145 lines
7.6 KiB
Python
Executable File
145 lines
7.6 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string
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import numpy as np
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from collections import defaultdict
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from optparse import OptionParser
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import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = scriptID.split()[1][:-3]
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def operator(stretch,strain,eigenvalues):
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return {
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'V#ln': np.log(eigenvalues) ,
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'U#ln': np.log(eigenvalues) ,
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'V#Biot': ( np.ones(3,'d') - 1.0/eigenvalues ) ,
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'U#Biot': ( eigenvalues - np.ones(3,'d') ) ,
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'V#Green': ( np.ones(3,'d') - 1.0/eigenvalues*eigenvalues) *0.5,
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'U#Green': ( eigenvalues*eigenvalues - np.ones(3,'d')) *0.5,
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}[stretch+'#'+strain]
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add column(s) containing given strains based on given stretches of requested deformation gradient column(s).
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""", version = scriptID)
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parser.add_option('-u','--right', dest='right', action='store_true',
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help='material strains based on right Cauchy--Green deformation, i.e., C and U [%default]')
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parser.add_option('-v','--left', dest='left', action='store_true',
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help='spatial strains based on left Cauchy--Green deformation, i.e., B and V [%default]')
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parser.add_option('-l','-0','--logarithmic', dest='logarithmic', action='store_true',
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help='calculate logarithmic strain tensor [%default]')
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parser.add_option('-b','-1','--biot', dest='biot', action='store_true',
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help='calculate biot strain tensor [%default]')
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parser.add_option('-g','-2','--green', dest='green', action='store_true',
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help='calculate green strain tensor [%default]')
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parser.add_option('-f','--defgrad', dest='defgrad', action='extend', type='string', metavar = '<string LIST>',
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help='heading(s) of columns containing deformation tensor values %default')
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parser.set_defaults(right = False)
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parser.set_defaults(left = False)
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parser.set_defaults(logarithmic = False)
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parser.set_defaults(biot = False)
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parser.set_defaults(green = False)
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parser.set_defaults(defgrad = ['f'])
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(options,filenames) = parser.parse_args()
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stretches = []
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stretch = {}
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strains = []
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if options.right: stretches.append('U')
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if options.left: stretches.append('V')
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if options.logarithmic: strains.append('ln')
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if options.biot: strains.append('Biot')
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if options.green: strains.append('Green')
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datainfo = { # list of requested labels per datatype
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'defgrad': {'len':9,
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'label':[]},
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}
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datainfo['defgrad']['label'] = options.defgrad
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# ------------------------------------------ setup file handles ------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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# ------------------------------------------ loop over input files ---------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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active = []
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column = defaultdict(dict)
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for label in datainfo['defgrad']['label']:
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key = '1_%s'%label
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if key not in table.labels:
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sys.stderr.write('column %s not found...\n'%key)
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else:
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active.append(label)
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column[label] = table.labels.index(key)
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# ------------------------------------------ assemble header ---------------------------------------
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for label in active:
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for theStretch in stretches:
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for theStrain in strains:
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table.labels_append(['%i_%s(%s)%s'%(i+1,theStrain,theStretch,
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{True: label,False: ''}[label!='f'])for i in xrange(9)]) # extend ASCII header with new labels
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table.head_write()
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# ------------------------------------------ process data ------------------------------------------
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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for label in active: # loop over all requested norms
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F = np.array(map(float,table.data[column[label]:
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column[label]+datainfo['defgrad']['len']]),'d').reshape(3,3)
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(U,S,Vh) = np.linalg.svd(F)
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R = np.dot(U,Vh)
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stretch['U'] = np.dot(np.linalg.inv(R),F)
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stretch['V'] = np.dot(F,np.linalg.inv(R))
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for theStretch in stretches:
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for i in range(9):
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if abs(stretch[theStretch][i%3,i//3]) < 1e-12: # kill nasty noisy data
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stretch[theStretch][i%3,i//3] = 0.0
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(D,V) = np.linalg.eig(stretch[theStretch]) # eigen decomposition (of symmetric matrix)
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for i,eigval in enumerate(D):
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if eigval < 0.0: # flip negative eigenvalues
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D[i] = -D[i]
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V[:,i] = -V[:,i]
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if np.dot(V[:,i],V[:,(i+1)%3]) != 0.0: # check each vector for orthogonality
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V[:,(i+1)%3] = np.cross(V[:,(i+2)%3],V[:,i]) # correct next vector
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V[:,(i+1)%3] /= np.sqrt(np.dot(V[:,(i+1)%3],V[:,(i+1)%3].conj())) # and renormalize (hyperphobic?)
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for theStrain in strains:
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d = operator(theStretch,theStrain,D) # operate on eigenvalues of U or V
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eps = (np.dot(V,np.dot(np.diag(d),V.T)).real).reshape(9) # build tensor back from eigenvalue/vector basis
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table.data_append(list(eps))
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output result -----------------------------------------
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outputAlive and table.output_flush() # just in case of buffered ASCII table
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table.input_close() # close input ASCII table (works for stdin)
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table.output_close() # close output ASCII table (works for stdout)
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if file['name'] != 'STDIN':
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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