Class MineralEQ3 represents a stoichiometric (fixed composition) incompressible substance based on EQ3's parameterization. More...

#include <MineralEQ3.h>

Inheritance diagram for MineralEQ3:

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Collaboration diagram for MineralEQ3:

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Public Member Functions
	MineralEQ3 ()
	Default constructor for the StoichSubstanceSSTP class. More...

	MineralEQ3 (const std::string &infile, std::string id="")
	Construct and initialize a StoichSubstanceSSTP ThermoPhase object directly from an ASCII input file. More...

	MineralEQ3 (XML_Node &phaseRef, const std::string &id="")
	Construct and initialize a StoichSubstanceSSTP ThermoPhase object directly from an XML database. More...

	MineralEQ3 (const MineralEQ3 &right)
	Copy constructor. More...

MineralEQ3 &	operator= (const MineralEQ3 &right)
	Assignment operator. More...

ThermoPhase *	duplMyselfAsThermoPhase () const
	Duplication function. More...

virtual int	eosType () const
	Equation of state flag. More...

virtual void	initThermoXML (XML_Node &phaseNode, const std::string &id)
	Initialize the phase parameters from an XML file. More...

virtual void	setParameters (int n, doublereal *const c)
	Set the equation of state parameters. More...

virtual void	getParameters (int &n, doublereal *const c) const
	Get the equation of state parameters in a vector. More...

virtual void	setParametersFromXML (const XML_Node &eosdata)
	Set equation of state parameter values from XML entries. More...

doublereal	LookupGe (const std::string &elemName)

void	convertDGFormation ()

Mechanical Equation of State
virtual doublereal	pressure () const
	Report the Pressure. Units: Pa. More...

virtual void	setPressure (doublereal p)
	Set the pressure at constant temperature. Units: Pa. 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...

Activities, Standard States, and Activity Concentrations
This section is largely handled by parent classes, since there is only one species. Therefore, the activity is equal to one.
virtual void	getActivityConcentrations (doublereal *c) const
	This method returns an array of generalized concentrations. 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	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	getUnitsStandardConc (doublereal *uA, int k=0, int sizeUA=6) const
	Returns the units of the standard and generalized concentrations. More...

Properties of the Standard State of the Species in the Solution
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	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	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	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...

Thermodynamic Values for the Species Reference States
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...

Public Member Functions inherited from StoichSubstanceSSTP
	StoichSubstanceSSTP ()
	Default constructor for the StoichSubstanceSSTP class. More...

	StoichSubstanceSSTP (const std::string &infile, std::string id="")
	Construct and initialize a StoichSubstanceSSTP ThermoPhase object directly from an ASCII input file. More...

	StoichSubstanceSSTP (XML_Node &phaseRef, const std::string &id="")
	Construct and initialize a StoichSubstanceSSTP ThermoPhase object directly from an XML database. More...

	StoichSubstanceSSTP (const StoichSubstanceSSTP &right)
	Copy constructor. More...

StoichSubstanceSSTP &	operator= (const StoichSubstanceSSTP &right)
	Assignment operator. More...

ThermoPhase *	duplMyselfAsThermoPhase () const
	Duplication function. More...

virtual void	initThermo ()

Public Member Functions inherited from SingleSpeciesTP
	SingleSpeciesTP ()
	Base empty constructor. More...

	SingleSpeciesTP (const SingleSpeciesTP &right)
	Copy constructor. More...

SingleSpeciesTP &	operator= (const SingleSpeciesTP &right)
	Assignment operator. More...

doublereal	enthalpy_mole () const
	Molar enthalpy. Units: J/kmol. More...

doublereal	intEnergy_mole () const
	Molar internal energy. Units: J/kmol. More...

doublereal	entropy_mole () const
	Molar entropy. Units: J/kmol/K. More...

doublereal	gibbs_mole () const
	Molar Gibbs function. Units: J/kmol. More...

doublereal	cp_mole () const
	Molar heat capacity at constant pressure. Units: J/kmol/K. More...

doublereal	cv_mole () const
	Molar heat capacity at constant volume. Units: J/kmol/K. 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 activity coefficients at the current solution temperature, pressure, and solution concentration. More...

