Vectorize operations referencing adjacent elements of a matrix

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I have made the simple code:
for i=2:xsize-1
for j=2:ysize-1
for n=2:zsize-1
matrix(i,j,n)=matrix(i,j,n)+0.2*(matrix(i,j,n)*6-matrix(i-1,j,n)-matrix(i+1,j,n)-matrix(i,j-1,n)-matrix(i,j+1,n)-matrix(i,j,n-1)-matrix(i,j,n+1));
end
end
end
This is part of a diffusion problem and it is particularly slow because the 3D matrix is large. Is it possible to vectorize an operation like this? How do you vectorize references to the matrix like this?

Accepted Answer

Andrei Bobrov
Andrei Bobrov on 18 Feb 2014
Edited: Andrei Bobrov on 18 Feb 2014
out = convn(matrix,cat(3,[0 0 0;0 -1 0;0 0 0],...
[0 -1 0;-1 1 -1;0 -1 0],...
[0 0 0;0 -1 0;0 0 0]),'valid');
  1 Comment
Christopher
Christopher on 19 Feb 2014
Edited: Christopher on 19 Feb 2014
Thanks! This gives about a factor of 20 speedup. The form I used is
newmatrix = convn(matrix,cat(3,[0 0 0; 0 rt 0; 0 0 0],...
[0 rt 0; rt 1-rt*6 rt; 0 rt 0],...
[0 0 0; 0 rt 0; 0 0 0]),'same');
where rt=0.2

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