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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_TISSUE_NETWORK_TRANSPORT_PROBLEMS_HH | ||
| 9 | #define DUMUX_TISSUE_NETWORK_TRANSPORT_PROBLEMS_HH | ||
| 10 | |||
| 11 | // # Initial, boundary conditions and sources (`problem.hh`) | ||
| 12 | // | ||
| 13 | // This file contains the __problem classes__ which defines the initial and boundary | ||
| 14 | // conditions and implements the coupling source terms. The file contains two | ||
| 15 | // problem classes: `TissueTransportProblem` and `NetworkTransportProblem` for the | ||
| 16 | // respective subdomains. The subdomain problem classes specify boundary and initial | ||
| 17 | // conditions for the subdomains separately. For this setup, we specify boundary fluxes | ||
| 18 | // via the `neumann` function (note that despite its name, the function allows you to | ||
| 19 | // implement both Neumann or Robin-type boundary conditions, weakly imposed). | ||
| 20 | // | ||
| 21 | // The subdomain problems are coupled to each other. This is evident from the | ||
| 22 | // coupling manager pointer that is stored in each subdomain problem (and the | ||
| 23 | // interface function `couplingManager()` giving access to the coupling manager object). | ||
| 24 | // This access is used in the `addPointSources()` and `pointSource(...)` functions. | ||
| 25 | // One point source (in this context) represents a quadrature point for the coupling | ||
| 26 | // condition integral. This means, we implement | ||
| 27 | // | ||
| 28 | // ```math | ||
| 29 | // \vert P \vert C_M D \bar{\varrho} (x^\bigcirc_\mathrm{T} - x_\mathrm{B}) w_i \mathrm{d}s_i | ||
| 30 | // ``` | ||
| 31 | // | ||
| 32 | // where $`w_i`$ is the weight and $`\mathrm{d}s_i`$ (units of m) the integration element at | ||
| 33 | // the quadrature point. The units of the resulting term is mol/s (tracer amount per meter and second), | ||
| 34 | // which are the units of the one-dimensional balance equation integrated over one dimensional control volumes. | ||
| 35 | // We are integrating conceptually over the surface of the vessel. The quantity | ||
| 36 | // $`x^\bigcirc_\mathrm{T}`$ is the perimeter average of the 3D mole fraction field. This is not | ||
| 37 | // directly visible in the code since the chosen coupling manager determined what to return here | ||
| 38 | // for the 1D and 3D mole fraction depending on the coupling scheme. | ||
| 39 | // | ||
| 40 | // [[content]] | ||
| 41 | // | ||
| 42 | // ### Include headers | ||
| 43 | // We use properties (compile-time parameterization) and parameters (run-time parameterization). | ||
| 44 | // Moreover, we need array types and the problem base class for porous medium problems. | ||
| 45 | #include <dumux/common/parameters.hh> | ||
| 46 | #include <dumux/common/properties.hh> | ||
| 47 | #include <dumux/common/boundarytypes.hh> | ||
| 48 | #include <dumux/common/numeqvector.hh> | ||
| 49 | #include <dumux/porousmediumflow/problem.hh> | ||
| 50 | // | ||
| 51 | // # The `TissueTransportProblem` class | ||
| 52 | // We start with the tissue transport with boundary, initial condition and sources. | ||
| 53 | // To set the initial condition, the problem reads some parameters from the configuration file | ||
| 54 | // `params.input`. Concentration is defined by $`c = \varrho x`$. This is usually a more | ||
| 55 | // convenient quantity which is why we read this from the configuration file. | ||
| 56 | // (What we read from the configuration file is entirely up to us. You can simply swap | ||
| 57 | // the parameter name in the `getParam` command and adapt the configuration file to provide the parameter.) | ||
| 58 | // | ||
| 59 | // [[codeblock]] | ||
| 60 | namespace Dumux { | ||
| 61 | template <class TypeTag> | ||
| 62 | class TissueTransportProblem : public PorousMediumFlowProblem<TypeTag> | ||
| 63 | { | ||
| 64 | // [[/codeblock]] | ||
| 65 | // [[details]] alias definitions and local variables | ||
| 66 | // [[codeblock]] | ||
| 67 | using ParentType = PorousMediumFlowProblem<TypeTag>; | ||
| 68 | using Scalar = GetPropType<TypeTag, Properties::Scalar>; | ||
| 69 | |||
| 70 | using GridGeometry = GetPropType<TypeTag, Properties::GridGeometry>; | ||
| 71 | using GridView = typename GridGeometry::GridView; | ||
| 72 | using FVElementGeometry = typename GridGeometry::LocalView; | ||
| 73 | using SubControlVolume = typename GridGeometry::SubControlVolume; | ||
| 74 | using SubControlVolumeFace = typename GridGeometry::SubControlVolumeFace; | ||
| 75 | |||
| 76 | using PrimaryVariables = GetPropType<TypeTag, Properties::PrimaryVariables>; | ||
| 77 | using ResidualVector = Dumux::NumEqVector<PrimaryVariables>; | ||
| 78 | using BoundaryTypes = Dumux::BoundaryTypes<PrimaryVariables::size()>; | ||
| 79 | using PointSource = GetPropType<TypeTag, Properties::PointSource>; | ||
| 80 | |||
| 81 | static constexpr int dim = GridView::dimension; | ||
| 82 | static constexpr int dimworld = GridView::dimensionworld; | ||
| 83 | |||
| 84 | using Element = typename GridView::template Codim<0>::Entity; | ||
| 85 | using GlobalPosition = typename Element::Geometry::GlobalCoordinate; | ||
| 86 | |||
| 87 | using CouplingManager = GetPropType<TypeTag, Properties::CouplingManager>; | ||
| 88 | |||
| 89 | static constexpr int phaseIdx = 0; | ||
| 90 | static constexpr int compIdx = 0; | ||
| 91 | |||
| 92 | static constexpr auto lowDimIdx = typename CouplingManager::MultiDomainTraits::template SubDomain<1>::Index(); | ||
| 93 | // [[/codeblock]] | ||
| 94 | // [[/details]] | ||
| 95 | // [[codeblock]] | ||
| 96 | public: | ||
| 97 | 1 | TissueTransportProblem(std::shared_ptr<const GridGeometry> gridGeometry, | |
| 98 | std::shared_ptr<CouplingManager> couplingManager, | ||
| 99 | const std::string& paramGroup = "") | ||
| 100 | : ParentType(gridGeometry, paramGroup) | ||
| 101 |
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5 | , couplingManager_(couplingManager) |
| 102 | { | ||
| 103 | //read parameters from input file | ||
| 104 |
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1 | name_ = getParam<std::string>("Problem.Name") + "_3d_transport"; |
| 105 | |||
| 106 |
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1 | freeD_ = getParam<Scalar>("Tracer.DiffusionCoefficient"); |
| 107 | |||
| 108 |
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1 | initialPeakConcentration_ = getParam<Scalar>("Tissue.Problem.InitialPeakConcentration", 1.0); // mmol/l |
| 109 |
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1 | initialCenter_ = getParam<GlobalPosition>("Tissue.Problem.InitialCenter"); |
| 110 |
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1 | initialStddev_ = getParam<GlobalPosition>("Tissue.Problem.InitialStddev"); |
| 111 | 1 | } | |
| 112 | |||
| 113 | // name (used for output) | ||
| 114 | const std::string& name() const | ||
| 115 |
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1 | { return name_; } |
| 116 | // [[/codeblock]] | ||
| 117 | // | ||
| 118 | // We set the initial condition as a Gaussian | ||
| 119 | // | ||
| 120 | // ```math | ||
| 121 | // x(t=0) = \frac{c}{\varrho} \operatorname{exp}\left( -\frac{x-x_0}{2 \sigma_x^2} | ||
| 122 | // -\frac{y-y_0}{2 \sigma_y^2}-\frac{z-z_0}{2 \sigma_z^2} \right) | ||
| 123 | //``` | ||
| 124 | // | ||
| 125 | // if the Gaussian is very wide, this essentially corresponds to a constant value. | ||
| 126 | // | ||
| 127 | // [[codeblock]] | ||
| 128 | // initial conditions (called when setting initial solution) | ||
| 129 | 8000 | PrimaryVariables initialAtPos(const GlobalPosition& globalPos) const | |
| 130 | { | ||
| 131 | return PrimaryVariables({ | ||
| 132 | 16000 | initialPeakConcentration_/1000*0.018*std::exp( | |
| 133 | 56000 | -(globalPos[0] - initialCenter_[0])*(globalPos[0] - initialCenter_[0])/(2*initialStddev_[0]*initialStddev_[0]) | |
| 134 | 56000 | -(globalPos[1] - initialCenter_[1])*(globalPos[1] - initialCenter_[1])/(2*initialStddev_[1]*initialStddev_[1]) | |
| 135 | 56000 | -(globalPos[2] - initialCenter_[2])*(globalPos[2] - initialCenter_[2])/(2*initialStddev_[2]*initialStddev_[2]) | |
| 136 | ) | ||
| 137 | 16000 | }); | |
| 138 | } | ||
| 139 | // [[/codeblock]] | ||
| 140 | |||
| 141 | // We set the boundary condition to boundary flux (or Neumann conditions) | ||
| 142 | // and specify zero flux everywhere for the tissue domain | ||
| 143 | // | ||
| 144 | // [[codeblock]] | ||
| 145 | ✗ | BoundaryTypes boundaryTypesAtPos(const GlobalPosition& globalPos) const | |
| 146 | { | ||
| 147 |
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484800 | BoundaryTypes values; |
| 148 |
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484800 | values.setAllNeumann(); |
| 149 | ✗ | return values; | |
| 150 | } | ||
| 151 | |||
| 152 | // flux boundaries (called for Neumann boundaries) | ||
| 153 | template<class ElementVolumeVariables, class ElementFluxVarsCache> | ||
| 154 | ✗ | ResidualVector neumann(const Element& element, | |
| 155 | const FVElementGeometry& fvGeometry, | ||
| 156 | const ElementVolumeVariables& elemVolVars, | ||
| 157 | const ElementFluxVarsCache& fluxCache, | ||
| 158 | const SubControlVolumeFace& scvf) const | ||
| 159 | { | ||
| 160 | // no-flow conditions / symmetry conditions | ||
| 161 | 484800 | ResidualVector values(0.0); | |
| 162 | ✗ | return values; | |
| 163 | } | ||
| 164 | // [[/codeblock]] | ||
| 165 | |||
| 166 | // Now follows the implementation of the point sources. The point sources | ||
| 167 | // are obtained from (and computed by) the coupling manager. The function | ||
| 168 | // `addPointSources` is called when we call `problem->computePointSourceMap()` | ||
| 169 | // in the `main.cc`. The mechanism is provided by the base problem we inherit | ||
| 170 | // from. Essentially all point sources computed by the coupling manager are | ||
| 171 | // located and assigned to the respective control volume. Finally, the | ||
| 172 | // function `pointSource` implements the actual value of the point source. | ||
| 173 | // (While this is linear in the primary variable here, note that you can | ||
| 174 | // also implement non-linear relations here, provided that a Newton solver | ||
| 175 | // is used in the main program.) The `source(...)` function allows to | ||
| 176 | // specify additional volumetric source terms (in units of mol/s/m^3), | ||
| 177 | // for example, some metabolic demand. | ||
| 178 | // | ||
| 179 | // [[codeblock]] | ||
| 180 | // this is needed for the 1d-3d coupling (realized via point source interface) | ||
| 181 | void addPointSources(std::vector<PointSource>& pointSources) const | ||
| 182 |
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1 | { pointSources = this->couplingManager().bulkPointSources(); } |
| 183 | |||
| 184 | // called for every point source (coupling term integration point) | ||
| 185 | template<class ElementVolumeVariables> | ||
| 186 | 322387 | void pointSource(PointSource& source, | |
| 187 | const Element &element, | ||
| 188 | const FVElementGeometry& fvGeometry, | ||
| 189 | const ElementVolumeVariables& elemVolVars, | ||
| 190 | const SubControlVolume &scv) const | ||
| 191 | { | ||
| 192 | // compute source at every integration point | ||
| 193 | 967161 | const Scalar x1D = this->couplingManager().lowDimPriVars(source.id())[compIdx]; | |
| 194 | 967161 | const Scalar x3D = this->couplingManager().bulkPriVars(source.id())[compIdx]; | |
| 195 | |||
| 196 | // get the segment radius (outer radius) | ||
| 197 | 967161 | const Scalar radius = this->couplingManager().radius(source.id()); | |
| 198 | |||
| 199 | // molar density (mol/m^3) (we assemble a mole balance equation instead of mass balance) | ||
| 200 | 322387 | const Scalar meanRhoMolar = 1000/0.018; | |
| 201 | |||
| 202 | // trans-membrane diffusive permeability | ||
| 203 | 967161 | const auto lowDimElementIdx = this->couplingManager().pointSourceData(source.id()).lowDimElementIdx(); | |
| 204 | 644774 | const Scalar lc = freeD_ | |
| 205 | 1289548 | * this->couplingManager().problem(lowDimIdx).spatialParams().membraneFactor(lowDimElementIdx); // m/s | |
| 206 | |||
| 207 | // diffusive flux across membrane | ||
| 208 | 322387 | auto transMembraneFlux = -2*M_PI*radius*lc*meanRhoMolar*(x3D - x1D); | |
| 209 | 322387 | transMembraneFlux *= source.quadratureWeight()*source.integrationElement(); | |
| 210 | |||
| 211 | 644774 | source = transMembraneFlux; | |
| 212 | 322387 | } | |
| 213 | |||
| 214 | // additional volumetric source term in mol/(s*m^3), i.e. metabolic consumption | ||
| 215 | // positive value means production into tissue, negative value means extraction from tissue | ||
| 216 | template<class ElementVolumeVariables> | ||
| 217 | ✗ | ResidualVector source(const Element &element, | |
| 218 | const FVElementGeometry& fvGeometry, | ||
| 219 | const ElementVolumeVariables& elemVolVars, | ||
| 220 | const SubControlVolume &scv) const | ||
| 221 | { | ||
| 222 |
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1634138 | return { 0.0 }; |
| 223 | } | ||
| 224 | // [[/codeblock]] | ||
| 225 | |||
| 226 | // Compute the current contrast agent amount in mole in the whole tissue | ||
| 227 | // This function is used from the main file to write output. | ||
| 228 | // | ||
| 229 | // [[codeblock]] | ||
| 230 | template<class SolutionVector, class GridVariables> | ||
| 231 | 101 | Scalar computeTracerAmount(const SolutionVector& sol, const GridVariables& gridVars) | |
| 232 | { | ||
| 233 | 101 | Scalar totalAmount(0.0); | |
| 234 |
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202 | auto fvGeometry = localView(this->gridGeometry()); |
| 235 |
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202 | auto elemVolVars = localView(gridVars.curGridVolVars()); |
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1616404 | for (const auto& element : elements(this->gridGeometry().gridView())) |
| 237 | { | ||
| 238 | 808000 | fvGeometry.bindElement(element); | |
| 239 | 808000 | elemVolVars.bindElement(element, fvGeometry, sol); | |
| 240 | |||
| 241 |
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3232000 | for (const auto& scv : scvs(fvGeometry)) |
| 242 | { | ||
| 243 | 808000 | const auto& volVars = elemVolVars[scv]; | |
| 244 | 808000 | const auto localAmount = volVars.porosity() | |
| 245 | 2424000 | *volVars.moleFraction(phaseIdx, compIdx)*volVars.molarDensity(phaseIdx) | |
| 246 | 808000 | *scv.volume()*volVars.extrusionFactor(); | |
| 247 | 808000 | totalAmount += localAmount; | |
| 248 | } | ||
| 249 | } | ||
| 250 | |||
| 251 | 101 | return totalAmount; | |
| 252 | } | ||
| 253 | // [[/codeblock]] | ||
| 254 | |||
| 255 | // [[details]] coupling manager interface function and private variables | ||
| 256 | // [[codeblock]] | ||
| 257 | // Get the coupling manager | ||
| 258 | const CouplingManager& couplingManager() const | ||
| 259 |
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1289550 | { return *couplingManager_; } |
| 260 | |||
| 261 | private: | ||
| 262 | static constexpr Scalar eps_ = 1.5e-7; | ||
| 263 | std::string name_; | ||
| 264 | |||
| 265 | Scalar freeD_; | ||
| 266 | Scalar initialPeakConcentration_; | ||
