implemented HWvC rate forms

Still tweaking a bunch of stuff:
* diffusion parameters
* precipitation
* total amounts of S, N, and Fe
* c_lim?
* diffusion in and out for O2 and CO2
working with HWcV changes
old changes
added script to extract rate and conc data

execute run_all first; this script references the variables that are
output by that script.
added some methane