Merge branch 'python-documentation' into drop-old-DADF5-support
This commit is contained in:
Martin Diehl
commit
6e1fe712c7
|
|
@ -12,8 +12,12 @@
|
|||
*.pbz2 binary
|
||||
|
||||
# ignore files from MSC.Marc in language statistics
|
||||
installation/mods_MarcMentat/20*/* linguist-vendored
|
||||
installation/mods_MarcMentat/** linguist-vendored
|
||||
src/Marc/include/* linguist-vendored
|
||||
installation/mods_MarcMentat/apply_DAMASK_modifications.py linguist-vendored=false
|
||||
|
||||
# ignore reference files for tests in language statistics
|
||||
python/tests/reference/* linguist-vendored
|
||||
python/tests/reference/** linguist-vendored
|
||||
|
||||
# ignore deprecated scripts
|
||||
processing/legacy/** linguist-vendored
|
||||
|
|
|
|||
|
|
@ -233,7 +233,7 @@ source_distribution:
|
|||
stage: deploy
|
||||
script:
|
||||
- cd $(mktemp -d)
|
||||
- $DAMASKROOT/PRIVATE/releasing/deployMe.sh $CI_COMMIT_SHA
|
||||
- $DAMASKROOT/PRIVATE/releasing/deploy.sh $DAMASKROOT $CI_COMMIT_SHA
|
||||
except:
|
||||
- master
|
||||
- release
|
||||
|
|
|
|||
2
PRIVATE
2
PRIVATE
|
|
@ -1 +1 @@
|
|||
Subproject commit 1490f97417664d6ae11d7ceafb6b98c9cc2dade1
|
||||
Subproject commit afffa8d04e110282e514a4e57d0bad9c76effe01
|
||||
|
|
@ -5,6 +5,7 @@ references:
|
|||
10.1016/j.ijplas.2020.102779
|
||||
- K. Sedighiani et al.,
|
||||
Mechanics of Materials, submitted
|
||||
output: [rho_dip, rho_mob]
|
||||
N_sl: [12, 12]
|
||||
b_sl: [2.49e-10, 2.49e-10]
|
||||
rho_mob_0: [2.81e12, 2.8e12]
|
||||
|
|
|
|||
|
|
@ -1,11 +1,4 @@
|
|||
"""
|
||||
Tools for pre and post processing of DAMASK simulations.
|
||||
|
||||
Modules that contain only one class (of the same name),
|
||||
are prefixed by a '_'. For example, '_colormap' contains
|
||||
a class called 'Colormap' which is imported as 'damask.Colormap'.
|
||||
|
||||
"""
|
||||
"""Tools for managing DAMASK simulations."""
|
||||
|
||||
from pathlib import Path as _Path
|
||||
import re as _re
|
||||
|
|
@ -15,7 +8,6 @@ with open(_Path(__file__).parent/_Path('VERSION')) as _f:
|
|||
version = _re.sub(r'^v','',_f.readline().strip())
|
||||
__version__ = version
|
||||
|
||||
# make classes directly accessible as damask.Class
|
||||
from . import util # noqa
|
||||
from . import seeds # noqa
|
||||
from . import tensor # noqa
|
||||
|
|
@ -23,6 +15,8 @@ from . import mechanics # noqa
|
|||
from . import solver # noqa
|
||||
from . import grid_filters # noqa
|
||||
from . import lattice # noqa
|
||||
#Modules that contain only one class (of the same name), are prefixed by a '_'.
|
||||
#For example, '_colormap' containsa class called 'Colormap' which is imported as 'damask.Colormap'.
|
||||
from ._rotation import Rotation # noqa
|
||||
from ._orientation import Orientation # noqa
|
||||
from ._table import Table # noqa
|
||||
|
|
|
|||
|
|
@ -91,6 +91,16 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
- 'lab': CIE Lab.
|
||||
- 'msh': Msh (for perceptual uniform interpolation).
|
||||
|
||||
Returns
|
||||
-------
|
||||
new : damask.Colormap
|
||||
Colormap within given bounds.
|
||||
|
||||
Examples
|
||||
--------
|
||||
>>> import damask
|
||||
>>> damask.Colormap.from_range((0,0,1),(0,0,0),'blue_to_black')
|
||||
|
||||
"""
|
||||
low_high = np.vstack((low,high))
|
||||
if model.lower() == 'rgb':
|
||||
|
|
@ -150,6 +160,16 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
This parameter is not used for matplotlib colormaps
|
||||
that are of type `ListedColormap`.
|
||||
|
||||
Returns
|
||||
-------
|
||||
new : damask.Colormap
|
||||
Predefined colormap.
|
||||
|
||||
Examples
|
||||
--------
|
||||
>>> import damask
|
||||
>>> damask.Colormap.from_predefined('strain')
|
||||
|
||||
"""
|
||||
# matplotlib presets
|
||||
try:
|
||||
|
|
@ -220,6 +240,11 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
damask.Colormap
|
||||
The reversed colormap.
|
||||
|
||||
Examples
|
||||
--------
|
||||
>>> import damask
|
||||
>>> damask.Colormap.from_predefined('stress').reversed()
|
||||
|
||||
"""
|
||||
rev = super(Colormap,self).reversed(name)
|
||||
return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
|
||||
|
|
@ -239,8 +264,8 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
|
||||
Returns
|
||||
-------
|
||||
f
|
||||
File handle
|
||||
f : file object
|
||||
File handle with write access.
|
||||
|
||||
"""
|
||||
if fname is None:
|
||||
|
|
|
|||
|
|
@ -60,54 +60,6 @@ class ConfigMaterial(Config):
|
|||
return super(ConfigMaterial,cls).load(fname)
|
||||
|
||||
|
||||
@staticmethod
|
||||
def from_table(table,**kwargs):
|
||||
"""
|
||||
Generate from an ASCII table.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
table : damask.Table
|
||||
Table that contains material information.
|
||||
**kwargs
|
||||
Keyword arguments where the key is the name and the value specifies
|
||||
the label of the data column in the table.
|
||||
|
||||
Examples
|
||||
--------
|
||||
>>> import damask
|
||||
>>> import damask.ConfigMaterial as cm
|
||||
>>> t = damask.Table.load('small.txt')
|
||||
>>> t
|
||||
pos pos pos qu qu qu qu phase homog
|
||||
0 0 0 0 0.19 0.8 0.24 -0.51 Aluminum SX
|
||||
1 1 0 0 0.8 0.19 0.24 -0.51 Steel SX
|
||||
1 1 1 0 0.8 0.19 0.24 -0.51 Steel SX
|
||||
>>> cm.from_table(t,O='qu',phase='phase',homogenization='homog')
|
||||
material:
|
||||
- constituents:
|
||||
- O: [0.19, 0.8, 0.24, -0.51]
|
||||
v: 1.0
|
||||
phase: Aluminum
|
||||
homogenization: SX
|
||||
- constituents:
|
||||
- O: [0.8, 0.19, 0.24, -0.51]
|
||||
v: 1.0
|
||||
phase: Steel
|
||||
homogenization: SX
|
||||
homogenization: {}
|
||||
phase: {}
|
||||
|
||||
"""
|
||||
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)
|
||||
kwargs_ = {k:np.atleast_1d(v[idx].squeeze()) for k,v in kwargs_.items()}
|
||||
|
||||
return ConfigMaterial().material_add(**kwargs_)
|
||||
|
||||
|
||||
@staticmethod
|
||||
def load_DREAM3D(fname,
|
||||
grain_data=None,cell_data=None,cell_ensemble_data='CellEnsembleData',
|
||||
|
|
@ -181,9 +133,69 @@ class ConfigMaterial(Config):
|
|||
return base_config.material_add(**constituent,homogenization='direct')
|
||||
|
||||
|
||||
@staticmethod
|
||||
def from_table(table,**kwargs):
|
||||
"""
|
||||
Generate from an ASCII table.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
table : damask.Table
|
||||
Table that contains material information.
|
||||
**kwargs
|
||||
Keyword arguments where the key is the name and the value specifies
|
||||
the label of the data column in the table.
|
||||
|
||||
Examples
|
||||
--------
|
||||
>>> import damask
|
||||
>>> import damask.ConfigMaterial as cm
|
||||
>>> t = damask.Table.load('small.txt')
|
||||
>>> t
|
||||
pos pos pos qu qu qu qu phase homog
|
||||
0 0 0 0 0.19 0.8 0.24 -0.51 Aluminum SX
|
||||
1 1 0 0 0.8 0.19 0.24 -0.51 Steel SX
|
||||
1 1 1 0 0.8 0.19 0.24 -0.51 Steel SX
|
||||
>>> cm.from_table(t,O='qu',phase='phase',homogenization='homog')
|
||||
material:
|
||||
- constituents:
|
||||
- O: [0.19, 0.8, 0.24, -0.51]
|
||||
v: 1.0
|
||||
phase: Aluminum
|
||||
homogenization: SX
|
||||
- constituents:
|
||||
- O: [0.8, 0.19, 0.24, -0.51]
|
||||
v: 1.0
|
||||
phase: Steel
|
||||
homogenization: SX
|
||||
homogenization: {}
|
||||
phase: {}
|
||||
|
||||
"""
|
||||
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)
|
||||
kwargs_ = {k:np.atleast_1d(v[idx].squeeze()) for k,v in kwargs_.items()}
|
||||
|
||||
return ConfigMaterial().material_add(**kwargs_)
|
||||
|
||||
|
||||
@property
|
||||
def is_complete(self):
|
||||
"""Check for completeness."""
|
||||
"""
|
||||
Check for completeness.
|
||||
|
||||
Only the general file layout is considered.
|
||||
This check does not consider whether parameters for
|
||||
a particular phase/homogenization model are missing.
|
||||
|
||||
Returns
|
||||
-------
|
||||
complete : bool
|
||||
Whether the material.yaml definition is complete.
|
||||
|
||||
"""
|
||||
ok = True
|
||||
for top_level in ['homogenization','phase','material']:
|
||||
ok &= top_level in self
|
||||
|
|
@ -236,7 +248,19 @@ class ConfigMaterial(Config):
|
|||
|
||||
@property
|
||||
def is_valid(self):
|
||||
"""Check for valid content."""
|
||||
"""
|
||||
Check for valid content.
|
||||
|
||||
Only the generic file content is considered.
|
||||
This check does not consider whether parameters for a
|
||||
particular phase/homogenization mode are out of bounds.
|
||||
|
||||
Returns
|
||||
-------
|
||||
valid : bool
|
||||
Whether the material.yaml definition is valid.
|
||||
|
||||
"""
|
||||
ok = True
|
||||
|
||||
if 'phase' in self:
|
||||
|
|
@ -282,7 +306,7 @@ class ConfigMaterial(Config):
|
|||
|
||||
Returns
|
||||
-------
|
||||
cfg : damask.ConfigMaterial
|
||||
updated : damask.ConfigMaterial
|
||||
Updated material configuration.
|
||||
|
||||
"""
|
||||
|
|
@ -311,7 +335,7 @@ class ConfigMaterial(Config):
|
|||
|
||||
Returns
|
||||
-------
|
||||
cfg : damask.ConfigMaterial
|
||||
updated : damask.ConfigMaterial
|
||||
Updated material configuration.
