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module opt_group
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!This module contains all code associated with dislocations
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use parameters
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use elements
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use subroutines
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use box
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implicit none
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integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2
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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), centroid(3), vertices(3,3),disp_vec(3)
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logical :: displace, delete, max_remesh, refine
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integer, allocatable :: element_index(:), atom_index(:)
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public
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contains
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subroutine group(arg_pos)
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!Main calling function for the group option
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integer, intent(inout) :: arg_pos
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print *, '-----------------------Option Group-------------------------'
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group_ele_num = 0
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group_atom_num = 0
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remesh_size=0
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displace=.false.
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delete=.false.
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max_remesh=.false.
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refine = .false.
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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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call parse_group(arg_pos)
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call get_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(remesh_size > 0) call remesh_group
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if(delete) call delete_group
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if(refine) call refine_group
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end subroutine group
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subroutine parse_group(arg_pos)
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!Parse the group command
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integer, intent(inout) :: arg_pos
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integer :: i,arglen
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character(len=100) :: textholder
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real(kind=dp) bwidth, wheight
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!Parse type and shape command
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, type, arglen)
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if (arglen==0) STOP "Missing select_type in group command"
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select case(trim(adjustl(type)))
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case('atoms', 'elements', 'both')
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continue
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case default
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print *, "Select_type ", trim(adjustl(type)), " is not an accept group selection criteria. ", &
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"Please select from atoms, nodes, or both."
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end select
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, shape, arglen)
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if (arglen==0) STOP "Missing group_shape in group command"
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!Now parse the arguments required by the user selected shape
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select case(trim(adjustl(shape)))
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case('block')
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do i= 1, 6
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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 block boundary in group command"
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call parse_pos(int((i+1)/2), textholder, block_bd(i))
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end do
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case('wedge')
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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 normal dim in group wedge command"
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read(textholder,*) dim1
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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 normal dim in group wedge command"
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read(textholder,*) dim2
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do i = 1, 3
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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 centroid in group wedge command"
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call parse_pos(i, textholder, centroid(i))
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end do
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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 base width in group wedge command"
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read(textholder,*) bwidth
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!Calculate the vertex positions
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vertices(:,1) = centroid
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vertices(dim2,1) = 0.0_dp
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do i = 1, 3
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if (i == dim1) then
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if (bwidth > 0) then
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vertices(i,2) = box_bd(2*i)
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vertices(i,3) = box_bd(2*i)
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else if (bwidth < 0) then
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vertices(i,2) = box_bd(2*i-1)
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vertices(i,3) = box_bd(2*i-1)
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else
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print *, "bwidth cannot be 0 in wedge shaped group"
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stop 3
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end if
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else if (i == dim2) then
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vertices(i,2) = 0.0_dp
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vertices(i,3) = 0.0_dp
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else
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vertices(i,2) = centroid(i) + bwidth
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vertices(i,3) = centroid(i) - bwidth
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end if
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end do
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case default
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print *, "Group shape ", trim(adjustl(shape)), " is not currently accepted. Please check documentation ", &
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"for accepted group shapes."
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end select
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!Now parse the additional options which may be present
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do while(.true.)
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if(arg_pos > command_argument_count()) exit
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!Pull out the next argument which should either be a keyword or an option
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arg_pos=arg_pos+1
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call get_command_argument(arg_pos, textholder)
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textholder=adjustl(textholder)
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!Choose what to based on what the option string is
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select case(trim(textholder))
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case('displace')
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displace = .true.
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do i = 1,3
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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 vector component for shift command"
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read(textholder, *) disp_vec(i)
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end do
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case('refine')
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refine=.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('max')
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max_remesh =.true.
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case('delete')
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delete=.true.
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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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exit
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end select
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end do
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end subroutine parse_group
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subroutine get_group
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!This subroutine finds all elements and/or atoms within the group boundaries
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!specified by the user.
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integer :: i, inod, ibasis
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integer, allocatable :: resize_array(:)
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real(kind=dp) :: r_center(3)
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select case(trim(adjustl(shape)))
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case('block')
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print *, "Group has block shape with boundaries: ", block_bd
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case ('crack')
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print *, "Group has crack shape with dim1", dim1, "and dim2", dim2, "and vertices ", vertices
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end select
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!Allocate variables to arbitrary size
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allocate(element_index(1024), atom_index(1024))
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!Check the type to see whether we need to find the elements within the group
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select case(trim(adjustl(type)))
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case('elements', 'both')
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do i = 1, ele_num
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r_center(:) = 0.0_dp
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do inod = 1, ng_node(lat_ele(i))
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do ibasis = 1, basisnum(lat_ele(i))
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r_center = r_center + r_node(:,ibasis,inod,i)/(basisnum(lat_ele(i))*ng_node(lat_ele(i)))
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end do
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end do
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if (in_group(r_center)) then
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group_ele_num = group_ele_num + 1
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if(group_ele_num > size(element_index)) then
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allocate(resize_array(size(element_index) + 1024))
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resize_array(1:group_ele_num-1) = element_index
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resize_array(group_ele_num:) = 0
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call move_alloc(resize_array, element_index)
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end if
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element_index(group_ele_num) = i
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end if
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end do
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end select
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!Check the type to see if we need to find the atoms within the group
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select case(trim(adjustl(type)))
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case('atoms','both')
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do i = 1, atom_num
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if(in_group(r_atom(:,i))) then
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group_atom_num = group_atom_num + 1
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if (group_atom_num > size(atom_index)) then
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allocate(resize_array(size(atom_index) + 1024))
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resize_array(1:group_atom_num -1) = atom_index
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resize_array(group_atom_num:) = 0
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call move_alloc(resize_array, atom_index)
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end if
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atom_index(group_atom_num) = i
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end if
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end do
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end select
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print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
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end subroutine get_group
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subroutine displace_group
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!This subroutine applies a displacement to elements/atoms in the groups
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integer :: i, inod, ibasis
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print *, "Elements/atoms in group displaced by ", disp_vec
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!Displace atoms
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do i = 1, group_atom_num
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r_atom(:,atom_index(i)) = r_atom(:,atom_index(i)) + disp_vec
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end do
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!Displace elements
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do i = 1, group_ele_num
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do inod = 1, ng_node(lat_ele(element_index(i)))
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do ibasis = 1, basisnum(lat_ele(element_index(i)))
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r_node(:,ibasis,inod,element_index(i)) = r_node(:,ibasis,inod,element_index(i)) + disp_vec
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end do
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end do
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end do
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!If we don't include the wrap command then we have to increase the size of the box
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if (.not.(wrap_flag)) then
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do i = 1,3
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if (disp_vec(i) < -lim_zero) then
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box_bd(2*i-1) = box_bd(2*i-1) - disp_vec(i)
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else if (disp_vec(i) > lim_zero) then
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box_bd(2*i) = box_bd(2*i) + disp_vec(i)
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end if
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end do
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end if
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end subroutine displace_group
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subroutine refine_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, orig_atom_num
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real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3)
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!Refining to atoms
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if(group_ele_num > 0) then
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orig_atom_num = atom_num
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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
