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Nektar::BidomainRoth Class Reference

A model for cardiac conduction. More...

#include <BidomainRoth.h>

Inheritance diagram for Nektar::BidomainRoth:
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Collaboration diagram for Nektar::BidomainRoth:
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Public Member Functions

virtual ~BidomainRoth ()
 Desctructor. More...
 
- Public Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
virtual SOLVER_UTILS_EXPORT ~UnsteadySystem ()
 Destructor. More...
 
SOLVER_UTILS_EXPORT NekDouble GetTimeStep (const Array< OneD, const Array< OneD, NekDouble > > &inarray)
 Calculate the larger time-step mantaining the problem stable. More...
 
- Public Member Functions inherited from Nektar::SolverUtils::EquationSystem
virtual SOLVER_UTILS_EXPORT ~EquationSystem ()
 Destructor. More...
 
SOLVER_UTILS_EXPORT void SetUpTraceNormals (void)
 
SOLVER_UTILS_EXPORT void InitObject ()
 Initialises the members of this object. More...
 
SOLVER_UTILS_EXPORT void DoInitialise ()
 Perform any initialisation necessary before solving the problem. More...
 
SOLVER_UTILS_EXPORT void DoSolve ()
 Solve the problem. More...
 
SOLVER_UTILS_EXPORT void TransCoeffToPhys ()
 Transform from coefficient to physical space. More...
 
SOLVER_UTILS_EXPORT void TransPhysToCoeff ()
 Transform from physical to coefficient space. More...
 
SOLVER_UTILS_EXPORT void Output ()
 Perform output operations after solve. More...
 
SOLVER_UTILS_EXPORT NekDouble LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
 Linf error computation. More...
 
SOLVER_UTILS_EXPORT std::string GetSessionName ()
 Get Session name. More...
 
template<class T >
boost::shared_ptr< T > as ()
 
SOLVER_UTILS_EXPORT void ResetSessionName (std::string newname)
 Reset Session name. More...
 
SOLVER_UTILS_EXPORT LibUtilities::SessionReaderSharedPtr GetSession ()
 Get Session name. More...
 
SOLVER_UTILS_EXPORT MultiRegions::ExpListSharedPtr GetPressure ()
 Get pressure field if available. More...
 
SOLVER_UTILS_EXPORT void PrintSummary (std::ostream &out)
 Print a summary of parameters and solver characteristics. More...
 
SOLVER_UTILS_EXPORT void SetLambda (NekDouble lambda)
 Set parameter m_lambda. More...
 
SOLVER_UTILS_EXPORT void EvaluateFunction (Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
 Evaluates a function as specified in the session file. More...
 
SOLVER_UTILS_EXPORT void EvaluateFunction (std::vector< std::string > pFieldNames, Array< OneD, Array< OneD, NekDouble > > &pFields, const std::string &pName, const int domain=0)
 Populate given fields with the function from session. More...
 
SOLVER_UTILS_EXPORT void EvaluateFunction (std::vector< std::string > pFieldNames, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields, const std::string &pName, const int domain=0)
 Populate given fields with the function from session. More...
 
SOLVER_UTILS_EXPORT void EvaluateFunction (std::string pFieldName, Array< OneD, NekDouble > &pArray, const std::string &pFunctionName, const NekDouble &pTime=0.0, const int domain=0)
 
SOLVER_UTILS_EXPORT std::string DescribeFunction (std::string pFieldName, const std::string &pFunctionName, const int domain)
 Provide a description of a function for a given field name. More...
 
SOLVER_UTILS_EXPORT void InitialiseBaseFlow (Array< OneD, Array< OneD, NekDouble > > &base)
 Perform initialisation of the base flow. More...
 
SOLVER_UTILS_EXPORT void SetInitialConditions (NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
 Initialise the data in the dependent fields. More...
 
SOLVER_UTILS_EXPORT void EvaluateExactSolution (int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
 Evaluates an exact solution. More...
 
SOLVER_UTILS_EXPORT NekDouble L2Error (unsigned int field, const Array< OneD, NekDouble > &exactsoln, bool Normalised=false)
 Compute the L2 error between fields and a given exact solution. More...
 
SOLVER_UTILS_EXPORT NekDouble L2Error (unsigned int field, bool Normalised=false)
 Compute the L2 error of the fields. More...
 
SOLVER_UTILS_EXPORT Array< OneD, NekDouble > ErrorExtraPoints (unsigned int field)
 Compute error (L2 and L_inf) over an larger set of quadrature points return [L2 Linf]. More...
 
SOLVER_UTILS_EXPORT void WeakAdvectionGreensDivergenceForm (const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
 Compute the inner product $ (\nabla \phi \cdot F) $. More...
 
SOLVER_UTILS_EXPORT void WeakAdvectionDivergenceForm (const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
 Compute the inner product $ (\phi, \nabla \cdot F) $. More...
 
SOLVER_UTILS_EXPORT void WeakAdvectionNonConservativeForm (const Array< OneD, Array< OneD, NekDouble > > &V, const Array< OneD, const NekDouble > &u, Array< OneD, NekDouble > &outarray, bool UseContCoeffs=false)
 Compute the inner product $ (\phi, V\cdot \nabla u) $. More...
 
f SOLVER_UTILS_EXPORT void AdvectionNonConservativeForm (const Array< OneD, Array< OneD, NekDouble > > &V, const Array< OneD, const NekDouble > &u, Array< OneD, NekDouble > &outarray, Array< OneD, NekDouble > &wk=NullNekDouble1DArray)
 Compute the non-conservative advection. More...
 
SOLVER_UTILS_EXPORT void WeakDGAdvection (const Array< OneD, Array< OneD, NekDouble > > &InField, Array< OneD, Array< OneD, NekDouble > > &OutField, bool NumericalFluxIncludesNormal=true, bool InFieldIsInPhysSpace=false, int nvariables=0)
 Calculate the weak discontinuous Galerkin advection. More...
 
SOLVER_UTILS_EXPORT void WeakDGDiffusion (const Array< OneD, Array< OneD, NekDouble > > &InField, Array< OneD, Array< OneD, NekDouble > > &OutField, bool NumericalFluxIncludesNormal=true, bool InFieldIsInPhysSpace=false)
 Calculate weak DG Diffusion in the LDG form. More...
 
SOLVER_UTILS_EXPORT void Checkpoint_Output (const int n)
 Write checkpoint file of m_fields. More...
 
SOLVER_UTILS_EXPORT void Checkpoint_Output (const int n, MultiRegions::ExpListSharedPtr &field, std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
 Write checkpoint file of custom data fields. More...
 
SOLVER_UTILS_EXPORT void Checkpoint_BaseFlow (const int n)
 Write base flow file of m_fields. More...
 
SOLVER_UTILS_EXPORT void WriteFld (const std::string &outname)
 Write field data to the given filename. More...
 
SOLVER_UTILS_EXPORT void WriteFld (const std::string &outname, MultiRegions::ExpListSharedPtr &field, std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
 Write input fields to the given filename. More...
 
SOLVER_UTILS_EXPORT void ImportFld (const std::string &infile, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields)
 Input field data from the given file. More...
 
SOLVER_UTILS_EXPORT void ImportFldToMultiDomains (const std::string &infile, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields, const int ndomains)
 Input field data from the given file to multiple domains. More...
 
SOLVER_UTILS_EXPORT void ImportFld (const std::string &infile, std::vector< std::string > &fieldStr, Array< OneD, Array< OneD, NekDouble > > &coeffs)
 Output a field. Input field data into array from the given file. More...
 
SOLVER_UTILS_EXPORT void ImportFld (const std::string &infile, MultiRegions::ExpListSharedPtr &pField, std::string &pFieldName)
 Output a field. Input field data into ExpList from the given file. More...
 
SOLVER_UTILS_EXPORT void ScanForHistoryPoints ()
 Builds map of which element holds each history point. More...
 
SOLVER_UTILS_EXPORT void WriteHistoryData (std::ostream &out)
 Probe each history point and write to file. More...
 
SOLVER_UTILS_EXPORT void SessionSummary (SummaryList &vSummary)
 Write out a session summary. More...
 
SOLVER_UTILS_EXPORT Array< OneD, MultiRegions::ExpListSharedPtr > & UpdateFields ()
 
SOLVER_UTILS_EXPORT LibUtilities::FieldMetaDataMap & UpdateFieldMetaDataMap ()
 Get hold of FieldInfoMap so it can be updated. More...
 
SOLVER_UTILS_EXPORT NekDouble GetFinalTime ()
 Return final time. More...
 
SOLVER_UTILS_EXPORT int GetNcoeffs ()
 
SOLVER_UTILS_EXPORT int GetNcoeffs (const int eid)
 
SOLVER_UTILS_EXPORT int GetNumExpModes ()
 
SOLVER_UTILS_EXPORT const Array< OneD, int > GetNumExpModesPerExp ()
 
SOLVER_UTILS_EXPORT int GetNvariables ()
 
SOLVER_UTILS_EXPORT const std::string GetVariable (unsigned int i)
 
SOLVER_UTILS_EXPORT int GetTraceTotPoints ()
 
SOLVER_UTILS_EXPORT int GetTraceNpoints ()
 
SOLVER_UTILS_EXPORT int GetExpSize ()
 
SOLVER_UTILS_EXPORT int GetPhys_Offset (int n)
 
SOLVER_UTILS_EXPORT int GetCoeff_Offset (int n)
 
SOLVER_UTILS_EXPORT int GetTotPoints ()
 
SOLVER_UTILS_EXPORT int GetTotPoints (int n)
 
SOLVER_UTILS_EXPORT int GetNpoints ()
 
SOLVER_UTILS_EXPORT int GetNumElmVelocity ()
 
SOLVER_UTILS_EXPORT int GetSteps ()
 
SOLVER_UTILS_EXPORT NekDouble GetTimeStep ()
 
SOLVER_UTILS_EXPORT void CopyFromPhysField (const int i, Array< OneD, NekDouble > &output)
 
SOLVER_UTILS_EXPORT void CopyToPhysField (const int i, Array< OneD, NekDouble > &output)
 
SOLVER_UTILS_EXPORT void SetStepsToOne ()
 
SOLVER_UTILS_EXPORT void ZeroPhysFields ()
 
SOLVER_UTILS_EXPORT void FwdTransFields ()
 
SOLVER_UTILS_EXPORT void GetFluxVector (const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
 
SOLVER_UTILS_EXPORT void GetFluxVector (const int i, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &fluxX, Array< OneD, Array< OneD, NekDouble > > &fluxY)
 
SOLVER_UTILS_EXPORT void GetFluxVector (const int i, const int j, Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &flux)
 
SOLVER_UTILS_EXPORT void NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
 
SOLVER_UTILS_EXPORT void NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numfluxX, Array< OneD, Array< OneD, NekDouble > > &numfluxY)
 
SOLVER_UTILS_EXPORT void NumFluxforScalar (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &uflux)
 
SOLVER_UTILS_EXPORT void NumFluxforVector (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &qfield, Array< OneD, Array< OneD, NekDouble > > &qflux)
 
SOLVER_UTILS_EXPORT void SetModifiedBasis (const bool modbasis)
 
SOLVER_UTILS_EXPORT int NoCaseStringCompare (const string &s1, const string &s2)
 Perform a case-insensitive string comparison. More...
 
virtual SOLVER_UTILS_EXPORT bool v_NegatedOp ()
 Virtual function to identify if operator is negated in DoSolve. More...
 

Static Public Member Functions

static SolverUtils::EquationSystemSharedPtr create (const LibUtilities::SessionReaderSharedPtr &pSession)
 Creates an instance of this class. More...
 

Static Public Attributes

static std::string className
 Name of class. More...
 

Protected Member Functions

 BidomainRoth (const LibUtilities::SessionReaderSharedPtr &pSession)
 Constructor. More...
 
virtual void v_InitObject ()
 Init object for UnsteadySystem class. More...
 
void DoImplicitSolve (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, NekDouble time, NekDouble lambda)
 Solve for the diffusion term. More...
 
void DoOdeRhs (const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
 Computes the reaction terms $f(u,v)$ and $g(u,v)$. More...
 
virtual void v_SetInitialConditions (NekDouble initialtime, bool dumpInitialConditions, const int domain)
 Sets a custom initial condition. More...
 
virtual void v_GenerateSummary (SummaryList &s)
 Prints a summary of the model parameters. More...
 
- Protected Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
SOLVER_UTILS_EXPORT UnsteadySystem (const LibUtilities::SessionReaderSharedPtr &pSession)
 Initialises UnsteadySystem class members. More...
 
SOLVER_UTILS_EXPORT NekDouble MaxTimeStepEstimator ()
 Get the maximum timestep estimator for cfl control. More...
 
virtual SOLVER_UTILS_EXPORT void v_DoSolve ()
 Solves an unsteady problem. More...
 
virtual SOLVER_UTILS_EXPORT void v_DoInitialise ()
 Sets up initial conditions. More...
 
virtual SOLVER_UTILS_EXPORT void v_AppendOutput1D (Array< OneD, Array< OneD, NekDouble > > &solution1D)
 Print the solution at each solution point in a txt file. More...
 
virtual SOLVER_UTILS_EXPORT void v_NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numflux)
 
virtual SOLVER_UTILS_EXPORT void v_NumericalFlux (Array< OneD, Array< OneD, NekDouble > > &physfield, Array< OneD, Array< OneD, NekDouble > > &numfluxX, Array< OneD, Array< OneD, NekDouble > > &numfluxY)
 
virtual SOLVER_UTILS_EXPORT void v_NumFluxforScalar (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &uflux)
 
virtual SOLVER_UTILS_EXPORT void v_NumFluxforVector (const Array< OneD, Array< OneD, NekDouble > > &ufield, Array< OneD, Array< OneD, Array< OneD, NekDouble > > > &qfield, Array< OneD, Array< OneD, NekDouble > > &qflux)
 
virtual SOLVER_UTILS_EXPORT NekDouble v_GetTimeStep (const Array< OneD, const Array< OneD, NekDouble > > &inarray)
 Return the timestep to be used for the next step in the time-marching loop. More...
 
virtual SOLVER_UTILS_EXPORT bool v_PreIntegrate (int step)
 
virtual SOLVER_UTILS_EXPORT bool v_PostIntegrate (int step)
 
virtual SOLVER_UTILS_EXPORT bool v_SteadyStateCheck (int step)
 
SOLVER_UTILS_EXPORT void CheckForRestartTime (NekDouble &time)
 
- Protected Member Functions inherited from Nektar::SolverUtils::EquationSystem
SOLVER_UTILS_EXPORT EquationSystem (const LibUtilities::SessionReaderSharedPtr &pSession)
 Initialises EquationSystem class members. More...
 
int nocase_cmp (const string &s1, const string &s2)
 
SOLVER_UTILS_EXPORT void SetBoundaryConditions (NekDouble time)
 Evaluates the boundary conditions at the given time. More...
 
virtual SOLVER_UTILS_EXPORT NekDouble v_LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
 Virtual function for the L_inf error computation between fields and a given exact solution. More...
 
virtual SOLVER_UTILS_EXPORT NekDouble v_L2Error (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray, bool Normalised=false)
 Virtual function for the L_2 error computation between fields and a given exact solution. More...
 
virtual SOLVER_UTILS_EXPORT void v_TransCoeffToPhys ()
 Virtual function for transformation to physical space. More...
 
virtual SOLVER_UTILS_EXPORT void v_TransPhysToCoeff ()
 Virtual function for transformation to coefficient space. More...
 
virtual SOLVER_UTILS_EXPORT void v_EvaluateExactSolution (unsigned int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
 
SOLVER_UTILS_EXPORT void SetUpBaseFields (SpatialDomains::MeshGraphSharedPtr &mesh)
 
SOLVER_UTILS_EXPORT void ImportFldBase (std::string pInfile, SpatialDomains::MeshGraphSharedPtr pGraph)
 
virtual SOLVER_UTILS_EXPORT void v_Output (void)
 
virtual SOLVER_UTILS_EXPORT MultiRegions::ExpListSharedPtr v_GetPressure (void)
 
virtual SOLVER_UTILS_EXPORT void v_ExtraFldOutput (std::vector< Array< OneD, NekDouble > > &fieldcoeffs, std::vector< std::string > &variables)
 

Private Member Functions

void LoadStimuli ()
 

Private Attributes

CellModelSharedPtr m_cell
 Cell model. More...
 
std::vector< StimulusSharedPtr > m_stimulus
 
StdRegions::VarCoeffMap m_vardiffi
 
StdRegions::VarCoeffMap m_vardiffe
 
StdRegions::VarCoeffMap m_vardiffie
 
NekDouble m_chi
 
NekDouble m_capMembrane
 
NekDouble m_stimDuration
 Stimulus current. More...
 

Friends

class MemoryManager< BidomainRoth >
 

Additional Inherited Members

- Public Attributes inherited from Nektar::SolverUtils::UnsteadySystem
NekDouble m_cflSafetyFactor
 CFL safety factor (comprise between 0 to 1). More...
 
- Protected Types inherited from Nektar::SolverUtils::EquationSystem
enum  HomogeneousType { eHomogeneous1D, eHomogeneous2D, eHomogeneous3D, eNotHomogeneous }
 Parameter for homogeneous expansions. More...
 
- Protected Attributes inherited from Nektar::SolverUtils::UnsteadySystem
int m_infosteps
 Number of time steps between outputting status information. More...
 
LibUtilities::TimeIntegrationWrapperSharedPtr m_intScheme
 Wrapper to the time integration scheme. More...
 
LibUtilities::TimeIntegrationSchemeOperators m_ode
 The time integration scheme operators to use. More...
 
LibUtilities::TimeIntegrationSolutionSharedPtr m_intSoln
 
NekDouble m_epsilon
 
bool m_explicitDiffusion
 Indicates if explicit or implicit treatment of diffusion is used. More...
 
bool m_explicitAdvection
 Indicates if explicit or implicit treatment of advection is used. More...
 
bool m_explicitReaction
 Indicates if explicit or implicit treatment of reaction is used. More...
 
bool m_homoInitialFwd
 Flag to determine if simulation should start in homogeneous forward transformed state. More...
 
std::vector< int > m_intVariables
 
std::vector< FilterSharedPtr > m_filters
 
- Protected Attributes inherited from Nektar::SolverUtils::EquationSystem
LibUtilities::CommSharedPtr m_comm
 Communicator. More...
 
LibUtilities::SessionReaderSharedPtr m_session
 The session reader. More...
 
LibUtilities::FieldIOSharedPtr m_fld
 Field input/output. More...
 
map< std::string, Array< OneD, Array< OneD, float > > > m_interpWeights
 Map of the interpolation weights for a specific filename. More...
 
map< std::string, Array< OneD, Array< OneD, unsigned int > > > m_interpInds
 Map of the interpolation indices for a specific filename. More...
 
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
 Array holding all dependent variables. More...
 
Array< OneD, MultiRegions::ExpListSharedPtr > m_base
 Base fields. More...
 
