Tersoff-style three-body potential for PtC developed by Albe, Nordlund, and Averback (2002) v004

Tobias Brink; Karsten Albe; Kai Nordlund; Robert S. Averback

doi:10.25950/78d69967

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Tersoff_LAMMPS_AlbeNordlundAverback_2002_PtC__MO_500121566391_004

Interatomic potential for Carbon (C), Platinum (Pt).
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Title A single sentence description.	Tersoff-style three-body potential for PtC developed by Albe, Nordlund, and Averback (2002) v004
Description A short description of the Model describing its key features including for example: type of model (pair potential, 3-body potential, EAM, etc.), modeled species (Ac, Ag, ..., Zr), intended purpose, origin, and so on.	Tersoff-style potential for PtC by Albe, Nordlund, and Averback. The C-C interaction is potential II from Brenner, Phys. Rev. B 42, 9458 (1990) without the overbinding correction.
Species The supported atomic species.	C, Pt
Disclaimer A statement of applicability provided by the contributor, informing users of the intended use of this KIM Item.	None

Contributor	Tobias Brink
Maintainer	Tobias Brink
Implementer	Tobias Brink
Developer	Karsten Albe Kai Nordlund Robert S. Averback
Published on KIM	2021
How to Cite	This Model originally published in [1-3] is archived in OpenKIM [4-7]. [1] Albe K, Nordlund K, Averback RS. Modeling the metal-semiconductor interaction: Analytical bond-order potential for platinum-carbon. Physical Review B. 2002May;65(19):195124. doi:10.1103/PhysRevB.65.195124 — (Primary Source) A primary source is a reference directly related to the item documenting its development, as opposed to other sources that are provided as background information. [2] Brenner DW. Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films. Physical Review B. 1990Nov;42(15):9458–71. doi:10.1103/PhysRevB.42.9458 [3] Brenner DW. Erratum: Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films. Physical Review B. 1992Jul;46(3):1948–. doi:10.1103/PhysRevB.46.1948.2 [4] Brink T, Albe K, Nordlund K, Averback RS. Tersoff-style three-body potential for PtC developed by Albe, Nordlund, and Averback (2002) v004. OpenKIM; 2021. doi:10.25950/78d69967 [5] Brink T, Thompson AP, Farrell DE, Wen M, Tersoff J, Nord J, et al. Model driver for Tersoff-style potentials ported from LAMMPS v005. OpenKIM; 2021. doi:10.25950/9a7dc96c [6] Tadmor EB, Elliott RS, Sethna JP, Miller RE, Becker CA. The potential of atomistic simulations and the Knowledgebase of Interatomic Models. JOM. 2011;63(7):17. doi:10.1007/s11837-011-0102-6 [7] Elliott RS, Tadmor EB. Knowledgebase of Interatomic Models (KIM) Application Programming Interface (API). OpenKIM; 2011. doi:10.25950/ff8f563a Click here to download the above citation in BibTeX format.
Citations This panel presents information regarding the papers that have cited the interatomic potential (IP) whose page you are on. The OpenKIM machine learning based Deep Citation framework is used to determine whether the citing article actually used the IP in computations (denoted by "USED") or only provides it as a background citation (denoted by "NOT USED"). For more details on Deep Citation and how to work with this panel, click the documentation link at the top of the panel. The word cloud to the right is generated from the abstracts of IP principle source(s) (given below in "How to Cite") and the citing articles that were determined to have used the IP in order to provide users with a quick sense of the types of physical phenomena to which this IP is applied. The bar chart shows the number of articles that cited the IP per year. Each bar is divided into green (articles that USED the IP) and blue (articles that did NOT USE the IP). Users are encouraged to correct Deep Citation errors in determination by clicking the speech icon next to a citing article and providing updated information. This will be integrated into the next Deep Citation learning cycle, which occurs on a regular basis. OpenKIM acknowledges the support of the Allen Institute for AI through the Semantic Scholar project for providing citation information and full text of articles when available, which are used to train the Deep Citation ML algorithm.	This panel provides information on past usage of this interatomic potential (IP) powered by the OpenKIM Deep Citation framework. The word cloud indicates typical applications of the potential. The bar chart shows citations per year of this IP (bars are divided into articles that used the IP (green) and those that did not (blue)). The complete list of articles that cited this IP is provided below along with the Deep Citation determination on usage. See the Deep Citation documentation for more information. 119 Citations (29 used) Show Model Used Show All Help us to determine which of the papers that cite this potential actually used it to perform calculations. If you know, click the . X. Ge et al., “Distinguishing contributions of ceramic matrix and binder metal to the plasticity of nanocrystalline cermets,” IUCrJ. 2020. link Times cited: 4 Abstract: Contributions to plasticity from hard matrix and binder meta… read more Abstract: Contributions to plasticity from hard matrix and binder metal in nanocrystalline cermets were studied by molecular dynamics simulations. read less Y. Zhang et al., “Molecular‐Scale Modeling and Multiscale Experiments on the Elastic Properties of HR‐2 Steel Affected by Hydrogen,” steel research international. 2019. link Times cited: 0 Abstract: Austenitic stainless steel is used in hydrogen containers. T… read more Abstract: Austenitic stainless steel is used in hydrogen containers. The hydrogen embrittlement has drawn much attention. In this paper, in situ measurement by neutron stress spectrometer and neutron scattering is carried out during quasi‐static tensile tests. Based on the information at the micro‐ and macro‐scale obtained through these measurements, a molecular‐scale simulation system with different numbers of grain boundaries is established. With the Tersoff potential parameters fitted by Kuopanportti, the change rates of the elastic modulus and yield limit of the steel with different concentrations of hydrogen can be calculated. read less T. Lühmann et al., “Screening and engineering of colour centres in diamond,” Journal of Physics D: Applied Physics. 2018. link Times cited: 61 Abstract: We present a high throughput and systematic method for the s… read more Abstract: We present a high throughput and systematic method for the screening of colour centres in diamond with the aim of searching for and reproducibly creating new optical centres down to the single defect level, potentially of interest for a wide range of diamond-based quantum applications. The screening method presented here should, moreover, help to identify some already indexed defects among hundreds in diamond (Zaitsev 2001 Optical Properties of Diamond (Berlin: Springer)) but also some promising defects of a still unknown nature, such as the recently discovered ST1 centre (Lee et al 2013 Nat. Nanotechnol. 8 487; John et al 2017 New J. Phys. 19 053008). We use ion implantation in a systematic manner to implant several chemical elements. Ion implantation has the advantage of addressing single atoms inside the bulk with defined depth and high lateral resolution, but the disadvantage of producing intrinsic defects. The implanted samples are annealed in vacuum at different temperatures (between 600 °C and 1600 °C with 200 °C steps) and fully characterised at each step in order to follow the evolution of the defects: formation, dissociation, diffusion, re-formation and charge state, at the ensemble level and, if possible, at the single centre level. We review the unavoidable ion implantation defects (such as the GR1 and 3H centres), discuss ion channeling and thermal annealing and estimate the diffusion of the vacancies, nitrogen and hydrogen. We use different characterisation methods best suited for our study (from widefield fluorescence down to sub-diffraction optical imaging of single centres) and discuss reproducibility issues due to diamond and defect inhomogeneities. Nitrogen is also implanted for reference, taking advantage of the considerable knowledge on NV centres as a versatile sensor in order to retrieve or deduce the conditions and local environment in which the different implanted chemical elements are embedded. We show here the preliminary promising results of a long-term study and focus on the elements O, Mg, Ca, F and P from which fluorescent centres were found. read less C. Herbig, E. Åhlgren, and T. Michely, “Blister-free ion beam patterning of supported graphene,” Nanotechnology. 2017. link Times cited: 4 Abstract: Ion irradiation of metal supported two-dimensional layers re… read more Abstract: Ion irradiation of metal supported two-dimensional layers results over a broad parameter space in noble gas trapping at the interface of the two-dimensional layer and the metal substrate. Trapping may give rise to the formation of gas filled blisters which deteriorate the structural and electronic properties of graphene. Here, we investigate the dependence of noble gas trapping at a graphene/Ir(111) interface and of graphene sputtering on the angle of incidence using scanning tunneling microscopy. Our experimental results are compared to dedicated molecular dynamics simulations. We find that at large impact angles of ≈ 80 ° graphene can be eroded without noble gas trapping and thereby establish conditions for nanopatterning without concomitant blister formation. read less E. Safi, J. Polvi, A. Lasa, and K. Nordlund, “Atomistic simulations of deuterium irradiation on iron-based alloys in future fusion reactors,” Nuclear materials and energy. 2016. link Times cited: 2 C. Herbig et al., “Xe irradiation of graphene on Ir(111): From trapping to blistering,” Physical Review B. 2015. link Times cited: 21 Abstract: Using x-ray photoelectron spectroscopy, thermal desorption s… read more Abstract: Using x-ray photoelectron spectroscopy, thermal desorption spectroscopy, and scanning tunneling microscopy, we show that upon keV Xe+ irradiation of graphene on Ir(111), Xe atoms are trapped under the graphene. Upon annealing, aggregation of Xe leads to graphene bulges and blisters. The efficient trapping is an unexpected and remarkable phenomenon given the absence of chemical binding of Xe to Ir and to graphene, the weak interaction of a perfect graphene layer with Ir(111), as well as the substantial damage to graphene due to irradiation. By combining molecular dynamics simulations and density functional theory calculations with our experiments, we uncover the mechanism of trapping. We describe ways to avoid blister formation during graphene growth, and also demonstrate how ion implantation can be used to intentionally create blisters without introducing damage to the graphene layer. Our approach may provide a pathway to synthesize new materials at a substrate-2D material interface or to enable confined reactions at high pressures and temperatures. (Less) read less S. Standop et al., “Ion impacts on graphene/Ir(111): interface channeling, vacancy funnels, and a nanomesh.,” Nano letters. 2013. link Times cited: 75 Abstract: By combining ion beam experiments and atomistic simulations … read more Abstract: By combining ion beam experiments and atomistic simulations we study the production of defects in graphene on Ir(111) under grazing incidence of low energy Xe ions. We demonstrate that the ions are channeled in between graphene and the substrate, giving rise to chains of vacancy clusters with their edges bending down toward the substrate. These clusters self-organize to a graphene nanomesh via thermally activated diffusion as their formation energy varies within the graphene moiré supercell. read less M. Moldovan et al., “On the Evolution of Pt Nanoparticles on Few-Layer Graphene Supports in the High-Temperature Range,” Journal of Physical Chemistry C. 2012. link Times cited: 45 Abstract: Controlling the size, dispersion, and shape of nanoparticles… read more Abstract: Controlling the size, dispersion, and shape of nanoparticles (NPs) in the high-temperature range is a key topic for the development of new technologies with applications in the particular fields of catalysis and energy storage. In this article, we present an approach combining in situ transmission electron microscopy (TEM), electron tomography (ET), and molecular dynamics (MD) calculations for assessing the evolution of Pt NPs deposited onto few-layer graphene supports. Spherical Pt NPs with average sizes of 2 nm located preferentially at the support topographical defects (e.g., steps and edges) diffuse and coalesce along these defects, such that, after annealing to 700 °C, the nanoparticles were located exclusively here. Their dispersion remained significant; only the particle size distribution changed from mono- to bimodal. This statistical variation is discussed herein by reviewing fundamental issues such as the NP–support interaction and NP faceting, diffusion, and subsequent sintering in the high-tem... read less I. Fampiou and A. Ramasubramaniam, “Binding of Pt Nanoclusters to Point Defects in Graphene: Adsorption, Morphology, and Electronic Structure,” Journal of Physical Chemistry C. 2012. link Times cited: 214 Abstract: Graphene nanosheets serve as excellent support materials in … read more Abstract: Graphene nanosheets serve as excellent support materials in the synthesis of advanced metal nanoparticle–graphene electrocatalysts. In this study, we employ a combination of density functional theory and bond-order potential calculations to perform a systematic investigation of the adsorption energetics, structural features, and electronic structure of platinum nanoclusters supported on both defective and defect-free graphene. We establish a hierarchy of point defects and their reconstructions that can act as strong trapping sites for platinum nanoclusters and inhibit catalyst sintering. We demonstrate that the preferred low-energy structure of supported platinum nanoclusters are neither high-symmetry structures (e.g., icosahedral, cuboctahedral) nor readily derived from moderate structural distortions of high-symmetry structures, as is often assumed in computational models. Rather, supported nanoparticles assume open, low-symmetry shapes much like those observed in earlier computational work on annealing... read less H. Ramézani, I. Ellien, Z. E. Oufir, N. Mathieu, S. Delpeux, and S. Bhatia, “Clustering of caffeine in water and its adsorption in activated carbon: Molecular simulations and experiments,” Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2023. link Times cited: 0 N. Gui, Q. Wang, X. Zhang, X. Yang, J. Tu, and S. Jiang, “Diffusion and Thermo-Driven Migration of Silver, Palladium and Ruthenium Nanoparticles in Cubic Sic Matrix Using Molecular Dynamics,” SSRN Electronic Journal. 2022. link Times cited: 1 Z. E. Oufir, H. Ramézani, N. Mathieu, S. Delpeux, and S. Bhatia, “Influence of force field used in carbon nanostructure reconstruction on simulated phenol adsorption isotherms in aqueous medium,” Journal of Molecular Liquids. 2021. link Times cited: 2 S. So, J.-Y. Kim, D. Kim, and J.-H. Lee, “Recovery of thermal transport in atomic-layer-deposition-healed defective graphene,” Carbon. 2021. link Times cited: 2 N. Chen, D. Huang, E. Heller, D. Cardimona, and F. Gao, “Atomistic simulation of displacement damage and effective nonionizing energy loss in InAs,” Physical Review Materials. 2021. link Times cited: 6 Abstract: A molecular dynamics (MD) method, along with the analytical … read more Abstract: A molecular dynamics (MD) method, along with the analytical bond-order potential, is applied to study defect production in InAs. This potential is modified to obtain a better description for point-defect properties and is extended for proper applications in radiation damage simulation. By using this modified potential, the threshold displacement energy $({E}_{d})$, as one of the crucial parameters in radiation damage studies, is calculated over thousands of crystallographic directions for incorporating spatial anisotropy. However, the ${E}_{d}$ dependence on directions is found to be relatively weak. The defect production, clustering, and evolution in InAs are further investigated for the energies of the primary knock-on atom (PKA) ranging from 500 eV to 40 keV. A nonlinear defect production is seen with increasing PKA energy. This nonlinearity, which is associated with the direct-impact amorphization, is very distinctive for PKA energies ranging from 1 to 20 keV. Based on the damage density evaluated from molecular dynamics simulations, a theoretical model is developed for determining nonionizing energy loss (NIEL), which can be used for quantifying the electronic device degradation in a space radiation environment. The NIELs of InAs for proton, alpha, and Xe particles are calculated from the displacement threshold up to 60 MeV in comparison with available data so as to validate our model in the current study. read less M. Eghbalian, R. Ansari, and S. Rouhi, “Mechanical properties of oxygen-functionalized silicon carbide nanotubes: A molecular dynamics study,” Physica B-condensed Matter. 2021. link Times cited: 11 X. Zhu and X. Cheng, “Molecular dynamics study of tilt grain boundary evolution during the growth of beryllium thin films,” Journal of Crystal Growth. 2020. link Times cited: 0 I. Matrane, M. Mazroui, R. Ferrando, M. Badawi, and S. Lebègue, “Adsorption and diffusion of Pt, Cu, Ag and Au on missing row reconstructed Pt(110) surfaces: An ab initio investigation,” Surface Science. 2019. link Times cited: 2 J. Byggmästar, M. J. Nagel, K. Albe, K. Henriksson, and K. Nordlund, “Analytical interatomic bond-order potential for simulations of oxygen defects in iron,” Journal of Physics: Condensed Matter. 2019. link Times cited: 11 Abstract: We present an analytical bond-order potential for the Fe–O s… read more Abstract: We present an analytical bond-order potential for the Fe–O system, capable of reproducing the basic properties of wüstite as well as the energetics of oxygen impurities in -iron. The potential predicts binding energies of various small oxygen-vacancy clusters in -iron in good agreement with density functional theory results, and is therefore suitable for simulations of oxygen-based defects in iron. We apply the potential in simulations of the stability and structure of Fe/FeO interfaces and FeO precipitates in iron, and observe that the shape of FeO precipitates can change due to formation of well-defined Fe/FeO interfaces. The interface with crystalline Fe also ensures that the precipitates never become fully amorphous, no matter how small they are. read less E. Hodille, J. Byggmästar, E. Safi, and K. Nordlund, “Molecular dynamics simulation of beryllium oxide irradiated by deuterium ions: sputtering and reflection,” Journal of Physics: Condensed Matter. 2019. link Times cited: 10 Abstract: The sputtering and reflection properties of wurtzite berylli… read more Abstract: The sputtering and reflection properties of wurtzite beryllium oxide (BeO) subjected to deuterium (D) ions bombardment at 300 K with ion energy between 10 eV and 200 eV is studied by classical molecular dynamics. Cumulative irradiations of wurtzite BeO show a D concentration threshold above which an ‘unphysical dramatic’ sputtering is observed. From the cumulative irradiations, simulation cells with different D concentrations are used to run non-cumulative irradiations at different concentrations. Using a D concentration close to the experimentally determined saturation concentration (0.12 atomic fraction), the simulations are able to reproduce accurately the experimental sputtering yield of BeO materials. The processes driving the sputtering of beryllium (Be) and oxygen (O) atoms as molecules are subsequently determined. At low irradiation energy, between 10 eV and 80 eV, swift chemical sputtering (SCS) is dominant and produces mostly ODz molecules. At high energy, the sputtered molecules are mostly BexOy molecules (mainly BeO dimer). Four different processes are associated to the formation of such molecules: the physical sputtering of BeO dimer, the delayed SCS not involving D ions and the detachment-induced sputtering. The physical sputtering of BeO dimer can be delayed if the sputtering event implies two interactions with the incoming ion (first interaction in its way in the material, the other in its way out if it is backscattered). The detachment-induced sputtering is a characteristic feature of the ‘dramatic’ sputtering and is mainly observed when the concentration of D is close to the threshold leading to this sputtering regime. read less M. Mock and K. Albe, “Modelling of dislocation-solute interaction in ODS steels: Analytic bond-order potential for the iron-yttrium system,” Journal of Nuclear Materials. 2018. link Times cited: 6 Q. Feng, X. Song, H. Xie, H. Wang, X. Liu, and F. Yin, “Deformation and plastic coordination in WC-Co composite — Molecular dynamics simulation of nanoindentation,” Materials & Design. 2017. link Times cited: 53 Y. Cai, Y.-L. Chen, Y. Shimizu, S. Ito, W. Gao, and L. Zhang, “Molecular dynamics simulation of subnanometric tool-workpiece contact on a force sensor-integrated fast tool servo for ultra-precision microcutting,” Applied Surface Science. 2016. link Times cited: 12 E. Elkoraychy, K. Sbiaai, M. Mazroui, Y. Boughaleb, and R. Ferrando, “Numerical study of hetero-adsorption and diffusion on (100) and (110) surfaces of Cu, Ag and Au,” Surface Science. 2015. link Times cited: 34 M. Petisme, M. Gren, and G. Wahnström, “Molecular dynamics simulation of WC/WC grain boundary sliding resistance in WC–Co cemented carbides at high temperature,” International Journal of Refractory Metals & Hard Materials. 2015. link Times cited: 29 P. He, D. Xu, T. Lin, and Z. Jiao, “Joint properties between carbon nanotube and gold at different energy levels from molecular dynamics,” Computational Materials Science. 2013. link Times cited: 8 M. Müller, P. Erhart, and K. Albe, “Thermodynamics of L 1 0 ordering in FePt nanoparticles studied by Monte Carlo simulations based on an analytic bond-order potential,” Physical Review B. 2007. link Times cited: 64 Abstract: The size dependence of the order-disorder transition in FePt… read more Abstract: The size dependence of the order-disorder transition in FePt nanoparticles with an $L{1}_{0}$ structure is investigated by means of Monte Carlo simulations based on an analytic bond-order potential for FePt. A cross parametrization for the Fe-Pt interaction is proposed, which complements existing potentials for the constituents Fe and Pt. This FePt potential properly describes structural properties of ordered and disordered phases, surface energies, and the $L{1}_{0}$ to $A1$ transition temperature in bulk FePt. The potential is applied for examining the ordering behavior in small particles. The observed lowering of the order-disorder transition temperature with decreasing particle size confirms previous lattice-based Monte Carlo simulations [M. M\"uller and K. Albe, Phys. Rev. B 72, 094203 (2005)]. Although a distinctly higher amount of surface induced disorder is found in comparison to previous studies based on lattice-type Hamiltonians, the presence of lattice strain caused by the tetragonal distortion of the $L{1}_{0}$ structure does not have a significant influence on the depression of the ordering temperature with decreasing particle size. read less S. Nagao, K. Nordlund, and R. Nowak, “Anisotropic elasticity of IVB transition-metal mononitrides determined by ab initio calculations,” Physical Review B. 2006. link Times cited: 43 Abstract: Elastic parameters of IVB transition-metal mononitrides, TiN… read more Abstract: Elastic parameters of IVB transition-metal mononitrides, TiN, ZrN, and HfN in the cubic NaCl crystal structure have been calculated by means of density-functional theory with the generalized gradient approximation. The elastic constants c{sub 11}, c{sub 12}, and c{sub 44} were shown to be sufficiently converged with the density of the k-point mesh in the deformed Brillouin zone to discuss the elastic anisotropy of the systems. It was found that the anisotropy coefficient {kappa}{identical_to}(c{sub 11}-c{sub 12})/2c{sub 44} increases with the atomic number of the metal element, i.e., HfN exhibits as strong anisotropy as {kappa}=2.02. The Young's modulus of HfN along is approximately two times higher than that along . Moreover, analysis of the deformation energy by the applied strain modes shows that this elastic anisotropy originates from the strong covalent bonding between metal and nitrogen atoms along . read less K. Albe and M. Müller, “Cluster Diffusion and Island Formation on fcc(111) Metal Surfaces Studied by Atomic Scale Computer Simulations.” 2005. link Times cited: 1 K. Nordlund, J. Nord, A. Krasheninnikov, and K. Albe, “Atomic-scale simulations of radiation effects in GaN and carbon nanotubes,” MRS Proceedings. 2003. link Times cited: 0 Abstract: Gallium nitride and carbon nanotubes have received wide inte… read more Abstract: Gallium nitride and carbon nanotubes have received wide interest in the materials research community since the mid-1990's. The former material is already in use in optoelectronics applications, while the latter is considered to be extremely promising in a wide range of materials. Common to both materials is that ion irradiation may be useful for modifying their properties. In this paper we overview our recent molecular dynamics simulations results on ion irradiation of these materials. We employ such potentials to study the basic physics of how ion irradiation affects these materials. In particular we discuss the reasons for the high radiation hardness of GaN, and the surprising nature of vacancies and interstitials in carbon nanotubes read less J. Kim and A. Caron, “Friction and Degradation of Graphite: A Nanotribological Approach,” Tribology Letters. 2023. link Times cited: 0 R. Villarreal et al., “Bond Defects in Graphene Created by Ultralow Energy Ion Implantation,” SSRN Electronic Journal. 2022. link Times cited: 2 Abstract: Ultralow energy (ULE) ion implantation is increasingly being… read more Abstract: Ultralow energy (ULE) ion implantation is increasingly being applied to the modification of 2D materials, in particular, for substitutional doping and intercalation of graphene [1][2] . Implantation-induced defects, whether desired or not, have a strong impact on the properties of graphene [3] . While significant research has been devoted to vacancy-related defects, disorder induced by ion irradiation in the ULE limit, that is, for energies below the vacancy-formation threshold, remains poorly understood. Here, we focus on that regime and report the formation of defects from the breaking of C-C sp2 bonds and formation of C-substrate bonds The bond defect our understanding of disorder induced in graphene read less X. Wang and F. Duan, “Damage Behavior Between Two Pt(111) Surfaces with Adsorbed Benzene Molecules,” Tribology Letters. 2022. link Times cited: 0 D. Chrobak, A. Majtyka-Piłat, G. Ziółkowski, and A. Chrobak, “Interatomic Potential for InP,” Materials. 2022. link Times cited: 0 Abstract: Classical modeling of structural phenomena occurring in InP … read more Abstract: Classical modeling of structural phenomena occurring in InP crystal, for example plastic deformation caused by contact force, requires an interatomic interaction potential that correctly describes not only the elastic properties of indium phosphide but also the pressure-induced reversible phase transition B3↔B1. In this article, a new parametrization of the analytical bond-order potential has been developed for InP. The potential reproduces fundamental physical properties (lattice parameters, cohesive energy, stiffness coefficients) of the B3 and B1 phases in good agreement with first-principles calculations. The proposed interaction model describes the reversibility of the pressure-induced B3↔B1 phase transition as well as the formation of native point defects in the B3 phase. read less M. Eghbalian, R. Ansari, and S. Rouhi, “Effects of geometrical parameters and functionalization percentage on the mechanical properties of oxygenated single-walled carbon nanotubes,” Journal of Molecular Modeling. 2021. link Times cited: 8 Z. E. Oufir, H. Ramézani, N. Mathieu, and S. Delpeux, “Impact of adsorbent carbons and carbon surface conductivity on adsorption capacity of CO2, CH4, N2 and gas separation,” Computational Materials Science. 2021. link Times cited: 8 P. Steinmann, A. Smith, E. Birang, A. McBride, and A. Javili, “Atomistic two-, three- and four-body potentials. Spatial and material settings,” Journal of The Mechanics and Physics of Solids. 2021. link Times cited: 5 G.-U. Jeong and B.-J. Lee, “Interatomic potentials for Pt-C and Pd-C systems and a study of structure-adsorption relationship in large Pt/graphene system,” Computational Materials Science. 2020. link Times cited: 4 G. Plummer and G. Tucker, “Bond-order potentials for theTi3AlC2andTi3SiC2MAX phases,” Physical Review B. 2019. link Times cited: 12 J. Fang, X. Liu, H. Lu, X. Liu, and X. Song, “Crystal defects responsible for mechanical behaviors of a WC-Co composite at room and high temperatures - a simulation study.,” Acta crystallographica Section B, Structural science, crystal engineering and materials. 2019. link Times cited: 11 Abstract: The microstructure evolution and changes in the structures o… read more Abstract: The microstructure evolution and changes in the structures of crystal defects of the nanocrystalline WC-Co composite in the process of uniaxial compression were studied by simulations at both room and high temperatures. The deformation processes were demonstrated as a function of stress and temperature for the stages prior to and after yielding of the composite. The Peierls stresses were evaluated for Co and WC dislocations with increasing temperature. The deformation mechanisms for each stage of the stress-strain curve were disclosed, in which the effect of temperature was clarified. It was found that with the increase of stress, from elastic deformation to plastic deformation then to yielding of the composite, the dominant mechanisms are grain boundary migration, formation and motion of dislocations in Co, concurrent motion and reaction of dislocations in Co and WC, and then rotation of WC grains in combination with motion of Co and WC dislocations. At the yielding stage, sliding of WC grain boundaries plays an increasingly important role in the contribution to plastic deformation at high temperatures. With strain the proportion of mobile dislocations decreases, and dislocations pile up at triple junctions of WC grains, WC/WC grain boundaries and WC/Co phase boundaries in priority order, leading to the nucleation and propagation of microcracks in these regions. read less J. Harrison, J. Schall, S. Maskey, P. Mikulski, M. T. Knippenberg, and B. Morrow, “Review of force fields and intermolecular potentials used in atomistic computational materials research,” Applied Physics Reviews. 2018. link Times cited: 99 Abstract: Molecular simulation is a powerful computational tool for a … read more Abstract: Molecular simulation is a powerful computational tool for a broad range of applications including the examination of materials properties and accelerating drug discovery. At the heart of molecular simulation is the analytic potential energy function. These functions span the range of complexity from very simple functions used to model generic phenomena to complex functions designed to model chemical reactions. The complexity of the mathematical function impacts the computational speed and is typically linked to the accuracy of the results obtained from simulations that utilize the function. One approach to improving accuracy is to simply add more parameters and additional complexity to the analytic function. This approach is typically used in non-reactive force fields where the functional form is not derived from quantum mechanical principles. The form of other types of potentials, such as the bond-order potentials, is based on quantum mechanics and has led to varying levels of accuracy and transferability. When selecting a potential energy function for use in molecular simulations, the accuracy, transferability, and computational speed must all be considered. In this focused review, some of the more commonly used potential energy functions for molecular simulations are reviewed with an eye toward presenting their general forms, strengths, and weaknesses.Molecular simulation is a powerful computational tool for a broad range of applications including the examination of materials properties and accelerating drug discovery. At the heart of molecular simulation is the analytic potential energy function. These functions span the range of complexity from very simple functions used to model generic phenomena to complex functions designed to model chemical reactions. The complexity of the mathematical function impacts the computational speed and is typically linked to the accuracy of the results obtained from simulations that utilize the function. One approach to improving accuracy is to simply add more parameters and additional complexity to the analytic function. This approach is typically used in non-reactive force fields where the functional form is not derived from quantum mechanical principles. The form of other types of potentials, such as the bond-order potentials, is based on quantum mechanics and has led to varying levels of accuracy and transferabilit... read less L. S. I. Liyanage et al., “From Electrons to Atoms: Designing an Interatomic Potential for Fe-C Alloys.” 