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

.github/pull_request_template.md

@@ -13,7 +13,7 @@ Fixes # (issue)
 # Checklist
 
 - [ ] I have performed a self-review of my own code
-- [ ] I have run [clang-format](https://docs.openmc.org/en/latest/devguide/styleguide.html#automatic-formatting) on any C++ source files (if applicable)
+- [ ] I have run [clang-format](https://docs.openmc.org/en/latest/devguide/styleguide.html#automatic-formatting) (version 15) on any C++ source files (if applicable)
 - [ ] I have followed the [style guidelines](https://docs.openmc.org/en/latest/devguide/styleguide.html#python) for Python source files (if applicable)
 - [ ] I have made corresponding changes to the documentation (if applicable)
 - [ ] I have added tests that prove my fix is effective or that my feature works (if applicable)

CMakeLists.txt

@@ -3,8 +3,8 @@ project(openmc C CXX)
 
 # Set version numbers
 set(OPENMC_VERSION_MAJOR 0)
-set(OPENMC_VERSION_MINOR 13)
-set(OPENMC_VERSION_RELEASE 4)
+set(OPENMC_VERSION_MINOR 14)
+set(OPENMC_VERSION_RELEASE 0)
 set(OPENMC_VERSION ${OPENMC_VERSION_MAJOR}.${OPENMC_VERSION_MINOR}.${OPENMC_VERSION_RELEASE})
 configure_file(include/openmc/version.h.in "${CMAKE_BINARY_DIR}/include/openmc/version.h" @ONLY)
 
@@ -120,6 +120,7 @@ if(OPENMC_USE_DAGMC)
     message(FATAL_ERROR "Discovered DAGMC Version: ${DAGMC_VERSION}. \
     Please update DAGMC to version 3.2.0 or greater.")
   endif()
+  message(STATUS "Found DAGMC: ${DAGMC_DIR} (version ${DAGMC_VERSION})")
 endif()
 
 #===============================================================================

docs/source/conf.py

@@ -69,9 +69,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "0.13"
+version = "0.14"
 # The full version, including alpha/beta/rc tags.
-release = "0.13.4"
+release = "0.14.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/devguide/styleguide.rst

@@ -29,6 +29,10 @@ whenever a file is saved. For example, `Visual Studio Code
 <https://code.visualstudio.com/docs/cpp/cpp-ide#_code-formatting>`_ includes
 support for running clang-format.
 
+.. note::
+    OpenMC's CI uses `clang-format` version 15. A different version of `clang-format`
+    may produce different line changes and as a result fail the CI test.
+
 Miscellaneous
 -------------
 

docs/source/devguide/tests.rst

@@ -59,6 +59,31 @@ If you want to view testing output on failure run::
 
     ctest --output-on-failure
 
+Possible Reasons for Test Failures
+----------------------------------
+
+You may find that when you run the test suite, not everything passes. First,
+make sure you have satisfied all the prerequisites above. After you have done
+that, consider the following:
+
+- When building OpenMC, make sure you run CMake with
+  ``-DCMAKE_BUILD_TYPE=Debug``. Building with a release build will result in
+  some test failures due to differences in which compiler optimizations are
+  used.
+- Because tallies involve the sum of many floating point numbers, the
+  non-associativity of floating point numbers can result in different answers
+  especially when the number of threads is high (different order of operations).
+  Thus, if you are running on a CPU with many cores, you may need to limit the
+  number of OpenMP threads used. It is recommended to set the
+  :envvar:`OMP_NUM_THREADS` environment variable to 2.
+- Recent versions of NumPy use instruction dispatch that may generate different
+  results depending the particular ISA that you are running on. To avoid issues,
+  you may need to disable AVX512 instructions. This can be done by setting the
+  :envvar:`NPY_DISABLE_CPU_FEATURES` environment variable to "AVX512F
+  AVX512_SKX". When NumPy/SciPy are built against OpenBLAS, you may also need to
+  limit the number of threads that OpenBLAS uses internally; this can be done by
+  setting the :envvar:`OPENBLAS_NUM_THREADS` environment variable to 1.
+
 Generating XML Inputs
 ---------------------
 

docs/source/io_formats/summary.rst

@@ -60,9 +60,11 @@ The current version of the summary file format is 6.0.
            - **coefficients** (*double[]*) -- Array of coefficients that define
              the surface. See :ref:`surface_element` for what coefficients are
              defined for each surface type.
-           - **boundary_condition** (*char[]*) -- Boundary condition applied to
-             the surface. Can be 'transmission', 'vacuum', 'reflective', or
-             'periodic'.
+           - **boundary_type** (*char[]*) -- Boundary condition applied to
+             the surface. Can be 'transmission', 'vacuum', 'reflective',
+             'periodic', or 'white'.
+           - **albedo** (*double*) -- Boundary albedo as a positive multiplier
+             of particle weight. If absent, it is assumed to be 1.0.
            - **geom_type** (*char[]*) -- Type of geometry used to create the cell.
              Either 'csg' or 'dagmc'.
 

