DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method Aradi, B; Hourahine, B; Frauenheim, Th
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
07/2007, Letnik:
111, Številka:
26
Journal Article
Recenzirano
A new Fortran 95 implementation of the DFTB (density functional-based tight binding) method has been developed, where the sparsity of the DFTB system of equations has been exploited. Conventional ...dense algebra is used only to evaluate the eigenproblems of the system and long-range Coulombic terms, but drop-in O(N) or O(N 2) modules are planned to replace the small code sections that these entail. The developed sparse storage structure is discussed in detail, and a short overview of other features of the new code is given.
Recent experimental observations suggested that the presence of oxygen vacancies on TiO2 surfaces affects the adsorption mode of formic acid ( Xu, M. ; Catal. Today 2012, 182, 12 ). Here we use ...density functional theory and the hybrid density functional HSE06 form for the exchange–correlation functional to determine the atomic geometry and band structure of single molecules on TiO2(101) surfaces. We show that formic acid adsorbs dissociatively on both perfect and defective surfaces with no overlap between oxygen defect states and molecular states, leading to no change in the adsorption mode. We propose that both relaxation experienced by the surface atoms due to the presence of vacancies and molecule adsorption affect the electronic structure of the surface, leading to stabilization of the monodentate mode.
A model for diamond nucleation by energetic species (for example, bias-enhanced nucleation) is proposed. It involves spontaneous bulk nucleation of a diamond embryo cluster in a dense, amorphous ...carbon hydrogenated matrix; stabilization of the cluster by favorable boundary conditions of nucleation sites and hydrogen termination; and ion bombardment-induced growth through a preferential displacement mechanism. The model is substantiated by density functional tight-binding molecular dynamics simulations and an experimental study of the structure of bias-enhanced and ion beam-nucleated films. The model is also applicable to the nucleation of other materials by energetic species, such as cubic boron nitride.
We outline recent developments in quantum mechanical atomistic modelling of complex materials properties that combine the efficiency of semi‐empirical quantum‐chemistry and tight‐binding approaches ...with the accuracy and transferability of more sophisticated density‐functional and post‐Hartree‐Fock methods with the aim to perform highly predictive materials simulations of technological relevant sizes in physics, chemistry and biology. Following Harris, Foulkes and Haydock, the methods are based on an expansion of the Kohn‐Sham total energy in density‐functional theory (DFT) with respect to charge density fluctuations at a given reference density. While the zeroth order approach is equivalent to a common standard non‐self‐consistent tight‐binding (TB) scheme, at second order by variationally treating the approximate Kohn‐Sham energy a transparent, parameter‐free, and readily calculable expression for generalized Hamiltonian matrix elements may be derived. These matrix elements are modified by a Self‐Consistent redistribution of Mulliken Charges (SCC). Besides the usual “band‐structure” and short‐range repulsive terms the final approximate Kohn‐Sham energy explicitly includes Coulomb interaction between charge fluctuations. The new SCC‐scheme is shown to successfully apply to problems, where defficiencies within the non‐SCC standard TB‐approach become obvious. These cover defect calculations and surface studies in polar semiconductors (see M. Haugk et al. of this special issue), spectroscopic studies of organic light‐emitting thin films, briefly outlined in the present article, and atomistic investigations of biomolecules (see M. Elstner et al. of this special issue).
Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of ...quantum mechanics−molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.
Self-Interaction and Strong Correlation in DFTB Hourahine, B; Sanna, S; Aradi, B ...
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
07/2007, Letnik:
111, Številka:
26
Journal Article
Recenzirano
The density functional based tight-binding (DFTB) method can benefit substantially from a number of developments in density functional theory (DFT) while also providing a simple analytical proving ...ground for new extensions. This contribution begins by demonstrating the variational nature of charge-self-consistent DFTB (SCC-DFTB), proving the presence of a defined ground-state in this class of methods. Because the ground state of the SCC-DFTB method itself can be qualitatively incorrect for some systems, suitable forms of the recent LDA+U functionals for SCC-DFTB are also presented. This leads to both a new semilocal self-interaction correction scheme and a new physical argument for the choice of parameters in the LDA+U method. The locality of these corrections can only partly repair the HOMO−LUMO gap and chemical potential discontinuity, hence a novel method for introducing this further physics into the method is also presented, leading to exact derivative discontinuities in this theory at low computational cost. The prototypical system NiO is used as an illustration for these developments.
We employ density‐functional theory (DFT) within the generalized‐gradient approximation (GGA) to investigate the formation energies, electronic structure, and magnetic properties of N impurities in ...zinc oxide (ZnO) nanowires. While the subsurface position is the preferential site for the N dopants in bare nanowires, upon hydrogen passivation N atoms segregate to surface sites. Additionally we show that the defect levels in these ultra‐thin wires are deeper than the ones in bulk ZnO, suggesting strong quantum dimensional effects. Finally we investigate the possibility of ferromagnetism induced by N in ZnO nanowires. Our spin‐polarized calculations show that, although N introduces a small net magnetic moment in ZnO, the interaction between N dopants is weak and strongly dependent on the N position.
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