Array< OneD, MultiRegions::ExpListSharedPtr > m_derivedfields
 Array holding all dependent variables. More...
 
SpatialDomains::BoundaryConditionsSharedPtr m_boundaryConditions
 Pointer to boundary conditions object. More...
 
SpatialDomains::MeshGraphSharedPtr m_graph
 Pointer to graph defining mesh. More...
 
std::string m_sessionName
 Name of the session. More...
 
NekDouble m_time
 Current time of simulation. More...
 
NekDouble m_fintime
 Finish time of the simulation. More...
 
NekDouble m_timestep
 Time step size. More...
 
NekDouble m_lambda
 Lambda constant in real system if one required. More...
 
NekDouble m_checktime
 Time between checkpoints. More...
 
int m_steps
 Number of steps to take. More...
 
int m_checksteps
 Number of steps between checkpoints. More...
 
int m_spacedim
 Spatial dimension (>= expansion dim). More...
 
int m_expdim
 Expansion dimension. More...
 
bool m_singleMode
 Flag to determine if single homogeneous mode is used. More...
 
bool m_halfMode
 Flag to determine if half homogeneous mode is used. More...
 
bool m_multipleModes
 Flag to determine if use multiple homogenenous modes are used. More...
 
bool m_useFFT
 Flag to determine if FFT is used for homogeneous transform. More...
 
bool m_homogen_dealiasing
 Flag to determine if dealiasing is used for homogeneous simulations. More...
 
bool m_specHP_dealiasing
 Flag to determine if dealisising is usde for the Spectral/hp element discretisation. More...
 
enum MultiRegions::ProjectionType m_projectionType
 Type of projection; e.g continuous or discontinuous. More...
 
Array< OneD, Array< OneD, NekDouble > > m_traceNormals
 Array holding trace normals for DG simulations in the forwards direction. More...
 
Array< OneD, Array< OneD, Array< OneD, NekDouble > > > m_gradtan
 1 x nvariable x nq More...
 
Array< OneD, Array< OneD, Array< OneD, NekDouble > > > m_tanbasis
 2 x m_spacedim x nq More...
 
Array< OneD, bool > m_checkIfSystemSingular
 Flag to indicate if the fields should be checked for singularity. More...
 
LibUtilities::FieldMetaDataMap m_fieldMetaDataMap
 Map to identify relevant solver info to dump in output fields. More...
 
int m_NumQuadPointsError
 Number of Quadrature points used to work out the error. More...
 
enum HomogeneousType m_HomogeneousType
 
NekDouble m_LhomX
 physical length in X direction (if homogeneous) More...
 
NekDouble m_LhomY
 physical length in Y direction (if homogeneous) More...
 
NekDouble m_LhomZ
 physical length in Z direction (if homogeneous) More...
 
int m_npointsX
 number of points in X direction (if homogeneous) More...
 
int m_npointsY
 number of points in Y direction (if homogeneous) More...
 
int m_npointsZ
 number of points in Z direction (if homogeneous) More...
 
int m_HomoDirec
 number of homogenous directions More...
 
int m_NumMode
 Mode to use in case of single mode analysis. More...
 

Detailed Description

A model for cardiac conduction.

Definition at line 48 of file BidomainRoth.h.

Constructor & Destructor Documentation

Nektar::BidomainRoth::~BidomainRoth ( )
virtual

Desctructor.

Definition at line 325 of file BidomainRoth.cpp.

326 {
327 
328 }
Nektar::BidomainRoth::BidomainRoth ( const LibUtilities::SessionReaderSharedPtr &  pSession)
protected

Constructor.

Definition at line 57 of file BidomainRoth.cpp.

59  : UnsteadySystem(pSession)
60 {
61 }
Nektar::SolverUtils::UnsteadySystem::UnsteadySystem
SOLVER_UTILS_EXPORT UnsteadySystem(const LibUtilities::SessionReaderSharedPtr &pSession)
Initialises UnsteadySystem class members.
Definition: UnsteadySystem.cpp:65

Member Function Documentation

static SolverUtils::EquationSystemSharedPtr Nektar::BidomainRoth::create ( const LibUtilities::SessionReaderSharedPtr &  pSession)
inlinestatic

Creates an instance of this class.

Definition at line 54 of file BidomainRoth.h.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr().

56  {
57  SolverUtils::EquationSystemSharedPtr p =
58  MemoryManager<BidomainRoth>::AllocateSharedPtr(pSession);
59  p->InitObject();
60  return p;
61  }
Nektar::MemoryManager::AllocateSharedPtr
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
Definition: NekMemoryManager.hpp:235
Nektar::SolverUtils::EquationSystemSharedPtr
boost::shared_ptr< EquationSystem > EquationSystemSharedPtr
A shared pointer to an EquationSystem object.
Definition: EquationSystem.h:56
void Nektar::BidomainRoth::DoImplicitSolve ( const Array< OneD, const Array< OneD, NekDouble > > &  inarray,
Array< OneD, Array< OneD, NekDouble > > &  outarray,
NekDouble  time,
NekDouble  lambda 
)
protected

Solve for the diffusion term.

Parameters
inarrayInput array.
outarrayOutput array.
timeCurrent simulation time.
lambdaTimestep.

Definition at line 337 of file BidomainRoth.cpp.

References Nektar::StdRegions::eFactorLambda, m_capMembrane, m_chi, Nektar::SolverUtils::EquationSystem::m_fields, m_vardiffe, Nektar::NullFlagList, and Vmath::Smul().

Referenced by v_InitObject().

342 {
343  int nq = m_fields[0]->GetNpoints();
344 
345  StdRegions::ConstFactorMap factorsHelmholtz;
346  // lambda = \Delta t
347  factorsHelmholtz[StdRegions::eFactorLambda]
348  = 1.0/lambda*m_chi*m_capMembrane;
349 
350  // ------------------------------
351  // Solve Helmholtz problem for Vm
352  // ------------------------------
353  // Multiply 1.0/timestep
354  //Vmath::Vadd(nq, inarray[0], 1, ggrad, 1, m_fields[0]->UpdatePhys(), 1);
355  Vmath::Smul(nq, -factorsHelmholtz[StdRegions::eFactorLambda], inarray[0], 1,
356  m_fields[0]->UpdatePhys(), 1);
357 
358  // Solve a system of equations with Helmholtz solver and transform
359  // back into physical space.
360  m_fields[0]->HelmSolve(m_fields[0]->GetPhys(),
361  m_fields[0]->UpdateCoeffs(), NullFlagList,
362  factorsHelmholtz, m_vardiffe);
363 
364  m_fields[0]->BwdTrans( m_fields[0]->GetCoeffs(),
365  m_fields[0]->UpdatePhys());
366  m_fields[0]->SetPhysState(true);
367 
368  // Copy the solution vector (required as m_fields must be set).
369  outarray[0] = m_fields[0]->GetPhys();
370 }
Nektar::StdRegions::ConstFactorMap
std::map< ConstFactorType, NekDouble > ConstFactorMap
Definition: StdRegions.hpp:248
Nektar::BidomainRoth::m_vardiffe
StdRegions::VarCoeffMap m_vardiffe
Definition: BidomainRoth.h:104
Vmath::Smul
void Smul(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Scalar multiply y = alpha*y.
Definition: Vmath.cpp:199
Nektar::SolverUtils::EquationSystem::m_fields
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
Definition: EquationSystem.h:423
Nektar::NullFlagList
static FlagList NullFlagList
An empty flag list.
Definition: NektarUnivTypeDefs.hpp:108
void Nektar::BidomainRoth::DoOdeRhs ( const Array< OneD, const Array< OneD, NekDouble > > &  inarray,
Array< OneD, Array< OneD, NekDouble > > &  outarray,
const NekDouble  time 
)
protected

Computes the reaction terms $f(u,v)$ and $g(u,v)$.

Definition at line 376 of file BidomainRoth.cpp.

References Nektar::StdRegions::eFactorLambda, Nektar::StdRegions::eVarCoeffD00, Nektar::StdRegions::eVarCoeffD11, Nektar::StdRegions::eVarCoeffD22, m_cell, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::EquationSystem::m_session, m_stimulus, m_vardiffi, m_vardiffie, Nektar::NullFlagList, Vmath::Smul(), Vmath::Vadd(), and Vmath::Vmul().

Referenced by v_InitObject().

380 {
381  int nq = m_fields[0]->GetNpoints();
382 
383  // Compute I_ion
384  m_cell->TimeIntegrate(inarray, outarray, time);
385 
386  // Compute I_stim
387  for (unsigned int i = 0; i < m_stimulus.size(); ++i)
388  {
389  m_stimulus[i]->Update(outarray, time);
390  }
391 
392  Array<OneD, NekDouble> ggrad0(nq), ggrad1(nq), ggrad2(nq), ggrad(nq);
393  StdRegions::ConstFactorMap factorsPoisson;
394  factorsPoisson[StdRegions::eFactorLambda] = 0.0;
395 
396  // ----------------------------
397  // Compute \nabla g_i \nabla Vm
398  // ----------------------------
399  m_fields[0]->PhysDeriv(inarray[0], ggrad0, ggrad1, ggrad2);
400  m_fields[0]->PhysDeriv(0, ggrad0, ggrad0);
401  m_fields[0]->PhysDeriv(1, ggrad1, ggrad1);
402  m_fields[0]->PhysDeriv(2, ggrad2, ggrad2);
403  if (m_session->DefinesFunction("IntracellularAnisotropicConductivity") &&
404  m_session->DefinesFunction("ExtracellularAnisotropicConductivity"))
405  {
406  Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD00], 1, ggrad0,
407  1, ggrad0, 1);
408  Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD11], 1, ggrad1,
409  1, ggrad1, 1);
410  Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD22], 1, ggrad2,
411  1, ggrad2, 1);
412  }
413  // Add partial derivatives together
414  Vmath::Vadd(nq, ggrad0, 1, ggrad1, 1, ggrad, 1);
415  Vmath::Vadd(nq, ggrad2, 1, ggrad, 1, ggrad, 1);
416 
417  Vmath::Smul(nq, -1.0, ggrad, 1, m_fields[1]->UpdatePhys(), 1);
418 
419  // ----------------------------
420  // Solve Poisson problem for Ve
421  // ----------------------------
422  m_fields[1]->HelmSolve(m_fields[1]->GetPhys(),
423  m_fields[1]->UpdateCoeffs(), NullFlagList, factorsPoisson,
424  m_vardiffie);
425  m_fields[1]->BwdTrans(m_fields[1]->GetCoeffs(),
426  m_fields[1]->UpdatePhys());
427  m_fields[1]->SetPhysState(true);
428 
429  // ------------------------------
430  // Compute Laplacian of Ve (forcing term)
431  // ------------------------------
432  m_fields[1]->PhysDeriv(m_fields[1]->GetPhys(), ggrad0, ggrad1, ggrad2);
433  m_fields[1]->PhysDeriv(0, ggrad0, ggrad0);
434  m_fields[1]->PhysDeriv(1, ggrad1, ggrad1);
435  m_fields[1]->PhysDeriv(2, ggrad2, ggrad2);
436  if (m_session->DefinesFunction("IntracellularAnisotropicConductivity") &&
437  m_session->DefinesFunction("ExtracellularAnisotropicConductivity"))
438  {
439  Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD00], 1, ggrad0,
440  1, ggrad0, 1);
441  Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD11], 1, ggrad1,
442  1, ggrad1, 1);
443  Vmath::Vmul(nq, m_vardiffi[StdRegions::eVarCoeffD22], 1, ggrad2,
444  1, ggrad2, 1);
445  }
446  // Add partial derivatives together
447  Vmath::Vadd(nq, ggrad0, 1, ggrad1, 1, ggrad, 1);
448  Vmath::Vadd(nq, ggrad2, 1, ggrad, 1, ggrad, 1);
449 
450  Vmath::Vadd(nq, ggrad, 1, outarray[0], 1, outarray[0], 1);
451 }
Nektar::StdRegions::ConstFactorMap
std::map< ConstFactorType, NekDouble > ConstFactorMap
Definition: StdRegions.hpp:248
Nektar::BidomainRoth::m_stimulus
std::vector< StimulusSharedPtr > m_stimulus
Definition: BidomainRoth.h:101
Vmath::Smul
void Smul(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Scalar multiply y = alpha*y.
Definition: Vmath.cpp:199
Nektar::BidomainRoth::m_vardiffie
StdRegions::VarCoeffMap m_vardiffie
Definition: BidomainRoth.h:105
Nektar::BidomainRoth::m_cell
CellModelSharedPtr m_cell
Cell model.
Definition: BidomainRoth.h:99
Nektar::SolverUtils::EquationSystem::m_fields
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
Definition: EquationSystem.h:423
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:415
Nektar::BidomainRoth::m_vardiffi
StdRegions::VarCoeffMap m_vardiffi
Definition: BidomainRoth.h:103
Vmath::Vadd
void Vadd(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Add vector z = x+y.
Definition: Vmath.cpp:285
Vmath::Vmul
void Vmul(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Multiply vector z = x*y.
Definition: Vmath.cpp:169
Nektar::NullFlagList
static FlagList NullFlagList
An empty flag list.
Definition: NektarUnivTypeDefs.hpp:108
void Nektar::BidomainRoth::LoadStimuli ( )
private
void Nektar::BidomainRoth::v_GenerateSummary ( SummaryList &  s)
protectedvirtual

Prints a summary of the model parameters.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 471 of file BidomainRoth.cpp.

References m_cell.

472 {
473  UnsteadySystem::v_GenerateSummary(s);
474  m_cell->GenerateSummary(s);
475 }
Nektar::BidomainRoth::m_cell
CellModelSharedPtr m_cell
Cell model.
Definition: BidomainRoth.h:99
void Nektar::BidomainRoth::v_InitObject ( )
protectedvirtual

Init object for UnsteadySystem class.

Initialization object for UnsteadySystem class.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 67 of file BidomainRoth.cpp.

References ASSERTL0, Nektar::LibUtilities::NekFactory< tKey, tBase, >::CreateInstance(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineImplicitSolve(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineOdeRhs(), DoImplicitSolve(), DoOdeRhs(), Nektar::SolverUtils::EquationSystem::EvaluateFunction(), Nektar::StdRegions::eVarCoeffD00, Nektar::StdRegions::eVarCoeffD01, Nektar::StdRegions::eVarCoeffD02, Nektar::StdRegions::eVarCoeffD11, Nektar::StdRegions::eVarCoeffD12, Nektar::StdRegions::eVarCoeffD22, Nektar::GetCellModelFactory(), Nektar::Stimulus::LoadStimuli(), m_capMembrane, m_cell, m_chi, Nektar::SolverUtils::UnsteadySystem::m_explicitDiffusion, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::UnsteadySystem::m_filters, Nektar::SolverUtils::UnsteadySystem::m_intVariables, Nektar::SolverUtils::UnsteadySystem::m_ode, Nektar::SolverUtils::EquationSystem::m_session, Nektar::SolverUtils::EquationSystem::m_spacedim, m_stimulus, m_vardiffe, m_vardiffi, m_vardiffie, Vmath::Sadd(), Nektar::FilterCheckpointCellModel::SetCellModel(), Vmath::Smul(), Vmath::Vadd(), Vmath::Vmul(), and Nektar::SolverUtils::EquationSystem::WriteFld().

68 {
69  UnsteadySystem::v_InitObject();
70 
71  m_session->LoadParameter("Chi", m_chi);
72  m_session->LoadParameter("Cm", m_capMembrane);
73 
74  std::string vCellModel;
75  m_session->LoadSolverInfo("CELLMODEL", vCellModel, "");
76 
77  ASSERTL0(vCellModel != "", "Cell Model not specified.");
78 
79  m_cell = GetCellModelFactory().CreateInstance(
80  vCellModel, m_session, m_fields[0]);
81 
82  m_intVariables.push_back(0);
83 
84  // Load variable coefficients
85  StdRegions::VarCoeffType varCoeffEnum[6] = {
86  StdRegions::eVarCoeffD00,
87  StdRegions::eVarCoeffD01,
88  StdRegions::eVarCoeffD11,
89  StdRegions::eVarCoeffD02,
90  StdRegions::eVarCoeffD12,
91  StdRegions::eVarCoeffD22
92  };
93  std::string varCoeffString[6] = {"xx","xy","yy","xz","yz","zz"};
94  std::string aniso_var[3] = {"fx", "fy", "fz"};
95 
96  const int nq = m_fields[0]->GetNpoints();
97 
98  // Allocate storage for variable coeffs and initialize to 1.
99  for (int i = 0, k = 0; i < m_spacedim; ++i)
100  {
101  for (int j = 0; j < i+1; ++j)
102  {
103  if (i == j)
104  {
105  m_vardiffi[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
106  m_vardiffe[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
107  m_vardiffie[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
108  }
109  else
110  {
111  m_vardiffi[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 0.0);
112  m_vardiffe[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 0.0);
113  m_vardiffie[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 0.0);
114  }
115  ++k;
116  }
117  }
118 
119  // Apply fibre map f \in [0,1], scale to conductivity range
120  // [o_min,o_max], specified by the session parameters o_min and o_max
121  if (m_session->DefinesFunction("ExtracellularAnisotropicConductivity"))
122  {
123  if (m_session->DefinesCmdLineArgument("verbose"))
124  {
125  cout << "Loading Extracellular Anisotropic Fibre map." << endl;
126  }
127 
128  NekDouble o_min = m_session->GetParameter("o_min");
129  NekDouble o_max = m_session->GetParameter("o_max");
130  int k = 0;
131 
132  Array<OneD, NekDouble> vTemp_i;
133  Array<OneD, NekDouble> vTemp_j;
134 
135  /*
136  * Diffusivity matrix D is upper triangular and defined as
137  * d_00 d_01 d_02
138  * d_11 d_12
139  * d_22
140  *
141  * Given a principle fibre direction _f_ the diffusivity is given
142  * by
143  * d_ij = { D_2 + (D_1 - D_2) f_i f_j if i==j
144  * { (D_1 - D_2) f_i f_j if i!=j
145  *
146  * The vector _f_ is given in terms of the variables fx,fy,fz in the
147  * function AnisotropicConductivity. The values of D_1 and D_2 are
148  * the parameters o_max and o_min, respectively.
149  */
150 
151  // Loop through columns of D
152  for (int j = 0; j < m_spacedim; ++j)
153  {
154  ASSERTL0(m_session->DefinesFunction(
155  "ExtracellularAnisotropicConductivity",
156  aniso_var[j]),
157  "Function 'AnisotropicConductivity' not correctly "
158  "defined.");
159  EvaluateFunction(aniso_var[j], vTemp_j,
160  "ExtracellularAnisotropicConductivity");
161 
162  // Loop through rows of D
163  for (int i = 0; i < j + 1; ++i)
164  {
165  ASSERTL0(m_session->DefinesFunction(
166  "ExtracellularAnisotropicConductivity",
167  aniso_var[i]),
168  "Function 'ExtracellularAnisotropicConductivity' not "
169  "correctly defined.");
170 
171  EvaluateFunction(aniso_var[i], vTemp_i,
172  "ExtracellularAnisotropicConductivity");
173 
174  Vmath::Vmul(nq, vTemp_i, 1, vTemp_j, 1,
175  m_vardiffe[varCoeffEnum[k]], 1);
176 
177  Vmath::Smul(nq, o_max-o_min,
178  m_vardiffe[varCoeffEnum[k]], 1,
179  m_vardiffe[varCoeffEnum[k]], 1);
180 
181  if (i == j)
182  {
183  Vmath::Sadd(nq, o_min,
184  m_vardiffe[varCoeffEnum[k]], 1,
185  m_vardiffe[varCoeffEnum[k]], 1);
186  }
187 
188  }
189  }
190  }
191 
192  // Apply fibre map f \in [0,1], scale to conductivity range
193  // [o_min,o_max], specified by the session parameters o_min and o_max
194  if (m_session->DefinesFunction("IntracellularAnisotropicConductivity"))
195  {
196  if (m_session->DefinesCmdLineArgument("verbose"))
197  {
198  cout << "Loading Anisotropic Fibre map." << endl;
199  }
200 
201  NekDouble o_min = m_session->GetParameter("o_min");
202  NekDouble o_max = m_session->GetParameter("o_max");
203  int k = 0;
204 
205  Array<OneD, NekDouble> vTemp_i;
206  Array<OneD, NekDouble> vTemp_j;
207 
208  /*
209  * Diffusivity matrix D is upper triangular and defined as
210  * d_00 d_01 d_02
211  * d_11 d_12
212  * d_22
213  *
214  * Given a principle fibre direction _f_ the diffusivity is given
215  * by
216  * d_ij = { D_2 + (D_1 - D_2) f_i f_j if i==j
217  * { (D_1 - D_2) f_i f_j if i!=j
218  *
219  * The vector _f_ is given in terms of the variables fx,fy,fz in the
220  * function AnisotropicConductivity. The values of D_1 and D_2 are
221  * the parameters o_max and o_min, respectively.
222  */
223 
224  // Loop through columns of D
225  for (int j = 0; j < m_spacedim; ++j)
226  {
227  ASSERTL0(m_session->DefinesFunction(
228  "IntracellularAnisotropicConductivity",
229  aniso_var[j]),
230  "Function 'IntracellularAnisotropicConductivity' not "
231  "correctly defined.");
232 
233  EvaluateFunction(aniso_var[j], vTemp_j,
234  "IntracellularAnisotropicConductivity");
235 
236  // Loop through rows of D
237  for (int i = 0; i < j + 1; ++i)
238  {
239  ASSERTL0(m_session->DefinesFunction(
240  "IntracellularAnisotropicConductivity",
241  aniso_var[i]),
242  "Function 'IntracellularAnisotropicConductivity' not "
243  "correctly defined.");
244  EvaluateFunction(aniso_var[i], vTemp_i,
245  "IntracellularAnisotropicConductivity");
246 
247  Vmath::Vmul(nq, vTemp_i, 1, vTemp_j, 1,
248  m_vardiffi[varCoeffEnum[k]], 1);
249 
250  Vmath::Smul(nq, o_max-o_min,
251  m_vardiffi[varCoeffEnum[k]], 1,
252  m_vardiffi[varCoeffEnum[k]], 1);
253 
254  if (i == j)
255  {
256  Vmath::Sadd(nq, o_min,
257  m_vardiffi[varCoeffEnum[k]], 1,
258  m_vardiffi[varCoeffEnum[k]], 1);
259  }
260 
261  Vmath::Vadd(nq, m_vardiffe[varCoeffEnum[k]], 1,
262  m_vardiffi[varCoeffEnum[k]], 1,
263  m_vardiffie[varCoeffEnum[k]], 1);
264 
265  ++k;
266  }
267  }
268  }
269 
270 
271  // Write out conductivity values
272  for (int j = 0, k = 0; j < m_spacedim; ++j)
273  {
274  // Loop through rows of D
275  for (int i = 0; i < j + 1; ++i)
276  {
277  // Transform variable coefficient and write out to file.
278  m_fields[0]->FwdTrans_IterPerExp(m_vardiffi[varCoeffEnum[k]],
279  m_fields[0]->UpdateCoeffs());
280  std::stringstream filenamei;
281  filenamei << "IConductivity_" << varCoeffString[k] << ".fld";
282  WriteFld(filenamei.str());
283 
284  // Transform variable coefficient and write out to file.
285  m_fields[0]->FwdTrans_IterPerExp(m_vardiffe[varCoeffEnum[k]],
286  m_fields[0]->UpdateCoeffs());
287  std::stringstream filenamee;
288  filenamee << "EConductivity_" << varCoeffString[k] << ".fld";
289  WriteFld(filenamee.str());
290 
291  ++k;
292  }
293  }
294 
295  // Search through the loaded filters and pass the cell model to any
296  // CheckpointCellModel filters loaded.
297  int k = 0;
298  const LibUtilities::FilterMap& f = m_session->GetFilters();
299  LibUtilities::FilterMap::const_iterator x;
300  for (x = f.begin(); x != f.end(); ++x, ++k)
301  {
302  if (x->first == "CheckpointCellModel")
303  {
304  boost::shared_ptr<FilterCheckpointCellModel> c
305  = boost::dynamic_pointer_cast<FilterCheckpointCellModel>(
306  m_filters[k]);
307  c->SetCellModel(m_cell);
308  }
309  }
310 
311  // Load stimuli
312  m_stimulus = Stimulus::LoadStimuli(m_session, m_fields[0]);
313 
314  if (!m_explicitDiffusion)
315  {
316  m_ode.DefineImplicitSolve (&BidomainRoth::DoImplicitSolve, this);
317  }
318  m_ode.DefineOdeRhs(&BidomainRoth::DoOdeRhs, this);
319 }
ASSERTL0
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:161
Nektar::BidomainRoth::DoOdeRhs
void DoOdeRhs(const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time)
Computes the reaction terms and .
Definition: BidomainRoth.cpp:376
Nektar::LibUtilities::NekFactory::CreateInstance
tBaseSharedPtr CreateInstance(tKey idKey BOOST_PP_COMMA_IF(MAX_PARAM) BOOST_PP_ENUM_BINARY_PARAMS(MAX_PARAM, tParam, x))
Create an instance of the class referred to by idKey.
Definition: NekFactory.hpp:162
Nektar::SolverUtils::UnsteadySystem::m_explicitDiffusion
bool m_explicitDiffusion
Indicates if explicit or implicit treatment of diffusion is used.
Definition: UnsteadySystem.h:73
Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineImplicitSolve
void DefineImplicitSolve(FuncPointerT func, ObjectPointerT obj)
Definition: TimeIntegrationScheme.h:208
Nektar::SolverUtils::UnsteadySystem::m_ode
LibUtilities::TimeIntegrationSchemeOperators m_ode
The time integration scheme operators to use.
Definition: UnsteadySystem.h:67
Nektar::FilterCheckpointCellModel::SetCellModel
void SetCellModel(CellModelSharedPtr &pCellModel)
Definition: FilterCheckpointCellModel.h:69
Nektar::BidomainRoth::m_vardiffe
StdRegions::VarCoeffMap m_vardiffe
Definition: BidomainRoth.h:104
Nektar::Stimulus::LoadStimuli
static std::vector< StimulusSharedPtr > LoadStimuli(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Definition: Stimulus.cpp:93
Nektar::BidomainRoth::m_stimulus
std::vector< StimulusSharedPtr > m_stimulus
Definition: BidomainRoth.h:101
Nektar::BidomainRoth::DoImplicitSolve
void DoImplicitSolve(const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, NekDouble time, NekDouble lambda)
Solve for the diffusion term.
Definition: BidomainRoth.cpp:337
Vmath::Smul
void Smul(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Scalar multiply y = alpha*y.
Definition: Vmath.cpp:199
Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineOdeRhs
void DefineOdeRhs(FuncPointerT func, ObjectPointerT obj)
Definition: TimeIntegrationScheme.h:184
Nektar::LibUtilities::FilterMap
std::vector< std::pair< std::string, FilterParams > > FilterMap
Definition: SessionReader.h:66
Nektar::SolverUtils::EquationSystem::m_spacedim
int m_spacedim
Spatial dimension (>= expansion dim).
Definition: EquationSystem.h:449
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:43
Nektar::SolverUtils::EquationSystem::EvaluateFunction
SOLVER_UTILS_EXPORT void EvaluateFunction(Array< OneD, Array< OneD, NekDouble > > &pArray, std::string pFunctionName, const NekDouble pTime=0.0, const int domain=0)
Evaluates a function as specified in the session file.
Definition: EquationSystem.cpp:684
Vmath::Sadd
void Sadd(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Add vector y = alpha + x.
Definition: Vmath.cpp:301
Nektar::BidomainRoth::m_vardiffie
StdRegions::VarCoeffMap m_vardiffie
Definition: BidomainRoth.h:105
Nektar::GetCellModelFactory
CellModelFactory & GetCellModelFactory()
Definition: CellModel.cpp:45
Nektar::SolverUtils::EquationSystem::WriteFld
SOLVER_UTILS_EXPORT void WriteFld(const std::string &outname)
Write field data to the given filename.
Definition: EquationSystem.cpp:2004
Nektar::BidomainRoth::m_cell
CellModelSharedPtr m_cell
Cell model.
Definition: BidomainRoth.h:99
Nektar::SolverUtils::EquationSystem::m_fields
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
Definition: EquationSystem.h:423
Nektar::SolverUtils::EquationSystem::m_session
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
Definition: EquationSystem.h:415
Nektar::BidomainRoth::m_vardiffi
StdRegions::VarCoeffMap m_vardiffi
Definition: BidomainRoth.h:103
Nektar::SolverUtils::UnsteadySystem::m_filters
std::vector< FilterSharedPtr > m_filters
Definition: UnsteadySystem.h:84
Vmath::Vadd
void Vadd(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Add vector z = x+y.
Definition: Vmath.cpp:285
Vmath::Vmul
void Vmul(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Multiply vector z = x*y.
Definition: Vmath.cpp:169
void Nektar::BidomainRoth::v_SetInitialConditions ( NekDouble  initialtime,
bool  dumpInitialConditions,
const int  domain 
)
protectedvirtual

Sets a custom initial condition.

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 457 of file BidomainRoth.cpp.

References m_cell.

460 {
461  EquationSystem::v_SetInitialConditions(initialtime,
462  dumpInitialConditions,
463  domain);
464  m_cell->Initialise();
465 }
Nektar::BidomainRoth::m_cell
CellModelSharedPtr m_cell
Cell model.
Definition: BidomainRoth.h:99

Friends And Related Function Documentation

friend class MemoryManager< BidomainRoth >
friend

Definition at line 51 of file BidomainRoth.h.

Member Data Documentation

string Nektar::BidomainRoth::className
static
Initial value:
= SolverUtils::GetEquationSystemFactory().RegisterCreatorFunction(
"BidomainRoth",
BidomainRoth::create,
"Bidomain Roth model of cardiac electrophysiology.")

Name of class.

Registers the class with the Factory.

Definition at line 64 of file BidomainRoth.h.

NekDouble Nektar::BidomainRoth::m_capMembrane
private

Definition at line 108 of file BidomainRoth.h.

Referenced by DoImplicitSolve(), and v_InitObject().

CellModelSharedPtr Nektar::BidomainRoth::m_cell
private

Cell model.

Definition at line 99 of file BidomainRoth.h.

Referenced by DoOdeRhs(), v_GenerateSummary(), v_InitObject(), and v_SetInitialConditions().

NekDouble Nektar::BidomainRoth::m_chi
private

Definition at line 107 of file BidomainRoth.h.

Referenced by DoImplicitSolve(), and v_InitObject().

NekDouble Nektar::BidomainRoth::m_stimDuration
private

Stimulus current.

Definition at line 111 of file BidomainRoth.h.

std::vector<StimulusSharedPtr> Nektar::BidomainRoth::m_stimulus
private

Definition at line 101 of file BidomainRoth.h.

Referenced by DoOdeRhs(), and v_InitObject().

StdRegions::VarCoeffMap Nektar::BidomainRoth::m_vardiffe
private

Definition at line 104 of file BidomainRoth.h.

Referenced by DoImplicitSolve(), and v_InitObject().

StdRegions::VarCoeffMap Nektar::BidomainRoth::m_vardiffi
private

Definition at line 103 of file BidomainRoth.h.

Referenced by DoOdeRhs(), and v_InitObject().

StdRegions::VarCoeffMap Nektar::BidomainRoth::m_vardiffie
private

Definition at line 105 of file BidomainRoth.h.

Referenced by DoOdeRhs(), and v_InitObject().

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