Migrating Sutton-Chen from Fortran over to C++

Added GB module to the C++ side, got rid of it on the fortran side.

builds

well, it compiles, but still segfaults

removing cruft (atom numbers, do_pot, do_stress) from many modules and
force managers

Adding property set to svn entries

Added missing cstdio include lines for gcc 4.4 compatibility

removing MPI responsibilities from the lowest level force routines.  This is
in preparation for migrating these routines (LJ, electrostatic, eam, suttonchen,
gay-berne, sticky) to C++

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

General bug-fixes and other changes to make particle pots work with
the Helfand Energy correlation function

Only build SMIPDynamics and register it if we have qhull

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.

Exclude is gone.  Replaced by a generic PairList to handle 1-2, 1-3, and
1-4 interactions as well as the exclude list

Changes for implementing Amber force field:  Added Inversions and
worked on BaseAtomTypes so that they'd function with the fortran side.

Adding infrastructure for Amber force field.

Checking in changes for Hefland moment calculations

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.

Changes for MnM forcefield.

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

Fixed a bug in NeighborListNeighbors.

Fixing an implementation problem

Adding the ability to compute Center of Mass properties on
reading in a dump file.  DumpReader must be told if it needs
to do this, however.

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

fixes for open babel

fixing bond order parameter code

fixed the half self term for wolf electrostatics and OOPSE now chooses a cutoff radius dependent alpha for damped electrostatics

adding NgammaT integrator

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.

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

Adding spherical boundary conditions to LD integrator

fixed a spelling error

Changes to cutoff radius setting to a more logical procedure - still may change...

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

Long range potential return from fortran is already accumulated, it should not be accumulated again;
nGroupTypesCol is not initialized; GroupMaxCutoffCol is not allocated;

Fixed issue with symbol naming and added call to set force options in SimCreator.

made some minor changes to allow compilation with the portland group
compilers

Got rid of spurious printing out of junk

Cutoff Mixing fixes

register openbabel readers/writers

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

Added a keyword for output of forces and torques

again, changing how we deal with summation and screening methods

changed the default switching radius to 85% of rcut

fix an index mismathcing between c and fortran

Customized StatWriter is working

Fix to forceManager to pass potential array to fortran.

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

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

xlf found a bug that ifc missed...

it builds now, but there are known issues - particularly with reaction field...

changes to include the coulombicCorrection selector

made some changes for implementing the wolf potential

Changes to remove angular momentum.

adding keyword printPressureTensor

adding NPAT and NPrT integrators

Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...

fix some warning messages

refactory lattice

fix a typo in MultipoleAtomTypesSectionParser

clean up SimInfo; modify the images of SelectionExpression.html

First commit of the new restraints code

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

SPRNG eradication project

remove default parameter from MersenneTwister.hpp which causes all kinds of trouble.
Refactory random number generator

replace SPRNG by MTRand

adding OOPSERandNumGen

Corrected filename collision for EAM on Mac OS X

using PhysMem - RSSMem to estimate avaliable memory

fix a bug in BlockSnapshotManager

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

fix a bug in BlockSnapshotManager.hpp

fix a bug in calculating  bytes per stuntdouble

maximum length defaults to the cutoff radius

dynamicProps in progress

adding dynamicProps

fix a bug in determing the global index for rigidbodies

remove some useless files

(1) complete section parser's error message
(2) add GhostTorsion
(3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor

no message

merging new_design branch into OOPSE-2.0

Don't remember what I did

char* -> string

DataStorage passes unit test

more classes get reconstructed

fixey fixey the breakey breakey

Snapshot and SnapshotManager in progress

replace old GebericData with  new GenericData

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

namespace problem prevented linking

Cleaning up a bit

change Makefile to relative path

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Import of OOPSE v. 2.0