With a THERMOCALC software (or other Calphad products such as MTDATA and PANDAT) you can predict the equilibrium thermodynamic properties of alloy, e.g. phase diagram. using such a phase diagram, you can predict the phases developed at a certain temperature and chemical composition, which enables to determine the mechanical and physical properties.
I think that molecular dynamics can be helpfull ; in the case of ordered alloys single crystals it is relatively simple. The free of charge lammps software (http://lammps.sandia.gov/) can be used for this .