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
parent
5814262f55
commit
f598e3b6ed
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@ -115,7 +115,7 @@ def vtk_writeASCII_mesh(mesh,data,res):
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cmds = [\
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'# vtk DataFile Version 3.1',
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'powered by 3Dvisualize',
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'powered by $Id$',
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS %i float'%N1,
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@ -124,19 +124,19 @@ def vtk_writeASCII_mesh(mesh,data,res):
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]
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# cells
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for i in range (res[2]):
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for j in range (res[1]):
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for k in range (res[0]):
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base = i*(res[1]+1)*(res[2]+1)+j*(res[1]+1)+k
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for z in range (res[2]):
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for y in range (res[1]):
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for x in range (res[0]):
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base = z*(res[1]+1)*(res[0]+1)+y*(res[0]+1)+x
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cmds.append('8 '+'\t'.join(map(str,[ \
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base,
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base+1,
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base+res[1]+2,
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base+res[1]+1,
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base+(res[1]+1)*(res[2]+1),
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base+(res[1]+1)*(res[2]+1)+1,
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base+(res[1]+1)*(res[2]+1)+res[1]+2,
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base+(res[1]+1)*(res[2]+1)+res[1]+1,
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base+res[0]+2,
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base+res[0]+1,
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base+(res[1]+1)*(res[0]+1),
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base+(res[1]+1)*(res[0]+1)+1,
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base+(res[1]+1)*(res[0]+1)+res[0]+2,
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base+(res[1]+1)*(res[0]+1)+res[0]+1,
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])))
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cmds += [\
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'CELL_TYPES %i'%N,
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@ -177,24 +177,26 @@ def gmsh_writeASCII_mesh(mesh,data,res):
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'%i'%N,
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]
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# cells
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n_elem = 0
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for i in range (res[2]):
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for j in range (res[1]):
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for k in range (res[0]):
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base = i*(res[1]+1)*(res[2]+1)+j*(res[1]+1)+k
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for z in range (res[2]):
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for y in range (res[1]):
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for x in range (res[0]):
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base = z*(res[1]+1)*(res[0]+1)+y*(res[0]+1)+x
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n_elem +=1
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cmds.append('\t'.join(map(str,[ \
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n_elem,
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'5',
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base,
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base+1,
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base+res[1]+2,
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base+res[1]+1,
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base+(res[1]+1)*(res[2]+1),
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base+(res[1]+1)*(res[2]+1)+1,
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base+(res[1]+1)*(res[2]+1)+res[1]+2,
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base+(res[1]+1)*(res[2]+1)+res[1]+1,
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base+res[0]+2,
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base+res[0]+1,
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base+(res[1]+1)*(res[0]+1),
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base+(res[1]+1)*(res[0]+1)+1,
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base+(res[1]+1)*(res[0]+1)+res[0]+2,
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base+(res[1]+1)*(res[0]+1)+res[0]+1,
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])))
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cmds += [\
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'ElementData',
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'1',
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@ -228,7 +230,7 @@ def vtk_writeASCII_points(coordinates,data,res):
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cmds = [\
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'# vtk DataFile Version 3.1',
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'powered by 3Dvisualize',
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'powered by $Id$',
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS %i float'%N,
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@ -267,7 +269,7 @@ def vtk_writeASCII_box(diag,defgrad):
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cmds = [\
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'# vtk DataFile Version 3.1',
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'powered by 3Dvisualize',
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'powered by $Id$',
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS 8 float',
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@ -285,7 +287,7 @@ def vtk_writeASCII_box(diag,defgrad):
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# ----------------------- MAIN -------------------------------
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parser = OptionParser(option_class=extendedOption, usage='%prog [options] datafile', description = """
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Produce VTK file from data field.
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Produce VTK file from data field. Coordinates are taken from (consecutive) ip.x, ip.y, and ip.z columns.
