Merge branch 'development' into vector-mechanics

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

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

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@ -15,7 +15,7 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) 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 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 struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
@ -62,7 +62,7 @@ if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) 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 grid_original = geom.grid
damask.util.croak(geom) damask.util.croak(geom)
@ -174,4 +174,4 @@ for name in filenames:
origin = geom.origin, origin = geom.origin,
comments = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])], 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)

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

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

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@ -213,9 +213,8 @@ class Geom:
if not keyword.startswith('head') or header_length < 3: if not keyword.startswith('head') or header_length < 3:
raise TypeError('Header length information missing or invalid') raise TypeError('Header length information missing or invalid')
content = f.readlines()
comments = [] comments = []
content = f.readlines()
for i,line in enumerate(content[:header_length]): for i,line in enumerate(content[:header_length]):
items = line.split('#')[0].lower().strip().split() items = line.split('#')[0].lower().strip().split()
key = items[0] if items else '' key = items[0] if items else ''
@ -247,7 +246,7 @@ class Geom:
raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}') raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
if not np.any(np.mod(material,1) != 0.0): # no float present if not np.any(np.mod(material,1) != 0.0): # no float present
material = material.astype('int') material = material.astype('int') - (1 if material.min() > 0 else 0)
return Geom(material.reshape(grid,order='F'),size,origin,comments) return Geom(material.reshape(grid,order='F'),size,origin,comments)
@ -510,7 +509,7 @@ class Geom:
Parameters 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. Filename to write. Valid extension is .vtr, it will be appended if not given.
compress : bool, optional compress : bool, optional
Compress with zlib algorithm. Defaults to True. Compress with zlib algorithm. Defaults to True.

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@ -803,7 +803,7 @@ class Orientation(Rotation):
return np.all(components >= 0.0,axis=-1) 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. 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 : numpy.ndarray of shape (...,3)
Vector to colorize. Vector to colorize.
in_SST : bool, optional
Consider symmetrically equivalent orientations such that poles are located in SST.
Defaults to True.
proper : bool, optional proper : bool, optional
Consider only vectors with z >= 0, hence combine two neighboring SSTs (with mirrored colors). Consider only vectors with z >= 0, hence combine two neighboring SSTs (with mirrored colors).
Defaults to False. 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: Inverse pole figure color of the e_3 direction for a crystal in "Cube" orientation with cubic symmetry:
>>> o = damask.Orientation(lattice='cubic') >>> o = damask.Orientation(lattice='cubic')
>>> o.IPF_color(o.to_SST([0,0,1])) >>> o.IPF_color([0,0,1])
array([1., 0., 0.]) array([1., 0., 0.])
References References
@ -1076,7 +1079,7 @@ class Orientation(Rotation):
@classmethod @classmethod
def Bravais_to_Miller(cls,uvtw=None,hkil=None): def Bravais_to_Miller(cls,*,uvtw=None,hkil=None):
""" """
Transform 4 MillerBravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl). Transform 4 MillerBravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
@ -1104,7 +1107,7 @@ class Orientation(Rotation):
@classmethod @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 MillerBravais indices of crystal direction [uvtw] or plane normal (hkil). Transform 3 Miller indices to 4 MillerBravais indices of crystal direction [uvtw] or plane normal (hkil).
@ -1133,7 +1136,7 @@ class Orientation(Rotation):
return np.einsum('il,...l',basis,axis) 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. 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) 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). 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)) 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). Calculate lab frame vector along lattice direction [uvw] or plane normal (hkl).

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

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

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

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