removed Geom.homogenization from shell scripts
This commit is contained in:
Philip Eisenlohr
parent
683161d479
commit
997f7dfa05
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit fa2885da8604c3ac46f64670393f04678dd1f45b
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Subproject commit 86f77da4aec6cb52bbcc2724f00a6cf6a7dc6e91
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@ -52,16 +52,11 @@ parser.add_option('-q', '--quaternion',
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type = 'string',
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metavar='string',
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help = 'name of the dataset containing pointwise/average orientation as quaternion [%default]')
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parser.add_option('--homogenization',
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dest = 'homogenization',
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type = 'int', metavar = 'int',
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help = 'homogenization index to be used [%default]')
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parser.set_defaults(pointwise = 'CellData',
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quaternion = 'Quats',
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phase = 'Phases',
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microstructure = 'FeatureIds',
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homogenization = 1,
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)
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(options, filenames) = parser.parse_args()
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@ -150,8 +145,7 @@ for name in filenames:
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header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
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+ config_header
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geom = damask.Geom(microstructure,size,origin,
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homogenization=options.homogenization,comments=header)
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geom = damask.Geom(microstructure,size,origin,comments=header)
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damask.util.croak(geom)
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geom.save_ASCII(os.path.splitext(name)[0]+'.geom',compress=False)
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@ -52,10 +52,6 @@ parser.add_option('-p', '--periods',
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dest = 'periods',
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type = 'int', metavar = 'int',
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help = 'number of repetitions of unit cell [%default]')
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parser.add_option('--homogenization',
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dest = 'homogenization',
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type = 'int', metavar = 'int',
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help = 'homogenization index to be used [%default]')
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parser.add_option('--m',
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dest = 'microstructure',
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type = 'int', nargs = 2, metavar = 'int int',
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@ -66,7 +62,6 @@ parser.set_defaults(type = minimal_surfaces[0],
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periods = 1,
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grid = (16,16,16),
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size = (1.0,1.0,1.0),
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homogenization = 1,
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microstructure = (1,2),
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)
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@ -85,7 +80,6 @@ microstructure = np.where(options.threshold < surface[options.type](x,y,z),
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options.microstructure[1],options.microstructure[0])
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geom=damask.Geom(microstructure,options.size,
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homogenization=options.homogenization,
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comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
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damask.util.croak(geom)
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@ -57,10 +57,6 @@ parser.add_option('-w', '--omega',
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dest='omega',
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type='float', metavar = 'float',
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help='rotation angle around normal of osteon [%default]')
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parser.add_option( '--homogenization',
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dest='homogenization',
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type='int', metavar = 'int',
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help='homogenization index to be used [%default]')
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parser.set_defaults(canal = 25e-6,
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osteon = 100e-6,
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@ -70,7 +66,7 @@ parser.set_defaults(canal = 25e-6,
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amplitude = 60,
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size = (300e-6,300e-6),
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grid = (512,512),
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homogenization = 1)
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)
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(options,filename) = parser.parse_args()
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@ -139,7 +135,7 @@ header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
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+ config_header
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geom = damask.Geom(microstructure.reshape(grid),
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size,-size/2,
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homogenization=options.homogenization,comments=header)
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comments=header)
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damask.util.croak(geom)
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geom.save_ASCII(sys.stdout if name is None else name,compress=False)
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@ -44,14 +44,9 @@ parser.add_option('--axes',
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dest = 'axes',
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type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
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help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]')
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parser.add_option('--homogenization',
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dest = 'homogenization',
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type = 'int', metavar = 'int',
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help = 'homogenization index to be used [%default]')
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parser.set_defaults(homogenization = 1,
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pos = 'pos',
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parser.set_defaults(pos = 'pos',
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)
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(options,filenames) = parser.parse_args()
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@ -102,7 +97,7 @@ for name in filenames:
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header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
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+ config_header
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geom = damask.Geom(microstructure,size,origin,
