vectorized equivalent orientation calculation
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cdda556e18
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@ -159,7 +159,7 @@ class Symmetry:
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@property
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@property
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def symmetry_operations(self):
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def symmetry_operations(self):
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"""List (or single element) of symmetry operations as rotations."""
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"""Symmetry operations as Rotations."""
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if self.lattice == 'cubic':
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if self.lattice == 'cubic':
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symQuats = [
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symQuats = [
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[ 1.0, 0.0, 0.0, 0.0 ],
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[ 1.0, 0.0, 0.0, 0.0 ],
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@ -236,7 +236,7 @@ class Symmetry:
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if (len(rodrigues) != 3):
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if (len(rodrigues) != 3):
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raise ValueError('Input is not a Rodrigues-Frank vector.\n')
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raise ValueError('Input is not a Rodrigues-Frank vector.\n')
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if np.any(rodrigues == np.inf): return False
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if np.any(rodrigues == np.inf): return False # ToDo: MD: not sure if needed
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Rabs = abs(rodrigues)
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Rabs = abs(rodrigues)
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@ -3,7 +3,7 @@ import numpy as np
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from . import Lattice
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from . import Lattice
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from . import Rotation
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from . import Rotation
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class Orientation:
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class Orientation: # make subclass or Rotation?
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"""
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"""
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Crystallographic orientation.
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Crystallographic orientation.
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@ -39,8 +39,6 @@ class Orientation:
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else:
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else:
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self.rotation = Rotation.from_quaternion(rotation) # assume quaternion
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self.rotation = Rotation.from_quaternion(rotation) # assume quaternion
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# if self.rotation.quaternion.shape != (4,):
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# raise NotImplementedError('Support for multiple rotations missing')
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def disorientation(self,
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def disorientation(self,
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other,
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other,
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@ -94,20 +92,25 @@ class Orientation:
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Rotation._qu2ro(self.rotation.as_quaternion())[l][...,:3]\
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Rotation._qu2ro(self.rotation.as_quaternion())[l][...,:3]\
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*Rotation._qu2ro(self.rotation.as_quaternion())[l][...,3])\
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*Rotation._qu2ro(self.rotation.as_quaternion())[l][...,3])\
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for l in range(self.rotation.shape[0])]
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for l in range(self.rotation.shape[0])]
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def inFZ(self):
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def inFZ(self):
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return self.lattice.symmetry.inFZ(self.rotation.as_Rodrigues(vector=True))
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return self.lattice.symmetry.inFZ(self.rotation.as_Rodrigues(vector=True))
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def equivalent_vec(self):
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@property
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"""List of orientations which are symmetrically equivalent."""
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def equivalent(self):
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if not self.rotation.shape:
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"""
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return [self.__class__(q*self.rotation,self.lattice) \
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Return orientations which are symmetrically equivalent.
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for q in self.lattice.symmetry.symmetryOperations()]
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else:
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One dimension (length according to symmetrically equivalent orientations)
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return np.reshape([self.__class__(q*Rotation.from_quaternion(self.rotation.as_quaternion()[l]),self.lattice) \
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is added to the left of the rotation array.
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for q in self.lattice.symmetry.symmetryOperations() \
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for l in range(self.rotation.shape[0])], \
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"""
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(len(self.lattice.symmetry.symmetryOperations()),self.rotation.shape[0]))
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symmetry_operations = self.lattice.symmetry.symmetry_operations
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q = np.block([self.rotation.quaternion]*symmetry_operations.shape[0])
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r = Rotation(q.reshape(symmetry_operations.shape+self.rotation.quaternion.shape))
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return self.__class__(symmetry_operations.broadcast_to(r.shape)@r,self.lattice)
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def equivalentOrientations(self,members=[]):
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def equivalentOrientations(self,members=[]):
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@ -130,7 +133,7 @@ class Orientation:
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[self.__class__(o*Rotation.from_quaternion(self.rotation.as_quaternion()[l])\
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[self.__class__(o*Rotation.from_quaternion(self.rotation.as_quaternion()[l])\
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,r['lattice']) for o in r['rotations'] for l in range(self.rotation.shape[0])]
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,r['lattice']) for o in r['rotations'] for l in range(self.rotation.shape[0])]
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,(len(r['rotations']),self.rotation.shape[0]))
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,(len(r['rotations']),self.rotation.shape[0]))
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def relatedOrientations(self,model):
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def relatedOrientations(self,model):
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"""List of orientations related by the given orientation relationship."""
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"""List of orientations related by the given orientation relationship."""
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@ -129,6 +129,7 @@ class Rotation:
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self.quaternion[...,1:] *= -1
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self.quaternion[...,1:] *= -1
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return self
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return self
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#@property
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def inversed(self):
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def inversed(self):
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"""Inverse rotation/backward rotation."""
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"""Inverse rotation/backward rotation."""
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return self.copy().inverse()
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return self.copy().inverse()
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@ -139,6 +140,7 @@ class Rotation:
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self.quaternion[self.quaternion[...,0] < 0.0] *= -1
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self.quaternion[self.quaternion[...,0] < 0.0] *= -1
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return self
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return self
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#@property
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def standardized(self):
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def standardized(self):
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"""Quaternion representation with positive real part."""
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"""Quaternion representation with positive real part."""
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return self.copy().standardize()
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return self.copy().standardize()
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@ -154,11 +156,12 @@ class Rotation:
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Rotation to which the misorientation is computed.
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Rotation to which the misorientation is computed.
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"""
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"""
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return other*self.inversed()
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return other@self.inversed()
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def broadcast_to(self,shape):
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def broadcast_to(self,shape):
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if isinstance(shape,int): shape = (shape,)
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if isinstance(shape,int):
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shape = (shape,)
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N = np.prod(shape)//np.prod(self.shape,dtype=int)
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N = np.prod(shape)//np.prod(self.shape,dtype=int)
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q = np.block([np.repeat(self.quaternion[...,0:1],N).reshape(shape+(1,)),
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q = np.block([np.repeat(self.quaternion[...,0:1],N).reshape(shape+(1,)),
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@ -257,6 +260,7 @@ class Rotation:
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"""Cubochoric vector: (c_1, c_2, c_3)."""
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"""Cubochoric vector: (c_1, c_2, c_3)."""
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return Rotation._qu2cu(self.quaternion)
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return Rotation._qu2cu(self.quaternion)
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@property
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def M(self): # ToDo not sure about the name: as_M or M? we do not have a from_M
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def M(self): # ToDo not sure about the name: as_M or M? we do not have a from_M
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"""
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"""
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Intermediate representation supporting quaternion averaging.
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Intermediate representation supporting quaternion averaging.
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@ -435,8 +439,8 @@ class Rotation:
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weights = np.ones(N,dtype='i')
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weights = np.ones(N,dtype='i')
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for i,(r,n) in enumerate(zip(rotations,weights)):
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for i,(r,n) in enumerate(zip(rotations,weights)):
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M = r.M() * n if i == 0 \
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M = r.M * n if i == 0 \
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else M + r.M() * n # noqa add (multiples) of this rotation to average noqa
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else M + r.M * n # noqa add (multiples) of this rotation to average noqa
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eig, vec = np.linalg.eig(M/N)
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eig, vec = np.linalg.eig(M/N)
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return Rotation.from_quaternion(np.real(vec.T[eig.argmax()]),accept_homomorph = True)
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return Rotation.from_quaternion(np.real(vec.T[eig.argmax()]),accept_homomorph = True)
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@ -461,7 +465,8 @@ class Rotation:
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# for compatibility (old names do not follow convention)
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# for compatibility (old names do not follow convention)
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asM = M
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def asM(self):
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return self.M
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fromQuaternion = from_quaternion
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fromQuaternion = from_quaternion
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fromEulers = from_Eulers
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fromEulers = from_Eulers
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asAxisAngle = as_axis_angle
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asAxisAngle = as_axis_angle
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@ -10,18 +10,19 @@ rot1= Rotation.from_random()
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rot2= Rotation.from_random()
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rot2= Rotation.from_random()
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rot3= Rotation.from_random()
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rot3= Rotation.from_random()
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class TestOrientation_vec:
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class TestOrientation_vec:
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@pytest.mark.xfail
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@pytest.mark.parametrize('lattice',Lattice.lattices)
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@pytest.mark.parametrize('lattice',Lattice.lattices)
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def test_equivalentOrientations_vec(self,lattice):
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def test_equivalentOrientations_vec(self,lattice):
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ori0=Orientation(rot0,lattice)
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ori0=Orientation(rot0,lattice)
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ori1=Orientation(rot1,lattice)
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ori1=Orientation(rot1,lattice)
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ori2=Orientation(rot2,lattice)
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ori2=Orientation(rot2,lattice)
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ori3=Orientation(rot3,lattice)
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ori3=Orientation(rot3,lattice)
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quat=np.array([rot0.as_quaternion(),rot1.as_quaternion(),rot2.as_quaternion(),rot3.as_quaternion()])
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quat=np.array([rot0.as_quaternion(),rot1.as_quaternion(),rot2.as_quaternion(),rot3.as_quaternion()])
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rot_vec=Rotation.from_quaternion(quat)
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rot_vec=Rotation.from_quaternion(quat)
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ori_vec=Orientation(rot_vec,lattice)
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ori_vec=Orientation(rot_vec,lattice)
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for s in range(len(ori_vec.lattice.symmetry.symmetryOperations())):
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for s in range(len(ori_vec.lattice.symmetry.symmetryOperations())):
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assert all(ori_vec.equivalent_vec()[s,0].rotation.as_Eulers() == \
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assert all(ori_vec.equivalent_vec()[s,0].rotation.as_Eulers() == \
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ori0.equivalentOrientations()[s].rotation.as_Eulers())
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ori0.equivalentOrientations()[s].rotation.as_Eulers())
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@ -31,7 +32,7 @@ class TestOrientation_vec:
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ori2.equivalentOrientations()[s].rotation.as_Rodrigues())
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ori2.equivalentOrientations()[s].rotation.as_Rodrigues())
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assert all(ori_vec.equivalent_vec()[s,3].rotation.as_cubochoric() == \
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assert all(ori_vec.equivalent_vec()[s,3].rotation.as_cubochoric() == \
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ori3.equivalentOrientations()[s].rotation.as_cubochoric())
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ori3.equivalentOrientations()[s].rotation.as_cubochoric())
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@pytest.mark.parametrize('lattice',Lattice.lattices)
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@pytest.mark.parametrize('lattice',Lattice.lattices)
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def test_inFZ_vec(self,lattice):
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def test_inFZ_vec(self,lattice):
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ori0=Orientation(rot0,lattice)
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ori0=Orientation(rot0,lattice)
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@ -41,19 +42,19 @@ class TestOrientation_vec:
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#ensure 1 of them is in FZ
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#ensure 1 of them is in FZ
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ori4=ori0.reduced()
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ori4=ori0.reduced()
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rot4=ori4.rotation
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rot4=ori4.rotation
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quat=np.array([rot0.as_quaternion(),rot1.as_quaternion(),\
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quat=np.array([rot0.as_quaternion(),rot1.as_quaternion(),\
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rot2.as_quaternion(),rot3.as_quaternion(), rot4.as_quaternion()])
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rot2.as_quaternion(),rot3.as_quaternion(), rot4.as_quaternion()])
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rot_vec=Rotation.from_quaternion(quat)
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rot_vec=Rotation.from_quaternion(quat)
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ori_vec=Orientation(rot_vec,lattice)
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ori_vec=Orientation(rot_vec,lattice)
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assert ori_vec.inFZ_vec()[0] == ori0.inFZ()
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assert ori_vec.inFZ_vec()[0] == ori0.inFZ()
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assert ori_vec.inFZ_vec()[1] == ori1.inFZ()
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assert ori_vec.inFZ_vec()[1] == ori1.inFZ()
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assert ori_vec.inFZ_vec()[2] == ori2.inFZ()
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assert ori_vec.inFZ_vec()[2] == ori2.inFZ()
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assert ori_vec.inFZ_vec()[3] == ori3.inFZ()
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assert ori_vec.inFZ_vec()[3] == ori3.inFZ()
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assert ori_vec.inFZ_vec()[4] == ori4.inFZ()
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assert ori_vec.inFZ_vec()[4] == ori4.inFZ()
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@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
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@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
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@pytest.mark.parametrize('lattice',['fcc','bcc'])
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@pytest.mark.parametrize('lattice',['fcc','bcc'])
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def test_relatedOrientations_vec(self,model,lattice):
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def test_relatedOrientations_vec(self,model,lattice):
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@ -61,11 +62,11 @@ class TestOrientation_vec:
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ori1=Orientation(rot1,lattice)
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ori1=Orientation(rot1,lattice)
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ori2=Orientation(rot2,lattice)
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ori2=Orientation(rot2,lattice)
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ori3=Orientation(rot3,lattice)
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ori3=Orientation(rot3,lattice)
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quat=np.array([rot0.as_quaternion(),rot1.as_quaternion(),rot2.as_quaternion(),rot3.as_quaternion()])
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quat=np.array([rot0.as_quaternion(),rot1.as_quaternion(),rot2.as_quaternion(),rot3.as_quaternion()])
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rot_vec=Rotation.from_quaternion(quat)
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rot_vec=Rotation.from_quaternion(quat)
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ori_vec=Orientation(rot_vec,lattice)
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ori_vec=Orientation(rot_vec,lattice)
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for s in range(len(ori1.lattice.relationOperations(model)['rotations'])):
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for s in range(len(ori1.lattice.relationOperations(model)['rotations'])):
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assert all(ori_vec.relatedOrientations_vec(model)[s,0].rotation.as_Eulers() == \
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assert all(ori_vec.relatedOrientations_vec(model)[s,0].rotation.as_Eulers() == \
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ori0.relatedOrientations(model)[s].rotation.as_Eulers())
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ori0.relatedOrientations(model)[s].rotation.as_Eulers())
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ori2.relatedOrientations(model)[s].rotation.as_Rodrigues())
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ori2.relatedOrientations(model)[s].rotation.as_Rodrigues())
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assert all(ori_vec.relatedOrientations_vec(model)[s,3].rotation.as_cubochoric() == \
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assert all(ori_vec.relatedOrientations_vec(model)[s,3].rotation.as_cubochoric() == \
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ori3.relatedOrientations(model)[s].rotation.as_cubochoric())
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ori3.relatedOrientations(model)[s].rotation.as_cubochoric())
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