[QE-users] Error in Calculating the d2ns_bare matrix in ph.x
Timrov Iurii
iurii.timrov at epfl.ch
Sun Oct 4 23:37:48 CEST 2020
Dear Mohaddeseh,
Maybe you can try to use more nodes (more RAM)?
Some other comments:
- It is better to try the Davidson diagonalisation method for the SCF calculation
- conv_thr = 1.0d-6 is too large. Try to use 1.0d-12 - 1.0d-15
- If you start the Phonon calculation from scratch (using the PW data) then do not set recover=.true.
- I suggest to use QE 6.6
Greetings,
Iurii
--
Dr. Iurii TIMROV
Postdoctoral Researcher
STI - IMX - THEOS and NCCR - MARVEL
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users <users-bounces at lists.quantum-espresso.org> on behalf of Mohad Abbasnejad <mohaddeseh.abbasnejad at gmail.com>
Sent: Saturday, October 3, 2020 8:24:42 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Error in Calculating the d2ns_bare matrix in ph.x
Thank you Dear Timrov for your reply
I am using QE 6.4, 96 cores with 2 nods. This is my scf and ph input:
&control
calculation='scf',
verbosity = 'low',
restart_mode = 'from_scratch',
prefix = 'structure',
tstress = .true.,
tprnfor = .true.,
forc_conv_thr = 1.0D-4,
pseudo_dir ='./',
outdir='./',
nstep=3000,
wf_collect=.true.
/
&SYSTEM
ibrav=0,
nat=16,
ntyp=4,
ecutwfc=54,
ecutrho=540,
occupations='smearing',
degauss=0.002,
smearing='mv',
lda_plus_u=.true.,
hubbard_u(1)=0.8,
hubbard_u(2)=0.8,
hubbard_u(3)=0.8,
nspin=2, starting_magnetization(1)=-0.25 ,starting_magnetization(2)=0.5, starting_magnetization(3)=-0.25,
/
&electrons
diagonalization='cg',
mixing_mode = 'plain',
mixing_beta = 0.4,
conv_thr = 1.0d-6,
electron_maxstep=600
/
&IONS
ion_dynamics = 'bfgs',
/
&cell
cell_dynamics = 'bfgs',
/
ATOMIC_SPECIES
Ti1 47.867 Ti.pbe-sp-van_ak.UPF
Ti2 47.867 Ti.pbe-sp-van_ak.UPF
Ti3 47.867 Ti.pbe-sp-van_ak.UPF
O 15.9994 O.pbe-van_ak.UPF
K_POINTS {automatic}
6 6 6 0 0 0
CELL_PARAMETERS (bohr)
10.111134720 -4.796028450 0.354034142
10.111109901 4.795974443 0.354015885
-4.375766517 -0.000014854 14.056013806
ATOMIC_POSITIONS (crystal)
Ti3 0.741339363 0.966762327 0.108086076
Ti3 0.258660637 0.033237673 0.891913924
Ti1 0.033235159 0.258661350 0.391913045
Ti1 0.966764841 0.741338650 0.608086955
Ti2 0.500000000 0.500000000 -0.000000000
Ti2 0.500000000 0.500000000 0.500000000
O 0.859056256 0.497199239 0.608571821
O 0.140943744 0.502800761 0.391428179
O 0.502800036 0.140945565 0.891430700
O 0.497199964 0.859054435 0.108569300
O 0.294040535 0.896343128 0.451238915
O 0.705959465 0.103656872 0.548761085
O 0.103655829 0.705960410 1.048758989
O 0.896344171 0.294039590 -0.048758989
O 0.681593682 0.318406936 0.249999781
O 0.318406318 0.681593064 0.750000219
and phinput file as follow:
Electron-phonon coefficients for structure
&inputph
tr2_ph=1.0d-14,
prefix = 'structure',
outdir='./',
fildyn='structure.dyn',
alpha_mix(1)=0.1,
trans=.true.,
ldisp=.true.
recover=.true.,
nq1=2, nq2=2, nq3=2
/
Best regards
Mohaddeseh
On Fri, Oct 2, 2020 at 11:27 AM Timrov Iurii <iurii.timrov at epfl.ch<mailto:iurii.timrov at epfl.ch>> wrote:
Dear Mohaddeseh,
Please check the posting guidelines:
https://www.quantum-espresso.org/forum
In particular, you should tell us which version of QE do you use, provide input and output files (e.g. via Google Drive), tell us how do you run the job (how many cores, how many k pools, etc.), which compilers and libraries do you use.
But my guess is that your job crashes because you do not have enough RAM.
Greetings,
Iurii
--
Dr. Iurii TIMROV
Postdoctoral Researcher
STI - IMX - THEOS and NCCR - MARVEL
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users <users-bounces at lists.quantum-espresso.org<mailto:users-bounces at lists.quantum-espresso.org>> on behalf of Mohad Abbasnejad <mohaddeseh.abbasnejad at gmail.com<mailto:mohaddeseh.abbasnejad at gmail.com>>
Sent: Thursday, October 1, 2020 9:03:12 PM
To: Quantum ESPRESSO users Forum
Subject: [QE-users] Error in Calculating the d2ns_bare matrix in ph.x
Hello QE users
When I am trying to calculate the d2ns_bare matrix for LDA+U phonon calculation of my structure, I am faced with this error:
Calculating the d2ns_bare matrix. It might take a while!
k point # 1 out of 224
k point # 2 out of 224
k point # 3 out of 224
k point # 4 out of 224
k point # 5 out of 224
k point # 6 out of 224
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k point # 18 out of 224
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k point # 24 out of 224
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k point # 36 out of 224
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k point # 68 out of 224
k point # 69 out of 224
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k point # 77 out of 224
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k point # 80 out of 224
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k point # 86 out of 224
k point # 87 out of 224
k point # 88 out of 224
k point # 89 out of 224
k point # 90 out of 224
Application 2461263 exit codes: 174
Application 2461263 exit signals: Killed
Application 2461263 resources: utime ~48102s, stime ~486s, Rss ~326644, inblocks ~0, outblocks ~183880
Any comments would be appreciated.
Thank you in advance.
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.abbasnejad at gmail.com<mailto:mohaddeseh.abbasnejad at gmail.com>
Website: academicstaff.uk.ac.ir/moabbasnejad<http://academicstaff.uk.ac.ir/moabbasnejad>
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---------------------------------------------------------
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.abbasnejad at gmail.com<mailto:mohaddeseh.abbasnejad at gmail.com>
Website: academicstaff.uk.ac.ir/moabbasnejad<http://academicstaff.uk.ac.ir/moabbasnejad>
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