[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
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--
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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