void AqueousKinetics::updateROP()
{
_update_rates_T();
_update_rates_C();
if (m_ROP_ok) {
return;
}
// copy rate coefficients into ropf
m_ropf = m_rfn;
// multiply by perturbation factor
multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
// copy the forward rates to the reverse rates
m_ropr = m_ropf;
// for reverse rates computed from thermochemistry, multiply the forward
// rates copied into m_ropr by the reciprocals of the equilibrium constants
multiply_each(m_ropr.begin(), m_ropr.end(), m_rkcn.begin());
// multiply ropf by concentration products
m_reactantStoich.multiply(m_conc.data(), m_ropf.data());
// for reversible reactions, multiply ropr by concentration products
m_revProductStoich.multiply(m_conc.data(), m_ropr.data());
for (size_t j = 0; j != nReactions(); ++j) {
m_ropnet[j] = m_ropf[j] - m_ropr[j];
}
m_ROP_ok = true;
}
/**
*
* getFwdRateConstants():
*
* Update the rate of progress for the reactions.
* This key routine makes sure that the rate of progress vectors
* located in the solid kinetics data class are up to date.
*/
void GasKinetics::
getFwdRateConstants(doublereal* kfwd)
{
_update_rates_C();
_update_rates_T();
// copy rate coefficients into ropf
copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
// multiply ropf by enhanced 3b conc for all 3b rxns
if (!concm_3b_values.empty()) {
m_3b_concm.multiply(&m_ropf[0], &concm_3b_values[0]);
}
/*
* This routine is hardcoded to replace some of the values
* of the ropf vector.
*/
if (m_nfall) {
processFalloffReactions();
}
// multiply by perturbation factor
multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
for (size_t i = 0; i < m_ii; i++) {
kfwd[i] = m_ropf[i];
}
}
/**
* Update the rates of progress of the reactions in the reaciton
* mechanism. This routine operates on internal data.
*/
void InterfaceKinetics::getFwdRateConstants(doublereal* kfwd) {
_update_rates_T();
_update_rates_C();
const vector_fp& rf = m_kdata->m_rfn;
// copy rate coefficients into kfwd
copy(rf.begin(), rf.end(), kfwd);
// multiply by perturbation factor
multiply_each(kfwd, kfwd + nReactions(), m_perturb.begin());
}
void AqueousKinetics::getFwdRateConstants(doublereal* kfwd)
{
_update_rates_T();
_update_rates_C();
// copy rate coefficients into ropf
m_ropf = m_rfn;
// multiply by perturbation factor
multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
for (size_t i = 0; i < nReactions(); i++) {
kfwd[i] = m_ropf[i];
}
}
//====================================================================================================================
void GasKinetics::updateROP()
{
_update_rates_C();
_update_rates_T();
if (m_ROP_ok) {
return;
}
// copy rate coefficients into ropf
copy(m_rfn.begin(), m_rfn.end(), m_ropf.begin());
// multiply ropf by enhanced 3b conc for all 3b rxns
if (!concm_3b_values.empty()) {
m_3b_concm.multiply(&m_ropf[0], &concm_3b_values[0]);
}
if (m_nfall) {
processFalloffReactions();
}
// multiply by perturbation factor
multiply_each(m_ropf.begin(), m_ropf.end(), m_perturb.begin());
// copy the forward rates to the reverse rates
copy(m_ropf.begin(), m_ropf.end(), m_ropr.begin());
// for reverse rates computed from thermochemistry, multiply
// the forward rates copied into m_ropr by the reciprocals of
// the equilibrium constants
multiply_each(m_ropr.begin(), m_ropr.end(), m_rkcn.begin());
// multiply ropf by concentration products
m_rxnstoich.multiplyReactants(&m_conc[0], &m_ropf[0]);
//m_reactantStoich.multiply(m_conc.begin(), ropf.begin());
// for reversible reactions, multiply ropr by concentration
// products
m_rxnstoich.multiplyRevProducts(&m_conc[0], &m_ropr[0]);
//m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
for (size_t j = 0; j != m_ii; ++j) {
m_ropnet[j] = m_ropf[j] - m_ropr[j];
}
m_ROP_ok = true;
}
/**
* Update the rates of progress of the reactions in the reaciton
* mechanism. This routine operates on internal data.
*/
void InterfaceKinetics::updateROP() {
_update_rates_T();
_update_rates_C();
if (m_kdata->m_ROP_ok) return;
const vector_fp& rf = m_kdata->m_rfn;
const vector_fp& m_rkc = m_kdata->m_rkcn;
array_fp& ropf = m_kdata->m_ropf;
array_fp& ropr = m_kdata->m_ropr;
array_fp& ropnet = m_kdata->m_ropnet;
// copy rate coefficients into ropf
copy(rf.begin(), rf.end(), ropf.begin());
// multiply by perturbation factor
multiply_each(ropf.begin(), ropf.end(), m_perturb.begin());
// copy the forward rates to the reverse rates
copy(ropf.begin(), ropf.end(), ropr.begin());
// for reverse rates computed from thermochemistry, multiply
// the forward rates copied into m_ropr by the reciprocals of
// the equilibrium constants
multiply_each(ropr.begin(), ropr.end(), m_rkc.begin());
// multiply ropf by concentration products
m_rxnstoich.multiplyReactants(DATA_PTR(m_conc), DATA_PTR(ropf));
//m_reactantStoich.multiply(m_conc.begin(), ropf.begin());
// for reversible reactions, multiply ropr by concentration
// products
m_rxnstoich.multiplyRevProducts(DATA_PTR(m_conc),
DATA_PTR(ropr));
//m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
// do global reactions
//m_globalReactantStoich.power(m_conc.begin(), ropf.begin());
for (int j = 0; j != m_ii; ++j) {
ropnet[j] = ropf[j] - ropr[j];
}
m_kdata->m_ROP_ok = true;
}
/**
* Get the equilibrium constants of all reactions, whether
* reversible or not.
*/
void GasKinetics::getEquilibriumConstants(doublereal* kc)
{
_update_rates_T();
thermo().getStandardChemPotentials(&m_grt[0]);
fill(m_rkcn.begin(), m_rkcn.end(), 0.0);
// compute Delta G^0 for all reactions
m_rxnstoich.getReactionDelta(m_ii, &m_grt[0], &m_rkcn[0]);
doublereal rrt = 1.0/(GasConstant * thermo().temperature());
for (size_t i = 0; i < m_ii; i++) {
kc[i] = exp(-m_rkcn[i]*rrt + m_dn[i]*m_logStandConc);
}
// force an update of T-dependent properties, so that m_rkcn will
// be updated before it is used next.
m_temp = 0.0;
}
void AqueousKinetics::getEquilibriumConstants(doublereal* kc)
{
_update_rates_T();
thermo().getStandardChemPotentials(m_grt.data());
fill(m_rkcn.begin(), m_rkcn.end(), 0.0);
for (size_t k = 0; k < thermo().nSpecies(); k++) {
doublereal logStandConc_k = thermo().logStandardConc(k);
m_grt[k] -= GasConstant * m_temp * logStandConc_k;
}
// compute Delta G^0 for all reactions
getReactionDelta(m_grt.data(), m_rkcn.data());
doublereal rrt = 1.0 / thermo().RT();
for (size_t i = 0; i < nReactions(); i++) {
kc[i] = exp(-m_rkcn[i]*rrt);
}
// force an update of T-dependent properties, so that m_rkcn will
// be updated before it is used next.
m_temp = 0.0;
}
/**
* Update the rates of progress of the reactions in the reaction
* mechanism. This routine operates on internal data.
*/
void InterfaceKinetics::updateROP() {
_update_rates_T();
_update_rates_C();
if (m_kdata->m_ROP_ok) return;
const vector_fp& rf = m_kdata->m_rfn;
const vector_fp& m_rkc = m_kdata->m_rkcn;
array_fp& ropf = m_kdata->m_ropf;
array_fp& ropr = m_kdata->m_ropr;
array_fp& ropnet = m_kdata->m_ropnet;
// copy rate coefficients into ropf
copy(rf.begin(), rf.end(), ropf.begin());
// multiply by perturbation factor
multiply_each(ropf.begin(), ropf.end(), m_perturb.begin());
// copy the forward rates to the reverse rates
copy(ropf.begin(), ropf.end(), ropr.begin());
// for reverse rates computed from thermochemistry, multiply
// the forward rates copied into m_ropr by the reciprocals of
// the equilibrium constants
multiply_each(ropr.begin(), ropr.end(), m_rkc.begin());
// multiply ropf by concentration products
m_rxnstoich.multiplyReactants(DATA_PTR(m_conc), DATA_PTR(ropf));
//m_reactantStoich.multiply(m_conc.begin(), ropf.begin());
// for reversible reactions, multiply ropr by concentration
// products
m_rxnstoich.multiplyRevProducts(DATA_PTR(m_conc),
DATA_PTR(ropr));
//m_revProductStoich.multiply(m_conc.begin(), ropr.begin());
// do global reactions
//m_globalReactantStoich.power(m_conc.begin(), ropf.begin());
for (int j = 0; j != m_ii; ++j) {
ropnet[j] = ropf[j] - ropr[j];
}
/*
* For reactions involving multiple phases, we must check that the phase
* being consumed actually exists. This is particularly important for
* phases that are stoichiometric phases containing one species with a unity activity
*/
if (m_phaseExistsCheck) {
for (int j = 0; j != m_ii; ++j) {
if ((ropr[j] > ropf[j]) && (ropr[j] > 0.0)) {
for (int p = 0; p < nPhases(); p++) {
if (m_rxnPhaseIsProduct[j][p]) {
if (! m_phaseExists[p]) {
ropnet[j] = 0.0;
ropr[j] = ropf[j];
if (ropf[j] > 0.0) {
for (int rp = 0; rp < nPhases(); rp++) {
if (m_rxnPhaseIsReactant[j][rp]) {
if (! m_phaseExists[rp]) {
ropnet[j] = 0.0;
ropr[j] = ropf[j] = 0.0;;
}
}
}
}
}
}
if (m_rxnPhaseIsReactant[j][p]) {
if (! m_phaseIsStable[p]) {
ropnet[j] = 0.0;
ropr[j] = ropf[j];
}
}
}
} else if ((ropf[j] > ropr[j]) && (ropf[j] > 0.0)) {
for (int p = 0; p < nPhases(); p++) {
if (m_rxnPhaseIsReactant[j][p]) {
if (! m_phaseExists[p]) {
ropnet[j] = 0.0;
ropf[j] = ropr[j];
if (ropf[j] > 0.0) {
for (int rp = 0; rp < nPhases(); rp++) {
if (m_rxnPhaseIsProduct[j][rp]) {
if (! m_phaseExists[rp]) {
ropnet[j] = 0.0;
ropf[j] = ropr[j] = 0.0;
}
}
}
}
}
}
if (m_rxnPhaseIsProduct[j][p]) {
if (! m_phaseIsStable[p]) {
ropnet[j] = 0.0;
ropf[j] = ropr[j];
}
}
}
}
}
}
m_kdata->m_ROP_ok = true;
}
