DAMASK_EICMD/processing/pre/geom_fromMinimalSurface.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,math
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import numpy as np
from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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# --------------------------------------------------------------------
# MAIN
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# --------------------------------------------------------------------
minimal_surfaces = ['primitive','gyroid','diamond',]
surface = {
'primitive': lambda x,y,z: math.cos(x)+math.cos(y)+math.cos(z),
'gyroid': lambda x,y,z: math.sin(x)*math.cos(y)+math.sin(y)*math.cos(z)+math.cos(x)*math.sin(z),
'diamond': lambda x,y,z: math.cos(x-y)*math.cos(z)+math.sin(x+y)*math.sin(z),
}
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog', description = """
Generate a geometry file of a bicontinuous structure of given type.
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""", version = scriptID)
parser.add_option('-t','--type',
dest = 'type',
choices = minimal_surfaces, metavar = 'string',
help = 'type of minimal surface [primitive] {%s}' %(','.join(minimal_surfaces)))
parser.add_option('-f','--threshold',
dest = 'threshold',
type = 'float', metavar = 'float',
help = 'threshold value defining minimal surface [%default]')
parser.add_option('-g', '--grid',
dest = 'grid',
type = 'int', nargs = 3, metavar = 'int int int',
help = 'a,b,c grid of hexahedral box [%default]')
parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'x,y,z size of hexahedral box [%default]')
parser.add_option('-p', '--periods',
dest = 'periods',
type = 'int', metavar = 'int',
help = 'number of repetitions of unit cell [%default]')
parser.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index to be used [%default]')
parser.add_option('--m',
dest = 'microstructure',
type = 'int', nargs = 2, metavar = 'int int',
help = 'two microstructure indices to be used [%default]')
parser.add_option('-1', '--onedimensional',
dest = 'oneD',
action = 'store_true',
help = 'output geom file with two-dimensional data arrangement [%default]')
parser.set_defaults(type = minimal_surfaces[0],
threshold = 0.0,
periods = 1,
grid = (16,16,16),
size = (1.0,1.0,1.0),
homogenization = 1,
microstructure = (1,2),
oneD = False,
)
(options,filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = ['STDIN']
for name in filenames:
if not (name == 'STDIN' or os.path.exists(name)): continue
table = damask.ASCIItable(name = name, outname = name,
buffered = False, labeled = False, writeonly = True)
table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name != 'STDIN' else ''))
# ------------------------------------------ make grid -------------------------------------
info = {
'grid': np.array(options.grid),
'size': np.array(options.size),
'origin': np.zeros(3,'d'),
'microstructures': max(options.microstructure),
'homogenization': options.homogenization
}
#--- report ---------------------------------------------------------------------------------------
table.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
if errors != []:
table.croak(errors)
table.close(dismiss = True)
continue
#--- write header ---------------------------------------------------------------------------------
table.labels_clear()
table.info_clear()
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
"homogenization\t{homog}".format(homog=info['homogenization']),
"microstructures\t{microstructures}".format(microstructures=info['microstructures']),
])
table.head_write()
#--- write data -----------------------------------------------------------------------------------
X = options.periods*2.0*math.pi*(np.arange(options.grid[0])+0.5)/options.grid[0]
Y = options.periods*2.0*math.pi*(np.arange(options.grid[1])+0.5)/options.grid[1]
Z = options.periods*2.0*math.pi*(np.arange(options.grid[2])+0.5)/options.grid[2]
for z in xrange(options.grid[2]):
for y in xrange(options.grid[1]):
table.data_clear()
for x in xrange(options.grid[0]):
table.data_append(options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])])
if options.oneD:
table.data_write()
table.data_clear()
table.data_write()
table.close()