Exemple #1
0
void HTProcess::initializeConcreteProcess(
    NumLib::LocalToGlobalIndexMap const& dof_table,
    MeshLib::Mesh const& mesh,
    unsigned const integration_order)
{
    // For the staggered scheme, both processes are assumed to use the same
    // element order. Therefore the order of shape function can be fetched from
    // any set of the sets of process variables of the coupled processes. Here,
    // we take the one from the first process by setting process_id = 0.
    const int process_id = 0;
    ProcessLib::ProcessVariable const& pv = getProcessVariables(process_id)[0];

    if (_use_monolithic_scheme)
    {
        ProcessLib::createLocalAssemblers<MonolithicHTFEM>(
            mesh.getDimension(), mesh.getElements(), dof_table,
            pv.getShapeFunctionOrder(), _local_assemblers,
            mesh.isAxiallySymmetric(), integration_order,
            *_material_properties);
    }
    else
    {
        ProcessLib::createLocalAssemblers<StaggeredHTFEM>(
            mesh.getDimension(), mesh.getElements(), dof_table,
            pv.getShapeFunctionOrder(), _local_assemblers,
            mesh.isAxiallySymmetric(), integration_order, *_material_properties,
            _heat_transport_process_id, _hydraulic_process_id);
    }

    _secondary_variables.addSecondaryVariable(
        "darcy_velocity",
        makeExtrapolator(mesh.getDimension(), getExtrapolator(),
                         _local_assemblers,
                         &HTLocalAssemblerInterface::getIntPtDarcyVelocity));
}
Exemple #2
0
int main (int argc, char* argv[])
{
	LOGOG_INITIALIZE();
	logog::Cout* logogCout = new logog::Cout;
	BaseLib::LogogSimpleFormatter* formatter = new BaseLib::LogogSimpleFormatter;
	logogCout->SetFormatter(*formatter);

	TCLAP::CmdLine cmd("Reordering of mesh nodes to make OGS Data Explorer 5 meshes compatible with OGS6.\n" \
	                   "Method 1 is the re-ordering between DataExplorer 5 and DataExplorer 6 meshes,\n" \
	                   "Method 2 is the re-ordering with and without InSitu-Lib in OGS6.",
	                   ' ', "0.1");
	TCLAP::UnlabeledValueArg<std::string> input_mesh_arg("input_mesh",
	                                                     "the name of the input mesh file",
	                                                     true, "", "oldmesh.msh");
	cmd.add(input_mesh_arg);
	TCLAP::UnlabeledValueArg<std::string> output_mesh_arg("output_mesh",
	                                                      "the name of the output mesh file",
	                                                      true, "", "newmesh.vtu");
	cmd.add(output_mesh_arg);
	TCLAP::ValueArg<int> method_arg("m", "method", "reordering method selection", false,  1, "value");

	cmd.add(method_arg);
	cmd.parse(argc, argv);

	MeshLib::Mesh* mesh (FileIO::readMeshFromFile(input_mesh_arg.getValue().c_str()));

	INFO("Reordering nodes... ");
	if (!method_arg.isSet() || method_arg.getValue() == 1)
		reorderNodes(const_cast<std::vector<MeshLib::Element*>&>(mesh->getElements()));
	else if (method_arg.getValue() == 2)
		reorderNodes2(const_cast<std::vector<MeshLib::Element*>&>(mesh->getElements()));
	else
	{
		ERR ("Unknown re-ordering method. Exit program...");
		return 1;
	}

	FileIO::VtuInterface writer(mesh);
	writer.writeToFile(output_mesh_arg.getValue().c_str());

