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DAMASK_EICMD
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Merge remote-tracking branch 'origin/development' into misc-improvements

This commit is contained in:
Martin Diehl 2020-06-02 00:12:50 +02:00
parent a51cc39613 45878b9f63
commit ac9fddd9e9
21 changed files with 13 additions and 1093 deletions
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2
PRIVATE

@ -1 +1 @@
Subproject commit 8dde2a68538b7cffbe9d370e2b60be90a31627ab Subproject commit a6109acd264c683fd335b1d1f69934fc4a4078e3

2
VERSION
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@ -1 +1 @@
v2.0.3-2523-ge22e2cfe v2.0.3-2629-g404c0659

13
processing/post/addAPS34IDEstrainCoords.py
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@ -32,15 +32,12 @@ parser.add_option('--depth', dest='depth', metavar='string',
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
if options.frame is None: if options.frame is None:
parser.error('frame not specified') parser.error('frame not specified')
if options.depth is None: if options.depth is None:
parser.error('depth not specified') parser.error('depth not specified')
theta=-0.75*np.pi rot_to_TSL = damask.Rotation.from_axis_angle([-1,0,0,.75*np.pi])
RotMat2TSL=np.array([[1., 0., 0.],
[0., np.cos(theta), np.sin(theta)], # Orientation to account for -135 deg
[0., -np.sin(theta), np.cos(theta)]]) # rotation for TSL convention
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
@ -50,8 +47,6 @@ for name in filenames:
coord = - table.get(options.frame) coord = - table.get(options.frame)
coord[:,2] += table.get(options.depth)[:,0] coord[:,2] += table.get(options.depth)[:,0]
table.add('coord', table.add('coord',rot_to_TSL.broadcast_to(coord.shape[0]) @ coord,scriptID+' '+' '.join(sys.argv[1:]))
np.einsum('ijk,ik->ij',np.broadcast_to(RotMat2TSL,(coord.shape[0],3,3)),coord),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name) table.to_ASCII(sys.stdout if name is None else name)

183
processing/post/addCalculation.py
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@ -1,183 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser
import re
from collections.abc import Iterable
import math # noqa
import scipy # noqa
import scipy.linalg # noqa
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def listify(x):
return x if isinstance(x, Iterable) else [x]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add or alter column(s) with derived values according to user-defined arithmetic operation between column(s).
Column labels are tagged by '#label#' in formulas. Use ';' for ',' in functions.
Numpy is available as 'np'.
Special variables: #_row_# -- row index
Examples:
(1) magnitude of vector -- "np.linalg.norm(#vec#)"
(2) rounded root of row number -- "round(math.sqrt(#_row_#);3)"
""", version = scriptID)
parser.add_option('-l','--label',
dest = 'labels',
action = 'extend', metavar = '<string LIST>',
help = '(list of) new column labels')
parser.add_option('-f','--formula',
dest = 'formulas',
action = 'extend', metavar = '<string LIST>',
help = '(list of) formulas corresponding to labels')
parser.add_option('-c','--condition',
dest = 'condition', metavar='string',
help = 'condition to alter existing column data (optional)')
(options,filenames) = parser.parse_args()
if options.labels is None or options.formulas is None:
parser.error('no formulas and/or labels specified.')
if len(options.labels) != len(options.formulas):
parser.error('number of labels ({}) and formulas ({}) do not match.'.format(len(options.labels),len(options.formulas)))
for i in range(len(options.formulas)):
options.formulas[i] = options.formulas[i].replace(';',',')
# ------------------------------------- loop over input files --------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name)
except IOError:
continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header -------------------------------------------
table.head_read()
# --------------------------------------------------------------------------------------------------
specials = { \
'_row_': 0,
}
# --------------------------------------- evaluate condition ---------------------------------------
if options.condition is not None:
condition = options.condition # copy per file, since might be altered inline
breaker = False
for position,(all,marker,column) in enumerate(set(re.findall(r'#(([s]#)?(.+?))#',condition))): # find three groups
idx = table.label_index(column)
dim = table.label_dimension(column)
if idx < 0 and column not in specials:
damask.util.croak('column "{}" not found.'.format(column))
breaker = True
else:
if column in specials:
replacement = 'specials["{}"]'.format(column)
elif dim == 1: # scalar input
replacement = '{}(table.data[{}])'.format({ '':'float',
's#':'str'}[marker],idx) # take float or string value of data column
elif dim > 1: # multidimensional input (vector, tensor, etc.)
replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim) # use (flat) array representation
condition = condition.replace('#'+all+'#',replacement)
if breaker: continue # found mistake in condition evaluation --> next file
# ------------------------------------------ build formulas ----------------------------------------
evaluator = {}
for label,formula in zip(options.labels,options.formulas):
for column in re.findall(r'#(.+?)#',formula): # loop over column labels in formula
idx = table.label_index(column)
dim = table.label_dimension(column)
if column in specials:
replacement = 'specials["{}"]'.format(column)
elif dim == 1: # scalar input
replacement = 'float(table.data[{}])'.format(idx) # take float value of data column
elif dim > 1: # multidimensional input (vector, tensor, etc.)
replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim) # use (flat) array representation
else:
damask.util.croak('column {} not found, skipping {}...'.format(column,label))
options.labels.remove(label)
break
formula = formula.replace('#'+column+'#',replacement)
evaluator[label] = formula
# ---------------------------- separate requested labels into old and new --------------------------
veterans = list(set(options.labels)&set(table.labels(raw=False)+table.labels(raw=True)) ) # intersection of requested and existing
newbies = list(set(options.labels)-set(table.labels(raw=False)+table.labels(raw=True)) ) # requested but not existing
# ------------------------------------------ process data ------------------------------------------
firstLine = True
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
specials['_row_'] += 1 # count row
if firstLine:
firstLine = False
# ---------------------------- line 1: determine dimension of formulas -----------------------------
resultDim = {}
for label in list(options.labels): # iterate over stable copy
resultDim[label] = np.size(eval(evaluator[label])) # get dimension of formula[label]
if resultDim[label] == 0: options.labels.remove(label) # remove label if invalid result
for veteran in list(veterans):
if resultDim[veteran] != table.label_dimension(veteran):
damask.util.croak('skipping {} due to inconsistent dimension...'.format(veteran))
veterans.remove(veteran) # discard culprit
# ----------------------------------- line 1: assemble header --------------------------------------
for newby in newbies:
table.labels_append(['{}_{}'.format(i+1,newby) for i in range(resultDim[newby])]
if resultDim[newby] > 1 else newby)
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.head_write()
# -------------------------------------- evaluate formulas -----------------------------------------
if options.condition is None or eval(condition): # condition for veteran replacement fulfilled
for veteran in veterans: # evaluate formulas that overwrite
table.data[table.label_index(veteran):
table.label_index(veteran)+table.label_dimension(veteran)] = \
listify(eval(evaluator[veteran]))
for newby in newbies: # evaluate formulas that append
table.data_append(listify(eval(evaluator[newby])))
outputAlive = table.data_write() # output processed line
# ------------------------------------- output finalization ----------------------------------------
table.close() # close ASCII table

68
processing/post/addIPFcolor.py
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@ -1,68 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add RGB color value corresponding to TSL-OIM scheme for inverse pole figures.
""", version = scriptID)
parser.add_option('-p',
'--pole',
dest = 'pole',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'lab frame direction for inverse pole figure [%default]')
parser.add_option('-s',
'--symmetry',
dest = 'symmetry',
type = 'choice', choices = damask.Symmetry.lattices[1:], metavar='string',
help = 'crystal symmetry [%default] {{{}}} '.format(', '.join(damask.Symmetry.lattices[1:])))
parser.add_option('-o',
'--orientation',
dest = 'quaternion',
metavar = 'string',
help = 'label of crystal orientation given as unit quaternion [%default]')
parser.set_defaults(pole = (0.0,0.0,1.0),
quaternion = 'orientation',
symmetry = damask.Symmetry.lattices[-1],
)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
# damask.Orientation requires Bravais lattice, but we are only interested in symmetry
symmetry2lattice={'cubic':'fcc','hexagonal':'hex','tetragonal':'bct'}
lattice = symmetry2lattice[options.symmetry]
pole = np.array(options.pole)
pole /= np.linalg.norm(pole)
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)
orientation = table.get(options.quaternion)
color = np.empty((orientation.shape[0],3))
for i,o in enumerate(orientation):
color[i] = damask.Orientation(o,lattice = lattice).IPFcolor(pole)
table.add('IPF_{:g}{:g}{:g}_{sym}'.format(*options.pole,sym = options.symmetry.lower()),
color,
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

75
processing/post/addNorm.py
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@ -1,75 +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])
# definition of element-wise p-norms for matrices
# ToDo: better use numpy.linalg.norm
def norm(which,object):
if which == 'Abs': # p = 1
return sum(map(abs, object))
elif which == 'Frobenius': # p = 2
return np.sqrt(sum([x*x for x in object]))
elif which == 'Max': # p = inf
return max(map(abs, object))
else:
return -1
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add column(s) containing norm of requested column(s) being either vectors or tensors.
""", version = scriptID)
normChoices = ['abs','frobenius','max']
parser.add_option('-n','--norm',
dest = 'norm',
type = 'choice', choices = normChoices, metavar='string',
help = 'type of element-wise p-norm [frobenius] {%s}'%(','.join(map(str,normChoices))))
parser.add_option('-l','--label',
dest = 'labels',
action = 'extend', metavar = '<string LIST>',
help = 'heading of column(s) to calculate norm of')
parser.set_defaults(norm = 'frobenius',
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.norm.lower() not in normChoices:
parser.error('invalid norm ({}) specified.'.format(options.norm))
if options.labels is None:
parser.error('no data column specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for label in options.labels:
data = table.get(label)
data_norm = np.empty((data.shape[0],1))
for i,d in enumerate(data):
data_norm[i] = norm(options.norm.capitalize(),d)
table.add('norm{}({})'.format(options.norm.capitalize(),label),
data_norm,
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

50
processing/post/addPK2.py
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@ -1,50 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add column(s) containing Second Piola--Kirchhoff stress based on given column(s) of deformation
gradient and first Piola--Kirchhoff stress.
""", version = scriptID)
parser.add_option('-f','--defgrad',
dest = 'defgrad',
type = 'string', metavar = 'string',
help = 'heading of columns containing deformation gradient [%default]')
parser.add_option('-p','--stress',
dest = 'stress',
type = 'string', metavar = 'string',
help = 'heading of columns containing first Piola--Kirchhoff stress [%default]')
parser.set_defaults(defgrad = 'f',
stress = 'p',
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.add('S',
damask.mechanics.PK2(table.get(options.stress ).reshape(-1,3,3),
table.get(options.defgrad).reshape(-1,3,3)).reshape(-1,9),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

65
processing/post/addPole.py
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@ -1,65 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add coordinates of stereographic projection of given direction (pole) in crystal frame.
""", version = scriptID)
parser.add_option('-p',
'--pole',
dest = 'pole',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'crystal frame direction for pole figure [%default]')
parser.add_option('--polar',
dest = 'polar',
action = 'store_true',
help = 'output polar coordinates (r,φ) instead of Cartesian coordinates (x,y)')
parser.add_option('-o',
'--orientation',
dest = 'quaternion',
metavar = 'string',
help = 'label of crystal orientation given as unit quaternion [%default]')
parser.set_defaults(pole = (1.0,0.0,0.0),
quaternion = 'orientation',
)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
pole = np.array(options.pole)
pole /= np.linalg.norm(pole)
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)
orientation = table.get(options.quaternion)
poles = np.empty((orientation.shape[0],2))
for i,o in enumerate(orientation):
rotatedPole = damask.Rotation(o)*pole # rotate pole according to crystal orientation
(x,y) = rotatedPole[0:2]/(1.+abs(pole[2])) # stereographic projection
poles[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)] if options.polar else [x,y] # cartesian coordinates
table.add('pole_{}{}{}'.format(*options.pole),
poles,
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

58
processing/post/addSpectralDecomposition.py
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@ -1,58 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add column(s) containing eigenvalues and eigenvectors of requested symmetric tensor column(s).
""", version = scriptID)
parser.add_option('-t','--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'heading of columns containing tensor field values')
parser.add_option('--no-check',
dest = 'rh',
action = 'store_false',
help = 'skip check for right-handed eigenvector basis')
parser.set_defaults(rh = True,
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for tensor in options.tensor:
t = table.get(tensor).reshape(-1,3,3)
(u,v) = np.linalg.eigh(damask.mechanics.symmetric(t))
if options.rh: v[np.linalg.det(v) < 0.0,:,2] *= -1.0
for i,o in enumerate(['Min','Mid','Max']):
table.add('eigval{}({})'.format(o,tensor),u[:,i], scriptID+' '+' '.join(sys.argv[1:]))
for i,o in enumerate(['Min','Mid','Max']):
table.add('eigvec{}({})'.format(o,tensor),v[:,:,i],scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

98
processing/post/addStrainTensors.py
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@ -1,98 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def parameters(stretch,strain):
"""Albrecht Bertram: Elasticity and Plasticity of Large Deformations An Introduction (3rd Edition, 2012), p. 102."""
return {
'V#ln': ('V',0.0),
'U#ln': ('U',0.0),
'V#Biot': ('V',-.5),
'U#Biot': ('U',+.5),
'V#Green': ('V',-1.),
'U#Green': ('U',+1.),
}[stretch+'#'+strain]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add column(s) containing given strains based on given stretches of requested deformation gradient column(s).
""", version = scriptID)
parser.add_option('-u','--right',
dest = 'right',
action = 'store_true',
help = 'material strains based on right Cauchy--Green deformation, i.e., C and U')
parser.add_option('-v','--left',
dest = 'left',
action = 'store_true',
help = 'spatial strains based on left Cauchy--Green deformation, i.e., B and V')
parser.add_option('-0','--logarithmic',
dest = 'logarithmic',
action = 'store_true',
help = 'calculate logarithmic strain tensor')
parser.add_option('-1','--biot',
dest = 'biot',
action = 'store_true',
help = 'calculate biot strain tensor')
parser.add_option('-2','--green',
dest = 'green',
action = 'store_true',
help = 'calculate green strain tensor')
parser.add_option('-f','--defgrad',
dest = 'defgrad',
action = 'extend',
metavar = '<string LIST>',
help = 'heading(s) of columns containing deformation tensor values [%default]')
parser.set_defaults(
defgrad = ['f'],
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if len(options.defgrad) > 1:
options.defgrad = options.defgrad[1:]
stretches = []
strains = []
if options.right: stretches.append('U')
if options.left: stretches.append('V')
if options.logarithmic: strains.append('ln')
if options.biot: strains.append('Biot')
if options.green: strains.append('Green')
if options.defgrad is None:
parser.error('no data column specified.')
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
for defgrad in options.defgrad:
F = table.get(defgrad).reshape(-1,3,3)
for theStretch in stretches:
for theStrain in strains:
(t,m) = parameters(theStretch,theStrain)
label = '{}({}){}'.format(theStrain,theStretch,defgrad if defgrad != 'f' else '')
table.add(label,
damask.mechanics.strain_tensor(F,t,m).reshape(-1,9),
scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

