Using Sundials cvode solver

Hi All,

I'm currently using ode15s to solve a set of stiff differential equations.

[t, species]  = ode15s(@(t,s) factory(t,s), tspan , species0, options);

I would like to try solving the same set of odes using the CVODE solver in Sundials.

I checked some examples which show how to specify the solver type and use Sundials.

configsetObj = getconfigset(modelObj);
configsetObj.SolverType = 'sundials';
configsetObj.MaximumWallClock = 30;
configsetObj.MaximumNumberOfLogs = 100;
configsetObj.StopTime = 10;
[time, states] = sbiosimulate(modelObj);
plot(time,states)

I would like to know how modelObj should be defined.

[Deepa Maheshvare]

Hi All,

Any suggestions?

[Deepa Maheshvare]

Any suggestions?

[Walter Roberson]

No suggestions from me. I had no idea that facility existed until you asked your question.

[Deepa Maheshvare]

Thank you for the reponse.

I hope I could get some suggestions from the others.

[Star Strider]

I had to look that up. I found SUNDIALS Solvers as the only relevant documentation. I get the impression that these are stand-alone routines, however I have not explored the LLNL documentation for the software.

Answer 1

[Aditya]

Hi Deepa,

I understand that you want to solve set of stiff differential equations using the CVODE solver in Sundials and need help defining the “modelObj” for it.

To convert your ODE model to SimBiology, you can follow a direct approach by converting each differential equation into a rate rule. You can find an example of that here:

• https://www.mathworks.com/help/simbio/ug/rule-object.html#mw_fef86e0c-1589-4ff5-b866-0c8dfd230895

In addition, I recommend checking out the following resources to understand how to define a model object according to your specific needs.

• https://www.mathworks.com/help/simbio/ref/modelobject.html#bqu195b-7
• https://www.mathworks.com/help/simbio/gs/construct-a-simple-model.html

Hope this helps!

Answer 2

[Mike Croucher]

As of MATLAB R2024a, SUNDIALS is shipped with and supported directly in MATLAB. See my blog post for details

Faster Ordinary Differential Equations (ODEs) solvers and Sensitivity Analysis of Parameters: Introducing SUNDIALS support in MATLAB » The MATLAB Blog - MATLAB & Simulink (mathworks.com)

[Neil]

YOU FORGET TO MENTION WHICH VERSION OF SUNDIALS IS USED. ALSO COULD BE HELPFULL TO KNOW IF IT IS THE SAME WRAPPER THAT USES SIMBIOLOGY. THANKS

Answer 3

[Mohamed Elshami]

you need to redefine your problem instead of traditional method. In this definition you set the ode solver to your problem directly.

ode15s(@(t,s) factory(t,s), tspan , species0, options)

Starting from 2024 versions new solvers of sundials were added which are (cvodenonstiff, cvodestiff, and idas), to use any of them you should follow the updated new method to define ode functions, according your problem you need to rewrite it as follows:

d = ode(ODEFcn = @(t,s)[factory(t,s)]);
d.Solver = "cvodesStiff"; % or "cvodesNonstiff" , "idas" (all are sundials solvers)
d.InitialValue = species0;
d.InitialTime  = 0;
d.RelativeTolerance  = 1e-6;
d.AbsoluteTolerance  = 1e-6;
d.SolverOptions.MaxStep = 1e-2;
StartTime = 0;
StopTime  = 10;
Y = solve(d,StartTime,StopTime);

note that

• d: is an arbitrary object name just to further deal with the object handles (InitialValue, InitialTime,... etc).
• for the full list of handles of the ode object just type the object given name (d) in the command line then enter.