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

Adding a progress bar, and pAngle staticProps

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. 

Merging changes skipped in working copies of OOPSE into the OpenMD
tree, fixing make install

Removing CGAL from all code

Re-write of convex hull.

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

units for thermalConductivity, spelling error fixed

Parallel version of RNEMD

only create RNEMD object if we need it.

bug fix in DLM, added temperature profiles and uniform bins to RNEMD

Bug fix

fixed some bugs, added some logic to sort stuntdoubles

Added handlers to Integrator to call RNEMD at the right times.  Added initialization
to RNEMD to make sure values from the MD file are available.

Different method again for Langevin Dynamics.

Code clean-up. Removed old langevin code.

Fixed bug in variance.

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

Fixed Memory Leak in ConvexHull.

Returned old LD forces to SMIPDForceManager.

Work continues on constant pressure langevin dynamics.

Only build SMIPDynamics and register it if we have qhull

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

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

MnM interaction now works.

Fixed Langevin Dynamics and DLM

does ifdef check for computational geometry packages

Starting NPT Langevin. Added new force manager files.

Massive update to do virials (both atomic and cutoff-group) correctly.
The rigid body constraint contributions had been missing and this was
masked by the use of cutoff groups...

Added velocitizer utility program, added samples of its use to the
builder samples.

fixes to zang writing

MPI thermodynamic integration works now.

Massive changes for GB code with multiple ellipsoid types (a la
Cleaver's paper).

Also, changes in hydrodynamics code to make HydroProp a somewhat
smarter class (rather than just a struct).

Fixed a bug when spherical boundary conditions were off.

*** empty log message ***

NPrT might work now

Verify the correctness of Ellipsoid's hydrodynamics properties

LagevinDynamics is working?

Got rid of spurious printing out of timestep

OptionSectionParser get compiled

Customized StatWriter is working

Removed print statement for angular momentum and inertia tensor from velocitizer.

Changes to remove angular momentum.

dding resetIntegrator

Fix to print pressure tensor.

NPrT in progress

NPAT is working

adding NPAT and NPrT integrators

minor change to TI output

First commit of the new restraints code

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

fix compilation problem for g++ 3.4

adding MersenneTwister random number generator

fix a bug in VelocityVerletIntegrator : last frame is written twice

dynamicProps get built

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

forget to set maxIterNum_ in NVT

merging new_design branch into OOPSE-2.0

Improvements to restraints

Don't remember what I did

change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp

change Makefile to relative path

change the #include in source files