Merge branch 'development' into 'vtk-to-file-method'
# Conflicts: # python/tests/test_VTK.py
This commit is contained in:
Philip Eisenlohr
commit
6785062a10
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit a16d1e45a2ed925e12244b0879b9d7e5a58d973b
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Subproject commit 1ca2223c68475bbcb9da633353dbe4a98c18db0d
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2
README
2
README
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@ -8,6 +8,6 @@ Max-Planck-Str. 1
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40237 Düsseldorf
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Germany
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Email: DAMASK@mpie.de
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damask@mpie.de
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https://damask.mpie.de
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https://magit1.mpie.de
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@ -169,7 +169,7 @@ for name in filenames:
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# undo any changes involving immutable microstructures
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microstructure = np.where(immutable, microstructure_original,microstructure)
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damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]))
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geom=geom.duplicate(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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geom.to_file(sys.stdout if name is None else name,pack=False)
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@ -2,4 +2,3 @@
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omit = tests/*
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damask/_asciitable.py
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damask/_test.py
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damask/config/*
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@ -24,5 +24,4 @@ from . import solver # noqa
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Environment = _
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from ._asciitable import ASCIItable # noqa
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from ._test import Test # noqa
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from .config import Material # noqa
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from .util import extendableOption # noqa
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|
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@ -280,7 +280,7 @@ class Colormap(mpl.colors.ListedColormap):
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colors+=[i]+c
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out = [{
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'Creator':util.version_date('Colormap'),
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'Creator':util.execution_stamp('Colormap'),
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'ColorSpace':'RGB',
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'Name':colormap.name,
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'DefaultMap':True,
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@ -296,7 +296,7 @@ class Colormap(mpl.colors.ListedColormap):
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def _export_ASCII(colormap,fhandle=None):
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"""Write colormap to ASCII table."""
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labels = {'RGBA':4} if colormap.colors.shape[1] == 4 else {'RGB': 3}
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t = Table(colormap.colors,labels,f'Creator: {util.version_date("Colormap")}')
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t = Table(colormap.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
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if fhandle is None:
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with open(colormap.name.replace(' ','_')+'.txt', 'w') as f:
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@ -24,15 +24,15 @@ class Geom:
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Parameters
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----------
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microstructure : numpy.ndarray
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microstructure array (3D)
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Microstructure array (3D)
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size : list or numpy.ndarray
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physical size of the microstructure in meter.
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Physical size of the microstructure in meter.
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origin : list or numpy.ndarray, optional
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physical origin of the microstructure in meter.
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Physical origin of the microstructure in meter.
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homogenization : int, optional
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homogenization index.
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Homogenization index.
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comments : list of str, optional
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comments lines.
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Comment lines.
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"""
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self.set_microstructure(microstructure)
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@ -63,63 +63,73 @@ class Geom:
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return self.__copy__()
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def update(self,microstructure=None,size=None,origin=None,rescale=False):
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def duplicate(self,microstructure=None,size=None,origin=None,comments=None,autosize=False):
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"""
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Update microstructure and size.
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Create a duplicate having updated microstructure, size, and origin.
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Parameters
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----------
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microstructure : numpy.ndarray, optional
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microstructure array (3D).
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Microstructure array (3D).
|
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size : list or numpy.ndarray, optional
|
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physical size of the microstructure in meter.
|
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Physical size of the microstructure in meter.
|
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origin : list or numpy.ndarray, optional
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physical origin of the microstructure in meter.
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rescale : bool, optional
|
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ignore size parameter and rescale according to change of grid points.
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Physical origin of the microstructure in meter.
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comments : list of str, optional
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Comment lines.
|
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autosize : bool, optional
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Ignore size parameter and rescale according to change of grid points.
|
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|
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"""
|
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if size is not None and autosize:
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raise ValueError('Auto-sizing conflicts with explicit size parameter.')
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grid_old = self.get_grid()
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size_old = self.get_size()
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origin_old = self.get_origin()
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unique_old = self.N_microstructure
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max_old = np.nanmax(self.microstructure)
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dup = self.copy()
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dup.set_microstructure(microstructure)
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dup.set_origin(origin)
|
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|
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if size is not None and rescale:
|
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raise ValueError('Either set size explicitly or rescale automatically')
|
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|
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self.set_microstructure(microstructure)
|
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self.set_origin(origin)
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if comments is not None:
|
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dup.set_comments(comments)
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|
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if size is not None:
|
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self.set_size(size)
|
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elif rescale:
|
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self.set_size(self.get_grid()/grid_old*self.size)
|
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dup.set_size(size)
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elif autosize:
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dup.set_size(dup.get_grid()/grid_old*self.get_size())
|
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|
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message = [f'grid a b c: {util.srepr(grid_old," x ")}']
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if np.any(grid_old != self.get_grid()):
|
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message[-1] = util.delete(message[-1])
|
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return dup
|
||||
|
||||
|
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def diff(self,other):
|
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"""
|
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Report property differences of self relative to other.
|
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|
||||
Parameters
|
||||
----------
|
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other : Geom
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Geometry to compare self against.
|
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|
||||
"""
|
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message = []
|
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if np.any(other.get_grid() != self.get_grid()):
|
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message.append(util.delete(f'grid a b c: {util.srepr(other.get_grid()," x ")}'))
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message.append(util.emph( f'grid a b c: {util.srepr( self.get_grid()," x ")}'))
|
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|
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message.append(f'size x y z: {util.srepr(size_old," x ")}')
|
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if np.any(size_old != self.get_size()):
|
||||
message[-1] = util.delete(message[-1])
|
||||
if np.any(other.get_size() != self.get_size()):
|
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message.append(util.delete(f'size x y z: {util.srepr(other.get_size()," x ")}'))
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message.append(util.emph( f'size x y z: {util.srepr( self.get_size()," x ")}'))
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||||
|
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message.append(f'origin x y z: {util.srepr(origin_old," ")}')
|
||||
if np.any(origin_old != self.get_origin()):
|
||||
message[-1] = util.delete(message[-1])
|
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if np.any(other.get_origin() != self.get_origin()):
|
||||
message.append(util.delete(f'origin x y z: {util.srepr(other.get_origin()," ")}'))
|
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message.append(util.emph( f'origin x y z: {util.srepr( self.get_origin()," ")}'))
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||||
|
||||
message.append(f'# microstructures: {unique_old}')
|
||||
if unique_old != self.N_microstructure:
|
||||
message[-1] = util.delete(message[-1])
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message.append(util.emph(f'# microstructures: {self.N_microstructure}'))
|
||||
if other.N_microstructure != self.N_microstructure:
|
||||
message.append(util.delete(f'# materialpoints: {other.N_microstructure}'))
|
||||
message.append(util.emph( f'# materialpoints: { self.N_microstructure}'))
|
||||
|
||||
message.append(f'max microstructure: {max_old}')
|
||||
if max_old != np.nanmax(self.microstructure):
|
||||
message[-1] = util.delete(message[-1])
|
||||
message.append(util.emph(f'max microstructure: {np.nanmax(self.microstructure)}'))
|
||||
if np.nanmax(other.microstructure) != np.nanmax(self.microstructure):
|
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message.append(util.delete(f'max materialpoint: {np.nanmax(other.microstructure)}'))
|
||||
message.append(util.emph( f'max materialpoint: {np.nanmax( self.microstructure)}'))
|
||||
|
||||
return util.return_message(message)
|
||||
|
||||
|
|
@ -131,7 +141,7 @@ class Geom:
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|||
Parameters
|
||||
----------
|
||||
comments : list of str
|
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new comments.
|
||||
All comments.
|
||||
|
||||
"""
|
||||
self.comments = []
|
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|
|
@ -145,7 +155,7 @@ class Geom:
|
|||
Parameters
|
||||
----------
|
||||
comments : list of str
|
||||
new comments.
|
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New comments.
|
||||
|
||||
"""
|
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self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
|
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|
|
@ -172,6 +182,10 @@ class Geom:
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else:
|
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self.microstructure = np.copy(microstructure)
|
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|
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if self.microstructure.dtype in np.sctypes['float'] and \
|
||||
np.all(self.microstructure == self.microstructure.astype(int).astype(float)):
|
||||
self.microstructure = self.microstructure.astype(int)
|
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|
||||
if len(self.microstructure.shape) != 3:
|
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raise ValueError(f'Invalid microstructure shape {microstructure.shape}')
|
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elif self.microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
|
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|
|
@ -185,7 +199,7 @@ class Geom:
|
|||
Parameters
|
||||
----------
|
||||
size : list or numpy.ndarray
|
||||
physical size of the microstructure in meter.
|
||||
Physical size of the microstructure in meter.
|
||||
|
||||
"""
|
||||
if size is not None:
|
||||
|
|
@ -202,7 +216,7 @@ class Geom:
|
|||
Parameters
|
||||
----------
|
||||
origin : list or numpy.ndarray
|
||||
physical origin of the microstructure in meter
|
||||
Physical origin of the microstructure in meter.
|
||||
|
||||
"""
|
||||
if origin is not None:
|
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|
|
@ -219,12 +233,12 @@ class Geom:
|
|||
Parameters
|
||||
----------
|
||||
homogenization : int
|
||||
homogenization index
|
||||
Homogenization index.
|
||||
|
||||
"""
|
||||
if homogenization is not None:
|
||||
if not isinstance(homogenization,int) or homogenization < 1:
|
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raise TypeError(f'Invalid homogenization {homogenization}')
|
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raise TypeError(f'Invalid homogenization {homogenization}.')
|
||||
else:
|
||||
self.homogenization = homogenization
|
||||
|
||||
|
|
@ -286,13 +300,16 @@ class Geom:
|
|||
f = fname
|
||||
|
||||
f.seek(0)
|
||||
try:
|
||||
header_length,keyword = f.readline().split()[:2]
|
||||
header_length = int(header_length)
|
||||
content = f.readlines()
|
||||
|
||||
except ValueError:
|
||||
header_length,keyword = (-1, 'invalid')
|
||||
if not keyword.startswith('head') or header_length < 3:
|
||||
raise TypeError('Header length information missing or invalid')
|
||||
|
||||
content = f.readlines()
|
||||
|
||||
comments = []
|
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for i,line in enumerate(content[:header_length]):
|
||||
items = line.split('#')[0].lower().strip().split()
|
||||
|
|
@ -345,11 +362,12 @@ class Geom:
|
|||
|
||||
"""
|
||||
v = VTK.from_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
|
||||
grid = np.array(v.geom.GetDimensions())-1
|
||||
bbox = np.array(v.geom.GetBounds()).reshape(3,2).T
|
||||
comments = v.get_comments()
|
||||
grid = np.array(v.vtk_data.GetDimensions())-1
|
||||
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
|
||||
size = bbox[1] - bbox[0]
|
||||
|
||||
return Geom(v.get('materialpoint').reshape(grid,order='F'),size,bbox[0])
|
||||
return Geom(v.get('materialpoint').reshape(grid,order='F'),size,bbox[0],comments=comments)
|
||||
|
||||
|
||||
@staticmethod
|
||||
|
|
@ -398,8 +416,9 @@ class Geom:
|
|||
else:
|
||||
microstructure = microstructure.reshape(grid)
|
||||
|
||||
creator = util.version_date('Geom','from_Laguerre_tessellation')
|
||||
return Geom(microstructure+1,size,homogenization=1,comments=creator)
|
||||
return Geom(microstructure+1,size,homogenization=1,
|
||||
comments=util.execution_stamp('Geom','from_Laguerre_tessellation'),
|
||||
)
|
||||
|
||||
|
||||
@staticmethod
|
||||
|
|
@ -423,8 +442,9 @@ class Geom:
|
|||
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
|
||||
devNull,microstructure = KDTree.query(coords)
|
||||
|
||||
creator = util.version_date('Geom','from_Voronoi_tessellation')
|
||||
return Geom(microstructure.reshape(grid)+1,size,homogenization=1,comments=creator)
|
||||
return Geom(microstructure.reshape(grid)+1,size,homogenization=1,
|
||||
comments=util.execution_stamp('Geom','from_Voronoi_tessellation'),
|
||||
)
|
||||
|
||||
|
||||
def to_file(self,fname,pack=None):
|
||||
|
|
@ -511,6 +531,7 @@ class Geom:
|
|||
"""
|
||||
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
|
||||
v.add(self.microstructure.flatten(order='F'),'materialpoint')
|
||||
v.add_comments(self.comments)
|
||||
|
||||
if fname:
|
||||
v.to_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
|
||||
|
|
@ -518,8 +539,8 @@ class Geom:
|
|||
sys.stdout.write(v.__repr__())
|
||||
|
||||
|
||||
def show(self):
|
||||
"""Show raw content (as in file)."""
|
||||
def as_ASCII(self):
|
||||
"""Format geometry as human-readable ASCII."""
