A Methodology to Generate Crystal-based Molecular Structures for Atomistic Simulations

TL;DR

This paper introduces a systematic, open-source methodology and software tool for generating various crystal-based molecular structures, including slabs and Wulff shapes, for atomistic simulations in computational chemistry.

Contribution

The paper presents a new, integrated approach and software (LCC) for constructing diverse crystal structures with customizable boundary conditions, enhancing simulation input preparation.

Findings

Successfully generates crystal slabs with orthogonal PBC vectors.

Provides open-source software LCC for community use.

Demonstrates application through multiple example structures.

Abstract

We propose a systematic method to construct crystal-based molecular structures often needed as input for computational chemistry studies. These structures include crystal ``slabs" with periodic boundary conditions (PBCs) and non-periodic solids such as Wulff structures. We also introduce a method to build crystal slabs with orthogonal PBC vectors. These methods are integrated into our code, Los Alamos Crystal Cut (LCC), which is open source and thus fully available to the community. Examples showing the use of these methods are given throughout the manuscript.