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Python geom.detect_symm函数代码示例

原作者: [db:作者] 来自: [db:来源] 收藏 邀请

本文整理汇总了Python中pyscf.symm.geom.detect_symm函数的典型用法代码示例。如果您正苦于以下问题：Python detect_symm函数的具体用法？Python detect_symm怎么用？Python detect_symm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detect_symm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_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2: test_ghost

    def test_ghost(self):
        atoms = [
            ['Fe'  , ( 0.0,   0.0,   0.0)],
            ['O'   , (-1.3,   0.0,   0.0)],
            ['GHOST-O' , ( 1.3,   0.0,   0.0)],
            ['GHOST-O' , ( 0.0,  -1.3,   0.0)],
            ['O'   , ( 0.0,   1.3,   0.0)],]
        l, orig, axes = geom.detect_symm(atoms)
        self.assertEqual(l, 'C2v')
        self.assertAlmostEqual(axes[2,0]*axes[2,1], -.5)

        atoms = [
            ['Fe'  , ( 0.0,   0.0,   0.0)],
            ['O'   , (-1.3,   0.0,   0.0)],
            ['XO'  , ( 1.3,   0.0,   0.0)],
            ['GHOSTO' , ( 0.0,  -1.3,   0.0)],
            ['O'   , ( 0.0,   1.3,   0.0)],]
        l, orig, axes = geom.detect_symm(atoms)
        self.assertEqual(l, 'C2v')
        self.assertAlmostEqual(axes[2,0]*axes[2,1], -.5)

        atoms = [
            ['Fe'  , ( 0.0,   0.0,   0.0)],
            ['O'   , (-1.3,   0.0,   0.0)],
            ['X' , ( 1.3,   0.0,   0.0)],
            ['X' , ( 0.0,  -1.3,   0.0)],
            ['O'   , ( 0.0,   1.3,   0.0)],]
        l, orig, axes = geom.detect_symm(atoms)
        self.assertEqual(l, 'C2v')
        self.assertAlmostEqual(axes[2,0]*axes[2,1], -.5)
开发者ID:chrinide，项目名称:pyscf，代码行数:30，代码来源:test_geom.py


示例3: 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4: test_quasi_c2v

 def test_quasi_c2v(self):
     atoms = [
         ['Fe', ( 0.0000000000,   0.0055197721,   0.0055197721)],
         ['O' , (-1.3265475500,   0.0000000000,  -0.9445024777)],
         ['O' , ( 1.3265475500,   0.0000000000,  -0.9445024777)],
         ['O' , ( 0.0000000000,  -1.3265374484,   0.9444796669)],
         ['O' , ( 0.0000000000,   1.3265374484,   0.9444796669)],]
     l, orig, axes = geom.detect_symm(atoms)
     self.assertEqual(l, 'Cs')
     tolbak, geom.TOLERANCE = geom.TOLERANCE, 1e-2
     l, orig, axes = geom.detect_symm(atoms)
     self.assertEqual(l, 'C2v')
     geom.TOLERANCE = tolbak
开发者ID:pengdl，项目名称:pyscf，代码行数:13，代码来源:test_geom.py


示例5: test_c3v_1

    def test_c3v_1(self):
        mol = gto.M(atom='''
C   0.948065  -0.081406  -0.007893
C   0.462608  -0.144439   1.364854
N   0.077738  -0.194439   2.453356
H   0.591046   0.830035  -0.495369
H   0.591062  -0.944369  -0.576807
H   2.041481  -0.080642  -0.024174''')
        gpname, orig, axes = geom.detect_symm(mol._atom)
        self.assertEqual(gpname, 'C1')

        with lib.temporary_env(geom, TOLERANCE=1e-3):
            gpname, orig, axes = geom.detect_symm(mol._atom)
        self.assertEqual(gpname, 'C3v')
开发者ID:chrinide，项目名称:pyscf，代码行数:14，代码来源:test_geom.py


示例6: 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7: test_quasi_c2v

    def test_quasi_c2v(self):
        atoms = [
            ['Fe', ( 0.0000000000,   0.0055197721,   0.0055197721)],
            ['O' , (-1.3265475500,   0.0000000000,  -0.9445024777)],
            ['O' , ( 1.3265475500,   0.0000000000,  -0.9445024777)],
            ['O' , ( 0.0000000000,  -1.3265374484,   0.9444796669)],
            ['O' , ( 0.0000000000,   1.3265374484,   0.9444796669)],]
        l, orig, axes = geom.detect_symm(atoms)
        self.assertEqual(l, 'Cs')
        with lib.temporary_env(geom, TOLERANCE=1e-2):
            l, orig, axes = geom.detect_symm(atoms)
        self.assertEqual(l, 'C2v')

        with lib.temporary_env(geom, TOLERANCE=1e-1):
            l, orig, axes = geom.detect_symm(atoms)
        self.assertEqual(l, 'Td')
开发者ID:chrinide，项目名称:pyscf，代码行数:16，代码来源:test_geom.py


示例8: test_c2

 def test_c2(self):
     coords1 = numpy.dot(make4(2.5), 1)
     coords2 = make12(1.2)
     axes = geom._make_axes(coords2[1]-coords2[0], coords2[2])
     coords2 = numpy.dot(coords2, axes.T)
     atoms = [['C', c] for c in numpy.vstack((coords1,coords2))]
     gpname, orig, axes = geom.detect_symm(atoms)
     self.assertEqual(gpname, 'C2')
开发者ID:berquist，项目名称:pyscf，代码行数:8，代码来源:test_geom.py


示例9: test_s10

 def test_s10(self):
     numpy.random.seed(19)
     rotz = numpy.eye(3)
     rotz[:2,:2] = numpy.linalg.svd(numpy.random.random((2,2)))[0]
     coords1 = numpy.dot(make60(1.5, 3.0), u)
     coords2 = reduce(numpy.dot, (make20(1.1), rotz, u))
     atoms = [['C', c] for c in coords1] + [['C', c] for c in coords2]
     gpname, orig, axes = geom.detect_symm(atoms)
     self.assertEqual(gpname, 'S10')
开发者ID:berquist，项目名称:pyscf，代码行数:9，代码来源:test_geom.py


示例10: test_cs

    def test_cs(self):
        coords1 = make4(2.5)
        axes = geom._make_axes(coords1[1]-coords1[0], coords1[2])
        coords1 = numpy.dot(coords1, axes.T)
        coords2 = make12(1.2)
        axes = geom._make_axes(coords2[1]-coords2[0], coords2[2])
        coords2 = numpy.dot(coords2, axes.T)
        atoms = [['C', c] for c in numpy.vstack((coords1,coords2))]
        gpname, orig, axes = geom.detect_symm(atoms)
        self.assertEqual(gpname, 'Cs')

        numpy.random.seed(1)
        c0 = numpy.random.random((4,3))
        c0[:,1] *= .5
        c1 = c0.copy()
        c1[:,1] *= -1
        atoms = [['C', c] for c in numpy.vstack((c0,c1))]
        gpname, orig, axes = geom.detect_symm(atoms)
        self.assertEqual(gpname, 'Cs')
开发者ID:chrinide，项目名称:pyscf，代码行数:19，代码来源:test_geom.py


示例11: test_ih4

    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))
开发者ID:berquist，项目名称:pyscf，代码行数:10，代码来源:test_geom.py


示例12: 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13: 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14: test_oh2

    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))
开发者ID:berquist，项目名称:pyscf，代码行数:10，代码来源:test_geom.py


示例15: 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16: 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17: test_ih2

    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))
开发者ID:berquist，项目名称:pyscf，代码行数:11，代码来源:test_geom.py


示例18: 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19: 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20: test_s6

    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')
开发者ID:berquist，项目名称:pyscf，代码行数:12，代码来源:test_geom.py



注：本文中的pyscf.symm.geom.detect_symm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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