Current working changes

src/io.f90

@@ -907,7 +907,6 @@ module io
 
         !Read more useless data
         read(11,*) textholder
-        read(11,*) textholder
 
         !set max values and allocate variables 
         max_basisnum = maxval(basisnum)
@@ -915,6 +914,8 @@ module io
         call grow_ele_arrays(in_eles, in_atoms)
 
         !Now start reading the elements 
+        if(in_eles > 0) then
+            read(11,*) textholder
             do i = 1, in_eles 
                 read(11,*) j, etype, k, lat_type 
                 do inod = 1, 8
@@ -923,10 +924,15 @@ module io
                 end do 
                 call add_element(in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in)
             end do
+        end if
 
+        if(in_atoms > 0) then 
+
+            if (in_eles > 0) then 
                 !Read useless data 
                 read(11,*)  textholder
                 read(11,*) textholder
+            end if
 
             do i = 1, in_atoms
                 read(11,*) j, k, atom_type, r_in_atom(:)
@@ -941,5 +947,6 @@ module io
             sub_box_num = sub_box_num + 1
 
             call set_max_esize
+        end if
     end subroutine read_pycac
 end module io

src/opt_group.f90

@@ -8,9 +8,9 @@ module opt_group
     use box 
     implicit none
 
-    integer :: group_ele_num, group_atom_num, remesh_size,normal, remesh_type, dim1, dim2
+    integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2
     character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
-    real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), remesh_lat_pam
+    real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3) 
     logical :: displace, delete, max_remesh, refine
 
     integer, allocatable :: element_index(:), atom_index(:) 
@@ -160,14 +160,6 @@ module opt_group
                 call get_command_argument(arg_pos, textholder, arglen)
                 if (arglen==0) stop "Missing remesh element size in group command"
                 read(textholder, *) remesh_size
-                arg_pos = arg_pos + 1
-                call get_command_argument(arg_pos, textholder, arglen)
-                if (arglen==0) stop "Missing remesh lattice parameter in group command"
-                read(textholder, *) remesh_lat_pam
-                arg_pos = arg_pos + 1
-                call get_command_argument(arg_pos, textholder, arglen)
-                if (arglen==0) stop "Missing remesh type in group command"
-                read(textholder, *) remesh_type
             case('max')
                 max_remesh =.true.
             case('delete')
@@ -311,10 +303,10 @@ module opt_group
 
         integer :: i, j, k, ix, iy, iz, inod, ibasis, ie, type_interp(max_basisnum*max_esize**3), add_atom_num, orig_atom_num,   &
                    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, &
-                   max_loops, working_esize
+                   max_loops, working_esize, group_lat_num, lat_list(10), group_sbox_num, sbox_list(100), is, ilat
 
         real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3),  ori_inv(3,3),  r(3), &
-                         r_new_node(3,max_basisnum, max_ng_node), orient(3,3), group_in_lat(3,8)
+                         r_new_node(3,max_basisnum, max_ng_node), orient(3,3), group_in_lat(3,8), group_bd(6)
         logical, allocatable :: lat_points(:,:,:)
         character(len=100) :: remesh_ele_type
 
@@ -322,42 +314,103 @@ module opt_group
         !Right now we just hardcode only remeshing to elements
         remesh_ele_type = 'fcc'
 
-        !Get the orientations, this assumes that the orientation of the subbox for the first atom is the 
+        ! Determine which sub_boxes and lattices types are within in the group
-        !same as the rest of the atoms
+        group_sbox_num = 0
-        !If this assumption is false then the code will break and exit
+        group_lat_num = 0
-        orient = sub_box_ori(:, :, sbox_atom(atom_index(1)))
+        do i = 1, group_atom_num 
+            do j = 1, group_sbox_num
+                if (sbox_list(j) == sbox_atom(atom_index(i))) exit
+                group_sbox_num = group_sbox_num + 1 
+                sbox_list(group_sbox_num) = sbox_atom(atom_index(i))
+            end do
+
+            do j = 1, group_lat_num
+                if (basis_type(1,lat_list(j)) == type_atom(atom_index(i))) exit
+                group_lat_num = group_lat_num + 1 
+                do k = 1, lattice_types
+                    if (basis_type(1,k) == type_atom(atom_index(i))) lat_list(group_lat_num) = k
+                end do
+            end do 
+        end do 
+
+        do i = 1, group_ele_num
+            do j = 1, group_sbox_num
+                if (sbox_list(j) == sbox_ele(element_index(i))) exit
+                group_sbox_num = group_sbox_num + 1
+                sbox_list(group_sbox_num) = sbox_ele(element_index(i))
+            end do
+
+            do j = 1, group_lat_num
+                if (lat_list(group_lat_num) == lat_ele(element_index(i))) exit
+                group_lat_num = group_lat_num + 1
+                lat_list(group_lat_num) = lat_ele(element_index(i))
+            end do
+        end do
+
+        do is = 1, group_sbox_num 
+
+            orient = sub_box_ori(:, :, sbox_list(is))
             call matrix_inverse(orient,3,ori_inv)
 
-        !First calculate max position in lattice space to be able to allocate lat_points array, also sum the total numbers of 
+            do ilat = 1, group_lat_num
-        !degrees of freedom which are added
+
+                !First calculate max position in lattice space to be able to allocate lat_points array, also sum the total number
+                !of degrees of freedom which are added
                 dof = 0 
+                do j = 1, 3
+                    group_bd(2*j) = -huge(1.0_dp)
+                    group_bd(2*j-1) = huge(1.0_dp)
+                end do
+                do i = 1, group_atom_num
+                    if ((type_atom(atom_index(i)) == basis_type(1,ilat)).and.(sbox_atom(atom_index(i)) == is)) then
+                        do j =1 ,3
+                            if (r_atom(j,atom_index(i)) > group_bd(2*j)) group_bd(2*j) = r_atom(j,atom_index(i))
+                            if (r_atom(j,atom_index(i)) < group_bd(2*j-1)) group_bd(2*j-1) = r_atom(j,atom_index(i))
+                        end do
+                        dof = dof + 1
+                    end if
+                end do 
                 
-        select case(trim(adjustl(shape)))
+                do i = 1, group_ele_num
-            case('block')
+                    if ((lat_ele(element_index(i)) == ilat).and.(sbox_ele(element_index(i)) == is)) then 
-                group_in_lat = reshape((/ block_bd(1),block_bd(3),block_bd(5), &
+                        do inod =1, ng_node(ilat)
-                                          block_bd(2),block_bd(3),block_bd(5), &
+                            do ibasis = 1, basisnum(ilat)
-                                          block_bd(2),block_bd(4),block_bd(5), &
+                                do j = 1, 3
-                                          block_bd(1),block_bd(4),block_bd(5), &
+                                    r =r_node(j,ibasis,inod,element_index(i)) 
-                                          block_bd(1),block_bd(3),block_bd(6), &
+                                    if (r(j) > group_bd(2*j)) group_bd(2*j) = r(j)
-                                          block_bd(2),block_bd(3),block_bd(6), &
+                                    if (r(j) < group_bd(2*j-1)) group_bd(2*j-1) = r(j)
-                                          block_bd(2),block_bd(4),block_bd(6), &
+                                end do
-                                          block_bd(1),block_bd(4),block_bd(6) /), [3,8])
+                            end do
-
+                        end do
-                group_in_lat = matmul(fcc_inv, matmul(ori_inv, group_in_lat/remesh_lat_pam))
+                        dof = dof + size_ele(element_index(i))**3
+                    end if
+                end do
+
+                !If for some reason there are no dof in this loop then cycle out
+                if(dof == 0) cycle
+
+                group_in_lat = reshape((/ group_bd(1),group_bd(3),group_bd(5), &
+                                          group_bd(2),group_bd(3),group_bd(5), &
+                                          group_bd(2),group_bd(4),group_bd(5), &
+                                          group_bd(1),group_bd(4),group_bd(5), &
+                                          group_bd(1),group_bd(3),group_bd(6), &
+                                          group_bd(2),group_bd(3),group_bd(6), &
+                                          group_bd(2),group_bd(4),group_bd(6), &
+                                          group_bd(1),group_bd(4),group_bd(6) /), [3,8])
+
+                group_in_lat = matmul(fcc_inv, matmul(ori_inv, group_in_lat/lapa(ilat)))
                 do i = 1, 3
                     bd_in_lat(2*i-1) = nint(minval(group_in_lat(i,:)))
                     bd_in_lat(2*i) = nint(maxval(group_in_lat(i,:)))
                 end do
 
-        end select 
-
                 allocate(lat_points(bd_in_lat(2)-bd_in_lat(1)+10, bd_in_lat(4)-bd_in_lat(3)+10, bd_in_lat(6)-bd_in_lat(5)+10))
                 lat_points(:,:,:) = .false.
                 dof = 0
 
                 !Now place all group atoms and group interpolated atoms into lat_points
                 do i = 1, group_atom_num
-            r = r_atom(:,atom_index(i))/remesh_lat_pam
+                    r = r_atom(:,atom_index(i))/lapa(ilat)
                     r = matmul(fcc_inv,matmul(ori_inv,r))
                     do j = 1, 3
                         r_lat(j) = nint(r(j))
@@ -377,13 +430,13 @@ module opt_group
                     ie = element_index(i)
                     call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
                     do j = 1, size_ele(ie)**3 * basisnum(lat_ele(ie))
-                r = r_interp(:,j)/remesh_lat_pam
+                        r = r_interp(:,j)/lapa(ilat)
                         r = matmul(fcc_inv,matmul(ori_inv,r))
                         do k = 1, 3
                             r_lat(k) = nint(r(k))
                         end do 
-                !Do a check to make sure the code is working and that lattice points aren't being written on top of each other. 
+                        !Do a check to make sure the code is working and that lattice points aren't being written on top of each  
-                !This is primarily a debugging statement
+                        !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 
@@ -435,18 +488,18 @@ module opt_group
                                     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(remesh_type)
+                                        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))*remesh_lat_pam
+                                           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.
+                                        !Add the element, for the sbox we just set it to the same sbox that we get the orientation 
-                                !In this case it is from the sbox of the first atom in the group.
+                                        !from. In this case it is from the sbox of the first atom in the group.
-                                call add_element(remesh_ele_type, working_esize, remesh_type, sbox_atom(atom_index(1)),r_new_node)
+                                        call add_element(remesh_ele_type, working_esize, ilat, sbox_atom(atom_index(1)),r_new_node)
 
                                     end if
                                 end if
@@ -465,13 +518,14 @@ module opt_group
                                     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))*remesh_lat_pam
+                               r = matmul(orient, matmul(fcc_mat, vlat))*lapa(ilat)
-                       call add_atom(remesh_type, sbox_atom(atom_index(1)), r)
+                               call add_atom(basis_type(1,ilat), sbox_atom(atom_index(1)), r)
                             end if
                         end do
                     end do 
                 end do
-        
+            end do
+        end do
 
         print *, "Remeshing has created ", ele_num-old_ele, " elements and ", atom_num-old_atom, " atoms."
     end subroutine remesh_group