#include <model_single_compartment.hh>

Inheritance diagram for Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >:

Public Types
using	State = typename Base::State

using	Grid = typename Traits::Grid

using	TimeQuantity = typename Traits::TimeQuantity

using	ScalarQuantity = typename Traits::RangeQuatinty

using	CompartmentEntitySet = typename Traits::CompartmentEntitySet

using	ScalarFiniteElementMap = typename Traits::ScalarFiniteElementMap

using	ScalarMergingStrategy = typename Traits::ScalarMergingStrategy

using	ScalarPreBasis = PDELab::PreBasis< ScalarMergingStrategy, ScalarFiniteElementMap, Constraints< CompartmentEntitySet > >

using	CompartmentMergingStrategy = typename Traits::CompartmentMergingStrategy

using	CompartmentPreBasis = PDELab::PreBasisVector< CompartmentMergingStrategy, ScalarPreBasis >

using	ResidualQuantity = ScalarQuantity

using	GridFunction = typename Base::GridFunction

Public Types inherited from Dune::Copasi::Model< Traits::Grid, Traits::CompartmentEntitySet, Traits::RangeQuatinty, Traits::TimeQuantity >
using	Grid = Grid_

using	GridView = GridView_

using	TimeQuantity = Traits::TimeQuantity

using	RangeQuatinty = Traits::RangeQuatinty

using	GridFunction = Dune::Functions::GridViewFunction< RangeQuatinty(typename GridView::template Codim< 0 >::Geometry::GlobalCoordinate), GridView >

Public Member Functions
	ModelSingleCompartment (std::shared_ptr< const FunctorFactory< Grid::dimensionworld > > functor_factory, std::shared_ptr< const CellData< typename Grid::LeafGridView, ScalarQuantity > > cell_data=nullptr)

std::unique_ptr< State >	make_state (const std::shared_ptr< const Grid > &, const ParameterTree &) const override

void	interpolate (State &, const std::unordered_map< std::string, GridFunction > &) const override

std::unordered_map< std::string, GridFunction >	make_initial (const Grid &, const ParameterTree &) const override

GridFunction	make_compartment_function (const std::shared_ptr< const State > &, std::string_view) const override

std::unique_ptr< PDELab::OneStep< State > >	make_step_operator (const State &, const ParameterTree &) const override

void	write_vtk (const State &, const std::filesystem::path &, bool=true) const override

std::map< std::string, double >	reduce (const State &, const ParameterTree &, const ParameterTree &={}) const override

Public Member Functions inherited from Dune::Copasi::Model< Traits::Grid, Traits::CompartmentEntitySet, Traits::RangeQuatinty, Traits::TimeQuantity >
	Model ()=default

	Model (const Model &)=delete

	Model (Model &&)=delete

Model &	operator= (const Model &)=delete

Model &	operator= (Model &&)=delete

virtual	~Model ()=default

virtual std::unique_ptr< State >	make_state (const std::shared_ptr< const Grid > &, const ParameterTree &) const=0

virtual void	interpolate (State &, const std::unordered_map< std::string, GridFunction > &) const=0

virtual std::unordered_map< std::string, GridFunction >	make_initial (const Grid &, const ParameterTree &) const=0

GridFunction	make_compartment_function (const State &state, std::string_view name) const

virtual GridFunction	make_compartment_function (const std::shared_ptr< const State > &, std::string_view) const=0

virtual std::nullptr_t	make_membrane_function (const State &, std::string_view) const

virtual std::nullptr_t	make_membrane_function (const std::shared_ptr< const State > &, std::string_view) const

virtual void	write_vtk (const State &, const std::filesystem::path &, bool) const

virtual std::unique_ptr< PDELab::OneStep< State > >	make_step_operator (const State &, const ParameterTree &) const=0

virtual std::map< std::string, double >	reduce (const State &, const ParameterTree &, const ParameterTree &={}) const

Static Public Member Functions
static CompartmentPreBasis	make_compartment_pre_basis (const CompartmentEntitySet &, std::string_view, const std::vector< std::string > &, const ParameterTree &={}, std::shared_ptr< const FunctorFactory< Grid::dimensionworld > >=nullptr)

Member Typedef Documentation

◆ CompartmentEntitySet

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::CompartmentEntitySet = typename Traits::CompartmentEntitySet

