Removed second build of active atom list to address issue #1025

[gtribello]

Description

@GiovanniBussi I think this change should give your speed up on the input you discussed in #1025. This also ensures that the code still works when you run with DomainDecomposition, however.

Target release

I would like my code to appear in release 2.10

Type of contribution

• [ x] changes to code or doc authored by PLUMED developers, or additions of code in the core or within the default modules
• [ ] changes to a module not authored by you
• [ ] new module contribution or edit of a module authored by you

Copyright

• [ x] I agree to transfer the copyright of the code I have written to the PLUMED developers or to the author of the code I am modifying.

• [ ] the module I added or modified contains a COPYRIGHT file with the correct license information. Code should be released under an open source license. I also used the command cd src && ./header.sh mymodulename in order to make sure the headers of the module are correct.

Tests

• [ ] I added a new regtest or modified an existing regtest to validate my changes.
• [ x] I verified that all regtests are passed successfully on GitHub Actions.

[GiovanniBussi]

@gtribello makes sense. It's however going to impact the MPI version, because in that case the function will be called.

I would merge this, then I'll be back when I will have done MPI tests :-)

[gtribello]

OK. I have some ideas as to what we can do to get this also working with the domain decomposition. They are more complicated to implement, however, so I would like some evidence that they will actually lead to measurable speedup before starting on them.