Tutorials

In this section, we will show how to set up the following systems:

• Wyoming Montmorillonite

• Illite

• Pyrophyllite

• Uley Nontronites

• Ferruginous Smectite

• Kaolinite

• Layered Double Hydroxide

The Pyrophyllite tutorial shows how to construct a system using only a .YAML file, the Nontronites tutorial discusses assigning iron distribution and oxidation and the Kaolinite tutorial shows a situation where invalid atom types are encountered by ClayCode.

All necessary input files can be found in the Tutorial directory. Each system has a corresponding .YAML file, and the exp_clay.csv file contains clay structures corresponding to the Clay Mineral Society’s Source Clays. ^1,2 Note, that Pyrophyllite’s composition is not given in the .CSV file as it is fully described in the .YAML file.

1

J Fripiat and H van Olphen, editors. Data Handbook for Clay Minerals and Other Non-metallic Minerals. Pergamon Press, 1979.

2

Clay Mineral Society. Physical and chemical data of source clays. URL: https://www.clays.org/sourceclays_data/.