Merge branch 'development' into Vectorize-Orientation
This commit is contained in:
Martin Diehl
commit
a7e3dd5a56
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|
@ -192,21 +192,6 @@ Post_addGradient:
|
|||
- master
|
||||
- release
|
||||
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||||
Post_ParaviewRelated:
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||||
stage: postprocessing
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||||
script: ParaviewRelated/test.py
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||||
except:
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||||
- master
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||||
- release
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||||
|
||||
Post_OrientationConversion:
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stage: postprocessing
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script:
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||||
- OrientationConversion/test.py
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||||
except:
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- master
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||||
- release
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||||
|
||||
Post_OrientationAverageMisorientation:
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stage: postprocessing
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||||
script:
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||||
|
|
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2
PRIVATE
2
PRIVATE
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|
@ -1 +1 @@
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Subproject commit a6109acd264c683fd335b1d1f69934fc4a4078e3
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Subproject commit 073913bf152b3c48f358dfbea5145807c0f7690d
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|
@ -27,7 +27,7 @@ SolidSolutionStrength 0.0 # Strength due to elements in solid solution
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### Dislocation glide parameters ###
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#per family
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Nslip 12 0
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Nslip 12
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slipburgers 2.72e-10 # Burgers vector of slip system [m]
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rhoedge0 1.0e12 # Initial edge dislocation density [m/m**3]
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rhoedgedip0 1.0 # Initial edged dipole dislocation density [m/m**3]
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|
|
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@ -1,56 +1,30 @@
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#!/usr/bin/env python3
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# Makes postprocessing routines accessible from everywhere.
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import os
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import sys
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from pathlib import Path
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import damask
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||||
damaskEnv = damask.Environment()
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||||
baseDir = damaskEnv.relPath('processing/')
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binDir = damaskEnv.relPath('bin/')
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env = damask.Environment()
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||||
bin_dir = env.root_dir/Path('bin')
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|
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if not os.path.isdir(binDir):
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os.mkdir(binDir)
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if not bin_dir.exists():
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bin_dir.mkdir()
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#define ToDo list
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processing_subDirs = ['pre',
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'post',
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]
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sys.stdout.write('\nsymbolic linking...\n')
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for sub_dir in ['pre','post']:
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the_dir = env.root_dir/Path('processing')/Path(sub_dir)
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|
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for subDir in processing_subDirs:
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theDir = os.path.abspath(os.path.join(baseDir,subDir))
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sys.stdout.write('\n'+binDir+' ->\n'+theDir+damask.util.deemph(' ...')+'\n')
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for theFile in os.listdir(theDir):
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theName,theExt = os.path.splitext(theFile)
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if theExt in ['.py']:
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src = os.path.abspath(os.path.join(theDir,theFile))
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sym_link = os.path.abspath(os.path.join(binDir,theName))
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if os.path.lexists(sym_link):
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os.remove(sym_link)
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output = theName+damask.util.deemph(theExt)
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else:
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output = damask.util.emph(theName)+damask.util.deemph(theExt)
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sys.stdout.write(damask.util.deemph('... ')+output+'\n')
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os.symlink(src,sym_link)
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for the_file in the_dir.glob('*.py'):
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src = the_dir/the_file
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dst = bin_dir/Path(the_file.with_suffix('').name)
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if dst.is_file(): dst.unlink() # dst.unlink(True) for Python >3.8
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dst.symlink_to(src)
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sys.stdout.write('\npruning broken links...\n')
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|
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brokenLinks = 0
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for filename in os.listdir(binDir):
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path = os.path.join(binDir,filename)
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||||
if os.path.islink(path) and not os.path.exists(path):
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sys.stdout.write(' '+damask.util.delete(path)+'\n')
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os.remove(path)
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brokenLinks += 1
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||||
|
||||
sys.stdout.write(('none.' if brokenLinks == 0 else '')+'\n')
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||||
for filename in bin_dir.glob('*'):
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if not filename.is_file():
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filename.unlink
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|
|
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|
|
@ -1,143 +0,0 @@
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#!/usr/bin/env python3
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import os
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import sys
|
||||
from io import StringIO
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from optparse import OptionParser
|
||||
|
||||
import numpy as np
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||||
|
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import damask
|
||||
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
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||||
scriptID = ' '.join([scriptName,damask.version])
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||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
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||||
Produces a binned grid of two columns from an ASCIItable, i.e. a two-dimensional probability density map.
|
||||
|
||||
""", version = scriptID)
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||||
|
||||
parser.add_option('-d','--data',
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||||
dest = 'data',
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||||
type = 'string', nargs = 2, metavar = 'string string',
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help = 'column labels containing x and y ')
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parser.add_option('-w','--weight',
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dest = 'weight',
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type = 'string', metavar = 'string',
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help = 'column label containing weight of (x,y) point')
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parser.add_option('-b','--bins',
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dest = 'bins',
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||||
type = 'int', nargs = 2, metavar = 'int int',
|
||||
help = 'number of bins in x and y direction [%default]')
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||||
parser.add_option('-t','--type',
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||||
dest = 'type',
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||||
type = 'string', nargs = 3, metavar = 'string string string',
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help = 'type (linear/log) of x, y, and z axis [%default]')
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||||
parser.add_option('-x','--xrange',
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dest = 'xrange',
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type = 'float', nargs = 2, metavar = 'float float',
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||||
help = 'min max limits in x direction (optional)')
|
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parser.add_option('-y','--yrange',
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||||
dest = 'yrange',
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||||
type = 'float', nargs = 2, metavar = 'float float',
|
||||
help = 'min max limits in y direction (optional)')
|
||||
parser.add_option('-z','--zrange',
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||||
dest = 'zrange',
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||||
type = 'float', nargs = 2, metavar = 'float float',
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||||
help = 'min max limits in z direction (optional)')
|
||||
parser.add_option('-i','--invert',
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||||
dest = 'invert',
|
||||
action = 'store_true',
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||||
help = 'invert probability density')
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parser.add_option('-r','--rownormalize',
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dest = 'normRow',
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||||
action = 'store_true',
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||||
help = 'normalize probability density in each row')
|
||||
parser.add_option('-c','--colnormalize',
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||||
dest = 'normCol',
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||||
action = 'store_true',
|
||||
help = 'normalize probability density in each column')
|
||||
|
||||
parser.set_defaults(bins = (10,10),
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||||
type = ('linear','linear','linear'),
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||||
xrange = (0.0,0.0),
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||||
yrange = (0.0,0.0),
|
||||
zrange = (0.0,0.0),
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||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
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||||
if filenames == []: filenames = [None]
|
||||
|
||||
minmax = np.array([options.xrange,options.yrange,options.zrange])
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||||
result = np.empty((options.bins[0],options.bins[1],3),'f')
|
||||
|
||||
if options.data is None: parser.error('no data columns specified.')
|
||||
|
||||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
data = np.hstack((table.get(options.data[0]),table.get(options.data[1])))
|
||||
|
||||
for c in (0,1): # check data minmax for x and y (i = 0 and 1)
|
||||
if (minmax[c] == 0.0).all(): minmax[c] = [data[:,c].min(),data[:,c].max()]
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||||
if options.type[c].lower() == 'log': # if log scale
|
||||
data[:,c] = np.log(data[:,c]) # change x,y coordinates to log
|
||||
minmax[c] = np.log(minmax[c]) # change minmax to log, too
|
||||
|
||||
delta = minmax[:,1]-minmax[:,0]
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||||
(grid,xedges,yedges) = np.histogram2d(data[:,0],data[:,1],
|
||||
bins=options.bins,
|
||||
range=minmax[:2],
|
||||
weights=table.get(options.weight) if options.weight else None)
|
||||
if options.normCol:
|
||||
for x in range(options.bins[0]):
|
||||
sum = np.sum(grid[x,:])
|
||||
if sum > 0.0:
|
||||
grid[x,:] /= sum
|
||||
if options.normRow:
|
||||
for y in range(options.bins[1]):
|
||||
sum = np.sum(grid[:,y])
|
||||
if sum > 0.0:
|
||||
grid[:,y] /= sum
|
||||
|
||||
if (minmax[2] == 0.0).all(): minmax[2] = [grid.min(),grid.max()] # auto scale from data
|
||||
if minmax[2,0] == minmax[2,1]:
|
||||
minmax[2,0] -= 1.
|
||||
minmax[2,1] += 1.
|
||||
if (minmax[2] == 0.0).all(): # no data in grid?
|
||||
damask.util.croak('no data found on grid...')
|
||||
minmax[2,:] = np.array([0.0,1.0]) # making up arbitrary z minmax
|
||||
if options.type[2].lower() == 'log':
|
||||
grid = np.log(grid)
|
||||
minmax[2] = np.log(minmax[2])
|
||||
|
||||
delta[2] = minmax[2,1]-minmax[2,0]
|
||||
|
||||
for x in range(options.bins[0]):
|
||||
for y in range(options.bins[1]):
|
||||
result[x,y,:] = [minmax[0,0]+delta[0]/options.bins[0]*(x+0.5),
|
||||
minmax[1,0]+delta[1]/options.bins[1]*(y+0.5),
|
||||
np.clip((grid[x,y]-minmax[2,0])/delta[2],0.0,1.0)]
|
||||
|
||||
for c in (0,1):
|
||||
if options.type[c].lower() == 'log': result[:,:,c] = np.exp(result[:,:,c])
|
||||
|
||||
if options.invert: result[:,:,2] = 1.0 - result[:,:,2]
|
||||
|
||||
comments = scriptID + '\t' + ' '.join(sys.argv[1:])
|
||||
shapes = {'bin_%s'%options.data[0]:(1,),'bin_%s'%options.data[1]:(1,),'z':(1,)}
|
||||
table = damask.Table(result.reshape(options.bins[0]*options.bins[1],3),shapes,[comments])
|
||||
if name:
|
||||
outname = os.path.join(os.path.dirname(name),'binned-{}-{}_'.format(*options.data) +
|
||||
('weighted-{}_'.format(options.weight) if options.weight else '') +
|
||||
os.path.basename(name))
|
||||
table.to_ASCII(outname)
|
||||
else:
|
||||
table.to_ASCII(sys.stdout)
|
||||
|
|
@ -1,65 +0,0 @@
|
|||
#!/usr/bin/env python3
|
||||
|
||||
import os
|
||||
import sys
|
||||
from io import StringIO
|
||||
from optparse import OptionParser
|
||||
|
||||
import numpy as np
|
||||
|
||||
import damask
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption,
|
||||
usage='%prog options [ASCIItable(s)]',
|
||||
description = 'Add scalars/vectors, tensors, and/or a RGB tuples from ASCIItable '
|
||||
+ 'to existing VTK file (.vtr/.vtu/.vtp).',
|
||||
version = scriptID)
|
||||
|
||||
parser.add_option( '--vtk',
|
||||
dest = 'vtk',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'VTK file name')
|
||||
parser.add_option('-d', '--data',
|
||||
dest = 'data',
|
||||
action = 'extend', metavar = '<string LIST>',
|
||||
help = 'scalar/vector value(s) label(s)')
|
||||
parser.add_option('-t', '--tensor',
|
||||
dest = 'tensor',
|
||||
action = 'extend', metavar = '<string LIST>',
|
||||
help = 'tensor (3x3) value label(s)')
|
||||
parser.add_option('-c', '--color',
|
||||
dest = 'color',
|
||||
action = 'extend', metavar = '<string LIST>',
|
||||
help = 'RGB color tuple label')
|
||||
|
||||
parser.set_defaults(data = [],
|
||||
tensor = [],
|
||||
color = [],
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
if not options.vtk:
|
||||
parser.error('No VTK file specified.')
|
||||
|
||||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
vtk = damask.VTK.from_file(options.vtk)
|
||||
|
||||
for data in options.data+options.tensor:
|
||||
vtk.add(table.get(data),data)
|
||||
for color in options.color:
|
||||
vtk.add((table.get(color)*255).astype(np.uint8),color)
|
||||
|
||||
vtk.write(options.vtk)
|
||||
|
|
@ -1,45 +0,0 @@
|
|||
#!/usr/bin/env python3
|
||||
|
||||
import os
|
||||
import sys
|
||||
from io import StringIO
|
||||
from optparse import OptionParser
|
||||
|
||||
import damask
|
||||
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Produce a VTK point cloud dataset based on coordinates given in an ASCIItable.
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-p',
|
||||
'--pos', '--position',
|
||||
dest = 'pos',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'label of coordinates [%default]')
|
||||
|
||||
parser.set_defaults(pos = 'pos',
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
v = damask.VTK.from_polyData(table.get(options.pos))
|
||||
|
||||
if name:
|
||||
v.write(os.path.splitext(name)[0])
|
||||
else:
|
||||
sys.stdout.write(v.__repr__())
|
||||
|
|
@ -1,58 +0,0 @@
|
|||
#!/usr/bin/env python3
|
||||
|
||||
import os
|
||||
import sys
|
||||
from io import StringIO
|
||||
from optparse import OptionParser
|
||||
|
||||
import damask
|
||||
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Create regular voxel grid from points in an ASCIItable.
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-m',
|
||||
'--mode',
|
||||
dest = 'mode',
|
||||
metavar='string',
|
||||
type = 'choice', choices = ['cell','point'],
|
||||
help = 'cell-centered or point-centered coordinates')
|
||||
parser.add_option('-p',
|
||||
'--pos', '--position',
|
||||
dest = 'pos',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'label of coordinates [%default]')
|
||||
|
||||
parser.set_defaults(mode = 'cell',
|
||||
pos = 'pos',
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
|
||||
if options.mode == 'cell':
|
||||
grid, size, origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
|
||||
elif options.mode == 'point':
|
||||
grid, size, origin = damask.grid_filters.node_coord0_gridSizeOrigin(table.get(options.pos))
|
||||
|
||||
v = damask.VTK.from_rectilinearGrid(grid,size,origin)
|
||||
|
||||
if name:
|
||||
v.write('{}_{}({})'.format(os.path.splitext(name)[0],options.pos,options.mode))
|
||||
else:
|
||||
sys.stdout.write(v.__repr__())
|
||||
|
|
@ -6,7 +6,7 @@ import numpy as np
|
|||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
sys.path.append(damask.solver.Marc().libraryPath())
|
||||
sys.path.append(str(damask.solver.Marc().library_path))
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
|
@ -198,13 +198,14 @@ def add_servoLinks(mfd_data,active=[True,True,True]): # directions on which to
|
|||
if mfd_data[i]['uid'] == 1705: del mfd_data[i]
|
||||
mfd_data.insert(i, links)
|
||||
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Set up servo linking to achieve periodic boundary conditions for a regular hexahedral mesh.
|
||||
Use *py_connection to operate on model presently opened in MSC.Mentat.
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-p', '--port',
|
||||
|
|
@ -229,10 +230,7 @@ if remote and filenames != []:
|
|||
if filenames == []: filenames = [None]
|
||||
|
||||
if remote:
|
||||
try: import py_mentat
|
||||
except:
|
||||
damask.util.croak('no valid Mentat release found.')
|
||||
sys.exit(-1)
|
||||
import py_mentat
|
||||
|
||||
damask.util.report(scriptName, 'waiting to connect...')
|
||||
filenames = [os.path.join(tempfile._get_default_tempdir(), next(tempfile._get_candidate_names()) + '.mfd')]
|
||||
|
|
@ -240,14 +238,14 @@ if remote:
|
|||
py_mentat.py_connect('',options.port)
|
||||
py_mentat.py_send('*set_save_formatted on')
|
||||
py_mentat.py_send('*save_as_model "{}" yes'.format(filenames[0]))
|
||||
py_mentat.py_get_int("nnodes()") # hopefully blocks until file is written
|
||||
except:
|
||||
damask.util.croak('failed. try setting Tools/Python/"Run as Separate Process" & "Initiate".')
|
||||
sys.exit()
|
||||
py_mentat.py_get_int("nnodes()")
|
||||
except py_mentat.InputError as err:
|
||||
damask.util.croak('{}. Try Tools/Python/"Run as Separate Process" & "Initiate".'.format(err))
|
||||
sys.exit(-1)
|
||||
damask.util.croak( 'connected...')
|
||||
|
||||
for name in filenames:
|
||||
while remote and not os.path.exists(name): time.sleep(0.5) # wait for Mentat to write MFD file
|
||||
while remote and not os.path.exists(name): time.sleep(0.5)
|
||||
with open( name,'r') if name is not None else sys.stdin as fileIn:
|
||||
damask.util.report(scriptName, name)
|
||||
mfd = parseMFD(fileIn)
|
||||
|
|
@ -257,5 +255,4 @@ for name in filenames:
|
|||
fileOut.write(asMFD(mfd))
|
||||
|
||||
if remote:
|
||||
try: py_mentat.py_send('*open_model "{}"'.format(filenames[0]))
|
||||
except: damask.util.croak('lost connection on sending open command for "{}".'.format(filenames[0]))
|
||||
py_mentat.py_send('*open_model "{}"'.format(filenames[0]))
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ import damask
|
|||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
sys.path.append(damask.solver.Marc().libraryPath())
|
||||
sys.path.append(str(damask.solver.Marc().library_path))
|
||||
|
||||
#-------------------------------------------------------------------------------------------------
|
||||
def outMentat(cmd,locals):
|
||||
|
|
|
|||
|
|
@ -1,9 +1,9 @@
|
|||
"""Tools for pre and post processing of DAMASK simulations."""
|
||||
import os as _os
|
||||
from pathlib import Path as _Path
|
||||
import re as _re
|
||||
|
||||
name = 'damask'
|
||||
with open(_os.path.join(_os.path.dirname(__file__),'VERSION')) as _f:
|
||||
with open(_Path(__file__).parent/_Path('VERSION')) as _f:
|
||||
version = _re.sub(r'^v','',_f.readline().strip())
|
||||
|
||||
# make classes directly accessible as damask.Class
|
||||
|
|
|
|||
|
|
@ -157,7 +157,7 @@ class ASCIItable():
|
|||
def head_write(self,
|
||||
header = True):
|
||||
"""Write current header information (info + labels)."""
|
||||
head = ['{}\theader'.format(len(self.info)+self.__IO__['labeled'])] if header else []
|
||||
head = [f"{len(self.info)+self.__IO__['labeled']}\theader"] if header else []
|
||||
head.append(self.info)
|
||||
if self.__IO__['labeled']:
|
||||
head.append('\t'.join(map(self._quote,self.tags)))
|
||||
|
|
@ -209,7 +209,7 @@ class ASCIItable():
|
|||
labelList.append(tags[id])
|
||||
else:
|
||||
label = tags[id][2:] # get label
|
||||
while id < len(tags) and tags[id] == '{}_{}'.format(dim,label): # check successors
|
||||
while id < len(tags) and tags[id] == f'{dim}_{label}': # check successors
|
||||
id += 1 # next label...
|
||||
dim += 1 # ...should be one higher dimension
|
||||
labelList.append(label) # reached end --> store
|
||||
|
|
|
|||
|
|
@ -1,4 +1,5 @@
|
|||
import numpy as np
|
||||
from . import util
|
||||
|
||||
class Color:
|
||||
"""Color representation in and conversion between different color-spaces."""
|
||||
|
|
@ -502,7 +503,7 @@ class Colormap:
|
|||
[RGB] colormap for use in paraview or gmsh, or as raw string, or array.
|
||||
|
||||
Arguments: name, format, steps, crop.
|
||||
Format is one of (paraview, gmsh, raw, list).
|
||||
Format is one of (paraview, gmsh, gom, raw, list).
|
||||
Crop selects a (sub)range in [-1.0,1.0].
|
||||
Generates sequential map if one limiting color is either white or black,
|
||||
diverging map otherwise.
|
||||
|
|
@ -511,23 +512,22 @@ class Colormap:
|
|||
frac = 0.5*(np.array(crop) + 1.0) # rescale crop range to fractions
|
||||
colors = [self.color(float(i)/(steps-1)*(frac[1]-frac[0])+frac[0]).express_as(model).color for i in range(steps)]
|
||||
if format == 'paraview':
|
||||
colormap = ['[\n {{\n "ColorSpace": "RGB", "Name": "{}", "DefaultMap": true,\n "RGBPoints" : ['.format(name)] \
|
||||
+ [' {:4d},{:8.6f},{:8.6f},{:8.6f},'.format(i,color[0],color[1],color[2],) \
|
||||
for i,color in enumerate(colors[:-1])] \
|
||||
+ [' {:4d},{:8.6f},{:8.6f},{:8.6f} '.format(len(colors),colors[-1][0],colors[-1][1],colors[-1][2],)] \
|
||||
colormap = [f'[\n {{\n "ColorSpace": "RGB", "Name": "{name}", "DefaultMap": true,\n "RGBPoints" : ['] \
|
||||
+ [f' {i:4d},{color[0]:8.6f},{color[1]:8.6f},{color[2]:8.6f}{"," if i+1<len(colors) else ""}' \
|
||||
for i,color in enumerate(colors)] \
|
||||
+ [' ]\n }\n]']
|
||||
|
||||
elif format == 'gmsh':
|
||||
colormap = ['View.ColorTable = {'] \
|
||||
+ [',\n'.join(['{%s}'%(','.join([str(x*255.0) for x in color])) for color in colors])] \
|
||||
+ [',\n'.join([','.join([str(x*255.0) for x in color]) for color in colors])] \
|
||||
+ ['}']
|
||||
|
||||
elif format == 'gom':
|
||||
colormap = ['1 1 ' + str(name)
|
||||
+ ' 9 ' + str(name)
|
||||
colormap = [ f'1 1 {name}'
|
||||
+ f' 9 {name}'
|
||||
+ ' 0 1 0 3 0 0 -1 9 \\ 0 0 0 255 255 255 0 0 255 '
|
||||
+ '30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 ' + str(len(colors))
|
||||
+ ' '.join([' 0 %s 255 1'%(' '.join([str(int(x*255.0)) for x in color])) for color in reversed(colors)])]
|
||||
+ f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {len(colors)}'
|
||||
+ ' '.join([f' 0 {util.srepr((255*np.array(c)).astype(int)," ")} 255 1' for c in reversed(colors)])]
|
||||
|
||||
elif format == 'raw':
|
||||
colormap = ['\t'.join(map(str,color)) for color in colors]
|
||||
|
|
|
|||
|
|
@ -1,11 +1,11 @@
|
|||
import os
|
||||
from pathlib import Path
|
||||
import tkinter
|
||||
|
||||
class Environment:
|
||||
|
||||
def __init__(self):
|
||||
"""Read and provide values of DAMASK configuration."""
|
||||
self.options = self._get_options()
|
||||
try:
|
||||
tk = tkinter.Tk()
|
||||
self.screen_width = tk.winfo_screenwidth()
|
||||
|
|
@ -15,17 +15,8 @@ class Environment:
|
|||
self.screen_width = 1024
|
||||
self.screen_height = 768
|
||||
|
||||
def relPath(self,relative = '.'):
|
||||
"""Return absolute path from path relative to DAMASK root."""
|
||||
return os.path.join(self.rootDir(),relative)
|
||||
|
||||
|
||||
def rootDir(self):
|
||||
"""Return DAMASK root path."""
