[Pw_forum] compiling with ifort
My suggestion is that you should put a list in the web contains which packages have been tested by you with which compiler and O.S., Or in which combination of package compiler and O.S. you know it is not working (at least for the examples you give). this will reduce all that kind of mails. thanks, eitan. -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130102/23928eff/attachment.html
[Pw_forum] compiling with ifort
On Wed, Jan 2, 2013 at 9:17 PM, eitan eidelstein wrote: > My suggestion is that you should put a list in the web contains which > packages have been tested by you with which compiler and O.S., Or in which > combination of package compiler and O.S. you know it is not working (at > least for the examples you give). this will reduce all that kind of mails. this is a good idea in theory, but doesn't work in practice. this information is already part of the Q-E documentation, but nobody seems to be reading it (as is confirmed by many other frequently re-asked questions that are well documented). http://www.quantum-espresso.org/wp-content/uploads/Doc/user_guide/node14.html axel. > thanks, eitan. > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] core-relax in hyperfine calculation (GIPAW)
Dear Jarkko, I changed the radial integration bound in 5.0.1. As a consequence results are slightly different from 4.3.2. The reason is that in 4.3.1 I got extremely bad HFCC for elements on the right columns in the periodic table (like oxygen). However the core-relaxation is still not accurate for such elements, and I'm investigating other relaxation schemes. Regarding metallic systems, yes for EFG/hyperfine, not yet for NMR/EPR. Best wishes, Davide On 01/02/2013 02:35 PM, Jarkko V?h?kangas wrote: > Hi, > > I'm starting to use QE 5.0.2 and corresponding GIPAW. I hThe compilation went > smoothly but I'm getting different core-relax contribution compared to GIPAW > 4.3.1 in H2O+ example. > > So, could tell me that which is correct one? Additionally, is it possible for > current GIPAW to calculate NMR/EPR properties to "metallic-like" systems > using smearing? > > Thanks and Regards > Jarkko V?h?kangas (PhD cand.) > University of oulu, Finland >
[Pw_forum] failure in trying to compute U
Hi all, I am trying to compute U for Mo in a molybdenum bronze, using Cococcioni's method. The calculation crashes. A file CRASH results with this content: %% task # 9 reading namelist system %% Standard output shows, after lines ... Max number of k-points (npk) = 4 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... Reading input from standard input these lines (repeated as many times as parallel processes involved): %% Error in routine read_namelists (17): reading namelist system %% stopping ... My input file is &control title = 'a0.05' calculation = 'scf' restart_mode='from_scratch' verbosity = 'high', prefix='namo6o17', etot_conv_thr = 2.0D-6 / &system ibrav=14, celldm(1)= 5.5325, celldm(2)=0.9974, celldm(3)=2.3467, celldm(4)=0.0, celldm(5)=0.0009076, celldm(6)=-0.49868442, nat= 24, ntyp= 4, ecutwfc=30.0, ecutrho=125.0, nbnd= 150, nspin=2, starting_magnetization(1)= 0.1, starting_magnetization(2)=-0.5, starting_magnetization(3)= 0.0, starting_magnetization(4)= 0.0, occupations='smearing', smearing='mp', degauss=0.01, lda_plus_u = .true., Hubbard_U(1)=1.d-8, Hubbard_U(2)=1.d-8, # (values used in the previous run) Hubbard_alpha(1)= 0.0, # this is alpha 0 applied on atom 1 (Mo) Hubbard_alpha(2)= 0.05, # this is alpha, only applied on atom 2 (also Mo) / &electrons diagonalization='cg' startingpot = 'namo6o17' # startingwfc = 'namo6o17' # (the corresponding files from the previous run are copied in the main working directory) diago_thr_init = 1.59E-10 # (from the previous run) mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-9, / ATOMIC_SPECIES ...(pseudopotentials for all species) ATOMIC_POSITIONS crystal (names and coordinates of 24 atoms) K_POINTS automatic 4 4 4 0 0 0 ?Any hint on the cause of the problem? Thanks, -- Jos? C. Conesa Instituto de Cat?lisis y Petroleoqu?mica, CSIC Marie Curie 2, Cantoblanco 28049 Madrid - Spain Tel. +34-915854766
[Pw_forum] Can QE outputs velocities in MD implemented by scf ?
