Data structure to hold all relevant information from the database file. More...

#include <PertinentGeochemicalSystem.h>

Public Member Functions
	ModelGeochemicalDatabase (const GeochemicalDatabaseReader &db)
	Constructor sets original_database.

bool	operator== (const ModelGeochemicalDatabase &rhs) const

Public Attributes
const GeochemicalDatabaseReader *	original_database
	a pointer to the original database used to build this ModelGeochemicalDatabase

std::unordered_map< std::string, unsigned >	basis_species_index
	basis_species_index[name] = index of the basis species, within all ModelGeochemicalDatabase internal datastrcutres, with given name

std::vector< std::string >	basis_species_name
	basis_species_name[j] = name of the j^th basis species

std::vector< bool >	basis_species_mineral
	basis_species_mineral[j] = true iff the j^th basis species is a mineral

std::vector< bool >	basis_species_gas
	basis_species_gas[j] = true iff the j^th basis species is a gas

std::vector< bool >	basis_species_transported
	basis_species_transported[j] = true iff the j^th basis species is transported in reactive-transport sims

std::vector< Real >	basis_species_charge
	all quantities have a charge (mineral charge = 0, gas charge = 0, oxide charge = 0)

std::vector< Real >	basis_species_radius
	all quantities have an ionic radius (Angstrom) for computing activity (mineral radius = 0, gas radius = 0, surface species radius = 0)

std::vector< Real >	basis_species_molecular_weight
	all quantities have a molecular weight (g)

std::vector< Real >	basis_species_molecular_volume
	all quantities have a molecular volume (cm^3) (only nonzero for minerals, however)

std::unordered_map< std::string, unsigned >	eqm_species_index
	eqm_species_index[name] = index of the equilibrium species (secondary aqueous species, redox couples in equilibrium with the aqueous solution, minerals in equilibrium with the aqueous solution, gases in equilibrium with the aqueous solution) within all ModelGeochemicalDatabase internal datastrcutres, with given name

std::vector< std::string >	eqm_species_name
	eqm_species_name[i] = name of the i^th eqm species

std::vector< bool >	eqm_species_mineral
	eqm_species_mineral[i] = true iff the i^th equilibrium species is a mineral

std::vector< bool >	eqm_species_gas
	eqm_species_gas[i] = true iff the i^th equilibrium species is a gas

std::vector< bool >	eqm_species_transported
	eqm_species_transported[i] = true iff the i^th eqm species is transported in reactive-transport sims

std::vector< Real >	eqm_species_charge
	all quantities have a charge (mineral charge = 0, gas charge = 0, oxide charge = 0)

std::vector< Real >	eqm_species_radius
	all quantities have an ionic radius (Angstrom) for computing activity (mineral radius = 0, gas radius = 0, surface species radius = 0)

std::vector< Real >	eqm_species_molecular_weight
	all quantities have a molecular weight (g)

std::vector< Real >	eqm_species_molecular_volume
	all quantities have a molecular volume (cm^3) (only nonzero for minerals, however)

DenseMatrix< Real >	eqm_stoichiometry
	eqm_stoichiometry(i, j) = stoichiometric coefficient for equilibrium species "i" in terms of the basis species "j"

DenseMatrix< Real >	eqm_log10K
	eqm_log10K(i, j) = log10(equilibrium constant) for i^th equilibrium species at the j^th temperature point

std::vector< std::string >	surface_sorption_name
	surface_sorption_name[k] = name of the mineral involved in surface sorption.

std::vector< Real >	surface_sorption_area
	surface_sorption_area[k] = specific surface area [m^2/g] for the k^th mineral involved in surface sorption.

std::vector< bool >	surface_sorption_related
	surface_sorption_related[j] = true iff the j^th equilibrium species is involved in surface sorption

std::vector< unsigned >	surface_sorption_number
	surface_sorption_number[j] = the index of the surface potential that should be used to modify the equilibrium constant for the j^th equilibrium species.

std::string	redox_lhs
	the name of the species on the left-hand side of the redox equations.

DenseMatrix< Real >	redox_stoichiometry
	redox_stoichiometry(i, j) = stoichiometric coefficients for i^th redox species that is in disequilibrium in terms of the j basis species.

DenseMatrix< Real >	redox_log10K
	redox_log10K(i, j) = log10(equilibrium constant) for i^th redox species at the j^th temperature point

std::unordered_map< std::string, SurfaceComplexationInfo >	surface_complexation_info
	Holds info on surface complexation, if any, in the model.

std::unordered_map< std::string, std::vector< Real > >	gas_chi
	Holds info on gas fugacity "chi" parameters.

std::unordered_map< std::string, unsigned >	kin_species_index
	kin_species_index[name] = index of the kinetic species, within all ModelGeochemicalDatabase internal datastrcutres, with given name

std::vector< std::string >	kin_species_name
	kin_species_name[j] = name of the j^th kinetic species

std::vector< bool >	kin_species_mineral
	kin_species_mineral[j] = true iff the j^th kinetic species is a mineral

std::vector< bool >	kin_species_transported
	kin_species_transported[j] = true iff the j^th kinetic species is transported in reactive-transport sims

std::vector< Real >	kin_species_charge
	all kinetic quantities have a charge (mineral charge = 0)

std::vector< Real >	kin_species_molecular_weight
	all quantities have a molecular weight (g/mol)

std::vector< Real >	kin_species_molecular_volume
	all quantities have a molecular volume (cm^3/mol) (only nonzero for minerals, however)

DenseMatrix< Real >	kin_log10K
	kin_log10K(i, j) = log10(equilibrium constant for the i^th kinetic species at the j^th temperature point

DenseMatrix< Real >	kin_stoichiometry
	kin_stoichiometry(i, j) = stoichiometric coefficient for kinetic species "i" in terms of the basis species "j"

std::vector< KineticRateDefinition >	kin_rate
	rates given to kinetic species.

std::vector< unsigned >	have_swapped_out_of_basis
	Species that have been swapped out of the basis.

std::vector< unsigned >	have_swapped_into_basis
	Species that have been swapped into the basis.

DenseMatrix< Real >	swap_to_original_basis
	Swap matrix that allows expression in terms of the original basis.

Detailed Description

Data structure to hold all relevant information from the database file.

Generally, the database file contains information on a lot more species than any numerical model considers. The ModelGeochemicalDatabase only holds the minimal information required for the numerical model. It also holds the information as std::vector and DenseMatrix data structures for numerical efficiency. This makes the ModelGeochemicalDatabase a little more obscure compared with the database file, but considering this information is used hundreds, maybe millions, of times per node during a single timestep, numerical efficiency is paramount.

Definition at line 101 of file PertinentGeochemicalSystem.h.

Constructor & Destructor Documentation

◆ ModelGeochemicalDatabase()

ModelGeochemicalDatabase::ModelGeochemicalDatabase ( const GeochemicalDatabaseReader & db )

inline

Constructor sets original_database.

Also initializes swap_to_original_basis to "nothing" in an attempt to reduce memory consumption

Definition at line 107 of file PertinentGeochemicalSystem.h.

    : original_database(&db), swap_to_original_basis(DenseMatrix<Real>())
  {
  }

Member Function Documentation

◆ operator==()

bool ModelGeochemicalDatabase::operator== ( const ModelGeochemicalDatabase & rhs ) const

inline

Definition at line 112 of file PertinentGeochemicalSystem.h.

  {
    return (original_database == rhs.original_database) &&
           (basis_species_index == rhs.basis_species_index) &&
           (basis_species_name == rhs.basis_species_name) &&
           (basis_species_mineral == rhs.basis_species_mineral) &&
           (basis_species_gas == rhs.basis_species_gas) &&
           (basis_species_transported == rhs.basis_species_transported) &&
           (basis_species_charge == rhs.basis_species_charge) &&
           (basis_species_radius == rhs.basis_species_radius) &&
           (basis_species_molecular_weight == rhs.basis_species_molecular_weight) &&
           (basis_species_molecular_volume == rhs.basis_species_molecular_volume) &&
           (eqm_species_index == rhs.eqm_species_index) &&
           (eqm_species_name == rhs.eqm_species_name) &&
           (eqm_species_mineral == rhs.eqm_species_mineral) &&
           (eqm_species_gas == rhs.eqm_species_gas) &&
           (eqm_species_transported == rhs.eqm_species_transported) &&
           (eqm_species_charge == rhs.eqm_species_charge) &&
           (eqm_species_radius == rhs.eqm_species_radius) &&
           (eqm_species_molecular_weight == rhs.eqm_species_molecular_weight) &&
           (eqm_species_molecular_volume == rhs.eqm_species_molecular_volume) &&
           (eqm_stoichiometry == rhs.eqm_stoichiometry) && (eqm_log10K == rhs.eqm_log10K) &&
           (surface_sorption_name == rhs.surface_sorption_name) &&
           (surface_sorption_area == rhs.surface_sorption_area) &&
           (surface_sorption_related == rhs.surface_sorption_related) &&
           (surface_sorption_number == rhs.surface_sorption_number) &&
           (redox_lhs == rhs.redox_lhs) && (redox_stoichiometry == rhs.redox_stoichiometry) &&
           (redox_log10K == rhs.redox_log10K) &&
           (surface_complexation_info == rhs.surface_complexation_info) &&
           (gas_chi == rhs.gas_chi) && (kin_species_index == rhs.kin_species_index) &&
           (kin_species_name == rhs.kin_species_name) &&
           (kin_species_mineral == rhs.kin_species_mineral) &&
           (kin_species_transported == rhs.kin_species_transported) &&
           (kin_species_charge == rhs.kin_species_charge) &&
           (kin_species_molecular_weight == rhs.kin_species_molecular_weight) &&
           (kin_species_molecular_volume == rhs.kin_species_molecular_volume) &&
           (kin_log10K == rhs.kin_log10K) && (kin_stoichiometry == rhs.kin_stoichiometry) &&
           (kin_rate == rhs.kin_rate) &&
           (have_swapped_out_of_basis == rhs.have_swapped_out_of_basis) &&
           (have_swapped_into_basis == rhs.have_swapped_into_basis) &&
           (swap_to_original_basis == rhs.swap_to_original_basis);
  };

Member Data Documentation

◆ basis_species_charge

std::vector<Real> ModelGeochemicalDatabase::basis_species_charge

all quantities have a charge (mineral charge = 0, gas charge = 0, oxide charge = 0)

Definition at line 177 of file PertinentGeochemicalSystem.h.

Referenced by GeochemicalSystem::alterChargeBalanceSpecies(), GeochemistrySpeciesSwapper::alterMGD(), GeochemistryActivityCoefficientsDebyeHuckel::buildActivityCoefficients(), GeochemicalSystem::checkAndInitialize(), GeochemicalSystem::computeJacobian(), PertinentGeochemicalSystem::createModel(), GeochemicalSystem::enforceChargeBalance(), GeochemicalSystem::enforceChargeBalanceIfSimple(), GeochemicalSystem::getResidualComponent(), GeochemicalSystem::getTotalChargeOld(), GeochemistryIonicStrength::ionicStrength(), operator==(), GeochemistryIonicStrength::stoichiometricIonicStrength(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), and TEST().

◆ basis_species_gas

std::vector<bool> ModelGeochemicalDatabase::basis_species_gas

basis_species_gas[j] = true iff the j^th basis species is a gas

Definition at line 171 of file PertinentGeochemicalSystem.h.

Referenced by GeochemicalSystem::addKineticRates(), GeochemistrySpeciesSwapper::alterMGD(), GeochemistryActivityCoefficientsDebyeHuckel::buildActivityCoefficients(), GeochemicalSystem::buildAlgebraicInfo(), GeochemicalSystem::changeConstraintToBulk(), GeochemicalSystem::changeConstraintToBulk(), GeochemicalSystem::checkAndInitialize(), PertinentGeochemicalSystem::createModel(), operator==(), GeochemistryConsoleOutput::output(), GeochemicalSystem::performSwap(), GeochemicalSystem::performSwapNoCheck(), GeochemicalSystem::setSolventMassAndFreeMolalityAndMineralMolesAndSurfacePotsAndKineticMoles(), GeochemicalSolver::swapNeeded(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), and GeochemicalSystem::updateBasisMolalityForKnownActivity().

◆ basis_species_index

std::unordered_map<std::string, unsigned> ModelGeochemicalDatabase::basis_species_index

basis_species_index[name] = index of the basis species, within all ModelGeochemicalDatabase internal datastrcutres, with given name

Definition at line 162 of file PertinentGeochemicalSystem.h.

Referenced by PertinentGeochemicalSystem::addKineticRate(), GeochemistrySpeciesSwapper::alterMGD(), GeochemicalSystem::buildAlgebraicInfo(), PertinentGeochemicalSystem::buildRedoxeInfo(), GeochemicalSystem::checkAndInitialize(), GeochemistrySpeciesSwapper::checkSwap(), GeochemistrySpeciesSwapper::checkSwap(), GeochemicalSystem::computeSorbingSurfaceArea(), GeochemistryQuantityAux::computeValue(), GeochemistrySpeciesSwapper::constructInverseMatrix(), PertinentGeochemicalSystem::createModel(), GeochemistrySpatialReactor::execute(), GeochemistryTimeDependentReactor::execute(), GeochemistryUnitConverter::fromMoles(), GeochemistryQuantityAux::GeochemistryQuantityAux(), GeochemistrySpatialReactor::GeochemistrySpatialReactor(), GeochemistryTimeDependentReactor::GeochemistryTimeDependentReactor(), GeochemicalModelInterrogator::knownActivity(), operator==(), GeochemistryConsoleOutput::output(), GeochemicalModelInterrogator::outputActivity(), GeochemicalModelInterrogator::outputTemperature(), GeochemistrySpeciesSwapper::performSwap(), GeochemistrySpeciesSwapper::performSwap(), GeochemistrySpeciesSwapper::performSwap(), GeochemicalSystem::performSwapNoCheck(), GeochemicalSystem::revertToOriginalChargeBalanceSpecies(), GeochemistryActivityCoefficientsDebyeHuckel::setInternalParameters(), GeochemicalSystem::setMineralRelatedFreeMoles(), GeochemicalSystem::setSolventMassAndFreeMolalityAndMineralMolesAndSurfacePotsAndKineticMoles(), GeochemistryIonicStrength::stoichiometricIonicStrength(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST_F(), TEST_F(), TEST_F(), TEST_F(), and TEST_F().

◆ basis_species_mineral

std::vector<bool> ModelGeochemicalDatabase::basis_species_mineral

basis_species_mineral[j] = true iff the j^th basis species is a mineral

Definition at line 168 of file PertinentGeochemicalSystem.h.

◆ basis_species_molecular_volume

std::vector<Real> ModelGeochemicalDatabase::basis_species_molecular_volume

all quantities have a molecular volume (cm^3) (only nonzero for minerals, however)

Definition at line 186 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemistryQuantityAux::computeValue(), PertinentGeochemicalSystem::createModel(), GeochemistryUnitConverter::fromMoles(), operator==(), TEST(), TEST(), TEST(), and TEST().

◆ basis_species_molecular_weight

std::vector<Real> ModelGeochemicalDatabase::basis_species_molecular_weight

all quantities have a molecular weight (g)

Definition at line 183 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemicalSystem::computeSorbingSurfaceArea(), GeochemistryQuantityAux::computeValue(), PertinentGeochemicalSystem::createModel(), GeochemistryUnitConverter::fromMoles(), GeochemistryTimeDependentReactor::newTemperature(), operator==(), GeochemistryConsoleOutput::output(), GeochemistryTimeDependentReactor::preSolveFlush(), TEST(), TEST(), TEST(), and TEST().

◆ basis_species_name

std::vector<std::string> ModelGeochemicalDatabase::basis_species_name

basis_species_name[j] = name of the j^th basis species

Definition at line 165 of file PertinentGeochemicalSystem.h.

Referenced by AddGeochemistrySolverAction::act(), PertinentGeochemicalSystem::addKineticRate(), GeochemicalSystem::addKineticRates(), GeochemistrySpeciesSwapper::alterMGD(), GeochemicalSystem::changeConstraintToBulk(), GeochemicalSystem::checkAndInitialize(), PertinentGeochemicalSystem::createModel(), GeochemistrySpeciesSwapper::findBestEqmSwap(), GeochemistryTimeDependentReactor::GeochemistryTimeDependentReactor(), operator==(), GeochemistryConsoleOutput::output(), GeochemicalModelInterrogator::outputActivity(), GeochemistryConsoleOutput::outputNernstInfo(), GeochemicalModelInterrogator::outputReaction(), GeochemicalModelInterrogator::outputTemperature(), GeochemistryTimeDependentReactor::postSolveFlowThrough(), GeochemistryTimeDependentReactor::preSolveDump(), GeochemicalSystem::setChargeBalanceSpecies(), GeochemicalSolver::solveSystem(), GeochemicalSolver::swapNeeded(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST_F(), and TEST_F().

◆ basis_species_radius

std::vector<Real> ModelGeochemicalDatabase::basis_species_radius

all quantities have an ionic radius (Angstrom) for computing activity (mineral radius = 0, gas radius = 0, surface species radius = 0)

Definition at line 180 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemistryActivityCoefficientsDebyeHuckel::buildActivityCoefficients(), PertinentGeochemicalSystem::createModel(), operator==(), TEST(), TEST(), TEST(), TEST(), and TEST().

◆ basis_species_transported

std::vector<bool> ModelGeochemicalDatabase::basis_species_transported

basis_species_transported[j] = true iff the j^th basis species is transported in reactive-transport sims

Definition at line 174 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemicalSystem::computeTransportedBulkFromMolalities(), PertinentGeochemicalSystem::createModel(), operator==(), TEST(), TEST(), TEST(), and TEST().

◆ eqm_log10K

DenseMatrix<Real> ModelGeochemicalDatabase::eqm_log10K

eqm_log10K(i, j) = log10(equilibrium constant) for i^th equilibrium species at the j^th temperature point

Definition at line 230 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), PertinentGeochemicalSystem::buildRedoxeInfo(), GeochemicalSystem::buildTemperatureDependentQuantities(), PertinentGeochemicalSystem::createModel(), operator==(), GeochemicalModelInterrogator::outputActivity(), GeochemicalModelInterrogator::outputReaction(), GeochemicalModelInterrogator::outputTemperature(), TEST(), TEST(), TEST(), and TEST().

◆ eqm_species_charge

std::vector<Real> ModelGeochemicalDatabase::eqm_species_charge

all quantities have a charge (mineral charge = 0, gas charge = 0, oxide charge = 0)

Definition at line 209 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemistryActivityCoefficientsDebyeHuckel::buildActivityCoefficients(), GeochemicalSystem::computeJacobian(), PertinentGeochemicalSystem::createModel(), GeochemicalSystem::getResidualComponent(), GeochemistryIonicStrength::ionicStrength(), operator==(), GeochemistryIonicStrength::stoichiometricIonicStrength(), GeochemicalSystem::surfaceSorptionModifier(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), and TEST().

◆ eqm_species_gas

std::vector<bool> ModelGeochemicalDatabase::eqm_species_gas

eqm_species_gas[i] = true iff the i^th equilibrium species is a gas

Definition at line 203 of file PertinentGeochemicalSystem.h.

Referenced by GeochemicalSystem::addKineticRates(), GeochemistrySpeciesSwapper::alterMGD(), GeochemistryActivityCoefficientsDebyeHuckel::buildActivityCoefficients(), GeochemicalSystem::changeConstraintToBulk(), GeochemicalSystem::computeEqmMolalities(), PertinentGeochemicalSystem::createModel(), GeochemistrySpeciesSwapper::findBestEqmSwap(), GeochemicalSystem::getEquilibriumActivity(), operator==(), GeochemistryConsoleOutput::output(), GeochemicalSystem::performSwap(), GeochemicalSystem::setSolventMassAndFreeMolalityAndMineralMolesAndSurfacePotsAndKineticMoles(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), and TEST().

◆ eqm_species_index

std::unordered_map<std::string, unsigned> ModelGeochemicalDatabase::eqm_species_index

eqm_species_index[name] = index of the equilibrium species (secondary aqueous species, redox couples in equilibrium with the aqueous solution, minerals in equilibrium with the aqueous solution, gases in equilibrium with the aqueous solution) within all ModelGeochemicalDatabase internal datastrcutres, with given name

Definition at line 194 of file PertinentGeochemicalSystem.h.

Referenced by PertinentGeochemicalSystem::addKineticRate(), GeochemistrySpeciesSwapper::alterMGD(), PertinentGeochemicalSystem::buildRedoxeInfo(), GeochemistrySpeciesSwapper::checkSwap(), GeochemistrySpeciesSwapper::checkSwap(), GeochemistryQuantityAux::computeValue(), PertinentGeochemicalSystem::createModel(), GeochemicalModelInterrogator::eqmSpeciesOfInterest(), GeochemistrySpatialReactor::execute(), GeochemistryTimeDependentReactor::execute(), GeochemistryUnitConverter::fromMoles(), GeochemistryQuantityAux::GeochemistryQuantityAux(), GeochemistrySpatialReactor::GeochemistrySpatialReactor(), GeochemistryTimeDependentReactor::GeochemistryTimeDependentReactor(), GeochemicalModelInterrogator::knownActivity(), operator==(), GeochemistryConsoleOutput::output(), GeochemicalModelInterrogator::outputActivity(), GeochemicalModelInterrogator::outputReaction(), GeochemicalModelInterrogator::outputTemperature(), GeochemistrySpeciesSwapper::performSwap(), GeochemistryActivityCoefficientsDebyeHuckel::setInternalParameters(), GeochemicalSystem::setMineralRelatedFreeMoles(), GeochemicalSystem::setSolventMassAndFreeMolalityAndMineralMolesAndSurfacePotsAndKineticMoles(), GeochemistryIonicStrength::stoichiometricIonicStrength(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST_F(), TEST_F(), TEST_F(), TEST_F(), TEST_F(), and TEST_F().

◆ eqm_species_mineral

std::vector<bool> ModelGeochemicalDatabase::eqm_species_mineral

eqm_species_mineral[i] = true iff the i^th equilibrium species is a mineral

Definition at line 200 of file PertinentGeochemicalSystem.h.

Referenced by AddGeochemistrySolverAction::act(), GeochemistrySpeciesSwapper::alterMGD(), GeochemistryActivityCoefficientsDebyeHuckel::buildActivityCoefficients(), GeochemicalSystem::computeEqmMolalities(), PertinentGeochemicalSystem::createModel(), GeochemistrySpeciesSwapper::findBestEqmSwap(), GeochemistryUnitConverter::fromMoles(), GeochemistryQuantityAux::GeochemistryQuantityAux(), GeochemistryTimeDependentReactor::GeochemistryTimeDependentReactor(), GeochemicalSystem::getEquilibriumActivity(), GeochemicalSystem::getSaturationIndices(), GeochemicalModelInterrogator::knownActivity(), operator==(), GeochemistryConsoleOutput::output(), GeochemicalSystem::setMineralRelatedFreeMoles(), GeochemicalSystem::setSolventMassAndFreeMolalityAndMineralMolesAndSurfacePotsAndKineticMoles(), GeochemicalSolver::swapNeeded(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), and TEST_F().

◆ eqm_species_molecular_volume

std::vector<Real> ModelGeochemicalDatabase::eqm_species_molecular_volume

all quantities have a molecular volume (cm^3) (only nonzero for minerals, however)

Definition at line 218 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemistryQuantityAux::computeValue(), PertinentGeochemicalSystem::createModel(), GeochemistryUnitConverter::fromMoles(), operator==(), TEST(), TEST(), TEST(), and TEST().

◆ eqm_species_molecular_weight

std::vector<Real> ModelGeochemicalDatabase::eqm_species_molecular_weight

all quantities have a molecular weight (g)

Definition at line 215 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemistryQuantityAux::computeValue(), PertinentGeochemicalSystem::createModel(), GeochemistryUnitConverter::fromMoles(), operator==(), GeochemistryConsoleOutput::output(), TEST(), TEST(), TEST(), and TEST().

◆ eqm_species_name

std::vector<std::string> ModelGeochemicalDatabase::eqm_species_name

eqm_species_name[i] = name of the i^th eqm species

Definition at line 197 of file PertinentGeochemicalSystem.h.

Referenced by AddGeochemistrySolverAction::act(), PertinentGeochemicalSystem::addKineticRate(), GeochemicalSystem::addKineticRates(), GeochemistrySpeciesSwapper::alterMGD(), GeochemistrySpeciesSwapper::checkSwap(), PertinentGeochemicalSystem::createModel(), GeochemicalModelInterrogator::eqmSpeciesOfInterest(), GeochemistrySpeciesSwapper::findBestEqmSwap(), GeochemistryTimeDependentReactor::GeochemistryTimeDependentReactor(), operator==(), GeochemistryConsoleOutput::output(), GeochemistryConsoleOutput::outputNernstInfo(), GeochemicalSystem::performSwap(), GeochemicalSolver::swapNeeded(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), and TEST_F().

◆ eqm_species_radius

std::vector<Real> ModelGeochemicalDatabase::eqm_species_radius

all quantities have an ionic radius (Angstrom) for computing activity (mineral radius = 0, gas radius = 0, surface species radius = 0)

Definition at line 212 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemistryActivityCoefficientsDebyeHuckel::buildActivityCoefficients(), PertinentGeochemicalSystem::createModel(), operator==(), TEST(), TEST(), TEST(), TEST(), and TEST().

◆ eqm_species_transported

std::vector<bool> ModelGeochemicalDatabase::eqm_species_transported

eqm_species_transported[i] = true iff the i^th eqm species is transported in reactive-transport sims

Definition at line 206 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemicalSystem::computeTransportedBulkFromMolalities(), PertinentGeochemicalSystem::createModel(), operator==(), TEST(), TEST(), TEST(), and TEST().

◆ eqm_stoichiometry

DenseMatrix<Real> ModelGeochemicalDatabase::eqm_stoichiometry

eqm_stoichiometry(i, j) = stoichiometric coefficient for equilibrium species "i" in terms of the basis species "j"

Definition at line 224 of file PertinentGeochemicalSystem.h.

