Fixed a bunch of stylistic and performance issues discovered via cppcheck.

Fixed a bunch of bugs in CubicSpline debug sections, ForceMatrix Decomp 
computing costhetas for non-existent rotation matrices, Hidden accumulator counts, and SMIPD non-coupling

Windows compilation fixes

Fixed some picky warnings from the new Intel compiler.

A bug fix in the electric field for the new electrostatic code.  Also comment fixes for Doxygen 

Merged trunk changes into the development branch

Adding an electric field and the architecture for external perturbations.   Fixing a bug in MultipoleAtomTypesSectionParser.

Code readability updates.

Added Fluctuating Charge Langevin propagator, and made it the default
fixed some errors on the one-center slater coulomb integrals, and some
parameters in PhysicalConstants.

Individual ForceField classes have been removed (they were essentially
all duplicates anyway).  

ForceField has moved to brains, and since only one force field is in
play at any time, the ForceFieldFactory and Register methods have been
removed.  

Adding more support structure for Fluctuating Charges.

qhull modifications for compilation 

Some fixes for CMake and single precision builds

First few fixes for explicit interactions.

fixing the build system

Splitting out ifstrstream into a header and an implementation.  This
means that much of the code that depends on it can be compiled only
once and the parallel I/O is concentrated into a few files.  To do
this, a number of files that relied on basic_ifstrstream to load the
mpi header had to be modified to manage their own headers.

Fixed a parallel bug in computing exclude lists.
Added file versioning information in MD files.
Still tracking down cutoff group bugs.

more bug fixes

changes for cell linked lists

Fortran removal

Well, it compiles and builds, but still has a bus error at runtime.

Starting migration of Morse to C++

Adding exception and reporting mechanism from ProtoMol to OpenMD.

Creating busticated version of OpenMD

Fixed  include file in ProgressBar.cpp for getenv.

fixing string bugs in ProgressBar

ProgressBar compilation fixes for linux

Added missing cstdio include lines for gcc 4.4 compatibility

Almost all of the changes necessary to create OpenMD out of our old
project (OOPSE-4)

added viscoConvert

A few simple mods to remove gcc compile warnings

Fixed MPI bug in opening elements.txt.

Added some logic to print out a special pair distance as a column in
the stat file.  To use this feature, use taggedAtomPair = "0, 10" and
printTaggedPairDistance = "true" in the md file.  Then, the distance
between integrableObjects 0 and 10 will be computed and printed in
the stat file on each statWrite.

Many fixes

Adding infrastructure for Amber force field.

updating configure process

fixed bug in physmem for 64 bit machines

fixing bugs in randomBuilder

Massive changes preparing for release of OOPSE-4: The main difference
is that the new MD file format (.md, .dump, .eor) now contains meta-data
information along with the configuration information.

Massive changes for GB code with multiple ellipsoid types (a la
Cleaver's paper).

Also, changes in hydrodynamics code to make HydroProp a somewhat
smarter class (rather than just a struct).

Adding single precision capabilities to the fortran side

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Many performance improvements

changed the interface a bit

Wiped the spline with derivatives and corrected a boundary comparision error by eliminating the check.  This algorithm REQUIRES known first derivatives at the endpoints.

Heavily modified interpolation module, also moved to "utils"

change the epsilon of numeric_limit

autoconf modernization and cruft removal

replace isType<int> with isInteger

the standard library came with SUN compiler does not have a conforming std::use_facet, define a macro
to handle it. Adding exception handling to SimCreator.

added missing include

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

OptionSectionParser get compiled

replace c++ style comment in c files

Breaky breaky!

NPrT in progress

Fixed gcc4 bug...

xemacs has been drafted to perform our indentation services

more memory leak are fixed

Further changes to vector_class destroy function.

Added code to delete vector.

OOPSE_itoa!

fix compilation problem for g++ 3.4

fix problem in sun

return residentMem in byte

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

bug fix for null termination

bugfixes for residentMem on LINUX

modifications to estimate memory in use by other processes
autoconf fixes
ps syntax checking
config.h file cleaning

dynamicProps get built

issue commented out in wildcards

minor change in BitSet

adding wildcard class; NameFinder is finished

Selection in progress

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

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

port to SGI platform

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

Adding Generic Tuple3 and Tuple4

more classes get reconstructed

remove some junk files

GenericData and PropertyMap  pass unit test.

more fortran name mangling

changed around findBegin

fix some bugs in Quaternion class

adding generic factory and vector test case

moved the getopt stuff

change Makefile to relative path

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Import of OOPSE v. 2.0