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MCCCS Towhee (Citation Manual)

 

 

Overview
    The ensembles, moves, and force fields that power Towhee come from a wide variety of sources. This section discusses how to use the towhee_citations output file as a starting place for acknowledging the contributions of others when writing up the results of your own research.

    This manual lists the references that are suggested in the towhee_citation file for each ensemble or Monte Carlo algorithm along with commentary on why those were chosen as the preferred references, and also sometimes includes a discussion about other papers that are relevant and also worth considering.
The Towhee Code
  • Martin 2013 suggested reference
    The history of the MCCCS Towhee project, along with a discussion of suggested simulation procedures for vapor-liquid simulation, and a review of papers that cited it prior to 2013.
  • http://towhee.sourceforge.net
Random Number Generators
    RANLUX
    • Lüscher 1994 suggested reference
      The original paper describing the algorithm used in RANLUX and also describes the luxury levels.
    • James 1994 suggested reference
      The original paper implementing the RANLUX algorithm.
    DX-1597-2-7
    • Deng 2005 suggested reference
      This paper describes many similar random number generators including the DX-1597-2-7.
    MRG32k3a
    • l'Ecuyer 1999 suggested reference
      Describes a family of random number generators including MRG32k3a.
    KISS99
    • G. Marsaglia posted this onto some internet newsgroups and there is no good journal reference.
Ensembles
    Canonical Ensemble
    • Metropolis et al. 1953 suggested reference
      This is the original Monte Carlo molecular simulation paper. While the system simulated was very primitive by modern standards (2-dimensional hard disks), they presented the general algorithm that is the basis for all subsequent Monte Carlo molecular simulations. Also the first use of the translation move (the only move required to sample the Canonical ensemble for monatomic molecules).
    Isobaric-isothermal Ensemble
    • McDonald 1972 suggested reference
      Presents the algorithm for the volume change move for continuous potentials in the pressence of a specified external pressure.
    Grand Canonical Ensemble
    • Norman 1969 suggested reference
      While this article was not known in the western literature until much later, it is the first paper describing the Grand Canonical ensemble using the Monte Carlo method for continuous potentials.
    • Rowley et al. 1975 additional reference
      Among the first publications in the western literature to present an algorithm and results for the Grand Canonical creation/removal move for continuous potentials. However, their method of keeping ficticious atoms in the system and transitioning them between real and imaginary is not the method used in Towhee for performing the insertion/deletion.
    Gibbs Ensemble (NVT or NpT)
    • Panagiotopoulos 1987 suggested reference
      The original Gibbs ensemble paper. Contains a derviation for the moves required for the NVT-Gibbs ensemble using arguments based upon the fluctuation theorm of Landau and Lifshitz. Despite the atypical starting place for deriving ensemble acceptance rules the only equation that does not agree with later work is the molecule transfer move (Eqn. 7).
    • Panagiotopoulos et al. 1988 suggested reference
      This follow-up to the original contains the derivations and acceptance rules for the NVT-Gibbs ensemble, the NpT-Gibbs ensemble, and an osmotic pressure Gibbs ensemble.
    • Smit et al. 1989 additional reference
      Contains detailed discussion about how the NVT-Gibbs ensemble free energy is the same as the Canonical ensemble free energy. Also analysis of why the Gibbs ensemble works better than many people originally expected it to, especially in its ability to predict the a critical point that does not suffer much from finite size effects.
Moves
    Isotropic Volume move (NpT)
    • McDonald 1972 suggested reference
      In either the Isobaric-isothermal or the Gibbs Isobaric-isothermal ensembles this move has not changed since the original Isobaric-isothermal paper.
    Isotropic Volume move (NVT)
    • Panagiotopoulos 1987 suggested reference
      The two-box volume exchange was first described in this paper using a maximum volume displacement. Towhee uses a maximum change based upon the logarithm of the ratio of box volumes.
    Anisotropic Volume move (NpT)
    • Yashonath and Rao 1985 suggested reference
      Perturbation of a single element of the hmatrix to change the volume in an anisotropic manner was first decribed in this paper.
    Rotational-bias molecule transfer
    • Cracknell et al. 1990 suggested reference
      The original description of the rotational-bias insertion algorithm.
    Configurational-bias molecule transfer
    • Mooij et al. 1992 suggested reference
      The original description of the configurational-bias molecule transfer algorithm. Note that while configurational-bias algorithms have advanced greatly since this paper, the general concept of the algorithm in the context of molecule transfer is essentially the same
    • Frenkel et al. 1992 additional reference
      The full paper version of the configurational-bias molecule transfer algorithm. Note that while configurational-bias algorithms have advanced greatly since this paper, the general concept of the algorithm in the context of molecule transfer is essentially the same

 

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Last updated: March 03, 2014