Surfkit: An atomic toolkit for surface modelling with molecular adsorption

Abstract

The surface model with molecular adsorption is critical to study various surface related functions by means of first principles approaches such as catalytic activity, energy storage, corrosion, charge transfer, ion adsorption, etc. However, as the atomic configurations in surface modelling become progressively complex, the public programs exhibit insufficient automation or even deficiency in the construction of specific surface-related models, e.g. the high-index surface slab, the bilayer/heterostructures and the adsorption configuration with specified symmetry. All these issues bring necessity to develop a user-friendly program that is dedicated to automatic surface modeling with the guidance of symmetry. In this work, we present an open-source program, termed as Surfkit, that is specifically developed for automatically constructing the complicated surface-related models for first-principles calculations. This program features three major functionalities, including the construction of complex surface model with minimal lattice dimension, the twisted bilayers or heterostructures with minimized misfit strain, and the molecular adsorption models with specified symmetry. Several options can be applied consecutively, allowing for a comprehensive workflow from a unit cell to complex surface model. We provide not only a throughout overview on various numerical methods and their implementation into Surfkit program, but some critical evaluations, specific tests and applications, demonstrating the capability of the program on each functionality.