Merge branch 'development' into avoid_data_copy_restart_MPI
This commit is contained in:
Martin Diehl
commit
7320120c5d
2
PRIVATE
2
PRIVATE
|
|
@ -1 +1 @@
|
|||
Subproject commit a4fed7a4b285496f547a7b940f6b6d54419f2384
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||||
Subproject commit ba046ace284515cb82020b3930206eab84ff3121
|
||||
|
|
@ -65,7 +65,7 @@ if filenames == []: parser.error('no input file specified.')
|
|||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
geom = damask.Grid.load_DREAM3D(name,options.basegroup,options.pointwise)
|
||||
geom = damask.Grid.load_DREAM3D(name,'FeatureIds')
|
||||
damask.util.croak(geom)
|
||||
|
||||
geom.save_ASCII(os.path.splitext(name)[0]+'.geom')
|
||||
|
|
|
|||
|
|
@ -27,12 +27,14 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
|
||||
References
|
||||
----------
|
||||
[1] DAMASK colormap theory
|
||||
https://www.kennethmoreland.com/color-maps/ColorMapsExpanded.pdf
|
||||
[2] DAMASK colormaps first use
|
||||
https://doi.org/10.1016/j.ijplas.2012.09.012
|
||||
[3] Matplotlib colormaps overview
|
||||
https://matplotlib.org/tutorials/colors/colormaps.html
|
||||
K. Moreland, Proceedings of the 5th International Symposium on Advances in Visual Computing, 2009
|
||||
https://doi.org/10.1007/978-3-642-10520-3_9
|
||||
|
||||
P. Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013
|
||||
https://doi.org/10.1016/j.ijplas.2012.09.012
|
||||
|
||||
Matplotlib colormaps overview
|
||||
https://matplotlib.org/tutorials/colors/colormaps.html
|
||||
|
||||
"""
|
||||
|
||||
|
|
@ -524,7 +526,7 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
|
||||
References
|
||||
----------
|
||||
http://www.ryanjuckett.com/programming/rgb-color-space-conversion
|
||||
https://www.easyrgb.com/en/math.php
|
||||
|
||||
"""
|
||||
rgb_lin = np.dot(np.array([
|
||||
|
|
@ -544,7 +546,7 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
|
||||
References
|
||||
----------
|
||||
http://www.ryanjuckett.com/programming/rgb-color-space-conversion
|
||||
https://www.easyrgb.com/en/math.php
|
||||
|
||||
"""
|
||||
rgb_lin = np.where(rgb>0.04045,((rgb+0.0555)/1.0555)**2.4,rgb/12.92)
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||||
|
|
|
|||
|
|
@ -1,4 +1,7 @@
|
|||
import os.path
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||||
|
||||
import numpy as np
|
||||
import h5py
|
||||
|
||||
from . import Config
|
||||
from . import Rotation
|
||||
|
|
@ -49,7 +52,7 @@ class ConfigMaterial(Config):
|
|||
@staticmethod
|
||||
def from_table(table,**kwargs):
|
||||
"""
|
||||
Load from an ASCII table.
|
||||
Generate from an ASCII table.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -85,7 +88,7 @@ class ConfigMaterial(Config):
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|||
phase: {}
|
||||
|
||||
"""
|
||||
kwargs_ = {k:table.get(v) for k,v in kwargs.items()}
|
||||
kwargs_ = {k:table.get(v) for k,v in kwargs.items()}
|
||||
|
||||
_,idx = np.unique(np.hstack(list(kwargs_.values())),return_index=True,axis=0)
|
||||
idx = np.sort(idx)
|
||||
|
|
@ -94,6 +97,79 @@ class ConfigMaterial(Config):
|
|||
return ConfigMaterial().material_add(**kwargs_)
|
||||
|
||||
|
||||
@staticmethod
|
||||
def load_DREAM3D(fname,
|
||||
grain_data=None,cell_data=None,cell_ensemble_data='CellEnsembleData',
|
||||
phases='Phases',Euler_angles='EulerAngles',phase_names='PhaseName',
|
||||
base_group=None):
|
||||
"""
|
||||
Load DREAM.3D (HDF5) file.
|
||||
|
||||
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.
|
||||
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
|
||||
Name of the group (folder) containing cell-wise data. Defaults to
|
||||
None in wich case it is automatically detected.
|
||||
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'.
|
||||
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
|
||||
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.
|
||||
|
||||
"""
|
||||
b = util.DREAM3D_base_group(fname) if base_group is None else base_group
|
||||
c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
|
||||
f = h5py.File(fname,'r')
|
||||
|
||||
if grain_data is None:
|
||||
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)
|
||||
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)
|
||||
|
||||
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
|
||||
|
||||
|
||||
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')
|
||||
|
||||
|
||||
@property
|
||||
def is_complete(self):
|
||||
"""Check for completeness."""
|
||||
|
|
|
|||
|
|
@ -256,35 +256,62 @@ class Grid:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
|
||||
def load_DREAM3D(fname,
|
||||
feature_IDs=None,cell_data=None,
|
||||
phases='Phases',Euler_angles='EulerAngles',
|
||||
base_group=None):
|
||||
"""
|
||||
Load from DREAM.3D file.
|
||||
Load DREAM.3D (HDF5) file.
|
||||
|
||||
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.ConfigMaterial.load_DREAM3D allows to get the
|
||||
corresponding material definition.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
Filename of the DREAM.3D file
|
||||
Filename of the DREAM.3D (HDF5) file.
|
||||
feature_IDs : str
|
||||
Name of the dataset containing the mapping between cells and
|
||||
grain-wise data. Defaults to 'None', in which case cell-wise
|
||||
data is used.
|
||||
cell_data : str
|
||||
Name of the group (folder) containing cell-wise data. Defaults to
|
||||
None in wich case it is automatically detected.
|
||||
phases : str
|
||||
Name of the dataset containing the phase ID. It is not used for
|
||||
grain-wise data, i.e. when feature_IDs is not None.
