updated to state-of-the art file handling etc
This commit is contained in:
Martin Diehl
parent
0874ebe096
commit
a0f9865133
|
|
@ -1,11 +1,16 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,re,sys,math
|
||||
import os,re,sys,math,string
|
||||
import numpy as np
|
||||
from collections import defaultdict
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
CoverA=1.587
|
||||
slipnormal_temp = [ # This is the real slip system information for hex aka titanium for now.
|
||||
scriptID = '$Id$'
|
||||
scriptName = scriptID.split()[1]
|
||||
|
||||
slipnormal_temp = [
|
||||
[0,0,0,1],
|
||||
[0,0,0,1],
|
||||
[0,0,0,1],
|
||||
|
|
@ -198,15 +203,21 @@ slipdirection = { \
|
|||
],
|
||||
}
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def applyEulers(phi1,Phi,phi2,x):
|
||||
""" transform x given in crystal coordinates to xbar returned in lab coordinates for Euler angles phi1,Phi,phi2 """
|
||||
|
||||
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)], \
|
||||
[ 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)], \
|
||||
[ math.sin(Phi)*math.sin(phi2), math.sin(Phi)*math.cos(phi2), math.cos(Phi)]]
|
||||
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)
|
||||
],
|
||||
[ 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)
|
||||
],
|
||||
[ math.sin(Phi)*math.sin(phi2),
|
||||
math.sin(Phi)*math.cos(phi2),
|
||||
math.cos(Phi)
|
||||
]]
|
||||
|
||||
xbar = [0,0,0]
|
||||
if len(x) == 3:
|
||||
|
|
@ -214,16 +225,12 @@ def applyEulers(phi1,Phi,phi2,x):
|
|||
xbar[i] = sum([eulerRot[i][j]*x[j] for j in range(3)])
|
||||
return xbar
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def normalize(x):
|
||||
|
||||
norm = math.sqrt(sum([x[i]*x[i] for i in range(len(x))]))
|
||||
|
||||
return [x[i]/norm for i in range(len(x))]
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
def crossproduct(x,y):
|
||||
|
||||
return [
|
||||
|
|
@ -232,37 +239,42 @@ def crossproduct(x,y):
|
|||
x[0]*y[1]-y[0]*x[1],
|
||||
]
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
parser = OptionParser(usage='%prog [options] [file]', description = """
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Add columns listing Schmid factors (and optional trace vector of selected system) for given Euler angles.
|
||||
Column headings need to have names 'phi1', 'Phi', 'phi2'.
|
||||
|
||||
$Id$
|
||||
""")
|
||||
""", version = string.replace(scriptID,'\n','\\n')
|
||||
)
|
||||
|
||||
parser.add_option('-l','--lattice', dest='lattice', choices=('fcc','bcc','hex'), \
|
||||
help='key for lattice type [%default]')
|
||||
parser.add_option('-d','--forcedirection', dest='forcedirection', type='int', nargs=3, \
|
||||
help='force direction in lab coordinates [%default]')
|
||||
parser.add_option('-n','--stressnormal', dest='stressnormal', type='int', nargs=3, \
|
||||
help='stress plane normal in lab coordinates [%default]')
|
||||
parser.add_option('-t','--trace', dest='traceplane', type='int', nargs=3, \
|
||||
help="normal (in lab coordinates) of plane on which the plane trace of the Schmid factor(s) is reported [%default]")
|
||||
parser.add_option('-r','--rank', dest='rank', type='int', \
|
||||
parser.add_option('-l','--lattice', dest='lattice', action='store', type='choice',
|
||||
choices=('fcc','bcc','hex'), metavar='string',
|
||||
help="type of neighborhood ('fcc','bcc','hex') [%default]")
|
||||
parser.add_option('--direction', dest='forcedirection', action='store', type='int', nargs=3, metavar='int int int',
|
||||
help='force direction in lab coordinates %default')
|
||||
parser.add_option('-n','--normal', dest='stressnormal', action='store', type='int', nargs=3, metavar='int int int',
|
||||
help='stress plane normal in lab coordinates ')
|
||||
parser.add_option('--trace', dest='traceplane', action='store', type='int', nargs=3, metavar='int int int',
|
||||
help='normal (in lab coordinates) of plane on which the plane trace of the Schmid factor(s) is reported')
|
||||
parser.add_option('--covera', dest='CoverA', action='store', type='float', metavar='float',
|
||||
help='C over A ratio for hexagonal systems')
|
||||
parser.add_option('-r','--rank', dest='rank', action='store', type='int', nargs=3, metavar='int int int',
|
||||
help="report trace of r'th highest Schmid factor [%default]")
|
||||
parser.add_option('-e', '--eulers', dest='eulers', action='store', type='string', metavar='string',
|
||||
help='Euler angles label')
|
||||
parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
|
||||
help = 'Euler angles are given in degrees [%default]')
|
||||
parser.set_defaults(lattice = 'fcc')
|
||||
parser.set_defaults(forcedirection = [0, 0, 1])
|
||||
parser.set_defaults(stressnormal = None)
|
||||
parser.set_defaults(traceplane = None)
|
||||
parser.set_defaults(rank = 0)
|
||||
parser.set_defaults(CoverA = 1.587)
|
||||
parser.set_defaults(eulers = 'eulerangles')
|
||||
|
||||
(options,filename) = parser.parse_args()
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
options.forcedirection = normalize(options.forcedirection)
|
||||
if options.stressnormal:
|
||||
|
|
@ -276,95 +288,105 @@ if options.traceplane:
|
|||
options.traceplane = normalize(options.traceplane)
|
||||
options.rank = min(options.rank,Nslipsystems[options.lattice])
|
||||
|
||||
# read from standard input unless input file specified
|
||||
if filename == []:
|
||||
file = sys.stdin
|
||||
elif os.path.exists(filename[0]):
|
||||
file = open(filename[0])
|
||||
datainfo = { # list of requested labels per datatype
|
||||
'vector': {'len':3,
|
||||
'label':[]},
|
||||
}
|
||||
|
||||
# read data
|
||||
content = file.readlines()
|
||||
file.close()
|
||||
datainfo['vector']['label'] += [options.eulers]
|
||||
|
||||
# get labels by either read the first row, or - if keyword header is present - the last line of the header
|
||||
headerlines = 1
|
||||
m = re.search('(\d+)\s*head', content[0].lower())
|
||||
if m:
|
||||
headerlines = int(m.group(1))+1
|
||||
labels = content[headerlines-1].split()
|
||||
data = content[headerlines:]
|
||||
toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
|
||||
|
||||
# Convert 4 Miller indices notation of hex to orthogonal 3 Miller indices notation
|
||||
if options.lattice=="hex":
|
||||
if options.lattice=='hex': # Convert 4 Miller indices notation of hex to orthogonal 3 Miller indices notation
|
||||
for i in range(Nslipsystems[options.lattice]):
|
||||
slipnormal[options.lattice][i][0]=slipnormal_temp[i][0]
|
||||
slipnormal[options.lattice][i][1]=(slipnormal_temp[i][0]+2.0*slipnormal_temp[i][1])/math.sqrt(3.0)
|
||||
slipnormal[options.lattice][i][2]=slipnormal_temp[i][3]/CoverA
|
||||
slipdirection[options.lattice][i][0]=slipdirection_temp[i][0]*1.5 # direction [uvtw]->[3u/2 (u+2v)*sqrt(3)/2 w*(c/a)] ,
|
||||
slipnormal[options.lattice][i][2]=slipnormal_temp[i][3]/options.CoverA
|
||||
slipdirection[options.lattice][i][0]=slipdirection_temp[i][0]*1.5 # direction [uvtw]->[3u/2 (u+2v)*sqrt(3)/2 w*(c/a)] ,
|
||||
slipdirection[options.lattice][i][1]=(slipdirection_temp[i][0]+2.0*slipdirection_temp[i][1])*(0.5*math.sqrt(3.0))
|
||||
slipdirection[options.lattice][i][2]=slipdirection_temp[i][3]*CoverA
|
||||
slipdirection[options.lattice][i][2]=slipdirection_temp[i][3]*options.CoverA
|
||||
|
||||
for i in range(Nslipsystems[options.lattice]):
|
||||
slipnormal[options.lattice][i]=normalize(slipnormal[options.lattice][i])
|
||||
slipdirection[options.lattice][i]=normalize(slipdirection[options.lattice][i])
|
||||
|
||||
for c in range(len(labels)):
|
||||
m = re.search('.*([Pp]hi\d*).*', labels[c])
|
||||
if m:
|
||||
if m.group(1).lower() == "phi1":
|
||||
phi1Column = c
|
||||
elif m.group(1).lower() == "phi":
|
||||
PhiColumn = c
|
||||
elif m.group(1).lower() == "phi2":
|
||||
phi2Column = c
|
||||
|
||||
output = '1\theader\n' + \
|
||||
'\t'.join(map(str,labels)) + \
|
||||
'\t' + \
|
||||
'\t'.join(['(%i)S(%i %i %i)[%i %i %i]'%(i+1,
|
||||
slipnormal[options.lattice][i][0],
|
||||
slipnormal[options.lattice][i][1],
|
||||
slipnormal[options.lattice][i][2],
|
||||
slipdirection[options.lattice][i][0],
|
||||
slipdirection[options.lattice][i][1],
|
||||
slipdirection[options.lattice][i][2],
|
||||
) for i in range(Nslipsystems[options.lattice])])
|
||||
if options.traceplane:
|
||||
if options.rank > 0:
|
||||
output += '\ttrace_x\ttrace_y\ttrace_z\tsystem'
|
||||
else:
|
||||
output += '\t' + '\t'.join(['(%i)tx\tty\ttz'%(i+1) for i in range(Nslipsystems[options.lattice])])
|
||||
output += '\n'
|
||||
|
||||
for line in data:
|
||||
items = line.split()[:len(labels)]
|
||||
if items == []:
|
||||
continue
|
||||
phi1 = math.radians(float(items[phi1Column]))
|
||||
Phi = math.radians(float(items[PhiColumn]))
|
||||
phi2 = math.radians(float(items[phi2Column]))
|
||||
S = [ sum( [applyEulers(phi1,Phi,phi2,normalize( slipnormal[options.lattice][slipsystem]))[i]*options.stressnormal[i] for i in range(3)] ) * \
|
||||
sum( [applyEulers(phi1,Phi,phi2,normalize(slipdirection[options.lattice][slipsystem]))[i]*options.forcedirection[i] for i in range(3)] ) \
|
||||
for slipsystem in range(Nslipsystems[options.lattice]) ]
|
||||
output += '\t'.join(items + map(str,S))
|
||||
if options.traceplane:
|
||||
trace = [crossproduct(options.traceplane,applyEulers(phi1,Phi,phi2,normalize(slipnormal[options.lattice][slipsystem]))) \
|
||||
for slipsystem in range(Nslipsystems[options.lattice]) ]
|
||||
if options.rank == 0:
|
||||
output += '\t' + '\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))])
|
||||
output += '\t' + '\t'.join(map(str,trace[SabsSorted[-options.rank][1]])) + '\t%i'%(1+SabsSorted[-options.rank][1])
|
||||
# for t in [normalize(crossproduct(options.traceplane,applyEulers(phi1,Phi,phi2,normalize(slipnormal[options.lattice][i])))) for i in range(12,24)]:
|
||||
# print '\t'.join(map(str,t))
|
||||
# print '\t'.join(map(lambda x: str(-x),t))
|
||||
# print '\t'.join(['0','0','0'])
|
||||
# print
|
||||
output += '\n'
|
||||
|
||||
if filename == []:
|
||||
print output
|
||||
# ------------------------------------------ setup file handles ---------------------------------------
|
||||
files = []
|
||||
if filenames == []:
|
||||
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
|
||||
else:
|
||||
file = open(filename[0],'w')
|
||||
file.write(output)
|
||||
file.close()
|
||||
for name in filenames:
|
||||
if os.path.exists(name):
|
||||
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
|
||||
|
||||
# ------------------------------------------ loop over input files ---------------------------------------
|
||||
for file in files:
|
||||
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
|
||||
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
|
||||
|
||||
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
|
||||
table.head_read() # read ASCII header info
|
||||
table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
|
||||
|
||||
active = defaultdict(list)
|
||||
column = defaultdict(dict)
|
||||
|
||||
for datatype,info in datainfo.items():
|
||||
for label in info['label']:
|
||||
foundIt = False
|
||||
for key in ['1_'+label,label]:
|
||||
if key in table.labels:
|
||||
foundIt = True
|
||||
active[datatype].append(label)
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
if not foundIt:
|
||||
file['croak'].write('column %s not found...\n'%label)
|
||||
break
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
|
||||
table.labels_append(['(%i)S(%i %i %i)[%i %i %i]'%(i+1,
|
||||
slipnormal[options.lattice][i][0],
|
||||
slipnormal[options.lattice][i][1],
|
||||
slipnormal[options.lattice][i][2],
|
||||
slipdirection[options.lattice][i][0],
|
||||
slipdirection[options.lattice][i][1],
|
||||
slipdirection[options.lattice][i][2],
|
||||
) for i in range(Nslipsystems[options.lattice])])
|
||||
|
||||
if options.traceplane:
|
||||
if options.rank > 0:
|
||||
table.labels_append('trace_x trace_y trace_z system')
|
||||
else:
|
||||
table.labels_append(['(%i)tx\tty\ttz'%(i+1) for i in range(Nslipsystems[options.lattice])])
|
||||
table.head_write()
|
||||
|
||||
# ------------------------------------------ process data ----------------------------------------
|
||||
outputAlive = True
|
||||
while outputAlive and table.data_read(): # read next data line of ASCII table
|
||||
[phi1,Phi,phi2] = Eulers=toRadians*np.array(map(\
|
||||
float,table.data[column['vector'][options.eulers]:\
|
||||
column['vector'][options.eulers]+datainfo['vector']['len']]))
|
||||
S = [ sum( [applyEulers(phi1,Phi,phi2,normalize( \
|
||||
slipnormal[options.lattice][slipsystem]))[i]*options.stressnormal[i] for i in range(3)] ) * \
|
||||
sum( [applyEulers(phi1,Phi,phi2,normalize( \
|
||||
slipdirection[options.lattice][slipsystem]))[i]*options.forcedirection[i] for i in range(3)] ) \
|
||||
for slipsystem in range(Nslipsystems[options.lattice]) ]
|
||||
table.data_append(S)
|
||||
if options.traceplane:
|
||||
trace = [crossproduct(options.traceplane,applyEulers(phi1,Phi,phi2,normalize(slipnormal[options.lattice][slipsystem]))) \
|
||||
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