Beispiel #1
0
// Creates a PropertyVector<unsigned> and maps it into a vtkDataArray-equivalent
TEST(MeshLibMappedPropertyVector, Unsigned)
{
    const std::size_t mesh_size = 5;
    const double length = 1.0;

    MeshLib::Mesh* mesh = MeshLib::MeshGenerator::generateRegularHexMesh(length, mesh_size);

    ASSERT_TRUE(mesh != nullptr);
    const std::size_t number_of_tuples(mesh_size*mesh_size*mesh_size);

    std::string const prop_name("TestProperty");
    auto* const properties =
        mesh->getProperties().createNewPropertyVector<unsigned>(
            prop_name, MeshLib::MeshItemType::Cell);
    properties->resize(number_of_tuples);
    std::iota(properties->begin(), properties->end(), 0);

    vtkNew<MeshLib::VtkMappedPropertyVectorTemplate<unsigned> > dataArray;
    dataArray->SetPropertyVector(*properties);

    ASSERT_EQ(dataArray->GetNumberOfComponents(), 1);
    ASSERT_EQ(dataArray->GetNumberOfTuples(), number_of_tuples);

    ASSERT_EQ(dataArray->GetValueReference(0), 0);
    double* range = dataArray->GetRange(0);
    ASSERT_EQ(range[0], 0);
    ASSERT_EQ(range[1], 0 + mesh->getNumberOfElements() - 1);

    delete mesh;
}
std::size_t ElementValueModification::setByElementType(MeshLib::Mesh &mesh, MeshElemType ele_type, int const new_value)
{
    MeshLib::PropertyVector<int>* property_value_vector = nullptr;
    try
    {
        property_value_vector = mesh.getProperties().getPropertyVector<int>(
            "MaterialIDs", MeshLib::MeshItemType::Cell, 1);
    }
    catch (std::runtime_error const& e)
    {
        ERR("%s", e.what());
        return 0;
    }

    std::vector<MeshLib::Element*> const& elements(mesh.getElements());
    std::size_t cnt(0);
    for (std::size_t k(0); k < elements.size(); k++)
    {
        if (elements[k]->getGeomType() != ele_type)
        {
            continue;
        }
        (*property_value_vector)[k] = new_value;
        cnt++;
    }

    return cnt;
}
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);
}
IntegrationPointMetaData getIntegrationPointMetaData(MeshLib::Mesh const& mesh,
                                                     std::string const& name)
{
    if (!mesh.getProperties().existsPropertyVector<char>(
            "IntegrationPointMetaData"))
    {
        OGS_FATAL(
            "Integration point data '%s' is present in the vtk field "
            "data but the required 'IntegrationPointMetaData' array "
            "is not available.",
            name.c_str());
    }
    auto const& mesh_property_ip_meta_data =
        *mesh.getProperties().template getPropertyVector<char>(
            "IntegrationPointMetaData");

    if (mesh_property_ip_meta_data.getMeshItemType() !=
        MeshLib::MeshItemType::IntegrationPoint)
    {
        OGS_FATAL("IntegrationPointMetaData array must be field data.");
    }

    // Find the current integration point data entry and extract the
    // meta data.
    auto const ip_meta_data = extractIntegrationPointMetaData(
        json::parse(mesh_property_ip_meta_data.begin(),
                    mesh_property_ip_meta_data.end()),
        name);

    return ip_meta_data;
}
Beispiel #5
0
void MeshSurfaceExtraction::getSurfaceAreaForNodes(const MeshLib::Mesh &mesh, std::vector<double> &node_area_vec)
{
	if (mesh.getDimension() == 2)
	{
		double total_area (0);

		// for each node, a vector containing all the element idget every element
		const std::vector<MeshLib::Node*> &nodes = mesh.getNodes();
		const size_t nNodes ( mesh.getNNodes() );
		node_area_vec.reserve(nNodes);
		for (size_t n=0; n<nNodes; ++n)
		{
			double node_area (0);

			std::vector<MeshLib::Element*> conn_elems = nodes[n]->getElements();
			const size_t nConnElems (conn_elems.size());

			for (size_t i=0; i<nConnElems; ++i)
			{
				const MeshLib::Element* elem (conn_elems[i]);
				const unsigned nElemParts = (elem->getGeomType() == MeshElemType::TRIANGLE) ? 3 : 4;
				const double area = conn_elems[i]->getContent() / nElemParts;
				node_area += area;
				total_area += area;
			}

