mirror of
https://github.com/openmc-dev/openmc.git
synced 2026-07-27 05:35:49 -04:00
Apply @paulromano 's suggestions from code review.
Co-Authored-By: Paul Romano <paul.k.romano@gmail.com>
This commit is contained in:
Patrick Shriwise
GitHub
parent
e7eceff2aa
commit
ca7cba57df
6 changed files with 74 additions and 99 deletions
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@ -488,7 +488,7 @@
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"tally.filters = [mesh_filter]\n",
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"tally.scores = ['heating', 'flux']\n",
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"tally.estimator = 'tracklength'\n",
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"model.tallies = (tally,)"
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"model.tallies = [tally]"
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]
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},
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{
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@ -99,8 +99,7 @@ public:
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int n_dimension_; //!< Number of dimensions
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};
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class StructuredMesh : public Mesh
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{
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class StructuredMesh : public Mesh {
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public:
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StructuredMesh() = default;
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StructuredMesh(pugi::xml_node node) : Mesh {node} {};
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@ -252,7 +251,7 @@ private:
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class UnstructuredMesh : public Mesh {
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typedef std::vector<std::pair<double, moab::EntityHandle>> UnstructuredMeshHits;
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using UnstructuredMeshHits = std::vector<std::pair<double, moab::EntityHandle>>;
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public:
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UnstructuredMesh() = default;
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@ -273,7 +272,7 @@ public:
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private:
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//! Finds all intersections with faces of the mesh.
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//! Find all intersections with faces of the mesh.
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//
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//! \param[in] start Staring location
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//! \param[in] dir Normalized particle direction
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@ -285,7 +284,7 @@ private:
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double track_len,
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UnstructuredMeshHits& hits) const;
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//! Calculates the volume for a given tetrahedron handle.
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//! Calculate the volume for a given tetrahedron handle.
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//
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// \param[in] tet MOAB EntityHandle of the tetrahedron
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double tet_volume(moab::EntityHandle tet) const;
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@ -297,12 +296,12 @@ private:
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//! \return MOAB EntityHandle of tet
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moab::EntityHandle get_tet(const Position& r) const;
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//! Returns the containing tet given a position
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inline moab::EntityHandle get_tet(const moab::CartVect& r) const {
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//! Return the containing tet given a position
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moab::EntityHandle get_tet(const moab::CartVect& r) const {
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return get_tet(Position(r[0], r[1], r[2]));
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};
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//! Check for point containment within a tet, uses
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//! Check for point containment within a tet; uses
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//! pre-computed barycentric data.
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//
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//! \param[in] r Position to check
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@ -317,13 +316,13 @@ private:
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//! \param[in] tets MOAB Range of tetrahedral elements
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void compute_barycentric_data(const moab::Range& tets);
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//! Translates a MOAB EntityHandle its corresponding bin.
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//! Translate a MOAB EntityHandle to its corresponding bin.
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//
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//! \param[in] eh MOAB EntityHandle to translate
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//! \return Mesh bin
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int get_bin_from_ent_handle(moab::EntityHandle eh) const;
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//! Translates a bin to its corresponding MOAB EntityHandle
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//! Translate a bin to its corresponding MOAB EntityHandle
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//! for the tetrahedron representing that bin.
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//
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//! \param[in] bin Bin value to translate
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@ -348,7 +347,7 @@ private:
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//! \return Index of the bin
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int get_index_from_bin(int bin) const;
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//! Builds a KDTree for all tetrahedra in the mesh. All
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//! Build a KDTree for all tetrahedra in the mesh. All
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//! triangles representing 2D faces of the mesh are
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//! added to the tree as well.
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//
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@ -359,7 +358,7 @@ private:
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//! or create them if they are not there
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//
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//! \param[in] score Name of the score
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//! \returns The MOAB value and error tag handles, respectively
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//! \return The MOAB value and error tag handles, respectively
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std::pair<moab::Tag, moab::Tag>
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get_score_tags(std::string score) const;
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@ -392,7 +391,7 @@ public:
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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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// \returns The centroid of the element
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// \return The centroid of the element
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Position centroid(moab::EntityHandle tet) const;
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//! Return a string represntation of the mesh bin
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@ -632,8 +632,7 @@ class UnstructuredMesh(MeshBase):
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@filename.setter
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def filename(self, filename):
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if filename is not None:
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cv.check_type('Unstructured Mesh filename: {}'.format(filename),
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filename, str)
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cv.check_type('Unstructured Mesh filename', filename, str)
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self._filename = filename
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else:
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self.filename = ''
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@ -663,8 +662,7 @@ class UnstructuredMesh(MeshBase):
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def __repr__(self):
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string = super().__repr__()
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string += '{0: <16}{1}{2}\n'.format('\tFilename', '=\t', self.filename)
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return string
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return string + '{: <16}=\t{}\n'.format('\tFilename', self.filename)
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@classmethod
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def from_hdf5(cls, group):
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@ -674,7 +672,7 @@ class UnstructuredMesh(MeshBase):
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mesh.filename = group['filename'][()].decode()
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vol_data = group['volumes'][()]
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centroids = group['centroids'][()]
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mesh.volumes = np.reshape(vol_data, (vol_data.shape[0], 1))
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mesh.volumes = np.reshape(vol_data, (vol_data.shape[0],))
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mesh.centroids = np.reshape(centroids, (vol_data.shape[0], 3))
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return mesh
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63
src/mesh.cpp
63
src/mesh.cpp
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@ -818,7 +818,7 @@ RegularMesh::count_sites(const Particle::Bank* bank,
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bool* outside) const
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{
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// Determine shape of array for counts
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std::size_t m = n_bins();
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std::size_t m = this->n_bins();
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std::vector<std::size_t> shape = {m};
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// Create array of zeros
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@ -1413,7 +1413,7 @@ openmc_extend_meshes(int32_t n, int32_t* index_start, int32_t* index_end)
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{
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if (index_start) *index_start = model::meshes.size();
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for (int i = 0; i < n; ++i) {
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model::meshes.push_back(std::move(std::make_unique<RegularMesh>()));
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model::meshes.push_back(std::make_unique<RegularMesh>());
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}
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if (index_end) *index_end = model::meshes.size() - 1;
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@ -1552,14 +1552,13 @@ UnstructuredMesh::UnstructuredMesh(pugi::xml_node node) : Mesh(node)
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// get the filename of the unstructured mesh to load
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if (check_for_node(node, "mesh_file")) {
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filename_ = get_node_value(node, "mesh_file");
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}
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else {
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} else {
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fatal_error("No filename supplied for unstructured mesh with ID: " +
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std::to_string(id_));
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}
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// create MOAB instance
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mbi_ = std::unique_ptr<moab::Interface>(new moab::Core());
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mbi_ = std::make_unique<moab::Core>();
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// create meshset to load mesh into
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moab::ErrorCode rval = mbi_->create_meshset(moab::MESHSET_SET, meshset_);
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if (rval != moab::MB_SUCCESS) {
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@ -1624,7 +1623,7 @@ UnstructuredMesh::build_kdtree(const moab::Range& all_tets)
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all_tets_and_tris.merge(all_tris);
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// create a kd-tree instance
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kdtree_ = std::unique_ptr<moab::AdaptiveKDTree>(new moab::AdaptiveKDTree(mbi_.get()));
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kdtree_ = std::make_unique<moab::AdaptiveKDTree>(mbi_.get());
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// build the tree
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rval = kdtree_->build_tree(all_tets_and_tris, &kdtree_root_);
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@ -1789,8 +1788,8 @@ UnstructuredMesh::get_tet(const Position& r) const
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// loop over the tets in this leaf, returning the containing tet if found
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for (const auto& tet : tets) {
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if (point_in_tet(pos, tet)) {
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return tet;
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if (point_in_tet(pos, tet)) {
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return tet;
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}
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}
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@ -1862,7 +1861,7 @@ UnstructuredMesh::compute_barycentric_data(const moab::Range& tets) {
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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, "mesh " + std::to_string(id_));
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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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@ -1872,8 +1871,8 @@ UnstructuredMesh::to_hdf5(hid_t group) const
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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(tet_volume(eh));
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Position c = centroid(eh);
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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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@ -1922,9 +1921,7 @@ UnstructuredMesh::point_in_tet(const moab::CartVect& r, moab::EntityHandle tet)
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int
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UnstructuredMesh::get_bin_from_index(int idx) const {
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if (idx >= n_bins()) {
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std::stringstream s;
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s << "Invalid bin index: " << idx;
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fatal_error(s);
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fatal_error(fmt::format("Invalid bin index: {}", idx));
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}
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return ehs_[idx] - ehs_[0];
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}
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@ -1951,9 +1948,7 @@ int
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UnstructuredMesh::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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std::stringstream s;
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s << "Invalid bin: " << bin;
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fatal_error(s);
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fatal_error(fmt::format("Invalid bin: {}", bin));
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}
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return bin;
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}
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@ -1961,9 +1956,7 @@ UnstructuredMesh::get_bin_from_ent_handle(moab::EntityHandle eh) const {
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moab::EntityHandle
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UnstructuredMesh::get_ent_handle_from_bin(int bin) const {
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if (bin >= n_bins()) {
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std::stringstream s;
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s << "Invalid bin index: " << bin;
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fatal_error(s);
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fatal_error(fmt::format("Invalid bin index: ", bin));
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}
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return ehs_[bin];
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}
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@ -1998,7 +1991,7 @@ UnstructuredMesh::centroid(moab::EntityHandle tet) const {
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// get the coordinates
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std::vector<moab::CartVect> coords(conn.size());
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rval = mbi_->get_coords(&conn.front(), conn.size(), coords[0].array());
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rval = mbi_->get_coords(conn.data(), conn.size(), coords[0].array());
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if (rval != moab::MB_SUCCESS) {
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warning("Failed to get the coordinates of a mesh element.");
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return {};
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@ -2016,9 +2009,7 @@ UnstructuredMesh::centroid(moab::EntityHandle tet) const {
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std::string
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UnstructuredMesh::bin_label(int bin) const {
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std::stringstream out;
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out << "Mesh Index (" << bin << ")";
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return out.str();
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return fmt::format("Mesh Index ({})", bin);
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};
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std::pair<moab::Tag, moab::Tag>
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@ -2031,7 +2022,7 @@ UnstructuredMesh::get_score_tags(std::string score) const {
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// create the value tag if not present and get handle
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double default_val = 0.0;
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auto val_string = score + "_value";
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auto val_string = score + "_mean";
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rval = mbi_->tag_get_handle(val_string.c_str(),
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1,
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moab::MB_TYPE_DOUBLE,
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@ -2039,9 +2030,8 @@ UnstructuredMesh::get_score_tags(std::string score) const {
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moab::MB_TAG_DENSE|moab::MB_TAG_CREAT,
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&default_val);
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if (rval != moab::MB_SUCCESS) {
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std::stringstream msg;
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msg << "Could not create or retrieve the value tag for the score " << score
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<< " on unstructured mesh " << id_;
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auto msg = fmt::format("Could not create or retrieve the value tag for the score {}"
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" on unstructured mesh {}", score, id_);
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fatal_error(msg);
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}
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@ -2067,26 +2057,26 @@ UnstructuredMesh::get_score_tags(std::string score) const {
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void
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UnstructuredMesh::add_score(std::string score) const {
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auto score_tags = get_score_tags(score);
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auto score_tags = this->get_score_tags(score);
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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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std::vector<double> values,
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std::vector<double> std_dev) const {
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auto score_tags = get_score_tags(score);
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auto score_tags = this->get_score_tags(score);
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// normalize tally values by element volume
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for (int i = 0; i < ehs_.size(); i++) {
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auto eh = get_ent_handle_from_bin(i);
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double volume = tet_volume(eh);
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auto eh = this->get_ent_handle_from_bin(i);
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double volume = this->tet_volume(eh);
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values[i] /= volume;
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std_dev[i] /= volume;
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}
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moab::ErrorCode rval;
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// set the score value
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rval = mbi_->tag_set_data(score_tags.first, ehs_, &values.front());
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rval = mbi_->tag_set_data(score_tags.first, ehs_, values.data());
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if (rval != moab::MB_SUCCESS) {
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std::stringstream msg;
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msg << "Failed to set the tally value for score '" << score << "' "
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@ -2095,7 +2085,7 @@ UnstructuredMesh::set_score_data(const std::string& score,
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}
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// set the error value
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rval = mbi_->tag_set_data(score_tags.second, ehs_, &std_dev.front());
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rval = mbi_->tag_set_data(score_tags.second, ehs_, std_dev.data());
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if (rval != moab::MB_SUCCESS) {
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std::stringstream msg;
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msg << "Failed to set the tally value for score '" << score << "' "
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@ -2144,12 +2134,11 @@ void read_meshes(pugi::xml_node root)
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model::meshes.push_back(std::make_unique<RegularMesh>(node));
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} else if (mesh_type == "rectilinear") {
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model::meshes.push_back(std::make_unique<RectilinearMesh>(node));
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}
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#ifdef DAGMC
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else if (mesh_type == "unstructured") {
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} else if (mesh_type == "unstructured") {
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model::meshes.push_back(std::make_unique<UnstructuredMesh>(node));
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#else
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else if (mesh_type == "unstructured") {
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} else if (mesh_type == "unstructured") {
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fatal_error("Unstructured mesh support is disabled.");
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#endif
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} else {
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@ -699,7 +699,7 @@ void write_unstructured_mesh_results() {
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// warning and skip writing the mesh
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if (tally->filters().size() > 1) {
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warning(fmt::format("Skipping unstructured mesh writing for tally "
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"{0}. More than one filter is present on the tally.",
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"{}. More than one filter is present on the tally.",
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tally->id_));
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break;
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}
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@ -711,7 +711,7 @@ void write_unstructured_mesh_results() {
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for (int i_nuc = 0; i_nuc < tally->nuclides_.size(); i_nuc++) {
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// index for this nuclide and score
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int nuc_score_idx = i_score + i_nuc * tally->scores_.size();
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int nuc_score_idx = i_score + i_nuc*tally->scores_.size();
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// construct result vectors
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std::vector<double> mean_vec, std_dev_vec;
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@ -731,12 +731,8 @@ void write_unstructured_mesh_results() {
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std::string score_name = tally->score_name(i_score);
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auto score_str = fmt::format("{0}_{1}",
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score_name,
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nuclide_name);
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umesh->set_score_data(score_str,
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mean_vec,
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std_dev_vec);
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auto score_str = fmt::format("{}_{}", score_name, nuclide_name);
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umesh->set_score_data(score_str, mean_vec, std_dev_vec);
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}
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}
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@ -1,4 +1,3 @@
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from collections import defaultdict
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import glob
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from itertools import product
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import os
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@ -18,8 +17,6 @@ TETS_PER_VOXEL = 12
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class UnstructuredMeshTest(PyAPITestHarness):
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def __init__(self, statepoint_name, **kwargs):
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super().__init__(statepoint_name)
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@ -47,11 +44,7 @@ class UnstructuredMeshTest(PyAPITestHarness):
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materials.append(fuel_mat)
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zirc_mat = openmc.Material(name="zircaloy")
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zirc_mat.add_nuclide("Zr90", 0.5145)
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zirc_mat.add_nuclide("Zr91", 0.1122)
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zirc_mat.add_nuclide("Zr92", 0.1715)
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zirc_mat.add_nuclide("Zr94", 0.1738)
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zirc_mat.add_nuclide("Zr96", 0.028)
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zirc_mat.add_element("Zr", 1.0)
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zirc_mat.set_density("g/cc", 5.77)
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materials.append(zirc_mat)
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@ -64,14 +57,14 @@ class UnstructuredMeshTest(PyAPITestHarness):
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materials.export_to_xml()
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### Geometry ###
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fuel_min_x = openmc.XPlane(x0=-5.0, name="minimum x")
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fuel_max_x = openmc.XPlane(x0=5.0, name="maximum x")
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fuel_min_x = openmc.XPlane(-5.0, name="minimum x")
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fuel_max_x = openmc.XPlane(5.0, name="maximum x")
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fuel_min_y = openmc.YPlane(y0=-5.0, name="minimum y")
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fuel_max_y = openmc.YPlane(y0=5.0, name="maximum y")
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fuel_min_y = openmc.YPlane(-5.0, name="minimum y")
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fuel_max_y = openmc.YPlane(5.0, name="maximum y")
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fuel_min_z = openmc.ZPlane(z0=-5.0, name="minimum z")
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fuel_max_z = openmc.ZPlane(z0=5.0, name="maximum z")
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fuel_min_z = openmc.ZPlane(-5.0, name="minimum z")
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fuel_max_z = openmc.ZPlane(5.0, name="maximum z")
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fuel_cell = openmc.Cell(name="fuel")
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fuel_cell.region = +fuel_min_x & -fuel_max_x & \
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||||
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@ -79,21 +72,21 @@ class UnstructuredMeshTest(PyAPITestHarness):
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+fuel_min_z & -fuel_max_z
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fuel_cell.fill = fuel_mat
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||||
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clad_min_x = openmc.XPlane(x0=-6.0, name="minimum x")
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clad_max_x = openmc.XPlane(x0=6.0, name="maximum x")
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||||
clad_min_x = openmc.XPlane(-6.0, name="minimum x")
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clad_max_x = openmc.XPlane(6.0, name="maximum x")
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clad_min_y = openmc.YPlane(y0=-6.0, name="minimum y")
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clad_max_y = openmc.YPlane(y0=6.0, name="maximum y")
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clad_min_y = openmc.YPlane(-6.0, name="minimum y")
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clad_max_y = openmc.YPlane(6.0, name="maximum y")
|
||||
|
||||
clad_min_z = openmc.ZPlane(z0=-6.0, name="minimum z")
|
||||
clad_max_z = openmc.ZPlane(z0=6.0, name="maximum z")
|
||||
clad_min_z = openmc.ZPlane(-6.0, name="minimum z")
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||||
clad_max_z = openmc.ZPlane(6.0, name="maximum z")
|
||||
|
||||
clad_cell = openmc.Cell(name="clad")
|
||||
clad_cell.region = (-fuel_min_x | +fuel_max_x | \
|
||||
-fuel_min_y | +fuel_max_y | \
|
||||
clad_cell.region = (-fuel_min_x | +fuel_max_x |
|
||||
-fuel_min_y | +fuel_max_y |
|
||||
-fuel_min_z | +fuel_max_z) & \
|
||||
(+clad_min_x & -clad_max_x & \
|
||||
+clad_min_y & -clad_max_y & \
|
||||
(+clad_min_x & -clad_max_x &
|
||||
+clad_min_y & -clad_max_y &
|
||||
+clad_min_z & -clad_max_z)
|
||||
clad_cell.fill = zirc_mat
|
||||
|
||||
|
|
@ -124,19 +117,16 @@ class UnstructuredMeshTest(PyAPITestHarness):
|
|||
boundary_type='vacuum')
|
||||
|
||||
water_cell = openmc.Cell(name="water")
|
||||
water_cell.region = (-clad_min_x | +clad_max_x | \
|
||||
-clad_min_y | +clad_max_y | \
|
||||
water_cell.region = (-clad_min_x | +clad_max_x |
|
||||
-clad_min_y | +clad_max_y |
|
||||
-clad_min_z | +clad_max_z) & \
|
||||
(+water_min_x & -water_max_x & \
|
||||
+water_min_y & -water_max_y & \
|
||||
(+water_min_x & -water_max_x &
|
||||
+water_min_y & -water_max_y &
|
||||
+water_min_z & -water_max_z)
|
||||
water_cell.fill = water_mat
|
||||
|
||||
# create a containing universe
|
||||
root_univ = openmc.Universe()
|
||||
root_univ.add_cells([fuel_cell, clad_cell, water_cell])
|
||||
|
||||
geom = openmc.Geometry(root=root_univ)
|
||||
geom = openmc.Geometry([fuel_cell, clad_cell, water_cell])
|
||||
|
||||
geom.export_to_xml()
|
||||
|
||||
|
|
@ -256,14 +246,17 @@ class UnstructuredMeshTest(PyAPITestHarness):
|
|||
if os.path.exists(f):
|
||||
os.remove(f)
|
||||
|
||||
param_values = ( ('collision', 'tracklength'), # estimators
|
||||
(True, False), # geometry outside of the mesh
|
||||
( (333, 90, 77), tuple() ) ) # location of holes in the mesh
|
||||
|
||||
param_values = (['collision', 'tracklength'], # estimators
|
||||
[True, False], # geometry outside of the mesh
|
||||
[(333, 90, 77), (,)]) # location of holes in the mesh
|
||||
test_cases = []
|
||||
for estimator, holes, ext_geom in product(*param_values):
|
||||
test_cases.append({'estimator' : estimator,
|
||||
'external_geom' : ext_geom,
|
||||
'holes' : holes})
|
||||
|
||||
|
||||
@pytest.mark.parametrize("opts", test_cases)
|
||||
def test_unstructured_mesh(opts):
|
||||
harness = UnstructuredMeshTest('statepoint.10.h5', kwargs=opts)
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue