Cantera  2.2.1
MineralEQ3 Class Reference

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...

MineralEQ3operator= (const MineralEQ3 &right)
Assignment operator. More...

ThermoPhaseduplMyselfAsThermoPhase () 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...

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

ThermoPhaseduplMyselfAsThermoPhase () 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...

SingleSpeciesTPoperator= (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...

ThermoPhaseoperator= (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 SpeciesThermospeciesThermo (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...

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

XML_Nodexml () 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_fpmolecularWeights () 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...

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_fpatomicWeights () 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 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...

Add an element, checking for uniqueness The uniqueness is checked by comparing the string symbol. More...

Add all elements referenced in an XML_Node tree. More...

void freezeElements ()

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< Speciesspecies (const std::string &name) const
Return the Species object for the named species. More...

shared_ptr< Speciesspecies (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...

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
SpeciesThermom_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...

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.

 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.

 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.

 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: