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Merge branch 'misc-improvements' into 'development' 

Misc improvements

See merge request damask/DAMASK!181
This commit is contained in:
Jaber 2020-06-22 13:24:00 +02:00
parent 01f21a9e3b c6a5bb8a3b
commit 17212b27dc
11 changed files with 337 additions and 175 deletions
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2
examples/ConfigFiles/Phase_DisloUCLA_Tungsten.config
View File

@ -27,7 +27,7 @@ SolidSolutionStrength 0.0 # Strength due to elements in solid solution
### Dislocation glide parameters ###
#per family
Nslip 12 0
Nslip 12
slipburgers 2.72e-10 # Burgers vector of slip system [m]
rhoedge0 1.0e12 # Initial edge dislocation density [m/m**3]
rhoedgedip0 1.0 # Initial edged dipole dislocation density [m/m**3]

280
python/damask/_rotation.py
View File

@ -20,8 +20,8 @@ class Rotation:
when viewing from the end point of the rotation axis towards the origin.
- rotations will be interpreted in the passive sense.
- Euler angle triplets are implemented using the Bunge convention,
with the angular ranges as [0, 2π],[0, π],[0, 2π].
- the rotation angle ω is limited to the interval [0, π].
with the angular ranges as [0,2π], [0,π], [0,2π].
- the rotation angle ω is limited to the interval [0,π].
- the real part of a quaternion is positive, Re(q) > 0
- P = -1 (as default).
@ -49,7 +49,8 @@ class Rotation:
Parameters
----------
quaternion : numpy.ndarray, optional
Unit quaternion that follows the conventions. Use .from_quaternion to perform a sanity check.
Unit quaternion in positive real hemisphere.
Use .from_quaternion to perform a sanity check.
"""
self.quaternion = quaternion.copy()
@ -73,7 +74,7 @@ class Rotation:
raise NotImplementedError('Support for multiple rotations missing')
return '\n'.join([
'Quaternion: (real={:.3f}, imag=<{:+.3f}, {:+.3f}, {:+.3f}>)'.format(*(self.quaternion)),
'Matrix:\n{}'.format(self.as_matrix()),
'Matrix:\n{}'.format(np.round(self.as_matrix(),8)),
'Bunge Eulers / deg: ({:3.2f}, {:3.2f}, {:3.2f})'.format(*self.as_Eulers(degrees=True)),
])
@ -87,10 +88,6 @@ class Rotation:
other : numpy.ndarray or Rotation
Vector, second or fourth order tensor, or rotation object that is rotated.
Todo
----
Check rotation of 4th order tensor
"""
if isinstance(other, Rotation):
q_m = self.quaternion[...,0:1]
@ -99,7 +96,7 @@ class Rotation:
p_o = other.quaternion[...,1:]
q = (q_m*q_o - np.einsum('...i,...i',p_m,p_o).reshape(self.shape+(1,)))
p = q_m*p_o + q_o*p_m + _P * np.cross(p_m,p_o)
return self.__class__(np.block([q,p])).standardize()
return self.__class__(np.block([q,p]))._standardize()
elif isinstance(other,np.ndarray):
if self.shape + (3,) == other.shape:
@ -124,24 +121,24 @@ class Rotation:
else:
raise TypeError('Cannot rotate {}'.format(type(other)))
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 real part."""
def _standardize(self):
"""Standardize (ensure positive real hemisphere)."""
self.quaternion[self.quaternion[...,0] < 0.0] *= -1
return self
def standardized(self):
"""Quaternion representation with positive real part."""
return self.copy().standardize()
def inverse(self):
"""In-place inverse rotation (backward rotation)."""
self.quaternion[...,1:] *= -1
return self
def __invert__(self):
"""Inverse rotation (backward rotation)."""
return self.copy().inverse()
def inversed(self):
"""Inverse rotation (backward rotation)."""
return ~ self
def misorientation(self,other):
@ -154,7 +151,7 @@ class Rotation:
Rotation to which the misorientation is computed.
"""
return other*self.inversed()
return other@~self
def broadcast_to(self,shape):
