Change DdMdTrajectory to use uint positions.
Merge branch 'devel' of github.com:/dmorse/simpatico into devel
Adding Util::Bit::init() member function.
Changing Bit::init() to Bit::setMask()
Merge branch 'devel' of github.com:/dmorse/simpatico into devel
Adding groupMask to AtomContext.
Adding groups and DdMdGroupTrajectoryWriter
Editing diblock/N32/dd example
Add groups() to DdMd::Atom class.
Small edits to Atom and AtomArray docs.
Moving src/spAn -> src/tools.
Editing manual to reflect SpAn -> Tools change.
Updating TODO lists.
Moving tools/ to scripts/
Updating TODO lists.
Removing doc/notes/tools files
Merge branch 'devel' into files
Cleaning up makefile, python scripts.
Editing src/config.mk and tools/patterns.mk
Changing makefile for ChainMaker program