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'.
More work on StuntDouble, Atom, DirectionalAtom and RigidBody
remove old Vector3d.hpp from application/simpleBuilder
Minor change in next_combination
Done with combination
change documentation of next_combination.hpp
ReplaceWildCard is working
adding replace wildcard function
Minor change
STL next_permutation like next_combination is working
fix of setDipoles
forgot to advance lines in the shapeFile
fixed duplicate declaration foo
Adding Generic TupleMatcher, wild char matching is on the way
Adding Generic Tuple3 and Tuple4
bug fix
subclass foo
more char* -> string conversion
char* -> string
Making ShapeType into a ShapeAtomType, fixing some isXXX
define name collision
forcefield refactoring for shapes
DataStorage passes unit test
Changes to help advance shapes
Changes to Shapes force field reader
Snaphot and SnapshotTestCase in progress
add getArray function to RectMatrix and Vector classes
adding GenericFactory Test Case. GenericFactory now can bed used to creat ForcefieldFactory and IntegratorFactory etc.
more classes get reconstructed
GenericFactory pass unit test
more work in Snapshot
Dear god! It runs and conserves energy!
strDUP not strCOPY
fixey fixey the breakey breakey
fixey fixey
Added un-busticated fortran files and c/Fortran interfaces
More on AtomType and DirectionalAtomType
Adding AtomType
Snapshot and SnapshotManager in progress
Breaky Breaky. Fixey Fixey.
remove some junk files
replace old GebericData with new GenericData
Added newLJtype to lj module.
Added interface for fortran lj module.
GenericData and PropertyMap pass unit test.
fixed a fortran name problem
Fortran/C++ interface de-obfuscation project appears to be complete! Woo hoo!
Fortran/C++ interface de-obfuscation project continues
Fortran/C++ interface de-obfuscation project (It is a very long story)
Math library pass the unit test
Snapshot and SnapshotManager in design phase
namespace problem prevented linking
fixed include
more fortran name mangling
yet more fortran renaming
Fortran name cleanup continues
fixing some broken fortran stuff
name sanity on the fortran side
except diagonalize(), all of functions in math library pass the test
Added correct prototypes for C-fortran interface functions.
Added correct prototypes for C-fortran interface functions.
more bugs get fixed at math library
Added new files for fortran interface.
regressing
working on shapes for portability
working on shapes
changed around findBegin
more bugs are fixed in Vector class
implement more test cases
more tests on math library
fix some bugs in Quaternion class
Your basic run of the mill real-valued versions of Y_l^m(\theta, \phi)
Working on getting Shapes into OOPSE
Added ShapeType
adding generic factory and vector test case
math library in progress
add quaternion class
fix a bunch of bugs
change const_cast to statc_const
fix a bug in basic_ifstrstream.hpp
fix include
fix incompatible declaration in jacobi
add checkFilename Option
adding basic_ifstrstream
math library in progress
FileReader in progress
Matrix in progress, test in isOrthogonal of SquareMatrix is failed by some reasons
adding PropertyMap class
adding RectMatrix
refactory vector and matrix classes
Remove some Makefile.in
add Vector3d.hpp and Matrix3x3d.hpp
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
moved the getopt stuff
more build fixes
Chris doesn't know about the OOPSE-2.0 directory structure yet
made the file reading in restraints more intelligent - no longer gives uninformative seg faults
cleaning up
Cleaning up a bit
move mpiSimulation_module to DarkSide
Started work merging shapes
define DEV_ROOT as relative path
change Makefile to relative path
remove StringUtils.c which cause headache in bulding libutils
change directory structure of application. Every executable file is replaced in seperate directory
move fortran files around to solve dependency problem
*** empty log message ***
add yacc and lex rules
change the #include in source files
Import of OOPSE v. 2.0