simplifications + more tests
This commit is contained in:
Martin Diehl
parent
de8e9b5fc1
commit
e18a5b8a1b
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@ -1,7 +1,5 @@
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import numpy as np
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from . import Rotation
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class Symmetry:
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"""
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@ -29,7 +27,6 @@ class Symmetry:
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raise KeyError(f'Crystal system "{system}" is unknown')
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self.system = system.lower() if isinstance(system,str) else system
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self.lattice = self.system # ToDo: for compatibility
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def __copy__(self):
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@ -219,6 +216,7 @@ class Symmetry:
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return np.ones_like(rho[...,0],dtype=bool)
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#ToDo: IPF color in separate function
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def in_SST(self,vector,proper=False,color=False):
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"""
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Check whether given vector falls into standard stereographic triangle of own symmetry.
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@ -311,9 +309,9 @@ class Symmetry:
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# ******************************************************************************************
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class Lattice: # ToDo: Make a subclass of Symmetry!
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"""
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Lattice system.
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Bravais lattice.
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Currently, this contains only a mapping from Bravais lattice to symmetry
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This contains only a mapping from Bravais lattice to symmetry
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and orientation relationships. It could include twin and slip systems.
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References
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@ -331,7 +329,7 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
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}
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def __init__(self, lattice):
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def __init__(self,lattice,c_over_a=None):
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"""
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New lattice of given type.
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@ -348,17 +346,17 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
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self.system = self.symmetry.system
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self.in_SST = self.symmetry.in_SST
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self.in_FZ = self.symmetry.in_FZ
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self.in_disorientation_SST = self.symmetry.in_disorientation_SST
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def __repr__(self):
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"""Report basic lattice information."""
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return 'Bravais lattice {} ({} symmetry)'.format(self.lattice,self.symmetry)
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return 'Bravais lattice {} ({} crystal system)'.format(self.lattice,self.symmetry)
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# Kurdjomov--Sachs orientation relationship for fcc <-> bcc transformation
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# from S. Morito et al., Journal of Alloys and Compounds 577:s587-s592, 2013
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# also see K. Kitahara et al., Acta Materialia 54:1279-1288, 2006
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KS = {'mapping':{'fcc':0,'bcc':1},
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_KS = {'mapping':{'fcc':0,'bcc':1},
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'planes': np.array([
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[[ 1, 1, 1],[ 0, 1, 1]],
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[[ 1, 1, 1],[ 0, 1, 1]],
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@ -412,7 +410,7 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
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# Greninger--Troiano orientation relationship for fcc <-> bcc transformation
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# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
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GT = {'mapping':{'fcc':0,'bcc':1},
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_GT = {'mapping':{'fcc':0,'bcc':1},
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'planes': np.array([
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[[ 1, 1, 1],[ 1, 0, 1]],
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[[ 1, 1, 1],[ 1, 1, 0]],
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@ -466,7 +464,7 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
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# Greninger--Troiano' orientation relationship for fcc <-> bcc transformation
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# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
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GTprime = {'mapping':{'fcc':0,'bcc':1},
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_GTprime = {'mapping':{'fcc':0,'bcc':1},
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'planes': np.array([
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[[ 7, 17, 17],[ 12, 5, 17]],
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[[ 17, 7, 17],[ 17, 12, 5]],
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@ -520,7 +518,7 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
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# Nishiyama--Wassermann orientation relationship for fcc <-> bcc transformation
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# from H. Kitahara et al., Materials Characterization 54:378-386, 2005
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NW = {'mapping':{'fcc':0,'bcc':1},
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_NW = {'mapping':{'fcc':0,'bcc':1},
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'planes': np.array([
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[[ 1, 1, 1],[ 0, 1, 1]],
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[[ 1, 1, 1],[ 0, 1, 1]],
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@ -550,7 +548,7 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
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# Pitsch orientation relationship for fcc <-> bcc transformation
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# from Y. He et al., Acta Materialia 53:1179-1190, 2005
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Pitsch = {'mapping':{'fcc':0,'bcc':1},
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_Pitsch = {'mapping':{'fcc':0,'bcc':1},
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'planes': np.array([
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[[ 0, 1, 0],[ -1, 0, 1]],
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[[ 0, 0, 1],[ 1, -1, 0]],
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@ -580,7 +578,7 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
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# Bain orientation relationship for fcc <-> bcc transformation
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# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
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Bain = {'mapping':{'fcc':0,'bcc':1},
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_Bain = {'mapping':{'fcc':0,'bcc':1},
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'planes': np.array([
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[[ 1, 0, 0],[ 1, 0, 0]],
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[[ 0, 1, 0],[ 0, 1, 0]],
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@ -590,7 +588,8 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
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[[ 0, 0, 1],[ 1, 0, 1]],
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[[ 1, 0, 0],[ 1, 1, 0]]],dtype='float')}
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def relationOperations(self,model):
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def relation_operations(self,model):
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"""
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Crystallographic orientation relationships for phase transformations.