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homogenization=options.homogenization,comments=header)
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comments=header)
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damask.util.croak(geom)
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geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False)
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@ -142,10 +142,6 @@ group.add_option('--without-config',
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dest = 'config',
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action = 'store_false',
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help = 'omit material configuration header')
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group.add_option('--homogenization',
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dest = 'homogenization',
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type = 'int', metavar = 'int',
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help = 'homogenization index to be used [%default]')
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group.add_option('--phase',
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dest = 'phase',
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type = 'int', metavar = 'int',
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@ -157,7 +153,6 @@ parser.set_defaults(pos = 'pos',
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weight = 'weight',
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microstructure = 'microstructure',
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eulers = 'euler',
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homogenization = 1,
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phase = 1,
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cpus = 2,
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laguerre = False,
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@ -225,7 +220,7 @@ for name in filenames:
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header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
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+ config_header
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geom = damask.Geom(indices.reshape(grid),size,origin,
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homogenization=options.homogenization,comments=header)
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comments=header)
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damask.util.croak(geom)
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geom.save_ASCII(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',compress=False)
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@ -41,7 +41,7 @@ parser.add_option('-N', '--iterations',
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help = 'curvature flow iterations [%default]')
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parser.add_option('-i', '--immutable',
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action = 'extend', dest = 'immutable', metavar = '<int LIST>',
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help = 'list of immutable microstructure indices')
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help = 'list of immutable material indices')
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parser.add_option('--ndimage',
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dest = 'ndimage', action='store_true',
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help = 'use ndimage.gaussian_filter in lieu of explicit FFT')
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@ -66,13 +66,13 @@ for name in filenames:
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grid_original = geom.grid
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damask.util.croak(geom)
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microstructure = np.tile(geom.microstructure,np.where(grid_original == 1, 2,1)) # make one copy along dimensions with grid == 1
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grid = np.array(microstructure.shape)
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materials = np.tile(geom.materials,np.where(grid_original == 1, 2,1)) # make one copy along dimensions with grid == 1
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grid = np.array(materials.shape)
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# --- initialize support data ---------------------------------------------------------------------
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# store a copy the initial microstructure to find locations of immutable indices
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microstructure_original = np.copy(microstructure)
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# store a copy of the initial material indices to find locations of immutable indices
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materials_original = np.copy(materials)
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if not options.ndimage:
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X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]]
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@ -88,14 +88,14 @@ for name in filenames:
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for smoothIter in range(options.N):
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interfaceEnergy = np.zeros(microstructure.shape,dtype=np.float32)
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interfaceEnergy = np.zeros(materials.shape,dtype=np.float32)
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for i in (-1,0,1):
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for j in (-1,0,1):
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for k in (-1,0,1):
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# assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
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interfaceEnergy = np.maximum(interfaceEnergy,
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getInterfaceEnergy(microstructure,np.roll(np.roll(np.roll(
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microstructure,i,axis=0), j,axis=1), k,axis=2)))
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getInterfaceEnergy(materials,np.roll(np.roll(np.roll(
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materials,i,axis=0), j,axis=1), k,axis=2)))
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# periodically extend interfacial energy array by half a grid size in positive and negative directions
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periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
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@ -129,13 +129,13 @@ for name in filenames:
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iterations = int(round(options.d*2.))-1),# fat boundary
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periodic_bulkEnergy[grid[0]//2:-grid[0]//2, # retain filled energy on fat boundary...
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2], # ...and zero everywhere else
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grid[2]//2:-grid[2]//2], # ...and zero everywhere else
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0.)).astype(np.complex64) *
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gauss).astype(np.float32)
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periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # periodically extend the smoothed bulk energy
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grid[2]//2:-grid[2]//2] # periodically extend the smoothed bulk energy
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# transform voxels close to interface region
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@ -143,33 +143,35 @@ for name in filenames:
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return_distances = False,
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return_indices = True) # want index of closest bulk grain
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periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # periodically extend the microstructure
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periodic_materials = np.tile(materials,(3,3,3))[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # periodically extend the geometry
