Convenience class which inherits from both EdgePhase and EdgeKinetics. More...
#include <Edge.h>
Inheritance diagram for Edge:
Collaboration diagram for Edge:
Public Member Functions | |
| Edge (const std::string &infile, std::string id, std::vector< ThermoPhase *> phases) | |
| bool | operator! () |
| bool | ready () const |
| Returns a bool indicating whether the object is ready for use. More... | |
 Public Member Functions inherited from EdgePhase | |
| EdgePhase (doublereal n0=1.0) | |
| Constructor. More... | |
| virtual std::string | type () const |
| String indicating the thermodynamic model implemented. More... | |
| virtual void | setParametersFromXML (const XML_Node &thermoData) |
| Set the Equation-of-State parameters by reading an XML Node Input. More... | |
| Public Member Functions inherited from SurfPhase | |
| SurfPhase (doublereal n0=1.0) | |
| Constructor. More... | |
| SurfPhase (const std::string &infile, const std::string &id) | |
| Construct and initialize a SurfPhase ThermoPhase object directly from an ASCII input file. More... | |
| SurfPhase (XML_Node &xmlphase) | |
| Construct and initialize a SurfPhase ThermoPhase object directly from an XML database. More... | |
| virtual doublereal | enthalpy_mole () const |
| Return the Molar Enthalpy. Units: J/kmol. More... | |
| virtual doublereal | intEnergy_mole () const |
| Return the Molar Internal Energy. Units: J/kmol. More... | |
| virtual doublereal | entropy_mole () const |
| Return the Molar Entropy. Units: J/kmol-K. More... | |
| virtual doublereal | cp_mole () const |
| Molar heat capacity at constant pressure. Units: J/kmol/K. More... | |
| virtual doublereal | cv_mole () const |
| Molar heat capacity at constant volume. Units: J/kmol/K. More... | |
| virtual void | getChemPotentials (doublereal *mu) const |
| Get the species chemical potentials. Units: J/kmol. More... | |
| virtual void | getPartialMolarEnthalpies (doublereal *hbar) const |
| Returns an array of partial molar enthalpies for the species in the mixture. More... | |
| virtual void | getPartialMolarEntropies (doublereal *sbar) const |
| Returns an array of partial molar entropies of the species in the solution. More... | |
| virtual void | getPartialMolarCp (doublereal *cpbar) const |
| Return an array of partial molar heat capacities for the species in the mixture. More... | |
| virtual void | getPartialMolarVolumes (doublereal *vbar) const |
| Return an array of partial molar volumes for the species in the mixture. More... | |
| virtual void | getStandardChemPotentials (doublereal *mu0) const |
| Get the array of chemical potentials at unit activity for the species at their standard states at the current T and P of the solution. More... | |
| virtual void | getActivityConcentrations (doublereal *c) const |
| Return a vector of activity concentrations for each species. More... | |
| virtual doublereal | standardConcentration (size_t k=0) const |
| Return the standard concentration for the kth species. More... | |
| virtual doublereal | logStandardConc (size_t k=0) const |
| Natural logarithm of the standard concentration of the kth species. More... | |
| virtual void | setParameters (int n, doublereal *const c) |
| Set the equation of state parameters from the argument list. More... | |
| virtual bool | addSpecies (shared_ptr< Species > spec) |
| virtual void | setStateFromXML (const XML_Node &state) |
| Set the initial state of the Surface Phase from an XML_Node. More... | |
| doublereal | siteDensity () |
| Returns the site density. More... | |
| virtual double | size (size_t k) const |
| Returns the number of sites occupied by one molecule of species k. More... | |
| void | setSiteDensity (doublereal n0) |
| Set the site density of the surface phase (kmol m-2) More... | |
| virtual void | getGibbs_RT (doublereal *grt) const |
| Get the nondimensional Gibbs functions for the species in their standard states at the current T and P of the solution. More... | |
| virtual void | getEnthalpy_RT (doublereal *hrt) const |
| Get the nondimensional Enthalpy functions for the species at their standard states at the current T and P of the solution. More... | |
| virtual void | getEntropy_R (doublereal *sr) const |
| Get the array of nondimensional Entropy functions for the standard state species at the current T and P of the solution. More... | |
| virtual void | getCp_R (doublereal *cpr) const |
| Get the nondimensional Heat Capacities at constant pressure for the species standard states at the current T and P of the solution. More... | |
| virtual void | getStandardVolumes (doublereal *vol) const |
| Get the molar volumes of the species standard states at the current T and P of the solution. More... | |
| virtual doublereal | pressure () const |
| Return the thermodynamic pressure (Pa). More... | |
| virtual void | setPressure (doublereal p) |
| Set the internally stored pressure (Pa) at constant temperature and composition. More... | |
| virtual void | getPureGibbs (doublereal *g) const |
| Get the Gibbs functions for the standard state of the species at the current T and P of the solution. More... | |
| virtual void | getGibbs_RT_ref (doublereal *grt) const |
| Returns the vector of nondimensional Gibbs Free Energies of the reference state at the current temperature of the solution and the reference pressure for the species. More... | |
| virtual void | getEnthalpy_RT_ref (doublereal *hrt) const |
| Returns the vector of nondimensional enthalpies of the reference state at the current temperature of the solution and the reference pressure for the species. More... | |
| virtual void | getEntropy_R_ref (doublereal *er) const |
| Returns the vector of nondimensional entropies of the reference state at the current temperature of the solution and the reference pressure for each species. More... | |
| virtual void | getCp_R_ref (doublereal *cprt) const |
| Returns the vector of nondimensional constant pressure heat capacities of the reference state at the current temperature of the solution and reference pressure for each species. More... | |
| void | setCoverages (const doublereal *theta) |
| Set the surface site fractions to a specified state. More... | |
| void | setCoveragesNoNorm (const doublereal *theta) |
| Set the surface site fractions to a specified state. More... | |
| void | setCoveragesByName (const std::string &cov) |
| Set the coverages from a string of colon-separated name:value pairs. More... | |
| void | setCoveragesByName (const compositionMap &cov) |
| Set the coverages from a map of name:value pairs. More... | |
| void | getCoverages (doublereal *theta) const |
| Return a vector of surface coverages. More... | |
| Public Member Functions inherited from ThermoPhase | |
| ThermoPhase () | |
| Constructor. More... | |
| doublereal | RT () const |
| Return the Gas Constant multiplied by the current temperature. More... | |
| virtual doublereal | refPressure () const |
| Returns the reference pressure in Pa. More... | |
| virtual doublereal | minTemp (size_t k=npos) const |
| Minimum temperature for which the thermodynamic data for the species or phase are valid. More... | |
| doublereal | Hf298SS (const size_t k) const |
| Report the 298 K Heat of Formation of the standard state of one species (J kmol-1) More... | |
| virtual void | modifyOneHf298SS (const size_t k, const doublereal Hf298New) |
| Modify the value of the 298 K Heat of Formation of one species in the phase (J kmol-1) More... | |
| virtual void | resetHf298 (const size_t k=npos) |
| Restore the original heat of formation of one or more species. More... | |
| virtual doublereal | maxTemp (size_t k=npos) const |
| Maximum temperature for which the thermodynamic data for the species are valid. More... | |
| bool | chargeNeutralityNecessary () const |
| Returns the chargeNeutralityNecessity boolean. More... | |
| virtual doublereal | gibbs_mole () const |
| Molar Gibbs function. Units: J/kmol. More... | |
| virtual doublereal | isothermalCompressibility () const |
| Returns the isothermal compressibility. Units: 1/Pa. More... | |
| virtual doublereal | thermalExpansionCoeff () const |
| Return the volumetric thermal expansion coefficient. Units: 1/K. More... | |
| void | setElectricPotential (doublereal v) |
| Set the electric potential of this phase (V). More... | |
| doublereal | electricPotential () const |
| Returns the electric potential of this phase (V). More... | |
| virtual int | activityConvention () const |
| This method returns the convention used in specification of the activities, of which there are currently two, molar- and molality-based conventions. More... | |
| virtual int | standardStateConvention () const |
| This method returns the convention used in specification of the standard state, of which there are currently two, temperature based, and variable pressure based. More... | |
| virtual void | getActivities (doublereal *a) const |
| Get the array of non-dimensional activities at the current solution temperature, pressure, and solution concentration. More... | |
| virtual void | getActivityCoefficients (doublereal *ac) const |
| Get the array of non-dimensional molar-based activity coefficients at the current solution temperature, pressure, and solution concentration. More... | |
| virtual void | getLnActivityCoefficients (doublereal *lnac) const |
| Get the array of non-dimensional molar-based ln activity coefficients at the current solution temperature, pressure, and solution concentration. More... | |
| virtual void | getChemPotentials_RT (doublereal *mu) const |
| Get the array of non-dimensional species chemical potentials These are partial molar Gibbs free energies. More... | |
| void | getElectrochemPotentials (doublereal *mu) const |
| Get the species electrochemical potentials. More... | |
| virtual void | getPartialMolarIntEnergies (doublereal *ubar) const |
| Return an array of partial molar internal energies for the species in the mixture. More... | |
| virtual void | getIntEnergy_RT (doublereal *urt) const |
| Returns the vector of nondimensional Internal Energies of the standard state species at the current T and P of the solution. More... | |
| virtual void | getGibbs_ref (doublereal *g) const |
| Returns the vector of the Gibbs function of the reference state at the current temperature of the solution and the reference pressure for the species. More... | |
| virtual void | getIntEnergy_RT_ref (doublereal *urt) const |
| Returns the vector of nondimensional internal Energies of the reference state at the current temperature of the solution and the reference pressure for each species. More... | |
| virtual void | getStandardVolumes_ref (doublereal *vol) const |
| Get the molar volumes of the species reference states at the current T and P_ref of the solution. More... | |
| doublereal | enthalpy_mass () const |
| Specific enthalpy. Units: J/kg. More... | |
| doublereal | intEnergy_mass () const |
| Specific internal energy. Units: J/kg. More... | |
| doublereal | entropy_mass () const |
| Specific entropy. Units: J/kg/K. More... | |
| doublereal | gibbs_mass () const |
| Specific Gibbs function. Units: J/kg. More... | |
| doublereal | cp_mass () const |
| Specific heat at constant pressure. Units: J/kg/K. More... | |
| doublereal | cv_mass () const |
| Specific heat at constant volume. Units: J/kg/K. More... | |
| virtual void | setState_TPX (doublereal t, doublereal p, const doublereal *x) |
| Set the temperature (K), pressure (Pa), and mole fractions. More... | |
| virtual void | setState_TPX (doublereal t, doublereal p, const compositionMap &x) |
| Set the temperature (K), pressure (Pa), and mole fractions. More... | |
| virtual void | setState_TPX (doublereal t, doublereal p, const std::string &x) |
| Set the temperature (K), pressure (Pa), and mole fractions. More... | |
| virtual void | setState_TPY (doublereal t, doublereal p, const doublereal *y) |
| Set the internally stored temperature (K), pressure (Pa), and mass fractions of the phase. More... | |
| virtual void | setState_TPY (doublereal t, doublereal p, const compositionMap &y) |
| Set the internally stored temperature (K), pressure (Pa), and mass fractions of the phase. More... | |
| virtual void | setState_TPY (doublereal t, doublereal p, const std::string &y) |
| Set the internally stored temperature (K), pressure (Pa), and mass fractions of the phase. More... | |
| virtual void | setState_TP (doublereal t, doublereal p) |
| Set the temperature (K) and pressure (Pa) More... | |
| virtual void | setState_PX (doublereal p, doublereal *x) |
| Set the pressure (Pa) and mole fractions. More... | |
| virtual void | setState_PY (doublereal p, doublereal *y) |
| Set the internally stored pressure (Pa) and mass fractions. More... | |
| virtual void | setState_HP (double h, double p, double tol=1e-9) |
| Set the internally stored specific enthalpy (J/kg) and pressure (Pa) of the phase. More... | |
| virtual void | setState_UV (double u, double v, double tol=1e-9) |
| Set the specific internal energy (J/kg) and specific volume (m^3/kg). More... | |
| virtual void | setState_SP (double s, double p, double tol=1e-9) |
| Set the specific entropy (J/kg/K) and pressure (Pa). More... | |
| virtual void | setState_SV (double s, double v, double tol=1e-9) |
| Set the specific entropy (J/kg/K) and specific volume (m^3/kg). More... | |
| virtual void | setState_ST (double s, double t, double tol=1e-9) |
| Set the specific entropy (J/kg/K) and temperature (K). More... | |
| virtual void | setState_TV (double t, double v, double tol=1e-9) |
| Set the temperature (K) and specific volume (m^3/kg). More... | |
| virtual void | setState_PV (double p, double v, double tol=1e-9) |
| Set the pressure (Pa) and specific volume (m^3/kg). More... | |
| virtual void | setState_UP (double u, double p, double tol=1e-9) |
| Set the specific internal energy (J/kg) and pressure (Pa). More... | |
| virtual void | setState_VH (double v, double h, double tol=1e-9) |
| Set the specific volume (m^3/kg) and the specific enthalpy (J/kg) More... | |
| virtual void | setState_TH (double t, double h, double tol=1e-9) |
| Set the temperature (K) and the specific enthalpy (J/kg) More... | |
| virtual void | setState_SH (double s, double h, double tol=1e-9) |
| Set the specific entropy (J/kg/K) and the specific enthalpy (J/kg) More... | |
| virtual void | setState_RP (doublereal rho, doublereal p) |
| Set the density (kg/m**3) and pressure (Pa) at constant composition. More... | |
| virtual void | setState_RPX (doublereal rho, doublereal p, const doublereal *x) |
| Set the density (kg/m**3), pressure (Pa) and mole fractions. More... | |
| virtual void | setState_RPX (doublereal rho, doublereal p, const compositionMap &x) |
| Set the density (kg/m**3), pressure (Pa) and mole fractions. More... | |
| virtual void | setState_RPX (doublereal rho, doublereal p, const std::string &x) |
| Set the density (kg/m**3), pressure (Pa) and mole fractions. More... | |
| virtual void | setState_RPY (doublereal rho, doublereal p, const doublereal *y) |
| Set the density (kg/m**3), pressure (Pa) and mass fractions. More... | |
| virtual void | setState_RPY (doublereal rho, doublereal p, const compositionMap &y) |
| Set the density (kg/m**3), pressure (Pa) and mass fractions. More... | |
| virtual void | setState_RPY (doublereal rho, doublereal p, const std::string &y) |
| Set the density (kg/m**3), pressure (Pa) and mass fractions. More... | |
| void | equilibrate (const std::string &XY, const std::string &solver="auto", double rtol=1e-9, int max_steps=50000, int max_iter=100, int estimate_equil=0, int log_level=0) |
| Equilibrate a ThermoPhase object. More... | |
| virtual void | setToEquilState (const doublereal *lambda_RT) |
| This method is used by the ChemEquil equilibrium solver. More... | |
| void | setElementPotentials (const vector_fp &lambda) |
| Stores the element potentials in the ThermoPhase object. More... | |
| bool | getElementPotentials (doublereal *lambda) const |
| Returns the element potentials stored in the ThermoPhase object. More... | |
| virtual bool | compatibleWithMultiPhase () const |
| Indicates whether this phase type can be used with class MultiPhase for equilibrium calculations. More... | |
| virtual doublereal | critTemperature () const |
| Critical temperature (K). More... | |
| virtual doublereal | critPressure () const |
| Critical pressure (Pa). More... | |
| virtual doublereal | critVolume () const |
| Critical volume (m3/kmol). More... | |
| virtual doublereal | critCompressibility () const |
| Critical compressibility (unitless). More... | |
| virtual doublereal | critDensity () const |
| Critical density (kg/m3). More... | |
| virtual doublereal | satTemperature (doublereal p) const |
| Return the saturation temperature given the pressure. More... | |
| virtual doublereal | satPressure (doublereal t) |
| Return the saturation pressure given the temperature. More... | |
| virtual doublereal | vaporFraction () const |
| Return the fraction of vapor at the current conditions. More... | |
| virtual void | setState_Tsat (doublereal t, doublereal x) |
| Set the state to a saturated system at a particular temperature. More... | |
| virtual void | setState_Psat (doublereal p, doublereal x) |
| Set the state to a saturated system at a particular pressure. More... | |
| virtual void | modifySpecies (size_t k, shared_ptr< Species > spec) |
| Modify the thermodynamic data associated with a species. More... | |
| void | saveSpeciesData (const size_t k, const XML_Node *const data) |
| Store a reference pointer to the XML tree containing the species data for this phase. More... | |
| const std::vector< const XML_Node * > & | speciesData () const |
| Return a pointer to the vector of XML nodes containing the species data for this phase. More... | |
| virtual MultiSpeciesThermo & | speciesThermo (int k=-1) |
| Return a changeable reference to the calculation manager for species reference-state thermodynamic properties. More... | |
| virtual void | initThermoFile (const std::string &inputFile, const std::string &id) |
| virtual void | initThermoXML (XML_Node &phaseNode, const std::string &id) |
| Import and initialize a ThermoPhase object using an XML tree. More... | |
| virtual void | initThermo () |
| Initialize the ThermoPhase object after all species have been set up. More... | |
| virtual void | getParameters (int &n, doublereal *const c) const |
| Get the equation of state parameters in a vector. More... | |
| virtual void | invalidateCache () |
| Invalidate any cached values which are normally updated only when a change in state is detected. More... | |
| virtual void | getdlnActCoeffds (const doublereal dTds, const doublereal *const dXds, doublereal *dlnActCoeffds) const |
| Get the change in activity coefficients wrt changes in state (temp, mole fraction, etc) along a line in parameter space or along a line in physical space. More... | |
| virtual void | getdlnActCoeffdlnX_diag (doublereal *dlnActCoeffdlnX_diag) const |
| Get the array of ln mole fraction derivatives of the log activity coefficients - diagonal component only. More... | |
| virtual void | getdlnActCoeffdlnN_diag (doublereal *dlnActCoeffdlnN_diag) const |
| Get the array of log species mole number derivatives of the log activity coefficients. More... | |
| virtual void | getdlnActCoeffdlnN (const size_t ld, doublereal *const dlnActCoeffdlnN) |
| Get the array of derivatives of the log activity coefficients with respect to the log of the species mole numbers. More... | |
| virtual void | getdlnActCoeffdlnN_numderiv (const size_t ld, doublereal *const dlnActCoeffdlnN) |
| virtual std::string | report (bool show_thermo=true, doublereal threshold=-1e-14) const |
| returns a summary of the state of the phase as a string More... | |
| virtual void | reportCSV (std::ofstream &csvFile) const |
| returns a summary of the state of the phase to a comma separated file. More... | |
| Public Member Functions inherited from Phase | |
