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Nektar::Monodomain Class Reference

A model for cardiac conduction. More...

#include <Monodomain.h>

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Public Member Functions

virtual ~Monodomain ()
 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

 Monodomain (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 Member Functions

void LoadStimuli ()

Private Attributes

CellModelSharedPtr m_cell
 Cell model.
std::vector< StimulusSharedPtrm_stimulus
StdRegions::VarCoeffMap m_vardiff
 Variable diffusivity.
NekDouble m_chi
NekDouble m_capMembrane
NekDouble m_stimDuration
 Stimulus current.

Friends

class MemoryManager< Monodomain >

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 50 of file Monodomain.h.

Constructor & Destructor Documentation

Nektar::Monodomain::~Monodomain ( )
virtual

Desctructor.

Definition at line 295 of file Monodomain.cpp.

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

Constructor.

Definition at line 70 of file Monodomain.cpp.

: UnsteadySystem(pSession)
{
}

Member Function Documentation

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

Creates an instance of this class.

Definition at line 56 of file Monodomain.h.

{
p->InitObject();
return p;
}
void Nektar::Monodomain::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 307 of file Monodomain.cpp.

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

Referenced by v_InitObject().

{
int nvariables = inarray.num_elements();
int nq = m_fields[0]->GetNpoints();
// lambda = \Delta t
// We solve ( \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)
{
// Multiply 1.0/timestep
Vmath::Smul(nq, -factors[StdRegions::eFactorLambda], inarray[i], 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_vardiff);
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::Monodomain::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 348 of file Monodomain.cpp.

References m_cell, and m_stimulus.

Referenced by v_InitObject().

{
// Compute I_ion
m_cell->TimeIntegrate(inarray, outarray, time);
// Compute I_stim
for (unsigned int i = 0; i < m_stimulus.size(); ++i)
{
m_stimulus[i]->Update(outarray, time);
}
}
void Nektar::Monodomain::LoadStimuli ( )
private

Referenced by v_InitObject().

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

Prints a summary of the model parameters.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 381 of file Monodomain.cpp.

References Nektar::SolverUtils::AddSummaryItem(), Nektar::LibUtilities::eFunctionTypeExpression, m_cell, and Nektar::SolverUtils::EquationSystem::m_session.

{
if (m_session->DefinesFunction("d00") &&
m_session->GetFunctionType("d00", "intensity")
{
AddSummaryItem(s, "Diffusivity-x",
m_session->GetFunction("d00", "intensity")->GetExpression());
}
if (m_session->DefinesFunction("d11") &&
m_session->GetFunctionType("d11", "intensity")
{
AddSummaryItem(s, "Diffusivity-y",
m_session->GetFunction("d11", "intensity")->GetExpression());
}
if (m_session->DefinesFunction("d22") &&
m_session->GetFunctionType("d22", "intensity")
{
AddSummaryItem(s, "Diffusivity-z",
m_session->GetFunction("d22", "intensity")->GetExpression());
}
m_cell->GenerateSummary(s);
}
void Nektar::Monodomain::v_InitObject ( )
protectedvirtual

Init object for UnsteadySystem class.

Initialization object for UnsteadySystem class.

Reimplemented from Nektar::SolverUtils::UnsteadySystem.

Definition at line 80 of file Monodomain.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(), 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_vardiff, Vmath::Sadd(), Nektar::FilterCheckpointCellModel::SetCellModel(), Vmath::Smul(), Vmath::Vmul(), and Nektar::SolverUtils::EquationSystem::WriteFld().

{
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.");
vCellModel, m_session, m_fields[0]);
m_intVariables.push_back(0);
// Load variable coefficients
StdRegions::VarCoeffType varCoeffEnum[6] = {
};
std::string varCoeffString[6] = {"xx","xy","yy","xz","yz","zz"};
std::string aniso_var[3] = {"fx", "fy", "fz"};
const int nq = m_fields[0]->GetNpoints();
const int nVarDiffCmpts = m_spacedim * (m_spacedim + 1) / 2;
// Allocate storage for variable coeffs and initialize to 1.
for (int i = 0, k = 0; i < m_spacedim; ++i)
{
for (int j = 0; j < i+1; ++j)
{
if (i == j)
{
m_vardiff[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 1.0);
}
else
{
m_vardiff[varCoeffEnum[k]] = Array<OneD, NekDouble>(nq, 0.0);
}
++k;
}
}
// Apply fibre map f \in [0,1], scale to conductivity range
// [o_min,o_max], specified by the session parameters o_min and o_max
if (m_session->DefinesFunction("AnisotropicConductivity"))
{
if (m_session->DefinesCmdLineArgument("verbose"))
{
cout << "Loading Anisotropic Fibre map." << endl;
}
NekDouble o_min = m_session->GetParameter("o_min");
NekDouble o_max = m_session->GetParameter("o_max");
int k = 0;
Array<OneD, NekDouble> vTemp_i;
Array<OneD, NekDouble> vTemp_j;
/*
* Diffusivity matrix D is upper triangular and defined as
* d_00 d_01 d_02
* d_11 d_12
* d_22
*
* Given a principle fibre direction _f_ the diffusivity is given
* by
* d_ij = { D_2 + (D_1 - D_2) f_i f_j if i==j
* { (D_1 - D_2) f_i f_j if i!=j
*
* The vector _f_ is given in terms of the variables fx,fy,fz in the
* function AnisotropicConductivity. The values of D_1 and D_2 are
* the parameters o_max and o_min, respectively.
*/
// Loop through columns of D
for (int j = 0; j < m_spacedim; ++j)
{
ASSERTL0(m_session->DefinesFunction("AnisotropicConductivity",
aniso_var[j]),
"Function 'AnisotropicConductivity' not correctly "
"defined.");
EvaluateFunction(aniso_var[j], vTemp_j,
"AnisotropicConductivity");
// Loop through rows of D
for (int i = 0; i < j + 1; ++i)
{
ASSERTL0(m_session->DefinesFunction(
"AnisotropicConductivity",aniso_var[i]),
"Function 'AnisotropicConductivity' not correctly "
"defined.");
EvaluateFunction(aniso_var[i], vTemp_i,
"AnisotropicConductivity");
Vmath::Vmul(nq, vTemp_i, 1, vTemp_j, 1,
m_vardiff[varCoeffEnum[k]], 1);
Vmath::Smul(nq, o_max-o_min,
m_vardiff[varCoeffEnum[k]], 1,
m_vardiff[varCoeffEnum[k]], 1);
if (i == j)
{
Vmath::Sadd(nq, o_min,
m_vardiff[varCoeffEnum[k]], 1,
m_vardiff[varCoeffEnum[k]], 1);
}
++k;
}
}
}
// Scale by scar map (range 0->1) derived from intensity map
// (range d_min -> d_max)
if (m_session->DefinesFunction("IsotropicConductivity"))
{
if (m_session->DefinesCmdLineArgument("verbose"))
{
cout << "Loading Isotropic Conductivity map." << endl;
}
const std::string varName = "intensity";
Array<OneD, NekDouble> vTemp;
EvaluateFunction(varName, vTemp, "IsotropicConductivity");
// If the d_min and d_max parameters are defined, then we need to
// rescale the isotropic conductivity to convert from the source
// domain (e.g. late-gad intensity) to conductivity
if ( m_session->DefinesParameter("d_min") ||
m_session->DefinesParameter("d_max") ) {
const NekDouble f_min = m_session->GetParameter("d_min");
const NekDouble f_max = m_session->GetParameter("d_max");
const NekDouble scar_min = 0.0;
const NekDouble scar_max = 1.0;
// Threshold based on d_min, d_max
for (int j = 0; j < nq; ++j)
{
vTemp[j] = (vTemp[j] < f_min ? f_min : vTemp[j]);
vTemp[j] = (vTemp[j] > f_max ? f_max : vTemp[j]);
}
// Rescale to s \in [0,1] (0 maps to d_max, 1 maps to d_min)
Vmath::Sadd(nq, -f_min, vTemp, 1, vTemp, 1);
Vmath::Smul(nq, -1.0/(f_max-f_min), vTemp, 1, vTemp, 1);
Vmath::Sadd(nq, 1.0, vTemp, 1, vTemp, 1);
Vmath::Smul(nq, scar_max - scar_min, vTemp, 1, vTemp, 1);
Vmath::Sadd(nq, scar_min, vTemp, 1, vTemp, 1);
}
// Scale anisotropic conductivity values
for (int i = 0; i < nVarDiffCmpts; ++i)
{
Vmath::Vmul(nq, vTemp, 1,
m_vardiff[varCoeffEnum[i]], 1,
m_vardiff[varCoeffEnum[i]], 1);
}
}
// Write out conductivity values
for (int j = 0, k = 0; j < m_spacedim; ++j)
{
// Loop through rows of D
for (int i = 0; i < j + 1; ++i)
{
// Transform variable coefficient and write out to file.
m_fields[0]->FwdTrans_IterPerExp(m_vardiff[varCoeffEnum[k]],
m_fields[0]->UpdateCoeffs());
std::stringstream filename;
filename << "Conductivity_" << varCoeffString[k] << ".fld";
WriteFld(filename.str());
++k;
}
}
// 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]);
}
}
// Load stimuli
{
}
}
void Nektar::Monodomain::v_SetInitialConditions ( NekDouble  initialtime,
bool  dumpInitialConditions,
const int  domain 
)
protectedvirtual

Sets a custom initial condition.

Reimplemented from Nektar::SolverUtils::EquationSystem.

Definition at line 367 of file Monodomain.cpp.

References m_cell.

{
dumpInitialConditions,
domain);
m_cell->Initialise();
}

Friends And Related Function Documentation

friend class MemoryManager< Monodomain >
friend

Definition at line 53 of file Monodomain.h.

Member Data Documentation

string Nektar::Monodomain::className
static
Initial value:
"Monodomain",
"Monodomain model of cardiac electrophysiology.")

Name of class.

Registers the class with the Factory.

Definition at line 65 of file Monodomain.h.

NekDouble Nektar::Monodomain::m_capMembrane
private

Definition at line 108 of file Monodomain.h.

Referenced by DoImplicitSolve(), and v_InitObject().

CellModelSharedPtr Nektar::Monodomain::m_cell
private

Cell model.

Definition at line 100 of file Monodomain.h.

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

NekDouble Nektar::Monodomain::m_chi
private

Definition at line 107 of file Monodomain.h.

Referenced by DoImplicitSolve(), and v_InitObject().

NekDouble Nektar::Monodomain::m_stimDuration
private

Stimulus current.

Definition at line 111 of file Monodomain.h.

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

Definition at line 102 of file Monodomain.h.

Referenced by DoOdeRhs(), and v_InitObject().

StdRegions::VarCoeffMap Nektar::Monodomain::m_vardiff
private

Variable diffusivity.

Definition at line 105 of file Monodomain.h.

Referenced by DoImplicitSolve(), and v_InitObject().