Merge remote-tracking branch 'origin/development' into internal-restructure
This commit is contained in:
Sharan Roongta
commit
c24d41ac4d
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@ -14,7 +14,6 @@ from . import tensor # noqa
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from . import mechanics # noqa
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from . import solver # noqa
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from . import grid_filters # noqa
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from . import lattice # noqa
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#Modules that contain only one class (of the same name), are prefixed by a '_'.
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#For example, '_colormap' containsa class called 'Colormap' which is imported as 'damask.Colormap'.
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from ._rotation import Rotation # noqa
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@ -110,13 +110,13 @@ class Colormap(mpl.colors.ListedColormap):
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low_,high_ = map(Colormap._rgb2msh,low_high)
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elif model.lower() == 'hsv':
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if np.any(low_high<0) or np.any(low_high[:,1:3]>1) or np.any(low_high[:,0]>360):
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if np.any(low_high<0) or np.any(low_high>[360,1,1]):
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raise ValueError(f'HSV color {low} | {high} are out of range.')
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low_,high_ = map(Colormap._hsv2msh,low_high)
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elif model.lower() == 'hsl':
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if np.any(low_high<0) or np.any(low_high[:,1:3]>1) or np.any(low_high[:,0]>360):
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if np.any(low_high<0) or np.any(low_high>[360,1,1]):
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raise ValueError(f'HSL color {low} | {high} are out of range.')
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low_,high_ = map(Colormap._hsl2msh,low_high)
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@ -5,6 +5,35 @@ import numpy as np
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from . import Rotation
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from . import util
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from . import tensor
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from . import _lattice
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_crystal_families = ['triclinic',
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'monoclinic',
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'orthorhombic',
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'tetragonal',
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'hexagonal',
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'cubic']
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_lattice_symmetries = {
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'aP': 'triclinic',
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'mP': 'monoclinic',
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'mS': 'monoclinic',
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'oP': 'orthorhombic',
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'oS': 'orthorhombic',
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'oI': 'orthorhombic',
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'oF': 'orthorhombic',
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'tP': 'tetragonal',
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'tI': 'tetragonal',
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'hP': 'hexagonal',
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'cP': 'cubic',
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'cI': 'cubic',
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'cF': 'cubic',
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}
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_parameter_doc = \
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"""lattice : str
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@ -33,7 +62,7 @@ class Orientation(Rotation):
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"""
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Representation of crystallographic orientation as combination of rotation and either crystal family or Bravais lattice.
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The crystal family is one of Orientation.crystal_families:
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The crystal family is one of:
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- triclinic
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- monoclinic
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@ -45,7 +74,7 @@ class Orientation(Rotation):
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and enables symmetry-related operations such as
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"equivalent", "reduced", "disorientation", "IPF_color", or "to_SST".
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The Bravais lattice is one of Orientation.lattice_symmetries:
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The Bravais lattice is given in the Pearson notation:
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- triclinic
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- aP : primitive
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@ -85,35 +114,6 @@ class Orientation(Rotation):
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"""
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crystal_families = ['triclinic',
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'monoclinic',
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'orthorhombic',
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'tetragonal',
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'hexagonal',
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'cubic']
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lattice_symmetries = {
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'aP': 'triclinic',
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'mP': 'monoclinic',
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'mS': 'monoclinic',
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'oP': 'orthorhombic',
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'oS': 'orthorhombic',
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'oI': 'orthorhombic',
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'oF': 'orthorhombic',
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'tP': 'tetragonal',
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'tI': 'tetragonal',
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'hP': 'hexagonal',
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'cP': 'cubic',
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'cI': 'cubic',
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'cF': 'cubic',
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}
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@util.extend_docstring(_parameter_doc)
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def __init__(self,
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rotation = None,
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@ -132,34 +132,17 @@ class Orientation(Rotation):
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Defaults to no rotation.
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"""
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from damask.lattice import kinematics
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Rotation.__init__(self) if rotation is None else Rotation.__init__(self,rotation=rotation)
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if ( lattice not in self.lattice_symmetries
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and lattice not in self.crystal_families):
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raise KeyError(f'Lattice "{lattice}" is unknown')
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self.family = None
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self.lattice = None
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self.a = None
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self.b = None
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self.c = None
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self.alpha = None
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self.beta = None
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self.gamma = None
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self.kinematics = None
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if lattice in self.lattice_symmetries:
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self.family = self.lattice_symmetries[lattice]
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if lattice in _lattice_symmetries:
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self.family = _lattice_symmetries[lattice]
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self.lattice = lattice
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self.a = 1 if a is None else a
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self.b = b
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self.c = c
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self.alpha = (np.radians(alpha) if degrees else alpha) if alpha is not None else None
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self.beta = (np.radians(beta) if degrees else beta) if beta is not None else None
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self.gamma = (np.radians(gamma) if degrees else gamma) if gamma is not None else None
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self.a = float(self.a) if self.a is not None else \
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(self.b / self.ratio['b'] if self.b is not None and self.ratio['b'] is not None else
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self.c / self.ratio['c'] if self.c is not None and self.ratio['c'] is not None else None)
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@ -171,9 +154,13 @@ class Orientation(Rotation):
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(self.a * self.ratio['c'] if self.a is not None and self.ratio['c'] is not None else
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self.b / self.ratio['b'] * self.ratio['c']
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if self.c is not None and self.ratio['b'] is not None and self.ratio['c'] is not None else None)
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self.alpha = self.alpha if self.alpha is not None else self.immutable['alpha'] if 'alpha' in self.immutable else None
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self.beta = self.beta if self.beta is not None else self.immutable['beta'] if 'beta' in self.immutable else None
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self.gamma = self.gamma if self.gamma is not None else self.immutable['gamma'] if 'gamma' in self.immutable else None
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self.alpha = np.radians(alpha) if degrees and alpha is not None else alpha
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self.beta = np.radians(beta) if degrees and beta is not None else beta
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self.gamma = np.radians(gamma) if degrees and gamma is not None else gamma
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if self.alpha is None and 'alpha' in self.immutable: self.alpha = self.immutable['alpha']
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if self.beta is None and 'beta' in self.immutable: self.beta = self.immutable['beta']
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if self.gamma is None and 'gamma' in self.immutable: self.gamma = self.immutable['gamma']
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if \
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(self.a is None) \
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@ -190,16 +177,22 @@ class Orientation(Rotation):
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> np.sum(np.roll([self.alpha,self.beta,self.gamma],r)[1:]) for r in range(3)]):
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raise ValueError ('Each lattice angle must be less than sum of others')
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if self.lattice in kinematics:
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master = kinematics[self.lattice]
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if self.lattice in _lattice.kinematics:
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master = _lattice.kinematics[self.lattice]
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self.kinematics = {}
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for m in master:
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self.kinematics[m] = {'direction':master[m][:,0:3],'plane':master[m][:,3:6]} \
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if master[m].shape[-1] == 6 else \
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{'direction':self.Bravais_to_Miller(uvtw=master[m][:,0:4]),
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'plane': self.Bravais_to_Miller(hkil=master[m][:,4:8])}
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elif lattice in self.crystal_families:
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self.family = lattice
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elif lattice in _crystal_families:
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self.family = lattice
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self.lattice = None
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self.a = self.b = self.c = None
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self.alpha = self.beta = self.gamma = None
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else:
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raise KeyError(f'Lattice "{lattice}" is unknown')
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def __repr__(self):
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@ -676,11 +669,9 @@ class Orientation(Rotation):
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https://doi.org/10.1016/j.actamat.2004.11.021
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"""
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from damask.lattice import relations
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if model not in relations:
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if model not in _lattice.relations:
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raise KeyError(f'Orientation relationship "{model}" is unknown')
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r = relations[model]
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r = _lattice.relations[model]
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if self.lattice not in r:
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raise KeyError(f'Relationship "{model}" not supported for lattice "{self.lattice}"')
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|
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@ -150,9 +150,8 @@ class VTK:
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----------
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fname : str or pathlib.Path
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Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.
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dataset_type : str, optional
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dataset_type : {'vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'}, optional
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Name of the vtk.vtkDataSet subclass when opening a .vtk file.
