FEMLAB can be used to model heap leach pad performance. Here is a description of the code:

FEMLAB is a powerful, interactive environment for modeling and solving scientific and engineering problems based on partial differential equations [1,2]. With it you can easily extend conventional models that address one branch of physics to state-of-the art multiphysics models that simultaneously involve multiple branches of science and engineering. Accessing this power, however, does not require that you have in-depth knowledge of mathematics or numerical analysis. Indeed, you can build many useful models simply by defining the relevant physical quantities rather than defining the equations directly.

And here is an abstract of a technical paper, Two-dimensional dynamic model of a copper sulphide ore bed by Sidborn et al. The paper that tells how the code was used to model heap leach pad performance:

A two-dimensional dynamic model for bioleaching of secondary copper minerals from a pile has been developed. Aeration of the pile is considered to be due to natural convection caused by the density gradient in the air within the bed. The rate of sulphide mineral dissolution is modeled according to the unreacted core model. The transport of ferric ions from the particle surface to the reaction zone is calculated considering film diffusion, diffusion within the particle and reaction kinetics. The rate of oxidation of the ferrous ion by bacteria attached to the ore surface is modeled using the Michaelis–Menten relationship. The influences of temperature, dissolved ferric iron and dissolved oxygen in the leaching solution are considered in the kinetic formulation.