|
||||
|
||||
"""
|
||||
|
|
@ -336,14 +360,17 @@ class ConfigMaterial(Config):
|
|||
|
||||
Returns
|
||||
-------
|
||||
cfg : damask.ConfigMaterial
|
||||
updated : damask.ConfigMaterial
|
||||
Updated material configuration.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Create a dual-phase steel microstructure for micromechanical simulations:
|
||||
|
||||
>>> import numpy as np
|
||||
>>> import damask
|
||||
>>> m = damask.ConfigMaterial().material_add(phase = ['Aluminum','Steel'],
|
||||
>>> m = damask.ConfigMaterial()
|
||||
>>> m = m.material_add(phase = ['Ferrite','Martensite'],
|
||||
... O = damask.Rotation.from_random(2),
|
||||
... homogenization = 'SX')
|
||||
>>> m
|
||||
|
|
@ -351,38 +378,43 @@ class ConfigMaterial(Config):
|
|||
- constituents:
|
||||
- O: [0.577764, -0.146299, -0.617669, 0.513010]
|
||||
v: 1.0
|
||||
phase: Aluminum
|
||||
phase: Ferrite
|
||||
homogenization: SX
|
||||
- constituents:
|
||||
- O: [0.184176, 0.340305, 0.737247, 0.553840]
|
||||
v: 1.0
|
||||
phase: Steel
|
||||
phase: Martensite
|
||||
homogenization: SX
|
||||
homogenization: {}
|
||||
phase: {}
|
||||
|
||||
>>> m = damask.ConfigMaterial().material_add(phase = np.array(['Austenite','Martensite']).reshape(1,2),
|
||||
Create a duplex stainless steel microstructure for forming simulations:
|
||||
|
||||
>>> import numpy as np
|
||||
>>> import damask
|
||||
>>> m = damask.ConfigMaterial()
|
||||
>>> m = m.material_add(phase = np.array(['Austenite','Ferrite']).reshape(1,2),
|
||||
... O = damask.Rotation.from_random((2,2)),
|
||||
... v = np.array([0.2,0.8]).reshape(1,2),
|
||||
... homogenization = ['A','B'])
|
||||
... homogenization = 'Taylor')
|
||||
>>> m
|
||||
material:
|
||||
- constituents:
|
||||
- phase: Austenite
|
||||
O: [0.659802978293224, 0.6953785848195171, 0.22426295326327111, -0.17554139512785227]
|
||||
v: 0.2
|
||||
- phase: Martensite
|
||||
- phase: Ferrite
|
||||
O: [0.49356745891301596, 0.2841806579193434, -0.7487679215072818, -0.339085707289975]
|
||||
v: 0.8
|
||||
homogenization: A
|
||||
homogenization: Taylor
|
||||
- constituents:
|
||||
- phase: Austenite
|
||||
O: [0.26542221365204055, 0.7268854930702071, 0.4474726435701472, -0.44828201137283735]
|
||||
v: 0.2
|
||||
- phase: Martensite
|
||||
- phase: Ferrite
|
||||
O: [0.6545817158479885, -0.08004812803625233, -0.6226561293931374, 0.4212059104577611]
|
||||
v: 0.8
|
||||
homogenization: B
|
||||
homogenization: Taylor
|
||||
homogenization: {}
|
||||
phase: {}
|
||||
|
||||
|
|
|
|||
|
|
@ -161,6 +161,11 @@ class Grid:
|
|||
Grid file to read. Valid extension is .vtr, which will be appended
|
||||
if not given.
|
||||
|
||||
Returns
|
||||
-------
|
||||
loaded : damask.Grid
|
||||
Grid-based geometry from file.
|
||||
|
||||
"""
|
||||
v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
|
||||
comments = v.get_comments()
|
||||
|
|
@ -190,6 +195,11 @@ class Grid:
|
|||
fname : str, pathlib.Path, or file handle
|
||||
Geometry file to read.
|
||||
|
||||
Returns
|
||||
-------
|
||||
loaded : damask.Grid
|
||||
Grid-based geometry from file.
|
||||
|
||||
"""
|
||||
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
|
||||
try:
|
||||
|
|
@ -281,6 +291,10 @@ class Grid:
|
|||
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.Grid
|
||||
Grid-based geometry from file.
|
||||
|
||||
"""
|
||||
b = util.DREAM3D_base_group(fname) if base_group is None else base_group
|
||||
|
|
@ -319,6 +333,11 @@ class Grid:
|
|||
Label(s) of the columns containing the material definition.
|
||||
Each unique combination of values results in one material ID.
|
||||
|
||||
Returns
|
||||
-------
|
||||
new : damask.Grid
|
||||
Grid-based geometry from values in table.
|
||||
|
||||
"""
|
||||
cells,size,origin = grid_filters.cellsSizeOrigin_coordinates0_point(table.get(coordinates))
|
||||
|
||||
|
|
@ -356,6 +375,11 @@ class Grid:
|
|||
periodic : Boolean, optional
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
Returns
|
||||
-------
|
||||
new : damask.Grid
|
||||
Grid-based geometry from tessellation.
|
||||
|
||||
"""
|
||||
if periodic:
|
||||
weights_p = np.tile(weights,27) # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
|
||||
|
|
@ -405,6 +429,11 @@ class Grid:
|
|||
periodic : Boolean, optional
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
Returns
|
||||
-------
|
||||
new : damask.Grid
|
||||
Grid-based geometry from tessellation.
|
||||
|
||||
"""
|
||||
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
|
||||
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
|
||||
|
|
@ -478,6 +507,11 @@ class Grid:
|
|||
materials : (int, int), optional
|
||||
Material IDs. Defaults to (1,2).
|
||||
|
||||
Returns
|
||||
-------
|
||||
new : damask.Grid
|
||||
Grid-based geometry from definition of minimal surface.
|
||||
|
||||
Notes
|
||||
-----
|
||||
The following triply-periodic minimal surfaces are implemented:
|
||||
|
|
@ -598,6 +632,11 @@ class Grid:
|
|||
periodic : Boolean, optional
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
# radius and center
|
||||
r = np.array(dimension)/2.0*self.size/self.cells if np.array(dimension).dtype in np.sctypes['int'] else \
|
||||
|
|
@ -638,6 +677,11 @@ class Grid:
|
|||
reflect : bool, optional
|
||||
Reflect (include) outermost layers. Defaults to False.
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
valid = ['x','y','z']
|
||||
if not set(directions).issubset(valid):
|
||||
|
|
@ -670,6 +714,11 @@ class Grid:
|
|||
Direction(s) along which the grid is flipped.
|
||||
Valid entries are 'x', 'y', 'z'.
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
valid = ['x','y','z']
|
||||
if not set(directions).issubset(valid):
|
||||
|
|
@ -695,6 +744,11 @@ class Grid:
|
|||
periodic : Boolean, optional
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
return Grid(material = ndimage.interpolation.zoom(
|
||||
self.material,
|
||||
|
|
@ -723,6 +777,11 @@ class Grid:
|
|||
periodic : Boolean, optional
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
def mostFrequent(arr,selection=None):
|
||||
me = arr[arr.size//2]
|
||||
|
|
@ -746,7 +805,15 @@ class Grid:
|
|||
|
||||
|
||||
def renumber(self):
|
||||
"""Renumber sorted material indices as 0,...,N-1."""
|
||||
"""
|
||||
Renumber sorted material indices as 0,...,N-1.
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
_,renumbered = np.unique(self.material,return_inverse=True)
|
||||
|
||||
return Grid(material = renumbered.reshape(self.cells),
|
||||
|
|
@ -767,6 +834,11 @@ class Grid:
|
|||
fill : int or float, optional
|
||||
Material index to fill the corners. Defaults to material.max() + 1.
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
if fill is None: fill = np.nanmax(self.material) + 1
|
||||
dtype = float if isinstance(fill,float) or self.material.dtype in np.sctypes['float'] else int
|
||||
|
|
@ -802,6 +874,11 @@ class Grid:
|
|||
fill : int or float, optional
|
||||
Material index to fill the background. Defaults to material.max() + 1.
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
if offset is None: offset = 0
|
||||
if fill is None: fill = np.nanmax(self.material) + 1
|
||||
|
|
@ -834,6 +911,11 @@ class Grid:
|
|||
to_material : iterable of ints
|
||||
New material indices.
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
def mp(entry,mapper):
|
||||
return mapper[entry] if entry in mapper else entry
|
||||
|
|
@ -849,7 +931,15 @@ class Grid:
|
|||
|
||||
|
||||
def sort(self):
|
||||
"""Sort material indices such that min(material) is located at (0,0,0)."""
|
||||
"""
|
||||
Sort material indices such that min(material) is located at (0,0,0).
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
a = self.material.flatten(order='F')
|
||||
from_ma = pd.unique(a)
|
||||
sort_idx = np.argsort(from_ma)
|
||||
|
|
@ -884,6 +974,11 @@ class Grid:
|
|||
periodic : Boolean, optional
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
Returns
|
||||
-------
|
||||
updated : damask.Grid
|
||||
Updated grid-based geometry.
|
||||
|
||||
"""
|
||||
def tainted_neighborhood(stencil,trigger):
|
||||
|
||||
|
|
|
|||
|
|
@ -8,15 +8,15 @@ from . import tensor
|
|||
|
||||
_parameter_doc = \
|
||||
"""lattice : str
|
||||
Either a crystal family out of [triclinic, monoclinic, orthorhombic, tetragonal, hexagonal, cubic]
|
||||
or a Bravais lattice out of [aP, mP, mS, oP, oS, oI, oF, tP, tI, hP, cP, cI, cF].
|
||||
When specifying a Bravais lattice, additional lattice parameters might be required:
|
||||
Either a crystal family out of {triclinic, monoclinic, orthorhombic, tetragonal, hexagonal, cubic}
|
||||
or a Bravais lattice out of {aP, mP, mS, oP, oS, oI, oF, tP, tI, hP, cP, cI, cF}.
|
||||
When specifying a Bravais lattice, additional lattice parameters might be required.
|
||||
a : float, optional
|
||||
Length of lattice parameter "a".
|
||||
Length of lattice parameter 'a'.
|
||||
b : float, optional
|
||||
Length of lattice parameter "b".
|
||||
Length of lattice parameter 'b'.
|
||||
c : float, optional
|
||||
Length of lattice parameter "c".
|
||||
Length of lattice parameter 'c'.
|
||||
alpha : float, optional
|
||||
Angle between b and c lattice basis.
|
||||
beta : float, optional
|
||||
|
|
|
|||
|
|
@ -57,11 +57,30 @@ def _empty_like(dataset,N_materialpoints,fill_float,fill_int):
|
|||
|
||||
class Result:
|
||||
"""
|
||||
Manipulate and read DADF5 files.
|
||||
Add data to and export data from a DADF5 file.
|
||||
|
||||
A DADF5 (DAMASK HDF5) file contain DAMASK results.
|
||||
Its group/folder structure reflects the layout in material.yaml.
|
||||
|
||||
This class provides a customable 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'
|
||||
and first Piola-Kirchhoff stress 'P', add the Mises equivalent of the
|
||||
Cauchy stress, and export it to VTK (file) and numpy.ndarray (memory).
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r.add_Cauchy()
|
||||
>>> r.add_equivalent_Mises('sigma')
|
||||
>>> r.save_VTK()
|
||||
>>> r_last = r.view('increments',-1)
|
||||
>>> sigma_vM_last = r_last.get('sigma_vM')
|
||||
|
||||
DADF5 (DAMASK HDF5) files contain DAMASK results.
|
||||
The group/folder structure reflects the input data
|
||||
in material.yaml.
|
||||
"""
|
||||
|
||||
def __init__(self,fname):
|
||||
|
|
@ -95,10 +114,10 @@ class Result:
|
|||
|
||||
self.N_materialpoints, self.N_constituents = np.shape(f[f'cell_to/phase'])
|
||||
|
||||
self.homogenizations = [m.decode() for m in np.unique(f[f'cell_to/homogenization']['label'])]
|
||||
self.homogenizations = sorted(self.homogenizations,key=util.natural_sort)
|
||||
self.phases = [c.decode() for c in np.unique(f[f'cell_to/phase']['label'])]
|
||||
self.phases = sorted(self.phases,key=util.natural_sort)
|
||||
self.homogenization = f[f'cell_to/homogenization']['label'].astype('str')
|
||||
self.homogenizations = sorted(np.unique(self.homogenization),key=util.natural_sort)
|
||||
self.phase = f[f'cell_to/phase']['label'].astype('str')
|
||||
self.phases = sorted(np.unique(self.phase),key=util.natural_sort)
|
||||
|
||||
self.fields = []
|
||||
for c in self.phases:
|
||||
|
|
@ -154,6 +173,11 @@ class Result:
|
|||
Name of datasets; supports '?' and '*' wildcards.
|
||||
True is equivalent to '*', False is equivalent to [].
|
||||
|
||||
Returns
|
||||
-------
|
||||
view : damask.Result
|
||||
Modified or new view on the DADF5 file.
|
||||
|
||||
"""
|
||||
# allow True/False and string arguments
|
||||
if datasets is True:
|
||||
|
|
@ -166,6 +190,7 @@ class Result:
|
|||
if what == 'increments':
|
||||
choice = [c if isinstance(c,str) and c.startswith('increment_') else
|
||||
f'increment_{c}' for c in choice]
|
||||
if datasets == -1: choice = [self.increments[-1]]
|
||||
elif what == 'times':
|
||||
what = 'increments'
|
||||
if choice == ['*']:
|
||||
|
|
@ -197,15 +222,31 @@ class Result:
|
|||
return dup
|
||||
|
||||
|
||||
def allow_modification(self):
|
||||
"""Allow to overwrite existing data."""
|
||||
def modification_enable(self):
|
||||
"""
|
||||
Allow to modify existing data.
|
||||
|
||||
Returns
|
||||
-------
|
||||
modified_view : damask.Result
|
||||
View where data is not write-protected.
|
||||
|
||||
"""
|
||||
print(util.warn('Warning: Modification of existing datasets allowed!'))
|
||||
dup = self.copy()
|
||||
dup._allow_modification = True
|
||||
return dup
|
||||
|
||||
def disallow_modification(self):
|
||||
"""Disallow to overwrite existing data (default case)."""
|
||||
def modification_disable(self):
|
||||
"""
|
||||
Disallow to modify existing data (default case).
|
||||
|
||||
Returns
|
||||
-------
|
||||
modified_view : damask.Result
|
||||
View where data is write-protected.
|
||||
|
||||
"""
|
||||
dup = self.copy()
|
||||
dup._allow_modification = False
|
||||
return dup
|
||||
|
|
@ -213,7 +254,7 @@ class Result:
|
|||
|
||||
def increments_in_range(self,start,end):
|
||||
"""
|
||||
Select all increments within a given range.
|
||||
Get all increments within a given range.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -222,6 +263,11 @@ class Result:
|
|||
end : int or str
|
||||
End increment.
|
||||
|
||||
Returns
|
||||
-------
|
||||
increments : list of ints
|
||||
Increment number of all increments within the given bounds.
|
||||
|
||||
"""
|
||||
selected = []
|
||||
for i,inc in enumerate([int(i[10:]) for i in self.increments]):
|
||||
|
|
@ -233,7 +279,7 @@ class Result:
|
|||
|
||||
def times_in_range(self,start,end):
|
||||
"""
|
||||
Select all increments within a given time range.
|
||||
Get all increments within a given time range.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -242,6 +288,11 @@ class Result:
|
|||
end : float
|
||||
Time of end increment.
|
||||
|
||||
Returns
|
||||
-------
|
||||
times : list of float
|
||||
Simulation time of all increments within the given bounds.
|
||||
|
||||
"""
|
||||
selected = []
|
||||
for i,time in enumerate(self.times):
|
||||
|
|
@ -262,6 +313,25 @@ class Result:
|
|||
Name of datasets; supports '?' and '*' wildcards.
|
||||
True is equivalent to '*', False is equivalent to [].
|
||||
|
||||
Returns
|
||||
-------
|
||||
view : damask.Result
|
||||
View with where selected attributes are visible.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Get a view that shows only results from the initial configuration:
|
||||
|
||||
>>> import damask
|
||||
>>> 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]:
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r_t10to40 = r.view('times',r.times_in_range(10.0,40.0))
|
||||
|
||||
"""
|
||||
return self._manage_view('set',what,datasets)
|
||||
|
||||
|
|
@ -278,6 +348,20 @@ class Result:
|
|||
Name of datasets; supports '?' and '*' wildcards.
|
||||
True is equivalent to '*', False is equivalent to [].
|
||||
|
||||
Returns
|
||||
-------
|
||||
modified_view : damask.Result
|
||||
View with more visible attributes.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Get a view that shows only results from first and last increment:
|
||||
|
||||
>>> import damask
|
||||
>>> r_empty = damask.Result('my_file.hdf5').view('increments',False)
|
||||
>>> r_first = r_empty.view_more('increments',0)
|
||||
>>> r_first_and_last = r.first.view_more('increments',-1)
|
||||
|
||||
"""
|
||||
return self._manage_view('add',what,datasets)
|
||||
|
||||
|
|
@ -294,37 +378,98 @@ class Result:
|
|||
Name of datasets; supports '?' and '*' wildcards.
|
||||
True is equivalent to '*', False is equivalent to [].
|
||||
|
||||
Returns
|
||||
-------
|
||||
modified_view : damask.Result
|
||||
View with less visible attributes.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Get a view that does not show the undeformed configuration:
|
||||
|
||||
>>> import damask
|
||||
>>> r_all = damask.Result('my_file.hdf5')
|
||||
>>> r_deformed = r_all.view_less('increments',0)
|
||||
|
||||
"""
|
||||
return self._manage_view('del',what,datasets)
|
||||
|
||||
|
||||
def rename(self,name_old,name_new):
|
||||
def rename(self,name_src,name_dst):
|
||||
"""
|
||||
Rename dataset.
|
||||
Rename/move datasets (within the same group/folder).
|
||||
|
||||
This operation is discouraged because the history of the
|
||||
data becomes untracable and scientific integrity cannot be
|
||||
ensured.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
name_old : str
|
||||
Name of the dataset to be renamed.
|
||||
name_new : str
|
||||
New name of the dataset.
|
||||
name_src : str
|
||||
Name of the datasets to be renamed.
|
||||
name_dst : str
|
||||
New name of the datasets.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Rename datasets containing the deformation gradient from 'F' to 'def_grad':
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r_unprotected = r.modification_enable()
|
||||
>>> r_unprotected.rename('F','def_grad')
|
||||
|
||||
"""
|
||||
if not self._allow_modification:
|
||||
raise PermissionError('Rename operation not permitted')
|
||||
raise PermissionError('Renaming datasets not permitted')
|
||||
|
||||
with h5py.File(self.fname,'a') as f:
|
||||
for inc in self.visible['increments']:
|
||||
for ty in ['phase','homogenization']:
|
||||
for label in self.visible[ty+'s']:
|
||||
for field in self.visible['fields']:
|
||||
path_old = '/'.join([inc,ty,label,field,name_old])
|
||||
path_new = '/'.join([inc,ty,label,field,name_new])
|
||||
if path_old in f.keys():
|
||||
f[path_new] = f[path_old]
|
||||
f[path_new].attrs['renamed'] = f'original name: {name_old}' if h5py3 else \
|
||||
f'original name: {name_old}'.encode()
|
||||
del f[path_old]
|
||||
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
|
||||
path_src = '/'.join([inc,ty,label,field,name_src])
|
||||
path_dst = '/'.join([inc,ty,label,field,name_dst])
|
||||
if path_src in f.keys():
|
||||
f[path_dst] = f[path_src]
|
||||
f[path_dst].attrs['renamed'] = f'original name: {name_src}' if h5py3 else \
|
||||
f'original name: {name_src}'.encode()
|
||||
del f[path_src]
|
||||
|
||||
|
||||
def remove(self,name):
|
||||
"""
|
||||
Remove/delete datasets.
|
||||
|
||||
This operation is discouraged because the history of the
|
||||
data becomes untracable and scientific integrity cannot be
|
||||
ensured.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
name : str
|
||||
Name of the datasets to be deleted.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Delete the deformation gradient 'F':
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r_unprotected = r.modification_enable()
|
||||
>>> r_unprotected.remove('F')
|
||||
|
||||
"""
|
||||
if not self._allow_modification:
|
||||
raise PermissionError('Removing datasets not permitted')
|
||||
|
||||
with h5py.File(self.fname,'a') as f:
|
||||
for inc in self.visible['increments']:
|
||||
for ty in ['phase','homogenization']:
|
||||
for label in self.visible[ty+'s']:
|
||||
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
|
||||
path = '/'.join([inc,ty,label,field,name])
|
||||
if path in f.keys(): del f[path]
|
||||
|
||||
|
||||
def list_data(self):
|
||||
|
|
@ -337,7 +482,7 @@ class Result:
|
|||
msg = ' '.join([msg,f'{ty}\n'])
|
||||
for label in self.visible[ty+'s']:
|
||||
msg = ' '.join([msg,f'{label}\n'])
|
||||
for field in self.visible['fields']:
|
||||
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
|
||||
msg = ' '.join([msg,f'{field}\n'])
|
||||
for d in f['/'.join([inc,ty,label,field])].keys():
|
||||
dataset = f['/'.join([inc,ty,label,field,d])]
|
||||
|
|
@ -357,7 +502,7 @@ class Result:
|
|||
|
||||
@property
|
||||
def coordinates0_point(self):
|
||||
"""Return initial coordinates of the cell centers."""
|
||||
"""Initial/undeformed cell center coordinates."""
|
||||
if self.structured:
|
||||
return grid_filters.coordinates0_point(self.cells,self.size,self.origin).reshape(-1,3,order='F')
|
||||
else:
|
||||
|
|
@ -366,7 +511,7 @@ class Result:
|
|||
|
||||
@property
|
||||
def coordinates0_node(self):
|
||||
"""Return initial coordinates of the cell centers."""
|
||||
"""Initial/undeformed nodal coordinates."""
|
||||
if self.structured:
|
||||
return grid_filters.coordinates0_node(self.cells,self.size,self.origin).reshape(-1,3,order='F')
|
||||
else:
|
||||
|
|
@ -375,6 +520,7 @@ class Result:
|
|||
|
||||
@property
|
||||
def geometry0(self):
|
||||
"""Initial/undeformed geometry."""
|
||||
if self.structured:
|
||||
return VTK.from_rectilinear_grid(self.cells,self.size,self.origin)
|
||||
else:
|
||||
|
|
@ -403,7 +549,7 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
x : str
|
||||
Label of scalar, vector, or tensor dataset to take absolute value of.
|
||||
Name of scalar, vector, or tensor dataset to take absolute value of.
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_absolute,{'x':x})
|
||||
|
|
@ -424,24 +570,51 @@ class Result:
|
|||
'creator': 'add_calculation'
|
||||
}
|
||||
}
|
||||
def add_calculation(self,label,formula,unit='n/a',description=None):
|
||||
def add_calculation(self,name,formula,unit='n/a',description=None):
|
||||
"""
|
||||
Add result of a general formula.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
label : str
|
||||
Label of resulting dataset.
|
||||
name : str
|
||||
Name of resulting dataset.
|
||||
formula : str
|
||||
Formula to calculate resulting dataset. Existing datasets are referenced by '#TheirLabel#'.
|
||||
Formula to calculate resulting dataset. Existing datasets are referenced by '#TheirName#'.
|
||||
unit : str, optional
|
||||
Physical unit of the result.
|
||||
description : str, optional
|
||||
Human-readable description of the result.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Add total dislocation density, i.e. the sum of mobile dislocation
|
||||
density 'rho_mob' and dislocation dipole density 'rho_dip' over
|
||||
all slip systems:
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r.add_calculation('rho_mob_total','np.sum(#rho_mob#,axis=1)',
|
||||
... '1/m²','total mobile dislocation density')
|
||||
>>> r.add_calculation('rho_dip_total','np.sum(#rho_dip#,axis=1)',
|
||||
... '1/m²','total dislocation dipole density')
|
||||
>>> r.add_calculation('rho_total','#rho_dip_total#+#rho_mob_total',
|
||||
... '1/m²','total dislocation density')
|
||||
|
||||
Add Mises equivalent of the Cauchy stress without storage of
|
||||
intermediate results. Define a user function for better readability:
|
||||
|
||||
>>> import damask
|
||||
>>> def equivalent_stress(F,P):
|
||||
... sigma = damask.mechanics.stress_Cauchy(F=F,P=P)
|
||||
... 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',
|
||||
... 'Mises equivalent of the Cauchy stress')
|
||||
|
||||
"""
|
||||
dataset_mapping = {d:d for d in set(re.findall(r'#(.*?)#',formula))} # datasets used in the formula
|
||||
args = {'formula':formula,'label':label,'unit':unit,'description':description}
|
||||
args = {'formula':formula,'label':name,'unit':unit,'description':description}
|
||||
self._add_generic_pointwise(self._add_calculation,dataset_mapping,args)
|
||||
|
||||
|
||||
|
|
@ -465,9 +638,9 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
P : str, optional
|
||||
Label of the dataset containing the first Piola-Kirchhoff stress. Defaults to 'P'.
|
||||
Name of the dataset containing the first Piola-Kirchhoff stress. Defaults to 'P'.
|
||||
F : str, optional
|
||||
Label of the dataset containing the deformation gradient. Defaults to 'F'.
|
||||
Name of the dataset containing the deformation gradient. Defaults to 'F'.
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_stress_Cauchy,{'P':P,'F':F})
|
||||
|
|
@ -491,7 +664,15 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
T : str
|
||||
Label of tensor dataset.
|
||||
Name of tensor dataset.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Add the determinant of plastic deformation gradient 'F_p':
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r.add_determinant('F_p')
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_determinant,{'T':T})
|
||||
|
|
@ -515,7 +696,7 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
T : str
|
||||
Label of tensor dataset.
|
||||
Name of tensor dataset.