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microstructure = periodic_microstructure[index[0],
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index[1],
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index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # extent grains into interface region
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materials = periodic_materials[index[0],
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index[1],
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index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
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grid[1]//2:-grid[1]//2,
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grid[2]//2:-grid[2]//2] # extent grains into interface region
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# replace immutable microstructures with closest mutable ones
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index = ndimage.morphology.distance_transform_edt(np.in1d(microstructure,options.immutable).reshape(grid),
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# replace immutable materials with closest mutable ones
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index = ndimage.morphology.distance_transform_edt(np.in1d(materials,options.immutable).reshape(grid),
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return_distances = False,
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return_indices = True)
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microstructure = microstructure[index[0],
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index[1],
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index[2]]
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materials = materials[index[0],
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index[1],
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index[2]]
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immutable = np.zeros(microstructure.shape, dtype=np.bool)
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# find locations where immutable microstructures have been in original structure
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immutable = np.zeros(materials.shape, dtype=np.bool)
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# find locations where immutable materials have been in original structure
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for micro in options.immutable:
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immutable += microstructure_original == micro
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immutable += materials_original == micro
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# undo any changes involving immutable microstructures
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microstructure = np.where(immutable, microstructure_original,microstructure)
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# undo any changes involving immutable materials
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materials = np.where(immutable, materials_original,materials)
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geom = geom.duplicate(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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geom.save_ASCII(sys.stdout if name is None else name,compress=False)
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damask.Geom(materials = materials[0:grid_original[0],0:grid_original[1],0:grid_original[2]],
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size = geom.size,
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origin = geom.origin,
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comments = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
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)\
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.save_ASCII(sys.stdout if name is None else name,compress=False)
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@ -30,7 +30,7 @@ class myThread (threading.Thread):
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def run(self):
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global bestSeedsUpdate
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global bestSeedsVFile
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global nMicrostructures
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global nMaterials
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global delta
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global points
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global target
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@ -70,7 +70,7 @@ class myThread (threading.Thread):
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selectedMs = []
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direction = []
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for i in range(NmoveGrains):
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selectedMs.append(random.randrange(1,nMicrostructures))
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selectedMs.append(random.randrange(1,nMaterials))
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direction.append((np.random.random()-0.5)*delta)
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@ -101,11 +101,11 @@ class myThread (threading.Thread):
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#--- evaluate current seeds file ------------------------------------------------------------------
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perturbedGeom = damask.Geom.load_ASCII(perturbedGeomVFile)
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myNmicrostructures = len(np.unique(perturbedGeom.microstructure))
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currentData=np.bincount(perturbedGeom.microstructure.ravel())[1:]/points
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myNmaterials = len(np.unique(perturbedGeom.materials))
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currentData=np.bincount(perturbedGeom.materials.ravel())[1:]/points
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currentError=[]
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currentHist=[]
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for i in range(nMicrostructures): # calculate the deviation in all bins per histogram
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for i in range(nMaterials): # calculate the deviation in all bins per histogram
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currentHist.append(np.histogram(currentData,bins=target[i]['bins'])[0])
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currentError.append(np.sqrt(np.square(np.array(target[i]['histogram']-currentHist[i])).sum()))
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@ -117,12 +117,12 @@ class myThread (threading.Thread):
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bestMatch = match
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#--- count bin classes with no mismatch ----------------------------------------------------------------------
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myMatch=0
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for i in range(nMicrostructures):
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for i in range(nMaterials):
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if currentError[i] > 0.0: break
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myMatch = i+1
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if myNmicrostructures == nMicrostructures:
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for i in range(min(nMicrostructures,myMatch+options.bins)):
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if myNmaterials == nMaterials:
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for i in range(min(nMaterials,myMatch+options.bins)):
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if currentError[i] > target[i]['error']: # worse fitting, next try
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randReset = True
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break
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@ -141,25 +141,25 @@ class myThread (threading.Thread):
