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@ -8,7 +8,7 @@ module opt_group
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use box
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use box
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implicit none
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implicit none
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integer :: group_ele_num, group_atom_num
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integer :: group_ele_num, group_atom_num, remesh_size
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character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
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character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
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real(kind=dp) :: block_bd(6), disp_vec(3)
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real(kind=dp) :: block_bd(6), disp_vec(3)
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logical :: displace, wrap
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logical :: displace, wrap
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@ -24,6 +24,7 @@ module opt_group
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group_ele_num = 0
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group_ele_num = 0
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group_atom_num = 0
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group_atom_num = 0
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remesh_size=0
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if(allocated(element_index)) deallocate(element_index)
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if(allocated(element_index)) deallocate(element_index)
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if(allocated(atom_index)) deallocate(atom_index)
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if(allocated(atom_index)) deallocate(atom_index)
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@ -34,6 +35,7 @@ module opt_group
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!Now call the transformation functions for the group
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!Now call the transformation functions for the group
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if(displace) call displace_group
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if(displace) call displace_group
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if(remesh_size > 0) call remesh_group
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end subroutine group
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end subroutine group
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subroutine parse_group(arg_pos)
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subroutine parse_group(arg_pos)
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@ -94,6 +96,11 @@ module opt_group
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end do
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end do
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case('wrap')
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case('wrap')
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wrap = .true.
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wrap = .true.
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case('remesh')
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, textholder, arglen)
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if (arglen==0) stop "Missing remesh element size in group command"
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read(textholder, *) remesh_size
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case default
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case default
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!If it isn't an available option to opt_disl then we just exit
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!If it isn't an available option to opt_disl then we just exit
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exit
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exit
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@ -197,4 +204,44 @@ module opt_group
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end subroutine displace_group
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end subroutine displace_group
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subroutine remesh_group
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!This command is used to remesh the group to a desired element size
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integer :: i, j, ie, type_interp(max_basisnum*max_esize**3), add_atom_num
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real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3)
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!Refining to atoms and remeshing to elements are different processes so check which code we need to run
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select case(remesh_size)
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!Refining to atoms
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case(2)
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if(group_ele_num > 0) then
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!Estimate number of atoms we are adding, this doesn't have to be exact
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add_atom_num = group_ele_num*basisnum(lat_ele(element_index(1)))*size_ele(element_index(1))**3
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call grow_ele_arrays(0,add_atom_num)
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do i = 1, group_ele_num
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ie = element_index(i)
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!Get the interpolated atom positions
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call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
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!Loop over all interpolated atoms and add them to the system, we apply periodic boundaries here as well to make sure
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!they are in the box
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do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3
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call apply_periodic(r_interp(:,j))
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call add_atom(type_interp(j), r_interp(:,j))
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end do
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end do
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!Once all atoms are added we delete all of the elements
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call delete_elements(group_ele_num, element_index)
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end if
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!Remeshing to elements, currently not available
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case default
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print *, "Remeshing to elements is currently not available. Please refine to atoms by passing a remsh size of 2"
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end select
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end subroutine remesh_group
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end module opt_group
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end module opt_group
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