Reorganized source directories, added RNEMD and flucQ blocks for options parsing.
Fixed compilation issues
resolved
Merging Shenyu's RNEMD changes from openmd-1 into the development branch.
updated copyright notices
Merging changes from old branch into development branch
Creating busticated version of OpenMD
Adding property set to svn entries
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
added RNEMD scaling
Parallel version of RNEMD
Added a getStatus routine to check the temperatures
fixed some bugs, added some logic to sort stuntdoubles
Adding options to RNEMD for selecting particular StuntDoubles
Added handlers to Integrator to call RNEMD at the right times. Added initialization to RNEMD to make sure values from the MD file are available.
Adding RNEMD
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