CEPS
24.01
Cardiac ElectroPhysiology Simulator
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Bidomain equation main class.
Definition at line 36 of file BidomainProblem.hpp.
#include <BidomainProblem.hpp>
Data Structures | |
struct | UnknownsName |
name of unknowns in a struct More... | |
Public Member Functions | |
BidomainProblem (Geometry *g, InputParameters *=nullptr) | |
Constructor with input strings and geometry. More... | |
~BidomainProblem ()=default | |
Destructor. More... | |
void | defineUnknowns () override |
Transmembrane voltage and extracellular potential. 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... | |
void | run () override |
Run the simulation. 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 | defineBoundaryConditions () override |
For cardiac problems, use the "boundary stimulation" key to create boundary conditions using the same syntax as internal. 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... | |
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... | |
Protected Member Functions inherited from CardiacProblem | |
void | setupWithParameters (InputParameters *params) override |
Sets options from the parameters. More... | |
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 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... | |
Static Protected Attributes inherited from CepsObject | |
static Profiler | m_profiler |
The same profiler for each big object. More... | |
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explicit |
Constructor with input strings and geometry.
Definition at line 35 of file BidomainProblem.cpp.
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default |
Destructor.
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overridevirtual |
Transmembrane voltage and extracellular potential.
Implements AbstractPdeProblem.
Reimplemented in ExtendedBidomainProblem.
Definition at line 43 of file BidomainProblem.cpp.
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overridevirtual |
Returns a vector containing all unknowns that are cardiac unknowns (eg. vm, ui or ue)
Implements CardiacProblem.
Definition at line 57 of file BidomainProblem.cpp.
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overridevirtual |
asks each ionic model to fill the parts of the Vm vector with its initial value, fill ue with same value
Reimplemented from AbstractTimedPdeProblem.
Definition at line 75 of file BidomainProblem.cpp.
Unknown * BidomainProblem::getTMVUnknown | ( | ) | const |
Link to the single unknown of the problem.
Definition at line 63 of file BidomainProblem.cpp.
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overridevirtual |
Returns a vector containing all unknowns that are a TMV (especially useful for bilayer)
Implements CardiacProblem.
Definition at line 51 of file BidomainProblem.cpp.
Unknown * BidomainProblem::getUeUnknown | ( | ) | const |
Link to the single unknown of the problem.
Definition at line 69 of file BidomainProblem.cpp.
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overridevirtual |
Run the simulation.
Reimplemented from AbstractPdeProblem.
Reimplemented in ExtendedBidomainProblem.
Definition at line 90 of file BidomainProblem.cpp.