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DAMASK_EICMD
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python 3 compatible and modernized

This commit is contained in:
Martin Diehl 2016-10-27 22:41:50 +02:00
parent 99dc75c2fd
commit 6d9d25ea43
1 changed files with 87 additions and 95 deletions
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182
processing/pre/patchFromReconstructedBoundaries.py
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@ -13,7 +13,7 @@ scriptID = ' '.join([scriptName,damask.version])
try: # check for Python Image Lib try: # check for Python Image Lib
from PIL import Image,ImageDraw from PIL import Image,ImageDraw
ImageCapability = True ImageCapability = True
except: except ImportError:
ImageCapability = False ImageCapability = False
sys.path.append(damask.solver.Marc().libraryPath()) sys.path.append(damask.solver.Marc().libraryPath())
@ -21,7 +21,7 @@ sys.path.append(damask.solver.Marc().libraryPath())
try: # check for MSC.Mentat Python interface try: # check for MSC.Mentat Python interface
import py_mentat import py_mentat
MentatCapability = True MentatCapability = True
except: except ImportError:
MentatCapability = False MentatCapability = False
@ -344,7 +344,7 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
else: else:
myNeighbors[grainNeighbors[leg][side]] = 1 myNeighbors[grainNeighbors[leg][side]] = 1
if myNeighbors: # do I have any neighbors (i.e., non-bounding box segment) if myNeighbors: # do I have any neighbors (i.e., non-bounding box segment)
candidateGrains = sorted(myNeighbors.items(), key=lambda (k,v): (v,k), reverse=True) # sort grain counting candidateGrains = sorted(myNeighbors.iteritems(), key=lambda p: (p[1],p[0]), reverse=True) # sort grain counting
# most frequent one not yet seen? # most frequent one not yet seen?
rcData['grainMapping'].append(candidateGrains[0 if candidateGrains[0][0] not in rcData['grainMapping'] else 1][0]) # must be me then rcData['grainMapping'].append(candidateGrains[0 if candidateGrains[0][0] not in rcData['grainMapping'] else 1][0]) # must be me then
# special case of bi-crystal situation... # special case of bi-crystal situation...
@ -647,7 +647,6 @@ def job(grainNumber,grainMapping,twoD):
"*job_param univ_gas_const 8.314472", "*job_param univ_gas_const 8.314472",
"*job_param planck_radiation_2 1.4387752e-2", "*job_param planck_radiation_2 1.4387752e-2",
"*job_param speed_light_vacuum 299792458", "*job_param speed_light_vacuum 299792458",
# "*job_usersub_file /san/%s/FEM/DAMASK/code/mpie_cpfem_marc2010.f90 | subroutine definition"%(pwd.getpwuid(os.geteuid())[0].rpartition("\\")[2]),
"*job_option user_source:compile_save", "*job_option user_source:compile_save",
] ]
@ -750,7 +749,7 @@ def inside(x,y,points):
return inside return inside
# ------------------------- # -------------------------
def fftbuild(rcData,height,xframe,yframe,resolution,extrusion): def fftbuild(rcData,height,xframe,yframe,grid,extrusion):
"""Build array of grain numbers""" """Build array of grain numbers"""
maxX = -1.*sys.maxint maxX = -1.*sys.maxint
maxY = -1.*sys.maxint maxY = -1.*sys.maxint
@ -760,14 +759,14 @@ def fftbuild(rcData,height,xframe,yframe,resolution,extrusion):
maxY = max(maxY, y) maxY = max(maxY, y)
xsize = maxX+2*xframe # add framsize xsize = maxX+2*xframe # add framsize
ysize = maxY+2*yframe ysize = maxY+2*yframe
xres = int(round(resolution/2.0)*2) # use only even resolution xres = int(grid)
yres = int(round(xres/xsize*ysize/2.0)*2) # calculate other resolutions yres = int(xres/xsize*ysize)
zres = extrusion zres = extrusion
zsize = extrusion*min([xsize/xres,ysize/yres]) zsize = extrusion*min([xsize/xres,ysize/yres])
fftdata = {'fftpoints':[], \ fftdata = {'fftpoints':[], \
'resolution':(xres,yres,zres), \ 'grid':(xres,yres,zres), \
'dimension':(xsize,ysize,zsize)} 'size':(xsize,ysize,zsize)}
frameindex=len(rcData['grain'])+1 # calculate frame index as largest grain index plus one frameindex=len(rcData['grain'])+1 # calculate frame index as largest grain index plus one
dx = xsize/(xres) # calculate step sizes dx = xsize/(xres) # calculate step sizes
@ -841,8 +840,8 @@ parser.add_option('-x', '--xmargin', type='float', metavar = 'float',
dest='xmargin',help='margin in x in units of patch size [%default]') dest='xmargin',help='margin in x in units of patch size [%default]')
parser.add_option('-y', '--ymargin', type='float', metavar = 'float', parser.add_option('-y', '--ymargin', type='float', metavar = 'float',
dest='ymargin', help='margin in y in units of patch size [%default]') dest='ymargin', help='margin in y in units of patch size [%default]')
parser.add_option('-r', '--resolution', type='int', metavar = 'int', parser.add_option('-g', '--grid', type='int', metavar = 'int',
dest='resolution',help='number of Fourier points/Finite Elements across patch size + x_margin [%default]') dest='grid',help='number of Fourier points/Finite Elements across patch size + x_margin [%default]')
parser.add_option('-z', '--extrusion', type='int', metavar = 'int', parser.add_option('-z', '--extrusion', type='int', metavar = 'int',
dest='extrusion', help='number of repetitions in z-direction [%default]') dest='extrusion', help='number of repetitions in z-direction [%default]')
parser.add_option('-i', '--imagesize', type='int', metavar = 'int', parser.add_option('-i', '--imagesize', type='int', metavar = 'int',
@ -861,7 +860,7 @@ parser.set_defaults(output = [],
port = 40007, port = 40007,
xmargin = 0.0, xmargin = 0.0,
ymargin = 0.0, ymargin = 0.0,
resolution = 64, grid = 64,
extrusion = 2, extrusion = 2,
imgsize = 512, imgsize = 512,
M = (0.0,1.0,1.0,0.0), # M_11, M_12, M_21, M_22. x,y in RCB is y,x of Eulers!! M = (0.0,1.0,1.0,0.0), # M_11, M_12, M_21, M_22. x,y in RCB is y,x of Eulers!!
@ -903,14 +902,14 @@ rcData = rcbParser(boundarySegments,options.M,options.size,options.tolerance,opt
Minv = np.linalg.inv(np.array(options.M).reshape(2,2)) Minv = np.linalg.inv(np.array(options.M).reshape(2,2))
if 'rcb' in options.output: if 'rcb' in options.output:
print """# Header: print('# Header:\n'+
# '# \n'+
# Column 1-3: right hand average orientation (phi1, PHI, phi2 in radians) '# Column 1-3: right hand average orientation (phi1, PHI, phi2 in radians)\n'+
# Column 4-6: left hand average orientation (phi1, PHI, phi2 in radians) '# Column 4-6: left hand average orientation (phi1, PHI, phi2 in radians)\n'+
# Column 7: length (in microns) '# Column 7: length (in microns)\n'+
# Column 8: trace angle (in degrees) '# Column 8: trace angle (in degrees)\n'+
# Column 9-12: x,y coordinates of endpoints (in microns) '# Column 9-12: x,y coordinates of endpoints (in microns)\n'+
# Column 13-14: IDs of right hand and left hand grains""" '# Column 13-14: IDs of right hand and left hand grains')
for i,(left,right) in enumerate(rcData['neighbors']): for i,(left,right) in enumerate(rcData['neighbors']):
if rcData['segment'][i]: if rcData['segment'][i]:
first = np.dot(Minv,np.array([rcData['bounds'][0][0]+rcData['point'][rcData['segment'][i][0]][0]/rcData['scale'], first = np.dot(Minv,np.array([rcData['bounds'][0][0]+rcData['point'][rcData['segment'][i][0]][0]/rcData['scale'],
@ -919,12 +918,12 @@ if 'rcb' in options.output:
second = np.dot(Minv,np.array([rcData['bounds'][0][0]+rcData['point'][rcData['segment'][i][1]][0]/rcData['scale'], second = np.dot(Minv,np.array([rcData['bounds'][0][0]+rcData['point'][rcData['segment'][i][1]][0]/rcData['scale'],
rcData['bounds'][0][1]+rcData['point'][rcData['segment'][i][1]][1]/rcData['scale'], rcData['bounds'][0][1]+rcData['point'][rcData['segment'][i][1]][1]/rcData['scale'],
])) ]))
print ' '.join(map(str,orientationData[left-1]+orientationData[right-1])), print(' '.join(map(str,orientationData[left-1]+orientationData[right-1]))+
print np.linalg.norm(first-second), str(np.linalg.norm(first-second))+
print '0', '0'+
print ' '.join(map(str,first)), ' '.join(map(str,first))+
print ' '.join(map(str,second)), ' '.join(map(str,second))+
print ' '.join(map(str,[left,right])) ' '.join(map(str,[left,right])))
# ----- write image ----- # ----- write image -----
@ -934,28 +933,67 @@ if 'image' in options.output and options.imgsize > 0:
else: else:
damask.util.croak('...no image drawing possible (PIL missing)...') damask.util.croak('...no image drawing possible (PIL missing)...')
# ----- generate material.config -----
if any(output in options.output for output in ['spectral','mentat']):
config = []
config.append('<microstructure>')
for i,grain in enumerate(rcData['grainMapping']):
config+=['[grain{}]'.format(grain),
'crystallite\t1',
'(constituent)\tphase 1\ttexture {}\tfraction 1.0'.format(i+1)]
if (options.xmargin > 0.0):
config+=['[x-margin]',
'crystallite\t1',
'(constituent)\tphase 2\ttexture {}\tfraction 1.0\n'.format(len(rcData['grainMapping'])+1)]
if (options.ymargin > 0.0):
config+=['[y-margin]',
'crystallite\t1',
'(constituent)\tphase 2\ttexture {}\tfraction 1.0\n'.format(len(rcData['grainMapping'])+1)]
if (options.xmargin > 0.0 and options.ymargin > 0.0):
config+=['[xy-margin]',
'crystallite\t1',
'(constituent)\tphase 2\ttexture {}\tfraction 1.0\n'.format(len(rcData['grainMapping'])+1)]
if (options.xmargin > 0.0 or options.ymargin > 0.0):
config.append('[margin]')
config.append('<texture>')
for grain in rcData['grainMapping']:
config+=['[grain{}]'.format(grain),
'(gauss)\tphi1\t%f\tphi\t%f\tphi2\t%f\tscatter\t%f\tfraction\t1.0'\
%(math.degrees(orientationData[grain-1][0]),math.degrees(orientationData[grain-1][1]),\
math.degrees(orientationData[grain-1][2]),options.scatter)]
if (options.xmargin > 0.0 or options.ymargin > 0.0):
config+=['[margin]',
'(random)\t\tscatter\t0.0\tfraction\t1.0']
# ----- write spectral geom ----- # ----- write spectral geom -----
if 'spectral' in options.output: if 'spectral' in options.output:
fftdata = fftbuild(rcData, options.size, options.xmargin, options.ymargin, options.resolution, options.extrusion) fftdata = fftbuild(rcData, options.size, options.xmargin, options.ymargin, options.grid, options.extrusion)
geomFile = open(myName+'_'+str(int(fftdata['resolution'][0]))+'.geom','w') # open geom file for writing
geomFile.write('3\theader\n') # write header info
geomFile.write('grid a %i b %i c %i\n'%(fftdata['resolution'])) # grid resolution
geomFile.write('size x %f y %f z %f\n'%(fftdata['dimension'])) # size
geomFile.write('homogenization 1\n') # homogenization
for z in xrange(fftdata['resolution'][2]): # z repetions
for y in xrange(fftdata['resolution'][1]): # each x-row separately
geomFile.write('\t'.join(map(str,fftdata['fftpoints'][ y *fftdata['resolution'][0]:
(y+1)*fftdata['resolution'][0]]))+'\n') # grain indexes, x-row per line
geomFile.close() # close geom file
damask.util.croak('assigned {} out of {} (2D) Fourier points...'
.format(len(fftdata['fftpoints']),
int(fftdata['resolution'][0])*int(fftdata['resolution'][1])))
table = damask.ASCIItable(outname = myName+'_'+str(int(fftdata['grid'][0]))+'.geom',
labeled = False,
buffered = False)
table.labels_clear()
table.info_clear()
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=fftdata['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=fftdata['size']),
"homogenization\t1",
])
table.info_append(config)
table.head_write()
table.data = np.array(fftdata['fftpoints']*options.extrusion).\
reshape(fftdata['grid'][1]*fftdata['grid'][2],fftdata['grid'][0])
formatwidth = 1+int(math.log10(np.max(table.data)))
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
table.close()
# ----- write Mentat procedure -----
if 'mentat' in options.output: if 'mentat' in options.output:
if MentatCapability: if MentatCapability:
@ -964,19 +1002,19 @@ if 'mentat' in options.output:
cmds = [\ cmds = [\
init(), init(),
sample(options.size,rcData['dimension'][1]/rcData['dimension'][0],12,options.xmargin,options.ymargin), sample(options.size,rcData['dimension'][1]/rcData['size'][0],12,options.xmargin,options.ymargin),
patch(options.size,options.resolution,options.mesh,rcData), patch(options.size,options.grid,options.mesh,rcData),
gage(options.mesh,rcData), gage(options.mesh,rcData),
] ]
if not options.twoD: if not options.twoD:
cmds += [expand3D(options.size*(1.0+2.0*options.xmargin)/options.resolution*options.extrusion,options.extrusion),] cmds += [expand3D(options.size*(1.0+2.0*options.xmargin)/options.grid*options.extrusion,options.extrusion),]
cmds += [\ cmds += [\
cleanUp(options.size), cleanUp(options.size),
materials(), materials(),
initial_conditions(len(rcData['grain']),rcData['grainMapping']), initial_conditions(len(rcData['grain']),rcData['grainMapping']),
boundary_conditions(options.strainrate,options.size*(1.0+2.0*options.xmargin)/options.resolution*options.extrusion,\ boundary_conditions(options.strainrate,options.size*(1.0+2.0*options.xmargin)/options.grid*options.extrusion,\
options.size,rcData['dimension'][1]/rcData['dimension'][0],options.xmargin,options.ymargin), options.size,rcData['dimension'][1]/rcData['dimension'][0],options.xmargin,options.ymargin),
loadcase(options.strain/options.strainrate,options.increments,0.01), loadcase(options.strain/options.strainrate,options.increments,0.01),
job(len(rcData['grain']),rcData['grainMapping'],options.twoD), job(len(rcData['grain']),rcData['grainMapping'],options.twoD),
@ -996,51 +1034,5 @@ if 'mentat' in options.output:
else: else:
damask.util.croak('...no interaction with Mentat possible...') damask.util.croak('...no interaction with Mentat possible...')
with open(myName+'.config','w') as configFile:
# ----- write config data to file ----- configFile.write('\n'.join(config))
if 'mentat' in options.output or 'spectral' in options.output:
output = ''
output += '\n\n<homogenization>\n' + \
'\n[SX]\n' + \
'type\tisostrain\n' + \
'Ngrains\t1\n' + \
'\n\n<microstructure>\n'
for i,grain in enumerate(rcData['grainMapping']):
output += '\n[grain %i]\n'%grain + \
'crystallite\t1\n' + \
'(constituent)\tphase 1\ttexture %i\tfraction 1.0\n'%(i+1)
if (options.xmargin > 0.0):
output += '\n[x-margin]\n' + \
'crystallite\t1\n' + \
'(constituent)\tphase 2\ttexture %i\tfraction 1.0\n'%(len(rcData['grainMapping'])+1)
if (options.ymargin > 0.0):
output += '\n[y-margin]\n' + \
'crystallite\t1\n' + \
'(constituent)\tphase 2\ttexture %i\tfraction 1.0\n'%(len(rcData['grainMapping'])+1)
if (options.xmargin > 0.0 and options.ymargin > 0.0):
output += '\n[margin edge]\n' + \
'crystallite\t1\n' + \
'(constituent)\tphase 2\ttexture %i\tfraction 1.0\n'%(len(rcData['grainMapping'])+1)
output += '\n\n<crystallite>\n' + \
'\n[fillMeIn]\n' + \
'\n\n<phase>\n' + \
'\n[patch]\n'
if (options.xmargin > 0.0 or options.ymargin > 0.0):
output += '\n[margin]\n'
output += '\n\n<texture>\n\n'
for grain in rcData['grainMapping']:
output += '\n[grain %i]\n'%grain + \
'(gauss)\tphi1\t%f\tphi\t%f\tphi2\t%f\tscatter\t%f\tfraction\t1.0\n'\
%(math.degrees(orientationData[grain-1][0]),math.degrees(orientationData[grain-1][1]),\
math.degrees(orientationData[grain-1][2]),options.scatter)
if (options.xmargin > 0.0 or options.ymargin > 0.0):
output += '\n[margin]\n' + \
'(random)\t\tscatter\t0.0\tfraction\t1.0\n'
configFile = open(myName+'.config','w')
configFile.write(output)
configFile.close()