void	getChemPotentials_RT (doublereal *murt) const
	Get the array of non-dimensional species chemical potentials These are partial molar Gibbs free energies. More...

void	getChemPotentials (doublereal *mu) const
	Get the array of chemical potentials. More...

void	getElectrochemPotentials (doublereal *mu) const
	Get the species electrochemical potentials. Units: J/kmol. More...

void	getPartialMolarEnthalpies (doublereal *hbar) const
	Get the species partial molar enthalpies. Units: J/kmol. More...

virtual void	getPartialMolarIntEnergies (doublereal *ubar) const
	Get the species partial molar internal energies. Units: J/kmol. More...

void	getPartialMolarEntropies (doublereal *sbar) const
	Get the species partial molar entropy. Units: J/kmol K. More...

void	getPartialMolarCp (doublereal *cpbar) const
	Get the species partial molar Heat Capacities. Units: J/ kmol /K. More...

void	getPartialMolarVolumes (doublereal *vbar) const
	Get the species partial molar volumes. Units: m^3/kmol. More...

void	getPureGibbs (doublereal *gpure) const
	Get the dimensional Gibbs functions for the standard state of the species at the current T and P. More...

void	getStandardVolumes (doublereal *vbar) const
	Get the molar volumes of each species in their standard states at the current T and P of the solution. More...

virtual void	getEnthalpy_RT_ref (doublereal *hrt) const

virtual void	getGibbs_RT_ref (doublereal *grt) const

virtual void	getGibbs_ref (doublereal *g) const

virtual void	getEntropy_R_ref (doublereal *er) const

virtual void	getCp_R_ref (doublereal *cprt) const

void	setMassFractions (const doublereal *const y)
	Mass fractions are fixed, with Y[0] = 1.0. More...

void	setMoleFractions (const doublereal *const x)
	Mole fractions are fixed, with x[0] = 1.0. More...

virtual void	setState_HP (doublereal h, doublereal p, doublereal tol=1.e-8)
	Set the internally stored specific enthalpy (J/kg) and pressure (Pa) of the phase. More...

virtual void	setState_UV (doublereal u, doublereal v, doublereal tol=1.e-8)
	Set the specific internal energy (J/kg) and specific volume (m^3/kg). More...

virtual void	setState_SP (doublereal s, doublereal p, doublereal tol=1.e-8)
	Set the specific entropy (J/kg/K) and pressure (Pa). More...

virtual void	setState_SV (doublereal s, doublereal v, doublereal tol=1.e-8)
	Set the specific entropy (J/kg/K) and specific volume (m^3/kg). More...

Public Member Functions inherited from ThermoPhase
	ThermoPhase ()
	Constructor. More...

virtual	~ThermoPhase ()
	Destructor. Deletes the species thermo manager. More...

	ThermoPhase (const ThermoPhase &right)
	Copy Constructor for the ThermoPhase object. More...

ThermoPhase &	operator= (const ThermoPhase &right)
	Assignment operator. 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 int 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 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	cv_vib (int, double) const

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	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...

void	getElectrochemPotentials (doublereal *mu) const
	Get the species electrochemical potentials. More...

virtual void	getdPartialMolarVolumes_dT (doublereal *d_vbar_dT) const
	Return an array of derivatives of partial molar volumes wrt temperature for the species in the mixture. More...

virtual void	getdPartialMolarVolumes_dP (doublereal *d_vbar_dP) const
	Return an array of derivatives of partial molar volumes wrt pressure for the species in the mixture. More...

virtual void	getdStandardVolumes_dT (doublereal *d_vol_dT) const
	Get the derivative of the molar volumes of the species standard states wrt temperature at the current T and P of the solution. More...

virtual void	getdStandardVolumes_dP (doublereal *d_vol_dP) const
	Get the derivative molar volumes of the species standard states wrt pressure at the current T and P of the solution. 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...

virtual void	setReferenceComposition (const doublereal *const x)
	Sets the reference composition. More...

virtual void	getReferenceComposition (doublereal *const x) const
	Gets the reference composition. More...

doublereal	enthalpy_mass () const
	Specific enthalpy. More...

doublereal	intEnergy_mass () const
	Specific internal energy. More...

doublereal	entropy_mass () const
	Specific entropy. More...

doublereal	gibbs_mass () const
	Specific Gibbs function. More...

doublereal	cp_mass () const
	Specific heat at constant pressure. More...

doublereal	cv_mass () const
	Specific heat at constant volume. 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...

