Cantera  2.1.2
Public Member Functions | Protected Attributes | List of all members
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:
[legend]
Collaboration diagram for MineralEQ3:
[legend]

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 initThermo ()
 Internal initialization required after all species have been added. 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...
 
- 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 setState_TPX (doublereal t, doublereal p, const doublereal *x)
 Set the temperature (K), pressure (Pa), and mole fractions. More...
 
void setState_TPX (doublereal t, doublereal p, compositionMap &x)
 Set the temperature (K), pressure (Pa), and mole fractions. More...
 
void setState_TPX (doublereal t, doublereal p, const std::string &x)
 Set the temperature (K), pressure (Pa), and mole fractions. More...
 
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...
 
void setState_TPY (doublereal t, doublereal p, compositionMap &y)
 Set the internally stored temperature (K), pressure (Pa), and mass fractions of the phase. More...
 
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...
 
void setState_PX (doublereal p, doublereal *x)
 Set the pressure (Pa) and mole fractions. More...
 
void setState_PY (doublereal p, doublereal *y)
 Set the internally stored pressure (Pa) and mass fractions. 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...
 
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...
 
- 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 int 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 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 critDensity () const
 Critical density (kg/m3). 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) 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...
 
virtual void setState_TP (doublereal t, doublereal p)
 Set the temperature (K) and pressure (Pa) 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 ()
 Returns a reference to the XML_Node stored for the 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...
 
virtual void freezeSpecies ()
 Call when finished adding species. More...
 
bool speciesFrozen ()
 True if freezeSpecies has been called. More...
 
virtual bool ready () const
 
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 (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 (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, 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, 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...
 
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...
 
doublereal massFraction (size_t k) const
 Return the mass fraction of a single species. More...
 
doublereal massFraction (const std::string &name) const
 Return the mass fraction of a single species. More...
 
void getMoleFractions (doublereal *const x) const
 Get the species mole fraction vector. More...
 
virtual void setMoleFractions (const doublereal *const x)
 Set the mole fractions to the specified values There is no restriction on the sum of the 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 (const doublereal *const y)
 Set the mass fractions to the specified values and normalize them. More...
 
virtual void setMassFractions_NoNorm (const doublereal *const y)
 Set the mass fractions to the specified values without normalizing. More...
 
void getConcentrations (doublereal *const c) const
 Get the species concentrations (kmol/m^3). More...
 
doublereal concentration (const size_t k) const
 Concentration of species k. More...
 
virtual void setConcentrations (const doublereal *const conc)
 Set the concentrations to the specified values within the phase. More...
 
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_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...
 
void addElement (const std::string &symbol, doublereal weight=-12345.0)
 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...
 

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
 
doublereal m_tlast
 Last temperature used to evaluate the thermodynamic polynomial. More...
 
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...
 
- Protected Attributes inherited from Phase
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...
 

Additional Inherited Members

- 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 init (const vector_fp &mw)
 
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 97 of file MineralEQ3.h.

Constructor & Destructor Documentation

Default constructor for the StoichSubstanceSSTP class.

Definition at line 32 of file MineralEQ3.cpp.

Referenced by MineralEQ3::duplMyselfAsThermoPhase().

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

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

Parameters
infilename of the input file
idname of the phase id in the file. If this is blank, the first phase in the file is used.

Definition at line 37 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
phaseRefXML node pointing to a StoichSubstanceSSTP description
idId of the phase.

Definition at line 59 of file MineralEQ3.cpp.

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

MineralEQ3 ( const MineralEQ3 right)

Copy constructor.

Parameters
rightObject to be copied

Definition at line 78 of file MineralEQ3.cpp.

References MineralEQ3::operator=().

Member Function Documentation

MineralEQ3 & operator= ( const MineralEQ3 right)
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 103 of file MineralEQ3.cpp.

References MineralEQ3::MineralEQ3().

int eosType ( ) const
virtual

Equation of state flag.

Returns the value cStoichSubstance, defined in mix_defs.h.

Reimplemented from StoichSubstanceSSTP.

Definition at line 112 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 121 of file MineralEQ3.cpp.

References SingleSpeciesTP::m_press.

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
pPressure (units - Pa)

Reimplemented from StoichSubstanceSSTP.

Definition at line 126 of file MineralEQ3.cpp.

References SingleSpeciesTP::m_press.

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 131 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 136 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
cOutput array of generalized concentrations. The units depend upon the implementation of the reaction rate expressions within the phase.

Reimplemented from StoichSubstanceSSTP.

Definition at line 146 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
kOptional 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 151 of file MineralEQ3.cpp.

doublereal logStandardConc ( size_t  k = 0) const
virtual

Natural logarithm of the standard concentration of the kth species.

Parameters
kindex of the species (defaults to zero)

Reimplemented from StoichSubstanceSSTP.

Definition at line 156 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
mu0Output vector of chemical potentials. Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 174 of file MineralEQ3.cpp.

References Cantera::GasConstant, MineralEQ3::getGibbs_RT(), and Phase::temperature().

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
uAOutput 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
kspecies index. Defaults to 0.
sizeUAoutput int containing the size of the vector. Currently, this is equal to 6.
Deprecated:

Reimplemented from StoichSubstanceSSTP.

Definition at line 162 of file MineralEQ3.cpp.

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
hrtOutput vector of nondimensional standard state enthalpies. Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 180 of file MineralEQ3.cpp.

References Cantera::GasConstant, SingleSpeciesTP::getEnthalpy_RT_ref(), SingleSpeciesTP::m_p0, SingleSpeciesTP::m_press, Phase::molarDensity(), and Phase::temperature().

Referenced by MineralEQ3::getGibbs_RT().

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
srOutput vector of nondimensional standard state entropies. Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 188 of file MineralEQ3.cpp.

References SingleSpeciesTP::getEntropy_R_ref().

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
grtOutput vector of nondimensional standard state gibbs free energies Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 193 of file MineralEQ3.cpp.

References MineralEQ3::getEnthalpy_RT(), and SingleSpeciesTP::m_s0_R.

Referenced by MineralEQ3::getStandardChemPotentials().

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
cprOutput vector of nondimensional standard state heat capacities Length: m_kk.

Reimplemented from StoichSubstanceSSTP.

Definition at line 199 of file MineralEQ3.cpp.

References SingleSpeciesTP::_updateThermo(), and SingleSpeciesTP::m_cp0_R.

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

Reimplemented from StoichSubstanceSSTP.

Definition at line 205 of file MineralEQ3.cpp.

References SingleSpeciesTP::_updateThermo(), Cantera::GasConstant, SingleSpeciesTP::m_h0_RT, SingleSpeciesTP::m_p0, Phase::molarDensity(), and Phase::temperature().

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

Reimplemented from StoichSubstanceSSTP.

Definition at line 216 of file MineralEQ3.cpp.

References SingleSpeciesTP::_updateThermo(), Cantera::GasConstant, SingleSpeciesTP::m_h0_RT, SingleSpeciesTP::m_p0, Phase::molarDensity(), and Phase::temperature().

void initThermo ( )
virtual

Internal initialization required after all species have been added.

Initialize. This method is provided to allow subclasses to perform any initialization required after all species have been added. For example, it might be used to resize internal work arrays that must have an entry for each species. The base class implementation does nothing, and subclasses that do not require initialization do not need to overload this method. When importing a CTML phase description, this method is called just prior to returning from function importPhase.

See Also
importCTML.cpp

Reimplemented from StoichSubstanceSSTP.

Definition at line 227 of file MineralEQ3.cpp.

References StoichSubstanceSSTP::initThermo().

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
phaseNodeThis 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.
idID 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 250 of file MineralEQ3.cpp.

References XML_Node::attrib(), XML_Node::child(), ctml::getFloat(), ctml::getFloatDefaultUnits(), XML_Node::hasAttrib(), XML_Node::hasChild(), 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, Phase::m_speciesSize, MineralEQ3::m_V0_pr_tr, Phase::molecularWeight(), Phase::setDensity(), ThermoPhase::speciesData(), and Cantera::toSI().

void setParameters ( int  n,
doublereal *const  c 
)
virtual

Set the equation of state parameters.

Parameters
nnumber of parameters
carray of n coefficients c[0] = density of phase [ kg/m3 ]
Deprecated:
Use setDensity()

Reimplemented from StoichSubstanceSSTP.

Definition at line 235 of file MineralEQ3.cpp.

References Phase::setDensity(), and Cantera::warn_deprecated().

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

Get the equation of state parameters in a vector.

Parameters
nnumber of parameters
carray of n coefficients

For this phase:

Reimplemented from StoichSubstanceSSTP.

Definition at line 242 of file MineralEQ3.cpp.

References Phase::density(), and Cantera::warn_deprecated().

void setParametersFromXML ( const XML_Node eosdata)
virtual

Set equation of state parameter values from XML entries.

This method is called by function importPhase() in file importCTML.cpp 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
eosdataAn XML_Node object corresponding to the "thermo" entry for this phase in the input file.

Reimplemented from StoichSubstanceSSTP.

Definition at line 311 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 444 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 450 of file MineralEQ3.h.

Referenced by MineralEQ3::initThermoXML(), and 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 459 of file MineralEQ3.h.

Referenced by MineralEQ3::initThermoXML(), and 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 468 of file MineralEQ3.h.

Referenced by MineralEQ3::initThermoXML(), and 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 474 of file MineralEQ3.h.

Referenced by MineralEQ3::initThermoXML(), and MineralEQ3::operator=().

doublereal m_a
protected

a coefficient (cal gmol-1 K-1)

Definition at line 477 of file MineralEQ3.h.

Referenced by MineralEQ3::initThermoXML(), and MineralEQ3::operator=().

doublereal m_b
protected

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

Definition at line 480 of file MineralEQ3.h.

Referenced by MineralEQ3::initThermoXML(), and MineralEQ3::operator=().

doublereal m_c
protected

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

Definition at line 483 of file MineralEQ3.h.

Referenced by MineralEQ3::initThermoXML(), and MineralEQ3::operator=().


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