NQCDynamics.jl: A Julia Package for Nonadiabatic Quantum Classical Molecular Dynamics in the Condensed Phase

Abstract

Accurate and efficient methods to simulate nonadiabatic and quantum nuclear effects in high-dimensional and dissipative systems are crucial for the prediction of chemical dynamics in condensed phase. To facilitate effective development, code sharing and uptake of newly developed dynamics methods, it is important that software implementations can be easily accessed and built upon. Using the Julia programming language, we have developed the NQCDynamics.jl package which provides a framework for established and emerging methods for performing semiclassical and mixed quantum-classical dynamics in condensed phase. The code provides several interfaces to existing atomistic simulation frameworks, electronic structure codes, and machine learning representations. In addition to the existing methods, the package provides infrastructure for developing and deploying new dynamics methods which we hope will benefit reproducibility and code sharing in the field of condensed phase quantum dynamics. Herein, we present our code design choices and the specific Julia programming features from which they benefit. We further demonstrate the capabilities of the package on two examples of chemical dynamics in condensed phase: the population dynamics of the spin-boson model as described by a wide variety of semi-classical and mixed quantum-classical nonadiabatic methods and the reactive scattering of H2 on Ag(111) using the Molecular Dynamics with Electronic Friction method. Together, they exemplify the broad scope of the package to study effective model Hamiltonians and realistic atomistic systems.

arXiv comment19 pages, 8 figures; updated figures, added scaling data, added model E results

References in corpus (39)

• Gaussian Approximation Potentials: the accuracy of quantum mechanics, without the electrons
• SchNet - a deep learning architecture for molecules and materials
• SchNetPack: A Deep Learning Toolbox For Atomistic Systems
• Efficient stochastic thermostatting of path integral molecular dynamics
• i-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations
• Computing in Operations Research using Julia
• Robust and efficient configurational molecular sampling via Langevin Dynamics
• Machine learning enables long time scale molecular photodynamics simulations
• Perspective on integrating machine learning into computational chemistry and materials science
• Rational Construction of Stochastic Numerical Methods for Molecular Sampling
• Generalized spin mapping for quantum-classical dynamics
• Spin-mapping approach for nonadiabatic molecular dynamics
• Ab-initio tensorial electronic friction for molecules on metal surfaces: nonadiabatic vibrational relaxation
• Born-Oppenheimer Dynamics, Electronic Friction, and the Inclusion of Electron-Electron Interactions
• Distributions.jl: Definition and Modeling of Probability Distributions in the JuliaStats Ecosystem
• A Unified Theoretical Framework for Mapping Models for the Multi-State Hamiltonian
• Julia Language in Machine Learning: Algorithms, Applications, and Open Issues
• Mode specific electronic friction in dissociative chemisorption on metal surfaces: H${}_2$ on Ag(111)
• On the identity of the identity operator in nonadiabatic linearized semiclassical dynamics
• Reduced density matrix hybrid approach: An efficient and accurate method for adiabatic and non-adiabatic quantum dynamics
• Unified Formulation of Phase Space Mapping Approaches for Nonadiabatic Quantum Dynamics
• MLJ: A Julia package for composable machine learning
• Symmetry-Adapted High Dimensional Neural Network Representation of Electronic Friction Tensor of Adsorbates on Metals
• Cayley modification for strongly stable path-integral and ring-polymer molecular dynamics
• An analysis of nonadiabatic ring-polymer molecular dynamics and its application to vibronic spectra
• On the accuracy of surface hopping dynamics in condensed phase non-adiabatic problems
• Equivariant analytical mapping of first principles Hamiltonians to accurate and transferable materials models
• Dimension-free path-integral molecular dynamics without preconditioning
• Nonadiabatic semiclassical dynamics in the mixed quantum-classical initial value representation
• Negative Zero-Point-Energy Parameter in the Meyer-Miller Mapping Model for Nonadiabatic Dynamics
• Commutator Matrix in Phase Space Mapping Models for Nonadiabatic Quantum Dynamics
• Quantum-Classical Limit of Quantum Correlation Functions
• State Dependent Ring Polymer Molecular Dynamics for Investigating Excited Nonadiabatic Dynamics
• Thermal quantum time-correlation functions from classical-like dynamics
• Quantum Dynamics with Electronic Friction
• Black-box inhomogeneous preconditioning for self-consistent field iterations in density functional theory
• Electronic friction coefficients from the atom-in-jellium model for $Z=1-92$
• High-order geometric integrators for representation-free Ehrenfest dynamics
• A robust and efficient line search for self-consistent field iterations