[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


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