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Monodomain.h
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1 ///////////////////////////////////////////////////////////////////////////////
2 //
3 // File Monodomain.h
4 //
5 // For more information, please see: http://www.nektar.info
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7 // The MIT License
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9 // Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
10 // Department of Aeronautics, Imperial College London (UK), and Scientific
11 // Computing and Imaging Institute, University of Utah (USA).
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31 //
32 // Description: Monodomain cardiac electrophysiology homogenised model.
33 //
34 ///////////////////////////////////////////////////////////////////////////////
35 
36 #ifndef NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_MONODOMAIN_H
37 #define NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_MONODOMAIN_H
38 
42 
43 using namespace Nektar::SolverUtils;
44 
45 namespace Nektar
46 {
47 
48 
49  /// A model for cardiac conduction.
50  class Monodomain : public UnsteadySystem
51  {
52  public:
53  friend class MemoryManager<Monodomain>;
54 
55  /// Creates an instance of this class
58  {
60  p->InitObject();
61  return p;
62  }
63 
64  /// Name of class
65  static std::string className;
66 
67  /// Desctructor
68  virtual ~Monodomain();
69 
70  protected:
71  /// Constructor
72  Monodomain(
73  const LibUtilities::SessionReaderSharedPtr& pSession);
74 
75  virtual void v_InitObject();
76 
77  /// Solve for the diffusion term.
78  void DoImplicitSolve(
79  const Array<OneD, const Array<OneD, NekDouble> >&inarray,
80  Array<OneD, Array<OneD, NekDouble> >&outarray,
81  NekDouble time,
82  NekDouble lambda);
83 
84  /// Computes the reaction terms \f$f(u,v)\f$ and \f$g(u,v)\f$.
85  void DoOdeRhs(
86  const Array<OneD, const Array<OneD, NekDouble> >&inarray,
87  Array<OneD, Array<OneD, NekDouble> >&outarray,
88  const NekDouble time);
89 
90  /// Sets a custom initial condition.
91  virtual void v_SetInitialConditions(NekDouble initialtime,
92  bool dumpInitialConditions,
93  const int domain);
94 
95  /// Prints a summary of the model parameters.
96  virtual void v_GenerateSummary(SummaryList& s);
97 
98  private:
99  /// Cell model.
101 
102  std::vector<StimulusSharedPtr> m_stimulus;
103 
104  /// Variable diffusivity
106 
109 
110  /// Stimulus current
112 
113  void LoadStimuli();
114  };
115 
116 }
117 
118 #endif
static boost::shared_ptr< DataType > AllocateSharedPtr()
Allocate a shared pointer from the memory pool.
General purpose memory allocation routines with the ability to allocate from thread specific memory p...
std::vector< std::pair< std::string, std::string > > SummaryList
Definition: Misc.h:47
StdRegions::VarCoeffMap m_vardiff
Variable diffusivity.
Definition: Monodomain.h:105
NekDouble m_capMembrane
Definition: Monodomain.h:108
boost::shared_ptr< SessionReader > SessionReaderSharedPtr
Definition: MeshPartition.h:51
boost::shared_ptr< CellModel > CellModelSharedPtr
A shared pointer to an EquationSystem object.
Definition: CellModel.h:56
boost::shared_ptr< EquationSystem > EquationSystemSharedPtr
A shared pointer to an EquationSystem object.
CellModelSharedPtr m_cell
Cell model.
Definition: Monodomain.h:100
std::map< StdRegions::VarCoeffType, Array< OneD, NekDouble > > VarCoeffMap
Definition: StdRegions.hpp:227
Base class for unsteady solvers.
double NekDouble
std::vector< StimulusSharedPtr > m_stimulus
Definition: Monodomain.h:102
NekDouble m_stimDuration
Stimulus current.
Definition: Monodomain.h:111
static std::string className
Name of class.
Definition: Monodomain.h:65
A model for cardiac conduction.
Definition: Monodomain.h:50
static EquationSystemSharedPtr create(const LibUtilities::SessionReaderSharedPtr &pSession)
Creates an instance of this class.
Definition: Monodomain.h:56