Modules over orders, conjugacy classes of integral matrices, and abelian varieties over finite fields

Abstract: We give an algorithm to compute representatives of the conjugacy classes of semisimple square integral matrices with given minimal and characteristic polynomials. We also give an algorithm to compute the $\mathbb{F}_q$-isomorphism classes of abelian varieties over a finite field $\mathbb{F}_q$ which belong to an isogeny class determined by a characteristic polynomial $h$ of Frobenius when $h$ is ordinary, or $q$ is prime and $h$ has no real roots.