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GeochemicalSystem Member List

This is the complete list of members for GeochemicalSystem, including all inherited members.

_algebraic_indexGeochemicalSystemprivate
_basis_activityGeochemicalSystemprivate
_basis_activity_coefGeochemicalSystemprivate
_basis_activity_knownGeochemicalSystemprivate
_basis_indexGeochemicalSystemprivate
_basis_molalityGeochemicalSystemprivate
_bulk_moles_oldGeochemicalSystemprivate
_charge_balance_basis_indexGeochemicalSystemprivate
_charge_balance_speciesGeochemicalSystemprivate
_constrained_speciesGeochemicalSystemprivate
_constraint_meaningGeochemicalSystemprivate
_constraint_unitGeochemicalSystemprivate
_constraint_user_meaningGeochemicalSystemprivate
_constraint_valueGeochemicalSystemprivate
_eqm_activityGeochemicalSystemprivate
_eqm_activity_coefGeochemicalSystemprivate
_eqm_log10KGeochemicalSystemprivate
_eqm_molalityGeochemicalSystemprivate
_gacGeochemicalSystemprivate
_in_algebraic_systemGeochemicalSystemprivate
_isGeochemicalSystemprivate
_iters_to_make_consistentGeochemicalSystemprivate
_kin_log10KGeochemicalSystemprivate
_kin_molesGeochemicalSystemprivate
_kin_moles_oldGeochemicalSystemprivate
_mgdGeochemicalSystemprivate
_min_initial_molalityGeochemicalSystemprivate
_num_basisGeochemicalSystemprivate
_num_basis_in_algebraic_systemGeochemicalSystemprivate
_num_eqmGeochemicalSystemprivate
_num_in_algebraic_systemGeochemicalSystemprivate
_num_kinGeochemicalSystemprivate
_num_redoxGeochemicalSystemprivate
_num_surface_potGeochemicalSystemprivate
_original_charge_balance_speciesGeochemicalSystemprivate
_original_constraint_valueGeochemicalSystemprivate
_original_redox_lhsGeochemicalSystemprivate
_redox_log10KGeochemicalSystemprivate
_sorbing_surface_areaGeochemicalSystemprivate
_surface_pot_exprGeochemicalSystemprivate
_swap_inGeochemicalSystemprivate
_swap_outGeochemicalSystemprivate
_swapperGeochemicalSystemprivate
_temperatureGeochemicalSystemprivate
addKineticRates(Real dt, DenseVector< Real > &mole_additions, DenseMatrix< Real > &dmole_additions)GeochemicalSystem
addToBulkMoles(unsigned basis_ind, Real value)GeochemicalSystem
alterChargeBalanceSpecies(Real threshold_molality)GeochemicalSystem
alterSystemBecauseBulkChanged()GeochemicalSystemprivate
buildAlgebraicInfo(std::vector< bool > &in_algebraic_system, unsigned &num_basis_in_algebraic_system, unsigned &num_in_algebraic_system, std::vector< unsigned > &algebraic_index, std::vector< unsigned > &basis_index) constGeochemicalSystemprivate
buildKnownBasisActivities(std::vector< bool > &basis_activity_known, std::vector< Real > &basis_activity) constGeochemicalSystemprivate
buildTemperatureDependentQuantities(Real temperature)GeochemicalSystemprivate
changeConstraintToBulk(unsigned basis_ind)GeochemicalSystem
changeConstraintToBulk(unsigned basis_ind, Real value)GeochemicalSystem
checkAndInitialize(const std::vector< std::string > &kin_name, const std::vector< Real > &kin_initial, const std::vector< GeochemistryUnitConverter::GeochemistryUnit > &kin_unit)GeochemicalSystemprivate
closeSystem()GeochemicalSystem
computeAndGetEquilibriumActivity()GeochemicalSystem
computeBulk(std::vector< Real > &bulk_moles_old) constGeochemicalSystemprivate
computeBulkFromMolalities(unsigned basis_ind) constGeochemicalSystemprivate
computeConsistentConfiguration()GeochemicalSystem
computeEqmMolalities(std::vector< Real > &eqm_molality) constGeochemicalSystemprivate
