Detailed Description

template<typename ShapeFunction, int GlobalDim>
class ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >

Definition at line 206 of file ComponentTransportFEM.h.

#include <ComponentTransportFEM.h>

Inheritance diagram for ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >:

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Collaboration diagram for ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >:

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Public Member Functions
	LocalAssemblerData (MeshLib::Element const &element, std::size_t const local_matrix_size, NumLib::GenericIntegrationMethod const &integration_method, bool is_axially_symmetric, ComponentTransportProcessData const &process_data, std::vector< std::reference_wrapper< ProcessVariable > > const &transport_process_variables)

void	setChemicalSystemID (std::size_t const) override

void	initializeChemicalSystemConcrete (Eigen::VectorXd const &local_x, double const t) override

void	setChemicalSystemConcrete (Eigen::VectorXd const &local_x, double const t, double dt) override

void	postSpeciationCalculation (std::size_t const ele_id, double const t, double const dt) override

void	assemble (double const t, double const dt, std::vector< double > const &local_x, std::vector< double > const &, std::vector< double > &local_M_data, std::vector< double > &local_K_data, std::vector< double > &local_b_data) override

void	assembleBlockMatrices (GlobalDimVectorType const &b, int const component_id, double const t, double const dt, Eigen::Ref< const NodalVectorType > const &C_nodal_values, Eigen::Ref< const NodalVectorType > const &p_nodal_values, Eigen::Ref< LocalBlockMatrixType > KCC, Eigen::Ref< LocalBlockMatrixType > MCC, Eigen::Ref< LocalBlockMatrixType > MCp, Eigen::Ref< LocalBlockMatrixType > MpC, Eigen::Ref< LocalBlockMatrixType > Kpp, Eigen::Ref< LocalBlockMatrixType > Mpp, Eigen::Ref< LocalSegmentVectorType > Bp)

void	assembleKCmCn (int const component_id, double const t, double const dt, Eigen::Ref< LocalBlockMatrixType > KCmCn, double const stoichiometric_coefficient, double const kinetic_prefactor)

void	assembleForStaggeredScheme (double const t, double const dt, Eigen::VectorXd const &local_x, Eigen::VectorXd const &local_x_prev, int const process_id, std::vector< double > &local_M_data, std::vector< double > &local_K_data, std::vector< double > &local_b_data) override

void	assembleHydraulicEquation (double const t, double const dt, Eigen::VectorXd const &local_x, Eigen::VectorXd const &local_x_prev, std::vector< double > &local_M_data, std::vector< double > &local_K_data, std::vector< double > &local_b_data)

void	assembleHeatTransportEquation (double const t, double const dt, Eigen::VectorXd const &local_x, Eigen::VectorXd const &, std::vector< double > &local_M_data, std::vector< double > &local_K_data, std::vector< double > &)

void	assembleComponentTransportEquation (double const t, double const dt, Eigen::VectorXd const &local_x, Eigen::VectorXd const &local_x_prev, std::vector< double > &local_M_data, std::vector< double > &local_K_data, std::vector< double > &, int const transport_process_id)

void	assembleWithJacobianForStaggeredScheme (double const t, double const dt, Eigen::VectorXd const &local_x, Eigen::VectorXd const &local_x_prev, int const process_id, std::vector< double > &local_b_data, std::vector< double > &local_Jac_data) override

void	assembleWithJacobianHydraulicEquation (double const t, double const dt, Eigen::VectorXd const &local_x, Eigen::VectorXd const &local_x_prev, std::vector< double > &local_b_data, std::vector< double > &local_Jac_data)

void	assembleWithJacobianComponentTransportEquation (double const t, double const dt, Eigen::VectorXd const &local_x, Eigen::VectorXd const &local_x_prev, std::vector< double > &local_b_data, std::vector< double > &local_Jac_data, int const component_id)

void	assembleReactionEquationConcrete (double const t, double const dt, Eigen::VectorXd const &local_x, std::vector< double > &local_M_data, std::vector< double > &local_K_data, std::vector< double > &local_b_data, int const transport_process_id) override

std::vector< double > const &	getIntPtDarcyVelocity (const double t, std::vector< GlobalVector * > const &x, std::vector< NumLib::LocalToGlobalIndexMap const * > const &dof_table, std::vector< double > &cache) const override

std::vector< double > const &	calculateIntPtDarcyVelocity (const double t, Eigen::Ref< const NodalVectorType > const &p_nodal_values, Eigen::Ref< const NodalVectorType > const &C_nodal_values, std::vector< double > &cache) const

Eigen::Map< const Eigen::RowVectorXd >	getShapeMatrix (const unsigned integration_point) const override
	Provides the shape matrix at the given integration point.

Eigen::Vector3d	getFlux (MathLib::Point3d const &pnt_local_coords, double const t, std::vector< double > const &local_x) const override

void	computeSecondaryVariableConcrete (double const t, double const, Eigen::VectorXd const &local_x, Eigen::VectorXd const &) override

void	computeReactionRelatedSecondaryVariable (std::size_t const ele_id) override

std::vector< double > const &	getIntPtMolarFlux (const double t, std::vector< GlobalVector * > const &x, std::vector< NumLib::LocalToGlobalIndexMap const * > const &dof_tables, std::vector< double > &cache, int const component_id) const override

void	postTimestepConcrete (Eigen::VectorXd const &, Eigen::VectorXd const &, double const, double const, int const) override

Public Member Functions inherited from ProcessLib::ComponentTransport::ComponentTransportLocalAssemblerInterface
	ComponentTransportLocalAssemblerInterface ()=default

void	initializeChemicalSystem (std::size_t const mesh_item_id, std::vector< NumLib::LocalToGlobalIndexMap const * > const &dof_tables, std::vector< GlobalVector * > const &x, double const t)

void	setChemicalSystem (std::size_t const mesh_item_id, std::vector< NumLib::LocalToGlobalIndexMap const * > const &dof_tables, std::vector< GlobalVector * > const &x, double const t, double const dt)

void	assembleReactionEquation (std::size_t const mesh_item_id, std::vector< NumLib::LocalToGlobalIndexMap const * > const &dof_tables, std::vector< GlobalVector * > const &x, double const t, double const dt, GlobalMatrix &M, GlobalMatrix &K, GlobalVector &b, int const process_id)

Public Member Functions inherited from ProcessLib::LocalAssemblerInterface
virtual	~LocalAssemblerInterface ()=default

virtual void	setInitialConditions (std::size_t const mesh_item_id, std::vector< NumLib::LocalToGlobalIndexMap const * > const &dof_tables, std::vector< GlobalVector * > const &x, double const t, int const process_id)

virtual void	initialize (std::size_t const mesh_item_id, NumLib::LocalToGlobalIndexMap const &dof_table)

virtual void	preAssemble (double const, double const, std::vector< double > const &)

virtual void	assembleWithJacobian (double const t, double const dt, std::vector< double > const &local_x, std::vector< double > const &local_x_prev, std::vector< double > &local_b_data, std::vector< double > &local_Jac_data)

virtual void	computeSecondaryVariable (std::size_t const mesh_item_id, std::vector< NumLib::LocalToGlobalIndexMap const * > const &dof_tables, double const t, double const dt, std::vector< GlobalVector * > const &x, GlobalVector const &x_prev, int const process_id)

virtual void	preTimestep (std::size_t const mesh_item_id, NumLib::LocalToGlobalIndexMap const &dof_table, GlobalVector const &x, double const t, double const delta_t)

virtual void	postTimestep (std::size_t const mesh_item_id, std::vector< NumLib::LocalToGlobalIndexMap const * > const &dof_tables, std::vector< GlobalVector * > const &x, std::vector< GlobalVector * > const &x_prev, double const t, double const dt, int const process_id)

void	postNonLinearSolver (std::size_t const mesh_item_id, std::vector< NumLib::LocalToGlobalIndexMap const * > const &dof_tables, std::vector< GlobalVector * > const &x, std::vector< GlobalVector * > const &x_prev, double const t, double const dt, int const process_id)

virtual Eigen::Vector3d	getFlux (MathLib::Point3d const &, double const, std::vector< std::vector< double > > const &) const
	Fits to staggered scheme.

Public Member Functions inherited from NumLib::ExtrapolatableElement
virtual	~ExtrapolatableElement ()=default

Private Types
using	ShapeMatricesType = ShapeMatrixPolicyType<ShapeFunction, GlobalDim>

using	ShapeMatrices = typename ShapeMatricesType::ShapeMatrices

using	LocalBlockMatrixType

using	LocalSegmentVectorType

using	LocalMatrixType

using	LocalVectorType = Eigen::Matrix<double, Eigen::Dynamic, 1>

using	NodalVectorType = typename ShapeMatricesType::NodalVectorType

using	NodalRowVectorType = typename ShapeMatricesType::NodalRowVectorType

using	GlobalDimVectorType = typename ShapeMatricesType::GlobalDimVectorType

using	GlobalDimNodalMatrixType

using	GlobalDimMatrixType = typename ShapeMatricesType::GlobalDimMatrixType

Private Member Functions
double	getHeatEnergyCoefficient (MaterialPropertyLib::VariableArray const &vars, const double porosity, const double fluid_density, const double specific_heat_capacity_fluid, ParameterLib::SpatialPosition const &pos, double const t, double const dt)

GlobalDimMatrixType	getThermalConductivityDispersivity (MaterialPropertyLib::VariableArray const &vars, const double fluid_density, const double specific_heat_capacity_fluid, const GlobalDimVectorType &velocity, ParameterLib::SpatialPosition const &pos, double const t, double const dt)

NodalVectorType	getLocalTemperature (double const t, Eigen::VectorXd const &local_x)

Private Attributes
const int	temperature_index = -1

const int	first_concentration_index = -1

MeshLib::Element const &	_element

ComponentTransportProcessData const &	_process_data

NumLib::GenericIntegrationMethod const &	_integration_method

std::vector< std::reference_wrapper< ProcessVariable > > const	_transport_process_variables

std::vector< IntegrationPointData< GlobalDimNodalMatrixType > >	_ip_data

Static Private Attributes
static const int	pressure_index = 0

static const int	pressure_size = ShapeFunction::NPOINTS

static const int	temperature_size = ShapeFunction::NPOINTS

static const int	concentration_size

Member Typedef Documentation

◆ GlobalDimMatrixType

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::GlobalDimMatrixType = typename ShapeMatricesType::GlobalDimMatrixType

private

Definition at line 238 of file ComponentTransportFEM.h.

◆ GlobalDimNodalMatrixType

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::GlobalDimNodalMatrixType

private

Initial value:

typename ShapeMatricesType::GlobalDimNodalMatrixType

EigenFixedShapeMatrixPolicy::GlobalDimNodalMatrixType

MatrixType< GlobalDim, ShapeFunction::NPOINTS > GlobalDimNodalMatrixType

Definition ShapeMatrixPolicy.h:82

Definition at line 236 of file ComponentTransportFEM.h.

◆ GlobalDimVectorType

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::GlobalDimVectorType = typename ShapeMatricesType::GlobalDimVectorType

private

Definition at line 235 of file ComponentTransportFEM.h.

◆ LocalBlockMatrixType

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::LocalBlockMatrixType

private

Initial value:

 
        typename ShapeMatricesType::template MatrixType<pressure_size,
                                                        pressure_size>

Definition at line 222 of file ComponentTransportFEM.h.

◆ LocalMatrixType

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::LocalMatrixType

private

Initial value:

Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>

Definition at line 228 of file ComponentTransportFEM.h.

◆ LocalSegmentVectorType

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::LocalSegmentVectorType

private

Initial value:

typename ShapeMatricesType::template VectorType<pressure_size>

Definition at line 225 of file ComponentTransportFEM.h.

