Chaste Commit::30a3e656d4b131f8c595cc6eb2becd297337570f
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 archive & mMoveSolutionWithCells;
84 archive & mOldCellLocations;
85 }
86
92
96 std::map<CellPtr, c_vector<double, DIM> > mOldCellLocations;
97
98
99public:
100
112 ParabolicBoxDomainPdeModifier(boost::shared_ptr<AbstractLinearPde<DIM,DIM> > pPde=boost::shared_ptr<AbstractLinearPde<DIM,DIM> >(),
113 boost::shared_ptr<AbstractBoundaryCondition<DIM> > pBoundaryCondition=boost::shared_ptr<AbstractBoundaryCondition<DIM> >(),
114 bool isNeumannBoundaryCondition=true,
115 boost::shared_ptr<ChasteCuboid<DIM> > pMeshCuboid=boost::shared_ptr<ChasteCuboid<DIM> >(),
116 double stepSize=1.0,
117 Vec solution=nullptr);
118
122 ~ParabolicBoxDomainPdeModifier() override = default;
123
131 void UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM, DIM>& rCellPopulation) override;
132
141 void SetupSolve(AbstractCellPopulation<DIM, DIM>& rCellPopulation, std::string outputDirectory) override;
142
150 virtual std::shared_ptr<BoundaryConditionsContainer<DIM,DIM,1> > ConstructBoundaryConditionsContainer(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
151
162
173
179 void SetMoveSolutionWithCells(bool moveSolutionWithCells);
180
184 bool GetMoveSolutionWithCells() const;
185
192 void OutputSimulationModifierParameters(out_stream& rParamsFile) override;
193};
194
197
198namespace boost
199{
200namespace serialization
201{
202template<class Archive, unsigned DIM>
203inline void save_construct_data(
204 Archive & ar, const ParabolicBoxDomainPdeModifier<DIM> * t, const unsigned int file_version)
205{
206 if (t->GetSolution())
207 {
208 std::string archive_filename = ArchiveLocationInfo::GetArchiveDirectory() + "solution.vec";
209 PetscTools::DumpPetscObject(t->GetSolution(), archive_filename);
210 }
211}
212
213template<class Archive, unsigned DIM>
214inline void load_construct_data(
215 Archive & ar, ParabolicBoxDomainPdeModifier<DIM> * t, const unsigned int file_version)
216{
217 Vec solution = nullptr;
218
219 std::string archive_filename = ArchiveLocationInfo::GetArchiveDirectory() + "solution.vec";
220 FileFinder file_finder(archive_filename, RelativeTo::Absolute);
221
222 if (file_finder.Exists())
223 {
224 PetscTools::ReadPetscObject(solution, archive_filename);
225 }
226
228 boost::shared_ptr<AbstractBoundaryCondition<DIM> >(),
229 true,
230 boost::shared_ptr<ChasteCuboid<DIM> >(),
231 1.0,
232 solution);
233}
234}
235} // namespace ...
236
237#endif /*PARABOLICBOXDOMAINPDEMODIFIER_HPP_*/
gcov doesn't like this file...
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
static std::string GetArchiveDirectory()
~ParabolicBoxDomainPdeModifier() override=default
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)
void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation) override
void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory) override
std::map< CellPtr, c_vector< double, DIM > > mOldCellLocations
friend class boost::serialization::access
void OutputSimulationModifierParameters(out_stream &rParamsFile) override
void SetMoveSolutionWithCells(bool moveSolutionWithCells)
Vec InterpolateSolutionFromCellMovement(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
static void DumpPetscObject(const Mat &rMat, const std::string &rOutputFileFullPath)
static void ReadPetscObject(Mat &rMat, const std::string &rOutputFileFullPath, Vec rParallelLayout=nullptr)