docs/source/pythonapi/model.rst

@@ -11,8 +11,6 @@ Convenience Functions
    :template: myfunction.rst
 
    openmc.model.borated_water
-   openmc.model.hexagonal_prism
-   openmc.model.rectangular_prism
    openmc.model.subdivide
    openmc.model.pin
 
@@ -26,9 +24,11 @@ Composite Surfaces
 
    openmc.model.CruciformPrism
    openmc.model.CylinderSector
+   openmc.model.HexagonalPrism
    openmc.model.IsogonalOctagon
    openmc.model.Polygon
    openmc.model.RectangularParallelepiped
+   openmc.model.RectangularPrism
    openmc.model.RightCircularCylinder
    openmc.model.XConeOneSided
    openmc.model.YConeOneSided

docs/source/usersguide/geometry.rst

@@ -147,12 +147,13 @@ For many regions, a bounding-box can be determined automatically::
 While a bounding box can be determined for regions involving half-spaces of
 spheres, cylinders, and axis-aligned planes, it generally cannot be determined
 if the region involves cones, non-axis-aligned planes, or other exotic
-second-order surfaces. For example, the :func:`openmc.model.hexagonal_prism`
-function returns the interior region of a hexagonal prism; because it is bounded
-by a :class:`openmc.Plane`, trying to get its bounding box won't work::
+second-order surfaces. For example, the :class:`openmc.model.HexagonalPrism`
+class returns a hexagonal prism surface; because it utilizes a
+:class:`openmc.Plane`, trying to get the bounding box of its interior won't
+work::
 
-  >>> hex = openmc.model.hexagonal_prism()
-  >>> hex.bounding_box
+  >>> hex = openmc.model.HexagonalPrism()
+  >>> (-hex).bounding_box
   (array([-0.8660254,       -inf,       -inf]),
    array([ 0.8660254,        inf,        inf]))
 
@@ -172,13 +173,17 @@ surface. To specify a vacuum boundary condition, simply change the
    outer_surface = openmc.Sphere(r=100.0)
    outer_surface.boundary_type = 'vacuum'
 
-Reflective and periodic boundary conditions can be set with the strings
-'reflective' and 'periodic'. Vacuum and reflective boundary conditions can be
-applied to any type of surface. Periodic boundary conditions can be applied to
-pairs of planar surfaces. If there are only two periodic surfaces they will be
-matched automatically. Otherwise it is necessary to specify pairs explicitly
-using the :attr:`Surface.periodic_surface` attribute as in the following
-example::
+Reflective, periodic, and white boundary conditions can be set with the
+strings 'reflective', 'periodic', and 'white' respectively.
+Vacuum, reflective and white boundary conditions can be applied to any
+type of surface. The 'white' boundary condition supports diffuse particle
+reflection in contrast to specular reflection provided by the 'reflective'
+boundary condition.
+
+Periodic boundary conditions can be applied to pairs of planar surfaces.
+If there are only two periodic surfaces they will be matched automatically.
+Otherwise it is necessary to specify pairs explicitly using the
+:attr:`Surface.periodic_surface` attribute as in the following example::
 
   p1 = openmc.Plane(a=0.3, b=5.0, d=1.0, boundary_type='periodic')
   p2 = openmc.Plane(a=0.3, b=5.0, d=-1.0, boundary_type='periodic')
@@ -196,6 +201,20 @@ lies in the first quadrant of the Cartesian grid. If the geometry instead lies
 in the fourth quadrant, the :class:`YPlane` must be replaced by a
 :class:`Plane` with the normal vector pointing in the :math:`-y` direction.
 
+Additionally, 'reflective', 'periodic', and 'white' boundary conditions have
+an albedo parameter that can be used to modify the importance of particles
+that encounter the boundary. The albedo value specifies the ratio between
+the particle's importance after interaction with the boundary to its initial
+importance. The following example creates a reflective planar surface which
+reduces the reflected particles' importance by 33.3%::
+
+   x1 = openmc.XPlane(1.0, boundary_type='reflective', albedo=0.667)
+
+   # This is equivalent
+   x1 = openmc.XPlane(1.0)
+   x1.boundary_type = 'reflective'
+   x1.albedo = 0.667
+
 .. _usersguide_cells:
 
 -----
@@ -410,7 +429,7 @@ code would work::
   hexlat.universes = [outer_ring, middle_ring, inner_ring]
 
 If you need to create a hexagonal boundary (composed of six planar surfaces) for
-a hexagonal lattice, :func:`openmc.model.hexagonal_prism` can be used.
+a hexagonal lattice, :class:`openmc.model.HexagonalPrism` can be used.
 
 .. _usersguide_geom_export:
 

examples/assembly/assembly.py

@@ -99,11 +99,11 @@ def assembly_model():
     assembly.universes[gt_pos[:, 0], gt_pos[:, 1]] = guide_tube_pin()
 
     # Create outer boundary of the geometry to surround the lattice
-    outer_boundary = openmc.model.rectangular_prism(
+    outer_boundary = openmc.model.RectangularPrism(
         pitch, pitch, boundary_type='reflective')
 
     # Create a cell filled with the lattice
-    main_cell = openmc.Cell(fill=assembly, region=outer_boundary)
+    main_cell = openmc.Cell(fill=assembly, region=-outer_boundary)
 
     # Finally, create geometry by providing a list of cells that fill the root
     # universe

examples/custom_source/build_xml.py

@@ -8,8 +8,8 @@
 mats.export_to_xml()
 
 # Create a 5 cm x 5 cm box filled with iron
-box = openmc.model.rectangular_prism(10.0, 10.0, boundary_type='vacuum')
-cell = openmc.Cell(fill=iron, region=box)
+box = openmc.model.RectangularPrism(10.0, 10.0, boundary_type='vacuum')
+cell = openmc.Cell(fill=iron, region=-box)
 geometry = openmc.Geometry([cell])
 geometry.export_to_xml()
 

examples/parameterized_custom_source/build_xml.py

@@ -8,8 +8,8 @@
 mats.export_to_xml()
 
 # Create a 5 cm x 5 cm box filled with iron
-box = openmc.model.rectangular_prism(10.0, 10.0, boundary_type='vacuum')
-cell = openmc.Cell(fill=iron, region=box)
+box = openmc.model.RectangularPrism(10.0, 10.0, boundary_type='vacuum')
+cell = openmc.Cell(fill=iron, region=-box)
 geometry = openmc.Geometry([cell])
 geometry.export_to_xml()
 

examples/pincell/build_xml.py

@@ -43,13 +43,13 @@
 
 # Create a region represented as the inside of a rectangular prism
 pitch = 1.25984
-box = openmc.rectangular_prism(pitch, pitch, boundary_type='reflective')
+box = openmc.model.RectangularPrism(pitch, pitch, boundary_type='reflective')
 
 # Create cells, mapping materials to regions
 fuel = openmc.Cell(fill=uo2, region=-fuel_or)
 gap = openmc.Cell(fill=helium, region=+fuel_or & -clad_ir)
 clad = openmc.Cell(fill=zircaloy, region=+clad_ir & -clad_or)
-water = openmc.Cell(fill=borated_water, region=+clad_or & box)
+water = openmc.Cell(fill=borated_water, region=+clad_or & -box)
 
 # Create a geometry and export to XML
 geometry = openmc.Geometry([fuel, gap, clad, water])

examples/pincell_depletion/run_depletion.py

@@ -41,13 +41,13 @@
 fuel_or = openmc.ZCylinder(r=0.39218, name='Fuel OR')
 clad_ir = openmc.ZCylinder(r=0.40005, name='Clad IR')
 clad_or = openmc.ZCylinder(r=0.45720, name='Clad OR')
-box = openmc.model.rectangular_prism(pitch, pitch, boundary_type='reflective')
+box = openmc.model.RectangularPrism(pitch, pitch, boundary_type='reflective')
 
 # Define cells
 fuel = openmc.Cell(fill=uo2, region=-fuel_or)
 gap = openmc.Cell(fill=helium, region=+fuel_or & -clad_ir)
 clad = openmc.Cell(fill=zircaloy, region=+clad_ir & -clad_or)
-water = openmc.Cell(fill=borated_water, region=+clad_or & box)
+water = openmc.Cell(fill=borated_water, region=+clad_or & -box)
 
 # Define overall geometry
 geometry = openmc.Geometry([fuel, gap, clad, water])

examples/pincell_multigroup/build_xml.py

@@ -90,11 +90,11 @@
 
 # Create a region represented as the inside of a rectangular prism
 pitch = 1.26
-box = openmc.rectangular_prism(pitch, pitch, boundary_type='reflective')
+box = openmc.model.RectangularPrism(pitch, pitch, boundary_type='reflective')
 
 # Instantiate Cells
 fuel = openmc.Cell(fill=uo2, region=-fuel_or, name='fuel')
-moderator = openmc.Cell(fill=water, region=+fuel_or & box, name='moderator')
+moderator = openmc.Cell(fill=water, region=+fuel_or & -box, name='moderator')
 
 # Create a geometry with the two cells and export to XML
 geometry = openmc.Geometry([fuel, moderator])

include/openmc/boundary_condition.h

@@ -1,7 +1,10 @@
 #ifndef OPENMC_BOUNDARY_CONDITION_H
 #define OPENMC_BOUNDARY_CONDITION_H
 
+#include "openmc/hdf5_interface.h"
+#include "openmc/particle.h"
 #include "openmc/position.h"
+#include <fmt/core.h>
 
 namespace openmc {
 
@@ -22,8 +25,44 @@ class BoundaryCondition {
   //! \param surf The specific surface on the boundary the particle struck.
   virtual void handle_particle(Particle& p, const Surface& surf) const = 0;
 
+  //! Modify the incident particle's weight according to the boundary's albedo.
+  //! \param p The particle that struck the boundary.  This function calculates
+  //!   the reduction in the incident particle's weight as it interacts
+  //!   with a boundary. The lost weight is tallied before the remaining weight
+  //!   is reassigned to the incident particle. Implementations of the
+  //!   handle_particle function typically call this method in its body.
+  //! \param surf The specific surface on the boundary the particle struck.
+  void handle_albedo(Particle& p, const Surface& surf) const
+  {
+    if (!has_albedo())
+      return;
+    double initial_wgt = p.wgt();
+    // Treat the lost weight fraction as leakage, similar to VacuumBC.
+    // This ensures the lost weight is tallied properly.
+    p.wgt() *= (1.0 - albedo_);
+    p.cross_vacuum_bc(surf);
+    p.wgt() = initial_wgt * albedo_;
+  };
+
   //! Return a string classification of this BC.
   virtual std::string type() const = 0;
+
+  //! Write albedo data of this BC to hdf5.
+  void to_hdf5(hid_t surf_group) const
+  {
+    if (has_albedo()) {
+      write_string(surf_group, "albedo", fmt::format("{}", albedo_), false);
+    }
+  };
+
+  //! Set albedo of this BC.
+  void set_albedo(double albedo) { albedo_ = albedo; }
+
+  //! Return if this BC has an albedo.
+  bool has_albedo() const { return (albedo_ > 0.0); }
+
+private:
+  double albedo_ = -1.0;
 };
 
 //==============================================================================

include/openmc/surface.h

@@ -83,10 +83,10 @@ struct BoundingBox {
 
 class Surface {
 public:
-  int id_;                                          //!< Unique ID
-  std::string name_;                                //!< User-defined name
-  std::shared_ptr<BoundaryCondition> bc_ {nullptr}; //!< Boundary condition
-  GeometryType geom_type_;   //!< Geometry type indicator (CSG or DAGMC)
+  int id_;                           //!< Unique ID
+  std::string name_;                 //!< User-defined name
+  unique_ptr<BoundaryCondition> bc_; //!< Boundary condition
+  GeometryType geom_type_;           //!< Geometry type indicator (CSG or DAGMC)
   bool surf_source_ {false}; //!< Activate source banking for the surface?
 
   explicit Surface(pugi::xml_node surf_node);

openmc/__init__.py

@@ -36,7 +36,7 @@
 from .config import *
 
 # Import a few names from the model module
-from openmc.model import rectangular_prism, hexagonal_prism, Model
+from openmc.model import Model
 
 
-__version__ = '0.13.4-dev'
+__version__ = '0.14.0-dev'

openmc/bounding_box.py

@@ -9,7 +9,7 @@
 class BoundingBox:
     """Axis-aligned bounding box.
 
-    .. versionadded:: 0.13.4
+    .. versionadded:: 0.14.0
 
     Parameters
     ----------

openmc/cell.py

@@ -562,7 +562,7 @@ def clone(self, clone_materials=True, clone_regions=True,  memo=None):
     def plot(self, *args, **kwargs):
         """Display a slice plot of the cell.
 
-        .. versionadded:: 0.13.4
+        .. versionadded:: 0.14.0
 
         Parameters
         ----------

openmc/data/library.py

@@ -15,7 +15,7 @@ class DataLibrary(list):
     cross section data from a single file. The dictionary has keys 'path',
     'type', and 'materials'.
 
-    .. versionchanged:: 0.13.4
+    .. versionchanged:: 0.14.0
         This class now behaves like a list rather than requiring you to access
         the list of libraries through a special attribute.
 

openmc/deplete/abc.py

@@ -554,7 +554,7 @@ class Integrator(ABC):
     transfer_rates : openmc.deplete.TransferRates
         Instance of TransferRates class to perform continuous transfer during depletion
 
-        .. versionadded:: 0.13.4
+        .. versionadded:: 0.14.0
 
     """