status_t DLL_EXPORT kin_getdestructionrates_(const integer* n, doublereal* ddot) {
try {
Kinetics* k = _fkin(n);
k->getDestructionRates(ddot);
return 0;
}
catch (CanteraError) {handleError(); return -1;}
}
status_t DLL_EXPORT kin_getfwdratesofprogress_(const integer* n, doublereal* fwdROP) {
Kinetics* k = _fkin(n);
try {
k->getFwdRatesOfProgress(fwdROP);
return 0;
}
catch (CanteraError) {handleError(); return -1;}
}
status_t DLL_EXPORT kin_getnetratesofprogress_(const integer* n, doublereal* netROP) {
try {
Kinetics* k = _fkin(n);
k->getNetRatesOfProgress(netROP);
return 0;
}
catch (CanteraError) {handleError(); return -1;}
}
status_t kin_getnetratesofprogress_(const integer* n, doublereal* netROP)
{
try {
Kinetics* k = _fkin(n);
k->getNetRatesOfProgress(netROP);
} catch (...) {
return handleAllExceptions(-1, ERR);
}
return 0;
}
status_t kin_getdestructionrates_(const integer* n, doublereal* ddot)
{
try {
Kinetics* k = _fkin(n);
k->getDestructionRates(ddot);
} catch (...) {
return handleAllExceptions(-1, ERR);
}
return 0;
}
status_t kin_getnetproductionrates_(const integer* n, doublereal* wdot)
{
try {
Kinetics* k = _fkin(n);
k->getNetProductionRates(wdot);
} catch (...) {
return handleAllExceptions(-1, ERR);
}
return 0;
}
status_t kin_getequilibriumconstants_(const integer* n, doublereal* kc)
{
try {
Kinetics* k = _fkin(n);
k->getEquilibriumConstants(kc);
} catch (...) {
return handleAllExceptions(-1, ERR);
}
return 0;
}
status_t DLL_EXPORT kin_getreactionstring_(const integer* n, integer* i, char* buf, ftnlen lenbuf) {
try {
Kinetics* k = _fkin(n);
std::string r = k->reactionString(*i-1);
int lout = min(lenbuf,r.size());
std::copy(r.c_str(), r.c_str() + lout, buf);
for (int nn = lout; nn < lenbuf; nn++) buf[nn] = ' ';
return 0;
}
catch (CanteraError) {handleError(); return -1;}
}
status_t DLL_EXPORT kin_advancecoverages_(const integer* n, doublereal* tstep) {
try {
Kinetics* k = _fkin(n);
if (k->type() == cInterfaceKinetics) {
((InterfaceKinetics*)k)->advanceCoverages(*tstep);
}
else {
throw CanteraError("kin_advanceCoverages",
"wrong kinetics manager type");
}
return 0;
}
catch (CanteraError) {handleError(); return -1;}
}
status_t kin_advancecoverages_(const integer* n, doublereal* tstep)
{
try {
Kinetics* k = _fkin(n);
if (k->type() == cInterfaceKinetics) {
((InterfaceKinetics*)k)->advanceCoverages(*tstep);
} else {
throw CanteraError("kin_advanceCoverages",
"wrong kinetics manager type");
}
} catch (...) {
return handleAllExceptions(-1, ERR);
}
return 0;
}
status_t kin_getreactionstring_(const integer* n, integer* i, char* buf, ftnlen lenbuf)
{
try {
Kinetics* k = _fkin(n);
std::string r = k->reactionString(*i-1);
int lout = std::min(lenbuf, (int) r.size());
std::copy(r.c_str(), r.c_str() + lout, buf);
for (int nn = lout; nn < lenbuf; nn++) {
buf[nn] = ' ';
}
} catch (...) {
return handleAllExceptions(-1, ERR);
}
return 0;
}
status_t ctbuildsolutionfromxml(char* src, integer* ixml, char* id,
