Child class of IonIfBase specialized for each ionic model type. More...

#include <ION_IF.h>

Inheritance diagram for limpet::IonIf< T >:

Collaboration diagram for limpet::IonIf< T >:

Classes
class	LimpetArray
	Utility class for handling arrays of data used by IMPs. More...

Public Member Functions
	IonIf (const IonType &type, Target target, int num_node, const std::vector< std::reference_wrapper< IonType >> &plugins)
	Constructs an IonIf object. More...

	~IonIf ()
	Destroy the IMP. More...

T::params_type *	params () const
	Gets a pointer to the parameter structure for the current target. More...

SvTab &	sv_tab ()
	Gets the SV LimpetArray for the current target. More...

PrivateTab &	ion_private ()
	Gets the ion private LimpetArray for the current target. More...

PrivateVectorTab &	ion_private_vector ()

void *	get_sv_address () override
	Gets the raw address of the SV array for the current target. More...

std::size_t	get_sv_size () const override
	Gets the size of a SV structure. More...

void	set_target (Target target) override
	Set a new execution target for this IMP. More...

void	allocate_model_data ()
	Allocate memory for the IMP data for the current target. More...

void	initialize (double dt, GlobalData_t **impdat) override
	Override of the initialization function to add the initialization of the private structures. More...

void	copy_SVs_from (IonIfBase &other_base, bool alloc) override
	Copy state and private variables from another IMP. More...

void	copy_ion_private (IonIf< T > &other, has_rosenbrock_vector_type)
	Copy the ion private array from `other`. More...

void	copy_ion_private (IonIf< T > &other, has_rosenbrock_type)
	Copy the ion private array from `other`. More...

void	copy_ion_private (IonIf< T > &other, no_rosenbrock_type)
	This function does nothing (overload of copy_ion_private(IonIf<T>&, has_rosenbrock_type)). More...

void	init_ion_private (has_rosenbrock_vector_type)
	Initialize private data. More...

void	init_ion_private (has_rosenbrock_type)
	Initialize private data. More...

void	init_ion_private (no_rosenbrock_type)
	Doesn't do anything. More...

Public Member Functions inherited from limpet::IonIfBase
	IonIfBase (const IonType &type, Target target, int num_node, const std::vector< std::reference_wrapper< IonType >> &plugins)
	Constructor for IonIfBase. More...

virtual	~IonIfBase ()
	Virtual destructor declaration. More...

const IonType &	get_type () const
	Gets this IMP's model type. More...

int	get_num_node () const
	Gets the number of nodes handled by this IMP. More...

std::size_t	get_num_threads () const
	Gets the number of threads used for running this IMP. More...

IonIfBase *	parent () const
	Gets the parent IMP. More...

void	set_parent (IonIfBase *parent)

std::vector< IonIfBase * > &	plugins ()
	Returns a vector containing the plugins of this IMP. More...

uint32_t	get_reqdat () const
	Gets the data flags for this IMP's required data. More...

uint32_t	get_moddat () const
	Gets the data flags for this IMP's modified data. More...

void	set_moddat (uint32_t data)
	Set the data flag for this IMP's modified data. More...

cell_geom &	cgeom ()
	Gets the cell geometry data. More...

float	get_dt () const
	Gets the basic integration time step. More...

void	set_dt (float dt)
	Sets the basic integration time step. More...

ts &	get_tstp ()
	Gets the time stepper. More...

std::vector< LUT > &	tables ()
	Gets the array of state variables. More...

LUT *	tables_d () const
	Gets an array of LUTs. More...

size_t	get_n_tables_d () const
	Gets the size of the array returned by IonIf::tables_d. More...

Target	get_target () const

void	initialize_params ()
	Initializes user modifiable parameters with default values defined in the respective ionic models. More...

void	compute (int start, int end, GlobalData_t **data)
	Perform ionic model computation for 1 time step. More...

char *	fill_buf (char buf, int n, opencarp::Salt_list *l) const
	Appends the state variables to a buffer. More...

int	restore (opencarp::FILE_SPEC in, int n, const int pos, IIF_Mask_t mask, size_t offset, IMPinfo impinfo, const int *loc2canon)
	Reads in the state variables for an IMP. More...

int	dump_luts (bool zipped)
	Dumps array of LUTs to file. More...

void	destroy_luts ()
	Destroys array of LUTs. More...

void	tune (const char im_par, const char plugs, const char *plug_par)
	Tunes specific IMP parameters from files. More...

int	read_svs (FILE *file)
	Reads state variable values for one cell from a file. More...

int	write_svs (FILE *file, int node)

void	copy_plugins_from (IonIfBase &other)
	Copies the plugins of an IMP. More...

void	for_each (const std::function< void(IonIfBase &)> &consumer)
	Executes the `consumer` functions on this IMP and each of its plugins. More...

Additional Inherited Members
Public Attributes inherited from limpet::IonIfBase
int	miifIdx
	imp index within miif More...

Target	_target
	execution target for this IMP More...

Protected Attributes inherited from limpet::IonIfBase
ts	_tstp
	control time stepping More...

Detailed Description

template<typename T>
class limpet::IonIf< T >

Child class of IonIfBase specialized for each ionic model type.

The template parameter T should be an IonType class and should define some type aliases:

params_type: the type of the parameters structure used by the model
state_type: the type of the state variables structure used by the model
private_type: the type of the private structure used by the model (or void if none if used)

Definition at line 497 of file ION_IF.h.

Constructor & Destructor Documentation

◆ IonIf()

template<typename T>

limpet::IonIf< T >::IonIf	(	const IonType &	type,
		Target	target,
		int	num_node,
		const std::vector< std::reference_wrapper< IonType >> &	plugins
	)

inline

Constructs an IonIf object.

Note: see IonIfBase::IonIfBase for explanatiosn on the parameters

This constructor allocated all necessary memory for the IMP

Definition at line 675 of file ION_IF.h.

◆ ~IonIf()

template<typename T>

limpet::IonIf< T >::~IonIf ( )

inline

Destroy the IMP.

Note: This function should deallocate all memory used by the IMP

Definition at line 686 of file ION_IF.h.

Member Function Documentation

◆ allocate_model_data()

template<typename T>

void limpet::IonIf< T >::allocate_model_data ( )

inline

Allocate memory for the IMP data for the current target.

Definition at line 778 of file ION_IF.h.

◆ copy_ion_private() [1/3]

template<typename T>

void limpet::IonIf< T >::copy_ion_private	(	IonIf< T > &	other,
		has_rosenbrock_vector_type
	)

inline

Copy the ion private array from other.

Parameters

other IMP to copy the array from

Note: this function is an overload to use for models using the vectorized private data workspace

Definition at line 842 of file ION_IF.h.

◆ copy_ion_private() [2/3]

template<typename T>

void limpet::IonIf< T >::copy_ion_private	(	IonIf< T > &	other,
		has_rosenbrock_type
	)

inline

Copy the ion private array from other.

Parameters

other IMP to copy the array from

Note: this function is an overload to use for models using the private data workspace

Definition at line 859 of file ION_IF.h.

◆ copy_ion_private() [3/3]

template<typename T>

void limpet::IonIf< T >::copy_ion_private	(	IonIf< T > &	other,
		no_rosenbrock_type
	)

inline

This function does nothing (overload of copy_ion_private(IonIf<T>&, has_rosenbrock_type)).

This is used to avoid trying to copy data on models that don't use private data

Definition at line 868 of file ION_IF.h.

◆ copy_SVs_from()

template<typename T>

void limpet::IonIf< T >::copy_SVs_from	(	IonIfBase &	other_base,
		bool	alloc
	)

inlineoverridevirtual

Copy state and private variables from another IMP.

Precondition: other is of the same type as this (IonIf<T>); this handles the same amount of cells as other_base (this->get_num_nodes() == other.get_num_nodes())

Parameters

other_base	IMP to copy the values from (passed as IonIfBase)
alloc	whether to allocate new storage for the copied values

Warning: alloc is deprecated and is not used since the IonIf constructor should always allocate memory, and if the IMPs don't handle the same amount of cells (same size of SV table), the function should throw an exception.

Implements limpet::IonIfBase.

Definition at line 820 of file ION_IF.h.

◆ get_sv_address()

template<typename T>

void* limpet::IonIf< T >::get_sv_address ( )

inlineoverridevirtual

Gets the raw address of the SV array for the current target.

Returns: a raw pointer to the SV array

Implements limpet::IonIfBase.

Definition at line 743 of file ION_IF.h.

◆ get_sv_size()

template<typename T>

std::size_t limpet::IonIf< T >::get_sv_size ( ) const

inlineoverridevirtual

Gets the size of a SV structure.

Returns: the size of the state variable structure

Implements limpet::IonIfBase.

Definition at line 752 of file ION_IF.h.

◆ init_ion_private() [1/3]

template<typename T>

void limpet::IonIf< T >::init_ion_private ( has_rosenbrock_vector_type )

inline

Initialize private data.

Note: Overload for the vectorized private structures

Definition at line 875 of file ION_IF.h.

◆ init_ion_private() [2/3]

template<typename T>

void limpet::IonIf< T >::init_ion_private ( has_rosenbrock_type )

inline

Initialize private data.

Note: Overload for the private structures

Definition at line 896 of file ION_IF.h.

◆ init_ion_private() [3/3]

template<typename T>

void limpet::IonIf< T >::init_ion_private ( no_rosenbrock_type )

inline

Doesn't do anything.

Note: Overload for models without the need for a private structure

Definition at line 909 of file ION_IF.h.

◆ initialize()

template<typename T>

void limpet::IonIf< T >::initialize	(	double	dt,
		GlobalData_t **	impdat
	)

inlineoverridevirtual

Override of the initialization function to add the initialization of the private structures.

Parameters

dt	time step
impdata	data

Note: see IonIfBase::initialize

Reimplemented from limpet::IonIfBase.

Definition at line 801 of file ION_IF.h.

◆ ion_private()

template<typename T>

PrivateTab& limpet::IonIf< T >::ion_private ( )

inline

Gets the ion private LimpetArray for the current target.

Returns: a reference to the ion private array

Definition at line 727 of file ION_IF.h.

Here is the caller graph for this function:

◆ ion_private_vector()

template<typename T>

PrivateVectorTab& limpet::IonIf< T >::ion_private_vector ( )

inline

Definition at line 731 of file ION_IF.h.

Here is the caller graph for this function:

◆ params()

template<typename T>

T::params_type* limpet::IonIf< T >::params ( ) const

inline

Gets a pointer to the parameter structure for the current target.

Returns: a pointer to the parameters structure

Definition at line 702 of file ION_IF.h.

◆ set_target()

template<typename T>

void limpet::IonIf< T >::set_target ( Target target )

inlineoverridevirtual

Set a new execution target for this IMP.

Parameters

target the new target to set

A call to this function will trigger allocation of memory on the new target and a copy of memory from the old target to the new target.

Reimplemented from limpet::IonIfBase.

Definition at line 764 of file ION_IF.h.

◆ sv_tab()

template<typename T>

SvTab& limpet::IonIf< T >::sv_tab ( )

inline

Gets the SV LimpetArray for the current target.

Returns: a reference to the SV array

Definition at line 714 of file ION_IF.h.

Here is the caller graph for this function:

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

physics/limpet/src/ION_IF.h

Classes

Public Member Functions

Additional Inherited Members

Detailed Description

template<typename T> class limpet::IonIf< T >

Constructor & Destructor Documentation

◆ IonIf()

◆ ~IonIf()

Member Function Documentation

◆ allocate_model_data()

◆ copy_ion_private() [1/3]

◆ copy_ion_private() [2/3]

◆ copy_ion_private() [3/3]

◆ copy_SVs_from()

◆ get_sv_address()

◆ get_sv_size()

◆ init_ion_private() [1/3]

◆ init_ion_private() [2/3]

◆ init_ion_private() [3/3]

◆ initialize()

◆ ion_private()

◆ ion_private_vector()

◆ params()

◆ set_target()

◆ sv_tab()

template<typename T>
class limpet::IonIf< T >