make python functions examples more complete by adding exception handling and initializing variables

This reverts commit 4d915dba.

This is to avoid confusion to what LAMMPS considers to be an
integrator like Verlet and RESPA.

Removing the loop over atoms by using NumPy array indexing allows to recover
performance close to that of plain fix nve.

This includes an example of how to implement fix NVE in Python.

The library interface was extended to provide direct access to atom data using
numpy arrays. No data copies are made and numpy operations directly manipulate
memory of the native code.

To keep this numpy dependency optional, all functions are wrapped into the
lammps.numpy sub-object which is only loaded when accessed.

- move example folder to examples/USER/misc/
- comment out writing of trajectory files
- reduce run length (for easier testing for regressions)
- record example outputs for 1 and 4 MPI processes
- rename readme.md to README.md for visibility