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;

added splitDipole and fixed quadrupole stuff

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

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

fixed a file inclusion problem

fix compilation problem for g++ 3.4

Making small modifications to allow for use on MPI machines

Adding a modified version of MersenneTwister.hpp

adding basic_teebuf which can operate on multiple stream simutaneously.

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

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

maximum length defaults to the cutoff radius

dynamicProps get built

more work in dynamicProps

adding command line option to DynamicProps

adding dynamicProps

adding one more constructor to Snapshot to create customized DataStorage

adding support 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

forget to set maxIterNum_ in NVT

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

fixing for gnugetopt

no message

remove include Integrator.hpp in Minimizer

formatting

remove useless debug info

LinearVisitor get fixed

fix another bug in WATER.cpp

improved restraints - mpi should work fine

Improvements to restraints

working towards parallel restraints

Got rid of some write statements

current status of the debugging process

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

Shapes looks like it's working

shapes rcut calculator added

remove old Vector3d.hpp from application/simpleBuilder

Done with combination

ReplaceWildCard is working

Minor change

fix of setDipoles

fixed duplicate declaration foo

Adding Generic Tuple3 and Tuple4

subclass foo

char* -> string

define name collision

DataStorage passes unit test

Changes to Shapes force field reader

add getArray function to  RectMatrix and Vector classes

more classes get reconstructed

more work in Snapshot

strDUP not strCOPY

fixey fixey

More on AtomType and DirectionalAtomType

Snapshot and SnapshotManager in progress

remove some junk files

Added newLJtype to lj module.

GenericData and PropertyMap  pass unit test.

Fortran/C++ interface de-obfuscation project appears to be complete!  Woo hoo!

Fortran/C++ interface de-obfuscation project (It is a very long story)

Snapshot and SnapshotManager in design phase

fixed include

yet more fortran renaming

fixing some broken fortran stuff

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

implement more test cases

fix some bugs in Quaternion class

Working on getting Shapes into OOPSE

adding generic factory and vector test case

add quaternion class

change const_cast to statc_const

fix include

add checkFilename Option

math library in progress

Matrix in progress, test in isOrthogonal of SquareMatrix is failed by some reasons

adding RectMatrix

Remove some Makefile.in

change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp

more build fixes

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

Cleaning up a bit

Started work merging shapes

change Makefile to relative path

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

*** empty log message ***

change the #include in source files