fixes issues with pressure control and infrequent evaluation

Fixes a bug when pressure control in md-vv when nstcalcenergy is not a
multiple of nstpcouple or nsttcouple. This bug results in boxes slowly
expanding to unphysical sizes because the virial is
neglected in the second half of the md-vv calculation.

Also discovered that as part of the bug, global energies were being communicated
where they did not need to be when nstpcouple and nsttcouple are > 1 in the case
of md-vv, so redid some of the iteration counting and global communication to fix
this all together. In the process, this simplified some of the interation counting.

Change-Id: I3f77ba361fc88e03ccdfdde1b0be388ea46a8683
Quiet stderr output, particularly for multi-simulations

* removed printing of DD info to stderr
* printed multi-simulation information only once in places where
  repetition is clearly redundant (Some repetition remains,
  but only from each simulation master.)
* add option to not print result of multi-simulation check
  if it passed, so that we don't have to print things to
  stderr/stdout just because the .log file is not yet open
* printing of diagnostics about the number of MPI
  processes present when mdrun starts only goes (once) to
  each debug file, and not to stderr
* reduced printing of diagnostics about the number of OpenMP
  threads; now goes to stderr only on SIMMASTER, or
  once to each debug file
* clarified errors and informational messages about selecting
  the number of OpenMP threads

Fixes #1078, refs #1083

Change-Id: If782259bcd62ddd9be325393930080b70c5cfb4e
split off pick_nbnxn_resource from nbnxn_pick_nbnxn

Fixes #1049

Change-Id: Iadf46f40676551b9b58d0d3da5bdca0f94d4a3fb