Chaste  Release::3.4
AbstractBidomainSolver.hpp
1 /*
2 
3 Copyright (c) 2005-2016, University of Oxford.
4 All rights reserved.
5 
6 University of Oxford means the Chancellor, Masters and Scholars of the
7 University of Oxford, having an administrative office at Wellington
8 Square, Oxford OX1 2JD, UK.
9 
10 This file is part of Chaste.
11 
12 Redistribution and use in source and binary forms, with or without
13 modification, are permitted provided that the following conditions are met:
14  * Redistributions of source code must retain the above copyright notice,
15  this list of conditions and the following disclaimer.
16  * Redistributions in binary form must reproduce the above copyright notice,
17  this list of conditions and the following disclaimer in the documentation
18  and/or other materials provided with the distribution.
19  * Neither the name of the University of Oxford nor the names of its
20  contributors may be used to endorse or promote products derived from this
21  software without specific prior written permission.
22 
23 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29 GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30 HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31 LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32 OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33 
34 */
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 
213 
214 
215 #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