Fortran API

Fortran API#

The s-dftd3 library seamlessly integrates with other Fortran projects via module interfaces,

Note

Generally, all quantities used in the library are stored in atomic units.

Handling of geometries and structure#

The basic infrastructure to handle molecular and periodic structures is provided by the modular computation tool chain library. The library provides a structure type which is used to represent all geometry related informations in s-dftd3. A structure type can be constructed from arrays or read from a file.

The constructor is provided with the generic interface new and takes an array of atomic numbers (integer) or element symbols (character(len=*)) as well as the cartesian coordinates in Bohr. Additionally, the molecular charge and the number of unpaired electrons can be provided the charge and uhf keyword, respectively. To create a periodic structure the lattice parameters can be passed as 3 by 3 matrix with the lattice keyword.

An example for using the constructor is given here

subroutine example
   use mctc_env, only : wp
   use mctc_io, only : structure_type, new
   implicit none
   type(structure_type) :: mol
   real(wp), allocatable :: xyz(:, :)
   integer, allocatable :: num(:)

   num = [6, 1, 1, 1, 1]
   xyz = reshape([ &
     &  0.00000000000000_wp, -0.00000000000000_wp,  0.00000000000000_wp, &
     & -1.19220800552211_wp,  1.19220800552211_wp,  1.19220800552211_wp, &
     &  1.19220800552211_wp, -1.19220800552211_wp,  1.19220800552211_wp, &
     & -1.19220800552211_wp, -1.19220800552211_wp, -1.19220800552211_wp, &
     &  1.19220800552211_wp,  1.19220800552211_wp, -1.19220800552211_wp],&
     & [3, size(num)])

   call new(mol, num, xyz, charge=0.0_wp, uhf=0)

   ! ...
end subroutine example

To interact with common input file formats for structures the read_structure procedure is available. The file type is inferred from the name of the file automatically or if a file type hint is provided directly from the enumerator of available file types. The read_structure routine can also use an already opened unit, but in this case the file type hint is mandatory to select the correct format to read from.

subroutine example
   use mctc_env, only : error_type
   use mctc_io, only : structure_type, read_structure, file_type
   implicit none
   type(structure_type) :: mol
   type(error_type), allocatable :: error
   character(len=:), allocatable :: input

   input = "struc.xyz"

   call read_structure(mol, input, error, file_type%xyz)
   if (allocated(error)) then
      print '(a)', error%message
      stop 1
   end if

   ! ...
end subroutine example

The structure type as well as the error type are using only allocatable members and can therefore be used without requiring explicit deconstruction.

Certain members of the structure type should be considered immutable, like the number of atoms (nat), the identifiers for unique atoms (id) and the boundary conditions (periodic). To change those specific structure parameters the structure type and all dependent objects should be reconstructed to ensure a consistent setup. Other properties, like the geometry (xyz), molecular charge (charge), number of unpaired electrons (uhf) and lattice parameters (lattice) can be changed without requiring to reconstruct dependent objects like calculators or restart data.

Error handling#

The basic error handler is an allocatable derived type, available from mctc_env as error_type, which signals an error by its allocation status.

use mctc_env, only : error_type, fatal_error
implicit none
type(error_type), allocatable :: error

call always_ok(error)
if (allocated(error)) then
   print '(a)', "Unexpected failure:", error%message
end if

call always_failed(error)
if (allocated(error)) then
   print '(a)', "Error:", error%message
end if

contains
   subroutine always_ok(error)
      type(error_type), allocatable, intent(out) :: error
   end subroutine always_ok

   subroutine always_failed(error)
      type(error_type), allocatable, intent(out) :: error

      call fatal_error(error, "Message associated with this error")
   end subroutine always_failed
end

An unhandled error might get dropped by the next procedure call.

Performing calculations#

An example for performing a calculation with DFT-D3(BJ)-ATM is shown below

subroutine calc_dftd3(mol, method, energy, gradient, sigma, error)
   use mctc_env, only : wp, error_type
   use mctc_io, only : structure_type
   use dftd3, only : d3_model, d3_param, rational_damping_param, &
      & get_rational_damping, new_rational_damping, new_d3_model, &
      & get_dispersion, realspace_cutoff
   type(structure_type), intent(in) :: mol
   character(len=*), intent(in) :: method
   real(wp), intent(out) :: energy
   real(wp), intent(out) :: gradient(:, :)
   real(wp), intent(out) :: sigma(:, :)
   type(error_type), allocatable, intent(out) :: error
   type(d3_model) :: disp
   type(d3_param) :: inp
   type(rational_damping_param) :: param

   call get_rational_damping(inp, method, error, s9=1.0_wp)
   if (allocated(error)) return
   call new_rational_damping(param, inp)

   call new_d3_model(disp, mol)

   call get_dispersion(mol, disp, param, realspace_cutoff(), energy, &
      & gradient, sigma)

end subroutine calc_dftd3
Contents