Fixed a bunch of cppcheck warnings.

Fixed a bug in RigidBody, added a check for fixed vs. fluctuating charge

Only compute field for sites not excluded from the pairwise electrostatic contribution.
Also, now compute the mean field felt by the sites in a rigid body, and report that as
the rigid body's field.

Unified the computation of storageLayout into SimCreator, but that
value is stored in SimInfo.  We used to compute storageLayout values
in two places - now only one.

Merged trunk changes into the development branch

Massive multipole rewrite

Bug fixes for heat flux import

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.

Added files for fcc and pentagonal nanorod builders. Updated runMe in samples/builders to include nanorod builders.

fixing the build system

bug fixes

changes for new parallel architecture

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.

Fixed a potential bug.  If Ghost atoms have no electroFrame
(i.e. if they are DirectionalAtoms, but not dipoles), the GhostBend
and GhostTorsions would give nans.   We should be using getA instead
of getElectroFrame.

Fixing gradients for minimization

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

many changes to keep track of particle potentials for both bonded and non-bonded interactions

A few simple mods to remove gcc compile warnings

Inversion fixes and amber mostly working

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

Checking in changes for Hefland moment calculations

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

Adding single precision capabilities to c++ side

using setFrc in RigidBody::calcForcesAndTorques will discard if there are force and torque applied in rigid body itself. use addFrc instead.

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

streamlined reaction field for dipoles (now a good bit faster) and added reaction field for charges - still need to do charge-dipole RF

Don't remember what we did

erase output of inertia tensor. There is still something wrong with current implementation.

fix a bug in projecting the inertia tensor of
directional atom in rigibody into rigidbody's body frame (previous commit is wrong)

Rotation matrix multiplication order error

xemacs has been drafted to perform our indentation services

more memory leak are fixed

Fixing a bug in BitSet.cpp

Fix for compilation on the Sun

adding dynamicProps

adding missing implementation

(1)Cast wrong atom to DirectionalAtom in GhostTorsion
(2)get the wrong column of electroframe

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

port to SGI platform

isLinear and linearAxis are virtual in StuntDouble,
but are implemented by DirectionalAtom and RigidBody
In StuntDouble, they should return false and "-1" but
there should be logic to figure them out in the other
two classes

replace old GebericData with  new GenericData

define DEV_ROOT as relative path

change the #include in source files