A few simple mods to remove gcc compile warnings

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.

more changes for 1-2, 1-3, 1-4 interactions plus some initialization-ordering
fixes to make gcc -Wall happier.

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.

Fixed typo in LJinteraction types. LJ-metal appears to work now.

A bunch of minor changes to make MPI compilation faster than
the double compilation we do now...

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

Nothing important

More changes to MnM.

Structural change to how spohr atoms will be parsed. Will be more like bonds.

Massive update to do virials (both atomic and cutoff-group) correctly.
The rigid body constraint contributions had been missing and this was
masked by the use of cutoff groups...

Adding the ability to compute Center of Mass properties on
reading in a dump file.  DumpReader must be told if it needs
to do this, however.

fixing a wrapVector problem in staticProps, also making Shifted force
and electrostatic damping the default behavior

fixed the half self term for wolf electrostatics and OOPSE now chooses a cutoff radius dependent alpha for damped electrostatics

adding NgammaT integrator

fixed some bugs in DumpWriter, eliminated some extra printing of
debugging information

change the globals.cpp to make sure we can set targetPressure and surfaceTension to be negative.

removed printing of GBN and GBM from previous debugging

more efficient file reading for thermodynamic integration, and fixed some formatting

fixes for mpi thermodynamic integration, close to fully working...

fixed some typos

Massive changes for GB code with multiple ellipsoid types (a la
Cleaver's paper).

Also, changes in hydrodynamics code to make HydroProp a somewhat
smarter class (rather than just a struct).

Last bug showed up in 2 places, fixed the other one.

Adding single precision capabilities to c++ side

NPrT might work now

refactor Hydrodynamics module.

Removed MixingRule from Globals. Handled by forceField now.

Changed formating.

Made some changes to electrostatics for shifted-potential and shifted-force with mono and multipoles

Added energy scaling to section parsers.

More Sutton-Chen bug fixes.

Force option changes.

added copyright

Added forceOptions to section parser

Fix parsing error in OptionSectionParser

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

Adding  ParamConstraint.cpp

OptionSectionParser get compiled

Missed makefile for sutton-chen.

added in a 5th order polynomial switching function option

improvements in shifted-force

fixed a capitalization problem with NPT integrator initialization

Another bug fix

changing GB architecture

Change error message in Globals

Adding Parameter Constraint class

rewrite Globals

Added support for skinThickness keyword to Globals.

DumpReader using pure c++ io

adding zipstream.hpp

some fixes but even more breaking (cutting out the old way to do reaction field)

changes to include the coulombicCorrection selector

made some changes for implementing the wolf potential

working version of DensityPlot

NPrT in progress

fix bug in NPAT and NPrT

help

Fixed build issues under ifc7.

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

xemacs has been drafted to perform our indentation services

more memory leak are fixed

reinitialize buffer_stack_ptr in BASS parser

fixed a bug in MPI restraints

using map to replace link list

minor change

fix a bug in SectionParser (lineNo is not updated)

Dunno

avoid using const char*(hope can fixed the missing atom type problem)

adding soft potential to LJ Module

adding LipidTransVisitor, GofXyz is working now

adding dynamicProps

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

using c library to do conversion instead of using iostream due to a bug in
libstdc++(GCC 3.2)

remove useless debug info

improved restraints - mpi should work fine

replace old GebericData with  new GenericData

fix a bunch of bugs

fix a bug in basic_ifstrstream.hpp

add checkFilename Option

FileReader in progress

change Makefile to relative path

change the #include in source files