| 267 | GlobalPosition initialCenter_, initialStddev_; | ||
| 268 | |||
| 269 | std::shared_ptr<CouplingManager> couplingManager_; | ||
| 270 | }; | ||
| 271 | // [[/codeblock]] | ||
| 272 | // [[/details]] | ||
| 273 | // | ||
| 274 | // # The `NetworkTransportProblem` class | ||
| 275 | // We continue with the network transport with boundary, initial condition and sources. | ||
| 276 | // The implementation is quite similar to the tissue domain. | ||
| 277 | // This time the boundary function is more complex as we also take into account | ||
| 278 | // advective transport over the network boundaries to blood flow. | ||
| 279 | // | ||
| 280 | // [[codeblock]] | ||
| 281 | template <class TypeTag> | ||
| 282 | class NetworkTransportProblem : public PorousMediumFlowProblem<TypeTag> | ||
| 283 | { | ||
| 284 | // [[/codeblock]] | ||
| 285 | // [[details]] alias definitions and local variables | ||
| 286 | // [[codeblock]] | ||
| 287 | using ParentType = PorousMediumFlowProblem<TypeTag>; | ||
| 288 | |||
| 289 | using Scalar = GetPropType<TypeTag, Properties::Scalar>; | ||
| 290 | using PointSource = GetPropType<TypeTag, Properties::PointSource>; | ||
| 291 | using PrimaryVariables = GetPropType<TypeTag, Properties::PrimaryVariables>; | ||
| 292 | using ResidualVector = Dumux::NumEqVector<PrimaryVariables>; | ||
| 293 | using BoundaryTypes = Dumux::BoundaryTypes<PrimaryVariables::size()>; | ||
| 294 | |||
| 295 | using GridGeometry = GetPropType<TypeTag, Properties::GridGeometry>; | ||
| 296 | using GridView = typename GridGeometry::GridView; | ||
| 297 | using FVElementGeometry = typename GridGeometry::LocalView; | ||
| 298 | using SubControlVolume = typename GridGeometry::SubControlVolume; | ||
| 299 | using SubControlVolumeFace = typename GridGeometry::SubControlVolumeFace; | ||
| 300 | |||
| 301 | using Element = typename GridView::template Codim<0>::Entity; | ||
| 302 | using GlobalPosition = typename Element::Geometry::GlobalCoordinate; | ||
| 303 | |||
| 304 | using CouplingManager = GetPropType<TypeTag, Properties::CouplingManager>; | ||
| 305 | |||
| 306 | static constexpr int dim = GridView::dimension; | ||
| 307 | static constexpr int dimworld = GridView::dimensionworld; | ||
| 308 | static constexpr int compIdx = 0; | ||
| 309 | static constexpr int phaseIdx = 0; | ||
| 310 | // [[/codeblock]] | ||
| 311 | // [[/details]] | ||
| 312 | // [[codeblock]] | ||
| 313 | public: | ||
| 314 | // initialize problem instance | ||
| 315 | template<class GridData> | ||
| 316 | 1 | NetworkTransportProblem(std::shared_ptr<const GridGeometry> gridGeometry, | |
| 317 | std::shared_ptr<CouplingManager> couplingManager, | ||
| 318 | std::shared_ptr<GridData> gridData, | ||
| 319 | const std::string& paramGroup = "") | ||
| 320 | : ParentType(gridGeometry, paramGroup) | ||
| 321 |
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3 | , couplingManager_(couplingManager) |
| 322 | { | ||
| 323 | //read parameters from input file | ||
| 324 |
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1 | name_ = getParam<std::string>("Problem.Name") + "_1d_transport"; |
| 325 | |||
| 326 | // initial conditions | ||
| 327 |
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1 | initialNetworkConcentration_ = getParam<Scalar>("Network.Problem.InitialConcentration", 0.0); // mmol/l |
| 328 | |||
| 329 | // cross end-feet transport | ||
| 330 |
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1 | freeD_ = getParam<Scalar>("Tracer.DiffusionCoefficient"); |
| 331 | |||
| 332 | // clearance at sides by diffusion | ||
| 333 | // a boundaryMembraneCoefficient_ of zero means zero gradient / zero diffusive flux | ||
| 334 | // we can still have advective transport | ||
| 335 |
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1 | farFieldConcentration_ = getParam<Scalar>("Network.Problem.FarFieldConcentration", 0.0); // mmol/l |
| 336 |
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1 | boundaryMembraneCoefficient_ = getParam<Scalar>("Network.Problem.BoundaryMembraneCoefficient", 0.0); // dimensionless |
| 337 | |||
| 338 |
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3 | this->spatialParams().readGridParams(*gridData); |
| 339 | 1 | } | |
| 340 | |||
| 341 | // name (used for output) | ||
| 342 | const std::string& name() const | ||
| 343 |
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1 | { return name_; } |
| 344 | // [[/codeblock]] | ||
| 345 | // initial conditions (called when setting initial solution) | ||
| 346 | // convert concentration to mole fraction | ||
| 347 | // [[codeblock]] | ||
| 348 | ✗ | PrimaryVariables initialAtPos(const GlobalPosition& globalPos) const | |
| 349 | 3470 | { return { initialNetworkConcentration_/1000*0.018 }; } | |
| 350 | // [[/codeblock]] | ||
| 351 | // | ||
| 352 | // Set the boundary conditions. Note that we generalize the boundary conditions | ||
| 353 | // for diffusion to allow for a Robin-type boundary condition with a "far-field" | ||
| 354 | // concentration. This can be used to relax the constraint that there is absolutely | ||
| 355 | // no diffusive flux over the boundary (`coeff` $`= 0`$). | ||
| 356 | // | ||
| 357 | // [[codeblock]] | ||
| 358 | // type of boundary condition | ||
| 359 | ✗ | BoundaryTypes boundaryTypes(const Element& element, const SubControlVolumeFace& scvf) const | |
| 360 | { | ||
| 361 |
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25452 | BoundaryTypes bcTypes; |
| 362 |
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25452 | bcTypes.setAllNeumann(); // Robin / flux boundary conditions |
| 363 | ✗ | return bcTypes; | |
| 364 | } | ||
| 365 | |||
| 366 | // flux boundaries (called for Neumann boundaries) | ||
| 367 | template<class ElementVolumeVariables, class ElementFluxVarsCache> | ||
| 368 | 12726 | ResidualVector neumann(const Element& element, | |
| 369 | const FVElementGeometry& fvGeometry, | ||
| 370 | const ElementVolumeVariables& elemVolVars, | ||
| 371 | const ElementFluxVarsCache& fluxCache, | ||
| 372 | const SubControlVolumeFace& scvf) const | ||
| 373 | { | ||
| 374 | 12726 | ResidualVector values(0.0); | |
| 375 | |||
| 376 | // Robin type boundary condition with far field concentration c | ||
| 377 | // and conductance coefficient (dimensionless) | ||
| 378 | // -> 1.0 means the concentration c reached in 1 µm distance from the boundary | ||
| 379 | // -> if this coefficient is low this essentially means no-flow, if high this means direct outflow/inflow | ||
| 380 | ✗ | const auto robinFlux = [&](const auto& vv, const Scalar c, const Scalar coeff) | |
| 381 | { | ||
| 382 |
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12726 | return - (c/vv.molarDensity() - vv.moleFraction(0, compIdx)) |
| 383 | 12726 | *vv.molarDensity() | |
| 384 |
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12726 | *coeff * vv.effectiveDiffusionCoefficient(phaseIdx, phaseIdx, compIdx); |
| 385 | }; | ||
| 386 | |||
| 387 | 25452 | const auto& volVars = elemVolVars[scvf.insideScvIdx()]; | |
| 388 | |||
| 389 | // diffusive part | ||
| 390 |
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12726 | values[0] = robinFlux(volVars, farFieldConcentration_, boundaryMembraneCoefficient_); |
| 391 | |||
| 392 | // advection | ||
| 393 |
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25452 | const auto volumeFlux = this->spatialParams().volumeFlux(scvf.index()); |
| 394 |
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12726 | if (volumeFlux > 0) // outflow |
| 395 | 11716 | values[0] += volumeFlux*volVars.molarDensity()*volVars.moleFraction(0, compIdx)/(volVars.extrusionFactor()*scvf.area()); | |