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@ -612,8 +611,8 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
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https://doi.org/10.1016/j.actamat.2004.11.021
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"""
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models={'KS':self.KS, 'GT':self.GT, 'GT_prime':self.GTprime,
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'NW':self.NW, 'Pitsch': self.Pitsch, 'Bain':self.Bain}
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models={'KS':self._KS, 'GT':self._GT, 'GT_prime':self._GTprime,
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'NW':self._NW, 'Pitsch': self._Pitsch, 'Bain':self._Bain}
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try:
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relationship = models[model]
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except KeyError :
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@ -639,6 +638,8 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
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otherDir = miller[otherDir_id]/ np.linalg.norm(miller[otherDir_id])
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otherMatrix = np.array([otherDir,np.cross(otherPlane,otherDir),otherPlane])
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r['rotations'].append(Rotation.from_matrix(np.dot(otherMatrix.T,myMatrix)))
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r['rotations'].append(np.dot(otherMatrix.T,myMatrix))
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r['rotations'] = np.array(r['rotations'])
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return r
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@ -71,8 +71,8 @@ class Orientation: # ToDo: make subclass of lattice and Rotation?
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r = b*aInv
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for k in range(2):
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r.inverse()
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breaker = self.in_FZ \
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and (not SST or other.lattice.symmetry.inDisorientationSST(r.as_Rodrigues(vector=True)))
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breaker = self.lattice.in_FZ(r.as_Rodrigues(vector=True)) \
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and (not SST or other.lattice.in_disorientation_SST(r.as_Rodrigues(vector=True)))
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if breaker: break
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if breaker: break
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if breaker: break
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@ -90,40 +90,36 @@ class Orientation: # ToDo: make subclass of lattice and Rotation?
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@property
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def equivalent(self):
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"""
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Return orientations which are symmetrically equivalent.
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Orientations which are symmetrically equivalent.
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One dimension (length according to symmetrically equivalent orientations)
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One dimension (length according to number of symmetrically equivalent orientations)
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is added to the left of the Rotation array.
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"""
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s = self.lattice.symmetry.symmetry_operations
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s = s.reshape(s.shape[:1]+(1,)*len(self.rotation.shape)+(4,))
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s = Rotation(np.broadcast_to(s,s.shape[:1]+self.rotation.quaternion.shape))
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o = self.lattice.symmetry.symmetry_operations
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o = o.reshape(o.shape[:1]+(1,)*len(self.rotation.shape)+(4,))
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o = Rotation(np.broadcast_to(o,o.shape[:1]+self.rotation.quaternion.shape))
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r = np.broadcast_to(self.rotation.quaternion,s.shape[:1]+self.rotation.quaternion.shape)
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s = np.broadcast_to(self.rotation.quaternion,o.shape[:1]+self.rotation.quaternion.shape)
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return self.__class__(s@Rotation(r),self.lattice)
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return self.__class__(o@Rotation(s),self.lattice)
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def relatedOrientations_vec(self,model):
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"""List of orientations related by the given orientation relationship."""
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h = self.lattice.relationOperations(model)
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rot= h['rotations']
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op=np.array([o.as_quaternion() for o in rot])
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def related(self,model):
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"""
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Orientations related by the given orientation relationship.
