[QE-users] NEB unexpected crash
Mauro Sgroi
maurofrancesco.sgroi at gmail.com
Tue Sep 21 09:43:53 CEST 2021
Dear Takahiro Chiba,
normally I don't set the max_seconds option expecting that the job runs
undefinitively.
The large number of steps is due to difficulties in convergence.
I'm going to verify if the problem is due to the batch queue system.
Best regards,
Mauro.
Il giorno mar 21 set 2021 alle ore 06:54 Takahiro Chiba <
takahiro_chiba at eis.hokudai.ac.jp> ha scritto:
> Dear Sgroi,
>
> Because "max_seconds" is not written in the "&control" section, I
> think this is related to your batch queue. Could you make sure that
> your job is not interrupted or paused by the batch queue?
>
> P.S.
> I am surprised to see your huge nstep_path. Is it intentional?
>
> ---Sender---
> Takahiro Chiba
> 1st-year student at grad. school of chem. sci. and eng., Hokkaido Univ.
> Expected graduation date: Mar. 2023
> takahiro_chiba at eis.hokudai.ac.jp
> -----
>
> 2021年9月21日(火) 0:52 Mauro Sgroi <maurofrancesco.sgroi at gmail.com>:
> >
> > Dear QE users,
> > I'm writing to point out a strange behavior I'm facing using PWNEB.
> >
> > I'm trying to calculate the activation energy related to the movement of
> a Li-ion in NiO doped with one cobalt atom.
> >
> > My input is the following:
> > BEGIN
> > BEGIN_PATH_INPUT
> > &PATH
> > restart_mode = 'from_scratch'
> > string_method = 'neb'
> > nstep_path = 2500
> > ds = 1.D0
> > opt_scheme = "broyden"
> > num_of_images = 12
> > CI_scheme = "no-CI"
> > path_thr = 0.05D0
> > use_freezing = .true.
> > minimum_image = .true.
> > first_last_opt = .true.
> > opt_scheme ='broyden'
> > /
> > END_PATH_INPUT
> > BEGIN_ENGINE_INPUT
> > &CONTROL
> > outdir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/tmp/modalis2/NEB_CO_no_CI'
> > prefix = 'R_3m_ODH_NEB_Co'
> > pseudo_dir = '/workhpc/FCA/FCA_CRF_STRUT/sgroi/DATABASE/ESPRESSO'
> > /
> > &SYSTEM
> > degauss = 1.00000e-02
> > ecutrho = 3.25000e+02
> > ecutwfc = 5.00000e+01
> > ibrav = 0
> > nat = 47
> > nspin = 2
> > ntyp = 4
> > occupations = "smearing"
> > smearing = "gaussian"
> > starting_magnetization(1) = 0.00000e+00
> > starting_magnetization(2) = 0.50000e-01
> > starting_magnetization(3) = 0.00000e+00
> > starting_magnetization(4) = 0.00000e-01
> > lda_plus_u = .true.
