bool CModelExpansion::SetOfModelElements::addObject(const CCopasiObject* x)
{
if (dynamic_cast<const CCompartment*>(x))
{
addCompartment(dynamic_cast<const CCompartment*>(x));
return true;
}
if (dynamic_cast<const CMetab*>(x))
{
addMetab(dynamic_cast<const CMetab*>(x));
return true;
}
if (dynamic_cast<const CReaction*>(x))
{
addReaction(dynamic_cast<const CReaction*>(x));
return true;
}
if (dynamic_cast<const CModelValue*>(x))
{
addGlobalQuantity(dynamic_cast<const CModelValue*>(x));
return true;
}
if (dynamic_cast<const CEvent*>(x))
{
addEvent(dynamic_cast<const CEvent*>(x));
return true;
}
return false;
}
void AudioContext::resume(Promise&& promise)
{
if (isOfflineContext()) {
promise.reject(INVALID_STATE_ERR);
return;
}
if (m_state == State::Running) {
promise.resolve(nullptr);
return;
}
if (m_state == State::Closed || !m_destinationNode) {
promise.reject(0);
return;
}
addReaction(State::Running, WTFMove(promise));
if (!willBeginPlayback())
return;
lazyInitialize();
RefPtr<AudioContext> strongThis(this);
m_destinationNode->resume([strongThis] {
strongThis->setState(State::Running);
});
}
void AudioContext::suspend(Promise&& promise)
{
if (isOfflineContext()) {
promise.reject(INVALID_STATE_ERR);
return;
}
if (m_state == State::Suspended) {
promise.resolve(nullptr);
return;
}
if (m_state == State::Closed || m_state == State::Interrupted || !m_destinationNode) {
promise.reject(0);
return;
}
addReaction(State::Suspended, WTFMove(promise));
if (!willPausePlayback())
return;
lazyInitialize();
RefPtr<AudioContext> strongThis(this);
m_destinationNode->suspend([strongThis] {
strongThis->setState(State::Suspended);
});
}
void CModelExpansion::SetOfModelElements::fillComplete(const CModel* pModel)
{
if (!pModel)
return;
size_t i;
for (i = 0; i < pModel->getCompartments().size(); ++i)
addCompartment(pModel->getCompartments()[i]);
for (i = 0; i < pModel->getMetabolites().size(); ++i)
addMetab(pModel->getMetabolites()[i]);
for (i = 0; i < pModel->getReactions().size(); ++i)
addReaction(pModel->getReactions()[i]);
for (i = 0; i < pModel->getModelValues().size(); ++i)
addGlobalQuantity(pModel->getModelValues()[i]);
for (i = 0; i < pModel->getEvents().size(); ++i)
addEvent(pModel->getEvents()[i]);
}
void AudioContext::close(Promise&& promise)
{
if (isOfflineContext()) {
promise.reject(INVALID_STATE_ERR);
return;
}
if (m_state == State::Closed || !m_destinationNode) {
promise.resolve(nullptr);
return;
}
addReaction(State::Closed, WTFMove(promise));
lazyInitialize();
RefPtr<AudioContext> strongThis(this);
m_destinationNode->close([strongThis] {
strongThis->setState(State::Closed);
strongThis->uninitialize();
});
}
void CModelExpansion::SetOfModelElements::fillDependencies(const CModel* pModel)
{
if (!pModel) return;
//create a combined set of all elements we know are to be copied
std::set< const CCopasiObject * > combinedSet;
std::set<const CCompartment*>::const_iterator itComp;
for (itComp = mCompartments.begin(); itComp != mCompartments.end(); ++itComp)
{
std::set< const CCopasiObject * > tmp = (*itComp)->getDeletedObjects();
combinedSet.insert(tmp.begin(), tmp.end());
}
std::set<const CMetab*>::const_iterator itMetab;
for (itMetab = mMetabs.begin(); itMetab != mMetabs.end(); ++itMetab)
{
std::set< const CCopasiObject * > tmp = (*itMetab)->getDeletedObjects();
combinedSet.insert(tmp.begin(), tmp.end());
}
std::set<const CReaction*>::const_iterator itReac;
for (itReac = mReactions.begin(); itReac != mReactions.end(); ++itReac)
{
std::set< const CCopasiObject * > tmp = (*itReac)->getDeletedObjects();
combinedSet.insert(tmp.begin(), tmp.end());
}
std::set<const CModelValue*>::const_iterator itQuant;
for (itQuant = mGlobalQuantities.begin(); itQuant != mGlobalQuantities.end(); ++itQuant)
{
std::set< const CCopasiObject * > tmp = (*itQuant)->getDeletedObjects();
combinedSet.insert(tmp.begin(), tmp.end());
}
/* Events do not contain any relevant objects.
std::set<const CEvent*>::const_iterator itEvent;
for (itEvent = mEvents.begin(); itEvent != mEvents.end(); ++itEvent)
{
std::set< const CCopasiObject * > tmp = (*itEvent)->getDeletedObjects();
combinedSet.insert(tmp.begin(), tmp.end());
}
*/
//ask the model for the dependencies
std::set< const CCopasiObject * > reacs, metabs, comps, values, events;
pModel->appendDependentModelObjects(combinedSet, reacs, metabs, comps, values, events);
//incorporate the results into the local sets
std::set< const CCopasiObject * >::const_iterator it;
for (it = reacs.begin(); it != reacs.end(); ++it)
addReaction(dynamic_cast<const CReaction*>(*it));
for (it = metabs.begin(); it != metabs.end(); ++it)
addMetab(dynamic_cast<const CMetab*>(*it));
for (it = comps.begin(); it != comps.end(); ++it)
addCompartment(dynamic_cast<const CCompartment*>(*it));
for (it = values.begin(); it != values.end(); ++it)
addGlobalQuantity(dynamic_cast<const CModelValue*>(*it));
for (it = events.begin(); it != events.end(); ++it)
addEvent(dynamic_cast<const CEvent*>(*it));
}
//-----------------------------------------------------------------------------
// Function : ReactionNetwork::addReaction
// Purpose : Create a new named reaction in the network
// Special Notes :
// Scope : public
// Creator : Tom Russo, SNL, Electrical and Microsystems Modeling
// Creation Date : 03/20/06
//-----------------------------------------------------------------------------
void ReactionNetwork::addReaction(const std::string &name)
{
N_DEV_Reaction dummy;
addReaction(name, dummy);
}
// this one sets up dx*dy majority vote problems without diffusion
MajorityVoteProblem::MajorityVoteProblem(Real length, int dx, int dy, uint numMolecules, uint nReds, uint numEncounters, Real reactionProb, Real recognitionError, const std::string &initScriptsPath)
: DiffusionModel(length, dx, dy), m_individual(false), m_isNonDiffusive(true)
{
if (numEncounters < 3) {
std::cout <<"ERROR: Need at least three encounters!\n";
exit(1);
}
// this list will hold all red and green species
// we need (i^2+i)/2 species per red and green
// where i is the number of encounters after which the species "votes"
uint maxSpecies = (numEncounters*numEncounters+numEncounters)/2;
std::vector<gpgmp::Species *> speciesListRed(maxSpecies);
std::vector<gpgmp::Species *> speciesListGreen(maxSpecies);
// add species and reactions corresponding to scheme:
// Rxy - red, has encountered x red and y green robots
// Gxy - green, has encountered x red and y green robots
uint c=0;
for (uint i=0; i<numEncounters; i++) {
for (uint j=0; j<numEncounters-i; j++) {
// add species
std::ostringstream snamered;
snamered << "R"<<i<<j;
speciesListRed[c] = addSpecies(snamered.str(), 0.);
std::ostringstream snamegreen;
snamegreen << "G"<<i<<j;
speciesListGreen[c] = addSpecies(snamegreen.str(),0.);
// print out
std::cout <<"Added species "<<snamered.str()<<" and "<<snamegreen.str()<<".\n";
// increase counter;
c++;
}
} // create species
// set diffusivity and drift for species
setParameter("diffX", 0.);
setParameter("diffY", 0.);
setParameter("driftX", 0.);
setParameter("driftY", 0.);
// set homogeneous diffusivity and drift
setComputeDriftDiffusivityMethod(gpgmp::DT_HOMOGENEOUS);
// these are the actual reaction probabilities for the correct reaction and the error reaction
double kcorrect = reactionProb*(1.-2.*recognitionError-recognitionError*recognitionError);
double kwrong1 = reactionProb*recognitionError;
double kwrongb = reactionProb*recognitionError*recognitionError;
// add reactions
// Gxy+Rwz -> Gx+1y + Rwz+1
// Gxy+Rwz -> Gxy+1 + Rw+1z (for recognition error)
uint cg = 0;
uint totnreacts=0.; // just debug counter to count number of reactions
for (uint x=0; x<numEncounters; x++) {
for (uint y=0; y<numEncounters-x; y++) {
// to name the reaction
std::ostringstream snamers;
std::ostringstream snamerd;
std::ostringstream snamerdw;
// find source and target species for green
Species *Gxy = speciesListGreen[cg];
snamers << "G"<<x<<y<<"("<<Gxy->id()<<")";
Species *Txp1y;
Species *Txyp1;
if ((x+y)==(numEncounters-1)) {
// target species is either G00 or R00
if (x>=y) {
// turns red
Txp1y = speciesListRed[0];
snamerd <<"R00"<<"("<<Txp1y->id()<<")";
// wrong decision
if (x>y) {
Txyp1 = speciesListRed[0];
snamerdw <<"R00"<<"("<<Txyp1->id()<<")";
}
else {
Txyp1 = speciesListGreen[0];
snamerdw <<"G00"<<"("<<Txyp1->id()<<")";
}
} else {
// stays green
Txp1y = speciesListGreen[0];
snamerd <<"G00"<<"("<<Txp1y->id()<<")";
// and the wrong decision stays green too
Txyp1 = speciesListGreen[0];
snamerdw <<"G00"<<"("<<Txyp1->id()<<")";
}
} else {
// target species is Gx+1y
Txp1y = speciesListGreen[cg+(numEncounters-x)];
snamerd <<"G"<<x+1<<y<<"("<<Txp1y->id()<<")";
// or Gxy+1
Txyp1 = speciesListGreen[cg+1];
snamerdw <<"G"<<x<<y+1<<"("<<Txyp1->id()<<")";
}
// now pair with all red robots
uint cr=0;
for (uint w=0; w<numEncounters; w++) {
for (uint z=0; z<numEncounters-w; z++) {
// find source and target species for red
Species *Rxy = speciesListRed[cr];
std::ostringstream sss;
std::ostringstream ssd;
std::ostringstream ssdw;
sss << "R"<<w<<z << "("<<Rxy->id()<<")";
Species *Twzp1;
Species *Twp1z;
if ((w+z)==(numEncounters-1)) {
// target species is either G00 or R00
if (w>z) {
// stays red
Twzp1 = speciesListRed[0];
ssd <<"R00" << "("<<Twzp1->id()<<")";
// and the wrong decision .. stays red too
Twp1z = speciesListRed[0];
ssdw <<"R00" << "("<<Twp1z->id()<<")";
} else {
// stays green
Twzp1 = speciesListGreen[0];
ssd <<"G00" << "("<<Twzp1->id()<<")";
if (w==z) {
Twp1z = speciesListRed[0];
ssdw <<"R00" << "("<<Twp1z->id()<<")";
} else {
Twp1z = speciesListGreen[0];
ssdw <<"G00" << "("<<Twp1z->id()<<")";
}
}
} else {
// target species is Rw+1z
Twzp1 = speciesListRed[cr+1];
ssd <<"R"<<w<<z+1<< "("<<Twzp1->id()<<")";
// and Rwzp1
Twp1z = speciesListRed[cr+(numEncounters-w)];
ssdw <<"R"<<w+1<<z<< "("<<Twp1z->id()<<")";
}
std::ostringstream rname, rnamew;
rname <<snamers.str()<<" + "<<sss.str()<<" -> "<<snamerd.str()<<" + " << ssd.str();
std::cout <<"Adding reaction "<<rname.str()<<".\n";
totnreacts++;
Reaction *r = addReaction (rname.str(), kcorrect, Gxy, Rxy);
r->setProductStoichiometry(Txp1y, 1);
if (Txp1y == Twzp1)
r->setProductStoichiometry(Twzp1, 2);
else
r->setProductStoichiometry(Twzp1, 1);
// and add wrong reaction if needed
if (recognitionError > 0) {
// both wrong
rnamew <<snamers.str()<<" + "<<sss.str()<<" -> "<<snamerdw.str()<<" + " << ssdw.str();
std::cout <<"Adding errenous reaction "<<rnamew.str()<<".\n"<<std::flush;
totnreacts++;
r = addReaction(rnamew.str(), kwrongb, Gxy, Rxy);
r->setProductStoichiometry(Txyp1, 1);
if (Txyp1 == Twp1z)
r->setProductStoichiometry(Twp1z, 2);
else
r->setProductStoichiometry(Twp1z, 1);
std::ostringstream rnamew1, rnamew2;
// first wrong
rnamew1 <<snamers.str()<<" + "<<sss.str()<<" -> "<<snamerdw.str()<<" + " << ssd.str();
std::cout <<"Adding errenous reaction (first wrong) "<<rnamew1.str()<<".\n"<<std::flush;
totnreacts++;
r = addReaction(rnamew.str(), kwrong1, Gxy, Rxy);
r->setProductStoichiometry(Txyp1, 1);
if (Txyp1 == Twzp1)
r->setProductStoichiometry(Twzp1, 2);
else
r->setProductStoichiometry(Twzp1, 1);
// second wrong
rnamew2 <<snamers.str()<<" + "<<sss.str()<<" -> "<<snamerd.str()<<" + " << ssdw.str();
std::cout <<"Adding errenous reaction (second wrong) "<<rnamew2.str()<<".\n"<<std::flush;
totnreacts++;
r = addReaction(rnamew2.str(), kwrong1, Gxy, Rxy);
r->setProductStoichiometry(Txp1y, 1);
if (Txp1y == Twp1z)
r->setProductStoichiometry(Twp1z, 2);
else
r->setProductStoichiometry(Twp1z, 1);
}
// increase counter
cr++;
} // pair with red robots z
} // pair with red robots w
// increase counter
cg++;
} // green robots y
} // green robots x
// Gxy+Gwz -> Gxy+1 + Gwz+1
for (uint x=0; x<maxSpecies; x++) {
for (uint y=x; y<maxSpecies; y++) {
// get source species
Species *G1 = speciesListGreen[x];
Species *G2 = speciesListGreen[y];
// get target species 1
Species *T1;
Species *T1wrong;
// is it at marginal position?
if (isMarginal(x, numEncounters)) {
// check if over changeover limit (see notebook index_computations.nb)
if (x > getChangeoverLimit(x, numEncounters)) {
// change to red
T1 = speciesListRed[0];
T1wrong = speciesListRed[0];
} else {
T1 = speciesListGreen[0];
// wrong species
if (x==getChangeoverLimit(x, numEncounters))
T1wrong = speciesListRed[0];
else
T1wrong = speciesListGreen[0];
}
} else {
T1 = speciesListGreen[x+1];
T1wrong = speciesListGreen[getNextRedPosition(x, numEncounters)];
}
// get target species 2
Species *T2;
Species *T2wrong;
// is it at marginal position?
if (isMarginal(y, numEncounters)) {
// check if over changeover limit (see notebook index_computations.nb)
if (y > getChangeoverLimit(y, numEncounters)) {
// change to red
T2 = speciesListRed[0];
T2wrong = speciesListRed[0];
} else {
T2 = speciesListGreen[0];
// wrong species
if (y==getChangeoverLimit(y, numEncounters))
T2wrong = speciesListRed[0];
else
T2wrong = speciesListGreen[0];
}
} else {
T2 = speciesListGreen[y+1];
T2wrong = speciesListGreen[getNextRedPosition(y, numEncounters)];
}
// print reaction
std::stringstream rname;
rname <<G1->id()<<" + "<<G2->id()<<" -> "<< T1->id()<<" + "<<T2->id();
std::cout <<"Adding reaction "<<rname.str() <<"\n"<<std::flush;
// and add it
totnreacts++;
Reaction *r = addReaction(rname.str(), kcorrect, G1, G2);
r->setProductStoichiometry(T1, 1);
if (T1 == T2)
r->setProductStoichiometry(T2, 2);
else
r->setProductStoichiometry(T2, 1);
// wrong reactions
if (recognitionError > 0) {
// first wrong
std::stringstream rnamew1;
rnamew1 << G1->id() << " + " << G2->id() <<" -> "<< T1wrong->id() << " + "<<T2->id();
std::cout <<"Adding erreneous (first wrong) reaction "<<rnamew1.str()<<"\n"<<std::flush;
totnreacts++;
r = addReaction(rnamew1.str(), kwrong1, G1, G2);
r->setProductStoichiometry(T1wrong, 1);
if (T1wrong == T2)
r->setProductStoichiometry(T2, 2);
else
r->setProductStoichiometry(T2, 1);
// second wrong
std::stringstream rnamew2;
rnamew2 << G1->id() << " + " << G2->id() <<" -> "<< T1->id() << " + "<<T2wrong->id();
std::cout <<"Adding erreneous (second wrong) reaction "<<rnamew2.str()<<"\n"<<std::flush;
totnreacts++;
r = addReaction(rnamew2.str(), kwrong1, G1, G2);
r->setProductStoichiometry(T1, 1);
if (T1== T2wrong)
r->setProductStoichiometry(T2wrong, 2);
else
r->setProductStoichiometry(T2wrong, 1);
// both wrong
std::stringstream rnamewb;
rnamewb << G1->id() << " + " << G2->id() <<" -> "<< T1wrong->id() << " + "<<T2wrong->id();
std::cout <<"Adding erreneous (both wrong) reaction "<<rnamewb.str()<<"\n"<<std::flush;
totnreacts++;
r = addReaction(rnamewb.str(), kwrongb, G1, G2);
r->setProductStoichiometry(T1wrong, 1);
if (T1wrong == T2wrong)
r->setProductStoichiometry(T2wrong, 2);
else
r->setProductStoichiometry(T2wrong, 1);
}
}
}
// Rxy+Rwz -> Rxy+1 + Rwz+1
for (uint x=0; x<maxSpecies; x++) {
for (uint y=x; y<maxSpecies; y++) {
// get source species
Species *R1 = speciesListRed[x];
Species *R2 = speciesListRed[y];
// get target species 1
Species *T1;
Species *T1wrong;
// is it at marginal position?
if (isMarginal(x, numEncounters)) {
// check if over changeover limit (see notebook index_computations.nb)
if (x >= getChangeoverLimit(x, numEncounters)) {
// change to red
T1 = speciesListRed[0];
// wrong species
if (x == getChangeoverLimit(x, numEncounters))
T1wrong = speciesListGreen[0];
else
T1wrong = speciesListRed[0];
} else {
T1 = speciesListGreen[0];
T1wrong = speciesListGreen[0];
}
} else {
T1 = speciesListRed[getNextRedPosition(x, numEncounters)];
T1wrong = speciesListRed[x+1];
}
// get target species 2
Species *T2;
Species *T2wrong;
// is it at marginal position?
if (isMarginal(y, numEncounters)) {
// check if over changeover limit (see notebook index_computations.nb)
if (y >= getChangeoverLimit(y, numEncounters)) {
// change to red
T2 = speciesListRed[0];
// wrong species
if (y == getChangeoverLimit(y, numEncounters))
T2wrong = speciesListGreen[0];
else
T2wrong = speciesListRed[0];
} else {
T2 = speciesListGreen[0];
T2wrong = speciesListGreen[0];
}
} else {
T2 = speciesListRed[getNextRedPosition(y, numEncounters)];
T2wrong = speciesListRed[y+1];
}
// print reaction
std::stringstream rname;
rname <<R1->id()<<" + "<<R2->id()<<" -> "<< T1->id()<<" + "<<T2->id();
std::cout <<"Adding reaction "<<rname.str() <<"\n"<<std::flush;
// and add it
totnreacts++;
Reaction *r = addReaction(rname.str(), kcorrect, R1, R2);
r->setProductStoichiometry(T1, 1);
if (T1 == T2)
r->setProductStoichiometry(T2, 2);
else
r->setProductStoichiometry(T2, 1);
// wrong reactions
if (recognitionError > 0) {
// first wrong
std::stringstream rnamew1;
rnamew1 << R1->id() <<" + " << R2->id() <<" -> " << T1wrong->id() << " + " << T2->id();
std::cout <<"Adding erreneous (first wrong) reaction "<<rnamew1.str() << "\n" << std::flush;
totnreacts++;
r = addReaction(rnamew1.str(), kwrong1, R1, R2);
r->setProductStoichiometry(T1wrong, 1);
if (T1wrong == T2)
r->setProductStoichiometry(T2, 2);
else
r->setProductStoichiometry(T2, 1);
// second wrong
std::stringstream rnamew2;
rnamew2 << R1->id() <<" + " << R2->id() <<" -> " << T1->id() << " + " << T2wrong->id();
std::cout <<"Adding erreneous (second wrong) reaction "<<rnamew2.str() << "\n" << std::flush;
totnreacts++;
r = addReaction(rnamew2.str(), kwrong1, R1, R2);
r->setProductStoichiometry(T1, 1);
if (T1== T2wrong)
r->setProductStoichiometry(T2wrong, 2);
else
r->setProductStoichiometry(T2wrong, 1);
// both wrong
std::stringstream rnamewb;
rnamewb << R1->id() <<" + " << R2->id() <<" -> " << T1wrong->id() << " + " << T2wrong->id();
std::cout <<"Adding erreneous (both wrong) reaction "<<rnamewb.str() << "\n" << std::flush;
totnreacts++;
r = addReaction(rnamewb.str(), kwrongb, R1, R2);
r->setProductStoichiometry(T1wrong, 1);
if (T1wrong == T2wrong)
r->setProductStoichiometry(T2wrong, 2);
else
r->setProductStoichiometry(T2wrong, 1);
}
}
}
std::cout <<"Added "<<totnreacts<<" reactions.\n";
std::cout <<"Reaction propensities: no error = "<<kcorrect<<", one wrong = "<< kwrong1 <<" both wrong = "<<kwrongb
<<"Sum = "<<(kcorrect + 2. * kwrong1 + kwrongb)<<"\n"<<std::flush;
/*
// Gxy+Gwz -> Gxy+1 + Gwz+1
cg = 0;
totnreacts=0;
for (uint x=0; x<numEncounters; x++) {
for (uint y=0; y<numEncounters-x; y++) {
// to name the reaction
std::ostringstream snamers;
std::ostringstream snamerd;
// find source and target species for green
Species *Gxy = speciesListGreen[cg];
snamers << "G"<<x<<y<<"("<<Gxy->id()<<")";
Species *Txyp1;
if ((x+y)==(numEncounters-1)) {
// target species is either G00 or R00
if (x>y) {
// turns red
Txyp1 = speciesListRed[0];
snamerd <<"R00"<<"("<<Txyp1->id()<<")";
} else {
// stays green
Txyp1 = speciesListGreen[0];
snamerd <<"G00"<<"("<<Txyp1->id()<<")";
}
} else {
// target species is Gxyp1
Txyp1 = speciesListGreen[cg+1];
snamerd <<"G"<<x<<y+1<<"("<<Txyp1->id()<<")";
}
// now pair with all other green robots
for (uint w=x; w<numEncounters; w++) {
for (uint z=x; z<numEncounters-w; z++) {
// compute index to second source species
// TODODODODO: you'll need to continue here ..
// come up with a function to compute the speciesindex from w and z
// and then assign cgg to it
// and then compare to the notebook with nencounters=3 (mesoscopic_reactions.nb)
// and then you need to adapt the HDF5 writer too
// and then just do a couple of runs with this problem and see how it compares to spatial
uint cgg=getSpeciesIndexFrom2D(w, z, numEncounters);
// find source and target species for red
Species *GGxy = speciesListGreen[cgg];
std::ostringstream sss;
std::ostringstream ssd;
sss << "G"<<w<<z<<"("<<GGxy->id()<<")";
Species *Twzp1;
if ((w+z)==(numEncounters-1)) {
// target species is either G00 or R00
if (w>z) {
// turns red
Twzp1 = speciesListRed[0];
ssd <<"R00"<<"("<<Twzp1->id()<<")";
} else {
// stays green
Twzp1 = speciesListGreen[0];
ssd <<"G00"<<"("<<Twzp1->id()<<")";
}
} else {
// target species is Gwzp1
Twzp1 = speciesListGreen[cgg+1];
ssd <<"G"<<w<<z+1<<"("<<Twzp1->id()<<")";
}
std::stringstream rname;
rname << snamers.str()<<" + "<<sss.str()<<" -> "<<snamerd.str();
std::cout <<"Adding reaction "<< rname.str() <<" + " << ssd.str()<<".\n"<<std::flush;
totnreacts++;
Reaction *r = addReaction(rname.str(), reactionProb, Gxy, GGxy);
r->setProductStoichiometry(Txyp1, 1);
if (Twzp1 == Txyp1)
r->setProductStoichiometry(Twzp1, 2);
else
r->setProductStoichiometry(Twzp1, 1);
// increase counter
cgg++;
} // pair with other green robots z
} // pair with other green robots w
// increase counter
cg++;
} // green robots y
} // green robots x
std::cout <<"Added a total of "<<totnreacts<<" reactions in the green self-reaction part.\n";
exit(1);
// Rxy+Rwz -> Rxy+1 + Rwz+1
uint cr = 0;
for (uint x=0; x<numEncounters; x++) {
for (uint y=0; y<numEncounters-x; y++) {
// to name the reaction
std::ostringstream snamers;
std::ostringstream snamerd;
// find source and target species for green
Species *Rxy = speciesListRed[cr];
snamers << "R"<<x<<y<<"("<<Rxy->id()<<")";
Species *Txp1y;
if ((x+y)==(numEncounters-1)) {
// target species is either G00 or R00
if (x>=y) {
// turns red
Txp1y = speciesListRed[0];
snamerd <<"R00"<<"("<<Txp1y->id()<<")";
} else {
// stays green
Txp1y = speciesListGreen[0];
snamerd <<"G00"<<"("<<Txp1y->id()<<")";
}
} else {
// target species is Gxyp1
Txp1y = speciesListRed[cr+(numEncounters-x)];
snamerd <<"R"<<x+1<<y<<"("<<Txp1y->id()<<")";
}
// now pair with all other red robots
uint crr=0;
for (uint w=0; w<numEncounters; w++) {
for (uint z=0; z<numEncounters-w; z++) {
// find source and target species for red
Species *RRxy = speciesListRed[crr];
std::ostringstream sss;
std::ostringstream ssd;
sss << "R"<<w<<z<<"("<<RRxy->id()<<")";
Species *Twp1z;
if ((w+z)==(numEncounters-1)) {
// target species is either G00 or R00
if (w>=z) {
// turns red
Twp1z = speciesListRed[0];
ssd <<"R00"<<"("<<Twp1z->id()<<")";
} else {
// stays green
Twp1z = speciesListGreen[0];
ssd <<"G00"<<"("<<Twp1z->id()<<")";
}
} else {
// target species is Rwzp1
Twp1z = speciesListRed[crr+(numEncounters-w)];
ssd <<"R"<<w+1<<z<<"("<<Twp1z->id()<<")";
}
std::stringstream rname;
rname << snamers.str()<<" + "<<sss.str()<<" -> "<<snamerd.str()<<" + " << ssd.str();
std::cout <<"Adding reaction "<< rname.str() <<".\n";
Reaction *r = addReaction(rname.str(), reactionProb, Rxy, RRxy);
r->setProductStoichiometry(Txp1y, 1);
if (Txp1y == Twp1z)
r->setProductStoichiometry(Twp1z, 2);
else
r->setProductStoichiometry(Twp1z, 1);
// increase counter
crr++;
} // pair with other red robots z
} // pair with other red robots w
// increase counter
cr++;
} // green robots y
} // green robots x
*/
// distribute species randomly
/*
Compartment *source = addCompartment("Source", 0, 0, dx-1, dy-1);
source->setInitialAmount(speciesListRed[0], nReds, gpgmp::RandomDistribution);
source->setInitialAmount(speciesListGreen[0], numMolecules-nReds, gpgmp::RandomDistribution);
*/
// load init script
loadInitScript((boost::filesystem::path(initScriptsPath) / "init_majority_no_diffusion.py").string());
// add script parameters
setParameter("numMolecules", numMolecules);
setParameter("p", static_cast<float>(nReds)/static_cast<float>(numMolecules));
setRegenerateInitStates(true);
}
// sets up the toy model
//
MajorityVoteProblem::MajorityVoteProblem(Real length, int dx, int dy, uint numMolecules, uint nReds, Real reactionProb, const std::string &initScriptsPath)
: DiffusionModel(length, dx, dy), m_individual(false), m_isNonDiffusive(true)
{
// add four species R_0, R_1, G_0, G_1
Species *R0 = addSpecies("R0", 0.);
Species *R1 = addSpecies("R1", 0.);
Species *G0 = addSpecies("G0", 0.);
Species *G1 = addSpecies("G1", 0.);
// set diffusivity and drift for species
setParameter("diffX", 0.);
setParameter("diffY", 0.);
setParameter("driftX", 0.);
setParameter("driftY", 0.);
// set homogeneous diffusivity and drift
setComputeDriftDiffusivityMethod(gpgmp::DT_HOMOGENEOUS);
// add reactions
// R0 + G0 -> R1 + G1 (i)
Reaction *r1 = addReaction("R0 + G0 -> R1 + G1", reactionProb, R0, G0);
r1 -> setProductStoichiometry(R1, 1);
r1 -> setProductStoichiometry(G1, 1);
// R0 + G1 -> R1 + R0 (ii)
Reaction *r2 = addReaction("R0 + G1 -> R1 + R0", reactionProb, R0, G1);
r2 -> setProductStoichiometry(R1, 1);
r2 -> setProductStoichiometry(R0, 1);
// R1 + G0 -> G0 + G1 (iii)
Reaction *r3 = addReaction("R1 + G0 -> G0 + G1", reactionProb, R1, G0);
r3 -> setProductStoichiometry(G1, 1);
r3 -> setProductStoichiometry(G0, 1);
// R1 + G1 -> G0 + R0 (iv)
Reaction *r4 = addReaction("R1 + G1 -> G0 + R0", reactionProb, R1, G1);
r4 -> setProductStoichiometry(G0, 1);
r4 -> setProductStoichiometry(R0, 1);
// R0 + R1 -> R0 + R0 (v)
Reaction *r5 = addReaction("R0 + R1 -> R0 + R0", reactionProb, R0, R1);
r5 -> setProductStoichiometry(R0, 2);
// R1 + R1 -> R0 + R0 (vi)
Reaction *r6 = addReaction("R1 + R1 -> R0 + R0", reactionProb, R1, R1);
r6 -> setProductStoichiometry(R0, 2);
// G0 + G1 -> G0 + G0 (vii)
Reaction *r7 = addReaction("G0 + G1 -> G0 + G0", reactionProb, G0, G1);
r7 -> setProductStoichiometry(G0, 2);
// G1 + G1 -> G0 + G0 (viii)
Reaction *r8 = addReaction("G1 + G1 -> G0 + G0", reactionProb, G1, G1);
r8 -> setProductStoichiometry(G0, 2);
// load init script
loadInitScript((boost::filesystem::path(initScriptsPath) / "init_majority_no_diffusion.py").string());
// add script parameters
setParameter("numMolecules", numMolecules);
setParameter("p", static_cast<float>(nReds)/static_cast<float>(numMolecules));
setRegenerateInitStates(true);
}
MajorityVoteProblem::MajorityVoteProblem(Real length, int dx, int dy,
Real diffX, Real diffY,
Real mux, Real muy,
uint numMolecules, uint nReds,
uint numEncounters,
Real reactionProb,const std::string &initScriptsPath)
: DiffusionModel(length, dx, dy), m_individual(false), m_isNonDiffusive(false)
{
// this list will hold all red and green species
// we need (i^2+i)/2 species per red and green
// where i is the number of encounters after which the species "votes"
uint maxSpecies = (numEncounters*numEncounters+numEncounters)/2;
std::vector<gpgmp::Species *> speciesListRed(maxSpecies);
std::vector<gpgmp::Species *> speciesListGreen(maxSpecies);
// add species and reactions corresponding to scheme:
// Rxy - red, has encountered x red and y green robots
// Gxy - green, has encountered x red and y green robots
uint c=0;
for (uint i=0; i<numEncounters; i++) {
for (uint j=0; j<numEncounters-i; j++) {
// add species
std::ostringstream snamered;
snamered << "R"<<i<<j;
speciesListRed[c] = addSpecies(snamered.str(), diffX);
std::ostringstream snamegreen;
snamegreen << "G"<<i<<j;
speciesListGreen[c] = addSpecies(snamegreen.str(),diffX);
// print out
std::cout <<"Added species "<<snamered.str()<<" and "<<snamegreen.str()<<".\n";
// increase counter;
c++;
}
} // create species
// set diffusivity and drift for species
setParameter("diffX", diffX);
setParameter("diffY", diffY);
setParameter("driftX", mux);
setParameter("driftY", muy);
// set homogeneous diffusivity and drift
setComputeDriftDiffusivityMethod(gpgmp::DT_HOMOGENEOUS);
// add reactions
// Gxy+Rwz -> Gx+1y + Rwz+1
uint cg = 0;
for (uint x=0; x<numEncounters; x++) {
for (uint y=0; y<numEncounters-x; y++) {
// to name the reaction
std::ostringstream snamers;
std::ostringstream snamerd;
// find source and target species for green
Species *Gxy = speciesListGreen[cg];
snamers << "G"<<x<<y<<"("<<Gxy->id()<<")";
Species *Txp1y;
if ((x+y)==(numEncounters-1)) {
// target species is either G00 or R00
if (x>=y) {
// turns red
Txp1y = speciesListRed[0];
snamerd <<"R00"<<"("<<Txp1y->id()<<")";
} else {
// stays greenstd::map<std::string, std::vector<Real> > &propertiesA = speciesA->getIndividualProperties();
Txp1y = speciesListGreen[0];
snamerd <<"G00"<<"("<<Txp1y->id()<<")";
}
} else {
// target species is Gx+1y
Txp1y = speciesListGreen[cg+(numEncounters-x)];
snamerd <<"G"<<x+1<<y<<"("<<Txp1y->id()<<")";
}
// now pair with all red robots
uint cr=0;
for (uint w=0; w<numEncounters; w++) {
for (uint z=0; z<numEncounters-w; z++) {
// find source and target species for red
Species *Rxy = speciesListRed[cr];
std::ostringstream sss;
std::ostringstream ssd;
sss << "R"<<w<<z << "("<<Rxy->id()<<")";
Species *Twzp1;
if ((w+z)==(numEncounters-1)) {
// target species is either G00 or R00
if (w>z) {
// turns red
Twzp1 = speciesListRed[0];
ssd <<"R00" << "("<<Twzp1->id()<<")";
} else {
// stays green
Twzp1 = speciesListGreen[0];
ssd <<"G00" << "("<<Twzp1->id()<<")";
}
} else {
// target species is Rw+1z
Twzp1 = speciesListRed[cr+1];
ssd <<"R"<<w<<z+1<< "("<<Twzp1->id()<<")";
}
std::ostringstream rname;
rname <<snamers.str()<<" + "<<sss.str()<<" -> "<<snamerd.str()<<" + " << ssd.str();
std::cout <<"Adding reaction "<<rname.str()<<".\n";
Reaction *r = addReaction (rname.str(), reactionProb, Gxy, Rxy);
r->setProductStoichiometry(Txp1y, 1);
if (Txp1y == Twzp1)
r->setProductStoichiometry(Twzp1, 2);
else
r->setProductStoichiometry(Twzp1, 1);
// increase counter
cr++;
} // pair with red robots z
} // pair with red robots w
// increase counter
cg++;
} // green robots y
} // green robots x
// Gxy+Gwz -> Gxy+1 + Gwz+1
cg = 0;
for (uint x=0; x<numEncounters; x++) {
for (uint y=0; y<numEncounters-x; y++) {
// to name the reaction
std::ostringstream snamers;
std::ostringstream snamerd;
// find source and target species for green
Species *Gxy = speciesListGreen[cg];
