fixed a bug in waterBoxer for invalid water names

Some efficiency fixes (now computes Wigner 3-j coefficients only once
in the constructor).

fixing bond order parameter code

Following Rein ten Wolde article

more changes to BOP and SH

Bugfixes in BondOrderParameter and SphericalHarmonic

fixed bugs (mostly in BondOrderParameter)

Working on BondOrderParameter

changing configure script to process the new utilities

added the waterBoxer script

adding NgammaT integrator

removed extra file in Hydro.cpp

starting change of file formats

fixed a pvf bug

added dumpConverter

Adding a directory for scripts
Adding affineScale script

Beginnings of a order parameter.

MPI thermodynamic integration works now.

Add the RippleOP to calculate the orderparameter of the ripples.

replace double with RealType

fixed an initialization bug of Hxy.cpp.

fixed the bugs of Hxy.cpp.

Autoconf fixes for FFTW.  Multiple FFTW version support.

Changes to calculate undulation spectrum

missing makefile was hanging up 'make clean'

Change in siminfo used in nanoparticleBuilder.

Using OpenBabel element table to pick vdw radii for hydrodynamics
if the LJ sigma can't be found.

Added EAM atom types to Hydro models

*** empty log message ***

Fixed latticeOrt in shapedlatice and latticebuilder.

(1) RoughShell Model is working; (20)Adding a new option into Hydro which allows user to generate the beads only

Debugging changes to nanoparticle builder.

Adding position correlation function. The command line option for DynamicProps is now changed. --rcorr is for position correlation and --rmsd is for mean square displacement.

Added shaped lattice.

Fix a bug in friction calculation for ellipsoid

New version of Hydro is working now.

LagevinDynamics is working?

unit conversion for diffusion tensor is wrong

correcting the unit in HydrodynamicsModel

adding hydrodynamics module into build system

Fixed a double/int bug.  Surprised no one ever noticed before...

Bead Model is working

Changed Names of class files.

Fixing a bug which reads the wrong frame of trajectory file during analysis

Adding :LegendrePolynomial

Added Makefile for nanoparticle builder.

fixed some version info and the copyright date

fixing RhoZ

End of the Link --> List
Return of the Oject-Oriented
replace yacc/lex parser with antlr parser

compilation issue

rename mdinConverter to atom2mdin

nothing

rewrite Globals

Added code for nanoparticle builder to cvs.

fixed a bug and ran a simulation

Fixed bug in typo in nanorodBuilder.

adding DensityPlot into StaticProps

adding AtomNameVisitor to convert atom name to its base name; wrappingvisitor
now wrap back to the center of the mass; adding P2OrderParameter into StaticProps

Couple of changes for TAP water.  Need to parametrize.

Adding support for generic geometry to nanorodbuilder.

Fixed issues with nanoRodBuilder....

Version string in banner (and version numbers in config.h)

nanorodbuilder now exit's when libCGAL is not present.

more memory leak are fixed

fix memory leak in nanorodBuilder and simpleBuilder(forget to delete lattice)

refactory LatticeFactory and LatticeCreator

Changes to delete atypes...

forget to delete prepareVisitor in Dump2XYZ

avoid building parallel executable for dump2XYZ, simpleBuilder, staticProps and dynamicProps

adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into
ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;

adding basic_teebuf which can operate on multiple stream simutaneously.

adding LipidTransVisitor, GofXyz is working now

more bug get fixed

make processHistogram non-abstrct function

finish GofXyz

fix a bug in writing out the value of cosang

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

bug fix in StaticProps

default length for staticProps is 1/2 smallest length of first frame

refactory CorrelationFunction

more fix

fixed a bug in SimInfo::getCutoff()

dynamicProps get built

more work in dynamicProps

adding command line option to DynamicProps

adding dynamicProps

change the filenames

remove some useless files

adding GofR

update help info for Dump2XYZ

dump2Xyz now take advantage of selection library

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

formatting

merging new_design branch into OOPSE-2.0

remove old Vector3d.hpp from application/simpleBuilder

more build fixes

define DEV_ROOT as relative path

change directory structure of application. Every executable file is replaced in seperate directory

change the #include in source files