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127 lines
4.6 KiB
127 lines
4.6 KiB
module opt_delete
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use parameters
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use subroutines
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use elements
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use neighbors
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implicit none
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real(kind=dp) :: rc_off
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public
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contains
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subroutine run_delete(arg_pos)
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integer, intent(inout) :: arg_pos
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rc_off = -lim_zero
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!Main calling function for delete option.
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print *, '-----------------------Option Delete------------------------'
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call parse_delete(arg_pos)
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if (rc_off > 0.0_dp) call delete_overlap
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end subroutine run_delete
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subroutine parse_delete(arg_pos)
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!Parse the delete command
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integer, intent(inout) :: arg_pos
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integer :: arg_len
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character(len=100) :: textholder
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, textholder, arg_len)
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if(arg_len==0) stop "Missing argument to delete command"
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select case(textholder)
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case('overlap')
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arg_pos=arg_pos + 1
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call get_command_argument(arg_pos, textholder, arg_len)
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if(arg_len==0) stop "Missing argument to delete overlap command"
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read(textholder, *) rc_off
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case default
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print *, "Command ", trim(adjustl(textholder)), " is not accepted for option delete"
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stop 3
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end select
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arg_pos = arg_pos + 1
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end subroutine parse_delete
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subroutine delete_overlap
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!This subroutine deletes all overlapping atoms, which is defined as atoms which are separated by a distance of
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!less then rc_off
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integer :: i, c(3), ci, cj, ck, num_nei, nei, delete_num
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integer, dimension(atom_num) :: for_delete
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!These are the variables containing the cell list information
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integer, dimension(3) :: cell_num
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integer, allocatable :: num_in_cell(:,:,:), which_cell(:,:)
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integer, allocatable :: cell_list(:,:,:,:)
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allocate(which_cell(3,atom_num))
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!First pass the atom list and atom num to the algorithm which builds the cell list
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call build_cell_list(atom_num, r_atom, rc_off, cell_num, num_in_cell, cell_list, which_cell)
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!Now loop over every atom and figure out if it has neighbors within the rc_off
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delete_num = 0
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atom_loop: do i = 1, atom_num
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!c is the position of the cell that the atom belongs to
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c = which_cell(:,i)
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!Check to make sure it hasn't already been deleted
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if(all(c /= 0)) then
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!Now loop over all neighboring cells
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do ci = -1, 1, 1
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do cj = -1, 1, 1
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do ck = -1, 1, 1
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if (any((c + (/ ck, cj, ci /)) == 0)) cycle
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if( (c(1) + ck > cell_num(1)).or.(c(2) + cj > cell_num(2)).or. &
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(c(3) + ci > cell_num(3))) cycle
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do num_nei = 1, num_in_cell(c(1) + ck, c(2) + cj, c(3) + ci)
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nei = cell_list(num_nei,c(1) + ck, c(2) + cj, c(3) + ci)
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!Check to make sure the atom isn't the same index as the atom we are checking
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!and that the neighbor hasn't already been deleted
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if((nei /= i).and.(nei/= 0)) then
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!Now check to see if it is in the cutoff radius, if it is add it to the delete code
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if (norm2(r_atom(:,nei)-r_atom(:,i)) < rc_off) then
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delete_num = delete_num + 1
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for_delete(delete_num) = max(i,nei)
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!Now zero out the larger index
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if(i > nei) then
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which_cell(:,i) = 0
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cycle atom_loop
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else
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which_cell(:,nei) = 0
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cell_list(num_nei,c(1) + ck, c(2) + cj, c(3) + ci) = 0
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end if
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end if
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end if
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end do
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end do
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end do
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end do
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end if
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end do atom_loop
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print *, "Overlap command deletes ", delete_num, " atoms"
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!Now delete all the atoms
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call delete_atoms(delete_num, for_delete(1:delete_num))
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end subroutine delete_overlap
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end module opt_delete
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