diffpy.structure 3.2.0__py3-none-any.whl

diffpy/structure/spacegroupmod.py

@@ -0,0 +1,329 @@
+#!/usr/bin/env python
+# Copyright 2002 by PyMMLib Development Group, http://pymmlib.sourceforge.net/
+# This code is part of the PyMMLib distribution and governed by
+# its license. Please see the LICENSE_pymmlib file that should have been
+# included as part of this package.
+"""Symmetry operations as functions on vectors or arrays.
+"""
+
+import numpy
+
+# 64 unique rotation matricies
+Rot_Z_mY_X = numpy.array([[0.0, 0.0, 1.0], [0.0, -1.0, 0.0], [1.0, 0.0, 0.0]], float)
+Rot_Y_mX_mZ = numpy.array([[0.0, 1.0, 0.0], [-1.0, 0.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_XmY_X_mZ = numpy.array([[1.0, -1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_mX_Y_mZ = numpy.array([[-1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_X_mZ_Y = numpy.array([[1.0, 0.0, 0.0], [0.0, 0.0, -1.0], [0.0, 1.0, 0.0]], float)
+Rot_Y_mXY_Z = numpy.array([[0.0, 1.0, 0.0], [-1.0, 1.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_Y_mX_Z = numpy.array([[0.0, 1.0, 0.0], [-1.0, 0.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_XmY_X_Z = numpy.array([[1.0, -1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_mX_mXY_mZ = numpy.array([[-1.0, 0.0, 0.0], [-1.0, 1.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_Y_Z_X = numpy.array([[0.0, 1.0, 0.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0]], float)
+Rot_mY_mZ_X = numpy.array([[0.0, -1.0, 0.0], [0.0, 0.0, -1.0], [1.0, 0.0, 0.0]], float)
+Rot_X_Z_mY = numpy.array([[1.0, 0.0, 0.0], [0.0, 0.0, 1.0], [0.0, -1.0, 0.0]], float)
+Rot_XmY_mY_Z = numpy.array([[1.0, -1.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_Y_X_mZ = numpy.array([[0.0, 1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_Y_mZ_X = numpy.array([[0.0, 1.0, 0.0], [0.0, 0.0, -1.0], [1.0, 0.0, 0.0]], float)
+Rot_mXY_Y_Z = numpy.array([[-1.0, 1.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_mX_mY_mZ = numpy.array([[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_X_Y_mZ = numpy.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_mXY_mX_Z = numpy.array([[-1.0, 1.0, 0.0], [-1.0, 0.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_mZ_mY_mX = numpy.array([[0.0, 0.0, -1.0], [0.0, -1.0, 0.0], [-1.0, 0.0, 0.0]], float)
+Rot_X_mZ_mY = numpy.array([[1.0, 0.0, 0.0], [0.0, 0.0, -1.0], [0.0, -1.0, 0.0]], float)
+Rot_X_Y_Z = numpy.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_mY_mX_mZ = numpy.array([[0.0, -1.0, 0.0], [-1.0, 0.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_mY_X_Z = numpy.array([[0.0, -1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_Z_X_Y = numpy.array([[0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0]], float)
+Rot_X_XmY_Z = numpy.array([[1.0, 0.0, 0.0], [1.0, -1.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_mY_X_mZ = numpy.array([[0.0, -1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_mY_Z_mX = numpy.array([[0.0, -1.0, 0.0], [0.0, 0.0, 1.0], [-1.0, 0.0, 0.0]], float)
+Rot_mY_Z_X = numpy.array([[0.0, -1.0, 0.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0]], float)
+Rot_mX_mZ_mY = numpy.array([[-1.0, 0.0, 0.0], [0.0, 0.0, -1.0], [0.0, -1.0, 0.0]], float)
+Rot_mX_Z_Y = numpy.array([[-1.0, 0.0, 0.0], [0.0, 0.0, 1.0], [0.0, 1.0, 0.0]], float)
+Rot_mZ_mX_mY = numpy.array([[0.0, 0.0, -1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]], float)
