[QE-users] NEB unexpected crash
Takahiro Chiba
takahiro_chiba at eis.hokudai.ac.jp
Tue Sep 21 06:53:13 CEST 2021
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
More information about the users
mailing list