			node_area_vec.push_back(node_area);
		}

		INFO ("Total surface Area: %f", total_area);
	}
	else
		ERR ("Error in MeshSurfaceExtraction::getSurfaceAreaForNodes() - Given mesh is no surface mesh (dimension != 2).");
}
Beispiel #6
0
void LayeredVolume::addLayerBoundaries(const MeshLib::Mesh &layer, std::size_t nLayers)
{
	const unsigned nLayerBoundaries (nLayers-1);
	const std::size_t nNodes (layer.getNNodes());
	const std::vector<MeshLib::Element*> &layer_elements (layer.getElements());
	for (MeshLib::Element* elem : layer_elements)
	{
		const std::size_t nElemNodes (elem->getNBaseNodes());
		for (unsigned i=0; i<nElemNodes; ++i)
			if (elem->getNeighbor(i) == nullptr)
				for (unsigned j=0; j<nLayerBoundaries; ++j)
				{
					const std::size_t offset (j*nNodes);
					MeshLib::Node* n0 = _nodes[offset + elem->getNodeIndex(i)];
					MeshLib::Node* n1 = _nodes[offset + elem->getNodeIndex((i+1)%nElemNodes)];
					MeshLib::Node* n2 = _nodes[offset + nNodes + elem->getNodeIndex((i+1)%nElemNodes)];
					MeshLib::Node* n3 = _nodes[offset + nNodes + elem->getNodeIndex(i)];

					if (MathLib::Vector3(*n1, *n2).getLength() > std::numeric_limits<double>::epsilon())
					{
						const std::array<MeshLib::Node*,3> tri_nodes = {{ n0, n2, n1 }};
						_elements.push_back(new MeshLib::Tri(tri_nodes, nLayers+1+j));
					}
					if (MathLib::Vector3(*n0, *n3).getLength() > std::numeric_limits<double>::epsilon())
					{
						const std::array<MeshLib::Node*,3> tri_nodes = {{ n0, n3, n2 }};
						_elements.push_back(new MeshLib::Tri(tri_nodes, nLayers+1+j));
					}
				}
	}
}
void HeatTransportBHEProcess::initializeConcreteProcess(
    NumLib::LocalToGlobalIndexMap const& dof_table,
    MeshLib::Mesh const& mesh,
    unsigned const integration_order)
{
    // Quick access map to BHE's through element ids.
    std::unordered_map<std::size_t, BHE::BHETypes*> element_to_bhe_map;
    int const n_BHEs = _process_data._vec_BHE_property.size();
    for (int i = 0; i < n_BHEs; i++)
    {
        auto const& bhe_elements = _bheMeshData.BHE_elements[i];
        for (auto const& e : bhe_elements)
        {
            element_to_bhe_map[e->getID()] =
                &_process_data._vec_BHE_property[i];
        }
    }

    assert(mesh.getDimension() == 3);
    ProcessLib::HeatTransportBHE::createLocalAssemblers<
        HeatTransportBHELocalAssemblerSoil, HeatTransportBHELocalAssemblerBHE>(
        mesh.getElements(), dof_table, _local_assemblers, element_to_bhe_map,
        mesh.isAxiallySymmetric(), integration_order, _process_data);

    // Create BHE boundary conditions for each of the BHEs
    createBHEBoundaryConditionTopBottom(_bheMeshData.BHE_nodes);
}
// Creates a PropertyVector<double> and maps it into a vtkDataArray-equivalent
TEST(InSituLibMappedPropertyVector, Int)
{
	const size_t mesh_size = 5;
	const double length = 1.0;

	MeshLib::Mesh* mesh = MeshLib::MeshGenerator::generateRegularHexMesh(length, mesh_size);

	ASSERT_TRUE(mesh != nullptr);
	const std::size_t size(mesh_size*mesh_size*mesh_size);

	std::string const prop_name("TestProperty");
	boost::optional<MeshLib::PropertyVector<int> &> properties(
		mesh->getProperties().createNewPropertyVector<int>(prop_name,
			MeshLib::MeshItemType::Cell));
	(*properties).resize(size);
	std::iota((*properties).begin(), (*properties).end(), 1);

	vtkNew<InSituLib::VtkMappedPropertyVectorTemplate<int> > dataArray;
	dataArray->SetPropertyVector(*properties);

