[QE-users] problem with NEB calculation- "problem computing cholesky"

Takahiro Chiba takahiro_chiba at eis.hokudai.ac.jp
Mon Jan 31 10:50:48 CET 2022


Dear Roy,

>From my experience, you should try...
1. Add "-ndiag 1" to your command line. e.g. mpirun neb.x -ndiag 1 -i INP > OUT
It usually works, but if 1 didn't work,
2. Use diagonalization = 'cg' in &ELECTRONS section of your input. It
is much slower than the default, but is more robust.

---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
-----

2022年1月31日(月) 16:49 Aritri Roy <aritrits at kgpian.iitkgp.ac.in>:
>
> Hi,
> I am trying to investigate the Li-ion migration dynamics. I created one Li vacancy in one Li layer by removing one Li atom from it. Then I simulated one neighbouring Li migrates to the vacancy site. I want to calculate the activation energy of this process using the NEB method. But I am getting this error- "Error in routine  cdiaghg (403): problems computing cholesky" . Any help to resolve this error is highly appreciated. Below I have given my input file.
>
> BEGIN
> BEGIN_PATH_INPUT
> &PATH
> string_method = 'neb'
> nstep_path =50
> k_min = 0.4
> k_max = 0.6
> num_of_images = 7
> path_thr = 0.1
> CI_scheme = 'no-CI'
> /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
> &CONTROL
>
> pseudo_dir = '/scratch/puneetce/Aritri/NEB'
> prefix = 'ODH'
> outdir = './output/'
> /
> &SYSTEM
> ecutwfc = 20
> occupations = 'smearing'
> degauss = 0.02
> a     =  5.68580e+00
> c     =  1.41456e+01
> ibrav = 4
> nat   = 47
> ntyp  = 3
> /
> &ELECTRONS
> conv_thr = 1.e-5
> mixing_beta = 0.2
>
>
> /
>
> ATOMIC_SPECIES
> Co 58.9332 Co_pbe_v1.2.uspp.F.UPF
> O 15.9994 O_pbe_v1.2.uspp.F.UPF
> Li 6.941 li_pbe_v1.4.uspp.F.UPF
>
>
> K_POINTS {automatic}
>  4 4 2 0  0 0
>
> BEGIN_POSITIONS
>
> FIRST_IMAGE
> ATOMIC_POSITIONS {angstrom}
> Li      0.000000   0.000000   0.000000  0 0 0
> Li      1.421449   0.820674   4.715205  0 0 0
> Li     -0.000000   1.641348   9.430410 1 1 0
> Li      1.421449   2.462022   0.000000  0 0 0
> Li      2.842898   3.282696   4.715205  0 0 0
> Li     -1.421449   2.462022   0.000000  0 0 0
> Li      0.000000   3.282696   4.715205  0 0 0
> Li     -1.421449   4.103370   9.430410  0 0 0
> Li      2.842898   0.000000   0.000000  0 0 0
> Li      4.264347   0.820674   4.715205  0 0 0
> Li      2.842898   1.641348   9.430410  0 0 0
> Co     -0.000000   1.641348   2.357603  0 0 0
> Co      0.000000   0.000000   7.072808  0 0 0
> Co      1.421449   0.820674  11.788013  0 0 0
> Co     -1.421449   4.103370   2.357603 0 0 0
> Co     -1.421449   2.462022   7.072808  0 0 0
> Co      0.000000   3.282696  11.788013  0 0 0
> Co      2.842898   1.641348   2.357603 0 0 0
> Co      2.842898   0.000000   7.072808  0 0 0
> Co      4.264347   0.820674  11.788013  0 0 0
> Co      1.421449   4.103370   2.357603 0 0 0
> Co      1.421449   2.462022   7.072808  0 0 0
> Co      2.842898   3.282696  11.788013  0 0 0
> O       0.000000   0.000000   3.389106 0 0 0
> O       1.421449   0.820674   1.326100 0 0 0
> O       1.421449   0.820674   8.104311  0 0 0
> O      -0.000000   1.641348   6.041305 0 0 0
> O      -0.000000   1.641348  12.819516  0 0 0
> O       0.000000   0.000000  10.756510  0 0 0
> O      -1.421449   2.462022   3.389106  0 0 0