|
||||
f = StringIO()
|
||||
self.to_file(f)
|
||||
f.seek(0)
|
||||
|
|
@ -550,10 +571,10 @@ class Geom:
|
|||
R : damask.Rotation, optional
|
||||
Rotation of primitive. Defaults to no rotation.
|
||||
inverse : Boolean, optional
|
||||
Retain original microstructure within primitive and fill
|
||||
outside. Defaults to False.
|
||||
Retain original microstructure within primitive and fill outside.
|
||||
Defaults to False.
|
||||
periodic : Boolean, optional
|
||||
Repeat primitive over boundaries. Defaults to False.
|
||||
Repeat primitive over boundaries. Defaults to True.
|
||||
|
||||
"""
|
||||
# normalized 'radius' and center
|
||||
|
|
@ -563,11 +584,11 @@ class Geom:
|
|||
(np.array(center) - self.origin)/self.size
|
||||
|
||||
coords = grid_filters.cell_coord0(self.grid,np.ones(3)) \
|
||||
- (np.ones(3)*0.5 if periodic else c) # center if periodic
|
||||
- ((np.ones(3)-(1./self.grid if np.array(center).dtype in np.sctypes['int'] else 0))*0.5 if periodic else c) # periodic center is always at CoG
|
||||
coords_rot = R.broadcast_to(tuple(self.grid))@coords
|
||||
|
||||
with np.errstate(over='ignore',under='ignore'):
|
||||
mask = np.where(np.sum(np.abs(coords_rot/r)**(2.0**exponent),axis=-1) < 1,True,False)
|
||||
with np.errstate(all='ignore'):
|
||||
mask = np.where(np.sum(np.power(coords_rot/r,2.0**exponent),axis=-1) > 1.0,True,False)
|
||||
|
||||
if periodic: # translate back to center
|
||||
mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))
|
||||
|
|
@ -575,8 +596,9 @@ class Geom:
|
|||
fill_ = np.full_like(self.microstructure,np.nanmax(self.microstructure)+1 if fill is None else fill)
|
||||
ms = np.ma.MaskedArray(fill_,np.logical_not(mask) if inverse else mask)
|
||||
|
||||
self.add_comments(util.version_date('Geom','add_primitive'))
|
||||
return self.update(ms)
|
||||
return self.duplicate(ms,
|
||||
comments=self.get_comments()+[util.execution_stamp('Geom','add_primitive')],
|
||||
)
|
||||
|
||||
|
||||
def mirror(self,directions,reflect=False):
|
||||
|
|
@ -589,10 +611,10 @@ class Geom:
|
|||
Direction(s) along which the microstructure is mirrored.
|
||||
Valid entries are 'x', 'y', 'z'.
|
||||
reflect : bool, optional
|
||||
Reflect (include) outermost layers.
|
||||
Reflect (include) outermost layers. Defaults to False.
|
||||
|
||||
"""
|
||||
valid = {'x','y','z'}
|
||||
valid = ['x','y','z']
|
||||
if not set(directions).issubset(valid):
|
||||
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
|
||||
|
||||
|
|
@ -606,8 +628,31 @@ class Geom:
|
|||
if 'x' in directions:
|
||||
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
|
||||
|
||||
self.add_comments(util.version_date('Geom','mirror'))
|
||||
return self.update(ms,rescale=True)
|
||||
return self.duplicate(ms,
|
||||
comments=self.get_comments()+[util.execution_stamp('Geom','mirror')],
|
||||
autosize=True)
|
||||
|
||||
|
||||
def flip(self,directions):
|
||||
"""
|
||||
Flip microstructure along given directions.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
directions : iterable containing str
|
||||
Direction(s) along which the microstructure is flipped.
|
||||
Valid entries are 'x', 'y', 'z'.
|
||||
|
||||
"""
|
||||
valid = ['x','y','z']
|
||||
if not set(directions).issubset(valid):
|
||||
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
|
||||
|
||||
ms = np.flip(self.microstructure, (valid.index(d) for d in directions if d in valid))
|
||||
|
||||
return self.duplicate(ms,
|
||||
comments=self.get_comments()+[util.execution_stamp('Geom','flip')],
|
||||
)
|
||||
|
||||
|
||||
def scale(self,grid,periodic=True):
|
||||
|
|
@ -622,16 +667,15 @@ class Geom:
|
|||
Assume geometry to be periodic. Defaults to True.
|
||||
|
||||
"""
|
||||
self.add_comments(util.version_date('Geom','scale'))
|
||||
return self.update(
|
||||
ndimage.interpolation.zoom(
|
||||
return self.duplicate(ndimage.interpolation.zoom(
|
||||
self.microstructure,
|
||||
grid/self.get_grid(),
|
||||
output=self.microstructure.dtype,
|
||||
order=0,
|
||||
mode=('wrap' if periodic else 'nearest'),
|
||||
prefilter=False
|
||||
)
|
||||
),
|
||||
comments=self.get_comments()+[util.execution_stamp('Geom','scale')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -657,14 +701,14 @@ class Geom:
|
|||
else:
|
||||
return me
|
||||
|
||||
self.add_comments(util.version_date('Geom','clean'))
|
||||
return self.update(ndimage.filters.generic_filter(
|
||||
return self.duplicate(ndimage.filters.generic_filter(
|
||||
self.microstructure,
|
||||
mostFrequent,
|
||||
size=(stencil if selection is None else stencil//2*2+1,)*3,
|
||||
mode=('wrap' if periodic else 'nearest'),
|
||||
extra_keywords=dict(selection=selection),
|
||||
).astype(self.microstructure.dtype)
|
||||
).astype(self.microstructure.dtype),
|
||||
comments=self.get_comments()+[util.execution_stamp('Geom','clean')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -674,8 +718,9 @@ class Geom:
|
|||
for i, oldID in enumerate(np.unique(self.microstructure)):
|
||||
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
|
||||
|
||||
self.add_comments(util.version_date('Geom','renumber'))
|
||||
return self.update(renumbered)
|
||||
return self.duplicate(renumbered,
|
||||
comments=self.get_comments()+[util.execution_stamp('Geom','renumber')],
|
||||
)
|
||||
|
||||
|
||||
def rotate(self,R,fill=None):
|
||||
|
|
@ -709,8 +754,11 @@ class Geom:
|
|||
|
||||
origin = self.origin-(np.asarray(microstructure_in.shape)-self.grid)*.5 * self.size/self.grid
|
||||
|
||||
self.add_comments(util.version_date('Geom','rotate'))
|
||||
return self.update(microstructure_in,origin=origin,rescale=True)
|
||||
return self.duplicate(microstructure_in,
|
||||
origin=origin,
|
||||
comments=self.get_comments()+[util.execution_stamp('Geom','rotate')],
|
||||
autosize=True,
|
||||
)
|
||||
|
||||
|
||||
def canvas(self,grid=None,offset=None,fill=None):
|
||||
|
|
@ -724,16 +772,14 @@ class Geom:
|
|||
offset : numpy.ndarray of shape (3)
|
||||
Offset (measured in grid points) from old to new microstructure[0,0,0].
|
||||
fill : int or float, optional
|
||||
Microstructure index to fill the corners. Defaults to microstructure.max() + 1.
|
||||
Microstructure index to fill the background. Defaults to microstructure.max() + 1.
|
||||
|
||||
"""
|
||||
if fill is None: fill = np.nanmax(self.microstructure) + 1
|
||||
if offset is None: offset = 0
|
||||
dtype = float if int(fill) != fill or self.microstructure.dtype==np.float else int
|
||||
if fill is None: fill = np.nanmax(self.microstructure) + 1
|
||||
dtype = float if int(fill) != fill or self.microstructure.dtype in np.sctypes['float'] else int
|
||||
|
||||
canvas = np.full(self.grid if grid is None else grid,
|
||||
np.nanmax(self.microstructure)+1 if fill is None else fill,
|
||||
dtype)
|
||||
canvas = np.full(self.grid if grid is None else grid,fill,dtype)
|
||||
|
||||
LL = np.clip( offset, 0,np.minimum(self.grid, grid+offset))
|
||||
UR = np.clip( offset+grid, 0,np.minimum(self.grid, grid+offset))
|
||||
|
|
@ -742,8 +788,11 @@ class Geom:
|
|||
|
||||
canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.microstructure[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
|
||||
|
||||
self.add_comments(util.version_date('Geom','canvas'))
|
||||
return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
|
||||
return self.duplicate(canvas,
|
||||
origin=self.origin+offset*self.size/self.grid,
|
||||
comments=self.get_comments()+[util.execution_stamp('Geom','canvas')],
|
||||
autosize=True,
|
||||
)
|
||||
|
||||
|
||||
def substitute(self,from_microstructure,to_microstructure):
|
||||
|
|
@ -762,8 +811,9 @@ class Geom:
|
|||
for from_ms,to_ms in zip(from_microstructure,to_microstructure):
|
||||
substituted[self.microstructure==from_ms] = to_ms
|
||||
|
||||
self.add_comments(util.version_date('Geom','substitute'))
|
||||
return self.update(substituted)
|
||||
return self.duplicate(substituted,
|
||||
comments=self.get_comments()+[util.execution_stamp('Geom','substitute')],
|
||||
)
|
||||
|
||||
|
||||
def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
|
||||
|
|
@ -804,9 +854,10 @@ class Geom:
|
|||
mask = ndimage.filters.generic_filter(self.microstructure,
|
||||
tainted_neighborhood,
|
||||
size=1+2*vicinity,
|
||||
mode=('wrap' if periodic else 'nearest'),
|
||||
mode='wrap' if periodic else 'nearest',
|
||||
extra_keywords={'trigger':trigger})
|
||||
microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask))
|
||||
|
||||
self.add_comments(util.version_date('Geom','vicinity_offset'))
|
||||
return self.update(microstructure)
|
||||
return self.duplicate(microstructure,
|
||||
comments=self.get_comments()+[util.execution_stamp('Geom','vicinity_offset')],
|
||||
)
|
||||
|
|
|
|||
|
|
@ -164,16 +164,16 @@ class Symmetry:
|
|||
with np.errstate(invalid='ignore'):
|
||||
# using '*'/prod for 'and'
|
||||
if self.system == 'cubic':
|
||||
return np.where(np.prod(np.sqrt(2)-1. >= rho_abs,axis=-1) * \
|
||||
return np.where(np.prod(np.sqrt(2)-1. >= rho_abs,axis=-1) *
|
||||
(1. >= np.sum(rho_abs,axis=-1)),True,False)
|
||||
elif self.system == 'hexagonal':
|
||||
return np.where(np.prod(1. >= rho_abs,axis=-1) * \
|
||||
(2. >= np.sqrt(3)*rho_abs[...,0] + rho_abs[...,1]) * \
|
||||
(2. >= np.sqrt(3)*rho_abs[...,1] + rho_abs[...,0]) * \
|
||||
return np.where(np.prod(1. >= rho_abs,axis=-1) *
|
||||
(2. >= np.sqrt(3)*rho_abs[...,0] + rho_abs[...,1]) *
|
||||
(2. >= np.sqrt(3)*rho_abs[...,1] + rho_abs[...,0]) *
|
||||
(2. >= np.sqrt(3) + rho_abs[...,2]),True,False)
|
||||
elif self.system == 'tetragonal':
|
||||
return np.where(np.prod(1. >= rho_abs[...,:2],axis=-1) * \
|
||||
(np.sqrt(2) >= rho_abs[...,0] + rho_abs[...,1]) * \
|
||||
return np.where(np.prod(1. >= rho_abs[...,:2],axis=-1) *
|
||||
(np.sqrt(2) >= rho_abs[...,0] + rho_abs[...,1]) *
|
||||
(np.sqrt(2) >= rho_abs[...,2] + 1.),True,False)
|
||||
elif self.system == 'orthorhombic':
|
||||
return np.where(np.prod(1. >= rho_abs,axis=-1),True,False)
|
||||
|
|
@ -321,6 +321,7 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
|
|||
"""
|
||||
|
||||
lattices = {
|
||||
'iso': {'system':None},
|
||||
'triclinic':{'system':None},
|
||||
'bct': {'system':'tetragonal'},
|
||||
'hex': {'system':'hexagonal'},
|
||||
|
|
|
|||
|
|
@ -1,6 +1,5 @@
|
|||
import multiprocessing as mp
|
||||
import re
|
||||
import inspect
|
||||
import glob
|
||||
import os
|
||||
import datetime
|
||||
|
|
@ -401,6 +400,7 @@ class Result:
|
|||
if sets is True:
|
||||
groups.append(group)
|
||||
else:
|
||||
if group in f.keys():
|
||||
match = [e for e_ in [glob.fnmatch.filter(f[group].keys(),s) for s in sets] for e in e_]
|
||||
if len(set(match)) == len(sets): groups.append(group)
|
||||
return groups
|
||||
|
|
@ -536,7 +536,7 @@ class Result:
|
|||
'meta': {
|
||||
'Unit': x['meta']['Unit'],
|
||||
'Description': f"Absolute value of {x['label']} ({x['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_absolute'
|
||||
}
|
||||
}
|
||||
def add_absolute(self,x):
|
||||
|
|
@ -564,7 +564,7 @@ class Result:
|
|||
'meta': {
|
||||
'Unit': kwargs['unit'],
|
||||
'Description': f"{kwargs['description']} (formula: {kwargs['formula']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_calculation'
|
||||
}
|
||||
}
|
||||
def add_calculation(self,label,formula,unit='n/a',description=None):
|
||||
|
|
@ -598,7 +598,7 @@ class Result:
|
|||
'Description': "Cauchy stress calculated "
|
||||
f"from {P['label']} ({P['meta']['Description']})"
|
||||
f" and {F['label']} ({F['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_Cauchy'
|
||||
}
|
||||
}
|
||||
def add_Cauchy(self,P='P',F='F'):
|
||||
|
|
@ -624,7 +624,7 @@ class Result:
|
|||
'meta': {
|
||||
'Unit': T['meta']['Unit'],
|
||||
'Description': f"Determinant of tensor {T['label']} ({T['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_determinant'
|
||||
}
|
||||
}
|
||||
def add_determinant(self,T):
|
||||
|
|
@ -648,7 +648,7 @@ class Result:
|
|||
'meta': {
|
||||
'Unit': T['meta']['Unit'],
|
||||
'Description': f"Deviator of tensor {T['label']} ({T['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_deviator'
|
||||
}
|
||||
}
|
||||
def add_deviator(self,T):
|
||||
|
|
@ -679,7 +679,7 @@ class Result:
|
|||
'meta' : {
|
||||
'Unit': T_sym['meta']['Unit'],
|
||||
'Description': f"{label} eigenvalue of {T_sym['label']} ({T_sym['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_eigenvalue'
|
||||
}
|
||||
}
|
||||
def add_eigenvalue(self,T_sym,eigenvalue='max'):
|
||||
|
|
@ -712,7 +712,7 @@ class Result:
|
|||
'Unit': '1',
|
||||
'Description': f"Eigenvector corresponding to {label} eigenvalue"
|
||||
f" of {T_sym['label']} ({T_sym['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_eigenvector'
|
||||
}
|
||||
}
|
||||
def add_eigenvector(self,T_sym,eigenvalue='max'):
|
||||
|
|
@ -745,7 +745,7 @@ class Result:
|
|||
'Unit': '8-bit RGB',
|
||||
'Lattice': q['meta']['Lattice'],
|
||||
'Description': 'Inverse Pole Figure (IPF) colors along sample direction [{} {} {}]'.format(*m),
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_IPF_color'
|
||||
}
|
||||
}
|
||||
def add_IPF_color(self,q,l):
|
||||
|
|
@ -771,7 +771,7 @@ class Result:
|
|||
'meta': {
|
||||
'Unit': T_sym['meta']['Unit'],
|
||||
'Description': f"Maximum shear component of {T_sym['label']} ({T_sym['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_maximum_shear'
|
||||
}
|
||||
}
|
||||
def add_maximum_shear(self,T_sym):
|
||||
|
|
@ -798,7 +798,7 @@ class Result:
|
|||
'meta': {
|
||||
'Unit': T_sym['meta']['Unit'],
|
||||
'Description': f"Mises equivalent {t} of {T_sym['label']} ({T_sym['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_Mises'
|
||||
}
|
||||
}
|
||||
def add_Mises(self,T_sym):
|
||||
|
|
@ -834,7 +834,7 @@ class Result:
|
|||
'meta': {
|
||||
'Unit': x['meta']['Unit'],
|
||||
'Description': f"{o}-norm of {t} {x['label']} ({x['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_norm'
|
||||
}
|
||||
}
|
||||
def add_norm(self,x,ord=None):
|
||||
|
|
@ -862,7 +862,7 @@ class Result:
|
|||
'Description': "2. Piola-Kirchhoff stress calculated "
|
||||
f"from {P['label']} ({P['meta']['Description']})"
|
||||
f" and {F['label']} ({F['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_PK2'
|
||||
}
|
||||
}
|
||||
def add_PK2(self,P='P',F='F'):
|
||||
|
|
@ -898,7 +898,7 @@ class Result:
|
|||
'Unit': '1',
|
||||
'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\
|
||||
.format('Polar' if polar else 'Cartesian'),
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_pole'
|
||||
}
|
||||
}
|
||||
def add_pole(self,q,p,polar=False):
|
||||
|
|
@ -926,7 +926,7 @@ class Result:
|
|||
'meta': {
|
||||
'Unit': F['meta']['Unit'],
|
||||
'Description': f"Rotational part of {F['label']} ({F['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_rotational_part'
|
||||
}
|
||||
}
|
||||
def add_rotational_part(self,F):
|
||||
|
|
@ -950,7 +950,7 @@ class Result:
|
|||
'meta': {
|
||||
'Unit': T['meta']['Unit'],
|
||||
'Description': f"Spherical component of tensor {T['label']} ({T['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_spherical'
|
||||
}
|
||||
}
|
||||
def add_spherical(self,T):
|
||||
|
|
@ -974,7 +974,7 @@ class Result:
|
|||
'meta': {
|
||||
'Unit': F['meta']['Unit'],
|
||||
'Description': f"Strain tensor of {F['label']} ({F['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_strain_tensor'
|
||||
}
|
||||
}
|
||||
def add_strain_tensor(self,F='F',t='V',m=0.0):
|
||||
|
|
@ -1006,7 +1006,7 @@ class Result:
|
|||
'Unit': F['meta']['Unit'],
|
||||
'Description': '{} stretch tensor of {} ({})'.format('Left' if t.upper() == 'V' else 'Right',
|
||||
F['label'],F['meta']['Description']),
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
'Creator': 'add_stretch_tensor'
|
||||
}
|
||||
}
|
||||
def add_stretch_tensor(self,F='F',t='V'):
|
||||
|
|
@ -1065,6 +1065,10 @@ class Result:
|
|||
lock = mp.Manager().Lock()
|
||||
|
||||
groups = self.groups_with_datasets(datasets.values())
|
||||
if len(groups) == 0:
|
||||
print('No matching dataset found, no data was added.')
|
||||
return
|
||||
|
||||
default_arg = partial(self._job,func=func,datasets=datasets,args=args,lock=lock)
|
||||
|
||||
for result in util.show_progress(pool.imap_unordered(default_arg,groups),len(groups)):
|
||||
|
|
|
|||
|
|
@ -49,7 +49,7 @@ class Table:
|
|||
def _add_comment(self,label,shape,info):
|
||||
if info is not None:
|
||||
specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}'
|
||||
general = util.version_date('Table')
|
||||
general = util.execution_stamp('Table')
|
||||
self.comments.append(f'{specific} / {general}')
|
||||
|
||||
|
||||
|
|
@ -136,7 +136,7 @@ class Table:
|
|||
|
||||
content = f.readlines()
|
||||
|
||||
comments = [util.version_date('Table','from_ang')]
|
||||
comments = [util.execution_stamp('Table','from_ang')]
|
||||
for line in content:
|
||||
if line.startswith('#'):
|
||||
comments.append(line.strip())
|
||||
|
|
|
|||
|
|
@ -20,18 +20,19 @@ class VTK:
|
|||
High-level interface to VTK.
|
||||
"""
|
||||
|
||||
def __init__(self,geom):
|
||||
def __init__(self,vtk_data):
|
||||
"""
|
||||
Set geometry and topology.
|
||||
Initialize from vtk dataset.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
geom : subclass of vtk.vtkDataSet
|
||||
Description of geometry and topology. Valid types are vtk.vtkRectilinearGrid,
|
||||
vtk.vtkUnstructuredGrid, or vtk.vtkPolyData.
|
||||
vtk_data : subclass of vtk.vtkDataSet
|
||||
Description of geometry and topology, optionally with attached data.
|
||||
Valid types are vtk.vtkRectilinearGrid, vtk.vtkUnstructuredGrid,
|
||||
or vtk.vtkPolyData.
|
||||
|
||||
"""
|
||||
self.geom = geom
|
||||
self.vtk_data = vtk_data
|
||||
|
||||
|
||||
@staticmethod
|
||||
|
|
@ -51,15 +52,15 @@ class VTK:
|
|||
Spatial origin.
|
||||
|
||||
"""
|
||||
geom = vtk.vtkRectilinearGrid()
|
||||
geom.SetDimensions(*(grid+1))
|
||||
vtk_data = vtk.vtkRectilinearGrid()
|
||||
vtk_data.SetDimensions(*(grid+1))
|
||||
coord = [np_to_vtk(np.linspace(origin[i],origin[i]+size[i],grid[i]+1),deep=True) for i in [0,1,2]]
|
||||
[coord[i].SetName(n) for i,n in enumerate(['x','y','z'])]
|
||||
geom.SetXCoordinates(coord[0])
|
||||
geom.SetYCoordinates(coord[1])
|
||||
geom.SetZCoordinates(coord[2])
|
||||
vtk_data.SetXCoordinates(coord[0])
|
||||
vtk_data.SetYCoordinates(coord[1])
|
||||
vtk_data.SetZCoordinates(coord[2])
|
||||
|
||||
return VTK(geom)
|
||||
return VTK(vtk_data)
|
||||
|
||||
|
||||
@staticmethod
|
||||
|
|
@ -87,11 +88,11 @@ class VTK:
|
|||
connectivity),axis=1).ravel()
|
||||
cells.SetCells(connectivity.shape[0],np_to_vtkIdTypeArray(T,deep=True))
|
||||
|
||||
geom = vtk.vtkUnstructuredGrid()
|
||||
geom.SetPoints(vtk_nodes)
|
||||
geom.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
|
||||
vtk_data = vtk.vtkUnstructuredGrid()
|
||||
vtk_data.SetPoints(vtk_nodes)
|
||||
vtk_data.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
|
||||
|
||||
return VTK(geom)
|
||||
return VTK(vtk_data)
|
||||
|
||||
|
||||
@staticmethod
|
||||
|
|
@ -110,10 +111,10 @@ class VTK:
|
|||
vtk_points = vtk.vtkPoints()
|
||||
vtk_points.SetData(np_to_vtk(points))
|
||||
|
||||
geom = vtk.vtkPolyData()
|
||||
geom.SetPoints(vtk_points)
|
||||
vtk_data = vtk.vtkPolyData()
|
||||
vtk_data.SetPoints(vtk_points)
|
||||
|
||||
return VTK(geom)
|
||||
return VTK(vtk_data)
|
||||
|
||||
|
||||
@staticmethod
|
||||
|
|
@ -131,18 +132,20 @@ class VTK:
|
|||
|
||||
"""
|
||||
ext = Path(fname).suffix
|
||||
if ext == '.vtk' or dataset_type:
|
||||
if ext == '.vtk' or dataset_type is not None:
|
||||
reader = vtk.vtkGenericDataObjectReader()
|
||||
reader.SetFileName(str(fname))
|
||||
reader.Update()
|
||||
if dataset_type is None:
|
||||
raise TypeError('Dataset type for *.vtk file not given.')
|
||||
elif dataset_type.lower().endswith('rectilineargrid'):
|
||||
geom = reader.GetRectilinearGridOutput()
|
||||
reader.Update()
|
||||
vtk_data = reader.GetRectilinearGridOutput()
|
||||
elif dataset_type.lower().endswith('unstructuredgrid'):
|
||||
geom = reader.GetUnstructuredGridOutput()
|
||||
reader.Update()
|
||||
vtk_data = reader.GetUnstructuredGridOutput()
|
||||
elif dataset_type.lower().endswith('polydata'):
|
||||
geom = reader.GetPolyDataOutput()
|
||||
reader.Update()
|
||||
vtk_data = reader.GetPolyDataOutput()
|
||||
else:
|
||||
raise TypeError(f'Unknown dataset type {dataset_type} for vtk file')
|
||||
else:
|
||||
|
|
@ -157,9 +160,9 @@ class VTK:
|
|||
|
||||
reader.SetFileName(str(fname))
|
||||
reader.Update()
|
||||
geom = reader.GetOutput()
|
||||
vtk_data = reader.GetOutput()
|
||||
|
||||
return VTK(geom)
|
||||
return VTK(vtk_data)
|
||||
|
||||
@staticmethod
|
||||
def _write(writer):
|
||||
|
|
@ -177,11 +180,11 @@ class VTK:
|
|||
Write data in parallel background process. Defaults to True.
