Chaste Commit::30a3e656d4b131f8c595cc6eb2becd297337570f
AveragedSourceParabolicPde.hpp
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34*/
35
36#ifndef AVERAGESOURCEPARABOLICPDE_HPP_
37#define AVERAGESOURCEPARABOLICPDE_HPP_
38
40#include <boost/serialization/base_object.hpp>
41
42#include "AbstractCellPopulation.hpp"
43#include "TetrahedralMesh.hpp"
44#include "AbstractLinearParabolicPde.hpp"
45
65template<unsigned DIM>
67{
68 friend class TestCellBasedParabolicPdes;
69
70private:
71
80 template<class Archive>
81 void serialize(Archive & archive, const unsigned int version)
82 {
83 archive & boost::serialization::base_object<AbstractLinearParabolicPde<DIM, DIM> >(*this);
86 archive & mDiffusionCoefficient;
87 archive & mDuDtCoefficient;
88 archive & mScaleByCellVolume;
90 }
91
92protected:
93
96
99
102
105
108
111
113 std::vector<double> mCellDensityOnCoarseElements;
114
115public:
116
128 double constantSourceCoefficient=0.0,
129 double linearSourceCoefficient=0.0,
130 double diffusionCoefficient=1.0,
131 double duDtCoefficient=1.0,
132 bool scaleByCellVolume=false);
133
138
142 double GetConstantCoefficient() const;
143
147 double GetLinearCoefficient() const;
148
152 double GetDiffusionCoefficient() const;
153
157 double GetDuDtCoefficient() const;
158
162 bool GetScaleByCellVolume() const;
163
172 void virtual SetupSourceTerms(TetrahedralMesh<DIM, DIM>& rCoarseMesh, std::map<CellPtr, unsigned>* pCellPdeElementMap = nullptr);
173
181 double ComputeDuDtCoefficientFunction(const ChastePoint<DIM>& rX) override;
182
192 double ComputeSourceTerm(const ChastePoint<DIM>& rX,
193 double u,
194 Element<DIM, DIM>* pElement) override;
195
204 double ComputeSourceTermAtNode(const Node<DIM>& rNode, double u) override;
205
214 c_matrix<double,DIM,DIM> ComputeDiffusionTerm(const ChastePoint<DIM>& rX, Element<DIM, DIM>* pElement = nullptr) override;
215
221 double GetUptakeRateForElement(unsigned elementIndex);
222};
223
226
227namespace boost
228{
229namespace serialization
230{
234template<class Archive, unsigned DIM>
235inline void save_construct_data(
236 Archive & ar, const AveragedSourceParabolicPde<DIM>* t, const unsigned int file_version)
237{
238 // Save data required to construct instance
239 const AbstractCellPopulation<DIM, DIM>* p_cell_population = &(t->rGetCellPopulation());
240 ar & p_cell_population;
241}
242
246template<class Archive, unsigned DIM>
247inline void load_construct_data(
248 Archive & ar, AveragedSourceParabolicPde<DIM>* t, const unsigned int file_version)
249{
250 // Retrieve data from archive required to construct new instance
251 AbstractCellPopulation<DIM, DIM>* p_cell_population;
252 ar >> p_cell_population;
253
254 // Invoke inplace constructor to initialise instance
255 ::new(t)AveragedSourceParabolicPde<DIM>(*p_cell_population);
256}
257}
258} // namespace ...
259
260#endif /*AVERAGESOURCEPARABOLICPDE_HPP_*/
gcov doesn't like this file...
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
std::vector< double > mCellDensityOnCoarseElements
AbstractCellPopulation< DIM, DIM > & mrCellPopulation
double ComputeSourceTerm(const ChastePoint< DIM > &rX, double u, Element< DIM, DIM > *pElement) override
double ComputeDuDtCoefficientFunction(const ChastePoint< DIM > &rX) override
void serialize(Archive &archive, const unsigned int version)
c_matrix< double, DIM, DIM > ComputeDiffusionTerm(const ChastePoint< DIM > &rX, Element< DIM, DIM > *pElement=nullptr) override
friend class boost::serialization::access
double GetUptakeRateForElement(unsigned elementIndex)
double ComputeSourceTermAtNode(const Node< DIM > &rNode, double u) override
const AbstractCellPopulation< DIM > & rGetCellPopulation() const
virtual void SetupSourceTerms(TetrahedralMesh< DIM, DIM > &rCoarseMesh, std::map< CellPtr, unsigned > *pCellPdeElementMap=nullptr)
Definition Node.hpp:59