Exploiting symmetry to speed up symmetric nudge elastic band calculations

Juan Maria García Lastra*, Nicolai Rask Mathiesen, Tejs Vegge

*Corresponding author for this work

Research output: Contribution to journalConference abstract in journalResearchpeer-review

Abstract

Many transitions of interest such as diffusion mechanisms in crystalline structures (vacancy, defect and polaron migration), rotations of ligands on molecules, and even reactions at surfaces (surface migration) there is a reflection relating the initial and final geometries of the reaction. Finding minimum energy paths (MEPs) of thermally activated transitions in such systems with band methods like the nudge elastic band (NEB, which for more than 20 years has been the most popular method), can be speed up if the symmetry is exploited. Here we present the formal properties required from a system to guarantee a reflection symmetric MEP. We present an implementation to prepare and effectively speed up nudge elastic band calculations through symmetry considerations. The implementation contains methods to identify symmetry relations between two given atomic geometries that can be used for many other purposes. The method can also be combined with many other implementations intended for speeding up nudge elastic band calculations. The implementation is validated through examples, showing that the computational time for a NEB calculation can be reduced by a factor between 2 and 10, depending on the considered system.
Original languageEnglish
JournalAmerican Chemical Society. Abstracts of Papers (at the National Meeting)
Volume257
Number of pages1
ISSN0065-7727
Publication statusPublished - 2019
Event257th ACS National Meeting and Exposition - Orlando, United States
Duration: 31 Mar 20194 Apr 2019

Conference

Conference257th ACS National Meeting and Exposition
CountryUnited States
CityOrlando
Period31/03/201904/04/2019

Bibliographical note

Spring 2019 National Meeting & Expo (2019), Program Area: PHYS 611

Cite this

@article{20206c1b409846a1a4ab9ac48145f41f,
title = "Exploiting symmetry to speed up symmetric nudge elastic band calculations",
abstract = "Many transitions of interest such as diffusion mechanisms in crystalline structures (vacancy, defect and polaron migration), rotations of ligands on molecules, and even reactions at surfaces (surface migration) there is a reflection relating the initial and final geometries of the reaction. Finding minimum energy paths (MEPs) of thermally activated transitions in such systems with band methods like the nudge elastic band (NEB, which for more than 20 years has been the most popular method), can be speed up if the symmetry is exploited. Here we present the formal properties required from a system to guarantee a reflection symmetric MEP. We present an implementation to prepare and effectively speed up nudge elastic band calculations through symmetry considerations. The implementation contains methods to identify symmetry relations between two given atomic geometries that can be used for many other purposes. The method can also be combined with many other implementations intended for speeding up nudge elastic band calculations. The implementation is validated through examples, showing that the computational time for a NEB calculation can be reduced by a factor between 2 and 10, depending on the considered system.",
author = "{Garc{\'i}a Lastra}, {Juan Maria} and Mathiesen, {Nicolai Rask} and Tejs Vegge",
note = "Spring 2019 National Meeting & Expo (2019), Program Area: PHYS 611",
year = "2019",
language = "English",
volume = "257",
journal = "American Chemical Society. Abstracts of Papers (at the National Meeting)",
issn = "0065-7727",
publisher = "American Chemical Society",

}

Exploiting symmetry to speed up symmetric nudge elastic band calculations. / García Lastra, Juan Maria; Mathiesen, Nicolai Rask; Vegge, Tejs.

In: American Chemical Society. Abstracts of Papers (at the National Meeting), Vol. 257, 2019.

Research output: Contribution to journalConference abstract in journalResearchpeer-review

TY - ABST

T1 - Exploiting symmetry to speed up symmetric nudge elastic band calculations

AU - García Lastra, Juan Maria

AU - Mathiesen, Nicolai Rask

AU - Vegge, Tejs

N1 - Spring 2019 National Meeting & Expo (2019), Program Area: PHYS 611

PY - 2019

Y1 - 2019

N2 - Many transitions of interest such as diffusion mechanisms in crystalline structures (vacancy, defect and polaron migration), rotations of ligands on molecules, and even reactions at surfaces (surface migration) there is a reflection relating the initial and final geometries of the reaction. Finding minimum energy paths (MEPs) of thermally activated transitions in such systems with band methods like the nudge elastic band (NEB, which for more than 20 years has been the most popular method), can be speed up if the symmetry is exploited. Here we present the formal properties required from a system to guarantee a reflection symmetric MEP. We present an implementation to prepare and effectively speed up nudge elastic band calculations through symmetry considerations. The implementation contains methods to identify symmetry relations between two given atomic geometries that can be used for many other purposes. The method can also be combined with many other implementations intended for speeding up nudge elastic band calculations. The implementation is validated through examples, showing that the computational time for a NEB calculation can be reduced by a factor between 2 and 10, depending on the considered system.

AB - Many transitions of interest such as diffusion mechanisms in crystalline structures (vacancy, defect and polaron migration), rotations of ligands on molecules, and even reactions at surfaces (surface migration) there is a reflection relating the initial and final geometries of the reaction. Finding minimum energy paths (MEPs) of thermally activated transitions in such systems with band methods like the nudge elastic band (NEB, which for more than 20 years has been the most popular method), can be speed up if the symmetry is exploited. Here we present the formal properties required from a system to guarantee a reflection symmetric MEP. We present an implementation to prepare and effectively speed up nudge elastic band calculations through symmetry considerations. The implementation contains methods to identify symmetry relations between two given atomic geometries that can be used for many other purposes. The method can also be combined with many other implementations intended for speeding up nudge elastic band calculations. The implementation is validated through examples, showing that the computational time for a NEB calculation can be reduced by a factor between 2 and 10, depending on the considered system.

M3 - Conference abstract in journal

VL - 257

JO - American Chemical Society. Abstracts of Papers (at the National Meeting)

JF - American Chemical Society. Abstracts of Papers (at the National Meeting)

SN - 0065-7727

ER -