mdrun ignores -nt option value, except for 1
Setting the -nt option of mdrun seems to have no effect, except when used with a value of 1. Tested only with thread-MPI.
Make mdrun -nt work again
Moved several thread count checks and assignments to a new
check_and_update_hw_opt_3 to clarify the options processing.
Also reorganized the PME thread count checks to avoid unclear
error messages for corner cases.
Renamed bOMP to bHasOmpSupport for clarity.
Converted assert calls to GMX_RELEASE_ASSERT (and added new ones).