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The free energy of ion solvation can be decomposed into enthalpic and entropic contributions. This helps to understand the connection between the dielectric properties and the underlying forces. We present a simple linear-response model of screened charge interactions that provides an alternative understanding of solvation barriers. Moreover, it explains the "anti-Coulomb" interactions (attraction between like-charged ions and repulsion between opposite-charged ions) observed in both simulations and experiments. We show that this is a universal behavior associated to the non-local response function of any dielectric or metallic system., Comment: 10 + 9 pages, 8 + 14 figures

The presence of sharp peaks in the real part of the static dielectric response function are usually accepted as indication of charge or spin instabilities in a material. However, there are misconceptions that Fermi surface (FS) nesting guarantees a peak in the response function like in one-dimensional systems, and, in addition, response function matrix elements between empty and occupied states are usually considered of secondary importance and typically set to unity like in the free electron gas case. In this work, we explicitly show, through model systems and real materials, within the framework of density functional theory, that predictions about the peaks in the response function, using FS nesting and constant matrix elements yields erroneous conclusions. We find that the inclusion of the matrix elements completely alters the structure of the response function. In all the cases studied other than the one-dimensional case we find that the inclusion of matrix elements washes out the structure found with constant matrix elements. Our conclusion is that it is imperative to calculate the full response function, with matrix elements, when making predictions about instabilities in novel materials.

A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-nineties, SIESTA's flexibility, efficiency and free distribution has given advanced materials simulation capabilities to many groups worldwide. The core methodological scheme of SIESTA combines finite-support pseudo-atomic orbitals as basis sets, norm-conserving pseudopotentials, and a real-space grid for the representation of charge density and potentials and the computation of their associated matrix elements. Here we describe the more recent implementations on top of that core scheme, which include: full spin-orbit interaction, non-repeated and multiple-contact ballistic electron transport, DFT+U and hybrid functionals, time-dependent DFT, novel reduced-scaling solvers, density-functional perturbation theory, efficient Van der Waals non-local density functionals, and enhanced molecular-dynamics options. In addition, a substantial effort has been made in enhancing interoperability and interfacing with other codes and utilities, such as Wannier90 and the second-principles modelling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various postprocessing utilities. SIESTA has also been engaged in the Electronic Structure Library effort from its inception, which has allowed the sharing of various low level libraries, as well as data standards and support for them, in particular the PSML definition and library for transferable pseudopotentials, and the interface to the ELSI library of solvers. Code sharing is made easier by the new open-source licensing model of the program. This review also presents examples of application of the capabilities of the code, as well as a view of on-going and future developments., Comment: 29 pages, 23 figures

First-principles electronic structure calculations are very widely used thanks to the many successful software packages available. Their traditional coding paradigm is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, from the compiler up, with the exception of linear-algebra and message-passing libraries. This model has been quite successful for decades. The rapid progress in methodology, however, has resulted in an ever increasing complexity of those programs, which implies a growing amount of replication in coding and in the recurrent re-engineering needed to adapt to evolving hardware architecture. The Electronic Structure Library (\esl) was initiated by CECAM (European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure programs and redesign them as free, open-source libraries. They include "heavy-duty" ones with a high degree of parallelisation, and potential for adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by scientists when implementing new ideas. It is a community effort, undertaken by developers of various successful codes, now facing the challenges arising in the new model. This modular paradigm will improve overall coding efficiency and enable specialists (computer scientists or computational scientists) to use their skills more effectively. It will lead to a more sustainable and dynamic evolution of software as well as lower barriers to entry for new developers., Comment: Revised version as finally accepted by J. Chem. Phys. to appear within the Special Topic in Electronic Structure Software (version prior to JCP's typesetting and proofs)

