Allowing the script API to return atom IDs even in scalable computations

[giacomofiorin]

Issue raised in a conversation a few weeks ago between @HanatoK and Ashkan Fakharzadeh Ghaan at UIUC.

Debugging a Colvars configuration in NAMD can be confusing if all the atoms are only involved in centers of mass, and getatomids returns an empty vector.

The most direct solution could be to return all atom IDs, regardless of whether their coordinates are sent to Colvars for sequential computation. However, that would make the vector of atom IDs not match those of atomic coordinates or forces.

A possible alternative could be letting the script API handle atom groups as well, and warn the user when these are not empty when the user requests atom IDs. @HanatoK also proposed turning off scalable centers of mass when using these script API methods.