	INFO("VTU file written.");

	delete formatter;
	delete logogCout;
	LOGOG_SHUTDOWN();

	return 0;
}
Exemple #3
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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;
}
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);
}
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;
}
Exemple #6
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));
    }
}
Exemple #7
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));
					}
				}
	}
}
Exemple #8
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));
		}
	}
}
Exemple #9
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;
}
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));
}
Exemple #12
0
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;
}
Exemple #13
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();
}
const std::pair<unsigned, unsigned> MeshInformation::getValueBounds(const MeshLib::Mesh &mesh)
{
	const std::vector<MeshLib::Element*> &elements (mesh.getElements());
	const auto minmax = std::minmax_element(elements.cbegin(), elements.cend(),
        [](MeshLib::Element const*const a, MeshLib::Element const*const b)
            {
                return a->getValue() < b->getValue();
        });
	return std::make_pair<unsigned, unsigned>((*minmax.first)->getValue(), (*minmax.second)->getValue());
}
Exemple #15
0
VolumetricSourceTerm::VolumetricSourceTerm(
    MeshLib::Mesh const& source_term_mesh,
    std::unique_ptr<NumLib::LocalToGlobalIndexMap> source_term_dof_table,
    unsigned const integration_order, unsigned const shapefunction_order,
    Parameter<double> const& volumetric_source_term)
    : SourceTerm(std::move(source_term_dof_table)),
      _volumetric_source_term(volumetric_source_term)
{
    ProcessLib::createLocalAssemblers<VolumetricSourceTermLocalAssembler>(
        source_term_mesh.getDimension(), source_term_mesh.getElements(),
        *_source_term_dof_table, shapefunction_order, _local_assemblers,
        source_term_mesh.isAxiallySymmetric(), integration_order,
        _volumetric_source_term);
}
Exemple #16
0
SurfaceFlux::SurfaceFlux(
    MeshLib::Mesh& boundary_mesh,
    std::size_t bulk_property_number_of_components,
    unsigned const integration_order)
{
    DBUG("Create local balance assemblers.");
    // Populate the vector of local assemblers.
    _local_assemblers.resize(boundary_mesh.getElements().size());

    // needed to create dof table
    auto mesh_subset_all_nodes = std::make_unique<MeshLib::MeshSubset>(
        boundary_mesh, boundary_mesh.getNodes());

    // Collect the mesh subsets in a vector.
    std::vector<MeshLib::MeshSubset> all_mesh_subsets;
    std::generate_n(std::back_inserter(all_mesh_subsets),
                    bulk_property_number_of_components,
                    [&]() { return *mesh_subset_all_nodes; });

    // needed for creation of local assemblers
    auto dof_table = std::make_unique<NumLib::LocalToGlobalIndexMap const>(
        std::move(all_mesh_subsets), NumLib::ComponentOrder::BY_LOCATION);

    auto const bulk_element_ids =
        boundary_mesh.getProperties().template getPropertyVector<std::size_t>(
            "bulk_element_ids", MeshLib::MeshItemType::Cell, 1);
    auto const bulk_face_ids =
        boundary_mesh.getProperties().template getPropertyVector<std::size_t>(
            "bulk_face_ids", MeshLib::MeshItemType::Cell, 1);

    ProcessLib::createLocalAssemblers<SurfaceFluxLocalAssembler>(
        boundary_mesh.getDimension() + 1,  // or bulk_mesh.getDimension()?
        boundary_mesh.getElements(), *dof_table, 1, _local_assemblers,
        boundary_mesh.isAxiallySymmetric(), integration_order,
        *bulk_element_ids, *bulk_face_ids);
}
Exemple #17
0
void
detectHoles(MeshLib::Mesh const& mesh,
	std::vector<std::size_t> erase_elems,
	std::size_t const expected_n_holes)
{
	std::vector<MeshLib::Node*> nodes = MeshLib::copyNodeVector(mesh.getNodes());
	std::vector<MeshLib::Element*> elems = MeshLib::copyElementVector(mesh.getElements(),nodes);
	for (auto pos : erase_elems)
	{
		delete elems[pos];
		elems.erase(elems.begin()+pos);
	}
	MeshLib::Mesh mesh2("mesh2", nodes, elems);
	ASSERT_EQ(expected_n_holes, MeshLib::MeshValidation::detectHoles(mesh2));
};
const std::array<unsigned, 7> MeshInformation::getNumberOfElementTypes(const MeshLib::Mesh &mesh)
{
	std::array<unsigned, 7> n_element_types = {{0, 0, 0, 0, 0, 0, 0}};
	const std::vector<MeshLib::Element*> &elements (mesh.getElements());
	for (auto it = elements.begin(); it != elements.end(); ++it)
	{
		MeshElemType t = (*it)->getGeomType();
		if (t == MeshElemType::LINE) n_element_types[0]++;
		if (t == MeshElemType::TRIANGLE) n_element_types[1]++;
		if (t == MeshElemType::QUAD) n_element_types[2]++;
		if (t == MeshElemType::TETRAHEDRON) n_element_types[3]++;
		if (t == MeshElemType::HEXAHEDRON) n_element_types[4]++;
		if (t == MeshElemType::PYRAMID) n_element_types[5]++;
		if (t == MeshElemType::PRISM) n_element_types[6]++;
	}
	return n_element_types;
}
Exemple #19
0
bool LayeredVolume::createRasterLayers(const MeshLib::Mesh &mesh,
                                       const std::vector<GeoLib::Raster const*> &rasters,
                                       double minimum_thickness,
                                       double noDataReplacementValue)
{
	if (mesh.getDimension() != 2)
		return false;

