more changes to MnM.

Removed debug message from simcreator.

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...

Changes to add thetacorr to dynamic props and fixes to radial rcorr.

BSM has to talk to reader about center of mass properties

Added function to calculate volume based on ellipsoid definded by radius of gyration.

user selected dampingAlpha now gets set

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

refined the reaction field dielectric passing

fixed a DumpReader bug, took out extra printing statements in
residentMem and BlockSnapshotManager

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

starting change of file formats

Adding single precision capabilities to c++ side

LangevinDynamics in progress

Missing brace caused the last commit not to build

unifying function name in electrostatics

More Sutton-Chen bug fixes.

In order to compile MPI version, we need to cast const char* to void* for stringstream.str();
Previous Makefile use bjects of single version to make the MPI library;

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.

Adding handler for CLAY force field

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

OptionSectionParser get compiled

Sutton-Chen added to SimInfo

added in a 5th order polynomial switching function option

improvements in shifted-force

fixed a capitalization problem with NPT integrator initialization

Still had some globals toUpper problems - these changes should fix those...

merged reaction field with electrostatics.F90

rewrite Globals

fix a bug in creating cutoffGroup. When
cutoffGroup is turned off, there is a mismatch between group and
center of mass array

Added support for skinThickness keyword to Globals.

reaction field seems to work now, still need to do some testing...

fixed a capitalization error

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

adding c-side interface to change cutoff Policy

replace c++ style comment in c files

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

NPAT is working

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

xemacs has been drafted to perform our indentation services

more memory leak are fixed

refactory LatticeFactory and LatticeCreator

pairs inside cutoff group should not be excluded

adding exclude pairs for rigidbody and cutoff group

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

Fixing a bug in BitSet.cpp

info_ in Velocitizer is not initialized which causes a seg fault

fixed a file inclusion problem

fix compilation problem for g++ 3.4

adding MersenneTwister random number generator

The change of interface of BitSet cause a bug in SelectionEvaluation

change the default bin number

BlockSnapshotManager is using reference counting now

cast of NULL to satisfy xlc++

begin bug fix

fixed a bug in SimInfo::getCutoff()

dynamicProps get built

more work in dynamicProps

adding one more constructor to Snapshot to create customized DataStorage

adding SelectionManager into SimInfo

fix a bug in SimInfo, use number of cutoff stamp as counter to loop over rigidbody stamp

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

port to SGI platform

Improvements to restraints

More work on StuntDouble, Atom, DirectionalAtom and RigidBody

forcefield refactoring for shapes

Snaphot and SnapshotTestCase in progress

more work in Snapshot

fixey fixey

Breaky Breaky.   Fixey Fixey.

Fortran/C++ interface de-obfuscation project appears to be complete!  Woo hoo!

Snapshot and SnapshotManager in design phase

fix some bugs in Quaternion class

define DEV_ROOT as relative path

move fortran files around to solve dependency problem

change the #include in source files