Removing CGAL dependence

fixed a bug confusing id with localID, stopped adding NULLS to triangles also.

Re-write of ConvexHull.

Stupid parallel bug fixes. Why was this ever working?

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

Modifications to support RMSD calculations, removing classes we aren't using.

Removing unused tnt classes

adding jama and tnt libraries for various linear algebra routines

Different method again for Langevin Dynamics.

More attempts to get SMIPD to themostat properly

Fixed Memory Leak in ConvexHull.

Fixed nanovol so it now builds.

Case typo for Hull.hpp.

Inversion fixes and amber mostly working

Added files to module section of Makefile.

A bunch of minor changes to make MPI compilation faster than
the double compilation we do now...

updating configure process

Build fixes for include files.

Initial code for AlphaShape.

Check CGAL and qhull defines

Many fixes for Charmm-type torsions.

Changes to Build system.

Fixed more bugs and removed more CGAL.

Removed CGAL from OOPSE and replaced it with qhull.

Added preliminary support for CGAL and computation of convex hull.

Bugfixes in BondOrderParameter and SphericalHarmonic

Added utility function to winger3jm from slatac.

Adding single precision capabilities to c++ side

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refactor Hydrodynamics module.

adding Cholesky Decomposition

Adding Hydrodynamics Module

fix a bug in converting integer to double

Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X

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

using epsilon instead of 0.0 to avoid divergence in rotation matrix to quaternion transformation

added error function

Fixed build issues under ifc7.

xemacs has been drafted to perform our indentation services

Fixing a bug in BitSet.cpp

info_ in Velocitizer is not initialized which causes a seg fault

replace SPRNG by MTRand

adding OOPSERandNumGen

adding MersenneTwister random number generator

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

port to SGI platform

still debugging

add getArray function to  RectMatrix and Vector classes

Snapshot and SnapshotManager in progress

except diagonalize(), all of functions in math library pass the test

more bugs are fixed in Vector class

more tests on math library

Your basic run of the mill real-valued versions of Y_l^m(\theta, \phi)

math library in progress

fix incompatible declaration in jacobi

Matrix in progress, test in isOrthogonal of SquareMatrix is failed by some reasons

refactory vector and matrix classes

add Vector3d.hpp and  Matrix3x3d.hpp

define DEV_ROOT as relative path

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Import of OOPSE v. 2.0