Merge branch 'Results.read-.place' into 'development'

simplified handling of Result class

See merge request damask/DAMASK!363
This commit is contained in:
Philip Eisenlohr 2021-04-09 22:47:05 +00:00
commit 73b07eda4a
43 changed files with 1473 additions and 707 deletions

3
.gitattributes vendored
View File

@ -9,10 +9,11 @@
*.hdf5 binary *.hdf5 binary
*.pdf binary *.pdf binary
*.dream3d binary *.dream3d binary
*.pbz2 binary
# ignore files from MSC.Marc in language statistics # ignore files from MSC.Marc in language statistics
installation/mods_MarcMentat/20*/* linguist-vendored installation/mods_MarcMentat/20*/* linguist-vendored
src/marc/include/* linguist-vendored src/Marc/include/* linguist-vendored
# ignore reference files for tests in language statistics # ignore reference files for tests in language statistics
python/tests/reference/* linguist-vendored python/tests/reference/* linguist-vendored

@ -1 +1 @@
Subproject commit f1ac733d5eb90de1cdcaf79a261157c9034f8136 Subproject commit 1298124143e7e2901d0b9c2e79ab6388cb78a1e3

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@ -1,5 +1,3 @@
import os
import numpy as np import numpy as np
import h5py import h5py
@ -159,18 +157,18 @@ class ConfigMaterial(Config):
f = h5py.File(fname,'r') f = h5py.File(fname,'r')
if grain_data is None: if grain_data is None:
phase = f[os.path.join(b,c,phases)][()].flatten() phase = f['/'.join([b,c,phases])][()].flatten()
O = Rotation.from_Euler_angles(f[os.path.join(b,c,Euler_angles)]).as_quaternion().reshape(-1,4) # noqa O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
_,idx = np.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0) _,idx = np.unique(np.hstack([O,phase.reshape(-1,1)]),return_index=True,axis=0)
idx = np.sort(idx) idx = np.sort(idx)
else: else:
phase = f[os.path.join(b,grain_data,phases)][()] phase = f['/'.join([b,grain_data,phases])][()]
O = Rotation.from_Euler_angles(f[os.path.join(b,grain_data,Euler_angles)]).as_quaternion() # noqa O = Rotation.from_Euler_angles(f['/'.join([b,grain_data,Euler_angles])]).as_quaternion() # noqa
idx = np.arange(phase.size) idx = np.arange(phase.size)
if cell_ensemble_data is not None and phase_names is not None: if cell_ensemble_data is not None and phase_names is not None:
try: try:
names = np.array([s.decode() for s in f[os.path.join(b,cell_ensemble_data,phase_names)]]) names = np.array([s.decode() for s in f['/'.join([b,cell_ensemble_data,phase_names])]])
phase = names[phase] phase = names[phase]
except KeyError: except KeyError:
pass pass

View File

@ -69,9 +69,9 @@ class Grid:
copy = __copy__ copy = __copy__
def diff(self,other): def __eq__(self,other):
""" """
Report property differences of self relative to other. Test equality of other.
Parameters Parameters
---------- ----------
@ -79,28 +79,10 @@ class Grid:
Grid to compare self against. Grid to compare self against.
""" """
message = [] return (np.allclose(other.size,self.size)
if np.any(other.cells != self.cells): and np.allclose(other.origin,self.origin)
message.append(util.deemph(f'cells a b c: {util.srepr(other.cells," x ")}')) and np.all(other.cells == self.cells)
message.append(util.emph( f'cells a b c: {util.srepr( self.cells," x ")}')) and np.all(other.material == self.material))
if not np.allclose(other.size,self.size):
message.append(util.deemph(f'size x y z: {util.srepr(other.size," x ")}'))
message.append(util.emph( f'size x y z: {util.srepr( self.size," x ")}'))
if not np.allclose(other.origin,self.origin):
message.append(util.deemph(f'origin x y z: {util.srepr(other.origin," ")}'))
message.append(util.emph( f'origin x y z: {util.srepr( self.origin," ")}'))
if other.N_materials != self.N_materials:
message.append(util.deemph(f'# materials: {other.N_materials}'))
message.append(util.emph( f'# materials: { self.N_materials}'))
if np.nanmax(other.material) != np.nanmax(self.material):
message.append(util.deemph(f'max material: {np.nanmax(other.material)}'))
message.append(util.emph( f'max material: {np.nanmax( self.material)}'))
return util.return_message(message)
@property @property
@ -305,18 +287,18 @@ class Grid:
c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data c = util.DREAM3D_cell_data_group(fname) if cell_data is None else cell_data
f = h5py.File(fname, 'r') f = h5py.File(fname, 'r')
cells = f[os.path.join(b,'_SIMPL_GEOMETRY','DIMENSIONS')][()] cells = f['/'.join([b,'_SIMPL_GEOMETRY','DIMENSIONS'])][()]
size = f[os.path.join(b,'_SIMPL_GEOMETRY','SPACING')] * cells size = f['/'.join([b,'_SIMPL_GEOMETRY','SPACING'])] * cells
origin = f[os.path.join(b,'_SIMPL_GEOMETRY','ORIGIN')][()] origin = f['/'.join([b,'_SIMPL_GEOMETRY','ORIGIN'])][()]
if feature_IDs is None: if feature_IDs is None:
phase = f[os.path.join(b,c,phases)][()].reshape(-1,1) phase = f['/'.join([b,c,phases])][()].reshape(-1,1)
O = Rotation.from_Euler_angles(f[os.path.join(b,c,Euler_angles)]).as_quaternion().reshape(-1,4) # noqa O = Rotation.from_Euler_angles(f['/'.join([b,c,Euler_angles])]).as_quaternion().reshape(-1,4) # noqa
unique,unique_inverse = np.unique(np.hstack([O,phase]),return_inverse=True,axis=0) unique,unique_inverse = np.unique(np.hstack([O,phase]),return_inverse=True,axis=0)
ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \ ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse] np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
else: else:
ma = f[os.path.join(b,c,feature_IDs)][()].flatten() ma = f['/'.join([b,c,feature_IDs])][()].flatten()
return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','load_DREAM3D')) return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','load_DREAM3D'))

File diff suppressed because it is too large Load Diff

View File

@ -230,7 +230,6 @@ class Table:
f = fname f = fname
f.seek(0) f.seek(0)
f.seek(0)
comments = [] comments = []
line = f.readline().strip() line = f.readline().strip()
while line.startswith('#'): while line.startswith('#'):
@ -515,7 +514,7 @@ class Table:
""" """
if set(self.shapes) & set(other.shapes) or self.data.shape[0] != other.data.shape[0]: if set(self.shapes) & set(other.shapes) or self.data.shape[0] != other.data.shape[0]:
raise KeyError('Dublicated keys or row count mismatch') raise KeyError('Duplicated keys or row count mismatch')
else: else:
dup = self.copy() dup = self.copy()
dup.data = dup.data.join(other.data) dup.data = dup.data.join(other.data)

