Fix illegal memory access with FEP and OpenMP

The thread reduction masks for the perturbed non-bonded interaction force buffer are generated by range loops, but the range of the std:: vectors do not correspond to the actual size in use. This would lead to out of bounds access of the mask buffers, but not to illegal memory access, as the only old elements could be out range but the buffers would still have at least that size.

This might also affect performance, as too many buffer elements were flagged with old, no longer used, atom indices.