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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 | // ## The main file | ||
| 8 | // This files contains the main program flow for the biomineralization example. Here we can see the programme sequence and how the system is solved using newton's method. | ||
| 9 | // | ||
| 10 | // [[content]] | ||
| 11 | // | ||
| 12 | // ### Included header files | ||
| 13 | // <details> | ||
| 14 | // [[exclude]] | ||
| 15 | // Some generic includes. | ||
| 16 | #include <config.h> | ||
| 17 | #include <iostream> | ||
| 18 | #include <dumux/io/container.hh> | ||
| 19 | // [[/exclude]] | ||
| 20 | |||
| 21 | // These are DUNE helper classes related to parallel computations | ||
| 22 | #include <dune/common/parallel/mpihelper.hh> | ||
| 23 | |||
| 24 | // The following headers include functionality related to property definition or retrieval, as well as | ||
| 25 | // the retrieval of input parameters specified in the input file or via the command line. | ||
| 26 | #include <dumux/common/properties.hh> | ||
| 27 | #include <dumux/common/parameters.hh> | ||
| 28 | #include <dumux/common/initialize.hh> | ||
| 29 | |||
| 30 | // The following files contain the nonlinear Newtown method, the linear solver and the assembler | ||
| 31 | #include <dumux/nonlinear/newtonsolver.hh> | ||
| 32 | #include <dumux/linear/istlsolvers.hh> | ||
| 33 | #include <dumux/linear/linearalgebratraits.hh> | ||
| 34 | #include <dumux/linear/linearsolvertraits.hh> | ||
| 35 | #include <dumux/assembly/fvassembler.hh> | ||
| 36 | #include <dumux/assembly/diffmethod.hh> | ||
| 37 | |||
| 38 | // The following class provides a convenient way of writing of dumux simulation results to VTK format. | ||
| 39 | #include <dumux/io/vtkoutputmodule.hh> | ||
| 40 | |||
| 41 | // The gridmanager constructs a grid from the information in the input or grid file. There is a specification for the different supported grid managers. | ||
| 42 | // Many different Dune grid implementations are supported, of which a list can be found | ||
| 43 | // in `gridmanager.hh`. | ||
| 44 | #include <dumux/io/grid/gridmanager_yasp.hh> | ||
| 45 | |||
| 46 | // We include the problem file which defines initial and boundary conditions to describe our example problem | ||
| 47 | //remove #include "problem.hh" | ||
| 48 | #include "properties.hh" | ||
| 49 | // </details> | ||
| 50 | // | ||
| 51 | |||
| 52 | // ### The main function | ||
| 53 | // We will now discuss the main program flow implemented within the `main` function. | ||
| 54 | // At the beginning of each program using Dune, an instance `Dune::MPIHelper` has to | ||
| 55 | // be created. Moreover, we parse the run-time arguments from the command line and the | ||
| 56 | // input file: | ||
| 57 | // [[codeblock]] | ||
| 58 | 1 | int main(int argc, char** argv) try | |
| 59 | { | ||
| 60 | 1 | using namespace Dumux; | |
| 61 | |||
| 62 | // maybe initialize MPI and/or multithreading backend | ||
| 63 |
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1 | Dumux::initialize(argc, argv); |
| 64 |
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1 | const auto& mpiHelper = Dune::MPIHelper::instance(); |
| 65 | |||
| 66 | // parse command line arguments and input file | ||
| 67 |
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4 | Parameters::init(argc, argv); |
| 68 | // [[/codeblock]] | ||
| 69 | |||
| 70 | // For convenience we define the type tag for this problem. | ||
| 71 | // The type tags contain all the properties that are needed to run the simulations. | ||
| 72 | 1 | using TypeTag = Properties::TTag::MICPColumnSimpleChemistry; | |
| 73 | |||
| 74 | // ### Step 1: Create the grid | ||
| 75 | // The `GridManager` class creates the grid from information given in the input file. | ||
| 76 | // This can either be a grid file, or in the case of structured grids, one can specify the coordinates | ||
| 77 | // of the corners of the grid and the number of cells to be used to discretize each spatial direction. The latter is the case for this example. | ||
| 78 | // [[codeblock]] | ||
| 79 |
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2 | GridManager<GetPropType<TypeTag, Properties::Grid>> gridManager; |
