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Nektar::BidomainRoth Class Reference

A model for cardiac conduction. More...

#include <BidomainRoth.h>

Inheritance diagram for Nektar::BidomainRoth:
[legend]

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...
 
SOLVER_UTILS_EXPORT void SteadyStateResidual (int step, Array< OneD, NekDouble > &L2)
 
- 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 (bool DeclareField=true)
 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 >
std::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 ExtraFldOutput (std::vector< Array< OneD, NekDouble >> &fieldcoeffs, std::vector< std::string > &variables)
 
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 SessionFunctionSharedPtr GetFunction (std::string name, const MultiRegions::ExpListSharedPtr &field=MultiRegions::NullExpListSharedPtr, bool cache=false)
 Get a SessionFunction by name. 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, NekDoubleErrorExtraPoints (unsigned int field)
 Compute error (L2 and L_inf) over an larger set of quadrature points return [L2 Linf]. 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 SessionSummary (SummaryList &vSummary)
 Write out a session summary. More...
 
SOLVER_UTILS_EXPORT Array< OneD, MultiRegions::ExpListSharedPtr > & UpdateFields ()
 
SOLVER_UTILS_EXPORT LibUtilities::FieldMetaDataMapUpdateFieldMetaDataMap ()
 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 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 SetSteps (const int steps)
 
SOLVER_UTILS_EXPORT void ZeroPhysFields ()
 
SOLVER_UTILS_EXPORT void FwdTransFields ()
 
SOLVER_UTILS_EXPORT void SetModifiedBasis (const bool modbasis)
 
SOLVER_UTILS_EXPORT int GetCheckpointNumber ()
 
SOLVER_UTILS_EXPORT void SetCheckpointNumber (int num)
 
SOLVER_UTILS_EXPORT int GetCheckpointSteps ()
 
SOLVER_UTILS_EXPORT void SetCheckpointSteps (int num)
 
SOLVER_UTILS_EXPORT Array< OneD, const Array< OneD, NekDouble > > GetTraceNormals ()
 
SOLVER_UTILS_EXPORT void SetTime (const NekDouble time)
 
SOLVER_UTILS_EXPORT void SetInitialStep (const int step)
 
SOLVER_UTILS_EXPORT void SetBoundaryConditions (NekDouble time)
 Evaluates the boundary conditions at the given time. 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, const SpatialDomains::MeshGraphSharedPtr &pGraph)
 Creates an instance of this class. More...
 

Static Public Attributes

static std::string className
 Name of class. More...
 
- Static Public Attributes inherited from Nektar::SolverUtils::UnsteadySystem
static std::string cmdSetStartTime
 
static std::string cmdSetStartChkNum
 

Protected Member Functions

 BidomainRoth (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
 Constructor. More...
 
virtual void v_InitObject ()
 
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, const SpatialDomains::MeshGraphSharedPtr &pGraph)
 Initialises UnsteadySystem class members. More...
 
virtual SOLVER_UTILS_EXPORT void v_InitObject (bool DeclareField=true)
 Init object for UnsteadySystem class. 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 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_RequireFwdTrans ()
 
virtual SOLVER_UTILS_EXPORT void v_SteadyStateResidual (int step, Array< OneD, NekDouble > &L2)
 
SOLVER_UTILS_EXPORT void CheckForRestartTime (NekDouble &time, int &nchk)
 
SOLVER_UTILS_EXPORT void SVVVarDiffCoeff (const Array< OneD, Array< OneD, NekDouble >> vel, StdRegions::VarCoeffMap &varCoeffMap)
 Evaluate the SVV diffusion coefficient according to Moura's paper where it should proportional to h time velocity. More...
 
virtual SOLVER_UTILS_EXPORT bool UpdateTimeStepCheck ()
 
- Protected Member Functions inherited from Nektar::SolverUtils::EquationSystem
SOLVER_UTILS_EXPORT EquationSystem (const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
 Initialises EquationSystem class members. 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)
 
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< StimulusSharedPtrm_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...
 
NekDouble m_cflNonAcoustic
 
NekDouble m_CFLGrowth
 CFL growth rate. More...
 
NekDouble m_CFLEnd
 maximun cfl in cfl growth 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...
 
int m_abortSteps
 Number of steps between checks for abort conditions. More...
 
int m_filtersInfosteps
 Number of time steps between outputting filters information. More...
 
int m_nanSteps
 
LibUtilities::TimeIntegrationSchemeSharedPtr m_intScheme
 Wrapper to the time integration scheme. More...
 
LibUtilities::TimeIntegrationSchemeOperators m_ode
 The time integration scheme operators to use. More...
 
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...
 
NekDouble m_steadyStateTol
 Tolerance to which steady state should be evaluated at. More...
 
int m_steadyStateSteps
 Check for steady state at step interval. More...
 
NekDouble m_steadyStateRes = 1.0
 
NekDouble m_steadyStateRes0 = 1.0
 
Array< OneD, Array< OneD, NekDouble > > m_previousSolution
 Storage for previous solution for steady-state check. More...
 
std::ofstream m_errFile
 
std::vector< int > m_intVariables
 
std::vector< std::pair< std::string, FilterSharedPtr > > m_filters
 
NekDouble m_filterTimeWarning
 Number of time steps between outputting status information. More...
 
NekDouble m_TimeIntegLambda = 0.0
 coefff of spacial derivatives(rhs or m_F in GLM) in calculating the residual of the whole equation(used in unsteady time integrations) More...
 
bool m_flagImplicitItsStatistics
 
bool m_flagImplicitSolver = false
 
Array< OneD, NekDoublem_magnitdEstimat
 estimate the magnitude of each conserved varibles More...
 
Array< OneD, NekDoublem_locTimeStep
 local time step(notice only for jfnk other see m_cflSafetyFactor) More...
 
NekDouble m_inArrayNorm = -1.0
 
int m_TotLinItePerStep = 0
 
int m_StagesPerStep = 1
 
bool m_flagUpdatePreconMat
 
int m_maxLinItePerNewton
 
int m_TotNewtonIts = 0
 
int m_TotLinIts = 0
 
int m_TotImpStages = 0
 
bool m_CalcPhysicalAV = true
 flag to update artificial viscosity More...
 
- Protected Attributes inherited from Nektar::SolverUtils::EquationSystem
LibUtilities::CommSharedPtr m_comm
 Communicator. More...
 
bool m_verbose
 
bool m_root
 
LibUtilities::SessionReaderSharedPtr m_session
 The session reader. More...
 
std::map< std::string, SolverUtils::SessionFunctionSharedPtrm_sessionFunctions
 Map of known SessionFunctions. More...
 
LibUtilities::FieldIOSharedPtr m_fld
 Field input/output. More...
 
Array< OneD, MultiRegions::ExpListSharedPtrm_fields
 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...
 
int m_initialStep
 Number of the step where the simulation should begin. More...
 
NekDouble m_fintime
 Finish time of the simulation. More...
 
NekDouble m_timestep
 Time step size. More...
 
NekDouble m_timestepMax = -1.0
 Time step size. More...
 
NekDouble m_lambda
 Lambda constant in real system if one required. More...
 
NekDouble m_checktime
 Time between checkpoints. More...
 
NekDouble m_lastCheckTime
 
NekDouble m_TimeIncrementFactor
 
int m_nchk
 Number of checkpoints written so far. 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, 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...
 
Array< OneD, NekDoublem_movingFrameVelsxyz
 Moving frame of reference velocities. More...
 
Array< OneD, NekDoublem_movingFrameTheta
 Moving frame of reference angles with respect to the. More...
 
boost::numeric::ublas::matrix< NekDoublem_movingFrameProjMat
 Projection matrix for transformation between inertial and moving. 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...
 
- Static Protected Attributes inherited from Nektar::SolverUtils::EquationSystem
static std::string equationSystemTypeLookupIds []
 

Detailed Description

A model for cardiac conduction.

Definition at line 46 of file BidomainRoth.h.

Constructor & Destructor Documentation

◆ ~BidomainRoth()

Nektar::BidomainRoth::~BidomainRoth ( )
virtual

Desctructor.

Definition at line 306 of file BidomainRoth.cpp.

307 {
308 }

◆ BidomainRoth()

Nektar::BidomainRoth::BidomainRoth ( const LibUtilities::SessionReaderSharedPtr pSession,
const SpatialDomains::MeshGraphSharedPtr pGraph 
)
protected

Constructor.

Definition at line 56 of file BidomainRoth.cpp.

58  : UnsteadySystem(pSession, pGraph)
59 {
60 }
SOLVER_UTILS_EXPORT UnsteadySystem(const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
Initialises UnsteadySystem class members.

Member Function Documentation

◆ create()

static SolverUtils::EquationSystemSharedPtr Nektar::BidomainRoth::create ( const LibUtilities::SessionReaderSharedPtr pSession,
const SpatialDomains::MeshGraphSharedPtr pGraph 
)
inlinestatic

Creates an instance of this class.

Definition at line 52 of file BidomainRoth.h.

55  {
58  p->InitObject();
59  return p;
60  }
static std::shared_ptr< DataType > AllocateSharedPtr(const Args &...args)
Allocate a shared pointer from the memory pool.
std::shared_ptr< EquationSystem > EquationSystemSharedPtr
A shared pointer to an EquationSystem object.

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), and CellMLToNektar.cellml_metadata::p.

◆ DoImplicitSolve()

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 316 of file BidomainRoth.cpp.

320 {
321  int nq = m_fields[0]->GetNpoints();
322 
323  StdRegions::ConstFactorMap factorsHelmholtz;
324  // lambda = \Delta t
325  factorsHelmholtz[StdRegions::eFactorLambda] =
326  1.0 / lambda * m_chi * m_capMembrane;
327 
328  // ------------------------------
329  // Solve Helmholtz problem for Vm
330  // ------------------------------
331  // Multiply 1.0/timestep
332  // Vmath::Vadd(nq, inarray[0], 1, ggrad, 1, m_fields[0]->UpdatePhys(), 1);
333  Vmath::Smul(nq, -factorsHelmholtz[StdRegions::eFactorLambda], inarray[0], 1,
334  m_fields[0]->UpdatePhys(), 1);
335 
336  // Solve a system of equations with Helmholtz solver and transform
337  // back into physical space.
338  m_fields[0]->HelmSolve(m_fields[0]->GetPhys(), m_fields[0]->UpdateCoeffs(),
339  factorsHelmholtz, m_vardiffe);
340 
341  m_fields[0]->BwdTrans(m_fields[0]->GetCoeffs(), m_fields[0]->UpdatePhys());
342  m_fields[0]->SetPhysState(true);
343 
344  // Copy the solution vector (required as m_fields must be set).
345  outarray[0] = m_fields[0]->GetPhys();
346 }
StdRegions::VarCoeffMap m_vardiffe
Definition: BidomainRoth.h:101
Array< OneD, MultiRegions::ExpListSharedPtr > m_fields
Array holding all dependent variables.
std::map< ConstFactorType, NekDouble > ConstFactorMap
Definition: StdRegions.hpp:282
void Smul(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Scalar multiply y = alpha*x.
Definition: Vmath.cpp:248

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

Referenced by v_InitObject().

◆ DoOdeRhs()

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 351 of file BidomainRoth.cpp.

354 {
355  int nq = m_fields[0]->GetNpoints();
356 
357  // Compute I_ion
358  m_cell->TimeIntegrate(inarray, outarray, time);
359 
360  // Compute I_stim
361  for (unsigned int i = 0; i < m_stimulus.size(); ++i)
362  {
363  m_stimulus[i]->Update(outarray, time);
364  }
365 
366  Array<OneD, NekDouble> ggrad0(nq), ggrad1(nq), ggrad2(nq), ggrad(nq);
367  StdRegions::ConstFactorMap factorsPoisson;
368  factorsPoisson[StdRegions::eFactorLambda] = 0.0;
369 
370  // ----------------------------
371  // Compute \nabla g_i \nabla Vm
372  // ----------------------------
373  m_fields[0]->PhysDeriv(inarray[0], ggrad0, ggrad1, ggrad2);
374  m_fields[0]->PhysDeriv(0, ggrad0, ggrad0);
375  m_fields[0]->PhysDeriv(1, ggrad1, ggrad1);
376  m_fields[0]->PhysDeriv(2, ggrad2, ggrad2);
377  if (m_session->DefinesFunction("IntracellularAnisotropicConductivity") &&
378  m_session->DefinesFunction("ExtracellularAnisotropicConductivity"))
379  {
381  ggrad0, 1);
383  ggrad1, 1);
385  ggrad2, 1);
386  }
387  // Add partial derivatives together
388  Vmath::Vadd(nq, ggrad0, 1, ggrad1, 1, ggrad, 1);
389  Vmath::Vadd(nq, ggrad2, 1, ggrad, 1, ggrad, 1);
390 
391  Vmath::Smul(nq, -1.0, ggrad, 1, m_fields[1]->UpdatePhys(), 1);
392 
393  // ----------------------------
394  // Solve Poisson problem for Ve
395  // ----------------------------
396  m_fields[1]->HelmSolve(m_fields[1]->GetPhys(), m_fields[1]->UpdateCoeffs(),
397  factorsPoisson, m_vardiffie);
398  m_fields[1]->BwdTrans(m_fields[1]->GetCoeffs(), m_fields[1]->UpdatePhys());
399  m_fields[1]->SetPhysState(true);
400 
401  // ------------------------------
402  // Compute Laplacian of Ve (forcing term)
403  // ------------------------------
404  m_fields[1]->PhysDeriv(m_fields[1]->GetPhys(), ggrad0, ggrad1, ggrad2);
405  m_fields[1]->PhysDeriv(0, ggrad0, ggrad0);
406  m_fields[1]->PhysDeriv(1, ggrad1, ggrad1);
407  m_fields[1]->PhysDeriv(2, ggrad2, ggrad2);
408  if (m_session->DefinesFunction("IntracellularAnisotropicConductivity") &&
409  m_session->DefinesFunction("ExtracellularAnisotropicConductivity"))
410  {
412  ggrad0, 1);
414  ggrad1, 1);
416  ggrad2, 1);
417  }
418  // Add partial derivatives together
419  Vmath::Vadd(nq, ggrad0, 1, ggrad1, 1, ggrad, 1);
420  Vmath::Vadd(nq, ggrad2, 1, ggrad, 1, ggrad, 1);
421 
422  Vmath::Vadd(nq, ggrad, 1, outarray[0], 1, outarray[0], 1);
423 }
StdRegions::VarCoeffMap m_vardiffi
Definition: BidomainRoth.h:100
std::vector< StimulusSharedPtr > m_stimulus
Definition: BidomainRoth.h:98
CellModelSharedPtr m_cell
Cell model.
Definition: BidomainRoth.h:96
StdRegions::VarCoeffMap m_vardiffie
Definition: BidomainRoth.h:102
LibUtilities::SessionReaderSharedPtr m_session
The session reader.
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:209
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:359

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, Vmath::Smul(), Vmath::Vadd(), and Vmath::Vmul().

Referenced by v_InitObject().

◆ LoadStimuli()

void Nektar::BidomainRoth::LoadStimuli ( )
private

◆ v_GenerateSummary()

void Nektar::BidomainRoth::v_GenerateSummary ( SummaryList s)
protectedvirtual

Prints a summary of the model parameters.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 440 of file BidomainRoth.cpp.

441 {
443  m_cell->GenerateSummary(s);
444 }
virtual SOLVER_UTILS_EXPORT void v_GenerateSummary(SummaryList &s)
Print a summary of time stepping parameters.

References m_cell, and Nektar::SolverUtils::UnsteadySystem::v_GenerateSummary().

◆ v_InitObject()

void Nektar::BidomainRoth::v_InitObject ( )
protectedvirtual

Definition at line 65 of file BidomainRoth.cpp.

66 {
68 
69  m_session->LoadParameter("Chi", m_chi);
70  m_session->LoadParameter("Cm", m_capMembrane);
71 
72  std::string vCellModel;
73  m_session->LoadSolverInfo("CELLMODEL", vCellModel, "");
74 
75  ASSERTL0(vCellModel != "", "Cell Model not specified.");
76 
78  m_fields[0]);
79 
80  m_intVariables.push_back(0);
81 
82  // Load variable coefficients
83  StdRegions::VarCoeffType varCoeffEnum[6] = {
87  std::string varCoeffString[6] = {"xx", "xy", "yy", "xz", "yz", "zz"};
88  std::string aniso_var[3] = {"fx", "fy", "fz"};
89 
90  const int nq = m_fields[0]->GetNpoints();
91 
92  // Allocate storage for variable coeffs and initialize to 1.
93  for (int i = 0, k = 0; i < m_spacedim; ++i)
94  {
95  for (int j = 0; j < i + 1; ++j)
96  {
97  if (i == j)
98  {
99  m_vardiffi[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
100  m_vardiffe[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
101  m_vardiffie[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
102  }
103  else
104  {
105  m_vardiffi[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 0.0);
106  m_vardiffe[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 0.0);
107  m_vardiffie[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 0.0);
108  }
109  ++k;
110  }
111  }
112 
113  // Apply fibre map f \in [0,1], scale to conductivity range
114  // [o_min,o_max], specified by the session parameters o_min and o_max
115  if (m_session->DefinesFunction("ExtracellularAnisotropicConductivity"))
116  {
117  if (m_session->DefinesCmdLineArgument("verbose"))
118  {
119  cout << "Loading Extracellular Anisotropic Fibre map." << endl;
120  }
121 
122  NekDouble o_min = m_session->GetParameter("o_min");
123  NekDouble o_max = m_session->GetParameter("o_max");
124  int k = 0;
125 
126  Array<OneD, NekDouble> vTemp_i;
127  Array<OneD, NekDouble> vTemp_j;
128 
129  /*
130  * Diffusivity matrix D is upper triangular and defined as
131  * d_00 d_01 d_02
132  * d_11 d_12
133  * d_22
134  *
135  * Given a principle fibre direction _f_ the diffusivity is given
136  * by
137  * d_ij = { D_2 + (D_1 - D_2) f_i f_j if i==j
138  * { (D_1 - D_2) f_i f_j if i!=j
139  *
140  * The vector _f_ is given in terms of the variables fx,fy,fz in the
141  * function AnisotropicConductivity. The values of D_1 and D_2 are
142  * the parameters o_max and o_min, respectively.
143  */
144 
145  // Loop through columns of D
146  for (int j = 0; j < m_spacedim; ++j)
147  {
148  ASSERTL0(m_session->DefinesFunction(
149  "ExtracellularAnisotropicConductivity", aniso_var[j]),
150  "Function 'AnisotropicConductivity' not correctly "
151  "defined.");
152 
153  GetFunction("ExtracellularAnisotropicConductivity")
154  ->Evaluate(aniso_var[j], vTemp_j);
155 
156  // Loop through rows of D
157  for (int i = 0; i < j + 1; ++i)
158  {
159  ASSERTL0(
160  m_session->DefinesFunction(
161  "ExtracellularAnisotropicConductivity", aniso_var[i]),
162  "Function 'ExtracellularAnisotropicConductivity' not "
163  "correctly defined.");
164 
165  GetFunction("ExtracellularAnisotropicConductivity")
166  ->Evaluate(aniso_var[i], vTemp_i);
167 
168  Vmath::Vmul(nq, vTemp_i, 1, vTemp_j, 1,
169  m_vardiffe[varCoeffEnum[k]], 1);
170 
171  Vmath::Smul(nq, o_max - o_min, m_vardiffe[varCoeffEnum[k]], 1,
172  m_vardiffe[varCoeffEnum[k]], 1);
173 
174  if (i == j)
175  {
176  Vmath::Sadd(nq, o_min, m_vardiffe[varCoeffEnum[k]], 1,
177  m_vardiffe[varCoeffEnum[k]], 1);
178  }
179  }
180  }
181  }
182 
183  // Apply fibre map f \in [0,1], scale to conductivity range
184  // [o_min,o_max], specified by the session parameters o_min and o_max
185  if (m_session->DefinesFunction("IntracellularAnisotropicConductivity"))
186  {
187  if (m_session->DefinesCmdLineArgument("verbose"))
188  {
189  cout << "Loading Anisotropic Fibre map." << endl;
190  }
191 
192  NekDouble o_min = m_session->GetParameter("o_min");
193  NekDouble o_max = m_session->GetParameter("o_max");
194  int k = 0;
195 
196  Array<OneD, NekDouble> vTemp_i;
197  Array<OneD, NekDouble> vTemp_j;
198 
199  /*
200  * Diffusivity matrix D is upper triangular and defined as
201  * d_00 d_01 d_02
202  * d_11 d_12
203  * d_22
204  *
205  * Given a principle fibre direction _f_ the diffusivity is given
206  * by
207  * d_ij = { D_2 + (D_1 - D_2) f_i f_j if i==j
208  * { (D_1 - D_2) f_i f_j if i!=j
209  *
210  * The vector _f_ is given in terms of the variables fx,fy,fz in the
211  * function AnisotropicConductivity. The values of D_1 and D_2 are
212  * the parameters o_max and o_min, respectively.
213  */
214 
215  // Loop through columns of D
216  for (int j = 0; j < m_spacedim; ++j)
217  {
218  ASSERTL0(m_session->DefinesFunction(
219  "IntracellularAnisotropicConductivity", aniso_var[j]),
220  "Function 'IntracellularAnisotropicConductivity' not "
221  "correctly defined.");
222 
223  GetFunction("IntracellularAnisotropicConductivity")
224  ->Evaluate(aniso_var[j], vTemp_j);
225 
226  // Loop through rows of D
227  for (int i = 0; i < j + 1; ++i)
228  {
229  ASSERTL0(
230  m_session->DefinesFunction(
231  "IntracellularAnisotropicConductivity", aniso_var[i]),
232  "Function 'IntracellularAnisotropicConductivity' not "
233  "correctly defined.");
234  GetFunction("IntracellularAnisotropicConductivity")
235  ->Evaluate(aniso_var[i], vTemp_i);
236 
237  Vmath::Vmul(nq, vTemp_i, 1, vTemp_j, 1,
238  m_vardiffi[varCoeffEnum[k]], 1);
239 
240  Vmath::Smul(nq, o_max - o_min, m_vardiffi[varCoeffEnum[k]], 1,
241  m_vardiffi[varCoeffEnum[k]], 1);
242 
243  if (i == j)
244  {
245  Vmath::Sadd(nq, o_min, m_vardiffi[varCoeffEnum[k]], 1,
246  m_vardiffi[varCoeffEnum[k]], 1);
247  }
248 
249  Vmath::Vadd(nq, m_vardiffe[varCoeffEnum[k]], 1,
250  m_vardiffi[varCoeffEnum[k]], 1,
251  m_vardiffie[varCoeffEnum[k]], 1);
252 
253  ++k;
254  }
255  }
256  }
257 
258  // Write out conductivity values
259  for (int j = 0, k = 0; j < m_spacedim; ++j)
260  {
261  // Loop through rows of D
262  for (int i = 0; i < j + 1; ++i)
263  {
264  // Transform variable coefficient and write out to file.
265  m_fields[0]->FwdTransLocalElmt(m_vardiffi[varCoeffEnum[k]],
266  m_fields[0]->UpdateCoeffs());
267  std::stringstream filenamei;
268  filenamei << "IConductivity_" << varCoeffString[k] << ".fld";
269  WriteFld(filenamei.str());
270 
271  // Transform variable coefficient and write out to file.
272  m_fields[0]->FwdTransLocalElmt(m_vardiffe[varCoeffEnum[k]],
273  m_fields[0]->UpdateCoeffs());
274  std::stringstream filenamee;
275  filenamee << "EConductivity_" << varCoeffString[k] << ".fld";
276  WriteFld(filenamee.str());
277 
278  ++k;
279  }
280  }
281 
282  // Search through the loaded filters and pass the cell model to any
283  // CheckpointCellModel filters loaded.
284  for (auto &x : m_filters)
285  {
286  if (x.first == "CheckpointCellModel")
287  {
288  std::shared_ptr<FilterCheckpointCellModel> c =
289  std::dynamic_pointer_cast<FilterCheckpointCellModel>(x.second);
290  c->SetCellModel(m_cell);
291  }
292  }
293  // Load stimuli
295 
296  if (!m_explicitDiffusion)
297  {
299  }
301 }
#define ASSERTL0(condition, msg)
Definition: ErrorUtil.hpp:215
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.
void DoOdeRhs(const Array< OneD, const Array< OneD, NekDouble >> &inarray, Array< OneD, Array< OneD, NekDouble >> &outarray, const NekDouble time)
Computes the reaction terms and .
tBaseSharedPtr CreateInstance(tKey idKey, tParam... args)
Create an instance of the class referred to by idKey.
Definition: NekFactory.hpp:144
void DefineOdeRhs(FuncPointerT func, ObjectPointerT obj)
void DefineImplicitSolve(FuncPointerT func, ObjectPointerT obj)
int m_spacedim
Spatial dimension (>= expansion dim).
SOLVER_UTILS_EXPORT void WriteFld(const std::string &outname)
Write field data to the given filename.
SOLVER_UTILS_EXPORT SessionFunctionSharedPtr GetFunction(std::string name, const MultiRegions::ExpListSharedPtr &field=MultiRegions::NullExpListSharedPtr, bool cache=false)
Get a SessionFunction by name.
LibUtilities::TimeIntegrationSchemeOperators m_ode
The time integration scheme operators to use.
std::vector< std::pair< std::string, FilterSharedPtr > > m_filters
bool m_explicitDiffusion
Indicates if explicit or implicit treatment of diffusion is used.
virtual SOLVER_UTILS_EXPORT void v_InitObject(bool DeclareField=true)
Init object for UnsteadySystem class.
static std::vector< StimulusSharedPtr > LoadStimuli(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Definition: Stimulus.cpp:89
CellModelFactory & GetCellModelFactory()
Definition: CellModel.cpp:46
double NekDouble
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:384

References ASSERTL0, Nektar::LibUtilities::NekFactory< tKey, tBase, tParam >::CreateInstance(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineImplicitSolve(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineOdeRhs(), DoImplicitSolve(), DoOdeRhs(), Nektar::StdRegions::eVarCoeffD00, Nektar::StdRegions::eVarCoeffD01, Nektar::StdRegions::eVarCoeffD02, Nektar::StdRegions::eVarCoeffD11, Nektar::StdRegions::eVarCoeffD12, Nektar::StdRegions::eVarCoeffD22, Nektar::GetCellModelFactory(), Nektar::SolverUtils::EquationSystem::GetFunction(), 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(), Vmath::Smul(), Nektar::SolverUtils::UnsteadySystem::v_InitObject(), Vmath::Vadd(), Vmath::Vmul(), and Nektar::SolverUtils::EquationSystem::WriteFld().

◆ v_SetInitialConditions()

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 428 of file BidomainRoth.cpp.

431 {
432  EquationSystem::v_SetInitialConditions(initialtime, dumpInitialConditions,
433  domain);
434  m_cell->Initialise();
435 }
virtual SOLVER_UTILS_EXPORT void v_SetInitialConditions(NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)

References m_cell, and Nektar::SolverUtils::EquationSystem::v_SetInitialConditions().

Friends And Related Function Documentation

◆ MemoryManager< BidomainRoth >

friend class MemoryManager< BidomainRoth >
friend

Definition at line 1 of file BidomainRoth.h.

Member Data Documentation

◆ className

string Nektar::BidomainRoth::className
static
Initial value:
=
"BidomainRoth", BidomainRoth::create,
"Bidomain Roth model of cardiac electrophysiology.")
static SolverUtils::EquationSystemSharedPtr create(const LibUtilities::SessionReaderSharedPtr &pSession, const SpatialDomains::MeshGraphSharedPtr &pGraph)
Creates an instance of this class.
Definition: BidomainRoth.h:52
tKey RegisterCreatorFunction(tKey idKey, CreatorFunction classCreator, std::string pDesc="")
Register a class with the factory.
Definition: NekFactory.hpp:198
EquationSystemFactory & GetEquationSystemFactory()

Name of class.

Registers the class with the Factory.

Definition at line 63 of file BidomainRoth.h.

◆ m_capMembrane

NekDouble Nektar::BidomainRoth::m_capMembrane
private

Definition at line 105 of file BidomainRoth.h.

Referenced by DoImplicitSolve(), and v_InitObject().

◆ m_cell

CellModelSharedPtr Nektar::BidomainRoth::m_cell
private

Cell model.

Definition at line 96 of file BidomainRoth.h.

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

◆ m_chi

NekDouble Nektar::BidomainRoth::m_chi
private

Definition at line 104 of file BidomainRoth.h.

Referenced by DoImplicitSolve(), and v_InitObject().

◆ m_stimDuration

NekDouble Nektar::BidomainRoth::m_stimDuration
private

Stimulus current.

Definition at line 108 of file BidomainRoth.h.

◆ m_stimulus

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

Definition at line 98 of file BidomainRoth.h.

Referenced by DoOdeRhs(), and v_InitObject().

◆ m_vardiffe

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

Definition at line 101 of file BidomainRoth.h.

Referenced by DoImplicitSolve(), and v_InitObject().

◆ m_vardiffi

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

Definition at line 100 of file BidomainRoth.h.

Referenced by DoOdeRhs(), and v_InitObject().

◆ m_vardiffie

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

Definition at line 102 of file BidomainRoth.h.

Referenced by DoOdeRhs(), and v_InitObject().