|
||||
Defaults to 'Phases'.
|
||||
Euler_angles : str
|
||||
Name of the dataset containing the crystallographic orientation as
|
||||
Euler angles in radians It is not used for grain-wise data, i.e.
|
||||
when feature_IDs is not None. Defaults to 'EulerAngles'.
|
||||
base_group : str
|
||||
Name of the group (folder) below 'DataContainers',
|
||||
for example 'SyntheticVolumeDataContainer'.
|
||||
point_data : str, optional
|
||||
Name of the group (folder) containing the pointwise material data,
|
||||
for example 'CellData'. Defaults to None, in which case points are consecutively numbered.
|
||||
material : str, optional
|
||||
Name of the dataset containing the material ID.
|
||||
Defaults to 'FeatureIds'.
|
||||
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.
|
||||
|
||||
|
||||
"""
|
||||
root_dir ='DataContainers'
|
||||
b = util.DREAM3D_base_group(fname) if base_group is None else base_group
|
||||
c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
|
||||
f = h5py.File(fname, 'r')
|
||||
g = os.path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
|
||||
cells = f[os.path.join(g,'DIMENSIONS')][()]
|
||||
size = f[os.path.join(g,'SPACING')][()] * cells
|
||||
origin = f[os.path.join(g,'ORIGIN')][()]
|
||||
|
||||
ma = np.arange(cells.prod(),dtype=int) \
|
||||
if point_data is None else \
|
||||
np.reshape(f[os.path.join(root_dir,base_group,point_data,material)],cells.prod())
|
||||
cells = f[os.path.join(b,'_SIMPL_GEOMETRY','DIMENSIONS')][()]
|
||||
size = f[os.path.join(b,'_SIMPL_GEOMETRY','SPACING')] * cells
|
||||
origin = f[os.path.join(b,'_SIMPL_GEOMETRY','ORIGIN')][()]
|
||||
|
||||
if feature_IDs is None:
|
||||
phase = f[os.path.join(b,c,phases)][()].reshape(-1,1)
|
||||
O = Rotation.from_Euler_angles(f[os.path.join(b,c,Euler_angles)]).as_quaternion().reshape(-1,4) # noqa
|
||||
unique,unique_inverse = np.unique(np.hstack([O,phase]),return_inverse=True,axis=0)
|
||||
ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
|
||||
np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
|
||||
else:
|
||||
ma = f[os.path.join(b,c,feature_IDs)][()].flatten()
|
||||
|
||||
return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','load_DREAM3D'))
|
||||
|
||||
|
|
@ -482,18 +509,13 @@ class Grid:
|
|||
|
||||
References
|
||||
----------
|
||||
Sébastien B G Blanquer, Maike Werner, Markus Hannula, Shahriar Sharifi,
|
||||
Guillaume P R Lajoinie, David Eglin, Jari Hyttinen, André A Poot, and Dirk W Grijpma
|
||||
Surface curvature in triply-periodic minimal surface architectures as
|
||||
a distinct design parameter in preparing advanced tissue engineering scaffolds
|
||||
S.B.G. Blanquer et al., Biofabrication 9(2):025001, 2017
|
||||
https://doi.org/10.1088/1758-5090/aa6553
|
||||
|
||||
Meinhard Wohlgemuth, Nataliya Yufa, James Hoffman, and Edwin L. Thomas
|
||||
Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
|
||||
M. Wohlgemuth et al., Macromolecules 34(17):6083-6089, 2001
|
||||
https://doi.org/10.1021/ma0019499
|
||||
|
||||
Meng-Ting Hsieh, Lorenzo Valdevit
|
||||
Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
|
||||
M.-T. Hsieh and L. Valdevit, Software Impacts 6:100026, 2020
|
||||
https://doi.org/10.1016/j.simpa.2020.100026
|
||||
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -742,8 +742,7 @@ class Orientation(Rotation):
|
|||
|
||||
References
|
||||
----------
|
||||
C.T. Young and J.L. Lytton, J. Appl. Phys. 43:1408–1417, 1972
|
||||
"Computer Generation and Identification of Kikuchi Projections"
|
||||
C.T. Young and J.L. Lytton, Journal of Applied Physics 43:1408–1417, 1972
|
||||
https://doi.org/10.1063/1.1661333
|
||||
|
||||
"""
|
||||
|
|
@ -1070,8 +1069,7 @@ class Orientation(Rotation):
|
|||
|
||||
References
|
||||
----------
|
||||
J.C. Glez and J. Driver, J. Appl. Cryst. 34:280-288, 2001
|
||||
"Orientation distribution analysis in deformed grains"
|
||||
J.C. Glez and J. Driver, Journal of Applied Crystallography 34:280-288, 2001
|
||||
https://doi.org/10.1107/S0021889801003077
|
||||
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -357,10 +357,8 @@ class Rotation:
|
|||
|
||||
References
|
||||
----------
|
||||
Quaternion averaging
|
||||
F. Landis Markley, Yang Cheng, John L. Crassidis, Yaakov Oshman
|
||||
Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
|
||||
10.2514/1.28949
|
||||
F. Landis Markley et al., Journal of Guidance, Control, and Dynamics 30(4):1193-1197, 2007
|
||||
https://doi.org/10.2514/1.28949
|
||||
|
||||
"""
|
||||
def _M(quat):
|
||||
|
|
@ -859,7 +857,7 @@ class Rotation:
|
|||
|
||||
References
|
||||
----------
|
||||
P. Eisenlohr, F. Roters, Computational Materials Science 42(4), 670-678, 2008
|
||||
P. Eisenlohr and F. Roters, Computational Materials Science 42(4):670-678, 2008
|
||||
https://doi.org/10.1016/j.commatsci.2007.09.015
|
||||
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -9,6 +9,7 @@ from functools import reduce
|
|||
from optparse import Option
|
||||
|
||||
import numpy as np
|
||||
import h5py
|
||||
|
||||
from . import version
|
||||
|
||||
|
|
@ -27,7 +28,8 @@ __all__=[
|
|||
'extendableOption',
|
||||
'execution_stamp',
|
||||
'shapeshifter', 'shapeblender',
|
||||
'extend_docstring', 'extended_docstring'
|
||||
'extend_docstring', 'extended_docstring',
|
||||
'DREAM3D_base_group', 'DREAM3D_cell_data_group'
|
||||
]
|
||||
|
||||
####################################################################################################
|
||||
|
|
@ -376,6 +378,53 @@ def extended_docstring(f,extra_docstring):
|
|||
return _decorator
|
||||
|
||||
|
||||
def DREAM3D_base_group(fname):
|
||||
"""
|
||||
Determine the base group of a DREAM.3D file.
|
||||
|
||||
The base group is defined as the group (folder) that contains
|
||||
a 'SPACING' dataset in a '_SIMPL_GEOMETRY' group.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
Filename of the DREAM.3D (HDF5) file.
|
||||
|
||||
"""
|
||||
with h5py.File(fname,'r') as f:
|
||||
base_group = f.visit(lambda path: path.rsplit('/',2)[0] if '_SIMPL_GEOMETRY/SPACING' in path else None)
|
||||
|
||||
if base_group is None:
|
||||
raise ValueError(f'Could not determine base group in file {fname}.')
|
||||
|
||||
return base_group
|
||||
|
||||
def DREAM3D_cell_data_group(fname):
|
||||
"""
|
||||
Determine the cell data group of a DREAM.3D file.
|
||||
|
||||
The cell data group is defined as the group (folder) that contains
|
||||
a dataset in the base group whose length matches the total number
|
||||
of points as specified in '_SIMPL_GEOMETRY/DIMENSIONS'.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
Filename of the DREAM.3D (HDF5) file.
|
||||
|
||||
"""
|
||||
base_group = DREAM3D_base_group(fname)
|
||||
with h5py.File(fname,'r') as f:
|
||||
cells = tuple(f[os.path.join(base_group,'_SIMPL_GEOMETRY','DIMENSIONS')][()][::-1])
|
||||
cell_data_group = f[base_group].visititems(lambda path,obj: path.split('/')[0] \
|
||||
if isinstance(obj,h5py._hl.dataset.Dataset) and np.shape(obj)[:-1] == cells \
|
||||
else None)
|
||||
|
||||
if cell_data_group is None:
|
||||
raise ValueError(f'Could not determine cell data group in file {fname}/{base_group}.')
|
||||
|
||||
return cell_data_group
|
||||
|
||||
####################################################################################################
|
||||
# Classes
|
||||
####################################################################################################
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
../Grid/2phase_irregularGrid.dream3d
|
||||
|
|
@ -0,0 +1 @@
|
|||
../Grid/2phase_irregularGrid.json
|
||||
|
|
@ -0,0 +1 @@
|
|||
../Grid/2phase_irregularGrid.xdmf
|
||||
|
|
@ -0,0 +1 @@
|
|||
../Grid/measured.dream3d
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1 @@
|
|||
../Grid/measured.xdmf
|
||||
Binary file not shown.
|
|
@ -0,0 +1,764 @@
|
|||
{
|
||||
"0": {
|
||||
"CellEnsembleAttributeMatrixName": "CellEnsembleData",
|
||||
"CrystalStructuresArrayName": "CrystalStructures",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "StatsGenerator",
|
||||
"Filter_Name": "StatsGeneratorFilter",
|
||||
"Filter_Uuid": "{f642e217-4722-5dd8-9df9-cee71e7b26ba}",
|
||||
"PhaseNamesArrayName": "PhaseName",
|
||||
"PhaseTypesArrayName": "PhaseTypes",
|
||||
"StatsDataArray": {
|
||||
"1": {
|
||||
"AxisODF-Weights": {
|
||||
},
|
||||
"Bin Count": 34,
|
||||
"BinNumber": [
|
||||
0.03019738383591175,
|
||||
1.031197428703308,
|
||||
2.0321974754333496,
|
||||
3.0331974029541016,
|
||||
4.0341973304748535,
|
||||
5.0351972579956055,
|
||||
6.036197185516357,
|
||||
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|
||||
"FeaturePhasesArrayName": "Phases",
|
||||
"FilterVersion": "6.5.138",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Pack Primary Phases",
|
||||
"Filter_Name": "PackPrimaryPhases",
|
||||
"Filter_Uuid": "{84305312-0d10-50ca-b89a-fda17a353cc9}",
|
||||
"InputPhaseNamesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "PhaseName",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"InputPhaseTypesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "PhaseTypes",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"InputShapeTypesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "ShapeTypes",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"InputStatsArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "Statistics",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"MaskArrayPath": {
|
||||
"Attribute Matrix Name": "",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": ""
|
||||
},
|
||||
"NewAttributeMatrixPath": {
|
||||
"Attribute Matrix Name": "Synthetic Shape Parameters (Primary Phase)",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"NumFeaturesArrayName": "NumFeatures",
|
||||
"OutputCellAttributeMatrixPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"OutputCellEnsembleAttributeMatrixName": "CellEnsembleData",
|
||||
"OutputCellFeatureAttributeMatrixName": "Grain Data",
|
||||
"PeriodicBoundaries": 0,
|
||||
"SaveGeometricDescriptions": 0,
|
||||
"SelectedAttributeMatrixPath": {
|
||||
"Attribute Matrix Name": "",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": ""
|
||||
},
|
||||
"UseMask": 0
|
||||
},
|
||||
"4": {
|
||||
"BoundaryCellsArrayName": "BoundaryCells",
|
||||
"FeatureIdsArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "FeatureIds",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FilterVersion": "6.5.138",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Find Boundary Cells (Image)",
|
||||
"Filter_Name": "FindBoundaryCells",
|
||||
"Filter_Uuid": "{8a1106d4-c67f-5e09-a02a-b2e9b99d031e}",
|
||||
"IgnoreFeatureZero": 1,
|
||||
"IncludeVolumeBoundary": 0
|
||||
},
|
||||
"5": {
|
||||
"BoundaryCellsArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "BoundaryCells",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"CellPhasesArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "Phases",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FeatureGeneration": 0,
|
||||
"FeatureIdsArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "FeatureIds",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FeaturePhasesArrayPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "Phases",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FilterVersion": "6.5.138",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Insert Precipitate Phases",
|
||||
"Filter_Name": "InsertPrecipitatePhases",
|
||||
"Filter_Uuid": "{1e552e0c-53bb-5ae1-bd1c-c7a6590f9328}",
|
||||
"InputPhaseTypesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "PhaseTypes",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"InputShapeTypesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "ShapeTypes",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"InputStatsArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "Statistics",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"MaskArrayPath": {
|
||||
"Attribute Matrix Name": "",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": ""
|
||||
},
|
||||
"MatchRDF": 0,
|
||||
"NewAttributeMatrixPath": {
|
||||
"Attribute Matrix Name": "Synthetic Shape Parameters (Precipitate)",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"NumFeaturesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "NumFeatures",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"PeriodicBoundaries": 0,
|
||||
"PrecipInputFile": "C:/Users/work",
|
||||
"SaveGeometricDescriptions": 0,
|
||||
"SelectedAttributeMatrixPath": {
|
||||
"Attribute Matrix Name": "",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": ""
|
||||
},
|
||||
"UseMask": 0
|
||||
},
|
||||
"6": {
|
||||
"BoundaryCellsArrayName": "BoundaryCells",
|
||||
"CellFeatureAttributeMatrixPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FeatureIdsArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "FeatureIds",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FilterVersion": "6.5.138",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Find Feature Neighbors",
|
||||
"Filter_Name": "FindNeighbors",
|
||||
"Filter_Uuid": "{97cf66f8-7a9b-5ec2-83eb-f8c4c8a17bac}",
|
||||
"NeighborListArrayName": "NeighborList",
|
||||
"NumNeighborsArrayName": "NumNeighbors",
|
||||
"SharedSurfaceAreaListArrayName": "SharedSurfaceAreaList",
|
||||
"StoreBoundaryCells": 0,
|
||||
"StoreSurfaceFeatures": 1,
|
||||
"SurfaceFeaturesArrayName": "SurfaceFeatures"
|
||||
},
|
||||
"7": {
|
||||
"AvgQuatsArrayName": "AvgQuats",
|
||||
"CellEulerAnglesArrayName": "EulerAngles",
|
||||
"CrystalStructuresArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "CrystalStructures",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"FeatureEulerAnglesArrayName": "EulerAngles",
|
||||
"FeatureIdsArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "FeatureIds",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FeaturePhasesArrayPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "Phases",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"FilterVersion": "6.5.138",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Match Crystallography",
|
||||
"Filter_Name": "MatchCrystallography",
|
||||
"Filter_Uuid": "{7bfb6e4a-6075-56da-8006-b262d99dff30}",
|
||||
"InputStatsArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "Statistics",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"MaxIterations": 100,
|
||||
"NeighborListArrayPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "NeighborList",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"NumFeaturesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "NumFeatures",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"PhaseTypesArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "PhaseTypes",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"SharedSurfaceAreaListArrayPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "SharedSurfaceAreaList",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"SurfaceFeaturesArrayPath": {
|
||||
"Attribute Matrix Name": "Grain Data",
|
||||
"Data Array Name": "SurfaceFeatures",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"VolumesArrayName": "Volumes"
|
||||
},
|
||||
"8": {
|
||||
"CellEulerAnglesArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "EulerAngles",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"CellIPFColorsArrayName": "IPFColor",
|
||||
"CellPhasesArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "Phases",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"CrystalStructuresArrayPath": {
|
||||
"Attribute Matrix Name": "CellEnsembleData",
|
||||
"Data Array Name": "CrystalStructures",
|
||||
"Data Container Name": "StatsGeneratorDataContainer"
|
||||
},
|
||||
"FilterVersion": "6.5.138",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Generate IPF Colors",
|
||||
"Filter_Name": "GenerateIPFColors",
|
||||
"Filter_Uuid": "{a50e6532-8075-5de5-ab63-945feb0de7f7}",
|
||||
"GoodVoxelsArrayPath": {
|
||||
"Attribute Matrix Name": "CellData",
|
||||
"Data Array Name": "",
|
||||
"Data Container Name": "SyntheticVolumeDataContainer"
|
||||
},
|
||||
"ReferenceDir": {
|
||||
"x": 0,
|
||||
"y": 0,
|
||||
"z": 1
|
||||
},
|
||||
"UseGoodVoxels": 0
|
||||
},
|
||||
"9": {
|
||||
"FilterVersion": "1.2.812",
|
||||
"Filter_Enabled": true,
|
||||
"Filter_Human_Label": "Write DREAM.3D Data File",
|
||||
"Filter_Name": "DataContainerWriter",
|
||||
"Filter_Uuid": "{3fcd4c43-9d75-5b86-aad4-4441bc914f37}",
|
||||
"OutputFile": "C:\\Users\\work\\Desktop\\2phase_irregularGrid.dream3d",
|
||||
"WriteTimeSeries": 0,
|
||||
"WriteXdmfFile": 1
|
||||
},
|
||||
"PipelineBuilder": {
|
||||
"Name": "2phase_irregularGrid",
|
||||
"Number_Filters": 10,
|
||||
"Version": 6
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,42 @@
|
|||
<?xml version="1.0"?>
|
||||
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd"[]>
|
||||
<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
|
||||
<Domain>
|
||||
<!-- *************** START OF SyntheticVolumeDataContainer *************** -->
|
||||
<Grid Name="SyntheticVolumeDataContainer" GridType="Uniform">
|
||||
<Topology TopologyType="3DCoRectMesh" Dimensions="11 9 14 "></Topology>
|
||||
<Geometry Type="ORIGIN_DXDYDZ">
|
||||
<!-- Origin Z, Y, X -->
|
||||
<DataItem Format="XML" Dimensions="3">0 0 0</DataItem>
|
||||
<!-- DxDyDz (Spacing/Resolution) Z, Y, X -->
|
||||
<DataItem Format="XML" Dimensions="3">0.8 0.8 0.8</DataItem>
|
||||
</Geometry>
|
||||
<Attribute Name="BoundaryCells" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="10 8 13 1" NumberType="Char" Precision="1" >
|
||||
2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/BoundaryCells
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="EulerAngles" AttributeType="Vector" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="10 8 13 3" NumberType="Float" Precision="4" >
|
||||
2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/EulerAngles
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="FeatureIds" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="10 8 13 1" NumberType="Int" Precision="4" >
|
||||
2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/FeatureIds
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="IPFColor" AttributeType="Vector" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="10 8 13 3" NumberType="UChar" Precision="1" >
|
||||
2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/IPFColor
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Phases" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="10 8 13 1" NumberType="Int" Precision="4" >
|
||||
2phase_irregularGrid.dream3d:/DataContainers/SyntheticVolumeDataContainer/CellData/Phases
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
</Grid>
|
||||
<!-- *************** END OF SyntheticVolumeDataContainer *************** -->
|
||||
</Domain>
|
||||
</Xdmf>
|
||||
Binary file not shown.
