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Merge branch 'development' into Fortran-cleaning

This commit is contained in:
Martin Diehl 2021-04-13 21:25:08 +02:00
parent 1762245b69 e360e0de55
commit d47c116ebd
15 changed files with 675 additions and 616 deletions
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2
VERSION
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@ -1 +1 @@
v3.0.0-alpha2-829-g73b07eda4
v3.0.0-alpha2-866-g1be1a72a0

90
python/damask/_orientation.py
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@ -86,11 +86,11 @@ class Orientation(Rotation):
"""
crystal_families = ['triclinic',
'monoclinic',
'orthorhombic',
'tetragonal',
'hexagonal',
'cubic']
'monoclinic',
'orthorhombic',
'tetragonal',
'hexagonal',
'cubic']
lattice_symmetries = {
'aP': 'triclinic',
@ -136,8 +136,7 @@ class Orientation(Rotation):
Rotation.__init__(self) if rotation is None else Rotation.__init__(self,rotation=rotation)
if ( lattice is not None
and lattice not in self.lattice_symmetries
if ( lattice not in self.lattice_symmetries
and lattice not in self.crystal_families):
raise KeyError(f'Lattice "{lattice}" is unknown')
@ -206,7 +205,7 @@ class Orientation(Rotation):
def __repr__(self):
"""Represent."""
return '\n'.join(([] if self.lattice is None else [f'Bravais lattice {self.lattice}'])
+ ([] if self.family is None else [f'Crystal family {self.family}'])
+ ([f'Crystal family {self.family}'])
+ [super().__repr__()])
@ -239,7 +238,7 @@ class Orientation(Rotation):
"""
matching_type = all([hasattr(other,attr) and getattr(self,attr) == getattr(other,attr)
for attr in ['family','lattice','parameters']])
return np.logical_and(super().__eq__(other),matching_type)
return np.logical_and(matching_type,super(self.__class__,self.reduced).__eq__(other.reduced))
def __ne__(self,other):
"""
@ -254,6 +253,57 @@ class Orientation(Rotation):
return np.logical_not(self==other)
def isclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
"""
Report where values are approximately equal to corresponding ones of other Orientation.
Parameters
----------
other : Orientation
Orientation to compare against.
rtol : float, optional
Relative tolerance of equality.
atol : float, optional
Absolute tolerance of equality.
equal_nan : bool, optional
Consider matching NaN values as equal. Defaults to True.
Returns
-------
mask : numpy.ndarray bool
Mask indicating where corresponding orientations are close.
"""
matching_type = all([hasattr(other,attr) and getattr(self,attr) == getattr(other,attr)
for attr in ['family','lattice','parameters']])
return np.logical_and(matching_type,super(self.__class__,self.reduced).isclose(other.reduced))
def allclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
"""
Test whether all values are approximately equal to corresponding ones of other Orientation.
Parameters
----------
other : Orientation
Orientation to compare against.
rtol : float, optional
Relative tolerance of equality.
atol : float, optional
Absolute tolerance of equality.
equal_nan : bool, optional
Consider matching NaN values as equal. Defaults to True.
Returns
-------
answer : bool
Whether all values are close between both orientations.
"""
return np.all(self.isclose(other,rtol,atol,equal_nan))
def __mul__(self,other):
"""
Compose this orientation with other.
@ -491,9 +541,6 @@ class Orientation(Rotation):
is added to the left of the Rotation array.
"""
if self.family is None:
raise ValueError('Missing crystal symmetry')
o = self.symmetry_operations.broadcast_to(self.symmetry_operations.shape+self.shape,mode='right')
return self.copy(rotation=o*Rotation(self.quaternion).broadcast_to(o.shape,mode='left'))
@ -501,9 +548,6 @@ class Orientation(Rotation):
@property
def reduced(self):
"""Select symmetrically equivalent orientation that falls into fundamental zone according to symmetry."""
if self.family is None:
raise ValueError('Missing crystal symmetry')
eq = self.equivalent
ok = eq.in_FZ
ok &= np.cumsum(ok,axis=0) == 1
@ -532,9 +576,6 @@ class Orientation(Rotation):
https://doi.org/10.1107/S0108767391006864
"""
if self.family is None:
raise ValueError('Missing crystal symmetry')
rho_abs = np.abs(self.as_Rodrigues_vector(compact=True))*(1.-1.e-9)
with np.errstate(invalid='ignore'):
@ -575,9 +616,6 @@ class Orientation(Rotation):
https://doi.org/10.1107/S0108767391006864
"""
if self.family is None:
raise ValueError('Missing crystal symmetry')
rho = self.as_Rodrigues_vector(compact=True)*(1.0-1.0e-9)
with np.errstate(invalid='ignore'):
@ -728,8 +766,6 @@ class Orientation(Rotation):
'beta': np.pi/2.,
'gamma': np.pi/2.,
}
else:
raise KeyError(f'Crystal family "{self.family}" is unknown')
@property
@ -1026,8 +1062,6 @@ class Orientation(Rotation):
Bunge Eulers / deg: (11.40, 21.86, 0.60)
"""
if self.family is None or other.family is None:
raise ValueError('missing crystal symmetry')
if self.family != other.family:
raise NotImplementedError('disorientation between different crystal families')
@ -1084,9 +1118,6 @@ class Orientation(Rotation):
https://doi.org/10.1107/S0021889801003077
"""
if self.family is None:
raise ValueError('Missing crystal symmetry')
eq = self.equivalent
m = eq.misorientation(self[...,0].reshape((1,)+self.shape[:-1]+(1,))
.broadcast_to(eq.shape))\
@ -1128,9 +1159,6 @@ class Orientation(Rotation):
Index of symmetrically equivalent orientation that rotated vector to SST.
"""
if self.family is None:
raise ValueError('Missing crystal symmetry')
eq = self.equivalent
blend = util.shapeblender(eq.shape,np.array(vector).shape[:-1])
poles = eq.broadcast_to(blend,mode='right') @ np.broadcast_to(np.array(vector),blend+(3,))

9
python/damask/_result.py
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@ -1044,7 +1044,8 @@ class Result:
collection = ET.SubElement(domain, 'Grid')
collection.attrib={'GridType': 'Collection',
'CollectionType': 'Temporal'}
'CollectionType': 'Temporal',
'Name': 'Increments'}
time = ET.SubElement(collection, 'Time')
time.attrib={'TimeType': 'List'}
@ -1106,7 +1107,7 @@ class Result:
unit = f[name].attrs[u] if h5py3 else f[name].attrs[u].decode()
attributes.append(ET.SubElement(grid, 'Attribute'))
attributes[-1].attrib = {'Name': name.split('/',2)[2]+f' / {unit}',
attributes[-1].attrib = {'Name': '/'.join([ty,field,out])+f' / {unit}',
'Center': 'Cell',
'AttributeType': attribute_type_map[shape]}
data_items.append(ET.SubElement(attributes[-1], 'DataItem'))
@ -1265,7 +1266,7 @@ class Result:
if prune: r = util.dict_prune(r)
if flatten: r = util.dict_flatten(r)
return r
return None if (type(r) == dict and r == {}) else r
def place(self,output='*',flatten=True,prune=True,constituents=None,fill_float=np.nan,fill_int=0):
@ -1352,4 +1353,4 @@ class Result:
if prune: r = util.dict_prune(r)
if flatten: r = util.dict_flatten(r)
return r
return None if (type(r) == dict and r == {}) else r

66
python/damask/_rotation.py
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@ -103,29 +103,20 @@ class Rotation:
"""
Equal to other.
Equality is determined taking limited floating point precision into account.
See numpy.allclose for details.
Parameters
----------
other : Rotation
Rotation to check for equality.
"""
s = self.quaternion
o = other.quaternion
if self.shape == () == other.shape:
return np.allclose(s,o) or (np.isclose(s[0],0.0) and np.allclose(s,-1.0*o))
else:
return np.all(np.isclose(s,o),-1) + np.all(np.isclose(s,-1.0*o),-1) * np.isclose(s[...,0],0.0)
return np.logical_or(np.all(self.quaternion == other.quaternion,axis=-1),
np.all(self.quaternion == -1.0*other.quaternion,axis=-1))
def __ne__(self,other):
"""
Not equal to other.
Equality is determined taking limited floating point precision into
account. See numpy.allclose for details.
Parameters
----------
other : Rotation
@ -135,6 +126,57 @@ class Rotation:
return np.logical_not(self==other)
def isclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
"""
Report where values are approximately equal to corresponding ones of other Rotation.
Parameters
----------
other : Rotation
Rotation to compare against.
rtol : float, optional
Relative tolerance of equality.
atol : float, optional
Absolute tolerance of equality.
equal_nan : bool, optional
Consider matching NaN values as equal. Defaults to True.
Returns
-------
mask : numpy.ndarray bool
Mask indicating where corresponding rotations are close.
"""
s = self.quaternion
o = other.quaternion
return np.logical_or(np.all(np.isclose(s, o,rtol,atol,equal_nan),axis=-1),
np.all(np.isclose(s,-1.0*o,rtol,atol,equal_nan),axis=-1))
def allclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
"""
Test whether all values are approximately equal to corresponding ones of other Rotation.
Parameters
----------
other : Rotation
Rotation to compare against.
rtol : float, optional
Relative tolerance of equality.
atol : float, optional
Absolute tolerance of equality.
equal_nan : bool, optional
Consider matching NaN values as equal. Defaults to True.
Returns
-------
answer : bool
Whether all values are close between both rotations.
"""
return np.all(self.isclose(other,rtol,atol,equal_nan))
def __array__(self):
"""Initializer for numpy."""
return self.quaternion

2
python/damask/util.py
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@ -137,7 +137,7 @@ def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
Character length of bar. Defaults to 50.
"""
if N_iter == 1 or (hasattr(iterable,'__len__') and len(iterable) == 1):
if N_iter in [0,1] or (hasattr(iterable,'__len__') and len(iterable) <= 1):
for item in iterable:
yield item
else:

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python/tests/reference/Result/6grains6x7x8_single_phase_tensionY.xdmf
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4
python/tests/test_Config.py
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@ -53,7 +53,7 @@ class TestConfig:
def test_abstract_is_complete(self):
assert Config().is_complete is None
@pytest.mark.parametrize('data',[Rotation.from_random(),Orientation.from_random()])
@pytest.mark.parametrize('data',[Rotation.from_random(),Orientation.from_random(lattice='cI')])
def test_rotation_orientation(self,data):
assert str(Config(a=data)) == str(Config(a=data.as_quaternion()))

3
python/tests/test_ConfigMaterial.py
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@ -140,6 +140,5 @@ class TestConfigMaterial:
if update:
cur.save(ref_path/'measured.material.yaml')
for i,m in enumerate(ref['material']):
assert Rotation(m['constituents'][0]['O']) == \
Rotation(cur['material'][i]['constituents'][0]['O'])
assert Rotation(m['constituents'][0]['O']).isclose(Rotation(cur['material'][i]['constituents'][0]['O']))
assert cur.is_valid and cur['phase'] == ref['phase'] and cur['homogenization'] == ref['homogenization']

42
python/tests/test_Orientation.py
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@ -37,9 +37,15 @@ class TestOrientation:
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('shape',[None,5,(4,6)])
def test_close(self,lattice,shape):
R = Orientation.from_random(lattice=lattice,shape=shape)
assert R.isclose(R.reduced).all() and R.allclose(R.reduced)
@pytest.mark.parametrize('a,b',[
(dict(rotation=[1,0,0,0]),
dict(rotation=[0.5,0.5,0.5,0.5])),
(dict(rotation=[1,0,0,0],lattice='triclinic'),
dict(rotation=[0.5,0.5,0.5,0.5],lattice='triclinic')),
(dict(rotation=[1,0,0,0],lattice='cubic'),
dict(rotation=[1,0,0,0],lattice='hexagonal')),
@ -222,7 +228,7 @@ class TestOrientation:
blend = util.shapeblender(o.shape,p.shape)
for loc in np.random.randint(0,blend,(10,len(blend))):
assert o[tuple(loc[:len(o.shape)])].disorientation(p[tuple(loc[-len(p.shape):])]) \
== o.disorientation(p)[tuple(loc)]
.isclose(o.disorientation(p)[tuple(loc)])
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
def test_disorientation360(self,lattice):
@ -335,33 +341,9 @@ class TestOrientation:
o.family = invalid_family
o.symmetry_operations # noqa
def test_missing_symmetry_equivalent(self):
with pytest.raises(ValueError):
Orientation(lattice=None).equivalent # noqa
def test_missing_symmetry_reduced(self):
with pytest.raises(ValueError):
Orientation(lattice=None).reduced # noqa
def test_missing_symmetry_in_FZ(self):
with pytest.raises(ValueError):
Orientation(lattice=None).in_FZ # noqa
def test_missing_symmetry_in_disorientation_FZ(self):
with pytest.raises(ValueError):
Orientation(lattice=None).in_disorientation_FZ # noqa
def test_missing_symmetry_disorientation(self):
with pytest.raises(ValueError):
Orientation(lattice=None).disorientation(Orientation(lattice=None)) # noqa
def test_missing_symmetry_average(self):
with pytest.raises(ValueError):
Orientation(lattice=None).average() # noqa
def test_missing_symmetry_to_SST(self):
with pytest.raises(ValueError):
Orientation(lattice=None).to_SST(np.zeros(3)) # noqa
def test_invalid_rot(self):
with pytest.raises(TypeError):
Orientation.from_random(lattice='cubic') * np.ones(3)
def test_missing_symmetry_immutable(self):
with pytest.raises(KeyError):

33
python/tests/test_Result.py
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@ -65,14 +65,17 @@ class TestResult:
assert dict_equal(a,default.view('times','*').get('F'))
assert dict_equal(a,default.view('times',default.times_in_range(0.0,np.inf)).get('F'))
@pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations
@pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations
def test_view_none(self,default,what):
a = default.view(what,False).get('F')
b = default.view(what,[]).get('F')
n0 = default.view(what,False)
n1 = default.view(what,[])
assert a == b == {}
label = 'increments' if what == 'times' else what
@pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations
assert n0.get('F') is n1.get('F') is None and \
len(n0.visible[label]) == len(n1.visible[label]) == 0
@pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations
def test_view_more(self,default,what):
empty = default.view(what,False)
@ -81,14 +84,17 @@ class TestResult:
assert dict_equal(a,b)
@pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations
@pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations
def test_view_less(self,default,what):
full = default.view(what,True)
a = full.view_less(what,'*').get('F')
b = full.view_less(what,True).get('F')
n0 = full.view_less(what,'*')
n1 = full.view_less(what,True)
assert a == b == {}
label = 'increments' if what == 'times' else what
assert n0.get('F') is n1.get('F') is None and \
len(n0.visible[label]) == len(n1.visible[label]) == 0
def test_view_invalid(self,default):
with pytest.raises(AttributeError):
@ -189,7 +195,7 @@ class TestResult:
default.add_stress_Cauchy('P','F')
default.add_calculation('sigma_y','#sigma#',unit='y')
default.add_equivalent_Mises('sigma_y')
assert default.get('sigma_y_vM') == {}
assert default.get('sigma_y_vM') is None
def test_add_Mises_stress_strain(self,default):
default.add_stress_Cauchy('P','F')
@ -380,8 +386,8 @@ class TestResult:
pickle.dump(cur,f)
with bz2.BZ2File((ref_path/'get'/fname).with_suffix('.pbz2')) as f:
assert dict_equal(cur,pickle.load(f))
ref = pickle.load(f)
assert cur is None if ref is None else dict_equal(cur,ref)
@pytest.mark.parametrize('view,output,flatten,constituents,prune',
[({},['F','P','F','L_p','F_e','F_p'],True,True,None),
@ -405,4 +411,5 @@ class TestResult:
pickle.dump(cur,f)
with bz2.BZ2File((ref_path/'place'/fname).with_suffix('.pbz2')) as f:
assert dict_equal(cur,pickle.load(f))
ref = pickle.load(f)
assert cur is None if ref is None else dict_equal(cur,ref)

4
python/tests/test_Rotation.py
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@ -960,7 +960,7 @@ class TestRotation:
if axis_angle[3] > np.pi:
axis_angle[3] -= 2.*np.pi
axis_angle *= -1
assert R**pwr == Rotation.from_axis_angle(axis_angle)
assert (R**pwr).isclose(Rotation.from_axis_angle(axis_angle))
def test_rotate_inverse(self):
R = Rotation.from_random()
@ -1027,7 +1027,7 @@ class TestRotation:
def test_invariant(self):
R = Rotation.from_random()
assert R/R == R*R**(-1) == Rotation()
assert (R/R).isclose(R*R**(-1)) and (R/R).isclose(Rotation())
@pytest.mark.parametrize('item',[np.ones(3),np.ones((3,3)), np.ones((3,3,3,3))])
def test_apply(self,item):