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Nektar::Bidomain Class Reference

A model for cardiac conduction. More...

#include <Bidomain.h>

Inheritance diagram for Nektar::Bidomain:
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Public Member Functions

virtual ~Bidomain ()
 Desctructor.
- Public Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
virtual SOLVER_UTILS_EXPORT ~UnsteadySystem ()
 Destructor.
SOLVER_UTILS_EXPORT NekDouble GetTimeStep (const Array< OneD, const Array< OneD, NekDouble > > &inarray)
 Calculate the larger time-step mantaining the problem stable.
- Public Member Functions inherited from Nektar::SolverUtils::EquationSystem
virtual SOLVER_UTILS_EXPORT ~EquationSystem ()
 Destructor.
SOLVER_UTILS_EXPORT void SetUpTraceNormals (void)
SOLVER_UTILS_EXPORT void InitObject ()
 Initialises the members of this object.
SOLVER_UTILS_EXPORT void DoInitialise ()
 Perform any initialisation necessary before solving the problem.
SOLVER_UTILS_EXPORT void DoSolve ()
 Solve the problem.
SOLVER_UTILS_EXPORT void TransCoeffToPhys ()
 Transform from coefficient to physical space.
SOLVER_UTILS_EXPORT void TransPhysToCoeff ()
 Transform from physical to coefficient space.
SOLVER_UTILS_EXPORT void Output ()
 Perform output operations after solve.
SOLVER_UTILS_EXPORT NekDouble LinfError (unsigned int field, const Array< OneD, NekDouble > &exactsoln=NullNekDouble1DArray)
 Linf error computation.
SOLVER_UTILS_EXPORT std::string GetSessionName ()
 Get Session name.
template<class T >
boost::shared_ptr< T > as ()
SOLVER_UTILS_EXPORT void ResetSessionName (std::string newname)
 Reset Session name.
SOLVER_UTILS_EXPORT
LibUtilities::SessionReaderSharedPtr 
GetSession ()
 Get Session name.
SOLVER_UTILS_EXPORT
MultiRegions::ExpListSharedPtr 
GetPressure ()
 Get pressure field if available.
SOLVER_UTILS_EXPORT void PrintSummary (std::ostream &out)
 Print a summary of parameters and solver characteristics.
SOLVER_UTILS_EXPORT void SetLambda (NekDouble lambda)
 Set parameter m_lambda.
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.
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.
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.
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.
SOLVER_UTILS_EXPORT void InitialiseBaseFlow (Array< OneD, Array< OneD, NekDouble > > &base)
 Perform initialisation of the base flow.
SOLVER_UTILS_EXPORT void SetInitialConditions (NekDouble initialtime=0.0, bool dumpInitialConditions=true, const int domain=0)
 Initialise the data in the dependent fields.
SOLVER_UTILS_EXPORT void EvaluateExactSolution (int field, Array< OneD, NekDouble > &outfield, const NekDouble time)
 Evaluates an exact solution.
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.
SOLVER_UTILS_EXPORT NekDouble L2Error (unsigned int field, bool Normalised=false)
 Compute the L2 error of the fields.
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].
SOLVER_UTILS_EXPORT void WeakAdvectionGreensDivergenceForm (const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
 Compute the inner product $ (\nabla \phi \cdot F) $.
SOLVER_UTILS_EXPORT void WeakAdvectionDivergenceForm (const Array< OneD, Array< OneD, NekDouble > > &F, Array< OneD, NekDouble > &outarray)
 Compute the inner product $ (\phi, \nabla \cdot F) $.
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) $.
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.
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.
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.
SOLVER_UTILS_EXPORT void Checkpoint_Output (const int n)
 Write checkpoint file of m_fields.
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.
SOLVER_UTILS_EXPORT void Checkpoint_BaseFlow (const int n)
 Write base flow file of m_fields.
SOLVER_UTILS_EXPORT void WriteFld (const std::string &outname)
 Write field data to the given filename.
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.
SOLVER_UTILS_EXPORT void ImportFld (const std::string &infile, Array< OneD, MultiRegions::ExpListSharedPtr > &pFields)
 Input field data from the given file.
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.
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.
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.
SOLVER_UTILS_EXPORT void ScanForHistoryPoints ()
 Builds map of which element holds each history point.
SOLVER_UTILS_EXPORT void WriteHistoryData (std::ostream &out)
 Probe each history point and write to file.
SOLVER_UTILS_EXPORT void SessionSummary (SummaryList &vSummary)
 Write out a session summary.
SOLVER_UTILS_EXPORT Array
< OneD,
MultiRegions::ExpListSharedPtr > & 
UpdateFields ()
SOLVER_UTILS_EXPORT
LibUtilities::FieldMetaDataMap
UpdateFieldMetaDataMap ()
 Get hold of FieldInfoMap so it can be updated.
SOLVER_UTILS_EXPORT NekDouble GetFinalTime ()
 Return final time.
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.

Static Public Member Functions

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

Static Public Attributes

static std::string className
 Name of class.

Protected Member Functions

 Bidomain (const LibUtilities::SessionReaderSharedPtr &pSession)
 Constructor.
virtual void v_InitObject ()
 Init object for UnsteadySystem class.
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 $f(u,v)$ and $g(u,v)$.
virtual void v_SetInitialConditions (NekDouble initialtime, bool dumpInitialConditions, const int domain)
 Sets a custom initial condition.
virtual void v_GenerateSummary (SummaryList &s)
 Prints a summary of the model parameters.
- Protected Member Functions inherited from Nektar::SolverUtils::UnsteadySystem
SOLVER_UTILS_EXPORT UnsteadySystem (const LibUtilities::SessionReaderSharedPtr &pSession)
 Initialises UnsteadySystem class members.
SOLVER_UTILS_EXPORT NekDouble MaxTimeStepEstimator ()
 Get the maximum timestep estimator for cfl control.
virtual SOLVER_UTILS_EXPORT void v_DoSolve ()
 Solves an unsteady problem.
virtual SOLVER_UTILS_EXPORT void v_DoInitialise ()
 Sets up initial conditions.
virtual SOLVER_UTILS_EXPORT void v_AppendOutput1D (Array< OneD, Array< OneD, NekDouble > > &solution1D)
 Print the solution at each solution point in a txt file.
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.
virtual SOLVER_UTILS_EXPORT bool v_PreIntegrate (int step)
virtual SOLVER_UTILS_EXPORT bool v_PostIntegrate (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.
int nocase_cmp (const string &s1, const string &s2)
SOLVER_UTILS_EXPORT void SetBoundaryConditions (NekDouble time)
 Evaluates the boundary conditions at the given time.
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.
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.
virtual SOLVER_UTILS_EXPORT void v_TransCoeffToPhys ()
 Virtual function for transformation to physical space.
virtual SOLVER_UTILS_EXPORT void v_TransPhysToCoeff ()
 Virtual function for transformation to coefficient space.
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 Attributes

CellModelSharedPtr m_cell
 Cell model.
NekDouble m_chi
NekDouble m_capMembrane
NekDouble m_sigmaix
NekDouble m_sigmaiy
NekDouble m_sigmaiz
NekDouble m_sigmaex
NekDouble m_sigmaey
NekDouble m_sigmaez
StdRegions::VarCoeffMap m_vardiffi
StdRegions::VarCoeffMap m_vardiffie
Array< OneD, Array< OneD,
NekDouble > > 
tmp1
Array< OneD, Array< OneD,
NekDouble > > 
tmp2
Array< OneD, Array< OneD,
NekDouble > > 
tmp3
NekDouble m_stimDuration
 Stimulus current.

Friends

class MemoryManager< Bidomain >

Additional Inherited Members

- Public Attributes inherited from Nektar::SolverUtils::UnsteadySystem
NekDouble m_cflSafetyFactor
 CFL safety factor (comprise between 0 to 1).
- 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.
LibUtilities::TimeIntegrationWrapperSharedPtr m_intScheme
 Wrapper to the time integration scheme.
LibUtilities::TimeIntegrationSchemeOperators m_ode
 The time integration scheme operators to use.
LibUtilities::TimeIntegrationSolutionSharedPtr m_intSoln
NekDouble m_epsilon
bool m_explicitDiffusion
 Indicates if explicit or implicit treatment of diffusion is used.
bool m_explicitAdvection
 Indicates if explicit or implicit treatment of advection is used.
bool m_explicitReaction
 Indicates if explicit or implicit treatment of reaction is used.
bool m_homoInitialFwd
 Flag to determine if simulation should start in homogeneous forward transformed state.
std::vector< int > m_intVariables
std::vector< FilterSharedPtrm_filters

Detailed Description

A model for cardiac conduction.

Base model of cardiac electrophysiology of the form

\begin{align*} \frac{\partial u}{\partial t} = \nabla^2 u + J_{ion}, \end{align*}

where the reaction term, $J_{ion}$ is defined by a specific cell model.

This implementation, at present, treats the reaction terms explicitly and the diffusive element implicitly.

Definition at line 49 of file Bidomain.h.

Constructor & Destructor Documentation

Nektar::Bidomain::~Bidomain ( )
virtual

Desctructor.

Definition at line 177 of file Bidomain.cpp.

{
}
Nektar::Bidomain::Bidomain ( const LibUtilities::SessionReaderSharedPtr pSession)
protected

Constructor.

Definition at line 70 of file Bidomain.cpp.

: UnsteadySystem(pSession)
{
}

Member Function Documentation

static EquationSystemSharedPtr Nektar::Bidomain::create ( const LibUtilities::SessionReaderSharedPtr pSession)
inlinestatic

Creates an instance of this class.

Definition at line 55 of file Bidomain.h.

{
p->InitObject();
return p;
}
void Nektar::Bidomain::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 189 of file Bidomain.cpp.

References Nektar::StdRegions::eFactorLambda, m_capMembrane, m_chi, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::EquationSystem::m_session, Nektar::SolverUtils::EquationSystem::m_spacedim, m_vardiffi, m_vardiffie, Nektar::NullFlagList, Vmath::Smul(), Vmath::Vadd(), and Vmath::Vcopy().

Referenced by v_InitObject().

{
int nvariables = inarray.num_elements();
int nq = m_fields[0]->GetNpoints();
Array<OneD, NekDouble> grad0(nq), grad1(nq), grad2(nq), grad(nq);
Array<OneD, NekDouble> ggrad0(nq), ggrad1(nq), ggrad2(nq), ggrad(nq), temp(nq);
// We solve ( \sigma\nabla^2 - HHlambda ) Y[i] = rhs [i]
// inarray = input: \hat{rhs} -> output: \hat{Y}
// outarray = output: nabla^2 \hat{Y}
// where \hat = modal coeffs
for (int i = 0; i < nvariables; ++i)
{
// Only apply diffusion to first variable.
if (i > 1) {
Vmath::Vcopy(nq, &inarray[i][0], 1, &outarray[i][0], 1);
continue;
}
if (i == 0) {
factors[StdRegions::eFactorLambda] = (1.0/lambda)*(m_capMembrane*m_chi);
if (m_spacedim==1) {
// Take first partial derivative
m_fields[i]->PhysDeriv(inarray[1],ggrad0);
// Take second partial derivative
m_fields[i]->PhysDeriv(0,ggrad0,ggrad0);
// Multiply by Intracellular-Conductivity
if (m_session->DefinesFunction("IntracellularConductivity") && m_session->DefinesFunction("ExtracellularConductivity"))
{
Vmath::Smul(nq, m_session->GetParameter("sigmaix"), ggrad0, 1, ggrad0, 1);
}
// Add partial derivatives together
Vmath::Vcopy(nq, ggrad0, 1, ggrad, 1);
Vmath::Smul(nq, -1.0, ggrad, 1, ggrad, 1);
// Multiply 1.0/timestep/lambda
Vmath::Smul(nq, -factors[StdRegions::eFactorLambda], inarray[i], 1, temp, 1);
Vmath::Vadd(nq, ggrad, 1, temp, 1, m_fields[i]->UpdatePhys(), 1);
// Solve a system of equations with Helmholtz solver and transform
// back into physical space.
m_fields[i]->HelmSolve(m_fields[i]->GetPhys(), m_fields[i]->UpdateCoeffs(),NullFlagList,factors);
m_fields[i]->BwdTrans( m_fields[i]->GetCoeffs(), m_fields[i]->UpdatePhys());
m_fields[i]->SetPhysState(true);
// Copy the solution vector (required as m_fields must be set).
outarray[i] = m_fields[i]->GetPhys();
}
if (m_spacedim==2) {
// Take first partial derivative
m_fields[i]->PhysDeriv(inarray[1],ggrad0,ggrad1);
// Take second partial derivative
m_fields[i]->PhysDeriv(0,ggrad0,ggrad0);
m_fields[i]->PhysDeriv(1,ggrad1,ggrad1);
// Multiply by Intracellular-Conductivity
if (m_session->DefinesFunction("IntracellularConductivity") && m_session->DefinesFunction("ExtracellularConductivity"))
{
Vmath::Smul(nq, m_session->GetParameter("sigmaix"), ggrad0, 1, ggrad0, 1);
Vmath::Smul(nq, m_session->GetParameter("sigmaiy"), ggrad1, 1, ggrad1, 1);
}
// Add partial derivatives together
Vmath::Vadd(nq, ggrad0, 1, ggrad1, 1, ggrad, 1);
Vmath::Smul(nq, -1.0, ggrad, 1, ggrad, 1);
// Multiply 1.0/timestep/lambda
Vmath::Smul(nq, -factors[StdRegions::eFactorLambda], inarray[i], 1, temp, 1);
Vmath::Vadd(nq, ggrad, 1, temp, 1, m_fields[i]->UpdatePhys(), 1);
// Solve a system of equations with Helmholtz solver and transform
// back into physical space.
m_fields[i]->HelmSolve(m_fields[i]->GetPhys(), m_fields[i]->UpdateCoeffs(),NullFlagList,factors,m_vardiffi);
m_fields[i]->BwdTrans( m_fields[i]->GetCoeffs(), m_fields[i]->UpdatePhys());
m_fields[i]->SetPhysState(true);
// Copy the solution vector (required as m_fields must be set).
outarray[i] = m_fields[i]->GetPhys();
}
if (m_spacedim==3) {
// Take first partial derivative
m_fields[i]->PhysDeriv(inarray[1],ggrad0,ggrad1,ggrad2);
// Take second partial derivative
m_fields[i]->PhysDeriv(0,ggrad0,ggrad0);
m_fields[i]->PhysDeriv(1,ggrad1,ggrad1);
m_fields[i]->PhysDeriv(2,ggrad2,ggrad2);
// Multiply by Intracellular-Conductivity
if (m_session->DefinesFunction("IntracellularConductivity") && m_session->DefinesFunction("ExtracellularConductivity"))
{
Vmath::Smul(nq, m_session->GetParameter("sigmaix"), ggrad0, 1, ggrad0, 1);
Vmath::Smul(nq, m_session->GetParameter("sigmaiy"), ggrad1, 1, ggrad1, 1);
Vmath::Smul(nq, m_session->GetParameter("sigmaiz"), ggrad2, 1, ggrad2, 1);
}
// Add partial derivatives together
Vmath::Vadd(nq, ggrad0, 1, ggrad1, 1, ggrad, 1);
Vmath::Vadd(nq, ggrad2, 1, ggrad, 1, ggrad, 1);
Vmath::Smul(nq, -1.0, ggrad, 1, ggrad, 1);
// Multiply 1.0/timestep/lambda
Vmath::Smul(nq, -factors[StdRegions::eFactorLambda], inarray[i], 1, temp, 1);
Vmath::Vadd(nq, ggrad, 1, temp, 1, m_fields[i]->UpdatePhys(), 1);
// Solve a system of equations with Helmholtz solver and transform
// back into physical space.
m_fields[i]->HelmSolve(m_fields[i]->GetPhys(), m_fields[i]->UpdateCoeffs(),NullFlagList,factors,m_vardiffi);
m_fields[i]->BwdTrans( m_fields[i]->GetCoeffs(), m_fields[i]->UpdatePhys());
m_fields[i]->SetPhysState(true);
// Copy the solution vector (required as m_fields must be set).
outarray[i] = m_fields[i]->GetPhys();
}
}
if (i == 1) {
factors[StdRegions::eFactorLambda] = 0.0;
if (m_spacedim==1) {
// Take first partial derivative
m_fields[i]->PhysDeriv(m_fields[0]->UpdatePhys(),grad0);
// Take second derivative
m_fields[i]->PhysDeriv(0,grad0,grad0);
// Multiply by Intracellular-Conductivity
if (m_session->DefinesFunction("IntracellularConductivity") && m_session->DefinesFunction("ExtracellularConductivity"))
{
Vmath::Smul(nq, m_session->GetParameter("sigmaix"), grad0, 1, grad0, 1);
}
// and sum terms
Vmath::Vcopy(nq, grad0, 1, grad, 1);
Vmath::Smul(nq, (-1.0*m_session->GetParameter("sigmaix"))/(m_session->GetParameter("sigmaix")+m_session->GetParameter("sigmaix")), grad, 1, grad, 1);
// Now solve Poisson problem for \phi_e
m_fields[i]->SetPhys(grad);
m_fields[i]->HelmSolve(m_fields[i]->GetPhys(), m_fields[i]->UpdateCoeffs(), NullFlagList, factors);
m_fields[i]->BwdTrans( m_fields[i]->GetCoeffs(), m_fields[i]->UpdatePhys());
m_fields[i]->SetPhysState(true);
// Copy the solution vector (required as m_fields must be set).
outarray[i] = m_fields[i]->GetPhys();
}
if (m_spacedim==2) {
// Take first partial derivative
m_fields[i]->PhysDeriv(m_fields[0]->UpdatePhys(),grad0,grad1);
// Take second derivative
m_fields[i]->PhysDeriv(0,grad0,grad0);
m_fields[i]->PhysDeriv(1,grad1,grad1);
// Multiply by Intracellular-Conductivity
if (m_session->DefinesFunction("IntracellularConductivity") && m_session->DefinesFunction("ExtracellularConductivity"))
{
Vmath::Smul(nq, m_session->GetParameter("sigmaix"), grad0, 1, grad0, 1);
Vmath::Smul(nq, m_session->GetParameter("sigmaiy"), grad1, 1, grad1, 1);
}
// and sum terms
Vmath::Vadd(nq, grad0, 1, grad1, 1, grad, 1);
Vmath::Smul(nq, -1.0, grad, 1, grad, 1);
// Now solve Poisson problem for \phi_e
m_fields[i]->SetPhys(grad);
m_fields[i]->HelmSolve(m_fields[i]->GetPhys(), m_fields[i]->UpdateCoeffs(), NullFlagList, factors, m_vardiffie);
m_fields[i]->BwdTrans( m_fields[i]->GetCoeffs(), m_fields[i]->UpdatePhys());
m_fields[i]->SetPhysState(true);
// Copy the solution vector (required as m_fields must be set).
outarray[i] = m_fields[i]->GetPhys();
}
if (m_spacedim==3) {
// Take first partial derivative
m_fields[i]->PhysDeriv(m_fields[0]->UpdatePhys(),grad0,grad1,grad2);
// Take second derivative
m_fields[i]->PhysDeriv(0,grad0,grad0);
m_fields[i]->PhysDeriv(1,grad1,grad1);
m_fields[i]->PhysDeriv(2,grad2,grad2);
// Multiply by Intracellular-Conductivity
if (m_session->DefinesFunction("IntracellularConductivity") && m_session->DefinesFunction("ExtracellularConductivity"))
{
Vmath::Smul(nq, m_session->GetParameter("sigmaix"), grad0, 1, grad0, 1);
Vmath::Smul(nq, m_session->GetParameter("sigmaiy"), grad1, 1, grad1, 1);
Vmath::Smul(nq, m_session->GetParameter("sigmaiz"), grad2, 1, grad2, 1);
}
// and sum terms
Vmath::Vadd(nq, grad0, 1, grad1, 1, grad, 1);
Vmath::Vadd(nq, grad2, 1, grad, 1, grad, 1);
Vmath::Smul(nq, -1.0, grad, 1, grad, 1);
// Now solve Poisson problem for \phi_e
m_fields[i]->SetPhys(grad);
m_fields[i]->HelmSolve(m_fields[i]->GetPhys(), m_fields[i]->UpdateCoeffs(), NullFlagList, factors, m_vardiffie);
m_fields[i]->BwdTrans( m_fields[i]->GetCoeffs(), m_fields[i]->UpdatePhys());
m_fields[i]->SetPhysState(true);
// Copy the solution vector (required as m_fields must be set).
outarray[i] = m_fields[i]->GetPhys();
}
}
}
}
void Nektar::Bidomain::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 379 of file Bidomain.cpp.

References m_capMembrane, m_cell, Nektar::SolverUtils::EquationSystem::m_fields, Nektar::SolverUtils::EquationSystem::m_session, m_stimDuration, Vmath::Smul(), and Vmath::Vadd().

Referenced by v_InitObject().

{
int nq = m_fields[0]->GetNpoints();
m_cell->TimeIntegrate(inarray, outarray, time);
if (m_stimDuration > 0 && time < m_stimDuration)
{
Array<OneD,NekDouble> x0(nq);
Array<OneD,NekDouble> x1(nq);
Array<OneD,NekDouble> x2(nq);
Array<OneD,NekDouble> result(nq);
// get the coordinates
m_fields[0]->GetCoords(x0,x1,x2);
= m_session->GetFunction("Stimulus", "u");
ifunc->Evaluate(x0,x1,x2,time, result);
Vmath::Vadd(nq, outarray[0], 1, result, 1, outarray[0], 1);
}
Vmath::Smul(nq, 1.0/m_capMembrane, outarray[0], 1, outarray[0], 1);
}
void Nektar::Bidomain::v_GenerateSummary ( SummaryList s)
protectedvirtual

Prints a summary of the model parameters.

Update summary

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 417 of file Bidomain.cpp.

References ASSERTL0, and m_cell.

{
/// @TODO Update summary
ASSERTL0(false, "Update the generate summary");
//
// out << "\tChi : " << m_chi << endl;
// out << "\tCm : " << m_capMembrane << endl;
// if (m_session->DefinesFunction("IntracellularConductivity", "AnisotropicConductivityX") &&
// m_session->GetFunctionType("IntracellularConductivity", "AnisotropicConductivityX") == LibUtilities::eFunctionTypeExpression)
// {
// out << "\tIntra-Diffusivity-x : "
// << m_session->GetFunction("IntracellularConductivity", "AnisotropicConductivityX")->GetExpression()
// << endl;
// }
// if (m_session->DefinesFunction("IntracellularConductivity", "AnisotropicConductivityY") &&
// m_session->GetFunctionType("IntracellularConductivity", "AnisotropicConductivityY") == LibUtilities::eFunctionTypeExpression)
// {
// out << "\tIntra-Diffusivity-y : "
// << m_session->GetFunction("IntracellularConductivity", "AnisotropicConductivityY")->GetExpression()
// << endl;
// }
// if (m_session->DefinesFunction("IntracellularConductivity", "AnisotropicConductivityZ") &&
// m_session->GetFunctionType("IntracellularConductivity", "AnisotropicConductivityZ") == LibUtilities::eFunctionTypeExpression)
// {
// out << "\tIntra-Diffusivity-z : "
// << m_session->GetFunction("IntracellularConductivity", "AnisotropicConductivityZ")->GetExpression()
// << endl;
// }
// if (m_session->DefinesFunction("ExtracellularConductivity", "AnisotropicConductivityX") &&
// m_session->GetFunctionType("ExtracellularConductivity", "AnisotropicConductivityX") == LibUtilities::eFunctionTypeExpression)
// {
// out << "\tExtra-Diffusivity-x : "
// << m_session->GetFunction("ExtracellularConductivity", "AnisotropicConductivityX")->GetExpression()
// << endl;
// }
// if (m_session->DefinesFunction("ExtracellularConductivity", "AnisotropicConductivityY") &&
// m_session->GetFunctionType("ExtracellularConductivity", "AnisotropicConductivityY") == LibUtilities::eFunctionTypeExpression)
// {
// out << "\tExtra-Diffusivity-y : "
// << m_session->GetFunction("ExtracellularConductivity", "AnisotropicConductivityY")->GetExpression()
// << endl;
// }
// if (m_session->DefinesFunction("ExtracellularConductivity", "AnisotropicConductivityZ") &&
// m_session->GetFunctionType("ExtracellularConductivity", "AnisotropicConductivityZ") == LibUtilities::eFunctionTypeExpression)
// {
// out << "\tExtra-Diffusivity-z : "
// << m_session->GetFunction("ExtracellularConductivity", "AnisotropicConductivityZ")->GetExpression()
// << endl;
// }
m_cell->GenerateSummary(s);
}
void Nektar::Bidomain::v_InitObject ( )
protectedvirtual

Init object for UnsteadySystem class.

Initialization object for UnsteadySystem class.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 76 of file Bidomain.cpp.

References ASSERTL0, Nektar::LibUtilities::NekFactory< tKey, tBase, >::CreateInstance(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineImplicitSolve(), Nektar::LibUtilities::TimeIntegrationSchemeOperators::DefineOdeRhs(), DoImplicitSolve(), DoOdeRhs(), Nektar::StdRegions::eVarCoeffD00, Nektar::StdRegions::eVarCoeffD11, Nektar::StdRegions::eVarCoeffD22, Nektar::GetCellModelFactory(), 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_stimDuration, m_vardiffi, m_vardiffie, Nektar::FilterCheckpointCellModel::SetCellModel(), tmp1, tmp2, tmp3, and Vmath::Vadd().

{
m_session->LoadParameter("Chi", m_chi);
m_session->LoadParameter("Cm", m_capMembrane);
std::string vCellModel;
m_session->LoadSolverInfo("CELLMODEL", vCellModel, "");
ASSERTL0(vCellModel != "", "Cell Model not specified.");
m_intVariables.push_back(0);
m_intVariables.push_back(1);
// Load variable coefficients
StdRegions::VarCoeffType varCoeffEnum[3] = {
};
std::string varName[3] = {
"AnisotropicConductivityX",
"AnisotropicConductivityY",
"AnisotropicConductivityZ"
};
if (m_session->DefinesFunction("IntracellularConductivity") && m_session->DefinesFunction("ExtracellularConductivity"))
{
for (int i = 0; i < m_spacedim; ++i)
{
int nq = m_fields[0]->GetNpoints();
Array<OneD,NekDouble> x0(nq);
Array<OneD,NekDouble> x1(nq);
Array<OneD,NekDouble> x2(nq);
// get the coordinates
m_fields[0]->GetCoords(x0,x1,x2);
tmp1 = Array<OneD, const Array<OneD, NekDouble> >(nq);
tmp2 = Array<OneD, const Array<OneD, NekDouble> >(nq);
tmp3 = Array<OneD, const Array<OneD, NekDouble> >(nq);
tmp1[i] = Array<OneD, NekDouble>(nq);
tmp2[i] = Array<OneD, NekDouble>(nq);
tmp3[i] = Array<OneD, NekDouble>(nq);
= m_session->GetFunction("IntracellularConductivity", varName[i]);
= m_session->GetFunction("ExtracellularConductivity", varName[i]);
for(int j = 0; j < nq; j++)
{
tmp1[i][j] = ifunc1->Evaluate(x0[j],x1[j],x2[j],0.0);
tmp2[i][j] = ifunc2->Evaluate(x0[j],x1[j],x2[j],0.0);
}
Vmath::Vadd(nq, tmp1[i], 1, tmp2[i], 1, tmp3[i], 1);
m_vardiffi[varCoeffEnum[i]] = tmp1[i];
m_vardiffie[varCoeffEnum[i]] = tmp3[i];
}
}
if (m_session->DefinesParameter("StimulusDuration"))
{
ASSERTL0(m_session->DefinesFunction("Stimulus", "u"),
"Stimulus function not defined.");
m_session->LoadParameter("StimulusDuration", m_stimDuration);
}
else
{
}
// Search through the loaded filters and pass the cell model to any
// CheckpointCellModel filters loaded.
int k = 0;
const LibUtilities::FilterMap& f = m_session->GetFilters();
LibUtilities::FilterMap::const_iterator x;
for (x = f.begin(); x != f.end(); ++x, ++k)
{
if (x->first == "CheckpointCellModel")
{
boost::shared_ptr<FilterCheckpointCellModel> c
= boost::dynamic_pointer_cast<FilterCheckpointCellModel>(
m_filters[k]);
}
}
{
}
}
void Nektar::Bidomain::v_SetInitialConditions ( NekDouble  initialtime,
bool  dumpInitialConditions,
const int  domain 
)
protectedvirtual

Sets a custom initial condition.

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 406 of file Bidomain.cpp.

References m_cell.

{
EquationSystem::v_SetInitialConditions(initialtime, dumpInitialConditions, domain);
m_cell->Initialise();
}

Friends And Related Function Documentation

friend class MemoryManager< Bidomain >
friend

Definition at line 52 of file Bidomain.h.

Member Data Documentation

string Nektar::Bidomain::className
static
Initial value:
"Bidomain",
"Bidomain model of cardiac electrophysiology with 3D diffusion.")

Name of class.

Registers the class with the Factory.

Definition at line 64 of file Bidomain.h.

NekDouble Nektar::Bidomain::m_capMembrane
private

Definition at line 101 of file Bidomain.h.

Referenced by DoImplicitSolve(), DoOdeRhs(), and v_InitObject().

CellModelSharedPtr Nektar::Bidomain::m_cell
private

Cell model.

Definition at line 99 of file Bidomain.h.

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

NekDouble Nektar::Bidomain::m_chi
private

Definition at line 101 of file Bidomain.h.

Referenced by DoImplicitSolve(), and v_InitObject().

NekDouble Nektar::Bidomain::m_sigmaex
private

Definition at line 101 of file Bidomain.h.

NekDouble Nektar::Bidomain::m_sigmaey
private

Definition at line 101 of file Bidomain.h.

NekDouble Nektar::Bidomain::m_sigmaez
private

Definition at line 101 of file Bidomain.h.

NekDouble Nektar::Bidomain::m_sigmaix
private

Definition at line 101 of file Bidomain.h.

NekDouble Nektar::Bidomain::m_sigmaiy
private

Definition at line 101 of file Bidomain.h.

NekDouble Nektar::Bidomain::m_sigmaiz
private

Definition at line 101 of file Bidomain.h.

NekDouble Nektar::Bidomain::m_stimDuration
private

Stimulus current.

Definition at line 111 of file Bidomain.h.

Referenced by DoOdeRhs(), and v_InitObject().

StdRegions::VarCoeffMap Nektar::Bidomain::m_vardiffi
private

Definition at line 103 of file Bidomain.h.

Referenced by DoImplicitSolve(), and v_InitObject().

StdRegions::VarCoeffMap Nektar::Bidomain::m_vardiffie
private

Definition at line 104 of file Bidomain.h.

Referenced by DoImplicitSolve(), and v_InitObject().

Array<OneD, Array<OneD, NekDouble> > Nektar::Bidomain::tmp1
private

Definition at line 106 of file Bidomain.h.

Referenced by v_InitObject().

Array<OneD, Array<OneD, NekDouble> > Nektar::Bidomain::tmp2
private

Definition at line 107 of file Bidomain.h.

Referenced by v_InitObject().

Array<OneD, Array<OneD, NekDouble> > Nektar::Bidomain::tmp3
private

Definition at line 108 of file Bidomain.h.

Referenced by v_InitObject().