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Corrections after rebase.
This commit is contained in:
Patrick Shriwise
parent
66346e8356
commit
ff0af7d594
2 changed files with 133 additions and 92 deletions
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@ -37,62 +37,9 @@ extern std::unordered_map<int32_t, int32_t> mesh_map;
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} // namespace model
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class Mesh {
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public:
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// Constructor
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Mesh() {}; // empty constructor
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Mesh(pugi::xml_node node);
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//! Determine which bins were crossed by a particle
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//
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//! \param[in] p Particle to check
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//! \param[out] bins Bins that were crossed
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//! \param[out] lengths Fraction of tracklength in each bin
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virtual void bins_crossed(const Particle* p, std::vector<int>& bins,
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std::vector<double>& lengths) const = 0;
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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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virtual void to_hdf5(hid_t group) const = 0;
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//! Determine which surface bins were crossed by a particle
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//
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//! \param[in] p Particle to check
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//! \param[out] bins Surface bins that were crossed
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virtual void
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surface_bins_crossed(const Particle* p, std::vector<int>& bins) const = 0;
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//! Get bin at a given position in space
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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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virtual int get_bin(Position r) const = 0;
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virtual std::string get_label_for_bin(int bin) const = 0;
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//! Count number of bank sites in each mesh bin / energy bin
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//
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//! \param[in] bank Array of bank sites
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//! \param[out] Whether any bank sites are outside the mesh
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//! \return Array indicating number of sites in each mesh/energy bin
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virtual xt::xarray<double>
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count_sites(const std::vector<Particle::Bank>& bank, bool* outside) const;
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virtual double get_volume_frac(int bin = -1) const = 0;
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virtual int num_bins() const = 0;
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int id_ {-1}; //!< User-specified ID
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int n_dimension_; //!< Number of dimensions
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};
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//==============================================================================
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//! Tessellation of n-dimensional Euclidean space by congruent squares or cubes
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//==============================================================================
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class RegularMesh : public Mesh {
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class Mesh
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{
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public:
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// Constructors and destructor
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Mesh() = default;
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@ -171,6 +118,60 @@ public:
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xt::xtensor<double, 1> upper_right_; //!< Upper-right coordinates of mesh
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};
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// class Mesh {
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// public:
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// // Constructors
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// Mesh() = default;
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// Mesh(pugi::xml_node node);
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// // Destructor
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// virtual ~Mesh() = default;
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// //! Determine which bins were crossed by a particle
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// //
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// //! \param[in] p Particle to check
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// //! \param[out] bins Bins that were crossed
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// //! \param[out] lengths Fraction of tracklength in each bin
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// virtual void bins_crossed(const Particle* p, std::vector<int>& bins,
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// std::vector<double>& lengths) const = 0;
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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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// virtual void to_hdf5(hid_t group) const = 0;
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// //! Determine which surface bins were crossed by a particle
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// //
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// //! \param[in] p Particle to check
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// //! \param[out] bins Surface bins that were crossed
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// virtual void
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// surface_bins_crossed(const Particle* p, std::vector<int>& bins) const = 0;
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// //! Get bin at a given position in space
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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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// virtual int get_bin(Position r) const = 0;
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// virtual std::string get_label_for_bin(int bin) const = 0;
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// //! Count number of bank sites in each mesh bin / energy bin
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// //
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// //! \param[in] bank Array of bank sites
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// //! \param[out] Whether any bank sites are outside the mesh
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// //! \return Array indicating number of sites in each mesh/energy bin
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// virtual xt::xarray<double>
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// count_sites(const std::vector<Particle::Bank>& bank, bool* outside) const;
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// virtual double get_volume_frac(int bin = -1) const = 0;
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// virtual int num_bins() const = 0;
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// int id_ {-1}; //!< User-specified ID
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// int n_dimension_; //!< Number of dimensions
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// };
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//==============================================================================
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//! Tessellation of n-dimensional Euclidean space by congruent squares or cubes
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//==============================================================================
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@ -393,6 +394,15 @@ intersect_track(const moab::CartVect& start,
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//! \return MOAB EntityHandle of tet
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moab::EntityHandle get_ent_handle_from_bin(int bin) const;
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int get_bin_from_indices(const int* ijk) const override;
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void get_indices(Position r, int* ijk, bool* in_mesh) const override;
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void get_indices_from_bin(int bin, int* ijk) const override;
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std::pair<std::vector<double>, std::vector<double>>
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plot(Position plot_ll, Position plot_ur) const override;
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//! Builds 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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@ -420,9 +430,11 @@ public:
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std::string get_label_for_bin(int bin) const;
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double get_volume_frac(int bin = -1) const;
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// double get_volume_frac(int bin = -1) const;
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int num_bins() const;
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int n_bins() const override;
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int n_surface_bins() const override;
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std::string filename_; //<! Path to unstructured mesh file
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99
src/mesh.cpp
99
src/mesh.cpp
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@ -69,8 +69,6 @@ inline bool check_intersection_point(double x1, double x0, double y1,
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// Mesh implementation
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//==============================================================================
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Mesh::Mesh(pugi::xml_node node)
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{
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Mesh::Mesh(pugi::xml_node node) {
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// Copy mesh id
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if (check_for_node(node, "id")) {
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@ -800,7 +798,7 @@ RegularMesh::count_sites(const Particle::Bank* bank, int64_t length,
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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 = num_bins();
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std::size_t m = 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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@ -850,28 +848,22 @@ RegularMesh::count_sites(const Particle::Bank* bank, int64_t length,
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return counts;
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}
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std::string RegularMesh::get_label_for_bin(int bin) const {
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int ijk[n_dimension_];
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get_indices_from_bin(bin, ijk);
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// std::string RegularMesh::get_label_for_bin(int bin) const {
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// int ijk[n_dimension_];
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// get_indices_from_bin(bin, ijk);
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std::stringstream out;
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out << "Mesh Index (" << ijk[0];
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if (n_dimension_ > 1) out << ", " << ijk[1];
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if (n_dimension_ > 2) out << ", " << ijk[2];
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out << ")";
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// std::stringstream out;
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// out << "Mesh Index (" << ijk[0];
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// if (n_dimension_ > 1) out << ", " << ijk[1];
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// if (n_dimension_ > 2) out << ", " << ijk[2];
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// out << ")";
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return out.str();
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}
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// return out.str();
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// }
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double RegularMesh::get_volume_frac(int bin) const {
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return volume_frac_;
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}
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int RegularMesh::num_bins() const {
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int n_bins = 1;
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for (auto v : shape_) n_bins *= v;
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return n_bins;
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}
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// double RegularMesh::get_volume_frac(int bin) const {
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// return volume_frac_;
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// }
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//==============================================================================
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// RectilinearMesh implementation
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@ -1936,10 +1928,35 @@ UnstructuredMesh::point_in_tet(const moab::CartVect& r, moab::EntityHandle tet)
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return in_tet;
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}
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int
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UnstructuredMesh::get_bin_from_indices(const int* ijk) const {
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if (ijk[0] >= n_bins()) {
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std::stringstream s;
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s << "Invalid bin: " << ijk[0];
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fatal_error(s);
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}
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int bin = ehs_[ijk[0]] - ehs_[0];
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return bin;
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}
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void
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UnstructuredMesh::get_indices(Position r, int* ijk, bool* in_mesh) const {
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int bin = get_bin(r);
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ijk[0]= bin;
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*in_mesh = bin != -1;
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}
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void UnstructuredMesh::get_indices_from_bin(int bin, int* ijk) const {
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ijk[0] = 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 { return {}; }
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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 >= num_bins()) {
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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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@ -1949,7 +1966,7 @@ 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 >= num_bins()) {
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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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@ -1957,19 +1974,31 @@ UnstructuredMesh::get_ent_handle_from_bin(int bin) const {
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return ehs_[bin];
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}
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double UnstructuredMesh::get_volume_frac(int bin) const {
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if (bin == -1) { return 0.0; }
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if (bin > ehs_.size() || bin < -1) {
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std::stringstream msg;
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msg << "Invalid bin " << bin << " for umesh with id " << id_;
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fatal_error(msg);
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}
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moab::EntityHandle tet = get_ent_handle_from_bin(bin);
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return tet_volume(tet);
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// double UnstructuredMesh::get_volume_frac(int bin) const {
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// if (bin == -1) { return 0.0; }
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// if (bin > ehs_.size() || bin < -1) {
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// std::stringstream msg;
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// msg << "Invalid bin " << bin << " for umesh with id " << id_;
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// fatal_error(msg);
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// }
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// moab::EntityHandle tet = get_ent_handle_from_bin(bin);
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// return tet_volume(tet);
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// }
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int UnstructuredMesh::n_bins() const {
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return ehs_.size();
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}
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int UnstructuredMesh::num_bins() const {
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return ehs_.size();
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int UnstructuredMesh::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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rval = mbi_->get_entities_by_type(0, moab::MBTRI, tris);
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if (rval != moab::MB_SUCCESS) {
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warning("Failed to get all triangles in the mesh instance");
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return -1;
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}
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return 2 * tris.size();
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}
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#endif
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