File diff suppressed because one or more lines are too long
|
|
@ -0,0 +1,77 @@
|
|||
<?xml version="1.0"?>
|
||||
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd"[]>
|
||||
<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
|
||||
<Domain>
|
||||
<!-- *************** START OF Small IN100 *************** -->
|
||||
<Grid Name="Small IN100" GridType="Uniform">
|
||||
<Topology TopologyType="3DCoRectMesh" Dimensions="2 102 202 "></Topology>
|
||||
<Geometry Type="ORIGIN_DXDYDZ">
|
||||
<!-- Origin Z, Y, X -->
|
||||
<DataItem Format="XML" Dimensions="3">0 35 -294.7</DataItem>
|
||||
<!-- DxDyDz (Spacing/Resolution) Z, Y, X -->
|
||||
<DataItem Format="XML" Dimensions="3">0.35 0.35 0.35</DataItem>
|
||||
</Geometry>
|
||||
<Attribute Name="Confidence Index" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Confidence Index
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="EulerAngles" AttributeType="Vector" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 3" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/EulerAngles
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="FeatureIds" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Int" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/FeatureIds
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Fit" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Fit
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="IPFColor" AttributeType="Vector" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 3" NumberType="UChar" Precision="1" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/IPFColor
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Image Quality" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Image Quality
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Mask" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="uchar" Precision="1" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Mask
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="ParentIds" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Int" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/ParentIds
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Phases" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Int" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Phases
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="SEM Signal" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/SEM Signal
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="X Position" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/X Position
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
<Attribute Name="Y Position" AttributeType="Scalar" Center="Cell">
|
||||
<DataItem Format="HDF" Dimensions="1 101 201 1" NumberType="Float" Precision="4" >
|
||||
measured.dream3d:/DataContainers/Small IN100/EBSD Scan Data/Y Position
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
</Grid>
|
||||
<!-- *************** END OF Small IN100 *************** -->
|
||||
</Domain>
|
||||
</Xdmf>
|
||||
|
|
@ -1,11 +1,12 @@
|
|||
import os
|
||||
|
||||
import filecmp
|
||||
import pytest
|
||||
import numpy as np
|
||||
|
||||
from damask import ConfigMaterial
|
||||
from damask import Table
|
||||
from damask import Rotation
|
||||
from damask import Grid
|
||||
|
||||
@pytest.fixture
|
||||
def ref_path(ref_path_base):
|
||||
|
|
@ -108,3 +109,32 @@ class TestConfigMaterial:
|
|||
m = ConfigMaterial().material_add(**kw)
|
||||
assert len(m['material']) == N
|
||||
assert len(m['material'][0]['constituents']) == n
|
||||
|
||||
|
||||
@pytest.mark.parametrize('cell_ensemble_data',[None,'CellEnsembleData'])
|
||||
def test_load_DREAM3D(self,ref_path,cell_ensemble_data):
|
||||
grain_c = ConfigMaterial.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','Grain Data',
|
||||
cell_ensemble_data = cell_ensemble_data)
|
||||
point_c = ConfigMaterial.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d',
|
||||
cell_ensemble_data = cell_ensemble_data)
|
||||
|
||||
assert point_c.is_valid and grain_c.is_valid and \
|
||||
len(point_c['material'])+1 == len(grain_c['material'])
|
||||
|
||||
grain_m = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','FeatureIds').material.flatten()
|
||||
point_m = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d').material.flatten()
|
||||
|
||||
for i in np.unique(point_m):
|
||||
j = int(grain_m[(point_m==i).nonzero()[0][0]])
|
||||
assert np.allclose(point_c['material'][i]['constituents'][0]['O'],
|
||||
grain_c['material'][j]['constituents'][0]['O'])
|
||||
assert point_c['material'][i]['constituents'][0]['phase'] == \
|
||||
grain_c['material'][j]['constituents'][0]['phase']
|
||||
|
||||
|
||||
def test_load_DREAM3D_reference(self,tmp_path,ref_path,update):
|
||||
config = ConfigMaterial.load_DREAM3D(ref_path/'measured.dream3d')
|
||||
config.save(tmp_path/'material.yaml')
|
||||
if update:
|
||||
config.save(ref_path/'measured.material_yaml')
|
||||
assert config.is_valid and filecmp.cmp(tmp_path/'material.yaml',ref_path/'measured.material_yaml')