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_deviator,{'T':T})
|
||||
|
|
@ -546,7 +727,7 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
T_sym : str
|
||||
Label of symmetric tensor dataset.
|
||||
Name of symmetric tensor dataset.
|
||||
eigenvalue : str, optional
|
||||
Eigenvalue. Select from 'max', 'mid', 'min'. Defaults to 'max'.
|
||||
|
||||
|
|
@ -579,7 +760,7 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
T_sym : str
|
||||
Label of symmetric tensor dataset.
|
||||
Name of symmetric tensor dataset.
|
||||
eigenvalue : str, optional
|
||||
Eigenvalue to which the eigenvector corresponds.
|
||||
Select from 'max', 'mid', 'min'. Defaults to 'max'.
|
||||
|
|
@ -619,9 +800,17 @@ class Result:
|
|||
l : numpy.array of shape (3)
|
||||
Lab frame direction for inverse pole figure.
|
||||
q : str
|
||||
Label of the dataset containing the crystallographic orientation as quaternions.
|
||||
Name of the dataset containing the crystallographic orientation as quaternions.
|
||||
Defaults to 'O'.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Add the IPF color along [0,1,1] for orientation 'O':
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r.add_IPF_color(np.array([0,1,1]))
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_IPF_color,{'q':q},{'l':l})
|
||||
|
||||
|
|
@ -644,7 +833,7 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
T_sym : str
|
||||
Label of symmetric tensor dataset.
|
||||
Name of symmetric tensor dataset.
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_maximum_shear,{'T_sym':T_sym})
|
||||
|
|
@ -678,11 +867,25 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
T_sym : str
|
||||
Label of symmetric tensorial stress or strain dataset.
|
||||
Name of symmetric tensorial stress or strain dataset.
|
||||
kind : {'stress', 'strain', None}, optional
|
||||
Kind of the von Mises equivalent. Defaults to None, in which case
|
||||
it is selected based on the unit of the dataset ('1' -> strain, 'Pa' -> stress).
|
||||
|
||||
Examples
|
||||
--------
|
||||
Add the Mises equivalent of the Cauchy stress 'sigma':
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r.add_equivalent_Mises('sigma')
|
||||
|
||||
Add the Mises equivalent of the spatial logarithmic strain 'epsilon_V^0.0(F)':
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r.add_equivalent_Mises('epsilon_V^0.0(F)')
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_equivalent_Mises,{'T_sym':T_sym},{'kind':kind})
|
||||
|
||||
|
|
@ -717,7 +920,7 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
x : str
|
||||
Label of vector or tensor dataset.
|
||||
Name of vector or tensor dataset.
|
||||
ord : {non-zero int, inf, -inf, 'fro', 'nuc'}, optional
|
||||
Order of the norm. inf means NumPy’s inf object. For details refer to numpy.linalg.norm.
|
||||
|
||||
|
|
@ -745,9 +948,9 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
P : str, optional
|
||||
Label of first Piola-Kirchhoff stress dataset. Defaults to 'P'.
|
||||
Name of first Piola-Kirchhoff stress dataset. Defaults to 'P'.
|
||||
F : str, optional
|
||||
Label of deformation gradient dataset. Defaults to 'F'.
|
||||
Name of deformation gradient dataset. Defaults to 'F'.
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_stress_second_Piola_Kirchhoff,{'P':P,'F':F})
|
||||
|
|
@ -786,7 +989,7 @@ class Result:
|
|||
# Parameters
|
||||
# ----------
|
||||
# q : str
|
||||
# Label of the dataset containing the crystallographic orientation as quaternions.
|
||||
# Name of the dataset containing the crystallographic orientation as quaternions.
|
||||
# p : numpy.array of shape (3)
|
||||
# Crystallographic direction or plane.
|
||||
# polar : bool, optional
|
||||
|
|
@ -813,8 +1016,16 @@ class Result:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
F : str, optional
|
||||
Label of deformation gradient dataset.
|
||||
F : str
|
||||
Name of deformation gradient dataset.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Add the rotational part of deformation gradient 'F':
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r.add_rotation('F')
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_rotation,{'F':F})
|
||||
|
|
@ -838,7 +1049,15 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
T : str
|
||||
Label of tensor dataset.
|
||||
Name of tensor dataset.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Add the hydrostatic part of the Cauchy stress 'sigma':
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r.add_spherical('sigma')
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_spherical,{'T':T})
|
||||
|
|
@ -864,13 +1083,28 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
F : str, optional
|
||||
Label of deformation gradient dataset. Defaults to 'F'.
|
||||
Name of deformation gradient dataset. Defaults to 'F'.
|
||||
t : {'V', 'U'}, optional
|
||||
Type of the polar decomposition, 'V' for left stretch tensor and 'U' for right stretch tensor.
|
||||
Defaults to 'V'.
|
||||
m : float, optional
|
||||
Order of the strain calculation. Defaults to 0.0.
|
||||
|
||||
Examples
|
||||
--------
|
||||
Add the Biot strain based on the deformation gradient 'F':
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r.strain(t='U',m=0.5)
|
||||
|
||||
Add the plastic Euler-Almansi strain based on the
|
||||
plastic deformation gradient 'F_p':
|
||||
|
||||
>>> import damask
|
||||
>>> r = damask.Result('my_file.hdf5')
|
||||
>>> r.strain('F_p','V',-1)
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_strain,{'F':F},{'t':t,'m':m})
|
||||
|
||||
|
|
@ -894,7 +1128,7 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
F : str, optional
|
||||
Label of deformation gradient dataset. Defaults to 'F'.
|
||||
Name of deformation gradient dataset. Defaults to 'F'.
|
||||
t : {'V', 'U'}, optional
|
||||
Type of the polar decomposition, 'V' for left stretch tensor and 'U' for right stretch tensor.
|
||||
Defaults to 'V'.
|
||||
|
|
@ -947,7 +1181,7 @@ class Result:
|
|||
for inc in self.visible['increments']:
|
||||
for ty in ['phase','homogenization']:
|
||||
for label in self.visible[ty+'s']:
|
||||
for field in self.visible['fields']:
|
||||
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
|
||||
group = '/'.join([inc,ty,label,field])
|
||||
if set(datasets.values()).issubset(f[group].keys()): groups.append(group)
|
||||
|
||||
|
|
@ -1001,10 +1235,14 @@ class Result:
|
|||
"""
|
||||
Write XDMF file to directly visualize data in DADF5 file.
|
||||
|
||||
The XDMF format is only supported for structured grids
|
||||
with single phase and single constituent.
|
||||
For other cases use `save_VTK`.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
output : (list of) str
|
||||
Labels of the datasets to read.
|
||||
Names of the datasets included in the XDMF file.
|
||||
Defaults to '*', in which case all datasets are considered.
|
||||
|
||||
"""
|
||||
|
|
@ -1082,7 +1320,7 @@ class Result:
|
|||
|
||||
for ty in ['phase','homogenization']:
|
||||
for label in self.visible[ty+'s']:
|
||||
for field in self.visible['fields']:
|
||||
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
|
||||
for out in _match(output,f['/'.join([inc,ty,label,field])].keys()):
|
||||
name = '/'.join([inc,ty,label,field,out])
|
||||
shape = f[name].shape[1:]
|
||||
|
|
@ -1131,10 +1369,16 @@ class Result:
|
|||
"""
|
||||
Export to VTK cell/point data.
|
||||
|
||||
One VTK file per visible increment is created.
|
||||
For cell data, the VTK format is a rectilinear grid (.vtr) for
|
||||
grid-based simulations and an unstructured grid (.vtu) for
|
||||
mesh-baed simulations. For point data, the VTK format is poly
|
||||
data (.vtp).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
output : (list of) str, optional
|
||||
Labels of the datasets to place.
|
||||
Names of the datasets included in the VTK file.
|
||||
Defaults to '*', in which case all datasets are exported.
|
||||
mode : {'cell', 'point'}
|
||||
Export in cell format or point format.
|
||||
|
|
@ -1212,7 +1456,7 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
output : (list of) str
|
||||
Labels of the datasets to read.
|
||||
Names of the datasets to read.
|
||||
Defaults to '*', in which case all datasets are read.
|
||||
flatten : bool
|
||||
Remove singular levels of the folder hierarchy.
|
||||
|
|
@ -1264,7 +1508,7 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
output : (list of) str, optional
|
||||
Labels of the datasets to place.
|
||||
Names of the datasets to read.
|
||||
Defaults to '*', in which case all datasets are placed.
|
||||
flatten : bool
|
||||
Remove singular levels of the folder hierarchy.
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ class Rotation:
|
|||
- Euler angle triplets are implemented using the Bunge convention,
|
||||
with angular ranges of [0,2π], [0,π], [0,2π].
|
||||
- The rotation angle ω is limited to the interval [0,π].
|
||||
- The real part of a quaternion is positive, Re(q) > 0
|
||||
- The real part of a quaternion is positive, Re(q) ≥ 0
|
||||
- P = -1 (as default).
|
||||
|
||||
Examples
|
||||
|
|
@ -357,7 +357,7 @@ class Rotation:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
other : Rotation or list of Rotations.
|
||||
other : damask.Rotation
|
||||
|
||||
"""
|
||||
return self.copy(rotation=np.vstack(tuple(map(lambda x:x.quaternion,
|
||||
|
|
@ -365,12 +365,28 @@ class Rotation:
|
|||
|
||||
|
||||
def flatten(self,order = 'C'):
|
||||
"""Flatten array."""
|
||||
"""
|
||||
Flatten array.
|
||||
|
||||
Returns
|
||||
-------
|
||||
flattened : damask.Rotation
|
||||
Rotation flattened to single dimension.
|
||||
|
||||
"""
|
||||
return self.copy(rotation=self.quaternion.reshape((-1,4),order=order))
|
||||
|
||||
|
||||
def reshape(self,shape,order = 'C'):
|
||||
"""Reshape array."""
|
||||
"""
|
||||
Reshape array.
|
||||
|
||||
Returns
|
||||
-------
|
||||
reshaped : damask.Rotation
|
||||
Rotation of given shape.
|
||||
|
||||
"""
|
||||
if isinstance(shape,(int,np.integer)): shape = (shape,)
|
||||
return self.copy(rotation=self.quaternion.reshape(tuple(shape)+(4,),order=order))
|
||||
|
||||
|
|
@ -387,6 +403,11 @@ class Rotation:
|
|||
Where to preferentially locate missing dimensions.
|
||||
Either 'left' or 'right' (default).
|
||||
|
||||
Returns
|
||||
-------
|
||||
broadcasted : damask.Rotation
|
||||
Rotation broadcasted to given shape.
|
||||
|
||||
"""
|
||||
if isinstance(shape,(int,np.integer)): shape = (shape,)
|
||||
return self.copy(rotation=np.broadcast_to(self.quaternion.reshape(util.shapeshifter(self.shape,shape,mode)+(4,)),
|
||||
|
|
@ -404,7 +425,7 @@ class Rotation:
|
|||
|
||||
Returns
|
||||
-------
|
||||
average : Rotation
|
||||
average : damask.Rotation
|
||||
Weighted average of original Rotation field.
|
||||
|
||||
References
|
||||
|
|
@ -438,9 +459,14 @@ class Rotation:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
other : Rotation
|
||||
other : damask.Rotation
|
||||
Rotation to which the misorientation is computed.
|
||||
|
||||
Returns
|
||||
-------
|
||||
g : damask.Rotation
|
||||
Misorientation.
|
||||
|
||||
"""
|
||||
return other*~self
|
||||
|
||||
|
|
|
|||
|
|
@ -49,7 +49,7 @@ class Table:
|
|||
|
||||
Returns
|
||||
-------
|
||||
slice : Table
|
||||
slice : damask.Table
|
||||
Sliced part of the Table.
|
||||
|
||||
Examples
|
||||
|
|
@ -157,7 +157,7 @@ class Table:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
other : Table
|
||||
other : damask.Table
|
||||
Table to compare against.
|
||||
rtol : float, optional
|
||||
Relative tolerance of equality.
|
||||
|
|
@ -185,7 +185,7 @@ class Table:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
other : Table
|
||||
other : damask.Table
|
||||
Table to compare against.
|
||||
rtol : float, optional
|
||||
Relative tolerance of equality.
|
||||
|
|
@ -223,6 +223,11 @@ class Table:
|
|||
fname : file, str, or pathlib.Path
|
||||
Filename or file for reading.
