problem_tissue.hh

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#ifndef DUMUX_TISSUE_PROBLEM_HH
#define DUMUX_TISSUE_PROBLEM_HH
 
#include <dune/grid/yaspgrid.hh>
 
#include <dune/geometry/quadraturerules.hh>
#include <dune/geometry/referenceelements.hh>
#include <dune/localfunctions/lagrange/pqkfactory.hh>
 
#include <dumux/common/math.hh>
#include <dumux/common/parameters.hh>
#include <dumux/common/properties.hh>
#include <dumux/discretization/box.hh>
#include <dumux/discretization/cctpfa.hh>
 
#include <dumux/porousmediumflow/1p/model.hh>
#include <dumux/porousmediumflow/problem.hh>
#include <dumux/porousmediumflow/1p/incompressiblelocalresidual.hh>
 
#include <dumux/material/components/constant.hh>
#include <dumux/material/fluidsystems/1pliquid.hh>
 
#include <dumux/multidomain/embedded/couplingmanager1d3d.hh> // for coupling mode
 
#include "spatialparams_tissue.hh"
 
namespace Dumux {
 
template <class TypeTag>
class TissueProblem;
 
namespace Properties {
 
// Create new type tags
namespace TTag {
struct Tissue { using InheritsFrom = std::tuple<OneP>; };
struct TissueCC { using InheritsFrom = std::tuple<Tissue, CCTpfaModel>; };
struct TissueBox { using InheritsFrom = std::tuple<Tissue, BoxModel>; };
} // end namespace TTag
 
// Set the grid type
template<class TypeTag>
struct Grid<TypeTag, TTag::Tissue> { using type = Dune::YaspGrid<3, Dune::EquidistantOffsetCoordinates<GetPropType<TypeTag, Properties::Scalar>, 3> >; };
 
template<class TypeTag>
struct EnableGridGeometryCache<TypeTag, TTag::Tissue> { static constexpr bool value = true; };
template<class TypeTag>
struct EnableGridVolumeVariablesCache<TypeTag, TTag::Tissue> { static constexpr bool value = true; };
template<class TypeTag>
struct EnableGridFluxVariablesCache<TypeTag, TTag::Tissue> { static constexpr bool value = true; };
template<class TypeTag>
struct SolutionDependentAdvection<TypeTag, TTag::Tissue> { static constexpr bool value = false; };
template<class TypeTag>
struct SolutionDependentMolecularDiffusion<TypeTag, TTag::Tissue> { static constexpr bool value = false; };
template<class TypeTag>
struct SolutionDependentHeatConduction<TypeTag, TTag::Tissue> { static constexpr bool value = false; };
 
// Set the problem property
template<class TypeTag>
struct Problem<TypeTag, TTag::Tissue> { using type = TissueProblem<TypeTag>; };
 
// Set the problem property
template<class TypeTag>
struct LocalResidual<TypeTag, TTag::Tissue> { using type = OnePIncompressibleLocalResidual<TypeTag>; };
 
// the fluid system
template<class TypeTag>
struct FluidSystem<TypeTag, TTag::Tissue>
{
    using Scalar = GetPropType<TypeTag, Properties::Scalar>;
    using type = FluidSystems::OnePLiquid<Scalar, Components::Constant<1, Scalar> >;
};
 
// Set the spatial parameters
template<class TypeTag>
struct SpatialParams<TypeTag, TTag::Tissue>
{
    using type = TissueSpatialParams<GetPropType<TypeTag, Properties::GridGeometry>,
                                     GetPropType<TypeTag, Properties::Scalar>>;
};
} // end namespace Properties
 
 
template <class TypeTag>
class TissueProblem : public PorousMediumFlowProblem<TypeTag>
{
    using ParentType = PorousMediumFlowProblem<TypeTag>;
    using Scalar = GetPropType<TypeTag, Properties::Scalar>;
    using GridGeometry = GetPropType<TypeTag, Properties::GridGeometry>;
    using FVElementGeometry = typename GridGeometry::LocalView;
    using SubControlVolume = typename GridGeometry::SubControlVolume;
    using GridView = typename GridGeometry::GridView;
    using PrimaryVariables = GetPropType<TypeTag, Properties::PrimaryVariables>;
    using NumEqVector = GetPropType<TypeTag, Properties::NumEqVector>;
    using SolutionVector = GetPropType<TypeTag, Properties::SolutionVector>;
    using GridVariables = GetPropType<TypeTag, Properties::GridVariables>;
    using BoundaryTypes = GetPropType<TypeTag, Properties::BoundaryTypes>;
    using PointSource = GetPropType<TypeTag, Properties::PointSource>;
    using Indices = typename GetPropType<TypeTag, Properties::ModelTraits>::Indices;
    using Element = typename GridView::template Codim<0>::Entity;
    using GlobalPosition = typename GridGeometry::GlobalCoordinate;
 
    using CouplingManager = GetPropType<TypeTag, Properties::CouplingManager>;
 
public:
    TissueProblem(std::shared_ptr<const GridGeometry> gridGeometry,
                  std::shared_ptr<CouplingManager> couplingManager)
    : ParentType(gridGeometry, "Tissue")
    , couplingManager_(couplingManager)
    {
        // read parameters from input file
        name_  =  getParam<std::string>("Vtk.OutputName") + "_" + getParamFromGroup<std::string>(this->paramGroup(), "Problem.Name");
 
        exactPressure_.resize(this->gridGeometry().numDofs());
        for (const auto& element : elements(this->gridGeometry().gridView()))
        {
            auto fvGeometry = localView(this->gridGeometry());
            fvGeometry.bindElement(element);
 
            for (auto&& scv : scvs(fvGeometry))
                exactPressure_[scv.dofIndex()] = exactSolution(scv.dofPosition());
        }
    }
 
    const std::string& name() const
    { return name_; }
 
    Scalar temperature() const
    { return 273.15 + 37; } // in [K]
 
    // \}
 
    // \{
 
    BoundaryTypes boundaryTypesAtPos(const GlobalPosition &globalPos) const
    {
        BoundaryTypes values;
        values.setAllDirichlet();
        return values;
    }
 
    PrimaryVariables dirichletAtPos(const GlobalPosition &globalPos) const
    {
        PrimaryVariables values;
        values = exactSolution(globalPos);
        return values;
    }
 
    // \}
 
    // \{
 
    void addPointSources(std::vector<PointSource>& pointSources) const
    { pointSources = this->couplingManager().bulkPointSources(); }
 
    template<class ElementVolumeVariables>
    void pointSource(PointSource& source,
                     const Element &element,
                     const FVElementGeometry& fvGeometry,
                     const ElementVolumeVariables& elemVolVars,
                     const SubControlVolume &scv) const
    {
        // compute source at every integration point
        const Scalar pressure3D = this->couplingManager().bulkPriVars(source.id())[Indices::pressureIdx];
        const Scalar pressure1D = this->couplingManager().lowDimPriVars(source.id())[Indices::pressureIdx];
 
        // calculate the source
        const Scalar radius = this->couplingManager().radius(source.id());
        const Scalar beta = 2*M_PI/(2*M_PI + std::log(radius));
        const Scalar sourceValue = beta*(pressure1D - pressure3D);
        source = sourceValue*source.quadratureWeight()*source.integrationElement();
    }
 
    template<class ElementVolumeVariables,
             bool enable = (CouplingManager::couplingMode == EmbeddedCouplingMode::kernel),
             std::enable_if_t<enable, int> = 0>
    NumEqVector source(const Element &element,
                       const FVElementGeometry& fvGeometry,
                       const ElementVolumeVariables& elemVolVars,
                       const SubControlVolume &scv) const
    {
        static const Scalar kernelWidth = getParam<Scalar>("MixedDimension.KernelWidth");
        static const Scalar kernelFactor = std::log(kernelWidth)-9.0/10.0;
 
        NumEqVector source(0.0);
 
        const auto eIdx = this->gridGeometry().elementMapper().index(element);
        const auto& sourceIds = this->couplingManager().bulkSourceIds(eIdx);
        const auto& sourceWeights = this->couplingManager().bulkSourceWeights(eIdx);
 
        for (int i = 0; i < sourceIds.size(); ++i)
        {
            const auto id = sourceIds[i];
            const auto weight = sourceWeights[i];
 
            const Scalar radius = this->couplingManager().radius(id);
            const Scalar pressure3D = this->couplingManager().bulkPriVars(id)[Indices::pressureIdx];
            const Scalar pressure1D = this->couplingManager().lowDimPriVars(id)[Indices::pressureIdx];
 
            // calculate the source
            const Scalar beta = 2*M_PI/(2*M_PI + std::log(radius));
            const Scalar sourceValue = beta*(pressure1D - pressure3D / kernelFactor * std::log(radius));
 
            source[Indices::conti0EqIdx] += sourceValue*weight;
        }
 
        const auto volume = scv.volume()*elemVolVars[scv].extrusionFactor();
        source[Indices::conti0EqIdx] /= volume;
 
        return source;
    }
 
    template<class ElementVolumeVariables,
             bool enable = (CouplingManager::couplingMode == EmbeddedCouplingMode::kernel),
             std::enable_if_t<!enable, int> = 0>
    NumEqVector source(const Element &element,
                       const FVElementGeometry& fvGeometry,
                       const ElementVolumeVariables& elemVolVars,
                       const SubControlVolume &scv) const
    { return NumEqVector(0.0); }
 
    template<class MatrixBlock, class VolumeVariables>
    void addSourceDerivatives(MatrixBlock& block,
                              const Element& element,
                              const FVElementGeometry& fvGeometry,
                              const VolumeVariables& curElemVolVars,
                              const SubControlVolume& scv) const
    {
        const auto eIdx = this->gridGeometry().elementMapper().index(element);
 
        auto key = std::make_pair(eIdx, 0);
        if (this->pointSourceMap().count(key))
        {
            // call the solDependent function. Herein the user might fill/add values to the point sources
            // we make a copy of the local point sources here
            auto pointSources = this->pointSourceMap().at(key);
 
            // add the point source values to the local residual (negative sign is convention for source term)
            for (const auto& source : pointSources)
                block[0][0] -= this->couplingManager().pointSourceDerivative(source, Dune::index_constant<0>{}, Dune::index_constant<0>{});
        }
    }
 
    PrimaryVariables initialAtPos(const GlobalPosition &globalPos) const
    { return PrimaryVariables(0.0); }
 
    Scalar exactSolution(const GlobalPosition &globalPos) const
    {
        Dune::FieldVector<double, 2> xy({globalPos[0], globalPos[1]});
        if (CouplingManager::couplingMode == EmbeddedCouplingMode::cylindersources)
        {
            static const auto R = getParam<Scalar>("SpatialParams.Radius");
            if (xy.two_norm() > R)
                return -1.0*(1+globalPos[2])/(2*M_PI)*std::log(xy.two_norm());
            else
               return -1.0*(1+globalPos[2])/(2*M_PI)*std::log(R);
 
        }
        else if (CouplingManager::couplingMode == EmbeddedCouplingMode::kernel)
        {
            static const auto rho = getParam<Scalar>("MixedDimension.KernelWidth");
            const auto& r = xy.two_norm();
            if (xy.two_norm() >= rho)
                return -1.0*(1+globalPos[2])/(2*M_PI)*std::log(xy.two_norm());
            else
                return -1.0*(1+globalPos[2])/(2*M_PI)*(11.0/15.0*std::pow(r/rho, 5)
                                                       - 3.0/2.0*std::pow(r/rho, 4)
                                                       + 5.0/3.0*std::pow(r/rho, 2)
                                                       - 9.0/10.0 + std::log(rho));
        }
        else
            return -1.0*(1+globalPos[2])/(2*M_PI)*std::log(xy.two_norm());
    }
 
    void computeSourceIntegral(const SolutionVector& sol, const GridVariables& gridVars)
    {
        PrimaryVariables source(0.0);
        for (const auto& element : elements(this->gridGeometry().gridView()))
        {
            auto fvGeometry = localView(this->gridGeometry());
            fvGeometry.bindElement(element);
 
            auto elemVolVars = localView(gridVars.curGridVolVars());
            elemVolVars.bindElement(element, fvGeometry, sol);
 
            for (auto&& scv : scvs(fvGeometry))
            {
                auto pointSources = this->scvPointSources(element, fvGeometry, elemVolVars, scv);
                pointSources += this->source(element, fvGeometry, elemVolVars, scv);
                pointSources *= scv.volume()*elemVolVars[scv].extrusionFactor();
                source += pointSources;
            }
        }
 
        std::cout << "Global integrated source (3D): " << source << '\n';
    }
 
    template<class VtkOutputModule>
    void addVtkOutputFields(VtkOutputModule& vtk) const
    {
        vtk.addField(exactPressure_, "exact pressure");
    }
 
    const CouplingManager& couplingManager() const
    { return *couplingManager_; }
 
private:
    std::vector<Scalar> exactPressure_;
 
    static constexpr Scalar eps_ = 1.5e-7;
    std::string name_;
 
    std::shared_ptr<CouplingManager> couplingManager_;
};
 
} // end namespace Dumux
 
#endif