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Merge branch 'development' into Marc2020

This commit is contained in:
Franz Roters 2020-09-16 09:00:02 +02:00
parent dbb6c8f867 de4587c52e
commit b09b500159
178 changed files with 5387 additions and 4880 deletions
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7
.gitlab-ci.yml
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@ -141,13 +141,6 @@ Pre_General:
- release
###################################################################################################
Post_AverageDown:
stage: postprocessing
script: averageDown/test.py
except:
- master
- release
Post_ASCIItable:
stage: postprocessing
script: ASCIItable/test.py

2
PRIVATE

@ -1 +1 @@
Subproject commit 3fc9d58a35614fd8ffa1179e634431eb457d0150
Subproject commit c6dc3f116fc6007caf076772d5c29f0a0523544d

2
README
View File

@ -8,6 +8,6 @@ Max-Planck-Str. 1
40237 Düsseldorf
Germany
Email: DAMASK@mpie.de
damask@mpie.de
https://damask.mpie.de
https://magit1.mpie.de

2
VERSION
View File

@ -1 +1 @@
v2.0.3-2945-gb7e03364
v3.0.0-alpha-89-g23d61511

126
examples/SpectralMethod/Polycrystal/material.config
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@ -1,126 +0,0 @@
#-------------------#
<homogenization>
#-------------------#
[SX]
mech none
#-------------------#
<phase>
#-------------------#
[Aluminum_phenopowerlaw]
elasticity hooke
plasticity phenopowerlaw
(output) resistance_slip
(output) orientation # quaternion
(output) F # deformation gradient tensor
(output) Fe # elastic deformation gradient tensor
(output) Fp # plastic deformation gradient tensor
(output) P # first Piola-Kichhoff stress tensor
(output) Lp # plastic velocity gradient tensor
lattice_structure fcc
Nslip 12 # per family
c11 106.75e9
c12 60.41e9
c44 28.34e9
gdot0_slip 0.001
n_slip 20
tau0_slip 31e6 # per family
tausat_slip 63e6 # per family
a_slip 2.25
h0_slipslip 75e6
interaction_slipslip 1 1 1.4 1.4 1.4 1.4
#-------------------#
<microstructure>
#-------------------#
[Grain01]
(constituent) phase 1 texture 01 fraction 1.0
[Grain02]
(constituent) phase 1 texture 02 fraction 1.0
[Grain03]
(constituent) phase 1 texture 03 fraction 1.0
[Grain04]
(constituent) phase 1 texture 04 fraction 1.0
[Grain05]
(constituent) phase 1 texture 05 fraction 1.0
[Grain06]
(constituent) phase 1 texture 06 fraction 1.0
[Grain07]
(constituent) phase 1 texture 07 fraction 1.0
[Grain08]
(constituent) phase 1 texture 08 fraction 1.0
[Grain09]
(constituent) phase 1 texture 09 fraction 1.0
[Grain10]
(constituent) phase 1 texture 10 fraction 1.0
[Grain11]
(constituent) phase 1 texture 11 fraction 1.0
[Grain12]
(constituent) phase 1 texture 12 fraction 1.0
[Grain13]
(constituent) phase 1 texture 13 fraction 1.0
[Grain14]
(constituent) phase 1 texture 14 fraction 1.0
[Grain15]
(constituent) phase 1 texture 15 fraction 1.0
[Grain16]
(constituent) phase 1 texture 16 fraction 1.0
[Grain17]
(constituent) phase 1 texture 17 fraction 1.0
[Grain18]
(constituent) phase 1 texture 18 fraction 1.0
[Grain19]
(constituent) phase 1 texture 19 fraction 1.0
[Grain20]
(constituent) phase 1 texture 20 fraction 1.0
#-------------------#
<texture>
#-------------------#
[Grain01]
(gauss) phi1 0.0 Phi 0.0 phi2 0.0
[Grain02]
(gauss) phi1 257.468172 Phi 53.250534 phi2 157.331503
[Grain03]
(gauss) phi1 216.994815 Phi 94.418518 phi2 251.147231
[Grain04]
(gauss) phi1 196.157946 Phi 55.870978 phi2 21.68117
[Grain05]
(gauss) phi1 152.515728 Phi 139.769395 phi2 240.036018
[Grain06]
(gauss) phi1 232.521881 Phi 73.749222 phi2 241.429633
[Grain07]
(gauss) phi1 157.531396 Phi 135.503513 phi2 75.737722
[Grain08]
(gauss) phi1 321.03828 Phi 27.209843 phi2 46.413467
[Grain09]
(gauss) phi1 346.918594 Phi 87.495569 phi2 113.554206
[Grain10]
(gauss) phi1 138.038947 Phi 99.827132 phi2 130.935878
[Grain11]
(gauss) phi1 285.021014 Phi 118.092004 phi2 205.270837
[Grain12]
(gauss) phi1 190.402171 Phi 56.738068 phi2 157.896545
[Grain13]
(gauss) phi1 204.496042 Phi 95.031265 phi2 355.814582
[Grain14]
(gauss) phi1 333.21479 Phi 82.133355 phi2 36.736132
[Grain15]
(gauss) phi1 25.572981 Phi 164.242648 phi2 75.195632
[Grain16]
(gauss) phi1 31.366548 Phi 76.392403 phi2 58.071426
[Grain17]
(gauss) phi1 7.278623 Phi 77.044663 phi2 235.118997
[Grain18]
(gauss) phi1 299.743144 Phi 76.475096 phi2 91.184977
[Grain19]
(gauss) phi1 280.13643 Phi 27.439718 phi2 167.871878
[Grain20]
(gauss) phi1 313.204373 Phi 68.676053 phi2 87.993213

123
examples/SpectralMethod/Polycrystal/material.yaml Normal file
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@ -0,0 +1,123 @@
homogenization:
SX:
mech: {type: none}
microstructure:
- constituents:
- fraction: 1.0
orientation: [1.0, 0.0, 0.0, 0.0]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.7936696712125002, -0.28765777461664166, -0.3436487135089419, 0.4113964260949434]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.3986143167493579, -0.7014883552495493, 0.2154871765709027, 0.5500781677772945]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.28645844315788244, -0.022571491243423537, -0.467933059311115, -0.8357456192708106]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.33012772942625784, -0.6781865350268957, 0.6494525351030648, 0.09638521992649676]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.43596817439583935, -0.5982537129781701, 0.046599032277502436, 0.6707106499919265]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.169734823419553, -0.699615227367322, -0.6059581215838098, -0.33844257746495854]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.9698864809294915, 0.1729052643205874, -0.15948307917616958, 0.06315956884687175]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.46205660912967883, 0.3105054068891252, -0.617849551030653, 0.555294529545738]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.4512443497461787, -0.7636045534540555, -0.04739348426715133, -0.45939142396805815]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.2161856212656443, -0.6581450184826598, -0.5498086209601588, 0.4667112513346289]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.8753220715350803, -0.4561599367657419, -0.13298279533852678, -0.08969369719975541]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.11908260752431069, 0.18266024809834172, -0.7144822594012615, -0.664807992845101]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.751104669484278, 0.5585633382623958, -0.34579336397009175, 0.06538900566860861]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.08740438971703973, 0.8991264096610437, -0.4156704205935976, 0.10559485570696363]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.5584325870096193, 0.6016408353068798, -0.14280340445801173, 0.5529814994483859]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.4052725440888093, 0.25253073423599154, 0.5693263597910454, -0.669215876471182]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.7570164606888676, 0.15265448024694664, -0.5998021466848317, 0.20942796551297105]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.6987659297138081, -0.132172211261028, -0.19693254724422338, 0.6748883269678543]
phase: Aluminum
homogenization: SX
- constituents:
- fraction: 1.0
orientation: [0.7729330445886478, 0.21682179052722322, -0.5207379472917645, 0.2905078484066341]
phase: Aluminum
homogenization: SX
phase:
Aluminum:
elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
generic:
output: [F, P, Fe, Fp, Lp]
lattice: fcc
plasticity:
N_sl: [12]
a_sl: 2.25
atol_xi: 1.0
dot_gamma_0_sl: 0.001
h_0_sl_sl: 75e6
h_sl_sl: [1, 1, 1.4, 1.4, 1.4, 1.4]
n_sl: 20
output: [xi_sl]
xi_0_sl: [31e6]
xi_inf_sl: [63e6]
type: phenopowerlaw

2
processing/legacy/addAPS34IDEstrainCoords.py
View File

@ -49,4 +49,4 @@ for name in filenames:
table.add('coord',rot_to_TSL.broadcast_to(coord.shape[0]) @ coord,scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

2
processing/legacy/addCumulative.py
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@ -45,4 +45,4 @@ for name in filenames:
np.cumprod(table.get(label),0) if options.product else np.cumsum(table.get(label),0),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

184
processing/legacy/imageData.py
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@ -1,184 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser
import numpy as np
from PIL import Image
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 [file[s]]', description = """
Generate PNG image from data in given column (or 2D data of overall table).
""", version = scriptID)
parser.add_option('-l','--label',
dest = 'label',
type = 'string', metavar = 'string',
help = 'column containing data [all]')
parser.add_option('-r','--range',
dest = 'range',
type = 'float', nargs = 2, metavar = 'float float',
help = 'data range (min max) [auto]')
parser.add_option('--gap', '--transparent',
dest = 'gap',
type = 'float', metavar = 'float',
help = 'value to treat as transparent [%default]')
parser.add_option('-d','--dimension',
dest = 'dimension',
type = 'int', nargs = 2, metavar = 'int int',
help = 'data dimension (width height) [native]')
parser.add_option('--color',
dest = 'color',
type = 'string', metavar = 'string',
help = 'color scheme [%default]')
parser.add_option('--invert',
dest = 'invert',
action = 'store_true',
help = 'invert color scheme')
parser.add_option('--abs',
dest = 'abs',
action = 'store_true',
help = 'magnitude of values')
parser.add_option('--log',
dest = 'log',
action = 'store_true',
help = 'log10 of values')
parser.add_option('--fliplr',
dest = 'flipLR',
action = 'store_true',
help = 'flip around vertical axis')
parser.add_option('--flipud',
dest = 'flipUD',
action = 'store_true',
help = 'flip around horizontal axis')
parser.add_option('--crop',
dest = 'crop',
type = 'int', nargs = 4, metavar = 'int int int int',
help = 'pixels cropped on left, right, top, bottom')
parser.add_option('-N','--pixelsize',
dest = 'pixelsize',
type = 'int', metavar = 'int',
help = 'pixel per data point')
parser.add_option('-x','--pixelsizex',
dest = 'pixelsizex',
type = 'int', metavar = 'int',
help = 'pixel per data point along x')
parser.add_option('-y','--pixelsizey',
dest = 'pixelsizey',
type = 'int', metavar = 'int',
help = 'pixel per data point along y')
parser.add_option('--show',
dest = 'show',
action = 'store_true',
help = 'show resulting image')
parser.set_defaults(label = None,
range = [0.0,0.0],
gap = None,
dimension = [],
abs = False,
log = False,
flipLR = False,
flipUD = False,
color = "gray",
invert = False,
crop = [0,0,0,0],
pixelsize = 1,
pixelsizex = 1,
pixelsizey = 1,
show = False,
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.pixelsize > 1: (options.pixelsizex,options.pixelsizey) = [options.pixelsize]*2
# --- color palette ---------------------------------------------------------------------------------
theMap = damask.Colormap(predefined = options.color)
if options.invert: theMap = theMap.invert()
theColors = np.uint8(np.array(theMap.export(format = 'list',steps = 256))*255)
# --- loop over input files -------------------------------------------------------------------------
for name in filenames:
try:
table = damask.ASCIItable(name = name, labeled = options.label is not None, readonly = True)
except IOError:
continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ process data ------------------------------------------
missing_labels = table.data_readArray(options.label)
if len(missing_labels) > 0:
damask.util.croak('column {} not found.'.format(options.label))
table.close(dismiss = True) # close ASCIItable and remove empty file
continue
# convert data to values between 0 and 1 and arrange according to given options
if options.dimension != []: table.data = table.data.reshape(options.dimension[1],options.dimension[0])
if options.abs: table.data = np.abs(table.data)
if options.log: table.data = np.log10(table.data);options.range = np.log10(options.range)
if options.flipLR: table.data = np.fliplr(table.data)
if options.flipUD: table.data = np.flipud(table.data)
mask = np.logical_or(table.data == options.gap, np.isnan(table.data))\
if options.gap else np.logical_not(np.isnan(table.data)) # mask gap and NaN (if gap present)
if np.all(np.array(options.range) == 0.0):
options.range = [table.data[mask].min(),
table.data[mask].max()]
damask.util.croak('data range: {0} – {1}'.format(*options.range))
delta = max(options.range) - min(options.range)
avg = 0.5*(max(options.range) + min(options.range))
if delta * 1e8 <= avg: # delta around numerical noise
options.range = [min(options.range) - 0.5*avg, max(options.range) + 0.5*avg] # extend range to have actual data centered within
table.data = (table.data - min(options.range)) / \
(max(options.range) - min(options.range))
table.data = np.clip(table.data,0.0,1.0).\
repeat(options.pixelsizex,axis = 1).\
repeat(options.pixelsizey,axis = 0)
mask = mask.\
repeat(options.pixelsizex,axis = 1).\
repeat(options.pixelsizey,axis = 0)
(height,width) = table.data.shape
damask.util.croak('image dimension: {0} x {1}'.format(width,height))
im = Image.fromarray(np.dstack((theColors[np.array(255*table.data,dtype = np.uint8)],
255*mask.astype(np.uint8))), 'RGBA').\
crop(( options.crop[0],
options.crop[2],
width -options.crop[1],
height-options.crop[3]))
# ------------------------------------------ output result -----------------------------------------
im.save(sys.stdout if not name else
os.path.splitext(name)[0]+ \
('' if options.label is None else '_'+options.label)+ \
'.png',
format = "PNG")
table.close() # close ASCII table
if options.show: im.show()

134
processing/legacy/imageDataRGB.py
View File

@ -1,134 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser
import numpy as np
from PIL import Image
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 [file[s]]', description = """
Generate PNG image from data in given column vector containing RGB tuples.
""", version = scriptID)
parser.add_option('-l','--label',
dest = 'label',
type = 'string', metavar = 'string',
help = 'column containing RGB triplet')
parser.add_option('-d','--dimension',
dest = 'dimension',
type = 'int', nargs = 2, metavar = 'int int',
help = 'data dimension (width height)')
parser.add_option('--fliplr',
dest = 'flipLR',
action = 'store_true',
help = 'flip around vertical axis')
parser.add_option('--flipud',
dest = 'flipUD',
action = 'store_true',
help = 'flip around horizontal axis')
parser.add_option('--crop',
dest = 'crop',
type = 'int', nargs = 4, metavar = ' '.join(['int']*4),
help = 'pixels cropped on left, right, top, bottom')
parser.add_option('-N','--pixelsize',
dest = 'pixelsize',
type = 'int', metavar = 'int',
help = 'pixels per data point')
parser.add_option('-x','--pixelsizex',
dest = 'pixelsizex',
type = 'int', metavar = 'int',
help = 'pixels per data point along x')
parser.add_option('-y','--pixelsizey',
dest = 'pixelsizey',
type = 'int', metavar = 'int',
help = 'pixels per data point along y')
parser.add_option('--show',
dest = 'show',
action = 'store_true',
help = 'show resulting image')
parser.set_defaults(label = None,
dimension = [],
flipLR = False,
flipUD = False,
crop = [0,0,0,0],
pixelsize = 1,
pixelsizex = 1,
pixelsizey = 1,
show = False,
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.dimension == []: parser.error('dimension of data array missing')
if options.pixelsize > 1: (options.pixelsizex,options.pixelsizey) = [options.pixelsize]*2
# --- loop over input files -------------------------------------------------------------------------
for name in filenames:
try:
table = damask.ASCIItable(name = name, labeled = options.label is not None, readonly = True)
except IOError:
continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ process data ------------------------------------------
errors = []
missing_labels = table.data_readArray(options.label)
if len(missing_labels) > 0:
errors.append('column{} {} not found'.format('s' if len(missing_labels) > 1 else '',
', '.join(missing_labels)))
if table.label_dimension(options.label) != 3:
errors.append('column {} does not have dimension'.format(options.label))
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True) # close ASCII table file handles and delete output file
continue
# convert data to shape and arrange according to given options
if options.dimension != []: table.data = table.data.reshape(options.dimension[1],options.dimension[0],3)
if options.flipLR: table.data = np.fliplr(table.data)
if options.flipUD: table.data = np.flipud(table.data)
table.data = table.data.repeat(options.pixelsizex,axis=1).\
repeat(options.pixelsizey,axis=0)
table.data *= 1. if np.any(table.data > 1.0) else 255.0 # ensure 8 bit data range
(height,width,bands) = table.data.shape
damask.util.croak('image dimension: {0} x {1}'.format(width,height))
im = Image.fromarray(table.data.astype('uint8'), 'RGB').\
crop(( options.crop[0],
options.crop[2],
width -options.crop[1],
height-options.crop[3]))
# ------------------------------------------ output result -----------------------------------------
im.save(os.path.splitext(name)[0]+ \
('_'+options.label if options.label else '')+ \
'.png' if name else sys.stdout,
format = "PNG")
table.close() # close ASCII table
if options.show: im.show()

