Current working changes
This commit is contained in:
Alex Selimov
parent
9a484c86f6
commit
babf4e176d
55
src/io.f90
55
src/io.f90
@ -907,39 +907,46 @@ module io
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!Read more useless data
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read(11,*) textholder
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read(11,*) textholder
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!set max values and allocate variables
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max_basisnum = maxval(basisnum)
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max_ng_node = maxval(ng_node)
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call grow_ele_arrays(in_eles, in_atoms)
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!Now start reading the elements
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do i = 1, in_eles
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read(11,*) j, etype, k, lat_type
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do inod = 1, 8
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read(11, *) j, k, r_in(:,1,inod)
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r_in(:,1,inod) = r_in(:,1,inod) + newdisplace
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if(in_eles > 0) then
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read(11,*) textholder
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do i = 1, in_eles
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read(11,*) j, etype, k, lat_type
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do inod = 1, 8
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read(11, *) j, k, r_in(:,1,inod)
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r_in(:,1,inod) = r_in(:,1,inod) + newdisplace
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end do
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call add_element(in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in)
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end do
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end if
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if(in_atoms > 0) then
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if (in_eles > 0) then
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!Read useless data
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read(11,*) textholder
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read(11,*) textholder
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end if
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do i = 1, in_atoms
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read(11,*) j, k, atom_type, r_in_atom(:)
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r_in_atom = r_in_atom + newdisplace
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call add_atom(atom_type_map(atom_type), sub_box_num + 1, r_in_atom)
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end do
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call add_element(in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in)
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end do
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!Close file
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close(11)
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!Read useless data
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read(11,*) textholder
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read(11,*) textholder
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lattice_types = maxval(new_lattice_map)
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do i = 1, in_atoms
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read(11,*) j, k, atom_type, r_in_atom(:)
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r_in_atom = r_in_atom + newdisplace
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call add_atom(atom_type_map(atom_type), sub_box_num + 1, r_in_atom)
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end do
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!Close file
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close(11)
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sub_box_num = sub_box_num + 1
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lattice_types = maxval(new_lattice_map)
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sub_box_num = sub_box_num + 1
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call set_max_esize
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call set_max_esize
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end if
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end subroutine read_pycac
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end module io
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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,normal, remesh_type, dim1, dim2
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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), remesh_lat_pam
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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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@ -160,14 +160,6 @@ module opt_group
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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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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 lattice parameter in group command"
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read(textholder, *) remesh_lat_pam
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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 type in group command"
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read(textholder, *) remesh_type
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case('max')
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max_remesh =.true.
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case('delete')
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@ -311,10 +303,10 @@ module opt_group
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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
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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)
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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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@ -322,156 +314,218 @@ module opt_group
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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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!Get the orientations, this assumes that the orientation of the subbox for the first atom is the
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!same as the rest of the atoms
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!If this assumption is false then the code will break and exit
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orient = sub_box_ori(:, :, sbox_atom(atom_index(1)))
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call matrix_inverse(orient,3,ori_inv)
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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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!First calculate max position in lattice space to be able to allocate lat_points array, also sum the total numbers of
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!degrees of freedom which are added
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dof = 0
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select case(trim(adjustl(shape)))
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case('block')
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group_in_lat = reshape((/ block_bd(1),block_bd(3),block_bd(5), &
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block_bd(2),block_bd(3),block_bd(5), &
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block_bd(2),block_bd(4),block_bd(5), &
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block_bd(1),block_bd(4),block_bd(5), &
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block_bd(1),block_bd(3),block_bd(6), &
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block_bd(2),block_bd(3),block_bd(6), &
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block_bd(2),block_bd(4),block_bd(6), &
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block_bd(1),block_bd(4),block_bd(6) /), [3,8])
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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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group_in_lat = matmul(fcc_inv, matmul(ori_inv, group_in_lat/remesh_lat_pam))
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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
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end if
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end do
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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)
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do ibasis = 1, basisnum(ilat)
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do j = 1, 3
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r =r_node(j,ibasis,inod,element_index(i))
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if (r(j) > group_bd(2*j)) group_bd(2*j) = r(j)
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if (r(j) < group_bd(2*j-1)) group_bd(2*j-1) = r(j)
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end do
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end do
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end do
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dof = dof + size_ele(element_index(i))**3
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end if
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end do
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!If for some reason there are no dof in this loop then cycle out
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if(dof == 0) cycle
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group_in_lat = reshape((/ group_bd(1),group_bd(3),group_bd(5), &
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group_bd(2),group_bd(3),group_bd(5), &
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group_bd(2),group_bd(4),group_bd(5), &
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group_bd(1),group_bd(4),group_bd(5), &
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group_bd(1),group_bd(3),group_bd(6), &
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group_bd(2),group_bd(3),group_bd(6), &
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group_bd(2),group_bd(4),group_bd(6), &
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group_bd(1),group_bd(4),group_bd(6) /), [3,8])
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group_in_lat = matmul(fcc_inv, matmul(ori_inv, group_in_lat/lapa(ilat)))
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do i = 1, 3
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bd_in_lat(2*i-1) = nint(minval(group_in_lat(i,:)))
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bd_in_lat(2*i) = nint(maxval(group_in_lat(i,:)))
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end do
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end select
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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))
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lat_points(:,:,:) = .false.
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dof = 0
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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))
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lat_points(:,:,:) = .false.
