I am looking for open-source modelling software to study the microstructural development of cement hydration products (Calcium hydroxide, Calcium silicate hydrate, and Ettringite).
To be honest, there are plenty of software available where you could model the Cement Hydration and Degradation.
From my personal experience, the National Institute of Standards and Technology (NIST, USA) offer some models that are freely available to the general public.
Cement Hydration Modelling [Computer programs for modeling cement hydration and percolation processes] : ftp://ftp.nist.gov/pub/bfrl/bentz/cmml/educ-mod/windowsxp/ [for windows]
Documentation for these models is available at https://concrete.nist.gov/~garbocz/