From ea28bc8f062e3629c300084c766019cfa1410ba6 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 24 Mar 2016 16:19:49 +0100 Subject: [PATCH] restored script for calculation of nodal positions --- processing/post/nodesAroundCentres.py | 152 ++++++++++++++++++++++++++ 1 file changed, 152 insertions(+) create mode 100644 processing/post/nodesAroundCentres.py diff --git a/processing/post/nodesAroundCentres.py b/processing/post/nodesAroundCentres.py new file mode 100644 index 000000000..3a2624b16 --- /dev/null +++ b/processing/post/nodesAroundCentres.py @@ -0,0 +1,152 @@ +#!/usr/bin/env python +# -*- coding: UTF-8 no BOM -*- + +import os,sys,math,string +import numpy as np +from optparse import OptionParser +import damask + +scriptID = string.replace('$Id: addDeformedConfiguration.py 4500 2015-09-24 09:24:42Z MPIE\m.diehl $','\n','\\n') +scriptName = os.path.splitext(scriptID.split()[1])[0] + +#-------------------------------------------------------------------------------------------------- +def nodesAroundCentres(gDim,Favg,centres): +#-------------------------------------------------------------------------------------------------- + neighbor = np.array([0, 0, 0, + 1, 0, 0, + 1, 1, 0, + 0, 1, 0, + 0, 0, 1, + 1, 0, 1, + 1, 1, 1, + 0, 1, 1]).reshape(8,3) + +#-------------------------------------------------------------------------------------------------- +# building wrappedCentres = centroids + ghosts + diag = np.ones([3]) + wrappedCentres = np.zeros([3,grid[0]+2,grid[1]+2,grid[2]+2]) + wrappedCentres[0:3,1:grid[0]+1,1:grid[1]+1,1:grid[2]+1] = centres + for k in xrange(grid[2]+2): + for j in xrange(grid[1]+2): + for i in xrange(grid[0]+2): + if (k in [0,grid[2]+1] or j in [0,grid[1]+1] or i in[0,grid[0]+1]): + me = np.array([i,j,k],'i') # me on skin + shift = abs(grid+np.ones([3],'i')-2*me)/(grid+np.ones([3],'i'))*\ + np.sign(grid+np.ones([3],'i')-2*me) + lookup = np.array(me-diag+shift*grid,'i') + wrappedCentres[0:3,i, j, k] = \ + centres[0:3,lookup[0],lookup[1],lookup[2]] - np.dot(Favg, shift*gDim) + +#-------------------------------------------------------------------------------------------------- +# averaging + nodes = np.zeros([3,grid[0]+1,grid[1]+1,grid[2]+1]) + for k in xrange(grid[2]+1): + for j in xrange(grid[1]+1): + for i in xrange(grid[0]+1): + for n in xrange(8): + nodes[0:3,i,j,k] = \ + nodes[0:3,i,j,k] + wrappedCentres[0:3,i+neighbor[n,0],j+neighbor[n,1],k+neighbor[n,2] ] + + return nodes/8.0 + +# -------------------------------------------------------------------- +# 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('-f', '--defgrad',dest='defgrad', metavar = 'string', + help='heading of deformation gradient columns [%default]') +parser.add_option('-u', '--unitlength', dest='unitlength', type='float', metavar = 'float', + help='set unit length for 2D model [%default]') + +parser.set_defaults(deformed = 'ipinitialcoord') +parser.set_defaults(unitlength = 0.0) + +(options,filenames) = parser.parse_args() + +options.scaling += [1.0 for i in xrange(max(0,3-len(options.scaling)))] +scaling = map(float, options.scaling) + + +# --- loop over input files ------------------------------------------------------------------------- + +if filenames == []: filenames = [None] + +for name in filenames: + try: + table = damask.ASCIItable(name = name, + buffered = False) + except: continue + damask.util.report(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 != []: damask.util.croak(remarks) + if errors != []: + damask.util.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 != []: + damask.util.croak(errors) + table.close(dismiss = True) + continue + +# ------------------------------------------ assemble header --------------------------------------- + + table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) + for coord in xrange(3): + label = '{}_{}_{}'.format(coord+1,options.defgrad,options.coords) + if np.any(scaling) != 1.0: label+='_{}_{}_{}'.format(scaling) + if options.undeformed: label+='_undeformed' + table.labels_append([label]) # extend ASCII header with new labels + table.head_write() + +# ------------------------------------------ read deformation gradient field ----------------------- + centroids,Favg = deformedCoordsFFT(table.data[:,colF:colF+9].reshape(grid[0],grid[1],grid[2],3,3)) + +# ------------------------------------------ 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[z,y,x,:])) + outputAlive = table.data_write() + +# ------------------------------------------ output finalization ----------------------------------- + + table.close() # close ASCII tables