add Electrostatic AtomType Section Parser
add EAM AtomType Section Parser
add BondTypesSectionParser, BendTypesSectionParser and TorsionTypeSectionParser
minor change in DUFF and EAM
adding section parsers
adding section parsers
remove more useless files
remove more useless files
refactory integrator
add EAM
DUFF is almost done except error checking
DUFF is almost done except error checking
adding DUFF parser
adding DUFF parser
Adding NumericConstant class
remove more junk files
remove some junk files
refine QudraticBond
add QuadraticBendType.hpp
UreyBradleyBend and GhostBend
more types stuff and Chebyshev Polynomial
add PolynomialBondType, PolynomialBendType, PolynomialTorsionType, HarmonicBendType and CharmmTorsionType. Need to refine the design and add document for them
add PolynomialBondType
Adding Polynomial class
added some new stuff
BondType, BendType and TorsionType
adding DUFF class; adding checking statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
adding ForceFieldFactory and LJFF classes
finish DumpReader, DumpWriter.Next Step is LJFF and integrators
refactory, refactory, refactory
bug fix in hasMoreTokens
adding StringUtils, a c-style strtok like class, need unit test
SimCreator and SimInfo are ready for unit test
MoleculeCreator forget to create CutoffGroups for free atoms
OOPSE = Object-Obfuscated Parallel Simulation Engine
add Snapshot.cpp, remove useless mpiSimulation
more work on SimInfo
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
add a configurable StatWriter
mpiSimulation in progress
adding ForceManager
More to break
adding ForceField and TypeContainer classes
Fix Exclude class etc.
This commit was manufactured by cvs2svn to create branch 'new_design'.
Pain......
time to break SimSetup
adding Stats class
Adding SimCreator class(similar as SimSetup)
ForceFiled get compiled. Still a long way to go ......
mess up ......
Adding LocalIndexManager and Migrator. Need unit test
SimModel in progress
adding MemoryUtils which provide some functions for dealing with memory issue
adding SimModel(something similar as SimInfo)
Molecule, Atom, DirectionalAtom, RigidBody and StuntDouble classes get compiled
add initial version of Bond, Bend and Torsion.
adding BondType, BendType, TorsionType
break, break and break.....
This commit was manufactured by cvs2svn to create branch 'new_design'.
a bunch of hacks for the twoChain systems
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.
some work on trying to find the compression bug
begun work on removing templates and most of standard template library from OOPSE.
started work on template removal.
This commit was manufactured by cvs2svn to create branch 'new-templateless'.
started work on template removal
This commit was manufactured by cvs2svn to create branch 'no-template- branch'.
This commit was manufactured by cvs2svn to create branch 'templatesBranch10-28-03'.
Matt Meineke's dissertation Files
The OOPSE paper
Midwest Theoritcal Conference 2003
a generic template for parseing command line options.
New OOPSE Tree
this is an inital attempt to implement the new fortran interfaces
some intial version bookeeping
This commit was manufactured by cvs2svn to create branch 'stable-0_5'.
This commit was manufactured by cvs2svn to create branch 'stable-05'.
the 1st paper based on our lipidModel
This is the mpi version of simBASS
This commit was manufactured by cvs2svn to create branch 'serial-branch'.
my Canidacy paper
A pair of utilities to turn an xyz file into a sequence of povray rendered images.
This is the original proposal I gave in 2001
This is the RSA paper published in 2001
Matt's canidacy presentation
little utility for catting together dump files.
A half polished version of props
Counts the number of frames in a dump or xyz
tools for analyzing BASS simulation dumps
runs a simulation from a BASS file
translates BASS dumps to xyz files
makes a square lipid configuration
makes a square lipid configuration
forcefield parameter files for libmdtools
everything you need to make libmdtools
Standard project directories initialized by cvs2svn.