GlobalSparsityPattern computeSparsityPatternNonPETSc(
NumLib::LocalToGlobalIndexMap const& dof_table, MeshLib::Mesh const& mesh)
{
MeshLib::NodeAdjacencyTable node_adjacency_table;
node_adjacency_table.createTable(mesh.getNodes());
// A mapping mesh node id -> global indices
// It acts as a cache for dof table queries.
std::vector<std::vector<GlobalIndexType>> global_idcs;
global_idcs.reserve(mesh.getNumberOfNodes());
for (std::size_t n = 0; n < mesh.getNumberOfNodes(); ++n)
{
MeshLib::Location l(mesh.getID(), MeshLib::MeshItemType::Node, n);
global_idcs.push_back(dof_table.getGlobalIndices(l));
}
GlobalSparsityPattern sparsity_pattern(dof_table.dofSizeWithGhosts());
// Map adjacent mesh nodes to "adjacent global indices".
for (std::size_t n = 0; n < mesh.getNumberOfNodes(); ++n)
{
unsigned n_connected_dof = 0;
for (auto an : node_adjacency_table.getAdjacentNodes(n))
n_connected_dof += global_idcs[an].size();
for (auto global_index : global_idcs[n])
sparsity_pattern[global_index] = n_connected_dof;
}
return sparsity_pattern;
}
bool convertMeshToGeo(const MeshLib::Mesh &mesh, GeoLib::GEOObjects &geo_objects, double eps)
{
if (mesh.getDimension() != 2)
{
ERR ("Mesh to geometry conversion is only working for 2D meshes.");
return false;
}
// nodes to points conversion
std::string mesh_name(mesh.getName());
{
auto points = std::make_unique<std::vector<GeoLib::Point*>>();
points->reserve(mesh.getNumberOfNodes());
for (auto node_ptr : mesh.getNodes())
points->push_back(new GeoLib::Point(*node_ptr, node_ptr->getID()));
geo_objects.addPointVec(std::move(points), mesh_name, nullptr, eps);
}
const std::vector<std::size_t> id_map (geo_objects.getPointVecObj(mesh_name)->getIDMap());
// elements to surface triangles conversion
std::string const mat_name ("MaterialIDs");
auto bounds (MeshInformation::getValueBounds<int>(mesh, mat_name));
const unsigned nMatGroups(bounds.second-bounds.first+1);
auto sfcs = std::make_unique<std::vector<GeoLib::Surface*>>();
sfcs->reserve(nMatGroups);
auto const& points = *geo_objects.getPointVec(mesh_name);
for (unsigned i=0; i<nMatGroups; ++i)
sfcs->push_back(new GeoLib::Surface(points));
const std::vector<MeshLib::Element*> &elements = mesh.getElements();
const std::size_t nElems (mesh.getNumberOfElements());
MeshLib::PropertyVector<int> const*const materialIds =
mesh.getProperties().existsPropertyVector<int>("MaterialIDs")
? mesh.getProperties().getPropertyVector<int>("MaterialIDs")
: nullptr;
for (unsigned i=0; i<nElems; ++i)
{
auto surfaceId = !materialIds ? 0 : ((*materialIds)[i] - bounds.first);
MeshLib::Element* e (elements[i]);
if (e->getGeomType() == MeshElemType::TRIANGLE)
(*sfcs)[surfaceId]->addTriangle(id_map[e->getNodeIndex(0)], id_map[e->getNodeIndex(1)], id_map[e->getNodeIndex(2)]);
if (e->getGeomType() == MeshElemType::QUAD)
{
(*sfcs)[surfaceId]->addTriangle(id_map[e->getNodeIndex(0)], id_map[e->getNodeIndex(1)], id_map[e->getNodeIndex(2)]);
(*sfcs)[surfaceId]->addTriangle(id_map[e->getNodeIndex(0)], id_map[e->getNodeIndex(2)], id_map[e->getNodeIndex(3)]);
}
// all other element types are ignored (i.e. lines)
}
std::for_each(sfcs->begin(), sfcs->end(), [](GeoLib::Surface* sfc){ if (sfc->getNumberOfTriangles()==0) delete sfc; sfc = nullptr;});
auto sfcs_end = std::remove(sfcs->begin(), sfcs->end(), nullptr);
sfcs->erase(sfcs_end, sfcs->end());
geo_objects.addSurfaceVec(std::move(sfcs), mesh_name);
return true;
}
std::unique_ptr<DirichletBoundaryCondition> createDirichletBoundaryCondition(
BaseLib::ConfigTree const& config, MeshLib::Mesh const& bc_mesh,
NumLib::LocalToGlobalIndexMap const& dof_table_bulk, int const variable_id,
int const component_id,
const std::vector<std::unique_ptr<ProcessLib::ParameterBase>>& parameters)
{
DBUG("Constructing DirichletBoundaryCondition from config.");
//! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__type}
config.checkConfigParameter("type", "Dirichlet");
//! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__Dirichlet__parameter}
auto const param_name = config.getConfigParameter<std::string>("parameter");
DBUG("Using parameter %s", param_name.c_str());
auto& param = findParameter<double>(param_name, parameters, 1);
// In case of partitioned mesh the boundary could be empty, i.e. there is no
// boundary condition.
#ifdef USE_PETSC
// This can be extracted to createBoundaryCondition() but then the config
// parameters are not read and will cause an error.
// TODO (naumov): Add a function to ConfigTree for skipping the tags of the
// subtree and move the code up in createBoundaryCondition().
if (bc_mesh.getDimension() == 0 && bc_mesh.getNumberOfNodes() == 0 &&
bc_mesh.getNumberOfElements() == 0)
{
return nullptr;
}
#endif // USE_PETSC
return std::make_unique<DirichletBoundaryCondition>(
param, bc_mesh, dof_table_bulk, variable_id, component_id);
}
bool MeshLayerMapper::layerMapping(MeshLib::Mesh &new_mesh, GeoLib::Raster const& raster, double noDataReplacementValue = 0.0)
{
if (new_mesh.getDimension() != 2)
{
ERR("MshLayerMapper::layerMapping() - requires 2D mesh");
return false;
}
GeoLib::RasterHeader const& header (raster.getHeader());
const double x0(header.origin[0]);
const double y0(header.origin[1]);
const double delta(header.cell_size);
const std::pair<double, double> xDim(x0, x0 + header.n_cols * delta); // extension in x-dimension
const std::pair<double, double> yDim(y0, y0 + header.n_rows * delta); // extension in y-dimension
const std::size_t nNodes (new_mesh.getNumberOfNodes());
const std::vector<MeshLib::Node*> &nodes = new_mesh.getNodes();
for (unsigned i = 0; i < nNodes; ++i)
{
if (!raster.isPntOnRaster(*nodes[i]))
{
// use either default value or elevation from layer above
nodes[i]->updateCoordinates((*nodes[i])[0], (*nodes[i])[1], noDataReplacementValue);
continue;
}
double elevation (raster.interpolateValueAtPoint(*nodes[i]));
if (std::abs(elevation - header.no_data) < std::numeric_limits<double>::epsilon())
elevation = noDataReplacementValue;
nodes[i]->updateCoordinates((*nodes[i])[0], (*nodes[i])[1], elevation);
}
return true;
}
std::unique_ptr<PythonBoundaryCondition> createPythonBoundaryCondition(
BaseLib::ConfigTree const& config, MeshLib::Mesh const& boundary_mesh,
NumLib::LocalToGlobalIndexMap const& dof_table, std::size_t bulk_mesh_id,
int const variable_id, int const component_id,
unsigned const integration_order, unsigned const shapefunction_order,
unsigned const global_dim)
{
//! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__type}
config.checkConfigParameter("type", "Python");
//! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__Python__bc_object}
auto const bc_object = config.getConfigParameter<std::string>("bc_object");
//! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__Python__flush_stdout}
auto const flush_stdout = config.getConfigParameter("flush_stdout", false);
// Evaluate Python code in scope of main module
pybind11::object scope =
pybind11::module::import("__main__").attr("__dict__");
if (!scope.contains(bc_object))
OGS_FATAL(
"Function `%s' is not defined in the python script file, or there "
"was no python script file specified.",
bc_object.c_str());
auto* bc = scope[bc_object.c_str()]
.cast<PythonBoundaryConditionPythonSideInterface*>();
if (variable_id >= static_cast<int>(dof_table.getNumberOfVariables()) ||
component_id >= dof_table.getNumberOfVariableComponents(variable_id))
{
OGS_FATAL(
"Variable id or component id too high. Actual values: (%d, %d), "
"maximum values: (%d, %d).",
variable_id, component_id, dof_table.getNumberOfVariables(),
dof_table.getNumberOfVariableComponents(variable_id));
}
// In case of partitioned mesh the boundary could be empty, i.e. there is no
// boundary condition.
#ifdef USE_PETSC
// This can be extracted to createBoundaryCondition() but then the config
// parameters are not read and will cause an error.
// TODO (naumov): Add a function to ConfigTree for skipping the tags of the
// subtree and move the code up in createBoundaryCondition().
if (boundary_mesh.getDimension() == 0 &&
boundary_mesh.getNumberOfNodes() == 0 &&
boundary_mesh.getNumberOfElements() == 0)
{
return nullptr;
}
#endif // USE_PETSC
return std::make_unique<PythonBoundaryCondition>(
PythonBoundaryConditionData{
bc, dof_table, bulk_mesh_id,
dof_table.getGlobalComponent(variable_id, component_id),
boundary_mesh},
integration_order, shapefunction_order, global_dim, flush_stdout);
}
void testZCoords2D(MeshLib::Mesh const& input, MeshLib::Mesh const& output, double height)
{
std::size_t const nNodes (input.getNumberOfNodes());
for (std::size_t i=0; i<nNodes; ++i)
{
ASSERT_EQ((*input.getNode(i))[2], (*output.getNode(i))[2]);
ASSERT_EQ((*input.getNode(i))[2] + height, (*output.getNode(nNodes+i))[2]);
}
}
bool MeshLayerMapper::createRasterLayers(
MeshLib::Mesh const& mesh,
std::vector<GeoLib::Raster const*> const& rasters,
double minimum_thickness,
double noDataReplacementValue)
{
const std::size_t nLayers(rasters.size());
if (nLayers < 2 || mesh.getDimension() != 2)
{
ERR("MeshLayerMapper::createRasterLayers(): A 2D mesh and at least two rasters required as input.");
return false;
}
auto top = std::make_unique<MeshLib::Mesh>(mesh);
if (!layerMapping(*top, *rasters.back(), noDataReplacementValue))
return false;
auto bottom = std::make_unique<MeshLib::Mesh>(mesh);
if (!layerMapping(*bottom, *rasters[0], 0))
{
return false;
}
this->_minimum_thickness = minimum_thickness;
std::size_t const nNodes = mesh.getNumberOfNodes();
_nodes.reserve(nLayers * nNodes);
// number of triangles in the original mesh
std::size_t const nElems (std::count_if(mesh.getElements().begin(), mesh.getElements().end(),
[](MeshLib::Element const* elem)
{ return (elem->getGeomType() == MeshLib::MeshElemType::TRIANGLE);}));
_elements.reserve(nElems * (nLayers-1));
_materials.reserve(nElems * (nLayers-1));
// add bottom layer
std::vector<MeshLib::Node*> const& nodes = bottom->getNodes();
for (MeshLib::Node* node : nodes)
_nodes.push_back(new MeshLib::Node(*node));
// add the other layers
for (std::size_t i=0; i<nLayers-1; ++i)
addLayerToMesh(*top, i, *rasters[i+1]);
return true;
}
std::unique_ptr<RobinBoundaryCondition> createRobinBoundaryCondition(
BaseLib::ConfigTree const& config, MeshLib::Mesh const& bc_mesh,
NumLib::LocalToGlobalIndexMap const& dof_table, int const variable_id,
int const component_id, unsigned const integration_order,
unsigned const shapefunction_order, unsigned const global_dim,
std::vector<std::unique_ptr<ParameterLib::ParameterBase>> const& parameters)
{
DBUG("Constructing RobinBcConfig from config.");
//! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__type}
config.checkConfigParameter("type", "Robin");
//! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__Robin__alpha}
auto const alpha_name = config.getConfigParameter<std::string>("alpha");
//! \ogs_file_param{prj__process_variables__process_variable__boundary_conditions__boundary_condition__Robin__u_0}
auto const u_0_name = config.getConfigParameter<std::string>("u_0");
auto const& alpha =
ParameterLib::findParameter<double>(alpha_name, parameters, 1);
auto const& u_0 =
ParameterLib::findParameter<double>(u_0_name, parameters, 1);
// In case of partitioned mesh the boundary could be empty, i.e. there is no
// boundary condition.
