aselimov
5 years ago
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21be35041c
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# Install CACmb
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In order to build CACmb switch to the src repository and run:
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```
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make
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```
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Once this command is complete you can run:
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```
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sudo make install
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```
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in order to copy the installation to `/usr/local/bin`.
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subroutine call_option(option, arg_pos)
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use parameters
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use opt_disl
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use opt_group
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implicit none
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integer, intent(inout) :: arg_pos
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character(len=100), intent(in) :: option
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select case(trim(adjustl(option)))
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case('-dislgen', '-disloop')
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call dislocation(option, arg_pos)
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case('-group')
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call group(arg_pos)
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case('-ow')
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arg_pos = arg_pos + 1
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continue
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case default
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print *, 'Option ', trim(adjustl(option)), ' is not currently accepted. Skipping to next argument'
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arg_pos = arg_pos + 1
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end select
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end subroutine call_option
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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
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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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logical :: displace, wrap
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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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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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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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!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 dislgen 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 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('wrap')
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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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!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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!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_block_bd(r_center, block_bd)) 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_block_bd(r_atom(:,i),block_bd)) 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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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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!Now either apply periodic boundaries if wrap command was passed or adjust box dimensions
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!Now we check if we have to wrap the atoms, nodes are not wrapped. For elements the periodic
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!boundary conditions are applied in the actual CAC codes
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if(wrap) then
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do i = 1, atom_num
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call apply_periodic(r_atom(:,i))
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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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else
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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 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, 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 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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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 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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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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!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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