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dof = 0
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!Now place all group atoms and group interpolated atoms into lat_points
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do i = 1, group_atom_num
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r = r_atom(:,atom_index(i))/remesh_lat_pam
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r = matmul(fcc_inv,matmul(ori_inv,r))
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do j = 1, 3
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r_lat(j) = nint(r(j))
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end do
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!Do a check to make sure the code is working and that lattice points aren't being written on top of each other.
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!This is primarily a debugging statement
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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
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stop "Multiple atoms share same position in lat point array, this shouldn't happen"
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else
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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.
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dof = dof + 1
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end if
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end do
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!Now place interpolated atoms within lat_points array
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do i =1, group_ele_num
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ie = element_index(i)
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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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do j = 1, size_ele(ie)**3 * basisnum(lat_ele(ie))
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r = r_interp(:,j)/remesh_lat_pam
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r = matmul(fcc_inv,matmul(ori_inv,r))
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do k = 1, 3
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r_lat(k) = nint(r(k))
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end do
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!Do a check to make sure the code is working and that lattice points aren't being written on top of each other.
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!This is primarily a debugging statement
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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
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stop "Multiple atoms/interpolated atoms share same position in lat point array, this shouldn't happen"
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else
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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.
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dof = dof + 1
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end if
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end do
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end do
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print *, "Group has ", dof, " degrees of freedom to remesh"
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!Delete all elements and atoms to make space for new elements and atoms
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call delete_atoms(group_atom_num, atom_index)
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call delete_elements(group_ele_num, element_index)
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old_atom = atom_num
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old_ele = ele_num
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!Now run remeshing algorithm, not the most optimized or efficient but gets the job done
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!Figure out new looping boundaries
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bd_in_array(1) = bd_in_lat(2) - bd_in_lat(1) + 10
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bd_in_array(2) = bd_in_lat(4) - bd_in_lat(3) + 10
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bd_in_array(3) = bd_in_lat(6) - bd_in_lat(5) + 10
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if (max_remesh) then
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max_loops = (remesh_size-3)/2
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else
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max_loops = 1
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end if
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do j = 1, max_loops
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working_esize = remesh_size - 2*(j-1)
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ele = (working_esize-1)*cubic_cell
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zloop: do iz = 1, bd_in_array(3)
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yloop: do iy = 1, bd_in_array(2)
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xloop: do ix = 1, bd_in_array(1)
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if (lat_points(ix, iy,iz)) then
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r_new_node(:,:,:) = 0.0_dp
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!Check to see if the element overshoots the bound
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if (iz+working_esize-1 > bd_in_array(3)) then
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exit zloop
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else if (iy+working_esize-1 > bd_in_array(2)) then
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cycle zloop
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else if (ix+working_esize-1 > bd_in_array(1)) then
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cycle yloop
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end if
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if (all(lat_points(ix:ix+working_esize-1,iy:iy+working_esize-1,iz:iz+working_esize-1))) then
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do inod = 1, ng_node(remesh_type)
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vlat = ele(:,inod) + (/ix, iy, iz /)
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do i = 1, 3
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vlat(i) = vlat(i) + bd_in_lat(2*i-1)-5
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end do
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r_new_node(:,1,inod) = matmul(orient, matmul(fcc_mat, vlat))*remesh_lat_pam
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end do
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lat_points(ix:ix+working_esize-1,iy:iy+working_esize-1,iz:iz+working_esize-1) = .false.
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!Add the element, for the sbox we just set it to the same sbox that we get the orientation from.
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!In this case it is from the sbox of the first atom in the group.
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call add_element(remesh_ele_type, working_esize, remesh_type, sbox_atom(atom_index(1)),r_new_node)
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end if
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end if
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end do xloop
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end do yloop
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end do zloop
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end do
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!Now we have to add any leftover lattice points as atoms
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do iz = 1, bd_in_array(3)
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do iy=1, bd_in_array(2)
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do ix = 1, bd_in_array(1)
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if(lat_points(ix,iy,iz)) then
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vlat = (/ ix, iy, iz /)
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do i = 1, 3
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vlat(i) = vlat(i) + bd_in_lat(2*i-1)-5
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end do
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lat_points(ix,iy,iz) = .false.
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r = matmul(orient, matmul(fcc_mat, vlat))*remesh_lat_pam
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call add_atom(remesh_type, sbox_atom(atom_index(1)), r)
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!Now place all group atoms and group interpolated atoms into lat_points
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do i = 1, group_atom_num
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r = r_atom(:,atom_index(i))/lapa(ilat)
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r = matmul(fcc_inv,matmul(ori_inv,r))
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do j = 1, 3
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r_lat(j) = nint(r(j))
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end do
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!Do a check to make sure the code is working and that lattice points aren't being written on top of each other.
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!This is primarily a debugging statement
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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
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stop "Multiple atoms share same position in lat point array, this shouldn't happen"
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else
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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.
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dof = dof + 1
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end if
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end do
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!Now place interpolated atoms within lat_points array
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do i =1, group_ele_num
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ie = element_index(i)
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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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do j = 1, size_ele(ie)**3 * basisnum(lat_ele(ie))
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r = r_interp(:,j)/lapa(ilat)
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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
|
||||
end do
|
||||
|
||||
|
||||
print *, "Remeshing has created ", ele_num-old_ele, " elements and ", atom_num-old_atom, " atoms."
|
||||
end subroutine remesh_group
|
||||
|
||||
Loading…
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Reference in New Issue
Block a user