LJ.cpp has been updated to more correctly deal with nonbonded interactions (i.e. explicit interactions where the species are not necessarily defined to be lennardJones type atoms)
updated copyright notices
Merging changes from old branch into development branch
Fixes
Bug squashing
Well, the potential energy values are still garbage, but the LJ sample runs.
bug fixes
bug fixes (not done yet)
Added Atypes to new C++ force decomposition.
For efficiency, pointers instead of objects will be passed during main force loop.
a few more tweaks We're getting somewhat closer to deleting fortran.
still busted, but much progress
compiles, builds and runs, but is very slow
Less busted than it was on last check-in, but still won't completely build.
Many changes, and we're not quite done with this phase yet.
fixed some destructor bugs dealing with the TypeContainers
fixing c/fortran bugs
fixing calls
Added nonbonded directory. Compiles, links, runs, but gives incorrect answer.
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