From dfb49c3138da194b3f41b2e8f46639891aa5fc0a Mon Sep 17 00:00:00 2001
From: chen <chenzhang8722@gamil.com>
Date: Fri, 14 Oct 2016 14:32:20 -0400
Subject: [PATCH] as script for calc Cauchy stress in HDF5

no safe net in the script, following 'let-it-fail' design
---
 processing/post/h5_addCauchy.py | 62 +++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100755 processing/post/h5_addCauchy.py

diff --git a/processing/post/h5_addCauchy.py b/processing/post/h5_addCauchy.py
new file mode 100755
index 000000000..abcfefafe
--- /dev/null
+++ b/processing/post/h5_addCauchy.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python2.7
+# -*- coding: UTF-8 no BOM -*-
+
+import os
+import sys
+import damask
+import numpy as np
+from optparse import OptionParser
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID = ' '.join([scriptName, damask.version])
+
+
+def getCauchy(f, p):
+    """return Cauchy stress for given f and p"""
+    # [Cauchy] = (1/det(F)) * [P].[F_transpose]
+    f = f.reshape((3, 3))
+    p = p.reshape((3, 3))
+    return 1.0/np.linalg.det(f)*np.dot(p, f.T).reshape(9)
+
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+desp = "Add column(s) containing Cauchy stress based on given column(s)"
+desp += "of deformation gradient and first Piola--Kirchhoff stress."
+parser = OptionParser(option_class=damask.extendableOption,
+                      usage='%prog options [file[s]]',
+                      description=desp,
+                      version=scriptID)
+parser.add_option('-f', '--defgrad',
+                  dest='defgrad',
+                  type='string', metavar='string',
+                  help='heading for deformation gradient [%default]')
+parser.add_option('-p', '--stress',
+                  dest='stress',
+                  type='string', metavar='string',
+                  help='heading for first Piola--Kirchhoff stress [%default]')
+
+parser.set_defaults(defgrad='f',
+                    stress='p')
+
+(options, filenames) = parser.parse_args()
+
+# ----- loop over input H5 files ----- #
+for name in filenames:
+    try:
+        h5f = damask.H5Table(name, new_file=False)
+    except:
+        continue
+    damask.util.report(scriptName, name)
+
+    # ----- read in data ----- #
+    f = h5f.get_data("f")
+    p = h5f.get_data("p")
+
+    # ----- calculate Cauchy stress ----- #
+    cauchy = [getCauchy(f_i, p_i) for f_i, p_i in zip(f, p)]
+
+    # ----- write to HDF5 file ----- #
+    cmd_log = " ".join([scriptID, name])
+    h5f.add_data('Cauchy', np.array(cauchy), cmd_log=cmd_log)