75 results found
Zuehlsdorff TJ, Hine NDM, Spencer JS, et al., 2013, Linear-scaling time-dependent density-functional theory in the linear response formalism, JOURNAL OF CHEMICAL PHYSICS, Vol: 139, ISSN: 0021-9606
Lever G, Cole DJ, Hine NDM, et al., 2013, Electrostatic considerations affecting the calculated HOMO-LUMO gap in protein molecules, JOURNAL OF PHYSICS-CONDENSED MATTER, Vol: 25, ISSN: 0953-8984
Ratcliff LE, Haynes PD, 2013, Ab initio calculations of the optical absorption spectra of C-60-conjugated polymer hybrids, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 15, Pages: 13024-13031, ISSN: 1463-9076
Avraam PW, Hine NDM, Tangney P, et al., 2012, Fermi-level pinning can determine polarity in semiconductor nanorods, PHYSICAL REVIEW B, Vol: 85, ISSN: 1098-0121
Hine NDM, Avraam PW, Tangney P, et al., 2012, Linear-Scaling Density Functional Theory Simulations of Polar Semiconductor Nanorods, 3rd Workshop on Theory, Modelling and Computational Methods for Semiconductor Materials and Nanostructures (TMCS), Publisher: IOP PUBLISHING LTD, ISSN: 1742-6588
Hine NDM, Dziedzic J, Haynes PD, et al., 2011, Electrostatic interactions in finite systems treated with periodic boundary conditions: Application to linear-scaling density functional theory, JOURNAL OF CHEMICAL PHYSICS, Vol: 135, ISSN: 0021-9606
Ratcliff LE, Hine NDM, Haynes PD, 2011, Calculating optical absorption spectra for large systems using linear-scaling density functional theory, PHYSICAL REVIEW B, Vol: 84, ISSN: 2469-9950
Avraam PW, Hine NDM, Tangney P, et al., 2011, Factors influencing the distribution of charge in polar nanocrystals, PHYSICAL REVIEW B, Vol: 83, ISSN: 1098-0121
We perform first-principles calculations of wurtzite GaAs nanorods to explore the factors determining charge distributions in polar nanostructures. We show that both the direction and magnitude of the dipole moment d of a nanorod, and its electric field, depend sensitively on how its surfaces are terminated and do not depend strongly on the spontaneous polarization of the underlying lattice. We identify two physical mechanisms by which d is controlled by the surface termination, and we show that the excess charge on the nanorod ends is not strongly localized. We discuss the implications of these results for tuning nanocrystal properties, and for their growth and assembly.
Hine NDM, Robinson M, Haynes PD, et al., 2011, Accurate ionic forces and geometry optimization in linear-scaling density-functional theory with local orbitals, PHYSICAL REVIEW B, Vol: 83, ISSN: 1098-0121
Skylaris C-K, Haynes PD, Mostofi AA, et al., 2011, Linear-scaling density functional theory with the ONETEP program, 241st National Meeting and Exposition of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Al-Jamal KT, Nerl H, Mueller KH, et al., 2011, Cellular uptake mechanisms of functionalised multi-walled carbon nanotubes by 3D electron tomography imaging, NANOSCALE, Vol: 3, Pages: 2627-2635, ISSN: 2040-3364
Monserrat B, Haynes PD, 2010, Truncated spherical-wave basis set for first-principles pseudopotential calculations, JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, Vol: 43, ISSN: 1751-8113
Hine NDM, Haynes PD, Mostofi AA, et al., 2010, Linear-scaling density-functional simulations of charged point defects in Al2O3 using hierarchical sparse matrix algebra, JOURNAL OF CHEMICAL PHYSICS, Vol: 133, ISSN: 0021-9606
Robinson M, Haynes PD, 2010, Dynamical effects in ab initio NMR calculations: Classical force fields fitted to quantum forces, JOURNAL OF CHEMICAL PHYSICS, Vol: 133, ISSN: 0021-9606
Badinski A, Haynes PD, Trail JR, et al., 2010, Methods for calculating forces within quantum Monte Carlo simulations, J PHYS: CONDENS MATTER, Vol: 22, ISSN: 0953-8984
Atomic force calculations within the variational and diffusion quantum Monte Carlo methods are described. The advantages of calculating diffusion quantum Monte Carlo forces with the 'pure' rather than the 'mixed' probability distribution are discussed. An accurate and practical method for calculating forces using the pure distribution is presented and tested for the SiH molecule. The statistics of force estimators are explored and violations of the central limit theorem are found in some cases.
Robinson M, Haynes PD, 2009, Linear-scaling first-principles study of a quasicrystalline molecular material, CHEM PHYS LETT, Vol: 476, Pages: 73-77, ISSN: 0009-2614
Quasicrystals exhibit long-range order without translational periodicity by siting their constituent atoms on the nodes of a quasiperiodic tiling. Zhou and Harris [Z. Zhou, K. D. M. Harris, ChemPhysChem 7 (2006) 1649] have proposed engineering a 2D molecular quasicrystal where each node of a Penrose tiling is occupied by a discrete molecule, the 10,5-coronene. First-principles quantum-mechanical calculations have been performed on the stability and energetics of this molecule using the linear-scaling density-functional theory package ONETEP. The suitability of the 10,5-coronene as a molecular building block is confirmed and different design strategies are compared. (C) 2009 Elsevier B.V. All rights reserved.
Hine NDM, Haynes PD, Mostofi AA, et al., 2009, Linear-scaling density-functional theory with tens of thousands of atoms: Expanding the scope and scale of calculations with ONETEP, COMPUTER PHYSICS COMMUNICATIONS, Vol: 180, Pages: 1041-1053, ISSN: 0010-4655
Conduit GJ, Haynes PD, 2008, Diffusion Monte Carlo study of a valley-degenerate electron gas and application to quantum dots, PHYS REV B, Vol: 78, ISSN: 1098-0121
A many-flavor electron gas (MFEG) in a semiconductor with a valley degeneracy ranging between 6 and 24 was analyzed using diffusion Monte Carlo (DMC) calculations. The DMC results compare well to an analytic expression derived by one of us [Phys. Rev. B 78, 035111 (2008)] for the total energy to within +/- 1% over an order of magnitude range of density, which increases with valley degeneracy. For Bi2Te3 (sixfold valley degeneracy) the applicable charge-carrier densities are between 7x10(19) cm(-3) and 2x10(20) cm(-3). DMC calculations distinguished between an exact and a useful approximate expression for the 24-fold degenerate MFEG polarizability for wave numbers 2p(F)< q < 7p(F). The analytical result for the MFEG is generalized to inhomogeneous systems by means of a gradient correction; the validity range of this approach is obtained. Employed within a density-functional theory calculation this approximation compares well to DMC results for a quantum dot.
Silas P, Yates JR, Haynes PD, 2008, Density-functional investigation of the rhombohedral to simple-cubic phase transition of arsenic, PHYS REV B, Vol: 78, ISSN: 1098-0121
We report on our investigation of the crystal structure of arsenic under compression, focusing primarily on the pressure-induced A7 -> simple-cubic (sc) phase transition. The two-atom rhombohedral unit cell is subjected to pressures ranging from 0 to 200 GPa. For each given pressure, cell lengths and angles, as well as atomic positions, are allowed to vary until the fully relaxed structure is obtained. We find that the nearest- and next-nearest-neighbor distances give the clearest indication of the occurrence of a structural phase transition. Calculations are performed using the local-density approximation (LDA) and the Perdew-Burke-Ernzerhof and Perdew-Wang generalized gradient approximations (GGA-PBE and GGA-PW91) for the exchange-correlation functional. The A7 -> sc transition is found to occur at 21 +/- 1 GPa in the LDA, at 28 +/- 1 GPa in the GGA-PBE, and at 29 +/- 1 GPa in the GGA-PW91. No volume discontinuity is observed across the transition in any of the three cases. We use k-point grids as dense as 66x66x66 to enable us to present reliably converged results for the A7 -> sc transition of arsenic.
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.
Skylaris CK, Haynes PD, Mostofi AA, et al., 2008, Recent progress in linear-scaling density functional calculations with plane waves and pseudopotentials: the ONETEP code, JOURNAL OF PHYSICS-CONDENSED MATTER, Vol: 20
The ONETEP program employs the single-particle density matrix reformulation of Kohn-Sham density functional theory to achieve computational cost and memory requirements which increase only linearly with the number of atoms. As the code employs a plane wave basis set (in the form of periodic sinc functions) and pseudopotentials it is able to achieve levels of accuracy and systematic improvability comparable to those of conventional cubic-scaling plane wave approaches. The code has been developed with the aim of running efficiently on a variety of parallel architectures ranging from commodity clusters with tens of processors to large national facilities with thousands of processors. Recent and ongoing studies which we are performing with ONETEP involve problems ranging from materials to biomolecules to nanostructures.
Badinski A, Haynes PD, Needs RJ, 2008, Nodal Pulay terms for accurate diffusion quantum Monte Carlo forces, PHYS REV B, Vol: 77, ISSN: 1098-0121
Exact expressions are derived for forces within the mixed and pure fixed-node diffusion quantum Monte Carlo (DMC) methods. These expressions include the "nodal terms" which arise from the discontinuity in the gradient of the DMC wave function at the nodal surface. We devise a practical scheme for estimating the nodal terms, and demonstrate that their inclusion leads to very accurate forces.
Skylaris CK, Haynes PD, 2007, Achieving plane wave accuracy in linear-scaling density functional theory applied to periodic systems: A case study on crystalline silicon, J CHEM PHYS, Vol: 127, ISSN: 0021-9606
Linear-scaling methods for density functional theory promise to revolutionize the scope and scale of first-principles quantum mechanical calculations. Crystalline silicon has been the system of choice for exploratory tests of such methods in the literature, yet attempts at quantitative comparisons under linear-scaling conditions with traditional methods or experimental results have not been forthcoming. A detailed study using the ONETEP code is reported here, demonstrating for the first time that plane wave accuracy can be achieved in linear-scaling calculations on periodic systems. (C) 2007 American Institute of Physics.
Haynes PD, Skylaris CK, Mostofi AA, et al., 2006, ONETEP: linear-scaling density-functional theory with local orbitals and plane waves, PHYS STATUS SOLIDI B, Vol: 243, Pages: 2489-2499, ISSN: 0370-1972
Haynes PD, Skylaris CK, Mostofi AA, et al., 2006, Elimination of basis set superposition error in linear-scaling density-functional calculations with local orbitals optimised in situ, CHEM PHYS LETT, Vol: 422, Pages: 345-349, ISSN: 0009-2614
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. (c) 2006 Elsevier B.V. All rights reserved.
Skylaris CK, Haynes PD, Mostofi AA, et al., 2006, Implementation of linear-scaling plane wave density functional theory on parallel computers, PHYS STATUS SOLIDI B, Vol: 243, Pages: 973-988
We describe the algorithms we have developed for linear-scaling plane wave density functional calculations on parallel computers as implemented in the ONETEP program. We outline how ONETEP achieves plane wave accuracy with a computational cost which increases only linearly with the number of atoms by optimising directly the single-particle density matrix expressed in a psinc basis set. We describe in detail the novel algorithms we have developed for computing with the psinc basis set the quantities needed in the evaluation and optimisation of the total energy within our approach. For our parallel computations we use the general Message Passing Interface (MPI) library of subroutines to exchange data between processors. Accordingly, we have developed efficient schemes for distributing data and computational load to processors in a balanced manner. We describe these schemes in detail and in relation to our algorithms for computations with a psinc basis. Results of tests on different materials show that ONETEP is an efficient parallel code that should be able to take advantage of a wide range of parallel computer architectures. (c) 2006 WILEYNCH Verlag GmbH & Co. KGaA, Weinheim.
von Alfthan S, Haynes PD, Kaski K, et al., 2006, Are the structures of twist grain boundaries in silicon ordered at 0 K?, PHYS REV LETT, Vol: 96, ISSN: 0031-9007
Contrary to previous simulation results on the existence of amorphous intergranular films at high-angle twist grain boundaries (GBs) in elemental solids such as silicon, recent experimental results imply structural order in some high-angle boundaries. With a novel protocol for simulating twist GBs, which allows the number of atoms at the boundary to vary, we have found new low-energy ordered structures. We give a detailed exposition of the results for the simplest boundary. The validity of our results is confirmed by first-principles calculations.
Haynes PD, Mostofi AA, Skylaris CK, et al., 2006, ONETEP: linear-scaling density-functional theory with plane-waves, EMAG/NANO Conference on Imaging, Analysis and Fabrication on the Nanoscale, Publisher: IOP PUBLISHING LTD, Pages: 143-148, ISSN: 1742-6588
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 large-scale 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.
Skylaris CK, Haynes PD, Mostofi AA, et al., 2005, Using ONETEP for accurate and efficient O(N) density functional calculations, JOURNAL OF PHYSICS-CONDENSED MATTER, Vol: 17, Pages: 5757-5769, ISSN: 0953-8984
Skylaris CK, Haynes PD, Mostofi AA, et al., 2005, Introducing ONETEP: Linear-scaling density functional simulations on parallel computers, JOURNAL OF CHEMICAL PHYSICS, Vol: 122, ISSN: 0021-9606
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