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Python operations.SymmOp类代码示例

原作者: [db:作者] 来自: [db:来源] 收藏 邀请

本文整理汇总了Python中pymatgen.core.operations.SymmOp的典型用法代码示例。如果您正苦于以下问题:Python SymmOp类的具体用法?Python SymmOp怎么用?Python SymmOp使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。



在下文中一共展示了SymmOp类的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: _find_mirror

    def _find_mirror(self, axis):
        """
        Looks for mirror symmetry of specified type about axis.  Possible
        types are "h" or "vd".  Horizontal (h) mirrors are perpendicular to
        the axis while vertical (v) or diagonal (d) mirrors are parallel.  v
        mirrors has atoms lying on the mirror plane while d mirrors do
        not.
        """
        mirror_type = ""

        # First test whether the axis itself is the normal to a mirror plane.
        if self.is_valid_op(SymmOp.reflection(axis)):
            self.symmops.append(SymmOp.reflection(axis))
            mirror_type = "h"
        else:
            # Iterate through all pairs of atoms to find mirror
            for s1, s2 in itertools.combinations(self.centered_mol, 2):
                if s1.species_and_occu == s2.species_and_occu:
                    normal = s1.coords - s2.coords
                    if np.dot(normal, axis) < self.tol:
                        op = SymmOp.reflection(normal)
                        if self.is_valid_op(op):
                            self.symmops.append(op)
                            if len(self.rot_sym) > 1:
                                mirror_type = "d"
                                for v, r in self.rot_sym:
                                    if not np.linalg.norm(v - axis) < self.tol:
                                        if np.dot(v, normal) < self.tol:
                                            mirror_type = "v"
                                            break
                            else:
                                mirror_type = "v"
                            break

        return mirror_type
开发者ID:Lightslayer,项目名称:pymatgen,代码行数:35,代码来源:analyzer.py


示例2: test_structure_transform

    def test_structure_transform(self):
        # Test trivial case
        trivial = self.fit_r4.structure_transform(self.structure,
                                                  self.structure.copy())
        self.assertArrayAlmostEqual(trivial, self.fit_r4)

        # Test simple rotation
        rot_symm_op = SymmOp.from_axis_angle_and_translation([1, 1, 1], 55.5)
        rot_struct = self.structure.copy()
        rot_struct.apply_operation(rot_symm_op)
        rot_tensor = self.fit_r4.rotate(rot_symm_op.rotation_matrix)
        trans_tensor = self.fit_r4.structure_transform(self.structure, rot_struct)
        self.assertArrayAlmostEqual(rot_tensor, trans_tensor)

        # Test supercell
        bigcell = self.structure.copy()
        bigcell.make_supercell([2, 2, 3])
        trans_tensor = self.fit_r4.structure_transform(self.structure, bigcell)
        self.assertArrayAlmostEqual(self.fit_r4, trans_tensor)

        # Test rotated primitive to conventional for fcc structure
        sn = self.get_structure("Sn")
        sn_prim = SpacegroupAnalyzer(sn).get_primitive_standard_structure()
        sn_prim.apply_operation(rot_symm_op)
        rotated = self.fit_r4.rotate(rot_symm_op.rotation_matrix)
        transformed = self.fit_r4.structure_transform(sn, sn_prim)
        self.assertArrayAlmostEqual(rotated, transformed)
开发者ID:albalu,项目名称:pymatgen,代码行数:27,代码来源:test_tensors.py


示例3: from_spacegroup_number

 def from_spacegroup_number(sgnum):
     datadir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sg_data')
     filename = str(sgnum).zfill(3) + "*"
     files = sorted(glob.glob(os.path.join(datadir, filename)))
     with open(files[0], "r") as fid:
         symmops = []
         rots = []
         lines = fid.readlines()
         sgname = lines[0].strip()
         for i in xrange(1, len(lines)):
             toks = re.split(",", lines[i].strip())
             if len(toks) == 3:
                 rot = np.zeros((3, 3))
                 trans = [0, 0, 0]
                 for j in xrange(3):
                     tok = toks[j]
                     m = re.search("([\+\-]*)([xyz])", tok)
                     if m:
                         factor = -1 if m.group(1) == "-" else 1
                         loc = ord(m.group(2)) - 120
                         rot[j, loc] = factor
                         tok = re.sub("([\+\-]*)([xyz])", "", tok)
                         if tok.strip() != '':
                             trans[j] = eval(tok)
                     rots.append(rot)
                 symmops.append(SymmOp.from_rotation_matrix_and_translation_vector(rot, trans))
         return Spacegroup(sgname, sgnum, symmops)
开发者ID:chenweis,项目名称:pymatgen,代码行数:27,代码来源:spacegroup.py


示例4: align_axis

def align_axis(structure, axis='c', direction=(0, 0, 1)):
    """
    Rotates a structure so that the specified axis is along
    the [001] direction. This is useful for adding vacuum, and
    in general for using vasp compiled with no z-axis relaxation.

