Merge branch 'development' of magit1.mpie.de:damask/DAMASK into miscImprovements

DAMASK_env.zsh

@@ -41,7 +41,7 @@ if [ ! -z "$PS1" ]; then
   echo Max-Planck-Institut für Eisenforschung GmbH, Düsseldorf
   echo https://damask.mpie.de
   echo
-  echo Using environment with ...
+  echo "Using environment with ..."
   echo "DAMASK             $DAMASK_ROOT"
   echo "Spectral Solver    $SOLVER" 
   echo "Post Processing    $PROCESSING"

VERSION

@@ -1 +1 @@
-v2.0.1-35-g6c82641
+v2.0.1-43-g64ac05f

code/plastic_nonlocal.f90

@@ -1115,7 +1115,7 @@ allocate(nonSchmidProjection(3,3,4,maxTotalNslip,maxNinstances),
                                             
  initializeInstances: do phase = 1_pInt, size(phase_plasticity)
    NofMyPhase=count(material_phase==phase)
-   myPhase2: if (phase_plasticity(phase) == PLASTICITY_NONLOCAL_ID .and. NofMyPhase/=0) then
+   myPhase2: if (phase_plasticity(phase) == PLASTICITY_NONLOCAL_ID) then
      instance = phase_plasticityInstance(phase)
      !*** Inverse lookup of my slip system family and the slip system in lattice
      

lib/damask/asciitable.py

@@ -501,10 +501,10 @@ class ASCIItable():
       columns = []
       for i,(c,d) in enumerate(zip(indices[present],dimensions[present])):                          # for all valid labels ...
         # ... transparently add all components unless column referenced by number or with explicit dimension
-        columns += range(c,c + \
+        columns += range(c,c +
-                          (d if str(c) != str(labels[present[i]]) else \
+                          (d if str(c) != str(labels[present[i]]) else
                            1))                                                                      
-      use = np.array(columns)
+      use = np.array(columns) if len(columns) > 0 else None
 
       self.tags = list(np.array(self.tags)[use])                                                    # update labels with valid subset
 

processing/post/addMapped.py

@@ -2,6 +2,7 @@
 # -*- coding: UTF-8 no BOM -*-
 
 import os,sys
+import numpy as np
 from optparse import OptionParser
 import damask
 
@@ -28,7 +29,7 @@ parser.add_option('-o','--offset',
 parser.add_option('-l','--label',
                   dest = 'label',
                   action = 'extend', metavar = '<string LIST>',
-                  help='heading of column(s) to be mapped')
+                  help='column label(s) to be mapped')
 parser.add_option('-a','--asciitable',
                   dest = 'asciitable',
                   type = 'string', metavar = 'string',
@@ -49,12 +50,13 @@ if options.map is None:
 if options.asciitable is not None and os.path.isfile(options.asciitable):
 
   mappedTable = damask.ASCIItable(name = options.asciitable,
-                                  buffered = False, readonly = True) 
+                                  buffered = False,
+                                  readonly = True) 
   mappedTable.head_read()                                                                           # read ASCII header info of mapped table
   missing_labels = mappedTable.data_readArray(options.label)
 
   if len(missing_labels) > 0:
-    mappedTable.croak('column{} {} not found...'.format('s' if len(missing_labels) > 1 else '',', '.join(missing_labels)))
+    damask.util.croak('column{} {} not found...'.format('s' if len(missing_labels) > 1 else '',', '.join(missing_labels)))
 
 else:
   parser.error('no mapped ASCIItable given.')
@@ -64,9 +66,8 @@ else:
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:
+  try:    table = damask.ASCIItable(name = name,
-    table = damask.ASCIItable(name = name,
+                                    buffered = False)
-                              buffered = False)
   except: continue
   damask.util.report(scriptName,name)
 
@@ -96,7 +97,10 @@ for name in filenames:
 
   outputAlive = True
   while outputAlive and table.data_read():                                                          # read next data line of ASCII table
-    table.data_append(mappedTable.data[int(round(float(table.data[mappedColumn])))+options.offset-1]) # add all mapped data types
+    try:
+      table.data_append(mappedTable.data[int(round(float(table.data[mappedColumn])))+options.offset-1]) # add all mapped data types
+    except IndexError:
+      table.data_append(np.nan*np.ones_like(mappedTable.data[0]))
     outputAlive = table.data_write()                                                                # output processed line
 
 # ------------------------------------------ output finalization -----------------------------------  

processing/post/addSchmidfactors.py

@@ -167,7 +167,6 @@ force = np.array(options.force)
 force /= np.linalg.norm(force)
 
 if options.normal:
-  damask.util.croak('got normal')
   normal = np.array(options.normal)
   normal /= np.linalg.norm(normal)
   if abs(np.dot(force,normal)) > 1e-3: