explain model section

Usecases/README.md

@@ -286,7 +286,7 @@ Some explantion is given in that file on how to define substructuring classes.
 
 ### MODEL CONFIGURATION
 The model configuration block sets all model parameters: Which model is assumed, material parameters, relative permeabilties, pc-S relationships etc.
-lets look at the first part:
+Lets look at the first part:
 ~~~python
 # MODEL CONFIGURATION #########################################################
 isRichards = {
@@ -349,7 +349,7 @@ assumed, when set to `False`, the two-phase model.
 
 The relative permeabilities and pc-S relationships are set subsequently in
 the block:
- 
+
 ~~~python
 intrinsic_permeability = {
     1: 0.01,
@@ -380,6 +380,20 @@ S_pc_sym_prime = Spc["prime_symbolic"]
 sat_pressure_relationship = Spc["dolfin"]
 ~~~
 
+- `intrinsic_permeability`: each subdomain gets an intrinsic permeabilties. So far functions as intrinsic permeabilties have not been implemented. This is
+because the numbers stored in the `intrinsic_permeability` dictionary get multiplied with the functions defined in the `rel_perm_definition` in the code.
+
+- `rel_perm_definition`: The relative permeabilities get defined by calling a
+a keyword specifying the type of function.
+This gets then passed to the function
+`fts.generate_relative_permeability_dicts` which generate the actual dictionaries needed by the simulation.
+All this is defined in `../LDDsimulation/functions.py` and this has been done
+to have a central way to defining and reusing data functions.
+If you want to introduce other relative permeabilities, this is the place to do it.  
+- `Spc_on_subdomains`: The Spc get defined similarly to the relative permeablities by calling a a keyword specifying the type of function along with a dictionary of parameters. As in the case of the relative permeabilities
+the function `fts.generate_Spc_dicts(Spc_on_subdomains)` does the generation.
+Again, `../LDDsimulation/functions.py` is the place to start hacking to get other parametrisations going. 
+
 ### MANUFACTURED SOLUTION/SOURCE EXPRESSION
 ~~~python
 ###############################################################################