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