DeepModeling

DFTIO, initiated by the DeePTB team at the Beijing Institute of Science and Intelligence, is an efficient electronic structure data processing tool designed to convert electronic structure output information from various first-principles/quantum computation software into data formats that are easy for machine learning models to read.

In recent years, machine learning-based first-principles electronic structure models have developed rapidly, including but not limited to machine learning tight-binding models, Hamiltonian models, electronic density models, and functional models. With the advancement of these models, we have increasingly realized that the post-processing of output data from different electronic structure calculation software has become a common challenge for both developers and users.

Recently, Professor Han Ye's research team from the School of Materials Science and Engineering at Shandong University of Science and Technology utilized the Deep Potential (DP) model for molecular dynamics simulations. They conducted an in-depth analysis of the phonon dispersion relations, energy-volume curves, solid-liquid interfacial structures, and mechanical properties of Cu-Sn alloys. The results were validated against density functional theory (DFT) calculations, demonstrating excellent consistency.

The radial distribution function (RDF) results computed using the DP model revealed that the disordered atomic arrangements of Cu₁₀Sn₃ and CuSn structures at 1100 K are attributed to the broadening and shortening of RDF peaks at high temperatures, indicating reduced atomic coherence.

The findings were published in Computational Materials Science under the title "Research on Cu-Sn Machine Learning Interatomic Potential with Active Learning Strategy". Master's students Liu Jinyan and Zhang Guanghao were the co-first authors, with Professor Han Ye serving as the corresponding author.

On the journey toward developing a Large Atomic Model (LAM), the core Deep Potential development team has launched the OpenLAM initiative for the community. OpenLAM’s slogan is "Conquer the Periodic Table!" The project aims to create an open-source ecosystem centered on microscale large models, providing new infrastructure for microscopic scientific research and driving transformative advancements in microscale industrial design across fields such as materials, energy, and biopharmaceuticals.

Recently, Dr. Mei Jia from Shangqiu Normal University, Dr. Yongbin Zhuang from École Polytechnique Fédérale de Lausanne (EPFL), and Prof. Jun Cheng from Xiamen University conducted an in-depth study on the proton transfer mechanism at the SnO₂(110)/H₂O interface by combining ab initio molecular dynamics (AIMD) with the Deep Potential (DP) method. The team used AIMD to obtain the electronic structure of the interface system and applied the Deep Potential Molecular Dynamics (DPMD) model to accelerate molecular dynamics simulations, enabling larger-scale and longer-timescale simulations. This combination of methods allowed the researchers to analyze the free energy distributions of different proton transfer pathways in detail and to reveal the influence of the solvation environment on the proton transfer process.

The related findings have been published in the high-impact journal Precision Chemistry, under the title “Water-Mediated Proton Hopping Mechanisms at the SnO₂(110)/H₂O Interface from Ab Initio Deep Potential Molecular Dynamics.” Dr. Mei Jia and Dr. Yongbin Zhuang are the co-first authors, and Prof. Jun Cheng is the corresponding author.

This Notebook will approach DeePKS from an application perspective, using the perovskite system as a case study. It systematically presents the complete process of DeePKS model training and deployment, including:

1. Preparation of labeled data for the example system,
2. Model training, and
3. Result analysis.

Check out here: https://bohrium.dp.tech/collections/6242632852/

On July 15, 2024, Bilal Aslan from the University of Cape Town, Flavio Correa da Silva from the University of São Paulo, and Geoff Nitschke from the University of Cape Town collaborated to present their research titled “Multi-Objective Evolution for Chemical Product Design” at the Genetic and Evolutionary Computation Conference (GECCO). This study introduced a chemical product design method based on multi-objective evolutionary optimization. By innovatively integrating deep learning with evolutionary algorithms, the approach optimizes molecular properties and utilizes the Uni-Mol model to evaluate molecular toxicity, providing a novel solution for the design and optimization of chemical products.

The ReacNetGenerator project has officially joined the DeepModeling open-source community, aiming to further advance its development.

Project Homepage

https://github.com/deepmodeling/reacnetgenerator

DeepFlame is an open-source combustion fluid dynamics platform developed for the AI for Science era [1-3], aimed at overcoming the longstanding challenges of applying traditional Computational Fluid Dynamics (CFD) in the field of combustion. Since its release, DeepFlame has garnered significant interest and attention from both academia and industry, attracting a group of outstanding developers and users. This ongoing support has provided continuous momentum for DeepFlame's development and has been a crucial driving force in its application to real-world scenarios.

In recent years, research on aerosol or spray detonation propulsion using liquid fuels has been experiencing a resurgence, and supersonic combustion, such as detonation combustion in gas-liquid two-phase systems, has been gaining increasing attention. The DeepFlame team has captured these trending topics and, based on the OpenFOAM open-source library, coupled the Euler-Lagrange model into the high-speed flow solver dfHighSpeedFoam and the low-speed flow solver dfLowMachFoam. This enables the solvers to simulate two-phase reactive flows, thereby expanding the application scenarios of DeepFlame.

On August 19, 2024, Shuqi Lu and Zhifeng Gao from DP Technology, in collaboration with Professor Di He from Peking University, published a research article titled "Data-driven quantum chemical property prediction leveraging 3D conformations with Uni-Mol+" in Nature Communications. This study introduces Uni-Mol+, a deep learning algorithm that innovatively utilizes neural networks to iteratively optimize initial 3D molecular conformations, enabling precise prediction of quantum chemical properties. By progressively approximating Density Functional Theory (DFT) equilibrium conformations, Uni-Mol+ significantly enhances prediction accuracy, providing a powerful tool for high-throughput screening and new material design.

In 2023, the AI for Science Institute, Beijing team introduced the v1 version of the DeePTB method, which was published on arXiv and joined the DeepModeling community. After nearly a year of rigorous peer review, it was officially published on August 8, 2024, in the international academic journal Nature Communications with the title "Deep learning tight-binding approach for large-scale electronic simulations at finite temperatures with ab initio accuracy" [1], DOI: 10.1038/s41467-024-51006-4.

The v1 version of DeePTB focuses on developing a deep learning-based method for constructing tight-binding (TB) model Hamiltonians. Based on the Slater-Koster TB parameterization, it builds first-principles equivalent electronic models using a minimal-basis set. By incorporating the localized chemical environment of atoms/bonds into the TB parameters, DeePTB achieves TB Hamiltonian predictions with near-DFT accuracy across a range of key material systems. By integrating with software like DeePMD-kit and TBPLaS, it enables the calculation and simulation of electronic structure properties and photoelectric responses in large-scale systems of up to millions of atoms in finite-temperature ensembles. This groundbreaking advancement has garnered widespread attention in the academic community and was ultimately published in Nature Communications. For more technical details on the DeePTB version, interested readers can refer to the DeePTB article in Nat Commun 15, 6772 (2024).