question concern more the crystal class than the Bravais lattice actually. I was just wondering what the matrix of the cell parameters looks like in a case of non triclinic cell. I'm wondering how the fact that a=b for instance is "translated" in the matrix form of the cell parameters. One may also have less than six degree of freedom. Thank you, Eric. On 02/28/2011 05:24 AM, Paolo Giannozzi wrote: > On Feb 27, 2011, at 5:50 , Eric Germaneau wrote: > >> I'd like to know the relationships between the elements of the matrix >> of cell parameters for each Bravais lattices. > you would like to know...what exactly? P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of ChineseAcademy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110228/d9f26c77/attachment.htm From mohnish.iitk at gmail.com Tue Mar 1 07:08:13 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 1 Mar 2011 11:38:13 +0530 Subject: [Pw_forum] Conservation of spin on oxygen adsorption Message-ID: Dear QE users, I am doing O2 adsorption on metal clusters. I have the question of how to conserve the spin multiplicity of O2 molecule during adsorption. I tried searching in the forum archive but did not find it. Can anybody please help me? Thanks a lot. -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110301/44613d6f/attachment.htm From giannozz at democritos.it Tue Mar 1 10:03:21 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 1 Mar 2011 10:03:21 +0100 Subject: [Pw_forum] Conservation of spin on oxygen adsorption In-Reply-To: References: Message-ID: On Mar 1, 2011, at 7:08 , mohnish pandey wrote: > how to conserve the spin multiplicity of O2 molecule > during adsorption all you can do is to keep the total magnetization of the system (O2+metal cluster) fixed to the value for O2 far from the metal cluster (e.g. 2 if the meta cluster has no spi polarization) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From member at linkedin.com Wed Mar 2 10:39:05 2011 From: member at linkedin.com (Cecil Ouma via LinkedIn) Date: Wed, 2 Mar 2011 09:39:05 +0000 (UTC) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <639686514.367191.1299058745097.JavaMail.app@ela4-bed83.prod> LinkedIn ------------Cecil Ouma requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Cecil Accept invitation from Cecil Ouma http://www.linkedin.com/e/-iqpnjm-gks21atk-30/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I16858299_60/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_c3pvejAOe3kUdz59bRdkgkcPunpobP8TczsRejkOd38LrCBxbOYWrSlI/EML_comm_afe/ View invitation from Cecil Ouma http://www.linkedin.com/e/-iqpnjm-gks21atk-30/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I16858299_60/0MdBYVej8UdjwSckALqnpPbOYWrSlI/svi/ ------------------------------------------ Why might connecting with Cecil Ouma be a good idea? Have a question? Cecil Ouma's network will probably have an answer: You can use LinkedIn Answers to distribute your professional questions to Cecil Ouma and your extended network. You can get high-quality answers from experienced professionals. http://www.linkedin.com/e/-iqpnjm-gks21atk-30/ash/inv19_ayn/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110302/a2b20b55/attachment.htm From raamesh123 at rediffmail.com Wed Mar 2 13:46:37 2011 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 2 Mar 2011 12:46:37 -0000 Subject: [Pw_forum] =?utf-8?q?Parallel_computing?= Message-ID: <20110302124637.7671.qmail@f6mail-145-185.rediffmail.com> Dear All I am new to parallel calculation trying to learn from the USER GUIDE. My trial calculations are running in serial and with different no of processors say 4, 8 16 etc...but i am able to run only one calculation at a time... If i submit 3 or 4 jobs it crashes..... My query is am i missing something important in the path??? or I should install the package in the head node??? thank you with regards K. Ramesh Kumar IIT Madras 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/20110302/14b6f892/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Wed Mar 2 14:07:37 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 02 Mar 2011 14:07:37 +0100 Subject: [Pw_forum] Parallel computing In-Reply-To: <20110302124637.7671.qmail@f6mail-145-185.rediffmail.com> References: <20110302124637.7671.qmail@f6mail-145-185.rediffmail.com> Message-ID: On Wed, 02 Mar 2011 13:46:37 +0100, ramesh kumar wrote: > but i am able to run only one calculation > at a time... Dear Ramesh, it is not possible to run 2 or more calculations with the same prefix and outdir. Please check if this is your case. Otherwise, please provide more detail on your problem, at the very least the output generated before the crash. best regards -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From giannozz at democritos.it Wed Mar 2 16:53:27 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 2 Mar 2011 16:53:27 +0100 Subject: [Pw_forum] problems computing cholesky decomposition In-Reply-To: References: Message-ID: <27DCCE4A-6BEC-4AE9-8F40-2F80663DBA5B@democritos.it> On Feb 16, 2011, at 17:04 , YY wrote: > Here is the input file atomic positions are missing. This makes it impossible to run it P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From akrukau at indiana.edu Wed Mar 2 23:58:19 2011 From: akrukau at indiana.edu (Krukau, Aliaksandr) Date: Wed, 2 Mar 2011 17:58:19 -0500 Subject: [Pw_forum] Lattice constant for copper Message-ID: <20110302175819.hkx8o4qh88ww40cw@webmail.iu.edu> Dear QE users, I apologize if my question seems stupid to you. I am a complete QE newbie and could not find any answer in the tutorials. I am trying to find equilibrium lattice constant for copper with PBE and ultrasoft pseudopotentials. I ran scf calculations for face-centered cubic unit cell for a number of lattice constants: Lattice constant 6.65 a.u. ! total energy = -121.62734203 Ry Lattice constant 6.66 a.u. ! total energy = -121.62735421 Ry Lattice constant 6.67 a.u. ! total energy = -121.62734651 Ry Lattice constant 6.65 a.u. ! total energy = -121.62731956 Ry The minimum total energy is for the lattice constant 6.66 a.u. But this value drastically differs from the published PBE value of 6.86 a.u. (Phys. Rev. B, vol. 77, 05414 (2008), Table II). It also differs from the experimental value of 6.83 a.u. I attach the input file that I used for lattice constant 6.66 a.u. below the signature. Why is equilibrium lattice constant so low? Best regards, Alex Krukau, Indiana University ------------------------------------------------------ &control calculation='scf' pseudo_dir = '~/espresso-4.2.1/pseudo/ADDITIONAL', / &system ibrav = 2, celldm(1) = 6.66, nat= 1, ntyp= 1, ecutwfc = 120.0, ecutrho = 1000.0 occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01 / &electrons conv_thr=0.0000001 / ATOMIC_SPECIES Cu 63.546 Cu.pbe-n-van_ak.UPF ATOMIC_POSITIONS Cu 0.0 0.0 0.0 1 1 1 K_POINTS automatic 12 12 1 0 0 0 From ttduyle at gmail.com Thu Mar 3 00:15:15 2011 From: ttduyle at gmail.com (Duy Le) Date: Wed, 2 Mar 2011 18:15:15 -0500 Subject: [Pw_forum] Lattice constant for copper In-Reply-To: <20110302175819.hkx8o4qh88ww40cw@webmail.iu.edu> References: <20110302175819.hkx8o4qh88ww40cw@webmail.iu.edu> Message-ID: Did you check your k-point sampling? -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Wed, Mar 2, 2011 at 5:58 PM, Krukau, Aliaksandr wrote: > ? Dear QE users, > ? ?I apologize if my question seems stupid to you. I am a complete QE newbie > and could not find any answer in the tutorials. > ? ?I am trying to find equilibrium lattice constant for copper with PBE > and ultrasoft pseudopotentials. I ran scf calculations for face-centered cubic > unit cell for a number of lattice constants: > Lattice constant 6.65 a.u. ! ? ?total energy ? ? ? ? ? ? ?= > -121.62734203 Ry > Lattice constant 6.66 a.u. ! ? ?total energy ? ? ? ? ? ? ?= > -121.62735421 Ry > Lattice constant 6.67 a.u. ! ? ?total energy ? ? ? ? ? ? ?= > -121.62734651 Ry > Lattice constant 6.65 a.u. ! ? ?total energy ? ? ? ? ? ? ?= > -121.62731956 Ry > ? ?The minimum total energy is for the lattice constant 6.66 a.u. > But this value drastically differs from the published PBE value of 6.86 a.u. > (Phys. Rev. B, vol. 77, 05414 (2008), Table II). It also differs from > the experimental value of 6.83 a.u. I attach the input file that I used > for lattice constant 6.66 a.u. below the signature. > ? ?Why is equilibrium lattice constant so low? > Best regards, > Alex Krukau, > Indiana University > > ------------------------------------------------------ > &control > ? ?calculation='scf' > ? ?pseudo_dir = '~/espresso-4.2.1/pseudo/ADDITIONAL', > / > &system > ? ?ibrav = 2, > ? ?celldm(1) = 6.66, > ? ?nat= 1, > ? ?ntyp= 1, > ? ?ecutwfc = 120.0, > ? ?ecutrho = 1000.0 > ? ?occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01 > / > &electrons > ? ?conv_thr=0.0000001 > / > ATOMIC_SPECIES > Cu ?63.546 Cu.pbe-n-van_ak.UPF > ATOMIC_POSITIONS > Cu 0.0 0.0 0.0 ? ?1 ? 1 ? 1 > K_POINTS automatic > 12 12 1 0 0 0 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From germaneau at gucas.ac.cn Thu Mar 3 13:32:45 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 03 Mar 2011 07:32:45 -0500 Subject: [Pw_forum] Lattice constant for copper In-Reply-To: <499102391.08168@test1.gucas.ac.cn> References: <499102391.08168@test1.gucas.ac.cn> Message-ID: <4D6F8A6D.4040502@gucas.ac.cn> Hey, I'm a newbie too and I'm wondering how can you equilibrate the lattice constant by doing just a scf calculation. Also, it seems to me that only MD is able to reproduce experimental data since it takes into account the temperature and the pressure. Please, let me know if I'm wrong. Eric. On 03/02/2011 05:58 PM, Krukau, Aliaksandr wrote: > Dear QE users, > I apologize if my question seems stupid to you. I am a complete QE newbie > and could not find any answer in the tutorials. > I am trying to find equilibrium lattice constant for copper with PBE > and ultrasoft pseudopotentials. I ran scf calculations for face-centered cubic > unit cell for a number of lattice constants: > Lattice constant 6.65 a.u. ! total energy = > -121.62734203 Ry > Lattice constant 6.66 a.u. ! total energy = > -121.62735421 Ry > Lattice constant 6.67 a.u. ! total energy = > -121.62734651 Ry > Lattice constant 6.65 a.u. ! total energy = > -121.62731956 Ry > The minimum total energy is for the lattice constant 6.66 a.u. > But this value drastically differs from the published PBE value of 6.86 a.u. > (Phys. Rev. B, vol. 77, 05414 (2008), Table II). It also differs from > the experimental value of 6.83 a.u. I attach the input file that I used > for lattice constant 6.66 a.u. below the signature. > Why is equilibrium lattice constant so low? > Best regards, > Alex Krukau, > Indiana University > > ------------------------------------------------------ > &control > calculation='scf' > pseudo_dir = '~/espresso-4.2.1/pseudo/ADDITIONAL', > / > &system > ibrav = 2, > celldm(1) = 6.66, > nat= 1, > ntyp= 1, > ecutwfc = 120.0, > ecutrho = 1000.0 > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01 > / > &electrons > conv_thr=0.0000001 > / > ATOMIC_SPECIES > Cu 63.546 Cu.pbe-n-van_ak.UPF > ATOMIC_POSITIONS > Cu 0.0 0.0 0.0 1 1 1 > K_POINTS automatic > 12 12 1 0 0 0 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110303/97bd28ff/attachment-0001.htm From elbuesta at icqmail.com Thu Mar 3 01:05:15 2011 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Wed, 02 Mar 2011 19:05:15 -0500 Subject: [Pw_forum] Lattice constant for copper In-Reply-To: <20110302175819.hkx8o4qh88ww40cw@webmail.iu.edu> References: <20110302175819.hkx8o4qh88ww40cw@webmail.iu.edu> Message-ID: <8CDA74DCEB03B9F-194C-4528@webmail-d100.sysops.aol.com> Increase the number of k-points in the kz direction. Since you are dealing with an fcc, you should have something like 12x12x12 to have a reasonable description of a bulk structure. Other than that, I see no other errors in the input. Well, the cutoffs are kind of exagerated in my perspective given that you have a USPP, but depending on what you plan to do later, this could be right. And a too high cutoff is not an error, only a waste of time. I hope that helps. Fabio Negreiros -----Original Message----- From: Krukau, Aliaksandr To: pw_forum at pwscf.org Sent: Wed, Mar 2, 2011 11:58 pm Subject: [Pw_forum] Lattice constant for copper Dear QE users, I apologize if my question seems stupid to you. I am a complete QE newbie and could not find any answer in the tutorials. I am trying to find equilibrium lattice constant for copper with PBE and ultrasoft pseudopotentials. I ran scf calculations for face-centered cubic unit cell for a number of lattice constants: Lattice constant 6.65 a.u. ! total energy = -121.62734203 Ry Lattice constant 6.66 a.u. ! total energy = -121.62735421 Ry Lattice constant 6.67 a.u. ! total energy = -121.62734651 Ry Lattice constant 6.65 a.u. ! total energy = -121.62731956 Ry The minimum total energy is for the lattice constant 6.66 a.u. But this value drastically differs from the published PBE value of 6.86 a.u. (Phys. Rev. B, vol. 77, 05414 (2008), Table II). It also differs from the experimental value of 6.83 a.u. I attach the input file that I used for lattice constant 6.66 a.u. below the signature. Why is equilibrium lattice constant so low? Best regards, Alex Krukau, Indiana University ------------------------------------------------------ &control calculation='scf' pseudo_dir = '~/espresso-4.2.1/pseudo/ADDITIONAL', / &system ibrav = 2, celldm(1) = 6.66, nat= 1, ntyp= 1, ecutwfc = 120.0, ecutrho = 1000.0 occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01 / &electrons conv_thr=0.0000001 / ATOMIC_SPECIES Cu 63.546 Cu.pbe-n-van_ak.UPF ATOMIC_POSITIONS Cu 0.0 0.0 0.0 1 1 1 K_POINTS automatic 12 12 1 0 0 0 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110302/56e1273d/attachment.htm From akrukau at indiana.edu Thu Mar 3 01:21:27 2011 From: akrukau at indiana.edu (Krukau, Aliaksandr) Date: Wed, 2 Mar 2011 19:21:27 -0500 Subject: [Pw_forum] Lattice constant for copper In-Reply-To: References: <20110302175819.hkx8o4qh88ww40cw@webmail.iu.edu> Message-ID: <20110302192127.422wwa7s0ks8cs8s@webmail.iu.edu> Dear Duy Le and Fabio Negreiros, Thank you very much! I redid calculation with 12 x 12 x 12 k-point grid and got lattice constant of 6.86 a.u., as previously reported. Now I realize I put 12 x 12 x 1 grid by mistake. To Eric Germaneau: I calculate equilibrium lattice structure at OK by doing a number of 'relax' calculations at different lattice constants. For copper, there is only one atom in the basis, so 'relax' and 'scf' are equivalent. You are right, experimental lattice constant was measured at room temperature, and my calculation provides the lattice constant at OK. So I neglect the temperature dependence. But molecular dynamics can calculate lattice constant for non-zero temperature. Best regards, Alex Krukau, Indiana University Quoting Duy Le : > Did you check your k-point sampling? > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > From germaneau at gucas.ac.cn Thu Mar 3 16:51:15 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 03 Mar 2011 10:51:15 -0500 Subject: [Pw_forum] Lattice constant for copper In-Reply-To: <499106715.28821@test1.gucas.ac.cn> References: <20110302175819.hkx8o4qh88ww40cw@webmail.iu.edu> <499106715.28821@test1.gucas.ac.cn> Message-ID: <4D6FB8F3.1010905@gucas.ac.cn> Hey Alex, Thank you for the explanation. On 03/02/2011 07:21 PM, Krukau, Aliaksandr wrote: > Dear Duy Le and Fabio Negreiros, > Thank you very much! I redid calculation with 12 x 12 x 12 k-point > grid and got lattice constant of 6.86 a.u., as previously reported. Now > I realize I put 12 x 12 x 1 grid by mistake. > To Eric Germaneau: > I calculate equilibrium lattice structure at OK by doing a number > of 'relax' calculations at different lattice constants. For copper, > there is only one atom in the basis, so 'relax' and 'scf' are > equivalent. > You are right, experimental lattice constant was measured at room > temperature, and my calculation provides the lattice constant at OK. So > I neglect the temperature dependence. But molecular dynamics can > calculate lattice constant for non-zero temperature. > Best regards, > Alex Krukau, > Indiana University > > Quoting Duy Le: > >> Did you check your k-point sampling? >> -------------------------------------------------- >> Duy Le >> PhD Student >> Department of Physics >> University of Central Florida. >> >> "Men don't need hand to do things" >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110303/e118d478/attachment.htm From iurii.timrov at polytechnique.edu Thu Mar 3 09:49:47 2011 From: iurii.timrov at polytechnique.edu (Iurii TIMROV) Date: Thu, 3 Mar 2011 09:49:47 +0100 Subject: [Pw_forum] DOS: tetrahedron method + spin-orbit coupling Message-ID: <72c8451186febdfeddcce1b7f0727938.squirrel@theory.polytechnique.fr> Dear All, I have met the problem in the calculation of the density of states with the tetrahedron method, when the spin-orbit effect is included. 1. SCF calculation a) smearing + spin-orbit -> OK b) tetrahedra + no spin-orbit -> OK c) tetrahedra + spin-orbit -> error:"charge is wrong: smearing is needed" occupations = 'tetrahedra', lspinorb = .true. noncolin = .true. 2. NSCF calculation Say, I do the SCF calculation with the smearing technique, and spin-orbit is .true.. At this point everything is fine. Then I do the NSCF calculation with the tetrahedron method and spin-orbit is .true.. Here comes the problem. SCF: occupations = 'smearing', lspinorb = .true., noncolin = .true. NSCF: occupations = 'tetrahedra', lspinorb = .true., noncolin = .true. running the scf calculation... done running the nscf calculation...*** Process received signal *** Signal: Segmentation fault (11) Signal code: (128) Failing at address: (nil) /lib64/libpthread.so.0 [0x3120e0e4c0] /usr/local/lib/libopen-pal.so.0(_int_free+0x5e) [0x2b394aa66f9e] /usr/local/lib/libopen-pal.so.0(free+0xbd) [0x2b394aa674cd] ... Some details: * espresso version 4.1 * the PP was generated with the atomic code (fully relativistic case) * parallel run I will be thankful for any comments/suggestions concerning this problem! Best regards, Iurii Timrov Iurii TIMROV Doctorant (PhD student) Laboratoire des Solides Irradies Ecole Polytechnique F-91128 Palaiseau +33 1 69 33 45 08 timrov at theory.polytechnique.fr From nicola.marzari at materials.ox.ac.uk Thu Mar 3 10:30:21 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Thu, 03 Mar 2011 09:30:21 +0000 Subject: [Pw_forum] Lattice constant for copper In-Reply-To: <4D6F8A6D.4040502@gucas.ac.cn> References: <499102391.08168@test1.gucas.ac.cn> <4D6F8A6D.4040502@gucas.ac.cn> Message-ID: <4D6F5FAD.4010609@materials.ox.ac.uk> On 3/3/11 12:32 PM, Eric Germaneau wrote: > Hey, > > I'm a newbie too and I'm wondering how can you equilibrate the lattice > constant by doing just a scf calculation. > Also, it seems to me that only MD is able to reproduce experimental data > since it takes into account the temperature and the pressure. > Please, let me know if I'm wrong. > > Eric. > Dear Eric, All, just a brief comment re temperature - vibrational excitations follow Bose-Einstein statistics (nuclei are indistinguishable) rather than Maxwell-Boltzmann. Molecular dyanmics, though, will give you a Maxwell-Boltzmann distribution - these two differ, especially at temperatures below the Debye temperature. The more appropriate thing to do to calculate thermal expansion is to construct the free energy of the system adding the vibrational entropy, and minimize the free energy that at any given temperature as a function of celldm(1:6). Plenty of literature on the topic. nicola -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From raamesh123 at rediffmail.com Thu Mar 3 11:17:53 2011 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 3 Mar 2011 10:17:53 -0000 Subject: [Pw_forum] =?utf-8?q?Parallel_computing=3ALorenzo?= In-Reply-To: Message-ID: <1299108811.S.33032.26227.F.H.TnB3X2ZvcnVtLXJlcXVlc3RAcHdzY2Yub3JnAFB3X2ZvcnVtIERpZ2VzdCwgVm9sIDQ1LCBJc3N1ZSAy.f6-144-228.lb.old.1299147473.23375@webmail.rediffmail.com> Dear Lorenzo Yes sir you are right. I missed this simple fact. i changed prefix and outdir its working fine. Thankyou 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/20110303/39438ee5/attachment.htm From giannozz at democritos.it Thu Mar 3 12:42:44 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 3 Mar 2011 12:42:44 +0100 Subject: [Pw_forum] DOS: tetrahedron method + spin-orbit coupling In-Reply-To: <72c8451186febdfeddcce1b7f0727938.squirrel@theory.polytechnique.fr> References: <72c8451186febdfeddcce1b7f0727938.squirrel@theory.polytechnique.fr> Message-ID: On Mar 3, 2011, at 9:49 , Iurii TIMROV wrote: > I have met the problem in the calculation of the density of states > with > the tetrahedron method, when the spin-orbit effect is included. I think it is not currently implemented and requires some changes to the code P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From iurii.timrov at polytechnique.edu Thu Mar 3 14:16:31 2011 From: iurii.timrov at polytechnique.edu (Iurii TIMROV) Date: Thu, 3 Mar 2011 14:16:31 +0100 Subject: [Pw_forum] DOS: tetrahedron method + spin-orbit coupling In-Reply-To: References: <72c8451186febdfeddcce1b7f0727938.squirrel@theory.polytechnique.fr> Message-ID: > I think it is not currently implemented and requires some changes > to the code Dear Paolo, Thank you for the answer! I am currently looking in the code, and trying to to solve this problem. Best regards, Iurii Timrov Iurii TIMROV Doctorant (PhD student) Laboratoire des Solides Irradies Ecole Polytechnique F-91128 Palaiseau +33 1 69 33 45 08 timrov at theory.polytechnique.fr From giannozz at democritos.it Thu Mar 3 14:31:00 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 3 Mar 2011 14:31:00 +0100 Subject: [Pw_forum] DOS: tetrahedron method + spin-orbit coupling In-Reply-To: References: <72c8451186febdfeddcce1b7f0727938.squirrel@theory.polytechnique.fr> Message-ID: On Mar 3, 2011, at 14:16 , Iurii TIMROV wrote: > Thank you for the answer! I am currently looking in the code, and > trying > to to solve this problem. you will need for sure to modify routine sumkt as in the attached file. Not sure this will solve all problems, though P. -------------- next part -------------- A non-text attachment was scrubbed... Name: sumkt.f90 Type: application/octet-stream Size: 2933 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110303/50701bd4/attachment.obj -------------- next part -------------- --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mirnezhad.mm at gmail.com Thu Mar 3 15:06:22 2011 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Thu, 3 Mar 2011 06:06:22 -0800 Subject: [Pw_forum] QHA compiling Message-ID: Dear Developers, How can we compile the QHA package with gfortran as a compiler for fortran? Thanks for you reply mahdi Mirnejad From eyvaz_isaev at yahoo.com Thu Mar 3 16:06:46 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 3 Mar 2011 07:06:46 -0800 (PST) Subject: [Pw_forum] QHA compiling In-Reply-To: References: Message-ID: <137709.84542.qm@web65708.mail.ac4.yahoo.com> Dear Mahdi, It is very easy with the applied tar (I have introduced a small changes to vary fortran compiler). It is the same as in QE 4.2, without example files. Many changes (to support more Bravais lattices) will come in the next release. Any problem, please contact me. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: Mahdi Mirnezhad To: pw_forum Sent: Thu, March 3, 2011 5:06:22 PM Subject: [Pw_forum] QHA compiling Dear Developers, How can we compile the QHA package with gfortran as a compiler for fortran? Thanks for you reply mahdi Mirnejad _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- A non-text attachment was scrubbed... Name: QHA_1.tar.gz Type: application/x-gzip Size: 27333 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110303/bcf4d925/attachment-0001.bin From eyvaz_isaev at yahoo.com Thu Mar 3 16:54:40 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 3 Mar 2011 07:54:40 -0800 (PST) Subject: [Pw_forum] QHA compiling In-Reply-To: <137709.84542.qm@web65708.mail.ac4.yahoo.com> References: <137709.84542.qm@web65708.mail.ac4.yahoo.com> Message-ID: <355416.94432.qm@web65715.mail.ac4.yahoo.com> In addition to my previous mail: now one can edit make.inc file to change the compiler. Bests, Eyvaz. ----- Original Message ---- From: Eyvaz Isaev To: PWSCF Forum Sent: Thu, March 3, 2011 6:06:46 PM Subject: Re: [Pw_forum] QHA compiling Dear Mahdi, It is very easy with the applied tar (I have introduced a small changes to vary fortran compiler). It is the same as in QE 4.2, without example files. Many changes (to support more Bravais lattices) will come in the next release. Any problem, please contact me. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: Mahdi Mirnezhad To: pw_forum Sent: Thu, March 3, 2011 5:06:22 PM Subject: [Pw_forum] QHA compiling Dear Developers, How can we compile the QHA package with gfortran as a compiler for fortran? Thanks for you reply mahdi Mirnejad _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From mirnezhad.mm at gmail.com Thu Mar 3 17:45:20 2011 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Thu, 3 Mar 2011 08:45:20 -0800 Subject: [Pw_forum] QHA compiling In-Reply-To: <355416.94432.qm@web65715.mail.ac4.yahoo.com> References: <137709.84542.qm@web65708.mail.ac4.yahoo.com> <355416.94432.qm@web65715.mail.ac4.yahoo.com> Message-ID: Dear Prof. Eyvaz Isaev, Thanks for your replies. Where can i find the latest version of QHA. I can not find it in the latest version of esperesso (espresso-4.3a). Mahdi Mirnezhad On 3/3/11, Eyvaz Isaev wrote: > In addition to my previous mail: now one can edit make.inc file to change > the > compiler. > > Bests, > Eyvaz. > > > > ----- Original Message ---- > From: Eyvaz Isaev > To: PWSCF Forum > Sent: Thu, March 3, 2011 6:06:46 PM > Subject: Re: [Pw_forum] QHA compiling > > Dear Mahdi, > > It is very easy with the applied tar (I have introduced a small changes to > vary > fortran compiler). It is the same as in QE 4.2, without example files. > Many changes (to support more Bravais lattices) will come in the next > release. > > Any problem, please contact me. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > ----- Original Message ---- > From: Mahdi Mirnezhad > To: pw_forum > Sent: Thu, March 3, 2011 5:06:22 PM > Subject: [Pw_forum] QHA compiling > > Dear Developers, > How can we compile the QHA package with gfortran as a compiler for fortran? > > Thanks for you reply > > mahdi Mirnejad > _______________________________________________ > 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 Thu Mar 3 17:58:32 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 3 Mar 2011 08:58:32 -0800 (PST) Subject: [Pw_forum] QHA compiling In-Reply-To: References: <137709.84542.qm@web65708.mail.ac4.yahoo.com> <355416.94432.qm@web65715.mail.ac4.yahoo.com> Message-ID: <729416.59234.qm@web65716.mail.ac4.yahoo.com> Dear Mahdi, It was distributed together with QE 4.2. The latest version is in my laptop. I have to finish all the changes. If you have high symmetry crystals, you should not be worried about the latest version. Bests, Eyvaz. ----- Original Message ---- From: Mahdi Mirnezhad To: PWSCF Forum Sent: Thu, March 3, 2011 7:45:20 PM Subject: Re: [Pw_forum] QHA compiling Dear Prof. Eyvaz Isaev, Thanks for your replies. Where can i find the latest version of QHA. I can not find it in the latest version of esperesso (espresso-4.3a). Mahdi Mirnezhad On 3/3/11, Eyvaz Isaev wrote: > In addition to my previous mail: now one can edit make.inc file to change > the > compiler. > > Bests, > Eyvaz. > > > > ----- Original Message ---- > From: Eyvaz Isaev > To: PWSCF Forum > Sent: Thu, March 3, 2011 6:06:46 PM > Subject: Re: [Pw_forum] QHA compiling > > Dear Mahdi, > > It is very easy with the applied tar (I have introduced a small changes to > vary > fortran compiler). It is the same as in QE 4.2, without example files. > Many changes (to support more Bravais lattices) will come in the next > release. > > Any problem, please contact me. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > ----- Original Message ---- > From: Mahdi Mirnezhad > To: pw_forum > Sent: Thu, March 3, 2011 5:06:22 PM > Subject: [Pw_forum] QHA compiling > > Dear Developers, > How can we compile the QHA package with gfortran as a compiler for fortran? > > Thanks for you reply > > mahdi Mirnejad > _______________________________________________ > 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 mirnezhad.mm at gmail.com Thu Mar 3 18:21:54 2011 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Thu, 3 Mar 2011 09:21:54 -0800 Subject: [Pw_forum] QHA compiling In-Reply-To: <729416.59234.qm@web65716.mail.ac4.yahoo.com> References: <137709.84542.qm@web65708.mail.ac4.yahoo.com> <355416.94432.qm@web65715.mail.ac4.yahoo.com> <729416.59234.qm@web65716.mail.ac4.yahoo.com> Message-ID: Dear Prof. Eyvaz Isaev, Could you please provide a additional example for QHA? Thanks Mahdi On 3/3/11, Eyvaz Isaev wrote: > Dear Mahdi, > > It was distributed together with QE 4.2. > The latest version is in my laptop. I have to finish all the changes. > If you have high symmetry crystals, you should not be worried about the > latest > version. > > Bests, > Eyvaz. > > > > > ----- Original Message ---- > From: Mahdi Mirnezhad > To: PWSCF Forum > Sent: Thu, March 3, 2011 7:45:20 PM > Subject: Re: [Pw_forum] QHA compiling > > Dear Prof. Eyvaz Isaev, > Thanks for your replies. Where can i find the latest version of QHA. I > can not find it in the latest version of esperesso (espresso-4.3a). > > Mahdi Mirnezhad > > > > On 3/3/11, Eyvaz Isaev wrote: >> In addition to my previous mail: now one can edit make.inc file to change >> the >> compiler. >> >> Bests, >> Eyvaz. >> >> >> >> ----- Original Message ---- >> From: Eyvaz Isaev >> To: PWSCF Forum >> Sent: Thu, March 3, 2011 6:06:46 PM >> Subject: Re: [Pw_forum] QHA compiling >> >> Dear Mahdi, >> >> It is very easy with the applied tar (I have introduced a small changes to >> vary >> fortran compiler). It is the same as in QE 4.2, without example files. >> Many changes (to support more Bravais lattices) will come in the next >> release. >> >> Any problem, please contact me. >> >> Bests, >> Eyvaz. >> >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >> Sweden >> >> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >> Russia, >> >> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> >> ----- Original Message ---- >> From: Mahdi Mirnezhad >> To: pw_forum >> Sent: Thu, March 3, 2011 5:06:22 PM >> Subject: [Pw_forum] QHA compiling >> >> Dear Developers, >> How can we compile the QHA package with gfortran as a compiler for >> fortran? >> >> Thanks for you reply >> >> mahdi Mirnejad >> _______________________________________________ >> 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 eyvaz_isaev at yahoo.com Thu Mar 3 18:26:10 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 3 Mar 2011 09:26:10 -0800 (PST) Subject: [Pw_forum] QHA compiling In-Reply-To: References: <137709.84542.qm@web65708.mail.ac4.yahoo.com> <355416.94432.qm@web65715.mail.ac4.yahoo.com> <729416.59234.qm@web65716.mail.ac4.yahoo.com> Message-ID: <828817.77374.qm@web65709.mail.ac4.yahoo.com> Ok, I will send it to you personally. Bests, Eyvaz. ----- Original Message ---- From: Mahdi Mirnezhad To: PWSCF Forum Sent: Thu, March 3, 2011 8:21:54 PM Subject: Re: [Pw_forum] QHA compiling Dear Prof. Eyvaz Isaev, Could you please provide a additional example for QHA? Thanks Mahdi On 3/3/11, Eyvaz Isaev wrote: > Dear Mahdi, > > It was distributed together with QE 4.2. > The latest version is in my laptop. I have to finish all the changes. > If you have high symmetry crystals, you should not be worried about the > latest > version. > > Bests, > Eyvaz. > > > > > ----- Original Message ---- > From: Mahdi Mirnezhad > To: PWSCF Forum > Sent: Thu, March 3, 2011 7:45:20 PM > Subject: Re: [Pw_forum] QHA compiling > > Dear Prof. Eyvaz Isaev, > Thanks for your replies. Where can i find the latest version of QHA. I > can not find it in the latest version of esperesso (espresso-4.3a). > > Mahdi Mirnezhad > > > > On 3/3/11, Eyvaz Isaev wrote: >> In addition to my previous mail: now one can edit make.inc file to change >> the >> compiler. >> >> Bests, >> Eyvaz. >> >> >> >> ----- Original Message ---- >> From: Eyvaz Isaev >> To: PWSCF Forum >> Sent: Thu, March 3, 2011 6:06:46 PM >> Subject: Re: [Pw_forum] QHA compiling >> >> Dear Mahdi, >> >> It is very easy with the applied tar (I have introduced a small changes to >> vary >> fortran compiler). It is the same as in QE 4.2, without example files. >> Many changes (to support more Bravais lattices) will come in the next >> release. >> >> Any problem, please contact me. >> >> Bests, >> Eyvaz. >> >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >> Sweden >> >> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >> Russia, >> >> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> >> ----- Original Message ---- >> From: Mahdi Mirnezhad >> To: pw_forum >> Sent: Thu, March 3, 2011 5:06:22 PM >> Subject: [Pw_forum] QHA compiling >> >> Dear Developers, >> How can we compile the QHA package with gfortran as a compiler for >> fortran? >> >> Thanks for you reply >> >> mahdi Mirnejad >> _______________________________________________ >> 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 eyvaz_isaev at yahoo.com Thu Mar 3 18:30:51 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 3 Mar 2011 09:30:51 -0800 (PST) Subject: [Pw_forum] QHA compiling In-Reply-To: References: <137709.84542.qm@web65708.mail.ac4.yahoo.com> <355416.94432.qm@web65715.mail.ac4.yahoo.com> Message-ID: <233070.82792.qm@web65701.mail.ac4.yahoo.com> Well, I have seen you did not provide your affiliation. I will send an example file when you sign your e-mail. Bests, Eyvaz. ----- Original Message ---- From: Mahdi Mirnezhad To: PWSCF Forum Sent: Thu, March 3, 2011 7:45:20 PM Subject: Re: [Pw_forum] QHA compiling Dear Prof. Eyvaz Isaev, Thanks for your replies. Where can i find the latest version of QHA. I can not find it in the latest version of esperesso (espresso-4.3a). Mahdi Mirnezhad On 3/3/11, Eyvaz Isaev wrote: > In addition to my previous mail: now one can edit make.inc file to change > the > compiler. > > Bests, > Eyvaz. > > > > ----- Original Message ---- > From: Eyvaz Isaev > To: PWSCF Forum > Sent: Thu, March 3, 2011 6:06:46 PM > Subject: Re: [Pw_forum] QHA compiling > > Dear Mahdi, > > It is very easy with the applied tar (I have introduced a small changes to > vary > fortran compiler). It is the same as in QE 4.2, without example files. > Many changes (to support more Bravais lattices) will come in the next > release. > > Any problem, please contact me. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > ----- Original Message ---- > From: Mahdi Mirnezhad > To: pw_forum > Sent: Thu, March 3, 2011 5:06:22 PM > Subject: [Pw_forum] QHA compiling > > Dear Developers, > How can we compile the QHA package with gfortran as a compiler for fortran? > > Thanks for you reply > > mahdi Mirnejad > _______________________________________________ > 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 mirnezhad.mm at gmail.com Thu Mar 3 18:41:35 2011 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Thu, 3 Mar 2011 09:41:35 -0800 Subject: [Pw_forum] QHA compiling In-Reply-To: <233070.82792.qm@web65701.mail.ac4.yahoo.com> References: <137709.84542.qm@web65708.mail.ac4.yahoo.com> <355416.94432.qm@web65715.mail.ac4.yahoo.com> <233070.82792.qm@web65701.mail.ac4.yahoo.com> Message-ID: Dear Prof. Eyvaz Isaev, Thanks for your helps. Mahdi Mirnezhad Guilan University On 3/3/11, Eyvaz Isaev wrote: > Well, I have seen you did not provide your affiliation. > I will send an example file when you sign your e-mail. > > > Bests, > Eyvaz. > > > ----- Original Message ---- > From: Mahdi Mirnezhad > To: PWSCF Forum > Sent: Thu, March 3, 2011 7:45:20 PM > Subject: Re: [Pw_forum] QHA compiling > > Dear Prof. Eyvaz Isaev, > Thanks for your replies. Where can i find the latest version of QHA. I > can not find it in the latest version of esperesso (espresso-4.3a). > > Mahdi Mirnezhad > > > > On 3/3/11, Eyvaz Isaev wrote: >> In addition to my previous mail: now one can edit make.inc file to change >> the >> compiler. >> >> Bests, >> Eyvaz. >> >> >> >> ----- Original Message ---- >> From: Eyvaz Isaev >> To: PWSCF Forum >> Sent: Thu, March 3, 2011 6:06:46 PM >> Subject: Re: [Pw_forum] QHA compiling >> >> Dear Mahdi, >> >> It is very easy with the applied tar (I have introduced a small changes to >> vary >> fortran compiler). It is the same as in QE 4.2, without example files. >> Many changes (to support more Bravais lattices) will come in the next >> release. >> >> Any problem, please contact me. >> >> Bests, >> Eyvaz. >> >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >> Sweden >> >> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >> Russia, >> >> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> >> ----- Original Message ---- >> From: Mahdi Mirnezhad >> To: pw_forum >> Sent: Thu, March 3, 2011 5:06:22 PM >> Subject: [Pw_forum] QHA compiling >> >> Dear Developers, >> How can we compile the QHA package with gfortran as a compiler for >> fortran? >> >> Thanks for you reply >> >> mahdi Mirnejad >> _______________________________________________ >> 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 baroni at sissa.it Thu Mar 3 18:51:22 2011 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 3 Mar 2011 18:51:22 +0100 Subject: [Pw_forum] QHA compiling In-Reply-To: References: <137709.84542.qm@web65708.mail.ac4.yahoo.com> <355416.94432.qm@web65715.mail.ac4.yahoo.com> <233070.82792.qm@web65701.mail.ac4.yahoo.com> Message-ID: <87EFAA1B-D1AC-406F-AC38-B9F9E6A66162@sissa.it> Hi Eyvaz: why don't you keep everything on qe-forge? Stefano On Mar 3, 2011, at 6:41 PM, Mahdi Mirnezhad wrote: > Dear Prof. Eyvaz Isaev, > Thanks for your helps. > > Mahdi Mirnezhad > Guilan University > > On 3/3/11, Eyvaz Isaev wrote: >> Well, I have seen you did not provide your affiliation. >> I will send an example file when you sign your e-mail. >> >> >> Bests, >> Eyvaz. >> >> >> ----- Original Message ---- >> From: Mahdi Mirnezhad >> To: PWSCF Forum >> Sent: Thu, March 3, 2011 7:45:20 PM >> Subject: Re: [Pw_forum] QHA compiling >> >> Dear Prof. Eyvaz Isaev, >> Thanks for your replies. Where can i find the latest version of QHA. I >> can not find it in the latest version of esperesso (espresso-4.3a). >> >> Mahdi Mirnezhad >> >> >> >> On 3/3/11, Eyvaz Isaev wrote: >>> In addition to my previous mail: now one can edit make.inc file to change >>> the >>> compiler. >>> >>> Bests, >>> Eyvaz. >>> >>> >>> >>> ----- Original Message ---- >>> From: Eyvaz Isaev >>> To: PWSCF Forum >>> Sent: Thu, March 3, 2011 6:06:46 PM >>> Subject: Re: [Pw_forum] QHA compiling >>> >>> Dear Mahdi, >>> >>> It is very easy with the applied tar (I have introduced a small changes to >>> vary >>> fortran compiler). It is the same as in QE 4.2, without example files. >>> Many changes (to support more Bravais lattices) will come in the next >>> release. >>> >>> Any problem, please contact me. >>> >>> Bests, >>> Eyvaz. >>> >>> ------------------------------------------------------------------- >>> Prof. Eyvaz Isaev, >>> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >>> Sweden >>> >>> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >>> Russia, >>> >>> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >>> >>> >>> >>> ----- Original Message ---- >>> From: Mahdi Mirnezhad >>> To: pw_forum >>> Sent: Thu, March 3, 2011 5:06:22 PM >>> Subject: [Pw_forum] QHA compiling >>> >>> Dear Developers, >>> How can we compile the QHA package with gfortran as a compiler for >>> fortran? >>> >>> Thanks for you reply >>> >>> mahdi Mirnejad >>> _______________________________________________ >>> 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 --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110303/5461da5a/attachment.htm From smirshamsi at phys.ufl.edu Thu Mar 3 19:39:48 2011 From: smirshamsi at phys.ufl.edu (Sahar Mirshamsi) Date: Thu, 3 Mar 2011 13:39:48 -0500 (EST) Subject: [Pw_forum] Some questions about non-collinear calculation and penalty function Message-ID: Hi all, I have some questions regarding non-collinear calculation and using penalty function in pwscf. 1) In constaint_magnetization ='atomic', is starting magnetization as the target magnetization? I have read this post http://www.democritos.it/pipermail/pw_forum/2009-December/015342.html and also in input.f90 I found mcons(1,nt) = starting_magnetization(nt) * SIN( theta ) * COS( phi ) mcons(2,nt) = starting_magnetization(nt) * SIN( theta ) * SIN( phi ) mcons(3,nt) = starting_magnetization(nt) * COS( theta ) So it means both magnitude and direction of atomic magnetizations are constrained, is this correct? 2) If above statement is correct, then the same problem as posted in above link will still exist, since starting_magnetization=m/n, then for constraining the magnitude of magnetization to desired value, we should multiply the magnitude of magnetization by charge and then replace it as starting_magnitization, is this correct? 3) What is the relation between charge and magnetization printed in scf calculation with those which we can get with using projwf.x, I expect they should get almost same numbers but in scf output for carbons in Graphene nanoribbon I get charge=0.6 and magnetization=0.1 while in projwf.x output I get charge=4 and polarization=0.2-0.3 which the latest one makes more sense. 4) Also, in some cases of non-collinear calculation with using penalty function, when I track "estimated scf accuracy" it is decreasing till reaching the threshold and stopping the job while "total energy" is oscillating in some range instead of converging to a number , any idea what's the problem? 5) The total energy printed in scf calculation does not include constraint energy, right? It's just energy of the structure with the constraint configuration of magnetizations, right? I appreciate any help in finding the answers of these questions. Sahar Mishamsi Quantum Theory Project and Physics Department, University of Florida From abmus007 at gmail.com Thu Mar 3 23:06:59 2011 From: abmus007 at gmail.com (Abolore Musari) Date: Thu, 3 Mar 2011 16:06:59 -0600 Subject: [Pw_forum] atomic positions Message-ID: Dear QE Users, Am presently working on a system which is CaTiSiO5, symmetrie is monoclinic some of my input read nat=8 and the atomic coordinates I saw is for Ca, Si, Ti, and O1 O2 O3 which am assuming oxygen should be up to five (I mean we should still have for O4 and O5) instead of just three as reflected in the chemical formula. What can I do? Pls can any1 explain this to me. Thanks for ur usual anf favourable support. Musari Abolore A Ph.D student Department of Physics. University Of Agriculture, Abeokuta Nigeria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110303/a8423faf/attachment.htm From degironc at sissa.it Thu Mar 3 23:41:08 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 03 Mar 2011 23:41:08 +0100 Subject: [Pw_forum] atomic positions In-Reply-To: References: Message-ID: <4D701904.7060406@sissa.it> Dear Musari Abolore it is hard to explain you something about an input that you don't post.... where did you get that input from ? did you wrote it ? there are two input "cards" in pw.x ATOMIC_SPECIES where you specify your ntyp species, and ATOMIC_POSITIONS where you specify the nat atoms . what is the value of ntyp in your case ? have you more that an Oxygen type ? is your system magnetic ? the labels in the ATOMIC_POSITIONS list correspond to the ATOMIC_SPECIES above... how many Oxygen lines do you have in ATOMIC_POSITIONS ? stefano On 03/03/2011 11:06 PM, Abolore Musari wrote: > Dear QE Users, > Am presently working on a system which is CaTiSiO5, symmetrie is monoclinic > some of my input read nat=8 and the atomic coordinates I saw is for Ca, Si, > Ti, and O1 O2 O3 which am assuming oxygen should be up to five (I mean we > should still have for O4 and O5) instead of just three as reflected in the > chemical formula. What can I do? Pls can any1 explain this to me. > Thanks for ur usual anf favourable support. > > Musari Abolore A > Ph.D student > Department of Physics. > University Of Agriculture, Abeokuta > Nigeria > > > > _______________________________________________ > 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/20110303/0ca1e72d/attachment-0001.htm From germaneau at gucas.ac.cn Fri Mar 4 13:20:47 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Fri, 04 Mar 2011 07:20:47 -0500 Subject: [Pw_forum] atomic positions In-Reply-To: <499185031.24978@test1.gucas.ac.cn> References: <499185031.24978@test1.gucas.ac.cn> Message-ID: <4D70D91F.4050307@gucas.ac.cn> Hi Abolore, First of all, monoclinic is not a symmetry but a crystal class. Then, because of symmetry you may need only 3 oxygen to describe the asymmetric unit. Stefano is right, you'd better provide your input file. Do you know what is the space group of your crystal? Eric. On 03/03/2011 05:06 PM, Abolore Musari wrote: > Dear QE Users, > Am presently working on a system which is CaTiSiO5, symmetrie is > monoclinic some of my input read nat=8 and the atomic coordinates I > saw is for Ca, Si, Ti, and O1 O2 O3 which am assuming oxygen should > be up to five (I mean we should still have for O4 and O5) instead of > just three as reflected in the chemical formula. What can I do? Pls > can any1 explain this to me. > Thanks for ur usual anf favourable support. > > Musari Abolore A > Ph.D student > Department of Physics. > University Of Agriculture, Abeokuta > Nigeria > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/1a0c4126/attachment.htm From josepht at chips.ncsu.edu Fri Mar 4 00:18:44 2011 From: josepht at chips.ncsu.edu (Joe) Date: Thu, 03 Mar 2011 18:18:44 -0500 Subject: [Pw_forum] PP generation with ld1.x (transition metals with semicore states) Message-ID: <4D7021D4.7090603@chips.ncsu.edu> Hello everyone, Using ld1.x, I am trying to generate pseudopotentials for elements such as Hf, both scalar relativistic and fully relativistic. I have followed from the examples given in atomic_doc, and have been making ample use of Paolo Giannozzi's July 9th 2010 tutorial, "Notes on pseudopotential generation" (which is the version with full worked examples for Ti). The information provided by this arsenal as been sufficient to generate and test new USPP/NCPP for Si, C, N, O, and S, as well as "naive" USPP for Hf. Several of the issues I am reporting below have been mentioned within the pw_forum, and when applicable, I have tried (often with success) the prescriptions offered. First, let me share what I have "working". Below is the input file for a scalar relativistic USPP for Hf that does not contain semicore states. I have tested it for bulk hafnia and it reproduces published band structure data at fixed cell parameters and fixed atomic coordinates, but gives optimized structures at variance with those (using PBE-based PP) reported in the literature (for example, following from the review given in the 2008 NJP paper by Beltran, Munoz, and Hafner - NJP 10 063031); it agrees most closely with the NCPP PBE structures generated by Zhao and Vanderbilt in PRB 65 233106, except for the angle \beta, which is similar to that reported in PRB 65 174117. The basic summary is that the cell volume is larger than anything published. &input title='Hf', zed=72, rel=1, iswitch=3, config='[Xe] 4f14.0 5d2.0 6s2.0 6p0.0', dft='PBE', / &inputp lloc=0, pseudotype=3, file_pseudopw='Hf.srl-pbe-rrkjus.UPF', nlcc=.true., rcore=0.9, author='test', rho0=0.0001, / 4 6P 2 1 0.00 0.00 2.70 2.70 1 5D 3 2 2.00 0.00 1.90 2.30 1 5D 3 2 0.00 -0.18 1.90 2.30 1 6S 1 0 2.00 0.00 2.50 2.50 1 / &test nconf=5 file_pseudo='Hf.srl-pbe-rrkjus.UPF' ecutmin=20.0, ecutmax=50.0, decut=10.0 configts(1)='5d2.0 6s2.0 6p0.0' configts(2)='5d1.0 6s2.0 6p0.0' configts(3)='5d1.0 6s1.0 6p0.0' configts(4)='5d0.0 6s1.0 6p0.0' configts(5)='5d0.0 6s0.0 6p0.0' / Note that the test results for different charged (d-depleted) states of Hf are pretty bad. For those interested in using this as a starting point, an analogous fully relativistic USPP can be generated using the input file: &input title='Hf', zed=72, rel=2, iswitch=3, config='[Xe] 4f14.0 5d2.0 6s2.0 6p0.0', dft='PBE', / &inputp lloc=0, pseudotype=3, file_pseudopw='Hf.rel-pbe-rrkjus.UPF', nlcc=.true., rcore=0.9, author='test', / 7 6P 2 1 0.00 0.00 2.70 2.70 0.5 6P 2 1 0.00 0.00 2.70 2.70 1.5 5D 3 2 2.00 0.00 1.90 2.30 1.5 5D 3 2 0.00 -0.18 1.90 2.30 1.5 5D 3 2 0.00 0.00 1.90 2.30 2.5 5D 3 2 0.00 -0.18 1.90 2.30 2.5 6S 1 0 2.00 0.00 2.50 2.50 0.5 / &test nconf=3 file_pseudo='Hf.rel-pbe-rrkjus.UPF' ecutmin=20.0, ecutmax=80.0, decut=10.0 configts(1)='5d2.0 6s2.0' configts(2)='5d2.0 6s1.0 6p1.0' configts(3)='5d1.0 6s2.0 6p0.0' / The structural discrepancies persist for different oxygen USPP, different optimization procedures, and different sets of parameters (charge density cutoffs, convergence criteria, etc.). I am now trying to check if the structural properties can be improved by the inclusion of semicore states, and am starting with the "simplest" case, that of a scalar relativistic NCPP with explicit inclusion of 5S and 5P. After starting with the fewest number of projectors (one each for 5S, 5P, and 5D), and running into all kinds of problems (anyone who runs ld1.x knows about the kinds of mysterious errors that are generated, and the equally mysterious modifications which result in said errors disappearing), I searched the pw_forum and found the following thread: http://www.democritos.it/pipermail/pw_forum/2009-July/013453.html Following from this (and making the implicit corrections to the provided files in order to render them processable, such as modifying the 2nd column in the definition of the projectors), I have been working off of the following NCPP input file, &input title='Hf', zed=72, rel=1, iswitch=3, config='[Xe] 4f14 5d2 6s2 6p0', dft='PBE', / &inputp lloc=0, pseudotype=2, file_pseudopw='Hf.semicore.srl-pbe-rrkjus.UPF', nlcc=.f., author='test', rho0=0.01, / 5 5P 2 1 6.00 0.00 1.50 1.50 1 5P 2 1 0.00 -1.00 1.50 1.50 1 5D 3 2 2.00 0.00 1.90 1.90 1 5D 3 2 0.00 -0.20 1.90 1.90 1 5S 1 0 2.00 0.00 1.20 1.20 1 / &test nconf=1 file_pseudo='Hf.semicore.srl-pbe-rrkjus.UPF' ecutmin=20.0, ecutmax=50.0, decut=10.0 configts(1)='5s2 5p6 5d2 6s2 6p0', / and have been varying the energy for the empty 5P projector, changing lloc (and rcloc when applicable), toying with rho0, and fiddling with the cutoffs, to no avail. The latest error is the not-so-helpful: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from run_pseudo : error # 1 Errors in PS-KS equation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Changing parameters merely changes the error, it seems. I know this is a highly-specific cooking problem, but if anyone has any suggestions on how to proceed, I would be extremely grateful. With some help, hopefully I can generate a good, tested set of USPPs for Hf and fill in that blank on PWSCF's pseudopotential page! Joseph Turnbull NC State University From wang.riping.81 at gmail.com Fri Mar 4 01:48:51 2011 From: wang.riping.81 at gmail.com (Riping WANG) Date: Fri, 4 Mar 2011 09:48:51 +0900 Subject: [Pw_forum] nstep for CPMD average physical quantities Message-ID: Dear Forum, For QE-CPMD calcualtion, Could any told me how many nstep keeping is necessary to get average physical quantities? Thank you very much. WANG Riping 20101.3.4 -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), 1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/fe9c9d01/attachment.htm From wang.riping.81 at gmail.com Fri Mar 4 01:51:21 2011 From: wang.riping.81 at gmail.com (Riping WANG) Date: Fri, 4 Mar 2011 09:51:21 +0900 Subject: [Pw_forum] nstep for CPMD average physical quantities In-Reply-To: References: Message-ID: To add information, I use vc-relax, and I want to get average quantities at certain pressure and temperature. WANG Riping 2011.3.4 On 4 March 2011 09:48, Riping WANG wrote: > Dear Forum, > > For QE-CPMD calcualtion, Could any told me how many nstep keeping is > necessary to get average physical quantities? > Thank you very much. > > WANG Riping > 20101.3.4 > > > -- > > ****************************************************************************** > WANG Riping > Ph.D student, > Institute for Study of the Earth's Interior,Okayama University, > 827 Yamada, Misasa, Tottori-ken 682-0193, Japan > Tel: +81-858-43-3739(Office), 1215(Inst) > E-mail: wang.riping.81 at gmail.com > > ****************************************************************************** > > > > -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), 1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/f5454c02/attachment.htm From wang.riping.81 at gmail.com Fri Mar 4 01:58:41 2011 From: wang.riping.81 at gmail.com (Riping WANG) Date: Fri, 4 Mar 2011 09:58:41 +0900 Subject: [Pw_forum] atomic position in vc-relax CPMD Message-ID: Dear Forum, How can I get average atomic positions at at given pressure and temperature with vc-relax QE-cpmd? I set the following control model: &control calculation = 'vc-cp' , prefix = 'SiO2' , restart_mode = 'restart', nstep = 2000 , iprint = 1 , isave = 1 , dt = 5.0 , ndr = 54 , ndw = 54 , tstress = .TRUE. , tprnfor = .TRUE. , saverho = .TRUE. , disk_io = 'high' , But it print atomic position information in output file every 10 steps. I hope it print c information every 1 step. and then I can make average position by matlab. I am not sure about this method good or not. Could any one give comment? Thank you WANG Riping 2011.3.4 -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), 1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/a50e804b/attachment.htm From parthasarathi13 at gmail.com Fri Mar 4 06:31:52 2011 From: parthasarathi13 at gmail.com (partha sarathi ghosh) Date: Fri, 4 Mar 2011 11:01:52 +0530 Subject: [Pw_forum] PAW potential for Uranium Message-ID: Hello QE users, Can any one please share PAW potential for Uranium as it is not available in the QE potential list. Thanks in advance Partha Ghosh B.A.R.C. INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/f400ec3f/attachment.htm From dalcorso at sissa.it Fri Mar 4 08:56:08 2011 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Fri, 04 Mar 2011 08:56:08 +0100 Subject: [Pw_forum] PP generation with ld1.x (transition metals with semicore states) In-Reply-To: <4D7021D4.7090603@chips.ncsu.edu> References: <4D7021D4.7090603@chips.ncsu.edu> Message-ID: <1299225368.27875.3.camel@ulisse.cm.sissa.it> Did you try the Hf PP in pslibrary? http://qe-forge.org/projects/pslibrary/ These are still untested PPs, and it would be useful to have feedback from the users. Andrea On Thu, 2011-03-03 at 18:18 -0500, Joe wrote: > Hello everyone, > > Using ld1.x, I am trying to generate pseudopotentials for elements such > as Hf, both scalar relativistic and fully relativistic. I have followed > from the examples given in atomic_doc, and have been making ample use of > Paolo Giannozzi's July 9th 2010 tutorial, "Notes on pseudopotential > generation" (which is the version with full worked examples for Ti). > The information provided by this arsenal as been sufficient to generate > and test new USPP/NCPP for Si, C, N, O, and S, as well as "naive" USPP > for Hf. Several of the issues I am reporting below have been mentioned > within the pw_forum, and when applicable, I have tried (often with > success) the prescriptions offered. > > First, let me share what I have "working". Below is the input file for > a scalar relativistic USPP for Hf that does not contain semicore > states. I have tested it for bulk hafnia and it reproduces published > band structure data at fixed cell parameters and fixed atomic > coordinates, but gives optimized structures at variance with those > (using PBE-based PP) reported in the literature (for example, following > from the review given in the 2008 NJP paper by Beltran, Munoz, and > Hafner - NJP 10 063031); it agrees most closely with the NCPP PBE > structures generated by Zhao and Vanderbilt in PRB 65 233106, except for > the angle \beta, which is similar to that reported in PRB 65 174117. > The basic summary is that the cell volume is larger than anything published. > > &input > title='Hf', > zed=72, > rel=1, > iswitch=3, > config='[Xe] 4f14.0 5d2.0 6s2.0 6p0.0', > dft='PBE', > / > &inputp > lloc=0, > pseudotype=3, > file_pseudopw='Hf.srl-pbe-rrkjus.UPF', > nlcc=.true., > rcore=0.9, > author='test', > rho0=0.0001, > / > 4 > 6P 2 1 0.00 0.00 2.70 2.70 1 > 5D 3 2 2.00 0.00 1.90 2.30 1 > 5D 3 2 0.00 -0.18 1.90 2.30 1 > 6S 1 0 2.00 0.00 2.50 2.50 1 > / > &test > nconf=5 > file_pseudo='Hf.srl-pbe-rrkjus.UPF' > ecutmin=20.0, ecutmax=50.0, decut=10.0 > configts(1)='5d2.0 6s2.0 6p0.0' > configts(2)='5d1.0 6s2.0 6p0.0' > configts(3)='5d1.0 6s1.0 6p0.0' > configts(4)='5d0.0 6s1.0 6p0.0' > configts(5)='5d0.0 6s0.0 6p0.0' > / > > Note that the test results for different charged (d-depleted) states of > Hf are pretty bad. For those interested in using this as a starting > point, an analogous fully relativistic USPP can be generated using the > input file: > > &input > title='Hf', > zed=72, > rel=2, > iswitch=3, > config='[Xe] 4f14.0 5d2.0 6s2.0 6p0.0', > dft='PBE', > / > &inputp > lloc=0, > pseudotype=3, > file_pseudopw='Hf.rel-pbe-rrkjus.UPF', > nlcc=.true., > rcore=0.9, > author='test', > / > 7 > 6P 2 1 0.00 0.00 2.70 2.70 0.5 > 6P 2 1 0.00 0.00 2.70 2.70 1.5 > 5D 3 2 2.00 0.00 1.90 2.30 1.5 > 5D 3 2 0.00 -0.18 1.90 2.30 1.5 > 5D 3 2 0.00 0.00 1.90 2.30 2.5 > 5D 3 2 0.00 -0.18 1.90 2.30 2.5 > 6S 1 0 2.00 0.00 2.50 2.50 0.5 > / > &test > nconf=3 > file_pseudo='Hf.rel-pbe-rrkjus.UPF' > ecutmin=20.0, ecutmax=80.0, decut=10.0 > configts(1)='5d2.0 6s2.0' > configts(2)='5d2.0 6s1.0 6p1.0' > configts(3)='5d1.0 6s2.0 6p0.0' > / > > The structural discrepancies persist for different oxygen USPP, > different optimization procedures, and different sets of parameters > (charge density cutoffs, convergence criteria, etc.). > > I am now trying to check if the structural properties can be improved by > the inclusion of semicore states, and am starting with the "simplest" > case, that of a scalar relativistic NCPP with explicit inclusion of 5S > and 5P. After starting with the fewest number of projectors (one each > for 5S, 5P, and 5D), and running into all kinds of problems (anyone who > runs ld1.x knows about the kinds of mysterious errors that are > generated, and the equally mysterious modifications which result in said > errors disappearing), I searched the pw_forum and found the following > thread: > > http://www.democritos.it/pipermail/pw_forum/2009-July/013453.html > > Following from this (and making the implicit corrections to the provided > files in order to render them processable, such as modifying the 2nd > column in the definition of the projectors), I have been working off of > the following NCPP input file, > > &input > title='Hf', > zed=72, > rel=1, > iswitch=3, > config='[Xe] 4f14 5d2 6s2 6p0', > dft='PBE', > / > &inputp > lloc=0, > pseudotype=2, > file_pseudopw='Hf.semicore.srl-pbe-rrkjus.UPF', > nlcc=.f., > author='test', > rho0=0.01, > / > 5 > 5P 2 1 6.00 0.00 1.50 1.50 1 > 5P 2 1 0.00 -1.00 1.50 1.50 1 > 5D 3 2 2.00 0.00 1.90 1.90 1 > 5D 3 2 0.00 -0.20 1.90 1.90 1 > 5S 1 0 2.00 0.00 1.20 1.20 1 > / > &test > nconf=1 > file_pseudo='Hf.semicore.srl-pbe-rrkjus.UPF' > ecutmin=20.0, ecutmax=50.0, decut=10.0 > configts(1)='5s2 5p6 5d2 6s2 6p0', > / > > and have been varying the energy for the empty 5P projector, changing > lloc (and rcloc when applicable), toying with rho0, and fiddling with > the cutoffs, to no avail. The latest error is the not-so-helpful: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from run_pseudo : error # 1 > Errors in PS-KS equation > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Changing parameters merely changes the error, it seems. I know this is > a highly-specific cooking problem, but if anyone has any suggestions on > how to proceed, I would be extremely grateful. With some help, > hopefully I can generate a good, tested set of USPPs for Hf and fill in > that blank on PWSCF's pseudopotential page! > > Joseph Turnbull > NC State University > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it From giannozz at democritos.it Fri Mar 4 09:32:29 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 4 Mar 2011 09:32:29 +0100 Subject: [Pw_forum] nstep for CPMD average physical quantities In-Reply-To: References: Message-ID: <593A5EAC-948B-4046-8C02-F960ECAB3ACF@democritos.it> On Mar 4, 2011, at 1:48 , Riping WANG wrote: > For QE-CPMD calcualtion, Could any told me how many nstep > keeping is necessary to get average physical quantities? > the lenght of the simulation (nstep*dt) is more important than the number of steps. The answer depends upon the system and the physical property you want to calculate. The longer, the better, but in first-principle MD one typically cannot afford more than a few tens of ps. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Mar 4 09:35:45 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 4 Mar 2011 09:35:45 +0100 Subject: [Pw_forum] atomic position in vc-relax CPMD In-Reply-To: References: Message-ID: <347E1AE9-778E-4A93-A67E-415D83F1DCDA@democritos.it> On Mar 4, 2011, at 1:58 , Riping WANG wrote: > How can I get average atomic positions at at given pressure and > temperature > with vc-relax QE-cpmd? vc-relax = "variable-cell structural optimization". This is not the same as vc-cp = "Car-Parrinello molecular dynamics with variable cell" See code CPV/fpmdpp.f90 and input description in Doc/INPUT_CPPP* P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From rejmakp at gmail.com Fri Mar 4 11:04:40 2011 From: rejmakp at gmail.com (=?ISO-8859-2?Q?Pawe=B3_Rejmak?=) Date: Fri, 4 Mar 2011 11:04:40 +0100 Subject: [Pw_forum] GIPAW fails for large system Message-ID: Hi everyone I am the beginning user of QE and I am trying to calculate NMR shielding for Si atoms in hydrated calcium silicates using GIPAW. Unfortunately, all alculations for large systems, up to 200 atoms per unit cell, have failed. I have accomplished GIPAW calculations for smaller systems (up to 100 atoms, Davidson diagonalization), thus I am (almost) sure that everything is OK with my inputs, SCF calculations, pseudopotentials (taken from http://www.impmc.jussieu.fr/~software/gipaw/pseudopotentials.html) etc. and the source of problem is simply due to the size of studied system. With CG diagonalization I got error like this: task # 0 from cdiaghg : error # numbers in range 255-790 diagonalization (ZHEGV*) failed With Davidson diagonalization I got for example: forrtl: error (78): process killed (SIGTERM) Image PC Routine Line Source gipaw.x 400000000062C5E0 Unknown Unknown Unknown gipaw.x 40000000006568E0 Unknown Unknown Unknown gipaw.x 4000000000656110 Unknown Unknown Unknown gipaw.x 4000000000656B70 Unknown Unknown Unknown gipaw.x 4000000000655310 Unknown Unknown Unknown gipaw.x 4000000000652F50 Unknown Unknown Unknown gipaw.x 40000000003C4660 fft_scalar_mp_cft 761 fft_scalar.f90 gipaw.x 40000000003BC4B0 fft_parallel_mp_t 142 fft_parallel.f90 gipaw.x 40000000000F86C0 cft3s_ 52 cft3s.f90 gipaw.x 4000000000038740 h_psiq_ 74 h_psiq.f90 gipaw.x 4000000000042190 ch_psi_all_ 60 ch_psi_all.f90 gipaw.x 400000000003B360 cgsolve_all_ 190 cgsolve_all.f90 gipaw.x 4000000000037360 greenfunction_ 132 greenfunction.f90 gipaw.x 4000000000057EB0 suscept_crystal_I 319 suscept_crystal.f90 gipaw.x 400000000004FC40 suscept_crystal_ 125 suscept_crystal.f90 gipaw.x 4000000000024B90 MAIN__ 77 gipaw_main.f90 gipaw.x 4000000000004E90 Unknown Unknown Unknown libc.so.6.1 200000000052FC20 Unknown Unknown Unknown gipaw.x 4000000000004C80 Unknown Unknown Unknown Is there any solution to this problem? Should I simply increase amount of memory per process? (so far I have tried 30GB per process) Or maybe changing some constant value (like some fixed array dimension) in source code and compiling it again would help? Or is my system simply too large and should I abandon all hope?:( Thank you in advance for your help Pawel Rejmak, Donostia International Physics Center P. S. Inputs below. ######## PW input: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = 'tmp' , wf_collect = .TRUE. , pseudo_dir = '/scratch/prejmak/qecement1/pseudos' , disk_io = 'default' , verbosity = 'high' , / &SYSTEM ibrav = 14 , A = 6.746900, B = 14.952840, C = 26.451853, cosAB = -0.565691, cosAC = -0.078344, cosBC = -0.018083, nat = 194, ntyp = 4, ecutwfc = 80 , input_dft = PBE , / &ELECTRONS electron_maxstep = 300, conv_thr = 1.d-6 , startingpot = 'atomic' , startingwfc = 'atomic' , mixing_mode = 'local-TF' , mixing_beta = 0.1 , diagonalization = 'cg' , / ATOMIC_SPECIES Si 28.08550 Si.UPF O 15.99940 O.UPF Ca 40.07800 Ca.UPF H 1.00794 H.UPF ATOMIC_POSITIONS crystal Ca 0.24000 0.83000 0.55000 ... K_POINTS automatic 1 1 1 0 0 0 ########### GIPAW input: &inputgipaw job = 'nmr' prefix = 'pwscf' tmp_dir = 'tmp/' iverbosity = 1 q_gipaw = 0.01 spline_ps = .true. isolve = 0 use_nmr_macroscopic_shape = .true. / -- Dr. Pawe? Rejmak Donostia International Physics Center Paseo Manuel de Lardizabal 4 Donostia -San Sebastian, Spain From kucukben at sissa.it Fri Mar 4 11:40:58 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Fri, 04 Mar 2011 11:40:58 +0100 Subject: [Pw_forum] GIPAW fails for large system In-Reply-To: References: Message-ID: <20110304114058.9fmi4iwhkwko8gog@webmail.sissa.it> Dear Pawe? I think there is no reason why your calculations for large systems shouldnt work, else than the obvious memory problem. Please monitor the memory usage and adjust the resources accordingly. Note that in GIPAW, many arrays with size (# of planewaves, # of bands) and (#band, #band) are allocated. This easily increases the memory required compared to a correspoinding pw.x calculation. But yes i think it is a good idea to print some estimate of the memory required at the beginning of the run, similar to pw.x emine kucukbenli, phd student, sissa, italy ps: I think your "conv_thr = 1.d-6 " is a bit too loose to get good enough wavefunctions for GIPAW. ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From nicola.marzari at materials.ox.ac.uk Fri Mar 4 13:15:12 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Fri, 04 Mar 2011 12:15:12 +0000 Subject: [Pw_forum] Lattice constant for copper In-Reply-To: <4D70D72F.4040704@gucas.ac.cn> References: <499102391.08168@test1.gucas.ac.cn> <4D6F8A6D.4040502@gucas.ac.cn> <499139633.07732@test1.gucas.ac.cn> <4D70D72F.4040704@gucas.ac.cn> Message-ID: <4D70D7D0.3050606@materials.ox.ac.uk> On 3/4/11 12:12 PM, Eric Germaneau wrote: > Dear Professor Marzari, > > Thank you for your comment, but I'm getting very much confused now. > Well, I thought the Bose-Einstein statistics apply to bosons. > Are you talking about Fermi-Dirac statistics? > Actually, I imaged that Car-Parrinello molecular dynamics approach > considered the quantum statistic of electrons. > I'm going to look for some paper on this topic. > I thank you again, > > Eric. Hi Eric, vibrations (i.e. ionic motions) are actually bosons - so in car-parrinello or born-oppenheimer md we treat the electrons properly (with fermi-dirac statistics) but not the vibrations - our algorithms assume distinguishable particles, hence maxwell boltzmann. at room temperature the difference is significant - you can take into account bose einstein statistics in general terms using a path-integral formulation (that gives you statistical bose-einstein averages, and not real dynamics), or around equilibrium by calculating phonons (sinze you can write out analytically the partition function of a system of independent harmonic oscillators - look out for papers on the quasiharmonic approximations). you could also look at the recent work of ceriotti, bussi and parrinello - in particolar the second paper below. Best, nicola Colored Langevin equation for molecular dynamics simulations M. Ceriotti, G. Bussi and M. Parrinello, Langevin equation with colored noise for constant-temperature molecular dynamics simulations, Phys. Rev. Lett. 102, 020601 (2009) Preprint: arXiv:0812.1168 M. Ceriotti, G. Bussi and M. Parrinello, Nuclear quantum effects in solids using a colored-noise thermostat, Phys. Rev. Lett. 103, 030603 (2009) Preprint: arXiv:0903.4551 M. Ceriotti, G. Bussi and M. Parrinello, Colored-Noise Thermostats ? la Carte, J. Chem. Theory Comput. 6, 1170 (2010) -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From nicola.marzari at materials.ox.ac.uk Fri Mar 4 13:19:29 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Fri, 04 Mar 2011 12:19:29 +0000 Subject: [Pw_forum] nstep for CPMD average physical quantities In-Reply-To: References: Message-ID: <4D70D8D1.9050000@materials.ox.ac.uk> On 3/4/11 12:48 AM, Riping WANG wrote: > Dear Forum, > > For QE-CPMD calcualtion, Could any told me how many nstep keeping is > necessary to get average physical quantities? > Thank you very much. > > WANG Riping > 20101.3.4 Dear Riping, here are a few lectures (videos, and notes) on Car-Parrinello and Born-Oppenheimer: http://www.mcc.uiuc.edu/summerschool/2006/ nicola -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From m_pazoki at physics.sharif.edu Fri Mar 4 14:18:58 2011 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Fri, 4 Mar 2011 16:48:58 +0330 Subject: [Pw_forum] SAX Message-ID: Dear PWSCF users I need to continue my calculations in GW approximation.I find a package "sax" that is joint to espresso. But the last date of release of this program is some years ago. I also cant see anything about SAX in pwscf.org. Is this package is reliable? Is there any other choices for GW calculations in espresso? Thanks alot Meysam Pazoki SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/163d4f11/attachment.htm From smirshamsi at phys.ufl.edu Fri Mar 4 16:19:22 2011 From: smirshamsi at phys.ufl.edu (Sahar Mirshamsi) Date: Fri, 4 Mar 2011 10:19:22 -0500 (EST) Subject: [Pw_forum] Some questions about non-collinear calculation and penalty function In-Reply-To: Message-ID: On Thu, 3 Mar 2011, Sahar Mirshamsi wrote: any idea about answers of these questions? Sahar > Hi all, > I have some questions regarding non-collinear calculation and using > penalty function in pwscf. > 1) In constaint_magnetization ='atomic', is starting magnetization as the > target magnetization? I have read this post > http://www.democritos.it/pipermail/pw_forum/2009-December/015342.html > and also in input.f90 I found > mcons(1,nt) = starting_magnetization(nt) * SIN( theta ) * COS( > phi ) > mcons(2,nt) = starting_magnetization(nt) * SIN( theta ) * SIN( > phi ) > mcons(3,nt) = starting_magnetization(nt) * COS( theta ) > So it means both magnitude and direction of atomic magnetizations are > constrained, is this correct? > 2) If above statement is correct, then the same problem as posted in above > link will still exist, since starting_magnetization=m/n, then for > constraining the magnitude of magnetization to desired value, we should > multiply the magnitude of magnetization by charge and then replace it as > starting_magnitization, is this correct? > 3) What is the relation between charge and magnetization printed in scf > calculation with those which we can get with using projwf.x, I expect they > should get almost same numbers but in scf output for carbons in Graphene > nanoribbon I get charge=0.6 and magnetization=0.1 while in projwf.x output > I get charge=4 and polarization=0.2-0.3 which the latest one makes more > sense. > 4) Also, in some cases of non-collinear calculation with using penalty > function, when I track "estimated scf accuracy" it is decreasing till > reaching the threshold and stopping the job while "total energy" is > oscillating in some range instead of converging to a number , any idea > what's the problem? > 5) The total energy printed in scf calculation does not include constraint > energy, right? It's just energy of the structure with the constraint > configuration of magnetizations, right? > I appreciate any help in finding the answers of these questions. > > Sahar Mishamsi > Quantum Theory Project and Physics Department, > University of Florida > > > From agkvashnin at gmail.com Fri Mar 4 18:57:49 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Fri, 4 Mar 2011 20:57:49 +0300 Subject: [Pw_forum] Adding an email Message-ID: Add my email to this mailing list, please -- Sincerely yours Alexander G. Kvashnin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/2980f7ed/attachment.htm From agkvashnin at gmail.com Fri Mar 4 19:07:46 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Fri, 4 Mar 2011 21:07:46 +0300 Subject: [Pw_forum] problem in MPI running of QE (16 processors) Message-ID: Hello, I have some problem when I ran parallel version of QE (16 procs), I saw next line in output file Parallel version (MPI), running on 1 processors And it works using only 1 processor, but there is MPI version. Help me please in my problem Thank you! -- Sincerely yours Alexander G. Kvashnin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/8a1e429e/attachment.htm From eyvaz_isaev at yahoo.com Fri Mar 4 19:37:40 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 4 Mar 2011 10:37:40 -0800 (PST) Subject: [Pw_forum] problem in MPI running of QE (16 processors) In-Reply-To: References: Message-ID: <420647.20855.qm@web65714.mail.ac4.yahoo.com> Dear Alexander, How do you run a job? You should launch a command like (some parameters are omitted) mpirun -np 16 -maxtime 30 ./pw.x < scf.in >scf.out The easiest way to be added to the forum list is subscribing to this forum. Please visit http://www.pwscf.org/contacts.php Please also provide your affiliation. Best regards, Eyvaz.------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Alexander G. Kvashnin To: pw_forum at pwscf.org Sent: Fri, March 4, 2011 9:07:46 PM Subject: [Pw_forum] problem in MPI running of QE (16 processors) Hello, I have some problem when I ran parallel version of QE (16 procs), I saw next line in output file Parallel version (MPI), running on 1 processors And it works using only 1 processor, but there is MPI version. Help me please in my problem Thank you!-- Sincerely yours Alexander G. Kvashnin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/ca82a86f/attachment-0001.htm From agkvashnin at gmail.com Fri Mar 4 19:53:19 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Fri, 4 Mar 2011 21:53:19 +0300 Subject: [Pw_forum] problem in MPI running of QE (16 processors) In-Reply-To: <420647.20855.qm@web65714.mail.ac4.yahoo.com> References: <420647.20855.qm@web65714.mail.ac4.yahoo.com> Message-ID: I create PBS task on supercomputer MIPT-60 where I write mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt all other types of this line such as mpiexec -np 16 ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt doesn't work. Maybe this number of processor too small for parallel calculation to QE? On 4 March 2011 21:37, Eyvaz Isaev wrote: > Dear Alexander, > > How do you run a job? You should launch a command like (some parameters are > omitted) > mpirun -np 16 -maxtime 30 ./pw.x < scf.in >scf.out > > The easiest way to be added to the forum list is subscribing to this > forum. Please visit > http://www.pwscf.org/contacts.php > > Please also provide your affiliation. > > Best regards, > Eyvaz. > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > ------------------------------ > *From:* Alexander G. Kvashnin > *To:* pw_forum at pwscf.org > *Sent:* Fri, March 4, 2011 9:07:46 PM > *Subject:* [Pw_forum] problem in MPI running of QE (16 processors) > > Hello, > > I have some problem when I ran parallel version of QE (16 procs), I saw > next line in output file > > Parallel version (MPI), running on 1 processors > > And it works using only 1 processor, but there is MPI version. > Help me please in my problem > Thank you! > -- > Sincerely yours > Alexander G. Kvashnin > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Sincerely yours Alexander G. Kvashnin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/f278f9dd/attachment.htm From ttduyle at gmail.com Fri Mar 4 20:23:42 2011 From: ttduyle at gmail.com (Duy Le) Date: Fri, 4 Mar 2011 14:23:42 -0500 Subject: [Pw_forum] problem in MPI running of QE (16 processors) In-Reply-To: References: <420647.20855.qm@web65714.mail.ac4.yahoo.com> Message-ID: You can use: mpiexec --help or man mpiexec to see how to have correct command -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Fri, Mar 4, 2011 at 1:53 PM, Alexander G. Kvashnin wrote: > I create PBS task on supercomputer MIPT-60 where I write > > mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt > all other types of this line such as > mpiexec -np 16 ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt > > doesn't work. > Maybe this number of processor too small for parallel calculation to QE? > > > On 4 March 2011 21:37, Eyvaz Isaev wrote: >> >> Dear? Alexander, >> >> How do you run a job? You should launch a command like (some parameters >> are omitted) >> mpirun -np 16 -maxtime 30 ./pw.x < scf.in >scf.out >> >> The easiest way to be added to the forum list? is subscribing? to this >> forum. Please visit >> http://www.pwscf.org/contacts.php >> >> Please also provide your affiliation. >> >> Best regards, >> ?Eyvaz. >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >> Sweden >> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >> Russia, >> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> ________________________________ >> From: Alexander G. Kvashnin >> To: pw_forum at pwscf.org >> Sent: Fri, March 4, 2011 9:07:46 PM >> Subject: [Pw_forum] problem in MPI running of QE (16 processors) >> >> Hello, >> >> I have some problem when I ran parallel version of QE (16 procs), I saw >> next line in output file >> >> Parallel version (MPI), running on 1 processors >> And it works using only 1 processor, but there is MPI version. >> Help me please in my problem >> Thank you! >> -- >> Sincerely yours >> Alexander G. Kvashnin >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Sincerely yours > Alexander G. Kvashnin > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From josepht at chips.ncsu.edu Fri Mar 4 21:49:21 2011 From: josepht at chips.ncsu.edu (Joe) Date: Fri, 04 Mar 2011 15:49:21 -0500 Subject: [Pw_forum] PP generation with ld1.x (transition metals with semicore states) In-Reply-To: <1299225368.27875.3.camel@ulisse.cm.sissa.it> References: <4D7021D4.7090603@chips.ncsu.edu> <1299225368.27875.3.camel@ulisse.cm.sissa.it> Message-ID: <4D715051.8040607@chips.ncsu.edu> Hello, Thanks for pointing out the updated beta-PP library! I just tested the listed Hf pseudopotential - it reproduces AE states with different 5d occupancy much more closely than the (non-semi-core) USPP I had been testing. Some comments. First, the usage of the augmentation function flags is novel to me - is the called directive similar in spirit to the procedure used in Vanderbilt's code (called by 'nfix') to constrain the q-function pseudization so as to overcome (negative charge) problems during the descreening step? There are a few more fundamental (?) aspects I am also trying to understand. For example, the (slightly modified) USPP input file is: &input title='Hf', zed=72.0, rel=1, config='[Xe] 4f14 5d2.0 6s2 6p0', iswitch=3, dft='PBE' / &inputp pseudotype=3, file_pseudopw='Hf.srl-pbe-rrkjus.UPF', author='ADC', lloc=-1, rcloc=2.5, which_augfun='PSQ', rmatch_augfun=1.1, nlcc=.true., rcore=1.2, tm=.true. / 6 5S 1 0 2.00 0.00 1.50 1.60 0.0 6S 2 0 2.00 0.00 1.10 1.60 0.0 5P 2 1 6.00 0.00 1.50 1.60 0.0 6P 3 1 0.00 0.00 1.30 1.60 0.0 5D 3 2 2.00 0.00 1.60 1.70 0.0 5D 3 2 -2.00 0.30 1.60 1.70 0.0 / ! &test ! nconf=8, ! file_pseudo='Hf.srl-pbe-rrkjus.UPF' ! ecutmin=20.0, ecutmax=50.0, decut=10.0 ! configts(1)='5s2 5p6 5d2 6s2 6p0' ! configts(2)='5s2 5p6 5d1 6s2 6p0' ! configts(3)='5s2 5p6 5d0 6s2 6p0' ! configts(4)='5s2 5p6 5d2 6s1 6p0' ! configts(5)='5s2 5p6 5d2 6s0 6p0' ! configts(6)='5s2 5p6 5d1 6s0 6p0' ! configts(7)='5s2 5p6 5d0 6s0 6p0' ! configts(8)='5s2 5p6 5d1 6s1 6p0' ! / and I was wondering ("at risk of appearing a fool, in the hope of being less of one")...why (hopefully aside from "because it works"...but with PP generation, I can appreciate that sometimes that is as far as things go) do the 6S and 6P states have lower cutoffs compared to the 5S and 5P states (given that the localizations of these states follow the opposite trend)? Anyway, I will report the results of tests using this semi-core USPP in bulk systems. Thanks again! Joseph Turnbull NC State University On 03/04/2011 02:56 AM, Andrea Dal Corso wrote: > Did you try the Hf PP in pslibrary? > > http://qe-forge.org/projects/pslibrary/ > > These are still untested PPs, and it would be useful to have feedback > from the users. > &input > title='Hf', > zed=72.0, > rel=1, > config='[Xe] 4f14 5d2.0 6s2 6p0', > iswitch=3, > dft='PBE' > / > &inputp > pseudotype=3, > file_pseudopw='Hf.srl-pbe-rrkjus.UPF', > author='ADC', > lloc=-1, > rcloc=2.5, > which_augfun='PSQ', > rmatch_augfun=1.1, > nlcc=.true., > rcore=1.2, > tm=.true. > / > 6 > 5S 1 0 2.00 0.00 1.50 1.60 0.0 > 6S 2 0 2.00 0.00 1.10 1.60 0.0 > 5P 2 1 6.00 0.00 1.50 1.60 0.0 > 6P 3 1 0.00 0.00 1.30 2.10 0.0 > 5D 3 2 2.00 0.00 1.60 1.70 0.0 > 5D 3 2 -2.00 0.30 1.60 1.70 0.0 > / > !&test > ! nconf=8, > ! file_pseudo='Hf.srl-pbe-rrkjus.UPF' > ! ecutmin=20.0, ecutmax=50.0, decut=10.0 > ! configts(1)='5s2 5p6 5d2 6s2 6p0' > ! configts(2)='5s2 5p6 5d1 6s2 6p0' > ! configts(3)='5s2 5p6 5d0 6s2 6p0' > ! configts(4)='5s2 5p6 5d2 6s1 6p0' > ! configts(5)='5s2 5p6 5d2 6s0 6p0' > ! configts(6)='5s2 5p6 5d1 6s0 6p0' > ! configts(7)='5s2 5p6 5d0 6s0 6p0' > ! configts(8)='5s2 5p6 5d1 6s1 6p0' > ! / > > Andrea > > On Thu, 2011-03-03 at 18:18 -0500, Joe wrote: >> Hello everyone, >> >> Using ld1.x, I am trying to generate pseudopotentials for elements such >> as Hf, both scalar relativistic and fully relativistic. I have followed >> from the examples given in atomic_doc, and have been making ample use of >> Paolo Giannozzi's July 9th 2010 tutorial, "Notes on pseudopotential >> generation" (which is the version with full worked examples for Ti). >> The information provided by this arsenal as been sufficient to generate >> and test new USPP/NCPP for Si, C, N, O, and S, as well as "naive" USPP >> for Hf. Several of the issues I am reporting below have been mentioned >> within the pw_forum, and when applicable, I have tried (often with >> success) the prescriptions offered. >> >> First, let me share what I have "working". Below is the input file for >> a scalar relativistic USPP for Hf that does not contain semicore >> states. I have tested it for bulk hafnia and it reproduces published >> band structure data at fixed cell parameters and fixed atomic >> coordinates, but gives optimized structures at variance with those >> (using PBE-based PP) reported in the literature (for example, following >> from the review given in the 2008 NJP paper by Beltran, Munoz, and >> Hafner - NJP 10 063031); it agrees most closely with the NCPP PBE >> structures generated by Zhao and Vanderbilt in PRB 65 233106, except for >> the angle \beta, which is similar to that reported in PRB 65 174117. >> The basic summary is that the cell volume is larger than anything published. >> >> &input >> title='Hf', >> zed=72, >> rel=1, >> iswitch=3, >> config='[Xe] 4f14.0 5d2.0 6s2.0 6p0.0', >> dft='PBE', >> / >> &inputp >> lloc=0, >> pseudotype=3, >> file_pseudopw='Hf.srl-pbe-rrkjus.UPF', >> nlcc=.true., >> rcore=0.9, >> author='test', >> rho0=0.0001, >> / >> 4 >> 6P 2 1 0.00 0.00 2.70 2.70 1 >> 5D 3 2 2.00 0.00 1.90 2.30 1 >> 5D 3 2 0.00 -0.18 1.90 2.30 1 >> 6S 1 0 2.00 0.00 2.50 2.50 1 >> / >> &test >> nconf=5 >> file_pseudo='Hf.srl-pbe-rrkjus.UPF' >> ecutmin=20.0, ecutmax=50.0, decut=10.0 >> configts(1)='5d2.0 6s2.0 6p0.0' >> configts(2)='5d1.0 6s2.0 6p0.0' >> configts(3)='5d1.0 6s1.0 6p0.0' >> configts(4)='5d0.0 6s1.0 6p0.0' >> configts(5)='5d0.0 6s0.0 6p0.0' >> / >> >> Note that the test results for different charged (d-depleted) states of >> Hf are pretty bad. For those interested in using this as a starting >> point, an analogous fully relativistic USPP can be generated using the >> input file: >> >> &input >> title='Hf', >> zed=72, >> rel=2, >> iswitch=3, >> config='[Xe] 4f14.0 5d2.0 6s2.0 6p0.0', >> dft='PBE', >> / >> &inputp >> lloc=0, >> pseudotype=3, >> file_pseudopw='Hf.rel-pbe-rrkjus.UPF', >> nlcc=.true., >> rcore=0.9, >> author='test', >> / >> 7 >> 6P 2 1 0.00 0.00 2.70 2.70 0.5 >> 6P 2 1 0.00 0.00 2.70 2.70 1.5 >> 5D 3 2 2.00 0.00 1.90 2.30 1.5 >> 5D 3 2 0.00 -0.18 1.90 2.30 1.5 >> 5D 3 2 0.00 0.00 1.90 2.30 2.5 >> 5D 3 2 0.00 -0.18 1.90 2.30 2.5 >> 6S 1 0 2.00 0.00 2.50 2.50 0.5 >> / >> &test >> nconf=3 >> file_pseudo='Hf.rel-pbe-rrkjus.UPF' >> ecutmin=20.0, ecutmax=80.0, decut=10.0 >> configts(1)='5d2.0 6s2.0' >> configts(2)='5d2.0 6s1.0 6p1.0' >> configts(3)='5d1.0 6s2.0 6p0.0' >> / >> >> The structural discrepancies persist for different oxygen USPP, >> different optimization procedures, and different sets of parameters >> (charge density cutoffs, convergence criteria, etc.). >> >> I am now trying to check if the structural properties can be improved by >> the inclusion of semicore states, and am starting with the "simplest" >> case, that of a scalar relativistic NCPP with explicit inclusion of 5S >> and 5P. After starting with the fewest number of projectors (one each >> for 5S, 5P, and 5D), and running into all kinds of problems (anyone who >> runs ld1.x knows about the kinds of mysterious errors that are >> generated, and the equally mysterious modifications which result in said >> errors disappearing), I searched the pw_forum and found the following >> thread: >> >> http://www.democritos.it/pipermail/pw_forum/2009-July/013453.html >> >> Following from this (and making the implicit corrections to the provided >> files in order to render them processable, such as modifying the 2nd >> column in the definition of the projectors), I have been working off of >> the following NCPP input file, >> >> &input >> title='Hf', >> zed=72, >> rel=1, >> iswitch=3, >> config='[Xe] 4f14 5d2 6s2 6p0', >> dft='PBE', >> / >> &inputp >> lloc=0, >> pseudotype=2, >> file_pseudopw='Hf.semicore.srl-pbe-rrkjus.UPF', >> nlcc=.f., >> author='test', >> rho0=0.01, >> / >> 5 >> 5P 2 1 6.00 0.00 1.50 1.50 1 >> 5P 2 1 0.00 -1.00 1.50 1.50 1 >> 5D 3 2 2.00 0.00 1.90 1.90 1 >> 5D 3 2 0.00 -0.20 1.90 1.90 1 >> 5S 1 0 2.00 0.00 1.20 1.20 1 >> / >> &test >> nconf=1 >> file_pseudo='Hf.semicore.srl-pbe-rrkjus.UPF' >> ecutmin=20.0, ecutmax=50.0, decut=10.0 >> configts(1)='5s2 5p6 5d2 6s2 6p0', >> / >> >> and have been varying the energy for the empty 5P projector, changing >> lloc (and rcloc when applicable), toying with rho0, and fiddling with >> the cutoffs, to no avail. The latest error is the not-so-helpful: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from run_pseudo : error # 1 >> Errors in PS-KS equation >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> Changing parameters merely changes the error, it seems. I know this is >> a highly-specific cooking problem, but if anyone has any suggestions on >> how to proceed, I would be extremely grateful. With some help, >> hopefully I can generate a good, tested set of USPPs for Hf and fill in >> that blank on PWSCF's pseudopotential page! >> >> Joseph Turnbull >> NC State University >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Fri Mar 4 21:48:36 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 4 Mar 2011 12:48:36 -0800 (PST) Subject: [Pw_forum] QHA compiling In-Reply-To: <87EFAA1B-D1AC-406F-AC38-B9F9E6A66162@sissa.it> References: <137709.84542.qm@web65708.mail.ac4.yahoo.com> <355416.94432.qm@web65715.mail.ac4.yahoo.com> <233070.82792.qm@web65701.mail.ac4.yahoo.com> <87EFAA1B-D1AC-406F-AC38-B9F9E6A66162@sissa.it> Message-ID: <99969.5513.qm@web65711.mail.ac4.yahoo.com> Hi Sterfano, Indeed, it is a good question. I had the same idea several times ago. Probably, I should ask about a password for a developer. Hopefully, I will do that soon. Bests, Eyvaz. ________________________________ From: Stefano Baroni To: PWSCF Forum Sent: Thu, March 3, 2011 8:51:22 PM Subject: Re: [Pw_forum] QHA compiling Hi Eyvaz: why don't you keep everything on qe-forge? Stefano -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/d81dcb2f/attachment.htm From eyvaz_isaev at yahoo.com Fri Mar 4 23:30:24 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 4 Mar 2011 14:30:24 -0800 (PST) Subject: [Pw_forum] problem in MPI running of QE (16 processors) In-Reply-To: References: <420647.20855.qm@web65714.mail.ac4.yahoo.com> Message-ID: <13539.92083.qm@web65707.mail.ac4.yahoo.com> Well, again, we will appreciate, if you sign your e-mail providing your affiliation. I do not think it is related to CPU numbers. Is a job you launched finished properly? Bests, Eyvaz. ________________________________ From: Alexander G. Kvashnin To: PWSCF Forum Sent: Fri, March 4, 2011 9:53:19 PM Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors) I create PBS task on supercomputer MIPT-60 where I write mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt all other types of this line such as mpiexec -np 16 ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt doesn't work. Maybe this number of processor too small for parallel calculation to QE? On 4 March 2011 21:37, Eyvaz Isaev wrote: Dear Alexander, > >How do you run a job? You should launch a command like (some parameters are >omitted) > >mpirun -np 16 -maxtime 30 ./pw.x < scf.in >scf.out > >The easiest way to be added to the forum list is subscribing to this forum. >Please visit > >http://www.pwscf.org/contacts.php > >Please also provide your affiliation. > >Best regards, > > Eyvaz.------------------------------------------------------------------- >Prof. Eyvaz Isaev, >Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >Sweden > >Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >Russia, > >isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > ________________________________ From: Alexander G. Kvashnin >To: pw_forum at pwscf.org >Sent: Fri, March 4, 2011 9:07:46 PM >Subject: [Pw_forum] problem in MPI running of QE (16 processors) > > > >Hello, > > > >I have some problem when I ran parallel version of QE (16 procs), I saw next >line in output file > > > >Parallel version (MPI), running on 1 processors > > >And it works using only 1 processor, but there is MPI version. >Help me please in my problem >Thank you!-- > >Sincerely yours >Alexander G. Kvashnin > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > -- Sincerely yours Alexander G. Kvashnin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110304/a8fdd4b4/attachment-0001.htm From germaneau at gucas.ac.cn Sat Mar 5 15:35:39 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Sat, 05 Mar 2011 09:35:39 -0500 Subject: [Pw_forum] problem in MPI running of QE (16 processors) In-Reply-To: <499261641.14003@test1.gucas.ac.cn> References: <420647.20855.qm@web65714.mail.ac4.yahoo.com> <499261641.14003@test1.gucas.ac.cn> Message-ID: <4D724A3B.7040101@gucas.ac.cn> Duy Le is write, you should take a look to the man of mpiexec. It is "mpiexec -n" ! Have you tried to run small mpi program first in order to check whether your machine is well configured? On 03/04/2011 02:23 PM, Duy Le wrote: > You can use: > mpiexec --help > or > man mpiexec > to see how to have correct command > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > > On Fri, Mar 4, 2011 at 1:53 PM, Alexander G. Kvashnin > wrote: >> I create PBS task on supercomputer MIPT-60 where I write >> >> mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp> output.opt >> all other types of this line such as >> mpiexec -np 16 ../../espresso-4.2.1/bin/pw.x -in graph.inp> output.opt >> >> doesn't work. >> Maybe this number of processor too small for parallel calculation to QE? >> >> >> On 4 March 2011 21:37, Eyvaz Isaev wrote: >>> Dear Alexander, >>> >>> How do you run a job? You should launch a command like (some parameters >>> are omitted) >>> mpirun -np 16 -maxtime 30 ./pw.x< scf.in>scf.out >>> >>> The easiest way to be added to the forum list is subscribing to this >>> forum. Please visit >>> http://www.pwscf.org/contacts.php >>> >>> Please also provide your affiliation. >>> >>> Best regards, >>> Eyvaz. >>> ------------------------------------------------------------------- >>> Prof. Eyvaz Isaev, >>> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >>> Sweden >>> Theoretical Physics Department, Moscow State Institute of Steel& Alloys, >>> Russia, >>> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >>> >>> ________________________________ >>> From: Alexander G. Kvashnin >>> To: pw_forum at pwscf.org >>> Sent: Fri, March 4, 2011 9:07:46 PM >>> Subject: [Pw_forum] problem in MPI running of QE (16 processors) >>> >>> Hello, >>> >>> I have some problem when I ran parallel version of QE (16 procs), I saw >>> next line in output file >>> >>> Parallel version (MPI), running on 1 processors >>> And it works using only 1 processor, but there is MPI version. >>> Help me please in my problem >>> Thank you! >>> -- >>> Sincerely yours >>> Alexander G. Kvashnin >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> -- >> Sincerely yours >> Alexander G. Kvashnin >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110305/4c688f68/attachment.htm From cjobrien at ncsu.edu Sat Mar 5 04:59:38 2011 From: cjobrien at ncsu.edu (Christopher O'Brien) Date: Fri, 4 Mar 2011 22:59:38 -0500 Subject: [Pw_forum] Ionic forces not reducing In-Reply-To: <20110224100830.mq87cz62bogcw40w@webmail.sic.rm.cnr.it> References: <934A8BF3-C58D-4E31-A8F7-459F63D7730F@ncsu.edu> <20110224100830.mq87cz62bogcw40w@webmail.sic.rm.cnr.it> Message-ID: Thank you for your suggestions regarding my problem. In my case, a further decrease in the electronic convergence threshold, or increase in ecutrho, and ecutwfc had little effect. I usually work with supercells or NEB calculations with little or no symmetry. It turns out that the parameter that affected the most significant reduction in force was the "upscale" parameter. Your recommended value of 1.D3 was usually sufficient, but really difficult cases can be handled with 1.D4. This parameter seemed to be the 'magic bullet' for me when nothing else worked. Why is the default value so small (10.0)? =================================================================== Christopher J. O'Brien cjobrien at ncsu.edu https://sites.google.com/a/ncsu.edu/cjobrien/ Ph.D. Candidate Computational Materials Group Department of Materials Science & Engineering North Carolina State University __________________________________________________________________ Please send all documents in PDF. For Word documents: Please use the 'Save as PDF' option before sending. =================================================================== On Feb 24, 2011, at 4:08 AM, Giuseppe Mattioli wrote: > Dear Christopher > You should try to reduce conv_thr in &ELECTRONS, in order to have a more accurate calculation of forces and stress. Try, for instance, with conv_thr = 1.0d-9 (and with a lower mixing_beta, 0.2~0.3 or so, if the electronic calculation does not converge). > HTH > > Giuseppe > > Quoting Christopher O'Brien : > >> Below this is a super-cell of an interface of Cu2O and Ti. The problem is simply that the forc_conv_thr is not met within 100 iterations. etot_conv_thr is almost always met first (even decreasing etot_conv_thr to 1.0d-6). Typically, the force in this system decreases to ~0.01 Ry/B with a delta F on the same order of magnitude but fluctuates about this value. This means that I continually get the warning telling me to reduce the convergence threshold. Ideally I would like obtain a maximum force of ~1D-4. >> Does anyone have any suggestions? I am at a loss. >> >> Thanks in advance, >> Chris O'Brien >> >> >> title = 'Cu2O-Ti-case2' , >> calculation = 'vc-relax' , >> restart_mode = 'from_scratch' , >> wf_collect = .false. , >> outdir = './', >> wfcdir = './', >> pseudo_dir = '/share2/cjobrien/pseudo/', >> prefix = 'Cu2OTi', >> disk_io = 'low', >> verbosity = 'minimal', >> tstress = .true., >> tprnfor = .true., >> forc_conv_thr = 1.0d-4, >> etot_conv_thr = 1.0d-5, >> / >> &SYSTEM >> ibrav = 0, >> celldm(1) = 8.1878, >> nat = 14, >> ntyp = 3, >> ecutwfc = 30.0 , >> ecutrho = 300.0 , >> occupations = 'smearing' , >> smearing = 'mv' , >> degauss = 0.01 , >> / >> &ELECTRONS >> conv_thr = 1.0d-6 , >> mixing_beta = 0.7 , >> / >> &IONS >> ion_dynamics = 'bfgs', >> / >> &CELL >> cell_dynamics = 'bfgs', >> press = 0.0, >> cell_dofree = 'xyz', >> / >> CELL_PARAMETERS >> 0.929429709 0.0 0.0 >> 0.0 0.929429709 0.0 >> 0.0 0.0 2.924945006 >> ATOMIC_SPECIES >> Cu 58.70000 Cu.pw91-n-van_ak.UPF >> Ti 47.88000 Ti.pw91-nsp-van.UPF >> O 16.00000 O.pw91-van_ak.UPF >> ATOMIC_POSITIONS alat >> Cu 0 0 0 >> Cu 0.504691013 0.504691013 0 >> Cu 0.484702934 0.019988079 0.553031754 >> Cu 0.019988079 0.484702934 0.553031754 >> Cu 0.039976158 0.039976158 1.106063508 >> Cu 0.464714854 0.464714854 1.106063508 >> O 0.252345506 0.252345506 0.285738983 >> O 0.024221288 0.024221288 1.544049139 >> Ti 0.480469725 0.024221288 1.544049139 >> Ti 0.024221288 0.480469725 1.544049139 >> Ti 0.484702934 0.484702934 2.015504257 >> Ti 0.019988079 0.019988079 2.015504257 >> Ti 0.01575487 0.488936142 2.486959376 >> Ti 0.488936142 0.01575487 2.486959376 >> K_POINTS automatic >> 8 8 4 0 0 0 >> >> =================================================================== >> Christopher J. O'Brien >> cjobrien at ncsu.edu >> https://sites.google.com/a/ncsu.edu/cjobrien/ >> >> Ph.D. Candidate >> Computational Materials Group >> Department of Materials Science & Engineering >> North Carolina State University >> __________________________________________________________________ >> Please send all documents in PDF. >> For Word documents: Please use the 'Save as PDF' option before sending. >> =================================================================== >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > Giuseppe Mattioli > ISM-CNR, Italy > > > > From dalcorso at sissa.it Sat Mar 5 10:01:19 2011 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Sat, 05 Mar 2011 10:01:19 +0100 Subject: [Pw_forum] PP generation with ld1.x (transition metals with semicore states) In-Reply-To: <4D715051.8040607@chips.ncsu.edu> References: <4D7021D4.7090603@chips.ncsu.edu> <1299225368.27875.3.camel@ulisse.cm.sissa.it> <4D715051.8040607@chips.ncsu.edu> Message-ID: <1299315679.2083.7.camel@localhost.localdomain> On Fri, 2011-03-04 at 15:49 -0500, Joe wrote: > Hello, > > Thanks for pointing out the updated beta-PP library! I just tested the > listed Hf pseudopotential - it reproduces AE states with different 5d > occupancy much more closely than the (non-semi-core) USPP I had been > testing. > > Some comments. First, the usage of the augmentation function flags is > novel to me - is the called directive similar in spirit to the procedure > used in Vanderbilt's code (called by 'nfix') to constrain the q-function > pseudization so as to overcome (negative charge) problems during the > descreening step? > It is a pseudization of the Q functions as described for instance in Phys. Rev. B 47, 10142 (1993). > There are a few more fundamental (?) aspects I am also trying to > understand. For example, the (slightly modified) USPP input file is: > > &input > title='Hf', > zed=72.0, > rel=1, > config='[Xe] 4f14 5d2.0 6s2 6p0', > iswitch=3, > dft='PBE' > / > &inputp > pseudotype=3, > file_pseudopw='Hf.srl-pbe-rrkjus.UPF', > author='ADC', > lloc=-1, > rcloc=2.5, > which_augfun='PSQ', > rmatch_augfun=1.1, > nlcc=.true., > rcore=1.2, > tm=.true. > / > 6 > 5S 1 0 2.00 0.00 1.50 1.60 0.0 > 6S 2 0 2.00 0.00 1.10 1.60 0.0 > 5P 2 1 6.00 0.00 1.50 1.60 0.0 > 6P 3 1 0.00 0.00 1.30 1.60 0.0 > 5D 3 2 2.00 0.00 1.60 1.70 0.0 > 5D 3 2 -2.00 0.30 1.60 1.70 0.0 > / > ! &test > ! nconf=8, > ! file_pseudo='Hf.srl-pbe-rrkjus.UPF' > ! ecutmin=20.0, ecutmax=50.0, decut=10.0 > ! configts(1)='5s2 5p6 5d2 6s2 6p0' > ! configts(2)='5s2 5p6 5d1 6s2 6p0' > ! configts(3)='5s2 5p6 5d0 6s2 6p0' > ! configts(4)='5s2 5p6 5d2 6s1 6p0' > ! configts(5)='5s2 5p6 5d2 6s0 6p0' > ! configts(6)='5s2 5p6 5d1 6s0 6p0' > ! configts(7)='5s2 5p6 5d0 6s0 6p0' > ! configts(8)='5s2 5p6 5d1 6s1 6p0' > ! / > > and I was wondering ("at risk of appearing a fool, in the hope of being > less of one")...why (hopefully aside from "because it works"...but with > PP generation, I can appreciate that sometimes that is as far as things > go) do the 6S and 6P states have lower cutoffs compared to the 5S and 5P > states (given that the localizations of these states follow the opposite > trend)? > You are right I should clean up these inputs. However with the option PSQ the norm conserving radius is not used, so provided that it is smaller than the US radius it is irrelevant. Andrea > Anyway, I will report the results of tests using this semi-core USPP in > bulk systems. Thanks again! > > Joseph Turnbull > NC State University > > > On 03/04/2011 02:56 AM, Andrea Dal Corso wrote: > > Did you try the Hf PP in pslibrary? > > > > http://qe-forge.org/projects/pslibrary/ > > > > These are still untested PPs, and it would be useful to have feedback > > from the users. > > &input > > title='Hf', > > zed=72.0, > > rel=1, > > config='[Xe] 4f14 5d2.0 6s2 6p0', > > iswitch=3, > > dft='PBE' > > / > > &inputp > > pseudotype=3, > > file_pseudopw='Hf.srl-pbe-rrkjus.UPF', > > author='ADC', > > lloc=-1, > > rcloc=2.5, > > which_augfun='PSQ', > > rmatch_augfun=1.1, > > nlcc=.true., > > rcore=1.2, > > tm=.true. > > / > > 6 > > 5S 1 0 2.00 0.00 1.50 1.60 0.0 > > 6S 2 0 2.00 0.00 1.10 1.60 0.0 > > 5P 2 1 6.00 0.00 1.50 1.60 0.0 > > 6P 3 1 0.00 0.00 1.30 2.10 0.0 > > 5D 3 2 2.00 0.00 1.60 1.70 0.0 > > 5D 3 2 -2.00 0.30 1.60 1.70 0.0 > > / > > !&test > > ! nconf=8, > > ! file_pseudo='Hf.srl-pbe-rrkjus.UPF' > > ! ecutmin=20.0, ecutmax=50.0, decut=10.0 > > ! configts(1)='5s2 5p6 5d2 6s2 6p0' > > ! configts(2)='5s2 5p6 5d1 6s2 6p0' > > ! configts(3)='5s2 5p6 5d0 6s2 6p0' > > ! configts(4)='5s2 5p6 5d2 6s1 6p0' > > ! configts(5)='5s2 5p6 5d2 6s0 6p0' > > ! configts(6)='5s2 5p6 5d1 6s0 6p0' > > ! configts(7)='5s2 5p6 5d0 6s0 6p0' > > ! configts(8)='5s2 5p6 5d1 6s1 6p0' > > ! / > > > > Andrea > > > > On Thu, 2011-03-03 at 18:18 -0500, Joe wrote: > >> Hello everyone, > >> > >> Using ld1.x, I am trying to generate pseudopotentials for elements such > >> as Hf, both scalar relativistic and fully relativistic. I have followed > >> from the examples given in atomic_doc, and have been making ample use of > >> Paolo Giannozzi's July 9th 2010 tutorial, "Notes on pseudopotential > >> generation" (which is the version with full worked examples for Ti). > >> The information provided by this arsenal as been sufficient to generate > >> and test new USPP/NCPP for Si, C, N, O, and S, as well as "naive" USPP > >> for Hf. Several of the issues I am reporting below have been mentioned > >> within the pw_forum, and when applicable, I have tried (often with > >> success) the prescriptions offered. > >> > >> First, let me share what I have "working". Below is the input file for > >> a scalar relativistic USPP for Hf that does not contain semicore > >> states. I have tested it for bulk hafnia and it reproduces published > >> band structure data at fixed cell parameters and fixed atomic > >> coordinates, but gives optimized structures at variance with those > >> (using PBE-based PP) reported in the literature (for example, following > >> from the review given in the 2008 NJP paper by Beltran, Munoz, and > >> Hafner - NJP 10 063031); it agrees most closely with the NCPP PBE > >> structures generated by Zhao and Vanderbilt in PRB 65 233106, except for > >> the angle \beta, which is similar to that reported in PRB 65 174117. > >> The basic summary is that the cell volume is larger than anything published. > >> > >> &input > >> title='Hf', > >> zed=72, > >> rel=1, > >> iswitch=3, > >> config='[Xe] 4f14.0 5d2.0 6s2.0 6p0.0', > >> dft='PBE', > >> / > >> &inputp > >> lloc=0, > >> pseudotype=3, > >> file_pseudopw='Hf.srl-pbe-rrkjus.UPF', > >> nlcc=.true., > >> rcore=0.9, > >> author='test', > >> rho0=0.0001, > >> / > >> 4 > >> 6P 2 1 0.00 0.00 2.70 2.70 1 > >> 5D 3 2 2.00 0.00 1.90 2.30 1 > >> 5D 3 2 0.00 -0.18 1.90 2.30 1 > >> 6S 1 0 2.00 0.00 2.50 2.50 1 > >> / > >> &test > >> nconf=5 > >> file_pseudo='Hf.srl-pbe-rrkjus.UPF' > >> ecutmin=20.0, ecutmax=50.0, decut=10.0 > >> configts(1)='5d2.0 6s2.0 6p0.0' > >> configts(2)='5d1.0 6s2.0 6p0.0' > >> configts(3)='5d1.0 6s1.0 6p0.0' > >> configts(4)='5d0.0 6s1.0 6p0.0' > >> configts(5)='5d0.0 6s0.0 6p0.0' > >> / > >> > >> Note that the test results for different charged (d-depleted) states of > >> Hf are pretty bad. For those interested in using this as a starting > >> point, an analogous fully relativistic USPP can be generated using the > >> input file: > >> > >> &input > >> title='Hf', > >> zed=72, > >> rel=2, > >> iswitch=3, > >> config='[Xe] 4f14.0 5d2.0 6s2.0 6p0.0', > >> dft='PBE', > >> / > >> &inputp > >> lloc=0, > >> pseudotype=3, > >> file_pseudopw='Hf.rel-pbe-rrkjus.UPF', > >> nlcc=.true., > >> rcore=0.9, > >> author='test', > >> / > >> 7 > >> 6P 2 1 0.00 0.00 2.70 2.70 0.5 > >> 6P 2 1 0.00 0.00 2.70 2.70 1.5 > >> 5D 3 2 2.00 0.00 1.90 2.30 1.5 > >> 5D 3 2 0.00 -0.18 1.90 2.30 1.5 > >> 5D 3 2 0.00 0.00 1.90 2.30 2.5 > >> 5D 3 2 0.00 -0.18 1.90 2.30 2.5 > >> 6S 1 0 2.00 0.00 2.50 2.50 0.5 > >> / > >> &test > >> nconf=3 > >> file_pseudo='Hf.rel-pbe-rrkjus.UPF' > >> ecutmin=20.0, ecutmax=80.0, decut=10.0 > >> configts(1)='5d2.0 6s2.0' > >> configts(2)='5d2.0 6s1.0 6p1.0' > >> configts(3)='5d1.0 6s2.0 6p0.0' > >> / > >> > >> The structural discrepancies persist for different oxygen USPP, > >> different optimization procedures, and different sets of parameters > >> (charge density cutoffs, convergence criteria, etc.). > >> > >> I am now trying to check if the structural properties can be improved by > >> the inclusion of semicore states, and am starting with the "simplest" > >> case, that of a scalar relativistic NCPP with explicit inclusion of 5S > >> and 5P. After starting with the fewest number of projectors (one each > >> for 5S, 5P, and 5D), and running into all kinds of problems (anyone who > >> runs ld1.x knows about the kinds of mysterious errors that are > >> generated, and the equally mysterious modifications which result in said > >> errors disappearing), I searched the pw_forum and found the following > >> thread: > >> > >> http://www.democritos.it/pipermail/pw_forum/2009-July/013453.html > >> > >> Following from this (and making the implicit corrections to the provided > >> files in order to render them processable, such as modifying the 2nd > >> column in the definition of the projectors), I have been working off of > >> the following NCPP input file, > >> > >> &input > >> title='Hf', > >> zed=72, > >> rel=1, > >> iswitch=3, > >> config='[Xe] 4f14 5d2 6s2 6p0', > >> dft='PBE', > >> / > >> &inputp > >> lloc=0, > >> pseudotype=2, > >> file_pseudopw='Hf.semicore.srl-pbe-rrkjus.UPF', > >> nlcc=.f., > >> author='test', > >> rho0=0.01, > >> / > >> 5 > >> 5P 2 1 6.00 0.00 1.50 1.50 1 > >> 5P 2 1 0.00 -1.00 1.50 1.50 1 > >> 5D 3 2 2.00 0.00 1.90 1.90 1 > >> 5D 3 2 0.00 -0.20 1.90 1.90 1 > >> 5S 1 0 2.00 0.00 1.20 1.20 1 > >> / > >> &test > >> nconf=1 > >> file_pseudo='Hf.semicore.srl-pbe-rrkjus.UPF' > >> ecutmin=20.0, ecutmax=50.0, decut=10.0 > >> configts(1)='5s2 5p6 5d2 6s2 6p0', > >> / > >> > >> and have been varying the energy for the empty 5P projector, changing > >> lloc (and rcloc when applicable), toying with rho0, and fiddling with > >> the cutoffs, to no avail. The latest error is the not-so-helpful: > >> > >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >> from run_pseudo : error # 1 > >> Errors in PS-KS equation > >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >> > >> Changing parameters merely changes the error, it seems. I know this is > >> a highly-specific cooking problem, but if anyone has any suggestions on > >> how to proceed, I would be extremely grateful. With some help, > >> hopefully I can generate a good, tested set of USPPs for Hf and fill in > >> that blank on PWSCF's pseudopotential page! > >> > >> Joseph Turnbull > >> NC State University > >> > >> > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Sat Mar 5 10:24:55 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Sat, 5 Mar 2011 10:24:55 +0100 Subject: [Pw_forum] Ionic forces not reducing In-Reply-To: References: <934A8BF3-C58D-4E31-A8F7-459F63D7730F@ncsu.edu> <20110224100830.mq87cz62bogcw40w@webmail.sic.rm.cnr.it> Message-ID: <464D0A70-E831-4B98-9E82-2F46FE64AB5F@sissa.it> Dear Christopher, Il giorno 05/mar/2011, alle ore 04.59, Christopher O'Brien ha scritto: > Thank you for your suggestions regarding my problem. In my case, a further decrease in the electronic convergence threshold, or increase in ecutrho, and ecutwfc had little effect. I usually work with supercells or NEB calculations with little or no symmetry. > It turns out that the parameter that affected the most significant reduction in force was the "upscale" parameter. Your recommended value of 1.D3 was usually sufficient, but really difficult cases can be handled with 1.D4. This parameter seemed to be the 'magic bullet' for me when nothing else worked. Why is the default value so small (10.0)? There's really no magic bullet, it is just a straightforward method to save computer time. You could have chosen conv_thr=1.d-9 and upscale=10, or conv_thr=1.d-6 and upscale=1.d4, you would end up in both cases with an electronic convergence threshold of 1.d-10 when the optimization procedure requires that (i.e. close to the convergence, when forces are small and energy changes very little, because you need very accurate forces to locate the minimum with a good precision). The point is that at the beginning of the relaxation your system is usually far from the optimum ionic configuration, hence it is not worth to spend a lot of cpu time in computing very accurate forces. Defaults are often good, but cannot encompass all possible needs of the users. Regards GS > =================================================================== > Christopher J. O'Brien > cjobrien at ncsu.edu > https://sites.google.com/a/ncsu.edu/cjobrien/ > > Ph.D. Candidate > Computational Materials Group > Department of Materials Science & Engineering > North Carolina State University > __________________________________________________________________ > Please send all documents in PDF. > For Word documents: Please use the 'Save as PDF' option before sending. > =================================================================== > > On Feb 24, 2011, at 4:08 AM, Giuseppe Mattioli wrote: > >> Dear Christopher >> You should try to reduce conv_thr in &ELECTRONS, in order to have a more accurate calculation of forces and stress. Try, for instance, with conv_thr = 1.0d-9 (and with a lower mixing_beta, 0.2~0.3 or so, if the electronic calculation does not converge). >> HTH >> >> Giuseppe >> >> Quoting Christopher O'Brien : >> >>> Below this is a super-cell of an interface of Cu2O and Ti. The problem is simply that the forc_conv_thr is not met within 100 iterations. etot_conv_thr is almost always met first (even decreasing etot_conv_thr to 1.0d-6). Typically, the force in this system decreases to ~0.01 Ry/B with a delta F on the same order of magnitude but fluctuates about this value. This means that I continually get the warning telling me to reduce the convergence threshold. Ideally I would like obtain a maximum force of ~1D-4. >>> Does anyone have any suggestions? I am at a loss. >>> >>> Thanks in advance, >>> Chris O'Brien >>> >>> >>> title = 'Cu2O-Ti-case2' , >>> calculation = 'vc-relax' , >>> restart_mode = 'from_scratch' , >>> wf_collect = .false. , >>> outdir = './', >>> wfcdir = './', >>> pseudo_dir = '/share2/cjobrien/pseudo/', >>> prefix = 'Cu2OTi', >>> disk_io = 'low', >>> verbosity = 'minimal', >>> tstress = .true., >>> tprnfor = .true., >>> forc_conv_thr = 1.0d-4, >>> etot_conv_thr = 1.0d-5, >>> / >>> &SYSTEM >>> ibrav = 0, >>> celldm(1) = 8.1878, >>> nat = 14, >>> ntyp = 3, >>> ecutwfc = 30.0 , >>> ecutrho = 300.0 , >>> occupations = 'smearing' , >>> smearing = 'mv' , >>> degauss = 0.01 , >>> / >>> &ELECTRONS >>> conv_thr = 1.0d-6 , >>> mixing_beta = 0.7 , >>> / >>> &IONS >>> ion_dynamics = 'bfgs', >>> / >>> &CELL >>> cell_dynamics = 'bfgs', >>> press = 0.0, >>> cell_dofree = 'xyz', >>> / >>> CELL_PARAMETERS >>> 0.929429709 0.0 0.0 >>> 0.0 0.929429709 0.0 >>> 0.0 0.0 2.924945006 >>> ATOMIC_SPECIES >>> Cu 58.70000 Cu.pw91-n-van_ak.UPF >>> Ti 47.88000 Ti.pw91-nsp-van.UPF >>> O 16.00000 O.pw91-van_ak.UPF >>> ATOMIC_POSITIONS alat >>> Cu 0 0 0 >>> Cu 0.504691013 0.504691013 0 >>> Cu 0.484702934 0.019988079 0.553031754 >>> Cu 0.019988079 0.484702934 0.553031754 >>> Cu 0.039976158 0.039976158 1.106063508 >>> Cu 0.464714854 0.464714854 1.106063508 >>> O 0.252345506 0.252345506 0.285738983 >>> O 0.024221288 0.024221288 1.544049139 >>> Ti 0.480469725 0.024221288 1.544049139 >>> Ti 0.024221288 0.480469725 1.544049139 >>> Ti 0.484702934 0.484702934 2.015504257 >>> Ti 0.019988079 0.019988079 2.015504257 >>> Ti 0.01575487 0.488936142 2.486959376 >>> Ti 0.488936142 0.01575487 2.486959376 >>> K_POINTS automatic >>> 8 8 4 0 0 0 >>> >>> =================================================================== >>> Christopher J. O'Brien >>> cjobrien at ncsu.edu >>> https://sites.google.com/a/ncsu.edu/cjobrien/ >>> >>> Ph.D. Candidate >>> Computational Materials Group >>> Department of Materials Science & Engineering >>> North Carolina State University >>> __________________________________________________________________ >>> Please send all documents in PDF. >>> For Word documents: Please use the 'Save as PDF' option before sending. >>> =================================================================== >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> Giuseppe Mattioli >> ISM-CNR, Italy >> >> >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110305/380c84d6/attachment-0001.htm From sclauzer at sissa.it Sat Mar 5 10:34:15 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Sat, 5 Mar 2011 10:34:15 +0100 Subject: [Pw_forum] Adding an email In-Reply-To: References: Message-ID: <8AB9960D-008A-4634-BABD-3282797A0148@sissa.it> If you can post on this forum it means that your email address has already been included in the mailing list. To check or change your subscription options please go here http://www.democritos.it/mailman/options/pw_forum Regards, GS Il giorno 04/mar/2011, alle ore 18.57, Alexander G. Kvashnin ha scritto: > Add my email to this mailing list, please > > -- > Sincerely yours > Alexander G. Kvashnin > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110305/974877fa/attachment.htm From giannozz at democritos.it Sat Mar 5 10:59:48 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 5 Mar 2011 10:59:48 +0100 Subject: [Pw_forum] Ionic forces not reducing In-Reply-To: <464D0A70-E831-4B98-9E82-2F46FE64AB5F@sissa.it> References: <934A8BF3-C58D-4E31-A8F7-459F63D7730F@ncsu.edu> <20110224100830.mq87cz62bogcw40w@webmail.sic.rm.cnr.it> <464D0A70-E831-4B98-9E82-2F46FE64AB5F@sissa.it> Message-ID: On Mar 5, 2011, at 10:24 , Gabriele Sclauzero wrote: > Defaults are often good ...but not always. I think that once upon a time, the convergency threshold was reduced by a factor 1/update^2 (but the threshold iself was defined in a different way). A reduction of a factor 10 means a similar reduction in the error on energies, but only sqrt(10) or so in the error on forces. A default of 100 might be more appropriate, I think, given the current default on conv_thr (10^{-6}) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From w2agz at w2agz.com Sun Mar 6 03:08:30 2011 From: w2agz at w2agz.com (W2AGZ) Date: Sat, 5 Mar 2011 18:08:30 -0800 Subject: [Pw_forum] ph.x and Nesting Fermi Surfaces Message-ID: <007901cbdba3$65373460$2fa59d20$@w2agz.com> To All: I'm running some exercises on electron-phonon interactions in narrow band metal monolayers (actually tetragonal unit cells with "large" c/a parameters...and think doped transition metal oxides). In this quasi-2D system, several of the Fermi surfaces approach planarity (actually, "Fermi lines"), suggesting strong electron-phonon interaction should be driven by the "nesting" wave vector (think CDW and/or Peierls-Froehlich). However, I'm having difficulty seeing how to structure the input to ph.x to select this wavevector alone (or indeed if this is even possible with ph.x). Imagine a square-planar BZ with dimensions (0.5, 0.5) in 2pi/a units, with a "Fermi line" perpendicular to, and kf distance along the (1,1) direction from the BZ origin. Now, as far as I can see from the ph.x documentation, nq1, etc., is only for defining the Monkhorst-Pack grid for the desired phonon grid-mesh (and are integers anyway). In principle, one could set the "line of input" xq's to the desired kf (fractional values are presumably allowed), but which would have its origin at BZ center, whereas one would like to "drive" or "excite" the phonons at -kf, +kf together. I hope I've made the issue/question clear and haven't said anything egregriously stupid. Thanks in advance, Paul Grant IBM Research Staff Member Emeritus Visiting Scholar, Stanford -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110305/d39a87e2/attachment.htm From miguel.martinez at ehu.es Sun Mar 6 12:21:53 2011 From: miguel.martinez at ehu.es (Miguel =?ISO-8859-1?B?TWFydO1uZXo=?=) Date: Sun, 6 Mar 2011 11:21:53 +0000 Subject: [Pw_forum] ph.x and Nesting Fermi Surfaces In-Reply-To: <007901cbdba3$65373460$2fa59d20$@w2agz.com> References: <007901cbdba3$65373460$2fa59d20$@w2agz.com> Message-ID: <20110306112153.5e73c34d@mark> Dear Paul, If I understood you correctly, you want to run a ph.x calculation at a q of your choice such that q=2kf, right? In that case, you only need to specify ldisp =.false., not specify any nq1, nq2, nq3 and *after* the slash in the ph.x input, specify the q points at which you want the calculations done. Example 02 has ph.x calculate the phonon frequencies at X (and gamma) for Fm-3d Si and C, and fcc Ni at X. Hope it helps, Miguel On Sat, 5 Mar 2011 18:08:30 -0800 "W2AGZ" wrote: > To All: > > > > I'm running some exercises on electron-phonon interactions in narrow > band metal monolayers (actually tetragonal unit cells with "large" c/a > parameters...and think doped transition metal oxides). In this > quasi-2D system, several of the Fermi surfaces approach planarity > (actually, "Fermi lines"), suggesting strong electron-phonon > interaction should be driven by the "nesting" wave vector (think CDW > and/or Peierls-Froehlich). > > > > However, I'm having difficulty seeing how to structure the input to > ph.x to select this wavevector alone (or indeed if this is even > possible with ph.x). Imagine a square-planar BZ with dimensions (0.5, > 0.5) in 2pi/a units, with a "Fermi line" perpendicular to, and kf > distance along the (1,1) direction from the BZ origin. Now, as far > as I can see from the ph.x documentation, nq1, etc., is only for > defining the Monkhorst-Pack grid for the desired phonon grid-mesh > (and are integers anyway). In principle, one could set the "line of > input" xq's to the desired kf (fractional values are presumably > allowed), but which would have its origin at BZ center, whereas one > would like to "drive" or "excite" the phonons at -kf, +kf together. > > > > I hope I've made the issue/question clear and haven't said anything > egregriously stupid. > > > > Thanks in advance, > > > > Paul Grant > > IBM Research Staff Member Emeritus > > Visiting Scholar, Stanford > -- ---------------------------------------- Dr. Miguel Martinez Canales Department of Physics & Astronomy University College London Gower Street, London, WC1E 6BT (UK) Fax: +44 207 679 0595 Tlf: +44 207 678 3476 ---------------------------------------- "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 hqzhou at nju.edu.cn Mon Mar 7 05:52:19 2011 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 7 Mar 2011 12:52:19 +0800 Subject: [Pw_forum] problem in MPI running of QE (16 processors) References: <420647.20855.qm@web65714.mail.ac4.yahoo.com> Message-ID: <13B48858C1B74179AAC1FC6E6931DB47@solarflare> How did you apply number of node, procs per node in your job script? #PBS -l nodes=?:ppn=? zhou huiqun @earth sciences, nanjing university, china ----- Original Message ----- From: Alexander G. Kvashnin To: PWSCF Forum Sent: Saturday, March 05, 2011 2:53 AM Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors) I create PBS task on supercomputer MIPT-60 where I write mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt all other types of this line such as mpiexec -np 16 ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt doesn't work. Maybe this number of processor too small for parallel calculation to QE? On 4 March 2011 21:37, Eyvaz Isaev wrote: Dear Alexander, How do you run a job? You should launch a command like (some parameters are omitted) mpirun -np 16 -maxtime 30 ./pw.x < scf.in >scf.out The easiest way to be added to the forum list is subscribing to this forum. Please visit http://www.pwscf.org/contacts.php Please also provide your affiliation. Best regards, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ---------------------------------------------------------------------------- From: Alexander G. Kvashnin To: pw_forum at pwscf.org Sent: Fri, March 4, 2011 9:07:46 PM Subject: [Pw_forum] problem in MPI running of QE (16 processors) Hello, I have some problem when I ran parallel version of QE (16 procs), I saw next line in output file Parallel version (MPI), running on 1 processors And it works using only 1 processor, but there is MPI version. Help me please in my problem Thank you! -- Sincerely yours Alexander G. Kvashnin _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Sincerely yours Alexander G. Kvashnin ------------------------------------------------------------------------------ _______________________________________________ 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/20110307/df6b7939/attachment.htm From agkvashnin at gmail.com Mon Mar 7 07:31:16 2011 From: agkvashnin at gmail.com (Alexander Kvashnin) Date: Mon, 7 Mar 2011 09:31:16 +0300 Subject: [Pw_forum] =?utf-8?b?0J3QkDogUmU6ICBwcm9ibGVtIGluIE1QSSBydW5uaW5n?= =?utf-8?q?_of_QE_=2816_processors=29?= Message-ID: <4d747bc2.470ddf0a.44a4.2ea3@mx.google.com> Yes, I wrote #PBS -l nodes=16:ppn=4 And in userguide of MIPT-60 wrote,that mpiexec must choose number of processors automatically, that's why I didn't write anything else ? ----- ???????? ????????? ----- ??: Huiqun Zhou ??????????: 7 ????? 2011 ?. 7:52 ????: PWSCF Forum ????: Re: [Pw_forum] problem in MPI running of QE (16 processors) How did you apply number of node, procs per node in your job script? ? #PBS -l nodes=?:ppn=? ? zhou huiqun @earth sciences, nanjing university, china ? ----- Original Message ----- From: Alexander G. Kvashnin To: PWSCF Forum Sent: Saturday, March 05, 2011 2:53 AM Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors) I create PBS task on supercomputer MIPT-60 where I write? mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt all other types of this line such as? mpiexec -np 16 ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt does [??????? ?? ???? ????? ????????? ?????????] -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110307/cd2caef3/attachment.htm From prayerz.omo at gmail.com Mon Mar 7 07:56:40 2011 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Mon, 7 Mar 2011 07:56:40 +0100 Subject: [Pw_forum] =?utf-8?b?0J3QkDogUmU6IHByb2JsZW0gaW4gTVBJIHJ1bm5pbmcg?= =?utf-8?q?of_QE_=2816_processors=29?= In-Reply-To: <4d747bc2.470ddf0a.44a4.2ea3@mx.google.com> References: <4d747bc2.470ddf0a.44a4.2ea3@mx.google.com> Message-ID: Try to see if specifying the full paths help. E.g., try something like: mpiexec /home/MyDir/bin/pw.x -in /scratch/MyDir/graph.inp > /scratch/MyDir/graph.out (where /home/MyDir/bin is the full path to your pw.x and /scratch/MyDir/graph.inp is the full path to your output ....) ( I see you use "-in" instead of "<" to indicate the input. I don't know too much but _perhaps_ you could also _try_ using "<" instead of "-in") . o. On Mon, Mar 7, 2011 at 7:31 AM, Alexander Kvashnin wrote: > Yes, I wrote > > #PBS -l nodes=16:ppn=4 > > And in userguide of MIPT-60 wrote,that mpiexec must choose number of > processors automatically, that's why I didn't write anything else > > > ________________________________ > ????: Huiqun Zhou > ????????????????????: 7 ?????????? 2011 ??. 7:52 > ????????: PWSCF Forum > ????????: Re: [Pw_forum] problem in MPI running of QE (16 processors) > > How did you apply number of node, procs per node in your job > script? > > #PBS -l nodes=?:ppn=? > > zhou huiqun > @earth sciences, nanjing university, china > > > ----- Original Message ----- > From: Alexander G. Kvashnin > To: PWSCF Forum > Sent: Saturday, March 05, 2011 2:53 AM > Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors) > I create PBS task on supercomputer MIPT-60 where I write > > mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt > all other types of this line such as > mpiexec -np 16 ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt > > does > > [?????????????? ???? ????? ?? ??????? ?? ??? ?????????????? ? > ??????????????? ] > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ***************** Seek GOD! ************* From w2agz at w2agz.com Mon Mar 7 08:04:48 2011 From: w2agz at w2agz.com (W2AGZ) Date: Sun, 6 Mar 2011 23:04:48 -0800 Subject: [Pw_forum] ph.x and Nesting Fermi Surfaces In-Reply-To: <20110306112153.5e73c34d@mark> References: <007901cbdba3$65373460$2fa59d20$@w2agz.com> <20110306112153.5e73c34d@mark> Message-ID: <01a401cbdc95$f3e9e160$dbbda420$@w2agz.com> Miguel, thanks for getting back so quickly. Actually, I use what the ph.x docs call "line of input" feature failrly often to do "quicky" calculations of the "gamma point" e-p interaction. I'm familiar with example 2, but note, for Si, G and X are two separate calculations. I don't think you can specify two different q-points, e.g., at -kf, +kf as separate lines of input (I could be wrong). What I sort of have in mind is whether one could somehow specify as input to ph.x a "q-vector" spanning the points -kf to kf and calculate the net e-p coupling. For example, suppose kf = (0.25, 0.25, 0)(2pi/a units) and 2kf "connects" two mostly planar Fermi surfaces on opposite sides of the BZ. Physically, this an extremely unstable situation would result in a CDW phase transition doubling the unit cell (dimerization) and gapping the Fermi surface and should in principle yield a very large e-p coupling constant beforehand. I suspect ph.x, at present, doesn't have the capability to simulate this situation. Right now, I have a run going with a "line of input" for q(or kf) = (0.37, 0.37, 0) but it's taking a long time to converge. I will also try later 2kf (0.74, 0.74, 0) just to see what happens. Note these are not "high symmetry" points. Again, thanks for your feedback. -Paul -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Miguel Mart?nez Sent: Sunday, March 06, 2011 3:22 AM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] ph.x and Nesting Fermi Surfaces Dear Paul, If I understood you correctly, you want to run a ph.x calculation at a q of your choice such that q=2kf, right? In that case, you only need to specify ldisp =.false., not specify any nq1, nq2, nq3 and *after* the slash in the ph.x input, specify the q points at which you want the calculations done. Example 02 has ph.x calculate the phonon frequencies at X (and gamma) for Fm-3d Si and C, and fcc Ni at X. Hope it helps, Miguel On Sat, 5 Mar 2011 18:08:30 -0800 "W2AGZ" wrote: > To All: > > > > I'm running some exercises on electron-phonon interactions in narrow > band metal monolayers (actually tetragonal unit cells with "large" c/a > parameters...and think doped transition metal oxides). In this > quasi-2D system, several of the Fermi surfaces approach planarity > (actually, "Fermi lines"), suggesting strong electron-phonon > interaction should be driven by the "nesting" wave vector (think CDW > and/or Peierls-Froehlich). > > > > However, I'm having difficulty seeing how to structure the input to > ph.x to select this wavevector alone (or indeed if this is even > possible with ph.x). Imagine a square-planar BZ with dimensions (0.5, > 0.5) in 2pi/a units, with a "Fermi line" perpendicular to, and kf > distance along the (1,1) direction from the BZ origin. Now, as far as > I can see from the ph.x documentation, nq1, etc., is only for defining > the Monkhorst-Pack grid for the desired phonon grid-mesh (and are > integers anyway). In principle, one could set the "line of input" > xq's to the desired kf (fractional values are presumably allowed), but > which would have its origin at BZ center, whereas one would like to > "drive" or "excite" the phonons at -kf, +kf together. > > > > I hope I've made the issue/question clear and haven't said anything > egregriously stupid. > > > > Thanks in advance, > > > > Paul Grant > > IBM Research Staff Member Emeritus > > Visiting Scholar, Stanford > -- ---------------------------------------- Dr. Miguel Martinez Canales Department of Physics & Astronomy University College London Gower Street, London, WC1E 6BT (UK) Fax: +44 207 679 0595 Tlf: +44 207 678 3476 ---------------------------------------- "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 agkvashnin at gmail.com Mon Mar 7 08:30:31 2011 From: agkvashnin at gmail.com (Alexander Kvashnin) Date: Mon, 7 Mar 2011 10:30:31 +0300 Subject: [Pw_forum] =?utf-8?b?0J3QkDogUmU6ICDQndCQOiBSZTogcHJvYmxlbSBpbiBN?= =?utf-8?q?PI_running_of_QE_=2816_processors=29?= Message-ID: <4d748a0f.9a5bdf0a.447e.30f0@mx.google.com> Thanks, I tried to use "<" instead of "-in" it also didn't work. OK,I will try to use full paths for input and output, and answer about result. ----- ???????? ????????? ----- ??: Omololu Akin-Ojo ??????????: 7 ????? 2011 ?. 9:56 ????: PWSCF Forum ????: Re: [Pw_forum] ??: Re: problem in MPI running of QE (16 processors) Try to see if specifying the full paths help. E.g., try something like: mpiexec /home/MyDir/bin/pw.x -in /scratch/MyDir/graph.inp > /scratch/MyDir/graph.out (where /home/MyDir/bin is the full path to your pw.x and /scratch/MyDir/graph.inp is the full path to your output ....) ( I see you use "-in" instead of "<" to indicate the input. I don't know too much but _perhaps_ you could also _try_ using "<" instead of "-in") . o. On Mon, Mar 7, 2011 at 7:31 AM, Alexander Kvashnin wrote: > Yes, I wrote > > #PBS -l nodes=16:ppn=4 > > And in userguide of MIPT-60 wrote,that mpiexec must choose number of > processors automatically, that's why I didn't write anything else > > > ________________________________ > ????: Huiqun Zhou > ????????????????????: 7 ?????????? 2011 ??. 7:52 > ????????: PWSCF Forum > ????????: Re: [Pw_forum] problem in MPI running of QE (16 processors) > > How did you apply number of node, procs per node in your job > script? > > #PBS -l nodes=?:ppn=? > > zhou huiqun > @earth sciences, nanjing university, china > > > ----- Original Message ----- > From: Alexander G. Kvashnin > To: PWSCF Forum > Sent: Saturday, March 05, 2011 2:53 AM > Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors) > I create PBS task on supercomputer MIPT-60 where I write > > mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt > all other [??????? ?? ???? ????? ????????? ?????????] From wang.riping.81 at gmail.com Mon Mar 7 10:08:21 2011 From: wang.riping.81 at gmail.com (Riping WANG) Date: Mon, 7 Mar 2011 18:08:21 +0900 Subject: [Pw_forum] ecfixed makes the volume different? Message-ID: Dear Forum, Could anyone give me some hints about how to adjust "qcutz,q2sigma,ecfixed" in vc-cp? I have some difficulties. After wave function initialization, the input file are for zero pressure zero temperature are following. (After zero pressure zero temperature, I will elevate temperature with verlet algorithm.) But when I use different ecfixed with fixed qcutz and q2sigma, the volumes at equilibrium are different. some is close to that without "qcutz,q2sigma,ecfixed" used. some are 100 ( toal around 3000) different from that without "qcutz,q2sigma,ecfixed" used. (In my case, I am sure the fnosep, wmass, and emass is good enough.) I attached the voluem evolution figure. In the figure, from step 200-1200 is belong to the following input file. before 200 step is wave initialization, after 1200 step, I increased temperature. Thank you very much! WANG Riping 2011.3.7 &control calculation = 'vc-cp' , prefix = 'SiO2-mog' , restart_mode = 'restart' , nstep = 1000 , iprint = 1 , isave = 10 , dt = 5.0 , ndr = 51 , ndw = 52 , tstress = .TRUE. , tprnfor = .TRUE. , saverho = .TRUE. , disk_io = 'high' , /ekin_conv_thr = 1.0d-3 , /etot_conv_thr = 5.0d-3 , /forc_conv_thr = 1.0d-2 , pseudo_dir ='~/espresso/pseudo' , outdir = './' , / &system ibrav = 14 , celldm(1) = 16.021289268 , celldm(2) = 0.558448710 , celldm(3) = 1.245135500 , celldm(4) = -0.000028830 , celldm(5) = -0.007432130 , celldm(6) = 0.000064680 , nat = 36 , ntyp = 2 , ecutwfc = 30 , ecutrho = 240.0 , nr1b = 16 , nr2b = 16 , nr3b = 16 , qcutz = 150.0 , q2sigma = 2 , ecfixed = 16.8 , / &electrons electron_dynamics = 'sd' , emass = 400 , emass_cutoff = 3. , / &ions ion_dynamics = 'sd' , / &cell cell_dynamics = 'pr' , press = 0 , wmass = 300 , / ATOMIC_SPECIES O 16.00 O.pbe-van_ak.UPF Si 28.00 Si.pbe-n-van.UPF ATOMIC_POSITIONS (crystal) ... -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), 1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110307/172de12c/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: volume.p Type: application/octet-stream Size: 3736 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110307/172de12c/attachment.obj From iurii.timrov at polytechnique.edu Mon Mar 7 10:30:57 2011 From: iurii.timrov at polytechnique.edu (Iurii TIMROV) Date: Mon, 7 Mar 2011 10:30:57 +0100 Subject: [Pw_forum] DOS: tetrahedron method + spin-orbit coupling In-Reply-To: References: <72c8451186febdfeddcce1b7f0727938.squirrel@theory.polytechnique.fr> Message-ID: <57ca38983c9f84db2125e9ab31a91604.squirrel@theory.polytechnique.fr> > you will need for sure to modify routine sumkt as in the attached > file. Not sure this will solve all problems, though > > P. Dear Paolo, I managed to solve the problem. There are two routines which were modified, namely, "sumkt" (as you told), and "tweights" (both attached). The problem was that the case nspin=4 (i.e. noncolin=.true.) was treated not properly: there was a loop do ns=1,nspin ... enddo Now I replaced it by (in the spirit of dost.f90): if (nspin==4) then nspin0=1 else nspin0=nspin endif do ns=1,nspin0 ... enddo I tested the code with these modifications, it works correctly. This bug is still present in the latest cvs version of espresso. So, now it can be removed. Thank you very much for your help! Best regards, Iurii Timrov Iurii TIMROV Doctorant (PhD student) Laboratoire des Solides Irradies Ecole Polytechnique F-91128 Palaiseau +33 1 69 33 45 08 timrov at theory.polytechnique.fr -------------- next part -------------- A non-text attachment was scrubbed... Name: sumkt.f90 Type: text/x-fortran Size: 3009 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110307/dbfe6930/attachment.bin -------------- next part -------------- A non-text attachment was scrubbed... Name: tweights.f90 Type: text/x-fortran Size: 6818 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110307/dbfe6930/attachment-0001.bin From giannozz at democritos.it Mon Mar 7 11:54:38 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 7 Mar 2011 11:54:38 +0100 Subject: [Pw_forum] DOS: tetrahedron method + spin-orbit coupling In-Reply-To: <57ca38983c9f84db2125e9ab31a91604.squirrel@theory.polytechnique.fr> References: <72c8451186febdfeddcce1b7f0727938.squirrel@theory.polytechnique.fr> <57ca38983c9f84db2125e9ab31a91604.squirrel@theory.polytechnique.fr> Message-ID: <5F3184FF-5230-4E46-922F-F2BC0E93AB36@democritos.it> On Mar 7, 2011, at 10:30 , Iurii TIMROV wrote: > Thank you very much for your help! thank you very much for YOUR help! Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From agkvashnin at gmail.com Mon Mar 7 17:24:05 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Mon, 7 Mar 2011 19:24:05 +0300 Subject: [Pw_forum] =?koi8-r?b?7uE6IFJlOiBwcm9ibGVtIGluIE1QSSBydW5uaW5n?= =?koi8-r?b?IG9mIFFFICgxNiBwcm9jZXNzb3JzKQ==?= In-Reply-To: <3224748192828762160@unknownmsgid> References: <3224748192828762160@unknownmsgid> Message-ID: Dear all I tried to use full paths, but it didn't give positive results. It wrote an error message application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 On 7 March 2011 10:30, Alexander Kvashnin wrote: > Thanks, I tried to use "<" instead of "-in" it also didn't work. > OK,I will try to use full paths for input and output, and answer about > result. > > ----- ???????? ????????? ----- > ??: Omololu Akin-Ojo > ??????????: 7 ????? 2011 ?. 9:56 > ????: PWSCF Forum > ????: Re: [Pw_forum] ??: Re: problem in MPI running of QE (16 processors) > > Try to see if specifying the full paths help. > E.g., try something like: > > mpiexec /home/MyDir/bin/pw.x -in /scratch/MyDir/graph.inp > > /scratch/MyDir/graph.out > > (where /home/MyDir/bin is the full path to your pw.x and > /scratch/MyDir/graph.inp is the full path to your output ....) > > ( I see you use "-in" instead of "<" to indicate the input. I don't > know too much but _perhaps_ you could also _try_ using "<" instead of > "-in") . > > o. > > On Mon, Mar 7, 2011 at 7:31 AM, Alexander Kvashnin > wrote: > > Yes, I wrote > > > > #PBS -l nodes=16:ppn=4 > > > > And in userguide of MIPT-60 wrote,that mpiexec must choose number of > > processors automatically, that's why I didn't write anything else > > > > > > ________________________________ > > ????: Huiqun Zhou > > ????????????????????: 7 ?????????? 2011 ??. 7:52 > > ????????: PWSCF Forum > > ????????: Re: [Pw_forum] problem in MPI running of QE (16 processors) > > > > How did you apply number of node, procs per node in your job > > script? > > > > #PBS -l nodes=?:ppn=? > > > > zhou huiqun > > @earth sciences, nanjing university, china > > > > > > ----- Original Message ----- > > From: Alexander G. Kvashnin > > To: PWSCF Forum > > Sent: Saturday, March 05, 2011 2:53 AM > > Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors) > > I create PBS task on supercomputer MIPT-60 where I write > > > > mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt > > all other > > [??????? ?? ???? ????? ????????? ?????????] > -- Sincerely yours Alexander G. Kvashnin -------------------------------------------------------------------------------------------------------------------------------- Student Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110307/6fa9ea8b/attachment-0001.htm From ttduyle at gmail.com Mon Mar 7 18:08:56 2011 From: ttduyle at gmail.com (Duy Le) Date: Mon, 7 Mar 2011 12:08:56 -0500 Subject: [Pw_forum] =?koi8-r?b?7uE6IFJlOiBwcm9ibGVtIGluIE1QSSBydW5uaW5n?= =?koi8-r?b?IG9mIFFFICgxNiBwcm9jZXNzb3JzKQ==?= In-Reply-To: References: <3224748192828762160@unknownmsgid> Message-ID: You should make sure that the mpiexec is used correctly. Try one of these sameple in this link. http://hamilton.nuigalway.ie/teaching/AOS/NINE/mpi-first-examples.html -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Mon, Mar 7, 2011 at 11:24 AM, Alexander G. Kvashnin wrote: > Dear all > > I tried to use full paths, but it didn't give positive results. It wrote an > error message > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 > > On 7 March 2011 10:30, Alexander Kvashnin wrote: >> >> Thanks, I tried to use "<" instead of "-in" it also didn't work. >> OK,I will try to use full paths for input and output, and answer about >> result. >> >> ----- ???????? ????????? ----- >> ??: Omololu Akin-Ojo >> ??????????: 7 ????? 2011 ?. 9:56 >> ????: PWSCF Forum >> ????: Re: [Pw_forum] ??: Re: problem in MPI running of QE (16 processors) >> >> Try to see if specifying the full paths help. >> E.g., try something like: >> >> mpiexec /home/MyDir/bin/pw.x -in ?/scratch/MyDir/graph.inp > >> /scratch/MyDir/graph.out >> >> (where /home/MyDir/bin is the full path to your pw.x and >> /scratch/MyDir/graph.inp is the full path to your output ....) >> >> ( I see you use "-in" instead of "<" to indicate the input. I don't >> know too much but _perhaps_ you could also _try_ using "<" instead of >> "-in") . >> >> o. >> >> On Mon, Mar 7, 2011 at 7:31 AM, Alexander Kvashnin >> wrote: >> > Yes, I wrote >> > >> > #PBS -l nodes=16:ppn=4 >> > >> > And in userguide of MIPT-60 wrote,that mpiexec must choose number of >> > processors automatically, that's why I didn't write anything else >> > >> > >> > ________________________________ >> > ????: Huiqun Zhou >> > ????????????????????: 7 ?????????? 2011 ??. 7:52 >> > ????????: PWSCF Forum >> > ????????: Re: [Pw_forum] problem in MPI running of QE (16 processors) >> > >> > How did you apply number of node, procs per node in your job >> > script? >> > >> > #PBS -l nodes=?:ppn=? >> > >> > zhou huiqun >> > @earth sciences, nanjing university, china >> > >> > >> > ----- Original Message ----- >> > From: Alexander G. Kvashnin >> > To: PWSCF Forum >> > Sent: Saturday, March 05, 2011 2:53 AM >> > Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors) >> > I create PBS task on supercomputer MIPT-60 where I write >> > >> > mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt >> > all other >> >> [??????? ?? ???? ????? ????????? ?????????] > > > -- > Sincerely yours > Alexander G. Kvashnin > -------------------------------------------------------------------------------------------------------------------------------- > Student > Moscow Institute of Physics and Technology ? ? ? ? ?http://mipt.ru/ > 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia > > Junior research scientist > Technological Institute for Superhard > and Novel Carbon Materials > http://www.ntcstm.troitsk.ru/ > 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia > ================================================================ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From trambui at u.boisestate.edu Tue Mar 8 00:28:33 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Mon, 7 Mar 2011 16:28:33 -0700 Subject: [Pw_forum] calculation wouldn't run using espresso-4.2.1 but did run with espresso-4.1.3 Message-ID: Hi Everyone, I have post a question regarding the single atom calculation for carbon simple cubic system last month. I was using the ultra-soft pseudopotential of C as :C.pbe-van_ak.UPF. And the calculation ran fine using espresso-4.1.3 (oder version), but not for espresso-4.2.1 (latest version). So would you let me know what might have been my problem? was it my input file or the new version of quantum espresso? I also attached my input file here for more info. Regard, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110307/d3c8f9f3/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: a2.in Type: application/octet-stream Size: 482 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110307/d3c8f9f3/attachment.obj From trambui at u.boisestate.edu Tue Mar 8 00:36:26 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Mon, 7 Mar 2011 16:36:26 -0700 Subject: [Pw_forum] published PBE data Message-ID: Hi Everyone, I have one more quick question, would you introduce to me any PBE published work (references) for SiC data. Thank you very much, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110307/279f639a/attachment.htm From trambui at u.boisestate.edu Tue Mar 8 01:05:14 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Mon, 7 Mar 2011 17:05:14 -0700 Subject: [Pw_forum] calculation wouldn't run using espresso-4.2.1 but did run with espresso-4.1.3 In-Reply-To: <20110308004422.2pa7m3ezcwc0cwg0@webmail.sissa.it> References: <20110308004422.2pa7m3ezcwc0cwg0@webmail.sissa.it> Message-ID: Dear Emine, Thank you for your respond. And to answer your chain of questions :), this is what I have got - First my installation was successful. I have done tons of calculation for single silicon as well as silicon carbide system and everything works fine, except when it comes to this single carbon atom calculation. - Second, the erroe message was: "the convergence was not achieved after 100 interations" (so you can see that the i took really long for this calculation but no result was given in the end) - Third, we tried the calculation with my thesis advisor computer,it didn't work and gave out the same problem. - Forth, I have tried to do the calculation using older version of QE, and it worked!!, but again, isn't the newer version supposed to work better than the older one? not mention about the fact that it should give more accurate results. So now both my advisor and I couldn't figure out why it is not working with properly in espresso-4.2.1. and I really appreciate any help from everyone! Thank you, Tram On Mon, Mar 7, 2011 at 4:44 PM, Emine Kucukbenli wrote: > Dear Tram Bui, > Doesnt it bug you that such a simple calculation which almost 'tests' the > pw.x doesnt work in your installation but seems to work for everyone else? > :) > > ok, sorry lets get serious: was your installation successful? what is the > error message? how does it stop? can you reproduce the same problem in > another machine/compiler etc? > what have you done to locate the problem? > yadda yadda.. the usual questions which i think you should have asked > yourself before posting.. :) > > emine kucukbenli, phd student, sissa, italy > > > > Quoting Tram Bui : > > Hi Everyone, >> I have post a question regarding the single atom calculation for >> carbon >> simple cubic system last month. I was using the ultra-soft pseudopotential >> of C as :C.pbe-van_ak.UPF. And the calculation ran fine using >> espresso-4.1.3 >> (oder version), but not for espresso-4.2.1 (latest version). So would you >> let me know what might have been my problem? was it my input file or the >> new >> version of quantum espresso? I also attached my input file here for more >> info. >> >> Regard, >> Tram Bui >> >> M.S. Materials Science & Engineering >> trambui at u.boisestate.edu >> >> > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > -- Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110307/964f7482/attachment.htm From ttduyle at gmail.com Tue Mar 8 01:18:39 2011 From: ttduyle at gmail.com (Duy Le) Date: Mon, 7 Mar 2011 19:18:39 -0500 Subject: [Pw_forum] calculation wouldn't run using espresso-4.2.1 but did run with espresso-4.1.3 In-Reply-To: References: <20110308004422.2pa7m3ezcwc0cwg0@webmail.sissa.it> Message-ID: for isolated C, you need to do spin polarized calculation with the usage of occupation card. See example 11 for details. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Mon, Mar 7, 2011 at 7:05 PM, Tram Bui wrote: > Dear Emine, > ????? Thank you for your respond. And to answer your chain of questions :), > this is what I have got > -?? First my installation was successful. I have done tons of calculation > for single silicon as well as silicon carbide system and everything works > fine, except when it comes to this single carbon atom calculation. > -?? Second, the erroe message was: "the convergence was not achieved after > 100 interations" (so you can see that the i took really long for this > calculation but no result was given in the end) > -??? Third, we tried the calculation with my thesis advisor computer,it > didn't work and gave out the same problem. > -??? Forth, I have tried to do the calculation using older version of QE, > and it worked!!, but again, isn't the newer version supposed to work better > than the older one? not mention about the fact that it should give more > accurate results. > ??? So now both my advisor and I couldn't figure out why it is not working > with properly in espresso-4.2.1. and I really appreciate any help from > everyone! > > Thank you, > Tram > > On Mon, Mar 7, 2011 at 4:44 PM, Emine Kucukbenli wrote: >> >> Dear Tram Bui, >> Doesnt it bug you that such a simple calculation which almost 'tests' the >> pw.x doesnt work in your installation but seems to work for everyone else? >> :) >> >> ok, sorry lets get serious: was your installation successful? what is the >> error message? how does it stop? can you reproduce the same problem in >> another machine/compiler etc? >> what have you done to locate the problem? >> yadda yadda.. the usual questions which i think you should have asked >> ?yourself before posting.. :) >> >> emine kucukbenli, phd student, sissa, italy >> >> >> Quoting Tram Bui : >> >>> Hi Everyone, >>> ? ? I have post a question regarding the single atom calculation for >>> carbon >>> simple cubic system last month. I was using the ultra-soft >>> pseudopotential >>> of C as :C.pbe-van_ak.UPF. And the calculation ran fine using >>> espresso-4.1.3 >>> (oder version), but not for espresso-4.2.1 (latest version). So would you >>> let me know what might have been my problem? was it my input file or the >>> new >>> version of quantum espresso? I also attached my input file here for more >>> info. >>> >>> Regard, >>> Tram Bui >>> >>> M.S. Materials Science & Engineering >>> trambui at u.boisestate.edu >>> >> >> >> >> ---------------------------------------------------------------- >> ?SISSA Webmail https://webmail.sissa.it/ >> ?Powered by Horde http://www.horde.org/ >> >> > > > > -- > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From arvifis at gmail.com Tue Mar 8 01:28:49 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 7 Mar 2011 22:28:49 -0200 Subject: [Pw_forum] published PBE data In-Reply-To: References: Message-ID: I think that you should use google and will find many papers. Best. Arles V. Gil Rebaza Instituto de F?sica La Plata Argentina 2011/3/7 Tram Bui > Hi Everyone, > I have one more quick question, would you introduce to me any PBE > published work (references) for SiC data. > > Thank you very much, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110307/fa604adb/attachment.htm From hqzhou at nju.edu.cn Tue Mar 8 05:48:57 2011 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Tue, 8 Mar 2011 12:48:57 +0800 Subject: [Pw_forum] =?utf-8?b?0J3QkDogUmU6IHByb2JsZW0gaW4gTVBJIHJ1bm5pbmcg?= =?utf-8?q?of_QE_=2816_processors=29?= References: <3224748192828762160@unknownmsgid> Message-ID: <45F59831C0DA4FB89984C2E23F8B50FA@solarflare> Alexander, According to your reply to my message, you actually applied 64 CPU cores (16 nodes, 4 cores per node), this should have no problem unless the policy of using your cluster prohibited it. Once upon a time, we had such a policy on our cluster: an job occupies at most 32 CPU cores, otherwise put it into sequential queue. Maybe, you should ask your administrator whether there is such a policy ... zhou huiqun @earth sciences, nanjing university, china ----- Original Message ----- From: Alexander G. Kvashnin To: PWSCF Forum Sent: Tuesday, March 08, 2011 12:24 AM Subject: Re: [Pw_forum] ??: Re: problem in MPI running of QE (16 processors) Dear all I tried to use full paths, but it didn't give positive results. It wrote an error message application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 On 7 March 2011 10:30, Alexander Kvashnin wrote: Thanks, I tried to use "<" instead of "-in" it also didn't work. OK,I will try to use full paths for input and output, and answer about result. ----- ???????? ????????? ----- ??: Omololu Akin-Ojo ??????????: 7 ????? 2011 ?. 9:56 ????: PWSCF Forum ????: Re: [Pw_forum] ??: Re: problem in MPI running of QE (16 processors) Try to see if specifying the full paths help. E.g., try something like: mpiexec /home/MyDir/bin/pw.x -in /scratch/MyDir/graph.inp > /scratch/MyDir/graph.out (where /home/MyDir/bin is the full path to your pw.x and /scratch/MyDir/graph.inp is the full path to your output ....) ( I see you use "-in" instead of "<" to indicate the input. I don't know too much but _perhaps_ you could also _try_ using "<" instead of "-in") . o. On Mon, Mar 7, 2011 at 7:31 AM, Alexander Kvashnin wrote: > Yes, I wrote > > #PBS -l nodes=16:ppn=4 > > And in userguide of MIPT-60 wrote,that mpiexec must choose number of > processors automatically, that's why I didn't write anything else > > > ________________________________ > ????: Huiqun Zhou > ????????????????????: 7 ?????????? 2011 ??. 7:52 > ????????: PWSCF Forum > ????????: Re: [Pw_forum] problem in MPI running of QE (16 processors) > > How did you apply number of node, procs per node in your job > script? > > #PBS -l nodes=?:ppn=? > > zhou huiqun > @earth sciences, nanjing university, china > > > ----- Original Message ----- > From: Alexander G. Kvashnin > To: PWSCF Forum > Sent: Saturday, March 05, 2011 2:53 AM > Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors) > I create PBS task on supercomputer MIPT-60 where I write > > mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt > all other [??????? ?? ???? ????? ????????? ?????????] -- Sincerely yours Alexander G. Kvashnin -------------------------------------------------------------------------------------------------------------------------------- Student Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ ------------------------------------------------------------------------------ _______________________________________________ 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/20110308/05fec3d7/attachment-0001.htm From wang.riping.81 at gmail.com Tue Mar 8 06:15:21 2011 From: wang.riping.81 at gmail.com (Riping WANG) Date: Tue, 8 Mar 2011 14:15:21 +0900 Subject: [Pw_forum] atomic positions in xsf from cppp.x Message-ID: Dear Forum, when I use cppp.x to generate an xsf file for an vc-cp output file with nstep=1000, there will be cell vectors and atomic positions in xsf file. what is this cell vectors and atomic positions stand for? For average structure configuration of 1000 steps, or for average structure configuration of one period, just for the last configuration of the this calculation? Part of input file are following: &control calculation = 'vc-cp' , prefix = 'SiO2' , restart_mode = 'restart' , nstep = 1000 , ndr = 51 , ndw = 52 , Thank you very much. WANG Riping 2011.3.8 -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), 1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110308/2c5abb9d/attachment.htm From agkvashnin at gmail.com Tue Mar 8 10:06:29 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Tue, 8 Mar 2011 12:06:29 +0300 Subject: [Pw_forum] =?koi8-r?b?7uE6IFJlOiBwcm9ibGVtIGluIE1QSSBydW5uaW5n?= =?koi8-r?b?IG9mIFFFICgxNiBwcm9jZXNzb3JzKQ==?= In-Reply-To: <45F59831C0DA4FB89984C2E23F8B50FA@solarflare> References: <3224748192828762160@unknownmsgid> <45F59831C0DA4FB89984C2E23F8B50FA@solarflare> Message-ID: Previously I used also 16 nodes, when I calculate with ABINIT and there is no problem for its running. I asked my administrator about it, he said that anything alright with policy. On 8 March 2011 07:48, Huiqun Zhou wrote: > Alexander, > > According to your reply to my message, you actually applied 64 CPU cores > (16 nodes, 4 cores per node), this should have no problem unless the policy > of using your cluster prohibited it. Once upon a time, we had such a policy > on our cluster: an job occupies at most 32 CPU cores, otherwise put it into > sequential queue. > > Maybe, you should ask your administrator whether there is such a policy ... > > zhou huiqun > @earth sciences, nanjing university, china > > > ----- Original Message ----- > *From:* Alexander G. Kvashnin > *To:* PWSCF Forum > *Sent:* Tuesday, March 08, 2011 12:24 AM > *Subject:* Re: [Pw_forum] ??: Re: problem in MPI running of QE (16 > processors) > > Dear all > > I tried to use full paths, but it didn't give positive results. It wrote an > error message > > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 > > > On 7 March 2011 10:30, Alexander Kvashnin wrote: > >> Thanks, I tried to use "<" instead of "-in" it also didn't work. >> OK,I will try to use full paths for input and output, and answer about >> result. >> >> ----- ???????? ????????? ----- >> ??: Omololu Akin-Ojo >> ??????????: 7 ????? 2011 ?. 9:56 >> ????: PWSCF Forum >> ????: Re: [Pw_forum] ??: Re: problem in MPI running of QE (16 processors) >> >> Try to see if specifying the full paths help. >> E.g., try something like: >> >> mpiexec /home/MyDir/bin/pw.x -in /scratch/MyDir/graph.inp > >> /scratch/MyDir/graph.out >> >> (where /home/MyDir/bin is the full path to your pw.x and >> /scratch/MyDir/graph.inp is the full path to your output ....) >> >> ( I see you use "-in" instead of "<" to indicate the input. I don't >> know too much but _perhaps_ you could also _try_ using "<" instead of >> "-in") . >> >> o. >> >> On Mon, Mar 7, 2011 at 7:31 AM, Alexander Kvashnin >> wrote: >> > Yes, I wrote >> > >> > #PBS -l nodes=16:ppn=4 >> > >> > And in userguide of MIPT-60 wrote,that mpiexec must choose number of >> > processors automatically, that's why I didn't write anything else >> > >> > >> > ________________________________ >> > ????: Huiqun Zhou >> > ????????????????????: 7 ?????????? 2011 ??. 7:52 >> > ????????: PWSCF Forum >> > ????????: Re: [Pw_forum] problem in MPI running of QE (16 processors) >> > >> > How did you apply number of node, procs per node in your job >> > script? >> > >> > #PBS -l nodes=?:ppn=? >> > >> > zhou huiqun >> > @earth sciences, nanjing university, china >> > >> > >> > ----- Original Message ----- >> > From: Alexander G. Kvashnin >> > To: PWSCF Forum >> > Sent: Saturday, March 05, 2011 2:53 AM >> > Subject: Re: [Pw_forum] problem in MPI running of QE (16 processors) >> > I create PBS task on supercomputer MIPT-60 where I write >> > >> > mpiexec ../../espresso-4.2.1/bin/pw.x -in graph.inp > output.opt >> > all other >> >> [??????? ?? ???? ????? ????????? ?????????] >> > > > > -- > Sincerely yours > Alexander G. Kvashnin > > -------------------------------------------------------------------------------------------------------------------------------- > Student > Moscow Institute of Physics and Technology http://mipt.ru/ > 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia > > Junior research scientist > Technological Institute for Superhard > and Novel Carbon Materials > http://www.ntcstm.troitsk.ru/ > 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia > ================================================================ > > ------------------------------ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Sincerely yours Alexander G. Kvashnin -------------------------------------------------------------------------------------------------------------------------------- Student Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110308/de79756e/attachment.htm From giannozz at democritos.it Tue Mar 8 10:14:08 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 08 Mar 2011 10:14:08 +0100 Subject: [Pw_forum] =?utf-8?b?0J3QkDogUmU6IHByb2JsZW0gaW4gTVBJIHJ1bm5pbmcg?= =?utf-8?q?of_QE_=2816_processors=29?= In-Reply-To: References: <3224748192828762160@unknownmsgid> <45F59831C0DA4FB89984C2E23F8B50FA@solarflare> Message-ID: <4D75F360.1040508@democritos.it> Alexander G. Kvashnin wrote: > Previously I used also 16 nodes, when I calculate with ABINIT and there > is no problem for its running. I don't know why you cannot run QE in parallel, but I know for sure that it is not a QE problem: it is either a problem of your machine, or QE wasn't properly compiled for parallel execution. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From agkvashnin at gmail.com Tue Mar 8 10:17:12 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Tue, 8 Mar 2011 12:17:12 +0300 Subject: [Pw_forum] =?utf-8?b?0J3QkDogUmU6IHByb2JsZW0gaW4gTVBJIHJ1bm5pbmcg?= =?utf-8?q?of_QE_=2816_processors=29?= In-Reply-To: <4D75F360.1040508@democritos.it> References: <3224748192828762160@unknownmsgid> <45F59831C0DA4FB89984C2E23F8B50FA@solarflare> <4D75F360.1040508@democritos.it> Message-ID: OK, I'll try to contact with my administrator again and solve this problem about machine. Thank you! On 8 March 2011 12:14, Paolo Giannozzi wrote: > Alexander G. Kvashnin wrote: > > > Previously I used also 16 nodes, when I calculate with ABINIT and there > > is no problem for its running. > > I don't know why you cannot run QE in parallel, but I know for sure > that it is not a QE problem: it is either a problem of your machine, > or QE wasn't properly compiled for parallel execution. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely yours Alexander G. Kvashnin -------------------------------------------------------------------------------------------------------------------------------- Student Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110308/fdfcd781/attachment.htm From parthasarathi13 at gmail.com Tue Mar 8 11:52:30 2011 From: parthasarathi13 at gmail.com (partha sarathi ghosh) Date: Tue, 8 Mar 2011 16:22:30 +0530 Subject: [Pw_forum] pseudo potential for Yb and U Message-ID: Hello QE users, I need PAW potential (for QE use) for Yb and U in my calculation. If any one is having please shear with me. Can any one please give references for some documents containing making of PAW pp using QE for these kind of high Z elements which contains spin-orbit coupling. With warm regards Partha Ghosh B.A.R.C., INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110308/c6b5ed46/attachment.htm From giannozz at democritos.it Tue Mar 8 12:45:57 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 08 Mar 2011 12:45:57 +0100 Subject: [Pw_forum] calculation wouldn't run using espresso-4.2.1 but did run with espresso-4.1.3 In-Reply-To: References: <20110308004422.2pa7m3ezcwc0cwg0@webmail.sissa.it> Message-ID: <4D7616F5.8080401@democritos.it> Tram Bui wrote: > isn't the newer version supposed to work better than the older one? it is (after all this is why there are new versions) but new versions fix old bugs and introduce new ones. This is clearly a bug and will be fixed soon. Meanwhile, use K_POINTS tpiba 1 0.0 0.0 0.0 1.0 instead of K_POINTS gamma It is slower but it converges very quickly (it should converge exactly in the same way,but it doesn't, for some obscure reason) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From germaneau at gucas.ac.cn Wed Mar 9 18:30:21 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Wed, 09 Mar 2011 12:30:21 -0500 Subject: [Pw_forum] graphene's band gap Message-ID: <4D77B92D.2020602@gucas.ac.cn> Dear all, I'm trying to compute graphene's band gap but get stuck. From my understanding a scf calculation should provide the same energy for the highest occupied and lowest occupied level which means a zero gap. I played with the number a kpoints a finally got a band gap of 0.57 which is not null. The scf convergence looks good. I'm not (yet) an expert in DFT calculation so may did something wrong or misunderstood something here. So, I wonder if someone has already successfully performed such calculation. I have attached my input file. Thanks in advance, Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110309/ef0d15ff/attachment.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: 03_graphene.scf.