From 7d96bb7ce8d9e4096ce7ff6ac6d8179f26bc6f4c Mon Sep 17 00:00:00 2001
From: Philip	Eisenlohr <eisenlohr@egr.msu.edu>
Date: Mon, 3 Dec 2012 13:10:16 +0000
Subject: [PATCH] Add column(s) containing directional stiffness based on given
 cubic stiffness values C11, C12, and C44 (in consecutive columns)

---
 processing/post/addEhkl.py           | 141 +++++++++++++++++++++++++++
 processing/setup/setup_processing.py |   3 +-
 2 files changed, 143 insertions(+), 1 deletion(-)
 create mode 100755 processing/post/addEhkl.py

diff --git a/processing/post/addEhkl.py b/processing/post/addEhkl.py
new file mode 100755
index 000000000..fc7c8fe38
--- /dev/null
+++ b/processing/post/addEhkl.py
@@ -0,0 +1,141 @@
+#!/usr/bin/env python
+
+import os,re,sys,math,numpy,string,damask
+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 normalize(vec):
+    return vec/numpy.sqrt(numpy.inner(vec,vec))
+
+def E_hkl(stiffness,vec):   # stiffness = (c11,c12,c44)
+    v = normalize(vec)
+    S11 = (stiffness[0]+stiffness[1])/(stiffness[0]*stiffness[0]+stiffness[0]*stiffness[1]-2.0*stiffness[1]*stiffness[1])
+    S12 = (            -stiffness[1])/(stiffness[0]*stiffness[0]+stiffness[0]*stiffness[1]-2.0*stiffness[1]*stiffness[1])
+    S44 = 1.0/stiffness[2]
+
+    invE = S11-(S11-S12-0.5*S44)* (1.0 - \
+                 (v[0]**4+v[1]**4+v[2]**4) \
+            /#------------------------------------
+                 numpy.inner(v,v)**2 \
+                )
+
+    return 1.0/invE
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+
+parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
+Add column(s) containing directional stiffness
+based on given cubic stiffness values C11, C12, and C44 in consecutive columns.
+
+""" + string.replace('$Id$','\n','\\n')
+)
+
+parser.add_option('-c','--stiffness',   dest='vector', action='extend', type='string', \
+                                        help='heading of column containing C11 (followed by C12, C44) field values', \
+                                        metavar='<label>')
+parser.add_option('-d','--direction', \
+                       '--hkl',         dest='hkl', action='store', type='int', nargs=3, \
+                                        help='direction of elastic modulus %default')
+
+parser.set_defaults(vector = [])
+parser.set_defaults(hkl = [1,1,1])
+
+(options,filenames) = parser.parse_args()
+
+if len(options.vector)== 0:
+  parser.error('no data column specified...')
+
+datainfo = {                                                               # list of requested labels per datatype
+             'vector':     {'len':3,
+                            'label':[]},
+           }
+
+
+if options.vector  != None:    datainfo['vector']['label']  += options.vector
+
+
+# ------------------------------------------ setup file handles ---------------------------------------  
+
+files = []
+if filenames == []:
+  files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
+else:
+  for name in filenames:
+    if os.path.exists(name):
+      files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
+
+# ------------------------------------------ loop over input files ---------------------------------------  
+
+for file in files:
+  if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
+
+  table = damask.ASCIItable(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:]))
+
+# --------------- figure out columns to process
+  active = {}
+  column = {}
+  head = []
+
+  for datatype,info in datainfo.items():
+    for label in info['label']:
+      foundIt = False
+      for key in ['1_'+label,label]:
+        if key in table.labels:
+          foundIt = True
+          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)                   # remember columns of requested data
+          table.labels_append('E%i%i%i(%s)'%(options.hkl[0],
+                                               options.hkl[1],
+                                               options.hkl[2],label)) # extend ASCII header with new labels
+      if not foundIt:
+        file['croak'].write('column %s not found...\n'%label)
+       
+# ------------------------------------------ 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 stiffnesses
+        table.data_append(E_hkl(map(float,table.data[column[datatype][label]:\
+                                                    column[datatype][label]+datainfo[datatype]['len']]),options.hkl))
+    
+    table.data_write()                                                      # output processed line
+
+# ------------------------------------------ output result ---------------------------------------  
+
+  table.output_flush()                                                      # just in case of buffered ASCII table
+
+  if file['name'] != 'STDIN':
+    file['input'].close()                                                   # close input ASCII table
+    file['output'].close()                                                  # close output ASCII table
+    os.rename(file['name']+'_tmp',file['name'])                             # overwrite old one with tmp new
diff --git a/processing/setup/setup_processing.py b/processing/setup/setup_processing.py
index 3b5d2f1b9..ccb65daf7 100755
--- a/processing/setup/setup_processing.py
+++ b/processing/setup/setup_processing.py
@@ -98,7 +98,6 @@ bin_link = { \
                 ],
         'post' : [
                 '3Dvisualize.py',
-                'addCauchy.py',
                 'addCalculation.py',
                 'addDeterminant.py',
                 'addDeviator.py',
@@ -107,8 +106,10 @@ bin_link = { \
                 'addCurl.py',
                 'addMises.py',
                 'addNorm.py',
+                'addCauchy.py',
                 'addPK2.py',
                 'addStrainTensors.py',
+                'addEhkl.py',
                 'addCompatibilityMismatch.py',
                 'addDeformedConfiguration.py',
                 'averageDown.py',