Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
EllipticBoxDomainPdeModifier.hpp
1/*
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34*/
35
36#ifndef ELLIPTICBOXDOMAINPDEMODIFIER_HPP_
37#define ELLIPTICBOXDOMAINPDEMODIFIER_HPP_
38
40#include <boost/serialization/base_object.hpp>
41
42#include "AbstractBoxDomainPdeModifier.hpp"
43#include "BoundaryConditionsContainer.hpp"
44#include "PetscTools.hpp"
45#include "FileFinder.hpp"
46
65template<unsigned DIM>
67{
68 friend class TestEllipticBoxDomainPdeModifier;
69
70private:
71
81 template<class Archive>
82 void serialize(Archive & archive, const unsigned int version)
83 {
84 archive & boost::serialization::base_object<AbstractBoxDomainPdeModifier<DIM> >(*this);
85 }
86
87public:
88
100 EllipticBoxDomainPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde=boost::shared_ptr<AbstractLinearPde<DIM,DIM> >(),
101 boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition=boost::shared_ptr<AbstractBoundaryCondition<DIM> >(),
102 bool isNeumannBoundaryCondition=true,
103 boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid=boost::shared_ptr<ChasteCuboid<DIM> >(),
104 double stepSize=1.0,
105 Vec solution=nullptr);
106
111
119 virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
120
129 virtual void SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory);
130
138 virtual std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > ConstructBoundaryConditionsContainer(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
139
146 void OutputSimulationModifierParameters(out_stream& rParamsFile);
147};
148
151
152namespace boost
153{
154namespace serialization
155{
156template<class Archive, unsigned DIM>
157inline void save_construct_data(
158 Archive & ar, const EllipticBoxDomainPdeModifier<DIM> * t, const unsigned int file_version)
159{
160 if (t->GetSolution())
161 {
162 std::string archive_filename = ArchiveLocationInfo::GetArchiveDirectory() + "solution.vec";
163 PetscTools::DumpPetscObject(t->GetSolution(), archive_filename);
164 }
165}
166
167template<class Archive, unsigned DIM>
168inline void load_construct_data(
169 Archive & ar, EllipticBoxDomainPdeModifier<DIM> * t, const unsigned int file_version)
170{
171 Vec solution = nullptr;
172
173 std::string archive_filename = ArchiveLocationInfo::GetArchiveDirectory() + "solution.vec";
174 FileFinder file_finder(archive_filename, RelativeTo::Absolute);
175
176 if (file_finder.Exists())
177 {
178 PetscTools::ReadPetscObject(solution, archive_filename);
179 }
180
182 boost::shared_ptr<AbstractBoundaryCondition<DIM> >(),
183 true,
184 boost::shared_ptr<ChasteCuboid<DIM> >(),
185 1.0,
186 solution);
187}
188}
189} // namespace ...
190
191#endif /*ELLIPTICBOXDOMAINPDEMODIFIER_HPP_*/
gcov doesn't like this file...
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
static std::string GetArchiveDirectory()
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual std::shared_ptr< BoundaryConditionsContainer< DIM, DIM, 1 > > ConstructBoundaryConditionsContainer(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
friend class boost::serialization::access
void serialize(Archive &archive, const unsigned int version)
static void DumpPetscObject(const Mat &rMat, const std::string &rOutputFileFullPath)
static void ReadPetscObject(Mat &rMat, const std::string &rOutputFileFullPath, Vec rParallelLayout=nullptr)