Merge branch 'develop' into centre_for_cylinder_spherical_meshes

.github/workflows/ci.yml

@@ -34,9 +34,6 @@ jobs:
         vectfit: [n]
 
         include:
-          - python-version: 3.6
-            omp: n
-            mpi: n
           - python-version: 3.7
             omp: n
             mpi: n

docs/source/devguide/styleguide.rst

@@ -142,7 +142,7 @@ Style for Python code should follow PEP8_.
 
 Docstrings for functions and methods should follow numpydoc_ style.
 
-Python code should work with Python 3.6+.
+Python code should work with Python 3.7+.
 
 Use of third-party Python packages should be limited to numpy_, scipy_,
 matplotlib_, pandas_, and h5py_. Use of other third-party packages must be

docs/source/usersguide/install.rst

@@ -511,7 +511,7 @@ to install the Python package in :ref:`"editable" mode <devguide_editable>`.
 Prerequisites
 -------------
 
-The Python API works with Python 3.6+. In addition to Python itself, the API
+The Python API works with Python 3.7+. In addition to Python itself, the API
 relies on a number of third-party packages. All prerequisites can be installed
 using Conda_ (recommended), pip_, or through the package manager in most Linux
 distributions.

openmc/mesh.py

@@ -514,7 +514,7 @@ class RegularMesh(StructuredMesh):
     def from_domain(
         cls,
         domain,
-        dimension=[100, 100, 100],
+        dimension=(10, 10, 10),
         mesh_id=None,
         name=''
     ):
@@ -1147,6 +1147,76 @@ class CylindricalMesh(StructuredMesh):
 
         return mesh
 
+    @classmethod
+    def from_domain(
+        cls,
+        domain,
+        dimension=(10, 10, 10),
+        mesh_id=None,
+        phi_grid_bounds=(0.0, 2*pi),
+        name=''
+    ):
+        """Creates a regular CylindricalMesh from an existing openmc domain.
+
+        Parameters
+        ----------
+        domain : openmc.Cell or openmc.Region or openmc.Universe or openmc.Geometry
+            The object passed in will be used as a template for this mesh. The
+            bounding box of the property of the object passed will be used to
+            set the r_grid, z_grid ranges.
+        dimension : Iterable of int
+            The number of equally spaced mesh cells in each direction (r_grid,
+            phi_grid, z_grid)
+        mesh_id : int
+            Unique identifier for the mesh
+        phi_grid_bounds : numpy.ndarray
+            Mesh bounds points along the phi-axis in radians. The default value
+            is (0, 2π), i.e., the full phi range.
+        name : str
+            Name of the mesh
+
+        Returns
+        -------
+        openmc.RegularMesh
+            RegularMesh instance
+
+        """
+        cv.check_type(
+            "domain",
+            domain,
+            (openmc.Cell, openmc.Region, openmc.Universe, openmc.Geometry),
+        )
+
+        mesh = cls(mesh_id, name)
+
+        # loaded once to avoid reading h5m file repeatedly
+        cached_bb = domain.bounding_box
+        max_bounding_box_radius = max(
+            [
+                cached_bb[0][0],
+                cached_bb[0][1],
+                cached_bb[1][0],
+                cached_bb[1][1],
+            ]
+        )
+        mesh.r_grid = np.linspace(
+            0,
+            max_bounding_box_radius,
+            num=dimension[0]+1
+        )
+        mesh.phi_grid = np.linspace(
+            phi_grid_bounds[0],
+            phi_grid_bounds[1],
+            num=dimension[1]+1
+        )
+        mesh.z_grid = np.linspace(
+            cached_bb[0][2],
+            cached_bb[1][2],
+            num=dimension[2]+1
+        )
+
+        return mesh
+
     def to_xml_element(self):
         """Return XML representation of the mesh
 

setup.py

@@ -57,14 +57,14 @@ kwargs = {
         'Topic :: Scientific/Engineering'
         'Programming Language :: C++',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
     ],
 
     # Dependencies
-    'python_requires': '>=3.6',
+    'python_requires': '>=3.7',
     'install_requires': [
         'numpy>=1.9', 'h5py', 'scipy', 'ipython', 'matplotlib',
         'pandas', 'lxml', 'uncertainties'

src/state_point.cpp

@@ -527,6 +527,7 @@ hid_t h5banktype()
   H5Tinsert(banktype, "r", HOFFSET(SourceSite, r), postype);
   H5Tinsert(banktype, "u", HOFFSET(SourceSite, u), postype);
   H5Tinsert(banktype, "E", HOFFSET(SourceSite, E), H5T_NATIVE_DOUBLE);
+  H5Tinsert(banktype, "time", HOFFSET(SourceSite, time), H5T_NATIVE_DOUBLE);
   H5Tinsert(banktype, "wgt", HOFFSET(SourceSite, wgt), H5T_NATIVE_DOUBLE);
   H5Tinsert(banktype, "delayed_group", HOFFSET(SourceSite, delayed_group),
     H5T_NATIVE_INT);

tests/unit_tests/test_mesh_from_domain.py

@@ -16,6 +16,22 @@ def test_reg_mesh_from_cell():
     assert np.array_equal(mesh.upper_right, cell.bounding_box[1])
 
 
+def test_cylindrical_mesh_from_cell():
+    """Tests a CylindricalMesh can be made from a Cell and the specified
+    dimensions are propagated through. Cell is not centralized"""
+    cy_surface = openmc.ZCylinder(r=50)
+    z_surface_1 = openmc.ZPlane(z0=30)
+    z_surface_2 = openmc.ZPlane(z0=0)
+    cell = openmc.Cell(region=-cy_surface & -z_surface_1 & +z_surface_2)
+    mesh = openmc.CylindricalMesh.from_domain(cell, dimension=[2, 4, 3])
+
+    assert isinstance(mesh, openmc.CylindricalMesh)
+    assert np.array_equal(mesh.dimension, (2, 4, 3))
+    assert np.array_equal(mesh.r_grid, [0., 25., 50.])
+    assert np.array_equal(mesh.phi_grid, [0., 0.5*np.pi, np.pi, 1.5*np.pi, 2.*np.pi])
+    assert np.array_equal(mesh.z_grid, [0., 10., 20., 30.])
+
+
 def test_reg_mesh_from_region():
     """Tests a RegularMesh can be made from a Region and the default dimensions
     are propagated through. Region is not centralized"""
@@ -24,28 +40,48 @@ def test_reg_mesh_from_region():
 
     mesh = openmc.RegularMesh.from_domain(region)
     assert isinstance(mesh, openmc.RegularMesh)
-    assert np.array_equal(mesh.dimension, (100, 100, 100))  # default values
+    assert np.array_equal(mesh.dimension, (10, 10, 10))  # default values
     assert np.array_equal(mesh.lower_left, region.bounding_box[0])
     assert np.array_equal(mesh.upper_right, region.bounding_box[1])
 
 
+def test_cylindrical_mesh_from_region():
+    """Tests a CylindricalMesh can be made from a Region and the specified
+    dimensions and phi_grid_bounds are propagated through. Cell is centralized"""
+    cy_surface = openmc.ZCylinder(r=6)
+    z_surface_1 = openmc.ZPlane(z0=30)
+    z_surface_2 = openmc.ZPlane(z0=-30)
+    cell = openmc.Cell(region=-cy_surface & -z_surface_1 & +z_surface_2)
+    mesh = openmc.CylindricalMesh.from_domain(
+        cell,
+        dimension=(6, 2, 3),
+        phi_grid_bounds=(0., np.pi)
+    )
+
+    assert isinstance(mesh, openmc.CylindricalMesh)
+    assert np.array_equal(mesh.dimension, (6, 2, 3))
+    assert np.array_equal(mesh.r_grid, [0., 1., 2., 3., 4., 5., 6.])
+    assert np.array_equal(mesh.phi_grid, [0., 0.5*np.pi, np.pi])
+    assert np.array_equal(mesh.z_grid, [-30., -10., 10., 30.])
+
+
 def test_reg_mesh_from_universe():
-    """Tests a RegularMesh can be made from a Universe and the default dimensions
-    are propagated through. Universe is centralized"""
+    """Tests a RegularMesh can be made from a Universe and the default
+    dimensions are propagated through. Universe is centralized"""
     surface = openmc.Sphere(r=42)
     cell = openmc.Cell(region=-surface)
     universe = openmc.Universe(cells=[cell])
 
     mesh = openmc.RegularMesh.from_domain(universe)
     assert isinstance(mesh, openmc.RegularMesh)
-    assert np.array_equal(mesh.dimension, (100, 100, 100))  # default values
+    assert np.array_equal(mesh.dimension, (10, 10, 10))  # default values
     assert np.array_equal(mesh.lower_left, universe.bounding_box[0])
     assert np.array_equal(mesh.upper_right, universe.bounding_box[1])
 
 
 def test_reg_mesh_from_geometry():
-    """Tests a RegularMesh can be made from a Geometry and the default dimensions
-    are propagated through. Geometry is centralized"""
+    """Tests a RegularMesh can be made from a Geometry and the default
+    dimensions are propagated through. Geometry is centralized"""
     surface = openmc.Sphere(r=42)
     cell = openmc.Cell(region=-surface)
     universe = openmc.Universe(cells=[cell])
@@ -53,7 +89,7 @@ def test_reg_mesh_from_geometry():
 
     mesh = openmc.RegularMesh.from_domain(geometry)
     assert isinstance(mesh, openmc.RegularMesh)
-    assert np.array_equal(mesh.dimension, (100, 100, 100))  # default values
+    assert np.array_equal(mesh.dimension, (10, 10, 10))  # default values
     assert np.array_equal(mesh.lower_left, geometry.bounding_box[0])
     assert np.array_equal(mesh.upper_right, geometry.bounding_box[1])
 

tests/unit_tests/test_source_file.py

@@ -75,3 +75,25 @@ def test_wrong_source_attributes(run_in_tmpdir):
     with pytest.raises(RuntimeError) as excinfo:
         openmc.run()
     assert 'platypus, axolotl, narwhal' in str(excinfo.value)
+
+
+def test_source_file_transport(run_in_tmpdir):
+    # Create a source file with a single particle
+    particle = openmc.SourceParticle()
+    openmc.write_source_file([particle], 'source.h5')
+
+    # Created simple model to use source file
+    model = openmc.Model()
+    al = openmc.Material()
+    al.add_element('Al', 1.0)
+    al.set_density('g/cm3', 2.7)
+    sph = openmc.Sphere(r=10.0, boundary_type='vacuum')
+    cell = openmc.Cell(fill=al, region=-sph)
+    model.geometry = openmc.Geometry([cell])
+    model.settings.source = openmc.Source(filename='source.h5')
+    model.settings.particles = 10
+    model.settings.batches = 3
+    model.settings.run_mode = 'fixed source'
+
+    # Try running OpenMC
+    model.run()