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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 | * \file | ||
| 9 | * \ingroup PoreNetworkModels | ||
| 10 | * \brief Provides a grid manager for pore-network models | ||
| 11 | */ | ||
| 12 | #ifndef DUMUX_PORE_NETWORK_GRID_MANAGER_HH | ||
| 13 | #define DUMUX_PORE_NETWORK_GRID_MANAGER_HH | ||
| 14 | |||
| 15 | #if HAVE_DUNE_FOAMGRID | ||
| 16 | |||
| 17 | #include <iostream> | ||
| 18 | #include <algorithm> | ||
| 19 | #include <vector> | ||
| 20 | |||
| 21 | #include <dune/common/classname.hh> | ||
| 22 | #include <dune/common/exceptions.hh> | ||
| 23 | #include <dune/common/timer.hh> | ||
| 24 | |||
| 25 | // FoamGrid specific includes | ||
| 26 | #include <dune/foamgrid/foamgrid.hh> | ||
| 27 | #include <dune/foamgrid/dgffoam.hh> | ||
| 28 | |||
| 29 | #include <dumux/common/parameters.hh> | ||
| 30 | #include <dumux/common/exceptions.hh> | ||
| 31 | |||
| 32 | #include "griddata.hh" | ||
| 33 | #include "structuredlatticegridcreator.hh" | ||
| 34 | |||
| 35 | namespace Dumux::PoreNetwork { | ||
| 36 | |||
| 37 | /*! | ||
| 38 | * \ingroup PoreNetworkModels | ||
| 39 | * \brief A grid manager for pore-network models | ||
| 40 | */ | ||
| 41 | template<int dimWorld, class GData = Dumux::PoreNetwork::GridData<Dune::FoamGrid<1, dimWorld>>> | ||
| 42 | class GridManager | ||
| 43 | { | ||
| 44 | using GridType = Dune::FoamGrid<1, dimWorld>; | ||
| 45 | using Element = typename GridType::template Codim<0>::Entity; | ||
| 46 | using GlobalPosition = typename Element::Geometry::GlobalCoordinate; | ||
| 47 | |||
| 48 | public: | ||
| 49 | using Grid = GridType; | ||
| 50 | using GridData = GData; | ||
| 51 | |||
| 52 | 57 | void init(const std::string& paramGroup = "") | |
| 53 | { | ||
| 54 | 57 | Dune::Timer timer; | |
| 55 | 57 | paramGroup_ = paramGroup; | |
| 56 | |||
| 57 | // First try to create it from a DGF file in GridParameterGroup.File | ||
| 58 |
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171 | if (hasParamInGroup(paramGroup, "Grid.File")) |
| 59 | { | ||
| 60 |
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24 | makeGridFromDgfFile(getParamFromGroup<std::string>(paramGroup, "Grid.File")); |
| 61 | 24 | loadBalance(); | |
| 62 | } | ||
| 63 | else // no grid file found | ||
| 64 | { | ||
| 65 | // create a structured grid (1D grid or lattice grid) | ||
| 66 |
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99 | const auto numPores = getParamFromGroup<std::vector<unsigned int>>(paramGroup_, "Grid.NumPores"); |
| 67 |
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66 | if (numPores.size() == 1) |
| 68 |
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5 | createOneDGrid_(numPores[0]); |
| 69 |
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28 | else if (numPores.size() == dimWorld) |
| 70 |
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28 | makeGridFromStructuredLattice(); |
| 71 | else | ||
| 72 | ✗ | DUNE_THROW(ParameterException, | |
| 73 | "Grid.NumPores parameter has wrong size " << numPores.size() | ||
| 74 | << ". Should be 1 (for 1D grid) or " | ||
| 75 | << dimWorld << " (for structured lattice grid)." | ||
| 76 | ); | ||
| 77 | |||
| 78 |
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33 | loadBalance(); |
| 79 | } | ||
| 80 | |||
| 81 | 57 | timer.stop(); | |
| 82 |
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57 | const auto gridType = enableDgfGridPointer_ ? "grid from dgf file" : "generic grid from structured lattice"; |
| 83 | 171 | std::cout << "Creating " << gridType << " with " << grid().leafGridView().size(0) << " elements and " | |
| 84 | 171 | << grid().leafGridView().size(1) << " vertices took " << timer.elapsed() << " seconds." << std::endl; | |
| 85 | 57 | } | |
