Efficient Tensorized Evaluation of Permutation Invariant Polynomials for Representing Potential Energy Surfaces

IF 5.8 1区 化学 Q2 CHEMISTRY, PHYSICAL
Journal of Chemical Theory and Computation Pub Date : 2026-10-13 Epub Date: 2026-09-30 DOI:10.1021/acs.jctc.6c01659
Junhong Li, Kaisheng Song, Hua Guo, Jun Li
{"title":"Efficient Tensorized Evaluation of Permutation Invariant Polynomials for Representing Potential Energy Surfaces","authors":"Junhong Li,&nbsp;Kaisheng Song,&nbsp;Hua Guo,&nbsp;Jun Li","doi":"10.1021/acs.jctc.6c01659","DOIUrl":null,"url":null,"abstract":"<p>Permutation invariant polynomials (PIPs), together with\r\nrelated\r\npolynomial-based invariant descriptors such as fundamental invariants\r\n(FIs), are widely used in constructing high-fidelity global potential\r\nenergy surfaces (PESs) of molecules that contain identical atoms.\r\nAlthough the monomial symmetrization approach (MSA) enables fast evaluation\r\nof PIPs through recursive factorization, it leads to deeply nested\r\ncomputational graphs that may require large memory and are inefficient\r\nin modern automatic differentiation frameworks. In this work, we introduce\r\nJaxPIP, a JAX-based implementation that reformulates PIP/FI evaluation\r\ninto tensorized linear algebra operations. By replacing recursive\r\nfactorization with dense matrix operations combined with log-exp transformation\r\nand segmented summation, the evaluation becomes regular and GPU-friendly.\r\nThis allows efficient execution with just-in-time compilation and\r\nenables large-scale batch evaluation of energies and forces (as well\r\nas higher-order derivatives). The resulting architecture supports\r\nensemble simulations such as quasi-classical trajectory (QCT), path-integral\r\nmolecular dynamics (PIMD), and diffusion Monte Carlo (DMC) in a fully\r\nvectorized manner. As demonstrated in examples, JaxPIP provides a\r\npractical route for efficient simulations of molecular systems with\r\nscalable GPU execution.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"22 19","pages":"9940–9953"},"PeriodicalIF":5.8000,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Theory and Computation","FirstCategoryId":"92","ListUrlMain":"https://pubs.acs.org/doi/10.1021/acs.jctc.6c01659","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2026/9/30 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0

Abstract

Permutation invariant polynomials (PIPs), together with related polynomial-based invariant descriptors such as fundamental invariants (FIs), are widely used in constructing high-fidelity global potential energy surfaces (PESs) of molecules that contain identical atoms. Although the monomial symmetrization approach (MSA) enables fast evaluation of PIPs through recursive factorization, it leads to deeply nested computational graphs that may require large memory and are inefficient in modern automatic differentiation frameworks. In this work, we introduce JaxPIP, a JAX-based implementation that reformulates PIP/FI evaluation into tensorized linear algebra operations. By replacing recursive factorization with dense matrix operations combined with log-exp transformation and segmented summation, the evaluation becomes regular and GPU-friendly. This allows efficient execution with just-in-time compilation and enables large-scale batch evaluation of energies and forces (as well as higher-order derivatives). The resulting architecture supports ensemble simulations such as quasi-classical trajectory (QCT), path-integral molecular dynamics (PIMD), and diffusion Monte Carlo (DMC) in a fully vectorized manner. As demonstrated in examples, JaxPIP provides a practical route for efficient simulations of molecular systems with scalable GPU execution.

表示势能面的置换不变量多项式的有效张紧化
摘要置换不变量多项式(PIPs)与相关的基于多项式的不变量描述符如基本不变量(fi)一起被广泛用于构建含有相同原子的分子的高保真全局势能面(PESs)。尽管单项对称方法(MSA)能够通过递归分解快速评估pip,但它会导致深度嵌套的计算图,这可能需要大量内存,并且在现代自动微分框架中效率低下。在这项工作中,我们介绍了JaxPIP,这是一种基于jax的实现,它将PIP/FI评估重新表述为张紧化的线性代数操作。用密集矩阵运算代替递归分解,结合对数-exp变换和分段求和,使求值变得规则且对gpu友好。这允许有效地执行即时编译,并允许大规模批量评估能量和力(以及高阶导数)。所得到的体系结构以完全矢量化的方式支持集成模拟,如准经典轨迹(QCT)、路径积分分子动力学(PIMD)和扩散蒙特卡罗(DMC)。如示例所示,JaxPIP为具有可伸缩GPU执行的分子系统的有效模拟提供了实用途径。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信
小红书