Steven D. Kenny

Improved grid‐based algorithm for Bader charge allocation

An improvement to the grid‐based algorithm of Henkelman et al. for the calculation of Bader volumes is suggested, which more accurately calculates atomic properties as predicted by the theory of Atoms in Molecules. The CPU time required by the improved algorithm to perform the Bader analysis scales linearly with the number of interatomic surfaces in the system. The new algorithm corrects systematic deviations from the true Bader surface, calculated by the original method and also does not require explicit representation of the interatomic surfaces, resulting in a more robust method of partitioning charge density among atoms in the system. Applications of the method to some small systems are given and it is further demonstrated how the method can be used to define an energy per atom in ab initio calculations.

Molecular dynamic simulations of nanoscratching of silver (100)

The nanometric scale ploughing friction and wear behaviour of a pyramidal diamond indenter sliding against a face-centred cubic silver (100) surface is investigated by means of parallel molecular dynamic (MD) simulations of nanoindentation followed by nanoscratching. The relationship between the friction coefficient, the hardness and the indenter orientation is studied. The simulations were performed using three different indenter orientations. For each orientation, simulations were performed at an indentation depth of 5 and 10??, and a scratching length of 210??. In order to study the behaviour of the friction coefficient and the hardness as a function of depth we performed the simulations for one of the orientations at depths of 5, 10 and 30??. The simulations show that the friction coefficient is dependent on both the orientation of the indenter and the indentation depth. The results also show that the friction coefficient increases as the depth increases, whereas the contact pressure decreases and the scratch hardness decreases slightly. With a shallow indent of 5??, no sub-surface defects were observed beneath the scratch groove, but with the deeper indents of 10 and 30???dislocations in the {111} planes are observed beneath the scratch groove. These dislocations propagate in the direction; each dislocation consists of the intersection of stacking faults on two {111} planes and each stacking fault is bounded by two Shockley partial dislocations.

Atomistic modelling of ploughing friction in silver, iron and silicon

Molecular dynamics (MD) simulations of atomic-scale stick–slip have been performed for a diamond tip in contact with the (100) surface of fcc Ag, bcc Fe, Si and H-terminated Si, at a temperature of 300 K. Simulations were carried out at different support displacements between 5 and 15 A. The simulations illustrate the important mechanisms that take place during stick–slip. In particular, for the case of the metals they show a direct link between tip slip events and the emission of dislocations from the point of contact of the tip with the substrate. This occurs both during indentation and scratching. For the case of silicon, no slip events were observed and no subsurface dislocations were generated underneath the scratch groove. At the deeper support displacement of 15 A the silicon atoms undergo some local phase transformations and the atom coordination number varies between 5 and 8, with the majority being five-fold or six-fold coordinated. Both the dynamic and the static friction coefficients were found to be higher for Si compared to the corresponding values for H-terminated Si. Comparisons were made between the MD simulations and experimental measurements for indentation on the (100) surface of Si and Al. A good qualitative agreement was observed between the experimental and theoretical results. However, in both the cases of Si and metals the MD simulations give a contact pressure under load that is depth dependent and values that are higher than experimental nanohardness values.

The bonding sites and structure of C60 on the Si(100) surface

The possible structures of C60 on the Si(1 0 0) surface have been investigated using ab initio total energy minimisations. The results show that fullerenes bond to the silicon surface by breaking carbon–carbon double bonds. One electron from the broken bond is contributed to the carbon–silicon bond. The second electron is generally involved in forming a new π-bond within the fullerene cage, or, for the less energetically favourable structures, is delocalised over the surrounding bonds. The carbon–silicon bond formed is primarily covalent with some charge transfer.

Atomistic surface erosion and thin film growth modelled over realistic time scales

We present results of atomistic modelling of surface growth and sputtering using a multi-time scale molecular dynamics-on-the-fly kinetic Monte Carlo scheme which allows simulations to be carried out over realistic experimental times. The method uses molecular dynamics to model the fast processes and then calculates the diffusion barriers for the slow processes on-the-fly, without any preconceptions about what transitions might occur. The method is applied to the growth of metal and oxide materials at impact energies typical for both vapour deposition and magnetron sputtering. The method can be used to explain growth processes, such as the filling of vacancies and the formation of stacking faults. By tuning the variable experimental parameters on the computer, a parameter set for optimum crystalline growth can be determined. The method can also be used to model sputtering where the particle interactions with the surface occur at a higher energy. It is shown how a steady state can arise in which interstitial clusters are continuously being formed below the surface during an atom impact event which also recombine or diffuse to the surface between impact events. For fcc metals the near surface region remains basically crystalline during the erosion process with a pitted topography which soon attains a steady state roughness.

