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Merge remote-tracking branch 'origin/development' into drop-old-DADF5-support

This commit is contained in:
Martin Diehl 2021-04-25 17:34:14 +02:00
parent 18aa6f7f12 b7777bc746
commit d4a46b9be8
10 changed files with 80 additions and 44 deletions
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2
PRIVATE

@ -1 +1 @@
Subproject commit afffa8d04e110282e514a4e57d0bad9c76effe01
Subproject commit 7f0594060779d9a8a4e774d558134309ab77b96e

15
python/damask/_config.py
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@ -61,6 +61,11 @@ class Config(dict):
other : damask.Config or dict
Key-value pairs that update self.
Returns
-------
updated : damask.Config
Updated configuration.
"""
duplicate = self.copy()
duplicate.update(other)
@ -81,6 +86,11 @@ class Config(dict):
keys : iterable or scalar
Label of the key(s) to remove.
Returns
-------
updated : damask.Config
Updated configuration.
"""
duplicate = self.copy()
for k in keys if isinstance(keys, Iterable) and not isinstance(keys, str) else [keys]:
@ -98,6 +108,11 @@ class Config(dict):
fname : file, str, or pathlib.Path
Filename or file for writing.
Returns
-------
loaded : damask.Config
Configuration from file.
"""
try:
fhandle = open(fname)

17
python/damask/_configmaterial.py
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@ -54,7 +54,12 @@ class ConfigMaterial(Config):
Parameters
----------
fname : file, str, or pathlib.Path, optional
Filename or file for writing. Defaults to 'material.yaml'.
Filename or file to read from. Defaults to 'material.yaml'.
Returns
-------
loaded : damask.ConfigMaterial
Material configuration from file.
"""
return super(ConfigMaterial,cls).load(fname)
@ -103,6 +108,11 @@ class ConfigMaterial(Config):
and grain- or cell-wise data. Defaults to None, in which case
it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
Returns
-------
loaded : damask.ConfigMaterial
Material configuration from file.
"""
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
@ -146,6 +156,11 @@ class ConfigMaterial(Config):
Keyword arguments where the key is the name and the value specifies
the label of the data column in the table.
Returns
-------
new : damask.ConfigMaterial
Material configuration from values in table.
Examples
--------
>>> import damask

5
python/damask/_grid.py
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@ -1012,6 +1012,11 @@ class Grid:
Direction(s) along which the boundaries are determined.
Valid entries are 'x', 'y', 'z'. Defaults to 'xyz'.
Returns
-------
grain_boundaries : damask.VTK
VTK-based geometry of grain boundary network.
"""
valid = ['x','y','z']
if not set(directions).issubset(valid):

47
python/damask/_result.py
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@ -59,17 +59,17 @@ class Result:
"""
Add data to and export data from a DADF5 file.
A DADF5 (DAMASK HDF5) file contain DAMASK results.
A DADF5 (DAMASK HDF5) file contains DAMASK results.
Its group/folder structure reflects the layout in material.yaml.
This class provides a customable view on the DADF5 file.
This class provides a customizable view on the DADF5 file.
Upon initialization, all attributes are visible.
Derived quantities are added to the file and existing data is
exported based on the current view.
Examples
--------
Open 'my_file.hdf5', which needs to contain deformation gradient 'F'
Open 'my_file.hdf5', which is assumed to contain deformation gradient 'F'
and first Piola-Kirchhoff stress 'P', add the Mises equivalent of the
Cauchy stress, and export it to VTK (file) and numpy.ndarray (memory).
@ -224,12 +224,12 @@ class Result:
def modification_enable(self):
"""
Allow to modify existing data.
Allow modification of existing data.
Returns
-------
modified_view : damask.Result
View where data is not write-protected.
View without write-protection of existing data.
"""
print(util.warn('Warning: Modification of existing datasets allowed!'))
@ -239,12 +239,12 @@ class Result:
def modification_disable(self):
"""
Disallow to modify existing data (default case).
Prevent modification of existing data (default case).
Returns
-------
modified_view : damask.Result
View where data is write-protected.
View with write-protection of existing data.
"""
dup = self.copy()
@ -316,7 +316,7 @@ class Result:
Returns
-------
view : damask.Result
View with where selected attributes are visible.
View with only the selected attributes being visible.
Examples
--------
@ -326,7 +326,7 @@ class Result:
>>> r = damask.Result('my_file.hdf5')
>>> r_first = r.view('increment',0)
Get a view that shows all results of in simulation time [10,40]:
Get a view that shows all results between simulation times of 10 to 40:
>>> import damask
>>> r = damask.Result('my_file.hdf5')
@ -351,7 +351,7 @@ class Result:
Returns
-------
modified_view : damask.Result
View with more visible attributes.
View with additional visible attributes.
Examples
--------
@ -368,7 +368,7 @@ class Result:
def view_less(self,what,datasets):
"""
Delete from view.
Remove from view.
Parameters
----------
@ -381,11 +381,11 @@ class Result:
Returns
-------
modified_view : damask.Result
View with less visible attributes.
View with fewer visible attributes.
Examples
--------
Get a view that does not show the undeformed configuration:
Get a view that omits the undeformed configuration:
>>> import damask
>>> r_all = damask.Result('my_file.hdf5')
@ -570,16 +570,17 @@ class Result:
'creator': 'add_calculation'
}
}
def add_calculation(self,name,formula,unit='n/a',description=None):
def add_calculation(self,formula,name,unit='n/a',description=None):
"""
Add result of a general formula.
Parameters
----------
formula : str
Formula to calculate resulting dataset.
Existing datasets are referenced by '#TheirName#'.
name : str
Name of resulting dataset.
formula : str
Formula to calculate resulting dataset. Existing datasets are referenced by '#TheirName#'.
unit : str, optional
Physical unit of the result.
description : str, optional
@ -593,11 +594,11 @@ class Result:
>>> import damask
>>> r = damask.Result('my_file.hdf5')
>>> r.add_calculation('rho_mob_total','np.sum(#rho_mob#,axis=1)',
>>> r.add_calculation('np.sum(#rho_mob#,axis=1)','rho_mob_total',
... '1/m²','total mobile dislocation density')
>>> r.add_calculation('rho_dip_total','np.sum(#rho_dip#,axis=1)',
>>> r.add_calculation(''np.sum(#rho_dip#,axis=1)',rho_dip_total',
... '1/m²','total dislocation dipole density')
>>> r.add_calculation('rho_total','#rho_dip_total#+#rho_mob_total',
>>> r.add_calculation('#rho_dip_total#+#rho_mob_total','rho_total',
... '1/m²','total dislocation density')
Add Mises equivalent of the Cauchy stress without storage of
@ -609,7 +610,7 @@ class Result:
... return damask.mechanics.equivalent_stress_Mises(sigma)
>>> r = damask.Result('my_file.hdf5')
>>> r.enable_user_function(equivalent_stress)
>>> r.add_calculation('sigma_vM','equivalent_stress(#F#,#P#)','Pa',
>>> r.add_calculation('equivalent_stress(#F#,#P#)','sigma_vM','Pa',
... 'Mises equivalent of the Cauchy stress')
"""
@ -1378,7 +1379,7 @@ class Result:
Parameters
----------
output : (list of) str, optional
Names of the datasets included in the VTK file.
Names of the datasets to export to the VTK file.
Defaults to '*', in which case all datasets are exported.
mode : {'cell', 'point'}
Export in cell format or point format.
@ -1502,7 +1503,7 @@ class Result:
in the DADF5 file.
Multi-phase data is fused into a single output.
`place` is equivalent to `read` if only one phase/homogenization
`place` is equivalent to `get` if only one phase/homogenization
and one constituent is present.
Parameters
@ -1518,7 +1519,7 @@ class Result:
Remove branches with no data. Defaults to True.
constituents : (list of) int, optional
Constituents to consider.
Defaults to 'None', in which case all constituents are considered.
Defaults to None, in which case all constituents are considered.
fill_float : float
Fill value for non-existent entries of floating point type.
Defaults to NaN.

