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pyDFTD3 logo

DOI

This program will compute the Grimme D3-dispersion energy for a set of atomic Cartesian coordinates. This version implements both versions of short-range damping that appear in the literature (i.e., zero-damping and Becke-Johnson damping) provided the required parameters are specified manually, or the density functional can be automatically recognized from a Gaussian formatted output file - in which case default values will be used. This program was developed to analyze interatomic and intermolecular dispersion energies within the D3-scheme: if two molecules are recognized based on the interatomic connectivity then it is possible to ignore intramolecular terms.

If a density functional is not recognizable from the input/output file it will be necessary to specify the desired damping parameters. For zero-damping three terms (S6, S8 and RS6) are required. For Becke-Johnson damping four (S6, S8, A1, A2) are required.

The 3-body Axilrod-Teller-Muto 3-body dispersion terms can be switched on (they are not computed by default)

This program is no longer actively developed. Usage is now recommended through the GoodVibes program, where download of these files is necessary for this to function.

Examples

Structure files available in the examples directory

  1. D3-energy correction with zero-damping for a Gaussian output file. The density functional is parsed from the output and the appropriate damping parameters (s6, rs6, rs8) are applied automatically.
   D3-dispersion correction with zero-damping: detected B3LYP functional - using default zero-damping parameters
   Zero-damping parameters: s6 = 1.0 rs6 = 1.261 s8 = 1.703
   3-body term will not be calculated

                                     D3(R6)         D3(R8)         Total (au)
  formic_acid_dimer.log             -0.00088974    -0.50891629    -0.50980603
  1. D3-energy correction with BJ-damping for a Gaussian output file. The density functional is parsed from the output and the appropriate damping parameters (s6, s8, a1, a2) are applied automatically.
   D3-dispersion correction with Becke_Johnson damping: detected B3LYP functional - using default BJ-damping parameters
   BJ-damping parameters: s6 = 1 s8 = 1.9889 a1 = 0.3981 a2 = 4.4211
   3-body term will not be calculated

                                     D3(R6)         D3(R8)         Total (au)
  formic_acid_dimer.log             -0.00455241    -0.00457708    -0.00912948
  1. Pairwise breakdown of the D3(BJ) correction by atom pair.
  --- Pairwise interaction between atoms 1 and 2 : Edisp = -0.359915 kcal/mol -0.3599152449643698
  --- Pairwise interaction between atoms 1 and 3 : Edisp = -0.320618 kcal/mol -0.6805336005703304
  ...
  --- Pairwise interaction between atoms 8 and 10 : Edisp = -0.136812 kcal/mol -5.6753050880809095
  --- Pairwise interaction between atoms 9 and 10 : Edisp = -0.053534 kcal/mol -5.728838870721404
  1. D3-energy correction with BJ-damping for a Gaussian input file. The density functional is parsed from the route line. Based on the connectivity, we request only the intermolecular contributions to the D3-energy.
  Only computing intermolecular dispersion interactions! This is not the total D3-correction

  --- Ignoring interaction between atoms 1 and 2
  --- Ignoring interaction between atoms 1 and 3
  ...
  --- Ignoring interaction between atoms 8 and 10
  --- Ignoring interaction between atoms 9 and 10

                                     D3(R6)         D3(R8)         Total (au)
  formic_acid_dimer.com             -0.00152126    -0.00144858    -0.00296984
  1. D3-energy correction with BJ-damping for an XYZ or PDB input file. Either the density functional or the parameters have to be specified in this case.
  D3-dispersion correction with Becke_Johnson damping: detected B3LYP functional - using default BJ-damping parameters
  BJ-damping parameters: s6 = 1 s8 = 1.9889 a1 = 0.3981 a2 = 4.4211
  3-body term will not be calculated

                                     D3(R6)         D3(R8)         Total (au)
  formic_acid_dimer.xyz             -0.00455241    -0.00457708    -0.00912949

License: MIT

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Python version of Grimme's D3-dispersion correction for Gaussian input/output

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