From a614e769683fb9830fe228c3b1ce0b086ee52e12 Mon Sep 17 00:00:00 2001
From: Martin	Diehl <m.diehl@mpie.de>
Date: Tue, 7 Jan 2014 20:42:51 +0000
Subject: [PATCH] first post processing script for HDF5 output

---
 processing/post/addCauchyX.py | 86 +++++++++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)
 create mode 100755 processing/post/addCauchyX.py

diff --git a/processing/post/addCauchyX.py b/processing/post/addCauchyX.py
new file mode 100755
index 000000000..862bc547f
--- /dev/null
+++ b/processing/post/addCauchyX.py
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+
+import os,re,sys,math,string,h5py
+import numpy as np
+import 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)
+
+
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+
+parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
+Add column(s) containing Cauchy stress based on given column(s) of
+deformation gradient and first Piola--Kirchhoff stress.
+
+""" + string.replace('$Id$','\n','\\n')
+)
+
+
+parser.add_option('-f','--defgrad',     dest='defgrad', type='string', \
+                                        help='heading of columns containing deformation gradient [%default]')
+parser.add_option('-p','--stress',      dest='stress', type='string', \
+                                        help='heading of columns containing first Piola--Kirchhoff stress [%default]')
+parser.add_option('-o','--output',      dest='output', type='string', \
+                                        help='group containing requested data [%default]')
+parser.set_defaults(defgrad = 'f')
+parser.set_defaults(stress  = 'p')
+parser.set_defaults(output  = 'crystallite')
+
+(options,filenames) = parser.parse_args()
+
+if options.defgrad == None or options.stress == None or options.output == None:
+  parser.error('missing data column...')
+
+
+# ------------------------------------------ setup file handles ---------------------------------------  
+
+files = []
+for name in filenames:
+  if os.path.exists(name):
+    files.append({'name':name, 'file':h5py.File(name,"a")})
+
+# ------------------------------------------ loop over input files ------------------------------------  
+
+match=re.compile("increment[0-9]*")
+for myFile in files:
+  print(myFile['name'])
+
+# ------------------------------------------ loop over increments --------------------------------------- 
+  increments = [incs+"/"+options.output for incs in filter(match.search, myFile['file'].keys())]
+  for inc in increments:
+    print("Current Group: "+inc)
+    for instance in myFile['file'][inc].keys():
+      path = inc+"/"+instance
+      dsets = myFile['file'][path].keys()
+      if (options.defgrad in dsets and options.stress in dsets):
+        defgrad = myFile['file'][path+"/"+options.defgrad]
+        stress = myFile['file'][path+"/"+options.stress]
+        cauchy=np.zeros(np.shape(stress),'f')
+        for p in range(stress.shape[0]):
+          cauchy[p,...] = 1.0/np.linalg.det(defgrad[p,...])*np.dot(stress[p,...],defgrad[p,...].T)  # [Cauchy] = (1/det(F)) * [P].[F_transpose]
+        cauchyFile = myFile['file'][path].create_dataset("cauchy", data=cauchy)
+        cauchyFile.attrs['units'] = "Pa"
+
+  
+