Merge branch 'develop' into Sensitivity-Analysis

Author: Ebiwonjumi

CMakeLists.txt

@@ -426,6 +426,7 @@ list(APPEND libopenmc_SOURCES
   src/tallies/filter_surface.cpp
   src/tallies/filter_time.cpp
   src/tallies/filter_universe.cpp
+  src/tallies/filter_weight.cpp
   src/tallies/filter_zernike.cpp
   src/tallies/tally.cpp
   src/tallies/tally_scoring.cpp

docs/source/_images/sphere-mesh-vtk.png

@@ -144,15 +144,11 @@ Constructing Tallies
    openmc.SpatialLegendreFilter
    openmc.SphericalHarmonicsFilter
    openmc.TimeFilter
+   openmc.WeightFilter
    openmc.ZernikeFilter
    openmc.ZernikeRadialFilter
    openmc.ParentNuclideFilter
    openmc.ParticleFilter
-   openmc.RegularMesh
-   openmc.RectilinearMesh
-   openmc.CylindricalMesh
-   openmc.SphericalMesh
-   openmc.UnstructuredMesh
    openmc.MeshMaterialVolumes
    openmc.Trigger
    openmc.TallyDerivative
@@ -161,6 +157,20 @@ Constructing Tallies
    openmc.Tally
    openmc.Tallies
 
+Meshes
+------
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myclassinherit.rst
+
+   openmc.RegularMesh
+   openmc.RectilinearMesh
+   openmc.CylindricalMesh
+   openmc.SphericalMesh
+   openmc.UnstructuredMesh
+
 Geometry Plotting
 -----------------
 

docs/source/pythonapi/base.rst

@@ -93,6 +93,7 @@ Classes
    SensitivityTally
    UniverseFilter
    UnstructuredMesh
+   WeightFilter
    WeightWindows
    ZernikeFilter
    ZernikeRadialFilter

docs/source/pythonapi/capi.rst

@@ -91,3 +91,82 @@ from a statepoint file, the ``openmc.statepoint`` module can be used. An
 `example notebook`_ demontrates how to analyze and plot source information.
 
 .. _example notebook: https://nbviewer.jupyter.org/github/openmc-dev/openmc-notebooks/blob/main/post-processing.ipynb
+
+------------------------
+VTK Mesh File Generation
+------------------------
+
+VTK files of OpenMC meshes can be created using the
+:meth:`openmc.Mesh.write_data_to_vtk`  method. Data can be applied to the
+elements of the resulting mesh from mesh filter objects. This data can be
+provided either as a flat array or, in the case of structured meshes
+(:class:`~openmc.RegularMesh`, :class:`~openmc.RectilinearMesh`,
+:class:`~openmc.CylindricalMesh`, or :class:`SphericalMesh`), the data can be
+shaped with dimensions that match the dimensions of the mesh itself.
+
+
+.. image:: ../_images/sphere-mesh-vtk.png
+   :width: 400px
+   :align: center
+   :alt: OpenMC spherical mesh exported to VTK
+
+
+For all mesh types, if a flat data array is provided to the mesh, it is expected
+that the data is ordered in the same ordering as the :attr:`openmc.Mesh.indices`
+for that mesh object. When providing data directly from a tally, as shown below,
+a flat array for a given dataset can be passed directly to this method.
+
+::
+
+    # create model above
+
+    # create a mesh tally
+    mesh = openmc.RegularMesh()
+    mesh.dimension = [10, 20, 30]
+    mesh.lower_left = [-5, -10, -15]
+    mesh.upper_right = [5, 10, 15]
+    mesh_filter = openmc.MeshFilter(mesh)
+    tally = openmc.Tally()
+    tally.filters = [mesh_filter]
+    tally.scores = ['flux']
+
+    model.tallies = [tally]
+    model.run(apply_tally_results=True)
+
+    # provide the data as-is to the method
+    mesh.write_data_to_vtk('flux.vtk', {'flux-mean': tally.mean})
+
+The :class:`~openmc.Tally` object also provides a way to expand the dimensions
+of the mesh filter into a meaningful form where indexing the mesh filter
+dimensions results in intuitive slicing of structured meshes by setting
+``expand_dims=True`` when using :meth:`openmc.Tally.get_reshaped_data`. This
+reshaping does cause flat indexing of the data to change, however. As noted
+above, provided datasets are allowed to be shaped so long as such datasets have
+shapes that match the mesh dimensions. The ability to pass datasets in this way
+is useful when additional filters are applied to a tally. The example below
+demonstrates such a case for tally with both a :class:`~openmc.MeshFilter` and
+:class:`~openmc.EnergyFilter` applied.
+
+::
+
+    # create model above
+
+    # create a mesh tally with energy filter
+    mesh = openmc.RegularMesh()
+    mesh.dimension = [10, 20, 30]
+    mesh.lower_left = [-5, -10, -15]
+    mesh.upper_right = [5, 10, 15]
+    mesh_filter = openmc.MeshFilter(mesh)
+    energy_filter = openmc.EnergyFilter([0.0, 1.0, 20.0e6])
+    tally = openmc.Tally()
+    tally.filters = [mesh_filter, energy_filter]
+    tally.scores = ['flux']
+
+    model.tallies = [tally]
+    model.run(apply_tally_results=True)
+
+    # get the data with mesh dimensions expanded, squeeze out length-one dimensions (nuclides, scores)
+    flux = tally.get_reshaped_data(expand_dims=True).squeeze() # shape: (10, 20, 30, 2)
+
+    # write the lowest energy group to a VTK file
+    mesh.write_data_to_vtk('flux-group1.vtk', datasets={'flux-mean': flux[..., 0]})

docs/source/usersguide/processing.rst

@@ -33,7 +33,6 @@ class ElectronSubshell {
 
   int index_subshell; //!< index in SUBSHELLS
   int threshold;
-  double n_electrons;
   double binding_energy;
   vector<Transition> transitions;
 };
@@ -90,6 +89,11 @@ class PhotonInteraction {
   xt::xtensor<double, 1> binding_energy_;
   xt::xtensor<double, 1> electron_pdf_;
 
+  // Map subshells from Compton profile data obtained from Biggs et al,
+  // "Hartree-Fock Compton profiles for the elements" to ENDF/B atomic
+  // relaxation data
+  xt::xtensor<int, 1> subshell_map_;
+
   // Stopping power data
   double I_; // mean excitation energy
   xt::xtensor<int, 1> n_electrons_;

include/openmc/photon.h

@@ -45,6 +45,7 @@ enum class FilterType {
   SURFACE,
   TIME,
   UNIVERSE,
+  WEIGHT,
   ZERNIKE,
   ZERNIKE_RADIAL
 };

include/openmc/tallies/filter.h

@@ -0,0 +1,51 @@
+#ifndef OPENMC_TALLIES_FILTER_WEIGHT_H
+#define OPENMC_TALLIES_FILTER_WEIGHT_H
+
+#include <string>
+
+#include "openmc/span.h"
+#include "openmc/tallies/filter.h"
+#include "openmc/vector.h"
+
+namespace openmc {
+
+//==============================================================================
+//! Bins the weights of the particles.
+//==============================================================================
+
+class WeightFilter : public Filter {
+public:
+  //----------------------------------------------------------------------------
+  // Constructors, destructors
+
+  ~WeightFilter() = default;
+
+  //----------------------------------------------------------------------------
+  // Methods
+
+  std::string type_str() const override { return "weight"; }
+  FilterType type() const override { return FilterType::WEIGHT; }
+
+  void from_xml(pugi::xml_node node) override;
+
+  void get_all_bins(const Particle& p, TallyEstimator estimator,
+    FilterMatch& match) const override;
+
+  void to_statepoint(hid_t filter_group) const override;
+
+  std::string text_label(int bin) const override;
+
+  //----------------------------------------------------------------------------
+  // Accessors
+
+  const vector<double>& bins() const { return bins_; }
+  void set_bins(span<const double> bins);
+
+protected:
+  //----------------------------------------------------------------------------
+  // Data members
+  vector<double> bins_;
+};
+
+} // namespace openmc
+#endif // OPENMC_TALLIES_FILTER_WEIGHT_H

include/openmc/tallies/filter_weight.h

@@ -141,7 +141,9 @@ def apply_time_correction(
     time_correction_factors : dict
         Time correction factors as returned by :func:`time_correction_factors`
     index : int, optional
-        Index to use for the correction factors
+        Index of the time of interest. If N timesteps are provided in
+        :func:`time_correction_factors`, there are N + 1 times to select from.
+        The default is -1 which corresponds to the final time.
     sum_nuclides : bool
         Whether to sum over the parent nuclides
 

openmc/deplete/d1s.py

@@ -25,7 +25,7 @@
     'energyout', 'mu', 'musurface', 'polar', 'azimuthal', 'distribcell', 'delayedgroup',
     'energyfunction', 'cellfrom', 'materialfrom', 'legendre', 'spatiallegendre',
     'sphericalharmonics', 'zernike', 'zernikeradial', 'particle', 'cellinstance',
-    'collision', 'time', 'importance', 'parentnuclide'
+    'collision', 'time', 'importance', 'parentnuclide', 'weight'
 )
 
 _CURRENT_NAMES = (
@@ -2518,3 +2518,26 @@ def get_pandas_dataframe(self, data_size, stride, **kwargs):
             {self.short_name.lower(): filter_bins})])
 
         return df
+
+
+class WeightFilter(RealFilter):
+    """Bins tally events based on the incoming particle weight.
+
+    Parameters
+    ----------
+    Values : Iterable of float
+        A list or iterable of the weight boundaries, as float values.
+    filter_id : int
+        Unique identifier for the filter
+
+    Attributes
+    ----------
+    id : int
+        Unique identifier for the filter
+    bins : numpy.ndarray
+        An array of integer values representing the weights by which to filter
+    num_bins : int
+        The number of filter bins
+    values : numpy.ndarray
+        Array of weight boundaries
+    """