Merge branch 'develop' into cam_WP7_task3

tests/unit_tests/test_data_photon.py

@@ -2,6 +2,7 @@
 
 from collections.abc import Mapping, Callable
 import os
+from pathlib import Path
 
 import numpy as np
 import pandas as pd
@@ -144,3 +145,9 @@ def test_export_to_hdf5(tmpdir, element):
            element2.bremsstrahlung['electron_energy']).all()
     # Export to hdf5 again
     element2.export_to_hdf5(filename, 'w')
+
+def test_photodat_only(run_in_tmpdir):
+    endf_dir = Path(os.environ['OPENMC_ENDF_DATA'])
+    photoatomic_file = endf_dir / 'photoat' / 'photoat-001_H_000.endf'
+    data = openmc.data.IncidentPhoton.from_endf(photoatomic_file)
+    data.export_to_hdf5('tmp.h5', 'w')

tests/unit_tests/test_deplete_nuclide.py

@@ -149,12 +149,18 @@ def test_fission_yield_distribution():
     # __getitem__ return yields as a view into yield matrix
     assert orig_yields.yields.base is yield_dist.yield_matrix
 
-    # Fission yield feature uses scaled and incremented
+    # Scale and increment fission yields
     mod_yields = orig_yields * 2
     assert numpy.array_equal(orig_yields.yields * 2, mod_yields.yields)
     mod_yields += orig_yields
     assert numpy.array_equal(orig_yields.yields * 3, mod_yields.yields)
 
+    mod_yields = 2.0 * orig_yields
+    assert numpy.array_equal(orig_yields.yields * 2, mod_yields.yields)
+
+    mod_yields = numpy.float64(2.0) * orig_yields
+    assert numpy.array_equal(orig_yields.yields * 2, mod_yields.yields)
+
     # Failure modes for adding, multiplying yields
     similar = numpy.empty_like(orig_yields.yields)
     with pytest.raises(TypeError):

tests/unit_tests/test_source.py

@@ -34,3 +34,11 @@ def test_source_file():
     elem = src.to_xml_element()
     assert 'strength' in elem.attrib
     assert 'file' in elem.attrib
+
+def test_source_dlopen():
+    library = './libsource.so'
+    src = openmc.Source(library=library)
+    assert src.library == library
+
+    elem = src.to_xml_element()
+    assert 'library' in elem.attrib

tests/unit_tests/test_surface.py

@@ -2,6 +2,7 @@ from functools import partial
 from random import uniform, seed
 
 import numpy as np
+import math
 import openmc
 import pytest
 
@@ -139,6 +140,51 @@ def test_zplane():
     repr(s)
 
 
+def test_cylinder():
+    x0, y0, z0, r = 2, 3, 4, 2
+    dx, dy, dz = 1, -1, 1
+    s = openmc.Cylinder(x0=x0, y0=y0, z0=z0, dx=dx, dy=dy, dz=dz, r=r)
+    assert s.x0 == 2
+    assert s.y0 == 3
+    assert s.z0 == 4
+    assert s.dx == 1
+    assert s.dy == -1
+    assert s.dz == 1
+    assert s.r == 2
+
+    # Check bounding box
+    assert_infinite_bb(s)
+
+    # evaluate method
+    # |(p - p1) ⨯ (p - p2)|^2 / |p2 - p1|^2 - r^2
+    p1 = s._origin
+    p2 = p1 + s._axis
+    perp = np.array((1, -2, 1))*(1 / s._axis)
+    divisor = np.linalg.norm(p2 - p1)
+    pin = p1 + 5*s._axis # point inside cylinder
+    pout = np.array((4., 0., 2.5)) # point outside the cylinder
+    pon = p1 + s.r*perp / np.linalg.norm(perp) # point on cylinder
+    for p, fn in zip((pin, pout, pon), (np.less, np.greater, np.isclose)):
+        c1 = np.linalg.norm(np.cross(p - p1, p - p2)) / divisor
+        val = c1*c1 - s.r*s.r
+        p_eval = s.evaluate(p)
+        assert fn(p_eval, 0.)
+        assert p_eval == pytest.approx(val)
+
+    # translate method
+    st = s.translate((1.0, 1.0, 1.0))
+    assert st.x0 == s.x0 + 1
+    assert st.y0 == s.y0 + 1
+    assert st.z0 == s.z0 + 1
+    assert st.dx == s.dx
+    assert st.dy == s.dy
+    assert st.dz == s.dz
+    assert st.r == s.r
+
+    # Make sure repr works
+    repr(s)
+
+
 def test_xcylinder():
     y, z, r = 3, 5, 2
     s = openmc.XCylinder(y0=y, z0=z, r=r)
@@ -284,6 +330,58 @@ def cone_common(apex, r2, cls):
     repr(s)
 
 
+def test_cone():
+    x0, y0, z0, r2 = 2, 3, 4, 4
+    dx, dy, dz = 1, -1, 1
+    s = openmc.Cone(x0=x0, y0=y0, z0=z0, dx=dx, dy=dy, dz=dz, r2=r2)
+    assert s.x0 == 2
+    assert s.y0 == 3
+    assert s.z0 == 4
+    assert s.dx == 1
+    assert s.dy == -1
+    assert s.dz == 1
+    assert s.r2 == 4
+
+    # Check bounding box
+    assert_infinite_bb(s)
+
+    # evaluate method
+    # cos^2(theta) * ((p - p1))**2 - (d @ (p - p1))^2 
+    # The argument r2 for cones is actually tan^2(theta) so that
+    # cos^2(theta) = 1 / (1 + r2)
+    #
+    # This makes the evaluation equation shown below where p is the evaluation
+    # point (x, y, z) p1 is the apex (origin) of the cone and r2 is related to
+    # the aperature of the cone as described above
+    # (p - p1) @ (p - p1) / (1 + r2) - (d @ (p - p1))^2
+    # point inside
+    p1 = s._origin
+    d = s._axis
+    perp = np.array((1, -2, 1))*(1 / d)
+    perp /= np.linalg.norm(perp)
+    pin = p1 + 5*d # point inside cone
+    pout = p1 + 3.2*perp # point outside cone
+    pon = p1 + 3.2*d + 3.2*math.sqrt(s.r2)*perp # point on cone
+    for p, fn in zip((pin, pout, pon), (np.less, np.greater, np.isclose)):
+        val = np.sum((p - p1)**2) / (1 + s.r2) - np.sum((d @ (p - p1))**2)
+        p_eval = s.evaluate(p)
+        assert fn(p_eval, 0.)
+        assert p_eval == pytest.approx(val)
+
+    # translate method
+    st = s.translate((1.0, 1.0, 1.0))
+    assert st.x0 == s.x0 + 1
+    assert st.y0 == s.y0 + 1
+    assert st.z0 == s.z0 + 1
+    assert st.dx == s.dx
+    assert st.dy == s.dy
+    assert st.dz == s.dz
+    assert st.r2 == s.r2
+
+    # Make sure repr works
+    repr(s)
+
+
 def test_xcone():
     apex = (10, 0, 0)
     r2 = 4
@@ -339,7 +437,7 @@ def test_cylinder_from_points():
         p1 = np.array([xi(), xi(), xi()])
         p2 = np.array([xi(), xi(), xi()])
         r = uniform(1.0, 100.0)
-        s = openmc.model.cylinder_from_points(p1, p2, r)
+        s = openmc.Cylinder.from_points(p1, p2, r)
 
         # Points p1 and p2 need to be inside cylinder
         assert p1 in -s
@@ -369,24 +467,27 @@ def test_cylinder_from_points_axis():
 
     # (x - 3)^2 + (y - 4)^2 = 2^2
     # x^2 + y^2 - 6x - 8y + 21 = 0
-    s = openmc.model.cylinder_from_points((3., 4., 0.), (3., 4., 1.), 2.)
-    assert (s.a, s.b, s.c) == pytest.approx((1., 1., 0.))
-    assert (s.d, s.e, s.f) == pytest.approx((0., 0., 0.))
-    assert (s.g, s.h, s.j) == pytest.approx((-6., -8., 0.))
-    assert s.k == pytest.approx(21.)
+    s = openmc.Cylinder.from_points((3., 4., 0.), (3., 4., 1.), 2.)
+    a, b, c, d, e, f, g, h, j, k = s._get_base_coeffs()
+    assert (a, b, c) == pytest.approx((1., 1., 0.))
+    assert (d, e, f) == pytest.approx((0., 0., 0.))
+    assert (g, h, j) == pytest.approx((-6., -8., 0.))
+    assert k == pytest.approx(21.)
 
     # (y + 7)^2 + (z - 1)^2 = 3^2
     # y^2 + z^2 + 14y - 2z + 41 = 0
-    s = openmc.model.cylinder_from_points((0., -7, 1.), (1., -7., 1.), 3.)
-    assert (s.a, s.b, s.c) == pytest.approx((0., 1., 1.))
-    assert (s.d, s.e, s.f) == pytest.approx((0., 0., 0.))
-    assert (s.g, s.h, s.j) == pytest.approx((0., 14., -2.))
-    assert s.k == 41.
+    s = openmc.Cylinder.from_points((0., -7, 1.), (1., -7., 1.), 3.)
+    a, b, c, d, e, f, g, h, j, k = s._get_base_coeffs()
+    assert (a, b, c) == pytest.approx((0., 1., 1.))
+    assert (d, e, f) == pytest.approx((0., 0., 0.))
+    assert (g, h, j) == pytest.approx((0., 14., -2.))
+    assert k == 41.
 
     # (x - 2)^2 + (z - 5)^2 = 4^2
     # x^2 + z^2 - 4x - 10z + 13 = 0
-    s = openmc.model.cylinder_from_points((2., 0., 5.), (2., 1., 5.), 4.)
-    assert (s.a, s.b, s.c) == pytest.approx((1., 0., 1.))
-    assert (s.d, s.e, s.f) == pytest.approx((0., 0., 0.))
-    assert (s.g, s.h, s.j) == pytest.approx((-4., 0., -10.))
-    assert s.k == pytest.approx(13.)
+    s = openmc.Cylinder.from_points((2., 0., 5.), (2., 1., 5.), 4.)
+    a, b, c, d, e, f, g, h, j, k = s._get_base_coeffs()
+    assert (a, b, c) == pytest.approx((1., 0., 1.))
+    assert (d, e, f) == pytest.approx((0., 0., 0.))
+    assert (g, h, j) == pytest.approx((-4., 0., -10.))
+    assert k == pytest.approx(13.)