62
processing/post/rotateData.py
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@ -1,62 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Rotate vector and/or tensor column data by given angle around given axis.
""", version = scriptID)
parser.add_option('-d', '--data',
dest = 'data',
action = 'extend', metavar = '<string LIST>',
help = 'vector/tensor value(s) label(s)')
parser.add_option('-r', '--rotation',
dest = 'rotation',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'axis and angle to rotate data [%default]')
parser.add_option('--degrees',
dest = 'degrees',
action = 'store_true',
help = 'angles are given in degrees')
parser.set_defaults(rotation = (1.,1.,1.,0), # no rotation about (1,1,1)
degrees = False,
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if options.data is None:
parser.error('no data column specified.')
r = damask.Rotation.from_axis_angle(options.rotation,options.degrees,normalise=True)
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)
for data in options.data:
d = table.get(data)
if table.shapes[data] == (9,): d=d.reshape(-1,3,3)
d = r.broadcast_to(d.shape[0:1]) @ d
if table.shapes[data] == (9,): d=d.reshape(-1,9)
table.set(data,d,scriptID+' '+' '.join(sys.argv[1:]))
table.to_ASCII(sys.stdout if name is None else name)

89
processing/post/viewTable.py
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@ -1,89 +0,0 @@
#!/usr/bin/env python3
import os
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(usage='%prog options [ASCIItable(s)]', description = """
Show components of given ASCIItable(s).
""", version = scriptID)
parser.add_option('-a','--head',
dest = 'head',
action = 'store_true',
help = 'output complete header (info + labels)')
parser.add_option('-i','--info',
dest = 'info',
action = 'store_true',
help = 'output info lines')
parser.add_option('-l','--labels',
dest = 'labels',
action = 'store_true',
help = 'output labels')
parser.add_option('-d','--data',
dest = 'data',
action = 'store_true',
help = 'output data')
parser.add_option('-t','--table',
dest = 'table',
action = 'store_true',
help = 'output heading line for proper ASCIItable format')
parser.add_option('--nolabels',
dest = 'labeled',
action = 'store_false',
help = 'table has no labels')
parser.set_defaults(table = False,
head = False,
info = False,
labels = False,
data = False,
labeled = True,
)
(options,filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name, labeled = options.labeled, readonly = True)
except IOError:
continue
details = ', '.join(
(['header'] if options.table else []) +
(['info'] if options.head or options.info else []) +
(['labels'] if options.head or options.labels else []) +
(['data'] if options.data else []) +
[]
)
damask.util.report(scriptName,(name if name is not None else '') + ('' if details == '' else ' -- '+details))
# ------------------------------------------ output head ---------------------------------------
table.head_read()
if not (options.head or options.info): table.info_clear()
if not (options.head or (options.labels and options.labeled)): table.labels_clear()
table.head_write(header = options.table)
# ------------------------------------------ output data ---------------------------------------
outputAlive = options.data
while outputAlive and table.data_read(): # read next data line of ASCII table
outputAlive = table.data_write() # output line
table.close()

61
processing/pre/geom_canvas.py
View File

@ -1,61 +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 = """
Increases or decreases the (three-dimensional) canvas.
Grid can be given as absolute or relative values, e.g. 16 16 16 or 2x 0.5x 32.
""", version = scriptID)
parser.add_option('-g','--grid',
dest = 'grid',
type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
help = 'a,b,c grid of hexahedral box')
parser.add_option('-o','--offset',
dest = 'offset',
type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
help = 'a,b,c offset from old to new origin of grid [%default]')
parser.add_option('-f','--fill',
dest = 'fill',
type = 'float', metavar = 'int',
help = 'background microstructure index, defaults to max microstructure index + 1')
parser.set_defaults(offset = (0,0,0))
(options, filenames) = parser.parse_args()
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.asarray(options.offset)
if options.grid is not None:
grid = np.maximum(1,
np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
else int(n) for o,n in zip(geom.grid,options.grid)],dtype=int))
else:
grid = np.array(options.grid,dtype=int)
damask.util.croak(geom.canvas(grid,np.asarray(options.offset),options.fill))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

37
processing/pre/geom_check.py
View File

@ -1,37 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
Writes vtk file for visualization.
""", version = scriptID)
(options, filenames) = parser.parse_args()
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)
damask.util.croak(geom)
if name:
geom.to_vtk(os.path.splitext(name)[0])
else:
sys.stdout.write(geom.to_vtk())

33
processing/pre/geom_renumber.py
View File

@ -1,33 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
Renumber sorted microstructure indices to 1,...,N.
""", version=scriptID)
(options, filenames) = parser.parse_args()
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)
damask.util.croak(geom.renumber())
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

77
processing/pre/geom_rotate.py
View File

@ -1,77 +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 = """
Rotates original microstructure and embeddeds it into buffer material.
""", version=scriptID)
parser.add_option('-r', '--rotation',
dest='rotation',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'rotation given as axis and angle')
parser.add_option('-e', '--eulers',
dest = 'eulers',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
help = 'rotation given as Euler angles')
parser.add_option('-d', '--degrees',
dest = 'degrees',
action = 'store_true',
help = 'Euler angles/axis angle are given in degrees')
parser.add_option('-m', '--matrix',
dest = 'matrix',
type = 'float', nargs = 9, metavar = ' '.join(['float']*9),
help = 'rotation given as matrix')
parser.add_option('-q', '--quaternion',
dest = 'quaternion',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'rotation given as quaternion')
parser.add_option('-f', '--fill',
dest = 'fill',
type = 'float', metavar = 'int',
help = 'background microstructure index, defaults to max microstructure index + 1')
parser.set_defaults(degrees = False)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) < 3:
parser.error('more than one rotation specified.')
if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) > 3:
parser.error('no rotation specified.')
if options.quaternion is not None:
rot = damask.Rotation.from_quaternion(np.array(options.quaternion)) # we might need P=+1 here, too...
if options.rotation is not None:
rot = damask.Rotation.from_axis_angle(np.array(options.rotation),degrees=options.degrees,normalise=True,P=+1)
if options.matrix is not None:
rot = damask.Rotation.from_matrix(np.array(options.Matrix))
if options.eulers is not None:
rot = damask.Rotation.from_Eulers(np.array(options.eulers),degrees=options.degrees)
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)
damask.util.croak(geom.rotate(rot,options.fill))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

56
processing/pre/geom_translate.py
View File

@ -1,56 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser
from io import StringIO
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 = """
Translate microstructure indices (shift or substitute) and/or geometry origin.
""", version=scriptID)
parser.add_option('-o', '--origin',
dest = 'origin',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
help = 'offset from old to new origin of grid')
parser.add_option('-m', '--microstructure',
dest = 'microstructure',
type = 'int', metavar = 'int',
help = 'offset from old to new microstructure indices (after substitution)')
parser.add_option('-s', '--substitute',
dest = 'substitute',
action = 'extend', metavar = '<string LIST>',
help = 'substitutions of microstructure indices from,to,from,to,...')
parser.set_defaults(origin = (0.0,0.0,0.0),
microstructure = 0,
substitute = []
)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
sub = list(map(int,options.substitute))
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)
geom.substitute(sub[0::2],sub[1::2])
geom.set_origin(geom.origin+options.origin)
geom.set_microstructure(geom.microstructure+options.microstructure)
damask.util.croak(geom)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

39
processing/pre/seeds_check.py
View File

@ -1,39 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [seedfile(s)]', description = """
Writes vtk file for visualization.
""", version = scriptID)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
seeds = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
v = damask.VTK.from_polyData(seeds.get('pos'))
for label in seeds.shapes.keys():
if label == 'pos': pass
v.add(seeds.get(label),label)
if name:
v.write(os.path.splitext(name)[0])
else:
sys.stdout.write(v.__repr__())

17
python/damask/_result.py
View File

@ -1270,20 +1270,3 @@ class Result:
inc[3:].zfill(N_digits)) inc[3:].zfill(N_digits))
v.write(file_out) v.write(file_out)
###################################################################################################
# BEGIN DEPRECATED
def set_by_time(self,start,end):
"""
Set active increments based on start and end time.
Parameters
----------
start : float
start time (included)
end : float
end time (included)
"""
self._manage_selection('set','times',self.times_in_range(start,end))

1
python/damask/_rotation.py
View File

@ -158,6 +158,7 @@ class Rotation:
def broadcast_to(self,shape): def broadcast_to(self,shape):
if isinstance(shape,int): shape = (shape,)
if self.shape == (): if self.shape == ():
q = np.broadcast_to(self.quaternion,shape+(4,)) q = np.broadcast_to(self.quaternion,shape+(4,))
else: else:

20
src/mesh/mesh_mech_FEM.f90
View File

@ -71,7 +71,7 @@ subroutine FEM_mech_init(fieldBC)
PetscQuadrature :: mechQuad, functional PetscQuadrature :: mechQuad, functional
PetscDS :: mechDS PetscDS :: mechDS
PetscDualSpace :: mechDualSpace PetscDualSpace :: mechDualSpace
DMLabel, dimension(:),pointer :: pBCLabel DMLabel, dimension(:),pointer :: nolabel=> NULL()
DMLabel :: BCLabel DMLabel :: BCLabel
PetscInt, dimension(:), pointer :: pNumComp, pNumDof, pBcField, pBcPoint PetscInt, dimension(:), pointer :: pNumComp, pNumDof, pBcField, pBcPoint
@ -134,7 +134,7 @@ subroutine FEM_mech_init(fieldBC)
! Setup FEM mech boundary conditions ! Setup FEM mech boundary conditions
call DMGetLabel(mech_mesh,'Face Sets',BCLabel,ierr); CHKERRQ(ierr) call DMGetLabel(mech_mesh,'Face Sets',BCLabel,ierr); CHKERRQ(ierr)
call DMPlexLabelComplete(mech_mesh,BCLabel,ierr); CHKERRQ(ierr) call DMPlexLabelComplete(mech_mesh,BCLabel,ierr); CHKERRQ(ierr)
#if (PETSC_VERSION_MINOR < 11) #if (PETSC_VERSION_MINOR < 12)
call DMGetSection(mech_mesh,section,ierr); CHKERRQ(ierr) call DMGetSection(mech_mesh,section,ierr); CHKERRQ(ierr)
#else #else
call DMGetLocalSection(mech_mesh,section,ierr); CHKERRQ(ierr) call DMGetLocalSection(mech_mesh,section,ierr); CHKERRQ(ierr)
@ -180,8 +180,7 @@ subroutine FEM_mech_init(fieldBC)
call DMPlexCreateSection(mech_mesh,dimPlex,1,pNumComp,pNumDof, & call DMPlexCreateSection(mech_mesh,dimPlex,1,pNumComp,pNumDof, &
numBC,pBcField,pBcComps,pBcPoints,PETSC_NULL_IS,section,ierr) numBC,pBcField,pBcComps,pBcPoints,PETSC_NULL_IS,section,ierr)
#else #else
allocate(pBClabel(1),source=BClabel) call DMPlexCreateSection(mech_mesh,nolabel,pNumComp,pNumDof, &
call DMPlexCreateSection(mech_mesh,pBClabel,pNumComp,pNumDof, &
numBC,pBcField,pBcComps,pBcPoints,PETSC_NULL_IS,section,ierr) numBC,pBcField,pBcComps,pBcPoints,PETSC_NULL_IS,section,ierr)
#endif #endif
