Merge branch 'MiscImprovements' into development

processing/post/addCalculation.py

@@ -66,7 +66,7 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try: 
-    table = damask.ASCIItable(name = name, buffered = False)
+    table = damask.ASCIItable(name = name)
   except IOError: 
     continue
   damask.util.report(scriptName,name)

processing/post/addEhkl.py

@@ -61,8 +61,8 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try:
-    table = damask.ASCIItable(name = name, buffered = False)
+    table = damask.ASCIItable(name = name)
-  except:
+  except IOError:
     continue
   damask.util.report(scriptName,name)
 

processing/post/addLinked.py

@@ -47,9 +47,7 @@ if options.link is None:
 
 if options.asciitable is not None and os.path.isfile(options.asciitable):
 
-  linkedTable = damask.ASCIItable(name = options.asciitable,
+  linkedTable = damask.ASCIItable(name = options.asciitable, readonly = True) 
-                                  buffered = False,
-                                  readonly = True) 
   linkedTable.head_read()                                                                           # read ASCII header info of linked table
   linkDim = linkedTable.label_dimension(options.link[1])                                            # dimension of linking column
 
@@ -72,9 +70,10 @@ else:
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,
+  try:
-                                    buffered = False)
+    table = damask.ASCIItable(name = name)
-  except: continue
+  except IOError:
+    continue
   damask.util.report(scriptName,"{} {} <== {} {}".format(name,damask.util.deemph('@ '+options.link[0]),
                                                          options.asciitable,damask.util.deemph('@ '+options.link[1])))
 

processing/post/addOrientations.py

@@ -126,7 +126,7 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try: 
-    table = damask.ASCIItable(name = name, buffered = False)
+    table = damask.ASCIItable(name = name)
   except IOError:
     continue
   damask.util.report(scriptName,name)

processing/post/addSchmidfactors.py

@@ -182,9 +182,10 @@ slip_normal    /= np.tile(np.linalg.norm(slip_normal   ,axis=1),(3,1)).T
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,
+  try:
-                                    buffered = False)
+    table = damask.ASCIItable(name = name)
-  except: continue
+  except IOError:
+    continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ read header ------------------------------------------

processing/post/binXY.py

@@ -90,13 +90,14 @@ if options.weight is not None: labels += [options.weight]
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,
+  try:
+    table = damask.ASCIItable(name = name,
                               outname = os.path.join(os.path.dirname(name),
                                                     'binned-{}-{}_'.format(*options.data) +
                                                    ('weighted-{}_'.format(options.weight) if options.weight else '') +
-                                                           os.path.basename(name)) if name else name,
+                                                    os.path.basename(name)) if name else name)
-                                    buffered = False)
+  except IOError:
-  except: continue
+    continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ read header ------------------------------------------

processing/post/filterTable.py

@@ -21,7 +21,7 @@ def sortingList(labels,whitelistitems):
   names   = []
 
   for label in labels:
-    if re.match('^\d+_',label):
+    if re.match(r'^\d+_',label):
       indices.append(int(label.split('_',1)[0]))
       names.append(label.split('_',1)[1])
     else:
@@ -66,9 +66,10 @@ parser.set_defaults(condition = None,
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,
+  try:
-                                    buffered = False)
+    table = damask.ASCIItable(name = name)
-  except: continue
+  except IOError:
+    continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ assemble info ---------------------------------------  
@@ -143,7 +144,7 @@ for name in filenames:
     try:
       table.data_readArray(positions+1)                                                               # read desired columns (indexed 1,...)
       table.data_writeArray()                                                                         # directly write out
-    except:
+    except Exception:
       table.data_rewind()
       atOnce = False                                                                                  # data contains items that prevent array chunking
 

processing/post/groupTable.py

@@ -11,11 +11,12 @@ import damask
 
 
 def periodicAverage(coords, limits):
-  """Centroid in periodic domain, see https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions"""
+  """Centroid in periodic domain, see https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions."""
   theta     = 2.0*np.pi * (coords - limits[0])/(limits[1] - limits[0])
   theta_avg = np.pi + np.arctan2(-np.sin(theta).mean(axis=0), -np.cos(theta).mean(axis=0))
   return limits[0] + theta_avg * (limits[1] - limits[0])/2.0/np.pi
 
+
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
@@ -73,7 +74,7 @@ try:
                         globals().get(funcModule) or
                         __import__(funcModule), 
                         funcName)
-except:
+except Exception:
   mapFunction = None
 
 if options.label is []:
@@ -87,9 +88,10 @@ if not hasattr(mapFunction,'__call__'):
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:    table = damask.ASCIItable(name = name,
+  try:
-                                    buffered = False)
+    table = damask.ASCIItable(name = name)
-  except: continue
+  except IOError:
+    continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ sanity checks ---------------------------------------  

processing/post/histogram.py

@@ -76,10 +76,10 @@ else:
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:    table = damask.ASCIItable(name     = name,
+  try: 
-                                    buffered = False,
+    table = damask.ASCIItable(name = name, readonly = True)
-                                    readonly = True)
+  except IOError: 
-  except: continue
+    continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ read header ------------------------------------------

processing/post/imageData.py

@@ -117,11 +117,9 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try:
-    table = damask.ASCIItable(name = name,
+    table = damask.ASCIItable(name = name, labeled = options.label is not None, readonly = True)
-                              buffered = False,
+  except IOError:
-                              labeled = options.label is not None,
+    continue
-                              readonly = True)
-  except: continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ read header ------------------------------------------

processing/post/imageDataDeformed.py

@@ -114,11 +114,10 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try:
-    table = damask.ASCIItable(name = name,
+    table = damask.ASCIItable(name = name, readonly = True,
-                              buffered = False,
+                              labeled = options.label is not None)
-                              labeled = options.label is not None,
+  except IOError:
-                              readonly = True)
+    continue
-  except: continue
   table.report_name(scriptName,name)
 
 # ------------------------------------------ read header ------------------------------------------

processing/post/imageDataRGB.py

@@ -82,11 +82,10 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try:
-    table = damask.ASCIItable(name = name,
+    table = damask.ASCIItable(name = name, readonly = True,
-                              buffered = False,
+                              labeled = options.label is not None)
-                              labeled = options.label is not None,
+  except IOError:
-                              readonly = True)
+    continue
-  except: continue
   damask.util.report(scriptName,name)
 
 # ------------------------------------------ read header ------------------------------------------

processing/post/permuteData.py

@@ -51,8 +51,7 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try:
-    table = damask.ASCIItable(name = name,
+    table = damask.ASCIItable(name = name)
-                              buffered = False)
   except IOError:
     continue
   damask.util.report(scriptName,name)

processing/post/rotateData.py

@@ -52,9 +52,9 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try:
-    table = damask.ASCIItable(name = name,
+    table = damask.ASCIItable(name = name)
-                              buffered = False)
+  except IOError:
-  except: continue
+    continue
   damask.util.report(scriptName,name)
 
 # --- interpret header ----------------------------------------------------------------------------

processing/post/viewTable.py

@@ -60,9 +60,9 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try:
-    table = damask.ASCIItable(name = name,
+    table = damask.ASCIItable(name = name, labeled = options.labeled, readonly = True)
-                              buffered = False, labeled = options.labeled, readonly = True)
+  except IOError:
-  except: continue
+    continue
   details = ', '.join(
                       (['header'] if options.table                  else []) +
                       (['info']   if options.head or options.info   else []) +

processing/pre/hybridIA_linODFsampling.py

@@ -234,7 +234,7 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   try:
-    table = damask.ASCIItable(name = name, buffered = False, readonly=True)
+    table = damask.ASCIItable(name = name, readonly=True)
   except IOError:
     continue
   damask.util.report(scriptName,name)

processing/pre/patchFromReconstructedBoundaries.py

@@ -966,9 +966,7 @@ if any(output in options.output for output in ['spectral','mentat']):
 if 'spectral' in options.output:
   fftdata = fftbuild(rcData, options.size, options.xmargin, options.ymargin, options.grid, options.extrusion)
   
-  table = damask.ASCIItable(outname = myName+'_'+str(int(fftdata['grid'][0]))+'.geom',
+  table = damask.ASCIItable(outname = myName+'_'+str(int(fftdata['grid'][0]))+'.geom', labeled = False)
-                            labeled = False,
-                            buffered = False)
   table.labels_clear()
   table.info_clear()
   table.info_append([

processing/pre/seeds_fromRandom.py

@@ -14,7 +14,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 # ------------------------------------------ aux functions ---------------------------------
 
 def kdtree_search(cloud, queryPoints):
-  """Find distances to nearest neighbor among cloud (N,d) for each of the queryPoints (n,d)"""
+  """Find distances to nearest neighbor among cloud (N,d) for each of the queryPoints (n,d)."""
   n = queryPoints.shape[0]
   distances = np.zeros(n,dtype=float)
   tree = spatial.cKDTree(cloud)
@@ -24,6 +24,7 @@ def kdtree_search(cloud, queryPoints):
 
   return distances
 
+
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
@@ -132,9 +133,10 @@ random.seed(options.randomSeed)
 if filenames == []: filenames = [None]
 
 for name in filenames:
-  try:    table = damask.ASCIItable(outname = name,
+  try:
-                                    buffered = False)
+    table = damask.ASCIItable(outname = name)
-  except: continue
+  except IOError:
+    continue
   damask.util.report(scriptName,name)
 
 # --- sanity checks -------------------------------------------------------------------------

python/damask/geom.py

@@ -148,7 +148,7 @@ class Geom():
         """
         if microstructure is not None:
             if len(microstructure.shape) != 3:
-                raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape))
+                raise ValueError('Invalid microstructure shape {}'.format(microstructure.shape))
             elif microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
                 raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype))
             else:
@@ -169,7 +169,7 @@ class Geom():
             self.size = grid/np.max(grid)
         else:
             if len(size) != 3 or any(np.array(size)<=0):
-                raise ValueError('Invalid size {}'.format(*size))
+                raise ValueError('Invalid size {}'.format(size))
             else:
                 self.size = np.array(size)
 
@@ -185,7 +185,7 @@ class Geom():
         """
         if origin is not None:
             if len(origin) != 3:
-                raise ValueError('Invalid origin {}'.format(*origin))
+                raise ValueError('Invalid origin {}'.format(origin))
             else:
                 self.origin = np.array(origin)
 
@@ -297,7 +297,7 @@ class Geom():
             i += len(items)
         
         if i != grid.prod():
-            raise TypeError('Invalid file: expected {} entries,found {}'.format(grid.prod(),i))
+            raise TypeError('Invalid file: expected {} entries, found {}'.format(grid.prod(),i))
         
         microstructure = microstructure.reshape(grid,order='F')
         if not np.any(np.mod(microstructure.flatten(),1) != 0.0):                                   # no float present
@@ -458,7 +458,7 @@ class Geom():
         if not all(isinstance(d, str) for d in directions):
             raise TypeError('Directions are not of type str.')
         elif not set(directions).issubset(valid):
-            raise ValueError('Invalid direction specified {}'.format(*set(directions).difference(valid)))
+            raise ValueError('Invalid direction specified {}'.format(set(directions).difference(valid)))
 
         limits = [None,None] if reflect else [-2,0]
         ms = self.get_microstructure()

src/crystallite.f90

@@ -57,7 +57,6 @@ module crystallite
     crystallite_Li0, &                                                                              !< intermediate velocitiy grad at start of FE inc
     crystallite_partionedLi0                                                                        !< intermediate velocity grad at start of homog inc
   real(pReal),                dimension(:,:,:,:,:),    allocatable :: &
-    crystallite_subS0, &                                                                            !< 2nd Piola-Kirchhoff stress vector at start of crystallite inc
     crystallite_invFp, &                                                                            !< inverse of current plastic def grad (end of converged time step)
     crystallite_subFp0,&                                                                            !< plastic def grad at start of crystallite inc
     crystallite_invFi, &                                                                            !< inverse of current intermediate def grad (end of converged time step)
@@ -136,7 +135,6 @@ subroutine crystallite_init
   allocate(crystallite_S0(3,3,cMax,iMax,eMax),                source=0.0_pReal)
   allocate(crystallite_partionedS0(3,3,cMax,iMax,eMax),       source=0.0_pReal)
   allocate(crystallite_S(3,3,cMax,iMax,eMax),                 source=0.0_pReal)
-  allocate(crystallite_subS0(3,3,cMax,iMax,eMax),             source=0.0_pReal)
   allocate(crystallite_P(3,3,cMax,iMax,eMax),                 source=0.0_pReal)
   allocate(crystallite_F0(3,3,cMax,iMax,eMax),                source=0.0_pReal)
   allocate(crystallite_partionedF0(3,3,cMax,iMax,eMax),       source=0.0_pReal)
@@ -351,7 +349,6 @@ function crystallite_stress(dummyArgumentToPreventInternalCompilerErrorWithGCC)
         crystallite_subFi0(1:3,1:3,c,i,e) = crystallite_partionedFi0(1:3,1:3,c,i,e)
         crystallite_subLi0(1:3,1:3,c,i,e) = crystallite_partionedLi0(1:3,1:3,c,i,e)
         crystallite_subF0(1:3,1:3,c,i,e)  = crystallite_partionedF0(1:3,1:3,c,i,e)
-        crystallite_subS0(1:3,1:3,c,i,e)  = crystallite_partionedS0(1:3,1:3,c,i,e)
         crystallite_subFrac(c,i,e) = 0.0_pReal
         crystallite_subStep(c,i,e) = 1.0_pReal/num%subStepSizeCryst
         crystallite_todo(c,i,e) = .true.
@@ -397,7 +394,6 @@ function crystallite_stress(dummyArgumentToPreventInternalCompilerErrorWithGCC)
               crystallite_subLi0(1:3,1:3,c,i,e) = crystallite_Li  (1:3,1:3,c,i,e)
               crystallite_subFp0(1:3,1:3,c,i,e) = crystallite_Fp  (1:3,1:3,c,i,e)
               crystallite_subFi0(1:3,1:3,c,i,e) = crystallite_Fi  (1:3,1:3,c,i,e)
-              crystallite_subS0 (1:3,1:3,c,i,e) = crystallite_S   (1:3,1:3,c,i,e)
               !if abbrevation, make c and p private in omp
               plasticState(    material_phaseAt(c,e))%subState0(:,material_phaseMemberAt(c,i,e)) &
                 = plasticState(material_phaseAt(c,e))%state(    :,material_phaseMemberAt(c,i,e))