6
python/damask/_vtk.py
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@ -46,9 +46,9 @@ class VTK:
grid : iterable of int, len (3)
Number of cells along each dimension.
size : iterable of float, len (3)
Physical lengths along each dimension.
Physical length along each dimension.
origin : iterable of float, len (3), optional
Spatial origin coordinates.
Coordinates of grid origin.
Returns
-------
@ -161,7 +161,7 @@ class VTK:
"""
if not os.path.isfile(fname): # vtk has a strange error handling
raise FileNotFoundError(f'no such file: {fname}')
raise FileNotFoundError(f'No such file: {fname}')
ext = Path(fname).suffix
if ext == '.vtk' or dataset_type is not None:
reader = vtk.vtkGenericDataObjectReader()

4
python/damask/grid_filters.py
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@ -493,7 +493,7 @@ def node_to_point(node_data):
def coordinates0_valid(coordinates0):
"""
Check whether coordinates lie on a regular grid.
Check whether coordinates form a regular grid.
Parameters
----------
@ -503,7 +503,7 @@ def coordinates0_valid(coordinates0):
Returns
-------
valid : bool
Wheter the coordinates lie on a regular grid.
Whether the coordinates form a regular grid.
"""
try:

2
python/damask/solver/__init__.py
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@ -1,3 +1,3 @@
"""Run simulations directly from python."""
"""Run simulations directly from Python."""
from ._marc import Marc # noqa

14
python/tests/test_Result.py
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@ -110,14 +110,14 @@ class TestResult:
def test_add_calculation(self,default,tmp_path,mode):
if mode == 'direct':
default.add_calculation('x','2.0*np.abs(#F#)-1.0','-','my notes')
default.add_calculation('2.0*np.abs(#F#)-1.0','x','-','my notes')
else:
with open(tmp_path/'f.py','w') as f:
f.write("import numpy as np\ndef my_func(field):\n return 2.0*np.abs(field)-1.0\n")
sys.path.insert(0,str(tmp_path))
import f
default.enable_user_function(f.my_func)
default.add_calculation('x','my_func(#F#)','-','my notes')
default.add_calculation('my_func(#F#)','x','-','my notes')
in_memory = 2.0*np.abs(default.place('F'))-1.0
in_file = default.place('x')
@ -193,14 +193,14 @@ class TestResult:
def test_add_Mises_invalid(self,default):
default.add_stress_Cauchy('P','F')
default.add_calculation('sigma_y','#sigma#',unit='y')
default.add_calculation('#sigma#','sigma_y',unit='y')
default.add_equivalent_Mises('sigma_y')
assert default.get('sigma_y_vM') is None
def test_add_Mises_stress_strain(self,default):
default.add_stress_Cauchy('P','F')
default.add_calculation('sigma_y','#sigma#',unit='y')
default.add_calculation('sigma_x','#sigma#',unit='x')
default.add_calculation('#sigma#','sigma_y',unit='y')
default.add_calculation('#sigma#','sigma_x',unit='x')
default.add_equivalent_Mises('sigma_y',kind='strain')
default.add_equivalent_Mises('sigma_x',kind='stress')
assert not np.allclose(default.place('sigma_y_vM'),default.place('sigma_x_vM'))
@ -285,7 +285,7 @@ class TestResult:
time.sleep(2.)
try:
last.add_calculation('sigma','#sigma#*0.0+311.','not the Cauchy stress')
last.add_calculation('#sigma#*0.0+311.','sigma','not the Cauchy stress')
except ValueError:
pass
@ -362,7 +362,7 @@ class TestResult:
def test_XDMF(self,tmp_path,single_phase,update,ref_path):
for shape in [('scalar',()),('vector',(3,)),('tensor',(3,3)),('matrix',(12,))]:
for dtype in ['f4','f8','i1','i2','i4','i8','u1','u2','u4','u8']:
single_phase.add_calculation(f'{shape[0]}_{dtype}',f"np.ones(np.shape(#F#)[0:1]+{shape[1]},'{dtype}')")
single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape[1]},'{dtype}')",f'{shape[0]}_{dtype}')
fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'.xdmf'
os.chdir(tmp_path)
single_phase.save_XDMF()