DAMASK_EICMD/processing/pre/geom_fromOsteonGeometry.py

#!/usr/bin/env python3

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 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',
                  help='a,b grid of hexahedral box [%default]')
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',
                  help='Haversian canal radius [%default]')
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',
                  help='lamella width [%default]')
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',
                  help='vertical/horizontal osteon aspect ratio [%default]')
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',
                  help='homogenization index to be used [%default]')

parser.set_defaults(canal = 25e-6,
                    osteon = 100e-6,
                    aspect = 1.0,
                    omega = 0.0,
                    period = 5e-6,
                    amplitude = 60,
                    size = (300e-6,300e-6),
                    grid = (512,512),
                    homogenization = 1)

(options,filename) = parser.parse_args()


name = None if filename == [] else filename[0]
damask.util.report(scriptName,name)

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')

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*np.pi*(radius-options.canal)/options.period)

microstructure = np.where(radius < float(options.canal), 1,0)\
               + np.where(radius > float(options.osteon),2,0)

# extend to 3D
size = np.append(size,np.min(size/grid))
grid = np.append(grid,1)
microstructure = microstructure.reshape(microstructure.shape+(1,))

alphaOfGrain = np.zeros(grid[0]*grid[1],'d')
betaOfGrain  = np.zeros(grid[0]*grid[1],'d')

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 

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)))

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)
  
if name is None:
  sys.stdout.write(str(geom.show()))
else:
  geom.to_file(name)