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_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_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_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_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)
class TestGamessifier(unittest.TestCase):
"""Tests the Molecule class"""
def setUp(self):
"""Set up for every test"""
self.g = Gamessifier()
self.formaldehyde_xyz = Molecule([['O', [0, 1.394, 0]],
['C', [0, 0, 0]],
['H', [0.994, -0.492, 0]],
['H', [-0.994, -0.492, 0]]])
def test_read_mol(self):
"""Test reading a molecule from a file"""
tmp_geom_file = 'geom.xyz.tmp'
self.formaldehyde_xyz.write(tmp_geom_file)
self.g.read_mol(tmp_geom_file)
self.assertEqual(str(self.g.mol), str(self.formaldehyde_xyz))
os.remove(tmp_geom_file)
def test_read_basis_set(self):
"""Test reading a basis from a file"""
tmp_basis_file = 'basis.gbs.tmp1'
basis_set = BasisSet()
basis_set['B'] = Basis('B',
[BasisFunction('S', [0.2, 0.4], [0.3, 0.7])])
with open(tmp_basis_file, 'w') as f:
f.write(basis_set.print('gamess'))
self.g.read_basis_set(tmp_basis_file)
self.assertEqual(basis_set, self.g.basis_set)
os.remove(tmp_basis_file)
def test_read_ecp(self):
"""Testing reading an ecp file"""
tmp_ecp_file = 'ecp.dat.tmp'
ecp = """\
H-ECP NONE
C-ECP GEN 10 2
3 ----- d-ul potential -----
-10.0000000 1 357.3914469
-60.2990287 2 64.6477389
-10.4217834 2 16.0960833
O-ECP NONE"""
with open(tmp_ecp_file, 'w') as f:
f.write(ecp)
self.g.read_ecp(tmp_ecp_file)
os.remove(tmp_ecp_file)
def test_read_options(self):
"""Testing read options"""
self.g.read_options({})
self.assertEqual({}, self.g.options_dict)
self.assertEqual('', self.g.write_options_str())
options_dir = OrderedDict(
[['CONTRL', OrderedDict([['SCFTYP', 'RHF']])],
['SCF', OrderedDict([['DIRSCF', '.TRUE.']])]])
options_str = ' $CONTRL\n SCFTYP=RHF\n $END\n\n $SCF\n DIRSCF=.TRUE.\n $END\n\n'
self.g.read_options(options_dir)
self.assertEqual(options_str, self.g.write_options_str())
tmp_options_file = 'options.dat.tmp'
with open(tmp_options_file, 'w') as f:
f.write(options_str)
self.g.read_options(tmp_options_file)
def test_read_other_data(self):
"""Testing read_other_data"""
tmp_dat_file = 'dat.tmp'
vec = ' $VEC\n12 23 31\n33241 32523 11.0\n $END'
hess = ' $HESS\n32 43 987\n453 443 11.0\n $END'
data = 'Hey\n' + vec + ' \n random other text\n' + hess + '\n more text\n122\n'
with open(tmp_dat_file, 'w') as f:
f.write(data)
self.g.read_data(tmp_dat_file)
self.assertEqual(vec, self.g.vec)
self.assertEqual(hess, self.g.hess)
os.remove(tmp_dat_file)
def test_update_options(self):
"""Test update_options"""
self.g.vec = ' $VEC\n123132\n $END'
self.g.options_dict = {'GUESS': {'GUESS': 'HUCKEL'}}
self.g.update_options()
self.assertEqual('MOREAD', self.g.options_dict['GUESS']['GUESS'])
self.g.vec = ' '
def test_write_input(self):
"""Test writing an input to a basis file"""
tmp_basis_file = 'basis.gbs.tmp'
basis_set = BasisSet()
basis_set['H'] = Basis('H', [BasisFunction('S', [1], [1])])
basis_set['O'] = Basis(
'O', [BasisFunction('S', [1], [1]),
BasisFunction('S', [2], [1])])
basis_set['C'] = Basis('C', [
BasisFunction('S', [1], [1]),
BasisFunction('SP', [1, 2], [[0.4, 0.6], [0.1, 0.9]])
])
with open(tmp_basis_file, 'w') as f:
f.write(basis_set.print('gamess'))
tmp_geom_file = 'geom.xyz.tmp'
self.formaldehyde_xyz.write(tmp_geom_file)
tmp_ecp_file = 'ecp.dat.tmp'
ecp = """\
C-ECP GEN 10 2
3 ----- d-ul potential -----
-10.0000000 1 357.3914469
-60.2990287 2 64.6477389
-10.4217834 2 16.0960833
O-ECP NONE"""
with open(tmp_ecp_file, 'w') as f:
f.write(ecp)
tmp_options_file = 'options.dat.tmp'
options_str = ' $CONTRL\n SCFTYP=RHF\n $END\n\n $SCF\n DIRSCF=.TRUE.\n $END\n\n'
with open(tmp_options_file, 'w') as f:
f.write(options_str)
tmp_dat_file = 'dat.tmp'
vec = ' $VEC\n12 23 31\n33241 32523 11.0\n $END'
hess = ' $HESS\n32 43 987\n453 443 11.0\n $END'
data = 'Hey\n' + vec + ' \n random other text\n' + hess + '\n more text\n122\n'
with open(tmp_dat_file, 'w') as f:
f.write(data)
self.g.read(tmp_geom_file, tmp_basis_file, tmp_ecp_file,
tmp_options_file, tmp_dat_file)
tmp_input_file = 'input.inp.tmp'
self.g.write_input(tmp_input_file)
os.remove(tmp_geom_file)
os.remove(tmp_basis_file)
os.remove(tmp_ecp_file)
os.remove(tmp_options_file)
os.remove(tmp_input_file)
os.remove(tmp_dat_file)
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)
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)
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])
def setUp(self):
"""Set up for every test"""
self.g = Gamessifier()
self.formaldehyde_xyz = Molecule([['O', 0, 1.394, 0], ['C', 0, 0, 0], ['H', 0.994, -0.492, 0], ['H', -0.994, -0.492, 0]])
class TestGamessifier(unittest.TestCase):
"""Tests the Molecule class"""
def setUp(self):
"""Set up for every test"""
self.g = Gamessifier()
self.formaldehyde_xyz = Molecule([['O', 0, 1.394, 0], ['C', 0, 0, 0], ['H', 0.994, -0.492, 0], ['H', -0.994, -0.492, 0]])
def test_read_mol(self):
"""Test reading a molecule from a file"""
tmp_geom_file = 'geom.xyz.tmp'
self.formaldehyde_xyz.write(tmp_geom_file)
self.g.read_mol(tmp_geom_file)
self.assertEqual(str(self.g.mol), str(self.formaldehyde_xyz))
os.remove(tmp_geom_file)
def test_read_basis_set(self):
"""Test reading a basis from a file"""
tmp_basis_file = 'basis.gbs.tmp1'
basis_set = BasisSet()
basis_set['B'] = Basis('B', [BasisFunction('S', [0.2, 0.4], [0.3, 0.7])])
open(tmp_basis_file, 'w').write(basis_set.print('gamess'))
self.g.read_basis_set(tmp_basis_file)
self.assertEqual(basis_set, self.g.basis_set)
os.remove(tmp_basis_file)
def test_read_ecp(self):
"""Testing reading an ecp file"""
tmp_ecp_file = 'ecp.dat.tmp'
ecp = """\
H-ECP NONE
C-ECP GEN 10 2
3 ----- d-ul potential -----
-10.0000000 1 357.3914469
-60.2990287 2 64.6477389
-10.4217834 2 16.0960833
O-ECP NONE"""
open(tmp_ecp_file, 'w').write(ecp)
self.g.read_ecp(tmp_ecp_file)
os.remove(tmp_ecp_file)
def test_read_options(self):
"""Testing read options"""
self.g.read_options({})
self.assertEqual({}, self.g.options_dict)
self.assertEqual('', self.g.write_options_str())
options_dir = OrderedDict([
['CONTRL', OrderedDict([['SCFTYP', 'RHF']])],
['SCF', OrderedDict([['DIRSCF', '.TRUE.']])]
