Merged trunk changes into the development branch

Code readability updates.

Refactored Snapshot and Stats to use the Accumulator classes.  Collected
a number of methods into Thermo that belonged there.

Fixing some bugs in optimization, fixing status functions so that they
dump correctly (although some things are deferred until the Stats is
accumulator-based).

Individual ForceField classes have been removed (they were essentially
all duplicates anyway).  

ForceField has moved to brains, and since only one force field is in
play at any time, the ForceFieldFactory and Register methods have been
removed.  

Some fixes for CMake and single precision builds

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.

Debugging mainly

Fixes

Bug squashing

bug fixes

More fortran removal, and trimming out unused code

a few more tweaks   We're getting somewhat closer to deleting fortran.

More modifications for paralllel rewrite

compiles, builds and runs, but is very slow

getting closer to compiling

Moved switching functions and force options over to the C++ side, and
removed them from Fortran.

Doesn't build yet, but getting much closer...

Changes to remove more of the low level stuff from the fortran side.

Adding property set to svn entries

removing MPI responsibilities from the lowest level force routines.  This is
in preparation for migrating these routines (LJ, electrostatic, eam, suttonchen,
gay-berne, sticky) to C++

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.

SF Lennard-Jones was added for everyones' enjoyment.  The behavior is tethered to the electrostaticSummationMethod keyword.

Fixed a bug in NeighborListNeighbors.

Added interface to change number of neighbors in calculating neighbor list.

fixing a wrapVector problem in staticProps, also making Shifted force
and electrostatic damping the default behavior

fixed the half self term for wolf electrostatics and OOPSE now chooses a cutoff radius dependent alpha for damped electrostatics

Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants

Adding spherical boundary conditions to LD integrator

Changes to cutoff radius setting to a more logical procedure - still may change...

More Sutton-Chen bug fixes.

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

OptionSectionParser get compiled

added in a 5th order polynomial switching function option

improvements in shifted-force

fixed a capitalization problem with NPT integrator initialization

Still had some globals toUpper problems - these changes should fix those...

rewrite Globals

Added support for skinThickness keyword to Globals.

reaction field seems to work now, still need to do some testing...

fixed a capitalization error

some fixes but even more breaking (cutting out the old way to do reaction field)

adding c-side interface to change cutoff Policy

Changes to remove angular momentum.

OOPSE setup for TAP water.  It's not parametrized, but OOPSE will now let me run it...

more memory leak are fixed

clean up SimInfo; modify the images of SelectionExpression.html

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

begin bug fix

fixed a bug in SimInfo::getCutoff()

adding one more constructor to Snapshot to create customized DataStorage

fix a bug in SimInfo, use number of cutoff stamp as counter to loop over rigidbody stamp

fixey fixey the breakey breakey

change the #include in source files