incorporate SMD into ZConstraint,it does not sound a good choice, next commit will seperate SMD and ZConstraint

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Stripped out the hardwired LJ_rcut

Add one more file into Makefile.in

Substantial changes. OOPSE now has a working WATER.cpp forcefield and parser.
This involved changes to WATER.cpp and ForceFields amoung other files. One important
note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. This will be removed on
the next commit...

Changed default orientation in BASS to use Euler angles in the
following order: phi, theta, psi
Removed the ability to set orientation using a unit vector

Adding warning if sample time, status time, thermal time and reset time are not divisible by dt

added the following parameters to BASS:
   * useInitialExtendedSystemState
   * orthoBoxTolerance
   * useIntiTime => useInitialTime

fixed a stdlib.h include error in bass.l

fixed a little bug in the first time step, regarding the setting of ecr and est in fortran

replace c++ header stuff with more portable c header stuff
Also, mod file fixes and portability changes
Some fortran changes will need to be reversed.

added eam ForceField files to the init

fixed an eam mpi parmeter setup bug

added useInitTime to the BASS syntax.
   * useInitTime = false: sets the origin time to 0.0 regardless of the time stamp in the .init file
   * default=> useInitTime = true;

Removed NPTfm from Integrator.hpp.

Some small syntax cleaning in NPTfm and SimSetup

added NPT base class. NPTi is up to date. NPTf is not.

fix a bug at MPI version of PolicyByMass

fix bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to MPI_DOUBLE,
however, the corret type is MPI_INT. Therefore, when we turn on the
optimization flag, it causes a seg fault

user can setup seed in bass file now, if he does not specify any value for
seed, oopse will take the value of seconds of system time as seed

reformmating ZConstraint and fixe bug of error msg printing

harmonic potential & z-contraint method

debugging globals

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stable version of Z-Constraint

 Added Z constraint.

Added eam to simSetup and added changecutoffeam.

Fixed a current time initialization bug in InitFromFile.

more fixes for box changes

fixed some bugs, Changed entry_plug to info where appropriate

Checking in changes for NPTim

adding in dan's NPT stuff

fixed the bugs introduced by switching the periodic box to a matrix

Most of the integrator and NVT seem to be working now.

 doing some work on SimSetup to clean it up / get it to work with the new Integrator.

fixed up sysBuild to where it should now build our systems

Bug fix in progress for NPT

fixed a n mpi init bug in SimSetup. caused a miscalculation of nLocal.

Fixes for NPT / NVT

bug fixes

dipoles mostly work, but there is a memory leak somewhere.

fixed a bug where the Excludes were not being created properly

MPI buggy, fixed mpiRefresh issue.

Fixed a single processor segfault bug.

fixing some compile time bugs

LJ_FF has been converted to the new Molecule model. TraPPE_Ex is currently being updated.
SimSetups routines are writtten, but not yet called.

still working on the SimSetup routine. also fixed some things in Exclude.hpp

electrostatic changes for dipole / RF separation

New OOPSE Tree