TEST_F(RedlichKister_Test, activityCoeffs)
{
const std::string valid_file("../data/RedlichKisterVPSSTP_valid.xml");
initializeTestPhaseWithXML(valid_file);
test_phase->setState_TP(298., 1.);
// Test that mu0 + RT log(activityCoeff * MoleFrac) == mu
const double RT = GasConstant * 298.;
vector_fp mu0(2);
vector_fp activityCoeffs(2);
vector_fp chemPotentials(2);
double xmin = 0.6;
double xmax = 0.9;
int numSteps = 9;
double dx = (xmax-xmin)/(numSteps-1);
for(int i=0; i < numSteps; ++i)
{
const double r = xmin + i*dx;
set_r(r);
test_phase->getChemPotentials(&chemPotentials[0]);
test_phase->getActivityCoefficients(&activityCoeffs[0]);
test_phase->getStandardChemPotentials(&mu0[0]);
EXPECT_NEAR(chemPotentials[0], mu0[0] + RT*std::log(activityCoeffs[0] * r), 1.e-6);
EXPECT_NEAR(chemPotentials[1], mu0[1] + RT*std::log(activityCoeffs[1] * (1-r)), 1.e-6);
}
}
TEST(HMWSoln, fromScratch)
{
// Regression test based on HMW_test_3
HMWSoln p;
auto sH2O = make_species("H2O(l)", "H:2, O:1", h2oliq_nasa_coeffs);
auto sCl = make_species("Cl-", "Cl:1, E:1", 0.0,
298.15, -52.8716, 333.15, -52.8716, 1e5);
sCl->charge = -1;
auto sH = make_species("H+", "H:1, E:-1", 0.0, 298.15, 0.0, 333.15, 0.0, 1e5);
sH->charge = 1;
auto sNa = make_species("Na+", "Na:1, E:-1", 0.0,
298.15, -125.5213, 333.15, -125.5213, 1e5);
sNa->charge = 1;
auto sOH = make_species("OH-", "O:1, H:1, E:1", 0.0,
298.15, -91.523, 333.15, -91.523, 1e5);
sOH->charge = -1;
for (auto& s : {sH2O, sCl, sH, sNa, sOH}) {
p.addSpecies(s);
}
std::unique_ptr<PDSS_Water> ss(new PDSS_Water());
p.installPDSS(0, std::move(ss));
size_t k = 1;
for (double v : {1.3, 1.3, 1.3, 1.3}) {
std::unique_ptr<PDSS_ConstVol> ss(new PDSS_ConstVol());
ss->setMolarVolume(v);
p.installPDSS(k++, std::move(ss));
}
p.setPitzerTempModel("complex");
p.setA_Debye(1.175930);
p.initThermo();
set_hmw_interactions(p);
p.setMolalitiesByName("Na+:6.0997 Cl-:6.0996986044628 H+:2.1628E-9 OH-:1.3977E-6");
p.setState_TP(150 + 273.15, 101325);
size_t N = p.nSpecies();
vector_fp acMol(N), mf(N), activities(N), moll(N), mu0(N);
p.getMolalityActivityCoefficients(acMol.data());
p.getMoleFractions(mf.data());
p.getActivities(activities.data());
p.getMolalities(moll.data());
p.getStandardChemPotentials(mu0.data());
double acMolRef[] = {0.9341, 1.0191, 3.9637, 1.0191, 0.4660};
double mfRef[] = {0.8198, 0.0901, 0.0000, 0.0901, 0.0000};
double activitiesRef[] = {0.7658, 6.2164, 0.0000, 6.2164, 0.0000};
double mollRef[] = {55.5084, 6.0997, 0.0000, 6.0997, 0.0000};
double mu0Ref[] = {-317.175788, -186.014558, 0.0017225, -441.615429, -322.000412}; // kJ/gmol
for (size_t k = 0 ; k < N; k++) {
EXPECT_NEAR(acMol[k], acMolRef[k], 2e-4);
EXPECT_NEAR(mf[k], mfRef[k], 2e-4);
EXPECT_NEAR(activities[k], activitiesRef[k], 2e-4);
EXPECT_NEAR(moll[k], mollRef[k], 2e-4);
EXPECT_NEAR(mu0[k]/1e6, mu0Ref[k], 2e-6);
}
}
/**
* @test Test cosine of incidence angle (μ<SUB>0</SUB>)
* calculations in MaRC::OblateSpheroid.
