Merge branch 'ft--group-shell' into development
This commit is contained in:
Alex Selimov
commit
1c7c028dd8
@ -779,8 +779,7 @@ do i = 1, atom_num
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end do
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end do
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end subroutine
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end subroutine get_interp_pos
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subroutine alloc_dat_arrays(n,m)
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!This subroutine used to provide initial allocation for the atom and element data arrays
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@ -10,8 +10,8 @@ module opt_group
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integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2, random_num, group_type, notsize
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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), radius, bwidth
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logical :: displace, delete, max_remesh, refine, group_nodes, flip
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real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), radius, bwidth, shell_thickness
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logical :: displace, delete, max_remesh, refine, group_nodes, flip, efill, refinefill
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integer, allocatable :: element_index(:), atom_index(:)
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@ -22,7 +22,9 @@ module opt_group
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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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print *, '------------------------------------------------------------'
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print *, 'Option Group'
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print *, '------------------------------------------------------------'
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group_ele_num = 0
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group_atom_num = 0
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@ -48,6 +50,11 @@ module opt_group
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call refine_group
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end if
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if(refinefill) then
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call get_group
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call refinefill_group
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end if
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if(displace)then
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call get_group
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call displace_group
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@ -335,6 +342,28 @@ module opt_group
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if (arglen==0) STOP "Missing sphere radius in group command"
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read(textholder, *) radius
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case('shell')
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!First extract the shell centroid
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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 shell centroid in group command"
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call parse_pos(i, textholder, centroid(i))
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end do
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!Now get the radius
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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 shell radius in group command"
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read(textholder, *) radius
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!Now get the shell thickness
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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 shell thickness in group command"
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read(textholder, *) shell_thickness
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case('all')
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!Do nothing if the shape is all
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continue
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@ -364,6 +393,8 @@ module opt_group
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end do
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case('refine')
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refine=.true.
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case('refinefill')
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refinefill=.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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@ -382,6 +413,8 @@ module opt_group
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read(textholder, *) random_num
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case('flip')
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flip=.true.
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case('efill')
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efill=.true.
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case('type')
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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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@ -403,7 +436,7 @@ module opt_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, j, inod, ibasis, temp
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integer :: i, j, inod, ibasis, temp, node_in_out(max_ng_node)
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integer, allocatable :: resize_array(:)
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real(kind=dp) :: r_center(3), rand
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@ -433,16 +466,8 @@ module opt_group
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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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if(.not.(group_nodes)) then
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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).neqv.flip).and.(size_ele(i)/= notsize)) then
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if(in_group_ele(size_ele(i), lat_ele(i), r_node(:,:,:,i))) 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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@ -455,27 +480,6 @@ module opt_group
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end if
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end do
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else if(group_nodes) then
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eleloop: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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if ((in_group(r_node(:,ibasis,inod,i)).neqv.flip).and.(size_ele(i)/=notsize)) 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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cycle eleloop
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end if
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end do
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end do
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end do eleloop
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end if
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if(random_num > 0) then
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!If we have the random option enabled then we select random_num number of elements from the group and overwrite
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!the group with those elements
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@ -569,7 +573,7 @@ module opt_group
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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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!This command is used to refine the group to full atomistics
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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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@ -596,7 +600,110 @@ module opt_group
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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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end subroutine refine_group
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subroutine refinefill_group
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!This command is used to refine the group to full atomistics
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integer :: i, j, ie, type_interp(max_basisnum*max_esize**3), add_atom_num, orig_atom_num, m, n, o, esize, &
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ele(3,8), new_ele_num, ibasis, inod, vlat(3), nump_ele, added_points
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real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), rfill(3,max_basisnum,max_ng_node), ravg(3), ratom(3,max_basisnum)
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logical :: lat_points(max_esize, max_esize, max_esize)
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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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new_ele_num = 0
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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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!Find all possible elements that we can make while making sure they aren't in the group
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lat_points(1:size_ele(ie),1:size_ele(ie),1:size_ele(ie)) = .true.
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!Now calculate the number of elemets which are available for remeshing
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nump_ele = size_ele(ie)**3
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do o =1, size_ele(ie)
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do n = 1, size_ele(ie)
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do m =1, size_ele(ie)
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call get_interp_pos(m,n,o,i,rfill(:,:,1))
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ravg(:) = 0
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do ibasis = 1, basisnum(lat_ele(ie))
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ravg = ravg + rfill(:,ibasis, 1)/basisnum(lat_ele(ie))
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end do
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if( in_group(ravg)) then
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nump_ele = nump_ele - 1
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end if
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end do
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end do
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end do
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!Now start the remeshing loop for the element
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esize = size_ele(ie) - 2
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added_points=0
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do while(esize > min_efillsize)
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if(nump_ele < min_efillsize**3) then
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exit
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else if (nump_ele < esize**3) then
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esize = esize - 2
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else
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ele = cubic_cell*(esize-1)
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do o = 1, size_ele(ie) - esize
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do n = 1, size_ele(ie) - esize
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latloop:do m = 1, size_ele(ie) - esize
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do inod = 1, ng_node(lat_ele(ie))
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vlat = ele(:,inod) + (/ m, n, o /)
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if (.not.lat_points(vlat(1), vlat(2),vlat(3))) cycle latloop
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call get_interp_pos(vlat(1), vlat(2), vlat(3), ie, rfill(:,:,inod))
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end do
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!Check to make sure all lattice points exist for the current element
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if(any(.not.lat_points(m:m+esize-1, n:n+esize-1, o:o+esize-1))) cycle latloop
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if (.not.in_group_ele(esize, lat_ele(ie), rfill)) then
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nump_ele=nump_ele - esize**3
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lat_points(m:m+esize-1, n:n+esize-1, o:o+esize-1) = .false.
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call add_element(0,type_ele(ie), esize, lat_ele(ie), sbox_ele(ie), rfill)
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new_ele_num = new_ele_num + 1
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added_points = added_points + esize**3
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end if
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end do latloop
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end do
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end do
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esize=esize-2
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end if
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end do
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!Now add the leftover lattice points as atoms
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do o = 1, size_ele(ie)
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do n = 1, size_ele(ie)
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do m = 1, size_ele(ie)
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if(lat_points(m,n,o)) then
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call get_interp_pos(m,n,o, ie, ratom(:,:))
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do ibasis = 1, basisnum(lat_ele(ie))
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call apply_periodic(ratom(:,ibasis))
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call add_atom(0, basis_type(ibasis,lat_ele(ie)), sbox_ele(ie), ratom(:,ibasis))
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added_points=added_points + 1
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end do
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end if
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end do
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end do
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end do
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if (added_points /= (size_ele(ie)**3)) then
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print *, "Element ", ie, " is refined incorrectly in refinefill"
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end if
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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 and ", new_ele_num, &
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" elements."
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end if
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end subroutine refinefill_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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@ -900,6 +1007,11 @@ module opt_group
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end subroutine change_group_type
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subroutine split_group_elements
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!
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end subroutine split_group_elements
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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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@ -933,8 +1045,85 @@ module opt_group
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else
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in_group = .false.
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end if
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case('shell')
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rnorm = norm2(r(:) - centroid(:))
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if ((rnorm >= radius).and.(rnorm<=(radius + shell_thickness))) then
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in_group = .true.
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else
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in_group = .false.
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end if
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case('all')
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in_group = .true.
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end select
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end function in_group
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function in_group_ele(esize, elat, rn)
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!This figures out if the elements are in the group boundaries
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real(kind=dp), intent(in) :: rn(3,max_basisnum, max_ng_node)
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integer, intent(in) :: esize, elat
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logical :: in_group_ele
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integer :: i, inod, ibasis, node_in_out(max_ng_node)
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real(kind=dp) :: r_center(3)
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in_group_ele=.false.
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if(trim(adjustl(shape)) == 'shell') then
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node_in_out(:) = -1
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!First calculate whether each element node is within the shell region, inside the shell sphere, or outside the
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!shell region
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nodeloop:do inod = 1, ng_node(elat)
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r_center(:)=0.0_dp
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do ibasis = 1, basisnum(elat)
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r_center(:)= r_center(:) + rn(:,ibasis,inod)/basisnum(elat)
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end do
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if((in_group(rn(:, ibasis, inod)).neqv.flip).and.(size_ele(i)/=notsize)) then
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node_in_out(inod) = 2
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exit nodeloop
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end if
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shape ='sphere'
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if((in_group(rn(:, ibasis, inod)).neqv.flip).and.(esize/=notsize)) then
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node_in_out(inod) = 1
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else
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node_in_out(inod) = 0
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end if
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shape='shell'
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end do nodeloop
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!If any nodes are within the shell region, or if the shell region interescts an element then add it to the group
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if(any(node_in_out == 2).or.(any(node_in_out==1).and.(any(node_in_out==0)))) then
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in_group_ele=.true.
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return
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end if
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else if(.not.(group_nodes)) then
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r_center(:) = 0.0_dp
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do inod = 1, ng_node(elat)
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do ibasis = 1, basisnum(elat)
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r_center = r_center + rn(:,ibasis,inod)/(basisnum(elat)*ng_node(elat))
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end do
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end do
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if ((in_group(r_center).neqv.flip).and.(esize/= notsize)) then
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in_group_ele=.true.
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return
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end if
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else if(group_nodes) then
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r_center(:) = 0.0_dp
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do inod = 1, ng_node(elat)
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do ibasis = 1, basisnum(elat)
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if ((in_group(rn(:,ibasis,inod)).neqv.flip).and.(esize/=notsize)) then
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in_group_ele=.true.
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return
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end if
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end do
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end do
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end if
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end function in_group_ele
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end module opt_group
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