| Phase () | |
| Default constructor. More... | |
| Phase (const Phase &)=delete | |
| Phase & | operator= (const Phase &)=delete |
| XML_Node & | xml () const |
| Returns a const reference to the XML_Node that describes the phase. More... | |
| void | setXMLdata (XML_Node &xmlPhase) |
| Stores the XML tree information for the current phase. More... | |
| void | saveState (vector_fp &state) const |
| Save the current internal state of the phase. More... | |
| void | saveState (size_t lenstate, doublereal *state) const |
| Write to array 'state' the current internal state. More... | |
| void | restoreState (const vector_fp &state) |
| Restore a state saved on a previous call to saveState. More... | |
| void | restoreState (size_t lenstate, const doublereal *state) |
| Restore the state of the phase from a previously saved state vector. More... | |
| doublereal | molecularWeight (size_t k) const |
Molecular weight of species k. More... | |
| void | getMolecularWeights (vector_fp &weights) const |
| Copy the vector of molecular weights into vector weights. More... | |
| void | getMolecularWeights (doublereal *weights) const |
| Copy the vector of molecular weights into array weights. More... | |
| const vector_fp & | molecularWeights () const |
| Return a const reference to the internal vector of molecular weights. More... | |
| doublereal | charge (size_t k) const |
| Dimensionless electrical charge of a single molecule of species k The charge is normalized by the the magnitude of the electron charge. More... | |
| doublereal | chargeDensity () const |
| Charge density [C/m^3]. More... | |
| size_t | nDim () const |
| Returns the number of spatial dimensions (1, 2, or 3) More... | |
| void | setNDim (size_t ndim) |
| Set the number of spatial dimensions (1, 2, or 3). More... | |
| int | stateMFNumber () const |
| Return the State Mole Fraction Number. More... | |
| std::string | id () const |
| Return the string id for the phase. More... | |
| void | setID (const std::string &id) |
| Set the string id for the phase. More... | |
| std::string | name () const |
| Return the name of the phase. More... | |
| void | setName (const std::string &nm) |
| Sets the string name for the phase. More... | |
| std::string | elementName (size_t m) const |
| Name of the element with index m. More... | |
| size_t | elementIndex (const std::string &name) const |
| Return the index of element named 'name'. More... | |
| const std::vector< std::string > & | elementNames () const |
| Return a read-only reference to the vector of element names. More... | |
| doublereal | atomicWeight (size_t m) const |
| Atomic weight of element m. More... | |
| doublereal | entropyElement298 (size_t m) const |
| Entropy of the element in its standard state at 298 K and 1 bar. More... | |
| int | atomicNumber (size_t m) const |
| Atomic number of element m. More... | |
| int | elementType (size_t m) const |
| Return the element constraint type Possible types include: More... | |
| int | changeElementType (int m, int elem_type) |
| Change the element type of the mth constraint Reassigns an element type. More... | |
| const vector_fp & | atomicWeights () const |
| Return a read-only reference to the vector of atomic weights. More... | |
| size_t | nElements () const |
| Number of elements. More... | |
| void | checkElementIndex (size_t m) const |
| Check that the specified element index is in range. More... | |
| void | checkElementArraySize (size_t mm) const |
| Check that an array size is at least nElements(). More... | |
| doublereal | nAtoms (size_t k, size_t m) const |
Number of atoms of element m in species k. More... | |
| void | getAtoms (size_t k, double *atomArray) const |
| Get a vector containing the atomic composition of species k. More... | |
| size_t | speciesIndex (const std::string &name) const |
| Returns the index of a species named 'name' within the Phase object. More... | |
| std::string | speciesName (size_t k) const |
| Name of the species with index k. More... | |
| std::string | speciesSPName (int k) const |
| Returns the expanded species name of a species, including the phase name This is guaranteed to be unique within a Cantera problem. More... | |
| const std::vector< std::string > & | speciesNames () const |
| Return a const reference to the vector of species names. More... | |
| size_t | nSpecies () const |
| Returns the number of species in the phase. More... | |
| void | checkSpeciesIndex (size_t k) const |
| Check that the specified species index is in range. More... | |
| void | checkSpeciesArraySize (size_t kk) const |
| Check that an array size is at least nSpecies(). More... | |
| void | setMoleFractionsByName (const compositionMap &xMap) |
| Set the species mole fractions by name. More... | |
| void | setMoleFractionsByName (const std::string &x) |
| Set the mole fractions of a group of species by name. More... | |
| void | setMassFractionsByName (const compositionMap &yMap) |
| Set the species mass fractions by name. More... | |
| void | setMassFractionsByName (const std::string &x) |
| Set the species mass fractions by name. More... | |
| void | setState_TRX (doublereal t, doublereal dens, const doublereal *x) |
| Set the internally stored temperature (K), density, and mole fractions. More... | |
| void | setState_TRX (doublereal t, doublereal dens, const compositionMap &x) |
| Set the internally stored temperature (K), density, and mole fractions. More... | |
| void | setState_TRY (doublereal t, doublereal dens, const doublereal *y) |
| Set the internally stored temperature (K), density, and mass fractions. More... | |
| void | setState_TRY (doublereal t, doublereal dens, const compositionMap &y) |
| Set the internally stored temperature (K), density, and mass fractions. More... | |
| void | setState_TNX (doublereal t, doublereal n, const doublereal *x) |
| Set the internally stored temperature (K), molar density (kmol/m^3), and mole fractions. More... | |
| void | setState_TR (doublereal t, doublereal rho) |
| Set the internally stored temperature (K) and density (kg/m^3) More... | |
| void | setState_TX (doublereal t, doublereal *x) |
| Set the internally stored temperature (K) and mole fractions. More... | |
| void | setState_TY (doublereal t, doublereal *y) |
| Set the internally stored temperature (K) and mass fractions. More... | |
| void | setState_RX (doublereal rho, doublereal *x) |
| Set the density (kg/m^3) and mole fractions. More... | |
| void | setState_RY (doublereal rho, doublereal *y) |
| Set the density (kg/m^3) and mass fractions. More... | |
| compositionMap | getMoleFractionsByName (double threshold=0.0) const |
| Get the mole fractions by name. More... | |
