fixed an MPI compilation bug in GayBerne

added samples for the cutoff methods that Yang Zheng has been working on

added a few GB test cases

Changed the parameters for the Gay-Berne type

Customized StatWriter is working

bugtracking gb

fix some namespace issues in Globals

Adding samples for gb tests

Change error message in Globals

Adding .md files for GB/LJ tests

Adding some cutoff tests

Adding Parameter Constraint class

rewrite Globals

Don't remember what we did

Testing new cutoff methods

Breaky, Breaky: c-fortran interface now expects an array for pot.

More changes to MPI potential calculations.

Free some variables that weren't freed before.

Added code for nanoparticle builder to cvs.

Fixed MPI bug with Row and Column indexing of groupToGtype. We now have two seperate maps groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer that is set to groupToGtypeRow in the single processor version.

There is still something wrong with inertia tensor projection

fix a bug in creating cutoffGroup. When
cutoffGroup is turned off, there is a mismatch between group and
center of mass array

fixed an annoying mass ratio bug that results in simulation failure with massless particles

just some random changes when testing

fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame

fixed some samples

using epsilon instead of 0.0 to avoid divergence in rotation matrix to quaternion transformation

tracking down quaternion bug

fix a bug in convert rotation matrix to quaternion

Changed erfc to derfc and declared it to be external to fix issure with ifc7. Hopefully this will not cause a problem with other compilers where derfc is an intrinsic function.

Added support for skinThickness keyword to Globals.

fixing up some samples

turned rf on

added error function

Removed print statements for remove angular momentum.

DumpReader using pure c++ io

libz additions

adding zlib support for DumpWriter

adding zipstream.hpp

Fixed bugs in reaction field, now it appears as though it really is working...

Added keywords for compressed dump files.

fixing some summation method issues

moved a header file around

some fixes but even more breaking (cutting out the old way to do reaction field)

Fix a bug in DumpReader in case readFrame is called without calling getNFrames

Fixed bug where gtypeMaxCutoff was not initialized after creation. When maxval(gtypeMaxCutoff) was called, the largest random garbage value was returned from the array.

added in the undamped wolf, in the process of doing the damped wolf

just some testing

re-added Cl- and Na+

fix to put back calculation of r in do_prepair

Added nGroupsInRow for mpi build.

bugfix on the grouptype finding algorithm

Some bug hunting

Added allocation for gtypeCutoffmap etc..

wrote createGtypeCutoffMap

updated getEAMCut

Added eamType map to atid map.

added fCutoffPolicy.h

putting spaceballs back where they belong

Breaky Breaky BREAKY breaky breaky

fixes in progress

Changed cutoffs... Segfaults nicely now...

std::bind2nd is in <functional>

Added subroutine to set cuttoff for Interaction map and function in simulation.F90 to determine if a particular atype is present in a simulation.

More breaking and destruction of force code. Does not build at this point...

fixed a bug and ran a simulation

Changes to remove angular momentum.

Added method to remove system angular momentum to velocitizer and added method to calculate system angular momentum to siminfo.

Removed balance from doForces

Included a tap dimer for testing purposes

ran make cvslog

dding resetIntegrator

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

adding keyword printPressureTensor

NPrT in progress

fix bug in NPAT and NPrT

just some tap changes

added a tap example for testing purposes

Fixed merge issues between Kyle and Chris so OOPSE will actually build.

added gb

Couple of changes for TAP water.  Need to parametrize.

More geometry builder changes.

OOPSE setup for TAP water.  It's not parametrized, but OOPSE will now let me run it...

More changes to nanoRodBuilder....

Added TIP4P-Ew

Got rid of write statements and am closer to a working shapes

adding CharClassificationFunctor to fix the locale problem  of c++

axed because file causes havoc on Mac (capitalization confusion of filenames)

gmake in case people forget

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

xemacs has been drafted to perform our indentation services

fix make install

some samples are not installed correctly

Fixed a bug in RigidBodyStamp section of MoLocator

nanorodbuilder now exit's when libCGAL is not present.

Changed interface name for SGI Compiler

Change typo in CGAL.

added CGAL checks

Added destroy method to clean up memory

File not needed for nanoRodBuilder.

refactory lattice

refactory LatticeFactory and LatticeCreator

cleaned up vector_class memory leak fix by deallocating in reverse
order of how we allocated.  Also migrated MoLocator into utils directory

added lattice directory, so all of these files are now redundant

added lattice subdirectory

added quadrupole sample

destory atom type in fortran side

Fixed pointer memory leak in vector_class.

minor change to TI output

Added code to delete vector.

Importing nanoRodBuilder application (may not work yet).  ((Doesn't work yet.))
(((May never work....)))

fixing of the quadrupoles.  look!  it's divide by 3 like stone says!

change the parameter name in constructors

Fixed the uc and lc functions for GNU make versions < 3.80

quadrupole interactions should be working with a remaining question of interaction magnitude

oops...  messed up a sample

changes during debug of charge-dipole

reinitialize buffer_stack_ptr in BASS parser

fix a bug in converting rotation matrix to quaternion

LipidTranVisitor should do the wrapping

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

Make sure electrostatic_module provides data for reaction_field

constant back to correct value

VelocityVerletIntegrator already deletes and Nullifies restWriter,
so Integrator shouldn't do it.

first run at charge-quadrupole interactions

added some samples

pairs inside cutoff group should not be excluded

quadrupoles for SSD models

fixed a bug in MPI restraints

fixed a doxygen problem

updated some documentation

using map to replace link list

Oops...  MPI now builds...

added fortran-side support for split dipoles

fixing restraints

First commit of the new restraints code

fix compilation issue

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

new electrostatic module

removed #include lines for outdated charge and dipole interfaces

fixing a strange icc8 bug (we think).

Electrostatic Unification Project

Using OOPSE_itoa and checking a NULL left over from the LinkedList days

electrostatic unification project

Added a charge for Chlorine

SPRNG eradication project

avoid using const char*(hope can fixed the missing atom type problem)

info_ in Velocitizer is not initialized which causes a seg fault

Adding unit test for random number generator

fixed compilation problem

Change the name of test case

fix compilation problem for g++ 3.4

Fixed the damned build problem with the libraries not
being removed in make clean and make distclean (at least
we think it is fixed).

adding MersenneTwister random number generator

selection expression

adding documentation for selection expression

Added ssdrf sample

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