add script for adding von Mises equivalent to HDF5 file

processing/post/h5_addMises.py

@@ -0,0 +1,85 @@
+#!/usr/bin/env python2.7
+# -*- coding: UTF-8 no BOM -*-
+
+import os
+import sys
+import math
+import damask
+import numpy as np
+from optparse import OptionParser
+
+scriptName = os.path.splitext(os.path.basename(__file__))[0]
+scriptID = ' '.join([scriptName, damask.version])
+
+
+# ----- Helper functions ----- #
+def calcMises(what, tensor):
+    """calculate von Mises equivalent"""
+    dev = tensor - np.trace(tensor)/3.0*np.eye(3)
+    symdev = 0.5*(dev+dev.T)
+    return math.sqrt(np.sum(symdev*symdev.T) *
+                     {
+                     'stress': 3.0/2.0,
+                     'strain': 2.0/3.0,
+                     }[what.lower()])
+
+
+# --------------------------------------------------------------------
+#                                MAIN
+# --------------------------------------------------------------------
+desp = "Add von Mises equivalent values for symmetric part of requested"
+parser = OptionParser(option_class=damask.extendableOption,
+                      usage='%prog options [file[s]]',
+                      description=desp,
+                      version=scriptID)
+parser.add_option('-e', '--strain',
+                  dest='strain',
+                  metavar='string',
+                  help='name of dataset containing strain tensors')
+parser.add_option('-s', '--stress',
+                  dest='stress',
+                  metavar='string',
+                  help='name of dataset containing stress tensors')
+
+parser.set_defaults(strain=None, stress=None)
+
+(options, filenames) = parser.parse_args()
+
+# ----- Loop over input files ----- #
+for name in filenames:
+    try:
+        h5f = damask.H5Table(name, new_file=False)
+    except:
+        continue
+    damask.util.report(scriptName, name)
+
+    # TODO:
+    #   Could use some refactoring here
+    if options.stress is not None:
+        # extract stress tensor from HDF5
+        tnsr = h5f.get_data(options.stress)
+
+        # calculate von Mises equivalent row by row
+        vmStress = np.zeros(tnsr.shape[0])
+        for ri in xrange(tnsr.shape[0]):
+            stressTnsr = tnsr[ri, :].reshape(3, 3)
+            vmStress[ri] = calcMises('stress', stressTnsr)
+
+        # compose label
+        label = "Mises{}".format(options.stress)
+
+        # prepare log info
+        cmd_log = scriptID + '\t' + ' '.join(sys.argv[1:])
+
+        # write data to HDF5 file
+        h5f.add_data(label, vmStress, cmd_log=cmd_log)
+
+    if options.strain is not None:
+        tnsr = h5f.get_data(options.strain)
+        vmStrain = np.zeros(tnsr.shape[0])
+        for ri in xrange(tnsr.shape[0]):
+            strainTnsr = tnsr[ri, :].reshape(3, 3)
+            vmStrain[ri] = calcMises('strain', strainTnsr)
+        label = "Mises{}".format(options.strain)
+        cmd_log = scriptID + '\t' + ' '.join(sys.argv[1:])
+        h5f.add_data(label, vmStrain, cmd_log=cmd_log)