#ifdef USE_PETSC
// This can be extracted to createBoundaryCondition() but then the config
// parameters are not read and will cause an error.
// TODO (naumov): Add a function to ConfigTree for skipping the tags of the
// subtree and move the code up in createBoundaryCondition().
if (bc_mesh.getDimension() == 0 && bc_mesh.getNumberOfNodes() == 0 &&
bc_mesh.getNumberOfElements() == 0)
{
return nullptr;
}
#endif // USE_PETSC
return std::make_unique<RobinBoundaryCondition>(
integration_order, shapefunction_order, dof_table, variable_id,
component_id, global_dim, bc_mesh,
RobinBoundaryConditionData{alpha, u_0});
}
int main (int argc, char* argv[])
{
ApplicationsLib::LogogSetup logog_setup;
TCLAP::CmdLine cmd("Converts VTK mesh into OGS mesh.", ' ', "0.1");
TCLAP::ValueArg<std::string> mesh_in("i", "mesh-input-file",
"the name of the file containing the input mesh", true,
"", "file name of input mesh");
cmd.add(mesh_in);
TCLAP::ValueArg<std::string> mesh_out("o", "mesh-output-file",
"the name of the file the mesh will be written to", true,
"", "file name of output mesh");
cmd.add(mesh_out);
cmd.parse(argc, argv);
MeshLib::Mesh* mesh (MeshLib::IO::VtuInterface::readVTUFile(mesh_in.getValue()));
INFO("Mesh read: %d nodes, %d elements.", mesh->getNumberOfNodes(), mesh->getNumberOfElements());
MeshLib::IO::Legacy::MeshIO meshIO;
meshIO.setMesh(mesh);
meshIO.writeToFile(mesh_out.getValue());
return EXIT_SUCCESS;
}
void ElementTreeModel::setMesh(MeshLib::Mesh const& mesh)
{
this->clearView();
QList<QVariant> mesh_name;
mesh_name << "Name:" << QString::fromStdString(mesh.getName()) << "" << "" << "";
TreeItem* name_item = new TreeItem(mesh_name, _rootItem);
_rootItem->appendChild(name_item);
QList<QVariant> nodes_number;
nodes_number << "#Nodes: " << QString::number(mesh.getNumberOfNodes()) << "" << "";
TreeItem* nodes_item = new TreeItem(nodes_number, _rootItem);
_rootItem->appendChild(nodes_item);
QList<QVariant> elements_number;
elements_number << "#Elements: " << QString::number(mesh.getNumberOfElements()) << "" << "";
TreeItem* elements_item = new TreeItem(elements_number, _rootItem);
_rootItem->appendChild(elements_item);
const std::array<QString, 7> n_element_names = {{ "Lines:", "Triangles:", "Quads:", "Tetrahedra:", "Hexahedra:", "Pyramids:", "Prisms:" }};
const std::array<unsigned, 7>& n_element_types (MeshLib::MeshInformation::getNumberOfElementTypes(mesh));
for (std::size_t i=0; i<n_element_types.size(); ++i)
{
if (n_element_types[i])
{
QList<QVariant> elements_number;
elements_number << n_element_names[i] << QString::number(n_element_types[i]) << "" << "";
TreeItem* type_item = new TreeItem(elements_number, elements_item);
elements_item->appendChild(type_item);
}
}
QList<QVariant> bounding_box;
bounding_box << "Bounding Box" << "" << "" << "";
TreeItem* aabb_item = new TreeItem(bounding_box, _rootItem);
_rootItem->appendChild(aabb_item);
const GeoLib::AABB aabb (MeshLib::MeshInformation::getBoundingBox(mesh));
auto const& min = aabb.getMinPoint();
auto const& max = aabb.getMaxPoint();
QList<QVariant> min_aabb;
min_aabb << "Min:" << QString::number(min[0], 'f') << QString::number(min[1], 'f') << QString::number(min[2], 'f');
TreeItem* min_item = new TreeItem(min_aabb, aabb_item);
aabb_item->appendChild(min_item);
QList<QVariant> max_aabb;
max_aabb << "Max:" << QString::number(max[0], 'f') << QString::number(max[1], 'f') << QString::number(max[2], 'f');
