New electrostatic method, starting to do some performance tuning.

Fixed a bunch of cppcheck warnings.

Added a Harmonic Torsion Type, fixed some bugs in RNEMD and waterReplacer.

Performance increases for cubic spline.
Bug fix for electric field in parallel.
Cleaned up globals.
Started adding infrastructure for long range corrections.

New electrostatic bug fixes.

Merged trunk changes into the development branch

Massive multipole rewrite

Code readability updates.

Refactored Snapshot and Stats to use the Accumulator classes.  Collected
a number of methods into Thermo that belonged there.

fixed an uninitialized option bug, fixed gcc 4.6 compilation problems

Fixes for minimization

Reorganized source directories, added RNEMD and flucQ blocks for
options parsing.

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 more support structure for Fluctuating Charges.

Bugfixes (mostly related to particlePot and storageLayout).

Added an adapter layer between the AtomType and the rest of the code to 
handle the bolt-on capabilities of new types. 

Fixed a long-standing bug in how storageLayout was being set to the maximum
possible value.

Started to add infrastructure for Polarizable and fluc-Q calculations.

updated copyright notices

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.

Fixing cutoff groups

Fixes

Moved switching functions and force options over to the C++ side, and
removed them from Fortran.

Starting migration of Morse to C++

Added EAM.  Still segfaults but compiles.

Fixed a potentially serious bug in GhostBend and GhostTorsion.  We
were using A instead of A.transpose() where we need lab-frame
coordinates of the body-fixed axis.

Added tests to make sure requisite position & orientation information
are present in dump file.

Adding nan/inf detection to DumpWriter, fixing one message

more on the minimizer Frq -> Freq conversion

Removed hard-wired atom number, trying out the NULL returns in SimInfo.

Added preliminary code for Alpha Hull calculation using qhull.
Added preliminary support to SMIPD to support Alpha Hull.
Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. 
Preliminary changes for shadow hamiltonian integrator.
Chages to md files so they will work in openMD. 

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).

added options for RNEMD

Added new restraint infrastructure
Added MolecularRestraints
Added ObjectRestraints
Added RestraintStamp
Updated thermodynamic integration to use ObjectRestraints
Added Quaternion mathematics for twist swing decompositions
Significantly updated RestWriter and RestReader to use dump-like files
Added selections for x, y, and z coordinates of atoms
Removed monolithic Restraints class
Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody
Added some rotational capabilities to prinicpalAxisCalculator

Adding restraint keywords to Globals

Adding options to RNEMD for selecting particular StuntDoubles

More attempts to get SMIPD to themostat properly

Returned old LD forces to SMIPDForceManager.

Added large quantities of code for convex hull and constant pressure langevin dynamics.

Inversion fixes and amber mostly working

Many fixes

Changes required for Inversions and Base Atom types.  This will
break OOPSE badly for a few days or so...

Adding Trappe torsion types and fixing Opls types

Removed accidental print lines.

Fixed a bug in BlockSnapshotManager.

Changing functional form

updating configure process

Many fixes for Charmm-type torsions.

Non-bonded interactions added.

Addition of section parser for Spohr water-metal potential.

Changes to add thetacorr to dynamic props and fixes to radial rcorr.

Added interface to change number of neighbors in calculating neighbor list.

refined the reaction field dielectric passing

fixed a DumpReader bug, took out extra printing statements in
residentMem and BlockSnapshotManager

fixed TI MPI bug

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.

testing commit logger

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

MPI thermodynamic integration works now.

Fixed a spelling error and a bug in MPI Thermodynamic Integration on file read-in

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

Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)

Fix a bug of printing empty line in DumpWriter

Adding spherical boundary conditions to LD integrator

remove a unknown method

LangevinDynamics in progress

Added NPAT to Globals integrators.

filepp can not handle multiple line macro, just convert multiple line macro into single line macro.

instead of printing to std::cout, throwing an exception when error is found.

replace isType<int> with isInteger

More changes to forcefield options.

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.

Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.

Overloaded interface for dumpwriter.

Adding handler for CLAY force field

parsing by filepp

adding ForceFieldOptions

ForceField optional parameters....

Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen.

Added a keyword and ability to output forces and torques

changing how we deal with summation and screening methods

Customized StatWriter is working

fix some namespace issues in Globals

fix a seg fault when try copy a  string to event's err_msg, there are still tons of memory leaking problem in Globals

Constraints for parameters are working now

added default restraint spring constants into Globals

tracking down quaternion bug

fix a typo in DumpReader

adding zlib support for DumpWriter

Added keywords for compressed dump files.

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

adding c-side interface to change cutoff Policy

replace c++ style comment in c files

adding keyword printPressureTensor

NPAT is working

adding NPAT and NPrT integrators

added gb

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

Working on the shapes parser...

fix one more warning message in make_nodes

avoid multiple inherit in basic_ifstrstream

fix a typo in MultipoleAtomTypesSectionParser

LinkedList removal project starts now

Oops...  MPI now builds...

First commit of the new restraints code

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

Fixing a bug in BitSet.cpp

adding MersenneTwister random number generator

adding basic_teebuf which can operate on multiple stream simutaneously.

dynamicProps get built

fix a bug in SimInfo, use number of cutoff stamp as counter to loop over rigidbody stamp

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

port to SGI platform

merging new_design branch into OOPSE-2.0

Improvements to restraints

fix some bugs in Quaternion class

change const_cast to statc_const

fix include

adding basic_ifstrstream

define DEV_ROOT as relative path

add yacc and lex rules

Import of OOPSE v. 2.0