The origin of Calabi-Yau crystals in BPS states counting

We study the counting problem of BPS D-branes wrapping holomorphic cycles of a general toric Calabi-Yau manifold. We evaluate the Jeffrey-Kirwan residues for the flavoured Witten index for the supersymmetric quiver quantum mechanics on the worldvolume of the D-branes, and find that BPS degeneracies are described by a statistical mechanical model of crystal melting. For Calabi-Yau threefolds, we reproduce the crystal melting models long known in the literature. For Calabi-Yau fourfolds, however, we find that the crystal does not contain the full information for the BPS degeneracy and we need to explicitly evaluate non-trivial weights assigned to the crystal configurations. Our discussions treat Calabi-Yau threefolds and fourfolds on equal footing, and include discussions on elliptic and rational generalizations of the BPS states counting, connections to the mathematical definition of generalized Donaldson-Thomas invariants, examples of wall crossings, and of trialities in quiver gauge theories.