| doublereal | moleFraction (size_t k) const |
| Return the mole fraction of a single species. More... | |
| doublereal | moleFraction (const std::string &name) const |
| Return the mole fraction of a single species. More... | |
| compositionMap | getMassFractionsByName (double threshold=0.0) const |
| Get the mass fractions by name. More... | |
| doublereal | massFraction (size_t k) const |
| Return the mass fraction of a single species. More... | |
| doublereal | massFraction (const std::string &name) const |
| Return the mass fraction of a single species. More... | |
| void | getMoleFractions (doublereal *const x) const |
| Get the species mole fraction vector. More... | |
| virtual void | setMoleFractions (const doublereal *const x) |
| Set the mole fractions to the specified values. More... | |
| virtual void | setMoleFractions_NoNorm (const doublereal *const x) |
| Set the mole fractions to the specified values without normalizing. More... | |
| void | getMassFractions (doublereal *const y) const |
| Get the species mass fractions. More... | |
| const doublereal * | massFractions () const |
| Return a const pointer to the mass fraction array. More... | |
| virtual void | setMassFractions (const doublereal *const y) |
| Set the mass fractions to the specified values and normalize them. More... | |
| virtual void | setMassFractions_NoNorm (const doublereal *const y) |
| Set the mass fractions to the specified values without normalizing. More... | |
| void | getConcentrations (doublereal *const c) const |
| Get the species concentrations (kmol/m^3). More... | |
| doublereal | concentration (const size_t k) const |
| Concentration of species k. More... | |
| virtual void | setConcentrations (const doublereal *const conc) |
| Set the concentrations to the specified values within the phase. More... | |
| virtual void | setConcentrationsNoNorm (const double *const conc) |
| Set the concentrations without ignoring negative concentrations. More... | |
| doublereal | elementalMassFraction (const size_t m) const |
| Elemental mass fraction of element m. More... | |
| doublereal | elementalMoleFraction (const size_t m) const |
| Elemental mole fraction of element m. More... | |
| const doublereal * | moleFractdivMMW () const |
| Returns a const pointer to the start of the moleFraction/MW array. More... | |
| doublereal | temperature () const |
| Temperature (K). More... | |
| virtual doublereal | density () const |
| Density (kg/m^3). More... | |
| doublereal | molarDensity () const |
| Molar density (kmol/m^3). More... | |
| doublereal | molarVolume () const |
| Molar volume (m^3/kmol). More... | |
| virtual void | setDensity (const doublereal density_) |
| Set the internally stored density (kg/m^3) of the phase. More... | |
| virtual void | setMolarDensity (const doublereal molarDensity) |
| Set the internally stored molar density (kmol/m^3) of the phase. More... | |
| virtual void | setTemperature (const doublereal temp) |
| Set the internally stored temperature of the phase (K). More... | |
| doublereal | mean_X (const doublereal *const Q) const |
| Evaluate the mole-fraction-weighted mean of an array Q. More... | |
| doublereal | mean_X (const vector_fp &Q) const |
| Evaluate the mole-fraction-weighted mean of an array Q. More... | |
| doublereal | meanMolecularWeight () const |
| The mean molecular weight. Units: (kg/kmol) More... | |
| doublereal | sum_xlogx () const |
| Evaluate \( \sum_k X_k \log X_k \). More... | |
| size_t | addElement (const std::string &symbol, doublereal weight=-12345.0, int atomicNumber=0, doublereal entropy298=ENTROPY298_UNKNOWN, int elem_type=CT_ELEM_TYPE_ABSPOS) |
| Add an element. More... | |
| shared_ptr< Species > | species (const std::string &name) const |
| Return the Species object for the named species. More... | |
| shared_ptr< Species > | species (size_t k) const |
| Return the Species object for species whose index is k. More... | |
| void | ignoreUndefinedElements () |
| Set behavior when adding a species containing undefined elements to just skip the species. More... | |
| void | addUndefinedElements () |
| Set behavior when adding a species containing undefined elements to add those elements to the phase. More... | |
| void | throwUndefinedElements () |
| Set the behavior when adding a species containing undefined elements to throw an exception. More... | |
| Public Member Functions inherited from EdgeKinetics | |
| EdgeKinetics () | |
| Constructor. More... | |
| virtual std::string | kineticsType () const |
| Identifies the Kinetics manager type. More... | |
| Public Member Functions inherited from InterfaceKinetics | |
| InterfaceKinetics (thermo_t *thermo=0) | |
| Constructor. More... | |
| void | setElectricPotential (int n, doublereal V) |
| Set the electric potential in the nth phase. More... | |
| virtual void | updateROP () |
| Internal routine that updates the Rates of Progress of the reactions. More... | |
| void | _update_rates_T () |
| Update properties that depend on temperature. More... | |
| void | _update_rates_phi () |
| Update properties that depend on the electric potential. More... | |
| void | _update_rates_C () |
| Update properties that depend on the species mole fractions and/or concentration,. More... | |
| void | advanceCoverages (doublereal tstep) |
| Advance the surface coverages in time. More... | |
| void | solvePseudoSteadyStateProblem (int ifuncOverride=-1, doublereal timeScaleOverride=1.0) |
| Solve for the pseudo steady-state of the surface problem. More... | |
| void | setIOFlag (int ioFlag) |
| virtual void | updateMu0 () |
| Update the standard state chemical potentials and species equilibrium constant entries. More... | |
| void | updateKc () |
| Update the equilibrium constants and stored electrochemical potentials in molar units for all reversible reactions and for all species. More... | |
| void | applyVoltageKfwdCorrection (doublereal *const kfwd) |
| Apply modifications for the forward reaction rate for interfacial charge transfer reactions. More... | |
| void | convertExchangeCurrentDensityFormulation (doublereal *const kfwd) |
| When an electrode reaction rate is optionally specified in terms of its exchange current density, adjust kfwd to the standard reaction rate constant form and units. More... | |
| void | setPhaseExistence (const size_t iphase, const int exists) |
| Set the existence of a phase in the reaction object. More... | |
| void | setPhaseStability (const size_t iphase, const int isStable) |
| Set the stability of a phase in the reaction object. More... | |
| int | phaseExistence (const size_t iphase) const |
| Gets the phase existence int for the ith phase. More... | |
| int | phaseStability (const size_t iphase) const |
| Gets the phase stability int for the ith phase. More... | |
| virtual void | determineFwdOrdersBV (ElectrochemicalReaction &r, vector_fp &fwdFullorders) |
| virtual void | getEquilibriumConstants (doublereal *kc) |
| Equilibrium constant for all reactions including the voltage term. More... | |
| void | updateExchangeCurrentQuantities () |
| values needed to convert from exchange current density to surface reaction rate. More... | |
| virtual void | getDeltaGibbs (doublereal *deltaG) |
| Return the vector of values for the reaction Gibbs free energy change. More... | |
| virtual void | getDeltaElectrochemPotentials (doublereal *deltaM) |
| Return the vector of values for the reaction electrochemical free energy change. More... | |
| virtual void | getDeltaEnthalpy (doublereal *deltaH) |
| Return the vector of values for the reactions change in enthalpy. More... | |
| virtual void | getDeltaEntropy (doublereal *deltaS) |
| Return the vector of values for the reactions change in entropy. More... | |
| virtual void | getDeltaSSGibbs (doublereal *deltaG) |
| Return the vector of values for the reaction standard state Gibbs free energy change. More... | |
| virtual void | getDeltaSSEnthalpy (doublereal *deltaH) |
| Return the vector of values for the change in the standard state enthalpies of reaction. More... | |
| virtual void | getDeltaSSEntropy (doublereal *deltaS) |
| Return the vector of values for the change in the standard state entropies for each reaction. More... | |
| virtual void | getActivityConcentrations (doublereal *const conc) |
| Get the vector of activity concentrations used in the kinetics object. More... | |
| doublereal | electrochem_beta (size_t irxn) const |
| Return the charge transfer rxn Beta parameter for the ith reaction. More... | |
| virtual bool | isReversible (size_t i) |
| True if reaction i has been declared to be reversible. More... | |
| virtual void | getFwdRateConstants (doublereal *kfwd) |
| Return the forward rate constants. More... | |
| virtual void | getRevRateConstants (doublereal *krev, bool doIrreversible=false) |
| Return the reverse rate constants. More... | |
| double | effectivePreExponentialFactor (size_t irxn) |
| Return effective preexponent for the specified reaction. More... | |
| double | effectiveActivationEnergy_R (size_t irxn) |
| Return effective activation energy for the specified reaction. More... | |
| double | effectiveTemperatureExponent (size_t irxn) |
| Return effective temperature exponent for the specified reaction. More... | |
| virtual void | addPhase (thermo_t &thermo) |
| Add a phase to the kinetics manager object. More... | |
| virtual void | init () |
| Prepare the class for the addition of reactions, after all phases have been added. More... | |
| virtual void | resizeSpecies () |
| Resize arrays with sizes that depend on the total number of species. More... | |
| virtual bool | addReaction (shared_ptr< Reaction > r) |
| Add a single reaction to the mechanism. More... | |
| virtual void | modifyReaction (size_t i, shared_ptr< Reaction > rNew) |
| Modify the rate expression associated with a reaction. More... | |
| Public Member Functions inherited from Kinetics | |
| virtual std::pair< size_t, size_t > | checkDuplicates (bool throw_err=true) const |
| Check for unmarked duplicate reactions and unmatched marked duplicates. More... | |
| void | selectPhase (const doublereal *data, const thermo_t *phase, doublereal *phase_data) |
| Kinetics () | |
| Default constructor. More... | |
| virtual | ~Kinetics () |
| Kinetics (const Kinetics &)=delete | |
| Kinetics objects are not copyable or assignable. More... | |
| Kinetics & | operator= (const Kinetics &)=delete |
| size_t | nReactions () const |
| Number of reactions in the reaction mechanism. More... | |
| void | checkReactionIndex (size_t m) const |
| Check that the specified reaction index is in range Throws an exception if i is greater than nReactions() More... | |
| void | checkReactionArraySize (size_t ii) const |
| Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions(). More... | |
| void | checkSpeciesIndex (size_t k) const |
| Check that the specified species index is in range Throws an exception if k is greater than nSpecies()-1. More... | |
| void | checkSpeciesArraySize (size_t mm) const |
| Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies(). More... | |
| size_t | nPhases () const |
| The number of phases participating in the reaction mechanism. More... | |
| void | checkPhaseIndex (size_t m) const |
| Check that the specified phase index is in range Throws an exception if m is greater than nPhases() More... | |
| void | checkPhaseArraySize (size_t mm) const |
| Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases(). More... | |
| size_t | phaseIndex (const std::string &ph) |
| Return the phase index of a phase in the list of phases defined within the object. More... | |
| size_t | surfacePhaseIndex () |
| This returns the integer index of the phase which has ThermoPhase type cSurf. More... | |
| size_t | reactionPhaseIndex () |
| Phase where the reactions occur. More... | |
| thermo_t & | thermo (size_t n=0) |
| This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism. More... | |
| const thermo_t & | thermo (size_t n=0) const |
| size_t | nTotalSpecies () const |
| The total number of species in all phases participating in the kinetics mechanism. More... | |
| size_t | kineticsSpeciesIndex (size_t k, size_t n) const |
| The location of species k of phase n in species arrays. More... | |
| std::string | kineticsSpeciesName (size_t k) const |
| Return the name of the kth species in the kinetics manager. More... | |
| size_t | kineticsSpeciesIndex (const std::string &nm) const |
| This routine will look up a species number based on the input std::string nm. More... | |
| size_t | kineticsSpeciesIndex (const std::string &nm, const std::string &ph) const |
| This routine will look up a species number based on the input std::string nm. More... | |
| thermo_t & | speciesPhase (const std::string &nm) |
| This function looks up the name of a species and returns a reference to the ThermoPhase object of the phase where the species resides. More... | |
| thermo_t & | speciesPhase (size_t k) |
| This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the species' owning ThermoPhase object. More... | |
| size_t | speciesPhaseIndex (size_t k) |
| This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the index of the phase owning the species. More... | |
| virtual void | getFwdRatesOfProgress (doublereal *fwdROP) |
| Return the forward rates of progress of the reactions. More... | |
| virtual void | getRevRatesOfProgress (doublereal *revROP) |
| Return the Reverse rates of progress of the reactions. More... | |
| virtual void | getNetRatesOfProgress (doublereal *netROP) |
| Net rates of progress. More... | |
| virtual void | getReactionDelta (const doublereal *property, doublereal *deltaProperty) |
| Change in species properties. More... | |
| virtual void | getRevReactionDelta (const doublereal *g, doublereal *dg) |
| Given an array of species properties 'g', return in array 'dg' the change in this quantity in the reversible reactions. More... | |
| virtual void | getCreationRates (doublereal *cdot) |
| Species creation rates [kmol/m^3/s or kmol/m^2/s]. More... | |
| virtual void | getDestructionRates (doublereal *ddot) |
| Species destruction rates [kmol/m^3/s or kmol/m^2/s]. More... | |
| virtual void | getNetProductionRates (doublereal *wdot) |
| Species net production rates [kmol/m^3/s or kmol/m^2/s]. More... | |
| virtual double | reactantStoichCoeff (size_t k, size_t i) const |
| Stoichiometric coefficient of species k as a reactant in reaction i. More... | |
| virtual double | productStoichCoeff (size_t k, size_t i) const |
| Stoichiometric coefficient of species k as a product in reaction i. More... | |
| virtual doublereal | reactantOrder (size_t k, size_t i) const |
| Reactant order of species k in reaction i. More... | |
| virtual doublereal | productOrder (int k, int i) const |
| product Order of species k in reaction i. More... | |
| virtual int | reactionType (size_t i) const |
| Flag specifying the type of reaction. More... | |
| std::string | reactionString (size_t i) const |
| Return a string representing the reaction. More... | |
| std::string | reactantString (size_t i) const |
| Returns a string containing the reactants side of the reaction equation. More... | |
| std::string | productString (size_t i) const |
| Returns a string containing the products side of the reaction equation. More... | |
| shared_ptr< Reaction > | reaction (size_t i) |
| Return the Reaction object for reaction i. More... | |
| shared_ptr< const Reaction > | reaction (size_t i) const |
| void | skipUndeclaredSpecies (bool skip) |
| Determine behavior when adding a new reaction that contains species not defined in any of the phases associated with this kinetics manager. More... | |
| void | skipUndeclaredThirdBodies (bool skip) |
| Determine behavior when adding a new reaction that contains third-body efficiencies for species not defined in any of the phases associated with this kinetics manager. More... | |
| doublereal | multiplier (size_t i) const |
| The current value of the multiplier for reaction i. More... | |
| virtual void | setMultiplier (size_t i, doublereal f) |
| Set the multiplier for reaction i to f. More... | |
| virtual void | invalidateCache () |
Protected Attributes | |
| bool | m_ok |
| XML_Node * | m_r |
| Protected Attributes inherited from SurfPhase | |
| doublereal | m_n0 |
| Surface site density (kmol m-2) More... | |
| vector_fp | m_speciesSize |
| Vector of species sizes (number of sites occupied). length m_kk. More... | |
| doublereal | m_logn0 |
| log of the surface site density More... | |
| doublereal | m_press |
| Current value of the pressure (Pa) More... | |
| vector_fp | m_h0 |
| Temporary storage for the reference state enthalpies. More... | |
| vector_fp | m_s0 |
| Temporary storage for the reference state entropies. More... | |
| vector_fp | m_cp0 |
| Temporary storage for the reference state heat capacities. More... | |
| vector_fp | m_mu0 |
| Temporary storage for the reference state Gibbs energies. More... | |
| vector_fp | m_work |
| Temporary work array. More... | |
| vector_fp | m_logsize |
| vector storing the log of the size of each species. More... | |
| Protected Attributes inherited from ThermoPhase | |
| MultiSpeciesThermo | m_spthermo |
| Pointer to the calculation manager for species reference-state thermodynamic properties. More... | |
| std::vector< const XML_Node * > | m_speciesData |
| Vector of pointers to the species databases. More... | |
| doublereal | m_phi |
| Stored value of the electric potential for this phase. Units are Volts. More... | |
| vector_fp | m_lambdaRRT |
| Vector of element potentials. More... | |
| bool | m_hasElementPotentials |
| Boolean indicating whether there is a valid set of saved element potentials for this phase. More... | |
| bool | m_chargeNeutralityNecessary |
| Boolean indicating whether a charge neutrality condition is a necessity. More... | |
| int | m_ssConvention |
| Contains the standard state convention. More... | |
| doublereal | m_tlast |
| last value of the temperature processed by reference state More... | |
| Protected Attributes inherited from Phase | |
| ValueCache | m_cache |
| Cached for saved calculations within each ThermoPhase. More... | |
| size_t | m_kk |
| Number of species in the phase. More... | |
| size_t | m_ndim |
| Dimensionality of the phase. More... | |
| vector_fp | m_speciesComp |
| Atomic composition of the species. More... | |
| vector_fp | m_speciesCharge |
| Vector of species charges. length m_kk. More... | |
| std::map< std::string, shared_ptr< Species > > | m_species |
| UndefElement::behavior | m_undefinedElementBehavior |
| Flag determining behavior when adding species with an undefined element. More... | |
| Protected Attributes inherited from InterfaceKinetics | |
| vector_fp | m_grt |
| Temporary work vector of length m_kk. More... | |
| std::vector< size_t > | m_revindex |
| List of reactions numbers which are reversible reactions. More... | |
| Rate1< SurfaceArrhenius > | m_rates |
| Templated class containing the vector of reactions for this interface. More... | |
| bool | m_redo_rates |
| std::vector< size_t > | m_irrev |
| Vector of irreversible reaction numbers. More... | |
| vector_fp | m_conc |
| Array of concentrations for each species in the kinetics mechanism. More... | |
| vector_fp | m_actConc |
| Array of activity concentrations for each species in the kinetics object. More... | |
| vector_fp | m_mu0 |
| Vector of standard state chemical potentials for all species. More... | |
| vector_fp | m_mu |
| Vector of chemical potentials for all species. More... | |
| vector_fp | m_mu0_Kc |
| Vector of standard state electrochemical potentials modified by a standard concentration term. More... | |
| vector_fp | m_phi |
| Vector of phase electric potentials. More... | |
| vector_fp | m_pot |
| Vector of potential energies due to Voltages. More... | |
| vector_fp | deltaElectricEnergy_ |
| Storage for the net electric energy change due to reaction. More... | |
