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DCD trajectory output

Vermaas, Josh requested to merge vermaasj/PuReMD:dcdio into master

In order to more easily load trajectories into visualization tools like VMD, Chimera, and others, I've gone ahead and incorporated the dcdplugin that is used by other molecular simulation engines into PuReMD (at least in the PG-PuReMD branch that we've been using). Thus, now instead of writing the coordinates to the trj file, coordinates will be written to a dcd file, which can be loaded much faster by visualization tools.

There are some limits

  • Only implemented it for the "Simple" MPI I/O.
  • Commented out the writing of the coordinates to the trj file. In principle, it might be useful to make this an option, rather than obligatory, since the charges aren't written to a dcd file.

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