Stopping simulation early on event

Hello,

Is there a good way to stop a simulation early if an event occurs; i.e., stop the simulation as soon as the event is triggered? Also, I'd like to do this in a way that causes the objective function value to be infinite when using 'sbiofit'.

Thank you,

Abed

Answer 1

[Arthur Goldsipe]

Hi Abed,

Interesting question. The only way an event can stop a simulation early is if the event errors. sbiofit would handle such a siutation by returning Inf for the objective function value. Since you mentioned fitting, I generally recommend setting MaximumWallClock during fitting to ensure that things don't get stuck if a fit encounters a bad parameter value that results in a really long running simulation.

Ok, back to a simulation that errors. The only tricky thing with that is creating an event that is compatible with SimBiology's acceleration (that is, with the subset of the MATLAB language that can be used for code generation). Here's an example of modifying the Lotka-Volterra model to end early due to an event:

First, save the following function to myfunction.m:

function time = myfunction(time)
if time >= 0
    error("Ending simulation at time " + time);
end

Then, execute the following:

sbioloadproject('lotka');
threshold = m1.addparameter('threshold',1e6);
m1.addevent('y1 > threshold', 'z = myfunction(time)');
sbioaccelerate(m1);         % Ensure this model can be accelerated
simdata = sbiosimulate(m1); % Runs to completion
threshold.Value = 1e3;
simdata = sbiosimulate(m1); % Simulation errors

[Abed Alnaif]

Thank you, Arthur.