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s = op.reshape(op.shape[:1]+(1,)*len(self.rotation.shape)+(4,))
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s = Rotation(np.broadcast_to(s,s.shape[:1]+self.rotation.quaternion.shape))
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One dimension (length according to number of related orientations)
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is added to the left of the Rotation array.
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r = np.broadcast_to(self.rotation.quaternion,s.shape[:1]+self.rotation.quaternion.shape)
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r = Rotation(r)
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"""
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o = Rotation.from_matrix(self.lattice.relation_operations(model)['rotations']).as_quaternion()
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o = o.reshape(o.shape[:1]+(1,)*len(self.rotation.shape)+(4,))
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o = Rotation(np.broadcast_to(o,o.shape[:1]+self.rotation.quaternion.shape))
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return self.__class__(s@r,h['lattice'])
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s = np.broadcast_to(self.rotation.quaternion,o.shape[:1]+self.rotation.quaternion.shape)
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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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r = self.lattice.relationOperations(model)
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return [self.__class__(o*self.rotation,r['lattice']) for o in r['rotations']]
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return self.__class__(o@Rotation(s),self.lattice.relation_operations(model)['lattice'])
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@property
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@ -136,26 +132,31 @@ class Orientation: # ToDo: make subclass of lattice and Rotation?
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found = np.zeros_like(in_FZ[0],dtype=bool)
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q = self.rotation.quaternion[0]
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for s in range(in_FZ.shape[0]):
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#something fishy... why does q needs to be initialized?
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q = np.where(np.expand_dims(np.logical_and(in_FZ[s],~found),-1),eq.rotation.quaternion[s],q)
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found = np.logical_or(in_FZ[s],found)
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return self.__class__(q,self.lattice)
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# ToDo: vectorize
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def inversePole(self,
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axis,
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proper = False,
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SST = True):
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def inverse_pole(self,axis,proper=False,SST=True):
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"""Axis rotated according to orientation (using crystal symmetry to ensure location falls into SST)."""
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if SST: # pole requested to be within SST
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for i,o in enumerate(self.equivalent): # test all symmetric equivalent quaternions
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pole = o.rotation@axis # align crystal direction to axis
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if self.lattice.in_SST(pole,proper): break # found SST version
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else:
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pole = self.rotation@axis # align crystal direction to axis
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if SST:
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eq = self.equivalent
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pole = eq.rotation @ np.broadcast_to(axis/np.linalg.norm(axis),eq.rotation.shape+(3,))
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in_SST = self.lattice.in_SST(pole,proper=proper)
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# remove duplicates (occur for highly symmetric orientations)
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found = np.zeros_like(in_SST[0],dtype=bool)
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p = pole[0]
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for s in range(in_SST.shape[0]):
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p = np.where(np.expand_dims(np.logical_and(in_SST[s],~found),-1),pole[s],p)
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found = np.logical_or(in_SST[s],found)
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return p
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else:
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return self.rotation @ np.broadcast_to(axis/np.linalg.norm(axis),self.rotation.shape+(3,))
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return (pole,i if SST else 0)
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def IPF_color(self,axis): #ToDo axis or direction?
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@ -166,7 +167,7 @@ class Orientation: # ToDo: make subclass of lattice and Rotation?
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# remove duplicates (occur for highly symmetric orientations)
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found = np.zeros_like(in_SST[0],dtype=bool)
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c = np.empty(color.shape[1:])
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c = color[0]
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for s in range(in_SST.shape[0]):
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c = np.where(np.expand_dims(np.logical_and(in_SST[s],~found),-1),color[s],c)
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found = np.logical_or(in_SST[s],found)
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@ -28,6 +28,22 @@ def reference_dir(reference_dir_base):
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class TestOrientation:
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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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def test_relationship_vectorize(self,set_of_quaternions,lattice,model):
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result = Orientation(set_of_quaternions[:200].reshape(50,4,4),lattice).related(model)
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ref_qu = result.rotation.quaternion.reshape(-1,200,4)
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for i in range(200):
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single = Orientation(set_of_quaternions[i],lattice).related(model).rotation.quaternion
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assert np.allclose(ref_qu[:,i,:],single)
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@pytest.mark.parametrize('lattice',Lattice.lattices)
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def test_IPF_vectorize(self,set_of_quaternions,lattice):
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direction = np.random.random(3)*2.0-1
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oris = Orientation(Rotation(set_of_quaternions),lattice)[:200]
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for i,color in enumerate(oris.IPF_color(direction)):
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assert np.allclose(color,IPF_color(oris[i],direction))
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@pytest.mark.parametrize('color',[{'label':'red', 'RGB':[1,0,0],'direction':[0,0,1]},
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{'label':'green','RGB':[0,1,0],'direction':[0,1,1]},
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{'label':'blue', 'RGB':[0,0,1],'direction':[1,1,1]}])
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@ -45,15 +61,6 @@ class TestOrientation:
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for equivalent in ori.equivalent:
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assert np.allclose(color,equivalent.IPF_color(direction))
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@pytest.mark.parametrize('lattice',Lattice.lattices)
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def test_IPF_vectorize(self,set_of_quaternions,lattice):
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direction = np.random.random(3)*2.0-1
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oris = Orientation(Rotation(set_of_quaternions),lattice)[:200]
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for i,color in enumerate(oris.IPF_color(direction)):
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assert np.allclose(color,IPF_color(oris[i],direction))
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@pytest.mark.parametrize('lattice',Lattice.lattices)
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def test_reduced(self,set_of_quaternions,lattice):
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oris = Orientation(Rotation(set_of_quaternions),lattice)
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@ -65,8 +72,8 @@ class TestOrientation:
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@pytest.mark.parametrize('lattice',['fcc','bcc'])
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def test_relationship_forward_backward(self,model,lattice):
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ori = Orientation(Rotation.from_random(),lattice)
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for i,r in enumerate(ori.relatedOrientations(model)):
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ori2 = r.relatedOrientations(model)[i]
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for i,r in enumerate(ori.related(model)):
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ori2 = r.related(model)[i]
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misorientation = ori.rotation.misorientation(ori2.rotation)
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assert misorientation.asAxisAngle(degrees=True)[3]<1.0e-5
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@ -75,7 +82,7 @@ class TestOrientation:
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def test_relationship_reference(self,update,reference_dir,model,lattice):
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reference = os.path.join(reference_dir,'{}_{}.txt'.format(lattice,model))
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ori = Orientation(Rotation(),lattice)
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eu = np.array([o.rotation.as_Eulers(degrees=True) for o in ori.relatedOrientations(model)])
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eu = np.array([o.rotation.as_Eulers(degrees=True) for o in ori.related(model)])
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if update:
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coords = np.array([(1,i+1) for i,x in enumerate(eu)])
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table = damask.Table(eu,{'Eulers':(3,)})
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@ -1,41 +0,0 @@
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import pytest
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import numpy as np
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from damask import Rotation
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from damask import Orientation
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from damask import Lattice
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rot0= Rotation.from_random()
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rot1= Rotation.from_random()
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rot2= Rotation.from_random()
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rot3= Rotation.from_random()
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#disorientation
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#fromaverage
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#average
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class TestOrientation_vec:
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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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def test_relatedOrientations_vec(self,model,lattice):
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ori0=Orientation(rot0,lattice)
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ori1=Orientation(rot1,lattice)
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ori2=Orientation(rot2,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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ori_vec=Orientation(quat,lattice)
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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).rotation.as_Eulers()[s,0] == \
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ori0.relatedOrientations(model)[s].rotation.as_Eulers())
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assert all(ori_vec.relatedOrientations_vec(model).rotation.as_quaternion()[s,1] == \
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ori1.relatedOrientations(model)[s].rotation.as_quaternion())
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assert all(ori_vec.relatedOrientations_vec(model).rotation.as_Rodrigues()[s,2] == \
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ori2.relatedOrientations(model)[s].rotation.as_Rodrigues())
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assert all(ori_vec.relatedOrientations_vec(model).rotation.as_cubochoric()[s,3] == \
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ori3.relatedOrientations(model)[s].rotation.as_cubochoric())
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