Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
MonodomainProblem.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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15 this list of conditions and the following disclaimer.
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19 * Neither the name of the University of Oxford nor the names of its
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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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33
34*/
35
36#include "MonodomainProblem.hpp"
37
38#include "Exception.hpp"
39#include "ReplicatableVector.hpp"
40#include "MonodomainSolver.hpp"
41#include "OperatorSplittingMonodomainSolver.hpp"
42
43
44template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
46{
47 mpMonodomainTissue = new MonodomainTissue<ELEMENT_DIM,SPACE_DIM>(this->mpCellFactory, HeartConfig::Instance()->GetUseStateVariableInterpolation());
48 return mpMonodomainTissue;
49}
50
51template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
53{
54 assert(mpMonodomainTissue);
55 /*
56 * NOTE: The this->mpBoundaryConditionsContainer.get() lines below convert a
57 * boost::shared_ptr to a normal pointer, as this is what the solvers are
58 * expecting. We have to be a bit careful though as boost could decide to delete
59 * them whenever it feels like as it won't count the assembers as using them.
60 *
61 * As long as they are kept as member variables here for as long as they are
62 * required in the solvers it should all work OK.
63 */
64
65 if (HeartConfig::Instance()->GetUseReactionDiffusionOperatorSplitting())
66 {
68 mpMonodomainTissue,
69 this->mpBoundaryConditionsContainer.get());
70 }
71 else
72 {
73 return new MonodomainSolver<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,
74 mpMonodomainTissue,
75 this->mpBoundaryConditionsContainer.get());
76 }
77}
78
79template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
81 : AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, 1>(pCellFactory),
82 mpMonodomainTissue(NULL)
83{
84}
85
86template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
88 : AbstractCardiacProblem<ELEMENT_DIM, SPACE_DIM, 1>(),
89 mpMonodomainTissue(NULL)
90{
91}
92
93template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
97
98template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
100{
101 assert(mpMonodomainTissue != NULL);
102 return mpMonodomainTissue;
103}
104
105template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
107{
109 {
110 std::cout << "Solved to time " << time << "\n" << std::flush;
111 }
112
113 double v_max, v_min;
114
115 VecMax( this->mSolution, CHASTE_PETSC_NULLPTR, &v_max );
116 VecMin( this->mSolution, CHASTE_PETSC_NULLPTR, &v_min );
117
119 {
120 std::cout << " V = " << "[" <<v_min << ", " << v_max << "]" << "\n" << std::flush;
121 }
122}
123
124template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
130
131template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
133{
134 this->mpWriter->PutUnlimitedVariable(time);
135 this->mpWriter->PutVector(this->mVoltageColumnId, voltageVec);
137}
138
139// Explicit instantiation
140template class MonodomainProblem<1,1>;
141template class MonodomainProblem<1,2>;
142template class MonodomainProblem<1,3>;
143template class MonodomainProblem<2,2>;
144template class MonodomainProblem<3,3>;
145
146// Serialization for Boost >= 1.36
#define CHASTE_PETSC_NULLPTR
A macro to define PETSc null pointer based on the PETSc version.
#define EXPORT_TEMPLATE_CLASS2(CLASS, E, S)
void DefineExtraVariablesWriterColumns(bool extending)
virtual void DefineWriterColumns(bool extending)
static HeartConfig * Instance()
AbstractDynamicLinearPdeSolver< ELEMENT_DIM, SPACE_DIM, 1 > * CreateSolver()
MonodomainTissue< ELEMENT_DIM, SPACE_DIM > * GetMonodomainTissue()
AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM > * CreateCardiacTissue()
virtual void WriteOneStep(double time, Vec voltageVec)
void WriteInfo(double time)
virtual void DefineWriterColumns(bool extending)
static bool AmMaster()