|
||||
|
||||
Returns
|
||||
-------
|
||||
loaded : damask.Table
|
||||
Table data from file.
|
||||
|
||||
"""
|
||||
try:
|
||||
f = open(fname)
|
||||
|
|
@ -275,6 +280,11 @@ class Table:
|
|||
fname : file, str, or pathlib.Path
|
||||
Filename or file for reading.
|
||||
|
||||
Returns
|
||||
-------
|
||||
loaded : damask.Table
|
||||
Table data from file.
|
||||
|
||||
"""
|
||||
try:
|
||||
f = open(fname)
|
||||
|
|
@ -334,14 +344,14 @@ class Table:
|
|||
----------
|
||||
label : str
|
||||
Column label.
|
||||
data : np.ndarray
|
||||
data : numpy.ndarray
|
||||
New data.
|
||||
info : str, optional
|
||||
Human-readable information about the new data.
|
||||
|
||||
Returns
|
||||
-------
|
||||
table : Table
|
||||
updated : damask.Table
|
||||
Updated table.
|
||||
|
||||
"""
|
||||
|
|
@ -367,14 +377,14 @@ class Table:
|
|||
----------
|
||||
label : str
|
||||
Column label.
|
||||
data : np.ndarray
|
||||
data : numpy.ndarray
|
||||
Modified data.
|
||||
info : str, optional
|
||||
Human-readable information about the modified data.
|
||||
|
||||
Returns
|
||||
-------
|
||||
table : Table
|
||||
udated : damask.Table
|
||||
Updated table.
|
||||
|
||||
"""
|
||||
|
|
@ -402,7 +412,7 @@ class Table:
|
|||
|
||||
Returns
|
||||
-------
|
||||
table : Table
|
||||
udated : damask.Table
|
||||
Updated table.
|
||||
|
||||
"""
|
||||
|
|
@ -425,7 +435,7 @@ class Table:
|
|||
|
||||
Returns
|
||||
-------
|
||||
table : Table
|
||||
udated : damask.Table
|
||||
Updated table.
|
||||
|
||||
"""
|
||||
|
|
@ -451,7 +461,7 @@ class Table:
|
|||
|
||||
Returns
|
||||
-------
|
||||
table : Table
|
||||
udated : damask.Table
|
||||
Updated table.
|
||||
|
||||
"""
|
||||
|
|
@ -479,13 +489,13 @@ class Table:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
other : Table
|
||||
other : damask.Table
|
||||
Table to append.
|
||||
|
||||
Returns
|
||||
-------
|
||||
table : Table
|
||||
Concatenated table.
|
||||
udated : damask.Table
|
||||
Updated table.
|
||||
|
||||
"""
|
||||
if self.shapes != other.shapes or not self.data.columns.equals(other.data.columns):
|
||||
|
|
@ -504,13 +514,13 @@ class Table:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
other : Table
|
||||
other : damask.Table
|
||||
Table to join.
|
||||
|
||||
Returns
|
||||
-------
|
||||
table : Table
|
||||
Joined table.
|
||||
udated : damask.Table
|
||||
Updated table.
|
||||
|
||||
"""
|
||||
if set(self.shapes) & set(other.shapes) or self.data.shape[0] != other.data.shape[0]:
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@ import multiprocessing as mp
|
|||
from pathlib import Path
|
||||
|
||||
import numpy as np
|
||||
import numpy.ma as ma
|
||||
import vtk
|
||||
from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk
|
||||
from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray
|
||||
|
|
@ -51,6 +50,11 @@ class VTK:
|
|||
origin : iterable of float, len (3), optional
|
||||
Spatial origin coordinates.
|
||||
|
||||
Returns
|
||||
-------
|
||||
new : damask.VTK
|
||||
VTK-based geometry without nodal or cell data.
|
||||
|
||||
"""
|
||||
vtk_data = vtk.vtkRectilinearGrid()
|
||||
vtk_data.SetDimensions(*(np.array(grid)+1))
|
||||
|
|
@ -68,7 +72,7 @@ class VTK:
|
|||
"""
|
||||
Create VTK of type vtk.vtkUnstructuredGrid.
|
||||
|
||||
This is the common type for FEM solver results.
|
||||
This is the common type for mesh solver results.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -80,6 +84,11 @@ class VTK:
|
|||
cell_type : str
|
||||
Name of the vtk.vtkCell subclass. Tested for TRIANGLE, QUAD, TETRA, and HEXAHEDRON.
|
||||
|
||||
Returns
|
||||
-------
|
||||
new : damask.VTK
|
||||
VTK-based geometry without nodal or cell data.
|
||||
|
||||
"""
|
||||
vtk_nodes = vtk.vtkPoints()
|
||||
vtk_nodes.SetData(np_to_vtk(nodes))
|
||||
|
|
@ -110,6 +119,11 @@ class VTK:
|
|||
points : numpy.ndarray of shape (:,3)
|
||||
Spatial position of the points.
|
||||
|
||||
Returns
|
||||
-------
|
||||
new : damask.VTK
|
||||
VTK-based geometry without nodal or cell data.
|
||||
|
||||
"""
|
||||
N = points.shape[0]
|
||||
vtk_points = vtk.vtkPoints()
|
||||
|
|
@ -137,8 +151,13 @@ class VTK:
|
|||
fname : str or pathlib.Path
|
||||
Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.
|
||||
dataset_type : str, optional
|
||||
Name of the vtk.vtkDataSet subclass when opening a .vtk file. Valid types are vtkRectilinearGrid,
|
||||
vtkUnstructuredGrid, and vtkPolyData.
|
||||
Name of the vtk.vtkDataSet subclass when opening a .vtk file.
|
||||
Valid types are vtkRectilinearGrid, vtkUnstructuredGrid, and vtkPolyData.
|
||||
|
||||
Returns
|
||||
-------
|
||||
loaded : damask.VTK
|
||||
VTK-based geometry from file.
|
||||
|
||||
"""
|
||||
if not os.path.isfile(fname): # vtk has a strange error handling
|
||||
|
|
@ -149,13 +168,13 @@ class VTK:
|
|||
reader.SetFileName(str(fname))
|
||||
if dataset_type is None:
|
||||
raise TypeError('Dataset type for *.vtk file not given.')
|
||||
elif dataset_type.lower().endswith('rectilineargrid'):
|
||||
elif dataset_type.lower().endswith(('rectilineargrid','rectilinear_grid')):
|
||||
reader.Update()
|
||||
vtk_data = reader.GetRectilinearGridOutput()
|
||||
elif dataset_type.lower().endswith('unstructuredgrid'):
|
||||
elif dataset_type.lower().endswith(('unstructuredgrid','unstructured_grid')):
|
||||
reader.Update()
|
||||
vtk_data = reader.GetUnstructuredGridOutput()
|
||||
elif dataset_type.lower().endswith('polydata'):
|
||||
elif dataset_type.lower().endswith(('polydata','poly_data')):
|
||||
reader.Update()
|
||||
vtk_data = reader.GetPolyDataOutput()
|
||||
else:
|
||||
|
|
@ -246,7 +265,7 @@ class VTK:
|
|||
raise ValueError('No label defined for numpy.ndarray')
|
||||
|
||||
N_data = data.shape[0]
|
||||
data_ = np.where(data.mask,data.fill_value,data) if isinstance(data,ma.MaskedArray) else\
|
||||
data_ = np.where(data.mask,data.fill_value,data) if isinstance(data,np.ma.MaskedArray) else\
|
||||
data
|
||||
d = np_to_vtk((data_.astype(np.single) if data_.dtype in [np.double, np.longdouble] else
|
||||
data_).reshape(N_data,-1),deep=True) # avoid large files
|
||||
|
|
@ -277,6 +296,11 @@ class VTK:
|
|||
label : str
|
||||
Data label.
|
||||
|
||||
Returns
|
||||
-------
|
||||
data : numpy.ndarray
|
||||
Data stored under the given label.
|
||||
|
||||
"""
|
||||
cell_data = self.vtk_data.GetCellData()
|
||||
for a in range(cell_data.GetNumberOfArrays()):
|
||||
|
|
|
|||
|
|
@ -1,15 +1,14 @@
|
|||
"""
|
||||
Filters for operations on regular grids.
|
||||
|
||||
Notes
|
||||
-----
|
||||
The grids are defined as (x,y,z,...) where x is fastest and z is slowest.
|
||||
This convention is consistent with the layout in grid vtr files.
|
||||
|
||||
When converting to/from a plain list (e.g. storage in ASCII table),
|
||||
the following operations are required for tensorial data:
|
||||
|
||||
D3 = D1.reshape(cells+(-1,),order='F').reshape(cells+(3,3))
|
||||
D1 = D3.reshape(cells+(-1,)).reshape(-1,9,order='F')
|
||||
- D3 = D1.reshape(cells+(-1,),order='F').reshape(cells+(3,3))
|
||||
- D1 = D3.reshape(cells+(-1,)).reshape(-1,9,order='F')
|
||||
|
||||
"""
|
||||
from scipy import spatial as _spatial
|
||||
|
|
@ -29,10 +28,12 @@ def _ks(size,cells,first_order=False):
|
|||
Correction for first order derivatives, defaults to False.
|
||||
|
||||
"""
|
||||
k_sk = _np.where(_np.arange(cells[0])>cells[0]//2,_np.arange(cells[0])-cells[0],_np.arange(cells[0]))/size[0]
|
||||
k_sk = _np.where(_np.arange(cells[0])>cells[0]//2,
|
||||
_np.arange(cells[0])-cells[0],_np.arange(cells[0]))/size[0]
|
||||
if cells[0]%2 == 0 and first_order: k_sk[cells[0]//2] = 0 # Nyquist freq=0 for even cells (Johnson, MIT, 2011)
|
||||
|
||||
k_sj = _np.where(_np.arange(cells[1])>cells[1]//2,_np.arange(cells[1])-cells[1],_np.arange(cells[1]))/size[1]
|
||||
k_sj = _np.where(_np.arange(cells[1])>cells[1]//2,
|
||||
_np.arange(cells[1])-cells[1],_np.arange(cells[1]))/size[1]
|
||||
if cells[1]%2 == 0 and first_order: k_sj[cells[1]//2] = 0 # Nyquist freq=0 for even cells (Johnson, MIT, 2011)
|
||||
|
||||
k_si = _np.arange(cells[2]//2+1)/size[2]
|
||||
|
|
@ -40,74 +41,89 @@ def _ks(size,cells,first_order=False):
|
|||
return _np.stack(_np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij'), axis=-1)
|
||||
|
||||
|
||||
def curl(size,field):
|
||||
"""
|
||||
def curl(size,f):
|
||||
u"""
|
||||
Calculate curl of a vector or tensor field in Fourier space.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
Physical size of the periodic field.
|
||||
field : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
|
||||
f : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
|
||||
Periodic field of which the curl is calculated.
|
||||
|
||||
Returns
|
||||
-------
|
||||
∇ × f : numpy.ndarray
|
||||
Curl of f.
|
||||
|
||||
"""
|
||||
n = _np.prod(field.shape[3:])
|
||||
k_s = _ks(size,field.shape[:3],True)
|
||||
n = _np.prod(f.shape[3:])
|
||||
k_s = _ks(size,f.shape[:3],True)
|
||||
|
||||
e = _np.zeros((3, 3, 3))
|
||||
e[0, 1, 2] = e[1, 2, 0] = e[2, 0, 1] = +1.0 # Levi-Civita symbol
|
||||
e[0, 2, 1] = e[2, 1, 0] = e[1, 0, 2] = -1.0
|
||||
|
||||
field_fourier = _np.fft.rfftn(field,axes=(0,1,2))
|
||||
curl_ = (_np.einsum('slm,ijkl,ijkm ->ijks', e,k_s,field_fourier)*2.0j*_np.pi if n == 3 else # vector, 3 -> 3
|
||||
_np.einsum('slm,ijkl,ijknm->ijksn',e,k_s,field_fourier)*2.0j*_np.pi) # tensor, 3x3 -> 3x3
|
||||
f_fourier = _np.fft.rfftn(f,axes=(0,1,2))
|
||||
curl_ = (_np.einsum('slm,ijkl,ijkm ->ijks', e,k_s,f_fourier)*2.0j*_np.pi if n == 3 else # vector, 3 -> 3
|
||||
_np.einsum('slm,ijkl,ijknm->ijksn',e,k_s,f_fourier)*2.0j*_np.pi) # tensor, 3x3 -> 3x3
|
||||
|
||||
return _np.fft.irfftn(curl_,axes=(0,1,2),s=field.shape[:3])
|
||||
return _np.fft.irfftn(curl_,axes=(0,1,2),s=f.shape[:3])
|
||||
|
||||
|
||||
def divergence(size,field):
|
||||
"""
|
||||
def divergence(size,f):
|
||||
u"""
|
||||
Calculate divergence of a vector or tensor field in Fourier space.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
Physical size of the periodic field.