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20110309/ef0d15ff/attachment.asc From nkxirainbow at gmail.com Wed Mar 9 10:28:39 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 9 Mar 2011 17:28:39 +0800 Subject: [Pw_forum] graphene's band gap In-Reply-To: <4D77B92D.2020602@gucas.ac.cn> References: <4D77B92D.2020602@gucas.ac.cn> Message-ID: Dear Eric: The occupied and unoccupied bands touch each other only at M point(or K point, I forget it). You must include this point in you k-mesh. Furthermore, if you include spin-orbital coupling, the band gap will be opened at this point. On Thu, Mar 10, 2011 at 1:30 AM, Eric Germaneau wrote: > Dear all, > > I'm trying to compute graphene's band gap but get stuck. > From my understanding a scf calculation should provide the same energy for > the highest occupied and lowest occupied level which means a zero gap. > I played with the number a kpoints a finally got a band gap of 0.57 which > is not null. > The scf convergence looks good. > I'm not (yet) an expert in DFT calculation so may did something wrong or > misunderstood something here. > So, I wonder if someone has already successfully performed such > calculation. > I have attached my input file. > Thanks in advance, > > Eric. > > -- > * Be the change you wish to see in the world > * ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > * Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. * > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ____________________________________ Hui Wang School of physics, Fudan University, Shanghai, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110309/2ecade03/attachment.htm From metokal at gmail.com Wed Mar 9 13:02:41 2011 From: metokal at gmail.com (Mehmet Topsakal) Date: Wed, 9 Mar 2011 14:02:41 +0200 Subject: [Pw_forum] graphene's band gap In-Reply-To: References: <4D77B92D.2020602@gucas.ac.cn> Message-ID: Dear Eric, In addition, if you select 18x18x1 kpoints, your mesh should include both K and M points. But for a band-structure calculation, you should arrange a kpoints list along special directions, such as from GAMMA-to-M-to-K-to-GAMMA, and do a nscf calculation.... On Wed, Mar 9, 2011 at 11:28 AM, xirainbow wrote: > Dear Eric: > The occupied and unoccupied bands touch each other only at M point(or K > point, I forget it). > You must include this point in you k-mesh. > Furthermore, if you include spin-orbital coupling, the band gap will be > opened at this point. > > On Thu, Mar 10, 2011 at 1:30 AM, Eric Germaneau wrote: > >> Dear all, >> >> I'm trying to compute graphene's band gap but get stuck. >> From my understanding a scf calculation should provide the same energy for >> the highest occupied and lowest occupied level which means a zero gap. >> I played with the number a kpoints a finally got a band gap of 0.57 which >> is not null. >> The scf convergence looks good. >> I'm not (yet) an expert in DFT calculation so may did something wrong or >> misunderstood something here. >> So, I wonder if someone has already successfully performed such >> calculation. >> I have attached my input file. >> Thanks in advance, >> >> Eric. >> >> -- >> * Be the change you wish to see in the world >> * ? Mahatma Gandhi ? >> >> Dr. ?ric Germaneau >> >> College of Physical Sciences >> Graduate University of Chinese Academy of Sciences >> Yuquan Road 19A >> Beijing 100049 >> China >> >> * Please consider the environment before printing this email. >> Consid?rez svp l'environnement avant d'imprimer cet email. * >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ____________________________________ > Hui Wang > School of physics, Fudan University, Shanghai, China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Mehmet Topsakal (Ph.D. Student) UNAM-Institute of Materials Science and Nanotechnology. Bilkent University. 06800 Bilkent, Ankara/Turkey Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 http://www.researcherid.com/rid/A-5015-2010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110309/ceea9138/attachment.htm From germaneau at gucas.ac.cn Thu Mar 10 15:52:49 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 10 Mar 2011 09:52:49 -0500 Subject: [Pw_forum] graphene's band gap In-Reply-To: <499667167.05330@test1.gucas.ac.cn> References: <4D77B92D.2020602@gucas.ac.cn> <499667167.05330@test1.gucas.ac.cn> Message-ID: <4D78E5C1.5060003@gucas.ac.cn> Dear Mehmet and Hui Wang, That's what I did. From my calculations the occupied and unoccupied bands touch only at K point. I was just confused because the scf calculation does not output a zero gap. I mean the line "highest occupied, lowest unoccupied level" shows two different values and I expected them to be equal. So, it seems I did not too bad in fact. But how to experimentally get a zero gap then? Thanks, Eric. On 03/09/2011 07:02 AM, Mehmet Topsakal wrote: > Dear Eric, > > In addition, if you select 18x18x1 kpoints, your mesh should include > both K and M points. > > But for a band-structure calculation, you should arrange a kpoints > list along special directions, such as from GAMMA-to-M-to-K-to-GAMMA, > and do a nscf calculation.... > > > > On Wed, Mar 9, 2011 at 11:28 AM, xirainbow > wrote: > > Dear Eric: > The occupied and unoccupied bands touch each other only at M > point(or K point, I forget it). > You must include this point in you k-mesh. > Furthermore, if you include spin-orbital coupling, the band gap > will be opened at this point. > > On Thu, Mar 10, 2011 at 1:30 AM, Eric Germaneau > > wrote: > > Dear all, > > I'm trying to compute graphene's band gap but get stuck. > From my understanding a scf calculation should provide the > same energy for the highest occupied and lowest occupied level > which means a zero gap. > I played with the number a kpoints a finally got a band gap of > 0.57 which is not null. > The scf convergence looks good. > I'm not (yet) an expert in DFT calculation so may did > something wrong or misunderstood something here. > So, I wonder if someone has already successfully performed > such calculation. > I have attached my input file. > Thanks in advance, > > Eric. > > -- > /Be the change you wish to see in the world > / ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > /Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. / > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > ____________________________________ > Hui Wang > School of physics, Fudan University, Shanghai, China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > > Mehmet Topsakal (Ph.D. Student) > UNAM-Institute of Materials Science and Nanotechnology. > Bilkent University. 06800 Bilkent, Ankara/Turkey > Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 > http://www.researcherid.com/rid/A-5015-2010 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / ? Mahatma Gandhi ? Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110310/cee26e31/attachment.htm From ttduyle at gmail.com Thu Mar 10 02:57:30 2011 From: ttduyle at gmail.com (Duy Le) Date: Wed, 9 Mar 2011 20:57:30 -0500 Subject: [Pw_forum] graphene's band gap In-Reply-To: <4D78E5C1.5060003@gucas.ac.cn> References: <4D77B92D.2020602@gucas.ac.cn> <499667167.05330@test1.gucas.ac.cn> <4D78E5C1.5060003@gucas.ac.cn> Message-ID: On Thu, Mar 10, 2011 at 9:52 AM, Eric Germaneau wrote: > Dear Mehmet and Hui Wang, > > That's what I did. > From my calculations the occupied and unoccupied bands touch only at K > point. > I was just confused because the scf calculation does not output a zero gap. > I mean the line "highest occupied, lowest unoccupied level" shows two > different values and I expected them to be equal. This was just explained by Mehmet. Check it again > So, it seems I did not too bad in fact. > But how to experimentally get a zero gap then? > Thanks, > > ??????????????????? Eric. > -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" > On 03/09/2011 07:02 AM, Mehmet Topsakal wrote: > > Dear?Eric, > In addition,?if you select 18x18x1 kpoints, your mesh should include both K > and M points. > But for a band-structure calculation, you should arrange a kpoints list > along special directions, such as from GAMMA-to-M-to-K-to-GAMMA, and do a > nscf calculation.... > > > On Wed, Mar 9, 2011 at 11:28 AM, xirainbow wrote: >> >> Dear?Eric: >> The occupied and unoccupied bands touch each other only at M point(or K >> point, I forget it). >> You must include this point in you k-mesh. >> Furthermore, if you include spin-orbital coupling, the band gap will be >> opened at this point. >> >> On Thu, Mar 10, 2011 at 1:30 AM, Eric Germaneau >> wrote: >>> >>> Dear all, >>> >>> I'm trying to compute graphene's band gap but get stuck. >>> From my understanding a scf calculation should provide the same energy >>> for the highest occupied and lowest occupied level which means a zero gap. >>> I played with the number a kpoints a finally got a band gap of 0.57 which >>> is not null. >>> The scf convergence looks good. >>> I'm not (yet) an expert in DFT calculation so may did something wrong or >>> misunderstood something here. >>> So, I wonder if someone has already successfully performed such >>> calculation. >>> I have attached my input file. >>> Thanks in advance, >>> >>> ??????????????????????????????? Eric. >>> >>> -- >>> Be the change you wish to see in the world >>> ? Mahatma Gandhi ? >>> >>> Dr. ?ric Germaneau >>> >>> College of Physical Sciences >>> Graduate University of Chinese Academy of Sciences >>> Yuquan Road 19A >>> Beijing 100049 >>> China >>> >>> Please consider the environment before printing this email. >>> Consid?rez svp l'environnement avant d'imprimer cet email. >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> -- >> ____________________________________ >> Hui Wang >> School of physics, Fudan University, Shanghai, China >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > > Mehmet Topsakal? (Ph.D. Student) > UNAM-Institute of Materials Science and Nanotechnology. > Bilkent University. 06800 Bilkent, Ankara/Turkey > Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 > http://www.researcherid.com/rid/A-5015-2010 > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > Be the change you wish to see in the world > ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From germaneau at gucas.ac.cn Thu Mar 10 16:08:07 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 10 Mar 2011 10:08:07 -0500 Subject: [Pw_forum] graphene's band gap In-Reply-To: <499717133.23756@test1.gucas.ac.cn> References: <4D77B92D.2020602@gucas.ac.cn> <499667167.05330@test1.gucas.ac.cn> <4D78E5C1.5060003@gucas.ac.cn> <499717133.23756@test1.gucas.ac.cn> Message-ID: <4D78E957.8040901@gucas.ac.cn> Did you read what I said? Got it. By the way, I've just realized that I did not thank Mehmet and Hui Wang. On 03/09/2011 08:57 PM, Duy Le wrote: > On Thu, Mar 10, 2011 at 9:52 AM, Eric Germaneau wrote: >> Dear Mehmet and Hui Wang, >> >> That's what I did. >> From my calculations the occupied and unoccupied bands touch only at K >> point. >> I was just confused because the scf calculation does not output a zero gap. >> I mean the line "highest occupied, lowest unoccupied level" shows two >> different values and I expected them to be equal. > This was just explained by Mehmet. Check it again >> So, it seems I did not too bad in fact. >> But how to experimentally get a zero gap then? >> Thanks, >> >> Eric. >> > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" >> On 03/09/2011 07:02 AM, Mehmet Topsakal wrote: >> >> Dear Eric, >> In addition, if you select 18x18x1 kpoints, your mesh should include both K >> and M points. >> But for a band-structure calculation, you should arrange a kpoints list >> along special directions, such as from GAMMA-to-M-to-K-to-GAMMA, and do a >> nscf calculation.... >> >> >> On Wed, Mar 9, 2011 at 11:28 AM, xirainbow wrote: >>> Dear Eric: >>> The occupied and unoccupied bands touch each other only at M point(or K >>> point, I forget it). >>> You must include this point in you k-mesh. >>> Furthermore, if you include spin-orbital coupling, the band gap will be >>> opened at this point. >>> >>> On Thu, Mar 10, 2011 at 1:30 AM, Eric Germaneau >>> wrote: >>>> Dear all, >>>> >>>> I'm trying to compute graphene's band gap but get stuck. >>>> From my understanding a scf calculation should provide the same energy >>>> for the highest occupied and lowest occupied level which means a zero gap. >>>> I played with the number a kpoints a finally got a band gap of 0.57 which >>>> is not null. >>>> The scf convergence looks good. >>>> I'm not (yet) an expert in DFT calculation so may did something wrong or >>>> misunderstood something here. >>>> So, I wonder if someone has already successfully performed such >>>> calculation. >>>> I have attached my input file. >>>> Thanks in advance, >>>> >>>> Eric. >>>> >>>> -- >>>> Be the change you wish to see in the world >>>> ? Mahatma Gandhi ? >>>> >>>> Dr. ?ric Germaneau >>>> >>>> College of Physical Sciences >>>> Graduate University of Chinese Academy of Sciences >>>> Yuquan Road 19A >>>> Beijing 100049 >>>> China >>>> >>>> Please consider the environment before printing this email. >>>> Consid?rez svp l'environnement avant d'imprimer cet email. >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>> >>> >>> -- >>> ____________________________________ >>> Hui Wang >>> School of physics, Fudan University, Shanghai, China >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> -- >> >> Mehmet Topsakal (Ph.D. Student) >> UNAM-Institute of Materials Science and Nanotechnology. >> Bilkent University. 06800 Bilkent, Ankara/Turkey >> Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 >> http://www.researcherid.com/rid/A-5015-2010 >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> -- >> Be the change you wish to see in the world >> ? Mahatma Gandhi ? >> >> Dr. ?ric Germaneau >> >> College of Physical Sciences >> Graduate University of Chinese Academy of Sciences >> Yuquan Road 19A >> Beijing 100049 >> China >> >> Please consider the environment before printing this email. >> Consid?rez svp l'environnement avant d'imprimer cet email. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / ? Mahatma Gandhi ? Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110310/202e879a/attachment.htm From jamali at dena.kntu.ac.ir Thu Mar 10 09:03:28 2011 From: jamali at dena.kntu.ac.ir (Maryam Jamali) Date: Thu, 10 Mar 2011 11:33:28 +0330 (IRST) Subject: [Pw_forum] plotrho.x error Message-ID: <1159886392.2712.1299744208855.JavaMail.root@mail.kntu.ac.ir> Dear all, There are 155 atoms in my system. I want to calculate charge density, I runned pw.x and pp.x program without any problem and I got file.dat for charge density. when I running plotrho.x program, I got the following error: Error: too many atoms ( 155, max: 130) thankyou for any suggestions to plot charge. the input files for pp.x: &inputpp prefix = 'scf51' outdir = './' filplot = 'file1' plot_num= 0 / &plot nfile = 1 filepp(1) = 'file1' weight(1) = 1.0 iflag = 2 output_format = 2 fileout = 'file1.dat' e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=0.5, e2(3) = 0.0, x0(1) =-0.29166666, x0(2)=0.0, x0(3)=0.0275 nx=60, ny=60 / and for plotrho.x: file1.dat file1.ps 0.01 0.5 10 thank you in advance maryam jamali Ph.D student of physical chemistry K.N.T university of technology, tehran From cyrille.barreteau at cea.fr Thu Mar 10 08:38:23 2011 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Thu, 10 Mar 2011 08:38:23 +0100 Subject: [Pw_forum] local magnetic moment in non collinear calculations In-Reply-To: <4D78E957.8040901@gucas.ac.cn> References: <4D77B92D.2020602@gucas.ac.cn> <499667167.05330@test1.gucas.ac.cn> <4D78E5C1.5060003@gucas.ac.cn> <499717133.23756@test1.gucas.ac.cn> <4D78E957.8040901@gucas.ac.cn> Message-ID: <1299742703.21089.37.camel@spcsi25169> Dear all, I think I already asked this question once but do not remember the answer and could not find it in the archive.. When doing non collinear calculations (noncolin=.true.) the magnetic moment on each atom is printed out in the output file. If I remember well this local magnetic moment is integrated over a sphere (and is different from the lowdin charge analysis of projwfc). I just would like to know the radius of this sphere in order to compare my results with the ones obtained from a FLAPW calculation which by construction also integrates charges over a sphere. By the way it would also be interesting to have this local charge within standard LSDA (collinear) calculations. thanks in advance cyrille -- ================================================================== Cyrille Barreteau | phone : +33 (0)1 69 08 29 51 CEA Saclay | fax : +33 (0)1 69 08 84 46 IRAMIS SPCSI Bat 462 | email cyrille.barreteau at cea.fr 91191 Gif sur Yvette FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ home page: http://iramis.cea.fr/Pisp/cbarreteau/ Lab page: http://iramis.cea.fr/spcsi/ ================================================================== From mighfar at jncasr.ac.in Thu Mar 10 10:11:33 2011 From: mighfar at jncasr.ac.in (Mighfar Imam) Date: Thu, 10 Mar 2011 14:41:33 +0530 Subject: [Pw_forum] local magnetic moment in non collinear calculations In-Reply-To: <1299742703.21089.37.camel@spcsi25169> References: <4D77B92D.2020602@gucas.ac.cn> <499667167.05330@test1.gucas.ac.cn> <4D78E5C1.5060003@gucas.ac.cn> <499717133.23756@test1.gucas.ac.cn> <4D78E957.8040901@gucas.ac.cn> <1299742703.21089.37.camel@spcsi25169> Message-ID: <9e6f8e18a338d124b7dc51a17681b8b6.squirrel@mercury.jncasr.ac.in> Dear Cyrille, I think the value of this radius (in the units of alat) is written in the beginning of the output, as "new r_m", which, as the code says, is chosen to be a little smaller than half of the minimum distance between two atoms of the system. The PW/make_pointlists.f90 also says that it can be specified by the user but i don't know where and how this info can be put in the input file! Mighfar Imam, JNCASR, Bangalore India > Dear all, > > I think I already asked this question once but do not remember the > answer and could not find it in the archive.. > > When doing non collinear calculations (noncolin=.true.) the magnetic > moment on each atom is printed out in the output file. > If I remember well this local magnetic moment is integrated over a > sphere (and is different from the lowdin charge analysis of projwfc). > > I just would like to know the radius of this sphere in order to compare > my results with the ones obtained from a FLAPW calculation which by > construction also integrates charges over a sphere. > > By the way it would also be interesting to have this local charge within > standard LSDA (collinear) calculations. > > thanks in advance > > cyrille > > > > -- > ================================================================== > Cyrille Barreteau | phone : +33 (0)1 69 08 29 51 > CEA Saclay | fax : +33 (0)1 69 08 84 46 > IRAMIS SPCSI Bat 462 | email cyrille.barreteau at cea.fr > 91191 Gif sur Yvette FRANCE > ~~~~~~~~~~~~~~~~~~~~~~~~ > home page: http://iramis.cea.fr/Pisp/cbarreteau/ > Lab page: http://iramis.cea.fr/spcsi/ > ================================================================== > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Thu Mar 10 14:45:28 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Mar 2011 14:45:28 +0100 Subject: [Pw_forum] local magnetic moment in non collinear calculations In-Reply-To: <9e6f8e18a338d124b7dc51a17681b8b6.squirrel@mercury.jncasr.ac.in> References: <4D77B92D.2020602@gucas.ac.cn> <499667167.05330@test1.gucas.ac.cn> <4D78E5C1.5060003@gucas.ac.cn> <499717133.23756@test1.gucas.ac.cn> <4D78E957.8040901@gucas.ac.cn> <1299742703.21089.37.camel@spcsi25169> <9e6f8e18a338d124b7dc51a17681b8b6.squirrel@mercury.jncasr.ac.in> Message-ID: On Mar 10, 2011, at 10:11 , Mighfar Imam wrote: > The PW/make_pointlists.f90 also says that it can be specified by > the user where? I don't see it P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Mar 10 15:25:01 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Mar 2011 15:25:01 +0100 Subject: [Pw_forum] plotrho.x error In-Reply-To: <1159886392.2712.1299744208855.JavaMail.root@mail.kntu.ac.ir> References: <1159886392.2712.1299744208855.JavaMail.root@mail.kntu.ac.ir> Message-ID: <8BFAC961-B1D1-46C3-BD0F-68E30F4BF637@democritos.it> On Mar 10, 2011, at 9:03 , Maryam Jamali wrote: > Error: too many atoms ( 155, max: 130) there is no such error in PP/plotrho.f90 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From Heiles at cluster.pc.chemie.tu-darmstadt.de Thu Mar 10 15:42:55 2011 From: Heiles at cluster.pc.chemie.tu-darmstadt.de (Sven Heiles) Date: Thu, 10 Mar 2011 15:42:55 +0100 Subject: [Pw_forum] Bi pseudopotential Message-ID: <4D78E36F.2010509@cluster.pc.chemie.tu-darmstadt.de> Dear QE users. Our group started to use QE and tries to combine the code with a global structural search routine. For this purpose valence only pseudopotentials (PP) optimized for a low energy cutoff has to be used (at the cost of computational correcetness of course). As a test case we want to start with Bi. For this element only a relatively hard PP exists which incoperates a d semicore state. Since the converted FHI PP 5-electron PPs does not work very well I decided to try to create a own PP. Have done the tutorial for Si and the example calculation for Ti and everything seemed to work all right. Because I am not very familiar with the theory of the PP fitting routines I tried to progress for Bi in the same manner as for Si and Ti. So I started with: &input iswitch=3, rlderiv=2.20, eminld=-2.0,emaxld=1.0,deld=0.01d0,nld=3, rel=1,zed=83.0,config="[Xe] 4f14 5d10 6s2 6p3 6d-1",dft='PBE', / &inputp lloc=2,pseudotype=1,file_pseudopw='Bi.pbe-n-rrkj.UPF', zval=5.0,rho0=0.01 / 3 6S 1 0 2.00 0.00 2.20 2.20 6P 2 1 3.00 0.00 2.20 2.20 6D 3 2 0.00 -0.10 2.20 2.20 But unfourtunately this input file produces the error "phi has nodes before r_c". Therefore tried to change rho0 , rcore and rcut systematically without success. Therefore used tm=.true. which produced a PP which looked good. Depressingly the TM potential failed to converge for test calculations for the dimer. Therefore changed the following things in the input: config="[Xe] 4f14 5d10 6s2 6p3", lloc=1, and got rid of the 6D in the PP card. In this way I am able to generate a PP. The wavefunctions and the logDev look ok. But the performance for the Dimer is not really good (40 Ry Ecutoff, RhoCutoff= 8*Ecutoff) -> 2.52 AA bondlength compared to 2.66 AA experimentally. For example a Lanl2DZ calculation in NWChem with the same functional yields 2.64 AA. Additionally any influence of the 6D state is not descibed with the potential. Every time I want to change the settings for the PP the program produces an error. I am not able so far to write in the 6D channel or in two channels (pseudotype=2) or to generate a US-PP (pseudotype=3). Since I am far away from beeing an expert and this are only my first attempts I wondered if someone has any suggestions what I could try to improve the PP for Bi step by step. Best wishes Sven -- Dipl. Ing. Sven Heiles Technische Universit?t Darmstadt AK Sch?fer Eduard-Zintl-Institut Petersenstra?e 20 D-64287 Darmstadt ? Germany Phone: ++49-(0)6151-164397 Fax: ++49-(0)6151-166024 Web: http://www.tu-darmstadt.de/fb/ch/cluster/schaefer.tud From mighfar at jncasr.ac.in Thu Mar 10 16:35:38 2011 From: mighfar at jncasr.ac.in (Mighfar Imam) Date: Thu, 10 Mar 2011 21:05:38 +0530 Subject: [Pw_forum] local magnetic moment in non collinear calculations In-Reply-To: References: <4D77B92D.2020602@gucas.ac.cn> <499667167.05330@test1.gucas.ac.cn> <4D78E5C1.5060003@gucas.ac.cn> <499717133.23756@test1.gucas.ac.cn> <4D78E957.8040901@gucas.ac.cn> <1299742703.21089.37.camel@spcsi25169> <9e6f8e18a338d124b7dc51a17681b8b6.squirrel@mercury.jncasr.ac.in> Message-ID: <9b549a3d851d2d38283802e342c9f73a.squirrel@mercury.jncasr.ac.in> Dear Paolo, In PW/make_pointlists.f90: !In the input the integration radius r_m can be given, otherwise it is ! calculated here. So i thought it can be given in the input. I am sorry if i understood it wrong! Mighfar Imam JNCASR, Bangalore. > > On Mar 10, 2011, at 10:11 , Mighfar Imam wrote: > >> The PW/make_pointlists.f90 also says that it can be specified by >> the user > > where? I don't see it > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From smirshamsi at phys.ufl.edu Thu Mar 10 16:46:08 2011 From: smirshamsi at phys.ufl.edu (Sahar Mirshamsi) Date: Thu, 10 Mar 2011 10:46:08 -0500 (EST) Subject: [Pw_forum] Some questions about non-collinear calculation and penalty function In-Reply-To: Message-ID: Dear Paolo,Cyrille and Mighfar, It seems you guys are the most active ones in non-collinear field among forum users. I have posted these questions about two weeks ago and I did not get any response, can you please take a look at them and tell me your ideas about possible answers? Thanks, Sahar On Fri, 4 Mar 2011, Sahar Mirshamsi wrote: > On Thu, 3 Mar 2011, Sahar Mirshamsi wrote: > > any idea about answers of these questions? > > Sahar > > > > Hi all, > > I have some questions regarding non-collinear calculation and using > > penalty function in pwscf. > > 1) In constaint_magnetization ='atomic', is starting magnetization as the > > target magnetization? I have read this post > > http://www.democritos.it/pipermail/pw_forum/2009-December/015342.html > > and also in input.f90 I found > > mcons(1,nt) = starting_magnetization(nt) * SIN( theta ) * COS( > > phi ) > > mcons(2,nt) = starting_magnetization(nt) * SIN( theta ) * SIN( > > phi ) > > mcons(3,nt) = starting_magnetization(nt) * COS( theta ) > > So it means both magnitude and direction of atomic magnetizations are > > constrained, is this correct? > > 2) If above statement is correct, then the same problem as posted in above > > link will still exist, since starting_magnetization=m/n, then for > > constraining the magnitude of magnetization to desired value, we should > > multiply the magnitude of magnetization by charge and then replace it as > > starting_magnitization, is this correct? > > 3) What is the relation between charge and magnetization printed in scf > > calculation with those which we can get with using projwf.x, I expect they > > should get almost same numbers but in scf output for carbons in Graphene > > nanoribbon I get charge=0.6 and magnetization=0.1 while in projwf.x output > > I get charge=4 and polarization=0.2-0.3 which the latest one makes more > > sense. > > 4) Also, in some cases of non-collinear calculation with using penalty > > function, when I track "estimated scf accuracy" it is decreasing till > > reaching the threshold and stopping the job while "total energy" is > > oscillating in some range instead of converging to a number , any idea > > what's the problem? > > 5) The total energy printed in scf calculation does not include constraint > > energy, right? It's just energy of the structure with the constraint > > configuration of magnetizations, right? > > I appreciate any help in finding the answers of these questions. > > > > Sahar Mishamsi > > Quantum Theory Project and Physics Department, > > University of Florida > > > > > > > > From saqib.javaid at ipcms.u-strasbg.fr Thu Mar 10 17:50:38 2011 From: saqib.javaid at ipcms.u-strasbg.fr (saqib.javaid at ipcms.u-strasbg.fr) Date: Thu, 10 Mar 2011 17:50:38 +0100 Subject: [Pw_forum] Coverting PDOS from JM basis (spin-orbit, non-colinear case) to LS basis In-Reply-To: <9b549a3d851d2d38283802e342c9f73a.squirrel@mercury.jncasr.ac.in> References: <4D77B92D.2020602@gucas.ac.cn> <499667167.05330@test1.gucas.ac.cn> <4D78E5C1.5060003@gucas.ac.cn> <499717133.23756@test1.gucas.ac.cn> <4D78E957.8040901@gucas.ac.cn> <1299742703.21089.37.camel@spcsi25169> <9e6f8e18a338d124b7dc51a17681b8b6.squirrel@mercury.jncasr.ac.in> <9b549a3d851d2d38283802e342c9f73a.squirrel@mercury.jncasr.ac.in> Message-ID: <1299775838.4d79015ec48bc@ipcms.u-strasbg.fr> Dear PWSCF Users, I have been trying to get PDOS given in JM basis for spin-orbit and non-colinear case into LS basis (like in colinear case). For this purpose, i converted projections calculated in 'projwave_nc' subroutine ( array proj0(natomwfc,nbnd), presumably in JM basis ) to LS basis using clebsh-Gordon coefficients. However, PDOS obtained with this procedure does not give the correct spin moment for simple 3d metals. I would appreciate if you can point out any concpetual mistake in the method used or an alternative way to obtain PDOS in LS basis for spin orbit case. with best regards, saqib javaid Phd student, University of strasbourg, France ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From snd2mra at yahoo.com Thu Mar 10 18:45:30 2011 From: snd2mra at yahoo.com (Madan Mithra. L. M) Date: Thu, 10 Mar 2011 09:45:30 -0800 (PST) Subject: [Pw_forum] CVS Version download link Message-ID: <747134.51771.qm@web161304.mail.bf1.yahoo.com> Hello, I was able to download the CVS Version from qe-forge site earlier. Now the link is missing. Could you please direct me to the correct link ? Thank you - Madan ---------------------------------------- Madan Mithra .L.M Senior Research Fellow Dept.of Physics Indian Institute of Science Bangalore - 560 012 INDIA ......................................... e-mail : mit at physics.iisc.ernet.in : snd2mra at yahoo.com Phone : 91-80-22932313 (Lab) FAX : (080) 360 2602 ----------------------------------------- From crma at sissa.it Thu Mar 10 18:53:48 2011 From: crma at sissa.it (Changru Ma) Date: Thu, 10 Mar 2011 18:53:48 +0100 Subject: [Pw_forum] CVS Version download link In-Reply-To: <747134.51771.qm@web161304.mail.bf1.yahoo.com> References: <747134.51771.qm@web161304.mail.bf1.yahoo.com> Message-ID: <50FE61E0-7DB9-416C-BCC5-8FFF7DBC2244@sissa.it> Dear Madan, Anonymous CVS Access This project's CVS repository can be checked out through anonymous (pserver) CVS with the following instruction set. The module you wish to check out must be specified as the modulename. When prompted for a password for anonymous, simply press the Enter key. cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e login cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e checkout espresso Best wishes, Changru On 10 Mar, 2011, at 18:45, Madan Mithra. L. M wrote: > Hello, > > I was able to download the CVS Version from qe-forge site earlier. Now the > link is missing. Could you please direct me to the correct link ? > > Thank you > > - Madan > > ---------------------------------------- > Madan Mithra .L.M > Senior Research Fellow > Dept.of Physics > Indian Institute of Science > Bangalore - 560 012 > INDIA > ......................................... > e-mail : mit at physics.iisc.ernet.in > : snd2mra at yahoo.com > Phone : 91-80-22932313 (Lab) > FAX : (080) 360 2602 > ----------------------------------------- > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma --- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110310/cd9712e2/attachment-0001.htm From giannozz at democritos.it Thu Mar 10 19:22:15 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Mar 2011 19:22:15 +0100 Subject: [Pw_forum] CVS Version download link In-Reply-To: <747134.51771.qm@web161304.mail.bf1.yahoo.com> References: <747134.51771.qm@web161304.mail.bf1.yahoo.com> Message-ID: On Mar 10, 2011, at 18:45 , Madan Mithra. L. M wrote: > I was able to download the CVS Version from qe-forge site earlier. > Now the > link is missing. Could you please direct me to the correct link ? this is a consequence of the upgrade of the qe-forge software to a new version. It will be fixed indue time. Meanwhile you can use anonymous CVS, as explained by Changru. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Mar 10 19:28:19 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Mar 2011 19:28:19 +0100 Subject: [Pw_forum] Some questions about non-collinear calculation and penalty function In-Reply-To: References: Message-ID: On Mar 10, 2011, at 16:46 , Sahar Mirshamsi wrote: > Dear Paolo [...] It seems you guys are the most active > ones in non-collinear field I know nothing about non-collinear calculations P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Mar 10 19:36:06 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 10 Mar 2011 19:36:06 +0100 Subject: [Pw_forum] local magnetic moment in non collinear calculations In-Reply-To: <9b549a3d851d2d38283802e342c9f73a.squirrel@mercury.jncasr.ac.in> References: <4D77B92D.2020602@gucas.ac.cn> <499667167.05330@test1.gucas.ac.cn> <4D78E5C1.5060003@gucas.ac.cn> <499717133.23756@test1.gucas.ac.cn> <4D78E957.8040901@gucas.ac.cn> <1299742703.21089.37.camel@spcsi25169> <9e6f8e18a338d124b7dc51a17681b8b6.squirrel@mercury.jncasr.ac.in> <9b549a3d851d2d38283802e342c9f73a.squirrel@mercury.jncasr.ac.in> Message-ID: <3A651338-A6B2-413F-BDAB-BA56E5FDD443@democritos.it> On Mar 10, 2011, at 16:35 , Mighfar Imam wrote: > !In the input the integration radius r_m can be given, otherwise it is > ! calculated here. funny: the first half of the comment had been lost in the CVS version. > So i thought it can be given in the input. I am sorry if i > understood it > wrong! even the complete version was not a marvel of clarity. I think it was supposed to mean "if r_m is set to something, we use that value, if it is set to zero, we calculate it here". P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From akrukau at indiana.edu Thu Mar 10 22:29:57 2011 From: akrukau at indiana.edu (Krukau, Aliaksandr) Date: Thu, 10 Mar 2011 16:29:57 -0500 Subject: [Pw_forum] Memory usage in Quantum Espresso Message-ID: <20110310162957.25rqp2odogc4s0wg@webmail.iu.edu> Dear QE users, My desktop has Intel Core 2 Quad processor and 4GB RAM. However, when I run Quantum Espresso (QE) 4.1, the biggest PWSCF jobs that I manage to run use about 200MB of RAM. For bigger systems or tighter cutoffs, the calculations crash with a segmentation violation. Moreover, if I use QE 4.2.1, the calculation crash even when I use more than ~100MB. So I am restricted to the quite small systems, especially if I use the latest 4.2.1 version. The user guide mentions that old compilers can reduce the size of the system that PWSCF can treat. But I use relatively new version 9.0 of Portland group Fortran compilers. If I run 'limit' command, it shows 'memoryuse unlimited; stacksize unlimited'. I apologize for the naive questions, but why can PWSCF use only a small fraction of my total RAM? Or the line "per-process dynamical memory" in the output file does not show the total required memory? Is there a way to run bigger calculations without using parallel execution (maybe by compiler flags etc.)? Best regards, Alex Krukau, Indiana University From giannozz at democritos.it Fri Mar 11 08:45:14 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 11 Mar 2011 08:45:14 +0100 Subject: [Pw_forum] Memory usage in Quantum Espresso In-Reply-To: <20110310162957.25rqp2odogc4s0wg@webmail.iu.edu> References: <20110310162957.25rqp2odogc4s0wg@webmail.iu.edu> Message-ID: <803D2EC0-3F2B-45E7-8FAD-E67277CB525B@democritos.it> On Mar 10, 2011, at 22:29 , Krukau, Aliaksandr wrote: > The user guide mentions that old compilers can reduce the size > of the system that PWSCF can treat. But I use relatively new > version 9.0 of Portland group Fortran compilers. Either your compiler is buggy, or it requires some specific options to run a relatively large code like PWscf. If you paid real money for the PGI compiler, complain with the vendor. In the meantime, try a recent version of gfortran or a non-buggy version of the Intel compiler (latest v.11 should be ok) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sks.jnc at gmail.com Fri Mar 11 14:46:04 2011 From: sks.jnc at gmail.com (S. K. S.) Date: Fri, 11 Mar 2011 14:46:04 +0100 Subject: [Pw_forum] LDA-USPP for Ge Message-ID: Dear QE Friends, Does any one have LDA-USPP for Ge ? Does this scarcity mean that it is not good to use LDA for Ge ? Thanking you all, Saha SK R&D Assistant JNCASR Bangalore-560012 From parishok at gmail.com Fri Mar 11 19:37:02 2011 From: parishok at gmail.com (pari shok) Date: Fri, 11 Mar 2011 13:37:02 -0500 Subject: [Pw_forum] number of bands and degenerate states in supercell Message-ID: Hello, I have a question and I appreciate your help in advance. I am making a supercell by repeating a unit cell of SiC. Then, instead of 8 atom in a hexagonal structure, there are 72 atoms in a supercell. My question is about the number of bands. Theoretically, the number of bands would be just the same for the unit cell (32 in this case) and even if you increase them in the input file, they should just have degeneracy and overlap. However, they are not. I was wondering how I can interpret the bands. Yours P Shok UMD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110311/fb4d9123/attachment.htm From ttduyle at gmail.com Fri Mar 11 19:44:43 2011 From: ttduyle at gmail.com (Duy Le) Date: Fri, 11 Mar 2011 13:44:43 -0500 Subject: [Pw_forum] number of bands and degenerate states in supercell In-Reply-To: References: Message-ID: The logic is simple: #bands = #electrons/2+#unoccupied_bands If you increase the size of unit cell, #atoms increase as well, so do #electrons However, you will have something called band folding because the BZ shrinks. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Fri, Mar 11, 2011 at 1:37 PM, pari shok wrote: > Hello, > I have a question and I appreciate your help in advance. > I am making a supercell by repeating a unit cell of SiC. Then, instead of 8 > atom in a hexagonal structure, there are 72 atoms in a supercell. > My question is about the number of bands. > Theoretically, the number of bands would be just the same for the unit cell > (32 in this case) and even if you increase them in the input file, they > should just have degeneracy and overlap. However, they are not. > I was wondering how I can interpret the bands. > Yours > P Shok > UMD > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From lorenzo.paulatto at impmc.upmc.fr Fri Mar 11 20:38:26 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 11 Mar 2011 20:38:26 +0100 Subject: [Pw_forum] LDA-USPP for Ge In-Reply-To: References: Message-ID: In data 11 marzo 2011 alle ore 14:46:04, S. K. S. ha scritto: > Does any one have LDA-USPP for Ge ? > Does this scarcity mean that it is not good to use LDA for Ge ? Dear Saha, if I remember correctly, Germanium does not have a gap in LDA, i.e. it is metallic. regards -- Lorenzo Paulatto post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously (take note of the change!): phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From sclauzer at sissa.it Sat Mar 12 14:54:08 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Sat, 12 Mar 2011 14:54:08 +0100 Subject: [Pw_forum] number of bands and degenerate states in supercell In-Reply-To: References: Message-ID: <8E0365D0-B6EB-4FEB-BABA-5B63D1B9B678@sissa.it> Il giorno 11/mar/2011, alle ore 19.37, pari shok ha scritto: > Hello, > I have a question and I appreciate your help in advance. > I am making a supercell by repeating a unit cell of SiC. Then, instead of 8 atom in a hexagonal structure, there are 72 atoms in a supercell. > My question is about the number of bands. > Theoretically, the number of bands would be just the same for the unit cell (32 in this case) Why 32? Since you have 8 atoms per cell, either Si or C, the number of electrons should be 4*8=32, so nbnd=16 should be sufficient (for collinear calculations). > and even if you increase them in the input file, they should just have degeneracy and overlap. However, they are not. > I was wondering how I can interpret the bands. For this point, please refer to Duy Le's reply and perform a search about "band refolding" on the forum (or in any electronic structure book). HTH GS > Yours > P Shok > UMD > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110312/d1951b82/attachment.htm From zhaohscas at yahoo.com.cn Sun Mar 13 10:35:33 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Sun, 13 Mar 2011 17:35:33 +0800 Subject: [Pw_forum] The issue of PWgui-4.2. Message-ID: <1988635548.20110313173533@yahoo.com.cn> Dear All, Currently, I use PWgui-4.2 under windows xp and I meet the following errors when open a input file, say, the file shipped by PWgui-4.2 in the examples folder: \examples\pw\al.band.in: --------------------------------- can not find channel named "filee286f8" can not find channel named "filee286f8" while executing "close $fileChannel" (object "::gUI0" method "::guib::GUI::_openInput" body line 36) invoked from within "$cmd $moduleIdent $moduleName $moduleFile" (object "::gUI0" method "::guib::GUI::_toolbarCmd" body line 3) invoked from within "::gUI0 _toolbarCmd .gUI0_toolbaropen _openInput pw PW.X F:/zhaohs/etc/PWgui/PWgui-4.2/espresso-4.2/PWgui-4.2/modules/pw/pw.tcl" (in namespace inscope "::guib::GUI" script line 1) invoked from within "namespace inscope ::guib::GUI {::gUI0 _toolbarCmd .gUI0_toolbaropen _openInput pw PW.X F:/zhaohs/etc/PWgui/PWgui-4.2/espresso-4.2/PWgui-4.2/modules/pw..." invoked from within ".gUI0_toolbaropen.0 invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 24) invoked from within "tk::ButtonUp .gUI0_toolbaropen.0" (command bound to event) --------------------------------- Any hints on this issue? Thanks in advance. Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China GnuPG DSA: 0xD108493 2011-3-13 From tkaloni at gmail.com Sun Mar 13 17:22:24 2011 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Sun, 13 Mar 2011 19:22:24 +0300 Subject: [Pw_forum] problem with degauss and magnetization Message-ID: Dear Quantum Espresso users, I am trying to get the magnetization by creating one vacancy in 5x5 supercell of graphene. With different values of degauss the total magnetization is changing surprisingly. Is there anything wrong with my input ?. Could anybody please tell me some references where I can read detail about smearing and degauss ?. The total magnetization with different degauss are given as below, *degauss total magnetization 0.05 0.00 0.01 0.58 0.001 0.88 0.0001 0.88 * I am posting my input file below. &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = 'OUT/', pseudo_dir = '/home/kaloni/pseudo/', prefix = 'g', tstress=.true., / &SYSTEM ibrav = 4, a=12.199359575, b= 12.199359575, c=19.999668786, cosab= -0.5, cosac =0.0 , cosbc=0.0, nat= 49, ntyp= 1, ecutwfc = 40, ecutrho = 400, nspin =2, starting_magnetization = 1.0, occupations='smearing', smearing=' gaussian', degauss=0.05, nosym = .true., / &ELECTRONS mixing_beta = 0.3 conv_thr = 1.0d-9 / ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF ATOMIC_POSITIONS (crystal) C -0.000437574 -0.000580938 0.000000015 C 0.000878501 0.200420327 -0.000000008 C 0.001210858 0.399950578 -0.000000071 C -0.000312205 0.599509065 0.000000002 C -0.000716730 0.798976722 0.000000025 C 0.199479935 -0.000986699 -0.000000031 C 0.200591611 0.200243356 0.000000020 C 0.204951004 0.399348478 -0.000000039 C 0.200756083 0.599210178 -0.000000027 C 0.199615366 0.799016660 0.000000045 C 0.399828248 -0.000558044 -0.000000011 C 0.399613916 0.200154971 0.000000014 C 0.401785094 0.599046302 -0.000000047 C 0.400264884 0.799510584 0.000000019 C 0.600023737 0.000445858 -0.000000037 C 0.599500576 0.200387180 0.000000030 C 0.594152084 0.399266958 0.000000290 C 0.597008286 0.598889370 0.000000057 C 0.600448742 0.800956977 -0.000000036 C 0.800386518 0.000445469 -0.000000021 C 0.800217273 0.200473648 -0.000000180 C 0.798607049 0.399927530 0.000000120 C 0.798270617 0.599140827 0.000000073 C 0.799080030 0.799392409 -0.000000024 C 0.132951308 0.065395469 0.000000019 C 0.133142262 0.266027786 -0.000000014 C 0.135800585 0.466331814 -0.000000062 C 0.133194345 0.665806346 0.000000014 C 0.132633945 0.865364014 0.000000018 C 0.332386006 0.065362305 -0.000000012 C 0.329787525 0.259493844 0.000000003 C 0.336738546 0.468697263 -0.000000042 C 0.333671463 0.665846245 -0.000000020 C 0.333143624 0.865895587 0.000000044 C 0.533078996 0.066642011 -0.000000019 C 0.532824452 0.265959049 0.000000110 C 0.531539380 0.468474465 0.000000226 C 0.534652606 0.669416138 -0.000000013 C 0.533415252 0.867317865 -0.000000015 C 0.733533974 0.067101960 -0.000000071 C 0.733185901 0.266889900 -0.000000007 C 0.730336277 0.466262841 0.000000196 C 0.731928945 0.665704201 0.000000020 C 0.733842050 0.867300592 -0.000000017 C 0.933534511 0.066657775 0.000000016 C 0.933667182 0.266910925 -0.000000085 C 0.933067875 0.466263286 0.000000000 C 0.932454196 0.665766534 0.000000004 C 0.932632612 0.865835315 0.000000008 K_POINTS AUTOMATIC 4 4 1 1 1 1 Thanks Thaneshwor Prashad Kaloni -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110313/6442c24c/attachment.htm From skgupta.physics at gmail.com Sun Mar 13 17:36:01 2011 From: skgupta.physics at gmail.com (Sanjeev Kumar Gupta) Date: Sun, 13 Mar 2011 22:06:01 +0530 Subject: [Pw_forum] problem with degauss and magnetization In-Reply-To: References: Message-ID: for smearing, may be this paper will be good. http://prb.aps.org/pdf/PRB/v65/i3/e035111. Best Regards Sanjeev Gupta Dept. of Physics, Bhavnagar University, Bhavnagar-364022 On 13 March 2011 21:52, Thaneshwor Kaloni wrote: > Dear Quantum Espresso users, > > > I am trying to get the magnetization by creating one vacancy > in 5x5 supercell of graphene. > With different values of degauss the total magnetization is > changing surprisingly. Is there anything wrong with my input ?. > Could anybody please tell me some references where I > can read detail about smearing and degauss ?. > > > The total magnetization with different degauss are given as below, > > *degauss total magnetization > 0.05 0.00 > 0.01 0.58 > 0.001 0.88 > 0.0001 0.88 > > * > > I am posting my input file below. > > > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = 'OUT/', > pseudo_dir = '/home/kaloni/pseudo/', > prefix = 'g', > tstress=.true., > / > &SYSTEM > ibrav = 4, a=12.199359575, b= 12.199359575, > c=19.999668786, cosab= -0.5, cosac =0.0 , cosbc=0.0, > nat= 49, ntyp= 1, > ecutwfc = 40, > ecutrho = 400, > nspin =2, starting_magnetization = 1.0, > occupations='smearing', smearing=' gaussian', degauss=0.05, > nosym = .true., > > / > &ELECTRONS > mixing_beta = 0.3 > conv_thr = 1.0d-9 > / > ATOMIC_SPECIES > C 12.0107 C.pz-rrkjus.UPF > ATOMIC_POSITIONS (crystal) > C -0.000437574 -0.000580938 0.000000015 > C 0.000878501 0.200420327 -0.000000008 > C 0.001210858 0.399950578 -0.000000071 > C -0.000312205 0.599509065 0.000000002 > C -0.000716730 0.798976722 0.000000025 > C 0.199479935 -0.000986699 -0.000000031 > C 0.200591611 0.200243356 0.000000020 > C 0.204951004 0.399348478 -0.000000039 > C 0.200756083 0.599210178 -0.000000027 > C 0.199615366 0.799016660 0.000000045 > C 0.399828248 -0.000558044 -0.000000011 > C 0.399613916 0.200154971 0.000000014 > C 0.401785094 0.599046302 -0.000000047 > C 0.400264884 0.799510584 0.000000019 > C 0.600023737 0.000445858 -0.000000037 > C 0.599500576 0.200387180 0.000000030 > C 0.594152084 0.399266958 0.000000290 > C 0.597008286 0.598889370 0.000000057 > C 0.600448742 0.800956977 -0.000000036 > C 0.800386518 0.000445469 -0.000000021 > C 0.800217273 0.200473648 -0.000000180 > C 0.798607049 0.399927530 0.000000120 > C 0.798270617 0.599140827 0.000000073 > C 0.799080030 0.799392409 -0.000000024 > C 0.132951308 0.065395469 0.000000019 > C 0.133142262 0.266027786 -0.000000014 > C 0.135800585 0.466331814 -0.000000062 > C 0.133194345 0.665806346 0.000000014 > C 0.132633945 0.865364014 0.000000018 > C 0.332386006 0.065362305 -0.000000012 > C 0.329787525 0.259493844 0.000000003 > C 0.336738546 0.468697263 -0.000000042 > C 0.333671463 0.665846245 -0.000000020 > C 0.333143624 0.865895587 0.000000044 > C 0.533078996 0.066642011 -0.000000019 > C 0.532824452 0.265959049 0.000000110 > C 0.531539380 0.468474465 0.000000226 > C 0.534652606 0.669416138 -0.000000013 > C 0.533415252 0.867317865 -0.000000015 > C 0.733533974 0.067101960 -0.000000071 > C 0.733185901 0.266889900 -0.000000007 > C 0.730336277 0.466262841 0.000000196 > C 0.731928945 0.665704201 0.000000020 > C 0.733842050 0.867300592 -0.000000017 > C 0.933534511 0.066657775 0.000000016 > C 0.933667182 0.266910925 -0.000000085 > C 0.933067875 0.466263286 0.000000000 > C 0.932454196 0.665766534 0.000000004 > C 0.932632612 0.865835315 0.000000008 > K_POINTS AUTOMATIC > 4 4 1 1 1 1 > > > Thanks > > Thaneshwor Prashad Kaloni > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- With Kind Regards, Sanjeev K. Gupta -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110313/22cd6542/attachment.htm From luoxuhui at uic.edu Sun Mar 13 18:06:32 2011 From: luoxuhui at uic.edu (xuhui luo) Date: Sun, 13 Mar 2011 13:06:32 -0400 Subject: [Pw_forum] How to read two wave-functions in one program? Message-ID: Dear PWscf experts, I have a problem about fortran coding for reading two set of wave-functions in one program. Actually I can read one set of wavefunctions for one structure. Now I would like to read another set for a new structure after reading the first one and then calculate some quantities based on two sets. I find that O. Baris Malcioglu already posted a nice list about reading one set of wavefunction coefficients. But the problem for reading two sets is that a lot global variables, such as the variables in module 'kilist', will stay in memory and affect the next reading. I tried several ways to avoid this problem but didn't succeed. Because I am a newbie of mpi and fortran 90 coding, I ask for helps and ideas here. Thanks in advance. Xuhui Luo University of Illinois at Chicago From rfaccio at fq.edu.uy Sun Mar 13 18:12:37 2011 From: rfaccio at fq.edu.uy (Ricardo Faccio) Date: Sun, 13 Mar 2011 14:12:37 -0300 (UYT) Subject: [Pw_forum] problem with degauss and magnetization In-Reply-To: References: Message-ID: Hi Magnetism due to vacancies in graphene can be seen understood following the stoner criteria. It is a metallic system, with localized states at the Fermi level, mainly due to non bonding states, that present to many peaks at the Fermi level. So, it is important to get a good DOS, mainly at the Fermi level. A big degauss, smoothes the DOS, and thus affect the unbalance between Nup and Ndn electrons. For all of these reasons: - try to reduce degauss, until having a converged results: energy and total magnetic moment - take care about the number of kpoints, since it has important effects in the DOS, particularly at the Fermi level. Regards Ricardo ------------------------------------------------- Dr. Ricardo Faccio Prof. Adjunto de F?sica Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA Facultad de Qu?mica, Universidad de la Rep?blica Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio at fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > Dear Quantum Espresso users, > > > I am trying to get the magnetization by creating one vacancy > in 5x5 supercell of graphene. > With different values of degauss the total magnetization is > changing surprisingly. Is there anything wrong with my input ?. > Could anybody please tell me some references where I > can read detail about smearing and degauss ?. > > > The total magnetization with different degauss are given as below, > > *degauss total magnetization > 0.05 0.00 > 0.01 0.58 > 0.001 0.88 > 0.0001 0.88 > > * > > I am posting my input file below. > > > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = 'OUT/', > pseudo_dir = '/home/kaloni/pseudo/', > prefix = 'g', > tstress=.true., > / > &SYSTEM > ibrav = 4, a=12.199359575, b= 12.199359575, > c=19.999668786, cosab= -0.5, cosac =0.0 , cosbc=0.0, > nat= 49, ntyp= 1, > ecutwfc = 40, > ecutrho = 400, > nspin =2, starting_magnetization = 1.0, > occupations='smearing', smearing=' gaussian', degauss=0.05, > nosym = .true., > > / > &ELECTRONS > mixing_beta = 0.3 > conv_thr = 1.0d-9 > / > ATOMIC_SPECIES > C 12.0107 C.pz-rrkjus.UPF > ATOMIC_POSITIONS (crystal) > C -0.000437574 -0.000580938 0.000000015 > C 0.000878501 0.200420327 -0.000000008 > C 0.001210858 0.399950578 -0.000000071 > C -0.000312205 0.599509065 0.000000002 > C -0.000716730 0.798976722 0.000000025 > C 0.199479935 -0.000986699 -0.000000031 > C 0.200591611 0.200243356 0.000000020 > C 0.204951004 0.399348478 -0.000000039 > C 0.200756083 0.599210178 -0.000000027 > C 0.199615366 0.799016660 0.000000045 > C 0.399828248 -0.000558044 -0.000000011 > C 0.399613916 0.200154971 0.000000014 > C 0.401785094 0.599046302 -0.000000047 > C 0.400264884 0.799510584 0.000000019 > C 0.600023737 0.000445858 -0.000000037 > C 0.599500576 0.200387180 0.000000030 > C 0.594152084 0.399266958 0.000000290 > C 0.597008286 0.598889370 0.000000057 > C 0.600448742 0.800956977 -0.000000036 > C 0.800386518 0.000445469 -0.000000021 > C 0.800217273 0.200473648 -0.000000180 > C 0.798607049 0.399927530 0.000000120 > C 0.798270617 0.599140827 0.000000073 > C 0.799080030 0.799392409 -0.000000024 > C 0.132951308 0.065395469 0.000000019 > C 0.133142262 0.266027786 -0.000000014 > C 0.135800585 0.466331814 -0.000000062 > C 0.133194345 0.665806346 0.000000014 > C 0.132633945 0.865364014 0.000000018 > C 0.332386006 0.065362305 -0.000000012 > C 0.329787525 0.259493844 0.000000003 > C 0.336738546 0.468697263 -0.000000042 > C 0.333671463 0.665846245 -0.000000020 > C 0.333143624 0.865895587 0.000000044 > C 0.533078996 0.066642011 -0.000000019 > C 0.532824452 0.265959049 0.000000110 > C 0.531539380 0.468474465 0.000000226 > C 0.534652606 0.669416138 -0.000000013 > C 0.533415252 0.867317865 -0.000000015 > C 0.733533974 0.067101960 -0.000000071 > C 0.733185901 0.266889900 -0.000000007 > C 0.730336277 0.466262841 0.000000196 > C 0.731928945 0.665704201 0.000000020 > C 0.733842050 0.867300592 -0.000000017 > C 0.933534511 0.066657775 0.000000016 > C 0.933667182 0.266910925 -0.000000085 > C 0.933067875 0.466263286 0.000000000 > C 0.932454196 0.665766534 0.000000004 > C 0.932632612 0.865835315 0.000000008 > K_POINTS AUTOMATIC > 4 4 1 1 1 1 > > > Thanks > > Thaneshwor Prashad Kaloni > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------- Dr. Ricardo Faccio Prof. Adjunto de F?sica Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA Facultad de Qu?mica, Universidad de la Rep?blica Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio at fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm From hqzhou at nju.edu.cn Mon Mar 14 04:34:42 2011 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 14 Mar 2011 11:34:42 +0800 Subject: [Pw_forum] problem with degauss and magnetization References: Message-ID: <359B704897A34115A7134B299F1DD37F@solarflare> If I were you, I would try degauss=0.006, 0.004, 0.002 with dense enough k points and see the tendency. zhou huiqun @earth sciences, nanjing university, china ----- Original Message ----- From: Thaneshwor Kaloni To: pw_forum at pwscf.org Sent: Monday, March 14, 2011 12:22 AM Subject: [Pw_forum] problem with degauss and magnetization Dear Quantum Espresso users, I am trying to get the magnetization by creating one vacancy in 5x5 supercell of graphene. With different values of degauss the total magnetization is changing surprisingly. Is there anything wrong with my input ?. Could anybody please tell me some references where I can read detail about smearing and degauss ?. The total magnetization with different degauss are given as below, degauss total magnetization 0.05 0.00 0.01 0.58 0.001 0.88 0.0001 0.88 I am posting my input file below. &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , outdir = 'OUT/', pseudo_dir = '/home/kaloni/pseudo/', prefix = 'g', tstress=.true., / &SYSTEM ibrav = 4, a=12.199359575, b= 12.199359575, c=19.999668786, cosab= -0.5, cosac =0.0 , cosbc=0.0, nat= 49, ntyp= 1, ecutwfc = 40, ecutrho = 400, nspin =2, starting_magnetization = 1.0, occupations='smearing', smearing=' gaussian', degauss=0.05, nosym = .true., / &ELECTRONS mixing_beta = 0.3 conv_thr = 1.0d-9 / ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF ATOMIC_POSITIONS (crystal) C -0.000437574 -0.000580938 0.000000015 C 0.000878501 0.200420327 -0.000000008 C 0.001210858 0.399950578 -0.000000071 C -0.000312205 0.599509065 0.000000002 C -0.000716730 0.798976722 0.000000025 C 0.199479935 -0.000986699 -0.000000031 C 0.200591611 0.200243356 0.000000020 C 0.204951004 0.399348478 -0.000000039 C 0.200756083 0.599210178 -0.000000027 C 0.199615366 0.799016660 0.000000045 C 0.399828248 -0.000558044 -0.000000011 C 0.399613916 0.200154971 0.000000014 C 0.401785094 0.599046302 -0.000000047 C 0.400264884 0.799510584 0.000000019 C 0.600023737 0.000445858 -0.000000037 C 0.599500576 0.200387180 0.000000030 C 0.594152084 0.399266958 0.000000290 C 0.597008286 0.598889370 0.000000057 C 0.600448742 0.800956977 -0.000000036 C 0.800386518 0.000445469 -0.000000021 C 0.800217273 0.200473648 -0.000000180 C 0.798607049 0.399927530 0.000000120 C 0.798270617 0.599140827 0.000000073 C 0.799080030 0.799392409 -0.000000024 C 0.132951308 0.065395469 0.000000019 C 0.133142262 0.266027786 -0.000000014 C 0.135800585 0.466331814 -0.000000062 C 0.133194345 0.665806346 0.000000014 C 0.132633945 0.865364014 0.000000018 C 0.332386006 0.065362305 -0.000000012 C 0.329787525 0.259493844 0.000000003 C 0.336738546 0.468697263 -0.000000042 C 0.333671463 0.665846245 -0.000000020 C 0.333143624 0.865895587 0.000000044 C 0.533078996 0.066642011 -0.000000019 C 0.532824452 0.265959049 0.000000110 C 0.531539380 0.468474465 0.000000226 C 0.534652606 0.669416138 -0.000000013 C 0.533415252 0.867317865 -0.000000015 C 0.733533974 0.067101960 -0.000000071 C 0.733185901 0.266889900 -0.000000007 C 0.730336277 0.466262841 0.000000196 C 0.731928945 0.665704201 0.000000020 C 0.733842050 0.867300592 -0.000000017 C 0.933534511 0.066657775 0.000000016 C 0.933667182 0.266910925 -0.000000085 C 0.933067875 0.466263286 0.000000000 C 0.932454196 0.665766534 0.000000004 C 0.932632612 0.865835315 0.000000008 K_POINTS AUTOMATIC 4 4 1 1 1 1 Thanks Thaneshwor Prashad Kaloni ------------------------------------------------------------------------------ _______________________________________________ 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/20110314/fc72fb82/attachment.htm From lfhuang at theory.issp.ac.cn Mon Mar 14 08:07:18 2011 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 14 Mar 2011 15:07:18 +0800 Subject: [Pw_forum] =?utf-8?q?A_small_bug_of_QE_when_nat_=3E=3D_100=2C_and?= =?utf-8?q?_the_solution?= Message-ID: <20110314070718.20231.qmail@ms.hfcas.ac.cn> Dear QEers: When I was calculating vibrational frequencies for a system with nat >= 100, I noticed a small bug of QE. The calculation steps were: (1) pw.x for scf electronic calculation; (2) ph.x for linear-response calculation; (3) q2r.x for the reciprocal-to-real transformation; Then, QE claimed that: ###################### from read_f: error # 1 wrong na read ###################### the error message may be different at some computers, like: ################# end of file during read ...... ################# Although this error information has been reported many times on the PW_FORUM, this time, it is caused by "nat >=100". (1) The cause When nat >=100, some lines in *.dyn[123...] file (which includes the reciprocal dynamical matrix) will be like that: ************************************** 34 99 0.00000113 0.00000000 -0.00000895 0.00000000 0.00000474 0.00000000 -0.00002272 0.00000000 -0.00002000 0.00000000 -0.00001948 0.00000000 0.00002366 0.00000000 -0.00002707 0.00000000 0.00006012 0.00000000 34100 0.00006484 0.00000000 -0.00000418 0.00000000 -0.00003671 0.00000000 -0.00000097 0.00000000 -0.00000993 0.00000000 0.00001364 0.00000000 0.00003728 0.00000000 -0.00000805 0.00000000 0.00002762 0.00000000 ************************************** the sencond pair of atomic indices above get close to each other. When execute q2r.x, these two numbers are read together as one number, which is the cause of the error. (2) The solution vi espresso/PH/q2r.f90 go to the Line 586, which is: **************************** READ(1,*) i,j **************************** change it to be **************************** READ(1,'(2i3)') i,j **************************** then, compile QE again. May this could be of a little help to you. Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 Our group: http://theory.issp.ac.cn ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110314/2f9e1dde/attachment-0001.htm From srijan.india at gmail.com Mon Mar 14 12:35:00 2011 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Mon, 14 Mar 2011 12:35:00 +0100 Subject: [Pw_forum] Phonon Dispersion with LO-TO splitting Message-ID: Dear QE USERS, The QE code takes note of the presence of Z* and epsilon in the dynamical matrix file and will add to the dynamical matrix the non-analytic part corresponding to the given *q*=>0. The 3-fold degenerate optical modes are now split by the LO-TO splitting. Here, I would like to know, whether during POST-PROCESSING, is it possible to manually add the values of the Born-effective charge and dielectric constant (which has been taken from the Experiments and not the computed ones) in the "dynamical matrix file" so that after POST-PROCESSING one can get a phonon dispersion curve taking into account the experimental values of the Z* and Dielectric constant ? If yes, then in which file and where, one should add the Z* and Dielectric constant manually ? Looking forward to your kind reply. Thanking you and with my best regards, Srijan Kumar R&D Assistant JNCASR Bangalore 560064 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110314/abfb1c70/attachment.htm From giannozz at democritos.it Mon Mar 14 12:55:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Mar 2011 12:55:46 +0100 Subject: [Pw_forum] A small bug of QE when nat >= 100, and the solution In-Reply-To: <20110314070718.20231.qmail@ms.hfcas.ac.cn> References: <20110314070718.20231.qmail@ms.hfcas.ac.cn> Message-ID: <4D7E0242.8090605@democritos.it> lfhuang wrote: > When I was calculating vibrational frequencies for a system with > nat >= 100, I noticed a small bug of QE. which version? I think something simliar was fixed some time ago P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From ranjit.phy at gmail.com Mon Mar 14 13:08:57 2011 From: ranjit.phy at gmail.com (Ranjit Thapa) Date: Mon, 14 Mar 2011 17:38:57 +0530 Subject: [Pw_forum] parallel use of quanum espresso Message-ID: dear all, I am new about quantum espresso. I make a cluster for practice with two CPU (first one intel i7 processor (i.e 8 core) and other pentium IV processor (single core)). I run an example given in MPICH2-1.3.2. The results is well, i.e both the processor process and give the result. After that i load Quantum Espresso-4.2.1. It detect mpi parallel enviroment when i run an example given in the QE examples folder, using the comand ./run_example the reults is well but it only excute in 1 processor (but mpi is detected). I think have to use mpiexec command but, i am not able to find what command should i give for running the example in my cluster sytem (two different type of CPU). please help me -- Dr. Ranjit Thapa Research Associate Materials Simulation Lab. Department of Materials Science Indian Association for the Cultivation of Science KOL-700032 Mobile No: +91 9593936060, +91 9804101030 http://sites.google.com/site/ranjitphy/home -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110314/1a3e3a92/attachment.htm From eyvaz_isaev at yahoo.com Mon Mar 14 13:54:43 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 14 Mar 2011 05:54:43 -0700 (PDT) Subject: [Pw_forum] Phonon Dispersion with LO-TO splitting Message-ID: <921564.73512.qm@web65702.mail.ac4.yahoo.com> Dear Srijan, Z* and \epsilon, therefore, LO-TO splitting are for semiconductors/insulators. As you know, all valence bands are occupied, and conductivity bands are empty. Thus, you can omit the smearing keyword to let pw.x know that you deal with a semiconductor. Then you will got dyn1-file with Z* and \epsion, q2r.x and matdyn.x will take care about these parameters and LO-TO splitting. Having IFC (*.fc) file you can edit Z* and \epsilon. See example06 and /Doc/PH.txt. Best regards, Eyvaz. P.S. So, they are not related with postprocessing ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: Srijan Kumar Saha To: PWSCF Forum Sent: Mon, March 14, 2011 2:35:00 PM Subject: [Pw_forum] Phonon Dispersion with LO-TO splitting Dear QE USERS, The QE code takes note of the presence of Z* and epsilon in the dynamical matrix file and will add to the dynamical matrix the non-analytic part corresponding to the given q=>0. The 3-fold degenerate optical modes are now split by the LO-TO splitting. Here, I would like to know, whether during POST-PROCESSING, is it possible to manually add the values of the Born-effective charge and dielectric constant (which has been taken from the Experiments and not the computed ones) in the "dynamical matrix file" so that after POST-PROCESSING one can get a phonon dispersion curve taking into account the experimental values of the Z* and Dielectric constant ? If yes, then in which file and where, one should add the Z* and Dielectric constant manually ? Looking forward to your kind reply. Thanking you and with my best regards, Srijan Kumar R&D Assistant JNCASR Bangalore 560064 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110314/279344af/attachment.htm From nazari at iasbs.ac.ir Mon Mar 14 14:43:02 2011 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Mon, 14 Mar 2011 17:13:02 +0330 (IRST) Subject: [Pw_forum] phonon/reducing the number of normal modes In-Reply-To: <921564.73512.qm@web65702.mail.ac4.yahoo.com> References: <921564.73512.qm@web65702.mail.ac4.yahoo.com> Message-ID: <45799.85.185.211.90.1300110182.squirrel@mail.iasbs.ac.ir>
Dear all, Is it possible in phonon calculation?frequency of?restricted number?of atoms in the system are calculated? regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110314/0f0d51a8/attachment.htm From eyvaz_isaev at yahoo.com Mon Mar 14 15:31:43 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 14 Mar 2011 07:31:43 -0700 (PDT) Subject: [Pw_forum] phonon/reducing the number of normal modes In-Reply-To: <45799.85.185.211.90.1300110182.squirrel@mail.iasbs.ac.ir> References: <921564.73512.qm@web65702.mail.ac4.yahoo.com> <45799.85.185.211.90.1300110182.squirrel@mail.iasbs.ac.ir> Message-ID: <35713.14939.qm@web65714.mail.ac4.yahoo.com> Dear Fariba, It is possible. Please have a look at /DOC/INPUT_PH.txt for more details. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: "nazari at iasbs.ac.ir" To: PWSCF Forum Sent: Mon, March 14, 2011 4:43:02 PM Subject: [Pw_forum] phonon/reducing the number of normal modes Dear all, Is it possible in phonon calculation frequency of restricted number of atoms in the system are calculated? regards Fariba Nazari IASBS -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110314/ad57d321/attachment.htm From srijan.india at gmail.com Mon Mar 14 15:42:12 2011 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Mon, 14 Mar 2011 15:42:12 +0100 Subject: [Pw_forum] Phonon Dispersion with LO-TO splitting In-Reply-To: <921564.73512.qm@web65702.mail.ac4.yahoo.com> References: <921564.73512.qm@web65702.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz, Thanks a lot for your helpful reply. > Z* and \epsilon, therefore, LO-TO splitting are for semiconductors/insulators. > As you know, all valence bands are occupied, and conductivity bands are empty. Thus, > you can omit the smearing keyword to let pw.x know that you deal with a semiconductor. I agree with you. However, in practice, sometime smearing keyword needs to be used for a complicated semiconductor or insulator in order get a faster scf convergence. And hence, it is better to identify a system is non-metal or metal by its band-gap instead of smearing keyword. In particular, phonon code in QE complain a lot if the system is a spin-polarized insulator. For example, "fixed occupations and lsda need tot_magnetization", "The phonon code with constrained magnetization is not yet available", " IF (epsil.AND.lgauss) & CALL errore ('phq_readin', 'no elec. field with metals', 1)", etc. etc. Atleast for the last error, I guess, it is better if we write, " IF (epsil.AND.gap_zero) & CALL errore ('phq_readin', 'no elec. field with metals', 1)" in place of the current existing statement. Then it will give a chance to compute \epsil also for an insulating system which uses "smearing" keyword just for faster convergence. > See example06 For magnetic insulator, is there any further example which shows a phonon-dispersion with LO-TO splitting ? > P.S. So, they are not related with postprocessing I meant, postprocessing after ph.x. I thought, q2r.x and matdyn.x, plotband.x as post-processing of phonon code (ph.x) . Thanking you and with my best regards, Srijan Kumar R&D Assistant JNCASR Bangalore 560064 On Mon, Mar 14, 2011 at 1:54 PM, Eyvaz Isaev wrote: > Dear Srijan, > > Z* and \epsilon, therefore, LO-TO splitting are for > semiconductors/insulators. > As you know, all valence bands are occupied, and conductivity bands are > empty. Thus, > you can omit the smearing keyword to let pw.x know that you deal with a > semiconductor. > Then you will got dyn1-file with Z* and \epsion, q2r.x and matdyn.x will > take care about these > parameters and LO-TO splitting. > > Having IFC (*.fc) file you can edit Z* and \epsilon. > > See example06 and /Doc/PH.txt. > > Best regards, > Eyvaz. > P.S. So, they are not related with postprocessing > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110314/93a3669d/attachment-0001.htm From lfhuang at theory.issp.ac.cn Mon Mar 14 16:00:52 2011 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 14 Mar 2011 23:00:52 +0800 Subject: [Pw_forum] =?utf-8?q?A_small_bug_of_QE_when_nat_=3E=3D_100=2C_and?= =?utf-8?q?_the_solution?= Message-ID: <20110314150052.15348.qmail@ms.hfcas.ac.cn> Dear prof. P. Giannozzi: > From: Paolo Giannozzi > which version? I think something simliar was fixed some time ago versions 4.2.1, 4.1.1, 3.2.3 I have not read newer versions. Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 Our group: http://theory.issp.ac.cn ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110314/0f4c3e41/attachment.htm From giannozz at democritos.it Mon Mar 14 17:41:19 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Mar 2011 17:41:19 +0100 Subject: [Pw_forum] A small bug of QE when nat >= 100, and the solution In-Reply-To: <20110314150052.15348.qmail@ms.hfcas.ac.cn> References: <20110314150052.15348.qmail@ms.hfcas.ac.cn> Message-ID: <4D7E452F.2000503@democritos.it> It is fixed in the forthcoming new version (the correct fix is to increase the format when writing rather than use a fixed format when reading). Thank you anyway for reporting this P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From lfhuang at theory.issp.ac.cn Mon Mar 14 18:48:26 2011 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 15 Mar 2011 1:48:26 +0800 Subject: [Pw_forum] =?utf-8?q?A_small_bug_of_QE_when_nat_=3E=3D_100=2C_and?= =?utf-8?q?_the_solution?= Message-ID: <20110314174826.21503.qmail@ms.hfcas.ac.cn> Dear prof. P. Giannozzi: This bug also has not been fixed in the recent Version-4.3a, which I download from www.pwscf.org just now. Please look at the Line 708 of q2r.f90 in this version: ************************************* IF (ionode) READ(1,*) i,j ************************************* after change it to: ************************************* IF (ionode) READ(1,'(2i3)') i,j *************************************q2r.x can work for systems with nat>=100. > From: Paolo Giannozzi > which version? I think something simliar was fixed some time ago Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 Our group: http://theory.issp.ac.cn ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110315/645219aa/attachment.htm From giannozz at democritos.it Mon Mar 14 19:02:01 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 14 Mar 2011 19:02:01 +0100 Subject: [Pw_forum] A small bug of QE when nat >= 100, and the solution In-Reply-To: <20110314174826.21503.qmail@ms.hfcas.ac.cn> References: <20110314174826.21503.qmail@ms.hfcas.ac.cn> Message-ID: <4D7E5819.1030203@democritos.it> lfhuang wrote: > This bug also has not been fixed in the recent Version-4.3a this is the fix: $ diff espresso-4.2.1/PH/write_dyn_on_file.f90 espresso/PH/ 29c29 < write (iudyn, '(2i3)') na, nb --- > write (iudyn, '(2i5)') na, nb P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From nicola.marzari at materials.ox.ac.uk Mon Mar 14 19:07:49 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Mon, 14 Mar 2011 18:07:49 +0000 Subject: [Pw_forum] A small bug of QE when nat >= 100, and the solution In-Reply-To: <4D7E5819.1030203@democritos.it> References: <20110314174826.21503.qmail@ms.hfcas.ac.cn> <4D7E5819.1030203@democritos.it> Message-ID: <4D7E5975.50208@materials.ox.ac.uk> On 3/14/11 6:02 PM, Paolo Giannozzi wrote: > lfhuang wrote: > >> This bug also has not been fixed in the recent Version-4.3a > > this is the fix: > > $ diff espresso-4.2.1/PH/write_dyn_on_file.f90 espresso/PH/ > 29c29 > < write (iudyn, '(2i3)') na, nb > --- > > write (iudyn, '(2i5)') na, nb > > I tried it, but it doesn't work when nat>= 10000 . What shall I do? Please help. nicola -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From eyvaz_isaev at yahoo.com Mon Mar 14 21:36:32 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 14 Mar 2011 13:36:32 -0700 (PDT) Subject: [Pw_forum] Phonon Dispersion with LO-TO splitting In-Reply-To: References: <921564.73512.qm@web65702.mail.ac4.yahoo.com> Message-ID: <382234.60607.qm@web65714.mail.ac4.yahoo.com> Dear Srijan, > Thanks a lot for your helpful reply. You are welcome. >However, in practice, sometime smearing keyword needs to be used for a >complicated >semiconductor or insulator in order get a faster scf convergence. And hence, >it is better to identify a system is non-metal or metal by its band-gap instead >of smearing > >keyword. As you were interested in LO-TO splitting, in fact, I meant the Gamma point calculation only. >In particular, phonon code in QE complain a lot if the system is a >spin-polarized insulator. > >For example, "fixed occupations and lsda need tot_magnetization", >"The phonon code with constrained magnetization is not yet available", Yes, agree. Such kind systems still seem to be problematic. At least, to me. > " IF (epsil.AND.lgauss) & CALL errore ('phq_readin', 'no elec. field with >metals', 1)", etc. etc. But this one is correct from the physical basics. See any good textbook on solid state physics, or review by S.Baroni, , S. de Girocoli, A. Dal Corso and P. Giannozzi, Rev.Mod.Phys., 73, 515, 2001. >At least for the last error, I guess, it is better if we write, > " IF (epsil.AND.gap_zero) & CALL errore ('phq_readin', 'no elec. field with >metals', 1)" > in place of the current existing statement. Then it will give a chance to >compute \epsil also for > > an insulating system which uses "smearing" keyword just for faster convergence. I am not sure, this will fix the convergence problem. Besides, see the above-mentioned comment. This prevents an attempt to calculate Z* and \epsilon for metallic systems and is correct. >For magnetic insulator, is there any further example which shows a >phonon-dispersion with LO-TO splitting ? > In fact, I do not remember any such kind example. Bests, Eyvaz, ______________________________________ Departmenmt of Physics, Chemistry and Biology, Linkoping University, Sweden eyvaz_isaev at yahoo.com, isaev at ifm.liu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110314/d57bf69e/attachment.htm From jasotelo at gmail.com Mon Mar 14 21:54:04 2011 From: jasotelo at gmail.com (juan sotelo) Date: Mon, 14 Mar 2011 15:54:04 -0500 Subject: [Pw_forum] A small bug of QE when nat >= 100, and the solution In-Reply-To: <4D7E5975.50208@materials.ox.ac.uk> References: <20110314174826.21503.qmail@ms.hfcas.ac.cn> <4D7E5819.1030203@democritos.it> <4D7E5975.50208@materials.ox.ac.uk> Message-ID: It seems the problem could be solved by creating a fortran-format on the fly, e.g., ===== program foo ! hints from http://www.sdsc.edu/~tkaiser/f90.html implicit none character (len=30)fstr ! create a format on the fly integer n_dgts, na, nb na = 30000 nb = 1000000 n_dgts = floor(log10(abs(real(max(na,nb)))))+1 !create a format on the fly write(fstr,'("(2i",i4,")")')n_dgts+1 write(*,fstr) na, nb end program ===== Output: 30000 1000000 juan sotelo Dpto Fisica & Informatica & Matematica Univ. Per. Cayetano Heredia. Lima-Peru On Mon, Mar 14, 2011 at 1:07 PM, Nicola Marzari wrote: > On 3/14/11 6:02 PM, Paolo Giannozzi wrote: >> lfhuang wrote: >> >>> This bug also has not been fixed in the recent Version-4.3a >> >> this is the fix: >> >> $ diff espresso-4.2.1/PH/write_dyn_on_file.f90 espresso/PH/ >> 29c29 >> < ? ? ? ? ?write (iudyn, '(2i3)') na, nb >> --- >> ? > ? ? ? ? ?write (iudyn, '(2i5)') na, nb >> >> > > I tried it, but it doesn't work when nat>= 10000 . > What shall I do? Please help. > > ? ? ? ? ? ? ? ? ? ? ? ?nicola > > > -- > ---------------------------------------------------------------------- > Prof Nicola Marzari ? ?Department of Materials ? ?University of Oxford > Chair of Materials Modelling ?Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk ? ? http://mml.materials.ox.ac.uk/NM > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From ranjit.phy at gmail.com Tue Mar 15 10:17:06 2011 From: ranjit.phy at gmail.com (Ranjit Thapa) Date: Tue, 15 Mar 2011 14:47:06 +0530 Subject: [Pw_forum] parallel Message-ID: dear all, I am new about quantum espresso. I make a cluster for practice with two CPU (first one intel i7 processor (i.e 8 core) and other pentium IV processor (single core)). I run an example given in MPICH2-1.3.2. The results is well, i.e both the processor process and give the result. After that i load Quantum Espresso-4.2.1. It detect mpi parallel enviroment when i run an example given in the QE examples folder, using the comand ./run_example the reults is well but it only excute in 1 processor (but mpi is detected). I think have to use mpiexec command but, i am not able to find what command should i give for running the example in my cluster sytem (two different type of CPU). please help me -- Dr. Ranjit Thapa Research Associate Materials Simulation Lab. Department of Materials Science Indian Association for the Cultivation of Science KOL-700032 Mobile No: +91 9593936060, +91 9804101030 http://sites.google.com/site/ranjitphy/home -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110315/4f4a8014/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Tue Mar 15 10:24:52 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 15 Mar 2011 10:24:52 +0100 Subject: [Pw_forum] parallel In-Reply-To: References: Message-ID: In data 15 marzo 2011 alle ore 10:17:06, Ranjit Thapa ha scritto: > I think have to use mpiexec command but, i am not able to find what > command should i give for running the example in my cluster sytem (two > different > type of CPU). Dear Ranjit, it's all explained in examples/README, section 2. It's all about editing the file "nvironment_variables". best regards -- Lorenzo Paulatto post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously (take note of the change!): phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From sclauzer at sissa.it Tue Mar 15 10:39:18 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 15 Mar 2011 10:39:18 +0100 Subject: [Pw_forum] A small bug of QE when nat >= 100, and the solution In-Reply-To: References: <20110314174826.21503.qmail@ms.hfcas.ac.cn> <4D7E5819.1030203@democritos.it> <4D7E5975.50208@materials.ox.ac.uk> Message-ID: <31C2FBE0-A135-445D-8028-744D1D120088@sissa.it> Il giorno 14/mar/2011, alle ore 21.54, juan sotelo ha scritto: > It seems the problem could be solved by creating a fortran-format on > the fly, e.g., > ===== > program foo > ! hints from http://www.sdsc.edu/~tkaiser/f90.html > implicit none > character (len=30)fstr ! create a format on the fly > integer n_dgts, na, nb > na = 30000 > nb = 1000000 > n_dgts = floor(log10(abs(real(max(na,nb)))))+1 > !create a format on the fly > write(fstr,'("(2i",i4,")")')n_dgts+1 > write(*,fstr) na, nb > end program > ===== > Output: > 30000 1000000 This is a nice trick, but I'm not sure that all compilers will accept it. I remember complaints about the fact that the format string should be either a constant string or a pointer to a format line. Just for information, on which compilers have you tried? Thanks, GS ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110315/e74236cd/attachment.htm From johnsondr at ornl.gov Tue Mar 15 14:52:26 2011 From: johnsondr at ornl.gov (Johnson, D. Ray) Date: Tue, 15 Mar 2011 09:52:26 -0400 Subject: [Pw_forum] Pw_forum Subscription Message-ID: Please change my email address to: D Ray Johnson, drjsej at hughes.net Thank you. Regards, D Ray Johnson The Oak Ridge National Lab Oak Ridge, TN USA From degironc at sissa.it Tue Mar 15 15:02:46 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 15 Mar 2011 15:02:46 +0100 Subject: [Pw_forum] Pw_forum Subscription In-Reply-To: References: Message-ID: <4D7F7186.30508@sissa.it> unsubscribe and subscribe with the new address. cheers, stefano On 03/15/2011 02:52 PM, Johnson, D. Ray wrote: > Please change my email address to: D Ray Johnson, drjsej at hughes.net > Thank you. > > Regards, > > D Ray Johnson > The Oak Ridge National Lab > Oak Ridge, TN > USA > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Tue Mar 15 15:08:20 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Mar 2011 15:08:20 +0100 Subject: [Pw_forum] Pw_forum Subscription In-Reply-To: <4D7F7186.30508@sissa.it> References: <4D7F7186.30508@sissa.it> Message-ID: <4D7F72D4.2030905@democritos.it> Stefano de Gironcoli wrote: > unsubscribe and subscribe with the new address. no longer true, I think: it used to be not possible for a subscriber (and not even for the administator) to change the subscription address, but now everybody can do it. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From amiri_physics at yahoo.com Tue Mar 15 15:38:01 2011 From: amiri_physics at yahoo.com (peyman amiri) Date: Tue, 15 Mar 2011 07:38:01 -0700 (PDT) Subject: [Pw_forum] smearing Message-ID: <733035.72917.qm@web161715.mail.bf1.yahoo.com> Dear all users Can i use? " occupations='tetrahedra' " in my scf input file? i use this option and encounter with the message below: { from iosys : error #???????? 1 ???? tetrahedra should be used only for calculation of DOS} What is wrong? Thanks in advance ====================================== Peiman Amiri Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Iran Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 ------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110315/da4e3bc6/attachment.htm From max.n.popov at gmail.com Tue Mar 15 16:11:20 2011 From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=) Date: Tue, 15 Mar 2011 16:11:20 +0100 Subject: [Pw_forum] smearing In-Reply-To: <733035.72917.qm@web161715.mail.bf1.yahoo.com> References: <733035.72917.qm@web161715.mail.bf1.yahoo.com> Message-ID: Dear Peiman, yes, you can. In order to do so, one has to comment the following (two) lines in PW/input.f90: IF( calculation /= 'nscf' ) CALL errore( 'iosys', & 'tetrahedra should be used only for calculation of DOS', 1 ) and recompile the code again. Mind, that 'tetrahedra' has to be used for DOS or SCF only, forces and stresses are not reliable it this case (they are not variational). Best regards, Maxim. 