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 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 bool	addSpecies (shared_ptr< Species > spec)
	Add a Species to this Phase. 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...

void	setSpeciesThermo (SpeciesThermo *spthermo)
	Install a species thermodynamic property manager. More...

virtual SpeciesThermo &	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	installSlavePhases (Cantera::XML_Node *phaseNode)
	Add in species from Slave phases. More...

virtual void	setStateFromXML (const XML_Node &state)
	Set the initial state of the phase to the conditions specified in the state XML element. 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...

virtual	~Phase ()
	Destructor. More...

	Phase (const Phase &right)
	Copy Constructor. More...

Phase &	operator= (const Phase &right)
	Assignment operator. More...

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 Write to vector 'state' the current internal state. 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	size (size_t k) const
	This routine returns the size of species k. 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...

virtual bool	ready () const
	Returns a bool indicating whether the object is ready for use. 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 Throws an exception if m is greater than nElements()-1. More...

void	checkElementArraySize (size_t mm) const
	Check that an array size is at least nElements() Throws an exception if mm is less than 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 Throws an exception if k is greater than nSpecies()-1. More...

void	checkSpeciesArraySize (size_t kk) const
	Check that an array size is at least nSpecies() Throws an exception if kk is less than 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...

void	getMoleFractionsByName (compositionMap &x) const
	Get the mole fractions by name. 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_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_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...

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 Note the density of a phase is an independent variable. 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	mean_Y (const doublereal *const Q) const
	Evaluate the mass-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...

doublereal	sum_xlogQ (doublereal *const Q) const
	Evaluate \( \sum_k X_k \log Q_k \). 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...

void	addElement (const XML_Node &e)
	Add an element from an XML specification. More...

void	addUniqueElement (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, checking for uniqueness The uniqueness is checked by comparing the string symbol. More...

void	addUniqueElement (const XML_Node &e)
	Add an element, checking for uniqueness The uniqueness is checked by comparing the string symbol. More...

void	addElementsFromXML (const XML_Node &phase)
	Add all elements referenced in an XML_Node tree. More...

void	freezeElements ()
	Prohibit addition of more elements, and prepare to add species. More...

bool	elementsFrozen ()
	True if freezeElements has been called. More...

size_t	addUniqueElementAfterFreeze (const std::string &symbol, doublereal weight, int atomicNumber, doublereal entropy298=ENTROPY298_UNKNOWN, int elem_type=CT_ELEM_TYPE_ABSPOS)
	Add an element after elements have been frozen, checking for uniqueness The uniqueness is checked by comparing the string symbol. More...

void	addSpecies (const std::string &name, const doublereal *comp, doublereal charge=0.0, doublereal size=1.0)

void	addUniqueSpecies (const std::string &name, const doublereal *comp, doublereal charge=0.0, doublereal size=1.0)
	Add a species to the phase, checking for uniqueness of the name This routine checks for uniqueness of the string name. 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...

Protected Attributes
doublereal	m_Mu0_pr_tr
	Value of the Absolute Gibbs Free Energy NIST scale at T_r and P_r. More...

doublereal	m_Entrop_pr_tr
	Input value of S_j at Tr and Pr (cal gmol-1 K-1) More...

doublereal	m_deltaG_formation_pr_tr
	Input Value of deltaG of Formation at Tr and Pr (cal gmol-1) More...

doublereal	m_deltaH_formation_pr_tr
	Input Value of deltaH of Formation at Tr and Pr (cal gmol-1) More...

doublereal	m_V0_pr_tr
	Input Value of the molar volume at T_r and P_r. More...

doublereal	m_a
	a coefficient (cal gmol-1 K-1) More...

doublereal	m_b
	b coefficient (cal gmol-1 K-2) x 10^3 More...

doublereal	m_c
	c coefficient (cal K gmol-1 K) x 10^-5 More...