> O       0.000000   3.282696   1.326100 0 0 0
> O       0.000000   3.282696   8.104311  0 0 0
> O      -1.421449   4.103370   6.041305 0 0 0
> O      -1.421449   4.103370  12.819516  0 0 0
> O      -1.421449   2.462022  10.756510  0 0 0
> O       2.842898   0.000000   3.389106 0 0 0
> O       4.264347   0.820674   1.326100 0 0 0
> O       4.264347   0.820674   8.104311  0 0 0
> O       2.842898   1.641348   6.041305 0 0 0
> O       2.842898   1.641348  12.819516  0 0 0
> O       2.842898   0.000000  10.756510  0 0 0
> O       1.421449   2.462022   3.389106 0 0 0
> O       2.842898   3.282696   1.326100 0 0 0
> O       2.842898   3.282696   8.104311  0 0 0
> O       1.421449   4.103370   6.041305 0 0 0
> O       1.421449   4.103370  12.819516  0 0 0
> O       1.421449   2.462022  10.756510  0 0 0
>
> LAST_IMAGE
> ATOMIC_POSITIONS {angstrom}
> Li      0.000000   0.000000   0.000000  0 0 0
> Li      1.421449   0.820674   4.715205  0 0 0
> Li      1.421449   2.462022   0.000000  0 0 0
> Li      2.842898   3.282696   4.715205  0 0 0
> Li      1.421449   4.103370   9.430410 1 1 0
> Li     -1.421449   2.462022   0.000000  0 0 0
> Li      0.000000   3.282696   4.715205  0 0 0
> Li     -1.421449   4.103370   9.430410  0 0 0
> Li      2.842898   0.000000   0.000000  0 0 0
> Li      4.264347   0.820674   4.715205  0 0 0
> Li      2.842898   1.641348   9.430410  0 0 0
> Co     -0.000000   1.641348   2.357603  0 0 0
> Co      0.000000   0.000000   7.072808  0 0 0
> Co      1.421449   0.820674  11.788013  0 0 0
> Co     -1.421449   4.103370   2.357603  0 0 0
> Co     -1.421449   2.462022   7.072808  0 0 0
> Co      0.000000   3.282696  11.788013  0 0 0
> Co      2.842898   1.641348   2.357603  0 0 0
> Co      2.842898   0.000000   7.072808  0 0 0
> Co      4.264347   0.820674  11.788013  0 0 0
> Co      1.421449   4.103370   2.357603  0 0 0
> Co      1.421449   2.462022   7.072808  0 0 0
> Co      2.842898   3.282696  11.788013  0 0 0
> O       0.000000   0.000000   3.389106  0 0 0
> O       1.421449   0.820674   1.326100  0 0 0
> O       1.421449   0.820674   8.104311 0 0 0
> O      -0.000000   1.641348   6.041305 0 0 0
> O      -0.000000   1.641348  12.819516  0 0 0
> O       0.000000   0.000000  10.756510  0 0 0
> O      -1.421449   2.462022   3.389106 0 0 0
> O       0.000000   3.282696   1.326100  0 0 0
> O       0.000000   3.282696   8.104311 0 0 0
> O      -1.421449   4.103370   6.041305 0 0 0
> O      -1.421449   4.103370  12.819516  0 0 0
> O      -1.421449   2.462022  10.756510  0 0 0
> O       2.842898   0.000000   3.389106 0 0 0
> O       4.264347   0.820674   1.326100  0 0 0
> O       4.264347   0.820674   8.104311 0 0 0
> O       2.842898   1.641348   6.041305 0 0 0
> O       2.842898   1.641348  12.819516  0 0 0
> O       2.842898   0.000000  10.756510  0 0 0
> O       1.421449   2.462022   3.389106 0 0 0
> O       2.842898   3.282696   1.326100  0 0 0
> O       2.842898   3.282696   8.104311 0 0 0
> O       1.421449   4.103370   6.041305 0 0 0
> O       1.421449   4.103370  12.819516  0 0 0
> O       1.421449   2.462022  10.756510  0 0 0
> END_POSITIONS
>
> END_ENGINE_INPUT
> END
> Regards,
> Aritri Roy
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