class TestMolecule(unittest.TestCase):
"""Tests the Molecule class"""
def setUp(self):
"""Set up for every test"""
self.water_geom = [['H', [0, 0, 0]], ['O', [0, 0, 1]],
['H', [0, 1, 1]]]
self.water = Molecule(self.water_geom)
def test_len(self):
"""Testing __len__"""
self.assertEqual(len(self.water), 3)
def test_getsetdeleqinsert(self):
"""Test getting, setting and deleting atoms"""
self.assertEqual(self.water[0][0], 'H')
self.assertTrue(all(self.water[0][1] == np.array([0, 0, 0])))
del self.water[1]
self.assertEqual(self.water[1][0], 'H')
self.assertTrue(all(self.water[1][1] == np.array([0, 1, 1])))
self.water[0] = ['H', [0, 0, 0]]
self.water[1] = ['H', [0, -1, 1]]
self.assertEqual(self.water[1][0], 'H')
self.assertTrue(all(self.water[1][1] == np.array([0, -1, 1])))
self.water.insert(1, 'O', [0, 0, 1])
self.assertEqual(self.water[1][0], 'O')
self.assertTrue(all(self.water[1][1] == np.array([0, 0, 1])))
self.assertEqual(self.water[2][0], 'H')
self.assertTrue(all(self.water[2][1] == np.array([0, -1, 1])))
new_water = Molecule([['H', [0, 0, 0]], ['O', [0, 0, 1]],
['H', [0, -1, 1]]])
self.assertEqual(self.water, new_water)
def test_str(self):
"""Testing __str__"""
water_string = """\
H 0.00000000 0.00000000 0.00000000
O 0.00000000 0.00000000 1.00000000
H 0.00000000 1.00000000 1.00000000"""
self.assertEqual(str(self.water), water_string)
def test_check_atom(self):
"""Test check_atom throws errors correctly"""
atom, xyz = ['H', [0, 1, 2]]
self.assertTrue(Molecule.check_atom(atom, xyz))
self.assertRaises(SyntaxError, Molecule.check_atom, [[]], 'a')
self.assertRaises(TypeError, Molecule.check_atom, [[1, 2, 3]])
self.assertRaises(SyntaxError, Molecule.check_atom, [[0, 1, 2, 3]],
'a')
self.assertRaises(SyntaxError, Molecule.check_atom, ['H', [1]],
['a', [3]])
def test_check_geom(self):
"""Test check_geom throws errors correctly"""
self.assertTrue(Molecule.check_geom(self.water_geom))
# Zero-length geometries are valid
self.assertTrue(Molecule.check_geom([]))
self.assertRaises(ValueError, Molecule.check_geom, [[[1, 2, 3]]])
self.assertRaises(TypeError, Molecule.check_geom, ['H'],
[[[0, 1, 2, 3]]])
self.assertRaises(SyntaxError, Molecule.check_geom,
[['H', [1, 'a', 3]]])
def test_read_write_geometry(self):
"""Testing read and write"""
test_file = 'geom.xyz.tmp'
self.water.write(test_file, True)
mol = Molecule.read_from(test_file)
mol.name = 'H2O'
self.assertEqual(mol.geom, self.water.geom)
mol.write(test_file, style='latex')
latex_geom = '''\
\\begin{verbatim}
H 0.000000 0.000000 0.000000
O 0.000000 0.000000 1.000000
H 0.000000 1.000000 1.000000
\\end{verbatim}'''
with open(test_file) as f:
out_tex = f.read()
self.assertEqual(latex_geom, out_tex)
os.remove(test_file)
class TestMolecule(unittest.TestCase):
"""Tests the Molecule class"""
def setUp(self):
"""Set up for every test"""
self.water_geom = [['H', [0, 0, 0]],
['O', [0, 0, 1]],
['H', [0, 1, 1]]]
self.water = Molecule(self.water_geom)
def test_len(self):
"""Testing __len__"""
self.assertEqual(len(self.water), 3)
def test_getsetdeleqinsert(self):
