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Merge remote-tracking branch 'origin/output-rename' into internal-restructure

This commit is contained in:
Sharan Roongta 2021-03-27 13:40:15 +01:00
parent 3ad2d903ab 35c854b549
commit f909aee835
50 changed files with 68132 additions and 148 deletions
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2
VERSION
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@ -1 +1 @@
v3.0.0-alpha2-602-ge2d4ab427
v3.0.0-alpha2-646-gee8015cd5

2
examples/ConfigFiles/Phase_Isotropic_FreeSurface.yaml
View File

@ -1,4 +1,4 @@
Air:
FreeSurface:
lattice: aP
mechanical:
output: [F, P, F_e, F_p, L_p]

3
examples/ConfigFiles/Phase_Phenopowerlaw_Magnesium.yaml
View File

@ -20,9 +20,6 @@ Magnesium:
xi_0_sl: [10.0e6, 55.0e6, 0, 60.0e6, 0.0, 60.0e6]
xi_inf_sl: [40.0e6, 135.0e6, 0, 150.0e6, 0.0, 150.0e6]
xi_0_tw: [40e6, 0.0, 0.0, 60.0e6]
####################################################
# open for discussion
####################################################
a_sl: 2.25
dot_gamma_0_sl: 0.001
dot_gamma_0_tw: 0.001

2
examples/ConfigFiles/Phase_Phenopowerlaw_cpTi.yaml
View File

@ -8,7 +8,7 @@ cpTi:
output: [F, P, F_e, F_p, L_p, O]
elastic: {C_11: 160.0e9, C_12: 90.0e9, C_13: 66.0e9, C_33: 181.7e9, C_44: 46.5e9, type: hooke}
plastic:
N_sl: [3, 3, 0, 0, 12]
N_sl: [3, 3, 0, 6, 12]
a_sl: 2.0
dot_gamma_0_sl: 0.001
h_0_sl_sl: 200e6

0
examples/FEM/polyXtal/material.yaml → examples/mesh/material.yaml
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0
examples/FEM/polyXtal/numerics.config → examples/mesh/numerics.config
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0
examples/FEM/polyXtal/polyXtal_100grains.msh → examples/mesh/polyXtal_100grains.msh
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0
examples/FEM/polyXtal/polyXtal_20grains.msh → examples/mesh/polyXtal_20grains.msh
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0
examples/FEM/polyXtal/tensionZ.load → examples/mesh/tensionZ.load
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2
processing/pre/geom_fromDREAM3D.py
View File

@ -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')

18
python/damask/_colormap.py
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@ -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)

80
python/damask/_configmaterial.py
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@ -1,4 +1,7 @@
import os.path
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):
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."""

76
python/damask/_grid.py
View File

@ -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
"""

6
python/damask/_orientation.py
View File

@ -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
"""