2
processing/post/DADF5_postResults.py
View File

@ -60,4 +60,4 @@ for filename in options.filenames:
os.mkdir(dirname,0o755)
file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0],
inc[3:].zfill(N_digits))
table.to_ASCII(os.path.join(dirname,file_out))
table.to_file(os.path.join(dirname,file_out))

2
processing/post/addCompatibilityMismatch.py
View File

@ -191,4 +191,4 @@ for name in filenames:
volumeMismatch.reshape(-1,1,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

2
processing/post/addCurl.py
View File

@ -55,4 +55,4 @@ for name in filenames:
curl.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape),order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

2
processing/post/addDerivative.py
View File

@ -71,4 +71,4 @@ for name in filenames:
derivative(table.get(options.coordinates),table.get(label)),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

4
processing/post/addDisplacement.py
View File

@ -60,7 +60,7 @@ for name in filenames:
table.add('fluct({}).{}'.format(options.f,options.pos),
damask.grid_filters.node_displacement_fluct(size,F).reshape(-1,3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt')
table.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt')
else:
table.add('avg({}).{}'.format(options.f,options.pos),
damask.grid_filters.cell_displacement_avg(size,F).reshape(-1,3,order='F'),
@ -68,4 +68,4 @@ for name in filenames:
table.add('fluct({}).{}'.format(options.f,options.pos),
damask.grid_filters.cell_displacement_fluct(size,F).reshape(-1,3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

2
processing/post/addDivergence.py
View File

@ -55,4 +55,4 @@ for name in filenames:
div.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)//3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

2
processing/post/addEuclideanDistance.py
View File

@ -184,4 +184,4 @@ for name in filenames:
distance[i,:],
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

2
processing/post/addGaussian.py
View File

@ -73,4 +73,4 @@ for name in filenames:
mode = 'wrap' if options.periodic else 'nearest'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

2
processing/post/addGradient.py
View File

@ -55,4 +55,4 @@ for name in filenames:
grad.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)*3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

4
processing/post/addIndexed.py
View File

@ -57,8 +57,8 @@ for name in filenames:
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
indexedTable = damask.Table.from_ASCII(options.asciitable)
idx = np.reshape(table.get(options.index).astype(int) + options.offset,(-1))-1
for data in options.label:
table.add(data+'_addIndexed',indexedTable.get(data)[idx],scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

2
processing/post/addOrientations.py
View File

@ -147,4 +147,4 @@ for name in filenames:
if 'axisangle' in options.output:
table.add('om({})'.format(label),o.as_axisangle(options.degrees), scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

2
processing/post/addSchmidfactors.py
View File

@ -189,4 +189,4 @@ for name in filenames:
for i,label in enumerate(labels):
table.add(label,S[:,i],scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

98
processing/post/averageDown.py
View File

@ -1,98 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import scipy.ndimage
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 = """
Average each data block of size 'packing' into single values thus reducing the former grid to grid/packing.
""", version = scriptID)
parser.add_option('-c','--coordinates',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'column label of coordinates [%default]')
parser.add_option('-p','--packing',
dest = 'packing',
type = 'int', nargs = 3, metavar = 'int int int',
help = 'size of packed group [%default]')
parser.add_option('--shift',
dest = 'shift',
type = 'int', nargs = 3, metavar = 'int int int',
help = 'shift vector of packing stencil [%default]')
parser.add_option('-g', '--grid',
dest = 'grid',
type = 'int', nargs = 3, metavar = 'int int int',
help = 'grid in x,y,z (optional)')
parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'size in x,y,z (optional)')
parser.set_defaults(pos = 'pos',
packing = (2,2,2),
shift = (0,0,0),
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
packing = np.array(options.packing,dtype = int)
shift = np.array(options.shift, dtype = int)
prefix = 'averagedDown{}x{}x{}_'.format(*packing)
if any(shift != 0): prefix += 'shift{:+}{:+}{:+}_'.format(*shift)
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.grid is None or options.size is None):
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
else:
grid = np.array(options.grid,'i')
size = np.array(options.size,'d')
packing = np.where(grid == 1,1,packing) # reset packing to 1 where grid==1
shift = np.where(grid == 1,0,shift) # reset shift to 0 where grid==1
packedGrid = np.maximum(np.ones(3,'i'),grid//packing)
data = table.data.values.reshape(tuple(grid)+(-1,),order = 'F')
averagedDown = scipy.ndimage.filters.uniform_filter( \
np.roll(
np.roll(
np.roll(data,
-shift[0],axis = 0),
-shift[1],axis = 1),
-shift[2],axis = 2),
size = list(packing) + [1],
mode = 'wrap',
origin = list(-(packing//2)) + [0])\
[::packing[0],::packing[1],::packing[2],:].reshape((packedGrid.prod(),-1),order = 'F')
table = damask.Table(averagedDown,table.shapes,table.comments)
coords = damask.grid_filters.cell_coord0(packedGrid,size,shift/packedGrid*size+origin)
table.set(options.pos, coords.reshape(-1,3,order='F'))
outname = os.path.join(os.path.dirname(name),prefix+os.path.basename(name))
table.to_ASCII(sys.stdout if name is None else outname)

72
processing/post/blowUp.py
View File

@ -1,72 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
from scipy import ndimage
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 = """
Blows up each value to a surrounding data block of size 'packing' thus increasing the former resolution
to resolution*packing.
""", version = scriptID)
parser.add_option('-c','--coordinates',
dest = 'pos', metavar = 'string',
help = 'column label of coordinates [%default]')
parser.add_option('-p','--packing',
dest = 'packing', type = 'int', nargs = 3, metavar = 'int int int',
help = 'dimension of packed group [%default]')
parser.add_option('-g','--grid',
dest = 'resolution', type = 'int', nargs = 3, metavar = 'int int int',
help = 'grid in x,y,z (optional)')
parser.add_option('-s','--size',
dest = 'dimension', type = 'float', nargs = 3, metavar = 'int int int',
help = 'size in x,y,z (optional)')
parser.set_defaults(pos = 'pos',
packing = (2,2,2),
grid = (0,0,0),
size = (0.0,0.0,0.0),
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
options.packing = np.array(options.packing)
prefix = 'blowUp{}x{}x{}_'.format(*options.packing)
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)
grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
packing = np.array(options.packing,'i')
outSize = grid*packing
data = table.data.values.reshape(tuple(grid)+(-1,),order='F')
blownUp = ndimage.interpolation.zoom(data,tuple(packing)+(1,),order=0,mode='nearest').reshape(outSize.prod(),-1,order='F')
table = damask.Table(blownUp,table.shapes,table.comments)
coords = damask.grid_filters.cell_coord0(outSize,size,origin)
table.set(options.pos,coords.reshape(-1,3,order='F'))
table.set('elem',np.arange(1,outSize.prod()+1))
outname = os.path.join(os.path.dirname(name),prefix+os.path.basename(name))
table.to_ASCII(sys.stdout if name is None else outname)

2
processing/post/permuteData.py
View File

@ -58,4 +58,4 @@ for name in filenames:
rng.shuffle(uniques)
table.set(label,uniques[inverse], scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

198
processing/post/vtk2ang.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
import os
import sys
@ -11,54 +11,50 @@ import vtk
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# -----------------------------
def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize):
"""Returns header for ang file step size in micrometer"""
return '\n'.join([ \
'# TEM_PIXperUM 1.000000', \
'# x-star 1.000000', \
'# y-star 1.000000', \
'# z-star 1.000000', \
'# WorkingDistance 18.000000', \
'#', \
'# Phase 1', \
'# MaterialName XX', \
'# Formula XX', \
'# Info', \
'# Symmetry 43', \
'# LatticeConstants 2.870 2.870 2.870 90.000 90.000 90.000', \
'# NumberFamilies 1', \
'# hklFamilies 1 1 0 1 0.000000 1', \
'# Categories 0 0 0 0 0 ', \
'#', \
'# GRID: SqrGrid', \
'# XSTEP: ' + str(stepsize*1e6), \
'# YSTEP: ' + str(stepsize*1e6), \
'# NCOLS_ODD: ' + str(sizeFastIndex), \
'# NCOLS_EVEN: ' + str(sizeFastIndex), \
'# NROWS: ' + str(sizeSlowIndex), \
'#', \
'# OPERATOR: ' + string.replace('$Id$','\n','\\n'), \
'#', \
'# SAMPLEID: %s'%filename, \
'#', \
'# SCANID: ', \
'#', \
"""Returns header for ang file step size in micrometer."""
return '\n'.join([
'# TEM_PIXperUM 1.000000',
'# x-star 1.000000',
'# y-star 1.000000',
'# z-star 1.000000',
'# WorkingDistance 18.000000',
'#',
'# Phase 1',
'# MaterialName XX',
'# Formula XX',
'# Info',
'# Symmetry 43',
'# LatticeConstants 2.870 2.870 2.870 90.000 90.000 90.000',
'# NumberFamilies 1',
'# hklFamilies 1 1 0 1 0.000000 1',
'# Categories 0 0 0 0 0 ',
'#',
'# GRID: SqrGrid',
'# XSTEP: ' + str(stepsize*1e6),
'# YSTEP: ' + str(stepsize*1e6),
'# NCOLS_ODD: ' + str(sizeFastIndex),
'# NCOLS_EVEN: ' + str(sizeFastIndex),
'# NROWS: ' + str(sizeSlowIndex),
'#',
'# OPERATOR: ' + string.replace('$Id$','\n','\\n'),
'#',
'# SAMPLEID: {}'.format(filename),
'#',
'# SCANID: ',
'#',
]) + '\n'
# -----------------------------
def positiveRadians(angle):
"""Returns positive angle in radians from angle in degrees"""
angle = math.radians(float(angle))
while angle < 0.0:
angle += 2.0 * math.pi
return angle
"""Returns positive angle in radians from angle in degrees."""
return math.radians(float(angle)) % (2.*math.pi)
# -----------------------------
@ -67,7 +63,7 @@ def getDataLine(angles,x,y,validData=True):
Returns string of one line in ang file.
Convention in ang file: y coordinate comes first and is fastest index
positions in micrometer
positions in micrometer.
"""
info = {True: (9999.9, 1.0, 0,99999,0.0),
False: ( -1.0,-1.0,-1, -1,1.0)}
@ -75,18 +71,16 @@ def getDataLine(angles,x,y,validData=True):
%(tuple(map(positiveRadians,angles))+(y*1e6,x*1e6)+info[validData])
# --------------------------------------------------------------------
# MAIN FUNCTION STARTS HERE
# --------------------------------------------------------------------
parser = OptionParser(usage='%prog options [file[s]]', description = """
Builds a ang files from a vtk file.
""", version = scriptID)
parser.add_option('--disp','--displacement',dest='dispLabel',
parser.add_option('--disp','--displacement',dest='dispLabel',
metavar ='string',
help='label of displacements [%default]')
parser.add_option('--euler', dest='eulerLabel', nargs=3,
@ -110,11 +104,6 @@ parser.add_option('-s','--scale', dest='scale', type='float',
parser.add_option('-r','--resolution', dest='resolution', type='float',
metavar ='float',
help='scaling factor for resolution [%default]')
parser.add_option('--hex','--hexagonal', dest='hexagonal', action='store_true',
help='use in plane hexagonal grid')
parser.add_option('--interpolation', dest='interpolation', type='int',
metavar='float',
help='number of points for linear interpolation [%default]')
parser.add_option('--verbose', dest='verbose', action='store_true',
help='verbose mode')
parser.add_option('--visualize', dest='visualize', action='store_true',
@ -122,7 +111,6 @@ parser.add_option('--visualize', dest='visualize', action='store_true
parser.set_defaults(dispLabel = 'displacement')
parser.set_defaults(eulerLabel = ['1_1_eulerangles','1_2_eulerangles','1_3_eulerangles'])
parser.set_defaults(hexagonal = False)
parser.set_defaults(normal = [0.0,0.0,-1.0])
parser.set_defaults(up = [0.0,1.0,0.0])
parser.set_defaults(Nslices = 1)
@ -130,7 +118,6 @@ parser.set_defaults(distance = 0.0)
parser.set_defaults(scale = 1.0)
parser.set_defaults(resolution = 1.0)
parser.set_defaults(dispScaling = 1.0)
parser.set_defaults(interpolation = 1)
parser.set_defaults(verbose = False)
parser.set_defaults(visualize = False)
(options,filenames) = parser.parse_args()
@ -153,35 +140,26 @@ if np.dot(np.array(options.normal),np.array(options.up)) > 1e-3:
parser.error('normal vector and up vector have to be orthogonal')
# check for options that are not yet implemented
if options.interpolation > 1:
parser.error('interpolation not yet supported')
if options.hexagonal:
parser.error('hexagonal grid not yet supported')
#--- ITERATE OVER FILES AND PROCESS THEM
for filename in filenames:
if options.verbose: sys.stdout.write("\nREADING VTK FILE\n")
# Read the source file
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.Update()
reader.Update()
undeformedMesh = reader.GetOutput()
# Get euler angles from cell data
if options.verbose: sys.stdout.write("\nGETTING EULER ANGLES\n")
angles = {}
for i in range(reader.GetNumberOfScalarsInFile()):
scalarName = reader.GetScalarsNameInFile(i)
for i in range(undeformedMesh.GetPointData().GetNumberOfArrays()):
scalarName = undeformedMesh.GetPointData().GetArrayName(i)
if scalarName in options.eulerLabel:
angles[scalarName] = undeformedMesh.GetCellData().GetScalars(scalarName)
if options.verbose: sys.stdout.write(" found scalar with name %s\n"%scalarName)
@ -189,14 +167,14 @@ for filename in filenames:
for label in options.eulerLabel:
if label not in angles.keys():
parser.error('Could not find scalar data with name %s'%label)
# Get deformed mesh
if options.verbose: sys.stdout.write("\nDEFORM MESH\n")
warpVector = vtk.vtkWarpVector()
undeformedMesh.GetPointData().SetActiveVectors(options.dispLabel)
warpVector.SetInput(undeformedMesh)
warpVector.SetInputData(undeformedMesh)
warpVector.Update()
deformedMesh = warpVector.GetOutput()
box = deformedMesh.GetBounds() # bounding box in mesh system
@ -208,24 +186,24 @@ for filename in filenames:
# Get cell centers of deformed mesh (position of ips)
if options.verbose: sys.stdout.write("\nGETTING CELL CENTERS OF DEFORMED MESH\n")
cellCenter = vtk.vtkCellCenters()
cellCenter.SetVertexCells(0) # do not generate vertex cells, just points
cellCenter.SetInput(deformedMesh)
cellCenter.SetInputData(deformedMesh)
cellCenter.Update()
meshIPs = cellCenter.GetOutput()
# Get outer surface of deformed mesh
if options.verbose: sys.stdout.write("\nGETTING OUTER SURFACE OF DEFORMED MESH\n")
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInput(deformedMesh)
surfaceFilter.SetInputData(deformedMesh)
surfaceFilter.Update()
surface = surfaceFilter.GetOutput()
# Get coordinate system for ang files
# z-vector is normal to slices
# x-vector corresponds to the up-direction
@ -248,11 +226,11 @@ for filename in filenames:
# Get bounding box in rotated system (x,y,z)
if options.verbose: sys.stdout.write("\nGETTING BOUNDING BOX IN ROTATED SYSTEM\n")
rotatedbox = [[np.inf,-np.inf] for i in range(3)] # bounding box in rotated TSL system
for n in range(8): # loop over eight vertices of mesh bounding box
vert = np.array([box[0+(n/1)%2],
box[2+(n/2)%2],
box[4+(n/4)%2]]) # vertex in mesh system
rotatedbox = [[np.inf,-np.inf] for i in range(3)] # bounding box in rotated TSL system
for n in range(8): # loop over eight vertices of mesh bounding box
vert = np.array([box[0+(n//1)%2],
box[2+(n//2)%2],
box[4+(n//4)%2]]) # vertex in mesh system
rotatedvert = np.dot(R,vert) # vertex in rotated system
for i in range(3):
rotatedbox[i][0] = min(rotatedbox[i][0],rotatedvert[i])
@ -274,7 +252,7 @@ for filename in filenames:
for i in range(2):
Npoints.extend([int(math.ceil(extent[i] / options.resolution))])
correction.extend([float(Npoints[i]) * options.resolution - extent[i]])
if options.distance > 0.0:
if options.distance > 0.0:
Npoints.extend([int(math.ceil(extent[2] / options.distance))])
correction.extend([float(Npoints[2]) * options.distance - extent[2]])
else:
@ -282,8 +260,8 @@ for filename in filenames:
correction.extend([0.0])
options.distance = extent[2] / float(options.Nslices)
for i in range(3):
rotatedbox[i][0] = rotatedbox[i][0] - 0.5 * correction[i]
rotatedbox[i][1] = rotatedbox[i][1] + 0.5 * correction[i]
rotatedbox[i][0] -= 0.5 * correction[i]
rotatedbox[i][1] += 0.5 * correction[i]
extent[i] = rotatedbox[i][1] - rotatedbox[i][0]
NpointsPerSlice = Npoints[0] * Npoints[1]
totalNpoints = NpointsPerSlice * Npoints[2]
@ -301,20 +279,20 @@ for filename in filenames:
if options.verbose: sys.stdout.write("\nGENERATING POINTS FOR POINT GRID")
points = vtk.vtkPoints()
for k in range(Npoints[2]):
for j in range(Npoints[0]):
for j in range(Npoints[0]):
for i in range(Npoints[1]): # y is fastest index
rotatedpoint = np.array([rotatedbox[0][0] + (float(j) + 0.5) * options.resolution,
rotatedbox[1][0] + (float(i) + 0.5) * options.resolution,
rotatedbox[2][0] + (float(k) + 0.5) * options.distance ]) # point in rotated system
rotatedbox[1][0] + (float(i) + 0.5) * options.resolution,
rotatedbox[2][0] + (float(k) + 0.5) * options.distance ]) # point in rotated system
point = np.dot(R.T,rotatedpoint) # point in mesh system
points.InsertNextPoint(list(point))
if options.verbose:
if options.verbose:
sys.stdout.write("\rGENERATING POINTS FOR POINT GRID %d%%" %(100*(Npoints[1]*(k*Npoints[0]+j)+i+1)/totalNpoints))
sys.stdout.flush()
if options.verbose:
if options.verbose:
sys.stdout.write("\n number of slices: %i\n"%Npoints[2])
sys.stdout.write(" slice spacing: %.8f\n"%options.distance)
if Npoints[2] > 1:
if Npoints[2] > 1:
sys.stdout.write(" number of points per slice: %i = %i rows * %i points in row\n"%(NpointsPerSlice,Npoints[0],Npoints[1]))
sys.stdout.write(" grid resolution: %.8f\n"%options.resolution)
@ -324,7 +302,7 @@ for filename in filenames:
vertex = vtk.vtkVertex()
vertex.GetPointIds().SetId(0,i) # each vertex consists of exactly one (index 0) point with ID "i"
vertices.InsertNextCell(vertex)
if options.verbose:
if options.verbose:
sys.stdout.write("\rGENERATING VERTICES FOR POINT GRID %d%%" %(100*(i+1)/totalNpoints))
sys.stdout.flush()
@ -357,34 +335,34 @@ for filename in filenames:
if enclosedPoints.IsInside(i):
NenclosedPoints += 1
# here one could use faster(?) "FindClosestPoint" if only first nearest neighbor required
kdTree.FindClosestNPoints(options.interpolation,pointgrid.GetPoint(i),ids)
for j in range(ids.GetNumberOfIds()):
kdTree.FindClosestNPoints(1,pointgrid.GetPoint(i),ids)
for j in range(ids.GetNumberOfIds()):
gridToMesh[-1].extend([ids.GetId(j)])
if options.verbose:
if options.verbose:
sys.stdout.write("\rBUILDING MAPPING OF GRID POINTS %d%%" %(100*(i+1)/totalNpoints))
sys.stdout.flush()
if options.verbose:
sys.stdout.write("\n Number of points inside mesh geometry %i\n"%NenclosedPoints)
sys.stdout.write(" Number of points outside mesh geometry %i\n"%(totalNpoints - NenclosedPoints))
# ITERATE OVER SLICES AND CREATE ANG FILE
if options.verbose:
if options.verbose:
sys.stdout.write("\nWRITING OUT ANG FILES\n")
sys.stdout.write(" scaling all length with %f\n"%options.scale)
x0,y0,z0 = np.dot(R,pointgrid.GetPoint(0)) # first point on slice defines origin
for sliceN in range(Npoints[2]):
# Open file and write header
angfilename = eval('"'+eval("'%%s_slice%%0%ii.ang'%(math.log10(Npoints[2])+1)")+'"%(os.path.splitext(filename)[0],sliceN+1)')
with open(angfilename,'w') as angfile:
if options.verbose: sys.stdout.write(" %s\n"%angfilename)
angfile.write(getHeader(filename,Npoints[1],Npoints[0],options.resolution*options.scale))
for i in range(sliceN*NpointsPerSlice,(sliceN+1)*NpointsPerSlice): # Iterate over points on slice
# Get euler angles of closest IDs
@ -397,26 +375,26 @@ for filename in filenames:
phi[-1].extend([angles[options.eulerLabel[k]].GetValue(IP)])
else:
phi = [[720,720,720]] # fake angles
# Interpolate Euler angle
# NOT YET IMPLEMENTED, simply take the nearest neighbors values
interpolatedPhi = phi[0]
# write data to ang file
x,y,z = np.dot(R,pointgrid.GetPoint(i)) # point in rotated TSL system
x -= x0 # first point on slice defines origin
y -= y0 # first point on slice defines origin
x -= x0 # first point on slice defines origin
y -= y0 # first point on slice defines origin
x *= options.scale
y *= options.scale
angfile.write(getDataLine(interpolatedPhi,x,y,enclosedPoints.IsInside(i)))
# Visualize slices
if options.visualize:
meshMapper = vtk.vtkDataSetMapper()
meshMapper.SetInput(surface)
@ -426,11 +404,11 @@ for filename in filenames:
meshActor.GetProperty().SetOpacity(0.2)
meshActor.GetProperty().SetColor(1.0,1.0,0)
meshActor.GetProperty().BackfaceCullingOn()
boxpoints = vtk.vtkPoints()
for n in range(8):
P = [rotatedbox[0][(n/1)%2],
rotatedbox[1][(n/2)%2],
rotatedbox[1][(n/2)%2],
rotatedbox[2][(n/4)%2]]
boxpoints.InsertNextPoint(list(np.dot(R.T,np.array(P))))
box = vtk.vtkHexahedron()
@ -469,7 +447,7 @@ for filename in filenames:
renderer.AddActor(boxActor)
renderer.AddActor(gridActor)
renderer.SetBackground(1,1,1)
renderWindow.Render()
renderWindowInteractor.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
renderWindowInteractor.Start()