|
||||
return os.path.normpath(os.path.join(os.path.realpath(__file__),'../../../'))
|
||||
|
||||
|
||||
def _get_options(self):
|
||||
@property
|
||||
def options(self):
|
||||
options = {}
|
||||
for item in ['DAMASK_NUM_THREADS',
|
||||
'MSC_ROOT',
|
||||
|
|
@ -34,3 +25,13 @@ class Environment:
|
|||
options[item] = os.environ[item] if item in os.environ else None
|
||||
|
||||
return options
|
||||
|
||||
@property
|
||||
def root_dir(self):
|
||||
"""Return DAMASK root path."""
|
||||
return Path(__file__).parents[2]
|
||||
|
||||
|
||||
# for compatibility
|
||||
def rootDir(self):
|
||||
return str(self.root_dir)
|
||||
|
|
|
|||
|
|
@ -43,12 +43,12 @@ class Geom:
|
|||
def __repr__(self):
|
||||
"""Basic information on geometry definition."""
|
||||
return util.srepr([
|
||||
'grid a b c: {}'.format(' x '.join(map(str,self.get_grid ()))),
|
||||
'size x y z: {}'.format(' x '.join(map(str,self.get_size ()))),
|
||||
'origin x y z: {}'.format(' '.join(map(str,self.get_origin()))),
|
||||
'homogenization: {}'.format(self.get_homogenization()),
|
||||
'# microstructures: {}'.format(len(np.unique(self.microstructure))),
|
||||
'max microstructure: {}'.format(np.nanmax(self.microstructure)),
|
||||
f'grid a b c: {util.srepr(self.get_grid ()," x ")}',
|
||||
f'size x y z: {util.srepr(self.get_size ()," x ")}',
|
||||
f'origin x y z: {util.srepr(self.get_origin()," ")}',
|
||||
f'homogenization: {self.get_homogenization()}',
|
||||
f'# microstructures: {self.N_microstructure}',
|
||||
f'max microstructure: {np.nanmax(self.microstructure)}',
|
||||
])
|
||||
|
||||
|
||||
|
|
@ -71,7 +71,7 @@ class Geom:
|
|||
grid_old = self.get_grid()
|
||||
size_old = self.get_size()
|
||||
origin_old = self.get_origin()
|
||||
unique_old = len(np.unique(self.microstructure))
|
||||
unique_old = self.N_microstructure
|
||||
max_old = np.nanmax(self.microstructure)
|
||||
|
||||
if size is not None and rescale:
|
||||
|
|
@ -85,32 +85,32 @@ class Geom:
|
|||
elif rescale:
|
||||
self.set_size(self.get_grid()/grid_old*self.size)
|
||||
|
||||
message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))]
|
||||
message = [f'grid a b c: {util.srepr(grid_old," x ")}']
|
||||
if np.any(grid_old != self.get_grid()):
|
||||
message[-1] = util.delete(message[-1])
|
||||
message.append(util.emph('grid a b c: {}'.format(' x '.join(map(str,self.get_grid())))))
|
||||
message.append(util.emph(f'grid a b c: {util.srepr(self.get_grid()," x ")}'))
|
||||
|
||||
message.append('size x y z: {}'.format(' x '.join(map(str,size_old))))
|
||||
message.append(f'size x y z: {util.srepr(size_old," x ")}')
|
||||
if np.any(size_old != self.get_size()):
|
||||
message[-1] = util.delete(message[-1])
|
||||
message.append(util.emph('size x y z: {}'.format(' x '.join(map(str,self.get_size())))))
|
||||
message.append(util.emph(f'size x y z: {util.srepr(self.get_size()," x ")}'))
|
||||
|
||||
message.append('origin x y z: {}'.format(' '.join(map(str,origin_old))))
|
||||
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])
|
||||
message.append(util.emph('origin x y z: {}'.format(' '.join(map(str,self.get_origin())))))
|
||||
message.append(util.emph(f'origin x y z: {util.srepr(self.get_origin()," ")}'))
|
||||
|
||||
message.append('homogenization: {}'.format(self.get_homogenization()))
|
||||
message.append(f'homogenization: {self.get_homogenization()}')
|
||||
|
||||
message.append('# microstructures: {}'.format(unique_old))
|
||||
if unique_old != len(np.unique(self.microstructure)):
|
||||
message.append(f'# microstructures: {unique_old}')
|
||||
if unique_old != self.N_microstructure:
|
||||
message[-1] = util.delete(message[-1])
|
||||
message.append(util.emph('# microstructures: {}'.format(len(np.unique(self.microstructure)))))
|
||||
message.append(util.emph(f'# microstructures: {self.N_microstructure}'))
|
||||
|
||||
message.append('max microstructure: {}'.format(max_old))
|
||||
message.append(f'max microstructure: {max_old}')
|
||||
if max_old != np.nanmax(self.microstructure):
|
||||
message[-1] = util.delete(message[-1])
|
||||
message.append(util.emph('max microstructure: {}'.format(np.nanmax(self.microstructure))))
|
||||
message.append(util.emph(f'max microstructure: {np.nanmax(self.microstructure)}'))
|
||||
|
||||
return util.return_message(message)
|
||||
|
||||
|
|
@ -154,9 +154,9 @@ class Geom:
|
|||
"""
|
||||
if microstructure is not None:
|
||||
if len(microstructure.shape) != 3:
|
||||
raise ValueError('Invalid microstructure shape {}'.format(microstructure.shape))
|
||||
raise ValueError(f'Invalid microstructure shape {microstructure.shape}')
|
||||
elif microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
|
||||
raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype))
|
||||
raise TypeError(f'Invalid microstructue data type {microstructure.dtype}')
|
||||
else:
|
||||
self.microstructure = np.copy(microstructure)
|
||||
|
||||
|
|
@ -175,8 +175,8 @@ class Geom:
|
|||
grid = np.asarray(self.microstructure.shape)
|
||||
self.size = grid/np.max(grid)
|
||||
else:
|
||||
if len(size) != 3 or any(np.array(size)<=0):
|
||||
raise ValueError('Invalid size {}'.format(size))
|
||||
if len(size) != 3 or any(np.array(size) <= 0):
|
||||
raise ValueError(f'Invalid size {size}')
|
||||
else:
|
||||
self.size = np.array(size)
|
||||
|
||||
|
|
@ -193,7 +193,7 @@ class Geom:
|
|||
"""
|
||||
if origin is not None:
|
||||
if len(origin) != 3:
|
||||
raise ValueError('Invalid origin {}'.format(origin))
|
||||
raise ValueError(f'Invalid origin {origin}')
|
||||
else:
|
||||
self.origin = np.array(origin)
|
||||
|
||||
|
|
@ -210,7 +210,7 @@ class Geom:
|
|||
"""
|
||||
if homogenization is not None:
|
||||
if not isinstance(homogenization,int) or homogenization < 1:
|
||||
raise TypeError('Invalid homogenization {}'.format(homogenization))
|
||||
raise TypeError(f'Invalid homogenization {homogenization}')
|
||||
else:
|
||||
self.homogenization = homogenization
|
||||
|
||||
|
|
@ -222,7 +222,7 @@ class Geom:
|
|||
|
||||
@property
|
||||
def N_microstructure(self):
|
||||
return len(np.unique(self.microstructure))
|
||||
return np.unique(self.microstructure).size
|
||||
|
||||
|
||||
def get_microstructure(self):
|
||||
|
|
@ -257,11 +257,11 @@ class Geom:
|
|||
|
||||
def get_header(self):
|
||||
"""Return the full header (grid, size, origin, homogenization, comments)."""
|
||||
header = ['{} header'.format(len(self.comments)+4)] + self.comments
|
||||
header = [f'{len(self.comments)+4} header'] + self.comments
|
||||
header.append('grid a {} b {} c {}'.format(*self.get_grid()))
|
||||
header.append('size x {} y {} z {}'.format(*self.get_size()))
|
||||
header.append('origin x {} y {} z {}'.format(*self.get_origin()))
|
||||
header.append('homogenization {}'.format(self.get_homogenization()))
|
||||
header.append(f'homogenization {self.get_homogenization()}')
|
||||
return header
|
||||
|
||||
|
||||
|
|
@ -320,7 +320,7 @@ class Geom:
|
|||
i += len(items)
|
||||
|
||||
if i != grid.prod():
|
||||
raise TypeError('Invalid file: expected {} entries, found {}'.format(grid.prod(),i))
|
||||
raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
|
||||
|
||||
if not np.any(np.mod(microstructure,1) != 0.0): # no float present
|
||||
microstructure = microstructure.astype('int')
|
||||
|
|
@ -331,6 +331,7 @@ class Geom:
|
|||
@staticmethod
|
||||
def _find_closest_seed(seeds, weights, point):
|
||||
return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
|
||||
|
||||
@staticmethod
|
||||
def from_Laguerre_tessellation(grid,size,seeds,weights,periodic=True):
|
||||
"""
|
||||
|
|
@ -373,7 +374,7 @@ class Geom:
|
|||
else:
|
||||
microstructure = microstructure.reshape(grid)
|
||||
|
||||
#comments = 'geom.py:from_Laguerre_tessellation v{}'.format(version)
|
||||
#ToDo: comments = 'geom.py:from_Laguerre_tessellation v{}'.format(version)
|
||||
return Geom(microstructure+1,size,homogenization=1)
|
||||
|
||||
|
||||
|
|
@ -398,7 +399,7 @@ class Geom:
|
|||
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
|
||||
devNull,microstructure = KDTree.query(coords)
|
||||
|
||||
#comments = 'geom.py:from_Voronoi_tessellation v{}'.format(version)
|
||||
#ToDo: comments = 'geom.py:from_Voronoi_tessellation v{}'.format(version)
|
||||
return Geom(microstructure.reshape(grid)+1,size,homogenization=1)
|
||||
|
||||
|
||||
|
|
@ -418,7 +419,7 @@ class Geom:
|
|||
grid = self.get_grid()
|
||||
|
||||
if pack is None:
|
||||
plain = grid.prod()/np.unique(self.microstructure).size < 250
|
||||
plain = grid.prod()/self.N_microstructure < 250
|
||||
else:
|
||||
plain = not pack
|
||||
|
||||
|
|
@ -448,11 +449,11 @@ class Geom:
|
|||
if compressType is None:
|
||||
f.write('\n'.join(self.get_header())+'\n')
|
||||
elif compressType == '.':
|
||||
f.write('{}\n'.format(former))
|
||||
f.write(f'{former}\n')
|
||||
elif compressType == 'to':
|
||||
f.write('{} to {}\n'.format(start,former))
|
||||
f.write(f'{start} to {former}\n')
|
||||
elif compressType == 'of':
|
||||
f.write('{} of {}\n'.format(reps,former))
|
||||
f.write(f'{reps} of {former}\n')
|
||||
|
||||
compressType = '.'
|
||||
start = current
|
||||
|
|
@ -461,11 +462,11 @@ class Geom:
|
|||
former = current
|
||||
|
||||
if compressType == '.':
|
||||
f.write('{}\n'.format(former))
|
||||
f.write(f'{former}\n')
|
||||
elif compressType == 'to':
|
||||
f.write('{} to {}\n'.format(start,former))
|
||||
f.write(f'{start} to {former}\n')
|
||||
elif compressType == 'of':
|
||||
f.write('{} of {}\n'.format(reps,former))
|
||||
f.write(f'{reps} of {former}\n')
|
||||
|
||||
|
||||
def to_vtk(self,fname=None):
|
||||
|
|
@ -511,7 +512,7 @@ class Geom:
|
|||
if not all(isinstance(d, str) for d in directions):
|
||||
raise TypeError('Directions are not of type str.')
|
||||
elif not set(directions).issubset(valid):
|
||||
raise ValueError('Invalid direction specified {}'.format(set(directions).difference(valid)))
|
||||
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
|
||||
|
||||
limits = [None,None] if reflect else [-2,0]
|
||||
ms = self.get_microstructure()
|
||||
|
|
@ -523,7 +524,7 @@ class Geom:
|
|||
if 'x' in directions:
|
||||
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
|
||||
|
||||
#self.add_comments('geom.py:mirror v{}'.format(version)
|
||||
#ToDo: self.add_comments('geom.py:mirror v{}'.format(version)
|
||||
return self.update(ms,rescale=True)
|
||||
|
||||
|
||||
|
|
@ -537,7 +538,7 @@ class Geom:
|
|||
number of grid points in x,y,z direction.
|
||||
|
||||
"""
|
||||
#self.add_comments('geom.py:scale v{}'.format(version)
|
||||
#ToDo: self.add_comments('geom.py:scale v{}'.format(version)
|
||||
return self.update(
|
||||
ndimage.interpolation.zoom(
|
||||
self.microstructure,
|
||||
|
|
@ -564,7 +565,7 @@ class Geom:
|
|||
unique, inverse = np.unique(arr, return_inverse=True)
|
||||
return unique[np.argmax(np.bincount(inverse))]
|
||||
|
||||
#self.add_comments('geom.py:clean v{}'.format(version)
|
||||
#ToDo: self.add_comments('geom.py:clean v{}'.format(version)
|
||||
return self.update(ndimage.filters.generic_filter(
|
||||
self.microstructure,
|
||||
mostFrequent,
|
||||
|
|
@ -579,7 +580,7 @@ class Geom:
|
|||
for i, oldID in enumerate(np.unique(self.microstructure)):
|
||||
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
|
||||
|
||||
#self.add_comments('geom.py:renumber v{}'.format(version)
|
||||
#ToDo: self.add_comments('geom.py:renumber v{}'.format(version)
|
||||
return self.update(renumbered)
|
||||
|
||||
|
||||
|
|
@ -614,7 +615,7 @@ class Geom:
|
|||
|
||||
origin = self.origin-(np.asarray(microstructure_in.shape)-self.grid)*.5 * self.size/self.grid
|
||||
|
||||
#self.add_comments('geom.py:rotate v{}'.format(version)
|
||||
#ToDo: self.add_comments('geom.py:rotate v{}'.format(version)
|
||||
return self.update(microstructure_in,origin=origin,rescale=True)
|
||||
|
||||
|
||||
|
|
@ -646,7 +647,7 @@ class Geom:
|
|||
|
||||
canvas[l[0]:r[0],l[1]:r[1],l[2]:r[2]] = self.microstructure[L[0]:R[0],L[1]:R[1],L[2]:R[2]]
|
||||
|
||||
#self.add_comments('geom.py:canvas v{}'.format(version)
|
||||
#ToDo: self.add_comments('geom.py:canvas v{}'.format(version)
|
||||
return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
|
||||
|
||||
|
||||
|
|
@ -666,5 +667,5 @@ class Geom:
|
|||
for from_ms,to_ms in zip(from_microstructure,to_microstructure):
|
||||
substituted[self.microstructure==from_ms] = to_ms
|
||||
|
||||
#self.add_comments('geom.py:substitute v{}'.format(version)
|
||||
#ToDo: self.add_comments('geom.py:substitute v{}'.format(version)
|
||||
return self.update(substituted)
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ class Symmetry:
|
|||
|
||||
def __repr__(self):
|
||||
"""Readable string."""
|
||||
return '{}'.format(self.system)
|
||||
return f'{self.system}'
|
||||
|
||||
|
||||
def __eq__(self, other):
|
||||
|
|
@ -82,9 +82,9 @@ class Symmetry:
|
|||
|
||||
@property
|
||||
def symmetry_operations(self):
|
||||
"""Symmetry operations as Quaternions."""
|
||||
"""Symmetry operations as quaternions."""
|
||||
if self.system == 'cubic':
|
||||
symQuats = [
|
||||
sym_quats = [
|
||||
[ 1.0, 0.0, 0.0, 0.0 ],
|
||||
[ 0.0, 1.0, 0.0, 0.0 ],
|
||||
[ 0.0, 0.0, 1.0, 0.0 ],
|
||||
|
|
@ -111,7 +111,7 @@ class Symmetry:
|
|||
[-0.5*np.sqrt(2),-0.5*np.sqrt(2), 0.0, 0.0 ],
|
||||
]
|
||||
elif self.system == 'hexagonal':
|
||||
symQuats = [
|
||||
sym_quats = [
|
||||
[ 1.0, 0.0, 0.0, 0.0 ],
|
||||
[-0.5*np.sqrt(3), 0.0, 0.0, -0.5 ],
|
||||
[ 0.5, 0.0, 0.0, 0.5*np.sqrt(3) ],
|
||||
|
|
@ -126,7 +126,7 @@ class Symmetry:
|
|||
[ 0.0, 0.5*np.sqrt(3), 0.5, 0.0 ],
|
||||
]
|
||||
elif self.system == 'tetragonal':
|
||||
symQuats = [
|
||||
sym_quats = [
|
||||
[ 1.0, 0.0, 0.0, 0.0 ],
|
||||
[ 0.0, 1.0, 0.0, 0.0 ],
|
||||
[ 0.0, 0.0, 1.0, 0.0 ],
|
||||
|
|
@ -137,17 +137,17 @@ class Symmetry:
|
|||
[-0.5*np.sqrt(2), 0.0, 0.0, 0.5*np.sqrt(2) ],
|
||||
]
|
||||
elif self.system == 'orthorhombic':
|
||||
symQuats = [
|
||||
sym_quats = [
|
||||
[ 1.0,0.0,0.0,0.0 ],
|
||||
[ 0.0,1.0,0.0,0.0 ],
|
||||
[ 0.0,0.0,1.0,0.0 ],
|
||||
[ 0.0,0.0,0.0,1.0 ],
|
||||
]
|
||||
else:
|
||||
symQuats = [
|
||||
sym_quats = [
|
||||
[ 1.0,0.0,0.0,0.0 ],
|
||||
]
|
||||
return np.array(symQuats)
|
||||
return np.array(sym_quats)
|
||||
|
||||
|
||||
def in_FZ(self,rho):
|
||||
|
|
@ -350,7 +350,7 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
|
|||
|
||||
def __repr__(self):
|
||||
"""Report basic lattice information."""
|
||||
return 'Bravais lattice {} ({} crystal system)'.format(self.lattice,self.symmetry)
|
||||
return f'Bravais lattice {self.lattice} ({self.symmetry} crystal system)'
|
||||
|
||||
|
||||
# Kurdjomov--Sachs orientation relationship for fcc <-> bcc transformation
|
||||
|
|
@ -616,10 +616,10 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
|
|||
try:
|
||||
relationship = models[model]
|
||||
except KeyError :
|
||||
raise KeyError('Orientation relationship "{}" is unknown'.format(model))
|
||||
raise KeyError(f'Orientation relationship "{model}" is unknown')
|
||||
|
||||
if self.lattice not in relationship['mapping']:
|
||||
raise ValueError('Relationship "{}" not supported for lattice "{}"'.format(model,self.lattice))
|
||||
raise ValueError(f'Relationship "{model}" not supported for lattice "{self.lattice}"')
|
||||
|
||||
r = {'lattice':Lattice((set(relationship['mapping'])-{self.lattice}).pop()), # target lattice
|
||||
'rotations':[] }
|
||||
|
|
|
|||
|
|
@ -61,7 +61,7 @@ class Orientation: # ToDo: make subclass of lattice and Rotation?
|
|||
if self.lattice.symmetry != other.lattice.symmetry:
|
||||
raise NotImplementedError('disorientation between different symmetry classes not supported yet.')
