Never did this particular thing so this could be a long shot, but if you don't find anything else, you could try the Atomic Simulation Environment (ASE) and its various ways to preform molecular dynamics.

https://wiki.fysik.dtu.dk/ase/ase/md.html

In order to couple different physics you can use a multiphysic CFD software as COMSOL which is very efficient to model this problem type.

I would recommend it to my colleague Benoit Legras

You can see the ansys or comsol software

I do not work with this kind of problem, but I think you could do some research on FLUENT.

better to use Fluent as solver for heat transfer problems i think for meshing you need to use Gambit 6,2

My suggestion is, use some mathematics software like Mathcad and develop a set of coupled equations for a simple case like a flat plate, a tube or one sphere. If you really want to use a multiphysics software compare your result for a simple case with the result of the multiphysics suite. If this runs well you may create complicated surfaces in the multiphysics solution but I would check also the behaviour during single heat transfer and single reaction. Do not trust impressive pictures ! Try to disover the dominant phenomenon. For example dominant heat transfer resistance in the gas phase, solid can be modeled as ideally conductive, reaction fast compared to heat transfer... Sometimes there is a simplyfied solution to the problem which gives you a good first guess.

Thank you all and particular to Thorsten,

like Thorsten, I will try first in a simple case in mathematical software and then compare with Comsol that I began to learn. For the moment I learn more about and trying some equations.

Thanks for all.

I suggest you to work with - ansys multiphysics- wich include Mechanics and CFD .