Molecular wires are essential components for future nanoscale electronics. However, the preparation of individual long conductive molecules is still a challenge. MMX metal-organic polymers are quasi-one-dimensional sequences of single halide atoms (X) bridging subunits with two metal ions (MM) connected by organic ligands. They are excellent electrical conductors as bulk macroscopic crystals and as nanoribbons. However, according to theoretical calculations, the electrical conductance found in the experiments should be even higher. Here we demonstrate a novel and simple drop-casting procedure to isolate bundles of few to single MMX chains. Furthermore, we report an exponential dependence of the electrical resistance of one or two MMX chains as a function of their length that does not agree with predictions based on their theoretical band structure. We attribute this dependence to strong Anderson localization originated by structural defects. Theoretical modeling confirms that the current is limited by structural defects, mainly vacancies of iodine atoms, through which the current is constrained to flow. Nevertheless, measurable electrical transport along distances beyond 250 nm surpasses that of all other molecular wires reported so far. This work places in perspective the role of defects in one-dimensional wires and their importance for molecular electronics.

We present a simple view on band unfolding of the energy bands obtained from supercell calculations. It relies on the relationship between the local density of states in reciprocal space (qLDOS) and the fully unfolded band structure. This provides an intuitive and valid approach not only for periodic, but also for systems with no translational symmetry. By refolding into the primitive Brillouin zone of the pristine crystal we recover the conventional unfolded bands. We implement our algorithm in the SIESTA package and apply it to defects on Si and graphene., Comment: 8 pages, 10 figures

We describe a method, that we call data projection onto parameter space (DPPS), to optimize an energy functional of the electron density, so that it reproduces a dataset of experimental magnitudes. Our scheme, based on Bayes theorem, constrains the optimized functional not to depart unphysically from existing ab initio functionals. The resulting functional maximizes the probability of being the \correct" parametrization of a given functional form, in the sense of Bayes theory. The application of DPPS to water sheds new light on why density functional theory has performed rather poorly for liquid water, on what improvements are needed, and on the intrinsic limitations of the generalized gradient approximation to electron exchange and correlation. Finally, we present tests of our water-optimized functional, that we call vdW-DF-w, showing that it performs very well for a variety of condensed water systems., Comment: 10 pages, 10 figures

Finite-range numerical atomic orbitals are the basis functions of choice for several first principles methods, due to their flexibility and scalability. Generating and testing such basis sets, however, remains a significant challenge for the end user. We discuss these issues and present a new scheme for generating improved polarization orbitals of finite range. We then develop a series of high-accuracy basis sets for the water molecule, and report on their performance in describing the monomer and dimer, two phases of ice, and liquid water at ambient and high density. The tests are performed by comparison with plane-wave calculations, and show the atomic orbital basis sets to exhibit an excellent level of transferability and consistency. The highest-order bases (quadruple-zeta) are shown to give accuracies comparable to a plane-wave kinetic energy cutoff of at least ~1000 eV for quantities such as energy differences and ionic forces, as well as achieving significantly greater accuracies for total energies and absolute pressures., Comment: 17 pages, 14 figures

The isothermal compressibility of water is essential to understand its anomalous properties. We compute it by ab initio molecular dynamics simulations of 200 molecules at five densities, using two different van der Waals density functionals. While both functionals predict compressibilities within ~30% of experiment, only one of them accurately reproduces, within the uncertainty of the simulation, the density dependence of the self-diffusion coefficient in the anomalous region. The discrepancies between the two functionals are explained in terms of the low- and high-density structures of the liquid., Comment: 12 pages, 16 figures

We present ab initio results at the density functional theory level for the energetics and kinetics of H_2 and CH_4 in the SI clathrate hydrate. Our results complement a recent article by some of the authors [G. Roman-Perez et al., Phys. Rev. Lett. 105, 145901 (2010)] in that we show additional results of the energy landscape of H_2 and CH_4 in the various cages of the host material, as well as further results for energy barriers for all possible diffusion paths of H_2 and CH_4 through the water framework. We also report structural data of the low-pressure phase SI and the higher-pressure phases SII and SH.

We present a study of the adsorption and diffusion of CH4, CO2 and H2 molecules in clathrate hydrates using ab initio van der Waals density functional formalism [Dion et al. Phys. Rev. Lett. 92, 246401 (2004)]. We find that the adsorption energy is dominated by van der Waals interactions and that, without them, gas hydrates would not be stable. We calculate the maximum adsorption capacity as well as the maximum hydrocarbon size that can be adsorbed.The relaxation of the host lattice is essential for a good description of the diffusion activation energies, which are estimated to be of the order of 0.2, 0.4, and 1.0 eV for H2, CO2, and CH4, respectively., Comment: 4 pages, 4 figures, 3 tables

It is known that ab initio molecular dynamics (AIMD) simulations of liquid water, based on the generalized gradient approximation (GGA) to density functional theory (DFT), yield structural and diffusive properties in reasonable agreement with experiment only if artificially high temperatures are used in the simulations. The equilibrium density, at normal conditions, of DFT water has been recently shown by Schmidt et al. [J. Phys. chem. B, 113, 11959 (2009)] to be underestimated by different GGA functionals for exchange and correlation, and corrected by the addition of interatomic pair potentials to describe van derWaals (vdW) interactions. In this contribution we present a DFTAIMD study of liquid water using several GGA functionals as well as the van der Waals density functional (vdW-DF) of Dion et al. [Phys. Rev. Lett. 92, 246401(2004)]. As expected, we find that the density of water is grossly underestimated by GGA functionals. When a vdW-DF is used, the density improves drastically and the experimental diffusivity is reproduced without the need of thermal corrections. We analyze the origin of the density differences between all the functionals. We show that the vdW-DF increases the population of non-H-bonded interstitial sites, at distances between the first and second coordination shells. However, it excessively weakens the H-bond network, collapsing the second coordination shell. This structural problem is partially associated to the choice of GGA exchange in the vdW-DF. We show that a different choice for the exchange functional is enough to achieve an overall improvement both in structure and diffusivity., Comment: 11 pages, 9 figures, submitted. Revised version

Molecular hydrogen adsorption in a nanoporous metal organic framework structure (MOF-74) was studied via van der Waals density-functional calculations. The primary and secondary binding sites for H$_2$ were confirmed. The low-lying rotational and translational energy levels were calculated, based on the orientation and position dependent potential energy surface at the two binding sites. A consistent picture is obtained between the calculated rotational-translational transitions for different H$_2$ loadings and those measured by inelastic neutron scattering exciting the singlet to triplet (para to ortho) transition in H$_2$. The H$_2$ binding energy after zero point energy correction due to the rotational and translational motions is predicted to be $\sim$100 meV in good agreement with the experimental value of $\sim$90 meV., Comment: 5 pagers, 4 figures. added references

We present an efficient implementation of the van der Waals density functional of Dion et al [Phys. Rev. Lett. 92, 246401 (2004)], which expresses the nonlocal correlation energy as a double spacial integral. We factorize the integration kernel and use fast Fourier transforms to evaluate the selfconsistent potential, total energy, and atomic forces, in N log(N) operations. The resulting overhead in total computational cost, over semilocal functionals, is very moderate for medium and large systems. We apply the method to calculate the binding energies and the barriers for relative translation and rotation in double-wall carbon nanotubes., Comment: 4 pages, 1 figure, 1 table

We present first principles calculations of the atomic and electronic structure of electron-doped LaOFeAs. We find that whereas the undoped compound has an antiferromagnetic arrangement of magnetic moments at the Fe atoms, the doped system becomes non magnetic at a critical electron concentration. We have studied the electron-phonon interaction in the doped paramagnetic phase. For the $A_{1g}$ phonon, the separation between the As and Fe planes induces a non-collinear arrangement of the Fe magnetic moments. This arrangement is anti parallel for interactions mediated by As, and perpendicular for Fe-Fe direct interactions, thus avoiding frustration. This coupling of magnetism with vibrations induces anharmonicities and an electron-phonon interaction much larger than in the pure paramagnetic case. We propose that such enhanced interactions play an essential role in superconducting compounds close to an atiferromagnetic phase transition., Comment: 4 pages, 5 figures