2018. link Times cited: 0 J. García-Merino, C. Mercado-Zúñiga, C. L. Martínez-González, C. R. Torres-SanMiguel, J. R. Vargas-Garcia, and C. Torres‐Torres, “Magneto-conductive encryption assisted by third-order nonlinear optical effects in carbon/metal nanohybrids,” Materials Research Express. 2017. link Times cited: 10 Abstract: The influence of a magnetic field on electrical conductivity… read more Abstract: The influence of a magnetic field on electrical conductivity and the third-order nonlinear optical properties exhibited by carbon nanotubes decorated with platinum nanoparticles is reported. The experimental and numerical results of the nonlinear magneto-optics, magneto-conductivity and photo-thermal processes were analyzed. The simultaneous impact of optical absorptive nonlinearities and the magnetic field in the sample allowed us to encrypt information in the electronic signals by designing an exclusive-OR logic gate scheme. The samples were prepared in film form using a spray pyrolysis route and a chemical vapor deposition approach. The characterization of the morphological nature of the multiwall nanotubes was evaluated by transmission electron microscopy and x-ray techniques. A vectorial two-wave mixing method was conducted by using nanosecond pulses at 532 nm in order to estimate the nonlinear optical behavior in the nanohybrid materials explored. An important enhancement in the phonon-band-structured transport from the inclusion of nanoparticles in the nanotubes was numerically calculated. A distinguished modification in the transient dynamics of the photo-thermal transitions and Kerr nonlinearities was pointed out to be due to the metallic nanoparticles incorporated in the sample. An extraordinary evolution of the magneto-conductivity, together with a strong change in the optical Kerr transmittance exposed to the magnetic field in propagation through the nanostructures, was observed. read less H. Shi, S. Auerbach, and A. Ramasubramaniam, “First-Principles Predictions of Structure–Function Relationships of Graphene-Supported Platinum Nanoclusters,” Journal of Physical Chemistry C. 2016. link Times cited: 37 Abstract: Platinum-based materials play an important role as electroca… read more Abstract: Platinum-based materials play an important role as electrocatalysts in energy conversion technologies. Graphene-supported Pt nanoclusters were recently found to be promising electrocatalysts for fuel-cell applications due to their enhanced activity and tolerance to CO poisoning as well as their long-term stability toward sintering. However, structure–function relationships that underpin the improved performance of these catalysts are still not well understood. Here, we employ a combination of empirical potential simulations and density functional theory (DFT) calculations to investigate structure–function relationships of small PtN (N = 2–80) clusters on model carbon (graphene) supports. A bond-order empirical potential is employed within a genetic algorithm to go beyond local optimizations in obtaining minimum-energy structures of PtN clusters on pristine as well as defective graphene supports. Point defects in graphene strongly anchor Pt clusters and also appreciably affect the morphologies of small clu... read less S. Skowron, I. Lebedeva, A. Popov, and E. Bichoutskaia, “Energetics of atomic scale structure changes in graphene.,” Chemical Society reviews. 2015. link Times cited: 107 Abstract: The presence of defects in graphene has an essential influen… read more Abstract: The presence of defects in graphene has an essential influence on its physical and chemical properties. The formation, behaviour and healing of defects are determined by energetic characteristics of atomic scale structure changes. In this article, we review recent studies devoted to atomic scale reactions during thermally activated and irradiation-induced processes in graphene. The formation energies of vacancies, adatoms and topological defects are discussed. Defect formation, healing and migration are quantified in terms of activation energies (barriers) for thermally activated processes and by threshold energies for processes occurring under electron irradiation. The energetics of defects in the graphene interior and at the edge is analysed. The effects of applied strain and a close proximity of the edge on the energetics of atomic scale reactions are overviewed. Particular attention is given to problems where further studies are required. read less C. Herbig et al., “Interfacial carbon nanoplatelet formation by ion irradiation of graphene on iridium(111).,” ACS nano. 2014. link Times cited: 25 Abstract: We expose epitaxial graphene (Gr) on Ir(111) to low-energy n… read more Abstract: We expose epitaxial graphene (Gr) on Ir(111) to low-energy noble gas ion irradiation and investigate by scanning tunneling microscopy and atomistic simulations the behavior of C atoms detached from Gr due to ion impacts. Consistent with our density functional theory calculations, upon annealing Gr nanoplatelets nucleate at the Gr/Ir(111) interface from trapped C atoms initially displaced with momentum toward the substrate. Making use of the nanoplatelet formation phenomenon, we measure the trapping yield as a function of ion energy and species and compare the values to those obtained using molecular dynamics simulations. Thereby, complementary to the sputtering yield, the trapping yield is established as a quantity characterizing the response of supported 2D materials to ion exposure. Our findings shed light on the microscopic mechanisms of defect production in supported 2D materials under ion irradiation and pave the way toward precise control of such systems by ion beam engineering. read less X. W. Zhou, R. Jones, P. Hopkins, and T. Beechem, “Thermal boundary conductance between Al films and GaN nanowires investigated with molecular dynamics.,” Physical chemistry chemical physics : PCCP. 2014. link Times cited: 9 Abstract: GaN nanowires are being pursued for optoelectronic and high-… read more Abstract: GaN nanowires are being pursued for optoelectronic and high-power applications. In either use, increases in operating temperature reduce both performance and reliability making it imperative to minimize thermal resistances. Since interfaces significantly influence the thermal response of nanosystems, the thermal boundary resistance between GaN nanowires and metal contacts has major significance. In response, we have performed systematic molecular dynamics simulations to study the thermal boundary conductance between GaN nanowires and Al films as a function of nanowire dimensions, packing density, and the depth the nanowire is embedded into the metal contact. At low packing densities, the apparent Kapitza conductance between GaN nanowires and an aluminum film is shown to be larger than when contact is made between films of these same materials. This enhancement decreases toward the film-film limit, however, as the packing density increases. For densely packed nanowires, maximizing the Kapitza conductance can be achieved by embedding the nanowires into the films, as the conductance is found to be proportional to the total contact area. read less A. Meinander, C. Björkas, and K. Nordlund, “The effect of hydrocarbon chemistry on sputtering in mixed Be–C–H materials,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2013. link Times cited: 2 S. Peng et al., “Bond-Order Potential for Erbium-Hydride System,” Journal of Physical Chemistry C. 2011. link Times cited: 7 Abstract: Interatomic potentials for an Er-H system are derived based … read more Abstract: Interatomic potentials for an Er-H system are derived based on an analytical bond-order scheme. The model potentials provide a good description of the bulk properties and defect properties of hcp-Er, including lattice parameter, cohesive energy, elastic constants, point defect formation energies, surface and stacking fault energies. In addition to experimental data, a DFT method is used to construct the necessary database of different phases. We demonstrate that such potentials can reproduce the hydrogen behaviour in an alpha-phase Er-H system for a low hydrogen/metal ratio. Especially, the present potentials can be employed for modelling the energetics and structural properties of fcc ErH2, including lattice parameters, elastic constants, bulk modulus, Young's modulus and shear modulus, as well as the formation energies and migration barriers of point defects in ErH2. read less J. Los, C. Bichara, and R. Pellenq, “Tight binding within the fourth moment approximation: Efficient implementation and application to liquid Ni droplet diffusion on graphene.” 2011. link Times cited: 9 Abstract: (Received 8 February 2011; revised manuscript received 13 Ma… read more Abstract: (Received 8 February 2011; revised manuscript received 13 May 2011; published 31 August 2011)Application of the fourth moment approximation (FMA) to the local density of states within a tight bindingdescription to build a reactive, interatomic interaction potential for use in large scale molecular simulations,is a logical and signiﬁcant step forward to improve the second moment approximation, standing at the basisof several, widely used (semi-)empirical interatomic interaction models. In this paper we present a sufﬁcientlydetailed description of the FMA and its technical implications, containing the essential elements for an efﬁcientimplementationinasimulationcode.Usingarecent,existingFMA-basedmodelforC-Nisystems,weinvestigatedthesizedependenceofthediffusionofaliquidNiclusteronagraphenesheetandﬁndapowerlawdependenceofthediffusionconstantontheclustersize(numberofclusteratoms)withanexponentverycloseto−2 read less K. Vörtler, C. Björkas, D. Terentyev, L. Malerba, and K. Nordlund, “The effect of C concentration on radiation damage in Fe–Cr–C alloys,” Journal of Nuclear Materials. 2008. link Times cited: 28 E. Deligoz, Y. Ciftci, P. T. Jochym, and K. Çolakoǧlu, “The first principles study on PtC compound,” Materials Chemistry and Physics. 2008. link Times cited: 37 K. Nordlund and S. Dudarev, “Interatomic potentials for simulating radiation damage effects in metals,” Comptes Rendus Physique. 2008. link Times cited: 29 M. Müller and K. Albe, “Structural stability of multiply twinned FePt nanoparticles,” Acta Materialia. 2007. link Times cited: 32 J. Kang and H. Hwang, “Atomistic study of III-nitride nanotubes,” Computational Materials Science. 2004. link Times cited: 45 L. Corrales, “Computational methods to study radiation effects in oxide materials,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2004. link Times cited: 8 J. Nord, K. Nordlund, J. Keinonen, and K. Albe, “Molecular dynamics study of defect formation in GaN cascades,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2003. link Times cited: 62 S. M. Zamzamian, S. Feghhi, and M. Samadfam, “Theoretical and computational investigation on the radiation-induced point defects in cementite: Picosecond timescale,” Journal of Nuclear Materials. 2021. link Times cited: 1 K. Nordlund and F. Djurabekova, “Molecular Dynamics Simulations of Non-equilibrium Systems,” Handbook of Materials Modeling. 2020. link Times cited: 3 G. Ferguson and L. Curtiss, “Atomic-level modeling of organic electrolytes in lithium-ion batteries,” ChemInform. 2013. link Times cited: 5 X.-C. Li, X. Shu, Y. Liu, F. Gao, and G. Lu, “Modified analytical interatomic potential for a W–H system with defects,” Journal of Nuclear Materials. 2011. link Times cited: 100 A. Bagaturyants, M. A. Deminskii, A. Knizhnik, B. Potapkin, and S. Umanskii, “Chapter 9 Integrated Approach to Dielectric Film Growth Modeling: Growth Mechanisms and Kinetics.” 2007. link Times cited: 2 J. Schall, P. Mikulski, G. M. Chateauneuf, G. Gao, and J. Harrison, “Molecular Dynamics Simulations of Tribology.” 2007. link Times cited: 8 B. Thijsse, “Silicon potentials under (ion) attack: towards a new MEAM model,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2005. link Times cited: 24 K. Nordlund and R. Averback, “Point Defects in Metals.” 2005. link Times cited: 2 I. M. P. Espinosa, T. Jacobs, and A. Martini, “Atomistic Simulations of the Elastic Compression of Platinum Nanoparticles,” Nanoscale Research Letters. 2022. link Times cited: 6 I. M. P. Espinosa, T. Jacobs, and A. Martini, “Evaluation of Force Fields for Molecular Dynamics Simulations of Platinum in Bulk and Nanoparticle Forms.,” Journal of chemical theory and computation. 2021. link Times cited: 7 Abstract: Understanding the size- and shape-dependent properties of pl… read more Abstract: Understanding the size- and shape-dependent properties of platinum nanoparticles is critical for enabling the design of nanoparticle-based applications with optimal and potentially tunable functionality. Toward this goal, we evaluated nine different empirical potentials with the purpose of accurately modeling faceted platinum nanoparticles using molecular dynamics simulation. First, the potentials were evaluated by computing bulk and surface properties-surface energy, lattice constant, stiffness constants, and the equation of state-and comparing these to prior experimental measurements and quantum mechanics calculations. Then, the potentials were assessed in terms of the stability of cubic and icosahedral nanoparticles with faces in the {100} and {111} planes, respectively. Although none of the force fields predicts all the evaluated properties with perfect accuracy, one potential-the embedded atom method formalism with a specific parameter set-was identified as best able to model platinum in both bulk and nanoparticle forms. read less S. Nasiri et al., “Multilayer Structures of Graphene and Pt Nanoparticles: A Multiscale Computational Study,” Advanced Engineering Materials. 2020. link Times cited: 5 Abstract: Multiscale simulation study results of multilayer structures… read more Abstract: Multiscale simulation study results of multilayer structures consisting of graphene sheets with embedded Pt nanoparticles is reported. Density functional theory is used to understand the energetics of Pt–graphene interfaces and provide reference data for the parameterization of a Pt–graphene interaction potential. Molecular dynamics simulations then provide the conformation and energetics of graphene sheets with embedded Pt nanoparticles of varying density, form, and size. These results are interpreted using a continuum mechanical model of sheet deformation, and serve to parameterize a meso‐scale Monte Carlo model to investigate the question under which conditions the free volume around the Pt nanoparticles forms a percolating cluster, such that the structures can be used in catalytic applications. This article is concluded with a discussion of potential applications of such multilayer structures. read less N. Chen, Q. Peng, Z. Jiao, I. van Rooyen, W. Skerjanc, and F. Gao, “Analytical bond-order potential for silver, palladium, ruthenium and iodine bulk diffusion in silicon carbide,” Journal of Physics: Condensed Matter. 2019. link Times cited: 6 Abstract: The analytical bond-order potential has been developed for s… read more Abstract: The analytical bond-order potential has been developed for simulating fission product (Ag, Pd, Ru, and I) behavior in SiC, especially for their diffusion. We have proposed adding experimentally available elastic constants and physical properties of the elements as well as important defect formation energies calculated from density functional theory simulation to the list of typical properties as the extensive fitting database. The results from molecular dynamics simulations are in a reasonable agreement with defect properties and energy barriers of their experimental/computational counterparts. The successful validation of the new potential has established a good reliability and transferability of the potentials, which enables the ability of simulation in extended scale. The kinetic behavior such as diffusion of different interstitials is then realized by applying the new interatomic potentials. The bulk diffusion is less likely to dominate the transport of the four fission products under pure thermal condition, when we refer to their extremely small values of the effective diffusion coefficients. The interstitial mechanism is hard for Pd, Ru, and I to access due to the high formation energy and high migration energy. However, it is found that the migration energy of silver is relatively low, which indicates Ag diffusion via an interstitial mechanism being feasible, especially under irradiation condition, where massive interstitials can be formed in high-temperature nuclear reactors. read less J. Hur, “Modified potential for atomistic simulation of the growth of carbon materials from binary alloy catalysts.,” Physical chemistry chemical physics : PCCP. 2019. link Times cited: 3 Abstract: A new hybrid bond order potential has been developed and imp… read more Abstract: A new hybrid bond order potential has been developed and implemented to describe carbon-bimetallic alloy interactions, which are involved in the catalytic growth of carbon materials such as graphene and carbon nanotubes on the surface of binary alloy catalysts. In carefully adjusting the parameters, the potential energy fitting correlated with the results calculated from the density functional theory (DFT) method leads to a high quality empirical force field with an average error of <4.5% only. With the PES accuracy, in total 16 (n,m) have been successfully obtained from the MD trajectories in this work, and the structural evolution including random chirality and diameter formation has been identified. The newly modified force field is expected to be useful for modelling the spontaneous growth of carbon materials, particularly tubes on binary alloy clusters, giving an idea of how these C-C, C-M, and M-M interactions affect the growth behavior of carbon nanotubes. In addition, the new FF is only valid for liquid alloy nanoparticles at this time, but the use of solid alloy nanocatalysts with the new FF can be further employed for 2-D material growth such as graphene layer growth. read less Z. Fan, Y. Wang, X. Gu, P. Qian, Y. Su, and T. Ala‐Nissila, “A minimal Tersoff potential for diamond silicon with improved descriptions of elastic and phonon transport properties,” Journal of Physics: Condensed Matter. 2019. link Times cited: 10 Abstract: Silicon is an important material and many empirical interato… read more Abstract: Silicon is an important material and many empirical interatomic potentials have been developed for atomistic simulations of it. Among them, the Tersoff potential and its variants are the most popular ones. However, all the existing Tersoff-like potentials fail to reproduce the experimentally measured thermal conductivity of diamond silicon. Here we propose a modified Tersoff potential and develop an efficient open source code called GPUGA (graphics processing units genetic algorithm) based on the genetic algorithm and use it to fit the potential parameters against energy, virial and force data from quantum density functional theory calculations. This potential, which is implemented in the efficient open source GPUMD (graphics processing units molecular dynamics) code, gives significantly improved descriptions of the thermal conductivity and phonon dispersion of diamond silicon as compared to previous Tersoff potentials and at the same time well reproduces the elastic constants. Furthermore, we find that quantum effects on the thermal conductivity of diamond silicon at room temperature are non-negligible but small: using classical statistics underestimates the thermal conductivity by about 10% as compared to using quantum statistics. read less X. Zhu and Y. Lu, “Growth of beryllium thin films on beryllium (0001) surface: Influence of incident energy and incident angle by molecular dynamics simulation,” Journal of Applied Physics. 2018. link Times cited: 5 Abstract: The morphology and microstructure of metallic thin films syn… read more Abstract: The morphology and microstructure of metallic thin films synthesized by magnetron sputtering deposition are sensitive to incident energy and incident angle. The role of incident energy and incident angle in films’ morphology evolution of the beryllium thin films’ growth on beryllium (0001) surface was studied by molecular dynamics simulations. The analytical bond order potential was used to represent the interatomic interactions, and the common neighbor analysis algorithm for crystal structures was used for the structural characterization of the simulated films. It is found that when the incident energy is between 1 eV and 20 eV, the increased incident energy is beneficial to grow uniform crystal films and, when the incident energy is greater than 15 eV, the interstitial atoms formed inside the films. Furthermore, under the small incident angle conditions, the morphology of a smooth surface was formed, which means that the vertical incident conditions are desired for the growth of high quality films. In short, vertically inserted atoms with hyperthermal energy (5–10 eV) are more propitious for the growth of perfect crystal Be thin films. The obtained results can be used to guide the experiment. read less J. Byggmästar, E. Hodille, Y. Ferro, and K. Nordlund, “Analytical bond order potential for simulations of BeO 1D and 2D nanostructures and plasma-surface interactions,” Journal of Physics: Condensed Matter. 2018. link Times cited: 18 Abstract: An analytical interatomic bond order potential for the Be–O … read more Abstract: An analytical interatomic bond order potential for the Be–O system is presented. The potential is fitted and compared to a large database of bulk BeO and point defect properties obtained using density functional theory. Its main applications include simulations of plasma-surface interactions involving oxygen or oxide layers on beryllium, as well as simulations of BeO nanotubes and nanosheets. We apply the potential in a study of oxygen irradiation of Be surfaces, and observe the early stages of an oxide layer forming on the Be surface. Predicted thermal and elastic properties of BeO nanotubes and nanosheets are simulated and compared with published ab initio data. read less R. Gasper, H. Shi, and A. Ramasubramaniam, “Adsorption of CO on Low-Energy, Low-Symmetry Pt Nanoparticles: Energy Decomposition Analysis and Prediction via Machine-Learning Models,” Journal of Physical Chemistry C. 2017. link Times cited: 55 Abstract: We present a systematic analysis of CO adsorption on Pt nano… read more Abstract: We present a systematic analysis of CO adsorption on Pt nanoclusters in the 0.2–1.5 nm size range with the aim of unraveling size-dependent trends and developing predictive models for site-specific adsorption behavior. Using an empirical-potential-based genetic algorithm and density functional theory (DFT) modeling, we show that there exists a size window (40–70 atoms) over which Pt nanoclusters bind CO weakly, the binding energies being comparable to those on (111) or (100) facets. The size-dependent adsorption energy trends are, however, distinctly nonmonotonic and are not readily captured using traditional descriptors such as d-band energies or (generalized) coordination numbers of the Pt binding sites. Instead, by applying machine-learning algorithms, we show that multiple descriptors, broadly categorized as structural and electronic descriptors, are essential for qualitatively capturing the CO adsorption trends. Nevertheless, attaining quantitative accuracy requires further refinement, and we propose... read less A. Stukowski, E. Fransson, M. Mock, and P. Erhart, “Atomicrex—a general purpose tool for the construction of atomic interaction models,” Modelling and Simulation in Materials Science and Engineering. 2017. link Times cited: 17 Abstract: We introduce atomicrex, an open-source code for constructing… read more Abstract: We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands of atoms or more, because electronic structure methods become computationally too expensive at this scale. atomicrex covers a wide range of interatomic potential types and fulfills many needs in atomistic model development. As inputs, it supports experimental property values as well as ab initio energies and forces, to which models can be fitted using various optimization algorithms. The open architecture of atomicrex allows it to be used in custom model development scenarios beyond classical interatomic potentials while thanks to its Python interface it can be readily integrated e.g., with electronic structure calculations or machine learning algorithms. read less J. Polvi, K. Heinola, and K. Nordlund, “An interatomic potential for W–N interactions,” Modelling and Simulation in Materials Science and Engineering. 2016. link Times cited: 5 Abstract: N2 gas is routinely used as a seeding species in fusion plas… read more Abstract: N2 gas is routinely used as a seeding species in fusion plasma to control the amount of power emitted from the plasma by radiation to the tungsten walls of an ITER-like divertor. Nitrogen atoms interact with the plasma-facing materials beryllium and tungsten, and form chemical bonds with the wall surfaces, as well as with plasma hydrogen isotopes, thus raising a special interest in W–N and N–H interactions in the fusion community. In this work we describe the development of an analytical interatomic potential for W–N interactions and benchmark the potential against DFT calculation results for N defects in tungsten. read less P. Kuopanportti, E. Hayward, C. Fu, A. Kuronen, and K. Nordlund, “Interatomic FeH potential for irradiation and embrittlement simulations,” Computational Materials Science. 2016. link Times cited: 18 E. Helgee and A. Isacsson, “Adsorption of metal atoms at a buckled graphene grain boundary using model potentials,” AIP Advances. 2016. link Times cited: 4 Abstract: Two model potentials have been evaluated with regard to thei… read more Abstract: Two model potentials have been evaluated with regard to their ability to model adsorption of single metal atoms on a buckled graphene grain boundary. One of the potentials is a Lennard-Jones potential parametrized for gold and carbon, while the other is a bond-order potential parametrized for the interaction between carbon and platinum. Metals are expected to adsorb more strongly to grain boundaries than to pristine graphene due to their enhanced adsorption at point defects resembling those that constitute the grain boundary. Of the two potentials considered here, only the bond-order potential reproduces this behavior and predicts the energy of the adsorbate to be about 0.8 eV lower at the grain boundary than on pristine graphene. The Lennard-Jones potential predicts no significant difference in energy between adsorbates at the boundary and on pristine graphene. These results indicate that the Lennard-Jones potential is not suitable for studies of metal adsorption on defects in graphene, and that bond-order potentials are preferable. read less J. Harrison, M. Fallet, K. E. Ryan, B. L. Mooney, M. T. Knippenberg, and J. Schall, “Recent developments and simulations utilizing bond-order potentials,” Modelling and Simulation in Materials Science and Engineering. 2015. link Times cited: 12 Abstract: Bond-order potentials (BOPs) have been used successfully in … read more Abstract: Bond-order potentials (BOPs) have been used successfully in simulations of a wide range of processes. A brief overview of bond-order potentials is provided which focuses on the reactive empirical bond-order (REBO) potential for hydrocarbons (Brenner et al 2002 J. Phys.: Condens. Matter 14 783) and the large number of useful potentials it has spawned. Two specific extensions of the REBO potential that make use of its formalism are discussed. First, the 2B-SiCH potential (Schall and Harrison 2013 J. Phys. Chem. C 117 1323) makes the appropriate changes to the hydrocarbon REBO potential so that three atom types, Si, C, and H, can be modeled. Second, we recently added the electronegative element O, along with the associated charge terms, to the adaptive intermolecular REBO (AIREBO) potential (Stuart et al 2000 J. Chem. Phys. 112 6472). The resulting qAIREBO potential (Knippenberg et al 2012 J. Chem. Phys. 136 164701) makes use of the bond-order potential/split-charge (BOP/SQE) equilibration method (Mikulski et al 2009 J. Chem. Phys. 131 241105) and the Lagrangian approach to charge dynamics (Rick et al 1994 J. Chem. Phys. 101 6141). The integration of these two techniques allows for atomic charges to evolve with time during MD simulations: as a result, chemical reactions can be modeled in C-, O-, and H-containing systems. The usefulness of the 2B-SiCH potential for tribological investigations is demonstrated in molecular dynamics (MD) simulations of axisymmetric tips composed of Si and SiC placed in sliding contact with diamond(1 1 1) surfaces with varying amounts of hydrogen termination. The qAIREBO potential is used to investigate confinement of sub-monolayer coverages of water between nanostructured surfaces. read less L.-F. Wang, X. Shu, and G. Lu, “Comparison of two tungsten–helium interatomic potentials,” Journal of Materials Research. 2015. link Times cited: 4 Abstract: We have clarified the performance of two tungsten–helium ana… read more Abstract: We have clarified the performance of two tungsten–helium analytical interatomic potentials, one of which, developed by Li et al., is a bond-order potential, and another, developed by Juslin et al., is a combination of embedded atom method potential and pair potential. Using these two potentials, we have simulated and made a full comparison of formation energy and migration energy of different defects including helium and vacancy, binding energies of helium and vacancy with helium-vacancy cluster, surface energy, as well as melting point, with reference to the corresponding results from the first-principles and experiments. read less X. W. Zhou, D. Ward, M. Foster, and J. Zimmerman, “An analytical bond-order potential for the copper–hydrogen binary system,” Journal of Materials Science. 2015. link Times cited: 18 Z. Zhao et al., “Carbon coated face-centered cubic Ru-C nanoalloys.,” Nanoscale. 2014. link Times cited: 13 Abstract: Carbon-encapsulated ruthenium-carbon (Ru-C) nanoalloys were … read more Abstract: Carbon-encapsulated ruthenium-carbon (Ru-C) nanoalloys were synthesized by dynamic shocks. The Ru-C alloy shows a new fcc structure different from the original hcp structure of metal Ru. This fcc phase is assigned to a Ru32C4 solid solution with a lattice parameter of 3.868(2) Å and a bulk modulus KT0 of 272(12) GPa. The small amount of carbon in the solid solution enhances the thermodynamic and chemical stabilities with respect to pure Ru, as well as induces changes in the electronic properties, which have direct applications in improving the material's catalytic activity and selectivity. read less K. Nordlund, C. Björkas, T. Ahlgren, A. Lasa, and A. Sand, “Multiscale modelling of plasma–wall interactions in fusion reactor conditions,” Journal of Physics D: Applied Physics. 2014. link Times cited: 58 Abstract: The interaction of fusion reactor plasma with the material o… read more Abstract: The interaction of fusion reactor plasma with the material of the first wall involves a complex multitude of interlinked physical and chemical effects. Hence, modern theoretical treatment of it relies to a large extent on multiscale modelling, i.e. using different kinds of simulation approaches suitable for different length and time scales in connection with each other. In this review article, we overview briefly the physics and chemistry of plasma–wall interactions in tokamak-like fusion reactors, and present some of the most commonly used material simulation approaches relevant for the topic. We also give summaries of recent multiscale modelling studies of the effects of fusion plasma on the modification of the materials of the first wall, especially on swift chemical sputtering, mixed material formation and hydrogen isotope retention in tungsten. read less K. Nordlund and F. Djurabekova, “Multiscale modelling of irradiation in nanostructures,” Journal of Computational Electronics. 2014. link Times cited: 42 F. Kaatz and A. Bultheel, “Informational thermodynamic model for nanostructures,” Journal of Mathematical Chemistry. 2014. link Times cited: 9 K. Henriksson, C. Björkas, and K. Nordlund, “Atomistic simulations of stainless steels: a many-body potential for the Fe–Cr–C system,” Journal of Physics: Condensed Matter. 