From kyin.cn at gmail.com Mon Nov 1 04:01:46 2010 From: kyin.cn at gmail.com (Kun Yin) Date: Mon, 1 Nov 2010 11:01:46 +0800 Subject: [Pw_forum] set_irr error during phonon calculation Message-ID: Dear Users, I did two similar phonon runs after a same scf calculation. The only difference between the two phonon calculations is the dimension of q-point mesh. nq1=2,nq2=2,nq3=2 (in 1st ph.x run) nq1=2,nq2=2,nq3=1 (in 2nd ph.x run) The first calculation was successful to finish, while the second one met the following error and stopped. from set_irr: error# 2 npert > 6 This problem seems different from someone have asked before which could be solved by increasing max_irr_dim value in phcom.f90 file. Actually I didn't find max_irr_dim in this file in QE version 4.2 which I used. Any suggestions or help will be appreciated. Kun Yin Nanjing University,China Input of scf run: &CONTROL calculation = 'scf', outdir = '/state/partition1/kyin', prefix = 'qe', pseudo_dir = '/share/apps/qe_pseudo', restart_mode = 'from_scratch', title = 'qe', verbosity = 'high', / &SYSTEM celldm(1) = 1, ecutrho = 400, ecutwfc = 40, ibrav = 0, nat = 20, ntyp = 3, nr1=60,nr2=60,nr3=90 / &ELECTRONS conv_thr = 1.0d-9, mixing_mode = 'plain', / ATOMIC_SPECIES Mg 24.305 Mg.pw91-np-van.UPF Si 28.0855 Si.pw91-n-van.UPF O 15.9994 O.pw91-van_ak.UPF K_POINTS automatic 4 4 2 0 0 0 CELL_PARAMETERS (alat= 1.00000000) 7.646348501 0.000000000 0.000000000 0.000000000 8.393090445 0.000000000 0.000000000 0.000000000 11.365238746 ATOMIC_POSITIONS (crystal) Mg 0.533728470 0.589922896 0.250000000 Mg 0.466271530 0.410077104 0.750000000 Mg 0.033728470 0.910077104 0.750000000 Mg 0.966271530 0.089922896 0.250000000 Si 0.500000000 0.000000000 0.500000000 Si 0.500000000 0.000000000 0.000000000 Si 0.000000000 0.500000000 0.500000000 Si 0.000000000 0.500000000 0.000000000 O 0.125931013 0.465888786 0.250000000 O 0.874068987 0.534111214 0.750000000 O 0.625931013 0.034111214 0.750000000 O 0.374068987 0.965888786 0.250000000 O 0.171733094 0.187375245 0.559982148 O 0.828266906 0.812624755 0.440017852 O 0.828266906 0.812624755 0.059982148 O 0.171733094 0.187375245 0.940017852 O 0.671733094 0.312624755 0.440017852 O 0.328266906 0.687375245 0.559982148 O 0.328266906 0.687375245 0.940017852 O 0.671733094 0.312624755 0.059982148 Input of phonon run: Phonons &inputph amass(1)=24.3050, amass(2)=28.0855, amass(3)=15.9994, prefix='qe', outdir='/state/partition1/kyin' fildyn='qe.dyn', tr2_ph=1.0d-14, ldisp=.true. nq1=2,nq2=2,nq3=2 / From 1009ukumar at gmail.com Mon Nov 1 06:54:50 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Mon, 1 Nov 2010 11:24:50 +0530 Subject: [Pw_forum] odd # of electrons in primitive cell => metal ? Message-ID: Dear all QE users, My primitive unit cell contains odd # of electrons so it should be metallic. QE code indicates the system to be metallic. But experimentally it is an insulator with band gap ~1.2 eV. why am i not able to get the insulating nature of the system? IS there something wrong in the input file? or in DFT? ################################################################### PARTs OF input n output file are: &control calculation='scf', ! relax,scf,vc-relax verbosity='high', restart_mode='from_scratch', ! 'from_scratch', prefix='CuFeO2', !wf_collect=.true., tstress=.true., tprnfor=.true., etot_conv_thr=1.0D-6, forc_conv_thr=1.0D-5, pseudo_dir = './pseudo', outdir='./tmp', / &system ibrav=5,celldm(1)=11.31, celldm(4)=0.8718, nat= 4, ntyp= 3, !nbnd=24, ecutwfc=40, ecutrho=400, !occupations = 'smearing', !degauss = 0.005D0, !smearing='gaussian', nspin=1, / &electrons electron_maxstep=100, mixing_mode='local-TF', mixing_beta = 0.2, conv_thr = 1.0d-12, mixing_ndim=8, diagonalization='cg', / ATOMIC_SPECIES Cu 0.0 Cu.pbe-n-van_ak.UPF Fe 0.0 Fe.pbe-sp-van.UPF O 0.0 O.pbe-rrkjus.UPF ..... .... !!!!!!!!!!!!!!!!!!!!!! Part of ouput file !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from electrons : error # 1 stopping ... charge is wrong: smearing is needed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ##################################################################### With Kind regards, 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/20101101/b4d2b8f8/attachment.htm From prasenjit.jnc at gmail.com Mon Nov 1 08:03:52 2010 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Mon, 1 Nov 2010 12:33:52 +0530 Subject: [Pw_forum] odd # of electrons in primitive cell => metal ? In-Reply-To: References: Message-ID: Dear Sonu, QE is not predicting anything at all.....at least for the input you have given. The code is stopping with the error message. If your system has odd no. of electrons, you should do a spin polarized calculation with some smearing You should uncomment the following lines in your input files ??? occupations = 'smearing', ??? degauss = 0.005D0, ??? smearing='gaussian', ??? nspin=2, As for the question whether the calculations will predict your system to be metallic or not depends on other factors, like you should test the pseudopotentials you are increasing.......moreover in DFT usually band gaps are notoriously underestimated.....so you may not get close to the experimental value....however it should in principle predict the correct trends With regards, Prasenjit -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From barfi.koa at gmail.com Mon Nov 1 10:25:26 2010 From: barfi.koa at gmail.com (B. Koa) Date: Mon, 1 Nov 2010 12:55:26 +0330 Subject: [Pw_forum] GDIS Message-ID: This is the link : http://www.pwscf.org/tools.php , and GDIS is one of the recommended visualization softwares. Dear QE Users > > I can not visualize input and output files of QE by GDIS which has been > introduced in the TOOLS. Is there any trick ? or is it only useful to > visualize some specific properties ? Many Thanks > > > -- > B. Koa > NIT > > > Dear B. Koa > what is GDIS and what is TOOLS ? > Stefano de Gironcoli - SISSA and DEMOCRITOS > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101101/7d906d91/attachment.htm From eyvaz_isaev at yahoo.com Mon Nov 1 11:47:50 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 1 Nov 2010 03:47:50 -0700 (PDT) Subject: [Pw_forum] set_irr error during phonon calculation In-Reply-To: References: Message-ID: <631331.74231.qm@web65715.mail.ac4.yahoo.com> Hi, So, you got two different set of q-points with different symmetry. In fact, this is very famous error and you should find the solution if search QE forum archive). Just have a look at set_irr.f90, find line with "npert > 6" (line 192 in QE 4.2) and then take more neprt (number of irreducible presentations). Do not forget recompile the phonon code. 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: Kun Yin To: pw_forum at pwscf.org Sent: Mon, November 1, 2010 4:01:46 AM Subject: [Pw_forum] set_irr error during phonon calculation Dear Users, I did two similar phonon runs after a same scf calculation. The only difference between the two phonon calculations is the dimension of q-point mesh. nq1=2,nq2=2,nq3=2 (in 1st ph.x run) nq1=2,nq2=2,nq3=1 (in 2nd ph.x run) The first calculation was successful to finish, while the second one met the following error and stopped. from set_irr: error# 2 npert > 6 This problem seems different from someone have asked before which could be solved by increasing max_irr_dim value in phcom.f90 file. Actually I didn't find max_irr_dim in this file in QE version 4.2 which I used. Any suggestions or help will be appreciated. Kun Yin Nanjing University,China Input of scf run: &CONTROL calculation = 'scf', outdir = '/state/partition1/kyin', prefix = 'qe', pseudo_dir = '/share/apps/qe_pseudo', restart_mode = 'from_scratch', title = 'qe', verbosity = 'high', / &SYSTEM celldm(1) = 1, ecutrho = 400, ecutwfc = 40, ibrav = 0, nat = 20, ntyp = 3, nr1=60,nr2=60,nr3=90 / &ELECTRONS conv_thr = 1.0d-9, mixing_mode = 'plain', / ATOMIC_SPECIES Mg 24.305 Mg.pw91-np-van.UPF Si 28.0855 Si.pw91-n-van.UPF O 15.9994 O.pw91-van_ak.UPF K_POINTS automatic 4 4 2 0 0 0 CELL_PARAMETERS (alat= 1.00000000) 7.646348501 0.000000000 0.000000000 0.000000000 8.393090445 0.000000000 0.000000000 0.000000000 11.365238746 ATOMIC_POSITIONS (crystal) Mg 0.533728470 0.589922896 0.250000000 Mg 0.466271530 0.410077104 0.750000000 Mg 0.033728470 0.910077104 0.750000000 Mg 0.966271530 0.089922896 0.250000000 Si 0.500000000 0.000000000 0.500000000 Si 0.500000000 0.000000000 0.000000000 Si 0.000000000 0.500000000 0.500000000 Si 0.000000000 0.500000000 0.000000000 O 0.125931013 0.465888786 0.250000000 O 0.874068987 0.534111214 0.750000000 O 0.625931013 0.034111214 0.750000000 O 0.374068987 0.965888786 0.250000000 O 0.171733094 0.187375245 0.559982148 O 0.828266906 0.812624755 0.440017852 O 0.828266906 0.812624755 0.059982148 O 0.171733094 0.187375245 0.940017852 O 0.671733094 0.312624755 0.440017852 O 0.328266906 0.687375245 0.559982148 O 0.328266906 0.687375245 0.940017852 O 0.671733094 0.312624755 0.059982148 Input of phonon run: Phonons &inputph amass(1)=24.3050, amass(2)=28.0855, amass(3)=15.9994, prefix='qe', outdir='/state/partition1/kyin' fildyn='qe.dyn', tr2_ph=1.0d-14, ldisp=.true. nq1=2,nq2=2,nq3=2 / _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Mon Nov 1 12:08:58 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 1 Nov 2010 04:08:58 -0700 (PDT) Subject: [Pw_forum] odd # of electrons in primitive cell => metal ? In-Reply-To: References: Message-ID: <551692.37103.qm@web65714.mail.ac4.yahoo.com> Hi, As you have an oxide it is not so surprising. As an example I remember B1 NiO or FeO. You should apply, at least, LDA+U to get more correct bands (see /examples/example25). Yamboo or GW+Wannier might be another tools to fix the problem. 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: sonu kumar <1009ukumar at gmail.com> To: pw_forum at pwscf.org Sent: Mon, November 1, 2010 6:54:50 AM Subject: [Pw_forum] odd # of electrons in primitive cell => metal ? Dear all QE users, My primitive unit cell contains odd # of electrons so it should be metallic. QE code indicates the system to be metallic. But experimentally it is an insulator with band gap ~1.2 eV. why am i not able to get the insulating nature of the system? IS there something wrong in the input file? or in DFT? ################################################################### PARTs OF input n output file are: &control calculation='scf', ! relax,scf,vc-relax verbosity='high', restart_mode='from_scratch', ! 'from_scratch', prefix='CuFeO2', !wf_collect=.true., tstress=.true., tprnfor=.true., etot_conv_thr=1.0D-6, forc_conv_thr=1.0D-5, pseudo_dir = './pseudo', outdir='./tmp', / &system ibrav=5,celldm(1)=11.31, celldm(4)=0.8718, nat= 4, ntyp= 3, !nbnd=24, ecutwfc=40, ecutrho=400, !occupations = 'smearing', !degauss = 0.005D0, !smearing='gaussian', nspin=1, / &electrons electron_maxstep=100, mixing_mode='local-TF', mixing_beta = 0.2, conv_thr = 1.0d-12, mixing_ndim=8, diagonalization='cg', / ATOMIC_SPECIES Cu 0.0 Cu.pbe-n-van_ak.UPF Fe 0.0 Fe.pbe-sp-van.UPF O 0.0 O.pbe-rrkjus.UPF ..... .... !!!!!!!!!!!!!!!!!!!!!! Part of ouput file !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from electrons : error # 1 stopping ... charge is wrong: smearing is needed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ##################################################################### With Kind regards, 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/20101101/d7fcffb6/attachment.htm From kyin.cn at gmail.com Mon Nov 1 12:35:30 2010 From: kyin.cn at gmail.com (Kun Yin) Date: Mon, 1 Nov 2010 19:35:30 +0800 Subject: [Pw_forum] set_irr error during phonon calculation In-Reply-To: <631331.74231.qm@web65715.mail.ac4.yahoo.com> References: <631331.74231.qm@web65715.mail.ac4.yahoo.com> Message-ID: Hi, Eyvaz I have modified "npert > 6" to "> 9" in set_irr.f90 file and recompiled the ph.x program. The calculation runs without error message any more. Thank you! Bests, Kun 2010/11/1 Eyvaz Isaev : > Hi, > > So, you got two different set of q-points with different symmetry. > In fact, this is very famous error ?and you should find the solution if search > QE forum archive). > > Just have a look at set_irr.f90, find line with "npert > 6" (line 192 in QE 4.2) > and then take more neprt (number of irreducible presentations). Do not forget > recompile the phonon code. > > 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: Kun Yin > To: pw_forum at pwscf.org > Sent: Mon, November 1, 2010 4:01:46 AM > Subject: [Pw_forum] set_irr error during phonon calculation > > Dear Users, > > I did two similar phonon runs after a same scf calculation. The only > difference between the two phonon calculations is the dimension of > q-point mesh. > > ? ?nq1=2,nq2=2,nq3=2 (in 1st ph.x run) > ? ?nq1=2,nq2=2,nq3=1 (in 2nd ph.x run) > > The first calculation was successful to finish, while the second one > met the following error and stopped. > > ? ?from set_irr: error# 2 > ? ?npert > 6 > > This problem seems different from someone have asked before which > could be solved by increasing max_irr_dim value in phcom.f90 file. > Actually I didn't find max_irr_dim in this file in QE version 4.2 > which I used. > > Any suggestions or help will be appreciated. > > Kun Yin > Nanjing University,China > > Input of scf run: > > &CONTROL > ? calculation ? ? ? ? ?= ?'scf', > ? outdir ? ? ? ? ? ? ? = ?'/state/partition1/kyin', > ? prefix ? ? ? ? ? ? ? = ?'qe', > ? pseudo_dir ? ? ? ? ? = ?'/share/apps/qe_pseudo', > ? restart_mode ? ? ? ? = ?'from_scratch', > ? title ? ? ? ? ? ? ? ?= ?'qe', > ? verbosity ? ? ? ? ? ?= ?'high', > / > > &SYSTEM > ? celldm(1) ? ? ? ? ? ?= ?1, > ? ecutrho ? ? ? ? ? ? ?= ?400, > ? ecutwfc ? ? ? ? ? ? ?= ?40, > ? ibrav ? ? ? ? ? ? ? ?= ?0, > ? nat ? ? ? ? ? ? ? ? ?= ?20, > ? ntyp ? ? ? ? ? ? ? ? = ?3, > ? nr1=60,nr2=60,nr3=90 > / > > &ELECTRONS > ? conv_thr ? ? ? ? ? ? = ?1.0d-9, > ? mixing_mode ? ? ? ? ?= ?'plain', > / > > ATOMIC_SPECIES > ?Mg ? 24.305 ? Mg.pw91-np-van.UPF > ?Si ? 28.0855 ? Si.pw91-n-van.UPF > ?O ? 15.9994 ? O.pw91-van_ak.UPF > > K_POINTS automatic > ?4 ? 4 ? 2 ? 0 ? 0 ? 0 > > CELL_PARAMETERS (alat= ?1.00000000) > ? 7.646348501 ? 0.000000000 ? 0.000000000 > ? 0.000000000 ? 8.393090445 ? 0.000000000 > ? 0.000000000 ? 0.000000000 ?11.365238746 > > ATOMIC_POSITIONS (crystal) > Mg ? ? ? 0.533728470 ? 0.589922896 ? 0.250000000 > Mg ? ? ? 0.466271530 ? 0.410077104 ? 0.750000000 > Mg ? ? ? 0.033728470 ? 0.910077104 ? 0.750000000 > Mg ? ? ? 0.966271530 ? 0.089922896 ? 0.250000000 > Si ? ? ? 0.500000000 ? 0.000000000 ? 0.500000000 > > Si ? ? ? 0.500000000 ? 0.000000000 ? 0.000000000 > Si ? ? ? 0.000000000 ? 0.500000000 ? 0.500000000 > Si ? ? ? 0.000000000 ? 0.500000000 ? 0.000000000 > O ? ? ? ?0.125931013 ? 0.465888786 ? 0.250000000 > O ? ? ? ?0.874068987 ? 0.534111214 ? 0.750000000 > O ? ? ? ?0.625931013 ? 0.034111214 ? 0.750000000 > O ? ? ? ?0.374068987 ? 0.965888786 ? 0.250000000 > O ? ? ? ?0.171733094 ? 0.187375245 ? 0.559982148 > O ? ? ? ?0.828266906 ? 0.812624755 ? 0.440017852 > O ? ? ? ?0.828266906 ? 0.812624755 ? 0.059982148 > O ? ? ? ?0.171733094 ? 0.187375245 ? 0.940017852 > O ? ? ? ?0.671733094 ? 0.312624755 ? 0.440017852 > O ? ? ? ?0.328266906 ? 0.687375245 ? 0.559982148 > O ? ? ? ?0.328266906 ? 0.687375245 ? 0.940017852 > O ? ? ? ?0.671733094 ? 0.312624755 ? 0.059982148 > > Input of phonon run: > Phonons > &inputph > ?amass(1)=24.3050, > ?amass(2)=28.0855, > ?amass(3)=15.9994, > ?prefix='qe', > ?outdir='/state/partition1/kyin' > ?fildyn='qe.dyn', > ?tr2_ph=1.0d-14, > ?ldisp=.true. > ?nq1=2,nq2=2,nq3=2 > / > _______________________________________________ > 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 1009ukumar at gmail.com Mon Nov 1 15:59:44 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Mon, 1 Nov 2010 20:29:44 +0530 Subject: [Pw_forum] odd # of electrons in primitive cell => metal ? Message-ID: Dear Prof. Eyvaz and Prasenjit, Thank you for your reply. ############################################################### >As you have an oxide it is not so surprising. As an example I remember B1 NiO >or FeO,You should apply, at least, LDA+U to get more correct bands (see >/examples/example25). Yamboo or GW+Wannier might be another tools to fix the >problem. I also want to do phonons calculations....can i use LDA+U or Yamboo or GW+Wannier for this also.? or any other option? Also from physics point of view if i have an odd no. of electrons in primitive cell, then my system should be metallic, but actually it insulator...why is it so? . ########################################################### >If your system has odd no. of electrons, you should do a spin >polarized calculation with some smearing. will try whether can i get insulating nature? ############################################################ with kind regards, -- 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/20101101/2b3262fd/attachment.htm From eyvaz_isaev at yahoo.com Mon Nov 1 19:49:26 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 1 Nov 2010 11:49:26 -0700 (PDT) Subject: [Pw_forum] odd # of electrons in primitive cell => metal ? Message-ID: <732826.66095.qm@web65713.mail.ac4.yahoo.com> Hi, From: sonu kumar <1009ukumar at gmail.com> >I also want to do phonons calculations....can i use LDA+U No, not yet. Hopefully, Matteo can tell us more about this opportunity. >or Yamboo or GW+Wannier for this also.? or any other option? Neither Yamboo nor GW+Wannier can be used for phonon calculations. >Also from physics point of view if i have an odd no. of electrons in primitive >cell, >then my system should be metallic, but actually it insulator...why is it so? The reason is the Columb imteraction (repulsion) between d-electrons. There are some materials that should be metallic from DFT view of point, but they are insulators (Mott insulators). >>If your system has odd no. of electrons, you should do a spin >>polarized calculation with some smearing. >will try whether can i get insulating nature? Most likely, AFM calculations. 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101101/7fad3935/attachment.htm From eariel99 at gmail.com Mon Nov 1 20:17:20 2010 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Mon, 1 Nov 2010 16:17:20 -0300 Subject: [Pw_forum] GDIS Message-ID: Hi Koa, I use GDIS to visualize and modify some structures, and to produce images. GDIS can read XYZ files, and a number of other formats, but not a format of Quantum ESPRESSO. GDIS is the preferred interface of GULP and have capabilities for other packages, like SIESTA. It would be nice to have, and it may be easy to write, a script to transfom from and for PWSCF format. One advantage for Debian and Ubuntu users is that it is included in the distribution, hence apt-get install gdis, and it gets installs in your box. If you do not use GULP, or SIESTA, or other supported code, you may live without it. For my taste, the images of XCRYSDEN are prettier. GDIS has certain capabilities to generate supercells and surfaces, what is call, a builder. XCRYSDEN can do the same, but only if you also have CRYSTAL. Regards -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez They did it! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101101/af897225/attachment.htm From kucukben at sissa.it Mon Nov 1 23:09:51 2010 From: kucukben at sissa.it (Emine Kucukbenli) Date: Mon, 01 Nov 2010 23:09:51 +0100 Subject: [Pw_forum] norm conserving pseudopotential with multiple projectors and semicores Message-ID: <20101101230951.64ex6iz4gcs4c0sc@webmail.sissa.it> Dear all, Sorry if you have already received this, =========== Dear Sangkook Choi, Please sign your posts with your name and affiliation. You can find the information you need in the INPUT_LD1.* file in the Doc directory. > 1) is it possible to generate norm conserving pseudopotentials with multiple > projectors, and semicores by LD1? As far as I know, NC with multiple projectors correspond to pseudotype=2. "Semicore is tricky. Please read carefully the documentation on how to generate PP in atomic_doc/pseudo-gen.tex" quoting from P. Giannozzi. 2)nns is the principal quantum number in the "pseudo" atom. You can double check with this: number of nodes=nns-lls-1 In your case for nns: 5s=>1, 5p=>2, 5d=>3, 6s=>2,6p=>3 hope this helps, emine kucukbenli, phd student, sissa, italy. ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From giannozz at democritos.it Tue Nov 2 10:18:32 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 02 Nov 2010 10:18:32 +0100 Subject: [Pw_forum] GDIS In-Reply-To: References: Message-ID: <4CCFD768.7050003@democritos.it> B. Koa wrote: > This is the link : > > http://www.pwscf.org/tools.php , and GDIS is one of the recommended > visualization softwares. I added this link because somebody working on GDIS mentioned that there was a filter for reading PWscf output data. Unfortunately I cannot find the message and don't remember the details. Most likely it is a feature that is present only in the development version of GDIS. You may try to contact the developer(s) of GDIS or to download the CVS version of GDIS. Please let us know if the link is misleading Paolo -- Paolo Giannozzi, Democritos and University of Udine, Italy From janfelix.binder at epfl.ch Tue Nov 2 08:40:15 2010 From: janfelix.binder at epfl.ch (Jan Felix Binder) Date: Tue, 02 Nov 2010 08:40:15 +0100 Subject: [Pw_forum] GDIS In-Reply-To: References: Message-ID: <4CCFC05F.6050502@epfl.ch> Hi, if you use the CVS version, I can also read (and maybe write) input and output of pwscf. Eduardo Ariel Menendez Proupin wrote: > Hi Koa, > I use GDIS to visualize and modify some structures, and to produce > images. GDIS can read XYZ files, and a number of other formats, but > not a format of Quantum ESPRESSO. GDIS is the preferred interface of > GULP and have capabilities for other packages, like SIESTA. It would > be nice to have, and it may be easy to write, a script to transfom > from and for PWSCF format. One advantage for Debian and Ubuntu users > is that it is included in the distribution, hence apt-get install > gdis, and it gets installs in your box. If you do not use GULP, or > SIESTA, or other supported code, you may live without it. For my > taste, the images of XCRYSDEN are prettier. GDIS has certain > capabilities to generate supercells and surfaces, what is call, a > builder. XCRYSDEN can do the same, but only if you also have CRYSTAL. > > > Regards > > -- > > > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez > > > They did it! > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Tue Nov 2 10:27:46 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 02 Nov 2010 10:27:46 +0100 Subject: [Pw_forum] (no subject) In-Reply-To: References: Message-ID: <4CCFD992.1050304@democritos.it> amar shugani wrote: > I am trying to run nscf but the error is occuring > # From IOTK LIBRARY VERSION 1.2.0 > #UNRECOVERABLE ERROR (ierr=1) > #ERROR IN :iotk_scan_end (iotk_scan.spp:233) > #cvs revision :1.23 > #foundl > #ERROR IN :iotk_close_read(iotk_files.spp:645) > #cvs revision:1.20 obscure iotk errors are frequent with buggy compilers. If you want to know more, consider the following item in the "guidelines for posting": * Remember that even experts cannot guess where a problem lies in the absence of sufficient information. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Nov 2 10:29:10 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 02 Nov 2010 10:29:10 +0100 Subject: [Pw_forum] subject (was: no subject) In-Reply-To: <4CCFD992.1050304@democritos.it> References: <4CCFD992.1050304@democritos.it> Message-ID: <4CCFD9E6.3090209@democritos.it> Paolo Giannozzi wrote: > If you want to know more, consider the following item > in the "guidelines for posting": ...and also this one: * Choose a meaningful subject P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From nicola.marzari at materials.ox.ac.uk Tue Nov 2 11:53:07 2010 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Tue, 02 Nov 2010 10:53:07 +0000 Subject: [Pw_forum] distributed computing Message-ID: <4CCFED93.4000605@materials.ox.ac.uk> Dear all, a bit of hubris today - I got QE running on my cell phone... http://mml.materials.ox.ac.uk/Main/QEN900 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 1009ukumar at gmail.com Tue Nov 2 11:55:21 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Tue, 2 Nov 2010 16:25:21 +0530 Subject: [Pw_forum] odd # of electrons in primitive cell => metal ? Message-ID: Dear Prof. Eyvaz Isaev and QE forum, Thank you very much for your help. with kind regards, Sonu IITD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101102/7440a034/attachment.htm From giannozz at democritos.it Tue Nov 2 12:11:07 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 02 Nov 2010 12:11:07 +0100 Subject: [Pw_forum] distributed computing In-Reply-To: <4CCFED93.4000605@materials.ox.ac.uk> References: <4CCFED93.4000605@materials.ox.ac.uk> Message-ID: <4CCFF1CB.5030206@democritos.it> Nicola Marzari wrote: > a bit of hubris today - I got QE running on my cell phone... "I have always desired that the computer become one day as easy to use as the telephone. My dream has come true: now I don't understand my telephone any longer" (attributed to Bjarne Stroustrup, author of the C++ language) P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From prasenjit.jnc at gmail.com Tue Nov 2 13:12:57 2010 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Tue, 2 Nov 2010 17:42:57 +0530 Subject: [Pw_forum] distributed computing In-Reply-To: <4CCFED93.4000605@materials.ox.ac.uk> References: <4CCFED93.4000605@materials.ox.ac.uk> Message-ID: great :) Prasenjit On 2 November 2010 16:23, Nicola Marzari wrote: > > > Dear all, > > a bit of hubris today - I got QE running on my cell phone... > > http://mml.materials.ox.ac.uk/Main/QEN900 > > ? ? ? ? ? ? ? ? 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 > -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From w2agz at w2agz.com Tue Nov 2 18:00:29 2010 From: w2agz at w2agz.com (W2AGZ) Date: Tue, 2 Nov 2010 10:00:29 -0700 Subject: [Pw_forum] distributed computing In-Reply-To: <4CCFED93.4000605@materials.ox.ac.uk> References: <4CCFED93.4000605@materials.ox.ac.uk> Message-ID: <014d01cb7aaf$755fa8e0$601efaa0$@w2agz.com> A bit of hubris two and half years ago. I got QE running on my son's Playstation 3, calculated the Electronic Properties of Rocksalt CuO, and gave a talk on the results at the 2008 APS March Meeting (see slide 7). http://www.w2agz.com/Presentations/2009/03-16%20APS%20March%20Pittsburgh/APS %20March%202009%20Talk%20II.pdf Nicola, can we expect to hear from you later this month at Fall MRS? - Paul Grant w2agz at w2agz.com -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Nicola Marzari Sent: Tuesday, November 02, 2010 3:53 AM To: PWSCF Forum Subject: [Pw_forum] distributed computing Dear all, a bit of hubris today - I got QE running on my cell phone... http://mml.materials.ox.ac.uk/Main/QEN900 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 barfi.koa at gmail.com Tue Nov 2 19:10:20 2010 From: barfi.koa at gmail.com (B. Koa) Date: Tue, 2 Nov 2010 21:40:20 +0330 Subject: [Pw_forum] GDIS Message-ID: Dear Eduardo Many thanks for your detailed answer. > Hi Koa, > I use GDIS to visualize and modify some structures, and to produce images. > GDIS can read XYZ files, and a number of other formats, but not a format of > Quantum ESPRESSO. GDIS is the preferred interface of GULP and have > capabilities for other packages, like SIESTA. It would be nice to have, and > it may be easy to write, a script to transfom from and for PWSCF format. > One > advantage for Debian and Ubuntu users is that it is included in the > distribution, hence apt-get install gdis, and it gets installs in your box. > If you do not use GULP, or SIESTA, or other supported code, you may live > without it. For my taste, the images of XCRYSDEN are prettier. GDIS has > certain capabilities to generate supercells and surfaces, what is call, a > builder. XCRYSDEN can do the same, but only if you also have CRYSTAL. > > > Regards > > -- > > > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez > > B. Koa NIT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101102/d65738d8/attachment.htm From baroni at sissa.it Wed Nov 3 08:27:06 2010 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 3 Nov 2010 08:27:06 +0100 Subject: [Pw_forum] distributed computing In-Reply-To: <4CCFED93.4000605@materials.ox.ac.uk> References: <4CCFED93.4000605@materials.ox.ac.uk> Message-ID: <865E4F49-95CF-4FF4-B1EA-CE560C37E1AB@sissa.it> funny! SB On Nov 2, 2010, at 11:53 AM, Nicola Marzari wrote: > > > Dear all, > > a bit of hubris today - I got QE running on my cell phone... > > http://mml.materials.ox.ac.uk/Main/QEN900 > > 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 --- 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/20101103/d1ba8529/attachment-0001.htm From baroni at sissa.it Wed Nov 3 08:27:45 2010 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 3 Nov 2010 08:27:45 +0100 Subject: [Pw_forum] distributed computing In-Reply-To: <014d01cb7aaf$755fa8e0$601efaa0$@w2agz.com> References: <4CCFED93.4000605@materials.ox.ac.uk> <014d01cb7aaf$755fa8e0$601efaa0$@w2agz.com> Message-ID: <49B3CEBC-B0E6-4FCE-A215-13CA36BB0967@sissa.it> even funnier! SB On Nov 2, 2010, at 6:00 PM, W2AGZ wrote: > A bit of hubris two and half years ago. I got QE running on my son's > Playstation 3, calculated the Electronic Properties of Rocksalt CuO, and > gave a talk on the results at the 2008 APS March Meeting (see slide 7). > http://www.w2agz.com/Presentations/2009/03-16%20APS%20March%20Pittsburgh/APS > %20March%202009%20Talk%20II.pdf > > Nicola, can we expect to hear from you later this month at Fall MRS? > > - Paul Grant > w2agz at w2agz.com > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of Nicola Marzari > Sent: Tuesday, November 02, 2010 3:53 AM > To: PWSCF Forum > Subject: [Pw_forum] distributed computing > > > > Dear all, > > a bit of hubris today - I got QE running on my cell phone... > > http://mml.materials.ox.ac.uk/Main/QEN900 > > 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 > > > _______________________________________________ > 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/20101103/10bd9a74/attachment.htm From eariel99 at gmail.com Wed Nov 3 15:34:49 2010 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 3 Nov 2010 11:34:49 -0300 Subject: [Pw_forum] distributed computing Message-ID: Wonderfull!! It looks like the silicon calculation of example1. Can anyone provide the historical reference of the date and kind of computer that hosted the original calculation? > bit of hubris today - I got QE running on my cell phone... > http://mml.materials.ox.ac.uk/Main/QEN900 -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez They did it! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101103/8e1fe5a8/attachment.htm From shruba at gmail.com Wed Nov 3 18:40:44 2010 From: shruba at gmail.com (Shruba Gangopadhyay) Date: Wed, 3 Nov 2010 13:40:44 -0400 Subject: [Pw_forum] distributed computing In-Reply-To: References: Message-ID: Thats wonderful. It will be great if we can see that in QE site :)) Thanks Prof Marzari for sharing this with us. Shruba On Wed, Nov 3, 2010 at 10:34 AM, Eduardo Ariel Menendez Proupin < eariel99 at gmail.com> wrote: > Wonderfull!! It looks like the silicon calculation of example1. > > Can anyone provide the historical reference of the date and kind of > computer that hosted the original calculation? > > > bit of hubris today - I got QE running on my cell phone... > > > http://mml.materials.ox.ac.uk/Main/QEN900 > > -- > > > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez > > They did it! > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Shruba Gangopadhyay PhD candidate Department of Chemistry, NanoScience Technology Center 12424 Research Parkway, Suite 400 University of Central Florida Orlando, FL-32826 'friendship doubles joys and reduces sorrows by half' (Francis Bacon). -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101103/9d9c0133/attachment.htm From ssdhayal at gmail.com Wed Nov 3 18:41:13 2010 From: ssdhayal at gmail.com (Suman Dhayal) Date: Wed, 3 Nov 2010 12:41:13 -0500 Subject: [Pw_forum] distributed computing In-Reply-To: References: Message-ID: Yes, its the silicon calculation of example1.. I am attaching the config.log file so that you would have all the information about it. Thanks a lot, Harli On Wed, Nov 3, 2010 at 9:34 AM, Eduardo Ariel Menendez Proupin < eariel99 at gmail.com> wrote: > Wonderfull!! It looks like the silicon calculation of example1. > > Can anyone provide the historical reference of the date and kind of > computer that hosted the original calculation? > > > bit of hubris today - I got QE running on my cell phone... > > > http://mml.materials.ox.ac.uk/Main/QEN900 > > -- > > > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez > > They did it! > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101103/80250ab2/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: config.log Type: text/x-log Size: 39123 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101103/80250ab2/attachment-0001.bin From ssdhayal at gmail.com Wed Nov 3 18:42:35 2010 From: ssdhayal at gmail.com (Suman Dhayal) Date: Wed, 3 Nov 2010 12:42:35 -0500 Subject: [Pw_forum] distributed computing In-Reply-To: References: Message-ID: On Wed, Nov 3, 2010 at 12:41 PM, Suman Dhayal wrote: > Yes, its the silicon calculation of example1.. I am attaching the > config.log file so that you would have all the information about it. > > Thanks a lot, > > Harli > > On Wed, Nov 3, 2010 at 9:34 AM, Eduardo Ariel Menendez Proupin < > eariel99 at gmail.com> wrote: > >> Wonderfull!! It looks like the silicon calculation of example1. >> >> Can anyone provide the historical reference of the date and kind of >> computer that hosted the original calculation? >> >> > bit of hubris today - I got QE running on my cell phone... >> >> > http://mml.materials.ox.ac.uk/Main/QEN900 >> >> -- >> >> >> Eduardo Menendez >> Departamento de Fisica >> Facultad de Ciencias >> Universidad de Chile >> Phone: (56)(2)9787439 >> URL: http://fisica.ciencias.uchile.cl/~emenendez >> >> They did it! >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101103/72239155/attachment.htm From yukihiro_okuno at fujifilm.co.jp Fri Nov 5 02:42:05 2010 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Fri, 5 Nov 2010 10:42:05 +0900 Subject: [Pw_forum] Van der Waals interaction in PWSCF Message-ID: Dear PWSCF users and developers. I want to calculate the interaction of molecules which interact by Van der Waals forces. And , there are some developments of the treatment of Van der Waals interaction within density functional theory like, M.Dion et al Phys. Rev Lett. vol 92 246401 (2004) T.Thonhauser et al Phys.Rev.B vol 76 125112 (2007) and others. Are there any plan implement such a Van der Waals functional in PWSCF ? and, in PWSCF there are VdW directory and what this code calculate and how to use it ? There are no document in /Docs/INPUT_VdW. Sincerely, Yukihiro Okuno. From juanlopez415 at gmail.com Fri Nov 5 03:22:13 2010 From: juanlopez415 at gmail.com (Juan Manuel Lopez) Date: Thu, 4 Nov 2010 22:22:13 -0400 Subject: [Pw_forum] Van der Waals interaction in PWSCF In-Reply-To: References: Message-ID: Hi Yukihiro, QE have an implementation of VdW interactions done in this publication: Barone, V., Casarin, M., Forrer, D., Pavone, M., Sambi, M. & Vittadini, A.,*J. Comput. Chem. * *2009*,* 30*, 934-939. In order to do the SCF calculations including VdW interactions you only need to add this tag on the &SYSTEM part of the input: london=.true. That's it. Juan. On Thu, Nov 4, 2010 at 9:42 PM, wrote: > > Dear PWSCF users and developers. > > I want to calculate the interaction of molecules which interact > > by Van der Waals forces. > > And , there are some developments of the treatment of Van der Waals > > interaction within density functional theory like, > > M.Dion et al Phys. Rev Lett. vol 92 246401 (2004) > T.Thonhauser et al Phys.Rev.B vol 76 125112 (2007) > > and others. > > Are there any plan implement such a Van der Waals functional in PWSCF ? > > and, in PWSCF there are VdW directory and what this code calculate and > > how to use it ? There are no document in /Docs/INPUT_VdW. > > Sincerely, > > Yukihiro Okuno. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Best regards, -------------------------------------- Juan M. Lopez Encarnacion Research associate, Institute of Physics, Universidad Aut?noma de Santo Domingo, Dominican Republic Graduate Student Doctoral Program in Chemical Physics, University of Puerto Rico, Rio Piedras Campus P.O.Box 23343 San Juan, PR 00931-3343 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101104/eb522663/attachment.htm From Michael at ihpc.a-star.edu.sg Fri Nov 5 04:22:42 2010 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Fri, 5 Nov 2010 11:22:42 +0800 Subject: [Pw_forum] Van der Waals interaction in PWSCF In-Reply-To: References: Message-ID: <235887FC8686C543B24F9DF2A01CBE04030191C6@S3-EXCHMB03.shared-svc.local> Okuno-san: Barone et al. has implemented Grimme's DFT-D by adding london=.true. into the &SYSTEM tag. In my opinion, this has some limitations that Grimme has recently addressed but hasn't been implemented in Espresso yet. He calls it DFT-D3. If you want to use Dion's method, have a look at JuNoLo that reads the charge density generated from Espresso: Lazic, P. et al. JuNoLo - J?lich nonlocal code for parallel post-processing evaluation of vdW-DF correlation energy. Computer Physics Communications 181, 371-379 (2010). DOI: 10.1016/j.cpc.2009.09.016 Hope that helps, Mike michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of yukihiro_okuno at fujifilm.co.jp Sent: Friday, November 05, 2010 9:42 AM To: pw_forum at pwscf.org Subject: [Pw_forum] Van der Waals interaction in PWSCF Dear PWSCF users and developers. I want to calculate the interaction of molecules which interact by Van der Waals forces. And , there are some developments of the treatment of Van der Waals interaction within density functional theory like, M.Dion et al Phys. Rev Lett. vol 92 246401 (2004) T.Thonhauser et al Phys.Rev.B vol 76 125112 (2007) and others. Are there any plan implement such a Van der Waals functional in PWSCF ? and, in PWSCF there are VdW directory and what this code calculate and how to use it ? There are no document in /Docs/INPUT_VdW. Sincerely, Yukihiro Okuno. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum IHPC Values :: Impact :: Honesty :: Performance :: Co-operation This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From sclauzer at sissa.it Fri Nov 5 09:05:28 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 05 Nov 2010 09:05:28 +0100 Subject: [Pw_forum] Van der Waals interaction in PWSCF In-Reply-To: <235887FC8686C543B24F9DF2A01CBE04030191C6@S3-EXCHMB03.shared-svc.local> References: <235887FC8686C543B24F9DF2A01CBE04030191C6@S3-EXCHMB03.shared-svc.local> Message-ID: <4CD3BAC8.9040801@sissa.it> On 11/05/2010 04:22 AM, Michael Sullivan wrote: > Okuno-san: > > Barone et al. has implemented Grimme's DFT-D by adding london=.true. into the&SYSTEM tag. In my opinion, this has some limitations that Grimme has recently addressed but hasn't been implemented in Espresso yet. He calls it DFT-D3. > Just for the sake of completeness, I think that the version implemented in QE is DFT-D2, which should be better than DFT-D. However it would be worth to implement the new DFT-D3, if someone is willing. GS -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne From degironc at sissa.it Fri Nov 5 09:11:49 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 05 Nov 2010 09:11:49 +0100 Subject: [Pw_forum] Van der Waals interaction in PWSCF In-Reply-To: References: Message-ID: <4CD3BC45.3030004@sissa.it> In the QE tree there is a developing branch where the Dion et al. functional (including the self-consistent treatment for the potential by Thonhauser et al.) has been implemented (thanks to Tymo Thonhauser and coworkers). Some work on the stress tensor calculation had to be completed. It took longer than foreseen but is currently in very good shape. It is our aim to release these developments quite soon. VdW subdirectory contains some code that has been used to calculate the imaginary frequency polarizability of molecules (both fully from first principles and with an approximate scheme) and hence the C6 coefficients [see V-H Nguyen and SdG, PRB79 115105 (2009)]. It is , I think, still working but is not being used actively so be careful and report on strange behavior if you plan to use it. We are also working (but this is still far from a fully working release) on the implementation of RPA energy (and potential) in QE [see V-H Nguyen and SdG, PRB79 205114 (2009) and related work by Gilia Galli, Francois Gygi and coworkers]. all the best, Stefano de Gironcoli - SISSA and DEMOCRITOS yukihiro_okuno at fujifilm.co.jp wrote: > Dear PWSCF users and developers. > > I want to calculate the interaction of molecules which interact > > by Van der Waals forces. > > And , there are some developments of the treatment of Van der Waals > > interaction within density functional theory like, > > M.Dion et al Phys. Rev Lett. vol 92 246401 (2004) > T.Thonhauser et al Phys.Rev.B vol 76 125112 (2007) > > and others. > > Are there any plan implement such a Van der Waals functional in PWSCF ? > > and, in PWSCF there are VdW directory and what this code calculate and > > how to use it ? There are no document in /Docs/INPUT_VdW. > > Sincerely, > > Yukihiro Okuno. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From yukihiro_okuno at fujifilm.co.jp Fri Nov 5 11:20:25 2010 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Fri, 5 Nov 2010 19:20:25 +0900 Subject: [Pw_forum] Van der Waals interaction in PWSCF Message-ID: Dear PWSCF users and developers. Thank you for informing me on the VdW treatment of PWSCF, and I'm glad to know that the implementation of VdW is now going on. If possible, I want to test the Dion and Thonhauser's treatment of VdW interaction. If we get CVS version of espresso, can I use it ? I want to calculate the optimized distance between some molecules. Sincerely, Yukihiro Okuno. From martinez.s.luis at gmail.com Fri Nov 5 18:53:40 2010 From: martinez.s.luis at gmail.com (=?ISO-8859-1?Q?Luis_Mart=EDnez?=) Date: Fri, 5 Nov 2010 18:53:40 +0100 Subject: [Pw_forum] Total DOS and sum of PDOS don't overlap Message-ID: Dear QE users, I have performed a DOS calculation of a metal oxide system with some adsorbates. Then I plot the total DOS using the file myfile.pdos_tot, and I also plot the sum of the PDOS generated by the program sumpdos.x included in the Quantum Espresso package. In principle both plots should give the same, but what I see is that the DOS plots for the zone of the unoccupied bands do not overlap. In particular, the DOS area generated with the sumpdos.x program is considerably smaller. I can't understand why do I encounter this difference. Is there a reason for that? Thank you -- Luis Mart?nez Suarez Lehrstuhl fuer Theoretische Chemie Ruhr-Universitaet Bochum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101105/3c9ed0b2/attachment.htm From degironc at sissa.it Fri Nov 5 19:30:02 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 05 Nov 2010 19:30:02 +0100 Subject: [Pw_forum] Total DOS and sum of PDOS don't overlap In-Reply-To: References: Message-ID: <4CD44D2A.1010207@sissa.it> the integral of the dos on the energy axis (from -infty to +infty) is the total number of states in your system ... (the number of plane waves in your basis) .... can you figure out why ? the integral of the total pdos over the same interval is the total number of atomic wavefunctions over which one is projecting ... again, can you figure out why ? As NPW >> NATOMWFC no surprise they differ in some portion of the energy axis. Since approximations like LCAO are usually reasonable the occupied portion of the energy axis is usually well described but sooner or later the pdos must drop to zero while the dos likely goes on for a while (forever for infinite cutoff). hope this helps stefano Luis Mart?nez wrote: > Dear QE users, > > I have performed a DOS calculation of a metal oxide system with some > adsorbates. > Then I plot the total DOS using the file myfile.pdos_tot, and I also plot > the sum of the PDOS generated by the program sumpdos.x included in the > Quantum Espresso package. > In principle both plots should give the same, but what I see is that the DOS > plots for the zone of the unoccupied bands do not overlap. In particular, > the DOS area generated with the sumpdos.x program is considerably smaller. > I can't understand why do I encounter this difference. Is there a reason for > that? > > Thank you > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From wumindt2 at zju.edu.cn Fri Nov 5 22:02:11 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Sat, 06 Nov 2010 05:02:11 +0800 Subject: [Pw_forum] pseudopotential Message-ID: Dear All, I met some problem when printing the stress using different pseudopotentials. The structure i calculated is CO2 solid structure. Using the same structure, when the pseudopotentials are C.pbe-rrkjus.UPF and O.pbe-rrkjus.UPF, the stress tensor i got is entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= 175.92 0.00114704 0.00000000 0.00000000 168.74 0.00 0.00 0.00000000 0.00121085 0.00000007 0.00 178.12 0.01 0.00000000 0.00000007 0.00122973 0.00 0.01 180.90 However, when i changed the pseudopotential to C.pbe-mt_gipaw.UPF and O.pbe-van_gipaw.UPF , the stress tensot i got is entering subroutine stress ... total stress (Ry/bohr**3) (kbar) P= 252.11 0.00113269 0.00000000 0.00000000 166.62 0.00 0.00 0.00000000 0.00225526 0.00000002 0.00 331.76 0.00 0.00000000 0.00000002 0.00175342 0.00 0.00 257.94 Why we will get so much different stress using the different pseudopotential ? The structures i ued are exact same. Thanks for any help. With kind regards, Min Wu 2010-11-5 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/907af28f/attachment.htm From jiejiangnc at gmail.com Fri Nov 5 23:07:48 2010 From: jiejiangnc at gmail.com (Jie Jiang) Date: Fri, 5 Nov 2010 18:07:48 -0400 Subject: [Pw_forum] Constrained occupation Message-ID: Dear PWscf, It seems that I can define occupation by using 'occupations=from_input'. Is the occupation constrained in the SCF iterations. Can I use this way to calculate e-h excitation energy? Thanks in advance, Jie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101105/68ba21d9/attachment.htm From giannozz at democritos.it Fri Nov 5 23:10:15 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 5 Nov 2010 23:10:15 +0100 Subject: [Pw_forum] pseudopotential In-Reply-To: References: Message-ID: On Nov 5, 2010, at 22:02 , wumindt2 wrote: > C.pbe-rrkjus.UPF and O.pbe-rrkjus.UPF ultrasoft > C.pbe-mt_gipaw.UPF and O.pbe-van_gipaw.UPF norm-conserving, and quite hard. A cutoff that is appropriate for the former may ot be sufficient for the latter. This is the first thing to be verified. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From wumindt2 at zju.edu.cn Sat Nov 6 00:10:48 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Sat, 06 Nov 2010 07:10:48 +0800 Subject: [Pw_forum] pseudopotential Message-ID: Dear Paolo, I know the difference, and have already used different cutoff for norm-conserving PP adn ultrasoft PP. Best regards, Min Wu, 2010-11-5 >From: Paolo Giannozzi >Reply-To: >To: wumindt2 ,PWSCF Forum >Subject: Re: [Pw_forum] pseudopotential >Date: Fri, 5 Nov 2010 23:10:15 +0100 > > >On Nov 5, 2010, at 22:02 , wumindt2 wrote: > >> C.pbe-rrkjus.UPF and O.pbe-rrkjus.UPF > >ultrasoft > >> C.pbe-mt_gipaw.UPF and O.pbe-van_gipaw.UPF > >norm-conserving, and quite hard. A cutoff that is appropriate for the >former may ot be sufficient for the latter. This is the first thing >to be >verified. > >P. >--- >Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine >via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > > From jiejiangnc at gmail.com Sat Nov 6 00:20:34 2010 From: jiejiangnc at gmail.com (Jie Jiang) Date: Fri, 5 Nov 2010 19:20:34 -0400 Subject: [Pw_forum] Constrained occupation Message-ID: Dear All, Does 'occupations=from_input' mean occupations of individual states are fixed ? Can I define the occupations of the highest occupied state and lowest unoccupied state to be 1 and 1 to calculate the electron-hole excitation energy? Thanks for any comments. Jie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101105/e0d0a060/attachment.htm From wangqj1 at 126.com Sat Nov 6 02:55:06 2010 From: wangqj1 at 126.com (Q.J.Wang) Date: Sat, 6 Nov 2010 09:55:06 +0800 (CST) Subject: [Pw_forum] LDA+DMFT Message-ID: <1ed8ff7f.1991.12c1ee4e75e.Coremail.wangqj1@126.com> Dear pwscf developers I want to learn LDA+DMFT method, can you introduce some references which use LDA+DMFT shcemes. Besides, I have read the example of LDA+DMFT, so I want to know how to get the U and J parameters in the hamilt.in ? Could you give some introduction of DMFT for users? -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/8d5a9104/attachment.htm From jiejiangnc at gmail.com Sat Nov 6 03:50:45 2010 From: jiejiangnc at gmail.com (Jie Jiang) Date: Fri, 5 Nov 2010 22:50:45 -0400 Subject: [Pw_forum] Constrained occupation In-Reply-To: References: Message-ID: Dear All, Again, is it possible to do occupation constraint DFT calculations with PWscf? Can the option 'occupations=from_input' do that? If not, is there any suggestion on where and how to modify to include this function. Thanks, Jie On Fri, Nov 5, 2010 at 7:20 PM, Jie Jiang wrote: > Dear All, > > Does 'occupations=from_input' mean occupations of individual states > are fixed ? > > Can I define the occupations of the highest occupied state and lowest > unoccupied state to be 1 and 1 to calculate the electron-hole excitation > energy? > > Thanks for any comments. > > Jie > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101105/7a287514/attachment-0001.htm From abmus911 at yahoo.ie Sat Nov 6 07:18:43 2010 From: abmus911 at yahoo.ie (bayo mus) Date: Sat, 6 Nov 2010 06:18:43 +0000 (GMT) Subject: [Pw_forum] atomic positions Message-ID: <528817.14870.qm@web29603.mail.ird.yahoo.com> Dear all I need assistance on how to get atomic positions of a material am workn on which is KAlSi3O8 I would be so grateful for every informatn concerning this work Thanks Musari A.A Department of physics University of Agriculture Abeokuta, Nigeria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/61241324/attachment.htm From vera.klekovkina at gmail.com Sat Nov 6 08:26:38 2010 From: vera.klekovkina at gmail.com (Vera Klekovkina) Date: Sat, 6 Nov 2010 10:26:38 +0300 Subject: [Pw_forum] restart in phonon calculation Message-ID: Then I try to preform Restart in Phonon calculation it happens the error: from ph_writefile : error # 47 cannot open xml_recover file for writing stopping ... -- Best regards, Vera Klekovkina -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/09db8c6b/attachment.htm From degironc at sissa.it Sat Nov 6 08:39:57 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 06 Nov 2010 08:39:57 +0100 Subject: [Pw_forum] atomic positions In-Reply-To: <528817.14870.qm@web29603.mail.ird.yahoo.com> References: <528817.14870.qm@web29603.mail.ird.yahoo.com> Message-ID: <4CD5064D.8070909@sissa.it> Dear Bayo Mus looks like a derivative of SiO2 (silica) with 1/4 Si substituted by Al and some compensating (interstitial ?) alkali metal. Silica itself can crystallize in several structures (http://en.wikipedia.org/wiki/Sio2). If you have in mind a specific crystalline form of KAlSi3O8 you should look for its crystallographic information and Wyckoff positions. This information should be sufficient to set up an initial set of positions for a relaxation. stefano bayo mus wrote: > Dear all > I need assistance on how to get atomic positions of a material am workn on which > is KAlSi3O8 > > I would be so grateful for every informatn concerning this work > > > Thanks > Musari A.A > 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 > From archygu at gmail.com Sat Nov 6 09:22:59 2010 From: archygu at gmail.com (chenjie gu) Date: Sat, 6 Nov 2010 16:22:59 +0800 Subject: [Pw_forum] do the relaxation under external electric field Message-ID: Hi all, recently, I try to do the crystal relaxation calculation under exter electric field, however, i get some problems: 1. do we need to set the "startingwfc" from file, or just as from the atomic 2. when i do the relaxation, i get the error as follows: error: translated G= 0.00000000000000 0.00000000000000 -0.999999999833333 with crystal coordinates 0 0 -1 corresponds to ng= 2 but G(ng)= 0.00000000000000 0.00000000000000 -0.716486350935015 probably because G_par is NOT a reciprocal lattice vector Possible choices as smallest G_par: any one can share your experience or suggestion with me, thanks so much, regards, -- Yours Regards, chenjie GU EEE,Nanyang Technoligical University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/f717ebe6/attachment.htm From sclauzer at sissa.it Sat Nov 6 10:50:27 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Sat, 6 Nov 2010 10:50:27 +0100 Subject: [Pw_forum] Constrained occupation In-Reply-To: References: Message-ID: Dear Jie, The only result that you will get by insistently repeating your question every few hours is to irritate the other users, hence the probability that you get an answer will drop considerably. Also consider that from an european point of view you asked your question in the middle of the night. Il giorno 06/nov/2010, alle ore 03.50, Jie Jiang ha scritto: > Dear All, > > Again, is it possible to do occupation constraint DFT calculations with PWscf? > Can the option 'occupations=from_input' do that? This option is to fix occupation, not to constrain them, and it is usually used to force an electronic configuration for an atom or a molecule computed with plane waves in a big box. Constrained DFT is another thing, in my opinion, and I don't think it has been implemented in QE so far. > > If not, is there any suggestion on where and how to modify to include > this function. You should first read the relevant literature (if I remember well, Dederichs and Bluegel were the first to apply it), then devise an algorithm and implement it. If you are really willing to do so, I think you'll get some help from the core developers. Anyway, I don't think it is so straightforward to do. Regards, GS > > Thanks, > > Jie > > On Fri, Nov 5, 2010 at 7:20 PM, Jie Jiang wrote: > Dear All, > > Does 'occupations=from_input' mean occupations of individual states > are fixed ? > > Can I define the occupations of the highest occupied state and lowest > unoccupied state to be 1 and 1 to calculate the electron-hole excitation > energy? > > Thanks for any comments. > > Jie > > _______________________________________________ > 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/20101106/e35478ce/attachment.htm From degironc at sissa.it Sat Nov 6 11:18:24 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 06 Nov 2010 11:18:24 +0100 Subject: [Pw_forum] Constrained occupation In-Reply-To: References: Message-ID: <4CD52B70.1050005@sissa.it> Dear Jie, as Gabriele was saying constrained DFT is not implemented in PWscf: it is not so easy to force occupation of specific atomic-like levels in a plane-wave basis. Something related to this issue had to be considered when with Matteo Cococcioni we devised a way to calculate the U parameter in DFT+U approaches in a consistent way in a planewave basis set [see Cococcioni M, de Gironcoli S, PRB 71, 035105 (2005)]. The trick has been to force the occupation by adding localized potentials using atomic-projectors multiplied by some parameter alfa_I, where I is the index of the perturbed atom. In this way the energy as a function of alfa_I is the Legendre transform of the energy as a function of n_I (the occupation of the localized orbitals of atom I). Hence, by chosing an appropriate value of alpha_I you can control n_I. Variables associated with this features in the pw.x input are Hubbard_U and Hubbard_alpha; you may want to have a look if these may be useful to your purpose. Hope this helps, stefano Gabriele Sclauzero wrote: > Dear Jie, > > The only result that you will get by insistently repeating your question every few hours is to irritate the other users, hence the probability that you get an answer will drop considerably. Also consider that from an european point of view you asked your question in the middle of the night. > > > Il giorno 06/nov/2010, alle ore 03.50, Jie Jiang ha scritto: > > >> Dear All, >> >> Again, is it possible to do occupation constraint DFT calculations with PWscf? >> Can the option 'occupations=from_input' do that? >> > > This option is to fix occupation, not to constrain them, and it is usually used to force an electronic configuration for an atom or a molecule computed with plane waves in a big box. > > Constrained DFT is another thing, in my opinion, and I don't think it has been implemented in QE so far. > > >> If not, is there any suggestion on where and how to modify to include >> this function. >> > > You should first read the relevant literature (if I remember well, Dederichs and Bluegel were the first to apply it), then devise an algorithm and implement it. If you are really willing to do so, I think you'll get some help from the core developers. Anyway, I don't think it is so straightforward to do. > > Regards, > > GS > > >> Thanks, >> >> Jie >> >> On Fri, Nov 5, 2010 at 7:20 PM, Jie Jiang wrote: >> Dear All, >> >> Does 'occupations=from_input' mean occupations of individual states >> are fixed ? >> >> Can I define the occupations of the highest occupied state and lowest >> unoccupied state to be 1 and 1 to calculate the electron-hole excitation >> energy? >> >> Thanks for any comments. >> >> Jie >> >> _______________________________________________ >> 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 > From eyvaz_isaev at yahoo.com Sat Nov 6 11:46:06 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 6 Nov 2010 03:46:06 -0700 (PDT) Subject: [Pw_forum] restart in phonon calculation In-Reply-To: References: Message-ID: <342524.67194.qm@web65711.mail.ac4.yahoo.com> Dear Vera, Please have a look at your temporary directory, $TMP_DIR. If you have it, you have permission problem (you are not allowed to read the file). If you do your calculations on a supercomputer, most likely, you have a little chance to restart, as all temporary files are written to a scratch disk that will be cleaned after your job finished. Of course, you can try to copy your $TMP_DIR to your local disk, but it costs disk space. Instead, you can restart with options start_q=N1, last_q=N2 (N2 > or = N1) Please provide your affiliation. 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: Vera Klekovkina To: pw_forum at pwscf.org Sent: Sat, November 6, 2010 8:26:38 AM Subject: [Pw_forum] restart in phonon calculation Then I try to preform Restart in Phonon calculation it happens the error: from ph_writefile : error # 47 cannot open xml_recover file for writing stopping ... -- Best regards, Vera Klekovkina -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/28fd818b/attachment.htm From nicola.marzari at materials.ox.ac.uk Sat Nov 6 13:50:43 2010 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Sat, 06 Nov 2010 12:50:43 +0000 Subject: [Pw_forum] Constrained occupation In-Reply-To: <4CD52B70.1050005@sissa.it> References: <4CD52B70.1050005@sissa.it> Message-ID: <4CD54F23.2000009@materials.ox.ac.uk> On 11/6/10 10:18 AM, Stefano de Gironcoli wrote: > Dear Jie, > as Gabriele was saying constrained DFT is not implemented in PWscf: > it is not so easy to force occupation of specific atomic-like levels in > a plane-wave basis. Dear Jie, with Patrick Sit and Matteo Cococcioni we did implement constrained DFT in the cp code a few years ago - Patrick (cc'd here, now in Princeton) has a working version of the code (and hopefully it will at a certain point make it into the public distribution). At the end the procedure is similar to what Stefano has just described - one adds a penalty for occupation matrices on a chosen manifold that are different from a desired target - by making the penalty very large one can make it into an exact constraint, or one could impose directly a Lagrange multiplier. Any code that has a working version of DFT+U should be easy to modify to make it into constrained DFT - you change the orbitals onto which you make the projections, and add a penalty or a Lagrange multiplier to force approximately or exactly the constraint that you want. nicola PS: H.-L. Sit, M. Cococcioni, and N. Marzari, "Realistic, Quantitative Descriptions of Electron-Transfer Reactions: Diabatic Surfaces from First-Principles Molecular Dynamics," Phys. Rev. Lett. 97, 028303 (2006). Sit P. H.-L., Cococcioni M., Marzari N. "Car-Parrinello molecular dynamics in the DFT+U formalism: Structure and energetics of solvated ferrous and ferric ions" Journal of Electroanalytical Chemistry 607, 107-112, (2007) -- ---------------------------------------------------------------------- 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 masoudnahali at live.com Sat Nov 6 13:56:02 2010 From: masoudnahali at live.com (Masoud Nahali) Date: Sat, 6 Nov 2010 16:26:02 +0330 Subject: [Pw_forum] Total DOS and sum of PDOS don't overlap Message-ID: Dear Luis If I am correct , I feel that the non-orthonormality of atomic states on different atoms may affect the projected properties like PDOS. ** Best Wishes * ----------------- Masoud Nahali PhD Student of Physical Chemistry Sharif University of Technology * > > Stefano de Gironcoli : > > > the integral of the dos on the energy axis (from -infty to +infty) is > the total number of states in your system ... (the number of plane waves > in your basis) .... can you figure out why ? > the integral of the total pdos over the same interval is the total > number of atomic wavefunctions over which one is projecting ... again, > can you figure out why ? > As NPW >> NATOMWFC no surprise they differ in some portion of the energy > axis. > Since approximations like LCAO are usually reasonable the occupied > portion of the energy axis is usually well described but sooner or > later the pdos must drop to zero while the dos likely goes on for a > while (forever for infinite cutoff). > > hope this helps > stefano > > Luis wrote: > > > Dear QE users, > > > > I have performed a DOS calculation of a metal oxide system with some > > adsorbates. > > Then I plot the total DOS using the file myfile.pdos_tot, and I also plot > > the sum of the PDOS generated by the program sumpdos.x included in the > > Quantum Espresso package. > > In principle both plots should give the same, but what I see is that the > DOS > > plots for the zone of the unoccupied bands do not overlap. In particular, > > the DOS area generated with the sumpdos.x program is considerably > smaller. > > I can't understand why do I encounter this difference. Is there a reason > for > > that? > > > > Thank you > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/032b9766/attachment-0001.htm From jiejiangnc at gmail.com Sat Nov 6 21:40:10 2010 From: jiejiangnc at gmail.com (Jie Jiang) Date: Sat, 6 Nov 2010 16:40:10 -0400 Subject: [Pw_forum] Constrained occupation In-Reply-To: <4CD54F23.2000009@materials.ox.ac.uk> References: <4CD52B70.1050005@sissa.it> <4CD54F23.2000009@materials.ox.ac.uk> Message-ID: On Sat, Nov 6, 2010 at 8:50 AM, Nicola Marzari < nicola.marzari at materials.ox.ac.uk> wrote: > On 11/6/10 10:18 AM, Stefano de Gironcoli wrote: > > Dear Jie, > > as Gabriele was saying constrained DFT is not implemented in PWscf: > > it is not so easy to force occupation of specific atomic-like levels in > > a plane-wave basis. > > Dear Nicola, Stefano, and Gabriele, > > Thank you very much for your information, > > One thing I would like to emphasis is that I want to constrain electron > occupations of Kohn-Sham orbitals instead of atomic-like levels. The method is usually called Delta-scf DFT, > > Will this makes some differences in implementation ? Thanks in advance, Jie > Dear Jie, > > with Patrick Sit and Matteo Cococcioni we did implement constrained DFT > in the cp code a few years ago - Patrick (cc'd here, now in Princeton) > has a working version of the code (and hopefully it will at a certain > point make it into the public distribution). > > At the end the procedure is similar to what Stefano has just described - > one adds a penalty for occupation matrices on a chosen manifold > that are different from a desired target - by making the penalty very > large one can make it into an exact constraint, or one could impose > directly a Lagrange multiplier. > > Any code that has a working version of DFT+U should be easy to > modify to make it into constrained DFT - you change the orbitals > onto which you make the projections, and add a penalty or a > Lagrange multiplier to force approximately or exactly the constraint > that you want. > > nicola > > > > > PS: H.-L. Sit, M. Cococcioni, and N. Marzari, "Realistic, Quantitative > Descriptions of Electron-Transfer Reactions: Diabatic Surfaces from > First-Principles Molecular Dynamics," Phys. Rev. Lett. 97, 028303 > (2006). > > Sit P. H.-L., Cococcioni M., Marzari N. "Car-Parrinello molecular > dynamics in the DFT+U formalism: Structure and energetics of solvated > ferrous and ferric ions" Journal of Electroanalytical Chemistry 607, > 107-112, (2007) > -- > ---------------------------------------------------------------------- > 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/20101106/189df331/attachment.htm From giannozz at democritos.it Sat Nov 6 21:58:30 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 6 Nov 2010 21:58:30 +0100 Subject: [Pw_forum] restart in phonon calculation In-Reply-To: References: Message-ID: <45E0EDC9-98F1-483E-923B-FE987FB1D168@democritos.it> On Nov 6, 2010, at 8:26 , Vera Klekovkina wrote: > Then I try to preform Restart in Phonon calculation it happens the > error: > > from ph_writefile : error # 47 > cannot open xml_recover file for writing with so little information, it is impossible to say anything. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Nov 6 22:03:30 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 6 Nov 2010 22:03:30 +0100 Subject: [Pw_forum] Constrained occupation In-Reply-To: References: <4CD52B70.1050005@sissa.it> <4CD54F23.2000009@materials.ox.ac.uk> Message-ID: <100890AD-9B67-49CD-8139-8E1AB9D11994@democritos.it> On Nov 6, 2010, at 21:40 , Jie Jiang wrote: > One thing I would like to emphasis is that I want to constrain > electron > occupations of Kohn-Sham orbitals instead of atomic-like levels. The > method is usually called Delta-scf DFT you can do this if you use the Gamma-point (k=0) only, not in general P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From baroni at sissa.it Sat Nov 6 22:10:31 2010 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 6 Nov 2010 22:10:31 +0100 Subject: [Pw_forum] Constrained occupation In-Reply-To: <100890AD-9B67-49CD-8139-8E1AB9D11994@democritos.it> References: <4CD52B70.1050005@sissa.it> <4CD54F23.2000009@materials.ox.ac.uk> <100890AD-9B67-49CD-8139-8E1AB9D11994@democritos.it> Message-ID: Also, be advised that the larger the system, the more \delta SCF energies would approach KS orbital energies, because the charge-density distribution of an extended wavefunction tends to zero with the system size ... SB On Nov 6, 2010, at 10:03 PM, Paolo Giannozzi wrote: > > On Nov 6, 2010, at 21:40 , Jie Jiang wrote: > >> One thing I would like to emphasis is that I want to constrain >> electron >> occupations of Kohn-Sham orbitals instead of atomic-like levels. The >> method is usually called Delta-scf DFT > > you can do this if you use the Gamma-point (k=0) only, not in general > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, 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 --- 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/20101106/316a8ee1/attachment.htm From giannozz at democritos.it Sat Nov 6 22:33:00 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 6 Nov 2010 22:33:00 +0100 Subject: [Pw_forum] Total DOS and sum of PDOS don't overlap In-Reply-To: References: Message-ID: On Nov 6, 2010, at 13:56 , Masoud Nahali wrote: > If I am correct , I feel that the non-orthonormality > of atomic states on different atoms may affect > the projected properties like PDOS. it can affect projected properties because one can use different techniques to project over a non-orthonormal manifold, if I remember correctly. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jiejiangnc at gmail.com Sat Nov 6 22:49:44 2010 From: jiejiangnc at gmail.com (Jie Jiang) Date: Sat, 6 Nov 2010 17:49:44 -0400 Subject: [Pw_forum] Constrained occupation In-Reply-To: <100890AD-9B67-49CD-8139-8E1AB9D11994@democritos.it> References: <4CD52B70.1050005@sissa.it> <4CD54F23.2000009@materials.ox.ac.uk> <100890AD-9B67-49CD-8139-8E1AB9D11994@democritos.it> Message-ID: Dear Paolo, Thank you. you can do this if you use the Gamma-point (k=0) only, not in general > > Is it possible to extend to more k points. Jie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/bffa1f80/attachment.htm From nicola.marzari at materials.ox.ac.uk Sat Nov 6 22:50:30 2010 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Sat, 06 Nov 2010 21:50:30 +0000 Subject: [Pw_forum] Constrained occupation Message-ID: <4CD5CDA6.1090202@materials.ox.ac.uk> On 11/6/10 9:05 PM, Paolo Giannozzi wrote: > > On Nov 6, 2010, at 13:50 , Nicola Marzari wrote: > >> with Patrick Sit and Matteo Cococcioni we did implement constrained DFT >> in the cp code a few years ago - Patrick (cc'd here, now in Princeton) >> has a working version of the code (and hopefully it will at a certain >> point make it into the public distribution). > Paolo G. tells me it's actually already in the distribution, albeit with a somewhat sparse documentation (I think you meant "somewhat sparse", Paolo, correct?) 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 nicola.marzari at materials.ox.ac.uk Sat Nov 6 23:03:40 2010 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Sat, 06 Nov 2010 22:03:40 +0000 Subject: [Pw_forum] Constrained occupation In-Reply-To: References: <4CD52B70.1050005@sissa.it> <4CD54F23.2000009@materials.ox.ac.uk> <100890AD-9B67-49CD-8139-8E1AB9D11994@democritos.it> Message-ID: <4CD5D0BC.2040801@materials.ox.ac.uk> Dear Jie, you need to consider what "more k-points" means - if you do delta scf on a Bloch state you have a zero correction, as Stefano pointed out. You can do it on a Wannier function (a sum of Bloch states for all k-points), but then you do not have delta scf, and it's not very different from having it on, say, an atomic orbital. nicola On 11/6/10 9:49 PM, Jie Jiang wrote: > Dear Paolo, > > Thank you. > > you can do this if you use the Gamma-point (k=0) only, not in general > > > Is it possible to extend to more k points. > > Jie > -- ---------------------------------------------------------------------- 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 Sat Nov 6 23:03:52 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 6 Nov 2010 23:03:52 +0100 Subject: [Pw_forum] Constrained occupation In-Reply-To: References: <4CD52B70.1050005@sissa.it> <4CD54F23.2000009@materials.ox.ac.uk> <100890AD-9B67-49CD-8139-8E1AB9D11994@democritos.it> Message-ID: <391D7F4B-016A-4589-9E45-5802CF67D3AC@democritos.it> On Nov 6, 2010, at 22:49 , Jie Jiang wrote: > Is it possible to extend to more k points. no --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Sat Nov 6 23:06:22 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 6 Nov 2010 23:06:22 +0100 Subject: [Pw_forum] Constrained occupation In-Reply-To: <4CD5CDA6.1090202@materials.ox.ac.uk> References: <4CD5CDA6.1090202@materials.ox.ac.uk> Message-ID: On Nov 6, 2010, at 22:50 , Nicola Marzari wrote: > Paolo G. tells me it's actually already in the distribution in the CVS, or at least, I think so > albeit with a somewhat sparse documentation (I think you meant > "somewhat sparse", Paolo, correct?) "nonexistent" is a better description, I think P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From jiejiangnc at gmail.com Sat Nov 6 23:13:41 2010 From: jiejiangnc at gmail.com (Jie Jiang) Date: Sat, 6 Nov 2010 18:13:41 -0400 Subject: [Pw_forum] Constrained occupation In-Reply-To: <4CD5D0BC.2040801@materials.ox.ac.uk> References: <4CD52B70.1050005@sissa.it> <4CD54F23.2000009@materials.ox.ac.uk> <100890AD-9B67-49CD-8139-8E1AB9D11994@democritos.it> <4CD5D0BC.2040801@materials.ox.ac.uk> Message-ID: Dear Nicola > you need to consider what "more k-points" means - if you do > delta scf on a Bloch state you have a zero correction, as Stefano > pointed out. You can do it on a Wannier function (a sum of Bloch states > for all k-points), but then you do not have delta scf, and it's not > very different from having it on, say, an atomic orbital. > > I got your points. Thanks, Jie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/5a0c6706/attachment.htm From jiejiangnc at gmail.com Sat Nov 6 23:21:44 2010 From: jiejiangnc at gmail.com (Jie Jiang) Date: Sat, 6 Nov 2010 18:21:44 -0400 Subject: [Pw_forum] Constrained occupation In-Reply-To: <4CD5CDA6.1090202@materials.ox.ac.uk> References: <4CD5CDA6.1090202@materials.ox.ac.uk> Message-ID: Nice news. Thank you, Nicola. > Paolo G. tells me it's actually already in the distribution, albeit > with a somewhat sparse documentation (I think you meant "somewhat > sparse", Paolo, correct?) > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/dbc53050/attachment.htm From jiejiangnc at gmail.com Sat Nov 6 23:34:22 2010 From: jiejiangnc at gmail.com (Jie Jiang) Date: Sat, 6 Nov 2010 18:34:22 -0400 Subject: [Pw_forum] Constrained occupation In-Reply-To: References: <4CD5CDA6.1090202@materials.ox.ac.uk> Message-ID: Dear Paolo, in the CVS, or at least, I think so > > Thank you. "nonexistent" is a better description, I think > > > It will be helpful if anyone can briefly tell how to use it. Jie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/77c22ced/attachment.htm From jiejiangnc at gmail.com Sun Nov 7 02:11:47 2010 From: jiejiangnc at gmail.com (Jie Jiang) Date: Sat, 6 Nov 2010 21:11:47 -0400 Subject: [Pw_forum] Constrained occupation In-Reply-To: References: <4CD5CDA6.1090202@materials.ox.ac.uk> Message-ID: Dear Paolo in the CVS, or at least, I think so > > Do you know in which directories ? Thank you, Jie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101106/7a7a37e9/attachment.htm From giannozz at democritos.it Sun Nov 7 09:28:28 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 7 Nov 2010 09:28:28 +0100 Subject: [Pw_forum] Constrained occupation In-Reply-To: References: <4CD5CDA6.1090202@materials.ox.ac.uk> Message-ID: <6B67EA9F-B831-4F58-A25F-7D50B334DDF7@democritos.it> On Nov 7, 2010, at 2:11 , Jie Jiang wrote: > Do you know in which directories ? only in CP P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From abmus911 at yahoo.ie Mon Nov 8 08:31:04 2010 From: abmus911 at yahoo.ie (bayo mus) Date: Mon, 8 Nov 2010 07:31:04 +0000 (GMT) Subject: [Pw_forum] band structure Message-ID: <94203.92312.qm@web29610.mail.ird.yahoo.com> Dear all From the examples i learnt so far on QE about band structure, I observed that they r just fore simple system Si Ni Al e.t.c Please I want to ask if QE can be used to calculate the band structure of systems like SiO2, ZnO, KAl Si3O8 e.t.c. If yes then I would be grateful for any materials that would be of assistance. thanls Musari A.A University of Agriculture Nigeria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101108/5eed0462/attachment.htm From prayerz.omo at gmail.com Mon Nov 8 08:53:35 2010 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Mon, 8 Nov 2010 02:53:35 -0500 Subject: [Pw_forum] xml_recover problem with phonon (ph.x) restart job Message-ID: Ciao tutti, I am trying to re-start a phonon calculation job on an sp6 machine (CINECA) but I got the following error: cannot open xml_recover file for writing This error was reported in the past (see following link). Does anyone know how to quickly fix this problem? Alternatively, does anyone know where I can get version 4.05 of Quantum-Espresso? The poster of the message below said the restart works for version 4.05. http://qe-forge.org/tracker/?func=detail&atid=133&aid=27&group_id=10 Vi ringrazio. Omololu ICTP, Italy. -- ***************** Seek GOD! ************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101108/8a75289b/attachment.htm From giannozz at democritos.it Mon Nov 8 09:03:11 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 08 Nov 2010 09:03:11 +0100 Subject: [Pw_forum] xml_recover problem with phonon (ph.x) restart job In-Reply-To: References: Message-ID: <4CD7AEBF.20606@democritos.it> Omololu Akin-Ojo wrote: > Alternatively, does anyone know where I can get version 4.05 of > Quantum-Espresso? Download page (http://www.quantum-espresso.org/download.php), link "Previous versions" (http://www.quantum-espresso.org/previousVersion.php Reminder: only the latest version is maintained (i.e. bugs are fixed), and only for a limited amount of time. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From prayerz.omo at gmail.com Mon Nov 8 09:16:39 2010 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Mon, 8 Nov 2010 03:16:39 -0500 Subject: [Pw_forum] xml_recover problem with phonon (ph.x) restart job In-Reply-To: <4CD7AEBF.20606@democritos.it> References: <4CD7AEBF.20606@democritos.it> Message-ID: Thank you, Paolo. I will try it (ver. 4.0.5) anyway. If it's ph..x gives the same results as ver. 4.2/1, I will hope it is bug-free. La ringrazio. o. On Mon, Nov 8, 2010 at 3:03 AM, Paolo Giannozzi wrote: > Omololu Akin-Ojo wrote: > > > Alternatively, does anyone know where I can get version 4.05 of > > Quantum-Espresso? > > Download page (http://www.quantum-espresso.org/download.php), > link "Previous versions" > (http://www.quantum-espresso.org/previousVersion.php > > Reminder: only the latest version is maintained (i.e. bugs > are fixed), and only for a limited amount of time. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ***************** Seek GOD! ************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101108/be46ad11/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Mon Nov 8 11:24:11 2010 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 08 Nov 2010 11:24:11 +0100 Subject: [Pw_forum] band structure In-Reply-To: <94203.92312.qm@web29610.mail.ird.yahoo.com> References: <94203.92312.qm@web29610.mail.ird.yahoo.com> Message-ID: On Mon, 08 Nov 2010 08:31:04 +0100, bayo mus wrote: > From the examples i learnt so far on QE about band structure, I observed > that they r just fore simple system Si Ni Al e.t.c Please I want to ask > if QE can be used to calculate the band structure of systems like SiO2, > ZnO, KAl Si3O8 e.t.c. Dear Musari, those are just examples, of course you can compute the band structure for any material. > If yes then I would be grateful for any materials that would be of > assistance. The procedure is exactly the same as in the examples. If you have any specific problem, please ask. 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 elbuesta at icqmail.com Mon Nov 8 12:56:33 2010 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Mon, 08 Nov 2010 06:56:33 -0500 Subject: [Pw_forum] xml_recover problem with phonon (ph.x) restart job In-Reply-To: References: Message-ID: <8CD4D531F9079A6-C6C-6CE3@webmail-m102.sysops.aol.com> When that happens to me on cineca, removing all the temporary files on scratch except the "_phprefix.phsave" directory usually works for me, as suggested on the manual for phonon calculations. "This mechanism allows: 1) To recover part of the ph.x calculation even if the recover file or files are corrupted. You just remove the _phprefix.recover files from the tmp_dir directory. You can also remove all the _ph files and keep only the _phprefix.phsave directory. " But I have to admit that, nowadys, in order to avoid this error, I always split my phonon calculations into several smaller parts that can run in the time limit allowed by cineca. I hope it helps. Fabio Negreiros Ribeiro IPCF - CNR, Pisa - Italy -----Original Message----- From: Omololu Akin-Ojo To: pw_forum at pwscf.org Sent: Mon, Nov 8, 2010 8:53 am Subject: [Pw_forum] xml_recover problem with phonon (ph.x) restart job Ciao tutti, I am trying to re-start a phonon calculation job on an sp6 machine (CINECA) but I got the following error: cannot open xml_recover file for writing This error was reported in the past (see following link). Does anyone know how to quickly fix this problem? Alternatively, does anyone know where I can get version 4.05 of Quantum-Espresso? The poster of the message below said the restart works for version 4.05. http://qe-forge.org/tracker/?func=detail&atid=133&aid=27&group_id=10 Vi ringrazio. Omololu ICTP, Italy. -- ***************** Seek GOD! ************* _______________________________________________ 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/20101108/41734236/attachment.htm From eyvaz_isaev at yahoo.com Mon Nov 8 14:54:20 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 8 Nov 2010 05:54:20 -0800 (PST) Subject: [Pw_forum] LDA+DMFT In-Reply-To: <1ed8ff7f.1991.12c1ee4e75e.Coremail.wangqj1@126.com> References: <1ed8ff7f.1991.12c1ee4e75e.Coremail.wangqj1@126.com> Message-ID: <779254.76683.qm@web65701.mail.ac4.yahoo.com> Hi , > From: Q.J.Wang > I want to learn LDA+DMFT method, can you introduce some references which use >LDA+DMFT shcemes Search via Google the next very famous DMFT authors: Kotlyar, Georges, Lichtenshtein, Katsnelson. Then you can find (at least) 2 review papers by Georges and Katsnelson and many others. 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101108/3ada094b/attachment.htm From ssdhayal at gmail.com Mon Nov 8 21:49:39 2010 From: ssdhayal at gmail.com (Suman Dhayal) Date: Mon, 8 Nov 2010 14:49:39 -0600 Subject: [Pw_forum] X-ray emission spectra! Message-ID: hi, I want to do the calculations for the emission of X-rays when Hydrogen atom put into external electric field but I am not sure if I could do this using Quantum Espresso. It does talk about X-ray absorption spectra, so I was feeling that through the same guidelines if I could do the emission calculations? So I am very confused. If yes, which files could I get the appropriate information from, for making the input file for it and also the theoretical methods for it?? I will be very thankful for the kind help. Thank you so much, Harli -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101108/058bbbf7/attachment.htm From miaoms at mrl.ucsb.edu Tue Nov 9 04:48:58 2010 From: miaoms at mrl.ucsb.edu (Maosheng Miao) Date: Mon, 8 Nov 2010 19:48:58 -0800 Subject: [Pw_forum] atomic energy levels in pseudopotential generation Message-ID: <26A3497C-9EC4-49CF-8DB7-868F52043E92@mrl.ucsb.edu> Dear QE professionals, This is a question for pseudopotential generation, or rather for atomic calculations of DFT. I have been using 'atomic' to generate pseudopotentials. However, I found the following trend for energy levels. For example, comparing Rh and Ir orbital energies, I found: Rh: 5s -0.316 Ry 4d: -0.4366 Ry Ir: 6s -0.4653 Ry 5d: -0.5253 Ry I think the unit is in Ry. Am I right? I wonder whether the 5s level should be lower than 6s and 4d lower than 5d. The HF levels as shown in Harrison's book (Electronic structure and the properties of solids, Dover 1980) are in the increasing order while move from 4d to 5d transition metals. I attached the input for Rh which is taken from ~atomic_doc/pseudo_library/PBE/SR: &input title='Rh', zed=45., rel=1, config='[Kr] 4d7.0 5s2.0 5p0.0', iswitch=3, dft='PBE' / &inputp lloc=0, pseudotype=3, file_pseudopw='Rh_ScaRel.UPF', nlcc=.true., rcore=0.9, author='ADC', / 4 5P 2 1 0.00 0.00 2.40 2.40 1 4D 3 2 7.00 0.00 1.90 2.20 1 4D 3 2 0.00 -0.30 1.90 2.20 1 5S 1 0 2.00 0.00 2.20 2.20 1 Thanks for your help, Maosheng Maosheng Miao, Ph. D Materials Research Laboratory University of California Santa Barbara miaoms at mrl.ucsb.edu From ac.rain at inbox.com Tue Nov 9 08:19:37 2010 From: ac.rain at inbox.com (ac.rain at inbox.com) Date: Mon, 8 Nov 2010 23:19:37 -0800 Subject: [Pw_forum] QE: install problem, 4.2.1 Message-ID: Hi all, I am having some troubles getting Quantum Espresso to build on a Linux system (CentOS 5.5) x86_64. my current issue is getting passed the iotk error... export CC=gcc export MPIF90=mpf90 export PATH=/usr/local/mpich2-install/bin:$PATH (to make sure mpf90 location is in the $PATH, mpich2 was compiled with gfortran support!) export F90=gfortran after ./configure ,the "make all" output is shown below... # make all test -d bin || mkdir bin if test -e extlibs/archive/iotk-1.1.beta.tar.gz ; then \ ( cd extlibs ; make libiotk) ; fi make[1]: Entering directory `/home/user/espresso-4.2.1/extlibs' if test ! -d ../S3DE; then \ (gzip -dc archive/iotk-1.1.beta.tar.gz | (cd ../; tar -xvf -)) ; \ if test -e install/Makefile_iotk; then \ (cp install/Makefile_iotk ../S3DE/iotk/src/Makefile); fi; \ if test -e install/iotk_config.h; then \ (cp install/iotk_config.h ../S3DE/iotk/include/iotk_config.h); fi; fi cd ../S3DE/iotk/src; make lib+util; make[2]: Entering directory `/home/user/espresso-4.2.1/S3DE/iotk/src' O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_base.f90 make[2]: O3: Command not found make[2]: [iotk_base.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_attr_interf.f90 make[2]: O3: Command not found make[2]: [iotk_attr_interf.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_error_interf.f90 make[2]: O3: Command not found make[2]: [iotk_error_interf.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_misc_interf.f90 make[2]: O3: Command not found make[2]: [iotk_misc_interf.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_str_interf.f90 make[2]: O3: Command not found make[2]: [iotk_str_interf.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_attr+CHARACTER1_0.f90 make[2]: O3: Command not found make[2]: [iotk_attr+CHARACTER1_0.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_fmt_interf.f90 make[2]: O3: Command not found make[2]: [iotk_fmt_interf.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_xtox_interf.f90 make[2]: O3: Command not found make[2]: [iotk_xtox_interf.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_attr+COMPLEX1_0.f90 make[2]: O3: Command not found make[2]: [iotk_attr+COMPLEX1_0.o] Error 127 (ignored) ....I omitted 2 pages of errors here that look very similar to the above and below lines.... O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_unit_list.f90 make[2]: O3: Command not found make[2]: [iotk_unit_list.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_unit.f90 make[2]: O3: Command not found make[2]: [iotk_unit.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_write.f90 make[2]: O3: Command not found make[2]: [iotk_write.o] Error 127 (ignored) O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW -I../include -c iotk_xtox.f90 make[2]: O3: Command not found make[2]: [iotk_xtox.o] Error 127 (ignored) ar ruv libiotk.a iotk_attr+CHARACTER1_0.o iotk_attr+COMPLEX1_0.o iotk_attr+COMPLEX1_3.o iotk_attr+COMPLEX1_6.o iotk_attr+COMPLEX2_0.o iotk_attr+COMPLEX2_3.o iotk_attr+COMPLEX2_6.o iotk_attr+COMPLEX3_0.o iotk_attr+COMPLEX3_3.o iotk_attr+COMPLEX3_6.o iotk_attr+COMPLEX4_0.o iotk_attr+COMPLEX4_3.o iotk_attr+COMPLEX4_6.o iotk_attr.o iotk_attr+INTEGER1_0.o iotk_attr+INTEGER1_3.o iotk_attr+INTEGER1_6.o iotk_attr+INTEGER2_0.o iotk_attr+INTEGER2_3.o iotk_attr+INTEGER2_6.o iotk_attr+INTEGER3_0.o iotk_attr+INTEGER3_3.o iotk_attr+INTEGER3_6.o iotk_attr+INTEGER4_0.o iotk_attr+INTEGER4_3.o iotk_attr+INTEGER4_6.o iotk_attr_interf.o iotk_attr+LOGICAL1_0.o iotk_attr+LOGICAL1_3.o iotk_attr+LOGICAL1_6.o iotk_attr+LOGICAL2_0.o iotk_attr+LOGICAL2_3.o iotk_attr+LOGICAL2_6.o iotk_attr+LOGICAL3_0.o iotk_attr+LOGICAL3_3.o iotk_attr+LOGICAL3_6.o iotk_attr+LOGICAL4_0.o iotk_attr+LOGICAL4_3.o iotk_attr+LOGICAL4_6.o iotk_attr+REAL1_0.o iotk_attr+REAL1_3.o iotk_attr+REAL1_6.o iotk_attr+REAL2_0.o iotk_attr+REAL2_3.o iotk_attr+REAL2_6.o iotk_attr+REAL3_0.o iotk_attr+REAL3_3.o iotk_attr+REAL3_6.o iotk_attr+REAL4_0.o iotk_attr+REAL4_3.o iotk_attr+REAL4_6.o iotk_base.o iotk_dat+CHARACTER1_0.o iotk_dat+CHARACTER1_3.o iotk_dat+CHARACTER1_6.o iotk_dat+COMPLEX1_0.o iotk_dat+COMPLEX1_3.o iotk_dat+COMPLEX1_6.o iotk_dat+COMPLEX2_0.o iotk_dat+COMPLEX2_3.o iotk_dat+COMPLEX2_6.o iotk_dat+COMPLEX3_0.o iotk_dat+COMPLEX3_3.o iotk_dat+COMPLEX3_6.o iotk_dat+COMPLEX4_0.o iotk_dat+COMPLEX4_3.o iotk_dat+COMPLEX4_6.o iotk_dat.o iotk_dat+INTEGER1_0.o iotk_dat+INTEGER1_3.o iotk_dat+INTEGER1_6.o iotk_dat+INTEGER2_0.o iotk_dat+INTEGER2_3.o iotk_dat+INTEGER2_6.o iotk_dat+INTEGER3_0.o iotk_dat+INTEGER3_3.o iotk_dat+INTEGER3_6.o iotk_dat+INTEGER4_0.o iotk_dat+INTEGER4_3.o iotk_dat+INTEGER4_6.o iotk_dat_interf.o iotk_dat+LOGICAL1_0.o iotk_dat+LOGICAL1_3.o iotk_dat+LOGICAL1_6.o iotk_dat+LOGICAL2_0.o iotk_dat+LOGICAL2_3.o iotk_dat+LOGICAL2_6.o iotk_dat+LOGICAL3_0.o iotk_dat+LOGICAL3_3.o iotk_dat+LOGICAL3_6.o iotk_dat+LOGICAL4_0.o iotk_dat+LOGICAL4_3.o iotk_dat+LOGICAL4_6.o iotk_dat+REAL1_0.o iotk_dat+REAL1_3.o iotk_dat+REAL1_6.o iotk_dat+REAL2_0.o iotk_dat+REAL2_3.o iotk_dat+REAL2_6.o iotk_dat+REAL3_0.o iotk_dat+REAL3_3.o iotk_dat+REAL3_6.o iotk_dat+REAL4_0.o iotk_dat+REAL4_3.o iotk_dat+REAL4_6.o iotk_error.o iotk_error_interf.o iotk_files.o iotk_files_interf.o iotk_fmt.o iotk_fmt_interf.o iotk_misc.o iotk_misc_interf.o iotk_module.o iotk_scan.o iotk_scan_interf.o iotk_stream.o iotk_stream_interf.o iotk_str.o iotk_str_interf.o iotk_tool.o iotk_tool_interf.o iotk_unit.o iotk_unit_interf.o iotk_unit_list.o iotk_write.o iotk_write_interf.o iotk_xtox.o iotk_xtox_interf.o ar: creating libiotk.a ar: iotk_attr+CHARACTER1_0.o: No such file or directory make[2]: *** [libiotk.a] Error 1 make[2]: Leaving directory `/home/user/espresso-4.2.1/S3DE/iotk/src' make[1]: *** [libiotk] Error 2 make[1]: Leaving directory `/home/user/espresso-4.2.1/extlibs' make: *** [libiotk] Error 2 # As you can see it passes -03 to the shell instead of the compiler, I have Fortran and Gcc people telling me the problem is application-specific. Any help is appreciated. regards, nick - Linux Administrator ____________________________________________________________ Send any screenshot to your friends in seconds... Works in all emails, instant messengers, blogs, forums and social networks. TRY IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if2 for FREE From giannozz at democritos.it Tue Nov 9 11:11:47 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 09 Nov 2010 11:11:47 +0100 Subject: [Pw_forum] QE: install problem, 4.2.1 In-Reply-To: References: Message-ID: <4CD91E63.8000101@democritos.it> ac.rain at inbox.com wrote: > export CC=gcc > export MPIF90=mpf90 > export F90=gfortran "configure" sometimes doesn't like pre-set environment variables. Look into make.sys and complete it. Most likely MPIF90 of F90 are set to nothing P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giuseppe.mattioli at mlib.ism.cnr.it Tue Nov 9 11:59:21 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 9 Nov 2010 11:59:21 +0100 Subject: [Pw_forum] tddfpt.x manual Message-ID: <201011091159.22113.giuseppe.mattioli@mlib.ism.cnr.it> Dear all (or, I suppose, dear Ralph or Dario...) I 'm playing around with tddfpt.x. I've been at nanoexcite2010, so I should be able to set up something not so wrong. However, is there any manual hidden somewhere, just because I do not remember a couple of things? Yours Giuseppe -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00016 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From baroni at sissa.it Tue Nov 9 17:18:08 2010 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 9 Nov 2010 17:18:08 +0100 Subject: [Pw_forum] tddfpt.x manual In-Reply-To: <201011091159.22113.giuseppe.mattioli@mlib.ism.cnr.it> References: <201011091159.22113.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: a CPC paper is being prepared (since several months, already ...) if and when the purported authors will find the time to complete it, it will hopefully contain the info you are righteously looking for hold on, and we'll be back hopefully soon Stefano B On Nov 9, 2010, at 11:59 AM, Giuseppe Mattioli wrote: > > Dear all (or, I suppose, dear Ralph or Dario...) > I 'm playing around with tddfpt.x. I've been at nanoexcite2010, so I should be > able to set up something not so wrong. However, is there any manual hidden > somewhere, just because I do not remember a couple of things? > Yours > Giuseppe > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00016 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- 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/20101109/0f66320a/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Tue Nov 9 14:54:32 2010 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Tue, 9 Nov 2010 14:54:32 +0100 Subject: [Pw_forum] tddfpt.x manual In-Reply-To: References: <201011091159.22113.