C++ Mesh::getNumberOfNodes方法代码示例

GlobalSparsityPattern computeSparsityPatternNonPETSc(
    NumLib::LocalToGlobalIndexMap const& dof_table, MeshLib::Mesh const& mesh)
{
    MeshLib::NodeAdjacencyTable node_adjacency_table;
    node_adjacency_table.createTable(mesh.getNodes());

    // A mapping   mesh node id -> global indices
    // It acts as a cache for dof table queries.
    std::vector<std::vector<GlobalIndexType>> global_idcs;

    global_idcs.reserve(mesh.getNumberOfNodes());
    for (std::size_t n = 0; n < mesh.getNumberOfNodes(); ++n)
    {
        MeshLib::Location l(mesh.getID(), MeshLib::MeshItemType::Node, n);
        global_idcs.push_back(dof_table.getGlobalIndices(l));
    }

    GlobalSparsityPattern sparsity_pattern(dof_table.dofSizeWithGhosts());

    // Map adjacent mesh nodes to "adjacent global indices".
    for (std::size_t n = 0; n < mesh.getNumberOfNodes(); ++n)
    {
        unsigned n_connected_dof = 0;
        for (auto an : node_adjacency_table.getAdjacentNodes(n))
            n_connected_dof += global_idcs[an].size();
        for (auto global_index : global_idcs[n])
            sparsity_pattern[global_index] = n_connected_dof;
    }

    return sparsity_pattern;
}

bool convertMeshToGeo(const MeshLib::Mesh &mesh, GeoLib::GEOObjects &geo_objects, double eps)
{
    if (mesh.getDimension() != 2)
    {
        ERR ("Mesh to geometry conversion is only working for 2D meshes.");
        return false;
    }

    // nodes to points conversion
    std::string mesh_name(mesh.getName());
    {
        auto points = std::make_unique<std::vector<GeoLib::Point*>>();
        points->reserve(mesh.getNumberOfNodes());

        for (auto node_ptr : mesh.getNodes())
            points->push_back(new GeoLib::Point(*node_ptr, node_ptr->getID()));

        geo_objects.addPointVec(std::move(points), mesh_name, nullptr, eps);
    }
    const std::vector<std::size_t> id_map (geo_objects.getPointVecObj(mesh_name)->getIDMap());

    // elements to surface triangles conversion
    std::string const mat_name ("MaterialIDs");
    auto bounds (MeshInformation::getValueBounds<int>(mesh, mat_name));
    const unsigned nMatGroups(bounds.second-bounds.first+1);
    auto sfcs = std::make_unique<std::vector<GeoLib::Surface*>>();
    sfcs->reserve(nMatGroups);
    auto const& points = *geo_objects.getPointVec(mesh_name);
    for (unsigned i=0; i<nMatGroups; ++i)
        sfcs->push_back(new GeoLib::Surface(points));

    const std::vector<MeshLib::Element*> &elements = mesh.getElements();
    const std::size_t nElems (mesh.getNumberOfElements());

    MeshLib::PropertyVector<int> const*const materialIds =
        mesh.getProperties().existsPropertyVector<int>("MaterialIDs")
            ? mesh.getProperties().getPropertyVector<int>("MaterialIDs")
            : nullptr;

    for (unsigned i=0; i<nElems; ++i)
    {
        auto surfaceId = !materialIds ? 0 : ((*materialIds)[i] - bounds.first);
        MeshLib::Element* e (elements[i]);
        if (e->getGeomType() == MeshElemType::TRIANGLE)
            (*sfcs)[surfaceId]->addTriangle(id_map[e->getNodeIndex(0)], id_map[e->getNodeIndex(1)], id_map[e->getNodeIndex(2)]);
        if (e->getGeomType() == MeshElemType::QUAD)
        {
            (*sfcs)[surfaceId]->addTriangle(id_map[e->getNodeIndex(0)], id_map[e->getNodeIndex(1)], id_map[e->getNodeIndex(2)]);
            (*sfcs)[surfaceId]->addTriangle(id_map[e->getNodeIndex(0)], id_map[e->getNodeIndex(2)], id_map[e->getNodeIndex(3)]);
        }
        // all other element types are ignored (i.e. lines)
    }

    std::for_each(sfcs->begin(), sfcs->end(), [](GeoLib::Surface* sfc){ if (sfc->getNumberOfTriangles()==0) delete sfc; sfc = nullptr;});
    auto sfcs_end = std::remove(sfcs->begin(), sfcs->end(), nullptr);
    sfcs->erase(sfcs_end, sfcs->end());

    geo_objects.addSurfaceVec(std::move(sfcs), mesh_name);
    return true;
}

std::unique_ptr<DirichletBoundaryCondition> createDirichletBoundaryCondition(
    BaseLib::ConfigTree const& config, MeshLib::Mesh const& bc_mesh,
    NumLib::LocalToGlobalIndexMap const& dof_table_bulk, int const variable_id,
    int const component_id,
    const std::vector<std::unique_ptr<ProcessLib::ParameterBase>>& parameters)
{
    DBUG("Constructing DirichletBoundaryCondition from config.");
    //! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__type}
    config.checkConfigParameter("type", "Dirichlet");

    //! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__Dirichlet__parameter}
    auto const param_name = config.getConfigParameter<std::string>("parameter");
    DBUG("Using parameter %s", param_name.c_str());

    auto& param = findParameter<double>(param_name, parameters, 1);

    // In case of partitioned mesh the boundary could be empty, i.e. there is no
    // boundary condition.
#ifdef USE_PETSC
    // This can be extracted to createBoundaryCondition() but then the config
    // parameters are not read and will cause an error.
    // TODO (naumov): Add a function to ConfigTree for skipping the tags of the
    // subtree and move the code up in createBoundaryCondition().
    if (bc_mesh.getDimension() == 0 && bc_mesh.getNumberOfNodes() == 0 &&
        bc_mesh.getNumberOfElements() == 0)
    {
        return nullptr;
    }
#endif  // USE_PETSC

    return std::make_unique<DirichletBoundaryCondition>(
        param, bc_mesh, dof_table_bulk, variable_id, component_id);
}

bool MeshLayerMapper::layerMapping(MeshLib::Mesh &new_mesh, GeoLib::Raster const& raster, double noDataReplacementValue = 0.0)
{
    if (new_mesh.getDimension() != 2)
    {
        ERR("MshLayerMapper::layerMapping() - requires 2D mesh");
        return false;
    }

    GeoLib::RasterHeader const& header (raster.getHeader());
    const double x0(header.origin[0]);
    const double y0(header.origin[1]);
    const double delta(header.cell_size);

    const std::pair<double, double> xDim(x0, x0 + header.n_cols * delta); // extension in x-dimension
    const std::pair<double, double> yDim(y0, y0 + header.n_rows * delta); // extension in y-dimension

    const std::size_t nNodes (new_mesh.getNumberOfNodes());
    const std::vector<MeshLib::Node*> &nodes = new_mesh.getNodes();
    for (unsigned i = 0; i < nNodes; ++i)
    {
        if (!raster.isPntOnRaster(*nodes[i]))
        {
            // use either default value or elevation from layer above
            nodes[i]->updateCoordinates((*nodes[i])[0], (*nodes[i])[1], noDataReplacementValue);
            continue;
        }

        double elevation (raster.interpolateValueAtPoint(*nodes[i]));
        if (std::abs(elevation - header.no_data) < std::numeric_limits<double>::epsilon())
            elevation = noDataReplacementValue;
        nodes[i]->updateCoordinates((*nodes[i])[0], (*nodes[i])[1], elevation);
    }

    return true;
}

std::unique_ptr<PythonBoundaryCondition> createPythonBoundaryCondition(
    BaseLib::ConfigTree const& config, MeshLib::Mesh const& boundary_mesh,
    NumLib::LocalToGlobalIndexMap const& dof_table, std::size_t bulk_mesh_id,
    int const variable_id, int const component_id,
    unsigned const integration_order, unsigned const shapefunction_order,
    unsigned const global_dim)
{
    //! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__type}
    config.checkConfigParameter("type", "Python");

    //! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__Python__bc_object}
    auto const bc_object = config.getConfigParameter<std::string>("bc_object");
    //! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__Python__flush_stdout}
    auto const flush_stdout = config.getConfigParameter("flush_stdout", false);

    // Evaluate Python code in scope of main module
    pybind11::object scope =
        pybind11::module::import("__main__").attr("__dict__");

    if (!scope.contains(bc_object))
        OGS_FATAL(
            "Function `%s' is not defined in the python script file, or there "
            "was no python script file specified.",
            bc_object.c_str());

    auto* bc = scope[bc_object.c_str()]
                   .cast<PythonBoundaryConditionPythonSideInterface*>();

    if (variable_id >= static_cast<int>(dof_table.getNumberOfVariables()) ||
        component_id >= dof_table.getNumberOfVariableComponents(variable_id))
    {
        OGS_FATAL(
            "Variable id or component id too high. Actual values: (%d, %d), "
            "maximum values: (%d, %d).",
            variable_id, component_id, dof_table.getNumberOfVariables(),
            dof_table.getNumberOfVariableComponents(variable_id));
    }

    // In case of partitioned mesh the boundary could be empty, i.e. there is no
    // boundary condition.
#ifdef USE_PETSC
    // This can be extracted to createBoundaryCondition() but then the config
    // parameters are not read and will cause an error.
    // TODO (naumov): Add a function to ConfigTree for skipping the tags of the
    // subtree and move the code up in createBoundaryCondition().
    if (boundary_mesh.getDimension() == 0 &&
        boundary_mesh.getNumberOfNodes() == 0 &&
        boundary_mesh.getNumberOfElements() == 0)
    {
        return nullptr;
    }
#endif  // USE_PETSC

    return std::make_unique<PythonBoundaryCondition>(
        PythonBoundaryConditionData{
            bc, dof_table, bulk_mesh_id,
            dof_table.getGlobalComponent(variable_id, component_id),
            boundary_mesh},
        integration_order, shapefunction_order, global_dim, flush_stdout);
}

 void testZCoords2D(MeshLib::Mesh const& input, MeshLib::Mesh const& output, double height)
 {
     std::size_t const nNodes (input.getNumberOfNodes());
     for (std::size_t i=0; i<nNodes; ++i)
     {
         ASSERT_EQ((*input.getNode(i))[2], (*output.getNode(i))[2]);
         ASSERT_EQ((*input.getNode(i))[2] + height, (*output.getNode(nNodes+i))[2]);
     }
 }

bool MeshLayerMapper::createRasterLayers(
    MeshLib::Mesh const& mesh,
    std::vector<GeoLib::Raster const*> const& rasters,
    double minimum_thickness,
    double noDataReplacementValue)
{
    const std::size_t nLayers(rasters.size());
    if (nLayers < 2 || mesh.getDimension() != 2)
    {
        ERR("MeshLayerMapper::createRasterLayers(): A 2D mesh and at least two rasters required as input.");
        return false;
    }

    auto top = std::make_unique<MeshLib::Mesh>(mesh);
    if (!layerMapping(*top, *rasters.back(), noDataReplacementValue))
        return false;

    auto bottom = std::make_unique<MeshLib::Mesh>(mesh);
    if (!layerMapping(*bottom, *rasters[0], 0))
    {
        return false;
    }

    this->_minimum_thickness = minimum_thickness;
    std::size_t const nNodes = mesh.getNumberOfNodes();
    _nodes.reserve(nLayers * nNodes);

    // number of triangles in the original mesh
    std::size_t const nElems (std::count_if(mesh.getElements().begin(), mesh.getElements().end(),
        [](MeshLib::Element const* elem)
            { return (elem->getGeomType() == MeshLib::MeshElemType::TRIANGLE);}));
    _elements.reserve(nElems * (nLayers-1));
    _materials.reserve(nElems *  (nLayers-1));

    // add bottom layer
    std::vector<MeshLib::Node*> const& nodes = bottom->getNodes();
    for (MeshLib::Node* node : nodes)
        _nodes.push_back(new MeshLib::Node(*node));

    // add the other layers
    for (std::size_t i=0; i<nLayers-1; ++i)
        addLayerToMesh(*top, i, *rasters[i+1]);

    return true;
}

std::unique_ptr<RobinBoundaryCondition> createRobinBoundaryCondition(
    BaseLib::ConfigTree const& config, MeshLib::Mesh const& bc_mesh,
    NumLib::LocalToGlobalIndexMap const& dof_table, int const variable_id,
    int const component_id, unsigned const integration_order,
    unsigned const shapefunction_order, unsigned const global_dim,
    std::vector<std::unique_ptr<ParameterLib::ParameterBase>> const& parameters)
{
    DBUG("Constructing RobinBcConfig from config.");
    //! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__type}
    config.checkConfigParameter("type", "Robin");

    //! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__Robin__alpha}
    auto const alpha_name = config.getConfigParameter<std::string>("alpha");
    //! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__Robin__u_0}
    auto const u_0_name = config.getConfigParameter<std::string>("u_0");

    auto const& alpha =
        ParameterLib::findParameter<double>(alpha_name, parameters, 1);
    auto const& u_0 =
        ParameterLib::findParameter<double>(u_0_name, parameters, 1);

    // In case of partitioned mesh the boundary could be empty, i.e. there is no
    // boundary condition.
#ifdef USE_PETSC
    // This can be extracted to createBoundaryCondition() but then the config
    // parameters are not read and will cause an error.
    // TODO (naumov): Add a function to ConfigTree for skipping the tags of the
    // subtree and move the code up in createBoundaryCondition().
    if (bc_mesh.getDimension() == 0 && bc_mesh.getNumberOfNodes() == 0 &&
        bc_mesh.getNumberOfElements() == 0)
    {
        return nullptr;
    }
#endif  // USE_PETSC

    return std::make_unique<RobinBoundaryCondition>(
        integration_order, shapefunction_order, dof_table, variable_id,
        component_id, global_dim, bc_mesh,
        RobinBoundaryConditionData{alpha, u_0});
}

int main (int argc, char* argv[])
{
    ApplicationsLib::LogogSetup logog_setup;

    TCLAP::CmdLine cmd("Converts VTK mesh into OGS mesh.", ' ', "0.1");
    TCLAP::ValueArg<std::string> mesh_in("i", "mesh-input-file",
                                         "the name of the file containing the input mesh", true,
                                         "", "file name of input mesh");
    cmd.add(mesh_in);
    TCLAP::ValueArg<std::string> mesh_out("o", "mesh-output-file",
                                          "the name of the file the mesh will be written to", true,
                                          "", "file name of output mesh");
    cmd.add(mesh_out);
    cmd.parse(argc, argv);

    MeshLib::Mesh* mesh (MeshLib::IO::VtuInterface::readVTUFile(mesh_in.getValue()));
    INFO("Mesh read: %d nodes, %d elements.", mesh->getNumberOfNodes(), mesh->getNumberOfElements());

    MeshLib::IO::Legacy::MeshIO meshIO;
    meshIO.setMesh(mesh);
    meshIO.writeToFile(mesh_out.getValue());

    return EXIT_SUCCESS;
}

void ElementTreeModel::setMesh(MeshLib::Mesh const& mesh)
{
    this->clearView();

    QList<QVariant> mesh_name;
    mesh_name << "Name:" << QString::fromStdString(mesh.getName()) << "" << "" << "";
    TreeItem* name_item = new TreeItem(mesh_name, _rootItem);
    _rootItem->appendChild(name_item);

    QList<QVariant> nodes_number;
    nodes_number << "#Nodes: " << QString::number(mesh.getNumberOfNodes()) << "" << "";
    TreeItem* nodes_item = new TreeItem(nodes_number, _rootItem);
    _rootItem->appendChild(nodes_item);

    QList<QVariant> elements_number;
    elements_number << "#Elements: " << QString::number(mesh.getNumberOfElements()) << "" << "";
    TreeItem* elements_item = new TreeItem(elements_number, _rootItem);
    _rootItem->appendChild(elements_item);

    const std::array<QString, 7> n_element_names = {{ "Lines:", "Triangles:", "Quads:", "Tetrahedra:", "Hexahedra:", "Pyramids:", "Prisms:" }};
    const std::array<unsigned, 7>& n_element_types (MeshLib::MeshInformation::getNumberOfElementTypes(mesh));
    for (std::size_t i=0; i<n_element_types.size(); ++i)
    {
        if (n_element_types[i])
        {
            QList<QVariant> elements_number;
            elements_number << n_element_names[i] << QString::number(n_element_types[i]) << "" << "";
            TreeItem* type_item = new TreeItem(elements_number, elements_item);
            elements_item->appendChild(type_item);
        }
    }

    QList<QVariant> bounding_box;
    bounding_box << "Bounding Box" << "" << "" << "";
    TreeItem* aabb_item = new TreeItem(bounding_box, _rootItem);
    _rootItem->appendChild(aabb_item);

    const GeoLib::AABB aabb (MeshLib::MeshInformation::getBoundingBox(mesh));
    auto const& min = aabb.getMinPoint();
    auto const& max = aabb.getMaxPoint();

    QList<QVariant> min_aabb;
    min_aabb << "Min:" << QString::number(min[0], 'f') << QString::number(min[1], 'f') << QString::number(min[2], 'f');
    TreeItem* min_item = new TreeItem(min_aabb, aabb_item);
    aabb_item->appendChild(min_item);

    QList<QVariant> max_aabb;
    max_aabb << "Max:" << QString::number(max[0], 'f') << QString::number(max[1], 'f') << QString::number(max[2], 'f');
    TreeItem* max_item = new TreeItem(max_aabb, aabb_item);
    aabb_item->appendChild(max_item);