2013. link Times cited: 65 Abstract: Stainless steels found in real-world applications usually ha… read more Abstract: Stainless steels found in real-world applications usually have some C content in the base Fe–Cr alloy, resulting in hard and dislocation-pinning carbides—Fe3C (cementite) and Cr23C6—being present in the finished steel product. The higher complexity of the steel microstructure has implications, for example, for the elastic properties and the evolution of defects such as Frenkel pairs and dislocations. This makes it necessary to re-evaluate the effects of basic radiation phenomena and not simply to rely on results obtained from purely metallic Fe–Cr alloys. In this report, an analytical interatomic potential parameterization in the Abell–Brenner–Tersoff form for the entire Fe–Cr–C system is presented to enable such calculations. The potential reproduces, for example, the lattice parameter(s), formation energies and elastic properties of the principal Fe and Cr carbides (Fe3C, Fe5C2, Fe7C3, Cr3C2, Cr7C3, Cr23C6), the Fe–Cr mixing energy curve, formation energies of simple C point defects in Fe and Cr, and the martensite lattice anisotropy, with fair to excellent agreement with empirical results. Tests of the predictive power of the potential show, for example, that Fe–Cr nanowires and bulk samples become elastically stiffer with increasing Cr and C concentrations. High-concentration nanowires also fracture at shorter relative elongations than wires made of pure Fe. Also, tests with Fe3C inclusions show that these act as obstacles for edge dislocations moving through otherwise pure Fe. read less L. Pastewka, A. Klemenz, P. Gumbsch, and M. Moseler, “Screened empirical bond-order potentials for Si-C,” Physical Review B. 2013. link Times cited: 110 Abstract: Typical empirical bond-order potentials are short ranged and… read more Abstract: Typical empirical bond-order potentials are short ranged and give ductile instead of brittle behavior for materials such as crystalline silicon or diamond. Screening functions can be used to increase the range of these potentials. We outline a general procedure to combine screening functions with bond-order potentials that does not require to refit any of the potential's properties. We use this approach to modify Tersoff's [Phys. Rev. B 39, 5566 (1989)], Erhart & Albe's [Phys. Rev. B 71, 35211 (2005)] and Kumagai et al.'s [Comp. Mater. Sci. 39, 457 (2007)] Si, C and Si-C potentials. The resulting potential formulations correctly reproduce brittle materials response, and give an improved description of amorphous phases. read less P. Stoyanov et al., “Experimental and Numerical Atomistic Investigation of the Third Body Formation Process in Dry Tungsten/Tungsten-Carbide Tribo Couples,” Tribology Letters. 2013. link Times cited: 45 M. Backman, N. Juslin, and K. Nordlund, “Bond order potential for gold,” The European Physical Journal B. 2012. link Times cited: 11 T. Lee, M. Baskes, S. Valone, and J. Doll, “Atomistic modeling of thermodynamic equilibrium and polymorphism of iron,” Journal of Physics: Condensed Matter. 2012. link Times cited: 52 Abstract: We develop two new modified embedded-atom method (MEAM) pote… read more Abstract: We develop two new modified embedded-atom method (MEAM) potentials for elemental iron, intended to reproduce the experimental phase stability with respect to both temperature and pressure. These simple interatomic potentials are fitted to a wide variety of material properties of bcc iron in close agreement with experiments. Numerous defect properties of bcc iron and bulk properties of the two close-packed structures calculated with these models are in reasonable agreement with the available first-principles calculations and experiments. Performance at finite temperatures of these models has also been examined using Monte Carlo simulations. We attempt to reproduce the experimental iron polymorphism at finite temperature by means of free energy computations, similar to the procedure previously pursued by Müller et al (2007 J. Phys.: Condens. Matter 19 326220), and re-examine the adequacy of the conclusion drawn in the study by addressing two critical aspects missing in their analysis: (i) the stability of the hcp structure relative to the bcc and fcc structures and (ii) the compatibility between the temperature and pressure dependences of the phase stability. Using two MEAM potentials, we are able to represent all of the observed structural phase transitions in iron. We discuss that the correct reproductions of the phase stability among three crystal structures of iron with respect to both temperature and pressure are incompatible with each other due to the lack of magnetic effects in this class of empirical interatomic potential models. The MEAM potentials developed in this study correctly predict, in the bcc structure, the self-interstitial in the 〈110〉 orientation to be the most stable configuration, and the screw dislocation to have a non-degenerate core structure, in contrast to many embedded-atom method potentials for bcc iron in the literature. read less H. Hou, R. Wang, J. Wang, X. Liu, G. Chen, and P. Huang, “An analytic bond-order potential for the Fe–Cu system,” Modelling and Simulation in Materials Science and Engineering. 2012. link Times cited: 5 Abstract: An angular-dependent analytic bond-order potential (ABOP) fo… read more Abstract: An angular-dependent analytic bond-order potential (ABOP) for copper and Fe–Cu system was developed, based on the ABOP of pure iron introduced by Müller et al (2007 J. Phys.: Condens. Matter 19 326220). The potential parameters for the present ABOP model of copper were determined by fitting to the experimental data of the basic properties of fcc Cu and ab initio calculated properties of bcc Cu. The model predicts the vacancy formation energy in good agreement with the experimental result, although no vacancy formation information was used in the fitting of the model parameters. The melting point of Cu is also properly reproduced. The Fe–Cu binary system was described by adding two independent cross parameters in the potential model. The cross parameters were fitted using the ab initio data of the formation energies and lattice parameters of fictitious Fe–Cu alloys. The potential was applied to investigate the point defects and small defect clusters in dilute Fe–Cu alloys. The results were compared with the ab initio data and the values obtained with other potentials. read less I. Lebedeva, A. Knizhnik, A. Popov, and B. Potapkin, “Ni-assisted transformation of graphene flakes to fullerenes,” arXiv: Mesoscale and Nanoscale Physics. 2012. link Times cited: 34 Abstract: Transformation of graphene flakes to fullerenes assisted by … read more Abstract: Transformation of graphene flakes to fullerenes assisted by Ni clusters is investigated using molecular dynamics simulations. The bond-order potential for Ni-C systems is developed. The potential reproduces the experimental and first-principles data on the physical properties of pure Ni as well as on relative energies of carbon species on Ni surfaces and in Ni bulk. The potential is applied for molecular dynamics simulations of the transformation of graphene flakes consisting of 50 - 400 atoms with and without Ni clusters attached. Free fullerenes, fullerenes with Ni clusters attached from outside and fullerenes encapsulating Ni clusters (Ni endofullerenes) are observed to form in the presence of Ni clusters consisting of 5 - 80 atoms. Moreover, a new type of heterofullerenes with a patch made of a Ni cluster is found to form as an intermediate structure during the transformation. The Ni clusters are shown to reduce the activation energy for the graphene-fullerene transformation from 4.0 eV to 1.5 - 1.9 eV, providing the decrease of the minimal temperature at which such a transformation can be observed experimentally from about 1400 K for free graphene flakes to about 700 - 800 K. While the transformation of free graphene flakes is found to occur through formation of chains of two-coordinated carbon atoms at the flake edges, the mechanism of the Ni-assisted graphene-fullerene transformation is revealed to be based on the transfer of carbon atoms from the graphene flake to the Ni cluster and back. The way of controlled synthesis of endofullerenes with a transition metal cluster inside and heterofullerenes with a transition metal patch is also proposed. read less A. Dongare and B. Lamattina, “Deformation and Failure Mechanisms in Ceramic-Reinforced Metal-Matrix Composites at Atomic Scales.” 2011. link Times cited: 1 C. Björkas, K. Henriksson, M. Probst, and K. Nordlund, “A Be–W interatomic potential,” Journal of Physics: Condensed Matter. 2010. link Times cited: 29 Abstract: In this work, an interatomic potential for the beryllium–tun… read more Abstract: In this work, an interatomic potential for the beryllium–tungsten system is derived. It is the final piece of a potential puzzle, now containing all possible interactions between the fusion reactor materials beryllium, tungsten and carbon as well as the plasma hydrogen isotopes. The potential is suitable for plasma–wall interaction simulations and can describe the intermetallic Be2W and Be12W phases. The interaction energy between a Be surface and a W atom, and vice versa, agrees qualitatively with ab initio calculations. The potential can also reasonably describe BexWy molecules with x, y = 1, 2, 3, 4. read less A. Krasheninnikov and K. Nordlund, “Ion and electron irradiation-induced effects in nanostructured materials,” Journal of Applied Physics. 2010. link Times cited: 877 Abstract: A common misconception is that the irradiation of solids wit… read more Abstract: A common misconception is that the irradiation of solids with energetic electrons and ions has exclusively detrimental effects on the properties of target materials. In addition to the well-known cases of doping of bulk semiconductors and ion beam nitriding of steels, recent experiments show that irradiation can also have beneficial effects on nanostructured systems. Electron or ion beams may serve as tools to synthesize nanoclusters and nanowires, change their morphology in a controllable manner, and tailor their mechanical, electronic, and even magnetic properties. Harnessing irradiation as a tool for modifying material properties at the nanoscale requires having the full microscopic picture of defect production and annealing in nanotargets. In this article, we review recent progress in the understanding of effects of irradiation on various zero-dimensional and one-dimensional nanoscale systems, such as semiconductor and metal nanoclusters and nanowires, nanotubes, and fullerenes. We also consider the t... read less T. Ahlgren, K. Heinola, N. Juslin, and A. Kuronen, “Bond-order potential for point and extended defect simulations in tungsten,” Journal of Applied Physics. 2010. link Times cited: 80 Abstract: A reactive interatomic bond-order potential for bcc tungsten… read more Abstract: A reactive interatomic bond-order potential for bcc tungsten is presented. Special attention in the potential development was given for obtaining accurate formation and migration energies for point defects, making the potential useful in atomic scale simulations of point and extended defects. The potential was used to calculate binding energies and trapping distances for vacancies in vacancy clusters and the recombination radius for self-interstitial atom and monovacancy. read less C. Björkas, K. Vörtler, K. Nordlund, D. Nishijima, and R. Doerner, “Chemical sputtering of Be due to D bombardment,” New Journal of Physics. 2009. link Times cited: 66 Abstract: While covalently bonded materials such as carbon are well kn… read more Abstract: While covalently bonded materials such as carbon are well known to be eroded by chemical sputtering when exposed to plasmas or low-energy ion irradiation, pure metals have been believed to sputter only physically. The erosion of Be when subject to D bombardment was in this work measured at the PISCES-B facility and modelled with molecular dynamics simulations. During the experiments, a chemical effect was observed, since a fraction of the eroded Be was in the form of BeD molecules. This fraction decreased with increasing ion energy. The same trend was seen in the simulations and was explained by the swift chemical sputtering mechanism, showing that pure metals can, indeed, be sputtered chemically. D ions of only 7 eV can erode Be through this mechanism. read less K. Albe, J. Nord, and K. Nordlund, “Dynamic charge-transfer bond-order potential for gallium nitride,” Philosophical Magazine. 2009. link Times cited: 10 Abstract: We present an analytical interatomic potential for gallium n… read more Abstract: We present an analytical interatomic potential for gallium nitride which is based on a new environment-dependent dynamic charge-transfer model. The model consists of a short-ranged bond-order potential that accounts for covalent/metallic interactions and an ionic Coulomb potential with effective point charges that are dynamically adjusted. In contrast to established models, these point charges are distance-dependent and vary with the number and type of nearest neighbour atoms. The basic concepts stem from the idea of bond charges. We assume pairwise symmetric charge transfer between atoms of different type forming a bond. Charge contributions of all bonds to an atomic site are weighted and added, yielding the effective charge per atom. Mulliken charges, as obtained from density-functional theory calculations within the local-density approximation, are used for adjusting the parameters and functional form of the potential. The short-range contributions are chosen as angular-dependent many-body bond-order potentials, which can be understood as an extension of a Finnis–Sinclair type potential. read less C. Björkas et al., “Interatomic potentials for the Be–C–H system,” Journal of Physics: Condensed Matter. 2009. link Times cited: 65 Abstract: Analytical bond-order potentials for beryllium, beryllium ca… read more Abstract: Analytical bond-order potentials for beryllium, beryllium carbide and beryllium hydride are presented. The reactive nature of the formalism makes the potentials suitable for simulations of non-equilibrium processes such as plasma–wall interactions in fusion reactors. The Be and Be–C potentials were fitted to ab initio calculations as well as to experimental data of several different atomic configurations and Be–H molecule and defect data were used in determining the Be–H parameter set. Among other tests, sputtering, melting and quenching simulations were performed in order to check the transferability of the potentials. The antifluorite Be2C structure is well described by the Be–C potential and the hydrocarbon interactions are modelled by the established Brenner potentials. read less A. Dongare, L. Zhigilei, A. Rajendran, and B. Lamattina, “Interatomic potentials for atomic scale modeling of metal–matrix ceramic particle reinforced nanocomposites,” Composites Part B-engineering. 2009. link Times cited: 15 K. Henriksson and K. Nordlund, “Simulations of cementite: An analytical potential for the Fe-C system,” Physical Review B. 2009. link Times cited: 72 Abstract: An analytical bond-order interatomic potential has been deve… read more Abstract: An analytical bond-order interatomic potential has been developed for the iron-carbon system for use in molecular-dynamics and Monte Carlo simulations. The potential has been successfully fitted to cementite and Hagg carbide, which are most important crystalline polytypes among the many known metastable iron carbide phases. Predicted properties of other carbides and the simplest point defects are in good to reasonable agreement with available data from experiments and density-functional theory calculations. The potential correctly describes melting and recrystallization of cementite, making it useful for simulation of steels. We show that they correctly describe the metastability of cementite and can be used to model carbide growth and dissolution. read less K. Li, H. He, B. Xu, and B. Pan, “The stabilities of gallium nanowires with different phases encapsulated in a carbon nanotube,” Journal of Applied Physics. 