Protected Attributes inherited from SingleSpeciesTP
doublereal	m_press
	The current pressure of the solution (Pa) More...

doublereal	m_p0

vector_fp	m_h0_RT
	Dimensionless enthalpy at the (mtlast, m_p0) More...

vector_fp	m_cp0_R
	Dimensionless heat capacity at the (mtlast, m_p0) More...

vector_fp	m_s0_R
	Dimensionless entropy at the (mtlast, m_p0) More...

Protected Attributes inherited from ThermoPhase
SpeciesThermo *	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. 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...

std::vector< doublereal >	xMol_Ref
	Reference Mole Fraction Composition. 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_speciesSize
	Vector of species sizes. 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...

Additional Inherited Members
Public Attributes inherited from Phase
enum CT_RealNumber_Range_Behavior	realNumberRangeBehavior_
	Overflow behavior of real number calculations involving this thermo object. More...

Protected Member Functions inherited from SingleSpeciesTP
void	_updateThermo () const

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...

Detailed Description

Class MineralEQ3 represents a stoichiometric (fixed composition) incompressible substance based on EQ3's parameterization.

This class inherits from SingleSpeciesSSTP class. EQ's parameterization is mapped onto the Shomate polynomial class.

Specification of Species Standard State Properties

This class inherits from SingleSpeciesTP. It is assumed that the reference state thermodynamics may be obtained by a pointer to a populated species thermodynamic property manager class (see ThermoPhase::m_spthermo). How to relate pressure changes to the reference state thermodynamics is resolved at this level.

For an incompressible, stoichiometric substance, the molar internal energy is independent of pressure. Since the thermodynamic properties are specified by giving the standard-state enthalpy, the term \( P_0 \hat v\) is subtracted from the specified molar enthalpy to compute the molar internal energy. The entropy is assumed to be independent of the pressure.

The enthalpy function is given by the following relation.

\[ h^o_k(T,P) = h^{ref}_k(T) + \tilde v \left( P - P_{ref} \right) \]

For an incompressible, stoichiometric substance, the molar internal energy is independent of pressure. Since the thermodynamic properties are specified by giving the standard-state enthalpy, the term \( P_{ref} \tilde v\) is subtracted from the specified reference molar enthalpy to compute the molar internal energy.

\[ u^o_k(T,P) = h^{ref}_k(T) - P_{ref} \tilde v \]

The standard state heat capacity and entropy are independent of pressure. The standard state Gibbs free energy is obtained from the enthalpy and entropy functions.

Specification of Solution Thermodynamic Properties

All solution properties are obtained from the standard state species functions, since there is only one species in the phase.

Application within Kinetics Managers

The standard concentration is equal to 1.0. This means that the kinetics operator works on an (activities basis). Since this is a stoichiometric substance, this means that the concentration of this phase drops out of kinetics expressions.

An example of a reaction using this is a sticking coefficient reaction of a substance in an ideal gas phase on a surface with a bulk phase species in this phase. In this case, the rate of progress for this reaction, \( R_s \), may be expressed via the following equation:

\[ R_s = k_s C_{gas} \]

where the units for \( R_s \) are kmol m-2 s-1. \( C_{gas} \) has units of kmol m-3. Therefore, the kinetic rate constant, \( k_s \), has units of m s-1. Nowhere does the concentration of the bulk phase appear in the rate constant expression, since it's a stoichiometric phase and the activity is always equal to 1.0.

Definition at line 94 of file MineralEQ3.h.

Constructor & Destructor Documentation

MineralEQ3 ( )

inline

Default constructor for the StoichSubstanceSSTP class.

Definition at line 98 of file MineralEQ3.h.

MineralEQ3	(	const std::string &	infile,
		std::string	id = `""`
	)

Construct and initialize a StoichSubstanceSSTP ThermoPhase object directly from an ASCII input file.

Parameters

infile	name of the input file
id	name of the phase id in the file. If this is blank, the first phase in the file is used.

Definition at line 30 of file MineralEQ3.cpp.

References XML_Node::child(), Cantera::get_XML_File(), Cantera::get_XML_NameID(), and Cantera::importPhase().

MineralEQ3	(	XML_Node &	phaseRef,
		const std::string &	id = `""`
	)

Construct and initialize a StoichSubstanceSSTP ThermoPhase object directly from an XML database.