integer* ith, integer* ikin, ftnlen lensrc, ftnlen lenid)
{
try {
XML_Node* root = 0;
if (*ixml > 0) {
root = _xml(ixml);
}
thermo_t* t = _fth(ith);
Kinetics* k = _fkin(ikin);
XML_Node* x, *r=0;
if (root) {
r = &root->root();
}
std::string srcS = f2string(src, lensrc);
std::string idS = f2string(id, lenid);
if (srcS != "") {
x = get_XML_Node(srcS, r);
} else {
x = get_XML_Node(idS, r);
}
if (!x) {
return 0;
}
importPhase(*x, t);
k->addPhase(*t);
k->init();
installReactionArrays(*x, *k, x->id());
t->setState_TP(300.0, OneAtm);
if (r) {
if (&x->root() != &r->root()) {
delete &x->root();
}
} else {
delete &x->root();
}
} catch (...) {
return handleAllExceptions(-1, ERR);
}
return 0;
}
double Reactor::evalSurfaces(double t, double* ydot)
{
const vector_fp& mw = m_thermo->molecularWeights();
fill(m_sdot.begin(), m_sdot.end(), 0.0);
size_t loc = 0; // offset into ydot
double mdot_surf = 0.0; // net mass flux from surface
for (size_t i = 0; i < m_wall.size(); i++) {
Kinetics* kin = m_wall[i]->kinetics(m_lr[i]);
SurfPhase* surf = m_wall[i]->surface(m_lr[i]);
if (surf && kin) {
double rs0 = 1.0/surf->siteDensity();
size_t nk = surf->nSpecies();
double sum = 0.0;
surf->setTemperature(m_state[0]);
m_wall[i]->syncCoverages(m_lr[i]);
kin->getNetProductionRates(&m_work[0]);
size_t ns = kin->surfacePhaseIndex();
size_t surfloc = kin->kineticsSpeciesIndex(0,ns);
for (size_t k = 1; k < nk; k++) {
ydot[loc + k] = m_work[surfloc+k]*rs0*surf->size(k);
sum -= ydot[loc + k];
}
ydot[loc] = sum;
loc += nk;
double wallarea = m_wall[i]->area();
for (size_t k = 0; k < m_nsp; k++) {
m_sdot[k] += m_work[k]*wallarea;
mdot_surf += m_sdot[k] * mw[k];
}
}
}
return mdot_surf;
}
bool checkElectrochemReaction(const XML_Node& p, Kinetics& kin, const XML_Node& r)
{
// If other phases are involved in the reaction mechanism, they must be
// listed in a 'phaseArray' child element. Homogeneous mechanisms do not
// need to include a phaseArray element.
vector<string> phase_ids;
if (p.hasChild("phaseArray")) {
const XML_Node& pa = p.child("phaseArray");
getStringArray(pa, phase_ids);
}
phase_ids.push_back(p["id"]);
// Get reaction product and reactant information
Composition reactants = parseCompString(r.child("reactants").value());
Composition products = parseCompString(r.child("products").value());
// If the reaction has undeclared species don't perform electrochemical check
for (const auto& sp : reactants) {
if (kin.kineticsSpeciesIndex(sp.first) == npos) {
return true;
}
}
for (const auto& sp : products) {
if (kin.kineticsSpeciesIndex(sp.first) == npos) {
return true;
}
}
// Initialize the electron counter for each phase
std::vector<double> e_counter(phase_ids.size(), 0.0);
// Find the amount of electrons in the products for each phase
for (const auto& sp : products) {
const ThermoPhase& ph = kin.speciesPhase(sp.first);
size_t k = ph.speciesIndex(sp.first);
double stoich = sp.second;
for (size_t m = 0; m < phase_ids.size(); m++) {
if (phase_ids[m] == ph.id()) {
e_counter[m] += stoich * ph.charge(k);
break;
}
}
}
// Subtract the amount of electrons in the reactants for each phase
for (const auto& sp : reactants) {
const ThermoPhase& ph = kin.speciesPhase(sp.first);
size_t k = ph.speciesIndex(sp.first);
double stoich = sp.second;
for (size_t m = 0; m < phase_ids.size(); m++) {
if (phase_ids[m] == ph.id()) {
e_counter[m] -= stoich * ph.charge(k);
break;
}
}
}
// If the electrons change phases then the reaction is electrochemical
bool echemical = false;
for(size_t m = 0; m < phase_ids.size(); m++) {
if (fabs(e_counter[m]) > 1e-4) {
echemical = true;
break;
}
}
// If the reaction is electrochemical, ensure the reaction is identified as
// electrochemical. If not already specified beta is assumed to be 0.5
std::string type = ba::to_lower_copy(r["type"]);
if (!r.child("rateCoeff").hasChild("electrochem")) {
if ((type != "butlervolmer_noactivitycoeffs" &&
type != "butlervolmer" &&
type != "surfaceaffinity") &&
echemical) {
XML_Node& f = r.child("rateCoeff").addChild("electrochem","");
f.addAttribute("beta",0.5);
}
}
return true;
}
void IdealGasConstPressureReactor::evalEqs(doublereal time, doublereal* y,
doublereal* ydot, doublereal* params)
{
size_t nk;
m_thermo->restoreState(m_state);
Kinetics* kin;
size_t npar, ploc;
double mult;
// process sensitivity parameters
if (params) {
npar = m_pnum.size();
for (size_t n = 0; n < npar; n++) {
mult = m_kin->multiplier(m_pnum[n]);
m_kin->setMultiplier(m_pnum[n], mult*params[n]);
}
ploc = npar;
for (size_t m = 0; m < m_nwalls; m++) {
if (m_nsens_wall[m] > 0) {
m_wall[m]->setSensitivityParameters(m_lr[m], params + ploc);
ploc += m_nsens_wall[m];
}
}
}
m_Q = 0.0;
// compute wall terms
doublereal rs0, sum, wallarea;
double mcpdTdt = 0.0; // m * c_p * dT/dt
double dmdt = 0.0; // dm/dt (gas phase)
double* dYdt = ydot + 2;
m_thermo->getPartialMolarEnthalpies(&m_hk[0]);
SurfPhase* surf;
size_t lr, ns, loc = m_nsp+2, surfloc;
fill(m_sdot.begin(), m_sdot.end(), 0.0);
for (size_t i = 0; i < m_nwalls; i++) {
lr = 1 - 2*m_lr[i];
m_Q += lr*m_wall[i]->Q(time);
kin = m_wall[i]->kinetics(m_lr[i]);
surf = m_wall[i]->surface(m_lr[i]);
if (surf && kin) {
rs0 = 1.0/surf->siteDensity();
nk = surf->nSpecies();
sum = 0.0;
surf->setTemperature(m_state[0]);
m_wall[i]->syncCoverages(m_lr[i]);
kin->getNetProductionRates(DATA_PTR(m_work));
ns = kin->surfacePhaseIndex();
surfloc = kin->kineticsSpeciesIndex(0,ns);
for (size_t k = 1; k < nk; k++) {
ydot[loc + k] = m_work[surfloc+k]*rs0*surf->size(k);
sum -= ydot[loc + k];
}
ydot[loc] = sum;
loc += nk;
wallarea = m_wall[i]->area();
for (size_t k = 0; k < m_nsp; k++) {
m_sdot[k] += m_work[k]*wallarea;
}
}
}
const vector_fp& mw = m_thermo->molecularWeights();
const doublereal* Y = m_thermo->massFractions();
if (m_chem) {
m_kin->getNetProductionRates(&m_wdot[0]); // "omega dot"
}