*/
bool test_mu0()
{
auto const o =
std::make_unique<MaRC::OblateSpheroid>(prograde, a, c);
constexpr double sub_solar_lat = -65 * C::degree;
constexpr double sub_solar_lon = 135 * C::degree;
constexpr double lat = 47 * C::degree;
constexpr double lon = 330 * C::degree;
// Cosine of the incidence angle.
double const mu0 = o->mu0(sub_solar_lat,
sub_solar_lon,
lat,
lon);
// We assume the Sun is an infinite distance away from the body.
// Unit vector from the Sun to the center of the oblate spheroid
// (e.g. planet) in body coordindates.
MaRC::DVector const rs =
{
cos(sub_solar_lat) * cos(sub_solar_lon),
cos(sub_solar_lat) * sin(sub_solar_lon),
sin(sub_solar_lat)
};
double const radius = o->centric_radius(lat);
// Vector from the center of the oblate spheroid to the point on
// the surface at the given latitude and longitude.
MaRC::DVector const re = { radius * cos(lat) * cos(lon),
radius * cos(lat) * sin(lon),
radius * sin(lat) };
double const a2 = a * a;
double const c2 = c * c;
// Normal vector at (lat, lon) (i.e. grad(f(x, y, z))).
MaRC::DVector const rn = { 2 * re[0] / a2,
2 * re[1] / a2,
2 * re[2] / c2 };
// Cosine of angle between the Sun and the vector normal to the
// surface at (lat, lon), the incidence angle in this case.
double const mu0_2 = cos_included_angle(rs, rn);
return MaRC::almost_equal(mu0, mu0_2, ulps);
}
/// \brief Quantities constructor
///
/// Requires properties:
/// - everything required by euler::quantities
/// - free-stream Reynoldsh number
/// - stagnation Prandtl number
/// - Sutherland's constant
explicit Quantities(io::Properties properties) noexcept
: euler::Quantities(properties)
, ReInfty_(io::read<quantity::Dimensionless>(properties, "ReInfty"))
, Pr0_(io::read<quantity::Dimensionless>(properties, "Pr0"))
, S0_(io::read<quantity::Temperature>(properties, "Sutherland0"))
, sOverTref_(S0_ / T0_)
, sOverTrefP1_(sOverTref_ + 1.0)
, Re0_(Re_infinity() * mu_infinity() / (rho_infinity() * u_infinity())) {
std::cerr << "Free-stream variables: "
<< "ReInfty = " << ReInfty_ << " "
<< "muInfty = " << mu_infinity()
<< "\n";
std::cerr << "Stagnation variables: "
<< "Pr0 = " << Pr0_ << " "
<< "S0 = " << S0_ << " "
<< "Re0 = " << Re0_ << " "
<< "mu0 = " << mu0()
<< "\n";
}
void VCS_PROB::reportCSV(const std::string& reportFile)
{
size_t k;
size_t istart;
double vol = 0.0;
string sName;
FILE* FP = fopen(reportFile.c_str(), "w");
if (!FP) {
plogf("Failure to open file\n");
exit(EXIT_FAILURE);
}
double Temp = T;
std::vector<double> volPM(nspecies, 0.0);
std::vector<double> activity(nspecies, 0.0);
std::vector<double> ac(nspecies, 0.0);
std::vector<double> mu(nspecies, 0.0);
std::vector<double> mu0(nspecies, 0.0);
std::vector<double> molalities(nspecies, 0.0);
vol = 0.0;
size_t iK = 0;
for (size_t iphase = 0; iphase < NPhase; iphase++) {
istart = iK;
vcs_VolPhase* volP = VPhaseList[iphase];
//const Cantera::ThermoPhase *tptr = volP->ptrThermoPhase();
size_t nSpeciesPhase = volP->nSpecies();
volPM.resize(nSpeciesPhase, 0.0);
volP->sendToVCS_VolPM(VCS_DATA_PTR(volPM));
double TMolesPhase = volP->totalMoles();
double VolPhaseVolumes = 0.0;
for (k = 0; k < nSpeciesPhase; k++) {
iK++;
VolPhaseVolumes += volPM[istart + k] * mf[istart + k];
}
VolPhaseVolumes *= TMolesPhase;
vol += VolPhaseVolumes;
}
fprintf(FP,"--------------------- VCS_MULTIPHASE_EQUIL FINAL REPORT"
" -----------------------------\n");
fprintf(FP,"Temperature = %11.5g kelvin\n", Temp);
fprintf(FP,"Pressure = %11.5g Pascal\n", PresPA);
fprintf(FP,"Total Volume = %11.5g m**3\n", vol);
fprintf(FP,"Number Basis optimizations = %d\n", m_NumBasisOptimizations);
fprintf(FP,"Number VCS iterations = %d\n", m_Iterations);
iK = 0;
for (size_t iphase = 0; iphase < NPhase; iphase++) {
istart = iK;
vcs_VolPhase* volP = VPhaseList[iphase];
const Cantera::ThermoPhase<doublereal>* tp = volP->ptrThermoPhase();
string phaseName = volP->PhaseName;
size_t nSpeciesPhase = volP->nSpecies();
volP->sendToVCS_VolPM(VCS_DATA_PTR(volPM));
double TMolesPhase = volP->totalMoles();
//AssertTrace(TMolesPhase == m_mix->phaseMoles(iphase));
activity.resize(nSpeciesPhase, 0.0);
ac.resize(nSpeciesPhase, 0.0);
mu0.resize(nSpeciesPhase, 0.0);
mu.resize(nSpeciesPhase, 0.0);
volPM.resize(nSpeciesPhase, 0.0);
molalities.resize(nSpeciesPhase, 0.0);
int actConvention = tp->activityConvention();
tp->getActivities(VCS_DATA_PTR(activity));
tp->getActivityCoefficients(VCS_DATA_PTR(ac));
tp->getStandardChemPotentials(VCS_DATA_PTR(mu0));
tp->getPartialMolarVolumes(VCS_DATA_PTR(volPM));
tp->getChemPotentials(VCS_DATA_PTR(mu));
double VolPhaseVolumes = 0.0;
for (k = 0; k < nSpeciesPhase; k++) {
VolPhaseVolumes += volPM[k] * mf[istart + k];
}
VolPhaseVolumes *= TMolesPhase;
vol += VolPhaseVolumes;
if (actConvention == 1) {
const Cantera::MolalityVPSSTP* mTP = static_cast<const Cantera::MolalityVPSSTP*>(tp);
tp->getChemPotentials(VCS_DATA_PTR(mu));
mTP->getMolalities(VCS_DATA_PTR(molalities));
tp->getChemPotentials(VCS_DATA_PTR(mu));
if (iphase == 0) {
fprintf(FP," Name, Phase, PhaseMoles, Mole_Fract, "
"Molalities, ActCoeff, Activity,"
"ChemPot_SS0, ChemPot, mole_num, PMVol, Phase_Volume\n");
fprintf(FP," , , (kmol), , "
" , , ,"
" (J/kmol), (J/kmol), (kmol), (m**3/kmol), (m**3)\n");
}
for (k = 0; k < nSpeciesPhase; k++) {
sName = tp->speciesName(k);
fprintf(FP,"%12s, %11s, %11.3e, %11.3e, %11.3e, %11.3e, %11.3e,"
"%11.3e, %11.3e, %11.3e, %11.3e, %11.3e\n",
sName.c_str(),
phaseName.c_str(), TMolesPhase,