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@ -2,8 +2,8 @@ import os
import multiprocessing as mp import multiprocessing as mp
from pathlib import Path from pathlib import Path
import pandas as pd
import numpy as np import numpy as np
import numpy.ma as ma
import vtk import vtk
from vtk.util.numpy_support import numpy_to_vtk as np_to_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 from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray
@ -224,14 +224,14 @@ class VTK:
# Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data # Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
# Needs support for pd.DataFrame and/or table # Needs support for damask.Table
def add(self,data,label=None): def add(self,data,label=None):
""" """
Add data to either cells or points. Add data to either cells or points.
Parameters Parameters
---------- ----------
data : numpy.ndarray data : numpy.ndarray or numpy.ma.MaskedArray
Data to add. First dimension needs to match either Data to add. First dimension needs to match either
number of cells or number of points. number of cells or number of points.
label : str label : str
@ -246,8 +246,10 @@ class VTK:
raise ValueError('No label defined for numpy.ndarray') raise ValueError('No label defined for numpy.ndarray')
N_data = data.shape[0] N_data = data.shape[0]
d = np_to_vtk((data.astype(np.single) if data.dtype in [np.double, np.longdouble] else data_ = np.where(data.mask,data.fill_value,data) if isinstance(data,ma.MaskedArray) else\
data).reshape(N_data,-1),deep=True) # avoid large files 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
d.SetName(label) d.SetName(label)
if N_data == N_points: if N_data == N_points:
@ -256,8 +258,6 @@ class VTK:
self.vtk_data.GetCellData().AddArray(d) self.vtk_data.GetCellData().AddArray(d)
else: else:
raise ValueError(f'Cell / point count ({N_cells} / {N_points}) differs from data ({N_data}).') raise ValueError(f'Cell / point count ({N_cells} / {N_points}) differs from data ({N_data}).')
elif isinstance(data,pd.DataFrame):
raise NotImplementedError('pd.DataFrame')
elif isinstance(data,Table): elif isinstance(data,Table):
raise NotImplementedError('damask.Table') raise NotImplementedError('damask.Table')
else: else:

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@ -17,15 +17,16 @@ __all__=[
'srepr', 'srepr',
'emph','deemph','warn','strikeout', 'emph','deemph','warn','strikeout',
'execute', 'execute',
'natural_sort',
'show_progress', 'show_progress',
'scale_to_coprime', 'scale_to_coprime',
'project_stereographic', 'project_stereographic',
'hybrid_IA', 'hybrid_IA',
'return_message',
'execution_stamp', 'execution_stamp',
'shapeshifter', 'shapeblender', 'shapeshifter', 'shapeblender',
'extend_docstring', 'extended_docstring', 'extend_docstring', 'extended_docstring',
'DREAM3D_base_group', 'DREAM3D_cell_data_group' 'DREAM3D_base_group', 'DREAM3D_cell_data_group',
'dict_prune', 'dict_flatten'
] ]
# https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py # https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py
@ -58,10 +59,11 @@ def srepr(arg,glue = '\n'):
Glue used for joining operation. Defaults to \n. Glue used for joining operation. Defaults to \n.
""" """
if (not hasattr(arg, "strip") and if (not hasattr(arg, 'strip') and
(hasattr(arg, "__getitem__") or (hasattr(arg, '__getitem__') or
hasattr(arg, "__iter__"))): hasattr(arg, '__iter__'))):
return glue.join(str(x) for x in arg) return glue.join(str(x) for x in arg)
else:
return arg if isinstance(arg,str) else repr(arg) return arg if isinstance(arg,str) else repr(arg)
@ -112,6 +114,11 @@ def execute(cmd,wd='./',env=None):
return process.stdout, process.stderr return process.stdout, process.stderr
def natural_sort(key):
convert = lambda text: int(text) if text.isdigit() else text
return [ convert(c) for c in re.split('([0-9]+)', key) ]
def show_progress(iterable,N_iter=None,prefix='',bar_length=50): def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
""" """
Decorate a loop with a status bar. Decorate a loop with a status bar.
@ -130,7 +137,11 @@ def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
Character length of bar. Defaults to 50. Character length of bar. Defaults to 50.
""" """
status = _ProgressBar(N_iter if N_iter else len(iterable),prefix,bar_length) if N_iter == 1 or (hasattr(iterable,'__len__') and len(iterable) == 1):
for item in iterable:
yield item
else:
status = _ProgressBar(N_iter if N_iter is not None else len(iterable),prefix,bar_length)
for i,item in enumerate(iterable): for i,item in enumerate(iterable):
yield item yield item
@ -388,7 +399,7 @@ def DREAM3D_cell_data_group(fname):
""" """
base_group = DREAM3D_base_group(fname) base_group = DREAM3D_base_group(fname)
with h5py.File(fname,'r') as f: with h5py.File(fname,'r') as f:
cells = tuple(f[os.path.join(base_group,'_SIMPL_GEOMETRY','DIMENSIONS')][()][::-1]) cells = tuple(f['/'.join([base_group,'_SIMPL_GEOMETRY','DIMENSIONS'])][()][::-1])
cell_data_group = f[base_group].visititems(lambda path,obj: path.split('/')[0] \ cell_data_group = f[base_group].visititems(lambda path,obj: path.split('/')[0] \
if isinstance(obj,h5py._hl.dataset.Dataset) and np.shape(obj)[:-1] == cells \ if isinstance(obj,h5py._hl.dataset.Dataset) and np.shape(obj)[:-1] == cells \
else None) else None)
@ -399,29 +410,59 @@ def DREAM3D_cell_data_group(fname):
return cell_data_group return cell_data_group
#################################################################################################### def dict_prune(d):
# Classes
####################################################################################################
class return_message:
"""Object with formatted return message."""
def __init__(self,message):
""" """
Set return message. Recursively remove empty dictionaries.
Parameters Parameters
---------- ----------
message : str or list of str d : dict
message for output to screen Dictionary to prune.
Returns
-------
pruned : dict
Pruned dictionary.
""" """
self.message = message # https://stackoverflow.com/questions/48151953
new = {}
def __repr__(self): for k,v in d.items():
"""Return message suitable for interactive shells.""" if isinstance(v, dict):
return srepr(self.message) v = dict_prune(v)
if not isinstance(v,dict) or v != {}:
new[k] = v
return new
def dict_flatten(d):
"""
Recursively remove keys of single-entry dictionaries.
Parameters
----------
d : dict
Dictionary to flatten.
Returns
-------
flattened : dict
Flattened dictionary.
"""
if isinstance(d,dict) and len(d) == 1:
entry = d[list(d.keys())[0]]
new = dict_flatten(entry.copy()) if isinstance(entry,dict) else entry
else:
new = {k: (dict_flatten(v) if isinstance(v, dict) else v) for k,v in d.items()}
return new
####################################################################################################
# Classes
####################################################################################################
class _ProgressBar: class _ProgressBar:
""" """
Report progress of an interation as a status bar. Report progress of an interation as a status bar.

