Featured Column — COMPUTATIONAL PROGRAMS FOR PHYSICS

    To promote the sharing and cooperation of computer programs developed for physics, which helps to reduce the barrier and lighten the burden of program development for physicists, Chinese Physics B launches a new section, “Computational Programs for Physics” in 2023. 

    Both research papers and review articles are welcome. Good computational programs are the focus of this section, whereas new physics and results are not necessary for acceptance. A good program should contain at least one of these factors: accuracy, efficiency, new functionality, accessibility, expansibility, etc.

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    MatChat: A large language model and application service platform for materials science
    Zi-Yi Chen(陈子逸), Fan-Kai Xie(谢帆恺), Meng Wan(万萌), Yang Yuan(袁扬), Miao Liu(刘淼), Zong-Guo Wang(王宗国), Sheng Meng(孟胜), and Yan-Gang Wang(王彦棡)
    Chin. Phys. B, 2023, 32 (11): 118104.   DOI: 10.1088/1674-1056/ad04cb
    Abstract213)   HTML7)    PDF (587KB)(242)      
    The prediction of chemical synthesis pathways plays a pivotal role in materials science research. Challenges, such as the complexity of synthesis pathways and the lack of comprehensive datasets, currently hinder our ability to predict these chemical processes accurately. However, recent advancements in generative artificial intelligence (GAI), including automated text generation and question-answering systems, coupled with fine-tuning techniques, have facilitated the deployment of large-scale AI models tailored to specific domains. In this study, we harness the power of the LLaMA2-7B model and enhance it through a learning process that incorporates 13878 pieces of structured material knowledge data. This specialized AI model, named MatChat, focuses on predicting inorganic material synthesis pathways. MatChat exhibits remarkable proficiency in generating and reasoning with knowledge in materials science. Although MatChat requires further refinement to meet the diverse material design needs, this research undeniably highlights its impressive reasoning capabilities and innovative potential in materials science. MatChat is now accessible online and open for use, with both the model and its application framework available as open source. This study establishes a robust foundation for collaborative innovation in the integration of generative AI in materials science.
    Analysis of pseudo-random number generators in QMC-SSE method
    Dong-Xu Liu(刘东旭), Wei Xu(徐维), and Xue-Feng Zhang(张学锋)
    Chin. Phys. B, 2024, 33 (3): 037509.   DOI: 10.1088/1674-1056/ad1e69
    Abstract87)   HTML4)    PDF (514KB)(99)      
    In the quantum Monte Carlo (QMC) method, the pseudo-random number generator (PRNG) plays a crucial role in determining the computation time. However, the hidden structure of the PRNG may lead to serious issues such as the breakdown of the Markov process. Here, we systematically analyze the performance of different PRNGs on the widely used QMC method known as the stochastic series expansion (SSE) algorithm. To quantitatively compare them, we introduce a quantity called QMC efficiency that can effectively reflect the efficiency of the algorithms. After testing several representative observables of the Heisenberg model in one and two dimensions, we recommend the linear congruential generator as the best choice of PRNG. Our work not only helps improve the performance of the SSE method but also sheds light on the other Markov-chain-based numerical algorithms.
    DSAS: A new macromolecular substructure solution program based on the modified phase-retrieval algorithm
    Xingke Fu(付兴科), Zhenxi Tan(谭振希), Zhi Geng(耿直), Qian Liu(刘茜), and Wei Ding(丁玮)
    Chin. Phys. B, 2024, 33 (5): 056102.   DOI: 10.1088/1674-1056/ad3c33
    Abstract82)   HTML0)    PDF (1091KB)(88)      
    Considering the pivotal role of single-wavelength anomalous diffraction (SAD) in macromolecular crystallography, our objective was to introduce {DSAS}, a novel program designed for efficient anomalous scattering substructure determination. DSAS stands out with its core components: a modified phase-retrieval algorithm and automated parameter tuning. The software boasts an intuitive graphical user interface (GUI), facilitating seamless input of essential data and real-time monitoring. Extensive testing on DSAS has involved diverse datasets, encompassing proteins, nucleic acids, and various anomalous scatters such as sulfur (S), selenium (Se), metals, and halogens. The results confirm {DSAS}'s exceptional performance in accurately determining heavy atom positions, making it a highly effective tool in the field.
    Literature classification and its applications in condensed matter physics and materials science by natural language processing
    Siyuan Wu(吴思远), Tiannian Zhu(朱天念), Sijia Tu(涂思佳), Ruijuan Xiao(肖睿娟), Jie Yuan(袁洁), Quansheng Wu(吴泉生), Hong Li(李泓), and Hongming Weng(翁红明)
    Chin. Phys. B, 2024, 33 (5): 050704.   DOI: 10.1088/1674-1056/ad3c30
    Abstract69)   HTML1)    PDF (681KB)(42)      
    The exponential growth of literature is constraining researchers' access to comprehensive information in related fields. While natural language processing (NLP) may offer an effective solution to literature classification, it remains hindered by the lack of labelled dataset. In this article, we introduce a novel method for generating literature classification models through semi-supervised learning, which can generate labelled dataset iteratively with limited human input. We apply this method to train NLP models for classifying literatures related to several research directions, i.e., battery, superconductor, topological material, and artificial intelligence (AI) in materials science. The trained NLP `battery' model applied on a larger dataset different from the training and testing dataset can achieve F1 score of 0.738, which indicates the accuracy and reliability of this scheme. Furthermore, our approach demonstrates that even with insufficient data, the not-well-trained model in the first few cycles can identify the relationships among different research fields and facilitate the discovery and understanding of interdisciplinary directions.
    Quafu-Qcover: Explore combinatorial optimization problems on cloud-based quantum computers
    Hong-Ze Xu(许宏泽), Wei-Feng Zhuang(庄伟峰), Zheng-An Wang(王正安), Kai-Xuan Huang(黄凯旋), Yun-Hao Shi(时运豪), Wei-Guo Ma(马卫国), Tian-Ming Li(李天铭), Chi-Tong Chen(陈驰通), Kai Xu(许凯), Yu-Long Feng(冯玉龙), Pei Liu(刘培), Mo Chen(陈墨), Shang-Shu Li(李尚书), Zhi-Peng Yang(杨智鹏), Chen Qian(钱辰), Yu-Xin Jin(靳羽欣), Yun-Heng Ma(马运恒), Xiao Xiao(肖骁), Peng Qian(钱鹏), Yanwu Gu(顾炎武), Xu-Dan Chai(柴绪丹), Ya-Nan Pu(普亚南), Yi-Peng Zhang(张翼鹏), Shi-Jie Wei(魏世杰), Jin-Feng Zeng(增进峰), Hang Li(李行), Gui-Lu Long(龙桂鲁), Yirong Jin(金贻荣), Haifeng Yu(于海峰), Heng Fan(范桁), Dong E. Liu(刘东), and Meng-Jun Hu(胡孟军)
    Chin. Phys. B, 2024, 33 (5): 050302.   DOI: 10.1088/1674-1056/ad18ab
    Abstract99)   HTML2)    PDF (2109KB)(76)      
    We introduce Quafu-Qcover, an open-source cloud-based software package developed for solving combinatorial optimization problems using quantum simulators and hardware backends. Quafu-Qcover provides a standardized and comprehensive workflow that utilizes the quantum approximate optimization algorithm (QAOA). It facilitates the automatic conversion of the original problem into a quadratic unconstrained binary optimization (QUBO) model and its corresponding Ising model, which can be subsequently transformed into a weight graph. The core of Qcover relies on a graph decomposition-based classical algorithm, which efficiently derives the optimal parameters for the shallow QAOA circuit. Quafu-Qcover incorporates a dedicated compiler capable of translating QAOA circuits into physical quantum circuits that can be executed on Quafu cloud quantum computers. Compared to a general-purpose compiler, our compiler demonstrates the ability to generate shorter circuit depths, while also exhibiting superior speed performance. Additionally, the Qcover compiler has the capability to dynamically create a library of qubits coupling substructures in real-time, utilizing the most recent calibration data from the superconducting quantum devices. This ensures that computational tasks can be assigned to connected physical qubits with the highest fidelity. The Quafu-Qcover allows us to retrieve quantum computing sampling results using a task ID at any time, enabling asynchronous processing. Moreover, it incorporates modules for results preprocessing and visualization, facilitating an intuitive display of solutions for combinatorial optimization problems. We hope that Quafu-Qcover can serve as an instructive illustration for how to explore application problems on the Quafu cloud quantum computers.
    FL-Online: An x-ray crystallographic web-server for atomic-scale structure analysis of biomolecule
    Bintang Wang(王宾堂), Tongxin Niu(牛彤欣), Haifu Fan(范海福), and Wei Ding(丁玮)
    Chin. Phys. B, 2024, 33 (7): 076104.   DOI: 10.1088/1674-1056/ad47e5
    Abstract29)      PDF (920KB)(2)      
    FL-Online (http://fanlab.ac.cn) is an out-of-box modern web service featuring a user-friendly interface and simplified parameters, providing academic users with access to a series of online programs for biomolecular crystallography, including SAPI-online, OASIS-online, C-IPCAS-online and a series of upcoming software releases. Meanwhile, it is a highly scalable and maintainable web application framework that provides a powerful and flexible solution for academic web development needs. All the codes are open-source under MIT licenses in GitHub.