Initial porosity and permeability in respective laws
Currently, the initial porosity and permeability values in the respective laws for the mineralization model are treated as values of the clean, unreactive porous medium without any initial precipitates. However, there are many cases, just as in the 2pncmin test, where there is some dissolving mineral present initially. In such cases, the initial porosity and permeability as implemented now are misleading, as the initial porosity and permeability in the calculations will not be the input value, but those updated by the effect of the initial mineral volume fraction.
I think a good way to improve this would be to rename initialPorosity(...) and initialPermeability(...). But I do not yet have good suggestion except for maybe cleanP.(...), unreactiveP.(...), or referenceP.(...). Further, the values for referenceP.(...) should be calculated in the initialization of the spatial parameters based on the actual initial porosity and permeability values: referencePorosity_= initialPorosity_-sum(precipitateVolumeFractions); and accordingly for referencePermeability_ with the respective permeability law used.
Whatever we decide to do, we should be more clear about what the reference parameters (currently initialPorosity(...) and initialPermeability(...)) for the porosity and permeability laws really are. Are they the "clean-porous-medium" values or the "initial" values or some arbitrary reference?. In my opinion, the "initial" is too misleading as it is used right now.
update 1pncmin and 2pncmin to use referenceXY(), as the already define reference and not initial values