def test_shortened_properties_errors(self):
properties = {"name": ["2", "3"]}
with self.assertRaises(ValueError) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(
str(cm.exception),
"The length of property values is different from the number of "
+ "structures and the number of atoms, we can not guess the target. "
+ "Got n_atoms = 3, n_structures = 1, the length of property values "
+ "is 2, for the 'name' property",
)
properties = {"name": ase.Atoms("CO2")}
with self.assertRaises(ValueError) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(
str(cm.exception),
"Property values should be either list or numpy array, got "
+ "<class 'ase.atoms.Atoms'> instead",
)
properties = {"name": ["2", "3"]}
frames_single_atoms = [ase.Atoms("C"), ase.Atoms("H")]
with self.assertWarns(UserWarning) as cm:
data = create_input(frames=frames_single_atoms, properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "structure")
self.assertEqual(
cm.warning.args[0],
"The target of the property 'name' is ambiguous because there is the same "
+ "number of atoms and structures. Will assume target=structure. ",
)
def test_properties_also_in_frame(self):
properties = {"name": {"target": "atom", "values": [2, 3, 4]}}
frames = copy.deepcopy(TEST_FRAMES)
for frame in frames:
frame.info["name"] = "test"
with self.assertWarns(UserWarning) as cm:
data = create_input(frames=frames, properties=properties)
self.assertEqual(
str(cm.warning),
"ignoring the 'name' structure property coming from the "
+ "structures since it is already part of the properties",
)
self.assertEqual(data["properties"]["name"]["target"], "atom")
properties = {"name": {"target": "structure", "values": [2]}}
frames = copy.deepcopy(TEST_FRAMES)
for frame in frames:
frame.arrays["name"] = [0] * len(frame)
with self.assertWarns(UserWarning) as cm:
data = create_input(frames=frames, properties=properties)
self.assertEqual(
str(cm.warning),
"ignoring the 'name' atom property coming from the "
+ "structures since it is already part of the properties",
)
self.assertEqual(data["properties"]["name"]["target"], "structure")
def test_property_only(self):
properties = {"name": [2, 3, 4]}
data = create_input(properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "structure")
properties = {
"first": [2, 3, 4],
"second": np.array([[1, 2], [1, 2], [1, 2]]),
}
data = create_input(properties=properties)
self.assertEqual(data["properties"]["second[1]"]["target"], "structure")
self.assertEqual(data["properties"]["second[2]"]["target"], "structure")
# error: different size
properties = {"first": [2, 3, 4], "second": [2, 3, 4, 5]}
with self.assertRaises(Exception) as cm:
data = create_input(properties=properties)
self.assertEqual(
str(cm.exception),
"wrong size for property 'second': expected 3 elements, but got an array with 4 entries",
)
# error: target is not "structure"
properties = {"name": {"target": "atom", "values": [2]}}
with self.assertRaises(Exception) as cm:
data = create_input(properties=properties)
self.assertEqual(
str(cm.exception),
"property 'name' has a non-structure target, which is not allowed if frames are not provided",
)
def test_meta_conversions(self):
meta = {"name": 33}
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "33")
self.assertEqual(len(data["meta"].keys()), 1)
meta = {"name": ["foo", "bar"], "description": False}
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "['foo', 'bar']")
self.assertEqual(data["meta"]["description"], "False")
self.assertEqual(len(data["meta"].keys()), 2)
meta = {"name": "foo", "references": (3, False)}
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "foo")
self.assertEqual(len(data["meta"]["references"]), 2)
self.assertEqual(data["meta"]["references"][0], "3")
self.assertEqual(data["meta"]["references"][1], "False")
self.assertEqual(len(data["meta"].keys()), 2)
meta = {"name": "foo", "authors": (3, False)}
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "foo")
self.assertEqual(len(data["meta"]["authors"]), 2)
self.assertEqual(data["meta"]["authors"][0], "3")
self.assertEqual(data["meta"]["authors"][1], "False")
self.assertEqual(len(data["meta"].keys()), 2)
def test_structures(self):
data = create_input(BASE_FRAME)
