Atlas is not hand optimized. On the contrary, the whole idea behind Atlas is to perform, for each machine it is going to be installed on (for optimum performance, Atlas should be always compiled from source - never use pre-built Atlas installation, as it is probably not tuned exactly for the specific configuration of your machine), an extensive search (at Atlas compile time) through the space of relevant algorithm implementation parameters (for example, for matrix-matrix multiplication algorithm, that is typically implemented through block multiplication, the most important implementation parameter would be the size of the block), in order to find parameter values that would provide fastest calculations on this specific machine.