1304 lines
57 KiB
Python
1304 lines
57 KiB
Python
import inspect
|
||
|
||
import numpy as np
|
||
|
||
from . import Rotation
|
||
from . import util
|
||
from . import tensor
|
||
|
||
_parameter_doc = \
|
||
"""lattice : str
|
||
Either a crystal family out of [triclinic, monoclinic, orthorhombic, tetragonal, hexagonal, cubic]
|
||
or a Bravais lattice out of [aP, mP, mS, oP, oS, oI, oF, tP, tI, hP, cP, cI, cF].
|
||
When specifying a Bravais lattice, additional lattice parameters might be required:
|
||
a : float, optional
|
||
Length of lattice parameter "a".
|
||
b : float, optional
|
||
Length of lattice parameter "b".
|
||
c : float, optional
|
||
Length of lattice parameter "c".
|
||
alpha : float, optional
|
||
Angle between b and c lattice basis.
|
||
beta : float, optional
|
||
Angle between c and a lattice basis.
|
||
gamma : float, optional
|
||
Angle between a and b lattice basis.
|
||
degrees : bool, optional
|
||
Angles are given in degrees. Defaults to False.
|
||
|
||
"""
|
||
|
||
|
||
class Orientation(Rotation):
|
||
"""
|
||
Representation of crystallographic orientation as combination of rotation and either crystal family or Bravais lattice.
|
||
|
||
The crystal family is one of Orientation.crystal_families:
|
||
|
||
- triclinic
|
||
- monoclinic
|
||
- orthorhombic
|
||
- tetragonal
|
||
- hexagonal
|
||
- cubic
|
||
|
||
and enables symmetry-related operations such as
|
||
"equivalent", "reduced", "disorientation", "IPF_color", or "to_SST".
|
||
|
||
The Bravais lattice is one of Orientation.lattice_symmetries:
|
||
|
||
- aP : triclinic primitive
|
||
- mP : monoclinic primitive
|
||
- mS : ... base-centered
|
||
- oP : orthorhombic primitive
|
||
- oS : ... base-centered
|
||
- oI : ... body-centered
|
||
- oF : ... face-centered
|
||
- tP : tetragonal primitive
|
||
- tI : ... body-centered
|
||
- hP : hexagonal primitive
|
||
- cP : cubic primitive
|
||
- cI : ... body-centered
|
||
- cF : ... face-centered
|
||
|
||
and inherits the corresponding crystal family.
|
||
Specifying a Bravais lattice, compared to just the crystal family,
|
||
extends the functionality of Orientation objects to include operations such as
|
||
"Schmid", "related", or "to_pole" that require a lattice type and its parameters.
|
||
|
||
Examples
|
||
--------
|
||
An array of 3 x 5 random orientations reduced to the fundamental zone of tetragonal symmetry:
|
||
|
||
>>> damask.Orientation.from_random(shape=(3,5),lattice='tetragonal').reduced
|
||
|
||
"""
|
||
|
||
crystal_families = ['triclinic',
|
||
'monoclinic',
|
||
'orthorhombic',
|
||
'tetragonal',
|
||
'hexagonal',
|
||
'cubic']
|
||
|
||
lattice_symmetries = {
|
||
'aP': 'triclinic',
|
||
|
||
'mP': 'monoclinic',
|
||
'mS': 'monoclinic',
|
||
|
||
'oP': 'orthorhombic',
|
||
'oS': 'orthorhombic',
|
||
'oI': 'orthorhombic',
|
||
'oF': 'orthorhombic',
|
||
|
||
'tP': 'tetragonal',
|
||
'tI': 'tetragonal',
|
||
|
||
'hP': 'hexagonal',
|
||
|
||
'cP': 'cubic',
|
||
'cI': 'cubic',
|
||
'cF': 'cubic',
|
||
}
|
||
|
||
|
||
@util.extend_docstring(_parameter_doc)
|
||
def __init__(self,
|
||
rotation = None,
|
||
lattice = None,
|
||
a = None,b = None,c = None,
|
||
alpha = None,beta = None,gamma = None,
|
||
degrees = False):
|
||
"""
|
||
Initialize orientation object.
|
||
|
||
Parameters
|
||
----------
|
||
rotation : list, numpy.ndarray, Rotation, optional
|
||
Unit quaternion in positive real hemisphere.
|
||
Use .from_quaternion to perform a sanity check.
|
||
Defaults to no rotation.
|
||
|
||
"""
|
||
from damask.lattice import kinematics
|
||
|
||
Rotation.__init__(self) if rotation is None else Rotation.__init__(self,rotation=rotation)
|
||
|
||
if ( lattice is not None
|
||
and lattice not in self.lattice_symmetries
|
||
and lattice not in self.crystal_families):
|
||
raise KeyError(f'Lattice "{lattice}" is unknown')
|
||
|
||
self.family = None
|
||
self.lattice = None
|
||
self.a = None
|
||
self.b = None
|
||
self.c = None
|
||
self.alpha = None
|
||
self.beta = None
|
||
self.gamma = None
|
||
self.kinematics = None
|
||
|
||
if lattice in self.lattice_symmetries:
|
||
self.family = self.lattice_symmetries[lattice]
|
||
self.lattice = lattice
|
||
self.a = 1 if a is None else a
|
||
self.b = b
|
||
self.c = c
|
||
self.alpha = (np.radians(alpha) if degrees else alpha) if alpha is not None else None
|
||
self.beta = (np.radians(beta) if degrees else beta) if beta is not None else None
|
||
self.gamma = (np.radians(gamma) if degrees else gamma) if gamma is not None else None
|
||
|
||
self.a = float(self.a) if self.a is not None else \
|
||
(self.b / self.ratio['b'] if self.b is not None and self.ratio['b'] is not None else
|
||
self.c / self.ratio['c'] if self.c is not None and self.ratio['c'] is not None else None)
|
||
self.b = float(self.b) if self.b is not None else \
|
||
(self.a * self.ratio['b'] if self.a is not None and self.ratio['b'] is not None else
|
||
self.c / self.ratio['c'] * self.ratio['b']
|
||
if self.c is not None and self.ratio['b'] is not None and self.ratio['c'] is not None else None)
|
||
self.c = float(self.c) if self.c is not None else \
|
||
(self.a * self.ratio['c'] if self.a is not None and self.ratio['c'] is not None else
|
||
self.b / self.ratio['b'] * self.ratio['c']
|
||
if self.c is not None and self.ratio['b'] is not None and self.ratio['c'] is not None else None)
|
||
self.alpha = self.alpha if self.alpha is not None else self.immutable['alpha'] if 'alpha' in self.immutable else None
|
||
self.beta = self.beta if self.beta is not None else self.immutable['beta'] if 'beta' in self.immutable else None
|
||
self.gamma = self.gamma if self.gamma is not None else self.immutable['gamma'] if 'gamma' in self.immutable else None
|
||
|
||
if \
|
||
(self.a is None) \
|
||
or (self.b is None or ('b' in self.immutable and self.b != self.immutable['b'] * self.a)) \
|
||
or (self.c is None or ('c' in self.immutable and self.c != self.immutable['c'] * self.b)) \
|
||
or (self.alpha is None or ('alpha' in self.immutable and self.alpha != self.immutable['alpha'])) \
|
||
or (self.beta is None or ( 'beta' in self.immutable and self.beta != self.immutable['beta'])) \
|
||
or (self.gamma is None or ('gamma' in self.immutable and self.gamma != self.immutable['gamma'])):
|
||
raise ValueError (f'Incompatible parameters {self.parameters} for crystal family {self.family}')
|
||
|
||
if np.any(np.array([self.alpha,self.beta,self.gamma]) <= 0):
|
||
raise ValueError ('Lattice angles must be positive')
|
||
if np.any([np.roll([self.alpha,self.beta,self.gamma],r)[0]
|
||
> np.sum(np.roll([self.alpha,self.beta,self.gamma],r)[1:]) for r in range(3)]):
|
||
raise ValueError ('Each lattice angle must be less than sum of others')
|
||
|
||
if self.lattice in kinematics:
|
||
master = kinematics[self.lattice]
|
||
self.kinematics = {}
|
||
for m in master:
|
||
self.kinematics[m] = {'direction':master[m][:,0:3],'plane':master[m][:,3:6]} \
|
||
if master[m].shape[-1] == 6 else \
|
||
{'direction':self.Bravais_to_Miller(uvtw=master[m][:,0:4]),
|
||
'plane': self.Bravais_to_Miller(hkil=master[m][:,4:8])}
|
||
elif lattice in self.crystal_families:
|
||
self.family = lattice
|
||
|
||
|
||
def __repr__(self):
|
||
"""Represent."""
