Merge remote-tracking branch 'upstream/develop' into cmfd-capi

include/openmc/capi.h

@@ -60,7 +60,7 @@ extern "C" {
   int openmc_material_get_id(int32_t index, int32_t* id);
   int openmc_material_get_fissionable(int32_t index, bool* fissionable);
   int openmc_material_get_volume(int32_t index, double* volume);
-  int openmc_material_set_density(int32_t index, double density);
+  int openmc_material_set_density(int32_t index, double density, const char* units);
   int openmc_material_set_densities(int32_t index, int n, const char** name, const double* density);
   int openmc_material_set_id(int32_t index, int32_t id);
   int openmc_material_set_volume(int32_t index, double volume);
@@ -135,17 +135,10 @@ extern "C" {
 
   // Global variables
   extern char openmc_err_msg[256];
-  extern int32_t n_cells;
-  extern int32_t n_lattices;
-  extern int32_t n_materials;
   extern int n_nuclides;
-  extern int32_t n_plots;
   extern int32_t n_realizations;
   extern int32_t n_sab_tables;
-  extern int32_t n_sources;
-  extern int32_t n_surfaces;
   extern int32_t n_tallies;
-  extern int32_t n_universes;
 
   // Variables that are shared by necessity (can be removed from public header
   // later)

include/openmc/cell.h

@@ -39,16 +39,21 @@ constexpr int32_t OP_UNION        {std::numeric_limits<int32_t>::max() - 4};
 // Global variables
 //==============================================================================
 
+class Cell;
+class Universe;
+
+namespace model {
+
 extern "C" int32_t n_cells;
 
-class Cell;
 extern std::vector<Cell*> cells;
 extern std::unordered_map<int32_t, int32_t> cell_map;
 
-class Universe;
 extern std::vector<Universe*> universes;
 extern std::unordered_map<int32_t, int32_t> universe_map;
 
+} // namespace model
+
 //==============================================================================
 //! A geometry primitive that fills all space and contains cells.
 //==============================================================================
@@ -145,13 +150,13 @@ public:
 
   virtual ~Cell() {}
 };
- 
+
 class CSGCell : public Cell
 {
 public:
 
   CSGCell();
-  
+
   explicit CSGCell(pugi::xml_node cell_node);
 
   bool
@@ -163,7 +168,7 @@ public:
   void to_hdf5(hid_t group_id) const;
 
 
-  
+
 protected:
   bool contains_simple(Position r, Direction u, int32_t on_surface) const;
   bool contains_complex(Position r, Direction u, int32_t on_surface) const;
@@ -183,6 +188,6 @@ public:
 
 };
 #endif
- 
+
 } // namespace openmc
 #endif // OPENMC_CELL_H

include/openmc/constants.h

@@ -25,7 +25,7 @@ constexpr int VERSION_RELEASE {0};
 constexpr std::array<int, 3> VERSION {VERSION_MAJOR, VERSION_MINOR, VERSION_RELEASE};
 
 // HDF5 data format
-constexpr int HDF5_VERSION[] {1, 0};
+constexpr int HDF5_VERSION[] {2, 0};
 
 // Version numbers for binary files
 constexpr std::array<int, 2> VERSION_PARTICLE_RESTART {2, 0};

include/openmc/cross_sections.h

@@ -0,0 +1,67 @@
+#ifndef OPENMC_CROSS_SECTIONS_H
+#define OPENMC_CROSS_SECTIONS_H
+
+#include "pugixml.hpp"
+
+#include <string>
+#include <map>
+#include <vector>
+
+namespace openmc {
+
+//==============================================================================
+// Library class
+//==============================================================================
+
+class Library {
+public:
+  // Types, enums
+  enum class Type {
+    neutron = 1, photon = 3, thermal = 2, multigroup = 4, wmp = 5
+  };
+
+  // Constructors
+  Library() { };
+  Library(pugi::xml_node node, const std::string& directory);
+
+  // Comparison operator (for using in map)
+  bool operator<(const Library& other) {
+    return path_ < other.path_;
+  }
+
+  // Data members
+  Type type_; //!< Type of data library
+  std::vector<std::string> materials_; //!< Materials contained in library
+  std::string path_; //!< File path to library
+};
+
+using LibraryKey = std::pair<Library::Type, std::string>;
+
+//==============================================================================
+// Global variable declarations
+//==============================================================================
+
+namespace data {
+
+//!< Data libraries
+extern std::vector<Library> libraries;
+
+//! Maps (type, name) to index in libraries
+extern std::map<LibraryKey, std::size_t> library_map;
+
+} // namespace data
+
+//==============================================================================
+// Non-member functions
+//==============================================================================
+
+//! Read cross sections file (either XML or multigroup H5) and populate data
+//! libraries
+extern "C" void read_cross_sections_xml();
+
+//! Read cross_sections.xml and populate data libraries
+void read_ce_cross_sections_xml();
+
+} // namespace openmc
+
+#endif // OPENMC_CROSS_SECTIONS_H

include/openmc/dagmc.h

@@ -10,12 +10,24 @@
 
 namespace openmc {
 
+//==============================================================================
+// Global variables
+//==============================================================================
+
+namespace model {
+
 extern moab::DagMC* DAG;
 
+} // namespace model
+
+//==============================================================================
+// Non-member functions
+//==============================================================================
+
 extern "C" void load_dagmc_geometry();
 extern "C" void free_memory_dagmc();
 
-}
+} // namespace openmc
 
 #endif // DAGMC
 

include/openmc/eigenvalue.h

@@ -18,6 +18,8 @@ namespace openmc {
 // Global variables
 //==============================================================================
 
+namespace simulation {
+
 extern double keff_generation; //!<  Single-generation k on each processor
 extern std::array<double, 2> k_sum; //!< Used to reduce sum and sum_sq
 extern std::vector<double> entropy; //!< Shannon entropy at each generation
@@ -26,6 +28,8 @@ extern xt::xtensor<double, 1> source_frac; //!< Source fraction for UFS
 extern "C" int64_t n_bank;
 #pragma omp threadprivate(n_bank)
 
+} // namespace simulation
+
 //==============================================================================
 // Non-member functions
 //==============================================================================

include/openmc/geometry.h

@@ -13,10 +13,14 @@ namespace openmc {
 // Global variables
 //==============================================================================
 
-extern "C" int openmc_root_universe;
+namespace model {
+
+extern "C" int root_universe;
 
 extern std::vector<int64_t> overlap_check_count;
 
+} // namespace model
+
 //==============================================================================
 //! Check for overlapping cells at a particle's position.
 //==============================================================================

include/openmc/lattice.h

@@ -31,10 +31,14 @@ enum class LatticeType {
 //==============================================================================
 
 class Lattice;
-extern std::vector<Lattice*> lattices;
 
+namespace model {
+
+extern std::vector<Lattice*> lattices;
 extern std::unordered_map<int32_t, int32_t> lattice_map;
 
+} // namespace model
+
 //==============================================================================
 //! \class Lattice
 //! \brief Abstract type for ordered array of universes.

include/openmc/material.h

@@ -14,9 +14,14 @@ namespace openmc {
 //==============================================================================
 
 class Material;
+
+namespace model {
+
 extern std::vector<Material*> materials;
 extern std::unordered_map<int32_t, int32_t> material_map;
 
+} // namespace model
+
 //==============================================================================
 //! A substance with constituent nuclides and thermal scattering data
 //==============================================================================

include/openmc/mesh.h

@@ -17,6 +17,19 @@
 
 namespace openmc {
 
+//==============================================================================
+// Global variables
+//==============================================================================
+
+class RegularMesh;
+
+namespace model {
+
+extern std::vector<std::unique_ptr<RegularMesh>> meshes;
+extern std::unordered_map<int32_t, int32_t> mesh_map;
+
+} // namespace model
+
 //==============================================================================
 //! Tessellation of n-dimensional Euclidean space by congruent squares or cubes
 //==============================================================================
@@ -117,15 +130,6 @@ extern "C" void read_meshes(pugi::xml_node* root);
 //! \param[in] group HDF5 group
 extern "C" void meshes_to_hdf5(hid_t group);
 
