Efficient sampling of atomic configurational spaces.
By Lívia B. Pártay, A. P. Bart'ok, Gábor Csányi. 2009
101 citations recorded by the source corpus.
We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling (AIP Conf. Proc. 2004, 395; J. Bayesian Anal. 2006, 1, 833) and allows us to explore the entire potential energy surface (PES) efficiently in an unbiased way. The algorithm has two parameters which directly control the trade-off between the resolution with which the space is explored and the computational cost. We demonstrate the use of nested sampling on Lennard-Jones (LJ) clusters. Nested sampling provides a straightforward approximation for the partition function; thus, evaluating expectation values of arbitrary smooth operators at arbitrary temperatures becomes a simple postprocessing step. Access to absolute free energies allows us to determine the temperature-density phase diagram for LJ cluster stability. Even for relatively small clusters, the efficiency gain over parallel tempering in calculating the heat capacity is an order of magnitude or more. Furthermore, by analyzing the topology of the resulting samples, we are able to visualize the PES in a new and illuminating way. We identify a discretely valued order parameter with basins and suprabasins of the PES, allowing a straightforward and unambiguous definition of macroscopic states of an atomistic system and the evaluation of the associated free energies.
Subfields: Biomedical Engineering, Materials Chemistry, Molecular Biology
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Citations in the corpus
- On the inner workings of Monte Carlo codes (2013, methodology): “[256–259] DOS methods use a finite range of energies in practice, which means that the partition function can only be computed to within a multiplicative constant.”