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <201011091454.33044.giuseppe.mattioli@mlib.ism.cnr.it> Thanks Stefano. I was exactly looking for comments on input variables... I've checked the lr_readin.f90 file but it does not help very much. I shall wait for the new QE release... Giuseppe On Tuesday 09 November 2010 17:18:08 Stefano Baroni wrote: > a CPC paper is being prepared (since several months, already ...) > if and when the purported authors will find the time to complete it, it > will hopefully contain the info you are righteously looking for hold on, > and we'll be back hopefully soon > Stefano B > > On Nov 9, 2010, at 11:59 AM, Giuseppe Mattioli wrote: > > Dear all (or, I suppose, dear Ralph or Dario...) > > I 'm playing around with tddfpt.x. I've been at nanoexcite2010, so I > > should be able to set up something not so wrong. However, is there any > > manual hidden somewhere, just because I do not remember a couple of > > things? > > Yours > > Giuseppe > > > > -- > > ******************************************************** > > - Article premier - Les hommes naissent et demeurent > > libres et ?gaux en droits. Les distinctions sociales > > ne peuvent ?tre fond?es que sur l'utilit? commune > > - Article 2 - Le but de toute association politique > > est la conservation des droits naturels et > > imprescriptibles de l'homme. Ces droits sont la libert?, > > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > > ******************************************************** > > > > Giuseppe Mattioli > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > > v. Salaria Km 29,300 - C.P. 10 > > I 00016 - Monterotondo Stazione (RM) > > Tel + 39 06 90672836 - Fax +39 06 90672316 > > E-mail: > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > 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 -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00016 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From giannozz at democritos.it Tue Nov 9 17:33:22 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 09 Nov 2010 17:33:22 +0100 Subject: [Pw_forum] atomic energy levels in pseudopotential generation In-Reply-To: <26A3497C-9EC4-49CF-8DB7-868F52043E92@mrl.ucsb.edu> References: <26A3497C-9EC4-49CF-8DB7-868F52043E92@mrl.ucsb.edu> Message-ID: <4CD977D2.5020002@democritos.it> Maosheng Miao wrote: > comparing Rh and Ir orbital energies, I found: > Rh: 5s -0.316 Ry 4d: -0.4366 Ry > Ir: 6s -0.4653 Ry 5d: -0.5253 Ry > I think the unit is in Ry. Am I right? the units are explicitly printed out. Rh: n l nl e(Ry) e(Ha) e(eV) 1 0 1S 1( 2.00) -1693.6034 -846.8017 -23042.6466 2 0 2S 1( 2.00) -245.7815 -122.8908 -3344.0274 2 1 2P 1( 6.00) -220.2944 -110.1472 -2997.2583 3 0 3S 1( 2.00) -44.1540 -22.0770 -600.7458 3 1 3P 1( 6.00) -35.7754 -17.8877 -486.7489 4 0 4S 1( 2.00) -6.3286 -3.1643 -86.1056 4 1 4P 1( 6.00) -3.9598 -1.9799 -53.8752 3 2 3D 1(10.00) -22.3817 -11.1908 -304.5179 4 2 4D 1( 7.00) -0.6379 -0.3190 -8.6797 5 0 5S 1( 2.00) -0.3909 -0.1954 -5.3184 5 1 5P 1( 0.00) -0.0969 -0.0484 -1.3179 Ir: n l nl e(Ry) e(Ha) e(eV) 1 0 1S 1( 2.00) -5596.0964 -2798.0482 -76138.7642 2 0 2S 1( 2.00) -978.9319 -489.4659 -13319.0456 2 1 2P 1( 6.00) -850.3234 -425.1617 -11569.2380 3 0 3S 1( 2.00) -228.9657 -114.4829 -3115.2374 3 1 3P 1( 6.00) -191.3672 -95.6836 -2603.6837 4 0 4S 1( 2.00) -48.8466 -24.4233 -664.5923 4 1 4P 1( 6.00) -36.5182 -18.2591 -496.8555 3 2 3D 1(10.00) -150.0207 -75.0103 -2041.1353 5 0 5S 1( 2.00) -7.2018 -3.6009 -97.9857 5 1 5P 1( 6.00) -4.0203 -2.0101 -54.6985 4 2 4D 1(10.00) -21.3872 -10.6936 -290.9871 4 3 4F 1(14.00) -4.5710 -2.2855 -62.1917 5 2 5D 1( 7.00) -0.5253 -0.2627 -7.1474 6 0 6S 1( 2.00) -0.4653 -0.2327 -6.3312 6 1 6P 1( 0.00) -0.0894 -0.0447 -1.2158 P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Tue Nov 9 18:01:33 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 09 Nov 2010 18:01:33 +0100 Subject: [Pw_forum] QE: install problem, 4.2.1 In-Reply-To: References: Message-ID: <4CD97E6D.6020706@democritos.it> ac.rain at inbox.com wrote: > export MPIF90=mpf90 I think this is the problem: "mpf90" is not in the path or not existent and "configure" gets an empty string when it checks if it exists and works P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From miaoms at mrl.ucsb.edu Tue Nov 9 18:22:42 2010 From: miaoms at mrl.ucsb.edu (Maosheng Miao) Date: Tue, 9 Nov 2010 09:22:42 -0800 Subject: [Pw_forum] atomic energy levels in pseudopotential generation In-Reply-To: <4CD977D2.5020002@democritos.it> References: <26A3497C-9EC4-49CF-8DB7-868F52043E92@mrl.ucsb.edu> <4CD977D2.5020002@democritos.it> Message-ID: <6DBB8B18-F8F5-4C54-85B4-588DA3411261@mrl.ucsb.edu> Prof. Giannozzi, Thanks for answering my question. However, your number is different to mine. Could you post the input file for Rh and Ir? I assume they both use scalar relativity form. Thanks, Maosheng On Nov 9, 2010, at 8:33 AM, Paolo Giannozzi wrote: > Maosheng Miao wrote: > >> comparing Rh and Ir orbital energies, I found: >> Rh: 5s -0.316 Ry 4d: -0.4366 Ry >> Ir: 6s -0.4653 Ry 5d: -0.5253 Ry >> I think the unit is in Ry. Am I right? > > the units are explicitly printed out. > Rh: > > n l nl e(Ry) e(Ha) e(eV) > 1 0 1S 1( 2.00) -1693.6034 -846.8017 -23042.6466 > 2 0 2S 1( 2.00) -245.7815 -122.8908 -3344.0274 > 2 1 2P 1( 6.00) -220.2944 -110.1472 -2997.2583 > 3 0 3S 1( 2.00) -44.1540 -22.0770 -600.7458 > 3 1 3P 1( 6.00) -35.7754 -17.8877 -486.7489 > 4 0 4S 1( 2.00) -6.3286 -3.1643 -86.1056 > 4 1 4P 1( 6.00) -3.9598 -1.9799 -53.8752 > 3 2 3D 1(10.00) -22.3817 -11.1908 -304.5179 > 4 2 4D 1( 7.00) -0.6379 -0.3190 -8.6797 > 5 0 5S 1( 2.00) -0.3909 -0.1954 -5.3184 > 5 1 5P 1( 0.00) -0.0969 -0.0484 -1.3179 > > Ir: > n l nl e(Ry) e(Ha) e(eV) > 1 0 1S 1( 2.00) -5596.0964 -2798.0482 -76138.7642 > 2 0 2S 1( 2.00) -978.9319 -489.4659 -13319.0456 > 2 1 2P 1( 6.00) -850.3234 -425.1617 -11569.2380 > 3 0 3S 1( 2.00) -228.9657 -114.4829 -3115.2374 > 3 1 3P 1( 6.00) -191.3672 -95.6836 -2603.6837 > 4 0 4S 1( 2.00) -48.8466 -24.4233 -664.5923 > 4 1 4P 1( 6.00) -36.5182 -18.2591 -496.8555 > 3 2 3D 1(10.00) -150.0207 -75.0103 -2041.1353 > 5 0 5S 1( 2.00) -7.2018 -3.6009 -97.9857 > 5 1 5P 1( 6.00) -4.0203 -2.0101 -54.6985 > 4 2 4D 1(10.00) -21.3872 -10.6936 -290.9871 > 4 3 4F 1(14.00) -4.5710 -2.2855 -62.1917 > 5 2 5D 1( 7.00) -0.5253 -0.2627 -7.1474 > 6 0 6S 1( 2.00) -0.4653 -0.2327 -6.3312 > 6 1 6P 1( 0.00) -0.0894 -0.0447 -1.2158 > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at democritos.it Tue Nov 9 18:26:16 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 09 Nov 2010 18:26:16 +0100 Subject: [Pw_forum] atomic energy levels in pseudopotential generation In-Reply-To: <6DBB8B18-F8F5-4C54-85B4-588DA3411261@mrl.ucsb.edu> References: <26A3497C-9EC4-49CF-8DB7-868F52043E92@mrl.ucsb.edu> <4CD977D2.5020002@democritos.it> <6DBB8B18-F8F5-4C54-85B4-588DA3411261@mrl.ucsb.edu> Message-ID: <4CD98438.7080909@democritos.it> Maosheng Miao wrote: > your number is different to mine. Could you post the input file for Rh and Ir? &input atom='Rh', config='[Kr] 4d7.0 5s2.0 5p0.0', dft='PBE' / &input atom='Ir', config='[Xe] 4f14.0 5d7.0 6s2.0 6p0.0', dft='PBE' / -- Paolo Giannozzi, Democritos and University of Udine, Italy From miaoms at mrl.ucsb.edu Tue Nov 9 18:28:52 2010 From: miaoms at mrl.ucsb.edu (Maosheng Miao) Date: Tue, 9 Nov 2010 09:28:52 -0800 Subject: [Pw_forum] atomic energy levels in pseudopotential generation In-Reply-To: <4CD977D2.5020002@democritos.it> References: <26A3497C-9EC4-49CF-8DB7-868F52043E92@mrl.ucsb.edu> <4CD977D2.5020002@democritos.it> Message-ID: <405C1139-2876-4C84-8813-CDCFC03F3D80@mrl.ucsb.edu> Dear Prof. Giannozzi, I figured out the difference. I used configuration of [Kr]4d^8 5s^1 for Rh. and the sample file is [Kr]4d^7 5s^2. I think the ground state of Rh atom is [Kr]4d^8 5s^1. But for generation they should both work. Thanks a lot for your help. Best regards, Maosheng On Nov 9, 2010, at 8:33 AM, Paolo Giannozzi wrote: > Maosheng Miao wrote: > >> comparing Rh and Ir orbital energies, I found: >> Rh: 5s -0.316 Ry 4d: -0.4366 Ry >> Ir: 6s -0.4653 Ry 5d: -0.5253 Ry >> I think the unit is in Ry. Am I right? > > the units are explicitly printed out. > Rh: > > n l nl e(Ry) e(Ha) e(eV) > 1 0 1S 1( 2.00) -1693.6034 -846.8017 -23042.6466 > 2 0 2S 1( 2.00) -245.7815 -122.8908 -3344.0274 > 2 1 2P 1( 6.00) -220.2944 -110.1472 -2997.2583 > 3 0 3S 1( 2.00) -44.1540 -22.0770 -600.7458 > 3 1 3P 1( 6.00) -35.7754 -17.8877 -486.7489 > 4 0 4S 1( 2.00) -6.3286 -3.1643 -86.1056 > 4 1 4P 1( 6.00) -3.9598 -1.9799 -53.8752 > 3 2 3D 1(10.00) -22.3817 -11.1908 -304.5179 > 4 2 4D 1( 7.00) -0.6379 -0.3190 -8.6797 > 5 0 5S 1( 2.00) -0.3909 -0.1954 -5.3184 > 5 1 5P 1( 0.00) -0.0969 -0.0484 -1.3179 > > Ir: > n l nl e(Ry) e(Ha) e(eV) > 1 0 1S 1( 2.00) -5596.0964 -2798.0482 -76138.7642 > 2 0 2S 1( 2.00) -978.9319 -489.4659 -13319.0456 > 2 1 2P 1( 6.00) -850.3234 -425.1617 -11569.2380 > 3 0 3S 1( 2.00) -228.9657 -114.4829 -3115.2374 > 3 1 3P 1( 6.00) -191.3672 -95.6836 -2603.6837 > 4 0 4S 1( 2.00) -48.8466 -24.4233 -664.5923 > 4 1 4P 1( 6.00) -36.5182 -18.2591 -496.8555 > 3 2 3D 1(10.00) -150.0207 -75.0103 -2041.1353 > 5 0 5S 1( 2.00) -7.2018 -3.6009 -97.9857 > 5 1 5P 1( 6.00) -4.0203 -2.0101 -54.6985 > 4 2 4D 1(10.00) -21.3872 -10.6936 -290.9871 > 4 3 4F 1(14.00) -4.5710 -2.2855 -62.1917 > 5 2 5D 1( 7.00) -0.5253 -0.2627 -7.1474 > 6 0 6S 1( 2.00) -0.4653 -0.2327 -6.3312 > 6 1 6P 1( 0.00) -0.0894 -0.0447 -1.2158 > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From miaoms at mrl.ucsb.edu Tue Nov 9 18:29:23 2010 From: miaoms at mrl.ucsb.edu (Maosheng Miao) Date: Tue, 9 Nov 2010 09:29:23 -0800 Subject: [Pw_forum] atomic energy levels in pseudopotential generation In-Reply-To: <4CD98438.7080909@democritos.it> References: <26A3497C-9EC4-49CF-8DB7-868F52043E92@mrl.ucsb.edu> <4CD977D2.5020002@democritos.it> <6DBB8B18-F8F5-4C54-85B4-588DA3411261@mrl.ucsb.edu> <4CD98438.7080909@democritos.it> Message-ID: Thanks a lot. Maosheng On Nov 9, 2010, at 9:26 AM, Paolo Giannozzi wrote: > Maosheng Miao wrote: > >> your number is different to mine. Could you post the input file for Rh and Ir? > > &input > atom='Rh', > config='[Kr] 4d7.0 5s2.0 5p0.0', > dft='PBE' > / > > &input > atom='Ir', > config='[Xe] 4f14.0 5d7.0 6s2.0 6p0.0', > dft='PBE' > / > > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From wangqj1 at 126.com Wed Nov 10 01:27:04 2010 From: wangqj1 at 126.com (Q.J.Wang) Date: Wed, 10 Nov 2010 08:27:04 +0800 (CST) Subject: [Pw_forum] LDA+DMFT (Eyvaz Isaev) Message-ID: <7c105c82.c5d5.12c332dbd9d.Coremail.wangqj1@126.com> Dear Eyvaz Thank you very much for your help! Could you tell me how to get U and J use pwscf? -- Best regards Q.J.Wang XiangTan University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101110/61c83639/attachment.htm From brad.malone at gmail.com Wed Nov 10 02:00:25 2010 From: brad.malone at gmail.com (Brad Malone) Date: Tue, 9 Nov 2010 17:00:25 -0800 Subject: [Pw_forum] Details on "third order derivatives not implemented with GGA" error Message-ID: Hi, I am seeking more information on the error > from phq_setup : error # 1 > third order derivatives not implemented with GGA From brad.malone at gmail.com Wed Nov 10 02:59:44 2010 From: brad.malone at gmail.com (Brad Malone) Date: Tue, 9 Nov 2010 17:59:44 -0800 Subject: [Pw_forum] Details on "third order derivatives not implemented with GGA" error In-Reply-To: References: Message-ID: It appears that my last email was severely truncated on the mailing list (even though it looks fine in my outbox). Below is what is should have been: ----------------------- Hi, I am seeking more information on the error > from phq_setup : error # 1 > third order derivatives not implemented with GGA From brad.malone at gmail.com Wed Nov 10 03:02:06 2010 From: brad.malone at gmail.com (Brad Malone) Date: Tue, 9 Nov 2010 18:02:06 -0800 Subject: [Pw_forum] Details on "third order derivatives not implemented with GGA" error In-Reply-To: References: Message-ID: No idea why it is being truncated, so this time I'll start the email after the error message --------------- From ttduyle at gmail.com Wed Nov 10 04:04:02 2010 From: ttduyle at gmail.com (Duy Le) Date: Tue, 9 Nov 2010 22:04:02 -0500 Subject: [Pw_forum] Details on "third order derivatives not implemented with GGA" error In-Reply-To: References: Message-ID: FYI. There is NO truncation on the mailing list, we got all what you sent. You gmail did it. Click Show Quote Text for full email. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Tue, Nov 9, 2010 at 9:02 PM, Brad Malone wrote: > No idea why it is being truncated, so this time I'll start the email after > the error message > --------------- > From the forums: > > http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html > http://www.democritos.it/pipermail/pw_forum/2010-February.txt > > I understand that the third derivatives were never implemented and > that only the LDA part was calculated, for the Perdew Zunger > parameterization. Is this third derivative the third derivative that > is mentioned in the routine PH/raman_mat.f90 (i.e, the third > derivative of the energy with respect to the atomic displacements and > with respect to two electric fields, as described in Lazzeri and > Mauri, PRL 90,036401)? > > I am interested in getting a feel for what would be needed to > implement the third derivatives with GGA into the code, as well as > what sort of errors one might expect when using the third-order term > as currently coded with LDA pseudopotentials (comments in the forums > have hinted that the errors are likely small). The shift in the Raman > spectra for cd-Si is pretty minor when using a GGA pseudo compared to > that of an LDA calculation, but I wanted to be able to quantify the > error better for other systems where comparing the GGA raman spectra > to one calculated within LDA was not possible (e.g., when the system > doesn't exhibit a gap in LDA). > > Thanks for the help! > > Best, > Brad > UC Berkeley > > > On Tue, Nov 9, 2010 at 5:59 PM, Brad Malone wrote: > >> It appears that my last email was severely truncated on the mailing list >> (even though it looks fine in my outbox). Below is what is should have been: >> ----------------------- >> Hi, I am seeking more information on the error >> >> > from phq_setup : error # 1 >> > third order derivatives not implemented with GGA >> >> From the forums: >> >> http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html >> http://www.democritos.it/pipermail/pw_forum/2010-February.txt >> >> I understand that the third derivatives were never implemented and >> that only the LDA part was calculated, for the Perdew Zunger >> parameterization. Is this third derivative the third derivative that >> is mentioned in the routine PH/raman_mat.f90 (i.e, the third >> derivative of the energy with respect to the atomic displacements and >> with respect to two electric fields, as described in Lazzeri and >> Mauri, PRL 90,036401)? >> >> I am interested in getting a feel for what would be needed to >> implement the third derivatives with GGA into the code, as well as >> what sort of errors one might expect when using the third-order term >> as currently coded with LDA pseudopotentials (comments in the forums >> have hinted that the errors are likely small). The shift in the Raman >> spectra for cd-Si is pretty minor when using a GGA pseudo compared to >> that of an LDA calculation, but I wanted to be able to quantify the >> error better for other systems where comparing the GGA raman spectra >> to one calculated within LDA was not possible (e.g., when the system >> doesn't exhibit a gap in LDA). >> >> Thanks for the help! >> >> Best, >> Brad >> UC Berkeley >> >> On Tue, Nov 9, 2010 at 5:00 PM, Brad Malone wrote: >> >>> Hi, I am seeking more information on the error >>> >>> > from phq_setup : error # 1 >>> > third order derivatives not implemented with GGA >>> >>> From the forums: >>> >>> http://www.democritos.it/pipermail/pw_forum/2008-September/010123.html >>> http://www.democritos.it/pipermail/pw_forum/2010-February.txt >>> >>> I understand that the third derivatives were never implemented and >>> that only the LDA part was calculated, for the Perdew Zunger >>> parameterization. Is this third derivative the third derivative that >>> is mentioned in the routine PH/raman_mat.f90 (i.e, the third >>> derivative of the energy with respect to the atomic displacements and >>> with respect to two electric fields, as described in Lazzeri and >>> Mauri, PRL 90,036401)? >>> >>> I am interested in getting a feel for what would be needed to >>> implement the third derivatives with GGA into the code, as well as >>> what sort of errors one might expect when using the third-order term >>> as currently coded with LDA pseudopotentials (comments in the forums >>> have hinted that the errors are likely small). The shift in the Raman >>> spectra for cd-Si is pretty minor when using a GGA pseudo compared to >>> that of an LDA calculation, but I wanted to be able to quantify the >>> error better for other systems where comparing the GGA raman spectra >>> to one calculated within LDA was not possible (e.g., when the system >>> doesn't exhibit a gap in LDA). >>> >>> Thanks for the help! >>> >>> Best, >>> Brad >>> UC Berkeley >>> >> >> > > _______________________________________________ > 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/20101109/b6acd7dc/attachment.htm From ac.rain at inbox.com Wed Nov 10 04:31:59 2010 From: ac.rain at inbox.com (ac.rain at inbox.com) Date: Tue, 9 Nov 2010 19:31:59 -0800 Subject: [Pw_forum] QE: install problem, 4.2.1 In-Reply-To: <4CD97E6D.6020706@democritos.it> References: Message-ID: Hi Paolo, yes that was the problem. it seems configure writes over make.sys, the following I put in there and it seemed to compile most things. MPIF90 = mpif90 F90 = gfortran CC = gcc F77 = gfortran the "make all" output looks good now except for some output lines that say "make[2]: g: Command not found". So then I added a specification for "LD = ld" in the make.sys and it seemed to break it, make all now shows many "undefined references to `'" messages before failing at libiotk again. do I need to have something in the LD_LIBS = section of the make.sys ? or should I put it back to how it was with a blank LD= and ignore the g: error. the LD_LIBS line is not specified, the LDFLAGS line is set to -g. thanks, nick > -----Original Message----- > From: giannozz at democritos.it > Sent: Tue, 09 Nov 2010 18:01:33 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] QE: install problem, 4.2.1 > > ac.rain at inbox.com wrote: > >> export MPIF90=mpf90 > > I think this is the problem: "mpf90" is not in the path or not > existent and "configure" gets an empty string when it checks if > it exists and works > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ____________________________________________________________ Send your photos by email in seconds... TRY FREE IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if3 Works in all emails, instant messengers, blogs, forums and social networks. From yuminqian at gmail.com Wed Nov 10 04:48:18 2010 From: yuminqian at gmail.com (yumin qian) Date: Wed, 10 Nov 2010 11:48:18 +0800 Subject: [Pw_forum] How to get the wannier_band.dat file Message-ID: Dear PWscf user I want to get the band dispersion information using wannier orbital, I find the file wannier_ham.f90 the output date can be written in wannier_band.dat is anybody know what data is meaning? Are they the same with conventional band dispersion curve ? which parameter control the output data? -- Sincerely Y. M. Qian Laboratory of Condensed Matter Theory and Materials Computation Institute of Physics(IOP), Chinese Academy of Sciences(CAS) Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101110/bdf97c83/attachment.htm From dmitry at korotin.name Wed Nov 10 05:09:30 2010 From: dmitry at korotin.name (Dmitry Korotin) Date: Wed, 10 Nov 2010 09:09:30 +0500 Subject: [Pw_forum] How to get the wannier_band.dat file In-Reply-To: References: Message-ID: Dear, Y. M. Qian. Data in wannier_bands.dat are eigenvalues of Hamiltonian in Wannier functions basis. I suppose that it is definetly what you need. There are no special parameters that control the output. You are only able to generate or not to generate wannier_bands.dat during Hamiltonian matrix construction. Anyway, there are special example of wannier_ham.x run in standart QE examples. You are welcome to ask if you have any questions. 2010/11/10 yumin qian : > Dear PWscf user > ???? I want to get the band dispersion information using wannier orbital, I > find?the file? wannier_ham.f90?the output?date?can be written > in?wannier_band.dat > ???? is?anybody? know what data is?meaning??Are they the?same with > conventional band dispersion curve ?? which parameter control the output > data? > > -- > Sincerely Y. M. Qian > Laboratory of Condensed Matter Theory and Materials Computation > Institute of Physics(IOP), Chinese Academy of Sciences(CAS) > Tel:? + 8610 8264 9147 > E-Mail:yuminqian at gmail.com > P.O.Box 603?? Beijing 100190 > China > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best regards, Dmitry Korotin Institute of Metal Physics S. Kovalevskaya, 18 620041 Ekaterinburg GSP-170 Russia From padmaja_patnaik at yahoo.co.uk Wed Nov 10 05:25:17 2010 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Wed, 10 Nov 2010 04:25:17 +0000 (GMT) Subject: [Pw_forum] Problem in compilation Message-ID: <269374.93693.qm@web26101.mail.ukl.yahoo.com> Dear all I am trying to compile Quantum espresso on a linux machine. Have tried different versions but getting the same error after giving, make all command. Following is the error message. ar: creating libiotk.a ar: iotk_attr+CHARACTER1_0.o: No such file or directory make[2]: *** [libiotk.a] Error 1 make[2]: Leaving directory `/home/patnaik/espresso-4.0.5/iotk/src' make[1]: *** [lib+util] Error 2 make[1]: Leaving directory `/home/patnaik/espresso-4.0.5/iotk' make: *** [libiotk] Error 2 Please advise. Thanking in advance. 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/20101110/244313ea/attachment.htm From yuminqian at gmail.com Wed Nov 10 05:27:10 2010 From: yuminqian at gmail.com (yumin qian) Date: Wed, 10 Nov 2010 12:27:10 +0800 Subject: [Pw_forum] How to get the wannier_band.dat file In-Reply-To: References: Message-ID: Dear Dmitry Korotin Thanks for your reply, it is very kind of you Can you tell me the right procedure, from a conventional LDA band calculation to finally get the band dispersion using wannier basis? I need to compare how the wannier function will improve the result. Can it be used in the case of spin orbital coupling with LDA+U ? 2010/11/10 Dmitry Korotin > Dear, Y. M. Qian. > > Data in wannier_bands.dat are eigenvalues of Hamiltonian in Wannier > functions basis. I suppose that it is definetly what you need. > There are no special parameters that control the output. You are only > able to generate or not to generate wannier_bands.dat during > Hamiltonian matrix construction. > > Anyway, there are special example of wannier_ham.x run in standart QE > examples. > > You are welcome to ask if you have any questions. > > 2010/11/10 yumin qian : > > Dear PWscf user > > I want to get the band dispersion information using wannier orbital, > I > > find the file wannier_ham.f90 the output date can be written > > in wannier_band.dat > > is anybody know what data is meaning? Are they the same with > > conventional band dispersion curve ? which parameter control the output > > data? > > > > -- > > Sincerely Y. M. Qian > > Laboratory of Condensed Matter Theory and Materials Computation > > Institute of Physics(IOP), Chinese Academy of Sciences(CAS) > > Tel: + 8610 8264 9147 > > E-Mail:yuminqian at gmail.com > > P.O.Box 603 Beijing 100190 > > China > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > Best regards, > Dmitry Korotin > > Institute of Metal Physics > S. Kovalevskaya, 18 > 620041 Ekaterinburg GSP-170 > Russia > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely Y. M. Qian Laboratory of Condensed Matter Theory and Materials Computation Institute of Physics(IOP), Chinese Academy of Sciences(CAS) Tel: + 8610 8264 9147 E-Mail:yuminqian at gmail.com P.O.Box 603 Beijing 100190 China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101110/2f08b1b4/attachment-0001.htm From brad.malone at gmail.com Wed Nov 10 06:01:46 2010 From: brad.malone at gmail.com (Brad Malone) Date: Tue, 9 Nov 2010 21:01:46 -0800 Subject: [Pw_forum] Details on "third order derivatives not implemented with GGA" error Message-ID: > > > > FYI. > There is NO truncation on the mailing list, we got all what you sent. > You gmail did it. Click Show Quote Text for full email. > > That doesn't seem to be completely true. Check out the posts here http://www.democritos.it/pipermail/pw_forum/2010-November/date.html . What is seen on the digest is different than what is stored online at the site above for some reason. Best, Brad UC Berkeley -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101109/1ede7b72/attachment.htm From ttduyle at gmail.com Wed Nov 10 06:10:57 2010 From: ttduyle at gmail.com (Duy Le) Date: Wed, 10 Nov 2010 00:10:57 -0500 Subject: [Pw_forum] Details on "third order derivatives not implemented with GGA" error In-Reply-To: References: Message-ID: Okie. Check the email I sent. We got your email. Next time, you should not use > mark in front of any line. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Wed, Nov 10, 2010 at 12:01 AM, Brad Malone wrote: > >> >> FYI. >> There is NO truncation on the mailing list, we got all what you sent. >> You gmail did it. Click Show Quote Text for full email. >> >> > That doesn't seem to be completely true. Check out the posts here > http://www.democritos.it/pipermail/pw_forum/2010-November/date.html . What > is seen on the digest is different than what is stored online at the site > above for some reason. > > > > Best, > Brad > UC Berkeley > > > > > > _______________________________________________ > 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/20101110/38237224/attachment.htm From giannozz at democritos.it Wed Nov 10 08:07:35 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 10 Nov 2010 08:07:35 +0100 Subject: [Pw_forum] Details on "third order derivatives not implemented with GGA" error In-Reply-To: References: Message-ID: <6ACF7195-A125-43C7-A84C-90524C3D4A23@democritos.it> On Nov 10, 2010, at 3:02 , Brad Malone wrote: > No idea why it is being truncated it wasn't truncated, or at least, what I got was fine. Some mailers have trouble with lines starting with "From" P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Nov 10 08:33:20 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 10 Nov 2010 08:33:20 +0100 Subject: [Pw_forum] Problem in compilation In-Reply-To: <269374.93693.qm@web26101.mail.ukl.yahoo.com> References: <269374.93693.qm@web26101.mail.ukl.yahoo.com> Message-ID: <50430D28-C8C5-48AA-9824-CBB96B2EDA61@democritos.it> On Nov 10, 2010, at 5:25 , Padmaja Patnaik wrote: > Please advise - use the latest version - "make clean; ./configure; make pw". If it doesn't work, your machine is missing some essential ingredient. Look at the message from "configure" P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Wed Nov 10 08:35:50 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 10 Nov 2010 08:35:50 +0100 Subject: [Pw_forum] QE: install problem, 4.2.1 In-Reply-To: References: Message-ID: <76DB5D76-E113-4DC6-8841-BA84C59E7B7C@democritos.it> On Nov 10, 2010, at 4:31 , ac.rain at inbox.com wrote: > the following I put in there you shouldn't put there anything: configure will do the job > and it seemed to compile most things. > > MPIF90 = mpif90 > F90 = gfortran > CC = gcc > F77 = gfortran > > the "make all" output looks good now except for some output lines > that say "make[2]: g: Command not found". so it doesn't look good > So then I added a specification for "LD = ld" in the make.sys and > it seemed to break it you shouldn't add anything to make.sys P. --- Paolo Giannozzi, Dept of Chemistry&Physics, 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 Nov 10 09:31:09 2010 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 10 Nov 2010 08:31:09 +0000 Subject: [Pw_forum] LDA+DMFT (Eyvaz Isaev) In-Reply-To: <7c105c82.c5d5.12c332dbd9d.Coremail.wangqj1@126.com> References: <7c105c82.c5d5.12c332dbd9d.Coremail.wangqj1@126.com> Message-ID: <4CDA584D.8030500@materials.ox.ac.uk> On 11/10/10 12:27 AM, Q.J.Wang wrote: > Dear Eyvaz > Thank you very much for your help! Could you tell me how to get U and J > use pwscf? > On the multimedia section of Q-E (go to LEARN, then Multimedia Contents) there are links to the school held at UCSB, with tutorials and video. This is a good starting point for anyone wanting to learn how to use different features of Q-E. 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 gexiaoch at sissa.it Wed Nov 10 13:07:08 2010 From: gexiaoch at sissa.it (Xiaochuan Ge) Date: Wed, 10 Nov 2010 13:07:08 +0100 (CET) Subject: [Pw_forum] 'mesh' in LD1.x Message-ID: <59886.147.122.48.68.1289390828.squirrel@webmail.sissa.it> Hello everyone, My name is Ge Xiaochuan, a student in SISSA. I have a problem when I am using LD1.x to test the pseudo potential. This is my input file: ++++++++++++++++++++++++++++ &input title='Li', zed=3, rel=1, rlderiv=2.50, eminld=-4.0 emaxld=4.0 deld=0.02 nld=3, iswitch=2, config='[He] 2s1 2p0', dft='PBE', / &test nconf=1, file_pseudo='Li.pbe-n-van.UPF', configts(1)='2s1 2p0', / ++++++++++++++++++++++++++++ But I got this in output: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_pseudoup : error # 1 mesh not supported %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Actually I 'copy' the input file from the example: +++++++++++++++++++++++++++++++++++++ &input title='Rh', zed=45., rel=1, rlderiv=2.50, eminld=-4.0, emaxld=4.0, deld=0.02, nld=3, iswitch=2, config='[Kr] 4d7 5s2 5p0' dft='PBE', / &test nconf=1, file_pseudo='RhUSPBEnlcc.RRKJ3.UPF', configts(1)= '4d7 5s2 5p0' / ++++++++++++++++++++++++++++++++++++++ Which differs from my input only in the choice of atom. This example can be run successfully. I don't know why I got error with my input. Wish someone can kindly help me, thank you in advance! Ge Xiaochuan ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From degironc at sissa.it Wed Nov 10 13:55:34 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 10 Nov 2010 13:55:34 +0100 Subject: [Pw_forum] 'mesh' in LD1.x In-Reply-To: <59886.147.122.48.68.1289390828.squirrel@webmail.sissa.it> References: <59886.147.122.48.68.1289390828.squirrel@webmail.sissa.it> Message-ID: <4CDA9646.8000802@sissa.it> Dear Xiaochuan Ge, the problem is that the ld1 code works with a logarithmic radial mesh defined as r_i = exp (xmin + (i-1)*dx)/Z where the first point in NOT the origin but some point closeby, while the pseudopotentials generated by Vanderbilt's code use a logarotmic radial grid shifted in such a way that the first point is in the origin. What you need to do in order to use ld1is to re-interpolate the potential on the grid used by ld1. The code virtual.x in upftools mixes different pseudopotentials and performs this re-interpolation. Maybe one can use it directly or can easily modify it in order to make the conversion you need. stefano Xiaochuan Ge wrote: > Hello everyone, My name is Ge Xiaochuan, a student in SISSA. I have a > problem when I am using LD1.x to test the pseudo potential. > This is my input file: > ++++++++++++++++++++++++++++ > &input > title='Li', > zed=3, > rel=1, > rlderiv=2.50, > eminld=-4.0 > emaxld=4.0 > deld=0.02 > nld=3, > iswitch=2, > config='[He] 2s1 2p0', > dft='PBE', > / > &test > nconf=1, > file_pseudo='Li.pbe-n-van.UPF', > configts(1)='2s1 2p0', > / > ++++++++++++++++++++++++++++ > But I got this in output: > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_pseudoup : error # 1 > mesh not supported > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > Actually I 'copy' the input file from the example: > +++++++++++++++++++++++++++++++++++++ > &input > title='Rh', > zed=45., > rel=1, > rlderiv=2.50, > eminld=-4.0, > emaxld=4.0, > deld=0.02, > nld=3, > iswitch=2, > config='[Kr] 4d7 5s2 5p0' > dft='PBE', > / > &test > nconf=1, > file_pseudo='RhUSPBEnlcc.RRKJ3.UPF', > configts(1)= '4d7 5s2 5p0' > / > ++++++++++++++++++++++++++++++++++++++ > Which differs from my input only in the choice of atom. This example can > be run successfully. I don't know why I got error with my input. Wish > someone can kindly help me, thank you in advance! > > Ge Xiaochuan > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Wed Nov 10 15:03:33 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 10 Nov 2010 15:03:33 +0100 Subject: [Pw_forum] Details on "third order derivatives not implemented with GGA" error In-Reply-To: References: Message-ID: <4CDAA635.3040301@democritos.it> Brad Malone wrote: > Is this third derivative the third derivative that is mentioned > in the routine PH/raman_mat.f90 (i.e, the third derivative of the > energy with respect to the atomic displacements and with respect to > two electric fields, as described in Lazzeri and Mauri, PRL 90,036401)? no, it is $$ {\delta^3 E_{xc}([n]) \over \delta n({\bf r})\delta n({\bf r}')\delta n({\bf r}'')} = {\delta^2 V_{xc}(n({\bf r})) \over \delta n({\bf r}')\delta n({\bf r}'')} $$ > I am interested in getting a feel for what would be needed to > implement the third derivatives with GGA into the code a sizable amount of algebra and some coding. See PH/setup_dgc.f90 and PH/dgradcorr.f90 for derivatives of the XC functional P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From Lorenzo.Paulatto at impmc.upmc.fr Wed Nov 10 15:41:09 2010 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 10 Nov 2010 15:41:09 +0100 Subject: [Pw_forum] Details on "third order derivatives not implemented with GGA" error In-Reply-To: <4CDAA635.3040301@democritos.it> References: <4CDAA635.3040301@democritos.it> Message-ID: On Wed, 10 Nov 2010 15:03:33 +0100, Paolo Giannozzi wrote: >> I am interested in getting a feel for what would be needed to >> implement the third derivatives with GGA into the code > > a sizable amount of algebra and some coding. See PH/setup_dgc.f90 > and PH/dgradcorr.f90 for derivatives of the XC functional A PhD student here (T Wassman) has been implementing it for a few months now, he is currently testing it. It will be ready sooner or later, but don't hold your breath. If you want to get a feel, you can contact him directly (I'm not sure he's following this mailing list) he is Tobias.Wassmann at impmc.upmc.fr. cheers -- 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 gexiaoch at sissa.it Wed Nov 10 15:47:50 2010 From: gexiaoch at sissa.it (Xiaochuan Ge) Date: Wed, 10 Nov 2010 15:47:50 +0100 (CET) Subject: [Pw_forum] 'mesh' in LD1.x In-Reply-To: <4CDA9646.8000802@sissa.it> References: <59886.147.122.48.68.1289390828.squirrel@webmail.sissa.it> <4CDA9646.8000802@sissa.it> Message-ID: <45941.147.122.48.68.1289400470.squirrel@webmail.sissa.it> Pro Stefano, Thank you very much, I understand the problem now. But is there any manual or example to tell me how to make the input file of virtual.x. Say thank you again! Ge Xiaochuan > Dear Xiaochuan Ge, > > the problem is that the ld1 code works with a logarithmic radial mesh > defined as r_i = exp (xmin + (i-1)*dx)/Z where the first point in NOT > the origin but some point closeby, while the pseudopotentials generated > by Vanderbilt's code use a logarotmic radial grid shifted in such a way > that the first point is in the origin. > What you need to do in order to use ld1is to re-interpolate the > potential on the grid used by ld1. > The code virtual.x in upftools mixes different pseudopotentials and > performs this re-interpolation. Maybe one can use it directly or can > easily modify it in order to make the conversion you need. > > stefano > > > Xiaochuan Ge wrote: >> Hello everyone, My name is Ge Xiaochuan, a student in SISSA. I have a >> problem when I am using LD1.x to test the pseudo potential. >> This is my input file: >> ++++++++++++++++++++++++++++ >> &input >> title='Li', >> zed=3, >> rel=1, >> rlderiv=2.50, >> eminld=-4.0 >> emaxld=4.0 >> deld=0.02 >> nld=3, >> iswitch=2, >> config='[He] 2s1 2p0', >> dft='PBE', >> / >> &test >> nconf=1, >> file_pseudo='Li.pbe-n-van.UPF', >> configts(1)='2s1 2p0', >> / >> ++++++++++++++++++++++++++++ >> But I got this in output: >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from read_pseudoup : error # 1 >> mesh not supported >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> Actually I 'copy' the input file from the example: >> +++++++++++++++++++++++++++++++++++++ >> &input >> title='Rh', >> zed=45., >> rel=1, >> rlderiv=2.50, >> eminld=-4.0, >> emaxld=4.0, >> deld=0.02, >> nld=3, >> iswitch=2, >> config='[Kr] 4d7 5s2 5p0' >> dft='PBE', >> / >> &test >> nconf=1, >> file_pseudo='RhUSPBEnlcc.RRKJ3.UPF', >> configts(1)= '4d7 5s2 5p0' >> / >> ++++++++++++++++++++++++++++++++++++++ >> Which differs from my input only in the choice of atom. This example can >> be run successfully. I don't know why I got error with my input. Wish >> someone can kindly help me, thank you in advance! >> >> Ge Xiaochuan >> >> >> >> ---------------------------------------------------------------- >> SISSA Webmail https://webmail.sissa.it/ >> Powered by SquirrelMail http://www.squirrelmail.org/ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From degironc at sissa.it Wed Nov 10 15:49:13 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 10 Nov 2010 15:49:13 +0100 Subject: [Pw_forum] 'mesh' in LD1.x In-Reply-To: <45941.147.122.48.68.1289400470.squirrel@webmail.sissa.it> References: <59886.147.122.48.68.1289390828.squirrel@webmail.sissa.it> <4CDA9646.8000802@sissa.it> <45941.147.122.48.68.1289400470.squirrel@webmail.sissa.it> Message-ID: <4CDAB0E9.6050004@sissa.it> just run it interactively. It asks the name of the first and second pseudopotential and the fraction of mixing. stefano Xiaochuan Ge wrote: > Pro Stefano, > Thank you very much, I understand the problem now. But is there any manual > or example to tell me how to make the input file of virtual.x. Say thank > you again! > Ge Xiaochuan > > >> Dear Xiaochuan Ge, >> >> the problem is that the ld1 code works with a logarithmic radial mesh >> defined as r_i = exp (xmin + (i-1)*dx)/Z where the first point in NOT >> the origin but some point closeby, while the pseudopotentials generated >> by Vanderbilt's code use a logarotmic radial grid shifted in such a way >> that the first point is in the origin. >> What you need to do in order to use ld1is to re-interpolate the >> potential on the grid used by ld1. >> The code virtual.x in upftools mixes different pseudopotentials and >> performs this re-interpolation. Maybe one can use it directly or can >> easily modify it in order to make the conversion you need. >> >> stefano >> >> >> Xiaochuan Ge wrote: >> >>> Hello everyone, My name is Ge Xiaochuan, a student in SISSA. I have a >>> problem when I am using LD1.x to test the pseudo potential. >>> This is my input file: >>> ++++++++++++++++++++++++++++ >>> &input >>> title='Li', >>> zed=3, >>> rel=1, >>> rlderiv=2.50, >>> eminld=-4.0 >>> emaxld=4.0 >>> deld=0.02 >>> nld=3, >>> iswitch=2, >>> config='[He] 2s1 2p0', >>> dft='PBE', >>> / >>> &test >>> nconf=1, >>> file_pseudo='Li.pbe-n-van.UPF', >>> configts(1)='2s1 2p0', >>> / >>> ++++++++++++++++++++++++++++ >>> But I got this in output: >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> from read_pseudoup : error # 1 >>> mesh not supported >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> >>> Actually I 'copy' the input file from the example: >>> +++++++++++++++++++++++++++++++++++++ >>> &input >>> title='Rh', >>> zed=45., >>> rel=1, >>> rlderiv=2.50, >>> eminld=-4.0, >>> emaxld=4.0, >>> deld=0.02, >>> nld=3, >>> iswitch=2, >>> config='[Kr] 4d7 5s2 5p0' >>> dft='PBE', >>> / >>> &test >>> nconf=1, >>> file_pseudo='RhUSPBEnlcc.RRKJ3.UPF', >>> configts(1)= '4d7 5s2 5p0' >>> / >>> ++++++++++++++++++++++++++++++++++++++ >>> Which differs from my input only in the choice of atom. This example can >>> be run successfully. I don't know why I got error with my input. Wish >>> someone can kindly help me, thank you in advance! >>> >>> Ge Xiaochuan >>> >>> >>> >>> ---------------------------------------------------------------- >>> SISSA Webmail https://webmail.sissa.it/ >>> Powered by SquirrelMail http://www.squirrelmail.org/ >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From gexiaoch at sissa.it Wed Nov 10 16:01:50 2010 From: gexiaoch at sissa.it (Xiaochuan Ge) Date: Wed, 10 Nov 2010 16:01:50 +0100 (CET) Subject: [Pw_forum] 'mesh' in LD1.x In-Reply-To: <4CDAB0E9.6050004@sissa.it> References: <59886.147.122.48.68.1289390828.squirrel@webmail.sissa.it> <4CDA9646.8000802@sissa.it> <45941.147.122.48.68.1289400470.squirrel@webmail.sissa.it> <4CDAB0E9.6050004@sissa.it> Message-ID: <37440.147.122.48.68.1289401310.squirrel@webmail.sissa.it> Yes I tried it, but I am wondering if it is necessary to tell the code "Hey! Don't don't use the shifted grid!!" or the code will change the pp into the form available for LD1.x. Because after I get the NewPseudo.UPF, problem of mesh still exits when I use it. > just run it interactively. > It asks the name of the first and second pseudopotential and the > fraction of mixing. > stefano > > Xiaochuan Ge wrote: >> Pro Stefano, >> Thank you very much, I understand the problem now. But is there any >> manual >> or example to tell me how to make the input file of virtual.x. Say thank >> you again! >> Ge Xiaochuan >> >> >>> Dear Xiaochuan Ge, >>> >>> the problem is that the ld1 code works with a logarithmic radial >>> mesh >>> defined as r_i = exp (xmin + (i-1)*dx)/Z where the first point in NOT >>> the origin but some point closeby, while the pseudopotentials generated >>> by Vanderbilt's code use a logarotmic radial grid shifted in such a >>> way >>> that the first point is in the origin. >>> What you need to do in order to use ld1is to re-interpolate the >>> potential on the grid used by ld1. >>> The code virtual.x in upftools mixes different pseudopotentials and >>> performs this re-interpolation. Maybe one can use it directly or can >>> easily modify it in order to make the conversion you need. >>> >>> stefano >>> >>> >>> Xiaochuan Ge wrote: >>> >>>> Hello everyone, My name is Ge Xiaochuan, a student in SISSA. I have a >>>> problem when I am using LD1.x to test the pseudo potential. >>>> This is my input file: >>>> ++++++++++++++++++++++++++++ >>>> &input >>>> title='Li', >>>> zed=3, >>>> rel=1, >>>> rlderiv=2.50, >>>> eminld=-4.0 >>>> emaxld=4.0 >>>> deld=0.02 >>>> nld=3, >>>> iswitch=2, >>>> config='[He] 2s1 2p0', >>>> dft='PBE', >>>> / >>>> &test >>>> nconf=1, >>>> file_pseudo='Li.pbe-n-van.UPF', >>>> configts(1)='2s1 2p0', >>>> / >>>> ++++++++++++++++++++++++++++ >>>> But I got this in output: >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> from read_pseudoup : error # 1 >>>> mesh not supported >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> >>>> Actually I 'copy' the input file from the example: >>>> +++++++++++++++++++++++++++++++++++++ >>>> &input >>>> title='Rh', >>>> zed=45., >>>> rel=1, >>>> rlderiv=2.50, >>>> eminld=-4.0, >>>> emaxld=4.0, >>>> deld=0.02, >>>> nld=3, >>>> iswitch=2, >>>> config='[Kr] 4d7 5s2 5p0' >>>> dft='PBE', >>>> / >>>> &test >>>> nconf=1, >>>> file_pseudo='RhUSPBEnlcc.RRKJ3.UPF', >>>> configts(1)= '4d7 5s2 5p0' >>>> / >>>> ++++++++++++++++++++++++++++++++++++++ >>>> Which differs from my input only in the choice of atom. This example >>>> can >>>> be run successfully. I don't know why I got error with my input. Wish >>>> someone can kindly help me, thank you in advance! >>>> >>>> Ge Xiaochuan >>>> >>>> >>>> >>>> ---------------------------------------------------------------- >>>> SISSA Webmail https://webmail.sissa.it/ >>>> Powered by SquirrelMail http://www.squirrelmail.org/ >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> >> ---------------------------------------------------------------- >> SISSA Webmail https://webmail.sissa.it/ >> Powered by SquirrelMail http://www.squirrelmail.org/ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From eyvaz_isaev at yahoo.com Wed Nov 10 20:41:43 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 10 Nov 2010 11:41:43 -0800 (PST) Subject: [Pw_forum] LDA+DMFT (Eyvaz Isaev) In-Reply-To: <4CDA584D.8030500@materials.ox.ac.uk> References: <7c105c82.c5d5.12c332dbd9d.Coremail.wangqj1@126.com> <4CDA584D.8030500@materials.ox.ac.uk> Message-ID: <549546.80012.qm@web65702.mail.ac4.yahoo.com> Hi, In addition, see examples/example25. 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: Nicola Marzari To: PWSCF Forum Sent: Wed, November 10, 2010 9:31:09 AM Subject: Re: [Pw_forum] LDA+DMFT (Eyvaz Isaev) On 11/10/10 12:27 AM, Q.J.Wang wrote: > Dear Eyvaz > Thank you very much for your help! Could you tell me how to get U and J > use pwscf? > On the multimedia section of Q-E (go to LEARN, then Multimedia Contents) there are links to the school held at UCSB, with tutorials and video. This is a good starting point for anyone wanting to learn how to use different features of Q-E. 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 brad.malone at gmail.com Wed Nov 10 21:03:28 2010 From: brad.malone at gmail.com (Brad Malone) Date: Wed, 10 Nov 2010 12:03:28 -0800 Subject: [Pw_forum] Details on "third order derivatives not implemented with GGA" error In-Reply-To: References: Message-ID: Lorenzo and Paolo, Thanks for the replies, I appreciate it. I'll contact Tobias to inquire about the status. Best, Brad UC Berkeley On Tue, Nov 9, 2010 at 9:01 PM, Brad Malone wrote: > >> >> FYI. >> There is NO truncation on the mailing list, we got all what you sent. >> You gmail did it. Click Show Quote Text for full email. >> >> > That doesn't seem to be completely true. Check out the posts here > http://www.democritos.it/pipermail/pw_forum/2010-November/date.html . What > is seen on the digest is different than what is stored online at the site > above for some reason. > > > > Best, > Brad > UC Berkeley > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101110/014a4112/attachment.htm From ac.rain at inbox.com Thu Nov 11 05:13:56 2010 From: ac.rain at inbox.com (ac.rain at inbox.com) Date: Wed, 10 Nov 2010 20:13:56 -0800 Subject: [Pw_forum] QE: install problem, 4.2.1 In-Reply-To: <76DB5D76-E113-4DC6-8841-BA84C59E7B7C@democritos.it> References: Message-ID: Hi Paolo, I put the values into the configure and all looks well, not a single error. much appreciated, thank you. ./configure MPIF90=mpif90 CC=gcc F90=gfortran F77=gfortran make all 2>&1 | tee makeall.log regards, nick - Linux Administrator > -----Original Message----- > From: giannozz at democritos.it > Sent: Wed, 10 Nov 2010 08:35:50 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] QE: install problem, 4.2.1 > > > On Nov 10, 2010, at 4:31 , ac.rain at inbox.com wrote: > >> the following I put in there > > you shouldn't put there anything: configure will do the job > >> and it seemed to compile most things. >> >> MPIF90 = mpif90 >> F90 = gfortran >> CC = gcc >> F77 = gfortran >> >> the "make all" output looks good now except for some output lines >> that say "make[2]: g: Command not found". > > so it doesn't look good > >> So then I added a specification for "LD = ld" in the make.sys and >> it seemed to break it > > you shouldn't add anything to make.sys > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, 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 ____________________________________________________________ Send any screenshot to your friends in seconds... Works in all emails, instant messengers, blogs, forums and social networks. TRY IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if2 for FREE From raamesh123 at rediffmail.com Thu Nov 11 06:44:19 2010 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 11 Nov 2010 05:44:19 -0000 Subject: [Pw_forum] =?utf-8?q?Problem_in_compilation?= Message-ID: <20101111054419.52522.qmail@f6mail-145-153.rediffmail.com> Hi Padmaja Patnaik I have got a similar problem a year back....i dont whether it is same....but i got answer from Prof Paolo Please check this link It may be useful to you http://www.democritos.it/pipermail/pw_forum/2009-April/012446.html with regards ramesh 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/20101111/d9cf4817/attachment.htm From kajalmh18 at gmail.com Thu Nov 11 13:32:23 2010 From: kajalmh18 at gmail.com (kajal jindal) Date: Thu, 11 Nov 2010 18:02:23 +0530 Subject: [Pw_forum] cohesive energy calculation of Zn Message-ID: Hi all, I am calculating the cohesive energy of Zn and I am getting a value of -0.734 eV which is almost 50% of the experimental value of -1.35 eV.Can anybody plz suggest me what is going wrong with my calculation...I read the forum regarding it but still unable to resolve my problem.. Following are the input files that i used for the calculation of total energy of bulk Zn atom in the hexagonal crystal structure and isolated Zn atom respectively.. /* input file for bulk Zn atom in crystal */ &control calculation='scf', restart_mode='from_scratch', prefix='bZn' wf_collect=.true., pseudo_dir = '/home/kajaljindal/pseudo/', outdir= './' / &system ibrav = 4, nat= 2, ntyp= 1,celldm(1) = 5.0338, celldm(3) = 1.85829, ecutwfc = 60.0,ecutrho=300, occupations ='smearing',smearing='m-v', degauss=0.001,starting_magnetization(1)=0.5,nspin=2,nosym=.true., / &electrons mixing_beta = 0.1 mixing_mode = 'local-TF' mixing_ndim = 10 conv_thr = 1.0e-5 diagonalization = 'david' / ATOMIC_SPECIES Zn 65.39 Zn.pbe-van.UPF ATOMIC_POSITIONS {crystal} Zn 0.333333 0.666666997 0.249999990 Zn 0.666667 0.333333003 0.750000010 K_POINTS {automatic} 9 9 6 0 0 0 /* part of the corresponding output file */ total energy = -253.16323313 Ry Harris-Foulkes estimate = -253.16322516 Ry estimated scf accuracy < 0.00000202 Ry The total energy is the sum of the following terms: one-electron contribution = -133.25510851 Ry hartree contribution = 94.29714101 Ry xc contribution = -37.02058576 Ry ewald contribution = -177.18467547 Ry smearing contrib. (-TS) = -0.00000441 Ry total magnetization = 0.00 Bohr mag/cell absolute magnetization = 0.00 Bohr mag/cell /* input file for isolated atom */ &control calculation='scf', restart_mode='from_scratch', prefix='iZn' wf_collect=.true., pseudo_dir = '/home/kajaljindal/pseudo/', outdir= './' / &system ibrav = 4, nat= 1, ntyp= 1,celldm(1) = 5.0338, celldm(3) = 1.85829, ecutwfc = 60.0,ecutrho=300, occupations ='smearing',smearing='m-v', degauss=0.001,starting_magnetization(1)=0.5,nspin=2,nosym=.true., / &electrons mixing_beta = 0.1 mixing_mode = 'local-TF' mixing_ndim = 10 conv_thr = 1.0e-5 diagonalization = 'david' / ATOMIC_SPECIES Zn 65.39 Zn.pbe-van.UPF ATOMIC_POSITIONS {crystal} Zn 0.0 0.0 0.0 K_POINTS {automatic} 9 9 6 0 0 0 /* part of the corresponding output file */ total energy = -126.55461784 Ry Harris-Foulkes estimate = -126.55460743 Ry estimated scf accuracy < 0.00000039 Ry The total energy is the sum of the following terms: one-electron contribution = -125.24932971 Ry hartree contribution = 73.37661809 Ry xc contribution = -18.43093183 Ry ewald contribution = -56.25098076 Ry smearing contrib. (-TS) = 0.00000637 Ry total magnetization = 0.00 Bohr mag/cell absolute magnetization = 0.00 Bohr mag/cell I deduced twice the total energy for the isolated Zn atom from the energy for the bulk Zn atom in crystal to obtain the cohesive energy...Plz guide me where am i going wrong.... Thanks in advance.. sincerely, Miss Kajal (UTA)(University of Delhi) Junior Research Fellow -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101111/710d092f/attachment.htm From kucukben at sissa.it Thu Nov 11 13:56:25 2010 From: kucukben at sissa.it (Emine Kucukbenli) Date: Thu, 11 Nov 2010 13:56:25 +0100 Subject: [Pw_forum] cohesive energy calculation of Zn In-Reply-To: References: Message-ID: <20101111135625.eug9atelcgkccc44@webmail.sissa.it> Dear Kajal The problem might as well be something else, but take a look: > /* input file for isolated atom */ ... > &system > ibrav = 4, nat= 1, ntyp= 1,celldm(1) = 5.0338, celldm(3) = 1.85829, not that isolated perhaps.. emine kucukbenli, phd student, sissa, italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From mighfar at jncasr.ac.in Thu Nov 11 15:18:21 2010 From: mighfar at jncasr.ac.in (Mighfar Imam) Date: Thu, 11 Nov 2010 19:48:21 +0530 Subject: [Pw_forum] cohesive energy calculation of Zn In-Reply-To: References: Message-ID: Your isolated Zn atom is not isolated enough to be called as isolated! You have used the same unit cell for both the bulk and the Zn atom. Put the Zn atom in a bigger box! -mighfar > Hi all, > > I am calculating the cohesive energy of Zn and I > am getting a value of > -0.734 eV which is almost 50% of the > experimental value of -1.35 eV.Can > anybody plz suggest me what is going wrong with > my calculation...I read the > forum regarding it but still unable to resolve > my problem.. > Following are the input files that i used for > the calculation of total > energy of bulk Zn atom in the hexagonal crystal > structure and isolated Zn > atom respectively.. > /* input file for bulk Zn atom in crystal */ > &control > calculation='scf', > restart_mode='from_scratch', > prefix='bZn' > wf_collect=.true., > pseudo_dir = '/home/kajaljindal/pseudo/', > outdir= './' > / > &system > ibrav = 4, nat= 2, ntyp= 1,celldm(1) = > 5.0338, celldm(3) = 1.85829, > ecutwfc = 60.0,ecutrho=300, occupations > ='smearing',smearing='m-v', > degauss=0.001,starting_magnetization(1)=0.5,nspin=2,nosym=.true., > / > &electrons > mixing_beta = 0.1 > mixing_mode = 'local-TF' > mixing_ndim = 10 > conv_thr = 1.0e-5 > diagonalization = 'david' > / > > ATOMIC_SPECIES > Zn 65.39 Zn.pbe-van.UPF > > ATOMIC_POSITIONS {crystal} > Zn 0.333333 0.666666997 0.249999990 > Zn 0.666667 0.333333003 0.750000010 > > K_POINTS {automatic} > 9 9 6 0 0 0 > > /* part of the corresponding output file */ > total energy = > -253.16323313 Ry > Harris-Foulkes estimate = > -253.16322516 Ry > estimated scf accuracy < > 0.00000202 Ry > > The total energy is the sum of the > following terms: > > one-electron contribution = > -133.25510851 Ry > hartree contribution = > 94.29714101 Ry > xc contribution = > -37.02058576 Ry > ewald contribution = > -177.18467547 Ry > smearing contrib. (-TS) = > -0.00000441 Ry > > total magnetization = 0.00 Bohr > mag/cell > absolute magnetization = 0.00 Bohr > mag/cell > > /* input file for isolated atom */ > &control > calculation='scf', > restart_mode='from_scratch', > prefix='iZn' > wf_collect=.true., > pseudo_dir = '/home/kajaljindal/pseudo/', > outdir= './' > / > &system > ibrav = 4, nat= 1, ntyp= 1,celldm(1) = > 5.0338, celldm(3) = 1.85829, > ecutwfc = 60.0,ecutrho=300, occupations > ='smearing',smearing='m-v', > degauss=0.001,starting_magnetization(1)=0.5,nspin=2,nosym=.true., > / > &electrons > mixing_beta = 0.1 > mixing_mode = 'local-TF' > mixing_ndim = 10 > conv_thr = 1.0e-5 > diagonalization = 'david' > / > ATOMIC_SPECIES > Zn 65.39 Zn.pbe-van.UPF > > ATOMIC_POSITIONS {crystal} > Zn 0.0 0.0 0.0 > > K_POINTS {automatic} > 9 9 6 0 0 0 > > /* part of the corresponding output file */ > total energy = > -126.55461784 Ry > Harris-Foulkes estimate = > -126.55460743 Ry > estimated scf accuracy < > 0.00000039 Ry > > The total energy is the sum of the > following terms: > > one-electron contribution = > -125.24932971 Ry > hartree contribution = > 73.37661809 Ry > xc contribution = > -18.43093183 Ry > ewald contribution = > -56.25098076 Ry > smearing contrib. (-TS) = > 0.00000637 Ry > > total magnetization = 0.00 Bohr > mag/cell > absolute magnetization = 0.00 Bohr > mag/cell > > I deduced twice the total energy for the > isolated Zn atom from the energy > for the bulk Zn atom in crystal to obtain the > cohesive energy...Plz guide me > where am i going wrong.... > > Thanks in advance.. > sincerely, > Miss Kajal > (UTA)(University of Delhi) > Junior Research Fellow > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Thu Nov 11 17:02:25 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 11 Nov 2010 17:02:25 +0100 Subject: [Pw_forum] [Fwd: Workshop Computational Methods in Chemistry, ICCS 2011] Message-ID: <4CDC1391.4060303@democritos.it> --------------------------------------------------------------------- Workshop on Computational Methods in Chemistry http://www.uni-graz.at/tchwww/sax/CMC/ In conjunction with ICCS 2011 Tsukuba, Japan -- June 1-3, 2011 ---------------------------------------------------------------------- The development of software used in Computational Chemistry and/or Computational Materials Science is strongly influenced by the developments in hardware, operating systems, program paradigms and program languages. The goal of CMC is to bring together developer and user of HPC software to discuss advantages and disadvantages of strategies for teracomputing in these fields. Topic of CMC2011 is "Novel Architecture and Algorithms" * Emphasis on massive parallelization on many-core and hybrid CPU/GPU architectures * Possible impact of quantum computing on future software developments. Workshop Chairs: Alexander F. Sax, University of Graz Juerg Hutter, University of Zurich Program Committee: Stefan Goedecker, University of Basel Gundolf Haase, University of Graz Juerg Hutter, University of Zurich Alexander F. Sax, University of Graz Important dates and submission details can be found on http://www.iccs-meeting.org/ -- Paolo Giannozzi, Democritos and University of Udine, Italy From matteo at umn.edu Thu Nov 11 17:05:50 2010 From: matteo at umn.edu (Matteo Cococcioni) Date: Thu, 11 Nov 2010 10:05:50 -0600 Subject: [Pw_forum] cohesive energy calculation of Zn In-Reply-To: References: Message-ID: Dear Kajal, besides the fact that the isolated Zn is not really isolated in your calculations there are some other few things you may want to check. 