Add notes on the Fokker-Planck collision operator, linking to the ExC…

…ALIBUR report and giving input parameter information. Modify the index to feature this note and the note on magnetic geometry.

docs/src/fokker_planck_notes.md

@@ -0,0 +1,37 @@
+Fokker Planck collision operator
+===============================================
+
+We implement the nonlinear Fokker-Planck collision operator for self collisions 
+using the weak-form finite-element method. This is documented in the 
+[ExCALIBUR/NEPTUNE report 2070839-TN-07](https://excalibur-neptune.github.io/Documents/TN-07_AHigherOrderFiniteElementImplementationFullFlandauFokkerPlanckCollisionOperatorC.html).
+A publication based on this report is in progress. Full online documentation will follow.
+
+Input parameters
+===============================================
+
+A series of 0D2V Fokker-Planck input files can be found in
+
+    examples/fokker-planck/
+
+and examples of 1D2V pre-sheath simulations with the Fokker-Planck collision operator
+can be found in
+
+    examples/fokker-planck-1D2V/
+
+noting that the timestepping or resolution parameters may require modification to find
+a converged simulation.
+
+The basic input namelist is structured as follows
+```
+[fokker_planck_collisions]
+use_fokker_planck = true
+# nuii sets the normalised input C[F,F] Fokker-Planck collision frequency
+# for frequency_option = "manual"
+nuii = 1.0
+frequency_option = "manual"
+```
+Set `use_fokker_planck=false` to turn off Fokker-Planck collisions 
+without commenting out the namelist.
+The default option for `frequency_option = "reference_parameters"`, where `nuii` is set
+by the reference parameter inputs. Further specialised input parameters can be
+seen in the source at  `setup_fkpl_collisions_input()` in `moment_kinetics/src/fokker_planck.jl`.

docs/src/index.md

@@ -13,6 +13,8 @@ Pages = ["getting_started.md",
          "moment_constraints_notes.md",
          "boundary_conditions_notes.md",
          "external_sources_notes.md",
+         "fokker_planck_notes.md",
+         "geometry.md",
          "debugging-hints.md",
          "developing.md",
          "manual_setup.md",