Adding RNEMD

Cleaning up some cruft.

Stupid getRandomNumber return 4;

More attempts to get SMIPD to themostat properly

Fixed segfault in because of directional atom in SMIPD.

More changes to SMIPD. Attempting to find memory leak.

Fixed nanovol so it now builds.

Fixed makefile.

Adding back more missing files.

Added some logic to print out a special pair distance as a column in
the stat file.  To use this feature, use taggedAtomPair = "0, 10" and
printTaggedPairDistance = "true" in the md file.  Then, the distance
between integrableObjects 0 and 10 will be computed and printed in
the stat file on each statWrite.

Adding iterative looping to get better estimates of friction forces
from full-step velocities

updating configure process

Removed older version of openbabel from our code.  We now have a
configure check to see if openbabel is installed and then we link to
the stuff we need.  Conversion to OOPSE's md format is handled by only
one application (atom2md), so most of the work went on there.
ElementsTable still needs some work to function in parallel.

Fixed some bugs in LDForceManager.cpp

SF Lennard-Jones was added for everyones' enjoyment.  The behavior is tethered to the electrostaticSummationMethod keyword.

Spherical boundary conditions.

adding NgammaT integrator

Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants

testing GB, removing CM drift in Langevin Dynamics, fixing a memory
leak, adding a visitor

fix a bug in parsing HydroProp file

Adding single precision capabilities to c++ side

Adding spherical boundary conditions to LD integrator

Fix a bug in friction calculation for ellipsoid

refactor Hydrodynamics module.

LangevinDynamics in progress

End of the Link --> List
Return of the Oject-Oriented
replace yacc/lex parser with antlr parser

fixed a capitalization problem with NPT integrator initialization

rewrite Globals

Removed print statements for remove angular momentum.

Added method to remove system angular momentum to velocitizer and added method to calculate system angular momentum to siminfo.

adding resetIntegrator

adding keyword printPressureTensor

NPrT in progress

fix bug in NPAT and NPrT

xemacs has been drafted to perform our indentation services

VelocityVerletIntegrator already deletes and Nullifies restWriter,
so Integrator shouldn't do it.

info_ in Velocitizer is not initialized which causes a seg fault

replace SPRNG by MTRand

adding OOPSERandNumGen

adding basic_teebuf which can operate on multiple stream simutaneously.

maximum length defaults to the cutoff radius

forget to add eorWriter

fix a bug in loading initial extended system parameters

moved Package variable into subdirectory makefiles to speed up
the building process

improved restraints

Commented out some write statements

replace old GebericData with  new GenericData

define DEV_ROOT as relative path

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