Another fix to overlap command

src/opt_delete.f90

@@ -82,6 +82,7 @@ module opt_delete
         integer, dimension(3) :: cell_num
         integer, allocatable :: num_in_cell(:,:,:), which_cell(:,:)
         integer, allocatable :: cell_list(:,:,:,:)
+        logical :: deleted_atom(atom_num)
         
         allocate(which_cell(3,atom_num))
 
@@ -90,6 +91,7 @@ module opt_delete
 
         !Now loop over every atom and figure out if it has neighbors within the rc_off
         delete_num = 0
+        deleted_atom=.false.
         atom_loop: do i = 1, atom_num
             
             !c is the position of the cell that the atom belongs to 
@@ -113,7 +115,7 @@ module opt_delete
 
                                 !Check to make sure the atom isn't the same index as the atom we are checking 
                                 !and that the neighbor hasn't already been deleted
-                                if((nei /= i).and.(nei/= 0)) then 
+                                if((nei /= i).and.(.not.deleted_atom(nei))) then 
 
                                     !Now check to see if it is in the cutoff radius, if it is add it to the delete code
                                     if (norm2(r_atom(:,nei)-r_atom(:,i)) < rc_off) then 
@@ -121,8 +123,10 @@ module opt_delete
                                         delete_num = delete_num + 1
                                         if(first) then
                                             for_delete(delete_num) = min(i,nei)
+                                            deleted_atom(min(i,nei)) = .true.
                                         else
                                             for_delete(delete_num) = max(i,nei)
+                                            deleted_atom(max(i,nei)) = .true.
                                         end if
 
                                         !Now zero out the larger index