Nektar++
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Pages
Bidomain.h
Go to the documentation of this file.
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
14 // Permission is hereby granted, free of charge, to any person obtaining a
15 // copy of this software and associated documentation files (the "Software"),
16 // to deal in the Software without restriction, including without limitation
17 // the rights to use, copy, modify, merge, publish, distribute, sublicense,
18 // and/or sell copies of the Software, and to permit persons to whom the
19 // Software is furnished to do so, subject to the following conditions:
20 //
21 // The above copyright notice and this permission notice shall be included
22 // in all copies or substantial portions of the Software.
23 //
24 // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
25 // OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
26 // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
27 // THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
28 // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
29 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
30 // DEALINGS IN THE SOFTWARE.
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
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 
109 
110  /// Stimulus current
112  };
113 
114 }
115 
116 #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
static std::string className
Name of class.
Definition: Bidomain.h:64
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.
NekDouble m_sigmaiz
Definition: Bidomain.h:101
StdRegions::VarCoeffMap m_vardiffie
Definition: Bidomain.h:104
NekDouble m_stimDuration
Stimulus current.
Definition: Bidomain.h:111
std::map< StdRegions::VarCoeffType, Array< OneD, NekDouble > > VarCoeffMap
Definition: StdRegions.hpp:227
Base class for unsteady solvers.
double NekDouble
StdRegions::VarCoeffMap m_vardiffi
Definition: Bidomain.h:103
static EquationSystemSharedPtr create(const LibUtilities::SessionReaderSharedPtr &pSession)
Creates an instance of this class.
Definition: Bidomain.h:55
CellModelSharedPtr m_cell
Cell model.
Definition: Bidomain.h:99
Array< OneD, Array< OneD, NekDouble > > tmp1
Definition: Bidomain.h:106
A model for cardiac conduction.
Definition: Bidomain.h:49
Array< OneD, Array< OneD, NekDouble > > tmp2
Definition: Bidomain.h:107
Array< OneD, Array< OneD, NekDouble > > tmp3
Definition: Bidomain.h:108