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_detect_symm_c2h(self):
atoms = [['H' , (1., 0., 2.)],
['He', (0., 1., 0.)],
['H' , (1., 0., 0.)],
['H' , (-1.,0., 0.)],
['H' , (-1.,0.,-2.)],
['He', (0.,-1., 0.)]]
l, orig, axes = geom.detect_symm(atoms)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(l, 'C2h')
self.assertEqual(geom.symm_identical_atoms(l,atoms), [[0,4],[1,5],[2,3]])
self.assertTrue(geom.check_given_symm('C2h', atoms))
atoms = [['H' , (1., 0., 1.)],
['H' , (1., 0.,-1.)],
['He', (0., 0., 2.)],
['He', (2., 0.,-2.)],
['Li', (1., 1., 0.)],
['Li', (1.,-1., 0.)]]
l, orig, axes = geom.detect_symm(atoms)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(l, 'C2h')
self.assertEqual(geom.symm_identical_atoms(l,atoms),
[[0, 1], [2, 3], [4, 5]])
self.assertTrue(geom.check_given_symm('C2h', atoms))
def test_detect_symm_c2h(self):
atoms = [['H' , (1., 0., 2.)],
['He', (0., 1., 0.)],
['H' , (1., 0., 0.)],
['H' , (-1.,0., 0.)],
['H' , (-1.,0.,-2.)],
['He', (0.,-1., 0.)]]
l, orig, axes = geom.detect_symm(atoms)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(l, 'C2h')
self.assertEqual(geom.symm_identical_atoms(l,atoms), [[0,4],[1,5],[2,3]])
self.assertTrue(geom.check_given_symm('C2h', atoms))
atoms = [['H' , (1., 0., 1.)],
['H' , (1., 0.,-1.)],
['He', (0., 0., 2.)],
['He', (2., 0.,-2.)],
['Li', (1., 1., 0.)],
['Li', (1.,-1., 0.)]]
l, orig, axes = geom.detect_symm(atoms)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(l, 'C2h')
self.assertEqual(geom.symm_identical_atoms(l,atoms),
[[0, 1], [2, 3], [4, 5]])
self.assertTrue(geom.check_given_symm('C2h', atoms))
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_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_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_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_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_detect_symm_d2h_b(self):
atoms = [['H', (1., 0., 2.)], ['He', (0., 1., 0.)],
['H', (-1., 0., -2.)], ['He', (0., -1., 0.)]]
l, orig, axes = geom.detect_symm(atoms)
self.assertEqual(l, 'D2h')
atoms = geom.shift_atom(atoms, orig, axes)
self.assertTrue(geom.check_given_symm('D2h', atoms))
self.assertEqual(geom.symm_identical_atoms(l, atoms), [[0, 2], [1, 3]])
def test_detect_symm_c1(self):
atoms = [['H', (1., 0., 0.)], ['He', (0., 1., 0.)],
['Li', (0., 0., 1.)], ['Be', (.5, .5, .5)]]
l, orig, axes = geom.detect_symm(atoms)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(l, 'C1')
self.assertTrue(geom.check_given_symm('C1', atoms))
self.assertEqual(geom.symm_identical_atoms(l, atoms),
[[0], [1], [2], [3]])
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_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_detect_symm_d2h_b(self):
atoms = [['H' , (1., 0., 2.)],
['He', (0., 1., 0.)],
['H' , (-1.,0.,-2.)],
['He', (0.,-1., 0.)]]
l, orig, axes = geom.detect_symm(atoms)
self.assertEqual(l, 'D2h')
atoms = geom.shift_atom(atoms, orig, axes)
self.assertTrue(geom.check_given_symm('D2h', atoms))
self.assertEqual(geom.symm_identical_atoms(l,atoms), [[0,2],[1,3]])
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_detect_symm_d2_a(self):
atoms = [['H', (1., 0., 1.)], ['H', (1., 0., -1.)],
['He', (0., 0., 2.)], ['He', (2., 0., 2.)],
['He', (1., 1., -2.)], ['He', (1., -1., -2.)]]
l, orig, axes = geom.detect_symm(atoms)
self.assertEqual(l, 'D2d')
atoms = geom.shift_atom(atoms, orig, axes)
self.assertTrue(geom.check_given_symm('D2', atoms))
self.assertEqual(geom.symm_identical_atoms('D2', atoms),
[[0, 1], [2, 3, 4, 5]])
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_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_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_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_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_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_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_detect_symm_ci(self):
atoms = [['H', (1., 0., 0.)], ['He', (0., 1., 0.)],
['Li', (0., 0., 1.)], ['Be', (.5, .5, .5)],
['H', (-1., 0., 0.)], ['He', (0., -1., 0.)],
['Li', (0., 0., -1.)], ['Be', (-.5, -.5, -.5)]]
l, orig, axes = geom.detect_symm(atoms)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(l, 'Ci')
self.assertTrue(geom.check_given_symm('Ci', atoms))
self.assertEqual(geom.symm_identical_atoms(l, atoms),
[[0, 4], [1, 5], [2, 6], [3, 7]])
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_detect_symm_d2_b(self):
s2 = numpy.sqrt(.5)
atoms = [['C', (0., 0., 1.)], ['C', (0., 0., -1.)], ['H', (1, 0., 2.)],
['H', (-1, 0., 2.)], ['H', (s2, s2, -2.)],
['H', (-s2, -s2, -2.)]]
l, orig, axes = geom.detect_symm(atoms)
self.assertEqual(l, 'D2')
atoms = geom.shift_atom(atoms, orig, axes)
self.assertTrue(geom.check_given_symm('D2', atoms))
self.assertEqual(geom.symm_identical_atoms(l, atoms),
[[0, 1], [2, 3, 4, 5]])
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, 4], [1, 3], [2], [5]])
def test_detect_symm_c1(self):
atoms = [['H' , ( 1., 0., 0.)],
['He', ( 0., 1., 0.)],
['Li', ( 0., 0., 1.)],
['Be', ( .5, .5, .5)]]
l, orig, axes = geom.detect_symm(atoms)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(l, 'C1')
self.assertTrue(geom.check_given_symm('C1', atoms))
self.assertEqual(geom.symm_identical_atoms(l,atoms),
[[0], [1], [2], [3]])
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_detect_symm_cs3(self):
atoms = [['H', (2., 1., 0.)], ['He', (0., 1., 0.)],
['Li', (-1., 2., 0.)], ['Be', (1., 0., 0.)],
['S', (.5, 1., -3)], ['S', (.5, 1., 3)]]
coord = numpy.dot([a[1] for a in atoms], u)
atoms = [[atoms[i][0], c] for i, c in enumerate(coord)]
l, orig, axes = geom.detect_symm(atoms)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(l, 'Cs')
self.assertTrue(geom.check_given_symm('Cs', atoms))
self.assertEqual(geom.symm_identical_atoms(l, atoms),
[[0], [1], [2], [3], [4, 5]])
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_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, 'D2')
self.assertTrue(geom.check_given_symm('D2', 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_detect_symm_d2_a(self):
atoms = [['H' , (1., 0., 1.)],
['H' , (1., 0.,-1.)],
['He', (0., 0., 2.)],
['He', (2., 0., 2.)],
['He', (1., 1.,-2.)],
['He', (1.,-1.,-2.)]]
l, orig, axes = geom.detect_symm(atoms)
self.assertEqual(l, 'D2')
atoms = geom.shift_atom(atoms, orig, axes)
self.assertTrue(geom.check_given_symm('D2', atoms))
self.assertEqual(geom.symm_identical_atoms(l,atoms),
[[0, 1], [2, 3, 4, 5]])
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_detect_symm_d2_b(self):
s2 = numpy.sqrt(.5)
atoms = [['C', (0., 0., 1.)],
['C', (0., 0.,-1.)],
['H', ( 1, 0., 2.)],
['H', (-1, 0., 2.)],
['H', ( s2, s2,-2.)],
['H', (-s2,-s2,-2.)]]
l, orig, axes = geom.detect_symm(atoms)
self.assertEqual(l, 'D2')
atoms = geom.shift_atom(atoms, orig, axes)
self.assertTrue(geom.check_given_symm('D2', atoms))
self.assertEqual(geom.symm_identical_atoms(l,atoms),
[[0, 1], [2, 3, 4, 5]])
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, 1], [2], [3], [4, 5], [6], [7]])
def test_td3(self):
coords1 = make4(1.5)
coords2 = make4(1.9)
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], [1, 3], [2], [4], [5, 7], [6]])
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_detect_symm_s4(self):
atoms = [['H', (-1,-1.,-2.)],
['H', ( 1, 1.,-2.)],
['C', (-.9,-1.,-2.)],
['C', (.9, 1.,-2.)],
['H', ( 1,-1., 2.)],
['H', (-1, 1., 2.)],
['C', ( 1,-.9, 2.)],
['C', (-1, .9, 2.)],]
l, orig, axes = geom.detect_symm(atoms)
self.assertEqual(l, 'S4')
atoms = geom.shift_atom(atoms, orig, axes)
self.assertTrue(geom.check_given_symm('C2', atoms))
self.assertEqual(geom.symm_identical_atoms('C2',atoms),
[[0, 1], [2, 3], [4, 5], [6, 7]])
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_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_detect_symm_s4(self):
atoms = [['H', (-1,-1.,-2.)],
['H', ( 1, 1.,-2.)],
['C', (-.9,-1.,-2.)],
['C', (.9, 1.,-2.)],
['H', ( 1,-1., 2.)],
['H', (-1, 1., 2.)],
['C', ( 1,-.9, 2.)],
['C', (-1, .9, 2.)],]
l, orig, axes = geom.detect_symm(atoms)
self.assertEqual(l, 'S4')
atoms = geom.shift_atom(atoms, orig, axes)
self.assertTrue(geom.check_given_symm('C2', atoms))
self.assertEqual(geom.symm_identical_atoms('C2',atoms),
[[0, 1], [2, 3], [4, 5], [6, 7]])
def test_detect_symm_ci(self):
atoms = [['H' , ( 1., 0., 0.)],
['He', ( 0., 1., 0.)],
['Li', ( 0., 0., 1.)],
['Be', ( .5, .5, .5)],
['H' , (-1., 0., 0.)],
['He', ( 0.,-1., 0.)],
['Li', ( 0., 0.,-1.)],
['Be', (-.5,-.5,-.5)]]
l, orig, axes = geom.detect_symm(atoms)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(l, 'Ci')
self.assertTrue(geom.check_given_symm('Ci', atoms))
self.assertEqual(geom.symm_identical_atoms(l,atoms),
[[0, 4], [1, 5], [2, 6], [3, 7]])
def test_detect_symm_cs3(self):
atoms = [['H' , ( 2.,1., 0.)],
['He', ( 0.,1., 0.)],
['Li', (-1.,2., 0.)],
['Be', ( 1.,0., 0.)],
['S' , ( .5,1., -3)],
['S' , ( .5,1., 3)]]
coord = numpy.dot([a[1] for a in atoms], u)
atoms = [[atoms[i][0], c] for i,c in enumerate(coord)]
l, orig, axes = geom.detect_symm(atoms)
atoms = geom.shift_atom(atoms, orig, axes)
self.assertEqual(l, 'Cs')
self.assertTrue(geom.check_given_symm('Cs', atoms))
self.assertEqual(geom.symm_identical_atoms(l,atoms),
[[0], [1], [2], [3], [4, 5]])
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 = 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_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_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]])