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

processing/post/3Dvisualize.py

@@ -227,7 +227,7 @@ for filename in args:
   locol = -1
   
   for col,head in enumerate(headings):
-    if head == {True:'1_ipinitialcoord',False:'1_nodeinitialcoord'}[options.cell]:
+    if head == {True:'1_pos',False:'1_nodeinitialcoord'}[options.cell]:
       locol = col
       maxcol = max(maxcol,col+3)
       break

processing/post/mentat_colorMap.py

@@ -68,26 +68,29 @@ Interpolates colors between "lower_hsl" and "upper_hsl".
 """, version = scriptID)
 
 parser.add_option("-i","--inverse", action = "store_true", 
-                  dest = "inverse", \
+                  dest = "inverse",
-                  help = "invert legend [%default]")
+                  help = "invert legend")
 parser.add_option(     "--palette", action = "store_true", 
-                  dest = "palette", \
+                  dest = "palette",
-                  help = "output plain rgb palette integer values (0-255) [%default]")
+                  help = "output plain rgb palette integer values (0-255)")
 parser.add_option(     "--palettef", action = "store_true", 
-                  dest = "palettef", \
+                  dest = "palettef",
-                  help = "output plain rgb palette float values (0.0-1.0) [%default]")
+                  help = "output plain rgb palette float values (0.0-1.0)")
-parser.add_option("-p", "--port", type = "int",\
+parser.add_option("-p", "--port", type = "int",
-                  dest = "port",\
+                  dest = "port",
+                  metavar ='int',
                   help = "Mentat connection port [%default]")
-parser.add_option("-b", "--baseindex", type = "int",\
+parser.add_option("-b", "--baseindex", type = "int",
-                  dest = "baseIdx",\
+                  metavar ='int',
+                  dest = "baseIdx",
                   help = "base index of colormap [%default]")
-parser.add_option("-n", "--colorcount", type = "int",\
+parser.add_option("-n", "--colorcount", type = "int",
-                  dest = "colorcount",\
+                  metavar ='int',
+                  dest = "colorcount",
                   help = "number of colors [%default]")
-parser.add_option("-v", "--verbose", action="store_true",\
+parser.add_option("-v", "--verbose", action="store_true",
-                  dest = "verbose",\
+                  dest = "verbose",
-                  help = "write Mentat command stream also to STDOUT [%default]")
+                  help = "write Mentat command stream also to STDOUT")
 
 parser.set_defaults(port = 40007)
 parser.set_defaults(baseIdx = 32)

processing/post/postResults.py

@@ -643,63 +643,69 @@ of already processed data points for evaluation.
 
 """, version = scriptID)
 
-parser.add_option('-i','--info', action='store_true', dest='info', \
+parser.add_option('-i','--info', action='store_true', dest='info',
-                  help='list contents of resultfile [%default]')
+                  help='list contents of resultfile')
-parser.add_option('-l','--legacy', action='store_true', dest='legacy', \
+parser.add_option('-l','--legacy', action='store_true', dest='legacy',
                   help='data format of spectral solver is in legacy format (no MPI out)')
-parser.add_option('-n','--nodal', action='store_true', dest='nodal', \
+parser.add_option('-n','--nodal', action='store_true', dest='nodal',
-                  help='data is extrapolated to nodal value [%default]')
+                  help='data is extrapolated to nodal value')
-parser.add_option(    '--prefix', dest='prefix', \
+parser.add_option(    '--prefix', dest='prefix',
-                  help='prefix to result file name [%default]')
+                  metavar='string',
-parser.add_option(    '--suffix', dest='suffix', \
+                  help='prefix to result file name')
-                  help='suffix to result file name [%default]')
+parser.add_option(    '--suffix', dest='suffix',
-parser.add_option('-d','--dir', dest='dir', \
+                  metavar='string',
+                  help='suffix to result file name')
+parser.add_option('-d','--dir', dest='dir',
+                  metavar='string',
                   help='name of subdirectory to hold output [%default]')
-parser.add_option('-s','--split', action='store_true', dest='separateFiles', \
+parser.add_option('-s','--split', action='store_true', dest='separateFiles',
-                  help='split output per increment [%default]')
+                  help='split output per increment')
-parser.add_option('-r','--range', dest='range', type='int', nargs=3, \
+parser.add_option('-r','--range', dest='range', type='int', nargs=3,
+                  metavar='int int int',
                   help='range of positions (or increments) to output (start, end, step) [all]')
-parser.add_option('--increments', action='store_true', dest='getIncrements', \
+parser.add_option('--increments', action='store_true', dest='getIncrements',
-                  help='switch to increment range [%default]')
+                  help='switch to increment range')
-parser.add_option('-m','--map', dest='func', \
+parser.add_option('-m','--map', dest='func',
+                  metavar='string',
                   help='data reduction mapping [%default] out of min, max, avg, avgabs, sum, sumabs or user-lambda')
-parser.add_option('-p','--type', dest='filetype', \
+parser.add_option('-p','--type', dest='filetype',
+                  metavar = 'string',
                   help = 'type of result file [auto]')
 
 group_material = OptionGroup(parser,'Material identifier')
 
