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DAMASK_EICMD
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Merge branch 'development' into vector-mechanics

This commit is contained in:
Sharan Roongta 2020-11-22 12:02:29 +01:00
parent cca8649d10 c354a85f68
commit 24fabdec22
10 changed files with 33 additions and 31 deletions
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2
VERSION
View File

@ -1 +1 @@
v3.0.0-alpha-777-g523a0979e
v3.0.0-alpha-791-g662a033d9

8
processing/pre/geom_grainGrowth.py
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@ -15,8 +15,8 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0) # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
getInterfaceEnergy = lambda A,B: np.float32((A != B)*1.0) # 1.0 if A & B are distinct, 0.0 otherwise
struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
#--------------------------------------------------------------------------------------------------
@ -62,7 +62,7 @@ if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid_original = geom.grid
damask.util.croak(geom)
@ -174,4 +174,4 @@ for name in filenames:
origin = geom.origin,
comments = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
)\
.save_ASCII(sys.stdout if name is None else name)
.save(sys.stdout if name is None else name)

3
processing/pre/mentat_pbcOnBoxMesh.py
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@ -11,8 +11,6 @@ import numpy as np
import damask
sys.path.append(str(damask.solver.Marc().library_path))
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -235,6 +233,7 @@ if remote and filenames != []:
if filenames == []: filenames = [None]
if remote:
sys.path.append(str(damask.solver.Marc().library_path))
import py_mentat
damask.util.report(scriptName, 'waiting to connect...')

6
processing/pre/mentat_spectralBox.py
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@ -9,7 +9,6 @@ import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
sys.path.append(str(damask.solver.Marc().library_path))
#-------------------------------------------------------------------------------------------------
def outMentat(cmd,locals):
@ -185,9 +184,10 @@ parser.set_defaults(port = None,
if options.port is not None:
try:
sys.path.append(str(damask.solver.Marc().library_path))
import py_mentat
except ImportError:
parser.error('no valid Mentat release found.')
parser.error('no valid Mentat release found')
# --- loop over input files ------------------------------------------------------------------------
@ -196,7 +196,7 @@ if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
material = geom.material.flatten(order='F')
cmds = [\

11
python/damask/_geom.py
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@ -213,9 +213,8 @@ class Geom:
if not keyword.startswith('head') or header_length < 3:
raise TypeError('Header length information missing or invalid')
content = f.readlines()
comments = []
content = f.readlines()
for i,line in enumerate(content[:header_length]):
items = line.split('#')[0].lower().strip().split()
key = items[0] if items else ''
@ -228,7 +227,7 @@ class Geom:
else:
comments.append(line.strip())
material = np.empty(grid.prod()) # initialize as flat array
material = np.empty(grid.prod()) # initialize as flat array
i = 0
for line in content[header_length:]:
items = line.split('#')[0].split()
@ -246,8 +245,8 @@ class Geom:
if i != grid.prod():
raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
if not np.any(np.mod(material,1) != 0.0): # no float present
material = material.astype('int')
if not np.any(np.mod(material,1) != 0.0): # no float present
material = material.astype('int') - (1 if material.min() > 0 else 0)
return Geom(material.reshape(grid,order='F'),size,origin,comments)
@ -510,7 +509,7 @@ class Geom:
Parameters
----------
fname : str or or pathlib.Path
fname : str or pathlib.Path
Filename to write. Valid extension is .vtr, it will be appended if not given.
compress : bool, optional
Compress with zlib algorithm. Defaults to True.

17
python/damask/_orientation.py
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@ -803,7 +803,7 @@ class Orientation(Rotation):
return np.all(components >= 0.0,axis=-1)
def IPF_color(self,vector,proper=False):
def IPF_color(self,vector,in_SST=True,proper=False):
"""
Map vector to RGB color within standard stereographic triangle of own symmetry.
@ -811,6 +811,9 @@ class Orientation(Rotation):
----------
vector : numpy.ndarray of shape (...,3)
Vector to colorize.
in_SST : bool, optional
Consider symmetrically equivalent orientations such that poles are located in SST.
Defaults to True.
proper : bool, optional
Consider only vectors with z >= 0, hence combine two neighboring SSTs (with mirrored colors).
Defaults to False.
@ -825,7 +828,7 @@ class Orientation(Rotation):
Inverse pole figure color of the e_3 direction for a crystal in "Cube" orientation with cubic symmetry:
>>> o = damask.Orientation(lattice='cubic')
>>> o.IPF_color(o.to_SST([0,0,1]))
>>> o.IPF_color([0,0,1])
array([1., 0., 0.])
References
@ -1076,7 +1079,7 @@ class Orientation(Rotation):
@classmethod
def Bravais_to_Miller(cls,uvtw=None,hkil=None):
def Bravais_to_Miller(cls,*,uvtw=None,hkil=None):
"""
Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
@ -1104,7 +1107,7 @@ class Orientation(Rotation):
@classmethod
def Miller_to_Bravais(cls,uvw=None,hkl=None):
def Miller_to_Bravais(cls,*,uvw=None,hkl=None):
"""
Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).
@ -1133,7 +1136,7 @@ class Orientation(Rotation):
return np.einsum('il,...l',basis,axis)
def to_lattice(self,direction=None,plane=None):
def to_lattice(self,*,direction=None,plane=None):
"""
Calculate lattice vector corresponding to crystal frame direction or plane normal.
@ -1157,7 +1160,7 @@ class Orientation(Rotation):
return np.einsum('il,...l',basis,axis)
def to_frame(self,uvw=None,hkl=None,with_symmetry=False):
def to_frame(self,*,uvw=None,hkl=None,with_symmetry=False):
"""
Calculate crystal frame vector along lattice direction [uvw] or plane normal (hkl).
@ -1185,7 +1188,7 @@ class Orientation(Rotation):
np.einsum('il,...l',basis,axis))
def to_pole(self,uvw=None,hkl=None,with_symmetry=False):
def to_pole(self,*,uvw=None,hkl=None,with_symmetry=False):
"""
Calculate lab frame vector along lattice direction [uvw] or plane normal (hkl).

2
python/damask/_result.py
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@ -747,7 +747,7 @@ class Result:
'hex':'hP'}[q['meta']['Lattice']])
return {
'data': np.uint8(o.IPF_color(o.to_SST(l))*255),
'data': np.uint8(o.IPF_color(l)*255),
'label': 'IPFcolor_[{} {} {}]'.format(*m),
'meta' : {
'Unit': '8-bit RGB',

1
python/tests/test_Geom.py
View File

@ -74,6 +74,7 @@ class TestGeom:
def test_save_load_ASCII(self,default,tmp_path):
default.save_ASCII(tmp_path/'ASCII')
default.material -= 1
assert geom_equal(Geom.load_ASCII(tmp_path/'ASCII'),default)
def test_invalid_origin(self,default):

12
python/tests/test_Orientation.py
View File

@ -231,11 +231,11 @@ class TestOrientation:
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
@pytest.mark.parametrize('proper',[True,False])
def test_IPF_color_vectorization(self,lattice,shape,vector,proper):
@pytest.mark.parametrize('in_SST',[True,False])
def test_IPF_color_vectorization(self,lattice,shape,vector,proper,in_SST):
o = Orientation.from_random(lattice=lattice,shape=shape)
poles = o.to_SST(vector=vector,proper=proper)
for r, theO in zip(o.IPF_color(poles,proper=proper).reshape((-1,3)),o.flatten()):
assert np.allclose(r,theO.IPF_color(theO.to_SST(vector=vector,proper=proper),proper=proper))
for r, theO in zip(o.IPF_color(vector,in_SST=in_SST,proper=proper).reshape((-1,3)),o.flatten()):
assert np.allclose(r,theO.IPF_color(vector,in_SST=in_SST,proper=proper))
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('a,b',[
@ -263,14 +263,14 @@ class TestOrientation:
cube = Orientation(lattice='cubic')
for direction in set(permutations(np.array(color['direction']))):
assert np.allclose(np.array(color['RGB']),
cube.IPF_color(cube.to_SST(vector=np.array(direction),proper=proper),proper=proper))
cube.IPF_color(vector=np.array(direction),proper=proper))
@pytest.mark.parametrize('lattice',Orientation.crystal_families)
@pytest.mark.parametrize('proper',[True,False])
def test_IPF_equivalent(self,set_of_quaternions,lattice,proper):
direction = np.random.random(3)*2.0-1.0
o = Orientation(rotation=set_of_quaternions,lattice=lattice).equivalent
color = o.IPF_color(o.to_SST(vector=direction,proper=proper),proper=proper)
color = o.IPF_color(vector=direction,proper=proper)
assert np.allclose(np.broadcast_to(color[0,...],color.shape),color)
@pytest.mark.parametrize('lattice',Orientation.crystal_families)

2
python/tests/test_Result.py
View File

@ -178,7 +178,7 @@ class TestResult:
lattice={'fcc':'cF',
'bcc':'cI',
'hex':'hP'}[crystal_structure])
in_memory = np.uint8(c.IPF_color(c.to_SST(np.array(d)))*255)
in_memory = np.uint8(c.IPF_color(np.array(d))*255)
in_file = default.read_dataset(loc['color'])
assert np.allclose(in_memory,in_file)