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Valid types are vtkRectilinearGrid, vtkUnstructuredGrid, and vtkPolyData.
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Returns
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-------
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|
|
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@ -124,9 +124,6 @@ def strain(F,t,m):
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"""
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Calculate strain tensor (Seth–Hill family).
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For details refer to https://en.wikipedia.org/wiki/Finite_strain_theory and
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https://de.wikipedia.org/wiki/Verzerrungstensor
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Parameters
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----------
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F : numpy.ndarray of shape (...,3,3)
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@ -142,6 +139,11 @@ def strain(F,t,m):
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epsilon : numpy.ndarray of shape (...,3,3)
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Strain of F.
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References
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----------
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https://en.wikipedia.org/wiki/Finite_strain_theory
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https://de.wikipedia.org/wiki/Verzerrungstensor
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"""
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if t == 'V':
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w,n = _np.linalg.eigh(deformation_Cauchy_Green_left(F))
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@ -150,7 +152,6 @@ def strain(F,t,m):
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if m > 0.0:
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eps = 1.0/(2.0*abs(m)) * (+ _np.einsum('...j,...kj,...lj',w**m,n,n) - _np.eye(3))
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elif m < 0.0:
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eps = 1.0/(2.0*abs(m)) * (- _np.einsum('...j,...kj,...lj',w**m,n,n) + _np.eye(3))
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else:
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|
|
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|
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@ -1,3 +1,5 @@
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"""Miscellaneous helper functionality."""
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|
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import sys
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import datetime
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import os
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|
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@ -177,26 +179,36 @@ def execute(cmd,wd='./',env=None):
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|
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|
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def natural_sort(key):
|
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"""
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Natural sort.
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|
||||
For use in python's 'sorted'.
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|
||||
References
|
||||
----------
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https://en.wikipedia.org/wiki/Natural_sort_order
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|
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"""
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convert = lambda text: int(text) if text.isdigit() else text
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return [ convert(c) for c in re.split('([0-9]+)', key) ]
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|
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|
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def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
|
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"""
|
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Decorate a loop with a status bar.
|
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Decorate a loop with a progress bar.
|
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|
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Use similar like enumerate.
|
