mirror of
https://github.com/openmc-dev/openmc.git
synced 2026-07-26 05:05:30 -04:00
Restructuring unstructured mesh inheritance a bit.
This commit is contained in:
Patrick Shriwise
parent
651ef1255c
commit
b1af80697c
2 changed files with 86 additions and 86 deletions
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@ -284,6 +284,11 @@ public:
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std::string bin_label(int bin) const override;
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//! Write mesh data to an HDF5 group.
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//
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//! \param[in] group HDF5 group
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void to_hdf5(hid_t group) const;
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//! Add a variable to the mesh instance
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virtual void add_score(const std::string& var_name) = 0;
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@ -296,20 +301,24 @@ public:
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virtual Position centroid(int bin) const = 0;
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virtual double volume(int bin) const = 0;
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virtual std::string library() const = 0;
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// Data members
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std::string filename_;
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std::string filename_; //!< Path to unstructured mesh file
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};
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#ifdef DAGMC
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class UnstructuredMesh : public UnstructuredMeshBase {
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class MOABUnstructuredMesh : public UnstructuredMeshBase {
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public:
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UnstructuredMesh() = default;
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UnstructuredMesh(pugi::xml_node);
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UnstructuredMesh(const std::string& filename);
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~UnstructuredMesh() = default;
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MOABUnstructuredMesh() = default;
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MOABUnstructuredMesh(pugi::xml_node);
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MOABUnstructuredMesh(const std::string& filename);
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~MOABUnstructuredMesh() = default;
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void bins_crossed(const Particle& p,
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std::vector<int>& bins,
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@ -324,27 +333,26 @@ public:
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//! \param[out] bins Surface bins that were crossed
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void surface_bins_crossed(const Particle& p, std::vector<int>& bins) const;
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//! Write mesh data to an HDF5 group.
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//
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//! \param[in] group HDF5 group
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void to_hdf5(hid_t group) const;
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//! Get bin at a given position.
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//
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//! \param[in] r Position to get bin for
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//! \return Mesh bin
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int get_bin(Position r) const;
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std::string library() const override;
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int n_bins() const override;
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int n_surface_bins() const override;
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//! Retrieve a centroid for the mesh cell
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//
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// \param[in] tet MOAB EntityHandle of the tetrahedron
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// \param[in] bin Bin to return the volume for
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// \return The centroid of the element
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Position centroid(int bin) const override;
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double volume(int bin) const override;
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//! Add a score to the mesh instance
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void add_score(const std::string& score);
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@ -364,8 +372,6 @@ public:
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//! Write the mesh with any current tally data
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void write(std::string base_filename) const;
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std::string filename_; //!< Path to unstructured mesh file
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bool intersects(Position& r0, Position r1, int* ijk);
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private:
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@ -492,6 +498,8 @@ public:
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int get_bin(Position r) const override;
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std::string library() const override;
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int n_bins() const override;
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int n_surface_bins() const override;
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@ -504,8 +512,6 @@ public:
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void write(std::string filename) const override;
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void to_hdf5(hid_t group) const override;
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//! Add a variable to the libmesh mesh instance
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void add_score(const std::string& var_name) override;
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@ -514,6 +520,10 @@ public:
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std::vector<double> values,
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std::vector<double> std_dev) override;
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Position centroid(int bin) const override;
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double volume(int bin) const override;
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private:
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//! Setup method for the mesh. Builds data structures,
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@ -551,8 +561,6 @@ private:
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double first(const libMesh::Node& a,
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const libMesh::Node& b) const;
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Position centroid(int bin) const override;
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// Data members
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private:
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128
src/mesh.cpp
128
src/mesh.cpp
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@ -136,6 +136,30 @@ UnstructuredMeshBase::bin_label(int bin) const {
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return fmt::format("Mesh Index ({})", bin);
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};
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void
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UnstructuredMeshBase::to_hdf5(hid_t group) const
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{
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hid_t mesh_group = create_group(group, fmt::format("mesh {}", id_));
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write_dataset(mesh_group, "type", "unstructured");
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write_dataset(mesh_group, "filename", filename_);
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write_dataset(mesh_group, "library", this->library());
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// write volume of each tet
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std::vector<double> tet_vols;
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xt::xtensor<double, 2> centroids({this->n_bins(), 3});
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for (int i = 0; i < this->n_bins(); i++) {
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tet_vols.emplace_back(this->volume(i));
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auto c = this->centroid(i);
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xt::view(centroids, i, xt::all()) = xt::xarray<double>({c.x, c.y, c.z});
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}
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write_dataset(mesh_group, "volumes", tet_vols);
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write_dataset(mesh_group, "centroids", centroids);
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close_group(mesh_group);
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}
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//==============================================================================
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// RegularMesh implementation
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//==============================================================================
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@ -1404,7 +1428,7 @@ extern "C" int openmc_add_unstructured_mesh(const char filename[],
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bool valid_lib = false;
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#ifdef DAGMC
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if (library == "moab") {
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model::meshes.push_back(std::move(std::make_unique<UnstructuredMesh>(filename)));
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model::meshes.push_back(std::move(std::make_unique<MOABUnstructuredMesh>(filename)));
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valid_lib = true;
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}
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#endif
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@ -1590,16 +1614,16 @@ openmc_rectilinear_mesh_set_grid(int32_t index, const double* grid_x,
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#ifdef DAGMC
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UnstructuredMesh::UnstructuredMesh(pugi::xml_node node) : UnstructuredMeshBase(node) {
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MOABUnstructuredMesh::MOABUnstructuredMesh(pugi::xml_node node) : UnstructuredMeshBase(node) {
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initialize();
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}
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UnstructuredMesh::UnstructuredMesh(const std::string& filename) {
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MOABUnstructuredMesh::MOABUnstructuredMesh(const std::string& filename) {
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filename_ = filename;
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initialize();
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}
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void UnstructuredMesh::initialize() {
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void MOABUnstructuredMesh::initialize() {
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// create MOAB instance
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mbi_ = std::make_unique<moab::Core>();
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// load unstructured mesh file
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@ -1637,7 +1661,7 @@ void UnstructuredMesh::initialize() {
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}
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void
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UnstructuredMesh::build_kdtree(const moab::Range& all_tets)
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MOABUnstructuredMesh::build_kdtree(const moab::Range& all_tets)
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{
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moab::Range all_tris;
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int adj_dim = 2;
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@ -1672,7 +1696,7 @@ UnstructuredMesh::build_kdtree(const moab::Range& all_tets)
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}
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void
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UnstructuredMesh::intersect_track(const moab::CartVect& start,
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MOABUnstructuredMesh::intersect_track(const moab::CartVect& start,
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const moab::CartVect& dir,
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double track_len,
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std::vector<double>& hits) const {
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@ -1703,7 +1727,7 @@ UnstructuredMesh::intersect_track(const moab::CartVect& start,
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}
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void
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UnstructuredMesh::bins_crossed(const Particle& p,
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MOABUnstructuredMesh::bins_crossed(const Particle* p,
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std::vector<int>& bins,
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std::vector<double>& lengths) const
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{
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@ -1780,7 +1804,7 @@ UnstructuredMesh::bins_crossed(const Particle& p,
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};
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moab::EntityHandle
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UnstructuredMesh::get_tet(const Position& r) const
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MOABUnstructuredMesh::get_tet(const Position& r) const
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{
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moab::CartVect pos(r.x, r.y, r.z);
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// find the leaf of the kd-tree for this position
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@ -1807,7 +1831,13 @@ UnstructuredMesh::get_tet(const Position& r) const
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return 0;
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}
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double UnstructuredMesh::tet_volume(moab::EntityHandle tet) const {
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double MOABUnstructuredMesh::volume(int bin) const {
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return tet_volume(get_ent_handle_from_bin(bin));
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}
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std::string MOABUnstructuredMesh::library() const { return "moab"; }
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double MOABUnstructuredMesh::tet_volume(moab::EntityHandle tet) const {
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std::vector<moab::EntityHandle> conn;
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moab::ErrorCode rval = mbi_->get_connectivity(&tet, 1, conn);
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if (rval != moab::MB_SUCCESS) {
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@ -1823,13 +1853,13 @@ double UnstructuredMesh::tet_volume(moab::EntityHandle tet) const {
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return 1.0 / 6.0 * (((p[1] - p[0]) * (p[2] - p[0])) % (p[3] - p[0]));
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}
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void UnstructuredMesh::surface_bins_crossed(const Particle& p, std::vector<int>& bins) const {
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void MOABUnstructuredMesh::surface_bins_crossed(const Particle* p, std::vector<int>& bins) const {
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// TODO: Implement triangle crossings here
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throw std::runtime_error{"Unstructured mesh surface tallies are not implemented."};
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}
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int
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UnstructuredMesh::get_bin(Position r) const {
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MOABUnstructuredMesh::get_bin(Position r) const {
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moab::EntityHandle tet = get_tet(r);
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if (tet == 0) {
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return -1;
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@ -1839,7 +1869,7 @@ UnstructuredMesh::get_bin(Position r) const {
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}
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void
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UnstructuredMesh::compute_barycentric_data(const moab::Range& tets) {
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MOABUnstructuredMesh::compute_barycentric_data(const moab::Range& tets) {
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moab::ErrorCode rval;
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baryc_data_.clear();
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@ -1868,32 +1898,8 @@ UnstructuredMesh::compute_barycentric_data(const moab::Range& tets) {
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}
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}
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void
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UnstructuredMesh::to_hdf5(hid_t group) const
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{
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hid_t mesh_group = create_group(group, fmt::format("mesh {}", id_));
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write_dataset(mesh_group, "type", "unstructured");
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write_dataset(mesh_group, "filename", filename_);
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write_dataset(mesh_group, "library", "moab");
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// write volume of each tet
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std::vector<double> tet_vols;
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xt::xtensor<double, 2> centroids({ehs_.size(), 3});
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for (int i = 0; i < ehs_.size(); i++) {
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const auto& eh = ehs_[i];
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tet_vols.emplace_back(this->tet_volume(eh));
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Position c = this->centroid(eh);
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xt::view(centroids, i, xt::all()) = xt::xarray<double>({c.x, c.y, c.z});
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}
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write_dataset(mesh_group, "volumes", tet_vols);
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write_dataset(mesh_group, "centroids", centroids);
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close_group(mesh_group);
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}
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bool
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UnstructuredMesh::point_in_tet(const moab::CartVect& r, moab::EntityHandle tet) const {
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MOABUnstructuredMesh::point_in_tet(const moab::CartVect& r, moab::EntityHandle tet) const {
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moab::ErrorCode rval;
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@ -1928,7 +1934,7 @@ UnstructuredMesh::point_in_tet(const moab::CartVect& r, moab::EntityHandle tet)
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}
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int
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UnstructuredMesh::get_bin_from_index(int idx) const {
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MOABUnstructuredMesh::get_bin_from_index(int idx) const {
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if (idx >= n_bins()) {
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fatal_error(fmt::format("Invalid bin index: {}", idx));
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}
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@ -1936,25 +1942,25 @@ UnstructuredMesh::get_bin_from_index(int idx) const {
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}
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int
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UnstructuredMesh::get_index(const Position& r,
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MOABUnstructuredMesh::get_index(const Position& r,
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bool* in_mesh) const {
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int bin = get_bin(r);
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*in_mesh = bin != -1;
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return bin;
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}
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int UnstructuredMesh::get_index_from_bin(int bin) const {
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int MOABUnstructuredMesh::get_index_from_bin(int bin) const {
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return bin;
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}
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std::pair<std::vector<double>, std::vector<double>>
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UnstructuredMesh::plot(Position plot_ll, Position plot_ur) const {
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MOABUnstructuredMesh::plot(Position plot_ll, Position plot_ur) const {
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// TODO: Implement mesh lines
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return {};
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}
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int
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UnstructuredMesh::get_bin_from_ent_handle(moab::EntityHandle eh) const {
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MOABUnstructuredMesh::get_bin_from_ent_handle(moab::EntityHandle eh) const {
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int bin = eh - ehs_[0];
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if (bin >= n_bins()) {
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fatal_error(fmt::format("Invalid bin: {}", bin));
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@ -1963,18 +1969,18 @@ UnstructuredMesh::get_bin_from_ent_handle(moab::EntityHandle eh) const {
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}
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moab::EntityHandle
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UnstructuredMesh::get_ent_handle_from_bin(int bin) const {
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MOABUnstructuredMesh::get_ent_handle_from_bin(int bin) const {
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if (bin >= n_bins()) {
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fatal_error(fmt::format("Invalid bin index: ", bin));
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}
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return ehs_[0] + bin;
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}
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int UnstructuredMesh::n_bins() const {
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int MOABUnstructuredMesh::n_bins() const {
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return ehs_.size();
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}
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int UnstructuredMesh::n_surface_bins() const {
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int MOABUnstructuredMesh::n_surface_bins() const {
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// collect all triangles in the set of tets for this mesh
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moab::Range tris;
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moab::ErrorCode rval;
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@ -1987,7 +1993,7 @@ int UnstructuredMesh::n_surface_bins() const {
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}
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Position
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UnstructuredMesh::centroid(int bin) const {
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MOABUnstructuredMesh::centroid(int bin) const {
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moab::ErrorCode rval;
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auto tet = this->get_ent_handle_from_bin(bin);
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@ -2019,7 +2025,7 @@ UnstructuredMesh::centroid(int bin) const {
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}
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std::pair<moab::Tag, moab::Tag>
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UnstructuredMesh::get_score_tags(std::string score) const {
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MOABUnstructuredMesh::get_score_tags(std::string score) const {
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moab::ErrorCode rval;
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// add a tag to the mesh
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// all scores are treated as a single value
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@ -2061,7 +2067,7 @@ UnstructuredMesh::get_score_tags(std::string score) const {
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}
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void
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UnstructuredMesh::add_score(const std::string& score) {
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MOABUnstructuredMesh::add_score(const std::string& score) {
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auto score_tags = get_score_tags(score);
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}
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@ -2094,7 +2100,7 @@ void UnstructuredMesh::remove_score(std::string score) const {
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}
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void
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UnstructuredMesh::set_score_data(const std::string& score,
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MOABUnstructuredMesh::set_score_data(const std::string& score,
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std::vector<double> values,
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std::vector<double> std_dev) {
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auto score_tags = this->get_score_tags(score);
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@ -2126,7 +2132,7 @@ UnstructuredMesh::set_score_data(const std::string& score,
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}
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void
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UnstructuredMesh::write(std::string base_filename) const {
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MOABUnstructuredMesh::write(std::string base_filename) const {
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// add extension to the base name
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auto filename = base_filename + ".vtk";
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write_message(5, "Writing unstructured mesh {}...", filename);
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@ -2172,6 +2178,8 @@ LibMesh::centroid(int bin) const {
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return {centroid(0), centroid(1), centroid(2)};
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}
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std::string LibMesh::library() const { return "libmesh"; }
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void LibMesh::initialize() {
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// always 3 for unstructured meshes
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n_dimension_ = 3;
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@ -2358,23 +2366,7 @@ LibMesh::inside_tet(const libMesh::Point& r,
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return e->contains_point(r, FP_COINCIDENT);
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}
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void LibMesh::to_hdf5(hid_t group) const
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{
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hid_t mesh_group = create_group(group, "mesh " + std::to_string(id_));
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write_dataset(mesh_group, "type", "unstructured");
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write_dataset(mesh_group, "filename", filename_);
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write_dataset(mesh_group, "library", "libmesh");
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// write volume of each tet
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std::vector<double> tet_vols;
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for (int i = 0; i < m_->n_elem(); i++) {
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tet_vols.emplace_back(m_->elem_ref(i).volume());
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}
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write_dataset(mesh_group, "volumes", tet_vols);
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close_group(mesh_group);
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}
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double LibMesh::volume(int bin) const { return m_->elem_ref(bin).volume(); }
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#endif // LIBMESH
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@ -2407,7 +2399,7 @@ void read_meshes(pugi::xml_node root)
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#ifdef DAGMC
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}
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else if (mesh_type == "unstructured" && mesh_lib == "moab") {
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model::meshes.push_back(std::make_unique<UnstructuredMesh>(node));
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model::meshes.push_back(std::make_unique<MOABUnstructuredMesh>(node));
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#else
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} else if (mesh_type == "unstructured") {
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fatal_error("Unstructured mesh support is disabled.");
|
||||
|
|
|
|||
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Reference in a new issue