fixed TI MPI bug

Massive changes preparing for release of OOPSE-4: The main difference
is that the new MD file format (.md, .dump, .eor) now contains meta-data
information along with the configuration information.

testing commit logger

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

MPI thermodynamic integration works now.

Fixed a spelling error and a bug in MPI Thermodynamic Integration on file read-in

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

Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)

Fix a bug of printing empty line in DumpWriter

Adding spherical boundary conditions to LD integrator

remove a unknown method

LangevinDynamics in progress

Added NPAT to Globals integrators.

filepp can not handle multiple line macro, just convert multiple line macro into single line macro.

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

replace isType<int> with isInteger

More changes to forcefield options.

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.

Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.

Overloaded interface for dumpwriter.

Adding handler for CLAY force field

parsing by filepp

adding ForceFieldOptions

ForceField optional parameters....

Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen.

Added a keyword and ability to output forces and torques

changing how we deal with summation and screening methods

Customized StatWriter is working

fix some namespace issues in Globals

fix a seg fault when try copy a  string to event's err_msg, there are still tons of memory leaking problem in Globals

Constraints for parameters are working now

added default restraint spring constants into Globals

tracking down quaternion bug

fix a typo in DumpReader

adding zlib support for DumpWriter

Added keywords for compressed dump files.

Fix a bug in DumpReader in case readFrame is called without calling getNFrames

adding c-side interface to change cutoff Policy

replace c++ style comment in c files

adding keyword printPressureTensor

NPAT is working

adding NPAT and NPrT integrators

added gb

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

Working on the shapes parser...

fix one more warning message in make_nodes

avoid multiple inherit in basic_ifstrstream

fix a typo in MultipoleAtomTypesSectionParser

LinkedList removal project starts now

Oops...  MPI now builds...

First commit of the new restraints code

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

adding MersenneTwister random number generator

adding basic_teebuf which can operate on multiple stream simutaneously.

dynamicProps get built

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

merging new_design branch into OOPSE-2.0

Improvements to restraints

fix some bugs in Quaternion class

change const_cast to statc_const

fix include

adding basic_ifstrstream

define DEV_ROOT as relative path

add yacc and lex rules

Import of OOPSE v. 2.0