Chaste  Release::2017.1
AbstractBidomainSolver.hpp
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35 
36 #ifndef ABSTRACTBIDOMAINSOLVER_HPP_
37 #define ABSTRACTBIDOMAINSOLVER_HPP_
38 
39 #include "AbstractDynamicLinearPdeSolver.hpp"
40 #include "BidomainTissue.hpp"
41 #include "HeartConfig.hpp"
42 
48 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
49 class AbstractBidomainSolver : public AbstractDynamicLinearPdeSolver<ELEMENT_DIM,SPACE_DIM,2>
50 {
51 protected:
54 
57 
60 
63 
66 
70  std::vector<unsigned> mFixedExtracellularPotentialNodes;
71 
78 
85  void InitialiseForSolve(Vec initialSolution);
86 
98  virtual void CheckCompatibilityCondition();
99 
107  void PrepareForSetupLinearSystem(Vec existingSolution);
108 
125  virtual void FinaliseLinearSystem(Vec existingSolution);
126 
133  virtual Vec GenerateNullBasis() const;
134 
148  void FinaliseForBath(bool computeMatrix, bool computeVector);
149 
150 public:
159  AbstractBidomainSolver(bool bathSimulation,
161  BidomainTissue<SPACE_DIM>* pTissue,
163 
167  virtual ~AbstractBidomainSolver();
168 
179  void SetFixedExtracellularPotentialNodes(std::vector<unsigned> fixedExtracellularPotentialNodes);
180 
187  void SetRowForAverageOfPhiZeroed(unsigned rowMeanPhiEZero);
188 
193  {
194  return mpBoundaryConditions;
195  }
196 
203  {
204  assert(pBcc);
205  mpBoundaryConditions = pBcc;
206  // Note, in SetupLinearSystem()
207  // neumann_assembler->ResetBoundaryConditionsContainer(mpBcc)
208  // MUST be called every timestep, in case the bcc was reset.
209  }
210 };
211 
212 #endif /*ABSTRACTBIDOMAINSOLVER_HPP_*/
std::vector< unsigned > mFixedExtracellularPotentialNodes
virtual void CheckCompatibilityCondition()
void InitialiseForSolve(Vec initialSolution)
virtual void FinaliseLinearSystem(Vec existingSolution)
BidomainTissue< SPACE_DIM > * mpBidomainTissue
void SetFixedExtracellularPotentialNodes(std::vector< unsigned > fixedExtracellularPotentialNodes)
void FinaliseForBath(bool computeMatrix, bool computeVector)
BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > * mpBoundaryConditions
void ResetBoundaryConditionsContainer(BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBcc)
void PrepareForSetupLinearSystem(Vec existingSolution)
BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > * GetBoundaryConditions()
AbstractBidomainSolver(bool bathSimulation, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *pMesh, BidomainTissue< SPACE_DIM > *pTissue, BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 2 > *pBoundaryConditions)
void SetRowForAverageOfPhiZeroed(unsigned rowMeanPhiEZero)
virtual Vec GenerateNullBasis() const