Merging trunk changes 1812:1830 into development branch.

Merging trunk changes back to development branch

Various fixes required to compile OpenMD with the MS Visual C++ compiler

fixing the build system

Splitting out ifstrstream into a header and an implementation.  This
means that much of the code that depends on it can be compiled only
once and the parallel I/O is concentrated into a few files.  To do
this, a number of files that relied on basic_ifstrstream to load the
mpi header had to be modified to manage their own headers.

Creating busticated version of OpenMD

Fixed a bug where any program using selection syntax without qhull would fail. We only do a is fatal now if you try to use hullfinder.

Fixed a bug with rigid bodies and stuntdoubles. We now update the SD's before doing the distance find.

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

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

adding SelectionToken.cpp

xemacs has been drafted to perform our indentation services

change the parameter name in constructors

clean up SimInfo; modify the images of SelectionExpression.html

adding IndexFinder

adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into
ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;

change the suffix of output files;fix the problem of counting in staticProps

replace std::make_pair by VariablesType::value_type to make Sun Compiler happy

adding SelectionManager.cpp

support select internal index selection, for example, select DMPC.3

adding Makefile

selection library is working

selection library get built

more work in selection library

selection library in progress, except SelectionEvaluator, other files are compiled

Selection in progress