boost::shared_ptr<AbstractStimulusFunction> AbstractStimulusFactory<ELEMENT_DIM,SPACE_DIM>::CreateStimulusForNode(Node<SPACE_DIM>* pNode)
{
//this is the default implementation
boost::shared_ptr<ZeroStimulus> p_stim ( new ZeroStimulus() );
return p_stim;
}
void TestSteadyStateRunnerConverges(void) throw(Exception)
{
#ifdef CHASTE_CVODE
//////////// DEFINE PARAMETERS ///////////////
// Get the frequency
double hertz = 1.0;
///////// END DEFINE PARAMETERS ////////////////////////
// Setup a CVODE model that has empty solver and stimulus
boost::shared_ptr<RegularStimulus> p_stimulus;
boost::shared_ptr<AbstractIvpOdeSolver> p_solver;
boost::shared_ptr<AbstractCvodeCell> p_model(new CellShannon2004FromCellMLCvode(p_solver, p_stimulus));
// Get it to use the default stimulus from CellML
boost::shared_ptr<RegularStimulus> p_reg_stim = p_model->UseCellMLDefaultStimulus();
{ // Test that the steady state analysis throws a nice error if we try to run it with a non-RegularStimulus
boost::shared_ptr<ZeroStimulus> p_stim(new ZeroStimulus());
p_model->SetStimulusFunction(p_stim);
SteadyStateRunner bad_steady_runner(p_model);
TS_ASSERT_THROWS_THIS(bad_steady_runner.RunToSteadyState(),
"Steady State approximations only work for models with RegularStimulus objects.");
// Reset to a sensible stimulus function.
p_model->SetStimulusFunction(p_reg_stim);
}
p_reg_stim->SetPeriod(1000.0/hertz);
// Note that increasing the strictness of the tolerances here (default is 1e-5, 1e-7)
// actually leads to a faster convergence to steady state, as a model solved in
// a sloppy way might never actually get close to its true limit cycle!
p_model->SetTolerances(1e-6,1e-8);
/**
* STEADY STATE PACING EXPERIMENT
*/
/*
* HOW_TO_TAG Cardiac/Cell Models
* Get a cardiac cell model to (roughly) a steady state, given a regular stimulus, using the `SteadyStateRunner` class.
*/
SteadyStateRunner steady_runner(p_model);
bool result;
// Here we don't reach steady state by max num paces
steady_runner.SetMaxNumPaces(1u);
result = steady_runner.RunToSteadyState();
TS_ASSERT_EQUALS(result,false);
// Here we do reach the steady state OK.
steady_runner.SetMaxNumPaces(10000u);
result = steady_runner.RunToSteadyState();
TS_ASSERT_EQUALS(result,true);
// Your mileage may vary. 32-bit machine, default build gives 520 evaluations, 484 on recent 64-bit CVODE.
TS_ASSERT_LESS_THAN(steady_runner.GetNumEvaluations(),550u);
// For coverage
TS_ASSERT_THROWS_THIS(steady_runner.SetMaxNumPaces(0u),
"Please set a maximum number of paces that is positive");
#else
std::cout << "CVODE must be enabled for the steady state runner to work." << std::endl;
#endif //_CHASTE_CVODE
}
