Detailed Description

Definition at line 109 of file ChemicalSolverInterface.h.

#include <ChemicalSolverInterface.h>

Inheritance diagram for ChemistryLib::ChemicalSolverInterface:

Collaboration diagram for ChemistryLib::ChemicalSolverInterface:

Public Member Functions
	ChemicalSolverInterface (MeshLib::Mesh const &mesh, GlobalLinearSolver &linear_solver_)
std::vector< std::size_t > const &	activeElementIDs () const
virtual void	initialize ()
virtual void	initializeChemicalSystemConcrete (std::vector< double > const &, GlobalIndexType const &, MaterialPropertyLib::Medium const &, ParameterLib::SpatialPosition const &, double const)
virtual void	setChemicalSystemConcrete (std::vector< double > const &, GlobalIndexType const &, MaterialPropertyLib::Medium const *, MaterialPropertyLib::VariableArray const &, ParameterLib::SpatialPosition const &, double const, double const)
virtual void	setAqueousSolutionsPrevFromDumpFile ()
virtual void	executeSpeciationCalculation (double const dt)
virtual double	getConcentration (int const, GlobalIndexType const) const
virtual std::vector< std::string > const	getComponentList () const
virtual Eigen::SparseMatrix< double > const *	getStoichiometricMatrix () const
virtual double	getKineticPrefactor (std::size_t reaction_id) const
virtual void	updateVolumeFractionPostReaction (GlobalIndexType const &, MaterialPropertyLib::Medium const &, ParameterLib::SpatialPosition const &, double const, double const, double const)
virtual void	updatePorosityPostReaction (GlobalIndexType const &, MaterialPropertyLib::Medium const &, double &)
virtual void	computeSecondaryVariable (std::size_t const, std::vector< GlobalIndexType > const &)
virtual	~ChemicalSolverInterface ()=default

Public Attributes
std::vector< GlobalIndexType >	chemical_system_index_map
MeshLib::Mesh const &	_mesh
GlobalLinearSolver &	linear_solver

Private Attributes
std::vector< std::size_t >	active_element_ids_

Constructor & Destructor Documentation

◆ ChemicalSolverInterface()

ChemistryLib::ChemicalSolverInterface::ChemicalSolverInterface	(	MeshLib::Mesh const &	mesh,
		GlobalLinearSolver &	linear_solver_ )

inline

Definition at line 112 of file ChemicalSolverInterface.h.

        : _mesh(mesh), linear_solver(linear_solver_)
    {
        auto const* const bulk_element_ids = bulkElementIDs(_mesh);
        if (bulk_element_ids == nullptr)
        {
            OGS_FATAL(
                "The 'bulk_element_ids' property does not exist on the mesh "
                "{:s}.",
                _mesh.getName());
        }
        active_element_ids_.assign(bulk_element_ids->begin(),
                                   bulk_element_ids->end());
    }

References _mesh, active_element_ids_, linear_solver, and OGS_FATAL.

Referenced by ChemistryLib::PhreeqcIOData::PhreeqcIO::PhreeqcIO(), ChemistryLib::PhreeqcKernelData::PhreeqcKernel::PhreeqcKernel(), and ChemistryLib::SelfContainedSolverData::SelfContainedSolver::SelfContainedSolver().

◆ ~ChemicalSolverInterface()

virtual ChemistryLib::ChemicalSolverInterface::~ChemicalSolverInterface ( )

virtualdefault

Member Function Documentation

◆ activeElementIDs()

std::vector< std::size_t > const & ChemistryLib::ChemicalSolverInterface::activeElementIDs ( ) const

inline

Definition at line 128 of file ChemicalSolverInterface.h.

    {
        return active_element_ids_;
    }

References active_element_ids_.

◆ computeSecondaryVariable()

virtual void ChemistryLib::ChemicalSolverInterface::computeSecondaryVariable	(	std::size_t const	,
		std::vector< GlobalIndexType > const &	)

inlinevirtual

Reimplemented in ChemistryLib::PhreeqcIOData::PhreeqcIO.

Definition at line 236 of file ChemicalSolverInterface.h.

