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Bidomain.h
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1 ///////////////////////////////////////////////////////////////////////////////
2 //
3 // File Bidomain.h
4 //
5 // For more information, please see: http://www.nektar.info
6 //
7 // The MIT License
8 //
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).
12 //
13 // License for the specific language governing rights and limitations under
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31 //
32 // Description: Bidomain cardiac electrophysiology homogenised model.
33 //
34 ///////////////////////////////////////////////////////////////////////////////
35 
36 #ifndef NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_BIDOMAIN_H
37 #define NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_BIDOMAIN_H
38 
41 
42 using namespace Nektar::SolverUtils;
43 
44 namespace Nektar
45 {
46 
47 
48  /// A model for cardiac conduction.
49  class Bidomain : public UnsteadySystem
50  {
51  public:
52  friend class MemoryManager<Bidomain>;
53 
54  /// Creates an instance of this class
55  static EquationSystemSharedPtr create(
57  {
59  p->InitObject();
60  return p;
61  }
62 
63  /// Name of class
64  static std::string className;
65 
66  /// Desctructor
67  virtual ~Bidomain();
68 
69  protected:
70  /// Constructor
71  Bidomain(
72  const LibUtilities::SessionReaderSharedPtr& pSession);
73 
74  virtual void v_InitObject();
75 
76  /// Solve for the diffusion term.
77  void DoImplicitSolve(
78  const Array<OneD, const Array<OneD, NekDouble> >&inarray,
79  Array<OneD, Array<OneD, NekDouble> >&outarray,
80  NekDouble time,
81  NekDouble lambda);
82 
83  /// Computes the reaction terms \f$f(u,v)\f$ and \f$g(u,v)\f$.
84  void DoOdeRhs(
85  const Array<OneD, const Array<OneD, NekDouble> >&inarray,
86  Array<OneD, Array<OneD, NekDouble> >&outarray,
87  const NekDouble time);
88 
89  /// Sets a custom initial condition.
90  virtual void v_SetInitialConditions(NekDouble initialtime,
91  bool dumpInitialConditions,
92  const int domain);
93 
94  /// Prints a summary of the model parameters.
95  virtual void v_GenerateSummary(SummaryList& s);
96 
97  private:
98  /// Cell model.
100 
101  NekDouble m_chi, m_capMembrane, m_sigmaix, m_sigmaiy, m_sigmaiz, m_sigmaex, m_sigmaey, m_sigmaez;
102 
105 
106  Array<OneD, Array<OneD, NekDouble> > tmp1;
107  Array<OneD, Array<OneD, NekDouble> > tmp2;
108  Array<OneD, Array<OneD, NekDouble> > tmp3;
109 
110  /// Stimulus current
112  };
113 
114 }
115 
116 #endif