Dear Pietro, Thank you so much for your further suggestions. I will certainly give them a try. I should probably also update my version of Quantum Espresso and see if the issue persists.
All the best, Martina On Tue, Jul 31, 2018 at 4:25 AM, Pietro Delugas <[email protected]> wrote: > I don't know what to suggest. > > If the issue were the size of the wfc file ( I don't know why it should be > though ) you can run the postprocessing code using more processes , this > will split the .wfc file in as many files as the number of mpi processes. > > other thing one can try is to run scf with wf_collect set to false and > disk_io set to high and see if pw is able to write the .wfc files that then > could be read directly by the pp code ( which in this case must be executed > with the same number of processes as pw ) > > On 30/07/2018 15:56, Martina Lessio wrote: > > Dear Pietro and Lorenzo, > > Thanks so much for your prompt response, I really appreciate it. Here are > my answers to your questions: > - Pietro, thanks so much for explaining the process by which the .wfc1 > file gets created, I was obviously confused about it. I checked and, like > you said, I have .dat files in the folders corresponding to different > k-points in the .save folder. I also don't have a .wfc1 file right after > running the scf. So this all looks correct based on what you said. > I did not report the error message verbatim, the name of the .wfc1 file is > printed correctly in the post processing output. I will copy below my input > for the postprocessing code and also the full output I get in case it might > help understand the issue. > > - Lorenzo, yes, I double-checked and my scf calculation is converged. > > I would really appreciate any further suggestion. Once again, I did not > experience such issues with smaller supercell so maybe that gives us a clue > to what the issue is? > I am copying below the scf input, the PP input and the PP output with the > error message. > > Thank you so much! > > All the best, > Martina > > SCF input file: > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='MoTe2ml_super5x5relaxNOsoc_def_sm_scf', > wf_collect=.TRUE. > pseudo_dir = '/home/mlessio/espresso-5.4.0/pseudo/', > outdir='./' > / > &system > ibrav= 4, A=17.65, B=17.65, C=16.882, cosAB=-0.5, cosAC=0, cosBC=0, > nat= 75, ntyp= 2, > ecutwfc =60. > occupations='smearing', smearing='gaussian', degauss=0.01 > nspin=1 > / > &electrons > mixing_mode = 'plain' > mixing_beta = 0.2 > conv_thr = 1.0d-10 > / > ATOMIC_SPECIES > Te 127.6 Te_ONCV_PBE_FR-1.1.upf > Mo 95.96 Mo_ONCV_PBE_FR-1.0.upf > ATOMIC_POSITIONS {crystal} > Te 0.134763127 0.067705673 0.314838709 > Te 0.135581610 0.267790815 0.313767464 > Te 0.134763126 0.467057438 0.314838722 > Te 0.133426199 0.666852373 0.315066533 > Te 0.133426206 0.866573824 0.315066528 > Te 0.333830680 0.067661368 0.314045748 > Te 0.337736908 0.270977783 0.312935985 > Te 0.337736909 0.466759125 0.312935994 > Te 0.333830676 0.666169311 0.314045769 > Te 0.333147629 0.866573820 0.315066533 > Te 0.532942565 0.067705695 0.314838702 > Te 0.533240880 0.270977796 0.312935965 > Mo 0.533333335 0.466666657 0.289322903 > Te 0.533240864 0.662263084 0.312935994 > Te 0.532942569 0.865236902 0.314838722 > Te 0.733136182 0.066568083 0.315103907 > Te 0.732209205 0.267790808 0.313767451 > Te 0.729022255 0.466759128 0.312935965 > Te 0.729022252 0.662263081 0.312935985 > Te 0.732209231 0.864418420 0.313767464 > Te 0.933431927 0.066568091 0.315103913 > Te 0.933431915 0.266863851 0.315103907 > Te 0.932294341 0.467057436 0.314838702 > Te 0.932338652 0.666169315 0.314045748 > Te 0.932294331 0.865236897 0.314838709 > Te 0.133264211 0.066582612 0.099418260 > Te 0.132725778 0.266362898 0.098974905 > Te 0.133264209 0.466681585 0.099418245 > Te 0.133234326 0.666468628 0.099305464 > Te 0.133234334 0.866765696 0.099305470 > Te 0.333453459 0.066906928 0.098996402 > Te 0.331845525 0.265879796 0.094385362 > Te 0.331845522 0.465965727 0.094385355 > Te 0.333453453 0.666546534 0.098996380 > Te 0.333531374 0.866765693 0.099305464 > Te 0.533318419 0.066582631 0.099418267 > Te 0.534034274 0.265879815 0.094385388 > Te 0.533333335 0.466666657 0.085781188 > Te 0.534034262 0.668154471 0.094385355 > Te 0.533318422 0.866735819 0.099418245 > Te 0.733260257 0.066630122 0.099465712 > Te 0.733637120 0.266362893 0.098974923 > Te 0.734120236 0.465965734 0.094385388 > Te 0.734120239 0.668154464 0.094385362 > Te 0.733637148 0.867274252 0.098974905 > Te 0.933369890 0.066630128 0.099465706 > Te 0.933369876 0.266739776 0.099465712 > Te 0.933417405 0.466681582 0.099418267 > Te 0.933093092 0.666546536 0.098996402 > Te 0.933417392 0.866735813 0.099418260 > Mo 0.066910177 0.133342732 0.207211832 > Mo 0.066910181 0.333567419 0.207211831 > Mo 0.066714643 0.533429235 0.207488709 > Mo 0.066613591 0.733306803 0.206964121 > Mo 0.066714624 0.933285385 0.207488709 > Mo 0.267519938 0.134476688 0.206033961 > Mo 0.268356012 0.334177979 0.204473191 > Mo 0.267519939 0.533043231 0.206033959 > Mo 0.266693218 0.733306792 0.206964121 > Mo 0.266693225 0.933386407 0.206964121 > Mo 0.466956762 0.134476690 0.206033961 > Mo 0.468945823 0.337891653 0.201981378 > Mo 0.468945838 0.531054173 0.201981377 > Mo 0.466956758 0.732480091 0.206033959 > Mo 0.466570767 0.933285385 0.207488709 > Mo 0.666432579 0.133342735 0.207211833 > Mo 0.665821985 0.334177980 0.204473191 > Mo 0.662108323 0.531054164 0.201981378 > Mo 0.665821981 0.731644003 0.204473191 > Mo 0.666432565 0.933089829 0.207211831 > Mo 0.866666673 0.133333333 0.207317092 > Mo 0.866657239 0.333567418 0.207211833 > Mo 0.865523322 0.533043230 0.206033961 > Mo 0.865523308 0.732480089 0.206033961 > Mo 0.866657248 0.933089841 0.207211832 > K_POINTS {automatic} > 2 2 1 0 0 0 > > PP input file: > &inputpp > prefix='MoTe2ml_super5x5relaxNOsoc_def_sm_scf', > outdir='/home/mlessio/MoTe2/NormConservingPseudo/ > MONOLAYER/DEFECT_SIMULATION/RemoveSOC/5x5x1/nspin1/ > AddSmearing/PP_ILDOS/SCF/' > filplot = 'MoTe2ml_5x5noSOCdef_VB-0.4eV_VB' > plot_num= 10 > emin=2.0832 > emax=2.4832 > / > &plot > iflag=3 > output_format=6 > fileout='MoTe2ml_5x5noSOCdef_VB-0.4eV_VB.cube' > / > > PP output: > > ------------------------------------------------------------------------- > > [[27902,1],0]: A high-performance Open MPI point-to-point messaging module > > was unable to find any relevant network interfaces: > > > Module: OpenFabrics (openib) > > Host: compute-0-5 > > > Another transport will be used instead, although this may result in > > lower performance. > > > NOTE: You can disable this warning by setting the MCA parameter > > btl_base_warn_component_unused to 0. > > -------------------------------------------------------------------------- > > > Program POST-PROC v.5.4.0 starts on 29Jul2018 at 15:46:19 > > > This program is part of the open-source Quantum ESPRESSO suite > > for quantum simulation of materials; please cite > > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > > URL http://www.quantum-espresso.org";, > > in publications or presentations arising from this work. More details > at > > http://www.quantum-espresso.org/quote > > > Parallel version (MPI), running on 1 processors > > > Reading data from directory: > > /home/mlessio/MoTe2/NormConservingPseudo/MONOLAYER/DEFECT_SIMULATION/ > RemoveSOC/5x5x1/nspin1/AddSmearing/PP_ILDOS/SCF/ > MoTe2ml_super5x5relaxNOsoc_def_sm_scf.save > > > Info: using nr1, nr2, nr3 values from input > > > Info: using nr1, nr2, nr3 values from input > > > IMPORTANT: XC functional enforced from input : > > Exchange-correlation = PBE ( 1 4 3 4 0 0) > > Any further DFT definition will be discarded > > Please, verify this is what you really want > > > > G-vector sticks info > > -------------------- > > sticks: dense smooth PW G-vecs: dense smooth PW > > Sum 18421 18421 4741 1930105 1930105 251743 > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%% > > Error in routine diropn (10): > > error opening /home/mlessio/MoTe2/NormConservingPseudo/ > MONOLAYER/DEFECT_SIMULATION/RemoveSOC/5x5x1/nspin1/ > AddSmearing/PP_ILDOS/SCF/MoTe2ml_super5x5relaxNOsoc_def_sm_scf.wfc1 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%% > > > stopping ... > > -------------------------------------------------------------------------- > > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > > with errorcode 1. > > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > You may or may not see output from other processes, depending on > > exactly when Open MPI kills them. > > -------------------------------------------------------------------------- > > > On Mon, Jul 30, 2018 at 7:31 AM, Lorenzo Paulatto <[email protected]> > wrote: > >> Are you sure the calculation is converged? If it stops because the a max >> number of iterations has been reached (check the output carefully, or is >> not obvious) the wfc file won't be created, unless you set disk_io to some >> higher value (medium or high, I'm not sure). Of course the real problem >> would be that the scf does not converge. >> >> -- >> Lorenzo Paulatto >> Written on a virtual keyboard with real fingers >> >> On 29 Jul 2018 22:35, "Martina Lessio" <[email protected]> wrote: >> >> Dear all, >> >> I am running some simulations of defects in MoTe2 slabs with the goal of >> plotting the integrated local density of states. >> I have been using different supercell sizes in order to simulate >> different defect concentrations. However, when I use a relatively large >> supercell (5x5), I start incurring the problem that the scf run does not >> seem to print the .wfc1 (it only prints the .save folder). Due to the lack >> of the .wfc1 file the post processing code crashes with the following >> error message: >> >> Error in routine diropn (10): >> error opening filename.wfc1 >> >> I am having a hard time understanding the issue since I usually get the >> .wfc1 file when I run an scf using wf_collect=.true. on smaller supercells. >> My only guess is that this file is way too large to be printed given that >> this is a relatively large supercell. However, I checked with my cluster >> administrator and there should not be any space issue. >> I am copying below my input file for the scf run that fails to print the >> .wfc1 file (I am running version 5.4 of QE). >> >> Thank you in advance for your help. >> >> All the best, >> Martina >> >> -- >> Martina Lessio, Ph.D. >> Frontiers of Science Lecturer in Discipline >> Postdoctoral Research Scientist >> Department of Chemistry >> Columbia University >> >> Input file: >> >> >> &control >> calculation = 'scf' >> restart_mode='from_scratch', >> prefix='MoTe2ml_super5x5relaxNOsoc_def_sm_scf', >> wf_collect=.TRUE. >> pseudo_dir = '/home/mlessio/espresso-5.4.0/pseudo/', >> outdir='./' >> / >> >> >> &system >> ibrav= 4, A=17.65, B=17.65, C=16.882, cosAB=-0.5, cosAC=0, cosBC=0, >> nat= 75, ntyp= 2, >> ecutwfc =60. >> occupations='smearing', smearing='gaussian', degauss=0.01 >> nspin=1 >> / >> >> &electrons >> mixing_mode = 'plain' >> mixing_beta = 0.2 >> conv_thr = 1.0d-10 >> / >> >> ATOMIC_SPECIES >> Te 127.6 Te_ONCV_PBE_FR-1.1.upf >> Mo 95.96 Mo_ONCV_PBE_FR-1.0.upf >> >> ATOMIC_POSITIONS {crystal} >> Te 0.134763127 0.067705673 0.314838709 >> Te 0.135581610 0.267790815 0.313767464 >> Te 0.134763126 0.467057438 0.314838722 >> Te 0.133426199 0.666852373 0.315066533 >> Te 0.133426206 0.866573824 0.315066528 >> Te 0.333830680 0.067661368 0.314045748 >> Te 0.337736908 0.270977783 0.312935985 >> Te 0.337736909 0.466759125 0.312935994 >> Te 0.333830676 0.666169311 0.314045769 >> Te 0.333147629 0.866573820 0.315066533 >> Te 0.532942565 0.067705695 0.314838702 >> Te 0.533240880 0.270977796 0.312935965 >> Mo 0.533333335 0.466666657 0.289322903 >> Te 0.533240864 0.662263084 0.312935994 >> Te 0.532942569 0.865236902 0.314838722 >> Te 0.733136182 0.066568083 0.315103907 >> Te 0.732209205 0.267790808 0.313767451 >> Te 0.729022255 0.466759128 0.312935965 >> Te 0.729022252 0.662263081 0.312935985 >> Te 0.732209231 0.864418420 0.313767464 >> Te 0.933431927 0.066568091 0.315103913 >> Te 0.933431915 0.266863851 0.315103907 >> Te 0.932294341 0.467057436 0.314838702 >> Te 0.932338652 0.666169315 0.314045748 >> Te 0.932294331 0.865236897 0.314838709 >> Te 0.133264211 0.066582612 0.099418260 >> Te 0.132725778 0.266362898 0.098974905 >> Te 0.133264209 0.466681585 0.099418245 >> Te 0.133234326 0.666468628 0.099305464 >> Te 0.133234334 0.866765696 0.099305470 >> Te 0.333453459 0.066906928 0.098996402 >> Te 0.331845525 0.265879796 0.094385362 >> Te 0.331845522 0.465965727 0.094385355 >> Te 0.333453453 0.666546534 0.098996380 >> Te 0.333531374 0.866765693 0.099305464 >> Te 0.533318419 0.066582631 0.099418267 >> Te 0.534034274 0.265879815 0.094385388 >> Te 0.533333335 0.466666657 0.085781188 >> Te 0.534034262 0.668154471 0.094385355 >> Te 0.533318422 0.866735819 0.099418245 >> Te 0.733260257 0.066630122 0.099465712 >> Te 0.733637120 0.266362893 0.098974923 >> Te 0.734120236 0.465965734 0.094385388 >> Te 0.734120239 0.668154464 0.094385362 >> Te 0.733637148 0.867274252 0.098974905 >> Te 0.933369890 0.066630128 0.099465706 >> Te 0.933369876 0.266739776 0.099465712 >> Te 0.933417405 0.466681582 0.099418267 >> Te 0.933093092 0.666546536 0.098996402 >> Te 0.933417392 0.866735813 0.099418260 >> Mo 0.066910177 0.133342732 0.207211832 >> Mo 0.066910181 0.333567419 0.207211831 >> Mo 0.066714643 0.533429235 0.207488709 >> Mo 0.066613591 0.733306803 0.206964121 >> Mo 0.066714624 0.933285385 0.207488709 >> Mo 0.267519938 0.134476688 0.206033961 >> Mo 0.268356012 0.334177979 0.204473191 >> Mo 0.267519939 0.533043231 0.206033959 >> Mo 0.266693218 0.733306792 0.206964121 >> Mo 0.266693225 0.933386407 0.206964121 >> Mo 0.466956762 0.134476690 0.206033961 >> Mo 0.468945823 0.337891653 0.201981378 >> Mo 0.468945838 0.531054173 0.201981377 >> Mo 0.466956758 0.732480091 0.206033959 >> Mo 0.466570767 0.933285385 0.207488709 >> Mo 0.666432579 0.133342735 0.207211833 >> Mo 0.665821985 0.334177980 0.204473191 >> Mo 0.662108323 0.531054164 0.201981378 >> Mo 0.665821981 0.731644003 0.204473191 >> Mo 0.666432565 0.933089829 0.207211831 >> Mo 0.866666673 0.133333333 0.207317092 >> Mo 0.866657239 0.333567418 0.207211833 >> Mo 0.865523322 0.533043230 0.206033961 >> Mo 0.865523308 0.732480089 0.206033961 >> Mo 0.866657248 0.933089841 0.207211832 >> >> K_POINTS {automatic} >> 2 2 1 0 0 0 >> _______________________________________________ >> users mailing list >> [email protected] >> https://lists.quantum-espresso.org/mailman/listinfo/users >> >> >> >> _______________________________________________ >> users mailing list >> [email protected] >> https://lists.quantum-espresso.org/mailman/listinfo/users >> > > > > -- > Martina Lessio, Ph.D. > Frontiers of Science Lecturer in Discipline > Postdoctoral Research Scientist > Department of Chemistry > Columbia University > > > _______________________________________________ > users mailing > [email protected]https://lists.quantum-espresso.org/mailman/listinfo/users > > > > _______________________________________________ > users mailing list > [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > -- Martina Lessio, Ph.D. Frontiers of Science Lecturer in Discipline Postdoctoral Research Scientist Department of Chemistry Columbia University
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