Daniel Sanchez-Portal

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.

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.

Numerical atomic orbitals for linear-scaling calculations

The performance of basis sets made of numerical atomic orbitals is explored in density-functional calculations of solids and molecules. With the aim of optimizing basis quality while maintaining strict localization of the orbitals, as needed for linear-scaling calculations, several schemes have been tried. The best performance is obtained for the basis sets generated according to a new scheme presented here, a flexibilization of previous proposals. Strict localization is maintained while ensuring the continuity of the basis-function derivative at the cutoff radius. The basis sets are tested versus converged plane-wave calculations on a significant variety of systems, including covalent, ionic, and metallic. Satisfactory convergence is obtained for reasonably small basis sizes, with a clear improvement over previous schemes. The transferability of the obtained basis sets is tested in several cases and it is found to be satisfactory as well.

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.

Projection of plane-wave calculations into atomic orbitals

The projection of the eigenfunctions obtained in standard plane-wave first-principle electronic-structure calculations into atomic-orbital basis sets is proposed as a formal and practical link between the methods based on plane waves and the ones based on atomic orbitals. Given a candidate atomic basis, (i) its quality is evaluated by its projection into the plane-wave eigenfunctions, (ii) it is optimized by maximizing that projection, (iii) the associated tight-binding hamiltonian and energy bands are obtained, and (iv) population analysis is performed in a natural way. The proposed method replaces the traditional trial-and-error procedures of finding appropriate atomic bases and the fitting of bands to obtain tight-binding hamiltonians. Test calculations of some zincblende semiconductors are presented.

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.

Calculation of the optical response of atomic clusters using time-dependent density functional theory and local orbitals

We report on a general method for the calculation of the frequency-dependent optical response of clusters based upon time-dependent density functional theory (TDDFT). The implementation is done using explicit propagation in the time domain and a self-consistent program that uses a linear combination of atomic orbitals (LCAO). Our actual calculations employ the SIESTA program, which is designed to be fast and accurate for large clusters. We use the adiabatic local density approximation to account for exchange and correlation effects. Results are presented for the imaginary part of the linear polarizability,

Seeing molecular orbitals

\mathrm{Im}\ensuremath{\alpha}(\ensuremath{\omega}),

Electrons in Dry DNA from Density Functional Calculations

and the dipole strength function,