Merge branch 'python-style' into 'development'
Python style See merge request damask/DAMASK!132
This commit is contained in:
commit
31136100c6
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@ -131,12 +131,12 @@ def BallToCube(ball):
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# inverse M_1
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# inverse M_1
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cube = np.array([ Tinv[0], Tinv[1], (-1.0 if xyz3[2] < 0.0 else 1.0) * rs / np.sqrt(6.0/np.pi) ]) /sc
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cube = np.array([ Tinv[0], Tinv[1], (-1.0 if xyz3[2] < 0.0 else 1.0) * rs / np.sqrt(6.0/np.pi) ]) /sc
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# reverse the coordinates back to the regular order according to the original pyramid number
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# reverse the coordinates back to the regular order according to the original pyramid number
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cube = cube[p]
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cube = cube[p]
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return cube
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return cube
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def get_order(xyz):
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def get_order(xyz):
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"""
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"""
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Get order of the coordinates.
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Get order of the coordinates.
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@ -13,7 +13,9 @@ from .asciitable import ASCIItable # noqa
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from .config import Material # noqa
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from .config import Material # noqa
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from .colormaps import Colormap, Color # noqa
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from .colormaps import Colormap, Color # noqa
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from .orientation import Symmetry, Lattice, Rotation, Orientation # noqa
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from .rotation import Rotation # noqa
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from .lattice import Symmetry, Lattice# noqa
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from .orientation import Orientation # noqa
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from .result import Result # noqa
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from .result import Result # noqa
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from .result import Result as DADF5 # noqa
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from .result import Result as DADF5 # noqa
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@ -10,7 +10,6 @@ class Color():
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]
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]
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# ------------------------------------------------------------------
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def __init__(self,
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def __init__(self,
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model = 'RGB',
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model = 'RGB',
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color = np.zeros(3,'d')):
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color = np.zeros(3,'d')):
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@ -49,20 +48,17 @@ class Color():
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self.color = np.array(color,'d')
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self.color = np.array(color,'d')
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# ------------------------------------------------------------------
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def __repr__(self):
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def __repr__(self):
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"""Color model and values."""
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"""Color model and values."""
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return 'Model: %s Color: %s'%(self.model,str(self.color))
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return 'Model: %s Color: %s'%(self.model,str(self.color))
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# ------------------------------------------------------------------
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def __str__(self):
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def __str__(self):
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"""Color model and values."""
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"""Color model and values."""
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return self.__repr__()
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return self.__repr__()
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# ------------------------------------------------------------------
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def convert_to(self,toModel = 'RGB'):
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def convertTo(self,toModel = 'RGB'):
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"""
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"""
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Change the color model permanently.
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Change the color model permanently.
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@ -88,8 +84,7 @@ class Color():
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return self
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return self
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# ------------------------------------------------------------------
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def express_as(self,asModel = 'RGB'):
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def expressAs(self,asModel = 'RGB'):
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"""
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"""
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Return the color in a different model.
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Return the color in a different model.
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@ -99,7 +94,7 @@ class Color():
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color model
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color model
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"""
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"""
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return self.__class__(self.model,self.color).convertTo(asModel)
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return self.__class__(self.model,self.color).convert_to(asModel)
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@ -293,6 +288,7 @@ class Color():
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self.model = converted.model
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self.model = converted.model
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self.color = converted.color
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self.color = converted.color
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def _XYZ2CIELAB(self):
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def _XYZ2CIELAB(self):
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"""
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"""
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Convert CIE XYZ to CIE Lab.
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Convert CIE XYZ to CIE Lab.
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@ -498,13 +494,13 @@ class Colormap():
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def interpolate_linear(lo, hi, frac):
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def interpolate_linear(lo, hi, frac):
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"""Linear interpolation between lo and hi color at given fraction; output in model of lo color."""
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"""Linear interpolation between lo and hi color at given fraction; output in model of lo color."""
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interpolation = (1.0 - frac) * np.array(lo.color[:]) \
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interpolation = (1.0 - frac) * np.array(lo.color[:]) \
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+ frac * np.array(hi.expressAs(lo.model).color[:])
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+ frac * np.array(hi.express_as(lo.model).color[:])
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return Color(lo.model,interpolation)
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return Color(lo.model,interpolation)
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if self.interpolate == 'perceptualuniform':
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if self.interpolate == 'perceptualuniform':
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return interpolate_Msh(self.left.expressAs('MSH').color,
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return interpolate_Msh(self.left.express_as('MSH').color,
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self.right.expressAs('MSH').color,fraction)
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self.right.express_as('MSH').color,fraction)
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elif self.interpolate == 'linear':
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elif self.interpolate == 'linear':
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return interpolate_linear(self.left,
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return interpolate_linear(self.left,
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self.right,fraction)
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self.right,fraction)
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@ -528,7 +524,7 @@ class Colormap():
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"""
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"""
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format = format.lower() # consistent comparison basis
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format = format.lower() # consistent comparison basis
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frac = 0.5*(np.array(crop) + 1.0) # rescale crop range to fractions
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frac = 0.5*(np.array(crop) + 1.0) # rescale crop range to fractions
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colors = [self.color(float(i)/(steps-1)*(frac[1]-frac[0])+frac[0]).expressAs(model).color for i in range(steps)]
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colors = [self.color(float(i)/(steps-1)*(frac[1]-frac[0])+frac[0]).express_as(model).color for i in range(steps)]
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if format == 'paraview':
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if format == 'paraview':
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colormap = ['[\n {{\n "ColorSpace": "RGB", "Name": "{}", "DefaultMap": true,\n "RGBPoints" : ['.format(name)] \
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colormap = ['[\n {{\n "ColorSpace": "RGB", "Name": "{}", "DefaultMap": true,\n "RGBPoints" : ['.format(name)] \
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+ [' {:4d},{:8.6f},{:8.6f},{:8.6f},'.format(i,color[0],color[1],color[2],) \
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+ [' {:4d},{:8.6f},{:8.6f},{:8.6f},'.format(i,color[0],color[1],color[2],) \
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@ -269,7 +269,7 @@ class Geom():
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comments = []
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comments = []
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for i,line in enumerate(content[:header_length]):
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for i,line in enumerate(content[:header_length]):
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items = line.lower().strip().split()
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items = line.lower().strip().split()
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key = items[0] if len(items) > 0 else ''
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key = items[0] if items else ''
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if key == 'grid':
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if key == 'grid':
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grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
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grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
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elif key == 'size':
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elif key == 'size':
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@ -1,7 +1,7 @@
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from scipy import spatial
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from scipy import spatial
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import numpy as np
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import numpy as np
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def __ks(size,grid,first_order=False):
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def _ks(size,grid,first_order=False):
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"""
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"""
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Get wave numbers operator.
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Get wave numbers operator.
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@ -34,7 +34,7 @@ def curl(size,field):
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"""
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"""
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n = np.prod(field.shape[3:])
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n = np.prod(field.shape[3:])
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k_s = __ks(size,field.shape[:3],True)
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k_s = _ks(size,field.shape[:3],True)
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e = np.zeros((3, 3, 3))
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e = np.zeros((3, 3, 3))
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e[0, 1, 2] = e[1, 2, 0] = e[2, 0, 1] = +1.0 # Levi-Civita symbol
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e[0, 1, 2] = e[1, 2, 0] = e[2, 0, 1] = +1.0 # Levi-Civita symbol
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@ -58,7 +58,7 @@ def divergence(size,field):
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"""
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"""
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n = np.prod(field.shape[3:])
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n = np.prod(field.shape[3:])
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k_s = __ks(size,field.shape[:3],True)
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k_s = _ks(size,field.shape[:3],True)
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field_fourier = np.fft.rfftn(field,axes=(0,1,2))
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field_fourier = np.fft.rfftn(field,axes=(0,1,2))
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divergence = (np.einsum('ijkl,ijkl ->ijk', k_s,field_fourier)*2.0j*np.pi if n == 3 else # vector, 3 -> 1
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divergence = (np.einsum('ijkl,ijkl ->ijk', k_s,field_fourier)*2.0j*np.pi if n == 3 else # vector, 3 -> 1
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@ -78,7 +78,7 @@ def gradient(size,field):
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"""
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"""
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n = np.prod(field.shape[3:])
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n = np.prod(field.shape[3:])
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k_s = __ks(size,field.shape[:3],True)
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k_s = _ks(size,field.shape[:3],True)
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field_fourier = np.fft.rfftn(field,axes=(0,1,2))
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field_fourier = np.fft.rfftn(field,axes=(0,1,2))
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gradient = (np.einsum('ijkl,ijkm->ijkm', field_fourier,k_s)*2.0j*np.pi if n == 1 else # scalar, 1 -> 3
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gradient = (np.einsum('ijkl,ijkm->ijkm', field_fourier,k_s)*2.0j*np.pi if n == 1 else # scalar, 1 -> 3
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@ -110,6 +110,7 @@ def cell_coord0(grid,size,origin=np.zeros(3)):
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return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
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return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
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def cell_displacement_fluct(size,F):
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def cell_displacement_fluct(size,F):
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"""
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"""
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Cell center displacement field from fluctuation part of the deformation gradient field.
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Cell center displacement field from fluctuation part of the deformation gradient field.
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@ -124,7 +125,7 @@ def cell_displacement_fluct(size,F):
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"""
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"""
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integrator = 0.5j*size/np.pi
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integrator = 0.5j*size/np.pi
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k_s = __ks(size,F.shape[:3],False)
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k_s = _ks(size,F.shape[:3],False)
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k_s_squared = np.einsum('...l,...l',k_s,k_s)
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k_s_squared = np.einsum('...l,...l',k_s,k_s)
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k_s_squared[0,0,0] = 1.0
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k_s_squared[0,0,0] = 1.0
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@ -136,6 +137,7 @@ def cell_displacement_fluct(size,F):
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return np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
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return np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
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def cell_displacement_avg(size,F):
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def cell_displacement_avg(size,F):
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"""
|
"""
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Cell center displacement field from average part of the deformation gradient field.
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Cell center displacement field from average part of the deformation gradient field.
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@ -151,6 +153,7 @@ def cell_displacement_avg(size,F):
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F_avg = np.average(F,axis=(0,1,2))
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F_avg = np.average(F,axis=(0,1,2))
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return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),cell_coord0(F.shape[:3][::-1],size))
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return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),cell_coord0(F.shape[:3][::-1],size))
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def cell_displacement(size,F):
|
def cell_displacement(size,F):
|
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"""
|
"""
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Cell center displacement field from deformation gradient field.
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Cell center displacement field from deformation gradient field.
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@ -165,6 +168,7 @@ def cell_displacement(size,F):
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"""
|
"""
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return cell_displacement_avg(size,F) + cell_displacement_fluct(size,F)
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return cell_displacement_avg(size,F) + cell_displacement_fluct(size,F)
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def cell_coord(size,F,origin=np.zeros(3)):
|
def cell_coord(size,F,origin=np.zeros(3)):
|
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"""
|
"""
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Cell center positions.
|
Cell center positions.
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|
@ -181,6 +185,7 @@ def cell_coord(size,F,origin=np.zeros(3)):
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"""
|
"""
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return cell_coord0(F.shape[:3][::-1],size,origin) + cell_displacement(size,F)
|
return cell_coord0(F.shape[:3][::-1],size,origin) + cell_displacement(size,F)
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|
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|
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def cell_coord0_gridSizeOrigin(coord0,ordered=True):
|
def cell_coord0_gridSizeOrigin(coord0,ordered=True):
|
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"""
|
"""
|
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Return grid 'DNA', i.e. grid, size, and origin from array of cell positions.
|
Return grid 'DNA', i.e. grid, size, and origin from array of cell positions.
|
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|
@ -221,6 +226,7 @@ def cell_coord0_gridSizeOrigin(coord0,ordered=True):
|
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|
|
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return (grid,size,origin)
|
return (grid,size,origin)
|
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|
|
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|
|
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def coord0_check(coord0):
|
def coord0_check(coord0):
|
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"""
|
"""
|
||||||
Check whether coordinates lie on a regular grid.
|
Check whether coordinates lie on a regular grid.
|
||||||
|
@ -234,7 +240,6 @@ def coord0_check(coord0):
|
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cell_coord0_gridSizeOrigin(coord0,ordered=True)
|
cell_coord0_gridSizeOrigin(coord0,ordered=True)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def node_coord0(grid,size,origin=np.zeros(3)):
|
def node_coord0(grid,size,origin=np.zeros(3)):
|
||||||
"""
|
"""
|
||||||
Nodal positions (undeformed).
|
Nodal positions (undeformed).
|
||||||
|
@ -256,6 +261,7 @@ def node_coord0(grid,size,origin=np.zeros(3)):
|
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|
|
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return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
|
return np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
|
||||||
|
|
||||||
|
|
||||||
def node_displacement_fluct(size,F):
|
def node_displacement_fluct(size,F):
|
||||||
"""
|
"""
|
||||||
Nodal displacement field from fluctuation part of the deformation gradient field.
|
Nodal displacement field from fluctuation part of the deformation gradient field.
|
||||||
|
@ -270,6 +276,7 @@ def node_displacement_fluct(size,F):
|
||||||
"""
|
"""
|
||||||
return cell_2_node(cell_displacement_fluct(size,F))
|
return cell_2_node(cell_displacement_fluct(size,F))
|
||||||
|
|
||||||
|
|
||||||
def node_displacement_avg(size,F):
|
def node_displacement_avg(size,F):
|
||||||
"""
|
"""
|
||||||
Nodal displacement field from average part of the deformation gradient field.
|
Nodal displacement field from average part of the deformation gradient field.
|
||||||
|
@ -285,6 +292,7 @@ def node_displacement_avg(size,F):
|
||||||
F_avg = np.average(F,axis=(0,1,2))
|
F_avg = np.average(F,axis=(0,1,2))
|
||||||
return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),node_coord0(F.shape[:3][::-1],size))
|
return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),node_coord0(F.shape[:3][::-1],size))
|
||||||
|
|
||||||
|
|
||||||
def node_displacement(size,F):
|
def node_displacement(size,F):
|
||||||
"""
|
"""
|
||||||
Nodal displacement field from deformation gradient field.
|
Nodal displacement field from deformation gradient field.
|
||||||
|
@ -299,6 +307,7 @@ def node_displacement(size,F):
|
||||||
"""
|
"""
|
||||||
return node_displacement_avg(size,F) + node_displacement_fluct(size,F)
|
return node_displacement_avg(size,F) + node_displacement_fluct(size,F)
|
||||||
|
|
||||||
|
|
||||||
def node_coord(size,F,origin=np.zeros(3)):
|
def node_coord(size,F,origin=np.zeros(3)):
|
||||||
"""
|
"""
|
||||||
Nodal positions.
|
Nodal positions.
|
||||||
|
@ -315,6 +324,7 @@ def node_coord(size,F,origin=np.zeros(3)):
|
||||||
"""
|
"""
|
||||||
return node_coord0(F.shape[:3][::-1],size,origin) + node_displacement(size,F)
|
return node_coord0(F.shape[:3][::-1],size,origin) + node_displacement(size,F)
|
||||||
|
|
||||||
|
|
||||||
def cell_2_node(cell_data):
|
def cell_2_node(cell_data):
|
||||||
"""Interpolate periodic cell data to nodal data."""
|
"""Interpolate periodic cell data to nodal data."""
|
||||||
n = ( cell_data + np.roll(cell_data,1,(0,1,2))
|
n = ( cell_data + np.roll(cell_data,1,(0,1,2))
|
||||||
|
@ -323,6 +333,7 @@ def cell_2_node(cell_data):
|
||||||
|
|
||||||
return np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
|
return np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
|
||||||
|
|
||||||
|
|
||||||
def node_2_cell(node_data):
|
def node_2_cell(node_data):
|
||||||
"""Interpolate periodic nodal data to cell data."""
|
"""Interpolate periodic nodal data to cell data."""
|
||||||
c = ( node_data + np.roll(node_data,1,(0,1,2))
|
c = ( node_data + np.roll(node_data,1,(0,1,2))
|
||||||
|
@ -331,6 +342,7 @@ def node_2_cell(node_data):
|
||||||
|
|
||||||
return c[:-1,:-1,:-1]
|
return c[:-1,:-1,:-1]
|
||||||
|
|
||||||
|
|
||||||
def node_coord0_gridSizeOrigin(coord0,ordered=False):
|
def node_coord0_gridSizeOrigin(coord0,ordered=False):
|
||||||
"""
|
"""
|
||||||
Return grid 'DNA', i.e. grid, size, and origin from array of nodal positions.
|
Return grid 'DNA', i.e. grid, size, and origin from array of nodal positions.
|
||||||
|
|
|
@ -0,0 +1,641 @@
|
||||||
|
import numpy as np
|
||||||
|
|
||||||
|
from .rotation import Rotation
|
||||||
|
|
||||||
|
P = -1
|
||||||
|
|
||||||
|
# ******************************************************************************************
|
||||||
|
class Symmetry:
|
||||||
|
"""
|
||||||
|
Symmetry operations for lattice systems.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
https://en.wikipedia.org/wiki/Crystal_system
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
lattices = [None,'orthorhombic','tetragonal','hexagonal','cubic',]
|
||||||
|
|
||||||
|
def __init__(self, symmetry = None):
|
||||||
|
"""
|
||||||
|
Symmetry Definition.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
symmetry : str, optional
|
||||||
|
label of the crystal system
|
||||||
|
|
||||||
|
"""
|
||||||
|
if symmetry is not None and symmetry.lower() not in Symmetry.lattices:
|
||||||
|
raise KeyError('Symmetry/crystal system "{}" is unknown'.format(symmetry))
|
||||||
|
|
||||||
|
self.lattice = symmetry.lower() if isinstance(symmetry,str) else symmetry
|
||||||
|
|
||||||
|
|
||||||
|
def __copy__(self):
|
||||||
|
"""Copy."""
|
||||||
|
return self.__class__(self.lattice)
|
||||||
|
|
||||||
|
copy = __copy__
|
||||||
|
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
"""Readable string."""
|
||||||
|
return '{}'.format(self.lattice)
|
||||||
|
|
||||||
|
|
||||||
|
def __eq__(self, other):
|
||||||
|
"""
|
||||||
|
Equal to other.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Symmetry
|
||||||
|
Symmetry to check for equality.
|
||||||
|
|
||||||
|
"""
|
||||||
|
return self.lattice == other.lattice
|
||||||
|
|
||||||
|
def __neq__(self, other):
|
||||||
|
"""
|
||||||
|
Not Equal to other.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Symmetry
|
||||||
|
Symmetry to check for inequality.
|
||||||
|
|
||||||
|
"""
|
||||||
|
return not self.__eq__(other)
|
||||||
|
|
||||||
|
def __cmp__(self,other):
|
||||||
|
"""
|
||||||
|
Linear ordering.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Symmetry
|
||||||
|
Symmetry to check for for order.
|
||||||
|
|
||||||
|
"""
|
||||||
|
myOrder = Symmetry.lattices.index(self.lattice)
|
||||||
|
otherOrder = Symmetry.lattices.index(other.lattice)
|
||||||
|
return (myOrder > otherOrder) - (myOrder < otherOrder)
|
||||||
|
|
||||||
|
def symmetryOperations(self,members=[]):
|
||||||
|
"""List (or single element) of symmetry operations as rotations."""
|
||||||
|
if self.lattice == 'cubic':
|
||||||
|
symQuats = [
|
||||||
|
[ 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.lattice == 'hexagonal':
|
||||||
|
symQuats = [
|
||||||
|
[ 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.lattice == 'tetragonal':
|
||||||
|
symQuats = [
|
||||||
|
[ 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.lattice == 'orthorhombic':
|
||||||
|
symQuats = [
|
||||||
|
[ 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 ],
|
||||||
|
]
|
||||||
|
else:
|
||||||
|
symQuats = [
|
||||||
|
[ 1.0,0.0,0.0,0.0 ],
|
||||||
|
]
|
||||||
|
|
||||||
|
symOps = list(map(Rotation,
|
||||||
|
np.array(symQuats)[np.atleast_1d(members) if members != [] else range(len(symQuats))]))
|
||||||
|
try:
|
||||||
|
iter(members) # asking for (even empty) list of members?
|
||||||
|
except TypeError:
|
||||||
|
return symOps[0] # no, return rotation object
|
||||||
|
else:
|
||||||
|
return symOps # yes, return list of rotations
|
||||||
|
|
||||||
|
|
||||||
|
def inFZ(self,rodrigues):
|
||||||
|
"""
|
||||||
|
Check whether given Rodriques-Frank vector falls into fundamental zone of own symmetry.
|
||||||
|
|
||||||
|
Fundamental zone in Rodrigues space is point symmetric around origin.
|
||||||
|
"""
|
||||||
|
if (len(rodrigues) != 3):
|
||||||
|
raise ValueError('Input is not a Rodriques-Frank vector.\n')
|
||||||
|
|
||||||
|
if np.any(rodrigues == np.inf): return False
|
||||||
|
|
||||||
|
Rabs = abs(rodrigues)
|
||||||
|
|
||||||
|
if self.lattice == 'cubic':
|
||||||
|
return np.sqrt(2.0)-1.0 >= Rabs[0] \
|
||||||
|
and np.sqrt(2.0)-1.0 >= Rabs[1] \
|
||||||
|
and np.sqrt(2.0)-1.0 >= Rabs[2] \
|
||||||
|
and 1.0 >= Rabs[0] + Rabs[1] + Rabs[2]
|
||||||
|
elif self.lattice == 'hexagonal':
|
||||||
|
return 1.0 >= Rabs[0] and 1.0 >= Rabs[1] and 1.0 >= Rabs[2] \
|
||||||
|
and 2.0 >= np.sqrt(3)*Rabs[0] + Rabs[1] \
|
||||||
|
and 2.0 >= np.sqrt(3)*Rabs[1] + Rabs[0] \
|
||||||
|
and 2.0 >= np.sqrt(3) + Rabs[2]
|
||||||
|
elif self.lattice == 'tetragonal':
|
||||||
|
return 1.0 >= Rabs[0] and 1.0 >= Rabs[1] \
|
||||||
|
and np.sqrt(2.0) >= Rabs[0] + Rabs[1] \
|
||||||
|
and np.sqrt(2.0) >= Rabs[2] + 1.0
|
||||||
|
elif self.lattice == 'orthorhombic':
|
||||||
|
return 1.0 >= Rabs[0] and 1.0 >= Rabs[1] and 1.0 >= Rabs[2]
|
||||||
|
else:
|
||||||
|
return True
|
||||||
|
|
||||||
|
|
||||||
|
def inDisorientationSST(self,rodrigues):
|
||||||
|
"""
|
||||||
|
Check whether given Rodriques-Frank vector (of misorientation) falls into standard stereographic triangle of own symmetry.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
A. Heinz and P. Neumann, Acta Crystallographica Section A 47:780-789, 1991
|
||||||
|
https://doi.org/10.1107/S0108767391006864
|
||||||
|
|
||||||
|
"""
|
||||||
|
if (len(rodrigues) != 3):
|
||||||
|
raise ValueError('Input is not a Rodriques-Frank vector.\n')
|
||||||
|
R = rodrigues
|
||||||
|
|
||||||
|
epsilon = 0.0
|
||||||
|
if self.lattice == 'cubic':
|
||||||
|
return R[0] >= R[1]+epsilon and R[1] >= R[2]+epsilon and R[2] >= epsilon
|
||||||
|
elif self.lattice == 'hexagonal':
|
||||||
|
return R[0] >= np.sqrt(3)*(R[1]-epsilon) and R[1] >= epsilon and R[2] >= epsilon
|
||||||
|
elif self.lattice == 'tetragonal':
|
||||||
|
return R[0] >= R[1]-epsilon and R[1] >= epsilon and R[2] >= epsilon
|
||||||
|
elif self.lattice == 'orthorhombic':
|
||||||
|
return R[0] >= epsilon and R[1] >= epsilon and R[2] >= epsilon
|
||||||
|
else:
|
||||||
|
return True
|
||||||
|
|
||||||
|
|
||||||
|
def inSST(self,
|
||||||
|
vector,
|
||||||
|
proper = False,
|
||||||
|
color = False):
|
||||||
|
"""
|
||||||
|
Check whether given vector falls into standard stereographic triangle of own symmetry.
|
||||||
|
|
||||||
|
proper considers only vectors with z >= 0, hence uses two neighboring SSTs.
|
||||||
|
Return inverse pole figure color if requested.
