First commit of partial SpeciesBuilder class.
Commiting doc/notes/ddMd/Computes.
Merge branch 'devel' into topo
Merge branch 'devel' into topo
Commiting makefiles in src/chem directory
First commit of changes to move reservoir Species -> Simulation
Fixing Linear generator, unit tests.
Adding access to group id arrays in Species.
Fixing bug in SystemTest. McMd unit tests now all pass.
Adding atomGroups file (compiles, not tested).
Superficial changes, commit to sync
Moving Species::getAtom(Groups) to namespace global functions
Putting INTER_BOND ifdefs around everything with bonds in McMd
Merge branch 'devel' into species
Editing tests of Species and McSimulation
Added #ifdef INTER_BOND blocks to McMd::Species and dependent classes
Fixing McSimulationTest unit test, adding check to getAtomGroups.
Editing examples.
updating BUG/TODO for McMd examples
Cleaning up McMd::Group class template.