renamed script
updated to recent standard in io processing introduced "primitive" bicontinuous structure in addition to "diamond" and "gyroid"
This commit is contained in:
Philip Eisenlohr
parent
7cf2024be3
commit
c4c27860b2
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@ -0,0 +1,105 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,math,numpy
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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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# ----------------------- MAIN -------------------------------
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minimal_surfaces = ['primitive','gyroid','diamond',]
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surface = {
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'primitive': lambda x,y,z: math.cos(x)+math.cos(y)+math.cos(z),
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'gyroid': lambda x,y,z: math.sin(x)*math.cos(y)+math.sin(y)*math.cos(z)+math.cos(x)*math.sin(z),
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'diamond': lambda x,y,z: math.cos(x-y)*math.cos(z)+math.sin(x+y)*math.sin(z),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog', description = """
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Generate a geometry file of a bicontinuous structure of given type.
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""" + string.replace('$Id: spectral_geomCheck 994 2011-09-05 13:38:10Z MPIE\p.eisenlohr $','\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('-f','--threshold', dest='threshold', type='float', \
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help='threshold value defining minimal surface')
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parser.add_option('-r', '--resolution', dest='resolution', type='int', nargs=3, \
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help='a,b,c resolution of periodic box')
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parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs=3, \
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help='x,y,z dimension of periodic box')
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parser.add_option('-p', '--periods', dest='periods', type='int', \
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help='number of repetitions of unit cell')
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parser.add_option('--homogenization', dest='homogenization', type='int', \
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help='homogenization index to be used')
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parser.add_option('--phase', dest='phase', type='int', nargs = 2, \
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help='two phase indices to be used %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')
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parser.set_defaults(type = minimal_surfaces[0])
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parser.set_defaults(threshold = 0.0)
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parser.set_defaults(periods = 1)
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parser.set_defaults(resolution = numpy.array([16,16,16]))
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parser.set_defaults(dimension = numpy.array([1.0,1.0,1.0]))
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parser.set_defaults(homogenization = 1)
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parser.set_defaults(phase = [1,2])
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parser.set_defaults(twoD = False)
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(options, args) = parser.parse_args()
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# ------------------------------------------ setup file handles ---------------------------------------
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file = {'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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if numpy.any(options.resolution < 1):
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file['croak'].write('invalid resolution...\n')
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sys.exit()
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if numpy.any(options.dimension < 0.0):
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file['croak'].write('invalid dimension...\n')
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sys.exit()
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file['output'].write("4 header\n" + \
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"resolution\ta %i\tb %i\tc %i\n"%(options.resolution[0],options.resolution[1],options.resolution[2],) + \
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"dimension\tx %g\ty %g\tz %g\n"%(options.dimension[0],options.dimension[1],options.dimension[2],) + \
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"origin\tx 0\ty 0\tz 0\n" + \
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"homogenization %i\n"%options.homogenization
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)
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for z in xrange(options.resolution[2]):
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Z = options.periods*2.0*math.pi*(z+0.5)/options.resolution[2]
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for y in xrange(options.resolution[1]):
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Y = options.periods*2.0*math.pi*(y+0.5)/options.resolution[1]
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for x in xrange(options.resolution[0]):
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X = options.periods*2.0*math.pi*(x+0.5)/options.resolution[0]
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file['output'].write(\
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str({True:options.phase[0],False:options.phase[1]}[options.threshold > surface[options.type](X,Y,Z)]) + \
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{True:' ',False:'\n'}[options.twoD] )
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file['output'].write({True:'\n',False:''}[options.twoD])
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@ -1,75 +0,0 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,math
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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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# ----------------------- MAIN -------------------------------
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minimal_surfaces = ['gyroid','d']
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surface = {
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'gyroid': lambda x,y,z: math.sin(x)*math.cos(y)+math.sin(y)*math.cos(z)+math.cos(x)*math.sin(z),
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'd': lambda x,y,z: math.cos(z)*math.sin(x+y)+math.sin(z)*math.cos(x-y),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog', description = """
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Produce VTK point file from geom data
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""" + string.replace('$Id: spectral_geomCheck 994 2011-09-05 13:38:10Z MPIE\p.eisenlohr $','\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('-c', '--threshold', dest='threshold', type='float', \
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help='threshold value defining minimal surface')
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parser.add_option('-p', '--periods', dest='periods', type='int', \
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help='number of repetitions of unit cell')
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parser.add_option('-r', '--resolution', dest='resolution', type='int', nargs=3, \
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help='resolution in x, y, and z')
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parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs=3, \
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help='physical dimension in x, y, and z')
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parser.set_defaults(type = 'gyroid')
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parser.set_defaults(threshold = 0.5)
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parser.set_defaults(periods = 1)
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parser.set_defaults(resolution = [8,8,8])
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parser.set_defaults(dimension = [1.0,1.0,1.0])
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(options, args) = parser.parse_args()
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print "3 header"
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print "resolution\ta %i\tb %i\tc %i"%(options.resolution[0],options.resolution[1],options.resolution[2],)
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print "dimension\tx %g\ty %g\tz %g"%(options.dimension[0],options.dimension[1],options.dimension[2],)
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print "homogenization 1"
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for z in range(options.resolution[2]):
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for y in range(options.resolution[1]):
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for x in range(options.resolution[0]):
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print {True:'1',False:'2'}\
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[options.threshold >
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surface[options.type](options.periods*2.0*math.pi*x/options.resolution[0],
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options.periods*2.0*math.pi*y/options.resolution[1],
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options.periods*2.0*math.pi*z/options.resolution[2],
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)]
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@ -83,16 +83,16 @@ bin_link = { \
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'OIMang_hex2cub.py',
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'patchFromReconstructedBoundaries.py',
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'spectral_geomFromAng.py',
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'spectral_geomFromMinimalSurface.py',
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'randomSeeding.py',
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'geom_fromMinimalSurface.py',
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'geom_fromVoronoiTessellation.py',
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'geom_canvas.py',
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'geom_check.py',
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'geom_fromVoronoiTessellation.py',
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'geom_rescale.py',
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'geom_pack.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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'randomSeeding.py',
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],
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'post' : [
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'3Dvisualize.py',
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