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

Amritpal ghumman amritpalghumman at gmail.com
Fri Mar 15 15:23:12 CET 2024


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
For accurate timings, use 'sacct -j 11025262 -X
--format=Submit,Start,End,Elapsed'
======================================================================================
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