arXiv subjects

Jose M. Soler

Publications and source records attributed to Jose M. Soler.

At least 19 recordsLinked to original sources

arXiv2024

Anti-Coulomb ion-ion interactions: a theoretical and computational study

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.

cond-mat.soft↗

arXiv2020

Critical analysis of the response function in low dimensional materials

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.

cond-mat.mtrl-sci↗

arXiv2020

The CECAM Electronic Structure Library and the modular software development paradigm

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.

cond-mat.mtrl-sci↗

arXiv2020

SIESTA: recent developments and applications

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.

physics.comp-ph↗

arXiv2019

High electrical conductivity of single metal-organic chains

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.

cond-mat.mes-hall↗

arXiv2019

Band Unfolding Made Simple

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.

cond-mat.mtrl-sci↗

arXiv2016

Optimization of an exchange-correlation density functional for water

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.

physics.chem-ph↗

arXiv2011

Ab initio energetics and kinetics study of H_2 and CH_4 in the SI Clathrate Hydrate

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.

cond-mat.mtrl-sci↗

arXiv2010

Density, structure and dynamics of water: the effect of Van der Waals interactions

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.

cond-mat.mtrl-sci↗

arXiv2010

Stability, Adsorption and Diffusion of CH4, CO2 and H2 in Clathrate Hydrates

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.

cond-mat.mtrl-sci↗

arXiv2008

Efficient implementation of a van der Waals density functional: Application to double-wall carbon nanotubes

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.

cond-mat.mtrl-sci↗

arXiv2008

Anomalous electron-phonon interaction in doped LaOFeAs: a First Principles calculation

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.

cond-mat.supr-con↗

arXiv2008

Optimal Fourier filtering of a function that is strictly confined within a sphere

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.

cond-mat.mtrl-sci↗

arXiv2007

Dislocation formation from a surface step in semiconductors: an ab initio study

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.

cond-mat.mtrl-sci↗

arXiv2006

Separating the articles of authors with the same name

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.

cs.DL↗

arXiv2006

A Rational Indicator of Scientific Creativity

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.

physics.soc-ph↗

arXiv2006

Planar and cagelike structures of gold clusters: Density-functional pseudopotential calculations

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.

cond-mat.other↗

arXiv2006

Efficient and reliable method for the simulation of scanning tunneling images and spectra with local basis sets

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.

cond-mat.mtrl-sci↗