在图形处理单元上高效实施蒙特卡罗算法,模拟多孔材料中的吸附。

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL
Journal of Chemical Theory and Computation Pub Date : 2024-12-10 Epub Date: 2024-11-19 DOI:10.1021/acs.jctc.4c01058
Zhao Li, Kaihang Shi, David Dubbeldam, Mark Dewing, Christopher Knight, Álvaro Vázquez-Mayagoitia, Randall Q Snurr
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引用次数: 0

摘要

我们介绍了一个开源代码 gRASPA 在蒙特卡洛模拟速度和功能方面的改进,与蒙特卡洛的串行 CPU 实现相比,该代码利用图形处理器(GPU)实现了显著的性能提升。该代码支持多种蒙特卡罗模拟,包括典型集合(NVT)、大典型、NVT Gibbs、Widom 测试粒子插入和连续-分数分量蒙特卡罗。大规范过渡矩阵蒙特卡洛(GC-TMMC)的实现以及允许金属有机框架(MOF)结构的不同组分采用不同移动方式的新功能,分别体现了 gRASPA 在精确自由能计算和增强吸附研究方面的能力。高通量计算(HTC)模式的引入允许在单个 GPU 设备上进行许多蒙特卡罗模拟,以加速材料发现。该代码可结合机器学习(ML)势能,以 Mg-MOF-74 中二氧化碳吸附的大规范蒙特卡罗模拟为例进行说明,与使用传统力场的模拟相比,该模拟与实验的一致性要好得多。gRASPA 的开源性质促进了科学的可重复性和开放性,用户可以为代码添加功能,并根据自己的目的对其进行优化。代码采用 CUDA/C++ 和 SYCL/C++ 编写,以支持不同的 GPU 供应商。gRASPA 代码可通过 https://github.com/snurr-group/gRASPA 公开获取。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Efficient Implementation of Monte Carlo Algorithms on Graphical Processing Units for Simulation of Adsorption in Porous Materials.

We present enhancements in Monte Carlo simulation speed and functionality within an open-source code, gRASPA, which uses graphical processing units (GPUs) to achieve significant performance improvements compared to serial, CPU implementations of Monte Carlo. The code supports a wide range of Monte Carlo simulations, including canonical ensemble (NVT), grand canonical, NVT Gibbs, Widom test particle insertions, and continuous-fractional component Monte Carlo. Implementation of grand canonical transition matrix Monte Carlo (GC-TMMC) and a novel feature to allow different moves for the different components of metal-organic framework (MOF) structures exemplify the capabilities of gRASPA for precise free energy calculations and enhanced adsorption studies, respectively. The introduction of a High-Throughput Computing (HTC) mode permits many Monte Carlo simulations on a single GPU device for accelerated materials discovery. The code can incorporate machine learning (ML) potentials, and this is illustrated with grand canonical Monte Carlo simulations of CO2 adsorption in Mg-MOF-74 that show much better agreement with experiment than simulations using a traditional force field. The open-source nature of gRASPA promotes reproducibility and openness in science, and users may add features to the code and optimize it for their own purposes. The code is written in CUDA/C++ and SYCL/C++ to support different GPU vendors. The gRASPA code is publicly available at https://github.com/snurr-group/gRASPA.

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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.
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