updated to state-of-the art file handling etc
This commit is contained in:
Martin Diehl
parent
0874ebe096
commit
a0f9865133
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@ -1,11 +1,16 @@
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#!/usr/bin/env python
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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# -*- coding: UTF-8 no BOM -*-
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import os,re,sys,math
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import os,re,sys,math,string
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import numpy as np
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from collections import defaultdict
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from optparse import OptionParser
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from optparse import OptionParser
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import damask
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CoverA=1.587
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scriptID = '$Id$'
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slipnormal_temp = [ # This is the real slip system information for hex aka titanium for now.
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scriptName = scriptID.split()[1]
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slipnormal_temp = [
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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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[0,0,0,1],
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[0,0,0,1],
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[0,0,0,1],
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@ -198,15 +203,21 @@ slipdirection = { \
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],
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],
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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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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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""" 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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eulerRot = [[ math.cos(phi1)*math.cos(phi2) - math.cos(Phi)*math.sin(phi1)*math.sin(phi2),
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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.cos(phi1)*math.sin(phi2) - math.cos(Phi)*math.cos(phi2)*math.sin(phi1),
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[ math.sin(Phi)*math.sin(phi2), math.sin(Phi)*math.cos(phi2), math.cos(Phi)]]
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math.sin(Phi)*math.sin(phi1)
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],
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[ math.cos(phi2)*math.sin(phi1) + math.cos(Phi)*math.cos(phi1)*math.sin(phi2),
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math.cos(Phi)*math.cos(phi1)*math.cos(phi2) - math.sin(phi1)*math.sin(phi2),
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-math.sin(Phi)*math.cos(phi1)
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],
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[ math.sin(Phi)*math.sin(phi2),
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math.sin(Phi)*math.cos(phi2),
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math.cos(Phi)
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]]
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xbar = [0,0,0]
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xbar = [0,0,0]
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if len(x) == 3:
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if len(x) == 3:
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@ -214,16 +225,12 @@ def applyEulers(phi1,Phi,phi2,x):
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xbar[i] = sum([eulerRot[i][j]*x[j] for j 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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return xbar
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# --------------------------------------------------------------------
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def normalize(x):
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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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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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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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def crossproduct(x,y):
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return [
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return [
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@ -232,37 +239,42 @@ def crossproduct(x,y):
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x[0]*y[1]-y[0]*x[1],
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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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# --------------------------------------------------------------------
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# --------------------------------------------------------------------
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# MAIN
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# MAIN
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# --------------------------------------------------------------------
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# --------------------------------------------------------------------
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parser = OptionParser(usage='%prog [options] [file]', description = """
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', 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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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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""", version = string.replace(scriptID,'\n','\\n')
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""")
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)
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parser.add_option('-l','--lattice', dest='lattice', choices=('fcc','bcc','hex'), \
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parser.add_option('-l','--lattice', dest='lattice', action='store', type='choice',
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help='key for lattice type [%default]')
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choices=('fcc','bcc','hex'), metavar='string',
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parser.add_option('-d','--forcedirection', dest='forcedirection', type='int', nargs=3, \
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help="type of neighborhood ('fcc','bcc','hex') [%default]")
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help='force direction in lab coordinates [%default]')
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parser.add_option('--direction', dest='forcedirection', action='store', type='int', nargs=3, metavar='int int int',
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parser.add_option('-n','--stressnormal', dest='stressnormal', type='int', nargs=3, \
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help='force direction in lab coordinates %default')
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help='stress plane normal in lab coordinates [%default]')
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parser.add_option('-n','--normal', dest='stressnormal', action='store', type='int', nargs=3, metavar='int int int',
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parser.add_option('-t','--trace', dest='traceplane', type='int', nargs=3, \
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help='stress plane normal in lab coordinates ')
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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('--trace', dest='traceplane', action='store', type='int', nargs=3, metavar='int int int',
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parser.add_option('-r','--rank', dest='rank', type='int', \
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help='normal (in lab coordinates) of plane on which the plane trace of the Schmid factor(s) is reported')
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parser.add_option('--covera', dest='CoverA', action='store', type='float', metavar='float',
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help='C over A ratio for hexagonal systems')
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parser.add_option('-r','--rank', dest='rank', action='store', type='int', nargs=3, metavar='int int int',
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help="report trace of r'th highest Schmid factor [%default]")
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help="report trace of r'th highest Schmid factor [%default]")
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parser.add_option('-e', '--eulers', dest='eulers', action='store', type='string', metavar='string',
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help='Euler angles label')
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parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
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help = 'Euler angles are given in degrees [%default]')
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parser.set_defaults(lattice = 'fcc')
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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(forcedirection = [0, 0, 1])
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parser.set_defaults(stressnormal = None)
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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(traceplane = None)
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parser.set_defaults(rank = 0)
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parser.set_defaults(rank = 0)
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parser.set_defaults(CoverA = 1.587)
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parser.set_defaults(eulers = 'eulerangles')
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(options,filename) = parser.parse_args()
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(options,filenames) = parser.parse_args()
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options.forcedirection = normalize(options.forcedirection)
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options.forcedirection = normalize(options.forcedirection)
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if options.stressnormal:
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if options.stressnormal:
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@ -276,95 +288,105 @@ if options.traceplane:
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options.traceplane = normalize(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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options.rank = min(options.rank,Nslipsystems[options.lattice])
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# read from standard input unless input file specified
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datainfo = { # list of requested labels per datatype
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if filename == []:
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'vector': {'len':3,
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file = sys.stdin
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'label':[]},
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elif os.path.exists(filename[0]):
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}
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file = open(filename[0])
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# read data
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datainfo['vector']['label'] += [options.eulers]
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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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toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
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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': # 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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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][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][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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slipnormal[options.lattice][i][2]=slipnormal_temp[i][3]/options.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][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][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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slipdirection[options.lattice][i][2]=slipdirection_temp[i][3]*options.CoverA
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for i in range(Nslipsystems[options.lattice]):
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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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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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slipdirection[options.lattice][i]=normalize(slipdirection[options.lattice][i])
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for c in range(len(labels)):
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# ------------------------------------------ setup file handles ---------------------------------------
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m = re.search('.*([Pp]hi\d*).*', labels[c])
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files = []
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if m:
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if filenames == []:
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if m.group(1).lower() == "phi1":
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files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
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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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else:
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file = open(filename[0],'w')
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for name in filenames:
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file.write(output)
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if os.path.exists(name):
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file.close()
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files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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# ------------------------------------------ loop over input files ---------------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
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active = defaultdict(list)
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column = defaultdict(dict)
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for datatype,info in datainfo.items():
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for label in info['label']:
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foundIt = False
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for key in ['1_'+label,label]:
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if key in table.labels:
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foundIt = True
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active[datatype].append(label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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if not foundIt:
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file['croak'].write('column %s not found...\n'%label)
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break
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# ------------------------------------------ assemble header ---------------------------------------
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table.labels_append(['(%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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table.labels_append('trace_x trace_y trace_z system')
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else:
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table.labels_append(['(%i)tx\tty\ttz'%(i+1) for i in range(Nslipsystems[options.lattice])])
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table.head_write()
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# ------------------------------------------ process data ----------------------------------------
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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[phi1,Phi,phi2] = Eulers=toRadians*np.array(map(\
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float,table.data[column['vector'][options.eulers]:\
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column['vector'][options.eulers]+datainfo['vector']['len']]))
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S = [ sum( [applyEulers(phi1,Phi,phi2,normalize( \
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slipnormal[options.lattice][slipsystem]))[i]*options.stressnormal[i] for i in range(3)] ) * \
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sum( [applyEulers(phi1,Phi,phi2,normalize( \
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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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table.data_append(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]) ]
|
||||||
|
if options.rank == 0:
|
||||||
|
table.data_append('\t'.join(map(lambda x:'%f\t%f\t%f'%(x[0],x[1],x[2]),trace)))
|
||||||
|
elif options.rank > 0:
|
||||||
|
SabsSorted = sorted([(abs(S[i]),i) for i in range(len(S))])
|
||||||
|
table.data_append('\t'.join(map(str,trace[SabsSorted[-options.rank][1]])) + '\t%i'%(1+SabsSorted[-options.rank][1]))
|
||||||
|
outputAlive = table.data_write() # output processed line
|
||||||
|
|
||||||
|
# ------------------------------------------ output result ---------------------------------------
|
||||||
|
outputAlive and table.output_flush() # just in case of buffered ASCII table
|
||||||
|
|
||||||
|
file['input'].close() # close input ASCII table (works for stdin)
|
||||||
|
file['output'].close() # close output ASCII table (works for stdout)
|
||||||
|
if file['name'] != 'STDIN':
|
||||||
|
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue