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| 1 | // -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- | ||
| 2 | // vi: set et ts=4 sw=4 sts=4: | ||
| 3 | // | ||
| 4 | // SPDX-FileCopyrightInfo: Copyright © DuMux Project contributors, see AUTHORS.md in root folder | ||
| 5 | // SPDX-License-Identifier: GPL-3.0-or-later | ||
| 6 | // | ||
| 7 | |||
| 8 | #ifndef DUMUX_NETWORK_TISSUE_SPATIAL_PARAMS_HH | ||
| 9 | #define DUMUX_NETWORK_TISSUE_SPATIAL_PARAMS_HH | ||
| 10 | |||
| 11 | // # Spatial parameters (`spatialparams.hh`) | ||
| 12 | // | ||
| 13 | // This file contains the __Spatial parameter classes__ for each of the | ||
| 14 | // sub-problems. This header implements two classes: `TissueSpatialParams` | ||
| 15 | // and `NetworkSpatialParams`. | ||
| 16 | // | ||
| 17 | // [[content]] | ||
| 18 | // | ||
| 19 | // ### Include headers | ||
| 20 | // | ||
| 21 | #include <dune/common/fvector.hh> | ||
| 22 | #include <dumux/common/parameters.hh> | ||
| 23 | #include <dumux/porousmediumflow/fvspatialparams1p.hh> | ||
| 24 | // | ||
| 25 | // # The `TissueSpatialParams` class | ||
| 26 | // | ||
| 27 | // The tissue spatial parameter are relatively simple. | ||
| 28 | // All parameters are constant and are configured via the configuration file. | ||
| 29 | // This means the parameters can be changed at runtime (after compilation). | ||
| 30 | // | ||
| 31 | // [[codeblock]] | ||
| 32 | namespace Dumux { | ||
| 33 | template<class FVGridGeometry, class Scalar> | ||
| 34 |
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1 | class TissueSpatialParams |
| 35 | : public FVPorousMediumFlowSpatialParamsOneP<FVGridGeometry, Scalar, TissueSpatialParams<FVGridGeometry, Scalar>> | ||
| 36 | { | ||
| 37 | // [[/codeblock]] | ||
| 38 | // [[details]] alias definitions | ||
| 39 | // [[codeblock]] | ||
| 40 | using ThisType = TissueSpatialParams<FVGridGeometry, Scalar>; | ||
| 41 | using ParentType = FVPorousMediumFlowSpatialParamsOneP<FVGridGeometry, Scalar, ThisType>; | ||
| 42 | using GridView = typename FVGridGeometry::GridView; | ||
| 43 | using FVElementGeometry = typename FVGridGeometry::LocalView; | ||
| 44 | using SubControlVolume = typename FVGridGeometry::SubControlVolume; | ||
| 45 | using SubControlVolumeFace = typename FVGridGeometry::SubControlVolumeFace; | ||
| 46 | using Element = typename GridView::template Codim<0>::Entity; | ||
| 47 | using GlobalPosition = typename Element::Geometry::GlobalCoordinate; | ||
| 48 | // [[/codeblock]] | ||
| 49 | // [[/details]] alias definitions | ||
| 50 | // | ||
| 51 | // We read parameter from the configuration file. In this case | ||
| 52 | // all parameters are constants and are configurable at runtime | ||
| 53 | // through the configuration file. | ||
| 54 | // | ||
| 55 | // [[codeblock]] | ||
| 56 | public: | ||
| 57 | 1 | TissueSpatialParams(std::shared_ptr<const FVGridGeometry> fvGridGeometry) | |
| 58 |
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1 | : ParentType(fvGridGeometry) |
| 59 | { | ||
| 60 |
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1 | porosity_ = getParam<Scalar>("Tissue.SpatialParams.Porosity"); |
| 61 |
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1 | fluidDensity_ = getParam<Scalar>("Fluid.LiquidDensity", 1000); |
| 62 |
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1 | fluidMolarMass_ = getParam<Scalar>("Fluid.AverageMolarMass", 0.018); |
| 63 | 1 | } | |
| 64 | |||
| 65 | // porosity of the tissue | ||
| 66 | ✗ | Scalar porosityAtPos(const GlobalPosition& globalPos) const | |
| 67 | ✗ | { return porosity_; } | |
| 68 | // [[/codeblock]] | ||
| 69 | // | ||
| 70 | // The volume flux (interstitial fluid flow) is zero | ||
| 71 | // because we assume no relevant advection takes place. | ||
| 72 | // | ||
| 73 | // [[codeblock]] | ||
| 74 | template<class ElementVolumeVariables> | ||
| 75 | ✗ | Scalar volumeFlux(const Element &element, | |
| 76 | const FVElementGeometry& fvGeometry, | ||
| 77 | const ElementVolumeVariables& elemVolVars, | ||
| 78 | const SubControlVolumeFace& scvf) const | ||
| 79 | { | ||
| 80 | ✗ | return 0.0; | |
| 81 | } | ||
| 82 | // [[/codeblock]] | ||
| 83 | // | ||
| 84 | // The following interfaces are needed by the (relatively general) | ||
| 85 | // tracer model to compute the fluid state and the variables needed | ||
| 86 | // to evaluate the discrete model equation in the local residual. | ||
| 87 | // The constant temperature is needed for isothermal problem since | ||
| 88 | // some interfaces (generic material interfaces) sometimes require temperature | ||
| 89 | // as input. However, this does not mean that this temperature is in | ||
| 90 | // fact used. | ||
| 91 | // | ||
| 92 | // [[details]] fluid density, molar mass, temperature and private variables | ||
| 93 | // [[codeblock]] | ||
| 94 | // fluid density | ||
| 95 | ✗ | Scalar fluidDensity(const Element& element, const SubControlVolume& scv) const | |
| 96 | ✗ | { return fluidDensity_; } | |
| 97 | |||
| 98 | // fluid molar mass | ||
| 99 | ✗ | Scalar fluidMolarMass(const Element& element, const SubControlVolume& scv) const | |
| 100 | ✗ | { return fluidMolarMass_; } | |
| 101 | |||
| 102 | // This unused here but a required interface for isothermal problems | ||
| 103 | // passed to fluid property interfaces that may in general depend on temperature | ||
| 104 | Scalar temperature() const | ||
| 105 | { return 273.15 + 37.0; } | ||
| 106 | |||
| 107 | private: | ||
| 108 | Scalar porosity_; | ||
| 109 | Scalar fluidDensity_, fluidMolarMass_; | ||
| 110 | }; | ||
| 111 | //[[/codeblock]] | ||
| 112 | //[[/details]] | ||
| 113 | // | ||
| 114 | // # The `NetworkSpatialParams` class | ||
| 115 | // | ||
| 116 | // The network parameters contain two additional interfaces. | ||
| 117 | // First, the parameters from the grid are read in `readGridParams` | ||
| 118 | // called by the problem class that stores an owning point to the | ||
| 119 | // spatial parameters object. Second, the `extrusionFactor` interface | ||
| 120 | // is used to implement extrusion of a line to a cylinder by multiplying | ||
| 121 | // all areas with the cross-sectional area. Since the cross-sectional | ||
| 122 | // are depends on the radius this is a spatially-varying parameter. | ||
| 123 | // `extrusionFactor` always exists as a member function of the base class | ||
| 124 | // `FVPorousMediumFlowSpatialParamsOneP` and defaults to $`1.0`$ (no extrusion). | ||
| 125 | // | ||
| 126 | // [[codeblock]] | ||
| 127 | template<class GridGeometry, class Scalar> | ||
| 128 | class NetworkSpatialParams | ||
| 129 | : public FVPorousMediumFlowSpatialParamsOneP<GridGeometry, Scalar, NetworkSpatialParams<GridGeometry, Scalar>> | ||
| 130 | { | ||
| 131 | // [[/codeblock]] | ||
| 132 | // | ||
| 133 | // [[details]] alias definitions | ||
| 134 | // [[codeblock]] | ||
| 135 | using ThisType = NetworkSpatialParams<GridGeometry, Scalar>; | ||
| 136 | using ParentType = FVPorousMediumFlowSpatialParamsOneP<GridGeometry, Scalar, ThisType>; | ||
| 137 | using GridView = typename GridGeometry::GridView; | ||
| 138 | using FVElementGeometry = typename GridGeometry::LocalView; | ||
| 139 | using SubControlVolume = typename GridGeometry::SubControlVolume; | ||
| 140 | using SubControlVolumeFace = typename GridGeometry::SubControlVolumeFace; | ||
| 141 | using Element = typename GridView::template Codim<0>::Entity; | ||
| 142 | using GlobalPosition = typename Element::Geometry::GlobalCoordinate; | ||
| 143 | static constexpr int dimWorld = GridView::dimensionworld; | ||
| 144 | // [[/codeblock]] | ||
| 145 | // [[/details]] | ||
| 146 | // | ||
| 147 | // In the constructor, read several parameters from the configuration file | ||
| 148 | // [[codeblock]] | ||
| 149 | public: | ||
| 150 | 1 | NetworkSpatialParams(std::shared_ptr<const GridGeometry> gridGeometry) | |
| 151 |
