adding back files to be reviewed

include/openmc/material.h

@@ -0,0 +1,204 @@
+#ifndef OPENMC_MATERIAL_H
+#define OPENMC_MATERIAL_H
+
+#include <memory> // for unique_ptr
+#include <string>
+#include <unordered_map>
+#include <vector>
+
+#include <gsl/gsl>
+#include <hdf5.h>
+#include "pugixml.hpp"
+#include "xtensor/xtensor.hpp"
+
+#include "openmc/bremsstrahlung.h"
+#include "openmc/particle.h"
+
+namespace openmc {
+
+//==============================================================================
+// Global variables
+//==============================================================================
+
+class Material;
+
+namespace model {
+
+extern std::vector<std::unique_ptr<Material>> materials;
+extern std::unordered_map<int32_t, int32_t> material_map;
+
+} // namespace model
+
+//==============================================================================
+//! A substance with constituent nuclides and thermal scattering data
+//==============================================================================
+
+class Material
+{
+public:
+  //----------------------------------------------------------------------------
+  // Types
+  struct ThermalTable {
+    int index_table; //!< Index of table in data::thermal_scatt
+    int index_nuclide; //!< Index in nuclide_
+    double fraction; //!< How often to use table
+  };
+
+  //----------------------------------------------------------------------------
+  // Constructors, destructors, factory functions
+  Material() {};
+  explicit Material(pugi::xml_node material_node);
+  ~Material();
+
+  //----------------------------------------------------------------------------
+  // Methods
+
+  void calculate_xs(Particle& p) const;
+
+  //! Assign thermal scattering tables to specific nuclides within the material
+  //! so the code knows when to apply bound thermal scattering data
+  void init_thermal();
+
+  //! Set up mapping between global nuclides vector and indices in nuclide_
+  void init_nuclide_index();
+
+  //! Finalize the material, assigning tables, normalize density, etc.
+  void finalize();
+
+  //! Write material data to HDF5
+  void to_hdf5(hid_t group) const;
+
+  //! Add nuclide to the material
+  //
+  //! \param[in] nuclide Name of the nuclide
+  //! \param[in] density Density of the nuclide in [atom/b-cm]
+  void add_nuclide(const std::string& nuclide, double density);
+
+  //! Set atom densities for the material
+  //
+  //! \param[in] name Name of each nuclide
+  //! \param[in] density Density of each nuclide in [atom/b-cm]
+  void set_densities(const std::vector<std::string>& name,
+    const std::vector<double>& density);
+
+  //----------------------------------------------------------------------------
+  // Accessors
+
+  //! Get density in [atom/b-cm]
+  //! \return Density in [atom/b-cm]
+  double density() const { return density_; }
+
+  //! Get density in [g/cm^3]
+  //! \return Density in [g/cm^3]
+  double density_gpcc() const { return density_gpcc_; }
+
+  //! Get name
+  //! \return Material name
+  const std::string& name() const { return name_; }
+
+  //! Set name
+  void set_name(const std::string& name) { name_ = name; }
+
+  //! Set total density of the material
+  //
+  //! \param[in] density Density value
+  //! \param[in] units Units of density
+  void set_density(double density, gsl::cstring_span units);
+
+  //! Get nuclides in material
+  //! \return Indices into the global nuclides vector
+  gsl::span<const int> nuclides() const { return {nuclide_.data(), nuclide_.size()}; }
+
+  //! Get densities of each nuclide in material
+  //! \return Densities in [atom/b-cm]
+  gsl::span<const double> densities() const { return {atom_density_.data(), atom_density_.size()}; }
+
+  //! Get ID of material
+  //! \return ID of material
+  int32_t id() const { return id_; }
+
+  //! Assign a unique ID to the material
+  //! \param[in] Unique ID to assign. A value of -1 indicates that an ID
+  //!   should be automatically assigned.
+  void set_id(int32_t id);
+
+  //! Get whether material is fissionable
+  //! \return Whether material is fissionable
+  bool fissionable() const { return fissionable_; }
+
+  //! Get volume of material
+  //! \return Volume in [cm^3]
+  double volume() const;
+
+  //----------------------------------------------------------------------------
+  // Data
+  int32_t id_ {-1}; //!< Unique ID
+  std::string name_; //!< Name of material
+  std::vector<int> nuclide_; //!< Indices in nuclides vector
+  std::vector<int> element_; //!< Indices in elements vector
+  xt::xtensor<double, 1> atom_density_; //!< Nuclide atom density in [atom/b-cm]
+  double density_; //!< Total atom density in [atom/b-cm]
+  double density_gpcc_; //!< Total atom density in [g/cm^3]
+  double volume_ {-1.0}; //!< Volume in [cm^3]
+  bool fissionable_ {false}; //!< Does this material contain fissionable nuclides
+  bool depletable_ {false}; //!< Is the material depletable?
+  std::vector<bool> p0_; //!< Indicate which nuclides are to be treated with iso-in-lab scattering
+
+  // To improve performance of tallying, we store an array (direct address
+  // table) that indicates for each nuclide in data::nuclides the index of the
+  // corresponding nuclide in the nuclide_ vector. If it is not present in the
+  // material, the entry is set to -1.
+  std::vector<int> mat_nuclide_index_;
+
+  // Thermal scattering tables
+  std::vector<ThermalTable> thermal_tables_;
+
+  //! \brief Default temperature for cells containing this material.
+  //!
+  //! A negative value indicates no default temperature was specified.
+  double temperature_ {-1};
+
+  std::unique_ptr<Bremsstrahlung> ttb_;
+
+private:
+  //----------------------------------------------------------------------------
+  // Private methods
+
+  //! Calculate the collision stopping power
+  void collision_stopping_power(double* s_col, bool positron);
+
+  //! Initialize bremsstrahlung data
+  void init_bremsstrahlung();
+
+  //! Normalize density
+  void normalize_density();
+
+  void calculate_neutron_xs(Particle& p) const;
+  void calculate_photon_xs(Particle& p) const;
+
+  //----------------------------------------------------------------------------
+  // Private data members
+  gsl::index index_;
+};
+
+//==============================================================================
+// Non-member functions
+//==============================================================================
+
+//! Calculate Sternheimer adjustment factor
+double sternheimer_adjustment(const std::vector<double>& f, const
+  std::vector<double>& e_b_sq, double e_p_sq, double n_conduction, double
+  log_I, double tol, int max_iter);
+
+//! Calculate density effect correction
+double density_effect(const std::vector<double>& f, const std::vector<double>&
+  e_b_sq, double e_p_sq, double n_conduction, double rho, double E, double tol,
+  int max_iter);
+
+//! Read material data from materials.xml
+void read_materials_xml();
+
+void free_memory_material();
+
+} // namespace openmc
+#endif // OPENMC_MATERIAL_H