How to use this library?

How to use this library?#

This section contains a few self-contained examples on how to use D3.

Compute energy with rational damping#

This example shows how to compute the dispersion energy with the rational damping function.

energy.f90#
program test_simple_d3
   use, intrinsic :: iso_fortran_env, only : r8 => real64
   use mctc_env, only: error_type
   use mctc_io, only: structure_type, new
   use dftd3, only: d3_model, d3_param, rational_damping_param, get_rational_damping, &
      & new_rational_damping, new_d3_model, get_dispersion, realspace_cutoff
   implicit none

   character(len=:), allocatable :: method
   type(structure_type) :: mol
   type(error_type), allocatable :: error
   integer, allocatable :: num(:)
   real(r8), allocatable :: xyz(:, :)
   real(r8) :: energy

   type(d3_model) :: disp
   type(d3_param) :: inp
   type(rational_damping_param) :: param

   method = 'PBE0'
   num = [6, 1, 1, 1, 1]
   xyz = reshape([ &  ! coordinates in Bohr
     &  0.0000000_r8, -0.0000000_r8,  0.0000000_r8, &
     & -1.1922080_r8,  1.1922080_r8,  1.1922080_r8, &
     &  1.1922080_r8, -1.1922080_r8,  1.1922080_r8, &
     & -1.1922080_r8, -1.1922080_r8, -1.1922080_r8, &
     &  1.1922080_r8,  1.1922080_r8, -1.1922080_r8],&
     & [3, size(num)])
   call new(mol, num, xyz, charge=0.0_r8, uhf=0)

   call get_rational_damping(inp, method, error, s9=1.0_r8)
   if (allocated(error)) then
      print '(2a)', "Error: ", error%message
      return
   end if
   call new_rational_damping(param, inp)
   call new_d3_model(disp, mol)

   call get_dispersion(mol, disp, param, realspace_cutoff(), energy)
   print '(3a, f13.10, a)', 'Dispersion energy for ', method, '-D3(BJ) is ', energy, ' Hartree'

end program test_simple_d3
energy.c#
#include <stdio.h>
#include <stdbool.h>

#include "dftd3.h"

int main(void)
{
  dftd3_error error = dftd3_new_error();
  dftd3_structure mol = NULL;
  dftd3_model d3 = NULL;
  dftd3_param param = NULL;

  int nat = 5;
  int num[5] = {6, 1, 1, 1, 1};
  double xyz[15] = {  // coordinates in Bohr
     0.0000000, -0.0000000,  0.0000000,
    -1.1922080,  1.1922080,  1.1922080,
     1.1922080, -1.1922080,  1.1922080,
    -1.1922080, -1.1922080, -1.1922080,
     1.1922080,  1.1922080, -1.1922080};
  mol = dftd3_new_structure(error, nat, num, xyz, NULL, NULL);
  if (dftd3_check_error(error)) goto handle_error;

  char method[5] = "PBE0";
  param = dftd3_load_rational_damping(error, method, false);
  if (dftd3_check_error(error)) goto handle_error;

  d3 = dftd3_new_d3_model(error, mol);
  if (dftd3_check_error(error)) goto handle_error;

  double energy;
  dftd3_get_dispersion(error, mol, d3, param, &energy, NULL, NULL);
  if (dftd3_check_error(error)) goto handle_error;

  printf("Dispersion energy for %s-D3(BJ) is %13.10lf Hartree\n", method, energy);

  dftd3_delete(error);
  dftd3_delete(mol);
  dftd3_delete(d3);
  dftd3_delete(param);
  return 0;

handle_error:
  char msg[512];
  dftd3_get_error(error, msg, NULL);
  printf("Error: %s\n", msg);

  dftd3_delete(error);
  dftd3_delete(mol);
  dftd3_delete(d3);
  dftd3_delete(param);
  return 1;
}
energy.py#
import numpy as np
from dftd3.interface import RationalDampingParam, DispersionModel

num = np.array([6, 1, 1, 1, 1])
xyz = np.array(  # coordinates in Bohr
    [
        [ 0.0000000, -0.0000000,  0.0000000],
        [-1.1922080,  1.1922080,  1.1922080],
        [ 1.1922080, -1.1922080,  1.1922080],
        [-1.1922080, -1.1922080, -1.1922080],
        [ 1.1922080,  1.1922080, -1.1922080],
    ]
)
method = "PBE0"

model = DispersionModel(num, xyz)
res = model.get_dispersion(RationalDampingParam(method=method), grad=False)
print(f"Dispersion energy for {method}-D3(BJ) is {res['energy']:13.10f} Hartree")

To test this example you can install the dependencies with

mamba create d3 simple-dftd3 fortran-compiler pkg-config
mamba activate d3

mamba create d3 simple-dftd3 c-compiler pkg-config
mamba activate d3

mamba create d3 dftd3-python
mamba activate d3

You can run the example code with

❯ $FC energy.f90 $(pkg-config s-dftd3 mctc-lib --cflags --libs) && ./a.out
Dispersion energy for PBE0-D3(BJ) is -0.0009218696 Hartree

❯ $CC energy.c $(pkg-config s-dftd3 mctc-lib --cflags --libs) && ./a.out
Dispersion energy for PBE0-D3(BJ) is -0.0009218696 Hartree

❯ python energy.py
Dispersion energy for PBE0-D3(BJ) is -0.0009218696 Hartree
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