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for line in perturbedSeedsVFile:
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currentSeedsFile.write(line)
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bestSeedsVFile.write(line)
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for j in range(nMicrostructures): # save new errors for all bins
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for j in range(nMaterials): # save new errors for all bins
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target[j]['error'] = currentError[j]
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if myMatch > match: # one or more new bins have no deviation
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damask.util.croak( 'Stage {:d} cleared'.format(myMatch))
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match=myMatch
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sys.stdout.flush()
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break
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if i == min(nMicrostructures,myMatch+options.bins)-1: # same quality as before: take it to keep on moving
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if i == min(nMaterials,myMatch+options.bins)-1: # same quality as before: take it to keep on moving
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bestSeedsUpdate = time.time()
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perturbedSeedsVFile.seek(0)
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bestSeedsVFile.close()
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bestSeedsVFile = StringIO()
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bestSeedsVFile.writelines(perturbedSeedsVFile.readlines())
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for j in range(nMicrostructures):
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for j in range(nMaterials):
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target[j]['error'] = currentError[j]
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randReset = True
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else: #--- not all grains are tessellated
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damask.util.croak('Thread {:d}: Microstructure mismatch ({:d} microstructures mapped)'\
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.format(self.threadID,myNmicrostructures))
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damask.util.croak('Thread {:d}: Material mismatch ({:d} material indices mapped)'\
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.format(self.threadID,myNmaterials))
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randReset = True
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@ -217,10 +217,10 @@ points = np.array(options.grid).prod().astype('float')
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# ----------- calculate target distribution and bin edges
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targetGeom = damask.Geom.load_ASCII(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
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nMicrostructures = len(np.unique(targetGeom.microstructure))
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targetVolFrac = np.bincount(targetGeom.microstructure.flatten())/targetGeom.grid.prod().astype(np.float)
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nMaterials = len(np.unique(targetGeom.materials))
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targetVolFrac = np.bincount(targetGeom.materials.flatten())/targetGeom.grid.prod().astype(np.float)
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target = []
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for i in range(1,nMicrostructures+1):
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for i in range(1,nMaterials+1):
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targetHist,targetBins = np.histogram(targetVolFrac,bins=i) #bin boundaries
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target.append({'histogram':targetHist,'bins':targetBins})
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@ -233,7 +233,7 @@ else:
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bestSeedsVFile.write(damask.util.execute('seeds_fromRandom'+\
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' -g '+' '.join(list(map(str, options.grid)))+\
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' -r {:d}'.format(options.randomSeed)+\
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' -N '+str(nMicrostructures))[0])
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' -N '+str(nMaterials))[0])
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bestSeedsUpdate = time.time()
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# ----------- tessellate initial seed file to get and evaluate geom file
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@ -244,11 +244,11 @@ initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
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initialGeomVFile.seek(0)
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initialGeom = damask.Geom.load_ASCII(initialGeomVFile)
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if len(np.unique(targetGeom.microstructure)) != nMicrostructures:
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damask.util.croak('error. Microstructure count mismatch')
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if len(np.unique(targetGeom.materials)) != nMaterials:
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damask.util.croak('error. Material count mismatch')
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initialData = np.bincount(initialGeom.microstructure.flatten())/points
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for i in range(nMicrostructures):
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initialData = np.bincount(initialGeom.materials.flatten())/points
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for i in range(nMaterials):
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initialHist = np.histogram(initialData,bins=target[i]['bins'])[0]
|
||||
target[i]['error']=np.sqrt(np.square(np.array(target[i]['histogram']-initialHist)).sum())
|
||||
|
||||
|
|
@ -257,13 +257,13 @@ if target[0]['error'] > 0.0:
|
|||
target[0]['error'] *=((target[0]['bins'][0]-np.min(initialData))**2.0+
|
||||
(target[0]['bins'][1]-np.max(initialData))**2.0)**0.5
|
||||
match=0
|
||||
for i in range(nMicrostructures):
|
||||
for i in range(nMaterials):
|
||||
if target[i]['error'] > 0.0: break
|
||||
match = i+1
|
||||
|
||||
|
||||
if options.maxseeds < 1:
|
||||
maxSeeds = len(np.unique(initialGeom.microstructure))
|
||||
maxSeeds = len(np.unique(initialGeom.materials))
|
||||
else:
|
||||
maxSeeds = options.maxseeds
|
||||
|
||||
|
|
|
|||
|
|
@ -61,7 +61,7 @@ for name in filenames:
|
|||
'grid\ta {}\tb {}\tc {}'.format(*geom.grid),
|
||||
'size\tx {}\ty {}\tz {}'.format(*geom.size),
|
||||
'origin\tx {}\ty {}\tz {}'.format(*geom.origin),
|
||||
'homogenization\t{}'.format(geom.homogenization)]
|
||||
]
|
||||
|
||||
damask.Table(seeds[mask],{'pos':(3,)},comments)\
|
||||
.add('material',materials[mask].astype(int))\
|
||||
|
|
|
|||
|
|
@ -76,7 +76,7 @@ for name in filenames:
|
|||
g[2] = k + offset[2]
|
||||
g %= geom.grid
|
||||
seeds[n,0:3] = (g+0.5)/geom.grid # normalize coordinates to box
|
||||
seeds[n, 3] = geom.microstructure[g[0],g[1],g[2]]
|
||||
seeds[n, 3] = geom.materials[g[0],g[1],g[2]]
|
||||
if options.x: g[0] += 1
|
||||
if options.y: g[1] += 1
|
||||
n += 1
|
||||
|
|
@ -88,9 +88,9 @@ for name in filenames:
|
|||
'grid\ta {}\tb {}\tc {}'.format(*geom.grid),
|
||||
'size\tx {}\ty {}\tz {}'.format(*geom.size),
|
||||
'origin\tx {}\ty {}\tz {}'.format(*geom.origin),
|
||||
'homogenization\t{}'.format(geom.homogenization)]
|
||||
]
|
||||
|
||||
table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments)
|
||||
table.set('microstructure',table.get('microstructure').astype(np.int))\
|
||||
table = damask.Table(seeds,{'pos':(3,),'material':(1,)},comments)
|
||||
table.set('material',table.get('material').astype(np.int))\
|
||||
.save(sys.stdout if name is None else \
|
||||
os.path.splitext(name)[0]+f'_poked_{options.N}.seeds',legacy=True)
|
||||
|
|
|
|||
Loading…
Reference in New Issue