Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
AbstractPdeModifier.hpp
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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()