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@ -0,0 +1,678 @@
material:
- constituents:
- phase: A
O: [0.44698096036898677, -0.035696623617731814, 0.050331402131209624, -0.8924127532086364]
v: 0.125
- phase: A
O: [0.6226205515354057, 0.4257792272120092, -0.6365250917893261, 0.16090837766592916]
v: 0.125
- phase: A
O: [0.4319357791504236, 0.5804552577310466, 0.4870786336250474, 0.48913963356904305]
v: 0.125
- phase: A
O: [0.6712122425649047, -0.5315470950319967, 0.11982471915778993, -0.5025672570639611]
v: 0.125
- phase: A
O: [0.03979536866120591, -0.01919843067074171, -0.5618628311727827, 0.8260495795286167]
v: 0.125
- phase: A
O: [0.6951890945163803, -0.46325436790720337, 0.03393768848173515, -0.5485943371753935]
v: 0.125
- phase: A
O: [0.3489469292795834, -0.5959323325634578, -0.6067706771532161, 0.3936115355256417]
v: 0.125
- phase: A
O: [0.39500485674202723, -0.07573446369604235, -0.015761384830863343, -0.9154163167144754]
v: 0.125
homogenization: RGC
- constituents:
- phase: B
O: [0.9221278604171202, 0.32701451341562027, 0.15952215192749652, -0.1315081750406033]
v: 0.125
- phase: B
O: [0.8117843306311869, 0.4102779561929707, -0.18584663447455768, 0.37167085930736465]
v: 0.125
- phase: B
O: [0.6548302235705483, 0.6510678661349768, -0.3832730015357094, 0.02024396894884073]
v: 0.125
- phase: B
O: [0.04255709858343937, -0.3005730931619659, -0.3060125731417352, -0.9023308783957146]
v: 0.125
- phase: B
O: [0.6960740097259569, 0.16329320418261428, 0.6991228405747408, 0.006599715032396515]
v: 0.125
- phase: B
O: [0.48818278044780217, -0.664294296073913, 0.2679908412891581, 0.4985695238008905]
v: 0.125
- phase: B
O: [0.545426202615872, 0.179298582176746, -0.7847831868864313, -0.23340442478628137]
v: 0.125
- phase: B
O: [0.8566603715426528, 0.26967937521434965, -0.03159131558814077, 0.43864339866435076]
v: 0.125
homogenization: RGC
- constituents:
- phase: C
O: [0.140304599816322, -0.017971728003341014, -0.9895572782263894, 0.027713342853867628]
v: 0.125
- phase: C
O: [0.8096406385129331, 0.2395956967578664, -0.25531574170054405, -0.47105181307727034]
v: 0.125
- phase: C
O: [0.15570676199790476, -0.7501738841096782, 0.2328253832435299, -0.5989882209070811]
v: 0.125
- phase: C
O: [0.4595649941522109, 0.3331746723324176, 0.23957383093695328, 0.7876541331042811]
v: 0.125
- phase: C
O: [0.2969510261483044, 0.0027640644222379847, -0.8133130954773664, 0.5003341450894221]
v: 0.125
- phase: C
O: [0.114170281047612, -0.9068850613039258, 0.3701597984948465, -0.16585040273553361]
v: 0.125
- phase: C
O: [0.29658840046433166, -0.5331902828876833, 0.7365409179409275, 0.2919776004129383]
v: 0.125
- phase: C
O: [0.931315147629592, -0.2017743466108175, 0.30303719188324046, 0.010376376100021569]
v: 0.125
homogenization: RGC
- constituents:
- phase: A
O: [0.20901169650798976, 0.5778057521557359, -0.3628020593274987, 0.7005920990464581]
v: 0.125
- phase: B
O: [0.6025573623737024, 0.7345291803280383, 0.3086529661391562, 0.04609614722911203]
v: 0.125
- phase: C
O: [0.6402291970447783, -0.5402560454335561, -0.5285008279381848, -0.13753856002062462]
v: 0.125
- phase: A
O: [0.12506307996119548, 0.5336909245447153, 0.8344001590799459, 0.05752910234470594]
v: 0.125
- phase: B
O: [0.5504712846116686, -0.6241210958640075, 0.42061504390637533, 0.3612993320712448]
v: 0.125
- phase: C
O: [0.3135636745691277, 0.6574027353927014, 0.6044800436379738, -0.32265049563317466]
v: 0.125
- phase: A
O: [0.1619452502554878, -0.4269267792831907, -0.8080415555188633, 0.3722581169097929]
v: 0.125
- phase: A
O: [0.17044595054343245, 0.8646695166660998, -0.30004868613437863, -0.365055599656809]
v: 0.125
homogenization: RGC
- constituents:
- phase: B
O: [0.43255174377606787, 0.2026672781261794, 0.35000490906160386, 0.8058048938583007]
v: 0.125
- phase: B
O: [0.19591912697365416, -0.8181375036268687, 0.3260880890153691, -0.4311998133665892]
v: 0.125
- phase: A
O: [0.1373248436058589, -0.43524771427953446, -0.8885320171891298, -0.047033700395389226]
v: 0.125
- phase: A
O: [0.250519065956112, -0.7636612069861932, 0.5672425862778043, -0.17971534951065127]
v: 0.125
- phase: B
O: [0.600521695167639, -0.2273230963128902, 0.7563911883237204, -0.12478090295368073]
v: 0.125
- phase: A
O: [0.4281846857945264, 0.5284504248063085, 0.21428541450090705, 0.7010561921167584]
v: 0.125
- phase: A
O: [0.34007599923699156, 0.5500172687924186, 0.6138467460818403, -0.45279298923219496]
v: 0.125
- phase: A
O: [0.8581382626679844, -0.20034169756111123, 0.3134907520728513, -0.35381559424127107]
v: 0.125
homogenization: RGC
- constituents:
- phase: C
O: [0.18637512817696594, 0.9354389080016575, 0.2967480269088709, -0.04646471262558266]
v: 0.125
- phase: C
O: [0.33425800495572805, 0.24948308477875414, 0.7297193930640264, 0.5417927499686225]
v: 0.125
- phase: A
O: [0.11918214701666907, -0.4185869380028542, 0.618905484805619, -0.6538628235673086]
v: 0.125
- phase: A
O: [0.40732205687168244, -0.6166051531766635, -0.6737097202702335, -0.0014282419993970551]
v: 0.125
- phase: A
O: [0.68397144415648, 0.6848389352552103, 0.24111983008651763, 0.07099242125789083]
v: 0.125
- phase: C
O: [0.05719438496521803, 0.2575447319897859, 0.5020591650211859, -0.8236116245968056]
v: 0.125
- phase: A
O: [0.10565206937493385, -0.1109750475948143, 0.8781814355546643, 0.45312199824690885]
v: 0.125
- phase: A
O: [0.22821192086563635, -0.9595048060506683, -0.07745760541549483, -0.1458429487626446]
v: 0.125
homogenization: RGC
- constituents:
- phase: A
O: [0.5745354940858776, 0.6366614824775295, 0.3307586622977252, -0.39391601907009377]
v: 0.125
- phase: B
O: [0.3505113084912295, -0.6046500894621007, 0.6274019946374426, -0.34337563841687757]
v: 0.125
- phase: A
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v: 0.125
homogenization: RGC
- constituents:
- phase: A
O: [0.3735354245257942, -0.19362809638145217, 0.7860424876438061, 0.45289806196843757]
v: 0.125
- phase: A
O: [0.0320727653734856, -0.8866094001869422, 0.46133859224884993, 0.007862094078374177]
v: 0.125
- phase: A
O: [0.4437387774582536, 0.2752317472571834, 0.5589728539449029, -0.6441216742466462]
v: 0.125
- phase: A
O: [0.4189270336917096, -0.7997419507282093, 0.08375652034255085, 0.4217793238031132]
v: 0.125
- phase: A
O: [0.07774372790271536, 0.8494512032072281, -0.23549059135564554, 0.4657603971191082]
v: 0.125
- phase: A
O: [0.7403304241587872, 0.5263542470691401, -0.1337642666383515, -0.39619337529526266]
v: 0.125
- phase: A
O: [0.3862324493674717, -0.7790044035666689, 0.2926767318730596, 0.39789064439798927]
v: 0.125
- phase: A
O: [0.12717246708576896, 0.2790094483039878, 0.8667779585068207, -0.39328979394229346]
v: 0.125
homogenization: RGC
homogenization:
RGC:
N_constituents: 8
mechanical:
type: RGC
D_alpha: [4.0e-06, 4.0e-06, 2.0e-06]
a_g: [0.0, 0.0, 0.0]
c_alpha: 2.0
cluster_size: [2, 2, 2]
output: [M, Delta_V, avg_a_dot, max_a_dot]
xi_alpha: 10.0
phase:
A:
lattice: cF
mechanical:
output: [F, F_e, F_p, L_p]
elastic: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
plastic:
N_sl: [12]
a_sl: 2.25
atol_xi: 1.0
dot_gamma_0_sl: 0.001
h_0_sl_sl: 75e6
h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4]
n_sl: 20
output: [xi_sl]
type: phenopowerlaw
xi_0_sl: [31e6]
xi_inf_sl: [63e6]
B:
lattice: cI
mechanical:
output: [F, P, F_e, F_p, L_p, O]
elastic: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
plastic:
N_sl: [12]
a_sl: 2.25
atol_xi: 1.0
dot_gamma_0_sl: 0.001
h_0_sl_sl: 75e6
h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4]
n_sl: 20
output: [xi_sl]
type: phenopowerlaw
xi_0_sl: [31e6]
xi_inf_sl: [63e6]
C:
lattice: cI
mechanical:
output: [F]
elastic: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}

