def test_d5h(self):
atoms = ringhat(5, u)
atoms = atoms[5:]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'D5h')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'C2v')
self.assertTrue(geom.check_given_symm('C2v', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0], [1, 4], [2, 3], [5, 6]])
atoms = ringhat(5, u)
atoms = atoms[5:]
atoms[1][0] = 'C1'
gpname, orig, axes = geom.detect_symm(atoms, {'C':'ccpvdz','C1':'sto3g','N':'631g'})
self.assertEqual(gpname, 'C2v')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'C2v')
self.assertTrue(geom.check_given_symm('C2v', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0,2],[1],[3,4],[5,6]])
def test_t(self):
atoms = [['C', ( 1.0 ,-1.0 , 1.0 )],
['O', ( 1.0-.1,-1.0+.2, 1.0 )],
['O', ( 1.0 ,-1.0+.1, 1.0-.2)],
['O', ( 1.0-.2,-1.0 , 1.0-.1)],
['C', (-1.0 , 1.0 , 1.0 )],
['O', (-1.0+.1, 1.0-.2, 1.0 )],
['O', (-1.0 , 1.0-.1, 1.0-.2)],
['O', (-1.0+.2, 1.0 , 1.0-.1)],
['C', ( 1.0 , 1.0 ,-1.0 )],
['O', ( 1.0-.2, 1.0 ,-1.0+.1)],
['O', ( 1.0 , 1.0-.1,-1.0+.2)],
['O', ( 1.0-.1, 1.0-.2,-1.0 )],
['C', (-1.0 ,-1.0 ,-1.0 )],
['O', (-1.0 ,-1.0+.1,-1.0+.2)],
['O', (-1.0+.2,-1.0 ,-1.0+.1)],
['O', (-1.0+.1,-1.0+.2,-1.0 )]]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'T')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'D2')
self.assertTrue(geom.check_given_symm('D2', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 4, 8, 12], [1, 5, 11, 15],
[2, 6, 10, 13], [3, 7, 9, 14]])
def test_oh2(self):
coords1 = numpy.dot(make8(1.5), u)
atoms = [['C', c] for c in coords1]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'Oh')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'D2h')
self.assertTrue(geom.check_given_symm('D2h', atoms))
def test_ih4(self):
coords1 = make12(1.5)
atoms = [['C', c] for c in coords1]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'Ih')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'Ci')
self.assertTrue(geom.check_given_symm('Ci', atoms))
def test_d6h(self):
atoms = ringhat(6, u)
atoms = atoms[6:]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'D6h')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0,3],[1,2,4,5],[6,7]])
self.assertTrue(geom.check_given_symm('D2h', atoms))
def test_td1(self):
coords1 = numpy.dot(make4(1.5), u)
atoms = [['C', c] for c in coords1]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'Td')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'D2')
self.assertTrue(geom.check_given_symm('D2', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 1, 2, 3]])
def test_ih2(self):
coords1 = numpy.dot(make60(1.5, 3), u)
coords2 = numpy.dot(make12(1.1), u)
atoms = [['C', c] for c in coords1] + [['C', c] for c in coords2]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'Ih')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'Ci')
self.assertTrue(geom.check_given_symm('Ci', atoms))
def test_c5v(self):
atoms = ringhat(5, u)[5:-1]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'C5v')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'Cs')