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!here as well to make sure 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), sbox_ele(ie), 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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print *, group_ele_num, " elements of group are refined to ", atom_num -orig_atom_num, " atoms."
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end if
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end subroutine
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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, k, ix, iy, iz, inod, ibasis, ie, type_interp(max_basisnum*max_esize**3), add_atom_num, orig_atom_num, &
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current_esize, dof, max_lat(3), r_lat(3), ele(3,8), vlat(3), bd_in_lat(6), bd_in_array(3), old_ele, old_atom, &
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max_loops, working_esize, group_lat_num, lat_list(10), group_sbox_num, sbox_list(100), is, ilat
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real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), ori_inv(3,3), r(3), &
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r_new_node(3,max_basisnum, max_ng_node), orient(3,3), group_in_lat(3,8), group_bd(6)
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logical, allocatable :: lat_points(:,:,:)
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character(len=100) :: remesh_ele_type
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|
!Right now we just hardcode only remeshing to elements
|
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|
|
|
remesh_ele_type = 'fcc'
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|
! Determine which sub_boxes and lattices types are within in the group
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group_sbox_num = 0
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group_lat_num = 0
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|
do i = 1, group_atom_num
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do j = 1, group_sbox_num
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if (sbox_list(j) == sbox_atom(atom_index(i))) exit
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group_sbox_num = group_sbox_num + 1
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sbox_list(group_sbox_num) = sbox_atom(atom_index(i))
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|
end do
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do j = 1, group_lat_num
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if (basis_type(1,lat_list(j)) == type_atom(atom_index(i))) exit
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group_lat_num = group_lat_num + 1
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do k = 1, lattice_types
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if (basis_type(1,k) == type_atom(atom_index(i))) lat_list(group_lat_num) = k
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end do
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end do
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end do
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do i = 1, group_ele_num
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do j = 1, group_sbox_num
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if (sbox_list(j) == sbox_ele(element_index(i))) exit
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group_sbox_num = group_sbox_num + 1
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sbox_list(group_sbox_num) = sbox_ele(element_index(i))
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end do
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do j = 1, group_lat_num
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if (lat_list(group_lat_num) == lat_ele(element_index(i))) exit
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group_lat_num = group_lat_num + 1
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lat_list(group_lat_num) = lat_ele(element_index(i))
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end do
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end do
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do is = 1, group_sbox_num
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|
orient = sub_box_ori(:, :, sbox_list(is))
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|
call matrix_inverse(orient,3,ori_inv)
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|
do ilat = 1, group_lat_num
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|
!First calculate max position in lattice space to be able to allocate lat_points array, also sum the total number
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!of degrees of freedom which are added
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|
dof = 0
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|
do j = 1, 3
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|
|
group_bd(2*j) = -huge(1.0_dp)
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|
|
group_bd(2*j-1) = huge(1.0_dp)
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|
|
end do
|
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|
|
do i = 1, group_atom_num
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|
|
if ((type_atom(atom_index(i)) == basis_type(1,ilat)).and.(sbox_atom(atom_index(i)) == is)) then
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|
|
do j =1 ,3
|
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|
|
if (r_atom(j,atom_index(i)) > group_bd(2*j)) group_bd(2*j) = r_atom(j,atom_index(i))
|
|
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|
|
if (r_atom(j,atom_index(i)) < group_bd(2*j-1)) group_bd(2*j-1) = r_atom(j,atom_index(i))
|
|
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|
|
end do
|
|
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|
|
dof = dof + 1
|
|
|
|
|
end if
|
|
|
|
|
end do
|
|
|
|
|
|
|
|
|
|
do i = 1, group_ele_num
|
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|
|
if ((lat_ele(element_index(i)) == ilat).and.(sbox_ele(element_index(i)) == is)) then
|
|
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|
|
do inod =1, ng_node(ilat)
|
|
|
|
|
do ibasis = 1, basisnum(ilat)
|
|
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|
|
do j = 1, 3
|
|
|
|
|
r =r_node(j,ibasis,inod,element_index(i))
|
|
|
|
|
if (r(j) > group_bd(2*j)) group_bd(2*j) = r(j)
|
|
|
|
|
if (r(j) < group_bd(2*j-1)) group_bd(2*j-1) = r(j)
|
|
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|
|
end do
|
|
|
|
|
end do
|
|
|
|
|
end do
|
|
|
|
|
dof = dof + size_ele(element_index(i))**3
|
|
|
|
|
end if
|
|
|
|
|
end do
|
|
|
|
|
|
|
|
|
|
!If for some reason there are no dof in this loop then cycle out
|
|
|
|
|
if(dof == 0) cycle
|
|
|
|
|
|
|
|
|
|
group_in_lat = reshape((/ group_bd(1),group_bd(3),group_bd(5), &
|
|
|
|
|
group_bd(2),group_bd(3),group_bd(5), &
|
|
|
|
|
group_bd(2),group_bd(4),group_bd(5), &
|
|
|
|
|
group_bd(1),group_bd(4),group_bd(5), &
|
|
|
|
|
group_bd(1),group_bd(3),group_bd(6), &
|
|
|
|
|
group_bd(2),group_bd(3),group_bd(6), &
|
|
|
|
|
group_bd(2),group_bd(4),group_bd(6), &
|
|
|
|
|
group_bd(1),group_bd(4),group_bd(6) /), [3,8])
|
|
|
|
|
|
|
|
|
|
group_in_lat = matmul(fcc_inv, matmul(ori_inv, group_in_lat/lapa(ilat)))
|
|
|
|
|
do i = 1, 3
|
|
|
|
|
bd_in_lat(2*i-1) = nint(minval(group_in_lat(i,:)))
|
|
|
|
|
bd_in_lat(2*i) = nint(maxval(group_in_lat(i,:)))
|
|
|
|
|
end do
|
|
|
|
|
|
|
|
|
|
allocate(lat_points(bd_in_lat(2)-bd_in_lat(1)+10, bd_in_lat(4)-bd_in_lat(3)+10, bd_in_lat(6)-bd_in_lat(5)+10))
|
|
|
|
|
lat_points(:,:,:) = .false.
|
|
|
|
|
dof = 0
|
|
|
|
|
|
|
|
|
|
!Now place all group atoms and group interpolated atoms into lat_points
|
|
|
|
|
do i = 1, group_atom_num
|
|
|
|
|
r = r_atom(:,atom_index(i))/lapa(ilat)
|
|
|
|
|
r = matmul(fcc_inv,matmul(ori_inv,r))
|
|
|
|
|
do j = 1, 3
|
|
|
|
|
r_lat(j) = nint(r(j))
|
|
|
|
|
end do
|
|
|
|
|
!Do a check to make sure the code is working and that lattice points aren't being written on top of each other.
|
|
|
|
|
!This is primarily a debugging statement
|
|
|
|
|
if(lat_points(r_lat(1)-bd_in_lat(1)+5,r_lat(2)-bd_in_lat(3)+5,r_lat(3)-bd_in_lat(5)+5)) then
|
|
|
|
|
stop "Multiple atoms share same position in lat point array, this shouldn't happen"
|
|
|
|
|
else
|
|
|
|
|
lat_points(r_lat(1)-bd_in_lat(1)+5, r_lat(2)-bd_in_lat(3)+5, r_lat(3)-bd_in_lat(5)+5) = .true.
|
|
|
|
|
dof = dof + 1
|
|
|
|
|
end if
|
|
|
|
|
end do
|
|
|
|
|
|
|
|
|
|
!Now place interpolated atoms within lat_points array
|
|
|
|
|
do i =1, group_ele_num
|
|
|
|
|
ie = element_index(i)
|
|
|
|
|
call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
|
|
|
|
|
do j = 1, size_ele(ie)**3 * basisnum(lat_ele(ie))
|
|
|
|
|
r = r_interp(:,j)/lapa(ilat)
|
|
|
|
|
r = matmul(fcc_inv,matmul(ori_inv,r))
|
|
|
|
|
do k = 1, 3
|
|
|
|
|
r_lat(k) = nint(r(k))
|
|
|
|
|
end do
|
|
|
|
|
!Do a check to make sure the code is working and that lattice points aren't being written on top of each
|
|
|
|
|
!other. This is primarily a debugging statement
|
|
|
|
|
if(lat_points(r_lat(1)-bd_in_lat(1)+5,r_lat(2)-bd_in_lat(3)+5,r_lat(3)-bd_in_lat(5)+5)) then
|
|
|
|
|
stop "Multiple atoms/interpolated atoms share same position in lat point array, this shouldn't happen"
|
|
|
|
|
else
|
|
|
|
|
lat_points(r_lat(1)-bd_in_lat(1)+5, r_lat(2)-bd_in_lat(3)+5, r_lat(3)-bd_in_lat(5)+5) = .true.
|
|
|
|
|
dof = dof + 1
|
|
|
|
|
end if
|
|
|
|
|
end do
|
|
|
|
|
end do
|
|
|
|
|
|
|
|
|
|
print *, "Group has ", dof, " degrees of freedom to remesh"
|
|
|
|
|
|
|
|
|
|
!Delete all elements and atoms to make space for new elements and atoms
|
|
|
|
|
call delete_atoms(group_atom_num, atom_index)
|
|
|
|
|
call delete_elements(group_ele_num, element_index)
|
|
|
|
|
|
|
|
|
|
old_atom = atom_num
|
|
|
|
|
old_ele = ele_num
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
!Now run remeshing algorithm, not the most optimized or efficient but gets the job done
|
|
|
|
|
!Figure out new looping boundaries
|
|
|
|
|
bd_in_array(1) = bd_in_lat(2) - bd_in_lat(1) + 10
|
|
|
|
|
bd_in_array(2) = bd_in_lat(4) - bd_in_lat(3) + 10
|
|
|
|
|
bd_in_array(3) = bd_in_lat(6) - bd_in_lat(5) + 10
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
if (max_remesh) then
|
|
|
|
|
max_loops = (remesh_size-3)/2
|
|
|
|
|
else
|
|
|
|
|
max_loops = 1
|
|
|
|
|
end if
|
|
|
|
|
do j = 1, max_loops
|
|
|
|
|
working_esize = remesh_size - 2*(j-1)
|
|
|
|
|
ele = (working_esize-1)*cubic_cell
|
|
|
|
|
zloop: do iz = 1, bd_in_array(3)
|
|
|
|
|
yloop: do iy = 1, bd_in_array(2)
|
|
|
|
|
xloop: do ix = 1, bd_in_array(1)
|
|
|
|
|
if (lat_points(ix, iy,iz)) then
|
|
|
|
|
r_new_node(:,:,:) = 0.0_dp
|
|
|
|
|
|
|
|
|
|
!Check to see if the element overshoots the bound
|
|
|
|
|
if (iz+working_esize-1 > bd_in_array(3)) then
|
|
|
|
|
exit zloop
|
|
|
|
|
else if (iy+working_esize-1 > bd_in_array(2)) then
|
|
|
|
|
cycle zloop
|
|
|
|
|
else if (ix+working_esize-1 > bd_in_array(1)) then
|
|
|
|
|
cycle yloop
|
|
|
|
|
end if
|
|
|
|
|
|
|
|
|
|
if (all(lat_points(ix:ix+working_esize-1,iy:iy+working_esize-1,iz:iz+working_esize-1))) then
|
|
|
|
|
do inod = 1, ng_node(ilat)
|
|
|
|
|
vlat = ele(:,inod) + (/ix, iy, iz /)
|
|
|
|
|
do i = 1, 3
|
|
|
|
|
vlat(i) = vlat(i) + bd_in_lat(2*i-1)-5
|
|
|
|
|
end do
|
|
|
|
|
r_new_node(:,1,inod) = matmul(orient, matmul(fcc_mat, vlat))*lapa(ilat)
|
|
|
|
|
end do
|
|
|
|
|
|
|
|
|
|
lat_points(ix:ix+working_esize-1,iy:iy+working_esize-1,iz:iz+working_esize-1) = .false.
|
|
|
|
|
!Add the element, for the sbox we just set it to the same sbox that we get the orientation
|
|
|
|
|
!from. In this case it is from the sbox of the first atom in the group.
|
|
|
|
|
call add_element(remesh_ele_type, working_esize, ilat, sbox_atom(atom_index(1)),r_new_node)
|
|
|
|
|
|
|
|
|
|
end if
|
|
|
|
|
end if
|
|
|
|
|
end do xloop
|
|
|
|
|
end do yloop
|
|
|
|
|
end do zloop
|
|
|
|
|
end do
|
|
|
|
|
|
|
|
|
|
!Now we have to add any leftover lattice points as atoms
|
|
|
|
|
do iz = 1, bd_in_array(3)
|
|
|
|
|
do iy=1, bd_in_array(2)
|
|
|
|
|
do ix = 1, bd_in_array(1)
|
|
|
|
|
if(lat_points(ix,iy,iz)) then
|
|
|
|
|
vlat = (/ ix, iy, iz /)
|
|
|
|
|
do i = 1, 3
|
|
|
|
|
vlat(i) = vlat(i) + bd_in_lat(2*i-1)-5
|
|
|
|
|
end do
|
|
|
|
|
lat_points(ix,iy,iz) = .false.
|
|
|
|
|
r = matmul(orient, matmul(fcc_mat, vlat))*lapa(ilat)
|
|
|
|
|
call add_atom(basis_type(1,ilat), sbox_atom(atom_index(1)), r)
|
|
|
|
|
end if
|
|
|
|
|
end do
|
|
|
|
|
end do
|
|
|
|
|
end do
|
|
|
|
|
end do
|
|
|
|
|
end do
|
|
|
|
|
|
|
|
|
|
print *, "Remeshing has created ", ele_num-old_ele, " elements and ", atom_num-old_atom, " atoms."
|
|
|
|
|
end subroutine remesh_group
|
|
|
|
|
|
|
|
|
|
subroutine delete_group
|
|
|
|
|
!This subroutine deletes all atoms/elements within a group
|
|
|
|
|
|
|
|
|
|
print *, "Deleting group containing ", group_atom_num, " atoms and ", group_ele_num, " elements."
|
|
|
|
|
|
|
|
|
|
!Delete atoms
|
|
|
|
|
call delete_atoms(group_atom_num, atom_index)
|
|
|
|
|
|
|
|
|
|
!Delete elements
|
|
|
|
|
call delete_elements(group_ele_num, element_index)
|
|
|
|
|
|
|
|
|
|
end subroutine delete_group
|
|
|
|
|
|
|
|
|
|
function in_group(r)
|
|
|
|
|
!This subroutine determines if a point is within the group boundaries
|
|
|
|
|
real(kind=dp), intent(in) :: r(3)
|
|
|
|
|
logical :: in_group
|
|
|
|
|
select case(trim(adjustl(shape)))
|
|
|
|
|
case('block')
|
|
|
|
|
in_group=in_block_bd(r,block_bd)
|
|
|
|
|
case('wedge')
|
|
|
|
|
in_group = in_wedge_bd(r,vertices)
|
|
|
|
|
end select
|
|
|
|
|
end function in_group
|
|
|
|
|
end module opt_group
|
