double mitk::GeneralizedLinearModel::Predict( const vnl_vector<double> &c)
{
LogItLinking link;
double mu = 0;
int cols = m_B.size();
for (int i = 0; i < cols; ++i)
{
if (!m_AddConstantColumn)
mu += c(i)* m_B(i);
else if ( i == 0)
mu += 1* m_B(i);
else
mu += c(i-1)*m_B(i);
}
return link.InverseLink(mu);
}
vnl_vector<double> mitk::GeneralizedLinearModel::ExpMu(const vnl_matrix<double> &x)
{
LogItLinking link;
vnl_vector<double> mu(x.rows());
int cols = m_B.size();
for (unsigned int r = 0 ; r < mu.size(); ++r)
{
mu(r) = 0;
for (int c = 0; c < cols; ++c)
{
if (!m_AddConstantColumn)
mu(r) += x(r,c)*m_B(c);
else if ( c == 0)
mu(r) += m_B(c);
else
mu(r) += x(r,c-1)*m_B(c);
}
mu(r) = exp(-mu(r));
}
return mu;
}
/*
*
* Solve for the diffusional velocities in the Stefan-Maxwell equations
*
*/
void LiquidTransport::stefan_maxwell_solve() {
doublereal tmp;
size_t VIM = m_nDim;
m_B.resize(m_nsp, VIM);
//! grab a local copy of the molecular weights
const vector_fp& M = m_thermo->molecularWeights();
/*
* Update the concentrations in the mixture.
*/
update_conc();
double T = m_thermo->temperature();
m_thermo->getStandardVolumes(DATA_PTR(volume_specPM_));
m_thermo->getActivityCoefficients(DATA_PTR(actCoeffMolar_));
/*
* Calculate the electrochemical potential gradient. This is the
* driving force for relative diffusional transport.
*
* Here we calculate
*
* c_i * (grad (mu_i) + S_i grad T - M_i / dens * grad P
*
* This is Eqn. 13-1 p. 318 Newman. The original equation is from
* Hershfeld, Curtis, and Bird.
*
* S_i is the partial molar entropy of species i. This term will cancel
* out a lot of the grad T terms in grad (mu_i), therefore simplifying
* the expression.
*
* Ok I think there may be many ways to do this. One way is to do it via basis
* functions, at the nodes, as a function of the variables in the problem.
*
* For calculation of molality based thermo systems, we current get
* the molar based values. This may change.
*
* Note, we have broken the symmetry of the matrix here, due to
* consideratins involving species concentrations going to zero.
*
*/
for (size_t i = 0; i < m_nsp; i++) {
double xi_denom = m_molefracs_tran[i];
for (size_t a = 0; a < VIM; a++) {
m_ck_Grad_mu[a*m_nsp + i] =
m_chargeSpecies[i] * concTot_ * Faraday * m_Grad_V[a]
+ concTot_ * (volume_specPM_[i] - M[i]/dens_) * m_Grad_P[a]
+ concTot_ * GasConstant * T * m_Grad_lnAC[a*m_nsp+i] / actCoeffMolar_[i]
+ concTot_ * GasConstant * T * m_Grad_X[a*m_nsp+i] / xi_denom;
}
}
if (m_thermo->activityConvention() == cAC_CONVENTION_MOLALITY) {
int iSolvent = 0;
double mwSolvent = m_thermo->molecularWeight(iSolvent);
double mnaught = mwSolvent/ 1000.;
double lnmnaught = log(mnaught);
for (size_t i = 1; i < m_nsp; i++) {
for (size_t a = 0; a < VIM; a++) {
m_ck_Grad_mu[a*m_nsp + i] -=
m_concentrations[i] * GasConstant * m_Grad_T[a] * lnmnaught;
}
}
}
/*
* Just for Note, m_A(i,j) refers to the ith row and jth column.
* They are still fortran ordered, so that i varies fastest.
*/
switch (VIM) {
case 1: /* 1-D approximation */
m_B(0,0) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
m_A(0,j) = M[j] * m_concentrations[j];
}
for (size_t i = 1; i < m_nsp; i++){
m_B(i,0) = m_ck_Grad_mu[i] / (GasConstant * T);
m_A(i,i) = 0.0;
for (size_t j = 0; j < m_nsp; j++){
if (j != i) {
tmp = m_concentrations[j] / m_DiffCoeff_StefMax(i,j);
m_A(i,i) += tmp;
m_A(i,j) = - tmp;
}
}
}
//! invert and solve the system Ax = b. Answer is in m_B
solve(m_A, m_B);
break;
case 2: /* 2-D approximation */
m_B(0,0) = 0.0;
m_B(0,1) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
m_A(0,j) = M[j] * m_concentrations[j];
}
for (size_t i = 1; i < m_nsp; i++){
m_B(i,0) = m_ck_Grad_mu[i] / (GasConstant * T);
m_B(i,1) = m_ck_Grad_mu[m_nsp + i] / (GasConstant * T);
m_A(i,i) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
if (j != i) {
tmp = m_concentrations[j] / m_DiffCoeff_StefMax(i,j);
m_A(i,i) += tmp;
m_A(i,j) = - tmp;
}
}
}
//! invert and solve the system Ax = b. Answer is in m_B
solve(m_A, m_B);
break;
case 3: /* 3-D approximation */
m_B(0,0) = 0.0;
m_B(0,1) = 0.0;
m_B(0,2) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
m_A(0,j) = M[j] * m_concentrations[j];
}
for (size_t i = 1; i < m_nsp; i++){
m_B(i,0) = m_ck_Grad_mu[i] / (GasConstant * T);
m_B(i,1) = m_ck_Grad_mu[m_nsp + i] / (GasConstant * T);
m_B(i,2) = m_ck_Grad_mu[2*m_nsp + i] / (GasConstant * T);
m_A(i,i) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
if (j != i) {
tmp = m_concentrations[j] / m_DiffCoeff_StefMax(i,j);
m_A(i,i) += tmp;
m_A(i,j) = - tmp;
}
}
}
//! invert and solve the system Ax = b. Answer is in m_B
solve(m_A, m_B);
break;
default:
printf("uninmplemetnd\n");
throw CanteraError("routine", "not done");
break;
}
for (size_t a = 0; a < VIM; a++) {
for (size_t j = 0; j < m_nsp; j++) {
m_flux(j,a) = M[j] * m_concentrations[j] * m_B(j,a);
}
}
}
void AqueousTransport::stefan_maxwell_solve()
{
size_t VIM = 2;
m_B.resize(m_nsp, VIM);
// grab a local copy of the molecular weights
const vector_fp& M = m_thermo->molecularWeights();
// get the mean molecular weight of the mixture
//double M_mix = m_thermo->meanMolecularWeight();
// get the concentration of the mixture
//double rho = m_thermo->density();
//double c = rho/M_mix;
m_thermo->getMoleFractions(DATA_PTR(m_molefracs));
double T = m_thermo->temperature();
/* electrochemical potential gradient */
for (size_t i = 0; i < m_nsp; i++) {
for (size_t a = 0; a < VIM; a++) {
m_Grad_mu[a*m_nsp + i] = m_chargeSpecies[i] * Faraday * m_Grad_V[a]
+ (GasConstant*T/m_molefracs[i]) * m_Grad_X[a*m_nsp+i];
}
}
/*
* Just for Note, m_A(i,j) refers to the ith row and jth column.
* They are still fortran ordered, so that i varies fastest.