self.assertEqual(len(data["structures"]), 1)
self.assertEqual(data["structures"][0]["size"], 3)
self.assertEqual(data["structures"][0]["names"], ["C", "O", "O"])
self.assertEqual(data["structures"][0]["x"], [0, 1, 2])
self.assertEqual(data["structures"][0]["y"], [0, 1, 2])
self.assertEqual(data["structures"][0]["z"], [0, 1, 5])
self.assertEqual(data["structures"][0].get("cell"), None)
frame = BASE_FRAME.copy()
frame.cell = [23, 22, 11]
data = create_input([frame])
self.assertEqual(len(data["structures"]), 1)
self.assertEqual(data["structures"][0]["cell"],
[23, 0, 0, 0, 22, 0, 0, 0, 11])
frame = BASE_FRAME.copy()
frame.cell = [23, 22, 11, 120, 90, 70]
data = create_input([frame])
self.assertEqual(len(data["structures"]), 1)
self.assertEqual(
data["structures"][0]["cell"],
[
23.0,
0.0,
0.0,
7.5244431531647145,
20.673237657289985,
0.0,
0.0,
-5.852977748617515,
9.313573507209156,
],
)
def test_shortened_properties(self):
# atom property
properties = {"name": [2, 3, 4]}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "atom")
self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
self.assertEqual(len(data["properties"]["name"].keys()), 2)
# frame property
properties = {"name": [2]}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "structure")
self.assertEqual(data["properties"]["name"]["values"], [2])
self.assertEqual(len(data["properties"]["name"].keys()), 2)
# ndarray frame property
properties = {"name": np.array([[2, 4]])}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name[1]"]["target"], "structure")
self.assertEqual(data["properties"]["name[1]"]["values"], [2])
self.assertEqual(len(data["properties"]["name[1]"].keys()), 2)
self.assertEqual(data["properties"]["name[2]"]["target"], "structure")
self.assertEqual(data["properties"]["name[2]"]["values"], [4])
self.assertEqual(len(data["properties"]["name[2]"].keys()), 2)
# the initial properties object must not be changed
self.assertEqual(type(properties["name"]), np.ndarray)
def test_invalid_types_metadata(self):
properties = {"name": {"target": "atom", "values": [2, 3, 4], "units": False}}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["units"], "False")
properties = {
"name": {"target": "atom", "values": [2, 3, 4], "description": False}
}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["description"], "False")
def test_property_unknown_keys_warning(self):
properties = {
"name": {
"target": "atom",
"values": [2, 3, 4],
"what": False
}
}
with self.assertWarns(UserWarning) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(cm.warning.args,
("ignoring unexpected property key: what", ))
def test_ndarray_properties(self):
# shape N
properties = {
"name": {
"target": "atom",
"values": np.array([2, 3, 4])
}
}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "atom")
self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
self.assertEqual(len(data["properties"].keys()), 1)
# shape N
properties = {
"name": {
"target": "atom",
"values": np.array(["2", "3", "4"])
}
}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "atom")
self.assertEqual(data["properties"]["name"]["values"], ["2", "3", "4"])
self.assertEqual(len(data["properties"].keys()), 1)
# shape N x 1
properties = {
"name": {
"target": "atom",
"values": np.array([[2], [3], [4]])
}
}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "atom")
self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
self.assertEqual(len(data["properties"].keys()), 1)
# shape N x 3
properties = {
"name": {
"target": "atom",
"values": np.array([[1, 2, 4], [1, 2, 4], [1, 2, 4]]),
}
}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name[1]"]["target"], "atom")
self.assertEqual(data["properties"]["name[1]"]["values"], [1, 1, 1])
self.assertEqual(data["properties"]["name[2]"]["target"], "atom")
self.assertEqual(data["properties"]["name[2]"]["values"], [2, 2, 2])
self.assertEqual(data["properties"]["name[3]"]["target"], "atom")
self.assertEqual(data["properties"]["name[3]"]["values"], [4, 4, 4])
self.assertEqual(len(data["properties"].keys()), 3)
def test_invalid_target(self):
properties = {"name": {"values": [2, 3, 4]}}
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(str(cm.exception), "missing 'target' for the 'name' property")
