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I think you will want to look at the publications by James Wilson at Colorado State University who has been doing this kind of thing for quite large groups.


Probably you accumulated rotations wrong. At each step, you have a working matrix $D$ that starts from $D=A$ and should converge to a diagonal matrix, and a matrix $Q$ that accumulates all rotations performed on $D$. Print after each step $\|QDQ^T - A\|$, and see where it stops being small.

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