Add wedge group shape option to opt_group.f90, update the documentation, and add the relevant functions to functions.f90
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Alex Selimov
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README.md
10
README.md
@ -203,6 +203,14 @@ This selects a group residing in a block with edges perpendicular to the simulat
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`additional keywords`- Represents the various transformations which can be performed on a group. These additional keywords are given below.
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*Wedge*
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`-group nodes wedge dim1 dim2 bx by bz bw`
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This selects a group which are within a wedge shape. The options are given as follows:
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`dim1` - The dimension containing the plane normal of the wedge base.
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`dim2` - The thickness dimension. Wedge groups are currently required to span the entire cell thickness in one dimensions which is normal to the triangular face. This through thickness dimension is dim2.
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`bx by bz` - Centroid of the center of the base
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`bw` - Base width
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**Displace**
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```
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@ -323,4 +331,4 @@ Face 6: [5,6,7,8]
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Image for vertex numbers is:
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@ -155,8 +155,7 @@ END FUNCTION StrDnCase
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end function in_bd_lat
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function in_block_bd(v, box_bd)
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!This function returns whether a point is within a block in 3d
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!This function determines whether a point is within a block in 3d
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!Input/output
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real(kind=dp), dimension(3), intent(in) :: v
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real(kind=dp), dimension(6), intent(in) :: box_bd
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@ -180,6 +179,28 @@ END FUNCTION StrDnCase
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end do
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end function in_block_bd
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function in_wedge_bd(r,vertex)
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!This code determines whether the 2dimensional projection of a point lies within the 2 dimensional projection of a wedge.
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real(kind=dp), intent(in) :: r(3) !This is the point position
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real(kind=dp), intent(in) :: vertex(3,3) !These are the relevant vertex positions for the wedge
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real(kind=dp) :: v1(3), v2(3), v3(3), c1(3), c2(3) !Vertex vector to point and cross products
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integer :: i
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logical :: in_wedge_bd
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in_wedge_bd = .true.
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do i = 1, 3
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v1 = vertex(:,mod(i,3)+1) - vertex(:,i)
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v2 = r - vertex(:,i)
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v3 = vertex(:,mod(i+1,3)+1) - vertex(:,i)
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c1 = cross_product(v1,v2)
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c2 = cross_product(v1,v3)
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if(dot_product(c1,c2) < 0) then
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in_wedge_bd=.false.
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exit
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end if
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end do
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end function in_wedge_bd
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function lcm(a,b)
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!This function returns the smallest least common multiple of two numbers
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@ -8,9 +8,9 @@ module opt_group
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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, remesh_type
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integer :: group_ele_num, group_atom_num, remesh_size,normal, remesh_type, 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), disp_vec(3), remesh_lat_pam
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real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), remesh_lat_pam
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logical :: displace, delete, max_remesh, refine
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integer, allocatable :: element_index(:), atom_index(:)
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@ -56,6 +56,7 @@ module opt_group
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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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@ -79,10 +80,56 @@ module opt_group
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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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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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@ -141,54 +188,55 @@ module opt_group
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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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!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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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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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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@ -440,4 +488,16 @@ module opt_group
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call delete_elements(group_ele_num, element_index)
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end subroutine delete_group
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end module opt_group
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function in_group(r)
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!This subroutine determines if a point is within the group boundaries
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real(kind=dp), intent(in) :: r(3)
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logical :: in_group
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select case(trim(adjustl(shape)))
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case('block')
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in_group=in_block_bd(r,block_bd)
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case('wedge')
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in_group = in_wedge_bd(r,vertices)
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end select
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end function in_group
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end module opt_group
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