R-NEB: Accelerated Nudged Elastic Band Calculations by Use of Reflection Symmetry

被引:24
|
作者
Mathiesen, Nicolai Rask [1 ]
Jonsson, Hannes [1 ,2 ,3 ]
Vegge, Tejs [1 ]
Lastra, Juan Maria Garcia [1 ]
机构
[1] Tech Univ Denmark, Dept Energy Convers & Storage, Fys Vej, DK-2800 Lyngby, Denmark
[2] Univ Iceland, Inst Sci, IS-107 Reykjavik, Iceland
[3] Univ Iceland, Fac Phys Sci, IS-107 Reykjavik, Iceland
关键词
FINDING SADDLE-POINTS;
D O I
10.1021/acs.jctc.8b01229
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Many activated processes in materials science, physics, and chemistry, e.g. diffusion processes, have initial and final states related by symmetry. Identification of minimum energy paths in such systems with methods such as nudged elastic band (NEB) can gain substantial speed up if the symmetry is exploited. The identification of minimum energy paths and transition states for such processes constitute a large fraction of the CPU-usage within computational materials science; much of which is in essence redundant due to symmetry. Paths with a reflection symmetry can be calculated using about half the computational resources, and the activation energy can, for some transitions, be estimated with high precision with a speed up factor equal to the number of images used in a standard NEB calculation. We present the formal properties required for a system to guarantee a reflection symmetric minimum energy path and an implementation to prepare and effectively speed up nudged elastic band calculations through symmetry considerations. Five examples are given to show the versatility and effectiveness of the method and to validate the implementation. The method is implemented in the open source package Atomic Simulation Environment (ASE) and contains internal methods to identify symmetry relations between the given end point configurations.
引用
收藏
页码:3215 / 3222
页数:8
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  • [1] Nudged elastic band calculations accelerated with Gaussian process regression
    Koistinen, Olli-Pekka
    Dagbjartsdottir, Freyja B.
    Asgeirsson, Vilhjalmur
    Vehtari, Aki
    Jonsson, Hannes
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2017, 147 (15):
  • [2] Nudged Elastic Band Calculations Accelerated with Gaussian Process Regression Based on Inverse Interatomic Distances
    Koistinen, Olli-Pekka
    Asgeirsson, Vilhjalmur
    Vehtari, Aki
    Jonsson, Hannes
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (12) : 6738 - 6751
  • [3] Implementation of distortion symmetry for the nudged elastic band method with DiSPy
    Munro, Jason M.
    Liu, Vincent S.
    Gopalan, Venkatraman
    Dabo, Ismaila
    [J]. NPJ COMPUTATIONAL MATERIALS, 2019, 5 (1)
  • [4] Implementation of distortion symmetry for the nudged elastic band method with DiSPy
    Jason M. Munro
    Vincent S. Liu
    Venkatraman Gopalan
    Ismaila Dabo
    [J]. npj Computational Materials, 5
  • [5] Implementation of GPU-accelerated partial nudged elastic band method in AMBER
    Ghoreishi, Delaram
    Cerutti, David
    Roitberg, Adrian
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2019, 257
  • [6] Use of a nudged elastic band method in analysis of optical flow
    Xia S.
    [J]. Xia, Shengxiang (xias@sdjzu.edu.cn), 1600, Begell House Inc. (23): : 157 - 169
  • [7] Calculations of dislocation mobility using Nudged Elastic Band method and first principles DFT calculations
    Pizzagalli, L.
    Beauchamp, P.
    Jonsson, H.
    [J]. PHILOSOPHICAL MAGAZINE, 2008, 88 (01) : 91 - 100
  • [8] Machine Learning in Computational Chemistry: An Evaluation of Method Performance for Nudged Elastic Band Calculations
    Meyer, Ralf
    Schmuck, Klemens S.
    Hauser, Andreas W.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (11) : 6513 - 6523
  • [9] Calculating low energy reaction pathways in proteins and RNA: A QM/MM implementation of the nudged elastic band (NEB) method
    Walker, RC
    Mathews, DH
    Case, D
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2005, 229 : U791 - U792
  • [10] Calculations of Thermodynamic Characteristics of Vapor Interlayers with the Use of Gradient and Integral Density Functional Theories and Nudged Elastic Band Method
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    [J]. Colloid Journal, 2021, 83 : 558 - 565