1) ecutrho is normally larger than 5*ecutwfc for US PPs (typically 8* or more). did you check convergence of energy (at least) and maybe forces wrt this parameter? 2) do you really need such a small smearing and such a fine k-point grid? 3) conv_thr seems a bit high to me. hth Matteo On Thu, Nov 11, 2010 at 6:32 AM, kajal jindal wrote: > Hi all, > > I am calculating the cohesive energy of Zn and I am getting a value of > -0.734 eV which is almost 50% of the experimental value of -1.35 eV.Can > anybody plz suggest me what is going wrong with my calculation...I read the > forum regarding it but still unable to resolve my problem.. > Following are the input files that i used for the calculation of total > energy of bulk Zn atom in the hexagonal crystal structure and isolated Zn > atom respectively.. > /* input file for bulk Zn atom in crystal */ > &control > calculation='scf', > restart_mode='from_scratch', > prefix='bZn' > wf_collect=.true., > pseudo_dir = '/home/kajaljindal/pseudo/', > outdir= './' > / > &system > ibrav = 4, nat= 2, ntyp= 1,celldm(1) = 5.0338, celldm(3) = 1.85829, > ecutwfc = 60.0,ecutrho=300, occupations ='smearing',smearing='m-v', > degauss=0.001,starting_magnetization(1)=0.5,nspin=2,nosym=.true., > / > &electrons > mixing_beta = 0.1 > mixing_mode = 'local-TF' > mixing_ndim = 10 > conv_thr = 1.0e-5 > diagonalization = 'david' > / > > ATOMIC_SPECIES > Zn 65.39 Zn.pbe-van.UPF > > ATOMIC_POSITIONS {crystal} > Zn 0.333333 0.666666997 0.249999990 > Zn 0.666667 0.333333003 0.750000010 > > K_POINTS {automatic} > 9 9 6 0 0 0 > > /* part of the corresponding output file */ > total energy = -253.16323313 Ry > Harris-Foulkes estimate = -253.16322516 Ry > estimated scf accuracy < 0.00000202 Ry > > The total energy is the sum of the following terms: > > one-electron contribution = -133.25510851 Ry > hartree contribution = 94.29714101 Ry > xc contribution = -37.02058576 Ry > ewald contribution = -177.18467547 Ry > smearing contrib. (-TS) = -0.00000441 Ry > > total magnetization = 0.00 Bohr mag/cell > absolute magnetization = 0.00 Bohr mag/cell > > /* input file for isolated atom */ > &control > calculation='scf', > restart_mode='from_scratch', > prefix='iZn' > wf_collect=.true., > pseudo_dir = '/home/kajaljindal/pseudo/', > outdir= './' > / > &system > ibrav = 4, nat= 1, ntyp= 1,celldm(1) = 5.0338, celldm(3) = 1.85829, > ecutwfc = 60.0,ecutrho=300, occupations ='smearing',smearing='m-v', > degauss=0.001,starting_magnetization(1)=0.5,nspin=2,nosym=.true., > / > &electrons > mixing_beta = 0.1 > mixing_mode = 'local-TF' > mixing_ndim = 10 > conv_thr = 1.0e-5 > diagonalization = 'david' > / > ATOMIC_SPECIES > Zn 65.39 Zn.pbe-van.UPF > > ATOMIC_POSITIONS {crystal} > Zn 0.0 0.0 0.0 > > K_POINTS {automatic} > 9 9 6 0 0 0 > > /* part of the corresponding output file */ > total energy = -126.55461784 Ry > Harris-Foulkes estimate = -126.55460743 Ry > estimated scf accuracy < 0.00000039 Ry > > The total energy is the sum of the following terms: > > one-electron contribution = -125.24932971 Ry > hartree contribution = 73.37661809 Ry > xc contribution = -18.43093183 Ry > ewald contribution = -56.25098076 Ry > smearing contrib. (-TS) = 0.00000637 Ry > > total magnetization = 0.00 Bohr mag/cell > absolute magnetization = 0.00 Bohr mag/cell > > I deduced twice the total energy for the isolated Zn atom from the energy > for the bulk Zn atom in crystal to obtain the cohesive energy...Plz guide me > where am i going wrong.... > > Thanks in advance.. > sincerely, > Miss Kajal > (UTA)(University of Delhi) > Junior Research Fellow > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101111/e7f07798/attachment-0001.htm From eariel99 at gmail.com Thu Nov 11 21:45:24 2010 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Thu, 11 Nov 2010 17:45:24 -0300 Subject: [Pw_forum] PDOS for P symmetry lacking in Ni Message-ID: Hi, I am doing a tutorial example of calculation of the projected DOS in Ni. It produces the PDOS projected on S and D states, but not on P. There are no bound P valence states in nickel. Is that the cause for not having a P partial DOS? States with P-symmetry component may be present in an empty band. Is there an option to produce the P-PDOS? Support information: this is from the help file INPUT_PROJWFC.txt In the collinear case and the non-collinear, non spin-orbit case projected DOS are written to file "filpdos".pdos_atm#N(X)_wfc#M(l), where N = atom number , X = atom symbol, M = wfc number, l=s,p,d,f (one file per atomic wavefunction found in the pseudopotential file) this is the head of the pseudopotential Generated using Andrea Dal Corso code (rrkj3) Author: Andrea Dal Corso Generation date: unknown Info: Ni 1 The Pseudo was generated with a Scalar-Relativistic Calculation 1.70000000000E+00 Local Potential cutoff radius nl pn l occ Rcut Rcut US E pseu 4S 1 0 1.00 2.00000000000 2.50000000000 0.00000000000 4S 1 0 0.00 2.00000000000 2.50000000000 0.00000000000 4P 2 1 0.00 2.40000000000 2.60000000000 0.00000000000 4P 2 1 0.00 2.40000000000 2.60000000000 0.00000000000 3D 3 2 9.00 1.60000000000 2.50000000000 0.00000000000 3D 3 2 0.00 1.60000000000 2.50000000000 0.00000000000 Thanks -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez They did it! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101111/c42c876b/attachment.htm From member at linkedin.com Thu Nov 11 21:44:21 2010 From: member at linkedin.com (Weiguang Chen via LinkedIn) Date: Thu, 11 Nov 2010 12:44:21 -0800 (PST) Subject: [Pw_forum] Weiguang Chen wants to stay in touch on LinkedIn Message-ID: <842489657.4492871.1289508261798.JavaMail.app@ech3-cdn06.prod> LinkedIn ------------Weiguang Chen requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Weiguang Chen Accept invitation from Weiguang Chen http://www.linkedin.com/e/bpp12m-gge3xaqr-4y/XOi1HZwtMe9Ipae3GXPJ40oAN5nddd/blk/I113964098_5/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_dlYUej0QdzAPcj59bTtymAlJoBtCbP8Rcj4PcjgVe34LrCBxbOYWrSlI/EML_comm_afe/ View invitation from Weiguang Chen http://www.linkedin.com/e/bpp12m-gge3xaqr-4y/XOi1HZwtMe9Ipae3GXPJ40oAN5nddd/blk/I113964098_5/0RnPwVc3gSejcNckALqnpPbOYWrSlI/svi/ ------------------------------------------ Why might connecting with Weiguang Chen be a good idea? Have a question? Weiguang Chen's network will probably have an answer: You can use LinkedIn Answers to distribute your professional questions to Weiguang Chen and your extended network. You can get high-quality answers from experienced professionals. http://www.linkedin.com/e/bpp12m-gge3xaqr-4y/ash/inv19_ayn/ -- (c) 2010, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101111/11c6eff9/attachment.htm From juanlopez415 at gmail.com Thu Nov 11 22:30:44 2010 From: juanlopez415 at gmail.com (Juan Manuel Lopez) Date: Thu, 11 Nov 2010 17:30:44 -0400 Subject: [Pw_forum] PDOS for P symmetry lacking in Ni In-Reply-To: References: Message-ID: Hi Eduardo, This is because pseudopotential(PP), in need to choose a PP that include semicore states p in valance. I think you can use Ni.pbe-sp-mt_gipaw.UPF, download this from the QE website. On Thu, Nov 11, 2010 at 4:45 PM, Eduardo Ariel Menendez Proupin < eariel99 at gmail.com> wrote: > Hi, > I am doing a tutorial example of calculation of the projected DOS in Ni. It > produces the PDOS projected on S and D states, but not on P. > There are no bound P valence states in nickel. Is that the cause for not > having a P partial DOS? > > States with P-symmetry component may be present in an empty band. Is there > an option to produce the P-PDOS? > > > Support information: > this is from the help file INPUT_PROJWFC.txt > > In the collinear case and the non-collinear, non spin-orbit case > projected DOS are written to file "filpdos".pdos_atm#N(X)_wfc#M(l), > where N = atom number , X = atom symbol, M = wfc number, l=s,p,d,f > (one file per atomic wavefunction found in the pseudopotential file) > > > this is the head of the pseudopotential > > Generated using Andrea Dal Corso code (rrkj3) > > Author: Andrea Dal Corso Generation date: unknown > > Info: Ni > > 1 The Pseudo was generated with a Scalar-Relativistic > Calculation > 1.70000000000E+00 Local Potential cutoff radius > nl pn l occ Rcut Rcut US E pseu > 4S 1 0 1.00 2.00000000000 2.50000000000 0.00000000000 > 4S 1 0 0.00 2.00000000000 2.50000000000 0.00000000000 > 4P 2 1 0.00 2.40000000000 2.60000000000 0.00000000000 > 4P 2 1 0.00 2.40000000000 2.60000000000 0.00000000000 > 3D 3 2 9.00 1.60000000000 2.50000000000 0.00000000000 > 3D 3 2 0.00 1.60000000000 2.50000000000 0.00000000000 > > > > Thanks > -- > > > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez > > They did it! > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best regards, -------------------------------------- Juan M. Lopez Encarnacion Research associate, Institute of Physics, Universidad Aut?noma de Santo Domingo, Dominican Republic Graduate Student Doctoral Program in Chemical Physics, University of Puerto Rico, Rio Piedras Campus P.O.Box 23343 San Juan, PR 00931-3343 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101111/ee26a80c/attachment.htm From sclauzer at sissa.it Fri Nov 12 09:41:59 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 12 Nov 2010 09:41:59 +0100 Subject: [Pw_forum] PDOS for P symmetry lacking in Ni In-Reply-To: References: Message-ID: Dear Eduardo, I think that the PP you are using does not include the 4p wavefunctions 0 Version Number Ni Element US Ultrasoft pseudopotential T Nonlinear Core Correction SLA PW PBE PBE PBE Exchange-Correlation functional 10.00000000000 Z valence -72.87827664100 Total energy 0.0000000 0.0000000 Suggested cutoff for wfc and rho 2 Max angular momentum component 1203 Number of points in mesh 2 6 Number of Wavefunctions, Number of Projectors Wavefunctions nl l occ 4S 0 1.00 3D 2 9.00 probably because the 4p states have 0 occupation and the ld1.x code stores in the PP file only atomic wavefunctions with occupation > 0. Hence the projections on the 4p atomic wavefunctions cannot be computed because they are not available to the code. However, I think that the 4p wavefunctions are still computed by ld1.x when generating the PP, since there are beta projectors on the l=1 channel (grep BETA inside the PP file). You could try to modify the default behavior of ld1.x so that it will include those wavefunctions in the PP. Then the projection code should detect them in the PP data and compute the additional projections. HTH GS Il giorno 11/nov/2010, alle ore 21.45, Eduardo Ariel Menendez Proupin ha scritto: > Hi, > I am doing a tutorial example of calculation of the projected DOS in Ni. It produces the PDOS projected on S and D states, but not on P. > There are no bound P valence states in nickel. Is that the cause for not having a P partial DOS? > > States with P-symmetry component may be present in an empty band. Is there an option to produce the P-PDOS? > > > Support information: > this is from the help file INPUT_PROJWFC.txt > > In the collinear case and the non-collinear, non spin-orbit case > projected DOS are written to file "filpdos".pdos_atm#N(X)_wfc#M(l), > where N = atom number , X = atom symbol, M = wfc number, l=s,p,d,f > (one file per atomic wavefunction found in the pseudopotential file) > > > this is the head of the pseudopotential > > Generated using Andrea Dal Corso code (rrkj3) > Author: Andrea Dal Corso Generation date: unknown > Info: Ni > 1 The Pseudo was generated with a Scalar-Relativistic Calculation > 1.70000000000E+00 Local Potential cutoff radius > nl pn l occ Rcut Rcut US E pseu > 4S 1 0 1.00 2.00000000000 2.50000000000 0.00000000000 > 4S 1 0 0.00 2.00000000000 2.50000000000 0.00000000000 > 4P 2 1 0.00 2.40000000000 2.60000000000 0.00000000000 > 4P 2 1 0.00 2.40000000000 2.60000000000 0.00000000000 > 3D 3 2 9.00 1.60000000000 2.50000000000 0.00000000000 > 3D 3 2 0.00 1.60000000000 2.50000000000 0.00000000000 > > > > Thanks > -- > > > Eduardo Menendez > Departamento de Fisica > Facultad de Ciencias > Universidad de Chile > Phone: (56)(2)9787439 > URL: http://fisica.ciencias.uchile.cl/~emenendez > > They did it! > > _______________________________________________ > 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/20101112/ee5a799b/attachment.htm From sclauzer at sissa.it Fri Nov 12 09:50:11 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 12 Nov 2010 09:50:11 +0100 Subject: [Pw_forum] PDOS for P symmetry lacking in Ni In-Reply-To: References: Message-ID: <286C7C91-16D6-428F-A4A9-403467938481@sissa.it> I forgot that a problem may arise if the wavefunctions are not bound: even it the 4p levels are not bound, the code can use them to generate the beta projector since it needs the wavefunctions only up to the core radius. If you want to make projections on it you'll need instead to integrate the wavefunction also beyond the core radius. If the wavefunction is not bound this integral will not make much sense. If this is the case, what you can do is to fix the 4p pseudization energy to a small negative value. This might however complicate or hinder the PP generation procedure... GS Il giorno 12/nov/2010, alle ore 09.41, Gabriele Sclauzero ha scritto: > Dear Eduardo, > > I think that the PP you are using does not include the 4p wavefunctions > > 0 Version Number > Ni Element > US Ultrasoft pseudopotential > T Nonlinear Core Correction > SLA PW PBE PBE PBE Exchange-Correlation functional > 10.00000000000 Z valence > -72.87827664100 Total energy > 0.0000000 0.0000000 Suggested cutoff for wfc and rho > 2 Max angular momentum component > 1203 Number of points in mesh > 2 6 Number of Wavefunctions, Number of Projectors > Wavefunctions nl l occ > 4S 0 1.00 > 3D 2 9.00 > > > probably because the 4p states have 0 occupation and the ld1.x code stores in the PP file only atomic wavefunctions with occupation > 0. Hence the projections on the 4p atomic wavefunctions cannot be computed because they are not available to the code. > However, I think that the 4p wavefunctions are still computed by ld1.x when generating the PP, since there are beta projectors on the l=1 channel (grep BETA inside the PP file). You could try to modify the default behavior of ld1.x so that it will include those wavefunctions in the PP. Then the projection code should detect them in the PP data and compute the additional projections. > > > HTH > > GS > > Il giorno 11/nov/2010, alle ore 21.45, Eduardo Ariel Menendez Proupin ha scritto: > >> Hi, >> I am doing a tutorial example of calculation of the projected DOS in Ni. It produces the PDOS projected on S and D states, but not on P. >> There are no bound P valence states in nickel. Is that the cause for not having a P partial DOS? >> >> States with P-symmetry component may be present in an empty band. Is there an option to produce the P-PDOS? >> >> >> Support information: >> this is from the help file INPUT_PROJWFC.txt >> >> In the collinear case and the non-collinear, non spin-orbit case >> projected DOS are written to file "filpdos".pdos_atm#N(X)_wfc#M(l), >> where N = atom number , X = atom symbol, M = wfc number, l=s,p,d,f >> (one file per atomic wavefunction found in the pseudopotential file) >> >> >> this is the head of the pseudopotential >> >> Generated using Andrea Dal Corso code (rrkj3) >> Author: Andrea Dal Corso Generation date: unknown >> Info: Ni >> 1 The Pseudo was generated with a Scalar-Relativistic Calculation >> 1.70000000000E+00 Local Potential cutoff radius >> nl pn l occ Rcut Rcut US E pseu >> 4S 1 0 1.00 2.00000000000 2.50000000000 0.00000000000 >> 4S 1 0 0.00 2.00000000000 2.50000000000 0.00000000000 >> 4P 2 1 0.00 2.40000000000 2.60000000000 0.00000000000 >> 4P 2 1 0.00 2.40000000000 2.60000000000 0.00000000000 >> 3D 3 2 9.00 1.60000000000 2.50000000000 0.00000000000 >> 3D 3 2 0.00 1.60000000000 2.50000000000 0.00000000000 >> >> >> >> Thanks >> -- >> >> >> Eduardo Menendez >> Departamento de Fisica >> Facultad de Ciencias >> Universidad de Chile >> Phone: (56)(2)9787439 >> URL: http://fisica.ciencias.uchile.cl/~emenendez >> >> They did it! >> >> _______________________________________________ >> 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/20101112/ba46105e/attachment.htm From sclauzer at sissa.it Fri Nov 12 10:34:53 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 12 Nov 2010 10:34:53 +0100 Subject: [Pw_forum] PDOS for P symmetry lacking in Ni In-Reply-To: References: Message-ID: <494D10FD-7956-4576-9020-82BDFD8106BE@sissa.it> Sorry for continuously correcting myself... I realized that some PP on the website have atomic wavefunctions corresponding to atomic levels with occupations = 0 (see Au, for instance)... so I don't understand the logic for printing or not the wfcs in the PP file. GS Il giorno 12/nov/2010, alle ore 09.41, Gabriele Sclauzero ha scritto: > Dear Eduardo, > > I think that the PP you are using does not include the 4p wavefunctions > > 0 Version Number > Ni Element > US Ultrasoft pseudopotential > T Nonlinear Core Correction > SLA PW PBE PBE PBE Exchange-Correlation functional > 10.00000000000 Z valence > -72.87827664100 Total energy > 0.0000000 0.0000000 Suggested cutoff for wfc and rho > 2 Max angular momentum component > 1203 Number of points in mesh > 2 6 Number of Wavefunctions, Number of Projectors > Wavefunctions nl l occ > 4S 0 1.00 > 3D 2 9.00 > > > probably because the 4p states have 0 occupation and the ld1.x code stores in the PP file only atomic wavefunctions with occupation > 0. Hence the projections on the 4p atomic wavefunctions cannot be computed because they are not available to the code. > However, I think that the 4p wavefunctions are still computed by ld1.x when generating the PP, since there are beta projectors on the l=1 channel (grep BETA inside the PP file). You could try to modify the default behavior of ld1.x so that it will include those wavefunctions in the PP. Then the projection code should detect them in the PP data and compute the additional projections. > > > HTH > > GS > > Il giorno 11/nov/2010, alle ore 21.45, Eduardo Ariel Menendez Proupin ha scritto: > >> Hi, >> I am doing a tutorial example of calculation of the projected DOS in Ni. It produces the PDOS projected on S and D states, but not on P. >> There are no bound P valence states in nickel. Is that the cause for not having a P partial DOS? >> >> States with P-symmetry component may be present in an empty band. Is there an option to produce the P-PDOS? >> >> >> Support information: >> this is from the help file INPUT_PROJWFC.txt >> >> In the collinear case and the non-collinear, non spin-orbit case >> projected DOS are written to file "filpdos".pdos_atm#N(X)_wfc#M(l), >> where N = atom number , X = atom symbol, M = wfc number, l=s,p,d,f >> (one file per atomic wavefunction found in the pseudopotential file) >> >> >> this is the head of the pseudopotential >> >> Generated using Andrea Dal Corso code (rrkj3) >> Author: Andrea Dal Corso Generation date: unknown >> Info: Ni >> 1 The Pseudo was generated with a Scalar-Relativistic Calculation >> 1.70000000000E+00 Local Potential cutoff radius >> nl pn l occ Rcut Rcut US E pseu >> 4S 1 0 1.00 2.00000000000 2.50000000000 0.00000000000 >> 4S 1 0 0.00 2.00000000000 2.50000000000 0.00000000000 >> 4P 2 1 0.00 2.40000000000 2.60000000000 0.00000000000 >> 4P 2 1 0.00 2.40000000000 2.60000000000 0.00000000000 >> 3D 3 2 9.00 1.60000000000 2.50000000000 0.00000000000 >> 3D 3 2 0.00 1.60000000000 2.50000000000 0.00000000000 >> >> >> >> Thanks >> -- >> >> >> Eduardo Menendez >> Departamento de Fisica >> Facultad de Ciencias >> Universidad de Chile >> Phone: (56)(2)9787439 >> URL: http://fisica.ciencias.uchile.cl/~emenendez >> >> They did it! >> >> _______________________________________________ >> 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/20101112/7caa98c7/attachment-0001.htm From giannozz at democritos.it Fri Nov 12 10:48:12 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 12 Nov 2010 10:48:12 +0100 Subject: [Pw_forum] PDOS for P symmetry lacking in Ni In-Reply-To: <494D10FD-7956-4576-9020-82BDFD8106BE@sissa.it> References: <494D10FD-7956-4576-9020-82BDFD8106BE@sissa.it> Message-ID: <05911CFE-9024-4BCE-9DE1-07A425B2266A@democritos.it> On Nov 12, 2010, at 10:34 , Gabriele Sclauzero wrote: > I realized that some PP on the website have atomic wavefunctions > corresponding to atomic levels with occupations = 0 (see Au, for > instance)... > so I don't understand the logic for printing or not the wfcs in the > PP file. > I think the logic has changed: once upon a time atomic orbitals with zero occupancy were not written to file in the PP_WFC section, while now they are, if they are included in the reference configuration and are not unbound states P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eariel99 at gmail.com Fri Nov 12 14:09:59 2010 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Fri, 12 Nov 2010 10:09:59 -0300 Subject: [Pw_forum] OPTIONAL VARIABLES FOR RAMAN Message-ID: Hi, Where can I read the meaning of these options of the PHONON code ? ///--- OPTIONAL VARIABLES FOR RAMAN: +-------------------------------------------------------------------- Variable: eth_rps Type: REAL Default: 1.0d-9 Description: Threshold for calculation of Pc R |psi>. +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: eth_ns Type: REAL Default: 1.0e-12 Description: Threshold for non-scf wavefunction calculation. +-------------------------------------------------------------------- +-------------------------------------------------------------------- Variable: dek Type: REAL Default: 1.0e-3 Description: Delta_xk used for wavefunction derivation wrt k. -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez They did it! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101112/de75b6d8/attachment.htm From giannozz at democritos.it Fri Nov 12 22:47:23 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 12 Nov 2010 22:47:23 +0100 Subject: [Pw_forum] OPTIONAL VARIABLES FOR RAMAN In-Reply-To: References: Message-ID: <02AD0224-33BE-4917-BCE6-E60DD0FBABF5@democritos.it> On Nov 12, 2010, at 14:09 , Eduardo Ariel Menendez Proupin wrote: > Hi, Where can I read the meaning of these options of the PHONON code ? you can read the meaning of those options...in your message! Seriously: what you reported is more or less all the available documentation of those variables, which you shouldn't need to set in normal circumstances. In order to know more, you have to know the details of the algorithm > Variable: eth_rps > Description: Threshold for calculation of Pc R |psi>. more exactly, threshold used in the solution of the linear system (H-\epsilon_v) x |\psi_v> = [H,x]|\psi_v> > Variable: eth_ns > Description: Threshold for non-scf wavefunction calculation. Needed to calculate |\psi_{k+\delta q}> > Variable: dek > Description: Delta_xk used for wavefunction derivation wrt k. this is actually \delta q above, because du_q/dq, with u_q=periodic part of the wavefunction, is used in the calculation of second-order response No warranty - P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eariel99 at gmail.com Fri Nov 12 23:39:34 2010 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Fri, 12 Nov 2010 19:39:34 -0300 Subject: [Pw_forum] PDOS for P symmetry lacking in Ni Message-ID: Hi Gabriele, Thank you for your comments. I think that better than adding new capabilities to the ld1 program, and a new "opportunity" to users to curse pseudopotentials, it is easier to add to projwfc.x the capability to project onto a Slater or Gaussian orbital that the user can define giving a covalent or ionic radius. I know a popular code that uses just a constant function up to a given radius. Have a nice weekend Eduardo -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez They did it! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101112/b52b5653/attachment.htm From kajalmh18 at gmail.com Sat Nov 13 11:23:18 2010 From: kajalmh18 at gmail.com (kajal jindal) Date: Sat, 13 Nov 2010 15:53:18 +0530 Subject: [Pw_forum] cohesive energy calculation of Zn In-Reply-To: References: Message-ID: Hi all, Thanx a lot to all who helped me sorting my problem..your suggestions were really helpful for my problem... sincerely, Miss Kajal (UTA)(University of Delhi) Junior Research Fellow On Thu, Nov 11, 2010 at 9:35 PM, Matteo Cococcioni wrote: > > Dear Kajal, > > besides the fact that the isolated Zn is not really isolated in your > calculations there are some other > few things you may want to check. > > 1) ecutrho is normally larger than 5*ecutwfc for US PPs (typically 8* or > more). did you check convergence of energy (at least) and maybe forces wrt > this parameter? > > 2) do you really need such a small smearing and such a fine k-point grid? > > 3) conv_thr seems a bit high to me. > > hth > > Matteo > > > > On Thu, Nov 11, 2010 at 6:32 AM, kajal jindal wrote: > >> Hi all, >> >> I am calculating the cohesive energy of Zn and I am getting a value of >> -0.734 eV which is almost 50% of the experimental value of -1.35 eV.Can >> anybody plz suggest me what is going wrong with my calculation...I read the >> forum regarding it but still unable to resolve my problem.. >> Following are the input files that i used for the calculation of total >> energy of bulk Zn atom in the hexagonal crystal structure and isolated Zn >> atom respectively.. >> /* input file for bulk Zn atom in crystal */ >> &control >> calculation='scf', >> restart_mode='from_scratch', >> prefix='bZn' >> wf_collect=.true., >> pseudo_dir = '/home/kajaljindal/pseudo/', >> outdir= './' >> / >> &system >> ibrav = 4, nat= 2, ntyp= 1,celldm(1) = 5.0338, celldm(3) = 1.85829, >> ecutwfc = 60.0,ecutrho=300, occupations ='smearing',smearing='m-v', >> degauss=0.001,starting_magnetization(1)=0.5,nspin=2,nosym=.true., >> / >> &electrons >> mixing_beta = 0.1 >> mixing_mode = 'local-TF' >> mixing_ndim = 10 >> conv_thr = 1.0e-5 >> diagonalization = 'david' >> / >> >> ATOMIC_SPECIES >> Zn 65.39 Zn.pbe-van.UPF >> >> ATOMIC_POSITIONS {crystal} >> Zn 0.333333 0.666666997 0.249999990 >> Zn 0.666667 0.333333003 0.750000010 >> >> K_POINTS {automatic} >> 9 9 6 0 0 0 >> >> /* part of the corresponding output file */ >> total energy = -253.16323313 Ry >> Harris-Foulkes estimate = -253.16322516 Ry >> estimated scf accuracy < 0.00000202 Ry >> >> The total energy is the sum of the following terms: >> >> one-electron contribution = -133.25510851 Ry >> hartree contribution = 94.29714101 Ry >> xc contribution = -37.02058576 Ry >> ewald contribution = -177.18467547 Ry >> smearing contrib. (-TS) = -0.00000441 Ry >> >> total magnetization = 0.00 Bohr mag/cell >> absolute magnetization = 0.00 Bohr mag/cell >> >> /* input file for isolated atom */ >> &control >> calculation='scf', >> restart_mode='from_scratch', >> prefix='iZn' >> wf_collect=.true., >> pseudo_dir = '/home/kajaljindal/pseudo/', >> outdir= './' >> / >> &system >> ibrav = 4, nat= 1, ntyp= 1,celldm(1) = 5.0338, celldm(3) = 1.85829, >> ecutwfc = 60.0,ecutrho=300, occupations ='smearing',smearing='m-v', >> degauss=0.001,starting_magnetization(1)=0.5,nspin=2,nosym=.true., >> / >> &electrons >> mixing_beta = 0.1 >> mixing_mode = 'local-TF' >> mixing_ndim = 10 >> conv_thr = 1.0e-5 >> diagonalization = 'david' >> / >> ATOMIC_SPECIES >> Zn 65.39 Zn.pbe-van.UPF >> >> ATOMIC_POSITIONS {crystal} >> Zn 0.0 0.0 0.0 >> >> K_POINTS {automatic} >> 9 9 6 0 0 0 >> >> /* part of the corresponding output file */ >> total energy = -126.55461784 Ry >> Harris-Foulkes estimate = -126.55460743 Ry >> estimated scf accuracy < 0.00000039 Ry >> >> The total energy is the sum of the following terms: >> >> one-electron contribution = -125.24932971 Ry >> hartree contribution = 73.37661809 Ry >> xc contribution = -18.43093183 Ry >> ewald contribution = -56.25098076 Ry >> smearing contrib. (-TS) = 0.00000637 Ry >> >> total magnetization = 0.00 Bohr mag/cell >> absolute magnetization = 0.00 Bohr mag/cell >> >> I deduced twice the total energy for the isolated Zn atom from the energy >> for the bulk Zn atom in crystal to obtain the cohesive energy...Plz guide me >> where am i going wrong.... >> >> Thanks in advance.. >> sincerely, >> Miss Kajal >> (UTA)(University of Delhi) >> Junior Research Fellow >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Matteo Cococcioni > Department of Chemical Engineering and Materials Science, > University of Minnesota > 421 Washington Av. SE > Minneapolis, MN 55455 > Tel. +1 612 624 9056 Fax +1 612 626 7246 > > _______________________________________________ > 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/20101113/190b9301/attachment.htm From prasenjit.jnc at gmail.com Sat Nov 13 13:46:15 2010 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Sat, 13 Nov 2010 18:16:15 +0530 Subject: [Pw_forum] Photoemission Spectra Message-ID: Hi, I think it is possible to calculate the photo-emission spectra using QE (Phys. Rev. B 77, 195116 (2008)). Is it available publicly in the current distribution.....if so can somebody point me to some examples or some documentation as to how to do it? With regards, Prasenjit -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From w2agz at w2agz.com Sat Nov 13 21:02:32 2010 From: w2agz at w2agz.com (W2AGZ) Date: Sat, 13 Nov 2010 12:02:32 -0800 Subject: [Pw_forum] Example 12 Message-ID: <019101cb836d$b6cf3d60$246db820$@w2agz.com> To All... Running example 12 from QE 4.2.1 within an Ubuntu 10.04.1 distro results in the following abend messages: From m_pazoki at physics.sharif.edu Sun Nov 14 11:16:34 2010 From: m_pazoki at physics.sharif.edu (meysam pazoki) Date: Sun, 14 Nov 2010 13:46:34 +0330 Subject: [Pw_forum] Example 12 (W2AGZ) In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: meysam pazoki Date: Sun, Nov 14, 2010 at 1:42 PM Subject: Re: Example 12 (W2AGZ) To: pw_forum at pwscf.org Dear Paul I see this message.use ifort instead of gfortran. follow this link to install ifortran in ubuntu: http://software.intel.com/en-us/articles/using-intel-compilers-for-linux-with-ubuntu/ Best Regards meysam pazoki SUT -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101114/cb065e19/attachment.htm From abmus007 at gmail.com Sun Nov 14 13:09:44 2010 From: abmus007 at gmail.com (Abolore Musari) Date: Sun, 14 Nov 2010 06:09:44 -0600 Subject: [Pw_forum] atomic positions Message-ID: Dear QE user Pls I need to know how the atomic positions of the system used in the examples like Si, SiO2 e.t.c are gotten so that i can apply it for the material i would like to work on. In fact i would appreciate a detail explanation on this ccos I visited bilbao Crystallographic server and still couldnt get a clue on how to explore the website. thanks Adebayo Abdulganiy university of Ibadan Nigeria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101114/b5838923/attachment.htm From degironc at sissa.it Sun Nov 14 17:38:23 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 14 Nov 2010 17:38:23 +0100 Subject: [Pw_forum] atomic positions In-Reply-To: References: Message-ID: <4CE0107F.7060001@sissa.it> Dear Adebayo Abdulganiy there is no magic. what you need to know are the positions of all the atoms in your unit cell and the three fundamental lattice vectors that define the cell. If you do not have this information there is no way you can build the structure. Once you have it, the cell shape can be defined using the ibrav and celldm variables (see their definitions) or choosing ibrav=0 and explicitly giving the three vectors. The positions can be defined using carthesian coordinates (in bohr, angstrom or unit of celldm(1)) or crystal coordinates (that is as fractions of the three fundamental vectors defining the cell). Read the explanation given about the ATOMIC_POSITION card. stefano Abolore Musari wrote: > Dear QE user > Pls I need to know how the atomic positions of the system used in the > examples like Si, SiO2 e.t.c are gotten so that i can apply it for the > material i would like to work on. In fact i would appreciate a detail > explanation on this ccos I visited bilbao Crystallographic server and still > couldnt get a clue on how to explore the website. > > thanks > > Adebayo Abdulganiy > university of Ibadan > Nigeria > > > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From giannozz at democritos.it Sun Nov 14 22:32:12 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 14 Nov 2010 22:32:12 +0100 Subject: [Pw_forum] Example 12 In-Reply-To: <019101cb836d$b6cf3d60$246db820$@w2agz.com> References: <019101cb836d$b6cf3d60$246db820$@w2agz.com> Message-ID: On Nov 13, 2010, at 21:02 , W2AGZ wrote: > from gep_x : error # 38 error on zggev > > I smell a fortran compiler problem here > it might also be a library problem: zggev is a lapack routine, and sometimes machine-optimized lapack do not work as expected. That error used to be quite frequent in the past. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From raamesh123 at rediffmail.com Mon Nov 15 10:01:19 2010 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 15 Nov 2010 09:01:19 -0000 Subject: [Pw_forum] =?utf-8?q?atom_positions?= In-Reply-To: Message-ID: <1289808357.S.14580.30818.F.H.TnB3X2ZvcnVtLXJlcXVlc3RAcHdzY2Yub3JnAFB3X2ZvcnVtIERpZ2VzdCwgVm9sIDQxLCBJc3N1ZSAyNw__.f6-144-219.lb.1289811678.45236@webmail.rediffmail.com> Dear Abolore Musari To build a unit cell you need space group and atom positions information. Most of the crystal structure informations will be available in http://cst-www.nrl.navy.mil/lattice/ or in http://cci.lbl.gov/cctbx/explore_symmetry.html. I hope you are not expecting an answer on how to crack a crystal structure??? 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/20101115/56c4f104/attachment.htm From eyvaz_isaev at yahoo.com Mon Nov 15 19:11:38 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 15 Nov 2010 10:11:38 -0800 (PST) Subject: [Pw_forum] PostDoc position In-Reply-To: <909C9225-D927-4FB2-B97A-BEA262FD5518@sissa.it> References: <909C9225-D927-4FB2-B97A-BEA262FD5518@sissa.it> Message-ID: <158845.91787.qm@web65702.mail.ac4.yahoo.com> Dear QE users, We have one year PostDoc position in our Department of Physics, Chemistry and Biology (Linkoping University), that might be extended for the next year. The work requires intensive use of QE. Please contact me or Prof. Igor Abrikosov (abrikos at ifm.liu.se) if interested. 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 ssdhayal at gmail.com Mon Nov 15 20:53:53 2010 From: ssdhayal at gmail.com (Suman Dhayal) Date: Mon, 15 Nov 2010 13:53:53 -0600 Subject: [Pw_forum] XSPectra calculations! Message-ID: hi, Can anyone give some guidelines over how to do the XSpectra calculations please? I don't see any README file in the example XSPectra/ too. So I tried to just run it using ./run_example in the XSPectra/ but it doesn't find the xspectra.x file in the bin/ as it is not there. So please-please a little help in this. Thanks, Harli -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101115/bcd2b10d/attachment.htm From giannozz at democritos.it Mon Nov 15 21:17:14 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 15 Nov 2010 21:17:14 +0100 Subject: [Pw_forum] XSPectra calculations! In-Reply-To: References: Message-ID: On Nov 15, 2010, at 20:53 , Suman Dhayal wrote: > it doesn't find the xspectra.x file in the bin/ as it is not there make xspectra --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From Ari.P.Seitsonen at iki.fi Mon Nov 15 21:16:04 2010 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Mon, 15 Nov 2010 21:16:04 +0100 (CET) Subject: [Pw_forum] XSPectra calculations! In-Reply-To: References: Message-ID: Dear Harli, Did you execute 'make xspectra' in the directory of the source code? XSpectra is not created with 'make all', for example. After the compilation you might want to study carefully the 'run_example' and read some of the papers from Christos Gougoussis and Matteo Calandra on their applications of the code; those will also lead you to more references on the theory behind the code from the institute in Paris where they work/worked. Greetings from Zurich, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Physikalisch-Chemisches Institut der Universitaet Zuerich Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 On Mon, 15 Nov 2010, Suman Dhayal wrote: > hi, > > Can anyone give some guidelines over how to do the XSpectra calculations > please? I don't see any README file in the example XSPectra/ too. So I tried > to just run it using ./run_example in the XSPectra/ but it doesn't find the > xspectra.x file in the bin/ as it is not there. So please-please a little > help in this. > > Thanks, > > Harli > > From ssdhayal at gmail.com Mon Nov 15 21:44:24 2010 From: ssdhayal at gmail.com (Suman Dhayal) Date: Mon, 15 Nov 2010 14:44:24 -0600 Subject: [Pw_forum] XSPectra calculations! In-Reply-To: References: Message-ID: Dear Paolo, Thank you for the quick help. Dear Ari, Thank you for the guidelines and the references for reading, its really helpful of you. I was confused about whether I would have to separately make it or so. SO Thank You! I made it now and tried to run the example which did not run yet, it seems to be a format problem which I should be able to take care hopefully. If you would have a look at the error, it is like this : running xspectra.x ...At line 2089 of file xspectra.f90 (unit = 33, file = 'C.wfc') Fortran runtime error: End of file Error condition encountered during test: exit status = 2 Aborting If you have any quick guidelines I would really appreciate it else I would try to work on it by myself. Thank you so much, Harli On Mon, Nov 15, 2010 at 2:16 PM, Ari P Seitsonen wrote: > > Dear Harli, > > Did you execute 'make xspectra' in the directory of the source code? > XSpectra is not created with 'make all', for example. After the > compilation you might want to study carefully the 'run_example' and read > some of the papers from Christos Gougoussis and Matteo Calandra on their > applications of the code; those will also lead you to more references > on the theory behind the code from the institute in Paris where they > work/worked. > > Greetings from Zurich, > > apsi > > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > Physikalisch-Chemisches Institut der Universitaet Zuerich > Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 > > > On Mon, 15 Nov 2010, Suman Dhayal wrote: > > > hi, > > > > Can anyone give some guidelines over how to do the XSpectra calculations > > please? I don't see any README file in the example XSPectra/ too. So I > tried > > to just run it using ./run_example in the XSPectra/ but it doesn't find > the > > xspectra.x file in the bin/ as it is not there. So please-please a little > > help in this. > > > > Thanks, > > > > Harli > > > > > _______________________________________________ > 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/20101115/9ea5527f/attachment.htm From Ari.P.Seitsonen at iki.fi Mon Nov 15 21:54:36 2010 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Mon, 15 Nov 2010 21:54:36 +0100 (CET) Subject: [Pw_forum] XSPectra calculations! In-Reply-To: References: Message-ID: Dear Harli, Did you check that 1) the file 'C.wfc' is generated correctly (it's done inside the 'run_example_diamond'), and if yes 2) is it similar/same as 'reference/C.wfc'? If the two files 'C.wfc' do not match please check for any error messages during the execution of the script. Greetings, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Physikalisch-Chemisches Institut der Universitaet Zuerich Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 On Mon, 15 Nov 2010, Suman Dhayal wrote: > Dear Paolo, Thank you for the quick help. > > Dear Ari, Thank you for the guidelines and the references for reading, its > really helpful of you. I was confused about whether I would have to > separately make it or so. SO Thank You! I made it now and tried to run the > example which did not run yet, it seems to be a format problem which I > should be able to take care hopefully. If you would have a look at the > error, it is like this : > > running xspectra.x ...At line 2089 of file xspectra.f90 (unit = 33, file = > 'C.wfc') > Fortran runtime error: End of file > Error condition encountered during test: exit status = 2 > Aborting > > If you have any quick guidelines I would really appreciate it else I would > try to work on it by myself. > > Thank you so much, > > Harli > > On Mon, Nov 15, 2010 at 2:16 PM, Ari P Seitsonen > wrote: > > Dear Harli, > > ? Did you execute 'make xspectra' in the directory of the source > code? > XSpectra is not created with 'make all', for example. After the > compilation you might want to study carefully the 'run_example' > and read > some of the papers from Christos Gougoussis and Matteo Calandra > on their > applications of the code; those will also lead you to more > references > on the theory behind the code from the institute in Paris where > they > work/worked. > > ? ? Greetings from Zurich, > > ? ? ? ?apsi > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=* > =- > ? Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / > http://www.iki.fi/~apsi/ > ? Physikalisch-Chemisches Institut der Universitaet Zuerich > ? Tel: +41 44 63 54 497 ?