|
||||||
|
Bases are computed from
|
||||||
|
|
||||||
|
basis = {'cubic' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||||||
|
[1.,0.,1.]/np.sqrt(2.), # direction of green
|
||||||
|
[1.,1.,1.]/np.sqrt(3.)]).T), # direction of blue
|
||||||
|
'hexagonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||||||
|
[1.,0.,0.], # direction of green
|
||||||
|
[np.sqrt(3.),1.,0.]/np.sqrt(4.)]).T), # direction of blue
|
||||||
|
'tetragonal' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||||||
|
[1.,0.,0.], # direction of green
|
||||||
|
[1.,1.,0.]/np.sqrt(2.)]).T), # direction of blue
|
||||||
|
'orthorhombic' : np.linalg.inv(np.array([[0.,0.,1.], # direction of red
|
||||||
|
[1.,0.,0.], # direction of green
|
||||||
|
[0.,1.,0.]]).T), # direction of blue
|
||||||
|
}
|
||||||
|
"""
|
||||||
|
if self.lattice == '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.lattice == '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.lattice == '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.lattice == '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
|
||||||
|
if color:
|
||||||
|
return (True,np.zeros(3,'d'))
|
||||||
|
else:
|
||||||
|
return True
|
||||||
|
|
||||||
|
v = np.array(vector,dtype=float)
|
||||||
|
if proper: # check both improper ...
|
||||||
|
theComponents = np.around(np.dot(basis['improper'],v),12)
|
||||||
|
inSST = np.all(theComponents >= 0.0)
|
||||||
|
if not inSST: # ... and proper SST
|
||||||
|
theComponents = np.around(np.dot(basis['proper'],v),12)
|
||||||
|
inSST = np.all(theComponents >= 0.0)
|
||||||
|
else:
|
||||||
|
v[2] = abs(v[2]) # z component projects identical
|
||||||
|
theComponents = np.around(np.dot(basis['improper'],v),12) # for positive and negative values
|
||||||
|
inSST = np.all(theComponents >= 0.0)
|
||||||
|
|
||||||
|
if color: # have to return color array
|
||||||
|
if inSST:
|
||||||
|
rgb = np.power(theComponents/np.linalg.norm(theComponents),0.5) # smoothen color ramps
|
||||||
|
rgb = np.minimum(np.ones(3,dtype=float),rgb) # limit to maximum intensity
|
||||||
|
rgb /= max(rgb) # normalize to (HS)V = 1
|
||||||
|
else:
|
||||||
|
rgb = np.zeros(3,dtype=float)
|
||||||
|
return (inSST,rgb)
|
||||||
|
else:
|
||||||
|
return inSST
|
||||||
|
|
||||||
|
# code derived from https://github.com/ezag/pyeuclid
|
||||||
|
# suggested reading: http://web.mit.edu/2.998/www/QuaternionReport1.pdf
|
||||||
|
|
||||||
|
|
||||||
|
# ******************************************************************************************
|
||||||
|
class Lattice:
|
||||||
|
"""
|
||||||
|
Lattice system.
|
||||||
|
|
||||||
|
Currently, this contains only a mapping from Bravais lattice to symmetry
|
||||||
|
and orientation relationships. It could include twin and slip systems.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
https://en.wikipedia.org/wiki/Bravais_lattice
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
lattices = {
|
||||||
|
'triclinic':{'symmetry':None},
|
||||||
|
'bct':{'symmetry':'tetragonal'},
|
||||||
|
'hex':{'symmetry':'hexagonal'},
|
||||||
|
'fcc':{'symmetry':'cubic','c/a':1.0},
|
||||||
|
'bcc':{'symmetry':'cubic','c/a':1.0},
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def __init__(self, lattice):
|
||||||
|
"""
|
||||||
|
New lattice of given type.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
lattice : str
|
||||||
|
Bravais lattice.
|
||||||
|
|
||||||
|
"""
|
||||||
|
self.lattice = lattice
|
||||||
|
self.symmetry = Symmetry(self.lattices[lattice]['symmetry'])
|
||||||
|
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
"""Report basic lattice information."""
|
||||||
|
return 'Bravais lattice {} ({} symmetry)'.format(self.lattice,self.symmetry)
|
||||||
|
|
||||||
|
|
||||||
|
# Kurdjomov--Sachs orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from S. Morito et al., Journal of Alloys and Compounds 577:s587-s592, 2013
|
||||||
|
# also see K. Kitahara et al., Acta Materialia 54:1279-1288, 2006
|
||||||
|
KS = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, -1],[ 0, 1, 1]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ -1, 0, 1],[ -1, -1, 1]],
|
||||||
|
[[ -1, 0, 1],[ -1, 1, -1]],
|
||||||
|
[[ 0, 1, -1],[ -1, -1, 1]],
|
||||||
|
[[ 0, 1, -1],[ -1, 1, -1]],
|
||||||
|
[[ 1, -1, 0],[ -1, -1, 1]],
|
||||||
|
[[ 1, -1, 0],[ -1, 1, -1]],
|
||||||
|
[[ 1, 0, -1],[ -1, -1, 1]],
|
||||||
|
[[ 1, 0, -1],[ -1, 1, -1]],
|
||||||
|
[[ -1, -1, 0],[ -1, -1, 1]],
|
||||||
|
[[ -1, -1, 0],[ -1, 1, -1]],
|
||||||
|
[[ 0, 1, 1],[ -1, -1, 1]],
|
||||||
|
[[ 0, 1, 1],[ -1, 1, -1]],
|
||||||
|
[[ 0, -1, 1],[ -1, -1, 1]],
|
||||||
|
[[ 0, -1, 1],[ -1, 1, -1]],
|
||||||
|
[[ -1, 0, -1],[ -1, -1, 1]],
|
||||||
|
[[ -1, 0, -1],[ -1, 1, -1]],
|
||||||
|
[[ 1, 1, 0],[ -1, -1, 1]],
|
||||||
|
[[ 1, 1, 0],[ -1, 1, -1]],
|
||||||
|
[[ -1, 1, 0],[ -1, -1, 1]],
|
||||||
|
[[ -1, 1, 0],[ -1, 1, -1]],
|
||||||
|
[[ 0, -1, -1],[ -1, -1, 1]],
|
||||||
|
[[ 0, -1, -1],[ -1, 1, -1]],
|
||||||
|
[[ 1, 0, 1],[ -1, -1, 1]],
|
||||||
|
[[ 1, 0, 1],[ -1, 1, -1]]],dtype='float')}
|
||||||
|
|
||||||
|
# Greninger--Troiano orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
|
||||||
|
GT = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 1, 1, 1],[ 1, 0, 1]],
|
||||||
|
[[ 1, 1, 1],[ 1, 1, 0]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, -1, 1],[ -1, 0, 1]],
|
||||||
|
[[ -1, -1, 1],[ -1, -1, 0]],
|
||||||
|
[[ -1, -1, 1],[ 0, -1, 1]],
|
||||||
|
[[ -1, 1, 1],[ -1, 0, 1]],
|
||||||
|
[[ -1, 1, 1],[ -1, 1, 0]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 1, 0, 1]],
|
||||||
|
[[ 1, -1, 1],[ 1, -1, 0]],
|
||||||
|
[[ 1, -1, 1],[ 0, -1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 1, 1, 0]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 1, 0, 1]],
|
||||||
|
[[ -1, -1, 1],[ -1, -1, 0]],
|
||||||
|
[[ -1, -1, 1],[ 0, -1, 1]],
|
||||||
|
[[ -1, -1, 1],[ -1, 0, 1]],
|
||||||
|
[[ -1, 1, 1],[ -1, 1, 0]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ -1, 0, 1]],
|
||||||
|
[[ 1, -1, 1],[ 1, -1, 0]],
|
||||||
|
[[ 1, -1, 1],[ 0, -1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 1, 0, 1]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ -5,-12, 17],[-17, -7, 17]],
|
||||||
|
[[ 17, -5,-12],[ 17,-17, -7]],
|
||||||
|
[[-12, 17, -5],[ -7, 17,-17]],
|
||||||
|
[[ 5, 12, 17],[ 17, 7, 17]],
|
||||||
|
[[-17, 5,-12],[-17, 17, -7]],
|
||||||
|
[[ 12,-17, -5],[ 7,-17,-17]],
|
||||||
|
[[ -5, 12,-17],[-17, 7,-17]],
|
||||||
|
[[ 17, 5, 12],[ 17, 17, 7]],
|
||||||
|
[[-12,-17, 5],[ -7,-17, 17]],
|
||||||
|
[[ 5,-12,-17],[ 17, -7,-17]],
|
||||||
|
[[-17, -5, 12],[-17,-17, 7]],
|
||||||
|
[[ 12, 17, 5],[ 7, 17, 17]],
|
||||||
|
[[ -5, 17,-12],[-17, 17, -7]],
|
||||||
|
[[-12, -5, 17],[ -7,-17, 17]],
|
||||||
|
[[ 17,-12, -5],[ 17, -7,-17]],
|
||||||
|
[[ 5,-17,-12],[ 17,-17, -7]],
|
||||||
|
[[ 12, 5, 17],[ 7, 17, 17]],
|
||||||
|
[[-17, 12, -5],[-17, 7,-17]],
|
||||||
|
[[ -5,-17, 12],[-17,-17, 7]],
|
||||||
|
[[-12, 5,-17],[ -7, 17,-17]],
|
||||||
|
[[ 17, 12, 5],[ 17, 7, 17]],
|
||||||
|
[[ 5, 17, 12],[ 17, 17, 7]],
|
||||||
|
[[ 12, -5,-17],[ 7,-17,-17]],
|
||||||
|
[[-17,-12, 5],[-17,-7, 17]]],dtype='float')}
|
||||||
|
|
||||||
|
# Greninger--Troiano' orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
|
||||||
|
GTprime = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 7, 17, 17],[ 12, 5, 17]],
|
||||||
|
[[ 17, 7, 17],[ 17, 12, 5]],
|
||||||
|
[[ 17, 17, 7],[ 5, 17, 12]],
|
||||||
|
[[ -7,-17, 17],[-12, -5, 17]],
|
||||||
|
[[-17, -7, 17],[-17,-12, 5]],
|
||||||
|
[[-17,-17, 7],[ -5,-17, 12]],
|
||||||
|
[[ 7,-17,-17],[ 12, -5,-17]],
|
||||||
|
[[ 17, -7,-17],[ 17,-12, -5]],
|
||||||
|
[[ 17,-17, -7],[ 5,-17,-12]],
|
||||||
|
[[ -7, 17,-17],[-12, 5,-17]],
|
||||||
|
[[-17, 7,-17],[-17, 12, -5]],
|
||||||
|
[[-17, 17, -7],[ -5, 17,-12]],
|
||||||
|
[[ 7, 17, 17],[ 12, 17, 5]],
|
||||||
|
[[ 17, 7, 17],[ 5, 12, 17]],
|
||||||
|
[[ 17, 17, 7],[ 17, 5, 12]],
|
||||||
|
[[ -7,-17, 17],[-12,-17, 5]],
|
||||||
|
[[-17, -7, 17],[ -5,-12, 17]],
|
||||||
|
[[-17,-17, 7],[-17, -5, 12]],
|
||||||
|
[[ 7,-17,-17],[ 12,-17, -5]],
|
||||||
|
[[ 17, -7,-17],[ 5, -12,-17]],
|
||||||
|
[[ 17,-17, -7],[ 17, -5,-12]],
|
||||||
|
[[ -7, 17,-17],[-12, 17, -5]],
|
||||||
|
[[-17, 7,-17],[ -5, 12,-17]],
|
||||||
|
[[-17, 17, -7],[-17, 5,-12]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ 0, 1, -1],[ 1, 1, -1]],
|
||||||
|
[[ -1, 0, 1],[ -1, 1, 1]],
|
||||||
|
[[ 1, -1, 0],[ 1, -1, 1]],
|
||||||
|
[[ 0, -1, -1],[ -1, -1, -1]],
|
||||||
|
[[ 1, 0, 1],[ 1, -1, 1]],
|
||||||
|
[[ 1, -1, 0],[ 1, -1, -1]],
|
||||||
|
[[ 0, 1, -1],[ -1, 1, -1]],
|
||||||
|
[[ 1, 0, 1],[ 1, 1, 1]],
|
||||||
|
[[ -1, -1, 0],[ -1, -1, 1]],
|
||||||
|
[[ 0, -1, -1],[ 1, -1, -1]],
|
||||||
|
[[ -1, 0, 1],[ -1, -1, 1]],
|
||||||
|
[[ -1, -1, 0],[ -1, -1, -1]],
|
||||||
|
[[ 0, -1, 1],[ 1, -1, 1]],
|
||||||
|
[[ 1, 0, -1],[ 1, 1, -1]],
|
||||||
|
[[ -1, 1, 0],[ -1, 1, 1]],
|
||||||
|
[[ 0, 1, 1],[ -1, 1, 1]],
|
||||||
|
[[ -1, 0, -1],[ -1, -1, -1]],
|
||||||
|
[[ -1, 1, 0],[ -1, 1, -1]],
|
||||||
|
[[ 0, -1, 1],[ -1, -1, 1]],
|
||||||
|
[[ -1, 0, -1],[ -1, 1, -1]],
|
||||||
|
[[ 1, 1, 0],[ 1, 1, 1]],
|
||||||
|
[[ 0, 1, 1],[ 1, 1, 1]],
|
||||||
|
[[ 1, 0, -1],[ 1, -1, -1]],
|
||||||
|
[[ 1, 1, 0],[ 1, 1, -1]]],dtype='float')}
