CEPS: ExtendedBidomainProblem Class Reference

Detailed Description

Bidomain equation with extracardiac medium main class.

Definition at line 35 of file ExtendedBidomainProblem.hpp.

#include <ExtendedBidomainProblem.hpp>

Inheritance diagram for ExtendedBidomainProblem:

Data Structures
struct	UnknownsName
	name of unknowns in a struct More...

Public Member Functions
	ExtendedBidomainProblem (Geometry g, InputParameters =nullptr)
	Constructor from geometry and possibly parameters. More...

	~ExtendedBidomainProblem ()=default
	Destructor. More...

void	defineUnknowns () override
	Transmembrane voltage (mV) and Extracellular potential (mV) More...

void	run () override
	Run the simulation. More...

const CepsSet< CepsAttribute > &	getExtracardiacAttributes () const
	Get extracardiac attributes. More...

CepsSet< CepsAttribute >	getWholeDomainAttributes () const
	Get all attributes: tissue and extracardiac. More...

virtual CepsSet< CepsAttribute >	getAnodeAttributes () const
	Get cathode attributes if set. More...

virtual CepsSet< CepsAttribute >	getCathodeAttributes () const
	Get cathode attributes if set. More...

CepsBool	hasAnodalCathodalStimulation () const
	Has anodal and cathodal stimulation ? More...

void	defineBoundaryConditions () override
	Define the boundary conditions. More...

CepsBool	requireNullMean () const
	Tells if this problem requires a null mean constraint. More...

Public Member Functions inherited from BidomainProblem
	BidomainProblem (Geometry g, InputParameters =nullptr)
	Constructor with input strings and geometry. More...

	~BidomainProblem ()=default
	Destructor. More...

CepsVector< Unknown * >	getTMVUnknowns () const override
	Returns a vector containing all unknowns that are a TMV (especially useful for bilayer) More...

CepsVector< Unknown * >	getCardiacUnknowns () const override
	Returns a vector containing all unknowns that are cardiac unknowns (eg. vm, ui or ue) More...

Unknown *	getTMVUnknown () const
	Link to the single unknown of the problem. More...

Unknown *	getUeUnknown () const
	Link to the single unknown of the problem. More...

void	getInitialCondition (DHVecPtr v) const override
	asks each ionic model to fill the parts of the Vm vector with its initial value, fill ue with same value More...

Public Member Functions inherited from CardiacProblem
	CardiacProblem (Geometry g, InputParameters params=nullptr)
	Constructor with input file and geometry. More...

	~CardiacProblem () override
	Destructor. More...

void	getInitialCondition (DHVecPtr v) const override
	Zero + asks each ionic model to fill the parts of the Vm vector with its initial value. More...

CepsVector< AbstractIonicModel * >	getIonicModels () const
	Vector of all initd ionic models. More...

ScalarField< DegreeOfFreedom > *	getAm () const
	Link to Am coefficient. More...

ScalarField< DegreeOfFreedom > *	getCm () const
	Link to Cm coefficient. More...

TensorField< GeomCell > *	getSigmaI () const
	Link to intracellular conductivity. More...

TensorField< GeomCell > *	getSigmaE () const
	Link to extracellular conductivity. More...

const CepsSet< CepsAttribute > &	getTissueAttributes () const
	All attributes that localize tissue. More...

void	initializeEquation () override
	Initializes all the elements of the PDE from options. More...

void	initializeCm ()
	Sets the membrane conductivity from the input parameters. More...

void	initializeAm ()
	Set the surface of membrane from input parameters. More...

void	initializeIonicModels ()
	Creates and assign ionic models to tissue regions from input string. More...

virtual void	initializeConductivities ()
	Generates the functors that compute conductivity either from inputs or volume fraction. More...

virtual void	initializeConductivities (CepsString sigmaIOpts, CepsString sigmaEOpts, TensorField< GeomCell > &sigmaI, TensorField< GeomCell > &sigmaE, CepsString fiberOptions, CepsString suffix="")
	Generates the functors that compute conductivity either from inputs or volume fraction. More...

virtual void	initializeStimulations ()
	Generates stimulations and links them to ionic models. Called within define source terms. More...

void	defineSourceTerms () override
	For cardiac problem, only calls initializeStimulation. Can be overriden. More...

