last polishing on preprocessing scripts, documentation and scripts are all up to date.
added addSchmidfactors to post processing scripts
This commit is contained in:
Martin Diehl
parent
84c43741a6
commit
e635b06270
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@ -0,0 +1,369 @@
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#!/usr/bin/python
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import os,re,sys,math
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from optparse import OptionParser
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CoverA=1.587
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slipnormal_temp = [ # This is the real slip system information for hex aka titanium for now.
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[0,0,0,1],
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[0,0,0,1],
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[0,0,0,1],
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[0,1,-1,0],
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[-1,0,1,0],
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[1,-1,0,0],
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[0,1,-1,1],
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[-1,1,0,1],
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[-1,0,1,1],
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[0,-1,1,1],
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[1,-1,0,1],
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[1,0,-1,1],
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[0,1,-1,1],
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[0,1,-1,1],
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[-1,1,0,1],
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[-1,1,0,1],
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[-1,0,1,1],
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[-1,0,1,1],
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[0,-1,1,1],
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[0,-1,1,1],
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[1,-1,0,1],
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[1,-1,0,1],
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[1,0,-1,1],
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[1,0,-1,1],
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]
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slipdirection_temp = [
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[2,-1,-1,0],
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[-1,2,-1,0],
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[-1,-1,2,0],
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[2,-1,-1,0],
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[-1,2,-1,0],
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[-1,-1,2,0],
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[2,-1,-1,0],
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[1,1,-2,0],
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[-1,2,-1,0],
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[-2,1,1,0],
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[-1,-1,2,0],
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[1,-2,1,0],
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[-1,2,-1,3],
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[1,1,-2,3],
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[-2,1,1,3],
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[-1,2,-1,3],
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[-1,-1,2,3],
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[-2,1,1,3],
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[1,-2,1,3],
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[-1,-1,2,3],
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[2,-1,-1,3],
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[1,-2,1,3],
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[1,1,-2,3],
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[2,-1,-1,3],
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]
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# slip normals and directions according to cpfem implementation
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Nslipsystems = {'fcc': 12, 'bcc': 24, 'hex': 24}
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slipnormal = { \
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'fcc': [
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[1,1,1],
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[1,1,1],
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[1,1,1],
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[-1,-1,1],
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[-1,-1,1],
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[-1,-1,1],
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[1,-1,-1],
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[1,-1,-1],
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[1,-1,-1],
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[-1,1,-1],
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[-1,1,-1],
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[-1,1,-1],
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],
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'bcc': [
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[0,1,1],
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[0,1,1],
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[0,-1,1],
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[0,-1,1],
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[1,0,1],
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[1,0,1],
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[-1,0,1],
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[-1,0,1],
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[1,1,0],
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[1,1,0],
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[-1,1,0],
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[-1,1,0],
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[2,1,1],
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[-2,1,1],
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[2,-1,1],
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[2,1,-1],
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[1,2,1],
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[-1,2,1],
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[1,-2,1],
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[1,2,-1],
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[1,1,2],
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[-1,1,2],
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[1,-1,2],
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[1,1,-2],
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],
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'hex': [ # these are dummy numbers and are recalculated based on the above hex real slip systems.
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[1,1,0],
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[1,1,0],
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[1,0,1],
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[1,0,1],
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[0,1,1],
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[0,1,1],
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[1,-1,0],
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[1,-1,0],
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[-1,0,1],
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[-1,0,1],
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[0,-1,1],
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[0,-1,1],
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[2,-1,1],
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[1,-2,-1],
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[1,1,2],
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[2,1,1],
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[1,2,-1],
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[1,-1,2],
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[2,1,-1],
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[1,2,1],
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[1,-1,-2],
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[2,-1,-1],
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[1,-2,1],
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[1,1,-2],
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],
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}
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slipdirection = { \
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'fcc': [
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[0,1,-1],
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[-1,0,1],
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[1,-1,0],
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[0,-1,-1],
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[1,0,1],
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[-1,1,0],
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[0,-1,1],
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[-1,0,-1],
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[1,1,0],
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[0,1,1],
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[1,0,-1],
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[-1,-1,0],
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],
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'bcc': [
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[1,-1,1],
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[-1,-1,1],
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[1,1,1],
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[-1,1,1],
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[-1,1,1],
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[-1,-1,1],
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[1,1,1],
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[1,-1,1],
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[-1,1,1],
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[-1,1,-1],
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[1,1,1],
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[1,1,-1],
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[-1,1,1],
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[1,1,1],
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[1,1,-1],
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[1,-1,1],
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[1,-1,1],
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[1,1,-1],
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[1,1,1],
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[-1,1,1],
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[1,1,-1],
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[1,-1,1],
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[-1,1,1],
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[1,1,1],
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],
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'hex': [ # these are dummy numbers and are recalculated based on the above hex real slip systems.
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[-1,1,1],
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[1,-1,1],
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[-1,-1,1],
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[-1,1,1],
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[-1,-1,1],
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[1,-1,1],
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[1,1,1],
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[-1,-1,1],
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[1,-1,1],
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[1,1,1],
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[1,1,1],
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[-1,1,1],
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[1,1,-1],
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[1,1,-1],
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[1,1,-1],
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[1,-1,-1],
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[1,-1,-1],
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[1,-1,-1],
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[1,-1,1],
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[1,-1,1],
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[1,-1,1],
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[1,1,1],
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[1,1,1],
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[1,1,1],
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],
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}
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# --------------------------------------------------------------------
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def applyEulers(phi1,Phi,phi2,x):
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""" transform x given in crystal coordinates to xbar returned in lab coordinates for Euler angles phi1,Phi,phi2 """
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eulerRot = [[ math.cos(phi1)*math.cos(phi2) - math.cos(Phi)*math.sin(phi1)*math.sin(phi2), - math.cos(phi1)*math.sin(phi2) - math.cos(Phi)*math.cos(phi2)*math.sin(phi1), math.sin(Phi)*math.sin(phi1)], \
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[ math.cos(phi2)*math.sin(phi1) + math.cos(Phi)*math.cos(phi1)*math.sin(phi2), math.cos(Phi)*math.cos(phi1)*math.cos(phi2) - math.sin(phi1)*math.sin(phi2), -math.sin(Phi)*math.cos(phi1)], \
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[ math.sin(Phi)*math.sin(phi2), math.sin(Phi)*math.cos(phi2), math.cos(Phi)]]
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xbar = [0,0,0]
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if len(x) == 3:
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for i in range(3):
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xbar[i] = sum([eulerRot[i][j]*x[j] for j in range(3)])
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return xbar
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# --------------------------------------------------------------------
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def normalize(x):
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norm = math.sqrt(sum([x[i]*x[i] for i in range(len(x))]))
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return [x[i]/norm for i in range(len(x))]
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# --------------------------------------------------------------------
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def crossproduct(x,y):
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return [
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x[1]*y[2]-y[1]*x[2],
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x[2]*y[0]-y[2]*x[0],
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x[0]*y[1]-y[0]*x[1],
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]
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# --------------------------------------------------------------------
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(usage='%prog [options] [file]', description = """
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Add columns listing Schmid factors (and optional trace vector of selected system) for given Euler angles.
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Column headings need to have names 'phi1', 'Phi', 'phi2'.
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$Id$
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""")
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parser.add_option('-l','--lattice', dest='lattice', choices=('fcc','bcc','hex'), \
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help='key for lattice type [%default]')
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parser.add_option('-d','--forcedirection', dest='forcedirection', type='int', nargs=3, \
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help='force direction in lab coordinates [%default]')
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parser.add_option('-n','--stressnormal', dest='stressnormal', type='int', nargs=3, \
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help='stress plane normal in lab coordinates [%default]')
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parser.add_option('-t','--trace', dest='traceplane', type='int', nargs=3, \
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help="normal (in lab coordinates) of plane on which the plane trace of the Schmid factor(s) is reported [%default]")
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parser.add_option('-r','--rank', dest='rank', type='int', \
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help="report trace of r'th highest Schmid factor [%default]")
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parser.set_defaults(lattice = 'fcc')
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parser.set_defaults(forcedirection = [0, 0, 1])
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parser.set_defaults(stressnormal = None)
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parser.set_defaults(traceplane = None)
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parser.set_defaults(rank = 0)
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(options,filename) = parser.parse_args()
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options.forcedirection = normalize(options.forcedirection)
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if options.stressnormal:
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if abs(sum([options.forcedirection[i] * options.stressnormal[i] for i in range(3)])) < 1e-3:
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options.stressnormal = normalize(options.stressnormal)
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else:
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parser.error('stress plane normal not orthogonal to force direction')
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else:
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options.stressnormal = options.forcedirection
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if options.traceplane:
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options.traceplane = normalize(options.traceplane)
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options.rank = min(options.rank,Nslipsystems[options.lattice])
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# read from standard input unless input file specified
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if filename == []:
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file = sys.stdin
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elif os.path.exists(filename[0]):
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file = open(filename[0])
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# read data
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content = file.readlines()
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file.close()
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# get labels by either read the first row, or - if keyword header is present - the last line of the header
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headerlines = 1
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m = re.search('(\d+)\s*head', content[0].lower())
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if m:
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headerlines = int(m.group(1))+1
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labels = content[headerlines-1].split()
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data = content[headerlines:]
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# Convert 4 Miller indices notation of hex to orthogonal 3 Miller indices notation
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if options.lattice=="hex":
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for i in range(Nslipsystems[options.lattice]):
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slipnormal[options.lattice][i][0]=slipnormal_temp[i][0]
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slipnormal[options.lattice][i][1]=(slipnormal_temp[i][0]+2.0*slipnormal_temp[i][1])/math.sqrt(3.0)
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slipnormal[options.lattice][i][2]=slipnormal_temp[i][3]/CoverA
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slipdirection[options.lattice][i][0]=slipdirection_temp[i][0]*1.5 # direction [uvtw]->[3u/2 (u+2v)*sqrt(3)/2 w*(c/a)] ,
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slipdirection[options.lattice][i][1]=(slipdirection_temp[i][0]+2.0*slipdirection_temp[i][1])*(0.5*math.sqrt(3.0))
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slipdirection[options.lattice][i][2]=slipdirection_temp[i][3]*CoverA
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for i in range(Nslipsystems[options.lattice]):
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slipnormal[options.lattice][i]=normalize(slipnormal[options.lattice][i])
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slipdirection[options.lattice][i]=normalize(slipdirection[options.lattice][i])
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for c in range(len(labels)):
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m = re.search('.*([Pp]hi\d*).*', labels[c])
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if m:
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if m.group(1).lower() == "phi1":
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phi1Column = c
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elif m.group(1).lower() == "phi":
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PhiColumn = c
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elif m.group(1).lower() == "phi2":
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phi2Column = c
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output = '1\theader\n' + \
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'\t'.join(map(str,labels)) + \
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'\t' + \
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'\t'.join(['(%i)S(%i %i %i)[%i %i %i]'%(i+1,
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slipnormal[options.lattice][i][0],
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slipnormal[options.lattice][i][1],
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slipnormal[options.lattice][i][2],
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slipdirection[options.lattice][i][0],
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slipdirection[options.lattice][i][1],
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slipdirection[options.lattice][i][2],
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) for i in range(Nslipsystems[options.lattice])])
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if options.traceplane:
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if options.rank > 0:
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output += '\ttrace_x\ttrace_y\ttrace_z\tsystem'
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else:
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output += '\t' + '\t'.join(['(%i)tx\tty\ttz'%(i+1) for i in range(Nslipsystems[options.lattice])])
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output += '\n'
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for line in data:
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items = line.split()[:len(labels)]
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if items == []:
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continue
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phi1 = math.radians(float(items[phi1Column]))
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Phi = math.radians(float(items[PhiColumn]))
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phi2 = math.radians(float(items[phi2Column]))
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S = [ sum( [applyEulers(phi1,Phi,phi2,normalize( slipnormal[options.lattice][slipsystem]))[i]*options.stressnormal[i] for i in range(3)] ) * \
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sum( [applyEulers(phi1,Phi,phi2,normalize(slipdirection[options.lattice][slipsystem]))[i]*options.forcedirection[i] for i in range(3)] ) \
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for slipsystem in range(Nslipsystems[options.lattice]) ]
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output += '\t'.join(items + map(str,S))
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if options.traceplane:
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trace = [crossproduct(options.traceplane,applyEulers(phi1,Phi,phi2,normalize(slipnormal[options.lattice][slipsystem]))) \
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for slipsystem in range(Nslipsystems[options.lattice]) ]
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if options.rank == 0:
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output += '\t' + '\t'.join(map(lambda x:'%f\t%f\t%f'%(x[0],x[1],x[2]),trace))
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elif options.rank > 0:
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SabsSorted = sorted([(abs(S[i]),i) for i in range(len(S))])
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output += '\t' + '\t'.join(map(str,trace[SabsSorted[-options.rank][1]])) + '\t%i'%(1+SabsSorted[-options.rank][1])
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# for t in [normalize(crossproduct(options.traceplane,applyEulers(phi1,Phi,phi2,normalize(slipnormal[options.lattice][i])))) for i in range(12,24)]:
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# print '\t'.join(map(str,t))
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# print '\t'.join(map(lambda x: str(-x),t))
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# print '\t'.join(['0','0','0'])
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# print
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output += '\n'
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if filename == []:
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print output
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else:
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file = open(filename[0],'w')
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file.write(output)
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file.close()
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@ -46,9 +46,9 @@ Changes the (three-dimensional) canvas of a spectral geometry description.
