Dune::Copasi Namespace Reference

Namespaces
namespace	Concept
namespace	DiffusionReaction
namespace	ISTL

Classes
class	BitFlags
	Bit flags for enumerators. More...
class	BoundaryEntityMapper
	Mapper of boundary entities. More...
class	CellData
	Container for cell data of a grid view. More...
class	Constraints
	Constraints parser and operator for a leaf basis. More...
class	ExprTkParser
class	FunctorFactory
class	FunctorFactoryParser
struct	is_bitflags
	Bitflag indicator. More...
class	LinearSolver
class	LocalBasisCache
	This class describes a local basis cache. More...
struct	LocalDomain
class	LocalEquations
struct	Model
struct	ModelMultiCompartmentPkTraits
class	MuParser
class	OStreamRedirect
	Helper class to redirect std::ostream to a functor. More...
class	ParameterizedObjectFactoryWrapper
	simple wrapper that captures and exposes the keys of Dune::ParameterizedObjectFactory More...
class	Parser
class	ParserContext
class	SimpleAdaptiveStepper
	Adapt an stepper into a simple adaptive time stepper. More...
class	SymEngineParser
struct	TIFFFile
	Simple tiff file interface. More...
class	TIFFGrayscale
	This class describes a tiff grayscale. More...
class	TimeStepper
	Simple time stepper of one-step operators. More...

Enumerations
enum class	ParserType {   None , SymEngine , SymEngineSBML , MuParser ,   ExprTk }

Functions
template<class Enum >
constexpr std::enable_if_t< is_bitflags_v< Enum >, BitFlags< Enum > >	operator| (Enum lhs, Enum rhs)
	Bitwise or between two enums that may be bitflags.
template<class Enum >
constexpr std::enable_if_t< is_bitflags_v< Enum >, BitFlags< Enum > >	operator& (Enum lhs, Enum rhs)
	Bitwise and between two enums that may be bitflags.
template<class Enum >
constexpr std::enable_if_t< is_bitflags_v< Enum >, BitFlags< Enum > >	operator^ (Enum lhs, Enum rhs)
	Bitwise xor between two enums that may be bitflags.
template<class Enum >
constexpr std::enable_if_t< is_bitflags_v< Enum >, bool >	operator== (Enum lhs, Enum rhs)
	Return true if all flags of both enums (allowed to be bitflags) are equal.
template<class Enum >
constexpr std::enable_if_t< is_bitflags_v< Enum >, bool >	operator!= (Enum lhs, Enum rhs)
template<typename Exception , typename... Args>
auto	format_exception (Exception &&e, fmt::format_string< Args... > format, Args &&... args)
auto	ostream2spdlog ()
	Standard output redirection to spdlog.
template<Dune::Concept::GridView GV, class T >
void	cell_data_parser (const ParameterTree &grid_config, CellData< GV, T > &cell_data)
	Parse data file with cell data and add its values to cell data.
template<class GridView >
std::enable_if_t< Capabilities::hasSingleGeometryType< typename GridView::Grid >::v, bool > constexpr	has_single_geometry_type (const GridView &)
	Determines if grid view has a single geometry type.
template<class GridView >
std::enable_if_t< not Capabilities::hasSingleGeometryType< typename GridView::Grid >::v, bool >	has_single_geometry_type (const GridView &grid_view)
	Determines if grid view has a single geometry type.
template<Concept::MultiDomainGrid MDGrid, class CellDataType = double>
std::tuple< std::unique_ptr< MDGrid >, std::unique_ptr< CellData< typename MDGrid::LevelGridView, CellDataType > > >	make_multi_domain_grid_with_cell_data (Dune::ParameterTree &config, std::shared_ptr< const ParserContext > parser_context={})
	Creates a multi domain grid from a config file From given configuration file with grid and compartment section as described in the program documentation (–grid.* and –compartment.*), this funcition will read or create a grid and its sub-domains (or compartments). It will also assign a unique subdomain 'id' to each compartment in the configuration file. Finally, it will create a cell data with the contents of the gmsh_id if the file was read by gmsh, and the data files parsed with cell_data_parser.
template<Concept::MultiDomainGrid MDGrid>
std::unique_ptr< MDGrid >	make_multi_domain_grid (Dune::ParameterTree &config, std::shared_ptr< const ParserContext > parser_context={})
	Creates a multi domain grid from a config file From given configuration file with grid and compartment section as described in the program documentation (–grid.* and –compartment.*), this funcition will read or create a grid and its sub-domains (or compartments). It will also assign a unique subdomain 'id' to each compartment in the configuration file. Finally, it will create a cell data with the contents of the gmsh_id if the file was read by gmsh, and the data files parsed with cell_data_parser.
template<int dim>
void	mark_stripes (UGGrid< dim > &grid, bool mark_others=true)
	Mark stripes for refinement.
std::unique_ptr< Parser >	make_parser (ParserType parser_type=default_parser)
std::unique_ptr< Parser >	make_parser (std::string_view parser_type)

