Merge remote-tracking branch 'upstream/develop' into valgrind

include/openmc/capi.h

@@ -110,6 +110,7 @@ extern "C" {
   int openmc_tally_get_nuclides(int32_t index, int** nuclides, int* n);
   int openmc_tally_get_scores(int32_t index, int** scores, int* n);
   int openmc_tally_get_type(int32_t index, int32_t* type);
+  int openmc_tally_get_writable(int32_t index, bool* writable);
   int openmc_tally_reset(int32_t index);
   int openmc_tally_results(int32_t index, double** ptr, size_t shape_[3]);
   int openmc_tally_set_active(int32_t index, bool active);
@@ -119,6 +120,7 @@ extern "C" {
   int openmc_tally_set_nuclides(int32_t index, int n, const char** nuclides);
   int openmc_tally_set_scores(int32_t index, int n, const char** scores);
   int openmc_tally_set_type(int32_t index, const char* type);
+  int openmc_tally_set_writable(int32_t index, bool writable);
   int openmc_zernike_filter_get_order(int32_t index, int* order);
   int openmc_zernike_filter_get_params(int32_t index, double* x, double* y, double* r);
   int openmc_zernike_filter_set_order(int32_t index, int order);

include/openmc/cell.h

@@ -179,10 +179,10 @@ public:
 
   //! \brief Rotational tranfsormation of the filled universe.
   //
-  //! The vector is empty if there is no rotation.  Otherwise, the first three
-  //! values are the rotation angles respectively about the x-, y-, and z-, axes
-  //! in degrees.  The next 9 values give the rotation matrix in row-major
-  //! order.
+  //! The vector is empty if there is no rotation. Otherwise, the first 9 values
+  //! give the rotation matrix in row-major order. When the user specifies
+  //! rotation angles about the x-, y- and z- axes in degrees, these values are
+  //! also present at the end of the vector, making it of length 12.
   std::vector<double> rotation_;
 
   std::vector<int32_t> offset_;  //!< Distribcell offset table

include/openmc/constants.h

@@ -20,7 +20,7 @@ using double_4dvec = std::vector<std::vector<std::vector<std::vector<double>>>>;
 
 // OpenMC major, minor, and release numbers
 constexpr int VERSION_MAJOR {0};
-constexpr int VERSION_MINOR {11};
+constexpr int VERSION_MINOR {12};
 constexpr int VERSION_RELEASE {0};
 constexpr bool VERSION_DEV {true};
 constexpr std::array<int, 3> VERSION {VERSION_MAJOR, VERSION_MINOR, VERSION_RELEASE};

include/openmc/distribution_spatial.h

@@ -37,6 +37,24 @@ private:
   UPtrDist z_; //!< Distribution of z coordinates
 };
 
+//==============================================================================
+//! Distribution of points specified by spherical coordinates r,theta,phi
+//==============================================================================
+
+class SphericalIndependent : public SpatialDistribution {
+public:
+  explicit SphericalIndependent(pugi::xml_node node);
+
+  //! Sample a position from the distribution
+  //! \return Sampled position
+  Position sample() const;
+private:
+  UPtrDist r_; //!< Distribution of r coordinates
+  UPtrDist theta_; //!< Distribution of theta coordinates
+  UPtrDist phi_; //!< Distribution of phi coordinates
+  Position origin_; //!< Cartesian coordinates of the sphere center
+};
+
 //==============================================================================
 //! Uniform distribution of points over a box
 //==============================================================================

include/openmc/geometry_aux.h

@@ -7,9 +7,15 @@
 #include <cstdint>
 #include <string>
 #include <vector>
+#include <unordered_map>
 
 namespace openmc {
 
+namespace model {
+  extern std::unordered_map<int32_t, std::unordered_map<int32_t, int32_t>> universe_cell_counts;
+  extern std::unordered_map<int32_t, int32_t> universe_level_counts;
+} // namespace model
+
 void read_geometry_xml();
 
