write_xyz Module Reference

Functions/Subroutines
subroutine	xyz_writer (filename, configuration, setup, trajectory)
	Subroutine to write xyz file

Function/Subroutine Documentation

xyz_writer()

subroutine write_xyz::xyz_writer	(	character(len=*), intent(in)	filename,
		integer(array_int), dimension(:,:,:,:), intent(in)	configuration,
		type(run_params), intent(in)	setup,
		logical, optional	trajectory )

Subroutine to write xyz file

This is routine writes an xyz file of the current configuration, in the extended xyz format, (incl. lattice, element type and coordinates) with option to append configurations in a single trajectory file.

Author

C. D. Woodgate

L. B. Partay

Date

2024

Parameters

filename	Name of file to be created
configuration	Current atomic configuration
setup	Derived type containing simulation parameters
trajectory	Logical type, if true, configuration will be appended to the end of the file

Returns

None

Definition at line 40 of file write_xyz.f90.

    ! Simulation setup information
    type(run_params), intent(in) :: setup
 
    ! Data to write to file
    !integer(array_int), dimension(:,:,:,:), allocatable, intent(in) :: configuration
    integer(array_int), dimension(:,:,:,:), intent(in) :: configuration
 
    ! Option to open existing xyz file and append new configuration to the end
    logical, optional :: trajectory
 
    ! Sizes of grid
    integer, dimension(4) :: grid_sizes
 
    ! Filename to which to write
    character(len=*), intent(in) :: filename
 
    integer :: n_particles, i, j, k, l
    logical :: exist
    real(real64), dimension(3) :: pos
 
    n_particles = total_particle_count(setup, configuration)
 
    grid_sizes = shape(configuration)
 
    ! Check if we want to open new xyz, overwrite existing xyz or append existing xyz file
    if (present(trajectory)) then
 
      if (trajectory) then
        inquire(file=filename, exist=exist)
        if (exist) then
          open(7, file=filename, status="old", position="append", action="write")
        else
          open(7, file=filename, status="new", action="write")
        end if      
      end if
 
    else ! open xyz (if exists, will ovrewrite)
 
      open(unit=7, file=filename)
 
    endif  
 
    write(7, *) n_particles
 
    write(7,*) 'Lattice="',setup%lattice_parameter*setup%n_1, 0.0, 0.0 , &
                   &   0.0, setup%lattice_parameter*setup%n_2, 0.0 , &
                   &   0.0, 0.0, setup%lattice_parameter*setup%n_3,     '"'
 
!    if (present(trajectory)) then
!      if (trajectory) then
!        write(7,*) 'Lattice="',setup%lattice_parameter*setup%n_1, 0.0, 0.0 , &
!                       &   0.0, setup%lattice_parameter*setup%n_2, 0.0 , &
!                       &   0.0, 0.0, setup%lattice_parameter*setup%n_3,     '"'
!      end if          
!    else           
!      write(7,*) ''
!    end if
 
    do i=1, grid_sizes(1)
      do j=1, grid_sizes(2)
        do k=1, grid_sizes(3)
          do l=1, grid_sizes(4)
            if (configuration(i,j,k,l) .eq. 0) cycle
            pos = real(j-1)*setup%lattice_vectors(1,:) + &
                  real(k-1)*setup%lattice_vectors(2,:) + &
                  real(l-1)*setup%lattice_vectors(3,:) + &
                  real(i)*setup%basis_vectors
            pos = pos*setup%lattice_parameter
            write(7,*) setup%species_names(configuration(i,j,k,l)), pos(1),pos(2),pos(3)
          end do
        end do
      end do
    end do
 
    close(unit=7)
 

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