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DAMASK_EICMD
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not needed anymore

This commit is contained in:
Martin Diehl 2016-03-24 18:47:11 +01:00
parent 04d2148e61
commit 7423c1a06a
2 changed files with 0 additions and 267 deletions
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61
processing/post/addCauchyX.py
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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,string,h5py
import numpy as np
from optparse import OptionParser
import damask
# --------------------------------------------------------------------
# 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.
""" + string.replace('$Id$','\n','\\n')
)
parser.add_option('-f','--defgrad', dest='defgrad', \
help='heading of columns containing deformation gradient [%default]')
parser.add_option('-p','--stress', dest='stress', \
help='heading of columns containing first Piola--Kirchhoff stress [%default]')
parser.add_option('-o','--output', dest='output', \
help='group containing requested data [%default]')
parser.set_defaults(defgrad = 'f')
parser.set_defaults(stress = 'p')
parser.set_defaults(output = 'crystallite')
(options,filenames) = parser.parse_args()
if options.defgrad is None or options.stress is None or options.output is None:
parser.error('missing data column...')
# ------------------------------------------ setup file handles ---------------------------------------
files = []
for name in filenames:
if os.path.exists(name):
files.append({'name':name, 'file':h5py.File(name,"a")})
# ------------------------------------------ loop over input files ------------------------------------
for myFile in files:
print(myFile['name'])
# ------------------------------------------ loop over increments -------------------------------------
for inc in myFile['file']['increments'].keys():
print("Current Increment: "+inc)
for instance in myFile['file']['increments/'+inc+'/'+options.output].keys():
dsets = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance].keys()
if (options.defgrad in dsets and options.stress in dsets):
defgrad = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance+'/'+options.defgrad]
stress = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance+'/'+options.stress]
cauchy=np.zeros(np.shape(stress),'f')
for p in range(stress.shape[0]):
cauchy[p,...] = 1.0/np.linalg.det(defgrad[p,...])*np.dot(stress[p,...],defgrad[p,...].T) # [Cauchy] = (1/det(F)) * [P].[F_transpose]
cauchyFile = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance].create_dataset('cauchy', data=cauchy)
cauchyFile.attrs['units'] = 'Pa'

206
processing/pre/geom_fromAng.py
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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Generate geometry description and material configuration from EBSD data in given square-gridded 'ang' file.
Two phases can be discriminated based on threshold value in a given data column.
""", version = scriptID)
parser.add_option('--column', dest='column', type='int', metavar = 'int',
help='data column to discriminate between both phases [%default]')
parser.add_option('-t','--threshold', dest='threshold', type='float', metavar = 'float',
help='threshold value for phase discrimination [%default]')
parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int',
help='homogenization index for <microstructure> configuration [%default]')
parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int',
help='phase indices for <microstructure> configuration %default')
parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int',
help='crystallite index for <microstructure> configuration [%default]')
parser.add_option('-c','--compress', dest='compress', action='store_true',
help='lump identical microstructure and texture information [%default]')
parser.add_option('-a', '--axes', dest='axes', nargs = 3, metavar = 'string string string',
help='Euler angle coordinate system for <texture> configuration x,y,z = %default')
parser.add_option('-p', '--precision', dest='precision', choices=['0','1','2','3'], metavar = 'int',
help = 'euler angles decimal places for output format and compressing (0,1,2,3) [2]')
parser.set_defaults(column = 11,
threshold = 0.5,
homogenization = 1,
phase = [1,2],
crystallite = 1,
compress = False,
axes = ['y','x','-z'],
precision = '2',
)
(options,filenames) = parser.parse_args()
for i in options.axes:
if i.lower() not in ['x','+x','-x','y','+y','-y','z','+z','-z']:
parser.error('invalid axes %s %s %s' %(options.axes[0],options.axes[1],options.axes[2]))
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[-2]+'.geom' if name else name,
buffered = False, labeled = False)
except: continue
damask.util.report(scriptName,name)
info = {
'grid': np.ones(3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
'microstructures': 0,
'homogenization': options.homogenization
}
coords = [{},{},{1:True}]
pos = {'min':[ float("inf"), float("inf")],
'max':[-float("inf"),-float("inf")]}
phase = []
eulerangles = []
# --------------- read data -----------------------------------------------------------------------
errors = []
while table.data_read():
words = table.data
if words[0] == '#': # process initial comments/header block
if len(words) > 2:
if words[2].lower() == 'hexgrid':
errors.append('The file has HexGrid format. Please first convert to SquareGrid...')
break
else:
currPos = words[3:5]
for i in xrange(2):
coords[i][currPos[i]] = True
currPos = map(float,currPos)
for i in xrange(2):
pos['min'][i] = min(pos['min'][i],currPos[i])
pos['max'][i] = max(pos['max'][i],currPos[i])
eulerangles.append(map(math.degrees,map(float,words[:3])))
phase.append(options.phase[int(float(words[options.column-1]) > options.threshold)])
if errors != []:
damask.util.croak(errors)
continue
# --------------- determine size and grid ---------------------------------------------------------
info['grid'] = np.array(map(len,coords),'i')
info['size'][0:2] = info['grid'][0:2]/(info['grid'][0:2]-1.0)* \
np.array([pos['max'][0]-pos['min'][0],
pos['max'][1]-pos['min'][1]],'d')
info['size'][2]=info['size'][0]/info['grid'][0]
eulerangles = np.array(eulerangles,dtype='f').reshape(info['grid'].prod(),3)
phase = np.array(phase,dtype='i').reshape(info['grid'].prod())
limits = [360,180,360]
if any([np.any(eulerangles[:,i]>=limits[i]) for i in [0,1,2]]):
errors.append('Error: euler angles out of bound. Ang file might contain unidexed poins.')
for i,angle in enumerate(['phi1','PHI','phi2']):
for n in np.nditer(np.where(eulerangles[:,i]>=limits[i]),['zerosize_ok']):
errors.append('%s in line %i (%4.2f %4.2f %4.2f)\n'
%(angle,n,eulerangles[n,0],eulerangles[n,1],eulerangles[n,2]))
if errors != []:
damask.util.croak(errors)
continue
eulerangles=np.around(eulerangles,int(options.precision)) # round to desired precision
# ensure, that rounded euler angles are not out of bounds (modulo by limits)
for i,angle in enumerate(['phi1','PHI','phi2']):
eulerangles[:,i]%=limits[i]
# scale angles by desired precision and convert to int. create unique integer key from three euler angles by
# concatenating the string representation with leading zeros and store as integer and search unique euler angle keys.
# Texture IDs are the indices of the first occurrence, the inverse is used to construct the microstructure
# create a microstructure (texture/phase pair) for each point using unique texture IDs.
# Use longInt (64bit, i8) because the keys might be long
if options.compress:
formatString='{0:0>'+str(int(options.precision)+3)+'}'
euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int')
eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \
for i in xrange(info['grid'].prod())])
devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)
msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8')
devNull,msUnique,matPoints = np.unique(msFull.view('c16'),True,True)
matPoints+=1
microstructure = np.array([msFull[i] for i in msUnique]) # pick only unique microstructures
else:
texture = np.arange(info['grid'].prod())
microstructure = np.hstack( zip(texture,phase) ).reshape(info['grid'].prod(),2) # create texture/phase pairs
formatOut = 1+int(math.log10(len(texture)))
textureOut =['<texture>']
eulerFormatOut='%%%i.%if'%(int(options.precision)+4,int(options.precision))
outStringAngles='(gauss) phi1 '+eulerFormatOut+' Phi '+eulerFormatOut+' phi2 '+eulerFormatOut+' scatter 0.0 fraction 1.0'
for i in xrange(len(texture)):
textureOut += ['[Texture%s]'%str(i+1).zfill(formatOut),
'axes %s %s %s'%(options.axes[0],options.axes[1],options.axes[2]),
outStringAngles%tuple(eulerangles[texture[i],...])
]
formatOut = 1+int(math.log10(len(microstructure)))
microstructureOut =['<microstructure>']
for i in xrange(len(microstructure)):
microstructureOut += ['[Grain%s]'%str(i+1).zfill(formatOut),
'crystallite\t%i'%options.crystallite,
'(constituent)\tphase %i\ttexture %i\tfraction 1.0'%(microstructure[i,1],microstructure[i,0]+1)
]
info['microstructures'] = len(microstructure)
#--- report ---------------------------------------------------------------------------------------
damask.util.croak('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) +
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) +
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) +
'homogenization: %i\n'%info['homogenization'] +
'microstructures: %i\n\n'%info['microstructures'])
if np.any(info['grid'] < 1):
damask.util.croak('invalid grid a b c.\n')
continue
if np.any(info['size'] <= 0.0):
damask.util.croak('invalid size x y z.\n')
continue
#--- write data/header --------------------------------------------------------------------------------
table.info_clear()
table.info_append([' '.join([scriptID] + sys.argv[1:]),
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
"microstructures\t%i"%info['microstructures'],
"homogenization\t%i"%info['homogenization'],
] +
[line for line in microstructureOut + textureOut]
)
table.head_write()
if options.compress:
matPoints = matPoints.reshape((info['grid'][1],info['grid'][0]))
table.data = matPoints
table.data_writeArray('%%%ii'%(1+int(math.log10(np.amax(matPoints)))),delimiter=' ')
else:
table.output_write("1 to %i\n"%(info['microstructures']))
table.output_flush()
# --- output finalization --------------------------------------------------------------------------
table.close()