no need to split code over two files
This commit is contained in:
Martin Diehl
parent
92ca010b7c
commit
2826e61ea1
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@ -17,7 +17,6 @@ from . import grid_filters # noqa
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#Modules that contain only one class (of the same name), are prefixed by a '_'.
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#For example, '_colormap' containsa class called 'Colormap' which is imported as 'damask.Colormap'.
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from ._rotation import Rotation # noqa
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from ._lattice_family import LatticeFamily # noqa
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from ._crystal import Crystal # noqa
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from ._orientation import Orientation # noqa
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from ._table import Table # noqa
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@ -1,7 +1,6 @@
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import numpy as np
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from . import util
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from . import LatticeFamily
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from . import Rotation
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lattice_symmetries = {
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@ -26,7 +25,7 @@ lattice_symmetries = {
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}
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class Crystal(LatticeFamily):
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class Crystal():
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"""Lattice."""
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def __init__(self,*,
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@ -42,6 +41,8 @@ class Crystal(LatticeFamily):
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----------
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lattice : {'aP', 'mP', 'mS', 'oP', 'oS', 'oI', 'oF', 'tP', 'tI', 'hP', 'cP', 'cI', 'cF'}.
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Name of the Bravais lattice in Pearson notation.
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family : {'triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'hexagonal', 'cubic'}
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Name of the crystal family.
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a : float, optional
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Length of lattice parameter 'a'.
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b : float, optional
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@ -58,8 +59,10 @@ class Crystal(LatticeFamily):
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Angles are given in degrees. Defaults to False.
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"""
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super().__init__(family = lattice_symmetries[lattice] if family is None else family)
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if family not in [None] + list(self._immutable.keys()):
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raise KeyError(f'invalid crystal family "{family}"')
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self.family = lattice_symmetries[lattice] if family is None else family
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self.lattice = lattice
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if self.lattice is not None:
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@ -114,7 +117,9 @@ class Crystal(LatticeFamily):
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Lattice to check for equality.
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"""
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return self.lattice == other.lattice and self.parameters == other.parameters
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return self.lattice == other.lattice and \
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self.parameters == other.parameters and \
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self.family == other.family
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@property
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def parameters(self):
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@ -122,6 +127,75 @@ class Crystal(LatticeFamily):
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return (self.a,self.b,self.c,self.alpha,self.beta,self.gamma)
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@property
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def immutable(self):
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"""Return immutable lattice parameters."""
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return self._immutable[self.family]
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@property
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def basis(self):
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"""
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Corners of the standard triangle.
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Not yet defined for monoclinic.
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References
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----------
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Bases are computed from
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>>> basis = {
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... 'cubic' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
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... [1.,0.,1.]/np.sqrt(2.), # green
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... [1.,1.,1.]/np.sqrt(3.)]).T), # blue
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... 'hexagonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
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... [1.,0.,0.], # green
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... [np.sqrt(3.),1.,0.]/np.sqrt(4.)]).T), # blue
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... 'tetragonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
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... [1.,0.,0.], # green
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... [1.,1.,0.]/np.sqrt(2.)]).T), # blue
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... 'orthorhombic': np.linalg.inv(np.array([[0.,0.,1.], # direction of red
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... [1.,0.,0.], # green
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... [0.,1.,0.]]).T), # blue
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... }
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"""
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_basis = {
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'cubic': {'improper':np.array([ [-1. , 0. , 1. ],
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[ np.sqrt(2.) , -np.sqrt(2.) , 0. ],
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[ 0. , np.sqrt(3.) , 0. ] ]),
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'proper':np.array([ [ 0. , -1. , 1. ],
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[-np.sqrt(2.) , np.sqrt(2.) , 0. ],
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[ np.sqrt(3.) , 0. , 0. ] ]),
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},
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'hexagonal':
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{'improper':np.array([ [ 0. , 0. , 1. ],
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[ 1. , -np.sqrt(3.) , 0. ],
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[ 0. , 2. , 0. ] ]),
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'proper':np.array([ [ 0. , 0. , 1. ],
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[-1. , np.sqrt(3.) , 0. ],
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[ np.sqrt(3.) , -1. , 0. ] ]),
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},
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'tetragonal':
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{'improper':np.array([ [ 0. , 0. , 1. ],
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[ 1. , -1. , 0. ],
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[ 0. , np.sqrt(2.) , 0. ] ]),
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'proper':np.array([ [ 0. , 0. , 1. ],
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[-1. , 1. , 0. ],
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[ np.sqrt(2.) , 0. , 0. ] ]),
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},
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'orthorhombic':
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{'improper':np.array([ [ 0., 0., 1.],
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[ 1., 0., 0.],
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[ 0., 1., 0.] ]),
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'proper':np.array([ [ 0., 0., 1.],
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[-1., 0., 0.],
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[ 0., 1., 0.] ]),
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}}
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return _basis.get(self.family,None)
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@property
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def ratio(self):
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"""Return axes ratios of own lattice."""
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@ -717,3 +791,35 @@ class Crystal(LatticeFamily):
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],dtype=float),
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},
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}
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_immutable = {
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'cubic': {
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'b': 1.0,
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'c': 1.0,
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'alpha': np.pi/2.,
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'beta': np.pi/2.,
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'gamma': np.pi/2.,
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},
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'hexagonal': {
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'b': 1.0,
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'alpha': np.pi/2.,
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'beta': np.pi/2.,
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'gamma': 2.*np.pi/3.,
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},
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'tetragonal': {
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'b': 1.0,
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'alpha': np.pi/2.,
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'beta': np.pi/2.,
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'gamma': np.pi/2.,
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},
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'orthorhombic': {
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'alpha': np.pi/2.,
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'beta': np.pi/2.,
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'gamma': np.pi/2.,
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},
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'monoclinic': {
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'alpha': np.pi/2.,
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'gamma': np.pi/2.,
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},
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'triclinic': {}
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}
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@ -1,208 +0,0 @@
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import numpy as np
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from . import Rotation
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class LatticeFamily():
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def __init__(self,family):
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"""
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Symmetry-related operations for crystal family.
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Parameters
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----------
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family : {'triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'hexagonal', 'cubic'}
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Name of the crystal family.
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"""
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if family not in self._immutable.keys():
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raise KeyError(f'invalid crystal family "{family}"')
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self.family = family
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def __eq__(self,other):
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"""
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Equal to other.
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Parameters
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----------
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other : LatticeFamily
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Lattice family to check for equality.
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"""
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return self.family == other.family
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@property
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def symmetry_operations(self):
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"""Symmetry operations as Rotations."""
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return Rotation.from_quaternion(self._symmetry_operations[self.family],accept_homomorph=True)
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@property
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def immutable(self):
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"""Return immutable lattice parameters."""
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return self._immutable[self.family]
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@property
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def basis(self):
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"""
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Corners of the standard triangle.
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Not yet defined for monoclinic.
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References
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----------
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Bases are computed from
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>>> basis = {
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... 'cubic' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
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... [1.,0.,1.]/np.sqrt(2.), # green
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... [1.,1.,1.]/np.sqrt(3.)]).T), # blue
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... 'hexagonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
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... [1.,0.,0.], # green
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... [np.sqrt(3.),1.,0.]/np.sqrt(4.)]).T), # blue
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... 'tetragonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
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... [1.,0.,0.], # green
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... [1.,1.,0.]/np.sqrt(2.)]).T), # blue
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... 'orthorhombic': np.linalg.inv(np.array([[0.,0.,1.], # direction of red
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... [1.,0.,0.], # green
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... [0.,1.,0.]]).T), # blue
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... }
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"""
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return self._basis.get(self.family,None)
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_symmetry_operations = {
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'cubic': [
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[ 1.0, 0.0, 0.0, 0.0 ],
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[ 0.0, 1.0, 0.0, 0.0 ],
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[ 0.0, 0.0, 1.0, 0.0 ],
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[ 0.0, 0.0, 0.0, 1.0 ],
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[ 0.0, 0.0, 0.5*np.sqrt(2), 0.5*np.sqrt(2) ],
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[ 0.0, 0.0, 0.5*np.sqrt(2),-0.5*np.sqrt(2) ],
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[ 0.0, 0.5*np.sqrt(2), 0.0, 0.5*np.sqrt(2) ],
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[ 0.0, 0.5*np.sqrt(2), 0.0, -0.5*np.sqrt(2) ],
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[ 0.0, 0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0 ],
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[ 0.0, -0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0 ],
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[ 0.5, 0.5, 0.5, 0.5 ],
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[-0.5, 0.5, 0.5, 0.5 ],
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[-0.5, 0.5, 0.5, -0.5 ],
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[-0.5, 0.5, -0.5, 0.5 ],
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[-0.5, -0.5, 0.5, 0.5 ],
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[-0.5, -0.5, 0.5, -0.5 ],
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[-0.5, -0.5, -0.5, 0.5 ],
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[-0.5, 0.5, -0.5, -0.5 ],
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[-0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
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[ 0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
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[-0.5*np.sqrt(2), 0.0, 0.5*np.sqrt(2), 0.0 ],
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[-0.5*np.sqrt(2), 0.0, -0.5*np.sqrt(2), 0.0 ],
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[-0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0, 0.0 ],
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[-0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0, 0.0 ],
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],
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'hexagonal': [
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[ 1.0, 0.0, 0.0, 0.0 ],
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[-0.5*np.sqrt(3), 0.0, 0.0, -0.5 ],
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[ 0.5, 0.0, 0.0, 0.5*np.sqrt(3) ],
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[ 0.0, 0.0, 0.0, 1.0 ],
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[-0.5, 0.0, 0.0, 0.5*np.sqrt(3) ],
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[-0.5*np.sqrt(3), 0.0, 0.0, 0.5 ],
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[ 0.0, 1.0, 0.0, 0.0 ],
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[ 0.0, -0.5*np.sqrt(3), 0.5, 0.0 ],
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[ 0.0, 0.5, -0.5*np.sqrt(3), 0.0 ],
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[ 0.0, 0.0, 1.0, 0.0 ],
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[ 0.0, -0.5, -0.5*np.sqrt(3), 0.0 ],
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[ 0.0, 0.5*np.sqrt(3), 0.5, 0.0 ],
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],
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'tetragonal': [
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[ 1.0, 0.0, 0.0, 0.0 ],
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[ 0.0, 1.0, 0.0, 0.0 ],
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[ 0.0, 0.0, 1.0, 0.0 ],
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[ 0.0, 0.0, 0.0, 1.0 ],
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[ 0.0, 0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0 ],
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[ 0.0, -0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0 ],
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[ 0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
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[-0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
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],
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'orthorhombic': [
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[ 1.0,0.0,0.0,0.0 ],
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[ 0.0,1.0,0.0,0.0 ],
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[ 0.0,0.0,1.0,0.0 ],
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[ 0.0,0.0,0.0,1.0 ],
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],
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'monoclinic': [
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[ 1.0,0.0,0.0,0.0 ],
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[ 0.0,0.0,1.0,0.0 ],
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],
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'triclinic': [
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[ 1.0,0.0,0.0,0.0 ],
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]}
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_immutable = {
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'cubic': {
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'b': 1.0,
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'c': 1.0,
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'alpha': np.pi/2.,
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'beta': np.pi/2.,
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'gamma': np.pi/2.,
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},
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'hexagonal': {
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'b': 1.0,
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'alpha': np.pi/2.,
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'beta': np.pi/2.,
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'gamma': 2.*np.pi/3.,
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},
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'tetragonal': {
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'b': 1.0,
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'alpha': np.pi/2.,
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'beta': np.pi/2.,
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'gamma': np.pi/2.,
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},
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'orthorhombic': {
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'alpha': np.pi/2.,
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'beta': np.pi/2.,
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'gamma': np.pi/2.,
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},
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'monoclinic': {
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'alpha': np.pi/2.,
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'gamma': np.pi/2.,
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},
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'triclinic': {}
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}
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_basis = {
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'cubic': {'improper':np.array([ [-1. , 0. , 1. ],
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[ np.sqrt(2.) , -np.sqrt(2.) , 0. ],
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[ 0. , np.sqrt(3.) , 0. ] ]),
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'proper':np.array([ [ 0. , -1. , 1. ],
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[-np.sqrt(2.) , np.sqrt(2.) , 0. ],
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[ np.sqrt(3.) , 0. , 0. ] ]),
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},
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'hexagonal':
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{'improper':np.array([ [ 0. , 0. , 1. ],
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[ 1. , -np.sqrt(3.) , 0. ],
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[ 0. , 2. , 0. ] ]),
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'proper':np.array([ [ 0. , 0. , 1. ],
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[-1. , np.sqrt(3.) , 0. ],
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[ np.sqrt(3.) , -1. , 0. ] ]),
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},
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'tetragonal':
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{'improper':np.array([ [ 0. , 0. , 1. ],
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[ 1. , -1. , 0. ],
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[ 0. , np.sqrt(2.) , 0. ] ]),
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'proper':np.array([ [ 0. , 0. , 1. ],
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[-1. , 1. , 0. ],
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[ np.sqrt(2.) , 0. , 0. ] ]),
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},
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'orthorhombic':
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{'improper':np.array([ [ 0., 0., 1.],
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[ 1., 0., 0.],
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[ 0., 1., 0.] ]),
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'proper':np.array([ [ 0., 0., 1.],
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[-1., 0., 0.],
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[ 0., 1., 0.] ]),
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}}
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@ -753,6 +753,77 @@ class Orientation(Rotation,Crystal):
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return rgb
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@property
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def symmetry_operations(self):
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"""Symmetry operations as Rotations."""
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_symmetry_operations = {
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'cubic': [
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[ 1.0, 0.0, 0.0, 0.0 ],
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[ 0.0, 1.0, 0.0, 0.0 ],
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[ 0.0, 0.0, 1.0, 0.0 ],
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[ 0.0, 0.0, 0.0, 1.0 ],
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[ 0.0, 0.0, 0.5*np.sqrt(2), 0.5*np.sqrt(2) ],
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[ 0.0, 0.0, 0.5*np.sqrt(2),-0.5*np.sqrt(2) ],
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[ 0.0, 0.5*np.sqrt(2), 0.0, 0.5*np.sqrt(2) ],
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[ 0.0, 0.5*np.sqrt(2), 0.0, -0.5*np.sqrt(2) ],
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[ 0.0, 0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0 ],
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[ 0.0, -0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0 ],
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[ 0.5, 0.5, 0.5, 0.5 ],
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[-0.5, 0.5, 0.5, 0.5 ],
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[-0.5, 0.5, 0.5, -0.5 ],
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[-0.5, 0.5, -0.5, 0.5 ],
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[-0.5, -0.5, 0.5, 0.5 ],
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[-0.5, -0.5, 0.5, -0.5 ],
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[-0.5, -0.5, -0.5, 0.5 ],
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[-0.5, 0.5, -0.5, -0.5 ],
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[-0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
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[ 0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
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[-0.5*np.sqrt(2), 0.0, 0.5*np.sqrt(2), 0.0 ],
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[-0.5*np.sqrt(2), 0.0, -0.5*np.sqrt(2), 0.0 ],
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[-0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0, 0.0 ],
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[-0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0, 0.0 ],
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],
|
||||
'hexagonal': [
|
||||
[ 1.0, 0.0, 0.0, 0.0 ],
|
||||
[-0.5*np.sqrt(3), 0.0, 0.0, -0.5 ],
|
||||
[ 0.5, 0.0, 0.0, 0.5*np.sqrt(3) ],
|
||||
[ 0.0, 0.0, 0.0, 1.0 ],
|
||||
[-0.5, 0.0, 0.0, 0.5*np.sqrt(3) ],
|
||||
[-0.5*np.sqrt(3), 0.0, 0.0, 0.5 ],
|
||||
[ 0.0, 1.0, 0.0, 0.0 ],
|
||||
[ 0.0, -0.5*np.sqrt(3), 0.5, 0.0 ],
|
||||
[ 0.0, 0.5, -0.5*np.sqrt(3), 0.0 ],
|
||||
[ 0.0, 0.0, 1.0, 0.0 ],
|
||||
[ 0.0, -0.5, -0.5*np.sqrt(3), 0.0 ],
|
||||
[ 0.0, 0.5*np.sqrt(3), 0.5, 0.0 ],
|
||||
],
|
||||
'tetragonal': [
|
||||
[ 1.0, 0.0, 0.0, 0.0 ],
|
||||
[ 0.0, 1.0, 0.0, 0.0 ],
|
||||
[ 0.0, 0.0, 1.0, 0.0 ],
|
||||
[ 0.0, 0.0, 0.0, 1.0 ],
|
||||
[ 0.0, 0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0 ],
|
||||
[ 0.0, -0.5*np.sqrt(2), 0.5*np.sqrt(2), 0.0 ],
|
||||
[ 0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
|
||||
[-0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
|
||||
],
|
||||
'orthorhombic': [
|
||||
[ 1.0,0.0,0.0,0.0 ],
|
||||
[ 0.0,1.0,0.0,0.0 ],
|
||||
[ 0.0,0.0,1.0,0.0 ],
|
||||
[ 0.0,0.0,0.0,1.0 ],
|
||||
],
|
||||
'monoclinic': [
|
||||
[ 1.0,0.0,0.0,0.0 ],
|
||||
[ 0.0,0.0,1.0,0.0 ],
|
||||
],
|
||||
'triclinic': [
|
||||
[ 1.0,0.0,0.0,0.0 ],
|
||||
]}
|
||||
return Rotation.from_quaternion(_symmetry_operations[self.family],accept_homomorph=True)
|
||||
|
||||
|
||||
####################################################################################################
|
||||
# functions that require lattice, not just family
|
||||
|
||||
def to_pole(self,*,uvw=None,hkl=None,with_symmetry=False):
|
||||
|
|
|
|||
Loading…
Reference in New Issue