-//==============================================================================
-// Global variables
-//==============================================================================
-
-extern std::vector<std::unique_ptr<RegularMesh>> meshes;
-
-extern std::unordered_map<int32_t, int32_t> mesh_map;
-
-
 } // namespace openmc
 
 #endif // OPENMC_MESH_H

include/openmc/mgxs_interface.h

@@ -15,6 +15,8 @@ namespace openmc {
 // Global variables
 //==============================================================================
 
+namespace data {
+
 extern std::vector<Mgxs> nuclides_MG;
 extern std::vector<Mgxs> macro_xs;
 extern "C" int num_energy_groups;
@@ -22,6 +24,8 @@ extern std::vector<double> energy_bins;
 extern std::vector<double> energy_bin_avg;
 extern std::vector<double> rev_energy_bins;
 
+} // namespace data
+
 //==============================================================================
 // Mgxs data loading interface methods
 //==============================================================================

include/openmc/nuclide.h

@@ -14,11 +14,15 @@ namespace openmc {
 // Global variables
 //==============================================================================
 
+namespace data {
+
 // Minimum/maximum transport energy for each particle type. Order corresponds to
 // that of the ParticleType enum
 extern std::array<double, 2> energy_min;
 extern std::array<double, 2> energy_max;
 
+} // namespace data
+
 //===============================================================================
 //! Cached microscopic cross sections for a particular nuclide at the current
 //! energy

include/openmc/physics_mg.h

@@ -10,34 +10,29 @@
 
 namespace openmc {
 
-//TODO: Remove energy_bin_avg and material_xs parameters when they reside on
+//TODO: Remove material_xs parameters when they reside on
 // the C-side this should happen after materials, physics, input, and tallies
 // are brought over
 
 //! \brief samples particle behavior after a collision event.
 //! \param p Particle to operate on
-//! \param energy_bin_avg Average energy within each energy bin
 //! \param material_xs The cross section cache for the current material
 extern "C" void
-collision_mg(Particle* p, const double* energy_bin_avg,
-     const MaterialMacroXS* material_xs);
+collision_mg(Particle* p, const MaterialMacroXS* material_xs);
 
 //! \brief samples a reaction type.
 //!
 //! Note that there is special logic when suvival biasing is turned on since
 //! fission and disappearance are treated implicitly.
 //! \param p Particle to operate on
-//! \param energy_bin_avg Average energy within each energy bin
 //! \param material_xs The cross section cache for the current material
 void
-sample_reaction(Particle* p, const double* energy_bin_avg,
-     const MaterialMacroXS* material_xs);
+sample_reaction(Particle* p, const MaterialMacroXS* material_xs);
 
 //! \brief Samples the scattering event
 //! \param p Particle to operate on
-//! \param energy_bin_avg Average energy within each energy bin
 void
-scatter(Particle* p, const double* energy_bin_avg);
+scatter(Particle* p);
 
 //! \brief Determines the average total, prompt and delayed neutrons produced
 //! from fission and creates the appropriate bank sites.

include/openmc/plot.h

@@ -18,14 +18,14 @@ namespace openmc {
 // Global variables
 //===============================================================================
 
-extern int PLOT_LEVEL_LOWEST; //!< lower bound on plot universe level
+class Plot;
 
+namespace model {
+
+extern std::vector<Plot> plots; //!< Plot instance container
 extern std::unordered_map<int, int> plot_map; //!< map of plot ids to index
 
-extern "C" int32_t n_plots; //!< number of plots in openmc run
-
-class Plot;
-extern std::vector<Plot> plots; //!< Plot instance container
+} // namespace model
 
 //===============================================================================
 // RGBColor holds color information for plotted objects
@@ -124,8 +124,7 @@ void draw_mesh_lines(Plot pl, ImageData& data);
 //! Write a ppm image to file using a plot object's image data
 //! \param[in] plot object
 //! \param[out] image data associated with the plot object
-void output_ppm(Plot pl,
-                const ImageData& data);
+void output_ppm(Plot pl, const ImageData& data);
 
 //! Get the rgb color for a given particle position in a plot
 //! \param[in] particle with position for current pixel
@@ -141,7 +140,7 @@ void position_rgb(Particle p, Plot pl, RGBColor& rgb, int& id);
 //! \param[out] dataset pointer to voxesl data
 //! \param[out] pointer to memory space of voxel data
 void voxel_init(hid_t file_id, const hsize_t* dims, hid_t* dspace,
-                           hid_t* dset, hid_t* memspace);
+                hid_t* dset, hid_t* memspace);
 
 //! Write a section of the voxel data to hdf5
 //! \param[in] voxel slice
@@ -149,7 +148,8 @@ void voxel_init(hid_t file_id, const hsize_t* dims, hid_t* dspace,
 //! \param[out] dataset pointer to voxesl data
 //! \param[out] pointer to data to write
 void voxel_write_slice(int x, hid_t dspace, hid_t dset,
-                                  hid_t memspace, void* buf);
+                       hid_t memspace, void* buf);
+
 //! Close voxel file entities
 //! \param[in] data space to close
 //! \param[in] dataset to close

include/openmc/settings.h

@@ -52,7 +52,6 @@ extern "C" bool dagmc;                   //!< indicator of DAGMC geometry
 // Paths to various files
 extern std::string path_cross_sections;   //!< path to cross_sections.xml
 extern std::string path_input;            //!< directory where main .xml files resides
-extern std::string path_multipole;        //!< directory containing multipole files
 extern std::string path_output;           //!< directory where output files are written
 extern std::string path_particle_restart; //!< path to a particle restart file
 extern std::string path_source;
@@ -62,7 +61,7 @@ extern std::string path_statepoint;       //!< path to a statepoint file
 extern "C" int32_t index_entropy_mesh;  //!< Index of entropy mesh in global mesh array
 extern "C" int32_t index_ufs_mesh;      //!< Index of UFS mesh in global mesh array
 extern "C" int32_t index_cmfd_mesh;     //!< Index of CMFD mesh in global mesh array
- 
+
 extern "C" int32_t n_batches;      //!< number of (inactive+active) batches
 extern "C" int32_t n_inactive;     //!< number of inactive batches
 extern "C" int32_t gen_per_batch;  //!< number of generations per batch
@@ -77,6 +76,7 @@ extern "C" int n_max_batches;            //!< Maximum number of batches
 extern "C" int res_scat_method;          //!< resonance upscattering method
 extern "C" double res_scat_energy_min;   //!< Min energy in [eV] for res. upscattering
 extern "C" double res_scat_energy_max;   //!< Max energy in [eV] for res. upscattering
+extern std::vector<std::string> res_scat_nuclides;  //!< Nuclides using res. upscattering treatment
 extern "C" int run_mode;                 //!< Run mode (eigenvalue, fixed src, etc.)
 extern std::unordered_set<int> sourcepoint_batch; //!< Batches when source should be written
 extern std::unordered_set<int> statepoint_batch; //!< Batches when state should be written

include/openmc/source.h

@@ -16,6 +16,18 @@
 
 namespace openmc {
 
+//==============================================================================
+// Global variables
+//==============================================================================
+
+class SourceDistribution;
+
+namespace model {
+
+extern std::vector<SourceDistribution> external_sources;
+
+} // namespace model
+
 //==============================================================================
 //! External source distribution
 //==============================================================================
@@ -40,12 +52,6 @@ private:
   UPtrDist energy_; //!< Energy distribution
 };
 
-//==============================================================================
-// Global variables
-//==============================================================================
-
-extern std::vector<SourceDistribution> external_sources;
-
 //==============================================================================
 // Functions
 //==============================================================================

include/openmc/string_functions.h

@@ -1,20 +0,0 @@
-//! \file string_functions.h
-//! A collection of helper routines for C-strings and STL strings
-
-#ifndef OPENMC_STRING_FUNCTIONS_H
-#define OPENMC_STRING_FUNCTIONS_H
-
-#include <string>
-
-namespace openmc {
-
-std::string& strtrim(std::string& s);
-
-char* strtrim(char* c_str);
-
-void to_lower(std::string& str);
-
-int word_count(std::string const& str);
-
-} // namespace openmc
-#endif // STRING_FUNCTIONS_H

include/openmc/string_utils.h

@@ -1,42 +1,24 @@
 #ifndef OPENMC_STRING_UTILS_H
 #define OPENMC_STRING_UTILS_H
 
-#include <algorithm>
 #include <string>
 #include <vector>
 
 namespace openmc {
 
-inline std::vector<std::string>
-split(const std::string& in)
-{
-  std::vector<std::string> out;
+std::string& strtrim(std::string& s);
 
-  for (int i = 0; i < in.size(); ) {
-    // Increment i until we find a non-whitespace character.
-    if (std::isspace(in[i])) {
-      i++;
+char* strtrim(char* c_str);
 
-    } else {
-      // Find the next whitespace character at j.
-      int j = i + 1;
-      while (j < in.size() && std::isspace(in[j]) == 0) {j++;}
+void to_lower(std::string& str);
 
-      // Push-back everything between i and j.
-      out.push_back(in.substr(i, j-i));
-      i = j + 1; // j is whitespace so leapfrog to j+1
-    }
-  }
+int word_count(std::string const& str);
 
-  return out;
-}
+std::vector<std::string> split(const std::string& in);
 
-inline bool
-ends_with(const std::string& value, const std::string& ending)
-{
-  if (ending.size() > value.size()) return false;
-  return std::equal(ending.rbegin(), ending.rend(), value.rbegin());
-}
+bool ends_with(const std::string& value, const std::string& ending);
+
+bool starts_with(const std::string& value, const std::string& beginning);
 
 } // namespace openmc
 #endif // OPENMC_STRING_UTILS_H

include/openmc/surface.h

@@ -32,13 +32,15 @@ extern "C" const int BC_PERIODIC;
 // Global variables
 //==============================================================================
 
-extern "C" int32_t n_surfaces;
-
 class Surface;
-extern std::vector<Surface*> surfaces;
 
+namespace model {
+
+extern std::vector<Surface*> surfaces;
 extern std::map<int, int> surface_map;
 
+} // namespace model
+
 //==============================================================================
 //! Coordinates for an axis-aligned cube that bounds a geometric object.
 //==============================================================================

include/openmc/tallies/filter.h

@@ -29,7 +29,7 @@ public:
 // Without an explicit instantiation of vector<FilterMatch>, the Intel compiler
 // will complain about the threadprivate directive on filter_matches. Note that
 // this has to happen *outside* of the openmc namespace
-template class std::vector<openmc::FilterMatch>;
+extern template class std::vector<openmc::FilterMatch>;
 
 namespace openmc {
 
@@ -77,13 +77,20 @@ public:
 // Global variables
 //==============================================================================
 
-extern "C" int32_t n_filters;
+namespace simulation {
 
 extern std::vector<FilterMatch> filter_matches;
 #pragma omp threadprivate(filter_matches)
 
+} // namespace simulation
+
+namespace model {
+
+extern "C" int32_t n_filters;
 extern std::vector<std::unique_ptr<Filter>> tally_filters;
 
+} // namespace model
+
 //==============================================================================
 
 extern "C" void free_memory_tally_c();

include/openmc/timer.h

@@ -5,6 +5,27 @@
 
 namespace openmc {
 
+//==============================================================================
+// Global variables
+//==============================================================================
+
+class Timer;
+
+namespace simulation {
+
+extern Timer time_active;
+extern Timer time_bank;
+extern Timer time_bank_sample;
+extern Timer time_bank_sendrecv;
+extern Timer time_finalize;
+extern Timer time_inactive;
+extern Timer time_initialize;
+extern Timer time_tallies;
+extern Timer time_total;
+extern Timer time_transport;
+
+} // namespace simulation
+
 //==============================================================================
 //! Class for measuring time elapsed
 //==============================================================================
@@ -34,21 +55,6 @@ private:
   double elapsed_ {0.0}; //!< elasped time in [s]
 };
 
-//==============================================================================
-// Global variables
-//==============================================================================
-
-extern Timer time_active;
-extern Timer time_bank;
-extern Timer time_bank_sample;
-extern Timer time_bank_sendrecv;
-extern Timer time_finalize;
-extern Timer time_inactive;
-extern Timer time_initialize;
-extern Timer time_tallies;
-extern Timer time_total;
-extern Timer time_transport;
-
 //==============================================================================
 // Non-member functions
 //==============================================================================