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DAMASK_EICMD
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moderized 

needs some polishing with respect to array orders
This commit is contained in:
Martin Diehl 2019-05-29 09:40:56 +02:00
parent 6836a2eae8
commit 78f30684f8
1 changed files with 95 additions and 99 deletions
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194
processing/pre/geom_fromOsteonGeometry.py
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@ -1,46 +1,66 @@
#!/usr/bin/env python3 #!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math import os
import numpy as np import sys
from io import StringIO
from optparse import OptionParser from optparse import OptionParser
import numpy as np
import damask import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) scriptID = ' '.join([scriptName,damask.version])
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# MAIN # MAIN
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] [geomfile]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile]', description = """
Generate a geometry file of an osteon enclosing the Harvesian canal and separated by interstitial tissue. Generate description of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
The osteon phase is lamellar with a twisted plywood structure. The osteon phase is lamellar with a twisted plywood structure.
Its fiber orientation is oscillating by +/- amplitude within one period. Its fiber orientation is oscillating by +/- amplitude within one period.
""", version = scriptID) """, version = scriptID)
parser.add_option('-g', '--grid', dest='grid', type='int', nargs=2, metavar = 'int int', parser.add_option('-g', '--grid',
dest='grid', type='int',
nargs=2, metavar = 'int int',
help='a,b grid of hexahedral box [%default]') help='a,b grid of hexahedral box [%default]')
parser.add_option('-s', '--size', dest='size', type='float', nargs=2, metavar = 'float float', parser.add_option('-s', '--size',
dest='size',
type='float', nargs=2, metavar = 'float float',
help='x,y size of hexahedral box [%default]') help='x,y size of hexahedral box [%default]')
parser.add_option('-c', '--canal', dest='canal', type='float', metavar = 'float', parser.add_option('-c', '--canal',
dest='canal',
type='float', metavar = 'float',
help='Haversian canal radius [%default]') help='Haversian canal radius [%default]')
parser.add_option('-o', '--osteon', dest='osteon', type='float', metavar = 'float', parser.add_option('-o', '--osteon',
dest='osteon',
type='float', metavar = 'float',
help='horizontal osteon radius [%default]') help='horizontal osteon radius [%default]')
parser.add_option('-l', '--lamella', dest='period', type='float', metavar = 'float', parser.add_option('-l', '--lamella',
dest='period',
type='float', metavar = 'float',
help='lamella width [%default]') help='lamella width [%default]')
parser.add_option('-a', '--amplitude', dest='amplitude', type='float', metavar = 'float', parser.add_option('-a', '--amplitude',
dest='amplitude',
type='float', metavar = 'float',
help='amplitude of twisted plywood wiggle in deg [%default]') help='amplitude of twisted plywood wiggle in deg [%default]')
parser.add_option( '--aspect', dest='aspect', type='float', metavar = 'float', parser.add_option( '--aspect',
dest='aspect',
type='float', metavar = 'float',
help='vertical/horizontal osteon aspect ratio [%default]') help='vertical/horizontal osteon aspect ratio [%default]')
parser.add_option('-w', '--omega', dest='omega', type='float', metavar = 'float', parser.add_option('-w', '--omega',
dest='omega',
type='float', metavar = 'float',
help='rotation angle around normal of osteon [%default]') help='rotation angle around normal of osteon [%default]')
parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', parser.add_option( '--homogenization',
dest='homogenization',
type='int', metavar = 'int',
help='homogenization index to be used [%default]') help='homogenization index to be used [%default]')
parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int',
help='crystallite index to be used [%default]')
parser.set_defaults(canal = 25e-6, parser.set_defaults(canal = 25e-6,
osteon = 100e-6, osteon = 100e-6,
@ -50,107 +70,83 @@ parser.set_defaults(canal = 25e-6,
amplitude = 60, amplitude = 60,
size = (300e-6,300e-6), size = (300e-6,300e-6),
grid = (512,512), grid = (512,512),
homogenization = 1, homogenization = 1)
crystallite = 1)
(options,filename) = parser.parse_args() (options,filename) = parser.parse_args()
if np.any(np.array(options.grid) < 2):
parser('invalid grid a b c.')
if np.any(np.array(options.size) <= 0.0):
parser('invalid size x y z.')
# --- open input files ---------------------------------------------------------------------------- name = None if filename == [] else filename[0]
damask.util.report(scriptName,name)
if filename == []: filename = [None] options.omega *= np.pi/180.0 # rescale ro radians
rotation = np.array([[ np.cos(options.omega),np.sin(options.omega),],
table = damask.ASCIItable(outname = filename[0], [-np.sin(options.omega),np.cos(options.omega),]],'d')
buffered = False, labeled=False)
damask.util.report(scriptName,filename[0])
options.omega *= math.pi/180.0 # rescale ro radians
rotation = np.array([[ math.cos(options.omega),math.sin(options.omega),],
[-math.sin(options.omega),math.cos(options.omega),]],'d')
box = np.dot(np.array([[options.canal,0.],[0.,options.aspect*options.canal]]).transpose(),rotation) box = np.dot(np.array([[options.canal,0.],[0.,options.aspect*options.canal]]).transpose(),rotation)
grid = np.array(options.grid,'i')
size = np.array(options.size,'d')
info = { X0 = size[0]/grid[0]*\
'grid': np.ones(3,'i'), (np.tile(np.arange(grid[0]),(grid[1],1)) - grid[0]/2 + 0.5)
'size': np.ones(3,'d'), Y0 = size[1]/grid[1]*\
'origin': np.zeros(3,'d'), (np.tile(np.arange(grid[1]),(grid[0],1)).transpose() - grid[1]/2 + 0.5)
'microstructures': 3,
'homogenization': options.homogenization,
}
info['grid'][:2] = np.array(options.grid,'i')
info['size'][:2] = np.array(options.size,'d')
info['size'][2] = min(info['size'][0]/info['grid'][0],info['size'][1]/info['grid'][1])
info['origin'] = -info['size']/2.0
X0 = info['size'][0]/info['grid'][0]*\
(np.tile(np.arange(info['grid'][0]),(info['grid'][1],1)) - info['grid'][0]/2 + 0.5)
Y0 = info['size'][1]/info['grid'][1]*\
(np.tile(np.arange(info['grid'][1]),(info['grid'][0],1)).transpose() - info['grid'][1]/2 + 0.5)
X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega
Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega
radius = np.sqrt(X*X + Y*Y/options.aspect/options.aspect) radius = np.sqrt(X*X + Y*Y/options.aspect/options.aspect)
alpha = np.degrees(np.arctan2(Y/options.aspect,X)) alpha = np.degrees(np.arctan2(Y/options.aspect,X))
beta = options.amplitude*np.sin(2.0*math.pi*(radius-options.canal)/options.period) beta = options.amplitude*np.sin(2.0*np.pi*(radius-options.canal)/options.period)
microstructure = np.where(radius < float(options.canal),1,0) + np.where(radius > float(options.osteon),2,0) microstructure = np.where(radius < float(options.canal), 1,0)\
+ np.where(radius > float(options.osteon),2,0)
alphaOfGrain = np.zeros(info['grid'][0]*info['grid'][1],'d') # extend to 3D
betaOfGrain = np.zeros(info['grid'][0]*info['grid'][1],'d') size = np.append(size,np.min(size/grid))
for y in range(info['grid'][1]): grid = np.append(grid,1)
for x in range(info['grid'][0]): microstructure = microstructure.reshape(microstructure.shape+(1,))
if microstructure[y,x] == 0:
microstructure[y,x] = info['microstructures']
alphaOfGrain[info['microstructures']] = alpha[y,x]
betaOfGrain[ info['microstructures']] = beta[y,x]
info['microstructures'] += 1
#--- report --------------------------------------------------------------------------------------- alphaOfGrain = np.zeros(grid[0]*grid[1],'d')
damask.util.report_geom(info,['grid','size','origin','homogenization','microstructures']) betaOfGrain = np.zeros(grid[0]*grid[1],'d')
formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1))) i = 3
header = [scriptID + ' ' + ' '.join(sys.argv[1:])] for x in range(grid[0]):
header.append('<microstructure>') for y in range(grid[1]):
header.append('[canal]') if microstructure[y,x] == 0: #ToDo: Wrong order (y and x are flipped)
header.append('crystallite %i'%options.crystallite) microstructure[y,x] = i #ToDo: Wrong order (y and x are flipped)
header.append('(constituent)\tphase 1\ttexture 1\tfraction 1.0') alphaOfGrain[i] = alpha[y,x]
header.append('[interstitial]') betaOfGrain[ i] = beta[y,x]
header.append('crystallite %i'%options.crystallite) i+=1
header.append('(constituent)\tphase 2\ttexture 2\tfraction 1.0')
for i in range(3,info['microstructures']):
header.append('[Grain%s]'%(str(i).zfill(formatwidth)))
header.append('crystallite %i'%options.crystallite)
header.append('(constituent)\tphase 3\ttexture %s\tfraction 1.0'%(str(i).rjust(formatwidth)))
header.append('<texture>') formatwidth = 1+int(np.floor(np.log10(np.nanmax(microstructure)-1)))
header.append('[canal]') config_header = []
header.append('[interstitial]') config_header.append('<microstructure>')
for i in range(3,info['microstructures']): config_header.append('[canal]')
header.append('[Grain%s]'%(str(i).zfill(formatwidth))) config_header.append('crystallite 1')
header.append('(gauss)\tphi1 %g\tPhi %g\tphi2 0\tscatter 0.0\tfraction 1.0'\ config_header.append('(constituent)\tphase 1\ttexture 1\tfraction 1.0')
%(alphaOfGrain[i],betaOfGrain[i])) config_header.append('[interstitial]')
header.append([ config_header.append('crystallite 1')
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']), config_header.append('(constituent)\tphase 2\ttexture 2\tfraction 1.0')
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']), for i in range(3,np.max(microstructure)):
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']), config_header.append('[Grain%s]'%(str(i).zfill(formatwidth)))
"homogenization\t{homog}".format(homog=info['homogenization']), config_header.append('crystallite 1')
"microstructures\t{microstructures}".format(microstructures=info['microstructures'])]) config_header.append('(constituent)\tphase 3\ttexture %s\tfraction 1.0'%(str(i).rjust(formatwidth)))
config_header.append('<texture>')
config_header.append('[canal]')
config_header.append('[interstitial]')
for i in range(3,np.max(microstructure)):
config_header.append('[Grain%s]'%(str(i).zfill(formatwidth)))
config_header.append('(gauss)\tphi1 %g\tPhi %g\tphi2 0'%(alphaOfGrain[i],betaOfGrain[i]))
header = [scriptID + ' ' + ' '.join(sys.argv[1:])] + config_header
geom = damask.Geom(microstructure.reshape(grid),
size,-size/2,
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
table.info_append(header) if name is None:
table.head_write() sys.stdout.write(str(geom.show()))
else:
# --- write microstructure information ------------------------------------------------------------ geom.to_file(name)
table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
table.close()