135
processing/pre/geom_addPrimitive.py
View File

@ -1,135 +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 [geomfile(s)]', description = """
Inserts a primitive geometric object at a given position.
These objects can be boxes, cylinders, or ellipsoids.
""", version = scriptID)
parser.add_option('-c', '--center',
dest='center',
type='float', nargs = 3, metavar=' '.join(['float']*3),
help='a,b,c origin of primitive %default')
parser.add_option('-d', '--dimension',
dest='dimension',
type='float', nargs = 3, metavar=' '.join(['float']*3),
help='a,b,c extension of hexahedral box')
parser.add_option('-e', '--exponent',
dest='exponent',
type='float', nargs = 3, metavar=' '.join(['float']*3),
help='i,j,k exponents for axes: '+
'0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1), '+
'1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1), '+
'large values produce boxes, negative turn concave.')
parser.add_option('-f', '--fill',
dest='fill',
type='float', metavar = 'int',
help='microstructure index to fill primitive, defaults to max microstructure index + 1')
parser.add_option('-q', '--quaternion',
dest='quaternion',
type='float', nargs = 4, metavar=' '.join(['float']*4),
help = 'rotation of primitive as quaternion')
parser.add_option('-a', '--angleaxis',
dest='angleaxis',
type=float, nargs = 4, metavar=' '.join(['float']*4),
help = 'axis and angle to rotate primitive')
parser.add_option( '--degrees',
dest='degrees',
action='store_true',
help = 'angle is given in degrees')
parser.add_option( '--nonperiodic',
dest='periodic',
action='store_false',
help = 'wrap around edges')
parser.add_option( '--realspace',
dest='realspace',
action='store_true',
help = '-c and -d span [origin,origin+size] instead of [0,grid] coordinates')
parser.add_option( '--invert',
dest='inside',
action='store_false',
help = 'invert the volume filled by the primitive (inside/outside)')
parser.set_defaults(center = (.0,.0,.0),
degrees = False,
exponent = (20,20,20), # box shape by default
periodic = True,
realspace = False,
inside = True,
)
(options, filenames) = parser.parse_args()
if options.dimension is None:
parser.error('no dimension specified.')
if [options.angleaxis,options.quaternion].count(None) == 0:
parser.error('more than one rotation specified.')
if options.angleaxis is not None:
rotation = damask.Rotation.from_axis_angle(np.array(options.angleaxis),options.degrees,normalise=True)
elif options.quaternion is not None:
rotation = damask.Rotation.from_quaternion(options.quaternion)
else:
rotation = damask.Rotation()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid = geom.get_grid()
size = geom.get_size()
# scale to box of size [1.0,1.0,1.0]
if options.realspace:
center = (np.array(options.center) - geom.get_origin())/size
r = np.array(options.dimension)/size/2.0
else:
center = (np.array(options.center) + 0.5)/grid
r = np.array(options.dimension)/grid/2.0
if np.any(center<0.0) or np.any(center>=1.0): print('error')
offset = np.ones(3)*0.5 if options.periodic else center
mask = np.full(grid,False)
# High exponents can cause underflow & overflow - okay here, just compare to 1, so +infinity and 0 are fine
np.seterr(over='ignore', under='ignore')
e = 2.0**np.array(options.exponent)
for x in range(grid[0]):
for y in range(grid[1]):
for z in range(grid[2]):
coords = np.array([x+0.5,y+0.5,z+0.5])/grid
mask[x,y,z] = np.sum(np.abs((rotation*(coords-offset))/r)**e) < 1
if options.periodic:
shift = ((offset-center)*grid).astype(int)
mask = np.roll(mask,shift,(0,1,2))
if options.inside: mask = np.logical_not(mask)
fill = np.nanmax(geom.microstructure)+1 if options.fill is None else options.fill
damask.util.croak(geom.update(np.where(mask,geom.microstructure,fill)))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

2
processing/pre/geom_fromDREAM3D.py
View File

@ -154,4 +154,4 @@ for name in filenames:
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
geom.to_file(os.path.splitext(name)[0]+'.geom',pack=False)
geom.to_file(os.path.splitext(name)[0]+'.geom',format='ASCII',pack=False)

2
processing/pre/geom_fromMinimalSurface.py
View File

@ -89,4 +89,4 @@ geom=damask.Geom(microstructure,options.size,
comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
damask.util.croak(geom)
geom.to_file(sys.stdout if name is None else name,pack=False)
geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)

2
processing/pre/geom_fromOsteonGeometry.py
View File

@ -142,4 +142,4 @@ geom = damask.Geom(microstructure.reshape(grid),
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
geom.to_file(sys.stdout if name is None else name,pack=False)
geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)

3
processing/pre/geom_fromTable.py
View File

@ -105,4 +105,5 @@ for name in filenames:
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',
format='ASCII',pack=False)

3
processing/pre/geom_fromVoronoiTessellation.py
View File

@ -228,4 +228,5 @@ for name in filenames:
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)
geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',
format='ASCII',pack=False)

4
processing/pre/geom_grainGrowth.py
View File

@ -169,7 +169,7 @@ for name in filenames:
# undo any changes involving immutable microstructures
microstructure = np.where(immutable, microstructure_original,microstructure)
damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]))
geom=geom.duplicate(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)
geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)

85
processing/pre/geom_vicinityOffset.py
View File

@ -1,85 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
from scipy import ndimage
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def taintedNeighborhood(stencil,trigger=[],size=1):
me = stencil[stencil.shape[0]//2]
if len(trigger) == 0:
return np.any(stencil != me)
if me in trigger:
trigger = set(trigger)
trigger.remove(me)
trigger = list(trigger)
return np.any(np.in1d(stencil,np.array(trigger)))
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Offset microstructure index for points which see a microstructure different from themselves
(or listed as triggers) within a given (cubic) vicinity, i.e. within the region close to a grain/phase boundary.
""", version = scriptID)
parser.add_option('-v', '--vicinity',
dest = 'vicinity',
type = 'int', metavar = 'int',
help = 'voxel distance checked for presence of other microstructure [%default]')
parser.add_option('-o', '--offset',
dest='offset',
type = 'int', metavar = 'int',
help='offset (positive or negative) to tag microstructure indices, defaults to max microstructure index')
parser.add_option('-t', '--trigger',
dest = 'trigger',
action = 'extend', metavar = '<int LIST>',
help = 'list of microstructure indices triggering a change')
parser.add_option('-n', '--nonperiodic',
dest = 'mode',
action = 'store_const', const = 'nearest',
help = 'assume geometry to be non-periodic')
parser.set_defaults(vicinity = 1,
trigger = [],
mode = 'wrap',
)
(options, filenames) = parser.parse_args()
options.trigger = np.array(options.trigger, dtype=int)
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
offset = np.nanmax(geom.microstructure) if options.offset is None else options.offset
damask.util.croak(geom.update(np.where(ndimage.filters.generic_filter(
geom.microstructure,
taintedNeighborhood,
size=1+2*options.vicinity,mode=options.mode,
extra_arguments=(),
extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
geom.microstructure + offset,geom.microstructure)))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

11
processing/pre/mentat_pbcOnBoxMesh.py
View File

@ -1,9 +1,14 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import sys,os,re,time,tempfile
import numpy as np
import sys
import os
import re
import time
import tempfile
from optparse import OptionParser
import numpy as np
import damask
sys.path.append(str(damask.solver.Marc().library_path))

12
processing/pre/mentat_spectralBox.py
View File

@ -20,7 +20,6 @@ def outMentat(cmd,locals):
py_mentat.py_send(cmd)
else:
py_mentat.py_send(cmd)
return
#-------------------------------------------------------------------------------------------------
def outFile(cmd,locals,dest):
@ -31,7 +30,6 @@ def outFile(cmd,locals,dest):
dest.write(cmd+'\n')
else:
dest.write(cmd+'\n')
return
#-------------------------------------------------------------------------------------------------
def output(cmds,locals,dest):
@ -43,8 +41,6 @@ def output(cmds,locals,dest):
outMentat(str(cmd),locals)
else:
outFile(str(cmd),locals,dest)
return
#-------------------------------------------------------------------------------------------------
@ -105,7 +101,7 @@ def mesh(r,d):
#-------------------------------------------------------------------------------------------------
def material():
cmds = [\
return [\
"*new_mater standard",
"*mater_option general:state:solid",
"*mater_option structural:type:hypo_elast",
@ -119,12 +115,10 @@ def material():
"all_existing",
]
return cmds
#-------------------------------------------------------------------------------------------------
def geometry():
cmds = [\
return [\
"*geometry_type mech_three_solid",
# "*geometry_option red_integ_capacity:on",
"*add_geometry_elements",
@ -134,8 +128,6 @@ def geometry():
"all_existing",
]
return cmds
#-------------------------------------------------------------------------------------------------
def initial_conditions(homogenization,microstructures):

2
processing/pre/seeds_fromDistribution.py
View File

@ -90,7 +90,7 @@ class myThread (threading.Thread):
direction[i]*=2.
i+= 1
perturbedSeedsTable.set('pos',coords)
perturbedSeedsTable.to_ASCII(perturbedSeedsVFile)
perturbedSeedsTable.to_file(perturbedSeedsVFile)
#--- do tesselation with perturbed seed file ------------------------------------------------------
perturbedGeomVFile.close()

4
processing/pre/seeds_fromGeom.py
View File

@ -65,5 +65,5 @@ for name in filenames:
table = damask.Table(seeds[mask],{'pos':(3,)},comments)
table.add('microstructure',microstructure[mask])
table.to_ASCII(sys.stdout if name is None else \
os.path.splitext(name)[0]+'.seeds')
table.to_file(sys.stdout if name is None else \
os.path.splitext(name)[0]+'.seeds')

4
processing/pre/seeds_fromPokes.py
View File

@ -92,5 +92,5 @@ for name in filenames:
table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments)
table.set('microstructure',table.get('microstructure').astype(np.int))
table.to_ASCII(sys.stdout if name is None else \
os.path.splitext(name)[0]+'_poked_{}.seeds'.format(options.N))
table.to_file(sys.stdout if name is None else \
os.path.splitext(name)[0]+f'_poked_{options.N}.seeds')

2
processing/pre/seeds_fromRandom.py
View File

@ -162,4 +162,4 @@ for name in filenames:
else np.random.normal(loc = options.mean, scale = options.sigma, size = options.N)
table.add('weight',weights)
table.to_ASCII(sys.stdout if name is None else name)
table.to_file(sys.stdout if name is None else name)

1
python/.coveragerc
View File

@ -2,4 +2,3 @@
omit = tests/*
damask/_asciitable.py
damask/_test.py
damask/config/*

1
python/damask/__init__.py
View File

@ -24,5 +24,4 @@ from . import solver # noqa
Environment = _
from ._asciitable import ASCIItable # noqa
from ._test import Test # noqa
from .config import Material # noqa
from .util import extendableOption # noqa

54
python/damask/_colormap.py
View File

@ -8,8 +8,9 @@ if os.name == 'posix' and 'DISPLAY' not in os.environ:
mpl.use('Agg')
import matplotlib.pyplot as plt
from matplotlib import cm
from PIL import Image
import damask
from . import util
from . import Table
_eps = 216./24389.
@ -50,7 +51,7 @@ class Colormap(mpl.colors.ListedColormap):
Color definition for minimum value.
high : numpy.ndarray of shape (3)
Color definition for maximum value.
N : integer, optional
N : int, optional
The number of color quantization levels. Defaults to 256.
name : str, optional
The name of the colormap. Defaults to `DAMASK colormap`.
@ -161,6 +162,47 @@ class Colormap(mpl.colors.ListedColormap):
print(' '+', '.join(cat[1]))
def shade(self,field,bounds=None,gap=None):
"""
Generate PIL image of 2D field using colormap.
Parameters
----------
field : numpy.array of shape(:,:)
Data to be shaded.
bounds : iterable of len(2), optional
Colormap value range (low,high).
gap : field.dtype, optional
Transparent value. NaN will always be rendered transparent.
Returns
-------
PIL.Image
RGBA image of shaded data.
"""
N = len(self.colors)
mask = np.logical_not(np.isnan(field) if gap is None else \
np.logical_or (np.isnan(field), field == gap)) # mask NaN (and gap if present)
lo,hi = (field[mask].min(),field[mask].max()) if bounds is None else \
(min(bounds[:2]),max(bounds[:2]))
delta,avg = hi-lo,0.5*(hi+lo)
if delta * 1e8 <= avg: # delta is similar to numerical noise
hi,lo = hi+0.5*avg,lo-0.5*avg # extend range to have actual data centered within
return Image.fromarray(
(np.dstack((
self.colors[(np.round(np.clip((field-lo)/(hi-lo),0.0,1.0)*(N-1))).astype(np.uint16),:3],
mask.astype(float)
)
)*255
).astype(np.uint8),
mode='RGBA')
def show(self,aspect=10,vertical=False):
"""Show colormap as matplotlib figure."""
fig = plt.figure(figsize=(5/aspect,5) if vertical else (5,5/aspect))
@ -238,7 +280,7 @@ class Colormap(mpl.colors.ListedColormap):
colors+=[i]+c
out = [{
'Creator':f'damask.Colormap v{damask.version}',
'Creator':util.execution_stamp('Colormap'),
'ColorSpace':'RGB',
'Name':colormap.name,
'DefaultMap':True,
@ -254,13 +296,13 @@ class Colormap(mpl.colors.ListedColormap):
def _export_ASCII(colormap,fhandle=None):
"""Write colormap to ASCII table."""
labels = {'RGBA':4} if colormap.colors.shape[1] == 4 else {'RGB': 3}
t = Table(colormap.colors,labels,f'Creator: damask.Colormap v{damask.version}')
t = Table(colormap.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
if fhandle is None:
with open(colormap.name.replace(' ','_')+'.txt', 'w') as f:
t.to_ASCII(f,True)
t.to_file(f,new_style=True)
else:
t.to_ASCII(fhandle,True)
t.to_file(fhandle,new_style=True)
@staticmethod
def _export_GOM(colormap,fhandle=None):