|
||
return '\n'.join(([] if self.lattice is None else [f'Bravais lattice {self.lattice}'])
|
||
+ ([] if self.family is None else [f'Crystal family {self.family}'])
|
||
+ [super().__repr__()])
|
||
|
||
|
||
def __copy__(self,**kwargs):
|
||
"""Create deep copy."""
|
||
return self.__class__(rotation=kwargs['rotation'] if 'rotation' in kwargs else self.quaternion,
|
||
lattice =kwargs['lattice'] if 'lattice' in kwargs else self.lattice
|
||
if self.lattice is not None else self.family,
|
||
a =kwargs['a'] if 'a' in kwargs else self.a,
|
||
b =kwargs['b'] if 'b' in kwargs else self.b,
|
||
c =kwargs['c'] if 'c' in kwargs else self.c,
|
||
alpha =kwargs['alpha'] if 'alpha' in kwargs else self.alpha,
|
||
beta =kwargs['beta'] if 'beta' in kwargs else self.beta,
|
||
gamma =kwargs['gamma'] if 'gamma' in kwargs else self.gamma,
|
||
degrees =kwargs['degrees'] if 'degrees' in kwargs else None,
|
||
)
|
||
|
||
copy = __copy__
|
||
|
||
|
||
def __eq__(self,other):
|
||
"""
|
||
Equal to other.
|
||
|
||
Parameters
|
||
----------
|
||
other : Orientation
|
||
Orientation to check for equality.
|
||
|
||
"""
|
||
matching_type = all([hasattr(other,attr) and getattr(self,attr) == getattr(other,attr)
|
||
for attr in ['family','lattice','parameters']])
|
||
return np.logical_and(super().__eq__(other),matching_type)
|
||
|
||
def __ne__(self,other):
|
||
"""
|
||
Not equal to other.
|
||
|
||
Parameters
|
||
----------
|
||
other : Orientation
|
||
Orientation to check for equality.
|
||
|
||
"""
|
||
return np.logical_not(self==other)
|
||
|
||
|
||
def __mul__(self,other):
|
||
"""
|
||
Compose this orientation with other.
|
||
|
||
Parameters
|
||
----------
|
||
other : Rotation or Orientation
|
||
Object for composition.
|
||
|
||
Returns
|
||
-------
|
||
composition : Orientation
|
||
Compound rotation self*other, i.e. first other then self rotation.
|
||
|
||
"""
|
||
if isinstance(other,Orientation) or isinstance(other,Rotation):
|
||
return self.copy(rotation=Rotation.__mul__(self,Rotation(other.quaternion)))
|
||
else:
|
||
raise TypeError('Use "O@b", i.e. matmul, to apply Orientation "O" to object "b"')
|
||
|
||
|
||
@staticmethod
|
||
def _split_kwargs(kwargs,target):
|
||
"""
|
||
Separate keyword arguments in 'kwargs' targeted at 'target' from general keyword arguments of Orientation objects.
|
||
|
||
Parameters
|
||
----------
|
||
kwargs : dictionary
|
||
Contains all **kwargs.
|
||
target: method
|
||
Function to scan for kwarg signature.
|
||
|
||
Returns
|
||
-------
|
||
rot_kwargs: dictionary
|
||
Valid keyword arguments of 'target' function of Rotation class.
|
||
ori_kwargs: dictionary
|
||
Valid keyword arguments of Orientation object.
|
||
|
||
"""
|
||
kws = ()
|
||
for t in (target,Orientation.__init__):
|
||
kws += ({key: kwargs[key] for key in set(inspect.signature(t).parameters) & set(kwargs)},)
|
||
|
||
invalid_keys = set(kwargs)-(set(kws[0])|set(kws[1]))
|
||
if invalid_keys:
|
||
raise TypeError(f"{inspect.stack()[1][3]}() got an unexpected keyword argument '{invalid_keys.pop()}'")
|
||
|
||
return kws
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_random,_parameter_doc)
|
||
def from_random(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_random)
|
||
return cls(rotation=Rotation.from_random(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_quaternion,_parameter_doc)
|
||
def from_quaternion(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_quaternion)
|
||
return cls(rotation=Rotation.from_quaternion(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_Euler_angles,_parameter_doc)
|
||
def from_Euler_angles(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_Euler_angles)
|
||
return cls(rotation=Rotation.from_Euler_angles(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_axis_angle,_parameter_doc)
|
||
def from_axis_angle(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_axis_angle)
|
||
return cls(rotation=Rotation.from_axis_angle(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_basis,_parameter_doc)
|
||
def from_basis(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_basis)
|
||
return cls(rotation=Rotation.from_basis(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_matrix,_parameter_doc)
|
||
def from_matrix(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_matrix)
|
||
return cls(rotation=Rotation.from_matrix(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_Rodrigues_vector,_parameter_doc)
|
||
def from_Rodrigues_vector(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_Rodrigues_vector)
|
||
return cls(rotation=Rotation.from_Rodrigues_vector(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_homochoric,_parameter_doc)
|
||
def from_homochoric(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_homochoric)
|
||
return cls(rotation=Rotation.from_homochoric(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_cubochoric,_parameter_doc)
|
||
def from_cubochoric(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_cubochoric)
|
||
return cls(rotation=Rotation.from_cubochoric(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_spherical_component,_parameter_doc)
|
||
def from_spherical_component(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_spherical_component)
|
||
return cls(rotation=Rotation.from_spherical_component(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extended_docstring(Rotation.from_fiber_component,_parameter_doc)
|
||
def from_fiber_component(cls,**kwargs):
|
||
kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_fiber_component)
|
||
return cls(rotation=Rotation.from_fiber_component(**kwargs_rot),**kwargs_ori)
|
||
|
||
|
||
@classmethod
|
||
@util.extend_docstring(_parameter_doc)
|
||
def from_directions(cls,uvw,hkl,**kwargs):
|
||
"""
|
||
Initialize orientation object from two crystallographic directions.
|
||
|
||
Parameters
|
||
----------
|
||
uvw : list, numpy.ndarray of shape (...,3)
|
||
lattice direction aligned with lab frame x-direction.
|
||
hkl : list, numpy.ndarray of shape (...,3)
|
||
lattice plane normal aligned with lab frame z-direction.
|
||
|
||
"""
|
||
o = cls(**kwargs)
|
||
x = o.to_frame(uvw=uvw)
|
||
z = o.to_frame(hkl=hkl)
|
||
om = np.stack([x,np.cross(z,x),z],axis=-2)
|
||
return o.copy(rotation=Rotation.from_matrix(tensor.transpose(om/np.linalg.norm(om,axis=-1,keepdims=True))))
|
||
|
||
|
||
@property
|
||
def symmetry_operations(self):
|
||
"""Symmetry operations as Rotations."""
|
||
if self.family == 'cubic':
|
||
sym_quats = [
|
||
[ 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, 0.0, 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, 0.5*np.sqrt(2) ],
|
||
[ 0.0, 0.5*np.sqrt(2), 0.0, -0.5*np.sqrt(2) ],
|
||
[ 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, 0.5, 0.5, 0.5 ],
|
||
[-0.5, 0.5, 0.5, 0.5 ],
|
||
[-0.5, 0.5, 0.5, -0.5 ],
|
||
[-0.5, 0.5, -0.5, 0.5 ],
|
||
[-0.5, -0.5, 0.5, 0.5 ],
|
||
[-0.5, -0.5, 0.5, -0.5 ],
|
||
[-0.5, -0.5, -0.5, 0.5 ],
|
||
[-0.5, 0.5, -0.5, -0.5 ],
|
||
[-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) ],
|
||
[-0.5*np.sqrt(2), 0.0, 0.5*np.sqrt(2), 0.0 ],
|
||
[-0.5*np.sqrt(2), 0.0, -0.5*np.sqrt(2), 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, 0.0 ],
|
||
]
|
||
elif self.family == 'hexagonal':
|
||
sym_quats = [
|
||
[ 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 ],
|
||
]
|
||
elif self.family == 'tetragonal':
|
||
sym_quats = [
|
||
[ 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) ],
|
||
]
|
||
elif self.family == 'orthorhombic':
|
||
sym_quats = [
|
||
[ 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 ],
|
||
]
|
||
elif self.family == 'monoclinic':
|
||
sym_quats = [
|
||
[ 1.0,0.0,0.0,0.0 ],
|
||
[ 0.0,0.0,1.0,0.0 ],
|
||
]
|
||
elif self.family == 'triclinic':
|
||
sym_quats = [
|
||
[ 1.0,0.0,0.0,0.0 ],
|
||
]
|
||
else:
|
||
raise KeyError(f'Crystal family "{self.family}" is unknown')
|
||
|
||
return Rotation.from_quaternion(sym_quats,accept_homomorph=True)
|
||
|
||
|
||
@property
|
||
def equivalent(self):
|
||
"""
|
||
Orientations that are symmetrically equivalent.
|
||
|
||
One dimension (length corresponds to number of symmetrically equivalent orientations)
|
||
is added to the left of the Rotation array.
|
||
|
||
"""
|
||
if self.family is None:
|
||
raise ValueError('Missing crystal symmetry')
|
||
|
||
o = self.symmetry_operations.broadcast_to(self.symmetry_operations.shape+self.shape,mode='right')
|
||
return self.copy(rotation=o*Rotation(self.quaternion).broadcast_to(o.shape,mode='left'))
|
||
|
||
|
||
@property
|
||
def reduced(self):
|
||
"""Select symmetrically equivalent orientation that falls into fundamental zone according to symmetry."""
|
||
if self.family is None:
|
||
raise ValueError('Missing crystal symmetry')
|
||
|
||
eq = self.equivalent
|
||
ok = eq.in_FZ
|
||
ok &= np.cumsum(ok,axis=0) == 1
|
||
loc = np.where(ok)
|
||
sort = 0 if len(loc) == 1 else np.lexsort(loc[:0:-1])
|
||
return eq[ok][sort].reshape(self.shape)
|
||
|
||
|
||
@property
|
||
def in_FZ(self):
|
||
"""
|
||
Check whether orientation falls into fundamental zone of own symmetry.
|
||
|
||
Returns
|
||
-------
|
||
in : numpy.ndarray of quaternion.shape
|
||
Boolean array indicating whether Rodrigues-Frank vector falls into fundamental zone.
|
||
|
||
Notes
|
||
-----
|
||
Fundamental zones in Rodrigues space are point-symmetric around origin.
|
||
|
||
References
|
||
----------
|
||
A. Heinz and P. Neumann, Acta Crystallographica Section A 47:780-789, 1991
|
||
https://doi.org/10.1107/S0108767391006864
|
||
|
||
"""
|
||
if self.family is None:
|
||
raise ValueError('Missing crystal symmetry')
|
||
|
||
rho_abs = np.abs(self.as_Rodrigues_vector(compact=True))*(1.-1.e-9)
|
||
|
||
with np.errstate(invalid='ignore'):
|
||
# using '*'/prod for 'and'
|
||
if self.family == 'cubic':
|
||
return (np.prod(np.sqrt(2)-1. >= rho_abs,axis=-1) *
|
||
(1. >= np.sum(rho_abs,axis=-1))).astype(bool)
|
||
elif self.family == 'hexagonal':
|
||
return (np.prod(1. >= rho_abs,axis=-1) *
|
||
(2. >= np.sqrt(3)*rho_abs[...,0] + rho_abs[...,1]) *
|
||
(2. >= np.sqrt(3)*rho_abs[...,1] + rho_abs[...,0]) *
|
||
(2. >= np.sqrt(3) + rho_abs[...,2])).astype(bool)
|
||
elif self.family == 'tetragonal':
|
||
return (np.prod(1. >= rho_abs[...,:2],axis=-1) *
|
||
(np.sqrt(2) >= rho_abs[...,0] + rho_abs[...,1]) *
|
||
(np.sqrt(2) >= rho_abs[...,2] + 1.)).astype(bool)
|
||
elif self.family == 'orthorhombic':
|
||
return (np.prod(1. >= rho_abs,axis=-1)).astype(bool)
|
||
elif self.family == 'monoclinic':
|
||
return (1. >= rho_abs[...,1]).astype(bool)
|
||
else:
|
||
return np.all(np.isfinite(rho_abs),axis=-1)
|
||
|
||
|
||
@property
|
||
def in_disorientation_FZ(self):
|
||
"""
|
||
Check whether orientation falls into fundamental zone of disorientations.