|
||||
field : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
|
||||
f : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
|
||||
Periodic field of which the divergence is calculated.
|
||||
|
||||
Returns
|
||||
-------
|
||||
∇ · f : numpy.ndarray
|
||||
Divergence of f.
|
||||
|
||||
"""
|
||||
n = _np.prod(field.shape[3:])
|
||||
k_s = _ks(size,field.shape[:3],True)
|
||||
n = _np.prod(f.shape[3:])
|
||||
k_s = _ks(size,f.shape[:3],True)
|
||||
|
||||
field_fourier = _np.fft.rfftn(field,axes=(0,1,2))
|
||||
div_ = (_np.einsum('ijkl,ijkl ->ijk', k_s,field_fourier)*2.0j*_np.pi if n == 3 else # vector, 3 -> 1
|
||||
_np.einsum('ijkm,ijklm->ijkl',k_s,field_fourier)*2.0j*_np.pi) # tensor, 3x3 -> 3
|
||||
f_fourier = _np.fft.rfftn(f,axes=(0,1,2))
|
||||
div_ = (_np.einsum('ijkl,ijkl ->ijk', k_s,f_fourier)*2.0j*_np.pi if n == 3 else # vector, 3 -> 1
|
||||
_np.einsum('ijkm,ijklm->ijkl',k_s,f_fourier)*2.0j*_np.pi) # tensor, 3x3 -> 3
|
||||
|
||||
return _np.fft.irfftn(div_,axes=(0,1,2),s=field.shape[:3])
|
||||
return _np.fft.irfftn(div_,axes=(0,1,2),s=f.shape[:3])
|
||||
|
||||
|
||||
def gradient(size,field):
|
||||
"""
|
||||
Calculate gradient of a scalar or vector field in Fourier space.
|
||||
def gradient(size,f):
|
||||
u"""
|
||||
Calculate gradient of a scalar or vector fieldin Fourier space.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
Physical size of the periodic field.
|
||||
field : numpy.ndarray of shape (:,:,:,1) or (:,:,:,3)
|
||||
f : numpy.ndarray of shape (:,:,:,1) or (:,:,:,3)
|
||||
Periodic field of which the gradient is calculated.
|
||||
|
||||
Returns
|
||||
-------
|
||||
∇ f : numpy.ndarray
|
||||
Divergence of f.
|
||||
|
||||
"""
|
||||
n = _np.prod(field.shape[3:])
|
||||
k_s = _ks(size,field.shape[:3],True)
|
||||
n = _np.prod(f.shape[3:])
|
||||
k_s = _ks(size,f.shape[:3],True)
|
||||
|
||||
field_fourier = _np.fft.rfftn(field,axes=(0,1,2))
|
||||
grad_ = (_np.einsum('ijkl,ijkm->ijkm', field_fourier,k_s)*2.0j*_np.pi if n == 1 else # scalar, 1 -> 3
|
||||
_np.einsum('ijkl,ijkm->ijklm',field_fourier,k_s)*2.0j*_np.pi) # vector, 3 -> 3x3
|
||||
f_fourier = _np.fft.rfftn(f,axes=(0,1,2))
|
||||
grad_ = (_np.einsum('ijkl,ijkm->ijkm', f_fourier,k_s)*2.0j*_np.pi if n == 1 else # scalar, 1 -> 3
|
||||
_np.einsum('ijkl,ijkm->ijklm',f_fourier,k_s)*2.0j*_np.pi) # vector, 3 -> 3x3
|
||||
|
||||
return _np.fft.irfftn(grad_,axes=(0,1,2),s=field.shape[:3])
|
||||
return _np.fft.irfftn(grad_,axes=(0,1,2),s=f.shape[:3])
|
||||
|
||||
|
||||
def coordinates0_point(cells,size,origin=_np.zeros(3)):
|
||||
|
|
@ -123,6 +139,11 @@ def coordinates0_point(cells,size,origin=_np.zeros(3)):
|
|||
origin : numpy.ndarray, optional
|
||||
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
|
||||
Returns
|
||||
-------
|
||||
x_p_0 : numpy.ndarray
|
||||
Undeformed cell center coordinates.
|
||||
|
||||
"""
|
||||
start = origin + size/cells*.5
|
||||
end = origin + size - size/cells*.5
|
||||
|
|
@ -144,6 +165,11 @@ def displacement_fluct_point(size,F):
|
|||
F : numpy.ndarray
|
||||
Deformation gradient field.
|
||||
|
||||
Returns
|
||||
-------
|
||||
u_p_fluct : numpy.ndarray
|
||||
Fluctuating part of the cell center displacements.
|
||||
|
||||
"""
|
||||
integrator = 0.5j*size/_np.pi
|
||||
|
||||
|
|
@ -171,6 +197,11 @@ def displacement_avg_point(size,F):
|
|||
F : numpy.ndarray
|
||||
Deformation gradient field.
|
||||
|
||||
Returns
|
||||
-------
|
||||
u_p_avg : numpy.ndarray
|
||||
Average part of the cell center displacements.
|
||||
|
||||
"""
|
||||
F_avg = _np.average(F,axis=(0,1,2))
|
||||
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_point(F.shape[:3],size))
|
||||
|
|
@ -187,6 +218,11 @@ def displacement_point(size,F):
|
|||
F : numpy.ndarray
|
||||
Deformation gradient field.
|
||||
|
||||
Returns
|
||||
-------
|
||||
u_p : numpy.ndarray
|
||||
Cell center displacements.
|
||||
|
||||
"""
|
||||
return displacement_avg_point(size,F) + displacement_fluct_point(size,F)
|
||||
|
||||
|
|
@ -204,6 +240,11 @@ def coordinates_point(size,F,origin=_np.zeros(3)):
|
|||
origin : numpy.ndarray of shape (3), optional
|
||||
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
|
||||
Returns
|
||||
-------
|
||||
x_p : numpy.ndarray
|
||||
Cell center coordinates.
|
||||
|
||||
"""
|
||||
return coordinates0_point(F.shape[:3],size,origin) + displacement_point(size,F)
|
||||
|
||||
|
|
@ -220,6 +261,11 @@ def cellsSizeOrigin_coordinates0_point(coordinates0,ordered=True):
|
|||
Expect coordinates0 data to be ordered (x fast, z slow).
|
||||
Defaults to True.
|
||||
|
||||
Returns
|
||||
-------
|
||||
cells, size, origin : Three numpy.ndarray, each of shape (3)
|
||||
Information to reconstruct grid.
|
||||
|
||||
"""
|
||||
coords = [_np.unique(coordinates0[:,i]) for i in range(3)]
|
||||
mincorner = _np.array(list(map(min,coords)))
|
||||
|
|
@ -252,19 +298,6 @@ def cellsSizeOrigin_coordinates0_point(coordinates0,ordered=True):
|
|||
return (cells,size,origin)
|
||||
|
||||
|
||||
def coordinates0_check(coordinates0):
|
||||
"""
|
||||
Check whether coordinates lie on a regular grid.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
coordinates0 : numpy.ndarray
|
||||
Array of undeformed cell coordinates.
|
||||
|
||||
"""
|
||||
cellsSizeOrigin_coordinates0_point(coordinates0,ordered=True)
|
||||
|
||||
|
||||
def coordinates0_node(cells,size,origin=_np.zeros(3)):
|
||||
"""
|
||||
Nodal positions (undeformed).
|
||||
|
|
@ -278,6 +311,11 @@ def coordinates0_node(cells,size,origin=_np.zeros(3)):
|
|||
origin : numpy.ndarray of shape (3), optional
|
||||
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
|
||||
Returns
|
||||
-------
|
||||
x_n_0 : numpy.ndarray
|
||||
Undeformed nodal coordinates.
|
||||
|
||||
"""
|
||||
return _np.stack(_np.meshgrid(_np.linspace(origin[0],size[0]+origin[0],cells[0]+1),
|
||||
_np.linspace(origin[1],size[1]+origin[1],cells[1]+1),
|
||||
|
|
@ -296,6 +334,11 @@ def displacement_fluct_node(size,F):
|
|||
F : numpy.ndarray
|
||||
Deformation gradient field.
|
||||
|
||||
Returns
|
||||
-------
|
||||
u_n_fluct : numpy.ndarray
|
||||
Fluctuating part of the nodal displacements.
|
||||
|
||||
"""
|
||||
return point_to_node(displacement_fluct_point(size,F))
|
||||
|
||||
|
|
@ -311,6 +354,11 @@ def displacement_avg_node(size,F):
|
|||
F : numpy.ndarray
|
||||
Deformation gradient field.
|
||||
|
||||
Returns
|
||||
-------
|
||||
u_n_avg : numpy.ndarray
|
||||
Average part of the nodal displacements.
|
||||
|
||||
"""
|
||||
F_avg = _np.average(F,axis=(0,1,2))
|
||||
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_node(F.shape[:3],size))
|
||||
|
|
@ -327,6 +375,11 @@ def displacement_node(size,F):
|
|||
F : numpy.ndarray
|
||||
Deformation gradient field.
|
||||
|
||||
Returns
|
||||
-------
|
||||
u_p : numpy.ndarray
|
||||
Nodal displacements.
|
||||
|
||||
"""
|
||||
return displacement_avg_node(size,F) + displacement_fluct_node(size,F)
|
||||
|
||||
|
|
@ -344,28 +397,15 @@ def coordinates_node(size,F,origin=_np.zeros(3)):
|
|||
origin : numpy.ndarray of shape (3), optional
|
||||
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
|
||||
Returns
|
||||
-------
|
||||
x_n : numpy.ndarray
|
||||
Nodal coordinates.
|
||||
|
||||
"""
|
||||
return coordinates0_node(F.shape[:3],size,origin) + displacement_node(size,F)
|
||||
|
||||
|
||||
def point_to_node(cell_data):
|
||||
"""Interpolate periodic point data to nodal data."""
|
||||
n = ( cell_data + _np.roll(cell_data,1,(0,1,2))
|
||||
+ _np.roll(cell_data,1,(0,)) + _np.roll(cell_data,1,(1,)) + _np.roll(cell_data,1,(2,))
|
||||
+ _np.roll(cell_data,1,(0,1)) + _np.roll(cell_data,1,(1,2)) + _np.roll(cell_data,1,(2,0)))*0.125
|
||||
|
||||
return _np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
|
||||
|
||||
|
||||
def node_2_point(node_data):
|
||||
"""Interpolate periodic nodal data to point data."""
|
||||
c = ( node_data + _np.roll(node_data,1,(0,1,2))
|
||||
+ _np.roll(node_data,1,(0,)) + _np.roll(node_data,1,(1,)) + _np.roll(node_data,1,(2,))
|
||||
+ _np.roll(node_data,1,(0,1)) + _np.roll(node_data,1,(1,2)) + _np.roll(node_data,1,(2,0)))*0.125
|
||||
|
||||
return c[1:,1:,1:]
|
||||
|
||||
|
||||
def cellsSizeOrigin_coordinates0_node(coordinates0,ordered=True):
|
||||
"""
|
||||
Return grid 'DNA', i.e. cells, size, and origin from 1D array of nodal positions.
|
||||
|
|
@ -378,6 +418,11 @@ def cellsSizeOrigin_coordinates0_node(coordinates0,ordered=True):
|
|||
Expect coordinates0 data to be ordered (x fast, z slow).
|
||||
Defaults to True.
|
||||
|
||||
Returns
|
||||
-------
|
||||
cells, size, origin : Three numpy.ndarray, each of shape (3)
|
||||
Information to reconstruct grid.
|
||||
|
||||
"""
|
||||
coords = [_np.unique(coordinates0[:,i]) for i in range(3)]
|
||||
mincorner = _np.array(list(map(min,coords)))
|
||||
|
|
@ -402,6 +447,72 @@ def cellsSizeOrigin_coordinates0_node(coordinates0,ordered=True):
|
|||
return (cells,size,origin)
|
||||
|
||||
|
||||
def point_to_node(cell_data):
|
||||
"""
|
||||
Interpolate periodic point data to nodal data.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
cell_data : numpy.ndarray of shape (:,:,:,...)
