Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
ParabolicBoxDomainPdeModifier.hpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
4All rights reserved.
5
6University of Oxford means the Chancellor, Masters and Scholars of the
7University of Oxford, having an administrative office at Wellington
8Square, Oxford OX1 2JD, UK.
9
10This file is part of Chaste.
11
12Redistribution and use in source and binary forms, with or without
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.
16 * Redistributions in binary form must reproduce the above copyright notice,
17 this list of conditions and the following disclaimer in the documentation
18 and/or other materials provided with the distribution.
19 * Neither the name of the University of Oxford nor the names of its
20 contributors may be used to endorse or promote products derived from this
21 software without specific prior written permission.
22
23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33
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)