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Separated wrap option to reduce opy and pasted code. Fixed warnings and added wrapping when inserting a dislocation or loop

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Alex 2020-01-29 10:25:33 -05:00
parent 636ae9421b
commit dc42b7b925
11 changed files with 55 additions and 46 deletions
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18
src/opt_group.f90
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@ -11,7 +11,7 @@ module opt_group
integer :: group_ele_num, group_atom_num, remesh_size
character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
real(kind=dp) :: block_bd(6), disp_vec(3)
logical :: displace, wrap
logical :: displace
integer, allocatable :: element_index(:), atom_index(:)
@ -96,8 +96,6 @@ module opt_group
if (arglen==0) stop "Missing vector component for shift command"
read(textholder, *) disp_vec(i)
end do
case('wrap')
wrap = .true.
case('remesh')
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
@ -192,16 +190,8 @@ module opt_group
end do
end do
!Now either apply periodic boundaries if wrap command was passed or adjust box dimensions
!Now we check if we have to wrap the atoms, nodes are not wrapped. For elements the periodic
!boundary conditions are applied in the actual CAC codes
if(wrap) then
do i = 1, atom_num
call apply_periodic(r_atom(:,i))
end do
!If we don't include the wrap command then we have to increase the size of the box
else
if (.not.(wrap_flag)) then
do i = 1,3
if (disp_vec(i) < -lim_zero) then
box_bd(2*i-1) = box_bd(2*i-1) - disp_vec(i)
@ -235,8 +225,8 @@ module opt_group
!Get the interpolated atom positions
call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
!Loop over all interpolated atoms and add them to the system, we apply periodic boundaries here as well to make sure
!they are in the box
!Loop over all interpolated atoms and add them to the system, we apply periodic boundaries
!here as well to make sure they are in the box
do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3
call apply_periodic(r_interp(:,j))
call add_atom(type_interp(j), r_interp(:,j))