|
||
|
||
Returns
|
||
-------
|
||
in : numpy.ndarray of quaternion.shape
|
||
Boolean array indicating whether Rodrigues-Frank vector falls into disorientation FZ.
|
||
|
||
References
|
||
----------
|
||
A. Heinz and P. Neumann, Acta Crystallographica Section A 47:780-789, 1991
|
||
https://doi.org/10.1107/S0108767391006864
|
||
|
||
"""
|
||
if self.family is None:
|
||
raise ValueError('Missing crystal symmetry')
|
||
|
||
rho = self.as_Rodrigues_vector(compact=True)*(1.0-1.0e-9)
|
||
|
||
with np.errstate(invalid='ignore'):
|
||
if self.family == 'cubic':
|
||
return ((rho[...,0] >= rho[...,1]) &
|
||
(rho[...,1] >= rho[...,2]) &
|
||
(rho[...,2] >= 0)).astype(bool)
|
||
elif self.family == 'hexagonal':
|
||
return ((rho[...,0] >= rho[...,1]*np.sqrt(3)) &
|
||
(rho[...,1] >= 0) &
|
||
(rho[...,2] >= 0)).astype(bool)
|
||
elif self.family == 'tetragonal':
|
||
return ((rho[...,0] >= rho[...,1]) &
|
||
(rho[...,1] >= 0) &
|
||
(rho[...,2] >= 0)).astype(bool)
|
||
elif self.family == 'orthorhombic':
|
||
return ((rho[...,0] >= 0) &
|
||
(rho[...,1] >= 0) &
|
||
(rho[...,2] >= 0)).astype(bool)
|
||
elif self.family == 'monoclinic':
|
||
return ((rho[...,1] >= 0) &
|
||
(rho[...,2] >= 0)).astype(bool)
|
||
else:
|
||
return np.ones_like(rho[...,0],dtype=bool)
|
||
|
||
|
||
def relation_operations(self,model,return_lattice=False):
|
||
"""
|
||
Crystallographic orientation relationships for phase transformations.
|
||
|
||
Parameters
|
||
----------
|
||
model : str
|
||
Name of orientation relationship.
|
||
return_lattice : bool, optional
|
||
Return the target lattice in addition.
|
||
|
||
Returns
|
||
-------
|
||
operations : Rotations
|
||
Rotations characterizing the orientation relationship.
|
||
|
||
References
|
||
----------
|
||
S. Morito et al., Journal of Alloys and Compounds 577:s587-s592, 2013
|
||
https://doi.org/10.1016/j.jallcom.2012.02.004
|
||
|
||
K. Kitahara et al., Acta Materialia 54(5):1279-1288, 2006
|
||
https://doi.org/10.1016/j.actamat.2005.11.001
|
||
|
||
Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
|
||
https://doi.org/10.1107/S0021889805038276
|
||
|
||
H. Kitahara et al., Materials Characterization 54(4-5):378-386, 2005
|
||
https://doi.org/10.1016/j.matchar.2004.12.015
|
||
|
||
Y. He et al., Acta Materialia 53(4):1179-1190, 2005
|
||
https://doi.org/10.1016/j.actamat.2004.11.021
|
||
|
||
"""
|
||
from damask.lattice import relations
|
||
|
||
if model not in relations:
|
||
raise KeyError(f'Orientation relationship "{model}" is unknown')
|
||
r = relations[model]
|
||
|
||
if self.lattice not in r:
|
||
raise KeyError(f'Relationship "{model}" not supported for lattice "{self.lattice}"')
|
||
|
||
sl = self.lattice
|
||
ol = (set(r)-{sl}).pop()
|
||
m = r[sl]
|
||
o = r[ol]
|
||
|
||
p_,_p = np.zeros(m.shape[:-1]+(3,)),np.zeros(o.shape[:-1]+(3,))
|
||
p_[...,0,:] = m[...,0,:] if m.shape[-1] == 3 else self.Bravais_to_Miller(uvtw=m[...,0,0:4])
|
||
p_[...,1,:] = m[...,1,:] if m.shape[-1] == 3 else self.Bravais_to_Miller(hkil=m[...,1,0:4])
|
||
_p[...,0,:] = o[...,0,:] if o.shape[-1] == 3 else self.Bravais_to_Miller(uvtw=o[...,0,0:4])
|
||
_p[...,1,:] = o[...,1,:] if o.shape[-1] == 3 else self.Bravais_to_Miller(hkil=o[...,1,0:4])
|
||
|
||
return (Rotation.from_parallel(p_,_p),ol) \
|
||
if return_lattice else \
|
||
Rotation.from_parallel(p_,_p)
|
||
|
||
|
||
def related(self,model):
|
||
"""
|
||
Orientations derived from the given relationship.
|
||
|
||
One dimension (length according to number of related orientations)
|
||
is added to the left of the Rotation array.
|
||
|
||
"""
|
||
o,lattice = self.relation_operations(model,return_lattice=True)
|
||
target = Orientation(lattice=lattice)
|
||
o = o.broadcast_to(o.shape+self.shape,mode='right')
|
||
return self.copy(rotation=o*Rotation(self.quaternion).broadcast_to(o.shape,mode='left'),
|
||
lattice=lattice,
|
||
b = self.b if target.ratio['b'] is None else self.a*target.ratio['b'],
|
||
c = self.c if target.ratio['c'] is None else self.a*target.ratio['c'],
|
||
alpha = None if 'alpha' in target.immutable else self.alpha,
|
||
beta = None if 'beta' in target.immutable else self.beta,
|
||
gamma = None if 'gamma' in target.immutable else self.gamma,
|
||
)
|
||
|
||
|
||
@property
|
||
def parameters(self):
|
||
"""Return lattice parameters a, b, c, alpha, beta, gamma."""
|
||
return (self.a,self.b,self.c,self.alpha,self.beta,self.gamma)
|
||
|
||
|
||
@property
|
||
def immutable(self):
|
||
"""Return immutable parameters of own lattice."""
