MeshLib::Mesh* MshEditor::getMeshSurface(const MeshLib::Mesh &mesh, const double* dir)
{
INFO ("Extracting mesh surface...");
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);
// create new elements vector with newly created nodes
const size_t nNewElements (sfc_elements.size());
std::vector<MeshLib::Element*> new_elements(sfc_elements.size());
for (unsigned i=0; i<nNewElements; ++i)
{
MeshLib::Element* elem (sfc_elements[i]);
if (elem->getType() == MshElemType::TRIANGLE) {
MeshLib::Node** tri_nodes = new MeshLib::Node*[3];
for (unsigned k(0); k<3; k++)
tri_nodes[k] = sfc_nodes[node_id_map[elem->getNode(k)->getID()]];
new_elements[i] = new MeshLib::Tri(tri_nodes);
} else {
MeshLib::Node** quad_nodes = new MeshLib::Node*[4];
for (unsigned k(0); k<3; k++)
quad_nodes[k] = sfc_nodes[node_id_map[elem->getNode(k)->getID()]];
new_elements[i] = new MeshLib::Quad(quad_nodes);
}
delete sfc_elements[i];
}
return new Mesh("SurfaceMesh", sfc_nodes, new_elements);
}
static void checkJacobianDeterminant(const double detJ,
MeshLib::Element const& element)
{
if (detJ > 0) // The usual case
return;
if (detJ < 0)
{
ERR("det J = %g is negative for element %d.", detJ, element.getID());
#ifndef NDEBUG
std::cerr << element << "\n";
#endif // NDEBUG
OGS_FATAL("Please check the node numbering of the element.");
}
if (detJ == 0)
{
ERR("det J is zero for element %d.", element.getID());
#ifndef NDEBUG
std::cerr << element << "\n";
#endif // NDEBUG
OGS_FATAL(
"Please check whether:\n"
"\t the element nodes may have the same coordinates,\n"
"\t or the coordinates of all nodes are not given on the x-axis "
"for a 1D problem or in the xy-plane in the 2D case.");
}
}
bool BoundaryElementsAlongPolyline::includesAllEdgeNodeIDs(const std::vector<std::size_t> &vec_node_ids, const MeshLib::Element &edge, std::vector<std::size_t> &edge_node_distances) const
{
unsigned j=0;
for (; j<edge.getNumberOfBaseNodes(); j++) {
auto itr = std::find(vec_node_ids.begin(), vec_node_ids.end(), edge.getNodeIndex(j));
if (itr != vec_node_ids.end())
edge_node_distances.push_back(std::distance(vec_node_ids.begin(), itr));
else
break;
}
return (j==edge.getNumberOfBaseNodes());
}
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;
}
MeshLib::Mesh* MeshSurfaceExtraction::getMeshBoundary(const MeshLib::Mesh &mesh)
{
if (mesh.getDimension()==1)
return nullptr;
// For 3D meshes return the 2D surface
if (mesh.getDimension()==3)
{
MathLib::Vector3 dir(0,0,0);
return getMeshSurface(mesh, dir, 90);
}
// For 2D meshes return the boundary lines
std::vector<MeshLib::Node*> nodes = MeshLib::copyNodeVector(mesh.getNodes());
std::vector<MeshLib::Element*> boundary_elements;
std::vector<MeshLib::Element*> const& org_elems (mesh.getElements());
for (auto it=org_elems.begin(); it!=org_elems.end(); ++it)
{
MeshLib::Element* elem (*it);
std::size_t const n_edges (elem->getNEdges());
for (std::size_t i=0; i<n_edges; ++i)
if (elem->getNeighbor(i) == nullptr)
{
MeshLib::Element const*const edge (elem->getEdge(i));
boundary_elements.push_back(MeshLib::copyElement(edge, nodes));
delete edge;
}
}
MeshLib::Mesh* result = new MeshLib::Mesh("Boundary Mesh", nodes, boundary_elements);
MeshLib::NodeSearch ns(*result);
if (ns.searchUnused() == 0) {
return result;
} else {
auto removed = MeshLib::removeNodes(*result, ns.getSearchedNodeIDs(), result->getName());
delete result;
return removed;
}
}
void Mesh::setElementsConnectedToNodes()
{
const size_t nElements (_elements.size());
for (unsigned i=0; i<nElements; ++i)
{
MeshLib::Element* element = _elements[i];
const unsigned nNodes (element->getNNodes());
for (unsigned j=0; j<nNodes; ++j)
element->_nodes[j]->addElement(element);
}
#ifndef NDEBUG
// search for nodes that are not part of any element
unsigned count(0);
const size_t nNodes (_nodes.size());
for (unsigned i=0; i<nNodes; ++i)
if (_nodes[i]->getNElements() == 0)
{
WARN ("Node %d is not part of any element.", i);
++count;
}
if (count)
WARN ("%d unused mesh nodes found.", count);
#endif
}
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();
}
bool test(MeshLib::Element const& element)
{
using ShapeMatricesType = ShapeMatrixPolicyType<ShapeFunction, GlobalDim>;
using FemType =
NumLib::TemplateIsoparametric<ShapeFunction, ShapeMatricesType>;
// Test if the cast is possible.
bool const dynamic_cast_failed =
dynamic_cast<typename ShapeFunction::MeshElement const*>(&element) ==
nullptr;
EXPECT_FALSE(dynamic_cast_failed);
if (dynamic_cast_failed)
{
return false;
}
FemType fe{
static_cast<typename ShapeFunction::MeshElement const&>(element)};
bool result = true;
// For each node evaluate the shape functions at natural coordinates and
// test if only the corresponding shape function has value 1 and all others
// must return 0.
int const number_nodes = element.getNumberOfNodes();
for (int n = 0; n < number_nodes; ++n)
{
// Evaluate shape matrices at natural coordinates.
typename ShapeMatricesType::ShapeMatrices shape_matrices{
ShapeFunction::DIM, GlobalDim, ShapeFunction::NPOINTS};
// Compute only N, because for pyramid the detJ becomes zero at the
// apex, and we only use N in the following test anyway.
fe.template computeShapeFunctions<NumLib::ShapeMatrixType::N>(
NumLib::NaturalCoordinates<
typename ShapeFunction::MeshElement>::coordinates[n]
.data(),
shape_matrices, GlobalDim, false /* axial symmetry */);
auto const& N = shape_matrices.N;
for (int p = 0; p < static_cast<int>(ShapeFunction::NPOINTS); ++p)
{
if (p == n)
{
if (N[p] != 1)
{
EXPECT_EQ(1, N[p]) << "for n = " << n << ", p = " << p
<< " and dimension " << GlobalDim;
result = false;
}
}
else
{
if (N[p] != 0)
{
EXPECT_EQ(0, N[p]) << "for n = " << n << ", p = " << p
<< " and dimension " << GlobalDim;
result = false;
}
}
}
}
return result;
}
void MeshLayerMapper::addLayerToMesh(const MeshLib::Mesh &dem_mesh, unsigned layer_id, GeoLib::Raster const& raster)
{
const unsigned pyramid_base[3][4] =
{
{1, 3, 4, 2}, // Point 4 missing
{2, 4, 3, 0}, // Point 5 missing
{0, 3, 4, 1}, // Point 6 missing
};
std::size_t const nNodes = dem_mesh.getNumberOfNodes();
std::vector<MeshLib::Node*> const& nodes = dem_mesh.getNodes();
int const last_layer_node_offset = layer_id * nNodes;
// add nodes for new layer
for (std::size_t i=0; i<nNodes; ++i)
_nodes.push_back(getNewLayerNode(*nodes[i], *_nodes[last_layer_node_offset + i], raster, _nodes.size()));
std::vector<MeshLib::Element*> const& elems = dem_mesh.getElements();
std::size_t const nElems (dem_mesh.getNumberOfElements());
for (std::size_t i=0; i<nElems; ++i)
{
MeshLib::Element* elem (elems[i]);
if (elem->getGeomType() != MeshLib::MeshElemType::TRIANGLE)
continue;
unsigned node_counter(3), missing_idx(0);
std::array<MeshLib::Node*, 6> new_elem_nodes;
for (unsigned j=0; j<3; ++j)
{
new_elem_nodes[j] = _nodes[_nodes[last_layer_node_offset + elem->getNodeIndex(j)]->getID()];
new_elem_nodes[node_counter] = (_nodes[last_layer_node_offset + elem->getNodeIndex(j) + nNodes]);
if (new_elem_nodes[j]->getID() != new_elem_nodes[node_counter]->getID())
node_counter++;
else
missing_idx = j;
}
switch (node_counter)
{
case 6:
_elements.push_back(new MeshLib::Prism(new_elem_nodes));
_materials.push_back(layer_id);
break;
case 5:
std::array<MeshLib::Node*, 5> pyramid_nodes;
pyramid_nodes[0] = new_elem_nodes[pyramid_base[missing_idx][0]];
pyramid_nodes[1] = new_elem_nodes[pyramid_base[missing_idx][1]];
pyramid_nodes[2] = new_elem_nodes[pyramid_base[missing_idx][2]];
pyramid_nodes[3] = new_elem_nodes[pyramid_base[missing_idx][3]];
pyramid_nodes[4] = new_elem_nodes[missing_idx];
_elements.push_back(new MeshLib::Pyramid(pyramid_nodes));
_materials.push_back(layer_id);
break;
case 4:
std::array<MeshLib::Node*, 4> tet_nodes;
std::copy(new_elem_nodes.begin(), new_elem_nodes.begin() + node_counter, tet_nodes.begin());
_elements.push_back(new MeshLib::Tet(tet_nodes));
_materials.push_back(layer_id);
break;
default:
continue;
}
}
}
