/*
* molecularWeight()
*
* Returns the molecular weight of a species given the species index
*
* units = kg / kmol.
*/
doublereal Constituents::molecularWeight(int k) const {
if (k < 0 || k >= nSpecies()) {
throw SpeciesRangeError("Constituents::molecularWeight",
k, nSpecies());
}
return m_weight[k];
}
void ThermoPhase::reportCSV(std::ofstream& csvFile) const
{
int tabS = 15;
int tabM = 30;
csvFile.precision(8);
vector_fp X(nSpecies());
getMoleFractions(&X[0]);
std::vector<std::string> pNames;
std::vector<vector_fp> data;
getCsvReportData(pNames, data);
csvFile << setw(tabS) << "Species,";
for (size_t i = 0; i < pNames.size(); i++) {
csvFile << setw(tabM) << pNames[i] << ",";
}
csvFile << endl;
for (size_t k = 0; k < nSpecies(); k++) {
csvFile << setw(tabS) << speciesName(k) + ",";
if (X[k] > SmallNumber) {
for (size_t i = 0; i < pNames.size(); i++) {
csvFile << setw(tabM) << data[i][k] << ",";
}
csvFile << endl;
} else {
for (size_t i = 0; i < pNames.size(); i++) {
csvFile << setw(tabM) << 0 << ",";
}
csvFile << endl;
}
}
}
/*
* Returns the number of atoms of element \c m in species \c k.
*/
doublereal Constituents::nAtoms(int k, int m) const
{
const int m_mm = m_Elements->nElements();
if (m < 0 || m >=m_mm)
throw ElementRangeError("Constituents::nAtoms",m,nElements());
if (k < 0 || k >= nSpecies())
throw SpeciesRangeError("Constituents::nAtoms",k,nSpecies());
return m_speciesComp[m_mm * k + m];
}
void Phase::restoreState(size_t lenstate, const doublereal* state)
{
if (lenstate >= nSpecies() + 2) {
setMassFractions_NoNorm(state + 2);
setTemperature(state[0]);
setDensity(state[1]);
} else {
throw ArraySizeError("Phase::restoreState",
lenstate,nSpecies()+2);
}
}
/**
* Finished adding species, prepare to use them for calculation
* of mixture properties.
*/
void Phase::freezeSpecies() {
Constituents::freezeSpecies();
init(Constituents::molecularWeights());
int kk = nSpecies();
int nv = kk + 2;
m_data.resize(nv,0.0);
m_data[0] = 300.0;
m_data[1] = 0.001;
m_data[2] = 1.0;
//setState_TRY(300.0, density(), &m_data[2]);
m_kk = nSpecies();
}
void SurfPhase::
setCoveragesByName(std::string cov) {
int kk = nSpecies();
int k;
compositionMap cc;
for (k = 0; k < kk; k++) {
cc[speciesName(k)] = -1.0;
}
parseCompString(cov, cc);
doublereal c;
vector_fp cv(kk, 0.0);
bool ifound = false;
for (k = 0; k < kk; k++) {
c = cc[speciesName(k)];
if (c > 0.0) {
ifound = true;
cv[k] = c;
}
}
if (!ifound) {
throw CanteraError("SurfPhase::setCoveragesByName",
"Input coverages are all zero or negative");
}
setCoverages(DATA_PTR(cv));
}
/**
* @internal Initialize. This method is provided to allow
* subclasses to perform any initialization required after all
* species have been added. For example, it might be used to
* resize internal work arrays that must have an entry for
* each species. The base class implementation does nothing,
* and subclasses that do not require initialization do not
* need to overload this method. When importing a CTML phase
* description, this method is called just prior to returning
* from function importPhase.
*
* @see importCTML.cpp
*/
void StoichSubstanceSSTP::initThermo() {
/*
* Make sure there is one and only one species in this phase.
*/
m_kk = nSpecies();
if (m_kk != 1) {
throw CanteraError("initThermo",
"stoichiometric substances may only contain one species.");
}
doublereal tmin = m_spthermo->minTemp();
doublereal tmax = m_spthermo->maxTemp();
if (tmin > 0.0) m_tmin = tmin;
if (tmax > 0.0) m_tmax = tmax;
/*
* Store the reference pressure in the variables for the class.
*/
m_p0 = refPressure();
/*
* Resize temporary arrays.
*/
int leng = 1;
m_h0_RT.resize(leng);
m_cp0_R.resize(leng);
m_s0_R.resize(leng);
/*
* Call the base class thermo initializer
*/
SingleSpeciesTP::initThermo();
}
/**
* Get the mole fractions by name.
*/
void Phase::getMoleFractionsByName(compositionMap& x) const {
x.clear();
int kk = nSpecies();
for (int k = 0; k < kk; k++) {
x[speciesName(k)] = State::moleFraction(k);
}
}
void ThermoPhase::getActivities(doublereal* a) const
{
getActivityConcentrations(a);
for (size_t k = 0; k < nSpecies(); k++) {
a[k] /= standardConcentration(k);
}
}
void SingleSpeciesTP::initThermo()
{
/*
* Make sure there is one and only one species in this phase.
*/
if (nSpecies() != 1) {
throw CanteraError("initThermo",
"stoichiometric substances may only contain one species.");
}
/*
* Resize temporary arrays.
*/
m_h0_RT.resize(1);
m_cp0_R.resize(1);
m_s0_R.resize(1);
/*
* Make sure the species mole fraction is equal to 1.0;
*/
double x = 1.0;
ThermoPhase::setMoleFractions(&x);
/*
* Call the base class initThermo object.
*/
ThermoPhase::initThermo();
}
void Phase::setMassFractionsByName(const std::string& y) {
compositionMap yy;
int kk = nSpecies();
for (int k = 0; k < kk; k++) {
yy[speciesName(k)] = -1.0;
}
parseCompString(y, yy);
setMassFractionsByName(yy);
}
doublereal Phase::chargeDensity() const {
int k;
int nsp = nSpecies();
doublereal cdens = 0.0;
for (k = 0; k < nsp; k++)
cdens += charge(k)*State::moleFraction(k);
cdens *= Faraday;
return cdens;
}
void Phase::setMassFractionsByName(const compositionMap& yMap)
{
size_t kk = nSpecies();
vector_fp mf(kk, 0.0);
for (size_t k = 0; k < kk; k++) {
mf[k] = std::max(getValue(yMap, speciesName(k), 0.0), 0.0);
}
setMassFractions(&mf[0]);
}
/*
* setMolalitiesByNames()
*
* Set the molalities of the solutes by name
*/
void MolalityVPSSTP::setMolalitiesByName(const std::string& x)
{
compositionMap xx;
for (size_t k = 0; k < nSpecies(); k++) {
xx[speciesName(k)] = -1.0;
}
parseCompString(x, xx);
setMolalitiesByName(xx);
}
void Phase::setMoleFractionsByName(compositionMap& xMap) {
int kk = nSpecies();
doublereal x;
vector_fp mf(kk, 0.0);
for (int k = 0; k < kk; k++) {
x = xMap[speciesName(k)];
if (x > 0.0) mf[k] = x;
}
setMoleFractions(&mf[0]);
}
doublereal Phase::chargeDensity() const
{
size_t kk = nSpecies();
doublereal cdens = 0.0;
for (size_t k = 0; k < kk; k++) {
cdens += charge(k)*moleFraction(k);
}
cdens *= Faraday;
return cdens;
}
void MixtureFugacityTP::initLengths()
{
m_kk = nSpecies();
moleFractions_.resize(m_kk, 0.0);
moleFractions_[0] = 1.0;
m_h0_RT.resize(m_kk, 0.0);
m_cp0_R.resize(m_kk, 0.0);
m_g0_RT.resize(m_kk, 0.0);
m_s0_R.resize(m_kk, 0.0);
}
void Phase::setMassFractionsByName(compositionMap& yMap) {
int kk = nSpecies();
doublereal y;
vector_fp mf(kk, 0.0);
for (int k = 0; k < kk; k++) {
y = yMap[speciesName(k)];
if (y > 0.0) mf[k] = y;
}
setMassFractions(&mf[0]);
}
void Phase::setMoleFractionsByName(const std::string& x)
{
size_t kk = nSpecies();
compositionMap xx;
for (size_t k = 0; k < kk; k++) {
xx[speciesName(k)] = -1.0;
}
parseCompString(x, xx);
setMoleFractionsByName(xx);
}
void ThermoPhase::resetHf298(size_t k) {
if (k != npos) {
m_spthermo->resetHf298(k);
} else {
for (size_t k = 0; k < nSpecies(); k++) {
m_spthermo->resetHf298(k);
}
}
invalidateCache();
}
// Initialize lengths of local variables after all species have
// been identified.
void GibbsExcessVPSSTP::initLengths() {
m_kk = nSpecies();
moleFractions_.resize(m_kk);
lnActCoeff_Scaled_.resize(m_kk);
dlnActCoeffdT_Scaled_.resize(m_kk);
d2lnActCoeffdT2_Scaled_.resize(m_kk);
dlnActCoeffdlnX_diag_.resize(m_kk);
dlnActCoeffdlnN_diag_.resize(m_kk);
dlnActCoeffdlnN_.resize(m_kk, m_kk);
m_pp.resize(m_kk);
}
void IdealMolalSoln::initThermo()
{
MolalityVPSSTP::initThermo();
for (size_t k = 0; k < nSpecies(); k++) {
m_speciesMolarVolume[k] = providePDSS(k)->molarVolume();
}
if (IMS_typeCutoff_ == 2) {
calcIMSCutoffParams_();
}
setMoleFSolventMin(1.0E-5);
}
doublereal MixedSolventElectrolyte::cp_mole() const
{
size_t kk = nSpecies();
double cp = 0;
vector_fp cpbar(kk);
getPartialMolarCp(&cpbar[0]);
for (size_t i = 0; i < kk; i++) {
cp += moleFractions_[i]*cpbar[i];
}
return cp;
}
doublereal MixedSolventElectrolyte::entropy_mole() const
{
size_t kk = nSpecies();
double s = 0;
vector_fp sbar(kk);
getPartialMolarEntropies(&sbar[0]);
for (size_t i = 0; i < kk; i++) {
s += moleFractions_[i]*sbar[i];
}
return s;
}
doublereal MixedSolventElectrolyte::enthalpy_mole() const
{
size_t kk = nSpecies();
double h = 0;
vector_fp hbar(kk);
getPartialMolarEnthalpies(&hbar[0]);
for (size_t i = 0; i < kk; i++) {
h += moleFractions_[i]*hbar[i];
}
return h;
}
void Phase::getMoleFractionsByName(compositionMap& x) const
{
warn_deprecated("void Phase::getMoleFractionsByName(compositionMap&)",
"To be removed after Cantera 2.2. Use"
" 'compositionMap getMoleFractionsByName(double threshold)'"
" instead");
x.clear();
size_t kk = nSpecies();
for (size_t k = 0; k < kk; k++) {
x[speciesName(k)] = Phase::moleFraction(k);
}
}
void LatticePhase::initThermo() {
m_kk = nSpecies();
m_mm = nElements();
doublereal tmin = m_spthermo->minTemp();
doublereal tmax = m_spthermo->maxTemp();
if (tmin > 0.0) m_tmin = tmin;
if (tmax > 0.0) m_tmax = tmax;
m_p0 = refPressure();
m_h0_RT.resize(m_kk);
m_g0_RT.resize(m_kk);
m_cp0_R.resize(m_kk);
m_s0_R.resize(m_kk);
setMolarDensity(m_molar_density);
}
void Phase::setMoleFractionsByName(const std::string& x) {
compositionMap xx;
int kk = nSpecies();
for (int k = 0; k < kk; k++) {
xx[speciesName(k)] = -1.0;
}
parseCompString(x, xx);
setMoleFractionsByName(xx);
//int kk = nSpecies();
//vector_fp mf(kk);
//for (int k = 0; k < kk; k++) {
// mf[k] = xx[speciesName(k)];
//}
//setMoleFractions(mf.begin());
}
void LatticeSolidPhase::initThermo() {
m_kk = nSpecies();
m_mm = nElements();
m_x.resize(m_kk);
int n, nsp, k, loc = 0;
doublereal ndens;
m_molar_density = 0.0;
for (n = 0; n < m_nlattice; n++) {
nsp = m_lattice[n]->nSpecies();
ndens = m_lattice[n]->molarDensity();
for (k = 0; k < nsp; k++) {
m_x[loc] = ndens * m_lattice[n]->moleFraction(k);
loc++;
}
m_molar_density += ndens;
}
setMoleFractions(DATA_PTR(m_x));
// const vector<string>& spnames = speciesNames();
// int n, k, kl, namesize;
// int nl = m_sitedens.size();
// string s;
// m_lattice.resize(m_kk,-1);
// vector_fp conc(m_kk, 0.0);
// compositionMap xx;
// for (n = 0; n < nl; n++) {
// for (k = 0; k < m_kk; k++) {
// xx[speciesName(k)] = -1.0;
// }
// parseCompString(m_sp[n], xx);
// for (k = 0; k < m_kk; k++) {
// if (xx[speciesName(k)] != -1.0) {
// conc[k] = m_sitedens[n]*xx[speciesName(k)];
// m_lattice[k] = n;
// }
// }
// }
// for (k = 0; k < m_kk; k++) {
// if (m_lattice[k] == -1) {
// throw CanteraError("LatticeSolidPhase::"
// "setParametersFromXML","Species "+speciesName(k)
// +" not a member of any lattice.");
// }
// }
// setMoleFractions(DATA_PTR(conc));
}
void ConstDensityThermo::initThermo() {
m_kk = nSpecies();
m_mm = nElements();
doublereal tmin = m_spthermo->minTemp();
doublereal tmax = m_spthermo->maxTemp();
if (tmin > 0.0) m_tmin = tmin;
if (tmax > 0.0) m_tmax = tmax;
m_p0 = refPressure();
m_h0_RT.resize(m_kk);
m_g0_RT.resize(m_kk);
m_expg0_RT.resize(m_kk);
m_cp0_R.resize(m_kk);
m_s0_R.resize(m_kk);
m_pe.resize(m_kk, 0.0);
m_pp.resize(m_kk);
}
