pymatgen.symmetry.settings — pymatgen 2020.7.3 documentation

# Source code for pymatgen.symmetry.settings

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.

    """
    This module provides classes for non-standard space-group settings
    """

    from fractions import Fraction
    import numpy as np
    import re

    from pymatgen.core import Lattice
    from pymatgen.util.string import transformation_to_string
    from pymatgen.core.operations import MagSymmOp, SymmOp

    from typing import Union, List, Tuple

    __author__ = "Matthew Horton"
    __copyright__ = "Copyright 2017, The Materials Project"
    __version__ = "0.1"
    __maintainer__ = "Matthew Horton"
    __email__ = "mkhorton@lbl.gov"
    __status__ = "Development"
    __date__ = "Apr 2017"

    class JonesFaithfulTransformation:
        """
        Transformation for space-groups defined in a non-standard setting
        """

        def __init__(self, P, p):
            """
            Transform between settings using matrix P and origin shift vector p,
            using same notation as reference.

            Should initialize using `from_transformation_string` in Jones
            faithful notation, given by a string specifying both a
            transformation matrix and an origin shift, with parts delimited
            by a semi-colon. Best shown by example:

            * `a,b,c;0,0,0` is the identity (no change)
            * `-b+c,a+c,-a+b+c;0,0,0` is R3:r to R3:h (rhombohedral to
              hexagonal setting)
            * `a,b,c;-1/4,-1/4,-1/4` is Pnnn:1 to Pnnn:2 (change in origin
              choice)
            * `b,c,a;-1/2,-1/2,-1/2` is Bbab:1 to Ccca:2 (change settin
              and origin)

            Can transform points (coords), lattices and symmetry operations.

            Used for transforming magnetic space groups since these are
            commonly used in multiple settings, due to needing to transform
            between magnetic and non-magnetic settings.

            See: International Tables for Crystallography (2016). Vol. A,
            Chapter 1.5, pp. 75–106.
            """
            # using capital letters in violation of PEP8 to
            # be consistent with variables in supplied reference,
            # for easier debugging in future
            self._P, self._p = P, p

        @classmethod
        def from_transformation_string(cls, transformation_string="a,b,c;0,0,0"):
            """
            Construct SpaceGroupTransformation from its transformation string.
            :param P: matrix
            :param p: origin shift vector
            :return:
            """
            P, p = JonesFaithfulTransformation.parse_transformation_string(
                transformation_string)
            return cls(P, p)

        @classmethod
        def from_origin_shift(cls, origin_shift="0,0,0"):
            """
            Construct SpaceGroupTransformation from its origin shift string.
            :param p: origin shift vector
            :return:
            """
            P = np.identity(3)
            p = [float(Fraction(x)) for x in origin_shift.split(",")]
            return cls(P, p)

        @staticmethod
        def parse_transformation_string(transformation_string="a,b,c;0,0,0"):
            # type: (str) -> Tuple[List[List[float]], List[float]]
            """
            :return: transformation matrix & vector
            """
            try:
                a = np.array([1, 0, 0])
                b = np.array([0, 1, 0])
                c = np.array([0, 0, 1])
                b_change, o_shift = transformation_string.split(";")
                basis_change = b_change.split(",")
                origin_shift = o_shift.split(",")
                # add implicit multiplication symbols
                basis_change = [re.sub(
                    r'(?<=\w|\))(?=\() | (?<=\))(?=\w) | (?<=(\d|a|b|c))(?=([abc]))',
                    r'*', x, flags=re.X) for x in basis_change]
                # should be fine to use eval here but be mindful for security
                # reasons
                # see http://lybniz2.sourceforge.net/safeeval.html
                # could replace with regex? or sympy expression?
                P = np.array([eval(x, {"__builtins__": None},
                                   {'a': a, 'b': b, 'c': c}) for x in basis_change])
                P = P.transpose()  # by convention
                p = [float(Fraction(x)) for x in origin_shift]
                return (P, p)
            except Exception:
                raise ValueError("Failed to parse transformation string.")

        @property
        def P(self) -> List[List[float]]:
            """
            :return: transformation matrix
            """
            return self._P

        @property
        def p(self) -> List[float]:
            """

            :return: translation vector
            """
            return self._p

        @property
        def inverse(self) -> 'JonesFaithfulTransformation':
            """

            :return: JonesFaithfulTransformation
            """
            Q = np.linalg.inv(self.P)
            return JonesFaithfulTransformation(Q, -np.matmul(Q, self.p))

        @property
        def transformation_string(self) -> str:
            """
            :return: transformation string
            """
            return self._get_transformation_string_from_Pp(self.P, self.p)

        @staticmethod
        def _get_transformation_string_from_Pp(P: List[List[float]], p: List[float]) -> str:
            P = np.array(P).transpose()
            P_string = transformation_to_string(P, components=('a', 'b', 'c'))
            p_string = transformation_to_string(np.zeros((3, 3)), p)
            return P_string + ";" + p_string

        def transform_symmop(self, symmop: Union[SymmOp, MagSymmOp]) -> Union[SymmOp, MagSymmOp]:
            """
            Takes a symmetry operation and transforms it.
            :param symmop: SymmOp or MagSymmOp
            :return:
            """
            W = symmop.rotation_matrix
            w = symmop.translation_vector
            Q = np.linalg.inv(self.P)
            W_ = np.matmul(np.matmul(Q, W), self.P)
            I = np.identity(3)
            w_ = np.matmul(Q, (w + np.matmul(W - I, self.p)))
            w_ = np.mod(w_, 1.0)
            if isinstance(symmop, MagSymmOp):
                return MagSymmOp.from_rotation_and_translation_and_time_reversal(
                    rotation_matrix=W_, translation_vec=w_,
                    time_reversal=symmop.time_reversal, tol=symmop.tol)
            elif isinstance(symmop, SymmOp):
                return SymmOp.from_rotation_and_translation(
                    rotation_matrix=W_, translation_vec=w_, tol=symmop.tol)
            raise RuntimeError

        def transform_coords(self, coords: List[List[float]]) -> List[List[float]]:
            """
            Takes a list of co-ordinates and transforms them.
            :param coords: List of coords
            :return:
            """
            new_coords = []
            for x in coords:
                x = np.array(x)
                Q = np.linalg.inv(self.P)
                x_ = np.matmul(Q, (x - self.p))  # type: ignore
                new_coords.append(x_.tolist())
            return new_coords

        def transform_lattice(self, lattice):
            # type: (Lattice) -> Lattice
            """
            Takes a Lattice object and transforms it.
            :param lattice: Lattice
            :return:
            """
            return Lattice(np.matmul(lattice.matrix, self.P))

        def __eq__(self, other):
            return np.allclose(self.P, other.P) and np.allclose(self.p, other.p)

        def __str__(self):
            return str(JonesFaithfulTransformation.transformation_string)

        def __repr__(self):
            return "JonesFaithfulTransformation with P:\n{0}\nand p:\n{1}".format(
                self.P, self.p)