    Args:
        structure (Structure): Pymatgen Structure object to rotate.
        axis: Axis to be rotated. Can be 'a', 'b', 'c', or a 1x3 vector.
        direction (vector): Final axis to be rotated to.
    Returns:
        structure. Rotated to align axis along direction.
    """

    if axis == 'a':
        axis = structure.lattice._matrix[0]
    elif axis == 'b':
        axis = structure.lattice._matrix[1]
    elif axis == 'c':
        axis = structure.lattice._matrix[2]
    proj_axis = np.cross(axis, direction)
    if not(proj_axis[0] == 0 and proj_axis[1] == 0):
        theta = (
            np.arccos(np.dot(axis, direction)
            / (np.linalg.norm(axis) * np.linalg.norm(direction)))
        )
        R = get_rotation_matrix(proj_axis, theta)
        rotation = SymmOp.from_rotation_and_translation(rotation_matrix=R)
        structure.apply_operation(rotation)
    if axis == 'c' and direction == (0, 0, 1):
        structure.lattice._matrix[2][2] = abs(structure.lattice._matrix[2][2])

    return structure
开发者ID:henniggroup,项目名称:MPInterfaces,代码行数:33,代码来源:utils.py


示例5: parse_symmetry_operations

def parse_symmetry_operations(symmops_str_list):
    """
    Help method to parse the symmetry operations.

    Args:
        symmops_str_list:
            List of symmops strings of the form
            ['x, y, z', '-x, -y, z', '-y+1/2, x+1/2, z+1/2', ...]

    Returns:
        List of SymmOps
    """
    ops = []
    for op_str in symmops_str_list:
        rot_matrix = np.zeros((3, 3))
        trans = np.zeros(3)
        toks = op_str.strip().split(",")
        for i, tok in enumerate(toks):
            for m in re.finditer("([\+\-]*)\s*([x-z\d]+)/*(\d*)", tok):
                factor = -1 if m.group(1) == "-" else 1
                if m.group(2) in ("x", "y", "z"):
                    j = ord(m.group(2)) - 120
                    rot_matrix[i, j] = factor
                else:
                    num = float(m.group(2))
                    if m.group(3) != "":
                        num /= float(m.group(3))
                    trans[i] = factor * num
        op = SymmOp.from_rotation_and_translation(rot_matrix, trans)
        ops.append(op)
    return ops
开发者ID:jesuansito,项目名称:pymatgen,代码行数:31,代码来源:cifio.py


示例6: test_fit

    def test_fit(self):
        """
        Take two known matched structures
            1) Ensure match
            2) Ensure match after translation and rotations
            3) Ensure no-match after large site translation
            4) Ensure match after site shuffling
            """
        sm = StructureMatcher()

        self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))

        # Test rotational/translational invariance
        op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
                                                    np.array([0.4, 0.7, 0.9]))
        self.struct_list[1].apply_operation(op)
        self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))

        #Test failure under large atomic translation
        self.struct_list[1].translate_sites([0], [.4, .4, .2],
                                            frac_coords=True)
        self.assertFalse(sm.fit(self.struct_list[0], self.struct_list[1]))

        self.struct_list[1].translate_sites([0], [-.4, -.4, -.2],
                                            frac_coords=True)
        # random.shuffle(editor._sites)
        self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
        #Test FrameworkComporator
        sm2 = StructureMatcher(comparator=FrameworkComparator())
        lfp = read_structure(os.path.join(test_dir, "LiFePO4.cif"))
        nfp = read_structure(os.path.join(test_dir, "NaFePO4.cif"))
        self.assertTrue(sm2.fit(lfp, nfp))
        self.assertFalse(sm.fit(lfp, nfp))

        #Test anonymous fit.
        self.assertEqual(sm.fit_anonymous(lfp, nfp),
                         {Composition("Li"): Composition("Na")})
        self.assertAlmostEqual(sm.get_minimax_rms_anonymous(lfp, nfp)[0],
                               0.096084154118549828)

