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.
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