Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
AbstractPdeModifier.hpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
4All rights reserved.
5
6University of Oxford means the Chancellor, Masters and Scholars of the
7University of Oxford, having an administrative office at Wellington
8Square, Oxford OX1 2JD, UK.
9
10This file is part of Chaste.
11
12Redistribution and use in source and binary forms, with or without
13modification, 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
23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33
34*/
35
36#ifndef ABSTRACTPDEMODIFIER_HPP_
37#define ABSTRACTPDEMODIFIER_HPP_
38
40#include "ClassIsAbstract.hpp"
41#include <boost/shared_ptr.hpp>
42
43#include "AbstractCellBasedSimulationModifier.hpp"
44#include "TetrahedralMesh.hpp"
45#include "AbstractLinearPde.hpp"
46#include "AbstractBoundaryCondition.hpp"
47
53template<unsigned DIM>
55{
56private:
57
67 template<class Archive>
68 void serialize(Archive & archive, const unsigned int version)
69 {
70 archive & boost::serialization::base_object<AbstractCellBasedSimulationModifier<DIM,DIM> >(*this);
71 archive & mpPde;
72 archive & mpBoundaryCondition;
74 archive & mDependentVariableName;
75
76 // Note that archiving of mSolution is handled by the methods save/load_construct_data
77 archive & mOutputDirectory;
78 archive & mOutputGradient;
80 }
81
82protected:
83
87 boost::shared_ptr<AbstractLinearPde<DIM,DIM> > mpPde;
88
92 boost::shared_ptr<AbstractBoundaryCondition<DIM> > mpBoundaryCondition;
93
100
106
109
112
114 std::string mOutputDirectory;
115
118
124
127
132
133public:
134
144 AbstractPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde=NULL,
145 boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition=boost::shared_ptr<AbstractBoundaryCondition<DIM> >(),
146 bool isNeumannBoundaryCondition=true,
147 Vec solution=nullptr);
148
152 virtual ~AbstractPdeModifier();
153
157 boost::shared_ptr<AbstractLinearPde<DIM,DIM> > GetPde();
158
162 boost::shared_ptr<AbstractBoundaryCondition<DIM> > GetBoundaryCondition();
163
168
174 void SetDependentVariableName(const std::string& rName);
175
181 std::string& rGetDependentVariableName();
182
187
195 void SetUpSourceTermsForAveragedSourcePde(TetrahedralMesh<DIM,DIM>* pMesh, std::map<CellPtr, unsigned>* pCellPdeElementMap=nullptr);
196
201
205 Vec GetSolution() const;
206
211
221 virtual void SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory);
222
231
242
250 virtual void UpdateAtEndOfSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
251
257 bool GetOutputGradient();
258
264 void SetOutputGradient(bool outputGradient);
265
271 void SetOutputSolutionAtPdeNodes(bool outputSolutionAtPdeNodes);
272
280 void OutputSimulationModifierParameters(out_stream& rParamsFile);
281};
282
285
286#endif /*ABSTRACTPDEMODIFIER_HPP_*/
#define TEMPLATED_CLASS_IS_ABSTRACT_1_UNSIGNED(T)
gcov doesn't like this file...
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
virtual void UpdateAtEndOfOutputTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
boost::shared_ptr< AbstractLinearPde< DIM, DIM > > mpPde
void serialize(Archive &archive, const unsigned int version)
void SetOutputSolutionAtPdeNodes(bool outputSolutionAtPdeNodes)
void SetOutputGradient(bool outputGradient)
TetrahedralMesh< DIM, DIM > * mpFeMesh
TetrahedralMesh< DIM, DIM > * GetFeMesh() const
boost::shared_ptr< AbstractLinearPde< DIM, DIM > > GetPde()
virtual void UpdateAtEndOfSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
std::string & rGetDependentVariableName()
boost::shared_ptr< AbstractBoundaryCondition< DIM > > mpBoundaryCondition
void SetDependentVariableName(const std::string &rName)
friend class boost::serialization::access
void SetUpSourceTermsForAveragedSourcePde(TetrahedralMesh< DIM, DIM > *pMesh, std::map< CellPtr, unsigned > *pCellPdeElementMap=nullptr)
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)=0
boost::shared_ptr< AbstractBoundaryCondition< DIM > > GetBoundaryCondition()