io/grid/porenetwork/gridmanager.hh

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// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
// vi: set et ts=4 sw=4 sts=4:
//
// SPDX-FileCopyrightInfo: Copyright © DuMux Project contributors, see AUTHORS.md in root folder
// SPDX-License-Identifier: GPL-3.0-or-later
//
#ifndef DUMUX_PORE_NETWORK_GRID_MANAGER_HH
#define DUMUX_PORE_NETWORK_GRID_MANAGER_HH
 
#if HAVE_DUNE_FOAMGRID
 
#include <iostream>
#include <algorithm>
#include <vector>
 
#include <dune/common/classname.hh>
#include <dune/common/exceptions.hh>
#include <dune/common/timer.hh>
 
// FoamGrid specific includes
#include <dune/foamgrid/foamgrid.hh>
#include <dune/foamgrid/dgffoam.hh>
 
#include <dumux/common/parameters.hh>
#include <dumux/common/exceptions.hh>
 
#include "griddata.hh"
#include "structuredlatticegridcreator.hh"
 
namespace Dumux::PoreNetwork {
 
template<int dimWorld, class GData = Dumux::PoreNetwork::GridData<Dune::FoamGrid<1, dimWorld>>>
class GridManager
{
    using GridType = Dune::FoamGrid<1, dimWorld>;
    using Element = typename GridType::template Codim<0>::Entity;
    using GlobalPosition = typename Element::Geometry::GlobalCoordinate;
 
public:
    using Grid = GridType;
    using GridData = GData;
 
    void init(const std::string& paramGroup = "")
    {
        Dune::Timer timer;
        paramGroup_ = paramGroup;
 
        // First try to create it from a DGF file in GridParameterGroup.File
        if (hasParamInGroup(paramGroup, "Grid.File"))
        {
            makeGridFromDgfFile(getParamFromGroup<std::string>(paramGroup, "Grid.File"));
            loadBalance();
        }
        else // no grid file found
        {
            // create a structured grid (1D grid or lattice grid)
            const auto numPores = getParamFromGroup<std::vector<unsigned int>>(paramGroup_, "Grid.NumPores");
            if (numPores.size() == 1)
                createOneDGrid_(numPores[0]);
            else if (numPores.size() == dimWorld)
                makeGridFromStructuredLattice();
            else
                DUNE_THROW(ParameterException,
                    "Grid.NumPores parameter has wrong size " << numPores.size()
                    << ". Should be 1 (for 1D grid) or "
                    << dimWorld << " (for structured lattice grid)."
                );
 
            loadBalance();
        }
 
        timer.stop();
        const auto gridType = enableDgfGridPointer_ ?  "grid from dgf file" : "generic grid from structured lattice";
        std::cout << "Creating "  << gridType << " with " << grid().leafGridView().size(0) << " elements and "
                  << grid().leafGridView().size(1) << " vertices took " << timer.elapsed() << " seconds." << std::endl;
    }
 
    void makeGridFromDgfFile(const std::string& fileName)
    {
        // We found a file in the input file...does it have a supported extension?
        const std::string extension = getFileExtension(fileName);
        if (extension != "dgf")
            DUNE_THROW(Dune::IOError, "Grid type " << Dune::className<Grid>() << " only supports DGF (*.dgf) but the specified filename has extension: *."<< extension);
 
        enableDgfGridPointer_ = true;
        dgfGridPtr() = Dune::GridPtr<Grid>(fileName.c_str(), Dune::MPIHelper::getCommunicator());
        gridData_ = std::make_shared<GridData>(dgfGridPtr_, paramGroup_);
 
        if (getParamFromGroup<bool>(paramGroup_, "Grid.Sanitize", false))
            sanitizeGrid();
    }
 
    void makeGridFromStructuredLattice()
    {
        StructuredLatticeGridCreator<dimWorld> creator;
        creator.init(paramGroup_);
        gridPtr() = creator.gridPtr();
 
        gridData_ = std::make_shared<GridData>(gridPtr_, paramGroup_);
 
        if (getParamFromGroup<bool>(paramGroup_, "Grid.Sanitize", true))
            sanitizeGrid();
        else
            std::cout << "\nWARNING: Set Grid.Sanitize = true in order to remove insular patches of elements not connected to the boundary." << std::endl;
 
        gridData_->assignParameters();
    }
 
    std::string getFileExtension(const std::string& fileName) const
    {
        std::size_t i = fileName.rfind('.', fileName.length());
        if (i != std::string::npos)
            return(fileName.substr(i+1, fileName.length() - i));
        else
            DUNE_THROW(Dune::IOError, "Please provide and extension for your grid file ('"<< fileName << "')!");
        return "";
    }
 
