Python operations.SymmOp类代码示例

    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

    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)

 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)

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

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

    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)

 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)

    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))

    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!")

 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)

    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)

    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)

 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))

    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))

 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))