Public Member Functions inherited from HeatProblem
	HeatProblem (Geometry g, InputParameters p=nullptr, const CepsMathTensor &k=CepsMathTensor::Identity())
	Constructor from geometry and optional input file. More...

	~HeatProblem () override
	Destructor. More...

void	setupWithParameters (InputParameters *params) override
	Set attributes from input file. Parameters are passed as arguments in case one wants to use other parameters. More...

void	defineUnknowns () override
	Lists the unknowns of the problem (one here) More...

void	defineSourceTerms () override
	Lists the unknowns of the problem (one here) More...

virtual CepsMathTensor	getDiffusionTensor (Unknown *u=nullptr) const
	Diffusion tensor. More...

void	run () override
	Computes the solution. More...

Public Member Functions inherited from AbstractTimedPdeProblem
	AbstractTimedPdeProblem (Geometry geom, InputParameters params=nullptr)
	Constructor with geometry and optional parameters. More...

CepsReal	getStartTime () const override
	pde start time More...

CepsReal	getEndTime () const override
	pde end time More...

CepsReal	getTimeStep () const
	pde time step More...

void	setTimes (CepsReal tStart, CepsReal tEnd, CepsReal dt)
	Define the start and end times, also time step. More...

CepsReal	getSnapshotTime () const override
	Periodicity of outputs, in time units. More...

void	setSnapshotTime (CepsReal st)
	Periodicity of outputs, in time units. More...

virtual void	defineInitialCondition ()
	Sets the pointer on function for initial guess. Here it is set to nullptr, so it will be 0. More...

void	initializeEquation () override
	Initializes equations (unknowns, bc, source term) and creates the spatial discretization This method should be called at the start of run() methods. More...

CepsArray2< CepsArray3< CepsArray3< CepsReal > > >	getErrors () const
	Get the errors. More...

CepsBool	canComputeErrorAtTime (CepsReal t) const
	Tells if either analytic solution or reference solution has a snapshot at time t. More...

Public Member Functions inherited from AbstractPdeProblem
	AbstractPdeProblem (Geometry geom, InputParameters params=nullptr)
	Constructor with geometry and optional parameters. More...

virtual	~AbstractPdeProblem ()
	destructor More...

	AbstractPdeProblem (const AbstractPdeProblem &that)=delete
	No copy constructor. More...

AbstractPdeProblem &	operator= (const AbstractPdeProblem &that)=delete
	No assignment operator. More...

InputParameters *	getParameters () const
	Text parameters. More...

void	setProblemName (const CepsString &name)
	Set the name of the problem. More...

CepsString	getProblemName () const
	Get the name of the problem. More...

Geometry *	getGeometry () const
	Link to geometry on which the pb is defined. More...

AbstractDiscretization *	getSpatialDiscretization () const
	Link to the spatial discretization (FE, FV, etc) More...

void	setSpatialDiscretization (AbstractDiscretization *discr)
	Link to the spatial discretization (FE, FV, etc) More...

void	createSpatialDiscretization ()
	Compute the discretization structure. More...

const CepsVector< Unknown * > &	getUnknowns () const
	List of unknowns of the pb. More...

Unknown *	getUnknown (const CepsString &label) const
	Get an unknown by its name. More...

Unknown *	getUnknown (CepsUnknownIndex uid) const
	Get an unknown by its id. More...

CepsVector< Unknown * >	getSpatialUnknowns () const
	A vector of all unknowns of pb defined on cells or points. More...

CepsVector< Unknown * >	getZeroDUnknowns () const
	A vector of all zeroD unknowns of the pb. More...

const CepsVector< UnknownInteraction * > &	getUnknownsInteractions () const
	All the interactions between unknowns. More...

CepsBool	unknownsInteract (Unknown u1, Unknown u2, const CepsSet< CepsAttribute > &attrs={CepsUniversal}) const
	Tells if unknowns interact on an entity with attributes. More...

CepsBool	ignoreZeroDUnknownsForError () const
	Tells if 0D must not be taken into account in error computation. More...

CepsBool	hasAnalyticSolution () const
	Tells if there is an analytic or reference solution. More...