| 80 |
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2 | gridManager.init(); |
| 81 | |||
| 82 | // we compute on the leaf grid view | ||
| 83 |
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1 | const auto& leafGridView = gridManager.grid().leafGridView(); |
| 84 | // [[/codeblock]] | ||
| 85 | |||
| 86 | // ### Step 2: Setting up the problem | ||
| 87 | // We create and initialize the finite volume grid geometry, the problem, the linear system, including the jacobian matrix, the residual and the solution vector and the gridvariables. | ||
| 88 | // We need the finite volume geometry to build up the subcontrolvolumes (scv) and subcontrolvolume faces (scvf) for each element of the grid partition. | ||
| 89 | 1 | using GridGeometry = GetPropType<TypeTag, Properties::GridGeometry>; | |
| 90 |
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2 | auto gridGeometry = std::make_shared<GridGeometry>(leafGridView); |
| 91 | |||
| 92 | // We now instantiate the problem, in which we define the boundary and initial conditions. | ||
| 93 | 1 | using Problem = GetPropType<TypeTag, Properties::Problem>; | |
| 94 |
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2 | auto problem = std::make_shared<Problem>(gridGeometry); |
| 95 | |||
| 96 | // get some time loop parameters | ||
| 97 | 1 | using Scalar = GetPropType<TypeTag, Properties::Scalar>; | |
| 98 |
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1 | const auto tEnd = getParam<Scalar>("TimeLoop.TEnd"); |
| 99 |
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1 | const auto maxDt = getParam<Scalar>("TimeLoop.MaxTimeStepSize"); |
| 100 |
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1 | const auto dt = getParam<Scalar>("TimeLoop.DtInitial"); |
| 101 | |||
| 102 | // We initialize the solution vector | ||
| 103 | 1 | using SolutionVector = GetPropType<TypeTag, Properties::SolutionVector>; | |
| 104 |
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2 | SolutionVector x; |
| 105 |
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2 | problem->applyInitialSolution(x); |
| 106 |
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2 | auto xOld = x; |
| 107 | |||
| 108 | // on the basis of this solution, we initialize the grid variables | ||
| 109 | 1 | using GridVariables = GetPropType<TypeTag, Properties::GridVariables>; | |
| 110 |
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2 | auto gridVariables = std::make_shared<GridVariables>(problem, gridGeometry); |
| 111 |
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2 | gridVariables->init(x); |
| 112 | |||
| 113 | // We initialize the vtk output module. Each model has a predefined model specific output with relevant parameters for that model. | ||
| 114 | // [[codeblock]] | ||
| 115 |
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4 | VtkOutputModule<GridVariables, SolutionVector> vtkWriter(*gridVariables, x, problem->name()); |
| 116 | 1 | using VelocityOutput = GetPropType<TypeTag, Properties::VelocityOutput>; | |
| 117 |
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3 | vtkWriter.addVelocityOutput(std::make_shared<VelocityOutput>(*gridVariables)); |
| 118 |
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1 | GetPropType<TypeTag, Properties::IOFields>::initOutputModule(vtkWriter); //!< Add model specific output fields |
| 119 | // We add permeability as a specific output | ||
| 120 |
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2 | vtkWriter.addField(problem->getPermeability(), "Permeability"); |
| 121 | // We update the output fields before write | ||
| 122 |
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2 | problem->updateVtkOutput(x); |
| 123 |
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1 | vtkWriter.write(0.0); |
| 124 | // [[/codeblock]] | ||
| 125 | |||
| 126 | // We instantiate the time loop and define an episode index to keep track of the the actual episode number | ||
| 127 | // [[codeblock]] | ||
| 128 | 1 | int episodeIdx = 0; | |
| 129 | // We set the initial episodeIdx in the problem to zero | ||
| 130 |
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2 | problem->setEpisodeIdx(episodeIdx); |
| 131 | // We set the time loop with episodes (check points) | ||
| 132 |
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2 | auto timeLoop = std::make_shared<CheckPointTimeLoop<Scalar>>(0.0, dt, tEnd); |
| 133 |
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2 | timeLoop->setMaxTimeStepSize(maxDt); |
| 134 | // [[/codeblock]] | ||
| 135 | |||
| 136 | // ### Step 3 Setting episodes specified from file | ||
| 137 | // In this example we want to specify the injected reactant solutions at certain times. | ||
| 138 | // This is specified in an external file `injections_checkpoints.dat`. | ||
| 139 | // Within the following code block, the parameter file read and the time for the injection are extracted. | ||
| 140 | // Based on that, the checkpoints for the simulation are set. | ||
| 141 | |||
| 142 | // [[codeblock]] | ||
| 143 | // We use a time loop with episodes if an injection parameter file is specified in the input | ||
| 144 |
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5 | if (hasParam("Injection.NumInjections")) |
| 145 | { | ||
| 146 | // We first read the times of the checkpoints from the injection file | ||
| 147 |
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4 | const auto injectionCheckPoints = readFileToContainer<std::vector<double>>("injection_checkpoints.dat"); |
| 148 | |||
| 149 | // We set the time loop with episodes of various lengths as specified in the injection file | ||
| 150 | // set the episode ends /check points: | ||
| 151 |
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4 | timeLoop->setCheckPoint(injectionCheckPoints.begin(), injectionCheckPoints.end()); |
| 152 | |||
| 153 | // We also set the initial episodeIdx in the problem to zero, as in the problem the boundary conditions depend on the episode. | ||
| 154 |
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3 | problem->setEpisodeIdx(episodeIdx); |
| 155 | } | ||
| 156 | |||
| 157 | // If nothing specified, we do not need to use episodes | ||
| 158 | else | ||
| 159 | { | ||
| 160 | // In this case, we set the time loop with one big episodes | ||
| 161 | ✗ | timeLoop->setCheckPoint(tEnd); | |
| 162 | } | ||
| 163 | // [[/codeblock]] | ||
| 164 | |||
| 165 | // ### Step 4 Solving the instationary problem | ||
| 166 | |||
| 167 | // We create and initialize the assembler with a time loop for the transient problem. | ||
| 168 | // Within the time loop, we will use this assembler in each time step to assemble the linear system. | ||
| 169 | // Additionally the linear and non-linear solvers are set | ||
| 170 | // [[codeblock]] | ||
| 171 | 1 | using Assembler = FVAssembler<TypeTag, DiffMethod::numeric>; | |
| 172 |
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2 | auto assembler = std::make_shared<Assembler>(problem, gridGeometry, gridVariables, timeLoop, xOld); |
| 173 | |||
| 174 | // We set the linear solver | ||
| 175 | 1 | using LinearSolver = ILUBiCGSTABIstlSolver< | |
| 176 | LinearSolverTraits<GridGeometry>, LinearAlgebraTraitsFromAssembler<Assembler> | ||
| 177 | >; | ||
| 178 |
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2 | auto linearSolver = std::make_shared<LinearSolver>(); |
| 179 | |||
| 180 | // We set the non-linear solver | ||
| 181 | 1 | using NewtonSolver = NewtonSolver<Assembler, LinearSolver>; | |
| 182 |
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5 | NewtonSolver nonLinearSolver(assembler, linearSolver); |
| 183 | // [[/codeblock]] | ||
| 184 | |||
| 185 | // #### The time loop | ||
| 186 | // We start the time loop and solve a new time step as long as `tEnd` is not reached. In every time step, | ||
| 187 | // the problem is assembled and solved, the solution is updated, and when a checkpoint is reached the solution | ||
| 188 | // is written to a new vtk file. In addition, statistics related to CPU time, the current simulation time | ||
| 189 | // and the time step sizes used is printed to the terminal. | ||
| 190 | |||
| 191 | // [[codeblock]] | ||
| 192 |
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2 | timeLoop->start(); do |
| 193 | { | ||
| 194 | // We set the time and time step size to be used in the problem | ||
| 195 |
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1650 | problem->setTime( timeLoop->time() + timeLoop->timeStepSize() ); |
| 196 |
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1100 | problem->setTimeStepSize( timeLoop->timeStepSize() ); |
| 197 | |||
| 198 | // Solve the linear system with time step control | ||
| 199 |
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550 | nonLinearSolver.solve(x, *timeLoop); |
| 200 | |||
| 201 | // Update the old solution with the one computed in this time step and move to the next one | ||
| 202 |
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275 | xOld = x; |
| 203 |
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550 | gridVariables->advanceTimeStep(); |
| 204 |
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550 | timeLoop->advanceTimeStep(); |
| 205 | |||
| 206 | // We update the output fields before write | ||
| 207 |
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550 | problem->updateVtkOutput(x); |
| 208 | |||
| 209 | // We write vtk output on checkpoints or every 20th timestep | ||
| 210 |
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550 | if (timeLoop->timeStepIndex() % 20 == 0 || timeLoop->isCheckPoint()) |
| 211 | { | ||
| 212 | // update the output fields before write | ||
| 213 |
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36 | problem->updateVtkOutput(x); |
| 214 | |||
| 215 | // write vtk output | ||
| 216 |
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54 | vtkWriter.write(timeLoop->time()); |
| 217 | } | ||
| 218 | // We report statistics of this time step | ||
| 219 |
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550 | timeLoop->reportTimeStep(); |
| 220 | |||
| 221 | // If episodes/check points are used, we count episodes and update the episode indices in the main file and the problem. | ||
| 222 |
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1100 | if (hasParam("Injection.NumInjections") || hasParam("TimeLoop.EpisodeLength")) |
| 223 | { | ||
| 224 |
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550 | if (timeLoop->isCheckPoint()) |
| 225 | { | ||
| 226 | 6 | episodeIdx++; | |
| 227 | 12 | problem->setEpisodeIdx(episodeIdx); | |
| 228 | } | ||
| 229 | } | ||
| 230 | |||
| 231 | // set the new time step size that is suggested by the newton solver | ||
| 232 |
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1375 | timeLoop->setTimeStepSize(nonLinearSolver.suggestTimeStepSize(timeLoop->timeStepSize())); |
| 233 | |||
| 234 |
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550 | } while (!timeLoop->finished()); |
| 235 |
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2 | timeLoop->finalize(leafGridView.comm()); |
| 236 | // [[/codeblock]] | ||
| 237 | |||
| 238 |
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2 | if (mpiHelper.rank() == 0) |
| 239 |
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1 | Parameters::print(); |
| 240 | |||
| 241 | 1 | return 0; | |
| 242 | } | ||
| 243 | |||
| 244 | // ### Exception handling | ||
| 245 | // In this part of the main file we catch and print possible exceptions that could | ||
| 246 | // occur during the simulation. | ||
| 247 | // [[details]] error handler | ||
| 248 | // [[codeblock]] | ||
| 249 | // errors related to run-time parameters | ||
| 250 | ✗ | catch (const Dumux::ParameterException &e) | |
| 251 | { | ||
| 252 | ✗ | std::cerr << std::endl << e << " ---> Abort!" << std::endl; | |
| 253 | ✗ | return 1; | |
| 254 | } | ||
| 255 | ✗ | catch (const Dune::DGFException & e) | |
| 256 | { | ||
| 257 | ✗ | std::cerr << "DGF exception thrown (" << e << | |
| 258 | "). Most likely, the DGF file name is wrong " | ||
| 259 | "or the DGF file is corrupted, " | ||
| 260 | "e.g. missing hash at end of file or wrong number (dimensions) of entries." | ||
| 261 | ✗ | << " ---> Abort!" << std::endl; | |
| 262 | ✗ | return 2; | |
| 263 | } | ||
| 264 | ✗ | catch (const Dune::Exception &e) | |
| 265 | { | ||
| 266 | ✗ | std::cerr << "Dune reported error: " << e << " ---> Abort!" << std::endl; | |
| 267 | ✗ | return 3; | |
| 268 | } | ||
| 269 | // [[/codeblock]] | ||
| 270 | // [[/details]] | ||
| 271 | // [[/content]] | ||
| 272 |