674
python/damask/_geom.py
View File

@ -1,12 +1,14 @@
import sys
from io import StringIO
import copy
import multiprocessing
from io import StringIO
from functools import partial
import numpy as np
from scipy import ndimage,spatial
import damask
from . import environment
from . import Rotation
from . import VTK
from . import util
from . import grid_filters
@ -22,15 +24,15 @@ class Geom:
Parameters
----------
microstructure : numpy.ndarray
microstructure array (3D)
Microstructure array (3D)
size : list or numpy.ndarray
physical size of the microstructure in meter.
Physical size of the microstructure in meter.
origin : list or numpy.ndarray, optional
physical origin of the microstructure in meter.
homogenization : integer, optional
homogenization index.
Physical origin of the microstructure in meter.
homogenization : int, optional
Homogenization index.
comments : list of str, optional
comments lines.
Comment lines.
"""
self.set_microstructure(microstructure)
@ -43,74 +45,91 @@ class Geom:
def __repr__(self):
"""Basic information on geometry definition."""
return util.srepr([
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)}',
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'# materialpoints: {self.N_microstructure}',
f'max materialpoint: {np.nanmax(self.microstructure)}',
])
def update(self,microstructure=None,size=None,origin=None,rescale=False):
def __copy__(self):
"""Copy geometry."""
return copy.deepcopy(self)
def copy(self):
"""Copy geometry."""
return self.__copy__()
def duplicate(self,microstructure=None,size=None,origin=None,comments=None,autosize=False):
"""
Update microstructure and size.
Create a duplicate having updated microstructure, size, and origin.
Parameters
----------
microstructure : numpy.ndarray, optional
microstructure array (3D).
Microstructure array (3D).
size : list or numpy.ndarray, optional
physical size of the microstructure in meter.
Physical size of the microstructure in meter.
origin : list or numpy.ndarray, optional
physical origin of the microstructure in meter.
rescale : bool, optional
ignore size parameter and rescale according to change of grid points.
Physical origin of the microstructure in meter.
comments : list of str, optional
Comment lines.
autosize : bool, optional
Ignore size parameter and rescale according to change of grid points.
"""
grid_old = self.get_grid()
size_old = self.get_size()
origin_old = self.get_origin()
unique_old = self.N_microstructure
max_old = np.nanmax(self.microstructure)
if size is not None and autosize:
raise ValueError('Auto-sizing conflicts with explicit size parameter.')
if size is not None and rescale:
raise ValueError('Either set size explicitly or rescale automatically')
grid_old = self.get_grid()
dup = self.copy()
dup.set_microstructure(microstructure)
dup.set_origin(origin)
self.set_microstructure(microstructure)
self.set_origin(origin)
if comments is not None:
dup.set_comments(comments)
if size is not None:
self.set_size(size)
elif rescale:
self.set_size(self.get_grid()/grid_old*self.size)
dup.set_size(size)
elif autosize:
dup.set_size(dup.get_grid()/grid_old*self.get_size())
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(f'grid a b c: {util.srepr(self.get_grid()," x ")}'))
return dup
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(f'size x y z: {util.srepr(self.get_size()," x ")}'))
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(f'origin x y z: {util.srepr(self.get_origin()," ")}'))
def diff(self,other):
"""
Report property differences of self relative to other.
message.append(f'homogenization: {self.get_homogenization()}')
Parameters
----------
other : Geom
Geometry to compare self against.
message.append(f'# microstructures: {unique_old}')
if unique_old != self.N_microstructure:
message[-1] = util.delete(message[-1])
message.append(util.emph(f'# microstructures: {self.N_microstructure}'))
"""
message = []
if np.any(other.get_grid() != self.get_grid()):
message.append(util.delete(f'grid a b c: {util.srepr(other.get_grid()," x ")}'))
message.append(util.emph( f'grid a b c: {util.srepr( self.get_grid()," x ")}'))
message.append(f'max microstructure: {max_old}')
if max_old != np.nanmax(self.microstructure):
message[-1] = util.delete(message[-1])
message.append(util.emph(f'max microstructure: {np.nanmax(self.microstructure)}'))
if np.any(other.get_size() != self.get_size()):
message.append(util.delete(f'size x y z: {util.srepr(other.get_size()," x ")}'))
message.append(util.emph( f'size x y z: {util.srepr( self.get_size()," x ")}'))
if np.any(other.get_origin() != self.get_origin()):
message.append(util.delete(f'origin x y z: {util.srepr(other.get_origin()," ")}'))
message.append(util.emph( f'origin x y z: {util.srepr( self.get_origin()," ")}'))
if other.N_microstructure != self.N_microstructure:
message.append(util.delete(f'# materialpoints: {other.N_microstructure}'))
message.append(util.emph( f'# materialpoints: { self.N_microstructure}'))
if np.nanmax(other.microstructure) != np.nanmax(self.microstructure):
message.append(util.delete(f'max materialpoint: {np.nanmax(other.microstructure)}'))
message.append(util.emph( f'max materialpoint: {np.nanmax( self.microstructure)}'))
return util.return_message(message)
@ -122,7 +141,7 @@ class Geom:
Parameters
----------
comments : list of str
new comments.
All comments.
"""
self.comments = []
@ -136,7 +155,7 @@ class Geom:
Parameters
----------
comments : list of str
new comments.
New comments.
"""
self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
@ -146,20 +165,32 @@ class Geom:
"""
Replace the existing microstructure representation.
The complete microstructure is replaced (indcluding grid definition),
unless a masked array is provided in which case the grid dimensions
need to match and masked entries are not replaced.
Parameters
----------
microstructure : numpy.ndarray
microstructure array (3D).
microstructure : numpy.ndarray or numpy.ma.core.MaskedArray of shape (:,:,:)
Microstructure indices.
"""
if microstructure is not None:
if len(microstructure.shape) != 3:
raise ValueError(f'Invalid microstructure shape {microstructure.shape}')
elif microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
raise TypeError(f'Invalid microstructue data type {microstructure.dtype}')
if isinstance(microstructure,np.ma.core.MaskedArray):
self.microstructure = np.where(microstructure.mask,
self.microstructure,microstructure.data)
else:
self.microstructure = np.copy(microstructure)
if self.microstructure.dtype in np.sctypes['float'] and \
np.all(self.microstructure == self.microstructure.astype(int).astype(float)):
self.microstructure = self.microstructure.astype(int)
if len(self.microstructure.shape) != 3:
raise ValueError(f'Invalid microstructure shape {microstructure.shape}')
elif self.microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
raise TypeError(f'Invalid microstructure data type {microstructure.dtype}')
def set_size(self,size):
"""
@ -168,13 +199,10 @@ class Geom:
Parameters
----------
size : list or numpy.ndarray
physical size of the microstructure in meter.
Physical size of the microstructure in meter.
"""
if size is None:
grid = np.asarray(self.microstructure.shape)
self.size = grid/np.max(grid)
else:
if size is not None:
if len(size) != 3 or any(np.array(size) <= 0):
raise ValueError(f'Invalid size {size}')
else:
@ -188,7 +216,7 @@ class Geom:
Parameters
----------
origin : list or numpy.ndarray
physical origin of the microstructure in meter
Physical origin of the microstructure in meter.
"""
if origin is not None:
@ -204,13 +232,13 @@ class Geom:
Parameters
----------
homogenization : integer
homogenization index
homogenization : int
Homogenization index.
"""
if homogenization is not None:
if not isinstance(homogenization,int) or homogenization < 1:
raise TypeError(f'Invalid homogenization {homogenization}')
raise TypeError(f'Invalid homogenization {homogenization}.')
else:
self.homogenization = homogenization
@ -255,16 +283,6 @@ class Geom:
return self.comments[:]
def get_header(self):
"""Return the full header (grid, size, origin, homogenization, 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(f'homogenization {self.get_homogenization()}')
return header
@staticmethod
def from_file(fname):
"""
@ -273,7 +291,7 @@ class Geom:
Parameters
----------
fname : str or file handle
geometry file to read.
Geometry file to read.
"""
try:
@ -282,13 +300,16 @@ class Geom:
f = fname
f.seek(0)
header_length,keyword = f.readline().split()[:2]
header_length = int(header_length)
content = f.readlines()
try:
header_length,keyword = f.readline().split()[:2]
header_length = int(header_length)
except ValueError:
header_length,keyword = (-1, 'invalid')
if not keyword.startswith('head') or header_length < 3:
raise TypeError('Header length information missing or invalid')
content = f.readlines()
comments = []
for i,line in enumerate(content[:header_length]):
items = line.split('#')[0].lower().strip().split()
@ -328,6 +349,27 @@ class Geom:
return Geom(microstructure.reshape(grid,order='F'),size,origin,homogenization,comments)
@staticmethod
def from_vtr(fname):
"""
Read a VTK rectilinear grid.
Parameters
----------
fname : str or or pathlib.Path
Geometry file to read.
Valid extension is .vtr, it will be appended if not given.
"""
v = VTK.from_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
comments = v.get_comments()
grid = np.array(v.vtk_data.GetDimensions())-1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
size = bbox[1] - bbox[0]
return Geom(v.get('materialpoint').reshape(grid,order='F'),size,bbox[0],comments=comments)
@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)
@ -339,16 +381,16 @@ class Geom:
Parameters
----------
grid : numpy.ndarray of shape (3)
number of grid points in x,y,z direction.
grid : int numpy.ndarray of shape (3)
Number of grid points in x,y,z direction.
size : list or numpy.ndarray of shape (3)
physical size of the microstructure in meter.
Physical size of the microstructure in meter.
seeds : numpy.ndarray of shape (:,3)
position of the seed points in meter. All points need to lay within the box.
Position of the seed points in meter. All points need to lay within the box.
weights : numpy.ndarray of shape (seeds.shape[0])
weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
periodic : Boolean, optional
perform a periodic tessellation. Defaults to True.
Perform a periodic tessellation. Defaults to True.
"""
if periodic:
@ -362,7 +404,7 @@ class Geom:
seeds_p = seeds
coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
pool = multiprocessing.Pool(processes = int(damask.environment.options['DAMASK_NUM_THREADS']))
pool = multiprocessing.Pool(processes = int(environment.options['DAMASK_NUM_THREADS']))
result = pool.map_async(partial(Geom._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
pool.close()
pool.join()
@ -374,8 +416,9 @@ class Geom:
else:
microstructure = microstructure.reshape(grid)
#ToDo: comments = 'geom.py:from_Laguerre_tessellation v{}'.format(version)
return Geom(microstructure+1,size,homogenization=1)
return Geom(microstructure+1,size,homogenization=1,
comments=util.execution_stamp('Geom','from_Laguerre_tessellation'),
)
@staticmethod
@ -385,115 +428,203 @@ class Geom:
Parameters
----------
grid : numpy.ndarray of shape (3)
number of grid points in x,y,z direction.
grid : int numpy.ndarray of shape (3)
Number of grid points in x,y,z direction.
size : list or numpy.ndarray of shape (3)
physical size of the microstructure in meter.
Physical size of the microstructure in meter.
seeds : numpy.ndarray of shape (:,3)
position of the seed points in meter. All points need to lay within the box.
Position of the seed points in meter. All points need to lay within the box.
periodic : Boolean, optional
perform a periodic tessellation. Defaults to True.
Perform a periodic tessellation. Defaults to True.
"""
coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
devNull,microstructure = KDTree.query(coords)
#ToDo: comments = 'geom.py:from_Voronoi_tessellation v{}'.format(version)
return Geom(microstructure.reshape(grid)+1,size,homogenization=1)
return Geom(microstructure.reshape(grid)+1,size,homogenization=1,
comments=util.execution_stamp('Geom','from_Voronoi_tessellation'),
)
def to_file(self,fname,pack=None):
def to_file(self,fname,format='vtr',pack=None):
"""
Writes a geom file.
Parameters
----------
fname : str or file handle
geometry file to write.
Geometry file to write.
format : {'vtr', 'ASCII'}, optional
File format, defaults to 'vtr'. Available formats are:
- vtr: VTK rectilinear grid file, extension '.vtr'.
- ASCII: Plain text file, extension '.geom'.
pack : bool, optional
compress geometry with 'x of y' and 'a to b'.
Compress ASCII geometry with 'x of y' and 'a to b'.
"""
header = self.get_header()
grid = self.get_grid()
def _to_ASCII(geom,fname,pack=None):
"""
Writes a geom file.
if pack is None:
plain = grid.prod()/self.N_microstructure < 250
Parameters
----------
geom : Geom object
Geometry to write.
fname : str or file handle
Geometry file to write.
pack : bool, optional
Compress geometry with 'x of y' and 'a to b'.
"""
header = [f'{len(geom.comments)+4} header'] + geom.comments
header.append('grid a {} b {} c {}'.format(*geom.get_grid()))
header.append('size x {} y {} z {}'.format(*geom.get_size()))
header.append('origin x {} y {} z {}'.format(*geom.get_origin()))
header.append(f'homogenization {geom.get_homogenization()}')
grid = geom.get_grid()
if pack is None:
plain = grid.prod()/geom.N_microstructure < 250
else:
plain = not pack
if plain:
format_string = '%g' if geom.microstructure.dtype in np.sctypes['float'] else \
'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(geom.microstructure)))))
np.savetxt(fname,
geom.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
header='\n'.join(header), fmt=format_string, comments='')
else:
try:
f = open(fname,'w')
except TypeError:
f = fname
compressType = None
former = start = -1
reps = 0
for current in geom.microstructure.flatten('F'):
if abs(current - former) == 1 and (start - current) == reps*(former - current):
compressType = 'to'
reps += 1
elif current == former and start == former:
compressType = 'of'
reps += 1
else:
if compressType is None:
f.write('\n'.join(header)+'\n')
elif compressType == '.':
f.write(f'{former}\n')
elif compressType == 'to':
f.write(f'{start} to {former}\n')
elif compressType == 'of':
f.write(f'{reps} of {former}\n')
compressType = '.'
start = current
reps = 1
former = current
if compressType == '.':
f.write(f'{former}\n')
elif compressType == 'to':
f.write(f'{start} to {former}\n')
elif compressType == 'of':
f.write(f'{reps} of {former}\n')
def _to_vtr(geom,fname=None):
"""
Generates vtk rectilinear grid.
Parameters
----------
geom : Geom object
Geometry to write.
fname : str, optional
Filename to write. If no file is given, a string is returned.
Valid extension is .vtr, it will be appended if not given.
"""
v = VTK.from_rectilinearGrid(geom.grid,geom.size,geom.origin)
v.add(geom.microstructure.flatten(order='F'),'materialpoint')
v.add_comments(geom.comments)
if fname:
v.to_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
else:
sys.stdout.write(v.__repr__())
if format.lower() == 'ascii':
return _to_ASCII(self,fname,pack)
elif format.lower() == 'vtr':
return _to_vtr(self,fname)
else:
plain = not pack
raise TypeError(f'Unknown format {format}.')
if plain:
format_string = '%g' if self.microstructure.dtype in np.sctypes['float'] else \
'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure)))))
np.savetxt(fname,
self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
header='\n'.join(header), fmt=format_string, comments='')
else:
try:
f = open(fname,'w')
except TypeError:
f = fname
compressType = None
former = start = -1
reps = 0
for current in self.microstructure.flatten('F'):
if abs(current - former) == 1 and (start - current) == reps*(former - current):
compressType = 'to'
reps += 1
elif current == former and start == former:
compressType = 'of'
reps += 1
else:
if compressType is None:
f.write('\n'.join(self.get_header())+'\n')
elif compressType == '.':
f.write(f'{former}\n')
elif compressType == 'to':
f.write(f'{start} to {former}\n')
elif compressType == 'of':
f.write(f'{reps} of {former}\n')
compressType = '.'
start = current
reps = 1
former = current
if compressType == '.':
f.write(f'{former}\n')
elif compressType == 'to':
f.write(f'{start} to {former}\n')
elif compressType == 'of':
f.write(f'{reps} of {former}\n')
def as_ASCII(self,pack=False):
"""Format geometry as human-readable ASCII."""
f = StringIO()
self.to_file(f,'ASCII',pack)
f.seek(0)
return ''.join(f.readlines())
def to_vtk(self,fname=None):
def add_primitive(self,dimension,center,exponent,
fill=None,R=Rotation(),inverse=False,periodic=True):
"""
Generates vtk file.
Inserts a primitive geometric object at a given position.
Parameters
----------
fname : str, optional
vtk file to write. If no file is given, a string is returned.
dimension : int or float numpy.ndarray of shape(3)
Dimension (diameter/side length) of the primitive. If given as
integers, grid point locations (cell centers) are addressed.
If given as floats, coordinates are addressed.
center : int or float numpy.ndarray of shape(3)
Center of the primitive. If given as integers, grid point
locations (cell centers) are addressed.
If given as floats, coordinates are addressed.
exponent : numpy.ndarray of shape(3) or float
Exponents for the three axis.
0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1)
1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1)
fill : int, optional
Fill value for primitive. Defaults to microstructure.max() + 1.
R : damask.Rotation, optional
Rotation of primitive. Defaults to no rotation.
inverse : Boolean, optional
Retain original microstructure within primitive and fill outside.
Defaults to False.
periodic : Boolean, optional
Repeat primitive over boundaries. Defaults to True.
"""
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
v.add(self.microstructure.flatten(order='F'),'microstructure')
# normalized 'radius' and center
r = np.array(dimension)/self.grid/2.0 if np.array(dimension).dtype in np.sctypes['int'] else \
np.array(dimension)/self.size/2.0
c = (np.array(center) + .5)/self.grid if np.array(center).dtype in np.sctypes['int'] else \
(np.array(center) - self.origin)/self.size
if fname:
v.write(fname)
else:
sys.stdout.write(v.__repr__())
coords = grid_filters.cell_coord0(self.grid,np.ones(3)) \
- ((np.ones(3)-(1./self.grid if np.array(center).dtype in np.sctypes['int'] else 0))*0.5 if periodic else c) # periodic center is always at CoG
coords_rot = R.broadcast_to(tuple(self.grid))@coords
with np.errstate(all='ignore'):
mask = np.where(np.sum(np.power(coords_rot/r,2.0**exponent),axis=-1) > 1.0,True,False)
def show(self):
"""Show raw content (as in file)."""
f=StringIO()
self.to_file(f)
f.seek(0)
return ''.join(f.readlines())
if periodic: # translate back to center
mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))
fill_ = np.full_like(self.microstructure,np.nanmax(self.microstructure)+1 if fill is None else fill)
ms = np.ma.MaskedArray(fill_,np.logical_not(mask) if inverse else mask)
return self.duplicate(ms,
comments=self.get_comments()+[util.execution_stamp('Geom','add_primitive')],
)
def mirror(self,directions,reflect=False):
@ -503,15 +634,14 @@ class Geom:
Parameters
----------
directions : iterable containing str
direction(s) along which the microstructure is mirrored. Valid entries are 'x', 'y', 'z'.
Direction(s) along which the microstructure is mirrored.
Valid entries are 'x', 'y', 'z'.
reflect : bool, optional
reflect (include) outermost layers.
Reflect (include) outermost layers. Defaults to False.
"""
valid = {'x','y','z'}
if not all(isinstance(d, str) for d in directions):
raise TypeError('Directions are not of type str.')
elif not set(directions).issubset(valid):
valid = ['x','y','z']
if not set(directions).issubset(valid):
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
limits = [None,None] if reflect else [-2,0]
@ -524,54 +654,88 @@ class Geom:
if 'x' in directions:
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
#ToDo: self.add_comments('geom.py:mirror v{}'.format(version)
return self.update(ms,rescale=True)
return self.duplicate(ms,
comments=self.get_comments()+[util.execution_stamp('Geom','mirror')],
autosize=True)
def scale(self,grid):
def flip(self,directions):
"""
Flip microstructure along given directions.
Parameters
----------
directions : iterable containing str
Direction(s) along which the microstructure is flipped.
Valid entries are 'x', 'y', 'z'.
"""
valid = ['x','y','z']
if not set(directions).issubset(valid):
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
ms = np.flip(self.microstructure, (valid.index(d) for d in directions if d in valid))
return self.duplicate(ms,
comments=self.get_comments()+[util.execution_stamp('Geom','flip')],
)
def scale(self,grid,periodic=True):
"""
Scale microstructure to new grid.
Parameters
----------
grid : numpy.ndarray of shape (3)
number of grid points in x,y,z direction.
Number of grid points in x,y,z direction.
periodic : Boolean, optional
Assume geometry to be periodic. Defaults to True.
"""
#ToDo: self.add_comments('geom.py:scale v{}'.format(version)
return self.update(
ndimage.interpolation.zoom(
self.microstructure,
grid/self.get_grid(),
output=self.microstructure.dtype,
order=0,
mode='nearest',
prefilter=False
)
)
return self.duplicate(ndimage.interpolation.zoom(
self.microstructure,
grid/self.get_grid(),
output=self.microstructure.dtype,
order=0,
mode=('wrap' if periodic else 'nearest'),
prefilter=False
),
comments=self.get_comments()+[util.execution_stamp('Geom','scale')],
)
def clean(self,stencil=3):
def clean(self,stencil=3,selection=None,periodic=True):
"""
Smooth microstructure by selecting most frequent index within given stencil at each location.
Parameters
----------
stencil : int, optional
size of smoothing stencil.
Size of smoothing stencil.
selection : list, optional
Field values that can be altered. Defaults to all.
periodic : Boolean, optional
Assume geometry to be periodic. Defaults to True.
"""
def mostFrequent(arr):
unique, inverse = np.unique(arr, return_inverse=True)
return unique[np.argmax(np.bincount(inverse))]
def mostFrequent(arr,selection=None):
me = arr[arr.size//2]
if selection is None or me in selection:
unique, inverse = np.unique(arr, return_inverse=True)
return unique[np.argmax(np.bincount(inverse))]
else:
return me
#ToDo: self.add_comments('geom.py:clean v{}'.format(version)
return self.update(ndimage.filters.generic_filter(
self.microstructure,
mostFrequent,
size=(stencil,)*3
).astype(self.microstructure.dtype)
)
return self.duplicate(ndimage.filters.generic_filter(
self.microstructure,
mostFrequent,
size=(stencil if selection is None else stencil//2*2+1,)*3,
mode=('wrap' if periodic else 'nearest'),
extra_keywords=dict(selection=selection),
).astype(self.microstructure.dtype),
comments=self.get_comments()+[util.execution_stamp('Geom','clean')],
)
def renumber(self):
@ -580,8 +744,9 @@ class Geom:
for i, oldID in enumerate(np.unique(self.microstructure)):
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
#ToDo: self.add_comments('geom.py:renumber v{}'.format(version)
return self.update(renumbered)
return self.duplicate(renumbered,
comments=self.get_comments()+[util.execution_stamp('Geom','renumber')],
)
def rotate(self,R,fill=None):
@ -591,9 +756,9 @@ class Geom:
Parameters
----------
R : damask.Rotation
rotation to apply to the microstructure.
Rotation to apply to the microstructure.
fill : int or float, optional
microstructure index to fill the corners. Defaults to microstructure.max() + 1.
Microstructure index to fill the corners. Defaults to microstructure.max() + 1.
"""
if fill is None: fill = np.nanmax(self.microstructure) + 1
@ -615,8 +780,11 @@ class Geom:
origin = self.origin-(np.asarray(microstructure_in.shape)-self.grid)*.5 * self.size/self.grid
#ToDo: self.add_comments('geom.py:rotate v{}'.format(version)
return self.update(microstructure_in,origin=origin,rescale=True)
return self.duplicate(microstructure_in,
origin=origin,
comments=self.get_comments()+[util.execution_stamp('Geom','rotate')],
autosize=True,
)
def canvas(self,grid=None,offset=None,fill=None):
@ -626,46 +794,96 @@ class Geom:
Parameters
----------
grid : numpy.ndarray of shape (3)
number of grid points in x,y,z direction.
Number of grid points in x,y,z direction.
offset : numpy.ndarray of shape (3)
offset (measured in grid points) from old to new microstructue[0,0,0].
Offset (measured in grid points) from old to new microstructure[0,0,0].
fill : int or float, optional
microstructure index to fill the corners. Defaults to microstructure.max() + 1.
Microstructure index to fill the background. Defaults to microstructure.max() + 1.
"""
if fill is None: fill = np.nanmax(self.microstructure) + 1
if offset is None: offset = 0
dtype = float if int(fill) != fill or self.microstructure.dtype==np.float else int
if fill is None: fill = np.nanmax(self.microstructure) + 1
dtype = float if int(fill) != fill or self.microstructure.dtype in np.sctypes['float'] else int
canvas = np.full(self.grid if grid is None else grid,
fill if fill is not None else np.nanmax(self.microstructure)+1,dtype)
canvas = np.full(self.grid if grid is None else grid,fill,dtype)
l = np.clip( offset, 0,np.minimum(self.grid +offset,grid)) # noqa
r = np.clip( offset+self.grid,0,np.minimum(self.grid*2+offset,grid))
L = np.clip(-offset, 0,np.minimum(grid -offset,self.grid))
R = np.clip(-offset+grid, 0,np.minimum(grid*2 -offset,self.grid))
LL = np.clip( offset, 0,np.minimum(self.grid, grid+offset))
UR = np.clip( offset+grid, 0,np.minimum(self.grid, grid+offset))
ll = np.clip(-offset, 0,np.minimum( grid,self.grid-offset))
ur = np.clip(-offset+self.grid,0,np.minimum( grid,self.grid-offset))
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]]
canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.microstructure[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
#ToDo: self.add_comments('geom.py:canvas v{}'.format(version)
return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
return self.duplicate(canvas,
origin=self.origin+offset*self.size/self.grid,
comments=self.get_comments()+[util.execution_stamp('Geom','canvas')],
autosize=True,
)
def substitute(self,from_microstructure,to_microstructure):
"""
Substitude microstructure indices.
Substitute microstructure indices.
Parameters
----------
from_microstructure : iterable of ints
microstructure indices to be substituted.
Microstructure indices to be substituted.
to_microstructure : iterable of ints
new microstructure indices.
New microstructure indices.
"""
substituted = self.get_microstructure()
for from_ms,to_ms in zip(from_microstructure,to_microstructure):
substituted[self.microstructure==from_ms] = to_ms
#ToDo: self.add_comments('geom.py:substitute v{}'.format(version)
return self.update(substituted)
return self.duplicate(substituted,
comments=self.get_comments()+[util.execution_stamp('Geom','substitute')],
)
def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
"""
Offset microstructure index of points in the vicinity of xxx.
Different from themselves (or listed as triggers) within a given (cubic) vicinity,
i.e. within the region close to a grain/phase boundary.
ToDo: use include/exclude as in seeds.from_geom
Parameters
----------
vicinity : int, optional
Voxel distance checked for presence of other microstructure.
Defaults to 1.
offset : int, optional
Offset (positive or negative) to tag microstructure indices,
defaults to microstructure.max() + 1.
trigger : list of ints, optional
List of microstructure indices triggering a change.
Defaults to [], meaning that different neigboors trigger a change.
periodic : Boolean, optional
Assume geometry to be periodic. Defaults to True.
"""
def tainted_neighborhood(stencil,trigger):
me = stencil[stencil.shape[0]//2]
if len(trigger) == 0:
return np.any(stencil != me)
if me in trigger:
trigger = set(trigger)
trigger.remove(me)
trigger = list(trigger)
return np.any(np.in1d(stencil,np.array(trigger)))
offset_ = np.nanmax(self.microstructure) if offset is None else offset
mask = ndimage.filters.generic_filter(self.microstructure,
tainted_neighborhood,
size=1+2*vicinity,
mode='wrap' if periodic else 'nearest',
extra_keywords={'trigger':trigger})
microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask))
return self.duplicate(microstructure,
comments=self.get_comments()+[util.execution_stamp('Geom','vicinity_offset')],
)

13
python/damask/_lattice.py
View File

@ -164,16 +164,16 @@ class Symmetry:
with np.errstate(invalid='ignore'):
# using '*'/prod for 'and'
if self.system == 'cubic':
return np.where(np.prod(np.sqrt(2)-1. >= rho_abs,axis=-1) * \
return np.where(np.prod(np.sqrt(2)-1. >= rho_abs,axis=-1) *
(1. >= np.sum(rho_abs,axis=-1)),True,False)
elif self.system == 'hexagonal':
return np.where(np.prod(1. >= rho_abs,axis=-1) * \
(2. >= np.sqrt(3)*rho_abs[...,0] + rho_abs[...,1]) * \
(2. >= np.sqrt(3)*rho_abs[...,1] + rho_abs[...,0]) * \
return np.where(np.prod(1. >= rho_abs,axis=-1) *
(2. >= np.sqrt(3)*rho_abs[...,0] + rho_abs[...,1]) *
(2. >= np.sqrt(3)*rho_abs[...,1] + rho_abs[...,0]) *
(2. >= np.sqrt(3) + rho_abs[...,2]),True,False)
elif self.system == 'tetragonal':
return np.where(np.prod(1. >= rho_abs[...,:2],axis=-1) * \
(np.sqrt(2) >= rho_abs[...,0] + rho_abs[...,1]) * \
return np.where(np.prod(1. >= rho_abs[...,:2],axis=-1) *
(np.sqrt(2) >= rho_abs[...,0] + rho_abs[...,1]) *
(np.sqrt(2) >= rho_abs[...,2] + 1.),True,False)
elif self.system == 'orthorhombic':
return np.where(np.prod(1. >= rho_abs,axis=-1),True,False)
@ -321,6 +321,7 @@ class Lattice: # ToDo: Make a subclass of Symmetry!
"""
lattices = {
'iso': {'system':None},
'triclinic':{'system':None},
'bct': {'system':'tetragonal'},
'hex': {'system':'hexagonal'},

