In this paper, it is presented a novel strategy to optimize the determination of magnetic couplings by using ab initio calculations of the energy. This approach allows determining efficiently, in terms of a proposed effective magnetic spin model, an optimal set of magnetic configurations to be simulated by DFT methods. Moreover, a procedure to estimate the values of the coupling constants and their error bounds from the estimated energies is proposed. This method, based on Monte Carlo sampling, takes into account the accuracy of the ab-initio simulations. A strategy to refine models reusing previously computed configuration energies is also presented. We apply the method to determine a magnetic model for the recently synthesized material Bi3Mn4O12(NO3). Finally, an open source software that implements and automatizes the whole process is presented.