Over the last decades, simulations by discrete elements methods (DEM) have proven to be a reliable analysis tool in various domains of science and engineering. By providing access to the local physical mechanisms, DEM allows the exploration of microscopic based phenomena related to particles properties and interactions in various conditions and to revisit constitutive equations consequently. The growing computer power and memory now allow us to handle large collections of grains of various shapes and sizes by DEM simulations and in particular, it offers new perspectives in the exploration of the behavior of asteroids seen as self-gravitating and cohesive granular aggregates. In this paper we describe the Contact Dynamics (CD) method, a class of DEM based on non-smooth mechanics, and its implementation in the open-source software LMGC90. In contrast to more classical approach, Hard-and Soft-Sphere DEM, the CD method is based on an implicit time integration of the equations of motion and on a non-regularized formulation of mutual exclusion between particles. This numerical strategy is particularly relevant to the study of dense granular assemblies (even of large size) because it does not introduce numerical artefacts due to contact stiffness. So that it can be used for Small Body research, we implement a parallelised kd-tree and monitor the performance of the code as it simulates a number of granular systems. We provide examples of the simulation of the accretion of self-gravitating aggregates as well as their rotational disruption. We use the routines at our disposal in the code to monitor their behaviour through the entire evolution and find agreement with previous research.