refactor: Remove ConfigurationAtom::globalIndex().#2514
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This PR addresses #2418 and removes the highly unnecessary
ConfigurationAtom::globalIndex()function which used the internalmolecule_pointer and some pointer arithmetic to work out which index it was in the parentConfiguration. We already had anAtom::index_variable, so now we just set, update, and use that instead.Running the benchmarks on my system suggest a 5% or so gain in the force routines as a direct result of doing this.