40
python/damask/_result.py
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@ -66,12 +66,14 @@ class Result:
self.times = [round(f[i].attrs['time/s'],12) for i in self.increments] if self.version_minor < 12 else \
[round(f[i].attrs['t/s'],12) for i in self.increments]
self.N_materialpoints, self.N_constituents = np.shape(f['mapping/phase'])
grp = 'mapping' if self.version_minor < 12 else 'cell_to'
self.homogenizations = [m.decode() for m in np.unique(f['mapping/homogenization']
['Name' if self.version_minor < 12 else 'name'])]
self.phases = [c.decode() for c in np.unique(f['mapping/phase']
['Name' if self.version_minor < 12 else 'name'])]
self.N_materialpoints, self.N_constituents = np.shape(f[f'{grp}/phase'])
self.homogenizations = [m.decode() for m in np.unique(f[f'{grp}/homogenization']
['Name' if self.version_minor < 12 else 'label'])]
self.phases = [c.decode() for c in np.unique(f[f'{grp}/phase']
['Name' if self.version_minor < 12 else 'label'])]
self.out_type_ph = []
for c in self.phases:
@ -375,8 +377,9 @@ class Result:
inGeom = {}
inData = {}
# compatibility hack
name = 'Name' if self.version_minor < 12 else 'name'
member = 'Position' if self.version_minor < 12 else 'member'
name = 'Name' if self.version_minor < 12 else 'label'
member = 'Position' if self.version_minor < 12 else 'entry'
grp = 'mapping' if self.version_minor < 12 else 'cell_to'
with h5py.File(self.fname,'r') as f:
for dataset in sets:
for group in self.groups_with_datasets(dataset):
@ -387,11 +390,11 @@ class Result:
if prop == 'geometry':
inGeom[key] = inData[key] = np.arange(self.N_materialpoints)
elif prop == 'phase':
inGeom[key] = np.where(f['mapping/phase'][:,constituent][name] == str.encode(name))[0]
inData[key] = f['mapping/phase'][inGeom[key],constituent][member]
inGeom[key] = np.where(f[f'{grp}/phase'][:,constituent][name] == str.encode(name))[0]
inData[key] = f[f'{grp}/phase'][inGeom[key],constituent][member]
elif prop == 'homogenization':
inGeom[key] = np.where(f['mapping/homogenization'][name] == str.encode(name))[0]
inData[key] = f['mapping/homogenization'][inGeom[key].tolist()][member]
inGeom[key] = np.where(f[f'{grp}/homogenization'][name] == str.encode(name))[0]
inData[key] = f[f'{grp}/homogenization'][inGeom[key].tolist()][member]
shape = np.shape(f[path])
data = np.full((self.N_materialpoints,) + (shape[1:] if len(shape)>1 else (1,)),
np.nan,
@ -542,8 +545,9 @@ class Result:
"""
# compatibility hack
name = 'Name' if self.version_minor < 12 else 'name'
member = 'Position' if self.version_minor < 12 else 'member'
name = 'Name' if self.version_minor < 12 else 'label'
member = 'Position' if self.version_minor < 12 else 'entry'
grp = 'mapping' if self.version_minor < 12 else 'cell_to'
with h5py.File(self.fname,'r') as f:
shape = (self.N_materialpoints,) + np.shape(f[path[0]])[1:]
if len(shape) == 1: shape = shape +(1,)
@ -555,17 +559,17 @@ class Result:
dataset = np.array(f[pa])
continue
p = np.where(f['mapping/phase'][:,c][name] == str.encode(label))[0]
p = np.where(f[f'{grp}/phase'][:,c][name] == str.encode(label))[0]
if len(p)>0:
u = (f['mapping/phase'][member][p,c])
u = (f[f'{grp}/phase'][member][p,c])
a = np.array(f[pa])
if len(a.shape) == 1:
a=a.reshape([a.shape[0],1])
dataset[p,:] = a[u,:]
p = np.where(f['mapping/homogenization'][name] == str.encode(label))[0]
p = np.where(f[f'{grp}/homogenization'][name] == str.encode(label))[0]
if len(p)>0:
u = (f['mapping/homogenization'][member][p.tolist()])
u = (f[f'{grp}/homogenization'][member][p.tolist()])
a = np.array(f[pa])
if len(a.shape) == 1:
a=a.reshape([a.shape[0],1])
@ -1346,7 +1350,7 @@ class Result:
for o in self.iterate('out_type_ph'):
for c in range(self.N_constituents):
prefix = '' if self.N_constituents == 1 else f'constituent{c}/'
if o not in ['mechanics', 'mechanical']: # compatitbility hack
if o not in ['mechanics', 'mechanical']: # compatibility hack
for _ in self.iterate('phases'):
path = self.get_dataset_location(label)
if len(path) == 0:

8
python/damask/_rotation.py
View File

@ -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
"""

51
python/damask/util.py
View File

@ -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
####################################################################################################

1
python/tests/reference/ConfigMaterial/2phase_irregularGrid.dream3d Symbolic link
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@ -0,0 +1 @@
../Grid/2phase_irregularGrid.dream3d

1
python/tests/reference/ConfigMaterial/2phase_irregularGrid.json Symbolic link
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@ -0,0 +1 @@
../Grid/2phase_irregularGrid.json

