Merge branch 'misc-improvements' into 'development'
Misc improvements See merge request damask/DAMASK!181
This commit is contained in:
Jaber
commit
17212b27dc
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@ -27,7 +27,7 @@ SolidSolutionStrength 0.0 # Strength due to elements in solid solution
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### Dislocation glide parameters ###
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#per family
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Nslip 12 0
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Nslip 12
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slipburgers 2.72e-10 # Burgers vector of slip system [m]
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rhoedge0 1.0e12 # Initial edge dislocation density [m/m**3]
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rhoedgedip0 1.0 # Initial edged dipole dislocation density [m/m**3]
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@ -20,8 +20,8 @@ class Rotation:
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when viewing from the end point of the rotation axis towards the origin.
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- rotations will be interpreted in the passive sense.
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- Euler angle triplets are implemented using the Bunge convention,
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with the angular ranges as [0, 2π],[0, π],[0, 2π].
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- the rotation angle ω is limited to the interval [0, π].
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with the angular ranges as [0,2π], [0,π], [0,2π].
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- the rotation angle ω is limited to the interval [0,π].
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- the real part of a quaternion is positive, Re(q) > 0
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- P = -1 (as default).
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@ -49,7 +49,8 @@ class Rotation:
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Parameters
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----------
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quaternion : numpy.ndarray, optional
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Unit quaternion that follows the conventions. Use .from_quaternion to perform a sanity check.
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Unit quaternion in positive real hemisphere.
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Use .from_quaternion to perform a sanity check.
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"""
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self.quaternion = quaternion.copy()
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@ -73,7 +74,7 @@ class Rotation:
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raise NotImplementedError('Support for multiple rotations missing')
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return '\n'.join([
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'Quaternion: (real={:.3f}, imag=<{:+.3f}, {:+.3f}, {:+.3f}>)'.format(*(self.quaternion)),
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'Matrix:\n{}'.format(self.as_matrix()),
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'Matrix:\n{}'.format(np.round(self.as_matrix(),8)),
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'Bunge Eulers / deg: ({:3.2f}, {:3.2f}, {:3.2f})'.format(*self.as_Eulers(degrees=True)),
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])
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@ -87,10 +88,6 @@ class Rotation:
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other : numpy.ndarray or Rotation
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Vector, second or fourth order tensor, or rotation object that is rotated.
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Todo
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----
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Check rotation of 4th order tensor
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"""
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if isinstance(other, Rotation):
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q_m = self.quaternion[...,0:1]
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@ -99,7 +96,7 @@ class Rotation:
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p_o = other.quaternion[...,1:]
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q = (q_m*q_o - np.einsum('...i,...i',p_m,p_o).reshape(self.shape+(1,)))
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p = q_m*p_o + q_o*p_m + _P * np.cross(p_m,p_o)
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return self.__class__(np.block([q,p])).standardize()
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return self.__class__(np.block([q,p]))._standardize()
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elif isinstance(other,np.ndarray):
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if self.shape + (3,) == other.shape:
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@ -124,24 +121,24 @@ class Rotation:
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else:
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raise TypeError('Cannot rotate {}'.format(type(other)))
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def inverse(self):
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"""In-place inverse rotation/backward rotation."""
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self.quaternion[...,1:] *= -1
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return self
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def inversed(self):
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"""Inverse rotation/backward rotation."""
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return self.copy().inverse()
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def standardize(self):
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"""In-place quaternion representation with positive real part."""
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def _standardize(self):
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"""Standardize (ensure positive real hemisphere)."""
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self.quaternion[self.quaternion[...,0] < 0.0] *= -1
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return self
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def standardized(self):
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"""Quaternion representation with positive real part."""
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return self.copy().standardize()
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def inverse(self):
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"""In-place inverse rotation (backward rotation)."""
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self.quaternion[...,1:] *= -1
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return self
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def __invert__(self):
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"""Inverse rotation (backward rotation)."""
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return self.copy().inverse()
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def inversed(self):
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"""Inverse rotation (backward rotation)."""
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return ~ self
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def misorientation(self,other):
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@ -154,7 +151,7 @@ class Rotation:
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Rotation to which the misorientation is computed.
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"""
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return other*self.inversed()
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return other@~self
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def broadcast_to(self,shape):
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@ -169,7 +166,7 @@ class Rotation:
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return self.__class__(q)
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def average(self,other):
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def average(self,other): #ToDo: discuss calling for vectors
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"""
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Calculate the average rotation.
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@ -189,25 +186,31 @@ class Rotation:
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def as_quaternion(self):
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"""
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Unit quaternion [q, p_1, p_2, p_3].
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Represent as unit quaternion.
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Parameters
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----------
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quaternion : bool, optional
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return quaternion as DAMASK object.
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Returns
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-------
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q : numpy.ndarray of shape (...,4)
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Unit quaternion in positive real hemisphere: (q_0, q_1, q_2, q_3), |q|=1, q_0 ≥ 0.
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"""
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return self.quaternion
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return self.quaternion.copy()
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def as_Eulers(self,
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degrees = False):
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"""
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Bunge-Euler angles: (φ_1, ϕ, φ_2).
