Added NPA integrator

Removing vestiges of deprecated MPI:: namespace C++ MPI bindings

Fixes to deal with deprecation of MPI C++ bindings.  We've reverted back to the
C calls.

Added Legendre Correlation function (as a function of Z), working on architecture for Ewald
Fixed some bugs in FlucQ

MERGE OpenMD development 1783:1878 into trunk

Fixed some compilation warnings on the Linux side of things.

vss-rnemd

Added Momentum correlation function, imported changes from Vector from
development branch, updated comments in some integrators

This commit should allow EADM simulations to be run on the cluster. Main additions include EADM_FF.hpp/cpp as well as a system dipole correlation option in DynamicProps.

option binShift enables bin division shifts Lz/2N
option output3DTemp enables x,y,z dimensional temperature recording
disables angular momentum exchange for swapping algorithm
fixed a bug for swapping MPI code

Added NPTsz integrator to the makefile

fixed a bug where chi value wasn't being set in calcConservedQuantity.  I'm not
100% sure we actually need this routine here in NPTxyz (instead of inheriting
from NPTf), but if it is here, the variables need to be set...

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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Import of OOPSE v. 2.0