| SurfPhase * | m_surf |
| Pointer to the single surface phase. More... | |
| ImplicitSurfChem * | m_integrator |
| Pointer to the Implicit surface chemistry object. More... | |
| vector_fp | m_beta |
| Electrochemical transfer coefficient for the forward direction. More... | |
| std::vector< size_t > | m_ctrxn |
| Vector of reaction indexes specifying the id of the charge transfer reactions in the mechanism. More... | |
| std::vector< size_t > | m_ctrxn_BVform |
| Vector of Reactions which follow the Butler-Volmer methodology for specifying the exchange current density first. More... | |
| vector_int | m_ctrxn_ecdf |
| Vector of booleans indicating whether the charge transfer reaction rate constant is described by an exchange current density rate constant expression. More... | |
| vector_fp | m_StandardConc |
| Vector of standard concentrations. More... | |
| vector_fp | m_deltaG0 |
| Vector of delta G^0, the standard state Gibbs free energies for each reaction. More... | |
| vector_fp | m_deltaG |
| Vector of deltaG[] of reaction, the delta Gibbs free energies for each reaction. More... | |
| vector_fp | m_ProdStanConcReac |
| Vector of the products of the standard concentrations of the reactants. More... | |
| bool | m_ROP_ok |
| doublereal | m_temp |
| Current temperature of the data. More... | |
| doublereal | m_logtemp |
| Current log of the temperature. More... | |
| bool | m_has_coverage_dependence |
| Boolean flag indicating whether any reaction in the mechanism has a coverage dependent forward reaction rate. More... | |
| bool | m_has_electrochem_rxns |
| Boolean flag indicating whether any reaction in the mechanism has a beta electrochemical parameter. More... | |
| bool | m_has_exchange_current_density_formulation |
| Boolean flag indicating whether any reaction in the mechanism is described by an exchange current density expression. More... | |
| int | m_phaseExistsCheck |
| Int flag to indicate that some phases in the kinetics mechanism are non-existent. More... | |
| std::vector< bool > | m_phaseExists |
| Vector of booleans indicating whether phases exist or not. More... | |
| vector_int | m_phaseIsStable |
| Vector of int indicating whether phases are stable or not. More... | |
| std::vector< std::vector< bool > > | m_rxnPhaseIsReactant |
| Vector of vector of booleans indicating whether a phase participates in a reaction as a reactant. More... | |
| std::vector< std::vector< bool > > | m_rxnPhaseIsProduct |
| Vector of vector of booleans indicating whether a phase participates in a reaction as a product. More... | |
| std::vector< StickData > | m_stickingData |
| Data for sticking reactions. More... | |
| int | m_ioFlag |
| size_t | m_nDim |
| Number of dimensions of reacting phase (2 for InterfaceKinetics, 1 for EdgeKinetics) More... | |
| Protected Attributes inherited from Kinetics | |
| ValueCache | m_cache |
| Cache for saved calculations within each Kinetics object. More... | |
| size_t | m_kk |
| The number of species in all of the phases that participate in this kinetics mechanism. More... | |
| vector_fp | m_perturb |
| Vector of perturbation factors for each reaction's rate of progress vector. More... | |
| std::vector< shared_ptr< Reaction > > | m_reactions |
| Vector of Reaction objects represented by this Kinetics manager. More... | |
| std::vector< thermo_t * > | m_thermo |
| m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator More... | |
| std::vector< size_t > | m_start |
| m_start is a vector of integers specifying the beginning position for the species vector for the n'th phase in the kinetics class. More... | |
| std::map< std::string, size_t > | m_phaseindex |
| Mapping of the phase id, i.e., the id attribute in the XML phase element to the position of the phase within the kinetics object. More... | |
| size_t | m_surfphase |
| Index in the list of phases of the one surface phase. More... | |
| size_t | m_rxnphase |
| Phase Index where reactions are assumed to be taking place. More... | |
| size_t | m_mindim |
| number of spatial dimensions of lowest-dimensional phase. More... | |
| vector_fp | m_rfn |
| Forward rate constant for each reaction. More... | |
| vector_fp | m_rkcn |
| Reciprocal of the equilibrium constant in concentration units. More... | |
| vector_fp | m_ropf |
| Forward rate-of-progress for each reaction. More... | |
| vector_fp | m_ropr |
| Reverse rate-of-progress for each reaction. More... | |
| vector_fp | m_ropnet |
| Net rate-of-progress for each reaction. More... | |
| bool | m_skipUndeclaredSpecies |
| bool | m_skipUndeclaredThirdBodies |
| StoichManagerN | m_reactantStoich |
| Stoichiometry manager for the reactants for each reaction. More... | |
| StoichManagerN | m_revProductStoich |
| Stoichiometry manager for the products of reversible reactions. More... | |
| StoichManagerN | m_irrevProductStoich |
| Stoichiometry manager for the products of irreversible reactions. More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from ThermoPhase | |
| virtual void | getCsvReportData (std::vector< std::string > &names, std::vector< vector_fp > &data) const |
Fills names and data with the column names and species thermo properties to be included in the output of the reportCSV method. More... | |
| Protected Member Functions inherited from Phase | |
| void | setMolecularWeight (const int k, const double mw) |
| Set the molecular weight of a single species to a given value. More... | |
| virtual void | compositionChanged () |
| Apply changes to the state which are needed after the composition changes. More... | |
| Protected Member Functions inherited from InterfaceKinetics | |
| SurfaceArrhenius | buildSurfaceArrhenius (size_t i, InterfaceReaction &r, bool replace) |
| Build a SurfaceArrhenius object from a Reaction, taking into account the possible sticking coefficient form and coverage dependencies. More... | |
| void | applyStickingCorrection (double T, double *kf) |
| Protected Member Functions inherited from Kinetics | |
| double | checkDuplicateStoich (std::map< int, double > &r1, std::map< int, double > &r2) const |
Check whether r1 and r2 represent duplicate stoichiometries This function returns a ratio if two reactions are duplicates of one another, and 0.0 otherwise. More... | |
| void | checkReactionBalance (const Reaction &R) |
| Check that the specified reaction is balanced (same number of atoms for each element in the reactants and products). More... | |
Detailed Description
Convenience class which inherits from both EdgePhase and EdgeKinetics.
Member Function Documentation
◆ ready()
|
inlinevirtual |
The documentation for this class was generated from the following file:
