 |
CEPS
24.01
Cardiac ElectroPhysiology Simulator
|
|
CEPS
24.01
Cardiac ElectroPhysiology Simulator
|
Solves the monodomain problem with FBE, SBDF RK or CN schemes.
Definition at line 36 of file MonodomainSolver.hpp.
#include <MonodomainSolver.hpp>
Public Member Functions | |
| MonodomainSolver (MonodomainProblem *p) | |
| Constructor. More... | |
| virtual | ~MonodomainSolver ()=default |
| Destructor. More... | |
| void | initializeAssemblers () override |
| Sets the assemblers. More... | |
| MonodomainProblem * | getMonodomainProblem () const |
| Converts own pointer to abstract pde problem to cardiac problem. More... | |
 Public Member Functions inherited from CardiacSolver | |
| virtual | ~CardiacSolver () |
| Destructor. More... | |
| CardiacSolver (CardiacProblem *problem) | |
| Constructor with associated PDE problem. More... | |
| void | solve () override |
| Performs all iterations of the PDE solver. More... | |
| CepsString | getResultsLocationMessage () const |
| To be displayed at the end of computation. More... | |
| CardiacProblem * | getCardiacProblem () const |
| Converts own pointer to abstract pde problem to cardiac problem. More... | |
| ActivationTracker * | getActivationTracker () const |
| Link to activation tracker. More... | |
| Public Member Functions inherited from HeatSolver | |
| HeatSolver ()=delete | |
| Deleted constructor. More... | |
| HeatSolver (HeatProblem *problem) | |
| Constructor (valid with HeatProblem and PseudoWaveFrontProblem) More... | |
| ~HeatSolver () override | |
| Destructor. More... | |
| Public Member Functions inherited from FETimedSolver | |
| FETimedSolver ()=delete | |
| Deleted constructor. More... | |
| FETimedSolver (AbstractTimedPdeProblem *problem) | |
| Constructor (valid with HeatProblem and PseudoWaveFrontProblem) More... | |
| ~FETimedSolver () override | |
| Destructor. More... | |
| Public Member Functions inherited from AbstractTimedPdeSolver | |
| AbstractTimedPdeSolver (AbstractTimedPdeProblem *pb) | |
| Default constructor. More... | |
| virtual | ~AbstractTimedPdeSolver () |
| Destructor. More... | |
| void | solve () override |
| Solves the all PDE (all iterations) 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... | |
| CepsUInt | getExpectedNumberOfOutputs () const override |
| Number of files written. More... | |
| DHVecPtr | getSolution () const |
| Returns a copy of the distributed vector containing the current solution. More... | |
| void | enableErrorComputation () |
| Sets the comparison with analytic solution. More... | |
| CepsArray2< CepsArray3< CepsArray3< CepsReal > > > | getErrors () const |
| Gets the currently computed errors. First index selects absolute(0) or relative(1) second index select max on t(0), integral on t(1), or error at end of time interval(2) third index is L-inf, L1, L2 selector. More... | |
| Public Member Functions inherited from AbstractPdeSolver | |
| AbstractPdeSolver ()=delete | |
| Deleted default constructor. More... | |
| AbstractPdeSolver (AbstractPdeProblem *pb) | |
| Constructor with problem. More... | |
| AbstractPdeSolver (const AbstractPdeSolver &that)=delete | |
| No copy. More... | |
| AbstractPdeSolver & | operator= (const AbstractPdeSolver &that)=delete |
| No assignment. More... | |
| ~AbstractPdeSolver () override | |
| Destructor. More... | |
| void | disableOutput () |
| Stops output. More... | |
| void | enableOutput () |
| Starts output. More... | |
| TimeWriter * | getTimeWriter () const |
| Access to Time Writer to be able to add data. More... | |
| void | disableErrorComputation () |
| Sets the comparison with analytic solution. 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 | |
| Protected Member Functions inherited from CardiacSolver | |
| void | assembleAndSolve () override |
| Performs one iteration of the solver. More... | |
| CepsBool | finished () const override |
| Tells if simulation reached end time or, if enabled, all points have seen an AP. More... | |
| void | fillSourceTermsVector (CepsReal tn) override |
| Computes all contributions to source terms (ionic current, stimcurrent, field sources) with a loop on source terms. More... | |
| void | output (DHVecPtr dummy, CepsBool immediatWriting=true) override |
| Calls the appropriate post-processing and writing methods. More... | |
| Protected Member Functions inherited from HeatSolver | |
| void | initializeAssemblers () override |
| Creates the right type of assemblers for LHS and BCs. Needs to be overriden. More... | |
| HeatProblem * | getHeatProblem () const |
| Returns a pointer to the pb with appropriate type. More... | |
| Protected Member Functions inherited from FETimedSolver | |
| void | assembleAndSolve () override |
| Main routine used during solving, assemble the system depending on the scheme and solve the linear system. More... | |
| void | assembleAndSolveSBDF (CepsUInt nSteps) |
| Updates matrix and RHS for the SBDF numerical scheme. More... | |
| void | assembleAndSolveCN (CepsUInt nSteps) |
| Updates matrix and RHS for the CN numerical scheme. More... | |
| Protected Member Functions inherited from AbstractTimedPdeSolver | |
| AbstractTimedPdeProblem * | getTimedProblem () const |
| Returns a pointer with the appropriate type of pb. More... | |
| virtual void | displayProgress () const |
| Tells time. More... | |
| void | determineSolverType (CepsString s) |
| Initialize the type from parameter string. More... | |
| virtual void | allocateArrays () |
| Allocates the arrays with the correct number of multistep. More... | |
| void | updateAssemblers () override |
| Update assemblers and recompute everything is needed. More... | |
| virtual void | swapMultiStepPointers () |
| Swaps vectors of array pointers for next step (for multistep methods) More... | |
| Protected Member Functions inherited from AbstractPdeSolver | |
| virtual void | initializeWriter () |
| Creates the solution writer. More... | |
| Protected Attributes inherited from CardiacSolver | |
| ActivationTracker * | m_activationTracker |
| Output computation and writing. More... | |
| CepsVector< IonicSolver * > | m_ionSolvers |
| One solver per ionic model in the problem. More... | |
| CepsString | m_ionSolvOpts |
| Options for ionic ODE solvers. More... | |
| CepsBool | m_writeIIon |
| Flag for additional output. More... | |
| CepsBool | m_writeIapp |
| Flag for additional output. More... | |
| CepsReal | m_postProcessPeriod |
| Period of post process calculations. More... | |
| std::set< CepsUInt > | m_saveDepolarizationTime |
| Components of which to save depolarization times. More... | |
| CepsBool | m_stopAtCompleteActivation |
| stop when all points have activation time computed More... | |
| CepsBool | m_stopAtCompleteRepolarization |
| stop when all points have APD computed More... | |
| Protected Attributes inherited from FETimedSolver | |
| FiniteElements * | m_fe |
| Geometry and reference FE. More... | |
| DHVecPtr | m_temp1 |
| Temporary vector for assembly of source terms. More... | |
| DHVecPtr | m_temp2 |
| Temporary vector for assembly of source terms. More... | |
| Protected Attributes inherited from AbstractTimedPdeSolver | |
| DMatPtr | m_dtMat |
| Matrix of time derivative of the system. More... | |
| DVecPtr | m_timeDerEqsVec |
| Vector of 1 or 0, depending on whether the dof equation has a time derivative or not. More... | |
| DVecPtr | m_noTimeDerEqsVec |
| The opposite version of m_timeDerEqsVec, such as m_timeDerEqsVec + m_noTimeDerEqsVec = vec(1) More... | |
| DHVecPtr | m_uNp1 |
| Vectors of unknowns at time t^n+1. More... | |
| CepsVector< DHVecPtr > | m_uNm |
| Solution vectors at different time steps. Several vectors are needed for multi-step methods. (read u^{n-k}). m_uNm[0] is current solution. More... | |
| CepsString | m_type |
| Numerical scheme descriptor. More... | |
| CepsString | m_rkType |
| RK Method if the solver is of type "RK". More... | |
| CepsUInt | m_nbMultiSteps |
| Maximum number of steps needed to compute next solution (eg CN:2) More... | |
| TimeStepper * | m_timeStepper |
| Monitors time evolution. More... | |
| CepsVector< DHVecPtr > | m_regSourcesNm |
| Sources at previous steps (if problem has source terms) More... | |
| CepsVector< DHVecPtr > | m_lapSourcesNm |
| Sources at previous steps (if problem has laplace source terms) More... | |
| CepsVector< DHVecPtr > | m_rkF |
| RK methods: intermediate rates. More... | |
| CepsVector< DHVecPtr > | m_rkU |
| RK methods: intermediate evaluations. More... | |
| CepsReal | m_scaleSystem |
| A factor for both matrix and vector (typically 1/dt) More... | |
| CepsBool | m_cheatConvergence |
| If true, use exact solution for first steps of multi steps methods. More... | |
| CepsUInt | m_nbIterSnapshot |
| Output perdiodicity. More... | |
| Protected Attributes inherited from AbstractPdeSolver | |
| AbstractPdeProblem * | m_problem |
| Link to PDE to solve. More... | |
| AbstractDiscretization * | m_discretization |
| Link to PDE discretization. More... | |
| LinearSystem * | m_linearSystem |
| Linear system. More... | |
| DMatPtr | m_lhs |
| Left hand side of the system. More... | |
| DVecPtr | m_rhs |
| Right hand side of the system. More... | |
| AbstractAssembler * | m_opAsb |
| Assembler for the operator matrix. More... | |
| DMatPtr | m_opMat |
| Matrix of operator. More... | |
| AbstractAssembler * | m_bcAsb |
| Assembler for Robin and Neumann BCs. More... | |
| DMatPtr | m_bcMat |
| Matrix of boundary conditions. More... | |
| DVecPtr | m_bcVec |
| Vector of boundary conditions. More... | |
| AbstractAssembler * | m_lapSrcAsb |
| Assembler for laplace source terms. More... | |
| DMatPtr | m_lapSrcMat |
| Matrix used for laplace source terms. More... | |
| CepsBool | m_hasRegSrc |
| Flag telling if there are regular source terms. More... | |
| CepsBool | m_hasLapSrc |
| Flag telling if there are Delta f source terms. More... | |
| CepsBool | m_useMassLumping |
| Put the mass on the diagonal of the matrix. More... | |
| CepsBool | m_doOutput |
| Enables/disables outputs. More... | |
| VtkWriter * | m_writer |
| Manages output. More... | |
| TimeWriter * | m_timeWriter |
| Writer for time dependant data (even for static problems...) More... | |
| CepsBool | m_doError |
| Compute error wrt analytic solution or reference. More... | |
| PdeErrorCalculator * | m_errors |
| Error computation. More... | |
| Static Protected Attributes inherited from AbstractTimedPdeSolver | |
| static constexpr CepsReal | c_alphaSBDF [5] = {0., 1., 2. / 3., 6. / 11., 12. / 25.} |
| LHS coeffcients of the SBDF schemes. More... | |
| static constexpr CepsReal | c_alphaCN [3] = {0., 1., 1. / 2.} |
| LHS coeffcients of the CN scheme. More... | |
| static constexpr CepsReal | c_akSBDF [4][4] = {{1.}, {4. / 3., -1. / 3.}, {18. / 11., -9. / 11., 2. / 11.}, {48. / 25., -36. / 25., 16. / 25., -3. / 25.}} |
| RHS coeffcients of the SBDF schemes. More... | |
| Static Protected Attributes inherited from CepsObject | |
| static Profiler | m_profiler |
| The same profiler for each big object. More... | |
| MonodomainSolver::MonodomainSolver | ( | MonodomainProblem * | p | ) |
Constructor.
Definition at line 36 of file MonodomainSolver.cpp.
|
virtualdefault |
Destructor.
| MonodomainProblem * MonodomainSolver::getMonodomainProblem | ( | ) | const |
Converts own pointer to abstract pde problem to cardiac problem.
Definition at line 53 of file MonodomainSolver.cpp.
|
overridevirtual |
Sets the assemblers.
Implements AbstractPdeSolver.
Definition at line 42 of file MonodomainSolver.cpp.
1.9.1