|
||||
Data defined on the cell centers of a periodic grid.
|
||||
|
||||
Returns
|
||||
-------
|
||||
node_data : numpy.ndarray of shape (:,:,:,...)
|
||||
Data defined on the nodes of a periodic grid.
|
||||
|
||||
"""
|
||||
n = ( cell_data + _np.roll(cell_data,1,(0,1,2))
|
||||
+ _np.roll(cell_data,1,(0,)) + _np.roll(cell_data,1,(1,)) + _np.roll(cell_data,1,(2,))
|
||||
+ _np.roll(cell_data,1,(0,1)) + _np.roll(cell_data,1,(1,2)) + _np.roll(cell_data,1,(2,0)))*0.125
|
||||
|
||||
return _np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
|
||||
|
||||
|
||||
def node_to_point(node_data):
|
||||
"""
|
||||
Interpolate periodic nodal data to point data.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
node_data : numpy.ndarray of shape (:,:,:,...)
|
||||
Data defined on the nodes of a periodic grid.
|
||||
|
||||
Returns
|
||||
-------
|
||||
cell_data : numpy.ndarray of shape (:,:,:,...)
|
||||
Data defined on the cell centers of a periodic grid.
|
||||
|
||||
"""
|
||||
c = ( node_data + _np.roll(node_data,1,(0,1,2))
|
||||
+ _np.roll(node_data,1,(0,)) + _np.roll(node_data,1,(1,)) + _np.roll(node_data,1,(2,))
|
||||
+ _np.roll(node_data,1,(0,1)) + _np.roll(node_data,1,(1,2)) + _np.roll(node_data,1,(2,0)))*0.125
|
||||
|
||||
return c[1:,1:,1:]
|
||||
|
||||
|
||||
def coordinates0_valid(coordinates0):
|
||||
"""
|
||||
Check whether coordinates lie on a regular grid.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
coordinates0 : numpy.ndarray
|
||||
Array of undeformed cell coordinates.
|
||||
|
||||
Returns
|
||||
-------
|
||||
valid : bool
|
||||
Wheter the coordinates lie on a regular grid.
|
||||
|
||||
"""
|
||||
try:
|
||||
cellsSizeOrigin_coordinates0_point(coordinates0,ordered=True)
|
||||
return True
|
||||
except ValueError:
|
||||
return False
|
||||
|
||||
|
||||
def regrid(size,F,cells):
|
||||
"""
|
||||
Return mapping from coordinates in deformed configuration to a regular grid.
|
||||
|
|
|
|||
|
|
@ -1,4 +1,9 @@
|
|||
"""Finite-strain continuum mechanics."""
|
||||
"""
|
||||
Finite-strain continuum mechanics.
|
||||
|
||||
All routines operate on numpy.ndarrays of shape (...,3,3).
|
||||
|
||||
"""
|
||||
|
||||
from . import tensor as _tensor
|
||||
from . import _rotation
|
||||
|
|
@ -154,7 +159,6 @@ def strain(F,t,m):
|
|||
return eps
|
||||
|
||||
|
||||
|
||||
def stress_Cauchy(P,F):
|
||||
"""
|
||||
Calculate the Cauchy stress (true stress).
|
||||
|
|
|
|||
|
|
@ -24,6 +24,11 @@ def from_random(size,N_seeds,cells=None,rng_seed=None):
|
|||
A seed to initialize the BitGenerator. Defaults to None.
|
||||
If None, then fresh, unpredictable entropy will be pulled from the OS.
|
||||
|
||||
Returns
|
||||
-------
|
||||
coords : numpy.ndarray of shape (N_seeds,3)
|
||||
Seed coordinates in 3D space.
|
||||
|
||||
"""
|
||||
rng = _np.random.default_rng(rng_seed)
|
||||
if cells is None:
|
||||
|
|
@ -56,6 +61,11 @@ def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,rng_seed=
|
|||
A seed to initialize the BitGenerator. Defaults to None.
|
||||
If None, then fresh, unpredictable entropy will be pulled from the OS.
|
||||
|
||||
Returns
|
||||
-------
|
||||
coords : numpy.ndarray of shape (N_seeds,3)
|
||||
Seed coordinates in 3D space.
|
||||
|
||||
"""
|
||||
rng = _np.random.default_rng(rng_seed)
|
||||
coords = _np.empty((N_seeds,3))
|
||||
|
|
@ -94,6 +104,11 @@ def from_grid(grid,selection=None,invert=False,average=False,periodic=True):
|
|||
periodic : boolean, optional
|
||||
Center of gravity with periodic boundaries.
|
||||
|
||||
Returns
|
||||
-------
|
||||
coords, materials : numpy.ndarray of shape (:,3), numpy.ndarray of shape (:)
|
||||
Seed coordinates in 3D space, material IDs.
|
||||
|
||||
"""
|
||||
material = grid.material.reshape((-1,1),order='F')
|
||||
mask = _np.full(grid.cells.prod(),True,dtype=bool) if selection is None else \
|
||||
|
|
|
|||
|
|
@ -1,3 +1,3 @@
|
|||
"""Tools to control the various solvers."""
|
||||
"""Run simulations directly from python."""
|
||||
|
||||
from ._marc import Marc # noqa
|
||||
|
|
|
|||
|
|
@ -1,10 +1,7 @@
|
|||
"""
|
||||
Tensor operations.
|
||||
Tensor mathematics.
|
||||
|
||||
Notes
|
||||
-----
|
||||
This is not a tensor class, but a collection of routines
|
||||
to operate on numpy.ndarrays of shape (...,3,3).
|
||||
All routines operate on numpy.ndarrays of shape (...,3,3).
|
||||
|
||||
"""
|
||||
|
||||
|
|
|
|||
|
|
@ -49,7 +49,7 @@ _colors = {
|
|||
####################################################################################################
|
||||
def srepr(arg,glue = '\n'):
|
||||
r"""
|
||||
Join arguments with glue string.
|
||||
Join items with glue string.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -58,6 +58,11 @@ def srepr(arg,glue = '\n'):
|
|||
glue : str, optional
|
||||
Glue used for joining operation. Defaults to \n.
|
||||
|
||||
Returns
|
||||
-------
|
||||
joined : str
|
||||
String representation of the joined items.
|
||||
|
||||
"""
|
||||
if (not hasattr(arg, 'strip') and
|
||||
(hasattr(arg, '__getitem__') or
|
||||
|
|
@ -68,19 +73,71 @@ def srepr(arg,glue = '\n'):
|
|||
|
||||
|
||||
def emph(what):
|
||||
"""Formats string with emphasis."""
|
||||
"""
|
||||
Format with emphasis.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
-------
|
||||
formatted : str
|
||||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['bold']+srepr(what)+_colors['end_color']
|
||||
|
||||
def deemph(what):
|
||||
"""Formats string with deemphasis."""
|
||||
"""
|
||||
Format with deemphasis.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
-------
|
||||
formatted : str
|
||||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['dim']+srepr(what)+_colors['end_color']
|
||||
|
||||
def warn(what):
|
||||
"""Formats string for warning."""
|
||||
"""
|
||||
Format for warning.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
-------
|
||||
formatted : str
|
||||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['warning']+emph(what)+_colors['end_color']
|
||||
|
||||
def strikeout(what):
|
||||
"""Formats string as strikeout."""
|
||||
"""
|
||||
Format as strikeout.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
-------
|
||||
formatted : str
|
||||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['crossout']+srepr(what)+_colors['end_color']
|
||||
|
||||
|
||||
|
|
@ -97,6 +154,11 @@ def execute(cmd,wd='./',env=None):
|
|||
env : dict, optional
|
||||
Environment for execution.
|
||||
|
||||
Returns
|
||||
-------
|
||||
stdout, stderr : str
|
||||
Output of the executed command.
|
||||
|
||||
"""
|
||||
print(f"executing '{cmd}' in '{wd}'")
|
||||
process = subprocess.run(shlex.split(cmd),
|
||||
|
|
@ -157,6 +219,11 @@ def scale_to_coprime(v):
|
|||
v : numpy.ndarray of shape (:)
|
||||
Vector to scale.
|
||||
|
||||
Returns
|
||||
-------
|
||||
m : numpy.ndarray of shape (:)
|
||||
Vector scaled to co-prime numbers.
|
||||
|
||||
"""
|
||||
MAX_DENOMINATOR = 1000000
|
||||
|
||||
|
|
@ -371,9 +438,14 @@ def DREAM3D_base_group(fname):
|
|||
|
||||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
fname : str or pathlib.Path
|
||||
Filename of the DREAM.3D (HDF5) file.
|
||||
|
||||
Returns
|
||||
-------
|
||||
path : str
|
||||
Path to the base group.
|
||||
|
||||
"""
|
||||
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)
|
||||
|
|
@ -393,9 +465,14 @@ def DREAM3D_cell_data_group(fname):
|
|||
|
||||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
fname : str or pathlib.Path
|
||||
Filename of the DREAM.3D (HDF5) file.
|
||||
|
||||
Returns
|
||||
-------
|
||||
path : str
|
||||
Path to the cell data group.
|
||||
|
||||
"""
|
||||
base_group = DREAM3D_base_group(fname)
|
||||
with h5py.File(fname,'r') as f:
|
||||
|
|
|
|||
|
|
@ -271,7 +271,7 @@ class TestResult:
|
|||
|
||||
@pytest.mark.parametrize('overwrite',['off','on'])
|
||||
def test_add_overwrite(self,default,overwrite):
|
||||
last = default.view('times',default.times_in_range(0,np.inf)[-1])
|
||||
last = default.view('increments',-1)
|
||||
|
||||
last.add_stress_Cauchy()
|
||||
|
||||
|
|
@ -279,9 +279,9 @@ class TestResult:
|
|||
created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
|
||||
|
||||
if overwrite == 'on':
|
||||
last = last.allow_modification()
|
||||
last = last.modification_enable()
|
||||
else:
|
||||
last = last.disallow_modification()
|
||||
last = last.modification_disable()
|
||||
|
||||
time.sleep(2.)
|
||||
try:
|
||||
|
|
@ -301,14 +301,24 @@ class TestResult:
|
|||
def test_rename(self,default,allowed):
|
||||
if allowed == 'on':
|
||||
F = default.place('F')
|
||||
default = default.allow_modification()
|
||||
default = default.modification_enable()
|
||||
default.rename('F','new_name')
|
||||
assert np.all(F == default.place('new_name'))
|
||||
default = default.disallow_modification()
|
||||
default = default.modification_disable()
|
||||
|
||||
with pytest.raises(PermissionError):
|
||||
default.rename('P','another_new_name')
|
||||
|
||||
@pytest.mark.parametrize('allowed',['off','on'])
|
||||
def test_remove(self,default,allowed):
|
||||
if allowed == 'on':
|
||||
unsafe = default.modification_enable()
|
||||
unsafe.remove('F')
|
||||
assert unsafe.get('F') is None
|
||||
else:
|
||||
with pytest.raises(PermissionError):
|
||||
default.remove('F')
|
||||
|
||||
@pytest.mark.parametrize('mode',['cell','node'])
|
||||
def test_coordinates(self,default,mode):
|
||||
if mode == 'cell':
|
||||
|
|
|
|||
|
|
@ -60,7 +60,7 @@ class TestGridFilters:
|
|||
cell_field_x = np.interp(coordinates0_point_x,coordinates_node_x,node_field_x,period=np.pi*2.)