"""Test getting, setting and deleting atoms"""
self.assertEqual(self.water[0][0], 'H')
assert_almost_equal(self.water[0][1], np.array([0, 0, 0]))
del self.water[1]
self.assertEqual(self.water[1][0], 'H')
assert_almost_equal(self.water[1][1], np.array([0, 1, 1]))
self.water[0] = ['H', [0, 0, 0]]
self.water[1] = ['H', [0, -1, 1]]
self.assertEqual(self.water[1][0], 'H')
assert_almost_equal(self.water[1][1], np.array([0, -1, 1]))
self.water.insert(1, 'O', [0, 0, 1])
self.assertEqual(self.water[1][0], 'O')
assert_almost_equal(self.water[1][1], np.array([0, 0, 1]))
self.assertEqual(self.water[2][0], 'H')
assert_almost_equal(self.water[2][1], np.array([0, -1, 1]))
new_water = Molecule([['H', [0, 0, 0]], ['O', [0, 0, 1]], ['H', [0, -1, 1]]])
self.assertEqual(self.water, new_water)
def test_str(self):
"""Testing __str__"""
water_string = """\
H 0.00000000 0.00000000 0.00000000
O 0.00000000 0.00000000 1.00000000
H 0.00000000 1.00000000 1.00000000"""
self.assertEqual(str(self.water), water_string)
def test_check_atom(self):
"""Test check_atom throws errors correctly"""
atom, xyz = ['H', [0, 1, 2]]
self.assertTrue(Molecule.check_atom(atom, xyz))
self.assertRaises(SyntaxError, Molecule.check_atom, [[]], 'a')
self.assertRaises(TypeError, Molecule.check_atom, [[1, 2, 3]])
self.assertRaises(SyntaxError, Molecule.check_atom, [[0, 1, 2, 3]], 'a')
self.assertRaises(SyntaxError, Molecule.check_atom, ['H', [1]], ['a', [3]])
def test_check_geom(self):
"""Test check_geom throws errors correctly"""
self.assertTrue(Molecule.check_geom(self.water_geom))
# Zero-length geometries are valid
self.assertTrue(Molecule.check_geom([]))
self.assertRaises(ValueError, Molecule.check_geom, [[[1, 2, 3]]])
self.assertRaises(TypeError, Molecule.check_geom, ['H'], [[[0, 1, 2, 3]]])
def test_read_write_geometry(self):
"""Testing read and write"""
geom_file = 'geom.xyz.tmp'
self.water.write(geom_file, True)
mol = Molecule.read_from(geom_file)
mol.name = 'H2O'
self.assertEqual(mol.geom, self.water.geom)
mol.write(geom_file, style='latex')
latex_geom = '''\
\\begin{verbatim}
H 0.000000 0.000000 0.000000
O 0.000000 0.000000 1.000000
H 0.000000 1.000000 1.000000
\\end{verbatim}'''
with open(geom_file) as f:
out_tex = f.read()
self.assertEqual(latex_geom, out_tex)
os.remove(geom_file)
def test_com(self):
""" Test the center of mass """
water_com = np.array([0, 0.05595744, 0.94404256])
assert_almost_equal(self.water.center_of_mass(), water_com)
# Translations should shift the center of mass the same amount
translation = [7, 8, 9]
self.water.xyz += translation
assert_almost_equal(self.water.center_of_mass(), water_com + translation)
def test_moi_tensor(self):
""" Test the moment of inertia tensor """
water_moi_tensor = np.array([
[ 1.9028595, 0 , 0 ],
[ 0 , 0.9514297, -0.0563953],
[ 0 , -0.0563953, 0.9514297]
])
assert_almost_equal(self.water.moment_of_inertia_tensor(), water_moi_tensor)
# Translations should not change moi tensor
self.water.xyz += [7, 8, 9]
assert_almost_equal(self.water.moment_of_inertia_tensor(), water_moi_tensor)
class TestMolecule(unittest.TestCase):
"""Tests the Molecule class"""
def setUp(self):
"""Set up for every test"""
self.water_geom = [['H', [0, 0, 0]],
['O', [0, 0, 1]],
['H', [0, 1, 1]]]
self.water = Molecule(self.water_geom)
def test_len(self):
"""Testing __len__"""
self.assertEqual(len(self.water), 3)
def test_getsetdeleqinsert(self):
"""Test getting, setting and deleting atoms"""
self.assertEqual(self.water[0][0], 'H')
assert_almost_equal(self.water[0][1], np.array([0, 0, 0]))
del self.water[1]
self.assertEqual(self.water[1][0], 'H')
assert_almost_equal(self.water[1][1], np.array([0, 1, 1]))
self.water[0] = ['H', [0, 0, 0]]
self.water[1] = ['H', [0, -1, 1]]
self.assertEqual(self.water[1][0], 'H')
assert_almost_equal(self.water[1][1], np.array([0, -1, 1]))
self.water.insert(1, 'O', [0, 0, 1])
self.assertEqual(self.water[1][0], 'O')
assert_almost_equal(self.water[1][1], np.array([0, 0, 1]))
self.assertEqual(self.water[2][0], 'H')
assert_almost_equal(self.water[2][1], np.array([0, -1, 1]))
new_water = Molecule([['H', [0, 0, 0]], ['O', [0, 0, 1]], ['H', [0, -1, 1]]])
self.assertEqual(self.water, new_water)
def test_str(self):
"""Testing __str__"""
water_string = """\
H 0.00000000 0.00000000 0.00000000
O 0.00000000 0.00000000 1.00000000
H 0.00000000 1.00000000 1.00000000"""
self.assertEqual(str(self.water), water_string)
def test_check_atom(self):
"""Test check_atom throws errors correctly"""
atom, xyz = ['H', [0, 1, 2]]
self.assertTrue(Molecule.check_atom(atom, xyz))
self.assertRaises(SyntaxError, Molecule.check_atom, [[]], 'a')
self.assertRaises(TypeError, Molecule.check_atom, [[1, 2, 3]])
self.assertRaises(SyntaxError, Molecule.check_atom, [[0, 1, 2, 3]], 'a')
self.assertRaises(SyntaxError, Molecule.check_atom, ['H', [1]], ['a', [3]])
def test_check_geom(self):
"""Test check_geom throws errors correctly"""
self.assertTrue(Molecule.check_geom(self.water_geom))
# Zero-length geometries are valid
self.assertTrue(Molecule.check_geom([]))
self.assertRaises(ValueError, Molecule.check_geom, [[[1, 2, 3]]])
self.assertRaises(TypeError, Molecule.check_geom, ['H'], [[[0, 1, 2, 3]]])
def test_read_write_geometry(self):
"""Testing read and write"""
geom_file = 'geom.xyz.tmp'
self.water.write(geom_file, True)
mol = Molecule.read_from(geom_file)
mol.name = 'H2O'
self.assertEqual(mol.geom, self.water.geom)
mol.write(geom_file, style='latex')
latex_geom = '''\
\\begin{verbatim}
H 0.000000 0.000000 0.000000
O 0.000000 0.000000 1.000000
H 0.000000 1.000000 1.000000
\\end{verbatim}'''
with open(geom_file) as f:
out_tex = f.read()
self.assertEqual(latex_geom, out_tex)
os.remove(geom_file)
def test_com(self):
""" Test the center of mass """
water_com = np.array([0, 0.05595744, 0.94404256])
assert_almost_equal(self.water.center_of_mass(), water_com)
# Translations should shift the center of mass the same amount
translation = [7, 8, 9]
self.water.xyz += translation
assert_almost_equal(self.water.center_of_mass(), water_com + translation)
def test_moi_tensor(self):
""" Test the moment of inertia tensor """
water_moi_tensor = np.array([
[ 1.9028595, 0 , 0 ],
[ 0 , 0.9514297, -0.0563953],
[ 0 , -0.0563953, 0.9514297]
])
assert_almost_equal(self.water.moment_of_inertia_tensor(), water_moi_tensor)
# Translations should not change moi tensor
self.water.xyz += [7, 8, 9]
assert_almost_equal(self.water.moment_of_inertia_tensor(), water_moi_tensor)
def test_reorder(self):
""" Test the reordering of atoms """
w1 = self.water
w2 = w1.reorder([1, 0, 2])
assert w1[0][0] == w2[1][0]
assert all(w1[0][1] == w2[1][1])
assert w1[1][0] == w2[0][0]
assert all(w1[1][1] == w2[0][1])
assert w1[2][0] == w2[2][0]
assert all(w1[2][1] == w2[2][1])
class TestMolecule(unittest.TestCase):
"""Tests the Molecule class"""
def setUp(self):
"""Set up for every test"""
self.water = Molecule([['H', 0, 0, 10],
['O', 0, 0, 11],
['H', 0, -1, 11]])
def test_len(self):
"""Testing __len__"""
self.assertEqual(len(self.water), 3)
def test_getsetdeleqinsert(self):
"""Test getting, setting and deleting atoms"""
self.assertEqual(self.water[0], ['H', 0, 0, 10])
del self.water[1]
self.assertEqual(self.water[1], ['H', 0, -1, 11])
self.water[0] = ['H', 0, 0, 0]
self.water[1] = ['H', 0, 1, 1]
self.assertEqual(self.water[1], ['H', 0, 1, 1])
self.water.insert(1, ['O', 0, 0, 1])
self.assertEqual(self.water[1], ['O', 0, 0, 1])
self.assertEqual(self.water[2], ['H', 0, 1, 1])
self.assertEqual(self.water, Molecule([['H', 0, 0, 0], ['O', 0, 0, 1], ['H', 0, 1, 1]]))
def test_str(self):
"""Testing __str__"""
water_string = """\
H 0.00000000 0.00000000 10.00000000
O 0.00000000 0.00000000 11.00000000
H 0.00000000 -1.00000000 11.00000000"""
self.assertEqual(str(self.water), water_string)
def test_check_atom(self):
"""Test check_atom throws errors correctly"""
atom = ['H', 0, 1, 2]
self.assertTrue(Molecule.check_atom(atom))
self.assertRaises(SyntaxError, Molecule.check_atom, [[]])
self.assertRaises(SyntaxError, Molecule.check_atom, [[1, 2, 3]])
self.assertRaises(SyntaxError, Molecule.check_atom, [[0, 1, 2, 3]])
self.assertRaises(SyntaxError, Molecule.check_atom, [['H', 1, 'a', 3]])
def test_check_geom(self):
"""Test check_geom throws errors correctly"""
water = [['H', 0, 0, 0], ['O', 0, 0, 1], ['H', 0, 1, 1]]
self.assertTrue(Molecule.check_geom(water))
# Zero-length geometries are valid
self.assertTrue(Molecule.check_geom([]))
self.assertRaises(SyntaxError, Molecule.check_geom, [[[1, 2, 3]]])
self.assertRaises(SyntaxError, Molecule.check_geom, [[[0, 1, 2, 3]]])
self.assertRaises(SyntaxError, Molecule.check_geom, [[['H', 1, 'a', 3]]])
def test_read_write_geometry(self):
"""Testing read and write"""
test_file = 'geom.xyz.tmp'
self.water.write(test_file, True)
mol = Molecule()
mol.read(test_file)
mol.name = 'H2O'
self.assertEqual(mol.geom, self.water.geom)
mol.write(test_file, style='latex')
latex_geom = '''\
\\begin{verbatim}
H 0.000000 0.000000 10.000000
O 0.000000 0.000000 11.000000
H 0.000000 -1.000000 11.000000
\\end{verbatim}'''
with open(test_file) as f:
out_tex = f.read()
self.assertEqual(latex_geom, out_tex)
os.remove(test_file)
