SUNDIALS Solvers

SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) are part of a freely available third-party package developed at Lawrence Livermore National Laboratory. All other ODE solvers used for simulation of SimBiology® models, such as ode45 and ode15s, are part of the MATLAB® ODE suite. SimBiology currently (R2018b or later) uses SUNDIALS 3.1.0.

SimBiology always uses the SUNDIALS solver to perform sensitivity analysis on a model, regardless of what you have selected as the SolverType in the configuration set.

In addition, if you are estimating model parameters using sbiofit or the Fit Data program with one of these gradient-based estimation functions: fmincon, fminunc, lsqnonlin, or lsqcurvefit, SimBiology uses the SUNDIALS solver by default to calculate sensitivities and use them to improve fitting. If you are using sbiofit, you can turn off this sensitivity calculation feature by setting the 'SensitivityAnalysis' name-value pair argument to false. However, if you are using the Fit Data program, you cannot turn off this feature. It is recommended that you keep the sensitivity analysis feature on whenever possible for more accurate gradient approximations and better parameter fits.

When you specify sundials for the solver, the software chooses one of two SUNDIALS solvers, CVODE or IDA, as appropriate for your model:

  • CVODE is a solver for systems of ODEs, both nonstiff and stiff. This is used when a model has no algebraic rules.

  • IDA is a differential-algebraic equation (DAE) solver, used when one or more algebraic rules are present.

For more information on the SUNDIALS solvers, see https://www.llnl.gov/casc/sundials/description/description.html.

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