2009. link Times cited: 10 Abstract: For C–Ga systems, a classical potential is developed to desc… read more Abstract: For C–Ga systems, a classical potential is developed to describe the interaction between C and Ga atoms. By using this potential, we study the stabilities of the Ga nanowires with different phases encapsulated in a carbon nanotube (CNT). Simulations show that the encapsulated β-Ga and γ-Ga nanowires are more stable than the α-Ga nanowire in the CNT. Moreover, we find that such relative stabilities are mainly originated from the size effect of the Ga nanowires and the influence of the CNT. With performing molecular dynamics simulation at finite temperatures, the linear thermal expansion coefficient of an encapsulated Ga nanowire is predicted to be 1.38×10−4 K−1, being very close to the bulk value. The obtained stabilities as well as the thermal expansion feature of the concerned Ga nanowires are all consistent with experimental observations. read less C. Sanz-Navarro et al., “Molecular Dynamics Simulations of Carbon-Supported Ni Clusters Using the Reax Reactive Force Field,” Journal of Physical Chemistry C. 2008. link Times cited: 30 Abstract: Molecular dynamics simulations have been performed using a R… read more Abstract: Molecular dynamics simulations have been performed using a Reax force field for C/H/Ni systems to study the structural changes of an Ni_(100) cluster adsorbed on a carbon platelet. Three different edges of a carbon platelet are considered. We find a complete restructuring of the initial structure of the Ni_(100) clusters adsorbed on the armchair and zigzag edges. Nonetheless, the mean Ni−Ni bond length hardly changes. Several preferential sites on each of the graphite edges are identified. Diffusion of the entire cluster is found both for adsorption on the basal plane and for binding to a hydrogen terminated graphite edge. read less C. Acharya, D. I. Sullivan, and C. Turner, “Characterizing the Interaction of Pt and PtRu Clusters with Boron-Doped, Nitrogen-Doped, and Activated Carbon : Density Functional Theory Calculations and Parameterization,” Journal of Physical Chemistry C. 2008. link Times cited: 57 Abstract: Previous density functional theory calculations of Pt and Pt… read more Abstract: Previous density functional theory calculations of Pt and PtRu clusters on carbon supports have shown that the adsorption energies of these metal clusters increase substantially with substitutional boron defects in the carbon lattice. Here, the stability of metal clusters is further probed with substitutional nitrogen defects and surface functional groups. Also, the dynamics of Pt and Ru atoms on pure and boron-doped carbon are studied as a function of temperature using ab initio molecular dynamics (AIMD) simulations. Although the time scale accessible is limited, the AIMD simulations show reduced mobility on the boron-doped surface. In order to calculate additional dynamic properties of the systems, such as diffusion coefficients, the motion of the metal clusters should be studied for much longer periods of time, which can be accomplished by performing classical molecular dynamics (MD) simulations. Thus, we have parametrized our electronic structure calculations to an analytical Lennard-Jones (LJ) potent... read less D. Tainoff, L. Bardotti, F. Tournus, G. Guiraud, O. Boisron, and P. Mélinon, “Self-Organization of Size-Selected Bare Platinum Nanoclusters: Toward Ultra-dense Catalytic Systems,” Journal of Physical Chemistry C. 2008. link Times cited: 27 Abstract: Novel applications in catalysis rely on the design of tailor… read more Abstract: Novel applications in catalysis rely on the design of tailored nanoarchitectures. In this field, we present a new physical route, based on ultrahigh vacuum deposition of size-selected preformed clusters, leading to self-organization of platinum nanoparticles on the surface. The resulting array of “model” nanoclusters (i.e., size-selected and ligand-free) may provide a unique tool for future experimental and theoretical studies. A detailed analysis of the experimental and physical origins of the spontaneous organization of platinum nanoclusters is provided and points out the extreme importance of cluster-cluster and cluster-surface interactions. read less J. Schall, G. Gao, and J. Harrison, “Elastic constants of silicon materials calculated as a function of temperature using a parametrization of the second-generation reactive empirical bond-order potential,” Physical Review B. 2008. link Times cited: 48 Abstract: A parametrization for silicon is presented that is based on … read more Abstract: A parametrization for silicon is presented that is based on the second-generation reactive empirical bondorder REBO formalism Brenner, Shenderova, Harrison, Stuart, Ni, and Sinnott J. Phys.: Condens. Matter 14, 783 2002 . Because it shares the same analytic form as Brenner’s second-generation REBO, this new potential is a step toward a single potential that can model many atom systems that contain C, Si, and H, where bond breaking and bond making are important. The widespread use of Brenner’s REBO potential, its ability to model both zero-Kelvin elastic constants of diamond and the temperature dependence of the elastic constants, and the existence of parameters for many atom types were the motivating factors for obtaining this parametrization for Si. While Si-C-H classical bond-order potentials do exist, they are based on Brenner’s original formalism. This new parametrization is validated by examining the structure and stability of a large number of crystalline silicon structures, by examining the relaxation energies of point defects, the energies of silicon surfaces, the effects of adatoms on surface energies, and the structures of both liquid silicon and amorphous silicon. Finally, the elastic constants of diamond-cubic and amorphous silicon between 0 and 1100 K are calculated with this new parametrization and compared to values calculated using a previously published potential. read less M. Müller, P. Erhart, and K. Albe, “Analytic bond-order potential for bcc and fcc iron—comparison with established embedded-atom method potentials,” Journal of Physics: Condensed Matter. 2007. link Times cited: 177 Abstract: A new analytic bond-order potential for iron is presented th… read more Abstract: A new analytic bond-order potential for iron is presented that has been fitted to experimental data and results from first-principles calculations. The angular-dependent functional form allows a proper description of a large variety of bulk, surface and defect properties, including the Bain path, phonon dispersions, defect diffusivities and defect formation energies. By calculating Gibbs free energies of body-centred cubic (bcc) and face-centred cubic (fcc) iron as a function of temperature, we show that this potential is able to reproduce the transitions from α-iron to γ-iron and δ-iron before the melting point. The results are compared to four widely used embedded-atom-method potentials for iron. read less C. Björkas and K. Nordlund, “Comparative study of cascade damage in Fe simulated with recent potentials,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2007. link Times cited: 102 P. Erhart, N. Juslin, O. Goy, K. Nordlund, R. Müller, and K. Albe, “Analytic bond-order potential for atomistic simulations of zinc oxide,” Journal of Physics: Condensed Matter. 2006. link Times cited: 75 Abstract: An interatomic potential for zinc oxide and its elemental co… read more Abstract: An interatomic potential for zinc oxide and its elemental constituents is derived based on an analytical bond-order formalism. The model potential provides a good description of the bulk properties of various solid structures of zinc oxide including cohesive energies, lattice parameters, and elastic constants. For the pure elements zinc and oxygen the energetics and structural parameters of a variety of bulk phases and in the case of oxygen also molecular structures are reproduced. The dependence of thermal and point defect properties on the cutoff parameters is discussed. As exemplary applications the irradiation of bulk zinc oxide and the elastic response of individual nanorods are studied. read less K. Nordlund, “Atomistic simulations of plasma–wall interactions in fusion reactors,” Physica Scripta. 2006. link Times cited: 6 Abstract: Atomistic computer simulations, especially molecular dynamic… read more Abstract: Atomistic computer simulations, especially molecular dynamics, but also kinetic Monte Carlo simulations and electronic structure calculations, have proven to be a valuable tool for studying radiation effects in fusion reactor materials. In this paper, I will first review a few cases where these methods have given additional insights into the interaction between a fusion plasma and the first wall of a reactor. Then I will, in the spirit of the workshop theme of ‘new directions in plasma–wall interactions’ discuss some possible future avenues of research. read less N. Juslin et al., “Analytical interatomic potential for modeling nonequilibrium processes in the W–C–H system,” Journal of Applied Physics. 2005. link Times cited: 264 Abstract: A reactive interatomic potential based on an analytical bond… read more Abstract: A reactive interatomic potential based on an analytical bond-order scheme is developed for the ternary system W–C–H. The model combines Brenner’s hydrocarbon potential with parameter sets for W–W, W–C, and W–H interactions and is adjusted to materials properties of reference structures with different local atomic coordinations including tungsten carbide, W–H molecules, as well as H dissolved in bulk W. The potential has been tested in various scenarios, such as surface, defect, and melting properties, none of which were considered in the fitting. The intended area of application is simulations of hydrogen and hydrocarbon interactions with tungsten, which have a crucial role in fusion reactor plasma-wall interactions. Furthermore, this study shows that the angular-dependent bond-order scheme can be extended to second nearest-neighbor interactions, which are relevant in body-centered-cubic metals. Moreover, it provides a possibly general route for modeling metal carbides. © 2005 American Institute of Physics. DOI: 10.1063/1.2149492 read less J. Samela, J. Kotakoski, K. Nordlund, and J. Keinonen, “A quantitative and comparative study of sputtering yields in Au,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2005. link Times cited: 56 J. Chen and K. Y. Chan, “Size-dependent mobility of platinum cluster on a graphite surface,” Molecular Simulation. 2005. link Times cited: 24 Abstract: Molecular dynamics simulations of platinum (Pt) clusters on … read more Abstract: Molecular dynamics simulations of platinum (Pt) clusters on a graphite surface were performed to study their diffusion and aggregation. The Sutton-Chen many-body potential was used for the Pt–Pt interaction, whereas, a Steele potential was used to calculate the interaction between Pt atoms and carbon (C) atoms of graphite. The results show that at room temperature, the Pt clusters with less than 40 atoms are very mobile with a two-dimensional diffusion coefficient higher than 10−11m2 s−1, but decreasing rapidly with size. The diffusion coefficient of larger cluster has variable size-dependence with local minima at cluster sizes of 50 and 300 Pt atoms and a local maximum at cluster size of 100 atoms. In additional to the overall size of the Pt cluster or nanoparticle, the mismatch between the bottom layer of Pt and graphite also affected the overall Pt–graphite affinity and hence the Pt cluster mobility. The presence of a neighboring Pt cluster can greatly affect mobility. The aggregation of two 50-atom clusters to form a single cluster was observed with the simulation. The relatively stable short dumbbell-like structure of the new cluster resembles previous experimentally observed network of connected Pt nanoparticles on graphite. read less P. Erhart and K. Albe, “Analytical potential for atomistic simulations of silicon, carbon, and silicon carbide,” Physical Review B. 2005. link Times cited: 462 Abstract: We present an analytical bond-order potential for silicon, c… read more Abstract: We present an analytical bond-order potential for silicon, carbon, and silicon carbide that has been optimized by a systematic fitting scheme. The functional form is adopted from a preceding work {\}Phys. Rev. B 65, 195124 (2002) and is built on three independently fitted potentials for Si-Si, C-C, and Si-C interaction. For elemental silicon and carbon, the potential perfectly reproduces elastic properties and agrees very well with first-principles results for high-pressure phases. The formation enthalpies of point defects are reasonably reproduced. In the case of silicon stuctural features of the melt agree nicely with data taken from literature. For silicon carbide the dimer as well as the solid phases B1, B2, and B3 were considered. Again, elastic properties are very well reproduced including internal relaxations under shear. Comparison with first-principles data on point defect formation enthalpies shows fair agreement. The successful validation of the potentials for configurations ranging from the molecular to the bulk regime indicates the transferability of the potential model and makes it a good choice for atomistic simulations that sample a large configuration space. read less J. Kang and H. Hwang, “Molecular Dynamics Simulations of Single-wall GaN Nanotubes,” Molecular Simulation. 2004. link Times cited: 16 Abstract: We have investigated the structural properties and the therm… read more Abstract: We have investigated the structural properties and the thermal behavior of single-wall GaN nanotubes using atomistic simulations based on the Tersoff-type potential. The Tersoff potential for GaN has effectively described the properties of GaN nanotubes. The caloric curves of single-wall GaN nanotubes were divided into three regions corresponding to nanotube, disintegrating range and vapor. Since the stability or the stiffness of the tube decreased with increasing curving strain energy of sheet-to-tube, the disintegration temperatures of GaN nanotubes were closely related to the curving strain energy of sheet-to-tube. read less N. Ramanan, S. Roy, D. Lahiri, S. M. Sharma, and B. N. Dev, “Ascertaining the nanocluster formation within an ion-irradiated Pt/Ni/C multi-trilayer with X-ray absorption spectroscopy.,” Journal of synchrotron radiation. 2013. link Times cited: 0 Abstract: In this work nanoclusters formed in a Pt/Ni/C multi-trilayer… read more Abstract: In this work nanoclusters formed in a Pt/Ni/C multi-trilayer by the ion-irradiated method of synthesis are characterized. In particular, an attempt to understand the role of interfaces in the synthesis is made. With this objective, ion-irradiation-induced structural changes in a Pt/Ni/C multi-trilayer using X-ray absorption spectroscopy (at the Ni K-edge) in conjunction with the X-ray standing-wave technique are investigated. The XANES analysis identifies chemical binding at pristine Ni/C and Ni/Pt interfaces, in contrast with physical adsorption at the Pt/C interface. The chemical nature of the interfaces determines their relative stability with respect to irradiation and controls the extent of metallic diffusion. The most interesting structural change, upon irradiation, is the disruption of the Pt/C interface and subsequent migration of Pt atoms towards pre-diffused Ni atoms within the C layer, leading to the formation of Ni-centered Ni-Pt bimetallic nanoclusters (with Ni:Pt = 60:40). These clusters are highly disordered beyond their nearest neighbor and find wide-scale applications as, for example, magnetic devices etc. The implications of these findings on the design goals are discussed. read less H. Xie, X. Song, F. Yin, and Y. Zhang, “Effect of WC/Co coherency phase boundaries on Fracture toughness of the nanocrystalline cemented carbides,” Scientific Reports. 2016. link Times cited: 30 P. Brault and E. Neyts, “Molecular dynamics simulations of supported metal nanocatalyst formation by plasma sputtering,” Catalysis Today. 2015. link Times cited: 26 A. Krause, W. Weber, D. Pohl, B. Rellinghaus, M. Verheijen, and T. Mikolajick, “Investigation of embedded perovskite nanoparticles for enhanced capacitor permittivities.,” ACS applied materials & interfaces. 2014. link Times cited: 3 Abstract: Growth experiments show significant differences in the cryst… read more Abstract: Growth experiments show significant differences in the crystallization of ultrathin CaTiO3 layers on polycrystalline Pt surfaces. While the deposition of ultrathin layers below crystallization temperature inhibits the full layer crystallization, local epitaxial growth of CaTiO3 crystals on top of specific oriented Pt crystals occurs. The result is a formation of crystals embedded in an amorphous matrix. An epitaxial alignment of the cubic CaTiO3 ⟨111⟩ direction on top of the underlying Pt {111} surface has been observed. A reduced forming energy is attributed to an interplay of surface energies at the {111} interface of both materials and CaTiO3 nanocrystallites facets. The preferential texturing of CaTiO3 layers on top of Pt has been used in the preparation of ultrathin metal-insulator-metal capacitors with 5-30 nm oxide thickness. The effective CaTiO3 permittivity in the capacitor stack increases to 55 compared to capacitors with amorphous layers and a permittivity of 28. The isolated CaTiO3 crystals exhibit a passivation of the CaTiO3 grain surfaces by the surrounding amorphous matrix, which keeps the capacitor leakage current at ideally low values comparable for those of amorphous thin film capacitors. read less S. Norris, J. Samela, M. Vestberg, K. Nordlund, and M. Aziz, “Crater functions for compound materials: A route to parameter estimation in coupled-PDE models of ion bombardment,” Nuclear Instruments & Methods in Physics Research Section B-beam Interactions With Materials and Atoms. 2013. link Times cited: 17
Funding	Not available

Short KIM ID The unique KIM identifier code.	MO_500121566391_004
Extended KIM ID The long form of the KIM ID including a human readable prefix (100 characters max), two underscores, and the Short KIM ID. Extended KIM IDs can only contain alpha-numeric characters (letters and digits) and underscores and must begin with a letter.	Tersoff_LAMMPS_AlbeNordlundAverback_2002_PtC__MO_500121566391_004
DOI	10.25950/78d69967 https://doi.org/10.25950/78d69967 https://commons.datacite.org/doi.org/10.25950/78d69967
KIM Item Type Specifies whether this is a Portable Model (software implementation of an interatomic model); Portable Model with parameter file (parameter file to be read in by a Model Driver); Model Driver (software implementation of an interatomic model that reads in parameters).	Portable Model using Model Driver Tersoff_LAMMPS__MD_077075034781_005
Driver	Tersoff_LAMMPS__MD_077075034781_005
KIM API Version	2.2
Potential Type	tersoff

Previous Version	Tersoff_LAMMPS_AlbeNordlundAverback_2002_PtC__MO_500121566391_003

Verification Check Dashboard

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Grade	Name	Category	Brief Description	Full Results	Aux File(s)
P All elements claimed by model are supported in at least one of the tested configurations.	vc-species-supported-as-stated	mandatory	The model supports all species it claims to support; see full description.	Results	Files
P Periodic boundary conditions were correctly supported for all configurations that the model was able to compute.	vc-periodicity-support	mandatory	Periodic boundary conditions are handled correctly; see full description.	Results	Files
P Model energy has permutation symmetry for all configurations the model was able to compute.	vc-permutation-symmetry	mandatory	Total energy and forces are unchanged when swapping atoms of the same species; see full description.	Results	Files
A The letter grade A was assigned because the normalized error in the computation was 4.40264e-10 compared with a machine precision of 2.22045e-16. The letter grade was based on 'score=log10(error/eps)', with ranges A=[0, 7.5], B=(7.5, 10.0], C=(10.0, 12.5], D=(12.5, 15.0), F>15.0. 'A' is the best grade, and 'F' indicates failure.	vc-forces-numerical-derivative	consistency	Forces computed by the model agree with numerical derivatives of the energy; see full description.	Results	Files
P The model is C^1 continuous. This means that the model has continuous energy and continuous first derivative.	vc-dimer-continuity-c1	informational	The energy versus separation relation of a pair of atoms is C1 continuous (i.e. the function and its first derivative are continuous); see full description.	Results	Files
P Model energy and forces are invariant with respect to rigid-body motion (translation and rotation) for all configurations the model was able to compute.	vc-objectivity	informational	Total energy is unchanged and forces transform correctly under rigid-body translation and rotation; see full description.	Results	Files
P Model energy has inversion symmetry for all configurations the model was able to compute.	vc-inversion-symmetry	informational	Total energy is unchanged and forces change sign when inverting a configuration through the origin; see full description.	Results	Files
P No memory leak detected.	vc-memory-leak	informational	The model code does not have memory leaks (i.e. it releases all allocated memory at the end); see full description.	Results	Files
P All threads give identical results for tested case. Model appears to be thread-safe.	vc-thread-safe	mandatory	The model returns the same energy and forces when computed in serial and when using parallel threads for a set of configurations. Note that this is not a guarantee of thread safety; see full description.	Results	Files
N/A Unable to perform verification check due to an error.	vc-unit-conversion	mandatory	The model is able to correctly convert its energy and/or forces to different unit sets; see full description.	Results	Files

This bar chart plot shows the mono-atomic body-centered cubic (bcc) lattice constant predicted by the current model (shown in the unique color) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: Pt

Species: C

Cohesive Energy Graph

This graph shows the cohesive energy versus volume-per-atom for the current mode for four mono-atomic cubic phases (body-centered cubic (bcc), face-centered cubic (fcc), simple cubic (sc), and diamond). The curve with the lowest minimum is the ground state of the crystal if stable. (The crystal structure is enforced in these calculations, so the phase may not be stable.) Graphs are generated for each species supported by the model.

Species: Pt

Species: C

Diamond Lattice Constant

This bar chart plot shows the mono-atomic face-centered diamond lattice constant predicted by the current model (shown in the unique color) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: Pt

Species: C

Dislocation Core Energies

This graph shows the dislocation core energy of a cubic crystal at zero temperature and pressure for a specific set of dislocation core cutoff radii. After obtaining the total energy of the system from conjugate gradient minimizations, non-singular, isotropic and anisotropic elasticity are applied to obtain the dislocation core energy for each of these supercells with different dipole distances. Graphs are generated for each species supported by the model.

(No matching species)

FCC Elastic Constants

This bar chart plot shows the mono-atomic face-centered cubic (fcc) elastic constants predicted by the current model (shown in blue) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: C

Species: Pt

FCC Lattice Constant

This bar chart plot shows the mono-atomic face-centered cubic (fcc) lattice constant predicted by the current model (shown in red) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: C

Species: Pt

FCC Stacking Fault Energies

This bar chart plot shows the intrinsic and extrinsic stacking fault energies as well as the unstable stacking and unstable twinning energies for face-centered cubic (fcc) predicted by the current model (shown in blue) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: Pt

FCC Surface Energies

This bar chart plot shows the mono-atomic face-centered cubic (fcc) relaxed surface energies predicted by the current model (shown in blue) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: Pt

SC Lattice Constant

This bar chart plot shows the mono-atomic simple cubic (sc) lattice constant predicted by the current model (shown in the unique color) compared with the predictions for all other models in the OpenKIM Repository that support the species. The vertical bars show the average and standard deviation (one sigma) bounds for all model predictions. Graphs are generated for each species supported by the model.

Species: Pt

Species: C

Cubic Crystal Basic Properties Table

Species: C

Species: Pt

Tests

CohesiveEnergyVsLatticeConstant__TD_554653289799_003

Cohesive energy versus lattice constant curve for monoatomic cubic lattices v003

Creators:
Contributor: karls
Publication Year: 2019
DOI: https://doi.org/10.25950/64cb38c5

This Test Driver uses LAMMPS to compute the cohesive energy of a given monoatomic cubic lattice (fcc, bcc, sc, or diamond) at a variety of lattice spacings. The lattice spacings range from a_min (=a_min_frac*a_0) to a_max (=a_max_frac*a_0) where a_0, a_min_frac, and a_max_frac are read from stdin (a_0 is typically approximately equal to the equilibrium lattice constant). The precise scaling and number of lattice spacings sampled between a_min and a_0 (a_0 and a_max) is specified by two additional parameters passed from stdin: N_lower and samplespacing_lower (N_upper and samplespacing_upper). Please see README.txt for further details.

Test	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Cohesive energy versus lattice constant curve for bcc C v004	view	2894
Cohesive energy versus lattice constant curve for bcc Pt v004	view	2447
Cohesive energy versus lattice constant curve for diamond C v004	view	3203
Cohesive energy versus lattice constant curve for diamond Pt v004	view	2429
Cohesive energy versus lattice constant curve for fcc C v004	view	3387
Cohesive energy versus lattice constant curve for fcc Pt v004	view	2503
Cohesive energy versus lattice constant curve for sc C v004	view	2884
Cohesive energy versus lattice constant curve for sc Pt v004	view	2288

ElasticConstantsCubic__TD_011862047401_006

Elastic constants for cubic crystals at zero temperature and pressure v006

Creators: Junhao Li and Ellad Tadmor
Contributor: tadmor
Publication Year: 2019
DOI: https://doi.org/10.25950/5853fb8f

Computes the cubic elastic constants for some common crystal types (fcc, bcc, sc, diamond) by calculating the hessian of the energy density with respect to strain. An estimate of the error associated with the numerical differentiation performed is reported.

Test	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Elastic constants for bcc C at zero temperature v006	view	10861
Elastic constants for bcc Pt at zero temperature v006	view	21692
Elastic constants for diamond C at zero temperature v001	view	28704
Elastic constants for diamond Pt at zero temperature v001	view	26844
Elastic constants for fcc C at zero temperature v006	view	13716
Elastic constants for fcc Pt at zero temperature v006	view	5591
Elastic constants for sc C at zero temperature v006	view	5479
Elastic constants for sc Pt at zero temperature v006	view	5628

EquilibriumCrystalStructure__TD_457028483760_002

Equilibrium structure and energy for a crystal structure at zero temperature and pressure v002

Creators:
Contributor: ilia
Publication Year: 2024
DOI: https://doi.org/10.25950/2f2c4ad3

Computes the equilibrium crystal structure and energy for an arbitrary crystal at zero temperature and applied stress by performing symmetry-constrained relaxation. The crystal structure is specified using the AFLOW prototype designation. Multiple sets of free parameters corresponding to the crystal prototype may be specified as initial guesses for structure optimization. No guarantee is made regarding the stability of computed equilibria, nor that any are the ground state.

