DAMASK_EICMD/processing/post/addDeformedConfiguration.py

128 lines
5.2 KiB
Python
Executable File

#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string
import numpy as np
from collections import defaultdict
from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
Add deformed configuration of given initial coordinates.
Operates on periodic three-dimensional x,y,z-ordered data sets.
""", version = scriptID)
parser.add_option('-c','--coordinates',
dest = 'coords',
type = 'string', metavar = 'string',
help = 'column label of coordinates [%default]')
parser.add_option('-f','--defgrad',
dest = 'defgrad',
type = 'string', metavar = 'string',
help = 'column label of deformation gradient [%default]')
parser.add_option('--scaling',
dest = 'scaling',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
help = 'x/y/z scaling of displacement fluctuation')
parser.set_defaults(coords = 'ipinitialcoord',
defgrad = 'f',
scaling = [1.,1.,1.],
)
(options,filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False)
except: continue
table.report_name(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
errors = []
remarks = []
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
if table.label_dimension(options.defgrad) != 9: errors.append('deformation gradient {} is not a tensor.'.format(options.defgrad))
else: colF = table.label_index(options.defgrad)
if remarks != []: table.croak(remarks)
if errors != []:
table.croak(errors)
table.close(dismiss = True)
continue
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray()
coords = [np.unique(table.data[:,colCoord+i]) for i in xrange(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other spacings
N = grid.prod()
if N != len(table.data): errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*grid))
if errors != []:
table.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header ---------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
for coord in xrange(3):
table.labels_append(['{}_{}.{}'.format(coord+1,options.defgrad,options.coords) ]) # extend ASCII header with new labels
table.head_write()
# ------------------------------------------ read deformation gradient field -----------------------
table.data_rewind()
F = np.array([0.0 for i in xrange(N*9)]).reshape([3,3]+grid.tolist())
idx = 0
while table.data_read():
(x,y,z) = damask.util.gridLocation(idx,grid) # figure out (x,y,z) position from line count
idx += 1
F[0:3,0:3,x,y,z] = np.array(map(float,table.data[table.label_index(options.defgrad):\
table.label_index(options.defgrad)+9]),'d').reshape(3,3)
# ------------------------------------------ calculate coordinates ---------------------------------
Favg = damask.core.math.tensorAvg(F)
centroids = damask.core.mesh.deformedCoordsFFT(size,F,Favg)
# ------------------------------------------ process data ------------------------------------------
table.data_rewind()
idx = 0
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
(x,y,z) = damask.util.gridLocation(idx,grid) # figure out (x,y,z) position from line count
idx += 1
table.data_append(list(centroids[:,x,y,z]))
outputAlive = table.data_write()
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables