Atomic latin squares have indivisible structure which mimics that of the cyclic groups of prime order. They are related to perfect $1$-factorisations of complete bipartite graphs. Only one example of an atomic latin square of a composite order (namely 27) was previously known. We show that this one example can be generated by an established method of constructing latin squares using cyclotomic orthomorphisms in finite fields. The same method is used in this paper to construct atomic latin squares of composite orders 25, 49, 121, 125, 289, 361, 625, 841, 1369, 1849, 2809, 4489, 24649 and 39601. It is also used to construct many new atomic latin squares of prime order and perfect $1$-factorisations of the complete graph $K_{q+1}$ for many prime powers $q$. As a result, existence of such a factorisation is shown for the first time for $q$ in $\big\{$529, 2809, 4489, 6889, 11449, 11881, 15625, 22201, 24389, 24649, 26569, 29929, 32041, 38809, 44521, 50653, 51529, 52441, 63001, 72361, 76729, 78125, 79507, 103823, 148877, 161051, 205379, 226981, 300763, 357911, 371293, 493039, 571787$\big\}$. We show that latin squares built by the 'orthomorphism method' have large automorphism groups and we discuss conditions under which different orthomorphisms produce isomorphic latin squares. We also introduce an invariant called the train of a latin square, which proves to be useful for distinguishing non-isomorphic examples.