|
||
if self.family == 'triclinic':
|
||
return {}
|
||
if self.family == 'monoclinic':
|
||
return {
|
||
'alpha': np.pi/2.,
|
||
'gamma': np.pi/2.,
|
||
}
|
||
if self.family == 'orthorhombic':
|
||
return {
|
||
'alpha': np.pi/2.,
|
||
'beta': np.pi/2.,
|
||
'gamma': np.pi/2.,
|
||
}
|
||
if self.family == 'tetragonal':
|
||
return {
|
||
'b': 1.0,
|
||
'alpha': np.pi/2.,
|
||
'beta': np.pi/2.,
|
||
'gamma': np.pi/2.,
|
||
}
|
||
if self.family == 'hexagonal':
|
||
return {
|
||
'b': 1.0,
|
||
'alpha': np.pi/2.,
|
||
'beta': np.pi/2.,
|
||
'gamma': 2.*np.pi/3.,
|
||
}
|
||
if self.family == 'cubic':
|
||
return {
|
||
'b': 1.0,
|
||
'c': 1.0,
|
||
'alpha': np.pi/2.,
|
||
'beta': np.pi/2.,
|
||
'gamma': np.pi/2.,
|
||
}
|
||
else:
|
||
raise KeyError(f'Crystal family "{self.family}" is unknown')
|
||
|
||
|
||
@property
|
||
def ratio(self):
|
||
"""Return axes ratios of own lattice."""
|
||
_ratio = { 'hexagonal': {'c': np.sqrt(8./3.)}}
|
||
|
||
return dict(b = self.immutable['b']
|
||
if 'b' in self.immutable else
|
||
_ratio[self.family]['b'] if self.family in _ratio and 'b' in _ratio[self.family] else None,
|
||
c = self.immutable['c']
|
||
if 'c' in self.immutable else
|
||
_ratio[self.family]['c'] if self.family in _ratio and 'c' in _ratio[self.family] else None,
|
||
)
|
||
|
||
|
||
@property
|
||
def basis_real(self):
|
||
"""
|
||
Calculate orthogonal real space crystal basis.
|
||
|
||
References
|
||
----------
|
||
C.T. Young and J.L. Lytton, Journal of Applied Physics 43:1408–1417, 1972
|
||
https://doi.org/10.1063/1.1661333
|
||
|
||
"""
|
||
if None in self.parameters:
|
||
raise KeyError('Missing crystal lattice parameters')
|
||
return np.array([
|
||
[1,0,0],
|
||
[np.cos(self.gamma),np.sin(self.gamma),0],
|
||
[np.cos(self.beta),
|
||
(np.cos(self.alpha)-np.cos(self.beta)*np.cos(self.gamma)) /np.sin(self.gamma),
|
||
np.sqrt(1 - np.cos(self.alpha)**2 - np.cos(self.beta)**2 - np.cos(self.gamma)**2
|
||
+ 2 * np.cos(self.alpha) * np.cos(self.beta) * np.cos(self.gamma))/np.sin(self.gamma)],
|
||
],dtype=float).T \
|
||
* np.array([self.a,self.b,self.c])
|
||
|
||
|
||
@property
|
||
def basis_reciprocal(self):
|
||
"""Calculate reciprocal (dual) crystal basis."""
|
||
return np.linalg.inv(self.basis_real.T)
|
||
|
||
|
||
def in_SST(self,vector,proper=False):
|
||
"""
|
||
Check whether given crystal frame vector falls into standard stereographic triangle of own symmetry.
|
||
|
||
Parameters
|
||
----------
|
||
vector : numpy.ndarray of shape (...,3)
|
||
Vector to check.
|
||
proper : bool, optional
|
||
Consider only vectors with z >= 0, hence combine two neighboring SSTs.
|
||
Defaults to False.
|
||
|
||
Returns
|
||
-------
|
||
in : numpy.ndarray of shape (...)
|
||
Boolean array indicating whether vector falls into SST.
|
||
|
||
References
|
||
----------
|
||
Bases are computed from
|
||
|
||
>>> basis = {
|
||
... 'cubic' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||
... [1.,0.,1.]/np.sqrt(2.), # green
|
||
... [1.,1.,1.]/np.sqrt(3.)]).T), # blue
|
||
... 'hexagonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||
... [1.,0.,0.], # green
|
||
... [np.sqrt(3.),1.,0.]/np.sqrt(4.)]).T), # blue
|
||
... 'tetragonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||
... [1.,0.,0.], # green
|
||
... [1.,1.,0.]/np.sqrt(2.)]).T), # blue
|
||
... 'orthorhombic': np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||
... [1.,0.,0.], # green
|
||
... [0.,1.,0.]]).T), # blue
|
||
... }
|
||
|
||
"""
|
||
if not isinstance(vector,np.ndarray) or vector.shape[-1] != 3:
|
||
raise ValueError('Input is not a field of three-dimensional vectors.')
|
||
|
||
if self.family == 'cubic':
|
||
basis = {'improper':np.array([ [-1. , 0. , 1. ],
|
||
[ np.sqrt(2.) , -np.sqrt(2.) , 0. ],
|
||
[ 0. , np.sqrt(3.) , 0. ] ]),
|
||
'proper':np.array([ [ 0. , -1. , 1. ],
|
||
[-np.sqrt(2.) , np.sqrt(2.) , 0. ],
|
||
[ np.sqrt(3.) , 0. , 0. ] ]),
|
||
}
|
||
elif self.family == 'hexagonal':
|
||
basis = {'improper':np.array([ [ 0. , 0. , 1. ],
|
||
[ 1. , -np.sqrt(3.) , 0. ],
|
||
[ 0. , 2. , 0. ] ]),
|
||
'proper':np.array([ [ 0. , 0. , 1. ],
|
||
[-1. , np.sqrt(3.) , 0. ],
|
||
[ np.sqrt(3.) , -1. , 0. ] ]),
|
||
}
|
||
elif self.family == 'tetragonal':
|
||
basis = {'improper':np.array([ [ 0. , 0. , 1. ],
|
||
[ 1. , -1. , 0. ],
|
||
[ 0. , np.sqrt(2.) , 0. ] ]),
|
||
'proper':np.array([ [ 0. , 0. , 1. ],
|
||
[-1. , 1. , 0. ],
|
||
[ np.sqrt(2.) , 0. , 0. ] ]),
|
||
}
|
||
elif self.family == 'orthorhombic':
|
||
basis = {'improper':np.array([ [ 0., 0., 1.],
|
||
[ 1., 0., 0.],
|
||
[ 0., 1., 0.] ]),
|
||
'proper':np.array([ [ 0., 0., 1.],
|
||
[-1., 0., 0.],
|
||
[ 0., 1., 0.] ]),
|
||
}
|
||
else: # direct exit for unspecified symmetry
|
||
return np.ones_like(vector[...,0],bool)
|
||
|
||
if proper:
|
||
components_proper = np.around(np.einsum('...ji,...i',
|
||
np.broadcast_to(basis['proper'], vector.shape+(3,)),
|
||
vector), 12)
|
||
components_improper = np.around(np.einsum('...ji,...i',
|
||
np.broadcast_to(basis['improper'], vector.shape+(3,)),
|
||
vector), 12)
|
||
return np.all(components_proper >= 0.0,axis=-1) \
|
||
| np.all(components_improper >= 0.0,axis=-1)
|
||
else:
|
||
components = np.around(np.einsum('...ji,...i',
|
||
np.broadcast_to(basis['improper'], vector.shape+(3,)),
|
||
np.block([vector[...,:2],np.abs(vector[...,2:3])])), 12)
|
||
|
||
return np.all(components >= 0.0,axis=-1)
|
||
|
||
|
||
def IPF_color(self,vector,in_SST=True,proper=False):
|
||
"""
|
||
Map vector to RGB color within standard stereographic triangle of own symmetry.