|
||||||
|
|
||||||
|
# Nishiyama--Wassermann orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from H. Kitahara et al., Materials Characterization 54:378-386, 2005
|
||||||
|
NW = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, 1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ 1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, -1, 1],[ 0, 1, 1]],
|
||||||
|
[[ -1, -1, 1],[ 0, 1, 1]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ 2, -1, -1],[ 0, -1, 1]],
|
||||||
|
[[ -1, 2, -1],[ 0, -1, 1]],
|
||||||
|
[[ -1, -1, 2],[ 0, -1, 1]],
|
||||||
|
[[ -2, -1, -1],[ 0, -1, 1]],
|
||||||
|
[[ 1, 2, -1],[ 0, -1, 1]],
|
||||||
|
[[ 1, -1, 2],[ 0, -1, 1]],
|
||||||
|
[[ 2, 1, -1],[ 0, -1, 1]],
|
||||||
|
[[ -1, -2, -1],[ 0, -1, 1]],
|
||||||
|
[[ -1, 1, 2],[ 0, -1, 1]],
|
||||||
|
[[ 2, -1, 1],[ 0, -1, 1]], #It is wrong in the paper, but matrix is correct
|
||||||
|
[[ -1, 2, 1],[ 0, -1, 1]],
|
||||||
|
[[ -1, -1, -2],[ 0, -1, 1]]],dtype='float')}
|
||||||
|
|
||||||
|
# Pitsch orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from Y. He et al., Acta Materialia 53:1179-1190, 2005
|
||||||
|
Pitsch = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 0, 1, 0],[ -1, 0, 1]],
|
||||||
|
[[ 0, 0, 1],[ 1, -1, 0]],
|
||||||
|
[[ 1, 0, 0],[ 0, 1, -1]],
|
||||||
|
[[ 1, 0, 0],[ 0, -1, -1]],
|
||||||
|
[[ 0, 1, 0],[ -1, 0, -1]],
|
||||||
|
[[ 0, 0, 1],[ -1, -1, 0]],
|
||||||
|
[[ 0, 1, 0],[ -1, 0, -1]],
|
||||||
|
[[ 0, 0, 1],[ -1, -1, 0]],
|
||||||
|
[[ 1, 0, 0],[ 0, -1, -1]],
|
||||||
|
[[ 1, 0, 0],[ 0, -1, 1]],
|
||||||
|
[[ 0, 1, 0],[ 1, 0, -1]],
|
||||||
|
[[ 0, 0, 1],[ -1, 1, 0]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ 1, 0, 1],[ 1, -1, 1]],
|
||||||
|
[[ 1, 1, 0],[ 1, 1, -1]],
|
||||||
|
[[ 0, 1, 1],[ -1, 1, 1]],
|
||||||
|
[[ 0, 1, -1],[ -1, 1, -1]],
|
||||||
|
[[ -1, 0, 1],[ -1, -1, 1]],
|
||||||
|
[[ 1, -1, 0],[ 1, -1, -1]],
|
||||||
|
[[ 1, 0, -1],[ 1, -1, -1]],
|
||||||
|
[[ -1, 1, 0],[ -1, 1, -1]],
|
||||||
|
[[ 0, -1, 1],[ -1, -1, 1]],
|
||||||
|
[[ 0, 1, 1],[ -1, 1, 1]],
|
||||||
|
[[ 1, 0, 1],[ 1, -1, 1]],
|
||||||
|
[[ 1, 1, 0],[ 1, 1, -1]]],dtype='float')}
|
||||||
|
|
||||||
|
# Bain orientation relationship for fcc <-> bcc transformation
|
||||||
|
# from Y. He et al., Journal of Applied Crystallography 39:72-81, 2006
|
||||||
|
Bain = {'mapping':{'fcc':0,'bcc':1},
|
||||||
|
'planes': np.array([
|
||||||
|
[[ 1, 0, 0],[ 1, 0, 0]],
|
||||||
|
[[ 0, 1, 0],[ 0, 1, 0]],
|
||||||
|
[[ 0, 0, 1],[ 0, 0, 1]]],dtype='float'),
|
||||||
|
'directions': np.array([
|
||||||
|
[[ 0, 1, 0],[ 0, 1, 1]],
|
||||||
|
[[ 0, 0, 1],[ 1, 0, 1]],
|
||||||
|
[[ 1, 0, 0],[ 1, 1, 0]]],dtype='float')}
|
||||||
|
|
||||||
|
def relationOperations(self,model):
|
||||||
|
"""
|
||||||
|
Crystallographic orientation relationships for phase transformations.
|
||||||
|
|
||||||
|
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
|
||||||
|
|
||||||
|
"""
|
||||||
|
models={'KS':self.KS, 'GT':self.GT, 'GT_prime':self.GTprime,
|
||||||
|
'NW':self.NW, 'Pitsch': self.Pitsch, 'Bain':self.Bain}
|
||||||
|
try:
|
||||||
|
relationship = models[model]
|
||||||
|
except KeyError :
|
||||||
|
raise KeyError('Orientation relationship "{}" is unknown'.format(model))
|
||||||
|
|
||||||
|
if self.lattice not in relationship['mapping']:
|
||||||
|
raise ValueError('Relationship "{}" not supported for lattice "{}"'.format(model,self.lattice))
|
||||||
|
|
||||||
|
r = {'lattice':Lattice((set(relationship['mapping'])-{self.lattice}).pop()), # target lattice
|
||||||
|
'rotations':[] }
|
||||||
|
|
||||||
|
myPlane_id = relationship['mapping'][self.lattice]
|
||||||
|
otherPlane_id = (myPlane_id+1)%2
|
||||||
|
myDir_id = myPlane_id +2
|
||||||
|
otherDir_id = otherPlane_id +2
|
||||||
|
|
||||||
|
for miller in np.hstack((relationship['planes'],relationship['directions'])):
|
||||||
|
myPlane = miller[myPlane_id]/ np.linalg.norm(miller[myPlane_id])
|
||||||
|
myDir = miller[myDir_id]/ np.linalg.norm(miller[myDir_id])
|
||||||
|
myMatrix = np.array([myDir,np.cross(myPlane,myDir),myPlane])
|
||||||
|
|
||||||
|
otherPlane = miller[otherPlane_id]/ np.linalg.norm(miller[otherPlane_id])
|
||||||
|
otherDir = miller[otherDir_id]/ np.linalg.norm(miller[otherDir_id])
|
||||||
|
otherMatrix = np.array([otherDir,np.cross(otherPlane,otherDir),otherPlane])
|
||||||
|
|
||||||
|
r['rotations'].append(Rotation.fromMatrix(np.dot(otherMatrix.T,myMatrix)))
|
||||||
|
|
||||||
|
return r
|
File diff suppressed because it is too large
Load Diff
|
@ -0,0 +1,837 @@
|
||||||
|
import numpy as np
|
||||||
|
|
||||||
|
from . import Lambert
|
||||||
|
|
||||||
|
P = -1
|
||||||
|
|
||||||
|
def iszero(a):
|
||||||
|
return np.isclose(a,0.0,atol=1.0e-12,rtol=0.0)
|
||||||
|
|
||||||
|
|
||||||
|
class Rotation:
|
||||||
|
u"""
|
||||||
|
Orientation stored with functionality for conversion to different representations.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
D. Rowenhorst et al., Modelling and Simulation in Materials Science and Engineering 23:083501, 2015
|
||||||
|
https://doi.org/10.1088/0965-0393/23/8/083501
|
||||||
|
|
||||||
|
Conventions
|
||||||
|
-----------
|
||||||
|
Convention 1: Coordinate frames are right-handed.
|
||||||
|
Convention 2: A rotation angle ω is taken to be positive for a counterclockwise rotation
|
||||||
|
when viewing from the end point of the rotation axis towards the origin.
|
||||||
|
Convention 3: Rotations will be interpreted in the passive sense.
|
||||||
|
Convention 4: Euler angle triplets are implemented using the Bunge convention,
|
||||||
|
with the angular ranges as [0, 2π],[0, π],[0, 2π].
|
||||||
|
Convention 5: The rotation angle ω is limited to the interval [0, π].
|
||||||
|
Convention 6: the real part of a quaternion is positive, Re(q) > 0
|
||||||
|
Convention 7: P = -1 (as default).
|
||||||
|
|
||||||
|
Usage
|
||||||
|
-----
|
||||||
|
Vector "a" (defined in coordinate system "A") is passively rotated
|
||||||
|
resulting in new coordinates "b" when expressed in system "B".
|
||||||
|
b = Q * a
|
||||||
|
b = np.dot(Q.asMatrix(),a)
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
__slots__ = ['quaternion']
|
||||||
|
|
||||||
|
def __init__(self,quaternion = np.array([1.0,0.0,0.0,0.0])):
|
||||||
|
"""
|
||||||
|
Initializes to identity unless specified.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
quaternion : numpy.ndarray, optional
|
||||||
|
Unit quaternion that follows the conventions. Use .fromQuaternion to perform a sanity check.
|
||||||
|
|
||||||
|
"""
|
||||||
|
self.quaternion = quaternion.copy()
|
||||||
|
|
||||||
|
def __copy__(self):
|
||||||
|
"""Copy."""
|
||||||
|
return self.__class__(self.quaternion)
|
||||||
|
|
||||||
|
copy = __copy__
|
||||||
|
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
"""Orientation displayed as unit quaternion, rotation matrix, and Bunge-Euler angles."""
|
||||||
|
return '\n'.join([
|
||||||
|
'Quaternion: (real={:.3f}, imag=<{:+.3f}, {:+.3f}, {:+.3f}>)'.format(*(self.quaternion)),
|
||||||
|
'Matrix:\n{}'.format(self.asMatrix()),
|
||||||
|
'Bunge Eulers / deg: ({:3.2f}, {:3.2f}, {:3.2f})'.format(*self.asEulers(degrees=True)),
|
||||||
|
])
|
||||||
|
|
||||||
|
|
||||||
|
def __mul__(self, other):
|
||||||
|
"""
|
||||||
|
Multiplication.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : numpy.ndarray or Rotation
|
||||||
|
Vector, second or fourth order tensor, or rotation object that is rotated.
|
||||||
|
|
||||||
|
Todo
|
||||||
|
----
|
||||||
|
Document details active/passive)
|
||||||
|
considere rotation of (3,3,3,3)-matrix
|
||||||
|
|
||||||
|
"""
|
||||||
|
if isinstance(other, Rotation): # rotate a rotation
|
||||||
|
self_q = self.quaternion[0]
|
||||||
|
self_p = self.quaternion[1:]
|
||||||
|
other_q = other.quaternion[0]
|
||||||
|
other_p = other.quaternion[1:]
|
||||||
|
R = self.__class__(np.append(self_q*other_q - np.dot(self_p,other_p),
|
||||||
|
self_q*other_p + other_q*self_p + P * np.cross(self_p,other_p)))
|
||||||
|
return R.standardize()
|
||||||
|
elif isinstance(other, (tuple,np.ndarray)):
|
||||||
|
if isinstance(other,tuple) or other.shape == (3,): # rotate a single (3)-vector or meshgrid
|
||||||
|
A = self.quaternion[0]**2.0 - np.dot(self.quaternion[1:],self.quaternion[1:])
|
||||||
|
B = 2.0 * ( self.quaternion[1]*other[0]
|
||||||
|
+ self.quaternion[2]*other[1]
|
||||||
|
+ self.quaternion[3]*other[2])
|
||||||
|
C = 2.0 * P*self.quaternion[0]
|
||||||
|
|
||||||
|
return np.array([
|
||||||
|
A*other[0] + B*self.quaternion[1] + C*(self.quaternion[2]*other[2] - self.quaternion[3]*other[1]),
|
||||||
|
A*other[1] + B*self.quaternion[2] + C*(self.quaternion[3]*other[0] - self.quaternion[1]*other[2]),
|
||||||
|
A*other[2] + B*self.quaternion[3] + C*(self.quaternion[1]*other[1] - self.quaternion[2]*other[0]),
|
||||||
|
])
|
||||||
|
elif other.shape == (3,3,): # rotate a single (3x3)-matrix
|
||||||
|
return np.dot(self.asMatrix(),np.dot(other,self.asMatrix().T))
|
||||||
|
elif other.shape == (3,3,3,3,):
|
||||||
|
raise NotImplementedError
|
||||||
|
else:
|
||||||
|
return NotImplemented
|
||||||
|
else:
|
||||||
|
return NotImplemented
|
||||||
|
|
||||||
|
|
||||||
|
def inverse(self):
|
||||||
|
"""In-place inverse rotation/backward rotation."""
|
||||||
|
self.quaternion[1:] *= -1
|
||||||
|
return self
|
||||||
|
|
||||||
|
def inversed(self):
|
||||||
|
"""Inverse rotation/backward rotation."""
|
||||||
|
return self.copy().inverse()
|
||||||
|
|
||||||
|
|
||||||
|
def standardize(self):
|
||||||
|
"""In-place quaternion representation with positive q."""
|
||||||
|
if self.quaternion[0] < 0.0: self.quaternion*=-1
|
||||||
|
return self
|
||||||
|
|
||||||
|
def standardized(self):
|
||||||
|
"""Quaternion representation with positive q."""
|
||||||
|
return self.copy().standardize()
|
||||||
|
|
||||||
|
|
||||||
|
def misorientation(self,other):
|
||||||
|
"""
|
||||||
|
Get Misorientation.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Rotation
|
||||||
|
Rotation to which the misorientation is computed.
|
||||||
|
|
||||||
|
"""
|
||||||
|
return other*self.inversed()
|
||||||
|
|
||||||
|
|
||||||
|
def average(self,other):
|
||||||
|
"""
|
||||||
|
Calculate the average rotation.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
other : Rotation
|
||||||
|
Rotation from which the average is rotated.
|
||||||
|
|
||||||
|
"""
|
||||||
|
return Rotation.fromAverage([self,other])
|
||||||
|
|
||||||
|
|
||||||
|
################################################################################################
|
||||||
|
# convert to different orientation representations (numpy arrays)
|
||||||
|
|
||||||
|
def asQuaternion(self):
|
||||||
|
"""
|
||||||
|
Unit quaternion [q, p_1, p_2, p_3] unless quaternion == True: damask.quaternion object.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
quaternion : bool, optional
|
||||||
|
return quaternion as DAMASK object.
|
||||||
|
|
||||||
|
"""
|
||||||
|
return self.quaternion
|
||||||
|
|
||||||
|
def asEulers(self,
|
||||||
|
degrees = False):
|
||||||
|
"""
|
||||||
|
Bunge-Euler angles: (φ_1, ϕ, φ_2).
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
degrees : bool, optional
|
||||||
|
return angles in degrees.
|
||||||
|
|
||||||
|
"""
|
||||||
|
eu = Rotation.qu2eu(self.quaternion)
|
||||||
|
if degrees: eu = np.degrees(eu)
|
||||||
|
return eu
|
||||||
|
|
||||||
|
def asAxisAngle(self,
|
||||||
|
degrees = False,
|
||||||
|
pair = False):
|
||||||
|
"""
|
||||||
|
Axis angle representation [n_1, n_2, n_3, ω] unless pair == True: ([n_1, n_2, n_3], ω).
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
degrees : bool, optional
|
||||||
|
return rotation angle in degrees.
|
||||||
|
pair : bool, optional
|
||||||
|
return tuple of axis and angle.
|
||||||
|
|
||||||
|
"""
|
||||||
|
ax = Rotation.qu2ax(self.quaternion)
|
||||||
|
if degrees: ax[3] = np.degrees(ax[3])
|
||||||
|
return (ax[:3],np.degrees(ax[3])) if pair else ax
|
||||||
|
|
||||||
|
def asMatrix(self):
|
||||||
|
"""Rotation matrix."""
|
||||||
|
return Rotation.qu2om(self.quaternion)
|
||||||
|
|
||||||
|
def asRodrigues(self,
|
||||||
|
vector = False):
|
||||||
|
"""
|
||||||
|
Rodrigues-Frank vector representation [n_1, n_2, n_3, tan(ω/2)] unless vector == True: [n_1, n_2, n_3] * tan(ω/2).
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
vector : bool, optional
|
||||||
|
return as actual Rodrigues--Frank vector, i.e. rotation axis scaled by tan(ω/2).
|
||||||
|
|
||||||
|
"""
|
||||||
|
ro = Rotation.qu2ro(self.quaternion)
|
||||||
|
return ro[:3]*ro[3] if vector else ro
|
||||||
|
|
||||||
|
def asHomochoric(self):
|
||||||
|
"""Homochoric vector: (h_1, h_2, h_3)."""
|
||||||
|
return Rotation.qu2ho(self.quaternion)
|
||||||
|
|
||||||
|
def asCubochoric(self):
|
||||||
|
"""Cubochoric vector: (c_1, c_2, c_3)."""
|
||||||
|
return Rotation.qu2cu(self.quaternion)
|
||||||
|
|
||||||
|
def asM(self):
|
||||||
|
"""
|
||||||
|
Intermediate representation supporting quaternion averaging.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
F. Landis Markley et al., Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
|
||||||
|
https://doi.org/10.2514/1.28949
|
||||||
|
|
||||||
|
"""
|
||||||
|
return np.outer(self.quaternion,self.quaternion)
|
||||||
|
|
||||||
|
|
||||||
|
################################################################################################
|
||||||
|
# static constructors. The input data needs to follow the convention, options allow to
|
||||||
|
# relax these convections
|
||||||
|
@staticmethod
|
||||||
|
def fromQuaternion(quaternion,
|
||||||
|
acceptHomomorph = False,
|
||||||
|
P = -1):
|
||||||
|
|
||||||
|
qu = quaternion if isinstance(quaternion,np.ndarray) and quaternion.dtype == np.dtype(float) \
|
||||||
|
else np.array(quaternion,dtype=float)
|
||||||
|
if P > 0: qu[1:4] *= -1 # convert from P=1 to P=-1
|
||||||
|
if qu[0] < 0.0:
|
||||||
|
if acceptHomomorph:
|
||||||
|
qu *= -1.
|
||||||
|
else:
|
||||||
|
raise ValueError('Quaternion has negative first component.\n{}'.format(qu[0]))
|
||||||
|
if not np.isclose(np.linalg.norm(qu), 1.0):
|
||||||
|
raise ValueError('Quaternion is not of unit length.\n{} {} {} {}'.format(*qu))
|
||||||
|
|
||||||
|
return Rotation(qu)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromEulers(eulers,
|
||||||
|
degrees = False):
|
||||||
|
|
||||||
|
eu = eulers if isinstance(eulers, np.ndarray) and eulers.dtype == np.dtype(float) \
|
||||||
|
else np.array(eulers,dtype=float)
|
||||||
|
eu = np.radians(eu) if degrees else eu
|
||||||
|
if np.any(eu < 0.0) or np.any(eu > 2.0*np.pi) or eu[1] > np.pi:
|
||||||
|
raise ValueError('Euler angles outside of [0..2π],[0..π],[0..2π].\n{} {} {}.'.format(*eu))
|
||||||
|
|
||||||
|
return Rotation(Rotation.eu2qu(eu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromAxisAngle(angleAxis,
|
||||||
|
degrees = False,
|
||||||
|
normalise = False,
|
||||||
|
P = -1):
|
||||||
|
|
||||||
|
ax = angleAxis if isinstance(angleAxis, np.ndarray) and angleAxis.dtype == np.dtype(float) \
|
||||||
|
else np.array(angleAxis,dtype=float)
|
||||||
|
if P > 0: ax[0:3] *= -1 # convert from P=1 to P=-1
|
||||||
|
if degrees: ax[ 3] = np.radians(ax[3])
|
||||||
|
if normalise: ax[0:3] /= np.linalg.norm(ax[0:3])
|
||||||
|
if ax[3] < 0.0 or ax[3] > np.pi:
|
||||||
|
raise ValueError('Axis angle rotation angle outside of [0..π].\n'.format(ax[3]))
|
||||||
|
if not np.isclose(np.linalg.norm(ax[0:3]), 1.0):
|
||||||
|
raise ValueError('Axis angle rotation axis is not of unit length.\n{} {} {}'.format(*ax[0:3]))
|
||||||
|
|
||||||
|
return Rotation(Rotation.ax2qu(ax))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromBasis(basis,
|
||||||
|
orthonormal = True,
|
||||||
|
reciprocal = False,
|
||||||
|
):
|
||||||
|
|
||||||
|
om = basis if isinstance(basis, np.ndarray) else np.array(basis).reshape((3,3))
|
||||||
|
if reciprocal:
|
||||||
|
om = np.linalg.inv(om.T/np.pi) # transform reciprocal basis set
|
||||||
|
orthonormal = False # contains stretch
|
||||||
|
if not orthonormal:
|
||||||
|
(U,S,Vh) = np.linalg.svd(om) # singular value decomposition
|
||||||
|
om = np.dot(U,Vh)
|
||||||
|
if not np.isclose(np.linalg.det(om),1.0):
|
||||||
|
raise ValueError('matrix is not a proper rotation.\n{}'.format(om))
|
||||||
|
if not np.isclose(np.dot(om[0],om[1]), 0.0) \
|
||||||
|
or not np.isclose(np.dot(om[1],om[2]), 0.0) \
|
||||||
|
or not np.isclose(np.dot(om[2],om[0]), 0.0):
|
||||||
|
raise ValueError('matrix is not orthogonal.\n{}'.format(om))
|
||||||
|
|
||||||
|
return Rotation(Rotation.om2qu(om))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromMatrix(om,
|
||||||
|
):
|
||||||
|
|
||||||
|
return Rotation.fromBasis(om)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromRodrigues(rodrigues,
|
||||||
|
normalise = False,
|
||||||
|
P = -1):
|
||||||
|
|
||||||
|
ro = rodrigues if isinstance(rodrigues, np.ndarray) and rodrigues.dtype == np.dtype(float) \
|
||||||
|
else np.array(rodrigues,dtype=float)
|
||||||
|
if P > 0: ro[0:3] *= -1 # convert from P=1 to P=-1
|
||||||
|
if normalise: ro[0:3] /= np.linalg.norm(ro[0:3])
|
||||||
|
if not np.isclose(np.linalg.norm(ro[0:3]), 1.0):
|
||||||
|
raise ValueError('Rodrigues rotation axis is not of unit length.\n{} {} {}'.format(*ro[0:3]))
|
||||||
|
if ro[3] < 0.0:
|
||||||
|
raise ValueError('Rodriques rotation angle not positive.\n'.format(ro[3]))
|
||||||
|
|
||||||
|
return Rotation(Rotation.ro2qu(ro))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromHomochoric(homochoric,
|
||||||
|
P = -1):
|
||||||
|
|
||||||
|
ho = homochoric if isinstance(homochoric, np.ndarray) and homochoric.dtype == np.dtype(float) \
|
||||||
|
else np.array(homochoric,dtype=float)
|
||||||
|
if P > 0: ho *= -1 # convert from P=1 to P=-1
|
||||||
|
|
||||||
|
return Rotation(Rotation.ho2qu(ho))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromCubochoric(cubochoric,
|
||||||
|
P = -1):
|
||||||
|
|
||||||
|
cu = cubochoric if isinstance(cubochoric, np.ndarray) and cubochoric.dtype == np.dtype(float) \
|
||||||
|
else np.array(cubochoric,dtype=float)
|
||||||
|
ho = Rotation.cu2ho(cu)
|
||||||
|
if P > 0: ho *= -1 # convert from P=1 to P=-1
|
||||||
|
|
||||||
|
return Rotation(Rotation.ho2qu(ho))
|
||||||
|
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromAverage(rotations,
|
||||||
|
weights = []):
|
||||||
|
"""
|
||||||
|
Average rotation.
