NanoCap: A framework for generating capped carbon nanotubes and fullerenes

NanoCap provides both libraries and a standalone application for the construction of capped nanotubes of arbitrary chirality and fullerenes of any radius. Structures are generated by constructing a set of optimal dual graph topologies which are subsequently optimised using a carbon interatomic potential. Combining this approach with a GUI featuring 3D rendering capabilities allows for the rapid inspection of physically sensible structures which can be used as input for molecular simulation

Variable timestep algorithm for molecular dynamics simulation of non-equilibrium processes

A simple, yet robust variable timestep algorithm is developed for use in molecular dynamics simulations of energetic processes. Single-particle Kepler orbits are studied to study the relationship between trajectory properties and the critical timestep for constant integration error. Over a wide variety of conditions the magnitude of the maximum force is found to correlate linearly with the inverse critical timestep. Other quantities used in the literature such as the time derivative of the force and the product of the velocity and force also show reasonable correlations, but not to the same extent. Application of the corresponding metric ||Fmax||Δt||Fmax||Δt in molecular dynamics simulation of radiation damage in graphite shows that the scheme is both straightforward to implement and effective. In tests on a 1 keV cascade the timestep varies by over two orders of magnitude with minimal loss of energy conservation

Effect of microstructure on the thermal conductivity of disordered carbon

Computational methods are used to control the degree of structural order in a variety of carbonmaterials containing primarily sp2 bonding. Room-temperature thermal conductivities arecomputed using non-equilibrium molecular dynamics. Our results reproduce experimental data foramorphous and glassy carbons and confirm previously proposed structural models for vitreouscarbons. An atomistic model is developed for highly oriented thin films seen experimentally, with amaximum computed thermal conductivity of 35 W m1 K1. This value is much higher than thatof the amorphous and glassy structures, demonstrating that the microstructure influences thethermal conductivity more strongly than the density

Structural dependence of threshold displacement energies in rutile, anatase and brookite TiO2

Systematic molecular dynamics simulations of low energy cascades have been performed to examine how threshold displacement events are affected by changes in crystal structure. Exploiting the structural proximity of the rutile, anatase and brookite polymorphs of TiO2, a quantitative examination of defect production has been carried out including detailed defect analysis and the determination of values of the threshold displacement energy (Ed). Across all polymorphs comparable values of Ed are reported for oxygen at around 20 eV, with the value for Ti in rutile (73 ± 2 eV) significantly higher than that in brookite (34 ± 1 eV) and anatase (39 ± 1 eV). Quantifying defect formation probability as a function of Primary Knock-on Atom (PKA) energy, simulations in rutile indicate a consistent reduction in defect formation at energies higher than Ed relative to anatase and brookite. Defect cluster analysis reveals a significant proportion of di-Frenkel pairs in anatase at Ti PKA energies around Ed. These clusters, which are stabilised by the localisation of two Frenkel pairs, are associated with a recombination barrier of approximately 0.19 eV. As such, annihilation is likely under typical a experimental condition which suggests an expected increase in the measured Ti value of Ed. Identical O defect populations produced at the threshold by the O PKA in both rutile and anatase explain the comparable values of Ed. At higher O PKA energies, the commencement of defect production on both sublattices in anatase is observed in contrast to the confinement of defects to the O sublattice in rutile. The overall trends reported are consistent with in-situ irradiation experiments and thermal spike simulations, suggesting the contrasting radiation response of the polymorphs of TiO2 is apparent during the initial stages of defect production

Molecular dynamics simulations of the transformation of carbon peapods into double-walled carbon nanotubes

The transformation of carbon peapods (encapsulated fullerenes in nanotubes) into doublewalled nanotubes was studied using molecular dynamics simulation. The simulations reproduce the two main trends known experimentally: the production of low-defect nanotubes and the templating effect of the outer tube. The process involves a low-temperature polymerization of the fullerenes followed by higher temperature self-assembly into a tube. Modelling of this second stage is made possible by the use of the Environment-Dependent Interaction Potential, a large number of atoms and long-time annealing. Analysis shows that the outer tube acts as a container for the self-assembly process, analogous to previous simulations and experiments in which free surfaces, either external or internal, template the formation of highly ordered sp2 phases

Electronic structure models of phosphorus 0-doped silicon

We report a density-functional theory treatment of phosphorus 0-doped silicon. Using large asymmetric unit cells with up to 800 atoms, we obtain first-principles doping potentials, band energies, and donor-electron distributions. The explicit and nonempirical description of both valence and donor electrons improves upon previous models of this system. The effects of overlapping 0-doping potentials in smaller systems are adequately captured using a uniform band alignment shift

Dehydroxylation of Kaolinite to Metakaolin - A Molecular Dynamics Study

The thermally induced transformation of kaolinite to metakaolin is simulated using molecular dynamics through a step-wise dehydroxylation approach. The simulation shows that the removal ofstructural 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-layerspacing. 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 are proportional to the amount of local disorder within the structure, which is governed by the degree oflocal 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

Electronic structure of two interacting phosphorus δ-doped layers in silicon

Density functional theory is used to quantify the interaction of a pair of 1/4-monolayer phosphorus δ-doped layers in silicon. We investigate changes in the electronic structure as the distance between the two δ-doped layers is altered and identify the onset of interactions between the transverse and longitudinal bands. The calculations show that the valley splitting is insensitive to the separation distance, while the interlayer band splittings are insensitive to the representation used to describe the dopant disorder. These observations are exploited in a hybrid model which enables the calculation of accurate splittings of realistically disordered systems at tractable computational cost

Graphitization of amorphous carbons: A comparative study of interatomic potentials

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 sp2 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