disable the water content temperarily. This needs big fix.
adding a test example of simple first order decay.
change the input files to simulate simple first order decay reaction.
adding the KRC file, where the first order decay reaction is defined.
fix the input files.
This was a bug and now fixed. For kinetic reactions, we do not make a difference btw basis and secondary species.
fix the same bug in REACT_GIA mode as in OPS mode.
adding the first order decay example running under GIA mode.
dt is not changing with elements, therefore move it to the outside of the element loop.
this F is never used, therefore remove.
use nnodes to represent the number of connecting nodes in one element.
The parameter "n_max_connect_nodes" is a very bad practise. We know examply how many nodes wo have in each element. Therefore move the place of initialization.
fix a warning msg.
remove unused theta_water_content.
fixing the same bug for module KIN_REACT_GIA.
fixing one bug here. The position of res44 was wrong.
we need porosity/water_content values on the RHS of the equation. As our mass matrix assembly also contains the porosity values.

This fix will make the curve right for KIN_REACT_GIA module. The fix for REACT_GIA module will come later.
following the revious commit, adding the porosity/water content values to the RHS of the equation in the REACT_GIA module.
The mass lumping parts in these two files actually forgot to factorize localF. Therefore, they will cause the effective reaction rate not the same as the real reaction rate!
Now the result of HC_decay_1Du exmaple is correct. Do not need full output. Just every 10 steps.