ScalarFunction *	getAnalyticSolution () const
	Pointer on analytic or refScalarFunction solution. More...

virtual void	defineAnalyticSolution ()
	Set directly the analytic function, default sets no solution, unless there is a collection of reference solution files, provided at init or from parameters. More...

void	setReferenceSolution (const CepsString &baseFiles, CepsReal snapDt)
	Externally define the referece solution from files. Can be used for convergence tests. More...

CepsBool	usesReferenceSolution () const
	Tells if analytic solution and if it is loaded from files. More...

CepsReal	getReferenceSolutionOutputPeriod () const
	Output dt of reference. More...

FunctionDictionary *	getFunctionDictionary () const
	Get functions manager. More...

void	setFunctionDictionary (FunctionDictionary *)
	Set functions manager. More...

BoundaryConditionManager *	getBoundaryConditionManager () const
	Get boundary condition manager. More...

void	setBoundaryConditionManager (BoundaryConditionManager *bcm)
	Set boundary condition manager. More...

SourceTermManager *	getSourceTermManager () const
	Get boundary condition manager. More...

void	setSourceTermManager (SourceTermManager *stm)
	Set boundary condition manager. More...

CepsString	getOutputFileBase () const
	Output file name includes the directory. More...

void	setOutputFileBase (CepsString fileName)
	Output file name includes the directory. More...

CepsOutputFormat	getOutputFormat () const
	Tells if output is binary or ascii. More...

void	setOutputFormat (CepsOutputFormat opt)
	Enable/disable binary output. More...

CepsBool	writesGlobalIndices () const
	Tells if global indices are written on top of solution. More...

void	writeGlobalIndices (CepsBool opt)
	Activate/deactivate global indices writing. More...

CepsVector< CepsReal3D >	getProbePoints () const
	Returns points where single data output should be written. More...

Public Member Functions inherited from CepsObject
	CepsObject ()=default
	default constructor More...

	CepsObject (const CepsObject &)=default
	Copy constructor. More...

virtual	~CepsObject ()=default
	Destructor. More...

CepsObject &	operator= (const CepsObject &)=default
	Assignment operator. More...

CepsObject *	toBaseObject ()
	Returns a pointer to CepsObject class. More...

const CepsObject *	toBaseObject () const
	Returns a pointer to CepsObject class, const version. More...

Profiler *	getProfiler () const
	Access to profiler. More...

Protected Member Functions
void	setupWithParameters (InputParameters *params) override
	Sets options from the parameters. More...

Protected Member Functions inherited from CardiacProblem
void	createFibersAndConductivities (CepsString fiberOptions, TensorField< GeomCell > &sigmaI, TensorField< GeomCell > &sigmaE, CepsString suffix="")
	Creates the entries in the dictionary for each direction of fibers from file This is splitted from initializeConductivities for BilayerMonodomain where several fiber orientations exist per cell. More...

Protected Member Functions inherited from AbstractPdeProblem
void	addUnknown (const CepsString &label, CepsSet< CepsAttribute > attrs={}, CepsLocationFlag flag=CepsLocationFlag::Point, const CepsString &unit="")
	Register a new unknown. More...

void	addZeroDUnknown (CepsString label, const CepsString &unit="")
	Register a new unknown, defined outside of geometry. More...

void	addUnknownInteraction (CepsString label1, CepsString label2, CepsSet< CepsAttribute > attrs={})
	Register interaction between unknowns. Also sets the interaction within Unknown instances label1 and label2. More...

Protected Attributes
CepsString	m_extMediaAttrsOpts
	Text input for extracardiac regions attributes. More...

CepsSet< CepsAttribute >	m_extMediaAttrs
	Extracardiac regions attributes. More...

CepsString	m_biElecStimOpts
	Anodal and cathodal stimulation parameters, disabled if empty. More...

CepsString	m_robinCoeffs
	Robin coefficients. More...

CepsString	m_anodeAttrsOpts
	Text input for anode attributes. More...

CepsSet< CepsAttribute >	m_anodeAttrs
	Anode attributes. More...

CepsString	m_cathodeAttrsOpts
	Text input for cathode attributes. More...

CepsSet< CepsAttribute >	m_cathodeAttrs
	Cathode attributes. More...

Protected Attributes inherited from CardiacProblem
CepsString	m_CmOptions
	Options for membrance capacitance. More...

CepsString	m_AmOptions
	Options for membrane surface. More...

CepsString	m_ionOptions
	Options for ionic models. More...

CepsString	m_fibersOptions
	Options for fiber orientation. More...

CepsString	m_sigmaIOptions
	Options for intracellular conductivity. More...

CepsString	m_sigmaEOptions
	Options for extracellulat conductivity. More...

CepsString	m_volFracOptions
	Options for volume fraction. More...

CepsString	m_volFracItpFileI
	Options for volume fraction. More...

CepsString	m_volFracItpFileE
	Options for volume fraction. More...

CepsString	m_stimOptions
	Options for stimulation. More...

CepsString	m_bcStimOptions
	Options for stimulation, on boundary. More...

CepsSet< CepsAttribute >	m_tissueAttributes
	Identifier for the tissue region, default {-1}. More...

ScalarField< DegreeOfFreedom > *	m_Cm
	Membrane capacitance, may depend on x and t. More...

ScalarField< DegreeOfFreedom > *	m_Am
	Surface (cm2) of cell membrane per cm3 of myocardium. More...

CepsVector< AbstractIonicModel * >	m_ionicModels
	All ionic models defined on the tissue. More...

TensorField< GeomCell > *	m_sigmaI
	Intracellular conductivity, defined on cells. More...

TensorField< GeomCell > *	m_sigmaE
	Extracellulat conductivity, defined on cells. More...

ScalarField< GeomCell > *	m_volFrac
	Fraction of tissue made of valid myocytes. More...

Protected Attributes inherited from HeatProblem
CepsMathTensor	m_k
	Diffusion tensor. More...

Protected Attributes inherited from AbstractTimedPdeProblem
CepsReal	m_pdeStartTime
	Initial time. More...

CepsReal	m_pdeEndTime
	End time. More...

CepsReal	m_pdeTimeStep
	Time Step for the PDE. More...

CepsReal	m_pdeSnapshotTime
	Periodicity of outputs. More...

ScalarFunction *	m_initialCondition
	Function defining the initial condition, which is 0 if pointer is null. More...

CepsArray2< CepsArray3< CepsArray3< CepsReal > > >	m_errors
	Will store Linf, L1 and L2 relative errors. More...

Protected Attributes inherited from AbstractPdeProblem
CepsString	m_name
	Name of the problem. More...

Geometry *	m_geom
	Link to geometry on which the pb is defined. More...

InputParameters *	m_parameters
	Input file data. More...

AbstractDiscretization *	m_discr
	Discretization method (eg FE for now) More...

CepsBool	m_ownedDiscr
	True if instance used new to create discretization. More...

CepsVector< Unknown * >	m_unknowns
	All maths unknowns of the problem. More...

CepsVector< UnknownInteraction * >	m_unknownsInteractions
	Describes how unknowns interact. More...

ScalarFunction *	m_analyticSolution
	analytic or reference solution More...

CepsBool	m_ownedRefSol
	Flag for reference ownership. More...

CepsString	m_refSolFiles
	base name of reference solution file, if any More...

CepsReal	m_refSolSnapDt
	reference solution output period More...

FunctionDictionary *	m_functions
	Collection of custom functions. More...

BoundaryConditionManager *	m_boundaryConditions
	All BCs should be there. More...

SourceTermManager *	m_sourceTerms
	All source terms. More...

CepsBool	m_ownedFunctions
	True if instance used new to create dictionary. More...

CepsBool	m_ownedBCs
	True if instance used new to create BC manager. More...

CepsBool	m_ownedSrcs
	True if instance used new to create src term manager. More...

CepsString	m_outputFileBase
	File names prefix. More...

CepsOutputFormat	m_outputFormat
	Output format selector. More...

CepsBool	m_writeGlobalIDs
	Writes CEPS indices as well. More...

CepsVector< CepsReal3D >	m_probePoints
	Single point data outputs. More...

CepsBool	m_ignoreZeroDError
	Ignore 0D unknowns when computing errors. More...

Additional Inherited Members
Public Types inherited from AbstractPdeProblem
using	ScalarFunction = ceps::Function< CepsReal(CepsStandardArgs)>
	Typedef for analytic solution. More...

Static Public Attributes inherited from AbstractTimedPdeProblem
static constexpr CepsBool	isStatic = false
	Flag for static/timed. More...

Static Protected Attributes inherited from CepsObject
static Profiler	m_profiler
	The same profiler for each big object. More...