Bugfix: LCAO and periodic systems

Description

Bugfix for LCAO in periodic systems.

In periodic systems, the distance between two atomic centers can be larger than the sum of the radius, and they can still overlap because of periodic copies. This never occurs in small systems, this is probably this went unnoticed before.

News snippet

Bugfix for LCAO in periodic systems.

Checklist

• I have checked that my code follows the Octopus coding standards
• I have added tests for all the new features added in this request.