-group_material.add_option('--homogenization', dest='homog', \
+group_material.add_option('--homogenization', dest='homog',
-                          help='homogenization identifier (as string or integer [%default])', metavar='<ID>')
+                          help='homogenization identifier (as string or integer [%default])', metavar='string')
-group_material.add_option('--crystallite', dest='cryst', \
+group_material.add_option('--crystallite', dest='cryst',
-                          help='crystallite identifier (as string or integer [%default])', metavar='<ID>')
+                          help='crystallite identifier (as string or integer [%default])', metavar='string')
-group_material.add_option('--phase', dest='phase', \
+group_material.add_option('--phase', dest='phase',
-                          help='phase identifier (as string or integer [%default])', metavar='<ID>')
+                          help='phase identifier (as string or integer [%default])', metavar='string')
 
 group_special  = OptionGroup(parser,'Special outputs')
 
-group_special.add_option('-t','--time', action='store_true', dest='time', \
+group_special.add_option('-t','--time', action='store_true', dest='time',
                          help='output time of increment [%default]')
-group_special.add_option('-f','--filter', dest='filter', \
+group_special.add_option('-f','--filter', dest='filter',
-                         help='condition(s) to filter results [%default]', metavar='<CODE>')
+                         help='condition(s) to filter results [%default]', metavar='string')
-group_special.add_option('--separation', action='extend', dest='sep', \
+group_special.add_option('--separation', action='extend', dest='sep',
-                         help='properties to separate results [%default]', metavar='<LIST>')
+                         help='properties to separate results [%default]', metavar='<string LIST>')
-group_special.add_option('--sort', action='extend', dest='sort', \
+group_special.add_option('--sort', action='extend', dest='sort',
-                         help='properties to sort results [%default]', metavar='<LIST>')
+                         help='properties to sort results [%default]', metavar='<string LIST>')
 
 group_general  = OptionGroup(parser,'General outputs')
 
-group_general.add_option('--ns', action='extend', dest='nodalScalar', \
+group_general.add_option('--ns', action='extend', dest='nodalScalar',
-                         help='nodal scalars to extract', metavar='<LIST>')
+                         help='nodal scalars to extract', metavar='<string LIST>')
-group_general.add_option('--es', action='extend', dest='elemScalar', \
+group_general.add_option('--es', action='extend', dest='elemScalar',
-                         help='elemental scalars to extract', metavar='<LIST>')
+                         help='elemental scalars to extract', metavar='<string LIST>')
-group_general.add_option('--et', action='extend', dest='elemTensor', \
+group_general.add_option('--et', action='extend', dest='elemTensor',
-                         help='elemental tensors to extract', metavar='<LIST>')
+                         help='elemental tensors to extract', metavar='<string LIST>')
-group_general.add_option('--ho', action='extend', dest='homogenizationResult', \
+group_general.add_option('--ho', action='extend', dest='homogenizationResult',
-                         help='homogenization results to extract', metavar='<LIST>')
+                         help='homogenization results to extract', metavar='<string LIST>')
-group_general.add_option('--cr', action='extend', dest='crystalliteResult', \
+group_general.add_option('--cr', action='extend', dest='crystalliteResult',
-                         help='crystallite results to extract', metavar='<LIST>')
+                         help='crystallite results to extract', metavar='<string LIST>')
-group_general.add_option('--co', action='extend', dest='constitutiveResult', \
+group_general.add_option('--co', action='extend', dest='constitutiveResult',
-                         help='constitutive results to extract', metavar='<LIST>')
+                         help='constitutive results to extract', metavar='<string LIST>')
 
 parser.add_option_group(group_material)
 parser.add_option_group(group_general)

processing/post/vtk2ang.py

@@ -81,30 +81,39 @@ Builds a ang files from a vtk file.
 """, version = scriptID)
 
