[Show abstract][Hide abstract] ABSTRACT: We have used ab initio total energy plane wave pseudopotential methods to perform the first completely ab initio investigation of the atomic and electronic structure of a grain boundary in a transition metal oxide. The ∑ = 15 (210) tilt boundary in rutile TiG2 is studied using the conjugate gradients iterative minimisation technique for performing total energy calculations within the LDA and pseudopotential approximations. The stability of the experimentally observed translation state of the boundary is confirmed, and some insight is gained into its electronic structure.
[Show abstract][Hide abstract] ABSTRACT: Plane wave basis sets are widely used in ab initio electronic structure calculations even though such an expansion in terms of extended states does not provide a natural way of quantifying local atomic properties. To overcome this deficiency we have implemented a scheme for projection of plane wave states onto a localised basis set. This approach is used to calculate atomic charges and bond populations, and is illustrated by application to a selection of small molecules. Finally, we calculate the changes in these quantities induced by adsorption of a molecule onto a zeolite substrate. Thus, using the procedure described in this paper, plane wave calculations can yield the same information as traditional quantum chemical methods.
[Show abstract][Hide abstract] ABSTRACT: An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semi-empirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans, gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.
Molecular Physics 12/2010; February 20(3-1998):365-370. DOI:10.1080/002689798169032 · 1.72 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We present calculations of formation energies of defects in an ionic solid (Al(2)O(3)) extrapolated to the dilute limit, corresponding to a simulation cell of infinite size. The large-scale calculations required for this extrapolation are enabled by developments in the approach to parallel sparse matrix algebra operations, which are central to linear-scaling density-functional theory calculations. The computational cost of manipulating sparse matrices, whose sizes are determined by the large number of basis functions present, is greatly improved with this new approach. We present details of the sparse algebra scheme implemented in the ONETEP code using hierarchical sparsity patterns, and demonstrate its use in calculations on a wide range of systems, involving thousands of atoms on hundreds to thousands of parallel processes.
The Journal of Chemical Physics 09/2010; 133(11):114111. DOI:10.1063/1.3492379 · 2.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A modification of the MM-PBSA technique for calculating binding affinities of biomolecular complexes is presented. Classical molecular dynamics is used to explore the motion of the extended interface between two peptides derived from the BRC4 repeat of BRCA2 and the eukaryotic recombinase RAD51. The resulting trajectory is sampled using the linear-scaling density functional theory code, onetep, to determine from first principles, and with high computational efficiency, the relative free energies of binding of the ˜2800 atom receptor-ligand complexes. This new method provides the basis for computational interrogation of protein-protein and protein-ligand interactions, within fields ranging from chemical biological studies to small molecule binding behaviour, with both unprecedented chemical accuracy and affordable computational expense.
[Show abstract][Hide abstract] ABSTRACT: ONETEP is an ab initio electronic structure package for total energy calculations within density-functional theory. It combines ‘linear scaling’, in that the total computational effort scales only linearly with system size, with ‘plane-wave’ accuracy, in that the convergence of the total energy is systematically improvable in the manner typical of conventional plane-wave pseudopotential methods. We present recent progress on improving the performance, and thus in effect the feasible scope and scale, of calculations with ONETEP on parallel computers comprising large clusters of commodity servers. Our recent improvements make calculations of tens of thousands of atoms feasible, even on fewer than 100 cores. Efficient scaling with number of atoms and number of cores is demonstrated up to 32,768 atoms on 64 cores.
[Show abstract][Hide abstract] ABSTRACT: When a brittle material is loaded to the limit of its strength, it fails by the nucleation and propagation of a crack. The conditions for crack propagation are created by stress concentration in the region of the crack tip and depend on macroscopic parameters such as the geometry and dimensions of the specimen. The way the crack propagates, however, is entirely determined by atomic-scale phenomena, because brittle crack tips are atomically sharp and propagate by breaking the variously oriented interatomic bonds, one at a time, at each point of the moving crack front. The physical interplay of multiple length scales makes brittle fracture a complex 'multi-scale' phenomenon. Several intermediate scales may arise in more complex situations, for example in the presence of microdefects or grain boundaries. The occurrence of various instabilities in crack propagation at very high speeds is well known, and significant advances have been made recently in understanding their origin. Here we investigate low-speed propagation instabilities in silicon using quantum-mechanical hybrid, multi-scale modelling and single-crystal fracture experiments. Our simulations predict a crack-tip reconstruction that makes low-speed crack propagation unstable on the (111) cleavage plane, which is conventionally thought of as the most stable cleavage plane. We perform experiments in which this instability is observed at a range of low speeds, using an experimental technique designed for the investigation of fracture under low tensile loads. Further simulations explain why, conversely, at moderately high speeds crack propagation on the (110) cleavage plane becomes unstable and deflects onto (111) planes, as previously observed experimentally.
[Show abstract][Hide abstract] ABSTRACT: ONETEP is a linear scaling code for performing first-principles total energy calculations within density-functional theory (DFT). The method is based on the density-matrix formulation of DFT and involves the iterative minimization of the total energy with respect to a set of local orbitals and a density kernel. An overview is given of the kernel optimization methods proposed in the literature and implemented in ONETEP, focusing in particular on the constraints of compatibility, idempotency and normalization that must be applied. A method is proposed for locating the chemical potential which may be useful in applying the normalization constraint and analysing the electronic structure near the Fermi level.
[Show abstract][Hide abstract] ABSTRACT: Ab initio calculations are presented of the cohesive energies of aluminium in a number of diverse hypothetical structures which span a wide range of the coordination number, C, from C = 0 to C = 12. The calculations have been performed to investigate the nature of multi-atom bonding, its dependence on C and to form a database for testing and developing empirical and semi-empirical models. The results support the saturation of cohesive energy for large C predicted by several simple theoretical models. Calculations on the same structures using semi-empirical schemes suggest that these methods might have a greater degree of accuracy than had previously been believed.
[Show abstract][Hide abstract] ABSTRACT: An overview is presented of the method used to parallelize a set of total energy pseudopotential codes on a 64-node i860 Meiko Computing Surface and a 32-node Intel iPSC/860 Hypercube. These codes have been used to calculate the surface energies and relaxed structures of the 3 × 3, 5 × 5 and 7 × 7 Takayanagi reconstructions of the (111) surface of silicon. It is found that the 7 × 7 reconstruction has the lowest energy and that structural trends across the series of reconstructions can be related to the degree of charge transfer from the adatoms to the rest atoms.
Physica Scripta 01/2007; 1992(T45):265. DOI:10.1088/0031-8949/1992/T45/057 · 1.13 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Basis set superposition error (BSSE) in density-functional calculations occurs when the extended Kohn–Sham orbitals are expanded in localised basis sets, but is absent when a plane-wave basis is used. Elimination of BSSE is essential for the accurate description of intermolecular forces. Linear-scaling methods are formulated in terms of local orbitals, making plane-waves an inappropriate choice of basis. In this work the BSSE in linear-scaling methods is studied in the context of hydrogen bonds. In particular it is shown that BSSE is eliminated by optimizing the local orbitals in situ using a systematic basis set equivalent to a set of plane-waves.
Chemical Physics Letters 05/2006; 422(4):345-349. DOI:10.1016/j.cplett.2006.02.086 · 1.90 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We review the main features of a recently proposed molecular dynamics method in which quantum mechanical calculations are embedded in a classical force model within a unified scheme free of boundary region and transferability problems. The scheme is based on the idea of augmenting a parametrized analytic force model by incorporating in it the quantum mechanical information necessary to compute accurate trajectories. This is achieved through a suitable fitting procedure in which the parameters of a classical inter-atomic force field are adjusted at run time to reproduce high-accuracy results which are computed separately on system subsets by tight-binding or DFT-based “black box” computing engines.
[Show abstract][Hide abstract] ABSTRACT: This paper provides a general overview of the methodology implemented in onetep (Order-N Electronic Total Energy Package), a parallel density-functional theory code for largescale first-principles quantum-mechanical calculations. The distinctive features of onetep are linear-scaling in both computational effort and resources, obtained by making well-controlled approximations which enable simulations to be performed with plane-wave accuracy. Titanium dioxide clusters of increasing size designed to mimic surfaces are studied to demonstrate the accuracy and scaling of onetep.
Journal of Physics Conference Series 02/2006; 26(1):143. DOI:10.1088/1742-6596/26/1/034
[Show abstract][Hide abstract] ABSTRACT: We present the temperature dependence of the growth rate of carbon nanofibers by plasma-enhanced chemical vapor deposition with Ni, Co, and Fe catalysts. We extrapolate a common low activation energy of 0.23-0.4 eV, much lower than for thermal deposition. The carbon diffusion on the catalyst surface and the stability of the precursor molecules, C2H2 or CH4, are investigated by ab initio plane wave density functional calculations. We find a low activation energy of 0.4 eV for carbon surface diffusion on Ni and Co (111) planes, much lower than for bulk diffusion. The energy barrier for C2H2 and CH4 dissociation is at least 1.3 eV and 0.9 eV, respectively, on Ni(111) planes or step edges. Hence, the rate-limiting step for plasma-enhanced growth is carbon diffusion on the catalyst surface, while an extra barrier is present for thermal growth due to gas decomposition.