The structure of C60 and endohedral C60 on the Si{100} surface

The possible structures of C60 on the Si{1 0 0} surface in the four dimer position over the dimer trench have been investigated using ab initio total energy minimisations. Four possible structures have been found. The fullerenes bond to the silicon surface by breaking carbon–carbon double bonds. One electron from the broken bond is contributed to the carbon–silicon bond. The second electron is involved in forming a new π-bond within the fullerene cage. The carbon–silicon bond is primarily covalent with some charge transfer. Some discussion of endohedral fullerenes is also given.

Silicon potentials investigated using density functional theory fitted neural networks

We present a method for fitting neural networks to geometric and energetic data sets. We then apply this method by fitting a neural network to a set of data generated using the local density approximation for systems composed entirely of silicon. In order to generate atomic potential energy data, we use the Bader analysis scheme to partition the total system energy among the constituent atoms. We then demonstrate the transferability of the neural network potential by fitting to various bulk, surface, and cluster systems.

Density functional study of a typical thiol tethered on a gold surface : ruptures under normal or parallel stretch

The mechanical and dynamical properties of a model Au(111)/thiol surface system were investigated by using localized atomic-type orbital density functional theory in the local density approximation. Relaxing the system gives a configuration where the sulfur atom forms covalent bonds to two adjacent gold atoms as the lowest energy structure. Investigations based on ab initio molecular dynamics simulations at 300, 350 and 370 K show that this tethering system is stable. The rupture behaviour between the thiol and the surface was studied by displacing the free end of the thiol. Calculated energy profiles show a process of multiple successive ruptures that account for experimental observations. The process features successive ruptures of the two Au–S bonds followed by the extraction of one S-bonded Au atom from the surface. The force required to rupture the thiol from the surface was found to be dependent on the direction in which the thiol was displaced, with values comparable with AFM measurements. These results aid the understanding of failure dynamics of Au(111)-thiol-tethered biosurfaces in microfluidic devices where fluidic shear and normal forces are of concern.

Molecular dynamics simulations of nanoindentation and nanotribology

We present results of parallel molecular dynamics simulations of nanoindentation and nanotribology experiments. The models we have developed describe both the sample and the indenter atomistically and model the effect of the cantilevers in an atomic force microscope through the use of springs. We show that the simulations are in good qualitative agreement with experiment and help to elucidate many of the mechanisms that take place during these processes. In particular, we illustrate the role that dislocations play both in nanoindentation and also in stick–slip. Further to this we show how real-time visualization and computational steering have been employed in these simulations to capture the dynamical events that take place.

Modelling the growth of ZnO thin films by PVD methods and the effects of post-annealing

Results are presented for modelling of the evaporation and magnetron sputter deposition of Zn(x)O(y) onto an O-terminated ZnO (0001¯) wurtzite surface. Growth was simulated through a combination of molecular dynamics (MD) and an on-the-fly kinetic Monte Carlo (otf-KMC) method, which finds diffusion pathways and barriers without prior knowledge of transitions. We examine the effects of varying experimental parameters, such as substrate bias, distribution of the deposition species and annealing temperature. It was found when comparing evaporation and sputtering growth that the latter process results in a denser and more crystalline structure, due to the higher deposition energy of the arriving species. The evaporation growth also exhibits more stacking faults than the sputtered growth. Post-annealing at 770 K did not allow complete recrystallization, resulting in films which still had stacking faults where monolayers formed in the zinc blende phase, whereas annealing at 920 K enabled the complete recrystallization of some films to the wurtzite structure. At the latter temperature atoms could also sometimes be locked in the zinc blende phase after annealing. When full recrystallization did not take place, both wurtzite and zinc blende phases were seen in the same layer, resulting in a phase boundary. Investigation of the various distributions of deposition species showed that, during evaporation, the best quality film resulted from a stoichiometric distribution where only ZnO clusters were deposited. During sputtering, however, the best quality film resulted from a slightly O rich distribution. Two stoichiometric distributions, one involving mainly ZnO clusters and the other involving mainly single species, showed that the distribution of deposition species makes a huge impact on the grown film. The deposition of predominantly single species causes many more O atoms at the surface to be sputtered or reflected, resulting in an O deficiency of up to 18% in the deposited film and therefore resulting in more stacking faults and phase boundaries. The methods used allow analysis of key mechanisms that occur during the growth process and give hints as to the optimum conditions under which complete crystalline layers can form.