def test_set_radii(self):
atom = Atom("H", [0, 0, 0])
self.assertEqual(atom._radii, 0.32)
atom = Atom("X", [0, 0, 0]) # ghost atom
self.assertEqual(atom._radii, 0.0)
with self.assertRaises(ValueError):
atom = Atom("NotAnElement", [0, 0, 0])
atom = Atom()
atom.element = "NotAnElement"
with self.assertLogs(logger=Atom.LOG, level="WARNING"):
atom._set_radii()
def test_store_atoms(self):
atoms_read = self.read_xyz(TestAtoms.small_mol)
atoms_manual = []
mol = []
with open(TestAtoms.small_mol) as f:
# split xyz file into info matrix
tmp = f.read()
tmp = tmp.split("\n")
for line in tmp:
line = line.strip().split()
if len(line):
mol += [line]
# remove atom number and comment line
mol = mol[2:]
for i, line in enumerate(mol):
a = Atom()
a.element = line[0]
a.coords = np.array(line[1:4], dtype=float)
a.flag = False
a.name = str(i + 1)
a.tags = set([i])
atoms_manual += [a]
# test manual and **kwargs assignment match
for a, b in zip(atoms_read, atoms_manual):
self.assertEqual(a.element, b.element)
self.assertTrue(np.linalg.norm(a.coords - b.coords) < 10**(-8))
self.assertEqual(a.name, b.name)
self.assertEqual(a.tags, b.tags)
# should have automatic lookup of _radii
self.assertTrue(a._radii is not None)
# transform back into xyz format for verification
atom_matrix = []
for a in atoms_read:
tmp = [str(a.element)]
for c in a.coords:
tmp += ["{:7.5f}".format(c)]
atom_matrix += [tmp]
for a, b in zip(mol, atom_matrix):
a = ' '.join(a)
b = ' '.join(b)
self.assertEqual(a, b)
return