cleaned

processing/pre/geom_fromMinimalSurface.py

@@ -1,30 +1,33 @@
 #!/usr/bin/env python3
-# -*- coding: UTF-8 no BOM -*-
 
 import os
 import sys
-import math
-import numpy as np
 from optparse import OptionParser
+
+import numpy as np
+
 import damask
 
+
 scriptName = os.path.splitext(os.path.basename(__file__))[0]
 scriptID   = ' '.join([scriptName,damask.version])
 
+
+minimal_surfaces = ['primitive','gyroid','diamond']
+
+surface = {
+            'primitive': lambda x,y,z: np.cos(x)+np.cos(y)+np.cos(z),
+            'gyroid':    lambda x,y,z: np.sin(x)*np.cos(y)+np.sin(y)*np.cos(z)+np.cos(x)*np.sin(z),
+            'diamond':   lambda x,y,z: np.cos(x-y)*np.cos(z)+np.sin(x+y)*np.sin(z),
+          }
+
+
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------
 
-minimal_surfaces = ['primitive','gyroid','diamond',]
-
-surface = {
-            'primitive': lambda x,y,z: math.cos(x)+math.cos(y)+math.cos(z),
-            'gyroid':    lambda x,y,z: math.sin(x)*math.cos(y)+math.sin(y)*math.cos(z)+math.cos(x)*math.sin(z),
-            'diamond':   lambda x,y,z: math.cos(x-y)*math.cos(z)+math.sin(x+y)*math.sin(z),
-          }
-
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] [geomfile]', description = """
-Generate a geometry file of a bicontinuous structure of given type.
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile]', description = """
+Generate a bicontinuous structure of given type.
 
 """, version = scriptID)
 
@@ -57,6 +60,7 @@ parser.add_option('--m',
                   dest = 'microstructure',
                   type = 'int', nargs = 2, metavar = 'int int',
                   help = 'two microstructure indices to be used [%default]')
+
 parser.set_defaults(type = minimal_surfaces[0],
                     threshold = 0.0,
                     periods = 1,
@@ -68,24 +72,23 @@ parser.set_defaults(type = minimal_surfaces[0],
 
 (options,filenames) = parser.parse_args()
 
-# --- loop over input files -------------------------------------------------------------------------
 
 if filenames == []: filenames = [None]
 
 for name in filenames:
   damask.util.report(scriptName,name)
 
-  X = options.periods*2.0*math.pi*(np.arange(options.grid[0])+0.5)/options.grid[0]
-  Y = options.periods*2.0*math.pi*(np.arange(options.grid[1])+0.5)/options.grid[1]
-  Z = options.periods*2.0*math.pi*(np.arange(options.grid[2])+0.5)/options.grid[2]
+  X = options.periods*2.0*np.pi*(np.arange(options.grid[0])+0.5)/options.grid[0]
+  Y = options.periods*2.0*np.pi*(np.arange(options.grid[1])+0.5)/options.grid[1]
+  Z = options.periods*2.0*np.pi*(np.arange(options.grid[2])+0.5)/options.grid[2]
 
   microstructure = np.empty(options.grid,dtype='int')
-  for z in range(options.grid[2]):
+  for x in range(options.grid[0]):
     for y in range(options.grid[1]):
-      for x in range(options.grid[0]):
+      for z in range(options.grid[2]):
         microstructure[x,y,z]=options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])]
   
-  geom=damask.Geom(options.size,microstructure,options.homogenization,
+  geom=damask.Geom(microstructure,options.size,options.homogenization,
                    comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
 
   damask.util.croak(geom)

processing/pre/geom_fromVoronoiTessellation.py

@@ -3,7 +3,6 @@
 import os
 import sys 
 import multiprocessing
-from io import StringIO
 from optparse import OptionParser,OptionGroup
 
 import numpy as np
@@ -101,6 +100,7 @@ def laguerreTessellation(undeformed, coords, weights, grains, periodic = True, c
 # closestSeed is modulo number of original seed points (i.e. excluding periodic copies)
   return grains[closestSeeds%coords.shape[0]]                                                   
 
+
 # --------------------------------------------------------------------
 #                                MAIN
 # --------------------------------------------------------------------

processing/pre/geom_grainGrowth.py

@@ -2,6 +2,7 @@
 
 import os
 import sys
+from io import StringIO
 from optparse import OptionParser
 
 import numpy as np

processing/pre/geom_pack.py

@@ -2,6 +2,7 @@
 
 import os
 import sys
+from io import StringIO
 from optparse import OptionParser
 
 import damask
@@ -49,7 +50,7 @@ for name in filenames:
       compressType = 'of'
       reps += 1
     else:
-      if   compressType == None:
+      if   compressType is None:
         out = []
       elif compressType == '.':
         out.append('{}\n'.format(former))

python/damask/geom.py

@@ -9,7 +9,6 @@ class Geom():
 
   def __init__(self,microstructure,size,homogenization=1,comments=[]):
     """New geometry definition from array of microstructures and size"""
-
     if len(microstructure.shape) != 3:
       raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape))
     elif microstructure.dtype not in [int,float]: