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DAMASK_EICMD
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corrected mixup of Fortran (1,2,3,...) indexing to Python (0,1,2,...) style. 

fixed erroneous array indexing in neighborhood calculation.
This commit is contained in:
Philip Eisenlohr 2011-04-14 10:11:23 +00:00
parent 5814262f55
commit f598e3b6ed
2 changed files with 70 additions and 60 deletions
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80
processing/post/3Dvisualize
View File

@ -115,7 +115,7 @@ def vtk_writeASCII_mesh(mesh,data,res):
cmds = [\ cmds = [\
'# vtk DataFile Version 3.1', '# vtk DataFile Version 3.1',
'powered by 3Dvisualize', 'powered by $Id$',
'ASCII', 'ASCII',
'DATASET UNSTRUCTURED_GRID', 'DATASET UNSTRUCTURED_GRID',
'POINTS %i float'%N1, 'POINTS %i float'%N1,
@ -124,19 +124,19 @@ def vtk_writeASCII_mesh(mesh,data,res):
] ]
# cells # cells
for i in range (res[2]): for z in range (res[2]):
for j in range (res[1]): for y in range (res[1]):
for k in range (res[0]): for x in range (res[0]):
base = i*(res[1]+1)*(res[2]+1)+j*(res[1]+1)+k base = z*(res[1]+1)*(res[0]+1)+y*(res[0]+1)+x
cmds.append('8 '+'\t'.join(map(str,[ \ cmds.append('8 '+'\t'.join(map(str,[ \
base, base,
base+1, base+1,
base+res[1]+2, base+res[0]+2,
base+res[1]+1, base+res[0]+1,
base+(res[1]+1)*(res[2]+1), base+(res[1]+1)*(res[0]+1),
base+(res[1]+1)*(res[2]+1)+1, base+(res[1]+1)*(res[0]+1)+1,
base+(res[1]+1)*(res[2]+1)+res[1]+2, base+(res[1]+1)*(res[0]+1)+res[0]+2,
base+(res[1]+1)*(res[2]+1)+res[1]+1, base+(res[1]+1)*(res[0]+1)+res[0]+1,
]))) ])))
cmds += [\ cmds += [\
'CELL_TYPES %i'%N, 'CELL_TYPES %i'%N,
@ -177,24 +177,26 @@ def gmsh_writeASCII_mesh(mesh,data,res):
'%i'%N, '%i'%N,
] ]
# cells
n_elem = 0 n_elem = 0
for i in range (res[2]): for z in range (res[2]):
for j in range (res[1]): for y in range (res[1]):
for k in range (res[0]): for x in range (res[0]):
base = i*(res[1]+1)*(res[2]+1)+j*(res[1]+1)+k base = z*(res[1]+1)*(res[0]+1)+y*(res[0]+1)+x
n_elem +=1 n_elem +=1
cmds.append('\t'.join(map(str,[ \ cmds.append('\t'.join(map(str,[ \
n_elem, n_elem,
'5', '5',
base, base,
base+1, base+1,
base+res[1]+2, base+res[0]+2,
base+res[1]+1, base+res[0]+1,
base+(res[1]+1)*(res[2]+1), base+(res[1]+1)*(res[0]+1),
base+(res[1]+1)*(res[2]+1)+1, base+(res[1]+1)*(res[0]+1)+1,
base+(res[1]+1)*(res[2]+1)+res[1]+2, base+(res[1]+1)*(res[0]+1)+res[0]+2,
base+(res[1]+1)*(res[2]+1)+res[1]+1, base+(res[1]+1)*(res[0]+1)+res[0]+1,
]))) ])))
cmds += [\ cmds += [\
'ElementData', 'ElementData',
'1', '1',
@ -228,7 +230,7 @@ def vtk_writeASCII_points(coordinates,data,res):
cmds = [\ cmds = [\
'# vtk DataFile Version 3.1', '# vtk DataFile Version 3.1',
'powered by 3Dvisualize', 'powered by $Id$',
'ASCII', 'ASCII',
'DATASET UNSTRUCTURED_GRID', 'DATASET UNSTRUCTURED_GRID',
'POINTS %i float'%N, 'POINTS %i float'%N,
@ -267,7 +269,7 @@ def vtk_writeASCII_box(diag,defgrad):
cmds = [\ cmds = [\
'# vtk DataFile Version 3.1', '# vtk DataFile Version 3.1',
'powered by 3Dvisualize', 'powered by $Id$',
'ASCII', 'ASCII',
'DATASET UNSTRUCTURED_GRID', 'DATASET UNSTRUCTURED_GRID',
'POINTS 8 float', 'POINTS 8 float',
@ -285,7 +287,7 @@ def vtk_writeASCII_box(diag,defgrad):
# ----------------------- MAIN ------------------------------- # ----------------------- MAIN -------------------------------
parser = OptionParser(option_class=extendedOption, usage='%prog [options] datafile', description = """ parser = OptionParser(option_class=extendedOption, usage='%prog [options] datafile', description = """
Produce VTK file from data field. Produce VTK file from data field. Coordinates are taken from (consecutive) ip.x, ip.y, and ip.z columns.
$Id$ $Id$
""") """)
@ -361,33 +363,37 @@ for filename in args:
maxcol = max(maxcol,col+1) maxcol = max(maxcol,col+1)
break break
values = numpy.array(sorted([map(transliterateToFloat,line.split()[:maxcol]) for line in content[headrow+1:]],
values = numpy.array([map(transliterateToFloat,line.split()[:maxcol]) for line in content[headrow+1:]],'d') key=lambda x:(x[ipcol+0],x[ipcol+1],x[ipcol+2])), # sort with z as fastest and x as slowest index
'd')
N = len(values) N = len(values)
grid = [{},{},{}] grid = [{},{},{}]
for i in range(N): for j in range(3):
grid[0][str(values[i,ipcol+0])] = True for i in range(N):
grid[1][str(values[i,ipcol+1])] = True grid[j][str(values[i,ipcol+j])] = True
grid[2][str(values[i,ipcol+2])] = True
res = numpy.array([len(grid[0]),\ res = numpy.array([len(grid[0]),\
len(grid[1]),\ len(grid[1]),\
len(grid[2]),],'i') len(grid[2]),],'i')
dim = numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\ dim = numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\ max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),]*res/(res-numpy.ones(3)), 'd') max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),]*res/(res-numpy.ones(3)), 'd')
print 'resolution',res print 'resolution',res
print 'dimension',dim print 'dimension',dim
defgrad_av = postprocessingMath.tensor_avg(res[0],res[1],res[2],\ defgrad_av = postprocessingMath.tensor_avg(res[0],res[1],res[2],\
numpy.reshape(values[:,column['tensor'][options.defgrad]: numpy.reshape(values[:,column['tensor'][options.defgrad]:
column['tensor'][options.defgrad]+9], column['tensor'][options.defgrad]+9],
(res[0],res[1],res[2],3,3))) (res[0],res[1],res[2],3,3)))
print 'avg F\n',defgrad_av
centroids = postprocessingMath.deformed_fft(res[0],res[1],res[2],dim,\ centroids = postprocessingMath.deformed_fft(res[0],res[1],res[2],dim,\
numpy.reshape(values[:,column['tensor'][options.defgrad]: numpy.reshape(values[:,column['tensor'][options.defgrad]:
column['tensor'][options.defgrad]+9], column['tensor'][options.defgrad]+9],
(res[0],res[1],res[2],3,3)),defgrad_av,1.0) (res[0],res[1],res[2],3,3)),defgrad_av,1.0)
print 'centroids\n',centroids
ms = postprocessingMath.mesh(res[0],res[1],res[2],dim,defgrad_av,centroids) ms = postprocessingMath.mesh(res[0],res[1],res[2],dim,defgrad_av,centroids)
print 'mesh\n',ms
fields = {\ fields = {\
'tensors': {},\ 'tensors': {},\

50
processing/post/postprocessingMath.f90
View File

@ -274,6 +274,7 @@ end function math_mul33x33
subroutine mesh(res_x,res_y,res_z,geomdim,defgrad_av,centroids,nodes) subroutine mesh(res_x,res_y,res_z,geomdim,defgrad_av,centroids,nodes)
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
implicit none implicit none
real*8 geomdim(3) real*8 geomdim(3)
integer res_x, res_y, res_z integer res_x, res_y, res_z
real*8 wrappedCentroids(res_x+2,res_y+2,res_z+2,3) real*8 wrappedCentroids(res_x+2,res_y+2,res_z+2,3)
@ -281,14 +282,14 @@ subroutine mesh(res_x,res_y,res_z,geomdim,defgrad_av,centroids,nodes)
real*8 centroids(res_x ,res_y ,res_z ,3) real*8 centroids(res_x ,res_y ,res_z ,3)
integer, dimension(3,8) :: neighbor = reshape((/ & integer, dimension(3,8) :: neighbor = reshape((/ &
0, 0, 0,& 0, 0, 0, &
1, 0, 0,& 1, 0, 0, &
1, 1, 0,& 1, 1, 0, &
0, 1, 0,& 0, 1, 0, &
0, 0, 1,& 0, 0, 1, &
1, 0, 1,& 1, 0, 1, &
1, 1, 1,& 1, 1, 1, &
0, 1, 1 & 0, 1, 1 &
/), & /), &
(/3,8/)) (/3,8/))
@ -296,33 +297,36 @@ subroutine mesh(res_x,res_y,res_z,geomdim,defgrad_av,centroids,nodes)
real*8, dimension(3,3) :: defgrad_av real*8, dimension(3,3) :: defgrad_av
integer, dimension(3) :: diag, shift, lookup, me, res integer, dimension(3) :: diag, shift, lookup, me, res
nodes = 0.0
diag = 1 diag = 1
shift = 0 shift = 0
lookup = 0 lookup = 0
res = (/res_x,res_y,res_z/) res = (/res_x,res_y,res_z/)
wrappedCentroids=0.0 wrappedCentroids = 0.0
wrappedCentroids(2:res_x+1,2:res_y+1,2:res_z+1,:) = centroids wrappedCentroids(2:res_x+1,2:res_y+1,2:res_z+1,:) = centroids
do k=0, res_z+1 do k = 0,res_z+1
do j=0, res_y+1 do j = 0,res_y+1
do i=0, res_x+1 do i = 0,res_x+1
if (k==0 .or. k==res_z+1 .or. & if (k==0 .or. k==res_z+1 .or. & ! z skin
j==0 .or. j==res_y+1 .or. & j==0 .or. j==res_y+1 .or. & ! y skin
i==0 .or. i==res_x+1 ) then i==0 .or. i==res_x+1 ) then ! x skin
me = (/i,j,k/) me = (/i,j,k/) ! me on skin
shift = sign(abs(res+diag-2*me)/(res+diag),res+diag-2*me) shift = sign(abs(res+diag-2*me)/(res+diag),res+diag-2*me)
lookup = me-diag+shift*res lookup = me-diag+shift*res
wrappedCentroids(i+1,j+1,k+1,:) = centroids(lookup(1)+1,lookup(2)+1,lookup(3)+1,:)- & wrappedCentroids(i+1,j+1,k+1,:) = centroids(lookup(1)+1,lookup(2)+1,lookup(3)+1,:) - &
matmul(defgrad_av, shift*geomdim) matmul(defgrad_av, shift*geomdim)
endif endif
enddo; enddo; enddo enddo; enddo; enddo
do k=0, res_z do k = 0,res_z
do j=0, res_y do j = 0,res_y
do i=0, res_x do i = 0,res_x
do n=1,8 do n = 1,8
nodes(i+1,j+1,k+1,:) = nodes(i+1,j+1,k+1,:) + wrappedCentroids(i+1+neighbor(n,1),j+1+neighbor(n,2),k+1+neighbor(n,3),:) nodes(i+1,j+1,k+1,:) = nodes(i+1,j+1,k+1,:) + wrappedCentroids(i+1+neighbor(1,n), &
j+1+neighbor(2,n), &
k+1+neighbor(3,n), :)
enddo; enddo; enddo; enddo enddo; enddo; enddo; enddo
nodes = nodes/8.0 nodes = nodes/8.0