computeFreeMineralMoles(std::vector< Real > &basis_molality) constGeochemicalSystemprivate
computeJacobian(const DenseVector< Real > &res, DenseMatrix< Real > &jac, const DenseVector< Real > &mole_additions, const DenseMatrix< Real > &dmole_additions) constGeochemicalSystem
computeRemainingBasisActivities(std::vector< Real > &basis_activity) constGeochemicalSystemprivate
computeSorbingSurfaceArea(std::vector< Real > &sorbing_surface_area) constGeochemicalSystemprivate
computeTransportedBulkFromMolalities(std::vector< Real > &transported_bulk) constGeochemicalSystem
ConstraintMeaningEnum enum nameGeochemicalSystem
ConstraintUserMeaningEnum enum nameGeochemicalSystem
enforceChargeBalance()GeochemicalSystem
enforceChargeBalance(std::vector< Real > &constraint_value, std::vector< Real > &bulk_moles_old) constGeochemicalSystemprivate
enforceChargeBalanceIfSimple(std::vector< Real > &constraint_value, std::vector< Real > &bulk_moles_old) constGeochemicalSystemprivate
GeochemicalSystem(ModelGeochemicalDatabase &mgd, GeochemistryActivityCoefficients &gac, GeochemistryIonicStrength &is, GeochemistrySpeciesSwapper &swapper, const std::vector< std::string > &swap_out_of_basis, const std::vector< std::string > &swap_into_basis, const std::string &charge_balance_species, const std::vector< std::string > &constrained_species, const std::vector< Real > &constraint_value, const MultiMooseEnum &constraint_unit, const MultiMooseEnum &constraint_user_meaning, Real initial_temperature, unsigned iters_to_make_consistent, Real min_initial_molality, const std::vector< std::string > &kin_name, const std::vector< Real > &kin_initial_moles, const MultiMooseEnum &kin_unit)GeochemicalSystem
GeochemicalSystem(ModelGeochemicalDatabase &mgd, GeochemistryActivityCoefficients &gac, GeochemistryIonicStrength &is, GeochemistrySpeciesSwapper &swapper, const std::vector< std::string > &swap_out_of_basis, const std::vector< std::string > &swap_into_basis, const std::string &charge_balance_species, const std::vector< std::string > &constrained_species, const std::vector< Real > &constraint_value, const std::vector< GeochemistryUnitConverter::GeochemistryUnit > &constraint_unit, const std::vector< ConstraintUserMeaningEnum > &constraint_user_meaning, Real initial_temperature, unsigned iters_to_make_consistent, Real min_initial_molality, const std::vector< std::string > &kin_name, const std::vector< Real > &kin_initial, const std::vector< GeochemistryUnitConverter::GeochemistryUnit > &kin_unit)GeochemicalSystem
GeochemicalSystem(const GeochemicalSystem &src)=defaultGeochemicalSystem
getAlgebraicBasisValues() constGeochemicalSystem
getAlgebraicIndexOfBasisSystem() constGeochemicalSystem
getAlgebraicVariableDenseValues() constGeochemicalSystem
getAlgebraicVariableValues() constGeochemicalSystem
getBasisActivity(unsigned i) constGeochemicalSystem
getBasisActivity() constGeochemicalSystem
getBasisActivityCoefficient(unsigned i) constGeochemicalSystem
getBasisActivityCoefficient() constGeochemicalSystem
getBasisActivityKnown() constGeochemicalSystem
getBasisIndexOfAlgebraicSystem() constGeochemicalSystem
getBulkMolesOld() constGeochemicalSystem
getBulkOldInOriginalBasis() constGeochemicalSystem
getChargeBalanceBasisIndex() constGeochemicalSystem
getConstraintMeaning() constGeochemicalSystem
getEquilibriumActivity(unsigned eqm_ind) constGeochemicalSystem
getEquilibriumActivityCoefficient(unsigned j) constGeochemicalSystem
getEquilibriumActivityCoefficient() constGeochemicalSystem
getEquilibriumMolality(unsigned j) constGeochemicalSystem
getEquilibriumMolality() constGeochemicalSystem
getInAlgebraicSystem() constGeochemicalSystem
getIonicStrength() constGeochemicalSystem
getKineticLog10K(unsigned kin) constGeochemicalSystem
getKineticLog10K() constGeochemicalSystem
getKineticMoles(unsigned kin) constGeochemicalSystem
getKineticMoles() constGeochemicalSystem
getLog10K(unsigned j) constGeochemicalSystem
getModelGeochemicalDatabase() constGeochemicalSystem
getNumBasisInAlgebraicSystem() constGeochemicalSystem
getNumInAlgebraicSystem() constGeochemicalSystem
getNumInBasis() constGeochemicalSystem
getNumInEquilibrium() constGeochemicalSystem
getNumKinetic() constGeochemicalSystem
getNumRedox() constGeochemicalSystem
getNumSurfacePotentials() constGeochemicalSystem
getOriginalRedoxLHS() constGeochemicalSystem
getRedoxLog10K(unsigned red) constGeochemicalSystem
getResidualComponent(unsigned algebraic_ind, const DenseVector< Real > &mole_additions) constGeochemicalSystem
getSaturationIndices() constGeochemicalSystem
getSolventMassAndFreeMolalityAndMineralMoles() constGeochemicalSystem
getSolventWaterMass() constGeochemicalSystem
getSorbingSurfaceArea() constGeochemicalSystem
getStoichiometricIonicStrength() constGeochemicalSystem
getSurfaceCharge(unsigned sp) constGeochemicalSystem
getSurfacePotential(unsigned sp) constGeochemicalSystem
getSwapper() constGeochemicalSystem
getTemperature() constGeochemicalSystem
getTotalChargeOld() constGeochemicalSystem
getTransportedBulkInOriginalBasis() constGeochemicalSystem
initBulkAndFree(std::vector< Real > &bulk_moles_old, std::vector< Real > &basis_molality) constGeochemicalSystemprivate
initialize()GeochemicalSystem
log10ActivityProduct(unsigned eqm_j) constGeochemicalSystemprivate
log10KineticActivityProduct(unsigned kin) constGeochemicalSystem
log10RedoxActivityProduct(unsigned red) constGeochemicalSystem
operator=(const GeochemicalSystem &src)GeochemicalSysteminline
operator==(const GeochemicalSystem &rhs) constGeochemicalSysteminline
performSwap(unsigned swap_out_of_basis, unsigned swap_into_basis)GeochemicalSystem
performSwapNoCheck(unsigned swap_out_of_basis, unsigned swap_into_basis)GeochemicalSystem
revertToOriginalChargeBalanceSpecies()GeochemicalSystem
setAlgebraicVariables(const DenseVector< Real > &algebraic_var)GeochemicalSystem
setChargeBalanceSpecies(unsigned new_charge_balance_index)GeochemicalSystemprivate
setConstraintValue(unsigned basis_ind, Real value)GeochemicalSystem
setKineticMoles(unsigned kin, Real moles)GeochemicalSystem
setMineralRelatedFreeMoles(Real value)GeochemicalSystem
setModelGeochemicalDatabase(const ModelGeochemicalDatabase &mgd)GeochemicalSystem
setSolventMassAndFreeMolalityAndMineralMolesAndSurfacePotsAndKineticMoles(const std::vector< std::string > &names, const std::vector< Real > &values, const std::vector< bool > &constraints_from_molalities)GeochemicalSystem
setTemperature(Real temperature)GeochemicalSystem
surfacePotPrefactor(unsigned sp) constGeochemicalSystemprivate
surfaceSorptionModifier(unsigned eqm_j) constGeochemicalSystemprivate
updateBasisMolalityForKnownActivity(std::vector< Real > &basis_molality) constGeochemicalSystemprivate
updateOldWithCurrent(const DenseVector< Real > &mole_additions)GeochemicalSystem
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