void Phase::addUniqueSpecies(const std::string& name_, const doublereal* comp,
doublereal charge_, doublereal size_)
{
for (size_t k = 0; k < m_kk; k++) {
if (m_speciesNames[k] == name_) {
// We have found a match. Do some compatibility checks.
for (size_t i = 0; i < m_mm; i++) {
if (comp[i] != m_speciesComp[k * m_mm + i]) {
throw CanteraError("addUniqueSpecies",
"Duplicate species have different "
"compositions: " + name_);
}
}
if (charge_ != m_speciesCharge[k]) {
throw CanteraError("addUniqueSpecies",
"Duplicate species have different "
"charges: " + name_);
}
if (size_ != m_speciesSize[k]) {
throw CanteraError("addUniqueSpecies",
"Duplicate species have different "
"sizes: " + name_);
}
return;
}
}
addSpecies(name_, comp, charge_, size_);
}
/**
Sets up the species and the source compartment. We use the pre-defined
drift-diffusion method gpgmp::DT_ORNSTEIN_UHLENBECK and set the kernel
parameters accordingly.
\see setComputeDriftDiffusivityMethod
\see setParameter
*/
OrnsteinUhlenbeckProblem::OrnsteinUhlenbeckProblem(Real length, int dx, int dy,
Real diffusivityX, Real diffusivityY,
Real gxx, Real gxy, Real gyx, Real gyy,
int numMolecules)
: DiffusionModel(length, dx, dy)
{
// one species
Species *speciesA = addSpecies("A", 1.);
// set boundary mask
const cl_int4 boundaryMask = {{1, 1, 1, 1}};
const cl_int4 sourceMask = {{0, 0, 0, 0}};
setBoundaryMasks(boundaryMask, sourceMask);
// add source compartment
Compartment *compartmentSource = new Compartment("TrueSource", dx/4,dy/4, dx/4, dy/4);
compartmentSource->setInitialAmount(speciesA, numMolecules, gpgmp::HomogeneousDistribution);
addCompartment(compartmentSource);
// add user parameters for kernel
setParameter("diffX", diffusivityX);
setParameter("diffY", diffusivityY);
setParameter("gammaXX", gxx);
setParameter("gammaXY", gxy);
setParameter("gammaYX", gyx);
setParameter("gammaYY", gyy);
// set OU method
setComputeDriftDiffusivityMethod(gpgmp::DT_ORNSTEIN_UHLENBECK);
}
/*
*
* addUniqueSpecies():
*
* Add a species to a Constituents object. This routine will
* first check to see if the species is already part of the
* phase. It does this via a string comparison with the
* existing species in the phase.
*/
void Constituents::
addUniqueSpecies(const std::string& name, const doublereal* comp,
doublereal charge, doublereal size) {
vector<string>::const_iterator it = m_speciesNames.begin();
for (int k = 0; k < m_kk; k++) {
if (*it == name) {
/*
* We have found a match. At this point we could do some
* compatibility checks. However, let's just return for the
* moment without specifying any error.
*/
int m_mm = m_Elements->nElements();
for (int i = 0; i < m_mm; i++) {
if (comp[i] != m_speciesComp[m_kk * m_mm + i]) {
throw CanteraError("addUniqueSpecies",
"Duplicate species have different "
"compositions: " + *it);
}
}
if (charge != m_speciesCharge[m_kk]) {
throw CanteraError("addUniqueSpecies",
"Duplicate species have different "
"charges: " + *it);
}
if (size != m_speciesSize[m_kk]) {
throw CanteraError("addUniqueSpecies",
"Duplicate species have different "
"sizes: " + *it);
}
return;
}
++it;
}
addSpecies(name, comp, charge, size);
}
int PopDynSEGA::addSpecies(lua_State* luaState)
{
Species* species = (Species*)Orbit<PopDynSEGA>::pointer(luaState, 1);
unsigned int id = addSpecies(species);
lua_pushinteger(luaState, id);
return 1;
}
TEST(LatticeSolidPhase, fromScratch)
{
auto base = make_shared<StoichSubstance>();
base->setName("Li7Si3(S)");
base->setDensity(1390.0);
auto sLi7Si3 = make_shomate2_species("Li7Si3(S)", "Li:7 Si:3", li7si3_shomate_coeffs);
base->addSpecies(sLi7Si3);
base->initThermo();
auto interstital = make_shared<LatticePhase>();
interstital->setName("Li7Si3_Interstitial");
auto sLii = make_const_cp_species("Li(i)", "Li:1", 298.15, 0, 2e4, 2e4);
auto sVac = make_const_cp_species("V(i)", "", 298.15, 8.98e4, 0, 0);
sLii->extra["molar_volume"] = 0.2;
interstital->setSiteDensity(10.46344);
interstital->addSpecies(sLii);
interstital->addSpecies(sVac);
interstital->initThermo();
interstital->setMoleFractionsByName("Li(i):0.01 V(i):0.99");
LatticeSolidPhase p;
p.addLattice(base);
p.addLattice(interstital);
p.setLatticeStoichiometry(parseCompString("Li7Si3(S):1.0 Li7Si3_Interstitial:1.0"));
p.initThermo();
p.setState_TP(725, 10 * OneAtm);
// Regression test based on modified version of Li7Si3_ls.xml
EXPECT_NEAR(p.enthalpy_mass(), -2077821.9295456698, 1e-6);
double mu_ref[] = {-4.62717474e+08, -4.64248485e+07, 1.16370186e+05};
double vol_ref[] = {0.09557086, 0.2, 0.09557086};
vector_fp mu(p.nSpecies());
vector_fp vol(p.nSpecies());
p.getChemPotentials(mu.data());
p.getPartialMolarVolumes(vol.data());
for (size_t k = 0; k < p.nSpecies(); k++) {
EXPECT_NEAR(mu[k], mu_ref[k], 1e-7*fabs(mu_ref[k]));
EXPECT_NEAR(vol[k], vol_ref[k], 1e-7);
}
}
void LatticeSolidPhase::initThermo()
{
size_t kk = 0;
size_t kstart = 0;
lkstart_.resize(m_lattice.size() + 1);
size_t loc = 0;
for (size_t n = 0; n < m_lattice.size(); n++) {
LatticePhase* lp = m_lattice[n];
vector_fp constArr(lp->nElements());
const vector_fp& aws = lp->atomicWeights();
for (size_t es = 0; es < lp->nElements(); es++) {
addElement(lp->elementName(es), aws[es], lp->atomicNumber(es),
lp->entropyElement298(es), lp->elementType(es));
}
kstart = kk;
for (size_t k = 0; k < lp->nSpecies(); k++) {
addSpecies(lp->species(k));
kk++;
}
// Add in the lattice stoichiometry constraint
if (n > 0) {
string econ = fmt::format("LC_{}_{}", n, id());
size_t m = addElement(econ, 0.0, 0, 0.0, CT_ELEM_TYPE_LATTICERATIO);
size_t mm = nElements();
size_t nsp0 = m_lattice[0]->nSpecies();
for (size_t k = 0; k < nsp0; k++) {
m_speciesComp[k * mm + m] = -theta_[0];
}
for (size_t k = 0; k < lp->nSpecies(); k++) {
size_t ks = kstart + k;
m_speciesComp[ks * mm + m] = theta_[n];
}
}
size_t nsp = m_lattice[n]->nSpecies();
lkstart_[n] = loc;
for (size_t k = 0; k < nsp; k++) {
m_x[loc] =m_lattice[n]->moleFraction(k) / (double) m_lattice.size();
loc++;
}
lkstart_[n+1] = loc;
}
setMoleFractions(m_x.data());
ThermoPhase::initThermo();
}
TEST(IonsFromNeutralConstructor, fromScratch)
{
auto neutral = make_shared<MargulesVPSSTP>();
auto sKCl = make_shomate_species("KCl(L)", "K:1 Cl:1", kcl_shomate_coeffs);
neutral->addSpecies(sKCl);
std::unique_ptr<PDSS_ConstVol> ssKCl(new PDSS_ConstVol());
ssKCl->setMolarVolume(0.03757);
neutral->installPDSS(0, std::move(ssKCl));
neutral->initThermo();
IonsFromNeutralVPSSTP p;
p.setNeutralMoleculePhase(neutral);
auto sKp = make_shared<Species>("K+", parseCompString("K:1"), 1);
auto sClm = make_shared<Species>("Cl-", parseCompString("Cl:1"), -1);
sClm->extra["special_species"] = true;
p.addSpecies(sKp);
p.addSpecies(sClm);
std::unique_ptr<PDSS_IonsFromNeutral> ssKp(new PDSS_IonsFromNeutral());
std::unique_ptr<PDSS_IonsFromNeutral> ssClm(new PDSS_IonsFromNeutral());
ssKp->setNeutralSpeciesMultiplier("KCl(L)", 1.2);
ssClm->setNeutralSpeciesMultiplier("KCl(L)", 1.5);
ssClm->setSpecialSpecies();
p.installPDSS(0, std::move(ssKp));
p.installPDSS(1, std::move(ssClm));
p.initThermo();
ASSERT_EQ((int) p.nSpecies(), 2);
p.setState_TPX(500, 2e5, "K+:0.1, Cl-:0.1");
vector_fp mu(p.nSpecies());
p.getChemPotentials(mu.data());
// Values for regression testing only -- same as XML test
EXPECT_NEAR(p.density(), 1984.3225978174073, 1e-6);
EXPECT_NEAR(p.enthalpy_mass(), -8035317241137.971, 1e-1);
EXPECT_NEAR(mu[0], -4.66404010e+08, 1e1);
EXPECT_NEAR(mu[1], -2.88157298e+06, 1e-1);
}
FixedChemPotSSTP::FixedChemPotSSTP(const std::string& Ename, doublereal val) :
chemPot_(0.0)
{
std::string pname = Ename + "Fixed";
setID(pname);
setName(pname);
setNDim(3);
addElement(Ename);
auto sp = make_shared<Species>(pname, parseCompString(Ename + ":1.0"));
double c[4] = {298.15, val, 0.0, 0.0};
shared_ptr<SpeciesThermoInterpType> stit(
newSpeciesThermoInterpType("const_cp", 0.1, 1e30, OneAtm, c));
sp->thermo = stit;
addSpecies(sp);
initThermo();
m_p0 = OneAtm;
m_tlast = 298.15;
setChemicalPotential(val);
// Create an XML_Node entry for this species
XML_Node s("species", 0);
s.addAttribute("name", pname);
std::string aaS = Ename + ":1";
s.addChild("atomArray", aaS);
XML_Node& tt = s.addChild("thermo");
XML_Node& ss = tt.addChild("Simple");
ss.addAttribute("Pref", "1 bar");
ss.addAttribute("Tmax", "5000.");
ss.addAttribute("Tmin", "100.");
ss.addChild("t0", "298.15");
ss.addChild("cp0", "0.0");
std::string sval = fp2str(val);
ss.addChild("h", sval);
ss.addChild("s", "0.0");
saveSpeciesData(0, &s);
}
// 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);
}
