Merge remote-tracking branch 'origin/development' into stress-ramp-loadcase

.gitlab-ci.yml

@@ -25,6 +25,7 @@ before_script:
     fi
   - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $TESTROOT/GitLabCI.queue) != 1 ];
       do sleep 5m;
+      echo -e "Currently queued pipelines:\n$(cat $TESTROOT/GitLabCI.queue)\n";
     done
   - source $DAMASKROOT/env/DAMASK.sh
   - cd $DAMASKROOT/PRIVATE/testing
@@ -87,6 +88,7 @@ checkout:
     - echo $CI_PIPELINE_ID >> $TESTROOT/GitLabCI.queue
     - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $TESTROOT/GitLabCI.queue) != 1 ];
         do sleep 5m;
+        echo -e "Currently queued pipelines:\n$(cat $TESTROOT/GitLabCI.queue)\n";
       done
   script:
     - mkdir -p $DAMASKROOT

PRIVATE

@@ -1 +1 @@
-Subproject commit 555f3e01f2b5cf43ade1bd48423b890adca21771
+Subproject commit 2550bf655aebe61ce459718323ba38b1ac205a7f

VERSION

@@ -1 +1 @@
-v3.0.0-alpha-233-g190f8a82
+v3.0.0-alpha-321-g0f6495430

processing/legacy/addAPS34IDEstrainCoords.py

@@ -42,11 +42,10 @@ rot_to_TSL = damask.Rotation.from_axis_angle([-1,0,0,.75*np.pi])
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
+
     coord      = - table.get(options.frame)
     coord[:,2] += table.get(options.depth)[:,0]
 
-    table.add('coord',rot_to_TSL.broadcast_to(coord.shape[0]) @ coord,scriptID+' '+' '.join(sys.argv[1:]))
-
-    table.to_file(sys.stdout if name is None else name)
+    table.add('coord',rot_to_TSL.broadcast_to(coord.shape[0]) @ coord,scriptID+' '+' '.join(sys.argv[1:]))\
+         .save((sys.stdout if name is None else name),legacy=True)

processing/legacy/addCumulative.py

@@ -39,10 +39,10 @@ if options.labels is None:
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     for label in options.labels:
-        table.add('cum_{}({})'.format('prod'     if options.product else 'sum',label),
-                  np.cumprod(table.get(label),0) if options.product else np.cumsum(table.get(label),0),
-                  scriptID+' '+' '.join(sys.argv[1:]))
+        table = table.add('cum_{}({})'.format('prod'     if options.product else 'sum',label),
+                          np.cumprod(table.get(label),0) if options.product else np.cumsum(table.get(label),0),
+                          scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name),legacy=True)

processing/post/DADF5_postResults.py

@@ -38,8 +38,8 @@ for filename in options.filenames:
     N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
     N_digits = 5 # hack to keep test intact
     for inc in damask.util.show_progress(results.iterate('increments'),len(results.increments)):
-        table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)})
-        table = table.add('pos',coords.reshape(-1,3))
+        table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)})\
+                      .add('pos',coords.reshape(-1,3))
 
         results.pick('materialpoints',False)
         results.pick('constituents',  True)
@@ -60,4 +60,4 @@ for filename in options.filenames:
             os.mkdir(dirname,0o755)
         file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0],
                                          inc[3:].zfill(N_digits))
-        table.to_file(os.path.join(dirname,file_out))
+        table.save(os.path.join(dirname,file_out),legacy=True)

processing/post/addCompatibilityMismatch.py

@@ -172,7 +172,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
   damask.util.report(scriptName,name)
 
-  table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+  table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
   grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
   F = table.get(options.defgrad).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3))
@@ -191,4 +191,4 @@ for name in filenames:
                       volumeMismatch.reshape(-1,1,order='F'),
                       scriptID+' '+' '.join(sys.argv[1:]))
 
-  table.to_file(sys.stdout if name is None else name)
+  table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addCurl.py

@@ -43,7 +43,7 @@ if options.labels is None: parser.error('no data column specified.')
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
     for label in options.labels:
@@ -55,4 +55,4 @@ for name in filenames:
                           curl.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape),order='F'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addDerivative.py

@@ -14,9 +14,9 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
 def derivative(coordinates,what):
-  
+
   result = np.empty_like(what)
-  
+
   # use differentiation by interpolation
   # as described in http://www2.math.umd.edu/~dlevy/classes/amsc466/lecture-notes/differentiation-chap.pdf
 
@@ -31,7 +31,7 @@ def derivative(coordinates,what):
                    (coordinates[0] - coordinates[1])
   result[-1,:]   = (what[-1,:] - what[-2,:]) / \
                    (coordinates[-1] - coordinates[-2])
-  
+
   return result
 
 
@@ -65,10 +65,10 @@ if options.labels is None:
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     for label in options.labels:
         table = table.add('d({})/d({})'.format(label,options.coordinates),
                           derivative(table.get(options.coordinates),table.get(label)),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addDisplacement.py

@@ -47,25 +47,25 @@ parser.set_defaults(f   = 'f',
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
     F = table.get(options.f).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3))
     if options.nodal:
-        table = damask.Table(damask.grid_filters.node_coord0(grid,size).reshape(-1,3,order='F'),
+        damask.Table(damask.grid_filters.node_coord0(grid,size).reshape(-1,3,order='F'),
                      {'pos':(3,)})\
               .add('avg({}).{}'.format(options.f,options.pos),
                    damask.grid_filters.node_displacement_avg(size,F).reshape(-1,3,order='F'),
                    scriptID+' '+' '.join(sys.argv[1:]))\
               .add('fluct({}).{}'.format(options.f,options.pos),
                    damask.grid_filters.node_displacement_fluct(size,F).reshape(-1,3,order='F'),
-                    scriptID+' '+' '.join(sys.argv[1:]))
-        table.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt')
+                    scriptID+' '+' '.join(sys.argv[1:]))\
+               .save((sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt'), legacy=True)
     else:
-        table = table.add('avg({}).{}'.format(options.f,options.pos),
+        table.add('avg({}).{}'.format(options.f,options.pos),
                   damask.grid_filters.cell_displacement_avg(size,F).reshape(-1,3,order='F'),
                   scriptID+' '+' '.join(sys.argv[1:]))\
              .add('fluct({}).{}'.format(options.f,options.pos),
                   damask.grid_filters.cell_displacement_fluct(size,F).reshape(-1,3,order='F'),
-                  scriptID+' '+' '.join(sys.argv[1:]))
-        table.to_file(sys.stdout if name is None else name)
+                  scriptID+' '+' '.join(sys.argv[1:]))\
+             .save((sys.stdout if name is None else name), legacy=True)

processing/post/addDivergence.py

@@ -43,7 +43,7 @@ if options.labels is None: parser.error('no data column specified.')
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
     for label in options.labels:
@@ -55,4 +55,4 @@ for name in filenames:
                           div.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)//3,order='F'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addEuclideanDistance.py

@@ -142,7 +142,7 @@ for i,feature in enumerate(features):
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
     neighborhood = neighborhoods[options.neighborhood]
@@ -158,7 +158,7 @@ for name in filenames:
         diffToNeighbor[:,:,:,i] = ndimage.convolve(microstructure,stencil)                          # compare ID at each point...
                                                                                                     # ...to every one in the specified neighborhood
                                                                                                     # for same IDs at both locations ==> 0
-  
+
     diffToNeighbor = np.sort(diffToNeighbor)                                                        # sort diff such that number of changes in diff (steps)...
                                                                                                     # ...reflects number of unique neighbors
     uniques = np.where(diffToNeighbor[1:-1,1:-1,1:-1,0] != 0, 1,0)                                  # initialize unique value counter (exclude myself [= 0])
@@ -184,4 +184,4 @@ for name in filenames:
                           distance[i,:],
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addGaussian.py

@@ -63,7 +63,7 @@ if options.labels is None: parser.error('no data column specified.')
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     damask.grid_filters.coord0_check(table.get(options.pos))
 
     for label in options.labels:
@@ -73,4 +73,4 @@ for name in filenames:
                                                           mode = 'wrap' if options.periodic else 'nearest'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addGradient.py

@@ -43,7 +43,7 @@ if options.labels is None: parser.error('no data column specified.')
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
     for label in options.labels:
@@ -55,4 +55,4 @@ for name in filenames:
                           grad.reshape(tuple(grid)+(-1,)).reshape(-1,np.prod(shape)*3,order='F'),
                           scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addOrientations.py

@@ -110,7 +110,7 @@ R = damask.Rotation.from_axis_angle(np.array(options.labrotation),options.degree
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     if   options.eulers is not None:
         label = options.eulers
@@ -147,4 +147,4 @@ for name in filenames:
     if 'axisangle' in options.output:
         table = table.add('om({})'.format(label),o.as_axisangle(options.degrees), scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/addSchmidfactors.py

@@ -175,7 +175,7 @@ labels = ['S[{direction[0]:.1g}_{direction[1]:.1g}_{direction[2]:.1g}]'
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     o = damask.Rotation.from_quaternion(table.get(options.quaternion))
 
@@ -189,4 +189,4 @@ for name in filenames:
     for i,label in enumerate(labels):
         table = table.add(label,S[:,i],scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/post/filterTable.py

@@ -27,7 +27,7 @@ def sortingList(labels,whitelistitems):
     else:
       indices.append(0)
       names.append(label)
-      
+
   return [indices,names,whitelistitems]
 
 
@@ -72,11 +72,11 @@ for name in filenames:
     continue
   damask.util.report(scriptName,name)
 
-# ------------------------------------------ assemble info ---------------------------------------  
+# ------------------------------------------ assemble info ---------------------------------------
 
   table.head_read()
 
-# ------------------------------------------ process data ---------------------------------------  
+# ------------------------------------------ process data ---------------------------------------
 
   specials = { \
                '_row_': 0,
@@ -103,12 +103,12 @@ for name in filenames:
             else np.lexsort(sortingList(labels,whitelistitem))                                      # reorder if unique, i.e. no "-1" in whitelistitem
   else:
     order = range(len(labels))                                                                      # maintain original order of labels
-  
+
 # --------------------------------------- evaluate condition ---------------------------------------
   if options.condition is not None:
     condition = options.condition                                                                   # copy per file, since might be altered inline
     breaker = False
-  
+
     for position,(all,marker,column) in enumerate(set(re.findall(r'#(([s]#)?(.+?))#',condition))):              # find three groups
       idx = table.label_index(column)
       dim = table.label_dimension(column)
@@ -123,11 +123,11 @@ for name in filenames:
                                                         's#':'str'}[marker],idx)                      # take float or string value of data column
         elif dim > 1:                                                                                 # multidimensional input (vector, tensor, etc.)
           replacement = 'np.array(table.data[{}:{}],dtype=float)'.format(idx,idx+dim)                 # use (flat) array representation
-       
+
         condition = condition.replace('#'+all+'#',replacement)
-    
+
     if breaker: continue                                                                              # found mistake in condition evaluation --> next file
-  
+
 # ------------------------------------------ assemble header ---------------------------------------
 
   table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
@@ -138,7 +138,7 @@ for name in filenames:
 # ------------------------------------------ process and output data ------------------------------------------
 
   positions = np.array(positions)[order]
-  
+
   atOnce = options.condition is None
   if atOnce:                                                                                          # read full array and filter columns
     try:

processing/post/permuteData.py

@@ -47,7 +47,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     randomSeed = int(os.urandom(4).hex(), 16) if options.randomSeed is None else options.randomSeed # random seed per file
     rng = np.random.default_rng(randomSeed)
@@ -58,4 +58,4 @@ for name in filenames:
         rng.shuffle(uniques)
         table = table.set(label,uniques[inverse], scriptID+' '+' '.join(sys.argv[1:]))
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save((sys.stdout if name is None else name), legacy=True)

processing/pre/geom_fromDREAM3D.py

@@ -52,16 +52,11 @@ parser.add_option('-q', '--quaternion',
                   type = 'string',
                   metavar='string',
                   help = 'name of the dataset containing pointwise/average orientation as quaternion [%default]')
-parser.add_option('--homogenization',
-                  dest = 'homogenization',
-                  type = 'int', metavar = 'int',
-                  help = 'homogenization index to be used [%default]')
 
 parser.set_defaults(pointwise      = 'CellData',
                     quaternion     = 'Quats',
                     phase          = 'Phases',
                     microstructure = 'FeatureIds',
-                    homogenization = 1,
                    )
 
 (options, filenames) = parser.parse_args()
@@ -150,8 +145,7 @@ for name in filenames:
 
   header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
          + config_header
-  geom = damask.Geom(microstructure,size,origin,
-                     homogenization=options.homogenization,comments=header)
+  geom = damask.Geom(microstructure,size,origin,comments=header)
   damask.util.croak(geom)
 
-  geom.to_file(os.path.splitext(name)[0]+'.geom',format='ASCII',pack=False)
+  geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False)

processing/pre/geom_fromMinimalSurface.py

@@ -52,10 +52,6 @@ parser.add_option('-p', '--periods',
                   dest = 'periods',
                   type = 'int', metavar = 'int',
                   help = 'number of repetitions of unit cell [%default]')
-parser.add_option('--homogenization',
-                  dest = 'homogenization',
-                  type = 'int', metavar = 'int',
-                  help = 'homogenization index to be used [%default]')
 parser.add_option('--m',
                   dest = 'microstructure',
                   type = 'int', nargs = 2, metavar = 'int int',
@@ -66,7 +62,6 @@ parser.set_defaults(type = minimal_surfaces[0],
                     periods = 1,
                     grid = (16,16,16),
                     size = (1.0,1.0,1.0),
-                    homogenization = 1,
                     microstructure = (1,2),
                    )
 
@@ -85,8 +80,7 @@ microstructure = np.where(options.threshold < surface[options.type](x,y,z),
                           options.microstructure[1],options.microstructure[0])
 
 geom=damask.Geom(microstructure,options.size,
-                 homogenization=options.homogenization,
                  comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
 damask.util.croak(geom)
 
-geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)
+geom.save_ASCII(sys.stdout if name is None else name,compress=False)

processing/pre/geom_fromOsteonGeometry.py

@@ -57,10 +57,6 @@ parser.add_option('-w', '--omega',
                   dest='omega',
                   type='float', metavar = 'float',
                   help='rotation angle around normal of osteon [%default]')
-parser.add_option(      '--homogenization',
-                  dest='homogenization',
-                  type='int', metavar = 'int',
-                  help='homogenization index to be used [%default]')
 
 parser.set_defaults(canal = 25e-6,
                     osteon = 100e-6,
@@ -70,7 +66,7 @@ parser.set_defaults(canal = 25e-6,
                     amplitude = 60,
                     size = (300e-6,300e-6),
                     grid = (512,512),
-                    homogenization = 1)
+                   )
 
 (options,filename) = parser.parse_args()
 
@@ -139,7 +135,7 @@ header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
        + config_header
 geom = damask.Geom(microstructure.reshape(grid),
                    size,-size/2,
-                   homogenization=options.homogenization,comments=header)
+                   comments=header)
 damask.util.croak(geom)
 
-geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)
+geom.save_ASCII(sys.stdout if name is None else name,compress=False)

processing/pre/geom_fromTable.py

@@ -44,14 +44,9 @@ parser.add_option('--axes',
                   dest = 'axes',
                   type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
                   help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]')
-parser.add_option('--homogenization',
-                  dest = 'homogenization',
-                  type = 'int', metavar = 'int',
-                  help = 'homogenization index to be used [%default]')
 
 
-parser.set_defaults(homogenization = 1,
-                    pos            = 'pos',
+parser.set_defaults(pos            = 'pos',
                    )
 
 (options,filenames) = parser.parse_args()
@@ -68,7 +63,7 @@ if options.axes is not None and not set(options.axes).issubset(set(['x','+x','-x
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
     table.sort_by(['{}_{}'.format(i,options.pos) for i in range(3,0,-1)])                           # x fast, y slow
     grid,size,origin = damask.grid_filters.cell_coord0_gridSizeOrigin(table.get(options.pos))
 
@@ -102,8 +97,7 @@ for name in filenames:
     header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
            + config_header
     geom = damask.Geom(microstructure,size,origin,
-                       homogenization=options.homogenization,comments=header)
+                       comments=header)
     damask.util.croak(geom)
 
-    geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',
-                 format='ASCII',pack=False)
+    geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False)

processing/pre/geom_fromVoronoiTessellation.py

@@ -142,10 +142,6 @@ group.add_option('--without-config',
                  dest = 'config',
                  action = 'store_false',
                  help = 'omit material configuration header')
-group.add_option('--homogenization',
-                 dest = 'homogenization',
-                 type = 'int', metavar = 'int',
-                 help = 'homogenization index to be used [%default]')
 group.add_option('--phase',
                  dest = 'phase',
                  type = 'int', metavar = 'int',
@@ -157,7 +153,6 @@ parser.set_defaults(pos            = 'pos',
                     weight         = 'weight',
                     microstructure = 'microstructure',
                     eulers         = 'euler',
-                    homogenization = 1,
                     phase          = 1,
                     cpus           = 2,
                     laguerre       = False,
@@ -171,7 +166,7 @@ if filenames == []: filenames = [None]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     size   = np.ones(3)
     origin = np.zeros(3)
@@ -225,8 +220,7 @@ for name in filenames:
     header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
            + config_header
     geom = damask.Geom(indices.reshape(grid),size,origin,
-                       homogenization=options.homogenization,comments=header)
+                       comments=header)
     damask.util.croak(geom)
 
-    geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',
-                 format='ASCII',pack=False)
+    geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False)

processing/pre/geom_grainGrowth.py

@@ -41,7 +41,7 @@ parser.add_option('-N', '--iterations',
                   help = 'curvature flow iterations [%default]')
 parser.add_option('-i', '--immutable',
                   action = 'extend', dest = 'immutable', metavar = '<int LIST>',
-                  help = 'list of immutable microstructure indices')
+                  help = 'list of immutable material indices')
 parser.add_option('--ndimage',
                   dest = 'ndimage', action='store_true',
                   help = 'use ndimage.gaussian_filter in lieu of explicit FFT')
@@ -62,17 +62,17 @@ if filenames == []: filenames = [None]
 for name in filenames:
   damask.util.report(scriptName,name)
 
-  geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
+  geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
-  grid_original = geom.get_grid()
+  grid_original = geom.grid
   damask.util.croak(geom)
-  microstructure = np.tile(geom.microstructure,np.where(grid_original == 1, 2,1))                   # make one copy along dimensions with grid == 1
-  grid = np.array(microstructure.shape)
+  material = np.tile(geom.material,np.where(grid_original == 1, 2,1))                   # make one copy along dimensions with grid == 1
+  grid = np.array(material.shape)
 
 # --- initialize support data ---------------------------------------------------------------------
 
-# store a copy the initial microstructure to find locations of immutable indices
-  microstructure_original = np.copy(microstructure)
+# store a copy of the initial material indices to find locations of immutable indices
+  material_original = np.copy(material)
 
   if not options.ndimage:
     X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]]
@@ -88,14 +88,14 @@ for name in filenames:
 
   for smoothIter in range(options.N):
 
-    interfaceEnergy = np.zeros(microstructure.shape,dtype=np.float32)
+    interfaceEnergy = np.zeros(material.shape,dtype=np.float32)
     for i in (-1,0,1):
       for j in (-1,0,1):
         for k in (-1,0,1):
           # assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
           interfaceEnergy = np.maximum(interfaceEnergy,
-                                       getInterfaceEnergy(microstructure,np.roll(np.roll(np.roll(
-                                                          microstructure,i,axis=0), j,axis=1), k,axis=2)))
+                                       getInterfaceEnergy(material,np.roll(np.roll(np.roll(
+                                                          material,i,axis=0), j,axis=1), k,axis=2)))
 
     # periodically extend interfacial energy array by half a grid size in positive and negative directions
     periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
@@ -129,13 +129,13 @@ for name in filenames:
                                                             iterations = int(round(options.d*2.))-1),# fat boundary
                          periodic_bulkEnergy[grid[0]//2:-grid[0]//2,                                 # retain filled energy on fat boundary...
                                              grid[1]//2:-grid[1]//2,
-                                             grid[2]//2:-grid[2]//2],                                # ...and zero everywhere else
+                                             grid[2]//2:-grid[2]//2],                               # ...and zero everywhere else
                          0.)).astype(np.complex64) *
                          gauss).astype(np.float32)
 
       periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
                                                                 grid[1]//2:-grid[1]//2,
-                                                                grid[2]//2:-grid[2]//2]              # periodically extend the smoothed bulk energy
+                                                                grid[2]//2:-grid[2]//2]             # periodically extend the smoothed bulk energy
 
 
     # transform voxels close to interface region
@@ -143,33 +143,35 @@ for name in filenames:
                                                       return_distances = False,
                                                       return_indices = True)                        # want index of closest bulk grain
 
-    periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]//2:-grid[0]//2,
-                                                              grid[1]//2:-grid[1]//2,
-                                                              grid[2]//2:-grid[2]//2]                # periodically extend the microstructure
+    periodic_material = np.tile(material,(3,3,3))[grid[0]//2:-grid[0]//2,
+                                                  grid[1]//2:-grid[1]//2,
+                                                  grid[2]//2:-grid[2]//2]                           # periodically extend the geometry
 
-    microstructure = periodic_microstructure[index[0],
-                                             index[1],
-                                             index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
-                                                                       grid[1]//2:-grid[1]//2,
-                                                                       grid[2]//2:-grid[2]//2]       # extent grains into interface region
+    material = periodic_material[index[0],
+                                index[1],
+                                index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
+                                                          grid[1]//2:-grid[1]//2,
+                                                          grid[2]//2:-grid[2]//2]                   # extent grains into interface region
 
-    # replace immutable microstructures with closest mutable ones
-    index = ndimage.morphology.distance_transform_edt(np.in1d(microstructure,options.immutable).reshape(grid),
+    # replace immutable materials with closest mutable ones
+    index = ndimage.morphology.distance_transform_edt(np.in1d(material,options.immutable).reshape(grid),
                                                       return_distances = False,
                                                       return_indices = True)
-    microstructure = microstructure[index[0],
-                                    index[1],
-                                    index[2]]
+    material = material[index[0],
+                          index[1],
+                          index[2]]
 
-    immutable = np.zeros(microstructure.shape, dtype=np.bool)
-    # find locations where immutable microstructures have been in original structure
+    immutable = np.zeros(material.shape, dtype=np.bool)
+    # find locations where immutable materials have been in original structure
     for micro in options.immutable:
-      immutable += microstructure_original == micro
+      immutable += material_original == micro
 
-    # undo any changes involving immutable microstructures
-    microstructure = np.where(immutable, microstructure_original,microstructure)
+    # undo any changes involving immutable materials
+    material = np.where(immutable, material_original,material)
 
-  geom=geom.duplicate(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])
-  geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
-
-  geom.to_file(sys.stdout if name is None else name,format='ASCII',pack=False)
+  damask.Geom(material = material[0:grid_original[0],0:grid_original[1],0:grid_original[2]],
+              size      = geom.size,
+              origin    = geom.origin,
+              comments  = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
+             )\
+        .save_ASCII(sys.stdout if name is None else name,compress=False)

processing/pre/hybridIA_linODFsampling.py

@@ -31,7 +31,7 @@ def binAsBins(bin,intervals):
   bins[1] = (bin//intervals[2]) % intervals[1]
   bins[2] = bin % intervals[2]
   return bins
-  
+
 def binsAsBin(bins,intervals):
   """Implode 3D bins into compound bin."""
   return (bins[0]*intervals[1] + bins[1])*intervals[2] + bins[2]
@@ -95,7 +95,7 @@ def directInversion (ODF,nSamples):
                                                                                         float(nInvSamples)/nOptSamples-1.0,
                                                                                         scale,nSamples))
   repetition = [None]*ODF['nBins']                                                                  # preallocate and clear
-    
+
   for bin in range(ODF['nBins']):                                                                   # loop over bins
     repetition[bin] = int(round(ODF['dV_V'][bin]*scale))                                            # calc repetition
 
@@ -105,7 +105,7 @@ def directInversion (ODF,nSamples):
   for bin in range(ODF['nBins']):
     set[i:i+repetition[bin]] = [bin]*repetition[bin]                                                # fill set with bin, i.e. orientation
     i += repetition[bin]                                                                            # advance set counter
-  
+
   orientations     = np.zeros((nSamples,3),'f')
   reconstructedODF = np.zeros(ODF['nBins'],'f')
   unitInc = 1.0/nSamples
@@ -117,7 +117,7 @@ def directInversion (ODF,nSamples):
     orientations[j] = np.degrees(Eulers)
     reconstructedODF[bin] += unitInc
     set[ex] = set[j]                                                                                # exchange orientations
-  
+
   return orientations, reconstructedODF
 
 
@@ -130,7 +130,7 @@ def MonteCarloEulers (ODF,nSamples):
   orientations     = np.zeros((nSamples,3),'f')
   reconstructedODF = np.zeros(ODF['nBins'],'f')
   unitInc = 1.0/nSamples
-  
+
   for j in range(nSamples):
     MC = maxdV_V*2.0
     bin = 0
@@ -153,7 +153,7 @@ def MonteCarloBins (ODF,nSamples):
   orientations     = np.zeros((nSamples,3),'f')
   reconstructedODF = np.zeros(ODF['nBins'],'f')
   unitInc = 1.0/nSamples
-  
+
   for j in range(nSamples):
     MC = maxdV_V*2.0
     bin = 0
@@ -173,14 +173,14 @@ def TothVanHoutteSTAT (ODF,nSamples):
   orientations     = np.zeros((nSamples,3),'f')
   reconstructedODF = np.zeros(ODF['nBins'],'f')
   unitInc = 1.0/nSamples
-  
+
   selectors = [random.random() for i in range(nSamples)]
   selectors.sort()
   indexSelector = 0
-  
+
   cumdV_V = 0.0
   countSamples = 0
-  
+
   for bin in range(ODF['nBins']) :
     cumdV_V += ODF['dV_V'][bin]
     while indexSelector < nSamples and selectors[indexSelector] < cumdV_V:
@@ -191,7 +191,7 @@ def TothVanHoutteSTAT (ODF,nSamples):
       indexSelector += 1
 
   damask.util.croak('created set of %i when asked to deliver %i'%(countSamples,nSamples))
-  
+
   return orientations, reconstructedODF
 
 
@@ -233,8 +233,8 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
   damask.util.report(scriptName,name)
-  
-  table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+
+  table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
   randomSeed = int(os.urandom(4).hex(),16)  if options.randomSeed is None else options.randomSeed  # random seed per file
   random.seed(randomSeed)
@@ -253,7 +253,7 @@ for name in filenames:
   if eulers.shape[0] != ODF['nBins']:
     damask.util.croak('expecting %i values but got %i'%(ODF['nBins'],eulers.shape[0]))
     continue
-  
+
 # ----- build binnedODF array and normalize ------------------------------------------------------
   sumdV_V = 0.0
   ODF['dV_V'] = [None]*ODF['nBins']
@@ -267,7 +267,7 @@ for name in filenames:
     if ODF['dV_V'][b] > 0.0:
       sumdV_V += ODF['dV_V'][b]
       ODF['nNonZero'] += 1
-  
+
   for b in range(ODF['nBins']):
     ODF['dV_V'][b] /= sumdV_V                                                            # normalize dV/V
 
@@ -277,19 +277,19 @@ for name in filenames:
                'Volume integral of ODF: %12.11f\n'%sumdV_V,
                'Reference Integral: %12.11f\n'%(ODF['limit'][0]*ODF['limit'][2]*(1-math.cos(ODF['limit'][1]))),
                ])
-                                                     
+
   Functions = {'IA': 'directInversion', 'STAT': 'TothVanHoutteSTAT', 'MC': 'MonteCarloBins'}
   method = Functions[options.algorithm]
 
   Orientations, ReconstructedODF = (globals()[method])(ODF,options.number)
-  
+
 # calculate accuracy of sample
   squaredDiff     = {'orig':0.0,method:0.0}
   squaredRelDiff  = {'orig':0.0,method:0.0}
   mutualProd      = {'orig':0.0,method:0.0}
   indivSum        = {'orig':0.0,method:0.0}
   indivSquaredSum = {'orig':0.0,method:0.0}
-  
+
   for bin in range(ODF['nBins']):
     squaredDiff[method] += (ODF['dV_V'][bin] - ReconstructedODF[bin])**2
     if ODF['dV_V'][bin] > 0.0:
@@ -299,7 +299,7 @@ for name in filenames:
     indivSquaredSum[method] += ReconstructedODF[bin]**2
   indivSum['orig'] += ODF['dV_V'][bin]
   indivSquaredSum['orig'] += ODF['dV_V'][bin]**2
-  
+
   damask.util.croak(['sqrt(N*)RMSD of ODFs:\t %12.11f'% math.sqrt(options.number*squaredDiff[method]),
                'RMSrD of ODFs:\t %12.11f'%math.sqrt(squaredRelDiff[method]),
                'rMSD of ODFs:\t %12.11f'%(squaredDiff[method]/indivSquaredSum['orig']),
@@ -311,10 +311,10 @@ for name in filenames:
                         (ODF['nNonZero']*math.sqrt((indivSquaredSum['orig']/ODF['nNonZero']-(indivSum['orig']/ODF['nNonZero'])**2)*\
                         (indivSquaredSum[method]/ODF['nNonZero']-(indivSum[method]/ODF['nNonZero'])**2)))),
               ])
-  
+
   if method == 'IA' and options.number < ODF['nNonZero']:
     strOpt = '(%i)'%ODF['nNonZero']
-  
+
   formatwidth = 1+int(math.log10(options.number))
 
   materialConfig = [
@@ -324,12 +324,12 @@ for name in filenames:
       '<microstructure>',
       '#-------------------#',
       ]
-  
+
   for i,ID in enumerate(range(options.number)):
     materialConfig += ['[Grain%s]'%(str(ID+1).zfill(formatwidth)),
                       '(constituent)   phase %i   texture %s   fraction 1.0'%(options.phase,str(ID+1).rjust(formatwidth)),
                      ]
-  
+
   materialConfig += [
       '#-------------------#',
       '<texture>',
@@ -338,12 +338,12 @@ for name in filenames:
 
   for ID in range(options.number):
     eulers = Orientations[ID]
-  
+
     materialConfig += ['[Grain%s]'%(str(ID+1).zfill(formatwidth)),
                      '(gauss)   phi1 {}   Phi {}   phi2 {}   scatter 0.0   fraction 1.0'.format(*eulers),
                      ]
 
-#--- output finalization -------------------------------------------------------------------------- 
+#--- output finalization --------------------------------------------------------------------------
 
   with (open(os.path.splitext(name)[0]+'_'+method+'_'+str(options.number)+'_material.config','w')) as outfile:
     outfile.write('\n'.join(materialConfig)+'\n')

processing/pre/mentat_spectralBox.py

@@ -42,7 +42,7 @@ def output(cmds,locals,dest):
       else:
         outFile(str(cmd),locals,dest)
 
-  
+
 #-------------------------------------------------------------------------------------------------
 def init():
   return [
@@ -100,7 +100,7 @@ def mesh(r,d):
 
 
 #-------------------------------------------------------------------------------------------------
-def material():
+def materials():
   return [\
   "*new_mater standard",
   "*mater_option general:state:solid",
@@ -114,7 +114,7 @@ def material():
   "*add_geometry_elements",
   "all_existing",
   ]
-  
+
 
 #-------------------------------------------------------------------------------------------------
 def geometry():
@@ -127,14 +127,14 @@ def geometry():
   "*element_type 7",
   "all_existing",
   ]
-  
+
 
 #-------------------------------------------------------------------------------------------------
-def initial_conditions(microstructures):
+def initial_conditions(material):
   elements = []
   element = 0
-  for id in microstructures:
-    element += 1 
+  for id in material:
+    element += 1
     if len(elements) < id:
       for i in range(id-len(elements)):
         elements.append([])
@@ -153,7 +153,7 @@ def initial_conditions(microstructures):
   for grain,elementList in enumerate(elements):
     cmds.append([\
             "*new_icond",
-            "*icond_name microstructure_%i"%(grain+1),
+            "*icond_name material_%i"%(grain+1),
             "*icond_type state_variable",
             "*icond_param_value state_var_id 2",
             "*icond_dof_value var %i"%(grain+1),
@@ -195,22 +195,22 @@ if filenames == []: filenames = [None]
 
 for name in filenames:
     damask.util.report(scriptName,name)
-    
-    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    microstructure = geom.get_microstructure().flatten(order='F')
+
+    geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    material = geom.material.flatten(order='F')
 
     cmds = [\
       init(),
       mesh(geom.grid,geom.size),
-      material(),
+      materials(),
       geometry(),
-      initial_conditions(microstructure),
+      initial_conditions(material),
       '*identify_sets',
       '*show_model',
       '*redraw',
       '*draw_automatic',
     ]
-    
+
     outputLocals = {}
     if options.port:
         py_mentat.py_connect('',options.port)

processing/pre/seeds_fromDistribution.py

@@ -30,7 +30,7 @@ class myThread (threading.Thread):
   def run(self):
     global bestSeedsUpdate
     global bestSeedsVFile
-    global nMicrostructures
+    global nMaterials
     global delta
     global points
     global target
@@ -70,7 +70,7 @@ class myThread (threading.Thread):
         selectedMs = []
         direction = []
         for i in range(NmoveGrains):
-          selectedMs.append(random.randrange(1,nMicrostructures))
+          selectedMs.append(random.randrange(1,nMaterials))
 
           direction.append((np.random.random()-0.5)*delta)
 
@@ -78,7 +78,7 @@ class myThread (threading.Thread):
       perturbedSeedsVFile = StringIO()
       myBestSeedsVFile.seek(0)
 
-      perturbedSeedsTable = damask.Table.from_ASCII(myBestSeedsVFile)
+      perturbedSeedsTable = damask.Table.load(myBestSeedsVFile)
       coords = perturbedSeedsTable.get('pos')
       i = 0
       for ms,coord in enumerate(coords):
@@ -89,8 +89,7 @@ class myThread (threading.Thread):
           coords[i]=newCoords
           direction[i]*=2.
           i+= 1
-      perturbedSeedsTable.set('pos',coords)
-      perturbedSeedsTable.to_file(perturbedSeedsVFile)
+      perturbedSeedsTable.set('pos',coords).save(perturbedSeedsVFile,legacy=True)
 
 #--- do tesselation with perturbed seed file ------------------------------------------------------
       perturbedGeomVFile.close()
@@ -101,12 +100,12 @@ class myThread (threading.Thread):
       perturbedGeomVFile.seek(0)
 
 #--- evaluate current seeds file ------------------------------------------------------------------
-      perturbedGeom = damask.Geom.from_file(perturbedGeomVFile)
-      myNmicrostructures = len(np.unique(perturbedGeom.microstructure))
-      currentData=np.bincount(perturbedGeom.microstructure.ravel())[1:]/points
+      perturbedGeom = damask.Geom.load_ASCII(perturbedGeomVFile)
+      myNmaterials = len(np.unique(perturbedGeom.material))
+      currentData = np.bincount(perturbedGeom.material.ravel())[1:]/points
       currentError=[]
       currentHist=[]
-      for i in range(nMicrostructures):                                                             # calculate the deviation in all bins per histogram
+      for i in range(nMaterials):                                                             # calculate the deviation in all bins per histogram
         currentHist.append(np.histogram(currentData,bins=target[i]['bins'])[0])
         currentError.append(np.sqrt(np.square(np.array(target[i]['histogram']-currentHist[i])).sum()))
 
@@ -118,12 +117,12 @@ class myThread (threading.Thread):
       bestMatch = match
 #--- count bin classes with no mismatch ----------------------------------------------------------------------
       myMatch=0
-      for i in range(nMicrostructures):
+      for i in range(nMaterials):
         if currentError[i] > 0.0: break
         myMatch = i+1
 
-      if myNmicrostructures == nMicrostructures:
-        for i in range(min(nMicrostructures,myMatch+options.bins)):
+      if myNmaterials == nMaterials:
+        for i in range(min(nMaterials,myMatch+options.bins)):
           if currentError[i] > target[i]['error']:                                                  # worse fitting, next try
             randReset = True
             break
@@ -142,25 +141,25 @@ class myThread (threading.Thread):
               for line in perturbedSeedsVFile:
                 currentSeedsFile.write(line)
                 bestSeedsVFile.write(line)
-            for j in range(nMicrostructures):                                                       # save new errors for all bins
+            for j in range(nMaterials):                                                       # save new errors for all bins
               target[j]['error'] = currentError[j]
             if myMatch > match:                                                                     # one or more new bins have no deviation
               damask.util.croak( 'Stage {:d}  cleared'.format(myMatch))
               match=myMatch
               sys.stdout.flush()
             break
-          if i == min(nMicrostructures,myMatch+options.bins)-1:                                     # same quality as before: take it to keep on moving
+          if i == min(nMaterials,myMatch+options.bins)-1:                                     # same quality as before: take it to keep on moving
             bestSeedsUpdate = time.time()
             perturbedSeedsVFile.seek(0)
             bestSeedsVFile.close()
             bestSeedsVFile = StringIO()
             bestSeedsVFile.writelines(perturbedSeedsVFile.readlines())
-            for j in range(nMicrostructures):
+            for j in range(nMaterials):
               target[j]['error'] = currentError[j]
             randReset = True
       else:                                                                                         #--- not all grains are tessellated
-        damask.util.croak('Thread {:d}: Microstructure mismatch ({:d} microstructures mapped)'\
-                                                         .format(self.threadID,myNmicrostructures))
+        damask.util.croak('Thread {:d}: Material mismatch ({:d} material indices mapped)'\
+                                                         .format(self.threadID,myNmaterials))
         randReset = True
 
 
@@ -213,15 +212,15 @@ if options.randomSeed is None:
   options.randomSeed = int(os.urandom(4).hex(),16)
 damask.util.croak(options.randomSeed)
 delta = options.scale/np.array(options.grid)
-baseFile=os.path.splitext(os.path.basename(options.seedFile))[0]
+baseFile = os.path.splitext(os.path.basename(options.seedFile))[0]
 points = np.array(options.grid).prod().astype('float')
 
 # ----------- calculate target distribution and bin edges
-targetGeom = damask.Geom.from_file(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
-nMicrostructures = len(np.unique(targetGeom.microstructure))
-targetVolFrac = np.bincount(targetGeom.microstructure.flatten())/targetGeom.grid.prod().astype(np.float)
-target=[]
-for i in range(1,nMicrostructures+1):
+targetGeom = damask.Geom.load_ASCII(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
+nMaterials = len(np.unique(targetGeom.material))
+targetVolFrac = np.bincount(targetGeom.material.flatten())/targetGeom.grid.prod().astype(np.float)
+target = []
+for i in range(1,nMaterials+1):
   targetHist,targetBins = np.histogram(targetVolFrac,bins=i) #bin boundaries
   target.append({'histogram':targetHist,'bins':targetBins})
 
@@ -234,7 +233,7 @@ else:
   bestSeedsVFile.write(damask.util.execute('seeds_fromRandom'+\
                                 ' -g '+' '.join(list(map(str, options.grid)))+\
                                 ' -r {:d}'.format(options.randomSeed)+\
-                                ' -N '+str(nMicrostructures))[0])
+                                ' -N '+str(nMaterials))[0])
 bestSeedsUpdate = time.time()
 
 # ----------- tessellate initial seed file to get and evaluate geom file
@@ -243,13 +242,13 @@ initialGeomVFile = StringIO()
 initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
                                ' -g '+' '.join(list(map(str, options.grid))),bestSeedsVFile)[0])
 initialGeomVFile.seek(0)
-initialGeom = damask.Geom.from_file(initialGeomVFile)
+initialGeom = damask.Geom.load_ASCII(initialGeomVFile)
 
-if len(np.unique(targetGeom.microstructure)) != nMicrostructures:
-  damask.util.croak('error. Microstructure count mismatch')
+if len(np.unique(targetGeom.material)) != nMaterials:
+  damask.util.croak('error. Material count mismatch')
 
-initialData = np.bincount(initialGeom.microstructure.flatten())/points
-for i in range(nMicrostructures):
+initialData = np.bincount(initialGeom.material.flatten())/points
+for i in range(nMaterials):
   initialHist = np.histogram(initialData,bins=target[i]['bins'])[0]
   target[i]['error']=np.sqrt(np.square(np.array(target[i]['histogram']-initialHist)).sum())
 
@@ -258,13 +257,13 @@ if target[0]['error'] > 0.0:
   target[0]['error'] *=((target[0]['bins'][0]-np.min(initialData))**2.0+
                         (target[0]['bins'][1]-np.max(initialData))**2.0)**0.5
 match=0
-for i in range(nMicrostructures):
+for i in range(nMaterials):
   if target[i]['error'] > 0.0: break
   match = i+1
 
 
 if options.maxseeds < 1:
-  maxSeeds = len(np.unique(initialGeom.microstructure))
+  maxSeeds = len(np.unique(initialGeom.material))
 else:
   maxSeeds = options.maxseeds
 
@@ -273,8 +272,8 @@ sys.stdout.flush()
 initialGeomVFile.close()
 
 # start mulithreaded monte carlo simulation
-threads=[]
-s=threading.Semaphore(1)
+threads = []
+s = threading.Semaphore(1)
 
 for i in range(options.threads):
   threads.append(myThread(i))

processing/pre/seeds_fromGeom.py

@@ -17,7 +17,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #--------------------------------------------------------------------------------------------------
 
 parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
-Create seed file taking microstructure indices from given geom file.
+Create seed file taking material indices from given geom file.
 Indices can be black-listed or white-listed.
 
 """, version = scriptID)
@@ -46,12 +46,12 @@ options.blacklist = [int(i) for i in options.blacklist]
 for name in filenames:
     damask.util.report(scriptName,name)
 
-    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
-    microstructure = geom.get_microstructure().reshape((-1,1),order='F')
+    geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    material = geom.material.reshape((-1,1),order='F')
 
-    mask = np.logical_and(np.in1d(microstructure,options.whitelist,invert=False) if options.whitelist else \
+    mask = np.logical_and(np.in1d(material,options.whitelist,invert=False) if options.whitelist else \
                           np.full(geom.grid.prod(),True,dtype=bool),
-                          np.in1d(microstructure,options.blacklist,invert=True)  if options.blacklist else \
+                          np.in1d(material,options.blacklist,invert=True)  if options.blacklist else \
                           np.full(geom.grid.prod(),True,dtype=bool))
 
     seeds = damask.grid_filters.cell_coord0(geom.grid,geom.size).reshape(-1,3,order='F')
@@ -61,8 +61,8 @@ for name in filenames:
                 'grid\ta {}\tb {}\tc {}'.format(*geom.grid),
                 'size\tx {}\ty {}\tz {}'.format(*geom.size),
                 'origin\tx {}\ty {}\tz {}'.format(*geom.origin),
-                'homogenization\t{}'.format(geom.homogenization)]
+                ]
 
-    table = damask.Table(seeds[mask],{'pos':(3,)},comments)
-    table = table.add('microstructure',microstructure[mask])
-    table.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.seeds')
+    damask.Table(seeds[mask],{'pos':(3,)},comments)\
+          .add('material',material[mask].astype(int))\
+          .save(sys.stdout if name is None else os.path.splitext(name)[0]+'.seeds',legacy=True)

processing/pre/seeds_fromPokes.py

@@ -52,7 +52,7 @@ options.box = np.array(options.box).reshape(3,2)
 
 for name in filenames:
     damask.util.report(scriptName,name)
-    geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
+    geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
 
     offset =(np.amin(options.box, axis=1)*geom.grid/geom.size).astype(int)
     box    = np.amax(options.box, axis=1) \
@@ -76,7 +76,7 @@ for name in filenames:
                 g[2] = k + offset[2]
                 g %= geom.grid
                 seeds[n,0:3] = (g+0.5)/geom.grid                                                    # normalize coordinates to box
-                seeds[n,  3] = geom.microstructure[g[0],g[1],g[2]]
+                seeds[n,  3] = geom.material[g[0],g[1],g[2]]
                 if options.x: g[0] += 1
                 if options.y: g[1] += 1
                 n += 1
@@ -88,9 +88,9 @@ for name in filenames:
                 'grid\ta {}\tb {}\tc {}'.format(*geom.grid),
                 'size\tx {}\ty {}\tz {}'.format(*geom.size),
                 'origin\tx {}\ty {}\tz {}'.format(*geom.origin),
-                'homogenization\t{}'.format(geom.homogenization)]
+               ]
 
-    table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments)
-    table.set('microstructure',table.get('microstructure').astype(np.int))
-    table.to_file(sys.stdout if name is None else \
-                  os.path.splitext(name)[0]+f'_poked_{options.N}.seeds')
+    table = damask.Table(seeds,{'pos':(3,),'material':(1,)},comments)
+    table.set('material',table.get('material').astype(np.int))\
+         .save(sys.stdout if name is None else \
+                     os.path.splitext(name)[0]+f'_poked_{options.N}.seeds',legacy=True)

processing/pre/seeds_fromRandom.py

@@ -154,12 +154,12 @@ for name in filenames:
                 'randomSeed\t{}'.format(options.randomSeed),
                ]
 
-    table = damask.Table(np.hstack((seeds,eulers)),{'pos':(3,),'euler':(3,)},comments)
-    table = table.add('microstructure',np.arange(options.microstructure,options.microstructure + options.N,dtype=int))
+    table = damask.Table(np.hstack((seeds,eulers)),{'pos':(3,),'euler':(3,)},comments)\
+                  .add('microstructure',np.arange(options.microstructure,options.microstructure + options.N,dtype=int))
 
     if options.weights:
         weights = np.random.uniform(low = 0, high = options.max, size = options.N) if options.max > 0.0 \
              else np.random.normal(loc = options.mean, scale = options.sigma, size = options.N)
         table = table.add('weight',weights)
 
-    table.to_file(sys.stdout if name is None else name)
+    table.save(sys.stdout if name is None else name,legacy=True)

python/damask/__init__.py

@@ -18,6 +18,7 @@ from ._lattice     import Symmetry, Lattice# noqa
 from ._orientation import Orientation      # noqa
 from ._result      import Result           # noqa
 from ._geom        import Geom             # noqa
+from ._material    import Material         # noqa
 from .             import solver           # noqa
 
 # deprecated

python/damask/_colormap.py

@@ -235,100 +235,128 @@ class Colormap(mpl.colors.ListedColormap):
         return Colormap(np.array(rev.colors),rev.name[:-4] if rev.name.endswith('_r_r') else rev.name)
 
 
-    def to_file(self,fname=None,format='ParaView'):
+
+    def save_paraview(self,fname=None):
         """
-        Export colormap to file for use in external programs.
+        Write colormap to JSON file for Paraview.
 
         Parameters
         ----------
         fname : file, str, or pathlib.Path, optional.
             Filename to store results. If not given, the filename will
-            consist of the name of the colormap and an extension that
-            depends on the file format.
-        format : {'ParaView', 'ASCII', 'GOM', 'gmsh'}, optional
-            File format, defaults to 'ParaView'. Available formats are:
-            - ParaView: JSON file, extension '.json'.
-            - ASCII: Plain text file, extension '.txt'.
-            - GOM: Aramis GOM (DIC), extension '.legend'.
-            - Gmsh: Gmsh FEM mesh-generator, extension '.msh'.
+            consist of the name of the colormap and extension '.json'.
 
         """
         if fname is not None:
             try:
-                f = open(fname,'w')
+                fhandle = open(fname,'w')
             except TypeError:
-                f = fname
+                fhandle = fname
         else:
-            f = None
+            fhandle = None
 
-        if format.lower() == 'paraview':
-            Colormap._export_paraview(self,f)
-        elif format.lower() == 'ascii':
-            Colormap._export_ASCII(self,f)
-        elif format.lower() == 'gom':
-            Colormap._export_GOM(self,f)
-        elif format.lower() == 'gmsh':
-            Colormap._export_gmsh(self,f)
-        else:
-            raise ValueError('Unknown output format: {format}.')
-
-    @staticmethod
-    def _export_paraview(colormap,fhandle=None):
-        """Write colormap to JSON file for Paraview."""
         colors = []
-        for i,c in enumerate(np.round(colormap.colors,6).tolist()):
+        for i,c in enumerate(np.round(self.colors,6).tolist()):
             colors+=[i]+c
 
         out = [{
                 'Creator':util.execution_stamp('Colormap'),
                 'ColorSpace':'RGB',
-                'Name':colormap.name,
+                'Name':self.name,
                 'DefaultMap':True,
                 'RGBPoints':colors
                }]
         if fhandle is None:
-            with open(colormap.name.replace(' ','_')+'.json', 'w') as f:
+            with open(self.name.replace(' ','_')+'.json', 'w') as f:
                 json.dump(out, f,indent=4)
         else:
             json.dump(out,fhandle,indent=4)
 
-    @staticmethod
-    def _export_ASCII(colormap,fhandle=None):
-        """Write colormap to ASCII table."""
-        labels = {'RGBA':4} if colormap.colors.shape[1] == 4 else {'RGB': 3}
-        t = Table(colormap.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
+
+    def save_ASCII(self,fname=None):
+        """
+        Write colormap to ASCII table.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path, optional.
+            Filename to store results. If not given, the filename will
+            consist of the name of the colormap and extension '.txt'.
+
+        """
+        if fname is not None:
+            try:
+                fhandle = open(fname,'w')
+            except TypeError:
+                fhandle = fname
+        else:
+            fhandle = None
+
+        labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
+        t = Table(self.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
 
         if fhandle is None:
-            with open(colormap.name.replace(' ','_')+'.txt', 'w') as f:
-                t.to_file(f,new_style=True)
+            with open(self.name.replace(' ','_')+'.txt', 'w') as f:
+                t.save(f)
         else:
-            t.to_file(fhandle,new_style=True)
+            t.save(fhandle)
 
-    @staticmethod
-    def _export_GOM(colormap,fhandle=None):
-        """Write colormap to GOM Aramis compatible format."""
+
+    def save_GOM(self,fname=None):
+        """
+        Write colormap to GOM Aramis compatible format.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path, optional.
+            Filename to store results. If not given, the filename will
+            consist of the name of the colormap and extension '.legend'.
+
+        """
+        if fname is not None:
+            try:
+                fhandle = open(fname,'w')
+            except TypeError:
+                fhandle = fname
+        else:
+            fhandle = None
         # ToDo: test in GOM
-        GOM_str = f'1 1 {colormap.name.replace(" ","_")} 9 {colormap.name.replace(" ","_")} ' \
+        GOM_str = '1 1 {name} 9 {name} '.format(name=self.name.replace(" ","_")) \
                 +  '0 1 0 3 0 0 -1 9 \\ 0 0 0 255 255 255 0 0 255 ' \
-                + f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {len(colormap.colors)}' \
-                + ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((colormap.colors*255).astype(int))]) \
+                + f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {len(self.colors)}' \
+                + ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(int))]) \
                 + '\n'
         if fhandle is None:
-            with open(colormap.name.replace(' ','_')+'.legend', 'w') as f:
+            with open(self.name.replace(' ','_')+'.legend', 'w') as f:
                 f.write(GOM_str)
         else:
             fhandle.write(GOM_str)
 
 
-    @staticmethod
-    def _export_gmsh(colormap,fhandle=None):
-        """Write colormap to Gmsh compatible format."""
+    def save_gmsh(self,fname=None):
+        """
+        Write colormap to Gmsh compatible format.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path, optional.
+            Filename to store results. If not given, the filename will
+            consist of the name of the colormap and extension '.msh'.
+
+        """
+        if fname is not None:
+            try:
+                fhandle = open(fname,'w')
+            except TypeError:
+                fhandle = fname
+        else:
+            fhandle = None
         # ToDo: test in gmsh
         gmsh_str = 'View.ColorTable = {\n' \
-                 +'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in colormap.colors[:,:3]*255]) \
+                 +'\n'.join([f'{c[0]},{c[1]},{c[2]},' for c in self.colors[:,:3]*255]) \
                  +'\n}\n'
         if fhandle is None:
-            with open(colormap.name.replace(' ','_')+'.msh', 'w') as f:
+            with open(self.name.replace(' ','_')+'.msh', 'w') as f:
                 f.write(gmsh_str)
         else:
             fhandle.write(gmsh_str)

python/damask/_material.py

@@ -0,0 +1,193 @@
+from io import StringIO
+import copy
+
+import yaml
+import numpy as np
+
+from . import Lattice
+from . import Rotation
+
+class NiceDumper(yaml.SafeDumper):
+    """Make YAML readable for humans."""
+
+    def write_line_break(self, data=None):
+        super().write_line_break(data)
+
+        if len(self.indents) == 1:
+            super().write_line_break()
+
+    def increase_indent(self, flow=False, indentless=False):
+        return super().increase_indent(flow, False)
+
+
+class Material(dict):
+    """Material configuration."""
+
+    def __repr__(self):
+        """Show as in file."""
+        output = StringIO()
+        self.save(output)
+        output.seek(0)
+        return ''.join(output.readlines())
+
+    @staticmethod
+    def load(fname):
+        """Load from yaml file."""
+        try:
+            fhandle = open(fname)
+        except TypeError:
+            fhandle = fname
+        return Material(yaml.safe_load(fhandle))
+
+    def save(self,fname='material.yaml'):
+        """
+        Save to yaml file.
+
+        Parameters
+        ----------
+        fname : file, str, or pathlib.Path
+            Filename or file for reading.
+
+        """
+        try:
+            fhandle = open(fname,'w')
+        except TypeError:
+            fhandle = fname
+        fhandle.write(yaml.dump(dict(self),width=256,default_flow_style=None,Dumper=NiceDumper))
+
+
+    @property
+    def is_complete(self):
+        """Check for completeness."""
+        ok = True
+        for top_level in ['homogenization','phase','microstructure']:
+            # ToDo: With python 3.8 as prerequisite we can shorten with :=
+            ok &= top_level in self
+            if top_level not in self: print(f'{top_level} entry missing')
+
+        if ok:
+           ok &= len(self['microstructure']) > 0
+           if len(self['microstructure']) < 1: print('Incomplete microstructure definition')
+
+        if ok:
+            homogenization = set()
+            phase          = set()
+            for i,v in enumerate(self['microstructure']):
+                if 'homogenization' in v:
+                    homogenization.add(v['homogenization'])
+                else:
+                    print(f'No homogenization specified in microstructure {i}')
+                    ok = False
+
+                if 'constituents' in v:
+                    for ii,vv in enumerate(v['constituents']):
+                        if 'orientation' not in vv:
+                            print('No orientation specified in constituent {ii} of microstructure {i}')
+                            ok = False
+                        if 'phase' in vv:
+                            phase.add(vv['phase'])
+                        else:
+                            print(f'No phase specified in constituent {ii} of microstructure {i}')
+                            ok = False
+
+            for k,v in self['phase'].items():
+                if 'lattice' not in v:
+                    print(f'No lattice specified in phase {k}')
+                    ok = False
+
+            #for k,v in self['homogenization'].items():
+            #    if 'N_constituents' not in v:
+            #        print(f'No. of constituents not specified in homogenization {k}'}
+            #        ok = False
+
+            if phase - set(self['phase']):
+                print(f'Phase(s) {phase-set(self["phase"])} missing')
+                ok = False
+            if homogenization - set(self['homogenization']):
+                print(f'Homogenization(s) {homogenization-set(self["homogenization"])} missing')
+                ok = False
+
+        return ok
+
+
+    @property
+    def is_valid(self):
+        """Check for valid file layout."""
+        ok = True
+
+        if 'phase' in self:
+            for k,v in self['phase'].items():
+                if 'lattice' in v:
+                    try:
+                        Lattice(v['lattice'])
+                    except KeyError:
+                        s = v['lattice']
+                        print(f"Invalid lattice: '{s}' in phase '{k}'")
+                        ok = False
+
+        if 'microstructure' in self:
+            for i,v in enumerate(self['microstructure']):
+                if 'constituents' in v:
+                    f = 0.0
+                    for c in v['constituents']:
+                        f+= float(c['fraction'])
+                        if 'orientation' in c:
+                            try:
+                                Rotation.from_quaternion(c['orientation'])
+                            except ValueError:
+                                o = c['orientation']
+                                print(f"Invalid orientation: '{o}' in microstructure '{i}'")
+                                ok = False
+                    if not np.isclose(f,1.0):
+                        print(f"Invalid total fraction '{f}' in microstructure '{i}'")
+                        ok = False
+
+        return ok
+
+
+    def microstructure_rename_phase(self,mapping,ID=None,constituent=None):
+        """
+        Change phase name in microstructure.
+
+        Parameters
+        ----------
+        mapping: dictionary
+            Mapping from old name to new name
+        ID: list of ints, optional
+            Limit renaming to selected microstructure IDs.
+        constituent: list of ints, optional
+            Limit renaming to selected constituents.
+
+        """
+        dup = copy.deepcopy(self)
+        for i,m in enumerate(dup['microstructure']):
+            if ID and i not in ID: continue
+            for c in m['constituents']:
+                if constituent is not None and c not in constituent: continue
+                try:
+                    c['phase'] = mapping[c['phase']]
+                except KeyError:
+                    continue
+        return dup
+
+
+    def microstructure_rename_homogenization(self,mapping,ID=None):
+        """
+        Change homogenization name in microstructure.
+
+        Parameters
+        ----------
+        mapping: dictionary
+            Mapping from old name to new name
+        ID: list of ints, optional
+            Limit renaming to selected homogenization IDs.
+
+        """
+        dup = copy.deepcopy(self)
+        for i,m in enumerate(dup['microstructure']):
+            if ID and i not in ID: continue
+            try:
+                m['homogenization'] = mapping[m['homogenization']]
+            except KeyError:
+                continue
+        return dup

python/damask/_result.py

@@ -1100,7 +1100,7 @@ class Result:
         pool.join()
 
 
-    def write_XDMF(self):
+    def save_XDMF(self):
         """
         Write XDMF file to directly visualize data in DADF5 file.
 
@@ -1196,7 +1196,7 @@ class Result:
             f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
 
 
-    def to_vtk(self,labels=[],mode='cell'):
+    def save_vtk(self,labels=[],mode='cell'):
         """
         Export to vtk cell/point data.
 
@@ -1268,4 +1268,4 @@ class Result:
             u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
             v.add(u,'u')
 
-            v.to_file(f'{self.fname.stem}_inc{inc[3:].zfill(N_digits)}')
+            v.save(f'{self.fname.stem}_inc{inc[3:].zfill(N_digits)}')

python/damask/_table.py

@@ -27,8 +27,11 @@ class Table:
         self.comments = [] if comments_ is None else [c for c in comments_]
         self.data = pd.DataFrame(data=data)
         self.shapes = { k:(v,) if isinstance(v,(np.int,int)) else v for k,v in shapes.items() }
-        self._label_condensed()
+        self._label_uniform()
 
+    def __repr__(self):
+        """Brief overview."""
+        return util.srepr(self.comments)+'\n'+self.data.__repr__()
 
     def __copy__(self):
         """Copy Table."""
@@ -39,7 +42,7 @@ class Table:
         return self.__copy__()
 
 
-    def _label_flat(self):
+    def _label_discrete(self):
         """Label data individually, e.g. v v v ==> 1_v 2_v 3_v."""
         labels = []
         for label,shape in self.shapes.items():
@@ -48,8 +51,8 @@ class Table:
         self.data.columns = labels
 
 
-    def _label_condensed(self):
-        """Label data condensed, e.g. 1_v 2_v 3_v ==> v v v."""
+    def _label_uniform(self):
+        """Label data uniformly, e.g. 1_v 2_v 3_v ==> v v v."""
         labels = []
         for label,shape in self.shapes.items():
             labels += [label] * int(np.prod(shape))
@@ -64,12 +67,15 @@ class Table:
 
 
     @staticmethod
-    def from_ASCII(fname):
+    def load(fname):
         """
-        Create table from ASCII file.
+        Load ASCII table file.
 
-        The first line can indicate the number of subsequent header lines as 'n header',
-        alternatively first line is the header and comments are marked by '#' ('new style').
+        In legacy style, the first line indicates the number of
+        subsequent header lines as "N header", with the last header line being
+        interpreted as column labels.
+        Alternatively, initial comments are marked by '#', with the first non-comment line
+        containing the column labels.
         Vector data column labels are indicated by '1_v, 2_v, ..., n_v'.
         Tensor data column labels are indicated by '3x3:1_T, 3x3:2_T, ..., 3x3:9_T'.
 
@@ -119,9 +125,9 @@ class Table:
         return Table(data,shapes,comments)
 
     @staticmethod
-    def from_ang(fname):
+    def load_ang(fname):
         """
-        Create table from TSL ang file.
+        Load ang file.
 
         A valid TSL ang file needs to contains the following columns:
         * Euler angles (Bunge notation) in radians, 3 floats, label 'eu'.
@@ -289,9 +295,9 @@ class Table:
 
         """
         dup = self.copy()
-        dup._label_flat()
+        dup._label_discrete()
         dup.data.sort_values(labels,axis=0,inplace=True,ascending=ascending)
-        dup._label_condensed()
+        dup._label_uniform()
         dup.comments.append(f'sorted {"ascending" if ascending else "descending"} by {labels}')
         return dup
 
@@ -338,59 +344,38 @@ class Table:
             return dup
 
 
-    def to_file(self,fname,format='ASCII',new_style=False):
+    def save(self,fname,legacy=False):
         """
-        Store as plain text file.
+        Save as plain text file.
 
         Parameters
         ----------
         fname : file, str, or pathlib.Path
             Filename or file for writing.
-        format : {ASCII'}, optional
-            File format, defaults to 'ASCII'. Available formats are:
-            - ASCII: Plain text file, extension '.txt'.
-        new_style : Boolean, optional
-            Write table in new style, indicating header lines by comment sign ('#') only.
+        legacy : Boolean, optional
+            Write table in legacy style, indicating header lines by "N header"
+            in contrast to using comment sign ('#') at beginning of lines.
 
         """
-        def _to_ASCII(table,fname,new_style=False):
-            """
-            Store as plain text file.
+        seen = set()
+        labels = []
+        for l in [x for x in self.data.columns if not (x in seen or seen.add(x))]:
+            if self.shapes[l] == (1,):
+                labels.append(f'{l}')
+            elif len(self.shapes[l]) == 1:
+                labels += [f'{i+1}_{l}' \
+                          for i in range(self.shapes[l][0])]
+            else:
+                labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
+                          for i in range(np.prod(self.shapes[l]))]
 
-            Parameters
-            ----------
-            table : Table object
-                Table to write.
-            fname : file, str, or pathlib.Path
-                Filename or file for writing.
-            new_style : Boolean, optional
-                Write table in new style, indicating header lines by comment sign ('#') only.
+        header = ([f'{len(self.comments)+1} header'] + self.comments) if legacy else \
+                  [f'# {comment}' for comment in self.comments]
 
-            """
-            seen = set()
-            labels = []
-            for l in [x for x in table.data.columns if not (x in seen or seen.add(x))]:
-                if table.shapes[l] == (1,):
-                    labels.append(f'{l}')
-                elif len(table.shapes[l]) == 1:
-                    labels += [f'{i+1}_{l}' \
-                              for i in range(table.shapes[l][0])]
-                else:
-                    labels += [f'{util.srepr(table.shapes[l],"x")}:{i+1}_{l}' \
-                              for i in range(np.prod(table.shapes[l]))]
+        try:
+            fhandle = open(fname,'w')
+        except TypeError:
+            fhandle = fname
 
-            header = [f'# {comment}' for comment in table.comments] if new_style else \
-                     [f'{len(table.comments)+1} header'] + table.comments
-
-            try:
-                f = open(fname,'w')
-            except TypeError:
-                f = fname
-
-            for line in header + [' '.join(labels)]: f.write(line+'\n')
-            table.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)
-
-        if format.lower() == 'ascii':
-            return _to_ASCII(self,fname,new_style)
-        else:
-            raise TypeError(f'Unknown format {format}.')
+        for line in header + [' '.join(labels)]: fhandle.write(line+'\n')
+        self.data.to_csv(fhandle,sep=' ',na_rep='nan',index=False,header=False)

python/damask/_test.py

@@ -228,7 +228,7 @@ class Test:
 
   def copy_Base2Current(self,sourceDir,sourcefiles=[],targetfiles=[]):
 
-    source=os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir))
+    source = os.path.normpath(os.path.join(self.dirBase,'../../..',sourceDir))
     if len(targetfiles) == 0: targetfiles = sourcefiles
     for i,f in enumerate(sourcefiles):
       try:
@@ -287,30 +287,30 @@ class Test:
 
     import numpy as np
     logging.info('\n '.join(['comparing',File1,File2]))
-    table = damask.Table.from_ASCII(File1)
-    len1=len(table.comments)+2
-    table = damask.Table.from_ASCII(File2)
-    len2=len(table.comments)+2
+    table = damask.Table.load(File1)
+    len1 = len(table.comments)+2
+    table = damask.Table.load(File2)
+    len2 = len(table.comments)+2
 
     refArray = np.nan_to_num(np.genfromtxt(File1,missing_values='n/a',skip_header = len1,autostrip=True))
     curArray = np.nan_to_num(np.genfromtxt(File2,missing_values='n/a',skip_header = len2,autostrip=True))
 
     if len(curArray) == len(refArray):
       refArrayNonZero = refArray[refArray.nonzero()]
-      curArray = curArray[refArray.nonzero()]
-      max_err=np.max(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
-      max_loc=np.argmax(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
+      curArray        = curArray[refArray.nonzero()]
+      max_err = np.   max(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
+      max_loc = np.argmax(abs(refArrayNonZero[curArray.nonzero()]/curArray[curArray.nonzero()]-1.))
       refArrayNonZero = refArrayNonZero[curArray.nonzero()]
-      curArray = curArray[curArray.nonzero()]
+      curArray        = curArray[curArray.nonzero()]
       print(f' ********\n * maximum relative error {max_err} between {refArrayNonZero[max_loc]} and {curArray[max_loc]}\n ********')
       return max_err
     else:
-       raise Exception('mismatch in array size to compare')
+       raise Exception(f'mismatch in array sizes ({len(refArray)} and {len(curArray)}) to compare')
 
 
   def compare_ArrayRefCur(self,ref,cur=''):
 
-    if cur =='': cur = ref
+    if cur == '': cur = ref
     refName = self.fileInReference(ref)
     curName = self.fileInCurrent(cur)
     return self.compare_Array(refName,curName)
@@ -331,7 +331,7 @@ class Test:
     logging.info('\n '.join(['comparing ASCII Tables',file0,file1]))
     if normHeadings == '': normHeadings = headings0
 
-# check if comparison is possible and determine lenght of columns
+# check if comparison is possible and determine length of columns
     if len(headings0) == len(headings1) == len(normHeadings):
       dataLength = len(headings0)
       length       = [1   for i in range(dataLength)]
@@ -399,10 +399,8 @@ class Test:
       if any(norm[i]) == 0.0 or absTol[i]:
         norm[i] = [1.0 for j in range(line0-len(skipLines))]
         absTol[i] = True
-        if perLine:
-          logging.warning(f"At least one norm of \"{headings0[i]['label']}\" in first table is 0.0, using absolute tolerance")
-        else:
-          logging.warning(f"Maximum norm of \"{headings0[i]['label']}\" in first table is 0.0, using absolute tolerance")
+        logging.warning(f'''{"At least one" if perLine else "Maximum"} norm of
+                            "{headings0[i]['label']}" in first table is 0.0, using absolute tolerance''')
 
     line1 = 0
     while table1.data_read():                                                  # read next data line of ASCII table
@@ -418,20 +416,18 @@ class Test:
 
     logging.info(' ********')
     for i in range(dataLength):
-      if absTol[i]:
-        logging.info(f" * maximum absolute error {maxError[i]} between {headings0[i]['label']} and {headings1[i]['label']}")
-      else:
-        logging.info(f" * maximum relative error {maxError[i]} between {headings0[i]['label']} and {headings1[i]['label']}")
+      logging.info(f''' * maximum {'absolute' if absTol[i] else 'relative'} error {maxError[i]}
+                       between {headings0[i]['label']} and {headings1[i]['label']}''')
     logging.info(' ********')
     return maxError
 
 
   def compare_TablesStatistically(self,
-                     files = [None,None],                                      # list of file names
-                     columns = [None],                                         # list of list of column labels (per file)
-                     meanTol = 1.0e-4,
-                     stdTol = 1.0e-6,
-                     preFilter = 1.0e-9):
+                                  files = [None,None],                                      # list of file names
+                                  columns = [None],                                         # list of list of column labels (per file)
+                                  meanTol = 1.0e-4,
+                                  stdTol = 1.0e-6,
+                                  preFilter = 1.0e-9):
     """
     Calculate statistics of tables.
 
@@ -440,9 +436,9 @@ class Test:
     if not (isinstance(files, Iterable) and not isinstance(files, str)):       # check whether list of files is requested
       files = [str(files)]
 
-    tables = [damask.Table.from_ASCII(filename) for filename in files]
+    tables = [damask.Table.load(filename) for filename in files]
     for table in tables:
-      table._label_flat()
+      table._label_discrete()
 
     columns += [columns[0]]*(len(files)-len(columns))                          # extend to same length as files
     columns = columns[:len(files)]                                             # truncate to same length as files
@@ -462,7 +458,7 @@ class Test:
 
     data = []
     for table,labels in zip(tables,columns):
-      table._label_condensed()
+      table._label_uniform()
       data.append(np.hstack(list(table.get(label) for label in labels)))
 
 
@@ -471,12 +467,11 @@ class Test:
       normBy = (np.abs(data[i]) + np.abs(data[i-1]))*0.5
       normedDelta = np.where(normBy>preFilter,delta/normBy,0.0)
       mean = np.amax(np.abs(np.mean(normedDelta,0)))
-      std = np.amax(np.std(normedDelta,0))
+      std  = np.amax(np.std(normedDelta,0))
       logging.info(f'mean: {mean:f}')
       logging.info(f'std:  {std:f}')
 
-    return (mean<meanTol) & (std < stdTol)
-
+    return (mean < meanTol) & (std < stdTol)
 
 
   def compare_Tables(self,
@@ -491,7 +486,7 @@ class Test:
 
     if len(files) < 2: return True                                             # single table is always close to itself...
 
-    tables = [damask.Table.from_ASCII(filename) for filename in files]
+    tables = [damask.Table.load(filename) for filename in files]
 
     columns += [columns[0]]*(len(files)-len(columns))                          # extend to same length as files
     columns = columns[:len(files)]                                             # truncate to same length as files
@@ -580,7 +575,7 @@ class Test:
 
     if culprit == 0:
       count = len(self.variants) if self.options.select is None else len(self.options.select)
-      msg = 'Test passed.' if count == 1 else f'All {count} tests passed.'
+      msg = ('Test passed.' if count == 1 else f'All {count} tests passed.') + '\a\a\a'
     elif culprit == -1:
       msg = 'Warning: could not start test...'
       ret = 0

python/damask/_vtk.py

@@ -118,7 +118,7 @@ class VTK:
 
 
     @staticmethod
-    def from_file(fname,dataset_type=None):
+    def load(fname,dataset_type=None):
         """
         Create VTK from file.
 
@@ -168,7 +168,7 @@ class VTK:
     def _write(writer):
         """Wrapper for parallel writing."""
         writer.Write()
-    def to_file(self,fname,parallel=True,compress=True):
+    def save(self,fname,parallel=True,compress=True):
         """
         Write to file.
 
@@ -178,6 +178,8 @@ class VTK:
             Filename for writing.
         parallel : boolean, optional
             Write data in parallel background process. Defaults to True.
+        compress : bool, optional
+            Compress with zlib algorithm. Defaults to True.
 
         """
         if   isinstance(self.vtk_data,vtk.vtkRectilinearGrid):

python/damask/util.py

@@ -117,6 +117,7 @@ def execute(cmd,
     initialPath = os.getcwd()
     myEnv = os.environ if env is None else env
     os.chdir(wd)
+    print(f"executing '{cmd}' in '{wd}'")
     process = subprocess.Popen(shlex.split(cmd),
                                stdout = subprocess.PIPE,
                                stderr = subprocess.PIPE,
@@ -128,7 +129,7 @@ def execute(cmd,
     stdout = stdout.decode('utf-8').replace('\x08','')
     stderr = stderr.decode('utf-8').replace('\x08','')
     if process.returncode != 0:
-        raise RuntimeError(f'{cmd} failed with returncode {process.returncode}')
+        raise RuntimeError(f"'{cmd}' failed with returncode {process.returncode}")
     return stdout, stderr
 
 
@@ -172,8 +173,9 @@ def scale_to_coprime(v):
     m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(np.int)
     m = m//reduce(np.gcd,m)
 
-    if not np.allclose(v[v.nonzero()]/m[v.nonzero()],v[v.nonzero()][0]/m[m.nonzero()][0]):
-        raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
+    with np.errstate(invalid='ignore'):
+        if not np.allclose(np.ma.masked_invalid(v/m),v[np.argmax(abs(v))]/m[np.argmax(abs(v))]):
+            raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
 
     return m
 

python/tests/reference/Geom/clean_2_1+2+3_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAZwAAAA==eF7t0rcOgmAAhVEgNmyo2AuoWN//BR04EwsJcfzvcvabL47qxcFOJg177HPAIUdMOeaEU844Z8YFl1wx55obbrnjngceeeKZFxYseeWNd1Z88MkX3/zwy+Z/wf8YOqzX1uEPlgwHCA==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_2_1+2+3_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAagAAAA==eF7t0rkOglAARFExLrgCKuKuqLj8/w9acCoSY7B+05x+cqNOvSj4l92GPfY54JAxRxxzwilnnDNhyowLLrlizjULbrjljnseeOSJZ15Y8sob76z44JMvvtn8L9jObz2GDuv96vADk5QHBg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_2_1_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAZAAAAA==eF7t0scRglAAQEEBAyZUMCuomPtv0ANbgMNw/O+yDbyo1xQFWxkzYZ8DDjliyjEnnHLGOTMuuOSKOQuuueGWO+554JEnnlmy4oVX3ljzzgeffPHND7+Mg50aPmz698MfmvQHCg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_2_1_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_2_None_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAAGwAAAA==eF5jZIAAxlF6lB4AmmmUpogeDUfKaAD7jwDw
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_2_None_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAAGQAAAA==eF5jZIAAxlF6lB4AmmmUHqUHkAYA/M8A8Q==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_1+2+3_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAZwAAAA==eF7t0rcOgmAAhVEgNmyo2AuoWN//BR04EwsJcfzvcvabL47qxcFOJg177HPAIUdMOeaEU844Z8YFl1wx55obbrnjngceeeKZFxYseeWNd1Z88MkX3/zwy+Z/wf8YOqzX1uEPlgwHCA==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_1+2+3_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAagAAAA==eF7t0rkOglAARFExLrgCKuKuqLj8/w9acCoSY7B+05x+cqNOvSj4l92GPfY54JAxRxxzwilnnDNhyowLLrlizjULbrjljnseeOSJZ15Y8sob76z44JMvvtn8L9jObz2GDuv96vADk5QHBg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_1_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAZAAAAA==eF7t0scRglAAQEEBAyZUMCuomPtv0ANbgMNw/O+yDbyo1xQFWxkzYZ8DDjliyjEnnHLGOTMuuOSKOQuuueGWO+554JEnnlmy4oVX3ljzzgeffPHND7+Mg50aPmz698MfmvQHCg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_1_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_None_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAAIgAAAA==eF5jZIAAxlGaLJoJjSakntr6hzqN7v9RepSmJw0AC04A9Q==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_3_None_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAALwAAAA==eF5jZIAAxlGaLJoJjSakHpc+cvUTUkdrmlL3j9KU0dROF5TqH2iaVPcDAALOANU=
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_1+2+3_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAcQAAAA==eF7t0rkOglAUBFAxKu6igvsKrv//gxYcm9fQGEPBNKe6yc1kolaZqPEndthljzH7HHDIEceccMoZE8654JIpM6645oZb7rjngUeeeOaFV+YseOOdDz754pthf+3Aqr7rdv9vw3+/NjssU7XDD0/8BuQ=
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_1+2+3_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAYQAAAA==eF7t0scVglAAAEHgqZgBA2ZExdR/gx6YCpDj38s0sEnUlgR7ccAhR0w55oRTzjjngktmzFlwxTU33LLkjnseeOSJZ15Y8cqaN975YMMnX3zzwy/j4F+GD9u6fvgD+gwHCA==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_1_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATgAAAA==eF4FwUEKgCAUBNCO4rIWX8ZJsbxA5/iUFqQVBJ2/9zZt+p52yXeza816mW+0sBCtz6HCGGSPE1wJjMX0BCGYhTQuJLrkKfDA0P0d3xK6
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="41">
         AQAAAACAAAAABQAAZAAAAA==eF7t0scRglAAQEEBAyZUMCuomPtv0ANbgMNw/O+yDbyo1xQFWxkzYZ8DDjliyjEnnHLGOTMuuOSKOQuuueGWO+554JEnnlmy4oVX3ljzzgeffPHND7+Mg50aPmz698MfmvQHCg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_1_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF5LScxNLM7Wc0/Nz9VLzklNzFMoM9Yz0DPQTcwpyEjUNTI31U03tzAwTDM1Mk9T0DAyMDLQNbDUNTJSMDS1MjK0MgFyTQwMNBkAHc8SuA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="2" RangeMax="41">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="2" RangeMax="41">
         AQAAAACAAAAABQAAZAAAAA==eF7t0rcSglAARFEHE0bAgBkE8///oAWnF8b2bXP6nRv1mkXBv+xzwCFHHDPmhFPOOOeCSyZMmXHFNTfcMueOex545IlnXliw5JUVa95454NPvvjmh79+DXYzdNisbYdfSqMHMg==
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_None_False.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwdEJgDAMBUBH6ad+JLzElmoXcI6grYKtCoLze7dZs/fkJd+N15rtct/IYJDV5zDSGGiPE6QEjcX1CgVhJlUnIakkLwQPDN0PHdcSuQ==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAAIAAAAA==eF5jZIAAxlF6lB4AmokAPdj1DzRNyP2jNH4aAMufANU=
       </DataArray>
     </CellData>

python/tests/reference/Geom/clean_4_None_True.vtr

@@ -1,11 +1,16 @@
 <?xml version="1.0"?>
 <VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
   <RectilinearGrid WholeExtent="0 8 0 5 0 4">
+    <FieldData>
+      <Array type="String" Name="comments" NumberOfTuples="1" format="binary">
+        AQAAAACAAABJAAAATwAAAA==eF4FwVEKgCAQBcCO4md97PJcE9MLdI6ltCCtIOj8zuza9Lt4zU/jrWa9ze8YDNL6nkoSPB1hgS1eQjGjQECIJGKsT2KTi4QZmIYOHg4SwA==
+      </Array>
+    </FieldData>
   <Piece Extent="0 8 0 5 0 4">
     <PointData>
     </PointData>
     <CellData>
-      <DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
+      <DataArray type="Int64" Name="material" format="binary" RangeMin="1" RangeMax="2">
         AQAAAACAAAAABQAAMAAAAA==eF5jYoAAJhw0IwEalz566aeUptT+oa6fUppS+4e6fkppSu0f6voppSm1HwBAngDh
       </DataArray>
     </CellData>

python/tests/reference/Material/material.yaml

@@ -0,0 +1,42 @@
+homogenization:
+  SX:
+    mech: {type: none}
+  Taylor:
+    mech: {type: isostrain, N_constituents: 2}
+
+microstructure:
+  - constituents:
+      - fraction: 1.0
+        orientation: [1.0, 0.0, 0.0, 0.0]
+        phase: Aluminum
+    homogenization: SX
+  - constituents:
+      - fraction: 1.0
+        orientation: [0.7936696712125002, -0.28765777461664166, -0.3436487135089419, 0.4113964260949434]
+        phase: Aluminum
+    homogenization: SX
+  - constituents:
+      - fraction: 1.0
+        orientation: [0.3986143167493579, -0.7014883552495493, 0.2154871765709027, 0.5500781677772945]
+        phase: Aluminum
+    homogenization: SX
+  - homogenization: Taylor
+    constituents:
+      - fraction: .5
+        orientation: [0.28645844315788244, -0.022571491243423537, -0.467933059311115, -0.8357456192708106]
+        phase: Aluminum
+      - fraction: .5
+        orientation: [0.3986143167493579, -0.7014883552495493, 0.2154871765709027, 0.5500781677772945]
+        phase: Steel
+
+phase:
+  Aluminum:
+    elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
+    generic:
+      output: [F, P, Fe, Fp, Lp]
+    lattice: fcc
+  Steel:
+    elasticity: {C_11: 233.3e9, C_12: 135.5e9, C_44: 118.0e9, type: hooke}
+    generic:
+      output: [F, P, Fe, Fp, Lp]
+    lattice: bcc

python/tests/reference/Rotation/Visualize_hybridIA_sampling.ipynb

@@ -0,0 +1,276 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import damask\n",
+    "\n",
+    "from pathlib import Path"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "orientations,rODF = damask.Rotation.from_ODF('hybridIA_ODF.txt',\n",
+    "                                             2**14,\n",
+    "                                             degrees=True,\n",
+    "                                             reconstruct=True,\n",
+    "                                             fractions=True,\n",
+    "                                             seed=0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "VTK = damask.VTK.from_rectilinearGrid([36,36,36],[90,90,90])\n",
+    "VTK.add(damask.Table.from_ASCII('hybridIA_ODF.txt').get('intensity'),'intensity')\n",
+    "VTK.add(rODF.flatten(order='F'),'rODF')\n",
+    "VTK.to_file('hybridIA_ODF.vtr')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Help on class VTK in module damask._vtk:\n",
+      "\n",
+      "class VTK(builtins.object)\n",
+      " |  VTK(geom)\n",
+      " |  \n",
+      " |  Spatial visualization (and potentially manipulation).\n",
+      " |  \n",
+      " |  High-level interface to VTK.\n",
+      " |  \n",
+      " |  Methods defined here:\n",
+      " |  \n",
+      " |  __init__(self, geom)\n",
+      " |      Set geometry and topology.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      geom : subclass of vtk.vtkDataSet\n",
+      " |          Description of geometry and topology. Valid types are vtk.vtkRectilinearGrid,\n",
+      " |          vtk.vtkUnstructuredGrid, or vtk.vtkPolyData.\n",
+      " |  \n",
+      " |  __repr__(self)\n",
+      " |      ASCII representation of the VTK data.\n",
+      " |  \n",
+      " |  add(self, data, label=None)\n",
+      " |      Add data to either cells or points.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      data : numpy.ndarray\n",
+      " |          Data to add. First dimension need to match either\n",
+      " |          number of cells or number of points\n",
+      " |      label : str\n",
+      " |          Data label.\n",
+      " |  \n",
+      " |  add_comments(self, comments)\n",
+      " |      Add Comments.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      comments : str or list of str\n",
+      " |          Comments to add.\n",
+      " |  \n",
+      " |  get(self, label)\n",
+      " |      Get either cell or point data.\n",
+      " |      \n",
+      " |      Cell data takes precedence over point data, i.e. this\n",
+      " |      function assumes that labels are unique among cell and\n",
+      " |      point data.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      label : str\n",
+      " |          Data label.\n",
+      " |  \n",
+      " |  get_comments(self)\n",
+      " |      Return the comments.\n",
+      " |  \n",
+      " |  set_comments(self, comments)\n",
+      " |      Set Comments.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      comments : str or list of str\n",
+      " |          Comments.\n",
+      " |  \n",
+      " |  show(self)\n",
+      " |      Render.\n",
+      " |      \n",
+      " |      See http://compilatrix.com/article/vtk-1 for further ideas.\n",
+      " |  \n",
+      " |  write(self, fname, parallel=True)\n",
+      " |      Write to file.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      fname : str or pathlib.Path\n",
+      " |          Filename for writing.\n",
+      " |      parallel : boolean, optional\n",
+      " |          Write data in parallel background process. Defaults to True.\n",
+      " |  \n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Static methods defined here:\n",
+      " |  \n",
+      " |  from_file(fname, dataset_type=None)\n",
+      " |      Create VTK from file.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      fname : str or pathlib.Path\n",
+      " |          Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.\n",
+      " |      dataset_type : str, optional\n",
+      " |          Name of the vtk.vtkDataSet subclass when opening an .vtk file. Valid types are vtkRectilinearGrid,\n",
+      " |          vtkUnstructuredGrid, and vtkPolyData.\n",
+      " |  \n",
+      " |  from_polyData(points)\n",
+      " |      Create VTK of type vtk.polyData.\n",
+      " |      \n",
+      " |      This is the common type for point-wise data.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      points : numpy.ndarray of shape (:,3)\n",
+      " |          Spatial position of the points.\n",
+      " |  \n",
+      " |  from_rectilinearGrid(grid, size, origin=array([0., 0., 0.]))\n",
+      " |      Create VTK of type vtk.vtkRectilinearGrid.\n",
+      " |      \n",
+      " |      This is the common type for results from the grid solver.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      grid : numpy.ndarray of shape (3) of np.dtype = int\n",
+      " |          Number of cells.\n",
+      " |      size : numpy.ndarray of shape (3)\n",
+      " |          Physical length.\n",
+      " |      origin : numpy.ndarray of shape (3), optional\n",
+      " |          Spatial origin.\n",
+      " |  \n",
+      " |  from_unstructuredGrid(nodes, connectivity, cell_type)\n",
+      " |      Create VTK of type vtk.vtkUnstructuredGrid.\n",
+      " |      \n",
+      " |      This is the common type for results from FEM solvers.\n",
+      " |      \n",
+      " |      Parameters\n",
+      " |      ----------\n",
+      " |      nodes : numpy.ndarray of shape (:,3)\n",
+      " |          Spatial position of the nodes.\n",
+      " |      connectivity : numpy.ndarray of np.dtype = int\n",
+      " |          Cell connectivity (0-based), first dimension determines #Cells, second dimension determines #Nodes/Cell.\n",
+      " |      cell_type : str\n",
+      " |          Name of the vtk.vtkCell subclass. Tested for TRIANGLE, QUAD, TETRA, and HEXAHEDRON.\n",
+      " |  \n",
+      " |  ----------------------------------------------------------------------\n",
+      " |  Data descriptors defined here:\n",
+      " |  \n",
+      " |  __dict__\n",
+      " |      dictionary for instance variables (if defined)\n",
+      " |  \n",
+      " |  __weakref__\n",
+      " |      list of weak references to the object (if defined)\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "help(damask.VTK)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "a,b=np.radians(([90,90],[45,45]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([1.57079633, 1.57079633])"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "a"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([0.78539816, 0.78539816])"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "b"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

python/tests/test_Colormap.py

@@ -75,41 +75,36 @@ class TestColormap:
             assert np.allclose(Colormap._xyz2msh(xyz),msh,atol=1.e-6,rtol=0)
 
 
-    @pytest.mark.parametrize('format',['ASCII','paraview','GOM','Gmsh'])
+    @pytest.mark.parametrize('format',['ASCII','paraview','GOM','gmsh'])
     @pytest.mark.parametrize('model',['rgb','hsv','hsl','xyz','lab','msh'])
     def test_from_range(self,model,format,tmpdir):
         N = np.random.randint(2,256)
-        c = Colormap.from_range(np.random.rand(3),np.random.rand(3),model=model,N=N)
-        c.to_file(tmpdir/'color_out',format=format)
+        c = Colormap.from_range(np.random.rand(3),np.random.rand(3),model=model,N=N)    # noqa
+        eval(f'c.save_{format}(tmpdir/"color_out")')
 
-    @pytest.mark.parametrize('format',['ASCII','paraview','GOM','Gmsh'])
+    @pytest.mark.parametrize('format',['ASCII','paraview','GOM','gmsh'])
     @pytest.mark.parametrize('name',['strain','gnuplot','Greys','PRGn','viridis'])
     def test_from_predefined(self,name,format,tmpdir):
         N = np.random.randint(2,256)
-        c = Colormap.from_predefined(name,N)
+        c = Colormap.from_predefined(name,N)                                            # noqa
         os.chdir(tmpdir)
-        c.to_file(format=format)
+        eval(f'c.save_{format}()')
 
     @pytest.mark.parametrize('format,name',[('ASCII','test.txt'),
                                             ('paraview','test.json'),
                                             ('GOM','test.legend'),
-                                            ('Gmsh','test.msh')
+                                            ('gmsh','test.msh')
                                            ])
     def test_write_filehandle(self,format,name,tmpdir):
-        c = Colormap.from_predefined('Dark2')
+        c = Colormap.from_predefined('Dark2')                                           # noqa
         fname = tmpdir/name
-        with open(fname,'w') as f:
-            c.to_file(f,format=format)
+        with open(fname,'w') as f:                                                      # noqa
+            eval(f'c.save_{format}(f)')
         for i in range(10):
             if fname.exists(): return
             time.sleep(.5)
         assert False
 
-    def test_write_invalid_format(self):
-        c = Colormap.from_predefined('Dark2')
-        with pytest.raises(ValueError):
-            c.to_file(format='invalid')
-
     @pytest.mark.parametrize('model',['rgb','hsv','hsl','lab','invalid'])
     def test_invalid_color(self,model):
         with pytest.raises(ValueError):
@@ -119,13 +114,13 @@ class TestColormap:
         c_1 = Colormap.from_predefined('stress')
         c_2 = c_1.reversed()
         assert (not np.allclose(c_1.colors,c_2.colors)) and \
-                np.allclose(c_1.colors,c_2.reversed().colors)
+                    np.allclose(c_1.colors,c_2.reversed().colors)
 
     def test_invert(self):
         c_1 = Colormap.from_predefined('strain')
         c_2 = ~c_1
-        assert (not np.allclose(c_1.colors,c_2.colors)) and \
-                np.allclose(c_1.colors,(~c_2).colors)
+        assert (not np.allclose(c_1.colors,  c_2.colors)) and \
+                    np.allclose(c_1.colors,(~c_2).colors)
 
     def test_add(self):
         c = Colormap.from_predefined('jet')
@@ -149,16 +144,16 @@ class TestColormap:
     @pytest.mark.parametrize('format,ext',[('ASCII','.txt'),
                                            ('paraview','.json'),
                                            ('GOM','.legend'),
-                                           ('Gmsh','.msh')
+                                           ('gmsh','.msh')
                                           ])
     def test_compare_reference(self,format,ext,tmpdir,reference_dir,update):
         name = 'binary'
-        c = Colormap.from_predefined(name)
+        c = Colormap.from_predefined(name)                                              # noqa
         if update:
             os.chdir(reference_dir)
-            c.to_file(format=format)
+            eval(f'c.save_{format}()')
         else:
             os.chdir(tmpdir)
-            c.to_file(format=format)
+            eval(f'c.save_{format}()')
             time.sleep(.5)
             assert filecmp.cmp(tmpdir/(name+ext),reference_dir/(name+ext))

python/tests/test_Geom.py

@@ -11,9 +11,9 @@ from damask import util
 
 
 def geom_equal(a,b):
-    return np.all(a.get_microstructure() == b.get_microstructure()) and \
-           np.all(a.get_grid()           == b.get_grid()) and \
-           np.allclose(a.get_size(), b.get_size()) and \
+    return np.all(a.material == b.material) and \
+           np.all(a.grid     == b.grid) and \
+           np.allclose(a.size, b.size) and \
            str(a.diff(b)) == str(b.diff(a))
 
 @pytest.fixture
@@ -33,115 +33,89 @@ def reference_dir(reference_dir_base):
 
 class TestGeom:
 
-    @pytest.mark.parametrize('flavor',['plain','explicit'])
-    def test_duplicate(self,default,flavor):
-        if flavor == 'plain':
-            modified = default.duplicate()
-        elif flavor == 'explicit':
-            modified = default.duplicate(
-                            default.get_microstructure(),
-                            default.get_size(),
-                            default.get_origin()
-                           )
-        print(modified)
-        assert geom_equal(default,modified)
-
     def test_diff_equal(self,default):
         assert str(default.diff(default)) == ''
 
+
     def test_diff_not_equal(self,default):
-        new = Geom(default.microstructure[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
+        new = Geom(default.material[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
         assert str(default.diff(new)) != ''
 
 
-    @pytest.mark.parametrize('masked',[True,False])
-    def test_set_microstructure(self,default,masked):
-        old = default.get_microstructure()
-        new = np.random.randint(200,size=default.grid)
-        default.set_microstructure(np.ma.MaskedArray(new,np.full_like(new,masked)))
-        assert np.all(default.microstructure==(old if masked else new))
-
-
     def test_write_read_str(self,default,tmpdir):
-        default.to_file(str(tmpdir/'default.geom'),format='ASCII')
-        new = Geom.from_file(str(tmpdir/'default.geom'))
+        default.save_ASCII(str(tmpdir/'default.geom'))
+        new = Geom.load_ASCII(str(tmpdir/'default.geom'))
         assert geom_equal(default,new)
 
+
     def test_write_read_file(self,default,tmpdir):
         with open(tmpdir/'default.geom','w') as f:
-            default.to_file(f,format='ASCII',pack=True)
+            default.save_ASCII(f,compress=True)
         with open(tmpdir/'default.geom') as f:
-            new = Geom.from_file(f)
+            new = Geom.load_ASCII(f)
         assert geom_equal(default,new)
 
-    def test_write_as_ASCII(self,default,tmpdir):
-        with open(tmpdir/'str.geom','w') as f:
-            f.write(default.as_ASCII())
-        with open(tmpdir/'str.geom') as f:
-            new = Geom.from_file(f)
-        assert geom_equal(default,new)
 
     def test_read_write_vtr(self,default,tmpdir):
-        default.to_file(tmpdir/'default',format='vtr')
+        default.save(tmpdir/'default')
         for _ in range(10):
             time.sleep(.2)
             if os.path.exists(tmpdir/'default.vtr'): break
 
-        new = Geom.from_vtr(tmpdir/'default.vtr')
+        new = Geom.load(tmpdir/'default.vtr')
         assert geom_equal(new,default)
 
+
     def test_invalid_geom(self,tmpdir):
         with open('invalid_file','w') as f:
             f.write('this is not a valid header')
         with open('invalid_file','r') as f:
             with pytest.raises(TypeError):
-                Geom.from_file(f)
+                Geom.load_ASCII(f)
+
 
     def test_invalid_vtr(self,tmpdir):
         v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
-        v.to_file(tmpdir/'no_materialpoint.vtr')
+        v.save(tmpdir/'no_materialpoint.vtr')
         for _ in range(10):
             time.sleep(.2)
             if os.path.exists(tmpdir/'no_materialpoint.vtr'): break
         with pytest.raises(ValueError):
-            Geom.from_vtr(tmpdir/'no_materialpoint.vtr')
+            Geom.load(tmpdir/'no_materialpoint.vtr')
 
 
-    @pytest.mark.parametrize('pack',[True,False])
-    def test_pack(self,default,tmpdir,pack):
-        default.to_file(tmpdir/'default.geom',format='ASCII',pack=pack)
-        new = Geom.from_file(tmpdir/'default.geom')
+    @pytest.mark.parametrize('compress',[True,False])
+    def test_compress(self,default,tmpdir,compress):
+        default.save_ASCII(tmpdir/'default.geom',compress=compress)
+        new = Geom.load_ASCII(tmpdir/'default.geom')
         assert geom_equal(new,default)
 
-    def test_invalid_combination(self,default):
-        with pytest.raises(ValueError):
-            default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(3), autosize=True)
 
     def test_invalid_size(self,default):
         with pytest.raises(ValueError):
-            default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(2))
+            Geom(default.material[1:,1:,1:],
+                 size=np.ones(2))
+
 
     def test_invalid_origin(self,default):
         with pytest.raises(ValueError):
-            default.duplicate(default.microstructure[1:,1:,1:],origin=np.ones(4))
+            Geom(default.material[1:,1:,1:],
+                 size=np.ones(3),
+                 origin=np.ones(4))
 
-    def test_invalid_microstructure_size(self,default):
-        microstructure = np.ones((3,3))
+
+    def test_invalid_materials_shape(self,default):
+        material = np.ones((3,3))
         with pytest.raises(ValueError):
-            default.duplicate(microstructure)
+            Geom(material,
+                 size=np.ones(3))
 
-    def test_invalid_microstructure_type(self,default):
-        microstructure = np.random.randint(1,300,(3,4,5))==1
-        with pytest.raises(TypeError):
-            default.duplicate(microstructure)
 
-    def test_invalid_homogenization(self,default):
+    def test_invalid_materials_type(self,default):
+        material = np.random.randint(1,300,(3,4,5))==1
         with pytest.raises(TypeError):
-            default.set_homogenization(homogenization=0)
+            Geom(material)
 
-    def test_invalid_write_format(self,default):
-        with pytest.raises(TypeError):
-            default.to_file(format='invalid')
 
     @pytest.mark.parametrize('directions,reflect',[
                                                    (['x'],        False),
@@ -154,10 +128,11 @@ class TestGeom:
         modified = default.mirror(directions,reflect)
         tag = f'directions={"-".join(directions)}_reflect={reflect}'
         reference = reference_dir/f'mirror_{tag}.geom'
-        if update: modified.to_file(reference)
-        assert geom_equal(Geom.from_file(reference),
+        if update: modified.save_ASCII(reference)
+        assert geom_equal(Geom.load_ASCII(reference),
                           modified)
 
+
     @pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
     def test_mirror_invalid(self,default,directions):
         with pytest.raises(ValueError):
@@ -175,17 +150,20 @@ class TestGeom:
         modified = default.flip(directions)
         tag = f'directions={"-".join(directions)}'
         reference = reference_dir/f'flip_{tag}.geom'
-        if update: modified.to_file(reference)
-        assert geom_equal(Geom.from_file(reference),
+        if update: modified.save_ASCII(reference)
+        assert geom_equal(Geom.load_ASCII(reference),
                           modified)
 
+
     def test_flip_invariant(self,default):
         assert geom_equal(default,default.flip([]))
 
+
     @pytest.mark.parametrize('direction',[['x'],['x','y']])
     def test_flip_double(self,default,direction):
         assert geom_equal(default,default.flip(direction).flip(direction))
 
+
     @pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
     def test_flip_invalid(self,default,directions):
         with pytest.raises(ValueError):
@@ -199,14 +177,15 @@ class TestGeom:
         current = default.clean(stencil,selection,periodic)
         reference = reference_dir/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
         if update and stencil > 1:
-            current.to_file(reference,format='vtr')
+            current.save(reference)
             for _ in range(10):
                 time.sleep(.2)
                 if os.path.exists(reference.with_suffix('.vtr')): break
-        assert geom_equal(Geom.from_vtr(reference) if stencil > 1 else default,
+        assert geom_equal(Geom.load(reference) if stencil > 1 else default,
                           current
                          )
 
+
     @pytest.mark.parametrize('grid',[
                                      (10,11,10),
                                      [10,13,10],
@@ -220,26 +199,33 @@ class TestGeom:
         modified = default.scale(grid)
         tag = f'grid={util.srepr(grid,"-")}'
         reference = reference_dir/f'scale_{tag}.geom'
-        if update: modified.to_file(reference)
-        assert geom_equal(Geom.from_file(reference),
+        if update: modified.save_ASCII(reference)
+        assert geom_equal(Geom.load_ASCII(reference),
                           modified)
 
+
     def test_renumber(self,default):
-        microstructure = default.get_microstructure()
-        for m in np.unique(microstructure):
-            microstructure[microstructure==m] = microstructure.max() + np.random.randint(1,30)
-        modified = default.duplicate(microstructure)
+        material = default.material.copy()
+        for m in np.unique(material):
+            material[material==m] = material.max() + np.random.randint(1,30)
+        modified = Geom(material,
+                        default.size,
+                        default.origin)
         assert not geom_equal(modified,default)
         assert geom_equal(default,
                           modified.renumber())
 
+
     def test_substitute(self,default):
         offset = np.random.randint(1,500)
-        modified = default.duplicate(default.get_microstructure() + offset)
+        modified = Geom(default.material + offset,
+                        default.size,
+                        default.origin)
         assert not geom_equal(modified,default)
         assert geom_equal(default,
-                          modified.substitute(np.arange(default.microstructure.max())+1+offset,
-                                              np.arange(default.microstructure.max())+1))
+                          modified.substitute(np.arange(default.material.max())+1+offset,
+                                              np.arange(default.material.max())+1))
+
 
     @pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]),
                                            np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
@@ -249,21 +235,24 @@ class TestGeom:
             modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True))
         assert geom_equal(default,modified)
 
+
     @pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0],
                                        [0.0,32.0,240.0]])
     def test_rotate(self,default,update,reference_dir,Eulers):
         modified = default.rotate(Rotation.from_Eulers(Eulers,degrees=True))
         tag = f'Eulers={util.srepr(Eulers,"-")}'
         reference = reference_dir/f'rotate_{tag}.geom'
-        if update: modified.to_file(reference)
-        assert geom_equal(Geom.from_file(reference),
+        if update: modified.save_ASCII(reference)
+        assert geom_equal(Geom.load_ASCII(reference),
                           modified)
 
+
     def test_canvas(self,default):
         grid = default.grid
         grid_add = np.random.randint(0,30,(3))
         modified = default.canvas(grid + grid_add)
-        assert np.all(modified.microstructure[:grid[0],:grid[1],:grid[2]] == default.microstructure)
+        assert np.all(modified.material[:grid[0],:grid[1],:grid[2]] == default.material)
+
 
     @pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random()*8),
                                                 (np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))])
@@ -276,13 +265,14 @@ class TestGeom:
                                          np.random.rand()*4,
                                          np.random.randint(20)])
     def test_add_primitive_shift(self,center1,center2,diameter,exponent):
-        """Same volume fraction for periodic microstructures and different center."""
+        """Same volume fraction for periodic geometries and different center."""
         o = np.random.random(3)-.5
         g = np.random.randint(8,32,(3))
         s = np.random.random(3)+.5
         G_1 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center1,exponent)
         G_2 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center2,exponent)
-        assert np.count_nonzero(G_1.microstructure!=2) == np.count_nonzero(G_2.microstructure!=2)
+        assert np.count_nonzero(G_1.material!=2) == np.count_nonzero(G_2.material!=2)
+
 
     @pytest.mark.parametrize('center',[np.random.randint(4,10,(3)),
                                        np.random.randint(2,10),
@@ -299,6 +289,7 @@ class TestGeom:
         G_2 = Geom(np.ones(g,'i'),[1.,1.,1.]).add_primitive(.3,center,1,fill,Rotation.from_Eulers(eu),inverse,periodic=periodic)
         assert geom_equal(G_1,G_2)
 
+
     @pytest.mark.parametrize('trigger',[[1],[]])
     def test_vicinity_offset(self,trigger):
         offset = np.random.randint(2,4)
@@ -317,13 +308,15 @@ class TestGeom:
 
         geom = Geom(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)
 
-        assert np.all(m2==geom.microstructure)
+        assert np.all(m2==geom.material)
+
 
     @pytest.mark.parametrize('periodic',[True,False])
     def test_vicinity_offset_invariant(self,default,periodic):
-        old = default.get_microstructure()
-        default.vicinity_offset(trigger=[old.max()+1,old.min()-1])
-        assert np.all(old==default.microstructure)
+        offset = default.vicinity_offset(trigger=[default.material.max()+1,
+                                                  default.material.min()-1])
+        assert np.all(offset.material==default.material)
+
 
     @pytest.mark.parametrize('periodic',[True,False])
     def test_tessellation_approaches(self,periodic):
@@ -335,6 +328,7 @@ class TestGeom:
         Laguerre = Geom.from_Laguerre_tessellation(grid,size,seeds,np.ones(N_seeds),periodic)
         assert geom_equal(Laguerre,Voronoi)
 
+
     def test_Laguerre_weights(self):
         grid   = np.random.randint(10,20,3)
         size   = np.random.random(3) + 1.0
@@ -344,17 +338,18 @@ class TestGeom:
         ms     = np.random.randint(1, N_seeds+1)
         weights[ms-1] = np.random.random()
         Laguerre = Geom.from_Laguerre_tessellation(grid,size,seeds,weights,np.random.random()>0.5)
-        assert np.all(Laguerre.microstructure == ms)
+        assert np.all(Laguerre.material == ms)
+
 
     @pytest.mark.parametrize('approach',['Laguerre','Voronoi'])
     def test_tessellate_bicrystal(self,approach):
         grid  = np.random.randint(5,10,3)*2
         size  = grid.astype(np.float)
         seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
-        microstructure = np.ones(grid)
-        microstructure[:,grid[1]//2:,:] = 2
+        material = np.ones(grid)
+        material[:,grid[1]//2:,:] = 2
         if   approach == 'Laguerre':
             geom = Geom.from_Laguerre_tessellation(grid,size,seeds,np.ones(2),np.random.random()>0.5)
         elif approach == 'Voronoi':
             geom = Geom.from_Voronoi_tessellation(grid,size,seeds,            np.random.random()>0.5)
-        assert np.all(geom.microstructure == microstructure)
+        assert np.all(geom.material == material)

python/tests/test_Material.py

@@ -0,0 +1,61 @@
+import os
+
+import pytest
+
+from damask import Material
+
+@pytest.fixture
+def reference_dir(reference_dir_base):
+    """Directory containing reference results."""
+    return reference_dir_base/'Material'
+
+
+class TestMaterial:
+    
+    @pytest.mark.parametrize('fname',[None,'test.yaml'])
+    def test_load_save(self,reference_dir,tmp_path,fname):
+        reference = Material.load(reference_dir/'material.yaml')
+        os.chdir(tmp_path)
+        if fname is None:
+            reference.save()
+            new = Material.load('material.yaml')
+        else:
+            reference.save(fname)
+            new = Material.load(fname)
+        assert reference == new
+
+    def test_valid_complete(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        assert material_config.is_valid and material_config.is_complete
+
+    def test_invalid_lattice(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        material_config['phase']['Aluminum']['lattice']='fxc'
+        assert not material_config.is_valid
+    
+    def test_invalid_orientation(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        material_config['microstructure'][0]['constituents'][0]['orientation']=[0,0,0,0]
+        assert not material_config.is_valid
+    
+    def test_invalid_fraction(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        material_config['microstructure'][0]['constituents'][0]['fraction']=.9
+        assert not material_config.is_valid
+    
+
+    @pytest.mark.parametrize('item',['homogenization','phase','microstructure'])
+    def test_incomplete_missing(self,reference_dir,item):
+        material_config = Material.load(reference_dir/'material.yaml')
+        del material_config[item]
+        assert not material_config.is_complete
+    
+    def test_incomplete_wrong_phase(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        new = material_config.microstructure_rename_phase({'Steel':'FeNbC'})
+        assert not new.is_complete
+    
+    def test_incomplete_wrong_homogenization(self,reference_dir):
+        material_config = Material.load(reference_dir/'material.yaml')
+        new = material_config.microstructure_rename_homogenization({'Taylor':'isostrain'})
+        assert not new.is_complete

python/tests/test_Orientation.py

@@ -106,8 +106,8 @@ class TestOrientation:
             coords = np.array([(1,i+1) for i,x in enumerate(eu)])
             table = Table(eu,{'Eulers':(3,)})
             table = table.add('pos',coords)
-            table.to_ASCII(reference)
-        assert np.allclose(eu,Table.from_ASCII(reference).get('Eulers'))
+            table.save(reference)
+        assert np.allclose(eu,Table.load(reference).get('Eulers'))
 
     @pytest.mark.parametrize('lattice',Lattice.lattices)
     def test_disorientation360(self,lattice):
@@ -129,4 +129,3 @@ class TestOrientation:
         eqs = [r for r in R_1.equivalent]
         R_2 = Orientation.from_average(eqs)
         assert np.allclose(R_1.rotation.quaternion,R_2.rotation.quaternion)
-

python/tests/test_Result.py

@@ -339,8 +339,8 @@ class TestResult:
     @pytest.mark.parametrize('output',['F',[],['F','P']])
     def test_vtk(self,tmp_path,default,output):
         os.chdir(tmp_path)
-        default.to_vtk(output)
+        default.save_vtk(output)
 
     def test_XDMF(self,tmp_path,single_phase):
         os.chdir(tmp_path)
-        single_phase.write_XDMF()
+        single_phase.save_XDMF()

python/tests/test_Rotation.py

@@ -461,7 +461,7 @@ def mul(me, other):
         if other.shape == (3,):
             A = me.quaternion[0]**2.0 - np.dot(me.quaternion[1:],me.quaternion[1:])
             B = 2.0 * np.dot(me.quaternion[1:],other)
-            C = 2.0 * _P*me.quaternion[0]
+            C = 2.0 * _P *   me.quaternion[0]
 
             return A*other + B*me.quaternion[1:] + C * np.cross(me.quaternion[1:],other)
 
@@ -496,9 +496,8 @@ class TestRotation:
             o = backward(forward(m))
             ok = np.allclose(m,o,atol=atol)
             if np.isclose(rot.as_quaternion()[0],0.0,atol=atol):
-                ok = ok or np.allclose(m*-1.,o,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and np.isclose(np.linalg.norm(o),1.0)
+                ok |= np.allclose(m*-1.,o,atol=atol)
+            assert ok and np.isclose(np.linalg.norm(o),1.0), f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._om2qu,Rotation._qu2om),
                                                  (Rotation._om2eu,Rotation._eu2om),
@@ -512,8 +511,7 @@ class TestRotation:
             m = rot.as_matrix()
             o = backward(forward(m))
             ok = np.allclose(m,o,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and np.isclose(np.linalg.det(o),1.0)
+            assert ok and np.isclose(np.linalg.det(o),1.0), f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._eu2qu,Rotation._qu2eu),
                                                  (Rotation._eu2om,Rotation._om2eu),
@@ -531,9 +529,9 @@ class TestRotation:
             ok = ok or np.allclose(np.where(np.isclose(m,u),m-u,m),np.where(np.isclose(o,u),o-u,o),atol=atol)
             if np.isclose(m[1],0.0,atol=atol) or np.isclose(m[1],np.pi,atol=atol):
                 sum_phi = np.unwrap([m[0]+m[2],o[0]+o[2]])
-                ok = ok or np.isclose(sum_phi[0],sum_phi[1],atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and (np.zeros(3)-1.e-9 <= o).all() and (o <= np.array([np.pi*2.,np.pi,np.pi*2.])+1.e-9).all()
+                ok |= np.isclose(sum_phi[0],sum_phi[1],atol=atol)
+            assert ok and (np.zeros(3)-1.e-9 <= o).all() \
+                      and (o <= np.array([np.pi*2.,np.pi,np.pi*2.])+1.e-9).all(), f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._ax2qu,Rotation._qu2ax),
                                                  (Rotation._ax2om,Rotation._om2ax),
@@ -548,9 +546,8 @@ class TestRotation:
             o = backward(forward(m))
             ok = np.allclose(m,o,atol=atol)
             if np.isclose(m[3],np.pi,atol=atol):
-                ok = ok or np.allclose(m*np.array([-1.,-1.,-1.,1.]),o,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0) and o[3]<=np.pi+1.e-9
+                ok |= np.allclose(m*np.array([-1.,-1.,-1.,1.]),o,atol=atol)
+            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0) and o[3]<=np.pi+1.e-9, f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._ro2qu,Rotation._qu2ro),
                                                  #(Rotation._ro2om,Rotation._om2ro),
@@ -566,8 +563,7 @@ class TestRotation:
             o = backward(forward(m))
             ok = np.allclose(np.clip(m,None,cutoff),np.clip(o,None,cutoff),atol=atol)
             ok = ok or np.isclose(m[3],0.0,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0)
+            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0), f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._ho2qu,Rotation._qu2ho),
                                                  (Rotation._ho2om,Rotation._om2ho),
@@ -581,8 +577,7 @@ class TestRotation:
             m = rot.as_homochoric()
             o = backward(forward(m))
             ok = np.allclose(m,o,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and np.linalg.norm(o) < _R1 + 1.e-9
+            assert ok and np.linalg.norm(o) < _R1 + 1.e-9, f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('forward,backward',[(Rotation._cu2qu,Rotation._qu2cu),
                                                  (Rotation._cu2om,Rotation._om2cu),
@@ -598,8 +593,7 @@ class TestRotation:
             ok = np.allclose(m,o,atol=atol)
             if np.count_nonzero(np.isclose(np.abs(o),np.pi**(2./3.)*.5)):
                 ok = ok or np.allclose(m*-1.,o,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and np.max(np.abs(o)) < np.pi**(2./3.) * 0.5 + 1.e-9
+            assert ok and np.max(np.abs(o)) < np.pi**(2./3.) * 0.5 + 1.e-9, f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._qu2om,qu2om),
                                                    (Rotation._qu2eu,qu2eu),
@@ -612,8 +606,7 @@ class TestRotation:
         vectorized(qu.reshape(qu.shape[0]//2,-1,4))
         co = vectorized(qu)
         for q,c in zip(qu,co):
-            print(q,c)
-            assert np.allclose(single(q),c) and np.allclose(single(q),vectorized(q))
+            assert np.allclose(single(q),c) and np.allclose(single(q),vectorized(q)), f'{q},{c}'
 
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._om2qu,om2qu),
@@ -625,8 +618,7 @@ class TestRotation:
         vectorized(om.reshape(om.shape[0]//2,-1,3,3))
         co = vectorized(om)
         for o,c in zip(om,co):
-            print(o,c)
-            assert np.allclose(single(o),c) and np.allclose(single(o),vectorized(o))
+            assert np.allclose(single(o),c) and np.allclose(single(o),vectorized(o)), f'{o},{c}'
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._eu2qu,eu2qu),
                                                    (Rotation._eu2om,eu2om),
@@ -638,8 +630,7 @@ class TestRotation:
         vectorized(eu.reshape(eu.shape[0]//2,-1,3))
         co = vectorized(eu)
         for e,c in zip(eu,co):
-            print(e,c)
-            assert np.allclose(single(e),c) and np.allclose(single(e),vectorized(e))
+            assert np.allclose(single(e),c) and np.allclose(single(e),vectorized(e)), f'{e},{c}'
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._ax2qu,ax2qu),
                                                    (Rotation._ax2om,ax2om),
@@ -651,8 +642,7 @@ class TestRotation:
         vectorized(ax.reshape(ax.shape[0]//2,-1,4))
         co = vectorized(ax)
         for a,c in zip(ax,co):
-            print(a,c)
-            assert np.allclose(single(a),c) and np.allclose(single(a),vectorized(a))
+            assert np.allclose(single(a),c) and np.allclose(single(a),vectorized(a)), f'{a},{c}'
 
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._ro2ax,ro2ax),
@@ -663,8 +653,7 @@ class TestRotation:
         vectorized(ro.reshape(ro.shape[0]//2,-1,4))
         co = vectorized(ro)
         for r,c in zip(ro,co):
-            print(r,c)
-            assert np.allclose(single(r),c) and np.allclose(single(r),vectorized(r))
+            assert np.allclose(single(r),c) and np.allclose(single(r),vectorized(r)), f'{r},{c}'
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._ho2ax,ho2ax),
                                                    (Rotation._ho2cu,ho2cu)])
@@ -674,8 +663,7 @@ class TestRotation:
         vectorized(ho.reshape(ho.shape[0]//2,-1,3))
         co = vectorized(ho)
         for h,c in zip(ho,co):
-            print(h,c)
-            assert np.allclose(single(h),c) and np.allclose(single(h),vectorized(h))
+            assert np.allclose(single(h),c) and np.allclose(single(h),vectorized(h)), f'{h},{c}'
 
     @pytest.mark.parametrize('vectorized, single',[(Rotation._cu2ho,cu2ho)])
     def test_cubochoric_vectorization(self,set_of_rotations,vectorized,single):
@@ -684,8 +672,7 @@ class TestRotation:
         vectorized(cu.reshape(cu.shape[0]//2,-1,3))
         co = vectorized(cu)
         for u,c in zip(cu,co):
-            print(u,c)
-            assert np.allclose(single(u),c) and np.allclose(single(u),vectorized(u))
+            assert np.allclose(single(u),c) and np.allclose(single(u),vectorized(u)), f'{u},{c}'
 
     @pytest.mark.parametrize('func',[Rotation.from_axis_angle])
     def test_normalization_vectorization(self,func):
@@ -703,9 +690,8 @@ class TestRotation:
             o = Rotation.from_Eulers(rot.as_Eulers(degrees),degrees).as_quaternion()
             ok = np.allclose(m,o,atol=atol)
             if np.isclose(rot.as_quaternion()[0],0.0,atol=atol):
-                ok = ok or np.allclose(m*-1.,o,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and np.isclose(np.linalg.norm(o),1.0)
+                ok |= np.allclose(m*-1.,o,atol=atol)
+            assert ok and np.isclose(np.linalg.norm(o),1.0), f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('P',[1,-1])
     @pytest.mark.parametrize('normalize',[True,False])
@@ -717,12 +703,12 @@ class TestRotation:
             o = Rotation.from_axis_angle(rot.as_axis_angle(degrees)*c,degrees,normalize,P).as_Eulers()
             u = np.array([np.pi*2,np.pi,np.pi*2])
             ok = np.allclose(m,o,atol=atol)
-            ok = ok or np.allclose(np.where(np.isclose(m,u),m-u,m),np.where(np.isclose(o,u),o-u,o),atol=atol)
+            ok |= np.allclose(np.where(np.isclose(m,u),m-u,m),np.where(np.isclose(o,u),o-u,o),atol=atol)
             if np.isclose(m[1],0.0,atol=atol) or np.isclose(m[1],np.pi,atol=atol):
                 sum_phi = np.unwrap([m[0]+m[2],o[0]+o[2]])
-                ok = ok or np.isclose(sum_phi[0],sum_phi[1],atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and (np.zeros(3)-1.e-9 <= o).all() and (o <= np.array([np.pi*2.,np.pi,np.pi*2.])+1.e-9).all()
+                ok |= np.isclose(sum_phi[0],sum_phi[1],atol=atol)
+            assert ok and (np.zeros(3)-1.e-9 <= o).all() \
+                      and (o <= np.array([np.pi*2.,np.pi,np.pi*2.])+1.e-9).all(), f'{m},{o},{rot.as_quaternion()}'
 
     def test_matrix(self,set_of_rotations):
         for rot in set_of_rotations:
@@ -731,8 +717,8 @@ class TestRotation:
             ok = np.allclose(m,o,atol=atol)
             if np.isclose(m[3],np.pi,atol=atol):
                 ok = ok or np.allclose(m*np.array([-1.,-1.,-1.,1.]),o,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0) and o[3]<=np.pi+1.e-9
+            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0) \
+                      and o[3]<=np.pi+1.e-9, f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('P',[1,-1])
     @pytest.mark.parametrize('normalize',[True,False])
@@ -742,8 +728,7 @@ class TestRotation:
             m = rot.as_matrix()
             o = Rotation.from_Rodrigues(rot.as_Rodrigues()*c,normalize,P).as_matrix()
             ok = np.allclose(m,o,atol=atol)
-            print(m,o)
-            assert ok and np.isclose(np.linalg.det(o),1.0)
+            assert ok and np.isclose(np.linalg.det(o),1.0), f'{m},{o}'
 
     @pytest.mark.parametrize('P',[1,-1])
     def test_homochoric(self,set_of_rotations,P):
@@ -753,8 +738,7 @@ class TestRotation:
             o = Rotation.from_homochoric(rot.as_homochoric()*P*-1,P).as_Rodrigues()
             ok = np.allclose(np.clip(m,None,cutoff),np.clip(o,None,cutoff),atol=atol)
             ok = ok or np.isclose(m[3],0.0,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0)
+            assert ok and np.isclose(np.linalg.norm(o[:3]),1.0), f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('P',[1,-1])
     def test_cubochoric(self,set_of_rotations,P):
@@ -762,8 +746,7 @@ class TestRotation:
             m = rot.as_homochoric()
             o = Rotation.from_cubochoric(rot.as_cubochoric()*P*-1,P).as_homochoric()
             ok = np.allclose(m,o,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and np.linalg.norm(o) < (3.*np.pi/4.)**(1./3.) + 1.e-9
+            assert ok and np.linalg.norm(o) < (3.*np.pi/4.)**(1./3.) + 1.e-9, f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('P',[1,-1])
     @pytest.mark.parametrize('accept_homomorph',[True,False])
@@ -774,9 +757,8 @@ class TestRotation:
             o = Rotation.from_quaternion(rot.as_quaternion()*c,accept_homomorph,P).as_cubochoric()
             ok = np.allclose(m,o,atol=atol)
             if np.count_nonzero(np.isclose(np.abs(o),np.pi**(2./3.)*.5)):
-                ok = ok or np.allclose(m*-1.,o,atol=atol)
-            print(m,o,rot.as_quaternion())
-            assert ok and o.max() < np.pi**(2./3.)*0.5+1.e-9
+                ok |= np.allclose(m*-1.,o,atol=atol)
+            assert ok and o.max() < np.pi**(2./3.)*0.5+1.e-9, f'{m},{o},{rot.as_quaternion()}'
 
     @pytest.mark.parametrize('reciprocal',[True,False])
     def test_basis(self,set_of_rotations,reciprocal):
@@ -858,8 +840,7 @@ class TestRotation:
         for rot in set_of_rotations:
             v = rot.broadcast_to((5,)) @ data
             for i in range(data.shape[0]):
-                print(i-data[i])
-                assert np.allclose(mul(rot,data[i]),v[i])
+                assert np.allclose(mul(rot,data[i]),v[i]), f'{i-data[i]}'
 
 
     @pytest.mark.parametrize('data',[np.random.rand(3),
@@ -926,34 +907,39 @@ class TestRotation:
     @pytest.mark.parametrize('sigma',[5,10,15,20])
     @pytest.mark.parametrize('N',[1000,10000,100000])
     def test_spherical_component(self,N,sigma):
-        c = Rotation.from_random()
-        o = Rotation.from_spherical_component(c,sigma,N)
-        _, angles = c.misorientation(o).as_axis_angle(pair=True,degrees=True)
-        angles[::2] *= -1                                                                           # flip angle for every second to symmetrize distribution
+        p = []
+        for run in range(5):
+            c = Rotation.from_random()
+            o = Rotation.from_spherical_component(c,sigma,N)
+            _, angles = c.misorientation(o).as_axis_angle(pair=True,degrees=True)
+            angles[::2] *= -1                                                                       # flip angle for every second to symmetrize distribution
+
+            p.append(stats.normaltest(angles)[1])
 
-        p = stats.normaltest(angles)[1]
         sigma_out = np.std(angles)
-        print(f'\np: {p}, sigma ratio {sigma/sigma_out}')
-        assert (.9 < sigma/sigma_out < 1.1) and p > 0.001
+        p = np.average(p)
+        assert (.9 < sigma/sigma_out < 1.1) and p > 1e-2, f'{sigma/sigma_out},{p}'
 
 
     @pytest.mark.parametrize('sigma',[5,10,15,20])
     @pytest.mark.parametrize('N',[1000,10000,100000])
     def test_from_fiber_component(self,N,sigma):
-        """https://en.wikipedia.org/wiki/Full_width_at_half_maximum."""
-        alpha = np.random.random(2)*np.pi
-        beta  = np.random.random(2)*np.pi
+        p = []
+        for run in range(5):
+             alpha = np.random.random()*2*np.pi,np.arccos(np.random.random())
+             beta  = np.random.random()*2*np.pi,np.arccos(np.random.random())
 
-        f_in_C = np.array([np.sin(alpha[0])*np.cos(alpha[1]), np.sin(alpha[0])*np.sin(alpha[1]), np.cos(alpha[0])])
-        f_in_S = np.array([np.sin(beta[0] )*np.cos(beta[1] ), np.sin(beta[0] )*np.sin(beta[1] ), np.cos(beta[0] )])
-        ax = np.append(np.cross(f_in_C,f_in_S), - np.arccos(np.dot(f_in_C,f_in_S)))
-        n = Rotation.from_axis_angle(ax if ax[3] > 0.0 else ax*-1.0 ,normalize=True)                # rotation to align fiber axis in crystal and sample system
+             f_in_C = np.array([np.sin(alpha[0])*np.cos(alpha[1]), np.sin(alpha[0])*np.sin(alpha[1]), np.cos(alpha[0])])
+             f_in_S = np.array([np.sin(beta[0] )*np.cos(beta[1] ), np.sin(beta[0] )*np.sin(beta[1] ), np.cos(beta[0] )])
+             ax = np.append(np.cross(f_in_C,f_in_S), - np.arccos(np.dot(f_in_C,f_in_S)))
+             n = Rotation.from_axis_angle(ax if ax[3] > 0.0 else ax*-1.0 ,normalize=True)           # rotation to align fiber axis in crystal and sample system
 
-        o = Rotation.from_fiber_component(alpha,beta,np.radians(sigma),N,False)
-        angles = np.arccos(np.clip(np.dot(o@np.broadcast_to(f_in_S,(N,3)),n@f_in_S),-1,1))
-        dist   = np.array(angles) * (np.random.randint(0,2,N)*2-1)
+             o = Rotation.from_fiber_component(alpha,beta,np.radians(sigma),N,False)
+             angles = np.arccos(np.clip(np.dot(o@np.broadcast_to(f_in_S,(N,3)),n@f_in_S),-1,1))
+             dist   = np.array(angles) * (np.random.randint(0,2,N)*2-1)
+
+             p.append(stats.normaltest(dist)[1])
 
-        p = stats.normaltest(dist)[1]
         sigma_out = np.degrees(np.std(dist))
-        print(f'\np: {p}, sigma ratio {sigma/sigma_out}')
-        assert (.9 < sigma/sigma_out < 1.1) and p > 0.001
+        p = np.average(p)
+        assert (.9 < sigma/sigma_out < 1.1) and p > 1e-2, f'{sigma/sigma_out},{p}'

python/tests/test_Table.py

@@ -35,50 +35,50 @@ class TestTable:
 
     @pytest.mark.parametrize('mode',['str','path'])
     def test_write_read(self,default,tmpdir,mode):
-        default.to_file(tmpdir/'default.txt')
+        default.save(tmpdir/'default.txt')
         if   mode == 'path':
-            new = Table.from_ASCII(tmpdir/'default.txt')
+            new = Table.load(tmpdir/'default.txt')
         elif mode == 'str':
-            new = Table.from_ASCII(str(tmpdir/'default.txt'))
+            new = Table.load(str(tmpdir/'default.txt'))
         assert all(default.data==new.data) and default.shapes == new.shapes
 
     def test_write_read_file(self,default,tmpdir):
         with open(tmpdir/'default.txt','w') as f:
-            default.to_file(f)
+            default.save(f)
         with open(tmpdir/'default.txt') as f:
-            new = Table.from_ASCII(f)
+            new = Table.load(f)
         assert all(default.data==new.data) and default.shapes == new.shapes
 
-    def test_write_read_new_style(self,default,tmpdir):
-        with open(tmpdir/'new_style.txt','w') as f:
-            default.to_file(f,new_style=True)
-        with open(tmpdir/'new_style.txt') as f:
-            new = Table.from_ASCII(f)
+    def test_write_read_legacy_style(self,default,tmpdir):
+        with open(tmpdir/'legacy.txt','w') as f:
+            default.save(f,legacy=True)
+        with open(tmpdir/'legacy.txt') as f:
+            new = Table.load(f)
         assert all(default.data==new.data) and default.shapes == new.shapes
 
     def test_write_invalid_format(self,default,tmpdir):
         with pytest.raises(TypeError):
-            default.to_file(tmpdir/'shouldnotbethere.txt',format='invalid')
+            default.save(tmpdir/'shouldnotbethere.txt',format='invalid')
 
     @pytest.mark.parametrize('mode',['str','path'])
     def test_read_ang(self,reference_dir,mode):
         if   mode == 'path':
-            new = Table.from_ang(reference_dir/'simple.ang')
+            new = Table.load_ang(reference_dir/'simple.ang')
         elif mode == 'str':
-            new = Table.from_ang(str(reference_dir/'simple.ang'))
+            new = Table.load_ang(str(reference_dir/'simple.ang'))
         assert new.data.shape == (4,10) and \
                new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
 
     def test_read_ang_file(self,reference_dir):
         f = open(reference_dir/'simple.ang')
-        new = Table.from_ang(f)
+        new = Table.load_ang(f)
         assert new.data.shape == (4,10) and \
                new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
 
     @pytest.mark.parametrize('fname',['datatype-mix.txt','whitespace-mix.txt'])
     def test_read_strange(self,reference_dir,fname):
         with open(reference_dir/fname) as f:
-            Table.from_ASCII(f)
+            Table.load(f)
 
     def test_set(self,default):
         d = default.set('F',np.zeros((5,3,3)),'set to zero').get('F')
@@ -166,7 +166,7 @@ class TestTable:
         x = np.random.random((5,12))
         t = Table(x,{'F':(3,3),'v':(3,)},['random test data'])
         unsort = t.get('4_F')
-        sort = t.sort_by('4_F').get('4_F')
+        sort   = t.sort_by('4_F').get('4_F')
         assert np.all(np.sort(unsort,0)==sort)
 
     def test_sort_revert(self):
@@ -179,6 +179,6 @@ class TestTable:
         t = Table(np.array([[0,1,],[2,1,]]),
                   {'v':(2,)},
                   ['test data'])\
-                  .add('s',np.array(['b','a']))\
-                  .sort_by('s')
+            .add('s',np.array(['b','a']))\
+            .sort_by('s')
         assert np.all(t.get('1_v') == np.array([2,0]).reshape(2,1))

python/tests/test_VTK.py

@@ -32,22 +32,22 @@ class TestVTK:
         origin = np.random.random(3)
         v = VTK.from_rectilinearGrid(grid,size,origin)
         string = v.__repr__()
-        v.to_file(tmp_path/'rectilinearGrid',False)
-        vtr = VTK.from_file(tmp_path/'rectilinearGrid.vtr')
+        v.save(tmp_path/'rectilinearGrid',False)
+        vtr = VTK.load(tmp_path/'rectilinearGrid.vtr')
         with open(tmp_path/'rectilinearGrid.vtk','w') as f:
             f.write(string)
-        vtk = VTK.from_file(tmp_path/'rectilinearGrid.vtk','VTK_rectilinearGrid')
+        vtk = VTK.load(tmp_path/'rectilinearGrid.vtk','VTK_rectilinearGrid')
         assert(string == vtr.__repr__() == vtk.__repr__())
 
     def test_polyData(self,tmp_path):
         points = np.random.rand(100,3)
         v = VTK.from_polyData(points)
         string = v.__repr__()
-        v.to_file(tmp_path/'polyData',False)
-        vtp = VTK.from_file(tmp_path/'polyData.vtp')
+        v.save(tmp_path/'polyData',False)
+        vtp = VTK.load(tmp_path/'polyData.vtp')
         with open(tmp_path/'polyData.vtk','w') as f:
             f.write(string)
-        vtk = VTK.from_file(tmp_path/'polyData.vtk','polyData')
+        vtk = VTK.load(tmp_path/'polyData.vtk','polyData')
         assert(string == vtp.__repr__() == vtk.__repr__())
 
     @pytest.mark.parametrize('cell_type,n',[
@@ -62,11 +62,11 @@ class TestVTK:
         connectivity = np.random.choice(np.arange(n),n,False).reshape(-1,n)
         v = VTK.from_unstructuredGrid(nodes,connectivity,cell_type)
         string = v.__repr__()
-        v.to_file(tmp_path/'unstructuredGrid',False)
-        vtu = VTK.from_file(tmp_path/'unstructuredGrid.vtu')
+        v.save(tmp_path/'unstructuredGrid',False)
+        vtu = VTK.load(tmp_path/'unstructuredGrid.vtu')
         with open(tmp_path/'unstructuredGrid.vtk','w') as f:
             f.write(string)
-        vtk = VTK.from_file(tmp_path/'unstructuredGrid.vtk','unstructuredgrid')
+        vtk = VTK.load(tmp_path/'unstructuredGrid.vtk','unstructuredgrid')
         assert(string == vtu.__repr__() == vtk.__repr__())
 
 
@@ -75,8 +75,8 @@ class TestVTK:
         v = VTK.from_polyData(points)
         fname_s = tmp_path/'single.vtp'
         fname_p = tmp_path/'parallel.vtp'
-        v.to_file(fname_s,False)
-        v.to_file(fname_p,True)
+        v.save(fname_s,False)
+        v.save(fname_p,True)
         for i in range(10):
             if os.path.isfile(fname_p) and filecmp.cmp(fname_s,fname_p):
                 assert(True)
@@ -90,11 +90,11 @@ class TestVTK:
                                                   ('this_file_does_not_exist.vtx', None)])
     def test_invalid_dataset_type(self,name,dataset_type):
         with pytest.raises(TypeError):
-            VTK.from_file(name,dataset_type)
+            VTK.load(name,dataset_type)
 
     def test_invalid_extension_write(self,default):
         with pytest.raises(ValueError):
-            default.to_file('default.txt')
+            default.save('default.txt')
 
     def test_invalid_get(self,default):
         with pytest.raises(ValueError):
@@ -115,8 +115,8 @@ class TestVTK:
 
     def test_comments(self,tmp_path,default):
         default.add_comments(['this is a comment'])
-        default.to_file(tmp_path/'with_comments',parallel=False)
-        new = VTK.from_file(tmp_path/'with_comments.vtr')
+        default.save(tmp_path/'with_comments',parallel=False)
+        new = VTK.load(tmp_path/'with_comments.vtr')
         assert new.get_comments() == ['this is a comment']
 
     def test_compare_reference_polyData(self,update,reference_dir,tmp_path):
@@ -124,9 +124,9 @@ class TestVTK:
         polyData = VTK.from_polyData(points)
         polyData.add(points,'coordinates')
         if update:
-             polyData.to_file(reference_dir/'polyData')
+             polyData.save(reference_dir/'polyData')
         else:
-             reference = VTK.from_file(reference_dir/'polyData.vtp')
+             reference = VTK.load(reference_dir/'polyData.vtp')
              assert polyData.__repr__() == reference.__repr__() and \
                     np.allclose(polyData.get('coordinates'),points)
 
@@ -139,8 +139,8 @@ class TestVTK:
         rectilinearGrid.add(c,'cell')
         rectilinearGrid.add(n,'node')
         if update:
-             rectilinearGrid.to_file(reference_dir/'rectilinearGrid')
+             rectilinearGrid.save(reference_dir/'rectilinearGrid')
         else:
-             reference = VTK.from_file(reference_dir/'rectilinearGrid.vtr')
+             reference = VTK.load(reference_dir/'rectilinearGrid.vtr')
              assert rectilinearGrid.__repr__() == reference.__repr__() and \
                     np.allclose(rectilinearGrid.get('cell'),c)

python/tests/test_util.py

@@ -18,8 +18,8 @@ class TestUtil:
 
     @pytest.mark.parametrize('input,output',
                             [
-                            ([2,0],[1,0]),
-                            ([0.5,0.5],[1,1]),
+                            ([0,-2],[0,-1]),
+                            ([-0.5,0.5],[-1,1]),
                             ([1./2.,1./3.],[3,2]),
                             ([2./3.,1./2.,1./3.],[4,3,2]),
                             ])
@@ -30,4 +30,4 @@ class TestUtil:
 
     def test_lackofprecision(self):
         with pytest.raises(ValueError):
-            util.scale_to_coprime(np.array([1/3333,1,1]))
+            util.scale_to_coprime(np.array([1/333.333,1,1]))

src/CPFEM.f90

@@ -106,7 +106,7 @@ subroutine CPFEM_init
     num_commercialFEM, &
     debug_CPFEM
 
-  print'(/,a)', ' <<<+-  CPFEM init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  CPFEM init  -+>>>'; flush(IO_STDOUT)
 
   allocate(CPFEM_cs(               6,discretization_nIP,discretization_nElem), source= 0.0_pReal)
   allocate(CPFEM_dcsdE(          6,6,discretization_nIP,discretization_nElem), source= 0.0_pReal)
@@ -132,7 +132,7 @@ subroutine CPFEM_init
     print'(a32,1x,6(i8,1x))',   'CPFEM_cs:              ', shape(CPFEM_cs)
     print'(a32,1x,6(i8,1x))',   'CPFEM_dcsdE:           ', shape(CPFEM_dcsdE)
     print'(a32,1x,6(i8,1x),/)', 'CPFEM_dcsdE_knownGood: ', shape(CPFEM_dcsdE_knownGood)
-    flush(6)
+    flush(IO_STDOUT)
   endif
 
 end subroutine CPFEM_init
@@ -250,7 +250,7 @@ subroutine CPFEM_general(mode, ffn, ffn1, temperature_inp, dt, elFE, ip, cauchyS
           '<< CPFEM >> stress/MPa at elFE ip ',   elFE, ip, CPFEM_cs(1:6,ip,elCP)*1.0e-6_pReal
         print'(a,i8,1x,i2,/,6(12x,6(f10.3,1x)/))', &
           '<< CPFEM >> Jacobian/GPa at elFE ip ', elFE, ip, transpose(CPFEM_dcsdE(1:6,1:6,ip,elCP))*1.0e-9_pReal
-        flush(6)
+        flush(IO_STDOUT)
     endif
 
   endif

src/CPFEM2.f90

@@ -76,7 +76,7 @@ end subroutine CPFEM_initAll
 !--------------------------------------------------------------------------------------------------
 subroutine CPFEM_init
 
-  print'(/,a)', ' <<<+-  CPFEM init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  CPFEM init  -+>>>'; flush(IO_STDOUT)
 
   if (interface_restartInc > 0) call crystallite_restartRead
 

src/IO.f90

@@ -7,8 +7,8 @@
 !--------------------------------------------------------------------------------------------------
 module IO
   use, intrinsic :: ISO_fortran_env, only: &
-    OUTPUT_UNIT, &
-    ERROR_UNIT
+    IO_STDOUT => OUTPUT_UNIT, &
+    IO_STDERR => ERROR_UNIT
 
   use prec
 
@@ -20,7 +20,7 @@ module IO
   character, parameter, public :: &
     IO_EOL = new_line('DAMASK'), &                                                                  !< end of line character
     IO_COMMENT = '#'
-  character(len=*), parameter, private :: &
+  character(len=*), parameter :: &
     IO_DIVIDER = '───────────────────'//&
                  '───────────────────'//&
                  '───────────────────'//&
@@ -42,7 +42,7 @@ module IO
     IO_stringAsBool, &
     IO_error, &
     IO_warning, &
-    OUTPUT_UNIT
+    IO_STDOUT
 
 contains
 
@@ -52,7 +52,7 @@ contains
 !--------------------------------------------------------------------------------------------------
 subroutine IO_init
 
-  print'(/,a)', ' <<<+-  IO init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  IO init  -+>>>'; flush(IO_STDOUT)
 
   call selfTest
 
@@ -543,29 +543,29 @@ subroutine IO_error(error_ID,el,ip,g,instance,ext_msg)
   end select
 
   !$OMP CRITICAL (write2out)
-  write(ERROR_UNIT,'(/,a)')                ' ┌'//IO_DIVIDER//'┐'
-  write(ERROR_UNIT,'(a,24x,a,40x,a)')      ' │','error',                                             '│'
-  write(ERROR_UNIT,'(a,24x,i3,42x,a)')     ' │',error_ID,                                            '│'
-  write(ERROR_UNIT,'(a)')                  ' ├'//IO_DIVIDER//'┤'
+  write(IO_STDERR,'(/,a)')                ' ┌'//IO_DIVIDER//'┐'
+  write(IO_STDERR,'(a,24x,a,40x,a)')      ' │','error',                                             '│'
+  write(IO_STDERR,'(a,24x,i3,42x,a)')     ' │',error_ID,                                            '│'
+  write(IO_STDERR,'(a)')                  ' ├'//IO_DIVIDER//'┤'
   write(formatString,'(a,i6.6,a,i6.6,a)') '(1x,a4,a',max(1,len_trim(msg)),',',&
                                                      max(1,72-len_trim(msg)-4),'x,a)'
-  write(ERROR_UNIT,formatString)            '│ ',trim(msg),                                          '│'
+  write(IO_STDERR,formatString)            '│ ',trim(msg),                                          '│'
   if (present(ext_msg)) then
     write(formatString,'(a,i6.6,a,i6.6,a)') '(1x,a4,a',max(1,len_trim(ext_msg)),',',&
                                                        max(1,72-len_trim(ext_msg)-4),'x,a)'
-    write(ERROR_UNIT,formatString)          '│ ',trim(ext_msg),                                      '│'
+    write(IO_STDERR,formatString)          '│ ',trim(ext_msg),                                      '│'
   endif
   if (present(el)) &
-    write(ERROR_UNIT,'(a19,1x,i9,44x,a3)') ' │ at element    ',el,                                   '│'
+    write(IO_STDERR,'(a19,1x,i9,44x,a3)') ' │ at element    ',el,                                   '│'
   if (present(ip)) &
-    write(ERROR_UNIT,'(a19,1x,i9,44x,a3)') ' │ at IP         ',ip,                                   '│'
+    write(IO_STDERR,'(a19,1x,i9,44x,a3)') ' │ at IP         ',ip,                                   '│'
   if (present(g)) &
-    write(ERROR_UNIT,'(a19,1x,i9,44x,a3)') ' │ at constituent',g,                                    '│'
+    write(IO_STDERR,'(a19,1x,i9,44x,a3)') ' │ at constituent',g,                                    '│'
   if (present(instance)) &
-    write(ERROR_UNIT,'(a19,1x,i9,44x,a3)') ' │ at instance   ',instance,                             '│'
-  write(ERROR_UNIT,'(a,69x,a)')            ' │',                                                     '│'
-  write(ERROR_UNIT,'(a)')                  ' └'//IO_DIVIDER//'┘'
-  flush(ERROR_UNIT)
+    write(IO_STDERR,'(a19,1x,i9,44x,a3)') ' │ at instance   ',instance,                             '│'
+  write(IO_STDERR,'(a,69x,a)')            ' │',                                                     '│'
+  write(IO_STDERR,'(a)')                  ' └'//IO_DIVIDER//'┘'
+  flush(IO_STDERR)
   call quit(9000+error_ID)
   !$OMP END CRITICAL (write2out)
 
@@ -628,27 +628,27 @@ subroutine IO_warning(warning_ID,el,ip,g,ext_msg)
     end select
 
   !$OMP CRITICAL (write2out)
-  write(ERROR_UNIT,'(/,a)')                ' ┌'//IO_DIVIDER//'┐'
-  write(ERROR_UNIT,'(a,24x,a,38x,a)')      ' │','warning',                                           '│'
-  write(ERROR_UNIT,'(a,24x,i3,42x,a)')     ' │',warning_ID,                                          '│'
-  write(ERROR_UNIT,'(a)')                  ' ├'//IO_DIVIDER//'┤'
+  write(IO_STDERR,'(/,a)')                ' ┌'//IO_DIVIDER//'┐'
+  write(IO_STDERR,'(a,24x,a,38x,a)')      ' │','warning',                                           '│'
+  write(IO_STDERR,'(a,24x,i3,42x,a)')     ' │',warning_ID,                                          '│'
+  write(IO_STDERR,'(a)')                  ' ├'//IO_DIVIDER//'┤'
   write(formatString,'(a,i6.6,a,i6.6,a)') '(1x,a4,a',max(1,len_trim(msg)),',',&
                                                      max(1,72-len_trim(msg)-4),'x,a)'
-  write(ERROR_UNIT,formatString)            '│ ',trim(msg),                                          '│'
+  write(IO_STDERR,formatString)            '│ ',trim(msg),                                          '│'
   if (present(ext_msg)) then
     write(formatString,'(a,i6.6,a,i6.6,a)') '(1x,a4,a',max(1,len_trim(ext_msg)),',',&
                                                        max(1,72-len_trim(ext_msg)-4),'x,a)'
-    write(ERROR_UNIT,formatString)          '│ ',trim(ext_msg),                                      '│'
+    write(IO_STDERR,formatString)          '│ ',trim(ext_msg),                                      '│'
   endif
   if (present(el)) &
-    write(ERROR_UNIT,'(a19,1x,i9,44x,a3)') ' │ at element    ',el,                                   '│'
+    write(IO_STDERR,'(a19,1x,i9,44x,a3)') ' │ at element    ',el,                                   '│'
   if (present(ip)) &
-    write(ERROR_UNIT,'(a19,1x,i9,44x,a3)') ' │ at IP         ',ip,                                   '│'
+    write(IO_STDERR,'(a19,1x,i9,44x,a3)') ' │ at IP         ',ip,                                   '│'
   if (present(g)) &
-    write(ERROR_UNIT,'(a19,1x,i9,44x,a3)') ' │ at constituent',g,                                    '│'
-  write(ERROR_UNIT,'(a,69x,a)')            ' │',                                                     '│'
-  write(ERROR_UNIT,'(a)')                  ' └'//IO_DIVIDER//'┘'
-  flush(ERROR_UNIT)
+    write(IO_STDERR,'(a19,1x,i9,44x,a3)') ' │ at constituent',g,                                    '│'
+  write(IO_STDERR,'(a,69x,a)')            ' │',                                                     '│'
+  write(IO_STDERR,'(a)')                  ' └'//IO_DIVIDER//'┘'
+  flush(IO_STDERR)
   !$OMP END CRITICAL (write2out)
 
 end subroutine IO_warning

src/base64.f90

@@ -27,7 +27,7 @@ contains
 !--------------------------------------------------------------------------------------------------
 subroutine base64_init
 
-  print'(/,a)', ' <<<+-  base64 init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  base64 init  -+>>>'; flush(IO_STDOUT)
 
   call selfTest
 

src/config.f90

@@ -35,7 +35,7 @@ contains
 !--------------------------------------------------------------------------------------------------
 subroutine config_init
 
-  print'(/,a)', ' <<<+-  config init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  config init  -+>>>'; flush(IO_STDOUT)
 
   call parse_material
   call parse_numerics
@@ -59,7 +59,7 @@ subroutine parse_material
     inquire(file=fname,exist=fileExists)
     if(.not. fileExists) call IO_error(100,ext_msg=fname)
   endif
-  print*, 'reading '//fname; flush(6)
+  print*, 'reading '//fname; flush(IO_STDOUT)
   config_material => YAML_parse_file(fname)
 
 end subroutine parse_material
@@ -75,7 +75,7 @@ subroutine parse_numerics
   config_numerics => emptyDict
   inquire(file='numerics.yaml', exist=fexist)
   if (fexist) then
-    print*, 'reading numerics.yaml'; flush(6)
+    print*, 'reading numerics.yaml'; flush(IO_STDOUT)
     config_numerics => YAML_parse_file('numerics.yaml')
   endif
 
@@ -92,7 +92,7 @@ subroutine parse_debug
   config_debug => emptyDict
   inquire(file='debug.yaml', exist=fexist)
   fileExists: if (fexist) then
-    print*, 'reading debug.yaml'; flush(6)
+    print*, 'reading debug.yaml'; flush(IO_STDOUT)
     config_debug => YAML_parse_file('debug.yaml')
   endif fileExists
 

src/constitutive.f90

@@ -446,7 +446,7 @@ subroutine constitutive_init
   call damage_init
   call thermal_init
 
-  print'(/,a)', ' <<<+-  constitutive init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  constitutive init  -+>>>'; flush(IO_STDOUT)
 
   constitutive_source_maxSizeDotState = 0
   PhaseLoop2:do p = 1,phases%length

src/constitutive_plastic_disloTungsten.f90

@@ -100,7 +100,7 @@ module function plastic_disloTungsten_init() result(myPlasticity)
 
   myPlasticity = plastic_active('disloTungsten')
   Ninstance = count(myPlasticity)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
   if(Ninstance == 0) return
   
   print*, 'Cereceda et al., International Journal of Plasticity 78:242–256, 2016'

src/constitutive_plastic_dislotwin.f90

@@ -147,7 +147,7 @@ module function plastic_dislotwin_init() result(myPlasticity)
 
   myPlasticity = plastic_active('dislotwin')
   Ninstance = count(myPlasticity)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
   if(Ninstance == 0) return
   
   print*, 'Ma and Roters, Acta Materialia 52(12):3603–3612, 2004'

src/constitutive_plastic_isotropic.f90

@@ -71,7 +71,7 @@ module function plastic_isotropic_init() result(myPlasticity)
 
   myPlasticity = plastic_active('isotropic')
   Ninstance = count(myPlasticity)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
   if(Ninstance == 0) return
 
   print*, 'Maiti and Eisenlohr, Scripta Materialia 145:37–40, 2018'

src/constitutive_plastic_kinehardening.f90

@@ -83,7 +83,7 @@ module function plastic_kinehardening_init() result(myPlasticity)
 
   myPlasticity = plastic_active('kinehardening')
   Ninstance = count(myPlasticity)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
   if(Ninstance == 0) return
 
   allocate(param(Ninstance))

src/constitutive_plastic_none.f90

@@ -35,7 +35,7 @@ module function plastic_none_init() result(myPlasticity)
   enddo
 
   Ninstance = count(myPlasticity)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
   if(Ninstance == 0) return
 
   do p = 1, phases%length

src/constitutive_plastic_nonlocal.f90

@@ -189,7 +189,7 @@ module function plastic_nonlocal_init() result(myPlasticity)
 
   myPlasticity = plastic_active('nonlocal')
   Ninstance = count(myPlasticity)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
   if(Ninstance == 0) then
     call geometry_plastic_nonlocal_disable
     return

src/constitutive_plastic_phenopowerlaw.f90

@@ -92,7 +92,7 @@ module function plastic_phenopowerlaw_init() result(myPlasticity)
 
   myPlasticity = plastic_active('phenopowerlaw')
   Ninstance = count(myPlasticity)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
   if(Ninstance == 0) return
 
   allocate(param(Ninstance))

src/crystallite.f90

@@ -294,7 +294,7 @@ subroutine crystallite_init
     print'(a42,1x,i10)', '    # of elements:                       ', eMax
     print'(a42,1x,i10)', '    # of integration points/element:     ', iMax
     print'(a42,1x,i10)', 'max # of constituents/integration point: ', cMax
-    flush(6)
+    flush(IO_STDOUT)
   endif
 
 #endif
@@ -1561,7 +1561,7 @@ subroutine crystallite_restartWrite
   integer(HID_T) :: fileHandle, groupHandle
   character(len=pStringLen) :: fileName, datasetName
 
-  print*, ' writing field and constitutive data required for restart to file';flush(6)
+  print*, ' writing field and constitutive data required for restart to file';flush(IO_STDOUT)
 
   write(fileName,'(a,i0,a)') trim(getSolverJobName())//'_',worldrank,'.hdf5'
   fileHandle = HDF5_openFile(fileName,'a')

src/damage_local.f90

@@ -49,7 +49,7 @@ subroutine damage_local_init
     homog, &
     homogDamage
 
-  print'(/,a)', ' <<<+-  damage_local init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  damage_local init  -+>>>'; flush(IO_STDOUT)
 
 !----------------------------------------------------------------------------------------------
 ! read numerics parameter and do sanity check

src/element.f90

@@ -922,7 +922,7 @@ subroutine tElement_init(self,elemType)
 
   self%nIPneighbors = size(self%IPneighbor,1)
 
-  print'(/,a)', ' <<<+-  element_init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  element_init  -+>>>'; flush(IO_STDOUT)
 
   print*, 'element type:      ',self%elemType
   print*, '  geom type:       ',self%geomType

src/grid/DAMASK_grid.f90

@@ -24,7 +24,7 @@ program DAMASK_grid
   use grid_damage_spectral
   use grid_thermal_spectral
   use results
-
+  
   implicit none
 
 !--------------------------------------------------------------------------------------------------
@@ -88,7 +88,7 @@ program DAMASK_grid
     mech_updateCoords
   procedure(grid_mech_spectral_basic_restartWrite), pointer :: &
     mech_restartWrite
-
+  
   external :: &
     quit
   class (tNode), pointer :: &
@@ -97,18 +97,18 @@ program DAMASK_grid
 
 !--------------------------------------------------------------------------------------------------
 ! init DAMASK (all modules)
-
-  call CPFEM_initAll
-  print'(/,a)',   ' <<<+-  DAMASK_spectral init  -+>>>'; flush(6)
-
+ 
+  call CPFEM_initAll 
+  print'(/,a)',   ' <<<+-  DAMASK_spectral init  -+>>>'; flush(IO_STDOUT)
+  
   print*, 'Shanthraj et al., Handbook of Mechanics of Materials, 2019'
   print*, 'https://doi.org/10.1007/978-981-10-6855-3_80'
 
 !--------------------------------------------------------------------------------------------------
 ! initialize field solver information
   nActiveFields = 1
-  if(any(thermal_type == THERMAL_conduction_ID)) nActiveFields = nActiveFields + 1
-  if(any(damage_type  == DAMAGE_nonlocal_ID   )) nActiveFields = nActiveFields + 1
+  if (any(thermal_type  == THERMAL_conduction_ID  )) nActiveFields = nActiveFields + 1
+  if (any(damage_type   == DAMAGE_nonlocal_ID     )) nActiveFields = nActiveFields + 1
   allocate(solres(nActiveFields))
   allocate(newLoadCase%ID(nActiveFields))
 
@@ -123,16 +123,16 @@ program DAMASK_grid
 
 !--------------------------------------------------------------------------------------------------
 ! assign mechanics solver depending on selected type
-
+ 
   debug_grid => config_debug%get('grid',defaultVal=emptyList)
-  select case (trim(num_grid%get_asString('solver', defaultVal = 'Basic')))
+  select case (trim(num_grid%get_asString('solver', defaultVal = 'Basic'))) 
     case ('Basic')
       mech_init         => grid_mech_spectral_basic_init
       mech_forward      => grid_mech_spectral_basic_forward
       mech_solution     => grid_mech_spectral_basic_solution
       mech_updateCoords => grid_mech_spectral_basic_updateCoords
       mech_restartWrite => grid_mech_spectral_basic_restartWrite
-
+  
     case ('Polarisation')
      if(debug_grid%contains('basic')) &
         call IO_warning(42, ext_msg='debug Divergence')
@@ -141,7 +141,7 @@ program DAMASK_grid
       mech_solution     => grid_mech_spectral_polarisation_solution
       mech_updateCoords => grid_mech_spectral_polarisation_updateCoords
       mech_restartWrite => grid_mech_spectral_polarisation_restartWrite
-
+  
     case ('FEM')
      if(debug_grid%contains('basic')) &
         call IO_warning(42, ext_msg='debug Divergence')
@@ -150,24 +150,24 @@ program DAMASK_grid
       mech_solution     => grid_mech_FEM_solution
       mech_updateCoords => grid_mech_FEM_updateCoords
       mech_restartWrite => grid_mech_FEM_restartWrite
-
+  
     case default
       call IO_error(error_ID = 891, ext_msg = trim(num_grid%get_asString('solver')))
-
+  
   end select
-
+  
 
 !--------------------------------------------------------------------------------------------------
-! reading information from load case file and to sanity checks
+! reading information from load case file and to sanity checks 
   fileContent = IO_readlines(trim(interface_loadFile))
   if(size(fileContent) == 0) call IO_error(307,ext_msg='No load case specified')
-
+  
   allocate (loadCases(0))                                                                           ! array of load cases
   do currentLoadCase = 1, size(fileContent)
     line = fileContent(currentLoadCase)
     if (IO_isBlank(line)) cycle
     chunkPos = IO_stringPos(line)
-
+  
     do i = 1, chunkPos(1)                                                                           ! reading compulsory parameters for loadcase
       select case (IO_lc(IO_stringValue(line,chunkPos,i)))
         case('l','fdot','dotf','f')
@@ -180,7 +180,7 @@ program DAMASK_grid
     enddo
     if ((N_def /= N_n) .or. (N_n /= N_t) .or. N_n < 1) &                                            ! sanity check
       call IO_error(error_ID=837,el=currentLoadCase,ext_msg = trim(interface_loadFile))             ! error message for incomplete loadcase
-
+  
     newLoadCase%stress%myType='p'
     field = 1
     newLoadCase%ID(field) = FIELD_MECH_ID                                                           ! mechanical active by default
@@ -192,7 +192,7 @@ program DAMASK_grid
       field = field + 1
       newLoadCase%ID(field) = FIELD_DAMAGE_ID
     endif damageActive
-
+  
     call newLoadCase%rot%fromEulers(real([0.0,0.0,0.0],pReal))
     readIn: do i = 1, chunkPos(1)
       select case (IO_lc(IO_stringValue(line,chunkPos,i)))
@@ -211,7 +211,7 @@ program DAMASK_grid
             if (temp_maskVector(j)) temp_valueVector(j) = IO_floatValue(line,chunkPos,i+j)          ! read value where applicable
           enddo
           newLoadCase%deformation%mask   = transpose(reshape(temp_maskVector,[ 3,3]))               ! mask in 3x3 notation
-          newLoadCase%deformation%values = math_9to33(temp_valueVector)                             ! values in 3x3 notation
+          newLoadCase%deformation%values    = math_9to33(temp_valueVector)                          ! values in 3x3 notation
         case('p','stress', 's')
           temp_valueVector = 0.0_pReal
           do j = 1, 9
@@ -219,7 +219,7 @@ program DAMASK_grid
             if (temp_maskVector(j)) temp_valueVector(j) = IO_floatValue(line,chunkPos,i+j)          ! read value where applicable
           enddo
           newLoadCase%stress%mask   = transpose(reshape(temp_maskVector,[ 3,3]))
-          newLoadCase%stress%values = math_9to33(temp_valueVector)
+          newLoadCase%stress%values      = math_9to33(temp_valueVector)
         case('t','time','delta')                                                                    ! increment time
           newLoadCase%time = IO_floatValue(line,chunkPos,i+1)
         case('n','incs','increments')                                                               ! number of increments
@@ -256,9 +256,9 @@ program DAMASK_grid
           call newLoadCase%rot%fromMatrix(math_9to33(temp_valueVector))
       end select
     enddo readIn
-
+  
     newLoadCase%followFormerTrajectory = merge(.true.,.false.,currentLoadCase > 1)                  ! by default, guess from previous load case
-
+  
     reportAndCheck: if (worldrank == 0) then
       write (loadcase_string, '(i0)' ) currentLoadCase
       print'(/,a,i0)', ' load case: ', currentLoadCase
@@ -277,29 +277,29 @@ program DAMASK_grid
       endif
       do i = 1, 3; do j = 1, 3
         if(newLoadCase%deformation%mask(i,j)) then
-          write(6,'(2x,f12.7)',advance='no') newLoadCase%deformation%values(i,j)
+          write(IO_STDOUT,'(2x,f12.7)',advance='no') newLoadCase%deformation%values(i,j)
         else
-          write(6,'(2x,12a)',advance='no') '     *      '
+          write(IO_STDOUT,'(2x,12a)',advance='no') '     *      '
           endif
-        enddo; write(6,'(/)',advance='no')
+        enddo; write(IO_STDOUT,'(/)',advance='no')
       enddo
       if (any(newLoadCase%stress%mask .eqv. newLoadCase%deformation%mask)) errorID = 831            ! exclusive or masking only
       if (any(newLoadCase%stress%mask .and. transpose(newLoadCase%stress%mask) .and. (math_I3<1))) &
         errorID = 838                                                                               ! no rotation is allowed by stress BC
       print*, ' stress / GPa:'
       do i = 1, 3; do j = 1, 3
-        if(newLoadCase%stress%mask(i,j)) then
-          write(6,'(2x,f12.7)',advance='no') newLoadCase%stress%values(i,j)*1e-9_pReal
+        if(newLoadCase%stress%maskLogical(i,j)) then
+          write(IO_STDOUT,'(2x,f12.7)',advance='no') newLoadCase%stress%values(i,j)*1e-9_pReal
         else
-          write(6,'(2x,12a)',advance='no') '     *      '
+          write(IO_STDOUT,'(2x,12a)',advance='no') '     *      '
         endif
-        enddo; write(6,'(/)',advance='no')
+        enddo; write(IO_STDOUT,'(/)',advance='no')
       enddo
       if (any(abs(matmul(newLoadCase%rot%asMatrix(), &
                          transpose(newLoadCase%rot%asMatrix()))-math_I3) > &
                  reshape(spread(tol_math_check,1,9),[ 3,3]))) errorID = 846                         ! given rotation matrix contains strain
       if (any(dNeq(newLoadCase%rot%asMatrix(), math_I3))) &
-        write(6,'(2x,a,/,3(3(3x,f12.7,1x)/))',advance='no') 'rotation of loadframe:',&
+        write(IO_STDOUT,'(2x,a,/,3(3(3x,f12.7,1x)/))',advance='no') 'rotation of loadframe:',&
                  transpose(newLoadCase%rot%asMatrix())
       if (newLoadCase%time < 0.0_pReal) errorID = 834                                               ! negative time increment
       print'(a,f0.3)', ' time: ', newLoadCase%time
@@ -322,13 +322,13 @@ program DAMASK_grid
     select case (loadCases(1)%ID(field))
       case(FIELD_MECH_ID)
         call mech_init
-
+      
       case(FIELD_THERMAL_ID)
         call grid_thermal_spectral_init
-
+  
       case(FIELD_DAMAGE_ID)
         call grid_damage_spectral_init
-
+  
     end select
   enddo
 
@@ -339,22 +339,22 @@ program DAMASK_grid
       open(newunit=statUnit,file=trim(getSolverJobName())//'.sta',form='FORMATTED',status='REPLACE')
       write(statUnit,'(a)') 'Increment Time CutbackLevel Converged IterationsNeeded'                ! statistics file
       if (debug_grid%contains('basic')) print'(/,a)', ' header of statistics file written out'
-      flush(6)
+      flush(IO_STDOUT)
     else writeHeader
       open(newunit=statUnit,file=trim(getSolverJobName())//&
                                   '.sta',form='FORMATTED', position='APPEND', status='OLD')
     endif writeHeader
   endif
-
+  
   writeUndeformed: if (interface_restartInc < 1) then
     print'(/,a)', ' ... writing initial configuration to file ........................'
     call CPFEM_results(0,0.0_pReal)
   endif writeUndeformed
-
+  
   loadCaseLooping: do currentLoadCase = 1, size(loadCases)
     time0 = time                                                                                    ! load case start time
     guess = loadCases(currentLoadCase)%followFormerTrajectory                                       ! change of load case? homogeneous guess for the first inc
-
+  
     incLooping: do inc = 1, loadCases(currentLoadCase)%incs
       totalIncsCounter = totalIncsCounter + 1
 
@@ -379,13 +379,13 @@ program DAMASK_grid
         endif
       endif
       timeinc = timeinc * real(subStepFactor,pReal)**real(-cutBackLevel,pReal)                      ! depending on cut back level, decrease time step
-
+  
       skipping: if (totalIncsCounter <= interface_restartInc) then                                  ! not yet at restart inc?
         time = time + timeinc                                                                       ! just advance time, skip already performed calculation
         guess = .true.                                                                              ! QUESTION:why forced guessing instead of inheriting loadcase preference
       else skipping
         stepFraction = 0                                                                            ! fraction scaled by stepFactor**cutLevel
-
+  
         subStepLooping: do while (stepFraction < subStepFactor**cutBackLevel)
           remainingLoadCaseTime = loadCases(currentLoadCase)%time+time0 - time
           time = time + timeinc                                                                     ! forward target time
@@ -402,7 +402,7 @@ program DAMASK_grid
           write(incInfo,'(4(a,i0))') &
                   'Increment ',totalIncsCounter,'/',sum(loadCases%incs),&
                   '-', stepFraction,'/',subStepFactor**cutBackLevel
-          flush(6)
+          flush(IO_STDOUT)
 
 !--------------------------------------------------------------------------------------------------
 ! forward fields
@@ -414,7 +414,7 @@ program DAMASK_grid
                         deformation_BC     = loadCases(currentLoadCase)%deformation, &
                         stress_BC          = loadCases(currentLoadCase)%stress, &
                         rotation_BC        = loadCases(currentLoadCase)%rot)
-
+  
               case(FIELD_THERMAL_ID); call grid_thermal_spectral_forward(cutBack)
               case(FIELD_DAMAGE_ID);  call grid_damage_spectral_forward(cutBack)
             end select
@@ -435,9 +435,9 @@ program DAMASK_grid
                 case(FIELD_DAMAGE_ID)
                   solres(field) = grid_damage_spectral_solution(timeinc,timeIncOld)
               end select
-
+  
               if (.not. solres(field)%converged) exit                                               ! no solution found
-
+  
             enddo
             stagIter = stagIter + 1
             stagIterate =            stagIter < stagItMax &
@@ -471,20 +471,20 @@ program DAMASK_grid
             if (worldrank == 0) close(statUnit)
             call quit(0)                                                                            ! quit
           endif
-
+  
         enddo subStepLooping
-
+  
         cutBackLevel = max(0, cutBackLevel - 1)                                                     ! try half number of subincs next inc
-
+  
         if (all(solres(:)%converged)) then
           print'(/,a,i0,a)', ' increment ', totalIncsCounter, ' converged'
         else
           print'(/,a,i0,a)', ' increment ', totalIncsCounter, ' NOT converged'
-        endif; flush(6)
-
+        endif; flush(IO_STDOUT)
+  
         if (mod(inc,loadCases(currentLoadCase)%outputFrequency) == 0) then                          ! at output frequency
           print'(1/,a)', ' ... writing results to file ......................................'
-          flush(6)
+          flush(IO_STDOUT)
           call CPFEM_results(totalIncsCounter,time)
         endif
         if (mod(inc,loadCases(currentLoadCase)%restartFrequency) == 0) then
@@ -492,17 +492,17 @@ program DAMASK_grid
           call CPFEM_restartWrite
         endif
       endif skipping
-
+  
      enddo incLooping
-
+  
   enddo loadCaseLooping
-
-
+ 
+ 
 !--------------------------------------------------------------------------------------------------
 ! report summary of whole calculation
   print'(/,a)', ' ###########################################################################'
   if (worldrank == 0) close(statUnit)
-
+  
   call quit(0)                                                                                      ! no complains ;)
-
+  
 end program DAMASK_grid

src/grid/discretization_grid.f90

@@ -56,7 +56,7 @@ subroutine discretization_grid_init(restart)
     myGrid                                                                                          !< domain grid of this process
 
   integer,     dimension(:),   allocatable :: &
-    microstructureAt
+    materialAt
 
   integer :: &
     j, &
@@ -65,12 +65,12 @@ subroutine discretization_grid_init(restart)
   integer(C_INTPTR_T) :: &
     devNull, z, z_offset
 
-  print'(/,a)', ' <<<+-  discretization_grid init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  discretization_grid init  -+>>>'; flush(IO_STDOUT)
 
   if(index(interface_geomFile,'.vtr') /= 0) then
-    call readVTR(grid,geomSize,origin,microstructureAt)
+    call readVTR(grid,geomSize,origin,materialAt)
   else
-    call readGeom(grid,geomSize,origin,microstructureAt)
+    call readGeom(grid,geomSize,origin,materialAt)
   endif
 
   print'(/,a,3(i12  ))',  ' grid     a b c: ', grid
@@ -102,10 +102,9 @@ subroutine discretization_grid_init(restart)
 
 !--------------------------------------------------------------------------------------------------
 ! general discretization
-  microstructureAt = microstructureAt(product(grid(1:2))*grid3Offset+1: &
-                                      product(grid(1:2))*(grid3Offset+grid3))                       ! reallocate/shrink in case of MPI
+  materialAt = materialAt(product(grid(1:2))*grid3Offset+1:product(grid(1:2))*(grid3Offset+grid3))  ! reallocate/shrink in case of MPI
 
-  call discretization_init(microstructureAt, &
+  call discretization_init(materialAt, &
                            IPcoordinates0(myGrid,mySize,grid3Offset), &
                            Nodes0(myGrid,mySize,grid3Offset),&
                            merge((grid(1)+1) * (grid(2)+1) * (grid3+1),&                            ! write bottom layer
@@ -147,7 +146,7 @@ end subroutine discretization_grid_init
 !> @details important variables have an implicit "save" attribute. Therefore, this function is
 ! supposed to be called only once!
 !--------------------------------------------------------------------------------------------------
-subroutine readGeom(grid,geomSize,origin,microstructure)
+subroutine readGeom(grid,geomSize,origin,material)
 
   integer,     dimension(3), intent(out) :: &
     grid                                                                                            ! grid   (across all processes!)
@@ -155,7 +154,7 @@ subroutine readGeom(grid,geomSize,origin,microstructure)
     geomSize, &                                                                                     ! size   (across all processes!)
     origin                                                                                          ! origin (across all processes!)
   integer,     dimension(:), intent(out), allocatable :: &
-    microstructure
+    material
 
   character(len=:),      allocatable :: rawData
   character(len=65536)               :: line
@@ -167,7 +166,7 @@ subroutine readGeom(grid,geomSize,origin,microstructure)
     startPos, endPos, &
     myStat, &
     l, &                                                                                            !< line counter
-    c, &                                                                                            !< counter for # microstructures in line
+    c, &                                                                                            !< counter for # materials in line
     o, &                                                                                            !< order of "to" packing
     e, &                                                                                            !< "element", i.e. spectral collocation point
     i, j
@@ -266,7 +265,7 @@ subroutine readGeom(grid,geomSize,origin,microstructure)
   if(any(geomSize < 0.0_pReal)) &
     call IO_error(error_ID = 842, ext_msg='size (readGeom)')
 
-  allocate(microstructure(product(grid)), source = -1)                                              ! too large in case of MPI (shrink later, not very elegant)
+  allocate(material(product(grid)), source = -1)                                              ! too large in case of MPI (shrink later, not very elegant)
 
 !--------------------------------------------------------------------------------------------------
 ! read and interpret content
@@ -281,18 +280,18 @@ subroutine readGeom(grid,geomSize,origin,microstructure)
 
     noCompression: if (chunkPos(1) /= 3) then
       c = chunkPos(1)
-      microstructure(e:e+c-1) =  [(IO_intValue(line,chunkPos,i+1), i=0, c-1)]
+      material(e:e+c-1) =  [(IO_intValue(line,chunkPos,i+1), i=0, c-1)]
     else noCompression
       compression: if (IO_lc(IO_stringValue(line,chunkPos,2))  == 'of') then
         c = IO_intValue(line,chunkPos,1)
-        microstructure(e:e+c-1) = [(IO_intValue(line,chunkPos,3),i = 1,IO_intValue(line,chunkPos,1))]
+        material(e:e+c-1) = [(IO_intValue(line,chunkPos,3),i = 1,IO_intValue(line,chunkPos,1))]
       else         if (IO_lc(IO_stringValue(line,chunkPos,2))  == 'to') then compression
         c = abs(IO_intValue(line,chunkPos,3) - IO_intValue(line,chunkPos,1)) + 1
         o = merge(+1, -1, IO_intValue(line,chunkPos,3) > IO_intValue(line,chunkPos,1))
-        microstructure(e:e+c-1) = [(i, i = IO_intValue(line,chunkPos,1),IO_intValue(line,chunkPos,3),o)]
+        material(e:e+c-1) = [(i, i = IO_intValue(line,chunkPos,1),IO_intValue(line,chunkPos,3),o)]
       else compression
         c = chunkPos(1)
-        microstructure(e:e+c-1) = [(IO_intValue(line,chunkPos,i+1), i=0, c-1)]
+        material(e:e+c-1) = [(IO_intValue(line,chunkPos,i+1), i=0, c-1)]
       endif compression
     endif noCompression
 
@@ -308,7 +307,7 @@ end subroutine readGeom
 !> @brief Parse vtk rectilinear grid (.vtr)
 !> @details https://vtk.org/Wiki/VTK_XML_Formats
 !--------------------------------------------------------------------------------------------------
-subroutine readVTR(grid,geomSize,origin,microstructure)
+subroutine readVTR(grid,geomSize,origin,material)
 
   integer,     dimension(3), intent(out) :: &
     grid                                                                                            ! grid   (across all processes!)
@@ -316,7 +315,7 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
     geomSize, &                                                                                     ! size   (across all processes!)
     origin                                                                                          ! origin (across all processes!)
   integer,     dimension(:), intent(out), allocatable :: &
-    microstructure
+    material
 
   character(len=:), allocatable :: fileContent, dataType, headerType
   logical :: inFile,inGrid,gotCoordinates,gotCellData,compressed
@@ -364,11 +363,9 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
       else
         if(index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then
           gotCellData = .true.
-          startPos = endPos + 2_pI64
           do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
-            endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
             if(index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
-                 getXMLValue(fileContent(startPos:endPos),'Name') == 'materialpoint' ) then
+                 getXMLValue(fileContent(startPos:endPos),'Name') == 'material' ) then
 
               if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
                 call IO_error(error_ID = 844, ext_msg='format (materialpoint)')
@@ -377,10 +374,11 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
               startPos = endPos + 2_pI64
               endPos  = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
               s = startPos + verify(fileContent(startPos:endPos),IO_WHITESPACE,kind=pI64) -1_pI64   ! start (no leading whitespace)
-              microstructure = as_Int(fileContent(s:endPos),headerType,compressed,dataType)
+              material = as_Int(fileContent(s:endPos),headerType,compressed,dataType)
               exit
             endif
             startPos = endPos + 2_pI64
+            endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
           enddo
         elseif(index(fileContent(startPos:endPos),'<Coordinates>',kind=pI64) /= 0_pI64) then
           gotCoordinates = .true.
@@ -415,10 +413,10 @@ subroutine readVTR(grid,geomSize,origin,microstructure)
 
   end do
 
-  if(.not. allocated(microstructure))       call IO_error(error_ID = 844, ext_msg='materialpoint not found')
-  if(size(microstructure) /= product(grid)) call IO_error(error_ID = 844, ext_msg='size(materialpoint)')
-  if(any(geomSize<=0))                      call IO_error(error_ID = 844, ext_msg='size')
-  if(any(grid<1))                           call IO_error(error_ID = 844, ext_msg='grid')
+  if(.not. allocated(material))       call IO_error(error_ID = 844, ext_msg='material data not found')
+  if(size(material) /= product(grid)) call IO_error(error_ID = 844, ext_msg='size(material)')
+  if(any(geomSize<=0))                call IO_error(error_ID = 844, ext_msg='size')
+  if(any(grid<1))                     call IO_error(error_ID = 844, ext_msg='grid')
 
   contains
 

src/grid/grid_damage_spectral.f90

@@ -205,10 +205,10 @@ function grid_damage_spectral_solution(timeinc,timeinc_old) result(solution)
   call VecMax(solution_vec,devNull,phi_max,ierr); CHKERRQ(ierr)
   if (solution%converged) &
     print'(/,a)', ' ... nonlocal damage converged .....................................'
-  write(6,'(/,a,f8.6,2x,f8.6,2x,e11.4,/)',advance='no') ' Minimum|Maximum|Delta Damage      = ',&
+  write(IO_STDOUT,'(/,a,f8.6,2x,f8.6,2x,e11.4,/)',advance='no') ' Minimum|Maximum|Delta Damage      = ',&
                                                           phi_min, phi_max, stagNorm
   print'(/,a)', ' ==========================================================================='
-  flush(6) 
+  flush(IO_STDOUT) 
 
 end function grid_damage_spectral_solution
 

src/grid/grid_mech_FEM.f90

@@ -116,7 +116,7 @@ subroutine grid_mech_FEM_init
     num_grid, &
     debug_grid
 
-  print'(/,a)', ' <<<+-  grid_mech_FEM init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  grid_mech_FEM init  -+>>>'; flush(IO_STDOUT)
 
 !-------------------------------------------------------------------------------------------------
 ! debugging options
@@ -408,7 +408,7 @@ subroutine grid_mech_FEM_restartWrite
   call DMDAVecGetArrayF90(mech_grid,solution_current,u_current,ierr); CHKERRQ(ierr)
   call DMDAVecGetArrayF90(mech_grid,solution_lastInc,u_lastInc,ierr); CHKERRQ(ierr)
 
-  print*, 'writing solver data required for restart to file'; flush(6)
+  print*, 'writing solver data required for restart to file'; flush(IO_STDOUT)
 
   write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
   fileHandle  = HDF5_openFile(fileName,'w')
@@ -476,7 +476,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,fnorm,reason,dummy,i
   print'(a,f12.2,a,es8.2,a,es9.2,a)',    ' error stress BC  = ', &
           err_BC/BCTol,    ' (',err_BC, ' Pa,  tol = ',BCTol,')'
   print'(/,a)', ' ==========================================================================='
-  flush(6)
+  flush(IO_STDOUT)
 
 end subroutine converged
 
@@ -510,11 +510,11 @@ subroutine formResidual(da_local,x_local, &
     totalIter = totalIter + 1
     print'(1x,a,3(a,i0))', trim(incInfo), ' @ Iteration ', num%itmin, '≤',totalIter+1, '≤', num%itmax
     if (debugRotation) &
-      write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
+      write(IO_STDOUT,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
               ' deformation gradient aim (lab) =', transpose(params%rotation_BC%rotate(F_aim,active=.true.))
-    write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
+    write(IO_STDOUT,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
               ' deformation gradient aim       =', transpose(F_aim)
-    flush(6)
+    flush(IO_STDOUT)
   endif newIteration
 
 !--------------------------------------------------------------------------------------------------

src/grid/grid_mech_spectral_basic.f90

@@ -106,7 +106,7 @@ subroutine grid_mech_spectral_basic_init
     num_grid, &
     debug_grid
 
-  print'(/,a)', ' <<<+-  grid_mech_spectral_basic init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  grid_mech_spectral_basic init  -+>>>'; flush(IO_STDOUT)
 
   print*, 'Eisenlohr et al., International Journal of Plasticity 46:37–53, 2013'
   print*, 'https://doi.org/10.1016/j.ijplas.2012.09.012'//IO_EOL
@@ -118,18 +118,18 @@ subroutine grid_mech_spectral_basic_init
 ! debugging options
   debug_grid => config_debug%get('grid', defaultVal=emptyList)
   debugRotation = debug_grid%contains('rotation')
-
+  
 !-------------------------------------------------------------------------------------------------
 ! read numerical parameters and do sanity checks
   num_grid => config_numerics%get('grid',defaultVal=emptyDict)
 
-  num%update_gamma    = num_grid%get_asBool ('update_gamma',   defaultVal=.false.)
-  num%eps_div_atol    = num_grid%get_asFloat('eps_div_atol',   defaultVal=1.0e-4_pReal)
-  num%eps_div_rtol    = num_grid%get_asFloat('eps_div_rtol',   defaultVal=5.0e-4_pReal)
-  num%eps_stress_atol = num_grid%get_asFloat('eps_stress_atol',defaultVal=1.0e3_pReal)
+  num%update_gamma    = num_grid%get_asBool   ('update_gamma',   defaultVal=.false.)
+  num%eps_div_atol    = num_grid%get_asFloat  ('eps_div_atol',   defaultVal=1.0e-4_pReal)
+  num%eps_div_rtol    = num_grid%get_asFloat  ('eps_div_rtol',   defaultVal=5.0e-4_pReal)
+  num%eps_stress_atol = num_grid%get_asFloat  ('eps_stress_atol',defaultVal=1.0e3_pReal)
   num%eps_stress_rtol = num_grid%get_asFloat('eps_stress_rtol',defaultVal=1.0e-3_pReal)
-  num%itmin           = num_grid%get_asInt  ('itmin',          defaultVal=1)
-  num%itmax           = num_grid%get_asInt  ('itmax',          defaultVal=250)
+  num%itmin           = num_grid%get_asInt    ('itmin',defaultVal=1)
+  num%itmax           = num_grid%get_asInt    ('itmax',defaultVal=250)
 
   if (num%eps_div_atol <= 0.0_pReal)             call IO_error(301,ext_msg='eps_div_atol')
   if (num%eps_div_rtol < 0.0_pReal)              call IO_error(301,ext_msg='eps_div_rtol')
@@ -137,7 +137,7 @@ subroutine grid_mech_spectral_basic_init
   if (num%eps_stress_rtol < 0.0_pReal)           call IO_error(301,ext_msg='eps_stress_rtol')
   if (num%itmax <= 1)                            call IO_error(301,ext_msg='itmax')
   if (num%itmin > num%itmax .or. num%itmin < 1)  call IO_error(301,ext_msg='itmin')
-
+   
 !--------------------------------------------------------------------------------------------------
 ! set default and user defined options for PETSc
   call PETScOptionsInsertString(PETSC_NULL_OPTIONS,'-mech_snes_type ngmres',ierr)
@@ -154,7 +154,7 @@ subroutine grid_mech_spectral_basic_init
 ! initialize solver specific parts of PETSc
   call SNESCreate(PETSC_COMM_WORLD,snes,ierr); CHKERRQ(ierr)
   call SNESSetOptionsPrefix(snes,'mech_',ierr);CHKERRQ(ierr)
-  localK            = 0
+  localK              = 0
   localK(worldrank) = grid3
   call MPI_Allreduce(MPI_IN_PLACE,localK,worldsize,MPI_INTEGER,MPI_SUM,PETSC_COMM_WORLD,ierr)
   call DMDACreate3d(PETSC_COMM_WORLD, &
@@ -370,7 +370,7 @@ subroutine grid_mech_spectral_basic_restartWrite
 
   call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)
 
-  print*, 'writing solver data required for restart to file'; flush(6)
+  print*, 'writing solver data required for restart to file'; flush(IO_STDOUT)
 
   write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
   fileHandle  = HDF5_openFile(fileName,'w')
@@ -436,7 +436,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
   print'(a,f12.2,a,es8.2,a,es9.2,a)',    ' error stress BC  = ', &
           err_BC/BCTol,    ' (',err_BC, ' Pa,  tol = ',BCTol,')'
   print'(/,a)', ' ==========================================================================='
-  flush(6)
+  flush(IO_STDOUT)
 
 end subroutine converged
 
@@ -471,11 +471,11 @@ subroutine formResidual(in, F, &
     totalIter = totalIter + 1
     print'(1x,a,3(a,i0))', trim(incInfo), ' @ Iteration ', num%itmin, '≤',totalIter, '≤', num%itmax
     if (debugRotation) &
-      write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
+      write(IO_STDOUT,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
               ' deformation gradient aim (lab) =', transpose(params%rotation_BC%rotate(F_aim,active=.true.))
-    write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
+    write(IO_STDOUT,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
               ' deformation gradient aim       =', transpose(F_aim)
-    flush(6)
+    flush(IO_STDOUT)
   endif newIteration
 
 !--------------------------------------------------------------------------------------------------
@@ -502,7 +502,7 @@ subroutine formResidual(in, F, &
 
 !--------------------------------------------------------------------------------------------------
 ! constructing residual
-  residuum = tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3)                                  ! Gamma*P gives correction towards div(P) = 0, so needs to be zero, too
+  residuum = tensorField_real(1:3,1:3,1:grid(1),1:grid(2),1:grid3)                                   ! Gamma*P gives correction towards div(P) = 0, so needs to be zero, too
 
 end subroutine formResidual
 

src/grid/grid_mech_spectral_polarisation.f90

@@ -119,7 +119,7 @@ subroutine grid_mech_spectral_polarisation_init
     num_grid, &
     debug_grid
 
-  print'(/,a)', ' <<<+-  grid_mech_spectral_polarisation init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  grid_mech_spectral_polarisation init  -+>>>'; flush(IO_STDOUT)
 
   print*, 'Shanthraj et al., International Journal of Plasticity 66:31–45, 2015'
   print*, 'https://doi.org/10.1016/j.ijplas.2014.02.006'
@@ -428,7 +428,7 @@ subroutine grid_mech_spectral_polarisation_restartWrite
   F     => FandF_tau(0: 8,:,:,:)
   F_tau => FandF_tau(9:17,:,:,:)
 
-  print*, 'writing solver data required for restart to file'; flush(6)
+  print*, 'writing solver data required for restart to file'; flush(IO_STDOUT)
 
   write(fileName,'(a,a,i0,a)') trim(getSolverJobName()),'_',worldrank,'.hdf5'
   fileHandle  = HDF5_openFile(fileName,'w')
@@ -500,7 +500,7 @@ subroutine converged(snes_local,PETScIter,devNull1,devNull2,devNull3,reason,dumm
   print  '(a,f12.2,a,es8.2,a,es9.2,a)', ' error stress BC         = ', &
             err_BC/BCTol,    ' (',err_BC,  ' Pa,  tol = ',BCTol,')'
   print'(/,a)', ' ==========================================================================='
-  flush(6)
+  flush(IO_STDOUT)
 
 end subroutine converged
 
@@ -554,11 +554,11 @@ subroutine formResidual(in, FandF_tau, &
     totalIter = totalIter + 1
     print'(1x,a,3(a,i0))', trim(incInfo), ' @ Iteration ', num%itmin, '≤',totalIter, '≤', num%itmax
     if(debugRotation) &
-      write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
+      write(IO_STDOUT,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
               ' deformation gradient aim (lab) =', transpose(params%rotation_BC%rotate(F_aim,active=.true.))
-    write(6,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
+    write(IO_STDOUT,'(/,a,/,3(3(f12.7,1x)/))',advance='no') &
               ' deformation gradient aim       =', transpose(F_aim)
-    flush(6)
+    flush(IO_STDOUT)
   endif newIteration
 
 !--------------------------------------------------------------------------------------------------

src/grid/grid_thermal_spectral.f90

@@ -199,10 +199,10 @@ function grid_thermal_spectral_solution(timeinc,timeinc_old) result(solution)
   call VecMax(solution_vec,devNull,T_max,ierr); CHKERRQ(ierr)
   if (solution%converged) &
     print'(/,a)', ' ... thermal conduction converged ..................................'
-  write(6,'(/,a,f8.4,2x,f8.4,2x,f8.4,/)',advance='no') ' Minimum|Maximum|Delta Temperature / K = ',&
+  write(IO_STDOUT,'(/,a,f8.4,2x,f8.4,2x,f8.4,/)',advance='no') ' Minimum|Maximum|Delta Temperature / K = ',&
                                                         T_min, T_max, stagNorm
   print'(/,a)', ' ==========================================================================='
-  flush(6) 
+  flush(IO_STDOUT) 
 
 end function grid_thermal_spectral_solution
 

src/grid/spectral_utilities.f90

@@ -210,7 +210,7 @@ subroutine spectral_utilities_init
   if(debugPETSc) print'(3(/,a),/)', &
                  ' Initializing PETSc with debug options: ', &
                  trim(PETScDebug), &
-                 ' add more using the PETSc_Options keyword in numerics.yaml '; flush(6)
+                 ' add more using the PETSc_Options keyword in numerics.yaml '; flush(IO_STDOUT)
 
   num_grid => config_numerics%get('grid',defaultVal=emptyDict)
 
@@ -279,7 +279,7 @@ subroutine spectral_utilities_init
   if (pReal /= C_DOUBLE .or. kind(1) /= C_INT) error stop 'C and Fortran datatypes do not match'
   call fftw_set_timelimit(num_grid%get_asFloat('fftw_timelimit',defaultVal=-1.0_pReal))
 
-  print*, 'FFTW initialized'; flush(6)
+  print*, 'FFTW initialized'; flush(IO_STDOUT)
 
 !--------------------------------------------------------------------------------------------------
 ! MPI allocation
@@ -506,7 +506,7 @@ subroutine utilities_fourierGammaConvolution(fieldAim)
 
 
   print'(/,a)', ' ... doing gamma convolution ...............................................'
-  flush(6)
+  flush(IO_STDOUT)
 
 !--------------------------------------------------------------------------------------------------
 ! do the actual spectral method calculation (mechanical equilibrium)
@@ -576,7 +576,7 @@ real(pReal) function utilities_divergenceRMS()
   complex(pReal), dimension(3)   :: rescaledGeom
 
   print'(/,a)', ' ... calculating divergence ................................................'
-  flush(6)
+  flush(IO_STDOUT)
 
   rescaledGeom = cmplx(geomSize/scaledGeomSize,0.0_pReal)
 
@@ -620,7 +620,7 @@ real(pReal) function utilities_curlRMS()
   complex(pReal), dimension(3)   :: rescaledGeom
 
   print'(/,a)', ' ... calculating curl ......................................................'
-  flush(6)
+  flush(IO_STDOUT)
 
   rescaledGeom = cmplx(geomSize/scaledGeomSize,0.0_pReal)
 
@@ -700,9 +700,9 @@ function utilities_maskedCompliance(rot_BC,mask_stress,C)
 
     if(debugGeneral) then
       print'(/,a)', ' ... updating masked compliance ............................................'
-      write(6,'(/,a,/,9(9(2x,f12.7,1x)/))',advance='no') ' Stiffness C (load) / GPa =',&
+      write(IO_STDOUT,'(/,a,/,9(9(2x,f12.7,1x)/))',advance='no') ' Stiffness C (load) / GPa =',&
                                                    transpose(temp99_Real)*1.0e-9_pReal
-      flush(6)
+      flush(IO_STDOUT)
     endif
 
     do i = 1,9; do j = 1,9
@@ -722,9 +722,9 @@ function utilities_maskedCompliance(rot_BC,mask_stress,C)
     if (debugGeneral .or. errmatinv) then
       write(formatString, '(i2)') size_reduced
       formatString = '(/,a,/,'//trim(formatString)//'('//trim(formatString)//'(2x,es9.2,1x)/))'
-      write(6,trim(formatString),advance='no') ' C * S (load) ', &
+      write(IO_STDOUT,trim(formatString),advance='no') ' C * S (load) ', &
                                                              transpose(matmul(c_reduced,s_reduced))
-      write(6,trim(formatString),advance='no') ' S (load) ', transpose(s_reduced)
+      write(IO_STDOUT,trim(formatString),advance='no') ' S (load) ', transpose(s_reduced)
       if(errmatinv) call IO_error(error_ID=400,ext_msg='utilities_maskedCompliance')
     endif
     temp99_real = reshape(unpack(reshape(s_reduced,[size_reduced**2]),reshape(mask,[81]),0.0_pReal),[9,9])
@@ -735,9 +735,9 @@ function utilities_maskedCompliance(rot_BC,mask_stress,C)
   utilities_maskedCompliance = math_99to3333(temp99_Real)
 
   if(debugGeneral) then
-    write(6,'(/,a,/,9(9(2x,f10.5,1x)/),/)',advance='no') &
+    write(IO_STDOUT,'(/,a,/,9(9(2x,f10.5,1x)/),/)',advance='no') &
       ' Masked Compliance (load) * GPa =', transpose(temp99_Real)*1.0e9_pReal
-    flush(6)
+    flush(IO_STDOUT)
   endif
 
 end function utilities_maskedCompliance
@@ -822,7 +822,7 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
   real(pReal), dimension(2) :: valueAndRank                                                         !< pair of min/max norm of dPdF to synchronize min/max of dPdF
 
   print'(/,a)', ' ... evaluating constitutive response ......................................'
-  flush(6)
+  flush(IO_STDOUT)
 
   materialpoint_F  = reshape(F,[3,3,1,product(grid(1:2))*grid3])                                    ! set materialpoint target F to estimated field
 
@@ -832,13 +832,13 @@ subroutine utilities_constitutiveResponse(P,P_av,C_volAvg,C_minmaxAvg,&
   P_av = sum(sum(sum(P,dim=5),dim=4),dim=3) * wgt                                                   ! average of P
   call MPI_Allreduce(MPI_IN_PLACE,P_av,9,MPI_DOUBLE,MPI_SUM,PETSC_COMM_WORLD,ierr)
   if (debugRotation) &
-  write(6,'(/,a,/,3(3(2x,f12.4,1x)/))',advance='no') ' Piola--Kirchhoff stress (lab) / MPa =',&
+  write(IO_STDOUT,'(/,a,/,3(3(2x,f12.4,1x)/))',advance='no') ' Piola--Kirchhoff stress (lab) / MPa =',&
                                                       transpose(P_av)*1.e-6_pReal
   if(present(rotation_BC)) &
     P_av = rotation_BC%rotate(P_av)
-  write(6,'(/,a,/,3(3(2x,f12.4,1x)/))',advance='no') ' Piola--Kirchhoff stress       / MPa =',&
+  write(IO_STDOUT,'(/,a,/,3(3(2x,f12.4,1x)/))',advance='no') ' Piola--Kirchhoff stress       / MPa =',&
                                                       transpose(P_av)*1.e-6_pReal
-  flush(6)
+  flush(IO_STDOUT)
 
   dPdF_max = 0.0_pReal
   dPdF_norm_max = 0.0_pReal
@@ -1094,7 +1094,7 @@ subroutine utilities_saveReferenceStiffness
     fileUnit,ierr
 
   if (worldrank == 0) then
-    print'(a)', ' writing reference stiffness data required for restart to file'; flush(6)
+    print'(a)', ' writing reference stiffness data required for restart to file'; flush(IO_STDOUT)
     open(newunit=fileUnit, file=getSolverJobName()//'.C_ref',&
          status='replace',access='stream',action='write',iostat=ierr)
     if(ierr /=0) call IO_error(100,ext_msg='could not open file '//getSolverJobName()//'.C_ref')

src/homogenization.f90

@@ -186,7 +186,7 @@ subroutine homogenization_init
   materialpoint_F = materialpoint_F0                                                                ! initialize to identity
   allocate(materialpoint_P(3,3,discretization_nIP,discretization_nElem),              source=0.0_pReal)
 
-  print'(/,a)', ' <<<+-  homogenization init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  homogenization init  -+>>>'; flush(IO_STDOUT)
 
   num%nMPstate          = num_homogGeneric%get_asInt  ('nMPstate',     defaultVal=10)
   num%subStepMinHomog   = num_homogGeneric%get_asFloat('subStepMin',   defaultVal=1.0e-3_pReal)

src/homogenization_mech_RGC.f90

@@ -95,7 +95,7 @@ module subroutine mech_RGC_init(num_homogMech)
   print'(/,a)', ' <<<+-  homogenization_mech_rgc init  -+>>>'
 
   Ninstance = count(homogenization_type == HOMOGENIZATION_RGC_ID)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
 
   print*, 'Tjahjanto et al., International Journal of Material Forming 2(1):939–942, 2009'
   print*, 'https://doi.org/10.1007/s12289-009-0619-1'//IO_EOL
@@ -247,7 +247,7 @@ module subroutine mech_RGC_partitionDeformation(F,avgF,instance,of)
         print'(1x,3(e15.8,1x))',(F(i,j,iGrain), j = 1,3)
       enddo
       print*,' '
-      flush(6)
+      flush(IO_STDOUT)
     endif
 #endif
   enddo
@@ -376,7 +376,7 @@ module procedure mech_RGC_updateState
                '@ grain ',stresLoc(3),' in component ',stresLoc(1),stresLoc(2)
     print'(a,e15.8,a,i3,a,i2)',' Max residual: ',residMax, &
                ' @ iface ',residLoc(1),' in direction ',residLoc(2)
-    flush(6)
+    flush(IO_STDOUT)
   endif
 #endif
 
@@ -388,7 +388,7 @@ module procedure mech_RGC_updateState
     mech_RGC_updateState = .true.
 #ifdef DEBUG
     if (debugHomog%extensive .and. prm%of_debug == of) &
-      print*, '... done and happy'; flush(6)
+      print*, '... done and happy'; flush(IO_STDOUT)
 #endif
 
 !--------------------------------------------------------------------------------------------------
@@ -416,7 +416,7 @@ module procedure mech_RGC_updateState
       print'(a,e15.8,/)', ' Volume discrepancy: ',      dst%volumeDiscrepancy(of)
       print'(a,e15.8)',   ' Maximum relaxation rate: ', dst%relaxationRate_max(of)
       print'(a,e15.8,/)', ' Average relaxation rate: ', dst%relaxationRate_avg(of)
-      flush(6)
+      flush(IO_STDOUT)
     endif
 #endif
 
@@ -429,7 +429,7 @@ module procedure mech_RGC_updateState
 
 #ifdef DEBUG
     if (debugHomog%extensive .and. prm%of_debug == of) &
-      print'(a,/)', ' ... broken'; flush(6)
+      print'(a,/)', ' ... broken'; flush(IO_STDOUT)
 #endif
 
    return
@@ -437,7 +437,7 @@ module procedure mech_RGC_updateState
  else                                                                                               ! proceed with computing the Jacobian and state update
 #ifdef DEBUG
    if (debugHomog%extensive .and. prm%of_debug == of) &
-     print'(a,/)', ' ... not yet done'; flush(6)
+     print'(a,/)', ' ... not yet done'; flush(IO_STDOUT)
 #endif
 
  endif
@@ -499,7 +499,7 @@ module procedure mech_RGC_updateState
       print'(1x,100(e11.4,1x))',(smatrix(i,j), j = 1,3*nIntFaceTot)
     enddo
     print*,' '
-    flush(6)
+    flush(IO_STDOUT)
   endif
 #endif
 
@@ -559,7 +559,7 @@ module procedure mech_RGC_updateState
       print'(1x,100(e11.4,1x))',(pmatrix(i,j), j = 1,3*nIntFaceTot)
     enddo
     print*,' '
-    flush(6)
+    flush(IO_STDOUT)
   endif
 #endif
 
@@ -578,7 +578,7 @@ module procedure mech_RGC_updateState
       print'(1x,100(e11.4,1x))',(rmatrix(i,j), j = 1,3*nIntFaceTot)
     enddo
     print*,' '
-    flush(6)
+    flush(IO_STDOUT)
   endif
 #endif
 
@@ -593,7 +593,7 @@ module procedure mech_RGC_updateState
       print'(1x,100(e11.4,1x))',(jmatrix(i,j), j = 1,3*nIntFaceTot)
     enddo
     print*,' '
-    flush(6)
+    flush(IO_STDOUT)
   endif
 #endif
 
@@ -609,7 +609,7 @@ module procedure mech_RGC_updateState
       print'(1x,100(e11.4,1x))',(jnverse(i,j), j = 1,3*nIntFaceTot)
     enddo
     print*,' '
-    flush(6)
+    flush(IO_STDOUT)
   endif
 #endif
 
@@ -625,7 +625,7 @@ module procedure mech_RGC_updateState
     !$OMP CRITICAL (write2out)
     print'(a,i3,a,i3,a)',' RGC_updateState: ip ',ip,' | el ',el,' enforces cutback'
     print'(a,e15.8)',' due to large relaxation change = ',maxval(abs(drelax))
-    flush(6)
+    flush(IO_STDOUT)
     !$OMP END CRITICAL (write2out)
   endif
 
@@ -636,7 +636,7 @@ module procedure mech_RGC_updateState
       print'(1x,2(e15.8,1x))', stt%relaxationVector(i,of)
     enddo
     print*,' '
-    flush(6)
+    flush(IO_STDOUT)
   endif
 #endif
 

src/homogenization_mech_isostrain.f90

@@ -40,7 +40,7 @@ module subroutine mech_isostrain_init
   print'(/,a)',   ' <<<+-  homogenization_mech_isostrain init  -+>>>'
 
   Ninstance = count(homogenization_type == HOMOGENIZATION_ISOSTRAIN_ID)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
 
   allocate(param(Ninstance))                                                                        ! one container of parameters per instance
 

src/homogenization_mech_none.f90

@@ -21,7 +21,7 @@ module subroutine mech_none_init
   print'(/,a)', ' <<<+-  homogenization_mech_none init  -+>>>'
 
   Ninstance = count(homogenization_type == HOMOGENIZATION_NONE_ID)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
 
   do h = 1, size(homogenization_type)
     if (homogenization_type(h) /= HOMOGENIZATION_NONE_ID) cycle

src/kinematics_cleavage_opening.f90

@@ -49,7 +49,7 @@ module function kinematics_cleavage_opening_init(kinematics_length) result(myKin
 
   myKinematics = kinematics_active('cleavage_opening',kinematics_length)
   Ninstance = count(myKinematics)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
   if(Ninstance == 0) return
 
   phases => config_material%get('phase')

src/kinematics_slipplane_opening.f90

@@ -52,7 +52,7 @@ module function kinematics_slipplane_opening_init(kinematics_length) result(myKi
 
   myKinematics = kinematics_active('slipplane_opening',kinematics_length)
   Ninstance = count(myKinematics)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
   if(Ninstance == 0) return
 
   phases => config_material%get('phase')

src/kinematics_thermal_expansion.f90

@@ -42,7 +42,7 @@ module function kinematics_thermal_expansion_init(kinematics_length) result(myKi
 
   myKinematics = kinematics_active('thermal_expansion',kinematics_length)
   Ninstance = count(myKinematics)
-  print'(a,i2)', ' # instances: ',Ninstance; flush(6)
+  print'(a,i2)', ' # instances: ',Ninstance; flush(IO_STDOUT)
   if(Ninstance == 0) return
 
   phases => config_material%get('phase')

src/lattice.f90

@@ -457,7 +457,7 @@ subroutine lattice_init
     phase, &
     elasticity
  
-  print'(/,a)', ' <<<+-  lattice init  -+>>>'; flush(6)
+  print'(/,a)', ' <<<+-  lattice init  -+>>>'; flush(IO_STDOUT)
 
   phases => config_material%get('phase')
   Nphases = phases%length