Parameters

phaseRef	XML node pointing to a StoichSubstanceSSTP description
id	Id of the phase.

Definition at line 50 of file MineralEQ3.cpp.

References XML_Node::child(), and Cantera::importPhase().

MineralEQ3 ( const MineralEQ3 & right )

Copy constructor.

Parameters

right Object to be copied

Definition at line 66 of file MineralEQ3.cpp.

Member Function Documentation

MineralEQ3 & operator= ( const MineralEQ3 & right )

Assignment operator.

Parameters

right Object to be copied

Definition at line 72 of file MineralEQ3.cpp.

References MineralEQ3::m_a, MineralEQ3::m_b, MineralEQ3::m_c, MineralEQ3::m_deltaG_formation_pr_tr, MineralEQ3::m_deltaH_formation_pr_tr, MineralEQ3::m_Entrop_pr_tr, MineralEQ3::m_Mu0_pr_tr, and MineralEQ3::m_V0_pr_tr.

ThermoPhase * duplMyselfAsThermoPhase ( ) const

virtual

Duplication function.

This virtual function is used to create a duplicate of the current phase. It's used to duplicate the phase when given a ThermoPhase pointer to the phase.

Returns: It returns a ThermoPhase pointer.

Reimplemented from ThermoPhase.

Definition at line 90 of file MineralEQ3.cpp.

int eosType ( ) const

virtual

Equation of state flag.

Returns the value cStoichSubstance, defined in mix_defs.h.

Reimplemented from StoichSubstanceSSTP.

Definition at line 99 of file MineralEQ3.cpp.

doublereal pressure ( ) const

virtual

Report the Pressure. Units: Pa.

For an incompressible substance, the density is independent of pressure. This method simply returns the stored pressure value.

Reimplemented from StoichSubstanceSSTP.

Definition at line 108 of file MineralEQ3.cpp.

void setPressure ( doublereal p )

virtual

Set the pressure at constant temperature. Units: Pa.

For an incompressible substance, the density is independent of pressure. Therefore, this method only stores the specified pressure value. It does not modify the density.

Parameters

p	Pressure (units - Pa)

Reimplemented from StoichSubstanceSSTP.

Definition at line 113 of file MineralEQ3.cpp.

doublereal isothermalCompressibility ( ) const

virtual

Returns the isothermal compressibility. Units: 1/Pa.

The isothermal compressibility is defined as

\[ \kappa_T = -\frac{1}{v}\left(\frac{\partial v}{\partial P}\right)_T \]

Reimplemented from StoichSubstanceSSTP.

Definition at line 118 of file MineralEQ3.cpp.

doublereal thermalExpansionCoeff ( ) const

virtual

Return the volumetric thermal expansion coefficient. Units: 1/K.

The thermal expansion coefficient is defined as

\[ \beta = \frac{1}{v}\left(\frac{\partial v}{\partial T}\right)_P \]

Reimplemented from StoichSubstanceSSTP.

Definition at line 123 of file MineralEQ3.cpp.

void getActivityConcentrations ( doublereal * c ) const

virtual

This method returns an array of generalized concentrations.

\( C^a_k\) are defined such that \( a_k = C^a_k / C^0_k, \) where \( C^0_k \) is a standard concentration defined below and \( a_k \) are activities used in the thermodynamic functions. These activity (or generalized) concentrations are used by kinetics manager classes to compute the forward and reverse rates of elementary reactions.

For a stoichiometric substance, there is only one species, and the generalized concentration is 1.0.

Parameters

c	Output array of generalized concentrations. The units depend upon the implementation of the reaction rate expressions within the phase.

Reimplemented from StoichSubstanceSSTP.

Definition at line 132 of file MineralEQ3.cpp.

doublereal standardConcentration ( size_t k = 0 ) const

virtual

Return the standard concentration for the kth species.

The standard concentration \( C^0_k \) used to normalize the activity (i.e., generalized) concentration. This phase assumes that the kinetics operator works on an dimensionless basis. Thus, the standard concentration is equal to 1.0.

Parameters

k	Optional parameter indicating the species. The default is to assume this refers to species 0.

Returns: Returns The standard Concentration as 1.0

Reimplemented from StoichSubstanceSSTP.

Definition at line 137 of file MineralEQ3.cpp.

doublereal logStandardConc ( size_t k = 0 ) const

virtual

Natural logarithm of the standard concentration of the kth species.

Parameters

k	index of the species (defaults to zero)

Reimplemented from StoichSubstanceSSTP.

Definition at line 142 of file MineralEQ3.cpp.

void getStandardChemPotentials ( doublereal * mu0 ) const

virtual

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.

For a stoichiometric substance, there is no activity term in the chemical potential expression, and therefore the standard chemical potential and the chemical potential are both equal to the molar Gibbs function.

These are the standard state chemical potentials \( \mu^0_k(T,P) \). The values are evaluated at the current temperature and pressure of the solution

Parameters

mu0	Output vector of chemical potentials. Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 161 of file MineralEQ3.cpp.

void getUnitsStandardConc	(	doublereal *	uA,
		int	k = `0`,
		int	sizeUA = `6`
	)		const

virtual

Returns the units of the standard and generalized concentrations.

Note they have the same units, as their ratio is defined to be equal to the activity of the kth species in the solution, which is unitless.

This routine is used in print out applications where the units are needed. Usually, MKS units are assumed throughout the program and in the XML input files.

The base ThermoPhase class assigns the default quantities of (kmol/m3) for all species. Inherited classes are responsible for overriding the default values if necessary.

Parameters

uA

Output vector containing the units

uA[0] = kmol units - default  = 1
uA[1] = m    units - default  = -nDim(), the number of spatial
                              dimensions in the Phase class.
uA[2] = kg   units - default  = 0;
uA[3] = Pa(pressure) units - default = 0;
uA[4] = Temperature units - default = 0;
uA[5] = time units - default = 0

k species index. Defaults to 0.

sizeUA output int containing the size of the vector. Currently, this is equal to 6.

Deprecated:: To be removed after Cantera 2.2.

Reimplemented from StoichSubstanceSSTP.

Definition at line 147 of file MineralEQ3.cpp.

References Cantera::warn_deprecated().

void getEnthalpy_RT ( doublereal * hrt ) const

virtual

Get the nondimensional Enthalpy functions for the species at their standard states at the current T and P of the solution.

Parameters

hrt	Output vector of nondimensional standard state enthalpies. Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 167 of file MineralEQ3.cpp.

void getEntropy_R ( doublereal * sr ) const

virtual

Get the array of nondimensional Entropy functions for the standard state species at the current T and P of the solution.

Parameters

sr	Output vector of nondimensional standard state entropies. Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 175 of file MineralEQ3.cpp.

void getGibbs_RT ( doublereal * grt ) const

virtual

Get the nondimensional Gibbs functions for the species in their standard states at the current T and P of the solution.

Parameters

grt	Output vector of nondimensional standard state Gibbs free energies Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 180 of file MineralEQ3.cpp.

void getCp_R ( doublereal * cpr ) const

virtual

Get the nondimensional Heat Capacities at constant pressure for the species standard states at the current T and P of the solution.

Parameters

cpr	Output vector of nondimensional standard state heat capacities Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 186 of file MineralEQ3.cpp.

void getIntEnergy_RT ( doublereal * urt ) const

virtual

Returns the vector of nondimensional Internal Energies of the standard state species at the current T and P of the solution.

For an incompressible, stoichiometric substance, the molar internal energy is independent of pressure. Since the thermodynamic properties are specified by giving the standard-state enthalpy, the term \( P_{ref} \hat v\) is subtracted from the specified reference molar enthalpy to compute the standard state molar internal energy.

Parameters

urt	output vector of nondimensional standard state internal energies of the species. Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 192 of file MineralEQ3.cpp.

void getIntEnergy_RT_ref ( doublereal * urt ) const

virtual

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.

Parameters

urt	Output vector of nondimensional reference state internal energies of the species. Length: m_kk

Reimplemented from StoichSubstanceSSTP.

Definition at line 203 of file MineralEQ3.cpp.

void initThermoXML	(	XML_Node &	phaseNode,
		const std::string &	id
	)

virtual

Initialize the phase parameters from an XML file.

initThermoXML() (virtual from ThermoPhase)

This gets called from importPhase(). It processes the XML file after the species are set up. This is the main routine for reading in activity coefficient parameters.

