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]
<mailto:[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]
<mailto:[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
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--
Martina Lessio, Ph.D.
Frontiers of Science Lecturer in Discipline
Postdoctoral Research Scientist
Department of Chemistry
Columbia University
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