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
F. Landis Markley et al., Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
|
||||||
|
https://doi.org/10.2514/1.28949
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
rotations : list of Rotations
|
||||||
|
Rotations to average from
|
||||||
|
weights : list of floats, optional
|
||||||
|
Weights for each rotation used for averaging
|
||||||
|
|
||||||
|
"""
|
||||||
|
if not all(isinstance(item, Rotation) for item in rotations):
|
||||||
|
raise TypeError("Only instances of Rotation can be averaged.")
|
||||||
|
|
||||||
|
N = len(rotations)
|
||||||
|
if weights == [] or not weights:
|
||||||
|
weights = np.ones(N,dtype='i')
|
||||||
|
|
||||||
|
for i,(r,n) in enumerate(zip(rotations,weights)):
|
||||||
|
M = r.asM() * n if i == 0 \
|
||||||
|
else M + r.asM() * n # noqa add (multiples) of this rotation to average noqa
|
||||||
|
eig, vec = np.linalg.eig(M/N)
|
||||||
|
|
||||||
|
return Rotation.fromQuaternion(np.real(vec.T[eig.argmax()]),acceptHomomorph = True)
|
||||||
|
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def fromRandom():
|
||||||
|
r = np.random.random(3)
|
||||||
|
A = np.sqrt(r[2])
|
||||||
|
B = np.sqrt(1.0-r[2])
|
||||||
|
return Rotation(np.array([np.cos(2.0*np.pi*r[0])*A,
|
||||||
|
np.sin(2.0*np.pi*r[1])*B,
|
||||||
|
np.cos(2.0*np.pi*r[1])*B,
|
||||||
|
np.sin(2.0*np.pi*r[0])*A])).standardize()
|
||||||
|
|
||||||
|
|
||||||
|
####################################################################################################
|
||||||
|
# Code below available according to the following conditions on https://github.com/MarDiehl/3Drotations
|
||||||
|
####################################################################################################
|
||||||
|
# Copyright (c) 2017-2019, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
|
||||||
|
# Copyright (c) 2013-2014, Marc De Graef/Carnegie Mellon University
|
||||||
|
# All rights reserved.
|
||||||
|
#
|
||||||
|
# Redistribution and use in source and binary forms, with or without modification, are
|
||||||
|
# permitted provided that the following conditions are met:
|
||||||
|
#
|
||||||
|
# - Redistributions of source code must retain the above copyright notice, this list
|
||||||
|
# of conditions and the following disclaimer.
|
||||||
|
# - Redistributions in binary form must reproduce the above copyright notice, this
|
||||||
|
# list of conditions and the following disclaimer in the documentation and/or
|
||||||
|
# other materials provided with the distribution.
|
||||||
|
# - Neither the names of Marc De Graef, Carnegie Mellon University nor the names
|
||||||
|
# of its contributors may be used to endorse or promote products derived from
|
||||||
|
# this software without specific prior written permission.
|
||||||
|
#
|
||||||
|
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||||
|
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||||
|
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
||||||
|
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
|
||||||
|
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
||||||
|
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
||||||
|
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
||||||
|
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
|
||||||
|
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
|
||||||
|
# USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||||
|
####################################################################################################
|
||||||
|
#---------- Quaternion ----------
|
||||||
|
@staticmethod
|
||||||
|
def qu2om(qu):
|
||||||
|
"""Quaternion to rotation matrix."""
|
||||||
|
qq = qu[0]**2-(qu[1]**2 + qu[2]**2 + qu[3]**2)
|
||||||
|
om = np.diag(qq + 2.0*np.array([qu[1],qu[2],qu[3]])**2)
|
||||||
|
|
||||||
|
om[1,0] = 2.0*(qu[2]*qu[1]+qu[0]*qu[3])
|
||||||
|
om[0,1] = 2.0*(qu[1]*qu[2]-qu[0]*qu[3])
|
||||||
|
om[2,1] = 2.0*(qu[3]*qu[2]+qu[0]*qu[1])
|
||||||
|
om[1,2] = 2.0*(qu[2]*qu[3]-qu[0]*qu[1])
|
||||||
|
om[0,2] = 2.0*(qu[1]*qu[3]+qu[0]*qu[2])
|
||||||
|
om[2,0] = 2.0*(qu[3]*qu[1]-qu[0]*qu[2])
|
||||||
|
return om if P > 0.0 else om.T
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def qu2eu(qu):
|
||||||
|
"""Quaternion to Bunge-Euler angles."""
|
||||||
|
q03 = qu[0]**2+qu[3]**2
|
||||||
|
q12 = qu[1]**2+qu[2]**2
|
||||||
|
chi = np.sqrt(q03*q12)
|
||||||
|
|
||||||
|
if iszero(chi):
|
||||||
|
eu = np.array([np.arctan2(-P*2.0*qu[0]*qu[3],qu[0]**2-qu[3]**2), 0.0, 0.0]) if iszero(q12) else \
|
||||||
|
np.array([np.arctan2(2.0*qu[1]*qu[2],qu[1]**2-qu[2]**2), np.pi, 0.0])
|
||||||
|
else:
|
||||||
|
eu = np.array([np.arctan2((-P*qu[0]*qu[2]+qu[1]*qu[3])*chi, (-P*qu[0]*qu[1]-qu[2]*qu[3])*chi ),
|
||||||
|
np.arctan2( 2.0*chi, q03-q12 ),
|
||||||
|
np.arctan2(( P*qu[0]*qu[2]+qu[1]*qu[3])*chi, (-P*qu[0]*qu[1]+qu[2]*qu[3])*chi )])
|
||||||
|
|
||||||
|
# reduce Euler angles to definition range, i.e a lower limit of 0.0
|
||||||
|
eu = np.where(eu<0, (eu+2.0*np.pi)%np.array([2.0*np.pi,np.pi,2.0*np.pi]),eu)
|
||||||
|
return eu
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def qu2ax(qu):
|
||||||
|
"""
|
||||||
|
Quaternion to axis angle pair.
|
||||||
|
|
||||||
|
Modified version of the original formulation, should be numerically more stable
|
||||||
|
"""
|
||||||
|
if iszero(qu[1]**2+qu[2]**2+qu[3]**2): # set axis to [001] if the angle is 0/360
|
||||||
|
ax = [ 0.0, 0.0, 1.0, 0.0 ]
|
||||||
|
elif not iszero(qu[0]):
|
||||||
|
s = np.sign(qu[0])/np.sqrt(qu[1]**2+qu[2]**2+qu[3]**2)
|
||||||
|
omega = 2.0 * np.arccos(np.clip(qu[0],-1.0,1.0))
|
||||||
|
ax = [ qu[1]*s, qu[2]*s, qu[3]*s, omega ]
|
||||||
|
else:
|
||||||
|
ax = [ qu[1], qu[2], qu[3], np.pi]
|
||||||
|
return np.array(ax)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def qu2ro(qu):
|
||||||
|
"""Quaternion to Rodriques-Frank vector."""
|
||||||
|
if iszero(qu[0]):
|
||||||
|
ro = [qu[1], qu[2], qu[3], np.inf]
|
||||||
|
else:
|
||||||
|
s = np.linalg.norm([qu[1],qu[2],qu[3]])
|
||||||
|
ro = [0.0,0.0,P,0.0] if iszero(s) else \
|
||||||
|
[ qu[1]/s, qu[2]/s, qu[3]/s, np.tan(np.arccos(np.clip(qu[0],-1.0,1.0)))]
|
||||||
|
return np.array(ro)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def qu2ho(qu):
|
||||||
|
"""Quaternion to homochoric vector."""
|
||||||
|
omega = 2.0 * np.arccos(np.clip(qu[0],-1.0,1.0))
|
||||||
|
|
||||||
|
if iszero(omega):
|
||||||
|
ho = np.array([ 0.0, 0.0, 0.0 ])
|
||||||
|
else:
|
||||||
|
ho = np.array([qu[1], qu[2], qu[3]])
|
||||||
|
f = 0.75 * ( omega - np.sin(omega) )
|
||||||
|
ho = ho/np.linalg.norm(ho) * f**(1./3.)
|
||||||
|
return ho
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def qu2cu(qu):
|
||||||
|
"""Quaternion to cubochoric vector."""
|
||||||
|
return Rotation.ho2cu(Rotation.qu2ho(qu))
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Rotation matrix ----------
|
||||||
|
@staticmethod
|
||||||
|
def om2qu(om):
|
||||||
|
"""
|
||||||
|
Rotation matrix to quaternion.
|
||||||
|
|
||||||
|
The original formulation (direct conversion) had (numerical?) issues
|
||||||
|
"""
|
||||||
|
return Rotation.eu2qu(Rotation.om2eu(om))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def om2eu(om):
|
||||||
|
"""Rotation matrix to Bunge-Euler angles."""
|
||||||
|
if abs(om[2,2]) < 1.0:
|
||||||
|
zeta = 1.0/np.sqrt(1.0-om[2,2]**2)
|
||||||
|
eu = np.array([np.arctan2(om[2,0]*zeta,-om[2,1]*zeta),
|
||||||
|
np.arccos(om[2,2]),
|
||||||
|
np.arctan2(om[0,2]*zeta, om[1,2]*zeta)])
|
||||||
|
else:
|
||||||
|
eu = np.array([np.arctan2( om[0,1],om[0,0]), np.pi*0.5*(1-om[2,2]),0.0]) # following the paper, not the reference implementation
|
||||||
|
|
||||||
|
# reduce Euler angles to definition range, i.e a lower limit of 0.0
|
||||||
|
eu = np.where(eu<0, (eu+2.0*np.pi)%np.array([2.0*np.pi,np.pi,2.0*np.pi]),eu)
|
||||||
|
return eu
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def om2ax(om):
|
||||||
|
"""Rotation matrix to axis angle pair."""
|
||||||
|
ax=np.empty(4)
|
||||||
|
|
||||||
|
# first get the rotation angle
|
||||||
|
t = 0.5*(om.trace() -1.0)
|
||||||
|
ax[3] = np.arccos(np.clip(t,-1.0,1.0))
|
||||||
|
|
||||||
|
if iszero(ax[3]):
|
||||||
|
ax = [ 0.0, 0.0, 1.0, 0.0]
|
||||||
|
else:
|
||||||
|
w,vr = np.linalg.eig(om)
|
||||||
|
# next, find the eigenvalue (1,0j)
|
||||||
|
i = np.where(np.isclose(w,1.0+0.0j))[0][0]
|
||||||
|
ax[0:3] = np.real(vr[0:3,i])
|
||||||
|
diagDelta = np.array([om[1,2]-om[2,1],om[2,0]-om[0,2],om[0,1]-om[1,0]])
|
||||||
|
ax[0:3] = np.where(iszero(diagDelta), ax[0:3],np.abs(ax[0:3])*np.sign(-P*diagDelta))
|
||||||
|
return np.array(ax)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def om2ro(om):
|
||||||
|
"""Rotation matrix to Rodriques-Frank vector."""
|
||||||
|
return Rotation.eu2ro(Rotation.om2eu(om))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def om2ho(om):
|
||||||
|
"""Rotation matrix to homochoric vector."""
|
||||||
|
return Rotation.ax2ho(Rotation.om2ax(om))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def om2cu(om):
|
||||||
|
"""Rotation matrix to cubochoric vector."""
|
||||||
|
return Rotation.ho2cu(Rotation.om2ho(om))
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Bunge-Euler angles ----------
|
||||||
|
@staticmethod
|
||||||
|
def eu2qu(eu):
|
||||||
|
"""Bunge-Euler angles to quaternion."""
|
||||||
|
ee = 0.5*eu
|
||||||
|
cPhi = np.cos(ee[1])
|
||||||
|
sPhi = np.sin(ee[1])
|
||||||
|
qu = np.array([ cPhi*np.cos(ee[0]+ee[2]),
|
||||||
|
-P*sPhi*np.cos(ee[0]-ee[2]),
|
||||||
|
-P*sPhi*np.sin(ee[0]-ee[2]),
|
||||||
|
-P*cPhi*np.sin(ee[0]+ee[2]) ])
|
||||||
|
if qu[0] < 0.0: qu*=-1
|
||||||
|
return qu
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def eu2om(eu):
|
||||||
|
"""Bunge-Euler angles to rotation matrix."""
|
||||||
|
c = np.cos(eu)
|
||||||
|
s = np.sin(eu)
|
||||||
|
|
||||||
|
om = np.array([[+c[0]*c[2]-s[0]*s[2]*c[1], +s[0]*c[2]+c[0]*s[2]*c[1], +s[2]*s[1]],
|
||||||
|
[-c[0]*s[2]-s[0]*c[2]*c[1], -s[0]*s[2]+c[0]*c[2]*c[1], +c[2]*s[1]],
|
||||||
|
[+s[0]*s[1], -c[0]*s[1], +c[1] ]])
|
||||||
|
|
||||||
|
om[np.where(iszero(om))] = 0.0
|
||||||
|
return om
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def eu2ax(eu):
|
||||||
|
"""Bunge-Euler angles to axis angle pair."""
|
||||||
|
t = np.tan(eu[1]*0.5)
|
||||||
|
sigma = 0.5*(eu[0]+eu[2])
|
||||||
|
delta = 0.5*(eu[0]-eu[2])
|
||||||
|
tau = np.linalg.norm([t,np.sin(sigma)])
|
||||||
|
alpha = np.pi if iszero(np.cos(sigma)) else \
|
||||||
|
2.0*np.arctan(tau/np.cos(sigma))
|
||||||
|
|
||||||
|
if iszero(alpha):
|
||||||
|
ax = np.array([ 0.0, 0.0, 1.0, 0.0 ])
|
||||||
|
else:
|
||||||
|
ax = -P/tau * np.array([ t*np.cos(delta), t*np.sin(delta), np.sin(sigma) ]) # passive axis angle pair so a minus sign in front
|
||||||
|
ax = np.append(ax,alpha)
|
||||||
|
if alpha < 0.0: ax *= -1.0 # ensure alpha is positive
|
||||||
|
return ax
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def eu2ro(eu):
|
||||||
|
"""Bunge-Euler angles to Rodriques-Frank vector."""
|
||||||
|
ro = Rotation.eu2ax(eu) # convert to axis angle pair representation
|
||||||
|
if ro[3] >= np.pi: # Differs from original implementation. check convention 5
|
||||||
|
ro[3] = np.inf
|
||||||
|
elif iszero(ro[3]):
|
||||||
|
ro = np.array([ 0.0, 0.0, P, 0.0 ])
|
||||||
|
else:
|
||||||
|
ro[3] = np.tan(ro[3]*0.5)
|
||||||
|
return ro
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def eu2ho(eu):
|
||||||
|
"""Bunge-Euler angles to homochoric vector."""
|
||||||
|
return Rotation.ax2ho(Rotation.eu2ax(eu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def eu2cu(eu):
|
||||||
|
"""Bunge-Euler angles to cubochoric vector."""
|
||||||
|
return Rotation.ho2cu(Rotation.eu2ho(eu))
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Axis angle pair ----------
|
||||||
|
@staticmethod
|
||||||
|
def ax2qu(ax):
|
||||||
|
"""Axis angle pair to quaternion."""
|
||||||
|
if iszero(ax[3]):
|
||||||
|
qu = np.array([ 1.0, 0.0, 0.0, 0.0 ])
|
||||||
|
else:
|
||||||
|
c = np.cos(ax[3]*0.5)
|
||||||
|
s = np.sin(ax[3]*0.5)
|
||||||
|
qu = np.array([ c, ax[0]*s, ax[1]*s, ax[2]*s ])
|
||||||
|
return qu
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ax2om(ax):
|
||||||
|
"""Axis angle pair to rotation matrix."""
|
||||||
|
c = np.cos(ax[3])
|
||||||
|
s = np.sin(ax[3])
|
||||||
|
omc = 1.0-c
|
||||||
|
om=np.diag(ax[0:3]**2*omc + c)
|
||||||
|
|
||||||
|
for idx in [[0,1,2],[1,2,0],[2,0,1]]:
|
||||||
|
q = omc*ax[idx[0]] * ax[idx[1]]
|
||||||
|
om[idx[0],idx[1]] = q + s*ax[idx[2]]
|
||||||
|
om[idx[1],idx[0]] = q - s*ax[idx[2]]
|
||||||
|
return om if P < 0.0 else om.T
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ax2eu(ax):
|
||||||
|
"""Rotation matrix to Bunge Euler angles."""
|
||||||
|
return Rotation.om2eu(Rotation.ax2om(ax))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ax2ro(ax):
|
||||||
|
"""Axis angle pair to Rodriques-Frank vector."""
|
||||||
|
if iszero(ax[3]):
|
||||||
|
ro = [ 0.0, 0.0, P, 0.0 ]
|
||||||
|
else:
|
||||||
|
ro = [ax[0], ax[1], ax[2]]
|
||||||
|
# 180 degree case
|
||||||
|
ro += [np.inf] if np.isclose(ax[3],np.pi,atol=1.0e-15,rtol=0.0) else \
|
||||||
|
[np.tan(ax[3]*0.5)]
|
||||||
|
return np.array(ro)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ax2ho(ax):
|
||||||
|
"""Axis angle pair to homochoric vector."""
|
||||||
|
f = (0.75 * ( ax[3] - np.sin(ax[3]) ))**(1.0/3.0)
|
||||||
|
ho = ax[0:3] * f
|
||||||
|
return ho
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ax2cu(ax):
|
||||||
|
"""Axis angle pair to cubochoric vector."""
|
||||||
|
return Rotation.ho2cu(Rotation.ax2ho(ax))
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Rodrigues-Frank vector ----------
|
||||||
|
@staticmethod
|
||||||
|
def ro2qu(ro):
|
||||||
|
"""Rodriques-Frank vector to quaternion."""
|
||||||
|
return Rotation.ax2qu(Rotation.ro2ax(ro))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ro2om(ro):
|
||||||
|
"""Rodgrigues-Frank vector to rotation matrix."""
|
||||||
|
return Rotation.ax2om(Rotation.ro2ax(ro))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ro2eu(ro):
|
||||||
|
"""Rodriques-Frank vector to Bunge-Euler angles."""
|
||||||
|
return Rotation.om2eu(Rotation.ro2om(ro))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ro2ax(ro):
|
||||||
|
"""Rodriques-Frank vector to axis angle pair."""
|
||||||
|
ta = ro[3]
|
||||||
|
|
||||||
|
if iszero(ta):
|
||||||
|
ax = [ 0.0, 0.0, 1.0, 0.0 ]
|
||||||
|
elif not np.isfinite(ta):
|
||||||
|
ax = [ ro[0], ro[1], ro[2], np.pi ]
|
||||||
|
else:
|
||||||
|
angle = 2.0*np.arctan(ta)
|
||||||
|
ta = 1.0/np.linalg.norm(ro[0:3])
|
||||||
|
ax = [ ro[0]/ta, ro[1]/ta, ro[2]/ta, angle ]
|
||||||
|
return np.array(ax)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ro2ho(ro):
|
||||||
|
"""Rodriques-Frank vector to homochoric vector."""
|
||||||
|
if iszero(np.sum(ro[0:3]**2.0)):
|
||||||
|
ho = [ 0.0, 0.0, 0.0 ]
|
||||||
|
else:
|
||||||
|
f = 2.0*np.arctan(ro[3]) -np.sin(2.0*np.arctan(ro[3])) if np.isfinite(ro[3]) else np.pi
|
||||||
|
ho = ro[0:3] * (0.75*f)**(1.0/3.0)
|
||||||
|
return np.array(ho)
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ro2cu(ro):
|
||||||
|
"""Rodriques-Frank vector to cubochoric vector."""
|
||||||
|
return Rotation.ho2cu(Rotation.ro2ho(ro))
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Homochoric vector----------
|
||||||
|
@staticmethod
|
||||||
|
def ho2qu(ho):
|
||||||
|
"""Homochoric vector to quaternion."""
|
||||||
|
return Rotation.ax2qu(Rotation.ho2ax(ho))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ho2om(ho):
|
||||||
|
"""Homochoric vector to rotation matrix."""
|
||||||
|
return Rotation.ax2om(Rotation.ho2ax(ho))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ho2eu(ho):
|
||||||
|
"""Homochoric vector to Bunge-Euler angles."""
|
||||||
|
return Rotation.ax2eu(Rotation.ho2ax(ho))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ho2ax(ho):
|
||||||
|
"""Homochoric vector to axis angle pair."""
|
||||||
|
tfit = np.array([+1.0000000000018852, -0.5000000002194847,
|
||||||
|
-0.024999992127593126, -0.003928701544781374,
|
||||||
|
-0.0008152701535450438, -0.0002009500426119712,
|
||||||
|
-0.00002397986776071756, -0.00008202868926605841,
|
||||||
|
+0.00012448715042090092, -0.0001749114214822577,
|
||||||
|
+0.0001703481934140054, -0.00012062065004116828,
|
||||||
|
+0.000059719705868660826, -0.00001980756723965647,
|
||||||
|
+0.000003953714684212874, -0.00000036555001439719544])
|
||||||
|
# normalize h and store the magnitude
|
||||||
|
hmag_squared = np.sum(ho**2.)
|
||||||
|
if iszero(hmag_squared):
|
||||||
|
ax = np.array([ 0.0, 0.0, 1.0, 0.0 ])
|
||||||
|
else:
|
||||||
|
hm = hmag_squared
|
||||||
|
|
||||||
|
# convert the magnitude to the rotation angle
|
||||||
|
s = tfit[0] + tfit[1] * hmag_squared
|
||||||
|
for i in range(2,16):
|
||||||
|
hm *= hmag_squared
|
||||||
|
s += tfit[i] * hm
|
||||||
|
ax = np.append(ho/np.sqrt(hmag_squared),2.0*np.arccos(np.clip(s,-1.0,1.0)))
|
||||||
|
return ax
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ho2ro(ho):
|
||||||
|
"""Axis angle pair to Rodriques-Frank vector."""
|
||||||
|
return Rotation.ax2ro(Rotation.ho2ax(ho))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def ho2cu(ho):
|
||||||
|
"""Homochoric vector to cubochoric vector."""
|
||||||
|
return Lambert.BallToCube(ho)
|
||||||
|
|
||||||
|
|
||||||
|
#---------- Cubochoric ----------
|
||||||
|
@staticmethod
|
||||||
|
def cu2qu(cu):
|
||||||
|
"""Cubochoric vector to quaternion."""
|
||||||
|
return Rotation.ho2qu(Rotation.cu2ho(cu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def cu2om(cu):
|
||||||
|
"""Cubochoric vector to rotation matrix."""
|
||||||
|
return Rotation.ho2om(Rotation.cu2ho(cu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def cu2eu(cu):
|
||||||
|
"""Cubochoric vector to Bunge-Euler angles."""
|
||||||
|
return Rotation.ho2eu(Rotation.cu2ho(cu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def cu2ax(cu):
|
||||||
|
"""Cubochoric vector to axis angle pair."""
|
||||||
|
return Rotation.ho2ax(Rotation.cu2ho(cu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def cu2ro(cu):
|
||||||
|
"""Cubochoric vector to Rodriques-Frank vector."""
|
||||||
|
return Rotation.ho2ro(Rotation.cu2ho(cu))
|
||||||
|
|
||||||
|
@staticmethod
|
||||||
|
def cu2ho(cu):
|
||||||
|
"""Cubochoric vector to homochoric vector."""
|
||||||
|
return Lambert.CubeToBall(cu)
|
|
@ -40,55 +40,92 @@ class bcolors:
|
||||||
self.CROSSOUT = ''
|
self.CROSSOUT = ''
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def srepr(arg,glue = '\n'):
|
def srepr(arg,glue = '\n'):
|
||||||
"""Joins arguments as individual lines."""
|
r"""
|
||||||
|
Join arguments as individual lines.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
arg : iterable
|
||||||
|
Items to join.
|
||||||
|
glue : str, optional
|
||||||
|
Defaults to \n.
|
||||||
|
|
||||||
|
"""
|
||||||
if (not hasattr(arg, "strip") and
|
if (not hasattr(arg, "strip") and
|
||||||
(hasattr(arg, "__getitem__") or
|
(hasattr(arg, "__getitem__") or
|
||||||
hasattr(arg, "__iter__"))):
|
hasattr(arg, "__iter__"))):
|
||||||
return glue.join(str(x) for x in arg)
|
return glue.join(str(x) for x in arg)
|
||||||
return arg if isinstance(arg,str) else repr(arg)
|
return arg if isinstance(arg,str) else repr(arg)
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def croak(what, newline = True):
|
def croak(what, newline = True):
|
||||||
"""Writes formated to stderr."""
|
"""
|
||||||
if what is not None:
|
Write formated to stderr.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
what : str or iterable
|
||||||
|
Content to be displayed
|
||||||
|
newline : bool, optional
|
||||||
|
Separate items of what by newline. Defaults to True.
|
||||||
|
|
||||||
|
"""
|
||||||
|
if not what:
|
||||||
sys.stderr.write(srepr(what,glue = '\n') + ('\n' if newline else ''))
|
sys.stderr.write(srepr(what,glue = '\n') + ('\n' if newline else ''))
|
||||||
sys.stderr.flush()
|
sys.stderr.flush()
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def report(who = None,
|
def report(who = None,
|
||||||
what = None):
|
what = None):
|
||||||
"""Reports script and file name."""
|
"""
|
||||||
|
Reports script and file name.
|
||||||
|
|
||||||
|
DEPRECATED
|
||||||
|
|
||||||
|
"""
|
||||||
croak( (emph(who)+': ' if who is not None else '') + (what if what is not None else '') + '\n' )
|
croak( (emph(who)+': ' if who is not None else '') + (what if what is not None else '') + '\n' )
|
||||||
|
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def emph(what):
|
def emph(what):
|
||||||
"""Formats string with emphasis."""
|
"""Formats string with emphasis."""
|
||||||
return bcolors.BOLD+srepr(what)+bcolors.ENDC
|
return bcolors.BOLD+srepr(what)+bcolors.ENDC
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def deemph(what):
|
def deemph(what):
|
||||||
"""Formats string with deemphasis."""
|
"""Formats string with deemphasis."""
|
||||||
return bcolors.DIM+srepr(what)+bcolors.ENDC
|
return bcolors.DIM+srepr(what)+bcolors.ENDC
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def delete(what):
|
def delete(what):
|
||||||
"""Formats string as deleted."""
|
"""Formats string as deleted."""
|
||||||
return bcolors.DIM+srepr(what)+bcolors.ENDC
|
return bcolors.DIM+srepr(what)+bcolors.ENDC
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def strikeout(what):
|
def strikeout(what):
|
||||||
"""Formats string as strikeout."""
|
"""Formats string as strikeout."""
|
||||||
return bcolors.CROSSOUT+srepr(what)+bcolors.ENDC
|
return bcolors.CROSSOUT+srepr(what)+bcolors.ENDC
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
def execute(cmd,
|
def execute(cmd,
|
||||||
streamIn = None,
|
streamIn = None,
|
||||||
wd = './',
|
wd = './',
|
||||||
env = None):
|
env = None):
|
||||||
"""Executes a command in given directory and returns stdout and stderr for optional stdin."""
|
"""
|
||||||
|
Execute command.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
cmd : str
|
||||||
|
Command to be executed.
|
||||||
|
streanIn :, optional
|
||||||
|
Input (via pipe) for executed process.
|
||||||
|
wd : str, optional
|
||||||
|
Working directory of process. Defaults to ./ .
|
||||||
|
env :
|
||||||
|
Environment
|
||||||
|
|
||||||
|
"""
|
||||||
initialPath = os.getcwd()
|
initialPath = os.getcwd()
|
||||||
os.chdir(wd)
|
os.chdir(wd)
|
||||||
myEnv = os.environ if env is None else env
|
myEnv = os.environ if env is None else env
|
||||||
|
@ -102,15 +139,17 @@ def execute(cmd,
|
||||||
out = out.decode('utf-8').replace('\x08','')
|
out = out.decode('utf-8').replace('\x08','')
|
||||||
error = error.decode('utf-8').replace('\x08','')
|
error = error.decode('utf-8').replace('\x08','')
|
||||||
os.chdir(initialPath)
|
os.chdir(initialPath)
|
||||||
if process.returncode != 0: raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
|
if process.returncode != 0:
|
||||||
|
raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
|
||||||
return out,error
|
return out,error
|
||||||
|
|
||||||
# -----------------------------
|
|
||||||
class extendableOption(Option):
|
class extendableOption(Option):
|
||||||
"""
|
"""
|
||||||
Used for definition of new option parser action 'extend', which enables to take multiple option arguments.
|
Used for definition of new option parser action 'extend', which enables to take multiple option arguments.
|
||||||
|
|
||||||
Adopted from online tutorial http://docs.python.org/library/optparse.html
|
Adopted from online tutorial http://docs.python.org/library/optparse.html
|
||||||
|
DEPRECATED
|
||||||
"""
|
"""
|
||||||
|
|
||||||
ACTIONS = Option.ACTIONS + ("extend",)
|
ACTIONS = Option.ACTIONS + ("extend",)
|
||||||
|
@ -125,17 +164,24 @@ class extendableOption(Option):
|
||||||
else:
|
else:
|
||||||
Option.take_action(self, action, dest, opt, value, values, parser)
|
Option.take_action(self, action, dest, opt, value, values, parser)
|
||||||
|
|
||||||
# Print iterations progress
|
|
||||||
# from https://gist.github.com/aubricus/f91fb55dc6ba5557fbab06119420dd6a
|
|
||||||
def progressBar(iteration, total, prefix='', bar_length=50):
|
def progressBar(iteration, total, prefix='', bar_length=50):
|
||||||
"""
|
"""
|
||||||
Call in a loop to create terminal progress bar.
|
Call in a loop to create terminal progress bar.
|
||||||
|
|
||||||
@params:
|
From https://gist.github.com/aubricus/f91fb55dc6ba5557fbab06119420dd6a
|
||||||
iteration - Required : current iteration (Int)
|
|
||||||
total - Required : total iterations (Int)
|
Parameters
|
||||||
prefix - Optional : prefix string (Str)
|
----------
|
||||||
bar_length - Optional : character length of bar (Int)
|
iteration : int
|
||||||
|
Current iteration.
|
||||||
|
total : int
|
||||||
|
Total iterations.
|
||||||
|
prefix : str, optional
|
||||||
|
Prefix string.
|
||||||
|
bar_length : int, optional
|
||||||
|
Character length of bar. Defaults to 50.
|
||||||
|
|
||||||
"""
|
"""
|
||||||
fraction = iteration / float(total)
|
fraction = iteration / float(total)
|
||||||
if not hasattr(progressBar, "last_fraction"): # first call to function
|
if not hasattr(progressBar, "last_fraction"): # first call to function
|
||||||
|
@ -159,7 +205,8 @@ def progressBar(iteration, total, prefix='', bar_length=50):
|
||||||
|
|
||||||
sys.stderr.write('\r{} {} {}'.format(prefix, bar, remaining_time)),
|
sys.stderr.write('\r{} {} {}'.format(prefix, bar, remaining_time)),
|
||||||
|
|
||||||
if iteration == total: sys.stderr.write('\n')
|
if iteration == total:
|
||||||
|
sys.stderr.write('\n')
|
||||||
sys.stderr.flush()
|
sys.stderr.flush()
|
||||||
|
|
||||||
|
|
||||||
|
@ -199,3 +246,4 @@ class return_message():
|
||||||
def __repr__(self):
|
def __repr__(self):
|
||||||
"""Return message suitable for interactive shells."""
|
"""Return message suitable for interactive shells."""
|
||||||
return srepr(self.message)
|
return srepr(self.message)
|
||||||
|
|
||||||
|
|
|
@ -0,0 +1,65 @@
|
||||||
|
import os
|
||||||
|
from itertools import permutations
|
||||||
|
|
||||||
|
import pytest
|
||||||
|
import numpy as np
|
||||||
|
|
||||||
|
import damask
|
||||||
|
from damask import Rotation
|
||||||
|
from damask import Orientation
|
||||||
|
from damask import Lattice
|
||||||
|
|
||||||
|
n = 1000
|
||||||
|
|
||||||
|
@pytest.fixture
|
||||||
|
def default():
|
||||||
|
"""A set of n random rotations."""
|
||||||
|
return [Rotation.fromRandom() for r in range(n)]
|
||||||
|
|
||||||
|
@pytest.fixture
|
||||||
|
def reference_dir(reference_dir_base):
|
||||||
|
"""Directory containing reference results."""
|
||||||
|
return os.path.join(reference_dir_base,'Rotation')
|
||||||
|
|
||||||
|
|
||||||
|
class TestOrientation:
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('color',[{'label':'red', 'RGB':[1,0,0],'direction':[0,0,1]},
|
||||||
|
{'label':'green','RGB':[0,1,0],'direction':[0,1,1]},
|
||||||
|
{'label':'blue', 'RGB':[0,0,1],'direction':[1,1,1]}])
|
||||||
|
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
||||||
|
def test_IPF_cubic(self,default,color,lattice):
|
||||||
|
cube = damask.Orientation(damask.Rotation(),lattice)
|
||||||
|
for direction in set(permutations(np.array(color['direction']))):
|
||||||
|
assert np.allclose(cube.IPFcolor(direction),np.array(color['RGB']))
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('lattice',Lattice.lattices)
|
||||||
|
def test_IPF(self,lattice):
|
||||||
|
direction = np.random.random(3)*2.0-1
|
||||||
|
for rot in [Rotation.fromRandom() for r in range(n//100)]:
|
||||||
|
R = damask.Orientation(rot,lattice)
|
||||||
|
color = R.IPFcolor(direction)
|
||||||
|
for equivalent in R.equivalentOrientations():
|
||||||
|
assert np.allclose(color,R.IPFcolor(direction))
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
|
||||||
|
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
||||||
|
def test_relationship_forward_backward(self,model,lattice):
|
||||||
|
ori = Orientation(Rotation.fromRandom(),lattice)
|
||||||
|
for i,r in enumerate(ori.relatedOrientations(model)):
|
||||||
|
ori2 = r.relatedOrientations(model)[i]
|
||||||
|
misorientation = ori.rotation.misorientation(ori2.rotation)
|
||||||
|
assert misorientation.asAxisAngle(degrees=True)[3]<1.0e-5
|
||||||
|
|
||||||
|
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
|
||||||
|
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
||||||
|
def test_relationship_reference(self,update,reference_dir,model,lattice):
|
||||||
|
reference = os.path.join(reference_dir,'{}_{}.txt'.format(lattice,model))
|
||||||
|
ori = Orientation(Rotation(),lattice)
|
||||||
|
eu = np.array([o.rotation.asEulers(degrees=True) for o in ori.relatedOrientations(model)])
|
||||||
|
if update:
|
||||||
|
coords = np.array([(1,i+1) for i,x in enumerate(eu)])
|
||||||
|
table = damask.Table(eu,{'Eulers':(3,)})
|
||||||
|
table.add('pos',coords)
|
||||||
|
table.to_ASCII(reference)
|
||||||
|
assert np.allclose(eu,damask.Table.from_ASCII(reference).get('Eulers'))
|
|
@ -1,13 +1,9 @@
|
||||||
import os
|
import os
|
||||||
from itertools import permutations
|
|
||||||
|
|
||||||
import pytest
|
import pytest
|
||||||
import numpy as np
|
import numpy as np
|
||||||
|
|
||||||
import damask
|
|
||||||
from damask import Rotation
|
from damask import Rotation
|
||||||
from damask import Orientation
|
|
||||||
from damask import Lattice
|
|
||||||
|
|
||||||
n = 1000
|
n = 1000
|
||||||
|
|
||||||
|
@ -58,44 +54,3 @@ class TestRotation:
|
||||||
for rot in default:
|
for rot in default:
|
||||||
assert np.allclose(rot.asCubochoric(),
|
assert np.allclose(rot.asCubochoric(),
|
||||||
Rotation.fromQuaternion(rot.asQuaternion()).asCubochoric())
|
Rotation.fromQuaternion(rot.asQuaternion()).asCubochoric())
|
||||||
|
|
||||||
|
|
||||||
@pytest.mark.parametrize('color',[{'label':'red', 'RGB':[1,0,0],'direction':[0,0,1]},
|
|
||||||
{'label':'green','RGB':[0,1,0],'direction':[0,1,1]},
|
|
||||||
{'label':'blue', 'RGB':[0,0,1],'direction':[1,1,1]}])
|
|
||||||
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
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||||||
def test_IPF_cubic(self,default,color,lattice):
|
|
||||||
cube = damask.Orientation(damask.Rotation(),lattice)
|
|
||||||
for direction in set(permutations(np.array(color['direction']))):
|
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assert np.allclose(cube.IPFcolor(direction),np.array(color['RGB']))
|
|
||||||
|
|
||||||
@pytest.mark.parametrize('lattice',Lattice.lattices)
|
|
||||||
def test_IPF(self,lattice):
|
|
||||||
direction = np.random.random(3)*2.0-1
|
|
||||||
for rot in [Rotation.fromRandom() for r in range(n//100)]:
|
|
||||||
R = damask.Orientation(rot,lattice)
|
|
||||||
color = R.IPFcolor(direction)
|
|
||||||
for equivalent in R.equivalentOrientations():
|
|
||||||
assert np.allclose(color,R.IPFcolor(direction))
|
|
||||||
|
|
||||||
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
|
|
||||||
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
|
||||||
def test_relationship_forward_backward(self,model,lattice):
|
|
||||||
ori = Orientation(Rotation.fromRandom(),lattice)
|
|
||||||
for i,r in enumerate(ori.relatedOrientations(model)):
|
|
||||||
ori2 = r.relatedOrientations(model)[i]
|
|
||||||
misorientation = ori.rotation.misorientation(ori2.rotation)
|
|
||||||
assert misorientation.asAxisAngle(degrees=True)[3]<1.0e-5
|
|
||||||
|
|
||||||
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
|
|
||||||
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
|
||||||
def test_relationship_reference(self,update,reference_dir,model,lattice):
|
|
||||||
reference = os.path.join(reference_dir,'{}_{}.txt'.format(lattice,model))
|
|
||||||
ori = Orientation(Rotation(),lattice)
|
|
||||||
eu = np.array([o.rotation.asEulers(degrees=True) for o in ori.relatedOrientations(model)])
|
|
||||||
if update:
|
|
||||||
coords = np.array([(1,i+1) for i,x in enumerate(eu)])
|
|
||||||
table = damask.Table(eu,{'Eulers':(3,)})
|
|
||||||
table.add('pos',coords)
|
|
||||||
table.to_ASCII(reference)
|
|
||||||
assert np.allclose(eu,damask.Table.from_ASCII(reference).get('Eulers'))
|
|
||||||
|
|
Loading…
Reference in New Issue