@ -169,7 +166,7 @@ class Rotation:
return self.__class__(q)
def average(self,other):
def average(self,other): #ToDo: discuss calling for vectors
"""
Calculate the average rotation.
@ -189,25 +186,31 @@ class Rotation:
def as_quaternion(self):
"""
Unit quaternion [q, p_1, p_2, p_3].
Represent as unit quaternion.
Parameters
----------
quaternion : bool, optional
return quaternion as DAMASK object.
Returns
-------
q : numpy.ndarray of shape (...,4)
Unit quaternion in positive real hemisphere: (q_0, q_1, q_2, q_3), |q|=1, q_0 ≥ 0.
"""
return self.quaternion
return self.quaternion.copy()
def as_Eulers(self,
degrees = False):
"""
Bunge-Euler angles: (φ_1, ϕ, φ_2).
Represent as Bunge-Euler angles.
Parameters
----------
degrees : bool, optional
return angles in degrees.
Return angles in degrees.
Returns
-------
phi : numpy.ndarray of shape (...,3)
Bunge-Euler angles: (φ_1, ϕ, φ_2), φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]
unless degrees == True: φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360]
"""
eu = Rotation._qu2eu(self.quaternion)
@ -218,14 +221,21 @@ class Rotation:
degrees = False,
pair = False):
"""
Axis angle representation [n_1, n_2, n_3, ω] unless pair == True: ([n_1, n_2, n_3], ω).
Represent as axis angle pair.
Parameters
----------
degrees : bool, optional
return rotation angle in degrees.
Return rotation angle in degrees. Defaults to False.
pair : bool, optional
return tuple of axis and angle.
Return tuple of axis and angle. Defaults to False.
Returns
-------
axis_angle : numpy.ndarray of shape (...,4) unless pair == True:
tuple containing numpy.ndarray of shapes (...,3) and (...)
Axis angle pair: (n_1, n_2, n_3, ω), |n| = 1 and ω ∈ [0,π]
unless degrees = True: ω ∈ [0,180].
"""
ax = Rotation._qu2ax(self.quaternion)
@ -233,29 +243,60 @@ class Rotation:
return (ax[...,:3],ax[...,3]) if pair else ax
def as_matrix(self):
"""Rotation matrix."""
"""
Represent as rotation matrix.
Returns
-------
R : numpy.ndarray of shape (...,3,3)
Rotation matrix R, det(R) = 1, R.T∙R=I.
"""
return Rotation._qu2om(self.quaternion)
def as_Rodrigues(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).
Represent as Rodrigues-Frank vector with separated axis and angle argument.
Parameters
----------
vector : bool, optional
return as actual Rodrigues--Frank vector, i.e. rotation axis scaled by tan(ω/2).
Return as actual Rodrigues-Frank vector, i.e. axis
and angle argument are not separated.
Returns
-------
rho : numpy.ndarray of shape (...,4) unless vector == True:
numpy.ndarray of shape (...,3)
Rodrigues-Frank vector: [n_1, n_2, n_3, tan(ω/2)], |n| = 1 and ω ∈ [0,π].
"""
ro = Rotation._qu2ro(self.quaternion)
return ro[...,:3]*ro[...,3] if vector else ro
def as_homochoric(self):
"""Homochoric vector: (h_1, h_2, h_3)."""
"""
Represent as homochoric vector.
Returns
-------
h : numpy.ndarray of shape (...,3)
Homochoric vector: (h_1, h_2, h_3), |h| < 1/2*π^(2/3).
"""
return Rotation._qu2ho(self.quaternion)
def as_cubochoric(self):
"""Cubochoric vector: (c_1, c_2, c_3)."""
"""
Represent as cubochoric vector.
Returns
-------
c : numpy.ndarray of shape (...,3)
Cubochoric vector: (c_1, c_2, c_3), max(c_i) < 1/2*π^(2/3).
"""
return Rotation._qu2cu(self.quaternion)
def M(self): # ToDo not sure about the name: as_M or M? we do not have a from_M
@ -275,18 +316,34 @@ class Rotation:
# Static constructors. The input data needs to follow the conventions, options allow to
# relax the conventions.
@staticmethod
def from_quaternion(quaternion,
def from_quaternion(q,
accept_homomorph = False,
P = -1,
acceptHomomorph = None):
acceptHomomorph = None): # old name (for compatibility)
"""
Initialize from quaternion.
Parameters
----------
q : numpy.ndarray of shape (...,4)
Unit quaternion in positive real hemisphere: (q_0, q_1, q_2, q_3),
|q|=1, q_0 ≥ 0.
accept_homomorph : boolean, optional
Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
Defaults to False.
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
if acceptHomomorph is not None:
accept_homomorph = acceptHomomorph
qu = np.array(quaternion,dtype=float)
accept_homomorph = acceptHomomorph # for compatibility
qu = np.array(q,dtype=float)
if qu.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if P > 0: qu[...,1:4] *= -1 # convert from P=1 to P=-1
if P == 1: qu[...,1:4] *= -1
if accept_homomorph:
qu[qu[...,0] < 0.0] *= -1
else:
@ -298,10 +355,21 @@ class Rotation:
return Rotation(qu)
@staticmethod
def from_Eulers(eulers,
def from_Eulers(phi,
degrees = False):
"""
Initialize from Bunge-Euler angles.
eu = np.array(eulers,dtype=float)
Parameters
----------
phi : numpy.ndarray of shape (...,3)
Bunge-Euler angles: (φ_1, ϕ, φ_2), φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]
unless degrees == True: φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360].
degrees : boolean, optional
Bunge-Euler angles are given in degrees. Defaults to False.
"""
eu = np.array(phi,dtype=float)
if eu.shape[:-2:-1] != (3,):
raise ValueError('Invalid shape.')
@ -316,12 +384,29 @@ class Rotation:
degrees = False,
normalise = False,
P = -1):
"""
Initialize from Axis angle pair.
Parameters
----------
axis_angle : numpy.ndarray of shape (...,4)
Axis angle pair: [n_1, n_2, n_3, ω], |n| = 1 and ω ∈ [0,π]
unless degrees = True: ω ∈ [0,180].
degrees : boolean, optional
Angle ω is given in degrees. Defaults to False.
normalize: boolean, optional
Allow |n| ≠ 1. Defaults to False.
P : integer ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
ax = np.array(axis_angle,dtype=float)
if ax.shape[:-2:-1] != (4,):
raise ValueError('Invalid shape.')
if abs(P) != 1:
raise ValueError('P ∉ {-1,1}')
if P > 0: ax[...,0:3] *= -1 # convert from P=1 to P=-1
if P == 1: ax[...,0:3] *= -1
if degrees: ax[..., 3] = np.radians(ax[...,3])
if normalise: ax[...,0:3] /= np.linalg.norm(ax[...,0:3],axis=-1)
if np.any(ax[...,3] < 0.0) or np.any(ax[...,3] > np.pi):
@ -335,7 +420,19 @@ class Rotation:
def from_basis(basis,
orthonormal = True,
reciprocal = False):
"""
Initialize from lattice basis vectors.
Parameters
----------
basis : numpy.ndarray of shape (...,3,3)
Three lattice basis vectors in three dimensions.
orthonormal : boolean, optional
Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
reciprocal : boolean, optional
Basis vectors are given in reciprocal (instead of real) space. Defaults to False.
"""
om = np.array(basis,dtype=float)
if om.shape[:-3:-1] != (3,3):
raise ValueError('Invalid shape.')
@ -356,20 +453,43 @@ class Rotation:
return Rotation(Rotation._om2qu(om))
@staticmethod
def from_matrix(om):
def from_matrix(R):
"""
Initialize from rotation matrix.
return Rotation.from_basis(om)
Parameters
----------
R : numpy.ndarray of shape (...,3,3)
Rotation matrix: det(R) = 1, R.T∙R=I.
"""
return Rotation.from_basis(R)
@staticmethod
def from_Rodrigues(rodrigues,
def from_Rodrigues(rho,
normalise = False,
P = -1):
"""
Initialize from Rodrigues-Frank vector.
ro = np.array(rodrigues,dtype=float)
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)
if np.any(ro[...,3] < 0.0):
raise ValueError('Rodrigues vector rotation angle not positive.')
@ -379,14 +499,26 @@ class Rotation:
return Rotation(Rotation._ro2qu(ro))
@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)))
])

14
python/damask/util.py
View File

@ -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):

2
python/tests/test_Result.py
View File

@ -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')))

36
python/tests/test_Rotation.py
View File

@ -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))

11
python/tests/test_util.py Normal file
View File

@ -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==''

2
src/constitutive_plastic_dislotwin.f90
View File

@ -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')

4
src/crystallite.f90
View File

@ -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 :: &

2
src/discretization.f90
View File

@ -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)

157
src/mesh/discretization_mesh.f90
View File

@ -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
implicit none
private
integer, public, protected :: &
mesh_Nboundaries, &
mesh_NcpElemsGlobal
use DAMASK_interface
use IO
use debug
use discretization
use numerics
use FEsolving
use FEM_quadrature
use prec
integer :: &
mesh_NcpElems !< total number of CP elements in mesh
implicit none
private
integer, public, protected :: &
mesh_Nboundaries, &
mesh_NcpElemsGlobal
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
PetscInt, dimension(:), allocatable, public, protected :: &
mesh_boundaries
DM, public :: geomMesh
public :: &
discretization_mesh_init, &
mesh_FEM_build_ipVolumes, &
mesh_FEM_build_ipCoordinates
PetscInt, dimension(:), allocatable, public, protected :: &
mesh_boundaries
public :: &
discretization_mesh_init, &
mesh_FEM_build_ipVolumes, &
mesh_FEM_build_ipCoordinates
contains
@ -67,39 +64,33 @@ 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
PetscInt, pointer, dimension(:) :: pFaceSets
character(len=pStringLen), dimension(:), allocatable :: fileContent
IS :: faceSetIS
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)
@ -142,48 +133,42 @@ subroutine discretization_mesh_init(restart)
enddo
call DMClone(globalMesh,geomMesh,ierr)
CHKERRQ(ierr)
else
else
call DMPlexDistribute(globalMesh,0,sf,geomMesh,ierr)
CHKERRQ(ierr)
endif
endif
call DMDestroy(globalMesh,ierr); CHKERRQ(ierr)
call DMGetStratumSize(geomMesh,'depth',dimPlex,mesh_NcpElems,ierr)
CHKERRQ(ierr)
call DMGetStratumSize(geomMesh,'depth',0,mesh_Nnodes,ierr)
CHKERRQ(ierr)
FE_Nips(FE_geomtype(1)) = FEM_nQuadrature(dimPlex,integrationOrder)
mesh_maxNips = FE_Nips(1)
write(6,*) 'mesh_maxNips',mesh_maxNips
mesh_maxNips = FEM_nQuadrature(dimPlex,integrationOrder)
call mesh_FEM_build_ipCoordinates(dimPlex,FEM_quadrature_points(dimPlex,integrationOrder)%p)
call mesh_FEM_build_ipVolumes(dimPlex)
allocate (mesh_element (4,mesh_NcpElems)); mesh_element = 0
do j = 1, mesh_NcpElems
mesh_element( 1,j) = -1 ! DEPRECATED
mesh_element( 2,j) = mesh_elemType ! elem type
mesh_element( 3,j) = 1 ! homogenization
call DMGetLabelValue(geomMesh,'material',j-1,mesh_element(4,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
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)))]
allocate(microstructureAt(mesh_NcpElems))
allocate(homogenizationAt(mesh_NcpElems),source=1)
do j = 1, mesh_NcpElems
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')
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,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)
end subroutine discretization_mesh_init
@ -191,23 +176,23 @@ end subroutine discretization_mesh_init
!> @brief Calculates IP volume. Allocates global array 'mesh_ipVolume'
!--------------------------------------------------------------------------------------------------
subroutine mesh_FEM_build_ipVolumes(dimPlex)
PetscInt,intent(in):: dimPlex
PetscReal :: vol
PetscReal, pointer,dimension(:) :: pCent, pNorm
PetscInt :: cellStart, cellEnd, cell
PetscErrorCode :: ierr
allocate(mesh_ipVolume(mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
allocate(pCent(dimPlex))
allocate(pNorm(dimPlex))
do cell = cellStart, cellEnd-1
call DMPlexComputeCellGeometryFVM(geomMesh,cell,vol,pCent,pNorm,ierr)
call DMPlexComputeCellGeometryFVM(geomMesh,cell,vol,pCent,pNorm,ierr)
CHKERRQ(ierr)
mesh_ipVolume(:,cell+1) = vol/real(mesh_maxNips,pReal)
enddo
enddo
end subroutine mesh_FEM_build_ipVolumes
@ -219,20 +204,20 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
PetscInt, intent(in) :: dimPlex
PetscReal, intent(in) :: qPoints(mesh_maxNips*dimPlex)
PetscReal, pointer,dimension(:) :: pV0, pCellJ, pInvcellJ
PetscReal :: detJ
PetscInt :: cellStart, cellEnd, cell, qPt, dirI, dirJ, qOffset
PetscErrorCode :: ierr
allocate(mesh_ipCoordinates(3,mesh_maxNips,mesh_NcpElems),source=0.0_pReal)
allocate(pV0(dimPlex))
allocatE(pCellJ(dimPlex**2))
allocatE(pinvCellJ(dimPlex**2))
call DMPlexGetHeightStratum(geomMesh,0,cellStart,cellEnd,ierr); CHKERRQ(ierr)
do cell = cellStart, cellEnd-1 !< loop over all elements
do cell = cellStart, cellEnd-1 !< loop over all elements
call DMPlexComputeCellGeometryAffineFEM(geomMesh,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
CHKERRQ(ierr)
qOffset = 0
@ -246,7 +231,7 @@ subroutine mesh_FEM_build_ipCoordinates(dimPlex,qPoints)
enddo
qOffset = qOffset + dimPlex
enddo
enddo
enddo
end subroutine mesh_FEM_build_ipCoordinates

2
src/quaternions.f90
View File

@ -101,6 +101,8 @@ module quaternions
assignment(=), &
conjg, aimag, &
log, exp, &
abs, dot_product, &
inverse, &
real
contains