snamers << "G"<<x<<y<<"("<<Gxy->id()<<")";
Species *Txyp1;
if ((x+y)==(numEncounters-1)) {
// target species is either G00 or R00
if (x>y) {
// turns red
Txyp1 = speciesListRed[0];
snamerd <<"R00"<<"("<<Txyp1->id()<<")";
} else {
// stays green
Txyp1 = speciesListGreen[0];
snamerd <<"G00"<<"("<<Txyp1->id()<<")";
}
} else {
// target species is Gxyp1
Txyp1 = speciesListGreen[cg+1];
snamerd <<"G"<<x<<y+1<<"("<<Txyp1->id()<<")";
}
// now pair with all other green robots
uint cgg=0;
for (uint w=0; w<numEncounters; w++) {
for (uint z=0; z<numEncounters-w; z++) {
// find source and target species for red
Species *GGxy = speciesListGreen[cgg];
std::ostringstream sss;
std::ostringstream ssd;
sss << "G"<<w<<z<<"("<<GGxy->id()<<")";
Species *Twzp1;
if ((w+z)==(numEncounters-1)) {
// target species is either G00 or R00
if (w>z) {
// turns red
Twzp1 = speciesListRed[0];
ssd <<"R00"<<"("<<Twzp1->id()<<")";
} else {
// stays green
Twzp1 = speciesListGreen[0];
ssd <<"G00"<<"("<<Twzp1->id()<<")";
}
} else {
// target species is Gwzp1
Twzp1 = speciesListGreen[cgg+1];
ssd <<"G"<<w<<z+1<<"("<<Twzp1->id()<<")";
}
std::stringstream rname;
rname << snamers.str()<<" + "<<sss.str()<<" -> "<<snamerd.str();
std::cout <<"Adding reaction "<< rname.str() <<" + " << ssd.str()<<".\n";
Reaction *r = addReaction(rname.str(), reactionProb, Gxy, GGxy);
r->setProductStoichiometry(Txyp1, 1);
if (Twzp1 == Txyp1)
r->setProductStoichiometry(Twzp1, 2);
else
r->setProductStoichiometry(Twzp1, 1);
// increase counter
cgg++;
} // pair with other green robots z
} // pair with other green robots w
// increase counter
cg++;
} // green robots y
} // green robots x
// Rxy+Rwz -> Rxy+1 + Rwz+1
uint cr = 0;
for (uint x=0; x<numEncounters; x++) {
for (uint y=0; y<numEncounters-x; y++) {
// to name the reaction
std::ostringstream snamers;
std::ostringstream snamerd;
// find source and target species for green
Species *Rxy = speciesListRed[cr];
snamers << "R"<<x<<y<<"("<<Rxy->id()<<")";
Species *Txp1y;
if ((x+y)==(numEncounters-1)) {
// target species is either G00 or R00
if (x>=y) {
// turns red
Txp1y = speciesListRed[0];
snamerd <<"R00"<<"("<<Txp1y->id()<<")";
} else {
// stays green
Txp1y = speciesListGreen[0];
snamerd <<"G00"<<"("<<Txp1y->id()<<")";
}
} else {
// target species is Gxyp1
Txp1y = speciesListRed[cr+(numEncounters-x)];
snamerd <<"R"<<x+1<<y<<"("<<Txp1y->id()<<")";
}
// now pair with all other red robots
uint crr=0;
for (uint w=0; w<numEncounters; w++) {
for (uint z=0; z<numEncounters-w; z++) {
// find source and target species for red
Species *RRxy = speciesListRed[crr];
std::ostringstream sss;
std::ostringstream ssd;
sss << "R"<<w<<z<<"("<<RRxy->id()<<")";
Species *Twp1z;
if ((w+z)==(numEncounters-1)) {
// target species is either G00 or R00
if (w>=z) {
// turns red
Twp1z = speciesListRed[0];
ssd <<"R00"<<"("<<Twp1z->id()<<")";
} else {
// stays green
Twp1z = speciesListGreen[0];
ssd <<"G00"<<"("<<Twp1z->id()<<")";
}
} else {
// target species is Rwzp1
Twp1z = speciesListRed[crr+(numEncounters-w)];
ssd <<"R"<<w+1<<z<<"("<<Twp1z->id()<<")";
}
std::stringstream rname;
rname << snamers.str()<<" + "<<sss.str()<<" -> "<<snamerd.str()<<" + " << ssd.str();
std::cout <<"Adding reaction "<< rname.str() <<".\n";
Reaction *r = addReaction(rname.str(), reactionProb, Rxy, RRxy);
r->setProductStoichiometry(Txp1y, 1);
if (Txp1y == Twp1z)
r->setProductStoichiometry(Twp1z, 2);
else
r->setProductStoichiometry(Twp1z, 1);
// increase counter
crr++;
} // pair with other red robots z
} // pair with other red robots w
// increase counter
cr++;
} // green robots y
} // green robots x
// distribute species randomly
/*
Compartment *source = addCompartment("Source", 0, 0, dx-1, dy-1);
source->setInitialAmount(speciesListRed[0], nReds, gpgmp::RandomDistribution);
source->setInitialAmount(speciesListGreen[0], numMolecules-nReds, gpgmp::RandomDistribution);
*/
// load init script
loadInitScript((boost::filesystem::path(initScriptsPath) / "init_majority.py").string());
// add script parameters
setParameter("numMolecules", numMolecules);
setParameter("p", static_cast<float>(nReds)/static_cast<float>(numMolecules));
setRegenerateInitStates(true);
}