2011/3/15 peyman amiri > > Dear all users > Can i use " occupations='tetrahedra' " > in my scf input file? i use this option and encounter with the message > below: > > { from iosys : error # 1 > tetrahedra should be used only for calculation of DOS} > What is wrong? > Thanks in advance > ====================================== > Peiman Amiri > Computational Condensed Matter Research Lab > Physics Department, Isfahan University of Technology, Iran > > Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best regards, Max Popov Ph.D. student Materials center Leoben (MCL), Leoben, Austria. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110315/5474db58/attachment.htm From lfhuang at theory.issp.ac.cn Tue Mar 15 16:47:05 2011 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Tue, 15 Mar 2011 23:47:05 +0800 Subject: [Pw_forum] =?utf-8?q?sorting_phonons_by_magnitude_and_band_index?= Message-ID: <20110315154705.4016.qmail@ms.hfcas.ac.cn> Dear QEers: Sorting phonons by magnitude and band index are two ways to plot phonon dispersions. Especially, the later is important for the precise understanding of phonons and for the calculation of some physical parameters, like Gruneissen constants. I have written a small code (named sort_phon) to do these sorting tasks, which needs the output of Quantum ESPRESSO (matdyn.modes) as input. The code package can be download in the link below: http://bbs.sciencenet.cn/home.php?mod=space&uid=345795&do=blog&quickforward=1&id=422819 where an introductory tutorial and an example about graphene phonon dispersions is included. I sincerely hope it could bring you some convenience in your daily research. Best Wishes! Yours Sincerely L. F. Huang ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 Our group: http://theory.issp.ac.cn ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110315/bdd8d8f4/attachment-0001.htm From iurii.timrov at polytechnique.edu Tue Mar 15 18:46:35 2011 From: iurii.timrov at polytechnique.edu (Iurii TIMROV) Date: Tue, 15 Mar 2011 18:46:35 +0100 Subject: [Pw_forum] smearing In-Reply-To: References: <733035.72917.qm@web161715.mail.bf1.yahoo.com> Message-ID: Dear Maxim, Dear All, > yes, you can. In order to do so, one has to comment the following (two) > lines in PW/input.f90: > > IF( calculation /= 'nscf' ) CALL errore( 'iosys', & > 'tetrahedra should be used only for calculation of DOS', 1 ) > These lines are present in PW/input.f90 of espresso-4.2.1 In espresso-4.3a you will find somewhat different: ! replace "errore" with "infomsg" in the next line if you really want ! to perform a calculation with forces using tetrahedra ! IF( lforce ) CALL errore( 'iosys', & 'force calculation with tetrahedra not recommanded: use smearing',1) > Mind, that 'tetrahedra' has to be used for DOS or SCF only, forces and > stresses are > not reliable it this case (they are not variational). Could you recommend some paper where this statement was mentioned/discussed/proved? Thanks! Best regards, Iurii Timrov Iurii TIMROV Doctorant (PhD student) Laboratoire des Solides Irradies Ecole Polytechnique F-91128 Palaiseau +33 1 69 33 45 08 timrov at theory.polytechnique.fr From ttduyle at gmail.com Tue Mar 15 18:55:10 2011 From: ttduyle at gmail.com (Duy Le) Date: Tue, 15 Mar 2011 13:55:10 -0400 Subject: [Pw_forum] smearing In-Reply-To: References: <733035.72917.qm@web161715.mail.bf1.yahoo.com> Message-ID: On Tue, Mar 15, 2011 at 1:46 PM, Iurii TIMROV wrote: >> Mind, that 'tetrahedra' has to be used for DOS or SCF only, forces and >> stresses are >> not reliable it this case (they are not variational). > > Could you recommend some paper where this statement was > mentioned/discussed/proved? Thanks! > Should be in the original paper about this method, by Bl?chl et al 1994 -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" From agkvashnin at gmail.com Tue Mar 15 18:59:00 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Tue, 15 Mar 2011 20:59:00 +0300 Subject: [Pw_forum] smearing In-Reply-To: References: <733035.72917.qm@web161715.mail.bf1.yahoo.com> Message-ID: Dear all, When I used occupations='tetrahedra' in my scf calculation, everything was OK. And in another scf calculation I had the same error. I don't understand, why this error appear in one case and disappear in another. Can you explain me this situation, please? Thanks. 2011/3/15 ?????? ????? > Dear Peiman, > > yes, you can. In order to do so, one has to comment the following (two) > lines in PW/input.f90: > > IF( calculation /= 'nscf' ) CALL errore( 'iosys', & > 'tetrahedra should be used only for calculation of DOS', 1 ) > > and recompile the code again. > Mind, that 'tetrahedra' has to be used for DOS or SCF only, forces and > stresses are > not reliable it this case (they are not variational). > > Best regards, > Maxim. > > 2011/3/15 peyman amiri > >> >> Dear all users >> Can i use " occupations='tetrahedra' " >> in my scf input file? i use this option and encounter with the message >> below: >> >> { from iosys : error # 1 >> tetrahedra should be used only for calculation of DOS} >> What is wrong? >> Thanks in advance >> ====================================== >> Peiman Amiri >> Computational Condensed Matter Research Lab >> Physics Department, Isfahan University of Technology, Iran >> >> Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 >> ------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Best regards, Max Popov > Ph.D. student > Materials center Leoben (MCL), Leoben, Austria. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Sincerely yours Alexander G. Kvashnin -------------------------------------------------------------------------------------------------------------------------------- Student Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110315/be781ac8/attachment.htm From giannozz at democritos.it Tue Mar 15 19:00:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Mar 2011 19:00:46 +0100 Subject: [Pw_forum] smearing In-Reply-To: References: <733035.72917.qm@web161715.mail.bf1.yahoo.com> Message-ID: <4D7FA94E.7090005@democritos.it> Alexander G. Kvashnin wrote: > When I used occupations='tetrahedra' in my scf calculation, everything > was OK. And in another scf calculation I had the same error. > I don't understand, why this error appear in one case and disappear in > another. Can you explain me this situation, please? you have the error, you explain ... P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From max.n.popov at gmail.com Tue Mar 15 19:00:55 2011 From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=) Date: Tue, 15 Mar 2011 19:00:55 +0100 Subject: [Pw_forum] smearing In-Reply-To: References: <733035.72917.qm@web161715.mail.bf1.yahoo.com> Message-ID: Dear Iurii, thanks for the info! You can look in the original paper by P. Bloechl: PRB 49, 16223-16233(1994) (http://prb.aps.org/abstract/PRB/v49/i23/p16223_1). Best regards, Maxim. 2011/3/15 Iurii TIMROV > Dear Maxim, Dear All, > > > yes, you can. In order to do so, one has to comment the following (two) > > lines in PW/input.f90: > > > > IF( calculation /= 'nscf' ) CALL errore( 'iosys', & > > 'tetrahedra should be used only for calculation of DOS', 1 ) > > > > These lines are present in PW/input.f90 of espresso-4.2.1 > > In espresso-4.3a you will find somewhat different: > > ! replace "errore" with "infomsg" in the next line if you really want > ! to perform a calculation with forces using tetrahedra > ! > IF( lforce ) CALL errore( 'iosys', & > 'force calculation with tetrahedra not recommanded: use smearing',1) > > > Mind, that 'tetrahedra' has to be used for DOS or SCF only, forces and > > stresses are > > not reliable it this case (they are not variational). > > Could you recommend some paper where this statement was > mentioned/discussed/proved? Thanks! > > Best regards, > Iurii Timrov > > > Iurii TIMROV > Doctorant (PhD student) > Laboratoire des Solides Irradies > Ecole Polytechnique > F-91128 Palaiseau > +33 1 69 33 45 08 > timrov at theory.polytechnique.fr > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best regards, Max Popov Ph.D. student Materials center Leoben (MCL), Leoben, Austria. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110315/12e4931e/attachment.htm From giannozz at democritos.it Tue Mar 15 19:05:50 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Mar 2011 19:05:50 +0100 Subject: [Pw_forum] smearing In-Reply-To: References: <733035.72917.qm@web161715.mail.bf1.yahoo.com> Message-ID: <4D7FAA7E.4000908@democritos.it> Iurii TIMROV wrote: > In espresso-4.3a you will find somewhat different: I was fed up with the question "why can't I use tetrahedra in scf calculations". You want tetrahedra? we'll give you tetrahedra. After all as long as you do not calculate forces, things are ok (in principle and in practise; if you calculate forces they might also be ok in practice, not in principle) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 15 19:41:12 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 15 Mar 2011 19:41:12 +0100 Subject: [Pw_forum] How to read two wave-functions in one program? In-Reply-To: References: Message-ID: <4D7FB2C8.6070502@democritos.it> xuhui luo wrote: > I have a problem about fortran coding for reading two set of > wave-functions in one program. it depends upon what exactly you need. You may try to take inspiration from code PP/bands.f90, which does something similar P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From jasotelo at gmail.com Tue Mar 15 20:22:09 2011 From: jasotelo at gmail.com (juan sotelo) Date: Tue, 15 Mar 2011 14:22:09 -0500 Subject: [Pw_forum] A small bug of QE when nat >= 100, and the solution In-Reply-To: <31C2FBE0-A135-445D-8028-744D1D120088@sissa.it> References: <20110314174826.21503.qmail@ms.hfcas.ac.cn> <4D7E5819.1030203@democritos.it> <4D7E5975.50208@materials.ox.ac.uk> <31C2FBE0-A135-445D-8028-744D1D120088@sissa.it> Message-ID: > Just for information, on which compilers have you tried? GNU Fortran 4.5.0 Intel ifort 11.1.073 Both on a linux box with OpenSUSE 11.3 x64 juan sotelo Dpto. de Fisica&Informatica&Matematica Univ. Per. Cayetano Heredia. Lima-Peru From Heiles at cluster.pc.chemie.tu-darmstadt.de Tue Mar 15 22:21:04 2011 From: Heiles at cluster.pc.chemie.tu-darmstadt.de (Sven Heiles) Date: Tue, 15 Mar 2011 22:21:04 +0100 Subject: [Pw_forum] Bi pseudopotential In-Reply-To: <4D78E36F.2010509@cluster.pc.chemie.tu-darmstadt.de> References: <4D78E36F.2010509@cluster.pc.chemie.tu-darmstadt.de> Message-ID: <4D7FD840.1040404@cluster.pc.chemie.tu-darmstadt.de> Hi Paolo, Emine! Thanks for your reply tested your suggested US-PP which seem to work quite good. Will have a look tomorrow on the performance for the dimer and the bulk. Yesterday evening in a long night season I was able to find the problem with my parameters and was able to fit a multiple projector, scalar relativistic NC-PP for LDA and PBE functionals. The performance of the PPs seem to be good (only judging on the geometrical parameters; the electronic structure is a complete different topic of course) Bi2 (bondlength): PP-LDA PP-PBE PBE-Lanl2DZ Exp [1] 2.57 AA 2.636 AA 2.64 AA 2.66 AA Bi-A7 phase (see parameters in [2]) PP-LDA PP-PBE Theo[2] Exp[2] a0 = 4.573 AA a0 = 4.766 AA ao= 4.528 AA ao= 4.726 AA alpha = 58.271 alpha = 57.454 alpha = 58.93 alpha = 57.32 z = 0.237 z = 0.235 z = 0.238 z = 0.238 [1] Chem. Rev. 90 93 1990 [2] Phys. Scr. 37 785 1988 Thanks a lot again for your suggestions. Best wishes Sven Am 10.03.2011 15:42, schrieb Sven Heiles: > Dear QE users. > > Our group started to use QE and tries to combine the code with a global > structural search routine. For this purpose > valence only pseudopotentials (PP) optimized for a low energy cutoff has > to be used (at the cost of computational correcetness of > course). As a test case we want to start with Bi. For this element only > a relatively hard PP exists which incoperates a d semicore > state. Since the converted FHI PP 5-electron PPs does not work very well > I decided to try to create a own PP. > > Have done the tutorial for Si and the example calculation for Ti and > everything seemed to work all right. Because I am not very > familiar with the theory of the PP fitting routines I tried to progress > for Bi in the same manner as for Si and Ti. So I started with: > > &input > iswitch=3, rlderiv=2.20, eminld=-2.0,emaxld=1.0,deld=0.01d0,nld=3, > rel=1,zed=83.0,config="[Xe] 4f14 5d10 6s2 6p3 6d-1",dft='PBE', > / > &inputp > lloc=2,pseudotype=1,file_pseudopw='Bi.pbe-n-rrkj.UPF', zval=5.0,rho0=0.01 > / > 3 > 6S 1 0 2.00 0.00 2.20 2.20 > 6P 2 1 3.00 0.00 2.20 2.20 > 6D 3 2 0.00 -0.10 2.20 2.20 > > But unfourtunately this input file produces the error "phi has nodes > before r_c". Therefore > tried to change rho0 , rcore and rcut systematically without success. > Therefore used tm=.true. > which produced a PP which looked good. Depressingly the TM potential > failed to converge for > test calculations for the dimer. Therefore changed the following things > in the input: > config="[Xe] 4f14 5d10 6s2 6p3", lloc=1, and got rid of the 6D in the PP > card. > In this way I am able to generate a PP. The wavefunctions and the logDev > look ok. But the performance > for the Dimer is not really good (40 Ry Ecutoff, RhoCutoff= 8*Ecutoff) > -> 2.52 AA bondlength compared to > 2.66 AA experimentally. For example a Lanl2DZ calculation in NWChem with > the same functional yields > 2.64 AA. Additionally any influence of the 6D state is not descibed with > the potential. > > Every time I want to change the settings for the PP the program produces > an error. I am not able so far to write > in the 6D channel or in two channels (pseudotype=2) or to generate a > US-PP (pseudotype=3). > > Since I am far away from beeing an expert and this are only my first > attempts I wondered if someone has > any suggestions what I could try to improve the PP for Bi step by step. > > Best wishes > > Sven > -- Dipl. Ing. Sven Heiles Technische Universit?t Darmstadt AK Sch?fer Eduard-Zintl-Institut Petersenstra?e 20 D-64287 Darmstadt ? Germany Phone: ++49-(0)6151-164397 Fax: ++49-(0)6151-166024 Web: http://www.tu-darmstadt.de/fb/ch/cluster/schaefer.tud From luoxuhui at uic.edu Wed Mar 16 01:11:58 2011 From: luoxuhui at uic.edu (xuhui luo) Date: Tue, 15 Mar 2011 20:11:58 -0400 Subject: [Pw_forum] How to read two wave-functions in one program? Message-ID: Dear Paolo Giannozzi, Thanks for your reply. I just looked at bands.f90. The purpose of bands.f90 is to check the band correspondence by taking inner product of (n,k) and (n',k') states in one structure. But what I would like to do is to taking inner product of (n,k) from one structure and (n',k') from another perturbed structure. Thus I need to read two set of wavefunction at the same time. Do you have suggestions to deal with this situation? Thank you! >it depends upon what exactly you need. You may try to take >inspiration from code PP/bands.f90, which does something similar Xuhui Luo University of Illinois at Chicago and NIST From eariel99 at gmail.com Wed Mar 16 03:50:25 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Tue, 15 Mar 2011 23:50:25 -0300 Subject: [Pw_forum] smearing Message-ID: Alexander, I guess You have used different versions of PWSCF. There have been recent changes in the use of tetrahedra http://www.democritos.it/pipermail/pw_forum/2010-October/018478.html > ---------- Mensaje reenviado ---------- > From: "Alexander G. Kvashnin" > To: PWSCF Forum > Date: Tue, 15 Mar 2011 20:59:00 +0300 > Subject: Re: [Pw_forum] smearing > Dear all, > > When I used occupations='tetrahedra' in my scf calculation, everything was > OK. And in another scf calculation I had the same error. > I don't understand, why this error appear in one case and disappear in > another. > Can you explain me this situation, please? > Thanks. > > > -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110315/aa5e3859/attachment.htm From giannozz at democritos.it Wed Mar 16 08:28:13 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Mar 2011 08:28:13 +0100 Subject: [Pw_forum] How to read two wave-functions in one program? In-Reply-To: References: Message-ID: <85531BCA-7504-4C8A-8D87-EB3C4C9F51F4@democritos.it> On Mar 16, 2011, at 1:11 , xuhui luo wrote: > > But what I would like to do is to taking inner product of (n,k) > from one structure and (n',k') from another perturbed structure. > Thus I need to read two set of wavefunction at the same time. > Do you have suggestions to deal with this situation? > save wavefunctions in real space. It will be much easier: no problems with ordering of k+G vectors P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From parishok at gmail.com Wed Mar 16 10:09:18 2011 From: parishok at gmail.com (pari shok) Date: Wed, 16 Mar 2011 05:09:18 -0400 Subject: [Pw_forum] interpreting fermi level in smearing scenario Message-ID: Dear All, I made a SiC/SiO2 structure with QE. The code kept giving me "charge is wrong, smearing is needed", no matter what charges I used (even after correcting charges for several times. This is why I used smearing with degauss=0.018. Now that I get a fermi level, I was wondering how to interpret it for a semiconductor system. I guess that since the number of states in the gap is high,, the code considers it as a "metal system"; however, as I wrote, I don't know how to interpret the fermi level. I really appreciate your help and support. Thanks in advance. Yours P Shok UMD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110316/01bb9c01/attachment.htm From giannozz at democritos.it Wed Mar 16 10:23:06 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Mar 2011 10:23:06 +0100 Subject: [Pw_forum] atomic positions in xsf from cppp.x In-Reply-To: References: Message-ID: <785AB499-C244-444C-AEC9-5DD8B5E44028@democritos.it> On Mar 8, 2011, at 6:15 , Riping WANG wrote: > when I use cppp.x to generate an xsf file for an vc-cp output file > with nstep=1000 there will be cell vectors and atomic positions in > xsf file. what is this cell vectors and atomic positions stand for? I know nothing about cppp.x, but the code should read data a prescribed number of MD steps (nframes) and write atomic positions and cell vectors for each of them. See Doc/INPUT_CPPP.* and also the coe itself, CPV/fpmdpp.f90 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Mar 16 10:37:31 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Mar 2011 10:37:31 +0100 Subject: [Pw_forum] calculation wouldn't run using espresso-4.2.1 but did run with espresso-4.1.3 In-Reply-To: References: Message-ID: <2B5BCAFF-7941-4778-93D1-D8B0404D01CE@democritos.it> On Mar 8, 2011, at 24:28 , Tram Bui wrote: > I have post a question regarding the single atom calculation > for carbon simple cubic system last month [...] the calculation > ran fine using espresso-4.1.3 (older version), but not for > espresso-4.2.1 (latest version) the old version used to symmetrize tha charge density also for the Gamma case. The new version doesn't (it shouldn't be needed in principle). The problem is that in the specific case of atoms, you may have degenerate levels. The resulting charge density is in general not spherical. If you force it top be spherical, the code quickly converges to a solution. If you don't, it doesn't. This is a problem that arises only in isolated atoms, so I wouldn't attach much importance to it. And no, it is not a bug, contrary to what I said in a previous message. Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From glapenna at iccom.cnr.it Wed Mar 16 10:45:26 2011 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Wed, 16 Mar 2011 10:45:26 +0100 (CET) Subject: [Pw_forum] atomic positions in xsf from cppp.x In-Reply-To: <785AB499-C244-444C-AEC9-5DD8B5E44028@democritos.it> References: <785AB499-C244-444C-AEC9-5DD8B5E44028@democritos.it> Message-ID: Please, have a look in the xcrysden documentation: http://www.xcrysden.org/doc/XSF.html Giovanni ============================================================ Giovanni La Penna - National research council (Cnr) Institute for chemistry of organo-metallic compounds (Iccom) via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy tel.: +39 055 522-5264, fax: +39 055 522-5203 e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna skype: giovannilapenna ============================================================ > > On Mar 8, 2011, at 6:15 , Riping WANG wrote: > >> when I use cppp.x to generate an xsf file for an vc-cp output file >> with nstep=1000 there will be cell vectors and atomic positions in >> xsf file. what is this cell vectors and atomic positions stand for? > From amiri_physics at yahoo.com Wed Mar 16 10:41:53 2011 From: amiri_physics at yahoo.com (peyman amiri) Date: Wed, 16 Mar 2011 02:41:53 -0700 (PDT) Subject: [Pw_forum] spin-orbit coupling Message-ID: <225611.52215.qm@web161702.mail.bf1.yahoo.com> Dear all I want to apply the spin-orbit coupling in my system so I have some questions. 1. How can i choose the amount of spin-orbit interaction in my system? 2. For this purpose do i need to choose options nspin=2? or? noncolin=.true. ? Any suggestion will be appreciated ====================================== Peiman Amiri Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Iran Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 ------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110316/e852f897/attachment.htm From alain.allouche at univ-provence.fr Wed Mar 16 16:22:44 2011 From: alain.allouche at univ-provence.fr (Alain Allouche) Date: Wed, 16 Mar 2011 16:22:44 +0100 Subject: [Pw_forum] XSpectra on graphite slab Message-ID: Dear Espressionists, I tried to run the diamond example in espresso-4.2-examples/examples/ XSpectra_example and it works fine using espresso-4.2. Threfore I duplicated the diamond files to make the calculation on graphite and the input looks like: &control calculation='scf' restart_mode='from_scratch', ! restart_mode='restart', ! pseudo_dir = '/Users/allouche/pseudo_espresso/' ! pseudo_dir = '/homegpfs/rech/ams/rams001/pseudo_espresso/' pseudo_dir = '/home/allouche/pseudo_espresso' prefix='graphite' / &system ibrav = 4 a =9.880, b =9.880, c =20.0000 cosab = 0.0 cosac = 0.0 cosbc = -0.5 nat= 64 ntyp= 2, ecutwfc=40. tot_charge=+1.0, degauss=0.001 nspin = 1 london=.true. / &electrons mixing_beta = 0.3, startingwfc = 'file' / ATOMIC_SPECIES C 12 C_PBE_TM_2pj.UPF Ch 12 Ch_PBE_TM_2pj.UPF ATOMIC_POSITIONS crystal Ch 0.166589 0.083384 0.827761 C 0.249912 0.250043 0.827591 C 0.333380 0.166614 0.665253 C 0.250046 0.249946 0.665282 C 0.166590 0.333382 0.827797 C 0.249927 0.500060 0.827753 C 0.333381 0.416617 0.665261 C 0.250049 0.499953 0.665288 C 0.166617 0.583430 0.827809 C 0.249925 0.750054 0.827751 C 0.333382 0.666616 0.665260 C 0.250048 0.749950 0.665286 C 0.166616 0.833367 0.827787 C 0.249927 0.000045 0.827690 C 0.333384 0.916617 0.665257 C 0.250048 0.999946 0.665282 C 0.416586 0.083370 0.827522 C 0.499907 0.250007 0.827142 C 0.583384 0.166614 0.665248 C 0.500045 0.249945 0.665274 C 0.416562 0.333369 0.827235 C 0.499907 0.500070 0.827236 C 0.583381 0.416619 0.665246 C 0.500048 0.499951 0.665283 C 0.416589 0.583393 0.827627 C 0.499919 0.750051 0.827751 C 0.583381 0.666616 0.665259 C 0.500046 0.749950 0.665287 C 0.416552 0.833366 0.827806 C 0.499916 0.000042 0.827678 C 0.583386 0.916617 0.665253 C 0.500047 0.999947 0.665279 C 0.666599 0.083383 0.827729 C 0.749937 0.250040 0.827505 C 0.833385 0.166614 0.665243 C 0.750051 0.249946 0.665273 C 0.666613 0.333368 0.827149 C 0.749971 0.500070 0.827145 C 0.833384 0.416616 0.665248 C 0.750053 0.499953 0.665273 C 0.666611 0.583417 0.827236 C 0.749935 0.750067 0.827591 C 0.833383 0.666618 0.665251 C 0.750054 0.749954 0.665279 C 0.666599 0.833390 0.827795 C 0.749964 0.000070 0.827829 C 0.833383 0.916619 0.665245 C 0.750052 0.999950 0.665271 C 0.916596 0.083383 0.827854 C 0.999910 0.250017 0.827831 C 0.083378 0.166616 0.665246 C 0.000049 0.249946 0.665273 C 0.916598 0.333382 0.827732 C 0.999937 0.500062 0.827682 C 0.083381 0.416612 0.665255 C 0.000052 0.499951 0.665280 C 0.916611 0.583397 0.827525 C 0.999932 0.750051 0.827692 C 0.083381 0.666615 0.665256 C 0.000052 0.749950 0.665280 C 0.916597 0.833392 0.827762 C 0.999909 0.000071 0.827828 C 0.083381 0.916617 0.665250 C 0.000050 0.999949 0.665269 K_POINTS Automatic 6 6 1 0 0 0 FIRST PROBLEM: expresso-4.2 and 4.1 do not like atom Ch (they did for diamond): This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 40 processors K-points division: npool = 20 R & G space division: proc/pool = 2 Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... Atom Ch not found rank 0 in job 1 node07_41087 caused collective abort of all ranks exit status of rank 0: killed by signal 9 Only espresso-4.0.4 did like !!! so I tried it on diamond (for checking) and then on graphite again, it works SECOND PROBLEM: The data for XSpectra: &input_xspectra calculation='fermi_level', prefix='graphite', xread_wf=.true., xiabs=1 / &plot / &pseudos filecore='C.wfc', / &cut_occ / 6 6 1 0 0 0 The result: Program XSPECTRA v.4.2.1 starts on 16Mar2011 at 15:52:46 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 40 processors R & G space division: proc/pool = 40 bef Planes per process (thick) : nr3 = 160 npp = 4 ncplane = 6400 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 4 96 9750 4 96 9750 26 1358 2 4 96 9750 4 96 9750 26 1356 3 4 96 9750 4 96 9750 26 1356 4 4 96 9750 4 96 9750 26 1356 5 4 96 9750 4 96 9750 26 1356 6 4 96 9750 4 96 9750 26 1356 7 4 96 9748 4 96 9748 26 1356 8 4 96 9748 4 96 9748 26 1352 9 4 96 9750 4 96 9750 25 1347 10 4 96 9750 4 96 9750 26 1356 11 4 96 9750 4 96 9750 26 1356 12 4 96 9750 4 96 9750 26 1356 13 4 96 9750 4 96 9750 26 1356 14 4 97 9753 4 97 9753 26 1356 15 4 97 9753 4 97 9753 26 1356 16 4 96 9748 4 96 9748 26 1350 17 4 96 9748 4 96 9748 26 1350 18 4 96 9748 4 96 9748 26 1350 19 4 96 9748 4 96 9748 26 1350 20 4 96 9748 4 96 9748 26 1350 21 4 96 9748 4 96 9748 26 1350 22 4 96 9748 4 96 9748 26 1350 23 4 96 9748 4 96 9748 26 1350 24 4 96 9748 4 96 9748 26 1350 25 4 96 9748 4 96 9748 26 1350 26 4 97 9751 4 97 9751 26 1350 27 4 97 9751 4 97 9751 26 1358 28 4 97 9751 4 97 9751 26 1358 29 4 97 9751 4 97 9751 26 1358 30 4 97 9751 4 97 9751 26 1356 31 4 97 9751 4 97 9751 26 1356 32 4 97 9751 4 97 9751 26 1356 33 4 97 9751 4 97 9751 26 1356 34 4 97 9751 4 97 9751 26 1356 35 4 97 9751 4 97 9751 26 1356 36 4 97 9751 4 97 9751 26 1356 37 4 96 9748 4 96 9748 26 1356 38 4 96 9748 4 96 9748 26 1356 39 4 96 9748 4 96 9748 26 1356 40 4 96 9748 4 96 9748 26 1356 tot 160 3853 389985 160 3853 389985 1039 54169 af Approx. ram memory needed per proc in MB = 1.482000000000000E-003 k-points : nkstot= 20 -------------- Crystal Structure ------------ celldm(1:6) 18.67049419 1.00000000 2.02429150 0.00000000 0.00000000 0.00000000 direct lattice vectors 1.00000000 -0.50000000 0.00000000 0.00000000 0.86602540 0.00000000 0.00000000 0.00000000 2.02429150 reciprocal lattice vectors 1.00000000 0.00000000 0.00000000 0.57735027 1.15470054 0.00000000 0.00000000 0.00000000 0.49400000 nks= 20 nkstot= 20 ----k-point list [units 2*pi/celldm(1)], weight--------- 1 0.00000000 0.00000000 0.00000000 0.05555556 2 0.00000000 0.19245009 0.00000000 0.11111111 3 0.00000000 0.38490018 0.00000000 0.11111111 4 0.00000000 -0.57735027 0.00000000 0.05555556 5 0.16666667 0.28867513 0.00000000 0.11111111 6 0.16666667 0.48112522 0.00000000 0.11111111 7 0.33333333 0.57735027 0.00000000 0.11111111 8 -0.16666667 0.09622504 0.00000000 0.11111111 9 0.16666667 0.09622504 0.00000000 0.11111111 10 -0.33333333 0.19245009 0.00000000 0.11111111 11 0.33333333 0.19245009 0.00000000 0.11111111 12 0.50000000 -0.28867513 0.00000000 0.05555556 13 -0.50000000 -0.28867513 0.00000000 0.05555556 14 -0.16666667 0.28867513 0.00000000 0.11111111 15 0.33333333 0.00000000 0.00000000 0.11111111 16 -0.16666667 0.48112522 0.00000000 0.11111111 17 -0.33333333 0.38490018 0.00000000 0.11111111 18 0.50000000 0.09622504 0.00000000 0.11111111 19 -0.33333333 -0.38490018 0.00000000 0.11111111 20 0.50000000 -0.09622504 0.00000000 0.11111111 ------------------------------------------------- --- Polarisation and k vector [cartesian coordinates]---- xepsilon(:)= 1.00000000 0.00000000 0.00000000 xkvec(:)= 1.00000000 0.00000000 0.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% from main program : error # 63 Wrong xiabs!!! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% stopping ... rank 30 in job 1 node08_33288 caused collective abort of all ranks exit status of rank 30: killed by signal 9 rank 25 in job 1 node08_33288 caused collective abort of all ranks exit status of rank 25: killed by signal 9 rank 15 in job 1 node08_33288 caused collective abort of all ranks exit status of rank 15: killed by signal 9 rank 0 in job 1 node08_33288 caused collective abort of all ranks exit status of rank 0: killed by signal 9 Can somebody explain me the curious behavior of pw.x accepting Ch on diamond and not on graphite, and this "Wrong xiabs!!!" ?? Thank you in advance Dr. Alain ALLOUCHE Physique des Interactions Ioniques et Moleculaires CNRS / Universite de Provence Campus Saint Jerome Service 242 Avenue de l'Escadrille Normandie-Niemen 13397 Marseille Cedex 20 - France Tel : +33 (0) 4 91 28 85 76 Mobile:+33 681 84 80 66 Fax : +33 491.28.89.05 email: Alain.Allouche at univ-provence.fr From stewart at cnf.cornell.edu Wed Mar 16 16:41:44 2011 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Wed, 16 Mar 2011 11:41:44 -0400 Subject: [Pw_forum] XSpectra on graphite slab In-Reply-To: References: Message-ID: <4D80DA38.4040708@cnf.cornell.edu> Hi Alain, A quick question on your problem with the Ch atom. Did you have the corresponding pseudopotential, "Ch_PBE_TM_2pj.UPF" in the pseudo directory? Best regards, Derek ################################ Derek Stewart, Ph. D. Senior Research Associate ** New Webpage ** http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 On 3/16/2011 11:22 AM, Alain Allouche wrote: > Dear Espressionists, > I tried to run the diamond example in espresso-4.2-examples/examples/ > XSpectra_example and it works fine using espresso-4.2. Threfore I > duplicated the diamond files to make the calculation on graphite and > the input looks like: > > &control > calculation='scf' > restart_mode='from_scratch', > ! restart_mode='restart', > ! pseudo_dir = '/Users/allouche/pseudo_espresso/' > ! pseudo_dir = '/homegpfs/rech/ams/rams001/pseudo_espresso/' > pseudo_dir = '/home/allouche/pseudo_espresso' > prefix='graphite' > / > &system > ibrav = 4 > a =9.880, > b =9.880, > c =20.0000 > cosab = 0.0 > cosac = 0.0 > cosbc = -0.5 > nat= 64 > ntyp= 2, > ecutwfc=40. > tot_charge=+1.0, > degauss=0.001 > nspin = 1 > london=.true. > / > &electrons > mixing_beta = 0.3, > startingwfc = 'file' > / > ATOMIC_SPECIES > C 12 C_PBE_TM_2pj.UPF > Ch 12 Ch_PBE_TM_2pj.UPF > ATOMIC_POSITIONS crystal > Ch 0.166589 0.083384 0.827761 > C 0.249912 0.250043 0.827591 > C 0.333380 0.166614 0.665253 > C 0.250046 0.249946 0.665282 > C 0.166590 0.333382 0.827797 > C 0.249927 0.500060 0.827753 > C 0.333381 0.416617 0.665261 > C 0.250049 0.499953 0.665288 > C 0.166617 0.583430 0.827809 > C 0.249925 0.750054 0.827751 > C 0.333382 0.666616 0.665260 > C 0.250048 0.749950 0.665286 > C 0.166616 0.833367 0.827787 > C 0.249927 0.000045 0.827690 > C 0.333384 0.916617 0.665257 > C 0.250048 0.999946 0.665282 > C 0.416586 0.083370 0.827522 > C 0.499907 0.250007 0.827142 > C 0.583384 0.166614 0.665248 > C 0.500045 0.249945 0.665274 > C 0.416562 0.333369 0.827235 > C 0.499907 0.500070 0.827236 > C 0.583381 0.416619 0.665246 > C 0.500048 0.499951 0.665283 > C 0.416589 0.583393 0.827627 > C 0.499919 0.750051 0.827751 > C 0.583381 0.666616 0.665259 > C 0.500046 0.749950 0.665287 > C 0.416552 0.833366 0.827806 > C 0.499916 0.000042 0.827678 > C 0.583386 0.916617 0.665253 > C 0.500047 0.999947 0.665279 > C 0.666599 0.083383 0.827729 > C 0.749937 0.250040 0.827505 > C 0.833385 0.166614 0.665243 > C 0.750051 0.249946 0.665273 > C 0.666613 0.333368 0.827149 > C 0.749971 0.500070 0.827145 > C 0.833384 0.416616 0.665248 > C 0.750053 0.499953 0.665273 > C 0.666611 0.583417 0.827236 > C 0.749935 0.750067 0.827591 > C 0.833383 0.666618 0.665251 > C 0.750054 0.749954 0.665279 > C 0.666599 0.833390 0.827795 > C 0.749964 0.000070 0.827829 > C 0.833383 0.916619 0.665245 > C 0.750052 0.999950 0.665271 > C 0.916596 0.083383 0.827854 > C 0.999910 0.250017 0.827831 > C 0.083378 0.166616 0.665246 > C 0.000049 0.249946 0.665273 > C 0.916598 0.333382 0.827732 > C 0.999937 0.500062 0.827682 > C 0.083381 0.416612 0.665255 > C 0.000052 0.499951 0.665280 > C 0.916611 0.583397 0.827525 > C 0.999932 0.750051 0.827692 > C 0.083381 0.666615 0.665256 > C 0.000052 0.749950 0.665280 > C 0.916597 0.833392 0.827762 > C 0.999909 0.000071 0.827828 > C 0.083381 0.916617 0.665250 > C 0.000050 0.999949 0.665269 > K_POINTS Automatic > 6 6 1 0 0 0 > > FIRST PROBLEM: expresso-4.2 and 4.1 do not like atom Ch (they did for > diamond): > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please cite > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 > (2009); > URL http://www.quantum-espresso.org", > in publications or presentations arising from this work. More > details at > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > > Parallel version (MPI), running on 40 processors > K-points division: npool = 20 > R& G space division: proc/pool = 2 > > Current dimensions of program PWSCF are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > Waiting for input... > Atom Ch not found > rank 0 in job 1 node07_41087 caused collective abort of all ranks > exit status of rank 0: killed by signal 9 > > > Only espresso-4.0.4 did like !!! so I tried it on diamond (for > checking) and then on graphite again, it works > > SECOND PROBLEM: > The data for XSpectra: > &input_xspectra > calculation='fermi_level', > prefix='graphite', > xread_wf=.true., > xiabs=1 > / > &plot > / > &pseudos > filecore='C.wfc', > / > &cut_occ > / > 6 6 1 0 0 0 > > > The result: > > > Program XSPECTRA v.4.2.1 starts on 16Mar2011 at 15:52:46 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please acknowledge > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 > (2009); > URL http://www.quantum-espresso.org", > in publications or presentations arising from this work. More > details at > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > > Parallel version (MPI), running on 40 processors > R& G space division: proc/pool = 40 > bef > > Planes per process (thick) : nr3 = 160 npp = 4 ncplane = 6400 > > Proc/ planes cols G planes cols G columns G > Pool (dense grid) (smooth grid) (wavefct grid) > 1 4 96 9750 4 96 9750 26 1358 > 2 4 96 9750 4 96 9750 26 1356 > 3 4 96 9750 4 96 9750 26 1356 > 4 4 96 9750 4 96 9750 26 1356 > 5 4 96 9750 4 96 9750 26 1356 > 6 4 96 9750 4 96 9750 26 1356 > 7 4 96 9748 4 96 9748 26 1356 > 8 4 96 9748 4 96 9748 26 1352 > 9 4 96 9750 4 96 9750 25 1347 > 10 4 96 9750 4 96 9750 26 1356 > 11 4 96 9750 4 96 9750 26 1356 > 12 4 96 9750 4 96 9750 26 1356 > 13 4 96 9750 4 96 9750 26 1356 > 14 4 97 9753 4 97 9753 26 1356 > 15 4 97 9753 4 97 9753 26 1356 > 16 4 96 9748 4 96 9748 26 1350 > 17 4 96 9748 4 96 9748 26 1350 > 18 4 96 9748 4 96 9748 26 1350 > 19 4 96 9748 4 96 9748 26 1350 > 20 4 96 9748 4 96 9748 26 1350 > 21 4 96 9748 4 96 9748 26 1350 > 22 4 96 9748 4 96 9748 26 1350 > 23 4 96 9748 4 96 9748 26 1350 > 24 4 96 9748 4 96 9748 26 1350 > 25 4 96 9748 4 96 9748 26 1350 > 26 4 97 9751 4 97 9751 26 1350 > 27 4 97 9751 4 97 9751 26 1358 > 28 4 97 9751 4 97 9751 26 1358 > 29 4 97 9751 4 97 9751 26 1358 > 30 4 97 9751 4 97 9751 26 1356 > 31 4 97 9751 4 97 9751 26 1356 > 32 4 97 9751 4 97 9751 26 1356 > 33 4 97 9751 4 97 9751 26 1356 > 34 4 97 9751 4 97 9751 26 1356 > 35 4 97 9751 4 97 9751 26 1356 > 36 4 97 9751 4 97 9751 26 1356 > 37 4 96 9748 4 96 9748 26 1356 > 38 4 96 9748 4 96 9748 26 1356 > 39 4 96 9748 4 96 9748 26 1356 > 40 4 96 9748 4 96 9748 26 1356 > tot 160 3853 389985 160 3853 389985 1039 54169 > > af > > Approx. ram memory needed per proc in MB = 1.482000000000000E-003 > > k-points : nkstot= 20 > -------------- Crystal Structure ------------ > celldm(1:6) > 18.67049419 1.00000000 2.02429150 > 0.00000000 0.00000000 0.00000000 > direct lattice vectors > 1.00000000 -0.50000000 0.00000000 > 0.00000000 0.86602540 0.00000000 > 0.00000000 0.00000000 2.02429150 > reciprocal lattice vectors > 1.00000000 0.00000000 0.00000000 > 0.57735027 1.15470054 0.00000000 > 0.00000000 0.00000000 0.49400000 > nks= 20 nkstot= 20 > ----k-point list [units 2*pi/celldm(1)], weight--------- > 1 0.00000000 0.00000000 0.00000000 0.05555556 > 2 0.00000000 0.19245009 0.00000000 0.11111111 > 3 0.00000000 0.38490018 0.00000000 0.11111111 > 4 0.00000000 -0.57735027 0.00000000 0.05555556 > 5 0.16666667 0.28867513 0.00000000 0.11111111 > 6 0.16666667 0.48112522 0.00000000 0.11111111 > 7 0.33333333 0.57735027 0.00000000 0.11111111 > 8 -0.16666667 0.09622504 0.00000000 0.11111111 > 9 0.16666667 0.09622504 0.00000000 0.11111111 > 10 -0.33333333 0.19245009 0.00000000 0.11111111 > 11 0.33333333 0.19245009 0.00000000 0.11111111 > 12 0.50000000 -0.28867513 0.00000000 0.05555556 > 13 -0.50000000 -0.28867513 0.00000000 0.05555556 > 14 -0.16666667 0.28867513 0.00000000 0.11111111 > 15 0.33333333 0.00000000 0.00000000 0.11111111 > 16 -0.16666667 0.48112522 0.00000000 0.11111111 > 17 -0.33333333 0.38490018 0.00000000 0.11111111 > 18 0.50000000 0.09622504 0.00000000 0.11111111 > 19 -0.33333333 -0.38490018 0.00000000 0.11111111 > 20 0.50000000 -0.09622504 0.00000000 0.11111111 > ------------------------------------------------- > --- Polarisation and k vector [cartesian coordinates]---- > xepsilon(:)= 1.00000000 0.00000000 0.00000000 > xkvec(:)= 1.00000000 0.00000000 0.00000000 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > from main program : error # 63 > Wrong xiabs!!! > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > > stopping ... > rank 30 in job 1 node08_33288 caused collective abort of all ranks > exit status of rank 30: killed by signal 9 > rank 25 in job 1 node08_33288 caused collective abort of all ranks > exit status of rank 25: killed by signal 9 > rank 15 in job 1 node08_33288 caused collective abort of all ranks > exit status of rank 15: killed by signal 9 > rank 0 in job 1 node08_33288 caused collective abort of all ranks > exit status of rank 0: killed by signal 9 > > > Can somebody explain me the curious behavior of pw.x accepting Ch on > diamond and not on graphite, and this "Wrong xiabs!!!" ?? > > Thank you in advance > > > > Dr. Alain ALLOUCHE > Physique des Interactions Ioniques et Moleculaires > CNRS / Universite de Provence > Campus Saint Jerome Service 242 > Avenue de l'Escadrille Normandie-Niemen > 13397 Marseille Cedex 20 - France > Tel : +33 (0) 4 91 28 85 76 > Mobile:+33 681 84 80 66 > Fax : +33 491.28.89.05 > email: Alain.Allouche at univ-provence.fr > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > From alain.allouche at univ-provence.fr Wed Mar 16 17:02:18 2011 From: alain.allouche at univ-provence.fr (Alain Allouche) Date: Wed, 16 Mar 2011 17:02:18 +0100 Subject: [Pw_forum] XSpectra on graphite slab In-Reply-To: <4D80DA38.4040708@cnf.cornell.edu> References: <4D80DA38.4040708@cnf.cornell.edu> Message-ID: <9EA065FE-E732-4CBF-B5B0-5EE0838F50C2@univ-provence.fr> Hi Derek, Of course I have it taken from the XS example pseudo files, I used it first on the diamondh case (I just duplicate and adapted the data files) Best Alain Le 16 mars 11 ? 16:41, Derek Stewart a ?crit : > Hi Alain, > > A quick question on your problem with the Ch atom. Did you have the > corresponding pseudopotential, "Ch_PBE_TM_2pj.UPF" in the pseudo > directory? > > Best regards, > > Derek > > > > ################################ > Derek Stewart, Ph. D. > Senior Research Associate > ** New Webpage ** > http://sites.google.com/site/dft4nano/ > 250 Duffield Hall > Cornell Nanoscale Facility (CNF) > Ithaca, NY 14853 > stewart (at) cnf.cornell.edu > (607) 255-2856 > > > > On 3/16/2011 11:22 AM, Alain Allouche wrote: >> Dear Espressionists, >> I tried to run the diamond example in espresso-4.2-examples/examples/ >> XSpectra_example and it works fine using espresso-4.2. Threfore I >> duplicated the diamond files to make the calculation on graphite and >> the input looks like: >> >> &control >> calculation='scf' >> restart_mode='from_scratch', >> ! restart_mode='restart', >> ! pseudo_dir = '/Users/allouche/pseudo_espresso/' >> ! pseudo_dir = '/homegpfs/rech/ams/rams001/pseudo_espresso/' >> pseudo_dir = '/home/allouche/pseudo_espresso' >> prefix='graphite' >> / >> &system >> ibrav = 4 >> a =9.880, >> b =9.880, >> c =20.0000 >> cosab = 0.0 >> cosac = 0.0 >> cosbc = -0.5 >> nat= 64 >> ntyp= 2, >> ecutwfc=40. >> tot_charge=+1.0, >> degauss=0.001 >> nspin = 1 >> london=.true. >> / >> &electrons >> mixing_beta = 0.3, >> startingwfc = 'file' >> / >> ATOMIC_SPECIES >> C 12 C_PBE_TM_2pj.UPF >> Ch 12 Ch_PBE_TM_2pj.UPF >> ATOMIC_POSITIONS crystal >> Ch 0.166589 0.083384 0.827761 >> C 0.249912 0.250043 0.827591 >> C 0.333380 0.166614 0.665253 >> C 0.250046 0.249946 0.665282 >> C 0.166590 0.333382 0.827797 >> C 0.249927 0.500060 0.827753 >> C 0.333381 0.416617 0.665261 >> C 0.250049 0.499953 0.665288 >> C 0.166617 0.583430 0.827809 >> C 0.249925 0.750054 0.827751 >> C 0.333382 0.666616 0.665260 >> C 0.250048 0.749950 0.665286 >> C 0.166616 0.833367 0.827787 >> C 0.249927 0.000045 0.827690 >> C 0.333384 0.916617 0.665257 >> C 0.250048 0.999946 0.665282 >> C 0.416586 0.083370 0.827522 >> C 0.499907 0.250007 0.827142 >> C 0.583384 0.166614 0.665248 >> C 0.500045 0.249945 0.665274 >> C 0.416562 0.333369 0.827235 >> C 0.499907 0.500070 0.827236 >> C 0.583381 0.416619 0.665246 >> C 0.500048 0.499951 0.665283 >> C 0.416589 0.583393 0.827627 >> C 0.499919 0.750051 0.827751 >> C 0.583381 0.666616 0.665259 >> C 0.500046 0.749950 0.665287 >> C 0.416552 0.833366 0.827806 >> C 0.499916 0.000042 0.827678 >> C 0.583386 0.916617 0.665253 >> C 0.500047 0.999947 0.665279 >> C 0.666599 0.083383 0.827729 >> C 0.749937 0.250040 0.827505 >> C 0.833385 0.166614 0.665243 >> C 0.750051 0.249946 0.665273 >> C 0.666613 0.333368 0.827149 >> C 0.749971 0.500070 0.827145 >> C 0.833384 0.416616 0.665248 >> C 0.750053 0.499953 0.665273 >> C 0.666611 0.583417 0.827236 >> C 0.749935 0.750067 0.827591 >> C 0.833383 0.666618 0.665251 >> C 0.750054 0.749954 0.665279 >> C 0.666599 0.833390 0.827795 >> C 0.749964 0.000070 0.827829 >> C 0.833383 0.916619 0.665245 >> C 0.750052 0.999950 0.665271 >> C 0.916596 0.083383 0.827854 >> C 0.999910 0.250017 0.827831 >> C 0.083378 0.166616 0.665246 >> C 0.000049 0.249946 0.665273 >> C 0.916598 0.333382 0.827732 >> C 0.999937 0.500062 0.827682 >> C 0.083381 0.416612 0.665255 >> C 0.000052 0.499951 0.665280 >> C 0.916611 0.583397 0.827525 >> C 0.999932 0.750051 0.827692 >> C 0.083381 0.666615 0.665256 >> C 0.000052 0.749950 0.665280 >> C 0.916597 0.833392 0.827762 >> C 0.999909 0.000071 0.827828 >> C 0.083381 0.916617 0.665250 >> C 0.000050 0.999949 0.665269 >> K_POINTS Automatic >> 6 6 1 0 0 0 >> >> FIRST PROBLEM: expresso-4.2 and 4.1 do not like atom Ch (they did for >> diamond): >> >> This program is part of the open-source Quantum ESPRESSO suite >> for quantum simulation of materials; please cite >> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 >> (2009); >> URL http://www.quantum-espresso.org", >> in publications or presentations arising from this work. More >> details at >> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO >> >> Parallel version (MPI), running on 40 processors >> K-points division: npool = 20 >> R& G space division: proc/pool = 2 >> >> Current dimensions of program PWSCF are: >> Max number of different atomic species (ntypx) = 10 >> Max number of k-points (npk) = 40000 >> Max angular momentum in pseudopotentials (lmaxx) = 3 >> Waiting for input... >> Atom Ch not found >> rank 0 in job 1 node07_41087 caused collective abort of all ranks >> exit status of rank 0: killed by signal 9 >> >> >> Only espresso-4.0.4 did like !!! so I tried it on diamond (for >> checking) and then on graphite again, it works >> >> SECOND PROBLEM: >> The data for XSpectra: >> &input_xspectra >> calculation='fermi_level', >> prefix='graphite', >> xread_wf=.true., >> xiabs=1 >> / >> &plot >> / >> &pseudos >> filecore='C.wfc', >> / >> &cut_occ >> / >> 6 6 1 0 0 0 >> >> >> The result: >> >> >> Program XSPECTRA v.4.2.1 starts on 16Mar2011 at 15:52:46 >> >> This program is part of the open-source Quantum ESPRESSO suite >> for quantum simulation of materials; please acknowledge >> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 >> (2009); >> URL http://www.quantum-espresso.org", >> in publications or presentations arising from this work. More >> details at >> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO >> >> Parallel version (MPI), running on 40 processors >> R& G space division: proc/pool = 40 >> bef >> >> Planes per process (thick) : nr3 = 160 npp = 4 ncplane = >> 6400 >> >> Proc/ planes cols G planes cols G columns G >> Pool (dense grid) (smooth grid) (wavefct grid) >> 1 4 96 9750 4 96 9750 26 1358 >> 2 4 96 9750 4 96 9750 26 1356 >> 3 4 96 9750 4 96 9750 26 1356 >> 4 4 96 9750 4 96 9750 26 1356 >> 5 4 96 9750 4 96 9750 26 1356 >> 6 4 96 9750 4 96 9750 26 1356 >> 7 4 96 9748 4 96 9748 26 1356 >> 8 4 96 9748 4 96 9748 26 1352 >> 9 4 96 9750 4 96 9750 25 1347 >> 10 4 96 9750 4 96 9750 26 1356 >> 11 4 96 9750 4 96 9750 26 1356 >> 12 4 96 9750 4 96 9750 26 1356 >> 13 4 96 9750 4 96 9750 26 1356 >> 14 4 97 9753 4 97 9753 26 1356 >> 15 4 97 9753 4 97 9753 26 1356 >> 16 4 96 9748 4 96 9748 26 1350 >> 17 4 96 9748 4 96 9748 26 1350 >> 18 4 96 9748 4 96 9748 26 1350 >> 19 4 96 9748 4 96 9748 26 1350 >> 20 4 96 9748 4 96 9748 26 1350 >> 21 4 96 9748 4 96 9748 26 1350 >> 22 4 96 9748 4 96 9748 26 1350 >> 23 4 96 9748 4 96 9748 26 1350 >> 24 4 96 9748 4 96 9748 26 1350 >> 25 4 96 9748 4 96 9748 26 1350 >> 26 4 97 9751 4 97 9751 26 1350 >> 27 4 97 9751 4 97 9751 26 1358 >> 28 4 97 9751 4 97 9751 26 1358 >> 29 4 97 9751 4 97 9751 26 1358 >> 30 4 97 9751 4 97 9751 26 1356 >> 31 4 97 9751 4 97 9751 26 1356 >> 32 4 97 9751 4 97 9751 26 1356 >> 33 4 97 9751 4 97 9751 26 1356 >> 34 4 97 9751 4 97 9751 26 1356 >> 35 4 97 9751 4 97 9751 26 1356 >> 36 4 97 9751 4 97 9751 26 1356 >> 37 4 96 9748 4 96 9748 26 1356 >> 38 4 96 9748 4 96 9748 26 1356 >> 39 4 96 9748 4 96 9748 26 1356 >> 40 4 96 9748 4 96 9748 26 1356 >> tot 160 3853 389985 160 3853 389985 1039 54169 >> >> af >> >> Approx. ram memory needed per proc in MB = 1.482000000000000E-003 >> >> k-points : nkstot= 20 >> -------------- Crystal Structure ------------ >> celldm(1:6) >> 18.67049419 1.00000000 2.02429150 >> 0.00000000 0.00000000 0.00000000 >> direct lattice vectors >> 1.00000000 -0.50000000 0.00000000 >> 0.00000000 0.86602540 0.00000000 >> 0.00000000 0.00000000 2.02429150 >> reciprocal lattice vectors >> 1.00000000 0.00000000 0.00000000 >> 0.57735027 1.15470054 0.00000000 >> 0.00000000 0.00000000 0.49400000 >> nks= 20 nkstot= 20 >> ----k-point list [units 2*pi/celldm(1)], weight--------- >> 1 0.00000000 0.00000000 0.00000000 0.05555556 >> 2 0.00000000 0.19245009 0.00000000 0.11111111 >> 3 0.00000000 0.38490018 0.00000000 0.11111111 >> 4 0.00000000 -0.57735027 0.00000000 0.05555556 >> 5 0.16666667 0.28867513 0.00000000 0.11111111 >> 6 0.16666667 0.48112522 0.00000000 0.11111111 >> 7 0.33333333 0.57735027 0.00000000 0.11111111 >> 8 -0.16666667 0.09622504 0.00000000 0.11111111 >> 9 0.16666667 0.09622504 0.00000000 0.11111111 >> 10 -0.33333333 0.19245009 0.00000000 0.11111111 >> 11 0.33333333 0.19245009 0.00000000 0.11111111 >> 12 0.50000000 -0.28867513 0.00000000 0.05555556 >> 13 -0.50000000 -0.28867513 0.00000000 0.05555556 >> 14 -0.16666667 0.28867513 0.00000000 0.11111111 >> 15 0.33333333 0.00000000 0.00000000 0.11111111 >> 16 -0.16666667 0.48112522 0.00000000 0.11111111 >> 17 -0.33333333 0.38490018 0.00000000 0.11111111 >> 18 0.50000000 0.09622504 0.00000000 0.11111111 >> 19 -0.33333333 -0.38490018 0.00000000 0.11111111 >> 20 0.50000000 -0.09622504 0.00000000 0.11111111 >> ------------------------------------------------- >> --- Polarisation and k vector [cartesian coordinates]---- >> xepsilon(:)= 1.00000000 0.00000000 0.00000000 >> xkvec(:)= 1.00000000 0.00000000 0.00000000 >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> %%% >> %%%%%%%%% >> from main program : error # 63 >> Wrong xiabs!!! >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> %%% >> %%%%%%%%% >> >> stopping ... >> rank 30 in job 1 node08_33288 caused collective abort of all ranks >> exit status of rank 30: killed by signal 9 >> rank 25 in job 1 node08_33288 caused collective abort of all ranks >> exit status of rank 25: killed by signal 9 >> rank 15 in job 1 node08_33288 caused collective abort of all ranks >> exit status of rank 15: killed by signal 9 >> rank 0 in job 1 node08_33288 caused collective abort of all ranks >> exit status of rank 0: killed by signal 9 >> >> >> Can somebody explain me the curious behavior of pw.x accepting Ch on >> diamond and not on graphite, and this "Wrong xiabs!!!" ?? >> >> Thank you in advance >> >> >> >> Dr. Alain ALLOUCHE >> Physique des Interactions Ioniques et Moleculaires >> CNRS / Universite de Provence >> Campus Saint Jerome Service 242 >> Avenue de l'Escadrille Normandie-Niemen >> 13397 Marseille Cedex 20 - France >> Tel : +33 (0) 4 91 28 85 76 >> Mobile:+33 681 84 80 66 >> Fax : +33 491.28.89.05 >> email: Alain.Allouche at univ-provence.fr >> >> >> >> >> >> >> >> _______________________________________________ >> 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 tylergordon at u.boisestate.edu Wed Mar 16 18:49:21 2011 From: tylergordon at u.boisestate.edu (Tyler Gordon) Date: Wed, 16 Mar 2011 11:49:21 -0600 Subject: [Pw_forum] norm conserving Ti pseudopotential Message-ID: Hello, I am a new user of QE. I am looking for a norm conserving pseudopotential for Ti. If anybody has created it, may I request it? Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110316/37a1385c/attachment.htm From giannozz at democritos.it Wed Mar 16 18:54:13 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Mar 2011 18:54:13 +0100 Subject: [Pw_forum] norm conserving Ti pseudopotential In-Reply-To: References: Message-ID: <26608CB5-87C3-431A-A862-AA2A2D917381@democritos.it> On Mar 16, 2011, at 18:49 , Tyler Gordon wrote: > If anybody has created it, may I request it? you may, even if nobody has ever created one P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From nicola.marzari at materials.ox.ac.uk Wed Mar 16 19:01:57 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 16 Mar 2011 18:01:57 +0000 Subject: [Pw_forum] norm conserving Ti pseudopotential In-Reply-To: References: Message-ID: <4D80FB15.3000206@materials.ox.ac.uk> On 3/16/11 5:49 PM, Tyler Gordon wrote: > Hello, > I am a new user of QE. I am looking for a norm conserving > pseudopotential for Ti. If anybody has created it, may I request it? > Thank you. Worse case scenario: download/compile the fritz-haber pseudopotential code, generate the troullier-martins Ti there, and convert it to UPF with the fhi2upf tool in the upftools directory of Q-E. Check that it works in calculations where you use ultrasoft Ti instead. One question - any volunteer to convert the entire fritz-haber database in upf format ? nicola -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From giannozz at democritos.it Wed Mar 16 19:15:57 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Mar 2011 19:15:57 +0100 Subject: [Pw_forum] norm conserving Ti pseudopotential In-Reply-To: <4D80FB15.3000206@materials.ox.ac.uk> References: <4D80FB15.3000206@materials.ox.ac.uk> Message-ID: On Mar 16, 2011, at 19:01 , Nicola Marzari wrote: > Worse case scenario: download/compile the fritz-haber pseudopotential > code, generate the troullier-martins Ti there, and convert it to UPF > with the fhi2upf tool in the upftools directory of Q-E. this can be done directly with the "atomic" code in QE. Generating a single-channel norm-conserving PP without semi-core states is trivial and well documented. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From stewart at cnf.cornell.edu Wed Mar 16 19:20:21 2011 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Wed, 16 Mar 2011 14:20:21 -0400 Subject: [Pw_forum] norm conserving Ti pseudopotential In-Reply-To: <4D80FB15.3000206@materials.ox.ac.uk> References: <4D80FB15.3000206@materials.ox.ac.uk> Message-ID: <4D80FF65.1080700@cnf.cornell.edu> Hi Tyler and Nicola, I have put together a database of pseudopotentials at the following location: http://charter.cnf.cornell.edu This contains pseudopotentials from QE, Abinit, and Qbox. If you search under Ti, http://charter.cnf.cornell.edu/psplist.php?element=Ti you will find several in the fhi format. Nicola, it should be possible to write a script to grab the Abinit fhi pseudopotentials from the database and convert them with the fhi2upf tool and then automate some test calculations to make sure the transfer is correct. I haven't used fhi2upf before, but I'll look into it. For more information, you can also go to the NNIN virtual vault to find links to pseudopotential generators, converters, and online databases: http://www.nnin.org/nnin_comp_psp_vault.html Best regards, Derek ################################ Derek Stewart, Ph. D. Senior Research Associate ** New Webpage ** http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 On 3/16/2011 2:01 PM, Nicola Marzari wrote: > On 3/16/11 5:49 PM, Tyler Gordon wrote: >> Hello, >> I am a new user of QE. I am looking for a norm conserving >> pseudopotential for Ti. If anybody has created it, may I request it? >> Thank you. > > Worse case scenario: download/compile the fritz-haber pseudopotential > code, generate the troullier-martins Ti there, and convert it to UPF > with the fhi2upf tool in the upftools directory of Q-E. Check that it > works in calculations where you use ultrasoft Ti instead. > > One question - any volunteer to convert the entire fritz-haber database > in upf format ? > > nicola > From ma at nano.ku.dk Wed Mar 16 19:03:43 2011 From: ma at nano.ku.dk (Martin Andersson) Date: Wed, 16 Mar 2011 19:03:43 +0100 Subject: [Pw_forum] norm conserving Ti pseudopotential In-Reply-To: References: Message-ID: <4D80FB7F.20401@nano.ku.dk> You could try the pseudos at: http://fpmd.ucdavis.edu/potentials/index.htm and use the converter to UPF: http://eslab.ucdavis.edu/software/index.htm I know the converter works, but I have no idea how good the pseudopotentials are. Cheers, Martin Andersson University of Copenhagen On 3/16/2011 6:49 PM, Tyler Gordon wrote: > Hello, > I am a new user of QE. I am looking for a norm conserving > pseudopotential for Ti. If anybody has created it, may I request it? > Thank you. > > > _______________________________________________ > 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/20110316/30b3802b/attachment-0001.htm From giannozz at democritos.it Wed Mar 16 23:12:12 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 16 Mar 2011 23:12:12 +0100 Subject: [Pw_forum] XSpectra on graphite slab In-Reply-To: References: Message-ID: On Mar 16, 2011, at 16:22 , Alain Allouche wrote: > Can somebody explain me the curious behavior of pw.x accepting Ch > on diamond and not on graphite, and this "Wrong xiabs!!!" ?? I'll do half of the job. It is the "london" option that makes the difference. Actually "Ch" is not acceptable syntax, or, more exactly: function "atomic_number" accepts "X", "Xn", n=0,...,9, "X-*", "X_*", where X is any atomic symbol. "Xh" confuses it. Since such routine is not actually called, except in some special cases (DFT-D is one such cases), this has gine unnoticed until now P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From nicola.marzari at materials.ox.ac.uk Wed Mar 16 23:49:17 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 16 Mar 2011 22:49:17 +0000 Subject: [Pw_forum] norm conserving Ti pseudopotential In-Reply-To: References: <4D80FB15.3000206@materials.ox.ac.uk> Message-ID: <4D813E6D.4040001@materials.ox.ac.uk> On 3/16/11 6:15 PM, Paolo Giannozzi wrote: > > On Mar 16, 2011, at 19:01 , Nicola Marzari wrote: > >> Worse case scenario: download/compile the fritz-haber pseudopotential >> code, generate the troullier-martins Ti there, and convert it to UPF >> with the fhi2upf tool in the upftools directory of Q-E. > > this can be done directly with the "atomic" code in QE. Generating a > single-channel > norm-conserving PP without semi-core states is trivial and well > documented. > I agree - one still needs to choose core radii wisely, and avoid ghost states - so one could use those chosen by the fhi code. I also recall that Philippe Gosez, in his PhD thesis, had good/tested values - maybe one could ask him what he used. Thanks to Derek for pointing out the pseudo vault, as well. nicola ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From alain.allouche at univ-provence.fr Thu Mar 17 08:37:59 2011 From: alain.allouche at univ-provence.fr (Alain Allouche) Date: Thu, 17 Mar 2011 08:37:59 +0100 Subject: [Pw_forum] XSpectra on graphite slab In-Reply-To: References: Message-ID: Merci Paolo, I should have though by myself... But even without London, after the right results of pw, XSpectra gives the message which I had not with diamondh ------------------------------------------------- --- Polarisation and k vector [cartesian coordinates]---- xepsilon(:)= 1.00000000 0.00000000 0.00000000 xkvec(:)= 1.00000000 0.00000000 0.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% from main program : error # 63 Wrong xiabs!!! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% stopping ... using these data: &input_xspectra calculation='fermi_level', prefix='graphite', xread_wf=.true., xiabs=1 / &plot / &pseudos filecore='C.wfc', / &cut_occ / 6 6 1 0 0 0 I saw in the source that this error occurs when the atom's type is not found, but which one? I cannot understand regards Alain Le 16 mars 11 ? 23:12, Paolo Giannozzi a ?crit : > On Mar 16, 2011, at 16:22 , Alain Allouche wrote: > >> Can somebody explain me the curious behavior of pw.x accepting Ch >> on diamond and not on graphite, and this "Wrong xiabs!!!" ?? > > > I'll do half of the job. It is the "london" option that makes the > difference. > Actually "Ch" is not acceptable syntax, or, more exactly: function > "atomic_number" accepts "X", "Xn", n=0,...,9, "X-*", "X_*", where X > is any atomic symbol. "Xh" confuses it. Since such routine is not > actually > called, except in some special cases (DFT-D is one such cases), this > has > gine unnoticed until now > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sclauzer at sissa.it Thu Mar 17 10:03:57 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 17 Mar 2011 10:03:57 +0100 Subject: [Pw_forum] Some questions about non-collinear calculation and penalty function In-Reply-To: References: Message-ID: <4FD209FE-A822-4079-9147-8108F985F5DC@sissa.it> Dear Sahar, I'll try to reply to these question if I can Il giorno 03/mar/2011, alle ore 19.39, Sahar Mirshamsi ha scritto: > Hi all, > I have some questions regarding non-collinear calculation and using > penalty function in pwscf. > 1) In constaint_magnetization ='atomic', is starting magnetization as the > target magnetization? Yes, the starting_magnetization(:) are used both for the starting and the target local magnetizations in that case. > I have read this post > http://www.democritos.it/pipermail/pw_forum/2009-December/015342.html > and also in input.f90 I found > mcons(1,nt) = starting_magnetization(nt) * SIN( theta ) * COS( > phi ) > mcons(2,nt) = starting_magnetization(nt) * SIN( theta ) * SIN( > phi ) > mcons(3,nt) = starting_magnetization(nt) * COS( theta ) > So it means both magnitude and direction of atomic magnetizations are > constrained, is this correct? Yes, you can fix the direction using angle1 and angle2. > 2) If above statement is correct, then the same problem as posted in above > link will still exist, since starting_magnetization=m/n, then for > constraining the magnitude of magnetization to desired value, we should > multiply the magnitude of magnetization by charge and then replace it as > starting_magnitization, is this correct? I'm not sure I understand when you say > starting_magnetization=m/n Which part of the code are you speaking about? Can you specify where? If I understood correctly, I think that this kind of problem was fixed by Paolo after the forum discussion you are referring to. If you look in input.f90, the case with constraints has been distinguished from that without. In the former, the starting magnetization is no more normalized between -1 and 1 (search for SELECT CASE( trim( constrained_magnetization ) ) in that file) > 3) What is the relation between charge and magnetization printed in scf > calculation with those which we can get with using projwf.x, I expect they > should get almost same numbers but in scf output for carbons in Graphene > nanoribbon I get charge=0.6 and magnetization=0.1 while in projwf.x output > I get charge=4 and polarization=0.2-0.3 which the latest one makes more > sense. Such a large difference sound strange and suspicious to me. The two methods of computing local magnetic moments are different, but I believe they should not give contrasting results. There has been some recent discussion about the first method, which mainly concerns the subroutine make_pointlists.f90 (see recent posts on the forum and the subroutine itself). Is your atomic structure fully relaxed, or are there any atoms too close to each other? > 4) Also, in some cases of non-collinear calculation with using penalty > function, when I track "estimated scf accuracy" it is decreasing till > reaching the threshold and stopping the job while "total energy" is > oscillating in some range instead of converging to a number , any idea > what's the problem? is this range larger than the "estimated scf accuracy"? Please provide some example on this point. > 5) The total energy printed in scf calculation does not include constraint > energy, right? It's just energy of the structure with the constraint > configuration of magnetizations, right? > I appreciate any help in finding the answers of these questions. I'm not completely sure on this point, but it looks to me that the constraint energy is included through the potential, which is augmented in the add_bfield.f90 subroutine. The magnetic penalty energy is also computed and printed by the same subroutine (search for etcon). Not sure that the two energies are the same... What I think I have understood is that you should trust only the total energy for the system where the constraint is (almost) satisfied, implying that both constraint energy and constraining potential are very small. To achieve this you have to play with lambda: a bigger lambda gives a better fulfilment of the constraint, but at the same time convergence becomes much more difficult (depending on the system and on the starting configuration). HTH GS > > Sahar Mishamsi > Quantum Theory Project and Physics Department, > University of Florida > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110317/5f37cb35/attachment.htm From matteo.calandra at impmc.jussieu.fr Thu Mar 17 10:29:57 2011 From: matteo.calandra at impmc.jussieu.fr (matteo calandra) Date: Thu, 17 Mar 2011 10:29:57 +0100 Subject: [Pw_forum] XSpectra on graphite slab In-Reply-To: References: Message-ID: <20110317102957.11482cdsuwkho905@www1.impmc.upmc.fr> Dear Alain, as you can read in the manual of the XSPECTRA code, xiabs must be the type of the absorbing atom. In your case, as you put the Ch as the second atom type, then your xiabs must be 2. For what concerns the london option this has never been tested. I have no idea where the DFT-D part of the code is and how it interact with the rest. So it will probably not work. But this is an independent problem. Finally note that here http://cdsagenda5.ictp.it/full_display.php?agenda_id=3218 you can find my lectures on xspectra in which the case of diamond is treated. Convergence with respect to the cell size is very pathological in diamond. All the best, M. Quoting pw_forum-request at pwscf.org: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: XSpectra on graphite slab (Paolo Giannozzi) > 2. Re: norm conserving Ti pseudopotential (Nicola Marzari) > 3. Re: XSpectra on graphite slab (Alain Allouche) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 16 Mar 2011 23:12:12 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] XSpectra on graphite slab > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > On Mar 16, 2011, at 16:22 , Alain Allouche wrote: > >> Can somebody explain me the curious behavior of pw.x accepting Ch >> on diamond and not on graphite, and this "Wrong xiabs!!!" ?? > > > I'll do half of the job. It is the "london" option that makes the > difference. > Actually "Ch" is not acceptable syntax, or, more exactly: function > "atomic_number" accepts "X", "Xn", n=0,...,9, "X-*", "X_*", where X > is any atomic symbol. "Xh" confuses it. Since such routine is not > actually > called, except in some special cases (DFT-D is one such cases), this has > gine unnoticed until now > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 16 Mar 2011 22:49:17 +0000 > From: Nicola Marzari > Subject: Re: [Pw_forum] norm conserving Ti pseudopotential > To: PWSCF Forum > Cc: Paolo Giannozzi > Message-ID: <4D813E6D.4040001 at materials.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 3/16/11 6:15 PM, Paolo Giannozzi wrote: >> >> On Mar 16, 2011, at 19:01 , Nicola Marzari wrote: >> >>> Worse case scenario: download/compile the fritz-haber pseudopotential >>> code, generate the troullier-martins Ti there, and convert it to UPF >>> with the fhi2upf tool in the upftools directory of Q-E. >> >> this can be done directly with the "atomic" code in QE. Generating a >> single-channel >> norm-conserving PP without semi-core states is trivial and well >> documented. >> > > > I agree - one still needs to choose core radii wisely, and avoid > ghost states - so one could use those chosen by the fhi code. I also > recall that Philippe Gosez, in his PhD thesis, had good/tested values - > maybe one could ask him what he used. > > Thanks to Derek for pointing out the pseudo vault, as well. > > nicola > > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > > > ------------------------------ > > Message: 3 > Date: Thu, 17 Mar 2011 08:37:59 +0100 > From: Alain Allouche > Subject: Re: [Pw_forum] XSpectra on graphite slab > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes > > Merci Paolo, I should have though by myself... But even without > London, after the right results of pw, XSpectra gives the message > which I had not with diamondh > > ------------------------------------------------- > --- Polarisation and k vector [cartesian coordinates]---- > xepsilon(:)= 1.00000000 0.00000000 0.00000000 > xkvec(:)= 1.00000000 0.00000000 0.00000000 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > from main program : error # 63 > Wrong xiabs!!! > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > > stopping ... > > using these data: > > &input_xspectra > calculation='fermi_level', > prefix='graphite', > xread_wf=.true., > xiabs=1 > / > &plot > / > &pseudos > filecore='C.wfc', > / > &cut_occ > / > 6 6 1 0 0 0 > > I saw in the source that this error occurs when the atom's type is not > found, but which one? I cannot understand > regards > Alain > > > Le 16 mars 11 ? 23:12, Paolo Giannozzi a ?crit : > >> On Mar 16, 2011, at 16:22 , Alain Allouche wrote: >> >>> Can somebody explain me the curious behavior of pw.x accepting Ch >>> on diamond and not on graphite, and this "Wrong xiabs!!!" ?? >> >> >> I'll do half of the job. It is the "london" option that makes the >> difference. >> Actually "Ch" is not acceptable syntax, or, more exactly: function >> "atomic_number" accepts "X", "Xn", n=0,...,9, "X-*", "X_*", where X >> is any atomic symbol. "Xh" confuses it. Since such routine is not >> actually >> called, except in some special cases (DFT-D is one such cases), this >> has >> gine unnoticed until now >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 45, Issue 36 > **************************************** > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From alain.allouche at univ-provence.fr Thu Mar 17 11:14:35 2011 From: alain.allouche at univ-provence.fr (Alain Allouche) Date: Thu, 17 Mar 2011 11:14:35 +0100 Subject: [Pw_forum] XSpectra on graphite slab In-Reply-To: <20110317102957.11482cdsuwkho905@www1.impmc.upmc.fr> References: <20110317102957.11482cdsuwkho905@www1.impmc.upmc.fr> Message-ID: <74CFB73D-0464-45EB-AF34-3518AD598518@univ-provence.fr> Thank you Matteo, I saw that but I referred to the ATOM_LIST not the ATOM_TYPE, thanks again A. Le 17 mars 11 ? 10:29, matteo calandra a ?crit : > Dear Alain, > > as you can read in the manual of the XSPECTRA code, > xiabs must be the type of the absorbing atom. In your case, > as you put the Ch as the second atom type, then your xiabs > must be 2. > > For what concerns the london option this has never been tested. > I have no idea where the DFT-D part of the code is and how it > interact with > the rest. So it will probably not work. But this is an independent > problem. > > Finally note that here > > http://cdsagenda5.ictp.it/full_display.php?agenda_id=3218 > > you can find my lectures on xspectra in which the case of diamond is > treated. > Convergence with respect to the cell size is very pathological in > diamond. > > All the best, M. > > > > > Quoting pw_forum-request at pwscf.org: > >> Send Pw_forum mailing list submissions to >> pw_forum at pwscf.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.democritos.it/mailman/listinfo/pw_forum >> or, via email, send a message with subject or body 'help' to >> pw_forum-request at pwscf.org >> >> You can reach the person managing the list at >> pw_forum-owner at pwscf.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Pw_forum digest..." >> >> >> Today's Topics: >> >> 1. Re: XSpectra on graphite slab (Paolo Giannozzi) >> 2. Re: norm conserving Ti pseudopotential (Nicola Marzari) >> 3. Re: XSpectra on graphite slab (Alain Allouche) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 16 Mar 2011 23:12:12 +0100 >> From: Paolo Giannozzi >> Subject: Re: [Pw_forum] XSpectra on graphite slab >> To: PWSCF Forum >> Message-ID: >> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed >> >> On Mar 16, 2011, at 16:22 , Alain Allouche wrote: >> >>> Can somebody explain me the curious behavior of pw.x accepting Ch >>> on diamond and not on graphite, and this "Wrong xiabs!!!" ?? >> >> >> I'll do half of the job. It is the "london" option that makes the >> difference. >> Actually "Ch" is not acceptable syntax, or, more exactly: function >> "atomic_number" accepts "X", "Xn", n=0,...,9, "X-*", "X_*", where X >> is any atomic symbol. "Xh" confuses it. Since such routine is not >> actually >> called, except in some special cases (DFT-D is one such cases), >> this has >> gine unnoticed until now >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 16 Mar 2011 22:49:17 +0000 >> From: Nicola Marzari >> Subject: Re: [Pw_forum] norm conserving Ti pseudopotential >> To: PWSCF Forum >> Cc: Paolo Giannozzi >> Message-ID: <4D813E6D.4040001 at materials.ox.ac.uk> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> On 3/16/11 6:15 PM, Paolo Giannozzi wrote: >>> >>> On Mar 16, 2011, at 19:01 , Nicola Marzari wrote: >>> >>>> Worse case scenario: download/compile the fritz-haber >>>> pseudopotential >>>> code, generate the troullier-martins Ti there, and convert it to >>>> UPF >>>> with the fhi2upf tool in the upftools directory of Q-E. >>> >>> this can be done directly with the "atomic" code in QE. Generating a >>> single-channel >>> norm-conserving PP without semi-core states is trivial and well >>> documented. >>> >> >> >> I agree - one still needs to choose core radii wisely, and avoid >> ghost states - so one could use those chosen by the fhi code. I also >> recall that Philippe Gosez, in his PhD thesis, had good/tested >> values - >> maybe one could ask him what he used. >> >> Thanks to Derek for pointing out the pseudo vault, as well. >> >> nicola >> >> ---------------------------------------------------------------------- >> Prof Nicola Marzari Department of Materials University of >> Oxford >> Chair of Materials Modelling Director, Materials Modelling >> Laboratory >> nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/ >> NM >> >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 17 Mar 2011 08:37:59 +0100 >> From: Alain Allouche >> Subject: Re: [Pw_forum] XSpectra on graphite slab >> To: PWSCF Forum >> Message-ID: >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; >> delsp=yes >> >> Merci Paolo, I should have though by myself... But even without >> London, after the right results of pw, XSpectra gives the message >> which I had not with diamondh >> >> ------------------------------------------------- >> --- Polarisation and k vector [cartesian coordinates]---- >> xepsilon(:)= 1.00000000 0.00000000 0.00000000 >> xkvec(:)= 1.00000000 0.00000000 0.00000000 >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> %% >> %%%%%%%%% >> from main program : error # 63 >> Wrong xiabs!!! >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> %% >> %%%%%%%%% >> >> stopping ... >> >> using these data: >> >> &input_xspectra >> calculation='fermi_level', >> prefix='graphite', >> xread_wf=.true., >> xiabs=1 >> / >> &plot >> / >> &pseudos >> filecore='C.wfc', >> / >> &cut_occ >> / >> 6 6 1 0 0 0 >> >> I saw in the source that this error occurs when the atom's type is >> not >> found, but which one? I cannot understand >> regards >> Alain >> >> >> Le 16 mars 11 ? 23:12, Paolo Giannozzi a ?crit : >> >>> On Mar 16, 2011, at 16:22 , Alain Allouche wrote: >>> >>>> Can somebody explain me the curious behavior of pw.x accepting Ch >>>> on diamond and not on graphite, and this "Wrong xiabs!!!" ?? >>> >>> >>> I'll do half of the job. It is the "london" option that makes the >>> difference. >>> Actually "Ch" is not acceptable syntax, or, more exactly: function >>> "atomic_number" accepts "X", "Xn", n=0,...,9, "X-*", "X_*", where X >>> is any atomic symbol. "Xh" confuses it. Since such routine is not >>> actually >>> called, except in some special cases (DFT-D is one such cases), this >>> has >>> gine unnoticed until now >>> >>> P. >>> --- >>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >>> Phone +39-0432-558216, fax +39-0432-558222 >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> End of Pw_forum Digest, Vol 45, Issue 36 >> **************************************** >> > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum Dr. Alain ALLOUCHE Physique des Interactions Ioniques et Moleculaires CNRS / Universite de Provence Campus Saint Jerome Service 242 Avenue de l'Escadrille Normandie-Niemen 13397 Marseille Cedex 20 - France Tel : +33 (0) 4 91 28 85 76 Mobile:+33 681 84 80 66 Fax : +33 491.28.89.05 email: Alain.Allouche at univ-provence.fr From ranjit.phy at gmail.com Thu Mar 17 13:05:48 2011 From: ranjit.phy at gmail.com (Ranjit Thapa) Date: Thu, 17 Mar 2011 17:35:48 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 45, Issue 31 In-Reply-To: References: Message-ID: Dear all I follow the read me file but i want to know what exactly the command is for my system, cluster with two cpu and 8 core and othe single core. i.e total core 9 but (in the form 8 + 1) On Tue, Mar 15, 2011 at 9:17 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. parallel (Ranjit Thapa) > 2. Re: parallel (Lorenzo Paulatto) > 3. Re: A small bug of QE when nat >= 100, and the solution > (Gabriele Sclauzero) > 4. Pw_forum Subscription (Johnson, D. Ray) > 5. Re: Pw_forum Subscription (Stefano de Gironcoli) > 6. Re: Pw_forum Subscription (Paolo Giannozzi) > 7. smearing (peyman amiri) > 8. Re: smearing (?????? ?????) > 9. sorting phonons by magnitude and band index ( lfhuang ) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 Mar 2011 14:47:06 +0530 > From: Ranjit Thapa > Subject: [Pw_forum] parallel > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > dear all, > > I am new about quantum espresso. I make a cluster for practice with two CPU > (first one intel i7 processor (i.e 8 core) and other pentium IV processor > (single core)). I run an example > given in MPICH2-1.3.2. The results is well, i.e both the processor process > and give the result. > > After that i load Quantum Espresso-4.2.1. It detect mpi parallel enviroment > when i run an example given in the QE examples folder, using the comand > ./run_example > the reults is well but it only excute in 1 processor (but mpi is > detected). > > I think have to use mpiexec command but, i am not able to find what command > should i give for running the example in my cluster sytem (two different > type of CPU). > > please help me > > -- > Dr. Ranjit Thapa > Research Associate > Materials Simulation Lab. > Department of Materials Science > Indian Association for the Cultivation of Science > KOL-700032 > Mobile No: +91 9593936060, +91 9804101030 > http://sites.google.com/site/ranjitphy/home > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110315/4f4a8014/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Tue, 15 Mar 2011 10:24:52 +0100 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] parallel > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 15 marzo 2011 alle ore 10:17:06, Ranjit Thapa > ha scritto: > > I think have to use mpiexec command but, i am not able to find what > > command should i give for running the example in my cluster sytem (two > > different > > type of CPU). > > > Dear Ranjit, > it's all explained in examples/README, section 2. It's all about editing > the file "nvironment_variables". > > best regards > > > -- > Lorenzo Paulatto > post-doc @ IMPMC/UPMC - Universit? Paris 6 > phone: +33 (0)1 44 27 74 89 > www: http://www-int.impmc.upmc.fr/~paulatto/ > > previously (take note of the change!): > phd student @ SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > www: http://people.sissa.it/~paulatto/ > > > ------------------------------ > > Message: 3 > Date: Tue, 15 Mar 2011 10:39:18 +0100 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] A small bug of QE when nat >= 100, and the > solution > To: PWSCF Forum > Message-ID: <31C2FBE0-A135-445D-8028-744D1D120088 at sissa.it> > Content-Type: text/plain; charset="iso-8859-1" > > > Il giorno 14/mar/2011, alle ore 21.54, juan sotelo ha scritto: > > > It seems the problem could be solved by creating a fortran-format on > > the fly, e.g., > > ===== > > program foo > > ! hints from http://www.sdsc.edu/~tkaiser/f90.html > > implicit none > > character (len=30)fstr ! create a format on the fly > > integer n_dgts, na, nb > > na = 30000 > > nb = 1000000 > > n_dgts = floor(log10(abs(real(max(na,nb)))))+1 > > !create a format on the fly > > write(fstr,'("(2i",i4,")")')n_dgts+1 > > write(*,fstr) na, nb > > end program > > ===== > > Output: > > 30000 1000000 > > This is a nice trick, but I'm not sure that all compilers will accept it. I > remember complaints about the fact that the format string should be either a > constant string or a pointer to a format line. > Just for information, on which compilers have you tried? > > Thanks, > > > GS > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110315/e74236cd/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Tue, 15 Mar 2011 09:52:26 -0400 > From: "Johnson, D. Ray" > Subject: [Pw_forum] Pw_forum Subscription > To: "pw_forum at pwscf.org" > Message-ID: > Content-Type: text/plain; charset=iso-8859-1 > > Please change my email address to: D Ray Johnson, drjsej at hughes.net > Thank you. > > Regards, > > D Ray Johnson > The Oak Ridge National Lab > Oak Ridge, TN > USA > > > > ------------------------------ > > Message: 5 > Date: Tue, 15 Mar 2011 15:02:46 +0100 > From: Stefano de Gironcoli > Subject: Re: [Pw_forum] Pw_forum Subscription > To: PWSCF Forum > Message-ID: <4D7F7186.30508 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > unsubscribe and subscribe with the new address. > cheers, > stefano > > On 03/15/2011 02:52 PM, Johnson, D. Ray wrote: > > Please change my email address to: D Ray Johnson, drjsej at hughes.net > > Thank you. > > > > Regards, > > > > D Ray Johnson > > The Oak Ridge National Lab > > Oak Ridge, TN > > USA > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ------------------------------ > > Message: 6 > Date: Tue, 15 Mar 2011 15:08:20 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Pw_forum Subscription > To: PWSCF Forum > Message-ID: <4D7F72D4.2030905 at democritos.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Stefano de Gironcoli wrote: > > > unsubscribe and subscribe with the new address. > > no longer true, I think: it used to be not possible for a > subscriber (and not even for the administator) to change > the subscription address, but now everybody can do it. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > ------------------------------ > > Message: 7 > Date: Tue, 15 Mar 2011 07:38:01 -0700 (PDT) > From: peyman amiri > Subject: [Pw_forum] smearing > To: PWSCF Forum > Message-ID: <733035.72917.qm at web161715.mail.bf1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > > Dear all users > Can i use? " occupations='tetrahedra' " > in my scf input file? i use this option and encounter with the message > below: > > { from iosys : error #???????? 