Add log.lammps unit tests

The PyLammps class (within the LAMMPS Python interface) is used to pass commands to LAMMPS; while it can pass every command that can be used in LAMMPS, it can only request partial state information e.g. it can poll LAMMPS for the number of atoms in a simulation, but not the bond parameters. Therefore the testing of certain asking of the MDMC LAMMPS module (lammps_engine.py) is restricted to testing for fatal exceptions, rather than checking the state of LAMMPS has been set correctly.

As PyLammps generates a log.lammps file, which contains all of the commands run by LAMMPS, it is possible to determine the state from this log. Write a function to parse the log and use this to test whether the state has been set correctly in the unit tests. The unit tests to which this should be applied are indicated in the unit test docstrings.