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

lib/damask/result.py

@@ -2,12 +2,12 @@
 
 
 import numpy as np
-import sys
+#import sys
 
 try:
   import h5py
 except (ImportError) as e:
-  sys.stderr.write('\nREMARK: h5py module not available \n\n')
+  pass #  sys.stderr.write('\nREMARK: h5py module not available \n\n')
 
 class Result():
   """

lib/damask/test/test.py

@@ -336,16 +336,16 @@ class Test():
       key0    = ('1_' if     length[i]>1 else '') +    headings0[i]['label']
       key1    = ('1_' if     length[i]>1 else '') +    headings1[i]['label']
       normKey = ('1_' if normLength[i]>1 else '') + normHeadings[i]['label']
-      if key0 not in table0.labels:
+      if key0 not in table0.labels(raw = True):
         raise Exception('column {} not found in 1. table...\n'.format(key0))
-      elif key1 not in table1.labels:
+      elif key1 not in table1.labels(raw = True):
         raise Exception('column {} not found in 2. table...\n'.format(key1))
-      elif normKey not in table0.labels:
+      elif normKey not in table0.labels(raw = True):
         raise Exception('column {} not found in 1. table...\n'.format(normKey))
       else:
-        column[0][i]  = table0.labels.index(key0)
+        column[0][i]  = table0.label_index(key0)
-        column[1][i]  = table1.labels.index(key1)
+        column[1][i]  = table1.label_index(key1)
-        normColumn[i] = table0.labels.index(normKey)
+        normColumn[i] = table0.label_index(normKey)
     
     line0 = 0
     while table0.data_read():                                                  # read next data line of ASCII table
@@ -421,7 +421,7 @@ class Test():
     columns = columns[:len(files)]                                             # truncate to same length as files
 
     for i,column in enumerate(columns):
-      if column is None: columns[i] = tables[i].labels                         # if no column is given, read all
+      if column is None: columns[i] = tables[i].labels(raw = True)             # if no column is given, read all
 
     logging.info('comparing ASCIItables statistically')
     for i in xrange(len(columns)):
@@ -477,7 +477,7 @@ class Test():
     columns = columns[:len(files)]                                             # truncate to same length as files
 
     for i,column in enumerate(columns):
-      if column is None: columns[i] = tables[i].labels                         # if no column is given, read all
+      if column is None: columns[i] = tables[i].labels(raw = True)             # if no column is given, read all
 
     logging.info('comparing ASCIItables')
     for i in xrange(len(columns)):

processing/misc/yieldSurface.py

@@ -138,7 +138,7 @@ def principalStrs_Der(p, (s1, s2, s3, s4, s5, s6), dim, Karafillis=False):
     return np.array([np.dot(dSdI[:,:,i],dIdc[:,:,i]).T for i in xrange(num)]).T
 
 def invariant(sigmas):
-    I=np.zeros(3)
+    I = np.zeros(3)
     s11,s22,s33,s12,s23,s31 = sigmas
     I[0] = s11 + s22 + s33
     I[1] = s11*s22 + s22*s33 + s33*s11 - s12**2 - s23**2 - s31**2
@@ -1271,13 +1271,12 @@ def doSim(thread):
   table = damask.ASCIItable(refFile,readonly=True)
   table.head_read()
 
-  if options.fitting =='equivalentStrain':
+  thresholdKey = {'equivalentStrain':'Mises(ln(V))',
-    thresholdKey = 'Mises(ln(V))'
+                  'totalshear':       'totalshear',
-  elif options.fitting =='totalshear':
+                 }[options.fitting]
-    thresholdKey = 'totalshear'
 
   for l in [thresholdKey,'1_Cauchy']:
-    if l not in table.labels: damask.util.croak('%s not found'%l)
+    if l not in table.labels(raw = True): damask.util.croak('%s not found'%l)
   s.release()
 
   table.data_readArray(['%i_Cauchy'%(i+1) for i in xrange(9)]+[thresholdKey]+['%i_ln(V)'%(i+1) for i in xrange(9)])
@@ -1380,51 +1379,46 @@ parser.add_option('-e', '--exponent',  dest='exponent', type='float',
 parser.add_option('-u', '--uniaxial',  dest='eqStress', type='float',
                                        help='Equivalent stress',  metavar='float') 
 
-parser.set_defaults(min        = 12)
+parser.set_defaults(min        = 12,
-parser.set_defaults(max        = 30)
+                    max        = 30,
-parser.set_defaults(threads    = 4)
+                    threads    = 4,
-parser.set_defaults(yieldValue = (0.002,0.004,2))
+                    yieldValue = (0.002,0.004,2),
-parser.set_defaults(load       = (0.010,100,100.0))
+                    load       = (0.010,100,100.0),
-parser.set_defaults(criterion  = 'vonmises')
+                    criterion  = 'vonmises',
-parser.set_defaults(fitting    = 'totalshear')
+                    fitting    = 'totalshear',
-parser.set_defaults(geometry   = '20grains16x16x16')
+                    geometry   = '20grains16x16x16',
-parser.set_defaults(bounds     = None)
+                    bounds     = None,
-parser.set_defaults(dimension  = '3')
+                    dimension  = '3',
-parser.set_defaults(exponent   = -1.0)
+                    exponent   = -1.0,
+                   )
 
 options = parser.parse_args()[0]
 
-if not os.path.isfile(options.geometry+'.geom'):
+if options.threads < 1:
-  parser.error('geometry file %s.geom not found'%options.geometry)
+  parser.error('invalid number of threads {}'.format(options.threads))
-if not os.path.isfile('material.config'):
+if options.min < 0:
-  parser.error('material.config file not found')
+  parser.error('invalid minimum number of simulations {}'.format(options.min))
-if options.threads<1:
+if options.max < options.min:
-  parser.error('invalid number of threads %i'%options.threads)
-if options.min<0:
-  parser.error('invalid minimum number of simulations %i'%options.min)
-if options.max<options.min:
   parser.error('invalid maximum number of simulations (below minimum)')
-if options.yieldValue[0]>options.yieldValue[1]:
+if options.yieldValue[0] > options.yieldValue[1]:
   parser.error('invalid yield start (below yield end)')
 if options.yieldValue[2] != int(options.yieldValue[2]):
   parser.error('count must be an integer')
 
-if not os.path.isfile('numerics.config'):
+for check in [options.geometry+'.geom','numerics.config','material.config']:
-  damask.util.croak('numerics.config file not found')
+  if not os.path.isfile(check):
-if not os.path.isfile('material.config'):
+    damask.util.croak('"{}" file not found'.format(check))
-  damask.util.croak('material.config file not found')
 
 options.dimension = int(options.dimension)
 
-if options.criterion == 'hill1948': stressUnit = 1.0e9
+stressUnit = 1.0e9 if options.criterion == 'hill1948' else 1.0e6
-else                              : stressUnit = 1.0e6
 
 
 if options.dimension not in fitCriteria[options.criterion]['dimen']:
   parser.error('invalid dimension for selected criterion')
 
-if options.criterion not in ['vonmises','tresca','drucker','hill1984'] and options.eqStress is None:
+if options.criterion not in ['vonmises','tresca','drucker','hill1948'] and options.eqStress is None:
-   parser.error('please specifie an equivalent stress (e.g. fitting to von Mises)') 
+   parser.error('please specify an equivalent stress (e.g. fitting to von Mises)') 
 
 run = runFit(options.exponent, options.eqStress, options.dimension, options.criterion)
 

processing/post/addTable.py

@@ -29,33 +29,30 @@ parser.add_option('-a', '--add','--table',
 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)
+
   tables = []
   for addTable in options.table:
-    try:
+    try:    tables.append(damask.ASCIItable(name = addTable,
-      tables.append(damask.ASCIItable(name = addTable,
+                                            buffered = False,
-                                      buffered = False,
+                                            readonly = True)
-                                      readonly = True)
+                         )
-                   )
     except: continue
 
 # ------------------------------------------ read headers ------------------------------------------
 
   table.head_read()
-  for addTable in tables:
+  for addTable in tables: addTable.head_read()
-    addTable.head_read()
 
 # ------------------------------------------ assemble header --------------------------------------
 
   table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
 
-  for addTable in tables:
+  for addTable in tables: table.labels_append(addTable.labels(raw = True))                          # extend ASCII header with new labels
-    table.labels_append(addTable.labels)                                                            # extend ASCII header with new labels
 
   table.head_write()
 

processing/post/averageTable.py

@@ -37,8 +37,6 @@ if options.label is None:
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  damask.util.croak(name)
-
   try:    table = damask.ASCIItable(name = name,
                                     outname = os.path.join(
                                               os.path.split(name)[0],

processing/pre/geom_pack.py

@@ -91,11 +91,11 @@ for name in filenames:
         if   type == '':
           table.data = []
         elif type == '.':
-          table.data = [str(former)]
+          table.data = [former]
         elif type == 'to':
-          table.data = ['{0} to {1}'.format(former-reps+1,former)]
+          table.data = [former-reps+1,'to',former]
         elif type == 'of':
-          table.data = ['{0} of {1}'.format(reps,former)]
+          table.data = [reps,'of',former]
 
         outputAlive = table.data_write(delimiter = ' ')                                             # output processed line
 
@@ -106,9 +106,9 @@ for name in filenames:
       former = current
 
   table.data = {
-                '.' : [str(former)],
+                '.' : [former],
-                'to': ['%i to %i'%(former-reps+1,former)],
+                'to': [former-reps+1,'to',former],
-                'of': ['%i of %i'%(reps,former)],
+                'of': [reps,'of',former],
                }[type]
 
   outputAlive = table.data_write(delimiter = ' ')                                                   # output processed line