        #Test partial occupancies.
        s1 = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]],
                       [{"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}],
                       [[0, 0, 0], [0.25, 0.25, 0.25],
                        [0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
        s2 = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]],
                       [{"Fe": 0.25}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.75}],
                       [[0, 0, 0], [0.25, 0.25, 0.25],
                        [0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
        self.assertFalse(sm.fit(s1, s2))
        self.assertFalse(sm.fit(s2, s1))
        s2 = Structure([[3, 0, 0], [0, 3, 0], [0, 0, 3]],
                       [{"Fe": 0.25}, {"Fe": 0.25}, {"Fe": 0.25},
                        {"Fe": 0.25}],
                       [[0, 0, 0], [0.25, 0.25, 0.25],
                        [0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
        self.assertEqual(sm.fit_anonymous(s1, s2),
                         {Composition("Fe0.5"): Composition("Fe0.25")})

        self.assertAlmostEqual(sm.get_minimax_rms_anonymous(s1, s2)[0], 0)
开发者ID:leicheng,项目名称:pymatgen,代码行数:60,代码来源:test_structure_matcher.py


示例7: rotate

 def rotate(self, matrix, tol=1e-5):
     matrix = SquareTensor(matrix)
     if not matrix.is_rotation(tol):
         raise ValueError("Rotation matrix is not valid.")
     sop = SymmOp.from_rotation_and_translation(matrix,
                                                [0., 0., 0.])
     return self.transform(sop)
开发者ID:PDoakORNL,项目名称:pymatgen,代码行数:7,代码来源:tensors.py


示例8: test_find_all_mappings

    def test_find_all_mappings(self):
        m = np.array([[0.1, 0.2, 0.3], [-0.1, 0.2, 0.7], [0.6, 0.9, 0.2]])
        latt = Lattice(m)

        op = SymmOp.from_origin_axis_angle([0, 0, 0], [2, -1, 3], 40)
        rot = op.rotation_matrix
        scale = np.array([[0, 2, 0], [1, 1, 0], [0,0,1]])

        latt2 = Lattice(np.dot(rot, np.dot(scale, m).T).T)

        for (aligned_out, rot_out, scale_out) in latt.find_all_mappings(latt2):
            self.assertArrayAlmostEqual(np.inner(latt2.matrix, rot_out),
                                        aligned_out.matrix, 5)
            self.assertArrayAlmostEqual(np.dot(scale_out, latt.matrix),
                                        aligned_out.matrix)
            self.assertArrayAlmostEqual(aligned_out.lengths_and_angles, latt2.lengths_and_angles)
            self.assertFalse(np.allclose(aligned_out.lengths_and_angles,
                                         latt.lengths_and_angles))

        latt = Lattice.orthorhombic(9, 9, 5)
        self.assertEqual(len(list(latt.find_all_mappings(latt))), 16)

        #catch the singular matrix error
        latt = Lattice.from_lengths_and_angles([1,1,1], [10,10,10])
        for l, _, _ in latt.find_all_mappings(latt, ltol=0.05, atol=11):
            self.assertTrue(isinstance(l, Lattice))
开发者ID:zulissi,项目名称:pymatgen,代码行数:26,代码来源:test_lattice.py


示例9: test_init

    def test_init(self):
        fitter = StructureFitter(self.b, self.a)
        self.assertTrue(fitter.mapping_op != None, "No fit found!")

        #Now to try with rotated structure
        op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False, np.array([0, 0, 1]))
        editor = StructureEditor(self.a)
        editor.apply_operation(op)
        fitter = StructureFitter(self.b, editor.modified_structure)

        self.assertTrue(fitter.mapping_op != None, "No fit found!")

        #test with a supercell
        mod = SupercellMaker(self.a, scaling_matrix=[[2, 0, 0], [0, 1, 0], [0, 0, 1]])
        a_super = mod.modified_structure
        fitter = StructureFitter(self.b, a_super)
        self.assertTrue(fitter.mapping_op != None, "No fit found!")

        # Test with a structure with a translated point

        editor = StructureEditor(self.a)
        site = self.a[0]
        editor.delete_site(0)
        trans = np.random.randint(0, 1000, 3)
        editor.insert_site(0, site.species_and_occu, site.frac_coords + trans, False, False)
        fitter = StructureFitter(self.b, editor.modified_structure)
        self.assertTrue(fitter.mapping_op != None, "No fit found for translation {}!".format(trans))

        parser = CifParser(os.path.join(test_dir, "FePO4a.cif"))
        a = parser.get_structures()[0]
        parser = CifParser(os.path.join(test_dir, "FePO4b.cif"))
        b = parser.get_structures()[0]
        fitter = StructureFitter(b, a)
        self.assertTrue(fitter.mapping_op != None, "No fit found!")
开发者ID:chenweis,项目名称:pymatgen,代码行数:34,代码来源:test_structure_fitter.py


示例10: test_apply_operation

 def test_apply_operation(self):
     op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 90)
     self.structure.apply_operation(op)
     self.assertArrayAlmostEqual(
         self.structure.lattice.matrix,
         [[0.000000, 3.840198, 0.000000],
          [-3.325710, 1.920099, 0.000000],
          [2.217138, -0.000000, 3.135509]], 5)
开发者ID:leicheng,项目名称:pymatgen,代码行数:8,代码来源:test_structure.py


示例11: test_fit

    def test_fit(self):
        """
        Take two known matched structures
            1) Ensure match
            2) Ensure match after translation and rotations
            3) Ensure no-match after large site translation
            4) Ensure match after site shuffling
            """
        sm = StructureMatcher()

        self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))

        # Test rotational/translational invariance
        op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
                                                    np.array([0.4, 0.7, 0.9]))
        self.struct_list[1].apply_operation(op)
        self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))

        #Test failure under large atomic translation
        self.struct_list[1].translate_sites([0], [.4, .4, .2],
                                            frac_coords=True)
        self.assertFalse(sm.fit(self.struct_list[0], self.struct_list[1]))

        self.struct_list[1].translate_sites([0], [-.4, -.4, -.2],
                                            frac_coords=True)
        # random.shuffle(editor._sites)
        self.assertTrue(sm.fit(self.struct_list[0], self.struct_list[1]))
        #Test FrameworkComporator
        sm2 = StructureMatcher(comparator=FrameworkComparator())
        lfp = self.get_structure("LiFePO4")
        nfp = self.get_structure("NaFePO4")
        self.assertTrue(sm2.fit(lfp, nfp))
        self.assertFalse(sm.fit(lfp, nfp))

        #Test anonymous fit.
        self.assertEqual(sm.fit_anonymous(lfp, nfp), True)
        self.assertAlmostEqual(sm.get_rms_anonymous(lfp, nfp)[0],
                               0.060895871160262717)

        #Test partial occupancies.
        s1 = Structure(Lattice.cubic(3),
                       [{"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.5}],
                       [[0, 0, 0], [0.25, 0.25, 0.25],
                        [0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
        s2 = Structure(Lattice.cubic(3),
                       [{"Fe": 0.25}, {"Fe": 0.5}, {"Fe": 0.5}, {"Fe": 0.75}],
                       [[0, 0, 0], [0.25, 0.25, 0.25],
                        [0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
        self.assertFalse(sm.fit(s1, s2))
        self.assertFalse(sm.fit(s2, s1))
        s2 = Structure(Lattice.cubic(3),
                       [{"Mn": 0.5}, {"Mn": 0.5}, {"Mn": 0.5},
                        {"Mn": 0.5}],
                       [[0, 0, 0], [0.25, 0.25, 0.25],
                        [0.5, 0.5, 0.5], [0.75, 0.75, 0.75]])
        self.assertEqual(sm.fit_anonymous(s1, s2), True)

        self.assertAlmostEqual(sm.get_rms_anonymous(s1, s2)[0], 0)
开发者ID:eantono,项目名称:pymatgen,代码行数:58,代码来源:test_structure_matcher.py


示例12: __init__

    def __init__(self, axis, angle, angle_in_radians=False):
        """

        """
        self._axis = axis
        self._angle = angle
        self._angle_in_radians = angle_in_radians
        self._symmop = SymmOp.from_axis_angle_and_translation(
            self._axis, self._angle, self._angle_in_radians)
开发者ID:ATNDiaye,项目名称:pymatgen,代码行数:9,代码来源:standard_transformations.py


示例13: test_reflection

 def test_reflection(self):
     normal = np.random.rand(3)
     origin = np.random.rand(3)
     refl = SymmOp.reflection(normal, origin)
     point = np.random.rand(3)
     newcoord = refl.operate(point)
     # Distance to the plane should be negatives of each other.
     self.assertAlmostEqual(np.dot(newcoord - origin, normal),
                            -np.dot(point - origin, normal))
开发者ID:Lightslayer,项目名称:pymatgen,代码行数:9,代码来源:test_operations.py


