Adds cut-off checks for triclinic domain decomposition

With domain decomposition and 2 decomposition cells in a trilinic
dimension, the cut-off could be longer than the size of the
communicated domains. This could lead to some pairs close to cut-off
distance to be ignored in the force/energy calculations.
Fixes #1467

Change-Id: Id7e16d7f8fa0796d6adcf48ad6e8bbb0b88039ff