indentation issue in lammps reader
Automating building the nonbonded forces.

Now much more trivial to add forces.

Will need some cleanup to be operational, not too much.
Some bug fixes, and added nonbondeds.
continuation of rewrite of forcepairs and forcepairtypes

Not quite working, but structure should be inherently set.
minor organization, docstring formatting and removed use of python keyword "file"
typo in dihedral creation
More bugfixing and functionality addition for force reorganization
All unit tests from gromacs now run without -e.
G->G unit test tests are all working.

Note that additional angle support was installed trivially with a couple of data lines.
More cleaning; creation of most forcetypes are moved to routines.
fixes for directly reading in entires (vs. reading in via bond types).

This includes better unit tests that include both direct specification of
forces and specification through forcetypes
Additional cleaning of gromacs_topology parser
reorganization, added a water unit test, and velocity handling

Some gromacs reorganization for nonbondeds, and moving even some
short sections into their own functions.

Better handling of no velocities.  In gromacs, there is a difference between
zero velocities and no velocities, so now zero velocities are stored as None,
and for now, if those are none in LAMMPS and DESMOND, they are interpreted as zero.

Added a water unit test and did some bugfixing resulting from errors there.
Bug fix for previous.
Added support for reading/writing virtual sites in gromacs.
Added unit tests for virtual sites in Gromacs.
Updated FKBP tests.
Some bug fixes so that dihedrals now are found, dihedral energy isn't matching.
Fix for reading 2PPN (narrow columns with no spaces).
A number of changes for supporting pairs correctly.

Includes rewriting the automated script for incorporation of defaults.

added two new pair unit tests.

pairs2 having some problem.  It's with the explicitly stated pair.  Not sure
what the issue is, will probably have to dril down to gromacs debugging.