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Citing HOOMD-blue

  • Please cite the following papers in any work that uses 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
    • J. Glaser, T. D. Nguyen, J. A. Anderson, P. Liu, F. Spiga, J. A. Millan, D. C. Morse, S. C. Glotzer. Strong scaling of general-purpose molecular dynamics simulations on GPUs Computer Physics Communications 192: 97-107, July 2015. 10.1016/j.cpc.2015.02.028
  • If you utilize the HPMC component, please also cite
    • J. A. Anderson, M. E. Irrgang, and S. C. Glotzer. Scalable Metropolis Monte Carlo for simulation of hard shapes Computer Physics Communications 204: 21-30, July 2016. 10.1016/j.cpc.2016.02.024
  • If you utilize the DEM component, please also cite
    • M. Spellings, R. L. Marson, J. A. Anderson, and S. C. Glotzer. GPU accelerated Discrete Element Method (DEM) molecular dynamics for conservative, faceted particle simulations Journal of Computational Physics 334: 460-467, Apr 2017. 10.1016/j.jcp.2017.01.014
  • If you utilize the tree or stencil neighbor list, please also cite
    • M. P. Howard, J. A. Anderson, A. Nikoubashman, S. C. Glotzer, and A. Z. Panagiotopoulos. Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units Computer Physics Communications 203: 45-52, Mar 2016. 10.1016/j.cpc.2016.02.003
  • If you utilize the rigid body functionality, please 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, please 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, please 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, please 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, please 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