[DFTB-Plus-User] Error in DFTB Calculations with Periodic Boundry Conditions

Bálint Aradi aradi at uni-bremen.de
Wed Apr 10 08:39:40 CEST 2024


Dear Amritpal,

hard to say, without further detail. The error comes from the 
diagonalizer, so there are two likely reasons for the failure:

* Your geometry is ill defined (e.g. you have atoms very close to each other

* Your sk-files have some problems resulting in a non-positive definite 
overlap matrix.

Best regards,

Bálint

On 15.03.24 15:23, Amritpal ghumman wrote:
> Hello
> 
> I am trying to run my first DFTB Calculations with Periodic Boundry 
> Conditions. However getting error. Help is much appreciated.
> 
> 
> Geometry = VASPFormat {
> Au16 O24
> 1.0
>     3.9106853548765952    0.0000000000000000    0.0000000000000002
>     0.0000000000000017   10.5361816600000964    0.0000000000000006
>     0.0000000000000000    0.0000000000000000   12.8778397505124929
> Au O
> 16 24
> Cartesian
>     0.7554028999999995    0.3668195449999998    0.4543756549999999 Au3+
>     0.7554028999999995    0.6331804550000002    0.5456243450000001 Au3+
>     0.5054028999999995    0.3831804550000002    0.7043756549999999 Au3+
>     0.5054028999999995    0.6168195449999998    0.2956243450000001 Au3+
>     0.2554028999999995    0.3668195449999998    0.9543756549999999 Au3+
>     0.2554028999999995    0.6331804550000002    0.0456243450000002 Au3+
>     0.0054028999999995    0.3831804550000002    0.2043756549999998 Au3+
>     0.0054028999999995    0.6168195449999998    0.7956243450000001 Au3+
>     0.2554028999999995    0.8668195449999998    0.4543756549999999 Au3+
>     0.2554028999999995    0.1331804550000002    0.5456243450000001 Au3+
>     0.0054028999999995    0.8831804550000002    0.7043756549999999 Au3+
>     0.0054028999999995    0.1168195449999998    0.2956243450000001 Au3+
>     0.7554028999999995    0.8668195449999998    0.9543756549999999 Au3+
>     0.7554028999999995    0.1331804550000002    0.0456243450000002 Au3+
>     0.5054028999999995    0.8831804550000002    0.2043756549999998 Au3+
>     0.5054028999999995    0.1168195449999998    0.7956243450000001 Au3+
>     0.4378688299999998    0.5000000000000000    0.5000000000000000 O2-
>     0.6878688299999998    0.2500000000000000    0.2500000000000000 O2-
>     0.6221129349999996    0.2681219699999998    0.5821403449999998 O2-
>     0.6221129349999996    0.7318780300000003    0.4178596550000002 O2-
>     0.8721129349999996    0.5181219699999997    0.6678596550000002 O2-
>     0.8721129349999996    0.4818780300000002    0.3321403449999998 O2-
>     0.9378688299999998    0.5000000000000000    0.0000000000000000 O2-
>     0.1878688299999998    0.2500000000000000    0.7500000000000000 O2-
>     0.1221129349999996    0.2681219699999998    0.0821403449999998 O2-
>     0.1221129349999996    0.7318780300000003    0.9178596550000002 O2-
>     0.3721129349999996    0.5181219699999997    0.1678596550000002 O2-
>     0.3721129349999996    0.4818780300000002    0.8321403449999998 O2-
>     0.9378688299999998    0.0000000000000000    0.5000000000000000 O2-
>     0.1878688299999998    0.7500000000000000    0.2500000000000000 O2-
>     0.1221129349999996    0.7681219699999997    0.5821403449999998 O2-
>     0.1221129349999996    0.2318780300000003    0.4178596550000002 O2-
>     0.3721129349999996    0.0181219699999997    0.6678596550000002 O2-
>     0.3721129349999996    0.9818780300000003    0.3321403449999998 O2-
>     0.4378688299999998    0.0000000000000000    0.0000000000000000 O2-
>     0.6878688299999998    0.7500000000000000    0.7500000000000000 O2-
>     0.6221129349999996    0.7681219699999997    0.0821403449999998 O2-
>     0.6221129349999996    0.2318780300000003    0.9178596550000002 O2-
>     0.8721129349999996    0.0181219699999997    0.1678596550000002 O2-
>     0.8721129349999996    0.9818780300000003    0.8321403449999998 O2-
> }
> 
> Driver = ConjugateGradient {
>    MovedAtoms = 1:-1
>    MaxForceComponent = 1E-4
>    MaxSteps = 10000
>    LatticeOpt = No
>    OutputPrefix = "geom_opt"
> }
> 
> Hamiltonian = DFTB {
>    SCC = Yes
>    SCCTolerance = 1e-10
>    MaxSCCIterations = 20000
>    Mixer = Broyden {
>      MixingParameter = 0.99
> }
>    SlaterKosterFiles {
>      Au-Au = "/users/dsb22123/slab53/ausf/Au-Au.skf"
>      Au-O = "/users/dsb22123/slab53/ausf/Au-O.skf"
>      O-Au = "/users/dsb22123/slab53/ausf/O-Au.skf"
>      O-O = "/users/dsb22123/slab53/ausf/O-O.skf"
>    }
>    MaxAngularMomentum {
>      Au = "d"
>       O = "p"
>    }
> KPointsAndWeights = SupercellFolding {
>    6 0 0
>    0 2 0
>    0 0 1
>    0.5 0.5 0.5
> }
> 
> Filling = Fermi {
>      Temperature [kelvin] = 300
>    }
> }
> 
> 
> Options {}
> 
> Analysis {
>    CalculateForces = Yes
> }
> 
> ParserOptions {
>    ParserVersion = 7
> }
> 
> Loading compiler-rt version 2022.1.0
> Loading icc version 2022.1.0
> Loading tbb version 2021.6.0
> Loading mkl version 2022.1.0
> Loading mpi version 2021.6.0
> ===================================================================================
> SLURM Job ID:            11025262
> Submit time:             Fri Mar 15 14:17:12 GMT 2024 (Unix Epoch time: 
> 1710512232)
> Start time:              Fri Mar 15 14:18:40 GMT 2024 (Unix Epoch time: 
> 1710512320)
> No. nodes:               1
> No. tasks:               4
> Job name:                PP
> Account:                 tuttle-rmss
> QoS:                     normal
> Partition (queue):       dev
> Submit directory:        /users/dsb22123/periodic/quick
> Script name:             /users/dsb22123/periodic/quick/dftb-parallel.sh
> Master node:             dev1
> Nodes used:              dev1
> Task distribution:
> ===================================================================================
> 
> |===============================================================================
> |
> |  DFTB+ development version (commit: c741f96d, base: 22.2)
> |
> |  Copyright (C) 2006 - 2022  DFTB+ developers group
> |
> |===============================================================================
> |
> |  When publishing results obtained with DFTB+, please cite the following
> |  reference:
> |
> |  * DFTB+, a software package for efficient approximate density functional
> |    theory based atomistic simulations, J. Chem. Phys. 152, 124101 (2020).
> |    [doi: 10.1063/1.5143190]
> |
> |  You should also cite additional publications crediting the 
> parametrization
> |  data you use. Please consult the documentation of the SK-files for the
> |  references.
> |
> |===============================================================================
> 
> Reading input file 'dftb_in.hsd'
> Parser version: 12
> 
> --------------------------------------------------------------------------------
> ***  Converting input from parser version  7 to parser version 12 ...
> ***  Done.
> 
> Reading SK-files:
> /users/dsb22123/slab53/ausf/Au-Au.skf
> /users/dsb22123/slab53/ausf/Au-O.skf
> /users/dsb22123/slab53/ausf/O-O.skf
> Done.
> WARNING!
> -> This driver is deprecated and will be removed in future versions.
> Please use the GeometryOptimisation driver instead.
> Path: dftbplusinput/Driver/ConjugateGradient
> Line: 52-58 (File: dftb_in.hsd)
> 
> 
> 
> Processed input in HSD format written to 'dftb_pin.hsd'
> 
> Starting initialization...
> --------------------------------------------------------------------------------
> WARNING!
> -> Dipole printed for extended system : value printed is not well defined
> MPI processes:               4
> OpenMP threads:              1
> BLACS orbital grid size:     2 x 2
> BLACS atom grid size:        2 x 2
> Chosen random seed:          445064792
> Current stacksize:           unlimited
> Mode:                        Conjugate gradient relaxation
> Self consistent charges:     Yes
> SCC-tolerance:                 0.100000E-09
> Max. scc iterations:                  20000
> Shell resolved Hubbard:      No
> Spin polarisation:           No
> Nr. of up electrons:           160.000000
> Nr. of down electrons:         160.000000
> Periodic boundaries:         Yes
> Electronic solver:           Relatively robust
> Mixer:                       Broyden mixer
> Mixing parameter:                  0.990000
> Maximal SCC-cycles:                   20000
> Nr. of chrg. vec. in memory:          20000
> Nr. of moved atoms:                      40
> Max. nr. of geometry steps:           10000
> Force tolerance:               0.100000E-03
> Electronic temperature:              0.950045E-03 H      0.258520E-01 eV
> Initial charges:             Set automatically (system chrg:   0.000E+00)
> Included shells:            Au:  s, p, d
>                               O:  s, p
> K-points and weights:           1:  0.083333  0.250000  0.500000     
> 0.166667
>                                  2:  0.083333  0.750000  0.500000     
> 0.166667
>                                  3:  0.250000  0.250000  0.500000     
> 0.166667
>                                  4:  0.250000  0.750000  0.500000     
> 0.166667
>                                  5:  0.416667  0.250000  0.500000     
> 0.166667
>                                  6:  0.416667  0.750000  0.500000     
> 0.166667
> 
> K-points in absolute space:     1:  0.011276  0.012556  0.020546
>                                  2:  0.011276  0.037669  0.020546
>                                  3:  0.033829  0.012556  0.020546
>                                  4:  0.033829  0.037669  0.020546
>                                  5:  0.056382  0.012556  0.020546
>                                  6:  0.056382  0.037669  0.020546
> 
> Extra options:
>                               Mulliken analysis
> Force type                   original
> 
> --------------------------------------------------------------------------------
> 
> ***  Geometry step: 0
> 
>   iSCC Total electronic   Diff electronic      SCC error
> Scalapack operation failed!
> Scalapack operation failed!
> ppotrf in scalafx_ppotrf_dcomplex
> Info: 153
> Scalapack operation failed!
> ppotrf in scalafx_ppotrf_dcomplex
> Info: 153
> Scalapack operation failed!
> ppotrf in scalafx_ppotrf_dcomplex
> Info: 153
> ppotrf in scalafx_ppotrf_dcomplex
> Info: 153
> ===================================================================================
> SLURM job 11025262 ended:     Fri Mar 15 14:18:49 GMT 2024 (Unix Epoch 
> time: 1710512329)
> This is an estimated end time using the 'date' command from node 
> dev1.hpc.strath.ac.uk <http://dev1.hpc.strath.ac.uk>
> For accurate timings, use 'sacct -j 11025262 -X 
> --format=Submit,Start,End,Elapsed'
> ======================================================================================
> 
> _______________________________________________
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> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user

-- 
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/


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