Deleted 1 atom but Created 0 atoms in the same region

The problem you are having is explained on the change_box doc page:

After all the keywords have been processed, any shrink-wrap boundary conditions are invoked (see the boundary command) which may change simulation box boundaries, and atoms are migrated to new owning processors.

You have shrink-wrapped BC, and are trying to use change_box to grow

the box length in a shrink-wrapped dimension, then insert an atom
with create_atoms single in the extra space you created (that is outside
the original shrink-wrapped box).

You can’t do that, b/c change_box re-shrink-wraps the box after all the

changes you specify. I.e. you can’t override a shrink-wrapped boundary.

What you would need to do is use the boundary
option of change_box to change from shrink-wrapped to periodic boundaries

(with the new box size you want), then use create_atoms to add an atom,
then use change_box again to convert back to shrink-wrapped boundaries.


Hi Steve!

I will try this. It’s really helpful.

Thank you very much!

Best Regards

Wenqiang Liu