|
||
|
||
Parameters
|
||
----------
|
||
vector : numpy.ndarray of shape (...,3)
|
||
Vector to colorize.
|
||
in_SST : bool, optional
|
||
Consider symmetrically equivalent orientations such that poles are located in SST.
|
||
Defaults to True.
|
||
proper : bool, optional
|
||
Consider only vectors with z >= 0, hence combine two neighboring SSTs (with mirrored colors).
|
||
Defaults to False.
|
||
|
||
Returns
|
||
-------
|
||
rgb : numpy.ndarray of shape (...,3)
|
||
RGB array of IPF colors.
|
||
|
||
Examples
|
||
--------
|
||
Inverse pole figure color of the e_3 direction for a crystal in "Cube" orientation with cubic symmetry:
|
||
|
||
>>> o = damask.Orientation(lattice='cubic')
|
||
>>> o.IPF_color([0,0,1])
|
||
array([1., 0., 0.])
|
||
|
||
References
|
||
----------
|
||
Bases are computed from
|
||
|
||
>>> basis = {
|
||
... 'cubic' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||
... [1.,0.,1.]/np.sqrt(2.), # green
|
||
... [1.,1.,1.]/np.sqrt(3.)]).T), # blue
|
||
... 'hexagonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||
... [1.,0.,0.], # green
|
||
... [np.sqrt(3.),1.,0.]/np.sqrt(4.)]).T), # blue
|
||
... 'tetragonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||
... [1.,0.,0.], # green
|
||
... [1.,1.,0.]/np.sqrt(2.)]).T), # blue
|
||
... 'orthorhombic': np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||
... [1.,0.,0.], # green
|
||
... [0.,1.,0.]]).T), # blue
|
||
... }
|
||
|
||
"""
|
||
if np.array(vector).shape[-1] != 3:
|
||
raise ValueError('Input is not a field of three-dimensional vectors.')
|
||
|
||
vector_ = self.to_SST(vector,proper) if in_SST else \
|
||
self @ np.broadcast_to(vector,self.shape+(3,))
|
||
|
||
if self.family == 'cubic':
|
||
basis = {'improper':np.array([ [-1. , 0. , 1. ],
|
||
[ np.sqrt(2.) , -np.sqrt(2.) , 0. ],
|
||
[ 0. , np.sqrt(3.) , 0. ] ]),
|
||
'proper':np.array([ [ 0. , -1. , 1. ],
|
||
[-np.sqrt(2.) , np.sqrt(2.) , 0. ],
|
||
[ np.sqrt(3.) , 0. , 0. ] ]),
|
||
}
|
||
elif self.family == 'hexagonal':
|
||
basis = {'improper':np.array([ [ 0. , 0. , 1. ],
|
||
[ 1. , -np.sqrt(3.) , 0. ],
|
||
[ 0. , 2. , 0. ] ]),
|
||
'proper':np.array([ [ 0. , 0. , 1. ],
|
||
[-1. , np.sqrt(3.) , 0. ],
|
||
[ np.sqrt(3.) , -1. , 0. ] ]),
|
||
}
|
||
elif self.family == 'tetragonal':
|
||
basis = {'improper':np.array([ [ 0. , 0. , 1. ],
|
||
[ 1. , -1. , 0. ],
|
||
[ 0. , np.sqrt(2.) , 0. ] ]),
|
||
'proper':np.array([ [ 0. , 0. , 1. ],
|
||
[-1. , 1. , 0. ],
|
||
[ np.sqrt(2.) , 0. , 0. ] ]),
|
||
}
|
||
elif self.family == 'orthorhombic':
|
||
basis = {'improper':np.array([ [ 0., 0., 1.],
|
||
[ 1., 0., 0.],
|
||
[ 0., 1., 0.] ]),
|
||
'proper':np.array([ [ 0., 0., 1.],
|
||
[-1., 0., 0.],
|
||
[ 0., 1., 0.] ]),
|
||
}
|
||
else: # direct exit for unspecified symmetry
|
||
return np.zeros_like(vector_)
|
||
|
||
if proper:
|
||
components_proper = np.around(np.einsum('...ji,...i',
|
||
np.broadcast_to(basis['proper'], vector_.shape+(3,)),
|
||
vector_), 12)
|
||
components_improper = np.around(np.einsum('...ji,...i',
|
||
np.broadcast_to(basis['improper'], vector_.shape+(3,)),
|
||
vector_), 12)
|
||
in_SST = np.all(components_proper >= 0.0,axis=-1) \
|
||
| np.all(components_improper >= 0.0,axis=-1)
|
||
components = np.where((in_SST & np.all(components_proper >= 0.0,axis=-1))[...,np.newaxis],
|
||
components_proper,components_improper)
|
||
else:
|
||
components = np.around(np.einsum('...ji,...i',
|
||
np.broadcast_to(basis['improper'], vector_.shape+(3,)),
|
||
np.block([vector_[...,:2],np.abs(vector_[...,2:3])])), 12)
|
||
|
||
in_SST = np.all(components >= 0.0,axis=-1)
|
||
|
||
with np.errstate(invalid='ignore',divide='ignore'):
|
||
rgb = (components/np.linalg.norm(components,axis=-1,keepdims=True))**0.5 # smoothen color ramps
|
||
rgb = np.clip(rgb,0.,1.) # clip intensity
|
||
rgb /= np.max(rgb,axis=-1,keepdims=True) # normalize to (HS)V = 1
|
||
rgb[np.broadcast_to(~in_SST[...,np.newaxis],rgb.shape)] = 0.0
|
||
return rgb
|
||
|
||
|
||
def disorientation(self,other,return_operators=False):
|
||
"""
|
||
Calculate disorientation between myself and given other orientation.
|
||
|
||
Parameters
|
||
----------
|
||
other : Orientation
|
||
Orientation to calculate disorientation for.
|
||
Shape of other blends with shape of own rotation array.
|
||
For example, shapes of (2,3) for own rotations and (3,2) for other's result in (2,3,2) disorientations.
|
||
return_operators : bool, optional
|
||
Return index pair of symmetrically equivalent orientations that result in disorientation axis falling into FZ.
|
||
Defaults to False.
|
||
|
||
Returns
|
||
-------
|
||
disorientation : Orientation
|
||
Disorientation between self and other.
|
||
operators : numpy.ndarray int of shape (...,2), conditional
|
||
Index of symmetrically equivalent orientation that rotated vector to the SST.
|
||
|
||
Notes
|
||
-----
|
||
Currently requires same crystal family for both orientations.
|
||
For extension to cases with differing symmetry see A. Heinz and P. Neumann 1991 and 10.1107/S0021889808016373.
|
||
|
||
Examples
|
||
--------
|
||
Disorientation between two specific orientations of hexagonal symmetry:
|
||
|
||
>>> import damask
|
||
>>> a = damask.Orientation.from_Eulers(phi=[123,32,21],degrees=True,lattice='hexagonal')
|
||
>>> b = damask.Orientation.from_Eulers(phi=[104,11,87],degrees=True,lattice='hexagonal')
|
||
>>> a.disorientation(b)
|
||
Crystal family hexagonal
|
||
Quaternion: (real=0.976, imag=<+0.189, +0.018, +0.103>)
|
||
Matrix:
|
||
[[ 0.97831006 0.20710935 0.00389135]
|
||
[-0.19363288 0.90765544 0.37238141]
|
||
[ 0.07359167 -0.36505797 0.92807163]]
|
||
Bunge Eulers / deg: (11.40, 21.86, 0.60)
|
||
|
||
"""
|
||
if self.family is None or other.family is None:
|
||
raise ValueError('missing crystal symmetry')
|
||
if self.family != other.family:
|
||
raise NotImplementedError('disorientation between different crystal families')
|
||
|
||
blend = util.shapeblender(self.shape,other.shape)
|
||
s = self.equivalent
|
||
o = other.equivalent
|
||
|
||
s_ = s.reshape((s.shape[0],1)+ self.shape).broadcast_to((s.shape[0],o.shape[0])+blend,mode='right')
|
||
o_ = o.reshape((1,o.shape[0])+other.shape).broadcast_to((s.shape[0],o.shape[0])+blend,mode='right')
|
||
r_ = s_.misorientation(o_)
|
||
_r = ~r_
|
||
|
||
forward = r_.in_FZ & r_.in_disorientation_FZ
|
||
reverse = _r.in_FZ & _r.in_disorientation_FZ
|
||
ok = forward | reverse
|
||
ok &= (np.cumsum(ok.reshape((-1,)+ok.shape[2:]),axis=0) == 1).reshape(ok.shape)
|
||
r = np.where(np.any(forward[...,np.newaxis],axis=(0,1),keepdims=True),
|
||
r_.quaternion,
|
||
_r.quaternion)
|
||
loc = np.where(ok)
|
||
sort = 0 if len(loc) == 2 else np.lexsort(loc[:1:-1])
|
||
quat = r[ok][sort].reshape(blend+(4,))
|
||
|
||
return (
|
||
(self.copy(rotation=quat),
|
||
(np.vstack(loc[:2]).T)[sort].reshape(blend+(2,)))
|
||
if return_operators else
|
||
self.copy(rotation=quat)
|
||
)
|
||
|
||
|
||
def average(self,weights=None,return_cloud=False):
|
||
"""
|
||
Return orientation average over last dimension.
|
||
|
||
Parameters
|
||
----------
|
||
weights : numpy.ndarray, optional
|
||
Relative weights of orientations.
|
||
return_cloud : bool, optional
|
||
Return the set of symmetrically equivalent orientations that was used in averaging.
|
||
Defaults to False.
|
||
|
||
Returns
|
||
-------
|
||
average : Orientation
|
||
Weighted average of original Orientation field.
|
||
cloud : Orientations, conditional
|
||
Set of symmetrically equivalent orientations that were used in averaging.
|
||
|
||
References
|
||
----------
|
||
J.C. Glez and J. Driver, Journal of Applied Crystallography 34:280-288, 2001
|
||
https://doi.org/10.1107/S0021889801003077
|
||
|
||
"""
|
||
if self.family is None:
|
||
raise ValueError('Missing crystal symmetry')
|
||
|
||
eq = self.equivalent
|
||
m = eq.misorientation(self[...,0].reshape((1,)+self.shape[:-1]+(1,))
|
||
.broadcast_to(eq.shape))\
|
||
.as_axis_angle()[...,3]
|
||
r = Rotation(np.squeeze(np.take_along_axis(eq.quaternion,
|
||
np.argmin(m,axis=0)[np.newaxis,...,np.newaxis],
|
||
axis=0),
|
||
axis=0))
|
||
return (
|
||
(self.copy(rotation=Rotation(r).average(weights)),
|
||
self.copy(rotation=Rotation(r)))
|
||
if return_cloud else
|
||
self.copy(rotation=Rotation(r).average(weights))
|
||
)
|
||
|
||
|
||
def to_SST(self,vector,proper=False,return_operators=False):
|
||
"""
|
||
Rotate vector to ensure it falls into (improper or proper) standard stereographic triangle of crystal symmetry.
|
||
|
||
Parameters
|
||
----------
|
||
vector : numpy.ndarray of shape (...,3)
|
||
Lab frame vector to align with crystal frame direction.
|
||
Shape of other blends with shape of own rotation array.
|
||
For example, a rotation array of shape (3,2) and a (2,4) vector array result in (3,2,4) outputs.
|
||
proper : bool, optional
|
||
Consider only vectors with z >= 0, hence combine two neighboring SSTs.
|
||
Defaults to False.
|
||
return_operators : bool, optional
|
||
Return the symmetrically equivalent orientation that rotated vector to SST.
|
||
Defaults to False.
|
||
|
||
Returns
|
||
-------
|
||
vector_SST : numpy.ndarray of shape (...,3)
|
||
Rotated vector falling into SST.
|
||
operators : numpy.ndarray int of shape (...), conditional
|
||
Index of symmetrically equivalent orientation that rotated vector to SST.
|
||
|
||
"""
|
||
if self.family is None:
|
||
raise ValueError('Missing crystal symmetry')
|
||
|
||
eq = self.equivalent
|
||
blend = util.shapeblender(eq.shape,np.array(vector).shape[:-1])
|
||
poles = eq.broadcast_to(blend,mode='right') @ np.broadcast_to(np.array(vector),blend+(3,))
|
||
ok = self.in_SST(poles,proper=proper)
|
||
ok &= np.cumsum(ok,axis=0) == 1
|
||
loc = np.where(ok)
|
||
sort = 0 if len(loc) == 1 else np.lexsort(loc[:0:-1])
|
||
return (
|
||
(poles[ok][sort].reshape(blend[1:]+(3,)), (np.vstack(loc[:1]).T)[sort].reshape(blend[1:]))
|
||
if return_operators else
|
||
poles[ok][sort].reshape(blend[1:]+(3,))
|
||
)
|
||
|
||
|
||
@classmethod
|
||
def Bravais_to_Miller(cls,*,uvtw=None,hkil=None):
|
||
"""
|
||
Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
|
||
|
||
Parameters
|
||
----------
|
||
uvtw|hkil : numpy.ndarray of shape (...,4)
|
||
Miller–Bravais indices of crystallographic direction [uvtw] or plane normal (hkil).
|
||
|
||
Returns
|
||
-------
|
||
uvw|hkl : numpy.ndarray of shape (...,3)
|
||
Miller indices of [uvw] direction or (hkl) plane normal.
