KIMERA is a code designed to study of mineral dissolution. It implements a reversible Kinetic Monte Carlo (KMC) method to study the evolution of a dissolving system, obtaining the dissolution rate and information about the atomic scale dissolution mechanisms. KIMERA allows to define the dissolution process in multiple ways, using a wide diversity of event types to mimic the dissolution reactions, and define the mineral structure in great detail, including topographic defects, dislocations, point defects… It offers a good performance thanks to its parallelization and efficient algorithms within the KMC method. KIMERA is written in object-oriented C++, and it is distributed as open-source software. https://github.com/hegoimanzano/KIMERA
KIMERA was written by Pablo Martin, and the v1.0 release was published in December 2020.
To start dissolving your minerals with KIMERA, please check the github wiki: https://github.com/hegoimanzano/KIMERA/wiki. There, you will find instructions on how to compile the code and write your inpufile. There are also descriptions on the native KIMERA format used for restarting purposes, examples, and tests to guarantee the reproducibility.
Whenever you use KIMERA, please cite “Martin, P., Gaitero, J. J., Dolado, J. S., & Manzano, H. (2020). KIMERA: A Kinetic Montecarlo Code for Mineral Dissolution. Minerals, 10(9), 825” https://www.mdpi.com/2075-163X/10/9/825/htm
ReaxFF is a reactive force field created originally for hydrocarbons by Adri C.T van Duin and his coworkers in the Materials and Process Simulation Center group from Caltech University, and extended afterwards to inorganic systems. ReaxFF uses a bond-order formalism for bonding and angular interactions, together with a polarisable charge equilibration method (Qeq) to describe both reactive and non-reactive interactions between atoms.
ReaxFF potentials for cement based material were parameterized by H.Manzano and coworkers at MIT in 2012. The Ca/Si/O/H has been tested in crystalline calcium silicates, calcium silicate hydrates, crystal/water interfaces, and amorphous C-S-H. The provided files are the parameterization of the Si-Ca-O-H set already presented in a suitable form to use with two open-source well mantained codes: GULP and LAMMPS.
The files can be dowloaded from https://github.com/hegoimanzano/ReaxFF_cement
Whenever you use this ReaxFF parameters for Ca/O/H, please cite:
Hydration of Calcium Oxide Surface Predicted by Reactive Force Field Molecular Dynamics H.Manzano, M.J.Buehler, F-J.Ulm, R.J.M.Pellenq, A.C.T van Duin, Langmuir, 2012, 28 (9), 4187-4197.
Whenever you use this ReaxFF parameters for Si/Ca/O/H, please cite:
Confined water dissociation in microporous defective silicates: mechanism, dipole distribution, and impact on substrate properties H.Manzano, S.Moeini, F.Marinello, A.C.T van Duin, F-J.Ulm, R.J.M.Pellenq, Journal of the American Chemical Society, 2012, 134 (4), 2208-2215.
Please cite the ReaxFF method as:
The ReaxFF reactive force-field: development, applications and future directions. Senftle, T. P., Hong, S., Islam, M. M., Kylasa, S. B., Zheng, Y., Shin, Y. K., ... & Van Duin, A. C. (2016). npj Computational Materials, 2(1), 1-14.