|
||||
|
|
|
|||
|
|
@ -420,12 +420,31 @@ class TestGrid:
|
|||
t = Table(np.column_stack((coords.reshape(-1,3,order='F'),grid.material.flatten(order='F'))),{'c':3,'m':1})
|
||||
assert grid_equal(grid.sort().renumber(),Grid.from_table(t,'c',['m']))
|
||||
|
||||
|
||||
@pytest.mark.parametrize('periodic',[True,False])
|
||||
@pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
|
||||
def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
|
||||
grid=Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
|
||||
current=grid.get_grain_boundaries(periodic,direction)
|
||||
grid = Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
|
||||
current = grid.get_grain_boundaries(periodic,direction)
|
||||
if update:
|
||||
current.save(ref_path/f'get_grain_boundaries_8g12x15x20_{direction}_{periodic}.vtu',parallel=False)
|
||||
reference=VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
|
||||
reference = VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
|
||||
assert current.__repr__() == reference.__repr__()
|
||||
|
||||
|
||||
def test_load_DREAM3D(self,ref_path):
|
||||
grain = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d','FeatureIds')
|
||||
point = Grid.load_DREAM3D(ref_path/'2phase_irregularGrid.dream3d')
|
||||
|
||||
assert np.allclose(grain.origin,point.origin) and \
|
||||
np.allclose(grain.size,point.size) and \
|
||||
(grain.sort().material == point.material+1).all()
|
||||
|
||||
|
||||
def test_load_DREAM3D_reference(self,ref_path,update):
|
||||
current = Grid.load_DREAM3D(ref_path/'measured.dream3d')
|
||||
reference = Grid.load(ref_path/'measured')
|
||||
if update:
|
||||
current.save(ref_path/'measured.vtr')
|
||||
|
||||
assert grid_equal(current,reference)
|
||||
|
|
|
|||
|
|
@ -1,6 +1,10 @@
|
|||
import random
|
||||
import os
|
||||
|
||||
import pytest
|
||||
import numpy as np
|
||||
from scipy import stats
|
||||
import h5py
|
||||
|
||||
from damask import util
|
||||
|
||||
|
|
@ -102,3 +106,36 @@ class TestUtil:
|
|||
@pytest.mark.parametrize('style',[util.emph,util.deemph,util.warn,util.strikeout])
|
||||
def test_decorate(self,style):
|
||||
assert 'DAMASK' in style('DAMASK')
|
||||
|
||||
@pytest.mark.parametrize('complete',[True,False])
|
||||
def test_D3D_base_group(self,tmp_path,complete):
|
||||
base_group = ''.join(random.choices('DAMASK', k=10))
|
||||
with h5py.File(tmp_path/'base_group.dream3d','w') as f:
|
||||
f.create_group(os.path.join(base_group,'_SIMPL_GEOMETRY'))
|
||||
if complete:
|
||||
f[os.path.join(base_group,'_SIMPL_GEOMETRY')].create_dataset('SPACING',data=np.ones(3))
|
||||
|
||||
if complete:
|
||||
assert base_group == util.DREAM3D_base_group(tmp_path/'base_group.dream3d')
|
||||
else:
|
||||
with pytest.raises(ValueError):
|
||||
util.DREAM3D_base_group(tmp_path/'base_group.dream3d')
|
||||
|
||||
@pytest.mark.parametrize('complete',[True,False])
|
||||
def test_D3D_cell_data_group(self,tmp_path,complete):
|
||||
base_group = ''.join(random.choices('DAMASK', k=10))
|
||||
cell_data_group = ''.join(random.choices('KULeuven', k=10))
|
||||
cells = np.random.randint(1,50,3)
|
||||
with h5py.File(tmp_path/'cell_data_group.dream3d','w') as f:
|
||||
f.create_group(os.path.join(base_group,'_SIMPL_GEOMETRY'))
|
||||
f[os.path.join(base_group,'_SIMPL_GEOMETRY')].create_dataset('SPACING',data=np.ones(3))
|
||||
f[os.path.join(base_group,'_SIMPL_GEOMETRY')].create_dataset('DIMENSIONS',data=cells[::-1])
|
||||
f[base_group].create_group(cell_data_group)
|
||||
if complete:
|
||||
f[os.path.join(base_group,cell_data_group)].create_dataset('data',shape=np.append(cells,1))
|
||||
|
||||
if complete:
|
||||
assert cell_data_group == util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')
|
||||
else:
|
||||
with pytest.raises(ValueError):
|
||||
util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')
|
||||
|
|
|
|||
|
|
@ -93,7 +93,7 @@ subroutine DAMASK_interface_init
|
|||
#endif
|
||||
print*, achar(27)//'[0m'
|
||||
|
||||
print*, 'Roters et al., Computational Materials Science 158:420–478, 2019'
|
||||
print*, 'F. Roters et al., Computational Materials Science 158:420–478, 2019'
|
||||
print*, 'https://doi.org/10.1016/j.commatsci.2018.04.030'
|
||||
|
||||
print'(/,a)', ' Version: '//DAMASKVERSION
|
||||
|
|
|
|||
|
|
@ -118,7 +118,7 @@ program DAMASK_grid
|
|||
call CPFEM_initAll
|
||||
print'(/,a)', ' <<<+- DAMASK_grid init -+>>>'; flush(IO_STDOUT)
|
||||
|
||||
print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
|
||||
print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
|
||||
print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -75,7 +75,7 @@ subroutine grid_damage_spectral_init
|
|||
|
||||
print'(/,a)', ' <<<+- grid_spectral_damage init -+>>>'
|
||||
|
||||
print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
|
||||
print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
|
||||
print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
|
||||
|
||||
