Some cleanup from self-review

Author: pshriwise

cmake/OpenMCConfig.cmake.in

@@ -15,12 +15,6 @@ if(@LIBMESH_FOUND@)
   pkg_check_modules(LIBMESH REQUIRED libmesh IMPORTED_TARGET)
 endif()
 
-if(@LIBMESH_FOUND@)
-  include(FindPkgConfig)
-  set(ENV{PKG_CONFIG_PATH} "$ENV{PKG_CONFIG_PATH}:@LIBMESH_PC@")
-  pkg_check_modules(LIBMESH REQUIRED libmesh IMPORTED_TARGET)
-endif()
-
 if(NOT TARGET OpenMC::libopenmc)
   include("${OpenMC_CMAKE_DIR}/OpenMCTargets.cmake")
 endif()

include/openmc/mesh.h

@@ -24,15 +24,14 @@
 
 #ifdef LIBMESH
 #include "libmesh/bounding_box.h"
-#include "libmesh/libmesh.h"
+#include "libmesh/dof_map.h"
 #include "libmesh/elem.h"
 #include "libmesh/equation_systems.h"
 #include "libmesh/exodusII_io.h"
 #include "libmesh/explicit_system.h"
-#include "libmesh/dof_map.h"
+#include "libmesh/libmesh.h"
 #include "libmesh/mesh.h"
 #include "libmesh/point.h"
-#include "libmesh/sphere.h"
 #endif
 
 namespace openmc {
@@ -109,7 +108,6 @@ class Mesh
   virtual std::pair<std::vector<double>, std::vector<double>>
   plot(Position plot_ll, Position plot_ur) const = 0;
 
-  //! Get a label for the mesh bin
   //! Return a string representation of the mesh bin
   //
   //! \param[in] bin Mesh bin to generate a label for
@@ -285,6 +283,13 @@ class UnstructuredMesh : public Mesh {
   UnstructuredMesh(const std::string& filename);
 
   // Methods
+private:
+
+  //! Setup method for the mesh. Builds data structures,
+  //! element mapping, etc.
+  virtual void initialize() = 0;
+
+public:
 
   //! Add a variable to the mesh instance
   virtual void add_score(const std::string& var_name) = 0;
@@ -383,7 +388,7 @@ class MOABUnstructuredMesh : public UnstructuredMesh {
 
 private:
 
-  void initialize();
+  void initialize() override;
 
   //! Find all intersections with faces of the mesh.
   //
@@ -528,9 +533,7 @@ class LibMesh : public UnstructuredMesh {
 
 private:
 
-  //! Setup method for the mesh. Builds data structures,
-  //! element mapping, etc.
-  void initialize();
+  void initialize() override;
 
   //! Translate a bin value to an element pointer
   const libMesh::Elem* get_element_from_bin(int bin) const;

openmc/mesh.py

@@ -616,8 +616,8 @@ class UnstructuredMesh(MeshBase):
         Name of the mesh
     filename : str
         Name of the file containing the unstructured mesh
-    mesh_lib : str
-        Library used for the unstructured mesh tally
+    library : str
+        Mesh library used for the unstructured mesh tally
     volumes : Iterable of float
         Volumes of the unstructured mesh elements
     total_volume : float
@@ -627,12 +627,12 @@ class UnstructuredMesh(MeshBase):
         (1.0, 1.0, 1.0), ...]
     """
 
-    def __init__(self, filename, mesh_id=None, name=''):
+    def __init__(self, filename, library, mesh_id=None, name=''):
         super().__init__(mesh_id, name)
         self.filename = filename
         self._volumes = None
         self._centroids = None
-        self._library = 'moab'
+        self.library = library
 
     @property
     def filename(self):
@@ -645,12 +645,12 @@ def filename(self, filename):
 
     @property
     def library(self):
-        return self._mesh_lib
+        return self._library
 
     @library.setter
-    def library(self, mesh_lib):
-        cv.check_value('mesh_lib', mesh_lib, ('moab', 'libmesh'))
-        self._library = mesh_lib
+    def library(self, lib):
+        cv.check_value('mesh_lib', lib, ('moab', 'libmesh'))
+        self._library = lib
 
     @property
     def size(self):
@@ -786,13 +786,13 @@ def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
     def from_hdf5(cls, group):
         mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
         filename = group['filename'][()].decode()
+        library = group['library'][()].decode()
 
-        mesh = cls(filename, mesh_id=mesh_id)
+        mesh = cls(filename, library, mesh_id=mesh_id)
         vol_data = group['volumes'][()]
         centroids = group['centroids'][()]
         mesh.volumes = np.reshape(vol_data, (vol_data.shape[0],))
         mesh.centroids = np.reshape(centroids, (vol_data.shape[0], 3))
-        mesh.mesh_lib = group['library'][()].decode()
         mesh.size = mesh.volumes.size
 
         return mesh
@@ -810,8 +810,8 @@ def to_xml_element(self):
         element = ET.Element("mesh")
         element.set("id", str(self._id))
         element.set("type", "unstructured")
-        subelement = ET.SubElement(element, "filename")
         element.set("library", self._library)
+        subelement = ET.SubElement(element, "filename")
         subelement.text = self.filename
 
         return element
@@ -834,6 +834,5 @@ def from_xml_element(cls, elem):
         filename = get_text(elem, 'filename')
         library = get_text(elem, 'library')
 
-        mesh = cls(filename, mesh_id)
-        mesh.library = library
+        mesh = cls(filename, library, mesh_id)
         return mesh

src/finalize.cpp

@@ -192,5 +192,4 @@ int openmc_hard_reset()
   // Reset the random number generator state
   openmc::openmc_set_seed(DEFAULT_SEED);
   return 0;
-
-}
+}

src/initialize.cpp

@@ -55,7 +55,6 @@ int openmc_init(int argc, char* argv[], const void* intracomm)
   initialize_mpi(comm);
 #endif
 
-
   // Parse command-line arguments
   int err = parse_command_line(argc, argv);
   if (err) return err;
@@ -89,7 +88,6 @@ int openmc_init(int argc, char* argv[], const void* intracomm)
   }
 #endif
 
-
   // Initialize random number generator -- if the user specifies a seed, it
   // will be re-initialized later
   openmc::openmc_set_seed(DEFAULT_SEED);

src/tallies/filter_mesh.cpp

@@ -45,10 +45,6 @@ const
   }
 
   double total = std::accumulate(match.weights_.begin(), match.weights_.end(), 0.0);
-  // if ( fabs(1.0 - total) > FP_PRECISION) {
-  //   std::cout << "Total weight for score < 1.0 (" << total << ")" << std::endl;
-  // }
-
 }
 
 void

tests/regression_tests/unstructured_mesh/test.py

@@ -184,7 +184,7 @@ def test_unstructured_mesh(test_opts):
 
     ### Tallies ###
 
-    # create meshes
+    # create meshes and mesh filters
     regular_mesh = openmc.RegularMesh()
     regular_mesh.dimension = (10, 10, 10)
     regular_mesh.lower_left = (-10.0, -10.0, -10.0)
@@ -197,8 +197,7 @@ def test_unstructured_mesh(test_opts):
     else:
         mesh_filename = "test_mesh_tets.exo"
 
-    uscd_mesh = openmc.UnstructuredMesh(mesh_filename)
-    uscd_mesh.library = test_opts['library']
+    uscd_mesh = openmc.UnstructuredMesh(mesh_filename, test_opts['library'])
     uscd_filter = openmc.MeshFilter(mesh=uscd_mesh)
 
     # create tallies