    QList<QVariant> edges;
    edges << "Edge Length: " << "[" + QString::number(mesh.getMinEdgeLength(), 'f') + "," << QString::number(mesh.getMaxEdgeLength(), 'f') + "]" << "";
    TreeItem* edge_item = new TreeItem(edges, _rootItem);
    _rootItem->appendChild(edge_item);

    std::vector<std::string> const& vec_names (mesh.getProperties().getPropertyVectorNames());
    for (std::size_t i=0; i<vec_names.size(); ++i)
    {
        QList<QVariant> array_info;
        array_info << QString::fromStdString(vec_names[i]) + ": ";
        auto vec_bounds (MeshLib::MeshInformation::getValueBounds<int>(mesh, vec_names[i]));
        if (vec_bounds.second != std::numeric_limits<int>::max())
            array_info << "[" + QString::number(vec_bounds.first) + "," << QString::number(vec_bounds.second) + "]" << "";
        else
        {
            auto vec_bounds (MeshLib::MeshInformation::getValueBounds<double>(mesh, vec_names[i]));
            if (vec_bounds.second != std::numeric_limits<double>::max())
                array_info  << "[" + QString::number(vec_bounds.first) + "," << QString::number(vec_bounds.second) + "]" << "";
        }
        if (array_info.size() == 1)
            array_info << "[ ?" << "? ]" << "";
        TreeItem* vec_item = new TreeItem(array_info, _rootItem);
        _rootItem->appendChild(vec_item);
    }

    reset();

}

void MeshLayerMapper::addLayerToMesh(const MeshLib::Mesh &dem_mesh, unsigned layer_id, GeoLib::Raster const& raster)
{
    const unsigned pyramid_base[3][4] =
    {
        {1, 3, 4, 2}, // Point 4 missing
        {2, 4, 3, 0}, // Point 5 missing
        {0, 3, 4, 1}, // Point 6 missing
    };

    std::size_t const nNodes = dem_mesh.getNumberOfNodes();
    std::vector<MeshLib::Node*> const& nodes = dem_mesh.getNodes();
    int const last_layer_node_offset = layer_id * nNodes;

    // add nodes for new layer
    for (std::size_t i=0; i<nNodes; ++i)
        _nodes.push_back(getNewLayerNode(*nodes[i], *_nodes[last_layer_node_offset + i], raster, _nodes.size()));

    std::vector<MeshLib::Element*> const& elems = dem_mesh.getElements();
    std::size_t const nElems (dem_mesh.getNumberOfElements());

    for (std::size_t i=0; i<nElems; ++i)
    {
        MeshLib::Element* elem (elems[i]);
        if (elem->getGeomType() != MeshLib::MeshElemType::TRIANGLE)
            continue;
        unsigned node_counter(3), missing_idx(0);
        std::array<MeshLib::Node*, 6> new_elem_nodes;
        for (unsigned j=0; j<3; ++j)
        {
            new_elem_nodes[j] = _nodes[_nodes[last_layer_node_offset + elem->getNodeIndex(j)]->getID()];
            new_elem_nodes[node_counter] = (_nodes[last_layer_node_offset + elem->getNodeIndex(j) + nNodes]);
            if (new_elem_nodes[j]->getID() != new_elem_nodes[node_counter]->getID())
                node_counter++;
            else
                missing_idx = j;
        }

        switch (node_counter)
        {
        case 6:
            _elements.push_back(new MeshLib::Prism(new_elem_nodes));
            _materials.push_back(layer_id);
            break;
        case 5:
            std::array<MeshLib::Node*, 5> pyramid_nodes;
            pyramid_nodes[0] = new_elem_nodes[pyramid_base[missing_idx][0]];
            pyramid_nodes[1] = new_elem_nodes[pyramid_base[missing_idx][1]];
            pyramid_nodes[2] = new_elem_nodes[pyramid_base[missing_idx][2]];
            pyramid_nodes[3] = new_elem_nodes[pyramid_base[missing_idx][3]];
            pyramid_nodes[4] = new_elem_nodes[missing_idx];
            _elements.push_back(new MeshLib::Pyramid(pyramid_nodes));
            _materials.push_back(layer_id);
            break;
        case 4:
            std::array<MeshLib::Node*, 4> tet_nodes;
            std::copy(new_elem_nodes.begin(), new_elem_nodes.begin() + node_counter, tet_nodes.begin());
            _elements.push_back(new MeshLib::Tet(tet_nodes));
            _materials.push_back(layer_id);
            break;
        default:
            continue;
        }
    }
}