!-------------------------------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -105,10 +105,10 @@ subroutine grid_mechanical_spectral_basic_init
|
|||
|
||||
print'(/,a)', ' <<<+- grid_mechanical_spectral_basic init -+>>>'; flush(IO_STDOUT)
|
||||
|
||||
print*, 'Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
|
||||
print*, 'P. Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
|
||||
print*, 'https://doi.org/10.1016/j.ijplas.2012.09.012'//IO_EOL
|
||||
|
||||
print*, 'Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
|
||||
print*, 'P. Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
|
||||
print*, 'https://doi.org/10.1016/j.ijplas.2014.02.006'
|
||||
|
||||
!-------------------------------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -118,7 +118,7 @@ subroutine grid_mechanical_spectral_polarisation_init
|
|||
|
||||
print'(/,a)', ' <<<+- grid_mechanical_spectral_polarization init -+>>>'; flush(IO_STDOUT)
|
||||
|
||||
print*, 'Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
|
||||
print*, 'P. Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
|
||||
print*, 'https://doi.org/10.1016/j.ijplas.2014.02.006'
|
||||
|
||||
!-------------------------------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -75,7 +75,7 @@ subroutine grid_thermal_spectral_init(T_0)
|
|||
|
||||
print'(/,a)', ' <<<+- grid_thermal_spectral init -+>>>'
|
||||
|
||||
print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
|
||||
print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
|
||||
print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
|
||||
|
||||
!-------------------------------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -176,16 +176,16 @@ subroutine spectral_utilities_init
|
|||
|
||||
print'(/,a)', ' <<<+- spectral_utilities init -+>>>'
|
||||
|
||||
print*, 'Diehl, Diploma Thesis TU München, 2010'
|
||||
print*, 'M. Diehl, Diploma Thesis TU München, 2010'
|
||||
print*, 'https://doi.org/10.13140/2.1.3234.3840'//IO_EOL
|
||||
|
||||
print*, 'Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
|
||||
print*, 'P. Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
|
||||
print*, 'https://doi.org/10.1016/j.ijplas.2012.09.012'//IO_EOL
|
||||
|
||||
print*, 'Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
|
||||
print*, 'P. Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
|
||||
print*, 'https://doi.org/10.1016/j.ijplas.2014.02.006'//IO_EOL
|
||||
|
||||
print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
|
||||
print*, 'P. Shanthraj et al., Handbook of Mechanics of Materials, 2019'
|
||||
print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -287,20 +287,17 @@ subroutine materialpoint_stressAndItsTangent(dt,FEsolving_execIP,FEsolving_execE
|
|||
.and. NiterationMPstate < num%nMPstate)
|
||||
NiterationMPstate = NiterationMPstate + 1
|
||||
|
||||
call mechanical_partition(homogenization_F(1:3,1:3,ce),ce)
|
||||
converged = .true.
|
||||
do co = 1, myNgrains
|
||||
converged = converged .and. crystallite_stress(dt,co,ip,el)
|
||||
enddo
|
||||
|
||||
if (.not. doneAndHappy(1)) then
|
||||
call mechanical_partition(homogenization_F(1:3,1:3,ce),ce)
|
||||
converged = .true.
|
||||
do co = 1, myNgrains
|
||||
converged = converged .and. crystallite_stress(dt,co,ip,el)
|
||||
enddo
|
||||
|
||||
if (.not. converged) then
|
||||
doneAndHappy = [.true.,.false.]
|
||||
else
|
||||
doneAndHappy = mechanical_updateState(dt,homogenization_F(1:3,1:3,ce),ce)
|
||||
converged = all(doneAndHappy)
|
||||
endif
|
||||
if (converged) then
|
||||
doneAndHappy = mechanical_updateState(dt,homogenization_F(1:3,1:3,ce),ce)
|
||||
converged = all(doneAndHappy)
|
||||
else
|
||||
doneAndHappy = [.true.,.false.]
|
||||
endif
|
||||
|
||||
enddo convergenceLooping
|
||||
|
|
|
|||
|
|
@ -91,12 +91,11 @@ module subroutine mechanical_RGC_init(num_homogMech)
|
|||
|
||||
print'(a,i2)', ' # instances: ',count(homogenization_type == HOMOGENIZATION_RGC_ID); flush(IO_STDOUT)
|
||||
|
||||
print*, 'Tjahjanto et al., International Journal of Material Forming 2(1):939–942, 2009'
|
||||
print*, 'D.D. Tjahjanto et al., International Journal of Material Forming 2(1):939–942, 2009'
|
||||
print*, 'https://doi.org/10.1007/s12289-009-0619-1'//IO_EOL
|
||||
|
||||
print*, 'Tjahjanto et al., Modelling and Simulation in Materials Science and Engineering 18:015006, 2010'
|
||||
print*, 'https://doi.org/10.1088/0965-0393/18/1/015006'//IO_EOL
|
||||
|
||||
print*, 'D.D. Tjahjanto et al., Modelling and Simulation in Materials Science and Engineering 18:015006, 2010'
|
||||
print*, 'https://doi.org/10.1088/0965-0393/18/1/015006'//IO_EOL
|
||||
|
||||
|
||||
material_homogenization => config_material%get('homogenization')
|
||||
|
|
|
|||
|
|
@ -561,7 +561,7 @@ function integrateStress(F,subFp0,subFi0,Delta_t,co,ip,el) result(broken)
|
|||
cycle LpLoop
|
||||
endif
|
||||
|
||||
calculateJacobiLi: if (mod(jacoCounterLp, num%iJacoLpresiduum) == 0) then
|
||||
calculateJacobiLp: if (mod(jacoCounterLp, num%iJacoLpresiduum) == 0) then
|
||||
jacoCounterLp = jacoCounterLp + 1
|
||||
|
||||
do o=1,3; do p=1,3
|
||||
|
|
@ -573,7 +573,7 @@ function integrateStress(F,subFp0,subFi0,Delta_t,co,ip,el) result(broken)
|
|||
call dgesv(9,1,dRLp_dLp,9,devNull_9,temp_9,9,ierr) ! solve dRLp/dLp * delta Lp = -res for delta Lp
|
||||
if (ierr /= 0) return ! error
|
||||
deltaLp = - math_9to33(temp_9)
|
||||
endif calculateJacobiLi
|
||||
endif calculateJacobiLp
|
||||
|
||||
Lpguess = Lpguess &
|
||||
+ deltaLp * steplengthLp
|
||||
|
|
@ -601,7 +601,7 @@ function integrateStress(F,subFp0,subFi0,Delta_t,co,ip,el) result(broken)
|
|||
cycle LiLoop
|
||||
endif
|
||||
|
||||
calculateJacobiLp: if (mod(jacoCounterLi, num%iJacoLpresiduum) == 0) then
|
||||
calculateJacobiLi: if (mod(jacoCounterLi, num%iJacoLpresiduum) == 0) then
|
||||
jacoCounterLi = jacoCounterLi + 1
|
||||
|
||||
temp_33 = matmul(matmul(A,B),invFi_current)
|
||||
|
|
@ -620,7 +620,7 @@ function integrateStress(F,subFp0,subFi0,Delta_t,co,ip,el) result(broken)
|
|||
call dgesv(9,1,dRLi_dLi,9,devNull_9,temp_9,9,ierr) ! solve dRLi/dLp * delta Li = -res for delta Li
|
||||
if (ierr /= 0) return ! error
|
||||
deltaLi = - math_9to33(temp_9)
|
||||
endif calculateJacobiLp
|
||||
endif calculateJacobiLi
|
||||
|
||||
Liguess = Liguess &
|
||||
+ deltaLi * steplengthLi
|
||||
|
|
|
|||
|
|
@ -103,7 +103,7 @@ module function plastic_dislotungsten_init() result(myPlasticity)
|
|||
print'(/,a)', ' <<<+- phase:mechanical:plastic:dislotungsten init -+>>>'
|
||||
print'(a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
|
||||
|
||||
print*, 'Cereceda et al., International Journal of Plasticity 78:242–256, 2016'
|
||||
print*, 'D. Cereceda et al., International Journal of Plasticity 78:242–256, 2016'
|
||||
print*, 'https://dx.doi.org/10.1016/j.ijplas.2015.09.002'
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -150,13 +150,13 @@ module function plastic_dislotwin_init() result(myPlasticity)
|
|||
print'(/,a)', ' <<<+- phase:mechanical:plastic:dislotwin init -+>>>'
|
||||
print'(a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
|
||||
|
||||
print*, 'Ma and Roters, Acta Materialia 52(12):3603–3612, 2004'
|
||||
print*, 'A. Ma and F. Roters, Acta Materialia 52(12):3603–3612, 2004'
|
||||
print*, 'https://doi.org/10.1016/j.actamat.2004.04.012'//IO_EOL
|
||||
|
||||
print*, 'Roters et al., Computational Materials Science 39:91–95, 2007'
|
||||
print*, 'F. Roters et al., Computational Materials Science 39:91–95, 2007'
|
||||
print*, 'https://doi.org/10.1016/j.commatsci.2006.04.014'//IO_EOL
|
||||
|
||||
print*, 'Wong et al., Acta Materialia 118:140–151, 2016'
|
||||
print*, 'S.L. Wong et al., Acta Materialia 118:140–151, 2016'
|
||||
print*, 'https://doi.org/10.1016/j.actamat.2016.07.032'
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -71,7 +71,7 @@ module function plastic_isotropic_init() result(myPlasticity)
|
|||
print'(/,a)', ' <<<+- phase:mechanical:plastic:isotropic init -+>>>'
|
||||
print'(a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
|
||||
|
||||
print*, 'Maiti and Eisenlohr, Scripta Materialia 145:37–40, 2018'
|
||||
print*, 'T. Maiti and P. Eisenlohr, Scripta Materialia 145:37–40, 2018'
|
||||
print*, 'https://doi.org/10.1016/j.scriptamat.2017.09.047'
|
||||
|
||||
phases => config_material%get('phase')
|
||||
|
|
|
|||
|
|
@ -203,10 +203,10 @@ module function plastic_nonlocal_init() result(myPlasticity)
|
|||
print'(/,a)', ' <<<+- phase:mechanical:plastic:nonlocal init -+>>>'
|
||||
print'(a,i0)', ' # phases: ',Ninstances; flush(IO_STDOUT)
|
||||
|
||||
print*, 'Reuber et al., Acta Materialia 71:333–348, 2014'
|
||||
print*, 'C. Reuber et al., Acta Materialia 71:333–348, 2014'
|
||||
print*, 'https://doi.org/10.1016/j.actamat.2014.03.012'//IO_EOL
|
||||
|
||||
print*, 'Kords, Dissertation RWTH Aachen, 2014'
|
||||
print*, 'C. Kords, Dissertation RWTH Aachen, 2014'
|
||||
print*, 'http://publications.rwth-aachen.de/record/229993'
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -61,7 +61,7 @@ subroutine results_init(restart)
|
|||
|
||||
print'(/,a)', ' <<<+- results init -+>>>'; flush(IO_STDOUT)
|
||||
|
||||
print*, 'Diehl et al., Integrating Materials and Manufacturing Innovation 6(1):83–91, 2017'
|
||||
print*, 'M. Diehl et al., Integrating Materials and Manufacturing Innovation 6(1):83–91, 2017'
|
||||
print*, 'https://doi.org/10.1007/s40192-017-0084-5'//IO_EOL
|
||||
|
||||
if(.not. restart) then
|
||||
|
|
|
|||
|
|
@ -105,7 +105,7 @@ subroutine rotations_init
|
|||
|
||||
print'(/,a)', ' <<<+- rotations init -+>>>'; flush(IO_STDOUT)
|
||||
|
||||
print*, 'Rowenhorst et al., Modelling and Simulation in Materials Science and Engineering 23:083501, 2015'
|
||||
print*, 'D. Rowenhorst et al., Modelling and Simulation in Materials Science and Engineering 23:083501, 2015'
|
||||
print*, 'https://doi.org/10.1088/0965-0393/23/8/083501'
|
||||
|
||||
call selfTest
|
||||
|
|
|
|||
Loading…
Reference in New Issue