Robert Q. Topper

Professor of Chemistry

TransRot

TransRot is machine-portable software for carrying out simulated annealing Monte Carlo optimizations of atomic and molecular clusters, using pairwise effective potentials and employing "mag-walking" translational and rotational Monte Carlo moves together with "sawtooth" simulated annealing. The code is free and will run on any machine on which the Java Development Environment can be installed. Visit https://github.com/steventopper/Transrot to download and try it out!

The animation above shows a TransRot optimization of the octamer water cluster, (H2O)8, using the TIP3P potential. The sequence of repeated heating and cooling enhances the translational ergodicity of the calculation, and random magnification of the rotational stepsize helps the cluster move past local orientational barriers.

If you use TransRot, please cite the code as well as the following articles (and watch this space for more references).

  1. F.M. Torres, E. Agichtein, L. Grinberg, G. Yu, R.Q. Topper, A note on the application of the “Boltzmann simplex”-simulated annealing algorithm to global optimizations of argon and water clusters, Journal of Molecular Structure (THEOCHEM) 419, 85 (1997). DOI: https://doi.org/10.1016/S0166-1280(97)00195-4 
  2. R.Q. Topper, D.L. Freeman, D. Bergin, K. LaMarche, Computational techniques and strategies for Monte Carlo thermodynamic calculations with applications to nanoclusters, invited book chapter, Reviews in Computational Chemistry, Vol. 19, pp. 1-41, K.B. Lipkowitz, R. Larter and T.R. Cundari, Eds., Wiley-VCH/John Wiley and Sons, New York (2003). ISBN 0-471-23585-7. Viewable free at Google Books.
  3. R.Q. Topper, W. V. Feldmann, I. Markus, D. Bergin, P.R. Sweeney, Simulated annealing and density functional theory calculations of structural and energetic properties of the ammonium chloride clusters (NH4Cl)n, (NH4+)(NH4Cl)n and (Cl–)(NH4Cl)n, n = 1–13, Journal of Physical Chemistry A, 115 (38), pp. 10423-10432 (2011). https://pubs.acs.org/doi/10.1021/jp2069732 
  4. J.J. Biswakarma, V. Ciocoi, R.Q. Topper, Energetics, thermodynamics, and hydrogen bond diversity in ammonium halide clusters, Journal of Physical Chemistry A, 120(40), pp. 7924-7934 (2016). https://pubs.acs.org/doi/10.1021/acs.jpca.6b06788 

Reference (1) was the first use of a sawtooth simulated annealing scheme; (2) first described the use of magwalking for cluster calculations; (3) and (4) first demonstrated the use of this combination of methods.