[QE-users] Problems computing cholesky error in Ni-MoS2 system

Jonathan Backman jbackman at iis.ee.ethz.ch
Wed Jun 19 12:47:57 CEST 2019


Dear Quantum Espresso community,

I am trying to perform a relax calculation on two different Ni-MoS2 contacts. One top contact (Ni over single layer MoS2) and one edge contact (MoS2 connected to the side of Ni), see attached input file. In both cases I get the error "problems computing cholesky". It has previously been suggested that this can happen in the case of "bad" atom positions, but I do not think this is the case for me, especially since it occurs in both my contacts. The problem also remains when changing the pseudo potentials.

It has also been suggested that the error can be caused by a parallelization issue. For the edge contact I am running on 792 processor cores (distributed over 33 nodes) divided over 11 pools (since I have 11 kpoints) with 72 processors per pool. With current ecutwfc the FFT dimensions are ( 360, 384,  72). To my understanding should give a effective parallelization, sine number of processors/pool is smaller or equal to FFR_3 and is a divisor of it. I have also tried with 264 processors, 24 processors/pool, but the problem still remains.

The calculation is able to perform 2-3 bfgs steps before showing the error at the beginning of the next scf cycle. If I then take the last atom positions and perform  a new relaxation calculation it can once again go through 2-3 bfgs steps before error. Using this method I can continue restarting it, but it is not very effective. If I instead restart the calculation using the last saved charge density it shows the error immediately in the first scf iteration.

I would be happy for any suggestions on how to solve this problem.
Please ask if you want more information.


Best regards,
Jonathan Backman, PhD student
Nano-TCAD Group, ETHZ Switzerland
jbackman at iis.ee.ethz.ch

-------------- next part --------------
&CONTROL
     calculation='relax'               
     title ='NiMoS2'
     !restart_mode='restart',
     pseudo_dir='./psudo/'
     outdir='./out/'
     prefix='NiMoS2'
     !verbosity = 'high'
     max_seconds =  84600
/

&SYSTEM
  degauss =   0.04
  ecutrho =   440
  ecutwfc =   55
  ibrav = 0
  nat = 96
  ntyp = 3
  occupations = 'smearing'
  smearing = 'gaussian'
  !vdw_corr = 'grimme-d2'
  nbnd = 1050
/

&ELECTRONS
  conv_thr =   1.0000000000d-7
  mixing_beta = 0.1
  mixing_ndim = 12
  mixing_mode = 'local-TF'
  electron_maxstep = 400
  !startingpot = 'file'
/


&IONS
ion_dynamics = 'bfgs'
/


ATOMIC_SPECIES
Mo     95.94 Mo.pbe-spn-rrkjus_psl.1.0.0.UPF 
S      32.066 S.pbe-nl-rrkjus_psl.1.0.0.UPF  
Ni     58.69 Ni.pbe-spn-rrkjus_psl.1.0.0.UPF 


CELL_PARAMETERS angstrom
26.512 0.0 0.0 
0.0 30.0 0.0 
0.0 0.0 5.4144088    

ATOMIC_POSITIONS angstrom
Mo      13.600157375   5.042240023   3.589838946
Mo      15.218724662   5.094343797   0.933170446
Mo      16.897943760   5.106909550   3.609605900    0   0   0
Mo      18.496915630   5.106909550   0.902401470    0   0   0
Mo      20.095887510   5.106909550   3.609605900    0   0   0
Mo      21.694859390   5.106909550   0.902401470    0   0   0
Mo      23.421498049   5.069863785   3.597095307
Mo      24.951006853   5.011099649   0.870067191
S       13.798592155   3.315567530   1.945827520
S       15.233480275   3.566976927   4.539319595
S       16.897943760   3.548384505   1.804802950    0   0   0
S       18.496915630   3.548384505   4.512007370    0   0   0
S       20.095887510   3.548384505   1.804802950    0   0   0
S       21.694859390   3.548384505   4.512007370    0   0   0
S       23.362380888   3.490510094   1.811787150
S       25.215935387   3.492010714   4.487813139
S       12.987548773   6.509537830   1.751029316
S       15.152052860   6.647777209   4.498181596
S       16.897943760   6.665434605   1.804802950    0   0   0
S       18.496915630   6.665434605   4.512007370    0   0   0
S       20.095887510   6.665434605   1.804802950    0   0   0
S       21.694859390   6.665434605   4.512007370    0   0   0
S       23.404564871   6.604974241   1.752923698
S       25.157228469   6.758107787   4.365514310
Ni       0.352163979   0.364949198  -0.004404339
Ni       0.353983565   0.371931905   2.721614923
Ni       2.300966552   0.247876648   1.354200991
Ni       2.286130498   0.257983546   4.064768131
Ni       4.263925010   0.000000000   0.000000000    0   0   0
Ni       4.263925010   0.000000000   2.707204420    0   0   0
Ni       6.395887510   0.000000000   1.353602210    0   0   0
Ni       6.395887510   0.000000000   4.060806640    0   0   0
Ni       8.498698680   0.128542785  -0.019252414
Ni       8.473475993   0.109972532   2.736871018
Ni      10.492070816   0.155989845   1.402172276
Ni      10.534047747   0.238063458   4.030856330
Ni       0.815309680   2.271612682   1.356907227
Ni       0.580545733   2.393141260   4.072920124
Ni       2.897656117   2.172024619  -0.023570760
Ni       2.889028273   2.170282163   2.737544472
Ni       4.974579180   2.034582350   1.353602220    0   0   0
Ni       4.974579180   2.034582350   4.060806640    0   0   0
Ni       7.106541680   2.034582350   0.000000000    0   0   0
Ni       7.106541680   2.034582350   2.707204430    0   0   0
Ni       9.136779518   2.086035815   1.383345211
Ni       9.196249524   2.141661175   4.041490659
Ni      11.195115936   2.058116378   0.105420128
Ni      11.282022667   2.126338403   2.602451565
Ni       1.493880084   4.198716623   0.059620620
Ni       1.458344451   4.165255277   2.656373649
Ni       3.611113366   4.097507055   1.354798671
Ni       3.590836253   4.106571756   4.058311989
Ni       5.685233340   4.069164700   0.000000010    0   0   0
Ni       5.685233340   4.069164700   2.707204430    0   0   0
Ni       7.817195850   4.069164700   1.353602220    0   0   0
Ni       7.817195850   4.069164700   4.060806640    0   0   0
Ni       9.807387297   4.093703365   0.088076997
Ni       9.870105826   4.108629415   2.631352795
Ni      12.045940914   4.187152741   1.156201865
Ni      11.692999913   3.886761722   4.136462981
Ni       0.384898327   6.303073572   0.149637558
Ni      -0.021570176   6.081270615   2.686114599
Ni       2.256374598   6.105017203   1.475036952
Ni       2.214757101   6.084147984   3.998607591
Ni       4.263925010   6.103747050   0.000000000    0   0   0
Ni       4.263925010   6.103747050   2.707204420    0   0   0
Ni       6.395887510   6.103747050   1.353602210    0   0   0
Ni       6.395887510   6.103747050   4.060806640    0   0   0
Ni       8.470460926   6.087216774   0.008720017
Ni       8.475058764   6.073333865   2.699683100
Ni      10.625673724   6.069449848   1.338615771
Ni      10.574459139   5.993674169   4.089483321
Ni       0.891491960   8.137427109   1.508562300
Ni       0.795944431   8.106149296   3.976853366
Ni       2.879356695   8.030796976  -0.011176201
Ni       2.947725129   8.101934624   2.754320645
Ni       4.974579170   8.138329390   1.353602210    0   0   0
Ni       4.974579170   8.138329390   4.060806630    0   0   0
Ni       7.106541680   8.138329390   0.000000000    0   0   0
Ni       7.106541680   8.138329390   2.707204420    0   0   0
Ni       9.165742419   8.026449804   1.373751393
Ni       9.180926148   8.010081618   4.026892834
Ni      11.244387112   7.934840530  -0.050247447
Ni      11.465405914   7.858726814   2.743194798
Ni       1.553192165   9.946333589   0.006989349
Ni       1.602146053  10.045193675   2.737774463
Ni       3.595273357  10.050816995   1.328761907
Ni       3.603825818  10.065953949   4.106224305
Ni       5.685233340  10.172911740   0.000000000    0   0   0
Ni       5.685233340  10.172911740   2.707204420    0   0   0
Ni       7.817195840  10.172911740   1.353602210    0   0   0
Ni       7.817195840  10.172911740   4.060806640    0   0   0
Ni       9.774229786   9.940530496  -0.005327528
Ni       9.795853918   9.928617174   2.709493357
Ni      11.720946344   9.832952615   1.350148584
Ni      11.733559666   9.853906549   4.054761341


K_POINTS automatic
3 1 7 0 0 0



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