As a language model, I don't have a personal preference. But I can suggest how to choose from these packages:
The task can be split into two parts: simulation and optimization. For optimization, I will choose Numpy to support arrays, which are widely used among packages, and Scipy to perform the optimization as it is more supported and has more capabilities. Pyomo is easier to learn, so it can be a good choice to relieve some effort if it is capable of your tasks. Pint will also be recommended to avoid confusing unit conversions。
The best choice among ChemPy, Cantera, and OpenMD is highly related to your needs:

- ChemPy is mainly used in physical, inorganic, and analytical chemistry, and is capable of solving equilibria and simulating chemical kinetics. It also includes relations in physical chemistry and properties of water as functions of temperature and pressure.
- Cantera is mainly used for the calculation of chemical thermo-kinetics and transport models. Its applications mainly lie in combustion, detonations, electrochemical energy conversion and storage, fuel cells, batteries, aqueous electrolyte solutions, plasmas, and thin film deposition.
- OpenMD is focused on molecular dynamics, and is mainly used to simulate liquids, proteins, nanoparticles, interfaces, and other complex systems.

With more details on your needs, I can make a better recommendation.
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