Computational code supporting 'Modelling the floating-catalyst method for carbon nanotube production'

Computational code developed in association with PhD project: 'Modelling the floating-catalyst method for carbon nanotube production'. The main functionality of the code is in `base_optimiser`, this has all the underlying functions for constructing geometry, solving the flow, and setting up the adjoint optimisation. The main code for my thesis is found in the `reactor` folder. The Thiophene optimisation scripts (Chapter 6) can be found in the `reactor/hoecker/thiophene/absolute` folder. The particle modelling scripts (Chapter 9) can be found in `reactor/misc/cued_particles/` and the adjointised run (Chapter 10) can be found in `reactor/misc/cued_particles/adjoint`. This code requires FEniCS, DOLFIN, and python3 to run, see https://fenicsproject.org/ for details on how to set it up. I recommend using `anaconda`. The majority of the code runs on FEniCS 2018.1.0, but some older code might need adjustment to work with the new versions of FEniCS. Further dependencies are listed in `requirements.txt` for pip3 to install. `Pygmsh` is used for the mesh description. In addition, an installed version of `gmsh` is required to automatically generate meshes with the code. As the code has gone through continuous development over 4 years there are several scripts that do not work out of the box, but that need to be tweaked to run with the updated version of the code, and FEniCS.