|
||||
|
||||
"""
|
||||
if isinstance(self.geom,vtk.vtkRectilinearGrid):
|
||||
if isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
|
||||
writer = vtk.vtkXMLRectilinearGridWriter()
|
||||
elif isinstance(self.geom,vtk.vtkUnstructuredGrid):
|
||||
elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid):
|
||||
writer = vtk.vtkXMLUnstructuredGridWriter()
|
||||
elif isinstance(self.geom,vtk.vtkPolyData):
|
||||
elif isinstance(self.vtk_data,vtk.vtkPolyData):
|
||||
writer = vtk.vtkXMLPolyDataWriter()
|
||||
|
||||
default_ext = writer.GetDefaultFileExtension()
|
||||
|
|
@ -191,7 +194,7 @@ class VTK:
|
|||
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetInputData(self.geom)
|
||||
writer.SetInputData(self.vtk_data)
|
||||
|
||||
if parallel:
|
||||
try:
|
||||
|
|
@ -218,8 +221,8 @@ class VTK:
|
|||
Data label.
|
||||
|
||||
"""
|
||||
N_points = self.geom.GetNumberOfPoints()
|
||||
N_cells = self.geom.GetNumberOfCells()
|
||||
N_points = self.vtk_data.GetNumberOfPoints()
|
||||
N_cells = self.vtk_data.GetNumberOfCells()
|
||||
|
||||
if isinstance(data,np.ndarray):
|
||||
if label is None:
|
||||
|
|
@ -232,9 +235,9 @@ class VTK:
|
|||
d.SetName(label)
|
||||
|
||||
if data.shape[0] == N_cells:
|
||||
self.geom.GetCellData().AddArray(d)
|
||||
self.vtk_data.GetCellData().AddArray(d)
|
||||
elif data.shape[0] == N_points:
|
||||
self.geom.GetPointData().AddArray(d)
|
||||
self.vtk_data.GetPointData().AddArray(d)
|
||||
else:
|
||||
raise ValueError(f'Invalid shape {data.shape[0]}')
|
||||
elif isinstance(data,pd.DataFrame):
|
||||
|
|
@ -259,22 +262,22 @@ class VTK:
|
|||
Data label.
|
||||
|
||||
"""
|
||||
celldata = self.geom.GetCellData()
|
||||
for a in range(celldata.GetNumberOfArrays()):
|
||||
if celldata.GetArrayName(a) == label:
|
||||
return vtk_to_np(celldata.GetArray(a))
|
||||
cell_data = self.vtk_data.GetCellData()
|
||||
for a in range(cell_data.GetNumberOfArrays()):
|
||||
if cell_data.GetArrayName(a) == label:
|
||||
return vtk_to_np(cell_data.GetArray(a))
|
||||
|
||||
pointdata = self.geom.GetPointData()
|
||||
for a in range(celldata.GetNumberOfArrays()):
|
||||
if pointdata.GetArrayName(a) == label:
|
||||
return vtk_to_np(pointdata.GetArray(a))
|
||||
point_data = self.vtk_data.GetPointData()
|
||||
for a in range(point_data.GetNumberOfArrays()):
|
||||
if point_data.GetArrayName(a) == label:
|
||||
return vtk_to_np(point_data.GetArray(a))
|
||||
|
||||
raise ValueError(f'array "{label}" not found')
|
||||
|
||||
|
||||
def get_comments(self):
|
||||
"""Return the comments."""
|
||||
fielddata = self.geom.GetFieldData()
|
||||
fielddata = self.vtk_data.GetFieldData()
|
||||
for a in range(fielddata.GetNumberOfArrays()):
|
||||
if fielddata.GetArrayName(a) == 'comments':
|
||||
comments = fielddata.GetAbstractArray(a)
|
||||
|
|
@ -284,7 +287,7 @@ class VTK:
|
|||
|
||||
def set_comments(self,comments):
|
||||
"""
|
||||
Set Comments.
|
||||
Set comments.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -296,12 +299,12 @@ class VTK:
|
|||
s.SetName('comments')
|
||||
for c in [comments] if isinstance(comments,str) else comments:
|
||||
s.InsertNextValue(c)
|
||||
self.geom.GetFieldData().AddArray(s)
|
||||
self.vtk_data.GetFieldData().AddArray(s)
|
||||
|
||||
|
||||
def add_comments(self,comments):
|
||||
"""
|
||||
Add Comments.
|
||||
Add comments.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -309,15 +312,15 @@ class VTK:
|
|||
Comments to add.
|
||||
|
||||
"""
|
||||
self.set_comments(self.get_comments + ([comments] if isinstance(comments,str) else comments))
|
||||
self.set_comments(self.get_comments() + ([comments] if isinstance(comments,str) else comments))
|
||||
|
||||
|
||||
def __repr__(self):
|
||||
"""ASCII representation of the VTK data."""
|
||||
writer = vtk.vtkDataSetWriter()
|
||||
writer.SetHeader(f'# {util.version_date("VTK")}')
|
||||
writer.SetHeader(f'# {util.execution_stamp("VTK")}')
|
||||
writer.WriteToOutputStringOn()
|
||||
writer.SetInputData(self.geom)
|
||||
writer.SetInputData(self.vtk_data)
|
||||
writer.Write()
|
||||
return writer.GetOutputString()
|
||||
|
||||
|
|
@ -329,7 +332,7 @@ class VTK:
|
|||
See http://compilatrix.com/article/vtk-1 for further ideas.
|
||||
"""
|
||||
mapper = vtk.vtkDataSetMapper()
|
||||
mapper.SetInputData(self.geom)
|
||||
mapper.SetInputData(self.vtk_data)
|
||||
actor = vtk.vtkActor()
|
||||
actor.SetMapper(mapper)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,3 +0,0 @@
|
|||
"""Aggregator for configuration file handling."""
|
||||
|
||||
from .material import Material # noqa
|
||||
|
|
@ -1,282 +0,0 @@
|
|||
import re
|
||||
import os
|
||||
|
||||
from damask import util
|
||||
|
||||
class Section():
|
||||
def __init__(self,data = {'__order__':[]},part = ''):
|
||||
"""New material.config section."""
|
||||
classes = {
|
||||
'homogenization':Homogenization,
|
||||
'microstructure':Microstructure,
|
||||
'crystallite':Crystallite,
|
||||
'phase':Phase,
|
||||
'texture':Texture,
|
||||
}
|
||||
self.parameters = {}
|
||||
for key in data:
|
||||
self.parameters[key] = data[key] if isinstance(data[key], list) else [data[key]]
|
||||
|
||||
if '__order__' not in self.parameters:
|
||||
self.parameters['__order__'] = list(self.parameters.keys())
|
||||
if part.lower() in classes:
|
||||
self.__class__ = classes[part.lower()]
|
||||
self.__init__(data)
|
||||
|
||||
def add_multiKey(self,key,data):
|
||||
multiKey = '(%s)'%key
|
||||
if multiKey not in self.parameters: self.parameters[multiKey] = []
|
||||
if multiKey not in self.parameters['__order__']: self.parameters['__order__'] += [multiKey]
|
||||
self.parameters[multiKey] += [[item] for item in data] if isinstance(data, list) else [[data]]
|
||||
|
||||
def data(self):
|
||||
return self.parameters
|
||||
|
||||
|
||||
class Homogenization(Section):
|
||||
def __init__(self,data = {'__order__':[]}):
|
||||
"""New material.config <homogenization> section."""
|
||||
Section.__init__(self,data)
|
||||
|
||||
|
||||
class Crystallite(Section):
|
||||
def __init__(self,data = {'__order__':[]}):
|
||||
"""New material.config <crystallite> section."""
|
||||
Section.__init__(self,data)
|
||||
|
||||
|
||||
class Phase(Section):
|
||||
def __init__(self,data = {'__order__':[]}):
|
||||
"""New material.config <Phase> section."""
|
||||
Section.__init__(self,data)
|
||||
|
||||
|
||||
class Microstructure(Section):
|
||||
def __init__(self,data = {'__order__':[]}):
|
||||
"""New material.config <microstructure> section."""
|
||||
Section.__init__(self,data)
|
||||
|
||||
|
||||
class Texture(Section):
|
||||
def __init__(self,data = {'__order__':[]}):
|
||||
"""New material.config <texture> section."""
|
||||
Section.__init__(self,data)
|
||||
|
||||
def add_component(self,theType,properties):
|
||||
|
||||
scatter = properties['scatter'] if 'scatter' in list(map(str.lower,list(properties.keys()))) else 0.0
|
||||
fraction = properties['fraction'] if 'fraction' in list(map(str.lower,list(properties.keys()))) else 1.0
|
||||
|
||||
try:
|
||||
multiKey = theType.lower()
|
||||
except AttributeError:
|
||||
pass
|
||||
|
||||
if multiKey == 'gauss':
|
||||
self.add_multiKey(multiKey,'phi1 %g\tPhi %g\tphi2 %g\tscatter %g\tfraction %g'%(
|
||||
properties['eulers'][0],
|
||||
properties['eulers'][1],
|
||||
properties['eulers'][2],
|
||||
scatter,
|
||||
fraction,
|
||||
)
|
||||
)
|
||||
|
||||
|
||||
class Material():
|
||||
"""Read, manipulate, and write material.config files."""
|
||||
|
||||
def __init__(self,verbose=True):
|
||||
"""Generates ordered list of parts."""
|
||||
self.parts = [
|
||||
'homogenization',
|
||||
'crystallite',
|
||||
'phase',
|
||||
'texture',
|
||||
'microstructure',
|
||||
]
|
||||
self.data = {
|
||||
'homogenization': {'__order__': []},
|
||||
'microstructure': {'__order__': []},
|
||||
'crystallite': {'__order__': []},
|
||||
'phase': {'__order__': []},
|
||||
'texture': {'__order__': []},
|
||||
}
|
||||
self.verbose = verbose
|
||||
|
||||
def __repr__(self):
|
||||
"""Returns current data structure in material.config format."""
|
||||
me = []
|
||||
for part in self.parts:
|
||||
if self.verbose: print(f'processing <{part}>')
|
||||
me += ['',
|
||||
'#'*100,
|
||||
f'<{part}>',
|
||||
'#'*100,
|
||||
]
|
||||
for section in self.data[part]['__order__']:
|
||||
me += [f'[{section}] {"#"+"-"*max(0,96-len(section))}']
|
||||
for key in self.data[part][section]['__order__']:
|
||||
if key.startswith('(') and key.endswith(')'): # multiple (key)
|
||||
me += [f'{key}\t{" ".join(values)}' for values in self.data[part][section][key]]
|
||||
else: # plain key
|
||||
me += [f'{key}\t{util.srepr(self.data[part][section][key]," ")}']
|
||||
return '\n'.join(me) + '\n'
|
||||
|
||||
def parse(self, part=None, sections=[], content=None):
|
||||
|
||||
re_part = re.compile(r'^<(.+)>$') # pattern for part
|
||||
re_sec = re.compile(r'^\[(.+)\]$') # pattern for section
|
||||
|
||||
name_section = ''
|
||||
active = False
|
||||
|
||||
for line in content:
|
||||
line = line.split('#')[0].strip() # kill comments and extra whitespace
|
||||
line = line.split('/echo/')[0].strip() # remove '/echo/' tags
|
||||
line = line.lower() # be case insensitive
|
||||
|
||||
if line: # content survives...
|
||||
match_part = re_part.match(line)
|
||||
if match_part: # found <...> separator
|
||||
active = (match_part.group(1) == part) # only active in <part>
|
||||
continue
|
||||
if active:
|
||||
match_sec = re_sec.match(line)
|
||||
if match_sec: # found [section]
|
||||
name_section = match_sec.group(1) # remember name ...
|
||||
if '__order__' not in self.data[part]: self.data[part]['__order__'] = []
|
||||
self.data[part]['__order__'].append(name_section) # ... and position
|
||||
self.data[part][name_section] = {'__order__':[]}
|
||||
continue
|
||||
|
||||
if sections == [] or name_section in sections: # possibly restrict to subset
|
||||
items = line.split()
|
||||
if items[0] not in self.data[part][name_section]: # first encounter of key?
|
||||
self.data[part][name_section][items[0]] = [] # create item
|
||||
self.data[part][name_section]['__order__'].append(items[0])
|
||||
if items[0].startswith('(') and items[0].endswith(')'): # multiple "(key)"
|
||||
self.data[part][name_section][items[0]].append(items[1:])
|
||||
else: # plain key
|
||||
self.data[part][name_section][items[0]] = items[1:]
|
||||
|
||||
|
||||
|
||||
def read(self,filename=None):
|
||||
"""Read material.config file."""
|
||||
def recursiveRead(filename):
|
||||
"""Takes care of include statements like '{}'."""
|
||||
result = []
|
||||
re_include = re.compile(r'^{(.+)}$')
|
||||
with open(filename) as f: lines = f.readlines()
|
||||
for line in lines:
|
||||
match = re_include.match(line.split()[0]) if line.strip() else False
|
||||
result += [line] if not match else \
|
||||
recursiveRead(match.group(1) if match.group(1).startswith('/') else
|
||||
os.path.normpath(os.path.join(os.path.dirname(filename),match.group(1))))
|
||||
return result
|
||||
|
||||
c = recursiveRead(filename)
|
||||
for p in self.parts:
|
||||
self.parse(part=p, content=c)
|
||||
|
||||
def write(self,filename='material.config', overwrite=False):
|
||||
"""Write to material.config."""