+Rot_X_XmY_mZ = numpy.array([[1.0, 0.0, 0.0], [1.0, -1.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_mY_XmY_mZ = numpy.array([[0.0, -1.0, 0.0], [1.0, -1.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_Z_X_mY = numpy.array([[0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [0.0, -1.0, 0.0]], float)
+Rot_mZ_mY_X = numpy.array([[0.0, 0.0, -1.0], [0.0, -1.0, 0.0], [1.0, 0.0, 0.0]], float)
+Rot_X_Z_Y = numpy.array([[1.0, 0.0, 0.0], [0.0, 0.0, 1.0], [0.0, 1.0, 0.0]], float)
+Rot_Z_mX_mY = numpy.array([[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]], float)
+Rot_mX_Z_mY = numpy.array([[-1.0, 0.0, 0.0], [0.0, 0.0, 1.0], [0.0, -1.0, 0.0]], float)
+Rot_X_mY_Z = numpy.array([[1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_mY_mX_Z = numpy.array([[0.0, -1.0, 0.0], [-1.0, 0.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_Z_mY_mX = numpy.array([[0.0, 0.0, 1.0], [0.0, -1.0, 0.0], [-1.0, 0.0, 0.0]], float)
+Rot_mX_mY_Z = numpy.array([[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_Z_Y_X = numpy.array([[0.0, 0.0, 1.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]], float)
+Rot_mZ_Y_mX = numpy.array([[0.0, 0.0, -1.0], [0.0, 1.0, 0.0], [-1.0, 0.0, 0.0]], float)
+Rot_Y_Z_mX = numpy.array([[0.0, 1.0, 0.0], [0.0, 0.0, 1.0], [-1.0, 0.0, 0.0]], float)
+Rot_mY_XmY_Z = numpy.array([[0.0, -1.0, 0.0], [1.0, -1.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_mXY_Y_mZ = numpy.array([[-1.0, 1.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_mZ_mX_Y = numpy.array([[0.0, 0.0, -1.0], [-1.0, 0.0, 0.0], [0.0, 1.0, 0.0]], float)
+Rot_mX_mZ_Y = numpy.array([[-1.0, 0.0, 0.0], [0.0, 0.0, -1.0], [0.0, 1.0, 0.0]], float)
+Rot_mX_Y_Z = numpy.array([[-1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_X_mY_mZ = numpy.array([[1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_mZ_X_Y = numpy.array([[0.0, 0.0, -1.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0]], float)
+Rot_Y_mZ_mX = numpy.array([[0.0, 1.0, 0.0], [0.0, 0.0, -1.0], [-1.0, 0.0, 0.0]], float)
+Rot_mY_mZ_mX = numpy.array([[0.0, -1.0, 0.0], [0.0, 0.0, -1.0], [-1.0, 0.0, 0.0]], float)
+Rot_mZ_Y_X = numpy.array([[0.0, 0.0, -1.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]], float)
+Rot_Z_Y_mX = numpy.array([[0.0, 0.0, 1.0], [0.0, 1.0, 0.0], [-1.0, 0.0, 0.0]], float)
+Rot_mXY_mX_mZ = numpy.array([[-1.0, 1.0, 0.0], [-1.0, 0.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_XmY_mY_mZ = numpy.array([[1.0, -1.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_Z_mX_Y = numpy.array([[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, 1.0, 0.0]], float)
+Rot_mX_mXY_Z = numpy.array([[-1.0, 0.0, 0.0], [-1.0, 1.0, 0.0], [0.0, 0.0, 1.0]], float)
+Rot_Y_mXY_mZ = numpy.array([[0.0, 1.0, 0.0], [-1.0, 1.0, 0.0], [0.0, 0.0, -1.0]], float)
+Rot_mZ_X_mY = numpy.array([[0.0, 0.0, -1.0], [1.0, 0.0, 0.0], [0.0, -1.0, 0.0]], float)
+Rot_Y_X_Z = numpy.array([[0.0, 1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, 1.0]], float)
+
+# 32 unique translation vectors
+Tr_0_0_34 = numpy.array([0.0, 0.0, 3.0 / 4.0], float)
+Tr_12_0_34 = numpy.array([1.0 / 2.0, 0.0, 3.0 / 4.0], float)
+Tr_0_0_56 = numpy.array([0.0, 0.0, 5.0 / 6.0], float)
+Tr_12_0_12 = numpy.array([1.0 / 2.0, 0.0, 1.0 / 2.0], float)
+Tr_0_12_12 = numpy.array([0.0, 1.0 / 2.0, 1.0 / 2.0], float)
+Tr_12_0_14 = numpy.array([1.0 / 2.0, 0.0, 1.0 / 4.0], float)
+Tr_0_12_14 = numpy.array([0.0, 1.0 / 2.0, 1.0 / 4.0], float)
+Tr_14_14_14 = numpy.array([1.0 / 4.0, 1.0 / 4.0, 1.0 / 4.0], float)
+Tr_0_12_34 = numpy.array([0.0, 1.0 / 2.0, 3.0 / 4.0], float)
+Tr_34_14_14 = numpy.array([3.0 / 4.0, 1.0 / 4.0, 1.0 / 4.0], float)
+Tr_0_0_0 = numpy.array([0.0, 0.0, 0.0], float)
+Tr_23_13_56 = numpy.array([2.0 / 3.0, 1.0 / 3.0, 5.0 / 6.0], float)
+Tr_14_14_34 = numpy.array([1.0 / 4.0, 1.0 / 4.0, 3.0 / 4.0], float)
+Tr_12_12_0 = numpy.array([1.0 / 2.0, 1.0 / 2.0, 0.0], float)
+Tr_23_13_13 = numpy.array([2.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0], float)
+Tr_13_23_23 = numpy.array([1.0 / 3.0, 2.0 / 3.0, 2.0 / 3.0], float)
+Tr_12_12_12 = numpy.array([1.0 / 2.0, 1.0 / 2.0, 1.0 / 2.0], float)
+Tr_12_12_14 = numpy.array([1.0 / 2.0, 1.0 / 2.0, 1.0 / 4.0], float)
+Tr_14_34_14 = numpy.array([1.0 / 4.0, 3.0 / 4.0, 1.0 / 4.0], float)
+Tr_12_12_34 = numpy.array([1.0 / 2.0, 1.0 / 2.0, 3.0 / 4.0], float)
+Tr_0_0_23 = numpy.array([0.0, 0.0, 2.0 / 3.0], float)
+Tr_0_12_0 = numpy.array([0.0, 1.0 / 2.0, 0.0], float)
+Tr_14_34_34 = numpy.array([1.0 / 4.0, 3.0 / 4.0, 3.0 / 4.0], float)
+Tr_34_34_14 = numpy.array([3.0 / 4.0, 3.0 / 4.0, 1.0 / 4.0], float)
+Tr_12_0_0 = numpy.array([1.0 / 2.0, 0.0, 0.0], float)
+Tr_34_34_34 = numpy.array([3.0 / 4.0, 3.0 / 4.0, 3.0 / 4.0], float)
+Tr_0_0_13 = numpy.array([0.0, 0.0, 1.0 / 3.0], float)
+Tr_0_0_12 = numpy.array([0.0, 0.0, 1.0 / 2.0], float)
+Tr_13_23_16 = numpy.array([1.0 / 3.0, 2.0 / 3.0, 1.0 / 6.0], float)
+Tr_0_0_14 = numpy.array([0.0, 0.0, 1.0 / 4.0], float)
+Tr_0_0_16 = numpy.array([0.0, 0.0, 1.0 / 6.0], float)
+Tr_34_14_34 = numpy.array([3.0 / 4.0, 1.0 / 4.0, 3.0 / 4.0], float)
+
+
+class SymOp(object):
+    """The transformation of coordinates to a symmetry-related position.
+
+    The SymOp operation involves rotation and translation in cell coordinates.
+
+    Parameters
+    ----------
+    R : numpy.ndarray
+        The 3x3 matrix of rotation for this symmetry operation.
+    t : numpy.ndarray
+        The vector of translation in this symmetry operation.
+
+    Attributes
+    ----------
+    R : numpy.ndarray
+        The 3x3 matrix of rotation pertaining to unit cell coordinates.
+        This may be identity, simple rotation, improper rotation, mirror
+        or inversion. The determinant of *R* is either +1 or -1.
+    t : numpy.ndarray
+        The translation of cell coordinates applied after rotation *R*.
+    """
+
+    def __init__(self, R, t):
+        self.R = R
+        self.t = t
+        return
+
+    def __str__(self):
+        """Printable representation of this SymOp object."""
+        x = "[%6.3f %6.3f %6.3f %6.3f]\n" % (self.R[0, 0], self.R[0, 1], self.R[0, 2], self.t[0])
+        x += "[%6.3f %6.3f %6.3f %6.3f]\n" % (self.R[1, 0], self.R[1, 1], self.R[1, 2], self.t[1])
+        x += "[%6.3f %6.3f %6.3f %6.3f]\n" % (self.R[2, 0], self.R[2, 1], self.R[2, 2], self.t[2])
+        return x
+
+    def __call__(self, vec):
+        """Return symmetry-related position for the specified coordinates.
+
+        Parameters
+        ----------
+        vec : numpy.ndarray
+            The initial position in fractional cell coordinates.
+
+        Returns
+        -------
+        numpy.ndarray
+            The transformed position after this symmetry operation.
+        """
+        return numpy.dot(self.R, vec) + self.t
+
+    def __eq__(self, symop):
+        """Implement the ``self == symop`` test of equality.
+
+        Return ``True`` when *self* and *symop* difference is within
+        tiny round-off errors.
+        """
+        return numpy.allclose(self.R, symop.R) and numpy.allclose(self.t, symop.t)
+
+    def is_identity(self):
+        """Check if this SymOp is an identity operation.
+
+        Returns
+        -------
+        bool
+            ``True`` if this is an identity operation within a small round-off.
+            Return ``False`` otherwise.
+        """
+        rv = numpy.allclose(self.R, numpy.identity(3, float)) and numpy.allclose(self.t, numpy.zeros(3, float))
+        return rv
+
+
+# End of class SymOp
+
+
+class SpaceGroup(object):
+    """Definition and basic operations for a specific space group.
+
+    Provide standard names and all symmetry operations contained in
+    one space group.
+
+    Parameters
+    ----------
+    number : int
+        The space group number.
+    num_sym_equiv : int
+        The number of symmetry equivalent sites for a general position.
+    num_primitive_sym_equiv : int
+        The number of symmetry equivalent sites in a primitive unit cell.
+    short_name : str
+        The short Hermann-Mauguin symbol of the space group.
+    point_group_name : str
+        The point group of this space group.
+    crystal_system : str
+        The crystal system of this space group.
+    pdb_name : str
+        The full Hermann-Mauguin symbol of the space group.
+    symop_list : list of SymOp
+        The symmetry operations contained in this space group.
+
+    Attributes
+    ----------
+    number : int
+        A unique space group number. This may be incremented by
+        several thousands to facilitate unique values for multiple
+        settings of the same space group. Use ``number % 1000``
+        to get the standard space group number from International
+        Tables.
+    num_sym_equiv : int
+        The number of symmetry equivalent sites for a general position.
+    num_primitive_sym_equiv : int
+        The number of symmetry equivalent sites in a primitive unit cell.
+    short_name : str
+        The short Hermann-Mauguin symbol of the space group.
+    point_group_name : str
+        The point group to which this space group belongs to.
+    crystal_system : str
+        The crystal system of this space group. The possible values are
+        ``"TRICLINIC", "MONOCLINIC", "ORTHORHOMBIC", "TETRAGONAL",
+        "TRIGONAL" "HEXAGONAL", "CUBIC"``.
+    pdb_name : str
+        The full Hermann-Mauguin symbol of the space group.
+    symop_list : list of SymOp
+        A list of `SymOp` objects for all symmetry operations
+        in this space group.
+    """
+
+    def __init__(
+        self,
+        number=None,
+        num_sym_equiv=None,
+        num_primitive_sym_equiv=None,
+        short_name=None,
+        point_group_name=None,
+        crystal_system=None,
+        pdb_name=None,
+        symop_list=None,
+    ):
+
+        self.number = number
+        self.num_sym_equiv = num_sym_equiv
+        self.num_primitive_sym_equiv = num_primitive_sym_equiv
+        self.short_name = short_name
+        self.point_group_name = point_group_name
+        self.crystal_system = crystal_system
+        self.pdb_name = pdb_name
+        self.symop_list = symop_list
+
+    def __repr__(self):
+        """Return a string representation of the space group."""
+        return ("SpaceGroup #%i (%s, %s). Symmetry matrices: %i, " "point sym. matr.: %i") % (
+            self.number,
+            self.short_name,
+            self.crystal_system[0] + self.crystal_system[1:].lower(),
+            self.num_sym_equiv,
+            self.num_primitive_sym_equiv,
+        )
+
+    def iter_symops(self):
+        """Iterate over all symmetry operations in the space group.
+
+        Yields
+        ------
+        SymOp
+            Generate all symmetry operations for this space group.
+        """
+        return iter(self.symop_list)
+
+    def check_group_name(self, name):
+        """Check if given name matches this space group.
+
+        Parameters
+        ----------
+        name : str or int
+            The space group identifier, a string name or number.
+
+        Returns
+        -------
+        bool
+            ``True`` if the specified name matches one of the recognized
+            names of this space group or if it equals its `number`.
+            Return ``False`` otherwise.
+        """
+
+        if name == self.short_name:
+            return True
+        if name == self.pdb_name:
+            return True
+        if name == self.point_group_name:
+            return True
+        if name == self.number:
+            return True
+        return False
+
+    def iter_equivalent_positions(self, vec):
+        """Generate symmetry equivalent positions for the specified position.
+
+        The initial position must be in fractional coordinates and so
+        are the symmetry equivalent positions yielded by iteration.
+        This generates `num_sym_equiv` positions regardless of initial
+        coordinates being a special symmetry position or not.
+
+        Parameters
+        ----------
+        vec : numpy.ndarray
+            The initial position in fractional coordinates.
+
+        Yields
+        ------
+        numpy.ndarray
+            The symmetry equivalent positions in fractional coordinates.
+            The positions may be duplicate or outside of the ``0 <= x < 1``
+            unit cell bounds.
+        """
+        for symop in self.symop_list:
+            yield symop(vec)
+        pass
+
+
+# End of class SpaceGroup