Variables
std::vector< std::string >	axis_names
template<class T >
constexpr bool	is_bitflags_v = is_bitflags<T>::value
	Alias for Bitflag indicator.
const ParserType	default_parser

Enumeration Type Documentation

ParserType

enum class Dune::Copasi::ParserType

strong

Enumerator
None
SymEngine
SymEngineSBML
MuParser
ExprTk

Function Documentation

cell_data_parser()

template<Dune::Concept::GridView GV, class T >

void Dune::Copasi::cell_data_parser	(	const ParameterTree &	grid_config,
		CellData< GV, T > &	cell_data )

Parse data file with cell data and add its values to cell data.

The format of the file is documented in the config_opts.json. In particular, the cell index set in the file will be assigned to the index set of the grid view used to construct the cell data object. This means that this is mostly useful for leaf grid views and level 0 grid vies. Be careful to choose the correct one!

Author

Dylan Vermoortele

Template Parameters

GV	The grid view type
T	The type of the cell data values

Parameters

grid_config	A config containing sub-sections with the paths for each cell data file
cell_data	A cell data object to store the parsed cell data

format_exception()

template<typename Exception , typename... Args>

auto Dune::Copasi::format_exception ( Exception && e, fmt::format_string< Args... > format, Args &&... args )

inline

has_single_geometry_type() [1/2]

template<class GridView >

std::enable_if_t< Capabilities::hasSingleGeometryType< typename GridView::Grid >::v, bool > constexpr Dune::Copasi::has_single_geometry_type ( const GridView & )

constexpr

Determines if grid view has a single geometry type.

If the grid only knows about one geometry type at compile-time, this function is constexpr and always true. Notice however, that the countrary does not hold and the check is done at run-time.

Parameters

[in]

grid_view

The grid view

Template Parameters

GridView

The grid view type

Returns

True if single geometry type, False otherwise.

has_single_geometry_type() [2/2]

template<class GridView >

std::enable_if_t< not Capabilities::hasSingleGeometryType< typename GridView::Grid >::v, bool > Dune::Copasi::has_single_geometry_type

(

const GridView &

grid_view

)

Determines if grid view has a single geometry type.

If the grid only knows about one geometry type at compile-time, this function is constexpr and always true. Notice however, that the countrary does not hold and the check is done at run-time.

Parameters

[in]

grid_view

The grid view

Template Parameters

GridView

The grid view type

Returns

True if single geometry type, False otherwise.

make_multi_domain_grid()

template<Concept::MultiDomainGrid MDGrid>

std::unique_ptr< MDGrid > Dune::Copasi::make_multi_domain_grid	(	Dune::ParameterTree &	config,
		std::shared_ptr< const ParserContext >	parser_context = {} )

Creates a multi domain grid from a config file From given configuration file with grid and compartment section as described in the program documentation (–grid.* and –compartment.*), this funcition will read or create a grid and its sub-domains (or compartments). It will also assign a unique subdomain 'id' to each compartment in the configuration file. Finally, it will create a cell data with the contents of the gmsh_id if the file was read by gmsh, and the data files parsed with cell_data_parser.

Template Parameters

MDGrid	The type of the multidomain-grid
CellDataType	The type to store values in the cell data object

Parameters

config	The configuration file
parser_context	A parser context to interpret parsed math expression

Returns

std::pair<std::unique_ptr<MDGrid>, std::unique_ptr<CellData<typename MDGrid::LevelGridView, CellDataType>>> Pointer to the resulting grid and cell data

std::unique_ptr<MDGrid> Pointer to the resulting grid

make_multi_domain_grid_with_cell_data()

template<Concept::MultiDomainGrid MDGrid, class CellDataType = double>

std::tuple< std::unique_ptr< MDGrid >, std::unique_ptr< CellData< typename MDGrid::LevelGridView, CellDataType > > > Dune::Copasi::make_multi_domain_grid_with_cell_data	(	Dune::ParameterTree &	config,
		std::shared_ptr< const ParserContext >	parser_context = {} )

Creates a multi domain grid from a config file From given configuration file with grid and compartment section as described in the program documentation (–grid.* and –compartment.*), this funcition will read or create a grid and its sub-domains (or compartments). It will also assign a unique subdomain 'id' to each compartment in the configuration file. Finally, it will create a cell data with the contents of the gmsh_id if the file was read by gmsh, and the data files parsed with cell_data_parser.

Template Parameters

MDGrid	The type of the multidomain-grid
CellDataType	The type to store values in the cell data object

Parameters

config	The configuration file
parser_context	A parser context to interpret parsed math expression

Returns

std::pair<std::unique_ptr<MDGrid>, std::unique_ptr<CellData<typename MDGrid::LevelGridView, CellDataType>>> Pointer to the resulting grid and cell data

make_parser() [1/2]

std::unique_ptr< Parser > Dune::Copasi::make_parser

(

ParserType

parser_type = default_parser

)

make_parser() [2/2]

std::unique_ptr< Parser > Dune::Copasi::make_parser

(

std::string_view

parser_type

)

mark_stripes()

template<int dim>

void Dune::Copasi::mark_stripes	(	UGGrid< dim > &	grid,
		bool	mark_others = true )

Mark stripes for refinement.

If a cube element is surrounded by non-cubes in opposite sides such cube is understood to be part of a stripe of cubes. In such case, this method should mark the grid such that a stripe is a stripe after refinement (e.g. refine in the direction of perpendicular to the non cubes)

Parameters

	grid	The grid
[in]	mark_others	If true, mark non-stripe entities for refinement.

Template Parameters

dim	Dimension of the grid

operator!=()

template<class Enum >

constexpr std::enable_if_t< is_bitflags_v< Enum >, bool > Dune::Copasi::operator!= ( Enum lhs, Enum rhs )

inlineconstexpr

Return true if any flags of both enums (allowed to be bitflags) are different

operator&()

template<class Enum >

constexpr std::enable_if_t< is_bitflags_v< Enum >, BitFlags< Enum > > Dune::Copasi::operator& ( Enum lhs, Enum rhs )

inlineconstexpr

Bitwise and between two enums that may be bitflags.

operator==()

template<class Enum >

constexpr std::enable_if_t< is_bitflags_v< Enum >, bool > Dune::Copasi::operator== ( Enum lhs, Enum rhs )

inlineconstexpr

Return true if all flags of both enums (allowed to be bitflags) are equal.

operator^()

template<class Enum >

constexpr std::enable_if_t< is_bitflags_v< Enum >, BitFlags< Enum > > Dune::Copasi::operator^ ( Enum lhs, Enum rhs )

inlineconstexpr

Bitwise xor between two enums that may be bitflags.

operator|()

template<class Enum >

constexpr std::enable_if_t< is_bitflags_v< Enum >, BitFlags< Enum > > Dune::Copasi::operator| ( Enum lhs, Enum rhs )

inlineconstexpr

Bitwise or between two enums that may be bitflags.

ostream2spdlog()

auto Dune::Copasi::ostream2spdlog ( )

inline

Standard output redirection to spdlog.

During the lifetime of the obtained object, it will redirect every character streamed to std::cout, std::cerr, and std::clog towards the spdlog logging system

Variable Documentation

axis_names

std::vector<std::string> Dune::Copasi::axis_names

extern

default_parser

const ParserType Dune::Copasi::default_parser

extern

is_bitflags_v

template<class T >

constexpr bool Dune::Copasi::is_bitflags_v = is_bitflags<T>::value

constexpr

Alias for Bitflag indicator.