Jian Liu Research Group, Peking University

High-throughput computation of important properties of chemical systems with the latest theoretical chemistry methods is a fundamental quest from the realm of computational chemistry. We have been working on implementing our theory on existing or new quantum molecular dynamics computer programs to fulfill the requirement. We hope these programs can build a bridge between theorists and experimentalists, making convenient use of our novel path integral molecular dynamics and nonadiabatic dynamics methods.

Currently we have been developing the following programs:

hNaF: Nonadiabatic Field for Heterogeneous Hardware
PSiNAD: Phase Space Integrated Nonadiabatic Dynamics
PSiQMD: Phase Space Integrated Quantum Molecular Dynamics

Currently we have been working on adding the following features to the corresponding existing programs:

The "middle" scheme thermostat and barostat to Amber, AmberTools, GROMACS and DL-POLY

Introduction

PSiNad (Phase Space Integrated Nonadiabatic Dynamics) is an open-source framework specifically designed for simulating chemical and physical dynamics at atomic and molecular scales in condensed matter. It excels in classical and quantum dynamics simulations, accommodating small systems, few-body systems, reduced systems, and large many-particle systems such as molecules and condensed matter. PSiNad offers a robust, versatile platform with multiple interfaces for developing advanced algorithms, ensuring ease of use and accessibility with third-party language wrappers, such as Python.

PSiNad features a comprehensive array of models and solvers, including harmonic models, forcefield models, and ab initio interfaces, meeting diverse simulation needs. It supports a wide range of computational approaches, from classical dynamics based on Newtonian and Hamiltonian mechanics to sophisticated quantum dynamics incorporating quantum phase space approximations, quantum trajectories, path integral techniques, influence functional methods, and semi-classical wavepackets.

Continual development efforts focus on expanding the library of models and solvers, with community contributions highly encouraged. To further extend its accessibility, PSiNad is now available as a Python package (PyPSiNad).

Introduction

PSiQMD includes molecular dynamics, path integral molecular dynamics, path integral Liouville dynamics, nonadiabatic molecular dynamics, and so on. It not only collects progress of our coding in

hNaF
PSiNAD

and for

novel integrators of the "middle" thermostat-barostat scheme in AMBER, AmberTools, GROMACS

but also includes phase space quantum dynamics approaches and other trajectory-based dynamics/thermodynamics methods for real molecular systems.

Introduction

hNaF is a nonadiabatic dynamics program designed for ultra-high throughput model tests and method developments on heterogeneous computation platforms. Homemade computational platforms are usually equipped with specially designed heterogeneous hardwares, parallel interfaces and limited supports to the programming languages. By modularizing the computation tasks and separating out the parallel layers, hNaF enables us to test our new nonadiabatic dynamics methods rapidly, making full use of the homemade hardwares, for example, the new Sunway supercomputer.

The "middle" thermostat and barostat scheme in Amber, AmberTools, GROMACS and DL-POLY

[NEW!] We have implemented a recommended "middle" scheme for the isobaric-isothermal ensemble in molecular dynamics packages, e.g., AMBER, GROMACS, and DL-POLY. An detailed description is on the way.

We have implemented the efficient "middle" thermostat scheme into the lastest version of AmberTools since 2019. It can be obtained by following the instructions on the official website. For the users who can only use AmberTools18, the updated files for the "middle" scheme for AmberTools18 can be downloaded from the GitHub webpage.

The tutorial for the "middle" scheme is available on the webpage. One is also encouraged to read the AMBER manual for more details. The "middle" thermostat scheme has been implemented for MD for classical statistics as well as primitive PIMD for quantum statistics. It can be used together with QM/MM and enhanced sampling techniques (such as replica exchange) in AMBER. One can do ab initio PIMD or MD for the canonical ensemble by using AMBER combined with other quantum chemistry packages.

Jian Liu Group @PKU

Theoretical Chemistry / Chemical Dynamics

Overview

PSiNAD: Phase Space Integrated Nonadiabatic Dynamics

Introduction

PSiQMD: Phase Space Integrated Quantum Molecular Dynamics

Introduction

hNaF: Nonadiabatic Field for Heterogeneous Hardware

Introduction

The "middle" thermostat and barostat scheme in molecular dynamics programs

The "middle" thermostat and barostat scheme in Amber, AmberTools, GROMACS and DL-POLY