added script to make 27 periodic copies (3 in each dimension)
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Martin Diehl
parent
f1ad5007c2
commit
010d4c6e26
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@ -0,0 +1,151 @@
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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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import os,sys,math,string,re,numpy, damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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# -----------------------------
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class extendedOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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identifiers = {
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'resolution': ['a','b','c'],
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'dimension': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grains': lambda x: int(x),
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'resolution': lambda x: int(x),
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'origin': lambda x: float(x),
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'dimension': lambda x: float(x),
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'homogenization': lambda x: int(x),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Generate geometry description and material configuration by standard Voronoi tessellation of given seeds file.
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""" + string.replace('$Id$','\n','\\n')
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)
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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')
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parser.set_defaults(twoD = False)
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(options,filenames) = parser.parse_args()
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# ------------------------------------------ setup file handles ---------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name,
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'input':open(name),
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'output':open(name+'_tmp','w'),
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'croak':sys.stdout,
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})
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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(file['name']+'\n')
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firstline = file['input'].readline()
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m = re.search('(\d+)\s*head', firstline.lower())
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if m:
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headerlines = int(m.group(1))
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headers = [firstline]+[file['input'].readline() for i in range(headerlines)]
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else:
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headerlines = 1
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headers = firstline
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info = {'grains': 0,
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'resolution': numpy.array([0,0,0]),
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'dimension': numpy.array([1.0,1.0,1.0]),
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'origin': numpy.array([0.0,0.0,0.0]),
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'homogenization': 1,
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}
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new_header = []
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for header in headers:
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headitems = map(str.lower,header.split())
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if headitems[0] in mappings.keys():
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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info[headitems[0]][i] = \
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mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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content = []
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for line in file['input']:
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for word in line.split(): content.append(word)
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file['input'].close()
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content=numpy.reshape(numpy.tile(numpy.reshape(content,info['resolution']),(1,1,1,3,3,3)),
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info['resolution'].prod()*27)
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info['grains'] = max(numpy.array(content,'i'))
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file['croak'].write('grains: %i\n'%info['grains'] + \
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'resolution: %s\n'%(' x '.join(map(str,info['resolution']))) + \
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'dimension: %s\n'%(' x '.join(map(str,info['dimension']))) + \
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'origin: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'])
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new_header.append("grains\t%i\n"%( info['grains']))
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new_header.append("resolution\ta %i\tb %i\tc %i\n"%(
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info['resolution'][0]*3,
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info['resolution'][1]*3,
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info['resolution'][2]*3,))
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new_header.append("dimension\tx %f\ty %f\tz %f\n"%(
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info['dimension'][0],
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info['dimension'][1],
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info['dimension'][2],))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(
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info['origin'][0],
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info['origin'][1],
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info['origin'][2],))
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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# -------------------------------------- write data to file ----------------------------------
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formatwidth = 1+int(math.log10(info['grains']))
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file['output'].write('%i\theader\n'%(len(new_header)) + ''.join(new_header))
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for n in xrange(info['resolution'][1:3].prod()*9):
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file['output'].write({ True: ' ',
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False:'\n'}[options.twoD].\
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join(map(lambda x: str(x).rjust(formatwidth),\
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content[n*3*info['resolution'][0]:(n+1)*3*info['resolution'][0]]))+'\n')
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# ------------------------------------------ output finalization ---------------------------------------
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if file['name'] != 'STDIN':
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file['output'].close()
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os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0]+'_27periodicCopies.geom')
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@ -26,6 +26,7 @@ bin_link = { \
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'geom_check.py',
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'geom_rescale.py',
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'geom_pack.py',
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'geom_periodicCopies.py',
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'geom_unpack.py',
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'geom_translate.py',
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'geom_vicinityOffset.py',
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