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

This commit is contained in:
Aritra Chakraborty 2016-05-16 19:45:57 -04:00
parent 4a273f9cb3 49b02ac1f2
commit 8540748220
22 changed files with 119 additions and 90 deletions
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2
processing/post/3Dvisualize.py
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@ -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

33
processing/post/mentat_colorMap.py
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@ -68,26 +68,29 @@ Interpolates colors between "lower_hsl" and "upper_hsl".
""", version = scriptID)
parser.add_option("-i","--inverse", action = "store_true",
dest = "inverse", \
help = "invert legend [%default]")
dest = "inverse",
help = "invert legend")
parser.add_option( "--palette", action = "store_true",
dest = "palette", \
help = "output plain rgb palette integer values (0-255) [%default]")
dest = "palette",
help = "output plain rgb palette integer values (0-255)")
parser.add_option( "--palettef", action = "store_true",
dest = "palettef", \
help = "output plain rgb palette float values (0.0-1.0) [%default]")
parser.add_option("-p", "--port", type = "int",\
dest = "port",\
dest = "palettef",
help = "output plain rgb palette float values (0.0-1.0)")
parser.add_option("-p", "--port", type = "int",
dest = "port",
metavar ='int',
help = "Mentat connection port [%default]")
parser.add_option("-b", "--baseindex", type = "int",\
dest = "baseIdx",\
parser.add_option("-b", "--baseindex", type = "int",
metavar ='int',
dest = "baseIdx",
help = "base index of colormap [%default]")
parser.add_option("-n", "--colorcount", type = "int",\
dest = "colorcount",\
parser.add_option("-n", "--colorcount", type = "int",
metavar ='int',
dest = "colorcount",
help = "number of colors [%default]")
parser.add_option("-v", "--verbose", action="store_true",\
dest = "verbose",\
help = "write Mentat command stream also to STDOUT [%default]")
parser.add_option("-v", "--verbose", action="store_true",
dest = "verbose",
help = "write Mentat command stream also to STDOUT")
parser.set_defaults(port = 40007)
parser.set_defaults(baseIdx = 32)