 
-parser.add_option('--disp','--displacement',dest='dispLabel', \
+parser.add_option('--disp','--displacement',dest='dispLabel', 
+                                            metavar ='string',
                                             help='label of displacements [%default]')
-parser.add_option('--euler',                dest='eulerLabel', nargs=3, \
+parser.add_option('--euler',                dest='eulerLabel', nargs=3,
+                                            metavar ='string string string',
                                             help='labels of euler angles [%default]')
-parser.add_option('-n','--normal',          dest='normal', type='float', nargs=3, \
+parser.add_option('-n','--normal',          dest='normal', type='float', nargs=3,
+                                            metavar ='float float float',
                                             help='normal of slices in direction of increasing slice numbers [%default]')
 parser.add_option('-u','--up',              dest='up', type='float', nargs=3,
+                                            metavar ='float float float',
                                             help='up direction of slices [%default]')
-parser.add_option('-i','--slices',          dest='Nslices', type='int', \
+parser.add_option('-i','--slices',          dest='Nslices', type='int',
+                                            metavar ='int',
                                             help='number of slices [%default]')
-parser.add_option('-d','--distance',        dest='distance', type='float', \
+parser.add_option('-d','--distance',        dest='distance', type='float',
+                                            metavar ='float',
                                             help='slice distance [%default]')
-parser.add_option('-s','--scale',           dest='scale', type='float', \
+parser.add_option('-s','--scale',           dest='scale', type='float',
+                                            metavar ='float',
                                             help='scale length from vtk file [%default]')
 parser.add_option('-r','--resolution',      dest='resolution', type='float',
+                                            metavar ='float',
                                             help='scaling factor for resolution [%default]')
 parser.add_option('--hex','--hexagonal',    dest='hexagonal', action='store_true',
-                                            help='use in plane hexagonal grid [%default]')
+                                            help='use in plane hexagonal grid')
-parser.add_option('--interpolation',        dest='interpolation', type='int', \
+parser.add_option('--interpolation',        dest='interpolation', type='int',
+                                            metavar='float',
                                             help='number of points for linear interpolation [%default]')
 parser.add_option('--verbose',              dest='verbose', action='store_true',
-                                            help='verbose mode [%default]')
+                                            help='verbose mode')
 parser.add_option('--visualize',            dest='visualize', action='store_true',
-                                            help='visualize geometry [%default]')
+                                            help='visualize geometry')
 
 parser.set_defaults(dispLabel = 'displacement')
 parser.set_defaults(eulerLabel = ['1_1_eulerangles','1_2_eulerangles','1_3_eulerangles'])

processing/post/vtk_addPointcloudData.py

@@ -30,13 +30,15 @@ parser.add_option('-r', '--render',
                   dest = 'render',
                   action = 'store_true',
                   help = 'open output in VTK render window')
-parser.add_option('-s', '--scalar',   dest='scalar', action='extend', \
+parser.add_option('-s', '--scalar',   dest='scalar', action='extend',
+                  metavar ='<string LIST>',
                   help = 'scalar values')
 parser.add_option('-v', '--vector',
                   dest = 'vector',
                   action = 'extend', metavar = '<string LIST>',
                   help = 'vector value label(s)')
-parser.add_option('-c', '--color',   dest='color', action='extend', \
+parser.add_option('-c', '--color',   dest='color', action='extend',
+                  metavar ='<string LIST>',
                   help = 'RGB color tuples')
 
 parser.set_defaults(scalar = [],

processing/post/vtk_rectilinearGrid.py

@@ -21,6 +21,7 @@ Create regular voxel grid from points in an ASCIItable.
 parser.add_option('-m',
                   '--mode',
                   dest = 'mode',
+                  metavar='string',
                   type = 'choice', choices = ['cell','point'],
                   help = 'cell-centered or point-centered coordinates')
 parser.add_option('-p',

processing/pre/OIMlinear2linearODF.py

@@ -23,6 +23,7 @@ Transform the binned texture data from "TSL OIM Analysis" into linear ODF data,
 """, version = scriptID)
 
 parser.add_option('-s', '--symmetry', dest='symmetry', choices=sampleSym.keys(),
+                  metavar = 'string',
                   help='Sample symmetry {%s} [Triclinic]'%(' '.join(sampleSym.keys())))
                                      
 parser.set_defaults(symmetry = 'Triclinic')

processing/pre/abq_addUserOutput.py

@@ -49,7 +49,7 @@ def ParseOutputFormat(filename,what,me):
   return format
 
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] Abaqus.Inputfile(s)', description = """
 Transfer the output variables requested in the material.config to
 properly labelled user defined variables within the Abaqus input file (*.inp).
 

processing/pre/geom_addPrimitive.py

@@ -27,7 +27,7 @@ mappings = {
         'microstructures': lambda x: int(x),
           }
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
 Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description.
 Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids.
 

processing/pre/geom_canvas.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
 Changes the (three-dimensional) canvas of a spectral geometry description.
 Grid can be given as absolute or relative values, e.g. 16 16 16 or 2x 0.5x 32.
 

processing/pre/geom_clean.py

@@ -18,7 +18,7 @@ def mostFrequent(arr):
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
 Smooth geometry by selecting most frequent microstructure index within given stencil at each location.
 
 """, version=scriptID)

processing/pre/geom_fromMinimalSurface.py

@@ -21,7 +21,7 @@ surface = {
             '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', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] [geomfile]', description = """
 Generate a geometry file of a bicontinuous structure of given type.
 
 """, version = scriptID)

processing/pre/geom_fromOsteonGeometry.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] [geomfile]', description = """
 Generate a geometry file of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
 The osteon phase is lamellar with a twisted plywood structure.
 Its fiber orientation is oscillating by +/- amplitude within one period.

processing/pre/geom_fromTable.py

@@ -15,7 +15,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
 Generate geometry description and material configuration from position, phase, and orientation (or microstructure) data.
 
 """, version = scriptID)

processing/pre/geom_fromVoronoiTessellation.py

@@ -104,8 +104,8 @@ def laguerreTessellation(undeformed, coords, weights, grains, nonperiodic = Fals
 #                                MAIN
 # --------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [seedfile(s)]', description = """
-Generate geometry description and material configuration by standard Voronoi tessellation of given seeds file.
+Generate geometry description and material configuration by tessellation of given seeds file.
 
 """, version = scriptID)
 

processing/pre/geom_grainGrowth.py

@@ -14,7 +14,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] [geomfile(s)]', description = """
 Smoothens out interface roughness by simulated curvature flow.
 This is achieved by the diffusion of each initially sharply bounded grain volume within the periodic domain
 up to a given distance 'd' voxels.
@@ -28,7 +28,7 @@ parser.add_option('-N', '--smooth', dest='N', type='int', metavar='int',
                  help='N for curvature flow [%default]')
 parser.add_option('-r', '--renumber', dest='renumber', action='store_true',
                   help='renumber microstructure indices from 1...N [%default]')
-parser.add_option('-i', '--immutable', action='extend', dest='immutable', metavar = '<LIST>',
+parser.add_option('-i', '--immutable', action='extend', dest='immutable', metavar = '<int LIST>',
                   help='list of immutable microstructures')
 
 parser.set_defaults(d = 1)

processing/pre/geom_pack.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
 compress geometry files with ranges "a to b" and/or multiples "n of x".
 
 """, version = scriptID)

processing/pre/geom_rescale.py

@@ -13,7 +13,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
 Scales a geometry description independently in x, y, and z direction in terms of grid and/or size.
 Either absolute values or relative factors (like "0.25x") can be used.
 

processing/pre/geom_rotate.py

@@ -14,7 +14,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
 Rotates spectral geometry description.
 
 """, version=scriptID)

processing/pre/geom_toTable.py

@@ -14,7 +14,7 @@ scriptID   = ' '.join([scriptName,damask.version])
 #                                MAIN
 #--------------------------------------------------------------------------------------------------
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile[s]]', description = """
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
 Translate geom description into ASCIItable containing 1/2/3_pos and microstructure.
 
 """, version = scriptID)

processing/pre/marc_addUserOutput.py

@@ -55,7 +55,7 @@ def ParseOutputFormat(filename,what,me):
           format['outputs'].append([output,length])
   return format
 
-parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] Marc.inputfile(s)', description="""
+parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] Marc.Inputfile(s)', description="""
 Transfer the output variables requested in the material.config to
 properly labelled user defined variables within the Marc input file (*.dat).
 
@@ -70,20 +70,26 @@ Or have an existing set of user variables copied over from another *.dat file.
 
 
 parser.add_option('-n','--number', dest='number', type='int', \
+          metavar='int',
           help='maximum requested User Defined Variable [%default]')
 parser.add_option('--homogenization', dest='homog', \
+          metavar='string',
           help='homogenization identifier (as string or integer [%default])')
 parser.add_option('--crystallite', dest='cryst', \
+          metavar='string',
           help='crystallite identifier (as string or integer [%default])')
 parser.add_option('--phase', dest='phase', \
+          metavar='string',
           help='phase identifier (as string or integer [%default])')
 parser.add_option('--use', dest='useFile', \
+          metavar='string',
           help='Optionally parse output descriptors from '+
                'different <model_job>.outputZZZ file. Saves the effort '+
-               'to start a calculation for each job [%default])')
+               'to start a calculation for each job)')
 parser.add_option('--option', dest='damaskOption', \
+          metavar='string',
           help='Add damask option to input file '+
-               'for example: "periodic x z" [%default]')
+               'for example: "periodic x z"')
 parser.set_defaults(number = 0)
 parser.set_defaults(homog = '1')
 parser.set_defaults(cryst = '1')

processing/pre/table_fromOIMgrainFile.py

@@ -19,6 +19,7 @@ Adds header to OIM grain file to make it accesible as ASCII table
 
 parser.add_option('-l', '--labels',
                   dest   = 'labels',
+                  action = 'extend', metavar = '<string LIST>',
                   help   = 'lables of requested columns')
 
 parser.set_defaults(labels = ['1_euler','2_euler','3_euler',