Nektar++
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#include <FentonKarma.h>
Public Member Functions | |
FentonKarma (const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField) | |
Constructor. More... | |
virtual | ~FentonKarma () |
Destructor. More... | |
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... | |
unsigned int | GetNumCellVariables () |
std::string | GetCellVarName (unsigned int idx) |
Array< OneD, NekDouble > | GetCellSolutionCoeffs (unsigned int idx) |
Array< OneD, NekDouble > | GetCellSolution (unsigned int 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) |
Computes the reaction terms $f(u,v)$ and $g(u,v)$. More... | |
virtual void | v_GenerateSummary (SummaryList &s) |
Prints a summary of the model parameters. More... | |
virtual void | v_SetInitialConditions () |
virtual std::string | v_GetCellVarName (unsigned int idx) |
Protected Member Functions inherited from Nektar::CellModel | |
void | LoadCellModel () |
Private Types | |
enum | Variants { eBR, eMBR, eMLR1, eGP, eCF1, eCF2a, eCF2b, eCF2c, eCF3a, eCF3b } |
Static Private Attributes | |
static std::string | lookupIds [] |
static std::string | def |
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... | |
int | m_nq |
Number of physical points. More... | |
int | m_nvar |
Number of variables in cell model (inc. transmembrane voltage) More... | |
NekDouble | m_lastTime |
Timestep for pde model. More... | |
int | 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... | |
Definition at line 43 of file FentonKarma.h.
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Enumerator | |
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eBR | |
eMBR | |
eMLR1 | |
eGP | |
eCF1 | |
eCF2a | |
eCF2b | |
eCF2c | |
eCF3a | |
eCF3b |
Definition at line 105 of file FentonKarma.h.
Nektar::FentonKarma::FentonKarma | ( | const LibUtilities::SessionReaderSharedPtr & | pSession, |
const MultiRegions::ExpListSharedPtr & | pField | ||
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Constructor.
Initialise Fenton-Karma model parameters. k1 is k in the original model. k2 is an additional parameter introduced in Cherry&Fenton 2004. u_r and u_fi are introduced by Cherry&Fenton 2004 and is the same as u_c in the original model.
Definition at line 88 of file FentonKarma.cpp.
References ASSERTL0, C_m, eBR, eCF1, eCF2a, eCF2b, eCF2c, eCF3a, eCF3b, eGP, eMBR, eMLR1, g_fi_max, isCF3, k1, k2, Nektar::CellModel::m_gates, Nektar::CellModel::m_nvar, model_variant, tau_0, tau_d, tau_r, tau_si, tau_v1_minus, tau_v2_minus, tau_v_plus, tau_w_minus, tau_w_plus, tau_y_minus, tau_y_plus, u_c, u_csi, u_fi, u_r, u_v, and V_0.
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inlinestatic |
Creates an instance of this class.
Definition at line 47 of file FentonKarma.h.
References Nektar::MemoryManager< DataType >::AllocateSharedPtr().
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protectedvirtual |
Prints a summary of the model parameters.
Implements Nektar::CellModel.
Definition at line 392 of file FentonKarma.cpp.
References Nektar::SolverUtils::AddSummaryItem(), lookupIds, and model_variant.
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protectedvirtual |
Reimplemented from Nektar::CellModel.
Definition at line 411 of file FentonKarma.cpp.
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protectedvirtual |
Implements Nektar::CellModel.
Definition at line 399 of file FentonKarma.cpp.
References Vmath::Fill(), isCF3, Nektar::CellModel::m_cellSol, and Nektar::CellModel::m_nq.
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protectedvirtual |
Computes the reaction terms $f(u,v)$ and $g(u,v)$.
Implements Nektar::CellModel.
Definition at line 317 of file FentonKarma.cpp.
References ASSERTL0, isCF3, k1, k2, Nektar::CellModel::m_gates_tau, Nektar::CellModel::m_nq, tau_0, tau_d, tau_r, tau_si, tau_v1_minus, tau_v2_minus, tau_v_plus, tau_w_minus, tau_w_plus, u_c, u_csi, u_fi, u_r, and u_v.
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Definition at line 81 of file FentonKarma.h.
Referenced by FentonKarma().
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static |
Name of class.
Definition at line 56 of file FentonKarma.h.
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staticprivate |
Definition at line 120 of file FentonKarma.h.
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Definition at line 87 of file FentonKarma.h.
Referenced by FentonKarma().
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Definition at line 103 of file FentonKarma.h.
Referenced by FentonKarma(), v_SetInitialConditions(), and v_Update().
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Definition at line 98 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 99 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 119 of file FentonKarma.h.
Referenced by v_GenerateSummary().
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Definition at line 117 of file FentonKarma.h.
Referenced by FentonKarma(), and v_GenerateSummary().
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Definition at line 92 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 88 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 93 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 94 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 89 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 90 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 91 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 100 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 101 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 96 of file FentonKarma.h.
Referenced by FentonKarma().
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Definition at line 95 of file FentonKarma.h.
Referenced by FentonKarma().
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Definition at line 84 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 97 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 83 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 86 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 85 of file FentonKarma.h.
Referenced by FentonKarma(), and v_Update().
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Definition at line 82 of file FentonKarma.h.
Referenced by FentonKarma().