DAMASK_EICMD/processing/post/addStrainTensors.py

172 lines
7.7 KiB
Python
Executable File

#!/usr/bin/python
import os,re,sys,math,numpy,string,damask_tools
from optparse import OptionParser, Option
# -----------------------------
class extendableOption(Option):
# -----------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
def operator(how,vector):
return { \
'ln': numpy.log(vector)*1.0,\
'Biot': vector *1.0,\
'Green': vector*vector *0.5,\
}[how]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
Add column(s) containing given strains based on given stretches of requested deformation gradient column(s).
""" + string.replace('$Id$','\n','\\n')
)
parser.add_option('-u','--right', action='store_true', dest='right', \
help='calculate strains based on right Cauchy--Green deformation, i.e., C and U')
parser.add_option('-v','--left', action='store_true', dest='left', \
help='calculate strains based on left Cauchy--Green deformation, i.e., B and V')
parser.add_option('-l','--logarithmic', action='store_true', dest='logarithmic', \
help='calculate logarithmic strain tensor')
parser.add_option('-b','--biot', action='store_true', dest='biot', \
help='calculate biot strain tensor')
parser.add_option('-g','--green', action='store_true', dest='green', \
help='calculate green strain tensor')
parser.add_option('-f','--deformation', dest='defgrad', action='extend', type='string', \
help='heading(s) of columns containing deformation tensor values %default')
parser.set_defaults(right = False)
parser.set_defaults(left = False)
parser.set_defaults(logarithmic = False)
parser.set_defaults(biot = False)
parser.set_defaults(green = False)
parser.set_defaults(defgrad = ['f'])
(options,filenames) = parser.parse_args()
stretches = []
stretch = {}
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')
datainfo = { # list of requested labels per datatype
'defgrad': {'len':9,
'label':[]},
}
if options.defgrad != None: datainfo['defgrad']['label'] += options.defgrad
# ------------------------------------------ setup file handles ---------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')})
# ------------------------------------------ loop over input files ---------------------------------------
for file in files:
if file['name'] != 'STDIN': print file['name']
table = damask_tools.ASCII_TABLE(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
table.info_append(string.replace('$Id$','\n','\\n') + \
'\t' + ' '.join(sys.argv[1:]))
active = {}
column = {}
head = []
for datatype,info in datainfo.items():
for label in info['label']:
key = {True :'1_%s',
False:'%s' }[info['len']>1]%label
if key not in table.labels:
sys.stderr.write('column %s not found...\n'%key)
else:
if datatype not in active: active[datatype] = []
if datatype not in column: column[datatype] = {}
active[datatype].append(label)
column[datatype][label] = table.labels.index(key)
for theStretch in stretches:
for theStrain in strains:
table.labels_append(['%i_%s(%s)'%(i+1,theStrain,theStretch)
for i in xrange(datainfo['defgrad']['len'])]) # extend ASCII header with new labels
# ------------------------------------------ assemble header ---------------------------------------
table.head_write()
# ------------------------------------------ process data ---------------------------------------
while table.data_read(): # read next data line of ASCII table
for datatype,labels in active.items(): # loop over vector,tensor
for label in labels: # loop over all requested norms
F = numpy.array(map(float,table.data[column['defgrad'][active['defgrad'][0]]:
column['defgrad'][active['defgrad'][0]]+datainfo['defgrad']['len']]),'d').reshape(3,3)
(U,S,Vh) = numpy.linalg.svd(F)
R = numpy.dot(U,Vh)
stretch['U'] = numpy.dot(numpy.linalg.inv(R),F)
stretch['V'] = numpy.dot(F,numpy.linalg.inv(R))
for theStretch in stretches:
for i in range(9):
if abs(stretch[theStretch][i%3,i//3]) < 1e-15: # kill nasty noisy data
stretch[theStretch][i%3,i//3] = 0.0
(D,V) = numpy.linalg.eig(stretch[theStretch]) # eigen decomposition (of symmetric matrix)
for i,eigval in enumerate(D):
if eigval < 0.0: # flip negative eigenvalues
D[i] = -D[i]
V[:,i] = -V[:,i]
if numpy.dot(V[:,i],V[:,(i+1)%3]) != 0.0: # check each vector for orthogonality
V[:,(i+1)%3] = numpy.cross(V[:,(i+2)%3],V[:,i]) # correct next vector
V[:,(i+1)%3] /= numpy.sqrt(numpy.dot(V[:,(i+1)%3],V[:,(i+1)%3].conj())) # and renormalize (hyperphobic?)
for theStrain in strains:
d = operator(theStrain,D) # operate on eigenvalues of U or V
I = operator(theStrain,numpy.ones(3)) # operate on eigenvalues of I (i.e. [1,1,1])
eps = (numpy.dot(V,numpy.dot(numpy.diag(d),V.T)).real-numpy.diag(I)).reshape(9) # build tensor back from eigenvalue/vector basis
table.data_append(list(eps))
table.data_write() # output processed line
# ------------------------------------------ output result ---------------------------------------
table.output_flush() # just in case of buffered ASCII table
file['input'].close() # close input ASCII table
if file['name'] != 'STDIN':
file['output'].close # close output ASCII table
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new