◆ LocalVectorType

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::LocalVectorType = Eigen::Matrix<double, Eigen::Dynamic, 1>

private

Definition at line 230 of file ComponentTransportFEM.h.

◆ NodalRowVectorType

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::NodalRowVectorType = typename ShapeMatricesType::NodalRowVectorType

private

Definition at line 233 of file ComponentTransportFEM.h.

◆ NodalVectorType

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::NodalVectorType = typename ShapeMatricesType::NodalVectorType

private

Definition at line 232 of file ComponentTransportFEM.h.

◆ ShapeMatrices

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::ShapeMatrices = typename ShapeMatricesType::ShapeMatrices

private

Definition at line 220 of file ComponentTransportFEM.h.

◆ ShapeMatricesType

template<typename ShapeFunction , int GlobalDim>

using ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::ShapeMatricesType = ShapeMatrixPolicyType<ShapeFunction, GlobalDim>

private

Definition at line 219 of file ComponentTransportFEM.h.

Constructor & Destructor Documentation

◆ LocalAssemblerData()

template<typename ShapeFunction , int GlobalDim>

ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::LocalAssemblerData	(	MeshLib::Element const &	element,
		std::size_t const	local_matrix_size,
		NumLib::GenericIntegrationMethod const &	integration_method,
		bool	is_axially_symmetric,
		ComponentTransportProcessData const &	process_data,
		std::vector< std::reference_wrapper< ProcessVariable > > const &	transport_process_variables )

inline

Definition at line 241 of file ComponentTransportFEM.h.

        : temperature_index(process_data.isothermal ? -1
                                                    : ShapeFunction::NPOINTS),
          first_concentration_index(process_data.isothermal
                                        ? ShapeFunction::NPOINTS
                                        : 2 * ShapeFunction::NPOINTS),
          _element(element),
          _process_data(process_data),
          _integration_method(integration_method),
          _transport_process_variables(transport_process_variables)
    {
        (void)local_matrix_size;
 
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
        _ip_data.reserve(n_integration_points);
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        double const aperture_size = _process_data.aperture_size(0.0, pos)[0];
 
        auto const shape_matrices =
            NumLib::initShapeMatrices<ShapeFunction, ShapeMatricesType,
                                      GlobalDim>(element, is_axially_symmetric,
                                                 _integration_method);
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        for (unsigned ip = 0; ip < n_integration_points; ip++)
        {
            _ip_data.emplace_back(
                shape_matrices[ip].dNdx,
                _integration_method.getWeightedPoint(ip).getWeight() *
                    shape_matrices[ip].integralMeasure *
                    shape_matrices[ip].detJ * aperture_size);
 
            pos.setIntegrationPoint(ip);
 
            _ip_data[ip].porosity =
                medium[MaterialPropertyLib::PropertyType::porosity]
                    .template initialValue<double>(
                        pos, std::numeric_limits<double>::quiet_NaN() /*t*/);
 
            _ip_data[ip].pushBackState();
        }
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_element, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_integration_method, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_ip_data, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, ProcessLib::ComponentTransport::ComponentTransportProcessData::aperture_size, MeshLib::Element::getID(), MaterialPropertyLib::MaterialSpatialDistributionMap::getMedium(), NumLib::GenericIntegrationMethod::getNumberOfPoints(), MathLib::WeightedPoint::getWeight(), NumLib::GenericIntegrationMethod::getWeightedPoint(), NumLib::initShapeMatrices(), ProcessLib::ComponentTransport::ComponentTransportProcessData::media_map, MaterialPropertyLib::porosity, ParameterLib::SpatialPosition::setElementID(), and ParameterLib::SpatialPosition::setIntegrationPoint().

Member Function Documentation

◆ assemble()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assemble	(	double const	t,
		double const	dt,
		std::vector< double > const &	local_x,
		std::vector< double > const &	,
		std::vector< double > &	local_M_data,
		std::vector< double > &	local_K_data,
		std::vector< double > &	local_b_data )

inlineoverridevirtual

Reimplemented from ProcessLib::LocalAssemblerInterface.

Definition at line 453 of file ComponentTransportFEM.h.

    {
        auto const local_matrix_size = local_x.size();
        // Nodal DOFs include pressure
        int const num_nodal_dof = 1 + _transport_process_variables.size();
        // This assertion is valid only if all nodal d.o.f. use the same shape
        // matrices.
        assert(local_matrix_size == ShapeFunction::NPOINTS * num_nodal_dof);
 
        auto local_M = MathLib::createZeroedMatrix<LocalMatrixType>(
            local_M_data, local_matrix_size, local_matrix_size);
        auto local_K = MathLib::createZeroedMatrix<LocalMatrixType>(
            local_K_data, local_matrix_size, local_matrix_size);
        auto local_b = MathLib::createZeroedVector<LocalVectorType>(
            local_b_data, local_matrix_size);
 
        // Get block matrices
        auto Kpp = local_K.template block<pressure_size, pressure_size>(
            pressure_index, pressure_index);
        auto Mpp = local_M.template block<pressure_size, pressure_size>(
            pressure_index, pressure_index);
        auto Bp = local_b.template segment<pressure_size>(pressure_index);
 
        auto local_p = Eigen::Map<const NodalVectorType>(
            &local_x[pressure_index], pressure_size);
 
        auto const& b =
            _process_data
                .projected_specific_body_force_vectors[_element.getID()];
 
        auto const number_of_components = num_nodal_dof - 1;
        for (int component_id = 0; component_id < number_of_components;
             ++component_id)
        {
            /*  Partitioned assembler matrix
             *  |  pp | pc1 | pc2 | pc3 |
             *  |-----|-----|-----|-----|
             *  | c1p | c1c1|  0  |  0  |
             *  |-----|-----|-----|-----|
             *  | c2p |  0  | c2c2|  0  |
             *  |-----|-----|-----|-----|
             *  | c3p |  0  |  0  | c3c3|
             */
            auto concentration_index =
                pressure_size + component_id * concentration_size;
 
            auto KCC =
                local_K.template block<concentration_size, concentration_size>(
                    concentration_index, concentration_index);
            auto MCC =
                local_M.template block<concentration_size, concentration_size>(
                    concentration_index, concentration_index);
            auto MCp =
                local_M.template block<concentration_size, pressure_size>(
                    concentration_index, pressure_index);
            auto MpC =
                local_M.template block<pressure_size, concentration_size>(
                    pressure_index, concentration_index);
 
            auto local_C = Eigen::Map<const NodalVectorType>(
                &local_x[concentration_index], concentration_size);
 
            assembleBlockMatrices(b, component_id, t, dt, local_C, local_p, KCC,
                                  MCC, MCp, MpC, Kpp, Mpp, Bp);
 
            if (_process_data.chemical_solver_interface)
            {
                auto const stoichiometric_matrix =
                    _process_data.chemical_solver_interface
                        ->getStoichiometricMatrix();
 
                assert(stoichiometric_matrix);
 
                for (Eigen::SparseMatrix<double>::InnerIterator it(
                         *stoichiometric_matrix, component_id);
                     it;
                     ++it)
                {
                    auto const stoichiometric_coefficient = it.value();
                    auto const coupled_component_id = it.row();
                    auto const kinetic_prefactor =
                        _process_data.chemical_solver_interface
                            ->getKineticPrefactor(coupled_component_id);
 
                    auto const concentration_index =
                        pressure_size + component_id * concentration_size;
                    auto const coupled_concentration_index =
                        pressure_size +
                        coupled_component_id * concentration_size;
                    auto KCmCn = local_K.template block<concentration_size,
                                                        concentration_size>(
                        concentration_index, coupled_concentration_index);
 
                    // account for the coupling between components
                    assembleKCmCn(component_id, t, dt, KCmCn,
                                  stoichiometric_coefficient,
                                  kinetic_prefactor);
                }
            }
        }
    }

◆ assembleBlockMatrices()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleBlockMatrices	(	GlobalDimVectorType const &	b,
		int const	component_id,
		double const	t,
		double const	dt,
		Eigen::Ref< const NodalVectorType > const &	C_nodal_values,
		Eigen::Ref< const NodalVectorType > const &	p_nodal_values,
		Eigen::Ref< LocalBlockMatrixType >	KCC,
		Eigen::Ref< LocalBlockMatrixType >	MCC,
		Eigen::Ref< LocalBlockMatrixType >	MCp,
		Eigen::Ref< LocalBlockMatrixType >	MpC,
		Eigen::Ref< LocalBlockMatrixType >	Kpp,
		Eigen::Ref< LocalBlockMatrixType >	Mpp,
		Eigen::Ref< LocalSegmentVectorType >	Bp )

inline

Definition at line 560 of file ComponentTransportFEM.h.

    {
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        MaterialPropertyLib::VariableArray vars;
 
        // Get material properties
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        // Select the only valid for component transport liquid phase.
        auto const& phase = medium.phase("AqueousLiquid");
 
        // Assume that the component name is the same as the process variable
        // name. Components are shifted by one because the first one is always
        // pressure.
        auto const& component = phase.component(
            _transport_process_variables[component_id].get().getName());
 
        LocalBlockMatrixType KCC_Laplacian =
            LocalBlockMatrixType::Zero(concentration_size, concentration_size);
 
        std::vector<GlobalDimVectorType> ip_flux_vector;
        double average_velocity_norm = 0.0;
        if (!_process_data.non_advective_form)
        {
            ip_flux_vector.reserve(n_integration_points);
        }
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        for (unsigned ip(0); ip < n_integration_points; ++ip)
        {
            pos.setIntegrationPoint(ip);
 
            auto& ip_data = _ip_data[ip];
            auto const& dNdx = ip_data.dNdx;
            auto const& N = Ns[ip];
            auto const& w = ip_data.integration_weight;
            auto& porosity = ip_data.porosity;
 
            double C_int_pt = 0.0;
            double p_int_pt = 0.0;
 
            NumLib::shapeFunctionInterpolate(C_nodal_values, N, C_int_pt);
            NumLib::shapeFunctionInterpolate(p_nodal_values, N, p_int_pt);
 
            vars.concentration = C_int_pt;
            vars.liquid_phase_pressure = p_int_pt;
 
            // update according to a particular porosity model
            porosity = medium[MaterialPropertyLib::PropertyType::porosity]
                           .template value<double>(vars, pos, t, dt);
            vars.porosity = porosity;
 
            auto const& retardation_factor =
                component[MaterialPropertyLib::PropertyType::retardation_factor]
                    .template value<double>(vars, pos, t, dt);
 
            auto const& solute_dispersivity_transverse = medium.template value<
                double>(
                MaterialPropertyLib::PropertyType::transversal_dispersivity);
 
            auto const& solute_dispersivity_longitudinal =
                medium.template value<double>(
                    MaterialPropertyLib::PropertyType::
                        longitudinal_dispersivity);
 
            // Use the fluid density model to compute the density
            // TODO (renchao): concentration of which component as the argument
            // for calculation of fluid density
            auto const density =
                phase[MaterialPropertyLib::PropertyType::density]
                    .template value<double>(vars, pos, t, dt);
 
            auto const decay_rate =
                component[MaterialPropertyLib::PropertyType::decay_rate]
                    .template value<double>(vars, pos, t, dt);
 
            auto const& pore_diffusion_coefficient =
                MaterialPropertyLib::formEigenTensor<GlobalDim>(
                    component[MaterialPropertyLib::PropertyType::pore_diffusion]
                        .value(vars, pos, t, dt));
 
            auto const& K = MaterialPropertyLib::formEigenTensor<GlobalDim>(
                medium[MaterialPropertyLib::PropertyType::permeability].value(
                    vars, pos, t, dt));
 