	_elevation_epsilon = calcEpsilon(*rasters[0], *rasters.back());
	if (_elevation_epsilon <= 0)
		return false;

	// remove line elements, only tri + quad remain
	MeshLib::ElementSearch ex(mesh);
	ex.searchByElementType(MeshLib::MeshElemType::LINE);
	MeshLib::Mesh* top (removeElements(mesh, ex.getSearchedElementIDs(), "MeshLayer"));
	if (top==nullptr)
		top = new MeshLib::Mesh(mesh);

	if (!MeshLib::MeshLayerMapper::layerMapping(*top, *rasters.back(), noDataReplacementValue))
		return false;

	MeshLib::Mesh* bottom (new MeshLib::Mesh(*top));
	if (!MeshLib::MeshLayerMapper::layerMapping(*bottom, *rasters[0], 0))
	{
		delete top;
		return false;
	}

	this->_minimum_thickness = minimum_thickness;
	_nodes = MeshLib::copyNodeVector(bottom->getNodes());
	_elements = MeshLib::copyElementVector(bottom->getElements(), _nodes);
	delete bottom;

	// map each layer and attach to subsurface mesh
	const std::size_t nRasters (rasters.size());
	for (std::size_t i=1; i<nRasters; ++i)
		this->addLayerToMesh(*top, i, *rasters[i]);

	// close boundaries between layers
	this->addLayerBoundaries(*top, nRasters);
	this->removeCongruentElements(nRasters, top->getNElements());
	delete top;
	return true;
}
Exemple #20
0
std::vector<ElementErrorCode> MeshValidation::testElementGeometry(const MeshLib::Mesh &mesh, double min_volume)
{
    INFO ("Testing mesh element geometry:");
    const std::size_t nErrorCodes (static_cast<std::size_t>(ElementErrorFlag::MaxValue));
    unsigned error_count[nErrorCodes];
    std::fill_n(error_count, 4, 0);
    const std::size_t nElements (mesh.getNElements());
    const std::vector<MeshLib::Element*> &elements (mesh.getElements());
    std::vector<ElementErrorCode> error_code_vector;
    error_code_vector.reserve(nElements);

    for (std::size_t i=0; i<nElements; ++i)
    {
        const ElementErrorCode e = elements[i]->validate();
        error_code_vector.push_back(e);
        if (e.none())
            continue;

        // increment error statistics
        const std::bitset< static_cast<std::size_t>(ElementErrorFlag::MaxValue) > flags (static_cast< std::bitset<static_cast<std::size_t>(ElementErrorFlag::MaxValue)> >(e));
        for (unsigned j=0; j<nErrorCodes; ++j)
            error_count[j] += flags[j];
    }

    // if a larger volume threshold is given, evaluate elements again to add them even if they are formally okay
    if (min_volume > std::numeric_limits<double>::epsilon())
        for (std::size_t i=0; i<nElements; ++i)
            if (elements[i]->getContent() < min_volume)
                error_code_vector[i].set(ElementErrorFlag::ZeroVolume);

    // output
    const unsigned error_sum (static_cast<unsigned>(std::accumulate(error_count, error_count+nErrorCodes, 0.0)));
    if (error_sum != 0)
    {
        ElementErrorFlag flags[nErrorCodes] = { ElementErrorFlag::ZeroVolume, ElementErrorFlag::NonCoplanar,
                                                ElementErrorFlag::NonConvex,  ElementErrorFlag::NodeOrder };
        for (std::size_t i=0; i<nErrorCodes; ++i)
            if (error_count[i])
                INFO ("%d elements found with %s.", error_count[i], ElementErrorCode::toString(flags[i]).c_str());
    }
    else
        INFO ("No errors found.");
    return error_code_vector;
}
std::size_t ElementValueModification::setByElementType(MeshLib::Mesh &mesh, MeshElemType ele_type, int const new_value)
{
    auto* const property_value_vector =
        mesh.getProperties().getPropertyVector<int>("MaterialIDs");

    if (!property_value_vector)
    {
        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;
}
Exemple #22
0
    ExtrapolationTestProcess(MeshLib::Mesh const& mesh,
                             unsigned const integration_order)
        : _integration_order(integration_order),
          _mesh_subset_all_nodes(mesh, mesh.getNodes())
    {
        std::vector<MeshLib::MeshSubset> all_mesh_subsets{
            _mesh_subset_all_nodes};

        _dof_table = std::make_unique<NumLib::LocalToGlobalIndexMap>(
            std::move(all_mesh_subsets), NumLib::ComponentOrder::BY_COMPONENT);

        // Passing _dof_table works, because this process has only one variable
        // and the variable has exactly one component.
        _extrapolator =
            std::make_unique<ExtrapolatorImplementation>(*_dof_table);

        // createAssemblers(mesh);
        ProcessLib::createLocalAssemblers<LocalAssemblerData>(
            mesh.getDimension(), mesh.getElements(), *_dof_table, 1,
            _local_assemblers, mesh.isAxiallySymmetric(), _integration_order);
    }
std::vector<GeoLib::Point*> MeshSurfaceExtraction::getSurfaceNodes(const MeshLib::Mesh &mesh, const MathLib::Vector3 &dir, double angle)
{
	INFO ("Extracting surface nodes...");
	std::vector<MeshLib::Element*> sfc_elements;
	get2DSurfaceElements(mesh.getElements(), sfc_elements, dir, angle, mesh.getDimension());

	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);

	for (auto e : sfc_elements)
		delete e;

	const std::size_t nNodes (sfc_nodes.size());
	std::vector<GeoLib::Point*> surface_pnts(nNodes);
	for (std::size_t i=0; i<nNodes; ++i)
	{
		surface_pnts[i] = new GeoLib::Point(*(sfc_nodes[i]), sfc_nodes[i]->getID());
		delete sfc_nodes[i];
	}
	return surface_pnts;
}
Exemple #24
0
void PhaseFieldProcess<DisplacementDim>::initializeConcreteProcess(
    NumLib::LocalToGlobalIndexMap const& dof_table,
    MeshLib::Mesh const& mesh,
    unsigned const integration_order)
{
    ProcessLib::SmallDeformation::createLocalAssemblers<
        DisplacementDim, PhaseFieldLocalAssembler>(
        mesh.getElements(), dof_table, _local_assemblers,
        mesh.isAxiallySymmetric(), integration_order, _process_data);

    _secondary_variables.addSecondaryVariable(
        "sigma",
        makeExtrapolator(MathLib::KelvinVector::KelvinVectorType<
                             DisplacementDim>::RowsAtCompileTime,
                         getExtrapolator(), _local_assemblers,
                         &LocalAssemblerInterface::getIntPtSigma));

    _secondary_variables.addSecondaryVariable(
        "epsilon",
        makeExtrapolator(MathLib::KelvinVector::KelvinVectorType<
                             DisplacementDim>::RowsAtCompileTime,
                         getExtrapolator(), _local_assemblers,
                         &LocalAssemblerInterface::getIntPtEpsilon));
}
Exemple #25
0
TEST(MeshLib, Duplicate)
{
	MeshLib::Mesh* mesh (MeshLib::MeshGenerator::generateRegularQuadMesh(10, 5, 1));

	std::vector<MeshLib::Node*> new_nodes (MeshLib::copyNodeVector(mesh->getNodes()));
	std::vector<MeshLib::Element*> new_elements (MeshLib::copyElementVector(mesh->getElements(), new_nodes));

