  Lyman limit systems (LLSs) are dense hydrogen clouds with high enough HI
column densities to absorb Lyman continuum photons emitted from distant
quasars. Their high column densities imply an origin in dense environments;
however, the statistics and distribution of LLSs at high redshifts still remain
uncertain. In this paper, we use self-consistent radiative transfer
cosmological simulations from the "Cosmic Reionization On Computers" (CROC)
project to study the physical properties of LLSs at the tail end of cosmic
reionization at $z\sim6$. We generate 3000 synthetic quasar sightlines to
obtain a large number of LLS samples in the simulations. In addition, with the
high physical fidelity and resolution of CROC, we are able to quantify the
association between these LLS samples and nearby galaxies. Our results show
that the fraction LLSs spatially associated with nearby galaxies is increasing
with the HI column density. Moreover, we find that LLSs that are not near any
galaxy typically reside in filamentary structures connecting neighboring
galaxies in the intergalactic medium (IGM). This quantification of the
distribution and associations of LLSs to large scale structures informs our
understanding of the IGM-galaxy connection during the Epoch of Reionization,
and provides a theoretical basis for interpreting future observations.