mf[istart + k], molalities[k], ac[k], activity[k],
mu0[k]*1.0E-6, mu[k]*1.0E-6,
mf[istart + k] * TMolesPhase,
volPM[k], VolPhaseVolumes);
}
} else {
if (iphase == 0) {
fprintf(FP," Name, Phase, PhaseMoles, Mole_Fract, "
"Molalities, ActCoeff, Activity,"
" ChemPotSS0, ChemPot, mole_num, PMVol, Phase_Volume\n");
fprintf(FP," , , (kmol), , "
" , , ,"
" (J/kmol), (J/kmol), (kmol), (m**3/kmol), (m**3)\n");
}
for (k = 0; k < nSpeciesPhase; k++) {
molalities[k] = 0.0;
}
for (k = 0; k < nSpeciesPhase; k++) {
sName = tp->speciesName(k);
fprintf(FP,"%12s, %11s, %11.3e, %11.3e, %11.3e, %11.3e, %11.3e, "
"%11.3e, %11.3e,% 11.3e, %11.3e, %11.3e\n",
sName.c_str(),
phaseName.c_str(), TMolesPhase,
mf[istart + k], molalities[k], ac[k],
activity[k], mu0[k]*1.0E-6, mu[k]*1.0E-6,
mf[istart + k] * TMolesPhase,
volPM[k], VolPhaseVolumes);
}
}
#ifdef DEBUG_MODE
/*
* Check consistency: These should be equal
*/
tp->getChemPotentials(VCS_DATA_PTR(m_gibbsSpecies)+istart);
for (k = 0; k < nSpeciesPhase; k++) {
if (!vcs_doubleEqual(m_gibbsSpecies[istart+k], mu[k])) {
fprintf(FP,"ERROR: incompatibility!\n");
fclose(FP);
plogf("ERROR: incompatibility!\n");
exit(EXIT_FAILURE);
}
}
#endif
iK += nSpeciesPhase;
}
fclose(FP);
}
RcppExport SEXP nsem3b(SEXP data,
SEXP theta,
SEXP Sigma,
SEXP modelpar,
SEXP control
) {
// srand ( time(NULL) ); /* initialize random seed: */
Rcpp::NumericVector Theta(theta);
Rcpp::NumericMatrix D(data);
unsigned nobs = D.nrow(), k = D.ncol();
mat Data(D.begin(), nobs, k, false); // Avoid copying
Rcpp::NumericMatrix V(Sigma);
mat S(V.begin(), V.nrow(), V.ncol());
S(0,0) = 1;
mat iS = inv(S);
double detS = det(S);
Rcpp::List Modelpar(modelpar);
// Rcpp::IntegerVector _nlatent = Modelpar["nlatent"]; unsigned nlatent = _nlatent[0];
Rcpp::IntegerVector _ny0 = Modelpar["nvar0"]; unsigned ny0 = _ny0[0];
Rcpp::IntegerVector _ny1 = Modelpar["nvar1"]; unsigned ny1 = _ny1[0];
Rcpp::IntegerVector _ny2 = Modelpar["nvar2"]; unsigned ny2 = _ny2[0];
Rcpp::IntegerVector _npred0 = Modelpar["npred0"]; unsigned npred0 = _npred0[0];
Rcpp::IntegerVector _npred1 = Modelpar["npred1"]; unsigned npred1 = _npred1[0];
Rcpp::IntegerVector _npred2 = Modelpar["npred2"]; unsigned npred2 = _npred2[0];
Rcpp::List Control(control);
Rcpp::NumericVector _lambda = Control["lambda"]; double lambda = _lambda[0];
Rcpp::NumericVector _niter = Control["niter"]; double niter = _niter[0];
Rcpp::NumericVector _Dtol = Control["Dtol"]; double Dtol = _Dtol[0];
rowvec mu0(ny0), lambda0(ny0);
rowvec mu1(ny1), lambda1(ny1);
rowvec mu2(ny2), lambda2(ny2);
rowvec beta0(npred0);
rowvec beta1(npred1);
rowvec beta2(npred2);
rowvec gamma(2);
rowvec gamma2(2);
unsigned pos=0;
for (unsigned i=0; i<ny0; i++) {
mu0(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<ny1; i++) {
mu1(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<ny2; i++) {
mu2(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<ny0; i++) {
lambda0(i) = Theta[pos];
pos++;
}
lambda1(0) = 1;
for (unsigned i=1; i<ny1; i++) {
lambda1(i) = Theta[pos];
pos++;
}
lambda2(0) = 1;
for (unsigned i=1; i<ny2; i++) {
lambda2(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<npred0; i++) {
beta0(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<npred1; i++) {
beta1(i) = Theta[pos];
pos++;
}
for (unsigned i=0; i<npred2; i++) {
beta2(i) = Theta[pos];
pos++;
}
gamma(0) = Theta[pos]; gamma(1) = Theta[pos+1];
gamma2(0) = Theta[pos+2]; gamma2(1) = Theta[pos+3];
// cerr << "mu0=" << mu0 << endl;
// cerr << "mu1=" << mu1 << endl;
// cerr << "mu2=" << mu2 << endl;
// cerr << "lambda0=" << lambda0 << endl;
// cerr << "lambda1=" << lambda1 << endl;
// cerr << "lambda2=" << lambda2 << endl;
// cerr << "beta0=" << beta0 << endl;
// cerr << "beta1=" << beta1 << endl;
// cerr << "beta2=" << beta2 << endl;
// cerr << "gamma=" << gamma << endl;
// cerr << "gamma2=" << gamma2 << endl;
mat lap(nobs,4);
for (unsigned i=0; i<nobs; i++) {
rowvec newlap = laNRb(Data.row(i), iS, detS,
mu0, mu1, mu2,
lambda0, lambda1, lambda2,
beta0,beta1, beta2, gamma, gamma2,
Dtol,niter,lambda);
lap.row(i) = newlap;
}
List res;
res["indiv"] = lap;
res["logLik"] = sum(lap.col(0)) + (3-V.nrow())*log(2.0*datum::pi)*nobs/2;
res["norm0"] = (3-V.nrow())*log(2*datum::pi)/2;
return res;
}
void VCS_PROB::reportCSV(const std::string& reportFile)
{
FILE* FP = fopen(reportFile.c_str(), "w");
if (!FP) {
throw CanteraError("VCS_PROB::reportCSV", "Failure to open file");
}
vector_fp volPM(nspecies, 0.0);
vector_fp activity(nspecies, 0.0);
vector_fp ac(nspecies, 0.0);
vector_fp mu(nspecies, 0.0);
vector_fp mu0(nspecies, 0.0);
vector_fp molalities(nspecies, 0.0);
double vol = 0.0;
size_t iK = 0;
for (size_t iphase = 0; iphase < NPhase; iphase++) {
size_t istart = iK;
vcs_VolPhase* volP = VPhaseList[iphase];
size_t nSpeciesPhase = volP->nSpecies();
volPM.resize(nSpeciesPhase, 0.0);
volP->sendToVCS_VolPM(&volPM[0]);
double TMolesPhase = volP->totalMoles();
double VolPhaseVolumes = 0.0;
for (size_t k = 0; k < nSpeciesPhase; k++) {
iK++;
VolPhaseVolumes += volPM[istart + k] * mf[istart + k];
}
VolPhaseVolumes *= TMolesPhase;
vol += VolPhaseVolumes;
}
fprintf(FP,"--------------------- VCS_MULTIPHASE_EQUIL FINAL REPORT"
" -----------------------------\n");
fprintf(FP,"Temperature = %11.5g kelvin\n", T);
fprintf(FP,"Pressure = %11.5g Pascal\n", PresPA);
fprintf(FP,"Total Volume = %11.5g m**3\n", vol);
fprintf(FP,"Number Basis optimizations = %d\n", m_NumBasisOptimizations);
fprintf(FP,"Number VCS iterations = %d\n", m_Iterations);
