Compilation and portability fixes

Fixed a bunch of cppcheck warnings.

CLearing out some memory leaks

Fixes for Qhull static build strangeness

Bug fixes to get new parallel decomposition methods working without periodic boundary conditions.  
Updated volume in stats file correctly.
LangevinHull fixes for low viscosity values.

Updated the integrator conserved quantity so that it doesn't trail the other properties

Cleaning more cruft and unused variables.

Fixes to mdParser to handle vector assignments, fixes for VelocityVerletIntegrator deleting rnemd_ when it doesn't exist yet.

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.

Some bugfixes (CholeskyDecomposition), more work on fluctuating charges,
migrating stats stuff into frameData

Fixed a strange bug where setting tempSet to false would still require a targetTemp

Removed a line in Integrator.cpp where the forceMan_ was being initialized too early. Additionally, added a dummy value for rCut_ in ForceManager.cpp::setupCutoffs. JRM

Mostly whitespace

Fixed compilation issues

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.  

Merging Shenyu's RNEMD changes from openmd-1 into the development branch.

Adding the propagators for FlucQ

Some fixes for DataStorage issues.  Removed outdated zangle stuff that
has been replaced by the more modern restraints.

Fixes for compilation under LLVM compiler
Bug-fix for switching function in Gay-Berne

updated copyright notices

cleaning up the development branch a bit, removing cruft, etc.

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.

builds

Creating busticated version of OpenMD

Adding property set to svn entries

Cleanup of unit normal code in Triangle.cpp
SMIPD now call getUnitNormal instead of getNormal.

Parallel bugfix in RestraintForceManager
Reverted back to hydrodynamics on triangular plates for SMIPDForceManager
Removed thermalLength and thermalConductivity keywords from Globals.
Bug tracking in openmdformat (not yet resolved).

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

fixed a bug confusing id with localID, stopped adding NULLS to triangles also.

added RNEMD scaling

New hotness

Latest version of SMIPD with gamma set to thermal conductivity

Adding boundary element hydrodynamics to SMIPD.

Bug fixes and sanity checks for RNEMD (nBins should be even), check to make
sure we aren't selecting inappropriate numbers of integrable Objects

Added a getStatus routine to check the temperatures

Debugging, but still unstable

Adding options to RNEMD for selecting particular StuntDoubles

Adding RNEMD

Cleaning up some cruft.

Stupid getRandomNumber return 4;

More attempts to get SMIPD to themostat properly

Fixed segfault in because of directional atom in SMIPD.

More changes to SMIPD. Attempting to find memory leak.

Fixed nanovol so it now builds.

Fixed makefile.

Adding back more missing files.

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.

Adding iterative looping to get better estimates of friction forces
from full-step velocities

updating configure process

Removed older version of openbabel from our code.  We now have a
configure check to see if openbabel is installed and then we link to
the stuff we need.  Conversion to OOPSE's md format is handled by only
one application (atom2md), so most of the work went on there.
ElementsTable still needs some work to function in parallel.

Fixed some bugs in LDForceManager.cpp

SF Lennard-Jones was added for everyones' enjoyment.  The behavior is tethered to the electrostaticSummationMethod keyword.

Spherical boundary conditions.

adding NgammaT integrator

Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants

testing GB, removing CM drift in Langevin Dynamics, fixing a memory
leak, adding a visitor

fix a bug in parsing HydroProp file

Adding single precision capabilities to c++ side

Adding spherical boundary conditions to LD integrator

Fix a bug in friction calculation for ellipsoid

refactor Hydrodynamics module.

LangevinDynamics in progress

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

fixed a capitalization problem with NPT integrator initialization

rewrite Globals

Removed print statements for remove angular momentum.

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

adding resetIntegrator

adding keyword printPressureTensor

NPrT in progress

fix bug in NPAT and NPrT

xemacs has been drafted to perform our indentation services

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

info_ in Velocitizer is not initialized which causes a seg fault

replace SPRNG by MTRand

adding OOPSERandNumGen

adding basic_teebuf which can operate on multiple stream simutaneously.

maximum length defaults to the cutoff radius

forget to add eorWriter

fix a bug in loading initial extended system parameters

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

improved restraints

Commented out some write statements

replace old GebericData with  new GenericData

define DEV_ROOT as relative path

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