本文整理汇总了Python中pyscf.symm.geom.symm_identical_atoms函数的典型用法代码示例。如果您正苦于以下问题：Python symm_identical_atoms函数的具体用法？Python symm_identical_atoms怎么用？Python symm_identical_atoms使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了symm_identical_atoms函数的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: test_detect_symm_c2h
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))
开发者ID:berquist，项目名称:pyscf，代码行数:25，代码来源:test_geom.py
示例2: test_d5h
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:25，代码来源:test_geom.py
示例3: test_Coov
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:15，代码来源:test_geom.py
示例4: test_t
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:27，代码来源:test_geom.py
示例5: test_detect_symm_d2h_b
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:10，代码来源:test_geom.py
示例6: test_d6h
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))
开发者ID:berquist，项目名称:pyscf，代码行数:10，代码来源:test_geom.py
示例7: test_td1
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:11，代码来源:test_geom.py
示例8: test_c5v
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:11，代码来源:test_geom.py
示例9: test_c5h
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:11，代码来源:test_geom.py
示例10: test_detect_symm_c1
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:11，代码来源:test_geom.py
示例11: test_td2
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]])
开发者ID:diradical，项目名称:pyscf，代码行数:13，代码来源:test_geom.py
示例12: test_c2v
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))
开发者ID:berquist，项目名称:pyscf，代码行数:13，代码来源:test_geom.py
示例13: test_detect_symm_d2_a
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:13，代码来源:test_geom.py
示例14: test_detect_symm_d2_b
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:14，代码来源:test_geom.py
示例15: test_c3v
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:14，代码来源:test_geom.py
示例16: test_detect_symm_cs3
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:15，代码来源:test_geom.py
示例17: test_detect_symm_ci
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:15，代码来源:test_geom.py
示例18: test_detect_symm_s4
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:15，代码来源:test_geom.py
示例19: test_d5d
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]])
开发者ID:berquist，项目名称:pyscf，代码行数:15，代码来源:test_geom.py
示例20: test_s4
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))
开发者ID:berquist，项目名称:pyscf，代码行数:16，代码来源:test_geom.py
注：本文中的pyscf.symm.geom.symm_identical_atoms函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。 |
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