Improve documentation

[nedtaylor]

Fortran API documentation needs to be brought up to FORD standards so that we can have a compilable API documentation. Similar improvements are needed for the Python API and the Read_the_Docs.

Fortran API improvements

• src/fortran/lib/mod_cache.f90
• src/fortran/lib/mod_generator.f90
• src/fortran/lib/mod_geom_rw.f90
• src/fortran/lib/mod_geom_utils.f90
• src/fortran/lib/mod_help.f90
• src/fortran/lib/mod_intf_identifier.f90
• src/fortran/lib/mod_io_utils.F90
• src/fortran/lib/mod_io_utils_extd.F90
• src/fortran/lib/mod_lat_compare.f90
• src/fortran/lib/mod_misc.f90
• src/fortran/lib/mod_misc_linalg.f90
• src/fortran/lib/mod_misc_maths.f90
• src/fortran/lib/mod_misc_types.f90
• src/fortran/lib/mod_plane_matching.f90
• src/fortran/lib/mod_shifting.f90
• src/fortran/lib/mod_swapping.f90
• src/fortran/lib/mod_sym.f90
• src/fortran/lib/mod_terminations.f90
• src/fortran/artemis.f90
• src/wrapper/f90wrap_mod_generator.f90
• src/wrapper/f90wrap_geom_rw.f90
• src/wrapper/f90wrap_mod_misc_types.f90
• src/wrapper/f90wrap_artemis.f90

Python API improvements

• Generator.artemis_generator.get_all_structures_data
• Generator.artemis_generator.get_all_structures_mismatch
• Generator.artemis_generator.get_all_structures_transform
• Generator.artemis_generator.get_all_structures_shift
• Generator.artemis_generator.get_structure_data
• Generator.artemis_generator.get_structure_mismatch
• Generator.artemis_generator.get_structure_transform
• Generator.artemis_generator.get_structure_shift
• Generator.artemis_generator.set_tolerance
• Generator.artemis_generator.set_shift_method
• Generator.artemis_generator.set_swap_method
• Generator.artemis_generator.set_match_method
• Generator.artemis_generator.set_materials
• Generator.artemis_generator.set_surface_properties
• Generator.artemis_generator.reset_is_layered_lw
• Generator.artemis_generator.reset_is_layered_up
• Generator.artemis_generator.get_terminations_lw
• Generator.artemis_generator.get_terminations_up
• Generator.artemis_generator.get_interface_location
• Generator.artemis_generator.generate
• Generator.artemis_generator.regenerate
• Generator.artemis_generator.clear_structures
• Generator.artemis_generator.get_structures

Read_the_Docs improvements

• Tolerance parameters
• Lattice match method
  • Maths for lattice matching
• Interface alignment method (shifting)
  • Description of shifting methods
• Intermixing method (swapping)
• Tutorial/Generate terminations
• Tutorial/Generate interface
• Tutorial/Regenerate interface
• Tutorial/Generate shifts
• Tutorial/Generate swaps (point to RAFFLE?)
• Tutorial/Get interface data
  • Understanding this data
• Interfacing with RAFFLE