|
||||
i = 0
|
||||
outname = filename
|
||||
while os.path.exists(outname) and not overwrite:
|
||||
i += 1
|
||||
outname = f'{filename}_{i}'
|
||||
|
||||
if self.verbose: print(f'Writing material data to {outname}')
|
||||
with open(outname,'w') as f:
|
||||
f.write(str(self))
|
||||
return outname
|
||||
|
||||
def add_section(self, part=None, section=None, initialData=None, merge=False):
|
||||
"""Add Update."""
|
||||
part = part.lower()
|
||||
section = section.lower()
|
||||
if part not in self.parts: raise Exception(f'invalid part {part}')
|
||||
|
||||
if not isinstance(initialData, dict):
|
||||
initialData = initialData.data()
|
||||
|
||||
if section not in self.data[part]: self.data[part]['__order__'] += [section]
|
||||
if section in self.data[part] and merge:
|
||||
for existing in self.data[part][section]['__order__']: # replace existing
|
||||
if existing in initialData['__order__']:
|
||||
if existing.startswith('(') and existing.endswith(')'): # multiple (key)
|
||||
self.data[part][section][existing] += initialData[existing] # add new multiple entries to existing ones
|
||||
else: # regular key
|
||||
self.data[part][section][existing] = initialData[existing] # plain replice
|
||||
for new in initialData['__order__']: # merge new content
|
||||
if new not in self.data[part][section]['__order__']:
|
||||
self.data[part][section][new] = initialData[new]
|
||||
self.data[part][section]['__order__'] += [new]
|
||||
else:
|
||||
self.data[part][section] = initialData
|
||||
|
||||
|
||||
|
||||
|
||||
def add_microstructure(self, section='',
|
||||
components={}, # dict of phase,texture, and fraction lists
|
||||
):
|
||||
"""Experimental! Needs expansion to multi-constituent microstructures..."""
|
||||
microstructure = Microstructure()
|
||||
# make keys lower case (http://stackoverflow.com/questions/764235/dictionary-to-lowercase-in-python)
|
||||
components=dict((k.lower(), v) for k,v in components.items())
|
||||
|
||||
for key in ['phase','texture','fraction','crystallite']:
|
||||
if isinstance(components[key], list):
|
||||
for i, x in enumerate(components[key]):
|
||||
try:
|
||||
components[key][i] = x.lower()
|
||||
except AttributeError:
|
||||
pass
|
||||
else:
|
||||
try:
|
||||
components[key] = [components[key].lower()]
|
||||
except AttributeError:
|
||||
components[key] = [components[key]]
|
||||
|
||||
for (phase,texture,fraction,crystallite) in zip(components['phase'],components['texture'],
|
||||
components['fraction'],components['crystallite']):
|
||||
microstructure.add_multiKey('constituent','phase %i\ttexture %i\tfraction %g\ncrystallite %i'%(
|
||||
self.data['phase']['__order__'].index(phase)+1,
|
||||
self.data['texture']['__order__'].index(texture)+1,
|
||||
fraction,
|
||||
self.data['crystallite']['__order__'].index(crystallite)+1))
|
||||
|
||||
self.add_section('microstructure',section,microstructure)
|
||||
|
||||
|
||||
def change_value(self, part=None,
|
||||
section=None,
|
||||
key=None,
|
||||
value=None):
|
||||
if not isinstance(value,list):
|
||||
if not isinstance(value,str):
|
||||
value = '%s'%value
|
||||
value = [value]
|
||||
newlen = len(value)
|
||||
oldval = self.data[part.lower()][section.lower()][key.lower()]
|
||||
oldlen = len(oldval)
|
||||
print('changing %s:%s:%s from %s to %s '%(part.lower(),section.lower(),key.lower(),oldval,value))
|
||||
self.data[part.lower()][section.lower()][key.lower()] = value
|
||||
if newlen is not oldlen:
|
||||
print('Length of value was changed from %i to %i!'%(oldlen,newlen))
|
||||
|
||||
|
||||
def add_value(self, part=None,
|
||||
section=None,
|
||||
key=None,
|
||||
value=None):
|
||||
if not isinstance(value,list):
|
||||
if not isinstance(value,str):
|
||||
value = '%s'%value
|
||||
value = [value]
|
||||
print('adding %s:%s:%s with value %s '%(part.lower(),section.lower(),key.lower(),value))
|
||||
self.data[part.lower()][section.lower()][key.lower()] = value
|
||||
self.data[part.lower()][section.lower()]['__order__'] += [key.lower()]
|
||||
|
|
@ -22,7 +22,7 @@ __all__=[
|
|||
'scale_to_coprime',
|
||||
'return_message',
|
||||
'extendableOption',
|
||||
'version_date'
|
||||
'execution_stamp'
|
||||
]
|
||||
|
||||
####################################################################################################
|
||||
|
|
@ -178,10 +178,10 @@ def scale_to_coprime(v):
|
|||
return m
|
||||
|
||||
|
||||
def version_date(class_name,function_name=None):
|
||||
"""tbd."""
|
||||
_function_name = '' if function_name is None else f'.{function_name}'
|
||||
def execution_stamp(class_name,function_name=None):
|
||||
"""Timestamp the execution of a (function within a) class."""
|
||||
now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
|
||||
_function_name = '' if function_name is None else f'.{function_name}'
|
||||
return f'damask.{class_name}{_function_name} v{version} ({now})'
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -16,12 +16,11 @@ setuptools.setup(
|
|||
packages=setuptools.find_packages(),
|
||||
include_package_data=True,
|
||||
install_requires = [
|
||||
"pandas",
|
||||
"pandas", # requires numpy
|
||||
"scipy",
|
||||
"h5py",
|
||||
"h5py", # requires numpy
|
||||
"vtk",
|
||||
"matplotlib",
|
||||
"PIL",
|
||||
"matplotlib", # requires numpy, pillow
|
||||
],
|
||||
classifiers = [
|
||||
"Intended Audience :: Science/Research",
|
||||
|
|
|
|||
|
|
@ -26,13 +26,13 @@ def patch_datetime_now(monkeypatch):
|
|||
monkeypatch.setattr(datetime, 'datetime', mydatetime)
|
||||
|
||||
@pytest.fixture
|
||||
def version_date(monkeypatch):
|
||||
"""Set damask.util.version_date for reproducible tests results."""
|
||||
def version_date(class_name,function_name=None):
|
||||
def execution_stamp(monkeypatch):
|
||||
"""Set damask.util.execution_stamp for reproducible tests results."""
|
||||
def execution_stamp(class_name,function_name=None):
|
||||
_function_name = '' if function_name is None else f'.{function_name}'
|
||||
return f'damask.{class_name}{_function_name} v{patched_version} ({patched_date})'
|
||||
|
||||
monkeypatch.setattr(damask.util, 'version_date', version_date)
|
||||
monkeypatch.setattr(damask.util, 'execution_stamp', execution_stamp)
|
||||
|
||||
|
||||
def pytest_addoption(parser):
|
||||
|
|
|
|||
|
|
@ -1,25 +0,0 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
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||||
<RectilinearGrid WholeExtent="0 20 0 18 0 8">
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<Piece Extent="0 20 0 18 0 8">
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<PointData>
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||||
</PointData>
|
||||
<CellData>
|
||||
<DataArray type="Int32" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
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AQAAAACAAAAALQAANQAAAA==eF7t1CECACAMxLBj/380fhYwIyK2spWkmnWgt6b3AF65/avfegAAAAAAAAAAAMy0AfYtC2k=
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</DataArray>
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||||
</CellData>
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<Coordinates>
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<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
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</DataArray>
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<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
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||||
</DataArray>
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
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AQAAAACAAABIAAAAIgAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9Bkp/sAcAAU8I6Q==
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||||
</DataArray>
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||||
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||||
</Piece>
|
||||
</RectilinearGrid>
|
||||
</VTKFile>
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
<?xml version="1.0"?>
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||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
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||||
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
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<Piece Extent="0 8 0 5 0 4">
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<PointData>
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||||
</PointData>
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<CellData>
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<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
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||||
</DataArray>
|
||||
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<Coordinates>
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<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
|
||||
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
|
||||
</DataArray>
|
||||
</Coordinates>
|
||||
</Piece>
|
||||
</RectilinearGrid>
|
||||
</VTKFile>
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
|
||||
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
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||||
<Piece Extent="0 8 0 5 0 4">
|
||||
<PointData>
|
||||
</PointData>
|
||||
<CellData>
|
||||
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
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||||
</DataArray>
|
||||
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|
||||
<Coordinates>
|
||||
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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||||
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
|
||||
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
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||||
</DataArray>
|
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|
||||
</Piece>
|
||||
</RectilinearGrid>
|
||||
</VTKFile>
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
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<RectilinearGrid WholeExtent="0 8 0 5 0 4">
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<Piece Extent="0 8 0 5 0 4">
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<PointData>
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||||
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
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</DataArray>
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||||
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||||
<Coordinates>
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||||
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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||||
</DataArray>
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
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||||
</DataArray>
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||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
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||||
</DataArray>
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</RectilinearGrid>
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</VTKFile>
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||||
|
|
@ -0,0 +1,25 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
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||||
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
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||||
<Piece Extent="0 8 0 5 0 4">
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||||
<PointData>
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||||
</PointData>
|
||||
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|
||||
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
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||||
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||||
<Coordinates>
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||||
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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||||
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
|
||||
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
|
||||
</DataArray>
|
||||
</Coordinates>
|
||||
</Piece>
|
||||
</RectilinearGrid>
|
||||
</VTKFile>
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
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||||
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
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||||
<Piece Extent="0 8 0 5 0 4">
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||||
<PointData>
|
||||
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|
||||
<CellData>
|
||||
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||||
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||||
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||||
<Coordinates>
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||||
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||||
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|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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||||
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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||||
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
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||||
</DataArray>
|
||||
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|
||||
</Piece>
|
||||
</RectilinearGrid>
|
||||
</VTKFile>
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
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||||
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
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||||
<Piece Extent="0 8 0 5 0 4">
