run: fixed CRITICAL errors

index assignment! need accumarray to get the rates to accumulate on the
repeatedly used substrates
removed erroneous C-
got good crossing

precipitation is a prboem
fixed the leak

some diffusion and precipitation constants were misplaced
cleaned up some older scripts
added oxygen reservoir
improved rates function

moved total rate control inside
working

need to add coefficients back in
allows separate precipitation parameters
about to make major changes
some improvements for biomass