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Represent as Bunge-Euler angles.
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Parameters
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----------
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degrees : bool, optional
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return angles in degrees.
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Return angles in degrees.
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Returns
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-------
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phi : numpy.ndarray of shape (...,3)
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Bunge-Euler angles: (φ_1, ϕ, φ_2), φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]
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unless degrees == True: φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360]
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"""
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eu = Rotation._qu2eu(self.quaternion)
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@ -218,14 +221,21 @@ class Rotation:
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degrees = False,
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pair = False):
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"""
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Axis angle representation [n_1, n_2, n_3, ω] unless pair == True: ([n_1, n_2, n_3], ω).
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Represent as axis angle pair.
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Parameters
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----------
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degrees : bool, optional
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return rotation angle in degrees.
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Return rotation angle in degrees. Defaults to False.
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pair : bool, optional
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return tuple of axis and angle.
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Return tuple of axis and angle. Defaults to False.
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Returns
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-------
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axis_angle : numpy.ndarray of shape (...,4) unless pair == True:
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tuple containing numpy.ndarray of shapes (...,3) and (...)
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Axis angle pair: (n_1, n_2, n_3, ω), |n| = 1 and ω ∈ [0,π]
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unless degrees = True: ω ∈ [0,180].
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"""
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ax = Rotation._qu2ax(self.quaternion)
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@ -233,29 +243,60 @@ class Rotation:
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return (ax[...,:3],ax[...,3]) if pair else ax
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def as_matrix(self):
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"""Rotation matrix."""
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"""
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Represent as rotation matrix.
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Returns
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-------
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R : numpy.ndarray of shape (...,3,3)
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Rotation matrix R, det(R) = 1, R.T∙R=I.
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"""
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return Rotation._qu2om(self.quaternion)
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def as_Rodrigues(self,
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vector = False):
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"""
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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).
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Represent as Rodrigues-Frank vector with separated axis and angle argument.
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Parameters
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----------
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vector : bool, optional
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return as actual Rodrigues--Frank vector, i.e. rotation axis scaled by tan(ω/2).
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Return as actual Rodrigues-Frank vector, i.e. axis
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and angle argument are not separated.
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Returns
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-------
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rho : numpy.ndarray of shape (...,4) unless vector == True:
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numpy.ndarray of shape (...,3)
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Rodrigues-Frank vector: [n_1, n_2, n_3, tan(ω/2)], |n| = 1 and ω ∈ [0,π].
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"""
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ro = Rotation._qu2ro(self.quaternion)
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return ro[...,:3]*ro[...,3] if vector else ro
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def as_homochoric(self):
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"""Homochoric vector: (h_1, h_2, h_3)."""
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"""
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Represent as homochoric vector.
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Returns
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-------
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h : numpy.ndarray of shape (...,3)
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Homochoric vector: (h_1, h_2, h_3), |h| < 1/2*π^(2/3).
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"""
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return Rotation._qu2ho(self.quaternion)
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def as_cubochoric(self):
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"""Cubochoric vector: (c_1, c_2, c_3)."""
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"""
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Represent as cubochoric vector.
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Returns
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-------
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c : numpy.ndarray of shape (...,3)
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Cubochoric vector: (c_1, c_2, c_3), max(c_i) < 1/2*π^(2/3).
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"""
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return Rotation._qu2cu(self.quaternion)
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def M(self): # ToDo not sure about the name: as_M or M? we do not have a from_M
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@ -275,18 +316,34 @@ class Rotation:
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# Static constructors. The input data needs to follow the conventions, options allow to
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# relax the conventions.
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@staticmethod
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def from_quaternion(quaternion,
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def from_quaternion(q,
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accept_homomorph = False,
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P = -1,
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acceptHomomorph = None):
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acceptHomomorph = None): # old name (for compatibility)
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"""
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Initialize from quaternion.
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Parameters
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----------
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q : numpy.ndarray of shape (...,4)
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Unit quaternion in positive real hemisphere: (q_0, q_1, q_2, q_3),
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|q|=1, q_0 ≥ 0.
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accept_homomorph : boolean, optional
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Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
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Defaults to False.
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P : integer ∈ {-1,1}, optional
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Convention used. Defaults to -1.
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"""
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if acceptHomomorph is not None:
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accept_homomorph = acceptHomomorph
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qu = np.array(quaternion,dtype=float)
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accept_homomorph = acceptHomomorph # for compatibility
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qu = np.array(q,dtype=float)
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if qu.shape[:-2:-1] != (4,):
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raise ValueError('Invalid shape.')
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if abs(P) != 1:
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raise ValueError('P ∉ {-1,1}')
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if P > 0: qu[...,1:4] *= -1 # convert from P=1 to P=-1
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if P == 1: qu[...,1:4] *= -1
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if accept_homomorph:
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qu[qu[...,0] < 0.0] *= -1
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else:
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@ -298,10 +355,21 @@ class Rotation:
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return Rotation(qu)
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@staticmethod
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def from_Eulers(eulers,
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def from_Eulers(phi,
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degrees = False):
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"""
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Initialize from Bunge-Euler angles.
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eu = np.array(eulers,dtype=float)
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Parameters
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----------
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phi : numpy.ndarray of shape (...,3)
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Bunge-Euler angles: (φ_1, ϕ, φ_2), φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]
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unless degrees == True: φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360].
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degrees : boolean, optional
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Bunge-Euler angles are given in degrees. Defaults to False.
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"""
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eu = np.array(phi,dtype=float)
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if eu.shape[:-2:-1] != (3,):
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raise ValueError('Invalid shape.')
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@ -316,12 +384,29 @@ class Rotation:
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degrees = False,
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normalise = False,
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P = -1):
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"""
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Initialize from Axis angle pair.
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Parameters
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----------
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axis_angle : numpy.ndarray of shape (...,4)
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Axis angle pair: [n_1, n_2, n_3, ω], |n| = 1 and ω ∈ [0,π]
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unless degrees = True: ω ∈ [0,180].
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degrees : boolean, optional
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Angle ω is given in degrees. Defaults to False.
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normalize: boolean, optional
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Allow |n| ≠ 1. Defaults to False.
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P : integer ∈ {-1,1}, optional
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Convention used. Defaults to -1.
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"""
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ax = np.array(axis_angle,dtype=float)
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if ax.shape[:-2:-1] != (4,):
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raise ValueError('Invalid shape.')
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if abs(P) != 1:
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raise ValueError('P ∉ {-1,1}')
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if P > 0: ax[...,0:3] *= -1 # convert from P=1 to P=-1
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if P == 1: ax[...,0:3] *= -1
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if degrees: ax[..., 3] = np.radians(ax[...,3])
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if normalise: ax[...,0:3] /= np.linalg.norm(ax[...,0:3],axis=-1)
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if np.any(ax[...,3] < 0.0) or np.any(ax[...,3] > np.pi):
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@ -335,7 +420,19 @@ class Rotation:
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def from_basis(basis,
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orthonormal = True,
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reciprocal = False):
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"""
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Initialize from lattice basis vectors.
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Parameters
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----------
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basis : numpy.ndarray of shape (...,3,3)
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Three lattice basis vectors in three dimensions.
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orthonormal : boolean, optional
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Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
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reciprocal : boolean, optional
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Basis vectors are given in reciprocal (instead of real) space. Defaults to False.
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"""
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om = np.array(basis,dtype=float)
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if om.shape[:-3:-1] != (3,3):
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raise ValueError('Invalid shape.')
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|
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@ -356,20 +453,43 @@ class Rotation:
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return Rotation(Rotation._om2qu(om))
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@staticmethod
|
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def from_matrix(om):
|
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def from_matrix(R):
|
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"""
|
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Initialize from rotation matrix.
|
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|
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return Rotation.from_basis(om)
|
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Parameters
|
||||
----------
|
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R : numpy.ndarray of shape (...,3,3)
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Rotation matrix: det(R) = 1, R.T∙R=I.
|
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|
||||
"""
|
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return Rotation.from_basis(R)
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@staticmethod
|
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def from_Rodrigues(rodrigues,
|
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def from_Rodrigues(rho,
|
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normalise = False,
|
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P = -1):
|
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"""
|
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Initialize from Rodrigues-Frank vector.
|
||||
|
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ro = np.array(rodrigues,dtype=float)
|
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Parameters
|
||||
----------
|
||||
rho : numpy.ndarray of shape (...,4)
|
||||
Rodrigues-Frank vector (angle separated from axis).
|
||||
(n_1, n_2, n_3, tan(ω/2)), |n| = 1 and ω ∈ [0,π].
|
||||
normalize : boolean, optional
|
||||
Allow |n| ≠ 1. Defaults to False.
|
||||
P : integer ∈ {-1,1}, optional
|
||||
Convention used. Defaults to -1.
|
||||
|
||||
"""
|
||||
ro = np.array(rho,dtype=float)
|
||||
if ro.shape[:-2:-1] != (4,):
|
||||
raise ValueError('Invalid shape.')
|
||||
if abs(P) != 1:
|
||||
raise ValueError('P ∉ {-1,1}')
|
||||
|
||||
if P > 0: ro[...,0:3] *= -1 # convert from P=1 to P=-1
|
||||
if P == 1: ro[...,0:3] *= -1
|
||||
if normalise: ro[...,0:3] /= np.linalg.norm(ro[...,0:3],axis=-1)
|
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if np.any(ro[...,3] < 0.0):
|
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raise ValueError('Rodrigues vector rotation angle not positive.')
|
||||
|
|
@ -379,14 +499,26 @@ class Rotation:
|
|||
return Rotation(Rotation._ro2qu(ro))
|
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|
||||
@staticmethod
|
||||
def from_homochoric(homochoric,
|
||||
def from_homochoric(h,
|
||||
P = -1):
|
||||
"""
|
||||
Initialize from homochoric vector.
|
||||
|
||||
ho = np.array(homochoric,dtype=float)
|
||||
Parameters
|
||||
----------
|
||||
h : numpy.ndarray of shape (...,3)
|
||||
Homochoric vector: (h_1, h_2, h_3), |h| < (3/4*π)^(1/3).
|
||||
P : integer ∈ {-1,1}, optional
|
||||
Convention used. Defaults to -1.
|
||||
|
||||
"""
|
||||
ho = np.array(h,dtype=float)
|
||||
if ho.shape[:-2:-1] != (3,):
|
||||
raise ValueError('Invalid shape.')
|
||||
if abs(P) != 1:
|
||||
raise ValueError('P ∉ {-1,1}')
|
||||
|
||||
if P > 0: ho *= -1 # convert from P=1 to P=-1
|
||||
if P == 1: ho *= -1
|
||||
|
||||
if np.any(np.linalg.norm(ho,axis=-1) >_R1+1e-9):
|
||||
raise ValueError('Homochoric coordinate outside of the sphere.')
|
||||
|
|
@ -394,18 +526,30 @@ class Rotation:
|
|||
return Rotation(Rotation._ho2qu(ho))
|
||||
|
||||
@staticmethod
|
||||
def from_cubochoric(cubochoric,
|
||||
P = -1):
|
||||
def from_cubochoric(c,
|
||||
P = -1):
|
||||
"""
|
||||
Initialize from cubochoric vector.
|
||||
|
||||
cu = np.array(cubochoric,dtype=float)
|
||||
Parameters
|
||||
----------
|
||||
c : numpy.ndarray of shape (...,3)
|
||||
Cubochoric vector: (c_1, c_2, c_3), max(c_i) < 1/2*π^(2/3).
|
||||
P : integer ∈ {-1,1}, optional
|
||||
Convention used. Defaults to -1.
|
||||
|
||||
"""
|
||||
cu = np.array(c,dtype=float)
|
||||
if cu.shape[:-2:-1] != (3,):
|
||||
raise ValueError('Invalid shape.')
|
||||
if abs(P) != 1:
|
||||
raise ValueError('P ∉ {-1,1}')
|
||||
|
||||
if np.abs(np.max(cu))>np.pi**(2./3.) * 0.5+1e-9:
|
||||
raise ValueError('Cubochoric coordinate outside of the cube: {} {} {}.'.format(*cu))
|
||||
if np.abs(np.max(cu)) > np.pi**(2./3.) * 0.5+1e-9:
|
||||
raise ValueError('Cubochoric coordinate outside of the cube.')
|
||||
|
||||
ho = Rotation._cu2ho(cu)
|
||||
if P > 0: ho *= -1 # convert from P=1 to P=-1
|
||||
if P == 1: ho *= -1
|
||||
|
||||
return Rotation(Rotation._ho2qu(ho))
|
||||
|
||||
|
|
@ -458,7 +602,7 @@ class Rotation:
|
|||
np.cos(2.0*np.pi*r[...,1])*B,
|
||||
np.sin(2.0*np.pi*r[...,0])*A],axis=-1)
|
||||
|
||||
return Rotation(q.reshape(r.shape[:-1]+(4,)) if shape is not None else q).standardize()
|
||||
return Rotation(q.reshape(r.shape[:-1]+(4,)) if shape is not None else q)._standardize()
|
||||
|
||||
|
||||
# for compatibility (old names do not follow convention)
|
||||
|
|
@ -471,7 +615,7 @@ class Rotation:
|
|||
####################################################################################################
|
||||
# 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) 2017-2020, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
|
||||
# Copyright (c) 2013-2014, Marc De Graef/Carnegie Mellon University
|
||||
# All rights reserved.
|
||||
#
|
||||
|
|
@ -530,7 +674,7 @@ class Rotation:
|
|||
np.zeros(qu.shape[:-1]+(2,))]),
|
||||
np.where(np.abs(q03_s) < 1.0e-8,
|
||||
np.block([np.arctan2( 2.0*qu[...,1:2]*qu[...,2:3],qu[...,1:2]**2-qu[...,2:3]**2),
|
||||
np.broadcast_to(np.pi,qu.shape[:-1]+(1,)),
|
||||
np.broadcast_to(np.pi,qu[...,0:1].shape),
|
||||
np.zeros(qu.shape[:-1]+(1,))]),
|
||||
np.block([np.arctan2((-_P*q02+q13)*chi, (-_P*q01-q23)*chi),
|
||||
np.arctan2( 2.0*chi, q03_s-q12_s ),
|
||||
|
|
@ -553,7 +697,7 @@ class Rotation:
|
|||
s = np.sign(qu[...,0:1])/np.sqrt(qu[...,1:2]**2+qu[...,2:3]**2+qu[...,3:4]**2)
|
||||
omega = 2.0 * np.arccos(np.clip(qu[...,0:1],-1.0,1.0))
|
||||
ax = np.where(np.broadcast_to(qu[...,0:1] < 1.0e-8,qu.shape),
|
||||
np.block([qu[...,1:4],np.broadcast_to(np.pi,qu.shape[:-1]+(1,))]),
|
||||
np.block([qu[...,1:4],np.broadcast_to(np.pi,qu[...,0:1].shape)]),
|
||||
np.block([qu[...,1:4]*s,omega]))
|
||||
ax[np.isclose(qu[...,0],1.,rtol=0.0)] = [0.0, 0.0, 1.0, 0.0]
|
||||
return ax
|
||||
|
|
@ -564,7 +708,7 @@ class Rotation:
|
|||
with np.errstate(invalid='ignore',divide='ignore'):
|
||||
s = np.linalg.norm(qu[...,1:4],axis=-1,keepdims=True)
|
||||
ro = np.where(np.broadcast_to(np.abs(qu[...,0:1]) < 1.0e-12,qu.shape),
|
||||
np.block([qu[...,1:2], qu[...,2:3], qu[...,3:4], np.broadcast_to(np.inf,qu.shape[:-1]+(1,))]),
|
||||
np.block([qu[...,1:2], qu[...,2:3], qu[...,3:4], np.broadcast_to(np.inf,qu[...,0:1].shape)]),
|
||||
np.block([qu[...,1:2]/s,qu[...,2:3]/s,qu[...,3:4]/s,
|
||||
np.tan(np.arccos(np.clip(qu[...,0:1],-1.0,1.0)))
|
||||
])
|
||||
|
|
|
|||
|
|
@ -93,7 +93,7 @@ def strikeout(what):
|
|||
|
||||
|
||||
def execute(cmd,
|
||||
streamIn = None,
|
||||
stream_in = None,
|
||||
wd = './',
|
||||
env = None):
|
||||
"""
|
||||
|
|
@ -103,7 +103,7 @@ def execute(cmd,
|
|||
----------
|
||||
cmd : str
|
||||
Command to be executed.
