for debuging purposes, output intermediate values.
When calculating the rates of kinetic reactions, the input variables shall be concentrations, not eta and xi.
make sure that xi_kin_bar_old values are always passed to the local ODE problem,
and also set the starting point of ODE problem to these values.
The original code was obviously wrong.
passing on the concentrations to kinetic rate calculation, instead of passing xi and eta.
using concentrations to calculate drates/dxi.

After this commit, the "linear solver blow up" problem is solved. The simulation of monod2d can saftly run over 2500 seconds.