|
||||
|
||||
mySymEqs = self.equivalent if SST else self.equivalent[0] # take all or only first sym operation
|
||||
mySymEqs = self.equivalent if SST else self.equivalent[0] #ToDo: This is just me! # take all or only first sym operation
|
||||
otherSymEqs = other.equivalent
|
||||
|
||||
for i,sA in enumerate(mySymEqs):
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@ import os
|
|||
import datetime
|
||||
import xml.etree.ElementTree as ET
|
||||
import xml.dom.minidom
|
||||
from pathlib import Path
|
||||
from functools import partial
|
||||
|
||||
import h5py
|
||||
|
|
@ -50,8 +51,7 @@ class Result:
|
|||
self.version_minor = f.attrs['DADF5-minor']
|
||||
|
||||
if self.version_major != 0 or not 2 <= self.version_minor <= 6:
|
||||
raise TypeError('Unsupported DADF5 version {}.{} '.format(self.version_major,
|
||||
self.version_minor))
|
||||
raise TypeError(f'Unsupported DADF5 version {self.version_major}.{self.version_minor}')
|
||||
|
||||
self.structured = 'grid' in f['geometry'].attrs.keys()
|
||||
|
||||
|
|
@ -89,7 +89,7 @@ class Result:
|
|||
'con_physics': self.con_physics, 'mat_physics': self.mat_physics
|
||||
}
|
||||
|
||||
self.fname = os.path.abspath(fname)
|
||||
self.fname = Path(fname).absolute()
|
||||
|
||||
self._allow_modification = False
|
||||
|
||||
|
|
@ -107,7 +107,7 @@ class Result:
|
|||
self.pick('increments',all_selected_increments)
|
||||
|
||||
in_between = '' if len(all_selected_increments) < 3 else \
|
||||
''.join(['\n{}\n ...\n'.format(inc) for inc in all_selected_increments[1:-2]])
|
||||
''.join([f'\n{inc}\n ...\n' for inc in all_selected_increments[1:-2]])
|
||||
|
||||
return util.srepr(first + in_between + last)
|
||||
|
||||
|
|
@ -137,7 +137,7 @@ class Result:
|
|||
|
||||
if what == 'increments':
|
||||
choice = [c if isinstance(c,str) and c.startswith('inc') else
|
||||
'inc{}'.format(c) for c in choice]
|
||||
f'inc{c}' for c in choice]
|
||||
elif what == 'times':
|
||||
what = 'increments'
|
||||
if choice == ['*']:
|
||||
|
|
@ -412,21 +412,19 @@ class Result:
|
|||
message = ''
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
for i in self.iterate('increments'):
|
||||
message += '\n{} ({}s)\n'.format(i,self.times[self.increments.index(i)])
|
||||
message += f'\n{i} ({self.times[self.increments.index(i)]}s)\n'
|
||||
for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
|
||||
for oo in self.iterate(o):
|
||||
message += ' {}\n'.format(oo)
|
||||
message += f' {oo}\n'
|
||||
for pp in self.iterate(p):
|
||||
message += ' {}\n'.format(pp)
|
||||
message += f' {pp}\n'
|
||||
group = '/'.join([i,o[:-1],oo,pp]) # o[:-1]: plural/singular issue
|
||||
for d in f[group].keys():
|
||||
try:
|
||||
dataset = f['/'.join([group,d])]
|
||||
unit = f" / {dataset.attrs['Unit'].decode()}" if 'Unit' in dataset.attrs else ''
|
||||
description = dataset.attrs['Description'].decode()
|
||||
if 'Unit' in dataset.attrs:
|
||||
message += ' {} / ({}): {}\n'.format(d,dataset.attrs['Unit'].decode(),description)
|
||||
else:
|
||||
message += ' {}: {}\n'.format(d,description)
|
||||
message += f' {d}{unit}: {description}\n'
|
||||
except KeyError:
|
||||
pass
|
||||
return message
|
||||
|
|
@ -528,10 +526,10 @@ class Result:
|
|||
def _add_absolute(x):
|
||||
return {
|
||||
'data': np.abs(x['data']),
|
||||
'label': '|{}|'.format(x['label']),
|
||||
'label': f'|{x["label"]}|',
|
||||
'meta': {
|
||||
'Unit': x['meta']['Unit'],
|
||||
'Description': 'Absolute value of {} ({})'.format(x['label'],x['meta']['Description']),
|
||||
'Description': f"Absolute value of {x['label']} ({x['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -552,14 +550,14 @@ class Result:
|
|||
def _add_calculation(**kwargs):
|
||||
formula = kwargs['formula']
|
||||
for d in re.findall(r'#(.*?)#',formula):
|
||||
formula = formula.replace('#{}#'.format(d),"kwargs['{}']['data']".format(d))
|
||||
formula = formula.replace(f'#{d}#',f"kwargs['{d}']['data']")
|
||||
|
||||
return {
|
||||
'data': eval(formula),
|
||||
'label': kwargs['label'],
|
||||
'meta': {
|
||||
'Unit': kwargs['unit'],
|
||||
'Description': '{} (formula: {})'.format(kwargs['description'],kwargs['formula']),
|
||||
'Description': f"{kwargs['description']} (formula: {kwargs['formula']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -596,8 +594,9 @@ class Result:
|
|||
'label': 'sigma',
|
||||
'meta': {
|
||||
'Unit': P['meta']['Unit'],
|
||||
'Description': 'Cauchy stress calculated from {} ({}) and {} ({})'\
|
||||
.format(P['label'],P['meta']['Description'],F['label'],F['meta']['Description']),
|
||||
'Description': "Cauchy stress calculated "
|
||||
f"from {P['label']} ({P['meta']['Description']})"
|
||||
f" and {F['label']} ({F['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -620,10 +619,10 @@ class Result:
|
|||
def _add_determinant(T):
|
||||
return {
|
||||
'data': np.linalg.det(T['data']),
|
||||
'label': 'det({})'.format(T['label']),
|
||||
'label': f"det({T['label']})",
|
||||
'meta': {
|
||||
'Unit': T['meta']['Unit'],
|
||||
'Description': 'Determinant of tensor {} ({})'.format(T['label'],T['meta']['Description']),
|
||||
'Description': f"Determinant of tensor {T['label']} ({T['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -644,10 +643,10 @@ class Result:
|
|||
def _add_deviator(T):
|
||||
return {
|
||||
'data': mechanics.deviatoric_part(T['data']),
|
||||
'label': 's_{}'.format(T['label']),
|
||||
'label': f"s_{T['label']}",
|
||||
'meta': {
|
||||
'Unit': T['meta']['Unit'],
|
||||
'Description': 'Deviator of tensor {} ({})'.format(T['label'],T['meta']['Description']),
|
||||
'Description': f"Deviator of tensor {T['label']} ({T['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -675,10 +674,10 @@ class Result:
|
|||
|
||||
return {
|
||||
'data': mechanics.eigenvalues(T_sym['data'])[:,p],
|
||||
'label': 'lambda_{}({})'.format(eigenvalue,T_sym['label']),
|
||||
'label': f"lambda_{eigenvalue}({T_sym['label']})",
|
||||
'meta' : {
|
||||
'Unit': T_sym['meta']['Unit'],
|
||||
'Description': '{} eigenvalue of {} ({})'.format(label,T_sym['label'],T_sym['meta']['Description']),
|
||||
'Description': f"{label} eigenvalue of {T_sym['label']} ({T_sym['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -708,11 +707,11 @@ class Result:
|
|||
print('p',eigenvalue)
|
||||
return {
|
||||
'data': mechanics.eigenvectors(T_sym['data'])[:,p],
|
||||
'label': 'v_{}({})'.format(eigenvalue,T_sym['label']),
|
||||
'label': f"v_{eigenvalue}({T_sym['label']})",
|
||||
'meta' : {
|
||||
'Unit': '1',
|
||||
'Description': 'Eigenvector corresponding to {} eigenvalue of {} ({})'\
|
||||
.format(label,T_sym['label'],T_sym['meta']['Description']),
|
||||
'Description': f"Eigenvector corresponding to {label} eigenvalue"
|
||||
f" of {T_sym['label']} ({T_sym['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -768,10 +767,10 @@ class Result:
|
|||
def _add_maximum_shear(T_sym):
|
||||
return {
|
||||
'data': mechanics.maximum_shear(T_sym['data']),
|
||||
'label': 'max_shear({})'.format(T_sym['label']),
|
||||
'label': f"max_shear({T_sym['label']})",
|
||||
'meta': {
|
||||
'Unit': T_sym['meta']['Unit'],
|
||||
'Description': 'Maximum shear component of {} ({})'.format(T_sym['label'],T_sym['meta']['Description']),
|
||||
'Description': f"Maximum shear component of {T_sym['label']} ({T_sym['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -794,11 +793,11 @@ class Result:
|
|||
'stress'
|
||||
|
||||
return {
|
||||
'data': mechanics.Mises_strain(T_sym['data']) if t=='strain' else mechanics.Mises_stress(T_sym['data']),
|
||||
'label': '{}_vM'.format(T_sym['label']),
|
||||
'data': (mechanics.Mises_strain if t=='strain' else mechanics.Mises_stress)(T_sym['data']),
|
||||
'label': f"{T_sym['label']}_vM",
|
||||
'meta': {
|
||||
'Unit': T_sym['meta']['Unit'],
|
||||
'Description': 'Mises equivalent {} of {} ({})'.format(t,T_sym['label'],T_sym['meta']['Description']),
|
||||
'Description': f"Mises equivalent {t} of {T_sym['label']} ({T_sym['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -831,10 +830,10 @@ class Result:
|
|||
|
||||
return {
|
||||
'data': np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True),
|
||||
'label': '|{}|_{}'.format(x['label'],o),
|
||||
'label': f"|{x['label']}|_{o}",
|
||||
'meta': {
|
||||
'Unit': x['meta']['Unit'],
|
||||
'Description': '{}-norm of {} {} ({})'.format(o,t,x['label'],x['meta']['Description']),
|
||||
'Description': f"{o}-norm of {t} {x['label']} ({x['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -860,19 +859,20 @@ class Result:
|
|||
'label': 'S',
|
||||
'meta': {
|
||||
'Unit': P['meta']['Unit'],
|
||||
'Description': '2. Piola-Kirchhoff stress calculated from {} ({}) and {} ({})'\
|
||||
.format(P['label'],P['meta']['Description'],F['label'],F['meta']['Description']),
|
||||
'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:]
|
||||
}
|
||||
}
|
||||
def add_PK2(self,P='P',F='F'):
|
||||
"""
|
||||
Add second Piola-Kirchhoff calculated from first Piola-Kirchhoff stress and deformation gradient.
|
||||
Add second Piola-Kirchhoff stress calculated from first Piola-Kirchhoff stress and deformation gradient.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
P : str, optional
|
||||
Label first Piola-Kirchhoff stress dataset. Defaults to ‘P’.
|
||||
Label of first Piola-Kirchhoff stress dataset. Defaults to ‘P’.
|
||||
F : str, optional
|
||||
Label of deformation gradient dataset. Defaults to ‘F’.
|
||||
|
||||
|
|
@ -922,10 +922,10 @@ class Result:
|
|||
def _add_rotational_part(F):
|
||||
return {
|
||||
'data': mechanics.rotational_part(F['data']),
|
||||
'label': 'R({})'.format(F['label']),
|
||||
'label': f"R({F['label']})",
|
||||
'meta': {
|
||||
'Unit': F['meta']['Unit'],
|
||||
'Description': 'Rotational part of {} ({})'.format(F['label'],F['meta']['Description']),
|
||||
'Description': f"Rotational part of {F['label']} ({F['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -946,10 +946,10 @@ class Result:
|
|||
def _add_spherical(T):
|
||||
return {
|
||||
'data': mechanics.spherical_part(T['data']),
|
||||
'label': 'p_{}'.format(T['label']),
|
||||
'label': f"p_{T['label']}",
|
||||
'meta': {
|
||||
'Unit': T['meta']['Unit'],
|
||||
'Description': 'Spherical component of tensor {} ({})'.format(T['label'],T['meta']['Description']),
|
||||
'Description': f"Spherical component of tensor {T['label']} ({T['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -970,10 +970,10 @@ class Result:
|
|||
def _add_strain_tensor(F,t,m):
|
||||
return {
|
||||
'data': mechanics.strain_tensor(F['data'],t,m),
|
||||
'label': 'epsilon_{}^{}({})'.format(t,m,F['label']),
|
||||
'label': f"epsilon_{t}^{m}({F['label']})",
|
||||
'meta': {
|
||||
'Unit': F['meta']['Unit'],
|
||||
'Description': 'Strain tensor of {} ({})'.format(F['label'],F['meta']['Description']),
|
||||
'Description': f"Strain tensor of {F['label']} ({F['meta']['Description']})",
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
}
|
||||
|
|
@ -1000,11 +1000,11 @@ class Result:
|
|||
@staticmethod
|
||||
def _add_stretch_tensor(F,t):
|
||||
return {
|
||||
'data': mechanics.left_stretch(F['data']) if t == 'V' else mechanics.right_stretch(F['data']),
|
||||
'label': '{}({})'.format(t,F['label']),
|
||||
'data': (mechanics.left_stretch if t.upper() == 'V' else mechanics.right_stretch)(F['data']),
|
||||
'label': f"{t}({F['label']})",
|
||||
'meta': {
|
||||
'Unit': F['meta']['Unit'],
|
||||
'Description': '{} stretch tensor of {} ({})'.format('Left' if t == 'V' else 'Right',
|
||||
'Description': '{} stretch tensor of {} ({})'.format('Left' if t.upper() == 'V' else 'Right',
|
||||
F['label'],F['meta']['Description']),
|
||||
'Creator': inspect.stack()[0][3][1:]
|
||||
}
|
||||
|
|
@ -1040,7 +1040,7 @@ class Result:
|
|||
r = func(**datasets_in,**args)
|
||||
return [group,r]
|
||||
except Exception as err:
|
||||
print('Error during calculation: {}.'.format(err))
|
||||
print(f'Error during calculation: {err}.')
|
||||
return None
|
||||
|
||||
|
||||
|
|
@ -1051,14 +1051,17 @@ class Result:
|
|||
Parameters
|
||||
----------
|
||||
func : function
|
||||
Callback function that calculates a new dataset from one or more datasets per HDF5 group.
|
||||
Callback function that calculates a new dataset from one or
|
||||
more datasets per HDF5 group.
|
||||
datasets : dictionary
|
||||
Details of the datasets to be used: label (in HDF5 file) and arg (argument to which the data is parsed in func).
|
||||
Details of the datasets to be used: label (in HDF5 file) and
|
||||
arg (argument to which the data is parsed in func).
|
||||
args : dictionary, optional
|
||||
Arguments parsed to func.
|
||||
|
||||
"""
|
||||
pool = multiprocessing.Pool(int(Environment().options['DAMASK_NUM_THREADS']))
|
||||
num_threads = Environment().options['DAMASK_NUM_THREADS']
|
||||
pool = multiprocessing.Pool(int(num_threads) if num_threads is not None else None)
|
||||
lock = multiprocessing.Manager().Lock()
|
||||
|
||||
groups = self.groups_with_datasets(datasets.values())
|
||||
|
|
@ -1082,11 +1085,11 @@ class Result:
|
|||
|
||||
for l,v in result[1]['meta'].items():
|
||||
dataset.attrs[l]=v.encode()
|
||||
creator = 'damask.Result.{} v{}'.format(dataset.attrs['Creator'].decode(),version)
|
||||
creator = f"damask.Result.{dataset.attrs['Creator'].decode()} v{version}"
|
||||
dataset.attrs['Creator'] = creator.encode()
|
||||
|
||||
except (OSError,RuntimeError) as err:
|
||||
print('Could not add dataset: {}.'.format(err))
|
||||
print(f'Could not add dataset: {err}.')
|
||||
lock.release()
|
||||
|
||||
pool.close()
|
||||
|
|
@ -1119,7 +1122,7 @@ class Result:
|
|||
time_data = ET.SubElement(time, 'DataItem')
|
||||
time_data.attrib={'Format': 'XML',
|
||||
'NumberType': 'Float',
|
||||
'Dimensions': '{}'.format(len(self.times))}
|
||||
'Dimensions': f'{len(self.times)}'}
|
||||
time_data.text = ' '.join(map(str,self.times))
|
||||
|
||||
attributes = []
|
||||
|
|
@ -1160,7 +1163,7 @@ class Result:
|
|||
data_items[-1].attrib={'Format': 'HDF',
|
||||
'Precision': '8',
|
||||
'Dimensions': '{} {} {} 3'.format(*(self.grid+1))}
|
||||
data_items[-1].text='{}:/{}/geometry/u_n'.format(os.path.split(self.fname)[1],inc)
|
||||
data_items[-1].text=f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n'
|
||||
|
||||
for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
|
||||
for oo in getattr(self,o):
|
||||
|
|
@ -1175,17 +1178,17 @@ class Result:
|
|||
if (shape not in [(1,), (3,), (3,3)]) or dtype != np.float64: continue
|
||||
|
||||
attributes.append(ET.SubElement(grid, 'Attribute'))
|
||||
attributes[-1].attrib={'Name': '{}'.format(name.split('/',2)[2]),
|
||||
attributes[-1].attrib={'Name': name.split('/',2)[2],
|
||||
'Center': 'Cell',
|
||||
'AttributeType': 'Tensor'}
|
||||
data_items.append(ET.SubElement(attributes[-1], 'DataItem'))
|
||||
data_items[-1].attrib={'Format': 'HDF',
|
||||
'NumberType': 'Float',
|
||||
'Precision': '{}'.format(prec),
|
||||
'Precision': f'{prec}',
|
||||
'Dimensions': '{} {} {} {}'.format(*self.grid,np.prod(shape))}
|
||||
data_items[-1].text='{}:{}'.format(os.path.split(self.fname)[1],name)
|
||||
data_items[-1].text=f'{os.path.split(self.fname)[1]}:{name}'
|
||||
|
||||
with open(os.path.splitext(self.fname)[0]+'.xdmf','w') as f:
|
||||
with open(self.fname.with_suffix('.xdmf').name,'w') as f:
|
||||
f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
|
||||
|
||||
|
||||
|
|
@ -1261,7 +1264,4 @@ class Result:
|
|||
u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
|
||||
v.add(u,'u')
|
||||
|
||||
file_out = '{}_inc{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
|
||||
inc[3:].zfill(N_digits))
|
||||
|
||||
v.write(file_out)
|
||||
v.write(f'{self.fname.stem}_inc{inc[3:].zfill(N_digits)}')
|
||||
|
|
|
|||
|
|
@ -20,8 +20,8 @@ class Rotation:
|
|||
when viewing from the end point of the rotation axis towards the origin.
|
||||
- rotations will be interpreted in the passive sense.
|
||||
- Euler angle triplets are implemented using the Bunge convention,
|
||||
with the angular ranges as [0, 2π],[0, π],[0, 2π].
|
||||
- the rotation angle ω is limited to the interval [0, π].
|
||||
with the angular ranges as [0,2π], [0,π], [0,2π].
|
||||
- the rotation angle ω is limited to the interval [0,π].
|
||||
- the real part of a quaternion is positive, Re(q) > 0
|
||||
- P = -1 (as default).
|
||||
|
||||
|
|
@ -49,7 +49,8 @@ class Rotation:
|
|||
Parameters
|
||||
----------
|
||||
quaternion : numpy.ndarray, optional
|
||||
Unit quaternion that follows the conventions. Use .from_quaternion to perform a sanity check.
|
||||
Unit quaternion in positive real hemisphere.
|
||||
Use .from_quaternion to perform a sanity check.
|
||||
|
||||
"""
|
||||
if quaternion.shape[-1] != 4:
|
||||
|
|
@ -76,7 +77,7 @@ class Rotation:
|
|||
return 'Quaternions:\n'+str(self.quaternion) # ToDo: could be nicer ...
|
||||
return '\n'.join([
|
||||
'Quaternion: (real={:.3f}, imag=<{:+.3f}, {:+.3f}, {:+.3f}>)'.format(*(self.quaternion)),
|
||||
'Matrix:\n{}'.format(self.as_matrix()),
|
||||
'Matrix:\n{}'.format(np.round(self.as_matrix(),8)),
|
||||
'Bunge Eulers / deg: ({:3.2f}, {:3.2f}, {:3.2f})'.format(*self.as_Eulers(degrees=True)),
|
||||
])
|
||||
|
||||
|
|
@ -116,7 +117,7 @@ class Rotation:
|
|||
p_o = other.quaternion[...,1:]
|
||||
q = (q_m*q_o - np.einsum('...i,...i',p_m,p_o).reshape(self.shape+(1,)))
|
||||
p = q_m*p_o + q_o*p_m + _P * np.cross(p_m,p_o)
|
||||
return self.__class__(np.block([q,p])).standardize()
|
||||
return self.__class__(np.block([q,p]))._standardize()
|
||||
|
||||
elif isinstance(other,np.ndarray):
|
||||
if self.shape + (3,) == other.shape:
|
||||
|
|
@ -139,28 +140,26 @@ class Rotation:
|
|||
else:
|
||||
raise ValueError('Can only rotate vectors, 2nd order tensors, and 4th order tensors')
|
||||
else:
|
||||
raise TypeError('Cannot rotate {}'.format(type(other)))
|
||||
|
||||
def inverse(self):
|
||||
"""In-place inverse rotation/backward rotation."""
|
||||
self.quaternion[...,1:] *= -1
|
||||
return self
|
||||
|
||||
#@property
|
||||
def inversed(self):
|
||||
"""Inverse rotation/backward rotation."""
|
||||
return self.copy().inverse()
|
||||
raise TypeError(f'Cannot rotate {type(other)}')
|
||||
|
||||
|
||||
def standardize(self):
|
||||
"""In-place quaternion representation with positive real part."""
|
||||
def _standardize(self):
|
||||
"""Standardize (ensure positive real hemisphere)."""
|
||||
self.quaternion[self.quaternion[...,0] < 0.0] *= -1
|
||||
return self
|
||||
|
||||
#@property
|
||||
def standardized(self):
|
||||
"""Quaternion representation with positive real part."""
|
||||
return self.copy().standardize()
|
||||
def inverse(self):
|
||||
"""In-place inverse rotation (backward rotation)."""
|
||||
self.quaternion[...,1:] *= -1
|
||||
return self
|
||||
|
||||
def __invert__(self):
|
||||
"""Inverse rotation (backward rotation)."""
|
||||
return self.copy().inverse()
|
||||
|
||||
def inversed(self):
|
||||
"""Inverse rotation (backward rotation)."""
|
||||
return ~ self
|
||||
|
||||
|
||||
def misorientation(self,other):
|
||||
|
|
@ -173,7 +172,7 @@ class Rotation:
|
|||
Rotation to which the misorientation is computed.
|
||||
|
||||
"""
|
||||
return other*self.inversed()
|
||||
return other@~self
|
||||
|
||||
|
||||
def broadcast_to(self,shape):
|
||||
|
|
@ -188,7 +187,7 @@ class Rotation:
|
|||
return self.__class__(q)
|
||||
|
||||
|
||||
def average(self,other):
|
||||
def average(self,other): #ToDo: discuss calling for vectors
|
||||
"""
|
||||
Calculate the average rotation.
|
||||
|
||||
|
|
@ -208,25 +207,31 @@ class Rotation:
|
|||
|
||||
def as_quaternion(self):
|
||||
"""
|
||||
Unit quaternion [q, p_1, p_2, p_3].
|
||||
Represent as unit quaternion.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
quaternion : bool, optional
|
||||
return quaternion as DAMASK object.
|
||||
Returns
|
||||
-------
|
||||
q : numpy.ndarray of shape (...,4)
|
||||
Unit quaternion in positive real hemisphere: (q_0, q_1, q_2, q_3), |q|=1, q_0 ≥ 0.
|
||||
|
||||
"""
|
||||
return self.quaternion
|
||||
return self.quaternion.copy()
|
||||
|
||||
def as_Eulers(self,
|
||||
degrees = False):
|
||||
"""
|
||||
Bunge-Euler angles: (φ_1, ϕ, φ_2).
|
||||
Represent as Bunge-Euler angles.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
degrees : bool, optional
|
||||
return angles in degrees.
|
||||
Return angles in degrees.
|
||||
|
||||
Returns
|
||||
-------
|
||||
phi : numpy.ndarray of shape (...,3)
|
||||
Bunge-Euler angles: (φ_1, ϕ, φ_2), φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]
|
||||
unless degrees == True: φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360]
|
||||
|
||||
"""
|
||||
eu = Rotation._qu2eu(self.quaternion)
|
||||
|
|
@ -237,14 +242,21 @@ class Rotation:
|
|||
degrees = False,
|
||||
pair = False):
|
||||
"""
|
||||
Axis angle representation [n_1, n_2, n_3, ω] unless pair == True: ([n_1, n_2, n_3], ω).
|
||||
Represent as axis angle pair.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
degrees : bool, optional
|
||||
return rotation angle in degrees.
|
||||
Return rotation angle in degrees. Defaults to False.
|
||||
pair : bool, optional
|
||||
return tuple of axis and angle.
|
||||
Return tuple of axis and angle. Defaults to False.
|
||||
|
||||
Returns
|
||||
-------
|
||||
axis_angle : numpy.ndarray of shape (...,4) unless pair == True:
|
||||
tuple containing numpy.ndarray of shapes (...,3) and (...)
|
||||
Axis angle pair: (n_1, n_2, n_3, ω), |n| = 1 and ω ∈ [0,π]
|
||||
unless degrees = True: ω ∈ [0,180].
|
||||
|
||||
"""
|
||||
ax = Rotation._qu2ax(self.quaternion)
|
||||
|
|
@ -252,30 +264,60 @@ class Rotation:
|
|||
return (ax[...,:3],ax[...,3]) if pair else ax
|
||||
|
||||
def as_matrix(self):
|
||||
"""Rotation matrix."""
|
||||
"""
|
||||
Represent as rotation matrix.
|
||||
|
||||
Returns
|
||||
-------
|
||||
R : numpy.ndarray of shape (...,3,3)
|
||||
Rotation matrix R, det(R) = 1, R.T∙R=I.
|
||||
|
||||
"""
|
||||
return Rotation._qu2om(self.quaternion)
|
||||
|
||||
def as_Rodrigues(self,
|
||||
vector = False):
|
||||
"""
|
||||
Rodrigues-Frank vector representation [n_1, n_2, n_3, tan(ω/2)] unless vector == True: [n_1, n_2, n_3] * tan(ω/2).
|
||||
Represent as Rodrigues-Frank vector with separated axis and angle argument.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
vector : bool, optional
|
||||
return as actual Rodrigues--Frank vector, i.e. rotation axis scaled by tan(ω/2).
|
||||
Return as actual Rodrigues-Frank vector, i.e. axis
|
||||
and angle argument are not separated.
|
||||
|
||||
Returns
|
||||
-------
|
||||
rho : numpy.ndarray of shape (...,4) unless vector == True:
|
||||
numpy.ndarray of shape (...,3)
|
||||
Rodrigues-Frank vector: [n_1, n_2, n_3, tan(ω/2)], |n| = 1 and ω ∈ [0,π].
|
||||
|
||||
"""
|
||||
ro = Rotation._qu2ro(self.quaternion)
|
||||
with np.errstate(invalid='ignore'):
|
||||
return ro[...,:3]*ro[...,3:] if vector else ro
|
||||
return ro[...,:3]*ro[...,3:4] if vector else ro
|
||||
|
||||
def as_homochoric(self):
|
||||
"""Homochoric vector: (h_1, h_2, h_3)."""
|
||||
"""
|
||||
Represent as homochoric vector.
|
||||
|
||||
Returns
|
||||
-------
|
||||
h : numpy.ndarray of shape (...,3)
|
||||
Homochoric vector: (h_1, h_2, h_3), |h| < 1/2*π^(2/3).
|
||||
|
||||
"""
|
||||
return Rotation._qu2ho(self.quaternion)
|
||||
|
||||
def as_cubochoric(self):
|
||||
"""Cubochoric vector: (c_1, c_2, c_3)."""
|
||||
"""
|
||||
Represent as cubochoric vector.
|
||||
|
||||
Returns
|
||||
-------
|
||||
c : numpy.ndarray of shape (...,3)
|
||||
Cubochoric vector: (c_1, c_2, c_3), max(c_i) < 1/2*π^(2/3).
|
||||
|
||||
"""
|
||||
return Rotation._qu2cu(self.quaternion)
|
||||
|
||||
@property
|
||||
|
|
@ -296,18 +338,34 @@ class Rotation:
|
|||
# Static constructors. The input data needs to follow the conventions, options allow to
|
||||
# relax the conventions.
|
||||
@staticmethod
|
||||
def from_quaternion(quaternion,
|
||||
def from_quaternion(q,
|
||||
accept_homomorph = False,
|
||||
P = -1,
|
||||
acceptHomomorph = None):
|
||||
acceptHomomorph = None): # old name (for compatibility)
|
||||
"""
|
||||
Initialize from quaternion.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
q : numpy.ndarray of shape (...,4)
|
||||
Unit quaternion in positive real hemisphere: (q_0, q_1, q_2, q_3),
|
||||
|q|=1, q_0 ≥ 0.
|
||||
accept_homomorph : boolean, optional
|
||||
Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
|
||||
Defaults to False.
|
||||
P : integer ∈ {-1,1}, optional
|
||||
Convention used. Defaults to -1.
|
||||
|
||||
"""
|
||||
if acceptHomomorph is not None:
|
||||
accept_homomorph = acceptHomomorph
|
||||
qu = np.array(quaternion,dtype=float)
|
||||
accept_homomorph = acceptHomomorph # for compatibility
|
||||
qu = np.array(q,dtype=float)
|
||||
if qu.shape[:-2:-1] != (4,):
|
||||
raise ValueError('Invalid shape.')
|
||||
if abs(P) != 1:
|
||||
raise ValueError('P ∉ {-1,1}')
|
||||
|
||||
if P > 0: qu[...,1:4] *= -1 # convert from P=1 to P=-1
|
||||
if P == 1: qu[...,1:4] *= -1
|
||||
if accept_homomorph:
|
||||
qu[qu[...,0] < 0.0] *= -1
|
||||
else:
|
||||
|
|
@ -319,10 +377,21 @@ class Rotation:
|
|||
return Rotation(qu)
|
||||
|
||||
@staticmethod
|
||||
def from_Eulers(eulers,
|
||||
def from_Eulers(phi,
|
||||
degrees = False):
|
||||
"""
|
||||
Initialize from Bunge-Euler angles.
|
||||
|
||||
eu = np.array(eulers,dtype=float)
|
||||
Parameters
|
||||
----------
|
||||
phi : numpy.ndarray of shape (...,3)
|
||||
Bunge-Euler angles: (φ_1, ϕ, φ_2), φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π]
|
||||
unless degrees == True: φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360].
|
||||
degrees : boolean, optional
|
||||
Bunge-Euler angles are given in degrees. Defaults to False.
|
||||
|
||||
"""
|
||||
eu = np.array(phi,dtype=float)
|
||||
if eu.shape[:-2:-1] != (3,):
|
||||
raise ValueError('Invalid shape.')
|
||||
|
||||
|
|
@ -337,12 +406,29 @@ class Rotation:
|
|||
degrees = False,
|
||||
normalise = False,
|
||||
P = -1):
|
||||
"""
|
||||
Initialize from Axis angle pair.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
axis_angle : numpy.ndarray of shape (...,4)
|
||||
Axis angle pair: [n_1, n_2, n_3, ω], |n| = 1 and ω ∈ [0,π]
|
||||
unless degrees = True: ω ∈ [0,180].
|
||||
degrees : boolean, optional
|
||||
Angle ω is given in degrees. Defaults to False.
|
||||
normalize: boolean, optional
|
||||
Allow |n| ≠ 1. Defaults to False.
|
||||
P : integer ∈ {-1,1}, optional
|
||||
Convention used. Defaults to -1.
|
||||
|
||||
"""
|
||||
ax = np.array(axis_angle,dtype=float)
|
||||
if ax.shape[:-2:-1] != (4,):
|
||||
raise ValueError('Invalid shape.')
|
||||
if abs(P) != 1:
|
||||
raise ValueError('P ∉ {-1,1}')
|
||||
|
||||
if P > 0: ax[...,0:3] *= -1 # convert from P=1 to P=-1
|
||||
if P == 1: ax[...,0:3] *= -1
|
||||
if degrees: ax[..., 3] = np.radians(ax[...,3])
|
||||
if normalise: ax[...,0:3] /= np.linalg.norm(ax[...,0:3],axis=-1)
|
||||
if np.any(ax[...,3] < 0.0) or np.any(ax[...,3] > np.pi):
|
||||
|
|
@ -356,7 +442,19 @@ class Rotation:
|
|||
def from_basis(basis,
|
||||
orthonormal = True,
|
||||
reciprocal = False):
|
||||
"""
|
||||
Initialize from lattice basis vectors.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
basis : numpy.ndarray of shape (...,3,3)
|
||||
Three lattice basis vectors in three dimensions.
|
||||
orthonormal : boolean, optional
|
||||
Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
|
||||
reciprocal : boolean, optional
|
||||
Basis vectors are given in reciprocal (instead of real) space. Defaults to False.
|
||||
|
||||
"""
|
||||
om = np.array(basis,dtype=float)
|
||||
if om.shape[:-3:-1] != (3,3):
|
||||
raise ValueError('Invalid shape.')
|
||||
|
|
@ -377,20 +475,43 @@ class Rotation:
|
|||
return Rotation(Rotation._om2qu(om))
|
||||
|
||||
@staticmethod
|
||||
def from_matrix(om):
|
||||
def from_matrix(R):
|
||||
"""
|
||||
Initialize from rotation matrix.
|
||||
|
||||
return Rotation.from_basis(om)
|
||||
Parameters
|
||||
----------
|
||||
R : numpy.ndarray of shape (...,3,3)
|
||||
Rotation matrix: det(R) = 1, R.T∙R=I.
|
||||
|
||||
"""
|
||||
return Rotation.from_basis(R)
|
||||
|
||||
@staticmethod
|
||||
def from_Rodrigues(rodrigues,
|
||||
def from_Rodrigues(rho,
|
||||
normalise = False,
|
||||
P = -1):
|
||||
"""
|
||||
Initialize from Rodrigues-Frank vector.
|
||||
|
||||
ro = np.array(rodrigues,dtype=float)
|
||||
Parameters
|
||||
----------
|
||||
rho : numpy.ndarray of shape (...,4)
|
||||
Rodrigues-Frank vector (angle separated from axis).
|
||||
(n_1, n_2, n_3, tan(ω/2)), |n| = 1 and ω ∈ [0,π].
|
||||
normalize : boolean, optional
|
||||
Allow |n| ≠ 1. Defaults to False.
|
||||
P : integer ∈ {-1,1}, optional
|
||||
Convention used. Defaults to -1.
|
||||
|
||||
"""
|
||||
ro = np.array(rho,dtype=float)
|
||||
if ro.shape[:-2:-1] != (4,):
|
||||
raise ValueError('Invalid shape.')
|
||||
if abs(P) != 1:
|
||||
raise ValueError('P ∉ {-1,1}')
|
||||
|
||||
if P > 0: ro[...,0:3] *= -1 # convert from P=1 to P=-1
|
||||
if P == 1: ro[...,0:3] *= -1
|
||||
if normalise: ro[...,0:3] /= np.linalg.norm(ro[...,0:3],axis=-1)
|
||||
if np.any(ro[...,3] < 0.0):
|
||||
raise ValueError('Rodrigues vector rotation angle not positive.')
|
||||
|
|
@ -400,14 +521,26 @@ class Rotation:
|
|||
return Rotation(Rotation._ro2qu(ro))
|
||||
|
||||
@staticmethod
|
||||
def from_homochoric(homochoric,
|
||||
def from_homochoric(h,
|
||||
P = -1):
|
||||
"""
|
||||
Initialize from homochoric vector.
|
||||
|
||||
ho = np.array(homochoric,dtype=float)
|
||||
Parameters
|
||||
----------
|
||||
h : numpy.ndarray of shape (...,3)
|
||||
Homochoric vector: (h_1, h_2, h_3), |h| < (3/4*π)^(1/3).
|
||||
P : integer ∈ {-1,1}, optional
|
||||
Convention used. Defaults to -1.
|
||||
|
||||
"""
|
||||
ho = np.array(h,dtype=float)
|
||||
if ho.shape[:-2:-1] != (3,):
|
||||
raise ValueError('Invalid shape.')
|
||||
if abs(P) != 1:
|
||||
raise ValueError('P ∉ {-1,1}')
|
||||
|
||||
if P > 0: ho *= -1 # convert from P=1 to P=-1
|
||||
if P == 1: ho *= -1
|
||||
|
||||
if np.any(np.linalg.norm(ho,axis=-1) >_R1+1e-9):
|
||||
raise ValueError('Homochoric coordinate outside of the sphere.')
|
||||
|
|
@ -415,18 +548,30 @@ class Rotation:
|
|||
return Rotation(Rotation._ho2qu(ho))
|
||||
|
||||
@staticmethod
|
||||
def from_cubochoric(cubochoric,
|
||||
def from_cubochoric(c,
|
||||
P = -1):
|
||||
"""
|
||||
Initialize from cubochoric vector.
|
||||
|
||||
cu = np.array(cubochoric,dtype=float)
|
||||
Parameters
|
||||
----------
|
||||
c : numpy.ndarray of shape (...,3)
|
||||
Cubochoric vector: (c_1, c_2, c_3), max(c_i) < 1/2*π^(2/3).
|
||||
P : integer ∈ {-1,1}, optional
|
||||
Convention used. Defaults to -1.
|
||||
|
||||
"""
|
||||
cu = np.array(c,dtype=float)
|
||||
if cu.shape[:-2:-1] != (3,):
|
||||
raise ValueError('Invalid shape.')
|
||||
if abs(P) != 1:
|
||||
raise ValueError('P ∉ {-1,1}')
|
||||
|
||||
if np.abs(np.max(cu))>np.pi**(2./3.) * 0.5+1e-9:
|
||||
raise ValueError('Cubochoric coordinate outside of the cube: {} {} {}.'.format(*cu))
|
||||
if np.abs(np.max(cu)) > np.pi**(2./3.) * 0.5+1e-9:
|
||||
raise ValueError('Cubochoric coordinate outside of the cube.')
|
||||
|
||||
ho = Rotation._cu2ho(cu)
|
||||
if P > 0: ho *= -1 # convert from P=1 to P=-1
|
||||
if P == 1: ho *= -1
|
||||
|
||||
return Rotation(Rotation._ho2qu(ho))
|
||||
|
||||
|
|
@ -479,7 +624,7 @@ class Rotation:
|
|||
np.cos(2.0*np.pi*r[...,1])*B,
|
||||
np.sin(2.0*np.pi*r[...,0])*A],axis=-1)
|
||||
|
||||
return Rotation(q.reshape(r.shape[:-1]+(4,)) if shape is not None else q).standardize()
|
||||
return Rotation(q.reshape(r.shape[:-1]+(4,)) if shape is not None else q)._standardize()
|
||||
|
||||
|
||||
# for compatibility (old names do not follow convention)
|
||||
|
|
@ -493,7 +638,7 @@ class Rotation:
|
|||
####################################################################################################
|
||||
# Code below available according to the following conditions on https://github.com/MarDiehl/3Drotations
|
||||
####################################################################################################
|
||||
# Copyright (c) 2017-2019, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
|
||||
# Copyright (c) 2017-2020, Martin Diehl/Max-Planck-Institut für Eisenforschung GmbH
|
||||
# Copyright (c) 2013-2014, Marc De Graef/Carnegie Mellon University
|
||||
# All rights reserved.
|
||||
#
|
||||
|
|
@ -552,7 +697,7 @@ class Rotation:
|
|||
np.zeros(qu.shape[:-1]+(2,))]),
|
||||
np.where(np.abs(q03_s) < 1.0e-8,
|
||||
np.block([np.arctan2( 2.0*qu[...,1:2]*qu[...,2:3],qu[...,1:2]**2-qu[...,2:3]**2),
|
||||
np.broadcast_to(np.pi,qu.shape[:-1]+(1,)),
|
||||
np.broadcast_to(np.pi,qu[...,0:1].shape),
|
||||
np.zeros(qu.shape[:-1]+(1,))]),
|
||||
np.block([np.arctan2((-_P*q02+q13)*chi, (-_P*q01-q23)*chi),
|
||||
np.arctan2( 2.0*chi, q03_s-q12_s ),
|
||||
|
|
@ -575,7 +720,7 @@ class Rotation:
|
|||
s = np.sign(qu[...,0:1])/np.sqrt(qu[...,1:2]**2+qu[...,2:3]**2+qu[...,3:4]**2)
|
||||
omega = 2.0 * np.arccos(np.clip(qu[...,0:1],-1.0,1.0))
|
||||
ax = np.where(np.broadcast_to(qu[...,0:1] < 1.0e-8,qu.shape),
|
||||
np.block([qu[...,1:4],np.broadcast_to(np.pi,qu.shape[:-1]+(1,))]),
|
||||
np.block([qu[...,1:4],np.broadcast_to(np.pi,qu[...,0:1].shape)]),
|
||||
np.block([qu[...,1:4]*s,omega]))
|
||||
ax[np.isclose(qu[...,0],1.,rtol=0.0)] = [0.0, 0.0, 1.0, 0.0]
|
||||
return ax
|
||||
|
|
@ -586,7 +731,7 @@ class Rotation:
|
|||
with np.errstate(invalid='ignore',divide='ignore'):
|
||||
s = np.linalg.norm(qu[...,1:4],axis=-1,keepdims=True)
|
||||
ro = np.where(np.broadcast_to(np.abs(qu[...,0:1]) < 1.0e-12,qu.shape),
|
||||
np.block([qu[...,1:2], qu[...,2:3], qu[...,3:4], np.broadcast_to(np.inf,qu.shape[:-1]+(1,))]),
|
||||
np.block([qu[...,1:2], qu[...,2:3], qu[...,3:4], np.broadcast_to(np.inf,qu[...,0:1].shape)]),
|
||||
np.block([qu[...,1:2]/s,qu[...,2:3]/s,qu[...,3:4]/s,
|
||||
np.tan(np.arccos(np.clip(qu[...,0:1],-1.0,1.0)))
|
||||
])
|
||||
|
|
|
|||
|
|
@ -4,6 +4,7 @@ import pandas as pd
|
|||
import numpy as np
|
||||
|
||||
from . import version
|
||||
from . import util
|
||||
|
||||
class Table:
|
||||
"""Store spreadsheet-like data."""
|
||||
|
|
@ -24,7 +25,7 @@ class Table:
|
|||
"""
|
||||
self.comments = [] if comments is None else [c for c in comments]
|
||||
self.data = pd.DataFrame(data=data)
|
||||
self.shapes = shapes
|
||||
self.shapes = { k:(v,) if isinstance(v,(np.int,int)) else v for k,v in shapes.items() }
|
||||
self._label_condensed()
|
||||
|
||||
|
||||
|
|
@ -33,7 +34,7 @@ class Table:
|
|||
labels = []
|
||||
for label,shape in self.shapes.items():
|
||||
size = int(np.prod(shape))
|
||||
labels += ['{}{}'.format('' if size == 1 else '{}_'.format(i+1),label) for i in range(size)]
|
||||
labels += [('' if size == 1 else f'{i+1}_')+label for i in range(size)]
|
||||
self.data.columns = labels
|
||||
|
||||
|
||||
|
|
@ -47,8 +48,7 @@ class Table:
|
|||
|
||||
def _add_comment(self,label,shape,info):
|
||||
if info is not None:
|
||||
c = '{}{}: {}'.format(label,' '+str(shape) if np.prod(shape,dtype=int) > 1 else '',info)
|
||||
self.comments.append(c)
|
||||
self.comments.append(f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}')
|
||||
|
||||
|
||||
@staticmethod
|
||||
|
|
@ -126,8 +126,6 @@ class Table:
|
|||
Filename or file for reading.
|
||||
|
||||
"""
|
||||
shapes = {'eu':(3,), 'pos':(2,),
|
||||
'IQ':(1,), 'CI':(1,), 'ID':(1,), 'intensity':(1,), 'fit':(1,)}
|
||||
try:
|
||||
f = open(fname)
|
||||
except TypeError:
|
||||
|
|
@ -136,7 +134,7 @@ class Table:
|
|||
|
||||
content = f.readlines()
|
||||
|
||||
comments = ['table.py:from_ang v {}'.format(version)]
|
||||
comments = [f'table.py:from_ang v{version}']
|
||||
for line in content:
|
||||
if line.startswith('#'):
|
||||
comments.append(line.strip())
|
||||
|
|
@ -144,8 +142,11 @@ class Table:
|
|||
break
|
||||
|
||||
data = np.loadtxt(content)
|
||||
for c in range(data.shape[1]-10):
|
||||
shapes['n/a_{}'.format(c+1)] = (1,)
|
||||
|
||||
shapes = {'eu':3, 'pos':2, 'IQ':1, 'CI':1, 'ID':1, 'intensity':1, 'fit':1}
|
||||
remainder = data.shape[1]-sum(shapes.values())
|
||||
if remainder > 0: # 3.8 can do: if (remainder := data.shape[1]-sum(shapes.values())) > 0
|
||||
shapes['unknown'] = remainder
|
||||
|
||||
return Table(data,shapes,comments)
|
||||
|
||||
|
|
@ -234,7 +235,6 @@ class Table:
|
|||
|
||||
"""
|
||||
self.data.drop(columns=label,inplace=True)
|
||||
|
||||
del self.shapes[label]
|
||||
|
||||
|
||||
|
|
@ -251,8 +251,7 @@ class Table:
|
|||
|
||||
"""
|
||||
self.data.rename(columns={label_old:label_new},inplace=True)
|
||||
c = '{} => {}{}'.format(label_old,label_new,'' if info is None else ': {}'.format(info))
|
||||
self.comments.append(c)
|
||||
self.comments.append(f'{label_old} => {label_new}'+('' if info is None else f': {info}'))
|
||||
self.shapes = {(label if label != label_old else label_new):self.shapes[label] for label in self.shapes}
|
||||
|
||||
|
||||
|
|
@ -271,7 +270,7 @@ class Table:
|
|||
self._label_flat()
|
||||
self.data.sort_values(labels,axis=0,inplace=True,ascending=ascending)
|
||||
self._label_condensed()
|
||||
self.comments.append('sorted by [{}]'.format(', '.join(labels)))
|
||||
self.comments.append(f'sorted by [{", ".join(labels)}]')
|
||||
|
||||
|
||||
def append(self,other):
|
||||
|
|
@ -328,18 +327,18 @@ class Table:
|
|||
labels = []
|
||||
for l in [x for x in self.data.columns if not (x in seen or seen.add(x))]:
|
||||
if self.shapes[l] == (1,):
|
||||
labels.append('{}'.format(l))
|
||||
labels.append(f'{l}')
|
||||
elif len(self.shapes[l]) == 1:
|
||||
labels += ['{}_{}'.format(i+1,l) \
|
||||
labels += [f'{i+1}_{l}' \
|
||||
for i in range(self.shapes[l][0])]
|
||||
else:
|
||||
labels += ['{}:{}_{}'.format('x'.join([str(d) for d in self.shapes[l]]),i+1,l) \
|
||||
labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
|
||||
for i in range(np.prod(self.shapes[l]))]
|
||||
|
||||
if new_style:
|
||||
header = ['# {}'.format(comment) for comment in self.comments]
|
||||
header = [f'# {comment}' for comment in self.comments]
|
||||
else:
|
||||
header = ['{} header'.format(len(self.comments)+1)] \
|
||||
header = [f'{len(self.comments)+1} header'] \
|
||||
+ self.comments \
|
||||
|
||||
try:
|
||||
|
|
|
|||
|
|
@ -53,7 +53,7 @@ class Test:
|
|||
self.dirBase = os.path.dirname(os.path.realpath(sys.modules[self.__class__.__module__].__file__))
|
||||
|
||||
self.parser = OptionParser(option_class=damask.extendableOption,
|
||||
description = '{} (Test class version: {})'.format(self.description,damask.version),
|
||||
description = f'{self.description} (Test class version: {damask.version})',
|
||||
usage = './test.py [options]')
|
||||
self.parser.add_option("-k", "--keep",
|
||||
action = "store_true",
|
||||
|
|
@ -93,7 +93,7 @@ class Test:
|
|||
for variant,object in enumerate(self.variants):
|
||||
name = self.variantName(variant)
|
||||
if self.options.show:
|
||||
logging.critical('{}: {}'.format(variant+1,name))
|
||||
logging.critical(f'{variant+1}: {name}')
|
||||
elif self.options.select is not None \
|
||||
and not (name in self.options.select or str(variant+1) in self.options.select):
|
||||
pass
|
||||
|
|
@ -106,12 +106,12 @@ class Test:
|
|||
self.postprocess(variant)
|
||||
|
||||
if self.options.update:
|
||||
if self.update(variant) != 0: logging.critical('update for "{}" failed.'.format(name))
|
||||
if self.update(variant) != 0: logging.critical(f'update for "{name}" failed.')
|
||||
elif not (self.options.accept or self.compare(variant)): # no update, do comparison
|
||||
return variant+1 # return culprit
|
||||
|
||||
except Exception as e:
|
||||
logging.critical('exception during variant execution: "{}"'.format(str(e)))
|
||||
logging.critical(f'exception during variant execution: "{e}"')
|
||||
return variant+1 # return culprit
|
||||
return 0
|
||||
|
||||
|
|
@ -124,13 +124,13 @@ class Test:
|
|||
try:
|
||||
shutil.rmtree(self.dirCurrent())
|
||||
except FileNotFoundError:
|
||||
logging.warning('removal of directory "{}" not possible...'.format(self.dirCurrent()))
|
||||
logging.warning(f'removal of directory "{self.dirCurrent()}" not possible...')
|
||||
|
||||
try:
|
||||
os.mkdir(self.dirCurrent())
|
||||
return True
|
||||
except FileExistsError:
|
||||
logging.critical('creation of directory "{}" failed.'.format(self.dirCurrent()))
|
||||
logging.critical(f'creation of directory "{self.dirCurrent()}" failed.')
|
||||
return False
|
||||
|
||||
def prepareAll(self):
|
||||
|
|
@ -211,7 +211,7 @@ class Test:
|
|||
try:
|
||||
shutil.copy2(source,target)
|
||||
except FileNotFoundError:
|
||||
logging.critical('error copying {} to {}'.format(source,target))
|
||||
logging.critical(f'error copying {source} to {target}')
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
|
|
@ -222,7 +222,7 @@ class Test:
|
|||
try:
|
||||
shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
|
||||
except FileNotFoundError:
|
||||
logging.critical('Reference2Current: Unable to copy file "{}"'.format(f))
|
||||
logging.critical(f'Reference2Current: Unable to copy file "{f}"')
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
|
|
@ -235,7 +235,7 @@ class Test:
|
|||
shutil.copy2(os.path.join(source,f),self.fileInCurrent(targetfiles[i]))
|
||||
except FileNotFoundError:
|
||||
logging.error(os.path.join(source,f))
|
||||
logging.critical('Base2Current: Unable to copy file "{}"'.format(f))
|
||||
logging.critical(f'Base2Current: Unable to copy file "{f}"')
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
|
|
@ -246,7 +246,7 @@ class Test:
|
|||
try:
|
||||
shutil.copy2(self.fileInCurrent(f),self.fileInReference(targetfiles[i]))
|
||||
except FileNotFoundError:
|
||||
logging.critical('Current2Reference: Unable to copy file "{}"'.format(f))
|
||||
logging.critical(f'Current2Reference: Unable to copy file "{f}"')
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
|
|
@ -257,7 +257,7 @@ class Test:
|
|||
try:
|
||||
shutil.copy2(self.fileInProof(f),self.fileInCurrent(targetfiles[i]))
|
||||
except FileNotFoundError:
|
||||
logging.critical('Proof2Current: Unable to copy file "{}"'.format(f))
|
||||
logging.critical(f'Proof2Current: Unable to copy file "{f}"')
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
|
|
@ -267,7 +267,7 @@ class Test:
|
|||
try:
|
||||
shutil.copy2(self.fileInReference(f),self.fileInCurrent(targetfiles[i]))
|
||||
except FileNotFoundError:
|
||||
logging.critical('Current2Current: Unable to copy file "{}"'.format(f))
|
||||
logging.critical(f'Current2Current: Unable to copy file "{f}"')
|
||||
raise FileNotFoundError
|
||||
|
||||
|
||||
|
|
@ -302,9 +302,7 @@ class Test:
|
|||
max_loc=np.argmax(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
|
||||
refArrayNonZero = refArrayNonZero[curArray.nonzero()]
|
||||
curArray = curArray[curArray.nonzero()]
|
||||
print(' ********\n * maximum relative error {} between {} and {}\n ********'.format(max_err,
|
||||
refArrayNonZero[max_loc],
|
||||
curArray[max_loc]))
|
||||
print(f' ********\n * maximum relative error {max_err} between {refArrayNonZero[max_loc]} and {curArray[max_loc]}\n ********')
|
||||
return max_err
|
||||
else:
|
||||
raise Exception('mismatch in array size to compare')
|
||||
|
|
@ -350,7 +348,7 @@ class Test:
|
|||
|
||||
for i in range(dataLength):
|
||||
if headings0[i]['shape'] != headings1[i]['shape']:
|
||||
raise Exception('shape mismatch between {} and {} '.format(headings0[i]['label'],headings1[i]['label']))
|
||||
raise Exception(f"shape mismatch between {headings0[i]['label']} and {headings1[i]['label']}")
|
||||
shape[i] = headings0[i]['shape']
|
||||
for j in range(np.shape(shape[i])[0]):
|
||||
length[i] *= shape[i][j]
|
||||
|
|
@ -358,9 +356,7 @@ class Test:
|
|||
for j in range(np.shape(normShape[i])[0]):
|
||||
normLength[i] *= normShape[i][j]
|
||||
else:
|
||||
raise Exception('trying to compare {} with {} normed by {} data sets'.format(len(headings0),
|
||||
len(headings1),
|
||||
len(normHeadings)))
|
||||
raise Exception(f'trying to compare {len(headings0)} with {len(headings1)} normed by {len(normHeadings)} data sets')
|
||||
|
||||
table0 = damask.ASCIItable(name=file0,readonly=True)
|
||||
table0.head_read()
|
||||
|
|
@ -372,11 +368,11 @@ class Test:
|
|||
key1 = ('1_' if length[i]>1 else '') + headings1[i]['label']
|
||||
normKey = ('1_' if normLength[i]>1 else '') + normHeadings[i]['label']
|
||||
if key0 not in table0.labels(raw = True):
|
||||
raise Exception('column "{}" not found in first table...\n'.format(key0))
|
||||
raise Exception(f'column "{key0}" not found in first table...')
|
||||
elif key1 not in table1.labels(raw = True):
|
||||
raise Exception('column "{}" not found in second table...\n'.format(key1))
|
||||
raise Exception(f'column "{key1}" not found in second table...')
|
||||
elif normKey not in table0.labels(raw = True):
|
||||
raise Exception('column "{}" not found in first table...\n'.format(normKey))
|
||||
raise Exception(f'column "{normKey}" not found in first table...')
|
||||
else:
|
||||
column[0][i] = table0.label_index(key0)
|
||||
column[1][i] = table1.label_index(key1)
|
||||
|
|
@ -404,9 +400,9 @@ class Test:
|
|||
norm[i] = [1.0 for j in range(line0-len(skipLines))]
|
||||
absTol[i] = True
|
||||
if perLine:
|
||||
logging.warning('At least one norm of "{}" in first table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
|
||||
logging.warning(f"At least one norm of \"{headings0[i]['label']}\" in first table is 0.0, using absolute tolerance")
|
||||
else:
|
||||
logging.warning('Maximum norm of "{}" in first table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
|
||||
logging.warning(f"Maximum norm of \"{headings0[i]['label']}\" in first table is 0.0, using absolute tolerance")
|
||||
|
||||
line1 = 0
|
||||
while table1.data_read(): # read next data line of ASCII table
|
||||
|
|
@ -418,18 +414,14 @@ class Test:
|
|||
norm[i][line1-len(skipLines)])
|
||||
line1 +=1
|
||||
|
||||
if (line0 != line1): raise Exception('found {} lines in first table but {} in second table'.format(line0,line1))
|
||||
if (line0 != line1): raise Exception(f'found {line0} lines in first table but {line1} in second table')
|
||||
|
||||
logging.info(' ********')
|
||||
for i in range(dataLength):
|
||||
if absTol[i]:
|
||||
logging.info(' * maximum absolute error {} between {} and {}'.format(maxError[i],
|
||||
headings0[i]['label'],
|
||||
headings1[i]['label']))
|
||||
logging.info(f" * maximum absolute error {maxError[i]} between {headings0[i]['label']} and {headings1[i]['label']}")
|
||||
else:
|
||||
logging.info(' * maximum relative error {} between {} and {}'.format(maxError[i],
|
||||
headings0[i]['label'],
|
||||
headings1[i]['label']))
|
||||
logging.info(f" * maximum relative error {maxError[i]} between {headings0[i]['label']} and {headings1[i]['label']}")
|
||||
logging.info(' ********')
|
||||
return maxError
|
||||
|
||||
|
|
@ -480,8 +472,8 @@ class Test:
|
|||
normedDelta = np.where(normBy>preFilter,delta/normBy,0.0)
|
||||
mean = np.amax(np.abs(np.mean(normedDelta,0)))
|
||||
std = np.amax(np.std(normedDelta,0))
|
||||
logging.info('mean: {:f}'.format(mean))
|
||||
logging.info('std: {:f}'.format(std))
|
||||
logging.info(f'mean: {mean:f}')
|
||||
logging.info(f'std: {std:f}')
|
||||
|
||||
return (mean<meanTol) & (std < stdTol)
|
||||
|
||||
|
|
@ -521,7 +513,7 @@ class Test:
|
|||
|
||||
for i,(table,labels) in enumerate(zip(tables,columns)):
|
||||
if np.any(dimensions != [np.prod(table.shapes[c]) for c in labels]): # check data object consistency
|
||||
logging.critical('Table {} differs in data layout.'.format(files[i]))
|
||||
logging.critical(f'Table {files[i]} differs in data layout.')
|
||||
return False
|
||||
data.append(np.hstack(list(table.get(label) for label in labels)).astype(np.float)) # store
|
||||
|
||||
|
|
@ -537,19 +529,19 @@ class Test:
|
|||
|
||||
for i in range(len(data)):
|
||||
data[i] /= maximum # normalize each table
|
||||
logging.info('shape of data {}: {}'.format(i,data[i].shape))
|
||||
logging.info(f'shape of data {i}: {data[i].shape}')
|
||||
|
||||
if debug:
|
||||
violators = np.absolute(data[0]-data[1]) > atol + rtol*np.absolute(data[1])
|
||||
logging.info('shape of violators: {}'.format(violators.shape))
|
||||
logging.info(f'shape of violators: {violators.shape}')
|
||||
for j,culprits in enumerate(violators):
|
||||
goodguys = np.logical_not(culprits)
|
||||
if culprits.any():
|
||||
logging.info('{} has {}'.format(j,np.sum(culprits)))
|
||||
logging.info('deviation: {}'.format(np.absolute(data[0][j]-data[1][j])[culprits]))
|
||||
logging.info('data : {}'.format(np.absolute(data[1][j])[culprits]))
|
||||
logging.info('deviation: {}'.format(np.absolute(data[0][j]-data[1][j])[goodguys]))
|
||||
logging.info('data : {}'.format(np.absolute(data[1][j])[goodguys]))
|
||||
logging.info(f'{j} has {np.sum(culprits)}')
|
||||
logging.info(f'deviation: {np.absolute(data[0][j]-data[1][j])[culprits]}')
|
||||
logging.info(f'data : {np.absolute(data[1][j])[culprits]}')
|
||||
logging.info(f'deviation: {np.absolute(data[0][j]-data[1][j])[goodguys]}')
|
||||
logging.info(f'data : {np.absolute(data[1][j])[goodguys]}')
|
||||
|
||||
allclose = True # start optimistic
|
||||
for i in range(1,len(data)):
|
||||
|
|
@ -588,12 +580,12 @@ class Test:
|
|||
|
||||
if culprit == 0:
|
||||
count = len(self.variants) if self.options.select is None else len(self.options.select)
|
||||
msg = 'Test passed.' if count == 1 else 'All {} tests passed.'.format(count)
|
||||
msg = 'Test passed.' if count == 1 else f'All {count} tests passed.'
|
||||
elif culprit == -1:
|
||||
msg = 'Warning: could not start test...'
|
||||
ret = 0
|
||||
else:
|
||||
msg = 'Test "{}" failed.'.format(self.variantName(culprit-1))
|
||||
msg = f'Test "{self.variantName(culprit-1)}" failed.'
|
||||
|
||||
logging.critical('\n'.join(['*'*40,msg,'*'*40]) + '\n')
|
||||
return ret
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
import os
|
||||
from pathlib import Path
|
||||
|
||||
import pandas as pd
|
||||
import numpy as np
|
||||
|
|
@ -51,9 +51,11 @@ class VTK:
|
|||
"""
|
||||
geom = vtk.vtkRectilinearGrid()
|
||||
geom.SetDimensions(*(grid+1))
|
||||
geom.SetXCoordinates(np_to_vtk(np.linspace(origin[0],origin[0]+size[0],grid[0]+1),deep=True))
|
||||
geom.SetYCoordinates(np_to_vtk(np.linspace(origin[1],origin[1]+size[1],grid[1]+1),deep=True))
|
||||
geom.SetZCoordinates(np_to_vtk(np.linspace(origin[2],origin[2]+size[2],grid[2]+1),deep=True))
|
||||
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])
|
||||
|
||||
return VTK(geom)
|
||||
|
||||
|
|
@ -85,7 +87,7 @@ class VTK:
|
|||
|
||||
geom = vtk.vtkUnstructuredGrid()
|
||||
geom.SetPoints(vtk_nodes)
|
||||
geom.SetCells(eval('vtk.VTK_{}'.format(cell_type.split('_',1)[-1].upper())),cells)
|
||||
geom.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
|
||||
|
||||
return VTK(geom)
|
||||
|
||||
|
|
@ -119,17 +121,17 @@ class VTK:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
fname : str or pathlib.Path
|
||||
Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.
|
||||
dataset_type : str, optional
|
||||
Name of the vtk.vtkDataSet subclass when opening an .vtk file. Valid types are vtkRectilinearGrid,
|
||||
vtkUnstructuredGrid, and vtkPolyData.
|
||||
|
||||
"""
|
||||
ext = os.path.splitext(fname)[1]
|
||||
if ext == '.vtk':
|
||||
ext = Path(fname).suffix
|
||||
if ext == '.vtk' or dataset_type:
|
||||
reader = vtk.vtkGenericDataObjectReader()
|
||||
reader.SetFileName(fname)
|
||||
reader.SetFileName(str(fname))
|
||||
reader.Update()
|
||||
if dataset_type is None:
|
||||
raise TypeError('Dataset type for *.vtk file not given.')
|
||||
|
|
@ -140,7 +142,7 @@ class VTK:
|
|||
elif dataset_type.lower().endswith('polydata'):
|
||||
geom = reader.GetPolyDataOutput()
|
||||
else:
|
||||
raise TypeError('Unknown dataset type for vtk file {}'.format(dataset_type))
|
||||
raise TypeError(f'Unknown dataset type {dataset_type} for vtk file')
|
||||
else:
|
||||
if ext == '.vtr':
|
||||
reader = vtk.vtkXMLRectilinearGridReader()
|
||||
|
|
@ -149,9 +151,9 @@ class VTK:
|
|||
elif ext == '.vtp':
|
||||
reader = vtk.vtkXMLPolyDataReader()
|
||||
else:
|
||||
raise TypeError('Unknown file extension {}'.format(ext))
|
||||
raise TypeError(f'Unknown file extension {ext}')
|
||||
|
||||
reader.SetFileName(fname)
|
||||
reader.SetFileName(str(fname))
|
||||
reader.Update()
|
||||
geom = reader.GetOutput()
|
||||
|
||||
|
|
@ -164,7 +166,7 @@ class VTK:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
fname : str or pathlib.Path
|
||||
Filename for writing.
|
||||
|
||||
"""
|
||||
|
|
@ -176,10 +178,10 @@ class VTK:
|
|||
writer = vtk.vtkXMLPolyDataWriter()
|
||||
|
||||
default_ext = writer.GetDefaultFileExtension()
|
||||
name, ext = os.path.splitext(fname)
|
||||
ext = Path(fname).suffix
|
||||
if ext and ext != '.'+default_ext:
|
||||
raise ValueError('Given extension {} is not .{}'.format(ext,default_ext))
|
||||
writer.SetFileName('{}.{}'.format(name,default_ext))
|
||||
raise ValueError(f'Given extension {ext} does not match default .{default_ext}')
|
||||
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetInputData(self.geom)
|
||||
|
|
@ -214,7 +216,7 @@ class VTK:
|
|||
def __repr__(self):
|
||||
"""ASCII representation of the VTK data."""
|
||||
writer = vtk.vtkDataSetWriter()
|
||||
writer.SetHeader('# DAMASK.VTK v{}'.format(version))
|
||||
writer.SetHeader(f'# DAMASK.VTK v{version}')
|
||||
writer.WriteToOutputStringOn()
|
||||
writer.SetInputData(self.geom)
|
||||
writer.Write()
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
import re
|
||||
import os
|
||||
|
||||
from damask import util
|
||||
|
||||
class Section():
|
||||
def __init__(self,data = {'__order__':[]},part = ''):
|
||||
|
|
@ -94,7 +95,7 @@ class Material():
|
|||
'texture',
|
||||
'microstructure',
|
||||
]
|
||||
self.data = {\
|
||||
self.data = {
|
||||
'homogenization': {'__order__': []},
|
||||
'microstructure': {'__order__': []},
|
||||
'crystallite': {'__order__': []},
|
||||
|
|
@ -107,19 +108,19 @@ class Material():
|
|||
"""Returns current data structure in material.config format."""
|
||||
me = []
|
||||
for part in self.parts:
|
||||
if self.verbose: print('processing <{}>'.format(part))
|
||||
if self.verbose: print(f'processing <{part}>')
|
||||
me += ['',
|
||||
'#'*100,
|
||||
'<{}>'.format(part),
|
||||
f'<{part}>',
|
||||
'#'*100,
|
||||
]
|
||||
for section in self.data[part]['__order__']:
|
||||
me += ['[{}] {}'.format(section,'#'+'-'*max(0,96-len(section)))]
|
||||
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 += ['{}\t{}'.format(key,' '.join(values)) for values in self.data[part][section][key]]
|
||||
me += [f'{key}\t{" ".join(values)}' for values in self.data[part][section][key]]
|
||||
else: # plain key
|
||||
me += ['{}\t{}'.format(key,' '.join(map(str,self.data[part][section][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):
|
||||
|
|
@ -185,9 +186,9 @@ class Material():
|
|||
outname = filename
|
||||
while os.path.exists(outname) and not overwrite:
|
||||
i += 1
|
||||
outname = '{}_{}'.format(filename,i)
|
||||
outname = f'{filename}_{i}'
|
||||
|
||||
if self.verbose: print('Writing material data to {}'.format(outname))
|
||||
if self.verbose: print(f'Writing material data to {outname}')
|
||||
with open(outname,'w') as f:
|
||||
f.write(str(self))
|
||||
return outname
|
||||
|
|
@ -196,7 +197,7 @@ class Material():
|
|||
"""Add Update."""
|
||||
part = part.lower()
|
||||
section = section.lower()
|
||||
if part not in self.parts: raise Exception('invalid part {}'.format(part))
|
||||
if part not in self.parts: raise Exception(f'invalid part {part}')
|
||||
|
||||
if not isinstance(initialData, dict):
|
||||
initialData = initialData.data()
|
||||
|
|
|
|||
|
|
@ -233,7 +233,7 @@ def cell_coord0_gridSizeOrigin(coord0,ordered=True):
|
|||
origin[_np.where(grid==1)] = 0.0
|
||||
|
||||
if grid.prod() != len(coord0):
|
||||
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
|
||||
raise ValueError('Data count {len(coord0)} does not match grid {grid}.')
|
||||
|
||||
start = origin + delta*.5
|
||||
end = origin - delta*.5 + size
|
||||
|
|
@ -384,7 +384,7 @@ def node_coord0_gridSizeOrigin(coord0,ordered=True):
|
|||
origin = mincorner
|
||||
|
||||
if (grid+1).prod() != len(coord0):
|
||||
raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
|
||||
raise ValueError('Data count {len(coord0)} does not match grid {grid}.')
|
||||
|
||||
atol = _np.max(size)*5e-2
|
||||
if not (_np.allclose(coords[0],_np.linspace(mincorner[0],maxcorner[0],grid[0]+1),atol=atol) and \
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
import os
|
||||
import subprocess
|
||||
import shlex
|
||||
import string
|
||||
from pathlib import Path
|
||||
|
||||
from .._environment import Environment
|
||||
|
||||
|
|
@ -19,28 +19,24 @@ class Marc:
|
|||
|
||||
"""
|
||||
self.solver = 'Marc'
|
||||
try:
|
||||
self.version = int(version)
|
||||
except TypeError:
|
||||
self.version = -1
|
||||
self.version = version
|
||||
|
||||
|
||||
#--------------------------
|
||||
def libraryPath(self):
|
||||
@property
|
||||
def library_path(self):
|
||||
|
||||
path_MSC = Environment().options['MSC_ROOT']
|
||||
path_lib = '{}/mentat{}/shlib/linux64'.format(path_MSC,self.version)
|
||||
path_lib = Path(f'{path_MSC}/mentat{self.version}/shlib/linux64')
|
||||
|
||||
return path_lib if os.path.exists(path_lib) else ''
|
||||
return path_lib if path_lib.is_dir() else None
|
||||
|
||||
|
||||
#--------------------------
|
||||
def toolsPath(self):
|
||||
@property
|
||||
def tools_path(self):
|
||||
|
||||
path_MSC = Environment().options['MSC_ROOT']
|
||||
path_tools = '{}/marc{}/tools'.format(path_MSC,self.version)
|
||||
path_tools = Path(f'{path_MSC}/marc{self.version}/tools')
|
||||
|
||||
return path_tools if os.path.exists(path_tools) else ''
|
||||
return path_tools if path_tools.is_dir() else None
|
||||
|
||||
|
||||
#--------------------------
|
||||
|
|
@ -53,23 +49,23 @@ class Marc:
|
|||
):
|
||||
|
||||
|
||||
damaskEnv = Environment()
|
||||
env = Environment()
|
||||
|
||||
user = os.path.join(damaskEnv.relPath('src'),'DAMASK_marc{}.{}'.format(self.version,'f90' if compile else 'marc'))
|
||||
if not os.path.isfile(user):
|
||||
raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),user))
|
||||
usersub = env.root_dir/Path(f'src/DAMASK_marc{self.version}').with_suffix('.f90' if compile else '.marc')
|
||||
if not usersub.is_file():
|
||||
raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),usersub))
|
||||
|
||||
# Define options [see Marc Installation and Operation Guide, pp 23]
|
||||
script = 'run_damask_{}mp'.format(optimization)
|
||||
script = f'run_damask_{optimization}mp'
|
||||
|
||||
cmd = os.path.join(self.toolsPath(),script) + \
|
||||
cmd = str(self.tools_path/Path(script)) + \
|
||||
' -jid ' + model + '_' + job + \
|
||||
' -nprocd 1 -autorst 0 -ci n -cr n -dcoup 0 -b no -v no'
|
||||
|
||||
if compile: cmd += ' -u ' + user + ' -save y'
|
||||
else: cmd += ' -prog ' + os.path.splitext(user)[0]
|
||||
if compile: cmd += ' -u ' + str(usersub) + ' -save y'
|
||||
else: cmd += ' -prog ' + str(usersub.with_suffix(''))
|
||||
|
||||
print('job submission {} compilation: {}'.format('with' if compile else 'without',user))
|
||||
print('job submission {} compilation: {}'.format(('with' if compile else 'without'),usersub))
|
||||
if logfile: log = open(logfile, 'w')
|
||||
print(cmd)
|
||||
process = subprocess.Popen(shlex.split(cmd),stdout = log,stderr = subprocess.STDOUT)
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@ __all__=[
|
|||
####################################################################################################
|
||||
def srepr(arg,glue = '\n'):
|
||||
r"""
|
||||
Join arguments as individual lines.
|
||||
Join arguments with glue string.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -93,7 +93,7 @@ def strikeout(what):
|
|||
|
||||
|
||||
def execute(cmd,
|
||||
streamIn = None,
|
||||
stream_in = None,
|
||||
wd = './',
|
||||
env = None):
|
||||
"""
|
||||
|
|
@ -103,7 +103,7 @@ def execute(cmd,
|
|||
----------
|
||||
cmd : str
|
||||
Command to be executed.
|
||||
streanIn :, optional
|
||||
stream_in : file object, optional
|
||||
Input (via pipe) for executed process.
|
||||
wd : str, optional
|
||||
Working directory of process. Defaults to ./ .
|
||||
|
|
@ -119,14 +119,14 @@ def execute(cmd,
|
|||
stderr = subprocess.PIPE,
|
||||
stdin = subprocess.PIPE,
|
||||
env = myEnv)
|
||||
out,error = [i for i in (process.communicate() if streamIn is None
|
||||
else process.communicate(streamIn.read().encode('utf-8')))]
|
||||
stdout, stderr = [i for i in (process.communicate() if stream_in is None
|
||||
else process.communicate(stream_in.read().encode('utf-8')))]
|
||||
os.chdir(initialPath)
|
||||
out = out.decode('utf-8').replace('\x08','')
|
||||
error = error.decode('utf-8').replace('\x08','')
|
||||
stdout = stdout.decode('utf-8').replace('\x08','')
|
||||
stderr = stderr.decode('utf-8').replace('\x08','')
|
||||
if process.returncode != 0:
|
||||
raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
|
||||
return out,error
|
||||
raise RuntimeError(f'{cmd} failed with returncode {process.returncode}')
|
||||
return stdout, stderr
|
||||
|
||||
|
||||
def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
|
||||
|
|
@ -156,7 +156,7 @@ def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
|
|||
|
||||
def scale_to_coprime(v):
|
||||
"""Scale vector to co-prime (relatively prime) integers."""
