Four species two reactions

examples/four_species.py demonstrates how to use the plotting utilities plot_per_reaction_contribution and plot_jacobian. The reaction system is as follows:

\[\begin{split}A &\rightarrow B ~~~ & k_1=0.05 \\ 2C + B &\rightarrow D + B ~~~ & k_2=3.0\end{split}\]

$ python four_species.py --help

usage: four_species.py [-h] [-t TEND] [-N N] [-n NT] [-j] [-m MODE] [--logy]
                       [--logt] [-p] [-s SAVEFIG] [-v] [-g]

    Integrates the reaction system defined by
    :download:`four_species.json <examples/four_species.json>`


optional arguments:
  -h, --help            show this help message and exit
  -t TEND, --tend TEND  10.0
  -N N, --N N           1
  -n NT, --nt NT        500
  -j, --jac-spy         False
  -m MODE, --mode MODE  -
  --logy                False
  --logt                False
  -p, --plot            False
  -s SAVEFIG, --savefig SAVEFIG
                        'None'
  -v, --verbose         False
  -g, --graph           False

Here is an example generated by:

$ python four_species.py --plot --savefig four_species.png

Jacobian:

Per reaction contribution:

four_species.integrate_rd(tend=10.0, N=1, nt=500, jac_spy=False, mode=None, logy=False, logt=False, plot=False, savefig='None', verbose=False, graph=False)

Integrates the reaction system defined by four_species.json