address PR comments

include/openmc/bank.h

@@ -16,11 +16,11 @@ namespace openmc {
 
 namespace simulation {
 
-extern vector<ParticleBank> source_bank;
+extern vector<SourceSite> source_bank;
 
-extern SharedArray<ParticleBank> surf_source_bank;
+extern SharedArray<SourceSite> surf_source_bank;
 
-extern SharedArray<ParticleBank> fission_bank;
+extern SharedArray<SourceSite> fission_bank;
 
 extern vector<int64_t> progeny_per_particle;
 

include/openmc/cell.h

@@ -303,7 +303,7 @@ private:
   //! `partitions_.back()` gives the cells that lie on the positive side of
   //! `surfs_.back()`.  Otherwise, `partitions_[i]` gives cells sandwiched
   //! between `surfs_[i-1]` and `surfs_[i]`.
-  vector<std::vector<int32_t>> partitions_;
+  vector<vector<int32_t>> partitions_;
 };
 
 

include/openmc/constants.h

@@ -13,9 +13,9 @@
 
 namespace openmc {
 
-using double_2dvec = vector<std::vector<double>>;
-using double_3dvec = vector<std::vector<std::vector<double>>>;
-using double_4dvec = vector<std::vector<std::vector<std::vector<double>>>>;
+using double_2dvec = vector<vector<double>>;
+using double_3dvec = vector<vector<vector<double>>>;
+using double_4dvec = vector<vector<vector<vector<double>>>>;
 
 // ============================================================================
 // VERSIONING NUMBERS

include/openmc/cross_sections.h

@@ -65,8 +65,8 @@ void read_cross_sections_xml();
 //
 //! \param[in] nuc_temps Temperatures for each nuclide in [K]
 //! \param[in] thermal_temps Temperatures for each thermal scattering table in [K]
-void read_ce_cross_sections(const vector<std::vector<double>>& nuc_temps,
-  const vector<std::vector<double>>& thermal_temps);
+void read_ce_cross_sections(const vector<vector<double>>& nuc_temps,
+  const vector<vector<double>>& thermal_temps);
 
 //! Read cross_sections.xml and populate data libraries
 void read_ce_cross_sections_xml();

include/openmc/geometry_aux.h

@@ -42,8 +42,8 @@ void assign_temperatures();
 //!   table
 //==============================================================================
 
-void get_temperatures(vector<std::vector<double>>& nuc_temps,
-  vector<std::vector<double>>& thermal_temps);
+void get_temperatures(
+  vector<vector<double>>& nuc_temps, vector<vector<double>>& thermal_temps);
 
 //==============================================================================
 //! \brief Perform final setup for geometry

include/openmc/material.h

@@ -197,9 +197,9 @@ double sternheimer_adjustment(const vector<double>& f,
   double log_I, double tol, int max_iter);
 
 //! Calculate density effect correction
-double density_effect(const 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);
+double density_effect(const vector<double>& f, const 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();

include/openmc/mesh.h

@@ -122,7 +122,7 @@ public:
   //!   of the plot's axes.  For example an xy-slice plot will get back a vector
   //!   of x-coordinates and another of y-coordinates.  These vectors may be
   //!   empty for low-dimensional meshes.
-  virtual std::pair<vector<double>, std::vector<double>> plot(
+  virtual std::pair<vector<double>, vector<double>> plot(
     Position plot_ll, Position plot_ur) const = 0;
 
   //! Return a string representation of the mesh bin
@@ -159,7 +159,7 @@ public:
   //! \param[in] Number of bank sites
   //! \param[out] Whether any bank sites are outside the mesh
   xt::xtensor<double, 1> count_sites(
-    const ParticleBank* bank, int64_t length, bool* outside) const;
+    const SourceSite* bank, int64_t length, bool* outside) const;
 
   //! Get bin given mesh indices
   //
@@ -244,7 +244,7 @@ public:
 
   double negative_grid_boundary(int* ijk, int i) const override;
 
-  std::pair<vector<double>, std::vector<double>> plot(
+  std::pair<vector<double>, vector<double>> plot(
     Position plot_ll, Position plot_ur) const override;
 
   void to_hdf5(hid_t group) const override;
@@ -257,7 +257,7 @@ public:
   //! \param[out] Whether any bank sites are outside the mesh
   //! \return Array indicating number of sites in each mesh/energy bin
   xt::xtensor<double, 1> count_sites(
-    const ParticleBank* bank, int64_t length, bool* outside) const;
+    const SourceSite* bank, int64_t length, bool* outside) const;
 
   // Data members
   double volume_frac_; //!< Volume fraction of each mesh element
@@ -285,12 +285,12 @@ public:
 
   double negative_grid_boundary(int* ijk, int i) const override;
 
-  std::pair<vector<double>, std::vector<double>> plot(
+  std::pair<vector<double>, vector<double>> plot(
     Position plot_ll, Position plot_ur) const override;
 
   void to_hdf5(hid_t group) const override;
 
-  vector<std::vector<double>> grid_;
+  vector<vector<double>> grid_;
 
   int set_grid();
 };
@@ -382,7 +382,7 @@ public:
 
   int n_surface_bins() const override;
 
-  std::pair<vector<double>, std::vector<double>> plot(
+  std::pair<vector<double>, vector<double>> plot(
     Position plot_ll, Position plot_ur) const override;
 
   std::string library() const override;
@@ -534,7 +534,7 @@ public:
 
   int n_surface_bins() const override;
 
-  std::pair<vector<double>, std::vector<double>> plot(
+  std::pair<vector<double>, vector<double>> plot(
     Position plot_ll, Position plot_ur) const override;
 
   void add_score(const std::string& var_name) override;

include/openmc/mgxs.h

@@ -64,7 +64,7 @@ class Mgxs {
     void init(const std::string& in_name, double in_awr,
       const vector<double>& in_kTs, bool in_fissionable,
       AngleDistributionType in_scatter_format, bool in_is_isotropic,
-      const vector<double>& in_polar, const std::vector<double>& in_azimuthal);
+      const vector<double>& in_polar, const vector<double>& in_azimuthal);
 
     //! \brief Initializes the Mgxs object metadata from the HDF5 file
     //!
@@ -84,9 +84,8 @@ class Mgxs {
     //! @param micro_ts The temperature index of the microscopic objects that
     //!   corresponds to the temperature of interest.
     //! @param this_t The temperature index of the macroscopic object.
-    void combine(const vector<Mgxs*>& micros,
-      const std::vector<double>& scalars, const vector<int>& micro_ts,
-      int this_t);
+    void combine(const vector<Mgxs*>& micros, const vector<double>& scalars,
+      const vector<int>& micro_ts, int this_t);
 
     //! \brief Checks to see if this and that are able to be combined
     //!
@@ -124,7 +123,7 @@ class Mgxs {
     //! @param num_group number of energy groups
     //! @param num_delay number of delayed groups
     Mgxs(const std::string& in_name, const vector<double>& mat_kTs,
-      const vector<Mgxs*>& micros, const std::vector<double>& atom_densities,
+      const vector<Mgxs*>& micros, const vector<double>& atom_densities,
       int num_group, int num_delay);
 
     //! \brief Provides a cross section value given certain parameters

include/openmc/mgxs_interface.h

@@ -23,7 +23,7 @@ public:
   // of XS to read and the corresponding temperatures for each XS
   MgxsInterface(const std::string& path_cross_sections,
     const vector<std::string> xs_to_read,
-    const vector<std::vector<double>> xs_temps);
+    const vector<vector<double>> xs_temps);
 
   // Does things to construct after the nuclides and temperatures to
   // read have been specified.
@@ -31,7 +31,7 @@ public:
 
   // Set which nuclides and temperatures are to be read
   void set_nuclides_and_temperatures(
-    vector<std::string> xs_to_read, vector<std::vector<double>> xs_temps);
+    vector<std::string> xs_to_read, vector<vector<double>> xs_temps);
 
   // Add an Mgxs object to be managed
   void add_mgxs(
@@ -45,20 +45,20 @@ public:
   void create_macro_xs();
 
   // Get the kT values which are used in the OpenMC model
-  vector<std::vector<double>> get_mat_kTs();
+  vector<vector<double>> get_mat_kTs();
 
   int num_energy_groups_;
   int num_delayed_groups_;
   vector<std::string> xs_names_;                 // available names in HDF5 file
   vector<std::string> xs_to_read_;               // XS which appear in materials
-  vector<std::vector<double>> xs_temps_to_read_; // temperatures used
+  vector<vector<double>> xs_temps_to_read_;      // temperatures used
   std::string cross_sections_path_; // path to MGXS h5 file
   vector<Mgxs> nuclides_;
   vector<Mgxs> macro_xs_;
   vector<double> energy_bins_;
   vector<double> energy_bin_avg_;
   vector<double> rev_energy_bins_;
-  vector<std::vector<double>> nuc_temps_; // all available temperatures
+  vector<vector<double>> nuc_temps_; // all available temperatures
 };
 
 namespace data {

include/openmc/particle.h

@@ -51,7 +51,7 @@ public:
   //! site may have been produced from an external source, from fission, or
   //! simply as a secondary particle.
   //! \param src Source site data
-  void from_source(const ParticleBank* src);
+  void from_source(const SourceSite* src);
 
   // Coarse-grained particle events
   void event_calculate_xs();

include/openmc/particle_data.h

@@ -1,5 +1,5 @@
-#ifndef OPENMC_PARTICLE_REPRESENTATION_H
-#define OPENMC_PARTICLE_REPRESENTATION_H
+#ifndef OPENMC_PARTICLE_DATA_H
+#define OPENMC_PARTICLE_DATA_H
 
 #include "openmc/array.h"
 #include "openmc/constants.h"
@@ -40,7 +40,7 @@ enum class ParticleType { neutron, photon, electron, positron };
 //! NOTE: This structure is also used on the python side, and is defined
 //! in lib/core.py. Changes made to the type here must also be made to the
 //! python defintion.
-struct ParticleBank {
+struct SourceSite {
   Position r;
   Direction u;
   double E;
@@ -247,7 +247,7 @@ private:
   int stream_;                // current RNG stream
 
   // Secondary particle bank
-  vector<ParticleBank> secondary_bank_;
+  vector<SourceSite> secondary_bank_;
 
   int64_t current_work_; // current work index
 
@@ -255,7 +255,7 @@ private:
 
   vector<FilterMatch> filter_matches_; // tally filter matches
 
-  vector<std::vector<Position>> tracks_; // tracks for outputting to file
+  vector<vector<Position>> tracks_; // tracks for outputting to file
 
   vector<NuBank> nu_bank_; // bank of most recently fissioned particles
 
@@ -370,7 +370,7 @@ public:
   uint64_t* seeds() { return seeds_; }
   int& stream() { return stream_; }
 
-  ParticleBank& secondary_bank(const int& i) { return secondary_bank_[i]; }
+  SourceSite& secondary_bank(const int& i) { return secondary_bank_[i]; }
   decltype(secondary_bank_)& secondary_bank() { return secondary_bank_; }
   int64_t& current_work() { return current_work_; }
   const int64_t& current_work() const { return current_work_; }
@@ -450,4 +450,4 @@ public:
 
 } // namespace openmc
 
-#endif // OPENMC_PARTICLE_REPRESENTATION_H
+#endif // OPENMC_PARTICLE_DATA_H

include/openmc/physics.h

@@ -80,7 +80,7 @@ Direction sample_cxs_target_velocity(double awr, double E, Direction u, double k
   uint64_t* seed);
 
 void sample_fission_neutron(int i_nuclide, const Reaction& rx, double E_in,
-  ParticleBank* site, uint64_t* seed);
+  SourceSite* site, uint64_t* seed);
 
 //! handles all reactions with a single secondary neutron (other than fission),
 //! i.e. level scattering, (n,np), (n,na), etc.

include/openmc/physics_mg.h

@@ -7,7 +7,6 @@
 #include "openmc/capi.h"
 #include "openmc/nuclide.h"
 #include "openmc/particle.h"
-#include "openmc/vector.h"
 
 namespace openmc {
 

include/openmc/source.h

@@ -35,7 +35,7 @@ public:
   virtual ~Source() = default;
 
   // Methods that must be implemented
-  virtual ParticleBank sample(uint64_t* seed) const = 0;
+  virtual SourceSite sample(uint64_t* seed) const = 0;
 
   // Methods that can be overridden
   virtual double strength() const { return 1.0; }
@@ -54,7 +54,7 @@ public:
   //! Sample from the external source distribution
   //! \param[inout] seed Pseudorandom seed pointer
   //! \return Sampled site
-  ParticleBank sample(uint64_t* seed) const override;
+  SourceSite sample(uint64_t* seed) const override;
 
   // Properties
   ParticleType particle_type() const { return particle_; }
@@ -83,10 +83,10 @@ public:
   explicit FileSource(std::string path);
 
   // Methods
-  ParticleBank sample(uint64_t* seed) const override;
+  SourceSite sample(uint64_t* seed) const override;
 
 private:
-  vector<ParticleBank> sites_; //!< Source sites from a file
+  vector<SourceSite> sites_; //!< Source sites from a file
 };
 
 //==============================================================================
@@ -100,7 +100,7 @@ public:
   ~CustomSourceWrapper();
 
   // Defer implementation to custom source library
-  ParticleBank sample(uint64_t* seed) const override
+  SourceSite sample(uint64_t* seed) const override
   {
     return custom_source_->sample(seed);
   }
@@ -124,7 +124,7 @@ extern "C" void initialize_source();
 //! source strength
 //! \param[inout] seed Pseudorandom seed pointer
 //! \return Sampled source site
-ParticleBank sample_external_source(uint64_t* seed);
+SourceSite sample_external_source(uint64_t* seed);
 
 void free_memory_source();
 

include/openmc/state_point.h

@@ -16,7 +16,7 @@ vector<int64_t> calculate_surf_source_size();
 void write_source_point(const char* filename, bool surf_source_bank = false);
 void write_source_bank(hid_t group_id, bool surf_source_bank);
 void read_source_bank(
-  hid_t group_id, vector<ParticleBank>& sites, bool distribute);
+  hid_t group_id, vector<SourceSite>& sites, bool distribute);
 void write_tally_results_nr(hid_t file_id);
 void restart_set_keff();
 void write_unstructured_mesh_results();

include/openmc/vector.h

@@ -17,7 +17,7 @@
 #include <vector>
 
 namespace openmc {
-using std::vector;
+using vector;
 }
 
 #endif // OPENMC_VECTOR_H

include/openmc/xsdata.h

@@ -137,7 +137,7 @@ class XsData {
     //! @param micros Microscopic objects to combine.
     //! @param scalars Scalars to multiply the microscopic data by.
     void combine(
-      const vector<XsData*>& those_xs, const std::vector<double>& scalars);
+      const vector<XsData*>& those_xs, const vector<double>& scalars);
 
     //! \brief Checks to see if this and that are able to be combined
     //!