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||||
<PointData>
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||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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||||
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|
||||
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|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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||||
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
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||||
</DataArray>
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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||||
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
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||||
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|
||||
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|
||||
</Piece>
|
||||
</RectilinearGrid>
|
||||
</VTKFile>
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
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||||
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
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||||
<Piece Extent="0 8 0 5 0 4">
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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||||
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
|
||||
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
|
||||
</DataArray>
|
||||
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|
||||
</Piece>
|
||||
</RectilinearGrid>
|
||||
</VTKFile>
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
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||||
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
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||||
<Piece Extent="0 8 0 5 0 4">
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||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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|
@ -1,23 +1,23 @@
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||||
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
|
||||
<Piece Extent="0 8 0 5 0 4">
|
||||
<PointData>
|
||||
</PointData>
|
||||
<CellData>
|
||||
<DataArray type="Int32" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
|
||||
AQAAAACAAAAALQAAOQAAAA==eF7t1CESACAMA8HS/z8aX4OgCGDFuszJZERkMTbU1us9gFO6/+q23moPAAAAAAAAAADAnybPzQto
|
||||
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
|
||||
AQAAAACAAAAABQAAIAAAAA==eF5jZIAAxlF6lB4AmokAPdj1DzRNyP2jNH4aAMufANU=
|
||||
</DataArray>
|
||||
</CellData>
|
||||
<Coordinates>
|
||||
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
|
||||
AQAAAACAAACoAAAAVQAAAA==eF5jYICAWTNBYKU9hN5pb2IMAoeh/JP2EFUXoOKX7dPTQOAaVP6m/dkzIHAHqu4BVPwhVP1jqPwTqL5nUHUvoOpeQtW9hqp7A1X3Dqrugz0ASSZF3Q==
|
||||
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
|
||||
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
|
||||
AQAAAACAAACYAAAAVgAAAA==eF5jYIAAmeOFQLTGHkLvsQ8Fg6NQ/hn7IjDjIlT8qr1F32MgugGVv2MPMeUBVN1D+8cQBVD1T+3BymSeQ/W9sF8FBq+g+t/Yg4Ut3kHN+WAPAAVdQE4=
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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||||
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
|
||||
AQAAAACAAABIAAAAIgAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9Bkp/sAcAAU8I6Q==
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
|
||||
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
|
||||
</DataArray>
|
||||
</Coordinates>
|
||||
</Piece>
|
||||
|
|
|
|||
|
|
@ -1,23 +1,23 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
|
||||
<RectilinearGrid WholeExtent="0 20 0 18 0 8">
|
||||
<Piece Extent="0 20 0 18 0 8">
|
||||
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
|
||||
<Piece Extent="0 8 0 5 0 4">
|
||||
<PointData>
|
||||
</PointData>
|
||||
<CellData>
|
||||
<DataArray type="Int32" Name="materialpoint" format="binary" RangeMin="1" RangeMax="1">
|
||||
AQAAAACAAAAALQAAJAAAAA==eF7twwEJAAAMBKH7/qWXY6DgqqmqqqqqqqqqqqqqPnhyUwtB
|
||||
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
|
||||
AQAAAACAAAAABQAAMAAAAA==eF5jYoAAJhw0IwEalz566aeUptT+oa6fUppS+4e6fkppSu0f6voppSm1HwBAngDh
|
||||
</DataArray>
|
||||
</CellData>
|
||||
<Coordinates>
|
||||
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
|
||||
AQAAAACAAACoAAAAVQAAAA==eF5jYICAWTNBYKU9hN5pb2IMAoeh/JP2EFUXoOKX7dPTQOAaVP6m/dkzIHAHqu4BVPwhVP1jqPwTqL5nUHUvoOpeQtW9hqp7A1X3Dqrugz0ASSZF3Q==
|
||||
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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||||
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
|
||||
AQAAAACAAACYAAAAVgAAAA==eF5jYIAAmeOFQLTGHkLvsQ8Fg6NQ/hn7IjDjIlT8qr1F32MgugGVv2MPMeUBVN1D+8cQBVD1T+3BymSeQ/W9sF8FBq+g+t/Yg4Ut3kHN+WAPAAVdQE4=
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
|
||||
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
|
||||
AQAAAACAAABIAAAAIgAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9Bkp/sAcAAU8I6Q==
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
|
||||
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
|
||||
</DataArray>
|
||||
</Coordinates>
|
||||
</Piece>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,25 @@
|
|||
4 header
|
||||
grid a 8 b 5 c 4
|
||||
size x 8e-06 y 5e-06 z 4e-06
|
||||
origin x 0.0 y 0.0 z 0.0
|
||||
homogenization 1
|
||||
40 39 38 37 36 35 34 33
|
||||
32 31 30 29 28 27 26 25
|
||||
24 23 22 21 20 19 18 17
|
||||
16 15 14 13 12 11 10 9
|
||||
8 7 6 5 4 3 2 1
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
41 40 39 38 37 36 35 34
|
||||
33 32 31 30 29 28 27 26
|
||||
25 24 23 22 21 20 19 18
|
||||
17 16 15 14 13 12 11 10
|
||||
9 8 7 6 5 4 3 2
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
4 header
|
||||
grid a 8 b 5 c 4
|
||||
size x 8e-06 y 5e-06 z 4e-06
|
||||
origin x 0.0 y 0.0 z 0.0
|
||||
homogenization 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
9 8 7 6 5 4 3 2
|
||||
17 16 15 14 13 12 11 10
|
||||
25 24 23 22 21 20 19 18
|
||||
33 32 31 30 29 28 27 26
|
||||
41 40 39 38 37 36 35 34
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
8 7 6 5 4 3 2 1
|
||||
16 15 14 13 12 11 10 9
|
||||
24 23 22 21 20 19 18 17
|
||||
32 31 30 29 28 27 26 25
|
||||
40 39 38 37 36 35 34 33
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
4 header
|
||||
grid a 8 b 5 c 4
|
||||
size x 8e-06 y 5e-06 z 4e-06
|
||||
origin x 0.0 y 0.0 z 0.0
|
||||
homogenization 1
|
||||
33 34 35 36 37 38 39 40
|
||||
25 26 27 28 29 30 31 32
|
||||
17 18 19 20 21 22 23 24
|
||||
9 10 11 12 13 14 15 16
|
||||
1 2 3 4 5 6 7 8
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
34 35 36 37 38 39 40 41
|
||||
26 27 28 29 30 31 32 33
|
||||
18 19 20 21 22 23 24 25
|
||||
10 11 12 13 14 15 16 17
|
||||
2 3 4 5 6 7 8 9
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
4 header
|
||||
grid a 8 b 5 c 4
|
||||
size x 8e-06 y 5e-06 z 4e-06
|
||||
origin x 0.0 y 0.0 z 0.0
|
||||
homogenization 1
|
||||
40 39 38 37 36 35 34 33
|
||||
32 31 30 29 28 27 26 25
|
||||
24 23 22 21 20 19 18 17
|
||||
16 15 14 13 12 11 10 9
|
||||
8 7 6 5 4 3 2 1
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
2 2 2 2 2 2 2 2
|
||||
41 40 39 38 37 36 35 34
|
||||
33 32 31 30 29 28 27 26
|
||||
25 24 23 22 21 20 19 18
|
||||
17 16 15 14 13 12 11 10
|
||||
9 8 7 6 5 4 3 2
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
1 1 1 1 1 1 1 1
|
||||
|
|
@ -17,8 +17,8 @@ def reference_dir(reference_dir_base):
|
|||
class TestColormap:
|
||||
|
||||
@pytest.fixture(autouse=True)
|
||||
def _version_date(self, version_date):
|
||||
print('patched damask.util.version_date')
|
||||
def _execution_stamp(self, execution_stamp):
|
||||
print('patched damask.util.execution_stamp')
|
||||
|
||||
def test_conversion(self):
|
||||
specials = np.array([[0.,0.,0.],
|
||||
|
|
|
|||
|
|
@ -13,7 +13,8 @@ from damask import util
|
|||
def geom_equal(a,b):
|
||||
return np.all(a.get_microstructure() == b.get_microstructure()) and \
|
||||
np.all(a.get_grid() == b.get_grid()) and \
|
||||
np.allclose(a.get_size(), b.get_size())
|
||||
np.allclose(a.get_size(), b.get_size()) and \
|
||||
str(a.diff(b)) == str(b.diff(a))
|
||||
|
||||
@pytest.fixture
|
||||
def default():
|
||||
|
|
@ -32,15 +33,26 @@ def reference_dir(reference_dir_base):
|
|||
|
||||
class TestGeom:
|
||||
|
||||
def test_update(self,default):
|
||||
modified = default.copy()
|
||||
modified.update(
|
||||
@pytest.mark.parametrize('flavor',['plain','explicit'])
|
||||
def test_duplicate(self,default,flavor):
|
||||
if flavor == 'plain':
|
||||
modified = default.duplicate()
|
||||
elif flavor == 'explicit':
|
||||
modified = default.duplicate(
|
||||
default.get_microstructure(),
|
||||
default.get_size(),
|
||||
default.get_origin()
|
||||
)
|
||||
print(modified)
|
||||
assert geom_equal(modified,default)
|
||||
assert geom_equal(default,modified)
|
||||
|
||||
def test_diff_equal(self,default):
|
||||
assert str(default.diff(default)) == ''
|
||||
|
||||
def test_diff_not_equal(self,default):
|
||||
new = Geom(default.microstructure[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
|
||||
assert str(default.diff(new)) != ''
|
||||
|
||||
|
||||
@pytest.mark.parametrize('masked',[True,False])
|
||||
def test_set_microstructure(self,default,masked):
|
||||
|
|
@ -53,24 +65,25 @@ class TestGeom:
|
|||
def test_write_read_str(self,default,tmpdir):
|
||||
default.to_file(str(tmpdir/'default.geom'))
|
||||
new = Geom.from_file(str(tmpdir/'default.geom'))
|
||||
assert geom_equal(new,default)
|
||||
assert geom_equal(default,new)
|
||||
|
||||
def test_write_read_file(self,default,tmpdir):
|
||||
with open(tmpdir/'default.geom','w') as f:
|
||||
default.to_file(f)
|
||||
default.to_file(f,pack=True)
|
||||
with open(tmpdir/'default.geom') as f:
|
||||
new = Geom.from_file(f)
|
||||
assert geom_equal(new,default)
|
||||
assert geom_equal(default,new)
|
||||
|
||||
def test_write_show(self,default,tmpdir):
|
||||
def test_write_as_ASCII(self,default,tmpdir):
|
||||
with open(tmpdir/'str.geom','w') as f:
|
||||
f.write(default.show())
|
||||
f.write(default.as_ASCII())
|
||||
with open(tmpdir/'str.geom') as f:
|
||||
new = Geom.from_file(f)
|
||||
assert geom_equal(new,default)
|
||||
assert geom_equal(default,new)
|
||||
|
||||
def test_read_write_vtr(self,default,tmpdir):
|
||||
default.to_vtr(tmpdir/'default')
|
||||
print(default.to_vtr())
|
||||
for _ in range(10):
|
||||
time.sleep(.2)
|
||||
if os.path.exists(tmpdir/'default.vtr'): break
|
||||
|
|
@ -78,6 +91,13 @@ class TestGeom:
|
|||
new = Geom.from_vtr(tmpdir/'default.vtr')
|
||||
assert geom_equal(new,default)
|
||||
|
||||
def test_invalid_geom(self,tmpdir):
|
||||
with open('invalid_file','w') as f:
|
||||
f.write('this is not a valid header')
|
||||
with open('invalid_file','r') as f:
|
||||
with pytest.raises(TypeError):
|
||||
Geom.from_file(f)
|
||||
|
||||
def test_invalid_vtr(self,tmpdir):
|
||||
v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
|
||||
v.to_file(tmpdir/'no_materialpoint.vtr')
|
||||
|
|
@ -96,25 +116,25 @@ class TestGeom:
|
|||
|
||||
def test_invalid_combination(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
default.update(default.microstructure[1:,1:,1:],size=np.ones(3), rescale=True)
|
||||
default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(3), autosize=True)
|
||||
|
||||
def test_invalid_size(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
default.update(default.microstructure[1:,1:,1:],size=np.ones(2))
|
||||
default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(2))
|
||||
|
||||
def test_invalid_origin(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
default.update(default.microstructure[1:,1:,1:],origin=np.ones(4))
|
||||
default.duplicate(default.microstructure[1:,1:,1:],origin=np.ones(4))
|
||||
|
||||
def test_invalid_microstructure_size(self,default):
|
||||
microstructure = np.ones((3,3))
|
||||
with pytest.raises(ValueError):
|
||||
default.update(microstructure)
|
||||
default.duplicate(microstructure)
|
||||
|
||||
def test_invalid_microstructure_type(self,default):
|
||||
microstructure = np.random.randint(1,300,(3,4,5))==1
|
||||
with pytest.raises(TypeError):
|
||||
default.update(microstructure)
|
||||
default.duplicate(microstructure)
|
||||
|
||||
def test_invalid_homogenization(self,default):
|
||||
with pytest.raises(TypeError):
|
||||
|
|
@ -128,31 +148,61 @@ class TestGeom:
|
|||
]
|
||||
)
|
||||
def test_mirror(self,default,update,reference_dir,directions,reflect):
|
||||
modified = default.copy()
|
||||
modified.mirror(directions,reflect)
|
||||
modified = default.mirror(directions,reflect)
|
||||
tag = f'directions={"-".join(directions)}_reflect={reflect}'
|
||||
reference = reference_dir/f'mirror_{tag}.geom'
|
||||
if update: modified.to_file(reference)
|
||||
assert geom_equal(modified,Geom.from_file(reference))
|
||||
assert geom_equal(Geom.from_file(reference),
|
||||
modified)
|
||||
|
||||
@pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
|
||||
def test_mirror_invalid(self,default,directions):
|
||||
with pytest.raises(ValueError):
|
||||
default.mirror(directions)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('directions',[
|
||||
['x'],
|
||||
['x','y','z'],
|
||||
['z','x','y'],
|
||||
['y','z'],
|
||||
]
|
||||
)
|
||||
def test_flip(self,default,update,reference_dir,directions):
|
||||
modified = default.flip(directions)
|
||||
tag = f'directions={"-".join(directions)}'
|
||||
reference = reference_dir/f'flip_{tag}.geom'
|
||||
if update: modified.to_file(reference)
|
||||
assert geom_equal(Geom.from_file(reference),
|
||||
modified)
|
||||
|
||||
def test_flip_invariant(self,default):
|
||||
assert geom_equal(default,default.flip([]))
|
||||
|
||||
@pytest.mark.parametrize('direction',[['x'],['x','y']])
|
||||
def test_flip_double(self,default,direction):
|
||||
assert geom_equal(default,default.flip(direction).flip(direction))
|
||||
|
||||
@pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
|
||||
def test_flip_invalid(self,default,directions):
|
||||
with pytest.raises(ValueError):
|
||||
default.flip(directions)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('stencil',[1,2,3,4])
|
||||
@pytest.mark.parametrize('selection',[None,1,2])
|
||||
@pytest.mark.parametrize('selection',[None,[1],[1,2,3]])
|
||||
@pytest.mark.parametrize('periodic',[True,False])
|
||||
def test_clean(self,update,reference_dir,stencil,selection,periodic):
|
||||
current = Geom.from_vtr((reference_dir/'clean').with_suffix('.vtr'))
|
||||
current.clean(stencil,None if selection is None else [selection],periodic)
|
||||
reference = reference_dir/f'clean_{stencil}_{selection}_{periodic}'
|
||||
if update and stencil !=1:
|
||||
def test_clean(self,default,update,reference_dir,stencil,selection,periodic):
|
||||
current = default.clean(stencil,selection,periodic)
|
||||
reference = reference_dir/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
|
||||
if update and stencil > 1:
|
||||
current.to_vtr(reference)
|
||||
for _ in range(10):
|
||||
time.sleep(.2)
|
||||
if os.path.exists(reference.with_suffix('.vtr')): break
|
||||
assert geom_equal(current,Geom.from_vtr(reference if stencil !=1 else reference_dir/'clean'))
|
||||
assert geom_equal(Geom.from_vtr(reference) if stencil > 1 else default,
|
||||
current
|
||||
)
|
||||
|
||||
@pytest.mark.parametrize('grid',[
|
||||
(10,11,10),
|
||||
|
|
@ -164,33 +214,29 @@ class TestGeom:
|
|||
]
|
||||
)
|
||||
def test_scale(self,default,update,reference_dir,grid):
|
||||
modified = default.copy()
|
||||
modified.scale(grid)
|
||||
modified = default.scale(grid)
|
||||
tag = f'grid={util.srepr(grid,"-")}'
|
||||
reference = reference_dir/f'scale_{tag}.geom'
|
||||
if update: modified.to_file(reference)
|
||||
assert geom_equal(modified,Geom.from_file(reference))
|
||||
assert geom_equal(Geom.from_file(reference),
|
||||
modified)
|
||||
|
||||
def test_renumber(self,default):
|
||||
modified = default.copy()
|
||||
microstructure = modified.get_microstructure()
|
||||
microstructure = default.get_microstructure()
|
||||
for m in np.unique(microstructure):
|
||||
microstructure[microstructure==m] = microstructure.max() + np.random.randint(1,30)
|
||||
modified.update(microstructure)
|
||||
modified = default.duplicate(microstructure)
|
||||
assert not geom_equal(modified,default)
|
||||
modified.renumber()
|
||||
assert geom_equal(modified,default)
|
||||
assert geom_equal(default,
|
||||
modified.renumber())
|
||||
|
||||
def test_substitute(self,default):
|
||||
modified = default.copy()
|
||||
microstructure = modified.get_microstructure()
|
||||
offset = np.random.randint(1,500)
|
||||
microstructure += offset
|
||||
modified.update(microstructure)
|
||||
modified = default.duplicate(default.get_microstructure() + offset)
|
||||
assert not geom_equal(modified,default)
|
||||
assert geom_equal(default,
|
||||
modified.substitute(np.arange(default.microstructure.max())+1+offset,
|
||||
np.arange(default.microstructure.max())+1)
|
||||
assert geom_equal(modified,default)
|
||||
np.arange(default.microstructure.max())+1))
|
||||
|
||||
@pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]),
|
||||
np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
|
||||
|
|
@ -198,40 +244,58 @@ class TestGeom:
|
|||
modified = default.copy()
|
||||
for i in range(np.rint(360/axis_angle[3]).astype(int)):
|
||||
modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True))
|
||||
assert geom_equal(modified,default)
|
||||
assert geom_equal(default,modified)
|
||||
|
||||
@pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0],
|
||||
[0.0,32.0,240.0]])
|
||||
def test_rotate(self,default,update,reference_dir,Eulers):
|
||||
modified = default.copy()
|
||||
modified.rotate(Rotation.from_Eulers(Eulers,degrees=True))
|
||||
modified = default.rotate(Rotation.from_Eulers(Eulers,degrees=True))
|
||||
tag = f'Eulers={util.srepr(Eulers,"-")}'
|
||||
reference = reference_dir/f'rotate_{tag}.geom'
|
||||
if update: modified.to_file(reference)
|
||||
assert geom_equal(modified,Geom.from_file(reference))
|
||||
assert geom_equal(Geom.from_file(reference),
|
||||
modified)
|
||||
|
||||
def test_canvas(self,default):
|
||||
grid = default.grid
|
||||
grid_add = np.random.randint(0,30,(3))
|
||||
modified = default.copy()
|
||||
modified.canvas(modified.grid + grid_add)
|
||||
e = default.grid
|
||||
assert np.all(modified.microstructure[:e[0],:e[1],:e[2]] == default.microstructure)
|
||||
modified = default.canvas(grid + grid_add)
|
||||
assert np.all(modified.microstructure[:grid[0],:grid[1],:grid[2]] == default.microstructure)
|
||||
|
||||
@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random(3)),
|
||||
@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random()*8),
|
||||
(np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))])
|
||||
@pytest.mark.parametrize('diameter',[np.random.random(3)*.5,
|
||||
np.random.randint(4,10,(3))])
|
||||
def test_add_primitive(self,diameter,center1,center2):
|
||||
np.random.randint(4,10,(3)),
|
||||
np.random.rand(),
|
||||
np.random.randint(30)])
|
||||
@pytest.mark.parametrize('exponent',[np.random.random(3)*.5,
|
||||
np.random.randint(4,10,(3)),
|
||||
np.random.rand()*4,
|
||||
np.random.randint(20)])
|
||||
def test_add_primitive_shift(self,center1,center2,diameter,exponent):
|
||||
"""Same volume fraction for periodic microstructures and different center."""
|
||||
o = np.random.random(3)-.5
|
||||
g = np.random.randint(8,32,(3))
|
||||
s = np.random.random(3)+.5
|
||||
G_1 = Geom(np.ones(g,'i'),s,o)
|
||||
G_2 = Geom(np.ones(g,'i'),s,o)
|
||||
G_1.add_primitive(diameter,center1,1)
|
||||
G_2.add_primitive(diameter,center2,1)
|
||||
G_1 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center1,exponent)
|
||||
G_2 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center2,exponent)
|
||||
assert np.count_nonzero(G_1.microstructure!=2) == np.count_nonzero(G_2.microstructure!=2)
|
||||
|
||||
@pytest.mark.parametrize('center',[np.random.randint(4,10,(3)),
|
||||
np.random.randint(2,10),
|
||||
np.random.rand()*4,
|
||||
np.random.rand(3)*10])
|
||||
@pytest.mark.parametrize('inverse',[True,False])
|
||||
@pytest.mark.parametrize('periodic',[True,False])
|
||||
def test_add_primitive_rotation(self,center,inverse,periodic):
|
||||
"""Rotation should not change result for sphere (except for discretization errors)."""
|
||||
g = np.array([32,32,32])
|
||||
fill = np.random.randint(10)+2
|
||||
eu=np.array([np.random.randint(4),np.random.randint(2),np.random.randint(4)])*.5*np.pi
|
||||
G_1 = Geom(np.ones(g,'i'),[1.,1.,1.]).add_primitive(.3,center,1,fill,inverse=inverse,periodic=periodic)
|
||||
G_2 = Geom(np.ones(g,'i'),[1.,1.,1.]).add_primitive(.3,center,1,fill,Rotation.from_Eulers(eu),inverse,periodic=periodic)
|
||||
assert geom_equal(G_1,G_2)
|
||||
|
||||
@pytest.mark.parametrize('trigger',[[1],[]])
|
||||
def test_vicinity_offset(self,trigger):
|
||||
offset = np.random.randint(2,4)
|
||||
|
|
@ -248,8 +312,7 @@ class TestGeom:
|
|||
if len(trigger) > 0:
|
||||
m2[m==1] = 1
|
||||
|
||||
geom = Geom(m,np.random.rand(3))
|
||||
geom.vicinity_offset(vicinity,offset,trigger=trigger)
|
||||
geom = Geom(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)
|
||||
|
||||
assert np.all(m2==geom.microstructure)
|
||||
|
||||
|
|
|
|||
|
|
@ -13,8 +13,19 @@ def reference_dir(reference_dir_base):
|
|||
"""Directory containing reference results."""
|
||||
return reference_dir_base/'VTK'
|
||||
|
||||
@pytest.fixture
|
||||
def default():
|
||||
"""Simple VTK."""
|
||||
grid = np.array([5,6,7],int)
|
||||
size = np.array([.6,1.,.5])
|
||||
return VTK.from_rectilinearGrid(grid,size)
|
||||
|
||||
class TestVTK:
|
||||
|
||||
@pytest.fixture(autouse=True)
|
||||
def _execution_stamp(self, execution_stamp):
|
||||
print('patched damask.util.execution_stamp')
|
||||
|
||||
def test_rectilinearGrid(self,tmp_path):
|
||||
grid = np.random.randint(5,10,3)*2
|
||||
size = np.random.random(3) + 1.0
|
||||
|
|
@ -77,10 +88,36 @@ class TestVTK:
|
|||
@pytest.mark.parametrize('name,dataset_type',[('this_file_does_not_exist.vtk', None),
|
||||
('this_file_does_not_exist.vtk','vtk'),
|
||||
('this_file_does_not_exist.vtx', None)])
|
||||
def test_invalid_dataset_type(self,dataset_type,name):
|
||||
def test_invalid_dataset_type(self,name,dataset_type):
|
||||
with pytest.raises(TypeError):
|
||||
VTK.from_file('this_file_does_not_exist.vtk',dataset_type)
|
||||
VTK.from_file(name,dataset_type)
|
||||
|
||||
def test_invalid_extension_write(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
default.write('default.txt')
|
||||
|
||||
def test_invalid_get(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
default.get('does_not_exist')
|
||||
|
||||
def test_invalid_add_shape(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
default.add(np.ones(3),'valid')
|
||||
|
||||
def test_invalid_add_missing_label(self,default):
|
||||
data = np.random.randint(9,size=np.prod(np.array(default.vtk_data.GetDimensions())-1))
|
||||
with pytest.raises(ValueError):
|
||||
default.add(data)
|
||||
|
||||
def test_invalid_add_type(self,default):
|
||||
with pytest.raises(TypeError):
|
||||
default.add('invalid_type','valid')
|
||||
|
||||
def test_comments(self,tmp_path,default):
|
||||
default.add_comments(['this is a comment'])
|
||||
default.write(tmp_path/'with_comments',parallel=False)
|
||||
new = VTK.from_file(tmp_path/'with_comments.vtr')
|
||||
assert new.get_comments() == ['this is a comment']
|
||||
|
||||
def test_compare_reference_polyData(self,update,reference_dir,tmp_path):
|
||||
points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze()
|
||||
|
|
@ -90,7 +127,8 @@ class TestVTK:
|
|||
polyData.write(reference_dir/'polyData')
|
||||
else:
|
||||
reference = VTK.from_file(reference_dir/'polyData.vtp')
|
||||
assert polyData.__repr__() == reference.__repr__()
|
||||
assert polyData.__repr__() == reference.__repr__() and \
|
||||
np.allclose(polyData.get('coordinates'),points)
|
||||
|
||||
def test_compare_reference_rectilinearGrid(self,update,reference_dir,tmp_path):
|
||||
grid = np.array([5,6,7],int)
|
||||
|
|
@ -104,4 +142,5 @@ class TestVTK:
|
|||
rectilinearGrid.write(reference_dir/'rectilinearGrid')
|
||||
else:
|
||||
reference = VTK.from_file(reference_dir/'rectilinearGrid.vtr')
|
||||
assert rectilinearGrid.__repr__() == reference.__repr__()
|
||||
assert rectilinearGrid.__repr__() == reference.__repr__() and \
|
||||
np.allclose(rectilinearGrid.get('cell'),c)
|
||||
|
|
|
|||
|
|
@ -15,7 +15,6 @@ module discretization
|
|||
discretization_nElem
|
||||
|
||||
integer, public, protected, dimension(:), allocatable :: &
|
||||
discretization_homogenizationAt, &
|
||||
discretization_microstructureAt
|
||||
|
||||
real(pReal), public, protected, dimension(:,:), allocatable :: &
|
||||
|
|
@ -38,12 +37,11 @@ contains
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief stores the relevant information in globally accesible variables
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine discretization_init(homogenizationAt,microstructureAt,&
|
||||
subroutine discretization_init(microstructureAt,&
|
||||
IPcoords0,NodeCoords0,&
|
||||
sharedNodesBegin)
|
||||
|
||||
integer, dimension(:), intent(in) :: &
|
||||
homogenizationAt, &
|
||||
microstructureAt
|
||||
real(pReal), dimension(:,:), intent(in) :: &
|
||||
IPcoords0, &
|
||||
|
|
@ -56,7 +54,6 @@ subroutine discretization_init(homogenizationAt,microstructureAt,&
|
|||
discretization_nElem = size(microstructureAt,1)
|
||||
discretization_nIP = size(IPcoords0,2)/discretization_nElem
|
||||
|
||||
discretization_homogenizationAt = homogenizationAt
|
||||
discretization_microstructureAt = microstructureAt
|
||||
|
||||
discretization_IPcoords0 = IPcoords0
|
||||
|
|
|
|||
|
|
@ -53,8 +53,7 @@ subroutine discretization_grid_init(restart)
|
|||
myGrid !< domain grid of this process
|
||||
|
||||
integer, dimension(:), allocatable :: &
|
||||
microstructureAt, &
|
||||
homogenizationAt
|
||||
microstructureAt
|
||||
|
||||
integer :: &
|
||||
j, &
|
||||
|
|
@ -65,7 +64,7 @@ subroutine discretization_grid_init(restart)
|
|||
|
||||
write(6,'(/,a)') ' <<<+- discretization_grid init -+>>>'; flush(6)
|
||||
|
||||
call readGeom(grid,geomSize,origin,microstructureAt,homogenizationAt)
|
||||
call readGeom(grid,geomSize,origin,microstructureAt)
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! grid solver specific quantities
|
||||
|
|
@ -94,10 +93,8 @@ subroutine discretization_grid_init(restart)
|
|||
! general discretization
|
||||
microstructureAt = microstructureAt(product(grid(1:2))*grid3Offset+1: &
|
||||
product(grid(1:2))*(grid3Offset+grid3)) ! reallocate/shrink in case of MPI
|
||||
homogenizationAt = homogenizationAt(product(grid(1:2))*grid3Offset+1: &
|
||||
product(grid(1:2))*(grid3Offset+grid3)) ! reallocate/shrink in case of MPI
|
||||
|
||||
call discretization_init(homogenizationAt,microstructureAt, &
|
||||
call discretization_init(microstructureAt, &
|
||||
IPcoordinates0(myGrid,mySize,grid3Offset), &
|
||||
Nodes0(myGrid,mySize,grid3Offset),&
|
||||
merge((grid(1)+1) * (grid(2)+1) * (grid3+1),& ! write bottom layer
|
||||
|
|
@ -139,7 +136,7 @@ end subroutine discretization_grid_init
|
|||
!> @details important variables have an implicit "save" attribute. Therefore, this function is
|
||||
! supposed to be called only once!
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine readGeom(grid,geomSize,origin,microstructure,homogenization)
|
||||
subroutine readGeom(grid,geomSize,origin,microstructure)
|
||||
|
||||
integer, dimension(3), intent(out) :: &
|
||||
grid ! grid (for all processes!)
|
||||
|
|
@ -147,8 +144,7 @@ subroutine readGeom(grid,geomSize,origin,microstructure,homogenization)
|
|||
geomSize, & ! size (for all processes!)
|
||||
origin ! origin (for all processes!)
|
||||
integer, dimension(:), intent(out), allocatable :: &
|
||||
microstructure, &
|
||||
homogenization
|
||||
microstructure
|
||||
|
||||
character(len=:), allocatable :: rawData
|
||||
character(len=65536) :: line
|
||||
|
|
@ -249,24 +245,18 @@ subroutine readGeom(grid,geomSize,origin,microstructure,homogenization)
|
|||
enddo
|
||||
endif
|
||||
|
||||
case ('homogenization')
|
||||
if (chunkPos(1) > 1) h = IO_intValue(line,chunkPos,2)
|
||||
|
||||
end select
|
||||
|
||||
enddo
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! sanity checks
|
||||
if(h < 1) &
|
||||
call IO_error(error_ID = 842, ext_msg='homogenization (readGeom)')
|
||||
if(any(grid < 1)) &
|
||||
call IO_error(error_ID = 842, ext_msg='grid (readGeom)')
|
||||
if(any(geomSize < 0.0_pReal)) &
|
||||
call IO_error(error_ID = 842, ext_msg='size (readGeom)')
|
||||
|
||||
allocate(microstructure(product(grid)), source = -1) ! too large in case of MPI (shrink later, not very elegant)
|
||||
allocate(homogenization(product(grid)), source = h) ! too large in case of MPI (shrink later, not very elegant)
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! read and interpret content
|
||||
|
|
|
|||
|
|
@ -52,8 +52,7 @@ subroutine discretization_marc_init
|
|||
type(tElement) :: elem
|
||||
|
||||
integer, dimension(:), allocatable :: &
|
||||
microstructureAt, &
|
||||
homogenizationAt
|
||||
microstructureAt
|
||||
integer:: &
|
||||
Nnodes, & !< total number of nodes in the mesh
|
||||
Nelems, & !< total number of elements in the mesh
|
||||
|
|
@ -84,7 +83,7 @@ subroutine discretization_marc_init
|
|||
mesh_unitlength = num_commercialFEM%get_asFloat('unitlength',defaultVal=1.0_pReal) ! set physical extent of a length unit in mesh
|
||||
if (mesh_unitlength <= 0.0_pReal) call IO_error(301,ext_msg='unitlength')
|
||||
|
||||
call inputRead(elem,node0_elem,connectivity_elem,microstructureAt,homogenizationAt)
|
||||
call inputRead(elem,node0_elem,connectivity_elem,microstructureAt)
|
||||
nElems = size(connectivity_elem,2)
|
||||
|
||||
if (debug_e < 1 .or. debug_e > nElems) call IO_error(602,ext_msg='element')
|
||||
|
|
@ -104,7 +103,7 @@ subroutine discretization_marc_init
|
|||
call buildIPcoordinates(IP_reshaped,reshape(connectivity_cell,[elem%NcellNodesPerCell,&
|
||||
elem%nIPs*nElems]),node0_cell)
|
||||
|
||||
call discretization_init(microstructureAt,homogenizationAt,&
|
||||
call discretization_init(microstructureAt,&
|
||||
IP_reshaped,&
|
||||
node0_cell)
|
||||
|
||||
|
|
@ -173,7 +172,7 @@ end subroutine writeGeometry
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief Read mesh from marc input file
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine inputRead(elem,node0_elem,connectivity_elem,microstructureAt,homogenizationAt)
|
||||
subroutine inputRead(elem,node0_elem,connectivity_elem,microstructureAt)
|
||||
|
||||
type(tElement), intent(out) :: elem
|
||||
real(pReal), dimension(:,:), allocatable, intent(out) :: &
|
||||
|
|
@ -181,8 +180,7 @@ subroutine inputRead(elem,node0_elem,connectivity_elem,microstructureAt,homogeni
|
|||
integer, dimension(:,:), allocatable, intent(out) :: &
|
||||
connectivity_elem
|
||||
integer, dimension(:), allocatable, intent(out) :: &
|
||||
microstructureAt, &
|
||||
homogenizationAt
|
||||
microstructureAt
|
||||
|
||||
integer :: &
|
||||
fileFormatVersion, &
|
||||
|
|
@ -228,7 +226,7 @@ subroutine inputRead(elem,node0_elem,connectivity_elem,microstructureAt,homogeni
|
|||
|
||||
connectivity_elem = inputRead_connectivityElem(nElems,elem%nNodes,inputFile)
|
||||
|
||||
call inputRead_microstructureAndHomogenization(microstructureAt,homogenizationAt, &
|
||||
call inputRead_microstructure(microstructureAt, &
|
||||
nElems,elem%nNodes,nameElemSet,mapElemSet,&
|
||||
initialcondTableStyle,inputFile)
|
||||
end subroutine inputRead
|
||||
|
|
@ -677,14 +675,13 @@ end function inputRead_connectivityElem
|
|||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief Stores homogenization and microstructure ID
|
||||
!> @brief Store microstructure ID
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine inputRead_microstructureAndHomogenization(microstructureAt,homogenizationAt, &
|
||||
subroutine inputRead_microstructure(microstructureAt,&
|
||||
nElem,nNodes,nameElemSet,mapElemSet,initialcondTableStyle,fileContent)
|
||||
|
||||
integer, dimension(:), allocatable, intent(out) :: &
|
||||
microstructureAt, &
|
||||
homogenizationAt
|
||||
microstructureAt
|
||||
integer, intent(in) :: &
|
||||
nElem, &
|
||||
nNodes, & !< number of nodes per element
|
||||
|
|
@ -700,7 +697,6 @@ subroutine inputRead_microstructureAndHomogenization(microstructureAt,homogeniza
|
|||
|
||||
|
||||
allocate(microstructureAt(nElem),source=0)
|
||||
allocate(homogenizationAt(nElem),source=0)
|
||||
|
||||
do l = 1, size(fileContent)
|
||||
chunkPos = IO_stringPos(fileContent(l))
|
||||
|
|
@ -719,8 +715,7 @@ subroutine inputRead_microstructureAndHomogenization(microstructureAt,homogeniza
|
|||
contInts = continuousIntValues(fileContent(l+k+m+1:),nElem,nameElemSet,mapElemSet,size(nameElemSet)) ! get affected elements
|
||||
do i = 1,contInts(1)
|
||||
e = mesh_FEM2DAMASK_elem(contInts(1+i))
|
||||
if (sv == 2) microstructureAt(e) = myVal
|
||||
if (sv == 3) homogenizationAt(e) = myVal
|
||||
if (sv == 3) microstructureAt(e) = myVal
|
||||
enddo
|
||||
if (initialcondTableStyle == 0) m = m + 1
|
||||
enddo
|
||||
|
|
@ -728,7 +723,7 @@ subroutine inputRead_microstructureAndHomogenization(microstructureAt,homogeniza
|
|||
endif
|
||||
enddo
|
||||
|
||||
end subroutine inputRead_microstructureAndHomogenization
|
||||
end subroutine inputRead_microstructure
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@ module material
|
|||
damage_initialPhi !< initial damage per each homogenization
|
||||
|
||||
integer, dimension(:), allocatable, public, protected :: & ! (elem)
|
||||
material_homogenizationAt !< homogenization ID of each element (copy of discretization_homogenizationAt)
|
||||
material_homogenizationAt !< homogenization ID of each element
|
||||
integer, dimension(:,:), allocatable, public, target :: & ! (ip,elem) ToDo: ugly target for mapping hack
|
||||
material_homogenizationMemberAt !< position of the element within its homogenization instance
|
||||
integer, dimension(:,:), allocatable, public, protected :: & ! (constituent,elem)
|
||||
|
|
@ -241,7 +241,6 @@ subroutine material_parseHomogenization
|
|||
homogDamage
|
||||
|
||||
integer :: h
|
||||
logical, dimension(:), allocatable :: homogenization_active
|
||||
|
||||
material_homogenization => material_root%get('homogenization')
|
||||
material_Nhomogenization = material_homogenization%length
|
||||
|
|
@ -253,13 +252,9 @@ subroutine material_parseHomogenization
|
|||
allocate(thermal_typeInstance(material_Nhomogenization), source=0)
|
||||
allocate(damage_typeInstance(material_Nhomogenization), source=0)
|
||||
allocate(homogenization_Ngrains(material_Nhomogenization), source=0)
|
||||
allocate(homogenization_active(material_Nhomogenization), source=.false.) !!!!!!!!!!!!!!!
|
||||
allocate(thermal_initialT(material_Nhomogenization), source=300.0_pReal)
|
||||
allocate(damage_initialPhi(material_Nhomogenization), source=1.0_pReal)
|
||||
|
||||
forall (h = 1:material_Nhomogenization) &
|
||||
homogenization_active(h) = any(discretization_homogenizationAt == h) !ToDo: SR: needed??
|
||||
|
||||
do h=1, material_Nhomogenization
|
||||
homog => material_homogenization%get(h)
|
||||
homogMech => homog%get('mech')
|
||||
|
|
@ -317,7 +312,7 @@ subroutine material_parseHomogenization
|
|||
damage_typeInstance(h) = count(damage_type (1:h) == damage_type (h))
|
||||
enddo
|
||||
|
||||
homogenization_maxNgrains = maxval(homogenization_Ngrains,homogenization_active)
|
||||
homogenization_maxNgrains = maxval(homogenization_Ngrains)
|
||||
|
||||
|
||||
end subroutine material_parseHomogenization
|
||||
|
|
|
|||
|
|
@ -77,7 +77,6 @@ subroutine discretization_mesh_init(restart)
|
|||
IS :: faceSetIS
|
||||
PetscErrorCode :: ierr
|
||||
integer, dimension(:), allocatable :: &
|
||||
homogenizationAt, &
|
||||
microstructureAt
|
||||
class(tNode), pointer :: &
|
||||
num_mesh
|
||||
|
|
@ -165,7 +164,6 @@ subroutine discretization_mesh_init(restart)
|
|||
call mesh_FEM_build_ipVolumes(dimPlex)
|
||||
|
||||
allocate(microstructureAt(mesh_NcpElems))
|
||||
allocate(homogenizationAt(mesh_NcpElems),source=1)
|
||||
do j = 1, mesh_NcpElems
|
||||
call DMGetLabelValue(geomMesh,'material',j-1,microstructureAt(j),ierr)
|
||||
CHKERRQ(ierr)
|
||||
|
|
@ -179,7 +177,7 @@ subroutine discretization_mesh_init(restart)
|
|||
|
||||
allocate(mesh_node0(3,mesh_Nnodes),source=0.0_pReal)
|
||||
|
||||
call discretization_init(microstructureAt,homogenizationAt,&
|
||||
call discretization_init(microstructureAt,&
|
||||
reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &
|
||||
mesh_node0)
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue