Publications describing the ONETEP code

In publications arising from the use of ONETEP please cite

Introducing ONETEP: Linear-scaling density functional simulations on parallel computers
C.-K. Skylaris, P. D. Haynes, A. A. Mostofi and M. C. Payne, J. Chem. Phys. 122, 084119 (2005) ONLINE JOURNAL

In publications making extensive use of forces and geometry optimisation, please also cite

Accurate ionic forces and geometry optimisation in linear scaling density-functional theory with local orbitals
N. D. M. Hine, M. Robinson, P. D. Haynes, C.-K. Skylaris, M. C. Payne and A. A. Mostofi, Phys. Rev. B 83, 195102 (2011). ONLINE JOURNAL

For a general overview of the ONETEP method please see

ONETEP: linear-scaling density-functional theory with plane waves
P. D. Haynes, C.-K. Skylaris, A. A. Mostofi and M. C. Payne, Psi-k Newsletter 72, 78-91 (December 2005) PDF

Publications related to linear-scaling methods by members and associates of the ONETEP Developers' Group

(Reverse chronological order)

2013

Simulations of Nanocrystals Under Pressure: Combining Electronic Enthalpy and Linear-Scaling Density-Functional Theory
Niccolò R. C. Corsini, Andrea Greco, Nicholas D. M. Hine, Carla Molteni, Peter D. Haynes
Submitted (2013). arXiv.
Ab initio calculations of the optical absorption spectra of C60-conjugated polymer hybrids
L. E. Ratcliff and P. D. Haynes
Phys. Chem. Chem. Phys. (in press, 2013). arXiv.
Linear-scaling time-dependent density-functional theory in the linear response formalism
T. J. Zuehlsdorff, N. D. M. Hine, J. S. Spencer, N. M. Harrison, D. J. Riley, and P. D. Haynes
Submitted (2013). arXiv.
Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning
L. P. Lee , D. J. Cole , C.-K. Skylaris , W. L. Jorgensen , and M. C. Payne
J. Chem. Theory Comput. (in press, 2013). ONLINE JOURNAL.
Electrostatic considerations affecting the calculated HOMO-LUMO gap in protein molecules
G. Lever, D. J. Cole, N. D. M. Hine, P. D. Haynes, and M. C. Payne
Journal of Physics: Condensed Matter 25, 152101 (Fast Track Communication) (2013). ONLINE JOURNAL.
Importance of many body effects in the kernel of hemoglobin for ligand binding
C. Weber, D. D. O'Regan, N. D. M. Hine, P. B. Littlewood, G. Kotliar and M. C. Payne,
Physical Review Letters, 110, 106402 (2013). ONLINE JOURNAL.
Self-assembled quantum dots in a nanowire system for quantum photonics
M. Heiss, Y. Fontana, A. Gustafsson, G. Wüst, C. Magen, D. D. O'Regan, J. W. Luo, B. Ketterer, S. Conesa-Boj, A. V. Kuhlmann, J. Houel, E. Russo-Averchi, J. R. Morante, M. Cantoni, N. Marzari, J. Arbiol, A. Zunger, R. J. Warburton, and A. Fontcuberta i Morral,
Nature Materials 12, 439–444 (2013). ONLINE JOURNAL
Natural bond orbital analysis in the ONETEP code: Applications to large protein systems
L. P. Lee, D. J. Cole, M. C. Payne, and C.-K. Skylaris, J. Comp.Chem. 34, 429 (2013). ONLINE JOURNAL

2012

Bromophenyl functionalization of carbon nanotubes: an ab initio study
J. Beaudin, J. Laflamme Janssen, N. D. M. Hine, P. D. Haynes, and M. Cote, Submitted (2012). arXiv.
Interactions of carbon nanomaterials with amyloidogenic peptides: insights from multiscale theoretical simulations
A. J. Makarucha, N. Todorova, N. D. M. Hine, A. A. Mostofi, I. Yarovsky, Submitted (2012).
Report on the CECAM/ESF-Psi-k Workshop "Efficient localised orbitals for large systems, strong correlations and excitations", Cambridge, 2-5 July 2012.
D. D. O'Regan, S. M.-M. Dubois, P. Umari, and P. D. Haynes,
Psi-k Newsletter 113 (October 2012). PDF
Pulay forces from localized orbitals optimized in situ using a psinc basis set
A. Ruiz-Serrano, N. D. M. Hine, and C.-K. Skylaris,
J. Chem. Phys. 136, 234101 (2012) ONLINE JOURNAL
Vanadium dioxide : A Peierls-Mott insulator stable against disorder
C. Weber, D. D. O'Regan, N. D. M. Hine, M. C. Payne, G. Kotliar and P. B. Littlewood,
Physical Review Letters 108, 256402 (2012). ONLINE JOURNAL.
Large-scale DFT calculations in implicit solvent - a case study on the T4 lysozyme L99A/M102Q protein
J. Dziedzic, S. J. Fox, T. Fox, C. S. Tautermann, and C.-K. Skylaris, Int. J. Quantum Chem 113, 771, (2013) ONLINE JOURNAL.
Linear-Scaling Density Functional Theory Simulations of Polar Semiconductor Nanorods
N. D. M. Hine, P. W. Avraam, P. Tangney, P. D. Haynes,
J. Phys. Conf. Ser 367, 012002 (2012). ONLINE JOURNAL
Generalized Wannier functions: a comparison of molecular electric dipole polarizabilities
D. D. O'Regan, M. C. Payne, and A. A. Mostofi,
Phys. Rev. B 85, 193101 (2012). ONLINE JOURNAL
Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U
D. J. Cole, D. D. O'Regan, and M. C. Payne,
J. Phys. Chem. Lett. 3, 1448 (2012). ONLINE JOURNAL
Fermi level pinning can determine polarity in semiconductor nanorods
P. W. Avraam, N. D. M. Hine, P. Tangney, P. D. Haynes
Phys. Rev. B 85, 115404 (2012). ONLINE JOURNAL
Linear-scaling DFT+U with full local orbital optimization
D. D. O'Regan, N. D. M. Hine, M. C. Payne and A. A. Mostofi,
Phys. Rev. B 85, 085107 (2012). ONLINE JOURNAL
Optimised Projections for the Ab Initio Simulation of Large and Strongly Correlated Systems,
D. D. O'Regan, (Springer, Berlin, Heidelberg, 2012) 1st Ed., Springer Theses XVI, 225p., ISBN 978-3-642-23237-4. ONLINE BOOK

2011

Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules
S. J. Fox., C. Pittock, T. Fox, C. Tautermann, N. Malcolm, and C.-K. Skylaris.
J. Chem. Phys. 135, 224107 (2011). ONLINE JOURNAL
Electrostatic Interactions in Finite Systems treated with Periodic Boundary Conditions: Application to Linear-Scaling Density Functional Theory
N. D. M. Hine, J. Dziedzic, P. D. Haynes, C.-K. Skylaris
J. Chem. Phys. 135, 204103 (2011). ONLINE JOURNAL
Calculating optical absorption spectra for large systems using linear-scaling density-functional theory
L. E. Ratcliff, N. D. M. Hine, and P. D. Haynes
Phys. Rev. B. 84, 165131 (2011). ONLINE JOURNAL
Minimal parameter implicit solvent model for ab initio electronic structure calculations
J. Dziedzic, H. H. Helal, C.-K. Skylaris, A. A. Mostofi, and M. C. Payne.
Europhysics Letters 95, 43001 (2011). ONLINE JOURNAL
The silicon vacancy: insights from large-scale electronic structure calculations and maximally-localized Wannier functions
F. Corsetti, A. A. Mostofi,
Phys. Rev. B. 84, 035209 (2011). ONLINE JOURNAL
Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity
D. J. Cole, E. Rajendra, M. Roberts-Thomson, B. Hardwick, G. J. McKenzie, M. C. Payne, A. R. Venkitaraman and C.-K. Skylaris,
PLoS Comput Biol 7(7): e1002096 (2011). ONLINE JOURNAL
Subspace representations in ab initio methods for strongly correlated systems,
D. D. O'Regan, M. C. Payne and A. A. Mostofi,
Phys. Rev. B 83, 245124 (2011). ONLINE JOURNAL
Factors influencing the distribution of charge in polar nanocrystals
P. W. Avraam, N. D. M. Hine, P. Tangney, P. D. Haynes,
Phys. Rev. B. 83 241402 (2011). ONLINE JOURNAL
Accurate ionic forces and geometry optimisation in linear scaling density-functional theory with local orbitals
N. D. M. Hine, M. Robinson, P. D. Haynes, C.-K. Skylaris, M. C. Payne and A. A. Mostofi, Phys. Rev. B 83, 195102 (2011). ONLINE JOURNAL
First principles-based calculations of free energy of binding: application to ligand binding in a self-assembling superstructure
S. Fox, H. Wallnoefer, T. Fox, C. Tautermann , and C.-K. Skylaris, J. Chem. Theor. Comput. 7, 1102 (2011). ONLINE JOURNAL

2010

Linear-scaling density-functional simulations of charged point defects in Al2O3 using hierarchical sparse matrix algebra
N. D. M. Hine, P. D. Haynes, A. A. Mostofi, and M. C. Payne, J. Chem. Phys. 133, 114111 (2010). ONLINE JOURNAL
Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations
D. J. Cole, C.-K. Skylaris, E. Rajendra, A. R. Venkitaraman and M. C. Payne, Europhysics Letters 91(3), 37004 (2010). ONLINE JOURNAL
Projector self-consistent DFT+U using non-orthogonal generalized Wannier functions
D. D. O'Regan, N. D. M. Hine, M. C. Payne and A. A. Mostofi, Phys. Rev. B 82, 081102(R) (2010). ONLINE JOURNAL
Large-scale first principles and tight-binding density functional theory calculations on hydrogen-passivated silicon nanorods
N. Zonias, P. Lagoudakis and C.-K. Skylaris, J. Phys.: Condens. Matter 22, 025303 (2010). ONLINE JOURNAL

2009

Linear-scaling first-principles study of a quasicrystalline molecular material
M. Robinson and P. D. Haynes, Chem. Phys. Lett. 476, 73 (2009). ONLINE JOURNAL
Linear-scaling density-functional theory with tens of thousands of atoms: Expanding the scope and scale of calculations with ONETEP
N. D. M. Hine, P. D. Haynes, A. A. Mostofi, C.-K. Skylaris and M. C. Payne, Computer Physics Communications 180, 1041 (2009). ONLINE JOURNAL
Including dispersion interactions in the ONETEP program for linear-scaling density functional theory calculations
Q. Hill and C.-K. Skylaris, Proc. R. Soc. A 465, 669 (2009) ONLINE JOURNAL

2008

Density kernel optimisation in the ONETEP code
P. D. Haynes, C.-K. Skylaris, A. A. Mostofi and M. C. Payne, J. Phys.: Cond. Mat. 20 (6), 294207 (2008) ONLINE JOURNAL
Recent progress in linear-scaling density functional calculations with plane waves and pseudopotentials: the ONETEP code
C.-K. Skylaris, P. D. Haynes, A. A. Mostofi and M. C. Payne, J. Phys.: Cond. Mat. 20 (6), 064209 (2008) ONLINE JOURNAL

2007

Achieving plane wave accuracy in linear-scaling density functional theory applied to periodic systems: A case study on crystalline silicon
C.-K. Skylaris and P. D. Haynes, J. Chem. Phys. 127, 164712 (2007) ONLINE JOURNAL
Report on the CECAM/ESF-Psi-k/CCP9 Workshop on "Linear-scaling ab initio Calculations, applications and future directions", Lyon, 3-6 September 2007
C.-K. Skylaris, P. D. Haynes, J.-L. Fattebert, D. R. Bowler and M. Gillan, (5 November 2007) PDF
ONETEP: linear-scaling density functional theory with plane-waves
A. A. Mostofi, P. D. Haynes, C.-K. Skylaris and M. C. Payne, Mol. Sim. 33 (7), 551 (2007) ONLINE JOURNAL

2006

ONETEP: linear-scaling density-functional theory with local orbitals and plane waves
P. D. Haynes, C.-K. Skylaris, A. A. Mostofi and M. C. Payne, phys. stat. sol. (b) 243, 2489-2499 (2006) ONLINE JOURNAL
Elimination of basis set superposition error in linear-scaling density-functional calculations with local orbitals optimised in situ
P. D. Haynes, C.-K. Skylaris, A. A. Mostofi and M. C. Payne, Chem. Phys. Lett 422, 345 (2006) ONLINE JOURNAL
ONETEP: linear-scaling density-functional theory with plane-waves
P. D. Haynes, A. A. Mostofi, C.-K. Skylaris and M. C. Payne, J. Phys.: Conf. Ser. 26, 143-148 (2006) ONLINE JOURNAL
Implementation of linear-scaling plane wave density functional theory on parallel computers
C.-K. Skylaris, P. D. Haynes, A. A. Mostofi and M. C. Payne, phys. stat. sol. (b) 243, 973-988 (2006) ONLINE JOURNAL
Novel structural features of CDK inhibition revealed by an ab initio computational method combined with dynamic simulations
L. Heady, M. Fernandez-Serra, R. L. Mancera, S. Joyce, A. R. Venkitaraman, E. Artacho, C.-K. Skylaris, L. Colombi Ciacchi and M. C. Payne, J. Med. Chem. 49, 5141 (2006) ONLINE JOURNAL

2005

ONETEP: linear-scaling density-functional theory with plane waves
P. D. Haynes, C.-K. Skylaris, A. A. Mostofi and M. C. Payne, Psi-k Newsletter 72, 78-91 (December 2005) PDF
Using ONETEP for accurate and efficient O(N) density functional calculations
C.-K. Skylaris, P. D. Haynes, A. A. Mostofi and M. C. Payne, J. Phys.: Condens. Matter 17, 5757-5769 (2005) ONLINE JOURNAL
Introducing ONETEP: Linear-scaling density functional simulations on parallel computers
C.-K. Skylaris, P. D. Haynes, A. A. Mostofi and M. C. Payne, J. Chem. Phys. 122, 084119 (2005) ONLINE JOURNAL

Pre-2005

Preconditioned iterative minimisation for linear-scaling electronic structure calculations
A. A. Mostofi, P. D. Haynes, C.-K. Skylaris and M. C. Payne, J. Chem. Phys. 119, 8842-8848 (2003) ONLINE JOURNAL
Comparison of variational real-space representations of the kinetic energy operator
C.-K. Skylaris, O. Diéguez, P. D. Haynes and M. C. Payne, Phys. Rev. B 66, 073103 (2002) ONLINE JOURNAL
Nonorthogonal generalized Wannier function pseudopotential plane-wave method
C.-K. Skylaris, A. A. Mostofi, P. D. Haynes, O. Diéguez and M. C. Payne, Phys. Rev. B 66, 035119 (2002) ONLINE JOURNAL
Total-energy calculations on a real space grid with localized functions and a plane-wave basis
A. A. Mostofi, C.-K. Skylaris, P. D. Haynes and M. C. Payne, Comput. Phys. Commun. 147, 788-802 (2002) ONLINE JOURNAL
Report on the CECAM/ESF STRUC-Psi-k Workshop on "Local Orbitals and Linear-scaling ab initio Calculations"
P. D. Haynes, D. R. Bowler and E. Artacho, Psi-k Newsletter 48, 36-66 (December 2001)
Accurate kinetic energy evaluation in electronic structure calculations with localized functions on real space grids
C.-K. Skylaris, A. A. Mostofi, P. D. Haynes, C. J. Pickard and M. C. Payne, Comput. Phys. Commun. 140, 315-322 (2001)
First-principles density-functional calculations using localized spherical-wave basis sets
C. K. Gan, P. D. Haynes and M. C. Payne, Phys. Rev. B 63, 205109 (2001)
Preconditioned conjugate gradient method for the sparse generalized eigenvalue problem in electronic structure calculations
C. K. Gan, P. D. Haynes and M. C. Payne, Comput. Phys. Commun. 134, 33-40 (2001)
An Ab Initio Linear-Scaling Scheme
P. D. Haynes and M. C. Payne, Molecular Simulation 25, 257-264 (2000)
On the Resolution of Identity Coulomb energy approximation in Density Functional Theory
C.-K. Skylaris, L. Gagliardi, N. C. Handy, A. G. Ioannou, S. Spencer and A. Willetts, J. Mol. Struct.: Theochem.501-502, 229-239 (2000)
Corrected penalty-functional method for linear-scaling calculations within density-functional theory
P. D. Haynes and M. C. Payne, Phys. Rev. B 59, 12173-12176 (1999)
Failure of density-matrix minimization methods for linear-scaling density-functional theory using the Kohn penalty-functional
P. D. Haynes and M. C. Payne, Solid State Commun. 108, 737-741 (1998)
An efficient method for calculating effective core potential integrals which involve projection operators
C.-K. Skylaris, L. Gagliardi, N. C. Handy, A. G. Ioannou, S. Spencer, A. Willetts and A. M. Simper. Chem. Phys. Lett. 296, 445-451 (1998)
Localised spherical-wave basis set for O(N) total-energy pseudopotential calculations
P. D. Haynes and M. C. Payne, Comput. Phys. Commun. 102, 17-27 (1997)

Selected Publications by the ONETEP Community

"Janus" Cyclic Peptides: A New Approach to Amyloid Fibril Inhibition? N. Todorova, L. Yeung, A. Hung, and I. Yarovsky, PLoS ONE 8(2), e57437 (2013) ONLINE JOURNAL
Comparative studies for evaluation of CO (2) fixation in the cavity of the Rubisco enzyme using QM, QM/MM and linear-scaling DFT methods
M. M. El-Hendawy, N. J. English, D. A. Mooney, J. Mol. Model., (2013) ONLINE JOURNAL
Defect motifs for spherical topologies
D. Wales, H. Mackay and E. L. Altschuler, Phys. Rev. B 79, 224115 (2009) ONLINE JOURNAL