Fix missing atomistic boundary flag on some elements after mesh repair
After the completion of the new repair algorithm, some elements in the atomistic region (which are adjacent to old bad elements) are missing the atomistic flag. This seems to result in errors when computing the forces on atoms which are the vertices of these elements.
The variable atomistic_bounds
should be enough to turn on after repair the atomistic flag of the elements within these atomistic_bounds
.
One can look only at the new set of elements generated in the repair and turn on their atomistic flag if they are within the atomistic_bounds
. (Check old repair algorithm which did not suffer from this problem).
Tasks:
-
Include a unit test to check all elements in the atomistic region have the atomistic flag after repair.
For this unit test, we can use an existing test where we have an atomistic mesh with bad elements.