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parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \
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help='a,b,c grid of hexahedral box [unchanged]')
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parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \
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help='x,y,z offset from old to new origin of grid %default')
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help='a,b,c offset from old to new origin of grid %default')
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parser.add_option('-f', '--fill', dest='fill', type='int', \
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help='(background) canvas grain index [autodetect]')
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help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
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parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
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help='output geom file with two-dimensional data arrangement [%default]')
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@ -117,7 +117,7 @@ boundaries, triple lines, and quadruple points.
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parser.add_option('-t','--type', dest='type', action='extend', type='string', \
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help='feature type (%s)'%(', '.join(map(lambda x:', '.join(x['names']),features))))
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parser.add_option('-n','--neighborhood', dest='neigborhood', action='store', type='string', \
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parser.add_option('-n','--neighborhood', dest='neigborhood', choices=neighborhoods.keys(), \
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help='type of neighborhood (%s) [neumann]'%(', '.join(neighborhoods.keys())))
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parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
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help='output geom file with two-dimensional data arrangement [%default]')
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@ -128,9 +128,6 @@ parser.set_defaults(twoD = False)
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(options,filenames) = parser.parse_args()
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options.neighborhood = options.neighborhood.lower()
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if options.neighborhood not in neighborhoods:
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parser.error('unknown neighborhood %s!'%options.neighborhood)
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feature_list = []
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for i,feature in enumerate(features):
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@ -40,8 +40,8 @@ Generate a geometry file of a bicontinuous structure of given type.
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-t','--type', dest='type', type='string', \
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help='type of minimal surface (%s)'%(','.join(minimal_surfaces)))
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parser.add_option('-t','--type', dest='type', choices=minimal_surfaces, \
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help='type of minimal surface (%s) [primitive]' %(','.join(minimal_surfaces)))
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parser.add_option('-f','--threshold', dest='threshold', type='float', \
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help='threshold value defining minimal surface [%default]')
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parser.add_option('-g', '--grid', dest='grid', type='int', nargs=3, \
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@ -51,7 +51,7 @@ parser.add_option('-s', '--size', dest='size', type='float', nargs=3, \
|
|||
parser.add_option('-p', '--periods', dest='periods', type='int', \
|
||||
help='number of repetitions of unit cell [%default]')
|
||||
parser.add_option('--homogenization', dest='homogenization', type='int', \
|
||||
help='homogenization index to be used [%defaults]')
|
||||
help='homogenization index to be used [%default]')
|
||||
parser.add_option('--m', dest='microstructure', type='int', nargs = 2, \
|
||||
help='two microstructure indices to be used %default')
|
||||
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
|
||||
|
|
|
|||
|
|
@ -40,7 +40,7 @@ Generate geometry description and material configuration by standard Voronoi tes
|
|||
)
|
||||
|
||||
parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \
|
||||
help='a,b,c grid of hexahedral box [from seed file]')
|
||||
help='a,b,c grid of hexahedral box [from seeds file]')
|
||||
parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, \
|
||||
help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
|
||||
parser.add_option('--homogenization', dest='homogenization', type='int', \
|
||||
|
|
|
|||
|
|
@ -48,7 +48,8 @@ i.e. within the region close to a grain/phase boundary.
|
|||
parser.add_option('-v', '--vicinity', dest='vicinity', type='int', \
|
||||
help='voxel distance checked for presence of other microstructure [%default]')
|
||||
parser.add_option('-m', '--microstructureoffset', dest='offset', type='int', \
|
||||
help='integer offset for tagged microstructure [autodetect]')
|
||||
help='offset (positive or negative) for tagged microstructure. '+
|
||||
'"0" selects maximum microstructure index [%default]')
|
||||
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
|
||||
help='output geom file with two-dimensional data arrangement')
|
||||
|
||||
|
|
|
|||
|
|
@ -789,10 +789,10 @@ reconstructed boundary file
|
|||
)
|
||||
|
||||
parser.add_option("-o", "--output", action='extend', dest='output', type='string', \
|
||||
help="types of output [image,mentat,procedure,spectral]")
|
||||
help="types of output [image, mentat, procedure, spectral]")
|
||||
parser.add_option("-p", "--port", type="int",\
|
||||
dest="port",\
|
||||
help="Mentat connection port")
|
||||
help="Mentat connection port [%default]")
|
||||
parser.add_option("-2", "--twodimensional", action="store_true",\
|
||||
dest="twoD",\
|
||||
help="twodimensional model [%default]")
|
||||
|
|
@ -804,16 +804,16 @@ parser.add_option("-e", "--strain", type="float",\
|
|||
help="final strain to reach in simulation [%default]")
|
||||
parser.add_option("--rate", type="float",\
|
||||
dest="strainrate",\
|
||||
help="(engineering) strain rate to simulate")
|
||||
help="(engineering) strain rate to simulate [%default]")
|
||||
parser.add_option("-N", "--increments", type="int",\
|
||||
dest="increments",\
|
||||
help="number of increments to take")
|
||||
help="number of increments to take [%default]")
|
||||
parser.add_option("-t", "--tolerance", type="float",\
|
||||
dest="tolerance",\
|
||||
help="relative tolerance of pixel positions to be swept")
|
||||
help="relative tolerance of pixel positions to be swept [%default]")
|
||||
parser.add_option("-m", "--mesh", choices=['dt_planar_trimesh','af_planar_trimesh','af_planar_quadmesh'],\
|
||||
dest="mesh",\
|
||||
help="algorithm and element type for automeshing [%default]")
|
||||
help="algorithm and element type for automeshing (dt_planar_trimesh, af_planar_trimesh, af_planar_quadmesh) [%default]")
|
||||
parser.add_option("-x", "--xmargin", type="float",\
|
||||
dest="xmargin",\
|
||||
help="margin in x in units of patch size [%default]")
|
||||
|
|
@ -828,22 +828,23 @@ parser.add_option("-z", "--extrusion", type="int",\
|
|||
help="number of repetitions in z-direction [%default]")
|
||||
parser.add_option("-i", "--imagesize", type="int",\
|
||||
dest="imgsize",\
|
||||
help="size of PNG image")
|
||||
help="size of PNG image [%default]")
|
||||
parser.add_option("-M", "--coordtransformation", type="float", nargs=4, \
|
||||
dest="M",\
|
||||
help="2x2 transformation from rcb to Euler coords ( = M . [x_rcb,y_rcb])")
|
||||
help="2x2 transformation from rcb to Euler coords [%default]")
|
||||
parser.add_option("--scatter", type="float",\
|
||||
dest="scatter",\
|
||||
help="orientation scatter [%default]")
|
||||
help="orientation scatter %default")
|
||||
|
||||
parser.set_defaults(output = [])
|
||||
parser.set_defaults(size = 1.0)
|
||||
parser.set_defaults(port = 40007)
|
||||
parser.set_defaults(xmargin = 0.0)
|
||||
parser.set_defaults(ymargin = 0.0)
|
||||
parser.set_defaults(resolution = 64)
|
||||
parser.set_defaults(extrusion = 2)
|
||||
parser.set_defaults(imgsize = 512)
|
||||
parser.set_defaults(M = [0.0,1.0,1.0,0]) # M_11, M_12, M_21, M_22. x,y in RCB is y,x of Eulers!!
|
||||
parser.set_defaults(M = [0.0,1.0,1.0,0.0]) # M_11, M_12, M_21, M_22. x,y in RCB is y,x of Eulers!!
|
||||
parser.set_defaults(tolerance = 1.0e-3)
|
||||
parser.set_defaults(scatter = 0.0)
|
||||
parser.set_defaults(strain = 0.2)
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ mappings = {
|
|||
|
||||
|
||||
parser = OptionParser(option_class=extendedOption, usage='%prog [options]', description = """
|
||||
Distribute given number of points randomly within the three-dimensional cube [0,0,0]--[1,1,1].
|
||||
Distribute given number of points randomly within the three-dimensional cube [0.0,0.0,0.0]--[1.0,1.0,1.0].
|
||||
Reports positions with random crystal orientations in seeds file format to STDOUT.
|
||||
""" + string.replace('$Id$','\n','\\n')
|
||||
)
|
||||
|
|
|
|||
|
|
@ -47,6 +47,7 @@ bin_link = { \
|
|||
'addMises.py',
|
||||
'addNorm.py',
|
||||
'addPK2.py',
|
||||
'addSchmidfactors.py',
|
||||
'addSpectralDecomposition.py',
|
||||
'addStrainTensors.py',
|
||||
'averageDown.py',
|
||||
|
|
|
|||
Loading…
Reference in New Issue