Fixes for restraints, renaming of UniformField

* Changed the stdDev printouts in RNEMD stats to the 95% confidence intervals
* Added the ability to specify non-bonded constraints in a molecule
* Added the ability to do selection offsets in the pAngle staticProps module

Fixes to deal with deprecation of MPI C++ bindings.  We've reverted back to the
C calls.

Quiet down a few warnings in MSVC

Some MPI include re-ordering to work with the Intel MPI implementation.

MERGE OpenMD development 1783:1878 into trunk

Updating MPI calls to C++, fixing a DumpWriter bug, cleaning cruft

Fixed some compilation warnings on the Linux side of things.

Various Windows compilation fixes

Fixed a clang compilation problem, added the ability to output
particle potential in the dump files.

Updated antlr, some minor formatting changes

Adding property set to svn entries

Added check for SGE to progress bar. If we are running under SGE, we should write to file SGE .o file. Under afs it is doubtful that the file will be flushed anyway making the information pointless.

ProgressBar should only print status when it is actually attached to a
tty.  This should quiet down those background jobs.

Adding a progress bar, and pAngle staticProps

Removing renamed files

units for thermalConductivity, spelling error fixed

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

Fixes for Inversions for use with Amber

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

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.

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

Fixed for MPI.

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.

fixed a DumpReader bug, took out extra printing statements in
residentMem and BlockSnapshotManager

testing GB, removing CM drift in Langevin Dynamics, fixing a memory
leak, adding a visitor

Adding single precision capabilities to c++ side

Getting fortran side prepped for single precision...

Complete rewrite of spline code and everything that uses it.

Since status.F90 is used by interpolation.F90, the former needs to be listed above the later in the Makefile.

added some logical flags

bug fixes for interpolation module

refactor Hydrodynamics module.

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

instead of printing to std::cout, throwing an exception when error is found.

make minor change to build oopse under solaris

fixed compilation problem for icc7

adding more checking for topology

compilation bug

ForceField optional parameters....

Added subroutine to set cuttoff for Interaction map and function in simulation.F90 to determine if a particular atype is present in a simulation.

adding SCDOrderParameter into StaticProps

Fixed build issues under ifc7.

adding CharClassificationFunctor to fix the locale problem  of c++

Fixed a bug in RigidBodyStamp section of MoLocator

cleaned up vector_class memory leak fix by deallocating in reverse
order of how we allocated.  Also migrated MoLocator into utils directory

Fixed pointer memory leak in vector_class.

added some stuff to clean out module files during "make clean"

Fixing a bug in BitSet.cpp

fix for compilation on the Sun

forget the const correctness for BitSet

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

*** empty log message ***

bugfixing residentMem

added residentMem

adding Algorithm.hpp

adding physmem

minor change in Bitset

fix BitSet

adding boost::any

adding selection library

fixing for gnugetopt

compile getopt and getopt1 if we need to

merging new_design branch into OOPSE-2.0

remove old Vector3d.hpp from application/simpleBuilder

Done with combination

ReplaceWildCard is working

Minor change

Adding Generic TupleMatcher, wild char matching is on the way

adding GenericFactory Test Case. GenericFactory now can bed used to creat
ForcefieldFactory and IntegratorFactory etc.

GenericFactory pass unit test

replace old GebericData with  new GenericData

namespace problem prevented linking

working on shapes for portability

more tests on math library

Working on getting Shapes into OOPSE

adding PropertyMap class

define DEV_ROOT as relative path

remove StringUtils.c which cause headache in bulding libutils

change the #include in source files