double GillespieIntegrator::integrate(double t, double hstep)
{
double tf = 0;
bool singleStep;
assert(hstep > 0 && "hstep must be > 0");
if (options.integratorFlags & VARIABLE_STEP)
{
if (options.minimumTimeStep > 0.0)
{
tf = t + options.minimumTimeStep;
singleStep = false;
}
else
{
tf = t + hstep;
singleStep = true;
}
}
else
{
tf = t + hstep;
singleStep = false;
}
Log(Logger::LOG_DEBUG) << "ssa(" << t << ", " << tf << ")";
// get the initial state vector
model->setTime(t);
model->getStateVector(stateVector);
while (t < tf)
{
// random uniform numbers
double r1 = urand();
double r2 = urand();
assert(r1 > 0 && r1 <= 1 && r2 >= 0 && r2 <= 1);
// sum of propensities
double s = 0;
// next time
double tau = 0;
// get the 'propensity' -- reaction rates
model->getReactionRates(nReactions, 0, reactionRates);
// sum the propensity
for (int k = 0; k < nReactions; k++)
{
Log(Logger::LOG_DEBUG) << "reac rate: " << k << ": "
<< reactionRates[k];
// if reaction rate is negative, that means reaction goes in reverse,
// this is fine, we just have to reverse the stoichiometry,
// but still need to sum the absolute value of the propensities
// to get tau.
s += std::abs(reactionRates[k]);
}
// sample tau
if (s > 0)
{
tau = -log(r1) / s;
}
else
{
// no reaction occurs
return std::numeric_limits<double>::infinity();
}
t = t + tau;
// select reaction
int reaction = -1;
double sp = 0.0;
r2 = r2 * s;
for (int i = 0; i < nReactions; ++i)
{
sp += std::abs(reactionRates[i]);
if (r2 < sp)
{
reaction = i;
break;
}
}
assert(reaction >= 0 && reaction < nReactions);
// update chemical species
// if rate is negative, means reaction goes in reverse, so
// multiply by sign
double sign = (reactionRates[reaction] > 0)
- (reactionRates[reaction] < 0);
for (int i = floatingSpeciesStart; i < stateVectorSize; ++i)
{
stateVector[i] = stateVector[i]
+ getStoich(i - floatingSpeciesStart, reaction)
* stoichScale * sign;
if(stateVector[i] < 0.0) {
Log(Logger::LOG_WARNING) << "Error, negative value of "
<< stateVector[i]
<< " encountred for floating species "
<< model->getFloatingSpeciesId(i - floatingSpeciesStart);
t = std::numeric_limits<double>::infinity();
}
}
// rates could be time dependent
model->setTime(t);
model->setStateVector(stateVector);
if (singleStep)
{
return t;
}
}
return t;
}
double GillespieIntegrator::integrate(double t, double hstep)
{
double tf = 0;
bool singleStep;
assert(hstep > 0 && "hstep must be > 0");
if (getValue("variable_step_size").convert<bool>())
{
if (getValue("minimum_time_step").convert<double>() > 0.0)
{
tf = t + getValue("minimum_time_step").convert<double>();
singleStep = false;
}
else
{
tf = t + hstep;
singleStep = true;
}
}
else
{
tf = t + hstep;
singleStep = false;
}
Log(Logger::LOG_DEBUG) << "ssa(" << t << ", " << tf << ")";
// get the initial state vector
model->setTime(t);
model->getStateVector(stateVector);
while (t < tf)
{
// random uniform numbers
double r1 = urand();
double r2 = urand();
assert(r1 > 0 && r1 <= 1 && r2 >= 0 && r2 <= 1);
// sum of propensities
double s = 0;
// next time
double tau = 0;
// get the 'propensity' -- reaction rates
model->getReactionRates(nReactions, 0, reactionRates);
// sum the propensity
for (int k = 0; k < nReactions; k++)
{
Log(Logger::LOG_DEBUG) << "reac rate: " << k << ": "
<< reactionRates[k];
// if reaction rate is negative, that means reaction goes in reverse,
// this is fine, we just have to reverse the stoichiometry,
// but still need to sum the absolute value of the propensities
// to get tau.
s += std::abs(reactionRates[k]);
}
// sample tau
if (s > 0)
{
tau = -log(r1) / s;
}
else
{
// no reaction occurs
return std::numeric_limits<double>::infinity();
}
t = t + tau;
// select reaction
int reaction = -1;
double sp = 0.0;
r2 = r2 * s;
for (int i = 0; i < nReactions; ++i)
{
sp += std::abs(reactionRates[i]);
if (r2 < sp)
{
reaction = i;
break;
}
}
assert(reaction >= 0 && reaction < nReactions);
// update chemical species
// if rate is negative, means reaction goes in reverse, so
// multiply by sign
double sign = (reactionRates[reaction] > 0)
- (reactionRates[reaction] < 0);
bool skip = false;
if (getValueAsBool("nonnegative")) {
// skip reactions which cause species amts to become negative
for (int i = floatingSpeciesStart; i < stateVectorSize; ++i) {
if (stateVector[i]
+ getStoich(i - floatingSpeciesStart, reaction)
* stoichScale * sign < 0.0) {
skip = true;
break;
}
}
}
if (!skip) {
for (int i = floatingSpeciesStart; i < stateVectorSize; ++i)
{
stateVector[i] = stateVector[i]
+ getStoich(i - floatingSpeciesStart, reaction)
* stoichScale * sign;
if (stateVector[i] < 0.0) {
Log(Logger::LOG_WARNING) << "Error, negative value of "
<< stateVector[i]
<< " encountred for floating species "
<< model->getFloatingSpeciesId(i - floatingSpeciesStart);
t = std::numeric_limits<double>::infinity();
}
}
}
// rates could be time dependent
model->setTime(t);
model->setStateVector(stateVector);
// events
bool triggered = false;
model->getEventTriggers(eventStatus.size(), NULL, eventStatus.size() ? &eventStatus[0] : NULL);
for(int k_=0; k_<eventStatus.size(); ++k_) {
if (eventStatus.at(k_))
triggered = true;
}
if (triggered) {
applyEvents(t, previousEventStatus);
}
if (eventStatus.size())
memcpy(&previousEventStatus[0], &eventStatus[0], eventStatus.size()*sizeof(unsigned char));
if (singleStep)
{
return t;
}
}
return t;
}
