HOOMD-blue: A Python']Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations

被引：364
作者：
Anderson, Joshua A. [1 ]
Glaser, Jens [1 ]
Glotzer, Sharon C. [1 ,2 ,3 ]
机构：
[1] Univ Michigan, Dept Chem Engn, Ann Arbor, MI 48109 USA
[2] Univ Michigan, Dept Mat Sci & Engn, Ann Arbor, MI 48109 USA
[3] Univ Michigan, Biointerfaces Inst, Ann Arbor, MI 48109 USA
来源：
COMPUTATIONAL MATERIALS SCIENCE | 2020年 / 173卷 / 173期
基金：
美国国家科学基金会;
关键词：
!text type='Python']Python[!/text; Molecular dynamics; Monte Carlo; Molecular simulation; GPU; CUDA; NONITERATIVE MATRIX-METHOD; PHASES;
D O I：
10.1016/j.commatsci.2019.109363
中图分类号：
T [工业技术];
学科分类号：
08 ;
摘要：
HOOMD-blue is a particle simulation engine designed for nano- and colloidal-scale molecular dynamics and hard particle Monte Carlo simulations. It has been actively developed since March 2007 and available open source since August 2008. HOOMD-blue is a Python package with a high performance C++/CUDA backend that we built from the ground up for GPU acceleration. The Python interface allows users to combine HOOMD-blue with other packages in the Python ecosystem to create simulation and analysis workflows. We employ software engineering practices to develop, test, maintain, and expand the code.
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页数：6
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共 55 条
  • [1] How to Professionally Develop Reusable Scientific Software-And When Not To
    Adorf, Carl S.
    Ramasubramani, Vyas
    Anderson, Joshua A.
    Glotzer, Sharon C.
    [J]. COMPUTING IN SCIENCE & ENGINEERING, 2019, 21 (02) : 66 - 79
  • [2] Simple data and workflow management with the signac framework
    Adorf, Carl S.
    Dodd, Paul M.
    Ramasubramani, Vyas
    Glotzer, Sharon C.
    [J]. COMPUTATIONAL MATERIALS SCIENCE, 2018, 146 : 220 - 229
  • [3] General purpose molecular dynamics simulations fully implemented on graphics processing units
    Anderson, Joshua A.
    Lorenz, Chris D.
    Travesset, A.
    [J]. JOURNAL OF COMPUTATIONAL PHYSICS, 2008, 227 (10) : 5342 - 5359
  • [4] Shape and Symmetry Determine Two-Dimensional Melting Transitions of Hard Regular Polygons
    Anderson, Joshua A.
    Antonaglia, James
    Millan, Jaime A.
    Engel, Michael
    Glotzer, Sharon C.
    [J]. PHYSICAL REVIEW X, 2017, 7 (02):
  • [5] Scalable Metropolis Monte Carlo for simulation of hard shapes
    Anderson, Joshua A.
    Irrgang, M. Eric
    Glotzer, Sharon C.
    [J]. COMPUTER PHYSICS COMMUNICATIONS, 2016, 204 : 21 - 30
  • [6] [Anonymous], [No title captured]
  • [7] [Anonymous], [No title captured]
  • [8] [Anonymous], [No title captured]
  • [9] [Anonymous], [No title captured]
  • [10] [Anonymous], 2019, Clang: A C Language Family Frontend for LLVM
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