Comment changes and typo corrections

include/cantera/kinetics/GasKinetics.h

@@ -139,7 +139,7 @@ class GasKinetics : public BulkKinetics
     //! @param ddX true: w.r.t mole fractions false: w.r.t species concentrations
     //! @return a sparse matrix of derivative contributions for each reaction of
     //! dimensions nTotalReactions by nTotalSpecies
-    Eigen::SparseMatrix<double> process_derivatives(StoichManagerN& stoich,
+    Eigen::SparseMatrix<double> calculateCompositionDerivatives(StoichManagerN& stoich,
                                                     const vector_fp& in, bool ddX=true);
 
     //! Helper function ensuring that all rate derivatives can be calculated

include/cantera/kinetics/InterfaceKinetics.h

@@ -307,7 +307,15 @@ class InterfaceKinetics : public Kinetics
 
     /**
      * Set/modify derivative settings. For the interface kinetics object this
-     * includes `"skip-cov-dep"`, `"skip-electrochem"`, and `"rtol-delta"`.
+     * includes `"skip-coverage-dependence"`, `"skip-electrochem"`, and `"rtol-delta"`.
+     *
+     *  - `skip-coverage-dependence` (boolean) ... if `true` (default), rate constant
+     *    coverage dependence is not considered when evaluating derivatives.
+     *  - `skip-electrochem` (boolean) ... if `true` (default), electrical charge is
+     *    not considered in evaluating the derivatives and these reactions are treated
+     *    as normal surface reactions.
+     *   - `rtol-delta` (double) ... relative tolerance used to perturb properties
+     *     when calculating numerical derivatives. The default value is 1e-8.
      *
      * @param settings  AnyMap containing settings determining derivative evaluation.
      */
@@ -335,14 +343,14 @@ class InterfaceKinetics : public Kinetics
     //! @param in  rate expression used for the derivative calculation
     //! @return a sparse matrix of derivative contributions for each reaction of
     //! dimensions nTotalReactions by nTotalSpecies
-    Eigen::SparseMatrix<double> process_derivatives(StoichManagerN& stoich,
+    Eigen::SparseMatrix<double> calculateCompositionDerivatives(StoichManagerN& stoich,
                                             const vector_fp& in);
 
     //! Helper function ensuring that all rate derivatives can be calculated
     //! @param name  method name used for error output
     //! @throw CanteraError if coverage dependence or electrochemical reactions are
     //! included
-    void assertDerivativesValid(const std::string& name);
+    void assertDerivativesValid(const string& name);
 
     //! @}
 

include/cantera/kinetics/InterfaceRate.h

@@ -44,11 +44,6 @@ struct InterfaceData : public BlowersMaselData
 
     virtual void update(double T) override;
 
-    virtual void update(double T, double P) override {
-        BlowersMaselData::update(T);
-        pressure = P;
-    }
-
     virtual void update(double T, const vector_fp& values) override;
 
     using BlowersMaselData::update;
@@ -72,9 +67,6 @@ struct InterfaceData : public BlowersMaselData
     vector_fp electricPotentials; //!< electric potentials of phases
     vector_fp standardChemPotentials; //!< standard state chemical potentials
     vector_fp standardConcentrations; //!< standard state concentrations
-
-    protected:
-        double m_pressure_buf; //!< buffered pressure
 };
 
 

include/cantera/zeroD/MoleReactor.h

@@ -39,7 +39,7 @@ class MoleReactor : public Reactor
 protected:
     //! Map all surface chemistry derivatives from concentration jacobian to
     //! A vector of triplets for the reactor
-    virtual void mapSurfJacobian(std::vector<Eigen::Triplet<double>> &strips);
+    virtual void addSurfaceJacobian(vector<Eigen::Triplet<double>> &triplets);
 
     //! Get moles of the system from mass fractions stored by thermo object
     //! @param y vector for moles to be put into

include/cantera/zeroD/ReactorNet.h

@@ -290,7 +290,7 @@ class ReactorNet : public FuncEval
     //!
     //! @warning  This method is an experimental part of the %Cantera
     //! API and may be changed or removed without notice.
-    Eigen::SparseMatrix<double> finiteDifferenceJacobian();
+    virtual Eigen::SparseMatrix<double> finiteDifferenceJacobian();
 
     //! Method to calculate the system jacobian
     //! @warning Depending on the particular implementation, this may return an

interfaces/cython/cantera/preconditioners.pyx

@@ -96,6 +96,9 @@ cdef class AdaptivePreconditioner(PreconditionerBase):
         self.preconditioner.printPreconditioner()
 
     property matrix:
+        """
+        Property to retrieve the latest internal preconditioner matrix.
+        """
         def __get__(self):
             cdef CxxSparseMatrix smat = self.preconditioner.matrix()
             return get_from_sparse(smat, smat.rows(), smat.cols())

src/kinetics/GasKinetics.cpp

@@ -403,7 +403,7 @@ void GasKinetics::getNetRatesOfProgress_ddC(double* drop)
     dNetRop -= dNetRop2;
 }
 
-Eigen::SparseMatrix<double> GasKinetics::process_derivatives(
+Eigen::SparseMatrix<double> GasKinetics::calculateCompositionDerivatives(
     StoichManagerN& stoich, const vector_fp& in, bool ddX)
 {
     Eigen::SparseMatrix<double> out;
@@ -453,7 +453,7 @@ Eigen::SparseMatrix<double> GasKinetics::fwdRatesOfProgress_ddX()
     // forward reaction rate coefficients
     vector_fp& rop_rates = m_rbuf0;
     processFwdRateCoefficients(rop_rates.data());
-    return process_derivatives(m_reactantStoich, rop_rates);
+    return calculateCompositionDerivatives(m_reactantStoich, rop_rates);
 }
 
 Eigen::SparseMatrix<double> GasKinetics::revRatesOfProgress_ddX()
@@ -464,7 +464,7 @@ Eigen::SparseMatrix<double> GasKinetics::revRatesOfProgress_ddX()
     vector_fp& rop_rates = m_rbuf0;
     processFwdRateCoefficients(rop_rates.data());
     processEquilibriumConstants(rop_rates.data());
-    return process_derivatives(m_revProductStoich, rop_rates);
+    return calculateCompositionDerivatives(m_revProductStoich, rop_rates);
 }
 
 Eigen::SparseMatrix<double> GasKinetics::netRatesOfProgress_ddX()
@@ -474,11 +474,11 @@ Eigen::SparseMatrix<double> GasKinetics::netRatesOfProgress_ddX()
     // forward reaction rate coefficients
     vector_fp& rop_rates = m_rbuf0;
     processFwdRateCoefficients(rop_rates.data());
-    Eigen::SparseMatrix<double> jac = process_derivatives(m_reactantStoich, rop_rates);
+    Eigen::SparseMatrix<double> jac = calculateCompositionDerivatives(m_reactantStoich, rop_rates);
 
     // reverse reaction rate coefficients
     processEquilibriumConstants(rop_rates.data());
-    return jac - process_derivatives(m_revProductStoich, rop_rates);
+    return jac - calculateCompositionDerivatives(m_revProductStoich, rop_rates);
 }
 
 Eigen::SparseMatrix<double> GasKinetics::fwdRatesOfProgress_ddN()
@@ -488,7 +488,7 @@ Eigen::SparseMatrix<double> GasKinetics::fwdRatesOfProgress_ddN()
     // forward reaction rate coefficients
     vector_fp& rop_rates = m_rbuf0;
     processFwdRateCoefficients(rop_rates.data());
-    return process_derivatives(m_reactantStoich, rop_rates, false);
+    return calculateCompositionDerivatives(m_reactantStoich, rop_rates, false);
 }
 
 Eigen::SparseMatrix<double> GasKinetics::revRatesOfProgress_ddN()
@@ -499,7 +499,7 @@ Eigen::SparseMatrix<double> GasKinetics::revRatesOfProgress_ddN()
     vector_fp& rop_rates = m_rbuf0;
     processFwdRateCoefficients(rop_rates.data());
     processEquilibriumConstants(rop_rates.data());
-    return process_derivatives(m_revProductStoich, rop_rates, false);
+    return calculateCompositionDerivatives(m_revProductStoich, rop_rates, false);
 }
 
 Eigen::SparseMatrix<double> GasKinetics::netRatesOfProgress_ddN()
@@ -509,12 +509,12 @@ Eigen::SparseMatrix<double> GasKinetics::netRatesOfProgress_ddN()
     // forward reaction rate coefficients
     vector_fp& rop_rates = m_rbuf0;
     processFwdRateCoefficients(rop_rates.data());
-    Eigen::SparseMatrix<double> jac = process_derivatives(m_reactantStoich, rop_rates,
+    Eigen::SparseMatrix<double> jac = calculateCompositionDerivatives(m_reactantStoich, rop_rates,
         false);
 
     // reverse reaction rate coefficients
     processEquilibriumConstants(rop_rates.data());
-    return jac - process_derivatives(m_revProductStoich, rop_rates, false);
+    return jac - calculateCompositionDerivatives(m_revProductStoich, rop_rates, false);
 }
 
 bool GasKinetics::addReaction(shared_ptr<Reaction> r, bool resize)

src/kinetics/InterfaceKinetics.cpp

@@ -29,12 +29,12 @@ InterfaceKinetics::~InterfaceKinetics()
 
 void InterfaceKinetics::resizeReactions()
 {
+    Kinetics::resizeReactions();
+
     // resize buffer
     m_rbuf0.resize(nReactions());
     m_rbuf1.resize(nReactions());
 
-    Kinetics::resizeReactions();
-
     for (auto& rates : m_interfaceRates) {
         rates->resize(nTotalSpecies(), nReactions(), nPhases());
         // @todo ensure that ReactionData are updated; calling rates->update
@@ -621,7 +621,7 @@ Eigen::SparseMatrix<double> InterfaceKinetics::fwdRatesOfProgress_ddN()
     // forward reaction rate coefficients
     vector_fp& rop_rates = m_rbuf0;
     processFwdRateCoefficients(rop_rates.data());
-    return process_derivatives(m_reactantStoich, rop_rates);
+    return calculateCompositionDerivatives(m_reactantStoich, rop_rates);
 }
 
 Eigen::SparseMatrix<double> InterfaceKinetics::revRatesOfProgress_ddN()
@@ -632,7 +632,7 @@ Eigen::SparseMatrix<double> InterfaceKinetics::revRatesOfProgress_ddN()
     vector_fp& rop_rates = m_rbuf0;
     processFwdRateCoefficients(rop_rates.data());
     processEquilibriumConstants(rop_rates.data());
-    return process_derivatives(m_revProductStoich, rop_rates);
+    return calculateCompositionDerivatives(m_revProductStoich, rop_rates);
 }
 
 Eigen::SparseMatrix<double> InterfaceKinetics::netRatesOfProgress_ddN()
@@ -642,18 +642,19 @@ Eigen::SparseMatrix<double> InterfaceKinetics::netRatesOfProgress_ddN()
     // forward reaction rate coefficients
     vector_fp& rop_rates = m_rbuf0;
     processFwdRateCoefficients(rop_rates.data());
-    Eigen::SparseMatrix<double> jac = process_derivatives(m_reactantStoich, rop_rates);
+    Eigen::SparseMatrix<double> jac = calculateCompositionDerivatives(m_reactantStoich,
+        rop_rates);
 
     // reverse reaction rate coefficients
     processEquilibriumConstants(rop_rates.data());
-    return jac - process_derivatives(m_revProductStoich, rop_rates);
+    return jac - calculateCompositionDerivatives(m_revProductStoich, rop_rates);
 }
 
 void InterfaceKinetics::setDerivativeSettings(const AnyMap& settings)
 {
     bool force = settings.empty();
-    if (force || settings.hasKey("skip-cov-dep")) {
-        m_jac_skip_cov_dependance = settings.getBool("skip-cov-dep",
+    if (force || settings.hasKey("skip-coverage-dependence")) {
+        m_jac_skip_cov_dependence = settings.getBool("skip-coverage-dependence",
             true);
     }
     if (force || settings.hasKey("skip-electrochem")) {
@@ -669,9 +670,8 @@ void InterfaceKinetics::processFwdRateCoefficients(double* ropf)
 {
     // evaluate rate constants and equilibrium constants at temperature and phi
     // (electric potential)
-    _update_rates_T();
     // get updated activities (rates updated below)
-    _update_rates_C();
+    updateROP();
     // copy rate coefficients into ropf
     copy(m_rfn.begin(), m_rfn.end(), ropf);
 
@@ -681,7 +681,7 @@ void InterfaceKinetics::processFwdRateCoefficients(double* ropf)
     }
 }
 
-Eigen::SparseMatrix<double> InterfaceKinetics::process_derivatives(
+Eigen::SparseMatrix<double> InterfaceKinetics::calculateCompositionDerivatives(
     StoichManagerN& stoich, const vector_fp& in)
 {
     Eigen::SparseMatrix<double> out;
@@ -692,9 +692,9 @@ Eigen::SparseMatrix<double> InterfaceKinetics::process_derivatives(
     return out;
 }
 
-void InterfaceKinetics::assertDerivativesValid(const std::string& name)
+void InterfaceKinetics::assertDerivativesValid(const string& name)
 {
-    if (!m_jac_skip_cov_dependance) {
+    if (!m_jac_skip_cov_dependence) {
         throw NotImplementedError(name, "Coverage-dependent reactions not supported.");
     }
     else if (!m_jac_skip_electrochem) {

src/kinetics/InterfaceRate.cpp

@@ -48,7 +48,6 @@ bool InterfaceData::update(const ThermoPhase& phase, const Kinetics& kin)
     }
 
     double T = phase.temperature();
-    double P = phase.pressure();
     bool changed = false;
     const auto& surf = dynamic_cast<const SurfPhase&>(
         kin.thermo(kin.reactionPhaseIndex()));
@@ -57,10 +56,6 @@ bool InterfaceData::update(const ThermoPhase& phase, const Kinetics& kin)
         density = surf.siteDensity();
         changed = true;
     }
-    if (P != pressure) {
-        pressure = P;
-        changed = true;
-    }
     if (T != temperature) {
         ReactionData::update(T);
         sqrtT = sqrt(T);

src/zeroD/IdealGasConstPressureMoleReactor.cpp

@@ -139,7 +139,7 @@ Eigen::SparseMatrix<double> IdealGasConstPressureMoleReactor::jacobian()
                 species_trips.emplace_back(it.row(), it.col(), it.value());
             }
         }
-        mapSurfJacobian(species_trips);
+        addSurfaceJacobian(species_trips);
         dnk_dnj.resize(ssize, ssize);
         dnk_dnj.setFromTriplets(species_trips.begin(), species_trips.end());
     }