Hello all, I am using scf to run the BO molecular dynamics (scf.x, not the cp.x code which uses CPMD). However, I did not see the output of of velocities. The .output files gives updated forces and coordinates, but there is no information about velocity. In the .save file, I also did not find it. I may get the velocity from updated coordinates in each step but that is a crude approximation. I wonder whether scf MD could output the velocity or not. Hopefully I just do not know this setup. Best, Tian -- Lan, Tian Ph.D. Candidate, Department of Applied Physics and Materials Science California Institute of Technology, Caltech M/C 138-78, Pasadena, CA, 91125 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130102/de44d1a4/attachment.html
[Pw_forum] Pseudo directory error
On Mon, Dec 31, 2012 at 4:30 AM, Bramha Pandey wrote: > Thanks Dear Axel and Ari for your elaborate explanation about non commercial > and free software. But we can see easiness compilation of all packages which > is included in espresso and there may be existing some problem with gfortron > which like me users can not check and correct where the problem is existing. > for example QHA package in > espresso is compiled only by ifort. what has that to do with the price of rice in china? ;) if you want to use the intel compiler, you need a valid license, and - as discussed - the non-commercial license does not apply to people working in academia. the fact that you have a broken gfortran installation on your machine doesn't justify using software in violation of its license. am i allowed to steal your car, because i couldn't pay for a cab?? apart from that, i contend that the code in question *does* compile correctly with gfortran, you probably simply need to update to a more recent version. if you believe, that the code itself is in error, please provide *proper* proof and report it to the gfortran or quantum espresso developers, depending on where you confirm the bug. axel. > > On Mon, Dec 31, 2012 at 12:16 AM, Ari P Seitsonen > wrote: >> >> >> Dear Branha Pandey, >> >> Axel managed to write the same things that I was planning to state as >> well - I know that one can download it without paying any money, but one has >> to accept the license agreements, and most scientists do not fulfill them. >> I'm also taking this as an academic "obligation": Since most of us indeed >> prefer free software, it would be better to use the "free" variant - in this >> case 'gcc'/'gfortran' - and help its developers improve its quality by >> reporting the remaining bugs to them. In this case the problem is probably >> already solved in the never versions of 'gfortran' though. >> >> Greetings and All the Best in 2013!, >> >> >>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 Sun, 30 Dec 2012, Bramha Pandey wrote: >> >>> Dear Ari, >>> you can downloaded ifortron for non-commercial purposes without any >>> restriction with license agreement. >>> >>> On Sun, Dec 30, 2012 at 11:35 PM, Ari P Seitsonen >>> >>> wrote: >>> >>> Dear Deepika, >>> >>> Newer versions of 'gfortran' should also work I believe. The >>> license agreements of the Intel compiler are quite restrictive - >>> well I guess most of the people either do not know or actively >>> ignore them. >>> >>> #> gfortran -v >>> >>> shows you which version you have installed on your machine. >>> >>> Greetings and Good Luck, >>> >>> 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 > > > > > -- > Thanks and Regards > Bramha Prasad Pandey > Indian School of Mines(ISM) > Dhanbad, INDIA. > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] execution problem when compiling with openmp and ifort
Hello, If I try to use QE.5.0.2 compiled with MPICC=icc CC=icc F90=ifort MPIF90=mpiifort F77=ifort MPIF77=ifort, all examples are o.k.. If I add --enable-openmp to the configure flags then examples 6,7,11 crashes: /home/eeitan/QE/espresso-5.0.2/PHonon/examples/example06 : starting This example shows how to use ph.x to calculate the phonons at X and Gamma of fcc-Pt using fully relativistic pseudo-potential and including spin-orbit coupling. executables directory: /home/eeitan/QE/espresso-5.0.2/bin pseudo directory: /home/eeitan/QE/espresso-5.0.2/pseudo temporary directory: /home/eeitan/tmp checking that needed directories and files exist... done running pw.x as: /home/eeitan/QE/espresso-5.0.2/bin/pw.x -nband 1 -ntg 1 running ph.x as: /home/eeitan/QE/espresso-5.0.2/bin/ph.x -nband 1 -ntg 1 cleaning /home/eeitan/tmp... done running the scf calculation for Pt with spin-orbit coupling.../home/eeitan/QE/espresso-5.0.2/bin/pw.x: symbol lookup error: /opt/intel/l_ics_2013.0.028/mkl/lib/inte l64/libmkl_intel_thread.so: undefined symbol: __kmpc_master Error condition encountered during test: exit status = 127 Aborting /home/eeitan/QE/espresso-5.0.2/PHonon/examples/example07 : starting This example tests pw.x and ph.x in several cases that require the noncollinear or the spin-orbit part of the code together with the gga. ph.x is used to calculate the phonons at X and Gamma of fcc-Pt with gga, and to calculate the phonons at X and Gamma of fcc-Ni to test the magnetic case with gga with or without spin-orbit executables directory: /home/eeitan/QE/espresso-5.0.2/bin pseudo directory: /home/eeitan/QE/espresso-5.0.2/pseudo temporary directory: /home/eeitan/tmp checking that needed directories and files exist... done running pw.x as: /home/eeitan/QE/espresso-5.0.2/bin/pw.x -nband 1 -ntg 1 running ph.x as: /home/eeitan/QE/espresso-5.0.2/bin/ph.x -nband 1 -ntg 1 cleaning /home/eeitan/tmp... done running scf pw.x for Pt with gga-pbe and spin-orbit coupling.../home/eeitan/QE/espresso-5.0.2/bin/pw.x: symbol lookup error: /opt/intel/l_ics_2013.0.028/mkl/lib/int el64/libmkl_intel_thread.so: undefined symbol: __kmpc_master Error condition encountered during test: exit status = 127 Aborting /home/eeitan/QE/espresso-5.0.2/PHonon/examples/example11 : starting This example calculates the phonon modes of relativistic Au at the gamma and X points with PAW in the noncollinear and spin-orbit case. executables directory: /home/eeitan/QE/espresso-5.0.2/bin pseudo directory: /home/eeitan/QE/espresso-5.0.2/pseudo temporary directory: /home/eeitan/tmp checking that needed directories and files exist... done running pw.x as: /home/eeitan/QE/espresso-5.0.2/bin/pw.x -nband 1 -ntg 1 running ph.x as: /home/eeitan/QE/espresso-5.0.2/bin/ph.x -nband 1 -ntg 1 cleaning /home/eeitan/tmp... done running the scf calculation for Au with PAW and spin-orbit... done running ph.x for Au at Gamma with PAW and spin-orbit... done running ph.x for Au at X with PAW and spin-orbit.../home/eeitan/QE/espresso-5.0.2/bin/ph.x: symbol lookup error: /opt/intel/l_ics_2013.0.028/mkl/lib/intel64/libmkl_ intel_thread.so: undefined symbol: __kmpc_master Error condition encountered during test: exit status = 127 Aborting thanks in addvance, Uri (Ben Gurion Univ. Israel). -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130102/5991b247/attachment.html
[Pw_forum] core-relax in hyperfine calculation (GIPAW)
Hi, I'm starting to use QE 5.0.2 and corresponding GIPAW. I hThe compilation went smoothly but I'm getting different core-relax contribution compared to GIPAW 4.3.1 in H2O+ example. Output from v.5.0.2: PRINCIPAL AXIS OF THE DIPOLAR COUPLINGS: O1Axx= 57.6603axis=( 0.99 0.001107 0.00) O1Ayy= 59.4428axis=( -0.001107 0.99 0.06) O1Azz= -117.1032axis=( 0.00 -0.06 1.00) H2Axx= -7.1733axis=( 0.00 -0.02 1.00) H2Ayy= -23.8786axis=( 0.554299 -0.832318 -0.02) H2Azz= 31.0518axis=( 0.832318 0.554299 0.01) H3Axx= -7.1727axis=( 0.00 -0.02 1.00) H3Ayy= -23.8779axis=( -0.554302 -0.832315 -0.02) H3Azz= 31.0505axis=( 0.832315 -0.554302 -0.01) ISOTROPIC (FERMI-CONTACT) COUPLINGS WITHOUT ZORA: USING CORE-RELAXATION METHOD: PRB 76, 035124 (2007) Warning: core-relaxation is an experimental feature - spin-densities in bohrradius^-3 - bareGIPAW core-relax total O10.0066670.337362 -0.2034290.140600 H2 -0.008880 -0.0062900.00 -0.015170 H3 -0.008875 -0.0062860.00 -0.015161 - Fermi contact in G - bareGIPAW core-relax total O1 -1.442135 -72.971400 44.001759 -30.411776 H2 -14.163000 -10.0319590.00 -24.194959 H3 -14.155300 -10.0264950.00 -24.181794 and form 4.3.1: PRINCIPAL AXIS OF THE DIPOLAR COUPLINGS: O1Axx= 57.6608axis=( 0.99 0.001114 0.00) O1Ayy= 59.4429axis=( -0.001114 0.99 0.05) O1Azz= -117.1037axis=( 0.00 -0.05 1.00) H2Axx= -7.1733axis=( 0.00 -0.02 1.00) H2Ayy= -23.8785axis=( 0.554300 -0.832317 -0.01) H2Azz= 31.0518axis=( 0.832317 0.554300 0.01) H3Axx= -7.1726axis=( 0.00 -0.02 1.00) H3Ayy= -23.8778axis=( -0.554303 -0.832315 -0.01) H3Azz= 31.0505axis=( 0.832315 -0.554303 -0.01) SPIN DENSITIES IN bohrradius^-3 WITHOUT ZORA: Warning: core-relaxation is an experimental feature bareGIPAW core-relax total O10.0066670.337358 -0.2928870.051138 H2 -0.008880 -0.0062900.00 -0.015169 H3 -0.008875 -0.0062860.00 -0.015161 ISOTROPIC (FERMI-CONTACT) COUPLINGS WITHOUT ZORA: Warning: core-relaxation is an experimental feature bareGIPAW core-relax total O1 -1.442085 -72.970443 63.351469 -11.061059 H2 -14.162531 -10.0315520.00 -24.194083 H3 -14.154765 -10.0260400.00 -24.180805 So, could tell me that which is correct one? Additionally, is it possible for current GIPAW to calculate NMR/EPR properties to "metallic-like" systems using smearing? Thanks and Regards Jarkko V?h?kangas (PhD cand.) University of oulu, Finland
[Pw_forum] Titanium Pseudopotential
Dear All, I am confused about occupations in Ti pseudopotential (no matter it is pbe, blyp, or anything else). In the UPF file, it is written like this : nl pn? l?? occ? 3S? 3? 0? 2.00? 3P? 3? 1? 6.00? 4S? 4? 0? 2.00? 3D? 3? 2? 1.00? Everyone knows that electron configuration of Ti is [Ar] 4s(2) 3d(2), so my questions are : 1) Why occupation of 3d in the UPF is 1, not 2 instead (according to Ti electron conf.) ? 2) In case I want to insert ion Ti4+ into my crystal system, how could I assure that the Ti pseudopotential is in 4+ ion state, not 3+ state ? Best regards, Iwan D. ? *** Iwan Darmadi ?Undergrad.Student - Department of Physics ?Universitas Indonesia -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130102/94ef7e5f/attachment.html
[Pw_forum] failure in trying to compute U
Hi Jose, You may use ! instead of # in your input. bests On Wed, Jan 2, 2013 at 12:35 PM, "Jos? C. Conesa" wrote: > # -- Jia Chen webpage: www.princeton.edu/~jiachen
[Pw_forum] what code actually loads xplor files? The edmplugin does not seem to execute and I can't find a py file.
sorry wrong address arrgggh can you please delete that... > From: marchywka at hotmail.com > To: pw_forum at pwscf.org > Subject: what code actually loads xplor files? The edmplugin does not seem to > execute and I can't find a py file. > Date: Wed, 2 Jan 2013 10:59:13 -0500 > > > > I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I > wanted to debug the > problem but can't get my debug statements to execute. The only thing that > greps for "xplor" > is a few pymol modules and plugin called edmplugin. If I rebuild the plugin > and relink pymol > nothing seems to change. Is this the right code? I also wanted to add a > loader for other > formats of density or vector fields and maybe do some rendering ( I have an > old viewer I wrote > with glut and thought I may be able to salvage parts of that for use here). > > Thanks. > > > > note new address > Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. > formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)<- leave > message 989-348-4796 (P)<- emergency > > >
[Pw_forum] what code actually loads xplor files? The edmplugin does not seem to execute and I can't find a py file.
I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the problem but can't get my debug statements to execute. The only thing that greps for "xplor" is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol nothing seems to change. Is this the right code? I also wanted to add a loader for other formats of density or vector fields and maybe do some rendering ( I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency
[Pw_forum] Error in 'nscf' calculation " from cdiaghg : diagonalization (ZHEGV*) failed"
Hi, Everyone, I get this error in my nscf calculation: from cdiaghg : error #99 1069 diagonalization (ZHEGV*) failed . I am basically running a TiO2 bulk calculation. The scf calculation runs fine. But I get the above error in the nscf calculation. The only difference in the nscf calculation is that I increase the number of bands to 100. Here is the input file for the scf calculation: &control prefix='Rutile', pseudo_dir='/scratch/scratchdirs/kopinjol/Calculations/Projects/TiO2/TiO 2/Rutile/Yambo', outdir='/scratch/scratchdirs/kopinjol/Calculations/Projects/TiO2/TiO2/Ru tile/Yambo/SAVE', / &system ibrav=6, celldm(1)=8.674, celldm(3)=0.645, nat=6, ntyp=2, ecutwfc = 50.0, occupations='fixed', nspin=1, nbnd=20, force_symmorphic=.true., nosym=.false., / &electrons diago_full_acc = .true., diago_thr_init = 1.0d-6, diagonalization='cg', / ATOMIC_SPECIES Ti 47.867 Ti.UPF O 15.99 O.UPF ATOMIC_POSITIONS bohr Ti0. 0. 0. Ti6.13831976 0. 2.79501944 O-2.38657872 0. 2.79501944 O 2.38657872 0. 2.79501944 O 6.13831976-2.38657872 0. O 6.13831976 2.38657872 0. K_POINTS automatic 8 8 8 0 0 0 And here is the input file for the nscf calculation: &control calculation='nscf' prefix='Rutile', pseudo_dir='/scratch/scratchdirs/kopinjol/Calculations/Projects/TiO2/TiO 2/Rutile/Yambo', outdir='/scratch/scratchdirs/kopinjol/Calculations/Projects/TiO2/TiO2/Ru tile/Yambo/SAVE', wf_collect=.true., verbosity='high', / &system ibrav=6, celldm(1)=8.674, celldm(3)=0.645, nat=6, ntyp=2, ecutwfc = 50.0, occupations='fixed', nspin=1, nbnd=100, force_symmorphic=.true., nosym=.false., / &electrons diago_full_acc = .true., diago_thr_init = 1.0d-4, diagonalization='cg', / ATOMIC_SPECIES Ti 47.867 Ti.UPF O 15.99 O.UPF ATOMIC_POSITIONS bohr Ti0. 0. 0. Ti6.13831976 0. 2.79501944 O-2.38657872 0. 2.79501944 O 2.38657872 0. 2.79501944 O 6.13831976-2.38657872 0. O 6.13831976 2.38657872 0. K_POINTS automatic 8 8 8 0 0 0 I would really appreciate any help. Thanks in advance, Kopinjol Baishya Graduate Student, Materials Modelling Group, Deptt. of Physics, University of Illinois, Chicago, IL 60607 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130102/adfc04e5/attachment.html
