Fix a bug in GofRAngle

fix for compilation on the Sun

adding LipidTransVisitor, GofXyz is working now

Updated copyright information

more bug get fixed

make processHistogram non-abstrct function

finish GofXyz

forget the const correctness for BitSet

return residentMem in byte

using PhysMem - RSSMem to estimate avaliable memory

change the suffix of output files;fix the problem of counting in staticProps

BlockSnapshotManager is using reference counting now

adding typedef to TokenMap, using TokenMapType::value_type instead of
std::make_pair to make Sun compiler happy

(1) adding #ifdef __RWSTD to make sun compiler happy
(2) fix pair density calculation problem when two selections intersect with each other

*** empty log message ***

bugfixing residentMem

added residentMem

ps niceness

fix a bug in BlockSnapshotManager.hpp

fix a bug in VelocityVerletIntegrator : last frame is written twice

refactory CorrelationFunction

fix a bug in calculating  bytes per stuntdouble

fixed a bug in CorrelationFunction

adding staticProps and dynamicProps into Makefile.in

adding Algorithm.hpp

dynamicProps in progress

adding dynamicProps

adding command line option for DynamicProps

adding SelectionManager.cpp

adding beginSelected, nextSelected method to SelectionManager

adding supprot for physmem

more work in StaticProps

adding GofRAngle

staticProps in progress

add getRigidBodyAt  function into Molecule class

support select internal index selection, for example, select DMPC.3

selection librarys added

issue commented out in wildcards

fix a bug in determing the global index for rigidbodies

selection library is working

IgnoreVisitor and XYZVisitor now use selection library

dump2Xyz now take advantage of selection library

adding missing implementation

selection library get built

remove some useless files

more work in selection library

selection library in progress, except SelectionEvaluator, other files are compiled

add SelectionCompiler.cpp

adding selection library

(1)Cast wrong atom to DirectionalAtom in GhostTorsion
(2)get the wrong column of electroframe

(1) complete section parser's error message
(2) add GhostTorsion
(3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor

fix a bug in loading initial extended system parameters

remove WATER.cpp

moved Package variable into subdirectory makefiles to speed up
the building process

added dummy subroutine to avoid empty unit, synchronized this dummy
routine between C and fortran

more fixes for gnugetopt

using c library to do conversion instead of using iostream due to a bug in
libstdc++(GCC 3.2)

fix a bug in global index

compile getopt and getopt1 if we need to

formatting

port to SGI platform

remove useless debug info

missing tab

LinearVisitor get fixed

remove some useless force fields

rename newDUFF.frc to DUFF2.frc

adding new EAM force field files

fix a bug in WATER.cpp when initializing the new Charge AtomType

merge WATER force field into DUFF

minor fix in DUFF

minor fix

replace misuse of using namespace std in header files

spell check

Addint StringTokenizerTestCase

improved restraints - mpi should work fine

oops...

Improvements to restraints

new DUFF forcefield

Fixed a mixing list bug that slowed down the force loop

working towards parallel restraints

Got rid of some write statements

Added the linear visitor

included visitors and minimizer

time to break SimSetup

isLinear and linearAxis are virtual in StuntDouble,
but are implemented by DirectionalAtom and RigidBody
In StuntDouble, they should return false and "-1" but
there should be logic to figure them out in the other
two classes

Breaky Breaky

testing force fields

mess up ......

these core classes get compiled

still debugging

shorter run

Remove some deprecated files

More work on StuntDouble, Atom, DirectionalAtom and RigidBody

Minor change in next_combination

change documentation of next_combination.hpp

adding replace wildcard function

STL next_permutation like next_combination is working

forgot to advance lines in the shapeFile

fixed duplicate declaration foo

next_combination in progress

STL Compatible combination sequence generator

a STL next_permutaion like next_combination function.

ReplaceWildCard(recursive version) is working, need refactoring. An iterative version is on the way

Adding Test Case for ReplaceWildCard

Adding Generic TupleMatcher, wild char matching is on the way

bug fix

more char* -> string conversion

Making ShapeType into a ShapeAtomType, fixing some isXXX

forcefield refactoring for shapes

DataStorage passes unit test

Changes to Shapes force field reader

add getArray function to  RectMatrix and Vector classes

more classes get reconstructed

Refactoring in progress

Dear god!  It runs and conserves energy!

fixey fixey the breakey breakey

fixey fixey

More on AtomType and DirectionalAtomType

Snapshot and SnapshotManager in progress

Breaky Breaky.   Fixey Fixey.

remove backup of  GenericData.hpp

Added newLJtype to lj module.

GenericData and PropertyMap  pass unit test.

adding generic data test case

Fortran/C++ interface de-obfuscation project continues

Math library pass the unit test

namespace problem prevented linking

more fortran name mangling

Fortran name cleanup continues

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 new files for fortran interface.

working on shapes for portability

changed around findBegin

fix some bugs in RectMatrixTestCase

more tests on math library

fix some bugs in Quaternion class

Working on getting Shapes into OOPSE

adding  vector test case

math library in progress

adding test file

change const_cast to statc_const

forget to use namespace oopse

adding ifstrstream test case

fix incompatible declaration in jacobi

adding test case for ifstrstream

add checkFilename Option

adding basic_ifstrstream

FileReader in progress

adding PropertyMap class

adding RectMatrix

Remove some Makefile.in

adding c++ coding style

fix a bug in filepp

filepp can be used to generate dependencies for c/c++ now

adding rules to move fortran 90 module to target directory

remove "use bytes" which causes problem in sgi machine

fix Makefile under water directory

Remove some Makefile.in

fix make install

add Makefile to sample directory

more build fixes

filepp can handle different fortran module case and suffix

Yeah yeah, we'lll get around to it later

made the file reading in restraints more intelligent - no longer gives uninformative seg faults

Cleaning up a bit

adding GNU make functions to combine all of the static libraries to a big library

move mpiSimulation_module to DarkSide

pass __FORTRAN90 instead of __F90 to filepp

more work on the parallel build

Started work merging shapes

add oopse_ as library prefix

A few minor build changes

make clean is smart enough to only remove object files belong to current package.
turn off silent mode

get the relative path by shell script

add PackageLibs;  fix dependency rule

Working on make stuff

fix dependencies rule

add print statment to rules

remove StringUtils.c which cause headache in bulding libutils

Keep that lib around, please.

move fortran files around to solve dependency problem

fix fortran dependency problem

adding include path to F90Options

change the #include in source files