*/
switch (VIM) {
case 1: /* 1-D approximation */
m_B(0,0) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
m_A(0,j) = 1.0;
}
for (size_t i = 1; i < m_nsp; i++) {
m_B(i,0) = m_concentrations[i] * m_Grad_mu[i] / (GasConstant * T);
for (size_t j = 0; j < m_nsp; j++) {
if (j != i) {
m_A(i,j) = m_molefracs[i] / (M[j] * m_DiffCoeff_StefMax(i,j));
m_A(i,i) -= m_molefracs[j] / (M[i] * m_DiffCoeff_StefMax(i,j));
} else if (j == i) {
m_A(i,i) = 0.0;
}
}
}
//! invert and solve the system Ax = b. Answer is in m_B
solve(m_A, m_B.ptrColumn(0));
m_flux = m_B;
break;
case 2: /* 2-D approximation */
m_B(0,0) = 0.0;
m_B(0,1) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
m_A(0,j) = 1.0;
}
for (size_t i = 1; i < m_nsp; i++) {
m_B(i,0) = m_concentrations[i] * m_Grad_mu[i] / (GasConstant * T);
m_B(i,1) = m_concentrations[i] * m_Grad_mu[m_nsp + i] / (GasConstant * T);
for (size_t j = 0; j < m_nsp; j++) {
if (j != i) {
m_A(i,j) = m_molefracs[i] / (M[j] * m_DiffCoeff_StefMax(i,j));
m_A(i,i) -= m_molefracs[j] / (M[i] * m_DiffCoeff_StefMax(i,j));
} else if (j == i) {
m_A(i,i) = 0.0;
}
}
}
//! invert and solve the system Ax = b. Answer is in m_B
//solve(m_A, m_B);
m_flux = m_B;
break;
case 3: /* 3-D approximation */
m_B(0,0) = 0.0;
m_B(0,1) = 0.0;
m_B(0,2) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
m_A(0,j) = 1.0;
}
for (size_t i = 1; i < m_nsp; i++) {
m_B(i,0) = m_concentrations[i] * m_Grad_mu[i] / (GasConstant * T);
m_B(i,1) = m_concentrations[i] * m_Grad_mu[m_nsp + i] / (GasConstant * T);
m_B(i,2) = m_concentrations[i] * m_Grad_mu[2*m_nsp + i] / (GasConstant * T);
for (size_t j = 0; j < m_nsp; j++) {
if (j != i) {
m_A(i,j) = m_molefracs[i] / (M[j] * m_DiffCoeff_StefMax(i,j));
m_A(i,i) -= m_molefracs[j] / (M[i] * m_DiffCoeff_StefMax(i,j));
} else if (j == i) {
m_A(i,i) = 0.0;
}
}
}
//! invert and solve the system Ax = b. Answer is in m_B
//solve(m_A, m_B);
m_flux = m_B;
break;
default:
printf("unimplemented\n");
throw CanteraError("routine", "not done");
break;
}
}
void LiquidTransport::stefan_maxwell_solve()
{
doublereal tmp;
m_B.resize(m_nsp, m_nDim, 0.0);
m_A.resize(m_nsp, m_nsp, 0.0);
//! grab a local copy of the molecular weights
const vector_fp& M = m_thermo->molecularWeights();
//! grad a local copy of the ion molar volume (inverse total ion concentration)
const doublereal vol = m_thermo->molarVolume();
/*
* Update the temperature, concentrations and diffusion coefficients in the mixture.
*/
update_T();
update_C();
if (!m_diff_temp_ok) {
updateDiff_T();
}
double T = m_thermo->temperature();
update_Grad_lnAC();
m_thermo->getActivityCoefficients(DATA_PTR(m_actCoeff));
/*
* Calculate the electrochemical potential gradient. This is the
* driving force for relative diffusional transport.
*
* Here we calculate
*
* X_i * (grad (mu_i) + S_i grad T - M_i / dens * grad P
*
* This is Eqn. 13-1 p. 318 Newman. The original equation is from
* Hershfeld, Curtis, and Bird.
*
* S_i is the partial molar entropy of species i. This term will cancel
* out a lot of the grad T terms in grad (mu_i), therefore simplifying
* the expression.
*
* Ok I think there may be many ways to do this. One way is to do it via basis
* functions, at the nodes, as a function of the variables in the problem.
*
* For calculation of molality based thermo systems, we current get
* the molar based values. This may change.
*
* Note, we have broken the symmetry of the matrix here, due to
* considerations involving species concentrations going to zero.
*/
for (size_t a = 0; a < m_nDim; a++) {
for (size_t i = 0; i < m_nsp; i++) {
m_Grad_mu[a*m_nsp + i] =
m_chargeSpecies[i] * Faraday * m_Grad_V[a]
+ GasConstant * T * m_Grad_lnAC[a*m_nsp+i];
}
}
if (m_thermo->activityConvention() == cAC_CONVENTION_MOLALITY) {
int iSolvent = 0;
double mwSolvent = m_thermo->molecularWeight(iSolvent);
double mnaught = mwSolvent/ 1000.;
double lnmnaught = log(mnaught);
for (size_t a = 0; a < m_nDim; a++) {
for (size_t i = 1; i < m_nsp; i++) {
m_Grad_mu[a*m_nsp + i] -=
m_molefracs[i] * GasConstant * m_Grad_T[a] * lnmnaught;
}
}
}
/*
* Just for Note, m_A(i,j) refers to the ith row and jth column.
* They are still fortran ordered, so that i varies fastest.
*/
double condSum1;
const doublereal invRT = 1.0 / (GasConstant * T);
switch (m_nDim) {
case 1: /* 1-D approximation */
m_B(0,0) = 0.0;
//equation for the reference velocity
for (size_t j = 0; j < m_nsp; j++) {
if (m_velocityBasis == VB_MOLEAVG) {
m_A(0,j) = m_molefracs_tran[j];
} else if (m_velocityBasis == VB_MASSAVG) {
m_A(0,j) = m_massfracs_tran[j];
} else if ((m_velocityBasis >= 0)
&& (m_velocityBasis < static_cast<int>(m_nsp))) {
// use species number m_velocityBasis as reference velocity
if (m_velocityBasis == static_cast<int>(j)) {
m_A(0,j) = 1.0;
} else {
m_A(0,j) = 0.0;
}
} else {
throw CanteraError("LiquidTransport::stefan_maxwell_solve",
"Unknown reference velocity provided.");
}
}
for (size_t i = 1; i < m_nsp; i++) {
m_B(i,0) = m_Grad_mu[i] * invRT;
m_A(i,i) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
if (j != i) {
tmp = m_molefracs_tran[j] * m_bdiff(i,j);
m_A(i,i) -= tmp;
m_A(i,j) = tmp;
}
}
}
//! invert and solve the system Ax = b. Answer is in m_B
solve(m_A, m_B);
condSum1 = 0;
for (size_t i = 0; i < m_nsp; i++) {
condSum1 -= Faraday*m_chargeSpecies[i]*m_B(i,0)*m_molefracs_tran[i]/vol;
}
break;
case 2: /* 2-D approximation */
m_B(0,0) = 0.0;
m_B(0,1) = 0.0;
//equation for the reference velocity
for (size_t j = 0; j < m_nsp; j++) {
if (m_velocityBasis == VB_MOLEAVG) {
m_A(0,j) = m_molefracs_tran[j];
} else if (m_velocityBasis == VB_MASSAVG) {
m_A(0,j) = m_massfracs_tran[j];
} else if ((m_velocityBasis >= 0)
&& (m_velocityBasis < static_cast<int>(m_nsp))) {
// use species number m_velocityBasis as reference velocity
if (m_velocityBasis == static_cast<int>(j)) {
m_A(0,j) = 1.0;
} else {
m_A(0,j) = 0.0;
}
} else {
throw CanteraError("LiquidTransport::stefan_maxwell_solve",
"Unknown reference velocity provided.");
}
}
for (size_t i = 1; i < m_nsp; i++) {
m_B(i,0) = m_Grad_mu[i] * invRT;
m_B(i,1) = m_Grad_mu[m_nsp + i] * invRT;
m_A(i,i) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
if (j != i) {
tmp = m_molefracs_tran[j] * m_bdiff(i,j);
m_A(i,i) -= tmp;
m_A(i,j) = tmp;
}
}
}
//! invert and solve the system Ax = b. Answer is in m_B
solve(m_A, m_B);
break;
case 3: /* 3-D approximation */
m_B(0,0) = 0.0;
m_B(0,1) = 0.0;
m_B(0,2) = 0.0;
//equation for the reference velocity
for (size_t j = 0; j < m_nsp; j++) {
if (m_velocityBasis == VB_MOLEAVG) {
m_A(0,j) = m_molefracs_tran[j];
} else if (m_velocityBasis == VB_MASSAVG) {
m_A(0,j) = m_massfracs_tran[j];
} else if ((m_velocityBasis >= 0)
&& (m_velocityBasis < static_cast<int>(m_nsp))) {
// use species number m_velocityBasis as reference velocity
if (m_velocityBasis == static_cast<int>(j)) {
m_A(0,j) = 1.0;
} else {
m_A(0,j) = 0.0;
}
} else {
throw CanteraError("LiquidTransport::stefan_maxwell_solve",
"Unknown reference velocity provided.");
}
}
for (size_t i = 1; i < m_nsp; i++) {
m_B(i,0) = m_Grad_mu[i] * invRT;
m_B(i,1) = m_Grad_mu[m_nsp + i] * invRT;
m_B(i,2) = m_Grad_mu[2*m_nsp + i] * invRT;
m_A(i,i) = 0.0;
for (size_t j = 0; j < m_nsp; j++) {
if (j != i) {
tmp = m_molefracs_tran[j] * m_bdiff(i,j);
m_A(i,i) -= tmp;
m_A(i,j) = tmp;
}
}
}
//! invert and solve the system Ax = b. Answer is in m_B
solve(m_A, m_B);
break;
default:
printf("unimplemented\n");
throw CanteraError("routine", "not done");
break;
}
for (size_t a = 0; a < m_nDim; a++) {
for (size_t j = 0; j < m_nsp; j++) {
m_Vdiff(j,a) = m_B(j,a);
m_flux(j,a) = concTot_ * M[j] * m_molefracs_tran[j] * m_B(j,a);
}
}
}
mitk::GeneralizedLinearModel::GeneralizedLinearModel(const vnl_matrix<double> &xData, const vnl_vector<double> &yData, bool addConstantColumn) :
m_AddConstantColumn(addConstantColumn)
{
EstimatePermutation(xData);
DistSimpleBinominal dist;
LogItLinking link;
vnl_matrix<double> x;
int rows = xData.rows();
int cols = m_Permutation.size();
vnl_vector<double> mu(rows);
vnl_vector<double> eta(rows);
vnl_vector<double> weightedY(rows);
vnl_matrix<double> weightedX(rows, cols);
vnl_vector<double> oldB(cols);
_UpdatePermXMatrix(xData, m_AddConstantColumn, m_Permutation, x);
_InitMuEta(&dist, &link, yData, mu, eta);
int iter = 0;
int iterLimit = 100;
double sqrtEps = sqrt(std::numeric_limits<double>::epsilon());
double convertCriterion =1e-6;
m_B.set_size(m_Permutation.size());
m_B.fill(0);
while (iter <= iterLimit)
{
++iter;
oldB = m_B;
// Do Row-wise operation. No Vector oepration at this point.
for (int r = 0; r<rows; ++r)
{
double deta = link.DLink(mu(r));
double zBuffer = eta(r) + (yData(r) - mu(r))*deta;
double sqrtWeight = 1 / (std::abs(deta) * dist.SqrtVariance(mu(r)));
weightedY(r) = zBuffer * sqrtWeight;
for (int c=0; c<cols; ++c)
{
weightedX(r,c) = x(r,c) * sqrtWeight;
}
}
vnl_qr<double> qr(weightedX);
m_B = qr.solve(weightedY);
eta = x * m_B;
for (int r = 0; r < rows; ++r)
{
mu(r) = link.InverseLink(eta(r));
}
bool stayInLoop = false;
for(int c= 0; c < cols; ++c)
{
stayInLoop |= std::abs( m_B(c) - oldB(c)) > convertCriterion * std::max(sqrtEps, std::abs(oldB(c)));
}
if (!stayInLoop)
break;
}
_FinalizeBVector(m_B, m_Permutation, xData.cols());
}