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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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A methodology to generate crystal-based molecular structures for atomistic simulations.

Christian F A Negre1, Andrew Alvarado1,2, Himanshu Singh1

  • 1Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America.

Journal of Physics. Condensed Matter : an Institute of Physics Journal
|March 8, 2023
PubMed
Summary
This summary is machine-generated.

This study presents a systematic method for creating crystal structures for computational chemistry. The open-source Los Alamos Crystal Cut (LCC) code facilitates building crystal slabs and non-periodic solids.

Keywords:
crystal structuresextended structuresmiller indicesquantum chemistryunit cells

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Area of Science:

  • Materials Science
  • Computational Chemistry
  • Crystallography

Background:

  • Computational chemistry studies often require accurate crystal-based molecular structures.
  • Generating these structures, especially with specific boundary conditions, can be complex.
  • Existing methods may lack flexibility for diverse crystallographic needs.

Purpose of the Study:

  • To introduce a systematic and versatile method for constructing crystal-based molecular structures.
  • To enable the creation of crystal slabs with periodic boundary conditions (PBCs) and non-periodic solids.
  • To provide an open-source computational tool for the scientific community.

Main Methods:

  • Development of a systematic approach to generate crystal slabs and Wulff shapes.
  • Implementation of methods for building crystal slabs with orthogonal PBC vectors.
  • Integration of these functionalities into the open-source Los Alamos Crystal Cut (LCC) software.

Main Results:

  • A robust and accessible method for constructing diverse crystal structures.
  • The LCC code provides a user-friendly interface for generating input structures.
  • Demonstration of the methods with practical examples within the manuscript.

Conclusions:

  • The proposed methods and LCC code offer a valuable resource for computational chemistry.
  • Facilitates the generation of essential crystal structures for simulations.
  • Promotes wider accessibility and reproducibility in materials modeling.