> > Hubbard_U(2) = 6.2
> > Hubbard_U(4) = 6.2
> > /
> > &ELECTRONS
> > conv_thr = 1.00000e-07
> > electron_maxstep = 300
> > mixing_beta = 1.00000e-01
> > startingpot = "atomic"
> > startingwfc = "atomic+random"
> > /
> > &IONS
> > /
> > ATOMIC_SPECIES
> > Li 6.94100 Li.pbe-sl-rrkjus_psl.1.0.0.UPF
> > Ni 58.69340 Ni.pbe-n-rrkjus_psl.1.0.0.UPF
> > O 15.99940 O.pbe-nl-rrkjus_psl.1.0.0.UPF
> > Co 58.93319 Co.pbe-n-rrkjus_psl.1.0.0.UPF
> > BEGIN_POSITIONS
> > FIRST_IMAGE
> > ATOMIC_POSITIONS {angstrom}
> > Ni -1.678337 2.906965 -4.880813 0 0 0
> > Ni 2.517505 -1.453482 0.000000 1 1 1
> > Co 1.678337 -2.906965 4.880813 1 1 1
> > Ni 0.845922 1.465179 -4.802724 0 0 0
> > Ni 2.517505 1.453482 0.000000 1 1 1
> > Ni 1.691843 0.000000 4.802724 1 1 1
> > Ni 0.845922 -1.465179 -4.802724 0 0 0
> > Ni 0.000000 2.906965 0.000000 1 1 1
> > Co 0.000000 0.000000 0.000000 1 1 1
> > Ni -0.845922 -1.465179 4.802724 1 1 1
> > Ni -0.845922 1.465179 4.802724 1 1 1
> > Ni -1.691843 0.000000 -4.802724 0 0 0
> > O 1.755223 0.000000 -5.980511 0 0 0
> > O 0.820882 -1.421809 -1.166320 0 0 0
> > O 0.086732 2.906965 3.715693 1 1 1
> > O -0.877611 1.520067 -5.980511 0 0 0
> > O 0.820882 1.421809 -1.166320 0 0 0
> > O 0.000000 0.000000 3.926037 1 1 1
> > O -0.877611 -1.520067 -5.980511 0 0 0
> > O -1.678337 2.906965 -0.877278 0 0 0
> > O -1.641764 0.000000 -1.166320 0 0 0
> > O 2.474140 1.528594 3.715693 1 1 1
> > O 2.474140 -1.528594 3.715693 1 1 1
> > O 1.678337 -2.906965 -5.671852 0 0 0
> > O 2.560871 -1.378371 -3.715693 0 0 0
> > O 1.678337 -2.906965 0.877278 1 1 1
> > O 0.877611 1.520067 5.980511 0 0 0
> > O 0.000000 0.000000 -3.926037 0 0 0
> > O 1.641764 0.000000 1.166320 1 1 1
> > O 0.877611 -1.520067 5.980511 0 0 0
> > O -0.086732 2.906965 -3.715693 0 0 0
> > O -0.820882 1.421809 1.166320 1 1 1
> > O -0.820882 -1.421809 1.166320 1 1 1
> > O -1.678337 2.906965 5.671852 0 0 0
> > O -1.755223 0.000000 5.980511 0 0 0
> > O 2.560871 1.378371 -3.715693 0 0 0
> > Li 2.517505 -1.453482 7.240013 0 0 0
> > Li 1.678337 -2.906965 -2.350686 0 0 0
> > Li 0.000000 0.000000 7.240013 0 0 0
> > Li 1.671002 0.000000 -2.405763 0 0 0
> > Li 0.835501 -1.447130 2.405763 1 1 1
> > Li 0.000000 2.906965 7.240013 0 0 0
> > Li -0.835501 1.447130 -2.405763 0 0 0
> > Li -0.835501 -1.447130 -2.405763 0 0 0
> > Li -1.678337 2.906965 2.350686 1 1 1
> > Li -1.671002 0.000000 2.405763 1 1 1
> > Li 2.517505 1.453482 7.240013 0 0 0
> > LAST_IMAGE
> > ATOMIC_POSITIONS {angstrom}
> > Ni -1.678337 2.906965 -4.880813 0 0 0
> > Ni 2.517505 -1.453482 0.000000 1 1 1
> > Co 1.678337 -2.906965 4.880813 1 1 1
> > Ni 0.845922 1.465179 -4.802724 0 0 0
> > Ni 2.517505 1.453482 0.000000 1 1 1
> > Ni 1.691843 0.000000 4.802724 1 1 1
> > Ni 0.845922 -1.465179 -4.802724 0 0 0
> > Ni 0.000000 2.906965 0.000000 1 1 1
> > Co 0.000000 0.000000 0.000000 1 1 1
> > Ni -0.845922 -1.465179 4.802724 1 1 1
> > Ni -0.845922 1.465179 4.802724 1 1 1
> > Ni -1.691843 0.000000 -4.802724 0 0 0
> > O 1.755223 0.000000 -5.980511 0 0 0
> > O 0.820882 -1.421809 -1.166320 0 0 0
> > O 0.086732 2.906965 3.715693 1 1 1
> > O -0.877611 1.520067 -5.980511 0 0 0
> > O 0.820882 1.421809 -1.166320 0 0 0
> > O 0.000000 0.000000 3.926037 1 1 1
> > O -0.877611 -1.520067 -5.980511 0 0 0
> > O -1.678337 2.906965 -0.877278 0 0 0
> > O -1.641764 0.000000 -1.166320 0 0 0
> > O 2.474140 1.528594 3.715693 1 1 1
> > O 2.474140 -1.528594 3.715693 1 1 1
> > O 1.678337 -2.906965 -5.671852 0 0 0
> > O 2.560871 -1.378371 -3.715693 0 0 0
> > O 1.678337 -2.906965 0.877278 1 1 1
> > O 0.877611 1.520067 5.980511 0 0 0
> > O 0.000000 0.000000 -3.926037 0 0 0
> > O 1.641764 0.000000 1.166320 1 1 1
> > O 0.877611 -1.520067 5.980511 0 0 0
> > O -0.086732 2.906965 -3.715693 0 0 0
> > O -0.820882 1.421809 1.166320 1 1 1
> > O -0.820882 -1.421809 1.166320 1 1 1
> > O -1.678337 2.906965 5.671852 0 0 0
> > O -1.755223 0.000000 5.980511 0 0 0
> > O 2.560871 1.378371 -3.715693 0 0 0
> > Li 2.517505 -1.453482 7.240013 0 0 0
> > Li 1.678337 -2.906965 -2.350686 0 0 0
> > Li 0.000000 0.000000 7.240013 0 0 0
> > Li 1.671002 0.000000 -2.405763 0 0 0
> > Li 0.835501 -1.447130 2.405763 1 1 1
> > Li 0.000000 2.906965 7.240013 0 0 0
> > Li -0.835501 1.447130 -2.405763 0 0 0
> > Li -0.835501 -1.447130 -2.405763 0 0 0
> > Li -1.678337 2.906965 2.350686 1 1 1
> > Li 0.835501 1.447130 2.405763 1 1 1
> > Li 2.517505 1.453482 7.240013 0 0 0
> > END_POSITIONS
> > K_POINTS { gamma }
> > CELL_PARAMETERS {angstrom}
> > 5.813929 0.000000 0.000000
> > 0.000000 5.813929 0.000000
> > 0.000000 0.000000 14.48002
> > END_ENGINE_INPUT
> > END
> >
> > The calculation stops with the following message:
> >
> > WARNING : scf convergence NOT achieved on image 11
> > cleaning-up extrapolation files
> > NEB : 5m11.32s CPU 5m16.54s WALL
> > This run was terminated on: 17:33: 4 20Sep2021
> >
> > but in image 11 output I've:
> > iteration #116 ecut= 50.00 Ry beta= 0.10
> > Davidson diagonalization with overlap
> > ethr = 1.92E-10, avg # of iterations = 1.0
> >
> > total cpu time spent up to now is 301.9 secs
> >
> > total energy = -2097.24718498 Ry
> > estimated scf accuracy < 0.00000057 Ry
> >
> > total magnetization = 9.00 Bohr mag/cell
> > absolute magnetization = 16.79 Bohr mag/cell
> >
> > iteration #117 ecut= 50.00 Ry beta= 0.10
> > Davidson diagonalization with overlap
> >
> > Program stopped by user request
> > Calculation stopped in k-point loop, point # 1
> > Calculation stopped in scf loop at iteration # 116
> >
> > What does " Program stopped by user request" it mean?
> > Is there a way to fix this behaviour?
> >
> > Thanks a lot and best regards,
> > Mauro Sgroi.
> > _______________________________________________
> > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> > users mailing list users at 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 at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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