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@ -0,0 +1,30 @@
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<CellData>
<DataArray type="Int64" Name="material" format="binary" RangeMin="0" RangeMax="3">
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@ -0,0 +1,17 @@
---
solver:
mechanical: spectral_basic
loadstep:
- boundary_conditions:
mechanical:
dot_F: [x, 0, 0,
0, -1.0e-3, 0,
0, 0, x]
P: [0, x, x,
x, x, x,
x, x, 0]
discretization:
t: 5
N: 10
f_out: 2

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@ -0,0 +1 @@
3b83384def67552ab7dd211efc0d54fd

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@ -0,0 +1 @@
c32c86ed50dbb39a93ca2a2ebe47d9cb

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@ -0,0 +1 @@
ead4f6fcaff174fddc041d701e54ac60

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@ -0,0 +1 @@
3f21254164f96de8ee4a28249ae72cc6

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@ -136,9 +136,9 @@ class TestConfigMaterial:
def test_load_DREAM3D_reference(self,tmp_path,ref_path,update): def test_load_DREAM3D_reference(self,tmp_path,ref_path,update):
cur = ConfigMaterial.load_DREAM3D(ref_path/'measured.dream3d') cur = ConfigMaterial.load_DREAM3D(ref_path/'measured.dream3d')
ref = ConfigMaterial.load(ref_path/'measured.material_yaml') ref = ConfigMaterial.load(ref_path/'measured.material.yaml')
if update: if update:
cur.save(ref_path/'measured.material_yaml') cur.save(ref_path/'measured.material.yaml')
for i,m in enumerate(ref['material']): for i,m in enumerate(ref['material']):
assert Rotation(m['constituents'][0]['O']) == \ assert Rotation(m['constituents'][0]['O']) == \
Rotation(cur['material'][i]['constituents'][0]['O']) Rotation(cur['material'][i]['constituents'][0]['O'])

View File

@ -14,8 +14,7 @@ from damask import grid_filters
def grid_equal(a,b): def grid_equal(a,b):
return np.all(a.material == b.material) and \ return np.all(a.material == b.material) and \
np.all(a.cells == b.cells) and \ np.all(a.cells == b.cells) and \
np.allclose(a.size, b.size) and \ np.allclose(a.size, b.size)
str(a.diff(b)) == str(b.diff(a))
@pytest.fixture @pytest.fixture
def default(): def default():
@ -42,13 +41,9 @@ class TestGrid:
def _patch_datetime_now(self, patch_datetime_now): def _patch_datetime_now(self, patch_datetime_now):
print('patched datetime.datetime.now') print('patched datetime.datetime.now')
def test_diff_equal(self,default):
assert str(default.diff(default)) == ''
def test_equal(self,default):
def test_diff_not_equal(self,default): assert default == default
new = Grid(default.material[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
assert str(default.diff(new)) != ''
def test_repr(self,default): def test_repr(self,default):
print(default) print(default)

View File

@ -1,12 +1,14 @@
import bz2
import pickle
import time import time
import shutil import shutil
import os import os
import sys import sys
import hashlib
from datetime import datetime from datetime import datetime
import pytest import pytest
import numpy as np import numpy as np
import h5py
from damask import Result from damask import Result
from damask import Rotation from damask import Rotation
@ -21,8 +23,7 @@ def default(tmp_path,ref_path):
fname = '12grains6x7x8_tensionY.hdf5' fname = '12grains6x7x8_tensionY.hdf5'
shutil.copy(ref_path/fname,tmp_path) shutil.copy(ref_path/fname,tmp_path)
f = Result(tmp_path/fname) f = Result(tmp_path/fname)
f.view('times',20.0) return f.view('times',20.0)
return f
@pytest.fixture @pytest.fixture
def single_phase(tmp_path,ref_path): def single_phase(tmp_path,ref_path):
@ -36,6 +37,17 @@ def ref_path(ref_path_base):
"""Directory containing reference results.""" """Directory containing reference results."""
return ref_path_base/'Result' return ref_path_base/'Result'
def dict_equal(d1, d2):
for k in d1:
if (k not in d2):
return False
else:
if type(d1[k]) is dict:
return dict_equal(d1[k],d2[k])
else:
if not np.allclose(d1[k],d2[k]):
return False
return True
class TestResult: class TestResult:
@ -44,51 +56,39 @@ class TestResult:
def test_view_all(self,default): def test_view_all(self,default):
default.view('increments',True) a = default.view('increments',True).get('F')
a = default.get_dataset_location('F')
default.view('increments','*')
b = default.get_dataset_location('F')
default.view('increments',default.increments_in_range(0,np.iinfo(int).max))
c = default.get_dataset_location('F')
default.view('times',True) assert dict_equal(a,default.view('increments','*').get('F'))
d = default.get_dataset_location('F') assert dict_equal(a,default.view('increments',default.increments_in_range(0,np.iinfo(int).max)).get('F'))
default.view('times','*')
e = default.get_dataset_location('F') assert dict_equal(a,default.view('times',True).get('F'))
default.view('times',default.times_in_range(0.0,np.inf)) assert dict_equal(a,default.view('times','*').get('F'))
f = default.get_dataset_location('F') assert dict_equal(a,default.view('times',default.times_in_range(0.0,np.inf)).get('F'))
assert a == b == c == d == e ==f
@pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations @pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations
def test_view_none(self,default,what): def test_view_none(self,default,what):
default.view(what,False) a = default.view(what,False).get('F')
a = default.get_dataset_location('F') b = default.view(what,[]).get('F')
default.view(what,[])
b = default.get_dataset_location('F')
assert a == b == [] assert a == b == {}
@pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations @pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations
def test_view_more(self,default,what): def test_view_more(self,default,what):
default.view(what,False) empty = default.view(what,False)
default.view_more(what,'*')
a = default.get_dataset_location('F')
default.view(what,True) a = empty.view_more(what,'*').get('F')
b = default.get_dataset_location('F') b = empty.view_more(what,True).get('F')
assert a == b assert dict_equal(a,b)
@pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations @pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations
def test_view_less(self,default,what): def test_view_less(self,default,what):
default.view(what,True) full = default.view(what,True)
default.view_less(what,'*')
a = default.get_dataset_location('F')
default.view(what,False) a = full.view_less(what,'*').get('F')
b = default.get_dataset_location('F') b = full.view_less(what,True).get('F')
assert a == b == [] assert a == b == {}
def test_view_invalid(self,default): def test_view_invalid(self,default):
with pytest.raises(AttributeError): with pytest.raises(AttributeError):
@ -96,10 +96,8 @@ class TestResult:
def test_add_absolute(self,default): def test_add_absolute(self,default):
default.add_absolute('F_e') default.add_absolute('F_e')
loc = {'F_e': default.get_dataset_location('F_e'), in_memory = np.abs(default.place('F_e'))
'|F_e|': default.get_dataset_location('|F_e|')} in_file = default.place('|F_e|')
in_memory = np.abs(default.read_dataset(loc['F_e'],0))
in_file = default.read_dataset(loc['|F_e|'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
@pytest.mark.parametrize('mode',['direct','function']) @pytest.mark.parametrize('mode',['direct','function'])
@ -115,77 +113,59 @@ class TestResult:
default.enable_user_function(f.my_func) default.enable_user_function(f.my_func)
default.add_calculation('x','my_func(#F#)','-','my notes') default.add_calculation('x','my_func(#F#)','-','my notes')
loc = {'F': default.get_dataset_location('F'), in_memory = 2.0*np.abs(default.place('F'))-1.0
'x': default.get_dataset_location('x')} in_file = default.place('x')
in_memory = 2.0*np.abs(default.read_dataset(loc['F'],0))-1.0
in_file = default.read_dataset(loc['x'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_stress_Cauchy(self,default): def test_add_stress_Cauchy(self,default):
default.add_stress_Cauchy('P','F') default.add_stress_Cauchy('P','F')
loc = {'F': default.get_dataset_location('F'), in_memory = mechanics.stress_Cauchy(default.place('P'), default.place('F'))
'P': default.get_dataset_location('P'), in_file = default.place('sigma')
'sigma':default.get_dataset_location('sigma')}
in_memory = mechanics.stress_Cauchy(default.read_dataset(loc['P'],0),
default.read_dataset(loc['F'],0))
in_file = default.read_dataset(loc['sigma'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_determinant(self,default): def test_add_determinant(self,default):
default.add_determinant('P') default.add_determinant('P')
loc = {'P': default.get_dataset_location('P'), in_memory = np.linalg.det(default.place('P'))
'det(P)':default.get_dataset_location('det(P)')} in_file = default.place('det(P)')
in_memory = np.linalg.det(default.read_dataset(loc['P'],0)).reshape(-1,1)
in_file = default.read_dataset(loc['det(P)'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_deviator(self,default): def test_add_deviator(self,default):
default.add_deviator('P') default.add_deviator('P')
loc = {'P' :default.get_dataset_location('P'), in_memory = tensor.deviatoric(default.place('P'))
's_P':default.get_dataset_location('s_P')} in_file = default.place('s_P')
in_memory = tensor.deviatoric(default.read_dataset(loc['P'],0))
in_file = default.read_dataset(loc['s_P'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
@pytest.mark.parametrize('eigenvalue,function',[('max',np.amax),('min',np.amin)]) @pytest.mark.parametrize('eigenvalue,function',[('max',np.amax),('min',np.amin)])
def test_add_eigenvalue(self,default,eigenvalue,function): def test_add_eigenvalue(self,default,eigenvalue,function):
default.add_stress_Cauchy('P','F') default.add_stress_Cauchy('P','F')
default.add_eigenvalue('sigma',eigenvalue) default.add_eigenvalue('sigma',eigenvalue)
loc = {'sigma' :default.get_dataset_location('sigma'), in_memory = function(tensor.eigenvalues(default.place('sigma')),axis=1)
'lambda':default.get_dataset_location(f'lambda_{eigenvalue}(sigma)')} in_file = default.place(f'lambda_{eigenvalue}(sigma)')
in_memory = function(tensor.eigenvalues(default.read_dataset(loc['sigma'],0)),axis=1,keepdims=True)
in_file = default.read_dataset(loc['lambda'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
@pytest.mark.parametrize('eigenvalue,idx',[('max',2),('mid',1),('min',0)]) @pytest.mark.parametrize('eigenvalue,idx',[('max',2),('mid',1),('min',0)])
def test_add_eigenvector(self,default,eigenvalue,idx): def test_add_eigenvector(self,default,eigenvalue,idx):
default.add_stress_Cauchy('P','F') default.add_stress_Cauchy('P','F')
default.add_eigenvector('sigma',eigenvalue) default.add_eigenvector('sigma',eigenvalue)
loc = {'sigma' :default.get_dataset_location('sigma'), in_memory = tensor.eigenvectors(default.place('sigma'))[:,idx]
'v(sigma)':default.get_dataset_location(f'v_{eigenvalue}(sigma)')} in_file = default.place(f'v_{eigenvalue}(sigma)')
in_memory = tensor.eigenvectors(default.read_dataset(loc['sigma'],0))[:,idx]
in_file = default.read_dataset(loc['v(sigma)'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
@pytest.mark.parametrize('d',[[1,0,0],[0,1,0],[0,0,1]]) @pytest.mark.parametrize('d',[[1,0,0],[0,1,0],[0,0,1]])
def test_add_IPF_color(self,default,d): def test_add_IPF_color(self,default,d):
default.add_IPF_color(d,'O') default.add_IPF_color(d,'O')
loc = {'O': default.get_dataset_location('O'), qu = default.place('O')
'color': default.get_dataset_location('IPFcolor_[{} {} {}]'.format(*d))} crystal_structure = qu.dtype.metadata['lattice']
qu = default.read_dataset(loc['O']).view(np.double).squeeze()
crystal_structure = default._get_attribute(default.get_dataset_location('O')[0],'lattice')
c = Orientation(rotation=qu,lattice=crystal_structure) c = Orientation(rotation=qu,lattice=crystal_structure)
in_memory = np.uint8(c.IPF_color(np.array(d))*255) in_memory = np.uint8(c.IPF_color(np.array(d))*255)
in_file = default.read_dataset(loc['color']) in_file = default.place('IPFcolor_({} {} {})'.format(*d))
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_maximum_shear(self,default): def test_add_maximum_shear(self,default):
default.add_stress_Cauchy('P','F') default.add_stress_Cauchy('P','F')
default.add_maximum_shear('sigma') default.add_maximum_shear('sigma')
loc = {'sigma' :default.get_dataset_location('sigma'), in_memory = mechanics.maximum_shear(default.place('sigma'))
'max_shear(sigma)':default.get_dataset_location('max_shear(sigma)')} in_file = default.place('max_shear(sigma)')
in_memory = mechanics.maximum_shear(default.read_dataset(loc['sigma'],0)).reshape(-1,1)
in_file = default.read_dataset(loc['max_shear(sigma)'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_Mises_strain(self,default): def test_add_Mises_strain(self,default):
@ -194,26 +174,22 @@ class TestResult:
default.add_strain('F',t,m) default.add_strain('F',t,m)
label = f'epsilon_{t}^{m}(F)' label = f'epsilon_{t}^{m}(F)'
default.add_equivalent_Mises(label) default.add_equivalent_Mises(label)
loc = {label :default.get_dataset_location(label), in_memory = mechanics.equivalent_strain_Mises(default.place(label))
label+'_vM':default.get_dataset_location(label+'_vM')} in_file = default.place(label+'_vM')
in_memory = mechanics.equivalent_strain_Mises(default.read_dataset(loc[label],0)).reshape(-1,1)
in_file = default.read_dataset(loc[label+'_vM'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_Mises_stress(self,default): def test_add_Mises_stress(self,default):
default.add_stress_Cauchy('P','F') default.add_stress_Cauchy('P','F')
default.add_equivalent_Mises('sigma') default.add_equivalent_Mises('sigma')
loc = {'sigma' :default.get_dataset_location('sigma'), in_memory = mechanics.equivalent_stress_Mises(default.place('sigma'))
'sigma_vM':default.get_dataset_location('sigma_vM')} in_file = default.place('sigma_vM')
in_memory = mechanics.equivalent_stress_Mises(default.read_dataset(loc['sigma'],0)).reshape(-1,1)
in_file = default.read_dataset(loc['sigma_vM'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_Mises_invalid(self,default): def test_add_Mises_invalid(self,default):
default.add_stress_Cauchy('P','F') default.add_stress_Cauchy('P','F')
default.add_calculation('sigma_y','#sigma#',unit='y') default.add_calculation('sigma_y','#sigma#',unit='y')
default.add_equivalent_Mises('sigma_y') default.add_equivalent_Mises('sigma_y')
assert default.get_dataset_location('sigma_y_vM') == [] assert default.get('sigma_y_vM') == {}
def test_add_Mises_stress_strain(self,default): def test_add_Mises_stress_strain(self,default):
default.add_stress_Cauchy('P','F') default.add_stress_Cauchy('P','F')
@ -221,26 +197,20 @@ class TestResult:
default.add_calculation('sigma_x','#sigma#',unit='x') default.add_calculation('sigma_x','#sigma#',unit='x')
default.add_equivalent_Mises('sigma_y',kind='strain') default.add_equivalent_Mises('sigma_y',kind='strain')
default.add_equivalent_Mises('sigma_x',kind='stress') default.add_equivalent_Mises('sigma_x',kind='stress')
loc = {'y' :default.get_dataset_location('sigma_y_vM'), assert not np.allclose(default.place('sigma_y_vM'),default.place('sigma_x_vM'))
'x' :default.get_dataset_location('sigma_x_vM')}
assert not np.allclose(default.read_dataset(loc['y'],0),default.read_dataset(loc['x'],0))
def test_add_norm(self,default): @pytest.mark.parametrize('ord',[1,2])
default.add_norm('F',1) @pytest.mark.parametrize('dataset,axis',[('F',(1,2)),('xi_sl',(1,))])
loc = {'F': default.get_dataset_location('F'), def test_add_norm(self,default,ord,dataset,axis):
'|F|_1':default.get_dataset_location('|F|_1')} default.add_norm(dataset,ord)
in_memory = np.linalg.norm(default.read_dataset(loc['F'],0),ord=1,axis=(1,2),keepdims=True) in_memory = np.linalg.norm(default.place(dataset),ord=ord,axis=axis,keepdims=True)
in_file = default.read_dataset(loc['|F|_1'],0) in_file = default.place(f'|{dataset}|_{ord}')
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_stress_second_Piola_Kirchhoff(self,default): def test_add_stress_second_Piola_Kirchhoff(self,default):
default.add_stress_second_Piola_Kirchhoff('P','F') default.add_stress_second_Piola_Kirchhoff('P','F')
loc = {'F':default.get_dataset_location('F'), in_memory = mechanics.stress_second_Piola_Kirchhoff(default.place('P'),default.place('F'))
'P':default.get_dataset_location('P'), in_file = default.place('S')
'S':default.get_dataset_location('S')}
in_memory = mechanics.stress_second_Piola_Kirchhoff(default.read_dataset(loc['P'],0),
default.read_dataset(loc['F'],0))
in_file = default.read_dataset(loc['S'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
@pytest.mark.skip(reason='requires rework of lattice.f90') @pytest.mark.skip(reason='requires rework of lattice.f90')
@ -248,30 +218,24 @@ class TestResult:
def test_add_pole(self,default,polar): def test_add_pole(self,default,polar):
pole = np.array([1.,0.,0.]) pole = np.array([1.,0.,0.])
default.add_pole('O',pole,polar) default.add_pole('O',pole,polar)
loc = {'O': default.get_dataset_location('O'), rot = Rotation(default.place('O'))
'pole': default.get_dataset_location('p^{}_[1 0 0)'.format(u'' if polar else 'xy'))}
rot = Rotation(default.read_dataset(loc['O']).view(np.double))
rotated_pole = rot * np.broadcast_to(pole,rot.shape+(3,)) rotated_pole = rot * np.broadcast_to(pole,rot.shape+(3,))
xy = rotated_pole[:,0:2]/(1.+abs(pole[2])) xy = rotated_pole[:,0:2]/(1.+abs(pole[2]))
in_memory = xy if not polar else \ in_memory = xy if not polar else \
np.block([np.sqrt(xy[:,0:1]*xy[:,0:1]+xy[:,1:2]*xy[:,1:2]),np.arctan2(xy[:,1:2],xy[:,0:1])]) np.block([np.sqrt(xy[:,0:1]*xy[:,0:1]+xy[:,1:2]*xy[:,1:2]),np.arctan2(xy[:,1:2],xy[:,0:1])])
in_file = default.read_dataset(loc['pole']) in_file = default.place('p^{}_[1 0 0)'.format(u'' if polar else 'xy'))
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_rotation(self,default): def test_add_rotation(self,default):
default.add_rotation('F') default.add_rotation('F')
loc = {'F': default.get_dataset_location('F'), in_memory = mechanics.rotation(default.place('F')).as_matrix()
'R(F)': default.get_dataset_location('R(F)')} in_file = default.place('R(F)')
in_memory = mechanics.rotation(default.read_dataset(loc['F'],0)).as_matrix()
in_file = default.read_dataset(loc['R(F)'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_spherical(self,default): def test_add_spherical(self,default):
default.add_spherical('P') default.add_spherical('P')
loc = {'P': default.get_dataset_location('P'), in_memory = tensor.spherical(default.place('P'),False)
'p_P': default.get_dataset_location('p_P')} in_file = default.place('p_P')
in_memory = tensor.spherical(default.read_dataset(loc['P'],0),False).reshape(-1,1)
in_file = default.read_dataset(loc['p_P'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_strain(self,default): def test_add_strain(self,default):
@ -279,26 +243,20 @@ class TestResult:
m = np.random.random()*2.0 - 1.0 m = np.random.random()*2.0 - 1.0