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5 | : ParentType(gridGeometry) |
| 152 | { | ||
| 153 |
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1 | fluidDensity_ = getParam<Scalar>("Fluid.LiquidDensity", 1000); |
| 154 |
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1 | fluidMolarMass_ = getParam<Scalar>("Fluid.AverageMolarMass", 0.018); |
| 155 |
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1 | membraneDiffusionFactor_ = getParam<Scalar>("Tracer.MembraneDiffusionFactor", 1e4); // 1/m |
| 156 | 1 | } | |
| 157 | // [[/codeblock]] | ||
| 158 | // | ||
| 159 | // Some interface functions that can be used, for example, in the problem class, to | ||
| 160 | // access spatial parameter. The interface `radius` is required by the 1D-3D coupling | ||
| 161 | // manager and is used to create the integration points for the coupling term | ||
| 162 | // | ||
| 163 | // [[codeblock]] | ||
| 164 | // this is used in the coupling so we use the outer radius of the network | ||
| 165 | Scalar radius(std::size_t eIdxGlobal) const | ||
| 166 | 11492 | { return outerRadius_[eIdxGlobal];} | |
| 167 | |||
| 168 | // the vessel radius (as given in the grid data) | ||
| 169 | Scalar vesselRadius(std::size_t eIdxGlobal) const | ||
| 170 | 697470 | { return vesselRadius_[eIdxGlobal];} | |
| 171 | |||
| 172 | // The membrane diffusion factor (1/m) to be multiplied with the free diffusion coefficient | ||
| 173 | ✗ | Scalar membraneFactor(std::size_t) const | |
| 174 | ✗ | { return membraneDiffusionFactor_; } | |
| 175 | |||
| 176 | // The blood volume flux (m^3/s) | ||
| 177 | Scalar volumeFlux(std::size_t scvfIndex) const | ||
| 178 |
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25452 | { return volumeFluxes_[scvfIndex]; } |
| 179 | |||
| 180 | // All space is available for flow | ||
| 181 | ✗ | Scalar porosityAtPos(const GlobalPosition& globalPos) const | |
| 182 | ✗ | { return 1.0; } | |
| 183 | |||
| 184 | // This unused here but a required interface for isothermal problems | ||
| 185 | // passed to fluid property interfaces that may in general depend on temperature | ||
| 186 | Scalar temperature() const | ||
| 187 | { return 273.15 + 37.0; } | ||
| 188 | |||
| 189 | // fluid density | ||
| 190 | ✗ | Scalar fluidDensity(const Element& element, const SubControlVolume& scv) const | |
| 191 | ✗ | { return fluidDensity_; } | |
| 192 | |||
| 193 | // fluid molar mass | ||
| 194 | ✗ | Scalar fluidMolarMass(const Element& element, const SubControlVolume& scv) const | |
| 195 | ✗ | { return fluidMolarMass_; } | |
| 196 | // [[/codeblock]] | ||
| 197 | |||
| 198 | // Cross-sectional area of network (computed via vessel lumen cross-sectional area) | ||
| 199 | // [[codeblock]] | ||
| 200 | template<class ElementSolution> | ||
| 201 | ✗ | Scalar extrusionFactor(const Element& element, | |
| 202 | const SubControlVolume& scv, | ||
| 203 | const ElementSolution& elemSol) const | ||
| 204 | { | ||
| 205 | 1046205 | const auto eIdx = this->gridGeometry().elementMapper().index(element); | |
| 206 | 348735 | const auto lumenRadius = vesselRadius(eIdx); | |
| 207 | 348735 | return M_PI*lumenRadius*lumenRadius; | |
| 208 | } | ||
| 209 | // [[/codeblock]] | ||
| 210 | // | ||
| 211 | // The following interface functions are used in the `main.cc` file | ||
| 212 | // for VTK output. For visualization in ParaView, it is nice to | ||
| 213 | // write out the vessel radius for ParaView's `Tube` filter. | ||
| 214 | // | ||
| 215 | // [[codeblock]] | ||
| 216 | // Get the vessel lumen radii for output | ||
| 217 | const std::vector<Scalar>& getVesselRadii() const | ||
| 218 |
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1 | { return vesselRadius_; } |
| 219 | |||
| 220 | // Get vessel segment length (for post-processing) | ||
| 221 | const std::vector<Scalar>& getVesselSegmentLengths() const | ||
| 222 |
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1 | { return vesselSegmentLength_; } |
| 223 | |||
| 224 | // Get the outer radii for output | ||
| 225 | const std::vector<Scalar>& getOuterRadii() const | ||
| 226 |
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1 | { return outerRadius_; } |
| 227 | // [[/codeblock]] | ||
| 228 | |||
| 229 | // Read params from dgf | ||
| 230 | // the grid file contains the vessel radius for each element | ||
| 231 | // [[codeblock]] | ||
| 232 | template<class GridData> | ||
| 233 | 1 | void readGridParams(const GridData& gridData) | |
| 234 | { | ||
| 235 | 1 | const auto& gg = this->gridGeometry(); | |
| 236 | 2 | const auto numElements = gg.gridView().size(0); | |
| 237 | 1 | vesselRadius_.resize(numElements); | |
| 238 | // the vessel segment length | ||
| 239 | 1 | vesselSegmentLength_.resize(numElements); | |
| 240 | // outer radius including layers outside lumen that are considered part of the membrane | ||
| 241 | 1 | outerRadius_.resize(numElements); | |
| 242 | |||
| 243 | // The grid view is a leafGridView. Parameters are only set on level 0. | ||
| 244 | // Elements have to inherit spatial parameters from their father. | ||
| 245 |
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3472 | for (const auto& element : elements(gg.gridView())) |
| 246 | { | ||
| 247 | 1735 | auto level0element = element; | |
| 248 |
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3470 | while (level0element.hasFather()) |
| 249 | ✗ | level0element = level0element.father(); | |
| 250 | |||
| 251 | 3470 | const auto eIdx = gg.elementMapper().index(element); | |
| 252 | 1735 | vesselRadius_[eIdx] = gridData.parameters(level0element)[0]; | |
| 253 | 1735 | vesselSegmentLength_[eIdx] = element.geometry().volume(); | |
| 254 | } | ||
| 255 | |||
| 256 | // outer radius adding endothelium and basement membrane | ||
| 257 |
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3471 | for (std::size_t eIdx = 0; eIdx < gg.gridView().size(0); ++eIdx) |
| 258 | 5205 | outerRadius_[eIdx] = vesselRadius_[eIdx] + 0.4e-6; | |
| 259 | 1 | } | |
| 260 | // [[/codeblock]] | ||
| 261 | // | ||
| 262 | // The blood volume flux for each (sub)-control-volume face | ||
| 263 | // is provided from the outside (from a blood-flow solver). | ||
| 264 | // The advection-diffusion model requires a volume flux | ||
| 265 | // at each (sub)-control-volume face. In case, for example, | ||
| 266 | // a velocity field is given instead, volume fluxes can be | ||
| 267 | // computed using the normal vector `scvf.unitOuterNormal()` | ||
| 268 | // of the (sub)-control-volume face. | ||
| 269 | // | ||
| 270 | // [[codeblock]] | ||
| 271 | // set the volume fluxes computed by a blood flow model | ||
| 272 | void setVolumeFluxes(const std::vector<Scalar>& fluxes) | ||
| 273 |
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1 | { volumeFluxes_ = fluxes; } |
| 274 | |||
| 275 | template<class ElementVolumeVariables> | ||
| 276 | ✗ | Scalar volumeFlux(const Element &element, | |
| 277 | const FVElementGeometry& fvGeometry, | ||
| 278 | const ElementVolumeVariables& elemVolVars, | ||
| 279 | const SubControlVolumeFace& scvf) const | ||
| 280 | { | ||
| 281 | ✗ | assert(!volumeFluxes_.empty()); | |
| 282 | ✗ | return volumeFluxes_[scvf.index()]; | |
| 283 | } | ||
| 284 | // [[/codeblock]] | ||
| 285 | // | ||
| 286 | // [[details]] private member variables | ||
| 287 | // [[codeblock]] | ||
| 288 | private: | ||
| 289 | Scalar porosity_; | ||
| 290 | Scalar fluidDensity_, fluidMolarMass_; | ||
| 291 | Scalar membraneDiffusionFactor_; | ||
| 292 | |||
| 293 | std::vector<Scalar> vesselRadius_; | ||
| 294 | std::vector<Scalar> vesselSegmentLength_; | ||
| 295 | std::vector<Scalar> outerRadius_; | ||
| 296 | std::vector<Scalar> volumeFluxes_; | ||
| 297 | }; | ||
| 298 | |||
| 299 | } // end namespace Dumux | ||
| 300 | // [[/codeblock]] | ||
| 301 | // [[/details]] | ||
| 302 | // [[/content]] | ||
| 303 | #endif | ||
| 304 |