We present an alternative method to filter a distribution, that is strictly confined within a sphere of given radius $r_c$, so that its Fourier transform is optimally confined within another sphere of radius $k_c$. In electronic structure methods, it can be used to generate optimized pseudopotentials, pseudocore charge distributions, and pseudo atomic orbital basis sets., Comment: 3 pages, 2 figures

The role of a simple surface defect, such as a step, for relaxing the stress applied to a semiconductor, has been investigated by means of large scale first principles calculations. Our results indicate that the step is the privileged site for initiating plasticity, with the formation and glide of 60$^\circ$ dislocations for both tensile and compressive deformations. We have also examined the effect of surface and step termination on the plastic mechanisms.

A model is proposed for the creation and transmission of scientific knowledge, based on the network of citations among research articles. The model allows to assign to each article a nonnegative value for its creativity, i. e. its creation of new knowledge. If the entire publication network is truncated to the first neighbors of an article (the n references that it makes and the m citations that it receives), its creativity value becomes a simple function of n and m. After splitting the creativity of each article among its authors, the cumulative creativity of an author is then proposed as an indicator of her or his merit of research. In contrast with other merit indicators, this creativity index yields similar values for the top scientists in two very different areas (life sciences and physics), thus offering good promise for interdisciplinary analyses., Comment: 5 pages, 2 figures

I describe a method to separate the articles of different authors with the same name. It is based on a distance between any two publications, defined in terms of the probability that they would have as many coincidences if they were drawn at random from all published documents. Articles with a given author name are then clustered according to their distance, so that all articles in a cluster belong very likely to the same author. The method has proven very useful in generating groups of papers that are then selected manually. This simplifies considerably citation analysis when the author publication lists are not available., Comment: 4 pages, 0 figures

We study why gold forms planar and cage-like clusters while copper and silver do not. We use density functional theory and norm-conserving pseudo-potentials with and without a scalar relativistic component. For the exchange-correlation functional we use both the generalized gradient (GGA) and the local density (LDA) approximations. We find that planar Au_n structures, with up to n = 11, have lower energy than the three-dimensional isomers only with scalar-relativistic pseudopotentials and the GGA. In all other calculations, with more than 6 or 7 noble metal atoms, we obtain three dimensional structures. In the total energy balance, kinetic energy favors planar and cage structures, while xc-energy favors 3D structures. As a second step, we construct cluster structures having only surface atoms with Oh, Td, and Ih symmetry. Then we select those with 2(l+1)**2 electrons (with l integer), which correspond to the filling of a spherical electronic shell formed by node-less one electron wave functions. Using scalar relativistic GGA molecular dynamics at T = 600K, we show that the cage-like structures of neutral Au32, Au50, and Au162 are meta-stable. The dipole polarizability of gold clusters corresponds to the linear response of 1.6 delocalized valence electrons, suggesting a strong screening of the valence interactions due to the d-electrons., Comment: 8 pages, 4 figures. (1) Dpto. de Fisica Teorica, Atomica y Optica, UVa, E-47011 Valladolid, Spain. (2) Dpto. de Fisica de la Materia Condensada, UAM, E-28049 Madrid, Spain

Based on Bardeen's perturbative approach to tunneling, we have found an expression for the current between tip and sample, which can be efficiently coded in order to perform fast ab initio simulations of STM images. Under the observation that the potential between the electrodes should be nearly flat at typical tunnel gaps, we have addressed the difficulty in the computation of the tunneling matrix elements by considering a vacuum region of constant potential delimited by two surfaces (each of them close to tip and sample respectively), then propagating tip and sample wave functions by means of the vacuum Green's function, to finally obtain a closed form in terms of convolutions. The current is then computed for every tip-sample relative position and for every bias voltage in one shot. The electronic structure of tip and sample is calculated at the same footing, within density functional theory, and independently. This allows us to carry out multiple simulations for a given surface with a database of different tips. We have applied this method to the Si(111)-(7x7) and Ge(111)-c(2x8) surfaces. Topographies and spectroscopic data, showing a very good agreement with experiments, are presented., Comment: 10 pages, 11 figures

Careful first-principles density functional calculations reveal the importance of hexagonal versus cubic stacking of closed packed planes of Pd as far as local magnetic properties are concerned. We find that, contrary to the stable face centered cubic phase, which is paramagnetic, the hexagonal close-packed phase of Pd is ferromagnetic with a magnetic moment of 0.35 $\mu_{B}$/atom. Our results show that two-dimensional defects with local hcp stacking, like twin boundaries and stacking faults, in the otherwise fcc Pd structure, increase the magnetic susceptibility. The (111) surface also increases the magnetic susceptibility and it becomes ferromagnetic in combination with an individual stacking fault or twin boundary close to it. On the contrary, we find that the (100) surface decreases the tendency to ferromagnetism. The results are consistent with the magnetic moment recently observed in small Pd nanoparticles, with a large surface area and a high concentration of two-dimensional stacking defects., Comment: 8 pages, 10 figures

We present a method to filter a distribution so that it is confined within a sphere of given radius r_c and, simultaneously, whose Fourier transform is optimally confined within a sphere of radius k_c. Our procedure may have several applications in the field of electronic structure methods, like the generation of optimized pseudopotentials and localized pseudocore charge distributions. As an example, we describe a particular application within the SIESTA method for density functional calculations, in removing the spurious rippling of the energy surface generated by the integrations in a real space grid., Comment: 6 pages, 6 figures

We present a very efficient and accurate method to simulate scanning tunneling microscopy images and spectra from first-principles density functional calculations. The wave-functions of the tip and sample are calculated separately on the same footing, and propagated far from the surface using the vacuum Green's function. This allows to express the Bardeen matrix elements in terms of convolutions, and to obtain the tunneling current at all tip positions and bias voltages in a single calculation. The efficiency of the method opens the door to real time determination of both tip and surface composition and structure, by comparing experiments to simulated images for a variety of precomputed tips. Comparison with the experimental topography and spectra of the Si(111)-(7x7) surface show a much better agreement with Si than with W tips, implying that the metallic tip is terminated by silicon., Comment: 4 pages, 4 figures

A functional $E_{xc}[\rho(\r,\epsilon)]$ is presented, in which the exchange and correlation energy of an electron gas depends on the local density of occupied states. A simple local parametrization scheme is proposed, entirely from first principles, based on the decomposition of the exchange-correlation hole in scattering states of different relative energies. In its practical Kohn-Sham-like form, the single-electron orbitals become the independent variables, and an explicit formula for the functional derivative is obtained., Comment: 5 pages. Expanded version. Will appear in Phys. Rev. B

We present two methods to accelerate first-principles structural relaxations, both based on the dynamical matrix obtained from a universal model of springs for bond stretching and bending. Despite its simplicity, the normal modes of this model Hessian represent excellent internal coordinates for molecules and solids irrespective of coordination, capturing not only the long-wavelength acoustic modes of large systems, but also the short-wavelength low-frequency modes that appear in complex systems. In the first method, the model Hessian is used to precondition a conjugate gradients minimization, thereby drastically reducing the effective spectral width and thus obtaining a substantial improvement of convergence. The same Hessian is used in the second method as a starting point of a quasi-Newton algorithm (Broyden's method and modifications thereof), reducing the number of steps needed to find the correct Hessian. Results for both methods are presented for geometry optimizations of clusters, slabs, and biomolecules, with speed-up factors between 2 and 8., Comment: 5 pages, 3 figures submites to Phys. Rev. B

We have developed and implemented a self-consistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical LCAO 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 of 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., Comment: 22 pages, 8 figures

We calculate from first principles the electronic structure, relaxation and magnetic moments in small Fe particles, applying the numerical local orbitals method in combination with norm-conserving pseudopotentials. The accuracy of the method in describing elastic properties and magnetic phase diagrams is tested by comparing benchmark results for different phases of crystalline iron to those obtained by an all-electron method. Our calculations for the bipyramidal Fe_5 cluster qualitatively and quantitatively confirm previous plane-wave results that predicted a non-collinear magnetic structure. For larger bcc-related (Fe_35) and fcc-related (Fe_38, Fe_43, Fe_62) particles, a larger inward relaxation of outer shells has been found in all cases, accompanied by an increase of local magnetic moments on the surface to beyond 3 mu_B., Comment: 15 pages with 6 embedded postscript figures, updated version, submitted to Eur.Phys.J.D

A potential disadvantage of real-space-grid electronic structure methods is the lack of a variational principle and the concomitant increase of total energy with grid refinement. We show that the origin of this feature is the systematic underestimation of the kinetic energy by the finite difference representation of the Laplacian operator. We present an alternative representation that provides a rigorous upper bound estimate of the true kinetic energy and we illustrate its properties with a harmonic oscillator potential. For a more realistic application, we study the convergence of the total energy of bulk silicon using a real-space-grid density-functional code and employing both the conventional and the alternative representations of the kinetic energy operator., Comment: 3 pages, 3 figures, 1 table. To appear in Phys. Rev. B. Contribution for the 10th anniversary of the eprint server

We describe a method for calculating the exchange and correlation (XC) contributions to the total energy, effective potential, and stress tensor in the generalized gradient approximation. We avoid using the analytical expressions for the functional derivatives of E_xc*rho, which depend on discontinuous second-order derivatives of the electron density rho. Instead, we first approximate E_xc by its integral in a real space grid, and then we evaluate its partial derivatives with respect to the density at the grid points. This ensures the exact consistency between the calculated total energy, potential, and stress, and it avoids the need of second-order derivatives. We show a few applications of the method, which requires only the value of the (spin) electron density in a grid (possibly nonuniform) and returns a conventional (local) XC potential., Comment: 7 pages, 3 figures

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., Comment: 2 pages, 0 figures

The adsorption of C60 on Si(111) has been studied by means of first-principles density functional calculations. A 2x2 adatom surface reconstruction was used to simulate the terraces of the 7x7 reconstruction. The structure of several possible adsorption configurations was optimized using the ab initio atomic forces, finding good candidates for two different adsorption states observed experimentally. While the C60 molecule remains closely spherical, the silicon substrate appears quite soft, especially the adatoms, which move substantially to form extra C-Si bonds, at the expense of breaking Si-Si bonds. The structural relaxation has a much larger effect on the adsorption energies, which strongly depend on the adsorption configuration, than on the charge transfer., Comment: 4 pages with 3 postscript figures, to appear in Surf. Science. (proceedings of the European Conference on Surface Science ECOSS-19, Sept 2000)

We have applied first-principles density-functional calculations to the study of the energetics, and the elastic and electronic properties of monatomic wires of Au, Cu, K, and Ca in linear and a planar-zigzag geometries. For Cu and Au wires, the zigzag distortion is favorable even when the linear wire is stretched, but this is not observed for K and Ca wires. In all the cases, the equilibrium structure is an equilateral zigzag (bond angle of 60$^{\rm o}$). Only in the case of Au, the zigzag geometry can also be stabilized for an intermediate bond angle of 131$^{\rm o}$. The relationship between the bond and wire lengths is qualitatively different for the metallic (Au, Cu and, K) and semiconducting (Ca) wires., Comment: 4 pages with 3 postscript figures. To appear in Surf. Science (proceedings of the European Conference on Surface Science, ECOSS-19, Madrid Sept. 2000)

We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT scheme, which is specially suited for systems with large numbers of atoms. As a first step towards the study of large DNA systems, in this work: (i) We establish the reliability of the approximations of our method (including pseudopotentials and basis sets) for the description of the hydrogen-bonded base pairs, by comparing our results with those of former calculations. We show that the interaction energies at Hartree-Fock geometries are in very good agreement with those of second order M{\o}ller-Plesset (MP2) perturbation theory (the most accurate technique that can be applied at present for system of the sizes of the base-pairs). (ii) We perform DFT structural optimizations for the 30 different DNA base-pairs, only three of which had been previously studied with DFT. Our results provide information on the effect of correlation on the structure of the other 27 base pairs, for which only Hartree-Fock geometries were formerly available., Comment: Submitted to J. Phys. Chem. B

We apply first principles calculations to study the opening of single-wall carbon nanotubes (SWNT's) by oxidation. We show that an oxygen rim can stabilize the edge of the open tube. The sublimation of CO$_2$ molecules from the rim with the subsequent closing of the tube changes from endothermic to exothermic as the tube radius increases, within the range of experimental feasible radii. We also obtain the energies for opening the tube at the cap and at the wall, the latter being significantly less favorable., Comment: 4 pages, 3 figures. Submitted to Phys. Rev. B

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., Comment: 4 pages, latex, 5 figures, submitted to PRL

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., Comment: 5 pages + 4 figures, submitted to Proc. Int. Conf. Solid State Spectroscopy (Sept 1999)

Using molecular dynamics simulations, with a realistic many-body embedded-atom potential, and a novel method to characterize local order, we study the structure of pure nickel during the rapid quench of the liquid and in the resulting glass. In contrast with previous simulations with pair potentials, we find more crystalline order and fewer icosahedra for slower quenching rates, resulting in a glass less stable against crystallization. It is shown that there is not a specific amorphous structure, only the arrest of the transition from liquid to crystal, resulting in small crystalline clusters immersed in an amorphous matrix with the same structure of the liquid., Comment: 4 pages, 4 ps figs., to appear in Phys. Rev. Lett

We present a method to perform fully selfconsistent density-functional calculations, which 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 $O(N)$ effort. The long range selfconsistent 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 $O(N)$ 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$_3$N$_4$. We apply the method to solve the existing controversy about the faceting of large icosahedral fullerenes by performing dynamical simulations on C$_{60}$, C$_{240}$, and C$_{540}$., Comment: RevTeX, 4 pages (2 figures included in the RevTeX file)

The projection of the eigenfunctions obtained in standard plane-wave first-principle calculations is used for analyzing atomic-orbital basis sets. The "spilling" defining the error in such a projection allows the evaluation of the quality of an atomic-orbital basis set for a given system and its systematic variational optimization. The same projection allows obtaining the band structure and the Hamiltonian matrix elements in the previously optimized atomic basis. The spilling is shown to correlate with the mean square error in the energy bands, indicating that the basis optimization via spilling minimization is qualitatively equivalent to the energy-minimization scheme, but involves a much smaller computational effort. The spilling minimization also allows the optimization of bases for uses different than total-energy calculations, like the description of the band gap in semiconductors. The method is applied to the characterization of finite-range pseudo-atomic orbitals {[}O. F. Sankey and D. J. Niklewski, Phys. Rev. B {\bf 40}, 3979 (1989){]} in comparison to infinite-range pseudo-atomic and Slater-type orbitals. The bases are evaluated and optimized for several zincblende semiconductors and for aluminum. The quality of the finite-range orbitals is found to be perfectly comparable to the others with the advantage of a limited range of interacions. A simple scheme is proposed to expand the basis without increasing the range. It is found that a double-$z$ basis substantially improves the basis performance on diamond, whereas $d$-polarization is required for Si and Al for similar results. Finally, the projection allows the chemical analysis of the plane-wave results via population analysis on the previously optimized atomic basis., Comment: 11 pages, RevTeX, plus 13 uuencoded, compressed, tared figures

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, ({\it i}) its quality is evaluated by its projection into the plane-wave eigenfunctions, ({\it ii}) it is optimized by maximizing that projection, ({\it iii}) the associated tight-binding Hamiltonian and energy bands are obtained, and ({\it 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., Comment: RevTex. 4 pages. 3 uuencoded compressed (tared) postscript figs. To appear in Solid St. Commun