adding StringUtils, a c-style strtok like class, need unit test

MoleculeCreator forget to create CutoffGroups for free atoms

add Snapshot.cpp, remove useless mpiSimulation

another painful day
(1) SimCreator, SimInfo, mpiSimulation
(2) DumpReader, DumpWriter (InitializeFrom File will be removed)
(3) ForceField (at least LJ) and BondType, BendType, TorsionType
(4)Integrator
(5)oopse.cpp
(6)visitors & Dump2XYZ
(7)SimpleBuilder
(8)Constraint & ZConstraint

mpiSimulation in progress

More to break

Fix Exclude class etc.

Pain......

adding Stats class

ForceFiled get compiled. Still a long way to go ......

Adding LocalIndexManager and Migrator. Need unit test

adding MemoryUtils which provide some functions for dealing with memory issue

Molecule, Atom, DirectionalAtom, RigidBody and StuntDouble classes get compiled

adding BondType, BendType, TorsionType

This commit was manufactured by cvs2svn to create branch 'new_design'.

fixed the "Sudden Death" bug.
	The box was not switching between orthorhombic and non-orthorhombic wrapping correctly.
	we added a fabs() to the check.which should fix it.

begun work on removing templates and most of standard template library from OOPSE.

This commit was manufactured by cvs2svn to create branch 'new-templateless'.

This commit was manufactured by cvs2svn to create branch 'no-template-
branch'.

Matt Meineke's dissertation Files

Midwest Theoritcal Conference 2003

New OOPSE Tree

some intial version bookeeping

This commit was manufactured by cvs2svn to create branch 'stable-05'.

This is the mpi version of simBASS

my Canidacy paper

This is the original proposal I gave in 2001

Matt's canidacy presentation

A half polished version of props

tools for analyzing BASS simulation dumps

translates BASS dumps to xyz files

makes a square lipid configuration

everything you need to make libmdtools