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'.
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
forgot the orientation line
fixed duplicate declaration foo
uncommented .in line
next_combination in progress
adding next_combination test case
STL Compatible combination sequence generator
bug fixed in GenerateCombination.hpp
a STL next_permutaion like next_combination function.
no message
ReplaceWildCard(recursive version) is working, need refactoring. An iterative version is on the way
ReplaceWildCard in progress
Adding Test Case for ReplaceWildCard
adding ReplaceWildCard.hpp, need test
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
adding sample shape directory
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
Refactoring in progress
more work in Snapshot
Dear god! It runs and conserves energy!
strDUP not strCOPY
fixey fixey the breakey breakey
compiler flags
fixey fixey
Added un-busticated fortran files and c/Fortran interfaces
More on AtomType and DirectionalAtomType
Adding AtomType
Snapshot and SnapshotManager in progress
adding test case for Snapshot and snapshotManager.
Breaky Breaky. Fixey Fixey.
remove some junk files
remove backup of GenericData.hpp
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
adding generic data test case
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
*** empty log message ***
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
fix some bugs in RectMatrixTestCase
implement more test cases
more tests on math library
adding more testing units
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 vector test case
adding generic factory and vector test case
math library in progress
add quaternion class
adding test file
fix a bunch of bugs
change const_cast to statc_const
fix a bug in basic_ifstrstream.hpp
forget to use namespace oopse
Changed optimization flags for XLF and XLC.
adding ifstrstream test case
fix include
fix incompatible declaration in jacobi
adding Makefile
adding test case for ifstrstream
add ifstrstreamTestCase
add checkFilename Option
add SquareMatrixTestCase class
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 testing unit
adding RectMatrix
refactory vector and matrix classes
Remove some Makefile.in
add Vector3d.hpp and Matrix3x3d.hpp
adding c++ coding style
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
fix a bug in filepp
using filepp to generate dependencies instead of compilers
filepp can be used to generate dependencies for c/c++ now
remove -module from F90Options
adding rules to move fortran 90 module to target directory
fixed makefile.in
remove "use bytes" which causes problem in sgi machine
add Makefile
fix Makefile under water directory
remove argon.dump and argon.eor from Makefile
Remove some Makefile.in
*** empty log message ***
fix make install
adding make install
add Makefile to sample directory
moved the getopt stuff
more build fixes
adding doxygen configuration file
filepp can handle different fortran module case and suffix
Chris doesn't know about the OOPSE-2.0 directory structure yet
Yeah yeah, we'lll get around to it later
cleaning up build process
made the file reading in restraints more intelligent - no longer gives uninformative seg faults
cleaning up
Cleaning up a bit
fix make statistics
adding GNU make functions to combine all of the static libraries to a big library
adding shared library flag
move mpiSimulation_module to DarkSide
building MPI version;using static library instead of shared library
pass __FORTRAN90 instead of __F90 to filepp
add make cvslog
more work on the parallel build
changes to backport declare flags
Started work merging shapes
remove sfmakedepend from cvs tree
add oopse_ as library prefix
fix a space trimming bug in filepp
A few minor build changes
adding fortran90 make dependency tool
make clean is smart enough to only remove object files belong to current package. turn off silent mode
define DEV_ROOT as relative path
get the relative path by shell script
eliminate DEV_ROOT by relative path
add PackageLibs; fix dependency rule
updates
Working on make stuff
If makefile does not exist, print error message
fix dependencies rule
still working on build process
add print statment to rules
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
Keep that lib around, please.
starting a configure version
move fortran files around to solve dependency problem
*** empty log message ***
fix fortran dependency problem
add yacc and lex rules
adding include path to F90Options
change suffix from .cc to .cpp
change the #include in source files
Import of OOPSE v. 2.0