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We perform a comparative study of six common carbon interatomic potentials: Tersoff, REBO-II, ReaxFF, EDIP, LCBOP-I and COMB3. To ensure fair comparison, all the potentials are used as implemented in the molecular dynamics package LAMMPS. Using the liquid quenching method we generate amorphous carbons at different densities, and subsequently anneal at high temperature. The amorphous carbon system provides a critical test of the transferability of the potential, while the annealing simulations illustrate the graphitization process and test bond-making and-breaking. A wide spread of behavior is seen across the six potentials, with quantities such as sp 2 fraction, radial distribution function, morphology, ring statistics, and 002 reflection intensity differing considerably. While none of the potentials is perfect, some perform particularly poorly. The lack of transferability can be traced to the details of the functional form, suggesting future directions in the development of carbon potentials.

Amorphous carbon networks are used to test various levels of theoretical approaches to molecular dynamics simulations. The density-functional theory as implemented in the Car-Parrinello method, nonorthogonal tightbinding method, the environment-dependent interaction potential ͑EDIP͒, and the Brenner potential are compared directly in liquid quench simulations containing 125 atoms at four densities. We find that at low densities the predictions of the Brenner potential are in agreement with those from density-functional theory, while structures produced by nonorthogonal tight-binding method compare well with density-functional theory at all densities. The tight-binding method does, however, find a slightly lower sp 3 fraction at high densities and the presence of singly coordinated atoms at low densities. The frequency of three-membered rings are underpredicted by the tight-binding and EDIP methods due to an overestimate of strain energy relative to densityfunctional theory and experiment. Aside from the small rings, and a slight underestimate in sp 3 fraction at the highest densities, the EDIP simulations are in very good agreement with density-functional theory. The EDIP method is also used to quantify the statistical variability of liquid quenching, and comparisons with film growth simulations verify that liquid quenching is a good representation of bulk amorphous carbon.

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Density functional calculations are performed to identify features observed in STM experiments after phosphine (PH3) dosing of the Si(001) surface. On the basis of a comprehensive survey of possible structures, energetics, and simulated STM images, three prominent STM features are assigned to structures containing surface bound PH2, PH, and P, respectively. Collectively, the assigned features outline for the first time a detailed mechanism of PH3 dissociation and P incorporation on Si(001).

The thermally induced transformation of kaolinite to metakoalin is simulated using molecular dynamics through a step-wise dehydroxylation approach. The simulation shows that the removal of structural water through dehydroxylation produces a distortion or buckling effect in the 1:1 Al-Si layers, which is due to the migration of the aluminium into vacant sites provided by the inter-layer spacing. The structural change is characterized by a loss of crystallinity and a concomitant change in aluminium coordination from octahedral to tetrahedral, with this study confirming the presence of 5-fold aluminium within the metakaolin structure. The degree and probability of Al migration is proportional to the amount of local disorder within the structure, which is governed by the degree of local hydroxyl group loss. This results in the formation of aluminium clusters within the layers. This study proposes that instead of a uniform structure, metakaolin exhibits regions of differing aluminium concentrations, which can have major effects in the reaction chemistry at those sites.

Within a full density functional theory framework we calculate the band structure and doping potential for phosphorus δ-doped silicon. We compare two different representations of the dopant plane; pseudo-atoms in which the nuclear charge is fractional between silicon and phosphorus, and explicit arrangements employing distinct silicon and phosphorus atoms. While the pseudo-atom approach offers several computational advantages, the explicit model calculations differ in a number of key points, including the valley splitting, the Fermi level and the width of the doping potential. These findings have implications for parameters used in device modelling.

Using density functional theory and guided by extensive scanning tunneling microscopy (STM) image data, we formulate a detailed mechanism for the dissociation of phosphine (PH3) molecules on the Si(001) surface at room temperature. We distinguish between a main sequence of dissociation that involves PH2+H, PH+2H, and P+3H as observable intermediates, and a secondary sequence that gives rise to PH+H, P+2H, and isolated phosphorus adatoms. The latter sequence arises because PH2 fragments are surprisingly mobile on Si(001) and can diffuse away from the third hydrogen atom that makes up the PH3 stoichiometry. Our calculated activation energies describe the competition between diffusion and dissociation pathways and hence provide a comprehensive model for the numerous adsorbate species observed in STM experiments.