self.assertTrue(geom.check_given_symm('Cs', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 1], [2, 4], [3], [5]])
def test_c5h(self):
atoms = ringhat(5, u)
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'C5h')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'Cs')
self.assertTrue(geom.check_given_symm('Cs', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0], [1], [2], [3], [4], [5], [6], [7], [8], [9], [10,11]])
def test_s6(self):
rotz = random_rotz()
atoms = ringhat(3, 1)[3:6] + ringhat(3, rotz)[:3]
rotz[2,2] = -1
rotz[:2,:2] = numpy.array(((.5, numpy.sqrt(3)/2),(-numpy.sqrt(3)/2, .5)))
r = numpy.dot([x[1] for x in atoms], rotz) - numpy.array((0,0,3.5))
atoms += list(zip([x[0] for x in atoms], r))
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'S6')
gpname, axes = geom.subgroup(gpname, axes)
self.assertEqual(gpname, 'C3')
def test_td2(self):
coords1 = make4(1.5)
coords2 = make4(1.9)
atoms = [['C', c] for c in coords1] + [['C', c] for c in coords2]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'Td')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'C2v')
self.assertTrue(geom.check_given_symm('C2v', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 1], [2, 3], [4, 5], [6, 7]])
def test_c2v(self):
atoms = ringhat(6, u)
atoms = atoms[6:]
atoms[1][0] = 'C1'
atoms[2][0] = 'C1'
basis = {'C': 'sto3g', 'N':'sto3g', 'C1':'ccpvdz'}
gpname, orig, axes = geom.detect_symm(atoms, basis)
self.assertEqual(gpname, 'C2v')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 3], [1, 2], [4, 5], [6, 7]])
self.assertTrue(geom.check_given_symm('C2', atoms, basis))
def test_c3v(self):
coords1 = numpy.dot(make4(1.5), u)
coords2 = numpy.dot(make4(1.9), u)
atoms = [['C', c] for c in coords1] + [['C', c] for c in coords2]
atoms[2][0] = 'C1'
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'C3v')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'Cs')
self.assertTrue(geom.check_given_symm('Cs', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 3], [1], [2], [4, 7], [5], [6]])
def test_s6(self):
numpy.random.seed(19)
rotz = numpy.eye(3)
rotz[:2,:2] = numpy.linalg.svd(numpy.random.random((2,2)))[0]
atoms = ringhat(3, 1)[3:6] + ringhat(3, numpy.dot(rotz, 1))[:3]
rotz[2,2] = -1
rotz[:2,:2] = numpy.array(((.5, numpy.sqrt(3)/2),(-numpy.sqrt(3)/2, .5)))
r = numpy.dot([x[1] for x in atoms], rotz) - numpy.array((0,0,3.5))
atoms += list(zip([x[0] for x in atoms], r))
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'S6')
gpname, axes = geom.subgroup(gpname, axes)
self.assertEqual(gpname, 'C3')
def test_d5d(self):
coord1 = ring(5)
coord2 = ring(5, numpy.pi/5)
coord1[:,2] = 1
coord2[:,2] =-1
atoms = [['H', c] for c in numpy.vstack((coord1,coord2))]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'D5d')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'C2h')
self.assertTrue(geom.check_given_symm('C2h', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 3, 5, 7], [1, 2, 8, 9], [4, 6]])
def test_Coov(self):
atoms = [['H', (0,0,0)], ['H', (0,0,-1)], ['H1', (0,0,1)]]
basis = {'H':'sto3g', 'H1':'6-31g'}