1 > ???? tetrahedra should be used only for calculation of DOS} > What is wrong? > Thanks in advance > ====================================== > > Peiman Amiri > > Computational Condensed Matter Research Lab > > Physics Department, Isfahan University of Technology, Iran > > > > Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 > > ------------------------------ > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110315/da4e3bc6/attachment-0001.htm > > ------------------------------ > > Message: 8 > Date: Tue, 15 Mar 2011 16:11:20 +0100 > From: ?????? ????? > Subject: Re: [Pw_forum] smearing > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Peiman, > > yes, you can. In order to do so, one has to comment the following (two) > lines in PW/input.f90: > > IF( calculation /= 'nscf' ) CALL errore( 'iosys', & > 'tetrahedra should be used only for calculation of DOS', 1 ) > > and recompile the code again. > Mind, that 'tetrahedra' has to be used for DOS or SCF only, forces and > stresses are > not reliable it this case (they are not variational). > > Best regards, > Maxim. > > 2011/3/15 peyman amiri > > > > > Dear all users > > Can i use " occupations='tetrahedra' " > > in my scf input file? i use this option and encounter with the message > > below: > > > > { from iosys : error # 1 > > tetrahedra should be used only for calculation of DOS} > > What is wrong? > > Thanks in advance > > ====================================== > > Peiman Amiri > > Computational Condensed Matter Research Lab > > Physics Department, Isfahan University of Technology, Iran > > > > Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > Best regards, Max Popov > Ph.D. student > Materials center Leoben (MCL), Leoben, Austria. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110315/5474db58/attachment-0001.htm > > ------------------------------ > > Message: 9 > Date: Tue, 15 Mar 2011 23:47:05 +0800 > From: " lfhuang " > Subject: [Pw_forum] sorting phonons by magnitude and band index > To: " pwscf forum " > Message-ID: <20110315154705.4016.qmail at ms.hfcas.ac.cn> > Content-Type: text/plain; charset="utf-8" > > > Dear QEers: > Sorting phonons by magnitude and band index are two ways to plot phonon > dispersions. Especially, the later is important for the precise > understanding of phonons and for the calculation of some physical > parameters, like Gruneissen constants. I have written a small code (named > sort_phon) to do these sorting tasks, which needs the output of Quantum > ESPRESSO (matdyn.modes) as input. The code package can be download in the > link below: > > http://bbs.sciencenet.cn/home.php?mod=space&uid=345795&do=blog&quickforward=1&id=422819 > where an introductory tutorial and an example about graphene phonon > dispersions is included. > I sincerely hope it could bring you some convenience in your daily > research. > Best Wishes! > Yours Sincerely > L. F. Huang ------ > ====================================================================== > L.F.Huang(???) DFT and phonon physics > ====================================================================== > Add: Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591464-326(office) > Fax: 86-551-5591434 > Our group: http://theory.issp.ac.cn > ====================================================================== > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110315/bdd8d8f4/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 45, Issue 31 > **************************************** > -- Dr. Ranjit Thapa Research Associate Materials Simulation Lab. Department of Materials Science Indian Association for the Cultivation of Science KOL-700032 Mobile No: +91 9593936060, +91 9804101030 http://sites.google.com/site/ranjitphy/home -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110317/1cf5f0ce/attachment-0001.htm From giannozz at democritos.it Thu Mar 17 14:04:30 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 17 Mar 2011 14:04:30 +0100 Subject: [Pw_forum] Pw_forum Digest, Vol 45, Issue 31 In-Reply-To: References: Message-ID: <268B5E44-DF4C-4A85-AE4A-D1A89CE6CEA2@democritos.it> On Mar 17, 2011, at 13:05 , Ranjit Thapa wrote: > I follow the read me file but i want to know what exactly > the command is for my system 0) please do not reply to a digest 1) your question makes as much sense as asking "I want to know what time exactly my wristwatch shows". P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From vinothrece at gmail.com Thu Mar 17 15:04:55 2011 From: vinothrece at gmail.com (vinoth r) Date: Thu, 17 Mar 2011 19:34:55 +0530 Subject: [Pw_forum] perpendicular saw like potential Message-ID: dear all, with this mail i attached my input file for saw like potential perpendicular to BN layer.could you help me whether i applied 1.4v(saw like potential) perpendicular to axis. thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110317/20d584ee/attachment.htm From vinothrece at gmail.com Thu Mar 17 16:06:02 2011 From: vinothrece at gmail.com (vinoth r) Date: Thu, 17 Mar 2011 20:36:02 +0530 Subject: [Pw_forum] saw like potential Message-ID: dear all, with this mail i attached my input file for saw like potential perpendicular to BN layer.could you help me whether i applied 1.4v(saw like potential) perpendicular to axis. thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110317/c5b9df3c/attachment.htm -------------- next part -------------- &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/home/vino/work/' , wfcdir = '/home/vino/work/' , pseudo_dir = '/home/vino/espresso-4.2.1/pseudo/' , verbosity = 'high' , tefield = .true. , / &SYSTEM ibrav = 4, celldm(1) = 2.456, celldm(3) = 16, nat = 4, ntyp = 2, ecutwfc = 400 , edir = 1 , emaxpos = 0.5D , eopreg = 0.5 , eamp = 2.72256676e-12 , / &ELECTRONS diagonalization = 'david' , / &IONS / ATOMIC_SPECIES N 14.00000 N.pz-nd-rrkjus.UPF B 10.00000 B.pz-vbc.UPF ATOMIC_POSITIONS angstrom N 0.000000000 0.000000000 4.560000000 B 1.230600000 0.710501000 4.560000000 B 0.000000000 0.000000000 8.000000000 N 1.230600000 0.710501000 8.000000000 K_POINTS automatic 36 36 1 0 0 0 From pnyawere at gmail.com Thu Mar 17 19:39:17 2011 From: pnyawere at gmail.com (Phillip Nyawere) Date: Thu, 17 Mar 2011 19:39:17 +0100 Subject: [Pw_forum] Vacancy energy Message-ID: Dear all, I am doing vacancy calculation of a flouride but I am obtaining positive energy for cation and negative energy for anion. The material is barium floride. Can someone help me understand this problem? -- Phillip W. Otieno Nyawere, Kabarak University, P.O. Box Private Bag - 20157, KABARAK Nakuru Kenya Tel +254728342054, pnyawere at gmail.com, potieno at kabarak.ac.ke God raises the meek from the ground and sits them with Kings. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110317/52e9c279/attachment.htm From germaneau at gucas.ac.cn Fri Mar 18 18:24:31 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Fri, 18 Mar 2011 13:24:31 -0400 Subject: [Pw_forum] constrained cell optimization Message-ID: <4D83954F.3090005@gucas.ac.cn> Dear all, I wish to do a constrained cell optimization by keeping constant the c axis of my hexagonal lattice. I tried to set "cell_dofree" but the program complains. So, can you please tell me whether there a way do to it. Thanks in advance, Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110318/57e3701a/attachment.htm From pnyawere at gmail.com Fri Mar 18 06:36:28 2011 From: pnyawere at gmail.com (Phillip Nyawere) Date: Fri, 18 Mar 2011 06:36:28 +0100 Subject: [Pw_forum] vacancy defect Message-ID: Hello all, I am calculating vacancy formation energy of barium flouride. I am using a super cell of 96 atoms. When I create barium vacancy and do a relax calculation, the vacancy energy is positive in sign. When i do the same for flouride ion, the vacancy energy turns to be negative. This energy is calculated by the formula E = E(vacancy) + E(single atom) - E(pure crystal). Both energies I hope should be positive. Thanks, -- Phillip W. Otieno Nyawere, Kabarak University, P.O. Box Private Bag - 20157, KABARAK Nakuru Kenya Tel +254728342054, pnyawere at gmail.com, potieno at kabarak.ac.ke God raises the meek from the ground and sits them with Kings. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110318/b3319864/attachment.htm From giannozz at democritos.it Fri Mar 18 08:30:11 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 18 Mar 2011 08:30:11 +0100 Subject: [Pw_forum] constrained cell optimization In-Reply-To: <4D83954F.3090005@gucas.ac.cn> References: <4D83954F.3090005@gucas.ac.cn> Message-ID: <19A2931D-A777-45C1-BE35-3091A8375C0F@democritos.it> On Mar 18, 2011, at 18:24 , Eric Germaneau wrote: > I tried to set "cell_dofree" but the program complains. > which version of which code complains how when you set cell_dofree to what? --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From janfelix.binder at epfl.ch Fri Mar 18 15:25:36 2011 From: janfelix.binder at epfl.ch (Jan Felix Binder) Date: Fri, 18 Mar 2011 15:25:36 +0100 Subject: [Pw_forum] saw like potential In-Reply-To: References: Message-ID: <4D836B60.3030608@epfl.ch> the axis perpendicular to the surface is the z-axis? then edir = 3 you should not use the same values for emaxpos and eoreg. Have a look on the example... On 03/17/2011 04:06 PM, vinoth r wrote: > > dear all, > with this mail i attached my input file for saw like > potential perpendicular to BN layer.could you help me whether i > applied 1.4v(saw like potential) perpendicular to axis. > > > thank you > > > _______________________________________________ > 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/20110318/86e05d5f/attachment.htm From germaneau at gucas.ac.cn Sat Mar 19 03:45:52 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Fri, 18 Mar 2011 22:45:52 -0400 Subject: [Pw_forum] constrained cell optimization In-Reply-To: <500433372.15826@test1.gucas.ac.cn> References: <4D83954F.3090005@gucas.ac.cn> <500433372.15826@test1.gucas.ac.cn> Message-ID: <4D8418E0.2020808@gucas.ac.cn> I'm sorry I had to provide more details. I use the last version (4.2.1). I set ibrav=4, calculation='vc-relax' and cell_dofree = 'x' (I also tried xy). The program crash with the following message: / from checkallsym : error # 2 not orthogonal operation/ What I'd like to do is to optimized the lattice parameter "a" and keep "c" constant. Thanks, Eric. On 03/18/2011 03:30 AM, Paolo Giannozzi wrote: > On Mar 18, 2011, at 18:24 , Eric Germaneau wrote: > >> I tried to set "cell_dofree" but the program complains. > which version of which code complains how when you > set cell_dofree to what? > > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110318/be6a657b/attachment.htm From agkvashnin at gmail.com Fri Mar 18 18:08:05 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Fri, 18 Mar 2011 20:08:05 +0300 Subject: [Pw_forum] Error in running bands.x Message-ID: Hello QE user, While I running my file for band structure calculation in out file I saw the error message : %%% from do_bands : error # 1 reading inputpp namelist %%% What does the problem with my input file? I write input file below &inputpp prefix='carbon', outdir='./', filband='carbon.band', lsym=.true., / Thank you! -- Sincerely yours Alexander G. Kvashnin -------------------------------------------------------------------------------------------------------------------------------- Student Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110318/3343919b/attachment.htm From agkvashnin at gmail.com Fri Mar 18 18:16:58 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Fri, 18 Mar 2011 20:16:58 +0300 Subject: [Pw_forum] Error in running bands.x In-Reply-To: References: Message-ID: I'm sorry for my question. Please if you can, don't spread it on pw_forum. Thank you. Sorry... On 18 March 2011 20:08, Alexander G. Kvashnin wrote: > Hello QE user, > > While I running my file for band structure calculation in out file I saw > the error message : > > %%% > from do_bands : error # 1 > reading inputpp namelist > %%% > > What does the problem with my input file? > I write input file below > > &inputpp > prefix='carbon', > outdir='./', > filband='carbon.band', > lsym=.true., > / > > Thank you! > > -- > Sincerely yours > Alexander G. Kvashnin > > -------------------------------------------------------------------------------------------------------------------------------- > Student > Moscow Institute of Physics and Technology http://mipt.ru/ > 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia > > Junior research scientist > Technological Institute for Superhard > and Novel Carbon Materials > http://www.ntcstm.troitsk.ru/ > 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia > ================================================================ > > -- Sincerely yours Alexander G. Kvashnin -------------------------------------------------------------------------------------------------------------------------------- Student Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110318/41ab8c0d/attachment.htm From faccin.giovani at gmail.com Fri Mar 18 21:05:04 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Fri, 18 Mar 2011 16:05:04 -0400 Subject: [Pw_forum] Is it possible to fix starting_ns_eigenvalue during many interactions? Message-ID: Dear pw.x users, In a DFT+U calculation, one can use the 'mixing_fixed_ns' parameter to force the system to converge using the initial ns configuration. For example, for a given atom, one can have this: *mixing_fixed_ns =100* (any large number fits). Initial setup: *atom 2 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000 * (at interaction 31, the calculation converges, and the system prints:) *atom 2 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000* Ok, so the ns eigenvalues remained fixed during the entire calculation, as it should be. Now I'd like to have this same behavior with an user given set of eigenvalues. For example, I can set: * starting_ns_eigenvalue(1,2,1) = 0.0 starting_ns_eigenvalue(2,2,1) = 0.0476060 starting_ns_eigenvalue(3,2,1) = 0.0476060 starting_ns_eigenvalue(4,2,1) = 0.9654373 starting_ns_eigenvalue(5,2,1) = 0.9954307* Now the same atom would yield this output: Calculation starts: * atom 2 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000 * iteration # 1 (modifies the default setup with scf): * atom 2 spin 2 eigenvalues: 0.0000004 0.0000074 0.0287535 0.2107956 0.2107956* Modify starting ns matrices according to input values enter write_ns (now the system will change the eigenvalues according to the starting_ns_eigenvalue) * atom 2 spin 2 eigenvalues: -0.0000000 0.0476060 0.0476060 0.9654373 0.9954307 *(This is the state I'd like to have fixed!) Calculation continues. At every interaction: * RESET ns to initial values (iter <= mixing_fixed_ns)* So that, on the end, I get this set of eigenvalues: * atom 2 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000* So the 'mixing_fixed_ns' appears to be fixing the eigenvalues not at the initial state one gives the program using 'starting_ns_eigenvalue'; instead, it's fixing it to the initial default configuration. Is it possible to configure pw.x to keep fixed an user set of eigenvalues, instead of the initial setup? In this example, I'd like the set of eigenvalues 0.0000000 0.0476060 0.0476060 0.9654373 0.9954307 to be fixed during the entire calculation. Should it be useful, I'm attaching an example input file and it's complete output, showing what I described above. What I really need here is to be able to force the the system to converge to a given state, even if this state is not the one with minimum energy. That's why I'm trying to impose specific eigenvalues. Perhaps there's a better way of doing this? Thank you very much! -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110318/471ad0da/attachment-0001.htm -------------- next part -------------- &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = './output' , pseudo_dir = '../pseudo/' , prefix = 'fe' , etot_conv_thr = 1.0D-9 , forc_conv_thr = 1.0D-6 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 1, celldm(1) = 15, nat = 2, ntyp = 1, ecutwfc = 100 , ecutrho = 300 , nbnd = 18, occupations = 'smearing' , degauss = 0.0005 , smearing = 'methfessel-paxton' , nspin = 2 , assume_isolated = 'martyna-tuckerman' starting_magnetization(1) = 0.9, lda_plus_u = .true. , Hubbard_U(1) = 3.1, starting_ns_eigenvalue(1,2,1) = 0.0 starting_ns_eigenvalue(2,2,1) = 0.0476060 starting_ns_eigenvalue(3,2,1) = 0.0476060 starting_ns_eigenvalue(4,2,1) = 0.9654373 starting_ns_eigenvalue(5,2,1) = 0.9954307 / &ELECTRONS conv_thr = 1.0e-9 , mixing_beta = 0.7 , diagonalization = 'david' , mixing_fixed_ns = 500, / ATOMIC_SPECIES Fe 58.69000 Fe.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Fe 2.070000000 0.000000000 0.000000000 Fe 0.000000000 0.000000000 0.000000000 K_POINTS automatic 1 1 1 1 1 1 -------------- next part -------------- Program PWSCF v.4.2.1 starts on 18Mar2011 at 15: 4:43 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 1 processors Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... file Fe.pbe-nd-rrkjus.UPF: wavefunction(s) 4S renormalized Subspace diagonalization in iterative solution of the eigenvalue problem: Too few procs for parallel algorithm: we need at least 4 procs per pool a serial algorithm will be used warning: symmetry operation # 2 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 3 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 13 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 14 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 25 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 28 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 39 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 40 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates Planes per process (thick) : nr3 = 90 npp = 90 ncplane = 8100 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 90 5385 296459 90 5385 296459 1925 63461 bravais-lattice index = 1 lattice parameter (a_0) = 15.0000 a.u. unit-cell volume = 3375.0000 (a.u.)^3 number of atoms/cell = 2 number of atomic types = 1 number of electrons = 16.00 number of Kohn-Sham states= 18 kinetic-energy cutoff = 100.0000 Ry charge density cutoff = 300.0000 Ry convergence threshold = 1.0E-09 mixing beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE (1434) EXX-fraction = 0.00 celldm(1)= 15.000000 celldm(2)= 0.000000 celldm(3)= 0.000000 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( 0.000000 1.000000 0.000000 ) a(3) = ( 0.000000 0.000000 1.000000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.000000 0.000000 0.000000 ) b(2) = ( 0.000000 1.000000 0.000000 ) b(3) = ( 0.000000 0.000000 1.000000 ) PseudoPot. # 1 for Fe read from file Fe.pbe-nd-rrkjus.UPF Pseudo is Ultrasoft + core correction, Zval = 8.0 Generated by new atomic code, or converted to UPF format Using radial grid of 957 points, 6 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 l(5) = 2 l(6) = 2 Q(r) pseudized with 0 coefficients atomic species valence mass pseudopotential Fe 8.00 58.69000 Fe( 1.00) Starting magnetic structure atomic species magnetization Fe 0.900 LDA+U calculation, Hubbard_lmax = 2 atomic species L Hubbard U Hubbard alpha Fe 2 0.227846 0.000000 8 Sym.Ops. (no inversion) Cartesian axes site n. atom positions (a_0 units) 1 Fe tau( 1) = ( 0.2607822 0.0000000 0.0000000 ) 2 Fe tau( 2) = ( 0.0000000 0.0000000 0.0000000 ) number of k points= 2 gaussian broad. (Ry)= 0.0005 ngauss = 1 cart. coord. in units 2pi/a_0 k( 1) = ( -0.5000000 -0.5000000 -0.5000000), wk = 1.0000000 k( 2) = ( -0.5000000 -0.5000000 -0.5000000), wk = 1.0000000 G cutoff = 1709.7950 ( 296459 G-vectors) FFT grid: ( 90, 90, 90) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 15.66 Mb ( 57016, 18) Atomic wavefunctions 10.44 Mb ( 57016, 12) NL pseudopotentials 31.32 Mb ( 57016, 36) Each V/rho on FFT grid 22.25 Mb ( 729000, 2) Each G-vector array 2.26 Mb ( 296459) G-vector shells 0.01 Mb ( 1428) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 62.64 Mb ( 57016, 72) Each subspace H/S matrix 0.08 Mb ( 72, 72) Each matrix 0.01 Mb ( 36, 18) Arrays for rho mixing 88.99 Mb ( 729000, 8) alpha, beta MT = 2.7999999999999998 0.17857142857142858 Check: negative/imaginary core charge= -0.000016 0.000000 Initial potential from superposition of free atoms starting charge 15.99873, renormalised to 16.00000 negative rho (up, down): 0.840E-05 0.442E-06 Parameters of the lda+U calculation: Number of iteration with fixed ns =500 Starting ns and Hubbard U : enter write_ns U( 1) = 3.1000 alpha( 1) = 0.0000 atom 1 Tr[ns(na)]= 6.0000000 atom 1 spin 1 atom 1 spin 1 eigenvalues: 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 atom 1 spin 2 atom 1 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 atom 2 Tr[ns(na)]= 6.0000000 atom 2 spin 1 atom 2 spin 1 eigenvalues: 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 atom 2 spin 2 atom 2 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 nsum = 12.0000000 exit write_ns Atomic wfc used for LDA+U Projector are NOT orthogonalized Starting wfc are 12 atomic + 6 random wfc total cpu time spent up to now is 18.36 secs per-process dynamical memory: 210.5 Mb Self-consistent Calculation iteration # 1 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 11.5 enter write_ns U( 1) = 3.1000 alpha( 1) = 0.0000 atom 1 Tr[ns(na)]= 5.4338797 atom 1 spin 1 atom 1 spin 1 eigenvalues: 0.9912601 0.9975801 0.9978221 0.9978221 0.9981564 eigenvectors 1 0.5000000 0.0000000 0.0000000 -0.8660254 -0.0000000 2 0.8660254 0.0000000 -0.0000000 0.5000000 0.0000000 3 0.0000000 0.3231293 0.0000000 0.0000000 -0.9463548 4 0.0000000 -0.9463548 -0.0000000 0.0000000 -0.3231293 5 0.0000000 -0.0000000 1.0000000 0.0000000 0.0000000 occupations 0.996 -0.000 -0.000 0.003 0.000 -0.000 0.998 -0.000 0.000 0.000 -0.000 -0.000 0.998 0.000 0.000 0.003 0.000 0.000 0.993 -0.000 0.000 0.000 0.000 -0.000 0.998 atom 1 spin 2 atom 1 spin 2 eigenvalues: 0.0000005 0.0000087 0.0287373 0.2112463 0.2112463 eigenvectors 1 0.8660254 0.0000000 0.0000000 0.5000000 -0.0000000 2 0.0000000 -0.0000000 -1.0000000 0.0000000 0.0000000 3 -0.5000000 -0.0000000 0.0000000 0.8660254 0.0000000 4 -0.0000000 0.4167215 -0.0000000 0.0000000 -0.9090342 5 0.0000000 -0.9090342 0.0000000 -0.0000000 -0.4167215 occupations 0.007 -0.000 0.000 -0.012 0.000 -0.000 0.211 -0.000 0.000 0.000 0.000 -0.000 0.000 -0.000 0.000 -0.012 0.000 -0.000 0.022 -0.000 0.000 0.000 0.000 -0.000 0.211 atom 2 Tr[ns(na)]= 5.4328473 atom 2 spin 1 atom 2 spin 1 eigenvalues: 0.9912596 0.9975606 0.9977966 0.9977966 0.9980812 eigenvectors 1 0.5000000 0.0000000 0.0000000 -0.8660254 -0.0000000 2 0.8660254 0.0000000 -0.0000000 0.5000000 0.0000000 3 0.0000000 0.3501070 0.0000000 0.0000000 -0.9367097 4 0.0000000 -0.9367097 -0.0000000 0.0000000 -0.3501070 5 0.0000000 -0.0000000 1.0000000 0.0000000 0.0000000 occupations 0.996 -0.000 -0.000 0.003 0.000 -0.000 0.998 -0.000 0.000 0.000 -0.000 -0.000 0.998 0.000 0.000 0.003 0.000 0.000 0.993 -0.000 0.000 0.000 0.000 -0.000 0.998 atom 2 spin 2 atom 2 spin 2 eigenvalues: 0.0000004 0.0000074 0.0287535 0.2107956 0.2107956 eigenvectors 1 0.8660254 0.0000000 0.0000000 0.5000000 -0.0000000 2 0.0000000 -0.0000000 -1.0000000 0.0000000 0.0000000 3 -0.5000000 -0.0000000 0.0000000 0.8660254 0.0000000 4 -0.0000000 0.4214217 -0.0000000 0.0000000 -0.9068648 5 0.0000000 -0.9068648 0.0000000 -0.0000000 -0.4214217 occupations 0.007 -0.000 0.000 -0.012 0.000 -0.000 0.211 -0.000 0.000 0.000 0.000 -0.000 0.000 -0.000 0.000 -0.012 0.000 -0.000 0.022 -0.000 0.000 0.000 0.000 -0.000 0.211 nsum = 10.8667269 exit write_ns Modify starting ns matrices according to input values enter write_ns U( 1) = 3.1000 alpha( 1) = 0.0000 atom 1 Tr[ns(na)]= 7.0387207 atom 1 spin 1 atom 1 spin 1 eigenvalues: 0.9912601 0.9975801 0.9978221 0.9978221 0.9981564 eigenvectors 1 0.5000000 0.0000000 0.0000000 -0.8660254 -0.0000000 2 0.8660254 0.0000000 -0.0000000 0.5000000 0.0000000 3 0.0000000 0.3332526 0.0000000 0.0000000 -0.9428376 4 0.0000000 -0.9428376 -0.0000000 0.0000000 -0.3332526 5 0.0000000 -0.0000000 1.0000000 0.0000000 0.0000000 occupations 0.996 -0.000 -0.000 0.003 0.000 -0.000 0.998 -0.000 0.000 0.000 -0.000 -0.000 0.998 0.000 0.000 0.003 0.000 0.000 0.993 -0.000 0.000 0.000 0.000 -0.000 0.998 atom 1 spin 2 atom 1 spin 2 eigenvalues: -0.0000000 0.0476060 0.0476060 0.9654373 0.9954307 eigenvectors 1 0.8660254 0.0000000 0.0000000 0.5000000 -0.0000000 2 -0.1016363 0.0000000 0.9791222 0.1760392 -0.0000000 3 -0.4895611 -0.0000000 -0.2032725 0.8479447 0.0000000 4 -0.0000000 0.4167215 -0.0000000 0.0000000 -0.9090342 5 0.0000000 -0.9090342 0.0000000 -0.0000000 -0.4167215 occupations 0.012 -0.000 -0.000 -0.021 0.000 -0.000 0.990 -0.000 0.000 0.011 -0.000 -0.000 0.048 -0.000 0.000 -0.021 0.000 -0.000 0.036 -0.000 0.000 0.011 0.000 -0.000 0.971 atom 2 Tr[ns(na)]= 7.0385747 atom 2 spin 1 atom 2 spin 1 eigenvalues: 0.9912596 0.9975606 0.9977966 0.9977966 0.9980812 eigenvectors 1 0.5000000 0.0000000 0.0000000 -0.8660254 -0.0000000 2 0.8660254 0.0000000 -0.0000000 0.5000000 0.0000000 3 0.0000000 0.4125984 0.0000000 0.0000000 -0.9109130 4 0.0000000 -0.9109130 -0.0000000 0.0000000 -0.4125984 5 0.0000000 -0.0000000 1.0000000 0.0000000 0.0000000 occupations 0.996 -0.000 -0.000 0.003 0.000 -0.000 0.998 -0.000 0.000 0.000 -0.000 -0.000 0.998 0.000 0.000 0.003 0.000 0.000 0.993 -0.000 0.000 0.000 0.000 -0.000 0.998 atom 2 spin 2 atom 2 spin 2 eigenvalues: -0.0000000 0.0476060 0.0476060 0.9654373 0.9954307 eigenvectors 1 0.8660254 0.0000000 0.0000000 0.5000000 -0.0000000 2 -0.4624456 -0.0000000 -0.3802318 0.8009793 0.0000000 3 0.1901159 0.0000000 -0.9248912 -0.3292904 0.0000000 4 -0.0000000 0.4214217 -0.0000000 0.0000000 -0.9068648 5 0.0000000 -0.9068648 0.0000000 -0.0000000 -0.4214217 occupations 0.012 -0.000 -0.000 -0.021 0.000 -0.000 0.990 -0.000 0.000 0.011 -0.000 -0.000 0.048 -0.000 0.000 -0.021 0.000 -0.000 0.036 -0.000 0.000 0.011 0.000 -0.000 0.971 nsum = 14.0772954 exit write_ns RESET ns to initial values (iter <= mixing_fixed_ns) total cpu time spent up to now is 63.22 secs total energy = -109.56880241 Ry Harris-Foulkes estimate = -110.68781016 Ry estimated scf accuracy < 1.54971595 Ry total magnetization = 12.00 Bohr mag/cell absolute magnetization = 12.00 Bohr mag/cell iteration # 2 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.69E-03, avg # of iterations = 3.0 RESET ns to initial values (iter <= mixing_fixed_ns) total cpu time spent up to now is 96.87 secs total energy = -110.18790510 Ry Harris-Foulkes estimate = -112.27467231 Ry estimated scf accuracy < 6.73753616 Ry total magnetization = 4.00 Bohr mag/cell absolute magnetization = 4.11 Bohr mag/cell iteration # 3 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.69E-03, avg # of iterations = 2.0 RESET ns to initial values (iter <= mixing_fixed_ns) total cpu time spent up to now is 128.28 secs total energy = -110.67113409 Ry Harris-Foulkes estimate = -110.85771078 Ry estimated scf accuracy < 2.44659746 Ry total magnetization = 6.00 Bohr mag/cell absolute magnetization = 6.17 Bohr mag/cell iteration # 4 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.69E-03, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) total cpu time spent up to now is 158.64 secs total energy = -110.67476165 Ry Harris-Foulkes estimate = -110.81051485 Ry estimated scf accuracy < 1.68872176 Ry total magnetization = 6.00 Bohr mag/cell absolute magnetization = 6.18 Bohr mag/cell iteration # 5 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.69E-03, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.176E-07 0.405E-08 total cpu time spent up to now is 188.11 secs total energy = -110.75139774 Ry Harris-Foulkes estimate = -110.75958072 Ry estimated scf accuracy < 0.12534928 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.12 Bohr mag/cell iteration # 6 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 7.83E-04, avg # of iterations = 2.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.331E-05 0.987E-03 total cpu time spent up to now is 219.24 secs total energy = -110.76694437 Ry Harris-Foulkes estimate = -110.76177260 Ry estimated scf accuracy < 0.06039123 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.17 Bohr mag/cell iteration # 7 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.77E-04, avg # of iterations = 2.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.420E-05 0.211E-02 total cpu time spent up to now is 250.49 secs total energy = -110.78322413 Ry Harris-Foulkes estimate = -110.81949761 Ry estimated scf accuracy < 0.46546960 Ry total magnetization = 6.00 Bohr mag/cell absolute magnetization = 6.41 Bohr mag/cell iteration # 8 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.77E-04, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.284E-03 0.121E-04 total cpu time spent up to now is 282.23 secs total energy = -110.70845864 Ry Harris-Foulkes estimate = -110.78568797 Ry estimated scf accuracy < 0.34448263 Ry total magnetization = 6.00 Bohr mag/cell absolute magnetization = 6.44 Bohr mag/cell iteration # 9 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.77E-04, avg # of iterations = 3.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.388E-03 0.103E-04 total cpu time spent up to now is 320.29 secs total energy = -110.76463767 Ry Harris-Foulkes estimate = -110.77304605 Ry estimated scf accuracy < 0.04964287 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.39 Bohr mag/cell iteration # 10 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.10E-04, avg # of iterations = 1.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.148E-04 0.726E-05 total cpu time spent up to now is 352.98 secs total energy = -110.76350147 Ry Harris-Foulkes estimate = -110.76755845 Ry estimated scf accuracy < 0.01520452 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.38 Bohr mag/cell iteration # 11 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.50E-05, avg # of iterations = 7.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.155E-04 0.719E-05 total cpu time spent up to now is 392.62 secs total energy = -110.76779053 Ry Harris-Foulkes estimate = -110.76836565 Ry estimated scf accuracy < 0.00323230 Ry total magnetization = 7.93 Bohr mag/cell absolute magnetization = 8.29 Bohr mag/cell iteration # 12 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 2.02E-05, avg # of iterations = 3.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.291E-04 0.113E-04 total cpu time spent up to now is 426.91 secs total energy = -110.76847976 Ry Harris-Foulkes estimate = -110.76816527 Ry estimated scf accuracy < 0.00081655 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.36 Bohr mag/cell iteration # 13 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.10E-06, avg # of iterations = 4.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.196E-04 0.882E-05 total cpu time spent up to now is 460.93 secs total energy = -110.76864253 Ry Harris-Foulkes estimate = -110.76861049 Ry estimated scf accuracy < 0.00154877 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 14 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.10E-06, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.190E-04 0.871E-05 total cpu time spent up to now is 491.11 secs total energy = -110.76849957 Ry Harris-Foulkes estimate = -110.76866933 Ry estimated scf accuracy < 0.00155698 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 15 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.10E-06, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.195E-04 0.859E-05 total cpu time spent up to now is 521.20 secs total energy = -110.76839415 Ry Harris-Foulkes estimate = -110.76851544 Ry estimated scf accuracy < 0.00096979 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 16 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.10E-06, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.188E-04 0.843E-05 total cpu time spent up to now is 550.79 secs total energy = -110.76833616 Ry Harris-Foulkes estimate = -110.76841286 Ry estimated scf accuracy < 0.00049899 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 17 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.12E-06, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.178E-04 0.839E-05 total cpu time spent up to now is 580.48 secs total energy = -110.76828820 Ry Harris-Foulkes estimate = -110.76836918 Ry estimated scf accuracy < 0.00019878 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 18 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.24E-06, avg # of iterations = 3.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.178E-04 0.840E-05 total cpu time spent up to now is 612.76 secs total energy = -110.76835280 Ry Harris-Foulkes estimate = -110.76835365 Ry estimated scf accuracy < 0.00001154 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 19 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 7.21E-08, avg # of iterations = 4.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.180E-04 0.834E-05 total cpu time spent up to now is 649.06 secs total energy = -110.76835740 Ry Harris-Foulkes estimate = -110.76835747 Ry estimated scf accuracy < 0.00000888 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 20 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.55E-08, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.180E-04 0.834E-05 total cpu time spent up to now is 679.01 secs total energy = -110.76835253 Ry Harris-Foulkes estimate = -110.76835792 Ry estimated scf accuracy < 0.00001487 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 21 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.55E-08, avg # of iterations = 2.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.182E-04 0.836E-05 total cpu time spent up to now is 709.94 secs total energy = -110.76835486 Ry Harris-Foulkes estimate = -110.76835488 Ry estimated scf accuracy < 0.00000147 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 22 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.20E-09, avg # of iterations = 3.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.181E-04 0.835E-05 total cpu time spent up to now is 742.52 secs total energy = -110.76835534 Ry Harris-Foulkes estimate = -110.76835533 Ry estimated scf accuracy < 0.00000246 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 23 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.20E-09, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.181E-04 0.835E-05 total cpu time spent up to now is 771.98 secs total energy = -110.76835548 Ry Harris-Foulkes estimate = -110.76835536 Ry estimated scf accuracy < 0.00000228 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 24 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.20E-09, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.180E-04 0.833E-05 total cpu time spent up to now is 801.18 secs total energy = -110.76835486 Ry Harris-Foulkes estimate = -110.76835549 Ry estimated scf accuracy < 0.00000255 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 25 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.20E-09, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.183E-04 0.846E-05 total cpu time spent up to now is 830.58 secs total energy = -110.76835498 Ry Harris-Foulkes estimate = -110.76835488 Ry estimated scf accuracy < 0.00000283 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 26 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.20E-09, avg # of iterations = 2.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.184E-04 0.852E-05 total cpu time spent up to now is 860.31 secs total energy = -110.76835592 Ry Harris-Foulkes estimate = -110.76835515 Ry estimated scf accuracy < 0.00000084 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 27 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.27E-09, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.185E-04 0.856E-05 total cpu time spent up to now is 889.83 secs total energy = -110.76835661 Ry Harris-Foulkes estimate = -110.76835595 Ry estimated scf accuracy < 0.00000048 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 28 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 2.99E-09, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.185E-04 0.855E-05 total cpu time spent up to now is 919.46 secs total energy = -110.76835660 Ry Harris-Foulkes estimate = -110.76835665 Ry estimated scf accuracy < 0.00000007 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 29 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 4.11E-10, avg # of iterations = 4.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.185E-04 0.855E-05 total cpu time spent up to now is 955.69 secs total energy = -110.76835665 Ry Harris-Foulkes estimate = -110.76835666 Ry estimated scf accuracy < 0.00000002 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 30 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.02E-10, avg # of iterations = 1.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.185E-04 0.855E-05 total cpu time spent up to now is 985.12 secs total energy = -110.76835607 Ry Harris-Foulkes estimate = -110.76835665 Ry estimated scf accuracy < 1.7E-09 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 31 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.07E-11, avg # of iterations = 3.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.185E-04 0.854E-05 total cpu time spent up to now is 1017.31 secs End of self-consistent calculation enter write_ns U( 1) = 3.1000 alpha( 1) = 0.0000 atom 1 Tr[ns(na)]= 6.0000000 atom 1 spin 1 atom 1 spin 1 eigenvalues: 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 atom 1 spin 2 atom 1 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 atom 2 Tr[ns(na)]= 6.0000000 atom 2 spin 1 atom 2 spin 1 eigenvalues: 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 atom 2 spin 2 atom 2 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 nsum = 12.0000000 exit write_ns ------ SPIN UP ------------ k =-0.5000-0.5000-0.5000 ( 57016 PWs) bands (ev): -10.0760 -10.0740 -9.7015 -9.7015 -9.5993 -9.5988 -9.5653 -7.8718 -7.8718 -7.6834 -6.2804 -3.5958 -1.9534 -1.9534 0.0623 0.0624 0.3984 1.1291 ------ SPIN DOWN ---------- k =-0.5000-0.5000-0.5000 ( 57016 PWs) bands (ev): -5.6617 -4.2120 -4.2120 -3.8909 -3.3885 -3.3842 -2.8676 -2.8663 -2.4253 -2.1497 -2.1497 -1.5092 -1.2947 -1.2947 0.8395 0.8395 1.2374 1.3773 the Fermi energy is -3.4524 ev ! total energy = -110.76835644 Ry Harris-Foulkes estimate = -110.76835607 Ry estimated scf accuracy < 1.7E-10 Ry The total energy is the sum of the following terms: one-electron contribution = -202.05900853 Ry hartree contribution = 110.92762605 Ry xc contribution = -52.54131955 Ry ewald contribution = 32.72206894 Ry Hubbard energy = 0.18227665 Ry smearing contrib. (-TS) = 0.00000000 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell convergence has been achieved in 31 iterations Forces acting on atoms (Ry/au): negative rho (up, down): 0.185E-04 0.854E-05 atom 1 type 1 force = 0.02076513 0.00000000 0.00000000 atom 2 type 1 force = -0.02076513 0.00000000 0.00000000 Total force = 0.029366 Total SCF correction = 0.000029 entering subroutine stress ... negative rho (up, down): 0.185E-04 0.854E-05 total stress (Ry/bohr**3) (kbar) P= 2009.64 0.01369711 0.00000000 0.00000000 2014.91 0.00 0.00 0.00000000 0.01364333 0.00000000 0.00 2007.00 0.00 0.00000000 0.00000000 0.01364333 0.00 0.00 2007.00 Writing output data file fe.save init_run : 17.82s CPU 18.29s WALL ( 1 calls) electrons : 972.07s CPU 998.95s WALL ( 1 calls) forces : 21.71s CPU 21.94s WALL ( 1 calls) stress : 74.52s CPU 76.48s WALL ( 1 calls) Called by init_run: wfcinit : 5.49s CPU 5.65s WALL ( 1 calls) potinit : 2.93s CPU 3.09s WALL ( 1 calls) Called by electrons: c_bands : 397.50s CPU 409.14s WALL ( 31 calls) sum_band : 246.60s CPU 250.62s WALL ( 31 calls) v_of_rho : 85.77s CPU 88.43s WALL ( 32 calls) newd : 226.99s CPU 228.45s WALL ( 32 calls) mix_rho : 20.42s CPU 20.79s WALL ( 31 calls) Called by c_bands: init_us_2 : 9.67s CPU 9.85s WALL ( 152 calls) cegterg : 381.24s CPU 390.16s WALL ( 62 calls) Called by *egterg: h_psi : 292.10s CPU 292.55s WALL ( 219 calls) s_psi : 25.75s CPU 25.80s WALL ( 241 calls) g_psi : 1.63s CPU 1.64s WALL ( 155 calls) cdiaghg : 0.19s CPU 0.20s WALL ( 217 calls) Called by h_psi: add_vuspsi : 21.46s CPU 21.47s WALL ( 219 calls) General routines calbec : 43.79s CPU 43.89s WALL ( 564 calls) cft3s : 258.88s CPU 259.64s WALL ( 7231 calls) davcio : 0.01s CPU 5.81s WALL ( 446 calls) Parallel routines PWSCF : 18m 6.46s CPU time, 18m36.32s WALL time This run was terminated on: 15:23:19 18Mar2011 =------------------------------------------------------------------------------= JOB DONE. =------------------------------------------------------------------------------= From 1009ukumar at gmail.com Sat Mar 19 06:53:03 2011 From: 1009ukumar at gmail.com (sonu kumar) Date: Sat, 19 Mar 2011 11:23:03 +0530 Subject: [Pw_forum] problems with current_iq ? Message-ID: Dear all QE users, while recovering phonon calculations, i am getting following error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_partial_ph : error # 1 problems with current_iq %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Initially i used large q-grid, but later on realized that it will take more time ,so reduced the q-grid and accordingly changed the q points etc. in xml file. Any suggestions or hints will be very useful. Thank you in advance. With regards, sk -- Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110319/9d751034/attachment.htm From bahaartv at gmail.com Sat Mar 19 22:49:14 2011 From: bahaartv at gmail.com (bahaareh tavakoli nejad) Date: Sat, 19 Mar 2011 14:49:14 -0700 Subject: [Pw_forum] Pw_forum Digest, Vol 45, Issue 41 In-Reply-To: References: Message-ID: please tell me if it is possible to convert UPF format from Quantumespresso to ABINIT format pseudopotentials? On 3/19/11, pw_forum-request at pwscf.org wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. problems with current_iq ? (sonu kumar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 19 Mar 2011 11:23:03 +0530 > From: sonu kumar <1009ukumar at gmail.com> > Subject: [Pw_forum] problems with current_iq ? > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all QE users, > > while recovering phonon calculations, i am getting following error: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_partial_ph : error # 1 > problems with current_iq > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Initially i used large q-grid, but later on realized that it will take > more time ,so reduced > the q-grid and accordingly changed the q points etc. in xml file. > > Any suggestions or hints will be very useful. > Thank you in advance. > > With regards, > sk > > > > -- > Sonu Kumar > > Phd Student > Physics Department > Indian Institute of Technology > Delhi-110016, India > web:-http://www.iitd.ac.in/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110319/9d751034/attachment.html > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 45, Issue 41 > **************************************** > From giannozz at democritos.it Sun Mar 20 17:05:50 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 20 Mar 2011 17:05:50 +0100 Subject: [Pw_forum] UPF=>Abinit (was: Pw_forum Digest, Vol 45, Issue 41) In-Reply-To: References: Message-ID: <8354A4EF-D7CB-4EF5-ADF7-BB649F4BCD2E@democritos.it> On Mar 19, 2011, at 22:49 , bahaareh tavakoli nejad wrote: > please tell me if it is possible to convert UPF format from > Quantumespresso to ABINIT format pseudopotentials? 0 ) please do not reply to a digest: see http://www.quantum-espresso.org/wiki/index.php/Pw_users 1) it is possible, but you have to write a converter. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From didi5158 at gmail.com Mon Mar 21 03:31:12 2011 From: didi5158 at gmail.com (Wang Di) Date: Mon, 21 Mar 2011 10:31:12 +0800 Subject: [Pw_forum] error in the Raman calculation Message-ID: Hello all: i wish to calculate the Raman spectra of the crystal with espresso 4.1.1 package. However, the calculation process was terminated in self-consistent calculation of representations. The error information was that: *Self-consistent Calculation cu003:1792: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 99 tl 100 cu003:1788: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 228 tl 229 cu003:1791: cu003:1794: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 228 tl 229 dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd 99 tl 100 rank 4 in job 1 cu004-ib_57947 caused collective abort of all ranks exit status of rank 4: killed by signal 9 * I have no idea to do with the case! Can you explain the reason causing the error and give some advises for the solution, any help is greatly appreciated. Best regards Wang ----------------------------------------------------------------- *Wang Di** The Crystal Lab,* *AnHui Institute of Optics and Fine Mechanics, *** *Chinese Academy of Sciences,** No350. , Shushanhu Road, Hefei, 230031, China**, E-mail: WangDiean at gmail.com** ,* ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110321/f18af41c/attachment.htm From giannozz at democritos.it Mon Mar 21 08:45:56 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 21 Mar 2011 08:45:56 +0100 Subject: [Pw_forum] error in the Raman calculation In-Reply-To: References: Message-ID: <248A6D21-4D84-445C-AFD2-3F4A2F7AF803@democritos.it> On Mar 21, 2011, at 3:31 , Wang Di wrote: > I have no idea to do with the case! find out where and under which circumstances the crash happens --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From lfhuang at theory.issp.ac.cn Mon Mar 21 10:18:05 2011 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 21 Mar 2011 17:18:05 +0800 Subject: [Pw_forum] =?utf-8?q?error_in_the_Raman_calculation?= Message-ID: <20110321091805.23390.qmail@ms.hfcas.ac.cn> Dear Wang, Di: It seems it is caused by the breakdown of certain computer node, not related with the QE code. How many atoms and what are the atomic types in your system? Your input file can tell us a lot of things. And how many cpus did you use? If it is due to the un-stability of the computer, I will inform the administrators of it. PS: Maybe it is better to think and test for enough times before submitting our problems on to the forum. And it is better to accompany a submitted problem with as much details as possible. Best Wishes! Yours Sincerely L. F. Huang > From: Wang Di > Subject: [Pw_forum] error in the Raman calculation > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello all: > i wish to calculate the Raman spectra of the crystal with espresso 4.1.1 > package. However, the calculation process was terminated in self-consistent > calculation of representations. The error information was that: > > *Self-consistent Calculation > cu003:1792: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, > max_cb 433 hd 99 tl 100 > cu003:1788: dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, > max_cb 433 hd 228 tl 229 > cu003:1791: cu003:1794: dapl_post_req resource ERR: dtos pending = 432, > max_dtos 432, max_cb 433 hd 228 tl 229 > dapl_post_req resource ERR: dtos pending = 432, max_dtos 432, max_cb 433 hd > 99 tl 100 > rank 4 in job 1 cu004-ib_57947 caused collective abort of all ranks > exit status of rank 4: killed by signal 9 * > > I have no idea to do with the case! Can you explain the reason causing the > error and give some advises for the solution, any help is greatly > appreciated. > > Best regards > Wang > > > ----------------------------------------------------------------- > *Wang Di** > The Crystal Lab,* > *AnHui Institute of Optics and Fine Mechanics, *** > *Chinese Academy of Sciences,** > No350. , Shushanhu Road, Hefei, 230031, China**, > E-mail: WangDiean at gmail.com** ,* > ----------------------------------------------------------------- ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 Our group: http://theory.issp.ac.cn ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110321/f44b3639/attachment.htm From amiri_physics at yahoo.com Mon Mar 21 17:31:35 2011 From: amiri_physics at yahoo.com (peyman amiri) Date: Mon, 21 Mar 2011 09:31:35 -0700 (PDT) Subject: [Pw_forum] (no subject) Message-ID: <957089.51164.qm@web161710.mail.bf1.yahoo.com> Dear all users Have anybody done the GW calculations by quantum-espresso till now? Regards. = = ====================================== Peiman Amiri Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Iran Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 ------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110321/b5f3acef/attachment.htm From liweig at mtu.edu Mon Mar 21 18:19:02 2011 From: liweig at mtu.edu (Liwei Geng) Date: Mon, 21 Mar 2011 13:19:02 -0400 (EDT) Subject: [Pw_forum] For help about Quantum Espresso In-Reply-To: <346374686.5783271300484277061.JavaMail.root@zcs-mbs03.it.mtu.edu> Message-ID: <220186805.6123861300727942108.JavaMail.root@zcs-mbs03.it.mtu.edu> Dear All, I am a newer to use Quantum Espresso. Could you please do me a favor to answer some little questions I met when using Quantum Espresso? 1. I am investigating the BaTiO3 crystal and used the best optimized parameter a=7.5344 Bohr. I used 'scf' to calculate the total energy. However, I obtained different values when using different number of cells. For example, when I use the unit cell, the total energy is -304 Ry, but when I use 1X1X2? supercell, I obtained E=-598Ry, i.e., -299Ry per unit cell, when I increased to 2X2X4 supercell (the input file is below these questions), I got E=-4766Ry, i.e., -298 Ry per unit cell. What is wrong? 2. Another strange result is when I?replaced two Ti atoms (Ti4+)?by two Fe atoms (Fe3+) and removed one O atom (O2-)?between them in the 2X2X4 supercell, I obtained even lower energy than the pure BaTiO3 crystal. What is wrong? It isnot reasonable, right? 3. I use the atom pseudopotential file, but Ba4+ or Fe3+ are both ions, should I?generate?their ionic pseudopotential files? Following is my input file. &control calculation = 'scf', prefix = 'BaTiO3', pseudo_dir='/work/01553/geng' / &system degauss=0.01 ibrav=6 celldm(1)=15.0688 celldm(3)=2 nat=80 ntyp=3 ecutwfc=30.0 ecutrho=300. / &electrons conv_thr = 1e-5, mixing_beta=0.7 / &IONS ion_dynamics='bfgs', / &CELL cell_dynamics='damp-w', / ATOMIC_SPECIES Ba 137.327 Ba.pbe-nsp-van.UPF Ti 47.867 Ti.pbe-sp-van_ak.UPF O 15.9994 O.pbe-van_ak.UPF ATOMIC_POSITIONS Ba 0.000 0.000 0.000 Ba 0.000 0.000 0.250 Ba 0.000 0.000 0.500 Ba 0.000 0.000 0.750 Ba 0.500 0.000 0.000 Ba 0.000 0.500 0.000 Ba 0.500 0.500 0.000 Ba 0.500 0.000 0.250 Ba 0.500 0.000 0.500 Ba 0.500 0.000 0.750 Ba 0.000 0.500 0.250 Ba 0.000 0.500 0.500 Ba 0.000 0.500 0.750 Ba 0.500 0.500 0.250 Ba 0.500 0.500 0.500 Ba 0.500 0.500 0.750 Ti 0.250 0.250 0.125 Ti 0.250 0.250 0.375 Ti 0.250 0.250 0.625 Ti 0.250 0.250 0.875 Ti 0.750 0.250 0.125 Ti 0.750 0.250 0.375 Ti 0.750 0.250 0.625 Ti 0.750 0.250 0.875 Ti 0.250 0.750 0.125 Ti 0.250 0.750 0.375 Ti 0.250 0.750 0.625 Ti 0.250 0.750 0.875 Ti 0.750 0.750 0.125 Ti 0.750 0.750 0.375 Ti 0.750 0.750 0.625 Ti 0.750 0.750 0.875 O 0.250 0.000 0.125 O 0.250 0.000 0.375 O 0.250 0.000 0.625 O 0.250 0.000 0.875 O 0.750 0.000 0.125 O 0.750 0.000 0.375 O 0.750 0.000 0.625 O 0.750 0.000 0.875 O 0.000 0.250 0.125 O 0.000 0.250 0.375 O 0.000 0.250 0.625 O 0.000 0.250 0.875 O 0.000 0.750 0.125 O 0.000 0.750 0.375 O 0.000 0.750 0.625 O 0.000 0.750 0.875 O 0.250 0.500 0.125 O 0.250 0.500 0.375 O 0.250 0.500 0.625 O 0.250 0.500 0.875 O 0.750 0.500 0.125 O 0.750 0.500 0.375 O 0.750 0.500 0.625 O 0.750 0.500 0.875 O 0.500 0.250 0.125 O 0.500 0.250 0.375 O 0.500 0.250 0.625 O 0.500 0.250 0.875 O 0.500 0.750 0.125 O 0.500 0.750 0.375 O 0.500 0.750 0.625 O 0.500 0.750 0.875 O 0.250 0.250 0.000 O 0.250 0.250 0.250 O 0.250 0.250 0.500 O 0.250 0.250 0.750 O 0.750 0.250 0.000 O 0.750 0.250 0.250 O 0.750 0.250 0.500 O 0.750 0.250 0.750 O 0.250 0.750 0.000 O 0.250 0.750 0.250 O 0.250 0.750 0.500 O 0.250 0.750 0.750 O 0.750 0.750 0.000 O 0.750 0.750 0.250 O 0.750 0.750 0.500 O 0.750 0.750 0.750 ? K_POINTS {automatic} 20 20 10 0 0 0 Thank you very much! Best regards, Liwei ? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110321/a9ac6383/attachment.htm From nicola.marzari at materials.ox.ac.uk Mon Mar 21 19:41:04 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Mon, 21 Mar 2011 18:41:04 +0000 Subject: [Pw_forum] For help about Quantum Espresso In-Reply-To: <220186805.6123861300727942108.JavaMail.root@zcs-mbs03.it.mtu.edu> References: <220186805.6123861300727942108.JavaMail.root@zcs-mbs03.it.mtu.edu> Message-ID: <4D879BC0.7070207@materials.ox.ac.uk> Dear Liwei 1) BT is an insulator, so no smearing. 6 6 6 1 1 1 is an ultracareful sampling for the cubic cell. use a much better convergence threshold for the electrons - 10-8 or 10-10. if you double the supercell, halve the kepoints in that direction - 6 6 3 1 1 1. Do not relax lattice parameter and ions, and make sure you get exactly the same values for the total energy. 2) you need to compare energies between the same amounts of matter, and it can easily become a very complex topic. try to read some extensive papers of people calculating the stability of non-stoichiometric oxides. 3) usually pseudos generated in neutral configurations are good enough - i.e. transferable enough. nicola On 3/21/11 5:19 PM, Liwei Geng wrote: > Dear All, > > I am a newer to use Quantum Espresso. Could you please do me a favor to > answer some little questions I met when using Quantum Espresso? > > 1. I am investigating the BaTiO3 crystal and used the best optimized > parameter a=7.5344 Bohr. I used 'scf' to calculate the total energy. > However, I obtained different values when using different number of > cells. For example, when I use the unit cell, the total energy is -304 > Ry, but when I use 1X1X2 supercell, I obtained E=-598Ry, i.e., -299Ry > per unit cell, when I increased to 2X2X4 supercell (the input file is > below these questions), I got E=-4766Ry, i.e., -298 Ry per unit cell. > What is wrong? > > 2. Another strange result is when I replaced two Ti atoms (Ti4+) by two > Fe atoms (Fe3+) and removed one O atom (O2-) between them in the 2X2X4 > supercell, I obtained even lower energy than the pure BaTiO3 crystal. > What is wrong? It isnot reasonable, right? > > 3. I use the atom pseudopotential file, but Ba4+ or Fe3+ are both ions, > should I generate their ionic pseudopotential files? > > Following is my input file. > > &control > > calculation = 'scf', > > prefix = 'BaTiO3', > > pseudo_dir='/work/01553/geng' > > / > > &system > > degauss=0.01 > > ibrav=6 > > celldm(1)=15.0688 > > celldm(3)=2 > > nat=80 > > ntyp=3 > > ecutwfc=30.0 > > ecutrho=300. > > / > > &electrons > > conv_thr = 1e-5, > > mixing_beta=0.7 > > / > > &IONS > > ion_dynamics='bfgs', > > / > > &CELL > > cell_dynamics='damp-w', > > / > > ATOMIC_SPECIES > > Ba 137.327 Ba.pbe-nsp-van.UPF > > Ti 47.867 Ti.pbe-sp-van_ak.UPF > > O 15.9994 O.pbe-van_ak.UPF > > ATOMIC_POSITIONS > > Ba 0.000 0.000 0.000 > > Ba 0.000 0.000 0.250 > > Ba 0.000 0.000 0.500 > > Ba 0.000 0.000 0.750 > > Ba 0.500 0.000 0.000 > > Ba 0.000 0.500 0.000 > > Ba 0.500 0.500 0.000 > > Ba 0.500 0.000 0.250 > > Ba 0.500 0.000 0.500 > > Ba 0.500 0.000 0.750 > > Ba 0.000 0.500 0.250 > > Ba 0.000 0.500 0.500 > > Ba 0.000 0.500 0.750 > > Ba 0.500 0.500 0.250 > > Ba 0.500 0.500 0.500 > > Ba 0.500 0.500 0.750 > > Ti 0.250 0.250 0.125 > > Ti 0.250 0.250 0.375 > > Ti 0.250 0.250 0.625 > > Ti 0.250 0.250 0.875 > > Ti 0.750 0.250 0.125 > > Ti 0.750 0.250 0.375 > > Ti 0.750 0.250 0.625 > > Ti 0.750 0.250 0.875 > > Ti 0.250 0.750 0.125 > > Ti 0.250 0.750 0.375 > > Ti 0.250 0.750 0.625 > > Ti 0.250 0.750 0.875 > > Ti 0.750 0.750 0.125 > > Ti 0.750 0.750 0.375 > > Ti 0.750 0.750 0.625 > > Ti 0.750 0.750 0.875 > > O 0.250 0.000 0.125 > > O 0.250 0.000 0.375 > > O 0.250 0.000 0.625 > > O 0.250 0.000 0.875 > > O 0.750 0.000 0.125 > > O 0.750 0.000 0.375 > > O 0.750 0.000 0.625 > > O 0.750 0.000 0.875 > > O 0.000 0.250 0.125 > > O 0.000 0.250 0.375 > > O 0.000 0.250 0.625 > > O 0.000 0.250 0.875 > > O 0.000 0.750 0.125 > > O 0.000 0.750 0.375 > > O 0.000 0.750 0.625 > > O 0.000 0.750 0.875 > > O 0.250 0.500 0.125 > > O 0.250 0.500 0.375 > > O 0.250 0.500 0.625 > > O 0.250 0.500 0.875 > > O 0.750 0.500 0.125 > > O 0.750 0.500 0.375 > > O 0.750 0.500 0.625 > > O 0.750 0.500 0.875 > > O 0.500 0.250 0.125 > > O 0.500 0.250 0.375 > > O 0.500 0.250 0.625 > > O 0.500 0.250 0.875 > > O 0.500 0.750 0.125 > > O 0.500 0.750 0.375 > > O 0.500 0.750 0.625 > > O 0.500 0.750 0.875 > > O 0.250 0.250 0.000 > > O 0.250 0.250 0.250 > > O 0.250 0.250 0.500 > > O 0.250 0.250 0.750 > > O 0.750 0.250 0.000 > > O 0.750 0.250 0.250 > > O 0.750 0.250 0.500 > > O 0.750 0.250 0.750 > > O 0.250 0.750 0.000 > > O 0.250 0.750 0.250 > > O 0.250 0.750 0.500 > > O 0.250 0.750 0.750 > > O 0.750 0.750 0.000 > > O 0.750 0.750 0.250 > > O 0.750 0.750 0.500 > > O 0.750 0.750 0.750 > > ? > > K_POINTS {automatic} > > 20 20 10 0 0 0 > > Thank you very much! > > Best regards, > > Liwei > > -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From padmaja_patnaik at yahoo.co.uk Tue Mar 22 05:57:47 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Tue, 22 Mar 2011 04:57:47 +0000 (GMT) Subject: [Pw_forum] Doubt in Curie temperature value Message-ID: <447810.38300.qm@web26103.mail.ukl.yahoo.com> Hi I am calculating the Curie Temperature for Iron. The experimental value for this is? 1043 K. I am getting the value as 2398.97 K. I am using the following way to calculate. Find out the ferromagnetic and anti-ferromagnetic energy of Fe. The difference between these two gives the value of J_0. Then, T_c = [2/3] [J_0/K_B] Please suggest me what is wrong? Why am I getting such a high value. On the other hand I am getting very low value for Ni, whose experimental Curie temperature is 627K and I am getting 315K. Thanking you in advance, regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110322/a72d2cfb/attachment.htm From didi5158 at gmail.com Tue Mar 22 13:25:53 2011 From: didi5158 at gmail.com (Wang Di) Date: Tue, 22 Mar 2011 20:25:53 +0800 Subject: [Pw_forum] error in the Raman calculation In-Reply-To: <20110321091805.23390.qmail@ms.hfcas.ac.cn> References: <20110321091805.23390.qmail@ms.hfcas.ac.cn> Message-ID: Dear Huang: Thanks for your advices, the input file for energy calculation was shown as: &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = '/lustre/AIOFM/gxgu/workLBO/11/temp/' , wfcdir = '/lustre/AIOFM/gxgu/workLBO/11/wftemp/' , pseudo_dir = '/home/AIOFM/gxgu/work/uspp/' , prefix = 'LBO' , etot_conv_thr = 1.0D-7 , forc_conv_thr = 5.0D-2 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 0, celldm(1) = 15.9630, nat = 36, ntyp = 3, ecutwfc = 80 , ecutrho = 640 , nosym = .false. , / &ELECTRONS conv_thr = 1.0D-9 , / CELL_PARAMETERS alat 0.968417930 0.000008220 0.000000000 -0.000005879 0.856162463 0.000000000 0.000000000 0.000000000 0.613950243 ATOMIC_SPECIES Li 6.94100 03-LiLi.GGA.fhi.UPF O 15.99940 08-O.GGA.fhi.UPF B 10.81100 05-B.GGA.fhi.UPF ATOMIC_POSITIONS crystal Li 0.082821278 0.067806279 0.948582148 B 0.008644463 0.666273464 0.809922417 B 0.197294156 0.441784814 0.008058571 B 0.155739762 0.749209155 0.189233598 O 0.084188233 0.501390357 0.808062459 O 0.119101858 0.290584988 0.153101264 O 0.058556173 0.801638318 0.983200264 O 0.257341210 0.090263679 0.689863953 O 0.845428098 0.125089922 0.885073710 Li 0.917178722 0.932193721 0.448582148 Li 0.417178778 0.567806424 0.448582105 Li 0.582821222 0.432193576 0.948582105 B 0.991355537 0.333726536 0.309922417 B 0.491356393 0.166273487 0.309923250 B 0.508643607 0.833726513 0.809923250 B 0.802705844 0.558215186 0.508058571 B 0.302705547 0.941784902 0.508059313 B 0.697294453 0.058215098 0.008059313 B 0.844260238 0.250790845 0.689233598 B 0.344259353 0.249207532 0.689232645 B 0.655740647 0.750792468 0.189232645 O 0.915811767 0.498609643 0.308062459 O 0.415811668 0.001389936 0.308062790 O 0.584188332 0.998610064 0.808062790 O 0.880898142 0.709415012 0.653101264 O 0.380897985 0.790585065 0.653102289 O 0.619102015 0.209414935 0.153102289 O 0.941443827 0.198361682 0.483200264 O 0.441444659 0.301638282 0.483200151 O 0.558555341 0.698361718 0.983200151 O 0.742658790 0.909736321 0.189863953 O 0.242658711 0.590262750 0.189863988 O 0.757341289 0.409737250 0.689863988 O 0.154571902 0.874910078 0.385073710 O 0.654572278 0.625088537 0.385075084 O 0.345427722 0.374911463 0.885075084 K_POINTS automatic 4 4 4 0 0 0 the input file for the phonon calculation was: phonon calculation for LBO &INPUTPH outdir = '/lustre/AIOFM/gxgu/workLBO/11/temp/' , prefix = 'LBO' , fildyn = 'LBO_IR.dynG' , fildrho = 'LBO_IR.drho' , trans = .true., epsil = .true., lraman = .true., amass(1) = 6.9410, amass(2) = 15.99940, amass(3) = 10.81100, tr2_ph = 1.0d-12 , / 0.0 0.0 0.0 the number of node used was 1 , cup was 8. The same calculation have been tested with difference parameters for some times, however, each calculation was terminated in self-consistent calculation of different representation. I don't know if the error is caused by my poor input parameter? Thank you very much for your help. Best Wishes ! Wang -- ----------------------------------------------------------------- *Wang Di** The Crystal Lab,* *AnHui Institute of Optics and Fine Mechanics, *** *Chinese Academy of Sciences,** No350. , Shushanhu Road, Hefei, 230031, China**, E-mail: WangDiean at gmail.com** ,* ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110322/4c9247c1/attachment.htm From giannozz at democritos.it Tue Mar 22 14:04:39 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 Mar 2011 14:04:39 +0100 Subject: [Pw_forum] error in the Raman calculation In-Reply-To: References: <20110321091805.23390.qmail@ms.hfcas.ac.cn> Message-ID: <1300799079.13890.8.camel@fe12lx.fisica.uniud.it> On Tue, 2011-03-22 at 20:25 +0800, Wang Di wrote: > ecutwfc = 80 , > ecutrho = 640 , you shouldn't specify a value for ecutrho different from 80*4 = 320 unless you have ultrasoft pseudopotentials .. > Li 6.94100 03-LiLi.GGA.fhi.UPF > O 15.99940 08-O.GGA.fhi.UPF > B 10.81100 05-B.GGA.fhi.UPF ...which you do not have, and in any case... > lraman = .true., ...are not impolemented for Raman calculations P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 22 14:08:03 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 Mar 2011 14:08:03 +0100 Subject: [Pw_forum] Doubt in Curie temperature value In-Reply-To: <447810.38300.qm@web26103.mail.ukl.yahoo.com> References: <447810.38300.qm@web26103.mail.ukl.yahoo.com> Message-ID: <1300799283.13890.13.camel@fe12lx.fisica.uniud.it> On Tue, 2011-03-22 at 04:57 +0000, Padmaja Patnaik wrote: > > I am calculating the Curie Temperature for Iron. > The experimental value for this is 1043 K. > I am getting the value as 2398.97 K. [...] > On the other hand I am getting very low value for Ni, > whose experimental Curie temperature is 627K and I am getting 315K. you didn't even specify which functional you used. One can get completely wrong results for magnetism in DFT, and you complain for a factor 2? P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From cyrille.barreteau at cea.fr Tue Mar 22 14:23:08 2011 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Tue, 22 Mar 2011 14:23:08 +0100 Subject: [Pw_forum] Doubt in Curie temperature value In-Reply-To: <447810.38300.qm@web26103.mail.ukl.yahoo.com> References: <447810.38300.qm@web26103.mail.ukl.yahoo.com> Message-ID: <1300800188.13808.12.camel@spcsi25169.extra.cea.fr> Dear Padmaja Patnaik There are several things wrong or at least approximative in your reasoning. -First your estimation of J_0 is quite crude at least for itinerant magnetism. A better estimate of J_0 would require a spin spiral calculation (not available within pwscf) and then a fit with Heisenberg model. -Second you only include first neighbors while it is well known that next nearest neighbors are very important especially for Iron. -last but not least: your estimation of T_c is based on mean field approximation which is known to overestimate the transition temperature.. Cyrille -- ============================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, B?timent 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ home page: http://iramis.cea.fr/Pisp/cyrille.barreteau/ Lab page: http://iramis.cea.fr/spcsi/ ============================================================= On Tue, 2011-03-22 at 04:57 +0000, Padmaja Patnaik wrote: > Hi > > I am calculating the Curie Temperature for Iron. The experimental > value for this is 1043 K. I am getting the value as 2398.97 K. I am > using the following way to calculate. > Find out the ferromagnetic and anti-ferromagnetic energy of Fe. The > difference between these two gives the value of J_0. Then, > T_c = [2/3] [J_0/K_B] > > Please suggest me what is wrong? Why am I getting such a high value. > On the other hand I am getting very low value for Ni, whose > experimental Curie temperature is 627K and I am getting 315K. > Thanking you in advance, > regards > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From kazempoor2000 at yahoo.com Tue Mar 22 15:24:07 2011 From: kazempoor2000 at yahoo.com (ali kazempour) Date: Tue, 22 Mar 2011 07:24:07 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: <957089.51164.qm@web161710.mail.bf1.yahoo.com> References: <957089.51164.qm@web161710.mail.bf1.yahoo.com> Message-ID: <938342.28520.qm@web114407.mail.gq1.yahoo.com> Dear Peyman In? CVS version you find some examples about? GW approximation with perturbative approach.?Could you tell me what do? you want? Further there are any codes in relation with esspresso?that do GW like Sax and yambo. Best ?Ali Kazempour Fritz-Haber-Institut fax : ++49-30-8413 4701 der Max-Planck-Gesellschaft Faradayweg 4-6 e-mail: kazempou at fhi-berlin.mpg.de D-14 195 Berlin-Dahlem / German ________________________________ From: peyman amiri To: pw_forum Sent: Mon, March 21, 2011 9:01:35 PM Subject: [Pw_forum] (no subject) Dear all users Have anybody done the GW calculations by quantum-espresso till now? Regards. = = ====================================== Peiman Amiri Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology, Iran Tel lab: +98 311 391 3733 Fax Office: +98311 391 3746 ------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110322/d9e6b533/attachment.htm From mehrnooshhazrati at gmail.com Tue Mar 22 16:16:39 2011 From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati) Date: Tue, 22 Mar 2011 18:46:39 +0330 Subject: [Pw_forum] XYZ for K-Points set Message-ID: Hi dear QE users, please tell me where can i find the X,Y,Z for K-Points set : G,F,Q,Z,G ( for the band structure calculations of an orthorhombic super cell . ) I wonder if you could help me. I thank you in advance. Regards Mehrnoosh -- Mehrnoosh Kh. Hazrati, Master Student of Computational Physical Chemistry, KNTU, Tehran. Phone : +989123436300 Mail : mehrnooshhazrati at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110322/1ec8c929/attachment-0001.htm From nakhmanson at anl.gov Tue Mar 22 16:21:50 2011 From: nakhmanson at anl.gov (Serge Nakhmanson) Date: Tue, 22 Mar 2011 10:21:50 -0500 Subject: [Pw_forum] XYZ for K-Points set In-Reply-To: References: Message-ID: <4D88BE8E.7070008@anl.gov> http://www.cryst.ehu.es/cryst/get_kvec.html Mehrnoosh Hazrati wrote: > Hi dear QE users, > > please tell me where can i find the X,Y,Z for K-Points set : G,F,Q,Z,G > ( for the band structure calculations of an orthorhombic super cell . ) > > I wonder if you could help me. > I thank you in advance. > > > Regards > > Mehrnoosh > > -- ********************************************************* 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 ********************************************************* From ttduyle at gmail.com Tue Mar 22 16:22:30 2011 From: ttduyle at gmail.com (Duy Le) Date: Tue, 22 Mar 2011 11:22:30 -0400 Subject: [Pw_forum] XYZ for K-Points set In-Reply-To: References: Message-ID: You can use xcrysden to find their coordinates. Or you can also use condensed matter text book. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Tue, Mar 22, 2011 at 11:16 AM, Mehrnoosh Hazrati wrote: > Hi dear QE users, > > please tell me where can i find the X,Y,Z for K-Points set? : G,F,Q,Z,G? ( > for the band structure calculations of an orthorhombic super cell .?) > > I wonder if you could help me. > I thank you in advance. > > Regards > > Mehrnoosh > > > -- > Mehrnoosh Kh. Hazrati, Master Student of Computational Physical Chemistry, > KNTU, Tehran. > Phone : +989123436300 > Mail : mehrnooshhazrati at gmail.com > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From mehrnooshhazrati at gmail.com Tue Mar 22 16:31:37 2011 From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati) Date: Tue, 22 Mar 2011 19:01:37 +0330 Subject: [Pw_forum] XYZ for K-Points set In-Reply-To: <4D88BE8E.7070008@anl.gov> References: <4D88BE8E.7070008@anl.gov> Message-ID: Thank you very much for your guidance On Tue, Mar 22, 2011 at 6:51 PM, Serge Nakhmanson wrote: > http://www.cryst.ehu.es/cryst/get_kvec.html > > Mehrnoosh Hazrati wrote: > > Hi dear QE users, > > > > please tell me where can i find the X,Y,Z for K-Points set : G,F,Q,Z,G > > ( for the band structure calculations of an orthorhombic super cell . ) > > > > I wonder if you could help me. > > I thank you in advance. > > > > > > Regards > > > > Mehrnoosh > > > > > > -- > ********************************************************* > 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 > -- Mehrnoosh Kh. Hazrati, Master Student of Computational Physical Chemistry, KNTU, Tehran. Phone : +989123436300 Mail : mehrnooshhazrati at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110322/27837135/attachment.htm From mikeat4999 at gmail.com Tue Mar 22 19:11:02 2011 From: mikeat4999 at gmail.com (mike at.) Date: Tue, 22 Mar 2011 21:11:02 +0300 Subject: [Pw_forum] core radius of pseudopotential for which matches real wave function Message-ID: hi, how can i tell the core radius ( cuttoff radius) , r_c , at which a pseudo potential is valid? ir for something like B.pz-vbc.UPF, how can i find out from which values the pseudo matches the *real* wavefunction? Regards M. O. ATAMBO. Undergrad , Moi University Chepkoilel University college Kenya. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110322/3ba08cc2/attachment.htm From eyvaz_isaev at yahoo.com Tue Mar 22 19:53:52 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 22 Mar 2011 11:53:52 -0700 (PDT) Subject: [Pw_forum] core radius of pseudopotential for which matches real wave function In-Reply-To: References: Message-ID: <352017.6788.qm@web65707.mail.ac4.yahoo.com> Dear Mike, I suppose, you should read an exciting paper "Pseudopotentials that work: From H to Pu" in Phys. Rev. B 26, 4199?4228 (1982) by G. B. Bachelet*, D. R. Hamann, and M. Schl?ter Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: mike at. To: Pw_forum at pwscf.org Sent: Tue, March 22, 2011 7:11:02 PM Subject: [Pw_forum] core radius of pseudopotential for which matches real wave function hi, how can i tell the core radius ( cuttoff radius) , r_c , at which a pseudo potential is valid? ir for something like B.pz-vbc.UPF, how can i find out from which values the pseudo matches the *real* wavefunction? Regards M. O. ATAMBO. Undergrad , Moi University Chepkoilel University college Kenya. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110322/3a9ce31a/attachment.htm From giannozz at democritos.it Tue Mar 22 21:22:03 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 22 Mar 2011 21:22:03 +0100 Subject: [Pw_forum] core radius of pseudopotential for which matches real wave function In-Reply-To: References: Message-ID: <28B17D02-FC4E-48E7-9428-BE924E87B6C6@democritos.it> On Mar 22, 2011, at 19:11 , mike at. wrote: > for something like B.pz-vbc.UPF, how can i find out from which > values the pseudo matches the *real* wavefunction? if should be written somewhere in the file, but for PPs converted from another format it is not always present. For a rough estimate, take the outermost maximum of the valence wave functions; or, make a PP calculation with ld1.x, compare the all-electron and pseudo-wavefunctions (if possible on the same electronic configuration used to generate the PP, if you know it available) For B.pz-vbc.UPF: Rc=1.5 for s and p (was written in the original file) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From trambui at u.boisestate.edu Tue Mar 22 22:52:33 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Tue, 22 Mar 2011 15:52:33 -0600 Subject: [Pw_forum] how to test if a generated file of pseudopotential is working or not Message-ID: Dear All, I have generated a Ultrasoft PP input file for Cs atom. And I know I need to test if my Cs' s pp file is working properly,but I don't know how to test run it. Would you let me know what command to use to how to run a test on my pp? Thank you very much, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110322/d06795ea/attachment.htm From faccin.giovani at gmail.com Wed Mar 23 01:25:31 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Wed, 23 Mar 2011 00:25:31 +0000 Subject: [Pw_forum] how to test if a generated file of pseudopotential is working or not In-Reply-To: References: Message-ID: Dear Tram, A few possibilities you might consider trying: 1 - Check if the logarithmic derivatives of the pseudo atomic wavefunctions are similar to the exact result. That's the first test to make! Usually the code that generates the pseudopotential has some kind of option to calculate these things. Many codes can create pseudopotentials for QE, so depends on which one you are using. 2 - Run a bulk standard calculation and see if equilibrium lattice constant/bulk modulus/bands are ok. 3 - Run a dimer calculation and see if the equilibrium distance/vibrational frequency is ok. I think that's the basic setup. I don't know the exact commands for all those things, but that's what you possibly should try to look for. Hope it helps you. Best, Giovani Faccin UFMS/Unicamp - Brazil 2011/3/22 Tram Bui > Dear All, > I have generated a Ultrasoft PP input file for Cs atom. And I know I > need to test if my Cs' s pp file is working properly,but I don't know how to > test run it. Would you let me know what command to use to how to run a test > on my pp? > > Thank you very much, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/f06c6b17/attachment-0001.htm From didi5158 at gmail.com Wed Mar 23 02:12:31 2011 From: didi5158 at gmail.com (Wang Di) Date: Wed, 23 Mar 2011 09:12:31 +0800 Subject: [Pw_forum] error in the Raman calculation In-Reply-To: <1300799079.13890.8.camel@fe12lx.fisica.uniud.it> References: <20110321091805.23390.qmail@ms.hfcas.ac.cn> <1300799079.13890.8.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Paolo: Thanks very much for your advices. When the pseudopotentials were changed without amendment of the ecutrho parameter, the error may be caused by my carelessness!!! Wang Di 2011/3/22 Paolo Giannozzi > On Tue, 2011-03-22 at 20:25 +0800, Wang Di wrote: > > > ecutwfc = 80 , > > ecutrho = 640 , > > you shouldn't specify a value for ecutrho different from 80*4 = 320 > unless you have ultrasoft pseudopotentials .. > > > Li 6.94100 03-LiLi.GGA.fhi.UPF > > O 15.99940 08-O.GGA.fhi.UPF > > B 10.81100 05-B.GGA.fhi.UPF > > ...which you do not have, and in any case... > > > lraman = .true., > > ...are not impolemented for Raman calculations > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ----------------------------------------------------------------- *Wang Di** The Crystal Lab,* *AnHui Institute of Optics and Fine Mechanics, *** *Chinese Academy of Sciences,** No350. , Shushanhu Road, Hefei, 230031, China**, E-mail: WangDiean at gmail.com** ,* ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/77450498/attachment.htm From germaneau at gucas.ac.cn Wed Mar 23 17:33:02 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Wed, 23 Mar 2011 12:33:02 -0400 Subject: [Pw_forum] graphite cell optimization failed Message-ID: <4D8A20BE.9020504@gucas.ac.cn> Dear all, I'm trying to optimize unit cell parameter of graphite. The problem is the c axis gets too long. Starting from published data my initial parameters are a=4.59203 Bohr and c=12.513 Bohr. The final values are 4.664 and 15.829 respectively. I need someone to explain to me what I did wrong, I've attached my input file. That's a basic calculation so it's very frustrating to not make it done. I thank you in advance, Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/f5e8af02/attachment.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: 02_graphite.vcrelax.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/f5e8af02/attachment.asc From lfhuang at theory.issp.ac.cn Wed Mar 23 06:35:12 2011 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Wed, 23 Mar 2011 13:35:12 +0800 Subject: [Pw_forum] =?utf-8?q?error_in_the_Raman_calculation?= Message-ID: <20110323053512.15736.qmail@ms.hfcas.ac.cn> Dear Wang, Di: In addition to the two important points mentioned by prof. P. Giannozzi (about E_cut and the un-compatiblility between GGA and lraman=.true.), Maybe other things need notion: (1) You can try to use the R&G division as the parallel scheme and increase the No. of cpus (e.g. 16) in order to decrease the memory in each cpu. Maybe it is caused by using too much memory in each cpu. (2) Maybe it is due to the un-stability of the computer, which has some problems these days. And the administrators are testing and checking it now. Best Wishes! Yours Sincerely L. F. Huang > From: Wang Di > Subject: Re: [Pw_forum] error in the Raman calculation > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Huang: > Thanks for your advices, the input file for energy calculation was shown as: > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > wf_collect = .true. , > outdir = '/lustre/AIOFM/gxgu/workLBO/11/temp/' , > wfcdir = '/lustre/AIOFM/gxgu/workLBO/11/wftemp/' , > pseudo_dir = '/home/AIOFM/gxgu/work/uspp/' , > prefix = 'LBO' , > etot_conv_thr = 1.0D-7 , > forc_conv_thr = 5.0D-2 , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 0, > celldm(1) = 15.9630, > nat = 36, > ntyp = 3, > ecutwfc = 80 , > ecutrho = 640 , > nosym = .false. , > / > &ELECTRONS > conv_thr = 1.0D-9 , > / > CELL_PARAMETERS alat > 0.968417930 0.000008220 0.000000000 > -0.000005879 0.856162463 0.000000000 > 0.000000000 0.000000000 0.613950243 > ATOMIC_SPECIES > Li 6.94100 03-LiLi.GGA.fhi.UPF > O 15.99940 08-O.GGA.fhi.UPF > B 10.81100 05-B.GGA.fhi.UPF > ATOMIC_POSITIONS crystal > Li 0.082821278 0.067806279 0.948582148 > B 0.008644463 0.666273464 0.809922417 > B 0.197294156 0.441784814 0.008058571 > B 0.155739762 0.749209155 0.189233598 > O 0.084188233 0.501390357 0.808062459 > O 0.119101858 0.290584988 0.153101264 > O 0.058556173 0.801638318 0.983200264 > O 0.257341210 0.090263679 0.689863953 > O 0.845428098 0.125089922 0.885073710 > Li 0.917178722 0.932193721 0.448582148 > Li 0.417178778 0.567806424 0.448582105 > Li 0.582821222 0.432193576 0.948582105 > B 0.991355537 0.333726536 0.309922417 > B 0.491356393 0.166273487 0.309923250 > B 0.508643607 0.833726513 0.809923250 > B 0.802705844 0.558215186 0.508058571 > B 0.302705547 0.941784902 0.508059313 > B 0.697294453 0.058215098 0.008059313 > B 0.844260238 0.250790845 0.689233598 > B 0.344259353 0.249207532 0.689232645 > B 0.655740647 0.750792468 0.189232645 > O 0.915811767 0.498609643 0.308062459 > O 0.415811668 0.001389936 0.308062790 > O 0.584188332 0.998610064 0.808062790 > O 0.880898142 0.709415012 0.653101264 > O 0.380897985 0.790585065 0.653102289 > O 0.619102015 0.209414935 0.153102289 > O 0.941443827 0.198361682 0.483200264 > O 0.441444659 0.301638282 0.483200151 > O 0.558555341 0.698361718 0.983200151 > O 0.742658790 0.909736321 0.189863953 > O 0.242658711 0.590262750 0.189863988 > O 0.757341289 0.409737250 0.689863988 > O 0.154571902 0.874910078 0.385073710 > O 0.654572278 0.625088537 0.385075084 > O 0.345427722 0.374911463 0.885075084 > K_POINTS automatic > 4 4 4 0 0 0 > > the input file for the phonon calculation was: > > phonon calculation for LBO > &INPUTPH > outdir = '/lustre/AIOFM/gxgu/workLBO/11/temp/' , > prefix = 'LBO' , > fildyn = 'LBO_IR.dynG' , > fildrho = 'LBO_IR.drho' , > trans = .true., > epsil = .true., > lraman = .true., > amass(1) = 6.9410, > amass(2) = 15.99940, > amass(3) = 10.81100, > tr2_ph = 1.0d-12 , > / > 0.0 0.0 0.0 > > the number of node used was 1 , cup was 8. The same calculation have been > tested with difference parameters for some times, however, each calculation > was terminated in self-consistent calculation of different representation. > > I don't know if the error is caused by my poor input parameter? > Thank you very much for your help. > > Best Wishes ! > > Wang > > > -- > ----------------------------------------------------------------- > *Wang Di** > The Crystal Lab,* > *AnHui Institute of Optics and Fine Mechanics, *** > *Chinese Academy of Sciences,** > No350. , Shushanhu Road, Hefei, 230031, China**, > E-mail: WangDiean at gmail.com** ,* > ----------------------------------------------------------------- > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110322/4c9247c1/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Tue, 22 Mar 2011 14:04:39 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] error in the Raman calculation > To: PWSCF Forum > Message-ID: > Content-Type: text/plain > > On Tue, 2011-03-22 at 20:25 +0800, Wang Di wrote: > > > ecutwfc = 80 , > > ecutrho = 640 , > > you shouldn't specify a value for ecutrho different from 80*4 = 320 > unless you have ultrasoft pseudopotentials .. > > > Li 6.94100 03-LiLi.GGA.fhi.UPF > > O 15.99940 08-O.GGA.fhi.UPF > > B 10.81100 05-B.GGA.fhi.UPF > > ...which you do not have, and in any case... > > > lraman = .true., > > ...are not impolemented for Raman calculations > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 Our group: http://theory.issp.ac.cn ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/835fc61f/attachment-0001.htm From mighfar at jncasr.ac.in Wed Mar 23 07:23:36 2011 From: mighfar at jncasr.ac.in (Mighfar Imam) Date: Wed, 23 Mar 2011 11:53:36 +0530 Subject: [Pw_forum] Doubt in Curie temperature value In-Reply-To: <447810.38300.qm@web26103.mail.ukl.yahoo.com> References: <447810.38300.qm@web26103.mail.ukl.yahoo.com> Message-ID: <619261686fa3080238e7f9602adbfda1.squirrel@mercury.jncasr.ac.in> I don't know how good an estimate of J_0 would be with this method, nevertheless, Curie temp marks the transition from ferro to para, not from ferro to antiferro! Mighfar Imam, JNCASR, Bangalore. > Hi > > I am calculating the Curie Temperature for Iron. The experimental value > for this is? 1043 K. I am getting the value as 2398.97 K. I am using the > following way to calculate. > Find out the ferromagnetic and anti-ferromagnetic energy of Fe. The > difference between these two gives the value of J_0. Then, > T_c = [2/3] [J_0/K_B] > > Please suggest me what is wrong? Why am I getting such a high value. On > the other hand I am getting very low value for Ni, whose experimental > Curie temperature is 627K and I am getting 315K. > Thanking you in advance, > regards > Padmaja Patnaik > > Research Scholar > > Dept of Physics > > IIT Bombay > > Mumbai, India > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mikeat4999 at gmail.com Wed Mar 23 07:47:59 2011 From: mikeat4999 at gmail.com (mike at.) Date: Wed, 23 Mar 2011 09:47:59 +0300 Subject: [Pw_forum] core radius of pseudopotential for which matches real wave function In-Reply-To: <28B17D02-FC4E-48E7-9428-BE924E87B6C6@democritos.it> References: <28B17D02-FC4E-48E7-9428-BE924E87B6C6@democritos.it> Message-ID: Hi, thanks for the help, how can one access the original file? Regards. On Tue, Mar 22, 2011 at 11:22 PM, Paolo Giannozzi wrote: > > On Mar 22, 2011, at 19:11 , mike at. wrote: > > > for something like B.pz-vbc.UPF, how can i find out from which > > values the pseudo matches the *real* wavefunction? > > if should be written somewhere in the file, but for PPs converted > from another format it is not always present. For a rough estimate, > take the outermost maximum of the valence wave functions; or, > make a PP calculation with ld1.x, compare the all-electron and > pseudo-wavefunctions (if possible on the same electronic > configuration used to generate the PP, if you know it available) > > For B.pz-vbc.UPF: Rc=1.5 for s and p (was written in the original > file) > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/c9314a0b/attachment.htm From didi5158 at gmail.com Wed Mar 23 08:01:48 2011 From: didi5158 at gmail.com (Wang Di) Date: Wed, 23 Mar 2011 15:01:48 +0800 Subject: [Pw_forum] error in the Raman calculation In-Reply-To: <20110323053512.15736.qmail@ms.hfcas.ac.cn> References: <20110323053512.15736.qmail@ms.hfcas.ac.cn> Message-ID: Dear Huang Thanks for your sincere help!!! Wang Di 2011/3/23 lfhuang > Dear Wang, Di: > In addition to the two important points mentioned by prof. P. Giannozzi > (about E_cut and the un-compatiblility between GGA and lraman=.true.), Maybe > other things need notion: > (1) You can try to use the R&G division as the parallel scheme and increase > the No. of cpus (e.g. 16) in order to decrease the memory in each cpu. Maybe > it is caused by using too much memory in each cpu. > (2) Maybe it is due to the un-stability of the computer, which has some > problems these days. And the administrators are testing and checking it now. > > > Best Wishes! > > Yours Sincerely > L. F. Huang > > > From: Wang Di > > Subject: Re: [Pw_forum] error in the Raman calculation > > To: PWSCF Forum > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Huang: > > Thanks for your advices, the input file for energy calculation was shown > as: > > > > &CONTROL > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > wf_collect = .true. , > > outdir = '/lustre/AIOFM/gxgu/workLBO/11/temp/' , > > wfcdir = '/lustre/AIOFM/gxgu/workLBO/11/wftemp/' , > > pseudo_dir = '/home/AIOFM/gxgu/work/uspp/' , > > prefix = 'LBO' , > > etot_conv_thr = 1.0D-7 , > > forc_conv_thr = 5.0D-2 , > > tstress = .true. , > > tprnfor = .true. , > > / > > &SYSTEM > > ibrav = 0, > > celldm(1) = 15.9630, > > nat = 36, > > ntyp = 3, > > ecutwfc = 80 , > > ecutrho = 640 , > > nosym = .false. , > > / > > &ELECTRONS > > conv_thr = 1.0D-9 , > > / > > CELL_PARAMETERS alat > > 0.968417930 0.000008220 0.000000000 > > -0.000005879 0.856162463 0.000000000 > > 0.000000000 0.000000000 0.613950243 > > ATOMIC_SPECIES > > Li 6.94100 03-LiLi.GGA.fhi.UPF > > O 15.99940 08-O.GGA.fhi.UPF > > B 10.81100 05-B.GGA.fhi.UPF > > ATOMIC_POSITIONS crystal > > Li 0.082821278 0.067806279 0.948582148 > > B 0.008644463 0.666273464 0.809922417 > > B 0.197294156 0.441784814 0.008058571 > > B 0.155739762 0.749209155 0.189233598 > > O 0.084188233 0.501390357 0.808062459 > > O 0.119101858 0.290584988 0.153101264 > > O 0.058556173 0.801638318 0.983200264 > > O 0.257341210 0.090263679 0.689863953 > > O 0.845428098 0.125089922 0.885073710 > > Li 0.917178722 0.932193721 0.448582148 > > Li 0.417178778 0.567806424 0.448582105 > > Li 0.582821222 0.432193576 0.948582105 > > B 0.991355537 0.333726536 0.309922417 > > B 0.491356393 0.166273487 0.309923250 > > B 0.508643607 0.833726513 0.809923250 > > B 0.802705844 0.558215186 0.508058571 > > B 0.302705547 0.941784902 0.508059313 > > B 0.697294453 0.058215098 0.008059313 > > B 0.844260238 0.250790845 0.689233598 > > B 0.344259353 0.249207532 0.689232645 > > B 0.655740647 0.750792468 0.189232645 > > O 0.915811767 0.498609643 0.308062459 > > O 0.415811668 0.001389936 0.308062790 > > O 0.584188332 0.998610064 0.808062790 > > O 0.880898142 0.709415012 0.653101264 > > O 0.380897985 0.790585065 0.653102289 > > O 0.619102015 0.209414935 0.153102289 > > O 0.941443827 0.198361682 0.483200264 > > O 0.441444659 0.301638282 0.483200151 > > O 0.558555341 0.698361718 0.983200151 > > O 0.742658790 0.909736321 0.189863953 > > O 0.242658711 0.590262750 0.189863988 > > O 0.757341289 0.409737250 0.689863988 > > O 0.154571902 0.874910078 0.385073710 > > O 0.654572278 0.625088537 0.385075084 > > O 0.345427722 0.374911463 0.885075084 > > K_POINTS automatic > > 4 4 4 0 0 0 > > > > the input file for the phonon calculation was: > > > > phonon calculation for LBO > > &INPUTPH > > outdir = '/lustre/AIOFM/gxgu/workLBO/11/temp/' , > > prefix = 'LBO' , > > fildyn = 'LBO_IR.dynG' , > > fildrho = 'LBO_IR.drho' , > > trans = .true., > > epsil = .true., > > lraman = .true., > > amass(1) = 6.9410, > > amass(2) = 15.99940, > > amass(3) = 10.81100, > > tr2_ph = 1.0d-12 , > > / > > 0.0 0.0 0.0 > > > > the number of node used was 1 , cup was 8. The same calculation have been > > > tested with difference parameters for some times, however, each > calculation > > was terminated in self-consistent calculation of different > representation. > > > > I don't know if the error is caused by my poor input parameter? > > Thank you very much for your help. > > > > Best Wishes ! > > > > Wang > > > > > > -- > > ----------------------------------------------------------------- > > *Wang Di** > > The Crystal Lab,* > > *AnHui Institute of Optics and Fine Mechanics, *** > > *Chinese Academy of Sciences,** > > No350. , Shushanhu Road, Hefei, 230031, China**, > > E-mail: WangDiean at gmail.com** ,* > > ----------------------------------------------------------------- > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110322/4c9247c1/attachment-0001.htm> > > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 22 Mar 2011 14:04:39 +0100 > > From: Paolo Giannozzi > > Subject: Re: [Pw_forum] error in the Raman calculation > > To: PWSCF Forum > > > Message-ID: > > Content-Type: text/plain > > > > > On Tue, 2011-03-22 at 20:25 +0800, Wang Di wrote: > > > > > ecutwfc = 80 , > > > ecutrho = 640 , > > > > you shouldn't specify a value for ecutrho different from 80*4 = 320 > > unless you have ultrasoft pseudopotentials .. > > > > > Li 6.94100 03-LiLi.GGA.fhi.UPF > > > O 15.99940 08-O.GGA.fhi.UPF > > > B 10.81100 05-B.GGA.fhi.UPF > > > > ...which you do not have, and in any case... > > > > > lraman = .true., > > > > ...are not impolemented for Raman calculations > > > > P. > > -- > > > > > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > > > ------ > ====================================================================== > L.F.Huang(???) DFT and phonon physics > ====================================================================== > Add: Research Laboratory for Computational Materials Sciences, > Instutue of Solid State Physics,the Chinese Academy of Sciences, > P.O.Box 1129, Hefei 230031, P.R.China > Tel: 86-551-5591464-326(office) > Fax: 86-551-5591434 > Our group: > > http://theory.issp.ac.cn > ====================================================================== > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ----------------------------------------------------------------- *Wang Di** The Crystal Lab,* *AnHui Institute of Optics and Fine Mechanics, *** *Chinese Academy of Sciences,** No350. , Shushanhu Road, Hefei, 230031, China**, E-mail: WangDiean at gmail.com** ,* ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/94c916a8/attachment-0001.htm From nkxirainbow at gmail.com Wed Mar 23 08:04:13 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 23 Mar 2011 15:04:13 +0800 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D8A20BE.9020504@gucas.ac.cn> References: <4D8A20BE.9020504@gucas.ac.cn> Message-ID: *Dear Eric.* *I met the same problem with you 3 years ago. But I did not fix it. I think it is related with the functional, which does not include dynamical dipole interaction.* * * *There are some discussion about the vander Waals interaction in PWSCF. I hope it will help you:)* *http://www.democritos.it/pipermail/pw_forum/2010-November/018516.html* * * *On Thu, Mar 24, 2011 at 12:33 AM, Eric Germaneau wrote: * > > * Dear all, > > I'm trying to optimize unit cell parameter of graphite. > The problem is the c axis gets too long. > Starting from published data my initial parameters are a=4.59203 Bohr and > c=12.513 Bohr. > The final values are 4.664 and 15.829 respectively. > I need someone to explain to me what I did wrong, I've attached my input > file. > That's a basic calculation so it's very frustrating to not make it done. > I thank you in advance, > > Eric. > > * > *-- > * * Be the change you wish to see in the world > ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. * > * > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > * * -- ____________________________________ Hui Wang School of physics, Fudan University, Shanghai, China* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/c3216f83/attachment.htm From cyrille.barreteau at cea.fr Wed Mar 23 08:34:43 2011 From: cyrille.barreteau at cea.fr (Cyrille Barreteau) Date: Wed, 23 Mar 2011 08:34:43 +0100 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D8A20BE.9020504@gucas.ac.cn> References: <4D8A20BE.9020504@gucas.ac.cn> Message-ID: <1300865683.13808.21.camel@spcsi25169.extra.cea.fr> Dear Eric I am not a specialist of Carbon but from what I have read (and heard) the interaction between two graphene layers is of Van der Waals nature. Therefore standard DFT is not very good. It seems that LDA is doing better than GGA with this respect. You could also try to include the semi-empirical dispersion term (proposed by Grimme) and now implemented if pwscf.. good luck cyrille -- ============================================================== Cyrille Barreteau phone : +33 (0)1 69 08 29 51 CEA Saclay fax : +33 (0)1 69 08 84 46 IRAMIS, SPCSI, B?timent 462 email cyrille.barreteau at cea.fr 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ home page: http://iramis.cea.fr/Pisp/cyrille.barreteau/ Lab page: http://iramis.cea.fr/spcsi/ ============================================================= On Wed, 2011-03-23 at 12:33 -0400, Eric Germaneau wrote: > Dear all, > > I'm trying to optimize unit cell parameter of graphite. > The problem is the c axis gets too long. > Starting from published data my initial parameters are a=4.59203 Bohr > and c=12.513 Bohr. > The final values are 4.664 and 15.829 respectively. > I need someone to explain to me what I did wrong, I've attached my > input file. > That's a basic calculation so it's very frustrating to not make it > done. > I thank you in advance, > > Eric. > > -- > Be the change you wish to see in the world > ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From masoudnahali at gmail.com Wed Mar 23 09:56:48 2011 From: masoudnahali at gmail.com (Masoud Nahali) Date: Wed, 23 Mar 2011 13:26:48 +0430 Subject: [Pw_forum] Re : graphite cell optimization failed Message-ID: Dear Eric Try london="true" to get improved answer; as you should know DFT is weak to calculate dispersion forces and by using the keyword one can include these forces semi-empirically. I hope it helps. Best Wishes Masoud -------------- Masoud Nahali, Sharif University of Technology Eric Wrote: Dear all, I'm trying to optimize unit cell parameter of graphite. The problem is the c axis gets too long. Starting from published data my initial parameters are a=4.59203 Bohr and c=12.513 Bohr. The final values are 4.664 and 15.829 respectively. I need someone to explain to me what I did wrong, I've attached my input file. That's a basic calculation so it's very frustrating to not make it done. I thank you in advance, Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau > College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/dd7527a4/attachment.htm From sclauzer at sissa.it Wed Mar 23 10:11:26 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 23 Mar 2011 10:11:26 +0100 Subject: [Pw_forum] how to test if a generated file of pseudopotential is working or not In-Reply-To: References: Message-ID: <0215037A-7B61-41D0-A488-28E611680BED@sissa.it> On top of this, before moving to the molecular or solid state calculations, one can perform some transferability tests with the atomic code (iswitch=2, see INPUT_LD1.txt). A good point to start learning the theory and practice of PP generation and testing may be the following: http://media.quantum-espresso.org/santa_barbara_2009_07/index.php (see lecture notes and labs of July 25) HTH GS Il giorno 23/mar/2011, alle ore 01.25, Giovani Faccin ha scritto: > Dear Tram, > > A few possibilities you might consider trying: > > 1 - Check if the logarithmic derivatives of the pseudo atomic wavefunctions are similar to the exact result. That's the first test to make! Usually the code that generates the pseudopotential has some kind of option to calculate these things. Many codes can create pseudopotentials for QE, so depends on which one you are using. > 2 - Run a bulk standard calculation and see if equilibrium lattice constant/bulk modulus/bands are ok. > 3 - Run a dimer calculation and see if the equilibrium distance/vibrational frequency is ok. > > I think that's the basic setup. I don't know the exact commands for all those things, but that's what you possibly should try to look for. > > Hope it helps you. > > Best, > > Giovani Faccin > UFMS/Unicamp - Brazil > > > 2011/3/22 Tram Bui > Dear All, > I have generated a Ultrasoft PP input file for Cs atom. And I know I need to test if my Cs' s pp file is working properly,but I don't know how to test run it. Would you let me know what command to use to how to run a test on my pp? > > Thank you very much, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Giovani > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/0b266fb3/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Wed Mar 23 10:12:53 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Wed, 23 Mar 2011 10:12:53 +0100 Subject: [Pw_forum] graphite cell optimization failed Message-ID: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> Dear all You can do better than the semiempirical "Grimme" correction. There is a new ab initio van der Waals correlation functional implemented in QE 4.3a. Try input_dft='vdW-DF', in the &sysytem list. By the way, what about a (semiempirical or ab initio) vdW scheme in cp.x? Is there any project going on? Yours Giuseppe Quoting Masoud Nahali : > Dear Eric > > Try london="true" to get improved answer; as you should know DFT is weak > to calculate dispersion forces and by using the keyword one can include > these forces semi-empirically. I hope it helps. > > Best Wishes > > Masoud > -------------- > Masoud Nahali, Sharif University of Technology > > > Eric Wrote: > > Dear all, > > I'm trying to optimize unit cell parameter of graphite. > The problem is the c axis gets too long. > Starting from published data my initial parameters are a=4.59203 Bohr > and c=12.513 Bohr. > The final values are 4.664 and 15.829 respectively. > I need someone to explain to me what I did wrong, I've attached my input > file. > That's a basic calculation so it's very frustrating to not make it done. > I thank you in advance, > > Eric. > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > Giuseppe Mattioli ISM-CNR Italy From sclauzer at sissa.it Wed Mar 23 10:22:11 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 23 Mar 2011 10:22:11 +0100 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> References: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> Message-ID: Dear Giuseppe, is there any concrete evidence that "ab initio" van der Waals vdW-DF is systematically better than Grimme's vdW? Are you aware of any paper comparing the latest version of the two methodologies (or "phisolophies", if you want), i.e. vdW-DF2 vs DFT-D3? Cheers, GS Il giorno 23/mar/2011, alle ore 10.12, giuseppe.mattioli at mlib.ism.cnr.it ha scritto: > > Dear all > You can do better than the semiempirical "Grimme" correction. There is > a new ab initio van der Waals correlation functional implemented in QE > 4.3a. Try input_dft='vdW-DF', in the &sysytem list. > By the way, what about a (semiempirical or ab initio) vdW scheme in > cp.x? Is there any project going on? > > Yours > > Giuseppe > > Quoting Masoud Nahali : > >> Dear Eric >> >> Try london="true" to get improved answer; as you should know DFT is weak >> to calculate dispersion forces and by using the keyword one can include >> these forces semi-empirically. I hope it helps. >> >> Best Wishes >> >> Masoud >> -------------- >> Masoud Nahali, Sharif University of Technology >> >> >> Eric Wrote: >> >> Dear all, >> >> I'm trying to optimize unit cell parameter of graphite. >> The problem is the c axis gets too long. >> Starting from published data my initial parameters are a=4.59203 Bohr >> and c=12.513 Bohr. >> The final values are 4.664 and 15.829 respectively. >> I need someone to explain to me what I did wrong, I've attached my input >> file. >> That's a basic calculation so it's very frustrating to not make it done. >> I thank you in advance, >> >> Eric. >> >> -- >> /Be the change you wish to see in the world >> / --- Mahatma Gandhi --- >> >> Dr. ?ric Germaneau > > >> >> College of Physical Sciences >> Graduate University of Chinese Academy of Sciences >> Yuquan Road 19A >> Beijing 100049 >> China >> > > Giuseppe Mattioli > ISM-CNR > Italy > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/7938c063/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Wed Mar 23 10:42:04 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 23 Mar 2011 10:42:04 +0100 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D8A20BE.9020504@gucas.ac.cn> References: <4D8A20BE.9020504@gucas.ac.cn> Message-ID: On Wed, 23 Mar 2011 17:33:02 +0100, Eric Germaneau wrote: > I'm trying to optimize unit cell parameter of graphite. > The problem is the c axis gets too long. > Starting from published data my initial parameters are a=4.59203 Bohr > and c=12.513 Bohr. > The final values are 4.664 and 15.829 respectively. > I need someone to explain to me what I did wrong, I've attached my input > file. Dear Eric, your input atomic positions are only specified to 4 significant digits: 0.3333 is not really 1/3. Hence you are loosing 18 out of 24 symmetry operation: I would suggest increasing the precision to 6 or 7 digits to recover them. With more symmetry you will be able to afford more kpoints, as graphite can be tricky to converge a 4x4x4 grid can not insufficient. I also doubt that you need 80Ry to converge an ultrasoft pseudopotential, but I assume you did your tests. Finally, your results seem to be in accord with other DFT calculation; considered you're using GGA they are actually quite good. In LDA the usual overbinding partially compensates for the lack of VdW interaction, while this effect does not occur for gradient-corrected functionals. best regards -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From giuseppe.mattioli at mlib.ism.cnr.it Wed Mar 23 10:48:54 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Wed, 23 Mar 2011 10:48:54 +0100 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: References: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> Message-ID: <20110323104854.f4nokxq1z40wcks0@webmail.sic.rm.cnr.it> Dear Gabriele > is there any concrete evidence that "ab initio" van der Waals > vdW-DF is systematically better than Grimme's vdW? Yes, at least in the case of molecule-surface interactions. There is a recent (2010) Grimme paper (I'm sorry, I cannot be more accurate today...) that reports an overestimate of the above interactions when using DFT-D2, currently implemented in QE. I've performed comparative tests (classical MM, DFT-D2, vdW-DF) on several molecules interacting with the non-polar 10-10 ZnO surface and I've obtained the best results (some of them comparable with experimental data, i.e., the thiophene ring) by using the vdW-DF approach. The DFT-D2 setup, however, is quite good for molecules in my experience, and can be tuned by changing the C6 coefficients by hand (QE/Modules/mm_dispersion.f90), following one of the available force fields (AMBER, CHARMM, ...). Maybe DFT-D3 and vdW-DF would converge to similar results... What about cp? Yours G. Quoting Gabriele Sclauzero : > Dear Giuseppe, > > is there any concrete evidence that "ab initio" van der Waals > vdW-DF is systematically better than Grimme's vdW? > Are you aware of any paper comparing the latest version of the two > methodologies (or "phisolophies", if you want), i.e. vdW-DF2 vs > DFT-D3? > > Cheers, > > GS > > > Il giorno 23/mar/2011, alle ore 10.12, > giuseppe.mattioli at mlib.ism.cnr.it ha scritto: > >> >> Dear all >> You can do better than the semiempirical "Grimme" correction. There is >> a new ab initio van der Waals correlation functional implemented in QE >> 4.3a. Try input_dft='vdW-DF', in the &sysytem list. >> By the way, what about a (semiempirical or ab initio) vdW scheme in >> cp.x? Is there any project going on? >> >> Yours >> >> Giuseppe >> >> Quoting Masoud Nahali : >> >>> Dear Eric >>> >>> Try london="true" to get improved answer; as you should know DFT is weak >>> to calculate dispersion forces and by using the keyword one can include >>> these forces semi-empirically. I hope it helps. >>> >>> Best Wishes >>> >>> Masoud >>> -------------- >>> Masoud Nahali, Sharif University of Technology >>> >>> >>> Eric Wrote: >>> >>> Dear all, >>> >>> I'm trying to optimize unit cell parameter of graphite. >>> The problem is the c axis gets too long. >>> Starting from published data my initial parameters are a=4.59203 Bohr >>> and c=12.513 Bohr. >>> The final values are 4.664 and 15.829 respectively. >>> I need someone to explain to me what I did wrong, I've attached my input >>> file. >>> That's a basic calculation so it's very frustrating to not make it done. >>> I thank you in advance, >>> >>> Eric. >>> >>> -- >>> /Be the change you wish to see in the world >>> / --- Mahatma Gandhi --- >>> >>> Dr. ?ric Germaneau >> > >>> >>> College of Physical Sciences >>> Graduate University of Chinese Academy of Sciences >>> Yuquan Road 19A >>> Beijing 100049 >>> China >>> >> >> Giuseppe Mattioli >> ISM-CNR >> Italy >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > From alain.allouche at univ-provence.fr Wed Mar 23 11:39:23 2011 From: alain.allouche at univ-provence.fr (Alain Allouche) Date: Wed, 23 Mar 2011 11:39:23 +0100 Subject: [Pw_forum] compiling QE 4.3a Message-ID: Dear all Compiling QE v 4.3a with Intel compiler I got the messages: mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 - nomodule -fpp -D__INTEL -D__FFTW -D__MPI -D__PARA -I../include -c iotk_scan_interf.f90 : warning #5117: Bad # preprocessor line which should be fatal then iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [VAL] subroutine iotk_stream_read_LOGICAL1(unit,header,val,setpos,getpos,noval,ierr) -------------------------------------------------^ iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [VAL] subroutine iotk_stream_read_INTEGER1(unit,header,val,setpos,getpos,noval,ierr) -------------------------------------------------^ iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [VAL] subroutine iotk_stream_read_REAL1(unit,header,val,setpos,getpos,noval,ierr) ----------------------------------------------^ iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [VAL] subroutine iotk_stream_read_REAL2(unit,header,val,setpos,getpos,noval,ierr) ----------------------------------------------^ iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [VAL] subroutine iotk_stream_read_COMPLEX1(unit,header,val,setpos,getpos,noval,ierr) -------------------------------------------------^ iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [VAL] subroutine iotk_stream_read_COMPLEX2(unit,header,val,setpos,getpos,noval,ierr) -------------------------------------------------^ iotk_stream.spp(54): warning #6843: A dummy argument with an explicit INTENT(OUT) declaration is not given an explicit value. [VAL] subroutine iotk_stream_read_CHARACTER1(unit,header,val,setpos,getpos,noval,ierr) ---------------------------------------------------^ Then make loclib_only make[3]: Nothing to be done for `loclib_only'. mpif90 -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 - nomodule -fpp -D__INTEL -D__FFTW -D__MPI -D__PARA -I../include -c iotk.f90 make loclib_only make[3]: Nothing to be done for `loclib_only'. And at the last step of pw compiling mpif90 -o pw.x \ pwscf.o libpw.a ../Modules/libqemod.a ../flib/ptools.a ../ flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -llapack -latlas / Volumes/Work/espresso-4.3a/lapack-3.2/lapack.a -latlas Undefined symbols: "___intel_sse2_strlen", referenced from: _get_md5 in clib.a(md5_from_file.o) _file_md5_ in clib.a(md5_from_file.o) ld: symbol(s) not found make[1]: *** [pw.x] Error 1 make: *** [pw] Error 2 Thanks for your help Alain Alain ALLOUCHE Physique des Interactions Ioniques et Moleculaires CNRS / Universite de Provence Campus Saint Jerome Service 242 email: Alain.Allouche at univ-provence.fr From lmartinsamos at gmail.com Wed Mar 23 12:00:14 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 23 Mar 2011 12:00:14 +0100 Subject: [Pw_forum] Fwd: compiling QE 4.3a In-Reply-To: References: Message-ID: Hi Alain, the warnings regarding iotk are not relevant. The messages "nothing to be done for ... " are normal. This are checks to see wheter things have to be compiled or not. The last message is realy an error message and it seems the your C compiler is not recognizing its own internal function call to STRLEN. Exactly which fortran and c compiler are you using? can you attach the make.sys file produced by the ESPRESSO configure? bests Layla 2011/3/23 Alain Allouche > Dear all > Compiling QE v 4.3a with Intel compiler I got the messages: > > mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 - > nomodule -fpp -D__INTEL -D__FFTW -D__MPI -D__PARA -I../include -c > iotk_scan_interf.f90 > : warning #5117: Bad # preprocessor line > > which should be fatal > > then > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_LOGICAL1(unit,header,val,setpos,getpos,noval,ierr) > -------------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_INTEGER1(unit,header,val,setpos,getpos,noval,ierr) > -------------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_REAL1(unit,header,val,setpos,getpos,noval,ierr) > ----------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_REAL2(unit,header,val,setpos,getpos,noval,ierr) > ----------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_COMPLEX1(unit,header,val,setpos,getpos,noval,ierr) > -------------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_COMPLEX2(unit,header,val,setpos,getpos,noval,ierr) > -------------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_CHARACTER1(unit,header,val,setpos,getpos,noval,ierr) > ---------------------------------------------------^ > > Then > > make loclib_only > make[3]: Nothing to be done for `loclib_only'. > mpif90 -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a > mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 - > nomodule -fpp -D__INTEL -D__FFTW -D__MPI -D__PARA -I../include -c > iotk.f90 > make loclib_only > make[3]: Nothing to be done for `loclib_only'. > > And at the last step of pw compiling > > mpif90 -o pw.x \ > pwscf.o libpw.a ../Modules/libqemod.a ../flib/ptools.a ../ > flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -llapack -latlas / > Volumes/Work/espresso-4.3a/lapack-3.2/lapack.a -latlas > Undefined symbols: > "___intel_sse2_strlen", referenced from: > _get_md5 in clib.a(md5_from_file.o) > _file_md5_ in clib.a(md5_from_file.o) > ld: symbol(s) not found > make[1]: *** [pw.x] Error 1 > make: *** [pw] Error 2 > > Thanks for your help > Alain > > > > > Alain ALLOUCHE > Physique des Interactions Ioniques et Moleculaires > CNRS / Universite de Provence > Campus Saint Jerome Service 242 > email: Alain.Allouche at univ-provence.fr > > > > > > > > _______________________________________________ > 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/20110323/a216f238/attachment.htm From anupvthomas at gmail.com Wed Mar 23 13:04:43 2011 From: anupvthomas at gmail.com (ANUP THOMAS) Date: Wed, 23 Mar 2011 17:34:43 +0530 Subject: [Pw_forum] Help for Calculating Organic Crystal Band Structure Message-ID: Dear All I, Anup Thomas, a novice in this field of solid state structure simulation. I would like to perform band structure calculations for some organic crystals. In my limited knowledge i could not find any one using Pwscf for organic crstals band structure. Would any one please let me know Pwscf can simulate the data? I will appreciate very much if you can give me more advices. -- Regards Anup Thomas SRF 7123 Computational Chemistry Lab of I and PC Division Indian Institute of Chemical Technology Hyderabad 500007 India "Praise the Lord, all you nations; extol him, all you peoples. For great is his love toward us, and the faithfulness of the Lord endures forever. Praise the Lord" -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/428f158a/attachment.htm From alain.allouche at univ-provence.fr Wed Mar 23 13:08:41 2011 From: alain.allouche at univ-provence.fr (Alain Allouche) Date: Wed, 23 Mar 2011 13:08:41 +0100 Subject: [Pw_forum] Fwd: compiling QE 4.3a In-Reply-To: References: Message-ID: Helle Layla, here is the make.sys Le 23 mars 11 ? 12:00, Layla Martin-Samos a ?crit : > > > Hi Alain, the warnings regarding iotk are not relevant. The messages > "nothing to be done for ... " are normal. This are checks to see > wheter things have to be compiled or not. The last message is realy > an error message and it seems the your C compiler is not recognizing > its own internal function call to STRLEN. Exactly which fortran and > c compiler are you using? can you attach the make.sys file produced > by the ESPRESSO configure? > > bests > > Layla > > > 2011/3/23 Alain Allouche > Dear all > Compiling QE v 4.3a with Intel compiler I got the messages: > > mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 - > nomodule -fpp -D__INTEL -D__FFTW -D__MPI -D__PARA -I../include -c > iotk_scan_interf.f90 > : warning #5117: Bad # preprocessor line > > which should be fatal > > then > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_LOGICAL1(unit,header,val,setpos,getpos,noval,ierr) > -------------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_INTEGER1(unit,header,val,setpos,getpos,noval,ierr) > -------------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_REAL1(unit,header,val,setpos,getpos,noval,ierr) > ----------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_REAL2(unit,header,val,setpos,getpos,noval,ierr) > ----------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_COMPLEX1(unit,header,val,setpos,getpos,noval,ierr) > -------------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_COMPLEX2(unit,header,val,setpos,getpos,noval,ierr) > -------------------------------------------------^ > iotk_stream.spp(54): warning #6843: A dummy argument with an explicit > INTENT(OUT) declaration is not given an explicit value. [VAL] > subroutine > iotk_stream_read_CHARACTER1(unit,header,val,setpos,getpos,noval,ierr) > ---------------------------------------------------^ > > Then > > make loclib_only > make[3]: Nothing to be done for `loclib_only'. > mpif90 -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a > mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 - > nomodule -fpp -D__INTEL -D__FFTW -D__MPI -D__PARA -I../include -c > iotk.f90 > make loclib_only > make[3]: Nothing to be done for `loclib_only'. > > And at the last step of pw compiling > > mpif90 -o pw.x \ > pwscf.o libpw.a ../Modules/libqemod.a ../flib/ptools.a ../ > flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -llapack -latlas / > Volumes/Work/espresso-4.3a/lapack-3.2/lapack.a -latlas > Undefined symbols: > "___intel_sse2_strlen", referenced from: > _get_md5 in clib.a(md5_from_file.o) > _file_md5_ in clib.a(md5_from_file.o) > ld: symbol(s) not found > make[1]: *** [pw.x] Error 1 > make: *** [pw] Error 2 > > Thanks for your help > Alain > > > > > Alain ALLOUCHE > Physique des Interactions Ioniques et Moleculaires > CNRS / Universite de Provence > Campus Saint Jerome Service 242 > email: Alain.Allouche at univ-provence.fr > > > > > > > > _______________________________________________ > 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. Alain ALLOUCHE Physique des Interactions Ioniques et Moleculaires CNRS / Universite de Provence Campus Saint Jerome Service 242 Avenue de l'Escadrille Normandie-Niemen 13397 Marseille Cedex 20 - France Tel : +33 (0) 4 91 28 85 76 Mobile:+33 681 84 80 66 Fax : +33 491.28.89.05 email: Alain.Allouche at univ-provence.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/f50d3ca3/attachment-0002.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: make.sys Type: application/octet-stream Size: 4395 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110323/f50d3ca3/attachment-0001.obj -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/f50d3ca3/attachment-0003.htm From nkxirainbow at gmail.com Wed Mar 23 13:40:12 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Wed, 23 Mar 2011 20:40:12 +0800 Subject: [Pw_forum] Help for Calculating Organic Crystal Band Structure In-Reply-To: References: Message-ID: I am fully convienced that pwscf can deal with organic crystal. But, I have no example. On 2011-03-23, ANUP THOMAS wrote: > Dear All > > I, Anup Thomas, a novice in this field of solid state structure > simulation. I would like to perform band structure calculations for some > organic crystals. In my limited knowledge i could not find any one using > Pwscf for organic crstals band structure. Would any one please let me know > Pwscf can simulate the data? > > I will appreciate very much if you can give me more advices. > > > > -- > Regards > > Anup Thomas > SRF 7123 > Computational Chemistry Lab of I and PC Division > Indian Institute of Chemical Technology > Hyderabad 500007 > India > > > "Praise the Lord, all you nations; extol him, all you peoples. > For great is his love toward us, and the faithfulness of the Lord endures > forever. > Praise the Lord" > -- ____________________________________ Hui Wang School of physics, Fudan University, Shanghai, China From sclauzer at sissa.it Wed Mar 23 13:57:46 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 23 Mar 2011 13:57:46 +0100 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <20110323104854.f4nokxq1z40wcks0@webmail.sic.rm.cnr.it> References: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> <20110323104854.f4nokxq1z40wcks0@webmail.sic.rm.cnr.it> Message-ID: <0098FC1B-C08B-4830-B7FA-CCEC05C4565F@sissa.it> Dear Giuseppe, I think your reply reached also the PW-forum, since I've received it twice, so everyone should have been able to read it. Il giorno 23/mar/2011, alle ore 10.48, giuseppe.mattioli at mlib.ism.cnr.it ha scritto: > Dear Gabriele > >> is there any concrete evidence that "ab initio" van der Waals >> vdW-DF is systematically better than Grimme's vdW? > > Yes, at least in the case of molecule-surface interactions. Maybe graphite is another story... with PBE-D2 you should get an interlayer spacing just 3.4% smaller than the experimental value, which is not so bad considering the much larger PBE error. > There is a > recent (2010) Grimme paper (I'm sorry, I cannot be more accurate > today...) Maybe this one: THE JOURNAL OF CHEMICAL PHYSICS 132, 154104 (2010) which is the paper introducing the D3 method (and a comparison with its predecessor D2) > that reports an overestimate of the above interactions when > using DFT-D2, currently implemented in QE. I've performed comparative > tests (classical MM, DFT-D2, vdW-DF) on several molecules interacting > with the non-polar 10-10 ZnO surface and I've obtained the best > results (some of them comparable with experimental data, i.e., the > thiophene ring) by using the vdW-DF approach. The DFT-D2 setup, > however, is quite good for molecules in my experience, and can be > tuned by changing the C6 coefficients by hand > (QE/Modules/mm_dispersion.f90), following one of the available force > fields (AMBER, CHARMM, ...). > Maybe DFT-D3 and vdW-DF would converge to > similar results... I can't tell this, but I know that DFT-D3 should include some notable improvements with respect to the D2 version, since it now takes into account some kind of local coordination of the atoms, atom-pair specific coefficients (from ab initio), and should also separate better the long range regime from the short range one. I know there is someone who offered to look at implementing the extension to D3, maybe it will be available in a few months time. > What about cp? No clear idea here. However I believe it should not be difficult to port DFT-D2 to CP, since it requires only atomic positions and the cell setup. These should be handled in a similar way in PW and CP. Gabriele > > Yours > > G. > > Quoting Gabriele Sclauzero : > >> Dear Giuseppe, >> >> is there any concrete evidence that "ab initio" van der Waals >> vdW-DF is systematically better than Grimme's vdW? >> Are you aware of any paper comparing the latest version of the two >> methodologies (or "phisolophies", if you want), i.e. vdW-DF2 vs >> DFT-D3? >> >> Cheers, >> >> GS >> >> >> Il giorno 23/mar/2011, alle ore 10.12, >> giuseppe.mattioli at mlib.ism.cnr.it ha scritto: >> >>> >>> Dear all >>> You can do better than the semiempirical "Grimme" correction. There is >>> a new ab initio van der Waals correlation functional implemented in QE >>> 4.3a. Try input_dft='vdW-DF', in the &sysytem list. >>> By the way, what about a (semiempirical or ab initio) vdW scheme in >>> cp.x? Is there any project going on? >>> >>> Yours >>> >>> Giuseppe >>> >>> Quoting Masoud Nahali : >>> >>>> Dear Eric >>>> >>>> Try london="true" to get improved answer; as you should know DFT is weak >>>> to calculate dispersion forces and by using the keyword one can include >>>> these forces semi-empirically. I hope it helps. >>>> >>>> Best Wishes >>>> >>>> Masoud >>>> -------------- >>>> Masoud Nahali, Sharif University of Technology >>>> >>>> >>>> Eric Wrote: >>>> >>>> Dear all, >>>> >>>> I'm trying to optimize unit cell parameter of graphite. >>>> The problem is the c axis gets too long. >>>> Starting from published data my initial parameters are a=4.59203 Bohr >>>> and c=12.513 Bohr. >>>> The final values are 4.664 and 15.829 respectively. >>>> I need someone to explain to me what I did wrong, I've attached my input >>>> file. >>>> That's a basic calculation so it's very frustrating to not make it done. >>>> I thank you in advance, >>>> >>>> Eric. >>>> >>>> -- >>>> /Be the change you wish to see in the world >>>> / --- Mahatma Gandhi --- >>>> >>>> Dr. ?ric Germaneau >>> > >>>> >>>> College of Physical Sciences >>>> Graduate University of Chinese Academy of Sciences >>>> Yuquan Road 19A >>>> Beijing 100049 >>>> China >>>> >>> >>> Giuseppe Mattioli >>> ISM-CNR >>> Italy >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> PH H2 462, Station 3, CH-1015 Lausanne >> >> > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/89586cbb/attachment.htm From daniel.forrer at unipd.it Wed Mar 23 14:56:15 2011 From: daniel.forrer at unipd.it (Daniel Forrer) Date: Wed, 23 Mar 2011 14:56:15 +0100 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <0098FC1B-C08B-4830-B7FA-CCEC05C4565F@sissa.it> References: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> <20110323104854.f4nokxq1z40wcks0@webmail.sic.rm.cnr.it> <0098FC1B-C08B-4830-B7FA-CCEC05C4565F@sissa.it> Message-ID: Dear Giuseppe and Gabriele I agree with Gabriele that PBE-D2 gives better results than vdw-DF in the case of graphite. About CP, some time ago I interfaced the DFT-D2 module of PWscf to cp.x. At that time, I used the 4.2 release of espresso, which is a little old now. I can send you that old package if you are interested. We also tested the DFT-D3 method on a couple of systems and, in my opinion, it does not give very exciting results. But interestingly, as suggested by Giuseppe, in some cases we found a good agreement between DFT-D3 and vdw-DF data. Hopefully the two series vdw-DF(n) and DFT-D(n+1) will converge to the same result :) regards daniel 2011/3/23 Gabriele Sclauzero > Dear Giuseppe, > > I think your reply reached also the PW-forum, since I've received it > twice, so everyone should have been able to read it. > > Il giorno 23/mar/2011, alle ore 10.48, giuseppe.mattioli at mlib.ism.cnr.itha scritto: > > Dear Gabriele > > is there any concrete evidence that "ab initio" van der Waals > > vdW-DF is systematically better than Grimme's vdW? > > > Yes, at least in the case of molecule-surface interactions. > > > Maybe graphite is another story... with PBE-D2 you should get an interlayer > spacing just 3.4% smaller than the experimental value, which is not so bad > considering the much larger PBE error. > > > There is a > recent (2010) Grimme paper (I'm sorry, I cannot be more accurate > today...) > > > Maybe this one: > THE JOURNAL OF CHEMICAL PHYSICS *132*, 154104 (2010) > which is the paper introducing the D3 method (and a comparison with its > predecessor D2) > > that reports an overestimate of the above interactions when > using DFT-D2, currently implemented in QE. I've performed comparative > tests (classical MM, DFT-D2, vdW-DF) on several molecules interacting > with the non-polar 10-10 ZnO surface and I've obtained the best > results (some of them comparable with experimental data, i.e., the > thiophene ring) by using the vdW-DF approach. The DFT-D2 setup, > however, is quite good for molecules in my experience, and can be > tuned by changing the C6 coefficients by hand > (QE/Modules/mm_dispersion.f90), following one of the available force > fields (AMBER, CHARMM, ...). > > Maybe DFT-D3 and vdW-DF would converge to > similar results... > > > I can't tell this, but I know that DFT-D3 should include some notable > improvements with respect to the D2 version, since it now takes into account > some kind of local coordination of the atoms, atom-pair specific > coefficients (from ab initio), and should also separate better the long > range regime from the short range one. I know there is someone who offered > to look at implementing the extension to D3, maybe it will be available in a > few months time. > > What about cp? > > > No clear idea here. However I believe it should not be difficult to port > DFT-D2 to CP, since it requires only atomic positions and the cell setup. > These should be handled in a similar way in PW and CP. > > > Gabriele > > > Yours > > G. > > Quoting Gabriele Sclauzero : > > Dear Giuseppe, > > > is there any concrete evidence that "ab initio" van der Waals > > vdW-DF is systematically better than Grimme's vdW? > > Are you aware of any paper comparing the latest version of the two > > methodologies (or "phisolophies", if you want), i.e. vdW-DF2 vs > > DFT-D3? > > > Cheers, > > > GS > > > > Il giorno 23/mar/2011, alle ore 10.12, > > giuseppe.mattioli at mlib.ism.cnr.it ha scritto: > > > > Dear all > > You can do better than the semiempirical "Grimme" correction. There is > > a new ab initio van der Waals correlation functional implemented in QE > > 4.3a. Try input_dft='vdW-DF', in the &sysytem list. > > By the way, what about a (semiempirical or ab initio) vdW scheme in > > cp.x? Is there any project going on? > > > Yours > > > Giuseppe > > > Quoting Masoud Nahali : > > > Dear Eric > > > Try london="true" to get improved answer; as you should know DFT is weak > > to calculate dispersion forces and by using the keyword one can include > > these forces semi-empirically. I hope it helps. > > > Best Wishes > > > Masoud > > -------------- > > Masoud Nahali, Sharif University of Technology > > > > Eric Wrote: > > > Dear all, > > > I'm trying to optimize unit cell parameter of graphite. > > The problem is the c axis gets too long. > > Starting from published data my initial parameters are a=4.59203 Bohr > > and c=12.513 Bohr. > > The final values are 4.664 and 15.829 respectively. > > I need someone to explain to me what I did wrong, I've attached my input > > file. > > That's a basic calculation so it's very frustrating to not make it done. > > I thank you in advance, > > > Eric. > > > -- > > /Be the change you wish to see in the world > > / --- Mahatma Gandhi --- > > > Dr. ?ric Germaneau > > > > > College of Physical Sciences > > Graduate University of Chinese Academy of Sciences > > Yuquan Road 19A > > Beijing 100049 > > China > > > > Giuseppe Mattioli > > ISM-CNR > > Italy > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > > PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > * PH H2 462, Station 3, CH-1015 Lausanne* > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ---------------------------------- Daniel Forrer Dipartimento di Scienze Chimiche Universit? degli Studi di Padova V. Marzolo 1, Padova mail daniel.forrer at unipd.it tel. +39 049 8275166 ---------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/b931d5d5/attachment-0001.htm From stewart at cnf.cornell.edu Wed Mar 23 15:33:00 2011 From: stewart at cnf.cornell.edu (Derek Stewart) Date: Wed, 23 Mar 2011 10:33:00 -0400 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D8A20BE.9020504@gucas.ac.cn> References: <4D8A20BE.9020504@gucas.ac.cn> Message-ID: <4D8A049C.8090900@cnf.cornell.edu> Hi Eric, I just wanted to follow up on Cyrille's comment. Density functional calculations for graphite based on the standard GGA exchange-correlation actually predict that the graphene layers don't bind together at all. So it is not surprising to see that you are getting very large unit cell values in the c direction. LDA exchange-correlation does a better job at getting the correct distance between graphene layers, HOWEVER, this is due to a lucky cancellation of errors. A quick test would be to rerun your structural relaxation with LDA to see if you get a more reasonable spacing between graphene layers. The root cause for your problems, as others on this forum, have mentioned is due to the fact that van der Waals interactions are not included in standard density functional theory (although QE now has some options available). In the end, the important question to ask is how much you expect van der Waals interactions to affect the property of graphite that you are interested. If it will make a minor contribution, then you may be able to just use the experimental distance between graphene layers in graphite or else use the LDA result. See the following article for a nice discussion on the LDA/GGA issue: "Hard numbers on soft matter", H. Rydberg, N. Jacobson, P. Hyldgaard, S. I. Simak, B. I. Lundqvist, and D. C. Langreth, Surface Science, 532-535, 606 (2003) http://dx.doi.org/10.1016/S0039-6028(03)00109-2 If you don't have access to the journal, I think there may be local copies of the article on one of the author's website if you google based on the title. Best regards, Derek ################################ Derek Stewart, Ph. D. Senior Research Associate ** New Webpage ** http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 On 3/23/2011 12:33 PM, Eric Germaneau wrote: > Dear all, > > I'm trying to optimize unit cell parameter of graphite. > The problem is the c axis gets too long. > Starting from published data my initial parameters are a=4.59203 Bohr > and c=12.513 Bohr. > The final values are 4.664 and 15.829 respectively. > I need someone to explain to me what I did wrong, I've attached my > input file. > That's a basic calculation so it's very frustrating to not make it done. > I thank you in advance, > > Eric. > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > /Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. / > > > _______________________________________________ > 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/20110323/c8424af4/attachment.htm From nicola.marzari at materials.ox.ac.uk Wed Mar 23 15:43:10 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 23 Mar 2011 14:43:10 +0000 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D8A049C.8090900@cnf.cornell.edu> References: <4D8A20BE.9020504@gucas.ac.cn> <4D8A049C.8090900@cnf.cornell.edu> Message-ID: <4D8A06FE.7080308@materials.ox.ac.uk> Dear Eric, All, indeed - a good example are the phonons: in order to get the right phonon dispersions in the Gamma-A direction (perpendicular to the planes, i.e. where vdW should matter) you need to have the right structure (i.e. the correct lattice spacing, that in GGA would require vdW), but if you impose the experimental lattice spacing you get the phonons correctly (and thus some of the tricky elastic constants) even *without* having a vdW term in the functional (btw, we discuss quantum-espresso graphite in a lot of detail in a 2005 PRB, with Nicolas Mounet - you could use those results as a sanity check for your calculations). nicola On 3/23/11 2:33 PM, Derek Stewart wrote: > Hi Eric, > > I just wanted to follow up on Cyrille's comment. Density functional > calculations for graphite based on the standard GGA exchange-correlation > actually predict that the graphene layers don't bind together at all. So > it is not surprising to see that you are getting very large unit cell > values in the c direction. LDA exchange-correlation does a better job at > getting the correct distance between graphene layers, HOWEVER, this is > due to a lucky cancellation of errors. A quick test would be to rerun > your structural relaxation with LDA to see if you get a more reasonable > spacing between graphene layers. > > The root cause for your problems, as others on this forum, have > mentioned is due to the fact that van der Waals interactions are not > included in standard density functional theory (although QE now has some > options available). In the end, the important question to ask is how > much you expect van der Waals interactions to affect the property of > graphite that you are interested. If it will make a minor contribution, > then you may be able to just use the experimental distance between > graphene layers in graphite or else use the LDA result. > > See the following article for a nice discussion on the LDA/GGA issue: > > "Hard numbers on soft matter", H. Rydberg, N. Jacobson, P. Hyldgaard, S. > I. Simak, B. I. Lundqvist, and D. C. Langreth, Surface Science, 532-535, > 606 (2003) > http://dx.doi.org/10.1016/S0039-6028(03)00109-2 > > If you don't have access to the journal, I think there may be local > copies of the article on one of the author's website if you google based > on the title. > > Best regards, > > Derek -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From guerrathiago at gmail.com Wed Mar 23 15:43:47 2011 From: guerrathiago at gmail.com (Thiago Guerra) Date: Wed, 23 Mar 2011 11:43:47 -0300 Subject: [Pw_forum] Help for Calculating Organic Crystal Band Structure (ANUP THOMAS) Message-ID: Hi Anup, i worked with organic crystals in PWscf and i had no problems. I studied the interaction of some molecules of organic crystals in oxides and metallic surfaces, and i made some pos processing calculations. I did not make organic crystals band structure yet, but i know that have some problems calculating some properties of organic crystals in DFT. You can find your information in some papers of Dr. G. E. Scuseria. He explain why one have problems calculating this properties in DFT. I hope have helped you. Best regards. _________________________ M. Sc. Thiago Guerra Programa de P?s Gradua??o em Engenharia de Defesa Instituto Militar de Engenharia (IME) Pra?a General Tib?rcio, 80 Praia Vermelha - Rio de Janeiro - RJ CEP: 22290-270 Brazil Mobile: (21) 8321-8971 E-mail: guerrathiago at gmail.com Dear All > > I, Anup Thomas, a novice in this field of solid state structure > simulation. I would like to perform band structure calculations for some > organic crystals. In my limited knowledge i could not find any one using > Pwscf for organic crstals band structure. Would any one please let me know > Pwscf can simulate the data? > > I will appreciate very much if you can give me more advices. > > > > -- > Regards > > Anup Thomas > SRF 7123 > Computational Chemistry Lab of I and PC Division > Indian Institute of Chemical Technology > Hyderabad 500007 > India > > > "Praise the Lord, all you nations; extol him, all you peoples. > For great is his love toward us, and the faithfulness of the Lord endures > forever. > Praise the Lord" > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110323/428f158a/attachment-0001.htm > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/3a097d5e/attachment.htm From metokal at gmail.com Wed Mar 23 15:56:20 2011 From: metokal at gmail.com (Mehmet Topsakal) Date: Wed, 23 Mar 2011 16:56:20 +0200 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D8A06FE.7080308@materials.ox.ac.uk> References: <4D8A20BE.9020504@gucas.ac.cn> <4D8A049C.8090900@cnf.cornell.edu> <4D8A06FE.7080308@materials.ox.ac.uk> Message-ID: Dear all, Once I had prepared a presentation in one of our group meetings which might be helpful in this discussion : http://www.unam.bilkent.edu.tr/mt2/random/vdW/ On Wed, Mar 23, 2011 at 4:43 PM, Nicola Marzari < nicola.marzari at materials.ox.ac.uk> wrote: > > > > Dear Eric, All, > > > indeed - a good example are the phonons: in order to get > the right phonon dispersions in the Gamma-A direction > (perpendicular to the planes, i.e. where vdW should matter) > you need to have the right structure (i.e. the correct lattice > spacing, that in GGA would require vdW), but if you impose the > experimental lattice spacing you get the phonons correctly > (and thus some of the tricky elastic constants) even *without* > having a vdW term in the functional (btw, we discuss > quantum-espresso graphite in a lot of detail in > a 2005 PRB, with Nicolas Mounet - you could use those results > as a sanity check for your calculations). > > nicola > > > On 3/23/11 2:33 PM, Derek Stewart wrote: > > Hi Eric, > > > > I just wanted to follow up on Cyrille's comment. Density functional > > calculations for graphite based on the standard GGA exchange-correlation > > actually predict that the graphene layers don't bind together at all. So > > it is not surprising to see that you are getting very large unit cell > > values in the c direction. LDA exchange-correlation does a better job at > > getting the correct distance between graphene layers, HOWEVER, this is > > due to a lucky cancellation of errors. A quick test would be to rerun > > your structural relaxation with LDA to see if you get a more reasonable > > spacing between graphene layers. > > > > The root cause for your problems, as others on this forum, have > > mentioned is due to the fact that van der Waals interactions are not > > included in standard density functional theory (although QE now has some > > options available). In the end, the important question to ask is how > > much you expect van der Waals interactions to affect the property of > > graphite that you are interested. If it will make a minor contribution, > > then you may be able to just use the experimental distance between > > graphene layers in graphite or else use the LDA result. > > > > See the following article for a nice discussion on the LDA/GGA issue: > > > > "Hard numbers on soft matter", H. Rydberg, N. Jacobson, P. Hyldgaard, S. > > I. Simak, B. I. Lundqvist, and D. C. Langreth, Surface Science, 532-535, > > 606 (2003) > > http://dx.doi.org/10.1016/S0039-6028(03)00109-2 > > > > If you don't have access to the journal, I think there may be local > > copies of the article on one of the author's website if you google based > > on the title. > > > > Best regards, > > > > Derek > -- > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Mehmet Topsakal (Ph.D. Student) UNAM-Institute of Materials Science and Nanotechnology. Bilkent University. 06800 Bilkent, Ankara/Turkey Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 http://www.researcherid.com/rid/A-5015-2010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/2226ef1f/attachment-0001.htm From giannozz at democritos.it Wed Mar 23 20:19:47 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 23 Mar 2011 20:19:47 +0100 Subject: [Pw_forum] compiling QE 4.3a In-Reply-To: References: Message-ID: <5BB874BC-1667-47C0-B8CA-9937B96A05BD@democritos.it> On Mar 23, 2011, at 11:39 , Alain Allouche wrote: > Undefined symbols: > "___intel_sse2_strlen", referenced from: > _get_md5 in clib.a(md5_from_file.o) > _file_md5_ in clib.a(md5_from_file.o) it looks like something strange in your intel fortran and/or C installation; or maybe mpif90 doesn't link the needed system library. See these links: http://software.intel.com/en-us/articles/unresolved-external-symbol- _intel_sse2_strlen/ http://software.intel.com/en-us/forums/showthread.php?t=67401 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From samolyuk at gmail.com Wed Mar 23 22:24:00 2011 From: samolyuk at gmail.com (German Samolyuk) Date: Wed, 23 Mar 2011 17:24:00 -0400 Subject: [Pw_forum] Doubt in Curie temperature value In-Reply-To: <447810.38300.qm@web26103.mail.ukl.yahoo.com> References: <447810.38300.qm@web26103.mail.ukl.yahoo.com> Message-ID: Hi, The difference between FM and AFM energies gives 2J_0, I think. It's easy to check for nearest neighbors interactions only. In this case for Fe your result is quite reasonable. Fe is itinerant ferromagnetic but with localized magnetic moments and Heisenberg model works quite good. You can look for exchange parameters calculated through linear response expression. There is a lot of publication on this topic. For Fe exchange potentials looks like: large first neighbors interactions and the oscillations. So the rest of neighbors almost compensate each other. Ni is a different story. I do not know if anybody can calculate Curie temperature in Ni correctly. It's significantly smaller and if I'm right and delta E = 2 J_0 result for Ni is even smaller in your calculations in agreement with other results. Sincerely, German Samolyuk, ORNL On Tue, Mar 22, 2011 at 12:57 AM, Padmaja Patnaik < padmaja_patnaik at yahoo.co.uk> wrote: > Hi > > I am calculating the Curie Temperature for Iron. The experimental value for > this is 1043 K. I am getting the value as 2398.97 K. I am using the > following way to calculate. > Find out the ferromagnetic and anti-ferromagnetic energy of Fe. The > difference between these two gives the value of J_0. Then, > T_c = [2/3] [J_0/K_B] > > Please suggest me what is wrong? Why am I getting such a high value. On the > other hand I am getting very low value for Ni, whose experimental Curie > temperature is 627K and I am getting 315K. > Thanking you in advance, > regards > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/19f5ba6e/attachment.htm From c.sun1 at uq.edu.au Thu Mar 24 00:51:44 2011 From: c.sun1 at uq.edu.au (Chenghua Sun) Date: Thu, 24 Mar 2011 09:51:44 +1000 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> References: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> Message-ID: <5682E80C36D6D449B2D4552B5884AE572A53CDAB@UQEXMB03.soe.uq.edu.au> Deal All, I didn't try QE4.3a yet, but I am wondering what is the theory basis for the first-principle vdW-DFT by 'vdW-DF' in QE 4.3a. Any improvement compared with semiempirical vdW scheme? In additional, is it applicable for all elements? Cheers, Chenghua ************************************************************ Chenghua Sun, PhD Australian Institute for Bioengineering and Nanotechnology Centre for Computational Molecular Science, Director The University of Queensland Postal Address: CCMS, AIBN Building #75, The University of Queensland Brisbane, Qld 4072, Australia Tel: +61 7 3346 3972 Fax : +61 7 3346 3992 Email: c.sun1 at uq.edu.au Web: http://web.aibn.uq.edu.au/cbn ************************************************************** ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of giuseppe.mattioli at mlib.ism.cnr.it [giuseppe.mattioli at mlib.ism.cnr.it] Sent: Wednesday, 23 March 2011 7:12 PM To: PWSCF Forum Subject: Re: [Pw_forum] graphite cell optimization failed Dear all You can do better than the semiempirical "Grimme" correction. There is a new ab initio van der Waals correlation functional implemented in QE 4.3a. Try input_dft='vdW-DF', in the &sysytem list. By the way, what about a (semiempirical or ab initio) vdW scheme in cp.x? Is there any project going on? Yours Giuseppe Quoting Masoud Nahali : > Dear Eric > > Try london="true" to get improved answer; as you should know DFT is weak > to calculate dispersion forces and by using the keyword one can include > these forces semi-empirically. I hope it helps. > > Best Wishes > > Masoud > -------------- > Masoud Nahali, Sharif University of Technology > > > Eric Wrote: > > Dear all, > > I'm trying to optimize unit cell parameter of graphite. > The problem is the c axis gets too long. > Starting from published data my initial parameters are a=4.59203 Bohr > and c=12.513 Bohr. > The final values are 4.664 and 15.829 respectively. > I need someone to explain to me what I did wrong, I've attached my input > file. > That's a basic calculation so it's very frustrating to not make it done. > I thank you in advance, > > Eric. > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > Giuseppe Mattioli ISM-CNR Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From nicola.marzari at materials.ox.ac.uk Thu Mar 24 01:03:29 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Thu, 24 Mar 2011 00:03:29 +0000 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <5682E80C36D6D449B2D4552B5884AE572A53CDAB@UQEXMB03.soe.uq.edu.au> References: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> <5682E80C36D6D449B2D4552B5884AE572A53CDAB@UQEXMB03.soe.uq.edu.au> Message-ID: <4D8A8A51.1080307@materials.ox.ac.uk> On 3/23/11 11:51 PM, Chenghua Sun wrote: > Deal All, > > I didn't try QE4.3a yet, but I am wondering what is the theory basis for the first-principle vdW-DFT by 'vdW-DF' in QE 4.3a. See "physical review" papers from Dion/Thonhauser/Langreth/Langreth Any improvement compared with semiempirical vdW scheme? In additional, is it applicable for all elements? I think so, but do not have extensive data. yes, it depends on the charge density, not on the elements. nicola ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From c.sun1 at uq.edu.au Thu Mar 24 03:19:59 2011 From: c.sun1 at uq.edu.au (Chenghua Sun) Date: Thu, 24 Mar 2011 12:19:59 +1000 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D8A8A51.1080307@materials.ox.ac.uk> References: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> <5682E80C36D6D449B2D4552B5884AE572A53CDAB@UQEXMB03.soe.uq.edu.au>, <4D8A8A51.1080307@materials.ox.ac.uk> Message-ID: <5682E80C36D6D449B2D4552B5884AE572A53CDAF@UQEXMB03.soe.uq.edu.au> Dear Nicola, Thanks for your reply. I installed the QE4.3a and run a test with input_dft = 'vdW-DF', but I got the error message below: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_kernel_table : error # 1 No \"vdW_kernel_table\" file could be found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% To fix it, should I install the kernel table or add some option with my compiling? Thanks. chenghua ************************************************************ Chenghua Sun, PhD Australian Institute for Bioengineering and Nanotechnology Centre for Computational Molecular Science, Director The University of Queensland Postal Address: CCMS, AIBN Building #75, The University of Queensland Brisbane, Qld 4072, Australia Tel: +61 7 3346 3972 Fax : +61 7 3346 3992 Email: c.sun1 at uq.edu.au Web: http://web.aibn.uq.edu.au/cbn ************************************************************** ________________________________________ From: Nicola Marzari [nicola.marzari at materials.ox.ac.uk] Sent: Thursday, 24 March 2011 10:03 AM Cc: Chenghua Sun; PWSCF Forum Subject: Re: [Pw_forum] graphite cell optimization failed On 3/23/11 11:51 PM, Chenghua Sun wrote: > Deal All, > > I didn't try QE4.3a yet, but I am wondering what is the theory basis for the first-principle vdW-DFT by 'vdW-DF' in QE 4.3a. See "physical review" papers from Dion/Thonhauser/Langreth/Langreth Any improvement compared with semiempirical vdW scheme? In additional, is it applicable for all elements? I think so, but do not have extensive data. yes, it depends on the charge density, not on the elements. nicola ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From tfcao at theory.issp.ac.cn Thu Mar 24 04:02:51 2011 From: tfcao at theory.issp.ac.cn (=?utf-8?B?5pu56IW+6aOe?=) Date: Thu, 24 Mar 2011 11:02:51 +0800 Subject: [Pw_forum] =?utf-8?q?mistake?= Message-ID: <20110324030251.9470.qmail@ms.hfcas.ac.cn> Hello QE users when I do nscf calculations about graphene with hydrogen absorbed on it . A mistake emerges .The information given in the graphene.nscf.out is "starting and expected charges diff " . Here is my input file: &CONTROL title = 'graphene layer' , calculation = 'nscf' , restart_mode = 'from_scratch' , outdir = './tmp' , pseudo_dir = '/home/tfcao/Quantum_Espresso/espresso-4.2.1/pseudo' , prefix = 'graphene' , / &SYSTEM ibrav = 4 , a = 4.9190243 , b = 4.9190243 , c = 10.000 , nat = 9 , ntyp = 2 , occupations = 'smearing' , nspin = 2 , starting_magnetization = 0.5 , tot_charge = 0.0 , degauss = 0.02 , smearing = 'mp' , ecutwfc = 30.0 , ecutrho = 300.0 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_mode = 'plain' , mixing_beta = 0.7 , diagonalization = 'david' , / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF H 1.00000 H.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.000000000 0.000000000 0.500000000 C 0.503477627 -0.000525285 0.499794370 C 0.000525751 0.496522777 0.499794376 C 0.501672324 0.498327941 0.534650360 C 0.162434585 0.329170689 0.501023074 C 0.671219505 0.328779898 0.500739924 C 0.167941491 0.832058258 0.505004338 C 0.670829095 0.837565209 0.501023094 H 0.502164437 0.497835558 0.647579435 K_POINTS 200 4.99999989E-03 0.0000000 0.0000000 1.0000000 9.99999978E-03 0.0000000 0.0000000 1.0000000 1.49999997E-02 0.0000000 0.0000000 1.0000000 1.99999996E-02 0.0000000 0.0000000 1.0000000 2.49999985E-02 0.0000000 0.0000000 1.0000000 2.99999993E-02 0.0000000 0.0000000 1.0000000 3.50000001E-02 0.0000000 0.0000000 1.0000000 3.99999991E-02 0.0000000 0.0000000 1.0000000 4.49999981E-02 0.0000000 0.0000000 1.0000000 4.99999970E-02 0.0000000 0.0000000 1.0000000 5.49999997E-02 0.0000000 0.0000000 1.0000000 5.99999987E-02 0.0000000 0.0000000 1.0000000 6.49999976E-02 0.0000000 0.0000000 1.0000000 7.00000003E-02 0.0000000 0.0000000 1.0000000 7.49999955E-02 0.0000000 0.0000000 1.0000000 7.99999982E-02 0.0000000 0.0000000 1.0000000 8.50000009E-02 0.0000000 0.0000000 1.0000000 8.99999961E-02 0.0000000 0.0000000 1.0000000 9.49999988E-02 0.0000000 0.0000000 1.0000000 9.99999940E-02 0.0000000 0.0000000 1.0000000 0.10500000 0.0000000 0.0000000 1.0000000 0.11000000 0.0000000 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0.35499999 0.0000000 0.0000000 1.0000000 0.35999998 0.0000000 0.0000000 1.0000000 0.36499998 0.0000000 0.0000000 1.0000000 0.37000000 0.0000000 0.0000000 1.0000000 0.37500000 0.0000000 0.0000000 1.0000000 0.38000000 0.0000000 0.0000000 1.0000000 0.38499999 0.0000000 0.0000000 1.0000000 0.38999999 0.0000000 0.0000000 1.0000000 0.39499998 0.0000000 0.0000000 1.0000000 0.39999998 0.0000000 0.0000000 1.0000000 0.40500000 0.0000000 0.0000000 1.0000000 0.41000000 0.0000000 0.0000000 1.0000000 0.41499999 0.0000000 0.0000000 1.0000000 0.41999999 0.0000000 0.0000000 1.0000000 0.42499998 0.0000000 0.0000000 1.0000000 0.42999998 0.0000000 0.0000000 1.0000000 0.43500000 0.0000000 0.0000000 1.0000000 0.44000000 0.0000000 0.0000000 1.0000000 0.44499999 0.0000000 0.0000000 1.0000000 0.44999999 0.0000000 0.0000000 1.0000000 0.45499998 0.0000000 0.0000000 1.0000000 0.45999998 0.0000000 0.0000000 1.0000000 0.46500000 0.0000000 0.0000000 1.0000000 0.47000000 0.0000000 0.0000000 1.0000000 0.47499999 0.0000000 0.0000000 1.0000000 0.47999999 0.0000000 0.0000000 1.0000000 0.48499998 0.0000000 0.0000000 1.0000000 0.48999998 0.0000000 0.0000000 1.0000000 0.49499997 0.0000000 0.0000000 1.0000000 0.50000000 0.0000000 0.0000000 1.0000000 0.49833301 3.33300000E-03 0.0000000 1.0000000 0.49666601 6.66600000E-03 0.0000000 1.0000000 0.49499899 9.99899954E-03 0.0000000 1.0000000 0.49333200 1.33320000E-02 0.0000000 1.0000000 0.49166501 1.66650005E-02 0.0000000 1.0000000 0.48999801 1.99979991E-02 0.0000000 1.0000000 0.48833099 2.33309995E-02 0.0000000 1.0000000 0.48666400 2.66640000E-02 0.0000000 1.0000000 0.48499700 2.99970005E-02 0.0000000 1.0000000 0.48333001 3.33300009E-02 0.0000000 1.0000000 0.48166299 3.66629995E-02 0.0000000 1.0000000 0.47999600 3.99959981E-02 0.0000000 1.0000000 0.47832900 4.33290005E-02 0.0000000 1.0000000 0.47666201 4.66619991E-02 0.0000000 1.0000000 0.47499499 4.99950014E-02 0.0000000 1.0000000 0.47332799 5.33280000E-02 0.0000000 1.0000000 0.47166100 5.66609986E-02 0.0000000 1.0000000 0.46999401 5.99940009E-02 0.0000000 1.0000000 0.46832699 6.33269995E-02 0.0000000 1.0000000 0.46665999 6.66600019E-02 0.0000000 1.0000000 0.46499300 6.99929968E-02 0.0000000 1.0000000 0.46332601 7.33259991E-02 0.0000000 1.0000000 0.46165901 7.66590014E-02 0.0000000 1.0000000 0.45999199 7.99919963E-02 0.0000000 1.0000000 0.45832500 8.33249986E-02 0.0000000 1.0000000 0.45665801 8.66580009E-02 0.0000000 1.0000000 0.45499101 8.99910033E-02 0.0000000 1.0000000 0.45332399 9.33239982E-02 0.0000000 1.0000000 0.45165700 9.66570005E-02 0.0000000 1.0000000 0.44999000 9.99900028E-02 0.0000000 1.0000000 0.44832301 0.10332300 0.0000000 1.0000000 0.44665599 0.10665600 0.0000000 1.0000000 0.44498900 0.10998900 0.0000000 1.0000000 0.44332200 0.11332200 0.0000000 1.0000000 0.44165501 0.11665500 0.0000000 1.0000000 0.43998799 0.11998800 0.0000000 1.0000000 0.43832099 0.12332100 0.0000000 1.0000000 0.43665400 0.12665400 0.0000000 1.0000000 0.43498701 0.12998700 0.0000000 1.0000000 0.43331999 0.13332000 0.0000000 1.0000000 0.43165299 0.13665301 0.0000000 1.0000000 0.42998600 0.13998599 0.0000000 1.0000000 0.42831901 0.14331900 0.0000000 1.0000000 0.42665201 0.14665200 0.0000000 1.0000000 0.42498499 0.14998500 0.0000000 1.0000000 0.42331800 0.15331800 0.0000000 1.0000000 0.42165101 0.15665101 0.0000000 1.0000000 0.41998398 0.15998399 0.0000000 1.0000000 0.41831699 0.16331699 0.0000000 1.0000000 0.41665000 0.16665000 0.0000000 1.0000000 0.41498300 0.16998300 0.0000000 1.0000000 0.41331601 0.17331600 0.0000000 1.0000000 0.41164899 0.17664900 0.0000000 1.0000000 0.40998200 0.17998201 0.0000000 1.0000000 0.40831500 0.18331499 0.0000000 1.0000000 0.40664801 0.18664800 0.0000000 1.0000000 0.40498102 0.18998100 0.0000000 1.0000000 0.40331399 0.19331400 0.0000000 1.0000000 0.40164700 0.19664700 0.0000000 1.0000000 0.39998001 0.19998001 0.0000000 1.0000000 0.39831299 0.20331299 0.0000000 1.0000000 0.39664599 0.20664600 0.0000000 1.0000000 0.39497900 0.20997900 0.0000000 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0.0000000 1.0000000 0.35330400 0.29330400 0.0000000 1.0000000 0.35163701 0.29663700 0.0000000 1.0000000 0.34996998 0.29997000 0.0000000 1.0000000 0.34830302 0.30330300 0.0000000 1.0000000 0.34663600 0.30663601 0.0000000 1.0000000 0.34496900 0.30996901 0.0000000 1.0000000 0.34330201 0.31330201 0.0000000 1.0000000 0.34163499 0.31663501 0.0000000 1.0000000 0.33996800 0.31996799 0.0000000 1.0000000 0.33830100 0.32330099 0.0000000 1.0000000 0.33663398 0.32663399 0.0000000 1.0000000 0.33496702 0.32996699 0.0000000 1.0000000 0.33329999 0.33329999 0.0000000 1.0000000 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/97c49b9a/attachment-0001.htm From metokal at gmail.com Thu Mar 24 04:47:26 2011 From: metokal at gmail.com (Mehmet Topsakal) Date: Thu, 24 Mar 2011 05:47:26 +0200 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <5682E80C36D6D449B2D4552B5884AE572A53CDAF@UQEXMB03.soe.uq.edu.au> References: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> <5682E80C36D6D449B2D4552B5884AE572A53CDAB@UQEXMB03.soe.uq.edu.au> <4D8A8A51.1080307@materials.ox.ac.uk> <5682E80C36D6D449B2D4552B5884AE572A53CDAF@UQEXMB03.soe.uq.edu.au> Message-ID: just run generate_vdW_kernel_table.x executable and wait for vdW_kernel_table file to appear. On Thu, Mar 24, 2011 at 4:19 AM, Chenghua Sun wrote: > Dear Nicola, > > Thanks for your reply. I installed the QE4.3a and run a test with > input_dft = 'vdW-DF', but I got the error message below: > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_kernel_table : error # 1 > No \"vdW_kernel_table\" file could be found > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > To fix it, should I install the kernel table or add some option with my > compiling? > > Thanks. > > chenghua > ************************************************************ > Chenghua Sun, PhD > Australian Institute for Bioengineering and Nanotechnology > Centre for Computational Molecular Science, Director > The University of Queensland > > Postal Address: > CCMS, AIBN Building #75, > The University of Queensland > Brisbane, Qld 4072, Australia > > Tel: +61 7 3346 3972 > Fax : +61 7 3346 3992 > Email: c.sun1 at uq.edu.au > Web: http://web.aibn.uq.edu.au/cbn > ************************************************************** > > ________________________________________ > From: Nicola Marzari [nicola.marzari at materials.ox.ac.uk] > Sent: Thursday, 24 March 2011 10:03 AM > Cc: Chenghua Sun; PWSCF Forum > Subject: Re: [Pw_forum] graphite cell optimization failed > > On 3/23/11 11:51 PM, Chenghua Sun wrote: > > Deal All, > > > > I didn't try QE4.3a yet, but I am wondering what is the theory basis for > the first-principle vdW-DFT by 'vdW-DF' in QE 4.3a. > > See "physical review" papers from Dion/Thonhauser/Langreth/Langreth > > Any improvement compared with semiempirical vdW scheme? In additional, > is it applicable for all elements? > > I think so, but do not have extensive data. yes, it depends on the > charge density, not on the elements. > > nicola > > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Mehmet Topsakal (Ph.D. Student) UNAM-Institute of Materials Science and Nanotechnology. Bilkent University. 06800 Bilkent, Ankara/Turkey Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 http://www.researcherid.com/rid/A-5015-2010 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/768e3155/attachment.htm From germaneau at gucas.ac.cn Thu Mar 24 18:45:59 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 24 Mar 2011 13:45:59 -0400 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <500855720.31742@test1.gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> Message-ID: <4D8B8357.8070802@gucas.ac.cn> Dear QE users, First of all I thank you all so much for your very useful replies and advices. I did again the calculation this time using 16x16x8 k-points with cold smearing as suggested in PRB 71, 205214 (2005). I've also increased the precision of the atomic coordinates. Finally, I preformed the calculation using GGA only, GGA+london, and LDA. I got the following results: GGA GGA - london LDA EXP a = 2.46854 angs a = 2.46283 angs a = 2.44424 a = 2.46067 c = 8.02141 angs c = 6.39949 angs c = 6.49579 c = 6.705 (6.67 at 0K) energy = -155.032 energy = -155.146 ev/atom energy = -155.481 ev/atom The DFT-D approach improve significatively the length of the c axis. I'm currently trying to do the same thing with the vdW-DF method implemented in QE 4.3a but the program crash with the error: / from ggen : error # 45126 too many g-vectors/ Best, Eric. On 03/23/2011 12:33 PM, Eric Germaneau wrote: > Dear all, > > I'm trying to optimize unit cell parameter of graphite. > The problem is the c axis gets too long. > Starting from published data my initial parameters are a=4.59203 Bohr > and c=12.513 Bohr. > The final values are 4.664 and 15.829 respectively. > I need someone to explain to me what I did wrong, I've attached my > input file. > That's a basic calculation so it's very frustrating to not make it done. > I thank you in advance, > > Eric. > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > /Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. / > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/00096532/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Thu Mar 24 08:12:37 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 24 Mar 2011 08:12:37 +0100 Subject: [Pw_forum] mistake In-Reply-To: <20110324030251.9470.qmail@ms.hfcas.ac.cn> References: <20110324030251.9470.qmail@ms.hfcas.ac.cn> Message-ID: In data 24 marzo 2011 alle ore 04:02:51, ??? ha scritto: > calculation = 'nscf' , > restart_mode = 'from_scratch' , Dear ???, you cannot do a nscf (NON-self-consistent field) calculation from scratch! You always have to start with an scf calculation, than you can do an nscf analysis starting from the pre-computed ground-state charge density. kind regards -- Lorenzo Paulatto post-doc @ IMPMC/UPMC - Universit? Paris 6 phone: +33 (0)1 44 27 74 89 www: http://www-int.impmc.upmc.fr/~paulatto/ previously (take note of the change!): phd student @ SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 www: http://people.sissa.it/~paulatto/ From giannozz at democritos.it Thu Mar 24 09:23:17 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 24 Mar 2011 09:23:17 +0100 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D8B8357.8070802@gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> Message-ID: <73A6AFB2-19FC-44B0-B9CD-24B4BDA82AB6@democritos.it> On Mar 24, 2011, at 18:45 , Eric Germaneau wrote: > I'm currently trying to do the same thing with the vdW-DF > method implemented in QE 4.3a but the program crash with the error: > > from ggen : error # 45126 > too many g-vectors very strange, since this error is in a part of the code that is not affected at all by vdW-DFT. You mean that if you run the same input with and without vdW-DFT, you get the error in the first case and not in the second? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mxchen.2011 at gmail.com Thu Mar 24 09:29:32 2011 From: mxchen.2011 at gmail.com (Mingxing Chen) Date: Thu, 24 Mar 2011 09:29:32 +0100 Subject: [Pw_forum] calculate third-order derivative of energy by D3 Message-ID: Dear all, Did anybody modify the PWSCF for calculations of the third-order derivative of energy on a general Qpoint configuration? Do you mind share the code with me? Any suggestion will be appreciated. Thanks a lot. Best regards, Mingxing Chen -- Mingxing Chen, Institute for Physical Chemistry University of Vienna Email: mxchen.2011 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/12a348b4/attachment.htm From giannozz at democritos.it Thu Mar 24 09:34:57 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 24 Mar 2011 09:34:57 +0100 Subject: [Pw_forum] core radius of pseudopotential for which matches real wave function In-Reply-To: References: <28B17D02-FC4E-48E7-9428-BE924E87B6C6@democritos.it> Message-ID: <5BB9D35C-01A0-45DC-89F2-DA820D29E66E@democritos.it> On Mar 23, 2011, at 7:47 , mike at. wrote: > thanks for the help, how can one access the original file? ask the original author, if known... P. -------------- next part -------------- A non-text attachment was scrubbed... Name: B.vbc Type: application/octet-stream Size: 5555 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110324/43f09b52/attachment-0001.obj -------------- next part -------------- --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Mar 24 09:39:03 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 24 Mar 2011 09:39:03 +0100 Subject: [Pw_forum] Help for Calculating Organic Crystal Band Structure In-Reply-To: References: Message-ID: On Mar 23, 2011, at 13:04 , ANUP THOMAS wrote: > I, Anup Thomas, a novice in this field of solid state structure > simulation. novices should first of all read some literature introducing to the subject. > I would like to perform band structure calculations for some > organic crystals. > see the discussion on van der Waals bonded systems. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From tfcao at theory.issp.ac.cn Thu Mar 24 12:29:40 2011 From: tfcao at theory.issp.ac.cn (=?utf-8?B?5pu56IW+6aOe?=) Date: Thu, 24 Mar 2011 19:29:40 +0800 Subject: [Pw_forum] =?utf-8?q?Problem_about__lattice_Relaxation__calculati?= =?utf-8?q?on_____________Tengfei_Cao?= Message-ID: <20110324112940.17783.qmail@ms.hfcas.ac.cn> Dear QE users I am doing the lattice relaxation calculation about graphene with three Hydrogen atoms absorbed on it . But with one configuration ,the converge can not be achieved,and the calculation stopped . And what can be the reasons ? Any advice will be appreciated .Here is part of my output file: iteration #100 ecut= 30.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 8.12E-10, avg # of iterations = 1.5 negative rho (up, down): 0.545E-04 0.924E-04 total cpu time spent up to now is 70504.76 secs total energy = -690.13933279 Ry Harris-Foulkes estimate = -690.13933282 Ry estimated scf accuracy < 0.00000298 Ry total magnetization = 4.18 Bohr mag/cell absolute magnetization = 7.23 Bohr mag/cell End of self-consistent calculation convergence NOT achieved after 100 iterations: stopping Writing output data file graphene.save -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/115747cd/attachment.htm From alain.allouche at univ-provence.fr Thu Mar 24 13:24:27 2011 From: alain.allouche at univ-provence.fr (Alain Allouche) Date: Thu, 24 Mar 2011 13:24:27 +0100 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: References: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> <5682E80C36D6D449B2D4552B5884AE572A53CDAB@UQEXMB03.soe.uq.edu.au> <4D8A8A51.1080307@materials.ox.ac.uk> <5682E80C36D6D449B2D4552B5884AE572A53CDAF@UQEXMB03.soe.uq.edu.au> Message-ID: <168E4526-95FC-42E0-9A65-72DF4AF524F8@univ-provence.fr> I have exactly the same problem with ifort on my MacPro and gfortran on my AMD cluster %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% from read_kernel_table : error # 1 No \"vdW_kernel_table\" file could be found %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%% Le 24 mars 11 ? 04:47, Mehmet Topsakal a ?crit : > just run generate_vdW_kernel_table.x executable and wait for > vdW_kernel_table file to appear. > > > On Thu, Mar 24, 2011 at 4:19 AM, Chenghua Sun > wrote: > Dear Nicola, > > Thanks for your reply. I installed the QE4.3a and run a test with > input_dft = 'vdW-DF', but I got the error message below: > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > from read_kernel_table : error # 1 > No \"vdW_kernel_table\" file could be found > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%% > > > To fix it, should I install the kernel table or add some option with > my compiling? > > Thanks. > > chenghua > ************************************************************ > Chenghua Sun, PhD > Australian Institute for Bioengineering and Nanotechnology > Centre for Computational Molecular Science, Director > The University of Queensland > > Postal Address: > CCMS, AIBN Building #75, > The University of Queensland > Brisbane, Qld 4072, Australia > > Tel: +61 7 3346 3972 > Fax : +61 7 3346 3992 > Email: c.sun1 at uq.edu.au > Web: http://web.aibn.uq.edu.au/cbn > ************************************************************** > > ________________________________________ > From: Nicola Marzari [nicola.marzari at materials.ox.ac.uk] > Sent: Thursday, 24 March 2011 10:03 AM > Cc: Chenghua Sun; PWSCF Forum > Subject: Re: [Pw_forum] graphite cell optimization failed > > On 3/23/11 11:51 PM, Chenghua Sun wrote: > > Deal All, > > > > I didn't try QE4.3a yet, but I am wondering what is the theory > basis for the first-principle vdW-DFT by 'vdW-DF' in QE 4.3a. > > See "physical review" papers from Dion/Thonhauser/Langreth/Langreth > > Any improvement compared with semiempirical vdW scheme? In additional, > is it applicable for all elements? > > I think so, but do not have extensive data. yes, it depends on the > charge density, not on the elements. > > nicola > > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > Mehmet Topsakal (Ph.D. Student) > UNAM-Institute of Materials Science and Nanotechnology. > Bilkent University. 06800 Bilkent, Ankara/Turkey > Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 > http://www.researcherid.com/rid/A-5015-2010 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum Dr. Alain ALLOUCHE Physique des Interactions Ioniques et Moleculaires CNRS / Universite de Provence Campus Saint Jerome Service 242 Avenue de l'Escadrille Normandie-Niemen 13397 Marseille Cedex 20 - France Tel : +33 (0) 4 91 28 85 76 Mobile:+33 681 84 80 66 Fax : +33 491.28.89.05 email: Alain.Allouche at univ-provence.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/237a8f05/attachment.htm From germaneau at gucas.ac.cn Fri Mar 25 01:38:08 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 24 Mar 2011 20:38:08 -0400 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <500969301.28413@test1.gucas.ac.cn> References: <20110323101253.ozoc0a31ckscsw4g@webmail.sic.rm.cnr.it> <5682E80C36D6D449B2D4552B5884AE572A53CDAB@UQEXMB03.soe.uq.edu.au> <4D8A8A51.1080307@materials.ox.ac.uk> <5682E80C36D6D449B2D4552B5884AE572A53CDAF@UQEXMB03.soe.uq.edu.au> <500969301.28413@test1.gucas.ac.cn> Message-ID: <4D8BE3F0.6060302@gucas.ac.cn> Actually the file generated by generate_vdW_kernel_table.x, vdW_kernel_table, must be in the same directory as you pseudo-potentials. On 03/24/2011 08:24 AM, Alain Allouche wrote: > I have exactly the same problem with ifort on my MacPro and gfortran > on my AMD cluster > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_kernel_table : error # 1 > No \"vdW_kernel_table\" file could be found > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > Le 24 mars 11 ? 04:47, Mehmet Topsakal a ?crit : > >> just run generate_vdW_kernel_table.x executable and wait for >> vdW_kernel_table file to appear. >> >> >> On Thu, Mar 24, 2011 at 4:19 AM, Chenghua Sun > > wrote: >> >> Dear Nicola, >> >> Thanks for your reply. I installed the QE4.3a and run a test with >> input_dft = 'vdW-DF', but I got the error message below: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from read_kernel_table : error # 1 >> No \"vdW_kernel_table\" file could be found >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> To fix it, should I install the kernel table or add some option >> with my compiling? >> >> Thanks. >> >> chenghua >> ************************************************************ >> Chenghua Sun, PhD >> Australian Institute for Bioengineering and Nanotechnology >> Centre for Computational Molecular Science, Director >> The University of Queensland >> >> Postal Address: >> CCMS, AIBN Building #75, >> The University of Queensland >> Brisbane, Qld 4072, Australia >> >> Tel: +61 7 3346 3972 >> Fax : +61 7 3346 3992 >> Email: c.sun1 at uq.edu.au >> Web: http://web.aibn.uq.edu.au/cbn >> ************************************************************** >> >> ________________________________________ >> From: Nicola Marzari [nicola.marzari at materials.ox.ac.uk >> ] >> Sent: Thursday, 24 March 2011 10:03 AM >> Cc: Chenghua Sun; PWSCF Forum >> Subject: Re: [Pw_forum] graphite cell optimization failed >> >> On 3/23/11 11:51 PM, Chenghua Sun wrote: >> > Deal All, >> > >> > I didn't try QE4.3a yet, but I am wondering what is the theory >> basis for the first-principle vdW-DFT by 'vdW-DF' in QE 4.3a. >> >> See "physical review" papers from Dion/Thonhauser/Langreth/Langreth >> >> Any improvement compared with semiempirical vdW scheme? In >> additional, >> is it applicable for all elements? >> >> I think so, but do not have extensive data. yes, it depends on the >> charge density, not on the elements. >> >> nicola >> >> ---------------------------------------------------------------------- >> Prof Nicola Marzari Department of Materials University of >> Oxford >> Chair of Materials Modelling Director, Materials Modelling >> Laboratory >> nicola.marzari at materials.ox.ac.uk >> >> http://mml.materials.ox.ac.uk/NM >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> -- >> >> Mehmet Topsakal (Ph.D. Student) >> UNAM-Institute of Materials Science and Nanotechnology. >> Bilkent University. 06800 Bilkent, Ankara/Turkey >> Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 >> http://www.researcherid.com/rid/A-5015-2010 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > Dr. Alain ALLOUCHE > Physique des Interactions Ioniques et Moleculaires > CNRS / Universite de Provence > Campus Saint Jerome Service 242 > Avenue de l'Escadrille Normandie-Niemen > 13397 Marseille Cedex 20 - France > Tel : +33 (0) 4 91 28 85 76 > Mobile:+33 681 84 80 66 > Fax : +33 491.28.89.05 > email: Alain.Allouche at univ-provence.fr > > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/ab9d0a31/attachment-0001.htm From julen.azpiroz at gmail.com Thu Mar 24 15:54:15 2011 From: julen.azpiroz at gmail.com (Julen Ibanez Azpiroz) Date: Thu, 24 Mar 2011 15:54:15 +0100 Subject: [Pw_forum] spin-orbit coupling In-Reply-To: <225611.52215.qm@web161702.mail.bf1.yahoo.com> References: <225611.52215.qm@web161702.mail.bf1.yahoo.com> Message-ID: Dear Peiman, As far as I know, in QE the spin-orbit coupling is taken into account by fully relativistic pseudopotentials, so you have to build this kind of PP for your atoms. Once you have them, I think that the way to include the it is to set lspinorb=.true. and also noncolin=.true. Best regards Julen Iba?ez University of the Basque Country, Condensed Matter Physics -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/f10f7d79/attachment.htm From davide.sangalli at gmail.com Thu Mar 24 17:37:00 2011 From: davide.sangalli at gmail.com (Davide Sangalli) Date: Thu, 24 Mar 2011 17:37:00 +0100 Subject: [Pw_forum] Born effective charges in spin polarized systems In-Reply-To: <4D8B709B.3030404@gmail.com> References: <4D8B709B.3030404@gmail.com> Message-ID: <4D8B732C.7080002@gmail.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/78047800/attachment-0001.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Zr0.75_O2_Fe0.25_ecut35_kpt444_ecutrho400_rc_pw.out Url: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/78047800/attachment-0002.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Zr0.75_O2_Fe0.25_ecut35_kpt444_ecutrho400_rc_ph_phonons+Z_zue.out Url: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/78047800/attachment-0001.asc -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Zr0.75_O2_Fe0.25_ecut35_kpt444_ecutrho400_rc_ph_eps+Z_zeu.out Url: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/78047800/attachment-0003.txt From srijan.india at gmail.com Thu Mar 24 19:08:46 2011 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Thu, 24 Mar 2011 19:08:46 +0100 Subject: [Pw_forum] Born effective charges in spin polarized systems In-Reply-To: <4D8B732C.7080002@gmail.com> References: <4D8B709B.3030404@gmail.com> <4D8B732C.7080002@gmail.com> Message-ID: Dear Davide, If possible, please attach the input files as well for a quicker and complete answer. regards, Srijan Kumar R&D Assistant JNCASR Bangalore 560064 On Thu, Mar 24, 2011 at 5:37 PM, Davide Sangalli wrote: > Dear Forum, > > I tried to use the ph code in order to compute Born effective charges > for a spin-polarized system. > The results I've obtained from the "zue" and the "zeu" methods are > different. > > The values for the Fe atom in one case are positive and in the other are > negative. > I've used the version of the code from the cvs repository > (which was working properly for a non-polarized system.) > > Any suggestion? > Attached the output of the two calculations and of the pwscf run. > > Thank you and best regards, > Davide > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110324/39a71531/attachment.htm From germaneau at gucas.ac.cn Fri Mar 25 12:17:31 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Fri, 25 Mar 2011 07:17:31 -0400 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <500954893.22959@test1.gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> Message-ID: <4D8C79CB.8040804@gucas.ac.cn> Dear Professor Giannozzi, I do not mean this error comes from vdW-DFT, I just report a fact that I've observed from my run. I've been trying with and without vdW-DFT and got the same error. Actually the optimization process looks good with vdW-DFT. I just don't understand the meaning of this error since it does not happen with the previous release. That's my be something obvious for experts but not yet for me. I'm going the the doc for the last version more carefully and let you know. Thank you, Eric. On 03/24/2011 04:23 AM, Paolo Giannozzi wrote: > On Mar 24, 2011, at 18:45 , Eric Germaneau wrote: > >> I'm currently trying to do the same thing with the vdW-DF >> method implemented in QE 4.3a but the program crash with the error: >> >> from ggen : error # 45126 >> too many g-vectors > very strange, since this error is in a part of the code that is > not affected at all by vdW-DFT. You mean that if you run the > same input with and without vdW-DFT, you get the error in > the first case and not in the second? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110325/e9c1dd20/attachment.htm From giannozz at democritos.it Fri Mar 25 08:25:38 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 25 Mar 2011 08:25:38 +0100 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D8C79CB.8040804@gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> <4D8C79CB.8040804@gucas.ac.cn> Message-ID: <141FBF01-AB8F-4AAB-B741-76026D886FAC@democritos.it> On Mar 25, 2011, at 12:17 , Eric Germaneau wrote: > That's my be something obvious for experts but not yet for me. it is not obvious at all: it is an internal error that should never show up. Please provide the input that produces such an error and specify if you run in parallel, and on how many processors P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From germaneau at gucas.ac.cn Fri Mar 25 20:40:25 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Fri, 25 Mar 2011 15:40:25 -0400 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <501037833.20213@test1.gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> <4D8C79CB.8040804@gucas.ac.cn> <501037833.20213@test1.gucas.ac.cn> Message-ID: <4D8CEFA9.6070608@gucas.ac.cn> I'm running it on parallel on a single quad core intel processor. Here is how I built QE: make clean export FFLAGS="-ffast-math -m64 -march=core2 -mtune=core2 -ftree-vectorize -O3" export CFLAGS=$FFLAGS ./configure --with-internal-blas --with-internal-lapack #--enable-openmp make all Here is how I execute it: mpiexec -n $NPROC $EXEC < 02_graphite.vcrelax.in > 02_graphite.vcrelax.out with $NPROC=4. I did the same thing with the previous version and did not get any issue. Thanks, Eric. On 03/25/2011 03:25 AM, Paolo Giannozzi wrote: > On Mar 25, 2011, at 12:17 , Eric Germaneau wrote: > >> That's my be something obvious for experts but not yet for me. > it is not obvious at all: it is an internal error that should never show > up. Please provide the input that produces such an error and > specify if you run in parallel, and on how many processors > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110325/a4d79f6a/attachment.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: 02_graphite.vcrelax.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20110325/a4d79f6a/attachment.txt From davide.sangalli at gmail.com Fri Mar 25 09:10:59 2011 From: davide.sangalli at gmail.com (Davide Sangalli) Date: Fri, 25 Mar 2011 09:10:59 +0100 Subject: [Pw_forum] Born effective charges in spin polarized systems In-Reply-To: References: <4D8B709B.3030404@gmail.com> <4D8B732C.7080002@gmail.com> Message-ID: <4D8C4E13.9040109@gmail.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110325/21889f7b/attachment.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Zr0.75_O2_Fe0.25_pw.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20110325/21889f7b/attachment.txt -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Zr0.75_O2_Fe0.25_ph_phonons+Z.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20110325/21889f7b/attachment.asc -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Zr0.75_O2_Fe0.25_ph_eps+Z.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20110325/21889f7b/attachment-0001.txt From giannozz at democritos.it Fri Mar 25 11:14:35 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 25 Mar 2011 11:14:35 +0100 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D8CEFA9.6070608@gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> <4D8C79CB.8040804@gucas.ac.cn> <501037833.20213@test1.gucas.ac.cn> <4D8CEFA9.6070608@gucas.ac.cn> Message-ID: <2453D16B-4C77-467B-974A-1309601B9F4F@democritos.it> On Mar 25, 2011, at 20:40 , Eric Germaneau wrote: > I did the same thing with the previous version and did not get any > issue. I have no such problem. Since your data contain restart_mode='restart', my guess is that the problem comes from a restart from inappropriate data P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From vinothrece at gmail.com Fri Mar 25 12:47:40 2011 From: vinothrece at gmail.com (vinoth r) Date: Fri, 25 Mar 2011 17:17:40 +0530 Subject: [Pw_forum] saw like potential Message-ID: Dear friends, i had one query. i need to apply 1.4V saw like potential. for eamp description given as Amplitude of the electric field in ***hartree***a.u; 1 a.u=51.4220632*10^10 v/m; i need to apply 1.4 voltage means how to convert in to ***hartree***a.u; i applied eamp = 2.72256676e-12 ,for 1.4 voltage.*i used all my units in a.u *; with this i attached my input file also. Thanks in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110325/672ac84f/attachment.htm -------------- next part -------------- &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/home/vino/work/' , wfcdir = '/home/vino/work/' , pseudo_dir = '/home/vino/espresso-4.2.1/pseudo/' , verbosity = 'high' , tefield = .true. , / &SYSTEM ibrav = 4, celldm(1) = 2.456, celldm(3) = 16, nat = 4, ntyp = 2, ecutwfc = 400 , edir = 3 , emaxpos = 0.5D , eopreg = 0.1D , eamp = 2.72256676e-12 , / &ELECTRONS diagonalization = 'david' , / &IONS / ATOMIC_SPECIES N 14.00000 N.pz-rrkjus.UPF B 10.00000 B.pz-vbc.UPF ATOMIC_POSITIONS angstrom N 0.000000000 0.000000000 4.560000000 B 1.230600000 0.710501000 4.560000000 B 0.000000000 0.000000000 8.000000000 N 1.230600000 0.710501000 8.000000000 K_POINTS automatic 36 36 1 0 0 0 From degironc at sissa.it Fri Mar 25 13:02:49 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 25 Mar 2011 13:02:49 +0100 Subject: [Pw_forum] saw like potential In-Reply-To: References: Message-ID: <4D8C8469.9070308@sissa.it> eamp is a measure of the additional electric field, you are talking of a potential energy difference.. you need to know/decide across which distance you want this potential drop to occur and define the electric field accordingly. stefano de Gironcoli On 03/25/2011 12:47 PM, vinoth r wrote: > Dear friends, > > i had one query. > > i need to apply 1.4V saw like potential. > for eamp description given as > > Amplitude of the electric field in ***hartree***a.u; > 1 a.u=51.4220632*10^10 v/m; > > i need to apply 1.4 voltage means how to convert in to ***hartree***a.u; > i applied eamp = 2.72256676e-12 ,for 1.4 voltage.*i used all my units in a.u > *; > > with this i attached my input file also. > > Thanks in advance > > > > _______________________________________________ > 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/20110325/164c43ac/attachment.htm From sclauzer at sissa.it Fri Mar 25 13:58:19 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 25 Mar 2011 13:58:19 +0100 Subject: [Pw_forum] I/O performance on BG/P systems Message-ID: <4D8C916B.8010800@sissa.it> Dear all, I've been running some large systems on BG/P and I've met surprisingly large timings for disk writing operations (wavefunctions). As an example, this is part of the timing for a system with 408 atoms, 904 KS states, and FFT grid: (220,220,512) General routines calbec : 1165.61s CPU 1165.61s WALL ( 337 calls) fft : 74.20s CPU 74.20s WALL ( 636 calls) ffts : 1.39s CPU 1.39s WALL ( 78 calls) fftw : 2042.87s CPU 2042.87s WALL ( 206112 calls) interpolate : 5.75s CPU 5.75s WALL ( 78 calls) davcio : 1083.30s CPU 1083.30s WALL ( 38 calls) The davcio cputime looks pretty high to me, compared to what I've seen in other computing clusters. I know that the BGP architecture is pretty different than what I've been using so far, but the system administrators claim that the IBM GPFS file system should be very efficient and fast. Before moving some complaints to the sysadmins, I would like to have some feedback from those of you who have used this kind of architecture. Are you aware of similar kind of I/O issues? Is there any performance tuning that can be done on the software/compiler side? Regards, Gabriele -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne From vinothrece at gmail.com Sat Mar 26 03:37:27 2011 From: vinothrece at gmail.com (vinoth r) Date: Sat, 26 Mar 2011 08:07:27 +0530 Subject: [Pw_forum] saw like potential In-Reply-To: <4D8C8469.9070308@sissa.it> References: <4D8C8469.9070308@sissa.it> Message-ID: thanks for your reply sir. On Fri, Mar 25, 2011 at 5:32 PM, Stefano de Gironcoli wrote: > eamp is a measure of the additional electric field, you are talking of a > potential energy difference.. > you need to know/decide across which distance you want this potential drop > to occur and define the electric field accordingly. > > stefano de Gironcoli > > > On 03/25/2011 12:47 PM, vinoth r wrote: > > Dear friends, > > i had one query. > > i need to apply 1.4V saw like potential. > for eamp description given as > > Amplitude of the electric field in ***hartree***a.u; > 1 a.u=51.4220632*10^10 v/m; > > i need to apply 1.4 voltage means how to convert in to ***hartree***a.u; > i applied eamp = 2.72256676e-12 ,for 1.4 voltage.*i used all my units in a.u > *; > > with this i attached my input file also. > > Thanks in advance > > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110326/5765614b/attachment.htm From vinothrece at gmail.com Sat Mar 26 07:00:09 2011 From: vinothrece at gmail.com (vinoth r) Date: Sat, 26 Mar 2011 11:30:09 +0530 Subject: [Pw_forum] saw like potential In-Reply-To: <4D836B60.3030608@epfl.ch> References: <4D836B60.3030608@epfl.ch> Message-ID: thanks for your reply sir On 3/18/11, Jan Felix Binder wrote: > the axis perpendicular to the surface is the z-axis? > then edir = 3 > you should not use the same values for emaxpos and eoreg. Have a look on > the example... > > > > On 03/17/2011 04:06 PM, vinoth r wrote: >> >> dear all, >> with this mail i attached my input file for saw like >> potential perpendicular to BN layer.could you help me whether i >> applied 1.4v(saw like potential) perpendicular to axis. >> >> >> thank you >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > From flux_ray12 at 163.com Sat Mar 26 07:39:33 2011 From: flux_ray12 at 163.com (=?GBK?B?0KFT?=) Date: Sat, 26 Mar 2011 14:39:33 +0800 (CST) Subject: [Pw_forum] Bug report: Segmentation Fault while vc-relax Message-ID: Dear QE developers: Hello. Thank you for the excellent work of QE, it is truely a very nice and powerful 1st-principle software. I have tested QE 4.3a for 2 weeks. It is exciting with TDDFPT, although it can only calculate GAMMA point now. However, when I used pw.x to find ground state via vc-relax method, the segmentation fault occurred while reading or wrting k-points. Sometimes it occurred after one or two scf circles, sometimes even at the beginning of forming k-grid. My system is Red Hat Enterprise Linux 6 Server x86_64. MPICH2 is used for MPI environment. FFTW3 has been installed. This problem happened both in AMD Athlon2 x2 and Intel i7 PC. I tried to degrade QE 4.3a to QE 4.2, then the vc-relax worked well with same input file. Looking forward the stable version of QE 4.3, and hoping that TDDFPT can calculate multi-kpoints. ---------------------------------------------------- ZrGe CMC Lab, MSE, Seoul Nat'l Univ., Seoul, S.Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110326/a1b4fe33/attachment.htm From giannozz at democritos.it Sat Mar 26 08:59:35 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 26 Mar 2011 08:59:35 +0100 Subject: [Pw_forum] Bug report: Segmentation Fault while vc-relax In-Reply-To: References: Message-ID: Please see: http://www.quantum-espresso.org/wiki/index.php/Bugs P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Mar 26 09:12:03 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 26 Mar 2011 09:12:03 +0100 Subject: [Pw_forum] I/O performance on BG/P systems In-Reply-To: <4D8C916B.8010800@sissa.it> References: <4D8C916B.8010800@sissa.it> Message-ID: <0F327142-3AB3-47B8-A6DA-723C9AFF135B@democritos.it> On Mar 25, 2011, at 13:58 , Gabriele Sclauzero wrote: > Before moving some complaints to the sysadmins, I would like to have > some feedback from those of you who have used this kind of > architecture. > Are you aware of similar kind of I/O issues? Is there any performance > tuning that can be done on the software/compiler side? I also noticed that reading/writing the CP restart file on a BG takes a sizable amount of time, in the order of a few minutes for a typical system suitable for BG. I had attributed this to the "gathering" of the distributed pieces of wavefunctions that are subsequently written to file by a single process, though; in your case, it is the I/O by each process that takes a lot of time. You may want to try to reduce the I/O to the strict minimum: work with one k-point per processor (use k-point parallelization if needed), use disk_io='low' (or 'none'): the code should write only at the end (or never). P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From daijiayu at nudt.edu.cn Sun Mar 27 11:30:09 2011 From: daijiayu at nudt.edu.cn (jiayudai) Date: Sun, 27 Mar 2011 17:30:09 +0800 Subject: [Pw_forum] Two limitations of TDDFPT? In-Reply-To: <501127336.31616@nudt.edu.cn> References: <501127336.31616@nudt.edu.cn> Message-ID: <110327173009735142209fd943273c74e68890b13fa6@nudt.edu.cn> Dear developers, When i tested the new package of TDDFPT, i found we can not do the calculations with two cases: with more than k-points (not Gamma only), and with electronic smearing method. Is it ture ? And if these two limitations can be overcome in the new release of the QE package of 4.3? Thanks a lot. Jiayu ---------------- -------------------------------------------Jiayu DaiDepartment of PhysicsNational University of Defense Technology, Changsha, 410073, P R China----------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110327/2dd8de15/attachment.htm From tfcao at theory.issp.ac.cn Sun Mar 27 16:37:28 2011 From: tfcao at theory.issp.ac.cn (=?utf-8?B?5pu56IW+6aOe?=) Date: Sun, 27 Mar 2011 22:37:28 +0800 Subject: [Pw_forum] =?utf-8?q?relaxation_process_stopped_without__reaching?= =?utf-8?q?_the__convergence____=22Tengfei_Cao=22?= Message-ID: <20110327143728.7765.qmail@ms.hfcas.ac.cn> Dear QE users I'm doing the relaxation calculation about graphene with hydrogen atoms absorbed on it .But for some configurations the calculation stopped by itself without achieving the convergence . I want to know what can be the reasons . What can I try to achieve the convergence .Any help will be greatly appreciated .Here is my input file: &CONTROL title = 'graphene layer' , calculation = 'relax' , restart_mode = 'restart' , outdir = './tmp' , pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' , prefix = 'graphene' , nstep = 400 , / &SYSTEM ibrav = 8 , a = 12.31 , b = 12.79312342 , c = 12.000 , nat = 66 , ntyp = 2 , occupations = 'smearing' , tot_charge = 0.0, nosym = .true. , degauss = 0.02 , smearing = 'mp' , nspin = 2 , starting_magnetization(1) = 0.9 , ecutwfc = 30.0 , ecutrho = 300.0 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_mode = 'local-TF' , mixing_beta = 0.7 , diagonalization = 'david' , / &IONS / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF H 1.0000 H.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.0000000 0.0000000 0.50000000 0 0 0 C 0.10000000 5.55555671E-02 0.50000000 C 0.10000000 0.16666667 0.50000000 C 0.0000000 0.22222224 0.50000000 C 0.0000000 0.33333334 0.50000000 C 0.10000000 0.38888890 0.50000000 C 0.10000000 0.50000000 0.50000000 C 0.0000000 0.55555558 0.50000000 C 0.0000000 0.66666669 0.50000000 C 0.10000000 0.72222227 0.50000000 C 0.10000000 0.83333337 0.50000000 C 0.0000000 0.88888896 0.50000000 C 0.20000000 0.0000000 0.50000000 C 0.30000001 5.55555671E-02 0.50000000 C 0.30000001 0.16666667 0.50000000 C 0.20000000 0.22222224 0.50000000 C 0.20000000 0.33333334 0.50000000 C 0.30000001 0.38888890 0.50000000 C 0.30000001 0.50000000 0.50000000 C 0.20000000 0.55555558 0.50000000 C 0.20000000 0.66666669 0.50000000 C 0.30000001 0.72222227 0.50000000 C 0.30000001 0.83333337 0.50000000 C 0.20000000 0.88888896 0.50000000 C 0.40000001 0.0000000 0.50000000 C 0.50000000 5.55555671E-02 0.50000000 C 0.50000000 0.16666667 0.50000000 C 0.40000001 0.22222224 0.50000000 C 0.40000001 0.33333334 0.50000000 C 0.50000000 0.38888890 0.50000000 C 0.50000000 0.50000000 0.50000000 C 0.40000001 0.55555558 0.50000000 C 0.40000001 0.66666669 0.50000000 C 0.50000000 0.72222227 0.50000000 C 0.50000000 0.83333337 0.50000000 C 0.40000001 0.88888896 0.50000000 C 0.60000002 0.0000000 0.50000000 C 0.70000005 5.55555671E-02 0.50000000 C 0.70000005 0.16666667 0.50000000 C 0.60000002 0.22222224 0.50000000 C 0.60000002 0.33333334 0.50000000 C 0.70000005 0.38888890 0.50000000 C 0.70000005 0.50000000 0.50000000 C 0.60000002 0.55555558 0.50000000 C 0.60000002 0.66666669 0.50000000 C 0.70000005 0.72222227 0.50000000 C 0.70000005 0.83333337 0.50000000 C 0.60000002 0.88888896 0.50000000 C 0.80000001 0.0000000 0.50000000 C 0.90000004 5.55555671E-02 0.50000000 C 0.90000004 0.16666667 0.50000000 C 0.80000001 0.22222224 0.50000000 C 0.80000001 0.33333334 0.50000000 C 0.90000004 0.38888890 0.50000000 C 0.90000004 0.50000000 0.50000000 C 0.80000001 0.55555558 0.50000000 C 0.80000001 0.66666669 0.50000000 C 0.90000004 0.72222227 0.50000000 C 0.90000004 0.83333337 0.50000000 C 0.80000001 0.88888896 0.50000000 H 0.40000000 0.66666667 0.60000000 H 0.50000000 0.50000000 0.60000000 H 0.60000000 0.66666667 0.600000000 H 0.00000000 0.00000000 0.600000000 H 0.90000000 5.55555671E-02 0.600000000 H 0.00000000 0.88888889 0.6000000000 K_POINTS automatic 5 5 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110327/aa426cea/attachment.htm From baroni at sissa.it Sun Mar 27 17:57:08 2011 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 27 Mar 2011 17:57:08 +0200 Subject: [Pw_forum] Two limitations of TDDFPT? In-Reply-To: <110327173009735142209fd943273c74e68890b13fa6@nudt.edu.cn> References: <501127336.31616@nudt.edu.cn> <110327173009735142209fd943273c74e68890b13fa6@nudt.edu.cn> Message-ID: <6F687496-7F1E-4FC4-B614-06E6C2D06A21@sissa.it> On Mar 27, 2011, at 11:30 AM, jiayudai wrote: > Dear developers, > > When i tested the new package of TDDFPT, i found we can not do the calculations with two cases: with more than k-points (not Gamma only), and with electronic smearing method. Is it ture ? > yes > And if these two limitations can be overcome in the new release of the QE package of 4.3? > no, I am afraid ... SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget 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/20110327/1bc26dea/attachment.htm From c.sun1 at uq.edu.au Sun Mar 27 22:49:33 2011 From: c.sun1 at uq.edu.au (Chenghua Sun) Date: Mon, 28 Mar 2011 06:49:33 +1000 Subject: [Pw_forum] relaxation process stopped without reaching the convergence "Tengfei Cao" In-Reply-To: <20110327143728.7765.qmail@ms.hfcas.ac.cn> References: <20110327143728.7765.qmail@ms.hfcas.ac.cn> Message-ID: <5682E80C36D6D449B2D4552B5884AE572A53CDBC@UQEXMB03.soe.uq.edu.au> Hi TengFei, You can reduce the conv_thr = 1.0d-8 (like 1.0d-3) and mixing_beta = 0.7 (how about 0.1 or 0.2) firstly and when it gets converged, you then improve it step by step. Hopefully it works. Chenghua -------------------------------------------------------------------------------------- Chenghua Sun, PhD ARC Centre of Excellence for Functional Nanomaterials Centre for Computational Molecular Science Australian Institute for Bioengineering and Nanotechnology, AIBN Building 75, The University of Queensland Qld 4072, Brisbane, Australia Tel (617) 33463972; Fax (617) 33463992 email: c.sun1 at uq.edu.au --------------------------------------------------------------------------------------- ________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of ??? [tfcao at theory.issp.ac.cn] Sent: Monday, 28 March 2011 12:37 AM To: pw_forum Subject: [Pw_forum] relaxation process stopped without reaching the convergence "Tengfei Cao" Dear QE users I'm doing the relaxation calculation about graphene with hydrogen atoms absorbed on it .But for some configurations the calculation stopped by itself without achieving the convergence . I want to know what can be the reasons . What can I try to achieve the convergence .Any help will be greatly appreciated .Here is my input file: &CONTROL title = 'graphene layer' , calculation = 'relax' , restart_mode = 'restart' , outdir = './tmp' , pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' , prefix = 'graphene' , nstep = 400 , / &SYSTEM ibrav = 8 , a = 12.31 , b = 12.79312342 , c = 12.000 , nat = 66 , ntyp = 2 , occupations = 'smearing' , tot_charge = 0.0, nosym = .true. , degauss = 0.02 , smearing = 'mp' , nspin = 2 , starting_magnetization(1) = 0.9 , ecutwfc = 30.0 , ecutrho = 300.0 , / &ELECTRONS conv_thr = 1.0d-8 , mixing_mode = 'local-TF' , mixing_beta = 0.7 , diagonalization = 'david' , / &IONS / ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF H 1.0000 H.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal C 0.0000000 0.0000000 0.50000000 0 0 0 C 0.10000000 5.55555671E-02 0.50000000 C 0.10000000 0.16666667 0.50000000 C 0.0000000 0.22222224 0.50000000 C 0.0000000 0.33333334 0.50000000 C 0.10000000 0.38888890 0.50000000 C 0.10000000 0.50000000 0.50000000 C 0.0000000 0.55555558 0.50000000 C 0.0000000 0.66666669 0.50000000 C 0.10000000 0.72222227 0.50000000 C 0.10000000 0.83333337 0.50000000 C 0.0000000 0.88888896 0.50000000 C 0.20000000 0.0000000 0.50000000 C 0.30000001 5.55555671E-02 0.50000000 C 0.30000001 0.16666667 0.50000000 C 0.20000000 0.22222224 0.50000000 C 0.20000000 0.33333334 0.50000000 C 0.30000001 0.38888890 0.50000000 C 0.30000001 0.50000000 0.50000000 C 0.20000000 0.55555558 0.50000000 C 0.20000000 0.66666669 0.50000000 C 0.30000001 0.72222227 0.50000000 C 0.30000001 0.83333337 0.50000000 C 0.20000000 0.88888896 0.50000000 C 0.40000001 0.0000000 0.50000000 C 0.50000000 5.55555671E-02 0.50000000 C 0.50000000 0.16666667 0.50000000 C 0.40000001 0.22222224 0.50000000 C 0.40000001 0.33333334 0.50000000 C 0.50000000 0.38888890 0.50000000 C 0.50000000 0.50000000 0.50000000 C 0.40000001 0.55555558 0.50000000 C 0.40000001 0.66666669 0.50000000 C 0.50000000 0.72222227 0.50000000 C 0.50000000 0.83333337 0.50000000 C 0.40000001 0.88888896 0.50000000 C 0.60000002 0.0000000 0.50000000 C 0.70000005 5.55555671E-02 0.50000000 C 0.70000005 0.16666667 0.50000000 C 0.60000002 0.22222224 0.50000000 C 0.60000002 0.33333334 0.50000000 C 0.70000005 0.38888890 0.50000000 C 0.70000005 0.50000000 0.50000000 C 0.60000002 0.55555558 0.50000000 C 0.60000002 0.66666669 0.50000000 C 0.70000005 0.72222227 0.50000000 C 0.70000005 0.83333337 0.50000000 C 0.60000002 0.88888896 0.50000000 C 0.80000001 0.0000000 0.50000000 C 0.90000004 5.55555671E-02 0.50000000 C 0.90000004 0.16666667 0.50000000 C 0.80000001 0.22222224 0.50000000 C 0.80000001 0.33333334 0.50000000 C 0.90000004 0.38888890 0.50000000 C 0.90000004 0.50000000 0.50000000 C 0.80000001 0.55555558 0.50000000 C 0.80000001 0.66666669 0.50000000 C 0.90000004 0.72222227 0.50000000 C 0.90000004 0.83333337 0.50000000 C 0.80000001 0.88888896 0.50000000 H 0.40000000 0.66666667 0.60000000 H 0.50000000 0.50000000 0.60000000 H 0.60000000 0.66666667 0.600000000 H 0.00000000 0.00000000 0.600000000 H 0.90000000 5.55555671E-02 0.600000000 H 0.00000000 0.88888889 0.6000000000 K_POINTS automatic 5 5 1 0 0 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/0436dcc4/attachment-0001.htm From germaneau at gucas.ac.cn Mon Mar 28 12:53:23 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Mon, 28 Mar 2011 06:53:23 -0400 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <501047928.23640@test1.gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> <4D8C79CB.8040804@gucas.ac.cn> <501037833.20213@test1.gucas.ac.cn> <4D8CEFA9.6070608@gucas.ac.cn> <501047928.23640@test1.gucas.ac.cn> Message-ID: <4D9068A3.9080205@gucas.ac.cn> Dear Professor Giannozzi, It seems you've edited the wrong file. I've attached it again. Yours, Eric. On 03/25/2011 06:14 AM, Paolo Giannozzi wrote: > On Mar 25, 2011, at 20:40 , Eric Germaneau wrote: > >> I did the same thing with the previous version and did not get any >> issue. > I have no such problem. Since your data contain restart_mode='restart', > my guess is that the problem comes from a restart from inappropriate > data > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/b280c0f1/attachment.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: 02_graphite.vcrelax.in Url: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/b280c0f1/attachment.txt From magda.birowska at gmail.com Mon Mar 28 12:37:32 2011 From: magda.birowska at gmail.com (Magdalena Birowska) Date: Mon, 28 Mar 2011 12:37:32 +0200 Subject: [Pw_forum] Is it possible to sitch on SOI and LDA+U ? Message-ID: Dear users, Is it possible to turn on at the same time Spin Orbit Iteraction and LDA+U corection? Best regards; Magdalena Birowska -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/4636d040/attachment.htm From nicola.marzari at materials.ox.ac.uk Mon Mar 28 13:01:26 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Mon, 28 Mar 2011 12:01:26 +0100 Subject: [Pw_forum] moving to Lausanne Message-ID: <4D906A86.9040707@materials.ox.ac.uk> Dear All, I'm arm twisting the forum for some personal reasons - I am moving to EPFL (Lausanne) in September, and so I wanted to announce this, and especially mention that I am keen in attracting bright and dedicated PhD students there - please find the ad in this link: http://mml.materials.ox.ac.uk/Main/Theos Many thanks, nicola -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From sclauzer at sissa.it Mon Mar 28 13:49:33 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 28 Mar 2011 13:49:33 +0200 Subject: [Pw_forum] Is it possible to sitch on SOI and LDA+U ? In-Reply-To: References: Message-ID: <32599095-9190-4848-AF67-54DF6FB94946@sissa.it> Il giorno 28/mar/2011, alle ore 12.37, Magdalena Birowska ha scritto: > Dear users, > > Is it possible to turn on at the same time Spin Orbit Iteraction and LDA+U corection? It would be nice, but the answer is no, unfortunately... Personally I know only one electronic structure code that has such a feature, it is the ELK all-electron code, see http://elk.sourceforge.net/ (under "Advanced"). HTH GS > > Best regards; > Magdalena Birowska > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/c2287713/attachment.htm From daijiayu at nudt.edu.cn Mon Mar 28 17:07:03 2011 From: daijiayu at nudt.edu.cn (jiayudai) Date: Mon, 28 Mar 2011 23:07:03 +0800 Subject: [Pw_forum] Two limitations of TDDFPT? In-Reply-To: <501259240.24495@nudt.edu.cn> References: <501259240.24495@nudt.edu.cn> Message-ID: <110328230703c1fd13ae4e181f95d5838ad6c7238370@nudt.edu.cn> > Dear developers, > > When i tested the new package of TDDFPT, i found we can not do the calculations with two cases: with more than k-points (not Gamma only), and with electronic smearing method. Is it ture ? > yes > And if these two limitations can be overcome in the new release of the QE package of 4.3? > no, I am afraid ... SB So so so so disappointed. If these two limitations existed, we can not do a lot of caculations. However, i found the more k-points calculations in your Tutorial file at some conference, where the 1*1*1 k-point is used. So, i think there should be no difficult to add this part in the code. Grazie. Jiayu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/e368d41c/attachment.htm From sclauzer at sissa.it Mon Mar 28 18:20:39 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 28 Mar 2011 18:20:39 +0200 Subject: [Pw_forum] Two limitations of TDDFPT? In-Reply-To: <110328230703c1fd13ae4e181f95d5838ad6c7238370@nudt.edu.cn> References: <501259240.24495@nudt.edu.cn> <110328230703c1fd13ae4e181f95d5838ad6c7238370@nudt.edu.cn> Message-ID: Il giorno 28/mar/2011, alle ore 17.07, jiayudai ha scritto: > > Dear developers, > > > > When i tested the new package of TDDFPT, i found we can not do the calculations with two cases: with more than k-points (not Gamma only), and with electronic smearing method. Is it ture ? > > > yes > > And if these two limitations can be overcome in the new release of the QE package of 4.3? > > > no, I am afraid ... > > SB > > > > So so so so disappointed. If these two limitations existed, we can not do a lot of caculations. If keen and willing developers didn't exist, probably you could not do ANY calculation with QE... but they exist, so you should be much happier for that! Cheers GS ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/5ca0b7a1/attachment.htm From giannozz at democritos.it Mon Mar 28 18:37:31 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 28 Mar 2011 18:37:31 +0200 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D9068A3.9080205@gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> <4D8C79CB.8040804@gucas.ac.cn> <501037833.20213@test1.gucas.ac.cn> <4D8CEFA9.6070608@gucas.ac.cn> <501047928.23640@test1.gucas.ac.cn> <4D9068A3.9080205@gucas.ac.cn> Message-ID: <1301330251.11450.6.camel@fe12lx.fisica.uniud.it> On Mon, 2011-03-28 at 06:53 -0400, Eric Germaneau wrote: > It seems you've edited the wrong file. I have edited what you sent. Anyway: now I see what is wrong. It is the final self-consistent calculation, performed as a test in order to verify the result with the basis ser calculated for the final cell (and not the initial one). I think it should be fixed now. More exactly: it shouldn't be any more wrong than it used to be , if the final cell is much larger than the starting one (the reason is that the FFT grid remains the same and may be no longer sufficient for a larger cell). Thank you for noticing this P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From baroni at sissa.it Mon Mar 28 20:29:33 2011 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 28 Mar 2011 20:29:33 +0200 Subject: [Pw_forum] Two limitations of TDDFPT? In-Reply-To: <110328230703c1fd13ae4e181f95d5838ad6c7238370@nudt.edu.cn> References: <501259240.24495@nudt.edu.cn> <110328230703c1fd13ae4e181f95d5838ad6c7238370@nudt.edu.cn> Message-ID: On Mar 28, 2011, at 5:07 PM, jiayudai wrote: > > So so so so disappointed. If these two limitations existed, we can not do a lot of caculations. No matter what the capabilities of any software may be they will always be finite. The number of things the same software cannot do is instead infinite. I conclude that the probability of disappointing at least one person in the universe is 1. The philosophy of any open-source endeavour, though, is that there is a finite probability that the disapponted person(s) instead of complaining, roll up their sleeves and implement the feature(s) they so badly need. This would give him/her the opportunity to give back to the developers' community some of the work that they have put in the development of the code. > However, i found the more k-points calculations in your Tutorial file at some conference, where the 1*1*1 k-point is used. So, i think there should be no difficult to add this part in the code. So do I ... > Grazie. Prego. Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/d9db730f/attachment.htm From Jennifer.Wohlwend.ctr at wpafb.af.mil Mon Mar 28 22:19:34 2011 From: Jennifer.Wohlwend.ctr at wpafb.af.mil (Wohlwend, Jennifer L CTR USAF AFMC AFRL/RXBT) Date: Mon, 28 Mar 2011 16:19:34 -0400 Subject: [Pw_forum] geometry optiiztion of metal clusters Message-ID: <9AC197D8D0788140BC98A478FB3852A88D9183@VFOHMLMC11.Enterprise.afmc.ds.af.mil> I'm trying to perform geometry optimization of some clusters and they are running extremely slow. For example a TiO2 anatase cluster of only 12 atoms has completed only a few self-consistent iterations after ~3 hours. I know I must be doing something wrong but I've not been able to spot it yet. For the TiO2 system, my input is as follows: &CONTROL title = Ti_relax , calculation = 'relax' , restart_mode = 'restart' , outdir = './' , wfcdir = './' , pseudo_dir = '/hafs15/jen7182/espresso/pseudo/' , lkpoint_dir = .true. , etot_conv_thr = 1.0D-6 , forc_conv_thr = 1.0D-6 , nstep = 120 , tstress = .true. , tprnfor = .true. , lberry = .false. , / &SYSTEM ibrav = 1, celldm(1) = 50.0000000, nat = 12, ntyp = 2, ecutwfc = 55 , ecutrho = 500 , occupations = 'smearing' , degauss = 0.02D0 , smearing = 'methfessel-paxton' , / &ELECTRONS conv_thr = 1.D-8 , / &IONS ion_dynamics = 'bfgs' , pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES Ti 47.87000 Ti.pw91-nsp-van.UPF 15.99960 O.pw91-van_ak.UPF ATOMIC_POSITIONS Ti 0.019646921155 -0.032104589149 0.072982942110 Ti -0.053021298671 0.015633269982 0.132549510485 Ti 0.057125188587 0.058771047647 0.164020158511 Ti 0.110388124153 0.105884441223 0.244068937730 O -0.023076017443 -0.044401500581 0.131365372724 O 0.035579202732 -0.080351647885 0.029496520030 O -0.037172544158 0.018329722652 0.066778689936 O 0.057973293750 0.014983392566 0.111654528302 O -0.014261394120 0.057693305910 0.168967680139 O 0.116729745829 0.144794684381 0.294813978638 O 0.083638150059 0.040575025164 0.225871612978 O 0.091668444256 0.117426432280 0.178170567176 K_POINTS automatic 4 4 4 1 1 1 Any help would be greatly appreciated!! Thank you! Jennifer Jennifer L. Wohlwend, Ph.D. Thermal Sciences and Materials Branch Materials and Manufacturing Directorate Air Force Research Laboratory 2941 Hobson Way B654 R015 Wright Patterson Air Force Base, OH 45433-7750 Ctr: Universal Technology Corporation Phone: (937) 656-4918 Email: jennifer.wohlwend.ctr at wpafb.af.mil -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/3872cb60/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/x-pkcs7-signature Size: 5738 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110328/3872cb60/attachment-0001.bin From jiachen at princeton.edu Mon Mar 28 22:48:57 2011 From: jiachen at princeton.edu (jia chen) Date: Mon, 28 Mar 2011 16:48:57 -0400 Subject: [Pw_forum] geometry optiiztion of metal clusters In-Reply-To: <9AC197D8D0788140BC98A478FB3852A88D9183@VFOHMLMC11.Enterprise.afmc.ds.af.mil> References: <9AC197D8D0788140BC98A478FB3852A88D9183@VFOHMLMC11.Enterprise.afmc.ds.af.mil> Message-ID: Dear Jennifer, For that large supercell, I think gamma point is enough. Bests On Mon, Mar 28, 2011 at 4:19 PM, Wohlwend, Jennifer L CTR USAF AFMC AFRL/RXBT wrote: > I?m trying to perform geometry optimization of some clusters and they are > running extremely slow. For example a TiO2 anatase cluster of only 12 atoms > has completed only a few self-consistent iterations after ~3 hours. I know I > must be doing something wrong but I?ve not been able to spot it yet. For the > TiO2 system, my input is as follows: > > &CONTROL > > ?????????????????????? title = Ti_relax , > > ???????????????? calculation = 'relax' , > > ??????????????? restart_mode = 'restart' , > > ????????????????????? outdir = './' , > > ????????????????????? wfcdir = './' , > > ????????????????? pseudo_dir = '/hafs15/jen7182/espresso/pseudo/' , > > ???????????????? lkpoint_dir = .true. , > > ?????????????? etot_conv_thr = 1.0D-6 , > > ?????????????? forc_conv_thr = 1.0D-6 , > > ?????????????????????? nstep = 120 , > > ???????????????????? tstress = .true. , > > ???????????????????? tprnfor = .true. , > > ????????????????????? lberry = .false. , > > ?/ > > ?&SYSTEM > > ?????????????????????? ibrav = 1, > > ?????????????????? celldm(1) = 50.0000000, > > ???????????????????????? nat = 12, > > ??????????????????????? ntyp = 2, > > ???????????????????? ecutwfc = 55 , > > ???????????????????? ecutrho = 500 , > > ???????????????? occupations = 'smearing' , > > ???????????????????? degauss = 0.02D0 , > > ??????????????????? smearing = 'methfessel-paxton' , > > ?/ > > ?&ELECTRONS > > ??????????????????? conv_thr = 1.D-8 , > > / > > ?&IONS > > ??????????????? ion_dynamics = 'bfgs' , > > ? pot_extrapolation = "second_order", > > ? wfc_extrapolation = "second_order", > > ?/ > > ATOMIC_SPECIES > > ??? Ti?? 47.87000? Ti.pw91-nsp-van.UPF > > 15.99960? O.pw91-van_ak.UPF > > ATOMIC_POSITIONS > > Ti????? 0.019646921155? -0.032104589149 0.072982942110 > > Ti????? -0.053021298671 0.015633269982? 0.132549510485 > > Ti????? 0.057125188587? 0.058771047647? 0.164020158511 > > Ti????? 0.110388124153? 0.105884441223? 0.244068937730 > > O?????? -0.023076017443 -0.044401500581 0.131365372724 > > O?????? 0.035579202732? -0.080351647885 0.029496520030 > > O?????? -0.037172544158 0.018329722652? 0.066778689936 > > O?????? 0.057973293750? 0.014983392566? 0.111654528302 > > O?????? -0.014261394120 0.057693305910? 0.168967680139 > > O?????? 0.116729745829? 0.144794684381? 0.294813978638 > > O?????? 0.083638150059? 0.040575025164? 0.225871612978 > > O?????? 0.091668444256? 0.117426432280? 0.178170567176 > > K_POINTS automatic > > 4 4 4?? 1 1 1 > > Any help would be greatly appreciated!! > > Thank you! > > Jennifer > > Jennifer L. Wohlwend, Ph.D. > > Thermal Sciences and Materials Branch > > Materials and Manufacturing Directorate > > Air Force Research Laboratory > > 2941 Hobson Way B654 R015 > > Wright Patterson Air Force Base, OH 45433-7750 > > Ctr: Universal Technology Corporation > > Phone: (937) 656-4918 > > Email: jennifer.wohlwend.ctr at wpafb.af.mil > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Jia Chen From ma at nano.ku.dk Mon Mar 28 22:50:29 2011 From: ma at nano.ku.dk (Martin Andersson) Date: Mon, 28 Mar 2011 22:50:29 +0200 Subject: [Pw_forum] geometry optiiztion of metal clusters In-Reply-To: <9AC197D8D0788140BC98A478FB3852A88D9183@VFOHMLMC11.Enterprise.afmc.ds.af.mil> References: <9AC197D8D0788140BC98A478FB3852A88D9183@VFOHMLMC11.Enterprise.afmc.ds.af.mil> Message-ID: <4D90F495.30102@nano.ku.dk> Hi, You don't need k-points with a cluster, so that should speed up things by a factor of 64. If you also use k-points gamma instead of automatic 1 1 1 0 0 0 you can gain some more as well. If you want further speed up you can put tqr=.true. under &electrons because you are using ultrasoft pseudopotentials. If you are able to reduce the cell size (which you have to check anyway) you can also gain significant time. Cheers, Martin Andersson University of Copenhagen On 3/28/2011 10:19 PM, Wohlwend, Jennifer L CTR USAF AFMC AFRL/RXBT wrote: > > I'm trying to perform geometry optimization of someclusters andthey > arerunning extremely slow. Forexamplea TiO2 anatase cluster of only 12 > atoms has completedonly a fewself-consistentiterationsafter ~3 hours. > IknowI must be doing something wrong but I've not been able to spot it > yet.For the TiO2 system, myinput is as follows: > > &CONTROL > > title = Ti_relax , > > calculation = 'relax' , > > restart_mode = 'restart' , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = '/hafs15/jen7182/espresso/pseudo/' , > > lkpoint_dir = .true. , > > etot_conv_thr = 1.0D-6 , > > forc_conv_thr = 1.0D-6 , > > nstep = 120 , > > tstress = .true. , > > tprnfor = .true. , > > lberry = .false. , > > / > > &SYSTEM > > ibrav = 1, > > celldm(1) = 50.0000000, > > nat = 12, > > ntyp = 2, > > ecutwfc = 55 , > > ecutrho = 500 , > > occupations = 'smearing' , > > degauss = 0.02D0 , > > smearing = 'methfessel-paxton' , > > / > > &ELECTRONS > > conv_thr = 1.D-8 , > > / > > &IONS > > ion_dynamics = 'bfgs' , > > pot_extrapolation = "second_order", > > wfc_extrapolation = "second_order", > > / > > ATOMIC_SPECIES > > Ti 47.87000 Ti.pw91-nsp-van.UPF > > 15.99960 O.pw91-van_ak.UPF > > ATOMIC_POSITIONS > > Ti 0.019646921155 -0.032104589149 0.072982942110 > > Ti -0.053021298671 0.015633269982 0.132549510485 > > Ti 0.057125188587 0.058771047647 0.164020158511 > > Ti 0.110388124153 0.105884441223 0.244068937730 > > O -0.023076017443 -0.044401500581 0.131365372724 > > O 0.035579202732 -0.080351647885 0.029496520030 > > O -0.037172544158 0.018329722652 0.066778689936 > > O 0.057973293750 0.014983392566 0.111654528302 > > O -0.014261394120 0.057693305910 0.168967680139 > > O 0.116729745829 0.144794684381 0.294813978638 > > O 0.083638150059 0.040575025164 0.225871612978 > > O 0.091668444256 0.117426432280 0.178170567176 > > K_POINTS automatic > > 4 4 4 1 1 1 > > Any help would be greatly appreciated!! > > Thank you! > > Jennifer > > ***Jennifer L. Wohlwend, Ph.D.* > > Thermal Sciences and Materials Branch > > Materials and Manufacturing Directorate > > Air Force Research Laboratory > > 2941 Hobson Way B654 R015 > > Wright Patterson Air Force Base, OH 45433-7750 > > Ctr: Universal Technology Corporation > > Phone: (937) 656-4918 > > Email:jennifer.wohlwend.ctr at wpafb.af.mil > > > _______________________________________________ > 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/20110328/3721cdf7/attachment.htm From germaneau at gucas.ac.cn Tue Mar 29 12:35:28 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Tue, 29 Mar 2011 06:35:28 -0400 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <501330069.12482@test1.gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> <4D8C79CB.8040804@gucas.ac.cn> <501037833.20213@test1.gucas.ac.cn> <4D8CEFA9.6070608@gucas.ac.cn> <501047928.23640@test1.gucas.ac.cn> <4D9068A3.9080205@gucas.ac.cn> <501330069.12482@test1.gucas.ac.cn> Message-ID: <4D91B5F0.2060801@gucas.ac.cn> On 03/28/2011 12:37 PM, Paolo Giannozzi wrote: > I think it should > be fixed now Dear Professor Giannozzi, When the new version available for download? Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/77cc681f/attachment-0001.htm From zdw2000 at gmail.com Tue Mar 29 01:14:22 2011 From: zdw2000 at gmail.com (Wei Zhou) Date: Tue, 29 Mar 2011 07:14:22 +0800 Subject: [Pw_forum] about the lambda and the int alpha2F Message-ID: dear users I want to calculate the elelectron-phonon coupling, but I found the lambda is always larger then int alpha2F, but if I increase the degauss larger than 1, then the lambda can equal the int alpha2F, but the degauss should be little than 1, so I fell puzzle, is there something wrong with me ? -- # degauss lambda int alpha2F N(Ef) 0.010 0.832693 0.648345 122.705 8.265196 0.020 0.829206 0.674542 123.132 8.626953 0.030 0.934942 0.748056 124.828 10.124415 0.040 0.992269 0.788636 125.307 10.954579 0.050 1.011396 0.801566 125.525 11.343069 0.060 1.023042 0.810451 125.690 11.551418 0.070 1.035084 0.820935 125.782 11.696555 0.080 1.047341 0.832322 125.801 11.819719 0.090 1.058079 0.842801 125.773 11.931143 0.100 1.066089 0.851119 125.728 12.031502 any help will be apprecialted ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com From eyvaz_isaev at yahoo.com Tue Mar 29 01:34:55 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 28 Mar 2011 16:34:55 -0700 (PDT) Subject: [Pw_forum] about the lambda and the int alpha2F In-Reply-To: References: Message-ID: <610358.88084.qm@web65703.mail.ac4.yahoo.com> Hi, Have you tried matdyn.x to calculate \lambda? Can you please send me your input file for lambda.x? > but if I increase the degauss larger than 1 In my experience, degauss up to 0.1 is sufficient to get converged \lambda. So, there is no need for such kind HUGE degauss. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: Wei Zhou To: PWSCF Forum Sent: Tue, March 29, 2011 1:14:22 AM Subject: [Pw_forum] about the lambda and the int alpha2F dear users I want to calculate the elelectron-phonon coupling, but I found the lambda is always larger then int alpha2F, but if I increase the degauss larger than 1, then the lambda can equal the int alpha2F, but the degauss should be little than 1, so I fell puzzle, is there something wrong with me ? -- # degauss lambda int alpha2F N(Ef) 0.010 0.832693 0.648345 122.705 8.265196 0.020 0.829206 0.674542 123.132 8.626953 0.030 0.934942 0.748056 124.828 10.124415 0.040 0.992269 0.788636 125.307 10.954579 0.050 1.011396 0.801566 125.525 11.343069 0.060 1.023042 0.810451 125.690 11.551418 0.070 1.035084 0.820935 125.782 11.696555 0.080 1.047341 0.832322 125.801 11.819719 0.090 1.058079 0.842801 125.773 11.931143 0.100 1.066089 0.851119 125.728 12.031502 any help will be apprecialted ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From izaakw89 at yahoo.com Tue Mar 29 01:44:56 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Mon, 28 Mar 2011 16:44:56 -0700 (PDT) Subject: [Pw_forum] Problem with pseudopotential In-Reply-To: References: Message-ID: <215415.11560.qm@web43407.mail.sp1.yahoo.com> Dear all, I was trying to calculate the workfunction for Cu(100) surface. When I plotted the planar average of Vbare+VH as a function of z, I found that Vbare+VH at some points is higher than Vbare+VH at the vacuum level. I have attached the file (planar-average-pbedrrkjus.pdf). I am also attaching the input file Cu100.in. Does this mean that the pseudopotential (Cu.pbe-d-rrkjus.UPF) is wrong? Why does it behave like this? When I do the same calculation with Cu.pbe-n-van_ak.UPF pseudopotential, then I get a reasonable graph (planar-average-pbevanak.pdf). Any suggestions/explanations would be greatly appreciated. Thank you. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/5c8596a2/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: planar-average-pbedrrkjus.pdf Type: application/pdf Size: 8268 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110328/5c8596a2/attachment-0002.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: planar-average-pbevanak.pdf Type: application/pdf Size: 7900 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110328/5c8596a2/attachment-0003.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: Cu100.in Type: application/octet-stream Size: 741 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110328/5c8596a2/attachment-0001.obj From arvifis at gmail.com Tue Mar 29 01:48:14 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 28 Mar 2011 20:48:14 -0300 Subject: [Pw_forum] geometry optiiztion of metal clusters In-Reply-To: <4D90F495.30102@nano.ku.dk> References: <9AC197D8D0788140BC98A478FB3852A88D9183@VFOHMLMC11.Enterprise.afmc.ds.af.mil> <4D90F495.30102@nano.ku.dk> Message-ID: perhaps you have a mistake in ATOMIC_SPECIES Ti 47.87000 Ti.pw91-nsp-van.UPF 15.99960 O.pw91-van_ak.UPF you forget out O symbol in the last line Best Arles V. Gil Rebaza IFLP - Argentina 2011/3/28 Martin Andersson > Hi, > > You don't need k-points with a cluster, so that should speed up things by a > factor of 64. If you also use k-points gamma instead of automatic 1 1 1 0 0 > 0 you can gain some more as well. If you want further speed up you can put > tqr=.true. under &electrons because you are using ultrasoft > pseudopotentials. If you are able to reduce the cell size (which you have to > check anyway) you can also gain significant time. > > Cheers, > Martin Andersson > University of Copenhagen > > > On 3/28/2011 10:19 PM, Wohlwend, Jennifer L CTR USAF AFMC AFRL/RXBT wrote: > > I?m trying to perform geometry optimization of some clusters and they arerunning extremely slow. > For example a TiO2 anatase cluster of only 12 atoms has completed only a > few self-consistent iterations after ~3 hours. I know I must be doing > something wrong but I?ve not been able to spot it yet. For the TiO2 > system, my input is as follows: > > &CONTROL > > title = Ti_relax , > > calculation = 'relax' , > > restart_mode = 'restart' , > > outdir = './' , > > wfcdir = './' , > > pseudo_dir = '/hafs15/jen7182/espresso/pseudo/' , > > lkpoint_dir = .true. , > > etot_conv_thr = 1.0D-6 , > > forc_conv_thr = 1.0D-6 , > > nstep = 120 , > > tstress = .true. , > > tprnfor = .true. , > > lberry = .false. , > > / > > &SYSTEM > > ibrav = 1, > > celldm(1) = 50.0000000, > > nat = 12, > > ntyp = 2, > > ecutwfc = 55 , > > ecutrho = 500 , > > occupations = 'smearing' , > > degauss = 0.02D0 , > > smearing = 'methfessel-paxton' , > > / > > &ELECTRONS > > conv_thr = 1.D-8 , > > / > > &IONS > > ion_dynamics = 'bfgs' , > > pot_extrapolation = "second_order", > > wfc_extrapolation = "second_order", > > / > > ATOMIC_SPECIES > > Ti 47.87000 Ti.pw91-nsp-van.UPF > > 15.99960 O.pw91-van_ak.UPF > > ATOMIC_POSITIONS > > Ti 0.019646921155 -0.032104589149 0.072982942110 > > Ti -0.053021298671 0.015633269982 0.132549510485 > > Ti 0.057125188587 0.058771047647 0.164020158511 > > Ti 0.110388124153 0.105884441223 0.244068937730 > > O -0.023076017443 -0.044401500581 0.131365372724 > > O 0.035579202732 -0.080351647885 0.029496520030 > > O -0.037172544158 0.018329722652 0.066778689936 > > O 0.057973293750 0.014983392566 0.111654528302 > > O -0.014261394120 0.057693305910 0.168967680139 > > O 0.116729745829 0.144794684381 0.294813978638 > > O 0.083638150059 0.040575025164 0.225871612978 > > O 0.091668444256 0.117426432280 0.178170567176 > > K_POINTS automatic > > 4 4 4 1 1 1 > > Any help would be greatly appreciated!! > > Thank you! > > Jennifer > > ***Jennifer L. Wohlwend, Ph.D.* > > Thermal Sciences and Materials Branch > > Materials and Manufacturing Directorate > > Air Force Research Laboratory > > 2941 Hobson Way B654 R015 > > Wright Patterson Air Force Base, OH 45433-7750 > > Ctr: Universal Technology Corporation > > Phone: (937) 656-4918 > > Email: jennifer.wohlwend.ctr at wpafb.af.mil > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110328/f350723e/attachment.htm From zdw2000 at gmail.com Tue Mar 29 03:30:34 2011 From: zdw2000 at gmail.com (Wei Zhou) Date: Tue, 29 Mar 2011 09:30:34 +0800 Subject: [Pw_forum] about the lambda and the int alpha2F In-Reply-To: <610358.88084.qm@web65703.mail.ac4.yahoo.com> References: <610358.88084.qm@web65703.mail.ac4.yahoo.com> Message-ID: first thank you for you reply. I calculate the lambla from the electron-phonon calculation similiar with the example 07, the lambda in fact should equal the int alpha2F, but in my case, it doesnot equal at tall, the lambda always large than int alpha2F the input file for lambla is as following #!/bin/sh cat > lambda.in < lambda.out 2011/3/29, Eyvaz Isaev : > Hi, > > Have you tried matdyn.x to calculate \lambda? > > Can you please send me your input file for lambda.x? > >> but if I increase the degauss larger than 1 > > In my experience, degauss up to 0.1 is sufficient to get converged \lambda. > So, > there is no need for such kind HUGE degauss. > > Bests, > Eyvaz. > > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > ----- Original Message ---- > From: Wei Zhou > To: PWSCF Forum > Sent: Tue, March 29, 2011 1:14:22 AM > Subject: [Pw_forum] about the lambda and the int alpha2F > > dear users > I want to calculate the elelectron-phonon coupling, but I found the > lambda is always larger then int alpha2F, but if I increase the > degauss larger than 1, then the lambda can equal the int alpha2F, but > the degauss should be little than 1, so I fell puzzle, is there > something wrong with me ? > -- # degauss lambda int alpha2F N(Ef) > 0.010 0.832693 0.648345 122.705 8.265196 > 0.020 0.829206 0.674542 123.132 8.626953 > 0.030 0.934942 0.748056 124.828 10.124415 > 0.040 0.992269 0.788636 125.307 10.954579 > 0.050 1.011396 0.801566 125.525 11.343069 > 0.060 1.023042 0.810451 125.690 11.551418 > 0.070 1.035084 0.820935 125.782 11.696555 > 0.080 1.047341 0.832322 125.801 11.819719 > 0.090 1.058079 0.842801 125.773 11.931143 > 0.100 1.066089 0.851119 125.728 12.031502 > > any help will be apprecialted > ZhouDawei > JiLin Universiyt ,ChangChun ,China > zdw2000 at gmail.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 > -- ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com From tfcao at theory.issp.ac.cn Tue Mar 29 04:18:19 2011 From: tfcao at theory.issp.ac.cn (=?utf-8?B?5pu56IW+6aOe?=) Date: Tue, 29 Mar 2011 10:18:19 +0800 Subject: [Pw_forum] =?utf-8?q?K=5Fpoint_selection____=28tengfei_cao=29?= Message-ID: <20110329021819.13310.qmail@ms.hfcas.ac.cn> Dear QE users: I want to do band structure the graphene with one hydrogen absorbed on it .And I have chosen the 2 x 2 supercell . So for this how can choose the K_point .Is it the same as the 1x1. Perhaps it is a silly question to you. But I do not fully understand this and need your help. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/493b8abc/attachment-0001.htm From sxu2 at ncsu.edu Tue Mar 29 04:26:53 2011 From: sxu2 at ncsu.edu (shu xu) Date: Mon, 28 Mar 2011 21:26:53 -0500 Subject: [Pw_forum] K_point selection (tengfei cao) In-Reply-To: <20110329021819.13310.qmail@ms.hfcas.ac.cn> References: <20110329021819.13310.qmail@ms.hfcas.ac.cn> Message-ID: if N N N 0 0 0 is k-points you used for 1x1, then use N/2 N/2 N/2 0 0 0 for 2X2 cell Shu On Mon, Mar 28, 2011 at 9:18 PM, ??? wrote: > Dear QE users: > I want to do band structure the graphene with one hydrogen absorbed on it > .And I have chosen the 2 x 2 supercell . So for this how can choose the > K_point .Is it the same as the 1x1. Perhaps it is a silly question to you. > But I do not fully understand this and need your help. Thank you. > > _______________________________________________ > 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/20110328/d0dffb14/attachment.htm From zdw2000 at gmail.com Tue Mar 29 04:48:42 2011 From: zdw2000 at gmail.com (Wei Zhou) Date: Tue, 29 Mar 2011 10:48:42 +0800 Subject: [Pw_forum] about the lambda and the int alpha2F In-Reply-To: References: <610358.88084.qm@web65703.mail.ac4.yahoo.com> Message-ID: as far as I know the lambda should equal integer vaule of alpha2F, that is "int alpha2F"but in my case the lambda always larger than int alpha2F,and another questions is; I donnot know how to choose the "degaussq" in the input file of lambda.x degaussq (THz):is gaussian smearing for sum over q. 2011/3/29, Wei Zhou : > first thank you for you reply. > I calculate the lambla from the electron-phonon calculation similiar > with the example 07, the lambda in fact should equal the int alpha2F, > but in my case, it doesnot equal at tall, the lambda always large than > int alpha2F > the input file for lambla is as following > #!/bin/sh > cat > lambda.in < 4.49 0.05000 1 > 24 > 0.0000000 0.0000000 0.0000000 0.0102041 > 0.0000000 0.0000000 0.1580773 0.0204082 > 0.0000000 0.0000000 -0.3161547 0.0102041 > 0.0000000 0.1649572 0.0000000 0.0612245 > 0.0000000 0.1649572 0.1580773 0.1224490 > 0.0000000 0.1649572 -0.3161547 0.0612245 > 0.0000000 0.3299144 0.0000000 0.0612245 > 0.0000000 0.3299144 0.1580773 0.1224490 > 0.0000000 0.3299144 -0.3161547 0.0612245 > 0.0000000 0.4948717 0.0000000 0.0612245 > 0.0000000 0.4948717 0.1580773 0.1224490 > 0.0000000 0.4948717 -0.3161547 0.0612245 > 0.1428571 0.2474358 0.0000000 0.0612245 > 0.1428571 0.2474358 0.1580773 0.1224490 > 0.1428571 0.2474358 -0.3161547 0.0612245 > 0.1428571 0.4123930 0.0000000 0.1224490 > 0.1428571 0.4123930 0.1580773 0.2448980 > 0.1428571 0.4123930 -0.3161547 0.1224490 > 0.1428571 0.5773503 0.0000000 0.0612245 > 0.1428571 0.5773503 0.1580773 0.1224490 > 0.1428571 0.5773503 -0.3161547 0.0612245 > 0.2857143 0.4948717 0.0000000 0.0612245 > 0.2857143 0.4948717 0.1580773 0.1224490 > 0.2857143 0.4948717 -0.3161547 0.0612245 > elph_1 > elph_2 > elph_3 > elph_4 > elph_5 > elph_6 > elph_7 > elph_8 > elph_9 > elph_10 > elph_11 > elph_12 > elph_13 > elph_14 > elph_15 > elph_16 > elph_17 > elph_18 > elph_19 > elph_20 > elph_21 > elph_22 > elph_23 > elph_24 > EOF > ./lambda.x < lambda.in > lambda.out > > > 2011/3/29, Eyvaz Isaev : >> Hi, >> >> Have you tried matdyn.x to calculate \lambda? >> >> Can you please send me your input file for lambda.x? >> >>> but if I increase the degauss larger than 1 >> >> In my experience, degauss up to 0.1 is sufficient to get converged >> \lambda. >> So, >> there is no need for such kind HUGE degauss. >> >> Bests, >> Eyvaz. >> >> >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping >> University, >> Sweden >> >> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >> Russia, >> >> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> >> ----- Original Message ---- >> From: Wei Zhou >> To: PWSCF Forum >> Sent: Tue, March 29, 2011 1:14:22 AM >> Subject: [Pw_forum] about the lambda and the int alpha2F >> >> dear users >> I want to calculate the elelectron-phonon coupling, but I found the >> lambda is always larger then int alpha2F, but if I increase the >> degauss larger than 1, then the lambda can equal the int alpha2F, but >> the degauss should be little than 1, so I fell puzzle, is there >> something wrong with me ? >> -- # degauss lambda int alpha2F N(Ef) >> 0.010 0.832693 0.648345 122.705 8.265196 >> 0.020 0.829206 0.674542 123.132 8.626953 >> 0.030 0.934942 0.748056 124.828 10.124415 >> 0.040 0.992269 0.788636 125.307 10.954579 >> 0.050 1.011396 0.801566 125.525 11.343069 >> 0.060 1.023042 0.810451 125.690 11.551418 >> 0.070 1.035084 0.820935 125.782 11.696555 >> 0.080 1.047341 0.832322 125.801 11.819719 >> 0.090 1.058079 0.842801 125.773 11.931143 >> 0.100 1.066089 0.851119 125.728 12.031502 >> >> any help will be apprecialted >> ZhouDawei >> JiLin Universiyt ,ChangChun ,China >> zdw2000 at gmail.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 >> > > > -- > ZhouDawei > JiLin Universiyt ,ChangChun ,China > zdw2000 at gmail.com > -- ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com From mayankaditya at gmail.com Tue Mar 29 06:00:15 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Tue, 29 Mar 2011 09:30:15 +0530 Subject: [Pw_forum] Error in phonon calculation using matdyn.x Message-ID: Dear All I am doing pwscf and phonon calculation for Y2O3. In 2x2x2 Q mesh it generates 6 irreducible q points (yo.dyn* files). The phonon frequency calculation using matdyn.x run I got error message 7.5000000000000000 from frc_blk : error # 1 wrong total_weight stopping ... What could be the possible error. Thanks -- Mayank kumar gupta Contact No- 9869834437 ? ? ? ? ? ? ? ? ? 8097400037 ? ? ? ? ? ? ? ?? 9220397437 From baroni at sissa.it Tue Mar 29 07:29:12 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 29 Mar 2011 07:29:12 +0200 Subject: [Pw_forum] Problem with pseudopotential In-Reply-To: <215415.11560.qm@web43407.mail.sp1.yahoo.com> References: <215415.11560.qm@web43407.mail.sp1.yahoo.com> Message-ID: <9D703350-5154-4059-8604-C508A409C28B@sissa.it> On Mar 29, 2011, at 1:44 AM, Izaak Williamson wrote: > Dear all, > I was trying to calculate the workfunction for Cu(100) surface. When I plotted the planar average of Vbare+VH as a function of z, I found that Vbare+VH at some points is higher than Vbare+VH at the vacuum level. I have attached the file (planar-average-pbedrrkjus.pdf). I am also attaching the input file Cu100.in. Does this mean that the pseudopotential (Cu.pbe-d-rrkjus.UPF) is wrong? No. (I mean, not necessarily) > Why does it behave like this? Why not? > When I do the same calculation with Cu.pbe-n-van_ak.UPF pseudopotential, then I get a reasonable graph (planar-average-pbevanak.pdf). Any suggestions/explanations would be greatly appreciated. the value of the bare potential at any atomic core is to a large extent arbitrary, and depends on many (unphysical) details of the pp construction, such as the choice of the core radius, the pseudization algorithm, the choice of the angular-momentum channel to be selected as reference ("local") potential ... > Thank you. you are most welcome Stefano B --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget 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/20110329/579ee27f/attachment.htm From anupvthomas at gmail.com Tue Mar 29 07:47:44 2011 From: anupvthomas at gmail.com (ANUP THOMAS) Date: Tue, 29 Mar 2011 11:17:44 +0530 Subject: [Pw_forum] Regarding Pwscf calculation - Organic Monoclinic Crystal Message-ID: Dear Pwscf Form Memebers I want to do band structure of monoclinic organic crystal -Napthalene. It will be highly helpfull if someone can help me how we can convert .cif file of a monoclinic crystal to pwscf input file. And also on K-path selection. Look forward to hear from you all. -- Regards Anup Thomas SRF 7123 Computational Chemistry Lab of I and PC Division Indian Institute of Chemical Technology Hyderabad 500007 India "Praise the Lord, all you nations; extol him, all you peoples. For great is his love toward us, and the faithfulness of the Lord endures forever. Praise the Lord" -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/bf2d3154/attachment-0001.htm From sclauzer at sissa.it Tue Mar 29 09:11:04 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 29 Mar 2011 09:11:04 +0200 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D91B5F0.2060801@gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> <4D8C79CB.8040804@gucas.ac.cn> <501037833.20213@test1.gucas.ac.cn> <4D8CEFA9.6070608@gucas.ac.cn> <501047928.23640@test1.gucas.ac.cn> <4D9068A3.9080205@gucas.ac.cn> <501330069.12482@test1.gucas.ac.cn> <4D91B5F0.2060801@gucas.ac.cn> Message-ID: <634DFD05-3AC9-4E1D-9905-1C42DB68D5A8@sissa.it> I think that Paolo has committed the changes yesterday, so you can already have access to them by downloading a copy of the distribution from the CVS repository. Please see here http://qe-forge.org/scm/?group_id=10 I'm not sure that the latest release (4.3b) which appears here http://qe-forge.org/frs/?group_id=10 includes those changes, since the creation date is quite far in the past... you should wait a reply from Paolo to be sure of this. Regards, Gabriele > On 03/28/2011 12:37 PM, Paolo Giannozzi wrote: >> >> I think it should >> be fixed now > Dear Professor Giannozzi, > > When the new version available for download? > > Eric. > > -- > Be the change you wish to see in the world > ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/6a776015/attachment.htm From giannozz at democritos.it Tue Mar 29 09:17:09 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 Mar 2011 09:17:09 +0200 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <634DFD05-3AC9-4E1D-9905-1C42DB68D5A8@sissa.it> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> <4D8C79CB.8040804@gucas.ac.cn> <501037833.20213@test1.gucas.ac.cn> <4D8CEFA9.6070608@gucas.ac.cn> <501047928.23640@test1.gucas.ac.cn> <4D9068A3.9080205@gucas.ac.cn> <501330069.12482@test1.gucas.ac.cn> <4D91B5F0.2060801@gucas.ac.cn> <634DFD05-3AC9-4E1D-9905-1C42DB68D5A8@sissa.it> Message-ID: <1301383029.13547.2.camel@fe12lx.fisica.uniud.it> On Tue, 2011-03-29 at 09:11 +0200, Gabriele Sclauzero wrote: > I'm not sure that the latest release (4.3b) which appears here > http://qe-forge.org/frs/?group_id=10 > includes those changes it should > since the creation date is quite far in the past... funny: the files were uploaded yeesterday evening ... P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From germaneau at gucas.ac.cn Tue Mar 29 21:43:59 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Tue, 29 Mar 2011 15:43:59 -0400 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <501382873.25523@test1.gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> <4D8C79CB.8040804@gucas.ac.cn> <501037833.20213@test1.gucas.ac.cn> <4D8CEFA9.6070608@gucas.ac.cn> <501047928.23640@test1.gucas.ac.cn> <4D9068A3.9080205@gucas.ac.cn> <501330069.12482@test1.gucas.ac.cn> <4D91B5F0.2060801@gucas.ac.cn> <634DFD05-3AC9-4E1D-9905-1C42DB68D5A8@sissa.it> <501382873.25523@test1.gucas.ac.cn> Message-ID: <4D92367F.2030005@gucas.ac.cn> On 03/29/2011 03:17 AM, Paolo Giannozzi wrote: > On Tue, 2011-03-29 at 09:11 +0200, Gabriele Sclauzero wrote: > >> I'm not sure that the latest release (4.3b) which appears here >> http://qe-forge.org/frs/?group_id=10 >> includes those changes > it should > >> since the creation date is quite far in the past... > funny: the files were uploaded yeesterday evening ... > > P. > I've just tried to compile the release 4.3b and got the error bellow: mpif90 -ffast-math -m64 -march=core2 -mtune=core2 -ftree-vectorize -O3 -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__MPI -D__PARA -I../include -I../iotk/src -I../Modules -I. -c casino2upf.f90 casino2upf.f90:34.72: dx !dx for Trail and Needs and standard QE 1 Error: Unexpected NAMELIST statement at (1) casino2upf.f90:37.16: READ(*,inputpp,iostat=ios) 1 Error: Symbol 'inputpp' at (1) has no IMPLICIT type make[1]: *** [casino2upf.o] Error 1 make[1]: Leaving directory `/home/germaneau/soft/science/DFT-codes/quantum_expresso/espresso-4.3b/upftools' make: *** [upf] Error 2 Here is what I did: ESPRESSO=espresso-4.3b #espresso-4.2.1 cd $ESPRESSO make clean export FFLAGS="-ffast-math -m64 -march=core2 -mtune=core2 -ftree-vectorize -O3" export CFLAGS=$FFLAGS ./configure --with-internal-blas --with-internal-lapack #--enable-openmp make all It worked for the version 4.2.1 and 4.3a. Yours, Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/d3cd6aed/attachment.htm From jibanez008 at ikasle.ehu.es Tue Mar 29 09:48:10 2011 From: jibanez008 at ikasle.ehu.es (Julen Ibanez Azpiroz) Date: Tue, 29 Mar 2011 09:48:10 +0200 Subject: [Pw_forum] nl(:) indexes of the FFT grid Message-ID: Dear all, I have a question regarding the indexes that give the correspondence between the FFT grid and the array of G vectors, the nl(:). After an nscf calculation, I would like to read these indexes used at each k point in the nscf calculation (I have used the option 'wf_collect=.true.' in the calculations so that data about the calculation is saved). I have looked in the directories of the k points in the outdir/prefix.save directory, in the gkvectors.dat file where data about the G vectors is stored, and there one can find, among other things, the indexes igk(:), 'index of G corresponding to a given index of k+G', but I was not able to find the nl(:) indexes. Neither I could find information about them in the files gvectors.dat or data-file.xml, in the .save directory. I was wondering if the nl(:) indexes are saved somewhere after a calculation, and if so where. Any suggestion will be really appreciated, thanks in advance. Julen -- ?======================================== Julen Iba?ez Azpiroz Materia Kondentsatuaren Fisika Saila Zientzia eta Teknologia Fakultatea Euskal Herriko Unibertsitatea 644 Posta Kutxatila, 48080 Bilbo, Spain Telefonoa: +34 946015326 Mail: jibanez008 at ikasle.ehu.es ======================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/b1a275f6/attachment.htm From sclauzer at sissa.it Tue Mar 29 09:49:16 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 29 Mar 2011 09:49:16 +0200 Subject: [Pw_forum] I/O performance on BG/P systems In-Reply-To: <0F327142-3AB3-47B8-A6DA-723C9AFF135B@democritos.it> References: <4D8C916B.8010800@sissa.it> <0F327142-3AB3-47B8-A6DA-723C9AFF135B@democritos.it> Message-ID: <4090C379-5D47-4916-945B-428D1B32F501@sissa.it> Il giorno 26/mar/2011, alle ore 09.12, Paolo Giannozzi ha scritto: > > On Mar 25, 2011, at 13:58 , Gabriele Sclauzero wrote: > >> Before moving some complaints to the sysadmins, I would like to have >> some feedback from those of you who have used this kind of >> architecture. >> Are you aware of similar kind of I/O issues? Is there any performance >> tuning that can be done on the software/compiler side? > > I also noticed that reading/writing the CP restart file on a BG takes a > sizable amount of time, in the order of a few minutes for a typical > system > suitable for BG. I had attributed this to the "gathering" of the > distributed > pieces of wavefunctions that are subsequently written to file by a > single > process, though; Are you referring to the wf_collect feature? I've not been using that, so I was supposing that each process writes independently its piece of wavefunctions (at least for PWscf), am I right? > in your case, it is the I/O by each process that > takes a > lot of time. Do you think that this might be a symptom of a GPFS problem or misconfiguration? Have you ever observed such a behavior? > You may want to try to reduce the I/O to the strict > minimum: > work with one k-point per processor (use k-point parallelization if > needed), Indeed that is what I am trying to do since I got aware of this problem, but it is sometimes painful because I am working with hexagonal cells and I sometimes end up with 6 k-points or, even worse, 9 or 15... moreover in BGP you can't reserve an arbitrary number of processors or nodes, but just a sub-partition of the machine, as you surely know. So I have sometimes to put some of the processors at rest. > use disk_io='low' (or 'none'): the code should write only at the end > (or never). I've tried to used disk_io='low' in some relax calculations, this might be a good compromise. However the code writes the wavefunctions only once at the end of the run. Wouldn't it be more reasonable to write them at the end of each ionic step? (just a personal opinion...) Thanks, GS > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/869b9bac/attachment.htm From giannozz at democritos.it Tue Mar 29 10:06:14 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 Mar 2011 10:06:14 +0200 Subject: [Pw_forum] graphite cell optimization failed In-Reply-To: <4D92367F.2030005@gucas.ac.cn> References: <500855720.31742@test1.gucas.ac.cn> <4D8B8357.8070802@gucas.ac.cn> <500954893.22959@test1.gucas.ac.cn> <4D8C79CB.8040804@gucas.ac.cn> <501037833.20213@test1.gucas.ac.cn> <4D8CEFA9.6070608@gucas.ac.cn> <501047928.23640@test1.gucas.ac.cn> <4D9068A3.9080205@gucas.ac.cn> <501330069.12482@test1.gucas.ac.cn> <4D91B5F0.2060801@gucas.ac.cn> <634DFD05-3AC9-4E1D-9905-1C42DB68D5A8@sissa.it> <501382873.25523@test1.gucas.ac.cn> <4D92367F.2030005@gucas.ac.cn> Message-ID: <1301385974.13547.27.camel@fe12lx.fisica.uniud.it> On Tue, 2011-03-29 at 15:43 -0400, Eric Germaneau wrote: > Error: Unexpected NAMELIST statement at (1) move the line WRITE(0,*) 'CASINO2UPF Converter' after the declaration of the namelist. Some compilers don't complain, but some do P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From giannozz at democritos.it Tue Mar 29 10:08:40 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 Mar 2011 10:08:40 +0200 Subject: [Pw_forum] nl(:) indexes of the FFT grid In-Reply-To: References: Message-ID: <1301386120.13547.30.camel@fe12lx.fisica.uniud.it> On Tue, 2011-03-29 at 09:48 +0200, Julen Ibanez Azpiroz wrote: > I was wondering if the nl(:) indexes are saved somewhere > after a calculation currently they aren't: quantities defined on the FFT grid are saved in real space P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From jibanez008 at ikasle.ehu.es Tue Mar 29 10:16:50 2011 From: jibanez008 at ikasle.ehu.es (Julen Ibanez Azpiroz) Date: Tue, 29 Mar 2011 10:16:50 +0200 Subject: [Pw_forum] nl(:) indexes of the FFT grid In-Reply-To: <1301386120.13547.30.camel@fe12lx.fisica.uniud.it> References: <1301386120.13547.30.camel@fe12lx.fisica.uniud.it> Message-ID: Dear Professor Giannozi, Thank you very much for your quick answer, Julen -- ?