Changed DumpReader to use linked lists instead of a vector. Fixed the makefile to build DumpReader.cpp Removed a comment output in Exclude.cpp Modified DumpWriter and Integrator to write an eor file every time a frame is written. This lets the .eor file represent the last written frame of a simulation.
Fixes in MPI force calc and in Trappe_Ex parsing.
fixed a bug where the Excludes were not being created properly
fixed a bug where excludes were not being initialized
fixed the compile time bugs, Source builds and links
bug fixes many bug fixes
fixed a couple of the "static" bugs in Atom and Exclude
still working on the SimSetup routine. also fixed some things in Exclude.hpp
Fixes in Atom and Exclude list
added an Exclude class with static arrays similar to the Atom class
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