])
options_str = ' $CONTRL\n SCFTYP=RHF\n $END\n\n $SCF\n DIRSCF=.TRUE.\n $END\n\n'
self.g.read_options(options_dir)
self.assertEqual(options_str, self.g.write_options_str())
tmp_options_file = 'options.dat.tmp'
open(tmp_options_file, 'w').write(options_str)
self.g.read_options(tmp_options_file)
def test_read_other_data(self):
"""Testing read_other_data"""
tmp_dat_file = 'dat.tmp'
vec = ' $VEC\n12 23 31\n33241 32523 11.0\n $END'
hess = ' $HESS\n32 43 987\n453 443 11.0\n $END'
data = 'Hey\n' + vec + ' \n random other text\n' + hess + '\n more text\n122\n'
open(tmp_dat_file, 'w').write(data)
self.g.read_data(tmp_dat_file)
self.assertEqual(vec, self.g.vec)
self.assertEqual(hess, self.g.hess)
os.remove(tmp_dat_file)
def test_update_options(self):
"""Test update_options"""
self.g.vec = ' $VEC\n123132\n $END'
self.g.options_dict = {'GUESS': {'GUESS': 'HUCKEL'}}
self.g.update_options()
self.assertEqual('MOREAD', self.g.options_dict['GUESS']['GUESS'])
self.g.vec = ' '
def test_write_input(self):
"""Test writing an input to a basis file"""
tmp_basis_file = 'basis.gbs.tmp'
basis_set = BasisSet()
basis_set['H'] = Basis('H', [BasisFunction('S', [1], [1])])
basis_set['O'] = Basis('O', [BasisFunction('S', [1], [1]), BasisFunction('S', [2], [1])])
basis_set['C'] = Basis('C', [BasisFunction('S', [1], [1]), BasisFunction('SP', [1, 2], [0.4, 0.6], [0.1, 0.9])])
open(tmp_basis_file, 'w').write(basis_set.print('gamess'))
tmp_geom_file = 'geom.xyz.tmp'
self.formaldehyde_xyz.write(tmp_geom_file)
tmp_ecp_file = 'ecp.dat.tmp'
ecp = """\
C-ECP GEN 10 2
3 ----- d-ul potential -----
-10.0000000 1 357.3914469
-60.2990287 2 64.6477389
-10.4217834 2 16.0960833
O-ECP NONE"""
open(tmp_ecp_file, 'w').write(ecp)
tmp_options_file = 'options.dat.tmp'
options_str = ' $CONTRL\n SCFTYP=RHF\n $END\n\n $SCF\n DIRSCF=.TRUE.\n $END\n\n'
open(tmp_options_file, 'w').write(options_str)
tmp_dat_file = 'dat.tmp'
vec = ' $VEC\n12 23 31\n33241 32523 11.0\n $END'
hess = ' $HESS\n32 43 987\n453 443 11.0\n $END'
data = 'Hey\n' + vec + ' \n random other text\n' + hess + '\n more text\n122\n'
open(tmp_dat_file, 'w').write(data)
self.g.read(tmp_geom_file, tmp_basis_file, tmp_ecp_file, tmp_options_file, tmp_dat_file)
tmp_input_file = 'input.inp.tmp'
self.g.write_input(tmp_input_file)
os.remove(tmp_geom_file)
os.remove(tmp_basis_file)
os.remove(tmp_ecp_file)
os.remove(tmp_options_file)
os.remove(tmp_input_file)
os.remove(tmp_dat_file)
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)
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 = 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)
def setUp(self):
"""Set up for every test"""
self.water = Molecule([['H', 0, 0, 10],
['O', 0, 0, 11],
['H', 0, -1, 11]])