gpname, orig, axes = geom.detect_symm(atoms, basis)
self.assertEqual(gpname, 'Coov')
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0], [1] ,[2]])
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'Coov')
self.assertTrue(geom.check_given_symm('Coov', atoms, basis))
self.assertTrue(geom.check_given_symm('C2v', atoms, basis))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0], [1], [2]])
def test_s4(self):
atoms = [['C', ( 0.5, 0 , 1)],
['O', ( 0.4, 0.2 , 1)],
['C', ( -0.5, 0 , 1)],
['O', ( -0.4, -0.2 , 1)],
['C', ( 0 , 0.5 , -1)],
['O', ( -0.2, 0.4 , -1)],
['C', ( 0 , -0.5 , -1)],
['O', ( 0.2, -0.4 , -1)]]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'S4')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 2], [1, 3], [4, 6], [5, 7]])
self.assertTrue(geom.check_given_symm('C2', atoms))
def test_ih1(self):
coords = make60(1.5, 1)
atoms = [['C', c] for c in coords]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'Ih')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'Cs')
self.assertTrue(geom.check_given_symm('Cs', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0], [1, 4], [2, 3], [5], [6, 9], [7, 8], [10, 25],
[11, 29], [12, 28], [13, 27], [14, 26], [15, 20],
[16, 24], [17, 23], [18, 22], [19, 21], [30],
[31, 34], [32, 33], [35, 50], [36, 54], [37, 53],
[38, 52], [39, 51], [40, 45], [41, 49], [42, 48],
[43, 47], [44, 46], [55], [56, 59], [57, 58]])
def test_ih1(self):
coords = numpy.dot(make60(1.5, 1), u)
atoms = [['C', c] for c in coords]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'Ih')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'Ci')
self.assertTrue(geom.check_given_symm('Ci', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 55], [1, 56], [2, 57], [3, 58], [4, 59],
[5, 30], [6, 31], [7, 32], [8, 33], [9, 34],
[10, 35], [11, 36], [12, 37], [13, 38], [14, 39],
[15, 40], [16, 41], [17, 42], [18, 43], [19, 44],
[20, 45], [21, 46], [22, 47], [23, 48], [24, 49],
[25, 50], [26, 51], [27, 52], [28, 53], [29, 54]])
def test_th(self):
atoms = [['C', ( 1.0 ,-1.0 , 1.0 )],
['O', ( 1.0-.1,-1.0+.2, 1.0 )],
['O', ( 1.0 ,-1.0+.1, 1.0-.2)],
['O', ( 1.0-.2,-1.0 , 1.0-.1)],
['C', ( 1.0 , 1.0 , 1.0 )],
['O', ( 1.0-.1, 1.0-.2, 1.0 )],
['O', ( 1.0 , 1.0-.1, 1.0-.2)],
['O', ( 1.0-.2, 1.0 , 1.0-.1)],
['C', (-1.0 , 1.0 , 1.0 )],
['O', (-1.0+.1, 1.0-.2, 1.0 )],
['O', (-1.0 , 1.0-.1, 1.0-.2)],
['O', (-1.0+.2, 1.0 , 1.0-.1)],
['C', (-1.0 ,-1.0 , 1.0 )],
['O', (-1.0+.1,-1.0+.2, 1.0 )],
['O', (-1.0 ,-1.0+.1, 1.0-.2)],
['O', (-1.0+.2,-1.0 , 1.0-.1)],
['C', ( 1.0 ,-1.0 ,-1.0 )],
['O', ( 1.0-.2,-1.0 ,-1.0+.1)],
['O', ( 1.0 ,-1.0+.1,-1.0+.2)],
['O', ( 1.0-.1,-1.0+.2,-1.0 )],
['C', ( 1.0 , 1.0 ,-1.0 )],
['O', ( 1.0-.2, 1.0 ,-1.0+.1)],
['O', ( 1.0 , 1.0-.1,-1.0+.2)],
['O', ( 1.0-.1, 1.0-.2,-1.0 )],
['C', (-1.0 , 1.0 ,-1.0 )],
['O', (-1.0+.2, 1.0 ,-1.0+.1)],
['O', (-1.0 , 1.0-.1,-1.0+.2)],
['O', (-1.0+.1, 1.0-.2,-1.0 )],
['C', (-1.0 ,-1.0 ,-1.0 )],
['O', (-1.0 ,-1.0+.1,-1.0+.2)],
['O', (-1.0+.2,-1.0 ,-1.0+.1)],
['O', (-1.0+.1,-1.0+.2,-1.0 )]]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'Th')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'D2')
self.assertTrue(geom.check_given_symm('D2', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 8, 20, 28], [1, 9, 23, 31],
[2, 10, 22, 29], [3, 11, 21, 30],
[4, 12, 16, 24], [5, 13, 19, 27],
[6, 14, 18, 26], [7, 15, 17, 25]])
def test_t(self):
atoms = [['C', (1.0, -1.0, 1.0)], ['O', (1.0 - .1, -1.0 + .2, 1.0)],
['O', (1.0, -1.0 + .1, 1.0 - .2)],
['O', (1.0 - .2, -1.0, 1.0 - .1)], ['C', (-1.0, 1.0, 1.0)],
['O', (-1.0 + .1, 1.0 - .2, 1.0)],
['O', (-1.0, 1.0 - .1, 1.0 - .2)],
['O', (-1.0 + .2, 1.0, 1.0 - .1)], ['C', (1.0, 1.0, -1.0)],
['O', (1.0 - .2, 1.0, -1.0 + .1)],
['O', (1.0, 1.0 - .1, -1.0 + .2)],
['O', (1.0 - .1, 1.0 - .2, -1.0)], ['C', (-1.0, -1.0, -1.0)],
['O', (-1.0, -1.0 + .1, -1.0 + .2)],
['O', (-1.0 + .2, -1.0, -1.0 + .1)],
['O', (-1.0 + .1, -1.0 + .2, -1.0)]]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'T')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'D2')
self.assertTrue(geom.check_given_symm('D2', atoms))
self.assertEqual(
geom.symm_identical_atoms(gpname, atoms),
[[0, 4, 8, 12], [1, 5, 11, 15], [2, 6, 10, 13], [3, 7, 9, 14]])
def test_th(self):
atoms = [['C', (1.0, -1.0, 1.0)], ['O', (1.0 - .1, -1.0 + .2, 1.0)],
['O', (1.0, -1.0 + .1, 1.0 - .2)],
['O', (1.0 - .2, -1.0, 1.0 - .1)], ['C', (1.0, 1.0, 1.0)],
['O', (1.0 - .1, 1.0 - .2, 1.0)],
['O', (1.0, 1.0 - .1, 1.0 - .2)],
['O', (1.0 - .2, 1.0, 1.0 - .1)], ['C', (-1.0, 1.0, 1.0)],
['O', (-1.0 + .1, 1.0 - .2, 1.0)],
['O', (-1.0, 1.0 - .1, 1.0 - .2)],
['O', (-1.0 + .2, 1.0, 1.0 - .1)], ['C', (-1.0, -1.0, 1.0)],
['O', (-1.0 + .1, -1.0 + .2, 1.0)],
['O', (-1.0, -1.0 + .1, 1.0 - .2)],
['O', (-1.0 + .2, -1.0, 1.0 - .1)], ['C', (1.0, -1.0, -1.0)],
['O', (1.0 - .2, -1.0, -1.0 + .1)],
['O', (1.0, -1.0 + .1, -1.0 + .2)],
['O', (1.0 - .1, -1.0 + .2, -1.0)], ['C', (1.0, 1.0, -1.0)],
['O', (1.0 - .2, 1.0, -1.0 + .1)],
['O', (1.0, 1.0 - .1, -1.0 + .2)],
['O', (1.0 - .1, 1.0 - .2, -1.0)], ['C', (-1.0, 1.0, -1.0)],
['O', (-1.0 + .2, 1.0, -1.0 + .1)],
['O', (-1.0, 1.0 - .1, -1.0 + .2)],
['O', (-1.0 + .1, 1.0 - .2, -1.0)], ['C', (-1.0, -1.0, -1.0)],
['O', (-1.0, -1.0 + .1, -1.0 + .2)],
['O', (-1.0 + .2, -1.0, -1.0 + .1)],
['O', (-1.0 + .1, -1.0 + .2, -1.0)]]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'Th')
gpname, axes = geom.subgroup(gpname, axes)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(gpname, 'D2')
self.assertTrue(geom.check_given_symm('D2', atoms))
self.assertEqual(geom.symm_identical_atoms(gpname, atoms),
[[0, 8, 20, 28], [1, 9, 23, 31], [2, 10, 22, 29],
[3, 11, 21, 30], [4, 12, 16, 24], [5, 13, 19, 27],
[6, 14, 18, 26], [7, 15, 17, 25]])
def test_c5(self):
atoms = ringhat(5, u)[:-1]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'C5')
gpname, axes = geom.subgroup(gpname, axes)
self.assertEqual(gpname, 'C1')
def test_c5(self):
atoms = ringhat(5, u)[:-1]
gpname, orig, axes = geom.detect_symm(atoms)
self.assertEqual(gpname, 'C5')
gpname, axes = geom.subgroup(gpname, axes)
self.assertEqual(gpname, 'C1')