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Classical interaction potentials for diverse materials from ab initio data: a review of potfit

Peter Brommer, Alexander Kiselev, Daniel Schopf, Philipp Beck, Johannes Roth and Hans-Rainer Trebin, Modelling Simul. Mater. Sci. Eng. 23 074002 (2015). doi:10.1088/0965-0393/23/7/074002

Force matching is an established technique to generate effective potentials for molecular dynamics simulations from first-principles data. This method has been implemented in the open source code potfit . Here, we present a review of the method and describe the main features of the code. Particular emphasis is placed on the features added since the initial release: interactions represented by analytical functions, differential evolution as optimization method, and a greatly extended set of interaction models. Beyond the initially present pair and embedded-atom method potentials, potfit can now also optimize angular dependent potentials, charge and dipolar interactions, and electron-temperature-dependent potentials. We demonstrate the functionality of these interaction models using three example systems: phonons in type I clathrates, fracture of α-alumina, and laser-irradiated silicon

Fri 18 Sep 2015, 13:42 | Tags: pbrommer

Effect of oxygen and nitrogen functionalization on the physical and electronic structure of graphene

Alexander J. Marsden, Peter Brommer, James J. Mudd, M. Adam Dyson, Robert Cook, María Asensio, Jose Avila, Ana Levy, Jeremy Sloan, David Quigley, Gavin R. Bell, and Neil R. Wilson, Nano Research (2015). doi: 10.1007/s12274-015-0768-0

Covalent functionalization of graphene offers opportunities for tailoring its properties and is an unavoidable consequence of some graphene synthesis techniques. However, the changes induced by the functionalization are not well understood. By using atomic sources to control the extent of the oxygen and nitrogen functionalization, we studied the evolution in the structure and properties at the atomic scale. Atomic oxygen reversibly introduces epoxide groups whilst, under similar conditions, atomic nitrogen irreversibly creates diverse functionalities including substitutional, pyridinic, and pyrrolic nitrogen. Atomic oxygen leaves the Fermi energy at the Dirac point (i.e., undoped), whilst atomic nitrogen results in a net n-doping; however, the experimental results are consistent with the dominant electronic effect for both being a transition from delocalized to localized states, and hence the loss of the signature electronic structure of graphene.

Mon 20 Jul 2015, 11:03 | Tags: pbrommer

Diffusion of point defects in crystalline silicon using the kinetic activation-relaxation technique method

Mickaël Trochet, Laurent Karim Béland, Jean-François Joly, Peter Brommer, and Normand Mousseau, Phys. Rev. B 91, 224106 (2015). doi:10.1103/PhysRevB.91.224106

We study point-defect diffusion in crystalline silicon using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities based on the activation-relaxation technique (ART nouveau), coupled to the standard Stillinger-Weber potential. We focus more particularly on the evolution of crystalline cells with one to four vacancies and one to four interstitials in order to provide a detailed picture of both the atomistic diffusion mechanisms and overall kinetics. We show formation energies, activation barriers for the ground state of all eight systems, and migration barriers for those systems that diffuse. Additionally, we characterize diffusion paths and special configurations such as dumbbell complex, di-interstitial (IV-pair+2I) superdiffuser, tetrahedral vacancy complex, and more. This study points to an unsuspected dynamical richness even for this apparently simple system that can only be uncovered by exhaustive and systematic approaches such as the kinetic activation-relaxation technique.

Thu 18 Jun 2015, 11:51 | Tags: pbrommer

Following atomistic kinetics on experimental timescales with the kinetic Activation–Relaxation Technique

N. Mousseau, L.K. Béland, P. Brommer, F. El-Mellouhi, J.-F. Joly, G.K. N'Tsouaglo, O. Restrepo, M. Trochet, Comp. Mater. Sci. 100 B, 111–123 (2015), doi:10.1016/j.commatsci.2014.11.047

The properties of materials, even at the atomic level, evolve on macroscopic time scales. Following this evolution through simulation has been a challenge for many years. For lattice-based activated diffusion, kinetic Monte Carlo has turned out to be an almost perfect solution. Various accelerated molecular dynamical schemes, for their part, have allowed the study on long time scale of relatively simple systems. There is still a need, however, for methods able to handle complex materials such as alloys and disordered systems. Here, we review the kinetic Activation–Relaxation Technique (k-ART), one of a handful of off-lattice kinetic Monte Carlo methods, with on-the-fly cataloging, that have been proposed in the last few years.

Mon 02 Mar 2015, 15:34 | Tags: pbrommer

P. Brommer and D. Quigley, 2014 J. Phys.: Condens. Matter 26 485501

Peter Brommer and David Quigley: Automated effective band structures for defective and mismatched supercells. J. Phys.: Condens. Matter 26 485501 (2014). doi: 10.1088/0953-8984/26/48/485501

In plane-wave density functional theory codes, defects and incommensurate structures are usually represented in supercells. However, interpretation of E versus k band structures is most effective within the primitive cell, where comparison to ideal structures and spectroscopy experiments are most natural. Popescu and Zunger recently described a method to derive effective band structures (EBS) from supercell calculations in the context of random alloys. In this paper, we present bs_sc2pc, an implementation of this method in the CASTEP code, which generates an EBS using the structural data of the supercell and the underlying primitive cell with symmetry considerations handled automatically. We demonstrate the functionality of our implementation in three test cases illustrating the efficacy of this scheme for capturing the effect of vacancies, substitutions and lattice mismatch on effective primitive cell band structures.

Thu 13 Nov 2014, 09:43 | Tags: pbrommer

P. Brommer et al. 2014 Phys. Rev. B 90 134109

Peter Brommer, Laurent Karim Béland, Jean-François Joly, and Normand Mousseau: Understanding long-time vacancy aggregation in iron: A kinetic activation-relaxation technique study. Physical Review B 90, 134109 (2014). doi:10.1103/PhysRevB.90.134109

Vacancy diffusion and clustering processes in body-centered-cubic (bcc) Fe are studied using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities. For monovacancies and divacancies, k-ART recovers previously published results while clustering in a 50-vacancy simulation box agrees with experimental estimates. Applying k-ART to the study of clustering pathways for systems containing from one to six vacancies, we find a rich set of diffusion mechanisms. In particular, we show that the path followed to reach a hexavacancy cluster influences greatly the associated mean-square displacement. Aggregation in a 50-vacancy box also shows a notable dispersion in relaxation time associated with effective barriers varying from 0.84 to 1.1 eV depending on the exact pathway selected. We isolate the effects of long-range elastic interactions between defects by comparing to simulations where those effects are deliberately suppressed. This allows us to demonstrate that in bcc Fe, suppressing long-range interactions mainly influences kinetics in the first 0.3 ms, slowing down quick energy release cascades seen more frequently in full simulations, whereas long-term behavior and final state are not significantly affected.

Tue 21 Oct 2014, 09:28 | Tags: pbrommer