示例14: test_find_mapping

    def test_find_mapping(self):
        m = np.array([[0.1, 0.2, 0.3], [-0.1, 0.2, 0.7], [0.6, 0.9, 0.2]])
        latt = Lattice(m)

        op = SymmOp.from_origin_axis_angle([0, 0, 0], [2, 3, 3], 35)
        rot = op.rotation_matrix
        scale = np.array([[1, 1, 0], [0, 1, 0], [0, 0, 1]])

        latt2 = Lattice(np.dot(rot, np.dot(scale, m).T).T)
        (aligned_out, rot_out, scale_out) = latt2.find_mapping(latt)
        self.assertAlmostEqual(abs(np.linalg.det(rot)), 1)

        rotated = SymmOp.from_rotation_and_translation(rot_out).operate_multi(latt.matrix)

        self.assertArrayAlmostEqual(rotated, aligned_out.matrix)
        self.assertArrayAlmostEqual(np.dot(scale_out, latt2.matrix), aligned_out.matrix)
        self.assertArrayAlmostEqual(aligned_out.lengths_and_angles, latt.lengths_and_angles)
        self.assertFalse(np.allclose(aligned_out.lengths_and_angles,
                                     latt2.lengths_and_angles))
开发者ID:zulissi,项目名称:pymatgen,代码行数:19,代码来源:test_lattice.py


示例15: _check_R2_axes_asym

 def _check_R2_axes_asym(self):
     """
     Test for 2-fold rotation along the principal axes. Used to handle
     asymetric top molecules.
     """
     for v in self.principal_axes:
         op = SymmOp.from_axis_angle_and_translation(v, 180)
         if self.is_valid_op(op):
             self.symmops.append(op)
             self.rot_sym.append((v, 2))
开发者ID:Lightslayer,项目名称:pymatgen,代码行数:10,代码来源:analyzer.py


示例16: test_list_based_functions

    def test_list_based_functions(self):
        # zeroed
        tc = TensorCollection([1e-4*Tensor(np.eye(3))]*4)
        for t in tc.zeroed():
            self.assertArrayEqual(t, np.zeros((3, 3)))
        for t in tc.zeroed(1e-5):
            self.assertArrayEqual(t, 1e-4*np.eye(3))
        self.list_based_function_check("zeroed", tc)
        self.list_based_function_check("zeroed", tc, tol=1e-5)

        # transform
        symm_op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30,
                                                         False, [0, 0, 1])
        self.list_based_function_check("transform", self.seq_tc, symm_op=symm_op)

        # symmetrized
        self.list_based_function_check("symmetrized", self.seq_tc)

        # rotation
        a = 3.14 * 42.5 / 180
        rotation = SquareTensor([[math.cos(a), 0, math.sin(a)], [0, 1, 0],
                                 [-math.sin(a), 0, math.cos(a)]])
        self.list_based_function_check("rotate", self.diff_rank, matrix=rotation)

        # is_symmetric
        self.assertFalse(self.seq_tc.is_symmetric())
        self.assertTrue(self.diff_rank.is_symmetric())

        # fit_to_structure
        self.list_based_function_check("fit_to_structure", self.diff_rank, self.struct)
        self.list_based_function_check("fit_to_structure", self.seq_tc, self.struct)

        # fit_to_structure
        self.list_based_function_check("fit_to_structure", self.diff_rank, self.struct)
        self.list_based_function_check("fit_to_structure", self.seq_tc, self.struct)

        # voigt
        self.list_based_function_check("voigt", self.diff_rank)

        # is_voigt_symmetric
        self.assertTrue(self.diff_rank.is_voigt_symmetric())
        self.assertFalse(self.seq_tc.is_voigt_symmetric())

        # Convert to ieee
        for entry in self.ieee_data[:2]:
            xtal = entry['xtal']
            tc = TensorCollection([entry['original_tensor']]*3)
            struct = entry['structure']
            self.list_based_function_check("convert_to_ieee", tc, struct)

        # from_voigt
        tc_input = [t for t in np.random.random((3, 6, 6))]
        tc = TensorCollection.from_voigt(tc_input)
        for t_input, t in zip(tc_input, tc):
            self.assertArrayAlmostEqual(Tensor.from_voigt(t_input), t)
开发者ID:albalu,项目名称:pymatgen,代码行数:55,代码来源:test_tensors.py


