 |
CEPS
24.01
Cardiac ElectroPhysiology Simulator
|
|
CEPS
24.01
Cardiac ElectroPhysiology Simulator
|
Bidomain equation with extracardiac medium and connected to a pacemaker main class.
Definition at line 38 of file PacemakerPoissonProblem.hpp.
#include <PacemakerPoissonProblem.hpp>
Data Structures | |
| class | PowerSupply |
| Power source function. More... | |
| struct | UnknownsName |
| Struct for all names of unknowns. More... | |
Public Member Functions | |
| PacemakerPoissonProblem (Geometry *g, InputParameters *=nullptr) | |
| Constructor from geometry and possibly parameters. More... | |
| virtual | ~PacemakerPoissonProblem ()=default |
| Destructor. More... | |
| void | getInitialCondition (DHVecPtr v0) const override |
| Zero and fill with initial conditions for vm and ue, and put QCets to Cets*AmpStim. More... | |
| void | defineUnknowns () override |
| Transmembrane voltage (mV), Extracellular potential (mV) and both potential of the pacemaker. More... | |
| void | defineBoundaryConditions () override |
| Define the boundary conditions. More... | |
| void | defineSourceTerms () override |
| Define the source terms. More... | |
| void | run () override |
| Run the simulation. More... | |
| CepsSet< CepsAttribute > | getAnodeAttributes () const |
| Get cathode attributes if set. More... | |
| CepsSet< CepsAttribute > | getCathodeAttributes () const |
| Get cathode attributes if set. More... | |
| Unknown * | getUFieldUnknown () const |
| Link to the u unknown of the problem. More... | |
| Unknown * | getUAnodeUnknown () const override |
| Link to the Up unknown of the problem. More... | |
| Unknown * | getUCathodeUnknown () const override |
| Link to the Um unknown of the problem. More... | |
| Unknown * | getVCetsUnknown () const override |
| Link to the VCets unknown of the problem. More... | |
| Unknown * | getVCtsUnknown () const override |
| Link to the VCts unknown of the problem. 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... | |
| Public Member Functions inherited from AbstractPacemakerProblem | |
| AbstractPacemakerProblem (Geometry *g, InputParameters *params=nullptr) | |
| Constructor with geometry and parameters. More... | |
| virtual | ~AbstractPacemakerProblem ()=default |
| Destructor. More... | |
| void | setStimulation (CepsReal amplitude, CepsReal duration) |
| Set the parameters of the stimulation. More... | |
| void | setStimulationAmplitude (CepsReal amplitude) |
| Set the amplitude of the stimulation. More... | |
| CepsReal | getStimulationAmplitude () const |
| Get the stimulation amplitude. More... | |
| void | setStimulationDuration (CepsReal duration) |
| Set the duration of the stimulation. More... | |
| CepsReal | getStimulationDuration () const |
| Get the stimulation duration. More... | |
| CepsReal | getStimulationPeriod () const |
| Get the stimulation period. More... | |
| CepsPacemakerPhase | getPhase (CepsReal t) const |
| Get the phase id of pacemaker cycle. More... | |
| CepsBool | isRechargingPhase (CepsReal t) const |
| Tells if the phase is a rehcarging phase. More... | |
| CepsReal | getRelativeTimeOnPhase (CepsReal t) const |
| Get the relative time of this pacemaker cycle step. More... | |
| CepsReal | getPacemakerDuration (CepsPacemakerPhase phase) const |
| Get the duration of a phase. More... | |
| CepsReal | getPacemakerCapacitance (CepsReal t) const |
| Get the equivalent capacitance of the pacemaker. More... | |
| CepsReal | getPacemakerCapacitanceCets (CepsReal t) const |
| Get the capacitance associated to the main capacitor of the device. More... | |
| CepsReal | getPacemakerCapacitanceCts (CepsReal t) const |
| Get the capacitance associated to the second capacitor of the pacemaker. More... | |
| CepsReal | getPacemakerResistance (CepsReal t) const |
| Get the equivalent resistance of the pacemaker. More... | |
| CepsReal | getPacemakerResistanceLittle (CepsReal t) const |
| Get the resistance used in the recharge circuit of the Cets. More... | |
| CepsReal | getWireResistanceAnodeLine (CepsReal t) const |
| Get the resistance used in to model the wire in anode line. More... | |
| CepsReal | getWireResistanceCathodeLine (CepsReal t) const |
| Get the resistance used in to model the wire in cathode line. More... | |
| void | setPulseOnlyMode (CepsBool value) |
| Set pacemaker in pulse only mode. More... | |
| CepsBool | isPulseOnlyMode () const |
| Tells if the pacemaker is in pulse only mode. More... | |
| void | setupWithParameters (InputParameters *params) |
| Sets options from the parameters. More... | |
| void | setupRunningProperties () |
| Sets running parameters like equivalent resistances and capacitances. More... | |
| Public Member Functions inherited from HoldsAnodeCathode< ParallelRCElectrode > | |
| HoldsAnodeCathode () | |
| Default constructor. More... | |
| HoldsAnodeCathode (InputParameters *params, Geometry *geom=nullptr) | |
| Constructor with parameters, pass geometry to compute measures. More... | |
| HoldsAnodeCathode (const CepsSet< CepsAttribute > &anodeAttrs, const CepsSet< CepsAttribute > &cathodeAttrs, Geometry *geom=nullptr) | |
| Constructor with sets of attributes, pass geometry to compute measures. More... | |
| virtual | ~HoldsAnodeCathode () |
| Destructor. More... | |
| CepsSet< CepsAttribute > & | getAnodeAttributes () const |
| Anode attributes. More... | |
| CepsSet< CepsAttribute > & | getCathodeAttributes () const |
| Cathode attributes. More... | |
| void | setElectrodesAttributes (const CepsSet< CepsAttribute > &anodeAttrs, const CepsSet< CepsAttribute > &cathodeAttrs, Geometry *geom=nullptr) |
| Sets the attributes. More... | |
| ParallelRCElectrode * | getAnode () const |
| Ptr to anode object. More... | |
| ParallelRCElectrode * | getCathode () const |
| Ptr to cathode object. More... | |
Protected Member Functions | |
| void | setupWithParameters (InputParameters *params) override |
| Sets options from the parameters. 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 Member Functions inherited from HoldsAnodeCathode< ParallelRCElectrode > | |
| void | checkCommonAttributes () |
| Check that anode and cathode do not share attributes. 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 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... | |
| Protected Attributes inherited from AbstractPacemakerProblem | |
| CepsReal | m_stimAmplitude |
| Amplitude of the stim [mV]. More... | |
| CepsReal | m_stimDuration |
| Duration of the stim [ms]. More... | |
| CepsBool | m_pmkPulseOnlyMode |
| Pulse only mode. More... | |
| CepsReal | m_pmkOffset |
| Offset duration [ms]. More... | |
| CepsReal | m_pmkPeriod |
| Period duration [ms], default 90bpm. More... | |
| CepsReal | m_pmkSwitch |
| Switch duration [ms]. More... | |
| CepsReal | m_pmkOcd |
| OCD duration [ms]. More... | |
| CepsUInt | m_pmkNSpikes |
| Number of spikes to do. More... | |
| CepsReal | m_pmkCets |
| CETS capacitance [uF]. More... | |
| CepsReal | m_pmkCts |
| CTS capacitance [uF]. More... | |
| CepsReal | m_pmkRgnd |
| GROUND resistance [kOhm]. More... | |
| CepsReal | m_pmkRpulse |
| PULSE resistance [kOhm]. More... | |
| CepsReal | m_pmkRwa |
| ANODE WIRE resistance [kOhm]. More... | |
| CepsReal | m_pmkRwc |
| CATHODE WIRE resistance [kOhm]. More... | |
| CepsReal | m_pmkRbig |
| BIG resistance [kOhm] during the waiting phase. More... | |
| CepsReal | m_pmkRlittle |
| LITTLE resistance [kOhm] used to recharge the CETS. More... | |
| CepsArray< CepsReal, CepsPacemakerPhaseSize > | m_pmkC |
| All equivalent capacitances depending on phase [uF]. More... | |
| CepsArray< CepsReal, CepsPacemakerPhaseSize > | m_pmkR |
| All equivalent resistances depending on phase [kOhm]. More... | |
| Protected Attributes inherited from HoldsAnodeCathode< ParallelRCElectrode > | |
| ParallelRCElectrode * | m_anode |
| Electrode object. More... | |
| ParallelRCElectrode * | m_cathode |
| Electrode object. More... | |
| Static Protected Attributes inherited from CepsObject | |
| static Profiler | m_profiler |
| The same profiler for each big object. More... | |
|
explicit |
Constructor from geometry and possibly parameters.
Definition at line 52 of file PacemakerPoissonProblem.cpp.
|
virtualdefault |
Destructor.
|
overridevirtual |
Define the boundary conditions.
Reimplemented from AbstractPdeProblem.
Definition at line 102 of file PacemakerPoissonProblem.cpp.
|
overridevirtual |
Define the source terms.
Reimplemented from AbstractPdeProblem.
Definition at line 106 of file PacemakerPoissonProblem.cpp.
|
overridevirtual |
Transmembrane voltage (mV), Extracellular potential (mV) and both potential of the pacemaker.
Implements AbstractPdeProblem.
Definition at line 78 of file PacemakerPoissonProblem.cpp.
| CepsSet< CepsAttribute > PacemakerPoissonProblem::getAnodeAttributes | ( | ) | const |
Get cathode attributes if set.
Definition at line 151 of file PacemakerPoissonProblem.cpp.
| CepsSet< CepsAttribute > PacemakerPoissonProblem::getCathodeAttributes | ( | ) | const |
Get cathode attributes if set.
Definition at line 157 of file PacemakerPoissonProblem.cpp.
|
overridevirtual |
Zero and fill with initial conditions for vm and ue, and put QCets to Cets*AmpStim.
Reimplemented from AbstractTimedPdeProblem.
Definition at line 63 of file PacemakerPoissonProblem.cpp.
|
overridevirtual |
Link to the Up unknown of the problem.
Implements AbstractPacemakerProblem.
Definition at line 169 of file PacemakerPoissonProblem.cpp.
|
overridevirtual |
Link to the Um unknown of the problem.
Implements AbstractPacemakerProblem.
Definition at line 175 of file PacemakerPoissonProblem.cpp.
| Unknown * PacemakerPoissonProblem::getUFieldUnknown | ( | ) | const |
Link to the u unknown of the problem.
Definition at line 163 of file PacemakerPoissonProblem.cpp.
|
overridevirtual |
Link to the VCets unknown of the problem.
Implements AbstractPacemakerProblem.
Definition at line 181 of file PacemakerPoissonProblem.cpp.
|
overridevirtual |
Link to the VCts unknown of the problem.
Implements AbstractPacemakerProblem.
Definition at line 187 of file PacemakerPoissonProblem.cpp.
|
overridevirtual |
Run the simulation.
Reimplemented from AbstractPdeProblem.
Definition at line 118 of file PacemakerPoissonProblem.cpp.
|
overrideprotectedvirtual |
Sets options from the parameters.
Reimplemented from AbstractPdeProblem.
Definition at line 193 of file PacemakerPoissonProblem.cpp.
1.9.1