Write and read mesh name attribute (openmc-dev#3221)

docs/source/io_formats/statepoint.rst

@@ -72,7 +72,10 @@ The current version of the statepoint file format is 18.1.
 
 **/tallies/meshes/mesh <uid>/**
 
-:Datasets: - **type** (*char[]*) -- Type of mesh.
+:Attributes: - **id** (*int*) -- ID of the mesh
+             - **type** (*char[]*) -- Type of mesh.
+
+:Datasets: - **name** (*char[]*) -- Name of the mesh.
            - **dimension** (*int*) -- Number of mesh cells in each dimension.
            - **Regular Mesh Only:**
               - **lower_left** (*double[]*) -- Coordinates of lower-left corner of

docs/source/io_formats/tallies.rst

@@ -109,7 +109,7 @@ The ``<tally>`` element accepts the following sub-elements:
                prematurely if there are no hits in any bins at the first
                evalulation. It is the user's responsibility to specify enough
                particles per batch to get a nonzero score in at least one bin.
-     
+
      *Default*: False
 
    :scores:
@@ -329,6 +329,11 @@ If a mesh is desired as a filter for a tally, it must be specified in a separate
 element with the tag name ``<mesh>``. This element has the following
 attributes/sub-elements:
 
+  :name:
+    An optional string name to identify the mesh in output files.
+
+    *Default*: ""
+
   :type:
     The type of mesh. This can be either "regular", "rectilinear",
     "cylindrical", "spherical", or "unstructured".

include/openmc/mesh.h

@@ -132,13 +132,18 @@ class Mesh {
 
   int32_t id() const { return id_; }
 
+  const std::string& name() const { return name_; }
+
   //! Set the mesh ID
   void set_id(int32_t id = -1);
 
+  //! Write the mesh data to an HDF5 group
+  void to_hdf5(hid_t group) const;
+
   //! Write mesh data to an HDF5 group
   //
   //! \param[in] group HDF5 group
-  virtual void to_hdf5(hid_t group) const = 0;
+  virtual void to_hdf5_inner(hid_t group) const = 0;
 
   //! Find the mesh lines that intersect an axis-aligned slice plot
   //
@@ -202,7 +207,8 @@ class Mesh {
   // Data members
   xt::xtensor<double, 1> lower_left_;  //!< Lower-left coordinates of mesh
   xt::xtensor<double, 1> upper_right_; //!< Upper-right coordinates of mesh
-  int id_ {-1};                        //!< User-specified ID
+  int id_ {-1};                        //!< Mesh ID
+  std::string name_;                   //!< User-specified name
   int n_dimension_ {-1};               //!< Number of dimensions
 };
 
@@ -410,7 +416,7 @@ class RegularMesh : public StructuredMesh {
   std::pair<vector<double>, vector<double>> plot(
     Position plot_ll, Position plot_ur) const override;
 
-  void to_hdf5(hid_t group) const override;
+  void to_hdf5_inner(hid_t group) const override;
 
   //! Get the coordinate for the mesh grid boundary in the positive direction
   //!
@@ -460,7 +466,7 @@ class RectilinearMesh : public StructuredMesh {
   std::pair<vector<double>, vector<double>> plot(
     Position plot_ll, Position plot_ur) const override;
 
-  void to_hdf5(hid_t group) const override;
+  void to_hdf5_inner(hid_t group) const override;
 
   //! Get the coordinate for the mesh grid boundary in the positive direction
   //!
@@ -506,7 +512,7 @@ class CylindricalMesh : public PeriodicStructuredMesh {
   std::pair<vector<double>, vector<double>> plot(
     Position plot_ll, Position plot_ur) const override;
 
-  void to_hdf5(hid_t group) const override;
+  void to_hdf5_inner(hid_t group) const override;
 
   double volume(const MeshIndex& ijk) const override;
 
@@ -570,7 +576,7 @@ class SphericalMesh : public PeriodicStructuredMesh {
   std::pair<vector<double>, vector<double>> plot(
     Position plot_ll, Position plot_ur) const override;
 
-  void to_hdf5(hid_t group) const override;
+  void to_hdf5_inner(hid_t group) const override;
 
   double r(int i) const { return grid_[0][i]; }
   double theta(int i) const { return grid_[1][i]; }
@@ -632,7 +638,7 @@ class UnstructuredMesh : public Mesh {
   void surface_bins_crossed(Position r0, Position r1, const Direction& u,
     vector<int>& bins) const override;
 
-  void to_hdf5(hid_t group) const override;
+  void to_hdf5_inner(hid_t group) const override;
 
   std::string bin_label(int bin) const override;
 

openmc/mesh.py

@@ -99,21 +99,40 @@ def from_hdf5(cls, group: h5py.Group):
             Instance of a MeshBase subclass
 
         """
+        mesh_type = 'regular' if 'type' not in group.attrs else group.attrs['type'].decode()
+        mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
+        mesh_name = '' if not 'name' in group else group['name'][()].decode()
 
-        mesh_type = group['type'][()].decode()
         if mesh_type == 'regular':
-            return RegularMesh.from_hdf5(group)
+            return RegularMesh.from_hdf5(group, mesh_id, mesh_name)
         elif mesh_type == 'rectilinear':
-            return RectilinearMesh.from_hdf5(group)
+            return RectilinearMesh.from_hdf5(group, mesh_id, mesh_name)
         elif mesh_type == 'cylindrical':
-            return CylindricalMesh.from_hdf5(group)
+            return CylindricalMesh.from_hdf5(group, mesh_id, mesh_name)
         elif mesh_type == 'spherical':
-            return SphericalMesh.from_hdf5(group)
+            return SphericalMesh.from_hdf5(group, mesh_id, mesh_name)
         elif mesh_type == 'unstructured':
-            return UnstructuredMesh.from_hdf5(group)
+            return UnstructuredMesh.from_hdf5(group, mesh_id, mesh_name)
         else:
             raise ValueError('Unrecognized mesh type: "' + mesh_type + '"')
 
+    def to_xml_element(self):
+        """Return XML representation of the mesh
+
+        Returns
+        -------
+        element : lxml.etree._Element
+            XML element containing mesh data
+
+        """
+        elem = ET.Element("mesh")
+
+        elem.set("id", str(self._id))
+        if self.name:
+            elem.set("name", self.name)
+
+        return elem
+
     @classmethod
     def from_xml_element(cls, elem: ET.Element):
         """Generates a mesh from an XML element
@@ -132,18 +151,21 @@ def from_xml_element(cls, elem: ET.Element):
         mesh_type = get_text(elem, 'type')
 
         if mesh_type == 'regular' or mesh_type is None:
-            return RegularMesh.from_xml_element(elem)
+            mesh = RegularMesh.from_xml_element(elem)
         elif mesh_type == 'rectilinear':
-            return RectilinearMesh.from_xml_element(elem)
+            mesh = RectilinearMesh.from_xml_element(elem)
         elif mesh_type == 'cylindrical':
-            return CylindricalMesh.from_xml_element(elem)
+            mesh = CylindricalMesh.from_xml_element(elem)
         elif mesh_type == 'spherical':
-            return SphericalMesh.from_xml_element(elem)
+            mesh = SphericalMesh.from_xml_element(elem)
         elif mesh_type == 'unstructured':
-            return UnstructuredMesh.from_xml_element(elem)
+            mesh = UnstructuredMesh.from_xml_element(elem)
         else:
             raise ValueError(f'Unrecognized mesh type "{mesh_type}" found.')
 
+        mesh.name = get_text(elem, 'name', default='')
+        return mesh
+
     def get_homogenized_materials(
             self,
             model: openmc.Model,
@@ -791,11 +813,9 @@ def __repr__(self):
         return string
 
     @classmethod
-    def from_hdf5(cls, group: h5py.Group):
-        mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
-
+    def from_hdf5(cls, group: h5py.Group, mesh_id: int, name: str):
         # Read and assign mesh properties
-        mesh = cls(mesh_id)
+        mesh = cls(mesh_id=mesh_id, name=name)
         mesh.dimension = group['dimension'][()]
         mesh.lower_left = group['lower_left'][()]
         if 'width' in group:
@@ -899,9 +919,7 @@ def to_xml_element(self):
             XML element containing mesh data
 
         """
-
-        element = ET.Element("mesh")
-        element.set("id", str(self._id))
+        element = super().to_xml_element()
 
         if self._dimension is not None:
             subelement = ET.SubElement(element, "dimension")
@@ -937,10 +955,6 @@ def from_xml_element(cls, elem: ET.Element):
         mesh_id = int(get_text(elem, 'id'))
         mesh = cls(mesh_id=mesh_id)
 
-        mesh_type = get_text(elem, 'type')
-        if mesh_type is not None:
-            mesh.type = mesh_type
-
         dimension = get_text(elem, 'dimension')
         if dimension is not None:
             mesh.dimension = [int(x) for x in dimension.split()]
@@ -1235,11 +1249,9 @@ def __repr__(self):
         return string
 
     @classmethod
-    def from_hdf5(cls, group: h5py.Group):
-        mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
-
+    def from_hdf5(cls, group: h5py.Group, mesh_id: int, name: str):
         # Read and assign mesh properties
-        mesh = cls(mesh_id=mesh_id)
+        mesh = cls(mesh_id=mesh_id, name=name)
         mesh.x_grid = group['x_grid'][()]
         mesh.y_grid = group['y_grid'][()]
         mesh.z_grid = group['z_grid'][()]
@@ -1279,8 +1291,7 @@ def to_xml_element(self):
 
         """
 
-        element = ET.Element("mesh")
-        element.set("id", str(self._id))
+        element = super().to_xml_element()
         element.set("type", "rectilinear")
 
         subelement = ET.SubElement(element, "x_grid")
@@ -1541,12 +1552,11 @@ def get_indices_at_coords(
         return (r_index, phi_index, z_index)
 
     @classmethod
-    def from_hdf5(cls, group: h5py.Group):
-        mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
-
+    def from_hdf5(cls, group: h5py.Group, mesh_id: int, name: str):
         # Read and assign mesh properties
         mesh = cls(
             mesh_id=mesh_id,
+            name=name,
             r_grid = group['r_grid'][()],
             phi_grid = group['phi_grid'][()],
             z_grid = group['z_grid'][()],
@@ -1647,8 +1657,7 @@ def to_xml_element(self):
 
         """
 
-        element = ET.Element("mesh")
-        element.set("id", str(self._id))
+        element = super().to_xml_element()
         element.set("type", "cylindrical")
 
         subelement = ET.SubElement(element, "r_grid")
@@ -1926,15 +1935,14 @@ def __repr__(self):
         return string
 
     @classmethod
-    def from_hdf5(cls, group: h5py.Group):
-        mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
-
+    def from_hdf5(cls, group: h5py.Group, mesh_id: int, name: str):
         # Read and assign mesh properties
         mesh = cls(
             r_grid = group['r_grid'][()],
             theta_grid = group['theta_grid'][()],
             phi_grid = group['phi_grid'][()],
             mesh_id=mesh_id,
+            name=name
         )
         if 'origin' in group:
             mesh.origin = group['origin'][()]
@@ -1951,8 +1959,7 @@ def to_xml_element(self):
 
         """
 
-        element = ET.Element("mesh")
-        element.set("id", str(self._id))
+        element = super().to_xml_element()
         element.set("type", "spherical")
 
         subelement = ET.SubElement(element, "r_grid")
@@ -2444,16 +2451,15 @@ def write_data_to_vtk(
         writer.Write()
 
     @classmethod
-    def from_hdf5(cls, group: h5py.Group):
-        mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
+    def from_hdf5(cls, group: h5py.Group, mesh_id: int, name: str):
         filename = group['filename'][()].decode()
         library = group['library'][()].decode()
         if 'options' in group.attrs:
             options = group.attrs['options'].decode()
         else:
             options = None
 
-        mesh = cls(filename=filename, library=library, mesh_id=mesh_id, options=options)
+        mesh = cls(filename=filename, library=library, mesh_id=mesh_id, name=name, options=options)
         mesh._has_statepoint_data = True
         vol_data = group['volumes'][()]
         mesh.volumes = np.reshape(vol_data, (vol_data.shape[0],))
@@ -2480,9 +2486,9 @@ def to_xml_element(self):
 
         """
 
-        element = ET.Element("mesh")
-        element.set("id", str(self._id))
+        element = super().to_xml_element()
         element.set("type", "unstructured")
+
         element.set("library", self._library)
         if self.options is not None:
             element.set('options', self.options)