	MeshLib::Mesh new_mesh ("new", new_nodes, new_elements);

	ASSERT_EQ (mesh->getNElements(), new_mesh.getNElements());
	ASSERT_EQ (mesh->getNNodes(), new_mesh.getNNodes());

	std::vector<std::size_t> del_idx(1,1);
	MeshLib::removeMeshNodes(*mesh, del_idx);

	ASSERT_EQ (mesh->getNElements(), new_mesh.getNElements()-2);
	ASSERT_EQ (mesh->getNNodes(), new_mesh.getNNodes()-2);

	ASSERT_DOUBLE_EQ (4.0, MathLib::sqrDist(*mesh->getNode(0), *new_mesh.getNode(0)));
	ASSERT_DOUBLE_EQ (0.0, MathLib::sqrDist(*mesh->getNode(0), *new_mesh.getNode(2)));

	ASSERT_DOUBLE_EQ (4.0, MathLib::sqrDist(*mesh->getElement(0)->getNode(0), *new_mesh.getElement(0)->getNode(0)));
	ASSERT_DOUBLE_EQ (0.0, MathLib::sqrDist(*mesh->getElement(0)->getNode(0), *new_mesh.getElement(2)->getNode(0)));
}
std::unique_ptr<MeshLib::Mesh> convertToLinearMesh(MeshLib::Mesh const& org_mesh, std::string const& new_mesh_name)
{
    std::vector<MeshLib::Node*> vec_new_nodes = MeshLib::copyNodeVector(MeshLib::getBaseNodes(org_mesh.getElements()));

    // create new elements with the quadratic nodes
    std::vector<MeshLib::Element*> vec_new_eles;
    for (MeshLib::Element const* e : org_mesh.getElements())
    {
        if (e->getCellType() == MeshLib::CellType::LINE3)
        {
            vec_new_eles.push_back(createLinearElement<MeshLib::Line>(
                e, vec_new_nodes));
        }
        else if (e->getCellType() == MeshLib::CellType::QUAD8)
        {
            vec_new_eles.push_back(createLinearElement<MeshLib::Quad>(
                e, vec_new_nodes));
        }
        else if (e->getCellType() == MeshLib::CellType::TRI6)
        {
            vec_new_eles.push_back(createLinearElement<MeshLib::Tri>(
                e, vec_new_nodes));
        }
        else if (e->getCellType() == MeshLib::CellType::HEX20)
        {
            vec_new_eles.push_back(createLinearElement<MeshLib::Hex>(
                e, vec_new_nodes));
        }
        else if (e->getCellType() == MeshLib::CellType::TET10)
        {
            vec_new_eles.push_back(createLinearElement<MeshLib::Tet>(
                e, vec_new_nodes));
        }
        else
        {
            OGS_FATAL("Mesh element type %s is not supported", MeshLib::CellType2String(e->getCellType()).c_str());
        }
    }

    auto new_mesh = std::make_unique<MeshLib::Mesh>(
        new_mesh_name, vec_new_nodes, vec_new_eles,
        org_mesh.getProperties().excludeCopyProperties(
            std::vector<MeshLib::MeshItemType>(1,
                                               MeshLib::MeshItemType::Node)));

    // copy property vectors for nodes
    MeshLib::Properties const& src_properties = org_mesh.getProperties();
    for (auto name : src_properties.getPropertyVectorNames())
    {
        if (!src_properties.existsPropertyVector<double>(name))
        {
            continue;
        }
        auto const* src_prop = src_properties.getPropertyVector<double>(name);
        if (src_prop->getMeshItemType() != MeshLib::MeshItemType::Node)
        {
            continue;
        }

        auto const n_src_comp = src_prop->getNumberOfComponents();
        auto new_prop =
            new_mesh->getProperties().createNewPropertyVector<double>(
                name, MeshLib::MeshItemType::Node, n_src_comp);
        new_prop->resize(new_mesh->getNumberOfNodes() * n_src_comp);

        // copy only base node values
        for (unsigned i=0; i<org_mesh.getNumberOfBaseNodes(); i++)
        {
            for (int j = 0; j < n_src_comp; j++)
            {
                (*new_prop)[i * n_src_comp + j] =
                    (*src_prop)[i * n_src_comp + j];
            }
        }
    }

    return new_mesh;
}
std::unique_ptr<MeshLib::Mesh> appendLinesAlongPolylines(
    const MeshLib::Mesh& mesh, const GeoLib::PolylineVec& ply_vec)
{
    // copy existing nodes and elements
    std::vector<MeshLib::Node*> vec_new_nodes = MeshLib::copyNodeVector(mesh.getNodes());
    std::vector<MeshLib::Element*> vec_new_eles = MeshLib::copyElementVector(mesh.getElements(), vec_new_nodes);

    auto const material_ids = materialIDs(mesh);
    int const max_matID =
        material_ids
            ? *(std::max_element(begin(*material_ids), end(*material_ids)))
            : 0;

    std::vector<int> new_mat_ids;
    const std::size_t n_ply (ply_vec.size());
    // for each polyline
    for (std::size_t k(0); k < n_ply; k++)
    {
        const GeoLib::Polyline* ply = (*ply_vec.getVector())[k];

        // search nodes on the polyline
        MeshGeoToolsLib::MeshNodesAlongPolyline mshNodesAlongPoly(
            mesh, *ply, mesh.getMinEdgeLength() * 0.5,
            MeshGeoToolsLib::SearchAllNodes::Yes);
        auto &vec_nodes_on_ply = mshNodesAlongPoly.getNodeIDs();
        if (vec_nodes_on_ply.empty()) {
            std::string ply_name;
            ply_vec.getNameOfElementByID(k, ply_name);
            INFO("No nodes found on polyline %s", ply_name.c_str());
            continue;
        }

        // add line elements
        for (std::size_t i=0; i<vec_nodes_on_ply.size()-1; i++) {
            std::array<MeshLib::Node*, 2> element_nodes;
            element_nodes[0] = vec_new_nodes[vec_nodes_on_ply[i]];
            element_nodes[1] = vec_new_nodes[vec_nodes_on_ply[i+1]];
            vec_new_eles.push_back(
                new MeshLib::Line(element_nodes, vec_new_eles.size()));
            new_mat_ids.push_back(max_matID+k+1);
        }
    }

    // generate a mesh
    const std::string name = mesh.getName() + "_with_lines";
    auto new_mesh =
        std::make_unique<MeshLib::Mesh>(name, vec_new_nodes, vec_new_eles);
    auto new_material_ids =
        new_mesh->getProperties().createNewPropertyVector<int>(
            "MaterialIDs", MeshLib::MeshItemType::Cell);
    if (!new_material_ids)
    {
        OGS_FATAL("Could not create MaterialIDs cell vector in new mesh.");
    }
    new_material_ids->reserve(new_mesh->getNumberOfElements());
    if (material_ids != nullptr)
    {
        std::copy(begin(*material_ids), end(*material_ids),
                  std::back_inserter(*new_material_ids));
    }
    else
    {
        new_material_ids->resize(mesh.getNumberOfElements());
    }
    std::copy(begin(new_mat_ids), end(new_mat_ids),
              std::back_inserter(*new_material_ids));
    return new_mesh;
}
Exemple #28
0
void getFractureMatrixDataInMesh(
        MeshLib::Mesh const& mesh,
        std::vector<MeshLib::Element*>& vec_matrix_elements,
        std::vector<MeshLib::Element*>& vec_fracture_elements,
        std::vector<MeshLib::Element*>& vec_fracture_matrix_elements,
        std::vector<MeshLib::Node*>& vec_fracture_nodes
        )
{
    IsCrackTip isCrackTip(mesh);

    // get vectors of matrix elements and fracture elements
    vec_matrix_elements.reserve(mesh.getNumberOfElements());
    for (MeshLib::Element* e : mesh.getElements())
    {
        if (e->getDimension() == mesh.getDimension())
            vec_matrix_elements.push_back(e);
        else
            vec_fracture_elements.push_back(e);
    }
    DBUG("-> found total %d matrix elements and %d fracture elements",
         vec_matrix_elements.size(), vec_fracture_elements.size());

    // get a vector of fracture nodes
    for (MeshLib::Element* e : vec_fracture_elements)
    {
        for (unsigned i=0; i<e->getNumberOfNodes(); i++)
        {
            if (isCrackTip(*e->getNode(i)))
                continue;
            vec_fracture_nodes.push_back(const_cast<MeshLib::Node*>(e->getNode(i)));
        }
    }
    std::sort(vec_fracture_nodes.begin(), vec_fracture_nodes.end(),
        [](MeshLib::Node* node1, MeshLib::Node* node2) { return (node1->getID() < node2->getID()); }
        );
    vec_fracture_nodes.erase(
                std::unique(vec_fracture_nodes.begin(), vec_fracture_nodes.end()),
                vec_fracture_nodes.end());
    DBUG("-> found %d nodes on the fracture", vec_fracture_nodes.size());

    // create a vector fracture elements and connected matrix elements,
    // which are passed to a DoF table
    // first, collect matrix elements
    for (MeshLib::Element *e : vec_fracture_elements)
    {
        for (unsigned i=0; i<e->getNumberOfBaseNodes(); i++)
        {
            MeshLib::Node const* node = e->getNode(i);
            if (isCrackTip(*node))
                continue;
            for (unsigned j=0; j<node->getNumberOfElements(); j++)
            {
                // only matrix elements
                if (node->getElement(j)->getDimension() == mesh.getDimension()-1)
                    continue;
                vec_fracture_matrix_elements.push_back(const_cast<MeshLib::Element*>(node->getElement(j)));
            }
        }
    }
    std::sort(vec_fracture_matrix_elements.begin(), vec_fracture_matrix_elements.end(),
        [](MeshLib::Element* p1, MeshLib::Element* p2) { return (p1->getID() < p2->getID()); }
        );
    vec_fracture_matrix_elements.erase(
                std::unique(vec_fracture_matrix_elements.begin(), vec_fracture_matrix_elements.end()),
                vec_fracture_matrix_elements.end());

    // second, append fracture elements
    vec_fracture_matrix_elements.insert(
                vec_fracture_matrix_elements.end(),
                vec_fracture_elements.begin(), vec_fracture_elements.end());
}
Exemple #29
0
TEST(MeshLib, ElementStatus)
{
	const unsigned width (100);
	const unsigned elements_per_side (20);
	MeshLib::Mesh* mesh (MeshLib::MeshGenerator::generateRegularQuadMesh(width, elements_per_side));
	MeshLib::ElementStatus status(mesh);
	const std::vector<MeshLib::Element*> elements (mesh->getElements());

	for (unsigned i=0; i<elements_per_side; ++i)
	{
		for (unsigned j=0; j<elements_per_side; ++j)
			elements[i*elements_per_side + j]->setValue(i);
	}

	// all elements active
	ASSERT_EQ (elements.size(), status.getNActiveElements());
	// all nodes active
	ASSERT_EQ (mesh->getNNodes(), status.getNActiveNodes());

	// set material 1 to false
	status.setMaterialStatus(1, false);
	ASSERT_EQ (elements.size()-elements_per_side, status.getNActiveElements());

	// set material 1 to false (again)
	status.setMaterialStatus(1, false);
	ASSERT_EQ (elements.size()-elements_per_side, status.getNActiveElements());

	// set material 0 to false
	status.setMaterialStatus(0, false);
	ASSERT_EQ (elements.size()-(2*elements_per_side), status.getNActiveElements());

	// active elements
	std::vector<std::size_t> active_elements (status.getActiveElements());
	ASSERT_EQ (active_elements.size(), status.getNActiveElements());

	// active nodes
	std::vector<std::size_t> active_nodes (status.getActiveNodes());
	ASSERT_EQ (active_nodes.size(), status.getNActiveNodes());

	// set element 1 to false (yet again)
	status.setElementStatus(1, false);
	status.getElementStatus(1);
	ASSERT_EQ (elements.size()-(2*elements_per_side), status.getNActiveElements());
	ASSERT_EQ (mesh->getNNodes()-(2*(elements_per_side+1)), status.getNActiveNodes());