properties = {"name": {"target": "atoms", "values": [2, 3, 4]}}
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(
str(cm.exception),
"the target must be 'atom' or 'structure' for the 'name' property",
)
def test_environment_wrong_type(self):
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, cutoff="3.5")
self.assertEqual(
str(cm.exception), "cutoff must be a float, got '3.5' of type <class 'str'>"
)
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, cutoff=False)
self.assertEqual(
str(cm.exception),
"cutoff must be a float, got 'False' of type <class 'bool'>",
)
def test_invalid_name(self):
properties = {"": {"target": "atom", "values": [2, 3, 4]}}
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(str(cm.exception),
"the name of a property can not be the empty string")
properties = {False: {"target": "atom", "values": [2, 3, 4]}}
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(
str(cm.exception),
"the name of a property name must be a string, " +
"got 'False' of type <class 'bool'>",
)
def test_environment(self):
data = create_input(frames=TEST_FRAMES + TEST_FRAMES, cutoff=3.5)
self.assertEqual(len(data["environments"]), 6)
for i, env in enumerate(data["environments"]):
self.assertEqual(env["structure"], i // 3)
self.assertEqual(env["center"], i % 3)
self.assertEqual(env["cutoff"], 3.5)
def test_meta_unknown_keys_warning(self):
meta = {"name": "foo", "what_is_this": "I don't know"}
with self.assertWarns(UserWarning) as cm:
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "foo")
self.assertEqual(len(data["meta"].keys()), 1)
self.assertEqual(str(cm.warning), "ignoring unexpected metadata: what_is_this")
def test_wrong_number_of_values(self):
properties = {"name": {"target": "atom", "values": [2, 3]}}
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(
str(cm.exception),
"wrong size for the property 'name' with target=='atom': "
+ "expected 3 values, got 2",
)
properties = {"name": {"target": "structure", "values": [2, 3, 5]}}
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(
str(cm.exception),
"wrong size for the property 'name' with target=='structure': "
+ "expected 1 values, got 3",
)
def test_arrays_as_atom_properties(self):
frame = BASE_FRAME.copy()
frame.arrays["bar"] = [4, 5, 6]
data = create_input([frame])
self.assertEqual(len(data["properties"].keys()), 1)
self.assertEqual(data["properties"]["bar"]["target"], "atom")
self.assertEqual(data["properties"]["bar"]["values"], [4, 5, 6])
self.assertEqual(data["properties"]["bar"].get("units"), None)
self.assertEqual(data["properties"]["bar"].get("description"), None)
def test_info_as_frame_properties(self):
frame = BASE_FRAME.copy()
frame.info["bar"] = 4
frame2 = BASE_FRAME.copy()
frame2.info["bar"] = 6
data = create_input([frame, frame2])
self.assertEqual(len(data["properties"].keys()), 1)
self.assertEqual(data["properties"]["bar"]["target"], "structure")
self.assertEqual(data["properties"]["bar"]["values"], [4, 6])
self.assertEqual(data["properties"]["bar"].get("units"), None)
self.assertEqual(data["properties"]["bar"].get("description"), None)
def test_properties(self):
# values are numbers
properties = {"name": {"target": "atom", "values": [2, 3, 4]}}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "atom")
self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
self.assertEqual(len(data["properties"]["name"].keys()), 2)
# values are strings
properties = {"name": {"target": "atom", "values": ["2", "3", "4"]}}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "atom")
self.assertEqual(data["properties"]["name"]["values"], ["2", "3", "4"])
self.assertEqual(len(data["properties"]["name"].keys()), 2)
properties = {
"name": {
"target": "atom",
"values": [2, 3, 4],
"description": "foo",
},
}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "atom")
self.assertEqual(data["properties"]["name"]["description"], "foo")
self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
self.assertEqual(len(data["properties"]["name"].keys()), 3)
properties = {
"name": {
"target": "atom",
"values": [2, 3, 4],
"units": "foo",
},
}
data = create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(data["properties"]["name"]["target"], "atom")
self.assertEqual(data["properties"]["name"]["units"], "foo")
self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
self.assertEqual(len(data["properties"]["name"].keys()), 3)
def test_meta(self):
meta = {}
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "<unknown>")
self.assertEqual(len(data["meta"].keys()), 1)
meta = {"name": ""}
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "<unknown>")
self.assertEqual(len(data["meta"].keys()), 1)
meta = {"name": "foo"}
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "foo")
self.assertEqual(len(data["meta"].keys()), 1)
meta = {"name": "foo", "description": "bar"}
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "foo")
self.assertEqual(data["meta"]["description"], "bar")
self.assertEqual(len(data["meta"].keys()), 2)
meta = {"name": "foo", "references": ["bar"]}
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "foo")
self.assertEqual(len(data["meta"]["references"]), 1)
self.assertEqual(data["meta"]["references"][0], "bar")
self.assertEqual(len(data["meta"].keys()), 2)
meta = {"name": "foo", "authors": ["bar"]}
data = create_input(frames=TEST_FRAMES, meta=meta)
self.assertEqual(data["meta"]["name"], "foo")
self.assertEqual(len(data["meta"]["authors"]), 1)
self.assertEqual(data["meta"]["authors"][0], "bar")
self.assertEqual(len(data["meta"].keys()), 2)
def test_wrong_property_type(self):
frame = BASE_FRAME.copy()
frame.arrays["bar"] = [{"f": 3}, {"f": 3}, {"f": 3}]
with self.assertWarns(UserWarning) as cm:
data = create_input(frame)
self.assertEqual(
cm.warning.args,
("value '{'f': 3}' of type '<class 'dict'>' for the 'bar' property "
+
"from ASE is not convertible to float or string, this property " +
"will be ignored.", ),
)
self.assertEqual(len(data["properties"].keys()), 0)
def test_different_info(self):
frame = BASE_FRAME.copy()
frame.info["bar"] = 4
frame.info["foo"] = False
frame2 = BASE_FRAME.copy()
frame2.info["bar"] = -1
frame2.info["baz"] = "test"
with self.assertWarns(UserWarning) as cm:
data = create_input([frame, frame2])
self.assertEqual(
cm.warning.args,
("the following structure properties properties are only defined "
+
"for a subset of frames: ['baz', 'foo']; they will be ignored", ),
)
self.assertEqual(len(data["properties"].keys()), 1)
self.assertEqual(data["properties"]["bar"]["target"], "structure")
self.assertEqual(data["properties"]["bar"]["values"], [4, -1])
self.assertEqual(data["properties"]["bar"].get("units"), None)
self.assertEqual(data["properties"]["bar"].get("description"), None)
def test_different_arrays(self):
frame = BASE_FRAME.copy()
frame.arrays["bar"] = [4, 5, 6]
frame.arrays["foo"] = [4, 5, 6]
frame2 = BASE_FRAME.copy()
frame2.arrays["bar"] = [-1, 2, 3]
frame2.arrays["baz"] = [33, 44, 55]
with self.assertWarns(UserWarning) as cm:
data = create_input([frame, frame2])
self.assertEqual(
cm.warning.args,
("the following atomic properties properties are only defined " +
"for a subset of frames: ['baz', 'foo']; they will be ignored", ),
)
self.assertEqual(len(data["properties"].keys()), 1)
self.assertEqual(data["properties"]["bar"]["target"], "atom")
self.assertEqual(data["properties"]["bar"]["values"],
[4, 5, 6, -1, 2, 3])
self.assertEqual(data["properties"]["bar"].get("units"), None)
self.assertEqual(data["properties"]["bar"].get("description"), None)
def test_invalid_values_types(self):
properties = {"name": {"target": "atom", "values": 3}}
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(str(cm.exception),
"unknown type (<class 'int'>) for property 'name'")
properties = {"name": {"target": "atom", "values": {"test": "bad"}}}
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(str(cm.exception),
"unknown type (<class 'dict'>) for property 'name'")
properties = {"name": {"target": "atom", "values": [{}, {}, {}]}}
with self.assertRaises(Exception) as cm:
create_input(frames=TEST_FRAMES, properties=properties)
self.assertEqual(
str(cm.exception),
"unsupported type in property 'name' values: should be string or number",
)
def test_arrays_numbers_postions_ignored(self):
data = create_input(BASE_FRAME)
self.assertEqual(len(BASE_FRAME.arrays.keys()), 2)
self.assertEqual(len(data["properties"].keys()), 0)
