GillespieIntegrator::GillespieIntegrator(ExecutableModel* m,
const SimulateOptions* o) :
model(m),
timeScale(1.0),
stoichScale(1.0),
stoichRows(0),
stoichCols(0),
stoichData(0),
seed(defaultSeed()) // default value for mersene twister
{
if (o)
{
this->options = *o;
}
nReactions = model->getNumReactions();
reactionRates = new double[nReactions];
reactionRatesBuffer = new double[nReactions];
stateVectorSize = model->getStateVector(0);
stateVector = new double[stateVectorSize];
stateVectorRate = new double[stateVectorSize];
floatingSpeciesStart = stateVectorSize - model->getNumIndFloatingSpecies();
assert(floatingSpeciesStart >= 0);
// get rows and columns
model->getStoichiometryMatrix(&stoichRows, &stoichCols, 0);
stoichData = new double[stoichRows * stoichCols];
// fill stoichData
model->getStoichiometryMatrix(&stoichRows, &stoichCols, &stoichData);
setEngineSeed(seed);
}
void GillespieIntegrator::resetSettings()
{
Solver::resetSettings();
// Set default integrator settings.
addSetting("seed", defaultSeed(), "Seed", "Set the seed into the random engine. (ulong)", "(ulong) Set the seed into the random engine.");
addSetting("variable_step_size",false, "Variable Step Size", "Perform a variable time step simulation. (bool)", "(bool) Enabling this setting will allow the integrator to adapt the size of each time step. This will result in a non-uniform time column.");
addSetting("initial_time_step", 0.0, "Initial Time Step", "Specifies the initial time step size. (double)", "(double) Specifies the initial time step size.");
addSetting("minimum_time_step", 0.0, "Minimum Time Step", "Specifies the minimum absolute value of step size allowed. (double)", "(double) The minimum absolute value of step size allowed.");
addSetting("maximum_time_step", 0.0, "Maximum Time Step", "Specifies the maximum absolute value of step size allowed. (double)", "(double) The maximum absolute value of step size allowed.");
addSetting("nonnegative", false, "Non-negative species only", "Prevents species amounts from going negative during a simulation. (bool)", "(bool) Enforce non-negative species constraint.");
}
