Changes to make MSVC happy

Removed inaccessible lines

Fixed some broken comments for use with Doxygen.
Made changes to allow topology-based force-field overrides in include files.
Fixed a calculation of box quadrupole moments for molecules with point dipoles.

Starting to add support for UniformGradient. 
Changed Vector3d input type to a more general std::vector<RealType> input.  This change alters RNEMD and UniformField inputs.

Discovered an old debugging region in OPLS torsions

Fixes to deal with deprecation of MPI C++ bindings.  We've reverted back to the
C calls.

Fixed a bend issue for James

Test for James

MERGE OpenMD development 1783:1878 into trunk

Fixed some compilation warnings on the Linux side of things.

Bug fixes for GB.  Now using strength parameter mixing ideas from Wu
et al. [J. Chem. Phys. 135, 155104 (2011)].  This helps get the
dissimilar particle mixing behavior to be the same whichever order the
two particles come in.  This does require that the force field file to
specify explicitly the values for epsilon in the cross (X), side-by-side (S), 
and end-to-end (E) configurations.

Updated antlr, some minor formatting changes

testing

added new CosineBendType

Added missing cstdio include lines for gcc 4.4 compatibility

Bug fixes in the SelectionEvaluator and SelectionCompiler
Added print option in Restraints

Returned old LD forces to SMIPDForceManager.

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.

fixed a strange compiler structure alignment problem with the
intel Mac compiler  (structs that cross between C and fortran
appear to need 8-byte boundary alignment on this compiler).

Changes for implementing Amber force field:  Added Inversions and
worked on BaseAtomTypes so that they'd function with the fortran side.

Adding infrastructure for Amber force field.

Code work on thiols and TraPPE torsions.

Changing functional form

Changes to MAW. New form of the potential and cleanup.

Formatting to prettify the code

removed MWM as an atom type property

Changes for Non-Bonded interactions.

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

Adding single precision capabilities to c++ side

adding transpose into SquareMatrix3; fix a bug in AtomStamp where orientation is not set correctly.

instead of printing to std::cout, throwing an exception when error is found.

the standard library came with SUN compiler does not have a conforming std::use_facet, define a macro
to handle it. Adding exception handling to SimCreator.

Fixed a bug in checkTorsion

adding more checking for topology

adding DataHolder

OptionSectionParser get compiled

Added suppport to atypes for MEAM and sutton-chen

Fixed merge issues between Kyle and Chris so OOPSE will actually build.

OOPSE setup for TAP water.  It's not parametrized, but OOPSE will now let me run it...

Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...

more memory leak are fixed

adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into
ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;

Electrostatic Unification Project

(1) complete section parser's error message
(2) add GhostTorsion
(3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor

port to SGI platform

still debugging

Making ShapeType into a ShapeAtomType, fixing some isXXX

strDUP not strCOPY

More on AtomType and DirectionalAtomType

Breaky Breaky.   Fixey Fixey.

Working on getting Shapes into OOPSE

define DEV_ROOT as relative path

change the #include in source files