 |
CEPS
24.01
Cardiac ElectroPhysiology Simulator
|
|
CEPS
24.01
Cardiac ElectroPhysiology Simulator
|
Two coupled monodomains.
Definition at line 36 of file BilayerMonodomainProblem.hpp.
#include <BilayerMonodomainProblem.hpp>
Data Structures | |
| struct | UnknownsName |
| name of unknowns in a struct More... | |
Public Member Functions | |
| BilayerMonodomainProblem (Geometry *g, InputParameters *=nullptr) | |
| Constructor with input strings and geometry. More... | |
| ~BilayerMonodomainProblem ()=default | |
| Destructor. More... | |
| void | defineUnknowns () override |
| A single unknown for transmembrane voltage. 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 * | getTMVUnknown1 () const |
| Link to the single unknown of the problem. More... | |
| Unknown * | getTMVUnknown2 () const |
| Link to the single unknown of the problem. More... | |
| TensorField< GeomCell > * | getSigmaI2 () const |
| Link to intracellular conductivity. More... | |
| TensorField< GeomCell > * | getSigmaE2 () const |
| Link to extracellular conductivity. More... | |
| void | run () override |
| Run the simulation. More... | |
| CepsReal | getCouplingStrength () const |
| coefficient that forces u1=u2 on coupled elements More... | |
| CepsSet< CepsAttribute > | getCouplingAttributes () const |
| where to apply coupling More... | |
| CepsBool | getCouplingAttrNeg () const |
| true if given attribute if for UNcoupled elements More... | |
| void | initializeConductivities () override |
| Sets the myocardium with physical properties for both layers. 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 (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... | |
Protected Member Functions | |
| void | setupWithParameters (InputParameters *p) override |
| Initializes the problem from text input file. 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 | |
| CepsReal | m_couplingStr |
| adds s*(u1-u2) on coupled elements More... | |
| CepsSet< CepsAttribute > | m_couplingAttrs |
| where to apply coupling More... | |
| CepsBool | m_couplingAttrNeg |
| true if given attribute is for UNcoupled elements More... | |
| CepsString | m_sigmaIOptions2 |
| Intracellular conductivity parameters string for layer 2. More... | |
| CepsString | m_sigmaEOptions2 |
| Extracellular conductivity parameters string for layer 2. More... | |
| CepsString | m_fibersOptions2 |
| Text input description. More... | |
| TensorField< GeomCell > * | m_sigmaI2 |
| Intracellular conductivity, defined on cells. More... | |
| TensorField< GeomCell > * | m_sigmaE2 |
| Extracellulat conductivity, defined on cells. 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... | |
|
explicit |
Constructor with input strings and geometry.
Definition at line 33 of file BilayerMonodomainProblem.cpp.
|
default |
Destructor.
|
overridevirtual |
A single unknown for transmembrane voltage.
Implements AbstractPdeProblem.
Definition at line 57 of file BilayerMonodomainProblem.cpp.
|
overridevirtual |
Returns a vector containing all unknowns that are cardiac unknowns (eg. vm, ui or ue)
Implements CardiacProblem.
Definition at line 70 of file BilayerMonodomainProblem.cpp.
| CepsSet< CepsAttribute > BilayerMonodomainProblem::getCouplingAttributes | ( | ) | const |
where to apply coupling
Definition at line 126 of file BilayerMonodomainProblem.cpp.
| CepsBool BilayerMonodomainProblem::getCouplingAttrNeg | ( | ) | const |
true if given attribute if for UNcoupled elements
Definition at line 132 of file BilayerMonodomainProblem.cpp.
| CepsReal BilayerMonodomainProblem::getCouplingStrength | ( | ) | const |
coefficient that forces u1=u2 on coupled elements
Definition at line 120 of file BilayerMonodomainProblem.cpp.
| TensorField< GeomCell > * BilayerMonodomainProblem::getSigmaE2 | ( | ) | const |
Link to extracellular conductivity.
Definition at line 94 of file BilayerMonodomainProblem.cpp.
| TensorField< GeomCell > * BilayerMonodomainProblem::getSigmaI2 | ( | ) | const |
Link to intracellular conductivity.
Definition at line 88 of file BilayerMonodomainProblem.cpp.
| Unknown * BilayerMonodomainProblem::getTMVUnknown1 | ( | ) | const |
Link to the single unknown of the problem.
Definition at line 76 of file BilayerMonodomainProblem.cpp.
| Unknown * BilayerMonodomainProblem::getTMVUnknown2 | ( | ) | const |
Link to the single unknown of the problem.
Definition at line 82 of file BilayerMonodomainProblem.cpp.
|
overridevirtual |
Returns a vector containing all unknowns that are a TMV (especially useful for bilayer)
Implements CardiacProblem.
Definition at line 64 of file BilayerMonodomainProblem.cpp.
|
overridevirtual |
Sets the myocardium with physical properties for both layers.
Reimplemented from CardiacProblem.
Definition at line 138 of file BilayerMonodomainProblem.cpp.
|
overridevirtual |
Run the simulation.
Reimplemented from AbstractPdeProblem.
Definition at line 100 of file BilayerMonodomainProblem.cpp.
|
overrideprotectedvirtual |
Initializes the problem from text input file.
Reimplemented from AbstractPdeProblem.
Definition at line 162 of file BilayerMonodomainProblem.cpp.
|
protected |
true if given attribute is for UNcoupled elements
Definition at line 112 of file BilayerMonodomainProblem.hpp.
|
protected |
where to apply coupling
Definition at line 111 of file BilayerMonodomainProblem.hpp.
|
protected |
adds s*(u1-u2) on coupled elements
Definition at line 110 of file BilayerMonodomainProblem.hpp.
|
protected |
Text input description.
Definition at line 117 of file BilayerMonodomainProblem.hpp.
|
protected |
Extracellulat conductivity, defined on cells.
Definition at line 120 of file BilayerMonodomainProblem.hpp.
|
protected |
Extracellular conductivity parameters string for layer 2.
Definition at line 115 of file BilayerMonodomainProblem.hpp.
|
protected |
Intracellular conductivity, defined on cells.
Definition at line 119 of file BilayerMonodomainProblem.hpp.
|
protected |
Intracellular conductivity parameters string for layer 2.
Definition at line 114 of file BilayerMonodomainProblem.hpp.
1.9.1