1
python/tests/reference/ConfigMaterial/2phase_irregularGrid.xdmf Symbolic link
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@ -0,0 +1 @@
../Grid/2phase_irregularGrid.xdmf

1
python/tests/reference/ConfigMaterial/measured.dream3d Symbolic link
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@ -0,0 +1 @@
../Grid/measured.dream3d

66831
python/tests/reference/ConfigMaterial/measured.material_yaml Normal file
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File diff suppressed because it is too large Load Diff

1
python/tests/reference/ConfigMaterial/measured.xdmf Symbolic link
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@ -0,0 +1 @@
../Grid/measured.xdmf

BIN
python/tests/reference/Grid/2phase_irregularGrid.dream3d Normal file
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Binary file not shown.

764
python/tests/reference/Grid/2phase_irregularGrid.json Normal file
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@ -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,
7.037197113037109,
8.03819751739502,
9.03919792175293,
10.04019832611084,
11.04119873046875,
12.04219913482666,
13.04319953918457,
14.04419994354248,
15.04520034790039,
16.046199798583984,
17.047199249267578,
18.048198699951172,
19.049198150634766,
20.05019760131836,
21.051197052001953,
22.052196502685547,
23.05319595336914,
24.054195404052734,
25.055194854736328,
26.056194305419922,
27.057193756103516,
28.05819320678711,
29.059192657470703,
30.060192108154297,
31.06119155883789,
32.062191009521484,
33.06319046020508
],
"BoundaryArea": 0,
"Crystal Symmetry": 1,
"FeatureSize Distribution": {
"Average": 0.5,
"Standard Deviation": 1
},
"FeatureSize Vs B Over A Distributions": {
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python/tests/reference/Grid/measured.xdmf Normal file
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@ -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>

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python/tests/reference/Result/12grains6x7x8_tensionY.hdf5
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python/tests/reference/Result/6grains6x7x8_single_phase_tensionY.hdf5
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34
python/tests/test_ConfigMaterial.py
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@ -1,11 +1,11 @@
import os
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 +108,35 @@ 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):
cur = ConfigMaterial.load_DREAM3D(ref_path/'measured.dream3d')
ref = ConfigMaterial.load(ref_path/'measured.material_yaml')
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 cur.is_valid and cur['phase'] == ref['phase'] and cur['homogenization'] == ref['homogenization']

25
python/tests/test_Grid.py
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@ -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)

37
python/tests/test_util.py
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@ -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')

2
src/DAMASK_interface.f90
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@ -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

2
src/grid/DAMASK_grid.f90
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@ -117,7 +117,7 @@ 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'

2
src/grid/grid_damage_spectral.f90
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@ -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'
!-------------------------------------------------------------------------------------------------

4
src/grid/grid_mech_spectral_basic.f90
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@ -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'
!-------------------------------------------------------------------------------------------------

2
src/grid/grid_mech_spectral_polarisation.f90
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@ -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'
!-------------------------------------------------------------------------------------------------

2
src/grid/grid_thermal_spectral.f90
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@ -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'
!-------------------------------------------------------------------------------------------------

8
src/grid/spectral_utilities.f90
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@ -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'
!--------------------------------------------------------------------------------------------------

29
src/homogenization.f90
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@ -276,8 +276,8 @@ subroutine materialpoint_stressAndItsTangent(dt,FEsolving_execIP,FEsolving_execE
call phase_restore(ce,.false.) ! wrong name (is more a forward function)
if(homogState(ho)%sizeState > 0) homogState(ho)%State(:,me) = homogState(ho)%State0(:,me)
if(damageState_h(ho)%sizeState > 0) damageState_h(ho)%State(:,me) = damageState_h(ho)%State0(:,me)
if(homogState(ho)%sizeState > 0) homogState(ho)%state(:,me) = homogState(ho)%state0(:,me)
if(damageState_h(ho)%sizeState > 0) damageState_h(ho)%state(:,me) = damageState_h(ho)%state0(:,me)
call damage_partition(ce)
doneAndHappy = [.false.,.true.]
@ -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
@ -450,7 +447,7 @@ subroutine homogenization_restartRead(fileHandle)
groupHandle(2) = HDF5_openGroup(groupHandle(1),material_name_homogenization(ho))
call HDF5_read(groupHandle(2),homogState(ho)%state,'omega') ! ToDo: should be done by mech
call HDF5_read(groupHandle(2),homogState(ho)%state0,'omega') ! ToDo: should be done by mech
call HDF5_closeGroup(groupHandle(2))

7
src/homogenization_mechanical_RGC.f90
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@ -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')

8
src/phase_mechanical.f90
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@ -492,7 +492,7 @@ 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
@ -504,7 +504,7 @@ 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
@ -532,7 +532,7 @@ 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)
@ -551,7 +551,7 @@ 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

4
src/phase_mechanical_plastic_dislotungsten.f90
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@ -103,8 +103,8 @@ 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*, 'https://dx.doi.org/10.1016/j.ijplas.2015.09.002'
print*, 'D. Cereceda et al., International Journal of Plasticity 78:242–256, 2016'
print*, 'https://doi.org/10.1016/j.ijplas.2015.09.002'
phases => config_material%get('phase')

6
src/phase_mechanical_plastic_dislotwin.f90
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@ -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'

2
src/phase_mechanical_plastic_isotropic.f90
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@ -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')

4
src/phase_mechanical_plastic_nonlocal.f90
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@ -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
src/results.f90
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@ -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
@ -71,7 +71,8 @@ subroutine results_init(restart)
call results_addAttribute('DAMASK_version',DAMASKVERSION)
call get_command(commandLine)
call results_addAttribute('call',trim(commandLine))
call results_closeGroup(results_addGroup('mapping'))
call results_closeGroup(results_addGroup('cell_to'))
call results_addAttribute('description','mappings to place data in space','cell_to')
call results_closeJobFile
endif
@ -431,8 +432,8 @@ subroutine results_mapping_phase(phaseAt,memberAtLocal,label)
integer(HID_T) :: &
loc_id, & !< identifier of group in file
dtype_id, & !< identifier of compound data type
name_id, & !< identifier of name (string) in compound data type
position_id, & !< identifier of position/index (integer) in compound data type
label_id, & !< identifier of label (string) in compound data type
entry_id, & !< identifier of entry (integer) in compound data type
dset_id, &
memspace_id, &
filespace_id, &
@ -497,21 +498,21 @@ subroutine results_mapping_phase(phaseAt,memberAtLocal,label)
call h5tcreate_f(H5T_COMPOUND_F, type_size_string + type_size_int, dtype_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, 'name', 0_SIZE_T, dt_id,hdferr)
call h5tinsert_f(dtype_id, 'label', 0_SIZE_T, dt_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, 'member', type_size_string, H5T_NATIVE_INTEGER, hdferr)
call h5tinsert_f(dtype_id, 'entry', type_size_string, H5T_NATIVE_INTEGER, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------
! create memory types for each component of the compound type
call h5tcreate_f(H5T_COMPOUND_F, type_size_string, name_id, hdferr)
call h5tcreate_f(H5T_COMPOUND_F, type_size_string, label_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(name_id, 'name', 0_SIZE_T, dt_id, hdferr)
call h5tinsert_f(label_id, 'label', 0_SIZE_T, dt_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tcreate_f(H5T_COMPOUND_F, type_size_int, position_id, hdferr)
call h5tcreate_f(H5T_COMPOUND_F, type_size_int, entry_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(position_id, 'member', 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dt_id, hdferr)
@ -533,14 +534,14 @@ subroutine results_mapping_phase(phaseAt,memberAtLocal,label)
call h5pset_preserve_f(plist_id, .true., hdferr)
if(hdferr < 0) error stop 'HDF5 error'
loc_id = results_openGroup('/mapping')
loc_id = results_openGroup('/cell_to')
call h5dcreate_f(loc_id, 'phase', dtype_id, filespace_id, dset_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5dwrite_f(dset_id, name_id, reshape(label(pack(phaseAtMaterialpoint,.true.)),myShape), &
call h5dwrite_f(dset_id, label_id, reshape(label(pack(phaseAtMaterialpoint,.true.)),myShape), &
myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
call h5dwrite_f(dset_id, position_id, reshape(pack(memberAtGlobal,.true.),myShape), &
call h5dwrite_f(dset_id, entry_id, reshape(pack(memberAtGlobal,.true.),myShape), &
myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
@ -557,9 +558,11 @@ subroutine results_mapping_phase(phaseAt,memberAtLocal,label)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dtype_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(name_id, hdferr)
call h5tclose_f(label_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(position_id, hdferr)
call h5tclose_f(entry_id, hdferr)
call executionStamp('cell_to/phase','cell ID and constituent ID to phase results')
end subroutine results_mapping_phase
@ -586,8 +589,8 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
integer(HID_T) :: &
loc_id, & !< identifier of group in file
dtype_id, & !< identifier of compound data type
name_id, & !< identifier of name (string) in compound data type
position_id, & !< identifier of position/index (integer) in compound data type
label_id, & !< identifier of label (string) in compound data type
entry_id, & !< identifier of entry (integer) in compound data type
dset_id, &
memspace_id, &
filespace_id, &
@ -653,21 +656,21 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
call h5tcreate_f(H5T_COMPOUND_F, type_size_string + type_size_int, dtype_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, 'name', 0_SIZE_T, dt_id,hdferr)
call h5tinsert_f(dtype_id, 'label', 0_SIZE_T, dt_id,hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(dtype_id, 'member', type_size_string, H5T_NATIVE_INTEGER, hdferr)
call h5tinsert_f(dtype_id, 'entry', type_size_string, H5T_NATIVE_INTEGER, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
!--------------------------------------------------------------------------------------------------
! create memory types for each component of the compound type
call h5tcreate_f(H5T_COMPOUND_F, type_size_string, name_id, hdferr)
call h5tcreate_f(H5T_COMPOUND_F, type_size_string, label_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(name_id, 'name', 0_SIZE_T, dt_id, hdferr)
call h5tinsert_f(label_id, 'label', 0_SIZE_T, dt_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tcreate_f(H5T_COMPOUND_F, type_size_int, position_id, hdferr)
call h5tcreate_f(H5T_COMPOUND_F, type_size_int, entry_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tinsert_f(position_id, 'member', 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
call h5tinsert_f(entry_id, 'entry', 0_SIZE_T, H5T_NATIVE_INTEGER, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dt_id, hdferr)
@ -689,14 +692,14 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
call h5pset_preserve_f(plist_id, .true., hdferr)
if(hdferr < 0) error stop 'HDF5 error'
loc_id = results_openGroup('/mapping')
loc_id = results_openGroup('/cell_to')
call h5dcreate_f(loc_id, 'homogenization', dtype_id, filespace_id, dset_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5dwrite_f(dset_id, name_id, reshape(label(pack(homogenizationAtMaterialpoint,.true.)),myShape), &
call h5dwrite_f(dset_id, label_id, reshape(label(pack(homogenizationAtMaterialpoint,.true.)),myShape), &
myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
call h5dwrite_f(dset_id, position_id, reshape(pack(memberAtGlobal,.true.),myShape), &
call h5dwrite_f(dset_id, entry_id, reshape(pack(memberAtGlobal,.true.),myShape), &
myShape, hdferr, file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if(hdferr < 0) error stop 'HDF5 error'
@ -713,11 +716,13 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(dtype_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(name_id, hdferr)
call h5tclose_f(label_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call h5tclose_f(position_id, hdferr)
call h5tclose_f(entry_id, hdferr)
if(hdferr < 0) error stop 'HDF5 error'
call executionStamp('cell_to/homogenization','cell ID to homogenization results')
end subroutine results_mapping_homogenization

2
src/rotations.f90
View File

@ -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