default.add_strain('F',t,m) default.add_strain('F',t,m)
label = f'epsilon_{t}^{m}(F)' label = f'epsilon_{t}^{m}(F)'
loc = {'F': default.get_dataset_location('F'), in_memory = mechanics.strain(default.place('F'),t,m)
label: default.get_dataset_location(label)} in_file = default.place(label)
in_memory = mechanics.strain(default.read_dataset(loc['F'],0),t,m)
in_file = default.read_dataset(loc[label],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_stretch_right(self,default): def test_add_stretch_right(self,default):
default.add_stretch_tensor('F','U') default.add_stretch_tensor('F','U')
loc = {'F': default.get_dataset_location('F'), in_memory = mechanics.stretch_right(default.place('F'))
'U(F)': default.get_dataset_location('U(F)')} in_file = default.place('U(F)')
in_memory = mechanics.stretch_right(default.read_dataset(loc['F'],0))
in_file = default.read_dataset(loc['U(F)'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_stretch_left(self,default): def test_add_stretch_left(self,default):
default.add_stretch_tensor('F','V') default.add_stretch_tensor('F','V')
loc = {'F': default.get_dataset_location('F'), in_memory = mechanics.stretch_left(default.place('F'))
'V(F)': default.get_dataset_location('V(F)')} in_file = default.place('V(F)')
in_memory = mechanics.stretch_left(default.read_dataset(loc['F'],0))
in_file = default.read_dataset(loc['V(F)'],0)
assert np.allclose(in_memory,in_file) assert np.allclose(in_memory,in_file)
def test_add_invalid(self,default): def test_add_invalid(self,default):
@ -307,48 +265,40 @@ class TestResult:
@pytest.mark.parametrize('overwrite',['off','on']) @pytest.mark.parametrize('overwrite',['off','on'])
def test_add_overwrite(self,default,overwrite): def test_add_overwrite(self,default,overwrite):
default.view('times',default.times_in_range(0,np.inf)[-1]) last = default.view('times',default.times_in_range(0,np.inf)[-1])
default.add_stress_Cauchy() last.add_stress_Cauchy()
loc = default.get_dataset_location('sigma')
with h5py.File(default.fname,'r') as f: created_first = last.place('sigma').dtype.metadata['created']
# h5py3 compatibility
try:
created_first = f[loc[0]].attrs['created'].decode()
except AttributeError:
created_first = f[loc[0]].attrs['created']
created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z') created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
if overwrite == 'on': if overwrite == 'on':
default.allow_modification() last = last.allow_modification()
else: else:
default.disallow_modification() last = last.disallow_modification()
time.sleep(2.) time.sleep(2.)
try: try:
default.add_calculation('sigma','#sigma#*0.0+311.','not the Cauchy stress') last.add_calculation('sigma','#sigma#*0.0+311.','not the Cauchy stress')
except ValueError: except ValueError:
pass pass
with h5py.File(default.fname,'r') as f:
# h5py3 compatibility created_second = last.place('sigma').dtype.metadata['created']
try:
created_second = f[loc[0]].attrs['created'].decode()
except AttributeError:
created_second = f[loc[0]].attrs['created']
created_second = datetime.strptime(created_second,'%Y-%m-%d %H:%M:%S%z') created_second = datetime.strptime(created_second,'%Y-%m-%d %H:%M:%S%z')
if overwrite == 'on': if overwrite == 'on':
assert created_first < created_second and np.allclose(default.read_dataset(loc),311.) assert created_first < created_second and np.allclose(last.place('sigma'),311.)
else: else:
assert created_first == created_second and not np.allclose(default.read_dataset(loc),311.) assert created_first == created_second and not np.allclose(last.place('sigma'),311.)
@pytest.mark.parametrize('allowed',['off','on']) @pytest.mark.parametrize('allowed',['off','on'])
def test_rename(self,default,allowed): def test_rename(self,default,allowed):
if allowed == 'on': if allowed == 'on':
F = default.read_dataset(default.get_dataset_location('F')) F = default.place('F')
default.allow_modification() default = default.allow_modification()
default.rename('F','new_name') default.rename('F','new_name')
assert np.all(F == default.read_dataset(default.get_dataset_location('new_name'))) assert np.all(F == default.place('new_name'))
default.disallow_modification() default = default.disallow_modification()
with pytest.raises(PermissionError): with pytest.raises(PermissionError):
default.rename('P','another_new_name') default.rename('P','another_new_name')
@ -363,10 +313,30 @@ class TestResult:
b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F') b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F')
assert np.allclose(a,b) assert np.allclose(a,b)
@pytest.mark.parametrize('output',['F',[],['F','P']]) # need to wait for writing in parallel, output order might change if select more then one
def test_vtk(self,tmp_path,default,output): @pytest.mark.parametrize('output',['F','*',['P']],ids=range(3))
@pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
@pytest.mark.parametrize('inc',[4,0],ids=range(2))
def test_vtk(self,request,tmp_path,ref_path,update,output,fname,inc):
result = Result(ref_path/fname).view('increments',inc)
os.chdir(tmp_path) os.chdir(tmp_path)
default.save_VTK(output) result.save_VTK(output)
fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vtr'
last = ''
for i in range(10):
if os.path.isfile(tmp_path/fname):
with open(fname) as f:
cur = hashlib.md5(f.read().encode()).hexdigest()
if cur == last:
break
else:
last = cur
time.sleep(.5)
if update:
with open((ref_path/'save_VTK'/request.node.name).with_suffix('.md5'),'w') as f:
f.write(cur)
with open((ref_path/'save_VTK'/request.node.name).with_suffix('.md5')) as f:
assert cur == f.read()
@pytest.mark.parametrize('mode',['point','cell']) @pytest.mark.parametrize('mode',['point','cell'])
def test_vtk_mode(self,tmp_path,single_phase,mode): def test_vtk_mode(self,tmp_path,single_phase,mode):
@ -387,3 +357,52 @@ class TestResult:
def test_XDMF_invalid(self,default): def test_XDMF_invalid(self,default):
with pytest.raises(TypeError): with pytest.raises(TypeError):
default.save_XDMF() default.save_XDMF()
@pytest.mark.parametrize('view,output,flatten,prune',
[({},['F','P','F','L_p','F_e','F_p'],True,True),
({'increments':3},'F',True,True),
({'increments':[1,8,3,4,5,6,7]},['F','P'],True,True),
({'phases':['A','B']},['F','P'],True,True),
({'phases':['A','C'],'homogenizations':False},['F','P','O'],True,True),
({'phases':False,'homogenizations':False},['F','P','O'],True,True),
({'phases':False},['Delta_V'],True,True),
({},['u_p','u_n'],False,False)],
ids=list(range(8)))
def test_get(self,update,request,ref_path,view,output,flatten,prune):
result = Result(ref_path/'4grains2x4x3_compressionY.hdf5')
for key,value in view.items():
result = result.view(key,value)
fname = request.node.name
cur = result.get(output,flatten,prune)
if update:
with bz2.BZ2File((ref_path/'get'/fname).with_suffix('.pbz2'),'w') as f:
pickle.dump(cur,f)
with bz2.BZ2File((ref_path/'get'/fname).with_suffix('.pbz2')) as f:
assert dict_equal(cur,pickle.load(f))
@pytest.mark.parametrize('view,output,flatten,constituents,prune',
[({},['F','P','F','L_p','F_e','F_p'],True,True,None),
({'increments':3},'F',True,True,[0,1,2,3,4,5,6,7]),
({'increments':[1,8,3,4,5,6,7]},['F','P'],True,True,1),
({'phases':['A','B']},['F','P'],True,True,[1,2]),
({'phases':['A','C'],'homogenizations':False},['F','P','O'],True,True,[0,7]),
({'phases':False,'homogenizations':False},['F','P','O'],True,True,[1,2,3,4]),
({'phases':False},['Delta_V'],True,True,[1,2,4]),
({},['u_p','u_n'],False,False,None)],
ids=list(range(8)))
def test_place(self,update,request,ref_path,view,output,flatten,prune,constituents):
result = Result(ref_path/'4grains2x4x3_compressionY.hdf5')
for key,value in view.items():
result = result.view(key,value)
fname = request.node.name
cur = result.place(output,flatten,prune,constituents)
if update:
with bz2.BZ2File((ref_path/'place'/fname).with_suffix('.pbz2'),'w') as f:
pickle.dump(cur,f)
with bz2.BZ2File((ref_path/'place'/fname).with_suffix('.pbz2')) as f:
assert dict_equal(cur,pickle.load(f))

View File

@ -4,6 +4,7 @@ import time
import pytest import pytest
import numpy as np import numpy as np
import numpy.ma as ma
from damask import VTK from damask import VTK
from damask import grid_filters from damask import grid_filters
@ -134,6 +135,15 @@ class TestVTK:
with pytest.raises(TypeError): with pytest.raises(TypeError):
default.add('invalid_type','valid') default.add('invalid_type','valid')
def test_add_masked(self,default):
data = np.random.rand(5*6*7,3)
masked = ma.MaskedArray(data,mask=data<.4,fill_value=42.)
default.add(masked,'D')
result_masked = str(default)
default.add(np.where(masked.mask,masked.fill_value,masked),'D')
assert result_masked == str(default)
def test_comments(self,tmp_path,default): def test_comments(self,tmp_path,default):
default.add_comments(['this is a comment']) default.add_comments(['this is a comment'])
default.save(tmp_path/'with_comments',parallel=False) default.save(tmp_path/'with_comments',parallel=False)

View File

@ -136,3 +136,25 @@ class TestUtil:
else: else:
with pytest.raises(ValueError): with pytest.raises(ValueError):
util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d') util.DREAM3D_cell_data_group(tmp_path/'cell_data_group.dream3d')
@pytest.mark.parametrize('full,reduced',[({}, {}),
({'A':{}}, {}),
({'A':{'B':{}}}, {}),
({'A':{'B':'C'}},)*2,
({'A':{'B':{},'C':'D'}}, {'A':{'C':'D'}})])
def test_prune(self,full,reduced):
assert util.dict_prune(full) == reduced
@pytest.mark.parametrize('full,reduced',[({}, {}),
({'A':{}}, {}),
({'A':'F'}, 'F'),
({'A':{'B':{}}}, {}),
({'A':{'B':'C'}}, 'C'),
({'A':1,'B':2},)*2,
({'A':{'B':'C','D':'E'}}, {'B':'C','D':'E'}),
({'B':'C','D':'E'},)*2,
({'A':{'B':{},'C':'D'}}, {'B':{},'C':'D'})])
def test_flatten(self,full,reduced):
assert util.dict_flatten(full) == reduced