| 396 | |||
| 397 | 12726 | return values; | |
| 398 | } | ||
| 399 | // [[/codeblock]] | ||
| 400 | // | ||
| 401 | // The point source implementation is symmetric to the implementation of the | ||
| 402 | // tissue domain. This is important such that the coupling condition is implemented | ||
| 403 | // in a mass-conservative way. | ||
| 404 | // | ||
| 405 | // [[codeblock]] | ||
| 406 | // this is needed for the 1d-3d coupling (realized via point source interface) | ||
| 407 | void addPointSources(std::vector<PointSource>& pointSources) const | ||
| 408 |
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1 | { pointSources = this->couplingManager().lowDimPointSources(); } |
| 409 | |||
| 410 | // called for every point source (coupling term integration point) | ||
| 411 | template<class ElementVolumeVariables> | ||
| 412 | 309825 | void pointSource(PointSource& source, | |
| 413 | const Element& element, | ||
| 414 | const FVElementGeometry& fvGeometry, | ||
| 415 | const ElementVolumeVariables& elemVolVars, | ||
| 416 | const SubControlVolume& scv) const | ||
| 417 | { | ||
| 418 | // compute source at every integration point | ||
| 419 | 929475 | const Scalar x1D = this->couplingManager().lowDimPriVars(source.id())[compIdx]; | |
| 420 | 929475 | const Scalar x3D = this->couplingManager().bulkPriVars(source.id())[compIdx]; | |
| 421 | |||
| 422 | // get the segment radius (outer PVS radius) | ||
| 423 | 929475 | const Scalar radius = this->couplingManager().radius(source.id()); | |
| 424 | |||
| 425 | // molar density (mol/m^3) (we assemble a mole balance equation instead of mass balance) | ||
| 426 | 309825 | const Scalar meanRhoMolar = 1000/0.018; | |
| 427 | |||
| 428 | // trans-membrane diffusive permeability | ||
| 429 | 619650 | const Scalar lc = freeD_ | |
| 430 | 619650 | * this->spatialParams().membraneFactor(scv.elementIndex()); // m/s | |
| 431 | |||
| 432 | // diffusive flux across membrane | ||
| 433 | 309825 | auto transMembraneFlux = 2*M_PI*radius*lc*meanRhoMolar*(x3D - x1D); | |
| 434 | 309825 | transMembraneFlux *= source.quadratureWeight()*source.integrationElement(); | |
| 435 | |||
| 436 | 619650 | source = transMembraneFlux; | |
| 437 | 309825 | } | |
| 438 | |||
| 439 | // additional volumetric source term in mol/(s*m^3), i.e. metabolic consumption | ||
| 440 | // positive value means production into blood, negative value means extraction from blood | ||
| 441 | template<class ElementVolumeVariables> | ||
| 442 | ✗ | ResidualVector source(const Element &element, | |
| 443 | const FVElementGeometry& fvGeometry, | ||
| 444 | const ElementVolumeVariables& elemVolVars, | ||
| 445 | const SubControlVolume &scv) const | ||
| 446 | { | ||
| 447 |
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369374 | return { 0.0 }; |
| 448 | } | ||
| 449 | // [[/codeblock]] | ||
| 450 | // [[details]] coupling manager function and internal variables (visibility: private) | ||
| 451 | // [[codeblock]] | ||
| 452 | // The coupling manager | ||
| 453 | const CouplingManager& couplingManager() const | ||
| 454 |
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1239302 | { return *couplingManager_; } |
| 455 | |||
| 456 | private: | ||
| 457 | std::string name_; | ||
| 458 | |||
| 459 | // parameters | ||
| 460 | Scalar freeD_; | ||
| 461 | |||
| 462 | Scalar initialNetworkConcentration_; // mmol/l | ||
| 463 | Scalar farFieldConcentration_; // mmol/l | ||
| 464 | Scalar boundaryMembraneCoefficient_; // dimensionless | ||
| 465 | |||
| 466 | std::shared_ptr<CouplingManager> couplingManager_; | ||
| 467 | }; | ||
| 468 | |||
| 469 | } //end namespace Dumux | ||
| 470 | // [[/codeblock]] | ||
| 471 | // [[/details]] | ||
| 472 | // [[/content]] | ||
| 473 | #endif | ||
| 474 |