Fix to formatting and cell neighbor loop algorithm

src/opt_delete.f90

@@ -42,12 +42,13 @@ module opt_delete
                 call get_command_argument(arg_pos, textholder, arg_len)
                 if(arg_len==0) stop "Missing argument to delete overlap command"
                 print *, textholder
-                read(*, textholder) rc_off
-
+                read(textholder, *) rc_off
             case default
                 print *, "Command ", trim(adjustl(textholder)), " is not accepted for option delete"
                 stop 3
         end select 
+
+        arg_pos = arg_pos + 1
     end subroutine parse_delete
 
     subroutine delete_overlap
@@ -79,6 +80,13 @@ module opt_delete
                 do ci = -1, 1, 1
                     do cj = -1, 1, 1
                         do ck = -1, 1, 1  
+
+                            if (any((c + (/ ck, cj, ci /)) == 0)) cycle 
+
+                            if( (c(1) + ck > cell_num(1)).or.(c(2) + cj > cell_num(2)).or. &
+                                (c(3) + ci > cell_num(3))) cycle
+
+
                             do num_nei = 1, num_in_cell(c(1) + ck, c(2) + cj, c(3) + ci)
                                 nei = cell_list(num_nei,c(1) + ck, c(2) + cj, c(3) + ci)
 
@@ -108,10 +116,10 @@ module opt_delete
                 end do 
             end if
 
-            !Now delete all the atoms
-            call delete_atoms(delete_num, for_delete(1:delete_num))
-
         end do atom_loop
 
+        print *, "Overlap command deletes ", delete_num, " atoms"
+        !Now delete all the atoms
+        call delete_atoms(delete_num, for_delete(1:delete_num))
     end subroutine delete_overlap
 end module opt_delete