◆ CompartmentMergingStrategy

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::CompartmentMergingStrategy = typename Traits::CompartmentMergingStrategy

◆ CompartmentPreBasis

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::CompartmentPreBasis = PDELab::PreBasisVector<CompartmentMergingStrategy, ScalarPreBasis>

◆ Grid

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::Grid = typename Traits::Grid

◆ GridFunction

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::GridFunction = typename Base::GridFunction

◆ ResidualQuantity

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::ResidualQuantity = ScalarQuantity

◆ ScalarFiniteElementMap

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::ScalarFiniteElementMap = typename Traits::ScalarFiniteElementMap

◆ ScalarMergingStrategy

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::ScalarMergingStrategy = typename Traits::ScalarMergingStrategy

◆ ScalarPreBasis

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::ScalarPreBasis = PDELab::PreBasis<ScalarMergingStrategy, ScalarFiniteElementMap, Constraints<CompartmentEntitySet> >

◆ ScalarQuantity

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::ScalarQuantity = typename Traits::RangeQuatinty

◆ State

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::State = typename Base::State

◆ TimeQuantity

template<class Traits >

using Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::TimeQuantity = typename Traits::TimeQuantity

Constructor & Destructor Documentation

◆ ModelSingleCompartment()

template<class Traits >

Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::ModelSingleCompartment	(	std::shared_ptr< const FunctorFactory< Grid::dimensionworld > >	functor_factory,
		std::shared_ptr< const CellData< typename Grid::LeafGridView, ScalarQuantity > >	cell_data = `nullptr`
	)

inlineexplicit

Member Function Documentation

◆ interpolate()

template<class Traits >

void Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::interpolate	(	State &	state,
		const std::unordered_map< std::string, GridFunction > &	initial
	)		const

override

◆ make_compartment_function()

template<class Traits >

ModelSingleCompartment< Traits >::GridFunction Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::make_compartment_function	(	const std::shared_ptr< const State > &	state,
		std::string_view	name
	)		const

override

◆ make_compartment_pre_basis()

template<class Traits >

auto Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::make_compartment_pre_basis	(	const CompartmentEntitySet &	entity_set,
		std::string_view	compartment_name,
		const std::vector< std::string > &	scalar_field_names,
		const ParameterTree &	scalar_fields_config = `{}`,
		std::shared_ptr< const FunctorFactory< Grid::dimensionworld > >	functor_factory = `nullptr`
	)

static

◆ make_initial()

template<class Traits >

auto Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::make_initial	(	const Grid &	grid,
		const ParameterTree &	config
	)		const

override

◆ make_state()

template<class Traits >

auto Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::make_state	(	const std::shared_ptr< const Grid > &	grid,
		const ParameterTree &	config
	)		const

override

◆ make_step_operator()

template<class Traits >

auto Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::make_step_operator	(	const State &	state,
		const ParameterTree &	config
	)		const

override

◆ reduce()

template<class Traits >

auto Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::reduce	(	const State &	state,
		const ParameterTree &	reduce_cfg,
		const ParameterTree &	domain_cfg = `{}`
	)		const

override

◆ write_vtk()

template<class Traits >

void Dune::Copasi::DiffusionReaction::ModelSingleCompartment< Traits >::write_vtk	(	const State &	state,
		const std::filesystem::path &	path,
		bool	append = `true`
	)		const

override

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

dune/copasi/model/diffusion_reaction/model_single_compartment.hh
dune/copasi/model/diffusion_reaction/model_single_compartment.impl.hh

Public Types

Public Member Functions

Static Public Member Functions

Member Typedef Documentation

◆ CompartmentEntitySet

◆ CompartmentMergingStrategy

◆ CompartmentPreBasis

◆ Grid

◆ GridFunction

◆ ResidualQuantity

◆ ScalarFiniteElementMap

◆ ScalarMergingStrategy

◆ ScalarPreBasis

◆ ScalarQuantity

◆ State

◆ TimeQuantity

Constructor & Destructor Documentation

◆ ModelSingleCompartment()

Member Function Documentation

◆ interpolate()

◆ make_compartment_function()

◆ make_compartment_pre_basis()

◆ make_initial()

◆ make_state()

◆ make_step_operator()

◆ reduce()

◆ write_vtk()