116 lines
4.8 KiB
Python
Executable File
116 lines
4.8 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,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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import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
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Add deformed configuration of given initial coordinates.
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Operates on periodic three-dimensional x,y,z-ordered data sets.
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""", version = scriptID)
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parser.add_option('-c','--coordinates',
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dest = 'coords',
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type = 'string', metavar = 'string',
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help = 'column label of coordinates [%default]')
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parser.add_option('-f','--defgrad',
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dest = 'defgrad',
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type = 'string', metavar = 'string',
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help = 'column label of deformation gradient [%default]')
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parser.add_option('--scaling',
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dest = 'scaling',
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type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
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help = 'x/y/z scaling of displacement fluctuation')
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parser.set_defaults(coords = 'ipinitialcoord',
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defgrad = 'f',
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scaling = [1.,1.,1.],
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)
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(options,filenames) = parser.parse_args()
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = ['STDIN']
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for name in filenames:
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if not (name == 'STDIN' or os.path.exists(name)): continue
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table = damask.ASCIItable(name = name, outname = name+'_tmp',
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buffered = False)
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table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name != 'STDIN' else ''))
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# ------------------------------------------ read header ------------------------------------------
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table.head_read()
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# ------------------------------------------ sanity checks ----------------------------------------
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errors = []
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remarks = []
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if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
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else: colCoord = table.label_index(options.coords)
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if table.label_dimension(options.defgrad) != 9: errors.append('deformation gradient {} is not a tensor.'.format(options.defgrad))
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else: colF = table.label_index(options.defgrad)
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if remarks != []: table.croak(remarks)
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if errors != []:
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table.croak(errors)
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table.close(dismiss = True)
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continue
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# --------------- figure out size and grid ---------------------------------------------------------
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table.data_readArray()
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coords = [{},{},{}]
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for i in xrange(len(table.data)):
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for j in xrange(3):
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coords[j][str(table.data[i,colCoord+j])] = True
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grid = np.array(map(len,coords),'i')
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size = grid/np.maximum(np.ones(3,'d'),grid-1.0)* \
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np.array([max(map(float,coords[0].keys()))-min(map(float,coords[0].keys())),\
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max(map(float,coords[1].keys()))-min(map(float,coords[1].keys())),\
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max(map(float,coords[2].keys()))-min(map(float,coords[2].keys())),\
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],'d') # size from bounding box, corrected for cell-centeredness
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size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other spacings
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N = grid.prod()
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# ------------------------------------------ assemble header ---------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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table.labels_append(['{}_{}.{}'%(coord+1,options.defgrad,options.coords) for coord in xrange(3)]) # extend ASCII header with new labels
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table.head_write()
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# ------------------------------------------ process deformation gradient --------------------------
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F = table.data[:,colF:colF+9].transpose().reshape([3,3]+list(options.dimension),order='F')
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Favg = damask.core.math.tensorAvg(F)
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centres = damask.core.mesh.deformedCoordsFFT(size,F,Favg,[1.0,1.0,1.0])
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stack = [table.data,centres]
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# ------------------------------------------ output result -----------------------------------------
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if len(stack) > 1: table.data = np.hstack(tuple(stack))
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table.data_writeArray('%.12g')
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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if name != 'STDIN': os.rename(name+'_tmp',name) # overwrite old one with tmp new
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