| 86 | |||
| 87 | /*! | ||
| 88 | * \brief Make a grid from a DGF file. | ||
| 89 | */ | ||
| 90 | 24 | void makeGridFromDgfFile(const std::string& fileName) | |
| 91 | { | ||
| 92 | // We found a file in the input file...does it have a supported extension? | ||
| 93 |
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48 | const std::string extension = getFileExtension(fileName); |
| 94 |
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24 | if (extension != "dgf") |
| 95 | ✗ | DUNE_THROW(Dune::IOError, "Grid type " << Dune::className<Grid>() << " only supports DGF (*.dgf) but the specified filename has extension: *."<< extension); | |
| 96 | |||
| 97 | 24 | enableDgfGridPointer_ = true; | |
| 98 |
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120 | dgfGridPtr() = Dune::GridPtr<Grid>(fileName.c_str(), Dune::MPIHelper::getCommunicator()); |
| 99 |
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24 | gridData_ = std::make_shared<GridData>(dgfGridPtr_, paramGroup_); |
| 100 | |||
| 101 |
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24 | if (getParamFromGroup<bool>(paramGroup_, "Grid.Sanitize", false)) |
| 102 |
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8 | sanitizeGrid(); |
| 103 | 24 | } | |
| 104 | |||
| 105 | /*! | ||
| 106 | * \brief Make a grid based on a structured lattice which allows to randomly delete elements based on Raoof et al. 2009 | ||
| 107 | */ | ||
| 108 | 28 | void makeGridFromStructuredLattice() | |
| 109 | { | ||
| 110 | 56 | StructuredLatticeGridCreator<dimWorld> creator; | |
| 111 |
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28 | creator.init(paramGroup_); |
| 112 |
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28 | gridPtr() = creator.gridPtr(); |
| 113 | |||
| 114 |
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28 | gridData_ = std::make_shared<GridData>(gridPtr_, paramGroup_); |
| 115 | |||
| 116 |
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28 | if (getParamFromGroup<bool>(paramGroup_, "Grid.Sanitize", true)) |
| 117 |
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20 | sanitizeGrid(); |
| 118 | else | ||
| 119 |
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16 | std::cout << "\nWARNING: Set Grid.Sanitize = true in order to remove insular patches of elements not connected to the boundary." << std::endl; |
| 120 | |||
| 121 |
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56 | gridData_->assignParameters(); |
| 122 | 28 | } | |
| 123 | |||
| 124 | /*! | ||
| 125 | * \brief Returns the filename extension of a given filename | ||
| 126 | */ | ||
| 127 | 24 | std::string getFileExtension(const std::string& fileName) const | |
| 128 | { | ||
| 129 |
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24 | std::size_t i = fileName.rfind('.', fileName.length()); |
| 130 |
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24 | if (i != std::string::npos) |
| 131 | 24 | return(fileName.substr(i+1, fileName.length() - i)); | |
| 132 | else | ||
| 133 | ✗ | DUNE_THROW(Dune::IOError, "Please provide and extension for your grid file ('"<< fileName << "')!"); | |
| 134 | return ""; | ||
| 135 | } | ||
| 136 | |||
| 137 | /*! | ||
| 138 | * \brief Returns a reference to the grid. | ||
| 139 | */ | ||
| 140 | 488 | Grid& grid() | |
| 141 |
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488 | { return enableDgfGridPointer_ ? *dgfGridPtr() : *gridPtr(); } |
| 142 | |||
| 143 | /*! | ||
| 144 | * \brief Returns the grid data. | ||
| 145 | */ | ||
| 146 | 59 | std::shared_ptr<GridData> getGridData() const | |
| 147 | { | ||
| 148 |
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59 | if (!gridData_) |
| 149 | ✗ | DUNE_THROW(Dune::IOError, "No grid data available"); | |
| 150 | |||
| 151 | 59 | return gridData_; | |
| 152 | } | ||
| 153 | |||
| 154 | /*! | ||
| 155 | * \brief Call loadBalance() function of the grid. | ||
| 156 | */ | ||
| 157 | 57 | void loadBalance() | |
| 158 | { | ||
| 159 |
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57 | if (Dune::MPIHelper::getCommunication().size() > 1) |
| 160 | { | ||
| 161 | // if we may have dgf parameters use load balancing of the dgf pointer | ||
| 162 | ✗ | if (enableDgfGridPointer_) | |
| 163 | { | ||
| 164 | ✗ | dgfGridPtr().loadBalance(); | |
| 165 | // update the grid data | ||
| 166 | ✗ | gridData_ = std::make_shared<GridData>(dgfGridPtr(), paramGroup_); | |
| 167 | } | ||
| 168 | else | ||
| 169 | ✗ | gridPtr()->loadBalance(); | |
| 170 | } | ||
| 171 | 57 | } | |
| 172 | |||
| 173 | /*! | ||
| 174 | * \brief post-processing to remove insular groups of elements that are not connected to a Dirichlet boundary | ||
| 175 | */ | ||
| 176 | 40 | void sanitizeGrid() | |
| 177 | { | ||
| 178 | // evaluate the coordination numbers to check if all pores are connected to at least one throat | ||
| 179 |
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80 | gridData_->getCoordinationNumbers(); |
| 180 | |||
| 181 | // for dgf grid, copy the data to persistent containers | ||
| 182 |
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40 | if (enableDgfGridPointer_) |
| 183 | 16 | gridData_->copyDgfData(); | |
| 184 | |||
| 185 |
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40 | const auto gridView = grid().leafGridView(); |
| 186 |
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40 | static const std::string sanitationMode = getParamFromGroup<std::string>(paramGroup_, "Grid.SanitationMode", "KeepLargestCluster"); |
| 187 | |||
| 188 | // find the elements to keep, all others will be deleted | ||
| 189 | 96 | const auto keepElement = [&] | |
| 190 | { | ||
| 191 |
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24 | if (sanitationMode == "UsePoreLabels") |
| 192 | 24 | return findElementsConnectedToPoreLabel(gridView); | |
| 193 |
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24 | else if (sanitationMode == "KeepLargestCluster") |
| 194 | 24 | return findElementsInLargestCluster(gridView); | |
| 195 | else | ||
| 196 | ✗ | DUNE_THROW(Dune::IOError, sanitationMode << "is not a valid sanitation mode. Use KeepLargestCluster or UsePoreLabels."); | |
| 197 | |||
| 198 | |||
| 199 | 24 | }(); | |
| 200 | |||
| 201 | 120 | if (std::none_of(keepElement.begin(), keepElement.end(), [](const bool i){return i;})) | |
| 202 | ✗ | DUNE_THROW(Dune::InvalidStateException, "sanitize() deleted all elements! Check your boundary face indices. " | |
| 203 | << "If the problem persists, add at least one of your boundary face indices to PruningSeedIndices"); | ||
| 204 | |||
| 205 | // remove the elements in the grid | ||
| 206 | 40 | std::size_t numDeletedElements = 0; | |
| 207 |
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40 | grid().preGrow(); |
| 208 |
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44855 | for (const auto& element : elements(gridView)) |
| 209 | { | ||
| 210 |
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44815 | const auto eIdx = gridView.indexSet().index(element); |
| 211 |
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89630 | if (!keepElement[eIdx]) |
| 212 | { | ||
| 213 |
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151 | grid().removeElement(element); |
| 214 | 151 | ++numDeletedElements; | |
| 215 | } | ||
| 216 | } | ||
| 217 | // triggers the grid growth process | ||
| 218 |
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40 | grid().grow(); |
| 219 |
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40 | grid().postGrow(); |
| 220 | |||
| 221 | // resize the parameters for dgf grids | ||
| 222 |
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40 | if (enableDgfGridPointer_) |
| 223 |
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16 | gridData_->resizeParameterContainers(); |
| 224 | |||
| 225 |
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40 | if (numDeletedElements > 0) |
| 226 |
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33 | std::cout << "\nDeleted " << numDeletedElements << " isolated elements.\n" << std::endl; |
| 227 | 40 | } | |
| 228 | |||
| 229 | /*! | ||
| 230 | * \brief Returns a vector of bool which entries are true for elements connected to pores at the boundary | ||
| 231 | * with a given pore label. | ||
| 232 | */ | ||
| 233 | ✗ | std::vector<bool> findElementsConnectedToPoreLabel(const typename Grid::LeafGridView& gridView) const | |
| 234 | { | ||
| 235 | // pruning -- remove elements not connected to a Dirichlet boundary (marker == 1) | ||
| 236 | ✗ | const auto pruningSeedIndices = getParamFromGroup<std::vector<int>>(paramGroup_, "Grid.PruningSeedIndices", std::vector<int>{1}); | |
| 237 | ✗ | std::vector<bool> elementIsConnected(gridView.size(0), false); | |
| 238 | |||
| 239 | ✗ | auto boundaryIdx = [&](const auto& vertex) | |
| 240 | { | ||
| 241 | ✗ | if (enableDgfGridPointer_) | |
| 242 | ✗ | return static_cast<int>(dgfGridPtr_.parameters(vertex)[gridData_->parameterIndex("PoreLabel")]); | |
| 243 | else | ||
| 244 | ✗ | return static_cast<int>(gridData_->poreLabelAtPosForGenericGrid(vertex.geometry().center())); | |
| 245 | }; | ||
| 246 | |||
| 247 | ✗ | for (const auto& element : elements(gridView)) | |
| 248 | { | ||
| 249 | ✗ | const auto eIdx = gridView.indexSet().index(element); | |
| 250 | ✗ | if (elementIsConnected[eIdx]) | |
| 251 | continue; | ||
| 252 | |||
| 253 | // try to find a seed from which to start the search process | ||
| 254 | ✗ | bool isSeed = false; | |
| 255 | ✗ | bool hasNeighbor = false; | |
| 256 | ✗ | for (const auto& intersection : intersections(gridView, element)) | |
| 257 | { | ||
| 258 | ✗ | auto vertex = element.template subEntity<1>(intersection.indexInInside()); | |
| 259 | // seed found | ||
| 260 | ✗ | if (std::any_of(pruningSeedIndices.begin(), pruningSeedIndices.end(), | |
| 261 | ✗ | [&]( const int i ){ return i == boundaryIdx(vertex); })) | |
| 262 | { | ||
| 263 | ✗ | isSeed = true; | |
| 264 | // break; | ||
| 265 | } | ||
| 266 | |||
| 267 | ✗ | if (intersection.neighbor()) | |
| 268 | ✗ | hasNeighbor = true; | |
| 269 | } | ||
| 270 | |||
| 271 | ✗ | if (!hasNeighbor) | |
| 272 | continue; | ||
| 273 | |||
| 274 | ✗ | if (isSeed) | |
| 275 | { | ||
| 276 | ✗ | elementIsConnected[eIdx] = true; | |
| 277 | |||
| 278 | // use iteration instead of recursion here because the recursion can get too deep | ||
| 279 | ✗ | recursivelyFindConnectedElements_(gridView, element, elementIsConnected); | |
| 280 | } | ||
| 281 | } | ||
| 282 | |||
| 283 | ✗ | return elementIsConnected; | |
| 284 | } | ||
| 285 | |||
| 286 | /*! | ||
| 287 | * \brief Returns a vector of bool which entries are true for elements located in the largest | ||
| 288 | * connected cluster of the network. | ||
| 289 | */ | ||
| 290 | 40 | std::vector<bool> findElementsInLargestCluster(const typename Grid::LeafGridView& gridView) const | |
| 291 | { | ||
| 292 | 40 | const auto clusteredElements = clusterElements(gridView); | |
| 293 | |||
| 294 |
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120 | const auto numClusters = *std::max_element(clusteredElements.begin(), clusteredElements.end()) + 1; |
| 295 |
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120 | std::cout << "\nFound " << numClusters << " unconnected clusters." << std::endl; |
| 296 | |||
| 297 | // count number of elements in individual clusters | ||
| 298 |