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$Id$
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""")
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@ -361,33 +363,37 @@ for filename in args:
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maxcol = max(maxcol,col+1)
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break
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values = numpy.array([map(transliterateToFloat,line.split()[:maxcol]) for line in content[headrow+1:]],'d')
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values = numpy.array(sorted([map(transliterateToFloat,line.split()[:maxcol]) for line in content[headrow+1:]],
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key=lambda x:(x[ipcol+0],x[ipcol+1],x[ipcol+2])), # sort with z as fastest and x as slowest index
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'd')
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N = len(values)
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grid = [{},{},{}]
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for i in range(N):
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grid[0][str(values[i,ipcol+0])] = True
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grid[1][str(values[i,ipcol+1])] = True
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grid[2][str(values[i,ipcol+2])] = True
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for j in range(3):
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for i in range(N):
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grid[j][str(values[i,ipcol+j])] = True
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res = numpy.array([len(grid[0]),\
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len(grid[1]),\
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len(grid[2]),],'i')
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dim = numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
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max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
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max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),]*res/(res-numpy.ones(3)), 'd')
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max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),]*res/(res-numpy.ones(3)), 'd')
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print 'resolution',res
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print 'dimension',dim
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defgrad_av = postprocessingMath.tensor_avg(res[0],res[1],res[2],\
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numpy.reshape(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9],
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(res[0],res[1],res[2],3,3)))
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numpy.reshape(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9],
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(res[0],res[1],res[2],3,3)))
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print 'avg F\n',defgrad_av
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centroids = postprocessingMath.deformed_fft(res[0],res[1],res[2],dim,\
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numpy.reshape(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9],
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(res[0],res[1],res[2],3,3)),defgrad_av,1.0)
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numpy.reshape(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9],
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(res[0],res[1],res[2],3,3)),defgrad_av,1.0)
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print 'centroids\n',centroids
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ms = postprocessingMath.mesh(res[0],res[1],res[2],dim,defgrad_av,centroids)
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print 'mesh\n',ms
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fields = {\
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'tensors': {},\
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@ -274,6 +274,7 @@ end function math_mul33x33
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subroutine mesh(res_x,res_y,res_z,geomdim,defgrad_av,centroids,nodes)
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!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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implicit none
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real*8 geomdim(3)
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integer res_x, res_y, res_z
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real*8 wrappedCentroids(res_x+2,res_y+2,res_z+2,3)
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@ -281,14 +282,14 @@ subroutine mesh(res_x,res_y,res_z,geomdim,defgrad_av,centroids,nodes)
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real*8 centroids(res_x ,res_y ,res_z ,3)
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integer, dimension(3,8) :: neighbor = reshape((/ &
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0, 0, 0,&
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1, 0, 0,&
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1, 1, 0,&
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0, 1, 0,&
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0, 0, 1,&
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1, 0, 1,&
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1, 1, 1,&
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0, 1, 1 &
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0, 0, 0, &
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1, 0, 0, &
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1, 1, 0, &
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0, 1, 0, &
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0, 0, 1, &
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1, 0, 1, &
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1, 1, 1, &
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0, 1, 1 &
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/), &
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(/3,8/))
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@ -296,33 +297,36 @@ subroutine mesh(res_x,res_y,res_z,geomdim,defgrad_av,centroids,nodes)
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real*8, dimension(3,3) :: defgrad_av
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integer, dimension(3) :: diag, shift, lookup, me, res
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nodes = 0.0
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diag = 1
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shift = 0
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lookup = 0
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res = (/res_x,res_y,res_z/)
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wrappedCentroids=0.0
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wrappedCentroids = 0.0
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wrappedCentroids(2:res_x+1,2:res_y+1,2:res_z+1,:) = centroids
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do k=0, res_z+1
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do j=0, res_y+1
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do i=0, res_x+1
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if (k==0 .or. k==res_z+1 .or. &
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j==0 .or. j==res_y+1 .or. &
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i==0 .or. i==res_x+1 ) then
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me = (/i,j,k/)
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do k = 0,res_z+1
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do j = 0,res_y+1
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do i = 0,res_x+1
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if (k==0 .or. k==res_z+1 .or. & ! z skin
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j==0 .or. j==res_y+1 .or. & ! y skin
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i==0 .or. i==res_x+1 ) then ! x skin
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me = (/i,j,k/) ! me on skin
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shift = sign(abs(res+diag-2*me)/(res+diag),res+diag-2*me)
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lookup = me-diag+shift*res
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wrappedCentroids(i+1,j+1,k+1,:) = centroids(lookup(1)+1,lookup(2)+1,lookup(3)+1,:)- &
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matmul(defgrad_av, shift*geomdim)
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wrappedCentroids(i+1,j+1,k+1,:) = centroids(lookup(1)+1,lookup(2)+1,lookup(3)+1,:) - &
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matmul(defgrad_av, shift*geomdim)
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endif
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enddo; enddo; enddo
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do k=0, res_z
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do j=0, res_y
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do i=0, res_x
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do n=1,8
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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),:)
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do k = 0,res_z
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do j = 0,res_y
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do i = 0,res_x
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do n = 1,8
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nodes(i+1,j+1,k+1,:) = nodes(i+1,j+1,k+1,:) + wrappedCentroids(i+1+neighbor(1,n), &
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j+1+neighbor(2,n), &
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k+1+neighbor(3,n), :)
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enddo; enddo; enddo; enddo
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nodes = nodes/8.0
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