            // Use the viscosity model to compute the viscosity
            auto const mu = phase[MaterialPropertyLib::PropertyType::viscosity]
                                .template value<double>(vars, pos, t, dt);
 
            GlobalDimMatrixType const K_over_mu = K / mu;
            GlobalDimVectorType const velocity =
                _process_data.has_gravity
                    ? GlobalDimVectorType(-K_over_mu *
                                          (dNdx * p_nodal_values - density * b))
                    : GlobalDimVectorType(-K_over_mu * dNdx * p_nodal_values);
 
            const double drho_dp =
                phase[MaterialPropertyLib::PropertyType::density]
                    .template dValue<double>(
                        vars,
                        MaterialPropertyLib::Variable::liquid_phase_pressure,
                        pos, t, dt);
 
            const double drho_dC =
                phase[MaterialPropertyLib::PropertyType::density]
                    .template dValue<double>(
                        vars, MaterialPropertyLib::Variable::concentration, pos,
                        t, dt);
 
            GlobalDimMatrixType const hydrodynamic_dispersion =
                NumLib::computeHydrodynamicDispersion(
                    _process_data.stabilizer, _element.getID(),
                    pore_diffusion_coefficient, velocity, porosity,
                    solute_dispersivity_transverse,
                    solute_dispersivity_longitudinal);
 
            const double R_times_phi(retardation_factor * porosity);
            GlobalDimVectorType const mass_density_flow = velocity * density;
            auto const N_t_N = (N.transpose() * N).eval();
 
            if (_process_data.non_advective_form)
            {
                MCp.noalias() += N_t_N * (C_int_pt * R_times_phi * drho_dp * w);
                MCC.noalias() += N_t_N * (C_int_pt * R_times_phi * drho_dC * w);
                KCC.noalias() -= dNdx.transpose() * mass_density_flow * N * w;
            }
            else
            {
                ip_flux_vector.emplace_back(mass_density_flow);
                average_velocity_norm += velocity.norm();
            }
            MCC.noalias() += N_t_N * (R_times_phi * density * w);
            KCC.noalias() += N_t_N * (decay_rate * R_times_phi * density * w);
            KCC_Laplacian.noalias() +=
                dNdx.transpose() * hydrodynamic_dispersion * dNdx * density * w;
 
            MpC.noalias() += N_t_N * (porosity * drho_dC * w);
 
            // Calculate Mpp, Kpp, and bp in the first loop over components
            if (component_id == 0)
            {
                Mpp.noalias() += N_t_N * (porosity * drho_dp * w);
                Kpp.noalias() +=
                    dNdx.transpose() * K_over_mu * dNdx * (density * w);
 
                if (_process_data.has_gravity)
                {
                    Bp.noalias() += dNdx.transpose() * K_over_mu * b *
                                    (density * density * w);
                }
            }
        }
 
        if (!_process_data.non_advective_form)
        {
            NumLib::assembleAdvectionMatrix<
                typename ShapeFunction::MeshElement>(
                _process_data.stabilizer,
                _ip_data,
                _process_data.shape_matrix_cache,
                ip_flux_vector,
                average_velocity_norm /
                    static_cast<double>(n_integration_points),
                KCC_Laplacian);
        }
 
        KCC.noalias() += KCC_Laplacian;
    }

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assemble().

◆ assembleComponentTransportEquation()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleComponentTransportEquation	(	double const	t,
		double const	dt,
		Eigen::VectorXd const &	local_x,
		Eigen::VectorXd const &	local_x_prev,
		std::vector< double > &	local_M_data,
		std::vector< double > &	local_K_data,
		std::vector< double > &	,
		int const	transport_process_id )

inline

Definition at line 1079 of file ComponentTransportFEM.h.

    {
        assert(static_cast<int>(local_x.size()) ==
               pressure_size +
                   concentration_size *
                       static_cast<int>(_transport_process_variables.size()) +
                   (_process_data.isothermal ? 0 : temperature_size));
 
        auto const local_p =
            local_x.template segment<pressure_size>(pressure_index);
 
        NodalVectorType local_T = getLocalTemperature(t, local_x);
 
        auto const local_C = local_x.template segment<concentration_size>(
            first_concentration_index +
            (transport_process_id - (_process_data.isothermal ? 1 : 2)) *
                concentration_size);
        auto const local_p_prev =
            local_x_prev.segment<pressure_size>(pressure_index);
 
        auto local_M = MathLib::createZeroedMatrix<LocalBlockMatrixType>(
            local_M_data, concentration_size, concentration_size);
        auto local_K = MathLib::createZeroedMatrix<LocalBlockMatrixType>(
            local_K_data, concentration_size, concentration_size);
 
        LocalBlockMatrixType KCC_Laplacian =
            LocalBlockMatrixType::Zero(concentration_size, concentration_size);
 
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        std::vector<GlobalDimVectorType> ip_flux_vector;
        double average_velocity_norm = 0.0;
        if (!_process_data.non_advective_form)
        {
            ip_flux_vector.reserve(n_integration_points);
        }
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        auto const& b =
            _process_data
                .projected_specific_body_force_vectors[_element.getID()];
 
        MaterialPropertyLib::VariableArray vars;
        MaterialPropertyLib::VariableArray vars_prev;
 
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        auto const& phase = medium.phase("AqueousLiquid");
        auto const component_id =
            transport_process_id - (_process_data.isothermal ? 1 : 2);
        auto const& component = phase.component(
            _transport_process_variables[component_id].get().getName());
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        for (unsigned ip(0); ip < n_integration_points; ++ip)
        {
            pos.setIntegrationPoint(ip);
 
            auto& ip_data = _ip_data[ip];
            auto const& dNdx = ip_data.dNdx;
            auto const& w = ip_data.integration_weight;
            auto const& N = Ns[ip];
            auto& porosity = ip_data.porosity;
            auto const& porosity_prev = ip_data.porosity_prev;
 
            double const C_int_pt = N.dot(local_C);
            double const p_int_pt = N.dot(local_p);
            double const T_int_pt = N.dot(local_T);
 
            vars.concentration = C_int_pt;
            vars.liquid_phase_pressure = p_int_pt;
            vars.temperature = T_int_pt;
 
            if (_process_data.temperature)
            {
                vars.temperature = N.dot(local_T);
            }
 
            // porosity
            {
                vars_prev.porosity = porosity_prev;
 
                porosity =
                    _process_data.chemically_induced_porosity_change
                        ? porosity_prev
                        : medium[MaterialPropertyLib::PropertyType::porosity]
                              .template value<double>(vars, vars_prev, pos, t,
                                                      dt);
 
                vars.porosity = porosity;
            }
 
            auto const& retardation_factor =
                component[MaterialPropertyLib::PropertyType::retardation_factor]
                    .template value<double>(vars, pos, t, dt);
 
            auto const& solute_dispersivity_transverse = medium.template value<
                double>(
                MaterialPropertyLib::PropertyType::transversal_dispersivity);
            auto const& solute_dispersivity_longitudinal =
                medium.template value<double>(
                    MaterialPropertyLib::PropertyType::
                        longitudinal_dispersivity);
 
            // Use the fluid density model to compute the density
            auto const density =
                phase[MaterialPropertyLib::PropertyType::density]
                    .template value<double>(vars, pos, t, dt);
            auto const decay_rate =
                component[MaterialPropertyLib::PropertyType::decay_rate]
                    .template value<double>(vars, pos, t, dt);
 
            auto const& pore_diffusion_coefficient =
                MaterialPropertyLib::formEigenTensor<GlobalDim>(
                    component[MaterialPropertyLib::PropertyType::pore_diffusion]
                        .value(vars, pos, t, dt));
 
            auto const& K = MaterialPropertyLib::formEigenTensor<GlobalDim>(
                medium[MaterialPropertyLib::PropertyType::permeability].value(
                    vars, pos, t, dt));
            // Use the viscosity model to compute the viscosity
            auto const mu = phase[MaterialPropertyLib::PropertyType::viscosity]
                                .template value<double>(vars, pos, t, dt);
 
            GlobalDimMatrixType const K_over_mu = K / mu;
            GlobalDimVectorType const velocity =
                _process_data.has_gravity
                    ? GlobalDimVectorType(-K_over_mu *
                                          (dNdx * local_p - density * b))
                    : GlobalDimVectorType(-K_over_mu * dNdx * local_p);
 
            GlobalDimMatrixType const hydrodynamic_dispersion =
                NumLib::computeHydrodynamicDispersion(
                    _process_data.stabilizer, _element.getID(),
                    pore_diffusion_coefficient, velocity, porosity,
                    solute_dispersivity_transverse,
                    solute_dispersivity_longitudinal);
 
            double const R_times_phi = retardation_factor * porosity;
            auto const N_t_N = (N.transpose() * N).eval();
 
            if (_process_data.non_advective_form)
            {
                const double drho_dC =
                    phase[MaterialPropertyLib::PropertyType::density]
                        .template dValue<double>(
                            vars, MaterialPropertyLib::Variable::concentration,
                            pos, t, dt);
                local_M.noalias() +=
                    N_t_N * (R_times_phi * C_int_pt * drho_dC * w);
            }
 
            local_M.noalias() += N_t_N * (R_times_phi * density * w);
 
            // coupling term
            if (_process_data.non_advective_form)
            {
                double const p_dot = (p_int_pt - N.dot(local_p_prev)) / dt;
 
                const double drho_dp =
                    phase[MaterialPropertyLib::PropertyType::density]
                        .template dValue<double>(vars,
                                                 MaterialPropertyLib::Variable::
                                                     liquid_phase_pressure,
                                                 pos, t, dt);
 
                local_K.noalias() +=
                    N_t_N * ((R_times_phi * drho_dp * p_dot) * w) -
                    dNdx.transpose() * velocity * N * (density * w);
            }
            else
            {
                ip_flux_vector.emplace_back(velocity * density);
                average_velocity_norm += velocity.norm();
            }
            local_K.noalias() +=
                N_t_N * (decay_rate * R_times_phi * density * w);
 
            KCC_Laplacian.noalias() += dNdx.transpose() *
                                       hydrodynamic_dispersion * dNdx *
                                       (density * w);
        }
 
        if (!_process_data.non_advective_form)
        {
            NumLib::assembleAdvectionMatrix<
                typename ShapeFunction::MeshElement>(
                _process_data.stabilizer, _ip_data,
                _process_data.shape_matrix_cache, ip_flux_vector,
                average_velocity_norm /
                    static_cast<double>(n_integration_points),
                KCC_Laplacian);
        }
        local_K.noalias() += KCC_Laplacian;
    }

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleForStaggeredScheme().

◆ assembleForStaggeredScheme()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleForStaggeredScheme	(	double const	t,
		double const	dt,
		Eigen::VectorXd const &	local_x,
		Eigen::VectorXd const &	local_x_prev,
		int const	process_id,
		std::vector< double > &	local_M_data,
		std::vector< double > &	local_K_data,
		std::vector< double > &	local_b_data )

inlineoverridevirtual

Reimplemented from ProcessLib::LocalAssemblerInterface.

Definition at line 795 of file ComponentTransportFEM.h.

    {
        if (process_id == _process_data.hydraulic_process_id)
        {
            assembleHydraulicEquation(t, dt, local_x, local_x_prev,
                                      local_M_data, local_K_data, local_b_data);
        }
        else if (process_id == _process_data.thermal_process_id)
        {
            assembleHeatTransportEquation(t, dt, local_x, local_x_prev,
                                          local_M_data, local_K_data,
                                          local_b_data);
        }
        else
        {
            // Go for assembling in an order of transport process id.
            assembleComponentTransportEquation(t, dt, local_x, local_x_prev,
                                               local_M_data, local_K_data,
                                               local_b_data, process_id);
        }
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleComponentTransportEquation(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHeatTransportEquation(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHydraulicEquation(), ProcessLib::ComponentTransport::ComponentTransportProcessData::hydraulic_process_id, and ProcessLib::ComponentTransport::ComponentTransportProcessData::thermal_process_id.

◆ assembleHeatTransportEquation()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHeatTransportEquation	(	double const	t,
		double const	dt,
		Eigen::VectorXd const &	local_x,
		Eigen::VectorXd const &	,
		std::vector< double > &	local_M_data,
		std::vector< double > &	local_K_data,
		std::vector< double > &	)

inline

Definition at line 951 of file ComponentTransportFEM.h.

    {
        assert(local_x.size() ==
               pressure_size + temperature_size + concentration_size);
 
        auto const local_p =
            local_x.template segment<pressure_size>(pressure_index);
        auto const local_T =
            local_x.template segment<temperature_size>(temperature_index);
 
        auto local_M = MathLib::createZeroedMatrix<LocalBlockMatrixType>(
            local_M_data, temperature_size, temperature_size);
        auto local_K = MathLib::createZeroedMatrix<LocalBlockMatrixType>(
            local_K_data, temperature_size, temperature_size);
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(this->_element.getID());
 
        auto const& process_data = this->_process_data;
        auto const& medium =
            *process_data.media_map.getMedium(this->_element.getID());
        auto const& liquid_phase = medium.phase("AqueousLiquid");
 
        auto const& b =
            _process_data
                .projected_specific_body_force_vectors[_element.getID()];
 
        MaterialPropertyLib::VariableArray vars;
 
        unsigned const n_integration_points =
            this->_integration_method.getNumberOfPoints();
 
        std::vector<GlobalDimVectorType> ip_flux_vector;
        double average_velocity_norm = 0.0;
        ip_flux_vector.reserve(n_integration_points);
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        for (unsigned ip(0); ip < n_integration_points; ip++)
        {
            pos.setIntegrationPoint(ip);
 
            auto const& ip_data = this->_ip_data[ip];
            auto const& dNdx = ip_data.dNdx;
            auto const& w = ip_data.integration_weight;
            auto const& N = Ns[ip];
 
            double p_at_xi = 0.;
            NumLib::shapeFunctionInterpolate(local_p, N, p_at_xi);
            double T_at_xi = 0.;
            NumLib::shapeFunctionInterpolate(local_T, N, T_at_xi);
 
            vars.temperature = T_at_xi;
            vars.liquid_phase_pressure = p_at_xi;
 
            vars.liquid_saturation = 1.0;
 
            auto const porosity =
                medium.property(MaterialPropertyLib::PropertyType::porosity)
                    .template value<double>(vars, pos, t, dt);
            vars.porosity = porosity;
 
            // Use the fluid density model to compute the density
            auto const fluid_density =
                liquid_phase
                    .property(MaterialPropertyLib::PropertyType::density)
                    .template value<double>(vars, pos, t, dt);
            vars.density = fluid_density;
            auto const specific_heat_capacity_fluid =
                liquid_phase
                    .property(MaterialPropertyLib::specific_heat_capacity)
                    .template value<double>(vars, pos, t, dt);
 
            // Assemble mass matrix
            local_M.noalias() += w *
                                 this->getHeatEnergyCoefficient(
                                     vars, porosity, fluid_density,
                                     specific_heat_capacity_fluid, pos, t, dt) *
                                 N.transpose() * N;
 
            // Assemble Laplace matrix
            auto const viscosity =
                liquid_phase
                    .property(MaterialPropertyLib::PropertyType::viscosity)
                    .template value<double>(vars, pos, t, dt);
 
            auto const intrinsic_permeability =
                MaterialPropertyLib::formEigenTensor<GlobalDim>(
                    medium
                        .property(
                            MaterialPropertyLib::PropertyType::permeability)
                        .value(vars, pos, t, dt));
 
            GlobalDimMatrixType const K_over_mu =
                intrinsic_permeability / viscosity;
            GlobalDimVectorType const velocity =
                process_data.has_gravity
                    ? GlobalDimVectorType(-K_over_mu *
                                          (dNdx * local_p - fluid_density * b))
                    : GlobalDimVectorType(-K_over_mu * dNdx * local_p);
 
            GlobalDimMatrixType const thermal_conductivity_dispersivity =
                this->getThermalConductivityDispersivity(
                    vars, fluid_density, specific_heat_capacity_fluid, velocity,
                    pos, t, dt);
 
            local_K.noalias() +=
                w * dNdx.transpose() * thermal_conductivity_dispersivity * dNdx;
 
            ip_flux_vector.emplace_back(velocity * fluid_density *
                                        specific_heat_capacity_fluid);
            average_velocity_norm += velocity.norm();
        }
 
        NumLib::assembleAdvectionMatrix<typename ShapeFunction::MeshElement>(
            process_data.stabilizer, this->_ip_data,
            _process_data.shape_matrix_cache, ip_flux_vector,
            average_velocity_norm / static_cast<double>(n_integration_points),
            local_K);
    }

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleForStaggeredScheme().

◆ assembleHydraulicEquation()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHydraulicEquation	(	double const	t,
		double const	dt,
		Eigen::VectorXd const &	local_x,
		Eigen::VectorXd const &	local_x_prev,
		std::vector< double > &	local_M_data,
		std::vector< double > &	local_K_data,
		std::vector< double > &	local_b_data )

inline

Definition at line 823 of file ComponentTransportFEM.h.

    {
        auto const local_p =
            local_x.template segment<pressure_size>(pressure_index);
        auto const local_C = local_x.template segment<concentration_size>(
            first_concentration_index);
        auto const local_C_prev =
            local_x_prev.segment<concentration_size>(first_concentration_index);
 
        NodalVectorType local_T = getLocalTemperature(t, local_x);
 
        auto local_M = MathLib::createZeroedMatrix<LocalBlockMatrixType>(
            local_M_data, pressure_size, pressure_size);
        auto local_K = MathLib::createZeroedMatrix<LocalBlockMatrixType>(
            local_K_data, pressure_size, pressure_size);
        auto local_b = MathLib::createZeroedVector<LocalSegmentVectorType>(
            local_b_data, pressure_size);
 
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        auto const& b =
            _process_data
                .projected_specific_body_force_vectors[_element.getID()];
 
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        auto const& phase = medium.phase("AqueousLiquid");
 
        MaterialPropertyLib::VariableArray vars;
        MaterialPropertyLib::VariableArray vars_prev;
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        for (unsigned ip(0); ip < n_integration_points; ++ip)
        {
            pos.setIntegrationPoint(ip);
 
            auto& ip_data = _ip_data[ip];
            auto const& dNdx = ip_data.dNdx;
            auto const& w = ip_data.integration_weight;
            auto const& N = Ns[ip];
            auto& porosity = ip_data.porosity;
            auto const& porosity_prev = ip_data.porosity_prev;
 
            double const C_int_pt = N.dot(local_C);
            double const p_int_pt = N.dot(local_p);
            double const T_int_pt = N.dot(local_T);
 
            vars.concentration = C_int_pt;
            vars.liquid_phase_pressure = p_int_pt;
            vars.temperature = T_int_pt;
 
            //  porosity
            {
                vars_prev.porosity = porosity_prev;
 
                porosity =
                    _process_data.chemically_induced_porosity_change
                        ? porosity_prev
                        : medium[MaterialPropertyLib::PropertyType::porosity]
                              .template value<double>(vars, vars_prev, pos, t,
                                                      dt);
 
                vars.porosity = porosity;
            }
 
            // Use the fluid density model to compute the density
            // TODO: Concentration of which component as one of arguments for
            // calculation of fluid density
            auto const density =
                phase[MaterialPropertyLib::PropertyType::density]
                    .template value<double>(vars, pos, t, dt);
 
            auto const& K = MaterialPropertyLib::formEigenTensor<GlobalDim>(
                medium[MaterialPropertyLib::PropertyType::permeability].value(
                    vars, pos, t, dt));
 
            // Use the viscosity model to compute the viscosity
            auto const mu = phase[MaterialPropertyLib::PropertyType::viscosity]
                                .template value<double>(vars, pos, t, dt);
 
            GlobalDimMatrixType const K_over_mu = K / mu;
 
            const double drho_dp =
                phase[MaterialPropertyLib::PropertyType::density]
                    .template dValue<double>(
                        vars,
                        MaterialPropertyLib::Variable::liquid_phase_pressure,
                        pos, t, dt);
            const double drho_dC =
                phase[MaterialPropertyLib::PropertyType::density]
                    .template dValue<double>(
                        vars, MaterialPropertyLib::Variable::concentration, pos,
                        t, dt);
 
            // matrix assembly
            local_M.noalias() += w * N.transpose() * porosity * drho_dp * N;
            local_K.noalias() +=
                w * dNdx.transpose() * density * K_over_mu * dNdx;
 
            if (_process_data.has_gravity)
            {
                local_b.noalias() +=
                    w * density * density * dNdx.transpose() * K_over_mu * b;
            }
 
            // coupling term
            {
                double const C_dot = (C_int_pt - N.dot(local_C_prev)) / dt;
 
                local_b.noalias() -=
                    w * N.transpose() * porosity * drho_dC * C_dot;
            }
        }
    }

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleForStaggeredScheme().

◆ assembleKCmCn()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleKCmCn	(	int const	component_id,
		double const	t,
		double const	dt,
		Eigen::Ref< LocalBlockMatrixType >	KCmCn,
		double const	stoichiometric_coefficient,
		double const	kinetic_prefactor )

inline

Definition at line 748 of file ComponentTransportFEM.h.

    {
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        MaterialPropertyLib::VariableArray vars;
 
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        auto const& phase = medium.phase("AqueousLiquid");
        auto const& component = phase.component(
            _transport_process_variables[component_id].get().getName());
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        for (unsigned ip(0); ip < n_integration_points; ++ip)
        {
            auto& ip_data = _ip_data[ip];
            auto const& w = ip_data.integration_weight;
            auto const& N = Ns[ip];
            auto& porosity = ip_data.porosity;
 
            auto const retardation_factor =
                component[MaterialPropertyLib::PropertyType::retardation_factor]
                    .template value<double>(vars, pos, t, dt);
 
            porosity = medium[MaterialPropertyLib::PropertyType::porosity]
                           .template value<double>(vars, pos, t, dt);
 
            auto const density =
                phase[MaterialPropertyLib::PropertyType::density]
                    .template value<double>(vars, pos, t, dt);
 
            KCmCn.noalias() -= w * N.transpose() * stoichiometric_coefficient *
                               kinetic_prefactor * retardation_factor *
                               porosity * density * N;
        }
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_element, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_integration_method, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_ip_data, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_transport_process_variables, MaterialPropertyLib::Phase::component(), MaterialPropertyLib::density, MeshLib::Element::getID(), MaterialPropertyLib::MaterialSpatialDistributionMap::getMedium(), getName(), NumLib::GenericIntegrationMethod::getNumberOfPoints(), ProcessLib::ComponentTransport::ComponentTransportProcessData::media_map, NumLib::ShapeMatrixCache::NsHigherOrder(), MaterialPropertyLib::Medium::phase(), MaterialPropertyLib::porosity, MaterialPropertyLib::retardation_factor, ParameterLib::SpatialPosition::setElementID(), and ProcessLib::ComponentTransport::ComponentTransportProcessData::shape_matrix_cache.

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assemble().

◆ assembleReactionEquationConcrete()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleReactionEquationConcrete	(	double const	t,
		double const	dt,
		Eigen::VectorXd const &	local_x,
		std::vector< double > &	local_M_data,
		std::vector< double > &	local_K_data,
		std::vector< double > &	local_b_data,
		int const	transport_process_id )

inlineoverridevirtual

Implements ProcessLib::ComponentTransport::ComponentTransportLocalAssemblerInterface.

Definition at line 1564 of file ComponentTransportFEM.h.

    {
        auto const local_C = local_x.template segment<concentration_size>(
            first_concentration_index +
            (transport_process_id - 1) * concentration_size);
 
        auto local_M = MathLib::createZeroedMatrix<LocalBlockMatrixType>(
            local_M_data, concentration_size, concentration_size);
        auto local_K = MathLib::createZeroedMatrix<LocalBlockMatrixType>(
            local_K_data, concentration_size, concentration_size);
        auto local_b = MathLib::createZeroedVector<LocalVectorType>(
            local_b_data, concentration_size);
 
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        MaterialPropertyLib::VariableArray vars;
        MaterialPropertyLib::VariableArray vars_prev;
 
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        auto const component_id = transport_process_id - 1;
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        for (unsigned ip(0); ip < n_integration_points; ++ip)
        {
            pos.setIntegrationPoint(ip);
 
            auto& ip_data = _ip_data[ip];
            auto const w = ip_data.integration_weight;
            auto const& N = Ns[ip];
            auto& porosity = ip_data.porosity;
            auto const& porosity_prev = ip_data.porosity_prev;
            auto const chemical_system_id = ip_data.chemical_system_id;
 
            double C_int_pt = 0.0;
            NumLib::shapeFunctionInterpolate(local_C, N, C_int_pt);
 
            vars.concentration = C_int_pt;
 
            auto const porosity_dot = (porosity - porosity_prev) / dt;
 
            // porosity
            {
                vars_prev.porosity = porosity_prev;
 
                porosity =
                    _process_data.chemically_induced_porosity_change
                        ? porosity_prev
                        : medium[MaterialPropertyLib::PropertyType::porosity]
                              .template value<double>(vars, vars_prev, pos, t,
                                                      dt);
            }
 
            local_M.noalias() += w * N.transpose() * porosity * N;
 
            local_K.noalias() += w * N.transpose() * porosity_dot * N;
 
            if (chemical_system_id == -1)
            {
                continue;
            }
 
            auto const C_post_int_pt =
                _process_data.chemical_solver_interface->getConcentration(
                    component_id, chemical_system_id);
 
            local_b.noalias() +=
                w * N.transpose() * porosity * (C_post_int_pt - C_int_pt) / dt;
        }
    }

◆ assembleWithJacobianComponentTransportEquation()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleWithJacobianComponentTransportEquation	(	double const	t,
		double const	dt,
		Eigen::VectorXd const &	local_x,
		Eigen::VectorXd const &	local_x_prev,
		std::vector< double > &	local_b_data,
		std::vector< double > &	local_Jac_data,
		int const	component_id )

inline

Definition at line 1414 of file ComponentTransportFEM.h.

    {
        auto const concentration_index =
            first_concentration_index + component_id * concentration_size;
 
        auto const p = local_x.template segment<pressure_size>(pressure_index);
        auto const c =
            local_x.template segment<concentration_size>(concentration_index);
        auto const c_prev =
            local_x_prev.segment<concentration_size>(concentration_index);
 
        NodalVectorType T;
        if (_process_data.temperature)
        {
            T = _process_data.temperature->getNodalValuesOnElement(_element, t);
        }
 
        auto local_Jac = MathLib::createZeroedMatrix<LocalBlockMatrixType>(
            local_Jac_data, concentration_size, concentration_size);
        auto local_rhs = MathLib::createZeroedVector<LocalSegmentVectorType>(
            local_b_data, concentration_size);
 
        LocalBlockMatrixType KCC_Laplacian =
            LocalBlockMatrixType::Zero(concentration_size, concentration_size);
 
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        std::vector<GlobalDimVectorType> ip_flux_vector;
        double average_velocity_norm = 0.0;
        ip_flux_vector.reserve(n_integration_points);
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        auto const& b =
            _process_data
                .projected_specific_body_force_vectors[_element.getID()];
 
        MaterialPropertyLib::VariableArray vars;
        MaterialPropertyLib::VariableArray vars_prev;
 
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        auto const& phase = medium.phase("AqueousLiquid");
        auto const& component = phase.component(
            _transport_process_variables[component_id].get().getName());
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        for (unsigned ip(0); ip < n_integration_points; ++ip)
        {
            pos.setIntegrationPoint(ip);
 
            auto& ip_data = _ip_data[ip];
            auto const& dNdx = ip_data.dNdx;
            auto const& w = ip_data.integration_weight;
            auto const& N = Ns[ip];
            auto& phi = ip_data.porosity;
            auto const& phi_prev = ip_data.porosity_prev;
 
            double const p_ip = N.dot(p);
            double const c_ip = N.dot(c);
 
            vars.liquid_phase_pressure = p_ip;
            vars.concentration = c_ip;
 
            if (_process_data.temperature)
            {
                vars.temperature = N.dot(T);
            }
 
            // porosity
            {
                vars_prev.porosity = phi_prev;
 
                phi = _process_data.chemically_induced_porosity_change
                          ? phi_prev
                          : medium[MaterialPropertyLib::PropertyType::porosity]
                                .template value<double>(vars, vars_prev, pos, t,
                                                        dt);
 
                vars.porosity = phi;
            }
 
            auto const R =
                component[MaterialPropertyLib::PropertyType::retardation_factor]
                    .template value<double>(vars, pos, t, dt);
 
            auto const alpha_T = medium.template value<double>(
                MaterialPropertyLib::PropertyType::transversal_dispersivity);
            auto const alpha_L = medium.template value<double>(
                MaterialPropertyLib::PropertyType::longitudinal_dispersivity);
 
            auto const rho = phase[MaterialPropertyLib::PropertyType::density]
                                 .template value<double>(vars, pos, t, dt);
            // first-order decay constant
            auto const alpha =
                component[MaterialPropertyLib::PropertyType::decay_rate]
                    .template value<double>(vars, pos, t, dt);
 
            auto const Dp = MaterialPropertyLib::formEigenTensor<GlobalDim>(
                component[MaterialPropertyLib::PropertyType::pore_diffusion]
                    .value(vars, pos, t, dt));
 
            auto const k = MaterialPropertyLib::formEigenTensor<GlobalDim>(
                medium[MaterialPropertyLib::PropertyType::permeability].value(
                    vars, pos, t, dt));
            auto const mu = phase[MaterialPropertyLib::PropertyType::viscosity]
                                .template value<double>(vars, pos, t, dt);
            // Darcy flux
            GlobalDimVectorType const q =
                _process_data.has_gravity
                    ? GlobalDimVectorType(-k / mu * (dNdx * p - rho * b))
                    : GlobalDimVectorType(-k / mu * dNdx * p);
 
            GlobalDimMatrixType const D = NumLib::computeHydrodynamicDispersion(
                _process_data.stabilizer, _element.getID(), Dp, q, phi, alpha_T,
                alpha_L);
 
            // matrix assembly
            local_Jac.noalias() +=
                w * rho * N.transpose() * phi * R * (alpha + 1 / dt) * N;
 
            KCC_Laplacian.noalias() += w * rho * dNdx.transpose() * D * dNdx;
 
            auto const cdot = (c - c_prev) / dt;
            local_rhs.noalias() -=
                w * rho * N.transpose() * phi * R * N * (cdot + alpha * c);
 
            ip_flux_vector.emplace_back(q * rho);
            average_velocity_norm += q.norm();
        }
 
        NumLib::assembleAdvectionMatrix<typename ShapeFunction::MeshElement>(
            _process_data.stabilizer, _ip_data,
            _process_data.shape_matrix_cache, ip_flux_vector,
            average_velocity_norm / static_cast<double>(n_integration_points),
            KCC_Laplacian);
 
        local_rhs.noalias() -= KCC_Laplacian * c;
 
        local_Jac.noalias() += KCC_Laplacian;
    }

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleWithJacobianForStaggeredScheme().

◆ assembleWithJacobianForStaggeredScheme()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleWithJacobianForStaggeredScheme	(	double const	t,
		double const	dt,
		Eigen::VectorXd const &	local_x,
		Eigen::VectorXd const &	local_x_prev,
		int const	process_id,
		std::vector< double > &	local_b_data,
		std::vector< double > &	local_Jac_data )

inlineoverridevirtual

Reimplemented from ProcessLib::LocalAssemblerInterface.

Definition at line 1285 of file ComponentTransportFEM.h.

    {
        if (process_id == _process_data.hydraulic_process_id)
        {
            assembleWithJacobianHydraulicEquation(t, dt, local_x, local_x_prev,
                                                  local_b_data, local_Jac_data);
        }
        else
        {
            int const component_id = process_id - 1;
            assembleWithJacobianComponentTransportEquation(
                t, dt, local_x, local_x_prev, local_b_data, local_Jac_data,
                component_id);
        }
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleWithJacobianComponentTransportEquation(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleWithJacobianHydraulicEquation(), and ProcessLib::ComponentTransport::ComponentTransportProcessData::hydraulic_process_id.

◆ assembleWithJacobianHydraulicEquation()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleWithJacobianHydraulicEquation	(	double const	t,
		double const	dt,
		Eigen::VectorXd const &	local_x,
		Eigen::VectorXd const &	local_x_prev,
		std::vector< double > &	local_b_data,
		std::vector< double > &	local_Jac_data )

inline

Definition at line 1305 of file ComponentTransportFEM.h.

    {
        auto const p = local_x.template segment<pressure_size>(pressure_index);
        auto const c = local_x.template segment<concentration_size>(
            first_concentration_index);
 
        auto const p_prev = local_x_prev.segment<pressure_size>(pressure_index);
        auto const c_prev =
            local_x_prev.segment<concentration_size>(first_concentration_index);
 
        auto local_Jac = MathLib::createZeroedMatrix<LocalBlockMatrixType>(
            local_Jac_data, pressure_size, pressure_size);
        auto local_rhs = MathLib::createZeroedVector<LocalSegmentVectorType>(
            local_b_data, pressure_size);
 
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
        auto const& b =
            _process_data
                .projected_specific_body_force_vectors[_element.getID()];
 
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        auto const& phase = medium.phase("AqueousLiquid");
 
        MaterialPropertyLib::VariableArray vars;
        MaterialPropertyLib::VariableArray vars_prev;
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        for (unsigned ip(0); ip < n_integration_points; ++ip)
        {
            pos.setIntegrationPoint(ip);
 
            auto& ip_data = _ip_data[ip];
            auto const& dNdx = ip_data.dNdx;
            auto const& w = ip_data.integration_weight;
            auto const& N = Ns[ip];
            auto& phi = ip_data.porosity;
            auto const& phi_prev = ip_data.porosity_prev;
 
            double const p_ip = N.dot(p);
            double const c_ip = N.dot(c);
 
            double const cdot_ip = (c_ip - N.dot(c_prev)) / dt;
 
            vars.liquid_phase_pressure = p_ip;
            vars.concentration = c_ip;
 
            //  porosity
            {
                vars_prev.porosity = phi_prev;
 
                phi = _process_data.chemically_induced_porosity_change
                          ? phi_prev
                          : medium[MaterialPropertyLib::PropertyType::porosity]
                                .template value<double>(vars, vars_prev, pos, t,
                                                        dt);
 
                vars.porosity = phi;
            }
 
            auto const rho = phase[MaterialPropertyLib::PropertyType::density]
                                 .template value<double>(vars, pos, t, dt);
 
            auto const k = MaterialPropertyLib::formEigenTensor<GlobalDim>(
                medium[MaterialPropertyLib::PropertyType::permeability].value(
                    vars, pos, t, dt));
 
            auto const mu = phase[MaterialPropertyLib::PropertyType::viscosity]
                                .template value<double>(vars, pos, t, dt);
 
            auto const drho_dp =
                phase[MaterialPropertyLib::PropertyType::density]
                    .template dValue<double>(
                        vars,
                        MaterialPropertyLib::Variable::liquid_phase_pressure,
                        pos, t, dt);
            auto const drho_dc =
                phase[MaterialPropertyLib::PropertyType::density]
                    .template dValue<double>(
                        vars, MaterialPropertyLib::Variable::concentration, pos,
                        t, dt);
 
            // matrix assembly
            local_Jac.noalias() += w * N.transpose() * phi * drho_dp / dt * N +
                                   w * dNdx.transpose() * rho * k / mu * dNdx;
 
            local_rhs.noalias() -=
                w * N.transpose() * phi *
                    (drho_dp * N * p_prev + drho_dc * cdot_ip) +
                w * rho * dNdx.transpose() * k / mu * dNdx * p;
 
            if (_process_data.has_gravity)
            {
                local_rhs.noalias() +=
                    w * rho * dNdx.transpose() * k / mu * rho * b;
            }
        }
    }

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleWithJacobianForStaggeredScheme().

◆ calculateIntPtDarcyVelocity()

template<typename ShapeFunction , int GlobalDim>

std::vector< double > const & ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::calculateIntPtDarcyVelocity	(	const double	t,
		Eigen::Ref< const NodalVectorType > const &	p_nodal_values,
		Eigen::Ref< const NodalVectorType > const &	C_nodal_values,
		std::vector< double > &	cache ) const

inline

Definition at line 1688 of file ComponentTransportFEM.h.

    {
        auto const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        cache.clear();
        auto cache_mat = MathLib::createZeroedMatrix<
            Eigen::Matrix<double, GlobalDim, Eigen::Dynamic, Eigen::RowMajor>>(
            cache, GlobalDim, n_integration_points);
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        auto const& b =
            _process_data
                .projected_specific_body_force_vectors[_element.getID()];
 
        MaterialPropertyLib::VariableArray vars;
 
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        auto const& phase = medium.phase("AqueousLiquid");
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        for (unsigned ip = 0; ip < n_integration_points; ++ip)
        {
            auto const& ip_data = _ip_data[ip];
            auto const& dNdx = ip_data.dNdx;
            auto const& N = Ns[ip];
            auto const& porosity = ip_data.porosity;
 
            pos.setIntegrationPoint(ip);
 
            double C_int_pt = 0.0;
            double p_int_pt = 0.0;
 
            NumLib::shapeFunctionInterpolate(C_nodal_values, N, C_int_pt);
            NumLib::shapeFunctionInterpolate(p_nodal_values, N, p_int_pt);
 
            vars.concentration = C_int_pt;
            vars.liquid_phase_pressure = p_int_pt;
            vars.porosity = porosity;
 
            // TODO (naumov) Temporary value not used by current material
            // models. Need extension of secondary variables interface.
            double const dt = std::numeric_limits<double>::quiet_NaN();
            auto const& K = MaterialPropertyLib::formEigenTensor<GlobalDim>(
                medium[MaterialPropertyLib::PropertyType::permeability].value(
                    vars, pos, t, dt));
            auto const mu = phase[MaterialPropertyLib::PropertyType::viscosity]
                                .template value<double>(vars, pos, t, dt);
            GlobalDimMatrixType const K_over_mu = K / mu;
 
            cache_mat.col(ip).noalias() = -K_over_mu * dNdx * p_nodal_values;
            if (_process_data.has_gravity)
            {
                auto const rho_w =
                    phase[MaterialPropertyLib::PropertyType::density]
                        .template value<double>(vars, pos, t, dt);
                // here it is assumed that the vector b is directed 'downwards'
                cache_mat.col(ip).noalias() += K_over_mu * rho_w * b;
            }
        }
 
        return cache;
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_element, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_integration_method, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_ip_data, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, MaterialPropertyLib::VariableArray::concentration, MathLib::createZeroedMatrix(), MaterialPropertyLib::density, MeshLib::Element::getID(), MaterialPropertyLib::MaterialSpatialDistributionMap::getMedium(), NumLib::GenericIntegrationMethod::getNumberOfPoints(), ProcessLib::ComponentTransport::ComponentTransportProcessData::has_gravity, MaterialPropertyLib::VariableArray::liquid_phase_pressure, ProcessLib::ComponentTransport::ComponentTransportProcessData::media_map, NumLib::ShapeMatrixCache::NsHigherOrder(), MaterialPropertyLib::permeability, MaterialPropertyLib::Medium::phase(), MaterialPropertyLib::VariableArray::porosity, ProcessLib::ComponentTransport::ComponentTransportProcessData::projected_specific_body_force_vectors, ParameterLib::SpatialPosition::setElementID(), ProcessLib::ComponentTransport::ComponentTransportProcessData::shape_matrix_cache, NumLib::detail::shapeFunctionInterpolate(), and MaterialPropertyLib::viscosity.

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::computeSecondaryVariableConcrete(), and ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getIntPtDarcyVelocity().

◆ computeReactionRelatedSecondaryVariable()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::computeReactionRelatedSecondaryVariable ( std::size_t const ele_id )

inlineoverridevirtual

Implements ProcessLib::ComponentTransport::ComponentTransportLocalAssemblerInterface.

Definition at line 1860 of file ComponentTransportFEM.h.

    {
        auto const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        if (_process_data.chemically_induced_porosity_change)
        {
            auto const& medium = *_process_data.media_map.getMedium(ele_id);
 
            for (auto& ip_data : _ip_data)
            {
                ip_data.porosity = ip_data.porosity_prev;
 
                _process_data.chemical_solver_interface
                    ->updatePorosityPostReaction(ip_data.chemical_system_id,
                                                 medium, ip_data.porosity);
            }
 
            (*_process_data.mesh_prop_porosity)[ele_id] =
                std::accumulate(_ip_data.begin(), _ip_data.end(), 0.,
                                [](double const s, auto const& ip)
                                { return s + ip.porosity; }) /
                n_integration_points;
        }
 
        std::vector<GlobalIndexType> chemical_system_indices;
        chemical_system_indices.reserve(n_integration_points);
        std::transform(_ip_data.begin(), _ip_data.end(),
                       std::back_inserter(chemical_system_indices),
                       [](auto const& ip_data)
                       { return ip_data.chemical_system_id; });
 
        _process_data.chemical_solver_interface->computeSecondaryVariable(
            ele_id, chemical_system_indices);
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_integration_method, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_ip_data, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, ProcessLib::ComponentTransport::ComponentTransportProcessData::chemical_solver_interface, ProcessLib::ComponentTransport::ComponentTransportProcessData::chemically_induced_porosity_change, ChemistryLib::ChemicalSolverInterface::computeSecondaryVariable(), MaterialPropertyLib::MaterialSpatialDistributionMap::getMedium(), NumLib::GenericIntegrationMethod::getNumberOfPoints(), ProcessLib::ComponentTransport::ComponentTransportProcessData::media_map, ProcessLib::ComponentTransport::ComponentTransportProcessData::mesh_prop_porosity, and ChemistryLib::ChemicalSolverInterface::updatePorosityPostReaction().

◆ computeSecondaryVariableConcrete()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::computeSecondaryVariableConcrete	(	double const	t,
		double const	,
		Eigen::VectorXd const &	local_x,
		Eigen::VectorXd const &	)

inlineoverridevirtual

Reimplemented from ProcessLib::LocalAssemblerInterface.

Definition at line 1834 of file ComponentTransportFEM.h.

    {
        auto const local_p =
            local_x.template segment<pressure_size>(pressure_index);
        auto const local_C = local_x.template segment<concentration_size>(
            first_concentration_index);
 
        std::vector<double> ele_velocity;
        calculateIntPtDarcyVelocity(t, local_p, local_C, ele_velocity);
 
        auto const n_integration_points =
            _integration_method.getNumberOfPoints();
        auto const ele_velocity_mat =
            MathLib::toMatrix(ele_velocity, GlobalDim, n_integration_points);
 
        auto const ele_id = _element.getID();
        Eigen::Map<LocalVectorType>(
            &(*_process_data.mesh_prop_velocity)[ele_id * GlobalDim],
            GlobalDim) =
            ele_velocity_mat.rowwise().sum() / n_integration_points;
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_element, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_integration_method, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::calculateIntPtDarcyVelocity(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::first_concentration_index, MeshLib::Element::getID(), NumLib::GenericIntegrationMethod::getNumberOfPoints(), ProcessLib::ComponentTransport::ComponentTransportProcessData::mesh_prop_velocity, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::pressure_index, and MathLib::toMatrix().

◆ getFlux()

template<typename ShapeFunction , int GlobalDim>

Eigen::Vector3d ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getFlux	(	MathLib::Point3d const &	,
		double const	,
		std::vector< double > const &	) const

inlineoverridevirtual

Computes the flux in the point p_local_coords that is given in local coordinates using the values from local_x. Fits to monolithic scheme.

Reimplemented from ProcessLib::LocalAssemblerInterface.

Definition at line 1772 of file ComponentTransportFEM.h.

    {
        auto const local_p = Eigen::Map<const NodalVectorType>(
            &local_x[pressure_index], pressure_size);
        auto const local_C = Eigen::Map<const NodalVectorType>(
            &local_x[first_concentration_index], concentration_size);
 
        // Eval shape matrices at given point
        // Note: Axial symmetry is set to false here, because we only need dNdx
        // here, which is not affected by axial symmetry.
        auto const shape_matrices =
            NumLib::computeShapeMatrices<ShapeFunction, ShapeMatricesType,
                                         GlobalDim>(
                _element, false /*is_axially_symmetric*/,
                std::array{pnt_local_coords})[0];
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
        auto const& b =
            _process_data
                .projected_specific_body_force_vectors[_element.getID()];
 
        MaterialPropertyLib::VariableArray vars;
 
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        auto const& phase = medium.phase("AqueousLiquid");
 
        // local_x contains the local concentration and pressure values
        double c_int_pt;
        NumLib::shapeFunctionInterpolate(local_C, shape_matrices.N, c_int_pt);
        vars.concentration = c_int_pt;
 
        double p_int_pt;
        NumLib::shapeFunctionInterpolate(local_p, shape_matrices.N, p_int_pt);
        vars.liquid_phase_pressure = p_int_pt;
 
        // TODO (naumov) Temporary value not used by current material models.
        // Need extension of secondary variables interface.
        double const dt = std::numeric_limits<double>::quiet_NaN();
        auto const K = MaterialPropertyLib::formEigenTensor<GlobalDim>(
            medium[MaterialPropertyLib::PropertyType::permeability].value(
                vars, pos, t, dt));
 
        auto const mu = phase[MaterialPropertyLib::PropertyType::viscosity]
                            .template value<double>(vars, pos, t, dt);
        GlobalDimMatrixType const K_over_mu = K / mu;
 
        GlobalDimVectorType q = -K_over_mu * shape_matrices.dNdx * local_p;
        auto const rho_w = phase[MaterialPropertyLib::PropertyType::density]
                               .template value<double>(vars, pos, t, dt);
        if (_process_data.has_gravity)
        {
            q += K_over_mu * rho_w * b;
        }
        Eigen::Vector3d flux(0.0, 0.0, 0.0);
        flux.head<GlobalDim>() = rho_w * q;
        return flux;
    }

◆ getHeatEnergyCoefficient()

template<typename ShapeFunction , int GlobalDim>

double ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getHeatEnergyCoefficient	(	MaterialPropertyLib::VariableArray const &	vars,
		const double	porosity,
		const double	fluid_density,
		const double	specific_heat_capacity_fluid,
		ParameterLib::SpatialPosition const &	pos,
		double const	t,
		double const	dt )

inlineprivate

Definition at line 2024 of file ComponentTransportFEM.h.

    {
        auto const& medium =
            *_process_data.media_map.getMedium(this->_element.getID());
        auto const& solid_phase = medium.phase("Solid");
 
        auto const specific_heat_capacity_solid =
            solid_phase
                .property(
                    MaterialPropertyLib::PropertyType::specific_heat_capacity)
                .template value<double>(vars, pos, t, dt);
 
        auto const solid_density =
            solid_phase.property(MaterialPropertyLib::PropertyType::density)
                .template value<double>(vars, pos, t, dt);
 
        return solid_density * specific_heat_capacity_solid * (1 - porosity) +
               fluid_density * specific_heat_capacity_fluid * porosity;
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, MaterialPropertyLib::density, MeshLib::Element::getID(), MaterialPropertyLib::MaterialSpatialDistributionMap::getMedium(), ProcessLib::ComponentTransport::ComponentTransportProcessData::media_map, MaterialPropertyLib::Medium::phase(), MaterialPropertyLib::Phase::property(), and MaterialPropertyLib::specific_heat_capacity.

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHeatTransportEquation().

◆ getIntPtDarcyVelocity()

template<typename ShapeFunction , int GlobalDim>

std::vector< double > const & ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getIntPtDarcyVelocity	(	const double	t,
		std::vector< GlobalVector * > const &	x,
		std::vector< NumLib::LocalToGlobalIndexMap const * > const &	dof_table,
		std::vector< double > &	cache ) const

inlineoverridevirtual

Implements ProcessLib::ComponentTransport::ComponentTransportLocalAssemblerInterface.

Definition at line 1646 of file ComponentTransportFEM.h.

    {
        assert(x.size() == dof_table.size());
 
        auto const n_processes = x.size();
        std::vector<std::vector<double>> local_x;
        local_x.reserve(n_processes);
 
        for (std::size_t process_id = 0; process_id < n_processes; ++process_id)
        {
            auto const indices =
                NumLib::getIndices(_element.getID(), *dof_table[process_id]);
            assert(!indices.empty());
            local_x.push_back(x[process_id]->get(indices));
        }
 
        // only one process, must be monolithic.
        if (n_processes == 1)
        {
            auto const local_p = Eigen::Map<const NodalVectorType>(
                &local_x[0][pressure_index], pressure_size);
            auto const local_C = Eigen::Map<const NodalVectorType>(
                &local_x[0][first_concentration_index], concentration_size);
            return calculateIntPtDarcyVelocity(t, local_p, local_C, cache);
        }
 
        // multiple processes, must be staggered.
        {
            constexpr int pressure_process_id = 0;
            constexpr int concentration_process_id = 1;
            auto const local_p = Eigen::Map<const NodalVectorType>(
                &local_x[pressure_process_id][0], pressure_size);
            auto const local_C = Eigen::Map<const NodalVectorType>(
                &local_x[concentration_process_id][0], concentration_size);
            return calculateIntPtDarcyVelocity(t, local_p, local_C, cache);
        }
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_element, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::calculateIntPtDarcyVelocity(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::concentration_size, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::first_concentration_index, MeshLib::Element::getID(), NumLib::getIndices(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::pressure_index, and ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::pressure_size.

◆ getIntPtMolarFlux()

template<typename ShapeFunction , int GlobalDim>

std::vector< double > const & ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getIntPtMolarFlux	(	const double	t,
		std::vector< GlobalVector * > const &	x,
		std::vector< NumLib::LocalToGlobalIndexMap const * > const &	dof_tables,
		std::vector< double > &	cache,
		int const	component_id ) const

inlineoverridevirtual

Implements ProcessLib::ComponentTransport::ComponentTransportLocalAssemblerInterface.

Definition at line 1897 of file ComponentTransportFEM.h.

    {
        std::vector<double> local_x_vec;
 
        auto const n_processes = x.size();
        for (std::size_t process_id = 0; process_id < n_processes; ++process_id)
        {
            auto const indices =
                NumLib::getIndices(_element.getID(), *dof_tables[process_id]);
            assert(!indices.empty());
            auto const local_solution = x[process_id]->get(indices);
            local_x_vec.insert(std::end(local_x_vec),
                               std::begin(local_solution),
                               std::end(local_solution));
        }
        auto const local_x = MathLib::toVector(local_x_vec);
 
        auto const p = local_x.template segment<pressure_size>(pressure_index);
        auto const c = local_x.template segment<concentration_size>(
            first_concentration_index + component_id * concentration_size);
 
        auto const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        cache.clear();
        auto cache_mat = MathLib::createZeroedMatrix<
            Eigen::Matrix<double, GlobalDim, Eigen::Dynamic, Eigen::RowMajor>>(
            cache, GlobalDim, n_integration_points);
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        auto const& b =
            _process_data
                .projected_specific_body_force_vectors[_element.getID()];
 
        MaterialPropertyLib::VariableArray vars;
 
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
        auto const& phase = medium.phase("AqueousLiquid");
 
        auto const& component = phase.component(
            _transport_process_variables[component_id].get().getName());
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        for (unsigned ip = 0; ip < n_integration_points; ++ip)
        {
            auto const& ip_data = _ip_data[ip];
            auto const& dNdx = ip_data.dNdx;
            auto const& N = Ns[ip];
            auto const& phi = ip_data.porosity;
 
            pos.setIntegrationPoint(ip);
 
            double const p_ip = N.dot(p);
            double const c_ip = N.dot(c);
 
            vars.concentration = c_ip;
            vars.liquid_phase_pressure = p_ip;
            vars.porosity = phi;
 
            double const dt = std::numeric_limits<double>::quiet_NaN();
 
            auto const& k = MaterialPropertyLib::formEigenTensor<GlobalDim>(
                medium[MaterialPropertyLib::PropertyType::permeability].value(
                    vars, pos, t, dt));
            auto const mu = phase[MaterialPropertyLib::PropertyType::viscosity]
                                .template value<double>(vars, pos, t, dt);
            auto const rho = phase[MaterialPropertyLib::PropertyType::density]
                                 .template value<double>(vars, pos, t, dt);
 
            // Darcy flux
            GlobalDimVectorType const q =
                _process_data.has_gravity
                    ? GlobalDimVectorType(-k / mu * (dNdx * p - rho * b))
                    : GlobalDimVectorType(-k / mu * dNdx * p);
 
            auto const alpha_T = medium.template value<double>(
                MaterialPropertyLib::PropertyType::transversal_dispersivity);
            auto const alpha_L = medium.template value<double>(
                MaterialPropertyLib::PropertyType::longitudinal_dispersivity);
            auto const Dp = MaterialPropertyLib::formEigenTensor<GlobalDim>(
                component[MaterialPropertyLib::PropertyType::pore_diffusion]
                    .value(vars, pos, t, dt));
 
            // Hydrodynamic dispersion
            GlobalDimMatrixType const D = NumLib::computeHydrodynamicDispersion(
                _process_data.stabilizer, _element.getID(), Dp, q, phi, alpha_T,
                alpha_L);
 
            cache_mat.col(ip).noalias() = q * c_ip - D * dNdx * c;
        }
 
        return cache;
    }

◆ getLocalTemperature()

template<typename ShapeFunction , int GlobalDim>

NodalVectorType ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getLocalTemperature	(	double const	t,
		Eigen::VectorXd const &	local_x )

inlineprivate

Definition at line 2089 of file ComponentTransportFEM.h.

    {
        NodalVectorType local_T;
        if (_process_data.isothermal)
        {
            if (_process_data.temperature)
            {
                local_T = _process_data.temperature->getNodalValuesOnElement(
                    _element, t);
            }
            else
            {
                local_T = NodalVectorType::Zero(temperature_size);
            }
        }
        else
        {
            local_T =
                local_x.template segment<temperature_size>(temperature_index);
        }
        return local_T;
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_element, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, ParameterLib::Parameter< T >::getNodalValuesOnElement(), ProcessLib::ComponentTransport::ComponentTransportProcessData::isothermal, ProcessLib::ComponentTransport::ComponentTransportProcessData::temperature, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::temperature_index, and ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::temperature_size.

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleComponentTransportEquation(), and ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHydraulicEquation().

◆ getShapeMatrix()

template<typename ShapeFunction , int GlobalDim>

Eigen::Map< const Eigen::RowVectorXd > ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getShapeMatrix ( const unsigned integration_point ) const

inlineoverridevirtual

Provides the shape matrix at the given integration point.

Implements NumLib::ExtrapolatableElement.

Definition at line 1762 of file ComponentTransportFEM.h.

    {
        auto const& N = _process_data.shape_matrix_cache.NsHigherOrder<
            typename ShapeFunction::MeshElement>()[integration_point];
 
        // assumes N is stored contiguously in memory
        return Eigen::Map<const Eigen::RowVectorXd>(N.data(), N.size());
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, NumLib::ShapeMatrixCache::NsHigherOrder(), and ProcessLib::ComponentTransport::ComponentTransportProcessData::shape_matrix_cache.

◆ getThermalConductivityDispersivity()

template<typename ShapeFunction , int GlobalDim>

GlobalDimMatrixType ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getThermalConductivityDispersivity	(	MaterialPropertyLib::VariableArray const &	vars,
		const double	fluid_density,
		const double	specific_heat_capacity_fluid,
		const GlobalDimVectorType &	velocity,
		ParameterLib::SpatialPosition const &	pos,
		double const	t,
		double const	dt )

inlineprivate

Definition at line 2048 of file ComponentTransportFEM.h.

    {
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
 
        auto thermal_conductivity =
            MaterialPropertyLib::formEigenTensor<GlobalDim>(
                medium
                    .property(
                        MaterialPropertyLib::PropertyType::thermal_conductivity)
                    .value(vars, pos, t, dt));
 
        auto const thermal_dispersivity_transversal =
            medium
                .property(MaterialPropertyLib::PropertyType::
                              thermal_transversal_dispersivity)
                .template value<double>();
 
        auto const thermal_dispersivity_longitudinal =
            medium
                .property(MaterialPropertyLib::PropertyType::
                              thermal_longitudinal_dispersivity)
                .template value<double>();
 
        // Thermal conductivity is moved outside and zero matrix is passed
        // instead due to multiplication with fluid's density times specific
        // heat capacity.
        return thermal_conductivity +
               fluid_density * specific_heat_capacity_fluid *
                   NumLib::computeHydrodynamicDispersion(
                       _process_data.stabilizer, _element.getID(),
                       GlobalDimMatrixType::Zero(GlobalDim, GlobalDim),
                       velocity, 0 /* phi */, thermal_dispersivity_transversal,
                       thermal_dispersivity_longitudinal);
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_element, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, NumLib::computeHydrodynamicDispersion(), MeshLib::Element::getID(), MaterialPropertyLib::MaterialSpatialDistributionMap::getMedium(), ProcessLib::ComponentTransport::ComponentTransportProcessData::media_map, ProcessLib::ComponentTransport::ComponentTransportProcessData::stabilizer, and MaterialPropertyLib::thermal_conductivity.