TreeItem* max_item = new TreeItem(max_aabb, aabb_item);
aabb_item->appendChild(max_item);
QList<QVariant> edges;
edges << "Edge Length: " << "[" + QString::number(mesh.getMinEdgeLength(), 'f') + "," << QString::number(mesh.getMaxEdgeLength(), 'f') + "]" << "";
TreeItem* edge_item = new TreeItem(edges, _rootItem);
_rootItem->appendChild(edge_item);
std::vector<std::string> const& vec_names (mesh.getProperties().getPropertyVectorNames());
for (std::size_t i=0; i<vec_names.size(); ++i)
{
QList<QVariant> array_info;
array_info << QString::fromStdString(vec_names[i]) + ": ";
auto vec_bounds (MeshLib::MeshInformation::getValueBounds<int>(mesh, vec_names[i]));
if (vec_bounds.second != std::numeric_limits<int>::max())
array_info << "[" + QString::number(vec_bounds.first) + "," << QString::number(vec_bounds.second) + "]" << "";
else
{
auto vec_bounds (MeshLib::MeshInformation::getValueBounds<double>(mesh, vec_names[i]));
if (vec_bounds.second != std::numeric_limits<double>::max())
array_info << "[" + QString::number(vec_bounds.first) + "," << QString::number(vec_bounds.second) + "]" << "";
}
if (array_info.size() == 1)
array_info << "[ ?" << "? ]" << "";
TreeItem* vec_item = new TreeItem(array_info, _rootItem);
_rootItem->appendChild(vec_item);
}
reset();
}
void MeshLayerMapper::addLayerToMesh(const MeshLib::Mesh &dem_mesh, unsigned layer_id, GeoLib::Raster const& raster)
{
const unsigned pyramid_base[3][4] =
{
{1, 3, 4, 2}, // Point 4 missing
{2, 4, 3, 0}, // Point 5 missing
{0, 3, 4, 1}, // Point 6 missing
};
std::size_t const nNodes = dem_mesh.getNumberOfNodes();
std::vector<MeshLib::Node*> const& nodes = dem_mesh.getNodes();
int const last_layer_node_offset = layer_id * nNodes;
// add nodes for new layer
for (std::size_t i=0; i<nNodes; ++i)
_nodes.push_back(getNewLayerNode(*nodes[i], *_nodes[last_layer_node_offset + i], raster, _nodes.size()));
std::vector<MeshLib::Element*> const& elems = dem_mesh.getElements();
std::size_t const nElems (dem_mesh.getNumberOfElements());
for (std::size_t i=0; i<nElems; ++i)
{
MeshLib::Element* elem (elems[i]);
if (elem->getGeomType() != MeshLib::MeshElemType::TRIANGLE)
continue;
unsigned node_counter(3), missing_idx(0);
std::array<MeshLib::Node*, 6> new_elem_nodes;
for (unsigned j=0; j<3; ++j)
{
new_elem_nodes[j] = _nodes[_nodes[last_layer_node_offset + elem->getNodeIndex(j)]->getID()];
new_elem_nodes[node_counter] = (_nodes[last_layer_node_offset + elem->getNodeIndex(j) + nNodes]);
if (new_elem_nodes[j]->getID() != new_elem_nodes[node_counter]->getID())
node_counter++;
else
missing_idx = j;
}
switch (node_counter)
{
case 6:
_elements.push_back(new MeshLib::Prism(new_elem_nodes));
_materials.push_back(layer_id);
break;
case 5:
std::array<MeshLib::Node*, 5> pyramid_nodes;
pyramid_nodes[0] = new_elem_nodes[pyramid_base[missing_idx][0]];
pyramid_nodes[1] = new_elem_nodes[pyramid_base[missing_idx][1]];
pyramid_nodes[2] = new_elem_nodes[pyramid_base[missing_idx][2]];
pyramid_nodes[3] = new_elem_nodes[pyramid_base[missing_idx][3]];
pyramid_nodes[4] = new_elem_nodes[missing_idx];
_elements.push_back(new MeshLib::Pyramid(pyramid_nodes));
_materials.push_back(layer_id);
break;
case 4:
std::array<MeshLib::Node*, 4> tet_nodes;
std::copy(new_elem_nodes.begin(), new_elem_nodes.begin() + node_counter, tet_nodes.begin());
_elements.push_back(new MeshLib::Tet(tet_nodes));
_materials.push_back(layer_id);
break;
default:
continue;
}
}
}