    Grid& grid()
    { return enableDgfGridPointer_ ? *dgfGridPtr() : *gridPtr(); }
 
    std::shared_ptr<GridData> getGridData() const
    {
        if (!gridData_)
            DUNE_THROW(Dune::IOError, "No grid data available");
 
        return gridData_;
    }
 
    void loadBalance()
    {
        if (Dune::MPIHelper::getCommunication().size() > 1)
        {
            // if we may have dgf parameters use load balancing of the dgf pointer
            if (enableDgfGridPointer_)
            {
                dgfGridPtr().loadBalance();
                // update the grid data
                gridData_ = std::make_shared<GridData>(dgfGridPtr(), paramGroup_);
            }
            else
                gridPtr()->loadBalance();
        }
    }
 
    void sanitizeGrid()
    {
        // evaluate the coordination numbers to check if all pores are connected to at least one throat
        gridData_->getCoordinationNumbers();
 
        // for dgf grid, copy the data to persistent containers
        if (enableDgfGridPointer_)
            gridData_->copyDgfData();
 
        const auto gridView = grid().leafGridView();
        static const std::string sanitationMode = getParamFromGroup<std::string>(paramGroup_, "Grid.SanitationMode", "KeepLargestCluster");
 
        // find the elements to keep, all others will be deleted
        const auto keepElement = [&]
        {
            if (sanitationMode == "UsePoreLabels")
                return findElementsConnectedToPoreLabel(gridView);
            else if (sanitationMode == "KeepLargestCluster")
                return findElementsInLargestCluster(gridView);
            else
                DUNE_THROW(Dune::IOError, sanitationMode << "is not a valid sanitation mode. Use KeepLargestCluster or UsePoreLabels.");
 
 
        }();
 
        if (std::none_of(keepElement.begin(), keepElement.end(), [](const bool i){return i;}))
            DUNE_THROW(Dune::InvalidStateException, "sanitize() deleted all elements! Check your boundary face indices. "
                << "If the problem persists, add at least one of your boundary face indices to PruningSeedIndices");
 
        // remove the elements in the grid
        std::size_t numDeletedElements = 0;
        grid().preGrow();
        for (const auto& element : elements(gridView))
        {
            const auto eIdx = gridView.indexSet().index(element);
            if (!keepElement[eIdx])
            {
                grid().removeElement(element);
                ++numDeletedElements;
            }
        }
        // triggers the grid growth process
        grid().grow();
        grid().postGrow();
 
        // resize the parameters for dgf grids
        if (enableDgfGridPointer_)
            gridData_->resizeParameterContainers();
 
        if (numDeletedElements > 0)
            std::cout << "\nDeleted " << numDeletedElements << " isolated elements.\n" << std::endl;
    }
 
    std::vector<bool> findElementsConnectedToPoreLabel(const typename Grid::LeafGridView& gridView) const
    {
        // pruning -- remove elements not connected to a Dirichlet boundary (marker == 1)
        const auto pruningSeedIndices = getParamFromGroup<std::vector<int>>(paramGroup_, "Grid.PruningSeedIndices", std::vector<int>{1});
        std::vector<bool> elementIsConnected(gridView.size(0), false);
 
        auto boundaryIdx = [&](const auto& vertex)
        {
            if (enableDgfGridPointer_)
                return static_cast<int>(dgfGridPtr_.parameters(vertex)[gridData_->parameterIndex("PoreLabel")]);
            else
                return static_cast<int>(gridData_->poreLabelAtPosForGenericGrid(vertex.geometry().center()));
        };
 
        for (const auto& element : elements(gridView))
        {
            const auto eIdx = gridView.indexSet().index(element);
            if (elementIsConnected[eIdx])
                continue;
 
            // try to find a seed from which to start the search process
            bool isSeed = false;
            bool hasNeighbor = false;
            for (const auto& intersection : intersections(gridView, element))
            {
                auto vertex = element.template subEntity<1>(intersection.indexInInside());
                // seed found
                if (std::any_of(pruningSeedIndices.begin(), pruningSeedIndices.end(),
                               [&]( const int i ){ return i == boundaryIdx(vertex); }))
                {
                    isSeed = true;
                    // break;
                }
 
                if (intersection.neighbor())
                    hasNeighbor = true;
            }
 
            if (!hasNeighbor)
                continue;
 
            if (isSeed)
            {
                elementIsConnected[eIdx] = true;
 
                // use iteration instead of recursion here because the recursion can get too deep
                recursivelyFindConnectedElements_(gridView, element, elementIsConnected);
            }
        }
 
        return elementIsConnected;
    }
 
    std::vector<bool> findElementsInLargestCluster(const typename Grid::LeafGridView& gridView) const
    {
        const auto clusteredElements = clusterElements(gridView);
 
        const auto numClusters = *std::max_element(clusteredElements.begin(), clusteredElements.end()) + 1;
        std::cout << "\nFound " << numClusters << " unconnected clusters." << std::endl;
 
        // count number of elements in individual clusters
        std::vector<std::size_t> clusterFrequency(numClusters);
        for (const auto clusterIdx : clusteredElements)
            clusterFrequency[clusterIdx] += 1;
 
        const auto largestCluster = std::max_element(clusterFrequency.begin(), clusterFrequency.end());
        const auto largestClusterIdx = std::distance(clusterFrequency.begin(), largestCluster);
 
        std::vector<bool> elementsInLargestCluster(gridView.size(0));
 
        for (int eIdx = 0; eIdx < clusteredElements.size(); ++eIdx)
            if (clusteredElements[eIdx] == largestClusterIdx)
                elementsInLargestCluster[eIdx] = true;
 
        return elementsInLargestCluster;
    }
 
    std::vector<std::size_t> clusterElements(const typename Grid::LeafGridView& gridView) const
    {
        std::vector<std::size_t> elementInCluster(gridView.size(0), 0); // initially, all elements are in pseudo cluster 0
        std::size_t clusterIdx = 0;
 
        for (const auto& element : elements(gridView))
        {
            const auto eIdx = gridView.indexSet().index(element);
            if (elementInCluster[eIdx]) // element already is in a cluster
                continue;
 
            ++clusterIdx;
            elementInCluster[eIdx] = clusterIdx;
 
            recursivelyFindConnectedElements_(gridView, element, elementInCluster, clusterIdx);
        }
 
        // make sure the clusters start with index zero
        for (auto& clusterIdx : elementInCluster)
            clusterIdx -= 1;
 
        return elementInCluster;
    }
 
protected:
 
    std::shared_ptr<Grid>& gridPtr()
    {
        if(!enableDgfGridPointer_)
            return gridPtr_;
        else
            DUNE_THROW(Dune::InvalidStateException, "You are using DGF. To get the grid pointer use method dgfGridPtr()!");
    }
 
    Dune::GridPtr<Grid>& dgfGridPtr()
    {
        if(enableDgfGridPointer_)
            return dgfGridPtr_;
        else
            DUNE_THROW(Dune::InvalidStateException, "The DGF grid pointer is only available if the grid was constructed with a DGF file!");
    }
 
    bool enableDgfGridPointer_ = false;
 
    std::shared_ptr<Grid> gridPtr_;
    Dune::GridPtr<Grid> dgfGridPtr_;
 
    std::shared_ptr<GridData> gridData_;
 
    std::string paramGroup_;
 
private:
 
    void createOneDGrid_(unsigned int numPores)
    {
        const auto lowerLeft = getParamFromGroup<GlobalPosition>(paramGroup_, "Grid.LowerLeft", GlobalPosition(0.0));
        const auto upperRight = getParamFromGroup<GlobalPosition>(paramGroup_, "Grid.UpperRight");
        const auto cells = numPores - 1;
 
        // create a step vector
        GlobalPosition step = upperRight;
        step -= lowerLeft, step /= cells;
 
        // make the grid (structured interval grid in dimworld space)
        Dune::GridFactory<Grid> factory;
 
        // create the vertices
        GlobalPosition globalPos = lowerLeft;
        for (unsigned int vIdx = 0; vIdx <= cells; vIdx++, globalPos += step)
            factory.insertVertex(globalPos);
 
        // create the cells
        for(unsigned int eIdx = 0; eIdx < cells; eIdx++)
            factory.insertElement(Dune::GeometryTypes::line, {eIdx, eIdx+1});
 
        gridPtr() = std::shared_ptr<Grid>(factory.createGrid());
        gridData_ = std::make_shared<GridData>(gridPtr_, paramGroup_);
        gridData_->assignParameters();
    }
 
    template<class T>
    void recursivelyFindConnectedElements_(const typename Grid::LeafGridView& gridView,
                                           const Element& element,
                                           std::vector<T>& elementIsConnected,
                                           T marker = 1) const
    {
        // use iteration instead of recursion here because the recursion can get too deep
        std::stack<Element> elementStack;
        elementStack.push(element);
        while (!elementStack.empty())
        {
            auto e = elementStack.top();
            elementStack.pop();
            for (const auto& intersection : intersections(gridView, e))
            {
                if (!intersection.boundary())
                {
                    auto outside = intersection.outside();
                    auto nIdx = gridView.indexSet().index(outside);
                    if (!elementIsConnected[nIdx])
                    {
                        elementIsConnected[nIdx] = marker;
                        elementStack.push(outside);
                    }
                }
            }
        }
    }
};
 
}
 
#endif // HAVE_DUNE_FOAMGRID
 
#endif