def test_rotation_analyser_is_initialised(self):
reference_points = np.array([[1.0, -1.0, 1.0], [-1.0, -1.0, -1.0],
[1.0, 1.0, -1.0], [-1.0, 1.0, 1.0]])
ra = RotationAnalyser(reference_points=reference_points)
self.assertEqual(ra.reference_points.shape, (1, 4, 3))
np.testing.assert_array_equal(ra.reference_points,
np.array([reference_points]))
def test_rotation_analyser_init_raises_error_for_misformed_reference_points(
self):
reference_points = np.array([[[1.0, -1.0, 1.0]],
[[-1.0, -1.0, -1.0], [1.0, 1.0, -1.0],
[-1.0, 1.0, 1.0]]])
with self.assertRaises(ValueError):
ra = RotationAnalyser(reference_points=reference_points)
def test_rotation_analyser_is_initialised_with_multiple_reference_geometries(
self):
reference_points = np.array([[[1.0, -1.0, 1.0], [-1.0, -1.0, -1.0]],
[[1.0, 1.0, -1.0], [-1.0, 1.0, 1.0]]])
ra = RotationAnalyser(reference_points=reference_points)
self.assertEqual(ra.reference_points.shape, (2, 2, 3))
np.testing.assert_array_equal(ra.reference_points, reference_points)
class TestRotationAnalyser(unittest.TestCase):
def setUp(self):
reference_points = np.array([[1.0, -1.0, 1.0], [-1.0, -1.0, -1.0],
[1.0, 1.0, -1.0], [-1.0, 1.0, 1.0]])
all_points = np.array([reference_points, reference_points * (-1.0)])
self.ra = RotationAnalyser(reference_points=all_points)
def test_polyhedron_orientation(self):
mock_polyhedron = Mock(spec=CoordinationPolyhedron)
mock_polyhedron.abstract_geometry = Mock(spec=AbstractGeometry)
mock_polyhedron.abstract_geometry.points_wocs_csc = Mock(
return_value='foo')
self.ra.discrete_orientation = Mock(return_value='bar')
orientation = self.ra.polyhedron_orientation(mock_polyhedron)
self.ra.discrete_orientation.assert_called_once_with('foo')
self.assertEqual(orientation, 'bar')
def setUp(self):
reference_points = np.array([[1.0, -1.0, 1.0], [-1.0, -1.0, -1.0],
[1.0, 1.0, -1.0], [-1.0, 1.0, 1.0]])
all_points = np.array([reference_points, reference_points * (-1.0)])
self.ra = RotationAnalyser(reference_points=all_points)
trajectory = Trajectory.from_xdatcars(filenames=[
'1/XDATCAR', '2/XDATCAR', '3/XDATCAR', '4/XDATCAR', '5/XDATCAR'
],
recipes=[ps4_recipe, sns4_recipe],
progress=True,
ncores=4)
reference_points = np.array([[1.0, -1.0, 1.0], [-1.0, -1.0, -1.0],
[1.0, 1.0, -1.0], [-1.0, 1.0, 1.0]])
reference_points.shape
all_points = np.array([reference_points, reference_points * (-1)])
all_points.shape
ra = RotationAnalyser(reference_points=all_points)
import math
n = len(trajectory.configurations[0].polyhedra)
# n = 2
all_orientations = []
all_angles = []
all_reference = []
for i in tqdm(range(n)):
angles = []
orientations = []
reference = []
for c in trajectory.configurations:
po = ra.polyhedron_orientation(c.polyhedra[i])
angles.append(po['rotational_distance'])