MLatom 3: A Platform for Machine Learning-Enhanced Computational Chemistry Simulations and Workflows

PO Dral, F Ge, YF Hou, P Zheng, Y Chen… - Journal of Chemical …, 2024 - ACS Publications
Machine learning (ML) is increasingly becoming a common tool in computational chemistry.
At the same time, the rapid development of ML methods requires a flexible software …

Searching configurations in uncertainty space: Active learning of high-dimensional neural network reactive potentials

Q Lin, L Zhang, Y Zhang, B Jiang - Journal of Chemical Theory …, 2021 - ACS Publications
Neural network (NN) potential energy surfaces (PESs) have been widely used in atomistic
simulations with ab initio accuracy. While constructing NN PESs, their training data points …

Exploring the mechanism of catalysis with the unified reaction valley approach (URVA)—A review

E Kraka, W Zou, Y Tao, M Freindorf - Catalysts, 2020 - mdpi.com
The unified reaction valley approach (URVA) differs from mainstream mechanistic studies,
as it describes a chemical reaction via the reaction path and the surrounding reaction valley …

REANN: A PyTorch-based end-to-end multi-functional deep neural network package for molecular, reactive, and periodic systems

Y Zhang, J Xia, B Jiang - The Journal of Chemical Physics, 2022 - pubs.aip.org
In this work, we present a general purpose deep neural network package for representing
energies, forces, dipole moments, and polarizabilities of atomistic systems. This so-called …

Automating the Development of High-Dimensional Reactive Potential Energy Surfaces with the robosurfer Program System

T Győri, G Czakó - Journal of Chemical Theory and Computation, 2019 - ACS Publications
The construction of high-dimensional global potential energy surfaces (PESs) from ab initio
data has been a major challenge for decades. Advances in computer hardware, electronic …

Reaction mechanism–explored with the unified reaction valley approach

E Kraka, JJ Antonio, M Freindorf - Chemical Communications, 2023 - pubs.rsc.org
One of the ultimate goals of chemistry is to understand and manipulate chemical reactions,
which implies the ability to monitor the reaction and its underlying mechanism at an atomic …

High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning

OT Unke, D Koner, S Patra, S Käser… - … Learning: Science and …, 2020 - iopscience.iop.org
An overview of computational methods to describe high-dimensional potential energy
surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy …

Bayesian machine learning approach to the quantification of uncertainties on ab initio potential energy surfaces

S Venturi, RL Jaffe, M Panesi - The Journal of Physical Chemistry …, 2020 - ACS Publications
This work introduces a novel methodology for the quantification of uncertainties associated
with potential energy surfaces (PESs) computed from first-principles quantum mechanical …

PES-Learn: An open-source software package for the automated generation of machine learning models of molecular potential energy surfaces

AS Abbott, JM Turney, B Zhang… - Journal of chemical …, 2019 - ACS Publications
We introduce a free and open-source software package (PES-Learn) which largely
automates the process of producing high-quality machine learning models of molecular …

Pitfalls in the n-mode representation of vibrational potentials

EL Yang, JJ Talbot, RJ Spencer… - The Journal of Chemical …, 2023 - pubs.aip.org
Simulations of anharmonic vibrational motion rely on computationally expedient
representations of the governing potential energy surface. The n-mode representation (n …