239 {

240 }

◆ executeSpeciationCalculation()

virtual void ChemistryLib::ChemicalSolverInterface::executeSpeciationCalculation ( double const dt )

inlinevirtual

Run PHREEQC for all local chemical systems for the current timestep.

Uses the state previously provided by initializeChemicalSystemConcrete() / setChemicalSystemConcrete() for each chemical_system_id. Each local system is advanced as an isolated batch reactor over \(\Delta t\): no mass is exchanged between different systems inside PHREEQC.

PHREEQC returns, for each system:

updated aqueous composition,
reaction / source terms \(R_{\alpha}\) for each transported component,
updated mineral amounts and saturation state.

After this call completes, these reacted values are available for porosity update and for assembling the reaction/source term in the transport equation.

Parameters

dt	Timestep size \(\Delta t\) used for kinetic reactions.

Reimplemented in ChemistryLib::PhreeqcIOData::PhreeqcIO, and ChemistryLib::PhreeqcKernelData::PhreeqcKernel.

Definition at line 175 of file ChemicalSolverInterface.h.

176 {

177 }

◆ getComponentList()

virtual std::vector< std::string > const ChemistryLib::ChemicalSolverInterface::getComponentList ( ) const

inlinevirtual

Reimplemented in ChemistryLib::PhreeqcIOData::PhreeqcIO.

Definition at line 186 of file ChemicalSolverInterface.h.

    {
        return {};
    }

◆ getConcentration()

virtual double ChemistryLib::ChemicalSolverInterface::getConcentration	(	int const	,
		GlobalIndexType const	) const

inlinevirtual

Reimplemented in ChemistryLib::PhreeqcIOData::PhreeqcIO.

Definition at line 179 of file ChemicalSolverInterface.h.

    {
        return std::numeric_limits<double>::quiet_NaN();
    }

◆ getKineticPrefactor()

virtual double ChemistryLib::ChemicalSolverInterface::getKineticPrefactor ( std::size_t reaction_id ) const

inlinevirtual

Reimplemented in ChemistryLib::SelfContainedSolverData::SelfContainedSolver.

Definition at line 196 of file ChemicalSolverInterface.h.

    {
        return std::numeric_limits<double>::quiet_NaN();
    }

◆ getStoichiometricMatrix()

virtual Eigen::SparseMatrix< double > const * ChemistryLib::ChemicalSolverInterface::getStoichiometricMatrix ( ) const

inlinevirtual

Reimplemented in ChemistryLib::SelfContainedSolverData::SelfContainedSolver.

Definition at line 191 of file ChemicalSolverInterface.h.

    {
        return nullptr;
    }

◆ initialize()

virtual void ChemistryLib::ChemicalSolverInterface::initialize ( )

inlinevirtual

Reimplemented in ChemistryLib::PhreeqcIOData::PhreeqcIO.

Definition at line 133 of file ChemicalSolverInterface.h.

133{}

◆ initializeChemicalSystemConcrete()

virtual void ChemistryLib::ChemicalSolverInterface::initializeChemicalSystemConcrete	(	std::vector< double > const &	,
		GlobalIndexType const &	,
		MaterialPropertyLib::Medium const &	,
		ParameterLib::SpatialPosition const &	,
		double const	)

inlinevirtual

Reimplemented in ChemistryLib::PhreeqcIOData::PhreeqcIO.

Definition at line 135 of file ChemicalSolverInterface.h.

140 {

141 }

◆ setAqueousSolutionsPrevFromDumpFile()

virtual void ChemistryLib::ChemicalSolverInterface::setAqueousSolutionsPrevFromDumpFile ( )

inlinevirtual

Reimplemented in ChemistryLib::PhreeqcIOData::PhreeqcIO.

Definition at line 153 of file ChemicalSolverInterface.h.

153{}

◆ setChemicalSystemConcrete()

virtual void ChemistryLib::ChemicalSolverInterface::setChemicalSystemConcrete	(	std::vector< double > const &	,
		GlobalIndexType const &	,
		MaterialPropertyLib::Medium const *	,
		MaterialPropertyLib::VariableArray const &	,
		ParameterLib::SpatialPosition const &	,
		double const	,
		double const	)

inlinevirtual

Reimplemented in ChemistryLib::PhreeqcIOData::PhreeqcIO.