double mdot_surf = 0.0; // net mass flux from surface
for (size_t k = 0; k < m_nsp; k++) {
// production in gas phase and from surfaces
dYdt[k] = (m_wdot[k] * m_vol + m_sdot[k]) * mw[k] / m_mass;
mdot_surf += m_sdot[k] * mw[k];
}
dmdt += mdot_surf;
// external heat transfer
mcpdTdt -= m_Q;
for (size_t n = 0; n < m_nsp; n++) {
// heat release from gas phase and surface reations
mcpdTdt -= m_wdot[n] * m_hk[n] * m_vol;
mcpdTdt -= m_sdot[n] * m_hk[n];
// dilution by net surface mass flux
dYdt[n] -= Y[n] * mdot_surf / m_mass;
}
// add terms for open system
if (m_open) {
// outlets
for (size_t i = 0; i < m_nOutlets; i++) {
dmdt -= m_outlet[i]->massFlowRate(time); // mass flow out of system
}
// inlets
for (size_t i = 0; i < m_nInlets; i++) {
double mdot_in = m_inlet[i]->massFlowRate(time);
dmdt += mdot_in; // mass flow into system
mcpdTdt += m_inlet[i]->enthalpy_mass() * mdot_in;
for (size_t n = 0; n < m_nsp; n++) {
double mdot_spec = m_inlet[i]->outletSpeciesMassFlowRate(n);
// flow of species into system and dilution by other species
dYdt[n] += (mdot_spec - mdot_in * Y[n]) / m_mass;
mcpdTdt -= m_hk[n] / mw[n] * mdot_spec;
}
}
}
ydot[0] = dmdt;
if (m_energy) {
ydot[1] = mcpdTdt / (m_mass * m_thermo->cp_mass());
} else {
ydot[1] = 0.0;
}
// reset sensitivity parameters
if (params) {
npar = m_pnum.size();
for (size_t n = 0; n < npar; n++) {
mult = m_kin->multiplier(m_pnum[n]);
m_kin->setMultiplier(m_pnum[n], mult/params[n]);
}
ploc = npar;
for (size_t m = 0; m < m_nwalls; m++) {
if (m_nsens_wall[m] > 0) {
m_wall[m]->resetSensitivityParameters(m_lr[m]);
ploc += m_nsens_wall[m];
}
}
}
}
void IdealGasReactor::evalEqs(doublereal time, doublereal* y,
doublereal* ydot, doublereal* params)
{
m_thermo->restoreState(m_state);
// process sensitivity parameters
if (params) {
size_t npar = m_pnum.size();
for (size_t n = 0; n < npar; n++) {
double mult = m_kin->multiplier(m_pnum[n]);
m_kin->setMultiplier(m_pnum[n], mult*params[n]);
}
size_t ploc = npar;
for (size_t m = 0; m < m_nwalls; m++) {
if (m_nsens_wall[m] > 0) {
m_wall[m]->setSensitivityParameters(m_lr[m], params + ploc);
ploc += m_nsens_wall[m];
}
}
}
m_vdot = 0.0;
m_Q = 0.0;
double mcvdTdt = 0.0; // m * c_v * dT/dt
double dmdt = 0.0; // dm/dt (gas phase)
double* dYdt = ydot + 3;
m_thermo->getPartialMolarIntEnergies(&m_uk[0]);
// compute wall terms
size_t loc = m_nsp+3;
fill(m_sdot.begin(), m_sdot.end(), 0.0);
for (size_t i = 0; i < m_nwalls; i++) {
int lr = 1 - 2*m_lr[i];
double vdot = lr*m_wall[i]->vdot(time);
m_vdot += vdot;
m_Q += lr*m_wall[i]->Q(time);
Kinetics* kin = m_wall[i]->kinetics(m_lr[i]);
SurfPhase* surf = m_wall[i]->surface(m_lr[i]);
if (surf && kin) {
double rs0 = 1.0/surf->siteDensity();
size_t nk = surf->nSpecies();
double sum = 0.0;
surf->setTemperature(m_state[0]);
m_wall[i]->syncCoverages(m_lr[i]);
kin->getNetProductionRates(DATA_PTR(m_work));
size_t ns = kin->surfacePhaseIndex();
size_t surfloc = kin->kineticsSpeciesIndex(0,ns);
