Slight improvements to GPU update/constraints initialization

Slight improvements to GPU update/constraints initialization

1. Assertions are updated to better correspond to the supported
   conditions.
2. The message in the log now depends on whether or not there are
   constraints in the system.
3. Redundant set(...)/setPbc(...) before the MD loop removed.

The getter for the total number of constraints is also added to
the Constraints class.

TODO: The assertions can be removed once the supported
      functionality is expanded.

Change-Id: I96e2b993f79cf721f7aa48b9af0eab6500c593ba