class TestAtom(unittest.TestCase):
atom_type = None
def setUp(self):
self.atom = Atom()
def tearDown(self):
del self.atom
def test_not_none(self):
self.assertIsNotNone(self.atom)
def test_data_object(self):
self.assertIsNotNone(self.atom.data_object)
test_name = create_object_attribute_test("atom", "name", "Test Name")
test_pn = create_object_attribute_test("atom", "pn", 3)
test_default_z = create_object_attribute_test("atom", "default_z", 5.3)
test_stretch_values = create_object_attribute_test("atom",
"stretch_values", True)
def test_parent(self):
parent_atom = Atom(name="Parent")
self.atom.parent = parent_atom
self.assertEqual(self.atom.parent, parent_atom)
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
class DummyComponent(object):
def get_interlayer_stretch_factors(self):
return lattice_d, factor
parent = DummyComponent()
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
def test_structure_factors(self):
import numpy as np
rng = 2.0 * np.sin(np.arange(30)) / 0.154056
res = self.atom.get_structure_factors(rng)
self.assertIsNotNone(res)
pass # end of class
class TestAtom(unittest.TestCase):
atom_type = None
def setUp(self):
self.atom = Atom()
def tearDown(self):
del self.atom
def test_not_none(self):
self.assertIsNotNone(self.atom)
def test_data_object(self):
self.assertIsNotNone(self.atom.data_object)
test_name = create_object_attribute_test("atom", "name", "Test Name")
test_pn = create_object_attribute_test("atom", "pn", 3)
test_default_z = create_object_attribute_test("atom", "default_z", 5.3)
test_stretch_values = create_object_attribute_test("atom", "stretch_values", True)
def test_parent(self):
parent_atom = Atom(name="Parent")
self.atom.parent = parent_atom
self.assertEqual(self.atom.parent, parent_atom)
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
class DummyComponent(object):
def get_interlayer_stretch_factors(self):
return lattice_d, factor
parent = DummyComponent()
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
def test_structure_factors(self):
import numpy as np
rng = 2.0 * np.sin(np.arange(30)) / 0.154056
res = self.atom.get_structure_factors(rng)
self.assertIsNotNone(res)
pass # end of class
class TestAtom(unittest.TestCase):
atom_type = None
def setUp(self):
self.atom = Atom()
def tearDown(self):
del self.atom
def get_mocked_hierarchy(self):
oxygen = Mock()
oxygen.name = "O1-"
hydrogen = Mock()
hydrogen.name = "H+"
project = Mock()
project.atom_types = [oxygen, hydrogen]
phase = Mock()
phase.attach_mock(project, 'project')
component = Mock()
component.attach_mock(phase, 'phase')
return oxygen, hydrogen, component, phase, project
def test_not_none(self):
self.assertIsNotNone(self.atom)
def test_data_object(self):
self.assertIsNotNone(self.atom.data_object)
test_name = create_object_attribute_test("atom", "name", "Test Name")
test_pn = create_object_attribute_test("atom", "pn", 3)
test_default_z = create_object_attribute_test("atom", "default_z", 5.3)
test_stretch_values = create_object_attribute_test("atom", "stretch_values", True)
def test_parent(self):
parent_atom = Atom(name="Parent")
self.atom.parent = parent_atom
self.assertEqual(self.atom.parent, parent_atom)
def test_set_atom_type(self):
oxygen, hydrogen, component, _, _ = self.get_mocked_hierarchy()
atom = Atom(
parent = component,
name = "O",
atom_type = oxygen,
)
atom.atom_type = hydrogen
self.assertEqual(atom.atom_type, hydrogen)
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
parent = Mock()
parent.configure_mock(**{
'get_interlayer_stretch_factors.return_value': (lattice_d, factor)
})
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
def test_structure_factors(self):
import numpy as np
rng = 2.0 * np.sin(np.arange(30)) / 0.154056
res = self.atom.get_structure_factors(rng)
self.assertIsNotNone(res)
def test_loads_atom_type_by_name(self):
atom_json_dict = {
"uuid": "878341b04e9e11e2b238150ae229a525",
"name": "O",
"default_z": 0.66,
"pn": 6.0,
"atom_type_name": "O1-"
}
oxygen, _, component, _, _ = self.get_mocked_hierarchy()
atom = Atom.from_json(parent = component, **atom_json_dict)
atom.resolve_json_references()
self.assertEqual(atom.atom_type, oxygen)
pass # end of class
class TestAtom(unittest.TestCase):
atom_type = None
def setUp(self):
self.atom = Atom()
def tearDown(self):
del self.atom
def get_mocked_hierarchy(self):
oxygen = Mock()
oxygen.name = "O1-"
hydrogen = Mock()
hydrogen.name = "H+"
project = Mock()
project.atom_types = [oxygen, hydrogen]
phase = Mock()
phase.attach_mock(project, 'project')
component = Mock()
component.attach_mock(phase, 'phase')
return oxygen, hydrogen, component, phase, project
def test_not_none(self):
self.assertIsNotNone(self.atom)
def test_data_object(self):
self.assertIsNotNone(self.atom.data_object)
test_name = create_object_attribute_test("atom", "name", "Test Name")
test_pn = create_object_attribute_test("atom", "pn", 3)
test_default_z = create_object_attribute_test("atom", "default_z", 5.3)
test_stretch_values = create_object_attribute_test("atom",
"stretch_values", True)
def test_parent(self):
parent_atom = Atom(name="Parent")
self.atom.parent = parent_atom
self.assertEqual(self.atom.parent, parent_atom)
def test_set_atom_type(self):
oxygen, hydrogen, component, _, _ = self.get_mocked_hierarchy()
atom = Atom(
parent=component,
name="O",
atom_type=oxygen,
)
atom.atom_type = hydrogen
self.assertEqual(atom.atom_type, hydrogen)
def test_z_calculations(self):
# Checks wether the atom can calculate stretched values:
# 1. When everything is set up the way it should be:
default_z = 9.0
lattice_d = 5.4
factor = 0.5
parent = Mock()
parent.configure_mock(**{
'get_interlayer_stretch_factors.return_value': (lattice_d, factor)
})
atom = Atom(parent=parent)
atom.stretch_values = True
atom.default_z = default_z
z = atom.z
self.assertEqual(z, lattice_d + (default_z - lattice_d) * factor)
# 2. When no component is set, but stretched is True: should not raise an error, but simple ignore the stretching
atom.parent = None
z = atom.z
def test_structure_factors(self):
import numpy as np
rng = 2.0 * np.sin(np.arange(30)) / 0.154056
res = self.atom.get_structure_factors(rng)
self.assertIsNotNone(res)
def test_loads_atom_type_by_name(self):
atom_json_dict = {
"uuid": "878341b04e9e11e2b238150ae229a525",
"name": "O",
"default_z": 0.66,
"pn": 6.0,
"atom_type_name": "O1-"
}
oxygen, _, component, _, _ = self.get_mocked_hierarchy()
atom = Atom.from_json(parent=component, **atom_json_dict)
atom.resolve_json_references()
self.assertEqual(atom.atom_type, oxygen)
pass # end of class
