Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
VolumeTrackingModifier.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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13modification, are permitted provided that the following conditions are met:
14 * Redistributions of source code must retain the above copyright notice,
15 this list of conditions and the following disclaimer.
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19 * Neither the name of the University of Oxford nor the names of its
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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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34*/
35
36#include "VolumeTrackingModifier.hpp"
37#include "MeshBasedCellPopulation.hpp"
38
39template<unsigned DIM>
44
45template<unsigned DIM>
49
50template<unsigned DIM>
52{
53 UpdateCellData(rCellPopulation);
54}
55
56template<unsigned DIM>
57void VolumeTrackingModifier<DIM>::SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory)
58{
59 /*
60 * We must update CellData in SetupSolve(), otherwise it will not have been
61 * fully initialised by the time we enter the main time loop.
62 */
63 UpdateCellData(rCellPopulation);
64}
65
66template<unsigned DIM>
68{
69 // Make sure the cell population is updated
70 rCellPopulation.Update();
71
81 if (bool(dynamic_cast<MeshBasedCellPopulation<DIM>*>(&rCellPopulation)))
82 {
83 static_cast<MeshBasedCellPopulation<DIM>*>(&(rCellPopulation))->CreateVoronoiTessellation();
84 }
85
86 // Iterate over cell population
87 for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = rCellPopulation.Begin();
88 cell_iter != rCellPopulation.End();
89 ++cell_iter)
90 {
91 // Get the volume of this cell
92 double cell_volume = rCellPopulation.GetVolumeOfCell(*cell_iter);
93
94 // Store the cell's volume in CellData
95 cell_iter->GetCellData()->SetItem("volume", cell_volume);
96 }
97}
98
99template<unsigned DIM>
101{
102 // No parameters to output, so just call method on direct parent class
104}
105
106// Explicit instantiation
107template class VolumeTrackingModifier<1>;
108template class VolumeTrackingModifier<2>;
109template class VolumeTrackingModifier<3>;
110
111// Serialization for Boost >= 1.36
114
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
virtual void OutputSimulationModifierParameters(out_stream &rParamsFile)=0
virtual double GetVolumeOfCell(CellPtr pCell)=0
virtual void Update(bool hasHadBirthsOrDeaths=true)=0
void OutputSimulationModifierParameters(out_stream &rParamsFile)
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
void UpdateCellData(AbstractCellPopulation< DIM, DIM > &rCellPopulation)