Merge branch '26_autodoc-2' into development
This commit is contained in:
commit
d2a9f55aaa
|
@ -482,24 +482,40 @@ AbaqusStd:
|
|||
script:
|
||||
- module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
|
||||
- $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT abaqus
|
||||
only:
|
||||
- development
|
||||
except:
|
||||
- master
|
||||
- release
|
||||
|
||||
Marc:
|
||||
stage: createDocumentation
|
||||
script:
|
||||
- module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
|
||||
- $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT marc
|
||||
only:
|
||||
- development
|
||||
except:
|
||||
- master
|
||||
- release
|
||||
|
||||
Spectral:
|
||||
stage: createDocumentation
|
||||
script:
|
||||
- module load $IntelCompiler $MPICH_Intel $PETSc_MPICH_Intel $Doxygen
|
||||
- $DAMASKROOT/PRIVATE/documenting/runDoxygen.sh $DAMASKROOT spectral
|
||||
only:
|
||||
- development
|
||||
except:
|
||||
- master
|
||||
- release
|
||||
|
||||
Processing:
|
||||
stage: createDocumentation
|
||||
script:
|
||||
- cd $DAMASKROOT/processing/pre
|
||||
- rm 3DRVEfrom2Dang.py abq_addUserOutput.py marc_addUserOutput.py
|
||||
- $DAMASKROOT/PRIVATE/documenting/scriptHelpToWiki.py --debug *.py
|
||||
- cd $DAMASKROOT/processing/post
|
||||
- rm marc_to_vtk.py vtk2ang.py
|
||||
- $DAMASKROOT/PRIVATE/documenting/scriptHelpToWiki.py --debug *.py
|
||||
except:
|
||||
- master
|
||||
- release
|
||||
|
||||
##################################################################################################
|
||||
backupData:
|
||||
|
|
2
PRIVATE
2
PRIVATE
|
@ -1 +1 @@
|
|||
Subproject commit 18ba1ba6a5e9ba446dc9311acf2acf2781614db1
|
||||
Subproject commit ddb0dae72af9012cca45d9fa5665da41815e88f7
|
|
@ -14,19 +14,14 @@ 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 [ASCIItable(s)]', description = """
|
||||
Transform X,Y,Z,F APS BeamLine 34 coordinates to x,y,z APS strain coordinates.
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-f',
|
||||
'--frame',
|
||||
dest='frame',
|
||||
metavar='string',
|
||||
help='APS X,Y,Z coords')
|
||||
parser.add_option('--depth',
|
||||
dest='depth',
|
||||
metavar='string',
|
||||
parser.add_option('-f','--frame',dest='frame', metavar='string',
|
||||
help='label of APS X,Y,Z coords')
|
||||
parser.add_option('--depth', dest='depth', metavar='string',
|
||||
help='depth')
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
|
|
@ -18,7 +18,7 @@ def listify(x):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add or alter column(s) with derived values according to user-defined arithmetic operation between column(s).
|
||||
Column labels are tagged by '#label#' in formulas. Use ';' for ',' in functions.
|
||||
Numpy is available as 'np'.
|
||||
|
@ -41,10 +41,7 @@ parser.add_option('-f','--formula',
|
|||
|
||||
parser.add_option('-c','--condition',
|
||||
dest = 'condition', metavar='string',
|
||||
help = 'condition to alter existing column data')
|
||||
|
||||
parser.set_defaults(condition = None,
|
||||
)
|
||||
help = 'condition to alter existing column data (optional)')
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
|
|
|
@ -13,8 +13,8 @@ scriptID = ' '.join([scriptName,damask.version])
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Add column(s) containing Cauchy stress based on given column(s) of deformation gradient and first Piola--Kirchhoff stress.
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add column containing Cauchy stress based on deformation gradient and first Piola--Kirchhoff stress.
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
|
|
|
@ -209,7 +209,7 @@ def shapeMismatch(size,F,nodes,centres):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add column(s) containing the shape and volume mismatch resulting from given deformation gradient.
|
||||
Operates on periodic three-dimensional x,y,z-ordered data sets.
|
||||
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Add cumulative (sum of first to current row) values for given label(s).
|
||||
""", version = scriptID)
|
||||
|
||||
|
@ -22,12 +22,9 @@ parser.add_option('-l','--label',
|
|||
action = 'extend', metavar = '<string LIST>',
|
||||
help = 'columns to cumulate')
|
||||
|
||||
parser.set_defaults(label = [],
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
if len(options.label) == 0:
|
||||
if options.label is None:
|
||||
parser.error('no data column(s) specified.')
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
|
|
@ -49,14 +49,14 @@ def curlFFT(geomdim,field):
|
|||
|
||||
curl_fourier = np.einsum(einsums[n],e,k_s,field_fourier)*TWOPIIMG
|
||||
|
||||
return np.fft.irfftn(curl_fourier,s=shapeFFT,axes=(0,1,2)).reshape([N,n])
|
||||
return np.fft.irfftn(curl_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n])
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add column(s) containing curl of requested column(s).
|
||||
Operates on periodic ordered three-dimensional data sets
|
||||
of vector and tensor fields.
|
||||
|
|
|
@ -34,7 +34,7 @@ def derivative(coordinates,what):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add column(s) containing numerical derivative of requested column(s) with respect to given coordinates.
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -20,7 +20,7 @@ def determinant(m):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add column(s) containing determinant of requested tensor column(s).
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -23,7 +23,7 @@ def deviator(m,spherical = False):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(2)]', description = """
|
||||
Add column(s) containing deviator of requested tensor column(s).
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -87,7 +87,7 @@ def displacementFluctFFT(F,grid,size,nodal=False,transformed=False):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] [ASCIItable(s)]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add displacments resulting from deformation gradient field.
|
||||
Operates on periodic three-dimensional x,y,z-ordered data sets.
|
||||
Outputs at cell centers or cell nodes (into separate file).
|
||||
|
@ -111,7 +111,6 @@ parser.add_option('--nodal',
|
|||
|
||||
parser.set_defaults(defgrad = 'f',
|
||||
pos = 'pos',
|
||||
nodal = False,
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
|
|
@ -45,7 +45,7 @@ def divFFT(geomdim,field):
|
|||
|
||||
div_fourier = np.einsum(einsums[n],k_s,field_fourier)*TWOPIIMG
|
||||
|
||||
return np.fft.irfftn(div_fourier,s=shapeFFT,axes=(0,1,2)).reshape([N,n//3])
|
||||
return np.fft.irfftn(div_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n//3])
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
|
|
@ -30,7 +30,7 @@ def E_hkl(stiffness,vec): # stiffness = (c11,c12,c44)
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add column(s) containing directional stiffness based on given cubic stiffness values C11, C12, and C44 in consecutive columns.
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -83,7 +83,7 @@ neighborhoods = {
|
|||
])
|
||||
}
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add column(s) containing Euclidean distance to grain structural features: boundaries, triple lines, and quadruple points.
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -15,7 +15,7 @@ scriptID = ' '.join([scriptName,damask.version])
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [ASCIItable(s)]', description = """
|
||||
Add column(s) containing Gaussian filtered values of requested column(s).
|
||||
Operates on periodic and non-periodic ordered three-dimensional data sets.
|
||||
For details see scipy.ndimage documentation.
|
||||
|
@ -34,12 +34,12 @@ parser.add_option('-o','--order',
|
|||
dest = 'order',
|
||||
type = int,
|
||||
metavar = 'int',
|
||||
help = 'order of the filter')
|
||||
help = 'order of the filter [%default]')
|
||||
parser.add_option('--sigma',
|
||||
dest = 'sigma',
|
||||
type = float,
|
||||
metavar = 'float',
|
||||
help = 'standard deviation')
|
||||
help = 'standard deviation [%default]')
|
||||
parser.add_option('--periodic',
|
||||
dest = 'periodic',
|
||||
action = 'store_true',
|
||||
|
@ -50,7 +50,6 @@ parser.add_option('--periodic',
|
|||
parser.set_defaults(pos = 'pos',
|
||||
order = 0,
|
||||
sigma = 1,
|
||||
periodic = False,
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
|
|
@ -45,14 +45,14 @@ def gradFFT(geomdim,field):
|
|||
k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3).astype('c16')
|
||||
grad_fourier = np.einsum(einsums[n],field_fourier,k_s)*TWOPIIMG
|
||||
|
||||
return np.fft.irfftn(grad_fourier,s=shapeFFT,axes=(0,1,2)).reshape([N,3*n])
|
||||
return np.fft.irfftn(grad_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,3*n])
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [ASCIItable(s)]', description = """
|
||||
Add column(s) containing gradient of requested column(s).
|
||||
Operates on periodic ordered three-dimensional data sets
|
||||
of vector and scalar fields.
|
||||
|
|
|
@ -28,9 +28,9 @@ parser.add_option('-d',
|
|||
help = 'disorientation threshold in degrees [%default]')
|
||||
parser.add_option('-s',
|
||||
'--symmetry',
|
||||
dest = 'symmetry',
|
||||
dest = 'symmetry', type = 'choice', choices = damask.Symmetry.lattices[1:],
|
||||
metavar = 'string',
|
||||
help = 'crystal symmetry [%default]')
|
||||
help = 'crystal symmetry [%default] {{{}}} '.format(', '.join(damask.Symmetry.lattices[1:])))
|
||||
parser.add_option('-o',
|
||||
'--orientation',
|
||||
dest = 'quaternion',
|
||||
|
@ -49,7 +49,7 @@ parser.add_option('--quiet',
|
|||
parser.set_defaults(disorientation = 5,
|
||||
verbose = True,
|
||||
quaternion = 'orientation',
|
||||
symmetry = 'cubic',
|
||||
symmetry = damask.Symmetry.lattices[-1],
|
||||
pos = 'pos',
|
||||
)
|
||||
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Add RGB color value corresponding to TSL-OIM scheme for inverse pole figures.
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Add data in column(s) of mapped ASCIItable selected from the row indexed by the value in a mapping column.
|
||||
Row numbers start at 1.
|
||||
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Add info lines to ASCIItable header.
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -23,11 +23,12 @@ parser.add_option('-i',
|
|||
dest = 'info', action = 'extend', metavar = '<string LIST>',
|
||||
help = 'items to add')
|
||||
|
||||
parser.set_defaults(info = [],
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
if options.info is None:
|
||||
parser.error('no info specified.')
|
||||
|
||||
# --- loop over input files ------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Add data of selected column(s) from (first) row of linked ASCIItable that shares the linking column value.
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -24,7 +24,7 @@ def Mises(what,tensor):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add vonMises equivalent values for symmetric part of requested strains and/or stresses.
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -38,13 +38,9 @@ parser.add_option('-s','--stress',
|
|||
action = 'extend', metavar = '<string LIST>',
|
||||
help = 'heading(s) of columns containing stress tensors')
|
||||
|
||||
parser.set_defaults(strain = [],
|
||||
stress = [],
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
if len(options.stress+options.strain) == 0:
|
||||
if options.stress is None and options.strain is None:
|
||||
parser.error('no data column specified...')
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
|
|
@ -9,6 +9,7 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
|||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
# definition of element-wise p-norms for matrices
|
||||
# ToDo: better use numpy.linalg.norm
|
||||
|
||||
def norm(which,object):
|
||||
|
||||
|
@ -18,12 +19,14 @@ def norm(which,object):
|
|||
return math.sqrt(sum([x*x for x in object]))
|
||||
elif which == 'Max': # p = inf
|
||||
return max(map(abs, object))
|
||||
else:
|
||||
return -1
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add column(s) containing norm of requested column(s) being either vectors or tensors.
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -43,6 +46,8 @@ parser.set_defaults(norm = 'frobenius',
|
|||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
if options.norm.lower() not in normChoices:
|
||||
parser.error('invalid norm ({}) specified.'.format(options.norm))
|
||||
if options.label is None:
|
||||
parser.error('no data column specified.')
|
||||
|
||||
|
|
|
@ -38,7 +38,7 @@ def check_matrix(M):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add quaternion and/or Bunge Euler angle representation of crystal lattice orientation.
|
||||
Orientation is given by quaternion, Euler angles, rotation matrix, or crystal frame coordinates
|
||||
(i.e. component vectors of rotation matrix).
|
||||
|
@ -68,12 +68,12 @@ parser.add_option('-R',
|
|||
'--labrotation',
|
||||
dest='labrotation',
|
||||
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
|
||||
help = 'angle and axis of additional lab frame rotation')
|
||||
help = 'angle and axis of additional lab frame rotation [%default]')
|
||||
parser.add_option('-r',
|
||||
'--crystalrotation',
|
||||
dest='crystalrotation',
|
||||
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
|
||||
help = 'angle and axis of additional crystal frame rotation')
|
||||
help = 'angle and axis of additional crystal frame rotation [%default]')
|
||||
parser.add_option('--eulers',
|
||||
dest = 'eulers',
|
||||
metavar = 'string',
|
||||
|
@ -106,7 +106,6 @@ parser.add_option('-z',
|
|||
parser.set_defaults(output = [],
|
||||
labrotation = (0.,1.,1.,1.), # no rotation about 1,1,1
|
||||
crystalrotation = (0.,1.,1.,1.), # no rotation about 1,1,1
|
||||
degrees = False,
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Add column(s) containing Second Piola--Kirchhoff stress based on given column(s) of deformation
|
||||
gradient and first Piola--Kirchhoff stress.
|
||||
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Add coordinates of stereographic projection of given direction (pole) in crystal frame.
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -35,7 +35,6 @@ parser.add_option('-o',
|
|||
|
||||
parser.set_defaults(pole = (1.0,0.0,0.0),
|
||||
quaternion = 'orientation',
|
||||
polar = False,
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
|
|
@ -103,7 +103,7 @@ slipSystems = {
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add columns listing Schmid factors (and optional trace vector of selected system) for given Euler angles.
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -115,7 +115,7 @@ parser.add_option('-l',
|
|||
help = 'type of lattice structure [%default] {}'.format(latticeChoices))
|
||||
parser.add_option('--covera',
|
||||
dest = 'CoverA', type = 'float', metavar = 'float',
|
||||
help = 'C over A ratio for hexagonal systems')
|
||||
help = 'C over A ratio for hexagonal systems [%default]')
|
||||
parser.add_option('-f',
|
||||
'--force',
|
||||
dest = 'force',
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Add column(s) containing eigenvalues and eigenvectors of requested symmetric tensor column(s).
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -25,7 +25,7 @@ def operator(stretch,strain,eigenvalues):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Add column(s) containing given strains based on given stretches of requested deformation gradient column(s).
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -56,16 +56,15 @@ parser.add_option('-f','--defgrad',
|
|||
metavar = '<string LIST>',
|
||||
help = 'heading(s) of columns containing deformation tensor values [%default]')
|
||||
|
||||
parser.set_defaults(right = False,
|
||||
left = False,
|
||||
logarithmic = False,
|
||||
biot = False,
|
||||
green = False,
|
||||
parser.set_defaults(
|
||||
defgrad = ['f'],
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
if len(options.defgrad) > 1:
|
||||
options.defgrad = options.defgrad[1:]
|
||||
|
||||
stretches = []
|
||||
strains = []
|
||||
|
||||
|
|
|
@ -12,7 +12,7 @@ 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 [ASCIItable(s)]', description = """
|
||||
Append data of ASCIItable(s).
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -24,6 +24,10 @@ parser.add_option('-a', '--add','--table',
|
|||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
if options.table is None:
|
||||
parser.error('no table specified.')
|
||||
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Average each data block of size 'packing' into single values thus reducing the former grid to grid/packing.
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -34,16 +34,14 @@ parser.add_option('--shift',
|
|||
parser.add_option('-g', '--grid',
|
||||
dest = 'grid',
|
||||
type = 'int', nargs = 3, metavar = 'int int int',
|
||||
help = 'grid in x,y,z [autodetect]')
|
||||
help = 'grid in x,y,z (optional)')
|
||||
parser.add_option('-s', '--size',
|
||||
dest = 'size',
|
||||
type = 'float', nargs = 3, metavar = 'float float float',
|
||||
help = 'size in x,y,z [autodetect]')
|
||||
help = 'size in x,y,z (optional)')
|
||||
parser.set_defaults(pos = 'pos',
|
||||
packing = (2,2,2),
|
||||
shift = (0,0,0),
|
||||
grid = (0,0,0),
|
||||
size = (0.0,0.0,0.0),
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
@ -92,7 +90,7 @@ for name in filenames:
|
|||
|
||||
table.data_readArray()
|
||||
|
||||
if (any(options.grid) == 0 or any(options.size) == 0.0):
|
||||
if (options.grid is None or options.size is None):
|
||||
grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
|
||||
else:
|
||||
grid = np.array(options.grid,'i')
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Produces a binned grid of two columns from an ASCIItable, i.e. a two-dimensional probability density map.
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -37,15 +37,15 @@ parser.add_option('-t','--type',
|
|||
parser.add_option('-x','--xrange',
|
||||
dest = 'xrange',
|
||||
type = 'float', nargs = 2, metavar = 'float float',
|
||||
help = 'min max value in x direction [autodetect]')
|
||||
help = 'min max limits in x direction (optional)')
|
||||
parser.add_option('-y','--yrange',
|
||||
dest = 'yrange',
|
||||
type = 'float', nargs = 2, metavar = 'float float',
|
||||
help = 'min max value in y direction [autodetect]')
|
||||
help = 'min max limits in y direction (optional)')
|
||||
parser.add_option('-z','--zrange',
|
||||
dest = 'zrange',
|
||||
type = 'float', nargs = 2, metavar = 'float float',
|
||||
help = 'min max value in z direction [autodetect]')
|
||||
help = 'min max limits in z direction (optional)')
|
||||
parser.add_option('-i','--invert',
|
||||
dest = 'invert',
|
||||
action = 'store_true',
|
||||
|
@ -64,9 +64,6 @@ parser.set_defaults(bins = (10,10),
|
|||
xrange = (0.0,0.0),
|
||||
yrange = (0.0,0.0),
|
||||
zrange = (0.0,0.0),
|
||||
invert = False,
|
||||
normRow = False,
|
||||
normCol = False,
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Blows up each value to a surrounding data block of size 'packing' thus increasing the former resolution
|
||||
to resolution*packing.
|
||||
|
||||
|
@ -27,10 +27,10 @@ parser.add_option('-p','--packing',
|
|||
help = 'dimension of packed group [%default]')
|
||||
parser.add_option('-g','--grid',
|
||||
dest = 'resolution', type = 'int', nargs = 3, metavar = 'int int int',
|
||||
help = 'resolution in x,y,z [autodetect]')
|
||||
help = 'grid in x,y,z (optional)')
|
||||
parser.add_option('-s','--size',
|
||||
dest = 'dimension', type = 'float', nargs = 3, metavar = 'int int int',
|
||||
help = 'dimension in x,y,z [autodetect]')
|
||||
help = 'size in x,y,z (optional)')
|
||||
parser.set_defaults(pos = 'pos',
|
||||
packing = (2,2,2),
|
||||
grid = (0,0,0),
|
||||
|
|
|
@ -30,7 +30,7 @@ def sortingList(labels,whitelistitems):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Filter rows according to condition and columns by either white or black listing.
|
||||
|
||||
Examples:
|
||||
|
|
|
@ -20,7 +20,7 @@ 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 [ASCIItable(s)]', description = """
|
||||
Apply a user-specified function to condense into a single row all those rows for which columns 'label' have identical values.
|
||||
Output table will contain as many rows as there are different (unique) values in the grouping column(s).
|
||||
Periodic domain averaging of coordinate values is supported.
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Permute all values in given column(s).
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -12,7 +12,7 @@ scriptID = ' '.join([scriptName,damask.version])
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] dfile[s]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
|
||||
Rename scalar, vectorial, and/or tensorial data header labels.
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Rotate vector and/or tensor column data by given angle around given axis.
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -29,7 +29,7 @@ parser.add_option('-r', '--rotation',
|
|||
parser.add_option('--degrees',
|
||||
dest = 'degrees',
|
||||
action = 'store_true',
|
||||
help = 'angles are given in degrees [%default]')
|
||||
help = 'angles are given in degrees')
|
||||
|
||||
parser.set_defaults(rotation = (0.,1.,1.,1.), # no rotation about 1,1,1
|
||||
degrees = False,
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Uniformly scale column values by given factor.
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Uniformly shift column values by given offset.
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Sort rows by given (or all) column label(s).
|
||||
|
||||
Examples:
|
||||
|
|
|
@ -12,7 +12,7 @@ scriptID = ' '.join([scriptName,damask.version])
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(usage='%prog [options] [file[s]]', description = """
|
||||
parser = OptionParser(usage='%prog options [ASCIItable(s)]', description = """
|
||||
Show components of given ASCIItable(s).
|
||||
|
||||
""", version = scriptID)
|
||||
|
|
|
@ -17,7 +17,7 @@ scriptID = ' '.join([scriptName,damask.version])
|
|||
msg = "Add scalars, vectors, and/or an RGB tuple from"
|
||||
msg += "an ASCIItable to existing VTK grid (.vtr/.vtk/.vtu)."
|
||||
parser = OptionParser(option_class=damask.extendableOption,
|
||||
usage='%prog options [file[s]]',
|
||||
usage='%prog options [ASCIItable(s)]',
|
||||
description = msg,
|
||||
version = scriptID)
|
||||
|
||||
|
@ -172,8 +172,7 @@ for name in filenames:
|
|||
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(rGrid)
|
||||
else: writer.SetInputData(rGrid)
|
||||
writer.SetInputData(rGrid)
|
||||
writer.Write()
|
||||
|
||||
# ------------------------------------------ render result ---------------------------------------
|
||||
|
|
|
@ -15,7 +15,7 @@ scriptID = ' '.join([scriptName,damask.version])
|
|||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption,
|
||||
usage='%prog options [file[s]]',
|
||||
usage='%prog options [ASCIItable(s)]',
|
||||
description = """Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp).""",
|
||||
version = scriptID)
|
||||
|
||||
|
@ -46,8 +46,6 @@ parser.add_option('-c', '--color', dest='color', action='extend',
|
|||
parser.set_defaults(data = [],
|
||||
tensor = [],
|
||||
color = [],
|
||||
inplace = False,
|
||||
render = False,
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
@ -151,14 +149,12 @@ for name in filenames:
|
|||
# ------------------------------------------ output result ---------------------------------------
|
||||
|
||||
Polydata.Modified()
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update()
|
||||
|
||||
writer = vtk.vtkXMLPolyDataWriter()
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtp' if options.inplace else '_added.vtp'))
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(Polydata)
|
||||
else: writer.SetInputData(Polydata)
|
||||
writer.SetInputData(Polydata)
|
||||
writer.Write()
|
||||
|
||||
# ------------------------------------------ render result ---------------------------------------
|
||||
|
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Produce a VTK point cloud dataset based on coordinates given in an ASCIItable.
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -78,7 +78,6 @@ for name in filenames:
|
|||
Polydata.SetPoints(Points)
|
||||
Polydata.SetVerts(Vertices)
|
||||
Polydata.Modified()
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: Polydata.Update()
|
||||
|
||||
# ------------------------------------------ output result ---------------------------------------
|
||||
|
||||
|
@ -94,8 +93,8 @@ for name in filenames:
|
|||
writer.SetHeader('# powered by '+scriptID)
|
||||
writer.WriteToOutputStringOn()
|
||||
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(Polydata)
|
||||
else: writer.SetInputData(Polydata)
|
||||
|
||||
writer.SetInputData(Polydata)
|
||||
|
||||
writer.Write()
|
||||
|
|
@ -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 [ASCIItable(s)]', description = """
|
||||
Create regular voxel grid from points in an ASCIItable.
|
||||
|
||||
""", version = scriptID)
|
||||
|
@ -125,8 +125,7 @@ for name in filenames:
|
|||
writer.SetHeader('# powered by '+scriptID)
|
||||
writer.WriteToOutputStringOn()
|
||||
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(rGrid)
|
||||
else: writer.SetInputData(rGrid)
|
||||
writer.SetInputData(rGrid)
|
||||
|
||||
writer.Write()
|
||||
|
||||
|
|
|
@ -25,7 +25,7 @@ mappings = {
|
|||
'microstructures': lambda x: int(x),
|
||||
}
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [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.
|
||||
|
||||
|
|
|
@ -18,7 +18,7 @@ def mostFrequent(arr):
|
|||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
|
||||
Smooth geometry by selecting most frequent microstructure index within given stencil at each location.
|
||||
|
||||
""", version=scriptID)
|
||||
|
|
|
@ -28,7 +28,7 @@ def kdtree_search(cloud, queryPoints):
|
|||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options]', description = """
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options', description = """
|
||||
Distribute given number of points randomly within (a fraction of) the three-dimensional cube [0.0,0.0,0.0]--[1.0,1.0,1.0].
|
||||
Reports positions with random crystal orientations in seeds file format to STDOUT.
|
||||
|
||||
|
|
Loading…
Reference in New Issue