Finalysing first step of performance improvement focusing on reducing
iteration CPU time by improving calculation of basic element functions,
which took a lot of the CPU time
Merging branches and fixing a number of important issues:
- Initial particles were not being assigned to the list of particles.
- List of particles was being erased every iteration, even if species
was not pushed.
These caused issues with the calculation of collisions when a species
was frozen.
Now, things should work properly. All particles are properly added to
the volume list and the list is erased ONLY if the species has been
updated.
I hope that collisions are now properly accounted for per species pair.
Now collisions can have a different time step.
Added species name to output names as it was starting to get confusing
in Gmsh for multiple species.
Output filenames adapted to match any number of iterations.