Referenced by GeochemicalSystem::addKineticRates(), GeochemistrySpeciesSwapper::alterMGD(), PertinentGeochemicalSystem::buildRedoxeInfo(), GeochemicalSystem::changeConstraintToBulk(), GeochemicalSystem::computeBulkFromMolalities(), GeochemicalSystem::computeFreeMineralMoles(), GeochemicalSystem::computeJacobian(), GeochemicalSystem::computeTransportedBulkFromMolalities(), GeochemistrySpeciesSwapper::constructInverseMatrix(), PertinentGeochemicalSystem::createModel(), GeochemistrySpatialReactor::execute(), GeochemistryTimeDependentReactor::execute(), GeochemistrySpeciesSwapper::findBestEqmSwap(), GeochemicalSystem::getEquilibriumActivity(), GeochemicalSystem::getResidualComponent(), GeochemicalSystem::log10ActivityProduct(), operator==(), GeochemistryConsoleOutput::output(), GeochemicalModelInterrogator::outputActivity(), GeochemicalModelInterrogator::outputReaction(), GeochemicalModelInterrogator::outputTemperature(), GeochemistryIonicStrength::stoichiometricIonicStrength(), GeochemicalSolver::swapNeeded(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST_F(), and TEST_F().

◆ gas_chi

std::unordered_map<std::string, std::vector<Real> > ModelGeochemicalDatabase::gas_chi

Holds info on gas fugacity "chi" parameters.

Note this is slow compared with storing info in a DenseMatrix, but it also saves memory over storing a lot of "zeroes" for non-gas species. I believe the slowness will not present a problem because fugacity parameters are typically only queried at the start of the simulation, or at most once per timestep. If the lookup becomes burdensome, change from unordered_map to DenseMatrix

Definition at line 298 of file PertinentGeochemicalSystem.h.

Referenced by PertinentGeochemicalSystem::createModel(), and operator==().

◆ have_swapped_into_basis

std::vector<unsigned> ModelGeochemicalDatabase::have_swapped_into_basis

Species that have been swapped into the basis.

Every time a swap is performed on the ModelGeochemicalDatabase, the equilibrium-index of the species added to the basis is appended to this list

Definition at line 355 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), operator==(), GeochemistryConsoleOutput::outputNernstInfo(), TEST(), TEST(), TEST(), and TEST().

◆ have_swapped_out_of_basis

std::vector<unsigned> ModelGeochemicalDatabase::have_swapped_out_of_basis

Species that have been swapped out of the basis.

Every time a swap is performed on the ModelGeochemicalDatabase, the basis-index of the species removed from the basis is appended to this list

Definition at line 348 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), operator==(), GeochemistryConsoleOutput::outputNernstInfo(), TEST(), TEST(), TEST(), and TEST().

◆ kin_log10K

DenseMatrix<Real> ModelGeochemicalDatabase::kin_log10K

kin_log10K(i, j) = log10(equilibrium constant for the i^th kinetic species at the j^th temperature point

Definition at line 328 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemicalSystem::buildTemperatureDependentQuantities(), PertinentGeochemicalSystem::createModel(), operator==(), TEST(), and TEST().

◆ kin_rate

std::vector<KineticRateDefinition> ModelGeochemicalDatabase::kin_rate

rates given to kinetic species.

See the method addKineticRate for a detailed description. This quantity is organised in such a way that a solver can loop through kin_rate, calculting the rates and applying them to the kin_rate[i].kinetic_species_index species

Definition at line 341 of file PertinentGeochemicalSystem.h.

Referenced by PertinentGeochemicalSystem::addKineticRate(), GeochemicalSystem::addKineticRates(), GeochemistrySpeciesSwapper::alterMGD(), operator==(), TEST(), and TEST().

◆ kin_species_charge

std::vector<Real> ModelGeochemicalDatabase::kin_species_charge

all kinetic quantities have a charge (mineral charge = 0)

Definition at line 316 of file PertinentGeochemicalSystem.h.

Referenced by PertinentGeochemicalSystem::createModel(), GeochemistryIonicStrength::ionicStrength(), operator==(), GeochemistryIonicStrength::stoichiometricIonicStrength(), TEST(), and TEST().

◆ kin_species_index

std::unordered_map<std::string, unsigned> ModelGeochemicalDatabase::kin_species_index

kin_species_index[name] = index of the kinetic species, within all ModelGeochemicalDatabase internal datastrcutres, with given name

Definition at line 304 of file PertinentGeochemicalSystem.h.

Referenced by PertinentGeochemicalSystem::addKineticRate(), GeochemicalSystem::checkAndInitialize(), GeochemistryQuantityAux::computeValue(), PertinentGeochemicalSystem::createModel(), GeochemistrySpatialReactor::execute(), GeochemistryTimeDependentReactor::execute(), GeochemistryUnitConverter::fromMoles(), GeochemistryQuantityAux::GeochemistryQuantityAux(), GeochemistrySpatialReactor::GeochemistrySpatialReactor(), GeochemistryTimeDependentReactor::GeochemistryTimeDependentReactor(), operator==(), GeochemicalSystem::setSolventMassAndFreeMolalityAndMineralMolesAndSurfacePotsAndKineticMoles(), GeochemistryIonicStrength::stoichiometricIonicStrength(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST_F(), and TEST_F().

◆ kin_species_mineral

std::vector<bool> ModelGeochemicalDatabase::kin_species_mineral

kin_species_mineral[j] = true iff the j^th kinetic species is a mineral

Definition at line 310 of file PertinentGeochemicalSystem.h.

Referenced by AddGeochemistrySolverAction::act(), PertinentGeochemicalSystem::createModel(), GeochemistryUnitConverter::fromMoles(), GeochemistryQuantityAux::GeochemistryQuantityAux(), GeochemistryTimeDependentReactor::GeochemistryTimeDependentReactor(), operator==(), GeochemistryConsoleOutput::output(), GeochemistryTimeDependentReactor::postSolveFlowThrough(), GeochemistryTimeDependentReactor::preSolveFlush(), GeochemicalSystem::setMineralRelatedFreeMoles(), and TEST().

◆ kin_species_molecular_volume

std::vector<Real> ModelGeochemicalDatabase::kin_species_molecular_volume

all quantities have a molecular volume (cm^3/mol) (only nonzero for minerals, however)

Definition at line 322 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistryQuantityAux::computeValue(), PertinentGeochemicalSystem::createModel(), GeochemistryUnitConverter::fromMoles(), operator==(), GeochemistryConsoleOutput::output(), TEST(), and TEST().

◆ kin_species_molecular_weight

std::vector<Real> ModelGeochemicalDatabase::kin_species_molecular_weight

all quantities have a molecular weight (g/mol)

Definition at line 319 of file PertinentGeochemicalSystem.h.

Referenced by GeochemicalSystem::addKineticRates(), GeochemistryQuantityAux::computeValue(), PertinentGeochemicalSystem::createModel(), GeochemistryUnitConverter::fromMoles(), GeochemistryTimeDependentReactor::newTemperature(), operator==(), GeochemistryConsoleOutput::output(), GeochemistryTimeDependentReactor::preSolveFlush(), TEST(), and TEST().

◆ kin_species_name

std::vector<std::string> ModelGeochemicalDatabase::kin_species_name

kin_species_name[j] = name of the j^th kinetic species

Definition at line 307 of file PertinentGeochemicalSystem.h.

Referenced by AddGeochemistrySolverAction::act(), GeochemicalSystem::checkAndInitialize(), PertinentGeochemicalSystem::createModel(), GeochemistryTimeDependentReactor::GeochemistryTimeDependentReactor(), operator==(), GeochemistryConsoleOutput::output(), GeochemistryTimeDependentReactor::postSolveFlowThrough(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), and TEST().

◆ kin_species_transported

std::vector<bool> ModelGeochemicalDatabase::kin_species_transported

kin_species_transported[j] = true iff the j^th kinetic species is transported in reactive-transport sims

Definition at line 313 of file PertinentGeochemicalSystem.h.

Referenced by PertinentGeochemicalSystem::createModel(), operator==(), and TEST().

◆ kin_stoichiometry

DenseMatrix<Real> ModelGeochemicalDatabase::kin_stoichiometry

kin_stoichiometry(i, j) = stoichiometric coefficient for kinetic species "i" in terms of the basis species "j"

Definition at line 334 of file PertinentGeochemicalSystem.h.

Referenced by GeochemicalSystem::addKineticRates(), GeochemistrySpeciesSwapper::alterMGD(), GeochemicalSystem::checkAndInitialize(), GeochemicalSystem::computeBulkFromMolalities(), GeochemicalSystem::computeFreeMineralMoles(), GeochemicalSystem::computeJacobian(), PertinentGeochemicalSystem::createModel(), GeochemicalSystem::getResidualComponent(), GeochemicalSystem::log10KineticActivityProduct(), operator==(), GeochemistryConsoleOutput::output(), GeochemistryTimeDependentReactor::postSolveFlowThrough(), GeochemistryTimeDependentReactor::preSolveFlush(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), and TEST().

◆ original_database

const GeochemicalDatabaseReader* ModelGeochemicalDatabase::original_database

a pointer to the original database used to build this ModelGeochemicalDatabase

Definition at line 156 of file PertinentGeochemicalSystem.h.

Referenced by GeochemicalSystem::buildTemperatureDependentQuantities(), operator==(), GeochemicalModelInterrogator::outputActivity(), GeochemicalModelInterrogator::outputReaction(), GeochemicalModelInterrogator::outputTemperature(), GeochemicalModelInterrogator::solveForT(), and TEST().

◆ redox_lhs

std::string ModelGeochemicalDatabase::redox_lhs

the name of the species on the left-hand side of the redox equations.

Upon creation of the model this is e-, but it may change due to swaps

Definition at line 261 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemicalSystem::checkAndInitialize(), PertinentGeochemicalSystem::createModel(), operator==(), GeochemistryConsoleOutput::outputNernstInfo(), and TEST().

◆ redox_log10K

DenseMatrix<Real> ModelGeochemicalDatabase::redox_log10K

redox_log10K(i, j) = log10(equilibrium constant) for i^th redox species at the j^th temperature point

Definition at line 282 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemicalSystem::buildTemperatureDependentQuantities(), PertinentGeochemicalSystem::createModel(), operator==(), and TEST().

◆ redox_stoichiometry

DenseMatrix<Real> ModelGeochemicalDatabase::redox_stoichiometry

redox_stoichiometry(i, j) = stoichiometric coefficients for i^th redox species that is in disequilibrium in terms of the j basis species.

These equations are all written with their left-hand sides being e-. For instance, the database contains the reactions Fe+++ = -0.5H20 + Fe++ + H+ + 0.25*O2(aq) e- = 0.5H2O - 0.25O2(aq)- H+ The first is a redox reaction, and assume the user has specified it is in disquilibrium (by specifying it is in the basis). If Fe++, H+ and O2(aq) are also in the basis then the two equations yield the single redox equation e- = -Fe+++ + Fe++ Then redox_stoichiometry will be -1 for j = Fe+++, and +1 for j = Fe++.

Definition at line 276 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), PertinentGeochemicalSystem::createModel(), GeochemicalSystem::log10RedoxActivityProduct(), operator==(), GeochemistryConsoleOutput::output(), GeochemistryConsoleOutput::outputNernstInfo(), and TEST().

◆ surface_complexation_info

std::unordered_map<std::string, SurfaceComplexationInfo> ModelGeochemicalDatabase::surface_complexation_info

Holds info on surface complexation, if any, in the model.

Note this is slow compared with storing information in a std::vector or DenseMatrix, but it also saves memory over storing a lot of "zeroes" for all species not involved in surface complexation

Definition at line 289 of file PertinentGeochemicalSystem.h.

Referenced by PertinentGeochemicalSystem::createModel(), operator==(), GeochemistryConsoleOutput::output(), and GeochemicalSystem::setMineralRelatedFreeMoles().

◆ surface_sorption_area

std::vector<Real> ModelGeochemicalDatabase::surface_sorption_area

surface_sorption_area[k] = specific surface area [m^2/g] for the k^th mineral involved in surface sorption.

Each mineral involved in surface sorption must have a surface_sorption_area prescribed it (in the database) and will be associated with a unique surface potential.

Definition at line 243 of file PertinentGeochemicalSystem.h.

Referenced by GeochemicalSystem::computeSorbingSurfaceArea(), PertinentGeochemicalSystem::createModel(), and operator==().

◆ surface_sorption_name

std::vector<std::string> ModelGeochemicalDatabase::surface_sorption_name

surface_sorption_name[k] = name of the mineral involved in surface sorption.

Each of these will be associated with a unique surface potential.

Definition at line 236 of file PertinentGeochemicalSystem.h.

Referenced by AddGeochemistrySolverAction::act(), GeochemicalSystem::computeSorbingSurfaceArea(), PertinentGeochemicalSystem::createModel(), GeochemistryQuantityAux::GeochemistryQuantityAux(), operator==(), GeochemistryConsoleOutput::output(), and GeochemicalSystem::setSolventMassAndFreeMolalityAndMineralMolesAndSurfacePotsAndKineticMoles().

◆ surface_sorption_number

std::vector<unsigned> ModelGeochemicalDatabase::surface_sorption_number

surface_sorption_number[j] = the index of the surface potential that should be used to modify the equilibrium constant for the j^th equilibrium species.

surface_sorption_number is only meaningful if surface_sorption_related[j] = true. 0 <= surface_sorption_number[:] < surface_sorption_name.size() = number of minerals involved in surface sorption = number of surface potentials in the simulation = surface_sorption_area.size().

Definition at line 255 of file PertinentGeochemicalSystem.h.

Referenced by GeochemicalSystem::computeJacobian(), PertinentGeochemicalSystem::createModel(), GeochemicalSystem::getResidualComponent(), operator==(), GeochemicalSystem::surfaceSorptionModifier(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), and TEST().

◆ surface_sorption_related

std::vector<bool> ModelGeochemicalDatabase::surface_sorption_related

surface_sorption_related[j] = true iff the j^th equilibrium species is involved in surface sorption

Definition at line 246 of file PertinentGeochemicalSystem.h.

Referenced by GeochemicalSystem::changeConstraintToBulk(), GeochemistrySpeciesSwapper::checkSwap(), GeochemicalSystem::computeJacobian(), PertinentGeochemicalSystem::createModel(), GeochemistrySpeciesSwapper::findBestEqmSwap(), GeochemicalSystem::getResidualComponent(), GeochemistryIonicStrength::ionicStrength(), operator==(), GeochemicalSystem::setMineralRelatedFreeMoles(), GeochemistryIonicStrength::stoichiometricIonicStrength(), GeochemicalSystem::surfaceSorptionModifier(), TEST(), TEST(), TEST(), TEST(), TEST(), TEST(), and TEST().

◆ swap_to_original_basis

DenseMatrix<Real> ModelGeochemicalDatabase::swap_to_original_basis

Swap matrix that allows expression in terms of the original basis.

When a swap is performed bulk_new = S^-1^T * bulk_old, where S is the swap matrix (and S^-1^T is the transposed inverse of S) Hence, upon multiple swaps (S_1 followed by S_2 followed by S_3, etc) bulk_new = S_n^-1^T * S_{n-1}^-1^T * ... * S_1^-1^T * bulk_original So bulk_original = (S_n * S_{n-1} * ... * S_1)^T * bulk_new swap_to_original_basis = S_n * S_{n-1} * ... * S_1 swap_to_original_basis is initialized to DenseMatrix<Real>(), ie, a zero-sized matrix, to reduce memory usage. The first time a swap is performed, it is set to the swap matrix generated in the GeochemistrySpeciesSwapper, and every time a swap is performed on the ModelGeochemicalDatabase this is updated

Definition at line 371 of file PertinentGeochemicalSystem.h.

Referenced by GeochemistrySpeciesSwapper::alterMGD(), GeochemicalSystem::getBulkOldInOriginalBasis(), GeochemicalSystem::getTransportedBulkInOriginalBasis(), operator==(), TEST(), TEST(), TEST(), TEST(), and TEST().

The documentation for this struct was generated from the following file:

geochemistry/include/utils/PertinentGeochemicalSystem.h

Public Member Functions

Public Attributes