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

View File

@ -1,46 +1,66 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] [geomfile]', description = """
Generate a geometry file of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile]', description = """
Generate description of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
The osteon phase is lamellar with a twisted plywood structure.
Its fiber orientation is oscillating by +/- amplitude within one period.
""", 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]')
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]')
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]')
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]')
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]')
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]')
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]')
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]')
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]')
parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int',
help='crystallite index to be used [%default]')
parser.set_defaults(canal = 25e-6,
osteon = 100e-6,
@ -50,107 +70,83 @@ parser.set_defaults(canal = 25e-6,
amplitude = 60,
size = (300e-6,300e-6),
grid = (512,512),
homogenization = 1,
crystallite = 1)
homogenization = 1)
(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]
table = damask.ASCIItable(outname = filename[0],
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')
options.omega *= np.pi/180.0 # rescale ro radians
rotation = np.array([[ np.cos(options.omega),np.sin(options.omega),],
[-np.sin(options.omega),np.cos(options.omega),]],'d')
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 = {
'grid': np.ones(3,'i'),
'size': np.ones(3,'d'),
'origin': np.zeros(3,'d'),
'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)
X0 = size[0]/grid[0]*\
(np.tile(np.arange(grid[0]),(grid[1],1)) - grid[0]/2 + 0.5)
Y0 = size[1]/grid[1]*\
(np.tile(np.arange(grid[1]),(grid[0],1)).transpose() - grid[1]/2 + 0.5)
X = X0*rotation[0,0] + Y0*rotation[0,1] # 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)
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')
betaOfGrain = np.zeros(info['grid'][0]*info['grid'][1],'d')
for y in range(info['grid'][1]):
for x in range(info['grid'][0]):
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
# extend to 3D
size = np.append(size,np.min(size/grid))
grid = np.append(grid,1)
microstructure = microstructure.reshape(microstructure.shape+(1,))
#--- report ---------------------------------------------------------------------------------------
damask.util.report_geom(info,['grid','size','origin','homogenization','microstructures'])
alphaOfGrain = np.zeros(grid[0]*grid[1],'d')
betaOfGrain = np.zeros(grid[0]*grid[1],'d')
formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1)))
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]
header.append('<microstructure>')
header.append('[canal]')
header.append('crystallite %i'%options.crystallite)
header.append('(constituent)\tphase 1\ttexture 1\tfraction 1.0')
header.append('[interstitial]')
header.append('crystallite %i'%options.crystallite)
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)))
i = 3
for x in range(grid[0]):
for y in range(grid[1]):
if microstructure[y,x] == 0: #ToDo: Wrong order (y and x are flipped)
microstructure[y,x] = i #ToDo: Wrong order (y and x are flipped)
alphaOfGrain[i] = alpha[y,x]
betaOfGrain[ i] = beta[y,x]
i+=1
header.append('<texture>')
header.append('[canal]')
header.append('[interstitial]')
for i in range(3,info['microstructures']):
header.append('[Grain%s]'%(str(i).zfill(formatwidth)))
header.append('(gauss)\tphi1 %g\tPhi %g\tphi2 0\tscatter 0.0\tfraction 1.0'\
%(alphaOfGrain[i],betaOfGrain[i]))
header.append([
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
"homogenization\t{homog}".format(homog=info['homogenization']),
"microstructures\t{microstructures}".format(microstructures=info['microstructures'])])
formatwidth = 1+int(np.floor(np.log10(np.nanmax(microstructure)-1)))
config_header = []
config_header.append('<microstructure>')
config_header.append('[canal]')
config_header.append('crystallite 1')
config_header.append('(constituent)\tphase 1\ttexture 1\tfraction 1.0')
config_header.append('[interstitial]')
config_header.append('crystallite 1')
config_header.append('(constituent)\tphase 2\ttexture 2\tfraction 1.0')
for i in range(3,np.max(microstructure)):
config_header.append('[Grain%s]'%(str(i).zfill(formatwidth)))
config_header.append('crystallite 1')
config_header.append('(constituent)\tphase 3\ttexture %s\tfraction 1.0'%(str(i).rjust(formatwidth)))
table.info_append(header)
table.head_write()
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]))
# --- write microstructure information ------------------------------------------------------------
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.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
table.close()
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)