Now molecules can keep track of their own IntegrableObjects (and RigidBodies). Also a bug-fix so that SimInfo can keep track of RigidBodies (which was done incorrectly before).
Changes for RigidBody dynamics (Somewhat extensive)
replace c++ header stuff with more portable c header stuff Also, mod file fixes and portability changes Some fortran changes will need to be reversed.
Added Z constraint.
more archaic code fixes
removing get_vx
Bug fix in progress for NPT
added a globalIndex counter to Molecule
fixes for NPT and NVT
Changes to integrate the NVT and NPT ensembles
Many fixes to add extended system
just little things like deleteing unused variables and such.
a few fixes to simError.h also some fixes to Molecule.hpp
Starting work on NPT
Fixes in MPI force calc and in Trappe_Ex parsing.
fixed a bug where the Excludes were not being created properly
fixed the compile time bugs, Source builds and links
fixed a few more bugs.
added the Molecule.cpp file
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