	ASSERT_EQ(dataArray->GetNumberOfComponents(), 1);
	ASSERT_EQ(dataArray->GetNumberOfTuples(), size);

	ASSERT_EQ(dataArray->GetValueReference(0), 1);
	double* range = dataArray->GetRange(0);
	ASSERT_EQ(range[0], 1);
	ASSERT_EQ(range[1], 1 + mesh->getNElements() - 1);

	delete mesh;
}
Beispiel #9
0
void LiquidFlowProcess::initializeConcreteProcess(
    NumLib::LocalToGlobalIndexMap const& dof_table,
    MeshLib::Mesh const& mesh,
    unsigned const integration_order)
{
    ProcessLib::ProcessVariable const& pv = getProcessVariables()[0];
    ProcessLib::createLocalAssemblers<LiquidFlowLocalAssembler>(
        mesh.getDimension(), mesh.getElements(), dof_table,
        pv.getShapeFunctionOrder(), _local_assemblers,
        mesh.isAxiallySymmetric(), integration_order, _gravitational_axis_id,
        _gravitational_acceleration, _material_properties);

    _secondary_variables.addSecondaryVariable(
        "darcy_velocity_x", 1,
        makeExtrapolator(
            getExtrapolator(), _local_assemblers,
            &LiquidFlowLocalAssemblerInterface::getIntPtDarcyVelocityX));

    if (mesh.getDimension() > 1)
    {
        _secondary_variables.addSecondaryVariable(
            "darcy_velocity_y", 1,
            makeExtrapolator(
                getExtrapolator(), _local_assemblers,
                &LiquidFlowLocalAssemblerInterface::getIntPtDarcyVelocityY));
    }
    if (mesh.getDimension() > 2)
    {
        _secondary_variables.addSecondaryVariable(
            "darcy_velocity_z", 1,
            makeExtrapolator(
                getExtrapolator(), _local_assemblers,
                &LiquidFlowLocalAssemblerInterface::getIntPtDarcyVelocityZ));
    }
}
std::size_t ElementValueModification::setByElementType(MeshLib::Mesh &mesh, MeshElemType ele_type, int const new_value)
{
    boost::optional<MeshLib::PropertyVector<int> &>
        optional_property_value_vec(
            mesh.getProperties().getPropertyVector<int>("MaterialIDs")
        );

    if (!optional_property_value_vec) {
        return 0;
    }

    MeshLib::PropertyVector<int> & property_value_vector(
        optional_property_value_vec.get()
    );

    std::vector<MeshLib::Element*> const& elements(mesh.getElements());
    std::size_t cnt(0);
    for (std::size_t k(0); k<elements.size(); k++) {
        if (elements[k]->getGeomType()!=ele_type)
            continue;
        property_value_vector[k] = new_value;
        cnt++;
    }

    return cnt;
}
void RichardsComponentTransportProcess::initializeConcreteProcess(
    NumLib::LocalToGlobalIndexMap const& dof_table,
    MeshLib::Mesh const& mesh,
    unsigned const integration_order)
{
    const int monolithic_process_id = 0;
    ProcessLib::ProcessVariable const& pv =
        getProcessVariables(monolithic_process_id)[0];
    ProcessLib::createLocalAssemblers<LocalAssemblerData>(
        mesh.getDimension(), mesh.getElements(), dof_table,
        pv.getShapeFunctionOrder(), _local_assemblers,
        mesh.isAxiallySymmetric(), integration_order, _process_data);

    _secondary_variables.addSecondaryVariable(
        "darcy_velocity",
        makeExtrapolator(mesh.getDimension(), getExtrapolator(),
                         _local_assemblers,
                         &RichardsComponentTransportLocalAssemblerInterface::
                             getIntPtDarcyVelocity));

    _secondary_variables.addSecondaryVariable(
        "saturation",
        makeExtrapolator(1, getExtrapolator(), _local_assemblers,
                         &RichardsComponentTransportLocalAssemblerInterface::
                             getIntPtSaturation));
}
Beispiel #12
0
std::unique_ptr<InitialCondition> createMeshPropertyInitialCondition(
    BaseLib::ConfigTree const& config,
    MeshLib::Mesh const& mesh,
    int const n_components)
{
	auto field_name = config.getConfParam<std::string>("field_name");
	DBUG("Using field_name %s", field_name.c_str());

	if (!mesh.getProperties().hasPropertyVector(field_name))
	{
		ERR("The required property %s does not exists in the mesh.",
		    field_name.c_str());
		std::abort();
	}
	auto const& property =
	    mesh.getProperties().template getPropertyVector<double>(field_name);
	if (!property)
	{
		ERR("The required property %s is not of the requested type.",
		    field_name.c_str());
		std::abort();
	}

	if (property->getNumberOfComponents() !=
	    static_cast<std::size_t>(n_components))
	{
		ERR("The required property %s has different number of components %d, "
		    "expected %d.",
		    field_name.c_str(), property->getNumberOfComponents(), n_components);
		std::abort();
	}
	return std::unique_ptr<InitialCondition>(
	    new MeshPropertyInitialCondition(*property));
}
Beispiel #13
0
std::unique_ptr<ParameterBase> createMeshPropertyParameter(
    BaseLib::ConfigTree const config, MeshLib::Mesh const& mesh)
{
	auto field_name = config.get_optional<std::string>("field_name");
	if (!field_name)
	{
		ERR("Could not find required parameter field_name.");
		std::abort();
	}
	DBUG("Using field_name %s", field_name->c_str());

	if (!mesh.getProperties().hasPropertyVector(*field_name))
	{
		ERR("The required property %s does not exists in the mesh.",
		    field_name->c_str());
		std::abort();
	}
	auto const& property =
	    mesh.getProperties().template getPropertyVector<double>(*field_name);
	if (!property)
	{
		ERR("The required property %s is not of the requested type.",
		    field_name->c_str());
		std::abort();
	}

	return std::unique_ptr<ParameterBase>(
	    new MeshPropertyParameter<double>(*property));
}
Beispiel #14
0
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;
}
Beispiel #15
0
void LayeredVolume::addLayerToMesh(const MeshLib::Mesh &dem_mesh, unsigned layer_id, GeoLib::Raster const& raster)
{
	const std::size_t nNodes (dem_mesh.getNNodes());
	const std::vector<MeshLib::Node*> &nodes (dem_mesh.getNodes());
	const std::size_t node_id_offset (_nodes.size());
	const std::size_t last_layer_node_offset (node_id_offset-nNodes);

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

	const std::vector<MeshLib::Element*> &layer_elements (dem_mesh.getElements());
	for (MeshLib::Element* elem : layer_elements)
	{
		if (elem->getGeomType() == MeshLib::MeshElemType::TRIANGLE)
		{
			std::array<MeshLib::Node*,3> tri_nodes = {{ _nodes[node_id_offset+elem->getNodeIndex(0)],
			                                            _nodes[node_id_offset+elem->getNodeIndex(1)],
			                                            _nodes[node_id_offset+elem->getNodeIndex(2)] }};
			_elements.push_back(new MeshLib::Tri(tri_nodes, layer_id));
		}
		else if (elem->getGeomType() == MeshLib::MeshElemType::QUAD)
		{
			std::array<MeshLib::Node*,4> quad_nodes = {{ _nodes[node_id_offset+elem->getNodeIndex(0)],
			                                             _nodes[node_id_offset+elem->getNodeIndex(1)],
			                                             _nodes[node_id_offset+elem->getNodeIndex(2)],
			                                             _nodes[node_id_offset+elem->getNodeIndex(3)] }};
			_elements.push_back(new MeshLib::Quad(quad_nodes, layer_id));
		}
	}
}
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);
}
Beispiel #17
0
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;
}
Beispiel #18
0
std::unique_ptr<ParameterBase> createMeshElementParameter(
    BaseLib::ConfigTree const& config, MeshLib::Mesh const& mesh)
{
    //! \ogs_file_param{parameter__type}
    config.checkConfigParameter("type", "MeshElement");
    //! \ogs_file_param{parameter__MeshElement__field_name}
    auto const field_name = config.getConfigParameter<std::string>("field_name");
    DBUG("Using field_name %s", field_name.c_str());

    if (!mesh.getProperties().hasPropertyVector(field_name)) {
        OGS_FATAL("The required property %s does not exists in the mesh.",
                  field_name.c_str());
    }

    // TODO other data types than only double
    auto const& property =
        mesh.getProperties().getPropertyVector<double>(field_name);
    if (!property) {
        OGS_FATAL("The mesh property `%s' is not of the requested type.",
                  field_name.c_str());
    }

    if (property->getMeshItemType() != MeshLib::MeshItemType::Cell) {
        OGS_FATAL("The mesh property `%s' is not an element property.",
                  field_name.c_str());
    }

    return std::unique_ptr<ParameterBase>(
        new MeshElementParameter<double>(*property));
}
Beispiel #19
0
std::vector<GeoLib::PointWithID*> MshEditor::getSurfaceNodes(const MeshLib::Mesh &mesh, const double *dir)
{
	INFO ("Extracting surface nodes...");
	const std::vector<MeshLib::Element*> all_elements (mesh.getElements());
	const std::vector<MeshLib::Node*> all_nodes (mesh.getNodes());

	std::vector<MeshLib::Element*> sfc_elements;
	get2DSurfaceElements(all_elements, sfc_elements, dir, mesh.getDimension());

	std::vector<MeshLib::Node*> sfc_nodes;
	std::vector<unsigned> node_id_map(mesh.getNNodes());
	get2DSurfaceNodes(all_nodes, sfc_nodes, sfc_elements, node_id_map);

	const unsigned nElements (sfc_elements.size());
	for (unsigned i=0; i<nElements; ++i)
		delete sfc_elements[i];

	const size_t nNodes (sfc_nodes.size());
	std::vector<GeoLib::PointWithID*> surface_pnts(nNodes);
	for (unsigned i=0; i<nNodes; ++i)
	{
		surface_pnts[i] = new GeoLib::PointWithID(sfc_nodes[i]->getCoords(), sfc_nodes[i]->getID());
		delete sfc_nodes[i];
	}
	return surface_pnts;
}
Beispiel #20
0
int main (int argc, char* argv[])
{
	LOGOG_INITIALIZE();
	logog::Cout* logog_cout (new logog::Cout);
	BaseLib::LogogSimpleFormatter *custom_format (new BaseLib::LogogSimpleFormatter);
	logog_cout->SetFormatter(*custom_format);

	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 (FileIO::BoostVtuInterface::readVTUFile(mesh_in.getValue()));
	INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());

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

	delete custom_format;
	delete logog_cout;
	LOGOG_SHUTDOWN();

	return 0;
}
Beispiel #21
0
void VtkMeshConverter::convertScalarArrays(vtkUnstructuredGrid& grid,
                                           MeshLib::Mesh& mesh)
{
    vtkPointData* point_data = grid.GetPointData();
    auto const n_point_arrays =
        static_cast<unsigned>(point_data->GetNumberOfArrays());
    for (unsigned i = 0; i < n_point_arrays; ++i)
        convertArray(*point_data->GetArray(i),
                     mesh.getProperties(),
                     MeshLib::MeshItemType::Node);

    vtkCellData* cell_data = grid.GetCellData();
    auto const n_cell_arrays =
        static_cast<unsigned>(cell_data->GetNumberOfArrays());
    for (unsigned i = 0; i < n_cell_arrays; ++i)
        convertArray(*cell_data->GetArray(i),
                     mesh.getProperties(),
                     MeshLib::MeshItemType::Cell);

    vtkFieldData* field_data = grid.GetFieldData();
    auto const n_field_arrays =
        static_cast<unsigned>(field_data->GetNumberOfArrays());
    for (unsigned i = 0; i < n_field_arrays; ++i)
        convertArray(
            *vtkDataArray::SafeDownCast(field_data->GetAbstractArray(i)),
            mesh.getProperties(),
            MeshLib::MeshItemType::IntegrationPoint);
}
Beispiel #22
0
void VtkVisPipelineView::convertVTKToOGSMesh()
{
	VtkVisPipelineItem* item = static_cast<VtkVisPipelineItem*>(
		static_cast<VtkVisPipeline*>(this->model())->getItem(this->selectionModel()->currentIndex()));
	vtkSmartPointer<vtkAlgorithm> algorithm = item->algorithm();


	vtkUnstructuredGrid* grid(NULL);
	vtkUnstructuredGridAlgorithm* ugAlg = vtkUnstructuredGridAlgorithm::SafeDownCast(algorithm);
	if (ugAlg)
		grid = ugAlg->GetOutput();
	else
	{
		// for old filetypes
		vtkGenericDataObjectReader* dataReader = vtkGenericDataObjectReader::SafeDownCast(algorithm);
		if (dataReader)
			grid = vtkUnstructuredGrid::SafeDownCast(dataReader->GetOutput());
		else
		{
			// for new filetypes
			vtkXMLUnstructuredGridReader* xmlReader = vtkXMLUnstructuredGridReader::SafeDownCast(algorithm);
			grid = vtkUnstructuredGrid::SafeDownCast(xmlReader->GetOutput());
		}
	}
	MeshLib::Mesh* mesh = MeshLib::VtkMeshConverter::convertUnstructuredGrid(grid);
	mesh->setName(item->data(0).toString().toStdString());
	emit meshAdded(mesh);
}
Beispiel #23
0
MeshLib::Mesh* MeshSurfaceExtraction::getMeshSurface(
    const MeshLib::Mesh& mesh, const MathLib::Vector3& dir, double angle,
    std::string const& subsfc_node_id_backup_prop_name)
{
	if (angle < 0 || angle > 90)
	{
		ERR ("Supported angle between 0 and 90 degrees only.");
		return nullptr;
	}

	INFO ("Extracting mesh surface...");
	std::vector<MeshLib::Element*> sfc_elements;
	get2DSurfaceElements(mesh.getElements(), sfc_elements, dir, angle, mesh.getDimension());

	if (sfc_elements.empty())
		return nullptr;

	std::vector<MeshLib::Node*> sfc_nodes;
	std::vector<std::size_t> node_id_map(mesh.getNNodes());
	get2DSurfaceNodes(sfc_nodes, mesh.getNNodes(), sfc_elements, node_id_map);

	// create new elements vector with newly created nodes
	std::vector<MeshLib::Element*> new_elements;
	new_elements.reserve(sfc_elements.size());
	for (auto elem = sfc_elements.cbegin(); elem != sfc_elements.cend(); ++elem)
	{
		unsigned const n_elem_nodes ((*elem)->getNBaseNodes());
		MeshLib::Node** new_nodes = new MeshLib::Node*[n_elem_nodes];
		for (unsigned k(0); k<n_elem_nodes; k++)
			new_nodes[k] = sfc_nodes[node_id_map[(*elem)->getNode(k)->getID()]];
		if ((*elem)->getGeomType() == MeshElemType::TRIANGLE)
			new_elements.push_back(new MeshLib::Tri(new_nodes));
		else {
			assert((*elem)->getGeomType() == MeshElemType::QUAD);
			new_elements.push_back(new MeshLib::Quad(new_nodes));
		}
		delete *elem;
	}

	std::vector<std::size_t> id_map;
	if (!subsfc_node_id_backup_prop_name.empty())
	{
		id_map.reserve(sfc_nodes.size());
		for (auto node = sfc_nodes.cbegin(); node != sfc_nodes.cend(); ++node)
			id_map.push_back((*node)->getID());
	}
	MeshLib::Mesh* result (new Mesh(mesh.getName()+"-Surface", sfc_nodes, new_elements));
	// transmit the original node ids of the subsurface mesh as a property
	if (!subsfc_node_id_backup_prop_name.empty()) {
		boost::optional<MeshLib::PropertyVector<std::size_t>&> orig_node_ids(
		    result->getProperties().createNewPropertyVector<std::size_t>(
		        subsfc_node_id_backup_prop_name , MeshLib::MeshItemType::Node, 1));
		if (orig_node_ids) {
			orig_node_ids->resize(id_map.size());
			std::copy(id_map.cbegin(), id_map.cend(), orig_node_ids->begin());
		}
	}
	return result;
}
Beispiel #24
0
 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]);
     }
 }
Beispiel #25
0
void TESProcess::initializeConcreteProcess(
    NumLib::LocalToGlobalIndexMap const& dof_table,
    MeshLib::Mesh const& mesh, unsigned const integration_order)
{
    ProcessLib::createLocalAssemblers<TESLocalAssembler>(
        mesh.getDimension(), mesh.getElements(), dof_table, _local_assemblers,
        mesh.isAxiallySymmetric(), integration_order, _assembly_params);

