arXiv subjects

Gábor Csányi

Publications and source records attributed to Gábor Csányi.

99 records · Page 6Linked to original sources

arXiv2014

Nested sampling for materials: the case of hard spheres

The recently introduced nested sampling algorithm allows the direct and efficient calculation of the partition function of atomistic systems. We demonstrate its applicability to condensed phase systems with periodic boundary conditions by studying the three dimensional hard sphere model. Having obtained the partition function, we show how easy it is to calculate the compressibility and the free energy as functions of the packing fraction and local order, verifying that the transition to crystallinity has a very small barrier, and that the entropic contribution of jammed states to the free energy is negligible for packing fractions above the phase transition. We quantify the previously proposed schematic phase diagram and estimate the extent of the region of jammed states. We find that within our samples, the maximally random jammed configuration is surprisingly disordered.

cond-mat.stat-mech↗

arXiv2013

On representing chemical environments

We review some recently published methods to represent atomic neighbourhood environments, and analyse their relative merits in terms of their faithfulness and suitability for fitting potential energy surfaces. The crucial properties that such representations (sometimes called descriptors) must have are differentiability with respect to moving the atoms, and invariance to the basic symmetries of physics: rotation, reflection, translation, and permutation of atoms of the same species. We demonstrate that certain widely used descriptors that initially look quite different are specific cases of a general approach, in which a finite set of basis functions with increasing angular wave numbers are used to expand the atomic neighbourhood density function. Using the example system of small clusters, we quantitatively show that this expansion needs to be carried to higher and higher wave numbers as the number of neighbours increases in order to obtain a faithful representation, and that variants of the descriptors converge at very different rates. We also propose an altogether new approach, called Smooth Overlap of Atomic Positions (SOAP), that sidesteps these difficulties by directly defining the similarity between any two neighbourhood environments, and show that it is still closely connected to the invariant descriptors. We test the performance of the various representations by fitting models to the potential energy surface of small silicon clusters and the bulk crystal.

physics.comp-ph↗

arXiv2010

Diffusive Nested Sampling

We introduce a general Monte Carlo method based on Nested Sampling (NS), for sampling complex probability distributions and estimating the normalising constant. The method uses one or more particles, which explore a mixture of nested probability distributions, each successive distribution occupying ~e^-1 times the enclosed prior mass of the previous distribution. While NS technically requires independent generation of particles, Markov Chain Monte Carlo (MCMC) exploration fits naturally into this technique. We illustrate the new method on a test problem and find that it can achieve four times the accuracy of classic MCMC-based Nested Sampling, for the same computational effort; equivalent to a factor of 16 speedup. An additional benefit is that more samples and a more accurate evidence value can be obtained simply by continuing the run for longer, as in standard MCMC.

stat.CO↗

arXiv2010

Efficient sampling of atomic configurational spaces

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 [Skilling J. (2004) In AIP Conference Proceedings, vol. 735, p. 395.; Skilling J. (2006) J of Bayesian Analysis 1:833-860.] 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 post-processing 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 more than an order of magnitude. Furthermore, by analysing the topology of the resulting samples we are able to visualise the PES in a new and illuminating way. We identify a discretely valued order parameter with basins and supra-basins of the PES allowing a straightforward and unambiguous definition of macroscopic states of an atomistic system and the evaluation of the associated free energies.

cond-mat.stat-mech↗

arXiv2009

Gaussian Approximation Potentials: the accuracy of quantum mechanics, without the electrons

We introduce a class of interatomic potential models that can be automatically generated from data consisting of the energies and forces experienced by atoms, derived from quantum mechanical calculations. The resulting model does not have a fixed functional form and hence is capable of modeling complex potential energy landscapes. It is systematically improvable with more data. We apply the method to bulk carbon, silicon and germanium and test it by calculating properties of the crystals at high temperatures. Using the interatomic potential to generate the long molecular dynamics trajectories required for such calculations saves orders of magnitude in computational cost.

physics.comp-ph↗

arXiv2004

Chemically active substitutional nitrogen impurity in carbon nanotubes

We investigate the nitrogen substitutional impurity in semiconducting zigzag and metallic armchair single-wall carbon nanotubes using ab initio density functional theory. At low concentrations (less than 1 atomic %), the defect state in a semiconducting tube becomes spatially localized and develops a flat energy level in the band gap. Such a localized state makes the impurity site chemically and electronically active. We find that if two neighboring tubes have their impurities facing one another, an intertube covalent bond forms. This finding opens an intriguing possibility for tunnel junctions, as well as the functionalization of suitably doped carbon nanotubes by selectively forming chemical bonds with ligands at the impurity site. If the intertube bond density is high enough, a highly packed bundle of interlinked single-wall nanotubes can form.

cond-mat.mtrl-sci↗

arXiv2004

Polynomial epidemics and clustering in contact networks

It is widely known that the spread of the HIV virus was slower than exponential in several populations, even at the very beginning of the epidemic. We show that this implies a significant reduction in the effective reproductive rate of the epidemic, and describe a general mechanism, related to the clustering properties of the disease transmission network, capable of explaining this reduction. Our considerations provide a new angle on polynomial epidemic processes, and may have implications for the choice of strategy against such epidemics.

q-bio.PE↗

arXiv2004

The fractal/small-world dichotomy in real-world networks

We draw attention to a clear dichotomy between small-world networks exhibiting exponential neighborhood growth, and fractal-like networks where neighborhoods grow according to a power law. This distinction is observed in a number of real-world networks, and is related to the degree correlations and geographical constraints. We conclude by pointing out that the status of human social networks in this dichotomy is far from clear.

cond-mat.stat-mech↗

arXiv2001

Improved tensor-product expansions for the two-particle density matrix

We present a new density-matrix functional within the recently introduced framework for tensor-product expansions of the two-particle density matrix. It performs well both for the homogeneous electron gas as well as atoms. For the homogeneous electron gas, it performs significantly better than all previous density-matrix functionals, becoming very accurate for high densities and outperforming Hartree-Fock at metallic valence electron densities. For isolated atoms and ions, it is on a par with previous density-matrix functionals and generalized gradient approximations to density-functional theory. We also present analytic results for the correlation energy in the low density limit of the free electron gas for a broad class of such functionals.

cond-mat.mtrl-sci↗