moderized
needs some polishing with respect to array orders
This commit is contained in:
Martin Diehl
parent
6836a2eae8
commit
78f30684f8
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@ -1,46 +1,66 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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import numpy as np
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import os
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import sys
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from io import StringIO
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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 [option(s)] [geomfile]', description = """
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Generate a geometry file of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
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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', dest='grid', type='int', nargs=2, metavar = 'int int',
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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', dest='size', type='float', nargs=2, metavar = 'float float',
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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', dest='canal', type='float', metavar = 'float',
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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', dest='osteon', type='float', metavar = 'float',
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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', dest='period', type='float', metavar = 'float',
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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', dest='amplitude', type='float', metavar = 'float',
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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', dest='aspect', type='float', metavar = 'float',
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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', dest='omega', type='float', metavar = 'float',
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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', dest='homogenization', type='int', metavar = 'int',
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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('--crystallite', dest='crystallite', type='int', metavar = 'int',
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help='crystallite 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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@ -50,107 +70,83 @@ 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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crystallite = 1)
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homogenization = 1)
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(options,filename) = parser.parse_args()
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if np.any(np.array(options.grid) < 2):
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parser('invalid grid a b c.')
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if np.any(np.array(options.size) <= 0.0):
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parser('invalid size x y z.')
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# --- open input files ----------------------------------------------------------------------------
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name = None if filename == [] else filename[0]
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damask.util.report(scriptName,name)
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if filename == []: filename = [None]
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table = damask.ASCIItable(outname = filename[0],
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buffered = False, labeled=False)
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damask.util.report(scriptName,filename[0])
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options.omega *= math.pi/180.0 # rescale ro radians
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rotation = np.array([[ math.cos(options.omega),math.sin(options.omega),],
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[-math.sin(options.omega),math.cos(options.omega),]],'d')
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options.omega *= np.pi/180.0 # rescale ro radians
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rotation = np.array([[ np.cos(options.omega),np.sin(options.omega),],
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[-np.sin(options.omega),np.cos(options.omega),]],'d')
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box = np.dot(np.array([[options.canal,0.],[0.,options.aspect*options.canal]]).transpose(),rotation)
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grid = np.array(options.grid,'i')
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size = np.array(options.size,'d')
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info = {
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'grid': np.ones(3,'i'),
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'size': np.ones(3,'d'),
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'origin': np.zeros(3,'d'),
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'microstructures': 3,
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'homogenization': options.homogenization,
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}
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info['grid'][:2] = np.array(options.grid,'i')
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info['size'][:2] = np.array(options.size,'d')
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info['size'][2] = min(info['size'][0]/info['grid'][0],info['size'][1]/info['grid'][1])
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info['origin'] = -info['size']/2.0
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X0 = info['size'][0]/info['grid'][0]*\
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(np.tile(np.arange(info['grid'][0]),(info['grid'][1],1)) - info['grid'][0]/2 + 0.5)
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Y0 = info['size'][1]/info['grid'][1]*\
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(np.tile(np.arange(info['grid'][1]),(info['grid'][0],1)).transpose() - info['grid'][1]/2 + 0.5)
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X0 = size[0]/grid[0]*\
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(np.tile(np.arange(grid[0]),(grid[1],1)) - grid[0]/2 + 0.5)
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Y0 = size[1]/grid[1]*\
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(np.tile(np.arange(grid[1]),(grid[0],1)).transpose() - grid[1]/2 + 0.5)
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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/options.aspect)
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alpha = np.degrees(np.arctan2(Y/options.aspect,X))
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beta = options.amplitude*np.sin(2.0*math.pi*(radius-options.canal)/options.period)
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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) + np.where(radius > float(options.osteon),2,0)
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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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alphaOfGrain = np.zeros(info['grid'][0]*info['grid'][1],'d')
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betaOfGrain = np.zeros(info['grid'][0]*info['grid'][1],'d')
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for y in range(info['grid'][1]):
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for x in range(info['grid'][0]):
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if microstructure[y,x] == 0:
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microstructure[y,x] = info['microstructures']
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alphaOfGrain[info['microstructures']] = alpha[y,x]
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betaOfGrain[ info['microstructures']] = beta[y,x]
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info['microstructures'] += 1
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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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#--- report ---------------------------------------------------------------------------------------
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damask.util.report_geom(info,['grid','size','origin','homogenization','microstructures'])
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alphaOfGrain = np.zeros(grid[0]*grid[1],'d')
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betaOfGrain = np.zeros(grid[0]*grid[1],'d')
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formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1)))
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header = [scriptID + ' ' + ' '.join(sys.argv[1:])]
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header.append('<microstructure>')
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header.append('[canal]')
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header.append('crystallite %i'%options.crystallite)
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header.append('(constituent)\tphase 1\ttexture 1\tfraction 1.0')
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header.append('[interstitial]')
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header.append('crystallite %i'%options.crystallite)
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header.append('(constituent)\tphase 2\ttexture 2\tfraction 1.0')
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for i in range(3,info['microstructures']):
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header.append('[Grain%s]'%(str(i).zfill(formatwidth)))
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header.append('crystallite %i'%options.crystallite)
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header.append('(constituent)\tphase 3\ttexture %s\tfraction 1.0'%(str(i).rjust(formatwidth)))
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i = 3
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for x in range(grid[0]):
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for y in range(grid[1]):
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if microstructure[y,x] == 0: #ToDo: Wrong order (y and x are flipped)
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microstructure[y,x] = i #ToDo: Wrong order (y and x are flipped)
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alphaOfGrain[i] = alpha[y,x]
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betaOfGrain[ i] = beta[y,x]
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i+=1
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header.append('<texture>')
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header.append('[canal]')
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header.append('[interstitial]')
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for i in range(3,info['microstructures']):
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header.append('[Grain%s]'%(str(i).zfill(formatwidth)))
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header.append('(gauss)\tphi1 %g\tPhi %g\tphi2 0\tscatter 0.0\tfraction 1.0'\
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%(alphaOfGrain[i],betaOfGrain[i]))
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header.append([
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"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
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"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
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"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
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"homogenization\t{homog}".format(homog=info['homogenization']),
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"microstructures\t{microstructures}".format(microstructures=info['microstructures'])])
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formatwidth = 1+int(np.floor(np.log10(np.nanmax(microstructure)-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('[Grain%s]'%(str(i).zfill(formatwidth)))
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config_header.append('crystallite 1')
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config_header.append('(constituent)\tphase 3\ttexture %s\tfraction 1.0'%(str(i).rjust(formatwidth)))
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table.info_append(header)
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table.head_write()
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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('[Grain%s]'%(str(i).zfill(formatwidth)))
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config_header.append('(gauss)\tphi1 %g\tPhi %g\tphi2 0'%(alphaOfGrain[i],betaOfGrain[i]))
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# --- write microstructure information ------------------------------------------------------------
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header = [scriptID + ' ' + ' '.join(sys.argv[1:])] + 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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table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
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table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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#--- output finalization --------------------------------------------------------------------------
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table.close()
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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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