forces/pair_trunc: take neighbour module as optional parameter

This enables the possibility to set the cell occupancy parameter to
a value that is not the default (0.4)
writers/h5md: extend on_write() for 6-element vectors

Six-dimensional vectors will be needed for saving the symmetric stress
tensor in HDF5 files.
gpu/thermodynamics: fix uninitialised potential energy accumulator

Although the results seem correct, it is better to initialise the
potential energy to zero on construction.
observables/thermodynamics: add stress tensor computation

Previously only the potential part of the stress tensor was available.
The additional accumulator in theromodynamics_kernel allows one to
compute the full stress tensor, i.e. both kinetic and potential parts.