63
python/damask/_result.py
View File

@ -1,6 +1,5 @@
import multiprocessing as mp
import re
import inspect
import glob
import os
import datetime
@ -49,7 +48,7 @@ class Result:
self.version_major = f.attrs['DADF5-major']
self.version_minor = f.attrs['DADF5-minor']
if self.version_major != 0 or not 2 <= self.version_minor <= 6:
if self.version_major != 0 or not 2 <= self.version_minor <= 7:
raise TypeError(f'Unsupported DADF5 version {self.version_major}.{self.version_minor}')
self.structured = 'grid' in f['geometry'].attrs.keys()
@ -401,8 +400,9 @@ class Result:
if sets is True:
groups.append(group)
else:
match = [e for e_ in [glob.fnmatch.filter(f[group].keys(),s) for s in sets] for e in e_]
if len(set(match)) == len(sets): groups.append(group)
if group in f.keys():
match = [e for e_ in [glob.fnmatch.filter(f[group].keys(),s) for s in sets] for e in e_]
if len(set(match)) == len(sets): groups.append(group)
return groups
@ -466,6 +466,11 @@ class Result:
return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str') # np.bytes_ to string
def enable_user_function(self,func):
globals()[func.__name__]=func
print(f'Function {func.__name__} enabled in add_calculation.')
def read_dataset(self,path,c=0,plain=False):
"""
Dataset for all points/cells.
@ -504,7 +509,7 @@ class Result:
else:
return dataset
@property
def cell_coordinates(self):
"""Return initial coordinates of the cell centers."""
if self.structured:
@ -513,6 +518,7 @@ class Result:
with h5py.File(self.fname,'r') as f:
return f['geometry/x_c'][()]
@property
def node_coordinates(self):
"""Return initial coordinates of the cell centers."""
if self.structured:
@ -530,7 +536,7 @@ class Result:
'meta': {
'Unit': x['meta']['Unit'],
'Description': f"Absolute value of {x['label']} ({x['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_absolute'
}
}
def add_absolute(self,x):
@ -558,10 +564,10 @@ class Result:
'meta': {
'Unit': kwargs['unit'],
'Description': f"{kwargs['description']} (formula: {kwargs['formula']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_calculation'
}
}
def add_calculation(self,label,formula,unit='n/a',description=None,vectorized=True):
def add_calculation(self,label,formula,unit='n/a',description=None):
"""
Add result of a general formula.
@ -575,13 +581,8 @@ class Result:
Physical unit of the result.
description : str, optional
Human-readable description of the result.
vectorized : bool, optional
Indicate whether the formula can be used in vectorized form. Defaults to ‘True’.
"""
if not vectorized:
raise NotImplementedError
dataset_mapping = {d:d for d in set(re.findall(r'#(.*?)#',formula))} # datasets used in the formula
args = {'formula':formula,'label':label,'unit':unit,'description':description}
self._add_generic_pointwise(self._add_calculation,dataset_mapping,args)
@ -597,7 +598,7 @@ class Result:
'Description': "Cauchy stress calculated "
f"from {P['label']} ({P['meta']['Description']})"
f" and {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_Cauchy'
}
}
def add_Cauchy(self,P='P',F='F'):
@ -623,7 +624,7 @@ class Result:
'meta': {
'Unit': T['meta']['Unit'],
'Description': f"Determinant of tensor {T['label']} ({T['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_determinant'
}
}
def add_determinant(self,T):
@ -647,7 +648,7 @@ class Result:
'meta': {
'Unit': T['meta']['Unit'],
'Description': f"Deviator of tensor {T['label']} ({T['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_deviator'
}
}
def add_deviator(self,T):
@ -678,7 +679,7 @@ class Result:
'meta' : {
'Unit': T_sym['meta']['Unit'],
'Description': f"{label} eigenvalue of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_eigenvalue'
}
}
def add_eigenvalue(self,T_sym,eigenvalue='max'):
@ -711,7 +712,7 @@ class Result:
'Unit': '1',
'Description': f"Eigenvector corresponding to {label} eigenvalue"
f" of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_eigenvector'
}
}
def add_eigenvector(self,T_sym,eigenvalue='max'):
@ -744,7 +745,7 @@ class Result:
'Unit': '8-bit RGB',
'Lattice': q['meta']['Lattice'],
'Description': 'Inverse Pole Figure (IPF) colors along sample direction [{} {} {}]'.format(*m),
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_IPF_color'
}
}
def add_IPF_color(self,q,l):
@ -770,7 +771,7 @@ class Result:
'meta': {
'Unit': T_sym['meta']['Unit'],
'Description': f"Maximum shear component of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_maximum_shear'
}
}
def add_maximum_shear(self,T_sym):
@ -797,7 +798,7 @@ class Result:
'meta': {
'Unit': T_sym['meta']['Unit'],
'Description': f"Mises equivalent {t} of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_Mises'
}
}
def add_Mises(self,T_sym):
@ -833,7 +834,7 @@ class Result:
'meta': {
'Unit': x['meta']['Unit'],
'Description': f"{o}-norm of {t} {x['label']} ({x['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_norm'
}
}
def add_norm(self,x,ord=None):
@ -861,7 +862,7 @@ class Result:
'Description': "2. Piola-Kirchhoff stress calculated "
f"from {P['label']} ({P['meta']['Description']})"
f" and {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_PK2'
}
}
def add_PK2(self,P='P',F='F'):
@ -897,7 +898,7 @@ class Result:
'Unit': '1',
'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\
.format('Polar' if polar else 'Cartesian'),
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_pole'
}
}
def add_pole(self,q,p,polar=False):
@ -925,7 +926,7 @@ class Result:
'meta': {
'Unit': F['meta']['Unit'],
'Description': f"Rotational part of {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_rotational_part'
}
}
def add_rotational_part(self,F):
@ -949,7 +950,7 @@ class Result:
'meta': {
'Unit': T['meta']['Unit'],
'Description': f"Spherical component of tensor {T['label']} ({T['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_spherical'
}
}
def add_spherical(self,T):
@ -973,7 +974,7 @@ class Result:
'meta': {
'Unit': F['meta']['Unit'],
'Description': f"Strain tensor of {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_strain_tensor'
}
}
def add_strain_tensor(self,F='F',t='V',m=0.0):
@ -1005,7 +1006,7 @@ class Result:
'Unit': F['meta']['Unit'],
'Description': '{} stretch tensor of {} ({})'.format('Left' if t.upper() == 'V' else 'Right',
F['label'],F['meta']['Description']),
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_stretch_tensor'
}
}
def add_stretch_tensor(self,F='F',t='V'):
@ -1064,6 +1065,10 @@ class Result:
lock = mp.Manager().Lock()
groups = self.groups_with_datasets(datasets.values())
if len(groups) == 0:
print('No matching dataset found, no data was added.')
return
default_arg = partial(self._job,func=func,datasets=datasets,args=args,lock=lock)
for result in util.show_progress(pool.imap_unordered(default_arg,groups),len(groups)):
@ -1263,4 +1268,4 @@ class Result:
u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
v.add(u,'u')
v.write(f'{self.fname.stem}_inc{inc[3:].zfill(N_digits)}')
v.to_file(f'{self.fname.stem}_inc{inc[3:].zfill(N_digits)}')

10
python/damask/_rotation.py
View File

@ -357,7 +357,7 @@ class Rotation:
accept_homomorph : boolean, optional
Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
Defaults to False.
P : integer ∈ {-1,1}, optional
P : int ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
@ -422,7 +422,7 @@ class Rotation:
Angle ω is given in degrees. Defaults to False.
normalize: boolean, optional
Allow |n| ≠ 1. Defaults to False.
P : integer ∈ {-1,1}, optional
P : int ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
@ -505,7 +505,7 @@ class Rotation:
(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
P : int ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
@ -534,7 +534,7 @@ class Rotation:
----------
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
P : int ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""
@ -561,7 +561,7 @@ class Rotation:
----------
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
P : int ∈ {-1,1}, optional
Convention used. Defaults to -1.
"""

74
python/damask/_table.py
View File

@ -3,7 +3,6 @@ import re
import pandas as pd
import numpy as np
from . import version
from . import util
class Table:
@ -49,7 +48,9 @@ class Table:
def _add_comment(self,label,shape,info):
if info is not None:
self.comments.append(f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}')
specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}'
general = util.execution_stamp('Table')
self.comments.append(f'{specific} / {general}')
@staticmethod
@ -135,7 +136,7 @@ class Table:
content = f.readlines()
comments = [f'table.py:from_ang v{version}']
comments = [util.execution_stamp('Table','from_ang')]
for line in content:
if line.startswith('#'):
comments.append(line.strip())
@ -312,7 +313,7 @@ class Table:
self.shapes[key] = other.shapes[key]
def to_ASCII(self,fname,new_style=False):
def to_file(self,fname,format='ASCII',new_style=False):
"""
Store as plain text file.
@ -320,32 +321,51 @@ class Table:
----------
fname : file, str, or pathlib.Path
Filename or file for writing.
format : {ASCII'}, optional
File format, defaults to 'ASCII'. Available formats are:
- ASCII: Plain text file, extension '.txt'.
new_style : Boolean, optional
Write table in new style, indicating header lines by comment sign ('#') only.
"""
seen = set()
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(f'{l}')
elif len(self.shapes[l]) == 1:
labels += [f'{i+1}_{l}' \
for i in range(self.shapes[l][0])]
else:
labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
for i in range(np.prod(self.shapes[l]))]
def _to_ASCII(table,fname,new_style=False):
"""
Store as plain text file.
if new_style:
header = [f'# {comment}' for comment in self.comments]
Parameters
----------
table : Table object
Table to write.
fname : file, str, or pathlib.Path
Filename or file for writing.
new_style : Boolean, optional
Write table in new style, indicating header lines by comment sign ('#') only.
"""
seen = set()
labels = []
for l in [x for x in table.data.columns if not (x in seen or seen.add(x))]:
if table.shapes[l] == (1,):
labels.append(f'{l}')
elif len(table.shapes[l]) == 1:
labels += [f'{i+1}_{l}' \
for i in range(table.shapes[l][0])]
else:
labels += [f'{util.srepr(table.shapes[l],"x")}:{i+1}_{l}' \
for i in range(np.prod(table.shapes[l]))]
header = [f'# {comment}' for comment in table.comments] if new_style else \
[f'{len(table.comments)+1} header'] + table.comments
try:
f = open(fname,'w')
except TypeError:
f = fname
for line in header + [' '.join(labels)]: f.write(line+'\n')
table.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)
if format.lower() == 'ascii':
return _to_ASCII(self,fname,new_style)
else:
header = [f'{len(self.comments)+1} header'] \
+ self.comments \
try:
f = open(fname,'w')
except TypeError:
f = fname
for line in header + [' '.join(labels)]: f.write(line+'\n')
self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)
raise TypeError(f'Unknown format {format}.')

173
python/damask/_vtk.py
View File

@ -6,8 +6,10 @@ import numpy as np
import vtk
from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk
from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray
from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
import damask
from . import util
from . import environment
from . import Table
@ -18,18 +20,19 @@ class VTK:
High-level interface to VTK.
"""
def __init__(self,geom):
def __init__(self,vtk_data):
"""
Set geometry and topology.
Initialize from vtk dataset.
Parameters
----------
geom : subclass of vtk.vtkDataSet
Description of geometry and topology. Valid types are vtk.vtkRectilinearGrid,
vtk.vtkUnstructuredGrid, or vtk.vtkPolyData.
vtk_data : subclass of vtk.vtkDataSet
Description of geometry and topology, optionally with attached data.
Valid types are vtk.vtkRectilinearGrid, vtk.vtkUnstructuredGrid,
or vtk.vtkPolyData.
"""
self.geom = geom
self.vtk_data = vtk_data
@staticmethod
@ -49,15 +52,15 @@ class VTK:
Spatial origin.
"""
geom = vtk.vtkRectilinearGrid()
geom.SetDimensions(*(grid+1))
vtk_data = vtk.vtkRectilinearGrid()
vtk_data.SetDimensions(*(grid+1))
coord = [np_to_vtk(np.linspace(origin[i],origin[i]+size[i],grid[i]+1),deep=True) for i in [0,1,2]]
[coord[i].SetName(n) for i,n in enumerate(['x','y','z'])]
geom.SetXCoordinates(coord[0])
geom.SetYCoordinates(coord[1])
geom.SetZCoordinates(coord[2])
vtk_data.SetXCoordinates(coord[0])
vtk_data.SetYCoordinates(coord[1])
vtk_data.SetZCoordinates(coord[2])
return VTK(geom)
return VTK(vtk_data)
@staticmethod
@ -85,11 +88,11 @@ class VTK:
connectivity),axis=1).ravel()
cells.SetCells(connectivity.shape[0],np_to_vtkIdTypeArray(T,deep=True))
geom = vtk.vtkUnstructuredGrid()
geom.SetPoints(vtk_nodes)
geom.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
vtk_data = vtk.vtkUnstructuredGrid()
vtk_data.SetPoints(vtk_nodes)
vtk_data.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
return VTK(geom)
return VTK(vtk_data)
@staticmethod
@ -108,10 +111,10 @@ class VTK:
vtk_points = vtk.vtkPoints()
vtk_points.SetData(np_to_vtk(points))
geom = vtk.vtkPolyData()
geom.SetPoints(vtk_points)
vtk_data = vtk.vtkPolyData()
vtk_data.SetPoints(vtk_points)
return VTK(geom)
return VTK(vtk_data)
@staticmethod
@ -129,18 +132,20 @@ class VTK:
"""
ext = Path(fname).suffix
if ext == '.vtk' or dataset_type:
if ext == '.vtk' or dataset_type is not None:
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(str(fname))
reader.Update()
if dataset_type is None:
raise TypeError('Dataset type for *.vtk file not given.')
elif dataset_type.lower().endswith('rectilineargrid'):
geom = reader.GetRectilinearGridOutput()
reader.Update()
vtk_data = reader.GetRectilinearGridOutput()
elif dataset_type.lower().endswith('unstructuredgrid'):
geom = reader.GetUnstructuredGridOutput()
reader.Update()
vtk_data = reader.GetUnstructuredGridOutput()
elif dataset_type.lower().endswith('polydata'):
geom = reader.GetPolyDataOutput()
reader.Update()
vtk_data = reader.GetPolyDataOutput()
else:
raise TypeError(f'Unknown dataset type {dataset_type} for vtk file')
else:
@ -155,15 +160,15 @@ class VTK:
reader.SetFileName(str(fname))
reader.Update()
geom = reader.GetOutput()
vtk_data = reader.GetOutput()
return VTK(geom)
return VTK(vtk_data)
@staticmethod
def _write(writer):
"""Wrapper for parallel writing."""
writer.Write()
def write(self,fname,parallel=True):
def to_file(self,fname,parallel=True):
"""
Write to file.
@ -175,11 +180,11 @@ class VTK:
Write data in parallel background process. Defaults to True.
"""
if isinstance(self.geom,vtk.vtkRectilinearGrid):
if isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
writer = vtk.vtkXMLRectilinearGridWriter()
elif isinstance(self.geom,vtk.vtkUnstructuredGrid):
elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid):
writer = vtk.vtkXMLUnstructuredGridWriter()
elif isinstance(self.geom,vtk.vtkPolyData):
elif isinstance(self.vtk_data,vtk.vtkPolyData):
writer = vtk.vtkXMLPolyDataWriter()
default_ext = writer.GetDefaultFileExtension()
@ -189,10 +194,14 @@ class VTK:
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
writer.SetInputData(self.geom)
writer.SetInputData(self.vtk_data)
if parallel:
mp_writer = mp.Process(target=self._write,args=(writer,))
mp_writer.start()
try:
mp_writer = mp.Process(target=self._write,args=(writer,))
mp_writer.start()
except TypeError:
writer.Write()
else:
writer.Write()
@ -200,9 +209,20 @@ class VTK:
# Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
# Needs support for pd.DataFrame and/or table
def add(self,data,label=None):
"""Add data to either cells or points."""
N_points = self.geom.GetNumberOfPoints()
N_cells = self.geom.GetNumberOfCells()
"""
Add data to either cells or points.
Parameters
----------
data : numpy.ndarray
Data to add. First dimension need to match either
number of cells or number of points
label : str
Data label.
"""
N_points = self.vtk_data.GetNumberOfPoints()
N_cells = self.vtk_data.GetNumberOfCells()
if isinstance(data,np.ndarray):
if label is None:
@ -215,9 +235,9 @@ class VTK:
d.SetName(label)
if data.shape[0] == N_cells:
self.geom.GetCellData().AddArray(d)
self.vtk_data.GetCellData().AddArray(d)
elif data.shape[0] == N_points:
self.geom.GetPointData().AddArray(d)
self.vtk_data.GetPointData().AddArray(d)
else:
raise ValueError(f'Invalid shape {data.shape[0]}')
elif isinstance(data,pd.DataFrame):
@ -228,12 +248,79 @@ class VTK:
raise TypeError
def get(self,label):
"""
Get either cell or point data.
Cell data takes precedence over point data, i.e. this
function assumes that labels are unique among cell and
point data.
Parameters
----------
label : str
Data label.
"""
cell_data = self.vtk_data.GetCellData()
for a in range(cell_data.GetNumberOfArrays()):
if cell_data.GetArrayName(a) == label:
return vtk_to_np(cell_data.GetArray(a))
point_data = self.vtk_data.GetPointData()
for a in range(point_data.GetNumberOfArrays()):
if point_data.GetArrayName(a) == label:
return vtk_to_np(point_data.GetArray(a))
raise ValueError(f'array "{label}" not found')
def get_comments(self):
"""Return the comments."""
fielddata = self.vtk_data.GetFieldData()
for a in range(fielddata.GetNumberOfArrays()):
if fielddata.GetArrayName(a) == 'comments':
comments = fielddata.GetAbstractArray(a)
return [comments.GetValue(i) for i in range(comments.GetNumberOfValues())]
return []
def set_comments(self,comments):
"""
Set comments.
Parameters
----------
comments : str or list of str
Comments.
"""
s = vtk.vtkStringArray()
s.SetName('comments')
for c in [comments] if isinstance(comments,str) else comments:
s.InsertNextValue(c)
self.vtk_data.GetFieldData().AddArray(s)
def add_comments(self,comments):
"""
Add comments.
Parameters
----------
comments : str or list of str
Comments to add.
"""
self.set_comments(self.get_comments() + ([comments] if isinstance(comments,str) else comments))
def __repr__(self):
"""ASCII representation of the VTK data."""
writer = vtk.vtkDataSetWriter()
writer.SetHeader(f'# damask.VTK v{damask.version}')
writer.SetHeader(f'# {util.execution_stamp("VTK")}')
writer.WriteToOutputStringOn()
writer.SetInputData(self.geom)
writer.SetInputData(self.vtk_data)
writer.Write()
return writer.GetOutputString()
@ -245,7 +332,7 @@ class VTK:
See http://compilatrix.com/article/vtk-1 for further ideas.
"""
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(self.geom)
mapper.SetInputData(self.vtk_data)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
@ -257,7 +344,7 @@ class VTK:
ren.AddActor(actor)
ren.SetBackground(0.2,0.2,0.2)
window.SetSize(damask.environment.screen_size[0],damask.environment.screen_size[1])
window.SetSize(environment.screen_size[0],environment.screen_size[1])
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(window)

3
python/damask/config/__init__.py
View File

@ -1,3 +0,0 @@
"""Aggregator for configuration file handling."""
from .material import Material # noqa

282
python/damask/config/material.py
View File

@ -1,282 +0,0 @@
import re
import os
from damask import util
class Section():
def __init__(self,data = {'__order__':[]},part = ''):
"""New material.config section."""
classes = {
'homogenization':Homogenization,
'microstructure':Microstructure,
'crystallite':Crystallite,
'phase':Phase,
'texture':Texture,
}
self.parameters = {}
for key in data:
self.parameters[key] = data[key] if isinstance(data[key], list) else [data[key]]
if '__order__' not in self.parameters:
self.parameters['__order__'] = list(self.parameters.keys())
if part.lower() in classes:
self.__class__ = classes[part.lower()]
self.__init__(data)
def add_multiKey(self,key,data):
multiKey = '(%s)'%key
if multiKey not in self.parameters: self.parameters[multiKey] = []
if multiKey not in self.parameters['__order__']: self.parameters['__order__'] += [multiKey]
self.parameters[multiKey] += [[item] for item in data] if isinstance(data, list) else [[data]]
def data(self):
return self.parameters
class Homogenization(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <homogenization> section."""
Section.__init__(self,data)
class Crystallite(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <crystallite> section."""
Section.__init__(self,data)
class Phase(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <Phase> section."""
Section.__init__(self,data)
class Microstructure(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <microstructure> section."""
Section.__init__(self,data)
class Texture(Section):
def __init__(self,data = {'__order__':[]}):
"""New material.config <texture> section."""
Section.__init__(self,data)
def add_component(self,theType,properties):
scatter = properties['scatter'] if 'scatter' in list(map(str.lower,list(properties.keys()))) else 0.0
fraction = properties['fraction'] if 'fraction' in list(map(str.lower,list(properties.keys()))) else 1.0
try:
multiKey = theType.lower()
except AttributeError:
pass
if multiKey == 'gauss':
self.add_multiKey(multiKey,'phi1 %g\tPhi %g\tphi2 %g\tscatter %g\tfraction %g'%(
properties['eulers'][0],
properties['eulers'][1],
properties['eulers'][2],
scatter,
fraction,
)
)
class Material():
"""Read, manipulate, and write material.config files."""
def __init__(self,verbose=True):
"""Generates ordered list of parts."""
self.parts = [
'homogenization',
'crystallite',
'phase',
'texture',
'microstructure',
]
self.data = {
'homogenization': {'__order__': []},
'microstructure': {'__order__': []},
'crystallite': {'__order__': []},
'phase': {'__order__': []},
'texture': {'__order__': []},
}
self.verbose = verbose
def __repr__(self):
"""Returns current data structure in material.config format."""
me = []
for part in self.parts:
if self.verbose: print(f'processing <{part}>')
me += ['',
'#'*100,
f'<{part}>',
'#'*100,
]
for section in self.data[part]['__order__']:
me += [f'[{section}] {"#"+"-"*max(0,96-len(section))}']
for key in self.data[part][section]['__order__']:
if key.startswith('(') and key.endswith(')'): # multiple (key)
me += [f'{key}\t{" ".join(values)}' for values in self.data[part][section][key]]
else: # plain key
me += [f'{key}\t{util.srepr(self.data[part][section][key]," ")}']
return '\n'.join(me) + '\n'
def parse(self, part=None, sections=[], content=None):
re_part = re.compile(r'^<(.+)>$') # pattern for part
re_sec = re.compile(r'^\[(.+)\]$') # pattern for section
name_section = ''
active = False
for line in content:
line = line.split('#')[0].strip() # kill comments and extra whitespace
line = line.split('/echo/')[0].strip() # remove '/echo/' tags
line = line.lower() # be case insensitive
if line: # content survives...
match_part = re_part.match(line)
if match_part: # found <...> separator
active = (match_part.group(1) == part) # only active in <part>
continue
if active:
match_sec = re_sec.match(line)
if match_sec: # found [section]
name_section = match_sec.group(1) # remember name ...
if '__order__' not in self.data[part]: self.data[part]['__order__'] = []
self.data[part]['__order__'].append(name_section) # ... and position
self.data[part][name_section] = {'__order__':[]}
continue
if sections == [] or name_section in sections: # possibly restrict to subset
items = line.split()
if items[0] not in self.data[part][name_section]: # first encounter of key?
self.data[part][name_section][items[0]] = [] # create item
self.data[part][name_section]['__order__'].append(items[0])
if items[0].startswith('(') and items[0].endswith(')'): # multiple "(key)"
self.data[part][name_section][items[0]].append(items[1:])
else: # plain key
self.data[part][name_section][items[0]] = items[1:]
def read(self,filename=None):
"""Read material.config file."""
def recursiveRead(filename):
"""Takes care of include statements like '{}'."""
result = []
re_include = re.compile(r'^{(.+)}$')
with open(filename) as f: lines = f.readlines()
for line in lines:
match = re_include.match(line.split()[0]) if line.strip() else False
result += [line] if not match else \
recursiveRead(match.group(1) if match.group(1).startswith('/') else
os.path.normpath(os.path.join(os.path.dirname(filename),match.group(1))))
return result
c = recursiveRead(filename)
for p in self.parts:
self.parse(part=p, content=c)
def write(self,filename='material.config', overwrite=False):
"""Write to material.config."""
i = 0
outname = filename
while os.path.exists(outname) and not overwrite:
i += 1
outname = f'{filename}_{i}'
if self.verbose: print(f'Writing material data to {outname}')
with open(outname,'w') as f:
f.write(str(self))
return outname
def add_section(self, part=None, section=None, initialData=None, merge=False):
"""Add Update."""
part = part.lower()
section = section.lower()
if part not in self.parts: raise Exception(f'invalid part {part}')
if not isinstance(initialData, dict):
initialData = initialData.data()
if section not in self.data[part]: self.data[part]['__order__'] += [section]
if section in self.data[part] and merge:
for existing in self.data[part][section]['__order__']: # replace existing
if existing in initialData['__order__']:
if existing.startswith('(') and existing.endswith(')'): # multiple (key)
self.data[part][section][existing] += initialData[existing] # add new multiple entries to existing ones
else: # regular key
self.data[part][section][existing] = initialData[existing] # plain replice
for new in initialData['__order__']: # merge new content
if new not in self.data[part][section]['__order__']:
self.data[part][section][new] = initialData[new]
self.data[part][section]['__order__'] += [new]
else:
self.data[part][section] = initialData
def add_microstructure(self, section='',
components={}, # dict of phase,texture, and fraction lists
):
"""Experimental! Needs expansion to multi-constituent microstructures..."""
microstructure = Microstructure()
# make keys lower case (http://stackoverflow.com/questions/764235/dictionary-to-lowercase-in-python)
components=dict((k.lower(), v) for k,v in components.items())
for key in ['phase','texture','fraction','crystallite']:
if isinstance(components[key], list):
for i, x in enumerate(components[key]):
try:
components[key][i] = x.lower()
except AttributeError:
pass
else:
try:
components[key] = [components[key].lower()]
except AttributeError:
components[key] = [components[key]]
for (phase,texture,fraction,crystallite) in zip(components['phase'],components['texture'],
components['fraction'],components['crystallite']):
microstructure.add_multiKey('constituent','phase %i\ttexture %i\tfraction %g\ncrystallite %i'%(
self.data['phase']['__order__'].index(phase)+1,
self.data['texture']['__order__'].index(texture)+1,
fraction,
self.data['crystallite']['__order__'].index(crystallite)+1))
self.add_section('microstructure',section,microstructure)
def change_value(self, part=None,
section=None,
key=None,
value=None):
if not isinstance(value,list):
if not isinstance(value,str):
value = '%s'%value
value = [value]
newlen = len(value)
oldval = self.data[part.lower()][section.lower()][key.lower()]
oldlen = len(oldval)
print('changing %s:%s:%s from %s to %s '%(part.lower(),section.lower(),key.lower(),oldval,value))
self.data[part.lower()][section.lower()][key.lower()] = value
if newlen is not oldlen:
print('Length of value was changed from %i to %i!'%(oldlen,newlen))
def add_value(self, part=None,
section=None,
key=None,
value=None):
if not isinstance(value,list):
if not isinstance(value,str):
value = '%s'%value
value = [value]
print('adding %s:%s:%s with value %s '%(part.lower(),section.lower(),key.lower(),value))
self.data[part.lower()][section.lower()][key.lower()] = value
self.data[part.lower()][section.lower()]['__order__'] += [key.lower()]

10
python/damask/solver/_marc.py
View File

@ -3,12 +3,12 @@ import shlex
import string
from pathlib import Path
import damask
from .. import environment
class Marc:
"""Wrapper to run DAMASK with MSCMarc."""
def __init__(self,version=damask.environment.options['MARC_VERSION']):
def __init__(self,version=environment.options['MARC_VERSION']):
"""
Create a Marc solver object.
@ -24,7 +24,7 @@ class Marc:
@property
def library_path(self):
path_MSC = damask.environment.options['MSC_ROOT']
path_MSC = environment.options['MSC_ROOT']
path_lib = Path(f'{path_MSC}/mentat{self.version}/shlib/linux64')
return path_lib if path_lib.is_dir() else None
@ -33,7 +33,7 @@ class Marc:
@property
def tools_path(self):
path_MSC = damask.environment.options['MSC_ROOT']
path_MSC = environment.options['MSC_ROOT']
path_tools = Path(f'{path_MSC}/marc{self.version}/tools')
return path_tools if path_tools.is_dir() else None
@ -49,7 +49,7 @@ class Marc:
):
usersub = damask.environment.root_dir/'src/DAMASK_marc'
usersub = environment.root_dir/'src/DAMASK_marc'
usersub = usersub.parent/(usersub.name + ('.f90' if compile else '.marc'))
if not usersub.is_file():
raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),usersub))

10
python/damask/util.py
View File

@ -9,6 +9,8 @@ from optparse import Option
import numpy as np
from . import version
# limit visibility
__all__=[
'srepr',
@ -20,6 +22,7 @@ __all__=[
'scale_to_coprime',
'return_message',
'extendableOption',
'execution_stamp'
]
####################################################################################################
@ -175,6 +178,13 @@ def scale_to_coprime(v):
return m
def execution_stamp(class_name,function_name=None):
"""Timestamp the execution of a (function within a) class."""
now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
_function_name = '' if function_name is None else f'.{function_name}'
return f'damask.{class_name}{_function_name} v{version} ({now})'
####################################################################################################
# Classes
####################################################################################################

5
python/setup.py
View File

@ -16,10 +16,11 @@ setuptools.setup(
packages=setuptools.find_packages(),
include_package_data=True,
install_requires = [
"pandas",
"pandas", # requires numpy
"scipy",
"h5py",
"h5py", # requires numpy
"vtk",
"matplotlib", # requires numpy, pillow
],
classifiers = [
"Intended Audience :: Science/Research",

35
python/tests/conftest.py
View File

@ -1,11 +1,38 @@
from pathlib import Path
import numpy as np
import datetime
import numpy as np
import pytest
# Use to monkeypatch damask.version (for comparsion to reference files that contain version information)
def pytest_configure():
pytest.dummy_version = '99.99.99-9999-pytest'
import damask
patched_version = '99.99.99-9999-pytest'
@pytest.fixture
def patch_damask_version(monkeypatch):
"""Set damask.version for reproducible tests results."""
monkeypatch.setattr(damask, 'version', patched_version)
patched_date = datetime.datetime(2019, 11, 2, 11, 58, 0)
@pytest.fixture
def patch_datetime_now(monkeypatch):
"""Set datetime.datetime.now for reproducible tests results."""
class mydatetime:
@classmethod
def now(cls):
return patched_date
monkeypatch.setattr(datetime, 'datetime', mydatetime)
@pytest.fixture
def execution_stamp(monkeypatch):
"""Set damask.util.execution_stamp for reproducible tests results."""
def execution_stamp(class_name,function_name=None):
_function_name = '' if function_name is None else f'.{function_name}'
return f'damask.{class_name}{_function_name} v{patched_version} ({patched_date})'
monkeypatch.setattr(damask.util, 'execution_stamp', execution_stamp)
def pytest_addoption(parser):

2
python/tests/reference/Colormap/binary.json
View File

@ -1,6 +1,6 @@
[
{
"Creator": "damask.Colormap v99.99.99-9999-pytest",
"Creator": "damask.Colormap v99.99.99-9999-pytest (2019-11-02 11:58:00)",
"ColorSpace": "RGB",
"Name": "binary",
"DefaultMap": true,

2
python/tests/reference/Colormap/binary.txt
View File

@ -1,4 +1,4 @@
# Creator: damask.Colormap v99.99.99-9999-pytest
# Creator: damask.Colormap v99.99.99-9999-pytest (2019-11-02 11:58:00)
1_RGBA 2_RGBA 3_RGBA 4_RGBA
1.0 1.0 1.0 1.0
0.996078431372549 0.996078431372549 0.996078431372549 1.0

BIN
python/tests/reference/Colormap/shade_None.png Normal file
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python/tests/reference/Colormap/shade_[2, 10].png Normal file
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25
python/tests/reference/Geom/clean_1_1+2+3_False.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_1_1+2+3_True.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_1_1_False.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_1_1_True.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
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1 1 18 38 2 2 17 37
1 1 3 23 2 2 2 22
1 1 7 27 2 2 6 26
1 1 11 31 2 2 10 30
1 1 15 35 2 2 14 34
1 1 19 39 2 2 18 38
1 1 4 24 2 2 3 23
1 1 8 28 2 2 7 27
1 1 12 32 2 2 11 31
1 1 16 36 2 2 15 35
1 1 20 40 2 2 19 39
1 1 5 25 2 2 4 24
1 1 9 29 2 2 8 28
1 1 13 33 2 2 12 32
1 1 17 37 2 2 16 36
1 1 21 41 2 2 20 40

25
python/tests/reference/Geom/clean_stencil=2.geom
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@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 2 2 2 1 1
1 1 1 2 2 2 2 1
1 1 1 6 2 2 2 5
1 1 1 10 2 2 2 9
1 1 1 14 2 2 2 13
1 1 1 2 2 2 2 1
1 1 1 2 2 2 2 1
1 1 1 6 2 2 2 5
1 1 1 10 2 2 2 9
1 1 1 14 2 2 2 13
1 1 1 3 2 2 2 2
1 1 1 3 2 2 2 2
1 1 1 7 2 2 2 6
1 1 1 11 2 2 2 10
1 1 1 15 2 2 2 14
1 1 1 4 2 2 2 3
1 1 1 4 2 2 2 3
1 1 1 8 2 2 2 7
1 1 1 12 2 2 2 11
1 1 1 16 2 2 2 15

25
python/tests/reference/Geom/clean_stencil=3.geom
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@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 2 2 2 2 21
1 1 1 2 2 2 2 21
1 1 1 2 2 2 2 25
1 1 1 2 2 2 2 29
1 1 1 2 2 2 2 37
1 1 1 2 2 2 2 21
1 1 1 2 2 2 2 21
1 1 1 2 2 2 2 25
1 1 1 2 2 2 2 29
1 1 1 2 2 2 2 37
1 1 1 2 2 2 2 22
1 1 1 2 2 2 2 22
1 1 1 2 2 2 2 26
1 1 1 2 2 2 2 30
1 1 1 2 2 2 2 38
1 1 1 2 2 2 2 24
1 1 1 2 2 2 2 24
1 1 1 2 2 2 2 28
1 1 1 2 2 2 2 32
1 1 1 2 2 2 2 40

25
python/tests/reference/Geom/clean_stencil=4.geom
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@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 2 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2
1 1 1 1 2 2 2 2

25
python/tests/reference/Geom/flip_directions=x-y-z.geom Normal file
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@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
40 39 38 37 36 35 34 33
32 31 30 29 28 27 26 25
24 23 22 21 20 19 18 17
16 15 14 13 12 11 10 9
8 7 6 5 4 3 2 1
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
41 40 39 38 37 36 35 34
33 32 31 30 29 28 27 26
25 24 23 22 21 20 19 18
17 16 15 14 13 12 11 10
9 8 7 6 5 4 3 2
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1

25
python/tests/reference/Geom/flip_directions=x.geom Normal file
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@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
9 8 7 6 5 4 3 2
17 16 15 14 13 12 11 10
25 24 23 22 21 20 19 18
33 32 31 30 29 28 27 26
41 40 39 38 37 36 35 34
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
8 7 6 5 4 3 2 1
16 15 14 13 12 11 10 9
24 23 22 21 20 19 18 17
32 31 30 29 28 27 26 25
40 39 38 37 36 35 34 33

25
python/tests/reference/Geom/flip_directions=y-z.geom Normal file
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@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
33 34 35 36 37 38 39 40
25 26 27 28 29 30 31 32
17 18 19 20 21 22 23 24
9 10 11 12 13 14 15 16
1 2 3 4 5 6 7 8
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
34 35 36 37 38 39 40 41
26 27 28 29 30 31 32 33
18 19 20 21 22 23 24 25
10 11 12 13 14 15 16 17
2 3 4 5 6 7 8 9
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1

25
python/tests/reference/Geom/flip_directions=z-x-y.geom Normal file
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@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
40 39 38 37 36 35 34 33
32 31 30 29 28 27 26 25
24 23 22 21 20 19 18 17
16 15 14 13 12 11 10 9
8 7 6 5 4 3 2 1
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
41 40 39 38 37 36 35 34
33 32 31 30 29 28 27 26
25 24 23 22 21 20 19 18
17 16 15 14 13 12 11 10
9 8 7 6 5 4 3 2
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1

160
python/tests/reference/Geom/mirror_directions=x-y-z_reflect=True.geom
View File

@ -3,83 +3,83 @@ grid a 16 b 10 c 8
size x 1.6e-05 y 1e-05 z 8e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 2 22 2 2 1 21 21 1 2 2 22 2 1 1
1 1 6 26 2 2 5 25 25 5 2 2 26 6 1 1
1 1 10 30 2 2 9 29 29 9 2 2 30 10 1 1
1 1 14 34 2 2 13 33 33 13 2 2 34 14 1 1
1 1 18 38 2 2 17 37 37 17 2 2 38 18 1 1
1 1 18 38 2 2 17 37 37 17 2 2 38 18 1 1
1 1 14 34 2 2 13 33 33 13 2 2 34 14 1 1
1 1 10 30 2 2 9 29 29 9 2 2 30 10 1 1
1 1 6 26 2 2 5 25 25 5 2 2 26 6 1 1
1 1 2 22 2 2 1 21 21 1 2 2 22 2 1 1
1 1 3 23 2 2 2 22 22 2 2 2 23 3 1 1
1 1 7 27 2 2 6 26 26 6 2 2 27 7 1 1
1 1 11 31 2 2 10 30 30 10 2 2 31 11 1 1
1 1 15 35 2 2 14 34 34 14 2 2 35 15 1 1
1 1 19 39 2 2 18 38 38 18 2 2 39 19 1 1
1 1 19 39 2 2 18 38 38 18 2 2 39 19 1 1
1 1 15 35 2 2 14 34 34 14 2 2 35 15 1 1
1 1 11 31 2 2 10 30 30 10 2 2 31 11 1 1
1 1 7 27 2 2 6 26 26 6 2 2 27 7 1 1
1 1 3 23 2 2 2 22 22 2 2 2 23 3 1 1
1 1 4 24 2 2 3 23 23 3 2 2 24 4 1 1
1 1 8 28 2 2 7 27 27 7 2 2 28 8 1 1
1 1 12 32 2 2 11 31 31 11 2 2 32 12 1 1
1 1 16 36 2 2 15 35 35 15 2 2 36 16 1 1
1 1 20 40 2 2 19 39 39 19 2 2 40 20 1 1
1 1 20 40 2 2 19 39 39 19 2 2 40 20 1 1
1 1 16 36 2 2 15 35 35 15 2 2 36 16 1 1
1 1 12 32 2 2 11 31 31 11 2 2 32 12 1 1
1 1 8 28 2 2 7 27 27 7 2 2 28 8 1 1
1 1 4 24 2 2 3 23 23 3 2 2 24 4 1 1
1 1 5 25 2 2 4 24 24 4 2 2 25 5 1 1
1 1 9 29 2 2 8 28 28 8 2 2 29 9 1 1
1 1 13 33 2 2 12 32 32 12 2 2 33 13 1 1
1 1 17 37 2 2 16 36 36 16 2 2 37 17 1 1
1 1 21 41 2 2 20 40 40 20 2 2 41 21 1 1
1 1 21 41 2 2 20 40 40 20 2 2 41 21 1 1
1 1 17 37 2 2 16 36 36 16 2 2 37 17 1 1
1 1 13 33 2 2 12 32 32 12 2 2 33 13 1 1
1 1 9 29 2 2 8 28 28 8 2 2 29 9 1 1
1 1 5 25 2 2 4 24 24 4 2 2 25 5 1 1
1 1 5 25 2 2 4 24 24 4 2 2 25 5 1 1
1 1 9 29 2 2 8 28 28 8 2 2 29 9 1 1
1 1 13 33 2 2 12 32 32 12 2 2 33 13 1 1
1 1 17 37 2 2 16 36 36 16 2 2 37 17 1 1
1 1 21 41 2 2 20 40 40 20 2 2 41 21 1 1
1 1 21 41 2 2 20 40 40 20 2 2 41 21 1 1
1 1 17 37 2 2 16 36 36 16 2 2 37 17 1 1
1 1 13 33 2 2 12 32 32 12 2 2 33 13 1 1
1 1 9 29 2 2 8 28 28 8 2 2 29 9 1 1
1 1 5 25 2 2 4 24 24 4 2 2 25 5 1 1
1 1 4 24 2 2 3 23 23 3 2 2 24 4 1 1
1 1 8 28 2 2 7 27 27 7 2 2 28 8 1 1
1 1 12 32 2 2 11 31 31 11 2 2 32 12 1 1
1 1 16 36 2 2 15 35 35 15 2 2 36 16 1 1
1 1 20 40 2 2 19 39 39 19 2 2 40 20 1 1
1 1 20 40 2 2 19 39 39 19 2 2 40 20 1 1
1 1 16 36 2 2 15 35 35 15 2 2 36 16 1 1
1 1 12 32 2 2 11 31 31 11 2 2 32 12 1 1
1 1 8 28 2 2 7 27 27 7 2 2 28 8 1 1
1 1 4 24 2 2 3 23 23 3 2 2 24 4 1 1
1 1 3 23 2 2 2 22 22 2 2 2 23 3 1 1
1 1 7 27 2 2 6 26 26 6 2 2 27 7 1 1
1 1 11 31 2 2 10 30 30 10 2 2 31 11 1 1
1 1 15 35 2 2 14 34 34 14 2 2 35 15 1 1
1 1 19 39 2 2 18 38 38 18 2 2 39 19 1 1
1 1 19 39 2 2 18 38 38 18 2 2 39 19 1 1
1 1 15 35 2 2 14 34 34 14 2 2 35 15 1 1
1 1 11 31 2 2 10 30 30 10 2 2 31 11 1 1
1 1 7 27 2 2 6 26 26 6 2 2 27 7 1 1
1 1 3 23 2 2 2 22 22 2 2 2 23 3 1 1
1 1 2 22 2 2 1 21 21 1 2 2 22 2 1 1
1 1 6 26 2 2 5 25 25 5 2 2 26 6 1 1
1 1 10 30 2 2 9 29 29 9 2 2 30 10 1 1
1 1 14 34 2 2 13 33 33 13 2 2 34 14 1 1
1 1 18 38 2 2 17 37 37 17 2 2 38 18 1 1
1 1 18 38 2 2 17 37 37 17 2 2 38 18 1 1
1 1 14 34 2 2 13 33 33 13 2 2 34 14 1 1
1 1 10 30 2 2 9 29 29 9 2 2 30 10 1 1
1 1 6 26 2 2 5 25 25 5 2 2 26 6 1 1
1 1 2 22 2 2 1 21 21 1 2 2 22 2 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
2 3 4 5 6 7 8 9 9 8 7 6 5 4 3 2
10 11 12 13 14 15 16 17 17 16 15 14 13 12 11 10
18 19 20 21 22 23 24 25 25 24 23 22 21 20 19 18
26 27 28 29 30 31 32 33 33 32 31 30 29 28 27 26
34 35 36 37 38 39 40 41 41 40 39 38 37 36 35 34
34 35 36 37 38 39 40 41 41 40 39 38 37 36 35 34
26 27 28 29 30 31 32 33 33 32 31 30 29 28 27 26
18 19 20 21 22 23 24 25 25 24 23 22 21 20 19 18
10 11 12 13 14 15 16 17 17 16 15 14 13 12 11 10
2 3 4 5 6 7 8 9 9 8 7 6 5 4 3 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
1 2 3 4 5 6 7 8 8 7 6 5 4 3 2 1
9 10 11 12 13 14 15 16 16 15 14 13 12 11 10 9
17 18 19 20 21 22 23 24 24 23 22 21 20 19 18 17
25 26 27 28 29 30 31 32 32 31 30 29 28 27 26 25
33 34 35 36 37 38 39 40 40 39 38 37 36 35 34 33
33 34 35 36 37 38 39 40 40 39 38 37 36 35 34 33
25 26 27 28 29 30 31 32 32 31 30 29 28 27 26 25
17 18 19 20 21 22 23 24 24 23 22 21 20 19 18 17
9 10 11 12 13 14 15 16 16 15 14 13 12 11 10 9
1 2 3 4 5 6 7 8 8 7 6 5 4 3 2 1
1 2 3 4 5 6 7 8 8 7 6 5 4 3 2 1
9 10 11 12 13 14 15 16 16 15 14 13 12 11 10 9
17 18 19 20 21 22 23 24 24 23 22 21 20 19 18 17
25 26 27 28 29 30 31 32 32 31 30 29 28 27 26 25
33 34 35 36 37 38 39 40 40 39 38 37 36 35 34 33
33 34 35 36 37 38 39 40 40 39 38 37 36 35 34 33
25 26 27 28 29 30 31 32 32 31 30 29 28 27 26 25
17 18 19 20 21 22 23 24 24 23 22 21 20 19 18 17
9 10 11 12 13 14 15 16 16 15 14 13 12 11 10 9
1 2 3 4 5 6 7 8 8 7 6 5 4 3 2 1
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 3 4 5 6 7 8 9 9 8 7 6 5 4 3 2
10 11 12 13 14 15 16 17 17 16 15 14 13 12 11 10
18 19 20 21 22 23 24 25 25 24 23 22 21 20 19 18
26 27 28 29 30 31 32 33 33 32 31 30 29 28 27 26
34 35 36 37 38 39 40 41 41 40 39 38 37 36 35 34
34 35 36 37 38 39 40 41 41 40 39 38 37 36 35 34
26 27 28 29 30 31 32 33 33 32 31 30 29 28 27 26
18 19 20 21 22 23 24 25 25 24 23 22 21 20 19 18
10 11 12 13 14 15 16 17 17 16 15 14 13 12 11 10
2 3 4 5 6 7 8 9 9 8 7 6 5 4 3 2
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

40
python/tests/reference/Geom/mirror_directions=x_reflect=False.geom
View File

@ -3,23 +3,23 @@ grid a 14 b 5 c 4
size x 1.4e-05 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 2 22 2 2 1 21 1 2 2 22 2 1
1 1 6 26 2 2 5 25 5 2 2 26 6 1
1 1 10 30 2 2 9 29 9 2 2 30 10 1
1 1 14 34 2 2 13 33 13 2 2 34 14 1
1 1 18 38 2 2 17 37 17 2 2 38 18 1
1 1 3 23 2 2 2 22 2 2 2 23 3 1
1 1 7 27 2 2 6 26 6 2 2 27 7 1
1 1 11 31 2 2 10 30 10 2 2 31 11 1
1 1 15 35 2 2 14 34 14 2 2 35 15 1
1 1 19 39 2 2 18 38 18 2 2 39 19 1
1 1 4 24 2 2 3 23 3 2 2 24 4 1
1 1 8 28 2 2 7 27 7 2 2 28 8 1
1 1 12 32 2 2 11 31 11 2 2 32 12 1
1 1 16 36 2 2 15 35 15 2 2 36 16 1
1 1 20 40 2 2 19 39 19 2 2 40 20 1
1 1 5 25 2 2 4 24 4 2 2 25 5 1
1 1 9 29 2 2 8 28 8 2 2 29 9 1
1 1 13 33 2 2 12 32 12 2 2 33 13 1
1 1 17 37 2 2 16 36 16 2 2 37 17 1
1 1 21 41 2 2 20 40 20 2 2 41 21 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1
2 3 4 5 6 7 8 9 8 7 6 5 4 3
10 11 12 13 14 15 16 17 16 15 14 13 12 11
18 19 20 21 22 23 24 25 24 23 22 21 20 19
26 27 28 29 30 31 32 33 32 31 30 29 28 27
34 35 36 37 38 39 40 41 40 39 38 37 36 35
2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2
1 2 3 4 5 6 7 8 7 6 5 4 3 2
9 10 11 12 13 14 15 16 15 14 13 12 11 10
17 18 19 20 21 22 23 24 23 22 21 20 19 18
25 26 27 28 29 30 31 32 31 30 29 28 27 26
33 34 35 36 37 38 39 40 39 38 37 36 35 34

96
python/tests/reference/Geom/mirror_directions=y-z_reflect=False.geom
View File

@ -3,51 +3,51 @@ grid a 8 b 8 c 6
size x 8e-06 y 8.000000000000001e-06 z 6e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 2 22 2 2 1 21
1 1 6 26 2 2 5 25
1 1 10 30 2 2 9 29
1 1 14 34 2 2 13 33
1 1 18 38 2 2 17 37
1 1 14 34 2 2 13 33
1 1 10 30 2 2 9 29
1 1 6 26 2 2 5 25
1 1 3 23 2 2 2 22
1 1 7 27 2 2 6 26
1 1 11 31 2 2 10 30
1 1 15 35 2 2 14 34
1 1 19 39 2 2 18 38
1 1 15 35 2 2 14 34
1 1 11 31 2 2 10 30
1 1 7 27 2 2 6 26
1 1 4 24 2 2 3 23
1 1 8 28 2 2 7 27
1 1 12 32 2 2 11 31
1 1 16 36 2 2 15 35
1 1 20 40 2 2 19 39
1 1 16 36 2 2 15 35
1 1 12 32 2 2 11 31
1 1 8 28 2 2 7 27
1 1 5 25 2 2 4 24
1 1 9 29 2 2 8 28
1 1 13 33 2 2 12 32
1 1 17 37 2 2 16 36
1 1 21 41 2 2 20 40
1 1 17 37 2 2 16 36
1 1 13 33 2 2 12 32
1 1 9 29 2 2 8 28
1 1 4 24 2 2 3 23
1 1 8 28 2 2 7 27
1 1 12 32 2 2 11 31
1 1 16 36 2 2 15 35
1 1 20 40 2 2 19 39
1 1 16 36 2 2 15 35
1 1 12 32 2 2 11 31
1 1 8 28 2 2 7 27
1 1 3 23 2 2 2 22
1 1 7 27 2 2 6 26
1 1 11 31 2 2 10 30
1 1 15 35 2 2 14 34
1 1 19 39 2 2 18 38
1 1 15 35 2 2 14 34
1 1 11 31 2 2 10 30
1 1 7 27 2 2 6 26
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17
18 19 20 21 22 23 24 25
26 27 28 29 30 31 32 33
34 35 36 37 38 39 40 41
26 27 28 29 30 31 32 33
18 19 20 21 22 23 24 25
10 11 12 13 14 15 16 17
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
1 2 3 4 5 6 7 8
9 10 11 12 13 14 15 16
17 18 19 20 21 22 23 24
25 26 27 28 29 30 31 32
33 34 35 36 37 38 39 40
25 26 27 28 29 30 31 32
17 18 19 20 21 22 23 24
9 10 11 12 13 14 15 16
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17
18 19 20 21 22 23 24 25
26 27 28 29 30 31 32 33
34 35 36 37 38 39 40 41
26 27 28 29 30 31 32 33
18 19 20 21 22 23 24 25
10 11 12 13 14 15 16 17

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