DAMASK_EICMD/processing/post/addStrainTensors

#!/usr/bin/python

import os,re,sys,math,numpy,string
from optparse import OptionParser, Option

def operator(how,vector):
  return { \
    'ln':    numpy.log(vector)*1.0,\
    'Biot':  vector           *1.0,\
    'Green': vector*vector    *0.5,\
         }[how]


# -----------------------------
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 prefixMultiply(what,len):

  return {True: ['%i_%s'%(i+1,what) for i in range(len)],
          False:[what]}[len>1]


# --------------------------------------------------------------------
#                                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('-m','--memory',      dest='memory', action='store_true', \
                                        help='load complete file into memory [%default]')
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(memory      = False)
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:
  print file['name']

  #  get labels by either read the first row, or - if keyword header is present - the last line of the header

  firstline = file['input'].readline()
  m = re.search('(\d+)\s*head', firstline.lower())
  if m:
    headerlines = int(m.group(1))
    passOn  = [file['input'].readline() for i in range(1,headerlines)]
    headers = file['input'].readline().split()
  else:
    headerlines = 1
    passOn  = []
    headers = firstline.split()

  if options.memory:
    data = file['input'].readlines()
  else:
    data = []

  for i,l in enumerate(headers):
    if l.startswith('1_'):
      if re.match('\d+_',l[2:]) or i == len(headers)-1 or not headers[i+1].endswith(l[2:]):
        headers[i] = l[2:]

  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 headers:
        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] = headers.index(key)
        for theStretch in stretches:
          for theStrain in strains:
            head += prefixMultiply('%s(%s)'%(theStrain,theStretch), 9)

# ------------------------------------------ assemble header ---------------------------------------  

  output = '%i\theader'%(headerlines+1) + '\n' + \
           ''.join(passOn) + \
           string.replace('$Id$','\n','\\n')+ '\t' + \
           ' '.join(sys.argv[1:]) + '\n' + \
           '\t'.join(headers + head) + '\n'                              # build extended header

  if not options.memory:
    file['output'].write(output)
    output = ''

# ------------------------------------------ read file ---------------------------------------  

  for line in {True  : data,
               False : file['input']}[options.memory]:
    items = line.split()[:len(headers)]
    if len(items) < len(headers):
      continue
  
    output += '\t'.join(items)

    for datatype,labels in active.items():
      for label in labels:
        defgrad = numpy.array(map(float,items[column[datatype][label]:
                                              column[datatype][label]+datainfo[datatype]['len']]),'d').reshape(3,3)
        (U,S,Vh) = numpy.linalg.svd(defgrad)
        R = numpy.dot(U,Vh)
        stretch['U'] = numpy.dot(numpy.linalg.inv(R),defgrad)
        stretch['V'] = numpy.dot(defgrad,numpy.linalg.inv(R))
        for theStretch in stretches:
          for i in range(9):
            if stretch[theStretch][i%3,i//3] < 1e-15:
              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
            output += '\t'+'\t'.join(map(str,eps))
         
          
    output += '\n'
  
    if not options.memory:
      file['output'].write(output)
      output = ''

  file['input'].close()

# ------------------------------------------ output result ---------------------------------------  

  if options.memory:
    file['output'].write(output)

  if file['name'] != 'STDIN':
    file['output'].close
    os.rename(file['name']+'_tmp',file['name'])