def test_wrong_symbol(self):
wrong_data = {
"atom_0": {
"sort": self._good_data["atom_0"]["sort"],
"symbol": "CA", # valid is Ca not CA
"coord": self._good_data["atom_0"]["coord"],
"mass": self._good_data["atom_0"]["mass"]
}
}
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data)
def test_wrong_mass(self):
wrong_data = {
"atom_0": {
"sort": self._good_data["atom_0"]["sort"],
"symbol": self._good_data["atom_0"]["symbol"],
"coord": self._good_data["atom_0"]["coord"],
"mass": -1.0
}
}
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data)
wrong_data["mass"] = 28 # int instead of float
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data)
def test_good_extract(self):
atoms_data = AtomsData(self._good_data)
data = atoms_data.extract()
elements = len(self._good_data)
for el in range(elements):
self.assertEqual(self._good_data["atom_%s" % el]["sort"],
data["atom_%s" % el]["sort"])
self.assertEqual(self._good_data["atom_%s" % el]["symbol"],
data["atom_%s" % el]["symbol"])
self.assertEqual(
True,
np.allclose(self._good_data["atom_%s" % el]["coord"],
data["atom_%s" % el]["coord"]))
self.assertEqual(self._good_data["atom_%s" % el]["mass"],
data["atom_%s" % el]["mass"])
def test_wrong_set(self):
data = {
"atom_1": self._good_data["atom_0"],
"atom_2": self._good_data["atom_1"]
}
with self.assertRaises(ValueError):
AtomsData(data)
def test_wrong_sort(self):
# too large
wrong_data = {
"atom_0": {
"sort": 2,
"symbol": self._good_data["atom_0"]["symbol"],
"coord": self._good_data["atom_0"]["coord"],
"mass": self._good_data["atom_0"]["mass"]
}
}
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data["atom_0"], n_atoms=1)
# negative
wrong_data["atom_0"]["sort"] = -1,
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data["atom_0"])
# string instead of number
wrong_data["atom_0"]["sort"] = "-1"
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data["atom_0"])
def test_wrong_coord(self):
wrong_data = {
"atom_0": {
"sort": self._good_data["atom_0"]["sort"],
"symbol": self._good_data["atom_0"]["symbol"],
"coord": "wrong",
"mass": self._good_data["atom_0"]["mass"]
}
}
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data)
wrong_data["coord"] = np.asarray([[1, 2], [4]])
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data)
wrong_data["coord"] = np.asarray([1, 2])
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data)
def test_wrong_atom(self):
wrong_data = {
"atom_0": {
"sort": self._good_data["atom_0"]["sort"],
"symbol": self._good_data["atom_0"]["symbol"],
"coord": self._good_data["atom_0"]["coord"],
"mass": self._good_data["atom_0"]["mass"]
}
}
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data)
wrong_data["atom"] = 2
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data)
wrong_data["atom"] = 3
with self.assertRaises(ValueError):
AtomsData._check_item(wrong_data)
def setUp(self):
self._tester = AtomsData(self._good_data)
def test_wrong_list(self):
# init while missing atom 0
with self.assertRaises(ValueError):
AtomsData({'atom_1': self._good_data["atom_1"]})
def test_wrong_num_atoms(self):
with self.assertRaises(ValueError):
# noinspection PyUnusedLocal
wrong_tester = AtomsData(num_atoms=-2)
def setUp(self):
self._tester = AtomsData(num_atoms=2)
class AtomsDataTest(unittest.TestCase):
_good_data = {
"atom_0": {
'sort': 0,
'symbol': 'Si',
'coord': np.asarray([0., 0., 0.]),
'mass': 28.085500
},
"atom_1": {
'sort': 1,
'symbol': 'Si',
'coord': np.asarray([0.25, 0.25, 0.25]),
'mass': 28.085500
}
}
def setUp(self):
self._tester = AtomsData(num_atoms=2)
# constructor
def test_wrong_num_atoms(self):
with self.assertRaises(ValueError):
# noinspection PyUnusedLocal
wrong_tester = AtomsData(num_atoms=-2)
# append
def test_wrong_sort(self):
# too large
wrong_data = {
"atom_0": {
"sort": 3,
"symbol": self._good_data["atom_0"]["symbol"],
"coord": self._good_data["atom_0"]["coord"],
"mass": self._good_data["atom_0"]["mass"]
}
}
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
wrong_data["atom_0"][
"sort"] = 2 # we count from zero so 2 is also to large
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
# negative
wrong_data["atom_0"]["sort"] = -1,
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
# string instead of number
wrong_data["atom_0"]["sort"] = "-1"
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
def test_wrong_symbol(self):
wrong_data = {
"atom_0": {
"sort": self._good_data["atom_0"]["sort"],
"symbol": "CA", # valid is Ca not CA
"coord": self._good_data["atom_0"]["coord"],
"mass": self._good_data["atom_0"]["mass"]
}
}
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
def test_wrong_coord(self):
wrong_data = {
"atom_0": {
"sort": self._good_data["atom_0"]["sort"],
"symbol": self._good_data["atom_0"]["symbol"],
"coord": "wrong",
"mass": self._good_data["atom_0"]["mass"]
}
}
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
wrong_data["coord"] = np.asarray([[1, 2], [4]])
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
wrong_data["coord"] = np.asarray([1, 2])
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
def test_wrong_atom(self):
wrong_data = {
"atom_0": {
"sort": self._good_data["atom_0"]["sort"],
"symbol": self._good_data["atom_0"]["symbol"],
"coord": self._good_data["atom_0"]["coord"],
"mass": self._good_data["atom_0"]["mass"]
}
}
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
wrong_data["atom"] = 2
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
wrong_data["atom"] = 3
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
def test_wrong_mass(self):
wrong_data = {
"atom_0": {
"sort": self._good_data["atom_0"]["sort"],
"symbol": self._good_data["atom_0"]["symbol"],
"coord": self._good_data["atom_0"]["coord"],
"mass": -1.0
}
}
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
wrong_data["mass"] = 28 # int instead of float
with self.assertRaises(ValueError):
self._tester._append(item=wrong_data)
# set
def test_wrong_list(self):
items = self._good_data["atom_0"] # dict data for one atom only
with self.assertRaises(ValueError):
self._tester.set(items=items)
def test_wrong_extra_append(self):
self._tester._append(self._good_data["atom_0"])
self._tester._append(self._good_data["atom_1"])
with self.assertRaises(ValueError):
self._tester._append({
'sort': 1,
'symbol': 'Si',
'coord': np.asarray([0.25, 0.25, 0.25]),
'mass': 28.085500
})
def test_wrong_set(self):
data = {}
data.update({"atom_1": self._good_data["atom_0"]})
data.update({"atom_2": self._good_data["atom_1"]})
with self.assertRaises(ValueError):
self._tester.set(items=data)
# extract
def wrong_size_of_data(self):
self._tester._append(self._good_data["atom_0"])
with self.assertRaises(ValueError):
self._tester.extract()
# valid situations
def test_good_append(self):
self._tester._append(self._good_data["atom_0"])
self._tester._append(self._good_data["atom_1"])
data = self._tester.extract()
elements = len(self._good_data)
for el in range(elements):
self.assertEqual(self._good_data["atom_%s" % el]["sort"],
data["atom_%s" % el]["sort"])
self.assertEqual(self._good_data["atom_%s" % el]["symbol"],
data["atom_%s" % el]["symbol"])
self.assertEqual(
True,
np.allclose(self._good_data["atom_%s" % el]["coord"],
data["atom_%s" % el]["coord"]))
self.assertEqual(self._good_data["atom_%s" % el]["mass"],
data["atom_%s" % el]["mass"])
def test_good_set(self):
self._tester.set(self._good_data)
data = self._tester.extract()
elements = len(self._good_data)
for el in range(elements):
self.assertEqual(self._good_data["atom_%s" % el]["sort"],
data["atom_%s" % el]["sort"])
self.assertEqual(self._good_data["atom_%s" % el]["symbol"],
data["atom_%s" % el]["symbol"])
self.assertEqual(
True,
np.allclose(self._good_data["atom_%s" % el]["coord"],
data["atom_%s" % el]["coord"]))
self.assertEqual(self._good_data["atom_%s" % el]["mass"],
data["atom_%s" % el]["mass"])