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160 | std::vector<std::size_t> clusterFrequency(numClusters); |
| 299 |
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89750 | for (const auto clusterIdx : clusteredElements) |
| 300 | 89630 | clusterFrequency[clusterIdx] += 1; | |
| 301 | |||
| 302 |
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120 | const auto largestCluster = std::max_element(clusterFrequency.begin(), clusterFrequency.end()); |
| 303 | 80 | const auto largestClusterIdx = std::distance(clusterFrequency.begin(), largestCluster); | |
| 304 | |||
| 305 |
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80 | std::vector<bool> elementsInLargestCluster(gridView.size(0)); |
| 306 | |||
| 307 |
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44855 | for (int eIdx = 0; eIdx < clusteredElements.size(); ++eIdx) |
| 308 |
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89630 | if (clusteredElements[eIdx] == largestClusterIdx) |
| 309 | 133992 | elementsInLargestCluster[eIdx] = true; | |
| 310 | |||
| 311 | 40 | return elementsInLargestCluster; | |
| 312 | } | ||
| 313 | |||
| 314 | /*! | ||
| 315 | * \brief Assigns a cluster index for each element. | ||
| 316 | */ | ||
| 317 | 40 | std::vector<std::size_t> clusterElements(const typename Grid::LeafGridView& gridView) const | |
| 318 | { | ||
| 319 | 80 | std::vector<std::size_t> elementInCluster(gridView.size(0), 0); // initially, all elements are in pseudo cluster 0 | |
| 320 | 40 | std::size_t clusterIdx = 0; | |
| 321 | |||
| 322 |
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44855 | for (const auto& element : elements(gridView)) |
| 323 | { | ||
| 324 |
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44815 | const auto eIdx = gridView.indexSet().index(element); |
| 325 |
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89630 | if (elementInCluster[eIdx]) // element already is in a cluster |
| 326 | continue; | ||
| 327 | |||
| 328 | 125 | ++clusterIdx; | |
| 329 | 125 | elementInCluster[eIdx] = clusterIdx; | |
| 330 | |||
| 331 |
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125 | recursivelyFindConnectedElements_(gridView, element, elementInCluster, clusterIdx); |
| 332 | } | ||
| 333 | |||
| 334 | // make sure the clusters start with index zero | ||
| 335 |
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89750 | for (auto& clusterIdx : elementInCluster) |
| 336 | 44815 | clusterIdx -= 1; | |
| 337 | |||
| 338 | 40 | return elementInCluster; | |
| 339 | } | ||
| 340 | |||
| 341 | protected: | ||
| 342 | |||
| 343 | /*! | ||
| 344 | * \brief Returns a reference to the grid pointer (std::shared_ptr<Grid>) | ||
| 345 | */ | ||
| 346 | 394 | std::shared_ptr<Grid>& gridPtr() | |
| 347 | { | ||
| 348 |
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394 | if(!enableDgfGridPointer_) |
| 349 | 394 | return gridPtr_; | |
| 350 | else | ||
| 351 | ✗ | DUNE_THROW(Dune::InvalidStateException, "You are using DGF. To get the grid pointer use method dgfGridPtr()!"); | |
| 352 | } | ||
| 353 | |||
| 354 | /*! | ||
| 355 | * \brief Returns a reference to the DGF grid pointer (Dune::GridPtr<Grid>). | ||
| 356 | */ | ||
| 357 | 151 | Dune::GridPtr<Grid>& dgfGridPtr() | |
| 358 | { | ||
| 359 |
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151 | if(enableDgfGridPointer_) |
| 360 | 151 | return dgfGridPtr_; | |
| 361 | else | ||
| 362 | ✗ | DUNE_THROW(Dune::InvalidStateException, "The DGF grid pointer is only available if the grid was constructed with a DGF file!"); | |
| 363 | } | ||
| 364 | |||
| 365 | /*! | ||
| 366 | * \brief A state variable if the DGF Dune::GridPtr has been enabled. | ||
| 367 | * It is always enabled if a DGF grid file was used to create the grid. | ||
| 368 | */ | ||
| 369 | bool enableDgfGridPointer_ = false; | ||
| 370 | |||
| 371 | std::shared_ptr<Grid> gridPtr_; | ||
| 372 | Dune::GridPtr<Grid> dgfGridPtr_; | ||
| 373 | |||
| 374 | std::shared_ptr<GridData> gridData_; | ||
| 375 | |||
| 376 | std::string paramGroup_; | ||
| 377 | |||
| 378 | private: | ||
| 379 | |||
| 380 | 5 | void createOneDGrid_(unsigned int numPores) | |
| 381 | { | ||
| 382 | 10 | const auto lowerLeft = getParamFromGroup<GlobalPosition>(paramGroup_, "Grid.LowerLeft", GlobalPosition(0.0)); | |
| 383 | 5 | const auto upperRight = getParamFromGroup<GlobalPosition>(paramGroup_, "Grid.UpperRight"); | |
| 384 | 5 | const auto cells = numPores - 1; | |
| 385 | |||
| 386 | // create a step vector | ||
| 387 | 5 | GlobalPosition step = upperRight; | |
| 388 | 10 | step -= lowerLeft, step /= cells; | |
| 389 | |||
| 390 | // make the grid (structured interval grid in dimworld space) | ||
| 391 | 10 | Dune::GridFactory<Grid> factory; | |
| 392 | |||
| 393 | // create the vertices | ||
| 394 | 5 | GlobalPosition globalPos = lowerLeft; | |
| 395 |
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89 | for (unsigned int vIdx = 0; vIdx <= cells; vIdx++, globalPos += step) |
| 396 |
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82 | factory.insertVertex(globalPos); |
| 397 | |||
| 398 | // create the cells | ||
| 399 |
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82 | for(unsigned int eIdx = 0; eIdx < cells; eIdx++) |
| 400 |
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308 | factory.insertElement(Dune::GeometryTypes::line, {eIdx, eIdx+1}); |
| 401 | |||
| 402 |
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5 | gridPtr() = std::shared_ptr<Grid>(factory.createGrid()); |
| 403 |
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5 | gridData_ = std::make_shared<GridData>(gridPtr_, paramGroup_); |
| 404 |
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10 | gridData_->assignParameters(); |
| 405 | 5 | } | |
| 406 | |||
| 407 | template<class T> | ||
| 408 | 178 | void recursivelyFindConnectedElements_(const typename Grid::LeafGridView& gridView, | |
| 409 | const Element& element, | ||
| 410 | std::vector<T>& elementIsConnected, | ||
| 411 | T marker = 1) const | ||
| 412 | { | ||
| 413 | // use iteration instead of recursion here because the recursion can get too deep | ||
| 414 | 356 | std::stack<Element> elementStack; | |
| 415 |
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178 | elementStack.push(element); |
| 416 |
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176968 | while (!elementStack.empty()) |
| 417 | { | ||
| 418 |
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89736 | auto e = elementStack.top(); |
| 419 | 88306 | elementStack.pop(); | |
| 420 |
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4933894 | for (const auto& intersection : intersections(gridView, e)) |
| 421 | { | ||
| 422 |
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2997780 | if (!intersection.boundary()) |
| 423 | { | ||
| 424 |
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1494584 | auto outside = intersection.outside(); |
| 425 |
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1494584 | auto nIdx = gridView.indexSet().index(outside); |
| 426 |
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2989168 | if (!elementIsConnected[nIdx]) |
| 427 | { | ||
| 428 |
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88128 | elementIsConnected[nIdx] = marker; |
| 429 |
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88128 | elementStack.push(outside); |
| 430 | } | ||
| 431 | } | ||
| 432 | } | ||
| 433 | } | ||
| 434 | 178 | } | |
| 435 | }; | ||
| 436 | |||
| 437 | } | ||
| 438 | |||
| 439 | #endif // HAVE_DUNE_FOAMGRID | ||
| 440 | |||
| 441 | #endif | ||
| 442 |