Merge pull request #67 from HaibingShao/haibing_working

taking the changes of safety protection in REDUCT_GIA
Merge branch 'haibing_working' into ops_kin
changing the input files according to Wenkui's updated definition.
change the input configuration of neckar_1D problem according to Wenkui's recommendation.
do not need output for every time step.
This was a bug and now fixed.
We should use the full list of chemical components to initialize the UserExp.
using the userExp.
try better numerical configuration.
this KRC setting will cause the decay of biomass instead of growth.

Notice the stoichiometry of 1.0 before Biomass. As the Biomass is on the left-hand-side of the equation, this will be -1.0 * rate.

Therefore, we multiply -1.0 on the rate expression, to get the correct rate.
loose the error tolerance and shorten the max nonlinear iteration.
max_time_steps set to 8640 sec.
fix a memory leak.
fix another memory leak.
this function cause run-time error while simulating monod2d problem. disbleing for now.
fall back to the backward Euler scheme for ODE.
a bit lose constrain on local problem.
also set Biomass_dummy initial value to 1.0e-6.
fixing the ODE part.
now the strict error tolerance should be fine.
add the input files for running seqdeg benchmark in ops mode.