Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
ImmersedBoundarySimulationModifier.hpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
4All rights reserved.
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10This file is part of Chaste.
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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
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19 * Neither the name of the University of Oxford nor the names of its
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21 software without specific prior written permission.
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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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33
34*/
35
36#ifndef IMMERSEDBOUNDARYSIMULATIONMODIFIER_HPP_
37#define IMMERSEDBOUNDARYSIMULATIONMODIFIER_HPP_
38
39// Chaste includes
40#include "AbstractCellBasedSimulationModifier.hpp"
41#include "ObsoleteBoxCollection.hpp"
43
44// Immersed boundary includes
45#include "AbstractImmersedBoundaryForce.hpp"
46#include "ImmersedBoundaryCellPopulation.hpp"
47#include "ImmersedBoundaryMesh.hpp"
48#include "ImmersedBoundaryArray.hpp"
49#include "ImmersedBoundary2dArrays.hpp"
50#include "ImmersedBoundaryFftInterface.hpp"
51#include "UniformGridRandomFieldGenerator.hpp"
52
53// Other includes
54#include <complex>
55#include <boost/serialization/base_object.hpp>
56
63template<unsigned DIM>
65{
66private:
67
70
80 template<class Archive>
81 void serialize(Archive & archive, const unsigned int version)
82 {
83 archive & boost::serialization::base_object<AbstractCellBasedSimulationModifier<DIM,DIM> >(*this);
84 }
85
88
91
94
97
100
102 double mFftNorm;
103
106
109
114 unsigned mNoiseSkip;
115
118
121
123 std::unique_ptr<ObsoleteBoxCollection<DIM>> mpBoxCollection;
124
126 std::vector<std::pair<Node<DIM>*, Node<DIM>*> > mNodePairs;
127
129 std::map<unsigned, std::set<unsigned> > mNodeNeighbours;
130
137
139 std::complex<double> mI;
140
142 std::vector<boost::shared_ptr<AbstractImmersedBoundaryForce<DIM> > > mForceCollection;
143
145 std::unique_ptr<ImmersedBoundary2dArrays<DIM>> mpArrays;
146
148 std::unique_ptr<ImmersedBoundaryFftInterface<DIM>> mpFftInterface;
149
151 std::unique_ptr<UniformGridRandomFieldGenerator<DIM>> mpRandomField;
152
160
168
175
182
187
193
199
205
214 double Delta1D(double dist, double spacing);
215
222 void Upwind2d(const multi_array<double, 3>& rInput, multi_array<double, 3>& rOutput);
223
230 void CalculateSourceGradients(const multi_array<double, 3>& rRhs, multi_array<double, 3>& rGradients);
231
237 void ZeroFieldSums(multi_array<double, 3>& rField);
238
239public:
240
245
250
258 virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
259
268 virtual void SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory);
269
276 void OutputSimulationModifierParameters(out_stream& rParamsFile);
277
281 void SetNodeNeighbourUpdateFrequency(unsigned newFrequency);
282
287
293 void AddImmersedBoundaryForce(boost::shared_ptr<AbstractImmersedBoundaryForce<DIM> > pForce);
294
298 void AddNormalNoise() const;
299
301 bool GetZeroFieldSums() const;
302
304 void SetZeroFieldSums(bool zeroFieldSums);
305
307 void SetReynoldsNumber(double reynoldsNumber);
308
310 double GetReynoldsNumber();
311
313 bool GetAdditiveNormalNoise() const;
314
316 void SetAdditiveNormalNoise(bool additiveNormalNoise);
317
319 double GetNoiseStrength() const;
320
322 void SetNoiseStrength(double noiseStrength);
323
325 unsigned GetNoiseSkip() const;
326
328 void SetNoiseSkip(unsigned noiseSkip);
329
331 double GetNoiseLengthScale() const;
332
334 void SetNoiseLengthScale(double noiseLengthScale);
335
336};
337
340
341#endif /*IMMERSEDBOUNDARYSIMULATIONMODIFIER_HPP_*/
gcov doesn't like this file...
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
std::unique_ptr< ImmersedBoundaryFftInterface< DIM > > mpFftInterface
void CalculateSourceGradients(const multi_array< double, 3 > &rRhs, multi_array< double, 3 > &rGradients)
void Upwind2d(const multi_array< double, 3 > &rInput, multi_array< double, 3 > &rOutput)
void SetupConstantMemberVariables(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void serialize(Archive &archive, const unsigned int version)
void AddImmersedBoundaryForce(boost::shared_ptr< AbstractImmersedBoundaryForce< DIM > > pForce)
std::vector< std::pair< Node< DIM > *, Node< DIM > * > > mNodePairs
virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void OutputSimulationModifierParameters(out_stream &rParamsFile)
std::map< unsigned, std::set< unsigned > > mNodeNeighbours
std::vector< boost::shared_ptr< AbstractImmersedBoundaryForce< DIM > > > mForceCollection
std::unique_ptr< ObsoleteBoxCollection< DIM > > mpBoxCollection
std::unique_ptr< ImmersedBoundary2dArrays< DIM > > mpArrays
std::unique_ptr< UniformGridRandomFieldGenerator< DIM > > mpRandomField
ImmersedBoundaryCellPopulation< DIM > * mpCellPopulation
virtual ~ImmersedBoundarySimulationModifier()=default
virtual void SetupSolve(AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
void UpdateFluidVelocityGrids(AbstractCellPopulation< DIM, DIM > &rCellPopulation)
void ZeroFieldSums(multi_array< double, 3 > &rField)
Definition Node.hpp:59