for (size_t k = 1; k < nk; k++) {
ydot[loc + k] = m_work[surfloc+k]*rs0*surf->size(k);
sum -= ydot[loc + k];
}
ydot[loc] = sum;
loc += nk;
double wallarea = m_wall[i]->area();
for (size_t k = 0; k < m_nsp; k++) {
m_sdot[k] += m_work[k]*wallarea;
}
}
}
const vector_fp& mw = m_thermo->molecularWeights();
const doublereal* Y = m_thermo->massFractions();
if (m_chem) {
m_kin->getNetProductionRates(&m_wdot[0]); // "omega dot"
}
double mdot_surf = 0.0; // net mass flux from surfaces
for (size_t k = 0; k < m_nsp; k++) {
// production in gas phase and from surfaces
dYdt[k] = (m_wdot[k] * m_vol + m_sdot[k]) * mw[k] / m_mass;
mdot_surf += m_sdot[k] * mw[k];
}
dmdt += mdot_surf;
// compression work and external heat transfer
mcvdTdt += - m_pressure * m_vdot - m_Q;
for (size_t n = 0; n < m_nsp; n++) {
// heat release from gas phase and surface reations
mcvdTdt -= m_wdot[n] * m_uk[n] * m_vol;
mcvdTdt -= m_sdot[n] * m_uk[n];
// dilution by net surface mass flux
dYdt[n] -= Y[n] * mdot_surf / m_mass;
}
// add terms for open system
if (m_open) {
// outlets
for (size_t i = 0; i < m_nOutlets; i++) {
double mdot_out = m_outlet[i]->massFlowRate(time);
dmdt -= mdot_out; // mass flow out of system
mcvdTdt -= mdot_out * m_pressure * m_vol / m_mass; // flow work
}
// inlets
for (size_t i = 0; i < m_nInlets; i++) {
double mdot_in = m_inlet[i]->massFlowRate(time);
dmdt += mdot_in; // mass flow into system
mcvdTdt += m_inlet[i]->enthalpy_mass() * mdot_in;
for (size_t n = 0; n < m_nsp; n++) {
double mdot_spec = m_inlet[i]->outletSpeciesMassFlowRate(n);
// flow of species into system and dilution by other species
dYdt[n] += (mdot_spec - mdot_in * Y[n]) / m_mass;
// In combintion with h_in*mdot_in, flow work plus thermal
// energy carried with the species
mcvdTdt -= m_uk[n] / mw[n] * mdot_spec;
}
}
}
ydot[0] = dmdt;
ydot[1] = m_vdot;
if (m_energy) {
ydot[2] = mcvdTdt / (m_mass * m_thermo->cv_mass());
} else {
ydot[2] = 0;
}
for (size_t i = 0; i < m_nv; i++) {
AssertFinite(ydot[i], "IdealGasReactor::evalEqs",
"ydot[" + int2str(i) + "] is not finite");
}
// reset sensitivity parameters
if (params) {
size_t npar = m_pnum.size();
for (size_t n = 0; n < npar; n++) {
double mult = m_kin->multiplier(m_pnum[n]);
m_kin->setMultiplier(m_pnum[n], mult/params[n]);
}
size_t ploc = npar;
for (size_t m = 0; m < m_nwalls; m++) {
if (m_nsens_wall[m] > 0) {
m_wall[m]->resetSensitivityParameters(m_lr[m]);
ploc += m_nsens_wall[m];
}
}
}
}
/*
* This virtual routine can be used to duplicate %Kinetics objects
* inherited from %Kinetics even if the application only has
* a pointer to %Kinetics to work with.
*
* These routines are basically wrappers around the derived copy
* constructor.
*/
Kinetics *Kinetics::duplMyselfAsKinetics(const std::vector<thermo_t*> & tpVector) const {
Kinetics* ko = new Kinetics(*this);
ko->assignShallowPointers(tpVector);
return ko;
}
/*
* Called by the integrator to evaluate ydot given y at time 'time'.
*/
void Reactor::evalEqs(doublereal time, doublereal* y,
doublereal* ydot, doublereal* params)
{
m_time = time;
m_thermo->restoreState(m_state);
// process sensitivity parameters
if (params) {
size_t npar = m_pnum.size();
for (size_t n = 0; n < npar; n++) {
double mult = m_kin->multiplier(m_pnum[n]);
m_kin->setMultiplier(m_pnum[n], mult*params[n]);
}
size_t ploc = npar;
for (size_t m = 0; m < m_nwalls; m++) {
if (m_nsens_wall[m] > 0) {
m_wall[m]->setSensitivityParameters(m_lr[m], params + ploc);
ploc += m_nsens_wall[m];
}
}
}
m_vdot = 0.0;
m_Q = 0.0;
// compute wall terms
size_t loc = m_nsp+2;
fill(m_sdot.begin(), m_sdot.end(), 0.0);
for (size_t i = 0; i < m_nwalls; i++) {
int lr = 1 - 2*m_lr[i];
double vdot = lr*m_wall[i]->vdot(time);
m_vdot += vdot;
m_Q += lr*m_wall[i]->Q(time);
Kinetics* kin = m_wall[i]->kinetics(m_lr[i]);
SurfPhase* surf = m_wall[i]->surface(m_lr[i]);
if (surf && kin) {
double rs0 = 1.0/surf->siteDensity();
size_t nk = surf->nSpecies();
double sum = 0.0;
surf->setTemperature(m_state[0]);
m_wall[i]->syncCoverages(m_lr[i]);
kin->getNetProductionRates(DATA_PTR(m_work));
size_t ns = kin->surfacePhaseIndex();
size_t surfloc = kin->kineticsSpeciesIndex(0,ns);
for (size_t k = 1; k < nk; k++) {
ydot[loc + k] = m_work[surfloc+k]*rs0*surf->size(k);
sum -= ydot[loc + k];
}
ydot[loc] = sum;
loc += nk;
double wallarea = m_wall[i]->area();
for (size_t k = 0; k < m_nsp; k++) {
m_sdot[k] += m_work[k]*wallarea;
}
}
}
// volume equation
ydot[1] = m_vdot;
/* species equations
* Equation is:
* \dot M_k = \hat W_k \dot\omega_k + \dot m_{in} Y_{k,in}
* - \dot m_{out} Y_{k} + A \dot s_k.
*/
const vector_fp& mw = m_thermo->molecularWeights();
if (m_chem) {
m_kin->getNetProductionRates(ydot+2); // "omega dot"
} else {
fill(ydot + 2, ydot + 2 + m_nsp, 0.0);
}
for (size_t n = 0; n < m_nsp; n++) {
ydot[n+2] *= m_vol; // moles/s/m^3 -> moles/s
ydot[n+2] += m_sdot[n];
ydot[n+2] *= mw[n];
}
/*
* Energy equation.
* \f[
* \dot U = -P\dot V + A \dot q + \dot m_{in} h_{in}
* - \dot m_{out} h.