======================================== Julen Iba?ez Azpiroz Materia Kondentsatuaren Fisika Saila Zientzia eta Teknologia Fakultatea Euskal Herriko Unibertsitatea 644 Posta Kutxatila, 48080 Bilbo, Spain Telefonoa: +34 946015326 Mail: jibanez008 at ikasle.ehu.es ======================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/58e77588/attachment.htm From nicola.marzari at materials.ox.ac.uk Tue Mar 29 11:32:59 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Tue, 29 Mar 2011 10:32:59 +0100 Subject: [Pw_forum] Problem with pseudopotential In-Reply-To: <215415.11560.qm@web43407.mail.sp1.yahoo.com> References: <215415.11560.qm@web43407.mail.sp1.yahoo.com> Message-ID: <4D91A74B.4040105@materials.ox.ac.uk> Dear Izaak, one of the graphs looks indeed very suspicious - it's the graph named "planar-average-pbedrrkjus.pdf", but labeled inside "Cu100 PP-van-ak 1vs2" (this is in itself is not a good sign :-)). Make sure you perform two identical calculations, with identical input files, and identical postprocessing, but only swap the pseudopotential name - first for the rrkjus pseudo, then for the ak-converted van pseudo. Calculate the average of the planar avarage, and then the work function (you could look at Phys. Rev. B 80, 235407 (2009) for an extensive discussion of these issues) - and see if you still get incorrect results. If you do, and everything else was absolutely identical, and one calculation gives a result that is in the experimental ballpark, and one gives a result that doesn't make sense, then the pseudopotential has a problem, and you should report it. Double check also that your structure is correct (plot it with xcrysden). Only superficial comment on the input is that you might need a bit more k-points and a bit less smearing for ultimate accuracy. nicola On 3/29/11 12:44 AM, Izaak Williamson wrote: > Dear all, > I was trying to calculate the workfunction for Cu(100) surface. When I > plotted the planar average of Vbare+VH as a function of z, I found that > Vbare+VH at some points is higher than Vbare+VH at the vacuum level. I > have attached the file (planar-average-pbedrrkjus.pdf). I am also > attaching the input file Cu100.in . Does this mean that > the pseudopotential (*Cu.pbe-d-rrkjus.UPF* > ) is > wrong? Why does it behave like this? > When I do the same calculation with *Cu.pbe-n-van_ak.UPF* > > pseudopotential, then I get a reasonable graph > (planar-average-pbevanak.pdf ). Any > suggestions/explanations would be greatly appreciated. > Thank you. > > -- > Izaak Williamson > Research Assistant > Physics Department > Boise State University > -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From balducci at univ.trieste.it Tue Mar 29 12:35:44 2011 From: balducci at univ.trieste.it (balducci at univ.trieste.it) Date: Tue, 29 Mar 2011 12:35:44 +0200 Subject: [Pw_forum] gfortran-4.6.0 and 4.3b Message-ID: <22519.1301394968@dschgrazlin2.units.it> Hello, apologies if I am missing some blatant point. Just tried to build 4.3b with the very recently released gfortran-4.6.0 (gfortran-4.5.2 works fine, but for the small bug already fixed by Check-in 8582). gfortran-4.6.0 chokes on pw2gw.f90 with: gfortran -O3 -g -x f95-cpp-input -D__FFTW3 -I../include -I../iotk/src -I../Modules -I../PW -I. -c pw2gw.f90 pw2gw.f90:460.26: CALL gen_us_vkb0(ik,npw,vkb0,size_tab,vec_tab,spline_ps,vec_tab_d2y) 1 Error: Dummy argument 'vec_tab_d2y' of procedure 'gen_us_vkb0' at (1) has an attribute that requires an explicit interface for this procedure As far as I seem to understand (and this is the reason for my report), looks like it is right: my fortran 90/95 book says that "a calling program unit must have an _explicit interface_ to a procedure if it is to use advanced fortran features such as keyword arguments or optional arguments" and vec_tab_d2y is declared as optional. As a matter of fact, this quick and dirty patch fixes the error: diff -c PP/pw2gw.f90.ORIG PP/pw2gw.f90 *** PP/pw2gw.f90.ORIG Tue Mar 29 11:51:03 2011 --- PP/pw2gw.f90 Tue Mar 29 11:51:03 2011 *************** *** 126,131 **** --- 126,156 ---- IMPLICIT NONE + INTERFACE + subroutine gen_us_vkb0 (ik,npw,vkb0,size_tab,vec_tab, spline_ps, vec_tab_d2y) + USE kinds, ONLY : DP, sgl + real(DP), intent(inout) ::vkb0(1:npw) + integer, intent(in) :: ik, npw + integer, intent(in) :: size_tab + real(DP), intent(in) :: vec_tab(1:size_tab) + real(DP), optional, intent(in) :: vec_tab_d2y(1:size_tab) + logical :: spline_ps + end subroutine gen_us_vkb0 + END INTERFACE + + INTERFACE + subroutine gen_us_djl (ik,npw,djl,size_tab,vec_tab, spline_ps, vec_tab_d2y) + USE kinds, ONLY : DP, sgl + real(DP), intent(inout) ::djl(1:npw) + integer, intent(in) :: ik, npw + integer, intent(in) :: size_tab + real(DP), intent(in) :: vec_tab(1:size_tab) + real(DP), optional, intent(in) :: vec_tab_d2y(1:size_tab) + logical :: spline_ps + end subroutine gen_us_djl + END INTERFACE + + LOGICAL, INTENT(in) :: use_gmaps INTEGER :: ii(16), ngw, nkpt, ig, ik, ir, n, i,j,k, io = 98, iband1, iband2 although my fortran book deprecates the use of INTERFACE in favor of stuffing the subroutine into a module. I report this in the hope of being of any use. (However, after fixing this, gfortran-4.6.0 crashes on fpmd2upf.f90 with: fpmd2upf.f90: In function 'fpmd2upf': fpmd2upf.f90:872:0: internal compiler error: Segmentation fault Please submit a full bug report, with preprocessed source if appropriate. See for instructions. OUCH!) thanks a lot for making q-e publicly available ciao gabriele -- Gabriele Balducci - Dipartimento di Scienze Chimiche - Via L. Giorgieri 1 I-34127 TRIESTE tel: I-040-5583957 fax: I-040-5583903 e-mail: balducci at units.it Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From eyvaz_isaev at yahoo.com Tue Mar 29 15:00:29 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 29 Mar 2011 06:00:29 -0700 (PDT) Subject: [Pw_forum] Error in phonon calculation using matdyn.x In-Reply-To: References: Message-ID: <616084.3211.qm@web65712.mail.ac4.yahoo.com> Hi, Find subroutine frc_blk(...) inside matdyn.f90 the next line: IF (ABS(total_weight-nr1*nr2*nr3).GT.1.0d-8) THEN Might be due to some numerical noise this condition is not fulfilled. Then try 1.d0d-7 (recompile matdyn.f90 using "make ph") and see what happens. If not, then one has to analyze your input files. Bests, Eyvaz. ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: mayank gupta To: pw_forum at pwscf.org Sent: Tue, March 29, 2011 6:00:15 AM Subject: [Pw_forum] Error in phonon calculation using matdyn.x Dear All I am doing pwscf and phonon calculation for Y2O3. In 2x2x2 Q mesh it generates 6 irreducible q points (yo.dyn* files). The phonon frequency calculation using matdyn.x run I got error message 7.5000000000000000 from frc_blk : error # 1 wrong total_weight stopping ... What could be the possible error. Thanks -- Mayank kumar gupta Contact No- 9869834437 8097400037 9220397437 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From degironc at sissa.it Tue Mar 29 15:14:46 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 29 Mar 2011 15:14:46 +0200 Subject: [Pw_forum] Error in phonon calculation using matdyn.x In-Reply-To: <616084.3211.qm@web65712.mail.ac4.yahoo.com> References: <616084.3211.qm@web65712.mail.ac4.yahoo.com> Message-ID: <4D91DB46.70307@sissa.it> increasing the threshold to 1.d-7 will probably not help.. I think the total weight you have is 7.5 instead of 8.0... is your cell very anisotropic ? try to increase the VERY VERY SAFE RANGE to 3 times nr1,nr2,nr3 ... stefano On 03/29/2011 03:00 PM, Eyvaz Isaev wrote: > Hi, > > Find subroutine frc_blk(...) inside matdyn.f90 the next line: > > IF (ABS(total_weight-nr1*nr2*nr3).GT.1.0d-8) THEN > > Might be due to some numerical noise this condition is not fulfilled. Then try > 1.d0d-7 (recompile matdyn.f90 using "make ph") and see what happens. If not, > then one has to analyze your input files. > > Bests, > Eyvaz. > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel& Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > ----- Original Message ---- > From: mayank gupta > To: pw_forum at pwscf.org > Sent: Tue, March 29, 2011 6:00:15 AM > Subject: [Pw_forum] Error in phonon calculation using matdyn.x > > Dear All I am doing pwscf and phonon calculation for Y2O3. In 2x2x2 Q > mesh it generates 6 irreducible q points (yo.dyn* files). The phonon > frequency calculation using matdyn.x run I got error message > > 7.5000000000000000 > from frc_blk : error # 1 > wrong total_weight > stopping ... > > What could be the possible error. > > > Thanks > > > > > > > From rajanpandey at gmail.com Tue Mar 29 16:28:18 2011 From: rajanpandey at gmail.com (Rajan Pandey) Date: Tue, 29 Mar 2011 19:58:18 +0530 Subject: [Pw_forum] Problem with newly implemented LDA -1/2 in atomic code (ld1) Message-ID: Dear Quantum Espresso Community, I built the latest release (perhaps alpha) of QE-4.3a. Tried to look into the latest LDA -1/2 (assumed to be similar to SIC) in atomic code (ld1), and from the available test case of Silicon, I decided to check if I get a corrected band gap of bulk Si (from example05). First I generated LDA - 0.5 pseudo (input deck for the same is supplied with the distribution). Subsequently, to run a band structure calculation of Si, I used the template in example05. First I did band structure calculation with Si.pz-vbc.UPF, and then another calculation with the LDA - 0.5 pseudo (Si.LDA.0.5.UPF). I checked the output of scf calculation of the latter (I am copying the portion from output): PseudoPot. # 1 for Si read from file Si.LDA.0.5.UPF MD5 check sum: ac6493edff0fd6b486246c8fa11d17dc Pseudo is Norm-conserving, Zval = 4.0 Generated using LDA-1/2 implemented by Leonardo Matheus Marion Jorge Using radial grid of 431 points, 2 beta functions with: l(1) = 0 l(2) = 1 atomic species valence mass pseudopotential Si 4.00 28.08600 Si( 1.00) 48 Sym.Ops. (with inversion) However, the end results of the two calculations are the same. That is the band structure and hence the band gap in two cases are same - nearly 50% underestimated. Not sure if I am missing something. I have attached the two scripts: run_example-0 ==> uses LDA pseudo, and run_example ==> uses LDA - 1/2 pseudo. I shall appreciate any suggestion. Thanks, and regards, Rajan Rajan K. Pandey, Ph.D. Advisory Research Engineer, Semiconductor Research & Development Center India Systems & Technology Engineering Lab IBM India Pvt. Ltd. MD3 1F B354 Manyata Embassy Business Park Nagawara, Outer Ring Road Bangalore - 560045, India Phone: +91-80-28061262 Mobile: +91-9901850981 Email: rajapand at in.ibm.com rajanpandey at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/a4c79c6c/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: run_example-0 Type: application/octet-stream Size: 5836 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110329/a4c79c6c/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: run_example Type: application/octet-stream Size: 5839 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110329/a4c79c6c/attachment-0003.obj From giannozz at democritos.it Tue Mar 29 16:53:56 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 29 Mar 2011 16:53:56 +0200 Subject: [Pw_forum] gfortran-4.6.0 and 4.3b In-Reply-To: <22519.1301394968@dschgrazlin2.units.it> References: <22519.1301394968@dschgrazlin2.units.it> Message-ID: <1301410436.13547.103.camel@fe12lx.fisica.uniud.it> On Tue, 2011-03-29 at 12:35 +0200, balducci at univ.trieste.it wrote: > I report this in the hope of being of any use. thank you. Fixed in the next release (very soon) > fpmd2upf.f90: In function 'fpmd2upf': > fpmd2upf.f90:872:0: internal compiler error: Segmentation fault > Please submit a full bug report, this will be needed only if you have pseudopotentials in the old FPMD format. If you have time, you may want to try what the error message suggests: file a bug report for gfortran (all internal compiler errors are, by definition, compiler bugs). It shouldn't be difficult to locate where the compiler runs into trouble, since the fpmd2upf code is rather simple. With a usable bug report, gfortran developers usually fix the bug in less than no time Paolo -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From nicola.marzari at materials.ox.ac.uk Tue Mar 29 17:22:39 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Tue, 29 Mar 2011 16:22:39 +0100 Subject: [Pw_forum] Problem with newly implemented LDA -1/2 in atomic code (ld1) In-Reply-To: References: Message-ID: <4D91F93F.2000903@materials.ox.ac.uk> Hi, If I understand correctly, you generated a lda-1/2 pseudo with the atomic code, but did a lda calculation on silicon with pwscf - so you will have gotten very similar but not perfectly identical results, of lda bulk silicon done with a consistent pseudo (lda) or an inconsistent pseudo . 2) not sure if lda-1/2 is in pwscf (I think not) or if it can be applied to solids. nicola On 3/29/11 3:28 PM, Rajan Pandey wrote: > Dear Quantum Espresso Community, > > I built the latest release (perhaps alpha) of QE-4.3a. Tried to look > into the latest LDA -1/2 (assumed to be similar to SIC) in atomic code > (ld1), and from the available test case of Silicon, > I decided to check if I get a corrected band gap of bulk Si (from > example05). First I generated LDA - 0.5 pseudo (input deck for the same > is supplied with the distribution). Subsequently, > to run a band structure calculation of Si, I used the template in > example05. First I did band structure calculation with Si.pz-vbc.UPF, > and then another calculation with the LDA - 0.5 pseudo (Si.LDA.0.5.UPF). > I checked the output of scf calculation of the latter (I am copying the > portion from output): > > > PseudoPot. # 1 for Si read from file Si.LDA.0.5.UPF > MD5 check sum: ac6493edff0fd6b486246c8fa11d17dc > Pseudo is Norm-conserving, Zval = 4.0 > Generated using LDA-1/2 implemented by Leonardo Matheus Marion Jorge > Using radial grid of 431 points, 2 beta functions with: > l(1) = 0 > l(2) = 1 > > atomic species valence mass pseudopotential > Si 4.00 28.08600 Si( 1.00) > > 48 Sym.Ops. (with inversion) > > However, the end results of the two calculations are the same. That is > the band structure and hence the band gap in two cases are same - nearly > 50% underestimated. > Not sure if I am missing something. I have attached the two scripts: > run_example-0 ==> uses LDA pseudo, and run_example ==> uses LDA - 1/2 > pseudo. > I shall appreciate any suggestion. > > Thanks, and regards, > > Rajan > -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From lmartinsamos at gmail.com Tue Mar 29 17:47:22 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Tue, 29 Mar 2011 17:47:22 +0200 Subject: [Pw_forum] Problem with newly implemented LDA -1/2 in atomic code (ld1) In-Reply-To: <4D91F93F.2000903@materials.ox.ac.uk> References: <4D91F93F.2000903@materials.ox.ac.uk> Message-ID: H, sometime ago LDA-1/2 in pwscf was working. I saw some numbers for TiO2 anatase, But I do not remember the details. i'll ask around bests regards Layla 2011/3/29 Nicola Marzari > > > Hi, > > If I understand correctly, you generated a lda-1/2 pseudo > with the atomic code, but did a lda calculation on silicon > with pwscf - so you will have gotten very similar but not perfectly > identical results, of lda bulk silicon done with a consistent > pseudo (lda) or an inconsistent pseudo . > > 2) not sure if lda-1/2 is in pwscf (I think not) or if it > can be applied to solids. > > nicola > > > > On 3/29/11 3:28 PM, Rajan Pandey wrote: > > Dear Quantum Espresso Community, > > > > I built the latest release (perhaps alpha) of QE-4.3a. Tried to look > > into the latest LDA -1/2 (assumed to be similar to SIC) in atomic code > > (ld1), and from the available test case of Silicon, > > I decided to check if I get a corrected band gap of bulk Si (from > > example05). First I generated LDA - 0.5 pseudo (input deck for the same > > is supplied with the distribution). Subsequently, > > to run a band structure calculation of Si, I used the template in > > example05. First I did band structure calculation with Si.pz-vbc.UPF, > > and then another calculation with the LDA - 0.5 pseudo (Si.LDA.0.5.UPF). > > I checked the output of scf calculation of the latter (I am copying the > > portion from output): > > > > > > PseudoPot. # 1 for Si read from file Si.LDA.0.5.UPF > > MD5 check sum: ac6493edff0fd6b486246c8fa11d17dc > > Pseudo is Norm-conserving, Zval = 4.0 > > Generated using LDA-1/2 implemented by Leonardo Matheus Marion > Jorge > > Using radial grid of 431 points, 2 beta functions with: > > l(1) = 0 > > l(2) = 1 > > > > atomic species valence mass pseudopotential > > Si 4.00 28.08600 Si( 1.00) > > > > 48 Sym.Ops. (with inversion) > > > > However, the end results of the two calculations are the same. That is > > the band structure and hence the band gap in two cases are same - nearly > > 50% underestimated. > > Not sure if I am missing something. I have attached the two scripts: > > run_example-0 ==> uses LDA pseudo, and run_example ==> uses LDA - 1/2 > > pseudo. > > I shall appreciate any suggestion. > > > > Thanks, and regards, > > > > Rajan > > > -- > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > _______________________________________________ > 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/20110329/bf9f7c2b/attachment.htm From faccin.giovani at gmail.com Tue Mar 29 18:16:22 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Tue, 29 Mar 2011 12:16:22 -0400 Subject: [Pw_forum] Fixing starting starting_ns_eigenvalue Message-ID: Hi all! Is it possible, in a LDA+U calculation, to fix the starting_ns eigenvalues for the entire calculation run, instead of just the second interaction? Specifically, I'd like to be able to track how a certain electronic configuration's associated energy varies when other parameters (ex: atomic distances) change. But in order to do that, I need to be able to impose specific electronic configurations for the system, even if those configurations are not the global energy mininum. Can that be done in QE? Thanks! -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/8ecf1c4c/attachment.htm From sclauzer at sissa.it Tue Mar 29 18:28:56 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 29 Mar 2011 18:28:56 +0200 Subject: [Pw_forum] Fixing starting starting_ns_eigenvalue In-Reply-To: References: Message-ID: Dear Giovani, have you tried with mixing_fixed_ns? Could you please provide your affiliation? Regards, GS mixing_fixed_ns Il giorno 29/mar/2011, alle ore 18.16, Giovani Faccin ha scritto: > Hi all! > > Is it possible, in a LDA+U calculation, to fix the starting_ns eigenvalues for the entire calculation run, instead of just the second interaction? > > Specifically, I'd like to be able to track how a certain electronic configuration's associated energy varies when other parameters (ex: atomic distances) change. But in order to do that, I need to be able to impose specific electronic configurations for the system, even if those configurations are not the global energy mininum. > > Can that be done in QE? > > Thanks! > > -- > Giovani > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/4e5cc563/attachment.htm From rajanpandey at gmail.com Tue Mar 29 18:39:55 2011 From: rajanpandey at gmail.com (Rajan Pandey) Date: Tue, 29 Mar 2011 22:09:55 +0530 Subject: [Pw_forum] Problem with newly implemented LDA -1/2 in atomic code (ld1) In-Reply-To: References: <4D91F93F.2000903@materials.ox.ac.uk> Message-ID: Hi Nicola, Your comment prompted me to get the reference [ L. G. Ferreira, M. Marques and L. K. Teles, Phys. Rev. B 78 125116 (2008) ] and try to figure out the way authors worked out LDA - 1/2 method, in general. From faccin.giovani at gmail.com Tue Mar 29 18:55:00 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Tue, 29 Mar 2011 12:55:00 -0400 Subject: [Pw_forum] Fixing starting starting_ns_eigenvalue In-Reply-To: References: Message-ID: Dear Gabriele, Yes, I tried mixing_fixed_ns. The problem is that this command fixes the initial occupation during all the run, not the occupation imposed on step 2 with starting_ns eigenvalues. I'm attaching an example input and output file that shows this happening. As you can see on the output.txt file, after iteraction 1 the program inserts the eigenvalues I wanted on atom 1 spin2 and atom 2 spin2. However, just after this it prints: RESET ns to initial values (iter <= mixing_fixed_ns) on every new iteration. Looking at the end of the calculation, you can see that the final states are exactly the default states from step 0. In other words, it overwrites the eigenvalues defined by starting_ns eigenvalues, placing the default initial occupations instead. Perhaps an "if" clause could be added to the code to manage situations when both mixing_fixed_ns and starting_ns eigenvalues are defined by the user? Or maybe I'm doing this all wrong? Regards, Giovani Faccin IFGW/Unicamp-Brazil 2011/3/29 Gabriele Sclauzero > Dear Giovani, > > have you tried with mixing_fixed_ns? > > Could you please provide your affiliation? > > > Regards, > > > GS > > mixing_fixed_ns > Il giorno 29/mar/2011, alle ore 18.16, Giovani Faccin ha scritto: > > Hi all! > > Is it possible, in a LDA+U calculation, to fix the starting_ns eigenvalues > for the entire calculation run, instead of just the second interaction? > > Specifically, I'd like to be able to track how a certain electronic > configuration's associated energy varies when other parameters (ex: atomic > distances) change. But in order to do that, I need to be able to impose > specific electronic configurations for the system, even if those > configurations are not the global energy mininum. > > Can that be done in QE? > > Thanks! > > -- > Giovani > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > * PH H2 462, Station 3, CH-1015 Lausanne* > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/b6606360/attachment-0001.htm -------------- next part -------------- &CONTROL calculation = 'scf' , restart_mode = 'from_scratch' , wf_collect = .true. , outdir = './output' , pseudo_dir = '../pseudo/' , prefix = 'fe' , etot_conv_thr = 1.0D-9 , forc_conv_thr = 1.0D-6 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 1, celldm(1) = 15, nat = 2, ntyp = 1, ecutwfc = 100 , ecutrho = 300 , nbnd = 18, occupations = 'smearing' , degauss = 0.0005 , smearing = 'methfessel-paxton' , nspin = 2 , assume_isolated = 'martyna-tuckerman' starting_magnetization(1) = 0.9, lda_plus_u = .true. , Hubbard_U(1) = 3.1, starting_ns_eigenvalue(1,2,1) = 0.0 starting_ns_eigenvalue(2,2,1) = 0.0476060 starting_ns_eigenvalue(3,2,1) = 0.0476060 starting_ns_eigenvalue(4,2,1) = 0.9654373 starting_ns_eigenvalue(5,2,1) = 0.9954307 / &ELECTRONS conv_thr = 1.0e-9 , mixing_beta = 0.7 , diagonalization = 'david' , mixing_fixed_ns = 500, / ATOMIC_SPECIES Fe 58.69000 Fe.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Fe 2.070000000 0.000000000 0.000000000 Fe 0.000000000 0.000000000 0.000000000 K_POINTS automatic 1 1 1 1 1 1 -------------- next part -------------- Program PWSCF v.4.2.1 starts on 18Mar2011 at 15: 4:43 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 1 processors Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... file Fe.pbe-nd-rrkjus.UPF: wavefunction(s) 4S renormalized Subspace diagonalization in iterative solution of the eigenvalue problem: Too few procs for parallel algorithm: we need at least 4 procs per pool a serial algorithm will be used warning: symmetry operation # 2 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 3 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 13 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 14 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 25 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 28 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 39 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates warning: symmetry operation # 40 not allowed. fractional translation: -0.2607822 0.0000000 0.0000000 in crystal coordinates Planes per process (thick) : nr3 = 90 npp = 90 ncplane = 8100 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 90 5385 296459 90 5385 296459 1925 63461 bravais-lattice index = 1 lattice parameter (a_0) = 15.0000 a.u. unit-cell volume = 3375.0000 (a.u.)^3 number of atoms/cell = 2 number of atomic types = 1 number of electrons = 16.00 number of Kohn-Sham states= 18 kinetic-energy cutoff = 100.0000 Ry charge density cutoff = 300.0000 Ry convergence threshold = 1.0E-09 mixing beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE (1434) EXX-fraction = 0.00 celldm(1)= 15.000000 celldm(2)= 0.000000 celldm(3)= 0.000000 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( 0.000000 1.000000 0.000000 ) a(3) = ( 0.000000 0.000000 1.000000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.000000 0.000000 0.000000 ) b(2) = ( 0.000000 1.000000 0.000000 ) b(3) = ( 0.000000 0.000000 1.000000 ) PseudoPot. # 1 for Fe read from file Fe.pbe-nd-rrkjus.UPF Pseudo is Ultrasoft + core correction, Zval = 8.0 Generated by new atomic code, or converted to UPF format Using radial grid of 957 points, 6 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 l(5) = 2 l(6) = 2 Q(r) pseudized with 0 coefficients atomic species valence mass pseudopotential Fe 8.00 58.69000 Fe( 1.00) Starting magnetic structure atomic species magnetization Fe 0.900 LDA+U calculation, Hubbard_lmax = 2 atomic species L Hubbard U Hubbard alpha Fe 2 0.227846 0.000000 8 Sym.Ops. (no inversion) Cartesian axes site n. atom positions (a_0 units) 1 Fe tau( 1) = ( 0.2607822 0.0000000 0.0000000 ) 2 Fe tau( 2) = ( 0.0000000 0.0000000 0.0000000 ) number of k points= 2 gaussian broad. (Ry)= 0.0005 ngauss = 1 cart. coord. in units 2pi/a_0 k( 1) = ( -0.5000000 -0.5000000 -0.5000000), wk = 1.0000000 k( 2) = ( -0.5000000 -0.5000000 -0.5000000), wk = 1.0000000 G cutoff = 1709.7950 ( 296459 G-vectors) FFT grid: ( 90, 90, 90) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 15.66 Mb ( 57016, 18) Atomic wavefunctions 10.44 Mb ( 57016, 12) NL pseudopotentials 31.32 Mb ( 57016, 36) Each V/rho on FFT grid 22.25 Mb ( 729000, 2) Each G-vector array 2.26 Mb ( 296459) G-vector shells 0.01 Mb ( 1428) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 62.64 Mb ( 57016, 72) Each subspace H/S matrix 0.08 Mb ( 72, 72) Each matrix 0.01 Mb ( 36, 18) Arrays for rho mixing 88.99 Mb ( 729000, 8) alpha, beta MT = 2.7999999999999998 0.17857142857142858 Check: negative/imaginary core charge= -0.000016 0.000000 Initial potential from superposition of free atoms starting charge 15.99873, renormalised to 16.00000 negative rho (up, down): 0.840E-05 0.442E-06 Parameters of the lda+U calculation: Number of iteration with fixed ns =500 Starting ns and Hubbard U : enter write_ns U( 1) = 3.1000 alpha( 1) = 0.0000 atom 1 Tr[ns(na)]= 6.0000000 atom 1 spin 1 atom 1 spin 1 eigenvalues: 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 atom 1 spin 2 atom 1 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 atom 2 Tr[ns(na)]= 6.0000000 atom 2 spin 1 atom 2 spin 1 eigenvalues: 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 atom 2 spin 2 atom 2 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 nsum = 12.0000000 exit write_ns Atomic wfc used for LDA+U Projector are NOT orthogonalized Starting wfc are 12 atomic + 6 random wfc total cpu time spent up to now is 18.36 secs per-process dynamical memory: 210.5 Mb Self-consistent Calculation iteration # 1 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 11.5 enter write_ns U( 1) = 3.1000 alpha( 1) = 0.0000 atom 1 Tr[ns(na)]= 5.4338797 atom 1 spin 1 atom 1 spin 1 eigenvalues: 0.9912601 0.9975801 0.9978221 0.9978221 0.9981564 eigenvectors 1 0.5000000 0.0000000 0.0000000 -0.8660254 -0.0000000 2 0.8660254 0.0000000 -0.0000000 0.5000000 0.0000000 3 0.0000000 0.3231293 0.0000000 0.0000000 -0.9463548 4 0.0000000 -0.9463548 -0.0000000 0.0000000 -0.3231293 5 0.0000000 -0.0000000 1.0000000 0.0000000 0.0000000 occupations 0.996 -0.000 -0.000 0.003 0.000 -0.000 0.998 -0.000 0.000 0.000 -0.000 -0.000 0.998 0.000 0.000 0.003 0.000 0.000 0.993 -0.000 0.000 0.000 0.000 -0.000 0.998 atom 1 spin 2 atom 1 spin 2 eigenvalues: 0.0000005 0.0000087 0.0287373 0.2112463 0.2112463 eigenvectors 1 0.8660254 0.0000000 0.0000000 0.5000000 -0.0000000 2 0.0000000 -0.0000000 -1.0000000 0.0000000 0.0000000 3 -0.5000000 -0.0000000 0.0000000 0.8660254 0.0000000 4 -0.0000000 0.4167215 -0.0000000 0.0000000 -0.9090342 5 0.0000000 -0.9090342 0.0000000 -0.0000000 -0.4167215 occupations 0.007 -0.000 0.000 -0.012 0.000 -0.000 0.211 -0.000 0.000 0.000 0.000 -0.000 0.000 -0.000 0.000 -0.012 0.000 -0.000 0.022 -0.000 0.000 0.000 0.000 -0.000 0.211 atom 2 Tr[ns(na)]= 5.4328473 atom 2 spin 1 atom 2 spin 1 eigenvalues: 0.9912596 0.9975606 0.9977966 0.9977966 0.9980812 eigenvectors 1 0.5000000 0.0000000 0.0000000 -0.8660254 -0.0000000 2 0.8660254 0.0000000 -0.0000000 0.5000000 0.0000000 3 0.0000000 0.3501070 0.0000000 0.0000000 -0.9367097 4 0.0000000 -0.9367097 -0.0000000 0.0000000 -0.3501070 5 0.0000000 -0.0000000 1.0000000 0.0000000 0.0000000 occupations 0.996 -0.000 -0.000 0.003 0.000 -0.000 0.998 -0.000 0.000 0.000 -0.000 -0.000 0.998 0.000 0.000 0.003 0.000 0.000 0.993 -0.000 0.000 0.000 0.000 -0.000 0.998 atom 2 spin 2 atom 2 spin 2 eigenvalues: 0.0000004 0.0000074 0.0287535 0.2107956 0.2107956 eigenvectors 1 0.8660254 0.0000000 0.0000000 0.5000000 -0.0000000 2 0.0000000 -0.0000000 -1.0000000 0.0000000 0.0000000 3 -0.5000000 -0.0000000 0.0000000 0.8660254 0.0000000 4 -0.0000000 0.4214217 -0.0000000 0.0000000 -0.9068648 5 0.0000000 -0.9068648 0.0000000 -0.0000000 -0.4214217 occupations 0.007 -0.000 0.000 -0.012 0.000 -0.000 0.211 -0.000 0.000 0.000 0.000 -0.000 0.000 -0.000 0.000 -0.012 0.000 -0.000 0.022 -0.000 0.000 0.000 0.000 -0.000 0.211 nsum = 10.8667269 exit write_ns Modify starting ns matrices according to input values enter write_ns U( 1) = 3.1000 alpha( 1) = 0.0000 atom 1 Tr[ns(na)]= 7.0387207 atom 1 spin 1 atom 1 spin 1 eigenvalues: 0.9912601 0.9975801 0.9978221 0.9978221 0.9981564 eigenvectors 1 0.5000000 0.0000000 0.0000000 -0.8660254 -0.0000000 2 0.8660254 0.0000000 -0.0000000 0.5000000 0.0000000 3 0.0000000 0.3332526 0.0000000 0.0000000 -0.9428376 4 0.0000000 -0.9428376 -0.0000000 0.0000000 -0.3332526 5 0.0000000 -0.0000000 1.0000000 0.0000000 0.0000000 occupations 0.996 -0.000 -0.000 0.003 0.000 -0.000 0.998 -0.000 0.000 0.000 -0.000 -0.000 0.998 0.000 0.000 0.003 0.000 0.000 0.993 -0.000 0.000 0.000 0.000 -0.000 0.998 atom 1 spin 2 atom 1 spin 2 eigenvalues: -0.0000000 0.0476060 0.0476060 0.9654373 0.9954307 eigenvectors 1 0.8660254 0.0000000 0.0000000 0.5000000 -0.0000000 2 -0.1016363 0.0000000 0.9791222 0.1760392 -0.0000000 3 -0.4895611 -0.0000000 -0.2032725 0.8479447 0.0000000 4 -0.0000000 0.4167215 -0.0000000 0.0000000 -0.9090342 5 0.0000000 -0.9090342 0.0000000 -0.0000000 -0.4167215 occupations 0.012 -0.000 -0.000 -0.021 0.000 -0.000 0.990 -0.000 0.000 0.011 -0.000 -0.000 0.048 -0.000 0.000 -0.021 0.000 -0.000 0.036 -0.000 0.000 0.011 0.000 -0.000 0.971 atom 2 Tr[ns(na)]= 7.0385747 atom 2 spin 1 atom 2 spin 1 eigenvalues: 0.9912596 0.9975606 0.9977966 0.9977966 0.9980812 eigenvectors 1 0.5000000 0.0000000 0.0000000 -0.8660254 -0.0000000 2 0.8660254 0.0000000 -0.0000000 0.5000000 0.0000000 3 0.0000000 0.4125984 0.0000000 0.0000000 -0.9109130 4 0.0000000 -0.9109130 -0.0000000 0.0000000 -0.4125984 5 0.0000000 -0.0000000 1.0000000 0.0000000 0.0000000 occupations 0.996 -0.000 -0.000 0.003 0.000 -0.000 0.998 -0.000 0.000 0.000 -0.000 -0.000 0.998 0.000 0.000 0.003 0.000 0.000 0.993 -0.000 0.000 0.000 0.000 -0.000 0.998 atom 2 spin 2 atom 2 spin 2 eigenvalues: -0.0000000 0.0476060 0.0476060 0.9654373 0.9954307 eigenvectors 1 0.8660254 0.0000000 0.0000000 0.5000000 -0.0000000 2 -0.4624456 -0.0000000 -0.3802318 0.8009793 0.0000000 3 0.1901159 0.0000000 -0.9248912 -0.3292904 0.0000000 4 -0.0000000 0.4214217 -0.0000000 0.0000000 -0.9068648 5 0.0000000 -0.9068648 0.0000000 -0.0000000 -0.4214217 occupations 0.012 -0.000 -0.000 -0.021 0.000 -0.000 0.990 -0.000 0.000 0.011 -0.000 -0.000 0.048 -0.000 0.000 -0.021 0.000 -0.000 0.036 -0.000 0.000 0.011 0.000 -0.000 0.971 nsum = 14.0772954 exit write_ns RESET ns to initial values (iter <= mixing_fixed_ns) total cpu time spent up to now is 63.22 secs total energy = -109.56880241 Ry Harris-Foulkes estimate = -110.68781016 Ry estimated scf accuracy < 1.54971595 Ry total magnetization = 12.00 Bohr mag/cell absolute magnetization = 12.00 Bohr mag/cell iteration # 2 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.69E-03, avg # of iterations = 3.0 RESET ns to initial values (iter <= mixing_fixed_ns) total cpu time spent up to now is 96.87 secs total energy = -110.18790510 Ry Harris-Foulkes estimate = -112.27467231 Ry estimated scf accuracy < 6.73753616 Ry total magnetization = 4.00 Bohr mag/cell absolute magnetization = 4.11 Bohr mag/cell iteration # 3 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.69E-03, avg # of iterations = 2.0 RESET ns to initial values (iter <= mixing_fixed_ns) total cpu time spent up to now is 128.28 secs total energy = -110.67113409 Ry Harris-Foulkes estimate = -110.85771078 Ry estimated scf accuracy < 2.44659746 Ry total magnetization = 6.00 Bohr mag/cell absolute magnetization = 6.17 Bohr mag/cell iteration # 4 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.69E-03, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) total cpu time spent up to now is 158.64 secs total energy = -110.67476165 Ry Harris-Foulkes estimate = -110.81051485 Ry estimated scf accuracy < 1.68872176 Ry total magnetization = 6.00 Bohr mag/cell absolute magnetization = 6.18 Bohr mag/cell iteration # 5 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.69E-03, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.176E-07 0.405E-08 total cpu time spent up to now is 188.11 secs total energy = -110.75139774 Ry Harris-Foulkes estimate = -110.75958072 Ry estimated scf accuracy < 0.12534928 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.12 Bohr mag/cell iteration # 6 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 7.83E-04, avg # of iterations = 2.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.331E-05 0.987E-03 total cpu time spent up to now is 219.24 secs total energy = -110.76694437 Ry Harris-Foulkes estimate = -110.76177260 Ry estimated scf accuracy < 0.06039123 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.17 Bohr mag/cell iteration # 7 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.77E-04, avg # of iterations = 2.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.420E-05 0.211E-02 total cpu time spent up to now is 250.49 secs total energy = -110.78322413 Ry Harris-Foulkes estimate = -110.81949761 Ry estimated scf accuracy < 0.46546960 Ry total magnetization = 6.00 Bohr mag/cell absolute magnetization = 6.41 Bohr mag/cell iteration # 8 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.77E-04, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.284E-03 0.121E-04 total cpu time spent up to now is 282.23 secs total energy = -110.70845864 Ry Harris-Foulkes estimate = -110.78568797 Ry estimated scf accuracy < 0.34448263 Ry total magnetization = 6.00 Bohr mag/cell absolute magnetization = 6.44 Bohr mag/cell iteration # 9 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.77E-04, avg # of iterations = 3.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.388E-03 0.103E-04 total cpu time spent up to now is 320.29 secs total energy = -110.76463767 Ry Harris-Foulkes estimate = -110.77304605 Ry estimated scf accuracy < 0.04964287 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.39 Bohr mag/cell iteration # 10 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.10E-04, avg # of iterations = 1.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.148E-04 0.726E-05 total cpu time spent up to now is 352.98 secs total energy = -110.76350147 Ry Harris-Foulkes estimate = -110.76755845 Ry estimated scf accuracy < 0.01520452 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.38 Bohr mag/cell iteration # 11 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.50E-05, avg # of iterations = 7.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.155E-04 0.719E-05 total cpu time spent up to now is 392.62 secs total energy = -110.76779053 Ry Harris-Foulkes estimate = -110.76836565 Ry estimated scf accuracy < 0.00323230 Ry total magnetization = 7.93 Bohr mag/cell absolute magnetization = 8.29 Bohr mag/cell iteration # 12 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 2.02E-05, avg # of iterations = 3.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.291E-04 0.113E-04 total cpu time spent up to now is 426.91 secs total energy = -110.76847976 Ry Harris-Foulkes estimate = -110.76816527 Ry estimated scf accuracy < 0.00081655 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.36 Bohr mag/cell iteration # 13 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.10E-06, avg # of iterations = 4.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.196E-04 0.882E-05 total cpu time spent up to now is 460.93 secs total energy = -110.76864253 Ry Harris-Foulkes estimate = -110.76861049 Ry estimated scf accuracy < 0.00154877 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 14 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.10E-06, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.190E-04 0.871E-05 total cpu time spent up to now is 491.11 secs total energy = -110.76849957 Ry Harris-Foulkes estimate = -110.76866933 Ry estimated scf accuracy < 0.00155698 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 15 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.10E-06, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.195E-04 0.859E-05 total cpu time spent up to now is 521.20 secs total energy = -110.76839415 Ry Harris-Foulkes estimate = -110.76851544 Ry estimated scf accuracy < 0.00096979 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 16 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.10E-06, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.188E-04 0.843E-05 total cpu time spent up to now is 550.79 secs total energy = -110.76833616 Ry Harris-Foulkes estimate = -110.76841286 Ry estimated scf accuracy < 0.00049899 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 17 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.12E-06, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.178E-04 0.839E-05 total cpu time spent up to now is 580.48 secs total energy = -110.76828820 Ry Harris-Foulkes estimate = -110.76836918 Ry estimated scf accuracy < 0.00019878 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 18 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.24E-06, avg # of iterations = 3.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.178E-04 0.840E-05 total cpu time spent up to now is 612.76 secs total energy = -110.76835280 Ry Harris-Foulkes estimate = -110.76835365 Ry estimated scf accuracy < 0.00001154 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 19 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 7.21E-08, avg # of iterations = 4.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.180E-04 0.834E-05 total cpu time spent up to now is 649.06 secs total energy = -110.76835740 Ry Harris-Foulkes estimate = -110.76835747 Ry estimated scf accuracy < 0.00000888 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 20 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.55E-08, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.180E-04 0.834E-05 total cpu time spent up to now is 679.01 secs total energy = -110.76835253 Ry Harris-Foulkes estimate = -110.76835792 Ry estimated scf accuracy < 0.00001487 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 21 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.55E-08, avg # of iterations = 2.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.182E-04 0.836E-05 total cpu time spent up to now is 709.94 secs total energy = -110.76835486 Ry Harris-Foulkes estimate = -110.76835488 Ry estimated scf accuracy < 0.00000147 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 22 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.20E-09, avg # of iterations = 3.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.181E-04 0.835E-05 total cpu time spent up to now is 742.52 secs total energy = -110.76835534 Ry Harris-Foulkes estimate = -110.76835533 Ry estimated scf accuracy < 0.00000246 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 23 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.20E-09, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.181E-04 0.835E-05 total cpu time spent up to now is 771.98 secs total energy = -110.76835548 Ry Harris-Foulkes estimate = -110.76835536 Ry estimated scf accuracy < 0.00000228 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 24 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.20E-09, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.180E-04 0.833E-05 total cpu time spent up to now is 801.18 secs total energy = -110.76835486 Ry Harris-Foulkes estimate = -110.76835549 Ry estimated scf accuracy < 0.00000255 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 25 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.20E-09, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.183E-04 0.846E-05 total cpu time spent up to now is 830.58 secs total energy = -110.76835498 Ry Harris-Foulkes estimate = -110.76835488 Ry estimated scf accuracy < 0.00000283 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 26 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 9.20E-09, avg # of iterations = 2.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.184E-04 0.852E-05 total cpu time spent up to now is 860.31 secs total energy = -110.76835592 Ry Harris-Foulkes estimate = -110.76835515 Ry estimated scf accuracy < 0.00000084 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 27 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.27E-09, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.185E-04 0.856E-05 total cpu time spent up to now is 889.83 secs total energy = -110.76835661 Ry Harris-Foulkes estimate = -110.76835595 Ry estimated scf accuracy < 0.00000048 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 28 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 2.99E-09, avg # of iterations = 1.0 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.185E-04 0.855E-05 total cpu time spent up to now is 919.46 secs total energy = -110.76835660 Ry Harris-Foulkes estimate = -110.76835665 Ry estimated scf accuracy < 0.00000007 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 29 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 4.11E-10, avg # of iterations = 4.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.185E-04 0.855E-05 total cpu time spent up to now is 955.69 secs total energy = -110.76835665 Ry Harris-Foulkes estimate = -110.76835666 Ry estimated scf accuracy < 0.00000002 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 30 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.02E-10, avg # of iterations = 1.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.185E-04 0.855E-05 total cpu time spent up to now is 985.12 secs total energy = -110.76835607 Ry Harris-Foulkes estimate = -110.76835665 Ry estimated scf accuracy < 1.7E-09 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell iteration # 31 ecut= 100.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.07E-11, avg # of iterations = 3.5 RESET ns to initial values (iter <= mixing_fixed_ns) negative rho (up, down): 0.185E-04 0.854E-05 total cpu time spent up to now is 1017.31 secs End of self-consistent calculation enter write_ns U( 1) = 3.1000 alpha( 1) = 0.0000 atom 1 Tr[ns(na)]= 6.0000000 atom 1 spin 1 atom 1 spin 1 eigenvalues: 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 atom 1 spin 2 atom 1 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 atom 2 Tr[ns(na)]= 6.0000000 atom 2 spin 1 atom 2 spin 1 eigenvalues: 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.000 atom 2 spin 2 atom 2 spin 2 eigenvalues: 0.2000000 0.2000000 0.2000000 0.2000000 0.2000000 eigenvectors 1 1.0000000 0.0000000 0.0000000 0.0000000 0.0000000 2 0.0000000 1.0000000 0.0000000 0.0000000 0.0000000 3 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 4 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 5 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 occupations 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.000 0.000 0.200 nsum = 12.0000000 exit write_ns ------ SPIN UP ------------ k =-0.5000-0.5000-0.5000 ( 57016 PWs) bands (ev): -10.0760 -10.0740 -9.7015 -9.7015 -9.5993 -9.5988 -9.5653 -7.8718 -7.8718 -7.6834 -6.2804 -3.5958 -1.9534 -1.9534 0.0623 0.0624 0.3984 1.1291 ------ SPIN DOWN ---------- k =-0.5000-0.5000-0.5000 ( 57016 PWs) bands (ev): -5.6617 -4.2120 -4.2120 -3.8909 -3.3885 -3.3842 -2.8676 -2.8663 -2.4253 -2.1497 -2.1497 -1.5092 -1.2947 -1.2947 0.8395 0.8395 1.2374 1.3773 the Fermi energy is -3.4524 ev ! total energy = -110.76835644 Ry Harris-Foulkes estimate = -110.76835607 Ry estimated scf accuracy < 1.7E-10 Ry The total energy is the sum of the following terms: one-electron contribution = -202.05900853 Ry hartree contribution = 110.92762605 Ry xc contribution = -52.54131955 Ry ewald contribution = 32.72206894 Ry Hubbard energy = 0.18227665 Ry smearing contrib. (-TS) = 0.00000000 Ry total magnetization = 8.00 Bohr mag/cell absolute magnetization = 8.37 Bohr mag/cell convergence has been achieved in 31 iterations Forces acting on atoms (Ry/au): negative rho (up, down): 0.185E-04 0.854E-05 atom 1 type 1 force = 0.02076513 0.00000000 0.00000000 atom 2 type 1 force = -0.02076513 0.00000000 0.00000000 Total force = 0.029366 Total SCF correction = 0.000029 entering subroutine stress ... negative rho (up, down): 0.185E-04 0.854E-05 total stress (Ry/bohr**3) (kbar) P= 2009.64 0.01369711 0.00000000 0.00000000 2014.91 0.00 0.00 0.00000000 0.01364333 0.00000000 0.00 2007.00 0.00 0.00000000 0.00000000 0.01364333 0.00 0.00 2007.00 Writing output data file fe.save init_run : 17.82s CPU 18.29s WALL ( 1 calls) electrons : 972.07s CPU 998.95s WALL ( 1 calls) forces : 21.71s CPU 21.94s WALL ( 1 calls) stress : 74.52s CPU 76.48s WALL ( 1 calls) Called by init_run: wfcinit : 5.49s CPU 5.65s WALL ( 1 calls) potinit : 2.93s CPU 3.09s WALL ( 1 calls) Called by electrons: c_bands : 397.50s CPU 409.14s WALL ( 31 calls) sum_band : 246.60s CPU 250.62s WALL ( 31 calls) v_of_rho : 85.77s CPU 88.43s WALL ( 32 calls) newd : 226.99s CPU 228.45s WALL ( 32 calls) mix_rho : 20.42s CPU 20.79s WALL ( 31 calls) Called by c_bands: init_us_2 : 9.67s CPU 9.85s WALL ( 152 calls) cegterg : 381.24s CPU 390.16s WALL ( 62 calls) Called by *egterg: h_psi : 292.10s CPU 292.55s WALL ( 219 calls) s_psi : 25.75s CPU 25.80s WALL ( 241 calls) g_psi : 1.63s CPU 1.64s WALL ( 155 calls) cdiaghg : 0.19s CPU 0.20s WALL ( 217 calls) Called by h_psi: add_vuspsi : 21.46s CPU 21.47s WALL ( 219 calls) General routines calbec : 43.79s CPU 43.89s WALL ( 564 calls) cft3s : 258.88s CPU 259.64s WALL ( 7231 calls) davcio : 0.01s CPU 5.81s WALL ( 446 calls) Parallel routines PWSCF : 18m 6.46s CPU time, 18m36.32s WALL time This run was terminated on: 15:23:19 18Mar2011 =------------------------------------------------------------------------------= JOB DONE. =------------------------------------------------------------------------------= From ttduyle at gmail.com Tue Mar 29 19:44:22 2011 From: ttduyle at gmail.com (Duy Le) Date: Tue, 29 Mar 2011 13:44:22 -0400 Subject: [Pw_forum] Type of pseudo potential using input_dft Message-ID: Dear all, It is a naive question. As I understand, if we specify input_dft=PBESol, PBE, revpbe... the code will override value from provided potentials. So, could any one please explain for me what type of pseudo potential (ultrasolf, normconserving, or paw) used if we use input_dft? Thank you. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" From degironc at sissa.it Tue Mar 29 22:33:15 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 29 Mar 2011 22:33:15 +0200 Subject: [Pw_forum] Type of pseudo potential using input_dft In-Reply-To: References: Message-ID: <4D92420B.5010601@sissa.it> the variable input_dft overwrites the exchange and correlation functional used in the calculation. It does not change any other detail of the pseudopotential file. ncpp/uspp/paw describe how the pseudoatom mimic the orthogonality to the (removed) core electrons. This is feature is not modified by input_dft stefano On 03/29/2011 07:44 PM, Duy Le wrote: > Dear all, > It is a naive question. > As I understand, if we specify input_dft=PBESol, PBE, revpbe... the > code will override value from provided potentials. > So, could any one please explain for me what type of pseudo potential > (ultrasolf, normconserving, or paw) used if we use input_dft? > > Thank you. > > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From degironc at sissa.it Tue Mar 29 23:34:47 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 29 Mar 2011 23:34:47 +0200 Subject: [Pw_forum] Fixing starting starting_ns_eigenvalue In-Reply-To: References: Message-ID: <4D925077.7060201@sissa.it> I think this is a bug ... The initial value of ns should be overwritten by the input request... A simple way to obtain this should be to replace, in electrons.f90, the line IF ( first .AND. istep == 0 .AND. & starting_pot == 'atomic' ) CALL ns_adj() by IF ( first .AND. istep == 0 .AND. & starting_pot == 'atomic' ) CALL ns_adj() ; rhoin%ns = rho%ns I updated the cvs version. stefano On 03/29/2011 06:55 PM, Giovani Faccin wrote: > Dear Gabriele, > > Yes, I tried mixing_fixed_ns. The problem is that this command fixes the > initial occupation during all the run, not the occupation imposed on step 2 > with starting_ns eigenvalues. I'm attaching an example input and output file > that shows this happening. > > As you can see on the output.txt file, after iteraction 1 the program > inserts the eigenvalues I wanted on atom 1 spin2 and atom 2 spin2. However, > just after this it prints: > > > RESET ns to initial values (iter<= mixing_fixed_ns) > > on every new iteration. Looking at the end of the calculation, you can see > that the final states are exactly the default states from step 0. In other > words, it overwrites the eigenvalues defined by starting_ns eigenvalues, > placing the default initial occupations instead. Perhaps an "if" clause > could be added to the code to manage situations when both mixing_fixed_ns > and starting_ns eigenvalues are defined by the user? Or maybe I'm doing this > all wrong? > > Regards, > > Giovani Faccin > > IFGW/Unicamp-Brazil > > > > > > 2011/3/29 Gabriele Sclauzero > >> Dear Giovani, >> >> have you tried with mixing_fixed_ns? >> >> Could you please provide your affiliation? >> >> >> Regards, >> >> >> GS >> >> mixing_fixed_ns >> Il giorno 29/mar/2011, alle ore 18.16, Giovani Faccin ha scritto: >> >> Hi all! >> >> Is it possible, in a LDA+U calculation, to fix the starting_ns eigenvalues >> for the entire calculation run, instead of just the second interaction? >> >> Specifically, I'd like to be able to track how a certain electronic >> configuration's associated energy varies when other parameters (ex: atomic >> distances) change. But in order to do that, I need to be able to impose >> specific electronic configurations for the system, even if those >> configurations are not the global energy mininum. >> >> Can that be done in QE? >> >> Thanks! >> >> -- >> Giovani >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> * PH H2 462, Station 3, CH-1015 Lausanne* >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > _______________________________________________ > 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/20110329/b73fb217/attachment.htm From liweig at mtu.edu Tue Mar 29 23:39:35 2011 From: liweig at mtu.edu (Liwei Geng) Date: Tue, 29 Mar 2011 17:39:35 -0400 (EDT) Subject: [Pw_forum] Valence state identification for BaTiO3 In-Reply-To: <1770338512.7926911301434677006.JavaMail.root@zcs-mbs03.it.mtu.edu> Message-ID: <1154044121.7927431301434775929.JavaMail.root@zcs-mbs03.it.mtu.edu> Dear all, I use atom pseudopotential files to do the scf calculation, but I can't know their valence state. Could?you tell me how to identify the valence state of each ion in?BaTiO3 using QE? Say, how can I know that the Ba is Ba2+ or O is O2-? Thanks, Liwei -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110329/8d733b92/attachment.htm From nicola.marzari at materials.ox.ac.uk Wed Mar 30 00:01:17 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Tue, 29 Mar 2011 23:01:17 +0100 Subject: [Pw_forum] Valence state identification for BaTiO3 In-Reply-To: <1154044121.7927431301434775929.JavaMail.root@zcs-mbs03.it.mtu.edu> References: <1154044121.7927431301434775929.JavaMail.root@zcs-mbs03.it.mtu.edu> Message-ID: <4D9256AD.4070607@materials.ox.ac.uk> On 3/29/11 10:39 PM, Liwei Geng wrote: > Dear all, > > I use atom pseudopotential files to do the scf calculation, but I can't > know their valence state. Could you tell me how to identify the valence > state of each ion in BaTiO3 using QE? Say, how can I know that the Ba is > Ba2+ or O is O2-? > > Thanks, > > Liwei > The oxidation state is a phenomenological concept, and not well defined. The closest physical thing is the Born effective charge. The number of valence electrons for any pseudopotential is given by Z valence, in the header of that pseudopotential file. nicola -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From mayankaditya at gmail.com Wed Mar 30 06:38:46 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Wed, 30 Mar 2011 10:08:46 +0530 Subject: [Pw_forum] Pw_forum Digest, Vol 45, Issue 71 In-Reply-To: References: Message-ID: Thanks Prof. Eyvaz Isaev. Mayank From vinothrece at gmail.com Wed Mar 30 08:59:54 2011 From: vinothrece at gmail.com (vinoth r) Date: Wed, 30 Mar 2011 12:29:54 +0530 Subject: [Pw_forum] emaxpos Message-ID: dear friends i had one query related to how to use the parameters emaxpos,eopreg,eamp to get 1.4V,-2 saw like potential. with this mail i attached the parameter description.could you help me how to apply saw like potential with 1.4V ,-2V. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110330/596cfbf0/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: eamp.png Type: image/png Size: 45961 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110330/596cfbf0/attachment-0002.png -------------- next part -------------- A non-text attachment was scrubbed... Name: eopreg.png Type: image/png Size: 50305 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110330/596cfbf0/attachment-0003.png From balducci at univ.trieste.it Wed Mar 30 09:49:50 2011 From: balducci at univ.trieste.it (balducci at univ.trieste.it) Date: Wed, 30 Mar 2011 09:49:50 +0200 Subject: [Pw_forum] 4.3b@sp.sp6.cineca.it Message-ID: <19065.1301471414@dschgrazlin2.units.it> Hello, here is another one which makes the fortran compiler at cineca's sp6 scream: *** ./espresso-4.3b/upftools/casino_pp.f90.ORIG Wed Mar 30 08:34:41 2011 --- ./espresso-4.3b/upftools/casino_pp.f90 Wed Mar 30 08:34:41 2011 *************** *** 137,149 **** pptr => phead ALLOCATE( pptr%channel(mesh_) ) ! READ(iunps, '("r*potential (L=",I1,") in Ry")'), l pptr%lquant=l READ(iunps, *) (pptr%channel(ir),ir=1,mesh_) DO ! READ(iunps, '("r*potential (L=",I1,") in Ry")', IOSTAT=ios), l IF (ios /= 0 ) THEN EXIT --- 137,149 ---- pptr => phead ALLOCATE( pptr%channel(mesh_) ) ! READ(iunps, '("r*potential (L=",I1,") in Ry")') l pptr%lquant=l READ(iunps, *) (pptr%channel(ir),ir=1,mesh_) DO ! READ(iunps, '("r*potential (L=",I1,") in Ry")', IOSTAT=ios) l IF (ios /= 0 ) THEN EXIT I am using this compiler on sp.sp6.cineca.it: IBM XL Fortran for AIX, V13.1 (5724-X15) Version: 13.01.0000.0004 ciao gabriele -- Gabriele Balducci - Dipartimento di Scienze Chimiche - Via L. Giorgieri 1 I-34127 TRIESTE tel: I-040-5583957 fax: I-040-5583903 e-mail: balducci at units.it Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From giannozz at democritos.it Wed Mar 30 10:50:41 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 30 Mar 2011 10:50:41 +0200 Subject: [Pw_forum] 4.3b@sp.sp6.cineca.it In-Reply-To: <19065.1301471414@dschgrazlin2.units.it> References: <19065.1301471414@dschgrazlin2.units.it> Message-ID: On Mar 30, 2011, at 9:49 , balducci at univ.trieste.it wrote: > here is another one which makes the fortran compiler at cineca's sp6 > scream it's non-standard syntax that most compilers accept (but some don't). Fixed, thank you P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Mar 30 11:09:15 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 30 Mar 2011 11:09:15 +0200 Subject: [Pw_forum] I/O performance on BG/P systems In-Reply-To: <4090C379-5D47-4916-945B-428D1B32F501@sissa.it> References: <4D8C916B.8010800@sissa.it> <0F327142-3AB3-47B8-A6DA-723C9AFF135B@democritos.it> <4090C379-5D47-4916-945B-428D1B32F501@sissa.it> Message-ID: On Mar 29, 2011, at 9:49 , Gabriele Sclauzero wrote: > Are you referring to the wf_collect feature? yes > I've not been using that, so I was supposing that each process > writes independently its piece of wavefunctions (at least for PWscf), > am I right? you are > Do you think that this might be a symptom of a GPFS problem or > misconfiguration? not sure > I've tried to used disk_io='low' in some relax calculations, this > might > be a good compromise. as long as you have sufficient memory to keep wavefunctions into RAM, this is the best solution > However the code writes the wavefunctions only once at the end of > the run. > Wouldn't it be more reasonable to write them at the end of each > ionic step?gh > (just a personal opinion...) it is not always possible to listen to all opinions...this behavior is easy to change, though: look for io_level in PW/electrons.f90 P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From sclauzer at sissa.it Wed Mar 30 11:20:00 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 30 Mar 2011 11:20:00 +0200 Subject: [Pw_forum] I/O performance on BG/P systems In-Reply-To: References: <4D8C916B.8010800@sissa.it> <0F327142-3AB3-47B8-A6DA-723C9AFF135B@democritos.it> <4090C379-5D47-4916-945B-428D1B32F501@sissa.it> Message-ID: Il giorno 30/mar/2011, alle ore 11.09, Paolo Giannozzi ha scritto: >> However the code writes the wavefunctions only once at the end of >> the run. >> Wouldn't it be more reasonable to write them at the end of each >> ionic step?gh >> (just a personal opinion...) > > it is not always possible to listen to all opinions... Indeed, I agree... > this behavior > is easy to > change, though: look for io_level in PW/electrons.f90 Do you think that having an additional optional level of I/O (let's say that it might be called "medium") would be too confusing for users? I could try to implement and test it. Merci, GS > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110330/dbadfd3b/attachment.htm From izaakw89 at yahoo.com Wed Mar 30 17:53:36 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Wed, 30 Mar 2011 08:53:36 -0700 (PDT) Subject: [Pw_forum] Problem with pseudopotential In-Reply-To: References: Message-ID: <417071.3840.qm@web43403.mail.sp1.yahoo.com> First of all, thank you so much for your replies. One more question: in the pbedrrkjus plot, there are maxima at the location of each atomic layer whereas the pbevanak plot has minima. What would cause this? Is it a problem? Both the calculations were done using exactly the same parameters but different pseudopotentials. I get the following values for workfunctions. Cu.pbe-d-rrkjus.UPF ---> 3.956405463 eV Cu.pbe-n-van_ak.UPF ---> 4.042282570 eV Experimental value ---> 4.59 eV I know that DFT-GGA calculations can underestimate the workfunctions of metal surfaces, but are these acceptable values (almost a 14% error)? Thank you again for all your help. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110330/6319f69a/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: planar-average-pbedrrkjus.pdf Type: application/pdf Size: 8682 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110330/6319f69a/attachment-0002.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: pbedrrkjus.in Type: application/octet-stream Size: 741 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110330/6319f69a/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: planar-average-pbevanak.pdf Type: application/pdf Size: 8449 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110330/6319f69a/attachment-0003.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: pbevanak.in Type: application/octet-stream Size: 741 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110330/6319f69a/attachment-0003.obj From giannozz at democritos.it Wed Mar 30 18:57:43 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 30 Mar 2011 18:57:43 +0200 Subject: [Pw_forum] I/O performance on BG/P systems In-Reply-To: References: <4D8C916B.8010800@sissa.it> <0F327142-3AB3-47B8-A6DA-723C9AFF135B@democritos.it> <4090C379-5D47-4916-945B-428D1B32F501@sissa.it> Message-ID: On Mar 30, 2011, at 11:20 , Gabriele Sclauzero wrote: > Do you think that having an additional optional level of I/O > (let's say that it might be called "medium") I propose 'rare', 'medium', 'well done' > would be too confusing for users? some users get confused no matter what > I could try to implement and test it. ok: just follow the "io_level" variable. Try first to understand what the actual behavior is (the documentation is not so clear on this point) and then think what it should be, if you have some clear ideas P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From leommj at usp.br Wed Mar 30 22:08:26 2011 From: leommj at usp.br (Leonardo Matheus) Date: Wed, 30 Mar 2011 17:08:26 -0300 Subject: [Pw_forum] Problem with newly implemented LDA -1/2 in atomic code (ld1) In-Reply-To: References: <4D91F93F.2000903@materials.ox.ac.uk> Message-ID: Hi, I'm Leonardo M M Jorge, the one who put the LDA-1/2 method on QE. And yes, it is working! You indeed have to create a new pseudopotential with ld1.x and the flag "iswitch=4" (among other options, shown in the example file atomic_doc/pseudo-LDA-0.5/si.lda.0.5.in ), and then use it on a standard LDA calculation. You obtained results very similar to standard LDA because one of these other options is not well set. When generating the pseudo, besides the electronic configuration used (of a half-ionized atom, hence the name -0.5 ), there is also another parameter needed: rcutv, which is the radius where you cut the perturbation. The value set on the example file (1.0) is too small; for Silicon these values should be somewhere around 3.6. To obtain the right value for this rcutv parameter you need to do several calculations, changing it by small steps, and then get the rcutv where the gap of the system is an extremum (maximum or minimum). The explanation why this works is written on the reference you just cited ( L. G. Ferreira, M. Marques and L. K. Teles, Phys. Rev. B 78 125116 (2008) ), but what's important is that it IS NOT a free parameter (one you keep changing until you get the result you want), as there is a procedure to obtain it. Also, as small variations of the rcutv parameters should give very small variations of the Electronic Gap (as it is an extremum for variations), we assume that you can obtain the right rcutv value for a small and simple system, and then use it on a bigger and more complex system (for a given atom; different atom kinds have different rcutv!). I hope I could explain the method for you, if you have any more questions feel free to write me. Leonardo Jorge PhD Student Universidade de S?o Paulo - Brazil From nicola.marzari at materials.ox.ac.uk Wed Mar 30 23:29:08 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 30 Mar 2011 22:29:08 +0100 Subject: [Pw_forum] Problem with pseudopotential In-Reply-To: <417071.3840.qm@web43403.mail.sp1.yahoo.com> References: <417071.3840.qm@web43403.mail.sp1.yahoo.com> Message-ID: <4D93A0A4.6020508@materials.ox.ac.uk> Dear Izaak, it seems that in Cu.pbe-d-rrkjus.UPF the average electrostatic potential inside the slab (i.e. the average over one layer of the planar average) would be higher than the vacuum level, so on electrostatic considerations a test charge would want to run away. So, I'm very baffled. Any one else has some suggestion? The two input files do look identical. The fermi energy that you print is the one given by the slab calculation (not really a good choice, unless you have a thick slab) or is given by calculating in bulk cu the position of the fermi energy with respect to the layer-average of the planar avarage, and then using that info in the slab calculation to position the fermi energy of the bulk, and obtain the work function? Last - a 14% is the last of the worries - LDA and GGA seem to be all over the place (have a look at the paper I had cited). nicola On 3/30/11 4:53 PM, Izaak Williamson wrote: > First of all, thank you so much for your replies. > > One more question: in the pbedrrkjus plot, there are maxima at the > location of each atomic layer whereas the pbevanak plot has minima. What > would cause this? Is it a problem? > > > Both the calculations were done using exactly the same parameters but > different pseudopotentials. I get the following values for workfunctions. > Cu.pbe-d-rrkjus.UPF ---> 3.956405463 eV > Cu.pbe-n-van_ak.UPF ---> 4.042282570 eV > Experimental value ---> 4.59 eV > > I know that DFT-GGA calculations can underestimate the workfunctions of > metal surfaces, but are these acceptable values (almost a 14% error)? > > Thank you again for all your help. > > > -- > Izaak Williamson > Research Assistant > Physics Department > Boise State University -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From zdw2000 at gmail.com Thu Mar 31 09:37:55 2011 From: zdw2000 at gmail.com (Wei Zhou) Date: Wed, 30 Mar 2011 23:37:55 -0800 Subject: [Pw_forum] about the degaussq in the calcualtion of phonon coupling Message-ID: Dear users; I rencently do some calculations about the electron-phonon calculation using pwscf. however,I feel puzzled about the input file of lamdba.x, I want to know how to choose the degaussq in the input file of lambda.x, and I found in my case, I only can let the lambda equal int alpha2F by using a very larger degaussq, larger than 1, I also have read the program of lambda.f90, found it is a gauss broadeding when sum the q. it is reasonable to use a degaussq larger than1? does anything wrong with me? any help will be apprecialted -- ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com From degironc at sissa.it Thu Mar 31 09:54:33 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 31 Mar 2011 09:54:33 +0200 Subject: [Pw_forum] Problem with pseudopotential In-Reply-To: <4D93A0A4.6020508@materials.ox.ac.uk> References: <417071.3840.qm@web43403.mail.sp1.yahoo.com> <4D93A0A4.6020508@materials.ox.ac.uk> Message-ID: <20110331095433.3e9bux89c8o44kks@webmail.sissa.it> Dear Izaak, The local part of the potential might be compensated by the non-local one .. Actually, in order to avoid ghost-states, I think that the local part is made as repulsive as possible at the atomic sites while the non-local part should add an attractive contribution. So maybe what you see is only one part of the picture because you are missing the non local terms. Having said that I don't know if this is actually the case in your system. If you plot the average charge density does it look reasonable or do you see it spilling out of the slab ? stefano Quoting Nicola Marzari : > > > Dear Izaak, > > > it seems that in Cu.pbe-d-rrkjus.UPF the average electrostatic potential > inside the slab (i.e. the average over one layer of the planar average) > would be higher than the vacuum level, so on electrostatic > considerations a test charge would want to run away. So, I'm very > baffled. Any one else has some suggestion? The two input files do look > identical. > > The fermi energy that you print is the one given by the slab calculation > (not really a good choice, unless you have a thick slab) > or is given by calculating in bulk cu the position of the fermi energy > with respect to the layer-average of the planar avarage, and then using > that info in the slab calculation to position the fermi energy of the > bulk, and obtain the work function? > > Last - a 14% is the last of the worries - LDA and GGA seem to be all > over the place (have a look at the paper I had cited). > > nicola > > > > On 3/30/11 4:53 PM, Izaak Williamson wrote: >> First of all, thank you so much for your replies. >> >> One more question: in the pbedrrkjus plot, there are maxima at the >> location of each atomic layer whereas the pbevanak plot has minima. What >> would cause this? Is it a problem? >> >> >> Both the calculations were done using exactly the same parameters but >> different pseudopotentials. I get the following values for workfunctions. >> Cu.pbe-d-rrkjus.UPF ---> 3.956405463 eV >> Cu.pbe-n-van_ak.UPF ---> 4.042282570 eV >> Experimental value ---> 4.59 eV >> >> I know that DFT-GGA calculations can underestimate the workfunctions of >> metal surfaces, but are these acceptable values (almost a 14% error)? >> >> Thank you again for all your help. >> >> >> -- >> Izaak Williamson >> Research Assistant >> Physics Department >> Boise State University > > > -- > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From eyvaz_isaev at yahoo.com Thu Mar 31 11:41:18 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 31 Mar 2011 02:41:18 -0700 (PDT) Subject: [Pw_forum] about the degaussq in the calcualtion of phonon coupling In-Reply-To: References: Message-ID: <707753.75511.qm@web65705.mail.ac4.yahoo.com> Dear Wei, As I noticed before, you do not need such kind HUGE degaussq. I always used ~0.1 and never had a problem. I have a question: how did you find q-points weight? Wrong weighting may affect your result. Best regards, Eyvaz ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ----- Original Message ---- From: Wei Zhou To: PWSCF Forum Sent: Thu, March 31, 2011 9:37:55 AM Subject: [Pw_forum] about the degaussq in the calcualtion of phonon coupling Dear users; I rencently do some calculations about the electron-phonon calculation using pwscf. however,I feel puzzled about the input file of lamdba.x, I want to know how to choose the degaussq in the input file of lambda.x, and I found in my case, I only can let the lambda equal int alpha2F by using a very larger degaussq, larger than 1, I also have read the program of lambda.f90, found it is a gauss broadeding when sum the q. it is reasonable to use a degaussq larger than1? does anything wrong with me? any help will be apprecialted -- ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From nkxirainbow at gmail.com Thu Mar 31 12:27:35 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 31 Mar 2011 18:27:35 +0800 Subject: [Pw_forum] Calculational equation of PDOS Message-ID: Dear all: I want to know the calculational equation of partial density of state(PDOS) in QE. I could not find the equation on any paper. I think it may be: \int_0^{Rcut} \Psi(\vec r)*R_n(r)*Y_{lm}(\theta,\phi)*r^2 dr d\theta d\phi. where the Psi(\vec r) is the KS wave function of solid. Y_{lm}(\theta,\phi) is the spherical harmonics. R_n(r) is the the radial wave function of a isolated atom. If I was right, what is the formation of R_n(r)? Thanks in advance:) -- ____________________________________ Hui Wang School of physics, Fudan University, Shanghai, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110331/0eb29963/attachment.htm From sclauzer at sissa.it Thu Mar 31 13:58:16 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 31 Mar 2011 13:58:16 +0200 Subject: [Pw_forum] Calculational equation of PDOS In-Reply-To: References: Message-ID: <2303D1A5-9350-4A9E-AB39-75C7D7D19A4D@sissa.it> Dear Wang, I remember that I put down a formula for that in my PhD thesis (http://www.sissa.it/cm/thesis/2010/SclauzeroG_PhDthesis.pdf), if this may help you (see eq. 2.74 at page 58). I'm sure you could find it in many other places, though. I believe there's no such thing as the Rcut you write in your formula below. As you say, the atomic wavefunctions are built from the radial part R_nl(r), which is taken from the pseudopotential file, and the spherical harmonics. However you should not forget that there is also structure factor which comes from the translation of the nucleus from the origin. The integral is done in reciprocal space for each k-point, hence a k-dependence is added to the atomic wavefunction when transforming it to the G-basis (have a look in PW/atomic_wfc.f90). The following paper might also be useful to you: Solid State Communications, Vol. 95, No. 10, pp. 685-690, 1995 HTH GS Il giorno 31/mar/2011, alle ore 12.27, xirainbow ha scritto: > Dear all: > I want to know the calculational equation of partial density of state(PDOS) in QE. > I could not find the equation on any paper. I think it may be: > \int_0^{Rcut} \Psi(\vec r)*R_n(r)*Y_{lm}(\theta,\phi)*r^2 dr d\theta d\phi. > where the Psi(\vec r) is the KS wave function of solid. Y_{lm}(\theta,\phi) is the spherical harmonics. R_n(r) is the the radial wave function of a isolated atom. > If I was right, what is the formation of R_n(r)? > > Thanks in advance:) > > -- > ____________________________________ > Hui Wang > School of physics, Fudan University, Shanghai, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110331/9d8ab4e6/attachment.htm From zdw2000 at gmail.com Thu Mar 31 15:11:56 2011 From: zdw2000 at gmail.com (Wei Zhou) Date: Thu, 31 Mar 2011 21:11:56 +0800 Subject: [Pw_forum] about the degaussq in the calcualtion of phonon coupling In-Reply-To: <707753.75511.qm@web65705.mail.ac4.yahoo.com> References: <707753.75511.qm@web65705.mail.ac4.yahoo.com> Message-ID: thank you for you replies. In fact I believe must choose a degaussq so that the?lambda? euqal the "int alpha2F" in the output file afer executing the lamdba.x, but I found if meet this condition, the gaussq must larger than 1. if I was wrong, then how to choose the value of degaussq. the samll q-points weight are come from a scf calculation results. is there anything wrong with me? SCF INPUT FILE . ../environment/environment_opt rm $TMP_DIR/* cat > ba.scf.in<< EOF &control calculation='scf' restart_mode='from_scratch', prefix='ba', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 4 celldm(1) =7.21969953 celldm(3) =1.511267317 nat = 2 ntyp = 1 ecutwfc =50, ecutrho=350 occupations='smearing', smearing='methfessel-paxton', degauss=0.022 / &electrons conv_thr = 1.0d-8 mixing_beta= 0.7 / ATOMIC_SPECIES Ba 137.327 Ba.ncpp ATOMIC_POSITIONS {crystal} Ba 0.333333330 0.666666000 0.250000000 Ba 0.666666660 0.333333000 0.750000000 K_POINTS {automatic} 7 7 4 0 0 0 EOF $PARA_PREFIX $PW_ROOT/pw.x $PARA_POSTFIX < ba.scf.in>ba.scf.out OUT SMALL-QPOINTS number of k points= 24 gaussian broad. (Ry)= 0.0220 ngauss = 1 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0102041 k( 2) = ( 0.0000000 0.0000000 0.1654241), wk = 0.0204082 k( 3) = ( 0.0000000 0.0000000 -0.3308482), wk = 0.0102041 k( 4) = ( 0.0000000 0.1649572 0.0000000), wk = 0.0612245 k( 5) = ( 0.0000000 0.1649572 0.1654241), wk = 0.1224490 k( 6) = ( 0.0000000 0.1649572 -0.3308482), wk = 0.0612245 k( 7) = ( 0.0000000 0.3299144 0.0000000), wk = 0.0612245 k( 8) = ( 0.0000000 0.3299144 0.1654241), wk = 0.1224490 k( 9) = ( 0.0000000 0.3299144 -0.3308482), wk = 0.0612245 k( 10) = ( 0.0000000 0.4948717 0.0000000), wk = 0.0612245 k( 11) = ( 0.0000000 0.4948717 0.1654241), wk = 0.1224490 k( 12) = ( 0.0000000 0.4948717 -0.3308482), wk = 0.0612245 k( 13) = ( 0.1428571 0.2474358 0.0000000), wk = 0.0612245 k( 14) = ( 0.1428571 0.2474358 0.1654241), wk = 0.1224490 k( 15) = ( 0.1428571 0.2474358 -0.3308482), wk = 0.0612245 k( 16) = ( 0.1428571 0.4123930 0.0000000), wk = 0.1224490 k( 17) = ( 0.1428571 0.4123930 0.1654241), wk = 0.2448980 k( 18) = ( 0.1428571 0.4123930 -0.3308482), wk = 0.1224490 k( 19) = ( 0.1428571 0.5773503 0.0000000), wk = 0.0612245 k( 20) = ( 0.1428571 0.5773503 0.1654241), wk = 0.1224490 k( 21) = ( 0.1428571 0.5773503 -0.3308482), wk = 0.0612245 k( 22) = ( 0.2857143 0.4948717 0.0000000), wk = 0.0612245 k( 23) = ( 0.2857143 0.4948717 0.1654241), wk = 0.1224490 k( 24) = ( 0.2857143 0.4948717 -0.3308482), wk = 0.0612245 2011/3/31, Eyvaz Isaev : > Dear Wei, > > As I noticed before, you do not need such kind HUGE degaussq. > I always used ~0.1 and never had a problem. > > I have a question: how did you find q-points weight? > Wrong weighting may affect your result. > > Best regards, > Eyvaz > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > ----- Original Message ---- > From: Wei Zhou > To: PWSCF Forum > Sent: Thu, March 31, 2011 9:37:55 AM > Subject: [Pw_forum] about the degaussq in the calcualtion of phonon coupling > > Dear users; > I rencently do some calculations about the electron-phonon > calculation using pwscf. however,I feel puzzled about the input file > of lamdba.x, I want to know how to choose the degaussq in the input > file of lambda.x, and I found in my case, I only can let the lambda > equal int alpha2F by using a very larger degaussq, larger than 1, I > also have read the program of lambda.f90, found it is a gauss > broadeding when sum the q. it is reasonable to use a degaussq larger > than1? does anything wrong with me? > any help will be apprecialted > -- > ZhouDawei > JiLin Universiyt ,ChangChun ,China > zdw2000 at gmail.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 > -- ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com From rajanpandey at gmail.com Thu Mar 31 20:48:06 2011 From: rajanpandey at gmail.com (Rajan Pandey) Date: Fri, 1 Apr 2011 00:18:06 +0530 Subject: [Pw_forum] Problem with newly implemented LDA -1/2 in atomic code (ld1) In-Reply-To: References: <4D91F93F.2000903@materials.ox.ac.uk> Message-ID: Hi Leonardo, Thanks a lot for the detailed description of LDA-1/2 in the atomic code. I appreciate it. Indeed, with CUT value of 3.67, I got the correct band-gap of Si. I went through one iteration of the paper, and I understand that the parameter CUT has to chosen such that it optimizes the excitation energy. However, It seems that there is no general rule for specifying the fraction of electronic charge to be removed from the valence electronic configuration. For group IV element it is 0.25 (C is), on the other hand for II-VI or III-V compound it is 0.5 for anion p or cation d. What about the transition metal with incomplete d orbital (for example Ti, Zr, V, Cr, Mn)? The only transition metal which was discussed in the paper is Zn, which has completely filled d orbital. Also, what about the fractional charge to be removed from the valence of f-block elements? Thank you, and best regards, Rajan On Thu, Mar 31, 2011 at 1:38 AM, Leonardo Matheus wrote: > Hi, > > I'm Leonardo M M Jorge, the one who put the LDA-1/2 method on QE. And > yes, it is working! > > You indeed have to create a new pseudopotential with ld1.x and the > flag "iswitch=4" (among other options, shown in the example file > atomic_doc/pseudo-LDA-0.5/si.lda.0.5.in ), and then use it on a > standard LDA calculation. > > You obtained results very similar to standard LDA because one of these > other options is not well set. When generating the pseudo, besides the > electronic configuration used (of a half-ionized atom, hence the name > -0.5 ), there is also another parameter needed: rcutv, which is the > radius where you cut the perturbation. The value set on the example > file (1.0) is too small; for Silicon these values should be somewhere > around 3.6. > > To obtain the right value for this rcutv parameter you need to do > several calculations, changing it by small steps, and then get the > rcutv where the gap of the system is an extremum (maximum or minimum). > The explanation why this works is written on the reference you just > cited ( L. G. Ferreira, M. Marques and L. K. Teles, Phys. Rev. B 78 > 125116 (2008) ), but what's important is that it IS NOT a free > parameter (one you keep changing until you get the result you want), > as there is a procedure to obtain it. > > Also, as small variations of the rcutv parameters should give very > small variations of the Electronic Gap (as it is an extremum for > variations), we assume that you can obtain the right rcutv value for a > small and simple system, and then use it on a bigger and more complex > system (for a given atom; different atom kinds have different rcutv!). > > I hope I could explain the method for you, if you have any more > questions feel free to write me. > > Leonardo Jorge > PhD Student > Universidade de S?o Paulo - Brazil > _______________________________________________ > 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/20110401/141f1488/attachment-0001.htm From izaakw89 at yahoo.com Thu Mar 31 23:26:48 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Thu, 31 Mar 2011 14:26:48 -0700 (PDT) Subject: [Pw_forum] Problem with pseudopotential Message-ID: <562843.64501.qm@web43413.mail.sp1.yahoo.com> Dear Stefano, I plotted the average charge and it seems reasonable to me for both the pseudopotentials. I am attaching both plots, it would be nice to get your input. Thank you. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110331/10fa4216/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: chdens-pbedrrkjus.pdf Type: application/pdf Size: 12023 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110331/10fa4216/attachment-0002.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: chdens-pbevanak.pdf Type: application/pdf Size: 12070 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110331/10fa4216/attachment-0003.pdf From izaakw89 at yahoo.com Thu Mar 31 23:46:51 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Thu, 31 Mar 2011 14:46:51 -0700 (PDT) Subject: [Pw_forum] Work function for Al100 in example files Message-ID: <398502.47742.qm@web43412.mail.sp1.yahoo.com> Dear all, I was looking at the example of the work function calculation for Al100 and noticed that the following celldm(1) and kpoints are used: For slab ---> celldm(1)= 5.4235090117, kpoints=3x3x1 For bulk ---> celldm(1)= 7.67000000, kpoints=3x3x3 With these values, one gets work functions of Wf1=4.15219 eV and Wf2=4.54641 eV. Since, celldm(1) for slab calculation is smaller than celldm(1) for bulk, shouldn't we use a higher k-mesh for the slab calculation? Is this correct? When I use a kmesh of 4x4x1, I get very different values of work functions: Wf1=4.0412 eV Wf2=3.82069 eV Does this make sense? Thank you. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110331/7c1f09cf/attachment.htm