forget to include <algorithm>
change license
change const static double data member to const double
forget namespace qualifier std::
change data type from logical to integer in AtomTypeProperties.h
change default name of DUFF force field to DUFF2.frc
adding constraints and minimizers into Makefile.in
remove some useless files
*** empty log message ***
minor fix
adding Rattle Algorithm
forget a '$' sign
missing tab in rules
create a register module to register force fields, integrators and minimizers
zconstraint method is working now
more work in zconstraint
ZConstraintForceManager in progress
constraint is almost working
simpleBuilder is working
simpleBuilder in progress
minimizer in progress
constraints in progress
minimizers in progress
fix a test command incompatiable problem
NPT is working now
Fix a bug in SimInfo which gives the invalid stamp id
parsing order three arrays in EAM parameter file is incorrect
add getMaxRcutFromAtomType into EAM
fix a bug in basic_ifstrstream
add EAM Force Field
add more force fields
fix bugs in getCom and getComVel (forget to call All_reduce in MPI version)
MPI in NVE is working
fix a bug in DumpReader. Master nodes does not brocast the total number of frames
more fix in MPI version
MPI version is built
forget to zero out the torque. Sticky and Dipole is working now
fix an index problem in eFrame matrix
sticky module get compiled
u_l -> eFrame for electrostatics u_l -> A for GB
u_l -> eFrame
sticky module now has the option for multiple sticky types
sticky
fix an interface inconsistency in lab2Bidy
Fix a bug in calculating torque in rigid body
fix a parsing bug in ElectroStaticAtomTypesSectionParser
Butane in NVT is working
NPT in progress
fix a bug in UseInitXSstate
no message
*** empty log message ***
fix atom type ident in Charge and Dipole Module
butane is working now
short range interaction for butane is correct.Still something wrong with long range one
fix a bug in Exclude List
fix a bug in filling MolMembership
add Integrator.cpp
NVE is working now, get the same result as OOPSE-1.0
rewind to old copy
What?
atid / c_ident confusion
NVE conserved energy, however, potential is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step 4 EAM Step 5 Shape Step 6 Constraint & Restraint
Dump2Xyz is also working, energy of NVE is not conserved
NVE is running
more missing function get implemented
Change interface of SimInfo
begin to fix bugs
Fixed a bug in countTokens in StringTokenizer
refine factory pattern to make it initialized correctly
oopse get built
still have two linking problem
change endl to std::endl
minor fix
remove StreamTokenizer
remove using namespace std in .cpp file
adding qulified name prefix std
replace string by std::string
replace misuse of using namespace std in header files
begin to fix linking problem
oopse get compiled, still has some linking problem
NVT get built
NVE get built
rename DumpWrite to DumpWriter
visitors get built
spell check
except integrator and constraint, other directories get built
refactory AtomType
minor change
Change NumericConstant
minor fix
io get built, next is integrator
brains get built
brains get built, io is next
fix Thermo
more get fixed
rename LocalndexManager.hpp to LocalIndexManager.hpp
Section Parsers get compiled
minor fixed
minor fixed
#inlcude statement can not be embedded
Polynomial passes unit test
rename QuarticTorsion.hpp to QuarticTorsionType.hpp
add CubicTorsionType and QuarticTorsionType
more file get fixed
add Trim Algorithm for std::string
remove some useless files
more files get fixed
part of io get built
types get built
types get built
rename some files
rename some files
more get built
UseTheForce get built
types and primitives get built
StringTokenizer passes unit test
change Makefile
add SetForceManager method to integrator
refactory NPT integrator
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.