Computational Implementation of Nudged Elastic Band, Rigid Rotation, and Corresponding Force Optimization.
Computational Implementation of Nudged Elastic Band, Rigid Rotation, and Corresponding Force Optimization.
复制标题
轻推弹力带、刚性旋转和相应力优化的计算实现。
DOI：
10.1021/acs.jctc.7b00360
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发表时间：
2017
影响因子：
5.5
通讯作者：
P. Clancy
中科院分区：
文献类型：
--
作者：
Henry C. Herbol;James M Stevenson;P. Clancy
轻推弹性带（NEB）算法是计算化学体系过渡态的主要方法。然而，目前的文献缺乏足够的指导用户希望实现NEB的一个关键部分，即优化方法。在这里，我们提供了以下六种梯度下降算法的实现细节：最速下降，快速最小Verlet，FIRE，共轭梯度，Broyden-Fletcher-Goldfarb-Shanno（BFGS）和有限内存BFGS（LBFGS）。我们还构建和实现了一个新的，加速回溯线搜索方法与部分Procrustes叠加，以改善现有的方法。通过两个测试案例的基准计算实现验证，CNX和BOX（其中X ∈ {H，Li，Na}）的异构化和丙氨酸二肽内的构象变化的研究。我们还与被称为原子模拟环境的成熟代码库进行了直接比较。
The nudged elastic band (NEB) algorithm is the leading method of calculating transition states in chemical systems. However, the current literature lacks adequate guidance for users wishing to implement a key part of NEB, namely, the optimization method. Here, we provide details of this implementation for the following six gradient descent algorithms: steepest descent, quick-min Verlet, FIRE, conjugate gradient, Broyden-Fletcher-Goldfarb-Shanno (BFGS), and limited-memory BFGS (LBFGS). We also construct and implement a new, accelerated backtracking line search method in concert with a partial Procrustes superimposition to improve upon existing methods. Validation is achieved through benchmark calculations of two test cases, the isomerization of CNX and BOX (where X ∈ {H, Li, Na}) and the study of a conformational change within an alanine dipeptide. We also make direct comparisons to the well-established codebase known as the atomic simulation environment.