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::setValue(string key, const Variant& val)
{
Integrator::setValue(key, val);
/* In addition to typically value-setting behavior, some settings require further changes
within CVODE. */
if (key == "seed")
{
try
{
unsigned long seed = val.convert<unsigned long>();
setEngineSeed(seed);
}
catch (std::exception& e)
{
std::stringstream ss;
ss << "Could not convert the value \"" << val.toString();
ss << "\" to an unsigned long integer. " << endl;
ss << "The seed must be a number between 0 and ";
ss << std::numeric_limits<unsigned long>::max();
ss << "; error message: " << e.what() << ".";
throw std::invalid_argument(ss.str());
}
}
}
void GillespieIntegrator::setSeed(const rr::Variant& value)
{
try
{
unsigned long seed = value.convert<unsigned long>();
this->seed = seed;
setEngineSeed(seed);
}
catch(std::exception& e)
{
std::stringstream ss;
ss << "Could not convert the value \"" << value.toString();
ss << "\" to an unsigned long integer. " << endl;
ss << "The seed must be a number between 0 and ";
ss << std::numeric_limits<unsigned long>::max();
ss << "; error message: " << e.what() << ".";
throw std::invalid_argument(ss.str());
}
}
void GillespieIntegrator::initializeFromModel() {
nReactions = model->getNumReactions();
reactionRates = new double[nReactions];
reactionRatesBuffer = new double[nReactions];
stateVectorSize = model->getStateVector(0);
stateVector = new double[stateVectorSize];
stateVectorRate = new double[stateVectorSize];
eventStatus = std::vector<unsigned char>(model->getEventTriggers(0, 0, 0), false);
previousEventStatus = std::vector<unsigned char>(model->getEventTriggers(0, 0, 0), false);
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(getValue("seed").convert<unsigned long>());
}