/**
* perform a stochastic ensemble calculation.
*
* :param: r an existing roadrunner obj, loaded with a mode.
* :param: n how many ensembles to run.
* :param: seed the seed value, use None to continue with previous
* random number stream.
* :param: start start time
* :param: stop stop time
* :param: ntps how many points display in the result.
*/
DoubleMatrix ensemble(RoadRunner &r, int n, unsigned long seed, double start, double stop, int npts) {
// set the seed value of the integrator
Integrator *itg = r.getIntegrator(Integrator::GILLESPIE);
itg->setItem("seed", seed);
// setup the simulation
// create a sim opt obj, loads itself with
// default values in ctor.
SimulateOptions o;
o.start = start;
o.duration = stop;
o.steps = npts;
// we should reset the model each time we simulate,
// set the RESET_MODEL bit.
o.flags |= SimulateOptions::RESET_MODEL;
o.integrator = Integrator::GILLESPIE;
// make a result var
DoubleMatrix result(npts+1, n+1);
for (int i = 0; i < n; ++i) {
const DoubleMatrix &sim = *r.simulate(&o);
// copy result data colum
for (int row = 0; row < npts+1; ++row) {
result(row, i+1) = sim(row, 1);
}
}
// copy result time column
const DoubleMatrix &sim = *r.getSimulationData();
// copy result data colum
for (int row = 0; row < npts+1; ++row) {
result(row, 0) = sim(row, 0);
}
return result;
}
