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Nektar::CellModelFitzHughNagumo Class Reference

FitzHugh-Nagumo model. More...

#include <FitzhughNagumo.h>

Inheritance diagram for Nektar::CellModelFitzHughNagumo:
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Public Member Functions

 CellModelFitzHughNagumo (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
 
virtual ~CellModelFitzHughNagumo ()
 
- Public Member Functions inherited from Nektar::CellModel
 CellModel (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
 
virtual ~CellModel ()
 
void Initialise ()
 Initialise the cell model storage and set initial conditions. More...
 
void TimeIntegrate (const Array< OneD, const Array< OneD, NekDouble >> &inarray, Array< OneD, Array< OneD, NekDouble >> &outarray, const NekDouble time)
 Time integrate the cell model by one PDE timestep. More...
 
void Update (const Array< OneD, const Array< OneD, NekDouble >> &inarray, Array< OneD, Array< OneD, NekDouble >> &outarray, const NekDouble time)
 Compute the derivatives of cell model variables. More...
 
void GenerateSummary (SummaryList &s)
 Print a summary of the cell model. More...
 
size_t GetNumCellVariables ()
 
std::string GetCellVarName (size_t idx)
 
Array< OneD, NekDouble > GetCellSolutionCoeffs (size_t idx)
 
Array< OneD, NekDouble > GetCellSolution (size_t idx)
 

Static Public Member Functions

static CellModelSharedPtr create (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
 Creates an instance of this class. More...
 

Static Public Attributes

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

Protected Member Functions

virtual void v_Update (const Array< OneD, const Array< OneD, NekDouble >> &inarray, Array< OneD, Array< OneD, NekDouble >> &outarray, const NekDouble time) override
 
virtual void v_GenerateSummary (SummaryList &s) override
 
virtual void v_SetInitialConditions () override
 
- Protected Member Functions inherited from Nektar::CellModel
virtual std::string v_GetCellVarName (size_t idx)
 
void LoadCellModel ()
 

Private Attributes

NekDouble m_beta
 
NekDouble m_epsilon
 
Array< OneD, NekDouble > m_uuu
 Temporary space for storing \(u^3\) when computing reaction term. More...
 

Additional Inherited Members

- Protected Attributes inherited from Nektar::CellModel
LibUtilities::SessionReaderSharedPtr m_session
 Session. More...
 
MultiRegions::ExpListSharedPtr m_field
 Transmembrane potential field from PDE system. More...
 
size_t m_nq
 Number of physical points. More...
 
size_t m_nvar
 Number of variables in cell model (inc. transmembrane voltage) More...
 
NekDouble m_lastTime
 Timestep for pde model. More...
 
size_t m_substeps
 Number of substeps to take. More...
 
Array< OneD, Array< OneD, NekDouble > > m_cellSol
 Cell model solution variables. More...
 
Array< OneD, Array< OneD, NekDouble > > m_wsp
 Cell model integration workspace. More...
 
bool m_useNodal
 Flag indicating whether nodal projection in use. More...
 
StdRegions::StdNodalTriExpSharedPtr m_nodalTri
 StdNodalTri for cell model calculations. More...
 
StdRegions::StdNodalTetExpSharedPtr m_nodalTet
 
Array< OneD, Array< OneD, NekDouble > > m_nodalTmp
 Temporary array for nodal projection. More...
 
std::vector< int > m_concentrations
 Indices of cell model variables which are concentrations. More...
 
std::vector< int > m_gates
 Indices of cell model variables which are gates. More...
 
Array< OneD, Array< OneD, NekDouble > > m_gates_tau
 Storage for gate tau values. More...
 

Detailed Description

FitzHugh-Nagumo model.

Definition at line 43 of file FitzhughNagumo.h.

Constructor & Destructor Documentation

◆ CellModelFitzHughNagumo()

Nektar::CellModelFitzHughNagumo::CellModelFitzHughNagumo ( const LibUtilities::SessionReaderSharedPtr &  pSession,
const MultiRegions::ExpListSharedPtr &  pField 
)

Definition at line 51 of file FitzhughNagumo.cpp.

54  : CellModel(pSession, pField)
55 {
56  pSession->LoadParameter("beta", m_beta, 0.0);
57  pSession->LoadParameter("epsilon", m_epsilon, 1.0);
58 
59  m_uuu = Array<OneD, NekDouble>(m_nq, 0.0);
60 
61  m_nvar = 2;
62  m_concentrations.push_back(1);
63 }
Nektar::CellModelFitzHughNagumo::m_uuu
Array< OneD, NekDouble > m_uuu
Temporary space for storing when computing reaction term.
Definition: FitzhughNagumo.h:81
Nektar::CellModel::m_concentrations
std::vector< int > m_concentrations
Indices of cell model variables which are concentrations.
Definition: CellModel.h:139
Nektar::CellModel::m_nq
size_t m_nq
Number of physical points.
Definition: CellModel.h:117
Nektar::CellModel::m_nvar
size_t m_nvar
Number of variables in cell model (inc. transmembrane voltage)
Definition: CellModel.h:119
Nektar::CellModel::CellModel
CellModel(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Definition: CellModel.cpp:66

References m_beta, Nektar::CellModel::m_concentrations, m_epsilon, Nektar::CellModel::m_nq, Nektar::CellModel::m_nvar, and m_uuu.

◆ ~CellModelFitzHughNagumo()

virtual Nektar::CellModelFitzHughNagumo::~CellModelFitzHughNagumo ( )
inlinevirtual

Definition at line 62 of file FitzhughNagumo.h.

63  {
64  }

Member Function Documentation

◆ create()

static CellModelSharedPtr Nektar::CellModelFitzHughNagumo::create ( const LibUtilities::SessionReaderSharedPtr &  pSession,
const MultiRegions::ExpListSharedPtr &  pField 
)
inlinestatic

Creates an instance of this class.

Definition at line 47 of file FitzhughNagumo.h.

50  {
51  return MemoryManager<CellModelFitzHughNagumo>::AllocateSharedPtr(
52  pSession, pField);
53  }
Nektar::MemoryManager::AllocateSharedPtr
static std::shared_ptr< DataType > AllocateSharedPtr(const Args &...args)
Allocate a shared pointer from the memory pool.
Definition: NekMemoryManager.hpp:168

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

◆ v_GenerateSummary()

void Nektar::CellModelFitzHughNagumo::v_GenerateSummary ( SummaryList &  s)
overrideprotectedvirtual

Implements Nektar::CellModel.

Definition at line 98 of file FitzhughNagumo.cpp.

99 {
100  SolverUtils::AddSummaryItem(s, "Cell model", "FitzHugh-Nagumo");
101  SolverUtils::AddSummaryItem(s, "Cell model beta", m_beta);
102 }
Nektar::SolverUtils::AddSummaryItem
void AddSummaryItem(SummaryList &l, const std::string &name, const std::string &value)
Adds a summary item to the summary info list.
Definition: Misc.cpp:49

References Nektar::SolverUtils::AddSummaryItem(), and m_beta.

◆ v_SetInitialConditions()

void Nektar::CellModelFitzHughNagumo::v_SetInitialConditions ( )
overrideprotectedvirtual

Implements Nektar::CellModel.

Definition at line 107 of file FitzhughNagumo.cpp.

108 {
109  Vmath::Fill(m_nq, 0.0, m_cellSol[0], 1);
110  Vmath::Fill(m_nq, 0.0, m_cellSol[1], 1);
111 }
Nektar::CellModel::m_cellSol
Array< OneD, Array< OneD, NekDouble > > m_cellSol
Cell model solution variables.
Definition: CellModel.h:126
Vmath::Fill
void Fill(int n, const T alpha, T *x, const int incx)
Fill a vector with a constant value.
Definition: Vmath.cpp:45

References Vmath::Fill(), Nektar::CellModel::m_cellSol, and Nektar::CellModel::m_nq.

◆ v_Update()

void Nektar::CellModelFitzHughNagumo::v_Update ( const Array< OneD, const Array< OneD, NekDouble >> &  inarray,
Array< OneD, Array< OneD, NekDouble >> &  outarray,
const NekDouble  time 
)
overrideprotectedvirtual

Implements Nektar::CellModel.

Definition at line 65 of file FitzhughNagumo.cpp.

68 {
69  boost::ignore_unused(time);
70 
71  NekDouble m_gamma = 0.5;
72 
73  // compute u^2: m_u = u*u
74  Vmath::Vmul(m_nq, &inarray[0][0], 1, &inarray[0][0], 1, &m_uuu[0], 1);
75 
76  // compute u^3: m_u = u*u*u
77  Vmath::Vmul(m_nq, &inarray[0][0], 1, &m_uuu[0], 1, &m_uuu[0], 1);
78 
79  // For u: (1/m_epsilon)*( u*-u*u*u/3 - v )
80  // physfield = u - (1.0/3.0)*u*u*u
81  Vmath::Svtvp(m_nq, (-1.0 / 3.0), &m_uuu[0], 1, &inarray[0][0], 1,
82  &outarray[0][0], 1);
83 
84  Vmath::Vsub(m_nq, &inarray[1][0], 1, &outarray[0][0], 1, &outarray[0][0],
85  1);
86  Vmath::Smul(m_nq, -1.0 / m_epsilon, &outarray[0][0], 1, &outarray[0][0], 1);
87 
88  // For v: m_epsilon*( u + m_beta - m_gamma*v )
89  Vmath::Svtvp(m_nq, -1.0 * m_gamma, &inarray[1][0], 1, &inarray[0][0], 1,
90  &outarray[1][0], 1);
91  Vmath::Sadd(m_nq, m_beta, &outarray[1][0], 1, &outarray[1][0], 1);
92  Vmath::Smul(m_nq, m_epsilon, &outarray[1][0], 1, &outarray[1][0], 1);
93 }
Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:43
Vmath::Vmul
void Vmul(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Multiply vector z = x*y.
Definition: Vmath.cpp:209
Vmath::Svtvp
void Svtvp(int n, const T alpha, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
svtvp (scalar times vector plus vector): z = alpha*x + y
Definition: Vmath.cpp:622
Vmath::Smul
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
Vmath::Sadd
void Sadd(int n, const T alpha, const T *x, const int incx, T *y, const int incy)
Add scalar y = alpha + x.
Definition: Vmath.cpp:384
Vmath::Vsub
void Vsub(int n, const T *x, const int incx, const T *y, const int incy, T *z, const int incz)
Subtract vector z = x-y.
Definition: Vmath.cpp:419

References m_beta, m_epsilon, Nektar::CellModel::m_nq, m_uuu, Vmath::Sadd(), Vmath::Smul(), Vmath::Svtvp(), Vmath::Vmul(), and Vmath::Vsub().

Member Data Documentation

◆ className

std::string Nektar::CellModelFitzHughNagumo::className
static
Initial value:
=
GetCellModelFactory().RegisterCreatorFunction(
"FitzHughNagumo", CellModelFitzHughNagumo::create,
"Phenomological model of squid nerve cell.")
Nektar::CellModelFitzHughNagumo::create
static CellModelSharedPtr create(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Creates an instance of this class.
Definition: FitzhughNagumo.h:47
Nektar::LibUtilities::NekFactory::RegisterCreatorFunction
tKey RegisterCreatorFunction(tKey idKey, CreatorFunction classCreator, std::string pDesc="")
Register a class with the factory.
Definition: NekFactory.hpp:198
Nektar::GetCellModelFactory
CellModelFactory & GetCellModelFactory()
Definition: CellModel.cpp:46

Name of class.

Registers the class with the Factory.

Definition at line 56 of file FitzhughNagumo.h.

◆ m_beta

NekDouble Nektar::CellModelFitzHughNagumo::m_beta
private

Definition at line 77 of file FitzhughNagumo.h.

Referenced by CellModelFitzHughNagumo(), v_GenerateSummary(), and v_Update().

◆ m_epsilon

NekDouble Nektar::CellModelFitzHughNagumo::m_epsilon
private

Definition at line 78 of file FitzhughNagumo.h.

Referenced by CellModelFitzHughNagumo(), and v_Update().

◆ m_uuu

Array<OneD, NekDouble> Nektar::CellModelFitzHughNagumo::m_uuu
private

Temporary space for storing \(u^3\) when computing reaction term.

Definition at line 81 of file FitzhughNagumo.h.

Referenced by CellModelFitzHughNagumo(), and v_Update().

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