示例17: fit_with_mapper

    def fit_with_mapper(self, mapper):
        coords = [[0.000000, 0.000000, 0.000000],
                  [0.000000, 0.000000, 1.089000],
                  [1.026719, 0.000000, -0.363000],
                  [-0.513360, -0.889165, -0.363000],
                  [-0.513360, 0.889165, -0.363000]]
        mol1 = Molecule(["C", "H", "H", "H", "H"], coords)
        op = SymmOp.from_origin_axis_angle([0, 0, 0], [0.1, 0.2, 0.3], 60)
        rotcoords = [op.operate(c) for c in coords]
        mol2 = Molecule(["C", "H", "H", "H", "H"], rotcoords)
        mm = MoleculeMatcher(mapper=mapper)
        self.assertTrue(mm.fit(mol1, mol2))

        mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "benzene2.xyz"))
        self.assertTrue(mm.fit(mol1, mol2))

        mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "t2.xyz"))
        self.assertFalse(mm.fit(mol1, mol2))

        mol1 = Molecule.from_file(os.path.join(test_dir, "c1.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "c2.xyz"))
        self.assertTrue(mm.fit(mol1, mol2))

        mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
        self.assertTrue(mm.fit(mol1, mol2))

        mol1 = Molecule.from_file(os.path.join(test_dir, "j1.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "j2.xyz"))
        self.assertTrue(mm.fit(mol1, mol2))

        mol1 = Molecule.from_file(os.path.join(test_dir, "ethene1.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "ethene2.xyz"))
        self.assertTrue(mm.fit(mol1, mol2))

        mol1 = Molecule.from_file(os.path.join(test_dir, "toluene1.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "toluene2.xyz"))
        self.assertTrue(mm.fit(mol1, mol2))

        mol1 = Molecule.from_file(os.path.join(test_dir, "cyclohexane1.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "cyclohexane2.xyz"))
        self.assertTrue(mm.fit(mol1, mol2))

        mol1 = Molecule.from_file(os.path.join(test_dir, "oxygen1.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "oxygen2.xyz"))
        self.assertTrue(mm.fit(mol1, mol2))

        mm = MoleculeMatcher(tolerance=0.001, mapper=mapper)
        mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
        self.assertFalse(mm.fit(mol1, mol2))
开发者ID:AtlasL,项目名称:pymatgen,代码行数:53,代码来源:test_molecule_matcher.py


示例18: __init__

    def __init__(self, int_symbol):
        """
        Initializes a Point Group from its international symbol.

        Args:
            int_symbol (str): International or Hermann-Mauguin Symbol.
        """
        self.symbol = int_symbol
        self.generators = [GENERATOR_MATRICES[c]
                           for c in POINT_GROUP_ENC[int_symbol]]
        self._symmetry_ops = set([SymmOp.from_rotation_and_translation(m)
                                  for m in self._generate_full_symmetry_ops()])
        self.order = len(self._symmetry_ops)
开发者ID:ornl-abinitio,项目名称:pymatgen,代码行数:13,代码来源:groups.py


示例19: __init__

    def __init__(self, int_symbol):
        """
        Initializes a Point Group from its international symbol.

        Args:
            int_symbol (str): International or Hermann-Mauguin Symbol.
        """
        self.symbol = int_symbol
        self.generators = [get_symm_data("generator_matrices")[c]
                           for c in get_symm_data("point_group_encoding")[int_symbol]]
        self._symmetry_ops = set([SymmOp.from_rotation_and_translation(m)
                                  for m in self._generate_full_symmetry_ops()])
        self.order = len(self._symmetry_ops)
开发者ID:albalu,项目名称:pymatgen,代码行数:13,代码来源:groups.py


示例20: test_find_mapping

    def test_find_mapping(self):
        m = np.array([[0.1, 0.2, 0.3], [-0.1, 0.2, 0.7], [0.6, 0.9, 0.2]])
        latt = Lattice(m)

        op = SymmOp.from_origin_axis_angle([0, 0, 0], [2, 3, 3], 35)
        rot = op.rotation_matrix
        scale = np.array([[1, 1, 0], [0, 1, 0], [0, 0, 1]])

        latt2 = Lattice(np.dot(rot, np.dot(scale, m).T).T)
        (latt, rot, scale2) = latt2.find_mapping(latt)
        self.assertAlmostEqual(abs(np.linalg.det(rot)), 1)
        self.assertTrue(np.allclose(scale2, scale) or
                        np.allclose(scale2, -scale))
开发者ID:akashneo,项目名称:pymatgen,代码行数:13,代码来源:test_lattice.py



注:本文中的pymatgen.core.operations.SymmOp类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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