Re: [QE-users] QE-6.6 Error in routine scale_sym_ops (4): incompatible FFT grid
On Mon, Nov 30, 2020 at 7:19 AM rekha sharma wrote: > > https://gitlab.com/QEF/q-e/-/merge_requests/1069 > > Could someone please help me what should I do to resolve this? > you should use symmetric atomic positions and cell vectors, not "quasi-symmetric" ones. Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Another question about continue a SCF or Optimization(vc-relax) job
On Sun, Nov 29, 2020 at 9:26 AM lisenzhiboda wrote: > In* opt1tc1 *I set restart_mode = "restart" in the input file > once again: restart_mode='restart' can be used ONLY to continue an interrupted calculation. See also this: https://gitlab.com/QEF/q-e/-/issues/252 In* opt1tc2* I just copy ATOMIC_POSITIONS and CELL_PARAMETERS data from > *opt1 *output file's final structure and set startingwfc = "file" . > then I got total energy = -3150.31950217 Ry . It's normal, > but I think the program didn't got the correct wavefunction for initial > guess. > you have to read the initial charge density as well: startingpot='file', or else the self-consistency with not-so-good starting charge will spoil starting good wavefunctions Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Installation problem regarding interoperability
It's a bug of gfortran versions < 4.9: see https://gcc.gnu.org/bugzilla/show_bug.cgi?id=50269 Paolo On Wed, Nov 25, 2020 at 1:20 PM Arif Emre Yarimbiyik wrote: > Hi, > I am trying to install QE following the instructions at > quantum-espresso.org. > I do not have any problem at configuring, however I get a C > interoperability error at the make stage: > > "Error: Assumed-shape array 'zmat' at (1) cannot be an argument to the > procedure 'c_loc' because it is not C interoperable > xmltools.f90:797.18: > >cp = c_loc(zvec) " > > As far as I understand, this is a problem regarding Fortran’s > multidimensional array support. I have the latest version of gcc-gfortran > running, but apparently that does not help. > I would appreciate any suggestions for solving this issue. > Regards, > Dr A. Emre Yarimbiyik > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Information about WFC file format
Try this link: https://gitlab.com/QEF/q-e/-/wikis/Format-of-wfc-files I have removed "(draft)" from the title and it has disappeared in the file name as well. Paolo On Fri, Nov 20, 2020 at 4:49 PM Aaron Friesz wrote: > Thanks for your reply, however, when I click on the link I come to a page > that states that the git project has no wiki pages. > > On Fri, Nov 20, 2020 at 3:12 AM Paolo Giannozzi > wrote: > >> You may find some information here: >>https://gitlab.com/QEF/q-e/-/wikis/Format-of-wfc-files-(draft) >> <https://urldefense.com/v3/__https://gitlab.com/QEF/q-e/-/wikis/Format-of-wfc-files-(draft)__;!!LIr3w8kk_Xxm!6oB_BYb5tZYHcDnzIyZPavGTpwzq8lyLr0JkV5F-hTuC7anQ78zQc-oAL6PZzw$> >> >> Paolo >> ___ >> Quantum ESPRESSO is supported by MaX ( >> https://urldefense.com/v3/__http://www.max-centre.eu__;!!LIr3w8kk_Xxm!6oB_BYb5tZYHcDnzIyZPavGTpwzq8lyLr0JkV5F-hTuC7anQ78zQc-q8pRC2og$ >> ) >> users mailing list users@lists.quantum-espresso.org >> >> https://urldefense.com/v3/__https://lists.quantum-espresso.org/mailman/listinfo/users__;!!LIr3w8kk_Xxm!6oB_BYb5tZYHcDnzIyZPavGTpwzq8lyLr0JkV5F-hTuC7anQ78zQc-rF5wgL0g$ > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Information about WFC file format
You may find some information here: https://gitlab.com/QEF/q-e/-/wikis/Format-of-wfc-files-(draft) Paolo ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Understanding Output of atomic_proj.xml
Projwfc.x computes "the projection of band states over atomic orbitals". If you just need atomic orbitals, it's not what you need Paolo On Wed, Nov 18, 2020 at 10:15 AM Didarul Alam wrote: > Hi Everyone > > For one of my projects, I need to calculate atomic wavefunction. For that, > I have used projwfc.x and it generates atomic_proj.xml in the output files. > But now, unfortunately, I could not understand the output file. Does anyone > have any experience with atomic_proj.xml file? Any kind of help will be > highly appreciated. > > Best > Didarul Alam > Graduate Student > Department of Physics > University of Central Florida > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] wrong offset
On Thu, Nov 19, 2020 at 10:12 AM José C. Conesa wrote: > Error in routine offset_atom_wfc (1): > wrong offset > Which may be the reason? > V_ONCV_PBE_FR-1.9.UPF contains no atomic wavefunctions Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] error compile gipaw
That's a different story: there is no GIPAW version aligned to QE v.6.6 anyway On Wed, Nov 18, 2020 at 4:57 PM Sangho Chung wrote: > Yes Paolo. I had the same issue with make pw, pp and all, so I redefined > cpp and it worked. > > But for gipaw, it is not working unfortunately. > > Regards, > Sangho > > On 18 Nov 2020, at 18:54, Paolo Giannozzi wrote: > > Looks quite the same as this one: > > https://www.mail-archive.com/users@lists.quantum-espresso.org/msg38781.html > Paolo > > On Tue, Nov 17, 2020 at 7:25 PM Sangho Chung > wrote: > >> Hello QE user, >> >> I am new to QE, and started compiling today. >> >> There was an error when I was trying to compile gipaw. Please have a look >> below error message and let me know what should be done. >> >> Best regards, >> Sangho >> >> >> kl-19943:qe-6.6 chuns0b$ make gipaw >> test -d bin || mkdir bin >> ( cd clib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= all >> || exit 1 ) >> make[1]: Nothing to be done for `all'. >> cd install ; /Library/Developer/CommandLineTools/usr/bin/make -f >> extlibs_makefile libiotk >> if test ! -d ../S3DE; then \ >> (gzip -dc ../archive/iotk-1.2.beta.tar.gz | (cd ../; tar -xvf -)) ; \ >> if test -e Makefile_iotk; then \ >> (cp Makefile_iotk ../S3DE/iotk/src/Makefile); fi; \ >> if test -e iotk_config.h; then \ >> (cp iotk_config.h ../S3DE/iotk/include/iotk_config.h); fi; fi >> cd ../S3DE/iotk/src; /Library/Developer/CommandLineTools/usr/bin/make >> lib+util; >> make[2]: Nothing to be done for `lib+util'. >> cd ../bin; ln -fs ../S3DE/iotk/tools/iotk .; \ >> ln -fs ../S3DE/iotk/src/iotk.x .; \ >> ln -fs ../S3DE/iotk/src/iotk_print_kinds.x .; \ >> # middle instruction needed for windows >> cd ../; rm -rf iotk ; ln -fs S3DE/iotk iotk >> cd install ; /Library/Developer/CommandLineTools/usr/bin/make -f >> extlibs_makefile libfox >> echo >> >> if test ! -d ../FoX; then \ >> mkdir ../FoX; \ >> (gzip -dc ../archive/fox.tgz | (cd ../FoX; tar -xvf -)); \ >> cd ../FoX/fox/; export FC=gfortran; export FCFLAGS=""; \ >> ./configure --prefix=/Users/chuns0b/QE/qe-6.6//FoX ;\ >> touch cp_test; \ >> if cp -p cp_test cp_test_1; then \ >> echo "cp -p works"; \ >> else \ >> find -type f | xargs sed -i 's/cp -p/cp/g'; \ >> fi; \ >> /Library/Developer/CommandLineTools/usr/bin/make install; cd ../; rm -fr >> fox;fi >> ( cd UtilXlib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= >> all || exit 1 ) >> make[1]: Nothing to be done for `all'. >> cd install ; /Library/Developer/CommandLineTools/usr/bin/make -f >> extlibs_makefile liblapack >> touch fake_liblapack.a >> rm fake_liblapack.a >> cd install ; /Library/Developer/CommandLineTools/usr/bin/make -f >> extlibs_makefile libcuda >> make[1]: Nothing to be done for `libcuda'. >> ( cd LAXlib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= >> all || exit 1 ) >> cpp -P -traditional -Uvector -D__FFTW -D__MPI -Duse_beef >> -I/Users/chuns0b/QE/qe-6.6//include >> -I/Users/chuns0b/QE/qe-6.6//FoX/finclude >> -I/Users/chuns0b/QE/qe-6.6//S3DE/iotk/include/ laxlib.h -o laxlib.fh >> ! >> ! Copyright (C) 2003-2013 Quantum ESPRESSO group >> ! This file is distributed under the terms of the >> ! GNU General Public License. See the file `License*laxlib.h:4:52: **warning: >> **missing terminating ' character [-Winvalid-pp-token]* >> ! GNU General Public License. See the file `License' >> * ^* >> ' >> ! in the root directory of the present distribution, >> ! or http://www.gnu.org/copyleft/gpl.txt . >> ! >>include 'laxlib_low.fh' >> include 'laxlib_mid.fh' >>include 'laxlib_hi.fh' >>include 'laxlib_param.fh' >> >>INTEGER, EXTERNAL :: ldim_block, ldim_cyclic, ldim_block_sca >> >> 1 warning generated. >> clang: *error: *no input files >> make[1]: *** [laxlib.fh] Error 1 >> make: *** [libla] Error 1 >> >> ___ >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu) >> users mailing list users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > __
Re: [QE-users] error compile gipaw
Looks quite the same as this one: https://www.mail-archive.com/users@lists.quantum-espresso.org/msg38781.html Paolo On Tue, Nov 17, 2020 at 7:25 PM Sangho Chung wrote: > Hello QE user, > > I am new to QE, and started compiling today. > > There was an error when I was trying to compile gipaw. Please have a look > below error message and let me know what should be done. > > Best regards, > Sangho > > > kl-19943:qe-6.6 chuns0b$ make gipaw > test -d bin || mkdir bin > ( cd clib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= all > || exit 1 ) > make[1]: Nothing to be done for `all'. > cd install ; /Library/Developer/CommandLineTools/usr/bin/make -f > extlibs_makefile libiotk > if test ! -d ../S3DE; then \ > (gzip -dc ../archive/iotk-1.2.beta.tar.gz | (cd ../; tar -xvf -)) ; \ > if test -e Makefile_iotk; then \ > (cp Makefile_iotk ../S3DE/iotk/src/Makefile); fi; \ > if test -e iotk_config.h; then \ > (cp iotk_config.h ../S3DE/iotk/include/iotk_config.h); fi; fi > cd ../S3DE/iotk/src; /Library/Developer/CommandLineTools/usr/bin/make > lib+util; > make[2]: Nothing to be done for `lib+util'. > cd ../bin; ln -fs ../S3DE/iotk/tools/iotk .; \ > ln -fs ../S3DE/iotk/src/iotk.x .; \ > ln -fs ../S3DE/iotk/src/iotk_print_kinds.x .; \ > # middle instruction needed for windows > cd ../; rm -rf iotk ; ln -fs S3DE/iotk iotk > cd install ; /Library/Developer/CommandLineTools/usr/bin/make -f > extlibs_makefile libfox > echo > > if test ! -d ../FoX; then \ > mkdir ../FoX; \ > (gzip -dc ../archive/fox.tgz | (cd ../FoX; tar -xvf -)); \ > cd ../FoX/fox/; export FC=gfortran; export FCFLAGS=""; \ > ./configure --prefix=/Users/chuns0b/QE/qe-6.6//FoX ;\ > touch cp_test; \ > if cp -p cp_test cp_test_1; then \ > echo "cp -p works"; \ > else \ > find -type f | xargs sed -i 's/cp -p/cp/g'; \ > fi; \ > /Library/Developer/CommandLineTools/usr/bin/make install; cd ../; rm -fr > fox;fi > ( cd UtilXlib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= > all || exit 1 ) > make[1]: Nothing to be done for `all'. > cd install ; /Library/Developer/CommandLineTools/usr/bin/make -f > extlibs_makefile liblapack > touch fake_liblapack.a > rm fake_liblapack.a > cd install ; /Library/Developer/CommandLineTools/usr/bin/make -f > extlibs_makefile libcuda > make[1]: Nothing to be done for `libcuda'. > ( cd LAXlib ; /Library/Developer/CommandLineTools/usr/bin/make TLDEPS= all > || exit 1 ) > cpp -P -traditional -Uvector -D__FFTW -D__MPI -Duse_beef > -I/Users/chuns0b/QE/qe-6.6//include > -I/Users/chuns0b/QE/qe-6.6//FoX/finclude > -I/Users/chuns0b/QE/qe-6.6//S3DE/iotk/include/ laxlib.h -o laxlib.fh > ! > ! Copyright (C) 2003-2013 Quantum ESPRESSO group > ! This file is distributed under the terms of the > ! GNU General Public License. See the file `License*laxlib.h:4:52: **warning: > **missing terminating ' character [-Winvalid-pp-token]* > ! GNU General Public License. See the file `License' > * ^* > ' > ! in the root directory of the present distribution, > ! or http://www.gnu.org/copyleft/gpl.txt . > ! >include 'laxlib_low.fh' >include 'laxlib_mid.fh' >include 'laxlib_hi.fh' >include 'laxlib_param.fh' > >INTEGER, EXTERNAL :: ldim_block, ldim_cyclic, ldim_block_sca > > 1 warning generated. > clang: *error: *no input files > make[1]: *** [laxlib.fh] Error 1 > make: *** [libla] Error 1 > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Sub optimal performance on 32 core AMD machine
On Tue, Nov 17, 2020 at 9:20 PM Pamela Whitfield wrote: Hyperthreading is necessary for the GPU version which works fine for DFTD2 > but not for DFTD3 - hence I use a CPU-only MPI-only version for the more > complex dispersion corrections. > If I remember correctly, there is no parallelization at all in DFT-D3 (while DFT-D2 is parallelized with both MPI and OpenMP) Paolo > My problems are probably very similar to Michal, a 2500 cubic Angstrom > cell is not that unusual so my runs are often measured in hours/days and > not minutes. I don't think any sane person is going to buy a Quadro GV100 > to save a few seconds! > > I'll now shut up and go away into my experimentalist corner > > Best regards > Pam Whitfield > > Hello Pamela, > I don't know whether it is clear or not, so I apologize if I repeat obvious > concepts. > I just bought a Threadripper 3990X with 64 core 128 threads. As far as I > remember the 3960X should have 24 core - 48 threads. > It is very very important to don't use more than 24 cores on 3960X . Simply > forget about hyperthreading. No need to disable it in the BIOS, but simply > count the real number of cores. > > I use gcc 9.3.0 and the new gcc 10 should be even better for AMD cpus. > With openblas 0.3.12 I found that my 8-cores home Ryzen 3800X is fast as a > Xeon 12 cores E5-2680 using quantum espresso 6.4.1 > Carlo > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Strange output for berry phase calculations; no check for insulator?
On Sat, Nov 14, 2020 at 9:13 PM Sergey Lisenkov wrote: Question: Does QE perform a check for the structure to be insulator before > proceeding with Berry phase calculation? No: QE complains and stops if you try a Berry phase calculation in a crystal treated as a metal (with tetrahedra or broadening), but it does not check whether the crystal you assumed to be an insulator is really one. Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] CASTEP to QE setup parameters conversions
On Sat, Nov 14, 2020 at 9:07 PM Husak Michal wrote: > For conv_thr the units are missing in the manual (but is is probably (a.u.) > >From the header: All quantities whose dimensions are not explicitly specified are in RYDBERG ATOMIC UNITS and from the description of conv_thr: Convergence threshold for selfconsistency: estimated energy error < conv_thr (note that conv_thr is extensive, like the total energy). So conv_thr is an energy, and is in Ry. > ecutrho equivalent is impossible to find in any CASTEP manual CASTEP uses norm-conserving pseudopotentials only, if I remember correctly, so the cutoff on the charge density (ecutrho) can be set to ecutrho=4*ecutwfc. Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Incorrect identification+generations of atoms in specialpositions (space_group options used).
On Thu, Nov 12, 2020 at 1:34 PM José Carlos Conesa Cegarra < jccon...@icp.csic.es> wrote: Last 11th of september I sent a similar question, but the answer, provided > by Paolo Giannozzi, did not clarify much. I can say that in that occasion I > was using qe-6.5. Should I use qe -6.6? > not necessarily so: the Wyckoff machinery is unchanged since two years, to the best of my knowledge. Instead you should have read my unclear answer again, or just the last sentence: *I suspect that one or more of the Ge positions are not exact Wyckoff positions but very close to them*, and verified it. There are just three Wyckoff Ge positions, and since atomic positions are expanded in the order they are provided, the problematic one seems to be the second: Ge 0.0 -0.49511 -0.50488 that looks almost like (0,-x,x). Almost. With 0.0 -0.49511 -0.50489 you get 56 atoms. not 59. Paolo > Regards, > > José C. Conesa > El 12/11/2020 a las 11:30, Pietro Delugas escribió: > > Hi > > which version of the code are you using ? > > > > with qe-6.6 using your parameters I got two positions > > > > site n. atom positions (alat units) > > 1 Zn tau( 1) = ( 0.4873906 2.5406690 > 1.4472625 ) > > 2 Zn tau( 2) = ( 0.3343454 0.8468897 > 0.4736359 ) > > > > With alat = 11.5468 a.u. > > > > alat = 11.5468 a.u. > > > > ibrav=-12 > > > > > > hope it helps > > greetings - Pietro > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Michal Husak > *Sent: *Thursday, November 12, 2020 10:34 AM > *To: *users@lists.quantum-espresso.org > *Subject: *[QE-users] Incorrect identification+generations of atoms in > specialpositions (space_group options used). > > > > I > > > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list > users@lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users > > -- > José C. Conesa > Research Professor > Instituto de Catálisis y Petroleoquímica, CSIC > Marie Curie, 2; Campus de Cantoblanco > 28028 Madrid (Spain) > Telef. +34 915854766 > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Incorrect identification+generations of atoms inspecialpositions (space_group options used).
On Thu, Nov 12, 2020 at 12:35 PM Pietro Delugas wrote: > It tells me atom 7 and 150 overlap, 7 should be > > O -0.503 0.4513 0.3517 > well, no, 7 and 150 in the list of all atoms, not of Wyckoff positions. Atom 7 is n.4 in the list: O -0.1486 0.54916 0.09311 atom 150 is n. 41: O -0.1486 -0.04916 0.09311 in crystal coordinates. Paolo As for 150 I don’t know, not very easy to spot in a short time. > > Pietro > > > > > > Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for > Windows 10 > > > > *From: *Michal Husak > *Sent: *Thursday, November 12, 2020 12:19 PM > *To: *Quantum ESPRESSO users Forum > *Subject: *Re: [QE-users] Incorrect identification+generations of atoms > inspecialpositions (space_group options used). > > > > H > > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] npw vs npwx
In principle, it doesn't matter: they are never (or should never be) used. In practice, they are set to zero Paolo On Thu, Nov 12, 2020 at 12:39 AM Andrew Xu wrote: > Thanks! > > Just out of curiosity, what values do the last npwx - npw entries of the > column (row) take? Are they all zero? > > Best, > Andrew > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] npw vs npwx
On Wed, Nov 11, 2020 at 7:29 PM Andrew Xu wrote: I'm confused why npw and npwx is used, instead of only npw or only npwx > npw = actual number of plane waves npwx= physical dimension of arrays containing plane-wave components The reason for the difference is that different k-points have different values of npw, so npwx is set to the maximum value of npw across k-points. Once upon a time, npwx was used to increase efficiency: setting it to an odd number, for obscure reasons related to memory access and memory banks, allowed to speed up some calculations, but I don't think this is done any longer. Paolo . Is this saying the number of columns of op(wfc) (which is the number of > rows of swfc) is npwx, but we only use the first npw columns of op(wfc) > (rows of swfc) because the entries in the last npwx - npw columns of > op(wfc) (rows of swfc) are all zero? > > Best regards, > Andrew > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Ris: Assign Initial velocity in CPMD
On Wed, Nov 11, 2020 at 5:01 PM Abhirup Patra
wrote:
> Even with the underscore, the error remains the same
Are you sure? This is the relevant piece of code. The error is issued in
routine "errore":
SELECT CASE ( TRIM(ion_velocities) )
CASE ('default')
CONTINUE
CASE ('change_step')
dt_old_ = tolp
CASE ('zero')
tzerop_= .TRUE.
CASE ('from_input')
tv0rd_ = .TRUE.
IF( .NOT. tavel ) CALL errore(' iosys ', &
' ION_VELOCITIES not present in stdin ', 1 )
CASE ('random')
tcap_ = .TRUE.
CASE DEFAULT
CALL errore(' control_flags ',' unknown ion_velocities
'//TRIM(ion_velocities), 1 )
END SELECT
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] Missing EOF in the input file causes confusing error message from pp.x chdens
It seems to me that the error message is correct. It's the fortran compiler
(or the fortran run-time library) that does not handle correctly that case.
Paolo
On Tue, Nov 10, 2020 at 6:57 AM 连云龙 wrote:
> Dear QE developers,
>
> I was trapped in an error from pp.x saying that
> -
> Message from routine chdens:
> namelist plot not found or invalid, exiting
> -
> but eventually this error is caused by a missing EOF after the final "/"
> in the input file.
> (I found solution here :
> https://www.mail-archive.com/users@lists.quantum-espresso.org/msg36019.html
> )
>
>
> To make the program easier to use for beginners, could you please revise
> the line
> -
> CALL infomsg ('chdens', 'namelist plot not found or invalid, exiting')
> -
> in .../qe-6.6/PP/src/chdens_module.f90 to give some more hints ? Strictly
> speaking, a missing EOF is not a problem of the content of the card
> "", but this line will be triggered by such an error and the error
> message is, at least to me, misleading.
>
>
> Have a good day,
> Yunlong
>
> --YunlongLIANORCID:
> https://orcid.org/-0002-9474-2181
> CSNS,DongguanNeutronScienceCenterDongguan,Guangdong,P.R.China连云龙中国散裂中子源中子科学部A1-629(内线303)中国广东省东莞市
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Phonon calculations using SCAN functionals
On Sun, Nov 8, 2020 at 5:12 PM p ul wrote: > Then the ph calculation didn't work because 'The phonon code with meta-GGA > functionals is not yet available' > this is the correct behavior: SCAN is a meta-GGA functional Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Mismatch between k-points from scf.out and q-point from system.dyn0
On Fri, Nov 6, 2020 at 11:14 PM Ashis Kundu wrote:
Why is there a mismatch between k-points from SCF and q-point from
> system.dyn0 (phonon calculation)?
> [...] Ideally they should be the same
>
they are the same, but the algorithms for generation and selection of the
irreducible sector are different for the two grids so the ordering and sign
may differ. Each of the points in the first set is either equal to or
equivalent to a point of the second set.
Please let me know if I am doing something wrong.
>
you aren't doing anything wrong. Or maybe you are: the scf input you sent
cannot produce the k-point grid you listed
Paolo
>
> The k-points generated from SCF
>
> number of k points= 8 Methfessel-Paxton smearing, width (Ry)=
> 0.0200
>cart. coord. in units 2pi/alat
> k(1) = ( 0.000 0.000 0.000), wk = 0.0740741
> k(2) = ( -0.333 0.000 0.0977788), wk = 0.2962963
> k(3) = ( -0.333 0.333 0.1955577), wk = 0.5925926
> k(4) = ( 0.333 0.333 -0.000), wk = 0.2962963
> k(5) = ( 0.000 0.000 0.1955577), wk = 0.1481481
> k(6) = ( 0.667 0.000 -0.000), wk = 0.1481481
> k(7) = ( 0.000 -0.333 -0.0977788), wk = 0.2962963
> k(8) = ( 0.000 0.667 0.000), wk = 0.1481481
>
> q-point from phonon calculations (a mesh of 3x3x3 is used)
>
> 0. 0. 0.
> -0. 0. 0.09777884
> 0. 0. 0.09777884
> -0. 0. 0.19555767
> 0. 0. -0.
> 0. 0. 0.19555767
> 0.6667 0. -0.
> 0. -0.6667 -0.
>
> Below are the SCF and phonon input file
>
> scf.in
> -
>
> calculation = 'scf'
> prefix = 'TaP'
> pseudo_dir = '../pp'
> outdir = './'
> wf_collect = .true.
> tprnfor = .true.
> tstress = .true.
> /
>
> ibrav = 7
> celldm(1) = 6.173529611
> celldm(3) = 3.409054
> nat = 4
> ntyp= 2
> ecutwfc = 100
> occupations = 'smearing'
> smearing= 'mp'
> degauss = 0.02
> /
>
> diagonalization = 'david'
> mixing_beta = 0.7
> conv_thr= 1.0d-10
> /
> ATOMIC_SPECIES
> Ta 180.948 Ta.pw-mt_fhi.UPF
> P 30.974 P.pw-mt_fhi.UPF
> ATOMIC_POSITIONS {alat}
> Ta 0.000 0.000 -0.0044625
> Ta 0.000 0.500 0.8478074
> P0.000 0.000 1.4178478
> P0.500 0.000 0.5655748
> K_POINTS {automatic}
> 15 15 15 0 0 0
>
> ph.in
>
> phonon
>
> prefix = 'TaP'
> fildyn = 'TaP.dyn'
> fildvscf = 'dvscf'
> ldisp= .true.
> epsil= .false.
> nq1 = 3
> nq2 = 3
> nq3 = 3
> tr2_ph = 1.0d-14
> /
>
>
> Best regards,
> Ashis
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Running efficiently on multiple nodes
Are there fast communications between the two nodes? if not, the parallel distributed 3D FFT will be very slow (note the time taken by fft_scatt_yz). You might find convenient to exploit k-point parallelization, that requires much less communication: for instance, "mpirun -n 32 pw.x -nk 2" (2 pools of 16 processors, each pool performing parallel FFT), but you have to figure out a way to convince the first pool of 16 processors on node 1, the second on node 2 (or vice versa, as long as FFT parallelization happens inside a node, k-point parallelization across nodes ) Paolo On Thu, Nov 5, 2020 at 7:29 PM Baer, Bradly via users < users@lists.quantum-espresso.org> wrote: > Paolo, > > Thank you for your suggestion. I will add recompiling to move to 6.6 to > my to do list. For now, I corrected the pseudopotential files as you > indicated and the calculation ran successfully. It has become slightly > faster, but still much slower than running on a single node (3:30s vs > 0:30s). Is there more that I should be doing to improve performance or is > my test problem too small to see the benefits of parallelization? > > Thanks, > Brad > > > Bradly Baer > Graduate Research Assistant, Walker Lab > Interdisciplinary Materials Science > Vanderbilt University > > > -- > *From:* users on behalf of > Paolo Giannozzi > *Sent:* Thursday, November 5, 2020 10:01 AM > *To:* Quantum ESPRESSO users Forum > *Subject:* Re: [QE-users] Running efficiently on multiple nodes > > On Thu, Nov 5, 2020 at 3:05 PM Baer, Bradly > wrote: > > > *Pseudo file Ga.pbe-dn-kjpaw_psl.1.0.0.UPF has been fixed on the fly.* > *To avoid this message in the future, permanently fix * > * your pseudo files following these instructions: * > *https://gitlab.com/QEF/q-e/blob/master/upftools/how_to_fix_upf.md > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitlab.com%2FQEF%2Fq-e%2Fblob%2Fmaster%2Fupftools%2Fhow_to_fix_upf.md=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C73a5a5e938ac4ee11cb808d881a440f4%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637401889751409012%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000=511bORLQwH1OKUCoHg%2BbMb5I%2FiOEuHIFEbDlNl28678%3D=0>* > > > This is a possible source of trouble if the output directory is not > visible to all processors. Please try one of the following: > - do what it is suggested (or simply: edit Ga.pbe-dn-kjpaw_psl.1.0.0.UPF, > replace all occurrences of "&" with "") > - get version 6.6, that reads the pseudopotential file on one processor > and broadcast its contents to all other processes > - get the development version, that in addition is not sensitive to the > presence of nonstandard "&" in the files, > > Paolo > > > > -Brad > > ---- > Bradly Baer > Graduate Research Assistant, Walker Lab > Interdisciplinary Materials Science > Vanderbilt University > > > -- > *From:* users on behalf of > Paolo Giannozzi > *Sent:* Thursday, November 5, 2020 2:33 AM > *To:* Quantum ESPRESSO users Forum > *Subject:* Re: [QE-users] Running efficiently on multiple nodes > > On Wed, Nov 4, 2020 at 11:28 PM Baer, Bradly > wrote: > > > Now that I have two nodes, the script for a single node results in a crash > shortly after reading in the pseudopotentials. > > > which version of QE are you using, and which crash do you obtain, with > which executable? > > Paolo > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > _ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2F=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C73a5a5e938ac4ee11cb808d881a440f4%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637401889751419008%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000=hFpaUoIPz4sX3DRUpP09MjX5XOrIVQEtwjR25n%2BUwlk%3D=0> > ) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers=04%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C73a5a5e938ac4ee11cb808d881a440f4%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637401889751419008%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000=5
Re: [QE-users] Running efficiently on multiple nodes
On Thu, Nov 5, 2020 at 3:05 PM Baer, Bradly wrote: > *Pseudo file Ga.pbe-dn-kjpaw_psl.1.0.0.UPF has been fixed on the fly.* > *To avoid this message in the future, permanently fix * > * your pseudo files following these instructions: * > *https://gitlab.com/QEF/q-e/blob/master/upftools/how_to_fix_upf.md > <https://gitlab.com/QEF/q-e/blob/master/upftools/how_to_fix_upf.md>* > This is a possible source of trouble if the output directory is not visible to all processors. Please try one of the following: - do what it is suggested (or simply: edit Ga.pbe-dn-kjpaw_psl.1.0.0.UPF, replace all occurrences of "&" with "") - get version 6.6, that reads the pseudopotential file on one processor and broadcast its contents to all other processes - get the development version, that in addition is not sensitive to the presence of nonstandard "&" in the files, Paolo > > > -Brad > > > Bradly Baer > Graduate Research Assistant, Walker Lab > Interdisciplinary Materials Science > Vanderbilt University > > > -- > *From:* users on behalf of > Paolo Giannozzi > *Sent:* Thursday, November 5, 2020 2:33 AM > *To:* Quantum ESPRESSO users Forum > *Subject:* Re: [QE-users] Running efficiently on multiple nodes > > On Wed, Nov 4, 2020 at 11:28 PM Baer, Bradly > wrote: > > > Now that I have two nodes, the script for a single node results in a crash > shortly after reading in the pseudopotentials. > > > which version of QE are you using, and which crash do you obtain, with > which executable? > > Paolo > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > _ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Updates on this mailing list
This is a test message, sent to test the mailing list after a system upgrade. You may ignore it, but maybe you shouldn't: there are frequent problems with posts coming from some providers (notably, @ymail.com) that bounce when delivered to some other providers (notably, @gmail.com). After a few bounces, delivery is disabled. It happened yesterday to some 160 emails. Apparently it is a consequence of DMARC, whatever it means. We are trying to solve the problem by updating the (rather old) mailing list software. Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Running efficiently on multiple nodes
On Wed, Nov 4, 2020 at 11:28 PM Baer, Bradly wrote: > Now that I have two nodes, the script for a single node results in a crash > shortly after reading in the pseudopotentials. > which version of QE are you using, and which crash do you obtain, with which executable? Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] "wrong offset" error when using SG15 pseudo
should find the 3d states. > > Best, > > Matteo > > > > Il giorno ven 30 ott 2020 alle ore 02:04 Sergey Lisenkov < > proff...@yandex.ru> ha scritto: > > Hello all, > > I tried to use DFT+U with SG15 pseudopotentials (from SG15 library, 2020 > version). First element in my structure is "Mn". I immediately got this > error message: > > > %% > Error in routine offset_atom_wfc (1): > wrong offset > > > %% > > Looking at the archives for similar error message, I found that it is > related that atomic element is not defined in "tabd.f90". But certainly Mn > element is implemented. > > When I changed pseudopotentials to different one, no such message appears. > > Could it mean that SG15 pseudopotentials are not suitable for the DFT+U > calculations? > > Thanks, > Sergey > > USF > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -- > Matteo Cococcioni > Department of Physics > University of Pavia > Via Bassi 6, I-27100 Pavia, Italy > tel +39-0382-987485 > e-mail matteo.cococci...@unipv.it > , > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > > , > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] information about PGI compiler v20+ download
*** >>>>> Sitangshu Bhattacharya (সিতাংশু ভট্টাচার্য), Ph.D >>>>> Assistant Professor, >>>>> Room No. 2221, CC-1, >>>>> Electronic Structure Theory Group, >>>>> Department of Electronics and Communication Engineering, >>>>> Indian Institute of Information Technology-Allahabad >>>>> Uttar Pradesh 211 012 >>>>> India >>>>> Telephone: 91-532-2922000 Extn.: 2131 >>>>> Web-page: http://profile.iiita.ac.in/sitangshu/ >>>>> Institute: http://www.iiita.ac.in/ >>>>> >>>>> >>>> >>>> -- >>>> ** >>>> Sitangshu Bhattacharya (সিতাংশু ভট্টাচার্য), Ph.D >>>> Assistant Professor, >>>> Room No. 2221, CC-1, >>>> Electronic Structure Theory Group, >>>> Department of Electronics and Communication Engineering, >>>> Indian Institute of Information Technology-Allahabad >>>> Uttar Pradesh 211 012 >>>> India >>>> Telephone: 91-532-2922000 Extn.: 2131 >>>> Web-page: http://profile.iiita.ac.in/sitangshu/ >>>> Institute: http://www.iiita.ac.in/ >>>> >>>> >>> >>> -- >>> ** >>> Sitangshu Bhattacharya (সিতাংশু ভট্টাচার্য), Ph.D >>> Assistant Professor, >>> Room No. 2221, CC-1, >>> Electronic Structure Theory Group, >>> Department of Electronics and Communication Engineering, >>> Indian Institute of Information Technology-Allahabad >>> Uttar Pradesh 211 012 >>> India >>> Telephone: 91-532-2922000 Extn.: 2131 >>> Web-page: http://profile.iiita.ac.in/sitangshu/ >>> Institute: http://www.iiita.ac.in/ >>> >>> >> >> -- >> ** >> Sitangshu Bhattacharya (সিতাংশু ভট্টাচার্য), Ph.D >> Assistant Professor, >> Room No. 2221, CC-1, >> Electronic Structure Theory Group, >> Department of Electronics and Communication Engineering, >> Indian Institute of Information Technology-Allahabad >> Uttar Pradesh 211 012 >> India >> Telephone: 91-532-2922000 Extn.: 2131 >> Web-page: http://profile.iiita.ac.in/sitangshu/ >> Institute: http://www.iiita.ac.in/ >> >> > > -- > ** > Sitangshu Bhattacharya (সিতাংশু ভট্টাচার্য), Ph.D > Assistant Professor, > Room No. 2221, CC-1, > Electronic Structure Theory Group, > Department of Electronics and Communication Engineering, > Indian Institute of Information Technology-Allahabad > Uttar Pradesh 211 012 > India > Telephone: 91-532-2922000 Extn.: 2131 > Web-page: http://profile.iiita.ac.in/sitangshu/ > Institute: http://www.iiita.ac.in/ > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] How to Calculate Charge Density Difference
Hi Guido >weight = 1, -1, -1 > are you sure this is an acceptable syntax? Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] mesh mismatch
There are two sets of problems in your PP file (not in the code): - at line 54, mesh_size="2000" is not correct, it should be the same as "mesh" (1035) a few lines below - the "index" attribute is missing in several xml tags. The simplest thing to do is to manually change "mesh_size" to 1035, then apply the attached patch (that disables the checks) and recompile. The previous version was silently overwriting the correct value of "mesh" over the bad one and was not performing many checks Paolo On Thu, Oct 22, 2020 at 5:16 PM Sergey Lisenkov wrote: > Dear all, > > I noticed that in developing version of QE several bugs related to DFT+U > were fixed so I tried to use the latest snapshot. However, I encountered a > problem with my PAW pseudopotentials from ATOMPAW: > > mismatch mesh > > that comes from upflib/read_upf_new.f90 > > I checked my UPF file and I see that meshes are different in some places > of the file, however v.6.6 is OK with that. > > Was something changed in the code as well? > > Thanks, > Sergey > > USF > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 upf.diff Description: Binary data ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] pseudopotential file reading error in 6.6a2-gpu
In file Pb_ONCV_PBE_FR-1.0.upf the "index" attribute of PP.BETA.N, N=1,..,14, should be index='N'. Apparently format I1 was used to write the index so when N > 10 the attribute has a funny value: index="*". Just edit the file and replace * with the corresponding index. Paolo On Fri, Oct 23, 2020 at 3:12 AM Zeeshan Ahmad wrote: > Hi, > > I obtain the following error (only in the gpu version) when I change my > ONCV pseudopotential to fully relativistic: > > FIO-F-225/list-directed read/internal file/lexical error-- unknown token > type. > In source file xmltools.f90, at line number 107 > > It seems to be due to the pseudopotential file reading error, similar to > https://www.vasp.at/forum/viewtopic.php?t=330 > > The pseudopotentials are SG15 ONCV downloaded from > http://www.quantum-simulation.org/potentials/sg15_oncv/ > (sg15_oncv_upf_2020-02-06.tar.gz > <http://www.quantum-simulation.org/potentials/sg15_oncv/sg15_oncv_upf_2020-02-06.tar.gz> > ) > > The input file which gives the error is: > (works fine for me when Pb_ONCV_PBE_FR-1.0.upf is replaced with > Pb_ONCV_PBE-1.2.upf) > > >title = '9009114.cif' > calculation = 'scf' > restart_mode = 'from_scratch' > outdir = 'scf' > pseudo_dir = './' > prefix = '9009114' > disk_io = 'none' >nstep = 400 > / > >ibrav = 4 >celldm(1) =8.60770253529410 >celldm(3) =1.53172338090011 > nat = 3 > ntyp = 2 > ecutwfc = 70 > / > > electron_maxstep = 200 > conv_thr = 1.0D-10 > mixing_beta = 0.7 > diagonalization = 'david' > / > > ATOMIC_SPECIES >Pb 207.20 Pb_ONCV_PBE_FR-1.0.upf > I 126.904000 I_ONCV_PBE-1.2.upf > ATOMIC_POSITIONS crystal > Pb 0.0 0.0 0.0 > I 0.3 0.7 0.26500 > I 0.7 0.4 0.73500 > K_POINTS automatic > 8 8 6 0 0 0 > > > Thanks, > Zeeshan > > > > > -- > Zeeshan Ahmad > Postdoctoral Researcher > Pritzker School of Molecular Engineering > University of Chicago > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] mesh mismatch
On Thu, Oct 22, 2020 at 5:16 PM Sergey Lisenkov wrote: I encountered a problem with my PAW pseudopotentials from ATOMPAW: > > mismatch mesh > > that comes from upflib/read_upf_new.f90 > > I checked my UPF file and I see that meshes are different in some places > of the file, however v.6.6 is OK with that. > > Was something changed in the code as well? > yes, the code reading the pseudopotentials has changed a lot, but it should read files exactly as before. Please provide the pseudopotential file. Paolo > > Thanks, > Sergey > > USF > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] [QE-GPU] nscf calculation problem
On Thu, Oct 22, 2020 at 4:36 PM lorenzo bastonero < lorenzo.baston...@edu.unito.it> wrote: > I need to calculate several bands (i.e. 8000) for GW calculations. it's not "several bands", it's "a lot of bands". QE is not optimized for such a case (and I don't think it will ever be). The printout of the amount of RAM is not meant to give a reliable estimate but just an order of magnitude Paolo > Running on 2 nodes with npool 2, the dynamical RAM per process is above > 16Gb. I tried out with npool 1, but I encountered the error "S matrix not > positive definite”. I decided then to try with 4 nodes and npool 2 with the > option diago_david_ndim='2', then the dyn RAM/process is 14.97Gb, so it has > to work now. But the calculation stops without the “CRASH” file and in the > output I got "2 total processes killed (some possibly by mpirun during > cleanup)”. In the slurm-output there are several segmentation fault error > messages. > I also discussed the problem with my supervisor but we are puzzled. > > Any suggestions on what to do? > > You’ll find attached the main outputs. > > Thanks for your precious time. > > Kind regards, > > Lorenzo Bastonero > > > -- > > > > > Indirizzo istituzionale di posta elettronica > degli studenti e dei laureati dell'Università degli Studi di > TorinoOfficial > University of Turin email address for students and graduates > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] pp.x does not seem to finish
On Thu, Oct 22, 2020 at 10:17 AM Thanh-Nam Huynh wrote: > When I set OMP_NUM_THREADS=64 and ran > mpirun -np 2 ... > in the output, the first lines were printed out twice. > Meanwhile, when I set OMP_NUM_THREADS=1 and ran > mpirun -np 40 ... > every line was printed out 40 times in the output file. > your executable is compiled for serial execution (that is: no MPI). You are running N independent copies of the same executable, one copy per processor. Paolo > Self-consistent Calculation > > iteration # 1 ecut=50.00 Ry beta= 0.30 > Davidson diagonalization with overlap > > total cpu time spent up to now is 1934.7 secs > > Self-consistent Calculation > > iteration # 1 ecut=50.00 Ry beta= 0.30 > Davidson diagonalization with overlap > > total cpu time spent up to now is 2017.0 secs > > Self-consistent Calculation > > iteration # 1 ecut=50.00 Ry beta= 0.30 > Davidson diagonalization with overlap > > total cpu time spent up to now is 2027.3 secs > > Self-consistent Calculation > > iteration # 1 ecut=50.00 Ry beta= 0.30 > Davidson diagonalization with overlap > > total cpu time spent up to now is 2062.5 secs > > Self-consistent Calculation > > iteration # 1 ecut=50.00 Ry beta= 0.30 > Davidson diagonalization with overlap > > total cpu time spent up to now is 2062.5 secs > > Self-consistent Calculation > > iteration # 1 ecut=50.00 Ry beta= 0.30 > Davidson diagonalization with overlap > > total cpu time spent up to now is 2069.4 secs > > Self-consistent Calculation > > iteration # 1 ecut=50.00 Ry beta= 0.30 > Davidson diagonalization with overlap > > total cpu time spent up to now is 2070.5 secs > > Self-consistent Calculation > > iteration # 1 ecut=50.00 Ry beta= 0.30 > Davidson diagonalization with overlap > > total cpu time spent up to now is 2089.3 secs > > I am not sure whether it affects the calculation time (I think it may), > but it is really annoying. Do you have any idea about this problem and how > to solve it? Thank you very much! > -- > *Huynh Thanh-Nam* > Department of Materials Science and Engineering, Chungnam National > University > Yuseong-gu, Daejeon 34134, Korea > Tel: (+82) 010 5719 1521 > _______ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] error in recovering phonon calculation
On Mon, Oct 19, 2020 at 7:35 AM Jacopo Simoni wrote: > > I am using recover=true > recover=.true., "dot true dot". Code version? Paolo On Sun, 18 Oct 2020 at 22:12, Oscar Baseggio wrote: > >> Dear Jacopo, >> It's hard to understand what's happening without the error, the only >> error that I see in your input is in recover. >> >> Recover =true, >>>> recover =.true., >> >> Best regards >> Oscar Baseggio >> >> >> Il 2020-10-19 01:35 Jacopo Simoni ha scritto: >> > Dear QE users, >> > I am running a phonon calculation, the calculation is quite long and >> > expensive so I need to restart it a couple of times before I complete >> > it. >> > The first run ends smoothly, but when I try to restart it I get an >> > error because it is not able to restart from the previous run. >> > This is my input file >> > >> > >> > phonons - mithrene >> > >> > recover=true, >> > max_seconds=39600, >> > tr2_ph=1.0d-12, >> > prefix='mthr', >> > ldisp=.true., >> > nq1=1, nq2=1, nq3=1, >> > amass(1)=107.86820, >> > amass(2)=78.96000, >> > amass(3)=12.01070, >> > amass(4)=1.00794, >> > outdir='/lustre/scratch3/turquoise/jacopo/mithrene3/data.save/', >> > fildyn='mthr.dyn', >> > / >> > %%% >> > I appreciate any suggestion. >> > Thanks, Jacopo Simoni >> > Research associate, Lawrence Berkeley National Lab. >> > ___ >> > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) >> > users mailing list users@lists.quantum-espresso.org >> > https://lists.quantum-espresso.org/mailman/listinfo/users >> ___ >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu) >> users mailing list users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users >> > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] fail to install qe 6.6 using /soft/compiler/intel/composer_xe_2013_sp1.0.080/bin/intel64/ifort
On Sun, Oct 18, 2020 at 1:26 PM Shaofeng Wang wrote: I am trying to install qe6.6 using > /soft/compiler/intel/composer_xe_2013_sp1.0.080/bin/intel64/ifort. But > the compiled pw.x can not run with the error as follow. > > [...] > pw.x 005F84FD pw_init_qexsd_inp 427 > pw_init_qexsd_input.f90 > > pw.x 005343F1 iosys_ 1683 > input.f90 > > pw.x 00625207 run_pwscf_ 91 > run_pwscf.f90 > > pw.x 0047041D MAIN__106 > pwscf.f90 > > Intel fortran v.2012 and 2013 have a problem with the way optional arguments are used in routine pw_init_qexsd_input.f90. Just comment it out: input data will not be written to xml file but this has no consequences Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] error in pw.x
On Sat, Oct 17, 2020 at 5:47 AM Sai vishnu wrote: this is my input file. > doesn't run: ibrav is not specified Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] not orthogonal operation in dos.x run only
On Fri, Oct 16, 2020 at 9:39 PM Lucas Dória wrote: > > So it is possible for a system to give satisfactory results in > optimization calculations, and yet show symmetry problems in further > routines? > The check that fails in your case is performed only in variable-cell MD and when data is read for further processing. So, yes, when you read your data you may discover that some symmetries that were assumed to be present during the scf calculation are no longer found, according to the criteria used to decide whether a symmetry is present or not. This typically happens when your system is at the border between symmetric and not symmetric. Also, my job using bands.x with the optimized structure for WS2 finished > without getting symmetry issues, which does not occur for dos.x and > projwfc.x calculations. > I don't think this can happen, because ALL codes that read data from the scf calculation perform the same check, so bands.x will fail as well. Anyway: you can just remove the check by deleting the line that calls "checkallsym" in PW/src/pw_restart.f90. It's a dumb check that makes more harm than good. Paolo > I will work on your tip and try to see if I can solve this problem by > re-submitting relax calculations with better parameters, but it is yet > strange to me why the 'not orthogonal operation' crash doesn't appear in > vc-relax calc, neither in scf and nscf calculations, and we just take note > of it in dos.x and projwfc.x routines. > > With regards, > > Lucas. > > ------ > *De:* users em nome de Paolo > Giannozzi > *Enviado:* sábado, 3 de outubro de 2020 13:06 > *Para:* Quantum ESPRESSO users Forum > *Assunto:* Re: [QE-users] not orthogonal operation in dos.x run only > > Obscure symmetry problems almost invariably come from the usage of "free" > Bravais lattice (ibrav=0) and almost-symmetric-but-not-enough lattice > vectors, or by almost-symmetric-but-not-enough atomic positions > > Paolo > > On Sat, Oct 3, 2020 at 6:36 PM Lucas Dória > wrote: > > Dear all, > > I ran into this problem while doing a dos.x calculation (nscf and scf > calculations finished succesfully): > > *'from checkallsym : error # 2* > *not orthogonal operation'* > > The structure is a WS2 bilayer. (WS2 is a layered material, we optimized > bulk structure and then added vaccum in z-direction to get bilayer > structure.) > > When i looked up for possible reasons and solutions, I found this problem > only occuring in vc-relax calculations. Our group did in fact optimized the > hexagonal structure, but vc-relax calculations finished succesfully. > > I add that we already studied electronic properties of another very > similar hexagonal structure, of the same point group, namely MoS2, and we > didn't get symmetry issues. (using v5.4 at the time) > > So, I don't know why this problem of 'not orthogonal operation' is > happening to WS2, and just in dos.x calculation, if it's a crash due to > symmetry breaking. We think that the only major differences between WS2 and > MoS2 are that W is heavier than Mo, and the PP used. But we are using an > optimized ecutwfc. > > Thanks in advance. QE-version used: 6.5. > > Lucas. > _______ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] convergence thresholds
Quick answer: no, there is no reason. Paolo On Thu, Oct 15, 2020 at 2:25 PM pboulet wrote: > Dear all, > > This question is more for developers. Is there a reason why the only > threshold reported in the output file is about the wave function? why not > the energy, and eventually forces and cell stress? > > Best, > Pascal > > > Pascal Boulet > — > *Professor in computational materials - DEPARTMENT OF CHEMISTRY* > University of Aix-Marseille - Avenue Escadrille Normandie Niemen - > F-13013 Marseille - FRANCE > Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 > Email : pascal.bou...@univ-amu.fr > > > > > > > > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] simple_ip error
On Wed, Oct 14, 2020 at 10:18 PM Anibal Thiago Bezerra < anibal.beze...@unifal-mg.edu.br> wrote: At line 47 of file input_simple_ip.f90 (unit = 5, file = 'stdin') > Fortran runtime error: End of file > apparently the code expects input from the terminal Paolo > Thanks a lot! > Best wishes! > > Anibal > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] error while calculating InAs phonon dispersion with QE 6.5
It's not easy because the DFT gap of InAs without spin-orbit is very small to nonexistent. You may try to include spin-orbit interactions (it is important for InAs) or, if you do not need the correct LO-TO splitting and dielectric constant, treat the system as a metal, with a small broadening (will not compute \epsilon and Z*) Paolo On Tue, Oct 13, 2020 at 9:34 PM Sheikh Ziauddin Ahmed wrote: > Thank you for the feedback, Paolo. Can you suggest any way of fixing this? > > On Tue, Oct 13, 2020 at 3:10 PM Paolo Giannozzi > wrote: > >> If you look at the value of \epsilon you will notice a very large value >> (likely a consequence of the smallness of the gap of InAs). In the force >> constant file, this appears as >> >> Paolo >> >> On Mon, Oct 12, 2020 at 3:53 PM Sheikh Ziauddin Ahmed < >> sza...@virginia.edu> wrote: >> >>> Hello >>> >>> I have been trying to calculate the InAs phonon dispersion using version >>> 6.5 but I am getting the following error while running matdyn.x: >>> >>> forrtl: severe (59): list-directed I/O syntax error, unit 1, file >>> /scratch/07250/sza9wz/III_V/InAs/phon2/InAs-6.fc >>> Image PCRoutineLine >>> Source >>> matdyn.x 04AE4253 Unknown Unknown >>> Unknown >>> matdyn.x 04B21DDC Unknown Unknown >>> Unknown >>> matdyn.x 04B1FFC6 Unknown Unknown >>> Unknown >>> matdyn.x 0043206F Unknown Unknown >>> Unknown >>> matdyn.x 0041209B Unknown Unknown >>> Unknown >>> matdyn.x 0040733E Unknown Unknown >>> Unknown >>> libc-2.17.so 2B85A8CE43D5 __libc_start_main Unknown >>> Unknown >>> matdyn.x 00407229 Unknown Unknown >>> Unknown >>> Error reading file header >>> forrtl: severe (59): list-directed I/O syntax error, unit 1, file >>> /scratch/07250/sza9wz/III_V/InAs/phon2/InAs-6.fc >>> Image PCRoutineLine >>> Source >>> matdyn.x 04AE4253 Unknown Unknown >>> Unknown >>> matdyn.x 04B21DDC Unknown Unknown >>> Unknown >>> matdyn.x 04B1FFC6 Unknown Unknown >>> Unknown >>> matdyn.x 0043206F Unknown Unknown >>> Unknown >>> matdyn.x 0041209B Unknown Unknown >>> Unknown >>> matdyn.x 0040733E Unknown Unknown >>> Unknown >>> libc-2.17.so 2B3D0A84E3D5 __libc_start_main Unknown >>> Unknown >>> matdyn.x 00407229 Unknown Unknown >>> Unknown >>> >>> >>> I am using the same input files for other materials and those are >>> working just fine. I am not sure what is causing the error for InAs. >>> >>> I am attaching the input files as well. >>> >>> Regards, >>> Sheikh >>> >>> -- >>> *Sheikh Ziauddin Ahmed * >>> PhD Candidate >>> Charles L. Brown Department of Electrical and Computer Engineering >>> University of Virginia >>> Email:sza9wz*@virginia.edu* >>> LinkedIn: https://www.linkedin.com/in/sheikh-ziauddin-ahmed >>> ___ >>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu) >>> users mailing list users@lists.quantum-espresso.org >>> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> >> >> -- >> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> ___ >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu) >> users mailing list users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -- > *Sheikh Ziauddin Ahmed * > PhD Candidate > Charles L. Brown Department of Electrical and Computer Engineering > University of Virginia > Email:sza9wz*@virginia.edu* > LinkedIn: https://www.linkedin.com/in/sheikh-ziauddin-ahmed > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] error while calculating InAs phonon dispersion with QE 6.5
If you look at the value of \epsilon you will notice a very large value (likely a consequence of the smallness of the gap of InAs). In the force constant file, this appears as Paolo On Mon, Oct 12, 2020 at 3:53 PM Sheikh Ziauddin Ahmed wrote: > Hello > > I have been trying to calculate the InAs phonon dispersion using version > 6.5 but I am getting the following error while running matdyn.x: > > forrtl: severe (59): list-directed I/O syntax error, unit 1, file > /scratch/07250/sza9wz/III_V/InAs/phon2/InAs-6.fc > Image PCRoutineLineSource > matdyn.x 04AE4253 Unknown Unknown Unknown > matdyn.x 04B21DDC Unknown Unknown Unknown > matdyn.x 04B1FFC6 Unknown Unknown Unknown > matdyn.x 0043206F Unknown Unknown Unknown > matdyn.x 0041209B Unknown Unknown Unknown > matdyn.x 0040733E Unknown Unknown Unknown > libc-2.17.so 2B85A8CE43D5 __libc_start_main Unknown > Unknown > matdyn.x 00407229 Unknown Unknown Unknown > Error reading file header > forrtl: severe (59): list-directed I/O syntax error, unit 1, file > /scratch/07250/sza9wz/III_V/InAs/phon2/InAs-6.fc > Image PCRoutineLineSource > matdyn.x 04AE4253 Unknown Unknown Unknown > matdyn.x 04B21DDC Unknown Unknown Unknown > matdyn.x 04B1FFC6 Unknown Unknown Unknown > matdyn.x 0043206F Unknown Unknown Unknown > matdyn.x 0041209B Unknown Unknown Unknown > matdyn.x 0040733E Unknown Unknown Unknown > libc-2.17.so 2B3D0A84E3D5 __libc_start_main Unknown > Unknown > matdyn.x 00407229 Unknown Unknown Unknown > > > I am using the same input files for other materials and those are working > just fine. I am not sure what is causing the error for InAs. > > I am attaching the input files as well. > > Regards, > Sheikh > > -- > *Sheikh Ziauddin Ahmed * > PhD Candidate > Charles L. Brown Department of Electrical and Computer Engineering > University of Virginia > Email:sza9wz*@virginia.edu* > LinkedIn: https://www.linkedin.com/in/sheikh-ziauddin-ahmed > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] FFT grid problems with ph.x
I think the problem (and the fix) is the same as here: https://gitlab.com/QEF/q-e/-/merge_requests/1069 Paolo On Tue, Oct 13, 2020 at 2:55 PM Jakob Kraus < jakob.kr...@physik.tu-freiberg.de> wrote: > Dear QE community, > > > my phonon calculation for AlN complains about > > > "Error in routine scale_sym_ops (4): incompatible FFT grid" > > > , whereas the scf calculation I performed beforehand went through > without any problems. > > > I've consulted the user guide and tried increasing the cutoffs for > wavefunction and density, to no avail. > > Additionally, I've tried playing around with the lattice constants and > setting the FFT grid by hand, to numbers > > that are divisible by 12, which did not help either. > > > Do you have any idea that could help me? I am pretty much stuck at this > point. > > Below is the original espresso.pwi input file for the scf calculation > that is performed before the phonon calculation. > > > Yours sincerely, > > > Jakob Kraus (Technische Universität Bergakademie Freiberg) > > > > > calculation = 'scf' > title= 'AlN_vib' > verbosity= 'high' > restart_mode = 'from_scratch' > tstress = .true. > tprnfor = .true. > outdir = './' > prefix = 'espresso' > pseudo_dir = '/home/kraus/theos_pp/pz.0.3.1/PSEUDOPOTENTIALS_NC' > / > > ibrav= 4 > ecutwfc = 190 > occupations = 'fixed' > nspin= 1 > ntyp = 2 > nat = 4 > celldm(1)= 5.877048275900463 > celldm(3)= 1.6012861736334407 > / > > electron_maxstep = 300 > conv_thr = 1e-10 > mixing_beta = 0.7 > / > > / > > / > > ATOMIC_SPECIES > Al 26.9815385 Al.pz-n-nc.UPF > N 14.007 N.pz-nc.UPF > > K_POINTS automatic > 5 5 5 0 0 0 > > ATOMIC_POSITIONS angstrom > Al 1.5550015550 0.8977787708 0.00 > Al -0.015550 1.7955602350 2.49 > N 1.5550015550 0.8977787708 1.902858 > N -0.015550 1.7955602350 4.392858 > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error in ph.x
On Tue, Oct 13, 2020 at 10:07 AM 连云龙 wrote: What are the recommended versions ? there are no recommended versions: nobody has the time to check all gcc versions. Recent versions should work. Those tested here work for sure: test-farm.quantum-espresso.org:8010/#/console. The older version for which I have a report is 4.8.4. It compiles v 6.5 but has a bug that prevents compilation of v 6.6. (in a part of the code that is used only in a few cases, so you can just comment it out if you are not interested to those cases) I got some mysterious errors in the compilation ... > such as? Paolo > -- > --- 连云龙 | Yunlong LIAN ORCID : > https://orcid.org/-0002-9474-2181 中国散裂中子源 | CSNS 中子科学部 | Dongguan > Neutron Science Center 中国广东省东莞市 | Dongguan, Guangdong, P. R. China > > -Original Messages- > *From:*"Paolo Giannozzi" > *Sent Time:*2020-10-13 15:55:32 (Tuesday) > *To:* "Quantum ESPRESSO users Forum" > *Cc:* > *Subject:* Re: [QE-users] Error in ph.x > > Note however that gfortran 4.8.3 is very old and may not be able to > compile QE (but it should be recognized by configure) > > Paolo > > On Tue, Oct 13, 2020 at 8:53 AM Lorenzo Paulatto > wrote: > >> You can compile qe 6.6 in exactly the same way as 6.3. If someone else >> did it for you ask him/her for help. >> >> kind regards >> >> On 10/13/20 5:43 AM, LEUNG Clarence wrote: >> > I also have mpiifor: >> > >> > which mpiifort >> > >> > >> /opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/bin/mpiifort >> > >> > Thanks! >> > >> > Best regards, >> > >> > LIANG Xiongyi >> > >> > Postdoctoral Fellow >> > >> > City University of Hong Kong >> > >> > *From: *LEUNG Clarence <mailto:liangxy...@hotmail.com> >> > *Sent: *2020年10月13日11:29 >> > *To: *Quantum ESPRESSO users Forum > users@lists.quantum-espresso.org> >> > *Subject: *Re: [QE-users] Error in ph.x >> > >> > Dear Lorenzo, >> > >> > Thanks for your suggestion. When I compile QE6.6, an error happens as >> > follows: >> > >> > configure error fortran could not compile .f90 files >> > >> > I have checked the gfortran in my PC: >> > >> > GNU Fortran (GCC) 4.8.3 20140911 (Red Hat 4.8.3-9) >> > >> > And its direction is /usr/bin/gfortran >> > >> > Thanks! >> > >> > Best regards, >> > >> > Clarence >> > >> > *From: *Lorenzo Paulatto <mailto:paul...@gmail.com> >> > *Sent: *2020年10月13日1:00 >> > *To: *users@lists.quantum-espresso.org >> > <mailto:users@lists.quantum-espresso.org> >> > *Subject: *Re: [QE-users] Error in ph.x >> > >> > use qe6.5 or 6.6 >> > regards >> > >> > On 10/12/20 6:52 PM, LEUNG Clarence wrote: >> >> The Version of QE I used is QE630. Thanks. >> >> >> >> >> >> >> >> Original message >> >> From: LEUNG Clarence >> >> Date: 13/10/2020 00:50 (GMT+08:00) >> >> To: users@lists.quantum-espresso.org >> >> Subject: [QE-users] Error in ph.x >> >> >> >> Dear QEuser, >> >> >> >> Recently, I come across a problem in runing ph.x as follow: >> >> >> >> >> >> %% >> >> Error in routine phq_readin (1): >> >> The phonon code with LDA+U is not yet available >> >> >> >> %% >> >> >> >> This is a system must include DFT+U method. If I do not use DFT+U in >> >> scf, it cannot converge even at 1000 steps. >> >> >> >> It is very appricated that give me some advices. >> >> >> >> Best regards, >> >> Clarence >> >> Postdoc >> >> Department of Materials Science and Engineering >> >> City Univeristy of Hong Kong >> >> >> >> >> >> ___ >> >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu < >> http://www.max-centre.eu>) >> >> users mailing list users@lists.quantum-espresso.org >> >> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> >> > >> > -- >> > Lorenzo Paulatto -
Re: [QE-users] Problem with bands_pp in quantum espresso
It's a known problem and has been explained more than once here. If you want to use symmetry, it is safe to explicitly specify the Bravais lattice (with the correct "ibrav") and exactly symmetric atomic positions, or better, space group and Wyckoff positions. You may still provide lattice vectors and no ibrav, and/or not-so-symmetric atomic positions though. It works, usually, but sometimes it doesn't and leads to funny errors. Alternatively, you may disable symmetry Paolo On Sun, Oct 11, 2020 at 12:10 PM Naharin Jannath < naharin.jannath...@gmail.com> wrote: > Hi.. > I have a problem, that is I am shown this error when i'm trying for > bands.x calculation for bands_pp file in quantum espresso.. it says - > > "Wrong classes for D_3d" > > What can i do now? someone said ' it is due to the inconsistency in the > symmetry tolerance in QE. The suggestion is to try to make the structure > symmetric up to 9 digits" I am not sure what I exactly need to do.. can > anyone help me? > > My scf input file - > > > calculation='scf' > prefix='aiida' > outdir='./.' > pseudo_dir='./.' > etot_conv_thr = 4.00d-05 > forc_conv_thr = 1.00d-04 > tprnfor = .true. > tstress = .true. > verbosity = 'high' > / > > ibrav = 0 > nat = 4 > ntyp = 2 > nspin = 2 > degauss = 1.4699723600d-02 > ecutrho = 3.20d+02 > ecutwfc = 4.00d+01 > occupations = 'smearing' > smearing = 'cold' > starting_magnetization(1) = 1.00d-01 > starting_magnetization(2) = 4.17d-01 > nosym = .TRUE. > / > > conv_thr = 8.00d-10 > electron_maxstep = 80 > mixing_beta = 4.00d-01 > / > ATOMIC_SPECIES > Cl 35.4527 cl_pbe_v1.4.uspp.F.UPF > Zr 91.224 Zr_pbe_v1.uspp.F.UPF > CELL_PARAMETERS (angstrom) >3.445706354000 0. 0. > -1.722852819000 2.984068617000 0. >0. 0. 25.910261154000 > ATOMIC_POSITIONS (crystal) > Zr 0.66567 0.33462 0.454088618 > Zr 0.33343 0.66925 0.545911352 > Cl 0.0 0.0 0.613045453 > Cl 0.0 0.0 0.386954577 > K_POINTS automatic > 11 11 2 0 0 0 > > > Bands input file - > > > calculation='bands' > prefix='aiida' > outdir='./.' > pseudo_dir='./.' > etot_conv_thr = 4.00d-05 > forc_conv_thr = 1.00d-04 > tprnfor = .true. > tstress = .true. > verbosity = 'high' > > / > > ibrav = 0 > nat = 4 > ntyp = 2 > nspin = 2 > occupations = 'smearing' > smearing = 'cold' > starting_magnetization(1) = 1.00d-01 > starting_magnetization(2) = 4.17d-01 > degauss = 1.4699723600d-02 > ecutrho = 3.20d+02 > ecutwfc = 4.00d+01 > / > > conv_thr = 8.00d-10 > electron_maxstep = 80 > mixing_beta = 4.00d-01 > / > ATOMIC_SPECIES > Cl 35.4527 cl_pbe_v1.4.uspp.F.UPF > Zr 91.224 Zr_pbe_v1.uspp.F.UPF > CELL_PARAMETERS (angstrom) >3.445706354000 0. 0. > -1.722852819000 2.984068617000 0. >0. 0. 25.910261154000 > ATOMIC_POSITIONS (crystal) > Zr 0.66567 0.33462 0.454088618 > Zr 0.33343 0.66925 0.545911352 > Cl 0.0 0.0 0.613045453 > Cl 0.0 0.0 0.386954577 > K_POINTS crystal_b > 8 > 0.00 0.00 0.00 30 ! G > 0.50 0.00 0.00 30 ! M > 0.33 0.33 0.00 30 ! K > 0.00 0.00 0.00 30 ! G > 0.00 0.00 0.50 30 ! A > 0.50 0.00 0.50 30 ! L > 0.33 0.33 0.50 30 ! H > 0.00 0.00 0.50 30 ! A > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Is there any problem if I use less ecutwfc and ecutrho than the suggested value in the pp file?
As long as your cutoffs are sufficiently good to get the desired accuracy on the targeted properties, there is no problem. The cutoffs suggested in the PP file are on the safe side and thus quite high, if I remember correctly. Paolo On Mon, Oct 12, 2020 at 2:56 PM ENDALE ABEBE wrote: > Dear Expertise > > The suggested values of the ecutrho and ecutwfc are making my calculation > expensive. For instance, in the pseudo potential file of Bi, > Bi.pbe-dn-kjpaw_psl.1.0.0.UPF > <https://www.quantum-espresso.org/upf_files/Bi.pbe-dn-kjpaw_psl.1.0.0.UPF>, > these are: > > Suggested minimum cutoff for wavefunctions: 45. Ry > Suggested minimum cutoff for charge density: 455. Ry > > Is there any problem if I use less values than these as much as the total > energy of the system converges? > > Thank you in advance for your response. > > With Regards > > -- > Endale Abebe > Program coordinator and Lecturer > Faculty of Materials Science and Engineering > Jimma Institute of Technology > Jimma University > P.O.Box 378, Jimma, Ethiopia > Mobile: +251921381598 > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Atoms switching after certain time step in cp.x
QE doesn't switch atoms as far as I know. Visualizers occasionally do: their algorithms sometimes cannot decide whether to visualize an atom or its periodic image and so you see atoms at the border of a box that disappear at one side and appear at the other side. If this is the case, there isn't anything wrong (but there isn't much that one can do either) Paolo On Tue, Oct 13, 2020 at 6:49 AM Abhirup Patra wrote: > Dear QE users and developers, > > Recently, I have performed some NVT simulation using cp.x for a molecule > on surface reaction, however, it looks like that after the 100-th step, > atoms in the molecule switch position with the atom of the bottom-most > metallic layer of the slab and then go back to the surface again after nth > time-step. > > I have converted .pos and .cel files to .xsf file using cppp.x with QE.6.6 > compiled with -D__OLDXML and visualized the xsf file in Xcrysden. My input > geometry is fine, meaning, nothing is switched after ionic relaxation. > > Any suggestions or tips about what might be the reason for this behavior? > > Thanks, > Abhirup > > -- > Abhirup Patra > Department of Chemistry > University of Pennsylvania > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error in ph.x
Note however that gfortran 4.8.3 is very old and may not be able to compile QE (but it should be recognized by configure) Paolo On Tue, Oct 13, 2020 at 8:53 AM Lorenzo Paulatto wrote: > You can compile qe 6.6 in exactly the same way as 6.3. If someone else > did it for you ask him/her for help. > > kind regards > > On 10/13/20 5:43 AM, LEUNG Clarence wrote: > > I also have mpiifor: > > > > which mpiifort > > > > > /opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/bin/mpiifort > > > > Thanks! > > > > Best regards, > > > > LIANG Xiongyi > > > > Postdoctoral Fellow > > > > City University of Hong Kong > > > > *From: *LEUNG Clarence <mailto:liangxy...@hotmail.com> > > *Sent: *2020年10月13日11:29 > > *To: *Quantum ESPRESSO users Forum users@lists.quantum-espresso.org> > > *Subject: *Re: [QE-users] Error in ph.x > > > > Dear Lorenzo, > > > > Thanks for your suggestion. When I compile QE6.6, an error happens as > > follows: > > > > configure error fortran could not compile .f90 files > > > > I have checked the gfortran in my PC: > > > > GNU Fortran (GCC) 4.8.3 20140911 (Red Hat 4.8.3-9) > > > > And its direction is /usr/bin/gfortran > > > > Thanks! > > > > Best regards, > > > > Clarence > > > > *From: *Lorenzo Paulatto <mailto:paul...@gmail.com> > > *Sent: *2020年10月13日1:00 > > *To: *users@lists.quantum-espresso.org > > <mailto:users@lists.quantum-espresso.org> > > *Subject: *Re: [QE-users] Error in ph.x > > > > use qe6.5 or 6.6 > > regards > > > > On 10/12/20 6:52 PM, LEUNG Clarence wrote: > >> The Version of QE I used is QE630. Thanks. > >> > >> > >> > >> Original message > >> From: LEUNG Clarence > >> Date: 13/10/2020 00:50 (GMT+08:00) > >> To: users@lists.quantum-espresso.org > >> Subject: [QE-users] Error in ph.x > >> > >> Dear QEuser, > >> > >> Recently, I come across a problem in runing ph.x as follow: > >> > >> > > %% > >> Error in routine phq_readin (1): > >> The phonon code with LDA+U is not yet available > >> > > %% > >> > >> This is a system must include DFT+U method. If I do not use DFT+U in > >> scf, it cannot converge even at 1000 steps. > >> > >> It is very appricated that give me some advices. > >> > >> Best regards, > >> Clarence > >> Postdoc > >> Department of Materials Science and Engineering > >> City Univeristy of Hong Kong > >> > >> > >> ___ > >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu < > http://www.max-centre.eu>) > >> users mailing list users@lists.quantum-espresso.org > >> https://lists.quantum-espresso.org/mailman/listinfo/users > >> > > > > -- > > Lorenzo Paulatto - Paris > > ___ > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu > > <http://www.max-centre.eu>) > > users mailing list users@lists.quantum-espresso.org > > https://lists.quantum-espresso.org/mailman/listinfo/users > > > > > > ___ > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > > users mailing list users@lists.quantum-espresso.org > > https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -- > Lorenzo Paulatto - Paris > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Is "block" a FORTRAN keyword? I see funny color in line qe-6.6/Modules/input_parameters.f90:656 when I open the file with VSCode or gedit
On Mon, Oct 12, 2020 at 11:09 AM 连云龙 wrote: When I open the source file input_parameters.f90 with VSCode or gedit, I > saw a highlighted word "block" in line 656. "block" is a bad choice for a variable name (it is also a fortran statement) but I don't think it is related to your compilation problem. If it were, you would get a different error message. The current (development version) file input_parameters.f90 has less than 1662 lines, by the way, so I don't see how it can fail at line 1703. Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Problem with bands_pp in quantum espresso
On Sun, Oct 11, 2020 at 12:10 PM Naharin Jannath < naharin.jannath...@gmail.com> wrote: > I am shown this error when i'm trying for bands.x calculation > [...] > Bands input file > does not look like an input file for bands.x Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Format of FFT grid for Potential
On Sat, Oct 10, 2020 at 5:52 AM Shivesh Sivakumar < shiveshsivaku...@gmail.com> wrote: > > For instance, my FFT grid has dimensions 40x54x180. If I understand > correctly, this means: > 1) The lattice constant along 'a' is divided into 40 points, along 'b' is > divided into 54 points and so on.. > in general, what is divided into 40, 54, 180 points are the three primitive lattice vectors generating the lattice 2) There are a total of 388800 (40*54*180) points printed, which correspond > to the potential at each point , starting with varying 'x' first, then 'y' > and then 'z'. Meaning, > the first 40 points in the output should be (0,0,0), (0.025,0,0) ... > (1,0,0). > (1,0,0) would be point 41 but is not in the grid, because it is equal to (0,0,0) (if your plot seems to miss something, that's why). Same for the two other directions. Xcrysden should output data in the same order as in FFT arrays: see point 6.3 of the developers' manual, https://www.quantum-espresso.org/Doc/developer_man/developer_man.html Paolo The next 40 points should be (0,1,0), (0.025,1,0) .. > (1,1,0). > Am I right in this regard? Any help would be much appreciated. > > Thanks, > Shivesh Sivakumar > University of Washington-Seattle > WA-98105 > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Is wfcdir still functional?
I think that wavefunctions are saved to file (in the internal format used by QE) at the end of each scf calculation in a structural optimization run, because of the way the interpolation algorithm works. If one doesn't use wave function interpolation there is no need to save the wavefunctions. I am not sure the current implementation is smart but improving it would require some work Paolo On Wed, Oct 7, 2020 at 4:39 PM Takahiro Chiba < takahiro_ch...@eis.hokudai.ac.jp> wrote: > Dear Mr. Marchand, Dr. Giannozzi, and all QE users, > > No "pwscf.wfcN" was found in "wfcdir" because he did calculation='scf' > and disk_io='low', I suspect. When I do "relax" calculation with > disk_io='low' option, QE 6.5 with intel MPI 18 on CentOS 6 does write > "pwscf.wfcN" in "wfcdir", where N is the number of MPI processes. > > By the way, I would be glad if you would change the default behavior > of 'wfcdir'. Like ESPRESSO_TMPDIR, using the ESPRESSO_WFCDIR > environment variable if set is better for me. > > Best regards, > > ---Sender--- > Takahiro Chiba > Undergraduate at Hokkaido University > takahiro_ch...@eis.hokudai.ac.jp > - > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Is wfcdir still functional?
Good point - Paolo On Thu, Oct 8, 2020 at 5:30 AM Takahiro Chiba < takahiro_ch...@eis.hokudai.ac.jp> wrote: > Dear Dr. Giannozzi, > > For QE input to be portable, not only wfcdir but also max_seconds > should be read from environment variables. Time limit differs with > batch queues. > > Best regards, > > ---Sender--- > Takahiro Chiba > Undergraduate at Hokkaido University > takahiro_ch...@eis.hokudai.ac.jp > - > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Band unfolding in QE v6.6
I don't know Bandup, but if it is well structured it should be quite easy to adapt it to the new format of data files. Otherwise, you may try "unfold" by Pietro Bonfà: https://bitbucket.org/bonfus/unfold-x/src/master/ Paolo On Thu, Oct 8, 2020 at 4:15 AM William Hewett < williamholmeshewe...@gmail.com> wrote: > Hi QE Users, > > I'm wanting to unfold a band structure calculation on a supercell, I've > tried Bandup (https://github.com/band-unfolding/bandup) however it seems > the current version of Bandup is not compatible with versions of QE post > 6.3. My calculation requires QE 6.6. > > Does anyone know if it is possible to use Bandup with QE v6.6, or suggest > an alternate unfolding code compatible with QE v6.6? > > Thanks > > Will Hewett > Postdoctoral Researcher > Victoria University of Wellington > New Zealand > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Is wfcdir still functional?
I think wfcdir is still used when wavefunctions are saved to disk during the scf calculation (option disk_io='high', that shouldn't be normally used) but not for writing the final data. Is there a good reason to use wfcdir? My opinion is that it should be deleted, together with outdir and pseudo_dir: values that depend upon the specific machine should be read from the command line or (better) from environment variables, not from input data. Input data should be portable. Paolo On Tue, Oct 6, 2020 at 11:09 PM Daniel Marchand wrote: > I am trying to make use of the wfcdir setting, but it seems that it does > nothing. For example, the code below works fine but wavefunction files are > saved to the outdir and not the wfcdir. I saw a post from 2011 that wfcdir > was working back then, but does anyone know if it's been deprecated? > > Best, > > Daniel Marchand (PhD student EPFL) > > > > calculation = 'scf' > disk_io = 'low' > etot_conv_thr = 1.00d-05 > forc_conv_thr = 1.00d-04 > outdir = MY_OUT_DIR > wfcdir = MY_WFC_DIR > prefix = 'aiida' > pseudo_dir = './pseudo/' > verbosity = 'high' > / > > ecutrho = 360 > ecutwfc = 30 > hubbard_u(2) = 4.406250d+00 > ibrav = 0 > lda_plus_u = .false. > lspinorb = .true. > nat = 2 > nbnd = 21 > noncolin = .true. > ntyp = 2 > occupations = 'tetrahedra_opt' > / > > conv_thr = 1.00d-08 > / > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Huge difference between Wall time and CPU time in electron-phonon calculation
If your cluster has a disk per node with a local (i.e., directly accessible by the node but not visible from other nodes) you may try to write data to that disk. It's a pain in the *** and may require some tweaking, but it might work. You need to ensure that the directories are there (they are created if missing only on the node performing I/O) and always run on the same set of processors (and hope that MPI keeps the same ordering) Paolo On Wed, Oct 7, 2020 at 1:21 PM pippo pippo wrote: > Dear Lorenzo and Michel, > > thank you for your reply. Yes, unfortunately I am using a small cluster > and, for memory issues, I cannot use the SSD-based local scratch. Thus I > am forced to use a > non-parallel NFS. From your answers, I understand that, given > the situation, the huge difference between the CPU and WALL time that I am > observing is reasonable. > Since I am facing a hardware limitation I guess I cannot do much to > improve the performances. I will try to find some solutions with the person > in charge of the cluster. > > Best Regards, > Raffaello Bianco > UPV/EHU - CFM > > On Wed, Sep 30, 2020 at 4:13 PM Michal Krompiec > wrote: > >> Dear Rafaello, >> Are you using a local (preferably SSD-based) scratch drive, or a very >> fast parallel file system? >> Best wishes, >> Michal Krompiec >> Merck KGaA >> >> On Wed, 30 Sep 2020 at 15:05, Raffaello Bianco < >> raffaello.bianco...@gmail.com> wrote: >> >>> Dear QE users and developers, >>> >>> I am doing an electron-phonon coupling calculation in this way (I am >>> using QE v 6.6). >>> First, I have done an scf calculation. Then, I have done a phonon >>> calculation where I have printed the dvscf files, with >>> >>>fildvscf = 'dvscf' >>> >>> Subsequently, I have done the electron-phonon calculation changing the >>> k-mesh grid, with >>> >>> trans= .false. >>> electron_phonon = 'simple' >>> >>> The calculation ends correctly, but for some q points I have noticed a >>> huge difference between >>> CPU and Wall time, like >>> >>> PHONON : 15h55m CPU 3d18h56m WALL >>> >>> From the report at the end of the output, the I/O davcio routine seems >>> to be the >>> "guilty": >>> >>> >>> General routines >>> davcio :107.89s CPU 263856.08s WALL ( 520331 calls) >>> >>> Parallel routines >>> >>> Electron-phonon coupling >>> elphon : 41730.55s CPU 309708.87s WALL ( 1 calls) >>> elphel : 41671.20s CPU 309625.04s WALL ( 60 calls) >>> >>> General routines >>> davcio :107.89s CPU 263856.08s WALL ( 520331 calls) >>> >>> This calculation was done with 10 processors and npool = 10, if I use >>> 40 processors and npool = 10 it is worse (as can probably be expected due >>> to the higher number of I / O operations). I have looked at the >>> documentation but I am not very familiar with these things, thus I still >>> have several doubts. Any suggestions on tests to do or how to improve >>> performance, or at least comments to clarify the problem, would be greatly >>> appreciated. >>> >>> Thank you for your time, >>> >>> Best, >>> Raffaello Bianco >>> >>> >>> ___ >>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu) >>> users mailing list users@lists.quantum-espresso.org >>> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> ___ >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu) >> users mailing list users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] gvectors.dat gone in QE 6.0 and beyond, how to extract it?
G-vectors are written to (but not read from) file "charge-density.dat" (default) or "charge-density.hdf5" (if HDF5 is enabled), together with the charge density. Note that it's not G-vectors that are written but Miller indices: G=i*b1+j*b2+k*b3, with b1,b2,b3 primitive reciprocal lattice vectors. See PW/src/io_rho_xml.f90 and routines read_rhog, write_rhog in Modules/io_base.f90 Paolo On Tue, Oct 6, 2020 at 3:32 PM Neven Golenić wrote: > Since the new format in QE, I am unable to find out where G vectors are > written, they used to be in the gvectors.dat file, however I cant find them > anywhere now. How can they be read in the new format? > > Help would be greatly appreciated. > > Kind Regards, > Nevensky, > > — > Lijepi pozdrav, > Neven Golenić > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] not orthogonal operation in dos.x run only
Obscure symmetry problems almost invariably come from the usage of "free" Bravais lattice (ibrav=0) and almost-symmetric-but-not-enough lattice vectors, or by almost-symmetric-but-not-enough atomic positions Paolo On Sat, Oct 3, 2020 at 6:36 PM Lucas Dória wrote: > Dear all, > > I ran into this problem while doing a dos.x calculation (nscf and scf > calculations finished succesfully): > > *'from checkallsym : error # 2* > *not orthogonal operation'* > > The structure is a WS2 bilayer. (WS2 is a layered material, we optimized > bulk structure and then added vaccum in z-direction to get bilayer > structure.) > > When i looked up for possible reasons and solutions, I found this problem > only occuring in vc-relax calculations. Our group did in fact optimized the > hexagonal structure, but vc-relax calculations finished succesfully. > > I add that we already studied electronic properties of another very > similar hexagonal structure, of the same point group, namely MoS2, and we > didn't get symmetry issues. (using v5.4 at the time) > > So, I don't know why this problem of 'not orthogonal operation' is > happening to WS2, and just in dos.x calculation, if it's a crash due to > symmetry breaking. We think that the only major differences between WS2 and > MoS2 are that W is heavier than Mo, and the PP used. But we are using an > optimized ecutwfc. > > Thanks in advance. QE-version used: 6.5. > > Lucas. > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Problems with Fe ONCV pseudopotential
On Wed, Sep 30, 2020 at 2:30 PM mkondrin wrote: May be "ONCV potentials" link in the QE site > (https://www.quantum-espresso.org/pseudopotentials) should be upgraded? > the previous link was selected because it provided PP files with pseudo-atomic orbitals. The last point of the README of https://github.com/pipidog/ONCVPSP contains this statement, that seems to explain what happened and why: * Use at your own risk! Although I used exactly the same input parameters as in the original ABINIT and SG15 database to regenerate ONCVPSPs in UPF format, the ONCVPSP code I used was v3.x where the original ABINIT and SG15 database were generate by v2.x. Therefore, the calculated results could be different. You should always double check your results carefully. Anyway, I have reverted the link to the original one (but won't answer complaints that "projwfc.x doesn't work" and the like) Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] compiling qe_6.6
Please see https://gitlab.com/QEF/q-e/-/issues/214 On Tue, Sep 29, 2020 at 12:20 PM Mohammad Moaddeli < mohammad.moadd...@gmail.com> wrote: > Dear all, > > I am trying to compile qe_6.6 using the following config: > > ./configure FC=mpif90 CC=mpicc > > make.inc file contains: > > DFLAGS = -D__FFTW -D__MPI -Duse_beef > > MPIF90 = mpif90 # --> from apt install mpich > F90 = gfortran > CC = mpicc > F77= gfortran > > However, I got the following error for "make pp": > --- > . > . > . > make[2]: Entering directory '/home/mohammad/Downloads/qe-6.6/PW/src' > make[2]: 'libpw.a' is up to date. > make[2]: Leaving directory '/home/mohammad/Downloads/qe-6.6/PW/src' > make[1]: Leaving directory '/home/mohammad/Downloads/qe-6.6/PW' > if test -d PP ; then \ > ( cd PP ; make TLDEPS= all || exit 1 ) ; fi > make[1]: Entering directory '/home/mohammad/Downloads/qe-6.6/PP' > if test -d src ; then \ > ( cd src ; make || exit 1 ) ; fi > make[2]: Entering directory '/home/mohammad/Downloads/qe-6.6/PP/src' > if test -n "" ; then \ > ( cd ../.. ; make || exit 1 ) ; fi > mpif90 -g -o average.x \ > average.o libpp.a ../../PW/src/libpw.a ../../Modules/libqemod.a > ../../upflib/libupf.a ../../KS_Solvers/libks_solvers.a > ../../FFTXlib/libqefft.a ../../LAXlib/libqela.a ../../UtilXlib/libutil.a > ../../dft-d3/libdftd3qe.a /home/mohammad/Downloads/qe-6.6//clib/clib.a > /home/mohammad/Downloads/qe-6.6//iotk/src/libiotk.a > /home/mohammad/Downloads/qe-6.6//LAPACK/liblapack.a > -L/home/mohammad/Downloads/qe-6.6//FoX/lib -lFoX_dom -lFoX_sax -lFoX_wxml > -lFoX_common -lFoX_utils -lFoX_fsys > /home/mohammad/Downloads/qe-6.6//LAPACK/libblas.a > /home/mohammad/Downloads/qe-6.6//LIBBEEF/libbeef.a > /home/mohammad/Downloads/qe-6.6//LIBBEEF/libbeef.a(beefun.o): In function > `beefx_': > beefun.c:(.text+0x71c5): undefined reference to `ddot_' > beefun.c:(.text+0x71f3): undefined reference to `ddot_' > beefun.c:(.text+0x72a3): undefined reference to `ddot_' > /home/mohammad/Downloads/qe-6.6//LIBBEEF/libbeef.a(beefun.o): In function > `beefxpot_': > beefun.c:(.text+0x79a3): undefined reference to `ddot_' > beefun.c:(.text+0x79f2): undefined reference to `ddot_' > /home/mohammad/Downloads/qe-6.6//LIBBEEF/libbeef.a(beefun.o):beefun.c:(.text+0x8224): > more undefined references to `ddot_' follow > collect2: error: ld returned 1 exit status > Makefile:85: recipe for target 'average.x' failed > make[2]: *** [average.x] Error 1 > make[2]: Leaving directory '/home/mohammad/Downloads/qe-6.6/PP/src' > Makefile:7: recipe for target 'all' failed > make[1]: *** [all] Error 1 > make[1]: Leaving directory '/home/mohammad/Downloads/qe-6.6/PP' > Makefile:97: recipe for target 'pp' failed > make: *** [pp] Error 1 > --- > > Any help will be greatly appreciated. > > > Mohammad Moaddeli > Department of Materials Science and Engineering, School of Engineering, > Shiraz University > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] OPENMP preprocessor tag
Hi, the __OPENMP preprocessing variable, with two underscores, has been
superseded by _OPENMP, with one underscore. All OpenMP-aware compilers
should automatically set _OPENMP. The contents of include/defs.h.README was
obsolete and has been updated recently.
Paolo
On Sun, Sep 27, 2020 at 11:12 AM Sergey Lisenkov wrote:
> Hello,
>
> May be this is not important or irrelevant, but I noticed when I select to
> build MPI/OpenMP hybrid version of QE ("--enable-openmp
> --enable-parallel"), configure script does not activate "-D__OPENMP" tag
> (as it shown in include/defs.h.README).
>
> Is this tag irrelevant for all practical purposes?
>
> Thanks,
> Sergey
> USF
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] ibrav -13
I think that the cif file and ibrav=0 case refer to the "conventional" cell, while the ibrav=-13 case is for the "primitive" cell. The former has twice the number of atoms of the latter, in addition to twice the volume. Using the information on the space group number and Wyckoff positions contained in the cif file, you can obtain the correct (?) structure in an easier way (see attached) Paolo On Sat, Sep 26, 2020 at 12:23 AM Carlo Nervi wrote: > > Dear QE developers, > I have a problem with ibrav -13. > The volume compute at first is too small from what it should be from a cif > file and differs if I run with ibrav=0 > > Attached please find the cif file, the input with ibrav=-13 and with > ibrav=0 > With ibrav=-13 the first volume is computed as > unit-cell volume =1198.4953 (a.u.)^3 > > With ibrav=0 the first volume is computed as > unit-cell volume =2396.9906 (a.u.)^3 > > These are the step 0 of the scf calculations. The right volume seems to be > that one with ibrav=0. > I will appreciate any suggestions. Am I doing something wrong? > Thank you, > Carlo > > -- > > > Prof. Carlo Nervi carlo.ne...@unito.it Tel:+39 0116707507/8 > Fax: +39 0116707855 - Dipartimento di Chimica, via > P. Giuria 7, 10125 Torino, Italy.http://lem.ch.unito.it/ > > ICCC 2020 5-10 July 2020, Rimini, Italy: http://www.iccc2020.com > International Conference on Coordination Chemistry (ICCC 2020) > > <http://www.iccc2020.com/> > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 test_sg.in Description: Binary data ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error in virtual_v2.x
It may not be the reason for the error you get, but: Pb is a PAW potential. I do not think VCA is implemented for PAW. Paolo On Fri, Sep 25, 2020 at 9:04 PM Sriram A wrote: > Dear Users and Experts, > I am trying to use VCA to mix UPF files for Pb and Sn, and Se and Te for a > High Entropy Alloy. Using virtual_v2.x gives me the following error. > Kindly help me rectify the same. > >> $ virtual_v2.x >> >> Generate the UPF pseudopotential for a virtual atom >> combining two pseudopootentials in UPF format >> >> Input PP file # 1 in UPF format > Pb.pbe-dn-kjpaw_psl.0.2.2.UPF >> file type is UPF v.2 >> >> Input PP file # 2 in UPF format > Sn_pbe_v1.uspp.F.UPF >> file type is UPF v.1 >> >> New Pseudo = x Pb.pbe-dn-kjpaw_psl.0.2.2.UPF + (1-x) Sn_pbe_v1.uspp.F.UPF >> mixing parameter x [0> DFT1=SLA PW PBX PBC, DFT2=SLA PW PBE PBE >> BEWARE! CHECK THAT THEY ARE THE SAME! >> pseudopotentials have different mesh >> 1281 891 >>1.1120511775055081E-005 0. >>98.818096677748585208.0913142860 >> pseudopotentials have different mesh >> capel =16570.458924195918 >> INTERPOLATE = T >> interpolate rho_atc >> done >> interpolate vloc0 >> interpolate betar >> interpolate betar >> interpolate betar >> interpolate betar >> interpolate betar >> interpolate betar >> upf(1)%lll =0 0 1 1 >> 2 2 >> upf(2)%lll =0 0 1 1 >> 2 2 >> pp_dij completed. >> pp_qij >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate qfunc >> done >> interpolate chi >> interpolate chi >> interpolate chi >> interpolate rho_at >> done >> At line 559 of file virtual_v2.f90 >> Fortran runtime error: Attempting to allocate already allocated variable >> 'upf_vca' >> >> Error termination. Backtrace: >> #0 0x7fd2d3b8f2ed in ??? >> #1 0x7fd2d3b8fed5 in ??? >> #2 0x7fd2d3b902a7 in ??? >> #3 0x5587508fddfd in compute_virtual_ >> at /home/sriram/qe-6.6/upflib/virtual_v2.f90:559 >> #4 0x5587508ffc07 in virtual_test >> at /home/sriram/qe-6.6/upflib/virtual_v2.f90:85 >> #5 0x5587508f286e in main >> at /home/sriram/qe-6.6/upflib/virtual_v2.f90:29 >> > > Thanks in advance, > *Sriram A* > B.Tech Metallurgical and Materials Engineering, > National Institute of Technology Tiruchirappalli > Tiruchirappalli 620015 > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Mo Pseudopotentials
According to the pseudopotential theory, the reference electronic configuration used to generate a pseudopotential shouldn't matter, as long as it is not too different from the one encountered in the molecule or solid. In practice, one may have to tweak the electronic configuration ii order to avoid ghost states, improve transferability, etc. Paolo On Tue, Sep 22, 2020 at 10:57 PM Victor Bermudez wrote: > Hello, > >I have a question about Mo pseudopotentials. The ground-state valence > configuration of a Mo atom is usually given as (4s)2 (5s)1 (4p)6 (4d)5 . > Some pseudopotentials use this configuration, while others use (4s)2 (5s)2 > (4p)6 (4d)4. Why the difference, and is it significant ? I suspect that it > doesn't matter because the SCF process should converge to the lowest-energy > configuration regardless of the starting configuration. Is that correct ? >Thank you in advance for your help. > > Best Wishes, > Vic Bermudez (US Naval Research Lab. - Retired) > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Orbital magnetization and GIPAW
As far as I know, the method described here is implemented: New J. Phys. 12, 053032 (2010), doi:10.1088/1367-2630/12/5/053032 See variable "lorbm" of pw.x. Note however that this option is unmaintained and may or may not work. Paolo On Wed, Sep 23, 2020 at 7:55 PM Malte Sachs < malte.sa...@chemie.uni-marburg.de> wrote: > Dear all, > > I have found a paper (PHYSICAL REVIEW B 81, 060409 R 2010 ) in which > the orbital magnetization of Fe,Co and Ni is calculated by the GIPAW > method. The authors mention that the method is implemented in Quantum > Espresso. However, I do not find any hint in the Quantum Espresso > distribution or at the GIPAW code. Can anybody tell me, where to find > this code or if it available at all? > > Thank you and best regards, > > Malte > > -- > Malte Sachs > Anorganische Chemie, Fluorchemie > Philipps-Universität Marburg > Hans-Meerwein-Straße 4 > 35032 Marburg (Paketpost: 35043 Marburg) > Tel.: +49 (0)6421 28 - 25 68 0 > http://www.uni-marburg.de/fb15/ag-kraus/ > > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Hybrid vc-relax
On Mon, Sep 21, 2020 at 6:47 PM Mona Asadinamin wrote: Considering that vc-relax is not implemented for hybrid functionals who told you that? it may be slow and not very robust, but it is implemented, as far as I know Paolo Best regards; > > > Mona Asadi Namin > > Graduate student > > Center for simulational physics > > University of Georgia > > -- > > Email:mon...@uga.ed u > > > > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] LO-TO splitting for Phonon DOS
On Tue, Sep 22, 2020 at 9:30 AM Jakob Kraus < jakob.kr...@physik.tu-freiberg.de> wrote: > > judging from the matdyn.f90 source file, it seems possible to include > LO-TO splitting in the calculation of the phonon DOS. > > However, I have not figured out the correct way to enter the direction > of the q vector in the matdyn input file. > it is explained in the header of matdyn.f90, from line 128: ! If q = 0, the direction qhat (q=>0) for the non-analytic part ! is extracted from the sequence of q-points as follows: ! qhat = q(n) - q(n-1) or qhat = q(n) - q(n+1) ! depending on which one is available and nonzero. ! For low-symmetry crystals, specify twice q = 0 in the list ! if you want to have q = 0 results for two different directions Paolo Chttps:// gitlab.com/QEF/q-e/-/commit/52d65b3cdbcc578c5e637082f5b82375471a242f > > Could you provide with an example of a matdyn input file that > incorporates LO-TO splitting in the direction of, let's say, q=(1,0,0)? > > > Moreover, I've noticed that, even though I've set epsil = .false. for > the phonon calculation for a metal, the ph.x code seems to calculate a > (wrong) dielectric tensor if ldisp = .true. > > Does ldisp somehow override epsil in this case? > > > Thank you very much in advance for your time and effort. > > It is very much appreciated. > > > Best regards, > > > Jakob Kraus > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] LO-TO splitting for Phonon DOS
On Tue, Sep 22, 2020 at 9:30 AM Jakob Kraus <
jakob.kr...@physik.tu-freiberg.de> wrote:
Moreover, I've noticed that, even though I've set epsil = .false. for
> the phonon calculation for a metal, the ph.x code seems to calculate a
> (wrong) dielectric tensor if ldisp = .true.
>
> Does ldisp somehow override epsil in this case?
>
not for metals, only for insulators ("metal" = "with broadening or
tetrahedra"). It was clarified a few days ago:
https://gitlab.com/QEF/q-e/-/commit/52d65b3cdbcc578c5e637082f5b82375471a242f
Paolo
>
> Thank you very much in advance for your time and effort.
>
> It is very much appreciated.
>
>
> Best regards,
>
>
> Jakob Kraus
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] f-orbital order in projwfc.x
On Mon, Sep 21, 2020 at 2:40 PM Soumyadeep wrote: In projwfc.x input description order of p,d orbitals are given > (https://www.quantum-espresso.org/Doc/INPUT_PROJWFC.html) Also those for f (and for any l>3) are given: > > Order of m-components for each l in the output: > > 1, cos(phi), sin(phi), cos(2*phi), sin(2*phi), .., cos(l*phi), sin(l*phi) > > The corresponding forms as functions of x,y,z, can be easily obtained as real combinations of usual spherical harmonics like those in this table: https://en.wikipedia.org/wiki/Table_of_spherical_harmonics#Spherical_harmonics Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Query regarding vdW-DF2 functional
On Mon, Sep 21, 2020 at 1:13 PM Dhvaneel Visaria < dhvaneel.visa...@iitb.ac.in> wrote: this convergence issue did not arise for no vdW functional & Grimme-D2 cases > Grimme-D2 has *NO* effect whatsoever on the convergence of the self-consistent procedure. Paolo > What could be the problem? > > Thanks & Regards, > Dhvaneel Visaria > IIT Bombay > > On Mon, 21 Sep 2020 at 15:02, Lorenzo Paulatto wrote: > >> > K_POINTS automatic >> >12 12 1 0 0 0 >> > >> k-point grid which have a dimension multiple of 3 are a frequent cause >> of troubles for graphene. Also, this is probably too coarse. >> >> hth >> >> -- >> Lorenzo Paulatto - Paris >> ___ >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) >> users mailing list users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Which pressure should I report on my work???
;> >> >> >> >> >> >> Hello Dear QE users >> >> >> >> >> I am studying the effect of pressure on >> >> the frequencies. >> >> >> In the experimental article, the >> >> pressure on the solid has been reported to be 7 >> >> kbar. >> >> >> >> >> >> >> >> When I put this pressure (7 kbar) on my >> >> structure and let it relax, the final pressure is >> >> calculated to be 6.57 kbar as the following. >> >> Therefore it is not exactly 7 kbar. >> >> >> >> >> >> >> >> >> >> Computing stress (Cartesian axis) and >> >> pressure >> >> >> >> >> >> total stress (Ry/bohr**3) >> >> (kbar) P=6.57 >> >> >>0.4467 0. -0. >> >> 6.57 0.00 -0.00 >> >> >>0. 0.4467 -0. >> >> 0.00 6.57 -0.00 >> >> >> -0. -0. 0.4467 >> >> -0.00 -0.00 6.57 >> >> >> >> >> >> >> >> >> >> >> >> >> MY QUESTION: Which pressure should I >> >> report on my paper; 7 kbar or 6.57 kbar? >> >> >> >> >> >> >> >> >> >> >> >> >> Any comments would be appreciated. >> >> >> >> >> >> >> >> Best regards >> >> >> >> >> Mohaddeseh >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> - >> >> >> Mohaddeseh Abbasnejad, >> >> >> Assistant Professor of Physics, >> >> >> Faculty of Physics, >> >> >> Shahid Bahonar University of Kerman, >> >> >> Kerman, Iran >> >> >> P.O. Box 76169-133 >> >> >> Tel: +98 34 31322199 >> >> >> Fax: +98 34 33257434 >> >> >> Cellphone: +98 917 731 7514 >> >> >> E-Mail: mohaddeseh.abbasne...@gmail.com >> >> >> Website: academicstaff.uk.ac.ir/moabbasnejad >> >> >> >> >> - >> >> >> >> >> >> >> >> >> >> >> >> ___ >> >> >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) >> >> >> users mailing list users@lists.quantum-espresso.org >> >> >> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ___ >> >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) >> >> users mailing list users@lists.quantum-espresso.org >> >> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> >> >> >> >> >> >> >> >> ___ >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) >> users mailing list users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> >> ___ >> >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) >> >> users mailing list users@lists.quantum-espresso.org >> >> https://lists.quantum-espresso.org/mailman/listinfo/users > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Getting wavefunctions from QE
On Sat, Sep 19, 2020 at 11:54 AM Andrew Xu wrote: Do you know if HDF5 format can also directly output wavefunctions in real > space, or just in reciprocal space? > currently, just reciprocal space -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Output of pw2casino
On Sat, Sep 19, 2020 at 12:40 PM Andrew Xu wrote: In the eigenvectors coefficients, I'd like to clarify what each ordered > pair represents. > Is each ordered pair one complex number with the real part in the first > index, and imaginary part the second index? > yes -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Output of wfck2r.x
On Fri, Sep 18, 2020 at 8:54 AM Andrew Xu wrote: I know it encodes KS orbitals in real-space, but it's not human-readable. > humans don't read KS orbitals. Alternatively, is there some program/option to turn it into a file with > numbers in base 10? > there is a namelist variable "loctave" that might do what you need. See the header of wfck2r.f90, and the code itself. The ordering of real-space wavefunctions is the same as for all real-space arrays and is described in the developers' manual. Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Getting wavefunctions from QE
Some time ago I wrote the attached piece of code that produces a simple
readable output.
Add it somewhere (for instance, at the end of PW/src/punch.f90) and add a
line
CALL simple_output ()
in some suitable place, such as e.g. after the line
CALL punch ('all')
in PW/src/run_pwscf.f90. Don't even think to use it for anything more
complex than simple crystals.You may also add a second line
CALL simple_test ()
that reads what has been written, fills the hamiltonian matrix,
diagonalizes it, and goes out of memory for anything more complex than
simple crystals.
It was working last time I used it, no warranty that it will work for you.
Paolo
On Thu, Sep 17, 2020 at 8:32 AM Andrew Xu wrote:
> Dear users,
>
> I'm trying to extract the wavefunctions in QE after running pw.x,
> preferably in non-binary format. In versions less than 6, these two links
> give me what I want (
> https://pw-forum.pwscf.narkive.com/UnDfSmzu/how-to-use-the-wave-functions,
> https://lists.quantum-espresso.org/pipermail/users/2011-June/020897.html);
> how can I do a similar thing for QE version 6?
>
> In particular (I'm using QE 6.3), I noticed the QExml_example in
> ~espresso/PP/ is missing in QE version 6, and when I do make qexml.x in
> ~espresso/PP/, I get errors. There's a qexml.f90 in Modules, but doing make
> qexml.f90, make qexml.o, make qexml_module.mod don't do anything.
>
> Best,
> Andy
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
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> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
!
! Copyright (C) 2019-2020 Paolo Giannozzi
! This file is distributed under the terms of the
! GNU General Public License. See the file `License'
! in the root directory of the present distribution,
! or http://www.gnu.org/copyleft/gpl.txt .
!
!
SUBROUTINE simple_output ( )
!
!
! Not-so-smart but easy-to-read output file for simple cases (e.g. Si)
!
USE kinds,ONLY : dp
USE io_global,ONLY : stdout
USE io_files, ONLY : iunpun, iunwfc, tmp_dir, prefix, postfix, nwordwfc
USE cell_base,ONLY : at, bg, alat, tpiba
USE ions_base,ONLy : nat, nsp, ityp, atm, tau
USE gvect,ONLY : ngm, mill
USE scf, ONLY : vrs
USE fft_rho, ONLY : rho_r2g
USE lsda_mod, ONLY : nspin
USE klist,ONLY : nks, xk, ngk, igk_k
USE uspp, ONLY : okvan, nkb, vkb, dvan, dvan_so
USE uspp_param, ONLY : nh
USE fft_base, ONLY : dffts
USE buffers, ONLY : get_buffer
USE spin_orb, ONLY : lspinorb, domag
USE wvfct,ONLY : nbnd, et
USE wavefunctions,ONLY : evc
!
IMPLICIT NONE
!
COMPLEX(dp), ALLOCATABLE :: vaux(:,:)
CHARACTER(LEN=256) :: fileout
INTEGER :: ig, is, ik, ikb, ibnd, na, nt
!
fileout = TRIM(tmp_dir) // TRIM( prefix ) // postfix // 'output.dat'
WRITE( UNIT = stdout, FMT = '(/,5X,"Writing simple output data file ",A)' ) &
fileout
iunpun = 4
OPEN ( UNIT = iunpun, FORM = 'formatted', STATUS = 'unknown', &
FILE = fileout )
WRITE(iunpun,'("# Primitive lattice vectors a_1, a_2, a_3 (a.u.)")')
WRITE(iunpun,*) alat*at(:,1), alat*at(:,2), alat*at(:,3)
WRITE(iunpun,'("# Reciprocal lattice vectors b_1, b_2, b_3 (a.u.)")')
WRITE(iunpun,*) tpiba*bg(:,1), tpiba*bg(:,2), tpiba*bg(:,3)
WRITE(iunpun,'("# Number of types of atom")')
WRITE(iunpun,*) nsp
WRITE(iunpun,'("# Number of atoms")')
WRITE(iunpun,*) nat
WRITE(iunpun,'("# Atomic species and positions (x, y, z, in a.u.)")')
DO na =1, nat
nt = ityp(na)
WRITE(iunpun,'(a,3e25.15)') atm(nt), alat*tau(:,na)
END DO
WRITE(iunpun,'("# number of G-vectors")')
WRITE(iunpun,*) ngm
WRITE(iunpun,'("# Miller indices: G=i_1*b_1+i_2*b_2+i_3*b_3")')
WRITE(iunpun,'(3i8)') (mill(:,ig), ig=1,ngm)
WRITE(iunpun,'("# number of spin components")')
WRITE(iunpun,*) nspin
IF ( nspin == 4 ) THEN
WRITE(iunpun,'("# magnetic, spin-orbit?")')
WRITE(iunpun,*) domag, lspinorb
END IF
ALLOCATE (vaux(ngm,nspin))
CALL rho_r2g (dffts, vrs, vaux )
WRITE(iunpun,'("# Local potential V(G) (one column per spin component)")')
DO is=1,nspin
WRITE(iunpun,'("# spin component n.",i4)') is
WRITE(iunpun,*) (vaux(ig,is), ig=1,ngm)
END DO
DEALLOCATE (vaux)
WRITE(iunpun,'("# US PP?")')
WRITE(iunpun,*) okvan
WRITE(iunpun,'("# Nonlocal PP coefficients Dlm")')
DO nt = 1, n
Re: [QE-users] error in nscf calculation
'nscf' calculations also compute the Fermi energy and occupations. If the number of bands (nbnd) you specify is smaller than the number of occupied bands, you get an error. Paolo On Tue, Sep 15, 2020 at 10:29 AM SHIVANI SAINI wrote: > Dear all, > > I am trying to calculate the electronic properties of van der Waals > heterostructure, calculations go smoothly for self consistent (scf.in > <https://www.researchgate.net/deref/http%3A%2F%2Fscf.in>) but for nscf > calculations I encountered an error "Error in routine efermig (1): internal > error, cannot bracket Ef". i tried to play with nbnd and cutoff energy and > also with mixing beta but every time i got the same error. > I am attaching the nscf.in > <https://www.researchgate.net/deref/http%3A%2F%2Fnscf.in> and nscf.out > file herewith, please help me to resolve the issue. > > > <https://www.researchgate.net/post/Problem_in_calculations_of_nscf_for_vdW_structure?_ec=topicPostOverviewAuthoredQuestions=true&_sg=yhR_UICF6NLex8DhvKQXc9mzE-c58CVPKXDFWxsLRLW2ZfL1hTZvDWR6iCzLPSfRVw> > > > > > Regards: > Shivani Saini > Research Scholar > Dept. of Applied Science > Indian Institute of Information Technology, Allahabad > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] QE-v6.6 Compile problem on Centos 8
https://gitlab.com/QEF/q-e/-/issues/214 On Tue, Sep 15, 2020 at 10:02 AM Kefan Chen wrote: > Hi there, > > I'm compiling QE-v6.6 on my Centos 8 machine. This machine has a QE-v6.5 > running normally. > > Here's the error info I got during 'make all': > > mpif90 -g -o average.x \ > average.o libpp.a ../../PW/src/libpw.a ../../Modules/libqemod.a > ../../upflib/libupf.a ../../KS_Solvers/libks_solvers.a > ../../FFTXlib/libqefft.a ../../LAXlib/libqela.a ../../UtilXlib/libutil.a > ../../dft-d3/libdftd3qe.a /home/small1/Downloads/qe-6.6//clib/clib.a > /home/small1/Downloads/qe-6.6//iotk/src/libiotk.a > /home/small1/Downloads/qe-6.6//LAPACK/liblapack.a > -L/home/small1/Downloads/qe-6.6//FoX/lib -lFoX_dom -lFoX_sax -lFoX_wxml > -lFoX_common -lFoX_utils -lFoX_fsys > /home/small1/Downloads/qe-6.6//LAPACK/libblas.a > /home/small1/Downloads/qe-6.6//LIBBEEF/libbeef.a > /home/small1/Downloads/qe-6.6//LIBBEEF/libbeef.a(beefun.o): In function > `beefx_': > beefun.c:(.text+0xb4b4): undefined reference to `ddot_' > beefun.c:(.text+0xb51a): undefined reference to `ddot_' > beefun.c:(.text+0xb5d1): undefined reference to `ddot_' > /home/small1/Downloads/qe-6.6//LIBBEEF/libbeef.a(beefun.o): In function > `beefxpot_': > beefun.c:(.text+0xbf13): undefined reference to `ddot_' > beefun.c:(.text+0xbf41): undefined reference to `ddot_' > /home/small1/Downloads/qe-6.6//LIBBEEF/libbeef.a(beefun.o):beefun.c:(.text+0xc71c): > more undefined references to `ddot_' follow > collect2: error: ld returned 1 exit status > make[2]: *** [Makefile:85: average.x] Error 1 > make[2]: Leaving directory '/home/small1/Downloads/qe-6.6/PP/src' > make[1]: *** [Makefile:7: all] Error 1 > make[1]: Leaving directory '/home/small1/Downloads/qe-6.6/PP' > make: *** [Makefile:97: pp] Error 1 > > I tried to search it online but I found no clue about it. Can anyone help > me with it? > > Thank you very much > > Kefan > > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error in routine pw_readfile
Note that pw.x automatically add a slash at the end of outdir, so if you specify outdir = '/home/hamed/Desktop/quartz/out' > the data is written to /home/hamed/Desktop/quartz/out/pwscf.save. GIPAW behaves differently: tmp_dir = '/home/hamed/Desktop/quartz/out' > Reading data from directory: > /home/hamed/Desktop/quartz/outpwscf.save > You should specify tmp_dir = '/home/hamed/Desktop/quartz/out/' (with a final /) instead Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Variation in ph.x results for QE 6.5 and QE 6.4
ASR is applied by auxiliary code, confusingly named "matdyn.x" and "dynmat.x" Paolo On Mon, Sep 14, 2020 at 9:42 AM Offermans Willem wrote: > Dear QE friends and Paolo, > > I’m sorry to break into this mail thread, but could you elaborate a bit on > “applying acoustic sum rule”. > > How is this done? > > > > Met vriendelijke groeten, > Mit freundlichen Grüßen, > With kind regards, > > > Willem Offermans > Researcher Electrocatalysis SCT > VITO NV | Boeretang 200 | 2400 Mol > Phone:+32(0)14335263 Mobile:+32(0)492182073 > > willem.offerm...@vito.be > > > On 14 Sep 2020, at 08:34, Paolo Giannozzi wrote: > > Apparently the largest discrepancies come from low-energy modes, in > particular zero-frequency acoustic modes (those with "negative" frequencies > that become zero when acoustic sum rule is applied). Even minor changes in > the way exchange-correlation is computed may lead to surprisingly large but > unphysical differences for those modes. > > Paolo > > On Sun, Sep 13, 2020 at 7:54 PM Unmesh Mondal < > unmesh.mon...@students.iiserpune.ac.in> wrote: > >> Dear all, >> I intend to calculate the vibrational modes of gas phase HCOOH (formic >> acid) molecule. >> >> The "ph.x" vibrational frequencies (in cm-1) of the system for the two >> versions of quantum espresso (6.5 and 6.4 : with same compilers) are: >> (QE 6.5) (QE 6.4) >> 1 -207.654081-207.686563 >> 2 -63.775769 -61.840758 >> 3 -55.090067 -57.158594 >> 4 -15.183543 -15.903109 >> 5 20.31166621.386665 >> 6 129.683418 129.214185 >> 7 615.352300615.209434 >> 8 676.597853676.547298 >> 9 999.285772999.331118 >> 10 1071.840671 1071.779138 >> 11 1253.496419 1253.514267 >> 12 1350.618940 1350.925730 >> 13 1735.698557 1735.582574 >> 142965.285270 2965.885980 >> 153665.961548 3665.948232 >> >> The maximum difference in any frequency for the two versions is about 2 >> cm-1. My question: >> Is the difference of 2 cm-1 within the error limit of ph.x >> calculations? What is the accuracy we expect in reporting the vibrational >> frequency (via ph.x)? >> >> Regards and Thanks >> Unmesh Mondal >> IISER Pune, India >> >> ___ >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso >> <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2Fquantum-espresso=02%7C01%7C%7Ceb09c593764540a31b7d08d858786b5c%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C0%7C637356621508435090=kTKqeX%2F%2F%2BO6kPNwef4FIkRfJEGe0%2F%2BN3PfxwhTEI0vM%3D=0> >> ) >> users mailing list users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users >> <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers=02%7C01%7C%7Ceb09c593764540a31b7d08d858786b5c%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C0%7C637356621508445049=3H9VxidE80u1fJGpErn5ia73gcU1wHWEO%2BBKUGsKTEo%3D=0> > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > Quantum ESPRESSO is supported by MaX ( > https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2Fquantum-espressodata=02%7C01%7C%7Ceb09c593764540a31b7d08d858786b5c%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C0%7C637356621508464957sdata=Ve%2ByVOhyxj96wsoUv84X01T7RhUF%2BsbovgeiBIRDERA%3Dreserved=0 > ) > users mailing list users@lists.quantum-espresso.org > > https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusersdata=02%7C01%7C%7Ceb09c593764540a31b7d08d858786b5c%7C9e2777ed82374ab992782c144d6f6da3%7C0%7C0%7C637356621508464957sdata=35lAnSluB8%2BFUxrP7RLiFDVqfOKa7Qs7Xi94ZtlXEq0%3Dreserved=0 > > > VITO Disclaimer: http://www.vito.be/e-maildisclaimer > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Variation in ph.x results for QE 6.5 and QE 6.4
Apparently the largest discrepancies come from low-energy modes, in particular zero-frequency acoustic modes (those with "negative" frequencies that become zero when acoustic sum rule is applied). Even minor changes in the way exchange-correlation is computed may lead to surprisingly large but unphysical differences for those modes. Paolo On Sun, Sep 13, 2020 at 7:54 PM Unmesh Mondal < unmesh.mon...@students.iiserpune.ac.in> wrote: > Dear all, > I intend to calculate the vibrational modes of gas phase HCOOH (formic > acid) molecule. > > The "ph.x" vibrational frequencies (in cm-1) of the system for the two > versions of quantum espresso (6.5 and 6.4 : with same compilers) are: > (QE 6.5) (QE 6.4) > 1 -207.654081-207.686563 > 2 -63.775769 -61.840758 > 3 -55.090067 -57.158594 > 4 -15.183543 -15.903109 > 5 20.31166621.386665 > 6 129.683418 129.214185 > 7 615.352300615.209434 > 8 676.597853676.547298 > 9 999.285772999.331118 > 10 1071.840671 1071.779138 > 11 1253.496419 1253.514267 > 12 1350.618940 1350.925730 > 13 1735.698557 1735.582574 > 142965.285270 2965.885980 > 153665.961548 3665.948232 > > The maximum difference in any frequency for the two versions is about 2 > cm-1. My question: > Is the difference of 2 cm-1 within the error limit of ph.x calculations? > What is the accuracy we expect in reporting the vibrational frequency (via > ph.x)? > > Regards and Thanks > Unmesh Mondal > IISER Pune, India > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] 2 questions on QE v6.6
On Mon, Sep 14, 2020 at 1:07 AM Kefan Chen wrote: > I noticed that QE v6.6 supports stress calculation for noncolinear cases. > Does it mean that I can run GGA noncolinear system relaxation? > you can, but it might be slow I cannot create executables for v6.6. All compiling processes went through > normally and I saw no error. > look more carefully and you will see one (do not use option -j of "make", it makes error messages hard to spot) . Paolo I just followed the same compiling procedure as v6.5 and I tried compiling > v6.5 again after I failed on v6.6 on the same machine and it worked fine. > > Anyone can help me with this? Thank you! > > Regards, > > Kefan > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] problem with number of atoms in pw.x
On Sat, Sep 12, 2020 at 12:43 PM Marcelo Albuquerque wrote: Would it be possible to run dist.x along with the input file to find out > which atom(s) is(are) positioned incorrectly? > not sure what you mean: dist.x reads the input file of pw.x. Have a look at PW/src/run_pwscf.f90 if you want to change its behavior (just locate "dist.x" in the code, it's very simple). Paolo --- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] problem with number of atoms in pw.x
; 37 N tau( 37) = ( -0.1577869 0.5010040 0.9975831 > ) > 38 Sn tau( 38) = ( -0.0014732 -0.4102001 1.2238930 > ) > 39 Sn tau( 39) = ( 0.3559803 0.2038242 1.2238930 > ) > 40 Sn tau( 40) = ( -0.3545071 0.2063759 1.2238930 > ) > 41 Sn tau( 41) = ( -0.0014732 0.4102001 0.5024774 > ) > 42 Sn tau( 42) = ( 0.3559803 -0.2038242 0.5024774 > ) > 43 Sn tau( 43) = ( -0.3545071 -0.2063759 0.5024774 > ) > 44 Ge tau( 44) = ( -0.3506754 0.2104528 0.5754626 > ) > 45 Ge tau( 45) = ( -0.0069197 -0.4089202 0.5754626 > ) > 46 Ge tau( 46) = ( 0.3575951 0.1984674 0.5754626 > ) > 47 Ge tau( 47) = ( 0.3575880 0.1984633 0.5754510 > ) > 48 Ge tau( 48) = ( -0.0069197 -0.4089120 0.5754510 > ) > 49 Ge tau( 49) = ( -0.3506683 0.2104487 0.5754510 > ) > 50 Ge tau( 50) = ( -0.1808480 0.3132379 0.8631852 > ) > 51 Ge tau( 51) = ( 0.3616960 -0.000 0.8631852 > ) > 52 Ge tau( 52) = ( -0.1808480 -0.3132379 0.8631852 > ) > 53 Sn tau( 53) = ( 0.1771154 -0.3067729 0.8631852 > ) > 54 Sn tau( 54) = ( -0.3542309 -0.000 0.8631852 > ) > 55 Sn tau( 55) = ( 0.1771154 0.3067729 0.8631852 > ) > 56 N tau( 56) = ( 0.000 -0.000 0.4022443 > ) > 57 N tau( 57) = ( -0.000 -0.000 1.3241261 > ) > 58 Sn tau( 58) = ( -0.000 -0.000 0.6427795 > ) > 59 Sn tau( 59) = ( 0.000 -0.000 1.0835909 > ) > > i.e. there are 3 Ge atoms more than expected (the count for the other > atoms is OK). And one can see that atoms 44/49, 45/48 and 46/47 are at > nearly the same positions. But of course with these positions added > automatically by pw.x the calculation cannot progress. How can this have > happened? There is something wrong here. > > Best regards, > > -- > José C. Conesa > Research Professor > Instituto de Catálisis y Petroleoquímica, CSIC > Marie Curie, 2; Campus de Cantoblanco > 28028 Madrid (Spain) > Telef. +34 915854766 > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error in routine read_xml_file
Do examples work? On Wed, Sep 9, 2020 at 5:51 PM hamed asadi wrote: > Dear Paolo; > Both versions are 6.5. > > Hamed > > On Wed, 9 Sep 2020, 19:15 Paolo Giannozzi, wrote: > >> Please verify that you are using the same versions of pw.x and gipaw.x to >> produce and read the xml file. >> >> Paolo >> >> On Wed, Sep 9, 2020 at 1:13 PM hamed asadi >> wrote: >> >>> dear all, >>> I am trying to run 'efg' calculation for quartz and working on VMware. >>> After scf calculation with mpirun and 2 cores, efg calculation lunched with >>> "mpirun -n 2 /home/hamed/qe-6.5/qe-gipaw/bin/gipaw.x -in >>> efg.out and unfortunately faced with following error: >>> >>> - >>> Program GIPAW v.6.5 starts on 4Sep2020 at 8: 3:54 >>> >>> This program is part of the open-source Quantum ESPRESSO suite >>> for quantum simulation of materials; please cite >>> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); >>> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017); >>> URL http://www.quantum-espresso.org;, >>> in publications or presentations arising from this work. More details >>> at >>> http://www.quantum-espresso.org/quote >>> >>> Serial version >>> >>> * This is GIPAW git revision >>> e4e5b4705a4bd05b622cb47ab228b3cc73e24bfb * >>> * you can cite: N. Varini et al., Comp. Phys. Comm. 184, 1827 >>> (2013) * >>> * in publications or presentations arising from this work. >>>* >>> >>> Parallelizing q-star over 1 images >>> >>> Reading xml data from directory: >>> >>> /home/hamed/Desktop/quartz/out/scf.savescf.save/ >>> Message from routine qexsd_readschema : >>> xml data file >>> /home/hamed/Desktop/quartz/out/scf.savescf.save/data-file-schema.x >>> >>> >>> %% >>> Error in routine read_xml_file (1): >>> fatal error reading xml file >>> >>> %% >>> >>> stopping ... >>> --- >>> Primary job terminated normally, but 1 process returned >>> a non-zero exit code.. Per user-direction, the job has been aborted. >>> --- >>> -- >>> mpirun detected that one or more processes exited with non-zero status, >>> thus causing >>> the job to be terminated. The first process to do so was: >>> >>> Process name: [[5058,1],0] >>> Exit code:1 >>> -- >>> >>> The output directory cheeked and xml file is presented. here is the >>> input file: >>> >>> >>> job = 'efg' >>> prefix = 'scf' >>> tmp_dir = '/home/hamed/Desktop/quartz/out/scf.save' >>> diagonalization = 'cg' >>> verbosity = 'high' >>> q_gipaw = 0.01 >>> spline_ps = .true. >>> use_nmr_macroscopic_shape = .true. >>> Q_efg(1) = 1.000 >>> Q_efg(2) = -2.558 >>> / >>> >>> I will appreciate any helps in this subject. >>> Truly yours, >>> Hamed Asadi >>> KN Toosi university of technology >>> ___ >>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso >>> ) >>> users mailing list users@lists.quantum-espresso.org >>> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> >> >> -- >> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> ___ >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) >> users mailing list users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] [External Email] Re: how to run ibrav2cell.x?
On Thu, Sep 10, 2020 at 12:52 AM Hari Paudyal wrote: > / > ibrav = 4 > celldm(1) = 5.82 > celldm(3) = 1.14 > should be > ibrav = 4 > celldm(1) = 5.82 > celldm(3) = 1.14 > / > Paolo > When I run ibrav2cell.x; ibrav2cell.x > I got the following error; > > > Error in routine latgen (236): > wrong celldm(1) > > > It looks like my input is not read at all. > > Could you please provide an input example and the way how it is run? I > appreciate it. > > Sincerely, > Hari > > > On Wed, Sep 9, 2020 at 4:34 AM Paolo Giannozzi > wrote: > >> On Wed, Sep 9, 2020 at 4:09 AM Hari Paudyal >> wrote: >> >> Can anyone help me how to use ibrav2cell.x? It says it read the standard >>> PW input >>> >> >> no, it says something different: >> WRITE(*,*) "This code reads a / namelist from standard input" >> WRITE(*,*) "containing ibrav and celldm(1..6) as in INPUT_PW." >> It is admittedly ambiguous: "containing ONLY ibrav and " would be >> clearer >> >> Paolo >> >> >> , but I could not run for my scf.in (PW_input) >>> >>> I used; ibrav2cell.x >> it does not work. >>> >>> On the other hand cell2ibrav.x is very easy to use and very helpful. >>> >>> I appreciate any suggestions. >>> >>> Sincerely, >>> Hari >>> ___ >>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso >>> ) >>> users mailing list users@lists.quantum-espresso.org >>> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> >> >> -- >> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> ___ >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) >> users mailing list users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Issue in WAN90_example
Wannier90 must be compiled ("make w90" should do the job), the
"run_example" script may need to be updated (it was written for a very old
version of the code), and the link from "qe-6.5/bin/wannier90.x" to the
executable must be in place
Paolo
On Wed, Sep 9, 2020 at 10:23 AM Poonam Kaushik
wrote:
> Dear All,
> I'm trying to replicate the results of WAN90_example in the reference
> /user/qe-6.5/PP/examples/WAN90_example. While I successfully completed scf
> and nscf calculations, I am facing the issue, during the run of
> $WAN_COMMAND -pp diamond.sa, and indeed there is no directory in the bin
> wannier90.x.
> "/user/qe-6.5/bin/wannier90.x' not existent or not executable".
> Can anyone please help to figure out this issue? I'll very thankful for
> any help.
>
> Thanks and regards,
> Poonam Sharma
>
> -
> Poonam Sharma
> Research Scholar
> Department of Physics
> Indian Institute of Technology Bombay
> Mumbai - 400076
> India.
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
users mailing list users@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error in routine read_xml_file
Please verify that you are using the same versions of pw.x and gipaw.x to produce and read the xml file. Paolo On Wed, Sep 9, 2020 at 1:13 PM hamed asadi wrote: > dear all, > I am trying to run 'efg' calculation for quartz and working on VMware. > After scf calculation with mpirun and 2 cores, efg calculation lunched with > "mpirun -n 2 /home/hamed/qe-6.5/qe-gipaw/bin/gipaw.x -in efg.out > and unfortunately faced with following error: > > - > Program GIPAW v.6.5 starts on 4Sep2020 at 8: 3:54 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please cite > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017); > URL http://www.quantum-espresso.org;, > in publications or presentations arising from this work. More details at > http://www.quantum-espresso.org/quote > > Serial version > > * This is GIPAW git revision > e4e5b4705a4bd05b622cb47ab228b3cc73e24bfb * > * you can cite: N. Varini et al., Comp. Phys. Comm. 184, 1827 (2013) > * > * in publications or presentations arising from this work. > * > > Parallelizing q-star over 1 images > > Reading xml data from directory: > > /home/hamed/Desktop/quartz/out/scf.savescf.save/ > Message from routine qexsd_readschema : > xml data file > /home/hamed/Desktop/quartz/out/scf.savescf.save/data-file-schema.x > > > %% > Error in routine read_xml_file (1): > fatal error reading xml file > > %% > > stopping ... > --- > Primary job terminated normally, but 1 process returned > a non-zero exit code.. Per user-direction, the job has been aborted. > --- > -- > mpirun detected that one or more processes exited with non-zero status, thus > causing > the job to be terminated. The first process to do so was: > > Process name: [[5058,1],0] > Exit code:1 > -- > > The output directory cheeked and xml file is presented. here is the input > file: > > > job = 'efg' > prefix = 'scf' > tmp_dir = '/home/hamed/Desktop/quartz/out/scf.save' > diagonalization = 'cg' > verbosity = 'high' > q_gipaw = 0.01 > spline_ps = .true. > use_nmr_macroscopic_shape = .true. > Q_efg(1) = 1.000 > Q_efg(2) = -2.558 > / > > I will appreciate any helps in this subject. > Truly yours, > Hamed Asadi > KN Toosi university of technology > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] how to run ibrav2cell.x?
On Wed, Sep 9, 2020 at 4:09 AM Hari Paudyal wrote: Can anyone help me how to use ibrav2cell.x? It says it read the standard PW > input > no, it says something different: WRITE(*,*) "This code reads a / namelist from standard input" WRITE(*,*) "containing ibrav and celldm(1..6) as in INPUT_PW." It is admittedly ambiguous: "containing ONLY ibrav and " would be clearer Paolo , but I could not run for my scf.in (PW_input) > > I used; ibrav2cell.x it does not work. > > On the other hand cell2ibrav.x is very easy to use and very helpful. > > I appreciate any suggestions. > > Sincerely, > Hari > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] How to get Bands of Specific Orbitals (Orbital Contribution)
That graph is generated by script qe-6.5/PP/examples/projected_bands_example/run_example using gnuplot Paolo On Sun, Sep 6, 2020 at 9:23 PM Stephen Zhang wrote: > Hi Everyone, > > I'm trying to replicate the results of example 2 in the > user/qe-6.5/PP/examples/example02/reference. While I successfully plotted > the fermi surface following the directions of README, can anyone please > help me figure out how they plotted the band structures of specific > orbitals (attached is the graph I'm trying to recreate). In the graph, they > managed to show the density of states (via color gradient), the band > structure, as well as the bands associated with each orbital (for Nickel, > they show the band structure for s and d orbitals). If anyone had > experience making this graph, I'd really appreciate any help you can give > me with this. > > Thank you so much, > Stephen > > > -- > *University of California, Berkeley* > *Department of Letter and Sciences* > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error in routine davcio (10)?
> > > > > > > *Warning: Process to core binding is enabled and OMP_NUM_THREADS is set to > non-zero (1) valueIf your program has OpenMP sections, this can cause > over-subscription of cores and consequently poor performanceTo avoid this, > please re-run your application after setting MV2_ENABLE_AFFINITY=0Use > MV2_USE_THREAD_WARNING=0 to suppress this message[cli_12]: aborting > job:application called MPI_Abort(MPI_COMM_WORLD, 1) - process > 12[mpiexec@golub220] HYDT_bscd_pbs_wait_for_completion > (tools/bootstrap/external/pbs_wait.c:67): tm_poll(obit_event) failed with > TM error 17002[mpiexec@golub220] HYDT_bsci_wait_for_completion > (tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting for > completion[proxy:0:0@golub220] HYD_pmcd_pmip_control_cmd_cb > (pm/pmiserv/pmip_cb.c:911): assert (!closed) failed[proxy:0:0@golub220] > HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback > returned error status[proxy:0:0@golub220] main (pm/pmiserv/pmip.c:202): > demux engine error waiting for event* > > > > On Fri, Aug 28, 2020 at 2:40 PM Vasilios Passias > wrote: > >> Hello fellow quantum espresso users. >> >> Recently, I tried running a relaxation calculation. The convergence >> thresholds on the total energy and total force are such that I need to run >> this relaxation calculation multiple times. The first relaxation run, with >> restart_mode = 'from_scratch' , ran fine for the max_time I had set. >> >> Then I set restart_mode = 'restart' and I ran this relaxation calculation >> again, expecting it to continue where it left off. >> >> Instead I got the following error: error in routine davcio (10): >> error while reading from file. >> >> All of the files associated with this error are in the same folder as my >> input and output files. Why is this happening? Should I just re-run this >> calculation? >> >> I have my input, output, job submission, and crash files attached in this >> email. >> >> >> Thank you for your time and input. >> > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] error during the new version (6.6) of Quantum ESSPRESSO instalation
I have been using the same version of the intel compiler + mpif90 until a few days ago (I just upgraded to 2020.2.254) with no problems. Intel compiler + mpiifort also works, when properly installed. There is a report of the same error, see my comments at the end of https://gitlab.com/QEF/q-e/-/issues/208 Paolo On Sun, Aug 30, 2020 at 4:39 PM Mohad Abbasnejad < mohaddeseh.abbasne...@gmail.com> wrote: > Dear Mohammad, > > Thanks alot. > I could compile it by setting the option to "mpif90". > However, after using the "make all" command, I received the following > message and the program stopped working. Any help would be appreciated. > > mpif90 -O3 -g -cpp -D__DFTI -D__MPI -D__SCALAPACK -Duse_beef > -I/opt/Source/q-e-qe-6.6//include -I/opt/Source/q-e-qe-6.6//FoX/finclude > -I/opt/Source/q-e-qe-6.6//S3DE/iotk/include/ > -I/opt/intel/compilers_and_libraries_2020.1.217/linux/mkl/include > -I/opt/Source/q-e-qe-6.6//FoX/finclude -c emend_upf.f90 > emend_upf.f90:29.16: > > OPEN (NEWUNIT = iun_source, FILE = TRIM(filename), STATUS = 'old', & > 1 > Error: Syntax error in OPEN statement at (1) > emend_upf.f90:44.16: > > OPEN (NEWUNIT = iun_dest, FILE = TRIM(tempname), STATUS = 'unknown', & > 1 > Error: Syntax error in OPEN statement at (1) > make[1]: *** [emend_upf.o] Error 1 > make[1]: Leaving directory `/opt/Source/q-e-qe-6.6/upflib' > make: *** [libupf] Error 1 > (base) [root@localhost q-e-qe-6.6]# > > Thanks > > Bests, > Mohaddeseh > > On Sun, Aug 30, 2020 at 4:55 PM Mohammad Moaddeli < > mohammad.moadd...@gmail.com> wrote: > >> Dear Dr. Abbasnejad, >> >> Try this: >> >> ./configure FC=mpiifort --with-scalapack=intel CC=mpiicc MPIF90=mpiifort >> F90=mpiifort F77=mpiifort >> >> Best, >> >> Mohammad >> >> Shiraz Uni >> >> On Sun, Aug 30, 2020 at 2:31 PM Mohad Abbasnejad < >> mohaddeseh.abbasne...@gmail.com> wrote: >> >>> Dear QE users, >>> >>> I am trying to install a new version of Quantum ESPRESSO (6.6). However, >>> I receive the following error message. Any help would be appreciated. >>> >>> (base) [Mohaddeseh@localhost q-e-qe-6.6]$ ./configure >>> checking build system type... x86_64-pc-linux-gnu >>> checking ARCH... x86_64 >>> checking setting AR... ... ar >>> checking setting ARFLAGS... ... ruv >>> checking for gfortran... gfortran >>> checking whether the Fortran compiler works... yes >>> checking for Fortran compiler default output file name... a.out >>> checking for suffix of executables... >>> checking whether we are cross compiling... no >>> checking for suffix of object files... o >>> checking whether we are using the GNU Fortran compiler... yes >>> checking whether gfortran accepts -g... yes >>> checking for mpiifort... mpiifort >>> checking whether we are using the GNU Fortran compiler... no >>> checking whether mpiifort accepts -g... no >>> checking version of mpiifort... unknown, assuming gfortran >>> checking for Fortran flag to compile .f90 files... unknown >>> configure: error: Fortran could not compile .f90 files >>> >>> The version of mpiifort is as following: >>> >>> (base) [Mohaddeseh@localhost q-e-qe-6.6]$ which mpiifort >>> >>> /opt/intel/compilers_and_libraries_2020.1.217/linux/mpi/intel64/bin/mpiifort >>> >>> Thanks in advance. >>> >>> Regards, >>> Mohaddeseh >>> >>> >>> >>> -- >>> - >>> Mohaddeseh Abbasnejad, >>> Assistant Professor of Physics, >>> Faculty of Physics, >>> Shahid Bahonar University of Kerman, >>> Kerman, Iran >>> P.O. Box 76169-133 >>> Tel: +98 34 31322199 >>> Fax: +98 34 33257434 >>> Cellphone: +98 917 731 7514 >>> E-Mail: mohaddeseh.abbasne...@gmail.com >>> Website: academicstaff.uk.ac.ir/moabbasnejad >>> - >>> >>> ___ >>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso >>> ) >>> users mailing list users@lists.quantum-espresso.org >>> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> ___ >> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) >> users mailing list users@lists.quantum-es
Re: [QE-users] Problems running make pw
Mac OS weridness as usual. In make.inc, between the line .h.fh: and the line $(CPP) $(CPPFLAGS) $< -o $*.fh add a line echo $(CPP) $(CPPFLAGS) $< -o $*.fh (there is a tabulator at the beginning of the line, not spaces). This should tell you what is the command that fails, so you can figure out why. Paolo On Sat, Aug 29, 2020 at 5:19 PM Aaron Celestian wrote: > Apologies, forgot to include that. This was the only error. After this, > then compilation stopped. > >include 'laxlib_low.fh' >include 'laxlib_mid.fh' >include 'laxlib_hi.fh' >include 'laxlib_param.fh' > >INTEGER, EXTERNAL :: ldim_block, ldim_cyclic, ldim_block_sca > > 1 warning generated. > clang: *error: *no input files > make[1]: *** [laxlib.fh] Error 1 > make: *** [libla] Error 1 > > > > > On Aug 28, 2020, at 11:38 PM, Paolo Giannozzi > wrote: > > On Sat, Aug 29, 2020 at 12:37 AM Aaron Celestian > wrote: > >> >> * f951:* *Warning:* Nonexistent include directory ' >> */Users/acelesti/QE//FoX/finclude*' [*-Wmissing-include-dirs*] >> mpif90 -O3 -g -fallow-argument-mismatch -cpp -D__FFTW -D__MPI -Duse_beef >> - I/Users/acelesti/QE//include -I/Users/acelesti/QE//FoX/finclude >> -I/Users/acelesti/QE//S3DE/iotk/include/ -c iotk_write.f90 >> > > this is a warning, not an error. Where is the error? > > Paolo > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Problems running make pw
On Sat, Aug 29, 2020 at 12:37 AM Aaron Celestian wrote: > > * f951:* *Warning:* Nonexistent include directory ' > */Users/acelesti/QE//FoX/finclude*' [*-Wmissing-include-dirs*] > mpif90 -O3 -g -fallow-argument-mismatch -cpp -D__FFTW -D__MPI -Duse_beef > - I/Users/acelesti/QE//include -I/Users/acelesti/QE//FoX/finclude > -I/Users/acelesti/QE//S3DE/iotk/include/ -c iotk_write.f90 > this is a warning, not an error. Where is the error? Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] [SUSPECT ATTACHMENT REMOVED] Error in routine davcio (10)?
On Fri, Aug 28, 2020 at 9:40 PM Vasilios Passias wrote: I have my input, output, job submission, and crash files attached in this > email. > you have, but the software of the mailing list didn't like them Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Wrong electron number in superposition of atomic charge densities
(Not-so-)Quick and dirty fix: run the atomic code for the Ti pseudopotential on the ground-state electronic configuration; replace the (pseudo-)atomic charge in the file with the one you get for the ground state. Only the starting charge will be affected. Paolo On Thu, Aug 27, 2020 at 5:28 PM Colonna Nicola (PSI) wrote: > Dear QE experts, > > > I recently perfomed a scf PBEsol calculation for Tb2Ti2O7 (attached the > input file). > > I would like to plot the difference between the scf charge density and > the superposition > > of atomic charge. For this purpose I used the PostProcessing tool > (plut_num = 9). > > > I expected the integral of this difference to be ~0 , but I found it to > be 4. After a quick check > > I realized that the Ti pseudopotetial (GBRV-1.4, > ti_pbesol_v1.4.uspp.F.UPF) was generated > > in an ionized configuration with just 1 electron (instead of 2 ) in the > 3d orbital. Since there > > are 4 Ti in the primitive cell, I think this is the reason for the odd > result described above. > > > Indeed during the initialization of a scf calculation for an isolated Ti > atom I got: > > > Initial potential from superposition of free atoms > Check: negative starting charge= -0.001319 > starting charge 10.6, renormalised to 12.0 > > However this renormalization is not done in the PP, and in any case I do > not think it would make sense there. > > > That said, my feeling is that I cannot completely trust the charge > density difference. > > Do you have any advise on how to solve this problem (beside changing > pseudo)? > > > Thank you in advance and best regards, > > > Nicola Colonna > > > > - > PAUL SCHERRER INSTITUT > Nicola S. Colonna > WHGA/150 > CH-5232 Villigen-PSI > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] a possible bug in QE 6.2.2
On Wed, Aug 26, 2020 at 5:05 PM Ranasinghe, Jayangani wrote: I am using qe 6.2.2 for calculating electron relaxation time using with the > epw package. > really? there is no such version: qe 6.2.1 maybe? About your problem: the 6.2.1 version is almost 3 years old. Nobody has the time to look for bugs in an old version. By the way: memory leaks are often the result of sloppy coding, but sometimes compilers or libraries are responsible Also note that the true amount of memory used by a code is one of the deepest mysteries of IT. Paolo > This calculation needs scf, ph, nscf and epw programs to run to the given > order. Because of this calculation is computationally demanding and has > many factors to optimize to get a convergent result, I wanted to use three > different supercomputer clusters. In order to check the consistency of the > result I ran the same calculation on the three computers. However, I > noticed the memory usage on each cluster is totally different. > > Computer 1: > > Memory Utilized: 8.36 GB (estimated maximum) > > Memory Efficiency: 2.23% of 375.00 GB (187.50 GB/node) > > Computer 2: > > Memory Utilized: 51.64 GB (estimated maximum) > > Memory Efficiency: 183.62% of 28.12 GB (1.76 GB/core) > > Computer 3: > > >Memory Utilized: 174.14 GB > > Memory Efficiency: 93.36% of 186.52 GB > > > > Further, ph.x calculation is crashed in the third computer. This program > needs to create 10 madyn files for my input. However, the third computer > generated only 4 matdyn files, but it finished the ph.out file without any > crashing. In the other two computers, this did not happen (but still the > memory usage is different). > > > > Our computer support says this could happen due to a bug in the QE > program. Could you please let me know if there is a problem in this version > of QE or any other reason for the issue. Thank you. > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] need help with the g-vector mapping
On Sat, Aug 22, 2020 at 3:26 PM Christoph Wolf wrote: > Coeff (dfftp%nl(igk_k(i,kp)))=evc (i, iband) > > (i goes from 1 to ngk for every k-point kp). Then we thought the g-vectors > would map as > > g1(dfftp%nl(igk_k(i,kp))) = g (1, igk_k(i,kp)) > > for the first component of the g-vector but that does not seem to be the > right way. > the right way is: xk(1,kp)+G(1,igk_k(i,kp)) = first component of i-th vector (k+G) corresponding to the i-th plane wave Paolo > Thanks in advance for your help and have a nice weekend! > > Chris > > -- > Postdoctoral Researcher > Center for Quantum Nanoscience, Institute for Basic Science > Ewha Womans University, Seoul, South Korea > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Norm Conserving PP in Supercell
Compare the scf and nscf results for the two sets of pseudopotentials, look for something suspicious? Paolo On Sat, Aug 22, 2020 at 5:24 PM Fariba Islam wrote: > Dear all, > I have written a code for supercell and used ONCV PP. The SCF calculation > converges but nscf calculation does not converge. When I change the pp and > use USPP the both scf and nscf calculation runs smoothly. But for epsilon.x > postprocessing I need ONCV. What should I do to solve this problem? > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] VASP POTCAR into Quantum Espresso formats
On Mon, Aug 17, 2020 at 9:49 PM Ilias Miroslav, doc. RNDr., PhD. < miroslav.il...@umb.sk> wrote: Is there a viable way to convert these POTCAR files into format suitable > for Quantum Espresso ? > it depends upon your definition of "viable" :-) Converting one pseudopotential format into another one implies the knowledge of what is present in each format and also of the correspondence between the quantities read from one format and those written into another one. This is typically easy for norm-conserving PPs, less so for ultrasoft PPs, even less so for PAW. Nobody will do that without a good reason. Paolo > Best, Miro > > PS: I asked similar question on Abinit forum, > https://forum.abinit.org/viewtopic.php?t=4469 . > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] vDW error for scf calculation
On Thu, Aug 20, 2020 at 10:04 AM Neeraj Kulhari < neerajkulhari041...@gmail.com> wrote: with vdw_corr=grimme-d2 or vdw_corr=grimme-d3 I am getting below error > the correct syntax is vdw_corr='grimme-d2' or vdw_corr='grimme-d3' Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] problem whem more than 1000 k-points
Let me understand: are you saying that there might be a problem with the so-called "here document" syntax: pw.x < EOF long input here EOF if the long input is too long? funny Paolo On Thu, Aug 20, 2020 at 11:53 AM aritz leonardo liceranzu wrote: > Dear Fanhao > > I have encountered the same problem and the solution is easy. It > doesn't have anything to do with QE. > > Simply create an independent nscf input file that contains the big > list of kpoints. Do not create the nscf input file within the same job > submission script using EOF. > > Then simply type pw.x < input and it should work. > > Best > Aritz > > > > Quoting Fanhao Jia <18329030...@163.com>: > > > Dear developers, > > I am doing a nscf calculation of GaAs with so many k-points. > > I can run the calculation if the number of k-points is 1000, and it > > is very fast to finish. > > But when I increase to 12*12*12=1728 k-points, the program does not > > really run, there is no output or error. > > I have increased the nkp in Module/parameter.f90 to 10, it > > doesn't help. Increasing cpus still doesn't help. > > I have attached my input. If you have any idea, please let me know. > > Best, > > Fanhao > > > > > > > >calculation = 'bands' > >pseudo_dir = '../' > > / > > > >ecutwfc = 60.0 > >ibrav = 0 > >nat = 2 > >ntyp = 2 > >nbnd=16 > > / > > > >electron_maxstep = 100 > >conv_thr = 1e-10 > >diago_full_acc = .true. > >diago_david_ndim = 4 > >mixing_ndim = 8 > >mixing_mode = 'plain' > >diagonalization = 'david' > >mixing_beta = 0.7 > > / > > CELL_PARAMETERS angstrom > >0.0 2.82675 2.82675 > >2.82675 0.0 2.82675 > >2.82675 2.82675 0.0 > > ATOMIC_SPECIES > >Ga 69.723 'Ga.UPF' > >As 74.9216 'As.UPF' > > ATOMIC_POSITIONS crystal > >Ga 0.0 0.0 0.0 > >As 0.25 0.25 0.25 > > K_POINTS crystal > > 1728 > > 0.0 0.0 0.0 1.0 > > 0.0 0.0 0.08333 1.0 > > 0.0 0.0 0.16667 1.0 > > 0.0 0.0 0.25000 1.0 > > 0.0 0.0 0.3 1.0 > > > > > > > > > > | | > > 贾帆豪 > > | > > | > > 18329030...@163.com > > | > > 签名由网易邮箱大师定制 > > > > > == > Aritz Leonardo Liceranzu > Department of Applied Physics II, > Faculty of Science and Technology, > University of the Basque Country (UPV/EHU) > Bº Sarriena s/n, 48940 Leioa, Spain > > Phone: +34-946015338, Fax: +34-946013500 > Mail: aritz.leona...@ehu.es https://aritzleonardo.wordpress.com/ > == > > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Problems running make pw
gcc 10? check for the presence of "-fallow-argument-mismatch" in compilation flags. "configure" should automatically add it, though. Paolo On Fri, Aug 14, 2020 at 12:33 AM Kelsey Levine wrote: > Dear QE Users, > > I am trying to set up Quantum Espresso 6.5 and have run into a problem > after running make pw. ./configure runs successfully, but make pw returns > the following: > *mp.f90:173:24:* > > 173 | CALL MPI_GATHER(mydata, 1, MPI_INTEGER, alldata, 1, > MPI_INTEGER, root, group, IERR) > |*1* > .. > 197 | CALL MPI_GATHER(mydata, msglen, MPI_INTEGER, alldata, > msglen, MPI_INTEGER, root, group, IERR) > |2 > *Error:* Rank mismatch between actual argument at *(1)* and actual > argument at (2) (rank-1 and scalar) > make[1]: *** [mp.o] Error 1 > make: *** [libutil] Error 1 > > The rank mismatch / type mismatch error displays numerous times before > the compilation actually stops, so I’m not sure if that is actually causing > the error 1 or if it is just a warning. It seems like it might be an issue > with the complier so I tried upgrading gcc to 11.0.3 but to no avail. I am > at a loss for how to solve this issue so any suggestions are appreciated. > > Thank You > Kelsey > Cornell University > ___ > Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) > users mailing list users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
