PyLammps now supports thermo_style entries such as c_msd[4]

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.

Also fixes some regressions due to command syntax changes

The interface of that function has changed and includes two additional
parameters, which haven't been added to the Python interface either.
This showed up by trying to run the simple.py example.

Based on material presented during MD Workshop at Temple University in
August 2016.

Thanks to Giacomo Fiorin for figuring this out with NAMD/Colvars.
This requires linking with -Xlinker -export-dynamic or equivalent,
which is the default when using python-config to provide linker flags.
We will fall back to loading the DSO in case the initial load fails.

0aebb2eabea6ae3f5365951335ac3d698ab9ad9e

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15668 f3b2605a-c512-4ea7-a41b-209d697bcdaa

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15634 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Make.py is now used to enable exceptions support

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15592 f3b2605a-c512-4ea7-a41b-209d697bcdaa

The return value of `lammps_get_last_error_message` now encodes if the last
error was recoverable or should cause an `MPI_Abort`. The driving code is
responsible of reacting to the error and calling `MPI_Abort` on the
communicator it passed to the LAMMPS instance.

Thermo data of the last run is now accessable through the `last_run.thermo`
property. This is a dictionary containing the data columns of thermo output.
All run data is kept as list and can be found in the `runs` property.
See issue #144

This implements the requested feature in issue #145. The `write_script`
method now gives you a way of dumping out all used commands into a
LAMMPS input script file.

Note: this also dumps all commands which are indirectly issued by PyLammps

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15533 f3b2605a-c512-4ea7-a41b-209d697bcdaa