90
processing/post/postResults.py
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@ -643,63 +643,69 @@ of already processed data points for evaluation.
""", version = scriptID)
parser.add_option('-i','--info', action='store_true', dest='info', \
help='list contents of resultfile [%default]')
parser.add_option('-l','--legacy', action='store_true', dest='legacy', \
parser.add_option('-i','--info', action='store_true', dest='info',
help='list contents of resultfile')
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', \
help='data is extrapolated to nodal value [%default]')
parser.add_option( '--prefix', dest='prefix', \
help='prefix to result file name [%default]')
parser.add_option( '--suffix', dest='suffix', \
help='suffix to result file name [%default]')
parser.add_option('-d','--dir', dest='dir', \
parser.add_option('-n','--nodal', action='store_true', dest='nodal',
help='data is extrapolated to nodal value')
parser.add_option( '--prefix', dest='prefix',
metavar='string',
help='prefix to result file name')
parser.add_option( '--suffix', dest='suffix',
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', \
help='split output per increment [%default]')
parser.add_option('-r','--range', dest='range', type='int', nargs=3, \
parser.add_option('-s','--split', action='store_true', dest='separateFiles',
help='split output per increment')
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', \
help='switch to increment range [%default]')
parser.add_option('-m','--map', dest='func', \
parser.add_option('--increments', action='store_true', dest='getIncrements',
help='switch to increment range')
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', \
help='homogenization identifier (as string or integer [%default])', metavar='<ID>')
group_material.add_option('--crystallite', dest='cryst', \
help='crystallite identifier (as string or integer [%default])', metavar='<ID>')
group_material.add_option('--phase', dest='phase', \
help='phase identifier (as string or integer [%default])', metavar='<ID>')
group_material.add_option('--homogenization', dest='homog',
help='homogenization identifier (as string or integer [%default])', metavar='string')
group_material.add_option('--crystallite', dest='cryst',
help='crystallite identifier (as string or integer [%default])', metavar='string')
group_material.add_option('--phase', dest='phase',
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', \
help='condition(s) to filter results [%default]', metavar='<CODE>')
group_special.add_option('--separation', action='extend', dest='sep', \
help='properties to separate results [%default]', metavar='<LIST>')
group_special.add_option('--sort', action='extend', dest='sort', \
help='properties to sort results [%default]', metavar='<LIST>')
group_special.add_option('-f','--filter', dest='filter',
help='condition(s) to filter results [%default]', metavar='string')
group_special.add_option('--separation', action='extend', dest='sep',
help='properties to separate results [%default]', metavar='<string LIST>')
group_special.add_option('--sort', action='extend', dest='sort',
help='properties to sort results [%default]', metavar='<string LIST>')
group_general = OptionGroup(parser,'General outputs')
group_general.add_option('--ns', action='extend', dest='nodalScalar', \
help='nodal scalars to extract', metavar='<LIST>')
group_general.add_option('--es', action='extend', dest='elemScalar', \
help='elemental scalars to extract', metavar='<LIST>')
group_general.add_option('--et', action='extend', dest='elemTensor', \
help='elemental tensors to extract', metavar='<LIST>')
group_general.add_option('--ho', action='extend', dest='homogenizationResult', \
help='homogenization results to extract', metavar='<LIST>')
group_general.add_option('--cr', action='extend', dest='crystalliteResult', \
help='crystallite results to extract', metavar='<LIST>')
group_general.add_option('--co', action='extend', dest='constitutiveResult', \
help='constitutive results to extract', metavar='<LIST>')
group_general.add_option('--ns', action='extend', dest='nodalScalar',
help='nodal scalars to extract', metavar='<string LIST>')
group_general.add_option('--es', action='extend', dest='elemScalar',
help='elemental scalars to extract', metavar='<string LIST>')
group_general.add_option('--et', action='extend', dest='elemTensor',
help='elemental tensors to extract', metavar='<string LIST>')
group_general.add_option('--ho', action='extend', dest='homogenizationResult',
help='homogenization results to extract', metavar='<string LIST>')
group_general.add_option('--cr', action='extend', dest='crystalliteResult',
help='crystallite results to extract', metavar='<string LIST>')
group_general.add_option('--co', action='extend', dest='constitutiveResult',
help='constitutive results to extract', metavar='<string LIST>')
parser.add_option_group(group_material)
parser.add_option_group(group_general)

29
processing/post/vtk2ang.py
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@ -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]')
parser.add_option('--interpolation', dest='interpolation', type='int', \
help='use in plane hexagonal grid')
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'])

6
processing/post/vtk_addPointcloudData.py
View File

@ -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 = [],

1
processing/post/vtk_rectilinearGrid.py
View File

@ -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',

3
processing/pre/OIMlinear2linearODF.py
View File

@ -23,7 +23,8 @@ 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(),
help='Sample symmetry {%s} [Triclinic]'%(' '.join(sampleSym.keys())))
metavar = 'string',
help='Sample symmetry {%s} [Triclinic]'%(' '.join(sampleSym.keys())))
parser.set_defaults(symmetry = 'Triclinic')

2
processing/pre/abq_addUserOutput.py
View File

@ -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).

2
processing/pre/geom_addPrimitive.py
View File

@ -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.

2
processing/pre/geom_canvas.py
View File

@ -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.

2
processing/pre/geom_clean.py
View File

@ -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)

2
processing/pre/geom_fromMinimalSurface.py
View File

@ -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)

2
processing/pre/geom_fromOsteonGeometry.py
View File

@ -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.

2
processing/pre/geom_fromTable.py
View File

@ -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)

4
processing/pre/geom_fromVoronoiTessellation.py
View File

@ -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 = """
Generate geometry description and material configuration by standard Voronoi tessellation of given seeds file.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [seedfile(s)]', description = """
Generate geometry description and material configuration by tessellation of given seeds file.
""", version = scriptID)

4
processing/pre/geom_grainGrowth.py
View File

@ -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)

2
processing/pre/geom_pack.py
View File

@ -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)

2
processing/pre/geom_rescale.py
View File

@ -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.

2
processing/pre/geom_rotate.py
View File

@ -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)

2
processing/pre/geom_toTable.py
View File

@ -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)

12
processing/pre/marc_addUserOutput.py
View File

@ -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')

1
processing/pre/table_fromOIMgrainFile.py
View File

@ -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',