Pablo Ordejón

The SIESTA method for ab initio order-N materials simulation

We have developed and implemented a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical linear combination of atomic orbitals basis set, which includes multiple-zeta and polarization orbitals. Exchange and correlation are treated with the local spin density or generalized gradient approximations. The basis functions and the electron density are projected on a real-space grid, in order to calculate the Hartree and exchange-correlation potentials and matrix elements, with a number of operations that scales linearly with the size of the system. We use a modified energy functional, whose minimization produces orthogonal wavefunctions and the same energy and density as the Kohn-Sham energy functional, without the need for an explicit orthogonalization. Additionally, using localized Wannier-like electron wavefunctions allows the computation time and memory required to minimize the energy to also scale linearly with the size of the system. Forces and stresses are also calculated efficiently and accurately, thus allowing structural relaxation and molecular dynamics simulations.An efficient method is described to handle mesh indexes in multidimensional problems like numerical integration of partial differential equations, lattice model simulations, and determination of atomic neighbor lists. By creating an extended mesh, beyond the periodic unit cell, the stride in memory between equivalent pairs of mesh points is independent of their position within the cell. This allows to contract the mesh indexes of all dimensions into a single index, avoiding modulo and other implicit index operations.

Density-functional method for nonequilibrium electron transport

We describe an ab initio method for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density-functional theory (DFT) as implemented in the well tested SIESTA approach (which uses nonlocal norm-conserving pseudopotentials to describe the effect of the core electrons, and linear combination of finite-range numerical atomic orbitals to describe the valence states). We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including self-consistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Greens functions. We relate the nonequilibrium Greens function expressions to the more transparent scheme involving the scattering states. As an illustration, the method is applied to three systems where we are able to compare our results to earlier ab initio DFT calculations or experiments, and we point out differences between this method and existing schemes. The systems considered are: (i) single atom carbon wires connected to aluminum electrodes with extended or finite cross section, (ii) single atom gold wires, and finally (iii) large carbon nanotube systems with point defects.

Self-consistent order- N density-functional calculations for very large systems

We present a method to perform fully self-consistent density-functional calculations that scales linearly with the system size and which is well suited for very large systems. It uses strictly localized pseudoatomic orbitals as basis functions. The sparse Hamiltonian and overlap matrices are calculated with an {ital O}({ital N}) effort. The long-range self-consistent potential and its matrix elements are computed in a real-space grid. The other matrix elements are directly calculated and tabulated as a function of the interatomic distances. The computation of the total energy and atomic forces is also done in {ital O}({ital N}) operations using truncated, Wannier-like localized functions to describe the occupied states, and a band-energy functional which is iteratively minimized with no orthogonality constraints. We illustrate the method with several examples, including carbon and silicon supercells with up to 1000 Si atoms and supercells of {beta}-C{sub 3}N{sub 4}. We apply the method to solve the existing controversy about the faceting of large icosahedral fullerenes by performing dynamical simulations on C{sub 60}, C{sub 240}, and C{sub 540}. {copyright} {ital 1996 The American Physical Society.}

Ab-initio structural, elastic, and vibrational properties of carbon nanotubes

A study based on ab initio calculations is presented on the structural, elastic, and vibrational properties of single-wall carbon nanotubes with different radii and chiralities. These properties are obtained using an implementation of pseudopotential-density-functional theory which allows calculations on systems with a large number of atoms per cell. Different quantities are monitored versus tube radius. The validity of expectations based on graphite is explored down to small radii, where some deviations appear related to the curvature-induced rehibridization of the carbon orbitals. Young moduli are found to be very similar to graphite and do not exhibit a systematic variation with either the radius or the chirality. The Poisson ratio also retains graphitic values except for a possible slight reduction for small radii. It shows, however, chirality dependence. The behavior of characteristic phonon branches as the breathing mode, twistons, and high-frequency optic modes, is also studied, the latter displaying a small chirality dependence at the top of the band. The results are compared with the predictions of the simple zone-folding approximation. Except for the known defficiencies of the zone-folding procedure in the low-frequency vibrational regions, it offers quite accurate results, even for relatively small radii.

LINEAR-SCALING AB-INITIO CALCULATIONS FOR LARGE AND COMPLEX SYSTEMS

A brief review of the Siesta project is presented in the context of linear-scaling density-functional methods for electronic-structure calculations and molecular-dynamics simulations of systems with a large number of atoms. Applications of the method to different systems are reviewed, including carbon nanotubes, gold nanostructures, adsorbates on silicon surfaces, and nucleic acids. Also, progress in atomic-orbital bases adapted to linear-scaling methodology is presented.

The SIESTA method; developments and applicability

Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.

Stiff Monatomic Gold Wires with a Spinning Zigzag Geometry

Using first principles density functional calculations, gold monatomic wires are found to exhibit a zigzag shape which remains under tension, becoming linear just before breaking. At room temperature they are found to spin, what explains the extremely long apparent interatomic distances shown by electron microscopy.The zigzag structure is stable if the tension is relieved, the wire holding its chainlike shape even as a free-standing cluster. This unexpected metallic-wire stiffness stems from the transverse quantization in the wire, as shown in a simple free electron model.

Tight-binding model and direct-gap/indirect-gap transition in single-layer and multilayer MoS2

In this paper we present a paradigmatic tight-binding model for single-layer as well as multilayered semiconducting MoS2 and similar transition metal dichalcogenides. We show that the electronic properties of multilayer systems can be reproduced in terms of a tight-binding modeling of the single-layer hopping terms by simply adding the proper interlayer hoppings ruled by the chalcogenide atoms. We show that such a tight-binding model makes it possible to understand and control in a natural way the transition between a direct-gap band structure, in single-layer systems, and an indirect gap in multilayer compounds in terms of a momentum/orbital selective interlayer splitting of the relevant valence and conduction bands. The model represents also a suitable playground to investigate in an analytical way strain and finite-size effects.

Real-Time TD-DFT Simulations in Dye Sensitized Solar Cells: The Electronic Absorption Spectrum of Alizarin Supported on TiO2 Nanoclusters

The structural and electronic properties of the alizarin dye supported on TiO2 nanoclusters have been examined by means of time-dependent density-functional (TD-DFT) calculations performed in the time-domain framework. The calculated electronic absorption spectrum of free alizarin shows a first band centered at 2.67 eV that upon adsorption features a red shift by 0.31 eV, in agreement with both experimental and previous theoretical work. This red shift arises from a relative stabilization of the dye LUMO when adsorbed. To analyze the dependence of the electronic properties of the dye-support couple on the size of metal-oxide nanoparticles, different models of (TiO2)n nanoclusters have been used (with n = 1, 2, 3, 6, 9, 15, and 38). As a conclusion, the minimal model is good enough to theoretically reproduce the main feature in the spectrum (i.e., the energy shift of the main band upon binding to TiO2). However, it fails in creating intermediate states which could play a significant role under real experimental conditions (dynamics of the electronic transfer). Indeed, as the size of the nanocluster grows, the dye LUMO moves from the edge to well inside the conduction band (Ti 3d band). On the other hand, to assess the consistency of the time-domain approach in the case of such systems, conventional (frequency-domain) TD-DFT calculations have been carried out. It is found that, as far as the functional and basis set are equivalent, both approaches lead to similar results. While for small systems the standard TD-DFT is better suited, for medium to large sized systems, the real-time TD-DFT becomes competitive and more efficient.

TranSIESTA: A Spice for Molecular Electronics

Abstract: Our recently developed method, TranSIESTA, enables modelling of molecular electronic devices under operation conditions. The method is based on density functional theory, and calculates the self‐consistent electronic structure of a nanostructure coupled to three‐dimensional electrodes with different electrochemical potentials. It uses a full atomistic ab initio description of both the electrodes and the nanoscale device. The calculations reveal information about the scattering states, transmission coefficients, electron current, and non‐equilibrium forces in the systems. In this paper we use the method to investigate the electrical properties of three ring phenyl‐ethynylene oligomers (OPE). We present results for the electrical effect of side groups and molecular conformations of the molecules. The calculations indicate that molecular switching and negative differential conductance (NDC) are related to rotations of the middle phenyl ring.