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DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments., Comment: 51 pages, 2 figures

It is imperative to accelerate the training of neural network force field such as Deep Potential, which usually requires thousands of images based on first-principles calculation and a couple of days to generate an accurate potential energy surface. To this end, we propose a novel optimizer named reorganized layer extended Kalman filtering (RLEKF), an optimized version of global extended Kalman filtering (GEKF) with a strategy of splitting big and gathering small layers to overcome the $O(N^2)$ computational cost of GEKF. This strategy provides an approximation of the dense weights error covariance matrix with a sparse diagonal block matrix for GEKF. We implement both RLEKF and the baseline Adam in our $\alpha$Dynamics package and numerical experiments are performed on 13 unbiased datasets. Overall, RLEKF converges faster with slightly better accuracy. For example, a test on a typical system, bulk copper, shows that RLEKF converges faster by both the number of training epochs ($\times$11.67) and wall-clock time ($\times$1.19). Besides, we theoretically prove that the updates of weights converge and thus are against the gradient exploding problem. Experimental results verify that RLEKF is not sensitive to the initialization of weights. The RLEKF sheds light on other AI-for-science applications where training a large neural network (with tons of thousands parameters) is a bottleneck.

The recently developed Deep Potential [Phys. Rev. Lett. 120, 143001, 2018] is a powerful method to represent general inter-atomic potentials using deep neural networks. The success of Deep Potential rests on the proper treatment of locality and symmetry properties of each component of the network. In this paper, we leverage its network structure to effectively represent the mapping from the atomic configuration to the electron density in Kohn-Sham density function theory (KS-DFT). By directly targeting at the self-consistent electron density, we demonstrate that the adapted network architecture, called the Deep Density, can effectively represent the electron density as the linear combination of contributions from many local clusters. The network is constructed to satisfy the translation, rotation, and permutation symmetries, and is designed to be transferable to different system sizes. We demonstrate that using a relatively small number of training snapshots, Deep Density achieves excellent performance for one-dimensional insulating and metallic systems, as well as systems with mixed insulating and metallic characters. We also demonstrate its performance for real three-dimensional systems, including small organic molecules, as well as extended systems such as water (up to $512$ molecules) and aluminum (up to $256$ atoms).

Real-time time-dependent density functional theory (RT-TDDFT) is known to be hindered by the very small time step (attosecond or smaller) needed in the numerical simulation due to the fast oscillation of electron wavefunctions, which significantly limits its range of applicability for the study of ultrafast dynamics. In this paper, we demonstrate that such oscillation can be considerably reduced by optimizing the gauge choice using the parallel transport formalism. RT-TDDFT calculations can thus be significantly accelerated using a combination of the parallel transport gauge and implicit integrators, and the resulting scheme can be used to accelerate any electronic structure software that uses a Schr\"odinger representation. Using absorption spectrum, ultrashort laser pulse, and Ehrenfest dynamics calculations for example, we show that the new method can utilize a time step that is on the order of $10\sim 100$ attoseconds in a planewave basis set, and is no less than $5\sim 10$ times faster when compared to the standard explicit 4th order Runge-Kutta time integrator. Thanks to the significant increase of the size of the time step, we also demonstrate that the new method is more than 10 times faster in terms of the wall clock time when compared to the standard explicit 4th order Runge-Kutta time integrator for silicon systems ranging from 32 to 1024 atoms