iK = 0;
for (size_t iphase = 0; iphase < NPhase; iphase++) {
size_t istart = iK;
vcs_VolPhase* volP = VPhaseList[iphase];
const ThermoPhase* tp = volP->ptrThermoPhase();
string phaseName = volP->PhaseName;
size_t nSpeciesPhase = volP->nSpecies();
volP->sendToVCS_VolPM(&volPM[0]);
double TMolesPhase = volP->totalMoles();
activity.resize(nSpeciesPhase, 0.0);
ac.resize(nSpeciesPhase, 0.0);
mu0.resize(nSpeciesPhase, 0.0);
mu.resize(nSpeciesPhase, 0.0);
volPM.resize(nSpeciesPhase, 0.0);
molalities.resize(nSpeciesPhase, 0.0);
int actConvention = tp->activityConvention();
tp->getActivities(&activity[0]);
tp->getActivityCoefficients(&ac[0]);
tp->getStandardChemPotentials(&mu0[0]);
tp->getPartialMolarVolumes(&volPM[0]);
tp->getChemPotentials(&mu[0]);
double VolPhaseVolumes = 0.0;
for (size_t k = 0; k < nSpeciesPhase; k++) {
VolPhaseVolumes += volPM[k] * mf[istart + k];
}
VolPhaseVolumes *= TMolesPhase;
vol += VolPhaseVolumes;
if (actConvention == 1) {
const MolalityVPSSTP* mTP = static_cast<const MolalityVPSSTP*>(tp);
tp->getChemPotentials(&mu[0]);
mTP->getMolalities(&molalities[0]);
tp->getChemPotentials(&mu[0]);
if (iphase == 0) {
fprintf(FP," Name, Phase, PhaseMoles, Mole_Fract, "
"Molalities, ActCoeff, Activity,"
"ChemPot_SS0, ChemPot, mole_num, PMVol, Phase_Volume\n");
fprintf(FP," , , (kmol), , "
" , , ,"
" (J/kmol), (J/kmol), (kmol), (m**3/kmol), (m**3)\n");
}
for (size_t k = 0; k < nSpeciesPhase; k++) {
std::string sName = tp->speciesName(k);
fprintf(FP,"%12s, %11s, %11.3e, %11.3e, %11.3e, %11.3e, %11.3e,"
"%11.3e, %11.3e, %11.3e, %11.3e, %11.3e\n",
sName.c_str(),
phaseName.c_str(), TMolesPhase,
mf[istart + k], molalities[k], ac[k], activity[k],
mu0[k]*1.0E-6, mu[k]*1.0E-6,
mf[istart + k] * TMolesPhase,
volPM[k], VolPhaseVolumes);
}
} else {
if (iphase == 0) {
fprintf(FP," Name, Phase, PhaseMoles, Mole_Fract, "
"Molalities, ActCoeff, Activity,"
" ChemPotSS0, ChemPot, mole_num, PMVol, Phase_Volume\n");
fprintf(FP," , , (kmol), , "
" , , ,"
" (J/kmol), (J/kmol), (kmol), (m**3/kmol), (m**3)\n");
}
for (size_t k = 0; k < nSpeciesPhase; k++) {
molalities[k] = 0.0;
}
for (size_t k = 0; k < nSpeciesPhase; k++) {
std::string sName = tp->speciesName(k);
fprintf(FP,"%12s, %11s, %11.3e, %11.3e, %11.3e, %11.3e, %11.3e, "
"%11.3e, %11.3e,% 11.3e, %11.3e, %11.3e\n",
sName.c_str(),
phaseName.c_str(), TMolesPhase,
mf[istart + k], molalities[k], ac[k],
activity[k], mu0[k]*1.0E-6, mu[k]*1.0E-6,
mf[istart + k] * TMolesPhase,
volPM[k], VolPhaseVolumes);
}
}
iK += nSpeciesPhase;
}
fclose(FP);
}
/// \brief $\mu = \overline{\mu} / \overline{\mu}_0$
inline quantity::Dimensionless mu
(const quantity::DynamicViscosity dynamicViscosity) const noexcept {
return dynamicViscosity / mu0();
}