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|
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Parameters
|
||||
----------
|
||||
iterable : iterable/function with yield statement
|
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iterable : iterable or function with yield statement
|
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Iterable (or function with yield statement) to be decorated.
|
||||
N_iter : int
|
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Total # of iterations. Needed if number of iterations can not be obtained as len(iterable).
|
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prefix : str, optional.
|
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N_iter : int, optional
|
||||
Total number of iterations. Required unless obtainable as len(iterable).
|
||||
prefix : str, optional
|
||||
Prefix string.
|
||||
bar_length : int, optional
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Character length of bar. Defaults to 50.
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Length of progress bar in characters. Defaults to 50.
|
||||
|
||||
"""
|
||||
if N_iter in [0,1] or (hasattr(iterable,'__len__') and len(iterable) <= 1):
|
||||
|
|
@ -509,6 +521,7 @@ def dict_prune(d):
|
|||
v = dict_prune(v)
|
||||
if not isinstance(v,dict) or v != {}:
|
||||
new[k] = v
|
||||
|
||||
return new
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ setuptools.setup(
|
|||
author='The DAMASK team',
|
||||
author_email='damask@mpie.de',
|
||||
description='DAMASK library',
|
||||
long_description='Python library for pre and post processing of DAMASK simulations',
|
||||
long_description='Python library for managing DAMASK simulations',
|
||||
url='https://damask.mpie.de',
|
||||
packages=setuptools.find_packages(),
|
||||
include_package_data=True,
|
||||
|
|
|
|||
|
|
@ -5,9 +5,10 @@ from itertools import permutations
|
|||
from damask import Rotation
|
||||
from damask import Orientation
|
||||
from damask import Table
|
||||
from damask import lattice
|
||||
from damask import util
|
||||
from damask import grid_filters
|
||||
from damask import _lattice as lattice
|
||||
from damask._orientation import _crystal_families as crystal_families
|
||||
|
||||
|
||||
@pytest.fixture
|
||||
|
|
@ -22,7 +23,7 @@ def set_of_rodrigues(set_of_quaternions):
|
|||
|
||||
class TestOrientation:
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('shape',[None,5,(4,6)])
|
||||
def test_equal(self,lattice,shape):
|
||||
R = Rotation.from_random(shape)
|
||||
|
|
@ -30,14 +31,14 @@ class TestOrientation:
|
|||
(Orientation(R,lattice) == Orientation(R,lattice)).all()
|
||||
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('shape',[None,5,(4,6)])
|
||||
def test_unequal(self,lattice,shape):
|
||||
R = Rotation.from_random(shape)
|
||||
assert not ( Orientation(R,lattice) != Orientation(R,lattice) if shape is None else \
|
||||
(Orientation(R,lattice) != Orientation(R,lattice)).any())
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('shape',[None,5,(4,6)])
|
||||
def test_close(self,lattice,shape):
|
||||
R = Orientation.from_random(lattice=lattice,shape=shape)
|
||||
|
|
@ -182,14 +183,14 @@ class TestOrientation:
|
|||
with pytest.raises(ValueError):
|
||||
Orientation(lattice='aP',a=1,b=2,c=3,alpha=45,beta=45,gamma=90.0001,degrees=True) # noqa
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('angle',[10,20,30,40])
|
||||
def test_average(self,angle,lattice):
|
||||
o = Orientation.from_axis_angle(lattice=lattice,axis_angle=[[0,0,1,10],[0,0,1,angle]],degrees=True)
|
||||
avg_angle = o.average().as_axis_angle(degrees=True,pair=True)[1]
|
||||
assert np.isclose(avg_angle,10+(angle-10)/2.)
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
def test_reduced_equivalent(self,lattice):
|
||||
i = Orientation(lattice=lattice)
|
||||
o = Orientation.from_random(lattice=lattice)
|
||||
|
|
@ -197,7 +198,7 @@ class TestOrientation:
|
|||
FZ = np.argmin(abs(eq.misorientation(i.broadcast_to(len(eq))).as_axis_angle(pair=True)[1]))
|
||||
assert o.reduced == eq[FZ]
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('N',[1,8,32])
|
||||
def test_disorientation(self,lattice,N):
|
||||
o = Orientation.from_random(lattice=lattice,shape=N)
|
||||
|
|
@ -215,7 +216,7 @@ class TestOrientation:
|
|||
.misorientation(p[n].equivalent[ops[n][1]])
|
||||
.as_quaternion())
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('a,b',[
|
||||
((2,3,2),(2,3,2)),
|
||||
((2,2),(4,4)),
|
||||
|
|
@ -230,20 +231,20 @@ class TestOrientation:
|
|||
assert o[tuple(loc[:len(o.shape)])].disorientation(p[tuple(loc[-len(p.shape):])]) \
|
||||
.isclose(o.disorientation(p)[tuple(loc)])
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
def test_disorientation360(self,lattice):
|
||||
o_1 = Orientation(Rotation(),lattice)
|
||||
o_2 = Orientation.from_Euler_angles(lattice=lattice,phi=[360,0,0],degrees=True)
|
||||
assert np.allclose((o_1.disorientation(o_2)).as_matrix(),np.eye(3))
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
|
||||
def test_reduced_vectorization(self,lattice,shape):
|
||||
o = Orientation.from_random(lattice=lattice,shape=shape)
|
||||
for r, theO in zip(o.reduced.flatten(),o.flatten()):
|
||||
assert r == theO.reduced
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
def test_reduced_corner_cases(self,lattice):
|
||||
# test whether there is always a sym-eq rotation that falls into the FZ
|
||||
N = np.random.randint(10,40)
|
||||
|
|
@ -253,7 +254,7 @@ class TestOrientation:
|
|||
assert evenly_distributed.shape == evenly_distributed.reduced.shape
|
||||
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
|
||||
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
|
||||
@pytest.mark.parametrize('proper',[True,False])
|
||||
|
|
@ -262,7 +263,7 @@ class TestOrientation:
|
|||
for r, theO in zip(o.to_SST(vector=vector,proper=proper).reshape((-1,3)),o.flatten()):
|
||||
assert np.allclose(r,theO.to_SST(vector=vector,proper=proper))
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
|
||||
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
|
||||
@pytest.mark.parametrize('proper',[True,False])
|
||||
|
|
@ -272,7 +273,7 @@ class TestOrientation:
|
|||
for r, theO in zip(o.IPF_color(vector,in_SST=in_SST,proper=proper).reshape((-1,3)),o.flatten()):
|
||||
assert np.allclose(r,theO.IPF_color(vector,in_SST=in_SST,proper=proper))
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('a,b',[
|
||||
((2,3,2),(2,3,2)),
|
||||
((2,2),(4,4)),
|
||||
|
|
@ -300,7 +301,7 @@ class TestOrientation:
|
|||
assert np.allclose(np.array(color['RGB']),
|
||||
cube.IPF_color(vector=np.array(direction),proper=proper))
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('proper',[True,False])
|
||||
def test_IPF_equivalent(self,set_of_quaternions,lattice,proper):
|
||||
direction = np.random.random(3)*2.0-1.0
|
||||
|
|
@ -308,13 +309,13 @@ class TestOrientation:
|
|||
color = o.IPF_color(vector=direction,proper=proper)
|
||||
assert np.allclose(np.broadcast_to(color[0,...],color.shape),color)
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
def test_in_FZ_vectorization(self,set_of_rodrigues,lattice):
|
||||
result = Orientation.from_Rodrigues_vector(rho=set_of_rodrigues.reshape((-1,4,4)),lattice=lattice).in_FZ.reshape(-1)
|
||||
for r,rho in zip(result,set_of_rodrigues[:len(result)]):
|
||||
assert r == Orientation.from_Rodrigues_vector(rho=rho,lattice=lattice).in_FZ
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
def test_in_disorientation_FZ_vectorization(self,set_of_rodrigues,lattice):
|
||||
result = Orientation.from_Rodrigues_vector(rho=set_of_rodrigues.reshape((-1,4,4)),
|
||||
lattice=lattice).in_disorientation_FZ.reshape(-1)
|
||||
|
|
@ -322,7 +323,7 @@ class TestOrientation:
|
|||
assert r == Orientation.from_Rodrigues_vector(rho=rho,lattice=lattice).in_disorientation_FZ
|
||||
|
||||
@pytest.mark.parametrize('proper',[True,False])
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
def test_in_SST_vectorization(self,lattice,proper):
|
||||
vecs = np.random.rand(20,4,3)
|
||||
result = Orientation(lattice=lattice).in_SST(vecs,proper).flatten()
|
||||
|
|
@ -393,7 +394,7 @@ class TestOrientation:
|
|||
a=a,b=b,c=c,
|
||||
alpha=alpha,beta=beta,gamma=gamma).related(relation) # noqa
|
||||
|
||||
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
|
||||
@pytest.mark.parametrize('lattice',crystal_families)
|
||||
@pytest.mark.parametrize('proper',[True,False])
|
||||
def test_in_SST(self,lattice,proper):
|
||||
assert Orientation(lattice=lattice).in_SST(np.zeros(3),proper)
|
||||
|
|
|
|||
|
|
@ -240,14 +240,12 @@ module phase
|
|||
real(pReal), dimension(6,6) :: C
|
||||
end function phase_homogenizedC
|
||||
|
||||
|
||||
module function phase_damage_C(C_homogenized,ph,en) result(C) ! ToDo: SR: better name?
|
||||
real(pReal), dimension(3,3,3,3), intent(in) :: C_homogenized
|
||||
integer, intent(in) :: ph,en
|
||||
real(pReal), dimension(3,3,3,3) :: C
|
||||
end function phase_damage_C
|
||||
|
||||
|
||||
module function phase_f_phi(phi,co,ce) result(f)
|
||||
integer, intent(in) :: ce,co
|
||||
real(pReal), intent(in) :: &
|
||||
|
|
|
|||
Loading…
Reference in New Issue