|
||||
MAX_DENOMINATOR = 1000
|
||||
MAX_DENOMINATOR = 1000000
|
||||
|
||||
def get_square_denominator(x):
|
||||
"""Denominator of the square of a number."""
|
||||
|
|
@ -166,10 +166,13 @@ def scale_to_coprime(v):
|
|||
"""Least common multiple."""
|
||||
return a * b // np.gcd(a, b)
|
||||
|
||||
denominators = [int(get_square_denominator(i)) for i in v]
|
||||
s = reduce(lcm, denominators) ** 0.5
|
||||
m = (np.array(v)*s).astype(np.int)
|
||||
return m//reduce(np.gcd,m)
|
||||
m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(np.int)
|
||||
m = m//reduce(np.gcd,m)
|
||||
|
||||
if not np.allclose(v[v.nonzero()]/m[v.nonzero()],v[v.nonzero()][0]/m[m.nonzero()][0]):
|
||||
raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
|
||||
|
||||
return m
|
||||
|
||||
|
||||
####################################################################################################
|
||||
|
|
@ -223,21 +226,20 @@ class _ProgressBar:
|
|||
self.start_time = datetime.datetime.now()
|
||||
self.last_fraction = 0.0
|
||||
|
||||
sys.stderr.write('{} {} 0% ETA n/a'.format(self.prefix, '░'*self.bar_length))
|
||||
sys.stderr.write(f"{self.prefix} {'░'*self.bar_length} 0% ETA n/a")
|
||||
sys.stderr.flush()
|
||||
|
||||
def update(self,iteration):
|
||||
|
||||
fraction = (iteration+1) / self.total
|
||||
filled_length = int(self.bar_length * fraction)
|
||||
|
||||
if int(self.bar_length * fraction) > int(self.bar_length * self.last_fraction):
|
||||
if filled_length > int(self.bar_length * self.last_fraction):
|
||||
bar = '█' * filled_length + '░' * (self.bar_length - filled_length)
|
||||
delta_time = datetime.datetime.now() - self.start_time
|
||||
remaining_time = (self.total - (iteration+1)) * delta_time / (iteration+1)
|
||||
remaining_time -= datetime.timedelta(microseconds=remaining_time.microseconds) # remove μs
|
||||
|
||||
filled_length = int(self.bar_length * fraction)
|
||||
bar = '█' * filled_length + '░' * (self.bar_length - filled_length)
|
||||
sys.stderr.write('\r{} {} {:>4.0%} ETA {}'.format(self.prefix, bar, fraction, remaining_time))
|
||||
sys.stderr.write(f'\r{self.prefix} {bar} {fraction:>4.0%} ETA {remaining_time}')
|
||||
sys.stderr.flush()
|
||||
|
||||
self.last_fraction = fraction
|
||||
|
|
@ -249,7 +251,7 @@ class _ProgressBar:
|
|||
|
||||
class bcolors:
|
||||
"""
|
||||
ASCII Colors.
|
||||
ASCII colors.
|
||||
|
||||
https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py
|
||||
https://stackoverflow.com/questions/287871
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
import os
|
||||
from pathlib import Path
|
||||
import numpy as np
|
||||
|
||||
import pytest
|
||||
|
|
@ -16,7 +16,7 @@ def update(request):
|
|||
@pytest.fixture
|
||||
def reference_dir_base():
|
||||
"""Directory containing reference results."""
|
||||
return os.path.join(os.path.dirname(__file__),'reference')
|
||||
return Path(__file__).parent/'reference'
|
||||
|
||||
@pytest.fixture
|
||||
def set_of_quaternions():
|
||||
|
|
|
|||
|
|
@ -0,0 +1,67 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
|
||||
<PolyData>
|
||||
<Piece NumberOfPoints="10" NumberOfVerts="0" NumberOfLines="0" NumberOfStrips="0" NumberOfPolys="0">
|
||||
<PointData>
|
||||
<DataArray type="Float64" Name="coordinates" NumberOfComponents="3" format="binary" RangeMin="0.7453559924999299" RangeMax="2.449489742783178">
|
||||
AQAAAACAAADwAAAAagAAAA==eF5jYMAGPuyXOV4IRHvsIfQZe8u+xxZ9j1/sh/Eh9B37IjDj4f5QMLhqD6Gf2odB+Pth6iD0G3sFiLn7ofqg+j/CxOH6IfRX+xCouRYQ+6H0D/sCqH6YuRD6D1wd1B9QmsEBxgcAJsNfhw==
|
||||
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
|
||||
<Value index="0">
|
||||
0.7453559925
|
||||
</Value>
|
||||
<Value index="1">
|
||||
2.4494897428
|
||||
</Value>
|
||||
</InformationKey>
|
||||
</DataArray>
|
||||
</PointData>
|
||||
<CellData>
|
||||
</CellData>
|
||||
<Points>
|
||||
<DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="0.7453559924999299" RangeMax="2.449489742783178">
|
||||
AQAAAACAAADwAAAAagAAAA==eF5jYMAGPuyXOV4IRHvsIfQZe8u+xxZ9j1/sh/Eh9B37IjDj4f5QMLhqD6Gf2odB+Pth6iD0G3sFiLn7ofqg+j/CxOH6IfRX+xCouRYQ+6H0D/sCqH6YuRD6D1wd1B9QmsEBxgcAJsNfhw==
|
||||
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
|
||||
<Value index="0">
|
||||
0.7453559925
|
||||
</Value>
|
||||
<Value index="1">
|
||||
2.4494897428
|
||||
</Value>
|
||||
</InformationKey>
|
||||
</DataArray>
|
||||
</Points>
|
||||
<Verts>
|
||||
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
|
||||
AAAAAACAAAAAAAAA
|
||||
</DataArray>
|
||||
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
|
||||
AAAAAACAAAAAAAAA
|
||||
</DataArray>
|
||||
</Verts>
|
||||
<Lines>
|
||||
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
|
||||
AAAAAACAAAAAAAAA
|
||||
</DataArray>
|
||||
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
|
||||
AAAAAACAAAAAAAAA
|
||||
</DataArray>
|
||||
</Lines>
|
||||
<Strips>
|
||||
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
|
||||
AAAAAACAAAAAAAAA
|
||||
</DataArray>
|
||||
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
|
||||
AAAAAACAAAAAAAAA
|
||||
</DataArray>
|
||||
</Strips>
|
||||
<Polys>
|
||||
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
|
||||
AAAAAACAAAAAAAAA
|
||||
</DataArray>
|
||||
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
|
||||
AAAAAACAAAAAAAAA
|
||||
</DataArray>
|
||||
</Polys>
|
||||
</Piece>
|
||||
</PolyData>
|
||||
</VTKFile>
|
||||
|
|
@ -0,0 +1,44 @@
|
|||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
|
||||
<RectilinearGrid WholeExtent="0 5 0 6 0 7">
|
||||
<Piece Extent="0 5 0 6 0 7">
|
||||
<PointData>
|
||||
<DataArray type="Float64" Name="node" NumberOfComponents="3" format="binary" RangeMin="0" RangeMax="1.268857754044952">
|
||||
AQAAAACAAACAHwAAywMAAA==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
|
||||
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
|
||||
<Value index="0">
|
||||
0
|
||||
</Value>
|
||||
<Value index="1">
|
||||
1.268857754
|
||||
</Value>
|
||||
</InformationKey>
|
||||
</DataArray>
|
||||
</PointData>
|
||||
<CellData>
|
||||
<DataArray type="Float64" Name="cell" NumberOfComponents="3" format="binary" RangeMin="0.10871961482881586" RangeMax="1.160792402743735">
|
||||
AQAAAACAAACwEwAAZQIAAA==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
|
||||
<InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
|
||||
<Value index="0">
|
||||
0.10871961483
|
||||
</Value>
|
||||
<Value index="1">
|
||||
1.1607924027
|
||||
</Value>
|
||||
</InformationKey>
|
||||
</DataArray>
|
||||
</CellData>
|
||||
<Coordinates>
|
||||
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.6">
|
||||
AQAAAACAAAAwAAAAJwAAAA==eF5jYICAHXKtrwN37LOH0Ofsua4vLrDlug7l37M3BoPH9gCdQxK6
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
|
||||
AQAAAACAAAA4AAAAIgAAAA==eF5jYICAUDA4ag+hr9pDRB9A+U/tV4HBK6j4B3sAk7wQqg==
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.5">
|
||||
AQAAAACAAABAAAAALAAAAA==eF5jYICASSqeQLTJHkIfsr+9LReITkP5l+zB3NvXoOK37SG6HtgDANusGUo=
|
||||
</DataArray>
|
||||
</Coordinates>
|
||||
</Piece>
|
||||
</RectilinearGrid>
|
||||
</VTKFile>
|
||||
|
|
@ -6,6 +6,7 @@ import numpy as np
|
|||
|
||||
from damask import Geom
|
||||
from damask import Rotation
|
||||
from damask import util
|
||||
|
||||
|
||||
def geom_equal(a,b):
|
||||
|
|
@ -85,8 +86,8 @@ class TestGeom:
|
|||
def test_mirror(self,default,update,reference_dir,directions,reflect):
|
||||
modified = copy.deepcopy(default)
|
||||
modified.mirror(directions,reflect)
|
||||
tag = 'directions={}_reflect={}'.format('-'.join(directions),reflect)
|
||||
reference = os.path.join(reference_dir,'mirror_{}.geom'.format(tag))
|
||||
tag = f'directions={"-".join(directions)}_reflect={reflect}'
|
||||
reference = os.path.join(reference_dir,f'mirror_{tag}.geom')
|
||||
if update: modified.to_file(reference)
|
||||
assert geom_equal(modified,Geom.from_file(reference))
|
||||
|
||||
|
|
@ -94,8 +95,8 @@ class TestGeom:
|
|||
def test_clean(self,default,update,reference_dir,stencil):
|
||||
modified = copy.deepcopy(default)
|
||||
modified.clean(stencil)
|
||||
tag = 'stencil={}'.format(stencil)
|
||||
reference = os.path.join(reference_dir,'clean_{}.geom'.format(tag))
|
||||
tag = f'stencil={stencil}'
|
||||
reference = os.path.join(reference_dir,f'clean_{tag}.geom')
|
||||
if update: modified.to_file(reference)
|
||||
assert geom_equal(modified,Geom.from_file(reference))
|
||||
|
||||
|
|
@ -111,8 +112,8 @@ class TestGeom:
|
|||
def test_scale(self,default,update,reference_dir,grid):
|
||||
modified = copy.deepcopy(default)
|
||||
modified.scale(grid)
|
||||
tag = 'grid={}'.format('-'.join([str(x) for x in grid]))
|
||||
reference = os.path.join(reference_dir,'scale_{}.geom'.format(tag))
|
||||
tag = f'grid={util.srepr(grid,"-")}'
|
||||
reference = os.path.join(reference_dir,f'scale_{tag}.geom')
|
||||
if update: modified.to_file(reference)
|
||||
assert geom_equal(modified,Geom.from_file(reference))
|
||||
|
||||
|
|
@ -150,8 +151,8 @@ class TestGeom:
|
|||
def test_rotate(self,default,update,reference_dir,Eulers):
|
||||
modified = copy.deepcopy(default)
|
||||
modified.rotate(Rotation.from_Eulers(Eulers,degrees=True))
|
||||
tag = 'Eulers={}-{}-{}'.format(*Eulers)
|
||||
reference = os.path.join(reference_dir,'rotate_{}.geom'.format(tag))
|
||||
tag = f'Eulers={util.srepr(Eulers,"-")}'
|
||||
reference = os.path.join(reference_dir,f'rotate_{tag}.geom')
|
||||
if update: modified.to_file(reference)
|
||||
assert geom_equal(modified,Geom.from_file(reference))
|
||||
|
||||
|
|
|
|||
|
|
@ -154,4 +154,4 @@ class TestSymmetry:
|
|||
def test_invalid_argument(self,function):
|
||||
s = Symmetry() # noqa
|
||||
with pytest.raises(ValueError):
|
||||
eval('s.{}(np.ones(4))'.format(function))
|
||||
eval(f's.{function}(np.ones(4))')
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@ class TestOrientation:
|
|||
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
|
||||
@pytest.mark.parametrize('lattice',['fcc','bcc'])
|
||||
def test_relationship_reference(self,update,reference_dir,model,lattice):
|
||||
reference = os.path.join(reference_dir,'{}_{}.txt'.format(lattice,model))
|
||||
reference = os.path.join(reference_dir,f'{lattice}_{model}.txt')
|
||||
ori = Orientation(Rotation(),lattice)
|
||||
eu = np.array([o.rotation.as_Eulers(degrees=True) for o in ori.related(model)])
|
||||
if update:
|
||||
|
|
|
|||
|
|
@ -137,7 +137,7 @@ class TestResult:
|
|||
default.add_Cauchy('P','F')
|
||||
default.add_eigenvalue('sigma',eigenvalue)
|
||||
loc = {'sigma' :default.get_dataset_location('sigma'),
|
||||
'lambda':default.get_dataset_location('lambda_{}(sigma)'.format(eigenvalue))}
|
||||
'lambda':default.get_dataset_location(f'lambda_{eigenvalue}(sigma)')}
|
||||
in_memory = function(mechanics.eigenvalues(default.read_dataset(loc['sigma'],0)),axis=1,keepdims=True)
|
||||
in_file = default.read_dataset(loc['lambda'],0)
|
||||
assert np.allclose(in_memory,in_file)
|
||||
|
|
@ -147,7 +147,7 @@ class TestResult:
|
|||
default.add_Cauchy('P','F')
|
||||
default.add_eigenvector('sigma',eigenvalue)
|
||||
loc = {'sigma' :default.get_dataset_location('sigma'),
|
||||
'v(sigma)':default.get_dataset_location('v_{}(sigma)'.format(eigenvalue))}
|
||||
'v(sigma)':default.get_dataset_location(f'v_{eigenvalue}(sigma)')}
|
||||
in_memory = mechanics.eigenvectors(default.read_dataset(loc['sigma'],0))[:,idx]
|
||||
in_file = default.read_dataset(loc['v(sigma)'],0)
|
||||
assert np.allclose(in_memory,in_file)
|
||||
|
|
@ -179,7 +179,7 @@ class TestResult:
|
|||
t = ['V','U'][np.random.randint(0,2)]
|
||||
m = np.random.random()*2.0 - 1.0
|
||||
default.add_strain_tensor('F',t,m)
|
||||
label = 'epsilon_{}^{}(F)'.format(t,m)
|
||||
label = f'epsilon_{t}^{m}(F)'
|
||||
default.add_Mises(label)
|
||||
loc = {label :default.get_dataset_location(label),
|
||||
label+'_vM':default.get_dataset_location(label+'_vM')}
|
||||
|
|
@ -248,7 +248,7 @@ class TestResult:
|
|||
t = ['V','U'][np.random.randint(0,2)]
|
||||
m = np.random.random()*2.0 - 1.0
|
||||
default.add_strain_tensor('F',t,m)
|
||||
label = 'epsilon_{}^{}(F)'.format(t,m)
|
||||
label = f'epsilon_{t}^{m}(F)'
|
||||
loc = {'F': default.get_dataset_location('F'),
|
||||
label: default.get_dataset_location(label)}
|
||||
in_memory = mechanics.strain_tensor(default.read_dataset(loc['F'],0),t,m)
|
||||
|
|
@ -302,8 +302,8 @@ class TestResult:
|
|||
|
||||
@pytest.mark.parametrize('allowed',['off','on'])
|
||||
def test_rename(self,default,allowed):
|
||||
F = default.read_dataset(default.get_dataset_location('F'))
|
||||
if allowed == 'on':
|
||||
F = default.read_dataset(default.get_dataset_location('F'))
|
||||
default.allow_modification()
|
||||
default.rename('F','new_name')
|
||||
assert np.all(F == default.read_dataset(default.get_dataset_location('new_name')))
|
||||
|
|
|
|||
|
|
@ -461,7 +461,7 @@ def mul(me, other):
|
|||
other_p = other.quaternion[1:]
|
||||
R = me.__class__(np.append(me_q*other_q - np.dot(me_p,other_p),
|
||||
me_q*other_p + other_q*me_p + _P * np.cross(me_p,other_p)))
|
||||
return R.standardize()
|
||||
return R._standardize()
|
||||
elif isinstance(other, np.ndarray):
|
||||
if other.shape == (3,):
|
||||
A = me.quaternion[0]**2.0 - np.dot(me.quaternion[1:],me.quaternion[1:])
|
||||
|
|
@ -481,9 +481,9 @@ def mul(me, other):
|
|||
axes = ((0, 2, 4, 6), (0, 1, 2, 3))
|
||||
return np.tensordot(RRRR, other, axes)
|
||||
else:
|
||||
raise ValueError('Can only rotate vectors, 2nd order ternsors, and 4th order tensors')
|
||||
raise ValueError('Can only rotate vectors, 2nd order tensors, and 4th order tensors')
|
||||
else:
|
||||
raise TypeError('Cannot rotate {}'.format(type(other)))
|
||||
raise TypeError(f'Cannot rotate {type(other)}')
|
||||
|
||||
|
||||
class TestRotation:
|
||||
|
|
@ -781,6 +781,10 @@ class TestRotation:
|
|||
rot = Rotation.from_basis(om,False,reciprocal=reciprocal)
|
||||
assert np.isclose(np.linalg.det(rot.as_matrix()),1.0)
|
||||
|
||||
@pytest.mark.parametrize('shape',[None,1,(4,4)])
|
||||
def test_random(self,shape):
|
||||
Rotation.from_random(shape)
|
||||
|
||||
@pytest.mark.parametrize('function',[Rotation.from_quaternion,
|
||||
Rotation.from_Eulers,
|
||||
Rotation.from_axis_angle,
|
||||
|
|
@ -793,6 +797,16 @@ class TestRotation:
|
|||
with pytest.raises(ValueError):
|
||||
function(invalid_shape)
|
||||
|
||||
@pytest.mark.parametrize('fr,to',[(Rotation.from_quaternion,'as_quaternion'),
|
||||
(Rotation.from_axis_angle,'as_axis_angle'),
|
||||
(Rotation.from_Rodrigues, 'as_Rodrigues'),
|
||||
(Rotation.from_homochoric,'as_homochoric'),
|
||||
(Rotation.from_cubochoric,'as_cubochoric')])
|
||||
def test_invalid_P(self,fr,to):
|
||||
R = Rotation.from_random(np.random.randint(8,32,(3))) # noqa
|
||||
with pytest.raises(ValueError):
|
||||
fr(eval(f'R.{to}()'),P=-30)
|
||||
|
||||
@pytest.mark.parametrize('shape',[None,(3,),(4,2)])
|
||||
def test_broadcast(self,shape):
|
||||
rot = Rotation.from_random(shape)
|
||||
|
|
@ -859,14 +873,18 @@ class TestRotation:
|
|||
phi_2 = 2*np.pi - phi_1
|
||||
R_1 = Rotation.from_Eulers(np.array([phi_1,0.,0.]))
|
||||
R_2 = Rotation.from_Eulers(np.array([0.,0.,phi_2]))
|
||||
assert np.allclose(data,R_2*(R_1*data))
|
||||
assert np.allclose(data,R_2@(R_1@data))
|
||||
|
||||
def test_rotate_inverse(self):
|
||||
R = Rotation.from_random()
|
||||
assert np.allclose(np.eye(3),(~R@R).as_matrix())
|
||||
|
||||
@pytest.mark.parametrize('data',[np.random.rand(3),
|
||||
np.random.rand(3,3),
|
||||
np.random.rand(3,3,3,3)])
|
||||
def test_rotate_inverse(self,data):
|
||||
def test_rotate_inverse_array(self,data):
|
||||
R = Rotation.from_random()
|
||||
assert np.allclose(data,R.inversed()*(R*data))
|
||||
assert np.allclose(data,~R@(R@data))
|
||||
|
||||
@pytest.mark.parametrize('data',[np.random.rand(4),
|
||||
np.random.rand(3,2),
|
||||
|
|
@ -883,3 +901,7 @@ class TestRotation:
|
|||
R = Rotation.from_random()
|
||||
with pytest.raises(TypeError):
|
||||
R*data
|
||||
|
||||
def test_misorientation(self):
|
||||
R = Rotation.from_random()
|
||||
assert np.allclose(R.misorientation(R).as_matrix(),np.eye(3))
|
||||
|
|
|
|||
|
|
@ -1,14 +1,13 @@
|
|||
import os
|
||||
|
||||
import pytest
|
||||
import numpy as np
|
||||
|
||||
from damask import VTK
|
||||
from damask import grid_filters
|
||||
|
||||
@pytest.fixture
|
||||
def reference_dir(reference_dir_base):
|
||||
"""Directory containing reference results."""
|
||||
return os.path.join(reference_dir_base,'Result')
|
||||
return reference_dir_base/'VTK'
|
||||
|
||||
class TestVTK:
|
||||
|
||||
|
|
@ -17,18 +16,24 @@ class TestVTK:
|
|||
size = np.random.random(3) + 1.0
|
||||
origin = np.random.random(3)
|
||||
v = VTK.from_rectilinearGrid(grid,size,origin)
|
||||
s = v.__repr__()
|
||||
v.write(os.path.join(tmp_path,'rectilinearGrid'))
|
||||
v = VTK.from_file(os.path.join(tmp_path,'rectilinearGrid.vtr'))
|
||||
assert(s == v.__repr__())
|
||||
string = v.__repr__()
|
||||
v.write(tmp_path/'rectilinearGrid')
|
||||
vtr = VTK.from_file(tmp_path/'rectilinearGrid.vtr')
|
||||
with open(tmp_path/'rectilinearGrid.vtk','w') as f:
|
||||
f.write(string)
|
||||
vtk = VTK.from_file(tmp_path/'rectilinearGrid.vtk','VTK_rectilinearGrid')
|
||||
assert(string == vtr.__repr__() == vtk.__repr__())
|
||||
|
||||
def test_polyData(self,tmp_path):
|
||||
points = np.random.rand(3,100)
|
||||
v = VTK.from_polyData(points)
|
||||
s = v.__repr__()
|
||||
v.write(os.path.join(tmp_path,'polyData'))
|
||||
v = VTK.from_file(os.path.join(tmp_path,'polyData.vtp'))
|
||||
assert(s == v.__repr__())
|
||||
string = v.__repr__()
|
||||
v.write(tmp_path/'polyData')
|
||||
vtp = VTK.from_file(tmp_path/'polyData.vtp')
|
||||
with open(tmp_path/'polyData.vtk','w') as f:
|
||||
f.write(string)
|
||||
vtk = VTK.from_file(tmp_path/'polyData.vtk','polyData')
|
||||
assert(string == vtp.__repr__() == vtk.__repr__())
|
||||
|
||||
@pytest.mark.parametrize('cell_type,n',[
|
||||
('VTK_hexahedron',8),
|
||||
|
|
@ -41,7 +46,43 @@ class TestVTK:
|
|||
nodes = np.random.rand(n,3)
|
||||
connectivity = np.random.choice(np.arange(n),n,False).reshape(-1,n)
|
||||
v = VTK.from_unstructuredGrid(nodes,connectivity,cell_type)
|
||||
s = v.__repr__()
|
||||
v.write(os.path.join(tmp_path,'unstructuredGrid'))
|
||||
v = VTK.from_file(os.path.join(tmp_path,'unstructuredGrid.vtu'))
|
||||
assert(s == v.__repr__())
|
||||
string = v.__repr__()
|
||||
v.write(tmp_path/'unstructuredGrid')
|
||||
vtu = VTK.from_file(tmp_path/'unstructuredGrid.vtu')
|
||||
with open(tmp_path/'unstructuredGrid.vtk','w') as f:
|
||||
f.write(string)
|
||||
vtk = VTK.from_file(tmp_path/'unstructuredGrid.vtk','unstructuredgrid')
|
||||
assert(string == vtu.__repr__() == vtk.__repr__())
|
||||
|
||||
@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):
|
||||
with pytest.raises(TypeError):
|
||||
VTK.from_file('this_file_does_not_exist.vtk',dataset_type)
|
||||
|
||||
|
||||
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()
|
||||
polyData = VTK.from_polyData(points)
|
||||
polyData.add(points,'coordinates')
|
||||
if update:
|
||||
polyData.write(reference_dir/'polyData')
|
||||
else:
|
||||
reference = VTK.from_file(reference_dir/'polyData.vtp')
|
||||
assert polyData.__repr__() == reference.__repr__()
|
||||
|
||||
def test_compare_reference_rectilinearGrid(self,update,reference_dir,tmp_path):
|
||||
grid = np.array([5,6,7],int)
|
||||
size = np.array([.6,1.,.5])
|
||||
rectilinearGrid = VTK.from_rectilinearGrid(grid,size)
|
||||
c = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
|
||||
n = grid_filters.node_coord0(grid,size).reshape(-1,3,order='F')
|
||||
rectilinearGrid.add(c,'cell')
|
||||
rectilinearGrid.add(n,'node')
|
||||
if update:
|
||||
rectilinearGrid.write(reference_dir/'rectilinearGrid')
|
||||
else:
|
||||
reference = VTK.from_file(reference_dir/'rectilinearGrid.vtr')
|
||||
assert rectilinearGrid.__repr__() == reference.__repr__()
|
||||
|
||||
|
|
|
|||
|
|
@ -30,8 +30,8 @@ class TestGridFilters:
|
|||
grid = np.random.randint(8,32,(3))
|
||||
size = np.random.random(3)
|
||||
origin = np.random.random(3)
|
||||
coord0 = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode)) # noqa
|
||||
_grid,_size,_origin = eval('grid_filters.{}_coord0_gridSizeOrigin(coord0.reshape(-1,3,order="F"))'.format(mode))
|
||||
coord0 = eval(f'grid_filters.{mode}_coord0(grid,size,origin)') # noqa
|
||||
_grid,_size,_origin = eval(f'grid_filters.{mode}_coord0_gridSizeOrigin(coord0.reshape(-1,3,order="F"))')
|
||||
assert np.allclose(grid,_grid) and np.allclose(size,_size) and np.allclose(origin,_origin)
|
||||
|
||||
def test_displacement_fluct_equivalence(self):
|
||||
|
|
@ -67,8 +67,8 @@ class TestGridFilters:
|
|||
origin= np.random.random(3)
|
||||
size = np.random.random(3) # noqa
|
||||
grid = np.random.randint(8,32,(3))
|
||||
shifted = eval('grid_filters.{}_coord0(grid,size,origin)'.format(mode))
|
||||
unshifted = eval('grid_filters.{}_coord0(grid,size)'.format(mode))
|
||||
shifted = eval(f'grid_filters.{mode}_coord0(grid,size,origin)')
|
||||
unshifted = eval(f'grid_filters.{mode}_coord0(grid,size)')
|
||||
if mode == 'cell':
|
||||
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid) +(3,)))
|
||||
elif mode == 'node':
|
||||
|
|
|
|||
|
|
@ -0,0 +1,33 @@
|
|||
import pytest
|
||||
import numpy as np
|
||||
from damask import util
|
||||
|
||||
|
||||
class TestUtil:
|
||||
|
||||
def test_execute_direct(self):
|
||||
out,err = util.execute('echo test')
|
||||
assert out=='test\n' and err==''
|
||||
|
||||
def test_execute_env(self):
|
||||
out,err = util.execute('sh -c "echo $test_for_execute"',env={'test_for_execute':'test'})
|
||||
assert out=='test\n' and err==''
|
||||
|
||||
def test_croak(self):
|
||||
util.croak('Burp!')
|
||||
|
||||
@pytest.mark.parametrize('input,output',
|
||||
[
|
||||
([2,0],[1,0]),
|
||||
([0.5,0.5],[1,1]),
|
||||
([1./2.,1./3.],[3,2]),
|
||||
([2./3.,1./2.,1./3.],[4,3,2]),
|
||||
])
|
||||
|
||||
def test_scale2coprime(self,input,output):
|
||||
assert np.allclose(util.scale_to_coprime(np.array(input)),
|
||||
np.array(output).astype(int))
|
||||
|
||||
def test_lackofprecision(self):
|
||||
with pytest.raises(ValueError):
|
||||
util.scale_to_coprime(np.array([1/3333,1,1]))
|
||||
128
src/CPFEM.f90
128
src/CPFEM.f90
|
|
@ -35,29 +35,15 @@ module CPFEM
|
|||
CPFEM_dcsdE !< Cauchy stress tangent
|
||||
real(pReal), dimension (:,:,:,:), allocatable, private :: &
|
||||
CPFEM_dcsdE_knownGood !< known good tangent
|
||||
integer(pInt), public :: &
|
||||
cycleCounter = 0_pInt, & !< needs description
|
||||
theInc = -1_pInt, & !< needs description
|
||||
lastLovl = 0_pInt !< lovl in previous call to marc hypela2
|
||||
real(pReal), public :: &
|
||||
theTime = 0.0_pReal, & !< needs description
|
||||
theDelta = 0.0_pReal
|
||||
logical, public :: &
|
||||
outdatedFFN1 = .false., & !< needs description
|
||||
lastIncConverged = .false., & !< needs description
|
||||
outdatedByNewInc = .false. !< needs description
|
||||
|
||||
logical, public, protected :: &
|
||||
CPFEM_init_done = .false. !< remember whether init has been done already
|
||||
logical, private :: &
|
||||
CPFEM_calc_done = .false. !< remember whether first ip has already calced the results
|
||||
integer(pInt), public :: &
|
||||
cycleCounter = 0_pInt !< needs description
|
||||
|
||||
integer(pInt), parameter, public :: &
|
||||
CPFEM_COLLECT = 2_pInt**0_pInt, &
|
||||
CPFEM_CALCRESULTS = 2_pInt**1_pInt, &
|
||||
CPFEM_AGERESULTS = 2_pInt**2_pInt, &
|
||||
CPFEM_BACKUPJACOBIAN = 2_pInt**3_pInt, &
|
||||
CPFEM_RESTOREJACOBIAN = 2_pInt**4_pInt
|
||||
CPFEM_CALCRESULTS = 2_pInt**0_pInt, &
|
||||
CPFEM_AGERESULTS = 2_pInt**1_pInt, &
|
||||
CPFEM_BACKUPJACOBIAN = 2_pInt**2_pInt, &
|
||||
CPFEM_RESTOREJACOBIAN = 2_pInt**3_pInt
|
||||
|
||||
public :: &
|
||||
CPFEM_general, &
|
||||
|
|
@ -68,14 +54,10 @@ contains
|
|||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief call (thread safe) all module initializations
|
||||
!> @brief call all module initializations
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine CPFEM_initAll(el,ip)
|
||||
subroutine CPFEM_initAll
|
||||
|
||||
integer(pInt), intent(in) :: el, & !< FE el number
|
||||
ip !< FE integration point number
|
||||
|
||||
CPFEM_init_done = .true.
|
||||
call DAMASK_interface_init
|
||||
call prec_init
|
||||
call IO_init
|
||||
|
|
@ -88,7 +70,7 @@ subroutine CPFEM_initAll(el,ip)
|
|||
call YAML_init
|
||||
call HDF5_utilities_init
|
||||
call results_init(.false.)
|
||||
call discretization_marc_init(ip, el)
|
||||
call discretization_marc_init
|
||||
call lattice_init
|
||||
call material_init(.false.)
|
||||
call constitutive_init
|
||||
|
|
@ -124,7 +106,7 @@ end subroutine CPFEM_init
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief perform initialization at first call, update variables and call the actual material model
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyStress, jacobian)
|
||||
subroutine CPFEM_general(mode, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyStress, jacobian)
|
||||
|
||||
integer(pInt), intent(in) :: elFE, & !< FE element number
|
||||
ip !< integration point number
|
||||
|
|
@ -133,24 +115,21 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
|
|||
ffn1 !< deformation gradient for t=t1
|
||||
integer(pInt), intent(in) :: mode !< computation mode 1: regular computation plus aging of results
|
||||
real(pReal), intent(in) :: temperature_inp !< temperature
|
||||
logical, intent(in) :: parallelExecution !< flag indicating parallel computation of requested IPs
|
||||
real(pReal), dimension(6), intent(out) :: cauchyStress !< stress as 6 vector
|
||||
real(pReal), dimension(6,6), intent(out) :: jacobian !< jacobian as 66 tensor (Consistent tangent dcs/dE)
|
||||
|
||||
real(pReal) J_inverse, & ! inverse of Jacobian
|
||||
rnd
|
||||
real(pReal), dimension (3,3) :: Kirchhoff, & ! Piola-Kirchhoff stress
|
||||
cauchyStress33 ! stress vector
|
||||
real(pReal), dimension (3,3) :: Kirchhoff ! Piola-Kirchhoff stress
|
||||
real(pReal), dimension (3,3,3,3) :: H_sym, &
|
||||
H, &
|
||||
jacobian3333 ! jacobian in Matrix notation
|
||||
H
|
||||
|
||||
integer(pInt) elCP, & ! crystal plasticity element number
|
||||
i, j, k, l, m, n, ph, homog, mySource
|
||||
logical updateJaco ! flag indicating if Jacobian has to be updated
|
||||
|
||||
real(pReal), parameter :: ODD_STRESS = 1e15_pReal, & !< return value for stress in case of ping pong dummy cycle
|
||||
ODD_JACOBIAN = 1e50_pReal !< return value for jacobian in case of ping pong dummy cycle
|
||||
real(pReal), parameter :: ODD_STRESS = 1e15_pReal, & !< return value for stress if terminallyIll
|
||||
ODD_JACOBIAN = 1e50_pReal !< return value for jacobian if terminallyIll
|
||||
|
||||
elCP = mesh_FEM2DAMASK_elem(elFE)
|
||||
|
||||
|
|
@ -159,9 +138,6 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
|
|||
write(6,'(/,a)') '#############################################'
|
||||
write(6,'(a1,a22,1x,i8,a13)') '#','element', elCP, '#'
|
||||
write(6,'(a1,a22,1x,i8,a13)') '#','ip', ip, '#'
|
||||
write(6,'(a1,a22,1x,f15.7,a6)') '#','theTime', theTime, '#'
|
||||
write(6,'(a1,a22,1x,f15.7,a6)') '#','theDelta', theDelta, '#'
|
||||
write(6,'(a1,a22,1x,i8,a13)') '#','theInc', theInc, '#'
|
||||
write(6,'(a1,a22,1x,i8,a13)') '#','cycleCounter', cycleCounter, '#'
|
||||
write(6,'(a1,a22,1x,i8,a13)') '#','computationMode',mode, '#'
|
||||
if (terminallyIll) &
|
||||
|
|
@ -174,13 +150,8 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
|
|||
if (iand(mode, CPFEM_RESTOREJACOBIAN) /= 0_pInt) &
|
||||
CPFEM_dcsde = CPFEM_dcsde_knownGood
|
||||
|
||||
!*** age results
|
||||
if (iand(mode, CPFEM_AGERESULTS) /= 0_pInt) call CPFEM_forward
|
||||
|
||||
|
||||
!*** collection of FEM input with returning of randomize odd stress and jacobian
|
||||
!* If no parallel execution is required, there is no need to collect FEM input
|
||||
if (.not. parallelExecution) then
|
||||
chosenThermal1: select case (thermal_type(material_homogenizationAt(elCP)))
|
||||
case (THERMAL_conduction_ID) chosenThermal1
|
||||
temperature(material_homogenizationAt(elCP))%p(thermalMapping(material_homogenizationAt(elCP))%p(ip,elCP)) = &
|
||||
|
|
@ -189,64 +160,22 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
|
|||
materialpoint_F0(1:3,1:3,ip,elCP) = ffn
|
||||
materialpoint_F(1:3,1:3,ip,elCP) = ffn1
|
||||
|
||||
elseif (iand(mode, CPFEM_COLLECT) /= 0_pInt) then
|
||||
call random_number(rnd)
|
||||
if (rnd < 0.5_pReal) rnd = rnd - 1.0_pReal
|
||||
CPFEM_cs(1:6,ip,elCP) = rnd * ODD_STRESS
|
||||
CPFEM_dcsde(1:6,1:6,ip,elCP) = ODD_JACOBIAN * math_identity2nd(6)
|
||||
chosenThermal2: select case (thermal_type(material_homogenizationAt(elCP)))
|
||||
case (THERMAL_conduction_ID) chosenThermal2
|
||||
temperature(material_homogenizationAt(elCP))%p(thermalMapping(material_homogenizationAt(elCP))%p(ip,elCP)) = &
|
||||
temperature_inp
|
||||
end select chosenThermal2
|
||||
materialpoint_F0(1:3,1:3,ip,elCP) = ffn
|
||||
materialpoint_F(1:3,1:3,ip,elCP) = ffn1
|
||||
CPFEM_calc_done = .false.
|
||||
endif
|
||||
|
||||
|
||||
!*** calculation of stress and jacobian
|
||||
if (iand(mode, CPFEM_CALCRESULTS) /= 0_pInt) then
|
||||
|
||||
!*** deformation gradient outdated or any actual deformation gradient differs more than relevantStrain from the stored one
|
||||
validCalculation: if (terminallyIll &
|
||||
.or. outdatedFFN1 &
|
||||
.or. any(abs(ffn1 - materialpoint_F(1:3,1:3,ip,elCP)) > defgradTolerance)) then
|
||||
if (any(abs(ffn1 - materialpoint_F(1:3,1:3,ip,elCP)) > defgradTolerance)) then
|
||||
if (iand(debug_level(debug_CPFEM), debug_levelBasic) /= 0_pInt) then
|
||||
write(6,'(a,1x,i8,1x,i2)') '<< CPFEM >> OUTDATED at elFE ip',elFE,ip
|
||||
write(6,'(a,/,3(12x,3(f10.6,1x),/))') '<< CPFEM >> FFN1 old:',&
|
||||
transpose(materialpoint_F(1:3,1:3,ip,elCP))
|
||||
write(6,'(a,/,3(12x,3(f10.6,1x),/))') '<< CPFEM >> FFN1 now:',transpose(ffn1)
|
||||
endif
|
||||
outdatedFFN1 = .true.
|
||||
endif
|
||||
validCalculation: if (terminallyIll) then
|
||||
call random_number(rnd)
|
||||
if (rnd < 0.5_pReal) rnd = rnd - 1.0_pReal
|
||||
CPFEM_cs(1:6,ip,elCP) = ODD_STRESS * rnd
|
||||
CPFEM_dcsde(1:6,1:6,ip,elCP) = ODD_JACOBIAN * math_identity2nd(6)
|
||||
|
||||
!*** deformation gradient is not outdated
|
||||
else validCalculation
|
||||
updateJaco = mod(cycleCounter,iJacoStiffness) == 0
|
||||
!* no parallel computation, so we use just one single elFE and ip for computation
|
||||
if (.not. parallelExecution) then
|
||||
FEsolving_execElem = elCP
|
||||
FEsolving_execIP = ip
|
||||
if (iand(debug_level(debug_CPFEM), debug_levelExtensive) /= 0_pInt) &
|
||||
write(6,'(a,i8,1x,i2)') '<< CPFEM >> calculation for elFE ip ',elFE,ip
|
||||
call materialpoint_stressAndItsTangent(updateJaco, dt)
|
||||
|
||||
!* parallel computation and calulation not yet done
|
||||
elseif (.not. CPFEM_calc_done) then
|
||||
if (iand(debug_level(debug_CPFEM), debug_levelExtensive) /= 0_pInt) &
|
||||
write(6,'(a,i8,a,i8)') '<< CPFEM >> calculation for elements ',FEsolving_execElem(1),&
|
||||
' to ',FEsolving_execElem(2)
|
||||
call materialpoint_stressAndItsTangent(updateJaco, dt)
|
||||
CPFEM_calc_done = .true.
|
||||
endif
|
||||
|
||||
!* map stress and stiffness (or return odd values if terminally ill)
|
||||
terminalIllness: if (terminallyIll) then
|
||||
|
||||
call random_number(rnd)
|
||||
|
|
@ -256,7 +185,7 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
|
|||
|
||||
else terminalIllness
|
||||
|
||||
! translate from P to CS
|
||||
! translate from P to sigma
|
||||
Kirchhoff = matmul(materialpoint_P(1:3,1:3,ip,elCP), transpose(materialpoint_F(1:3,1:3,ip,elCP)))
|
||||
J_inverse = 1.0_pReal / math_det33(materialpoint_F(1:3,1:3,ip,elCP))
|
||||
CPFEM_cs(1:6,ip,elCP) = math_sym33to6(J_inverse * Kirchhoff,weighted=.false.)
|
||||
|
|
@ -280,7 +209,6 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
|
|||
endif terminalIllness
|
||||
endif validCalculation
|
||||
|
||||
!* report stress and stiffness
|
||||
if ((iand(debug_level(debug_CPFEM), debug_levelExtensive) /= 0_pInt) &
|
||||
.and. ((debug_e == elCP .and. debug_i == ip) &
|
||||
.or. .not. iand(debug_level(debug_CPFEM), debug_levelSelective) /= 0_pInt)) then
|
||||
|
|
@ -293,35 +221,11 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
|
|||
|
||||
endif
|
||||
|
||||
!*** warn if stiffness close to zero
|
||||
if (all(abs(CPFEM_dcsdE(1:6,1:6,ip,elCP)) < 1e-10_pReal)) call IO_warning(601,elCP,ip)
|
||||
|
||||
!*** copy to output if using commercial FEM solver
|
||||
cauchyStress = CPFEM_cs (1:6, ip,elCP)
|
||||
jacobian = CPFEM_dcsdE(1:6,1:6,ip,elCP)
|
||||
|
||||
|
||||
!*** remember extreme values of stress ...
|
||||
cauchyStress33 = math_6toSym33(CPFEM_cs(1:6,ip,elCP),weighted=.false.)
|
||||
if (maxval(cauchyStress33) > debug_stressMax) then
|
||||
debug_stressMaxLocation = [elCP, ip]
|
||||
debug_stressMax = maxval(cauchyStress33)
|
||||
endif
|
||||
if (minval(cauchyStress33) < debug_stressMin) then
|
||||
debug_stressMinLocation = [elCP, ip]
|
||||
debug_stressMin = minval(cauchyStress33)
|
||||
endif
|
||||
!*** ... and Jacobian
|
||||
jacobian3333 = math_66toSym3333(CPFEM_dcsdE(1:6,1:6,ip,elCP),weighted=.false.)
|
||||
if (maxval(jacobian3333) > debug_jacobianMax) then
|
||||
debug_jacobianMaxLocation = [elCP, ip]
|
||||
debug_jacobianMax = maxval(jacobian3333)
|
||||
endif
|
||||
if (minval(jacobian3333) < debug_jacobianMin) then
|
||||
debug_jacobianMinLocation = [elCP, ip]
|
||||
debug_jacobianMin = minval(jacobian3333)
|
||||
endif
|
||||
|
||||
end subroutine CPFEM_general
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -43,8 +43,6 @@ module DAMASK_interface
|
|||
logical, protected, public :: symmetricSolver
|
||||
character(len=*), parameter, public :: INPUTFILEEXTENSION = '.dat'
|
||||
|
||||
logical, dimension(:,:), public, allocatable :: &
|
||||
calcMode !< calculate or collect (ping pong scheme)
|
||||
|
||||
public :: &
|
||||
DAMASK_interface_init, &
|
||||
|
|
@ -185,7 +183,7 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
|
|||
use CPFEM
|
||||
|
||||
implicit none
|
||||
!$ include "omp_lib.h" ! the openMP function library
|
||||
include "omp_lib.h" ! the openMP function library
|
||||
integer, intent(in) :: & ! according to MSC.Marc 2012 Manual D
|
||||
ngens, & !< size of stress-strain law
|
||||
nn, & !< integration point number
|
||||
|
|
@ -243,7 +241,18 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
|
|||
real(pReal), dimension(6) :: stress
|
||||
real(pReal), dimension(6,6) :: ddsdde
|
||||
integer :: computationMode, i, cp_en, node, CPnodeID
|
||||
!$ integer(4) :: defaultNumThreadsInt !< default value set by Marc
|
||||
integer(4) :: defaultNumThreadsInt !< default value set by Marc
|
||||
|
||||
integer(pInt), save :: &
|
||||
theInc = -1_pInt, & !< needs description
|
||||
lastLovl = 0_pInt !< lovl in previous call to marc hypela2
|
||||
real(pReal), save :: &
|
||||
theTime = 0.0_pReal, & !< needs description
|
||||
theDelta = 0.0_pReal
|
||||
logical, save :: &
|
||||
lastIncConverged = .false., & !< needs description
|
||||
outdatedByNewInc = .false., & !< needs description
|
||||
CPFEM_init_done = .false. !< remember whether init has been done already
|
||||
|
||||
if (iand(debug_level(debug_MARC),debug_LEVELBASIC) /= 0) then
|
||||
write(6,'(a,/,i8,i8,i2)') ' MSC.MARC information on shape of element(2), IP:', m, nn
|
||||
|
|
@ -260,116 +269,76 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
|
|||
transpose(ffn1)
|
||||
endif
|
||||
|
||||
!$ defaultNumThreadsInt = omp_get_num_threads() ! remember number of threads set by Marc
|
||||
!$ call omp_set_num_threads(DAMASK_NumThreadsInt) ! set number of threads for parallel execution set by DAMASK_NUM_THREADS
|
||||
defaultNumThreadsInt = omp_get_num_threads() ! remember number of threads set by Marc
|
||||
call omp_set_num_threads(1) ! no openMP
|
||||
|
||||
if (.not. CPFEM_init_done) call CPFEM_initAll(m(1),nn)
|
||||
if (.not. CPFEM_init_done) then
|
||||
CPFEM_init_done = .true.
|
||||
call CPFEM_initAll
|
||||
endif
|
||||
|
||||
computationMode = 0 ! save initialization value, since it does not result in any calculation
|
||||
if (lovl == 4 ) then ! jacobian requested by marc
|
||||
if (timinc < theDelta .and. theInc == inc .and. lastLovl /= lovl) & ! first after cutback
|
||||
computationMode = CPFEM_RESTOREJACOBIAN
|
||||
elseif (lovl == 6) then ! stress requested by marc
|
||||
computationMode = CPFEM_CALCRESULTS
|
||||
cp_en = mesh_FEM2DAMASK_elem(m(1))
|
||||
if (cptim > theTime .or. inc /= theInc) then ! reached "convergence"
|
||||
terminallyIll = .false.
|
||||
cycleCounter = -1 ! first calc step increments this to cycle = 0
|
||||
if (inc == 0) then ! >> start of analysis <<
|
||||
lastIncConverged = .false. ! no Jacobian backup
|
||||
outdatedByNewInc = .false. ! no aging of state
|
||||
calcMode = .false. ! pretend last step was collection
|
||||
lastIncConverged = .false.
|
||||
outdatedByNewInc = .false.
|
||||
lastLovl = lovl ! pretend that this is NOT the first after a lovl change
|
||||
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> start of analysis..! ',m(1),nn
|
||||
flush(6)
|
||||
else if (inc - theInc > 1) then ! >> restart of broken analysis <<
|
||||
lastIncConverged = .false. ! no Jacobian backup
|
||||
outdatedByNewInc = .false. ! no aging of state
|
||||
calcMode = .true. ! pretend last step was calculation
|
||||
lastIncConverged = .false.
|
||||
outdatedByNewInc = .false.
|
||||
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> restart of analysis..! ',m(1),nn
|
||||
flush(6)
|
||||
else ! >> just the next inc <<
|
||||
lastIncConverged = .true. ! request Jacobian backup
|
||||
outdatedByNewInc = .true. ! request aging of state
|
||||
calcMode = .true. ! assure last step was calculation
|
||||
lastIncConverged = .true.
|
||||
outdatedByNewInc = .true.
|
||||
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> new increment..! ',m(1),nn
|
||||
flush(6)
|
||||
endif
|
||||
else if ( timinc < theDelta ) then ! >> cutBack <<
|
||||
lastIncConverged = .false. ! no Jacobian backup
|
||||
outdatedByNewInc = .false. ! no aging of state
|
||||
lastIncConverged = .false.
|
||||
outdatedByNewInc = .false.
|
||||
terminallyIll = .false.
|
||||
cycleCounter = -1 ! first calc step increments this to cycle = 0
|
||||
calcMode = .true. ! pretend last step was calculation
|
||||
write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> cutback detected..! ',m(1),nn
|
||||
flush(6)
|
||||
endif ! convergence treatment end
|
||||
flush(6)
|
||||
|
||||
|
||||
if (usePingPong) then
|
||||
calcMode(nn,cp_en) = .not. calcMode(nn,cp_en) ! ping pong (calc <--> collect)
|
||||
if (calcMode(nn,cp_en)) then ! now --- CALC ---
|
||||
computationMode = CPFEM_CALCRESULTS
|
||||
if (lastLovl /= lovl) then ! first after ping pong
|
||||
call debug_reset() ! resets debugging
|
||||
outdatedFFN1 = .false.
|
||||
cycleCounter = cycleCounter + 1
|
||||
!mesh_cellnode = mesh_build_cellnodes() ! update cell node coordinates
|
||||
!call mesh_build_ipCoordinates() ! update ip coordinates
|
||||
endif
|
||||
if (outdatedByNewInc) then
|
||||
computationMode = ior(computationMode,CPFEM_AGERESULTS) ! calc and age results
|
||||
outdatedByNewInc = .false. ! reset flag
|
||||
endif
|
||||
else ! now --- COLLECT ---
|
||||
computationMode = CPFEM_COLLECT ! plain collect
|
||||
if (lastLovl /= lovl .and. & .not. terminallyIll) &
|
||||
call debug_info() ! first after ping pong reports (meaningful) debugging
|
||||
if (lastIncConverged) then
|
||||
computationMode = ior(computationMode,CPFEM_BACKUPJACOBIAN) ! collect and backup Jacobian after convergence
|
||||
lastIncConverged = .false. ! reset flag
|
||||
endif
|
||||
!do node = 1,theMesh%elem%nNodes
|
||||
!CPnodeID = mesh_element(4+node,cp_en)
|
||||
!mesh_node(1:ndeg,CPnodeID) = mesh_node0(1:ndeg,CPnodeID) + numerics_unitlength * dispt(1:ndeg,node)
|
||||
!enddo
|
||||
endif
|
||||
|
||||
else ! --- PLAIN MODE ---
|
||||
computationMode = CPFEM_CALCRESULTS ! always calc
|
||||
if (lastLovl /= lovl) then
|
||||
if (.not. terminallyIll) &
|
||||
call debug_info() ! first reports (meaningful) debugging
|
||||
call debug_reset() ! and resets debugging
|
||||
outdatedFFN1 = .false.
|
||||
cycleCounter = cycleCounter + 1
|
||||
!mesh_cellnode = mesh_build_cellnodes() ! update cell node coordinates
|
||||
!call mesh_build_ipCoordinates() ! update ip coordinates
|
||||
endif
|
||||
if (outdatedByNewInc) then
|
||||
computationMode = ior(computationMode,CPFEM_AGERESULTS)
|
||||
outdatedByNewInc = .false. ! reset flag
|
||||
outdatedByNewInc = .false.
|
||||
endif
|
||||
if (lastIncConverged) then
|
||||
computationMode = ior(computationMode,CPFEM_BACKUPJACOBIAN) ! backup Jacobian after convergence
|
||||
lastIncConverged = .false. ! reset flag
|
||||
endif
|
||||
computationMode = ior(computationMode,CPFEM_BACKUPJACOBIAN)
|
||||
lastIncConverged = .false.
|
||||
endif
|
||||
|
||||
theTime = cptim ! record current starting time
|
||||
theDelta = timinc ! record current time increment
|
||||
theInc = inc ! record current increment number
|
||||
theTime = cptim
|
||||
theDelta = timinc
|
||||
theInc = inc
|
||||
|
||||
endif
|
||||
lastLovl = lovl ! record lovl
|
||||
lastLovl = lovl
|
||||
|
||||
call CPFEM_general(computationMode,usePingPong,ffn,ffn1,t(1),timinc,m(1),nn,stress,ddsdde)
|
||||
call CPFEM_general(computationMode,ffn,ffn1,t(1),timinc,m(1),nn,stress,ddsdde)
|
||||
|
||||
d = ddsdde(1:ngens,1:ngens)
|
||||
s = stress(1:ndi+nshear)
|
||||
g = 0.0_pReal
|
||||
if(symmetricSolver) d = 0.5_pReal*(d+transpose(d))
|
||||
|
||||
!$ call omp_set_num_threads(defaultNumThreadsInt) ! reset number of threads to stored default value
|
||||
call omp_set_num_threads(defaultNumThreadsInt) ! reset number of threads to stored default value
|
||||
|
||||
end subroutine hypela2
|
||||
|
||||
|
|
|
|||
|
|
@ -830,7 +830,7 @@ module subroutine plastic_dislotwin_results(instance,group)
|
|||
'mobile dislocation density','1/m²')
|
||||
case('rho_dip')
|
||||
if(prm%sum_N_sl>0) call results_writeDataset(group,stt%rho_dip,'rho_dip',&
|
||||
'dislocation dipole density''1/m²')
|
||||
'dislocation dipole density','1/m²')
|
||||
case('gamma_sl')
|
||||
if(prm%sum_N_sl>0) call results_writeDataset(group,stt%gamma_sl,'gamma_sl',&
|
||||
'plastic shear','1')
|
||||
|
|
|
|||
|
|
@ -245,7 +245,7 @@ subroutine crystallite_init
|
|||
enddo
|
||||
!$OMP END PARALLEL DO
|
||||
|
||||
if(any(plasticState%nonlocal) .and. .not. usePingPong) call IO_error(601) ! exit if nonlocal but no ping-pong ToDo: Why not check earlier? or in nonlocal?
|
||||
!if(any(plasticState%nonlocal) .and. .not. usePingPong) call IO_error(601)
|
||||
|
||||
crystallite_partionedFp0 = crystallite_Fp0
|
||||
crystallite_partionedFi0 = crystallite_Fi0
|
||||
|
|
@ -276,9 +276,6 @@ subroutine crystallite_init
|
|||
write(6,'(a42,1x,i10)') 'max # of constituents/integration point: ', cMax
|
||||
flush(6)
|
||||
endif
|
||||
|
||||
call debug_info
|
||||
call debug_reset
|
||||
#endif
|
||||
|
||||
end subroutine crystallite_init
|
||||
|
|
@ -287,11 +284,9 @@ end subroutine crystallite_init
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief calculate stress (P)
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
function crystallite_stress(dummyArgumentToPreventInternalCompilerErrorWithGCC)
|
||||
function crystallite_stress()
|
||||
|
||||
logical, dimension(discretization_nIP,discretization_nElem) :: crystallite_stress
|
||||
real(pReal), intent(in), optional :: &
|
||||
dummyArgumentToPreventInternalCompilerErrorWithGCC
|
||||
real(pReal) :: &
|
||||
formerSubStep
|
||||
integer :: &
|
||||
|
|
|
|||
|
|
@ -49,26 +49,11 @@ module debug
|
|||
debug_i = 1, &
|
||||
debug_g = 1
|
||||
|
||||
integer, dimension(2), public :: &
|
||||
debug_stressMaxLocation = 0, &
|
||||
debug_stressMinLocation = 0, &
|
||||
debug_jacobianMaxLocation = 0, &
|
||||
debug_jacobianMinLocation = 0
|
||||
|
||||
|
||||
real(pReal), public :: &
|
||||
debug_stressMax = -huge(1.0_pReal), &
|
||||
debug_stressMin = huge(1.0_pReal), &
|
||||
debug_jacobianMax = -huge(1.0_pReal), &
|
||||
debug_jacobianMin = huge(1.0_pReal)
|
||||
|
||||
#ifdef PETSc
|
||||
character(len=1024), parameter, public :: &
|
||||
PETSCDEBUG = ' -snes_view -snes_monitor '
|
||||
#endif
|
||||
public :: debug_init, &
|
||||
debug_reset, &
|
||||
debug_info
|
||||
public :: debug_init
|
||||
|
||||
contains
|
||||
|
||||
|
|
@ -230,42 +215,4 @@ subroutine debug_init
|
|||
|
||||
end subroutine debug_init
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief resets all debug values
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine debug_reset
|
||||
|
||||
debug_stressMaxLocation = 0
|
||||
debug_stressMinLocation = 0
|
||||
debug_jacobianMaxLocation = 0
|
||||
debug_jacobianMinLocation = 0
|
||||
debug_stressMax = -huge(1.0_pReal)
|
||||
debug_stressMin = huge(1.0_pReal)
|
||||
debug_jacobianMax = -huge(1.0_pReal)
|
||||
debug_jacobianMin = huge(1.0_pReal)
|
||||
|
||||
end subroutine debug_reset
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief writes debug statements to standard out
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine debug_info
|
||||
|
||||
!$OMP CRITICAL (write2out)
|
||||
debugOutputCPFEM: if (iand(debug_level(debug_CPFEM),debug_LEVELBASIC) /= 0 &
|
||||
.and. any(debug_stressMinLocation /= 0) &
|
||||
.and. any(debug_stressMaxLocation /= 0) ) then
|
||||
write(6,'(2/,a,/)') ' Extreme values of returned stress and Jacobian'
|
||||
write(6,'(a39)') ' value el ip'
|
||||
write(6,'(a14,1x,e12.3,1x,i8,1x,i4)') ' stress min :', debug_stressMin, debug_stressMinLocation
|
||||
write(6,'(a14,1x,e12.3,1x,i8,1x,i4)') ' max :', debug_stressMax, debug_stressMaxLocation
|
||||
write(6,'(a14,1x,e12.3,1x,i8,1x,i4)') ' Jacobian min :', debug_jacobianMin, debug_jacobianMinLocation
|
||||
write(6,'(a14,1x,e12.3,1x,i8,1x,i4,/)') ' max :', debug_jacobianMax, debug_jacobianMaxLocation
|
||||
endif debugOutputCPFEM
|
||||
!$OMP END CRITICAL (write2out)
|
||||
|
||||
end subroutine debug_info
|
||||
|
||||
end module debug
|
||||
|
|
|
|||
|
|
@ -49,7 +49,7 @@ subroutine discretization_init(homogenizationAt,microstructureAt,&
|
|||
IPcoords0, &
|
||||
NodeCoords0
|
||||
integer, optional, intent(in) :: &
|
||||
sharedNodesBegin
|
||||
sharedNodesBegin !< index of first node shared among different processes (MPI)
|
||||
|
||||
write(6,'(/,a)') ' <<<+- discretization init -+>>>'; flush(6)
|
||||
|
||||
|
|
|
|||
|
|
@ -249,7 +249,8 @@ subroutine materialpoint_stressAndItsTangent(updateJaco,dt)
|
|||
NiterationHomog = 0
|
||||
|
||||
cutBackLooping: do while (.not. terminallyIll .and. &
|
||||
any(subStep(:,FEsolving_execELem(1):FEsolving_execElem(2)) > num%subStepMinHomog))
|
||||
any(subStep(FEsolving_execIP(1):FEsolving_execIP(2),&
|
||||
FEsolving_execElem(1):FEsolving_execElem(2)) > num%subStepMinHomog))
|
||||
|
||||
!$OMP PARALLEL DO PRIVATE(myNgrains)
|
||||
elementLooping1: do e = FEsolving_execElem(1),FEsolving_execElem(2)
|
||||
|
|
|
|||
|
|
@ -45,9 +45,7 @@ contains
|
|||
!> @brief initializes the mesh by calling all necessary private routines the mesh module
|
||||
!! Order and routines strongly depend on type of solver
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine discretization_marc_init(ip,el)
|
||||
|
||||
integer, intent(in) :: el, ip
|
||||
subroutine discretization_marc_init
|
||||
|
||||
real(pReal), dimension(:,:), allocatable :: &
|
||||
node0_elem, & !< node x,y,z coordinates (initially!)
|
||||
|
|
@ -70,7 +68,7 @@ subroutine discretization_marc_init(ip,el)
|
|||
real(pReal), dimension(:,:,:,:),allocatable :: &
|
||||
unscaledNormals
|
||||
|
||||
write(6,'(/,a)') ' <<<+- mesh init -+>>>'; flush(6)
|
||||
write(6,'(/,a)') ' <<<+- discretization_marc init -+>>>'; flush(6)
|
||||
|
||||
mesh_unitlength = numerics_unitlength ! set physical extent of a length unit in mesh
|
||||
|
||||
|
|
@ -83,10 +81,6 @@ subroutine discretization_marc_init(ip,el)
|
|||
FEsolving_execElem = [1,nElems]
|
||||
FEsolving_execIP = [1,elem%nIPs]
|
||||
|
||||
allocate(calcMode(elem%nIPs,nElems),source=.false.) ! pretend to have collected what first call is asking (F = I)
|
||||
calcMode(ip,mesh_FEM2DAMASK_elem(el)) = .true. ! first ip,el needs to be already pingponged to "calc"
|
||||
|
||||
|
||||
allocate(cellNodeDefinition(elem%nNodes-1))
|
||||
allocate(connectivity_cell(elem%NcellNodesPerCell,elem%nIPs,nElems))
|
||||
call buildCells(connectivity_cell,cellNodeDefinition,&
|
||||
|
|
|
|||
|
|
@ -36,9 +36,6 @@ module discretization_mesh
|
|||
mesh_maxNips !< max number of IPs in any CP element
|
||||
!!!! BEGIN DEPRECATED !!!!!
|
||||
|
||||
integer, dimension(:,:), allocatable :: &
|
||||
mesh_element !DEPRECATED
|
||||
|
||||
real(pReal), dimension(:,:), allocatable :: &
|
||||
mesh_ipVolume, & !< volume associated with IP (initially!)
|
||||
mesh_node0 !< node x,y,z coordinates (initially!)
|
||||
|
|
@ -67,15 +64,10 @@ subroutine discretization_mesh_init(restart)
|
|||
|
||||
logical, intent(in) :: restart
|
||||
|
||||
integer, dimension(1), parameter:: FE_geomtype = [1] !< geometry type of particular element type
|
||||
integer, dimension(1) :: FE_Nips !< number of IPs in a specific type of element
|
||||
|
||||
integer, allocatable, dimension(:) :: chunkPos
|
||||
integer :: dimPlex, &
|
||||
mesh_Nnodes, & !< total number of nodes in mesh
|
||||
j, l
|
||||
integer, parameter :: &
|
||||
mesh_ElemType=1 !< Element type of the mesh (only support homogeneous meshes)
|
||||
PetscSF :: sf
|
||||
DM :: globalMesh
|
||||
PetscInt :: nFaceSets
|
||||
|
|
@ -83,23 +75,22 @@ subroutine discretization_mesh_init(restart)
|
|||
character(len=pStringLen), dimension(:), allocatable :: fileContent
|
||||
IS :: faceSetIS
|
||||
PetscErrorCode :: ierr
|
||||
integer, dimension(:), allocatable :: &
|
||||
homogenizationAt, &
|
||||
microstructureAt
|
||||
|
||||
|
||||
write(6,'(/,a)') ' <<<+- mesh init -+>>>'
|
||||
|
||||
! read in file
|
||||
call DMPlexCreateFromFile(PETSC_COMM_WORLD,geometryFile,PETSC_TRUE,globalMesh,ierr)
|
||||
CHKERRQ(ierr)
|
||||
! get spatial dimension (2 or 3?)
|
||||
call DMGetDimension(globalMesh,dimPlex,ierr)
|
||||
CHKERRQ(ierr)
|
||||
write(6,*) 'dimension',dimPlex;flush(6)
|
||||
call DMGetStratumSize(globalMesh,'depth',dimPlex,mesh_NcpElemsGlobal,ierr)
|
||||
CHKERRQ(ierr)
|
||||
! get number of IDs in face sets (for boundary conditions?)
|
||||
call DMGetLabelSize(globalMesh,'Face Sets',mesh_Nboundaries,ierr)
|
||||
CHKERRQ(ierr)
|
||||
write(6,*) 'number of "Face Sets"',mesh_Nboundaries;flush(6)
|
||||
call MPI_Bcast(mesh_Nboundaries,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
|
||||
call MPI_Bcast(mesh_NcpElemsGlobal,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
|
||||
call MPI_Bcast(dimPlex,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr)
|
||||
|
|
@ -154,33 +145,27 @@ subroutine discretization_mesh_init(restart)
|
|||
call DMGetStratumSize(geomMesh,'depth',0,mesh_Nnodes,ierr)
|
||||
CHKERRQ(ierr)
|
||||
|
||||
FE_Nips(FE_geomtype(1)) = FEM_nQuadrature(dimPlex,integrationOrder)
|
||||
mesh_maxNips = FE_Nips(1)
|
||||
mesh_maxNips = FEM_nQuadrature(dimPlex,integrationOrder)
|
||||
|
||||
write(6,*) 'mesh_maxNips',mesh_maxNips
|
||||
call mesh_FEM_build_ipCoordinates(dimPlex,FEM_quadrature_points(dimPlex,integrationOrder)%p)
|
||||
call mesh_FEM_build_ipVolumes(dimPlex)
|
||||
|
||||
allocate (mesh_element (4,mesh_NcpElems)); mesh_element = 0
|
||||
allocate(microstructureAt(mesh_NcpElems))
|
||||
allocate(homogenizationAt(mesh_NcpElems),source=1)
|
||||
do j = 1, mesh_NcpElems
|
||||
mesh_element( 1,j) = -1 ! DEPRECATED
|
||||
mesh_element( 2,j) = mesh_elemType ! elem type
|
||||
mesh_element( 3,j) = 1 ! homogenization
|
||||
call DMGetLabelValue(geomMesh,'material',j-1,mesh_element(4,j),ierr)
|
||||
call DMGetLabelValue(geomMesh,'material',j-1,microstructureAt(j),ierr)
|
||||
CHKERRQ(ierr)
|
||||
end do
|
||||
|
||||
if (debug_e < 1 .or. debug_e > mesh_NcpElems) &
|
||||
call IO_error(602,ext_msg='element') ! selected element does not exist
|
||||
if (debug_i < 1 .or. debug_i > FE_Nips(FE_geomtype(mesh_element(2,debug_e)))) &
|
||||
call IO_error(602,ext_msg='IP') ! selected element does not have requested IP
|
||||
if (debug_e < 1 .or. debug_e > mesh_NcpElems) call IO_error(602,ext_msg='element')
|
||||
if (debug_i < 1 .or. debug_i > mesh_maxNips) call IO_error(602,ext_msg='IP')
|
||||
|
||||
FEsolving_execElem = [ 1,mesh_NcpElems ] ! parallel loop bounds set to comprise all DAMASK elements
|
||||
FEsolving_execIP = [1,FE_Nips(FE_geomtype(mesh_element(2,1)))]
|
||||
FEsolving_execElem = [1,mesh_NcpElems] ! parallel loop bounds set to comprise all DAMASK elements
|
||||
FEsolving_execIP = [1,mesh_maxNips]
|
||||
|
||||
allocate(mesh_node0(3,mesh_Nnodes),source=0.0_pReal)
|
||||
|
||||
call discretization_init(mesh_element(3,:),mesh_element(4,:),&
|
||||
call discretization_init(microstructureAt,homogenizationAt,&
|
||||
reshape(mesh_ipCoordinates,[3,mesh_maxNips*mesh_NcpElems]), &
|
||||
mesh_node0)
|
||||
|
||||
|
|
|
|||
|
|
@ -28,8 +28,6 @@ module numerics
|
|||
numerics_unitlength = 1.0_pReal, & !< determines the physical length of one computational length unit
|
||||
charLength = 1.0_pReal, & !< characteristic length scale for gradient problems
|
||||
residualStiffness = 1.0e-6_pReal !< non-zero residual damage
|
||||
logical, protected, public :: &
|
||||
usePingPong = .true.
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! field parameters:
|
||||
|
|
@ -133,8 +131,6 @@ subroutine numerics_init
|
|||
defgradTolerance = IO_floatValue(line,chunkPos,2)
|
||||
case ('ijacostiffness')
|
||||
iJacoStiffness = IO_intValue(line,chunkPos,2)
|
||||
case ('usepingpong')
|
||||
usepingpong = IO_intValue(line,chunkPos,2) > 0
|
||||
case ('unitlength')
|
||||
numerics_unitlength = IO_floatValue(line,chunkPos,2)
|
||||
|
||||
|
|
@ -221,7 +217,6 @@ subroutine numerics_init
|
|||
! writing parameters to output
|
||||
write(6,'(a24,1x,es8.1)') ' defgradTolerance: ',defgradTolerance
|
||||
write(6,'(a24,1x,i8)') ' iJacoStiffness: ',iJacoStiffness
|
||||
write(6,'(a24,1x,L8)') ' use ping pong scheme: ',usepingpong
|
||||
write(6,'(a24,1x,es8.1,/)')' unitlength: ',numerics_unitlength
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -101,6 +101,8 @@ module quaternions
|
|||
assignment(=), &
|
||||
conjg, aimag, &
|
||||
log, exp, &
|
||||
abs, dot_product, &
|
||||
inverse, &
|
||||
real
|
||||
|
||||
contains
|
||||
|
|
|
|||
Loading…
Reference in New Issue