Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition

Overview

HOOMD-blue stands for Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition. It performs general purpose particle dynamics simulations on a single workstation, taking advantage of NVIDIA GPUs to attain a level of performance equivalent to many processor cores on a fast cluster.

Object-oriented design patterns are used in HOOMD-blue so it versatile and expandable. Various types of potentials, integration methods and file formats are currently supported, and more are added with each release. The code is available and open source, so anyone can write a plugin or change the source to add additional functionality.

Simulations are configured and run using simple python scripts, allowing complete control over the force field choice, integrator, all parameters, how many time steps are run, etc... . The scripting system is designed to be as simple as possible to the non-programmer.

The HOOMD-blue development effort is led by the Glotzer group at the University of Michigan. Many groups from different universities have contributed code that is now part of the HOOMD-blue main package, see the credits page for the full list.

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Features

  • Executes particle dynamics simulations fast on NVIDIA GPUs
  • Supports Linux and Mac OS X
  • Pair Potentials - cutoff
    • CGCMM
    • DPD (dissipative particle dynamics)
    • EAM (embedded atom method)
    • Gaussian
    • Lennard-Jones
    • Morse
    • User-specified (tabulated)
    • Shifted Lennard-Jones
    • Yukawa
  • Pair Potentials - long range
    • PPPM Electrostatics
  • Bond Potentials
    • FENE
    • Harmonic
  • Angle Potentials
    • Harmonic
    • CGCMM
  • Dihedral/Improper Potentials
    • Harmonic
  • Wall Potentials
    • Lennard-Jones
  • Constraint forces
    • Constrain selected particles to the surface of a sphere
  • Integrators
    • Berendsen NVT
    • Brownian dynamics NVT, on free particles and rigid bodies
    • NPT, on free particles or rigid bodies
    • NVE, on free particles and rigid bodies
    • NVT, on free particles and rigid bodies
  • Energy minimization
    • FIRE
  • Dump file formats
    • HOOMD-blue's XML input format
    • MOL2
    • DCD
    • PDB
  • Simple and powerful python script interface for defining simulations
    • Specify any combination of potentials, integrators, etc...
    • Compute and set parameters
    • Read and write particle properties during a simulation
    • Read and write bond topology during a simulation
    • Specify initial conditions within a job script
  • Performs 2D and 3D simulations
  • Advanced built-in initial configuration generators
  • Human readable XML input files
  • Space-filling curve particle reordering to increase performance
  • Extensible object-oriented design. Additional features may be added in new classes contained in plugins.
  • Simulations can be visualized in real-time using VMD's IMD interface.
  • Pair potentials and forces may be varied smoothly to 0 at the cutoff
  • Real time analysis may be run at a non-linear rate
  • Temperature, pressure, and box size can be varied smoothly over a run
  • Flexible selection of particles for integration

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Citing HOOMD-blue

  • Include both of the following citations in any work that uses HOOMD-blue.
    • HOOMD-blue web page: http://codeblue.umich.edu/hoomd-blue
    • J. A. Anderson, C. D. Lorenz, and A. Travesset. General purpose molecular dynamics simulations fully implemented on graphics processing units Journal of Computational Physics 227(10): 5342-5359, May 2008. 10.1016/j.jcp.2008.01.047
  • If you utilize the rigid body functionality, also cite
    • T. D. Nguyen, C. L. Phillips, J. A. Anderson, and S. C. Glotzer. Rigid body constraints realized in massively-parallel molecular dynamics on graphics processing units Computer Physics Communications 182(11): 2313-2307, June 2011. 10.1016/j.cpc.2011.06.005
  • If you utilize the DPD functionality, also cite
    • C. L. Phillips, J. A. Anderson, and S. C. Glotzer. Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices Journal of Computational Physics 230(19): 7191-7201, Aug. 2011. 10.1016/j.jcp.2011.05.021
  • If you utilize the EAM functionality, also cite
    • I.V. Morozov, A.M. Kazennova, R.G. Bystryia, G.E. Normana, V.V. Pisareva, and V.V. Stegailova. Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs Computer Physics Communications 182(9): 1974-1978, 2011. 10.1016/j.cpc.2010.12.026
  • If you utilize the PPPM functionality, also cite
    • D. N. LeBard, B. G. Levine, P. Mertmann, S. A. Barr, A. Jusufi, S. Sanders, M. L. Klein, and A. Z. Panagiotopoulos. Self-assembly of coarse-grained ionic surfactants accelerated by graphics processing units Soft Matter 8: 2385-2397, 2012. 10.1039/c1sm06787g
  • If you utilize the CGCMM potential, also cite
    • B. G. Levine, D. N. LeBard, R. DeVane, W. Shinoda, A. Kohlmeyer, and M. L. Klein. Micellization studied by GPU-accelerated coarse-grained molecular dynamics Journal of Chemical Theory and Computation 7(12): 4135-4145, Oct. 2011. 10.1021/ct2005193

Download bibtex entries of these citations for import into your bibliography management software.

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Publications

Papers

2011

Rigid body constraints realized in massively-parallel molecular dynamics on graphics processing units
Trung Dac Nguyen, Carolyn L. Phillips, Joshua A. Anderson, and Sharon C. Glotzer
Computer Physics Communications, 182 (2011) p. 2307
DOI: doi:10.1016/j.cpc.2011.06.005

Pseudo-Random Number Generation for Brownian Dynamics and Dissipative Particle Dynamics Simulations on GPU Devices
Carolyn L. Phillips, Joshua A. Anderson, and Sharon C. Glotzer
Journal of Computational Physics, 230 (2011) p. 7191
DOI: doi:10.1016/j.jcp.2011.05.021

2008

Parallel Computing Experiences with CUDA
Michael Garland, et al.
IEEE Micro July/August 2008; 13-27

Molecular Dynamics on Graphic Processing Units: HOOMD to the Rescue.
Joshua A. Anderson and Alex Travesset
Computing in Science & Engineering 10(6) (2008).

General purpose molecular dynamics simulations fully implemented on graphics processing units
Joshua A. Anderson, Chris D. Lorenz, and Alex Travesset
Journal of Computational Physics 227 (2008) 5342-5359

DOI: 10.1016/j.jcp.2008.01.047
Download preprint

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Software using HOOMD-blue

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