Definition at line 143 of file ChemicalSolverInterface.h.

150 {

151 }

◆ updatePorosityPostReaction()

virtual void ChemistryLib::ChemicalSolverInterface::updatePorosityPostReaction	(	GlobalIndexType const &	,
		MaterialPropertyLib::Medium const &	,
		double &	)

inlinevirtual

Update porosity after chemical reactions.

This applies porosity changes caused by precipitation / dissolution in the local chemical system. The updated porosity can then be used to update flow parameters (e.g. permeability) in the next timestep.

Reimplemented in ChemistryLib::PhreeqcIOData::PhreeqcIO.

Definition at line 229 of file ChemicalSolverInterface.h.

233 {

234 }

◆ updateVolumeFractionPostReaction()

virtual void ChemistryLib::ChemicalSolverInterface::updateVolumeFractionPostReaction	(	GlobalIndexType const &	,
		MaterialPropertyLib::Medium const &	,
		ParameterLib::SpatialPosition const &	,
		double const	,
		double const	,
		double const	)

inlinevirtual

Apply mineral precipitation / dissolution to the solid fraction in OGS.

Called after executeSpeciationCalculation(). For a given chemical_system_id, this function updates the solid / mineral inventory and related volume fractions based on the PHREEQC results for the last timestep.

Typical effect:

change in mineral volume fraction at this location,
updated solid composition available to mechanics / flow.

Reimplemented in ChemistryLib::PhreeqcIOData::PhreeqcIO.

Definition at line 214 of file ChemicalSolverInterface.h.

219 {

220 }

Member Data Documentation

◆ _mesh

MeshLib::Mesh const& ChemistryLib::ChemicalSolverInterface::_mesh

Definition at line 246 of file ChemicalSolverInterface.h.

Referenced by ChemicalSolverInterface().

◆ active_element_ids_

std::vector<std::size_t> ChemistryLib::ChemicalSolverInterface::active_element_ids_

private

Definition at line 252 of file ChemicalSolverInterface.h.

Referenced by ChemicalSolverInterface(), and activeElementIDs().

◆ chemical_system_index_map

std::vector<GlobalIndexType> ChemistryLib::ChemicalSolverInterface::chemical_system_index_map

Definition at line 245 of file ChemicalSolverInterface.h.

Referenced by ChemistryLib::PhreeqcIOData::PhreeqcIO::initialize().

◆ linear_solver

GlobalLinearSolver& ChemistryLib::ChemicalSolverInterface::linear_solver

specify the linear solver used to solve the linearized reaction equation.

Definition at line 249 of file ChemicalSolverInterface.h.

Referenced by ChemicalSolverInterface(), ChemistryLib::PhreeqcIOData::PhreeqcIO::PhreeqcIO(), ChemistryLib::PhreeqcKernelData::PhreeqcKernel::PhreeqcKernel(), and ChemistryLib::SelfContainedSolverData::SelfContainedSolver::SelfContainedSolver().

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

ChemicalSolverInterface.h

Detailed Description

Public Member Functions

Public Attributes

Private Attributes

Constructor & Destructor Documentation

◆ ChemicalSolverInterface()

◆ ~ChemicalSolverInterface()

Member Function Documentation

◆ activeElementIDs()

◆ computeSecondaryVariable()

◆ executeSpeciationCalculation()

◆ getComponentList()

◆ getConcentration()

◆ getKineticPrefactor()

◆ getStoichiometricMatrix()

◆ initialize()

◆ initializeChemicalSystemConcrete()

◆ setAqueousSolutionsPrevFromDumpFile()

◆ setChemicalSystemConcrete()

◆ updatePorosityPostReaction()

◆ updateVolumeFractionPostReaction()

Member Data Documentation

◆ _mesh

◆ active_element_ids_

◆ chemical_system_index_map

◆ linear_solver