Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
ParabolicBoxDomainPdeModifier.hpp
1/*
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34*/
35
36#ifndef PARABOLICBOXDOMAINPDEMODIFIER_HPP_
37#define PARABOLICBOXDOMAINPDEMODIFIER_HPP_
38
40#include <boost/serialization/base_object.hpp>
41
42#include "AbstractBoxDomainPdeModifier.hpp"
43#include "BoundaryConditionsContainer.hpp"
44
63template<unsigned DIM>
65{
66 friend class TestParabolicBoxDomainPdeModifier;
67
68private:
69
79 template<class Archive>
80 void serialize(Archive & archive, const unsigned int version)
81 {
82 archive & boost::serialization::base_object<AbstractBoxDomainPdeModifier<DIM> >(*this);
83 }
84
85public:
86
98 ParabolicBoxDomainPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde=boost::shared_ptr<AbstractLinearPde<DIM,DIM> >(),
99 boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition=boost::shared_ptr<AbstractBoundaryCondition<DIM> >(),
100 bool isNeumannBoundaryCondition=true,
101 boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid=boost::shared_ptr<ChasteCuboid<DIM> >(),
102 double stepSize=1.0,
103 Vec solution=nullptr);
104
109
117 virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
118
127 virtual void SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory);
128
136 virtual std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > ConstructBoundaryConditionsContainer(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
137
146
153 void OutputSimulationModifierParameters(out_stream& rParamsFile);
154};
155
158
159namespace boost
160{
161namespace serialization
162{
163template<class Archive, unsigned DIM>
164inline void save_construct_data(
165 Archive & ar, const ParabolicBoxDomainPdeModifier<DIM> * t, const unsigned int file_version)
166{
167 if (t->GetSolution())
168 {
169 std::string archive_filename = ArchiveLocationInfo::GetArchiveDirectory() + "solution.vec";
170 PetscTools::DumpPetscObject(t->GetSolution(), archive_filename);
171 }
172}
173
174template<class Archive, unsigned DIM>
175inline void load_construct_data(
176 Archive & ar, ParabolicBoxDomainPdeModifier<DIM> * t, const unsigned int file_version)
177{
178 Vec solution = nullptr;
179
180 std::string archive_filename = ArchiveLocationInfo::GetArchiveDirectory() + "solution.vec";
181 FileFinder file_finder(archive_filename, RelativeTo::Absolute);
182
183 if (file_finder.Exists())
184 {
185 PetscTools::ReadPetscObject(solution, archive_filename);
186 }
187
189 boost::shared_ptr<AbstractBoundaryCondition<DIM> >(),
190 true,
191 boost::shared_ptr<ChasteCuboid<DIM> >(),
192 1.0,
193 solution);
194}
195}
196} // namespace ...
197
198#endif /*PARABOLICBOXDOMAINPDEMODIFIER_HPP_*/
gcov doesn't like this file...
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
static std::string GetArchiveDirectory()
void serialize(Archive &archive, const unsigned int version)
void SetupInitialSolutionVector(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual std::shared_ptr< BoundaryConditionsContainer< DIM, DIM, 1 > > ConstructBoundaryConditionsContainer(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
friend class boost::serialization::access
static void DumpPetscObject(const Mat &rMat, const std::string &rOutputFileFullPath)
static void ReadPetscObject(Mat &rMat, const std::string &rOutputFileFullPath, Vec rParallelLayout=nullptr)