/ ?Mobile: +41 79 71 90 935 > > > On Mon, 15 Nov 2010, Suman Dhayal wrote: > > > hi, > > > > Can anyone give some guidelines over how to do the XSpectra > calculations > > please? I don't see any README file in the example XSPectra/ too. So > I tried > > to just run it using ./run_example in the XSPectra/ but it doesn't > find the > > xspectra.x file in the bin/ as it is not there. So please-please a > little > > help in this. > > > > Thanks, > > > > Harli > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > From ssdhayal at gmail.com Tue Nov 16 06:58:25 2010 From: ssdhayal at gmail.com (Suman Dhayal) Date: Mon, 15 Nov 2010 23:58:25 -0600 Subject: [Pw_forum] Help! Message-ID: hi, I configured and compiled the code but when I run example01, it runs for Si but not for Al. It gives me a segmentation fault error and then says exit status as follows: This example shows how to use pw.x to calculate the total energy and the band structure of four simple systems: Si, Al, Cu, Ni. executables directory: /home/suman/Diff_folders/Diff_ Codes/espresso-4.2.1/bin pseudo directory: /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/espresso-4.2.1/pseudo temporary directory: /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file checking that needed directories and files exist... done running pw.x as: /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/pw.x running bands.x as: /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/bands.x cleaning /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done running the scf calculation for Si... done running the band-structure calculation for Si... done running the symmetry analysis for Si bands...Segmentation fault done cleaning /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done running the scf calculation for Al...Segmentation fault Error condition encountered during test: exit status = 139 Aborting Thanks for the help, Harli -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101115/0b3385a5/attachment-0001.htm From matteo.calandra at impmc.jussieu.fr Tue Nov 16 09:09:01 2010 From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra) Date: Tue, 16 Nov 2010 09:09:01 +0100 Subject: [Pw_forum] Help XSPectra calculation In-Reply-To: References: Message-ID: <4CE23C1D.3080704@impmc.jussieu.fr> Dear Suman Dhayal, fro; the output of your script it seems to me that you are not running at all the XSpectra example but the general QE example. And the segmentation fault that you find has little do to with xspectrq but this is connected with the bands.x file. The XSpectra examples are in another directory. M. >> >> >> > > ------------------------------ > > Message: 8 > Date: Mon, 15 Nov 2010 23:58:25 -0600 > From: Suman Dhayal > Subject: [Pw_forum] Help! > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > hi, > > I configured and compiled the code but when I run example01, it runs for Si > but not for Al. It gives me a segmentation fault error and then says exit > status as follows: > > This example shows how to use pw.x to calculate the total energy and > the band structure of four simple systems: Si, Al, Cu, Ni. > > executables directory: /home/suman/Diff_folders/Diff_ > Codes/espresso-4.2.1/bin > pseudo directory: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/espresso-4.2.1/pseudo > temporary directory: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file > checking that needed directories and files exist... done > > running pw.x as: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/pw.x > running bands.x as: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/bands.x > > cleaning > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > running the scf calculation for Si... done > running the band-structure calculation for Si... done > running the symmetry analysis for Si bands...Segmentation fault > done > cleaning > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > running the scf calculation for Al...Segmentation fault > Error condition encountered during test: exit status = 139 > Aborting > > Thanks for the help, > > Harli > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101115/0b3385a5/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 41, Issue 28 > **************************************** -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra From prayerz.omo at gmail.com Tue Nov 16 12:27:47 2010 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Tue, 16 Nov 2010 06:27:47 -0500 Subject: [Pw_forum] MPI_Bcast error from cp.x Message-ID: Ciao tutti, Pls does anyone know a simple way to fix this error which I got from running cp.x with 4 processors: ERROR: 0032-117 User pack or receive buffer is too small (32) in MPI_Bcast, task 1 ERROR: 0032-117 User pack or receive buffer is too small (16) in MPI_Bcast, task 2 ERROR: 0032-117 User pack or receive buffer is too small (32) in MPI_Bcast, task 3 I googled and found: http://publib.boulder.ibm.com/infocenter/clresctr/vxrx/index.jsp?topic=%2Fcom.ibm.cluster.pe_linux43.messages.doc%2F0032-117.html which says: 0032-117 Parallel Environment for Linux V4.3 Messages SA38-0648-01 User pack or receive buffer too small (number) in string, task number Explanation The buffer specified for the operation was too small to hold the message. In the PACK and UNPACK cases it is the space between current position and buffer end which is too small. User response Increase the size of the buffer or reduce the size of the message. Error Class: MPI_ERR_TRUNCATE -------------------------------------------------------------------------------- I actually don't have a clue in which part of the program I should increase/decrease buffer/message size. Thanks for any help. o. -- ***************** Seek GOD! ************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101116/6bcc4ac1/attachment.htm From giannozz at democritos.it Tue Nov 16 13:19:52 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 16 Nov 2010 13:19:52 +0100 Subject: [Pw_forum] MPI_Bcast error from cp.x In-Reply-To: References: Message-ID: <4CE276E8.1020304@democritos.it> Omololu Akin-Ojo wrote: > I actually don't have a clue in which part of the program > I should increase/decrease buffer/message size. you shouldn't increase/decrease anything. You should look in the output file if there are other error messages. Then you should verify whether this error is reproducible ([referrably by running it on a different machine). If it is, please provide code version, input data, execution detail so that the error can be reproduced. If it is not: your compiler or MPI libraries are, with very high probability, buggy P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From prayerz.omo at gmail.com Tue Nov 16 15:22:22 2010 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Tue, 16 Nov 2010 09:22:22 -0500 Subject: [Pw_forum] MPI_Bcast error from cp.x In-Reply-To: <4CE276E8.1020304@democritos.it> References: <4CE276E8.1020304@democritos.it> Message-ID: Thanks, Paolo. It turns out that if one is NOT using orthogonalization='ortho' in optimizing the electrons, the eigenvalues should not be computed: NOTE: eigenvalues are not computed without ortho (I got this warning on a 64bit Linux while it crashes on AIX machine with the error I reported previously: ERROR: 0032-117 User pack or receive buffer is too small) My way of getting around it is to avoid printing "physical quantities to standard output" as it seems the error comes at the printing step. So, I set iprint (and isave) in the &control section to something larger than my maximum number of steps, nstep. It is still running so I don't know what it will do at the end. Grazie ancora. o. On Tue, Nov 16, 2010 at 7:19 AM, Paolo Giannozzi wrote: > Omololu Akin-Ojo wrote: > > > I actually don't have a clue in which part of the program > > I should increase/decrease buffer/message size. > > you shouldn't increase/decrease anything. You should look in the > output file if there are other error messages. Then you should > verify whether this error is reproducible ([referrably by running > it on a different machine). If it is, please provide code version, > input data, execution detail so that the error can be reproduced. > If it is not: your compiler or MPI libraries are, with very high > probability, buggy > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ***************** Seek GOD! ************* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101116/95d7983a/attachment.htm From ssdhayal at gmail.com Tue Nov 16 15:57:46 2010 From: ssdhayal at gmail.com (Suman Dhayal) Date: Tue, 16 Nov 2010 08:57:46 -0600 Subject: [Pw_forum] Help XSPectra calculation In-Reply-To: <4CE23C1D.3080704@impmc.jussieu.fr> References: <4CE23C1D.3080704@impmc.jussieu.fr> Message-ID: Dear Matteo, Thank you for the quick response. Hmmmm, I want to run the XSpectra example which I did once but it did not run and aborted in between. So I went back to example01 as xspectra uses the output of 'pw.x' and 'gipaw.x'. So I got back to example01 and looked into the output files and I found that it's not run completely. The output files for Si are completely run but not for the Al, it stops in between only with the error message that I have posted here in the previous email. So the error message that I posted is from running example01 and not xspectra. And I have no idea, what may be wrong. So it would be very helpful if I could be guided a little over it. Thanks a lot, Harli On Tue, Nov 16, 2010 at 2:09 AM, Matteo Calandra < matteo.calandra at impmc.jussieu.fr> wrote: > Dear Suman Dhayal, > > fro; the output of your script it seems to me that you are not running > at all the XSpectra example but the general QE example. > And the segmentation fault that you find has little do to with xspectrq > but this is connected with the bands.x file. > > The XSpectra examples are in another directory. > > M. > > >> > >> > >> > > > > ------------------------------ > > > > Message: 8 > > Date: Mon, 15 Nov 2010 23:58:25 -0600 > > From: Suman Dhayal > > Subject: [Pw_forum] Help! > > To: PWSCF Forum > > Message-ID: > > > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > hi, > > > > I configured and compiled the code but when I run example01, it runs for > Si > > but not for Al. It gives me a segmentation fault error and then says exit > > status as follows: > > > > This example shows how to use pw.x to calculate the total energy and > > the band structure of four simple systems: Si, Al, Cu, Ni. > > > > executables directory: /home/suman/Diff_folders/Diff_ > > Codes/espresso-4.2.1/bin > > pseudo directory: > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/espresso-4.2.1/pseudo > > temporary directory: > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file > > checking that needed directories and files exist... done > > > > running pw.x as: > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/pw.x > > running bands.x as: > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/bands.x > > > > cleaning > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > > running the scf calculation for Si... done > > running the band-structure calculation for Si... done > > running the symmetry analysis for Si bands...Segmentation fault > > done > > cleaning > > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > > running the scf calculation for Al...Segmentation fault > > Error condition encountered during test: exit status = 139 > > Aborting > > > > Thanks for the help, > > > > Harli > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101115/0b3385a5/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 41, Issue 28 > > **************************************** > > > -- > * * * * > Matteo Calandra, Charge de Recherche (CR1) > Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris > Universit? Pierre et Marie Curie, tour 16, case 115 > 4 Place Jussieu, 75252 Paris Cedex 05 France > Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 > http://www.impmc.jussieu.fr/~calandra > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101116/c23e178c/attachment.htm From giannozz at democritos.it Tue Nov 16 16:38:58 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 16 Nov 2010 16:38:58 +0100 Subject: [Pw_forum] MPI_Bcast error from cp.x In-Reply-To: References: <4CE276E8.1020304@democritos.it> Message-ID: <4CE2A592.1070407@democritos.it> Omololu Akin-Ojo wrote: > It turns out that if one is NOT using orthogonalization='ortho' in > optimizing the electrons, the eigenvalues should not be computed this is completely irrelevant > My way of getting around it is to avoid printing "physical quantities to > standard output" as it seems the error comes at the printing step. what makes you think that the error comes at the printing step? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From 1009ukumar at gmail.com Tue Nov 16 17:04:23 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Tue, 16 Nov 2010 21:34:23 +0530 Subject: [Pw_forum] ERROR IN: iotk_scan_dat_aux and iotk_scan_dat of IOTK LIBRARY? Message-ID: Dear all QE users, i am getting errors in iotk while doing following tests: /tests$ ./check-pw.x.j Checking atom...passed Checking atom-lsda...passed Checking atom-pbe...discrepancy in pressure detected Reference: -14.44, You got: -14.43 Checking atom-sigmapbe...discrepancy in pressure detected Reference: -15.02, You got: -15.03 Checking berry...passed Checking berry, step 2 ...######################################################################################################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_dat_aux (iotk_dat.spp:664) # CVS Revision: 1.27 # ERROR IN: iotk_scan_dat (iotk_dat.spp:740) # CVS Revision: 1.27 # Error reading data name=z.2 rkind=8 rlen=-1 ######################################################################################################################## application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 FAILED with error condition! Input: berry.in2, Output: berry.out2, Reference: berry.ref2 Aborting I have this problem with Ubuntu OS, while i have no problem on Suse(SLED-11) and code works nicely there with same make.sys file. While executing "make all" command i got few warnings from iotk/src, which are : mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D_SCALAPACK -D__FFTW3 -D__MPI -D__PARA -I../include -I/extra/sonu/intel/composerxe-2011.0.084/mkl/include/fftw -I/extra/sonu/mpich2-install/include -c iotk_base.f90 ../include/iotk_config.h(104): warning #5117: Bad # preprocessor line # 21 "iotk_base.spp" 2 ----------------------^ mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D_SCALAPACK -D__FFTW3 -D__MPI -D__PARA -I../include -I/extra/sonu/intel/composerxe-2011.0.084/mkl/include/fftw -I/extra/sonu/mpich2-install/include -c iotk_attr_interf.f90 ../include/iotk_config.h(104): warning #5117: Bad # preprocessor line # 21 "iotk_attr_interf.spp" 2 -----------------------------^ mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D_SCALAPACK -D__FFTW3 -D__MPI -D__PARA -I../include -I/extra/sonu/intel/composerxe-2011.0.084/mkl/include/fftw -I/extra/sonu/mpich2-install/include -c iotk_error_interf.f90 ../include/iotk_config.h(104): warning #5117: Bad # preprocessor line # 21 "iotk_error_interf.spp" 2 ------------------------------^ mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D_SCALAPACK -D__FFTW3 -D__MPI -D__PARA -I../include -I/extra/sonu/intel/composerxe-2011.0.084/mkl/include/fftw -I/extra/sonu/mpich2-install/include -c iotk_attr+COMPLEX1_0.f90 iotk_attr.spp(221): remark #8291: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'. read(string(pos+1:pos1-1),"(G100.95)",iostat=iostat) tmpreal ---------------------------------^ i think something to do with config.h file of iotk. I shall be thankful for any kind of help. with regards, 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/20101116/dac25eef/attachment-0001.htm From prayerz.omo at gmail.com Tue Nov 16 17:08:11 2010 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Tue, 16 Nov 2010 17:08:11 +0100 Subject: [Pw_forum] MPI_Bcast error from cp.x In-Reply-To: <4CE2A592.1070407@democritos.it> References: <4CE276E8.1020304@democritos.it> <4CE2A592.1070407@democritos.it> Message-ID: On Tue, Nov 16, 2010 at 4:38 PM, Paolo Giannozzi wrote: > > Omololu Akin-Ojo wrote: > > > It turns out that if one is NOT using orthogonalization='ortho' in > > optimizing the electrons, the eigenvalues should not be computed > > this is completely irrelevant I think this is important. It seems that the problem is caused by an attempt to calculate the eigenvalues and this attempt is triggered by "iprint." > > > My way of getting around it is to avoid printing "physical quantities to > > standard output" as it seems the error comes at the printing step. > > what makes you think that the error comes at the printing step? The program crashes (AIX) or writes the warning message (Linux) at the point where it is supposed to print (iprint=X) "relevant physical quantities to standard output ..." -- and very reproducible for any X. Grazie ancora. o. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- ***************** Seek GOD! ************* From giannozz at democritos.it Tue Nov 16 17:30:58 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 16 Nov 2010 17:30:58 +0100 Subject: [Pw_forum] MPI_Bcast error from cp.x In-Reply-To: References: <4CE276E8.1020304@democritos.it> <4CE2A592.1070407@democritos.it> Message-ID: <4CE2B1C2.6070607@democritos.it> Omololu Akin-Ojo wrote: > The program crashes (AIX) or writes the warning message (Linux) at the > point where it is supposed to print (iprint=X) "relevant physical > quantities to standard output ..." -- and very reproducible for any X. please provide a test P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From julen.azpiroz at gmail.com Wed Nov 17 12:27:01 2010 From: julen.azpiroz at gmail.com (Julen Ibanez Azpiroz) Date: Wed, 17 Nov 2010 12:27:01 +0100 Subject: [Pw_forum] Plot given atomic orbital Message-ID: Hello I wanted to plot the 3D shape of an eigenstate at certain k point and certain band value. I used pp.x with 'plot_num=7' which plots the square of the eigenstate and the result was very nice (I used XCRYSDEN), but it is difficult for me to distinguish between the contribution of different atomic orbitals (s, p, d). I see that the executable projwfc.x does project the eigenstates onto localized atomic orbitals and calculate quantities such as Lowding charges, spilling parameter or projected DOS. I was wondering if there is an option in quantum-espresso to plot the contribution of these atomic orbitals in 3D (at certain k point and certain band value) in the way that pp.x plots the entire eigenstate. I couldnt find the answer neither in the forum nor in the Documentation of the package, so I would really appreciate if anyone knows if it is or not possible, thank you in advance, Julen Iba?ez University of the Basque Country -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101117/780f4ef8/attachment.htm From giannozz at democritos.it Wed Nov 17 12:56:07 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 17 Nov 2010 12:56:07 +0100 Subject: [Pw_forum] ERROR IN: iotk_scan_dat_aux and iotk_scan_dat of IOTK LIBRARY? In-Reply-To: References: Message-ID: <4CE3C2D7.6050707@democritos.it> sonu kumar wrote: > I have this problem with Ubuntu OS, while i have no problem on > Suse(SLED-11) and code works nicely there with same make.sys file. gfortran? have a look at this: http://www.quantum-espresso.org/user_guide/node14.html#SECTION00037430000000000000 > ../include/iotk_config.h(104): warning #5117: Bad # preprocessor line > # 21 "iotk_base.spp" 2 > ----------------------^ it shouldn't be important P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From 1009ukumar at gmail.com Wed Nov 17 14:37:10 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Wed, 17 Nov 2010 19:07:10 +0530 Subject: [Pw_forum] ERROR IN: iotk_scan_dat_aux and iotk_scan_dat of IOTK LIBRARY? Message-ID: Dear all QE users and respected Prof. Paolo Giannozzi, >>* I have this problem with Ubuntu OS, while i have no problem on *>>* Suse(SLED-11) and code works nicely there with same make.sys file. * >gfortran? have a look at this: >http://www.quantum-espresso.org/user_guide/node14.html#SECTION00037430000000000000 Not gfortan, I am using ifort, intel compiler. On ubuntu linux os, i am using latest intel fortran compiler (non-commercial version),*Intel? Fortran Composer XE 2011*. While on open-suse linux os or SLED-11 linux os, i used ifort-version-11.1.072,*Intel? Fortran Compiler Professional Edition. With kind regards, Sonu IITD * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101117/7be77a5c/attachment.htm From wumindt2 at zju.edu.cn Wed Nov 17 22:19:58 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Thu, 18 Nov 2010 05:19:58 +0800 Subject: [Pw_forum] wannier function Message-ID: Dear All QE user, I want to plot the localized wannier function of SiO2. In the QE user's guide, there are three wannier-related utilities. 1. "poor man wannier" code pmw.x. Is this only used in LDA+U calculation ? Besides, there isn't any discription of the parameters of this code. 2. Wannier90 code. 3. wannier_ham.x code. So which one is recommended ? Thanks for any help. With regards. Min Wu 2010-11-17 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/6b4007fb/attachment.htm From nicola.marzari at materials.ox.ac.uk Wed Nov 17 23:06:03 2010 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 17 Nov 2010 22:06:03 +0000 Subject: [Pw_forum] wannier function In-Reply-To: References: Message-ID: <1290031563.3421.6.camel@Nokia-N900-42-11> Wannier90. Nicola ----- Original message ----- > Dear All QE user, > > I want to plot the localized wannier function of SiO2. In the QE user's > guide, there are three wannier-related utilities. 1. "poor man wannier" > code pmw.x. Is this only used in LDA+U calculation ? Besides, there > isn't any discription of the parameters of this code. 2. Wannier90 code. > 3. wannier_ham.x code. > > So which one is recommended ? > > Thanks for any help. > > With regards. > > Min Wu > 2010-11-17 ? ATT00001.txt -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101117/2e196b7c/attachment.htm From tavana.ali at gmail.com Thu Nov 18 12:35:26 2010 From: tavana.ali at gmail.com (Ali Tavana) Date: Thu, 18 Nov 2010 15:05:26 +0330 Subject: [Pw_forum] Error in phonon calculation Message-ID: Dear QE users, When I want to calculate phonons for a q-point, I get this error running ph.x; ####################################### # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_dat_aux (iotk_dat.spp:664) # CVS Revision: 1.27 # ERROR IN: iotk_scan_dat (iotk_dat.spp:740) # CVS Revision: 1.27 # Error reading data name=z.1 rkind=8 rlen=-1 ################################################### Do u have any idea about it? -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/984a2b3e/attachment.htm From jtmullen at ncsu.edu Thu Nov 18 13:42:21 2010 From: jtmullen at ncsu.edu (Jeff Mullen) Date: Thu, 18 Nov 2010 07:42:21 -0500 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: Message-ID: Greetings, Can you post the input files for the SCF and phonon calculation? I assume you are using 4.2.1. Cheers Jeff NCSU Physics On Thu, Nov 18, 2010 at 6:35 AM, Ali Tavana wrote: > Dear QE users, > > When I want to calculate phonons for a q-point, I get this error running > ph.x; > > ####################################### > # FROM IOTK LIBRARY, VERSION 1.2.0 > # UNRECOVERABLE ERROR (ierr=1) > # ERROR IN: iotk_scan_dat_aux (iotk_dat.spp:664) > # CVS Revision: 1.27 > # ERROR IN: iotk_scan_dat (iotk_dat.spp:740) > # CVS Revision: 1.27 > # Error reading data > name=z.1 > rkind=8 > rlen=-1 > ################################################### > > > Do u have any idea about it? > > -- > Ali Tavana > PhD Candidate, > Magnet Research Lab. (MRL) > Sharif University of Technology, > Tehran, Iran. > Tel: +98 21 6616 4544 > > _______________________________________________ > 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/20101118/974ea809/attachment.htm From tavana.ali at gmail.com Thu Nov 18 14:02:37 2010 From: tavana.ali at gmail.com (Ali Tavana) Date: Thu, 18 Nov 2010 16:32:37 +0330 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: Message-ID: Yes, I am using 4.2.1 These are my input files: ====================================================== &control calculation='scf' restart_mode='from_scratch', prefix='La', pseudo_dir = './', outdir='./tmp' / &system ibrav=6, celldm(1) =7.616, celldm(3) =2.168, nat=8, ntyp=4, nspin = 1, ecutwfc = 24.0, ecutrho = 240.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.02 / &electrons conv_thr = 1.0e-10 mixing_beta = 0.7 / ATOMIC_SPECIES La 57 La.UPF Fe 26 Fe.UPF O 8 O.UPF As 33 As.UPF ATOMIC_POSITIONS crystal Fe 0.250000000 0.750000000 0.000000000 Fe 0.750000000 0.250000000 0.000000000 As 0.750000000 0.750000000 0.169696326 As 0.250000000 0.250000000 0.830303674 O 0.250000000 0.750000000 0.500000000 O 0.750000000 0.250000000 0.500000000 La 0.750000000 0.750000000 0.657729323 La 0.250000000 0.250000000 0.342270677 K_POINTS automatic 8 8 4 0 0 0 ===================================================== phonons at Gamma &inputph tr2_ph=1.0d-18, prefix='La', outdir='./tmp', fildyn='La.dyn', trans=.true., / 0.0 0.0 0.0 ====================================================== Bests, Ali -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 Fax:+98 21 4446 0799 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/d64b15e3/attachment.htm From padmaja_patnaik at yahoo.co.uk Thu Nov 18 14:26:54 2010 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Thu, 18 Nov 2010 13:26:54 +0000 (GMT) Subject: [Pw_forum] Finding Curie temperature Message-ID: <970149.49143.qm@web26103.mail.ukl.yahoo.com> Hi How can we calculate Curie temperature using quantum espresso? If anybody can explain, it can be very helpful for me. 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/20101118/3d78e692/attachment.htm From eyvaz_isaev at yahoo.com Thu Nov 18 14:54:53 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 18 Nov 2010 05:54:53 -0800 (PST) Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: Message-ID: <418841.93388.qm@web65702.mail.ac4.yahoo.com> Dear Ali, Possible reasons: 1. Compiler error - it seems, such kind error often happens with gfortran 2. Network problem 3. Corrupted data - try again. I do not think the error is caused by your input file. Nevertheless, you can try also the option ldisp=.true. with nq1=N1,nq2=N2,nq3=N3 and start_q=1, last_q=1 to calculate phonons at the Gamma point. Just to note, 10^{-18} looks VERY strong (and time consumable) criteria for phonon convergence threshold. The default value thr2_ph=10^{-12}. 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: Ali Tavana To: pw_forum at pwscf.org Sent: Thu, November 18, 2010 12:35:26 PM Subject: [Pw_forum] Error in phonon calculation Dear QE users, When I want to calculate phonons for a q-point, I get this error running ph.x; ####################################### # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_dat_aux (iotk_dat.spp:664) # CVS Revision: 1.27 # ERROR IN: iotk_scan_dat (iotk_dat.spp:740) # CVS Revision: 1.27 # Error reading data name=z.1 rkind=8 rlen=-1 ################################################### Do u have any idea about it? -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/63b0a487/attachment.htm From tavana.ali at gmail.com Thu Nov 18 15:13:27 2010 From: tavana.ali at gmail.com (Ali Tavana) Date: Thu, 18 Nov 2010 17:43:27 +0330 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: <418841.93388.qm@web65702.mail.ac4.yahoo.com> References: <418841.93388.qm@web65702.mail.ac4.yahoo.com> Message-ID: Dear Prof. Isaev, Thank you very much for your response. I tried what you suggested but it didn't solve my problem. - I use ifort (actually Intel Parallel Studio xe) on a core i7 processor (no networking) - Strong convergence criteria is because of the convergency tests . No correlation have been seen between it's value and the occurring error ;) The error still exists... sincerely yours, Ali -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 Fax:+98 21 4446 0799 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/1d1845ce/attachment.htm From tavana.ali at gmail.com Thu Nov 18 15:17:36 2010 From: tavana.ali at gmail.com (Ali Tavana) Date: Thu, 18 Nov 2010 17:47:36 +0330 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: <418841.93388.qm@web65702.mail.ac4.yahoo.com> Message-ID: Forgot to say, I tried the 4.2 version also and the error showed up again! This error doesn't happen for the example calculations!! I used the standard PPs from the official website of Qespresso instead of my own PPs, but it didn't help!!! -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 Fax:+98 21 4446 0799 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/3217a07c/attachment.htm From cvasse at hotmail.com Thu Nov 18 15:34:50 2010 From: cvasse at hotmail.com (Vasse chis) Date: Thu, 18 Nov 2010 15:34:50 +0100 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: , , Message-ID: Dear Ali, I've noticed that where you are supposed to write the atomic mass you've written the atomic number, i.e. instead of / ATOMIC_SPECIES La 57 La.UPF Fe 26 Fe.UPF O 8 O.UPF As 33 As.UPF It should read, / ATOMIC_SPECIES La 138.9055 La.UPF Fe 55.845 Fe.UPF O 15.9994 O.UPF As 74.9216 As.UPF This correction might help? Bests, Vasse From: tavana.ali at gmail.com Date: Thu, 18 Nov 2010 16:32:37 +0330 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Error in phonon calculation Yes, I am using 4.2.1 These are my input files: ====================================================== &control calculation='scf' restart_mode='from_scratch', prefix='La', pseudo_dir = './', outdir='./tmp' / &system ibrav=6, celldm(1) =7.616, celldm(3) =2.168, nat=8, ntyp=4, nspin = 1, ecutwfc = 24.0, ecutrho = 240.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.02 / &electrons conv_thr = 1.0e-10 mixing_beta = 0.7 / ATOMIC_SPECIES La 57 La.UPF Fe 26 Fe.UPF O 8 O.UPF As 33 As.UPF ATOMIC_POSITIONS crystal Fe 0.250000000 0.750000000 0.000000000 Fe 0.750000000 0.250000000 0.000000000 As 0.750000000 0.750000000 0.169696326 As 0.250000000 0.250000000 0.830303674 O 0.250000000 0.750000000 0.500000000 O 0.750000000 0.250000000 0.500000000 La 0.750000000 0.750000000 0.657729323 La 0.250000000 0.250000000 0.342270677 K_POINTS automatic 8 8 4 0 0 0 ===================================================== phonons at Gamma &inputph tr2_ph=1.0d-18, prefix='La', outdir='./tmp', fildyn='La.dyn', trans=.true., / 0.0 0.0 0.0 ====================================================== Bests, Ali -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 Fax:+98 21 4446 0799 _______________________________________________ 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/20101118/876b8b36/attachment-0001.htm From eyvaz_isaev at yahoo.com Thu Nov 18 15:47:18 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 18 Nov 2010 06:47:18 -0800 (PST) Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: <418841.93388.qm@web65702.mail.ac4.yahoo.com> Message-ID: <899908.28996.qm@web65712.mail.ac4.yahoo.com> Well, Then most likely, a compiler error. If I remember correctly, recently similar error with IOTK and the last Intel Compiler was posted. Try earlier version of IFC, gfortran, or g95 . I did not suggest that the convergence criteria might cause the error, I just noticed "it is VERY high". Bests, Eyvaz. ________________________________ From: Ali Tavana To: PWSCF Forum Sent: Thu, November 18, 2010 3:13:27 PM Subject: Re: [Pw_forum] Error in phonon calculation Dear Prof. Isaev, Thank you very much for your response. I tried what you suggested but it didn't solve my problem. - I use ifort (actually Intel Parallel Studio xe) on a core i7 processor (no networking) - Strong convergence criteria is because of the convergency tests . No correlation have been seen between it's value and the occurring error ;) The error still exists... sincerely yours, Ali -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 Fax:+98 21 4446 0799 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/29b3e38b/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Thu Nov 18 15:47:40 2010 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 18 Nov 2010 15:47:40 +0100 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: <418841.93388.qm@web65702.mail.ac4.yahoo.com> Message-ID: Are you running the 2 calculations with the same number of processors and pools? It should work anyway, but it's better to be sure On Thu, 18 Nov 2010 15:17:36 +0100, Ali Tavana wrote: > This error doesn't happen for the example calculations!! like, you can run example02 and example06 with no problems? -- 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 Nov 18 15:50:59 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 18 Nov 2010 15:50:59 +0100 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: <418841.93388.qm@web65702.mail.ac4.yahoo.com> References: <418841.93388.qm@web65702.mail.ac4.yahoo.com> Message-ID: <4CE53D53.8030505@democritos.it> Eyvaz Isaev wrote: > 10^{-18} looks VERY strong (and time consumable) criteria for > phonon convergence threshold. The default value thr2_ph=10^{-12}. for ultrasoft pseudopotentials, it's a safe criterion. The default is usually too large for US PP P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Nov 18 15:52:32 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 18 Nov 2010 15:52:32 +0100 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: , , Message-ID: <4CE53DB0.9050804@democritos.it> Vasse chis wrote: > This correction might help? it might be a good idea to use the correct masses, for sure, but this has nothing to do with the error, for sure P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From chakraa at tcd.ie Thu Nov 18 15:55:32 2010 From: chakraa at tcd.ie (Aurab) Date: Thu, 18 Nov 2010 14:55:32 +0000 Subject: [Pw_forum] Help! In-Reply-To: References: Message-ID: Hi, Segmentation fault indicates dynamic memory overflow. May be for Al, pseudopotentials are larger and it created large matrices that the system you are using was unable to handle. Are you running in parallel? Try using specific parallelisation parameters -npool -ndiag etc. See the Parallelism chapter of QE user guide for detailed instructions. Many regards, Aurab On 16 November 2010 05:58, Suman Dhayal wrote: > hi, > > I configured and compiled the code but when I run example01, it runs for Si > but not for Al. It gives me a segmentation fault error and then says exit > status as follows: > > This example shows how to use pw.x to calculate the total energy and > the band structure of four simple systems: Si, Al, Cu, Ni. > > executables directory: /home/suman/Diff_folders/Diff_ > Codes/espresso-4.2.1/bin > pseudo directory: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/espresso-4.2.1/pseudo > temporary directory: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file > checking that needed directories and files exist... done > > running pw.x as: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/pw.x > running bands.x as: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/bands.x > > cleaning > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > running the scf calculation for Si... done > running the band-structure calculation for Si... done > running the symmetry analysis for Si bands...Segmentation fault > done > cleaning > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > running the scf calculation for Al...Segmentation fault > Error condition encountered during test: exit status = 139 > Aborting > > Thanks for the help, > > Harli > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- =*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* Aurab D. Chakrabarty Postgraduate Student (Research) Room 2.22 The Lloyd Institute School of Physics Trinity College Dublin Dublin 2 Ireland Telephone: +353-1-896-8453 *=*=*=*=*=*=*=*=*=*=*=*=*=*=* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/cf67049c/attachment.htm From giannozz at democritos.it Thu Nov 18 16:04:48 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 18 Nov 2010 16:04:48 +0100 Subject: [Pw_forum] Help! In-Reply-To: References: Message-ID: <4CE54090.6020603@democritos.it> Aurab wrote: > Segmentation fault indicates dynamic memory overflow. May be for Al, > pseudopotentials are larger and it created large matrices that the > system you are using was unable to handle. thanks for the effort, but you should try harder. example01 can run without any problem on any machine, including the smallest ones, as long as they have a compiler that produces correct executables. Apparently most people in this list don't have one. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From tavana.ali at gmail.com Thu Nov 18 16:08:26 2010 From: tavana.ali at gmail.com (Ali Tavana) Date: Thu, 18 Nov 2010 18:38:26 +0330 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: <4CE53DB0.9050804@democritos.it> References: <4CE53DB0.9050804@democritos.it> Message-ID: Once I tried true atomic masses but didn't (and shouldn't) help as Prof. Giannozzi said. Interestingly when I do e-ph calculation for this case, it works! i.e. a dense scf (la2F=true) --> rare scf --> ph.x (elph=true)!!! -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 Fax:+98 21 4446 0799 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/8011b6fa/attachment.htm From samolyuk at gmail.com Thu Nov 18 16:16:31 2010 From: samolyuk at gmail.com (German Samolyuk) Date: Thu, 18 Nov 2010 10:16:31 -0500 Subject: [Pw_forum] Finding Curie temperature In-Reply-To: <970149.49143.qm@web26103.mail.ukl.yahoo.com> References: <970149.49143.qm@web26103.mail.ukl.yahoo.com> Message-ID: The simples way is to yse Heisenberg model. If you have system with well localized magnetic moments, the bcc iron is one of them, it will works pretty good. You can calculate total energy of ferromangnetically (FM) ordered state and anitferromagnetically (AFM) one. Depending on type of AFM the difference of these two energies gives you effective exchange parameter J_0. in mean field approximation the Curie temperature T_c=2/3 J_0. Or more complicate - you can map set of exchange parameters to set of energies for differently magnetically ordered states and obtain T_C from this Heisenberg hamiltonian. As I understand all other approaches wiil need modifications of the code. Best, German Samolyuk Oak Ridge National Lab USA On Thu, Nov 18, 2010 at 8:26 AM, Padmaja Patnaik < padmaja_patnaik at yahoo.co.uk> wrote: > Hi > > How can we calculate Curie temperature using quantum espresso? If anybody > can explain, it can be very helpful for me. > > 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/20101118/d0d152e8/attachment-0001.htm From eyvaz_isaev at yahoo.com Thu Nov 18 16:14:14 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 18 Nov 2010 07:14:14 -0800 (PST) Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: , , Message-ID: <876787.93253.qm@web65715.mail.ac4.yahoo.com> No. Even their (amass) absence in Ali's input file for phonons , I think, can not cause this error, they are read from a database. 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: Vasse chis To: pw_forum at pwscf.org Sent: Thu, November 18, 2010 3:34:50 PM Subject: Re: [Pw_forum] Error in phonon calculation Dear Ali, I've noticed that where you are supposed to write the atomic mass you've written the atomic number, i.e. instead of / ATOMIC_SPECIES La 57 La.UPF Fe 26 Fe.UPF O 8 O.UPF As 33 As.UPF It should read, / ATOMIC_SPECIES La 138.9055 La.UPF Fe 55.845 Fe.UPF O 15.9994 O.UPF As 74.9216 As.UPF This correction might help? Bests, Vasse ________________________________ From: tavana.ali at gmail.com Date: Thu, 18 Nov 2010 16:32:37 +0330 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Error in phonon calculation Yes, I am using 4.2.1 These are my input files: ====================================================== &control calculation='scf' restart_mode='from_scratch', prefix='La', pseudo_dir = './', outdir='./tmp' / &system ibrav=6, celldm(1) =7.616, celldm(3) =2.168, nat=8, ntyp=4, nspin = 1, ecutwfc = 24.0, ecutrho = 240.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.02 / &electrons conv_thr = 1.0e-10 mixing_beta = 0.7 / ATOMIC_SPECIES La 57 La.UPF Fe 26 Fe.UPF O 8 O.UPF As 33 As.UPF ATOMIC_POSITIONS crystal Fe 0.250000000 0.750000000 0.000000000 Fe 0.750000000 0.250000000 0.000000000 As 0.750000000 0.750000000 0.169696326 As 0.250000000 0.250000000 0.830303674 O 0.250000000 0.750000000 0.500000000 O 0.750000000 0.250000000 0.500000000 La 0.750000000 0.750000000 0.657729323 La 0.250000000 0.250000000 0.342270677 K_POINTS automatic 8 8 4 0 0 0 ===================================================== phonons at Gamma &inputph tr2_ph=1.0d-18, prefix='La', outdir='./tmp', fildyn='La.dyn', trans=.true., / 0.0 0.0 0.0 ====================================================== Bests, Ali -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 Fax:+98 21 4446 0799 _______________________________________________ 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/20101118/f043a7c4/attachment.htm From giannozz at democritos.it Thu Nov 18 17:31:57 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 18 Nov 2010 17:31:57 +0100 Subject: [Pw_forum] Plot given atomic orbital In-Reply-To: References: Message-ID: <4CE554FD.3020002@democritos.it> Julen Ibanez Azpiroz wrote: > I was wondering if there is an option in quantum-espresso to plot > the contribution of these atomic orbitals in 3D (at certain k point > and certain band value) in the way that pp.x plots the entire eigenstate not that I know P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From ssdhayal at gmail.com Thu Nov 18 17:00:27 2010 From: ssdhayal at gmail.com (Suman Dhayal) Date: Thu, 18 Nov 2010 10:00:27 -0600 Subject: [Pw_forum] Help! In-Reply-To: <4CE54090.6020603@democritos.it> References: <4CE54090.6020603@democritos.it> Message-ID: Thanks a lot Dr. Aurab for the guidelines and Dr. Paolo for the suggestion. On Thu, Nov 18, 2010 at 9:04 AM, Paolo Giannozzi wrote: > Aurab wrote: > > > Segmentation fault indicates dynamic memory overflow. May be for Al, > > pseudopotentials are larger and it created large matrices that the > > system you are using was unable to handle. > > thanks for the effort, but you should try harder. example01 can run > without any problem on any machine, including the smallest ones, as > long as they have a compiler that produces correct executables. > Apparently most people in this list don't have one. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/82242542/attachment.htm From julen.azpiroz at gmail.com Thu Nov 18 17:41:18 2010 From: julen.azpiroz at gmail.com (Julen Ibanez Azpiroz) Date: Thu, 18 Nov 2010 17:41:18 +0100 Subject: [Pw_forum] Plot given atomic orbital In-Reply-To: <4CE554FD.3020002@democritos.it> References: <4CE554FD.3020002@democritos.it> Message-ID: Thank you very much for the answer Prof. Giannozzi, Julen Iba?ez University of the Basque Country -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/cd2b907f/attachment.htm From giannozz at democritos.it Thu Nov 18 18:48:16 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 18 Nov 2010 18:48:16 +0100 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: Message-ID: <4CE566E0.4020002@democritos.it> Ali Tavana wrote: > Yes, I am using 4.2.1 > These are my input files: when does the error occur? in serial or parallel execution? is it reproducible? if not, the usual comment apply P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From tavana.ali at gmail.com Thu Nov 18 19:53:51 2010 From: tavana.ali at gmail.com (Ali Tavana) Date: Thu, 18 Nov 2010 22:23:51 +0330 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: <4CE566E0.4020002@democritos.it> References: <4CE566E0.4020002@democritos.it> Message-ID: It occurs in serial execution. I moved the folders to my desktop. After that, some times I see the error and some times not! For the case elph=true I never saw it. I'll try this situation on other computers. -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/34b558be/attachment.htm From eyvaz_isaev at yahoo.com Thu Nov 18 20:01:16 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 18 Nov 2010 11:01:16 -0800 (PST) Subject: [Pw_forum] QHA release Message-ID: <704508.72119.qm@web65710.mail.ac4.yahoo.com> Dear QE users, I have just released a new version of QHA code and you can download it from http://qe-forge.org/projects/qha/ The main changes are: 1. It should be faster 2. Support for bct type structure (a>c and a Hi I am using pp to get charge densities, and plot in gnuplot. It is all working fine (thanks to forum answers). I just have a question on units: I am assuming the output of pp is in C/m^3. Am I correct? Thanks in advance. Peter MIT, EECS, Cambridge, MA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101118/5960a20d/attachment-0001.htm From lorenzo.paulatto at impmc.upmc.fr Thu Nov 18 22:31:53 2010 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 18 Nov 2010 22:31:53 +0100 Subject: [Pw_forum] PP output In-Reply-To: <00ef01cb8753$4f812490$ee836db0$@edu> References: <00ef01cb8753$4f812490$ee836db0$@edu> Message-ID: In data 18 novembre 2010 alle ore 20:03:36, Peter O Orondo ha scritto: > I am using pp to get charge densities, and plot in gnuplot. It is all > working fine (thanks to forum answers). I just have a question on units: > I > am assuming the output of pp is in C/m^3. Am I correct? It is atomic units, namely qe/a0^3. a0 in the bohr radius, but I'm not sure if qe is 1 or sqrt(2). This issue has already been discussed on the mailing list a few times I think you should a be able to find a documented sensible answer in the archives. If you need to be 100% sure you will have to integrate it. -- 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 wang.riping.81 at gmail.com Fri Nov 19 01:56:56 2010 From: wang.riping.81 at gmail.com (Riping WANG) Date: Fri, 19 Nov 2010 09:56:56 +0900 Subject: [Pw_forum] cppp.x ---- IONS not found in data-file.xml Message-ID: Dear all, I have some trouble, could you please help me and give me suggestions ? After I modified the pseudo-dir and out-dir, and I did not change anything else. 1. cp.x < h2o_mol1.in 2. cp.x < h2o_mol2.in 3. cp.x < h2o_mol.cp-dens.in 4. cppp.x < h2o_mol.cppp-dens.in I run the following. The first three are ok. when I run the fourth commond: cppp.x the error shows that: %%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from cppp : error # 1 IONS not found in data-file.xml %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... STOP 2 My system is Thinkpad-X200 with Ubuntu 64bit system PC. Thanks very much. WANG Riping 2010.11.19 -- ****************************************************************************** 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/20101119/5ce1503f/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: examples_cp.tgz Type: application/x-gzip Size: 76726 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101119/5ce1503f/attachment-0001.bin From 1009ukumar at gmail.com Fri Nov 19 05:09:41 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Fri, 19 Nov 2010 09:39:41 +0530 Subject: [Pw_forum] Error in phonon calculation and during tests also? Message-ID: Dear all QE users and Ali, I am getting EXACTLY the same error, which is : ######################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_dat_aux (iotk_dat.spp:664) # CVS Revision: 1.27 # ERROR IN: iotk_scan_dat (iotk_dat.spp:740) # CVS Revision: 1.27 # Error reading data name=z.2 rkind=8 rlen=-1 ######################################################################### >It occurs in serial execution. i am getting it in parallel, not tried in serial. >I moved the folders to my desktop. After that, some times I see the error >and some times not! >For the case elph=true I never saw it. I'll try this situation on other >computers. I tried with both, phonon calculations and "tests" , and got the same error. So seems that it's not the problem with phonon input file or test input files. Also one thing, with scf calculations code finishes with no error. I am using latest intel fortran compiler (ifort-2011.0.084). I am at fix because of this error. Need Help. With regards, sonu IITD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101119/b9d89b0e/attachment.htm From 1009ukumar at gmail.com Fri Nov 19 05:19:49 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Fri, 19 Nov 2010 09:49:49 +0530 Subject: [Pw_forum] Error in phonon calculation and during tests also? In-Reply-To: References: Message-ID: Additionally: i tried with both espresso-4.2.1 and espresso-4.2. but getting same error with phonon and test calculations. Also i put the iotk from old version-3.2.3 into the 4.2.1 to compile the code, but got errors during compilations....did this just to see if code compiles or not? Sonu IITD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101119/234173a7/attachment.htm From yukihiro_okuno at fujifilm.co.jp Fri Nov 19 05:54:25 2010 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Fri, 19 Nov 2010 13:54:25 +0900 Subject: [Pw_forum] Reference of PWCOND Message-ID: Dear PWSCF users and developers. I want to know the reference (article) of PWCOND, because I'm interested to how to calculate conductivity by plane wave method. There are papers on calculation of conductivity like surface Green function method + abinitio method, but many of them are based on localized atomic orbital, so I want to know how to calculate the conductivity by plane wave method. Sincerely, Yukihiro Okuno. From nkxirainbow at gmail.com Fri Nov 19 07:36:59 2010 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 19 Nov 2010 14:36:59 +0800 Subject: [Pw_forum] Reference of PWCOND In-Reply-To: References: Message-ID: Dear Yukihiro Okuno: I think you can find important information at this websit: http://people.sissa.it/~smogunov/ As far as I know, PWCOND can only get the conductivity under zero bias voltage. On Fri, Nov 19, 2010 at 12:54 PM, wrote: > > Dear PWSCF users and developers. > > I want to know the reference (article) of PWCOND, because > > I'm interested to how to calculate conductivity by plane wave method. > > There are papers on calculation of conductivity like surface Green > > function method + abinitio method, but many of them are based on > > localized atomic orbital, so I want to know how to calculate > > the conductivity by plane wave method. > > Sincerely, > > > Yukihiro Okuno. > > _______________________________________________ > 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/20101119/0e05583c/attachment.htm From tavana.ali at gmail.com Fri Nov 19 08:12:35 2010 From: tavana.ali at gmail.com (Ali Tavana) Date: Fri, 19 Nov 2010 10:42:35 +0330 Subject: [Pw_forum] Error in phonon calculation In-Reply-To: References: <4CE566E0.4020002@democritos.it> Message-ID: Dear all, It seems that using gfortran instead of ifort solves the problem! Bests, Ali -- Ali Tavana PhD Candidate, Magnet Research Lab. (MRL) Sharif University of Technology, Tehran, Iran. Tel: +98 21 6616 4544 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101119/a400610b/attachment.htm From giannozz at democritos.it Fri Nov 19 09:34:51 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 19 Nov 2010 09:34:51 +0100 Subject: [Pw_forum] Error in phonon calculation and during tests also? In-Reply-To: References: Message-ID: <6F5A2FFB-D046-45BE-82FA-6084FE735F31@democritos.it> On Nov 19, 2010, at 5:09 , sonu kumar wrote > I am using latest intel fortran compiler (ifort-2011.0.084). > > I am at fix because of this error. Need Help. did you pay real money for your compiler? complain with Intel. If not, try a different compiler (or a different version of the same compiler) P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From glapenna at iccom.cnr.it Fri Nov 19 09:54:22 2010 From: glapenna at iccom.cnr.it (Giovanni La Penna) Date: Fri, 19 Nov 2010 09:54:22 +0100 (CET) Subject: [Pw_forum] cppp.x ---- IONS not found in data-file.xml In-Reply-To: References: Message-ID: If you use an older version of cppp.x (4.1.x) most of the analysis is performed correctly on data produced by versions 4.2.y. 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 Fri, 19 Nov 2010, Riping WANG wrote: > Dear all, > > > I have some trouble, could you please help me and give me suggestions ? > > After I modified the pseudo-dir and out-dir, > and I did not change anything else. > > 1. cp.x < h2o_mol1.in? > 2. cp.x < h2o_mol2.in? > 3. cp.x < h2o_mol.cp-dens.in > 4. cppp.x < h2o_mol.cppp-dens.in > > I run the following. The first three are ok. > when I run the fourth commond: cppp.x the error shows that: > > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%% > ???? from? cppp? : error #???????? 1 > ????? IONS not found in data-file.xml > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%% > > ???? stopping ... > STOP 2 > > > > My system is Thinkpad-X200 with Ubuntu 64bit system PC. > > > Thanks very much. > > WANG Riping > 2010.11.19 > -- > *************************************************************************** > *** > 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 > *************************************************************************** > *** > > > > > From lataprem29 at gmail.com Fri Nov 19 10:16:20 2010 From: lataprem29 at gmail.com (premlata pandit) Date: Fri, 19 Nov 2010 14:46:20 +0530 Subject: [Pw_forum] bulk modulus in orthorhombic structure Message-ID: Dear PWSCF users i wants to calculate equilibrium lattice parameter, bulk modulus in orthorhombic structure. i have calculated energies corresponding to different lattice constants, but in ev.x program there is no option for orthorhombic structure. so how to calculate bulk modulus and its pressure derivative in orthorhombic structure? Thanks in advance. -- With Regards and Thanks Premlata Pandit Ph.d. Student Barkatullah University Bhopal 462 026 (M.P) India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101119/394783be/attachment.htm From prayerz.omo at gmail.com Fri Nov 19 12:58:45 2010 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Fri, 19 Nov 2010 12:58:45 +0100 Subject: [Pw_forum] MPI_Bcast error from cp.x In-Reply-To: <4CE5549C.2090207@democritos.it> References: <4CE5549C.2090207@democritos.it> Message-ID: Thank you very much, Paolo. I appreciate this. I will write to the sys admins on CINECA and ask for an upgrade to 4.2. Grazie ancora. o. On Thu, Nov 18, 2010 at 5:30 PM, Paolo Giannozzi wrote: > Omololu Akin-Ojo wrote: > >> The attachment is a test case -- running it on 4 processors produced the >> error. > > it does, but only for version 4.1.3. There is no error on version 4.2 > and later > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > -- ***************** Seek GOD! ************* From Lorenzo.Paulatto at impmc.upmc.fr Fri Nov 19 13:03:49 2010 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 19 Nov 2010 13:03:49 +0100 Subject: [Pw_forum] Error in phonon calculation and during tests also? In-Reply-To: References: Message-ID: On Fri, 19 Nov 2010 05:19:49 +0100, sonu kumar <1009ukumar at gmail.com> wrote: > Additionally: > > i tried with both espresso-4.2.1 and espresso-4.2. but getting > same error with phonon and test calculations. > About one year ago I met a very similar problem with the sun compiler. After a long debugging session I was able to track it to a specific compiler bug: loop counter was not incremented at loop exit (for sufficiently complicated loops). Reducing optimization to 1 for compiling iotk solved the problem. -- 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 Fri Nov 19 13:19:03 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 19 Nov 2010 13:19:03 +0100 Subject: [Pw_forum] cppp.x ---- IONS not found in data-file.xml In-Reply-To: References: Message-ID: <71885007-F454-44B7-AC2E-35664EE2CCBE@democritos.it> On Nov 19, 2010, at 1:56 , Riping WANG wrote: > from cppp : error # 1 > IONS not found in data-file.xml > My system is Thinkpad-X200 with Ubuntu 64bit system PC. you didn't specify the most important thing: code version. Anyway: thanks to Giovanni's remark, I noticed that in recent versions of CPV/fpmdpp.f90, the following line: CALL iotk_scan_begin( dunit, "IONS", FOUND = found ) appears twice (at line number 173 and 175). This is obviously wrong. Remove one of the two lines and recompile Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From faridtaherkhani at gmail.com Fri Nov 19 16:54:39 2010 From: faridtaherkhani at gmail.com (farid taherkhani) Date: Fri, 19 Nov 2010 10:54:39 -0500 Subject: [Pw_forum] charge density in o2 molecule Message-ID: I am calculating charge density for simple case O2 molecule(oxygen), I obtained 2-D contour for charge density of o2 molecule.In post processing of o2 molecule, "o2 charge " file, was created , I do not know what is the content of "o2 charge" file? what are the variables ? As a matter of fact in "o2charge" file there are many numbers by 5 columns any many rows. I want to find the position of maximum charge density in o2 molecule. I do not know how can I do that? ( there is similar problem for post processing in "example 05" in PWSCF and there is charge density for " si charge" file). Any help will be appreciated. Best, Farid -- Farid Taherkhani PhD Student of Physical Chemistry Department of Chemistry Sharif University of Technology Tehran, Iran Tel: +989359464596 http://mehr.sharif.edu/~taherkhani/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101119/0d6f01c7/attachment.htm From giannozz at democritos.it Fri Nov 19 21:55:51 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 19 Nov 2010 21:55:51 +0100 Subject: [Pw_forum] charge density in o2 molecule In-Reply-To: References: Message-ID: <18FD5542-FD0B-425D-9F54-383CE3255741@democritos.it> On Nov 19, 2010, at 16:54 , farid taherkhani wrote: > I do not know what is the content of "o2 charge" file? > what are the variables ? As a matter of fact in "o2charge" > file there are many numbers by 5 columns any many rows. > I want to find the position of maximum charge density in > o2 molecule. I do not know how can I do that? files produced by post-processing codes are not for human consumption. If you want to see where the maximum is, the simplest way is to make a plot three-dimensional plot with XCrySDen or similar software P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From somnath.bhowmick at gmail.com Sat Nov 20 01:19:15 2010 From: somnath.bhowmick at gmail.com (Somnath) Date: Fri, 19 Nov 2010 18:19:15 -0600 Subject: [Pw_forum] Problem running pw4gww.x Message-ID: Hi, I have QE 4.2.1 installed with Intel Version 12.0.0 compilers. I am getting the following error while running GWW_examples: example01 and so on. running the pw4gww calculation at Gamma for C6H6...######################################################################################################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_dat_aux (iotk_dat.spp:664) # CVS Revision: 1.27 # ERROR IN: iotk_scan_dat (iotk_dat.spp:740) # CVS Revision: 1.27 # Error reading data name=z.1 rkind=8 rlen=-1 ######################################################################################################################## application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 The scf part is running fine and the pw4gww part is giving trouble. I am wondering whether it is a bug or there is some problem with my compilation ? thanks in advance. -- -------------------------------------------------- Somnath Bhowmick Room No. 201, Department of Mechanical Engineering & Materials Science. Rice University, 6100 Main Street. Houston, TX 77005-1827, USA. Office: 713 348 8079 Somnath.Bhowmick at rice.edu somnath.bhowmick at gmail.com http://somnath.bhowmick.googlepages.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101119/dfcc91cb/attachment.htm From giannozz at democritos.it Sat Nov 20 11:11:09 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 20 Nov 2010 11:11:09 +0100 Subject: [Pw_forum] Problem running pw4gww.x In-Reply-To: References: Message-ID: <4D08613F-D602-49E7-8614-DEAE55F9EA27@democritos.it> On Nov 20, 2010, at 1:19 , Somnath wrote: > # FROM IOTK LIBRARY, VERSION 1.2.0 > The scf part is running fine and the pw4gww part is giving trouble. > I am wondering whether it is a bug or there is some problem with > my compilation ? third message on the same subject in three days...enough to justify an item in the FAQ (not that anybody will read it). Just added: --- \paragraph{The code stops with a mysterious error in IOTK} IOTK is a toolkit that reads/writes XML files. There are frequent reports of mysterious errors with IOTK not finding some variable in the XML data file. If this error has no obvious explanation (e.g. the file is properly written and read, the searched variable is present, etc) and if it appears to be erratic or irreproducible (e.g. occurs only with version X of compiler Y), it is almost certainly due to a compiler bug. Try to reduce optimization level, or use a different compiler. If you paid real money for your compiler, complain with the vendor. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From 1009ukumar at gmail.com Sat Nov 20 14:22:02 2010 From: 1009ukumar at gmail.com (sonu kumar) Date: Sat, 20 Nov 2010 18:52:02 +0530 Subject: [Pw_forum] (solved) Error in phonon calculation and during tests also? Message-ID: Respected Prof. Paolo Giannozzi, Lorenzo Paulatto, Ali Tavana and all QE users, Thank you very much for your help. Problem is solved with gfortran compiler ( gcc version 4.4.1 ). All the tests and phonon calculations are working fine. >did you pay real money for your compiler? complain with Intel. >If not, try a different compiler (or a different version of the >same compiler) I used latest non-commercial version of intel fortran compiler. Will try to check with other intel compilers. >About one year ago I met a very similar problem with the sun compiler. >After a long debugging session I was able to track it to a specific >compiler bug: loop counter was not incremented at loop exit (for >sufficiently complicated loops). Reducing optimization to 1 for compiling >iotk solved the problem. will try with -O1 flag. 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/20101120/8e6625c7/attachment.htm From tavana.ali at gmail.com Sat Nov 20 14:31:12 2010 From: tavana.ali at gmail.com (Ali Tavana) Date: Sat, 20 Nov 2010 17:01:12 +0330 Subject: [Pw_forum] (solved) Error in phonon calculation and during tests also? In-Reply-To: References: Message-ID: The age of free trustful compilers is finished ;) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101120/31c63542/attachment.htm From sh.shapt at gmail.com Sun Nov 21 21:26:59 2010 From: sh.shapt at gmail.com (Shaptrishi Sharma) Date: Sun, 21 Nov 2010 20:26:59 +0000 Subject: [Pw_forum] valence electron charge density Message-ID: Hi, I would like to know does quantum espresso calculate only the valence electron charge density or it calculate the charge density of all electrons.As plane wave calculates only the valence electron charge density . Regards Shapt. DU, Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101121/4eb9c1a6/attachment.htm From eyvaz_isaev at yahoo.com Mon Nov 22 00:49:22 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 21 Nov 2010 15:49:22 -0800 (PST) Subject: [Pw_forum] valence electron charge density In-Reply-To: References: Message-ID: <758736.85991.qm@web65706.mail.ac4.yahoo.com> Dear Sharma, Congratulations! You have answered your own question. Now just think about, why? 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: Shaptrishi Sharma To: pw_forum at pwscf.org Sent: Sun, November 21, 2010 9:26:59 PM Subject: [Pw_forum] valence electron charge density Hi, I would like to know does quantum espresso calculate only the valence electron charge density or it calculate the charge density of all electrons.As plane wave calculates only the valence electron charge density . Regards Shapt. DU, Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101121/3af64b5e/attachment.htm From dhruv.singh at gmail.com Mon Nov 22 04:08:19 2010 From: dhruv.singh at gmail.com (DHRUV SINGH) Date: Sun, 21 Nov 2010 22:08:19 -0500 Subject: [Pw_forum] Multiple issues with graphene supercell calculations Message-ID: <8EFD229B-2BC3-496B-84D9-17CEDA9F8D19@gmail.com> Dear PWSCF users, I use a hexagonal unit cell with 2 basis atoms and lattice parameter (C-C bond length) of 2.6868 a.u. - this value was arrived at by energy minimization over a range of lattice parameters near this value. With a 16x16x1 kpoint grid it is seen that the energy per atom converges to -11.395192 Ry and the forces on the 2 atoms are zero (atleast until a good precision). The ultrasoft pseudopotential with the RRKJ modification is used for C and the results obtained are in excellent agreement with Marzari and Mounet PRB 71, 205214, 2005. The essentials of the input file and the forces from the 2 atom unit cell are shown below -------------------------------------------------------------------------------- &system ibrav=0, celldm(1)=2.6868, nat=2, ntyp=1, ecutwfc=40.0, ecutrho=480.0, degauss=0.03, nbnd=8 / &electrons mixing_beta = 0.5 conv_thr = 1.0d-8 / ATOMIC_SPECIES C 12.0 C.pbe-rrkjus.UPF CELL_PARAMETERS {hexagonal} 1.5 0.866025404 0.0 1.5 -0.866025404 0.0 0.0 0.0 20 ATOMIC_POSITIONS {crystal} C 0.0000000 0.0000000 0.0000000 C 1/3.0 1/3.0 0.0000000 atom 1 type 1 force = -0.00000000 -0.00000000 0.00000000 atom 2 type 1 force = 0.00000000 0.00000000 0.00000000 -------------------------------------------------------------------------------- Using this lattice parameter I then try to do supercell calculations with rectangular and hexagonal supercells and I am facing the following problems in the supercell scf calculations : i) With a 4 atom rectangular supercell and the same lattice parameter of 2.6868 au, atomic coordinates and input shown below, I find that the energy/atom coverges to -11.395182 Ry(very close to the 2 atom unit cell) for a 8x8x1 k point grid but there seem to be non-negligible net forces on all 4 atoms as shown below, -------------------------------------------------------------------------------- &system ibrav=0, celldm(1)=2.6868, nat=4, ntyp=1, ecutwfc=40.0, ecutrho=480.0, degauss=0.03, nbnd=16 / &electrons mixing_beta = 0.5 conv_thr = 1.0d-8 / CELL_PARAMETERS {cubic} 3.0 0.0 0.0 0.0 1.732050808 0.0 0.0 0.0 14 ATOMIC_POSITIONS {alat} C 0 0 0 C 1 0 0 C 1.5 0.866025404 0 C 2.5 0.866025404 0 -------------------------------------------------------------------------------- atom 1 type 1 force = 0.00310476 0.00000000 0.00000000 atom 2 type 1 force = -0.00310476 0.00000000 0.00000000 atom 3 type 1 force = 0.00310476 0.00000000 0.00000000 atom 4 type 1 force = -0.00310476 0.00000000 0.00000000 ii) With a 48 atom rectangular supercell and 2x2x1 kpoint grid I find energy/atom of -11.395152 Ry (again very close to the 2 atom unit cell) but non negligible forces: Forces on atom 1 are shown below atom 1 type 1 force = 0.00274639 0.00000000 0.00000000 The story is the same as I keep increasing the supercell size ... for 60 atoms the forces on atom 1 are atom 1 type 1 force = -0.00395744 0.00000000 0.00000000 The forces do not change even if I increase ecutwfc to 80.0 and ecutrho to 800.0. They also do not change if I increase the kpoint grid resolution iii) Hexagonal supercells: I get slightly better answers with a hexagonal supercell in terms of forces. For example a 32 atom hexagonal supercell of graphene gives me an energy/atom of 11.395194 Ry for a 4x4x1 kpoint grid. The force on 1 of the atoms is atom 2 type 1 force = 0.00001419 0.00000887 0.00000000 and the magnitude is similar for most other atoms. Once again I find that increasing ecutrho or ecutwfc doesnt matter. However a more serious problem is seen with the hexagonal supercell. I find that scf calculations do not converge for a 72 atom supercell, with the following trend: estimated scf accuracy < 7.42866516 Ry estimated scf accuracy < 2.47702692 Ry estimated scf accuracy < 0.05551173 Ry estimated scf accuracy < 0.02263262 Ry estimated scf accuracy < 0.01534456 Ry estimated scf accuracy < 0.00799064 Ry estimated scf accuracy < 0.00499060 Ry estimated scf accuracy < 0.00272207 Ry estimated scf accuracy < 0.00292201 Ry estimated scf accuracy < 0.00255637 Ry estimated scf accuracy < 0.00240574 Ry estimated scf accuracy < 0.00239154 Ry estimated scf accuracy < 0.00227859 Ry estimated scf accuracy < 0.00214441 Ry estimated scf accuracy < 0.00221359 Ry I also tried changing the parameters ecutrho to 600.0; nband to 400 (from 72*4); decreasing degauss to 0.03 and trying mixing_mode='local-TF' as suggested but that does not help convergence one bit. Please let me know if there is something else I could try which would help with these issues - decreasing the forces on each atom and helping convergence in the hexagonal supercell calculations. Thank you very much Dhruv Singh Graduate Student, Purdue University ME From hqzhou at nju.edu.cn Mon Nov 22 06:34:10 2010 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Mon, 22 Nov 2010 13:34:10 +0800 Subject: [Pw_forum] (solved) Error in phonon calculation and duringtests also? References: Message-ID: <68AB68C3F058417FBB99BE052B7B9D4D@solarflare> It's not nessarilly a problem of Intel compiler. I'm using Intel Compiler 11.1 064 and 072 on two different clusters and no problem occurred in compiling qe-espresso. You can try to clean your build and remove the folder S3DE, then compile again. zhou huiqun @earth sciences, nanjing university, china ----- Original Message ----- From: sonu kumar To: pw_forum at pwscf.org Sent: Saturday, November 20, 2010 9:22 PM Subject: Re: [Pw_forum] (solved) Error in phonon calculation and duringtests also? Respected Prof. Paolo Giannozzi, Lorenzo Paulatto, Ali Tavana and all QE users, Thank you very much for your help. Problem is solved with gfortran compiler ( gcc version 4.4.1 ). All the tests and phonon calculations are working fine. >did you pay real money for your compiler? complain with Intel. >If not, try a different compiler (or a different version of the >same compiler) I used latest non-commercial version of intel fortran compiler. Will try to check with other intel compilers. >About one year ago I met a very similar problem with the sun compiler. >After a long debugging session I was able to track it to a specific >compiler bug: loop counter was not incremented at loop exit (for >sufficiently complicated loops). Reducing optimization to 1 for compiling >iotk solved the problem. will try with -O1 flag. Sonu Kumar Phd Student Physics Department Indian Institute of Technology Delhi-110016, India web:-http://www.iitd.ac.in/ ------------------------------------------------------------------------------ _______________________________________________ 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/20101122/da297059/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Mon Nov 22 10:07:17 2010 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 22 Nov 2010 10:07:17 +0100 Subject: [Pw_forum] valence electron charge density In-Reply-To: References: Message-ID: In data 21 novembre 2010 alle ore 21:26:59, Shaptrishi Sharma ha scritto: > I would like to know does quantum espresso calculate only the valence > electron charge density or it calculate the charge density of all > electrons.As plane wave calculates only the valence electron charge > density. Dear Shaptrishi, because of the pseudopotential formalism, the code knows nothing of the all-electron charge: it is not possible to plot it. However, if you use *only* PAW datasets, you *can* plot the all electron charge using the pawplot.x utility. Keep in mind that the frozen-core approximation is still used, thus I'm not sure it is really useful. 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 Mon Nov 22 12:01:11 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 22 Nov 2010 12:01:11 +0100 Subject: [Pw_forum] Multiple issues with graphene supercell calculations In-Reply-To: <8EFD229B-2BC3-496B-84D9-17CEDA9F8D19@gmail.com> References: <8EFD229B-2BC3-496B-84D9-17CEDA9F8D19@gmail.com> Message-ID: <4015178D-DE6F-4069-B6E1-98E2BEC01C6C@sissa.it> Dear Singh, i) in the hexagonal cell the forces vanish by symmetry, that's why they are perfectly zero. In the rectangular cell this is no more the case. I think the problem arises because you did not specify the celldm(1) parameter with enough significant digits, perhaps, hence the structure does not correspond exactly to the optimal one. Then keep in mind that the cell is rectangular, thus in principle you should use a different number of k-points in the two directions. ii) I do not see the point of moving to larger supercells if you are in trouble with the small one. No reason to try such a high wfc and density cutoff either, in my opinion. iii) In the hexagonal cell the forces look good to me, for practical purposes they are sufficiently small to say that you are at the theoretical energy minimum. The energy is much closer to the one of the primitive cell because the k-point sampling is correct this time. About the 72 atom cell, well, first are you sure about the structure? If so, you need to specify your input file, otherwise if will be difficult to judge. HTH GS Il giorno 22/nov/2010, alle ore 04.08, DHRUV SINGH ha scritto: > Dear PWSCF users, > > I use a hexagonal unit cell with 2 basis atoms and lattice parameter (C-C bond length) of 2.6868 a.u. - this value was arrived at by energy minimization over a range of lattice parameters near this value. With a 16x16x1 kpoint grid it is seen that the energy per atom converges to -11.395192 Ry and the forces on the 2 atoms are zero (atleast until a good precision). The ultrasoft pseudopotential with the RRKJ modification is used for C and the results obtained are in excellent agreement with Marzari and Mounet PRB 71, 205214, 2005. > The essentials of the input file and the forces from the 2 atom unit cell are shown below > -------------------------------------------------------------------------------- > &system > ibrav=0, > celldm(1)=2.6868, > nat=2, > ntyp=1, > ecutwfc=40.0, > ecutrho=480.0, > degauss=0.03, > nbnd=8 > / > &electrons > mixing_beta = 0.5 > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > C 12.0 C.pbe-rrkjus.UPF > > CELL_PARAMETERS {hexagonal} > 1.5 0.866025404 0.0 > 1.5 -0.866025404 0.0 > 0.0 0.0 20 > ATOMIC_POSITIONS {crystal} > C 0.0000000 0.0000000 0.0000000 > C 1/3.0 1/3.0 0.0000000 > > atom 1 type 1 force = -0.00000000 -0.00000000 0.00000000 > atom 2 type 1 force = 0.00000000 0.00000000 0.00000000 > -------------------------------------------------------------------------------- > > Using this lattice parameter I then try to do supercell calculations with rectangular and hexagonal supercells and I am facing the following problems in the supercell scf calculations : > > i) With a 4 atom rectangular supercell and the same lattice parameter of 2.6868 au, atomic coordinates and input shown below, I find that the energy/atom coverges to -11.395182 Ry(very close to the 2 atom unit cell) for a 8x8x1 k point grid but there seem to be non-negligible net forces on all 4 atoms as shown below, > -------------------------------------------------------------------------------- > > &system > ibrav=0, > celldm(1)=2.6868, > nat=4, > ntyp=1, > ecutwfc=40.0, > ecutrho=480.0, > degauss=0.03, > nbnd=16 > / > &electrons > mixing_beta = 0.5 > conv_thr = 1.0d-8 > / > > CELL_PARAMETERS {cubic} > 3.0 0.0 0.0 > 0.0 1.732050808 0.0 > 0.0 0.0 14 > ATOMIC_POSITIONS {alat} > C 0 0 0 > C 1 0 0 > C 1.5 0.866025404 0 > C 2.5 0.866025404 0 > -------------------------------------------------------------------------------- > > atom 1 type 1 force = 0.00310476 0.00000000 0.00000000 > atom 2 type 1 force = -0.00310476 0.00000000 0.00000000 > atom 3 type 1 force = 0.00310476 0.00000000 0.00000000 > atom 4 type 1 force = -0.00310476 0.00000000 0.00000000 > > ii) With a 48 atom rectangular supercell and 2x2x1 kpoint grid I find energy/atom of -11.395152 Ry (again very close to the 2 atom unit cell) but non negligible forces: Forces on atom 1 are shown below > atom 1 type 1 force = 0.00274639 0.00000000 0.00000000 > The story is the same as I keep increasing the supercell size ... for 60 atoms the forces on atom 1 are > atom 1 type 1 force = -0.00395744 0.00000000 0.00000000 > The forces do not change even if I increase ecutwfc to 80.0 and ecutrho to 800.0. They also do not change if I increase the kpoint grid resolution > > iii) Hexagonal supercells: I get slightly better answers with a hexagonal supercell in terms of forces. For example a 32 atom hexagonal supercell of graphene gives me an energy/atom of 11.395194 Ry for a 4x4x1 kpoint grid. The force on 1 of the atoms is > atom 2 type 1 force = 0.00001419 0.00000887 0.00000000 > and the magnitude is similar for most other atoms. Once again I find that increasing ecutrho or ecutwfc doesnt matter. > > However a more serious problem is seen with the hexagonal supercell. I find that scf calculations do not converge for a 72 atom supercell, with the following trend: > > estimated scf accuracy < 7.42866516 Ry > estimated scf accuracy < 2.47702692 Ry > estimated scf accuracy < 0.05551173 Ry > estimated scf accuracy < 0.02263262 Ry > estimated scf accuracy < 0.01534456 Ry > estimated scf accuracy < 0.00799064 Ry > estimated scf accuracy < 0.00499060 Ry > estimated scf accuracy < 0.00272207 Ry > estimated scf accuracy < 0.00292201 Ry > estimated scf accuracy < 0.00255637 Ry > estimated scf accuracy < 0.00240574 Ry > estimated scf accuracy < 0.00239154 Ry > estimated scf accuracy < 0.00227859 Ry > estimated scf accuracy < 0.00214441 Ry > estimated scf accuracy < 0.00221359 Ry > > I also tried changing the parameters ecutrho to 600.0; nband to 400 (from 72*4); decreasing degauss to 0.03 and trying mixing_mode='local-TF' as suggested but that does not help convergence one bit. > > Please let me know if there is something else I could try which would help with these issues - decreasing the forces on each atom and helping convergence in the hexagonal supercell calculations. > > Thank you very much > Dhruv Singh > Graduate Student, Purdue University ME > > _______________________________________________ > 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/20101122/b3f651c8/attachment.htm From mpayami at aeoi.org.ir Mon Nov 22 11:57:55 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 22 Nov 2010 14:27:55 +0330 Subject: [Pw_forum] Problem with constraining an atomic position References: Message-ID: <63129C69C2A14B5D97DD714DCB7B60F6@b> Hi All, I have performed a simple "relax" job for a few-layered Al slab. The input file is similar to that in example03 but with an un(?)important difference that all z-coordinates are positive, starting from z=0.0 for the first layer: Al 0.00000 0.0000000 0.0000000 0 0 0 I have also constrined this z=0 atom to stay at that position during the relaxation. But, at the end all atoms (including the first one) are moved in the positive z direction. How can I handle it? Best regards, Mahmoud Payami, AEOI, Tehran, Iran From mpayami at aeoi.org.ir Mon Nov 22 13:11:31 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 22 Nov 2010 15:41:31 +0330 Subject: [Pw_forum] Problem with constraining an atomic position References: <63129C69C2A14B5D97DD714DCB7B60F6@b> Message-ID: Hi again, To be specific, I include the in and out files: -------------------------------------------- &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/tmp/' , pseudo_dir = './' , prefix = 'al' , forc_conv_thr = 1.d-4 , ! tstress = .true. , ! tprnfor = .true. , / &SYSTEM ibrav = 6, A = 0.28567113959937E+01 , B = 0.28567113959937E+01 , C = 32.3200000000000 , nat = 10, ntyp = 1 , ecutwfc = 70.0 , ecutrho = 200.0 , occupations = 'smearing' , degauss = 0.05 , smearing = 'methfessel-paxton' , / &ELECTRONS electron_maxstep = 200, conv_thr = 1.d-7 , mixing_beta = 0.3 , mixing_ndim = 5, / &IONS bfgs_ndim = 3, / ATOMIC_SPECIES Al 1.0 Al.pz-vbc.UPF ATOMIC_POSITIONS angstrom Al 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 0 0 0 Al 1.42835569799683 1.42835569799683 2.02000000000000 Al 0.000000000000000E+000 0.000000000000000E+000 4.04000000000000 Al 1.42835569799683 1.42835569799683 6.06000000000000 Al 0.000000000000000E+000 0.000000000000000E+000 8.08000000000000 Al 1.42835569799683 1.42835569799683 10.1000000000000 Al 0.000000000000000E+000 0.000000000000000E+000 12.1200000000000 Al 1.42835569799683 1.42835569799683 14.1400000000000 Al 0.000000000000000E+000 0.000000000000000E+000 16.1600000000000 Al 1.42835569799683 1.42835569799683 18.1800000000000 K_POINTS automatic 10 10 1 1 1 1 ------------------------------------- output: convergence has been achieved in 14 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000000 0.00000000 0.00006914 atom 2 type 1 force = 0.00000000 0.00000000 -0.00007622 atom 3 type 1 force = 0.00000000 0.00000000 -0.00000979 atom 4 type 1 force = 0.00000000 0.00000000 0.00000932 atom 5 type 1 force = 0.00000000 0.00000000 0.00004949 atom 6 type 1 force = 0.00000000 0.00000000 -0.00004534 atom 7 type 1 force = 0.00000000 0.00000000 -0.00001505 atom 8 type 1 force = 0.00000000 0.00000000 0.00001078 atom 9 type 1 force = 0.00000000 0.00000000 0.00007297 atom 10 type 1 force = 0.00000000 0.00000000 -0.00006530 Total force = 0.000159 Total SCF correction = 0.000092 SCF correction compared to forces is too large, reduce conv_thr bfgs converged in 16 scf cycles and 13 bfgs steps (criteria: energy < 0.10E-03, force < 0.10E-03) End of BFGS Geometry Optimization Final energy = -41.8150228286 Ry Begin final coordinates ATOMIC_POSITIONS (angstrom) Al 0.000000000 0.000000000 0.355841193 Al 1.428355698 1.428355698 2.318583884 Al 0.000000000 0.000000000 4.250222911 Al 1.428355698 1.428355698 6.193971098 Al 0.000000000 0.000000000 8.120043965 Al 1.428355698 1.428355698 10.059962875 Al 0.000000000 0.000000000 11.986071843 Al 1.428355698 1.428355698 13.929789648 Al 0.000000000 0.000000000 15.861401102 Al 1.428355698 1.428355698 17.824111471 End final coordinates Best regards, mahmoud > Hi All, > > I have performed a simple "relax" job for a few-layered Al slab. The input > file is similar to that in example03 but with an un(?)important difference > that all z-coordinates are positive, starting from z=0.0 for the first > layer: > > Al 0.00000 0.0000000 0.0000000 0 0 0 > > I have also constrined this z=0 atom to stay at that position during the > relaxation. But, at the end all atoms (including the first one) are moved > in > the positive z direction. How can I handle it? > Best regards, > Mahmoud Payami, AEOI, Tehran, Iran > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From neto.baldini at gmail.com Mon Nov 22 13:47:24 2010 From: neto.baldini at gmail.com (Ettore Baldini Neto) Date: Mon, 22 Nov 2010 10:47:24 -0200 Subject: [Pw_forum] Graphene structure Message-ID: Dear QE users, I'm kinda new with quantum espresso. I'm trying to relax a Graphene structure with 32C atoms plus one Ti atom at a given position and the structure do not converge. In what follows I copy the input. Could anyone give-me some hint? Is there anything wrong or that can be improved? I'm using the pp's from the QE data base. I'm planning to generate my own pp's soon. I'm using a k-point grid of 6x6x1 since with SIESTA (dzp basis) the energy and force convergence is achieved without problem. With best regards, ************************************************************ Dr. Ettore Baldini-Neto Wernher von Braun Center for Advanced Research Campinas, Brazil. ************************************************************ &CONTROL title = 'Graphene mono layer' calculation = "relax" , restart_mode = 'from_scratch' , outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' , pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' , etot_conv_thr = 1.0E-4 , forc_conv_thr = 1.0D-3 , nstep=50, dt=40, prefix='1MLG_Ti_H2', / &SYSTEM ibrav = 0., ntyp = 2 , nat = 33 , ecutwfc = 50.0 , ecutrho = 400.0, / &ELECTRONS electron_maxstep = 300., conv_thr = 1.0d-8 , mixing_mode = 'plain', mixing_beta = 0.5, diagonalization = 'cg' , diago_cg_maxiter = 50, / &IONS / CELL_PARAMETERS 16.12131954 9.383047808 0.0000000 0.00000000 18.658162370 0.0000000 0.0000000 0.0000000 56.6893424 ATOMIC_SPECIES C 12.0107 C.pbe-van_ak.UPF Ti 47.8670 Ti.pbe-sp-van_ak.UPF ATOMIC_POSITIONS angstrom C 2.89163 7.40219 1.8862 C 3.59292 8.63832 1.8826 C 3.60349 6.16702 1.8884 C 5.0186 8.64501 1.8612 C 5.0215 6.16598 1.8904 C 5.73302 7.40522 1.8718 C 1.47184 7.39616 1.891 C 2.89112 9.87066 1.886 C 2.89471 4.93264 1.8916 C 5.73319 9.8885 1.8612 C 5.73643 4.9413 1.8924 C 7.16348 7.41203 1.882 C 1.47474 4.9269 1.8924 C 0.762281 8.62783 1.8946 C 0.763134 6.16172 1.8914 C 1.4715 9.86335 1.8934 C 3.60341 11.1095 1.8868 C 5.02124 11.1239 1.882 C 3.60512 3.70156 1.8932 C 5.02645 3.70789 1.891 C 7.87807 8.65532 1.8816 C 7.16373 9.89497 1.872 C 7.16203 4.94814 1.8954 C 7.87619 6.17677 1.8996 C 5.73634 12.3522 1.8872 C 0.772689 3.69102 1.898 C 0.762793 1.22003 1.8968 C 7.87645 11.1337 1.8894 C 7.16203 12.3587 1.889 C 7.87201 13.5922 1.8942 C 2.89479 2.46619 1.8922 C 1.47482 2.45878 1.8952 Ti 6.41604 8.65974 3.74 K_POINTS {automatic} 6.0 6.0 1.0 1.0 1.0 1.0 From sclauzer at sissa.it Mon Nov 22 14:00:19 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 22 Nov 2010 14:00:19 +0100 Subject: [Pw_forum] Graphene structure In-Reply-To: References: Message-ID: <2130FA3A-6611-4AA9-A1BC-8F28BA451212@sissa.it> Ti has an open d shell in valence. Why don't you treat the system as metallic (i.e. use smearing)? Moreover you might need to take into account spin-polarization as well (nspin=2). HTH GS Il giorno 22/nov/2010, alle ore 13.47, Ettore Baldini Neto ha scritto: > Dear QE users, > > I'm kinda new with quantum espresso. I'm trying to relax a Graphene structure with 32C atoms plus one Ti atom at a given position and the structure do not converge. > In what follows I copy the input. Could anyone give-me some hint? Is there anything wrong or that can be improved? I'm using the pp's from the QE data base. I'm planning to generate my own pp's soon. > I'm using a k-point grid of 6x6x1 since with SIESTA (dzp basis) the energy and force convergence is achieved without problem. > > With best regards, > > ************************************************************ > Dr. Ettore Baldini-Neto > Wernher von Braun Center for Advanced Research > Campinas, Brazil. > ************************************************************ > > &CONTROL > title = 'Graphene mono layer' > calculation = "relax" , > restart_mode = 'from_scratch' , > outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' , > pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' , > etot_conv_thr = 1.0E-4 , > forc_conv_thr = 1.0D-3 , > nstep=50, > dt=40, > prefix='1MLG_Ti_H2', > / > &SYSTEM > ibrav = 0., > ntyp = 2 , > nat = 33 , > ecutwfc = 50.0 , > ecutrho = 400.0, > / > &ELECTRONS > electron_maxstep = 300., > conv_thr = 1.0d-8 , > mixing_mode = 'plain', > mixing_beta = 0.5, > diagonalization = 'cg' , > diago_cg_maxiter = 50, > / > &IONS > / > CELL_PARAMETERS > 16.12131954 9.383047808 0.0000000 > 0.00000000 18.658162370 0.0000000 > 0.0000000 0.0000000 56.6893424 > ATOMIC_SPECIES > C 12.0107 C.pbe-van_ak.UPF > Ti 47.8670 Ti.pbe-sp-van_ak.UPF > ATOMIC_POSITIONS angstrom > C 2.89163 7.40219 1.8862 > C 3.59292 8.63832 1.8826 > C 3.60349 6.16702 1.8884 > C 5.0186 8.64501 1.8612 > C 5.0215 6.16598 1.8904 > C 5.73302 7.40522 1.8718 > C 1.47184 7.39616 1.891 > C 2.89112 9.87066 1.886 > C 2.89471 4.93264 1.8916 > C 5.73319 9.8885 1.8612 > C 5.73643 4.9413 1.8924 > C 7.16348 7.41203 1.882 > C 1.47474 4.9269 1.8924 > C 0.762281 8.62783 1.8946 > C 0.763134 6.16172 1.8914 > C 1.4715 9.86335 1.8934 > C 3.60341 11.1095 1.8868 > C 5.02124 11.1239 1.882 > C 3.60512 3.70156 1.8932 > C 5.02645 3.70789 1.891 > C 7.87807 8.65532 1.8816 > C 7.16373 9.89497 1.872 > C 7.16203 4.94814 1.8954 > C 7.87619 6.17677 1.8996 > C 5.73634 12.3522 1.8872 > C 0.772689 3.69102 1.898 > C 0.762793 1.22003 1.8968 > C 7.87645 11.1337 1.8894 > C 7.16203 12.3587 1.889 > C 7.87201 13.5922 1.8942 > C 2.89479 2.46619 1.8922 > C 1.47482 2.45878 1.8952 > Ti 6.41604 8.65974 3.74 > K_POINTS {automatic} > 6.0 6.0 1.0 1.0 1.0 1.0 > > _______________________________________________ > 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/20101122/0425db68/attachment.htm From sclauzer at sissa.it Mon Nov 22 14:23:28 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 22 Nov 2010 14:23:28 +0100 Subject: [Pw_forum] Multiple issues with graphene supercell calculations In-Reply-To: <4015178D-DE6F-4069-B6E1-98E2BEC01C6C@sissa.it> References: <8EFD229B-2BC3-496B-84D9-17CEDA9F8D19@gmail.com> <4015178D-DE6F-4069-B6E1-98E2BEC01C6C@sissa.it> Message-ID: <4CEA6ED0.70108@sissa.it> On 11/22/2010 12:01 PM, Gabriele Sclauzero wrote: > Dear Singh, > > i) in the hexagonal cell the forces vanish by symmetry, that's why > they are perfectly zero. In the rectangular cell this is no more the > case. I think the problem arises because you did not specify the > celldm(1) parameter with enough significant digits, perhaps, hence the > structure does not correspond exactly to the optimal one. > Then keep in mind that the cell is rectangular, thus in principle > you should use a different number of k-points in the two directions. > > Indeed I found that if you use a 15x9x1 k-point grid, which is roughly equivalent to the 16x16x1 in the hexagonal cell, the forces are Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00037456 0.00000000 0.00000000 atom 2 type 1 force = -0.00037456 0.00000000 0.00000000 atom 3 type 1 force = 0.00037456 0.00000000 0.00000000 atom 4 type 1 force = -0.00037456 0.00000000 0.00000000 that is to say 10 times smaller than what you cited. Hence, if you want more precision you probably need to use better k-point sampling and C-C distances. GS -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne From giannozz at democritos.it Mon Nov 22 14:26:50 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 22 Nov 2010 14:26:50 +0100 Subject: [Pw_forum] Multiple issues with graphene supercell calculations In-Reply-To: <4CEA6ED0.70108@sissa.it> References: <8EFD229B-2BC3-496B-84D9-17CEDA9F8D19@gmail.com> <4015178D-DE6F-4069-B6E1-98E2BEC01C6C@sissa.it> <4CEA6ED0.70108@sissa.it> Message-ID: <5CB088BC-4C5F-4E82-8FF4-33FC25225170@democritos.it> On Nov 22, 2010, at 14:23 , Gabriele Sclauzero wrote: > Hence, if you want more precision you probably need to use > better k-point sampling and C-C distances. and better (i.e. smaller) self-consistenty convergence thresholds. The error on the energy is a quadratic function of the error on the charge density due to imperfect self-consistency; the error on forces is instead linear. P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mpayami at aeoi.org.ir Mon Nov 22 14:44:39 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 22 Nov 2010 17:14:39 +0330 Subject: [Pw_forum] Problem with constraining an atomic position References: <63129C69C2A14B5D97DD714DCB7B60F6@b> Message-ID: <86BDADDC488142BFB817B8709A7BBBD3@b> Now it is ok. I just rewrote the position of the first atom and deleted extra spaces between the parameter values. Bests, m. > Hi again, > To be specific, I include the in and out files: > -------------------------------------------- > &CONTROL > calculation = 'relax' , > restart_mode = 'from_scratch' , > outdir = '/tmp/' , > pseudo_dir = './' , > prefix = 'al' , > forc_conv_thr = 1.d-4 , > ! tstress = .true. , > ! tprnfor = .true. , > / > &SYSTEM > ibrav = 6, > A = 0.28567113959937E+01 , > B = 0.28567113959937E+01 , > C = 32.3200000000000 , > nat = 10, > ntyp = 1 , > ecutwfc = 70.0 , > ecutrho = 200.0 , > occupations = 'smearing' , > degauss = 0.05 , > smearing = 'methfessel-paxton' , > / > &ELECTRONS > electron_maxstep = 200, > conv_thr = 1.d-7 , > mixing_beta = 0.3 , > mixing_ndim = 5, > / > &IONS > bfgs_ndim = 3, > / > ATOMIC_SPECIES > Al 1.0 Al.pz-vbc.UPF > ATOMIC_POSITIONS angstrom > Al 0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000 > 0 0 0 > Al 1.42835569799683 1.42835569799683 2.02000000000000 > Al 0.000000000000000E+000 0.000000000000000E+000 4.04000000000000 > Al 1.42835569799683 1.42835569799683 6.06000000000000 > Al 0.000000000000000E+000 0.000000000000000E+000 8.08000000000000 > Al 1.42835569799683 1.42835569799683 10.1000000000000 > Al 0.000000000000000E+000 0.000000000000000E+000 12.1200000000000 > Al 1.42835569799683 1.42835569799683 14.1400000000000 > Al 0.000000000000000E+000 0.000000000000000E+000 16.1600000000000 > Al 1.42835569799683 1.42835569799683 18.1800000000000 > K_POINTS automatic > 10 10 1 1 1 1 > ------------------------------------- > > output: > > convergence has been achieved in 14 iterations > > Forces acting on atoms (Ry/au): > > atom 1 type 1 force = 0.00000000 0.00000000 0.00006914 > atom 2 type 1 force = 0.00000000 0.00000000 -0.00007622 > atom 3 type 1 force = 0.00000000 0.00000000 -0.00000979 > atom 4 type 1 force = 0.00000000 0.00000000 0.00000932 > atom 5 type 1 force = 0.00000000 0.00000000 0.00004949 > atom 6 type 1 force = 0.00000000 0.00000000 -0.00004534 > atom 7 type 1 force = 0.00000000 0.00000000 -0.00001505 > atom 8 type 1 force = 0.00000000 0.00000000 0.00001078 > atom 9 type 1 force = 0.00000000 0.00000000 0.00007297 > atom 10 type 1 force = 0.00000000 0.00000000 -0.00006530 > > Total force = 0.000159 Total SCF correction = 0.000092 > SCF correction compared to forces is too large, reduce conv_thr > > bfgs converged in 16 scf cycles and 13 bfgs steps > (criteria: energy < 0.10E-03, force < 0.10E-03) > > End of BFGS Geometry Optimization > > Final energy = -41.8150228286 Ry > Begin final coordinates > > ATOMIC_POSITIONS (angstrom) > Al 0.000000000 0.000000000 0.355841193 > Al 1.428355698 1.428355698 2.318583884 > Al 0.000000000 0.000000000 4.250222911 > Al 1.428355698 1.428355698 6.193971098 > Al 0.000000000 0.000000000 8.120043965 > Al 1.428355698 1.428355698 10.059962875 > Al 0.000000000 0.000000000 11.986071843 > Al 1.428355698 1.428355698 13.929789648 > Al 0.000000000 0.000000000 15.861401102 > Al 1.428355698 1.428355698 17.824111471 > End final coordinates > > > > Best regards, > mahmoud > > > > >> Hi All, >> >> I have performed a simple "relax" job for a few-layered Al slab. The >> input >> file is similar to that in example03 but with an un(?)important >> difference >> that all z-coordinates are positive, starting from z=0.0 for the first >> layer: >> >> Al 0.00000 0.0000000 0.0000000 0 0 0 >> >> I have also constrined this z=0 atom to stay at that position during the >> relaxation. But, at the end all atoms (including the first one) are moved >> in >> the positive z direction. How can I handle it? >> Best regards, >> Mahmoud Payami, AEOI, Tehran, Iran >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at democritos.it Mon Nov 22 14:54:13 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 22 Nov 2010 14:54:13 +0100 Subject: [Pw_forum] Problem with constraining an atomic position In-Reply-To: References: <63129C69C2A14B5D97DD714DCB7B60F6@b> Message-ID: <7684131E-D29F-491F-A1EF-DEB132D95207@democritos.it> On Nov 22, 2010, at 13:11 , Mahmoud Payami wrote: > ecutwfc = 70.0 , > ecutrho = 200.0 not a great idea: ecutrho should be 4*ecutwfc. By the way, 70Ry for Al is a VERY big cutoff P. --- Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From mpayami at aeoi.org.ir Mon Nov 22 15:13:08 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 22 Nov 2010 17:43:08 +0330 Subject: [Pw_forum] Problem with constraining an atomic position References: <63129C69C2A14B5D97DD714DCB7B60F6@b> <7684131E-D29F-491F-A1EF-DEB132D95207@democritos.it> Message-ID: <23C916D8B3584506A60A50397AFE312D@b> Dear Paolo, Thank you very much for reminding this point. For accuracy of some 3 decimals I checked, 40.0 is sufficient for ecutwf. Bests, m. > > On Nov 22, 2010, at 13:11 , Mahmoud Payami wrote: > >> ecutwfc = 70.0 , >> ecutrho = 200.0 > > not a great idea: ecutrho should be 4*ecutwfc. > By the way, 70Ry for Al is a VERY big cutoff > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, 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 hande at newton.physics.metu.edu.tr Mon Nov 22 14:23:57 2010 From: hande at newton.physics.metu.edu.tr (Hande Ustunel) Date: Mon, 22 Nov 2010 15:23:57 +0200 (EET) Subject: [Pw_forum] Graphene structure In-Reply-To: Message-ID: Dear Ettore, As with any structure including metals, you would need some sort of smearing. Try something like occupations='smearing' smearing='mv' degauss=0.01 in the &system portion of your input. You must however be informed about the usage of smearing since the number of k-points that will be sufficient for convergence will be degauss-dependent. I would read the papers refered to in the Doc/INPUT_PW.txt. As a rule of thumb soemthing like 0.01 or 0.02 are good smearing widths. Incidentally, our vacuum is a tad too large. This will ill-condition your problem (and consequently mess up your convergence) as well as increase the run-time. I would decrease it to something like 15 A. If these fail (which I doubt they will in your case) you can try one of the following remedies which sometimes work : 1) Increase number of kpoints. 2) Change the location of Ti slightly. 3) Change pseudo (if you can) 4) Change mixing mode and mixing beta. Hope this helps, Hande On Mon, 22 Nov 2010, Ettore Baldini Neto wrote: > Dear QE users, > > I'm kinda new with quantum espresso. I'm trying to relax a Graphene structure with 32C atoms plus one Ti atom at a given position and the structure do not converge. > In what follows I copy the input. Could anyone give-me some hint? Is there anything wrong or that can be improved? I'm using the pp's from the QE data base. I'm planning to generate my own pp's soon. > I'm using a k-point grid of 6x6x1 since with SIESTA (dzp basis) the energy and force convergence is achieved without problem. > > With best regards, > > ************************************************************ > Dr. Ettore Baldini-Neto > Wernher von Braun Center for Advanced Research > Campinas, Brazil. > ************************************************************ -- Hande Toffoli Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande From neto.baldini at gmail.com Mon Nov 22 17:01:56 2010 From: neto.baldini at gmail.com (Ettore Baldini Neto) Date: Mon, 22 Nov 2010 14:01:56 -0200 Subject: [Pw_forum] Graphene structure In-Reply-To: References: Message-ID: Thanks a lot Hande and Gabriele, best regards, Ettore On Nov 22, 2010, at 11:23 AM, Hande Ustunel wrote: > Dear Ettore, > > As with any structure including metals, you would need some sort of > smearing. > > Try something like > > occupations='smearing' > smearing='mv' > degauss=0.01 > > in the &system portion of your input. You must however be informed about > the usage of smearing since the number of k-points that will be sufficient > for convergence will be degauss-dependent. I would read the papers refered > to in the Doc/INPUT_PW.txt. As a rule of thumb soemthing like 0.01 or 0.02 > are good smearing widths. > > Incidentally, our vacuum is a tad too large. This will ill-condition your > problem (and consequently mess up your convergence) as well as increase the > run-time. I would decrease it to something like 15 A. > > If these fail (which I doubt they will in your case) you can try one of the > following remedies which sometimes work : > > 1) Increase number of kpoints. > 2) Change the location of Ti slightly. > 3) Change pseudo (if you can) > 4) Change mixing mode and mixing beta. > > Hope this helps, > Hande > > > On Mon, 22 Nov 2010, Ettore Baldini Neto wrote: > >> Dear QE users, >> >> I'm kinda new with quantum espresso. I'm trying to relax a Graphene structure with 32C atoms plus one Ti atom at a given position and the structure do not converge. >> In what follows I copy the input. Could anyone give-me some hint? Is there anything wrong or that can be improved? I'm using the pp's from the QE data base. I'm planning to generate my own pp's soon. >> I'm using a k-point grid of 6x6x1 since with SIESTA (dzp basis) the energy and force convergence is achieved without problem. >> >> With best regards, >> >> ************************************************************ >> Dr. Ettore Baldini-Neto >> Wernher von Braun Center for Advanced Research >> Campinas, Brazil. >> ************************************************************ > > -- > Hande Toffoli > Department of Physics > Office 439 > Middle East Technical University > Ankara 06531, Turkey > Tel : +90 312 210 3264 > http://www.physics.metu.edu.tr/~hande > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From dhruv.singh at gmail.com Mon Nov 22 19:18:23 2010 From: dhruv.singh at gmail.com (Dhruv Singh) Date: Mon, 22 Nov 2010 13:18:23 -0500 Subject: [Pw_forum] Multiple issues with graphene supercell calculations In-Reply-To: <5CB088BC-4C5F-4E82-8FF4-33FC25225170@democritos.it> References: <8EFD229B-2BC3-496B-84D9-17CEDA9F8D19@gmail.com> <4015178D-DE6F-4069-B6E1-98E2BEC01C6C@sissa.it> <4CEA6ED0.70108@sissa.it> <5CB088BC-4C5F-4E82-8FF4-33FC25225170@democritos.it> Message-ID: Thanks very much for the help regarding this topic.... I guess the hexagonal supercell is a better choice then and I will need to use a finer k point grid with tighter scf convergence criterion for better accuracy in forces. As an advice though, would you suggest that for subsequent force constant calculations - forces of the order of 1.0e-5 would not lead to unstable modes ? (I am using a supercell to calculate force constants rather than the ph.x codes because I later need to calculate third derivatives) As regards the 72 atom supercell scf calculations not converging, the corresponding input file is attached here. I increased the scf convergence threshold to 1.0e-3 in order to terminate the computation earlier (to check the results). I am attaching two output files-one with threshold 1.0e-8 and the other with 1.0e-3. Both of them use a 72 atom supercell and a 2x2x1 kpoint grid. Please let me know if you think tweaking a few parameters could help convergence. Thanks very much Dhruv On Mon, Nov 22, 2010 at 8:26 AM, Paolo Giannozzi wrote: > > On Nov 22, 2010, at 14:23 , Gabriele Sclauzero wrote: > >> Hence, if you want more precision you probably need to use >> better k-point sampling and C-C distances. > > and better (i.e. smaller) self-consistenty convergence thresholds. > The error on the energy is a quadratic function of the error on the > charge density due to imperfect self-consistency; the error on forces > is instead linear. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, 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 > -- Dhruv -------------- next part -------------- A non-text attachment was scrubbed... Name: gra.scf.in Type: application/octet-stream Size: 4820 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101122/c154e516/attachment-0003.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: gra2by2_thr1.0e-3.scf.out Type: application/octet-stream Size: 32857 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101122/c154e516/attachment-0004.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: gra2by2_thr1e-8.scf.out Type: application/octet-stream Size: 28263 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101122/c154e516/attachment-0005.obj From dhruv.singh at gmail.com Mon Nov 22 19:23:25 2010 From: dhruv.singh at gmail.com (Dhruv Singh) Date: Mon, 22 Nov 2010 13:23:25 -0500 Subject: [Pw_forum] Multiple issues with graphene supercell calculations In-Reply-To: References: <8EFD229B-2BC3-496B-84D9-17CEDA9F8D19@gmail.com> <4015178D-DE6F-4069-B6E1-98E2BEC01C6C@sissa.it> <4CEA6ED0.70108@sissa.it> <5CB088BC-4C5F-4E82-8FF4-33FC25225170@democritos.it> Message-ID: And as expected, the termination threshold of 1.0e-3 gives a rather lousy answer for forces and energy/atom of -11.39486969 Ry significantly different from the correct value of ~ -11.395192 Ry. I believe a finer kpoint grid should resolve the convergence issue to a certain extent (correct me if I am wrong) - but I am trying to understand if a well converged asnwer can be obtained even on a 2x2x1 kpoint grid. Thanks, Dhruv On Mon, Nov 22, 2010 at 1:18 PM, Dhruv Singh wrote: > Thanks very much for the help regarding this topic.... I guess the > hexagonal supercell is a better choice then and I will need ?to use a > finer k point grid with tighter scf convergence criterion for better > accuracy in forces. As an advice though, would you suggest that for > subsequent force constant calculations - forces of the order of 1.0e-5 > would not lead to unstable modes ? (I am using a supercell to > calculate force constants rather than the ph.x codes because I later > need to calculate third derivatives) > > As regards the 72 atom supercell scf calculations not converging, the > corresponding input file is attached here. I increased the scf > convergence threshold to 1.0e-3 in order to terminate the computation > earlier (to check the results). I am attaching two output files-one > with threshold 1.0e-8 and the other with 1.0e-3. Both of them use a 72 > atom supercell and a 2x2x1 kpoint grid. Please let me know if you > think tweaking a few parameters could help convergence. > > Thanks very much > > Dhruv > > On Mon, Nov 22, 2010 at 8:26 AM, Paolo Giannozzi wrote: >> >> On Nov 22, 2010, at 14:23 , Gabriele Sclauzero wrote: >> >>> Hence, if you want more precision you probably need to use >>> better k-point sampling and C-C distances. >> >> and better (i.e. smaller) self-consistenty convergence thresholds. >> The error on the energy is a quadratic function of the error on the >> charge density due to imperfect self-consistency; the error on forces >> is instead linear. >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics, 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 >> > > > > -- > Dhruv > -- Dhruv From wumindt2 at zju.edu.cn Mon Nov 22 22:31:48 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Tue, 23 Nov 2010 05:31:48 +0800 Subject: [Pw_forum] wannier function Message-ID: Dearl All, To incorporate wannier90 into PWSCF-4.2.1, do we need to copy pw2wannier90.f90 and wannier.f90 from wannier90 to PWSCF directory, and recompile the PWSCF, or just compile PWSCF and wannier90 individually? Thanks for any help. With Best regards, Min Wu 2010-11-22 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101123/966e7635/attachment.htm From wangweiphysics at yahoo.com.cn Tue Nov 23 03:49:48 2010 From: wangweiphysics at yahoo.com.cn (wangwei) Date: Tue, 23 Nov 2010 10:49:48 +0800 (CST) Subject: [Pw_forum] a2F.dos.1 Message-ID: <675148.23595.qm@web15207.mail.cnb.yahoo.com> Dear sir, I am calculating?phonon properties, the file a2F.dos.1 as follows: ? Eliashberg function a2F (per both spin) ?? frequencies in Rydberg ? DOS normalized to E in Rydberg: a2F_total, a2F(mode) ?????? 0.000061???? -0.00000891???? -0.00000529???? -0.00000367????? 0.00000005????? 0.00000000????? 0.00000000 ?????? 0.000000????? 0.00000000????? 0.00000000????? 0.00000000????? 0.00000000????? 0.00000000????? 0.00000000 ?????? 0.000000????? 0.00000000????? 0.00000000 ?????? 0.000183???? -0.00024046???? -0.00014282???? -0.00009910????? 0.00000146????? 0.00000000????? 0.00000000 ?????? 0.000000????? 0.00000000????? 0.00000000????? 0.00000000????? 0.00000000????? 0.00000000????? 0.00000000 ?????? 0.000000????? 0.00000000????? 0.00000000 ?????? 0.000305???? -0.00120382???? -0.00075069???? -0.00045991????? 0.00000678????? 0.00000000????? 0.00000000 ???? ............................? As we can read from header lines, the first column is frequency, the second column is a2F_total, but I do not understand what the last four columns stand for? Thanks for any reply! Best wishes! wangwei Huaibei Normal University From Michael at ihpc.a-star.edu.sg Tue Nov 23 07:28:58 2010 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Tue, 23 Nov 2010 14:28:58 +0800 Subject: [Pw_forum] QM/MM and/or external charges in QE In-Reply-To: References: Message-ID: <235887FC8686C543B24F9DF2A01CBE04030195B5@S3-EXCHMB03.shared-svc.local> PWSCFers: My colleague has this question/problem: ------------------------------------------------------------------------------------------------ We have a cluster of atoms (not necessarily periodical). One (small) region of this cluster must be treated by Quantum Mechanics, the rest can be treated semiclassically or classically. As in QM/MM, the semiclassical/classical calculation is performed first and the result is a spatial charge distribution. For the QM calculation, we need to do DFT considering the influence of the semiclassical/classical charge distribution. Would Quantum Espresso be able to handle DFT in the external electrostatic field created by the above-mentioned charge distribution? If the answer is yes, how do we technically do it? ------------------------------------------------------------------------------------------------ The related question that I have is this: Is there any way to introduce point charges into the DFT? This makes for a simple QM/MM method. Do we need to work out the electric field itself and input that in using something like tefield or lefield? Also, is there any work being done on interfacing QE with some MM package like what CPMD does with GROMACS (in what seems to be a rather clunky way)? Thanks for your help, Mike Sullivan michael at ihpc.a-star.edu.sg http://www.ihpc.a-star.edu.sg/ IHPC Values :: Impact :: Honesty :: Performance :: Co-operation This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From eyvaz_isaev at yahoo.com Tue Nov 23 09:52:26 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 23 Nov 2010 00:52:26 -0800 (PST) Subject: [Pw_forum] a2F.dos.1 In-Reply-To: <675148.23595.qm@web15207.mail.cnb.yahoo.com> References: <675148.23595.qm@web15207.mail.cnb.yahoo.com> Message-ID: <852382.8875.qm@web65701.mail.ac4.yahoo.com> Hi, Yes, the first column is energy, the second one is total a2F.dos, and last 15 columns stand for mode-projected a2F.dos for each mode. I suppose you have 5 atoms in your unit cell. 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: wangwei To: pw_forum at pwscf.org Sent: Tue, November 23, 2010 3:49:48 AM Subject: [Pw_forum] a2F.dos.1 Dear sir, I am calculating phonon properties, the file a2F.dos.1 as follows: Eliashberg function a2F (per both spin) frequencies in Rydberg DOS normalized to E in Rydberg: a2F_total, a2F(mode) 0.000061 -0.00000891 -0.00000529 -0.00000367 0.00000005 0.00000000 0.00000000 0.000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000000 0.00000000 0.00000000 0.000183 -0.00024046 -0.00014282 -0.00009910 0.00000146 0.00000000 0.00000000 0.000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.000000 0.00000000 0.00000000 0.000305 -0.00120382 -0.00075069 -0.00045991 0.00000678 0.00000000 0.00000000 ............................ As we can read from header lines, the first column is frequency, the second column is a2F_total, but I do not understand what the last four columns stand for? Thanks for any reply! Best wishes! wangwei Huaibei Normal University _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From janfelix.binder at epfl.ch Tue Nov 23 09:54:03 2010 From: janfelix.binder at epfl.ch (Jan Felix Binder) Date: Tue, 23 Nov 2010 09:54:03 +0100 Subject: [Pw_forum] wannier function In-Reply-To: References: Message-ID: <4CEB812B.2080806@epfl.ch> You should compile it individually. But you should use the same compiler. wumindt2 wrote: > Dearl All, > > To incorporate wannier90 into PWSCF-4.2.1, do we need to copy > pw2wannier90.f90 and wannier.f90 > from wannier90 to PWSCF directory, and recompile the PWSCF, or just > compile PWSCF and wannier90 individually? > > Thanks for any help. > > With Best regards, > > Min Wu > 2010-11-22 > ------------------------------------------------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From sclauzer at sissa.it Tue Nov 23 09:56:07 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 23 Nov 2010 09:56:07 +0100 Subject: [Pw_forum] Multiple issues with graphene supercell calculations In-Reply-To: References: <8EFD229B-2BC3-496B-84D9-17CEDA9F8D19@gmail.com> <4015178D-DE6F-4069-B6E1-98E2BEC01C6C@sissa.it> <4CEA6ED0.70108@sissa.it> <5CB088BC-4C5F-4E82-8FF4-33FC25225170@democritos.it> Message-ID: Il giorno 22/nov/2010, alle ore 19.18, Dhruv Singh ha scritto: > Thanks very much for the help regarding this topic.... I guess the > hexagonal supercell is a better choice then and I will need to use a If there's no specific reason for using a lower symmetry cell (as the tetragonal one you've been using previously), I think so. > finer k point grid with tighter scf convergence criterion for better > accuracy in forces. As an advice though, would you suggest that for > subsequent force constant calculations - forces of the order of 1.0e-5 That's a very tight threshold! i.e. 2 orders of magnitudes smaller than the default one... > would not lead to unstable modes ? (I am using a supercell to > calculate force constants rather than the ph.x codes because I later > need to calculate third derivatives) > > As regards the 72 atom supercell scf calculations not converging, the > corresponding input file is attached here. I increased the scf > convergence threshold to 1.0e-3 in order to terminate the computation > earlier (to check the results). I am attaching two output files-one > with threshold 1.0e-8 and the other with 1.0e-3. Both of them use a 72 > atom supercell and a 2x2x1 kpoint grid. Please let me know if you > think tweaking a few parameters could help convergence. Graphene has zero bandgap, hence you might need to include a broadening of the electronic occupations (i.e. you need to specify also occupations and smearing keywords, degauss is not sufficient). HTH GS > > Thanks very much > > Dhruv > > On Mon, Nov 22, 2010 at 8:26 AM, Paolo Giannozzi wrote: >> >> On Nov 22, 2010, at 14:23 , Gabriele Sclauzero wrote: >> >>> Hence, if you want more precision you probably need to use >>> better k-point sampling and C-C distances. >> >> and better (i.e. smaller) self-consistenty convergence thresholds. >> The error on the energy is a quadratic function of the error on the >> charge density due to imperfect self-consistency; the error on forces >> is instead linear. >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics, 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 >> > > > > -- > Dhruv > _______________________________________________ > 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/20101123/0a4f5241/attachment.htm From sclauzer at sissa.it Tue Nov 23 10:02:18 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 23 Nov 2010 10:02:18 +0100 Subject: [Pw_forum] Multiple issues with graphene supercell calculations In-Reply-To: References: <8EFD229B-2BC3-496B-84D9-17CEDA9F8D19@gmail.com> <4015178D-DE6F-4069-B6E1-98E2BEC01C6C@sissa.it> <4CEA6ED0.70108@sissa.it> <5CB088BC-4C5F-4E82-8FF4-33FC25225170@democritos.it> Message-ID: <2115A450-C80E-4B33-9629-47C018CAFE29@sissa.it> Il giorno 22/nov/2010, alle ore 19.23, Dhruv Singh ha scritto: > And as expected, the termination threshold of 1.0e-3 gives a rather > lousy answer for forces and energy/atom of -11.39486969 Ry > significantly different from the correct value of ~ -11.395192 Ry. I I wouldn't say "lousy"... you got what you asked for, that is to a say an accuracy of 1e-3 Ry on the total energy. > believe a finer kpoint grid should resolve the convergence issue to a > certain extent (correct me if I am wrong) - but I am trying to > understand if a well converged asnwer can be obtained even on a 2x2x1 > kpoint grid. if you use a n x n supercell, you should get the same accuracy of the primitive unit cell by reducing the k-point mesh accordingly (e.g. k_x/n k_y/n) GS > > Thanks, > Dhruv > > On Mon, Nov 22, 2010 at 1:18 PM, Dhruv Singh wrote: >> Thanks very much for the help regarding this topic.... I guess the >> hexagonal supercell is a better choice then and I will need to use a >> finer k point grid with tighter scf convergence criterion for better >> accuracy in forces. As an advice though, would you suggest that for >> subsequent force constant calculations - forces of the order of 1.0e-5 >> would not lead to unstable modes ? (I am using a supercell to >> calculate force constants rather than the ph.x codes because I later >> need to calculate third derivatives) >> >> As regards the 72 atom supercell scf calculations not converging, the >> corresponding input file is attached here. I increased the scf >> convergence threshold to 1.0e-3 in order to terminate the computation >> earlier (to check the results). I am attaching two output files-one >> with threshold 1.0e-8 and the other with 1.0e-3. Both of them use a 72 >> atom supercell and a 2x2x1 kpoint grid. Please let me know if you >> think tweaking a few parameters could help convergence. >> >> Thanks very much >> >> Dhruv >> >> On Mon, Nov 22, 2010 at 8:26 AM, Paolo Giannozzi wrote: >>> >>> On Nov 22, 2010, at 14:23 , Gabriele Sclauzero wrote: >>> >>>> Hence, if you want more precision you probably need to use >>>> better k-point sampling and C-C distances. >>> >>> and better (i.e. smaller) self-consistenty convergence thresholds. >>> The error on the energy is a quadratic function of the error on the >>> charge density due to imperfect self-consistency; the error on forces >>> is instead linear. >>> >>> P. >>> --- >>> Paolo Giannozzi, Dept of Chemistry&Physics, 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 >>> >> >> >> >> -- >> Dhruv >> > > > > -- > Dhruv > _______________________________________________ > 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/20101123/ac4d8b2d/attachment.htm From giannozz at democritos.it Tue Nov 23 17:03:43 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 23 Nov 2010 17:03:43 +0100 Subject: [Pw_forum] Problem with constraining an atomic position In-Reply-To: <63129C69C2A14B5D97DD714DCB7B60F6@b> References: <63129C69C2A14B5D97DD714DCB7B60F6@b> Message-ID: <4CEBE5DF.1070402@democritos.it> Mahmoud Payami wrote: > I have also constrined this z=0 atom to stay at that position during the > relaxation. But, at the end all atoms (including the first one) are moved I cannot reproduce this behavior. Which code version are you using? P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From marsamos at democritos.it Tue Nov 23 17:06:21 2010 From: marsamos at democritos.it (marsamos at democritos.it) Date: Tue, 23 Nov 2010 17:06:21 +0100 Subject: [Pw_forum] QM/MM and/or external charges in QE In-Reply-To: <235887FC8686C543B24F9DF2A01CBE04030195B5@S3-EXCHMB03.shared-svc.local> References: <235887FC8686C543B24F9DF2A01CBE04030195B5@S3-EXCHMB03.shared-svc.local> Message-ID: <20101123170621.s9ws1u776swcgs8w@mail.democritos.it> Dear Sullivan, at the moment there is a test version interfaced with Lammps. You should contact Riccardo Dimeo (dimeo at democritos.it), developer of the MS2 package (see at www.qe-forge.org) and piccinin at sissa.it, which is adding the electrostatic coupling for having more information. bests Layla Quoting Michael Sullivan : > PWSCFers: > > My colleague has this question/problem: > > ------------------------------------------------------------------------------------------------ > We have a cluster of atoms (not necessarily periodical). One (small) > region of this cluster must be treated by Quantum Mechanics, the rest > can be treated semiclassically or classically. As in QM/MM, the > semiclassical/classical calculation is performed first and the result > is a spatial charge distribution. For the QM calculation, we need to > do DFT considering the influence of the semiclassical/classical > charge distribution. > > Would Quantum Espresso be able to handle DFT in the external > electrostatic field created by the above-mentioned charge > distribution? If the answer is yes, how do we technically do it? > ------------------------------------------------------------------------------------------------ > > The related question that I have is this: Is there any way to > introduce point charges into the DFT? This makes for a simple QM/MM > method. Do we need to work out the electric field itself and input > that in using something like tefield or lefield? > > Also, is there any work being done on interfacing QE with some MM > package like what CPMD does with GROMACS (in what seems to be a > rather clunky way)? > > Thanks for your help, > > Mike Sullivan > michael at ihpc.a-star.edu.sg > http://www.ihpc.a-star.edu.sg/ > > > IHPC Values :: Impact :: Honesty :: Performance :: Co-operation > This email is confidential and may be privileged. If you are not the > intended recipient, please delete it and notify us immediately. > Please do not copy or use it for any purpose, or disclose its > contents to any other person. Thank you. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. L. Martin-Samos tel. +39 040 3787 429 CNR-DEMOCRITOS and International School for Advanced Studies (ISAS-SISSA) via Beirut 2-4 34151 Trieste Italy ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From wumindt2 at zju.edu.cn Tue Nov 23 17:13:31 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Wed, 24 Nov 2010 00:13:31 +0800 Subject: [Pw_forum] wannier function Message-ID: Thanks. BTW, can wannier90.x run with MPI support? And can it plot the wannier function of supercell structure with a defect? Cheers, Min Wu 2010-11-22 >From: Jan Felix Binder >Reply-To: >To: wumindt2 , PWSCF Forum >Subject: Re: [Pw_forum] wannier function >Date: Tue, 23 Nov 2010 09:54:03 +0100 > >You should compile it individually. But you should use the same compiler. > > > >wumindt2 wrote: >> Dearl All, >> >> To incorporate wannier90 into PWSCF-4.2.1, do we need to copy >> pw2wannier90.f90 and wannier.f90 >> from wannier90 to PWSCF directory, and recompile the PWSCF, or just >> compile PWSCF and wannier90 individually? >> >> Thanks for any help. >> >> With Best regards, >> >> Min Wu >> 2010-11-22 >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > From lanhaiping at gmail.com Tue Nov 23 18:27:20 2010 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 23 Nov 2010 12:27:20 -0500 Subject: [Pw_forum] wannier function In-Reply-To: References: Message-ID: no, w90 can only run in serial mode. yes, you can plot wannier function no matter it is insulator or metal. but you should have a read over the definition of mlwfs for metals. On Tue, Nov 23, 2010 at 11:13 AM, wumindt2 wrote: > Thanks. > BTW, can wannier90.x run with MPI support? And can it plot the wannier > function > of supercell structure with a defect? > > Cheers, > > Min Wu > 2010-11-22 > > >From: Jan Felix Binder > >Reply-To: > >To: wumindt2 , PWSCF Forum > >Subject: Re: [Pw_forum] wannier function > >Date: Tue, 23 Nov 2010 09:54:03 +0100 > > > >You should compile it individually. But you should use the same compiler. > > > > > > > >wumindt2 wrote: > >> Dearl All, > >> > >> To incorporate wannier90 into PWSCF-4.2.1, do we need to copy > >> pw2wannier90.f90 and wannier.f90 > >> from wannier90 to PWSCF directory, and recompile the PWSCF, or just > >> compile PWSCF and wannier90 individually? > >> > >> Thanks for any help. > >> > >> With Best regards, > >> > >> Min Wu > >> 2010-11-22 > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101123/635f9807/attachment.htm From andreas.linscheid at fu-berlin.de Tue Nov 23 18:51:53 2010 From: andreas.linscheid at fu-berlin.de (Andreas Linscheid) Date: Tue, 23 Nov 2010 18:51:53 +0100 Subject: [Pw_forum] Possible bugs in the electron-phonon calculation Message-ID: <4CEBFF39.40505@fu-berlin.de> Hello everybody. I want to implement a routine that writes out the el-ph matrix elements (no summation!) in order to use it as an input for our SCDFT code. On my way to doing so I think that I have found 2 bugs in the code. (I am working with version 4.2.1 of quantum espresso) 1) The first one is rather trivial (I hope ...) The Problem appears, if one adds the flags noinv=.true. and nosym=.true. to the scf and scf.fit calculation of example 07. The code crashes with "from lint : error # 10 cannot remap grid on k-point list" I was able to cure the crashing by simply removing the check of |deltam| < eps in elphon.f90, line 740 like this: @@ -740,10 +740,7 @@ subroutine lint ( nsym, s, minus_q, at, bg, npk, k1,k2,k3, & end do if ( sqrt ( deltap(1)**2 + & deltap(2)**2 + & - deltap(3)**2 ) < eps .or. ( minus_q .and. & - sqrt ( deltam(1)**2 + & - deltam(2)**2 + & - deltam(3)**2 ) < eps ) ) then + deltap(3)**2 ) < eps ) then eqBZ(nk) = n sBZ(nk) = ns go to 15 The condition checks for each symmetry also the inversion and stops if the k point matched. I think this is incorrect, as the inversions are separate symmetry operations that will be checked independently. If then the code is forced by hand to use no symmetry, where there are implicit symmetries not every point in the irreducible BZ is mapped and the check at the end of the routine fails. Clearly this is not a regular case ... (But it is in any case incorrect to store ns in sBZ(nk), where one should store the inversion ns+nsymq/2 ... ;-)) 2) The second problem is more severe. The flag trans=.false. seems to be not working any more. First I want to be a bit verbose why we actually need this. In our group, we extensively used trans since the k grid of the electron phonon calculation needs to be converged independently from the k grid for the phonon calculation. An interpolation (The way the elphsum routine works right now) may not always work. I don't know whether there are plans to remove that feature from the code in the next version, but I consider it a very useful tool. The problem with trans appears if one splits the electron phonon calculation of example 07 into two, (I have attached a slightly modified run script of example 07 ) i.e. does a ph calculation with elph=.false first and then an el-ph calculation with trans=.false and elph=.true.. According to the manual this procedure should be still correct, isn't it? The code crashes with: forrtl: severe (179): Cannot allocate array - overflow on array size calculation. Image PC Routine Line Source ph.x 0000000000EC72B6 Unknown Unknown Unknown ph.x 0000000000EC64B6 Unknown Unknown Unknown ph.x 0000000000E4493A Unknown Unknown Unknown ph.x 0000000000DF16F2 Unknown Unknown Unknown ph.x 0000000000E25CE9 Unknown Unknown Unknown ph.x 00000000004DB755 allocate_pert_ 25 allocate_pert.f90 ph.x 0000000000481B04 phq_setup_ 324 phq_setup.f90 ph.x 000000000046CDE2 initialize_ph_ 55 initialize_ph.f90 ph.x 0000000000452928 MAIN__ 97 phonon.f90 ph.x 0000000000452762 Unknown Unknown Unknown libc.so.6 00002B387BC8C4CA Unknown Unknown Unknown ph.x 00000000004526AA Unknown Unknown Unknown I was unable to solve the problem but this how far I got, tracing the error: > the crash is because npertx contains a random large integer when the t array is allocated in allocate_pert.f90 line 25 > this is because npert(:) contains random numbers when in init_representations.f90 line 97 npertx is computed > I figured that npert does not get initialized in set_irr.f90 because u_from_file is true (as it should be) and I think it should be read in from the xml file in _ph*.phsave/data-file.xml.[iq] where the data is stored. > I tried to make the code read that file 'by hand', however this file gets overwritten during the initialization of the phonon code and I don't know exactly where. I was unable to stop the code from overwriting the file data-file.xml.[iq] and correctly reading the data. As a workaround, I hacked the recover branch of the code in a dirty way to make it do what I want. This means to restart with a different k grid and compute el_ph_mat, then spit out the el-ph matrix elements in the basis of the modes. However, I would rather work with the trans branch as it is much cleaner and, according to the manual, intended exactly for such purpose. Then, if this is also of interest to other people, I can share this version as I am not messing up all the other part of the code. Thank you very much for your help! Andreas Linscheid PhD Student AG Gross --- Max-Planck-Institut f?r Mikrostrukturphysik Weinberg 2, 06120 Halle (Saale), Germany -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: run_example Url: http://www.democritos.it/pipermail/pw_forum/attachments/20101123/5f19de7d/attachment.asc From wangweiphysics at yahoo.com.cn Wed Nov 24 06:41:54 2010 From: wangweiphysics at yahoo.com.cn (wangwei) Date: Wed, 24 Nov 2010 13:41:54 +0800 (CST) Subject: [Pw_forum] a2F.dos.1 Message-ID: <978476.8104.qm@web15208.mail.cnb.yahoo.com> Dear Eyvaz, Thanks for youe relpy, and I clearly understand the meaning of file named a2F.dos.1 now. But I have?the other two?questions: what is the unit of Eliashberg function a2F? is it /Ry? How to calculate the partial phonon density of states? Thanks for any reply! Best wishes! wangwei Huaibei Normal University .? From mpayami at aeoi.org.ir Wed Nov 24 10:15:36 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 24 Nov 2010 12:45:36 +0330 Subject: [Pw_forum] Problem with constraining an atomic position References: <63129C69C2A14B5D97DD714DCB7B60F6@b> <4CEBE5DF.1070402@democritos.it> Message-ID: <4D296A503CDB470095E7231AF23B6B41@b> Dear Paolo, Thank you very much for your reply. It was solved. I just entered the positions of the atoms in a normal way (I mean without extra spaces between the coordinates). I use the QE-4.2.1. Best regards, m. > Mahmoud Payami wrote: > >> I have also constrined this z=0 atom to stay at that position during the >> relaxation. But, at the end all atoms (including the first one) are moved > > I cannot reproduce this behavior. Which code version are > you using? P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From mpayami at aeoi.org.ir Wed Nov 24 10:39:10 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 24 Nov 2010 13:09:10 +0330 Subject: [Pw_forum] on nosym=.true. References: <978476.8104.qm@web15208.mail.cnb.yahoo.com> Message-ID: <59461DA9D6D94740AD4CD23DFA8A42A8@b> Dear QE experts, I am doing slab calculations, and have let the interlayer spacings change along z-direction. I sometimes encounter the message: "the symmetry opetarion #... is not...", and sometimes this problem causes the program stop. However, I followed Eyvaz's suggestion in the forum and added "nosym=.true." in &SYSTEM. Now there is no complain about symmetry operation but the number of k-points has been increased. My question is: using "nosym=.true.", what symmetry operations are ignored, and where should I refer to find out which symmetry operation number refers to what? Best regards, Mahmoud Payami, Physics Group, AEOI, Tehran, Iran. From dalcorso at sissa.it Wed Nov 24 10:46:47 2010 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Wed, 24 Nov 2010 10:46:47 +0100 Subject: [Pw_forum] Possible bugs in the electron-phonon calculation In-Reply-To: <4CEBFF39.40505@fu-berlin.de> References: <4CEBFF39.40505@fu-berlin.de> Message-ID: <1290592007.12941.6.camel@ulisse.cm.sissa.it> Dear Andreas, Thank you very much for reporting this. Actually your point 2 is a real bug. ph_restart is not saving on file and reading the modes when trans=.false. and elph=.true. as it should. The fix is to change PH/ph_restart.f90 at lines 217, 804 and 862. These three lines are now: IF (trans.OR.zeu) THEN instead they should be: IF (trans.OR.zeu.OR.elph) THEN With this change your example is now running on my PC. I have corrected the cvs version. HTH, Andrea On Tue, 2010-11-23 at 18:51 +0100, Andreas Linscheid wrote: > Hello everybody. > > I want to implement a routine that writes out the el-ph matrix elements > (no summation!) in order to use it as an input for our SCDFT code. On my > way to doing so I think that I have found 2 bugs in the code. (I am > working with version 4.2.1 of quantum espresso) > > 1) The first one is rather trivial (I hope ...) > The Problem appears, if one adds the flags noinv=.true. and nosym=.true. > to the scf and scf.fit calculation of example 07. The code crashes with > > "from lint : error # 10 cannot remap grid on k-point list" > > I was able to cure the crashing by simply removing the check of |deltam| > < eps in elphon.f90, line 740 like this: > > @@ -740,10 +740,7 @@ subroutine lint ( nsym, s, minus_q, at, bg, npk, > k1,k2,k3, & > end do > if ( sqrt ( deltap(1)**2 + & > deltap(2)**2 + & > - deltap(3)**2 ) < eps .or. ( minus_q .and. & > - sqrt ( deltam(1)**2 + & > - deltam(2)**2 + & > - deltam(3)**2 ) < eps ) ) then > + deltap(3)**2 ) < eps ) then > eqBZ(nk) = n > sBZ(nk) = ns > go to 15 > > The condition checks for each symmetry also the inversion and stops if > the k point matched. I think this is incorrect, as the inversions are > separate symmetry operations that will be checked independently. If > then the code is forced by hand to use no symmetry, where there are > implicit symmetries not every point in the irreducible BZ is mapped and > the check at the end of the routine fails. Clearly this is not a regular > case ... (But it is in any case incorrect to store ns in sBZ(nk), where > one should store the inversion ns+nsymq/2 ... ;-)) > > 2) The second problem is more severe. The flag trans=.false. seems to be > not working any more. > First I want to be a bit verbose why we actually need this. > In our group, we extensively used trans since the k grid of the electron > phonon calculation needs to be converged independently from the k grid > for the phonon calculation. An interpolation (The way the elphsum > routine works right now) may not always work. > I don't know whether there are plans to remove that feature from the > code in the next version, but I consider it a very useful tool. > > The problem with trans appears if one splits the electron phonon > calculation of example 07 into two, (I have attached a slightly modified > run script of example 07 ) i.e. does a ph calculation with elph=.false > first and then an el-ph calculation with trans=.false and elph=.true.. > According to the manual this procedure should be still correct, isn't it? > The code crashes with: > > forrtl: severe (179): Cannot allocate array - overflow on array size > calculation. > Image PC Routine Line Source > ph.x 0000000000EC72B6 Unknown Unknown Unknown > ph.x 0000000000EC64B6 Unknown Unknown Unknown > ph.x 0000000000E4493A Unknown Unknown Unknown > ph.x 0000000000DF16F2 Unknown Unknown Unknown > ph.x 0000000000E25CE9 Unknown Unknown Unknown > ph.x 00000000004DB755 allocate_pert_ 25 > allocate_pert.f90 > ph.x 0000000000481B04 phq_setup_ 324 > phq_setup.f90 > ph.x 000000000046CDE2 initialize_ph_ 55 > initialize_ph.f90 > ph.x 0000000000452928 MAIN__ 97 > phonon.f90 > ph.x 0000000000452762 Unknown Unknown Unknown > libc.so.6 00002B387BC8C4CA Unknown Unknown Unknown > ph.x 00000000004526AA Unknown Unknown Unknown > > > I was unable to solve the problem but this how far I got, tracing the error: > > the crash is because npertx contains a random large integer when the > t array is allocated in allocate_pert.f90 line 25 > > this is because npert(:) contains random numbers when in > init_representations.f90 line 97 npertx is computed > > I figured that npert does not get initialized in set_irr.f90 because > u_from_file is true (as it should be) and I think it should be read in > from the xml file in _ph*.phsave/data-file.xml.[iq] where the data is > stored. > > I tried to make the code read that file 'by hand', however this file > gets overwritten during the initialization of the phonon code and I > don't know exactly where. > > I was unable to stop the code from overwriting the file > data-file.xml.[iq] and correctly reading the data. > > As a workaround, I hacked the recover branch of the code in a dirty way > to make it do what I want. This means to restart with a different k grid > and compute el_ph_mat, then spit out the el-ph matrix elements in the > basis of the modes. > However, I would rather work with the trans branch as it is much cleaner > and, according to the manual, intended exactly for such purpose. > Then, if this is also of interest to other people, I can share this > version as I am not messing up all the other part of the code. > > Thank you very much for your help! > > Andreas Linscheid > > PhD Student AG Gross --- Max-Planck-Institut f?r Mikrostrukturphysik > Weinberg 2, 06120 Halle (Saale), Germany > > > _______________________________________________ > 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 sclauzer at sissa.it Wed Nov 24 11:05:55 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 24 Nov 2010 11:05:55 +0100 Subject: [Pw_forum] on nosym=.true. In-Reply-To: <59461DA9D6D94740AD4CD23DFA8A42A8@b> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com> <59461DA9D6D94740AD4CD23DFA8A42A8@b> Message-ID: <211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it> Il giorno 24/nov/2010, alle ore 10.39, Mahmoud Payami ha scritto: > Dear QE experts, > I am doing slab calculations, and have let the interlayer spacings change > along z-direction. I sometimes encounter the message: "the symmetry > opetarion #... is not...", and sometimes this problem causes the program Do you mean "Warning: symmetry operation #N not allowed"? This is not an error, but simply a warning, please have a look here: http://www.quantum-espresso.org/user_guide/node50.html#SECTION0001110200000000000000 I doubt that this would cause the program to stop. > stop. However, I followed Eyvaz's suggestion in the forum and added > "nosym=.true." in &SYSTEM. Now there is no complain about symmetry operation > but the number of k-points has been increased. Of course, they cannot be reduced by symmetry since you asked the code to ignore any symmetry operation that might be present. > My question is: using > "nosym=.true.", what symmetry operations are ignored, and where should I All. > refer to find out which symmetry operation number refers to what? use verbosity = 'high' in namelist &control or look into the source code. HTH GS > Best regards, > Mahmoud Payami, > > Physics Group, AEOI, Tehran, Iran. > > > _______________________________________________ > 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/20101124/5a58c4b5/attachment.htm From mpayami at aeoi.org.ir Wed Nov 24 11:29:14 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 24 Nov 2010 13:59:14 +0330 Subject: [Pw_forum] on nosym=.true. References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b> <211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it> Message-ID: <379D51F547CB43829A96034D028E51A9@b> Dear Gabriele, Thank you very much for your reply. >Do you mean "Warning: symmetry operation #N not >allowed"? This is not an error, but simply a warning, Yes, it is. >I doubt that this would cause the program to stop. But it stops a process in the mpi running. > All. How can I constrain the system just ignore symmetry operations wrt the xoy plane (because the z coordinates change)? Bests, m. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101124/00887eed/attachment.htm From sclauzer at sissa.it Wed Nov 24 11:46:10 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 24 Nov 2010 11:46:10 +0100 Subject: [Pw_forum] on nosym=.true. In-Reply-To: <379D51F547CB43829A96034D028E51A9@b> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b> <211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it> <379D51F547CB43829A96034D028E51A9@b> Message-ID: <4CECECF2.6060008@sissa.it> On 11/24/2010 11:29 AM, Mahmoud Payami wrote: > Dear Gabriele, > Thank you very much for your reply. > >Do you mean "Warning: symmetry operation #N not >allowed"? This is > not an error, but simply a warning, > Yes, it is. > > >I doubt that this would cause the program to stop. > But it stops a process in the mpi running. At which point? Does it display some error message? You are not giving enough information to understand the problem. > > > All. > How can I constrain the system just ignore symmetry operations wrt the > xoy plane (because the z coordinates change)? I thought you had a slab geometry... if so, there should not be any symmetry operations involving a change in z coordinate (apart maybe a mirror plane and the inversion, depending on how you have built the slab). Then there are only operation involving x and y coordinates left. If you want to ignore those, then you should be left with no symmetries... What you can do is to very slightly displace some atoms in the xy plane such that some symmetry operations are not verified anymore. Anyway, if you want to remove a subset of symmetry operations in a systematic way I think you should modify the code. GS > Bests, > m. > > > _______________________________________________ > 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/20101124/2e5bd53a/attachment.htm From mpayami at aeoi.org.ir Wed Nov 24 11:46:46 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 24 Nov 2010 14:16:46 +0330 Subject: [Pw_forum] on nosym=.true. References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it> <379D51F547CB43829A96034D028E51A9@b> Message-ID: <7BCBF9FFDF4C48CA9AAEAA4918144828@b> Dear Gabriele, The message for stopping is: %%%%%%%%%%% from checkallsym : error # 1 some of the original symmetry operations not satisfied %%%%%%%%%%%%%%% stopping..... ------------ MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 0. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. ------------------------- Bests, m. Dear Gabriele, Thank you very much for your reply. >Do you mean "Warning: symmetry operation #N not >allowed"? This is not an error, but simply a warning, Yes, it is. >I doubt that this would cause the program to stop. But it stops a process in the mpi running. > All. How can I constrain the system just ignore symmetry operations wrt the xoy plane (because the z coordinates change)? Bests, m. ------------------------------------------------------------------------------ _______________________________________________ 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/20101124/bdb65e5a/attachment-0001.htm From mpayami at aeoi.org.ir Wed Nov 24 11:58:13 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 24 Nov 2010 14:28:13 +0330 Subject: [Pw_forum] on nosym=.true. References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b> <7BCBF9FFDF4C48CA9AAEAA4918144828@b> Message-ID: <8FCBD519728F4B50BAED47FFD2C5C9E2@b> Dear Gabriele, It stops after first scf calculation and declaring Total force, and afterward the ATOMIC_POSITIONS: ... ... convergence has been achieved in 23 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000000 0.00000000 0.00536688 atom 2 type 1 force = 0.00000000 0.00000000 0.00357281 atom 3 type 1 force = 0.00000000 0.00000000 -0.00247112 atom 4 type 1 force = 0.00000000 0.00000000 0.00167422 atom 5 type 1 force = 0.00000000 0.00000000 0.00068009 atom 6 type 1 force = 0.00000000 0.00000000 -0.00068009 atom 7 type 1 force = 0.00000000 0.00000000 -0.00167422 atom 8 type 1 force = 0.00000000 0.00000000 0.00247112 atom 9 type 1 force = 0.00000000 0.00000000 -0.00357281 atom 10 type 1 force = 0.00000000 0.00000000 -0.00536688 Total force = 0.008549 Total SCF correction = 0.000304 BFGS Geometry Optimization number of scf cycles = 1 number of bfgs steps = 0 energy new = -41.8258632643 Ry new trust radius = 0.2000000000 bohr new conv_thr = 0.0000001000 Ry ATOMIC_POSITIONS (angstrom) Al 0.000000000 0.000000000 0.000000000 0 0 0 Al 1.428355698 0.824661547 2.376728451 0 0 1 Al 2.856711396 1.649323093 4.634396299 0 0 1 Al 0.000000000 0.000000000 7.018212974 0 0 1 Al 1.428355698 0.824661547 9.338400235 0 0 1 Al 2.856711396 1.649323093 11.654055553 0 0 1 Al 0.000000000 0.000000000 13.974242813 0 0 1 Al 1.428355698 0.824661547 16.358059488 0 0 1 Al 2.856711396 1.649323093 18.615727337 0 0 1 Al 0.000000000 0.000000000 20.926010890 0 0 1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from checkallsym : error # 1 some of the original symmetry operations not satisfied %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 0. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun has exited due to process rank 0 with PID 5815 on node hpc9.ctpm.aeoi.org exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- Bests, m. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101124/222d725d/attachment.htm From mpayami at aeoi.org.ir Wed Nov 24 12:18:59 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 24 Nov 2010 14:48:59 +0330 Subject: [Pw_forum] on nosym=.true. References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b><7BCBF9FFDF4C48CA9AAEAA4918144828@b> <8FCBD519728F4B50BAED47FFD2C5C9E2@b> Message-ID: <38A9137B695749D0B613FA56741389A8@b> Dear Gabriele, I found the origin of the stop: I must NOT force any coordinates of any atom to remain fix. I just removed " 0 0 0" after the coordinates of the first atom and now it works at the expense that there is a whole translation of the system along the z-direction. Thank you again for your kind help. Bests, mahmoud -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101124/f89fc7d3/attachment.htm From eyvaz_isaev at yahoo.com Wed Nov 24 12:28:43 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 24 Nov 2010 03:28:43 -0800 (PST) Subject: [Pw_forum] on nosym=.true. In-Reply-To: <59461DA9D6D94740AD4CD23DFA8A42A8@b> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com> <59461DA9D6D94740AD4CD23DFA8A42A8@b> Message-ID: <359584.43782.qm@web65714.mail.ac4.yahoo.com> Dear Mahmoud, >I sometimes encounter the message: >"the symmetry opetarion #... is not ...", and sometimes this problem causes the >program stop Another way to overcome this message is specifying options nr1=N1,Nr2=N2,nr3=N3 Then you should not specify nosym=.true. >using "nosym=.true.", what symmetry operations are ignored, I suppose, all symmetry elements are ignored >where should I refer to find out which symmetry operation number refers to >what? In the &system section add verbosity='high' and have a look at output file. 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: Mahmoud Payami To: PWSCF Forum Sent: Wed, November 24, 2010 10:39:10 AM Subject: [Pw_forum] on nosym=.true. Dear QE experts, I am doing slab calculations, and have let the interlayer spacings change along z-direction. I sometimes encounter the message: "the symmetry opetarion #... is not...", and sometimes this problem causes the program stop. However, I followed Eyvaz's suggestion in the forum and added "nosym=.true." in &SYSTEM. Now there is no complain about symmetry operation but the number of k-points has been increased. My question is: using "nosym=.true.", what symmetry operations are ignored, and where should I refer to find out which symmetry operation number refers to what? Best regards, Mahmoud Payami, Physics Group, AEOI, Tehran, Iran. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From mpayami at aeoi.org.ir Wed Nov 24 12:45:56 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 24 Nov 2010 15:15:56 +0330 Subject: [Pw_forum] on nosym=.true. References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b> <359584.43782.qm@web65714.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz, Thank you very much for your comments. I have to learn more about the advanced (at least for me) the "nr1" switches. However, by not constraining any component of the atoms, the problem was solved. Best regards, mahmoud > Dear Mahmoud, > >>I sometimes encounter the message: >>"the symmetry opetarion #... is not ...", and sometimes this problem >>causes the >>program stop > > > Another way to overcome this message is specifying options > nr1=N1,Nr2=N2,nr3=N3 > Then you should not specify nosym=.true. > >>using "nosym=.true.", what symmetry operations are ignored, > > I suppose, all symmetry elements are ignored > >>where should I refer to find out which symmetry operation number refers >>to >>what? > > In the &system section add verbosity='high' and have a look at output > file. > > 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: Mahmoud Payami > To: PWSCF Forum > Sent: Wed, November 24, 2010 10:39:10 AM > Subject: [Pw_forum] on nosym=.true. > > Dear QE experts, > I am doing slab calculations, and have let the interlayer spacings change > along z-direction. I sometimes encounter the message: "the symmetry > opetarion #... is not...", and sometimes this problem causes the program > stop. However, I followed Eyvaz's suggestion in the forum and added > "nosym=.true." in &SYSTEM. Now there is no complain about symmetry > operation > but the number of k-points has been increased. My question is: using > "nosym=.true.", what symmetry operations are ignored, and where should I > refer to find out which symmetry operation number refers to what? > Best regards, > Mahmoud Payami, > > Physics Group, AEOI, Tehran, Iran. > > > _______________________________________________ > 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 Wed Nov 24 12:47:24 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 24 Nov 2010 03:47:24 -0800 (PST) Subject: [Pw_forum] on nosym=.true. In-Reply-To: <379D51F547CB43829A96034D028E51A9@b> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b> <211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it> <379D51F547CB43829A96034D028E51A9@b> Message-ID: <890486.26831.qm@web65702.mail.ac4.yahoo.com> From: Mahmoud Payami >>Do you mean "Warning: symmetry operation #N not >allowed"? This is not an >>error, but simply a warning, >Yes, it is. But this causes lowered symmetry that also leads to increased number of k-points. >How can I constrain the system just ignore symmetry operations wrt the >xoy >plane (because the z coordinates change)? If you mean changes only along Z-direction add cell_dofree=z. For ore info please have a look at INPUT_PW,txt in /Doc. Bests, Eyvaz. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101124/234b78e5/attachment-0001.htm From giannozz at democritos.it Wed Nov 24 13:24:06 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 24 Nov 2010 13:24:06 +0100 Subject: [Pw_forum] on nosym=.true. In-Reply-To: <38A9137B695749D0B613FA56741389A8@b> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b><7BCBF9FFDF4C48CA9AAEAA4918144828@b> <8FCBD519728F4B50BAED47FFD2C5C9E2@b> <38A9137B695749D0B613FA56741389A8@b> Message-ID: <4CED03E6.3020705@democritos.it> Mahmoud Payami wrote: > I must NOT force any coordinates of any atom to remain fix. I just > removed " 0 0 0" after the coordinates of the first atom and now it > works at the expense that there is a whole translation of the system > along the z-direction. this is an old and known problem. If you impose a constraint that breaks the symmetry, you will run into trouble because the number of k-points may change during the run. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From sclauzer at sissa.it Wed Nov 24 13:34:12 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 24 Nov 2010 13:34:12 +0100 Subject: [Pw_forum] on nosym=.true. In-Reply-To: <38A9137B695749D0B613FA56741389A8@b> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b><7BCBF9FFDF4C48CA9AAEAA4918144828@b> <8FCBD519728F4B50BAED47FFD2C5C9E2@b> <38A9137B695749D0B613FA56741389A8@b> Message-ID: <1C69FB80-F1BD-46DF-9BA8-30E28C011985@sissa.it> Il giorno 24/nov/2010, alle ore 12.18, Mahmoud Payami ha scritto: > Dear Gabriele, > > I found the origin of the stop: > I must NOT force any coordinates of any atom to remain fix. I just removed " 0 0 0" after the coordinates of the first atom and now it works at the expense that there is a whole translation of the system along the z-direction. By inspecting your forces I guess that this should not happen, because the slab is mirror symmetric wrt xy plane and so the forces are. Even if this is not the case, the translation of the whole slab should be small and should cause no problem (unless you have a sawtooth potential, maybe). Regards, GS > Thank you again for your kind help. > > Bests, > mahmoud > > > _______________________________________________ > 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/20101124/c1062120/attachment.htm From eyvaz_isaev at yahoo.com Wed Nov 24 15:06:47 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 24 Nov 2010 06:06:47 -0800 (PST) Subject: [Pw_forum] a2F.dos.1 In-Reply-To: <978476.8104.qm@web15208.mail.cnb.yahoo.com> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com> Message-ID: <911979.46443.qm@web65711.mail.ac4.yahoo.com> Hi, From: wangwei > I clearly understand the meaning of file named 2F.dos.1 now. Very good! > what is the unit of Eliashberg function a2F? is it /Ry? Ry, I suppose. > How to calculate the partial phonon density of states? Use QHA code for this purpose. See your QE directory to locate QHA suite. Bests, Eyvaz. ------------------------ IFM, Linkoping University, Sweden isaev at ifm.liu.se, eyvaz_isaev at yahoo.com _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From elie.moujaes at hotmail.co.uk Wed Nov 24 15:09:04 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 24 Nov 2010 14:09:04 +0000 Subject: [Pw_forum] band structure of a 60 atom grain boundary Message-ID: Dear all, I am trying to get the band structure of a 60-atom GB of graphene. The result is ok except that two of the bands should touch at some point and they are not touching. Could that be a probvlem in the convergence or in the set degauss value? Thanks Regards Elie Moujaes University of Nottingham NG7 2RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101124/1c39ea6e/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: GB60.bands.ps Type: application/postscript Size: 36709 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20101124/1c39ea6e/attachment-0001.ps From mpayami at aeoi.org.ir Wed Nov 24 19:34:36 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Wed, 24 Nov 2010 22:04:36 +0330 Subject: [Pw_forum] on nosym=.true. In-Reply-To: <4CED03E6.3020705@democritos.it> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b><7BCBF9FFDF4C48CA9AAEAA4918144828@b> <8FCBD519728F4B50BAED47FFD2C5C9E2@b> <38A9137B695749D0B613FA56741389A8@b> <4CED03E6.3020705@democritos.it> Message-ID: Dear Paolo, Thank you very much for your answer. It was a new experience for me. With kind regards, m. > > this is an old and known problem. If you impose a constraint > that breaks the symmetry, you will run into trouble because > the number of k-points may change during the run. > > P. > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From mpayami at aeoi.org.ir Wed Nov 24 19:42:46 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami Shabestari) Date: Wed, 24 Nov 2010 22:12:46 +0330 Subject: [Pw_forum] on nosym=.true. In-Reply-To: <1C69FB80-F1BD-46DF-9BA8-30E28C011985@sissa.it> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b><7BCBF9FFDF4C48CA9AAEAA4918144828@b> <8FCBD519728F4B50BAED47FFD2C5C9E2@b> <38A9137B695749D0B613FA56741389A8@b> <1C69FB80-F1BD-46DF-9BA8-30E28C011985@sissa.it> Message-ID: Dear Gabriele, As you mentioned, the translation was very small. Paolo pointed out that constraining the atoms leads to such a problem because during the relaxation, the number of k-points may change. Thank you again and cheers, mahmoud > > By inspecting your forces I guess that this should not happen, because > the slab is mirror symmetric wrt xy plane and so the forces are. Even > if this is not the case, the translation of the whole slab should be > small and should cause no problem (unless you have a sawtooth > potential, maybe). > > Regards, > > GS > > > Thank you again for your kind help. > > > > Bests, > > mahmoud > > > > > > _______________________________________________ > > 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 ssdhayal at gmail.com Thu Nov 25 04:37:19 2010 From: ssdhayal at gmail.com (Suman Dhayal) Date: Wed, 24 Nov 2010 21:37:19 -0600 Subject: [Pw_forum] Help! Message-ID: Hi, As far as I understand, we can use QE for solids. I am just wondering it is possible to do calculations for gaseous systems using QE? May be XSpectra calculations for example. I would appreciate any help and guidelines over it. Thanks, Suman -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101124/0e6fae72/attachment.htm From tkaloni at gmail.com Thu Nov 25 06:12:35 2010 From: tkaloni at gmail.com (Thaneshwor Kaloni) Date: Thu, 25 Nov 2010 10:42:35 +0530 Subject: [Pw_forum] Request Message-ID: Dear All, I have pasted the out put file below. I want to calculate the amount of charge transfer from boron site to carbon site. For example I have 2x2 supercell of graphene and I have replaced one carbon atom by Boron. Please suggest me. With Best Regards Thaneshwor P Kaloni SNBNCBS kolkata India. # E (eV) ldosup(E) ldosdw(E) pdosup(E) pdosdw(E) pdosup(E) pdosdw(E) pdosup(E) pdosdw(E) -21.020 -0.116E-06 -0.116E-06 -0.165E-09 -0.165E-09 -0.702E-07 -0.701E-07 -0.453E-07 -0.452E-07 -20.920 -0.773E-06 -0.773E-06 -0.103E-08 -0.103E-08 -0.466E-06 -0.466E-06 -0.306E-06 -0.306E-06 -20.820 -0.380E-05 -0.380E-05 -0.467E-08 -0.467E-08 -0.228E-05 -0.227E-05 -0.152E-05 -0.152E-05 -20.720 -0.134E-04 -0.134E-04 -0.150E-07 -0.150E-07 -0.795E-05 -0.795E-05 -0.540E-05 -0.539E-05 -20.620 -0.315E-04 -0.315E-04 -0.321E-07 -0.321E-07 -0.187E-04 -0.187E-04 -0.128E-04 -0.128E-04 -20.520 -0.392E-04 -0.392E-04 -0.348E-07 -0.348E-07 -0.231E-04 -0.231E-04 -0.161E-04 -0.161E-04 -20.420 0.261E-04 0.260E-04 0.292E-07 0.292E-07 0.152E-04 0.152E-04 0.108E-04 0.108E-04 -20.320 0.241E-03 0.241E-03 0.203E-06 0.203E-06 0.142E-03 0.142E-03 0.994E-04 0.994E-04 -20.220 0.593E-03 0.593E-03 0.410E-06 0.409E-06 0.350E-03 0.350E-03 0.242E-03 0.242E-03 -20.120 0.910E-03 0.910E-03 0.304E-06 0.304E-06 0.544E-03 0.544E-03 0.366E-03 0.366E-03 -20.020 0.978E-03 0.979E-03 -0.592E-06 -0.592E-06 0.595E-03 0.595E-03 0.384E-03 0.384E-03 -19.920 0.749E-03 0.749E-03 -0.166E-05 -0.166E-05 0.466E-03 0.467E-03 0.284E-03 0.284E-03 -19.820 0.389E-03 0.389E-03 0.882E-06 0.881E-06 0.249E-03 0.249E-03 0.139E-03 0.139E-03 -19.720 0.116E-03 0.116E-03 0.127E-04 0.127E-04 0.709E-04 0.710E-04 0.325E-04 0.325E-04 -19.620 0.119E-04 0.120E-04 0.338E-04 0.338E-04 -0.108E-04 -0.108E-04 -0.111E-04 -0.110E-04 -19.520 0.163E-04 0.162E-04 0.534E-04 0.534E-04 -0.228E-04 -0.228E-04 -0.143E-04 -0.143E-04 -19.420 0.425E-04 0.425E-04 0.598E-04 0.598E-04 -0.120E-04 -0.120E-04 -0.521E-05 -0.521E-05 -19.320 0.541E-04 0.541E-04 0.529E-04 0.529E-04 -0.266E-05 -0.266E-05 0.386E-05 0.386E-05 -19.220 0.519E-04 0.519E-04 0.406E-04 0.406E-04 0.148E-05 0.148E-05 0.986E-05 0.986E-05 -19.120 0.410E-04 0.410E-04 0.273E-04 0.273E-04 0.241E-05 0.241E-05 0.112E-04 0.112E-04 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101125/864d94d6/attachment.htm From mpayami at aeoi.org.ir Thu Nov 25 06:59:17 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Thu, 25 Nov 2010 09:29:17 +0330 Subject: [Pw_forum] on nosym=.true. References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b> <890486.26831.qm@web65702.mail.ac4.yahoo.com> Message-ID: <4F8FDB4C7BD34E32B7AFB76C485C7644@b> Dear Eyvaz, Thank you very much for "cell_dofree" switch. I looked at INPUT_PW and added "cell_dofree=z" in the &CELL namelist but in the output file I noticed that it is ignored with the message: Warning: card &CELL ignored Warning: card CELL_DOFREE=z ignored Am I committing a mistake in using that? Bests, mahmoud If you mean changes only along Z-direction add cell_dofree=z. For ore info please have a look at INPUT_PW,txt in /Doc. Bests, Eyvaz. ------------------------------------------------------------------------------ _______________________________________________ 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/20101125/6e57e33f/attachment.htm From degironc at sissa.it Thu Nov 25 07:14:18 2010 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 25 Nov 2010 07:14:18 +0100 Subject: [Pw_forum] on nosym=.true. In-Reply-To: <4F8FDB4C7BD34E32B7AFB76C485C7644@b> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b> <890486.26831.qm@web65702.mail.ac4.yahoo.com> <4F8FDB4C7BD34E32B7AFB76C485C7644@b> Message-ID: <20101125071418.702vbd4iskgow8oc@webmail.sissa.it> Dear Mahmoud Payami, are you specifing calc='vc-relax' in the &control namelist ? otherwise the code will skip the CELL part. I thnk that one should specify cell_dofree="z" (with z into quotation marks) stefano Quoting Mahmoud Payami : > Dear Eyvaz, > Thank you very much for "cell_dofree" switch. I looked at INPUT_PW > and added "cell_dofree=z" in the &CELL namelist but in the output > file I noticed that it is ignored with the message: > Warning: card &CELL ignored > Warning: card CELL_DOFREE=z ignored > > Am I committing a mistake in using that? > Bests, > mahmoud > > If you mean changes only along Z-direction add cell_dofree=z. For > ore info please have a look at INPUT_PW,txt in /Doc. > > Bests, > Eyvaz. > > > > > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > 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 mpayami at aeoi.org.ir Thu Nov 25 08:43:21 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Thu, 25 Nov 2010 11:13:21 +0330 Subject: [Pw_forum] on nosym=.true. References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b><890486.26831.qm@web65702.mail.ac4.yahoo.com><4F8FDB4C7BD34E32B7AFB76C485C7644@b> <20101125071418.702vbd4iskgow8oc@webmail.sissa.it> Message-ID: <7FA815C7D210438FB0EB4718EDB21844@b> Dear Stefano, Thank you. I followed your suggestion and it worked perfect. Cheers, mahmoud > Dear Mahmoud Payami, > are you specifing calc='vc-relax' in the &control namelist ? > otherwise the code will skip the CELL part. > I thnk that one should specify cell_dofree="z" (with z into quotation > marks) > > stefano > > Quoting Mahmoud Payami : > >> Dear Eyvaz, >> Thank you very much for "cell_dofree" switch. I looked at INPUT_PW >> and added "cell_dofree=z" in the &CELL namelist but in the output >> file I noticed that it is ignored with the message: >> Warning: card &CELL ignored >> Warning: card CELL_DOFREE=z ignored >> >> Am I committing a mistake in using that? >> Bests, >> mahmoud >> >> If you mean changes only along Z-direction add cell_dofree=z. For >> ore info please have a look at INPUT_PW,txt in /Doc. >> >> Bests, >> Eyvaz. >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From mpayami at aeoi.org.ir Thu Nov 25 09:22:25 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Thu, 25 Nov 2010 11:52:25 +0330 Subject: [Pw_forum] on nosym=.true. References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b><890486.26831.qm@web65702.mail.ac4.yahoo.com><4F8FDB4C7BD34E32B7AFB76C485C7644@b><20101125071418.702vbd4iskgow8oc@webmail.sissa.it> <7FA815C7D210438FB0EB4718EDB21844@b> Message-ID: Dear Stefano, I did "vc-relax" + "cell_dofree='z'" calculation with two input files: In the first, I constrained the position of the first atom (out of ten atoms) to remain unchanged, and in the second, I did not constrain any atom. The calculation of the first case completed successfully, but the unconstrined case stopped (after 12 scf cycles and 5 bfgs steps) with the message: ---------------------- trust_radius < trust_radius_min resetting bfgs history %%%%%%%%%%%%%%%% from bfgs : error #1 bfgs history already reset at previous step %%%%%%%%%%%%%%%%%% How can I handle it? Bests, mahmoud > Dear Stefano, > Thank you. I followed your suggestion and it worked perfect. > Cheers, > mahmoud > > >> Dear Mahmoud Payami, >> are you specifing calc='vc-relax' in the &control namelist ? >> otherwise the code will skip the CELL part. >> I thnk that one should specify cell_dofree="z" (with z into quotation >> marks) >> >> stefano >> >> Quoting Mahmoud Payami : >> >>> Dear Eyvaz, >>> Thank you very much for "cell_dofree" switch. I looked at INPUT_PW >>> and added "cell_dofree=z" in the &CELL namelist but in the output >>> file I noticed that it is ignored with the message: >>> Warning: card &CELL ignored >>> Warning: card CELL_DOFREE=z ignored >>> >>> Am I committing a mistake in using that? >>> Bests, >>> mahmoud >>> >>> If you mean changes only along Z-direction add cell_dofree=z. For >>> ore info please have a look at INPUT_PW,txt in /Doc. >>> >>> Bests, >>> Eyvaz. >>> >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> ---------------------------------------------------------------- >> SISSA Webmail https://webmail.sissa.it/ >> Powered by Horde http://www.horde.org/ >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From sclauzer at sissa.it Thu Nov 25 10:17:57 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 25 Nov 2010 10:17:57 +0100 Subject: [Pw_forum] on nosym=.true. In-Reply-To: <7FA815C7D210438FB0EB4718EDB21844@b> References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b><890486.26831.qm@web65702.mail.ac4.yahoo.com><4F8FDB4C7BD34E32B7AFB76C485C7644@b> <20101125071418.702vbd4iskgow8oc@webmail.sissa.it> <7FA815C7D210438FB0EB4718EDB21844@b> Message-ID: I don't see any point in doing a vc-relax with cell_dofree="z" for a slab with the surface plane perpendicular to the z axis (as it was in your first output file, if I understood correctly)... What's your real aim? GS Il giorno 25/nov/2010, alle ore 08.43, Mahmoud Payami ha scritto: > Dear Stefano, > Thank you. I followed your suggestion and it worked perfect. > Cheers, > mahmoud > > >> Dear Mahmoud Payami, >> are you specifing calc='vc-relax' in the &control namelist ? >> otherwise the code will skip the CELL part. >> I thnk that one should specify cell_dofree="z" (with z into quotation >> marks) >> >> stefano >> >> Quoting Mahmoud Payami : >> >>> Dear Eyvaz, >>> Thank you very much for "cell_dofree" switch. I looked at INPUT_PW >>> and added "cell_dofree=z" in the &CELL namelist but in the output >>> file I noticed that it is ignored with the message: >>> Warning: card &CELL ignored >>> Warning: card CELL_DOFREE=z ignored >>> >>> Am I committing a mistake in using that? >>> Bests, >>> mahmoud >>> >>> If you mean changes only along Z-direction add cell_dofree=z. For >>> ore info please have a look at INPUT_PW,txt in /Doc. >>> >>> Bests, >>> Eyvaz. >>> >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> ---------------------------------------------------------------- >> SISSA Webmail https://webmail.sissa.it/ >> Powered by Horde http://www.horde.org/ >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? 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/20101125/b65a1f38/attachment.htm From sclauzer at sissa.it Thu Nov 25 10:24:28 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 25 Nov 2010 10:24:28 +0100 Subject: [Pw_forum] Help! In-Reply-To: References: Message-ID: <6EBDC5A4-5841-4F15-91DC-5BBBA8CD7837@sissa.it> I can give you this advice: specify a meaningful and less generic subject in your post if you want real help ;) All of us sometimes need to be helped, of course, but you should put an effort to make it an easier task. And please specify your affiliation in your next posts. Thanks! GS Il giorno 25/nov/2010, alle ore 04.37, Suman Dhayal ha scritto: > Hi, > > As far as I understand, we can use QE for solids. I am just wondering it is possible to do calculations for gaseous systems using QE? May be XSpectra calculations for example. I would appreciate any help and guidelines over it. > > Thanks, > > Suman > _______________________________________________ > 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/20101125/3a93c232/attachment.htm From mpayami at aeoi.org.ir Thu Nov 25 11:42:50 2010 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Thu, 25 Nov 2010 14:12:50 +0330 Subject: [Pw_forum] on nosym=.true. References: <978476.8104.qm@web15208.mail.cnb.yahoo.com><59461DA9D6D94740AD4CD23DFA8A42A8@b><211E8269-8E46-4247-BA2E-CD16775D0606@sissa.it><379D51F547CB43829A96034D028E51A9@b><890486.26831.qm@web65702.mail.ac4.yahoo.com><4F8FDB4C7BD34E32B7AFB76C485C7644@b><20101125071418.702vbd4iskgow8oc@webmail.sissa.it><7FA815C7D210438FB0EB4718EDB21844@b> Message-ID: Dear Gabriele, Thank you for your reply. "vc-relax"+"cell_dofree="z"" work fine. I have to examine a little bit more to explore more details. Cheers, mahmoud I don't see any point in doing a vc-relax with cell_dofree="z" for a slab with the surface plane perpendicular to the z axis (as it was in your first output file, if I understood correctly)... What's your real aim? GS Il giorno 25/nov/2010, alle ore 08.43, Mahmoud Payami ha scritto: Dear Stefano, Thank you. I followed your suggestion and it worked perfect. Cheers, mahmoud Dear Mahmoud Payami, are you specifing calc='vc-relax' in the &control namelist ? otherwise the code will skip the CELL part. I thnk that one should specify cell_dofree="z" (with z into quotation marks) stefano Quoting Mahmoud Payami : Dear Eyvaz, Thank you very much for "cell_dofree" switch. I looked at INPUT_PW and added "cell_dofree=z" in the &CELL namelist but in the output file I noticed that it is ignored with the message: Warning: card &CELL ignored Warning: card CELL_DOFREE=z ignored Am I committing a mistake in using that? Bests, mahmoud If you mean changes only along Z-direction add cell_dofree=z. For ore info please have a look at INPUT_PW,txt in /Doc. Bests, Eyvaz. ------------------------------------------------------------------------------ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101125/5bc9f5ac/attachment-0001.htm From sks.jnc at gmail.com Thu Nov 25 12:16:20 2010 From: sks.jnc at gmail.com (S. K. S.) Date: Thu, 25 Nov 2010 12:16:20 +0100 Subject: [Pw_forum] cell_dofree Message-ID: Dear All, Is there any option in PWSCF which allow to move x, y and z axis, keeping volume unchanged ??? Thanking you all, Saha S.K. JNCASR Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101125/327fda39/attachment.htm From mighfar at jncasr.ac.in Thu Nov 25 13:46:11 2010 From: mighfar at jncasr.ac.in (Mighfar Imam) Date: Thu, 25 Nov 2010 18:16:11 +0530 Subject: [Pw_forum] cell_dofree In-Reply-To: References: Message-ID: <28ed3c9a9f270c0ee7eacbca88dc417f.squirrel@mercury.jncasr.ac.in> Dear Srijan, that's exactly what calculation='relax' does! Mighfar JNCASR, Bangalore > Is there any option in PWSCF which allow to move > > x, y and z axis, keeping volume unchanged ??? > > Thanking you all, > Saha S.K. > JNCASR > Bangalore > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From mighfar at jncasr.ac.in Thu Nov 25 13:50:04 2010 From: mighfar at jncasr.ac.in (Mighfar Imam) Date: Thu, 25 Nov 2010 18:20:04 +0530 Subject: [Pw_forum] cell_dofree In-Reply-To: <28ed3c9a9f270c0ee7eacbca88dc417f.squirrel@mercury.jncasr.ac.in> References: <28ed3c9a9f270c0ee7eacbca88dc417f.squirrel@mercury.jncasr.ac.in> Message-ID: <2428587ed1d1d03849048b6564887756.squirrel@mercury.jncasr.ac.in> I am sorry, i thought you were asking about x y z coordinates of atoms! -mighfar Dear Srijan, that's exactly what > calculation='relax' does! > > > Mighfar > JNCASR, Bangalore > > >> Is there any option in PWSCF which allow to >> move >> >> x, y and z axis, keeping volume unchanged ??? >> >> Thanking you all, >> Saha S.K. >> JNCASR >> Bangalore >> _______________________________________________ >> 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 sks.jnc at gmail.com Thu Nov 25 14:00:16 2010 From: sks.jnc at gmail.com (S. K. S.) Date: Thu, 25 Nov 2010 14:00:16 +0100 Subject: [Pw_forum] HOW TO COMPUTE Effective charge for FM INSULATOR using PWSCF? Message-ID: Dear all, The fixed occupations and lsda need nelup and neldw, and the phonon code with constrained magnetization is not yet available. Does it imply that the phonon calculation is not possible for fixed occupations and lsda???? regards, S. K. Saha JNCASR BANGALORE P.S. Dear Mighfar, it is okay, cheers!!!!! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101125/6ee5bcf9/attachment.htm From giannozz at democritos.it Thu Nov 25 14:30:18 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 25 Nov 2010 14:30:18 +0100 Subject: [Pw_forum] cell_dofree In-Reply-To: References: Message-ID: <4CEE64EA.1080806@democritos.it> S. K. S. wrote: > Is there any option in PWSCF which allow to move > x, y and z axis, keeping volume unchanged ??? yes, but only in the development (cvs) version P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Nov 25 14:36:10 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 25 Nov 2010 14:36:10 +0100 Subject: [Pw_forum] band structure of a 60 atom grain boundary In-Reply-To: References: Message-ID: <4CEE664A.4010701@democritos.it> Elie Moujaes wrote: > I am trying to get the band structure of a 60-atom GB of graphene. The > result is ok except that two of the bands should touch at some point and > they are not touching. Could that be a probvlem in the convergence or in > the set degauss value? or it could be that the point at which the bands touch is not where you think it is P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Thu Nov 25 14:49:08 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 25 Nov 2010 14:49:08 +0100 Subject: [Pw_forum] Request In-Reply-To: References: Message-ID: <4CEE6954.9070708@democritos.it> Thaneshwor Kaloni wrote: > Please suggest me. may I suggest you to better formulate your questions and to use a better subject? > # E (eV) ldosup(E) ldosdw(E) pdosup(E) pdosdw(E) pdosup(E) > pdosdw(E) pdosup(E) pdosdw(E) see last pages of: http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_magn.pdf P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From srijan.india at gmail.com Thu Nov 25 15:51:36 2010 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Thu, 25 Nov 2010 15:51:36 +0100 Subject: [Pw_forum] cell_dofree In-Reply-To: <4CEE64EA.1080806@democritos.it> References: <4CEE64EA.1080806@democritos.it> Message-ID: Dear Paolo, Thanks a lot for your reply. If I am not wrong, I think, I am using the CVS VERSION. The part of the program follows here: CASE ( 'all', 'default' ) iforceh = 1 CASE ( 'shape' ) iforceh = 1 fix_volume = .true. CASE ( 'volume' ) CALL errore(' init_dofree ', & ' cell_dofree = '//TRIM(cell_dofree)//' not yet implemented ', 1 ) CASE ('x') iforceh = 0 iforceh(1,1) = 1 I am not sure that CASE('shape') does the same thing I WANTED. And it is written that CASE ( 'volume' ) is not yet implemented. So, is there any other version that you mentioned ? regards, Saha S. K. JNCASR, Bangalore On Thu, Nov 25, 2010 at 2:30 PM, Paolo Giannozzi wrote: > S. K. S. wrote: > > > Is there any option in PWSCF which allow to move > > x, y and z axis, keeping volume unchanged ??? > > yes, but only in the development (cvs) version > > P. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101125/ee096b78/attachment.htm From giannozz at democritos.it Thu Nov 25 15:54:36 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 25 Nov 2010 15:54:36 +0100 Subject: [Pw_forum] cell_dofree In-Reply-To: References: <4CEE64EA.1080806@democritos.it> Message-ID: <4CEE78AC.90407@democritos.it> Srijan Kumar Saha wrote: > I am not sure that CASE('shape') does the same thing I WANTED. try. -- Paolo Giannozzi, Democritos and University of Udine, Italy From wumindt2 at zju.edu.cn Fri Nov 26 01:05:21 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Fri, 26 Nov 2010 08:05:21 +0800 Subject: [Pw_forum] wannier function Message-ID: Dear All, I have a problem using the wannier90.x. Does the wannier90.x can plot the wannier function above the fermi level, i.e. the unocuppied charge density? Thanks! Min Wu 2010-11-25 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101126/8a6a419e/attachment.htm From baroni at sissa.it Fri Nov 26 03:55:58 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 26 Nov 2010 08:25:58 +0530 Subject: [Pw_forum] Help! In-Reply-To: References: Message-ID: <8B9E913E-27A2-4AC3-9A5A-C21E01ADCDEF@sissa.it> yes, using "supercells" (see a textbook in electronic-structure calculations, such as Martin's, to see what a supercell is). As suggested by others, please always sign your posts including your affiliation and use a less generic "subject" field. SB On Nov 25, 2010, at 9:07 AM, Suman Dhayal wrote: > Hi, > > As far as I understand, we can use QE for solids. I am just wondering it is possible to do calculations for gaseous systems using QE? May be XSpectra calculations for example. I would appreciate any help and guidelines over it. > > Thanks, > > Suman > _______________________________________________ > 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/20101126/5c2a5101/attachment-0001.htm From baroni at sissa.it Fri Nov 26 03:48:48 2010 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 26 Nov 2010 08:18:48 +0530 Subject: [Pw_forum] wannier function In-Reply-To: References: Message-ID: <7E50BDCD-3602-4BC1-A810-457F987509E7@sissa.it> Not sure i understand what you mean, but the "unoccupied charge density" (i.e. the sum of the squared moduli of the unoccupied orbitals is infinite, for whatever reason you may need it). Or you rather mean the squared modulus of a specific Wannier function obtained from specific energy bands above the Fermi energy? SB On Nov 26, 2010, at 5:35 AM, wumindt2 wrote: > Dear All, > > I have a problem using the wannier90.x. > Does the wannier90.x can plot the wannier function above the fermi level, i.e. the unocuppied charge density? > > Thanks! > > Min Wu > 2010-11-25 > > _______________________________________________ > 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/20101126/0495017f/attachment.htm From wumindt2 at zju.edu.cn Fri Nov 26 04:39:11 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Fri, 26 Nov 2010 11:39:11 +0800 Subject: [Pw_forum] wannier function Message-ID: Hi Stefano, I want to plot the unoccupied state in an energy window, so it can be finite. Because i'm calculating the X-ray absorbtion spectra of SiO2. This is the reason i need the wannier function plotted in an energy window above the Fermi level. Cheers, Wu Min 2010-11-25 >From: Stefano Baroni >Reply-To: >To: wumindt2 ,PWSCF Forum >Subject: Re: [Pw_forum] wannier function >Date: Fri, 26 Nov 2010 08:18:48 +0530 > Not sure i understand what you mean, but the "unoccupied charge density" (i.e. the sum of the squared moduli of the unoccupied orbitals is infinite, for whatever reason you may need it). Or you rather mean the squared modulus of a specific Wannier function obtained from specific energy bands above the Fermi energy? SB On Nov 26, 2010, at 5:35 AM, wumindt2 wrote: Dear All, I have a problem using the wannier90.x. Does the wannier90.x can plot the wannier function above the fermi level, i.e. the unocuppied charge density? Thanks! Min Wu 2010-11-25 _______________________________________________ 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/20101126/cd9e1b32/attachment.htm From payam.norouzzadeh at gmail.com Fri Nov 26 07:28:23 2010 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Fri, 26 Nov 2010 09:58:23 +0330 Subject: [Pw_forum] equation of states Message-ID: Hello QE Users ev.x executable code as a part of QE can fit energy versus lattice constant curve to 4 different equation of states named birch1, birch2,keane and murnaghan.Does anyone know how can I find more information about these equation of states? Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101126/3b8b1638/attachment.htm From ma at nano.ku.dk Fri Nov 26 08:09:40 2010 From: ma at nano.ku.dk (Martin Andersson) Date: Fri, 26 Nov 2010 08:09:40 +0100 Subject: [Pw_forum] changing vdW radii for dispersion correction Message-ID: <4CEF5D34.90605@nano.ku.dk> Hi! I would like to use the DFT-D implemented in QE, but I would like to change the vdW radii used. How can I do this? Cheers, Martin Andersson, NanoGeoScience, University of Copenhagen From Michael at ihpc.a-star.edu.sg Fri Nov 26 08:44:35 2010 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Fri, 26 Nov 2010 15:44:35 +0800 Subject: [Pw_forum] changing vdW radii for dispersion correction In-Reply-To: <4CEF5D34.90605@nano.ku.dk> References: <4CEF5D34.90605@nano.ku.dk> Message-ID: <235887FC8686C543B24F9DF2A01CBE040301967A@S3-EXCHMB03.shared-svc.local> Martin: Have a look at the mm_dispersion.f90 file in the Modules folder. It's pretty obvious what to change. This is also the place you'd change the C6 if needed. Mike michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Martin Andersson Sent: Friday, November 26, 2010 3:10 PM To: pw_forum at pwscf.org Subject: [Pw_forum] changing vdW radii for dispersion correction Hi! I would like to use the DFT-D implemented in QE, but I would like to change the vdW radii used. How can I do this? Cheers, Martin Andersson, NanoGeoScience, University of Copenhagen _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum IHPC Values :: Impact :: Honesty :: Performance :: Co-operation This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From ssdhayal at gmail.com Fri Nov 26 08:57:33 2010 From: ssdhayal at gmail.com (Suman Dhayal) Date: Fri, 26 Nov 2010 01:57:33 -0600 Subject: [Pw_forum] Help! In-Reply-To: <8B9E913E-27A2-4AC3-9A5A-C21E01ADCDEF@sissa.it> References: <8B9E913E-27A2-4AC3-9A5A-C21E01ADCDEF@sissa.it> Message-ID: Dear Prof. Baroni, Thank you so much for the guidance and the Book's name. Its very helpful. And yes, sure I will include my affiliation in all the next posts and would try to be more specific. Thanks again, Suman On Thu, Nov 25, 2010 at 8:55 PM, Stefano Baroni wrote: > yes, using "supercells" (see a textbook in electronic-structure > calculations, such as Martin's, to see what a supercell is). As suggested by > others, please always sign your posts including your affiliation and use a > less generic "subject" field. SB > > On Nov 25, 2010, at 9:07 AM, Suman Dhayal wrote: > > Hi, > > As far as I understand, we can use QE for solids. I am just wondering it is > possible to do calculations for gaseous systems using QE? May be XSpectra > calculations for example. I would appreciate any help and guidelines over > it. > > Thanks, > > Suman > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101126/d2b0cac1/attachment-0001.htm From giannozz at democritos.it Fri Nov 26 10:57:38 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 26 Nov 2010 10:57:38 +0100 Subject: [Pw_forum] equation of states In-Reply-To: References: Message-ID: <4CEF8492.6070302@democritos.it> Payam Norouzzadeh wrote: > ev.x executable code as a part of QE can fit energy versus lattice > constant curve to 4 different equation of states named birch1, > birch2,keane and murnaghan.Does anyone know how can I find more > information about these equation of states? in the related literature (unfortunately in hard to find old issues of geophysical journals). There is a rather good wikipedia page: http://en.wikipedia.org/wiki/Birch?Murnaghan_equation_of_state P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at democritos.it Fri Nov 26 12:24:06 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 26 Nov 2010 12:24:06 +0100 Subject: [Pw_forum] (solved) Error in phonon calculation and duringtests also? In-Reply-To: <68AB68C3F058417FBB99BE052B7B9D4D@solarflare> References: <68AB68C3F058417FBB99BE052B7B9D4D@solarflare> Message-ID: <4CEF98D6.5070904@democritos.it> Huiqun Zhou wrote: > I'm using Intel Compiler 11.1 064 and 072 on two different > clusters and no problem occurred in compiling qe-espresso. in fact the problem shows up only in the newer ifort v.12.0.0. Apparently it miscompiles iotk. Previous versions are ok. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy From giacsport at libero.it Mon Nov 29 13:16:04 2010 From: giacsport at libero.it (giacsport at libero.it) Date: Mon, 29 Nov 2010 13:16:04 +0100 (CET) Subject: [Pw_forum] ibrav for Bmmb group Message-ID: <3030295.973961291032964727.JavaMail.defaultUser@defaultHost> Dear All, I would like to calculate a structure whose symmetry group is Bmmb. I know that is a orthorombic structure with the ab-plane adopted as a 2D plane. The unit cell is 1 atom of Ti and 2 of oxygen. Cartesian axes site n. atom positions (a_0 units) 1 Ti tau( 1) = ( 0.0000000 0.2500000 0.6800900 ) 2 O tau( 2) = ( 0.0000000 0.2500000 0.3832200 ) 3 O tau( 3) = ( 0.0000000 0.2500000 0.2180200 ) I tried setting ibrav = 8, celldm(1)=a (bohr), celldm(2)=b/a, celldm(3)=c/a and I got this message in the output ortho sub-group = 2* 2 procs warning: symmetry operation # 2 not allowed. fractional translation: 0.0000000 0.3862661 0.0000000 in crystal coordinates warning: symmetry operation # 7 not allowed. fractional translation: 0.0000000 0.3862661 0.0000000 in crystal coordinates Is the ibrav value not appropriate for the Bmmb space group? Can anybody kindly help me? Very best, Giacomo Giorgi, PhD. Tokyo University. From elie.moujaes at hotmail.co.uk Mon Nov 29 14:32:06 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 29 Nov 2010 13:32:06 +0000 Subject: [Pw_forum] wannier90.x missing Message-ID: Dear all, I am using the wannier functions to get the band structure in bilayer graphene. in expresso-4.2, I found all the executables (pw2wannier90.x, wannier_plot.x, etc..) except the wannier90.x executable that I need. I downloaded the folder W90 from the QE site and I found the the wannier90.f90 program. I tried to form the executable by tping: g95 wannier.f90 -o wannier but I got some errors. Is it possible to let me know where I can find the executable or how to form it given that I have the .f90 file. Regards Elie Moujaes University of Nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101129/d9f5a935/attachment.htm From sclauzer at sissa.it Mon Nov 29 15:12:17 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 29 Nov 2010 15:12:17 +0100 Subject: [Pw_forum] wannier90.x missing In-Reply-To: References: Message-ID: Have you tried with the following? make w90 BTW, if you simply type make, you'll get a list of all possible targets and what will be built for each of them GS Il giorno 29/nov/2010, alle ore 14.32, Elie Moujaes ha scritto: > Dear all, > > I am using the wannier functions to get the band structure in bilayer graphene. in expresso-4.2, I found all the executables (pw2wannier90.x, wannier_plot.x, etc..) except the wannier90.x executable that I need. I downloaded the folder W90 from the QE site and I found the the wannier90.f90 program. I tried to form the executable by tping: > > g95 wannier.f90 -o wannier but I got some errors. > > Is it possible to let me know where I can find the executable or how to form it given that I have the .f90 file. > > Regards > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? 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/20101129/d4da4fab/attachment.htm From sclauzer at sissa.it Mon Nov 29 15:15:12 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 29 Nov 2010 15:15:12 +0100 Subject: [Pw_forum] ibrav for Bmmb group In-Reply-To: <3030295.973961291032964727.JavaMail.defaultUser@defaultHost> References: <3030295.973961291032964727.JavaMail.defaultUser@defaultHost> Message-ID: Please have a look here: http://www.quantum-espresso.org/user_guide/node50.html#SECTION0001110200000000000000 You can try to play a bit the cutoff or with the FFT mesh size to avoid this. HTH GS Il giorno 29/nov/2010, alle ore 13.16, giacsport at libero.it ha scritto: > Dear All, > I would like to calculate a structure whose symmetry group is > Bmmb. I know that is a orthorombic structure with the ab-plane adopted as a 2D > plane. > The unit cell is 1 atom of Ti and 2 of oxygen. > Cartesian axes > site n. atom positions (a_0 units) > 1 Ti tau( 1) = ( 0.0000000 0.2500000 0.6800900 ) > 2 O tau( 2) = ( 0.0000000 0.2500000 0.3832200 ) > 3 O tau( 3) = ( 0.0000000 0.2500000 0.2180200 ) > > I tried setting ibrav = 8, > celldm(1)=a (bohr), > celldm(2)=b/a, > celldm(3)=c/a > > and I got this message in the output > > ortho sub-group = 2* 2 procs > > warning: symmetry operation # 2 not allowed. fractional translation: > 0.0000000 0.3862661 0.0000000 in crystal coordinates > warning: symmetry operation # 7 not allowed. fractional translation: > 0.0000000 0.3862661 0.0000000 in crystal coordinates > > Is the ibrav value not appropriate for the Bmmb space group? Can anybody > kindly help me? > Very best, > > Giacomo Giorgi, > PhD. Tokyo University. > > > _______________________________________________ > 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/20101129/0b9a641c/attachment.htm From elie.moujaes at hotmail.co.uk Mon Nov 29 16:41:46 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 29 Nov 2010 15:41:46 +0000 Subject: [Pw_forum] wannier90.x missing In-Reply-To: References: , Message-ID: Thanks for the reply.. I have tried make w90 before yes but it stopped giving me an error: cp: cannot create regular file `.../wannier90-1.2/make.sys` : no such file or directory make[1]: *** w90 error 1 make[1]: /espresso-4.2/plugins Regards Elie Moujaes From: sclauzer at sissa.it Date: Mon, 29 Nov 2010 15:12:17 +0100 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] wannier90.x missing Have you tried with the following? make w90 BTW, if you simply type make, you'll get a list of all possible targets and what will be built for each of them GS Il giorno 29/nov/2010, alle ore 14.32, Elie Moujaes ha scritto: Dear all, I am using the wannier functions to get the band structure in bilayer graphene. in expresso-4.2, I found all the executables (pw2wannier90.x, wannier_plot.x, etc..) except the wannier90.x executable that I need. I downloaded the folder W90 from the QE site and I found the the wannier90.f90 program. I tried to form the executable by tping: g95 wannier.f90 -o wannier but I got some errors. Is it possible to let me know where I can find the executable or how to form it given that I have the .f90 file. Regards Elie Moujaes University of Nottingham NG7 2RD UK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101129/6ec512c2/attachment.htm From sclauzer at sissa.it Mon Nov 29 17:00:32 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 29 Nov 2010 17:00:32 +0100 Subject: [Pw_forum] wannier90.x missing In-Reply-To: References: , Message-ID: <762EC8C9-7F13-4C25-A1B1-7D8A683A961D@sissa.it> I suppose that you must first download the wannier90 plugin from the qe-forge website http://qe-forge.org/frs/?group_id=10 put it in the right place and the retry. GS Il giorno 29/nov/2010, alle ore 16.41, Elie Moujaes ha scritto: > Thanks for the reply.. > > I have tried make w90 before yes but it stopped giving me an error: > > cp: cannot create regular file `.../wannier90-1.2/make.sys` : no such file or directory > make[1]: *** w90 error 1 > make[1]: /espresso-4.2/plugins > > Regards > > Elie Moujaes > > > > > From: sclauzer at sissa.it > Date: Mon, 29 Nov 2010 15:12:17 +0100 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] wannier90.x missing > > Have you tried with the following? > > make w90 > > BTW, if you simply type make, you'll get a list of all possible targets and what will be built for each of them > > GS > > Il giorno 29/nov/2010, alle ore 14.32, Elie Moujaes ha scritto: > > Dear all, > > I am using the wannier functions to get the band structure in bilayer graphene. in expresso-4.2, I found all the executables (pw2wannier90.x, wannier_plot.x, etc..) except the wannier90.x executable that I need. I downloaded the folder W90 from the QE site and I found the the wannier90.f90 program. I tried to form the executable by tping: > > g95 wannier.f90 -o wannier but I got some errors. > > Is it possible to let me know where I can find the executable or how to form it given that I have the .f90 file. > > Regards > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > ? 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 ? 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/20101129/ea297469/attachment-0001.htm From elie.moujaes at hotmail.co.uk Mon Nov 29 18:20:17 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 29 Nov 2010 17:20:17 +0000 Subject: [Pw_forum] wannier90.x missing In-Reply-To: <762EC8C9-7F13-4C25-A1B1-7D8A683A961D@sissa.it> References: , , , , <762EC8C9-7F13-4C25-A1B1-7D8A683A961D@sissa.it> Message-ID: Thanks again for ur help. I redownloaded the whole .tar file for wannier and untarred it and when I tried the command make wannier, I got an error : entering directory 'espresso-4.2/..../wannier90-1.2/src' ifort -O2 -c constants.f90 make [1] ifort command not found mak[1] *** [constants.o] error 127 make[1] leaving directory 'espresso-4.2/..../wannier90-1.2/src' make: *** [wannier] error 2 presumably related to the compiler (ifort which I dont have). I am using a cygwin interface to execute LIUNX commands. I guess the solution is to change the compiler command but from where? sorry for my limited knowledge about UNIX regards Elie Moujaes From: sclauzer at sissa.it Date: Mon, 29 Nov 2010 17:00:32 +0100 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] wannier90.x missing I suppose that you must first download the wannier90 plugin from the qe-forge website http://qe-forge.org/frs/?group_id=10 put it in the right place and the retry. GS Il giorno 29/nov/2010, alle ore 16.41, Elie Moujaes ha scritto: Thanks for the reply.. I have tried make w90 before yes but it stopped giving me an error: cp: cannot create regular file `.../wannier90-1.2/make.sys` : no such file or directory make[1]: *** w90 error 1 make[1]: /espresso-4.2/plugins Regards Elie Moujaes From: sclauzer at sissa.it Date: Mon, 29 Nov 2010 15:12:17 +0100 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] wannier90.x missing Have you tried with the following? make w90 BTW, if you simply type make, you'll get a list of all possible targets and what will be built for each of them GS Il giorno 29/nov/2010, alle ore 14.32, Elie Moujaes ha scritto: Dear all, I am using the wannier functions to get the band structure in bilayer graphene. in expresso-4.2, I found all the executables (pw2wannier90.x, wannier_plot.x, etc..) except the wannier90.x executable that I need. I downloaded the folder W90 from the QE site and I found the the wannier90.f90 program. I tried to form the executable by tping: g95 wannier.f90 -o wannier but I got some errors. Is it possible to let me know where I can find the executable or how to form it given that I have the .f90 file. Regards Elie Moujaes University of Nottingham NG7 2RD UK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ? 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 ? 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101129/649d663d/attachment.htm From giannozz at democritos.it Mon Nov 29 18:22:20 2010 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 29 Nov 2010 18:22:20 +0100 Subject: [Pw_forum] wannier90.x missing In-Reply-To: References: , , , , <762EC8C9-7F13-4C25-A1B1-7D8A683A961D@sissa.it> Message-ID: <4CF3E14C.5060506@democritos.it> re-run configure -- Paolo Giannozzi, Democritos and University of Udine, Italy From sama at ns.dcci.unipi.it Mon Nov 29 18:49:00 2010 From: sama at ns.dcci.unipi.it (sama at ns.dcci.unipi.it) Date: Mon, 29 Nov 2010 18:49:00 +0100 Subject: [Pw_forum] q2r and electron-phonon interaction Message-ID: Hi, I'm trying to calculate the electron-phonon interaction for a single graphene sheet. I took as a reference the example 07 given in the distribution and modified it accordingly. When arriving to run q2r.x, I have the following issue: # At line 357 of file q2r.f90 (unit = 51, file = 'a2Fq2r.51') # Fortran runtime error: Bad real number in item 1 of list input Of course, this error does not display when I set la2F=.false. in file q2r.in. Any suggestion? Samantha From elie.moujaes at hotmail.co.uk Mon Nov 29 19:08:07 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 29 Nov 2010 18:08:07 +0000 Subject: [Pw_forum] wannier90.x missing In-Reply-To: <4CF3E14C.5060506@democritos.it> References: , , , , , , , <762EC8C9-7F13-4C25-A1B1-7D8A683A961D@sissa.it>, , <4CF3E14C.5060506@democritos.it> Message-ID: Thanks very much...I missed that..sorry :) Thank you Regards > Date: Mon, 29 Nov 2010 18:22:20 +0100 > From: giannozz at democritos.it > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] wannier90.x missing > > re-run configure > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101129/46dccb4c/attachment.htm From w2agz at w2agz.com Mon Nov 29 20:06:59 2010 From: w2agz at w2agz.com (W2AGZ) Date: Mon, 29 Nov 2010 11:06:59 -0800 Subject: [Pw_forum] T>0 DFT Message-ID: <043d01cb8ff8$9b135d30$d13a1790$@w2agz.com> I'm sure several in the QE community have seen Helmut Eschrig's recent paper in PRB followed by Emil Prodan's Viewpoint commentary in Physics. Both can be found at http://physics.aps.org/viewpoint-for/10.1103/PhysRevB.82.205120. On the face of it, Eschrig's conclusions appear to be good news for DFT based on plane-wave representations such as QE, but I'd like to hear other views as well. As I believe the electron-phonon interaction depends on the functional derivative of the charge density (or equivalent potential)(see the conclusions in the PRB paper), is it indeed good news for extending the QE package to include e-p extensions to cover LDA+U, a tool I'd dearly like to have? I'm here at Fall MRS in Boston, and this morning there was an experimental talk concluding Si nanowires thinner than 5 nm were unstable (W2.5). Seems like a good QE exercise for some ambitious student out there. Paul Grant IBM Research Staff Member Emeritus -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101129/309f125a/attachment.htm From eyvaz_isaev at yahoo.com Mon Nov 29 20:17:22 2010 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 29 Nov 2010 11:17:22 -0800 (PST) Subject: [Pw_forum] q2r and electron-phonon interaction In-Reply-To: References: Message-ID: <253975.48718.qm@web65705.mail.ac4.yahoo.com> Hi, Most likely, you have a misprinted number. Please have a look at a2Fq2r.51 file to see if there is something like NaN or ***********. Please also provide your affiliation. 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: "sama at ns.dcci.unipi.it" To: pw_forum at pwscf.org Sent: Mon, November 29, 2010 6:49:00 PM Subject: [Pw_forum] q2r and electron-phonon interaction Hi, I'm trying to calculate the electron-phonon interaction for a single graphene sheet. I took as a reference the example 07 given in the distribution and modified it accordingly. When arriving to run q2r.x, I have the following issue: # At line 357 of file q2r.f90 (unit = 51, file = 'a2Fq2r.51') # Fortran runtime error: Bad real number in item 1 of list input Of course, this error does not display when I set la2F=.false. in file q2r.in. Any suggestion? Samantha _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From sama at ns.dcci.unipi.it Mon Nov 29 22:59:12 2010 From: sama at ns.dcci.unipi.it (sama at ns.dcci.unipi.it) Date: Mon, 29 Nov 2010 22:59:12 +0100 Subject: [Pw_forum] q2r and electron-phonon interaction In-Reply-To: <253975.48718.qm@web65705.mail.ac4.yahoo.com> References: <253975.48718.qm@web65705.mail.ac4.yahoo.com> Message-ID: Hi, I checked and in file a2Fq2r.51 there are no misprinted number. In line 358 of code q2r.f90 is read the variable *nstar*, which for count_q=2 takes the value nstar=3. In the next subroutine read_gamma the code expects then a series of information dimensioned 3, while actually in file a2Fq2r.51 the series is dimensioned 6. In this way, in the next count_q, the code does not find vriables deg, ef and dosscf, and then stops giving the reported error. The file a2Fq2r.51 is produced by QE, following the instructions. I hope the report is clear enough. Thanks for any suggestion, Samantha ----------------------------------------------------- Samantha Bruzzone Dept. of Electronic Engineering Pisa University, Italy > Hi, > > Most likely, you have a misprinted number. Please have a look at > a2Fq2r.51 file > to see if there is something like NaN or ***********. > > Please also provide your affiliation. > > 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: "sama at ns.dcci.unipi.it" > To: pw_forum at pwscf.org > Sent: Mon, November 29, 2010 6:49:00 PM > Subject: [Pw_forum] q2r and electron-phonon interaction > > > Hi, > > I'm trying to calculate the electron-phonon interaction for > a single graphene sheet. > I took as a reference the example 07 given in the distribution and > modified > it accordingly. > When arriving to run q2r.x, I have the following issue: > > # At line 357 of file q2r.f90 (unit = 51, file = 'a2Fq2r.51') > # Fortran runtime error: Bad real number in item 1 of list input > > Of course, this error does not display when I set la2F=.false. in file > q2r.in. > > Any suggestion? > > Samantha > > > _______________________________________________ > 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 wumindt2 at zju.edu.cn Tue Nov 30 00:59:13 2010 From: wumindt2 at zju.edu.cn (wumindt2) Date: Tue, 30 Nov 2010 07:59:13 +0800 Subject: [Pw_forum] wannier function Message-ID: Dearl all, I met an error when i try to calculate the wannier function of Si. The error is "Exiting....... param_get_projection: too many projections defined". What's the reason of this error? The input wannier.win file is shown below: "num_bands = 12 num_iter = 100 dis_num_iter = 100 iprint = 2 num_dump_cycles = 10 num_print_cycles = 10 length_unit = bohr num_wann = 4 dis_froz_max = 6.5 dis_win_max = 6.5 !! !! Bond-centred s-orbitals begin projections Si:sp3 end projections begin unit_cell_cart bohr -5.10 0.00 5.10 0.00 5.10 5.10 -5.10 5.10 0.00 end unit_cell_cart begin atoms_frac Si -0.25 0.75 -0.25 Si 0.00 0.00 0.00 end atoms_frac mp_grid = 4 4 4 begin kpoints ........ " In the wannier user-guide, there are several options for the defination of the projection. Such as "Si:l=0;l=1;l=2" , " Si: sp3", or "f=-0.125,-0.125, 0.375:s". So how to choose these different options? Thanks for any help. Min Wu 2010-11-29 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101130/b24b43ee/attachment.htm From spakinform at gmail.com Tue Nov 30 07:34:32 2010 From: spakinform at gmail.com (soroush pakseresht) Date: Tue, 30 Nov 2010 15:34:32 +0900 Subject: [Pw_forum] Pseudopotential for Nd Message-ID: Dear all I'm going to do GGA and GGA+SO calculations for some Nd based intermetallic compounds. However, there seems to be no pseudopotential available for Nd on pwscf homepage . I was wondering if somebody in this forum could kindly provide me with a reliable ultrasoft (or PAW) pseudopotential (possibly made using PBE) for Nd? Thanking you in advance, Soroush -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101130/d320729b/attachment.htm From spakinform at gmail.com Tue Nov 30 13:18:45 2010 From: spakinform at gmail.com (soroush pakseresht) Date: Tue, 30 Nov 2010 21:18:45 +0900 Subject: [Pw_forum] Pseudopotential for Nd Message-ID: Dear all I'm going to do GGA and GGA+SO calculations for some Nd based intermetallic compounds. However, there seems to be no pseudopotential available for Nd on pwscf homepage . I was wondering if somebody in this forum could kindly provide me with a reliable ultrasoft (or PAW) pseudopotential (possibly made using PBE) for Nd? Thanking you in advance, Soroush -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101130/e17bd9e7/attachment.htm From elie.moujaes at hotmail.co.uk Tue Nov 30 13:56:09 2010 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Tue, 30 Nov 2010 12:56:09 +0000 Subject: [Pw_forum] pw2wannier error Message-ID: Dear all, I am applying the pw2wannier90.x executable to bilayer graphene but I am getting the very famous error: Checking info from wannier.nnkp file Something wrong! rlatt(i,j) = 4.536660026280493 at(i,j)= 5.3304100000000005 I am using the version v3.2.3 of wannier90 so the precision to which the lattice vectors are written should be fine. The strange thing is that the values are not that close to each other. You will find attcahed the scf and the win files. Regards Elie Moujaes University of Nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... 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