148 lines
5.4 KiB
Python
Executable File
148 lines
5.4 KiB
Python
Executable File
#!/usr/bin/env python3
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import os
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import sys
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from optparse import OptionParser
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import numpy as np
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile]', description = """
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Generate description of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
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The osteon phase is lamellar with a twisted plywood structure.
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Its fiber orientation is oscillating by +/- amplitude within one period.
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""", version = scriptID)
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parser.add_option('-g', '--grid',
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dest='grid', type='int',
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nargs=2, metavar = 'int int',
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help='a,b grid of hexahedral box [%default]')
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parser.add_option('-s', '--size',
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dest='size',
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type='float', nargs=2, metavar = 'float float',
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help='x,y size of hexahedral box [%default]')
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parser.add_option('-c', '--canal',
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dest='canal',
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type='float', metavar = 'float',
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help='Haversian canal radius [%default]')
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parser.add_option('-o', '--osteon',
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dest='osteon',
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type='float', metavar = 'float',
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help='horizontal osteon radius [%default]')
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parser.add_option('-l', '--lamella',
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dest='period',
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type='float', metavar = 'float',
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help='lamella width [%default]')
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parser.add_option('-a', '--amplitude',
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dest='amplitude',
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type='float', metavar = 'float',
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help='amplitude of twisted plywood wiggle in deg [%default]')
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parser.add_option( '--aspect',
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dest='aspect',
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type='float', metavar = 'float',
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help='vertical/horizontal osteon aspect ratio [%default]')
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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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aspect = 1.0,
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omega = 0.0,
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period = 5e-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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(options,filename) = parser.parse_args()
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name = None if filename == [] else filename[0]
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damask.util.report(scriptName,name)
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omega = np.deg2rad(options.omega)
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rotation = np.array([[ np.cos(omega),np.sin(omega),],
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[-np.sin(omega),np.cos(omega),]])
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grid = np.array(options.grid,'i')
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size = np.array(options.size,'d')
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X0,Y0 = np.meshgrid(size[0]/grid[0] * (np.arange(grid[0]) - grid[0]/2 + 0.5),
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size[1]/grid[0] * (np.arange(grid[1]) - grid[1]/2 + 0.5), indexing='ij')
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X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega
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Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega
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radius = np.sqrt(X*X + Y*Y/options.aspect**2.0)
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alpha = np.degrees(np.arctan2(Y/options.aspect,X))
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beta = options.amplitude*np.sin(2.0*np.pi*(radius-options.canal)/options.period)
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microstructure = np.where(radius < float(options.canal), 1,0) \
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+ np.where(radius > float(options.osteon),2,0)
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# extend to 3D
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size = np.append(size,np.min(size/grid))
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grid = np.append(grid,1)
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microstructure = microstructure.reshape(microstructure.shape+(1,))
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Alpha = np.zeros(grid[0]*grid[1],'d')
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Beta = np.zeros(grid[0]*grid[1],'d')
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i = 3
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for y in range(grid[1]):
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for x in range(grid[0]):
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if microstructure[x,y] == 0:
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microstructure[x,y] = i
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Alpha[i] = alpha[x,y]
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Beta [i] = beta [x,y]
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i+=1
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config_header = []
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config_header.append('<microstructure>')
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config_header.append('[canal]')
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config_header.append('crystallite 1')
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config_header.append('(constituent)\tphase 1\ttexture 1\tfraction 1.0')
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config_header.append('[interstitial]')
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config_header.append('crystallite 1')
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config_header.append('(constituent)\tphase 2\ttexture 2\tfraction 1.0')
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for i in range(3,np.max(microstructure)):
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config_header.append('[Point{}]'.format(i-2))
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config_header.append('crystallite 1')
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config_header.append('(constituent)\tphase 3\ttexture {}\tfraction 1.0'.format(i))
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config_header.append('<texture>')
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config_header.append('[canal]')
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config_header.append('[interstitial]')
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for i in range(3,np.max(microstructure)):
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config_header.append('[Point{}]'.format(i-2))
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config_header.append('(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 0'.format(Alpha[i],Beta[i]))
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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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damask.util.croak(geom)
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if name is None:
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sys.stdout.write(str(geom.show()))
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else:
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geom.to_file(name)
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