Publications describing the ONETEP code


In publications arising from the use of ONETEP please cite

The ONETEP linear-scaling density functional theory program
J. C. A. Prentice, J. Aarons, J. C. Womack, A. E. A. Allen, L. Andrinopoulos, L. Anton, R. A. Bell, A. Bhandari, G. A. Bramley, R. J. Charlton, R. J. Clements, D. J. Cole, G. Constantinescu, F. Corsetti, S. M.-M. Dubois, K. K. B. Duff, J. M. Escartín, A. Greco, Q. Hill, L. P. Lee, E. Linscott, D. D. O'Regan, M. J. S. Phipps, L. E. Ratcliff, Á. Ruiz Serrano, E. W. Tait, G. Teobaldi, V. Vitale, N. Yeung, T. J. Zuehlsdorff, J. Dziedzic, P. D. Haynes, N. D. M. Hine, A. A. Mostofi, M. C. Payne, C.-K. Skylaris
J. Chem. Phys. 152, 174111 (2020) ONLINE JOURNAL

This supersedes the previous general reference paper, which now only need be cited as a reference to the fundamental underlying ideas and algorithms:

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)

2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 Pre-2005

2020

  • Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory \\ J. Dziedzic, A. Bhandari, L. Anton, C. Peng, J. C. Womack, M. Famili, D. Kramer, and C.-K. Skylaris. \\

J. Phys. Chem. C.

  • Electron localisation descriptors in ONETEP: a tool for interpreting localisation and bonding in large-scale DFT calculations \\ R. J. Clements, J. C. Womack, and C.-K. Skylaris. \\

Electron. Struct. (2020)

  • The role of electrostatics in enzymes: do biomolecular force fields reflect protein electric fields? \\ R. T. Bradshaw, J. Dziedzic, C.-K. Skylaris, and J. W. Essex.
    J. Chem. Inf. Model. (2020)
  • Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study
    G. Bramley, M.-T. Nguyen, V.-A. Glezakou, R. Rousseau, and C.-K. Skylaris.
    J. Chem. Theor. Comput. (2020)
  • Meta-analysis: the molecular organization of non-fullerene acceptors.
    P. Mondelli, G. Boschetto, P. Horton, P. Tiwana, C.-K. Skylaris, S. Coles, M. Krompiec, and G. Morse.
    Mater. Horiz. (2020)
  • ONETEP + TOSCAM: uniting dynamical mean field theory and linear-scaling density functional theory
    E. B. Linscott, D. J. Cole, N. D. M. Hine, M. C. Payne, C. Weber
    J. Chem. Theory Comput., in press (2020)
  • The ONETEP linear-scaling density functional theory program
    J. C. A. Prentice, J. Aarons, J. C. Womack, A. E. A. Allen, L. Andrinopoulos, L. Anton, R. A. Bell, A. Bhandari, G. A. Bramley, R. J. Charlton, R. J. Clements, D. J. Cole, G. Constantinescu, F. Corsetti, S. M.-M. Dubois, K. K. B. Duff, J. M. Escartín, A. Greco, Q. Hill, L. P. Lee, E. Linscott, D. D. O'Regan, M. J. S. Phipps, L. E. Ratcliff, Á. Ruiz Serrano, E. W. Tait, G. Teobaldi, V. Vitale, N. Yeung, T. J. Zuehlsdorff, J. Dziedzic, P. D. Haynes, N. D. M. Hine, A. A. Mostofi, M. C. Payne, C.-K. Skylaris
    J. Chem. Phys. 152, 174111 (2020) ONLINE JOURNAL
  • Combining embedded mean-field theory with linear-scaling density-functional theory
    J. C. A. Prentice, R. J. Charlton, A. A. Mostofi and P. D. Haynes
    J. Chem. Theory Comput. 16, 354 (2020) ONLINE JOURNAL

2019

  • Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields
    D. J. Cole, I. Cabeza de Vaca, W. L. Jorgensen
    MedChemComm, Advance Article (2019) ONLINE JOURNAL.
  • Mutually polarizable QM/MM model with in situ optimized localized basis functions
    J. Dziedzic, T. Head-Gordon, M. Head-Gordon, C.-K. Skylaris
    J. Chem. Phys. 150, 074103 (2019) ONLINE JOURNAL.
  • QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics
    J. T. Horton, A. E. A. Allen, L. S. Dodda, D. J. Cole
    J. Chem. Inf. Model. 59, 1366 (2019) ONLINE JOURNAL.
  • Resolution of the "exponent puzzle" for the Anderson transition in doped semiconductors
    E. G. Carnio, N. D. M. Hine, R. A. Roemer
    Phys Rev B (Rapid Comms) 99, 081201 (2019). ONLINE JOURNAL.
  • Introducing QUBE: Quantum Mechanical Bespoke Force Fields for Protein Simulations
    A. E. A. Allen, M. J. Robertson, M. C. Payne, D. J. Cole
    ChemRxiv preprint (2019) CHEMRXIV.
  • Determination of Secondary Species in Solution through Pump-Selective Transient Absorption Spectroscopy and Explicit-Solvent TDDFT
    M. A. P. Turner, M. D. Horbury, V. G. Stavros, and N. D. M. Hine
    J. Phys. Chem. A 123, 873 (2019). ONLINE JOURNAL.

2018

  • Band structure interpolation using optimized local orbitals from linear-scaling density functional theory
    L. E. Ratcliff, G. J. Conduit, N. D. M. Hine, and P. D. Haynes
    Phys. Rev. B 98, 125123 (2018). ONLINE JOURNAL.
  • Photophysics and Photochemistry of DNA Molecules - Electronic Excited States Leading to Thymine Dimerization
    J.-H. Li, T. J. Zuehlsdorff, M. C. Payne, and N. D. M. Hine
    J. Phys. Chem. C. 122, 11633 (2018). ONLINE JOURNAL
  • Ideal vs Real: Simulated Annealing of Experimentally Derived and Geometric Platinum Nanoparticles
    T. H. Ellaby, J. Aarons, A. Varambhia, L. Jones, P. Nellist, D. Özkaya, M. Sarwar, D. Thompsett, and C.-K. Skylaris.
    J. Phys. Condens. Matter. 30, 155301 (2018) ONLINE JOURNAL.
  • Implicit and explicit host effects on excitons in pentacene derivatives
    R. J. Charlton, R. M. Fogarty, S. Bogatko, T. J. Zuehlsdorff, N. D. M. Hine, M. Heeney, A. P. Horsfield, and P. D. Haynes
    J. Chem. Phys. 148, 104108 (2018) ONLINE JOURNAL.
  • DL_MG: A parallel multigrid Poisson and Poisson-Boltzmann solver for electronic structure calculations in vacuum and solution
    J. Womack, L. Anton, J. Dziedzic, P. Hasnip, M. Probert, and C.-K. Skylaris
    J. Chem. Theor. Comput. 14, 1412 (2018) ONLINE JOURNAL.
  • Electronic annealing Fermi operator expansion for DFT calculations on metallic systems
    J. Aarons and C.-K. Skylaris
    J. Chem. Phys. 148, 074017 (2018). ONLINE JOURNAL.
  • DFT calculation of oxygen adsorption on platinum nanoparticles: Coverage and size effects
    L.G. Verga, J. Aarons, M. Sarwar, D. Thompsett, A. E. Russell, and C-K. Skylaris
    Faraday Discuss. 208, 497 (2018) ONLINE JOURNAL.
  • Self-assembly of bis-salphen compounds: from semiflexible chains to webs of nanorings
    S. V. Pyrlin, N. D. M. Hine, A. W. Kleij and M. M. D. Ramos
    Soft Matter 14, 1181 (2018) ONLINE JOURNAL.

2017

  • Distance dependent photoacoustics revealed through DNA nanostructures,
    J. Joseph, K. N. Baumann, P. Koehler, T. J. Zuehlsdorff, D. J. Cole, J. Weber, S. E. Bohndiek and S. Hernández-Ainsa,
    Nanoscale, 2017,9, 16193-16199 ONLINE JOURNAL.
  • Spatially resolving density-dependent screening around a single charged atom in graphene
    FD. Wong, F. Corsetti, Y. Wang, V. W. Brar, H.-Z. Tsai, Q. Wu, R. K. Kawakami, A. Zettl, A. A. Mostofi, J. Lischner and M. F. Crommie
    Phys. Rev. B 95, 205419 (2017) ONLINE JOURNAL.
  • First-principles multiscale modelling of charged adsorbates on doped graphene
    F. Corsetti, A. A. Mostofi and J. Lischner
    2D Materials 4, 025070 (2017) ONLINE JOURNAL.
  • Predicting the oxygen binding properties of platinum nanoparticle ensembles by combining high-precision electron microscopy & DFT
    J. Aarons, L. Jones, A. Varambhia, K. E. MacArthur, D. Ozkaya, M. Sarwar, C.-K. Skylaris, and P. D. Nellist
    Nano Letters 17, 4003 (2017) ONLINE JOURNAL.
  • Evidence for Correlated Static Disorder in the Fenna-Matthews-Olson Complex
    A. S. Fokas, D. J. Cole, N. D. M. Hine, S. A. Wells, M. C. Payne, and A. W. Chin
    J. Phys. Chem. Lett 8, 2350 (2017) ONLINE JOURNAL.
  • Intuitive Density Functional Theory-Based Energy Decomposition Analysis for Protein–Ligand Interactions
    M. J. S. Phipps, T. Fox, C. S. Tautermann, and C.-K. Skylaris
    J. Chem. Theor. Comput. 13, 1837(2017) ONLINE JOURNAL.
  • Predicting solvatochromic shifts and colours of a solvated organic dye: The example of Nile Red
    T. J. Zuehlsdorff, P. D. Haynes, M. C. Payne, and N. D. M. Hine
    J. Chem. Phys. 146, 124504 (2017) ONLINE JOURNAL.
  • Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory
    V. Vitale, J. Dziedzic, A. Albaugh, A. M. N. Niklasson, T. Head-Gordon, and C.-K. Skylaris
    J. Chem. Phys. 146, 124115 (2017) ONLINE JOURNAL.
  • Determination of band offsets, hybridization and exciton binding in 2D semiconductor heterostructures
    N. R. Wilson, P. Nguyen, K. Seyler, P. Rivera, A. J. Marsden, Z. P. L. Laker, G. C. Constantinescu, V. Kandyba, A. Barinov, N. D. M. Hine, X Xu, D. H. Cobden
    Science Advances 3, e1601832 (2017) ONLINE JOURNAL arXiv.
  • Linear-scaling density functional simulations of the effect of crystallographic structure on electronic and optical properties of fullerene solvates
    H-T. Xue, G. Boschetto, M. Krompiec, G. E. Morse, F.-L. Tang, and C.-K. Skylaris
    Phys. Chem. Chem. Phys. 19, 5617 (2017). ONLINE JOURNAL.
  • Effect of Polymerization Statistics on the Electronic Properties of Copolymers for Organic Photovoltaics
    G. Boschetto, H.-T. Xue, J. Dziedzic, M. Krompiec, and C.-K. Skylaris
    J. Phys. Chem. C 121, 2529 (2017). ONLINE JOURNAL.
  • Unravelling the Roles of Size, Ligands and Pressure in the Piezochromic Properties of CdS Nanocrystals
    N. R. C. Corsini, N. D. M. Hine, P. D. Haynes and C. Molteni
    Nano Letters 17, 1042 (2017). ONLINE JOURNAL
  • Linear-Scaling Density Functional Theory using the Projector Augmented Wave Method
    N. D. M. Hine
    J. Phys. Condens. Matter 29, 024001 (2017). ONLINE JOURNAL

2016

  • Perspective: Methods for large-scale density functional calculations on metallic systems
    J. Aarons, M. Sarwar, D. Thompsett, and C.-K. Skylaris
    J. Chem. Phys. 145 220901 (2016) ONLINE JOURNAL
  • Effect of graphene support on large Pt nanoparticles
    L. G. Verga, J. Aarons, M. Sarwar, D. Thompsett, A. E. Russell and C.-K. Skylaris
    Phys. Chem. Chem. Phys. DOI: 10.1039/C6CP07334D ONLINE JOURNAL
  • Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package
    J. C. Womack, Narbe Mardirossian, Martin Head-Gordon, and Chris-Kriton Skylaris
    J. Chem. Phys. 145, 204114 (2016) ONLINE JOURNAL
  • Tuning the Role of Charge-Transfer States in Intramolecular Singlet Exciton Fission Through Side-Group Engineering
    S. Lukman, K. Chen, J. M. Hodgkiss, D. Turban, N. D. M. Hine, S. Dong, J. Wu, N. C. Greenham and A. J. Musser
    Nature Communications 7, 13622 (2016) ONLINE JOURNAL
  • Inapplicability of exact constraints and a minimal two-parameter generalization to the DFT+U based correction of self-interaction error
    G. Moynihan, G. Teobaldi, and D. D. O'Regan
    Phys. Rev. B 94, 220104(R) (2016) ONLINE JOURNAL
  • TINKTEP: A fully self-consistent, mutually-polarizable QM/MM approach based on the AMOEBA force field
    J. Dziedzic, Y. Mao, Y. Shao, J. Ponder, T. Head-Gordon, M. Head-Gordon, and C.-K. Skylaris.
    J. Chem. Phys, 145, 124106 (2016) ONLINE JOURNAL
  • Energy decomposition analysis based on absolutely localised molecular orbitals for large-scale density functional theory calculations in drug design.
    M. J. S. Phipps, T. Fox, C. S. Tautermann, and C.-K. Skylaris. J. Chem. Theory Comput. 12, 3135 (2016) ONLINE JOURNAL
  • Advanced Potential Energy Surfaces for Molecular Simulation
    A. Albaugh, H. A. Boateng, R. T. Bradshaw, O. N. Demerdash, J. Dziedzic, Y. Mao, D. T. Margul, J. M. Swails, Q. Zeng, D. A. Case, P. K. Eastman, J. W. Essex, M. Head-Gordon, V. S. Pande, J. W. Ponder, Y. Shao, C.-K. Skylaris, I. T. Todorov, M. E. Tuckerman, T. Head-Gordon
    J. Phys. Chem. B (2016) ONLINE JOURNAL
  • Chemically Selective Alternatives to Photoferroelectrics for Polarization-Enhanced Photocatalysis: the Untapped Potential of Hybrid Inorganic Nanotubes
    J. D. Elliott, E. Poli, I. Scivetti, L. E. Ratcliff, L. Andrinopoulos, J. Dziedzic, N. D. M. Hine, A. A. Mostofi, C.-K. Skylaris, P. D. Haynes, G. Teobaldi
    Advanced Science 1600153 (2016) ONLINE JOURNAL
  • Applications of large-scale density functional theory in biology
    D. J. Cole and N. D. M. Hine
    J. Phys. Condens. Matter 28, 393001 (2016) ONLINE JOURNAL
  • Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning
    D. J. Cole, J. Z. Vilseck, J. Tirado-Rives, M. C. Payne, and W. L. Jorgensen
    J. Chem. Theory Comput. 12, 2312 (2016) ONLINE JOURNAL
  • Optimization of constrained density functional theory
    D. D. O'Regan and G. Teobaldi
    Phys. Rev. B 94, 035159 (2016) ONLINE JOURNAL arXiv
  • Multi-purpose Black-Phosphorus/hBN heterostructures
    G. C. Constantinescu, N. D. M. Hine
    Nano Letters, 16, 2586 (2016). ONLINE JOURNAL
  • Simulation of electron energy loss spectra of nanomaterials with linear-scaling density functional theory
    E. W. Tait, L. E. Ratcliff, M. C. Payne, P. D. Haynes and N. D. M. Hine
    J. Phys: Condens Matter, 28 195202 (2016). ONLINE JOURNAL
  • Supercell convergence of charge-transfer energies in pentacene molecular crystals from constrained DFT
    D. H. P. Turban, G. Teobaldi, D. D. O'Regan, N. D. M. Hine
    Phys. Rev. B 93, 165102 (2016) ONLINE JOURNAL arXiv
  • Solvent effects on electronic excitations of an organic chromophore
    T. J. Zuehlsdorff, P. D. Haynes, F. Hanke, M. C. Payne, and N. D. M. Hine
    J. Chem. Theory Comput., 12, 1853 (2016). ONLINE JOURNAL
  • The potential of Imogolite nanotubes as (co-)photocatalyst: a linear-scaling Density Functional Theory study
    E. Poli, J. D. Elliott, L. E. Ratcliff, L. Andrinopoulos, J. Dziedzic, N. D. M. Hine, A. A. Mostofi, C.-K. Skylaris, P. D. Haynes and G. Teobaldi
    J. Phys. Condens. Matter, 28 074003 (2016). ONLINE JOURNAL

2015

  • Pressure-induced amorphisation and a new high density amorphous metallic phase in matrix-free Ge nanoparticles
    N. R. C. Corsini, W. R. Little, A. Karatutlu, Y. Zhang, O. Ersoy, P. D. Haynes, C. Molteni, N. D. M. Hine, I. Hernandez, J. Gonzalez, F. Rodriguez, V. V. Brazhkin, and A. Sapelkin
    Nano Letters 15, 7334 (2015). ONLINE JOURNAL
  • Linear-scaling time-dependent density-functional theory (TDDFT) beyond the Tamm-Dancoff approximation: obtaining efficiency and accuracy with in situ optimised local orbitals
    T. J. Zuehlsdorff, N. D. M. Hine, M. C. Payne, P. D. Haynes
    J. Chem. Phys. 143, 204107 (2015) ONLINE JOURNAL arXiv.
  • Large-scale density functional theory simulation of inorganic nanotubes: a case study on Imogolite nanotubes
    E. Poli, J. D. Elliott, N. D. M. Hine, A. A. Mostofi and G. Teobaldi
    Mater. Res. Innov. 19, S272 (2015). ONLINE JOURNAL.
  • Anharmonic infrared spectroscopy through the Fourier transform of time correlation function formalism in ONETEP
    V. Vitale, J. Dziedzic, S. Dubois, H. Fangohr, and C.-K. Skylaris
    J. Chem. Theory Comput., 11(7), 3321 (2015). ONLINE JOURNAL.
  • A "Stepping Stone" Approach for Obtaining Quantum Free Energies of Hydration
    C. Sampson, T. Fox, C. S. Tautermann, C. J. Woods, and C.-K. Skylaris
    J. Phys. Chem. B, 119, 7030 (2015). ONLINE JOURNAL.
  • Energy landscape and band-structure tuning in realistic MoS2/MoSe2 heterostructures
    G. C. Constantinescu and N. D. M. Hine
    Phys. Rev. B 91, 195416 (2015). ONLINE JOURNAL.
  • Electronic transport calculations in the ONETEP code: Implementation and applications
    R. A. Bell, S. M.-M. Dubois, M. C. Payne, A. A. Mostofi,
    Comput. Phys. Commun. 193, 78 (2015). ONLINE JOURNAL.
  • Identifying and tracing potential energy surfaces of electronic excitations with specific character via their transition origins: application to oxirane
    J-H. Li, T. J. Zuehlsdorff, M. C. Payne, N. D. M. Hine,
    Phys. Chem. Chem. Phys. 17, 12065 (2015). ONLINE JOURNAL arXiv.
  • Acid-Base Dissociation Mechanisms and Energetics at the Silica-Water Interface: An Activationless Process
    B. M. Lowe, C.-K. Skylaris, and N. G. Green
    Journal of Colloid and Interface Science, 451, 231 (2015). ONLINE JOURNAL

2014

  • Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms
    L. P. Lee, N. Gabaldon Limas , D. J. Cole , M. C. Payne , C.-K. Skylaris , and T. A. Manz,
    J. Chem. Theory Comput., 10, 5377 (2014). ONLINE JOURNAL.
  • Does water dope carbon nanotubes?
    R. A. Bell, M. C. Payne and A. A. Mostofi,
    J. Chem. Phys. 141, 164703 (2014). ONLINE JOURNAL.
  • Density functional theory calculations on entire proteins for free energies of binding: application to a model polar binding site
    S. J. Fox, J. Dziedzic, T. Fox, C. S. Tautermann, and C.-K. Skylaris,
    PROTEINS, 82, 3335 (2014). ONLINE JOURNAL.
  • Optimised three-dimensional Fourier interpolation: An analysis of techniques and application to a linear-scaling density functional theory code
    F. P. Russell, K. A. Wilkinson, Paul H. J. Kelly, and C.-K. Skylaris,
    Comput. Phys. Commun., 187, 8 (2014). ONLINE JOURNAL.
  • Hybrid MPI-OpenMP parallelism in the ONETEP linear-scaling electronic structure code: Application to the delamination of cellulose nano-fibrils
    K. A. Wilkinson, N. D. M. Hine, and C.-K. Skylaris,
    J. Chem. Theory Comput. 10, 4782 (2014). ONLINE JOURNAL.
  • Large-Scale Density Functional Theory Transition State Searching in Enzymes
    G. Lever, D. J. Cole, R. Lonsdale, K. E. Ranaghan, D. J. Wales, A. J. Mulholland, C.-K. Skylaris, and M. C. Payne,
    J. Phys. Chem. Lett., 5, 3614 (2014). ONLINE JOURNAL.
  • Renormalization of myoglobin–ligand binding energetics by quantum many-body effects
    C. Weber, D. J. Cole, D. D. O'Regan, and M. C. Payne,
    Proc. Natl. Acad. Sci. USA, 2014 111 (16) 5790-5795. ONLINE JOURNAL.

2013

  • Towards ab initio Optical Spectroscopy of the Fenna-Matthews-Olson Complex
    D. J. Cole, A. W. Chin, N. D. M. Hine, P. D. Haynes and M. C. Payne,
    J. Phys. Chem. Lett. 4, 4206 (2013). ONLINE JOURNAL.
  • Variationally localized search direction method for constrained optimization of non-orthogonal, localized orbitals in electronic structure calculations
    A. Ruiz-Serrano and C.-K. Skylaris,
    J. Chem. Phys 139, 164110 (2013). ONLINE JOURNAL.
  • Linear-scaling calculation of Hartree-Fock exchange energy with Non-orthogonal Generalised Wannier Functions
    J. Dziedzic, Q. O. Hill and C.-K. Skylaris,
    J. Chem. Phys 139, 214103 (2013). ONLINE JOURNAL.
  • Dimensionality of carbon nanomaterials determines the binding and dynamics of amyloidogenic peptides: multiscale theoretical simulations
    A. J. Makarucha, N. Todorova, N. D. M. Hine, A. A. Mostofi, I. Yarovsky, PLoS Comput Biol 9, e1003360 (2013). ONLINE JOURNAL
  • Porting ONETEP to Graphical Processing Unit based Coprocessors: 1. FFT box Operations
    K. Wilkinson and C.-K. Skylaris
    J. Comput. Chem. (July 2013). ONLINE JOURNAL
  • Free Energies of Binding from Large-Scale First Principles Quantum Mechanical Calculations: Application to Ligand Hydration Energies
    S. J. Fox, C. Pittock, C. S. Tautermann, T. Fox, C. Christ, N.O.J. Malcolm, J. W. Essex, and C.-K. Skylaris
    J. Phys. Chem. B 117, 9478 (2013). ONLINE JOURNAL.
  • Simulations of Nanocrystals Under Pressure: Combining Electronic Enthalpy and Linear-Scaling Density-Functional Theory
    N. R. C. Corsini, A. Greco, N. D. M. Hine, C. Molteni, P. D. Haynes
    J. Chem. Phys. 139, 084117 (2013). arXiv ONLINE JOURNAL.
  • Bromophenyl functionalization of carbon nanotubes: an ab initio study
    J. Beaudin, J. Laflamme Janssen, N. D. M. Hine, P. D. Haynes, and M. Cote,
    Nanotechnology 24, 375702 (2013). arXiv ONLINE JOURNAL.
  • 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
    J. Chem. Phys. 139, 064104 (2013). arXiv ONLINE JOURNAL.
  • A variational method for density functional theory calculations on metallic systems with thousands of atoms
    A. Ruiz-Serrano and C.-K. Skylaris
    J. Chem. Phys. 139, 054107 (2013). ONLINE JOURNAL.
  • Ab initio calculations of the optical absorption spectra of C60-conjugated polymer hybrids
    L. E. Ratcliff and P. D. Haynes
    Phys. Chem. Chem. Phys. 15, 13024 (2013). ONLINE JOURNAL.
  • 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. 9, 2981 (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 e ffects 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
  • Optical Absorption Spectra Calculated Using Linear-Scaling Density-Functional Theory,
    Laura Ratcliff, (Springer, Berlin, Heidelberg, 2013) 1st Ed., Springer Theses XI, 116p., ISBN 978-3-319-00338-2. ONLINE BOOK

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

  • Analysis of a capped carbon nanotube by linear-scaling density-functional theory, C. J. Edgcombe, S. M. Masur, E. B. Linscott, J. A. J. Whaley-Baldwin, and C. H. W. Barnes, Ultramicroscopy 198, 26 (2019) ONLINE JOURNAL
  • Graft-Induced Mid-Gap States in Functionalized Carbon Nanotubes, D. Bouilly, J. J. Laflamme, J. Cabana, M. Côté, and R. Martel, ACS Nano 9, 2626 (2015) ONLINE JOURNAL
  • Nanorings and rods interconnected by self-assembly mimicking an artificial network of neurons, M. V. Escárcega-Bobadilla, G. A. Zelada-Guillén, S. V. Pyrlin, M. Wegrzyn, M. M. D. Ramos, E. Giménez, A. Stewart, G. Maier and A. W. Kleij, Nature Communications 4, 2648 (2013) ONLINE JOURNAL
  • "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
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