 //==============================================================================

include/openmc/hdf5_interface.h

@@ -345,7 +345,7 @@ read_dataset(hid_t obj_id, const char* name, Position& r, bool indep=false)
 }
 
 template <typename T, std::size_t N>
-void read_dataset_as_shape(hid_t obj_id, const char* name,
+inline void read_dataset_as_shape(hid_t obj_id, const char* name,
                            xt::xtensor<T, N>& arr, bool indep=false)
 {
   hid_t dset = open_dataset(obj_id, name);
@@ -367,7 +367,7 @@ void read_dataset_as_shape(hid_t obj_id, const char* name,
 
 
 template <typename T, std::size_t N>
-void read_nd_vector(hid_t obj_id, const char* name, xt::xtensor<T, N>& result,
+inline void read_nd_vector(hid_t obj_id, const char* name, xt::xtensor<T, N>& result,
      bool must_have=false)
 {
   if (object_exists(obj_id, name)) {

include/openmc/mgxs.h

@@ -11,6 +11,7 @@
 
 #include "openmc/constants.h"
 #include "openmc/hdf5_interface.h"
+#include "openmc/particle.h"
 #include "openmc/xsdata.h"
 
 
@@ -110,7 +111,10 @@ class Mgxs {
     //!
     //! @param xs_id HDF5 group id for the cross section data.
     //! @param temperature Temperatures to read.
-    Mgxs(hid_t xs_id, const std::vector<double>& temperature);
+    //! @param num_group number of energy groups
+    //! @param num_delay number of delayed groups
+    Mgxs(hid_t xs_id, const std::vector<double>& temperature,
+        int num_group, int num_delay);
 
     //! \brief Constructor that initializes and populates all data to build a
     //!   macroscopic cross section from microscopic cross section.
@@ -119,8 +123,11 @@ class Mgxs {
     //! @param mat_kTs temperatures (in units of eV) that data is needed.
     //! @param micros Microscopic objects to combine.
     //! @param atom_densities Atom densities of those microscopic quantities.
+    //! @param num_group number of energy groups
+    //! @param num_delay number of delayed groups
     Mgxs(const std::string& in_name, const std::vector<double>& mat_kTs,
-         const std::vector<Mgxs*>& micros, const std::vector<double>& atom_densities);
+         const std::vector<Mgxs*>& micros, const std::vector<double>& atom_densities,
+         int num_group, int num_delay);
 
     //! \brief Provides a cross section value given certain parameters
     //!
@@ -137,6 +144,11 @@ class Mgxs {
     get_xs(int xstype, int gin, const int* gout, const double* mu,
       const int* dg);
 
+    inline double
+    get_xs(int xstype, int gin)
+    {return get_xs(xstype, gin, nullptr, nullptr, nullptr);}
+
+
     //! \brief Samples the fission neutron energy and if prompt or delayed.
     //!
     //! @param gin Incoming energy group.
@@ -156,15 +168,9 @@ class Mgxs {
 
     //! \brief Calculates cross section quantities needed for tracking.
     //!
-    //! @param gin Incoming energy group.
-    //! @param sqrtkT Temperature of the material.
-    //! @param u Incoming particle direction.
-    //! @param total_xs Resultant total cross section.
-    //! @param abs_xs Resultant absorption cross section.
-    //! @param nu_fiss_xs Resultant nu-fission cross section.
+    //! @param p The particle whose attributes set which MGXS to get.
     void
-    calculate_xs(int gin, double sqrtkT, Direction u,
-         double& total_xs, double& abs_xs, double& nu_fiss_xs);
+    calculate_xs(Particle& p);
 
     //! \brief Sets the temperature index in cache given a temperature
     //!

include/openmc/mgxs_interface.h

@@ -12,70 +12,71 @@
 namespace openmc {
 
 //==============================================================================
-// Global variables
+// Global MGXS data container structure
 //==============================================================================
 
+class MgxsInterface {
+public:
+
+  MgxsInterface() = default;
+
+  // Construct from path to cross sections file, as well as a list
+  // of XS to read and the corresponding temperatures for each XS
+  MgxsInterface(const std::string& path_cross_sections,
+                const std::vector<std::string> xs_to_read,
+                const std::vector<std::vector<double>> xs_temps);
+
+  // Does things to construct after the nuclides and temperatures to
+  // read have been specified.
+  void init();
+
+  // Set which nuclides and temperatures are to be read
+  void set_nuclides_and_temperatures(std::vector<std::string> xs_to_read,
+                                     std::vector<std::vector<double>> xs_temps);
+
+  // Add an Mgxs object to be managed
+  void add_mgxs(hid_t file_id, const std::string& name,
+         const std::vector<double>& temperature);
+
+  // Reads just the header of the cross sections file, to find
+  // min & max energies as well as the available XS
+  void read_header(const std::string& path_cross_sections);
+
+  // Calculate microscopic cross sections from nuclide macro XS
+  void create_macro_xs();
+
+  // Get the kT values which are used in the OpenMC model
+  std::vector<std::vector<double>> get_mat_kTs();
+
+  int num_energy_groups_;
+  int num_delayed_groups_;
+  std::vector<std::string> xs_names_; // available names in HDF5 file
+  std::vector<std::string> xs_to_read_; // XS which appear in materials
+  std::vector<std::vector<double>> xs_temps_to_read_; // temperatures used
+  std::string cross_sections_path_; // path to MGXS h5 file
+  std::vector<Mgxs> nuclides_;
+  std::vector<Mgxs> macro_xs_;
+  std::vector<double> energy_bins_;
+  std::vector<double> energy_bin_avg_;
+  std::vector<double> rev_energy_bins_;
+  std::vector<std::vector<double>> nuc_temps_; // all available temperatures
+};
+
 namespace data {
+  extern MgxsInterface mg;
+}
 
-extern std::vector<Mgxs> nuclides_MG;
-extern std::vector<Mgxs> macro_xs;
-extern int num_energy_groups;
-extern int num_delayed_groups;
-extern std::vector<double> energy_bins;
-extern std::vector<double> energy_bin_avg;
-extern std::vector<double> rev_energy_bins;
+// Puts available XS in MGXS file to globals so that when
+// materials are read, the MGXS specified in a material can
+// be ensured to be present in the available data.
+void put_mgxs_header_data_to_globals();
 
-} // namespace data
+// Set which nuclides and temperatures are to be read on
+// mg through global data
+void set_mg_interface_nuclides_and_temps();
 
-//==============================================================================
-// Mgxs data loading interface methods
-//==============================================================================
-
-void read_mgxs();
-
-void
-add_mgxs(hid_t file_id, const std::string& name,
-     const std::vector<double>& temperature);
-
-void create_macro_xs();
-
-std::vector<std::vector<double>> get_mat_kTs();
-
-void read_mg_cross_sections_header();
-
-//==============================================================================
-// Mgxs tracking/transport/tallying interface methods
-//==============================================================================
-
-extern "C" void
-calculate_xs_c(int i_mat, int gin, double sqrtkT, Direction u,
-     double& total_xs, double& abs_xs, double& nu_fiss_xs);
-
-double
-get_nuclide_xs(int index, int xstype, int gin, const int* gout,
-  const double* mu, const int* dg);
-
-inline double
-get_nuclide_xs(int index, int xstype, int gin)
-{return get_nuclide_xs(index, xstype, gin, nullptr, nullptr, nullptr);}
-
-double
-get_macro_xs(int index, int xstype, int gin, const int* gout,
-  const double* mu, const int* dg);
-
-inline double
-get_macro_xs(int index, int xstype, int gin)
-{return get_macro_xs(index, xstype, gin, nullptr, nullptr, nullptr);}
-
-//==============================================================================
-// General Mgxs methods
-//==============================================================================
-
-extern "C" void
-get_name_c(int index, int name_len, char* name);
-
-extern "C" double
-get_awr_c(int index);
+// After macro XS have been read, materials can be marked as fissionable
+void mark_fissionable_mgxs_materials();
 
 } // namespace openmc
 #endif // OPENMC_MGXS_INTERFACE_H

include/openmc/settings.h

@@ -31,7 +31,7 @@ extern "C" bool cmfd_run;             //!< is a CMFD run?
 extern "C" bool dagmc;                //!< indicator of DAGMC geometry
 extern "C" bool entropy_on;           //!< calculate Shannon entropy?
 extern bool legendre_to_tabular;      //!< convert Legendre distributions to tabular?
-extern bool output_summary;           //!< write summary.h5?
+extern "C" bool output_summary;       //!< write summary.h5?
 extern bool output_tallies;           //!< write tallies.out?
 extern bool particle_restart_run;     //!< particle restart run?
 extern "C" bool photon_transport;     //!< photon transport turned on?

include/openmc/tallies/tally.h

@@ -37,6 +37,8 @@ public:
 
   void set_active(bool active) { active_ = active; }
 
+  void set_writable(bool writable) { writable_ = writable; }
+
   void set_scores(pugi::xml_node node);
 
   void set_scores(const std::vector<std::string>& scores);
@@ -55,6 +57,8 @@ public:
 
   int32_t n_filter_bins() const {return n_filter_bins_;}
 
+  bool writable() const { return writable_;}
+
   //----------------------------------------------------------------------------
   // Other methods.
 
@@ -98,6 +102,9 @@ public:
   //! (e.g. specific cell, specific energy group, etc.)
   xt::xtensor<double, 3> results_;
 
+  //! True if this tally should be written to statepoint files
+  bool writable_ {true};
+
   //----------------------------------------------------------------------------
   // Miscellaneous public members.
 

include/openmc/volume_calc.h

@@ -2,12 +2,14 @@
 #define OPENMC_VOLUME_CALC_H
 
 #include "openmc/position.h"
+#include "openmc/tallies/trigger.h"
 
 #include "pugixml.hpp"
 #include "xtensor/xtensor.hpp"
 
 #include <string>
 #include <vector>
+#include <gsl/gsl>
 
 namespace openmc {
 
@@ -16,6 +18,7 @@ namespace openmc {
 //==============================================================================
 
 class VolumeCalculation {
+
 public:
   // Aliases, types
   struct Result {
@@ -23,6 +26,7 @@ public:
     std::vector<int> nuclides; //!< Index of nuclides
     std::vector<double> atoms; //!< Number of atoms for each nuclide
     std::vector<double> uncertainty; //!< Uncertainty on number of atoms
+    int iterations; //!< Number of iterations needed to obtain the results
   }; // Results for a single domain
 
   // Constructors
@@ -44,7 +48,9 @@ public:
 
   // Data members
   int domain_type_; //!< Type of domain (cell, material, etc.)
-  int n_samples_; //!< Number of samples to use
+  size_t n_samples_; //!< Number of samples to use
+  double threshold_ {-1.0}; //!< Error threshold for domain volumes
+  TriggerMetric trigger_type_ {TriggerMetric::not_active}; //!< Trigger metric for the volume calculation
   Position lower_left_; //!< Lower-left position of bounding box
   Position upper_right_; //!< Upper-right position of bounding box
   std::vector<int> domain_ids_; //!< IDs of domains to find volumes of

include/openmc/xsdata.h

@@ -22,6 +22,7 @@ namespace openmc {
 class XsData {
 
   private:
+
     //! \brief Reads scattering data from the HDF5 file
     void
     scatter_from_hdf5(hid_t xsdata_grp, size_t n_ang,
@@ -61,6 +62,9 @@ class XsData {
     void
     fission_matrix_no_delayed_from_hdf5(hid_t xsdata_grp, size_t n_ang);
 
+    //! Number of energy and delayed neutron groups
+    size_t n_g_, n_dg_;
+
   public:
 
     // The following quantities have the following dimensions:
@@ -98,7 +102,10 @@ class XsData {
     //! @param scatter_format The scattering representation of the file.
     //! @param n_pol Number of polar angles.
     //! @param n_azi Number of azimuthal angles.
-    XsData(bool fissionable, int scatter_format, int n_pol, int n_azi);
+    //! @param n_groups Number of energy groups.
+    //! @param n_d_groups Number of delayed neutron groups.
+    XsData(bool fissionable, int scatter_format, int n_pol, int n_azi,
+           size_t n_groups, size_t n_d_groups);
 
     //! \brief Loads the XsData object from the HDF5 file
     //!