added kevin results
Updated nmd.py to include lmpReadBin and nmdProc.

Included lmpReadBin which can read lammps binary files (confirmed) and nmdProc which
performs normal mode decomposition (still testing).
Working on lmppy
added simple python lammps example
organized ./examples
First examples of pypar/multiprocessing.

These are the first few examples of how to do pypar and multiprocessing in python, with the goal of eventually
implimenting nmd using these methods.
Muliprocessing shared mem and pypar fail.

Mpi cannot use the shared memory from the multiprocess class, it simply copies the array by the number of
processors.
Parallel lammps velocity pull working.

Parallel lammps velocity pull now works. I find it helps to think as one of the proc reading the script.
Maybe one area of impovement could be the loop to receive velocities
Added secondary files for
multi.py
Performance improvement, preallocate functions.

Preallocated lammps and pypar functions to reduce function lookups.
Turning the code into nmd code.

Right now stuck on how to efficently collect the velocities from lammps into one array.
Fixed the lammps run part. Debugging nmd.

Instead of using extract_variables which extracts the variables from each separate process, using gather_atoms
returns the whole position list all at once. Now nmd is in use of debugging. Currently the specED returned is
full of nans
Lammps successfully using gather_atoms.

Problem was lammps returns gather_atoms(\quote v \quote, 1, 3) in a single array of size (numAtoms*3). This
is indexed as vel1x vel1y vel1z vel2x vel2y ...
Lammps script not working with nve rescale.

The nve rescale leads to an exponential decrease the the SED. Possible going to try and run once script with the
rescale then push all the pos/vel/box size to another script.
Added ntpy.param.si