|
||
|
||
"""
|
||
if (uvtw is not None) ^ (hkil is None):
|
||
raise KeyError('Specify either "uvtw" or "hkil"')
|
||
axis,basis = (np.array(uvtw),np.array([[1,0,-1,0],
|
||
[0,1,-1,0],
|
||
[0,0, 0,1]])) \
|
||
if hkil is None else \
|
||
(np.array(hkil),np.array([[1,0,0,0],
|
||
[0,1,0,0],
|
||
[0,0,0,1]]))
|
||
return np.einsum('il,...l',basis,axis)
|
||
|
||
|
||
@classmethod
|
||
def Miller_to_Bravais(cls,*,uvw=None,hkl=None):
|
||
"""
|
||
Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).
|
||
|
||
Parameters
|
||
----------
|
||
uvw|hkl : numpy.ndarray of shape (...,3)
|
||
Miller indices of crystallographic direction [uvw] or plane normal (hkl).
|
||
|
||
Returns
|
||
-------
|
||
uvtw|hkil : numpy.ndarray of shape (...,4)
|
||
Miller–Bravais indices of [uvtw] direction or (hkil) plane normal.
|
||
|
||
"""
|
||
if (uvw is not None) ^ (hkl is None):
|
||
raise KeyError('Specify either "uvw" or "hkl"')
|
||
axis,basis = (np.array(uvw),np.array([[ 2,-1, 0],
|
||
[-1, 2, 0],
|
||
[-1,-1, 0],
|
||
[ 0, 0, 3]])/3) \
|
||
if hkl is None else \
|
||
(np.array(hkl),np.array([[ 1, 0, 0],
|
||
[ 0, 1, 0],
|
||
[-1,-1, 0],
|
||
[ 0, 0, 1]]))
|
||
return np.einsum('il,...l',basis,axis)
|
||
|
||
|
||
def to_lattice(self,*,direction=None,plane=None):
|
||
"""
|
||
Calculate lattice vector corresponding to crystal frame direction or plane normal.
|
||
|
||
Parameters
|
||
----------
|
||
direction|normal : numpy.ndarray of shape (...,3)
|
||
Vector along direction or plane normal.
|
||
|
||
Returns
|
||
-------
|
||
Miller : numpy.ndarray of shape (...,3)
|
||
lattice vector of direction or plane.
|
||
Use util.scale_to_coprime to convert to (integer) Miller indices.
|
||
|
||
"""
|
||
if (direction is not None) ^ (plane is None):
|
||
raise KeyError('Specify either "direction" or "plane"')
|
||
axis,basis = (np.array(direction),self.basis_reciprocal.T) \
|
||
if plane is None else \
|
||
(np.array(plane),self.basis_real.T)
|
||
return np.einsum('il,...l',basis,axis)
|
||
|
||
|
||
def to_frame(self,*,uvw=None,hkl=None,with_symmetry=False):
|
||
"""
|
||
Calculate crystal frame vector along lattice direction [uvw] or plane normal (hkl).
|
||
|
||
Parameters
|
||
----------
|
||
uvw|hkl : numpy.ndarray of shape (...,3)
|
||
Miller indices of crystallographic direction or plane normal.
|
||
with_symmetry : bool, optional
|
||
Calculate all N symmetrically equivalent vectors.
|
||
|
||
Returns
|
||
-------
|
||
vector : numpy.ndarray of shape (...,3) or (N,...,3)
|
||
Crystal frame vector (or vectors if with_symmetry) along [uvw] direction or (hkl) plane normal.
|
||
|
||
"""
|
||
if (uvw is not None) ^ (hkl is None):
|
||
raise KeyError('Specify either "uvw" or "hkl"')
|
||
axis,basis = (np.array(uvw),self.basis_real) \
|
||
if hkl is None else \
|
||
(np.array(hkl),self.basis_reciprocal)
|
||
return (self.symmetry_operations.broadcast_to(self.symmetry_operations.shape+axis.shape[:-1],mode='right')
|
||
@ np.broadcast_to(np.einsum('il,...l',basis,axis),self.symmetry_operations.shape+axis.shape)
|
||
if with_symmetry else
|
||
np.einsum('il,...l',basis,axis))
|
||
|
||
|
||
def to_pole(self,*,uvw=None,hkl=None,with_symmetry=False):
|
||
"""
|
||
Calculate lab frame vector along lattice direction [uvw] or plane normal (hkl).
|
||
|
||
Parameters
|
||
----------
|
||
uvw|hkl : numpy.ndarray of shape (...,3)
|
||
Miller indices of crystallographic direction or plane normal.
|
||
with_symmetry : bool, optional
|
||
Calculate all N symmetrically equivalent vectors.
|
||
|
||
Returns
|
||
-------
|
||
vector : numpy.ndarray of shape (...,3) or (N,...,3)
|
||
Lab frame vector (or vectors if with_symmetry) along [uvw] direction or (hkl) plane normal.
|
||
|
||
"""
|
||
v = self.to_frame(uvw=uvw,hkl=hkl,with_symmetry=with_symmetry)
|
||
return ~(self if self.shape+v.shape[:-1] == () else self.broadcast_to(self.shape+v.shape[:-1],mode='right')) \
|
||
@ np.broadcast_to(v,self.shape+v.shape)
|
||
|
||
|
||
def Schmid(self,mode):
|
||
u"""
|
||
Calculate Schmid matrix P = d ⨂ n in the lab frame for given lattice shear kinematics.
|
||
|
||
Parameters
|
||
----------
|
||
mode : str
|
||
Type of kinematics, i.e. 'slip' or 'twin'.
|
||
|
||
Returns
|
||
-------
|
||
P : numpy.ndarray of shape (...,N,3,3)
|
||
Schmid matrix for each of the N deformation systems.
|
||
|
||
Examples
|
||
--------
|
||
Schmid matrix (in lab frame) of slip systems of a face-centered
|
||
cubic crystal in "Goss" orientation.
|
||
|
||
>>> import damask
|
||
>>> import numpy as np
|
||
>>> np.set_printoptions(3,suppress=True,floatmode='fixed')
|
||
>>> damask.Orientation.from_Eulers(phi=[0,45,0],degrees=True,lattice='cF').Schmid('slip')[0]
|
||
array([[ 0.000, 0.000, 0.000],
|
||
[ 0.577, -0.000, 0.816],
|
||
[ 0.000, 0.000, 0.000]])
|
||
|
||
"""
|
||
d = self.to_frame(uvw=self.kinematics[mode]['direction'],with_symmetry=False)
|
||
p = self.to_frame(hkl=self.kinematics[mode]['plane'] ,with_symmetry=False)
|
||
P = np.einsum('...i,...j',d/np.linalg.norm(d,axis=-1,keepdims=True),
|
||
p/np.linalg.norm(p,axis=-1,keepdims=True))
|
||
|
||
return ~self.broadcast_to( self.shape+P.shape[:-2],mode='right') \
|
||
@ np.broadcast_to(P,self.shape+P.shape)
|