Vilhjálmur Ásgeirsson

arXiv2023

Improved Initialization of Optimal Path Calculations Using Sequential Traversal over the Image Dependent Pair Potential Surface

In reaction path optimization, such as the calculation of a minimum energy path (MEP) between given reactant and product configurations of atoms, it is advantageous to start with an initial guess where close proximity of atoms is avoided and bonds are not unnecessarily broken only to be reformed later. When the configurations of the atoms are described with Cartesian coordinates, a linear interpolation between the endpoints can be problematic, and a better option is provided by the so-called image dependent pair potential (IDPP) approach where interpolated pairwise distances are generated to form an objective function that can be used to generate an improved initial path. When started with a linear interpolation, this method can, however, still lead to unnecessary bond breaking in, for example, reactions where a molecular subgroup undergoes significant rotation. In the method presented here, this problem is addressed by constructing the path gradually, introducing images sequentially starting from the vicinity of the endpoints while the distance between images in the central region is larger. The distribution of images is controlled by systematically scaling the tightness of springs acting between the images until the desired number of images is obtained and they are evenly spaced. This procedure generates an initial path on the IDPP surface, a task that requires insignificant computational effort, as no evaluation of the energy of the system is needed. The calculation of the MEP, typically using electronic structure calculations, is then subsequently carried out in a way that makes efficient use of parallel computing with the nudged elastic band method. Several examples of reactions are given where the linear interpolation IDPP (LI-IDPP) method yields problematic paths with unnecessary bond breaking in some of the intermediate images, while the sequential IDPP (S-IDPP) method yields pat

physics.chem-ph↗

arXiv2017

Nudged elastic band calculations accelerated with Gaussian process regression

Minimum energy paths for transitions such as atomic and/or spin rearrangements in thermalized systems are the transition paths of largest statistical weight. Such paths are frequently calculated using the nudged elastic band method, where an initial path is iteratively shifted to the nearest minimum energy path. The computational effort can be large, especially when ab initio or electron density functional calculations are used to evaluate the energy and atomic forces. Here, we show how the number of such evaluations can be reduced by an order of magnitude using a Gaussian process regression approach where an approximate energy surface is generated and refined in each iteration. When the goal is to evaluate the transition rate within harmonic transition state theory, the evaluation of the Hessian matrix at the initial and final state minima can be carried out beforehand and used as input in the minimum energy path calculation, thereby improving stability and reducing the number of iterations needed for convergence. A Gaussian process model also provides an uncertainty estimate for the approximate energy surface, and this can be used to focus the calculations on the lesser-known part of the path, thereby reducing the number of needed energy and force evaluations to a half in the present calculations. The methodology is illustrated using the two-dimensional Müller-Brown potential surface and performance assessed on an established benchmark involving 13 rearrangement transitions of a heptamer island on a solid surface.

physics.chem-ph↗