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHeatTransportEquation().

◆ initializeChemicalSystemConcrete()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::initializeChemicalSystemConcrete	(	Eigen::VectorXd const &	local_x,
		double const	t )

inlineoverridevirtual

Implements ProcessLib::ComponentTransport::ComponentTransportLocalAssemblerInterface.

Definition at line 315 of file ComponentTransportFEM.h.

    {
        assert(_process_data.chemical_solver_interface);
 
        auto const& medium =
            *_process_data.media_map.getMedium(_element.getID());
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        for (unsigned ip = 0; ip < n_integration_points; ip++)
        {
            auto& ip_data = _ip_data[ip];
            auto const& N = Ns[ip];
            auto const& chemical_system_id = ip_data.chemical_system_id;
 
            auto const n_component = _transport_process_variables.size();
            std::vector<double> C_int_pt(n_component);
            for (unsigned component_id = 0; component_id < n_component;
                 ++component_id)
            {
                auto const concentration_index =
                    first_concentration_index +
                    component_id * concentration_size;
                auto const local_C =
                    local_x.template segment<concentration_size>(
                        concentration_index);
 
                NumLib::shapeFunctionInterpolate(local_C, N,
                                                 C_int_pt[component_id]);
            }
 
            _process_data.chemical_solver_interface
                ->initializeChemicalSystemConcrete(C_int_pt, chemical_system_id,
                                                   medium, pos, t);
        }
    }

◆ postSpeciationCalculation()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::postSpeciationCalculation	(	std::size_t const	ele_id,
		double const	t,
		double const	dt )

inlineoverridevirtual

Implements ProcessLib::ComponentTransport::ComponentTransportLocalAssemblerInterface.

Definition at line 426 of file ComponentTransportFEM.h.

    {
        if (!_process_data.chemically_induced_porosity_change)
        {
            return;
        }
 
        auto const& medium = *_process_data.media_map.getMedium(ele_id);
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(ele_id);
 
        for (auto& ip_data : _ip_data)
        {
            ip_data.porosity = ip_data.porosity_prev;
 
            _process_data.chemical_solver_interface
                ->updateVolumeFractionPostReaction(ip_data.chemical_system_id,
                                                   medium, pos,
                                                   ip_data.porosity, t, dt);
 
            _process_data.chemical_solver_interface->updatePorosityPostReaction(
                ip_data.chemical_system_id, medium, ip_data.porosity);
        }
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_ip_data, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, ProcessLib::ComponentTransport::ComponentTransportProcessData::chemical_solver_interface, ProcessLib::ComponentTransport::ComponentTransportProcessData::chemically_induced_porosity_change, MaterialPropertyLib::MaterialSpatialDistributionMap::getMedium(), ProcessLib::ComponentTransport::ComponentTransportProcessData::media_map, ParameterLib::SpatialPosition::setElementID(), ChemistryLib::ChemicalSolverInterface::updatePorosityPostReaction(), and ChemistryLib::ChemicalSolverInterface::updateVolumeFractionPostReaction().

◆ postTimestepConcrete()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::postTimestepConcrete	(	Eigen::VectorXd const &	,
		Eigen::VectorXd const &	,
		double const	,
		double const	,
		int const	)

inlineoverridevirtual

Reimplemented from ProcessLib::LocalAssemblerInterface.

Definition at line 2000 of file ComponentTransportFEM.h.

    {
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        for (unsigned ip = 0; ip < n_integration_points; ip++)
        {
            _ip_data[ip].pushBackState();
        }
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_integration_method, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_ip_data, and NumLib::GenericIntegrationMethod::getNumberOfPoints().

◆ setChemicalSystemConcrete()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::setChemicalSystemConcrete	(	Eigen::VectorXd const &	local_x,
		double const	t,
		double	dt )

inlineoverridevirtual

Implements ProcessLib::ComponentTransport::ComponentTransportLocalAssemblerInterface.

Definition at line 361 of file ComponentTransportFEM.h.

    {
        assert(_process_data.chemical_solver_interface);
 
        auto const& medium =
            _process_data.media_map.getMedium(_element.getID());
 
        MaterialPropertyLib::VariableArray vars;
        MaterialPropertyLib::VariableArray vars_prev;
 
        ParameterLib::SpatialPosition pos;
        pos.setElementID(_element.getID());
 
        auto const& Ns =
            _process_data.shape_matrix_cache
                .NsHigherOrder<typename ShapeFunction::MeshElement>();
 
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
 
        for (unsigned ip = 0; ip < n_integration_points; ip++)
        {
            auto& ip_data = _ip_data[ip];
            auto const& N = Ns[ip];
            auto& porosity = ip_data.porosity;
            auto const& porosity_prev = ip_data.porosity_prev;
            auto const& chemical_system_id = ip_data.chemical_system_id;
 
            auto const n_component = _transport_process_variables.size();
            std::vector<double> C_int_pt(n_component);
            for (unsigned component_id = 0; component_id < n_component;
                 ++component_id)
            {
                auto const concentration_index =
                    first_concentration_index +
                    component_id * concentration_size;
                auto const local_C =
                    local_x.template segment<concentration_size>(
                        concentration_index);
 
                NumLib::shapeFunctionInterpolate(local_C, N,
                                                 C_int_pt[component_id]);
            }
 
            {
                vars_prev.porosity = porosity_prev;
 
                porosity =
                    _process_data.chemically_induced_porosity_change
                        ? porosity_prev
                        : medium
                              ->property(
                                  MaterialPropertyLib::PropertyType::porosity)
                              .template value<double>(vars, vars_prev, pos, t,
                                                      dt);
 
                vars.porosity = porosity;
            }
 
            _process_data.chemical_solver_interface->setChemicalSystemConcrete(
                C_int_pt, chemical_system_id, medium, vars, pos, t, dt);
        }
    }

◆ setChemicalSystemID()

template<typename ShapeFunction , int GlobalDim>

void ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::setChemicalSystemID ( std::size_t const )

inlineoverridevirtual

Implements ProcessLib::ComponentTransport::ComponentTransportLocalAssemblerInterface.

Definition at line 295 of file ComponentTransportFEM.h.

    {
        assert(_process_data.chemical_solver_interface);
        // chemical system index map
        auto& chemical_system_index_map =
            _process_data.chemical_solver_interface->chemical_system_index_map;
 
        unsigned const n_integration_points =
            _integration_method.getNumberOfPoints();
        for (unsigned ip = 0; ip < n_integration_points; ip++)
        {
            _ip_data[ip].chemical_system_id =
                chemical_system_index_map.empty()
                    ? 0
                    : chemical_system_index_map.back() + 1;
            chemical_system_index_map.push_back(
                _ip_data[ip].chemical_system_id);
        }
    }

References ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_integration_method, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_ip_data, ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data, ProcessLib::ComponentTransport::ComponentTransportProcessData::chemical_solver_interface, ChemistryLib::ChemicalSolverInterface::chemical_system_index_map, and NumLib::GenericIntegrationMethod::getNumberOfPoints().

Member Data Documentation

◆ _element

template<typename ShapeFunction , int GlobalDim>

MeshLib::Element const& ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_element

private

Definition at line 2015 of file ComponentTransportFEM.h.

◆ _integration_method

template<typename ShapeFunction , int GlobalDim>

NumLib::GenericIntegrationMethod const& ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_integration_method

private

Definition at line 2018 of file ComponentTransportFEM.h.

◆ _ip_data

template<typename ShapeFunction , int GlobalDim>

std::vector<IntegrationPointData<GlobalDimNodalMatrixType> > ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_ip_data

private

Definition at line 2022 of file ComponentTransportFEM.h.

◆ _process_data

template<typename ShapeFunction , int GlobalDim>

ComponentTransportProcessData const& ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_process_data

private

Definition at line 2016 of file ComponentTransportFEM.h.

◆ _transport_process_variables

template<typename ShapeFunction , int GlobalDim>

std::vector<std::reference_wrapper<ProcessVariable> > const ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::_transport_process_variables

private

Definition at line 2020 of file ComponentTransportFEM.h.

◆ concentration_size

template<typename ShapeFunction , int GlobalDim>

const int ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::concentration_size

staticprivate

Initial value:

=

ShapeFunction::NPOINTS

Definition at line 216 of file ComponentTransportFEM.h.

◆ first_concentration_index

template<typename ShapeFunction , int GlobalDim>

const int ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::first_concentration_index = -1

private

Definition at line 212 of file ComponentTransportFEM.h.

◆ pressure_index

template<typename ShapeFunction , int GlobalDim>

const int ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::pressure_index = 0

staticprivate

Definition at line 210 of file ComponentTransportFEM.h.

◆ pressure_size

template<typename ShapeFunction , int GlobalDim>

const int ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::pressure_size = ShapeFunction::NPOINTS

staticprivate

Definition at line 214 of file ComponentTransportFEM.h.

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assemble(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleComponentTransportEquation(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHeatTransportEquation(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHydraulicEquation(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleWithJacobianHydraulicEquation(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getFlux(), and ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getIntPtDarcyVelocity().

◆ temperature_index

template<typename ShapeFunction , int GlobalDim>

const int ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::temperature_index = -1

private

Definition at line 211 of file ComponentTransportFEM.h.

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHeatTransportEquation(), and ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getLocalTemperature().

◆ temperature_size

template<typename ShapeFunction , int GlobalDim>

const int ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::temperature_size = ShapeFunction::NPOINTS

staticprivate

Definition at line 215 of file ComponentTransportFEM.h.

Referenced by ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleComponentTransportEquation(), ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::assembleHeatTransportEquation(), and ProcessLib::ComponentTransport::LocalAssemblerData< ShapeFunction, GlobalDim >::getLocalTemperature().

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

ProcessLib/ComponentTransport/ComponentTransportFEM.h

Detailed Description

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Member Typedef Documentation

◆ GlobalDimMatrixType

◆ GlobalDimNodalMatrixType

◆ GlobalDimVectorType

◆ LocalBlockMatrixType

◆ LocalMatrixType

◆ LocalSegmentVectorType

◆ LocalVectorType

◆ NodalRowVectorType

◆ NodalVectorType

◆ ShapeMatrices

◆ ShapeMatricesType

Constructor & Destructor Documentation

◆ LocalAssemblerData()

Member Function Documentation

◆ assemble()

◆ assembleBlockMatrices()

◆ assembleComponentTransportEquation()

◆ assembleForStaggeredScheme()

◆ assembleHeatTransportEquation()

◆ assembleHydraulicEquation()

◆ assembleKCmCn()

◆ assembleReactionEquationConcrete()

◆ assembleWithJacobianComponentTransportEquation()

◆ assembleWithJacobianForStaggeredScheme()

◆ assembleWithJacobianHydraulicEquation()

◆ calculateIntPtDarcyVelocity()

◆ computeReactionRelatedSecondaryVariable()

◆ computeSecondaryVariableConcrete()

◆ getFlux()

◆ getHeatEnergyCoefficient()

◆ getIntPtDarcyVelocity()

◆ getIntPtMolarFlux()

◆ getLocalTemperature()

◆ getShapeMatrix()

◆ getThermalConductivityDispersivity()

◆ initializeChemicalSystemConcrete()

◆ postSpeciationCalculation()

◆ postTimestepConcrete()

◆ setChemicalSystemConcrete()

◆ setChemicalSystemID()

Member Data Documentation

◆ _element

◆ _integration_method

◆ _ip_data

◆ _process_data

◆ _transport_process_variables

◆ concentration_size

◆ first_concentration_index

◆ pressure_index

◆ pressure_size

◆ temperature_index

◆ temperature_size