Working remesh command and remesh max command

src/io.f90

@@ -310,6 +310,9 @@ module io
 20      format('SCALARS lattice_type float', /&
                'LOOKUP_TABLE default')
 
+21      format('SCALARS esize float', /&
+               'LOOKUP_TABLE default')
+
         !First we write the vtk file containing the atoms
         open(unit=11, file='atoms_'//trim(adjustl(file)), action='write', status='replace',position='rewind')
 
@@ -358,6 +361,10 @@ module io
         do i = 1, ele_num
             write(11, '(i16)') lat_ele(i)
         end do
+        write(11,21)
+        do i = 1, ele_num
+            write(11, '(i16)') size_ele(i)
+        end do
         close(11)
     end subroutine
 
@@ -624,8 +631,13 @@ module io
         !Read in the box boundary and grow the current active box bd 
         read(11, *) temp_box_bd(:)
 
+        print *, "displace", displace
         do i = 1, 3
+            if (displace(i) > lim_zero) then 
                 newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
+            else
+                newdisplace=displace(i)
+            end if 
             temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
             temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
         end do 
@@ -717,7 +729,8 @@ module io
         !Read the atoms 
         do i = 1, in_atoms
             read(11,*) j, type, sbox, r(:)
-            call add_atom(new_type_to_type(type), sbox, r+newdisplace )
+            r = r+newdisplace
+            call add_atom(new_type_to_type(type), sbox, r)
         end do
 
         !Read the elements

src/opt_group.f90

@@ -29,7 +29,7 @@ module opt_group
         remesh_size=0
         displace=.false.
         delete=.false.
-        ! max_remesh=.false.
+        max_remesh=.false.
         refine = .false.
 
         if(allocated(element_index)) deallocate(element_index)
@@ -262,7 +262,9 @@ module opt_group
         !This command is used to remesh the group to a desired element size
 
         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
+                   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
+
         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)
         logical, allocatable :: lat_points(:,:,:)
@@ -352,31 +354,40 @@ module opt_group
         old_atom = atom_num
         old_ele = ele_num
 
+
+
         !Now run remeshing algorithm, not the most optimized or efficient but gets the job done
-
-        ele = (remesh_size-1)*cubic_cell
-
         !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-2)/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+remesh_size-1 > bd_in_array(3)) then
+                            if (iz+working_esize-1 > bd_in_array(3)) then
                                 exit zloop
-                        else if (iy+remesh_size-1 > bd_in_array(2)) then
+                            else if (iy+working_esize-1 > bd_in_array(2)) then
                                 cycle zloop
-                        else if (ix+remesh_size-1 > bd_in_array(1)) then 
+                            else if (ix+working_esize-1 > bd_in_array(1)) then 
                                 cycle yloop
                             end if  
 
-                        if (all(lat_points(ix:ix+remesh_size-1,iy:iy+remesh_size-1,iz:iz+remesh_size-1))) then 
+                            if (all(lat_points(ix:ix+working_esize-1,iy:iy+working_esize-1,iz:iz+working_esize-1))) then 
-                            do inod = 1, 8
+                                do inod = 1, ng_node(remesh_type)
                                     vlat = ele(:,inod) + (/ix, iy, iz /)
                                     do i = 1, 3
                                         vlat(i) = vlat(i) + bd_in_lat(2*i-1)-5
@@ -384,16 +395,17 @@ module opt_group
                                    r_new_node(:,1,inod) = matmul(orient, matmul(fcc_mat, vlat))*remesh_lat_pam
                                 end do 
 
-                            lat_points(ix:ix+remesh_size-1,iy:iy+remesh_size-1,iz:iz+remesh_size-1) = .false.
+                                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, remesh_size, remesh_type, sbox_atom(atom_index(1)),r_new_node)
+                                call add_element(remesh_ele_type, working_esize, remesh_type, 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)