Parameters

phaseNode	This object must be the phase node of a complete XML tree description of the phase, including all of the species data. In other words while "phase" must point to an XML phase object, it must have sibling nodes "speciesData" that describe the species in the phase.
id	ID of the phase. If nonnull, a check is done to see if phaseNode is pointing to the phase with the correct id.

Reimplemented from StoichSubstanceSSTP.

Definition at line 225 of file MineralEQ3.cpp.

References XML_Node::attrib(), XML_Node::child(), Cantera::getFloat(), Cantera::getFloatDefaultUnits(), XML_Node::hasAttrib(), XML_Node::hasChild(), and Cantera::toSI().

void setParameters	(	int	n,
		doublereal *const	c
	)

virtual

Set the equation of state parameters.

Parameters

n	number of parameters
c	array of n coefficients c[0] = density of phase [ kg/m3 ]

Reimplemented from StoichSubstanceSSTP.

Definition at line 214 of file MineralEQ3.cpp.

void getParameters	(	int &	n,
		doublereal *const	c
	)		const

virtual

Get the equation of state parameters in a vector.

Parameters

n	number of parameters
c	array of n coefficients

For this phase:

n = 1
c[0] = density of phase [ kg/m3 ]

Reimplemented from StoichSubstanceSSTP.

Definition at line 219 of file MineralEQ3.cpp.

void setParametersFromXML ( const XML_Node & eosdata )

virtual

Set equation of state parameter values from XML entries.

This method is called by function importPhase() when processing a phase definition in an input file. It should be overloaded in subclasses to set any parameters that are specific to that particular phase model. Note, this method is called before the phase is initialized with elements and/or species.

For this phase, the density of the phase is specified in this block.

Parameters

eosdata An XML_Node object corresponding to the "thermo" entry for this phase in the input file.

Reimplemented from StoichSubstanceSSTP.

Definition at line 279 of file MineralEQ3.cpp.

Member Data Documentation

doublereal m_Mu0_pr_tr

protected

Value of the Absolute Gibbs Free Energy NIST scale at T_r and P_r.

This is the NIST scale value of Gibbs free energy at T_r = 298.15 and P_r = 1 atm.

J kmol-1

Definition at line 421 of file MineralEQ3.h.

Referenced by MineralEQ3::operator=().

doublereal m_Entrop_pr_tr

protected

Input value of S_j at Tr and Pr (cal gmol-1 K-1)

Tr = 298.15 Pr = 1 atm

Definition at line 427 of file MineralEQ3.h.

Referenced by MineralEQ3::operator=().

doublereal m_deltaG_formation_pr_tr

protected

Input Value of deltaG of Formation at Tr and Pr (cal gmol-1)

Tr = 298.15 Pr = 1 atm

This is the delta G for the formation reaction of the ion from elements in their stable state at Tr, Pr.

Definition at line 436 of file MineralEQ3.h.

Referenced by MineralEQ3::operator=().

doublereal m_deltaH_formation_pr_tr

protected

Input Value of deltaH of Formation at Tr and Pr (cal gmol-1)

Tr = 298.15 Pr = 1 atm

This is the delta H for the formation reaction of the ion from elements in their stable state at Tr, Pr.

Definition at line 445 of file MineralEQ3.h.

Referenced by MineralEQ3::operator=().

doublereal m_V0_pr_tr

protected

Input Value of the molar volume at T_r and P_r.

cm^3 / gmol

Definition at line 451 of file MineralEQ3.h.

Referenced by MineralEQ3::operator=().

doublereal m_a

protected

a coefficient (cal gmol-1 K-1)

Definition at line 454 of file MineralEQ3.h.

Referenced by MineralEQ3::operator=().

doublereal m_b

protected

b coefficient (cal gmol-1 K-2) x 10^3

Definition at line 457 of file MineralEQ3.h.

Referenced by MineralEQ3::operator=().

doublereal m_c

protected

c coefficient (cal K gmol-1 K) x 10^-5

Definition at line 460 of file MineralEQ3.h.

Referenced by MineralEQ3::operator=().

The documentation for this class was generated from the following files:

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation