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Write and read mesh name attribute (#3221)
This commit is contained in:
Patrick Shriwise
GitHub
parent
de8132a5a4
commit
775c415122
8 changed files with 126 additions and 79 deletions
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@ -72,7 +72,10 @@ The current version of the statepoint file format is 18.1.
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**/tallies/meshes/mesh <uid>/**
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:Datasets: - **type** (*char[]*) -- Type of mesh.
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:Attributes: - **id** (*int*) -- ID of the mesh
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- **type** (*char[]*) -- Type of mesh.
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:Datasets: - **name** (*char[]*) -- Name of the mesh.
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- **dimension** (*int*) -- Number of mesh cells in each dimension.
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- **Regular Mesh Only:**
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- **lower_left** (*double[]*) -- Coordinates of lower-left corner of
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@ -109,7 +109,7 @@ The ``<tally>`` element accepts the following sub-elements:
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prematurely if there are no hits in any bins at the first
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evalulation. It is the user's responsibility to specify enough
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particles per batch to get a nonzero score in at least one bin.
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*Default*: False
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:scores:
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@ -329,6 +329,11 @@ If a mesh is desired as a filter for a tally, it must be specified in a separate
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element with the tag name ``<mesh>``. This element has the following
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attributes/sub-elements:
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:name:
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An optional string name to identify the mesh in output files.
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*Default*: ""
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:type:
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The type of mesh. This can be either "regular", "rectilinear",
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"cylindrical", "spherical", or "unstructured".
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@ -132,13 +132,18 @@ public:
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int32_t id() const { return id_; }
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const std::string& name() const { return name_; }
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//! Set the mesh ID
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void set_id(int32_t id = -1);
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//! Write the mesh data to an HDF5 group
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void to_hdf5(hid_t group) const;
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//! Write mesh data to an HDF5 group
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//
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//! \param[in] group HDF5 group
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virtual void to_hdf5(hid_t group) const = 0;
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virtual void to_hdf5_inner(hid_t group) const = 0;
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//! Find the mesh lines that intersect an axis-aligned slice plot
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//
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@ -202,7 +207,8 @@ public:
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// Data members
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xt::xtensor<double, 1> lower_left_; //!< Lower-left coordinates of mesh
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xt::xtensor<double, 1> upper_right_; //!< Upper-right coordinates of mesh
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int id_ {-1}; //!< User-specified ID
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int id_ {-1}; //!< Mesh ID
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std::string name_; //!< User-specified name
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int n_dimension_ {-1}; //!< Number of dimensions
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};
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@ -410,7 +416,7 @@ public:
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std::pair<vector<double>, vector<double>> plot(
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Position plot_ll, Position plot_ur) const override;
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void to_hdf5(hid_t group) const override;
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void to_hdf5_inner(hid_t group) const override;
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//! Get the coordinate for the mesh grid boundary in the positive direction
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//!
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@ -460,7 +466,7 @@ public:
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std::pair<vector<double>, vector<double>> plot(
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Position plot_ll, Position plot_ur) const override;
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void to_hdf5(hid_t group) const override;
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void to_hdf5_inner(hid_t group) const override;
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//! Get the coordinate for the mesh grid boundary in the positive direction
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//!
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@ -506,7 +512,7 @@ public:
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std::pair<vector<double>, vector<double>> plot(
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Position plot_ll, Position plot_ur) const override;
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void to_hdf5(hid_t group) const override;
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void to_hdf5_inner(hid_t group) const override;
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double volume(const MeshIndex& ijk) const override;
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@ -570,7 +576,7 @@ public:
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std::pair<vector<double>, vector<double>> plot(
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Position plot_ll, Position plot_ur) const override;
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void to_hdf5(hid_t group) const override;
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void to_hdf5_inner(hid_t group) const override;
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double r(int i) const { return grid_[0][i]; }
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double theta(int i) const { return grid_[1][i]; }
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@ -632,7 +638,7 @@ public:
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void surface_bins_crossed(Position r0, Position r1, const Direction& u,
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vector<int>& bins) const override;
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void to_hdf5(hid_t group) const override;
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void to_hdf5_inner(hid_t group) const override;
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std::string bin_label(int bin) const override;
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@ -99,21 +99,40 @@ class MeshBase(IDManagerMixin, ABC):
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Instance of a MeshBase subclass
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"""
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mesh_type = 'regular' if 'type' not in group.attrs else group.attrs['type'].decode()
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mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
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mesh_name = '' if not 'name' in group else group['name'][()].decode()
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mesh_type = group['type'][()].decode()
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if mesh_type == 'regular':
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return RegularMesh.from_hdf5(group)
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return RegularMesh.from_hdf5(group, mesh_id, mesh_name)
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elif mesh_type == 'rectilinear':
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return RectilinearMesh.from_hdf5(group)
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return RectilinearMesh.from_hdf5(group, mesh_id, mesh_name)
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elif mesh_type == 'cylindrical':
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return CylindricalMesh.from_hdf5(group)
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return CylindricalMesh.from_hdf5(group, mesh_id, mesh_name)
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elif mesh_type == 'spherical':
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return SphericalMesh.from_hdf5(group)
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return SphericalMesh.from_hdf5(group, mesh_id, mesh_name)
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elif mesh_type == 'unstructured':
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return UnstructuredMesh.from_hdf5(group)
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return UnstructuredMesh.from_hdf5(group, mesh_id, mesh_name)
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else:
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raise ValueError('Unrecognized mesh type: "' + mesh_type + '"')
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def to_xml_element(self):
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"""Return XML representation of the mesh
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Returns
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-------
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element : lxml.etree._Element
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XML element containing mesh data
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"""
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elem = ET.Element("mesh")
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elem.set("id", str(self._id))
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if self.name:
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elem.set("name", self.name)
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return elem
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@classmethod
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def from_xml_element(cls, elem: ET.Element):
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"""Generates a mesh from an XML element
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@ -132,18 +151,21 @@ class MeshBase(IDManagerMixin, ABC):
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mesh_type = get_text(elem, 'type')
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if mesh_type == 'regular' or mesh_type is None:
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return RegularMesh.from_xml_element(elem)
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mesh = RegularMesh.from_xml_element(elem)
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elif mesh_type == 'rectilinear':
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return RectilinearMesh.from_xml_element(elem)
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mesh = RectilinearMesh.from_xml_element(elem)
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elif mesh_type == 'cylindrical':
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return CylindricalMesh.from_xml_element(elem)
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mesh = CylindricalMesh.from_xml_element(elem)
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elif mesh_type == 'spherical':
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return SphericalMesh.from_xml_element(elem)
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mesh = SphericalMesh.from_xml_element(elem)
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elif mesh_type == 'unstructured':
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return UnstructuredMesh.from_xml_element(elem)
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mesh = UnstructuredMesh.from_xml_element(elem)
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else:
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raise ValueError(f'Unrecognized mesh type "{mesh_type}" found.')
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mesh.name = get_text(elem, 'name', default='')
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return mesh
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def get_homogenized_materials(
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self,
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model: openmc.Model,
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@ -791,11 +813,9 @@ class RegularMesh(StructuredMesh):
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return string
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@classmethod
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def from_hdf5(cls, group: h5py.Group):
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mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
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def from_hdf5(cls, group: h5py.Group, mesh_id: int, name: str):
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# Read and assign mesh properties
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mesh = cls(mesh_id)
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mesh = cls(mesh_id=mesh_id, name=name)
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mesh.dimension = group['dimension'][()]
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mesh.lower_left = group['lower_left'][()]
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if 'width' in group:
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@ -899,9 +919,7 @@ class RegularMesh(StructuredMesh):
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XML element containing mesh data
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"""
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element = ET.Element("mesh")
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element.set("id", str(self._id))
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element = super().to_xml_element()
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if self._dimension is not None:
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subelement = ET.SubElement(element, "dimension")
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@ -937,10 +955,6 @@ class RegularMesh(StructuredMesh):
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mesh_id = int(get_text(elem, 'id'))
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mesh = cls(mesh_id=mesh_id)
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mesh_type = get_text(elem, 'type')
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if mesh_type is not None:
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mesh.type = mesh_type
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dimension = get_text(elem, 'dimension')
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if dimension is not None:
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mesh.dimension = [int(x) for x in dimension.split()]
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@ -1235,11 +1249,9 @@ class RectilinearMesh(StructuredMesh):
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return string
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@classmethod
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def from_hdf5(cls, group: h5py.Group):
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mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
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def from_hdf5(cls, group: h5py.Group, mesh_id: int, name: str):
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# Read and assign mesh properties
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mesh = cls(mesh_id=mesh_id)
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mesh = cls(mesh_id=mesh_id, name=name)
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mesh.x_grid = group['x_grid'][()]
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mesh.y_grid = group['y_grid'][()]
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mesh.z_grid = group['z_grid'][()]
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@ -1279,8 +1291,7 @@ class RectilinearMesh(StructuredMesh):
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"""
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element = ET.Element("mesh")
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element.set("id", str(self._id))
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element = super().to_xml_element()
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element.set("type", "rectilinear")
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subelement = ET.SubElement(element, "x_grid")
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@ -1541,12 +1552,11 @@ class CylindricalMesh(StructuredMesh):
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return (r_index, phi_index, z_index)
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@classmethod
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def from_hdf5(cls, group: h5py.Group):
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mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
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def from_hdf5(cls, group: h5py.Group, mesh_id: int, name: str):
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# Read and assign mesh properties
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mesh = cls(
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mesh_id=mesh_id,
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name=name,
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r_grid = group['r_grid'][()],
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phi_grid = group['phi_grid'][()],
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z_grid = group['z_grid'][()],
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@ -1647,8 +1657,7 @@ class CylindricalMesh(StructuredMesh):
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"""
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element = ET.Element("mesh")
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element.set("id", str(self._id))
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element = super().to_xml_element()
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element.set("type", "cylindrical")
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subelement = ET.SubElement(element, "r_grid")
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@ -1926,15 +1935,14 @@ class SphericalMesh(StructuredMesh):
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return string
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@classmethod
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def from_hdf5(cls, group: h5py.Group):
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mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
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def from_hdf5(cls, group: h5py.Group, mesh_id: int, name: str):
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# Read and assign mesh properties
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mesh = cls(
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r_grid = group['r_grid'][()],
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theta_grid = group['theta_grid'][()],
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phi_grid = group['phi_grid'][()],
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mesh_id=mesh_id,
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name=name
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)
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if 'origin' in group:
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mesh.origin = group['origin'][()]
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@ -1951,8 +1959,7 @@ class SphericalMesh(StructuredMesh):
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"""
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element = ET.Element("mesh")
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element.set("id", str(self._id))
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element = super().to_xml_element()
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element.set("type", "spherical")
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subelement = ET.SubElement(element, "r_grid")
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@ -2444,8 +2451,7 @@ class UnstructuredMesh(MeshBase):
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writer.Write()
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@classmethod
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def from_hdf5(cls, group: h5py.Group):
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mesh_id = int(group.name.split('/')[-1].lstrip('mesh '))
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def from_hdf5(cls, group: h5py.Group, mesh_id: int, name: str):
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filename = group['filename'][()].decode()
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library = group['library'][()].decode()
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if 'options' in group.attrs:
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@ -2453,7 +2459,7 @@ class UnstructuredMesh(MeshBase):
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else:
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options = None
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mesh = cls(filename=filename, library=library, mesh_id=mesh_id, options=options)
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mesh = cls(filename=filename, library=library, mesh_id=mesh_id, name=name, options=options)
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mesh._has_statepoint_data = True
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vol_data = group['volumes'][()]
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mesh.volumes = np.reshape(vol_data, (vol_data.shape[0],))
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@ -2480,9 +2486,9 @@ class UnstructuredMesh(MeshBase):
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"""
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element = ET.Element("mesh")
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element.set("id", str(self._id))
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element = super().to_xml_element()
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element.set("type", "unstructured")
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element.set("library", self._library)
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if self.options is not None:
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element.set('options', self.options)
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55
src/mesh.cpp
55
src/mesh.cpp
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@ -109,6 +109,8 @@ Mesh::Mesh(pugi::xml_node node)
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{
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// Read mesh id
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id_ = std::stoi(get_node_value(node, "id"));
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if (check_for_node(node, "name"))
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name_ = get_node_value(node, "name");
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}
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void Mesh::set_id(int32_t id)
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@ -236,6 +238,28 @@ vector<Mesh::MaterialVolume> Mesh::material_volumes(
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return result;
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}
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void Mesh::to_hdf5(hid_t group) const
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{
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// Create group for mesh
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std::string group_name = fmt::format("mesh {}", id_);
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hid_t mesh_group = create_group(group, group_name.c_str());
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// Write mesh type
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write_attribute(mesh_group, "type", this->get_mesh_type());
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// Write mesh ID
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write_attribute(mesh_group, "id", id_);
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// Write mesh name
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write_dataset(mesh_group, "name", name_);
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// Write mesh data
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this->to_hdf5_inner(mesh_group);
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// Close group
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close_group(mesh_group);
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}
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//==============================================================================
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// Structured Mesh implementation
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//==============================================================================
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@ -389,11 +413,8 @@ std::string UnstructuredMesh::bin_label(int bin) const
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return fmt::format("Mesh Index ({})", bin);
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};
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void UnstructuredMesh::to_hdf5(hid_t group) const
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void UnstructuredMesh::to_hdf5_inner(hid_t mesh_group) const
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{
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hid_t mesh_group = create_group(group, fmt::format("mesh {}", id_));
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write_dataset(mesh_group, "type", mesh_type);
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write_dataset(mesh_group, "filename", filename_);
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write_dataset(mesh_group, "library", this->library());
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if (!options_.empty()) {
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@ -453,8 +474,6 @@ void UnstructuredMesh::to_hdf5(hid_t group) const
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write_dataset(mesh_group, "volumes", volumes);
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write_dataset(mesh_group, "connectivity", connectivity);
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write_dataset(mesh_group, "element_types", elem_types);
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close_group(mesh_group);
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}
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void UnstructuredMesh::set_length_multiplier(double length_multiplier)
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@ -948,17 +967,13 @@ std::pair<vector<double>, vector<double>> RegularMesh::plot(
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return {axis_lines[0], axis_lines[1]};
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}
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void RegularMesh::to_hdf5(hid_t group) const
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void RegularMesh::to_hdf5_inner(hid_t mesh_group) const
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{
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hid_t mesh_group = create_group(group, "mesh " + std::to_string(id_));
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write_dataset(mesh_group, "type", "regular");
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write_dataset(mesh_group, "dimension", get_x_shape());
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write_dataset(mesh_group, "lower_left", lower_left_);
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write_dataset(mesh_group, "upper_right", upper_right_);
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write_dataset(mesh_group, "width", width_);
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close_group(mesh_group);
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}
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xt::xtensor<double, 1> RegularMesh::count_sites(
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@ -1138,16 +1153,12 @@ std::pair<vector<double>, vector<double>> RectilinearMesh::plot(
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return {axis_lines[0], axis_lines[1]};
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}
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void RectilinearMesh::to_hdf5(hid_t group) const
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void RectilinearMesh::to_hdf5_inner(hid_t mesh_group) const
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{
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hid_t mesh_group = create_group(group, "mesh " + std::to_string(id_));
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write_dataset(mesh_group, "type", "rectilinear");
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write_dataset(mesh_group, "x_grid", grid_[0]);
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write_dataset(mesh_group, "y_grid", grid_[1]);
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write_dataset(mesh_group, "z_grid", grid_[2]);
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close_group(mesh_group);
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}
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double RectilinearMesh::volume(const MeshIndex& ijk) const
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@ -1417,17 +1428,13 @@ std::pair<vector<double>, vector<double>> CylindricalMesh::plot(
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return {axis_lines[0], axis_lines[1]};
|
||||
}
|
||||
|
||||
void CylindricalMesh::to_hdf5(hid_t group) const
|
||||
void CylindricalMesh::to_hdf5_inner(hid_t mesh_group) const
|
||||
{
|
||||
hid_t mesh_group = create_group(group, "mesh " + std::to_string(id_));
|
||||
|
||||
write_dataset(mesh_group, "type", "cylindrical");
|
||||
write_dataset(mesh_group, "r_grid", grid_[0]);
|
||||
write_dataset(mesh_group, "phi_grid", grid_[1]);
|
||||
write_dataset(mesh_group, "z_grid", grid_[2]);
|
||||
write_dataset(mesh_group, "origin", origin_);
|
||||
|
||||
close_group(mesh_group);
|
||||
}
|
||||
|
||||
double CylindricalMesh::volume(const MeshIndex& ijk) const
|
||||
|
|
@ -1733,17 +1740,13 @@ std::pair<vector<double>, vector<double>> SphericalMesh::plot(
|
|||
return {axis_lines[0], axis_lines[1]};
|
||||
}
|
||||
|
||||
void SphericalMesh::to_hdf5(hid_t group) const
|
||||
void SphericalMesh::to_hdf5_inner(hid_t mesh_group) const
|
||||
{
|
||||
hid_t mesh_group = create_group(group, "mesh " + std::to_string(id_));
|
||||
|
||||
write_dataset(mesh_group, "type", SphericalMesh::mesh_type);
|
||||
write_dataset(mesh_group, "r_grid", grid_[0]);
|
||||
write_dataset(mesh_group, "theta_grid", grid_[1]);
|
||||
write_dataset(mesh_group, "phi_grid", grid_[2]);
|
||||
write_dataset(mesh_group, "origin", origin_);
|
||||
|
||||
close_group(mesh_group);
|
||||
}
|
||||
|
||||
double SphericalMesh::volume(const MeshIndex& ijk) const
|
||||
|
|
|
|||
|
|
@ -308,7 +308,7 @@
|
|||
</settings>
|
||||
<tallies>
|
||||
<!--mesh-->
|
||||
<mesh id="1">
|
||||
<mesh id="1" name="mesh">
|
||||
<dimension>2 2</dimension>
|
||||
<lower_left>-50.0 -50.0</lower_left>
|
||||
<upper_right>50.0 50.0</upper_right>
|
||||
|
|
|
|||
|
|
@ -149,6 +149,9 @@ class TallySliceMergeTestHarness(PyAPITestHarness):
|
|||
sum2 = mesh_tally.summation(filter_type=openmc.MeshFilter,
|
||||
filter_bins=[(2, 1), (2, 2)])
|
||||
|
||||
mesh = mesh_tally.find_filter(openmc.MeshFilter).mesh
|
||||
assert mesh.name == 'mesh'
|
||||
|
||||
# Merge the mesh tally slices
|
||||
merge_tally = sum1.merge(sum2)
|
||||
|
||||
|
|
|
|||
|
|
@ -357,6 +357,27 @@ def test_CylindricalMesh_get_indices_at_coords():
|
|||
assert mesh.get_indices_at_coords([102, 199.1, 299]) == (0, 3, 0) # forth angle quadrant
|
||||
|
||||
|
||||
def test_mesh_name_roundtrip(run_in_tmpdir):
|
||||
|
||||
mesh = openmc.RegularMesh()
|
||||
mesh.name = 'regular-mesh'
|
||||
mesh.lower_left = (-1, -1, -1)
|
||||
mesh.width = (1, 1, 1)
|
||||
mesh.dimension = (1, 1, 1)
|
||||
|
||||
mesh_filter = openmc.MeshFilter(mesh)
|
||||
tally = openmc.Tally()
|
||||
tally.filters = [mesh_filter]
|
||||
tally.scores = ['flux']
|
||||
|
||||
openmc.Tallies([tally]).export_to_xml()
|
||||
|
||||
xml_tallies = openmc.Tallies.from_xml()
|
||||
|
||||
mesh = xml_tallies[0].find_filter(openmc.MeshFilter).mesh
|
||||
assert mesh.name == 'regular-mesh'
|
||||
|
||||
|
||||
def test_umesh_roundtrip(run_in_tmpdir, request):
|
||||
umesh = openmc.UnstructuredMesh(request.path.parent / 'test_mesh_tets.e', 'moab')
|
||||
umesh.output = True
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue