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));
}
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;
}
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;
}
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));
}
}
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 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::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));
}
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;
}
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());
}
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);
}
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);
}
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;
}
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;
}
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;
}
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;
}
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));
}
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;
}
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());
}
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());
}
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();
}