[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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