@ -315,7 +314,7 @@ subroutine FEM_mech_formResidual(dm_local,xx_local,f_local,dummy,ierr)
PetscReal, pointer,dimension(:) :: pV0, pCellJ, pInvcellJ, basisField, basisFieldDer PetscReal, pointer,dimension(:) :: pV0, pCellJ, pInvcellJ, basisField, basisFieldDer
PetscInt :: cellStart, cellEnd, cell, field, face, & PetscInt :: cellStart, cellEnd, cell, field, face, &
qPt, basis, comp, cidx, & qPt, basis, comp, cidx, &
numFields, depth ! < DEBUG numFields
PetscReal :: detFAvg PetscReal :: detFAvg
PetscReal :: BMat(dimPlex*dimPlex,cellDof) PetscReal :: BMat(dimPlex*dimPlex,cellDof)
@ -328,7 +327,7 @@ subroutine FEM_mech_formResidual(dm_local,xx_local,f_local,dummy,ierr)
allocate(pinvcellJ(dimPlex**2)) allocate(pinvcellJ(dimPlex**2))
allocate(x_scal(cellDof)) allocate(x_scal(cellDof))
#if (PETSC_VERSION_MINOR < 11) #if (PETSC_VERSION_MINOR < 12)
call DMGetSection(dm_local,section,ierr); CHKERRQ(ierr) call DMGetSection(dm_local,section,ierr); CHKERRQ(ierr)
#else #else
call DMGetLocalSection(dm_local,section,ierr); CHKERRQ(ierr) call DMGetLocalSection(dm_local,section,ierr); CHKERRQ(ierr)
@ -356,15 +355,8 @@ subroutine FEM_mech_formResidual(dm_local,xx_local,f_local,dummy,ierr)
! evaluate field derivatives ! evaluate field derivatives
do cell = cellStart, cellEnd-1 !< loop over all elements do cell = cellStart, cellEnd-1 !< loop over all elements
! BEGIN DEBUG
call PetscSectionGetNumFields(section,numFields,ierr) call PetscSectionGetNumFields(section,numFields,ierr)
CHKERRQ(ierr) CHKERRQ(ierr)
write(6,*) 'numFields', numFields
call DMPlexGetDepth(dm_local,depth,ierr)
CHKERRQ(ierr)
write(6,*) 'depth', depth
! END DEBUG
call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,ierr) !< get Dofs belonging to element call DMPlexVecGetClosure(dm_local,section,x_local,cell,x_scal,ierr) !< get Dofs belonging to element
CHKERRQ(ierr) CHKERRQ(ierr)
call DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,ierr) call DMPlexComputeCellGeometryAffineFEM(dm_local,cell,pV0,pCellJ,pInvcellJ,detJ,ierr)
@ -482,7 +474,7 @@ subroutine FEM_mech_formJacobian(dm_local,xx_local,Jac_pre,Jac,dummy,ierr)
call MatZeroEntries(Jac,ierr); CHKERRQ(ierr) call MatZeroEntries(Jac,ierr); CHKERRQ(ierr)
call DMGetDS(dm_local,prob,ierr); CHKERRQ(ierr) call DMGetDS(dm_local,prob,ierr); CHKERRQ(ierr)
call PetscDSGetTabulation(prob,0,basisField,basisFieldDer,ierr) call PetscDSGetTabulation(prob,0,basisField,basisFieldDer,ierr)
#if (PETSC_VERSION_MINOR < 11) #if (PETSC_VERSION_MINOR < 12)
call DMGetSection(dm_local,section,ierr); CHKERRQ(ierr) call DMGetSection(dm_local,section,ierr); CHKERRQ(ierr)
#else #else
call DMGetLocalSection(dm_local,section,ierr); CHKERRQ(ierr) call DMGetLocalSection(dm_local,section,ierr); CHKERRQ(ierr)