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.
If you have questions, or would like us to help you get a calculation set up for a particular kind of system, we're here for you! Please reach out to us at TopperNanoGroup _ at _ gmail.com .
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).
- R.Q. Topper, S.L. Topper, S. Lee, TransRot: A portable software package for simulated annealing Monte Carlo geometry optimization of atomic and molecular clusters, ACS Symposium Series eBook chapter (accepted for publication, 2022).
- 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
- 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
- R.Q. Topper, D.L. Freeman, D. Bergin, K. LaMarche, Computational techniques and strategies for Monte Carlo thermodynamic calculations with applications to nanoclusters, in 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.
- 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
Reference (5) was the first use of a sawtooth simulated annealing scheme; (4) describes the use of magwalking for cluster calculations; (2) and (3) first demonstrated the use of this combination of methods.