def test_linear(self):
coords = [[0.000000, 0.000000, 0.000000], [0.000000, 0.000000, 1.08],
[0, 0.000000, -1.08]]
mol = Molecule(["C", "H", "H"], coords)
a = PointGroupAnalyzer(mol)
self.assertEqual(a.sch_symbol, "D*h")
mol = Molecule(["C", "H", "N"], coords)
a = PointGroupAnalyzer(mol)
self.assertEqual(a.sch_symbol, "C*v")
def test_spherical(self):
a = PointGroupAnalyzer(CH4)
self.assertEqual(a.sch_symbol, "Td")
self.assertEqual(len(a.get_pointgroup()), 24)
a = PointGroupAnalyzer(PF6)
self.assertEqual(a.sch_symbol, "Oh")
self.assertEqual(len(a.get_pointgroup()), 48)
xyz = XYZ.from_file(os.path.join(test_dir, "c60.xyz"))
a = PointGroupAnalyzer(xyz.molecule)
self.assertEqual(a.sch_symbol, "Ih")
def test_dihedral(self):
a = PointGroupAnalyzer(C2H4)
self.assertEqual(a.sch_symbol, "D2h")
self.assertEqual(len(a.get_pointgroup()), 8)
a = PointGroupAnalyzer(BF3)
self.assertEqual(a.sch_symbol, "D3h")
self.assertEqual(len(a.get_pointgroup()), 12)
xyz = XYZ.from_file(os.path.join(test_dir, "b12h12.xyz"))
a = PointGroupAnalyzer(xyz.molecule)
self.assertEqual(a.sch_symbol, "D5d")
def test_cyclic(self):
a = PointGroupAnalyzer(H2O2)
self.assertEqual(a.sch_symbol, "C2")
self.assertEqual(len(a.get_pointgroup()), 2)
a = PointGroupAnalyzer(H2O)
self.assertEqual(a.sch_symbol, "C2v")
self.assertEqual(len(a.get_pointgroup()), 4)
a = PointGroupAnalyzer(NH3)
self.assertEqual(a.sch_symbol, "C3v")
self.assertEqual(len(a.get_pointgroup()), 6)
def test_spherical(self):
a = PointGroupAnalyzer(CH4)
self.assertEqual(a.sch_symbol, "Td")
self.assertEqual(len(a.get_pointgroup()), 24)
a = PointGroupAnalyzer(PF6)
self.assertEqual(a.sch_symbol, "Oh")
self.assertEqual(len(a.get_pointgroup()), 48)
xyz = XYZ.from_file(os.path.join(test_dir, "c60.xyz"))
a = PointGroupAnalyzer(xyz.molecule)
self.assertEqual(a.sch_symbol, "Ih")
def test_dihedral(self):
a = PointGroupAnalyzer(C2H4)
self.assertEqual(a.sch_symbol, "D2h")
self.assertEqual(len(a.get_pointgroup()), 8)
a = PointGroupAnalyzer(BF3)
self.assertEqual(a.sch_symbol, "D3h")
self.assertEqual(len(a.get_pointgroup()), 12)
xyz = XYZ.from_file(os.path.join(test_dir, "b12h12.xyz"))
a = PointGroupAnalyzer(xyz.molecule)
self.assertEqual(a.sch_symbol, "D5d")
def test_asym_top(self):
coords = [
[0.000000, 0.000000, 0.000000],
[0.000000, 0.000000, 1.08],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000],
]
mol = Molecule(["C", "H", "F", "Br", "Cl"], coords)
a = PointGroupAnalyzer(mol)
self.assertEqual(a.sch_symbol, "C1")
self.assertEqual(len(a.get_pointgroup()), 1)
coords = [
[0.000000, 0.000000, 1.08],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000],
]
cs_mol = Molecule(["H", "F", "Cl", "Cl"], coords)
a = PointGroupAnalyzer(cs_mol)
self.assertEqual(a.sch_symbol, "Cs")
self.assertEqual(len(a.get_pointgroup()), 2)
a = PointGroupAnalyzer(C2H2F2Br2)
self.assertEqual(a.sch_symbol, "Ci")
self.assertEqual(len(a.get_pointgroup()), 2)
def test_asym_top(self):
coords = [[0.000000, 0.000000, 0.000000], [0.000000, 0.000000, 1.08],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
mol = Molecule(["C", "H", "F", "Br", "Cl"], coords)
a = PointGroupAnalyzer(mol)
self.assertEqual(a.sch_symbol, "C1")
self.assertEqual(len(a.get_pointgroup()), 1)
coords = [[0.000000, 0.000000, 1.08], [1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
cs_mol = Molecule(["H", "F", "Cl", "Cl"], coords)
a = PointGroupAnalyzer(cs_mol)
self.assertEqual(a.sch_symbol, "Cs")
self.assertEqual(len(a.get_pointgroup()), 2)
a = PointGroupAnalyzer(C2H2F2Br2)
self.assertEqual(a.sch_symbol, "Ci")
self.assertEqual(len(a.get_pointgroup()), 2)
def test_cyclic(self):
a = PointGroupAnalyzer(H2O2)
self.assertEqual(a.sch_symbol, "C2")
self.assertEqual(len(a.get_pointgroup()), 2)
a = PointGroupAnalyzer(H2O)
self.assertEqual(a.sch_symbol, "C2v")
self.assertEqual(len(a.get_pointgroup()), 4)
a = PointGroupAnalyzer(NH3)
self.assertEqual(a.sch_symbol, "C3v")
self.assertEqual(len(a.get_pointgroup()), 6)
cs2 = read_mol(os.path.join(test_dir, "Carbon_Disulfide.xyz"))
a = PointGroupAnalyzer(cs2, eigen_tolerance=0.001)
self.assertEqual(a.sch_symbol, "C2v")
def test_cyclic(self):
a = PointGroupAnalyzer(H2O2)
self.assertEqual(a.sch_symbol, "C2")
self.assertEqual(len(a.get_pointgroup()), 2)
a = PointGroupAnalyzer(H2O)
self.assertEqual(a.sch_symbol, "C2v")
self.assertEqual(len(a.get_pointgroup()), 4)
a = PointGroupAnalyzer(NH3)
self.assertEqual(a.sch_symbol, "C3v")
self.assertEqual(len(a.get_pointgroup()), 6)
def test_cyclic(self):
a = PointGroupAnalyzer(H2O2)
self.assertEqual(a.sch_symbol, "C2")
self.assertEqual(len(a.get_pointgroup()), 2)
a = PointGroupAnalyzer(H2O)
self.assertEqual(a.sch_symbol, "C2v")
self.assertEqual(len(a.get_pointgroup()), 4)
a = PointGroupAnalyzer(NH3)
self.assertEqual(a.sch_symbol, "C3v")
self.assertEqual(len(a.get_pointgroup()), 6)
cs2 = read_mol(os.path.join(test_dir, "Carbon_Disulfide.xyz"))
a = PointGroupAnalyzer(cs2, eigen_tolerance=0.001)
self.assertEqual(a.sch_symbol, "C2v")