* \f]
*/
if (m_energy) {
ydot[0] = - m_thermo->pressure() * m_vdot - m_Q;
} else {
ydot[0] = 0.0;
}
// add terms for open system
if (m_open) {
const doublereal* mf = m_thermo->massFractions();
doublereal enthalpy = m_thermo->enthalpy_mass();
// outlets
for (size_t i = 0; i < m_nOutlets; i++) {
double mdot_out = m_outlet[i]->massFlowRate(time);
for (size_t n = 0; n < m_nsp; n++) {
ydot[2+n] -= mdot_out * mf[n];
}
if (m_energy) {
ydot[0] -= mdot_out * enthalpy;
}
}
// inlets
for (size_t i = 0; i < m_nInlets; i++) {
double mdot_in = m_inlet[i]->massFlowRate(time);
for (size_t n = 0; n < m_nsp; n++) {
ydot[2+n] += m_inlet[i]->outletSpeciesMassFlowRate(n);
}
if (m_energy) {
ydot[0] += mdot_in * m_inlet[i]->enthalpy_mass();
}
}
}
// reset sensitivity parameters
if (params) {
size_t npar = m_pnum.size();
for (size_t n = 0; n < npar; n++) {
double mult = m_kin->multiplier(m_pnum[n]);
m_kin->setMultiplier(m_pnum[n], mult/params[n]);
}
size_t ploc = npar;
for (size_t m = 0; m < m_nwalls; m++) {
if (m_nsens_wall[m] > 0) {
m_wall[m]->resetSensitivityParameters(m_lr[m]);
ploc += m_nsens_wall[m];
}
}
}
}
bool installReactionArrays(const XML_Node& p, Kinetics& kin,
std::string default_phase, bool check_for_duplicates)
{
int itot = 0;
// Search the children of the phase element for the XML element named
// reactionArray. If we can't find it, then return signaling having not
// found any reactions. Apparently, we allow multiple reactionArray elements
// here Each one will be processed sequentially, with the end result being
// purely additive.
vector<XML_Node*> rarrays = p.getChildren("reactionArray");
if (rarrays.empty()) {
return false;
}
for (size_t n = 0; n < rarrays.size(); n++) {
// Go get a reference to the current XML element, reactionArray. We will
// process this element now.
const XML_Node& rxns = *rarrays[n];
// The reactionArray element has an attribute called, datasrc. The value
// of the attribute is the XML element comprising the top of the tree of
// reactions for the phase. Find this datasrc element starting with the
// root of the current XML node.
const XML_Node* rdata = get_XML_Node(rxns["datasrc"], &rxns.root());
// If the reactionArray element has a child element named "skip", and if
// the attribute of skip called "species" has a value of "undeclared",
// we will set rxnrule.skipUndeclaredSpecies to 'true'. rxnrule is
// passed to the routine that parses each individual reaction so that
// the parser will skip all reactions containing an undefined species
// without throwing an error.
//
// Similarly, an attribute named "third_bodies" with the value of
// "undeclared" will skip undeclared third body efficiencies (while
// retaining the reaction and any other efficiencies).
if (rxns.hasChild("skip")) {
const XML_Node& sk = rxns.child("skip");
if (sk["species"] == "undeclared") {
kin.skipUndeclaredSpecies(true);
}
if (sk["third_bodies"] == "undeclared") {
kin.skipUndeclaredThirdBodies(true);
}
}
// Search for child elements called include. We only include a reaction
// if it's tagged by one of the include fields. Or, we include all
// reactions if there are no include fields.
vector<XML_Node*> incl = rxns.getChildren("include");
vector<XML_Node*> allrxns = rdata->getChildren("reaction");
// if no 'include' directive, then include all reactions
if (incl.empty()) {
for (size_t i = 0; i < allrxns.size(); i++) {
checkElectrochemReaction(p,kin,*allrxns[i]);
kin.addReaction(newReaction(*allrxns[i]));
++itot;
}
} else {
for (size_t nii = 0; nii < incl.size(); nii++) {
const XML_Node& ii = *incl[nii];
string imin = ii["min"];
string imax = ii["max"];
string::size_type iwild = string::npos;
if (imax == imin) {
iwild = imin.find("*");
if (iwild != string::npos) {
imin = imin.substr(0,iwild);
imax = imin;
}
}
for (size_t i = 0; i < allrxns.size(); i++) {
const XML_Node* r = allrxns[i];
string rxid;
if (r) {
rxid = r->attrib("id");
if (iwild != string::npos) {
rxid = rxid.substr(0,iwild);
}
// To decide whether the reaction is included or not we
// do a lexical min max and operation. This sometimes
// has surprising results.
if ((rxid >= imin) && (rxid <= imax)) {
checkElectrochemReaction(p,kin,*r);
kin.addReaction(newReaction(*r));
++itot;
}
}
}
}
}
}
if (check_for_duplicates) {
kin.checkDuplicates();
}
return true;
}