	// set element 1 to true
	status.setElementStatus(1, true);
	ASSERT_EQ (elements.size()-(2*elements_per_side)+1, status.getNActiveElements());
	ASSERT_EQ (mesh->getNNodes()-(2*(elements_per_side+1))+4, status.getNActiveNodes());
	ASSERT_EQ(status.getElementStatus(1), true);

	std::vector<std::size_t> active_elements_at_node (status.getActiveElementsAtNode(2));
	ASSERT_EQ(1u, active_elements_at_node.size());
	active_elements_at_node = status.getActiveElementsAtNode(22);
	ASSERT_EQ(1u, active_elements_at_node.size());
	active_elements_at_node = status.getActiveElementsAtNode(44);
	ASSERT_EQ(2u, active_elements_at_node.size());
	active_elements_at_node = status.getActiveElementsAtNode(102);
	ASSERT_EQ(4u, active_elements_at_node.size());

	status.setAll(true);
	ASSERT_EQ(elements.size(), status.getNActiveElements());
	ASSERT_EQ(mesh->getNNodes(), status.getNActiveNodes());

	status.setAll(false);
	ASSERT_EQ(0u, status.getNActiveElements());
	ASSERT_EQ(0u, status.getNActiveNodes());
}
Exemple #30
0
PostProcessTool::PostProcessTool(
    MeshLib::Mesh const& org_mesh,
    std::vector<MeshLib::Node*> const& vec_fracture_nodes,
    std::vector<MeshLib::Element*> const& vec_fracutre_matrix_elements)
    :_org_mesh(org_mesh)
{
    if (!org_mesh.getProperties().hasPropertyVector("displacement")
        || !org_mesh.getProperties().hasPropertyVector("displacement_jump1")
        || !org_mesh.getProperties().hasPropertyVector("levelset1")
        )
    {
        OGS_FATAL("The given mesh does not have relevant properties");
    }

    // clone nodes and elements
    std::vector<MeshLib::Node*> new_nodes(MeshLib::copyNodeVector(org_mesh.getNodes()));
    std::vector<MeshLib::Element*> new_eles(
        MeshLib::copyElementVector(org_mesh.getElements(), new_nodes));

    // duplicate fracture nodes
    for (auto const* org_node : vec_fracture_nodes)
    {
        auto duplicated_node = new MeshLib::Node(org_node->getCoords(), new_nodes.size());
        new_nodes.push_back(duplicated_node);
        _map_dup_newNodeIDs[org_node->getID()] = duplicated_node->getID();
    }

    // split elements using the new duplicated nodes
    auto prop_levelset = org_mesh.getProperties().getPropertyVector<double>("levelset1");
    for (auto const* org_e : vec_fracutre_matrix_elements)
    {
        // only matrix elements
        if (org_e->getDimension() != org_mesh.getDimension())
            continue;

        auto const eid = org_e->getID();

        // keep original if the element has levelset=0
        if ((*prop_levelset)[eid] == 0)
            continue;

        // replace fracture nodes with duplicated ones
        MeshLib::Element* e = new_eles[eid];
        for (unsigned i=0; i<e->getNumberOfNodes(); i++)
        {
            // only fracture nodes
            auto itr = _map_dup_newNodeIDs.find(e->getNodeIndex(i));
            if (itr == _map_dup_newNodeIDs.end())
                continue;

            // check if a node belongs to the particular fracture group
            auto itr2 = std::find_if(vec_fracture_nodes.begin(), vec_fracture_nodes.end(),
                                     [&](MeshLib::Node const*node) { return node->getID()==e->getNodeIndex(i);});
            if (itr2 == vec_fracture_nodes.end())
                continue;

            e->setNode(i, new_nodes[itr->second]);
        }
    }

    // new mesh
    _output_mesh.reset(new MeshLib::Mesh(org_mesh.getName(), new_nodes, new_eles));
    createProperties<int>();
    createProperties<double>();
    copyProperties<int>();
    copyProperties<double>();
    calculateTotalDisplacement();
}