Test	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hR10_166_5c v002	view	114038
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hR14_166_7c v002	view	121400
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hR2_166_c v002	view	66774
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hR4_166_2c v002	view	37975
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hR60_166_2h4i v002	view	177662
Equilibrium crystal structure and energy for CPt in AFLOW crystal prototype AB_cF8_216_a_c v002	view	109474
Equilibrium crystal structure and energy for CPt in AFLOW crystal prototype AB_cF8_225_a_b v002	view	98872
Equilibrium crystal structure and energy for CPt in AFLOW crystal prototype AB_cP2_221_a_b v002	view	58998
Equilibrium crystal structure and energy for CPt in AFLOW crystal prototype AB_hP2_187_a_d v002	view	80099

EquilibriumCrystalStructure__TD_457028483760_003

Equilibrium structure and energy for a crystal structure at zero temperature and pressure v003

Creators:
Contributor: ilia
Publication Year: 2025
DOI: https://doi.org/10.25950/866c7cfa

Computes the equilibrium crystal structure and energy for an arbitrary crystal at zero temperature and applied stress by performing symmetry-constrained relaxation. The crystal structure is specified using the AFLOW prototype designation. Multiple sets of free parameters corresponding to the crystal prototype may be specified as initial guesses for structure optimization. No guarantee is made regarding the stability of computed equilibria, nor that any are the ground state.

Test	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_cF16_227_c v003	view	402170
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_cF240_202_h2i v003	view	8903400
Equilibrium crystal structure and energy for Pt in AFLOW crystal prototype A_cF4_225_a v003	view	141145
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_cF8_227_a v003	view	384064
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_cI16_206_c v003	view	183921
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_cI16_229_f v003	view	195951
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_cI8_214_a v003	view	196200
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_cP1_221_a v003	view	146189
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_cP20_221_gj v003	view	338433
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hP12_194_bc2f v003	view	621028
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hP12_194_e2f v003	view	258000
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hP16_194_e3f v003	view	586273
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hP2_191_c v003	view	281280
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hP4_194_bc v003	view	152082
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hP4_194_f v003	view	166057
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hP8_194_ef v003	view	181733
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_mC16_12_4i v003	view	350820
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_oC16_65_mn v003	view	483832
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_oC16_65_pq v003	view	233075
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_oC8_65_gh v003	view	218311
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_oC8_67_m v003	view	142239
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_oI120_71_lmn6o v003	view	2885640
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_oP16_62_4c v003	view	278099
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_tI8_139_h v003	view	215220

GrainBoundaryCubicCrystalSymmetricTiltRelaxedEnergyVsAngle__TD_410381120771_003

Relaxed energy as a function of tilt angle for a symmetric tilt grain boundary within a cubic crystal v003

Creators:
Contributor: brunnels
Publication Year: 2022
DOI: https://doi.org/10.25950/2c59c9d6

Computes grain boundary energy for a range of tilt angles given a crystal structure, tilt axis, and material.

Test	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Relaxed energy as a function of tilt angle for a 100 symmetric tilt grain boundary in fcc Pt v000	view	39625572
Relaxed energy as a function of tilt angle for a 110 symmetric tilt grain boundary in fcc Pt v000	view	125223023
Relaxed energy as a function of tilt angle for a 111 symmetric tilt grain boundary in fcc Pt v000	view	51955827

LatticeConstant2DHexagonalEnergy__TD_034540307932_002

Cohesive energy and equilibrium lattice constant of hexagonal 2D crystalline layers v002

Creators: Ilia Nikiforov
Contributor: ilia
Publication Year: 2019
DOI: https://doi.org/10.25950/dd36239b

Given atomic species and structure type (graphene-like, 2H, or 1T) of a 2D hexagonal monolayer crystal, as well as an initial guess at the lattice spacing, this Test Driver calculates the equilibrium lattice spacing and cohesive energy using Polak-Ribiere conjugate gradient minimization in LAMMPS

Test	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Cohesive energy and equilibrium lattice constant of graphene v002		view	596

LatticeConstantCubicEnergy__TD_475411767977_007

Equilibrium lattice constant and cohesive energy of a cubic lattice at zero temperature and pressure v007

Creators: Daniel S. Karls and Junhao Li
Contributor: karls
Publication Year: 2019
DOI: https://doi.org/10.25950/2765e3bf

Equilibrium lattice constant and cohesive energy of a cubic lattice at zero temperature and pressure.

Test	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Equilibrium zero-temperature lattice constant for bcc C v007	view	4100
Equilibrium zero-temperature lattice constant for bcc Pt v007	view	6922
Equilibrium zero-temperature lattice constant for diamond C v007	view	9528
Equilibrium zero-temperature lattice constant for diamond Pt v007	view	9140
Equilibrium zero-temperature lattice constant for fcc C v007	view	4212
Equilibrium zero-temperature lattice constant for fcc Pt v007	view	8733
Equilibrium zero-temperature lattice constant for sc C v007	view	9349
Equilibrium zero-temperature lattice constant for sc Pt v007	view	6435

LatticeConstantHexagonalEnergy__TD_942334626465_005

Equilibrium lattice constants for hexagonal bulk structures at zero temperature and pressure v005

Creators: Daniel S. Karls and Junhao Li
Contributor: karls
Publication Year: 2019
DOI: https://doi.org/10.25950/c339ca32

Calculates lattice constant of hexagonal bulk structures at zero temperature and pressure by using simplex minimization to minimize the potential energy.

Test	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Equilibrium lattice constants for hcp Pt v005		view	27656

LinearThermalExpansionCoeffCubic__TD_522633393614_002

Linear thermal expansion coefficient of cubic crystal structures v002

Creators:
Contributor: mjwen
Publication Year: 2024
DOI: https://doi.org/10.25950/9d9822ec

This Test Driver uses LAMMPS to compute the linear thermal expansion coefficient at a finite temperature under a given pressure for a cubic lattice (fcc, bcc, sc, diamond) of a single given species.

Test	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Linear thermal expansion coefficient of diamond C at 293.15 K under a pressure of 0 MPa v002		view	5079299
Linear thermal expansion coefficient of fcc Pt at 293.15 K under a pressure of 0 MPa v002		view	4459176

PhononDispersionCurve__TD_530195868545_004

Phonon dispersion relations for an fcc lattice v004

Creators: Matt Bierbaum
Contributor: mattbierbaum
Publication Year: 2019
DOI: https://doi.org/10.25950/64f4999b

Calculates the phonon dispersion relations for fcc lattices and records the results as curves.

Test	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Phonon dispersion relations for fcc Pt v004		view	127069

StackingFaultFccCrystal__TD_228501831190_002

Stacking and twinning fault energies of an fcc lattice at zero temperature and pressure v002

Creators:
Contributor: SubrahmanyamPattamatta
Publication Year: 2019
DOI: https://doi.org/10.25950/b4cfaf9a

Intrinsic and extrinsic stacking fault energies, unstable stacking fault energy, unstable twinning energy, stacking fault energy as a function of fractional displacement, and gamma surface for a monoatomic FCC lattice at zero temperature and pressure.

Test	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Stacking and twinning fault energies for fcc Pt v002		view	69510454

SurfaceEnergyCubicCrystalBrokenBondFit__TD_955413365818_004

High-symmetry surface energies in cubic lattices and broken bond model v004

Creators: Matt Bierbaum
Contributor: mattbierbaum
Publication Year: 2019
DOI: https://doi.org/10.25950/6c43a4e6

Calculates the surface energy of several high symmetry surfaces and produces a broken-bond model fit. In latex form, the fit equations are given by:

E_{FCC} (\vec{n}) = p_1 (4 \left( |x+y| + |x-y| + |x+z| + |x-z| + |z+y| +|z-y|\right)) + p_2 (8 \left( |x| + |y| + |z|\right)) + p_3 (2 ( |x+ 2y + z| + |x+2y-z| + |x-2y + z| + |x-2y-z| + |2x+y+z| + |2x+y-z| +|2x-y+z| +|2x-y-z| +|x+y+2z| +|x+y-2z| +|x-y+2z| +|x-y-2z| ) + c

E_{BCC} (\vec{n}) = p_1 (6 \left( | x+y+z| + |x+y-z| + |-x+y-z| + |x-y+z| \right)) + p_2 (8 \left( |x| + |y| + |z|\right)) + p_3 (4 \left( |x+y| + |x-y| + |x+z| + |x-z| + |z+y| +|z-y|\right)) +c.

In Python, these two fits take the following form:

def BrokenBondFCC(params, index):

import numpy
x, y, z = index
x = x / numpy.sqrt(x**2.+y**2.+z**2.)
y = y / numpy.sqrt(x**2.+y**2.+z**2.)
z = z / numpy.sqrt(x**2.+y**2.+z**2.)

return params[0]*4* (abs(x+y) + abs(x-y) + abs(x+z) + abs(x-z) + abs(z+y) + abs(z-y)) + params[1]*8*(abs(x) + abs(y) + abs(z)) + params[2]*(abs(x+2*y+z) + abs(x+2*y-z) +abs(x-2*y+z) +abs(x-2*y-z) + abs(2*x+y+z) +abs(2*x+y-z) +abs(2*x-y+z) +abs(2*x-y-z) + abs(x+y+2*z) +abs(x+y-2*z) +abs(x-y+2*z) +abs(x-y-2*z))+params[3]

def BrokenBondBCC(params, x, y, z):

import numpy
x, y, z = index
x = x / numpy.sqrt(x**2.+y**2.+z**2.)
y = y / numpy.sqrt(x**2.+y**2.+z**2.)
z = z / numpy.sqrt(x**2.+y**2.+z**2.)

return params[0]*6*(abs(x+y+z) + abs(x-y-z) + abs(x-y+z) + abs(x+y-z)) + params[1]*8*(abs(x) + abs(y) + abs(z)) + params[2]*4* (abs(x+y) + abs(x-y) + abs(x+z) + abs(x-z) + abs(z+y) + abs(z-y)) + params[3]

Test	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Broken-bond fit of high-symmetry surface energies in fcc Pt v004		view	269775

VacancyFormationEnergyRelaxationVolume__TD_647413317626_001

Monovacancy formation energy and relaxation volume for cubic and hcp monoatomic crystals v001

Creators:
Contributor: efuem
Publication Year: 2023
DOI: https://doi.org/10.25950/fca89cea

Computes the monovacancy formation energy and relaxation volume for cubic and hcp monoatomic crystals.

Test	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Monovacancy formation energy and relaxation volume for fcc Pt		view	607075

VacancyFormationMigration__TD_554849987965_001

Vacancy formation and migration energies for cubic and hcp monoatomic crystals v001

Creators:
Contributor: efuem
Publication Year: 2023
DOI: https://doi.org/10.25950/c27ba3cd

Computes the monovacancy formation and migration energies for cubic and hcp monoatomic crystals.

Test	Test Results	Link to Test Results page	Benchmark time Usertime multiplied by the Whetstone Benchmark. This number can be used (approximately) to compare the performance of different models independently of the architecture on which the test was run. Measured in Millions of Whetstone Instructions (MWI)
Vacancy formation and migration energy for fcc Pt		view	5614962

Errors

DislocationCoreEnergyCubic__TD_452950666597_002

Test	Error Categories	Link to Error page
Dislocation core energy for fcc Pt computed at zero temperature for a set of dislocation core cutoff radii with burgers vector [0.5, 0.5, 0] along line direction [1, 1, 0] v000	other	view

ElasticConstantsHexagonal__TD_612503193866_004

Test	Error Categories	Link to Error page
Elastic constants for hcp Pt at zero temperature v004	other	view

EquilibriumCrystalStructure__TD_457028483760_000

Test	Error Categories	Link to Error page
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hP12_194_bc2f v000	other	view
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hR14_166_7c v000	other	view
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hR2_166_c v000	other	view
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_hR4_166_2c v000	other	view
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_oC16_65_mn v000	other	view
Equilibrium crystal structure and energy for C in AFLOW crystal prototype A_oC8_65_gh v000	other	view

LatticeConstantHexagonalEnergy__TD_942334626465_005

Test	Error Categories	Link to Error page
Equilibrium lattice constants for hcp C v005	other	view

PhononDispersionCurve__TD_530195868545_004

Test	Error Categories	Link to Error page
Phonon dispersion relations for fcc Pt v004	other	view

No Driver

Verification Check	Error Categories	Link to Error page
PeriodicitySupport__VC_895061507745_004	other	view

Files

CMakeLists.txt
LICENSE
Tersoff_AlbeNordlundAverback_2002_PtC.params
Tersoff_AlbeNordlundAverback_2002_PtC.settings
kimprovenance.edn
kimspec.edn

Download

Tersoff_LAMMPS_AlbeNordlundAverback_2002_PtC__MO_500121566391_004.txz	Tar+XZ	Linux and OS X archive
Tersoff_LAMMPS_AlbeNordlundAverback_2002_PtC__MO_500121566391_004.zip	Zip	Windows archive

Download Dependency

This Model requires a Model Driver. Archives for the Model Driver Tersoff_LAMMPS__MD_077075034781_005 appear below.

Tersoff_LAMMPS__MD_077075034781_005.txz	Tar+XZ	Linux and OS X archive
Tersoff_LAMMPS__MD_077075034781_005.zip	Zip	Windows archive

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Tersoff_LAMMPS_AlbeNordlundAverback_2002_PtC__MO_500121566391_004

Verification Check Dashboard

Visualizers (in-page)

BCC Lattice Constant

Cohesive Energy Graph

Diamond Lattice Constant

Dislocation Core Energies

FCC Elastic Constants

FCC Lattice Constant

FCC Stacking Fault Energies

FCC Surface Energies

SC Lattice Constant

Cubic Crystal Basic Properties Table

Tests

Errors

Files

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