src/zeroD/IdealGasMoleReactor.cpp

@@ -156,7 +156,7 @@ void IdealGasMoleReactor::eval(double time, double* LHS, double* RHS)
 Eigen::SparseMatrix<double> IdealGasMoleReactor::jacobian()
 {
     if (m_nv == 0) {
-        throw CanteraError("IdealGasConstPressureMoleReactor::jacobian",
+        throw CanteraError("IdealGasMoleReactor::jacobian",
                            "Reactor must be initialized first.");
     }
     // clear former jacobian elements
@@ -165,24 +165,25 @@ Eigen::SparseMatrix<double> IdealGasMoleReactor::jacobian()
     Eigen::SparseMatrix<double> dnk_dnj = m_kin->netProductionRates_ddN();
     // species size that accounts for surface species
     size_t ssize = m_nv - m_sidx;
-    // map concentration derivatives from surfaces to same vector
+    // map concentration derivatives from the surface chemistry jacobian
+    // to the reactor jacobian
     if (!m_surfaces.empty()) {
         std::vector<Eigen::Triplet<double>> species_trips(dnk_dnj.nonZeros());
         for (int k = 0; k < dnk_dnj.outerSize(); k++) {
             for (Eigen::SparseMatrix<double>::InnerIterator it(dnk_dnj, k); it; ++it) {
                 species_trips.emplace_back(it.row(), it.col(), it.value());
             }
         }
-        mapSurfJacobian(species_trips);
+        addSurfaceJacobian(species_trips);
         dnk_dnj.resize(ssize, ssize);
         dnk_dnj.setFromTriplets(species_trips.begin(), species_trips.end());
     }
+    // add species to species derivatives  elements to the jacobian
     // calculate ROP derivatives, excluding the terms where dnk/dnj is zero but
     // molarVolume * wdot is not, as it reduces matrix sparsity and diminishes
     // performance.
     for (int k = 0; k < dnk_dnj.outerSize(); k++) {
         for (Eigen::SparseMatrix<double>::InnerIterator it(dnk_dnj, k); it; ++it) {
-            // scale value by appropriate quantities.
             m_jac_trips.emplace_back(static_cast<int>(it.row() + m_sidx),
                 static_cast<int>(it.col() + m_sidx), it.value());
         }
@@ -223,10 +224,10 @@ Eigen::SparseMatrix<double> IdealGasMoleReactor::jacobian()
         m_kin->getNetProductionRates(netProductionRates.data());
         m_thermo->getPartialMolarCp(specificHeat.data());
         // surface phases
-        size_t shift = m_nsp;
+        size_t offset = m_nsp;
         for (auto S : m_surfaces) {
-            S->thermo()->getPartialMolarCp(specificHeat.data() + shift);
-            S->thermo()->getPartialMolarEnthalpies(internal_energy.data() + shift);
+            S->thermo()->getPartialMolarCp(specificHeat.data() + offset);
+            S->thermo()->getPartialMolarEnthalpies(internal_energy.data() + offset);
             // get additional net production rates
             auto curr_kin = S->kinetics();
             vector_fp prod_rates(curr_kin->nTotalSpecies());
@@ -238,10 +239,10 @@ Eigen::SparseMatrix<double> IdealGasMoleReactor::jacobian()
                 }
             }
             // scale production rates by areas
-            for (size_t i = shift; i < shift + S->thermo()->nSpecies(); i++) {
+            for (size_t i = offset; i < offset + S->thermo()->nSpecies(); i++) {
                 netProductionRates[i] *= S->area();
             }
-            shift += S->thermo()->nSpecies();
+            offset += S->thermo()->nSpecies();
         }
         // convert Cp to Cv for ideal gas as Cp - Cv = R
         for (size_t i = 0; i < m_nsp; i++) {
@@ -250,16 +251,16 @@ Eigen::SparseMatrix<double> IdealGasMoleReactor::jacobian()
         }
         // scale net production rates by  volume to get molar rate
         double qdot = internal_energy.dot(netProductionRates);
-        // find denominator ahead of time
+        // find the sum of n_i and cp_i
         double NCv = 0.0;
         double* moles = yCurrent.data() + m_sidx;
         for (size_t i = 0; i < ssize; i++) {
             NCv += moles[i] * specificHeat[i];
         }
-        // Make denominator beforehand
+        // make denominator beforehand
         double denom = 1 / (NCv * NCv);
         Eigen::VectorXd uk_dnkdnj_sums = dnk_dnj.transpose() * internal_energy;
-        // Add derivatives to jac by spanning columns
+        // add derivatives to jacobian
         for (size_t j = 0; j < ssize; j++) {
             m_jac_trips.emplace_back(0, static_cast<int>(j + m_sidx),
                 (specificHeat[j] * qdot - NCv * uk_dnkdnj_sums[j]) * denom);

src/zeroD/MoleReactor.cpp

@@ -84,7 +84,7 @@ void MoleReactor::evalSurfaces(double* LHS, double* RHS, double* sdot)
     }
 }
 
-void MoleReactor::mapSurfJacobian(std::vector<Eigen::Triplet<double>> &strips)
+void MoleReactor::addSurfaceJacobian(vector<Eigen::Triplet<double>> &triplets)
 {
     for (auto& S : m_surfaces) {
         // sync states
@@ -103,7 +103,7 @@ void MoleReactor::mapSurfJacobian(std::vector<Eigen::Triplet<double>> &strips)
                     double scalar = (row < m_nsp) ? m_vol : S->area();
                     scalar /= (col < m_nsp) ? m_vol : S->area();
                     // add to appropriate row and col
-                    strips.emplace_back(row, col, scalar * it.value());
+                    triplets.emplace_back(row, col, scalar * it.value());
                 }
             }
         }