DAMASK_EICMD/python/damask/_configmaterial.py

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import os.path
import numpy as np
import h5py
from . import Config
from . import Rotation
from . import Orientation
from . import util
class ConfigMaterial(Config):
"""
Material configuration.
Manipulate material configurations for storage in YAML format.
A complete material configuration file has the entries 'material',
'phase', and 'homogenization'. For use in DAMASK, it needs to be
stored as 'material.yaml'.
"""
def __init__(self,d=None):
"""
New material configuration.
Parameters
----------
d : dictionary, optional
Initial content. Defaults to None, in which case empty entries for
material, homogenization, and phase are created.
"""
super().__init__({'material': [], 'homogenization': {}, 'phase': {}} if d is None else d)
def save(self,fname='material.yaml',**kwargs):
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"""
Save to yaml file.
Parameters
----------
fname : file, str, or pathlib.Path, optional
Filename or file for writing. Defaults to 'material.yaml'.
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**kwargs
Keyword arguments parsed to yaml.dump.
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"""
super().save(fname,**kwargs)
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@classmethod
def load(cls,fname='material.yaml'):
"""
Load from yaml file.
Parameters
----------
fname : file, str, or pathlib.Path, optional
Filename or file for writing. Defaults to 'material.yaml'.
"""
return super(ConfigMaterial,cls).load(fname)
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@staticmethod
def from_table(table,**kwargs):
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"""
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Generate from an ASCII table.
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Parameters
----------
table : damask.Table
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Table that contains material information.
**kwargs
Keyword arguments where the key is the name and the value specifies
the label of the data column in the table.
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Examples
--------
>>> import damask
>>> import damask.ConfigMaterial as cm
>>> t = damask.Table.load('small.txt')
>>> t
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pos pos pos qu qu qu qu phase homog
0 0 0 0 0.19 0.8 0.24 -0.51 Aluminum SX
1 1 0 0 0.8 0.19 0.24 -0.51 Steel SX
1 1 1 0 0.8 0.19 0.24 -0.51 Steel SX
>>> cm.from_table(t,O='qu',phase='phase',homogenization='homog')
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material:
- constituents:
- O: [0.19, 0.8, 0.24, -0.51]
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v: 1.0
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phase: Aluminum
homogenization: SX
- constituents:
- O: [0.8, 0.19, 0.24, -0.51]
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v: 1.0
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phase: Steel
homogenization: SX
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homogenization: {}
phase: {}
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"""
kwargs_ = {k:table.get(v) for k,v in kwargs.items()}
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_,idx = np.unique(np.hstack(list(kwargs_.values())),return_index=True,axis=0)
idx = np.sort(idx)
kwargs_ = {k:np.atleast_1d(v[idx].squeeze()) for k,v in kwargs_.items()}
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return ConfigMaterial().material_add(**kwargs_)
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@staticmethod
def load_DREAM3D(fname,
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grain_data=None,cell_data=None,cell_ensemble_data='CellEnsembleData',
phases='Phases',Euler_angles='EulerAngles',phase_names='PhaseName',
base_group=None):
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"""
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Load DREAM.3D (HDF5) file.
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Data in DREAM.3D files can be stored per cell ('CellData')
and/or per grain ('Grain Data'). Per default, cell-wise data
is assumed.
damask.Grid.load_DREAM3D allows to get the corresponding geometry
for the grid solver.
Parameters
----------
fname : str
Filename of the DREAM.3D (HDF5) file.
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grain_data : str
Name of the group (folder) containing grain-wise data. Defaults
to None, in which case cell-wise data is used.
cell_data : str
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Name of the group (folder) containing cell-wise data. Defaults to
None in wich case it is automatically detected.
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cell_ensemble_data : str
Name of the group (folder) containing data of cell ensembles. This
group is used to inquire the name of the phases. Phases will get
numeric IDs if this group is not found. Defaults to 'CellEnsembleData'.
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phases : str
Name of the dataset containing the phase ID (cell-wise or grain-wise).
Defaults to 'Phases'.
Euler_angles : str
Name of the dataset containing the crystallographic orientation as
Euler angles in radians (cell-wise or grain-wise). Defaults to 'EulerAngles'.
phase_names : str
Name of the dataset containing the phase names. Phases will get
numeric IDs if this dataset is not found. Defaults to 'PhaseName'.
base_group : str
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Path to the group (folder) that contains geometry (_SIMPL_GEOMETRY),
and grain- or cell-wise data. Defaults to None, in which case
it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
"""
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b = util.DREAM3D_base_group(fname) if base_group is None else base_group
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c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
f = h5py.File(fname,'r')
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if grain_data is None:
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phase = f[os.path.join(b,c,phases)][()].flatten()
O = Rotation.from_Euler_angles(f[os.path.join(b,c,Euler_angles)]).as_quaternion().reshape(-1,4) # noqa
_,idx = np.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0)
idx = np.sort(idx)
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else:
phase = f[os.path.join(b,grain_data,phases)][()]
O = Rotation.from_Euler_angles(f[os.path.join(b,grain_data,Euler_angles)]).as_quaternion() # noqa
idx = np.arange(phase.size)
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if cell_ensemble_data is not None and phase_names is not None:
try:
names = np.array([s.decode() for s in f[os.path.join(b,cell_ensemble_data,phase_names)]])
phase = names[phase]
except KeyError:
pass
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base_config = ConfigMaterial({'phase':{k if isinstance(k,int) else str(k):'t.b.d.' for k in np.unique(phase)},
'homogenization':{'direct':{'N_constituents':1}}})
constituent = {k:np.atleast_1d(v[idx].squeeze()) for k,v in zip(['O','phase'],[O,phase])}
return base_config.material_add(**constituent,homogenization='direct')
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@property
def is_complete(self):
"""Check for completeness."""
ok = True
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for top_level in ['homogenization','phase','material']:
ok &= top_level in self
if top_level not in self: print(f'{top_level} entry missing')
if ok:
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ok &= len(self['material']) > 0
if len(self['material']) < 1: print('Incomplete material definition')
if ok:
homogenization = set()
phase = set()
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for i,v in enumerate(self['material']):
if 'homogenization' in v:
homogenization.add(v['homogenization'])
else:
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print(f'No homogenization specified in material {i}')
ok = False
if 'constituents' in v:
for ii,vv in enumerate(v['constituents']):
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if 'O' not in vv:
print('No orientation specified in constituent {ii} of material {i}')
ok = False
if 'phase' in vv:
phase.add(vv['phase'])
else:
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print(f'No phase specified in constituent {ii} of material {i}')
ok = False
for k,v in self['phase'].items():
if 'lattice' not in v:
print(f'No lattice specified in phase {k}')
ok = False
for k,v in self['homogenization'].items():
if 'N_constituents' not in v:
print(f'No. of constituents not specified in homogenization {k}')
ok = False
if phase - set(self['phase']):
print(f'Phase(s) {phase-set(self["phase"])} missing')
ok = False
if homogenization - set(self['homogenization']):
print(f'Homogenization(s) {homogenization-set(self["homogenization"])} missing')
ok = False
return ok
@property
def is_valid(self):
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"""Check for valid content."""
ok = True
if 'phase' in self:
for k,v in self['phase'].items():
if 'lattice' in v:
try:
Orientation(lattice=v['lattice'])
except KeyError:
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print(f"Invalid lattice '{v['lattice']}' in phase '{k}'")
ok = False
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if 'material' in self:
for i,m in enumerate(self['material']):
if 'constituents' in m:
v = 0.0
for c in m['constituents']:
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v += float(c['v'])
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if 'O' in c:
try:
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Rotation.from_quaternion(c['O'])
except ValueError:
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print(f"Invalid orientation '{c['O']}' in material '{i}'")
ok = False
if not np.isclose(v,1.0):
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print(f"Total fraction v = {v} ≠ 1 in material '{i}'")
ok = False
return ok
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def material_rename_phase(self,mapping,ID=None,constituent=None):
"""
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Change phase name in material.
Parameters
----------
mapping: dictionary
Mapping from old name to new name
ID: list of ints, optional
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Limit renaming to selected material IDs.
constituent: list of ints, optional
Limit renaming to selected constituents.
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Returns
-------
cfg : damask.ConfigMaterial
Updated material configuration.
"""
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dup = self.copy()
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for i,m in enumerate(dup['material']):
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if ID is not None and i not in ID: continue
for c in m['constituents']:
if constituent is not None and c not in constituent: continue
try:
c['phase'] = mapping[c['phase']]
except KeyError:
continue
return dup
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def material_rename_homogenization(self,mapping,ID=None):
"""
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Change homogenization name in material.
Parameters
----------
mapping: dictionary
Mapping from old name to new name
ID: list of ints, optional
Limit renaming to selected homogenization IDs.
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Returns
-------
cfg : damask.ConfigMaterial
Updated material configuration.
"""
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dup = self.copy()
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for i,m in enumerate(dup['material']):
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if ID is not None and i not in ID: continue
try:
m['homogenization'] = mapping[m['homogenization']]
except KeyError:
continue
return dup
def material_add(self,**kwargs):
"""
Add material entries.
Parameters
----------
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**kwargs
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Key-value pairs.
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Returns
-------
cfg : damask.ConfigMaterial
Updated material configuration.
Examples
--------
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>>> import numpy as np
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>>> import damask
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>>> m = damask.ConfigMaterial().material_add(phase = ['Aluminum','Steel'],
... O = damask.Rotation.from_random(2),
... homogenization = 'SX')
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>>> m
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material:
- constituents:
- O: [0.577764, -0.146299, -0.617669, 0.513010]
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v: 1.0
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phase: Aluminum
homogenization: SX
- constituents:
- O: [0.184176, 0.340305, 0.737247, 0.553840]
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v: 1.0
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phase: Steel
homogenization: SX
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homogenization: {}
phase: {}
>>> m = damask.ConfigMaterial().material_add(phase = np.array(['Austenite','Martensite']).reshape(1,2),
... O = damask.Rotation.from_random((2,2)),
... v = np.array([0.2,0.8]).reshape(1,2),
... homogenization = ['A','B'])
>>> m
material:
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- constituents:
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- phase: Austenite
O: [0.659802978293224, 0.6953785848195171, 0.22426295326327111, -0.17554139512785227]
v: 0.2
- phase: Martensite
O: [0.49356745891301596, 0.2841806579193434, -0.7487679215072818, -0.339085707289975]
v: 0.8
homogenization: A
- constituents:
- phase: Austenite
O: [0.26542221365204055, 0.7268854930702071, 0.4474726435701472, -0.44828201137283735]
v: 0.2
- phase: Martensite
O: [0.6545817158479885, -0.08004812803625233, -0.6226561293931374, 0.4212059104577611]
v: 0.8
homogenization: B
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homogenization: {}
phase: {}
"""
N,n,shaped = 1,1,{}
for k,v in kwargs.items():
shaped[k] = np.array(v)
s = shaped[k].shape[:-1] if k=='O' else shaped[k].shape
N = max(N,s[0]) if len(s)>0 else N
n = max(n,s[1]) if len(s)>1 else n
mat = [{'constituents':[{} for _ in range(n)]} for _ in range(N)]
if 'v' not in kwargs:
shaped['v'] = np.broadcast_to(1/n,(N,n))
for k,v in shaped.items():
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target = (N,n,4) if k=='O' else (N,n)
obj = np.broadcast_to(v.reshape(util.shapeshifter(v.shape,target,mode='right')),target)
for i in range(N):
if k in ['phase','O','v']:
for j in range(n):
mat[i]['constituents'][j][k] = obj[i,j].item() if isinstance(obj[i,j],np.generic) else obj[i,j]
else:
mat[i][k] = obj[i,0].item() if isinstance(obj[i,0],np.generic) else obj[i,0]
dup = self.copy()
dup['material'] = dup['material'] + mat if 'material' in dup else mat
return dup