Added warnings for ewald-geometry and surface-epsilon

ewald-geometry and surface-epsilon require the system dipole,
which will be incorrect when charge groups with net charge cross pbc.
grompp now checks and warns for this.
Refs #1645.

Change-Id: I02e317cbddb47256f942312ec53c5bab2b13be2a
Fixed triclinic 1xNx1 domain decomposition

With the Verlet scheme, 1D triclinic domain decomposition along
dimension y produces incorrect bounding boxes for the non-bonded grid.
This led to a lot of missing non-bonded interactions, which quickly
crashes any simulation affected by this.
Fixes #1631.

Change-Id: I9bd1fc9d983be839e0c9a8e62d47f6cf17684a03
Fix problem with mixed affinity mask on different nodes.

If task distribution (with slurm for instance) causes both fully
allocated and not-fully allocated nodes to be assigned to the job then
there may be tasks with a all-cores affinity mask and tasks with a
not-all-cores affinity masks.

Fixes #1613

Change-Id: I71c0daa43a5dd42da57bfd09037806ce1d9334b5
Merge branch release-4-6 into release-5-0

Conflicts:
	src/gromacs/gmxpreprocess/readir.c
(added content at same point in both branches)

Change-Id: I9df7cef8c2e4920461fb3d84806c58cf07c645e2