Put initialization in a separate function.

This is useful for the Python interface, as it does not need to know the
signatures of the communication functions.
Added a shared library target for use with Python.
Git ignore build products.
Added initial version of Python interface.
Not really needed.
Added local Git ignore file.
Renamed class.
Removed DBG prints and unneeded type casts.
Added potential energy getter.
Added method to get atom names.
Removed prelim_md, configure energy_ctrl by hand.
Renamed symbols to names.
Added an example for the Python interface.
Ignore LaTeX build output.
Removed old file.
Remove settings not needed.
Put declarations in interface file.
Major overhaul of Python interface - multiple replicas running in parallel.
Fix output buffering on stdout.
Added Python tools.