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11.05.2012: Reproducing Fig. 1 of Richards and Brentnall (2006)ΒΆ

To test if I am running the model correctly, I reproduced the left panel of Fig. 1 of Richards and Brentnall (2006) which shows the maximum P for a run with no viruses and starting with uniform initial conditions (so that advection and diffusion become unimportant) (Fig. 1, upper panel). To test that each simulation has reached a steady state after 8000 days, I also plot a convergence test in the lower panel of Fig. 1.

../../../../../../_images/Psmax_Psconv.png

Figure 1: (upper): same as the left panel of Fig. 1 of Richards and Brentnall (2006). (lower): difference in P between day 7800 and day 8000 to test the convergence of each run.

As you can see, we do not have exactly the same plot as in Richards and Brentnall but, I think, the difference is solely due to the resolution used. I tried to use as many points as possible without having to run the model for weeks. I do not know how Richards and Brentnall got this figure rapidly. Maybe they actually used an analytical solution. In any case, I am confident that I am running the model correctly. Notice, finally, in the lower panel that indeed, each simulation has converged to a steady solution after 8000 days.


Simulations made with manyruns_1.py in RESEARCH/MODELISATION/marine_viruses/current_version/runs/test_Richards_Brentnall_06. Plot made with plot_Psmax_Psconv.py in RESEARCH/MODELISATION/marine_viruses/current_version/runs/test_Richards_Brentnall_06/analysis/manyruns_1/