|
||||
cell_field = np.broadcast_to(cell_field_x.reshape(-1,1,1),cells)
|
||||
|
||||
assert np.allclose(cell_field,grid_filters.node_2_point(node_field))
|
||||
assert np.allclose(cell_field,grid_filters.node_to_point(node_field))
|
||||
|
||||
@pytest.mark.parametrize('mode',['point','node'])
|
||||
def test_coordinates0_origin(self,mode):
|
||||
|
|
@ -93,14 +93,24 @@ class TestGridFilters:
|
|||
F = np.broadcast_to(np.random.random((3,3)), tuple(cells)+(3,3))
|
||||
assert np.allclose(function(size,F),0.0)
|
||||
|
||||
@pytest.mark.parametrize('function',[grid_filters.coordinates0_check,
|
||||
grid_filters.cellsSizeOrigin_coordinates0_node,
|
||||
grid_filters.cellsSizeOrigin_coordinates0_point])
|
||||
@pytest.mark.parametrize('function',[grid_filters.cellsSizeOrigin_coordinates0_point,
|
||||
grid_filters.cellsSizeOrigin_coordinates0_node])
|
||||
def test_invalid_coordinates(self,function):
|
||||
invalid_coordinates = np.random.random((np.random.randint(12,52),3))
|
||||
with pytest.raises(ValueError):
|
||||
function(invalid_coordinates)
|
||||
|
||||
@pytest.mark.parametrize('function',[grid_filters.coordinates0_point,
|
||||
grid_filters.coordinates0_node])
|
||||
def test_valid_coordinates_check(self,function):
|
||||
valid_coordinates = function(np.random.randint(4,10,(3)),np.random.rand(3))
|
||||
assert grid_filters.coordinates0_valid(valid_coordinates.reshape(-1,3,order='F'))
|
||||
|
||||
def test_invalid_coordinates_check(self):
|
||||
invalid_coordinates = np.random.random((np.random.randint(12,52),3))
|
||||
assert not grid_filters.coordinates0_valid(invalid_coordinates)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('function',[grid_filters.cellsSizeOrigin_coordinates0_node,
|
||||
grid_filters.cellsSizeOrigin_coordinates0_point])
|
||||
def test_uneven_spaced_coordinates(self,function):
|
||||
|
|
|
|||
|
|
@ -40,7 +40,6 @@
|
|||
#include "phase_damage_isobrittle.f90"
|
||||
#include "phase_damage_isoductile.f90"
|
||||
#include "phase_damage_anisobrittle.f90"
|
||||
#include "phase_damage_anisoductile.f90"
|
||||
#include "homogenization.f90"
|
||||
#include "homogenization_mechanical.f90"
|
||||
#include "homogenization_mechanical_pass.f90"
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ module material
|
|||
integer, dimension(:,:), allocatable, public, protected :: & ! (constituent,elem)
|
||||
material_phaseAt, & !< phase ID of each element
|
||||
material_phaseID, & !< per (constituent,cell)
|
||||
material_phaseEntry !< per (constituent,cell
|
||||
material_phaseEntry !< per (constituent,cell)
|
||||
integer, dimension(:,:,:), allocatable, public, protected :: & ! (constituent,IP,elem)
|
||||
material_phaseMemberAt !< position of the element within its phase instance
|
||||
|
||||
|
|
|
|||
|
|
@ -12,8 +12,7 @@ submodule(phase) damage
|
|||
DAMAGE_UNDEFINED_ID, &
|
||||
DAMAGE_ISOBRITTLE_ID, &
|
||||
DAMAGE_ISODUCTILE_ID, &
|
||||
DAMAGE_ANISOBRITTLE_ID, &
|
||||
DAMAGE_ANISODUCTILE_ID
|
||||
DAMAGE_ANISOBRITTLE_ID
|
||||
end enum
|
||||
|
||||
|
||||
|
|
@ -34,10 +33,6 @@ submodule(phase) damage
|
|||
logical, dimension(:), allocatable :: mySources
|
||||
end function anisobrittle_init
|
||||
|
||||
module function anisoductile_init() result(mySources)
|
||||
logical, dimension(:), allocatable :: mySources
|
||||
end function anisoductile_init
|
||||
|
||||
module function isobrittle_init() result(mySources)
|
||||
logical, dimension(:), allocatable :: mySources
|
||||
end function isobrittle_init
|
||||
|
|
@ -62,10 +57,6 @@ submodule(phase) damage
|
|||
S
|
||||
end subroutine anisobrittle_dotState
|
||||
|
||||
module subroutine anisoductile_dotState(ph,me)
|
||||
integer, intent(in) :: ph,me
|
||||
end subroutine anisoductile_dotState
|
||||
|
||||
module subroutine isoductile_dotState(ph,me)
|
||||
integer, intent(in) :: ph,me
|
||||
end subroutine isoductile_dotState
|
||||
|
|
@ -75,11 +66,6 @@ submodule(phase) damage
|
|||
character(len=*), intent(in) :: group
|
||||
end subroutine anisobrittle_results
|
||||
|
||||
module subroutine anisoductile_results(phase,group)
|
||||
integer, intent(in) :: phase
|
||||
character(len=*), intent(in) :: group
|
||||
end subroutine anisoductile_results
|
||||
|
||||
module subroutine isobrittle_results(phase,group)
|
||||
integer, intent(in) :: phase
|
||||
character(len=*), intent(in) :: group
|
||||
|
|
@ -146,7 +132,6 @@ module subroutine damage_init
|
|||
where(isobrittle_init() ) phase_source = DAMAGE_ISOBRITTLE_ID
|
||||
where(isoductile_init() ) phase_source = DAMAGE_ISODUCTILE_ID
|
||||
where(anisobrittle_init()) phase_source = DAMAGE_ANISOBRITTLE_ID
|
||||
where(anisoductile_init()) phase_source = DAMAGE_ANISODUCTILE_ID
|
||||
endif
|
||||
|
||||
end subroutine damage_init
|
||||
|
|
@ -171,7 +156,7 @@ module function phase_f_phi(phi,co,ce) result(f)
|
|||
en = material_phaseEntry(co,ce)
|
||||
|
||||
select case(phase_source(ph))
|
||||
case(DAMAGE_ISOBRITTLE_ID,DAMAGE_ISODUCTILE_ID,DAMAGE_ANISOBRITTLE_ID,DAMAGE_ANISODUCTILE_ID)
|
||||
case(DAMAGE_ISOBRITTLE_ID,DAMAGE_ISODUCTILE_ID,DAMAGE_ANISOBRITTLE_ID)
|
||||
f = 1.0_pReal &
|
||||
- phi*damageState(ph)%state(1,en)
|
||||
case default
|
||||
|
|
@ -304,9 +289,6 @@ module subroutine damage_results(group,ph)
|
|||
case (DAMAGE_ANISOBRITTLE_ID) sourceType
|
||||
call anisobrittle_results(ph,group//'damage/')
|
||||
|
||||
case (DAMAGE_ANISODUCTILE_ID) sourceType
|
||||
call anisoductile_results(ph,group//'damage/')
|
||||
|
||||
end select sourceType
|
||||
|
||||
end subroutine damage_results
|
||||
|
|
@ -332,9 +314,6 @@ function phase_damage_collectDotState(ph,me) result(broken)
|
|||
case (DAMAGE_ISODUCTILE_ID) sourceType
|
||||
call isoductile_dotState(ph,me)
|
||||
|
||||
case (DAMAGE_ANISODUCTILE_ID) sourceType
|
||||
call anisoductile_dotState(ph,me)
|
||||
|
||||
case (DAMAGE_ANISOBRITTLE_ID) sourceType
|
||||
call anisobrittle_dotState(mechanical_S(ph,me), ph,me) ! correct stress?
|
||||
|
||||
|
|
|
|||
|
|
@ -1,138 +0,0 @@
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
!> @author Luv Sharma, Max-Planck-Institut für Eisenforschung GmbH
|
||||
!> @author Pratheek Shanthraj, Max-Planck-Institut für Eisenforschung GmbH
|
||||
!> @brief material subroutine incorporating anisotropic ductile damage source mechanism
|
||||
!> @details to be done
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
submodule(phase:damage) anisoductile
|
||||
|
||||
type :: tParameters !< container type for internal constitutive parameters
|
||||
real(pReal) :: &
|
||||
q !< damage rate sensitivity
|
||||
real(pReal), dimension(:), allocatable :: &
|
||||
gamma_crit !< critical plastic strain per slip system
|
||||
character(len=pStringLen), allocatable, dimension(:) :: &
|
||||
output
|
||||
end type tParameters
|
||||
|
||||
type(tParameters), dimension(:), allocatable :: param !< containers of constitutive parameters
|
||||
|
||||
contains
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief module initialization
|
||||
!> @details reads in material parameters, allocates arrays, and does sanity checks
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module function anisoductile_init() result(mySources)
|
||||
|
||||
logical, dimension(:), allocatable :: mySources
|
||||
|
||||
class(tNode), pointer :: &
|
||||
phases, &
|
||||
phase, &
|
||||
mech, &
|
||||
pl, &
|
||||
sources, &
|
||||
src
|
||||
integer :: Ninstances,Nmembers,ph
|
||||
integer, dimension(:), allocatable :: N_sl
|
||||
character(len=pStringLen) :: extmsg = ''
|
||||
|
||||
|
||||
mySources = source_active('anisoductile')
|
||||
if(count(mySources) == 0) return
|
||||
|
||||
print'(/,a)', ' <<<+- phase:damage:anisoductile init -+>>>'
|
||||
print'(a,i0)', ' # phases: ',count(mySources); flush(IO_STDOUT)
|
||||
|
||||
|
||||
phases => config_material%get('phase')
|
||||
allocate(param(phases%length))
|
||||
|
||||
do ph = 1, phases%length
|
||||
if(mySources(ph)) then
|
||||
phase => phases%get(ph)
|
||||
mech => phase%get('mechanical')
|
||||
pl => mech%get('plastic')
|
||||
sources => phase%get('damage')
|
||||
|
||||
|
||||
associate(prm => param(ph))
|
||||
src => sources%get(1)
|
||||
|
||||
N_sl = pl%get_as1dInt('N_sl',defaultVal=emptyIntArray)
|
||||
prm%q = src%get_asFloat('q')
|
||||
prm%gamma_crit = src%get_as1dFloat('gamma_crit',requiredSize=size(N_sl))
|
||||
|
||||
! expand: family => system
|
||||
prm%gamma_crit = math_expand(prm%gamma_crit,N_sl)
|
||||
|
||||
#if defined (__GFORTRAN__)
|
||||
prm%output = output_as1dString(src)
|
||||
#else
|
||||
prm%output = src%get_as1dString('output',defaultVal=emptyStringArray)
|
||||
#endif
|
||||
|
||||
! sanity checks
|
||||
if (prm%q <= 0.0_pReal) extmsg = trim(extmsg)//' q'
|
||||
if (any(prm%gamma_crit < 0.0_pReal)) extmsg = trim(extmsg)//' gamma_crit'
|
||||
|
||||
Nmembers=count(material_phaseID==ph)
|
||||
call phase_allocateState(damageState(ph),Nmembers,1,1,0)
|
||||
damageState(ph)%atol = src%get_asFloat('anisoDuctile_atol',defaultVal=1.0e-3_pReal)
|
||||
if(any(damageState(ph)%atol < 0.0_pReal)) extmsg = trim(extmsg)//' anisoductile_atol'
|
||||
|
||||
end associate
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! exit if any parameter is out of range
|
||||
if (extmsg /= '') call IO_error(211,ext_msg=trim(extmsg)//'(damage_anisoDuctile)')
|
||||
endif
|
||||
|
||||
enddo
|
||||
|
||||
|
||||
end function anisoductile_init
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief calculates derived quantities from state
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module subroutine anisoductile_dotState(ph,me)
|
||||
|
||||
integer, intent(in) :: &
|
||||
ph, &
|
||||
me
|
||||
|
||||
|
||||
associate(prm => param(ph))
|
||||
damageState(ph)%dotState(1,me) = sum(plasticState(ph)%slipRate(:,me)/(damage_phi(ph,me)**prm%q)/prm%gamma_crit)
|
||||
end associate
|
||||
|
||||
end subroutine anisoductile_dotState
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief writes results to HDF5 output file
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module subroutine anisoductile_results(phase,group)
|
||||
|
||||
integer, intent(in) :: phase
|
||||
character(len=*), intent(in) :: group
|
||||
|
||||
integer :: o
|
||||
|
||||
|
||||
associate(prm => param(phase), stt => damageState(phase)%state)
|
||||
outputsLoop: do o = 1,size(prm%output)
|
||||
select case(trim(prm%output(o)))
|
||||
case ('f_phi')
|
||||
call results_writeDataset(group,stt,trim(prm%output(o)),'driving force','J/m³')
|
||||
end select
|
||||
enddo outputsLoop
|
||||
end associate
|
||||
|
||||
end subroutine anisoductile_results
|
||||
|
||||
end submodule anisoductile
|
||||
|
|
@ -190,7 +190,7 @@ end function phase_thermal_collectDotState
|
|||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief Damage viscosity.
|
||||
!> @brief Thermal viscosity.
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module function phase_mu_T(co,ce) result(mu)
|
||||
|
||||
|
|
@ -205,7 +205,7 @@ end function phase_mu_T
|
|||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief Damage conductivity/diffusivity in reference configuration.
|
||||
!> @brief Thermal conductivity/diffusivity in reference configuration.
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module function phase_K_T(co,ce) result(K)
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue