WIP: more reasonable naming
This commit is contained in:
Martin Diehl
parent
b8b34080fe
commit
ce7018164f
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@ -5,7 +5,7 @@ from . import Rotation
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class Symmetry:
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"""
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Symmetry operations for lattice systems.
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Symmetry-related operations for crystal systems.
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References
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----------
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@ -13,34 +13,35 @@ class Symmetry:
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"""
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lattices = [None,'orthorhombic','tetragonal','hexagonal','cubic']
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crystal_systems = [None,'orthorhombic','tetragonal','hexagonal','cubic']
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def __init__(self, symmetry = None):
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def __init__(self, system = None):
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"""
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Symmetry Definition.
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Parameters
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----------
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symmetry : str, optional
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label of the crystal system
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system : {None,'orthorhombic','tetragonal','hexagonal','cubic'}, optional
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Name of the crystal system. Defaults to 'None'.
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"""
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if symmetry is not None and symmetry.lower() not in Symmetry.lattices:
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raise KeyError('Symmetry/crystal system "{}" is unknown'.format(symmetry))
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if system is not None and system.lower() not in self.crystal_systems:
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raise KeyError(f'Crystal system "{system}" is unknown')
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self.lattice = symmetry.lower() if isinstance(symmetry,str) else symmetry
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self.system = system.lower() if isinstance(system,str) else system
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self.lattice = self.system # for compatibility
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def __copy__(self):
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"""Copy."""
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return self.__class__(self.lattice)
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return self.__class__(self.system)
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copy = __copy__
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def __repr__(self):
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"""Readable string."""
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return '{}'.format(self.lattice)
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return '{}'.format(self.system)
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def __eq__(self, other):
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@ -53,7 +54,7 @@ class Symmetry:
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Symmetry to check for equality.
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"""
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return self.lattice == other.lattice
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return self.system == other.system
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def __neq__(self, other):
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"""
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@ -77,13 +78,13 @@ class Symmetry:
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Symmetry to check for for order.
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"""
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myOrder = Symmetry.lattices.index(self.lattice)
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otherOrder = Symmetry.lattices.index(other.lattice)
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myOrder = self.crystal_systems.index(self.system)
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otherOrder = self.crystal_systems.index(other.system)
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return (myOrder > otherOrder) - (myOrder < otherOrder)
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def symmetryOperations(self,members=[]):
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"""List (or single element) of symmetry operations as rotations."""
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if self.lattice == 'cubic':
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if self.system == 'cubic':
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symQuats = [
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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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@ -110,7 +111,7 @@ class Symmetry:
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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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elif self.lattice == 'hexagonal':
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elif self.system == 'hexagonal':
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symQuats = [
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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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@ -125,7 +126,7 @@ class Symmetry:
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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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elif self.lattice == 'tetragonal':
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elif self.system == 'tetragonal':
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symQuats = [
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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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@ -136,7 +137,7 @@ class Symmetry:
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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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elif self.lattice == 'orthorhombic':
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elif self.system == 'orthorhombic':
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symQuats = [
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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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@ -160,7 +161,7 @@ class Symmetry:
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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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if self.lattice == 'cubic':
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if self.system == 'cubic':
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symQuats = [
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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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@ -187,7 +188,7 @@ class Symmetry:
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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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elif self.lattice == 'hexagonal':
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elif self.system == 'hexagonal':
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symQuats = [
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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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@ -202,7 +203,7 @@ class Symmetry:
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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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elif self.lattice == 'tetragonal':
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elif self.system == 'tetragonal':
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symQuats = [
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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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@ -213,7 +214,7 @@ class Symmetry:
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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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elif self.lattice == 'orthorhombic':
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elif self.system == 'orthorhombic':
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symQuats = [
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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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@ -240,21 +241,21 @@ class Symmetry:
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Rabs = abs(rodrigues)
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if self.lattice == 'cubic':
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if self.system == 'cubic':
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return np.sqrt(2.0)-1.0 >= Rabs[0] \
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and np.sqrt(2.0)-1.0 >= Rabs[1] \
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and np.sqrt(2.0)-1.0 >= Rabs[2] \
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and 1.0 >= Rabs[0] + Rabs[1] + Rabs[2]
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elif self.lattice == 'hexagonal':
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elif self.system == 'hexagonal':
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return 1.0 >= Rabs[0] and 1.0 >= Rabs[1] and 1.0 >= Rabs[2] \
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and 2.0 >= np.sqrt(3)*Rabs[0] + Rabs[1] \
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and 2.0 >= np.sqrt(3)*Rabs[1] + Rabs[0] \
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and 2.0 >= np.sqrt(3) + Rabs[2]
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elif self.lattice == 'tetragonal':
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elif self.system == 'tetragonal':
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return 1.0 >= Rabs[0] and 1.0 >= Rabs[1] \
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and np.sqrt(2.0) >= Rabs[0] + Rabs[1] \
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and np.sqrt(2.0) >= Rabs[2] + 1.0
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elif self.lattice == 'orthorhombic':
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elif self.system == 'orthorhombic':
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return 1.0 >= Rabs[0] and 1.0 >= Rabs[1] and 1.0 >= Rabs[2]
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else:
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return True
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@ -275,13 +276,13 @@ class Symmetry:
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R = rodrigues
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epsilon = 0.0
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if self.lattice == 'cubic':
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if self.system == 'cubic':
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return R[0] >= R[1]+epsilon and R[1] >= R[2]+epsilon and R[2] >= epsilon
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elif self.lattice == 'hexagonal':
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elif self.system == 'hexagonal':
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return R[0] >= np.sqrt(3)*(R[1]-epsilon) and R[1] >= epsilon and R[2] >= epsilon
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elif self.lattice == 'tetragonal':
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elif self.system == 'tetragonal':
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return R[0] >= R[1]-epsilon and R[1] >= epsilon and R[2] >= epsilon
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elif self.lattice == 'orthorhombic':
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elif self.system == 'orthorhombic':
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return R[0] >= epsilon and R[1] >= epsilon and R[2] >= epsilon
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else:
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return True
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@ -313,7 +314,7 @@ class Symmetry:
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... }
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"""
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if self.lattice == 'cubic':
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if self.system == 'cubic':
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basis = {'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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@ -321,7 +322,7 @@ class Symmetry:
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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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elif self.lattice == 'hexagonal':
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elif self.system == 'hexagonal':
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basis = {'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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@ -329,7 +330,7 @@ class Symmetry:
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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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elif self.lattice == 'tetragonal':
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elif self.system == 'tetragonal':
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basis = {'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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@ -337,7 +338,7 @@ class Symmetry:
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[-1. , 1. , 0. ],
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[ np.sqrt(2.) , 0. , 0. ] ]),
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}
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elif self.lattice == 'orthorhombic':
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elif self.system == 'orthorhombic':
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basis = {'improper':np.array([ [ 0., 0., 1.],
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[ 1., 0., 0.],
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[ 0., 1., 0.] ]),
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@ -401,7 +402,7 @@ class Symmetry:
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... }
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"""
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if self.lattice == 'cubic':
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if self.system == 'cubic':
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basis = {'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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@ -409,7 +410,7 @@ class Symmetry:
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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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elif self.lattice == 'hexagonal':
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elif self.system == 'hexagonal':
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basis = {'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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@ -417,7 +418,7 @@ class Symmetry:
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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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elif self.lattice == 'tetragonal':
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elif self.system == 'tetragonal':
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basis = {'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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@ -425,7 +426,7 @@ class Symmetry:
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[-1. , 1. , 0. ],
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[ np.sqrt(2.) , 0. , 0. ] ]),
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}
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elif self.lattice == 'orthorhombic':
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elif self.system == 'orthorhombic':
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basis = {'improper':np.array([ [ 0., 0., 1.],
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[ 1., 0., 0.],
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[ 0., 1., 0.] ]),
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@ -13,26 +13,26 @@ class TestSymmetry:
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s = Symmetry(invalid_symmetry) # noqa
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def test_equal(self):
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symmetry = random.choice(Symmetry.lattices)
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symmetry = random.choice(Symmetry.crystal_systems)
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print(symmetry)
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assert Symmetry(symmetry) == Symmetry(symmetry)
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def test_not_equal(self):
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symmetries = random.sample(Symmetry.lattices,k=2)
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symmetries = random.sample(Symmetry.crystal_systems,k=2)
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assert Symmetry(symmetries[0]) != Symmetry(symmetries[1])
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@pytest.mark.parametrize('lattice',Symmetry.lattices)
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def test_inFZ(self,lattice):
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assert Symmetry(lattice).inFZ(np.zeros(3))
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@pytest.mark.parametrize('system',Symmetry.crystal_systems)
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def test_inFZ(self,system):
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assert Symmetry(system).inFZ(np.zeros(3))
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@pytest.mark.parametrize('lattice',Symmetry.lattices)
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def test_inDisorientationSST(self,lattice):
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assert Symmetry(lattice).inDisorientationSST(np.zeros(3))
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@pytest.mark.parametrize('system',Symmetry.crystal_systems)
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def test_inDisorientationSST(self,system):
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assert Symmetry(system).inDisorientationSST(np.zeros(3))
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@pytest.mark.parametrize('lattice',Symmetry.lattices)
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@pytest.mark.parametrize('system',Symmetry.crystal_systems)
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@pytest.mark.parametrize('proper',[True,False])
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def test_inSST(self,lattice,proper):
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assert Symmetry(lattice).inSST(np.zeros(3),proper)
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def test_inSST(self,system,proper):
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assert Symmetry(system).inSST(np.zeros(3),proper)
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@pytest.mark.parametrize('function',['inFZ','inDisorientationSST'])
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def test_invalid_argument(self,function):
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