|
||||
streanIn :, optional
|
||||
stream_in : file object, optional
|
||||
Input (via pipe) for executed process.
|
||||
wd : str, optional
|
||||
Working directory of process. Defaults to ./ .
|
||||
|
|
@ -119,14 +119,14 @@ def execute(cmd,
|
|||
stderr = subprocess.PIPE,
|
||||
stdin = subprocess.PIPE,
|
||||
env = myEnv)
|
||||
out,error = [i for i in (process.communicate() if streamIn is None
|
||||
else process.communicate(streamIn.read().encode('utf-8')))]
|
||||
stdout, stderr = [i for i in (process.communicate() if stream_in is None
|
||||
else process.communicate(stream_in.read().encode('utf-8')))]
|
||||
os.chdir(initialPath)
|
||||
out = out.decode('utf-8').replace('\x08','')
|
||||
error = error.decode('utf-8').replace('\x08','')
|
||||
stdout = stdout.decode('utf-8').replace('\x08','')
|
||||
stderr = stderr.decode('utf-8').replace('\x08','')
|
||||
if process.returncode != 0:
|
||||
raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
|
||||
return out,error
|
||||
return stdout, stderr
|
||||
|
||||
|
||||
def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
|
||||
|
|
|
|||
|
|
@ -302,8 +302,8 @@ class TestResult:
|
|||
|
||||
@pytest.mark.parametrize('allowed',['off','on'])
|
||||
def test_rename(self,default,allowed):
|
||||
F = default.read_dataset(default.get_dataset_location('F'))
|
||||
if allowed == 'on':
|
||||
F = default.read_dataset(default.get_dataset_location('F'))
|
||||
default.allow_modification()
|
||||
default.rename('F','new_name')
|
||||
assert np.all(F == default.read_dataset(default.get_dataset_location('new_name')))
|
||||
|
|
|
|||
|
|
@ -14,7 +14,7 @@ scatter=1.e-2
|
|||
|
||||
@pytest.fixture
|
||||
def default():
|
||||
"""A set of n random rotations."""
|
||||
"""A set of n rotations (corner cases and random)."""
|
||||
specials = np.array([
|
||||
[1.0, 0.0, 0.0, 0.0],
|
||||
#----------------------
|
||||
|
|
@ -170,7 +170,7 @@ def qu2ax(qu):
|
|||
|
||||
Modified version of the original formulation, should be numerically more stable
|
||||
"""
|
||||
if np.isclose(qu[0],1.,rtol=0.0): # set axis to [001] if the angle is 0/360
|
||||
if np.isclose(qu[0],1.,rtol=0.0): # set axis to [001] if the angle is 0/360
|
||||
ax = np.array([ 0.0, 0.0, 1.0, 0.0 ])
|
||||
elif qu[0] > 1.e-8:
|
||||
s = np.sign(qu[0])/np.sqrt(qu[1]**2+qu[2]**2+qu[3]**2)
|
||||
|
|
@ -534,7 +534,7 @@ def mul(me, other):
|
|||
other_p = other.quaternion[1:]
|
||||
R = me.__class__(np.append(me_q*other_q - np.dot(me_p,other_p),
|
||||
me_q*other_p + other_q*me_p + _P * np.cross(me_p,other_p)))
|
||||
return R.standardize()
|
||||
return R._standardize()
|
||||
elif isinstance(other, np.ndarray):
|
||||
if other.shape == (3,):
|
||||
A = me.quaternion[0]**2.0 - np.dot(me.quaternion[1:],me.quaternion[1:])
|
||||
|
|
@ -554,7 +554,7 @@ def mul(me, other):
|
|||
axes = ((0, 2, 4, 6), (0, 1, 2, 3))
|
||||
return np.tensordot(RRRR, other, axes)
|
||||
else:
|
||||
raise ValueError('Can only rotate vectors, 2nd order ternsors, and 4th order tensors')
|
||||
raise ValueError('Can only rotate vectors, 2nd order tensors, and 4th order tensors')
|
||||
else:
|
||||
raise TypeError('Cannot rotate {}'.format(type(other)))
|
||||
|
||||
|
|
@ -854,6 +854,10 @@ class TestRotation:
|
|||
rot = Rotation.from_basis(om,False,reciprocal=reciprocal)
|
||||
assert np.isclose(np.linalg.det(rot.as_matrix()),1.0)
|
||||
|
||||
@pytest.mark.parametrize('shape',[None,1,(4,4)])
|
||||
def test_random(self,shape):
|
||||
Rotation.from_random(shape)
|
||||
|
||||
@pytest.mark.parametrize('function',[Rotation.from_quaternion,
|
||||
Rotation.from_Eulers,
|
||||
Rotation.from_axis_angle,
|
||||
|
|
@ -866,6 +870,16 @@ class TestRotation:
|
|||
with pytest.raises(ValueError):
|
||||
