DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics

Han Wang, Linfeng Zhang, Jiequn Han, Weinan E

Research output: Contribution to journalArticle

43 Scopus citations

Abstract

Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in Python/C++ that has been designed to minimize the effort required to build deep learning based representation of potential energy and force field and to perform molecular dynamics. Potential applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems. DeePMD-kit is interfaced with TensorFlow, one of the most popular deep learning frameworks, making the training process highly automatic and efficient. On the other end, DeePMD-kit is interfaced with high-performance classical molecular dynamics and quantum (path-integral) molecular dynamics packages, i.e., LAMMPS and the i-PI, respectively. Thus, upon training, the potential energy and force field models can be used to perform efficient molecular simulations for different purposes. As an example of the many potential applications of the package, we use DeePMD-kit to learn the interatomic potential energy and forces of a water model using data obtained from density functional theory. We demonstrate that the resulted molecular dynamics model reproduces accurately the structural information contained in the original model. Program summary: Program Title: DeePMD-kit Program Files doi: http://dx.doi.org/10.17632/hvfh9yvncf.1 Licensing provisions: LGPL Programming language: Python/C++ Nature of problem: Modeling the many-body atomic interactions by deep neural network models. Running molecular dynamics simulations with the models. Solution method: The Deep Potential for Molecular Dynamics (DeePMD) method is implemented based on the deep learning framework TensorFlow. Supports for using a DeePMD model in LAMMPS and i-PI, for classical and quantum (path integral) molecular dynamics are provided. Additional comments including Restrictions and Unusual features: The code defines a data protocol such that the energy, force, and virial calculated by different third-party molecular simulation packages can be easily processed and used as model training data.

Original languageEnglish (US)
Pages (from-to)178-184
Number of pages7
JournalComputer Physics Communications
Volume228
DOIs
StatePublished - Jul 2018

All Science Journal Classification (ASJC) codes

  • Hardware and Architecture
  • Physics and Astronomy(all)

Keywords

  • Deep neural networks
  • Many-body potential energy
  • Molecular dynamics

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