    initializeSecondaryVariables();
}
Beispiel #26
0
void VtkMeshConverter::convertScalarArrays(vtkUnstructuredGrid &grid, MeshLib::Mesh &mesh)
{
    vtkPointData* point_data = grid.GetPointData();
    unsigned const n_point_arrays = static_cast<unsigned>(point_data->GetNumberOfArrays());
    for (unsigned i=0; i<n_point_arrays; ++i)
        convertArray(*point_data->GetArray(i), mesh.getProperties(), MeshLib::MeshItemType::Node);

    vtkCellData* cell_data = grid.GetCellData();
    unsigned const n_cell_arrays = static_cast<unsigned>(cell_data->GetNumberOfArrays());
    for (unsigned i=0; i<n_cell_arrays; ++i)
        convertArray(*cell_data->GetArray(i), mesh.getProperties(), MeshLib::MeshItemType::Cell);
}
Beispiel #27
0
int main(int argc, char *argv[])
{
	LOGOG_INITIALIZE();
	logog::Cout* logogCout = new logog::Cout;

	TCLAP::CmdLine cmd("Simple mesh loading test", ' ', "0.1");

	// Define a value argument and add it to the command line.
	// A value arg defines a flag and a type of value that it expects,
	// such as "-m meshfile".
	TCLAP::ValueArg<std::string> mesh_arg("m","mesh","input mesh file",true,"homer","string");

	// Add the argument mesh_arg to the CmdLine object. The CmdLine object
	// uses this Arg to parse the command line.
	cmd.add( mesh_arg );

	cmd.parse( argc, argv );

	std::string fname (mesh_arg.getValue());

	FileIO::MeshIO mesh_io;
#ifndef WIN32
	BaseLib::MemWatch mem_watch;
	unsigned long mem_without_mesh (mem_watch.getVirtMemUsage());
#endif
	BaseLib::RunTime run_time;
	run_time.start();
	MeshLib::Mesh* mesh = mesh_io.loadMeshFromFile(fname);
#ifndef WIN32
	unsigned long mem_with_mesh (mem_watch.getVirtMemUsage());
//	std::cout << "mem for mesh: " << (mem_with_mesh - mem_without_mesh)/(1024*1024) << " MB" << std::endl;
	INFO ("mem for mesh: %i MB", (mem_with_mesh - mem_without_mesh)/(1024*1024));
#endif
	run_time.stop();
//	std::cout << "time for reading: " << run_time.elapsed() << " s" << std::endl;
	INFO ("time for reading: %f s", run_time.elapsed());


	unsigned elem_id = 25000;
	const MeshLib::Element* e = mesh->getElement(elem_id);
	const size_t nElems = mesh->getNElements();
	for (unsigned i=0; i< e->getNNeighbors(); i++)
	{
		for (unsigned j=0; j< nElems; j++)
			if (mesh->getElement(j) == e->getNeighbor(i))
				std::cout << "neighbour of element " << elem_id << elem_id << " : " << j << std::endl;
	}

	delete mesh;
	delete logogCout;
	LOGOG_SHUTDOWN();
}
Beispiel #28
0
bool MeshLayerMapper::mapToStaticValue(MeshLib::Mesh &mesh, double value)
{
    if (mesh.getDimension() != 2)
    {
        ERR("MshLayerMapper::mapToStaticValue() - requires 2D mesh");
        return false;
    }

    std::vector<MeshLib::Node*> const& nodes (mesh.getNodes());
    for (MeshLib::Node* node : nodes)
        node->updateCoordinates((*node)[0], (*node)[1], value);
    return true;
}
Beispiel #29
0
// Project to parallels of YZ plane
TEST_F(ProjectionTest, ProjectToYZ)
{
    MathLib::Vector3 normal (1,0,0);
    std::size_t const n_nodes (_mesh->getNumberOfNodes());
    for (std::size_t p=0; p<10; p++)
    {
        MathLib::Point3d origin (std::array<double,3>{{static_cast<double>(p),0,0}});
        MeshLib::Mesh* result = MeshLib::projectMeshOntoPlane(*_mesh, origin, normal);
        for (std::size_t i=0; i<n_nodes; i++)
            ASSERT_NEAR(static_cast<double>(p), (*result->getNode(i))[0], std::numeric_limits<double>::epsilon());
        delete result;
    }
}
Beispiel #30
0
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;
}