ImmersedBoundarySimulationModifier.hpp

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*/
 
#ifndef IMMERSEDBOUNDARYSIMULATIONMODIFIER_HPP_
#define IMMERSEDBOUNDARYSIMULATIONMODIFIER_HPP_
 
// Chaste includes
#include "AbstractCellBasedSimulationModifier.hpp"
#include "ObsoleteBoxCollection.hpp"
#include "ChasteSerialization.hpp"
 
// Immersed boundary includes
#include "AbstractImmersedBoundaryForce.hpp"
#include "ImmersedBoundaryCellPopulation.hpp"
#include "ImmersedBoundaryMesh.hpp"
#include "ImmersedBoundary2dArrays.hpp"
#include "ImmersedBoundaryFftInterface.hpp"
#include "UniformGridRandomFieldGenerator.hpp"
 
// Other includes
#include <complex>
#include <boost/serialization/base_object.hpp>
#include <boost/multi_array.hpp>
 
template<unsigned DIM>
class ImmersedBoundarySimulationModifier : public AbstractCellBasedSimulationModifier<DIM,DIM>
{
private:
 
    friend class TestImmersedBoundarySimulationModifier;
 
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCellBasedSimulationModifier<DIM,DIM> >(*this);
    }
 
    ImmersedBoundaryMesh<DIM,DIM>* mpMesh;
 
    ImmersedBoundaryCellPopulation<DIM>* mpCellPopulation;
 
    unsigned mNodeNeighbourUpdateFrequency;
 
    double mGridSpacingX;
 
    double mGridSpacingY;
 
    double mFftNorm;
 
    bool mAdditiveNormalNoise;
 
    double mNoiseStrength;
 
    unsigned mNoiseSkip;
 
    double mNoiseLengthScale;
 
    bool mZeroFieldSums;
 
    std::unique_ptr<ObsoleteBoxCollection<DIM>> mpBoxCollection;
 
    std::vector<std::pair<Node<DIM>*, Node<DIM>*> > mNodePairs;
 
    std::map<unsigned, std::set<unsigned> > mNodeNeighbours;
 
    double mReynoldsNumber;
 
    std::complex<double> mI;
 
    std::vector<boost::shared_ptr<AbstractImmersedBoundaryForce<DIM> > > mForceCollection;
 
    std::unique_ptr<ImmersedBoundary2dArrays<DIM>> mpArrays;
 
    std::unique_ptr<ImmersedBoundaryFftInterface<DIM>> mpFftInterface;
 
    std::unique_ptr<UniformGridRandomFieldGenerator<DIM>> mpRandomField;
 
    void UpdateFluidVelocityGrids(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
 
    void SetupConstantMemberVariables(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
 
    void ClearForcesAndSources();
 
    void RecalculateAverageNodeSpacings();
 
    void AddImmersedBoundaryForceContributions();
 
    void PropagateForcesToFluidGrid();
 
    void PropagateFluidSourcesToGrid();
 
    void SolveNavierStokesSpectral();
 
    double Delta1D(double dist, double spacing);
 
    void Upwind2d(const multi_array<double, 3>& rInput, multi_array<double, 3>& rOutput);
 
    void CalculateSourceGradients(const multi_array<double, 3>& rRhs, multi_array<double, 3>& rGradients);
 
    void ZeroFieldSums(multi_array<double, 3>& rField);
 
public:
 
    ImmersedBoundarySimulationModifier();
 
    virtual ~ImmersedBoundarySimulationModifier() = default;
 
    virtual void UpdateAtEndOfTimeStep(AbstractCellPopulation<DIM,DIM>& rCellPopulation);
 
    virtual void SetupSolve(AbstractCellPopulation<DIM,DIM>& rCellPopulation, std::string outputDirectory);
 
    void OutputSimulationModifierParameters(out_stream& rParamsFile);
 
    void SetNodeNeighbourUpdateFrequency(unsigned newFrequency);
 
    unsigned GetNodeNeighbourUpdateFrequency();
 
    void AddImmersedBoundaryForce(boost::shared_ptr<AbstractImmersedBoundaryForce<DIM> > pForce);
 
    void AddNormalNoise() const;
 
    bool GetZeroFieldSums() const;
 
    void SetZeroFieldSums(bool zeroFieldSums);
 
    void SetReynoldsNumber(double reynoldsNumber);
 
    double GetReynoldsNumber();
 
    bool GetAdditiveNormalNoise() const;
 
    void SetAdditiveNormalNoise(bool additiveNormalNoise);
 
    double GetNoiseStrength() const;
 
    void SetNoiseStrength(double noiseStrength);
 
    unsigned GetNoiseSkip() const;
 
    void SetNoiseSkip(unsigned noiseSkip);
 
    double GetNoiseLengthScale() const;
 
    void SetNoiseLengthScale(double noiseLengthScale);
 
};
 
#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(ImmersedBoundarySimulationModifier)
 
#endif /*IMMERSEDBOUNDARYSIMULATIONMODIFIER_HPP_*/