function(invalid_shape)
|
||||
|
||||
@pytest.mark.parametrize('fr,to',[(Rotation.from_quaternion,'as_quaternion'),
|
||||
(Rotation.from_axis_angle,'as_axis_angle'),
|
||||
(Rotation.from_Rodrigues, 'as_Rodrigues'),
|
||||
(Rotation.from_homochoric,'as_homochoric'),
|
||||
(Rotation.from_cubochoric,'as_cubochoric')])
|
||||
def test_invalid_P(self,fr,to):
|
||||
R = Rotation.from_random(np.random.randint(8,32,(3))) # noqa
|
||||
with pytest.raises(ValueError):
|
||||
fr(eval('R.{}()'.format(to)),P=-30)
|
||||
|
||||
@pytest.mark.parametrize('shape',[None,(3,),(4,2)])
|
||||
def test_broadcast(self,shape):
|
||||
rot = Rotation.from_random(shape)
|
||||
|
|
@ -932,14 +946,18 @@ class TestRotation:
|
|||
phi_2 = 2*np.pi - phi_1
|
||||
R_1 = Rotation.from_Eulers(np.array([phi_1,0.,0.]))
|
||||
R_2 = Rotation.from_Eulers(np.array([0.,0.,phi_2]))
|
||||
assert np.allclose(data,R_2*(R_1*data))
|
||||
assert np.allclose(data,R_2@(R_1@data))
|
||||
|
||||
def test_rotate_inverse(self):
|
||||
R = Rotation.from_random()
|
||||
assert np.allclose(np.eye(3),(~R@R).as_matrix())
|
||||
|
||||
@pytest.mark.parametrize('data',[np.random.rand(3),
|
||||
np.random.rand(3,3),
|
||||
np.random.rand(3,3,3,3)])
|
||||
def test_rotate_inverse(self,data):
|
||||
def test_rotate_inverse_array(self,data):
|
||||
R = Rotation.from_random()
|
||||
assert np.allclose(data,R.inversed()*(R*data))
|
||||
assert np.allclose(data,~R@(R@data))
|
||||
|
||||
@pytest.mark.parametrize('data',[np.random.rand(4),
|
||||
np.random.rand(3,2),
|
||||
|
|
@ -956,3 +974,7 @@ class TestRotation:
|
|||
R = Rotation.from_random()
|
||||
with pytest.raises(TypeError):
|
||||
R*data
|
||||
|
||||
def test_misorientation(self):
|
||||
R = Rotation.from_random()
|
||||
assert np.allclose(R.misorientation(R).as_matrix(),np.eye(3))
|
||||
|
|
|
|||
|
|
@ -0,0 +1,11 @@
|
|||
from damask import util
|
||||
|
||||
class TestUtil:
|
||||
|
||||
def test_execute_direct(self):
|
||||
out,err = util.execute('echo test')
|
||||
assert out=='test\n' and err==''
|
||||
|
||||
def test_execute_env(self):
|
||||
out,err = util.execute('sh -c "echo $test_for_execute"',env={'test_for_execute':'test'})
|
||||
assert out=='test\n' and err==''
|
||||
|
|
@ -830,7 +830,7 @@ module subroutine plastic_dislotwin_results(instance,group)
|
|||
'mobile dislocation density','1/m²')
|
||||
case('rho_dip')
|
||||
if(prm%sum_N_sl>0) call results_writeDataset(group,stt%rho_dip,'rho_dip',&
|
||||
'dislocation dipole density''1/m²')
|
||||
'dislocation dipole density','1/m²')
|
||||
case('gamma_sl')
|
||||
if(prm%sum_N_sl>0) call results_writeDataset(group,stt%gamma_sl,'gamma_sl',&
|
||||
'plastic shear','1')
|
||||
|
|
|
|||
|
|
@ -284,11 +284,9 @@ end subroutine crystallite_init
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief calculate stress (P)
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
function crystallite_stress(dummyArgumentToPreventInternalCompilerErrorWithGCC)
|
||||
function crystallite_stress()
|
||||
|
||||
logical, dimension(discretization_nIP,discretization_nElem) :: crystallite_stress
|
||||
real(pReal), intent(in), optional :: &
|
||||
dummyArgumentToPreventInternalCompilerErrorWithGCC
|
||||
real(pReal) :: &
|
||||
formerSubStep
|
||||
integer :: &
|
||||
|
|
|
|||
|
|
@ -49,7 +49,7 @@ subroutine discretization_init(homogenizationAt,microstructureAt,&
|
|||
IPcoords0, &
|
||||
NodeCoords0
|
||||
integer, optional, intent(in) :: &
|
||||
sharedNodesBegin
|
||||
sharedNodesBegin !< index of first node shared among different processes (MPI)
|
||||
|
||||
write(6,'(/,a)') ' <<<+- discretization init -+>>>'; flush(6)
|
||||
|
||||
|
|
|
|||
|
|
@ -8,53 +8,50 @@ module discretization_mesh
|
|||
#include <petsc/finclude/petscdmplex.h>
|
||||
#include <petsc/finclude/petscis.h>
|
||||
#include <petsc/finclude/petscdmda.h>
|
||||
use PETScdmplex
|
||||
use PETScdmda
|
||||
use PETScis
|
||||
use PETScdmplex
|
||||
use PETScdmda
|
||||
use PETScis
|
||||
|
||||
use DAMASK_interface
|
||||
use IO
|
||||
use debug
|
||||
use discretization
|
||||
use numerics
|
||||
use FEsolving
|
||||
use FEM_quadrature
|
||||
use prec
|
||||
use DAMASK_interface
|
||||
use IO
|
||||
use debug
|
||||
use discretization
|
||||
use numerics
|
||||
use FEsolving
|
||||
use FEM_quadrature
|
||||
use prec
|
||||
|
||||
implicit none
|
||||
private
|
||||
implicit none
|
||||
private
|
||||
|
||||
integer, public, protected :: &
|
||||
mesh_Nboundaries, &
|
||||
mesh_NcpElemsGlobal
|
||||
integer, public, protected :: &
|
||||
mesh_Nboundaries, &
|
||||
mesh_NcpElemsGlobal
|
||||
|
||||
integer :: &
|
||||
mesh_NcpElems !< total number of CP elements in mesh
|
||||
integer :: &
|
||||
mesh_NcpElems !< total number of CP elements in mesh
|
||||
|
||||
!!!! BEGIN DEPRECATED !!!!!
|
||||
integer, public, protected :: &
|
||||
mesh_maxNips !< max number of IPs in any CP element
|
||||
integer, public, protected :: &
|
||||
mesh_maxNips !< max number of IPs in any CP element
|
||||
!!!! BEGIN DEPRECATED !!!!!
|
||||
|
||||
integer, dimension(:,:), allocatable :: &
|
||||
mesh_element !DEPRECATED
|
||||
real(pReal), dimension(:,:), allocatable :: &
|
||||
mesh_ipVolume, & !< volume associated with IP (initially!)
|
||||
mesh_node0 !< node x,y,z coordinates (initially!)
|
||||
|
||||
real(pReal), dimension(:,:), allocatable :: &
|
||||
mesh_ipVolume, & !< volume associated with IP (initially!)
|
||||
mesh_node0 !< node x,y,z coordinates (initially!)
|
||||
real(pReal), dimension(:,:,:), allocatable :: &
|
||||
mesh_ipCoordinates !< IP x,y,z coordinates (after deformation!)
|
||||
|
||||
real(pReal), dimension(:,:,:), allocatable :: &
|
||||
mesh_ipCoordinates !< IP x,y,z coordinates (after deformation!)
|
||||
DM, public :: geomMesh
|
||||
|
||||
DM, public :: geomMesh
|
||||
PetscInt, dimension(:), allocatable, public, protected :: &
|
||||
mesh_boundaries
|
||||
|
||||
PetscInt, dimension(:), allocatable, public, protected :: &
|
||||
mesh_boundaries
|
||||
|
||||
public :: &
|
||||
discretization_mesh_init, &
|
||||
mesh_FEM_build_ipVolumes, &
|
||||
mesh_FEM_build_ipCoordinates
|
||||
public :: &
|
||||
discretization_mesh_init, &
|
||||
mesh_FEM_build_ipVolumes, &
|
||||
mesh_FEM_build_ipCoordinates
|
||||
|
||||
contains
|
||||
|
||||
|
|
@ -67,15 +64,10 @@ subroutine discretization_mesh_init(restart)
|
|||
|
||||
logical, intent(in) :: restart
|
||||
|
||||
integer, dimension(1), parameter:: FE_geomtype = [1] !< geometry type of particular element type
|
||||
integer, dimension(1) :: FE_Nips !< number of IPs in a specific type of element
|
||||
|
||||
integer, allocatable, dimension(:) :: chunkPos
|
||||
integer :: dimPlex, &
|
||||
mesh_Nnodes, & !< total number of nodes in mesh
|
||||
j, l
|
||||
integer, parameter :: &
|
||||
mesh_ElemType=1 !< Element type of the mesh (only support homogeneous meshes)
|
||||
PetscSF :: sf
|
||||
DM :: globalMesh
|
||||
PetscInt :: nFaceSets
|
||||
|
|
@ -83,23 +75,22 @@ subroutine discretization_mesh_init(restart)
|
|||
character(len=pStringLen), dimension(:), allocatable :: fileContent
|
||||
IS :: faceSetIS
|
||||
PetscErrorCode :: ierr
|
||||
integer, dimension(:), allocatable :: &
|
||||
homogenizationAt, &
|
||||
microstructureAt
|
||||
|
||||
|
||||
write(6,'(/,a)') ' <<<+- mesh init -+>>>'
|
||||
|
||||
! read in file
|
||||
call DMPlexCreateFromFile(PETSC_COMM_WORLD,geometryFile,PETSC_TRUE,globalMesh,ierr)
|
||||
CHKERRQ(ierr)
|
||||
! get spatial dimension (2 or 3?)
|
||||
call DMGetDimension(globalMesh,dimPlex,ierr)
|
||||
CHKERRQ(ierr)
|
||||
write(6,*) 'dimension',dimPlex;flush(6)
|
||||
call DMGetStratumSize(globalMesh,'depth',dimPlex,mesh_NcpElemsGlobal,ierr)
|
||||
CHKERRQ(ierr)
|
||||
! get number of IDs in face sets (for boundary conditions?)
|
||||
call DMGetLabelSize(globalMesh,'Face Sets',mesh_Nboundaries,ierr)
|
||||
CHKERRQ(ierr)
|
||||
write(6,*) 'number of "Face Sets"',mesh_Nboundaries;flush(6)
|
||||
call MPI_Bcast(mesh_Nboundaries,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
|
||||
call MPI_Bcast(mesh_NcpElemsGlobal,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
|
||||
call MPI_Bcast(dimPlex,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
|
||||
|
|
@ -154,33 +145,27 @@ subroutine discretization_mesh_init(restart)
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call DMGetStratumSize(geomMesh,'depth',0,mesh_Nnodes,ierr)
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CHKERRQ(ierr)
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||||
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||||
FE_Nips(FE_geomtype(1)) = FEM_nQuadrature(dimPlex,integrationOrder)
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mesh_maxNips = FE_Nips(1)
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||||
mesh_maxNips = FEM_nQuadrature(dimPlex,integrationOrder)
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||||
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||||
write(6,*) 'mesh_maxNips',mesh_maxNips
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call mesh_FEM_build_ipCoordinates(dimPlex,FEM_quadrature_points(dimPlex,integrationOrder)%p)
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call mesh_FEM_build_ipVolumes(dimPlex)
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allocate (mesh_element (4,mesh_NcpElems)); mesh_element = 0
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||||
allocate(microstructureAt(mesh_NcpElems))
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||||
allocate(homogenizationAt(mesh_NcpElems),source=1)
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do j = 1, mesh_NcpElems
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||||
mesh_element( 1,j) = -1 ! DEPRECATED
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||||
mesh_element( 2,j) = mesh_elemType ! elem type
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||||
mesh_element( 3,j) = 1 ! homogenization
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||||
call DMGetLabelValue(geomMesh,'material',j-1,mesh_element(4,j),ierr)
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||||
call DMGetLabelValue(geomMesh,'material',j-1,microstructureAt(j),ierr)
|
||||
CHKERRQ(ierr)
|
||||
end do
|
||||
|
||||
if (debug_e < 1 .or. debug_e > mesh_NcpElems) &
|
||||
call IO_error(602,ext_msg='element') ! selected element does not exist
|
||||
if (debug_i < 1 .or. debug_i > FE_Nips(FE_geomtype(mesh_element(2,debug_e)))) &
|
||||
call IO_error(602,ext_msg='IP') ! selected element does not have requested IP
|
||||
if (debug_e < 1 .or. debug_e > mesh_NcpElems) call IO_error(602,ext_msg='element')
|
||||
if (debug_i < 1 .or. debug_i > mesh_maxNips) call IO_error(602,ext_msg='IP')
|
||||
|
||||
FEsolving_execElem = [ 1,mesh_NcpElems ] ! parallel loop bounds set to comprise all DAMASK elements
|
||||
FEsolving_execIP = [1,FE_Nips(FE_geomtype(mesh_element(2,1)))]
|
||||
FEsolving_execElem = [1,mesh_NcpElems] ! parallel loop bounds set to comprise all DAMASK elements
|
||||
FEsolving_execIP = [1,mesh_maxNips]
|
||||
|
||||
allocate(mesh_node0(3,mesh_Nnodes),source=0.0_pReal)
|
||||
|
||||
call discretization_init(mesh_element(3,:),mesh_element(4,:),&
|
||||
call discretization_init(microstructureAt,homogenizationAt,&
|
||||
reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &
|
||||
mesh_node0)
|
||||
|
||||
|
|
|
|||
|
|
@ -101,6 +101,8 @@ module quaternions
|
|||
assignment(=), &
|
||||
conjg, aimag, &
|
||||
log, exp, &
|
||||
abs, dot_product, &
|
||||
inverse, &
|
||||
real
|
||||
|
||||
contains
|
||||
|
|
|
|||
Loading…
Reference in New Issue