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We demonstrate an efficient method for high-accuracy ab initio simulations for semiconductor device technology development, such as high-k metal gate stack engineering and investigation of 2D material-based FET performance. The method combines the HSE06 hybrid density functional with linear combination of atomic orbitals (LCAO) basis sets, as implemented in the QuantumATK atomic-scale modeling platform. We show that HSE06-LCAO predicts accurate band energies and enables large-scale HSE06 simulations for systems comprising thousands of atoms using modest computational resources.

This paper presents a multiscale physics-based approach for evaluating DRAM cell retention time including variable retention time effects. The flow goes from ab-initio DFT simulation to high-sigma SPICE analysis, allowing for the evaluation of the causes and retention time related failure states for DRAM technologies.

This article is part of the JCP Special Topic on Electronic Structure Software., A review of the present status, recent enhancements, and applicability of the SIESTA program is presented. Since its debut in the mid-1990s, SIESTA’s flexibility, efficiency, and free distribution have 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 realspace 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, density functional theory (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 modeling it can be used for, an AiiDA plugin for workflow automatization, interface to Lua for steering SIESTA runs, and various post-processing 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, particularly the PSeudopotential Markup Language definition and library for transferable pseudopotentials, and the interface to the ELectronic Structure Infrastructure 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., Siesta development was historically supported by different Spanish National Plan projects (Project Nos. MEC-DGES-PB95-0202, MCyT-BFM2000-1312, MEC-BFM2003-03372, FIS2006-12117, FIS2009-12721, FIS2012-37549, FIS2015-64886-P, and RTC-2016-5681-7), the latter one together with Simune Atomistics Ltd. We are thankful for financial support from the Spanish Ministry of Science, Innovation and Universities through Grant No. PGC2018-096955-B. We acknowledge the Severo Ochoa Center of Excellence Program [Grant Nos. SEV-2015-0496 (ICMAB) and SEV-2017-0706 (ICN2)], the GenCat (Grant No. 2017SGR1506), and the European Union MaX Center of Excellence (EU-H2020 Grant No. 824143). P.G.-F. acknowledges support from Ramón y Cajal (Grant No. RyC-2013-12515). J.I.C. acknowledges Grant No. RTI2018-097895-B-C41. R.C. acknowledges the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodoswka-Curie Grant Agreement No. 665919. D.S.P, P.K., and P.B. acknowledge Grant No. MAT2016-78293-C6, FET-Open No. 863098, and UPV-EHU Grant No. IT1246-19. V. W. Yu was supported by a MolSSI Fellowship (U.S. NSF Award No. 1547580), and V.B. and V.W.Y. were supported by the ELSI Development by the NSF (Award No. 1450280).

First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the 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 codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and 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, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community., The authors would also like to thank the Psi-k network for having partially funded several of the ESL workshops. A.O., E.A., D.L.-D., S.G., E.K., A.A.M., and M.C.P. received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 676531 (Centre of Excellence project E-CAM). The same project has partly funded the extended software development workshops in which most of the ESL coding effort has happened. A.G., S.M., and E.A. acknowledge support from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 824143 (Centre of Excellence project MaX). M.A.L.M. acknowledges partial support from the DFG through Project No. MA-6786/1. D.G.A.S. was supported by the U.S. National Science Foundation (NSF) (Grant No. ACI1547580). M.C.P. acknowledges support from the EPSRC under Grant No. EP/P034616/1. A.A.M. acknowledges support from the Thomas Young Centre under Grant No. TYC-101, the Wannier Developers Group, and all of the authors and contributors of the wannier90 code (see Ref. 115 for a complete list). A.M.E. acknowledges support from CoSeC, the Computational Science Centre for Research Communities, through CCP5: The Computer Simulation of Condensed Phases (EPSRC Grant Nos. EP/M022617/1 and EP/P022308/1). A.G. and J.M.S. acknowledge Spain’s Ministry of Science (Grant No. PGC2018-096955-B-C42). E.A., A.G., and J.M.S. acknowledge Spain’s Ministry of Science (Grant No. FIS2015-64886- C5). Y.P., D.L.-D., and E.A. acknowledge support from the Spanish MINECO and EU Structural Investment Funds (Grant No. RTC2016-5681-7). M.L. acknowledges support from the EPRSC under Grant No. EP/M022668/1. M.L., M.J.T.O., and Y.P. acknowledge support from the EU COST action (Grant No. MP1306). J.M. was supported by the European Regional Development Fund (ERDF), project CEDAMNF (Reg. No. CZ.02.1.01/0.0/0.0/15-003/0000358). V.W.-Z.Y., W.P.H., Y.L., and V.B. acknowledge support from the National Science Foundation under Award No. ACI-1450280 (the ELSI project). V.W.-Z.Y. also acknowledges a MolSSI fellowship (NSF Award No. ACI-1547580). Simune Atomistics S.L. is thanked for allowing A.H.L. and Y.P. to contribute to the ESL, as is Synopsys, Inc., for the partial availability of F.C.

The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing $\beta$-strands. Its strength and structural stability are critical for its anchoring function in uropathogenic Escherichia coli bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations [A. Alonso-Caballero et al., Nature Commun. 9, 2758 (2018)]. In this work we perform a quantitative comparison between experiment and simulation, showing a good agreement in the underlying work values for the unfolding. The simulation results are then used to estimate the free energy difference for the detachment of FimG from the complementing strand of the neighbouring subunit in the chain, FimF. Finally, we show that the large free energy difference for the unravelling and detachment of the subunits which leads to the high stability of the chain is entirely entropic in nature., Comment: 9 pages, 5 figures

The effective interaction between electrons in two-dimensional materials can be modified by their environment, enabling control of electronic correlations and phases. Here, we study the dependence of electronic correlations in twisted bilayer graphene (tBLG) on the separation to the metallic gate(s) in two device configurations. Using an atomistic tight-binding model, we determine the Hubbard parameters of the flat bands as a function of gate separation, taking into account the screening from the metallic gate(s), the dielectric spacer layers and the tBLG itself. We determine the critical gate separation at which the Hubbard parameters become smaller than the critical value required for a transition from a correlated insulator state to a (semi-)metallic phase. We show how this critical gate separation depends on twist angle, doping and the device configuration. These calculations may help rationalise the reported differences between recent measurements of tBLG's phase diagram and suggests that correlated insulator states can be screened out in devices with thin dielectric layers., Comment: 9 pages, 9 figures

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys., Comment: Submitted to Journal of Physics: Condensed Matter

Twisted double bilayer graphene has recently emerged as an interesting moir\'e material that exhibits strong correlation phenomena that are tunable by an applied electric field. Here we study the atomic and electronic properties of three different graphene double bilayers: double bilayers composed of two AB stacked bilayers (AB/AB), double bilayers composed of two AA stacked bilayers (AA/AA) as well as heterosystems composed of one AB and one AA bilayer (AB/AA). The atomic structure is determined using classical force fields. We find that the inner layers of the double bilayer exhibit significant in-plane and out-of-plane relaxations, similar to twisted bilayer graphene. The relaxations of the outer layers depend on the stacking: atoms in AB bilayers follow the relaxations of the inner layers, while atoms in AA bilayers attempt to avoid higher-energy AA stacking. For the relaxed structures, we calculate the electronic band structures using the tight-binding method. All double bilayers exhibit flat bands at small twist angles, but the shape of the bands depends sensitively on the stacking of the outer layers. To gain further insight, we study the evolution of the band structure as the outer layers are rigidly moved away from the inner layers, while preserving their atomic relaxations. This reveals that the hybridization with the outer layers results in an additional flattening of the inner-layer flat band manifold. Our results establish AA/AA and AB/AA twisted double bilayers as interesting moir\'e materials with different flat band physics compared to the widely studied AB/AB system., Comment: 14 pages, 11 figures

We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the density matrix and the NGWFs are optimized with localization constraints. By taking advantage of localization, onetep is able to perform calculations including thousands of atoms with computational effort, which scales linearly with the number or atoms. The code has a large and diverse range of capabilities, explored in this paper, including different boundary conditions, various exchange-correlation functionals (with and without exact exchange), finite electronic temperature methods for metallic systems, methods for strongly correlated systems, molecular dynamics, vibrational calculations, time-dependent DFT, electronic transport, core loss spectroscopy, implicit solvation, quantum mechanical (QM)/molecular mechanical and QM-in-QM embedding, density of states calculations, distributed multipole analysis, and methods for partitioning charges and interactions between fragments. Calculations with onetep provide unique insights into large and complex systems that require an accurate atomic-level description, ranging from biomolecular to chemical, to materials, and to physical problems, as we show with a small selection of illustrative examples. onetep has always aimed to be at the cutting edge of method and software developments, and it serves as a platform for developing new methods of electronic structure simulation. We therefore conclude by describing some of the challenges and directions for its future developments and applications.

[EN] Integration of Shift-and-Invert Parallel Spectral Transformation (SIPs) eigensolver (as implemented in the SLEPc library) into an ab initio molecular dynamics package, SIESTA, is described. The effectiveness of the code is demonstrated on applications to polyethylene chains, boron nitride sheets, and bulk water clusters. For problems with the same number of orbitals, the performance of the SLEPc eigensolver depends on the sparsity of the matrices involved, favoring reduced dimensional systems such as polyethylene or boron nitride sheets in comparison to bulk systems like water clusters. For all problems investigated, performance of SIESTA-SIPs exceeds the performance of SIESTA with default solver (ScaLAPACK) at the larger number of cores and the larger number of orbitals. A method that improves the load-balance with each iteration in the self-consistency cycle by exploiting the emerging knowledge of the eigenvalue spectrum is demonstrated. (c) 2018 Wiley Periodicals, Inc., Contract grant sponsor: Argonne National Laboratory, and by Basic Energy Science, provided by the Director, Office of Science, of the U.S. Department of Energy; Contract grant number: DE-AC02-06CH11357; Contract grant sponsor: The U.S. Department of Energy Office of Science, Office of Basic Energy Sciences Division of Materials Science and Engineering; Contract grant number: DE-AC02-06CH11357; Contract grant sponsor: The Spanish Ministry of Economy and Competitiveness; Contract grant number: TIN2016-75985-P (including European Commission FEDER funds)

Uropathogenic Escherichia coli attach to tissues using pili type 1. Each pilus is composed by thousands of coiled FimA domains followed by the domains of the tip fibrillum, FimF-FimG-FimH. The domains are linked by non-covalent β-strands that must resist mechanical forces during attachment. Here, we use single-molecule force spectroscopy to measure the mechanical contribution of each domain to the stability of the pilus and monitor the oxidative folding mechanism of a single Fim domain assisted by periplasmic FimC and the oxidoreductase DsbA. We demonstrate that pilus domains bear high mechanical stability following a hierarchy by which domains close to the tip are weaker than those close to or at the pilus rod. During folding, this remarkable stability is achieved by the intervention of DsbA that not only forms strategic disulfide bonds but also serves as a chaperone assisting the folding of the domains., The pilus type 1 of uropathogenic E. coli must resist mechanical forces to remain attached to the epithelium. Here the authors use single-molecule force spectroscopy to demonstrate a hierarchy of mechanical stability among the pilus domains and show that the oxidoreductase DsbA also acts as a folding chaperone on the domains.

Motivated by the recent observation of correlated insulator states and unconventional superconductivity in twisted bilayer graphene, we study the dependence of electron correlations on the twist angle and reveal the existence of strong correlations over a narrow range of twist angles near the magic angle. Specifically, we determine the on-site and extended Hubbard parameters of the low-energy Wannier states using an atomistic quantum-mechanical approach. The ratio of the on-site Hubbard parameter and the width of the flat bands, which is an indicator of the strength of electron correlations, depends sensitively on the screening by the semiconducting substrate and the metallic gates. Including the effect of long-ranged Coulomb interactions significantly reduces electron correlations and explains the experimentally observed sensitivity of strong-correlation phenomena on twist angles.

Twisted bilayer graphene (tBLG) has recently emerged as a new platform for studying electron correlations, the strength of which can be controlled via the twist angle. Here, we study the effect of internal screening on electron-electron interactions in undoped tBLG. Using the random phase approximation, we find that the dielectric response of tBLG drastically increases near the magic angle and is highly twist-angle dependent. As a consequence of the abrupt change of the Fermi velocity as a function of wave vector, the screened interaction in real space exhibits attractive regions for certain twist angles near the magic angle. Attractive interactions can induce charge density waves and superconductivity and therefore our findings could be relevant to understand the microscopic origins of the recently observed strong correlation phenomena in undoped tBLG. The resulting screened Hubbard parameters are strongly reduced and exhibit a non-linear dependence on the twist angle. We also carry out calculations with the constrained random phase approximation and parametrize a twist-angle dependent Keldysh model for the resulting effective interaction., 14 pages, 7 figures

In this report for Deliverable 2.1 of E-CAM, 9 software modules in electronic structure, which are related to an Extended Software Development Workshop (ESDW) held by E-CAM in Zaragoza in June 2016, are presented. These modules are libraries intended to be leveraged during the development process of new applications that span most of the electronic structure community, but the main focus are codes that implement Density Functional Theory, which can be used to determine a wide range of properties of atoms, molecules, and materials. 9 modules are respectively named: LibOMM, MatrixSwitch, Libpspio, Libescdf, Poke, SQARE radial grid & function, SQARE ODE solvers, SQARE states and FDF. These include codes for solvers of localised orbitals, for computing on a grid and their documentation. In addition to the solvers, data format modules, a pseudopotential data file I/O operation module and intermediary interface layer module are also present in this document. A short description is written for each module as well as the codes where they have been implemented, followed by a link to the respective Merge-Request on the GitLab service of E-CAM. These merge requests contain detailed information about the code development, testing and documentation of the modules.

Electrons in two-dimensional graphene sheets behave as interacting chiral Dirac fermions and have unique screening properties due to their symmetry and reduced dimensionality. By using a combination of scanning tunneling spectroscopy (STM/STS) measurements and theoretical modeling we have characterized how graphene's massless charge carriers screen individual charged calcium atoms. A back-gated graphene device configuration has allowed us to directly visualize how the screening length for this system can be tuned with carrier density. Our results provide insight into electron-impurity and electron-electron interactions in a relativistic setting with important consequences for other graphene-based electronic devices., 4 figures

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aims to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures., Comment: 55 pages, 14 figures, 2 tables

The implementation of the orbital minimization method (OMM) for solving the self-consistent Kohn-Sham (KS) problem for electronic structure calculations in a basis of non-orthogonal numerical atomic orbitals of finite-range is reported. We explore the possibilities for using the OMM as an exact cubic-scaling solver for the KS problem, and compare its performance with that of explicit diagonalization in realistic systems. We analyze the efficiency of the method depending on the choice of line search algorithm and on two free parameters, the scale of the kinetic energy preconditioning and the eigenspectrum shift. The results of several timing tests are then discussed, showing that the OMM can achieve a noticeable speedup with respect to diagonalization even for minimal basis sets for which the number of occupied eigenstates represents a significant fraction of the total basis size (>15%). We investigate the hard and soft parallel scaling of the method on multiple cores, finding a performance equal to or better than diagonalization depending on the details of the OMM implementation. Finally, we discuss the possibility of making use of the natural sparsity of the operator matrices for this type of basis, leading to a method that scales linearly with basis size., 23 pages, 10 figures. Comput. Phys. Commun., in publication (2013)

Liquid water is not only of obvious importance but also extremely intriguing, displaying many anomalies that still challenge our understanding of such an a priori simple system. The same is true when looking at nanoconfined water: The liquid between constituents in a cell is confined to such dimensions, and there is already evidence that such water can behave very differently from its bulk counterpart. A striking finding has been reported from computer simulations for two-dimensionally confined water: The liquid displays continuous or discontinuous melting depending on its density. In order to understand this behavior, we have analyzed the melting exhibited by a bilayer of nanoconfined water by means of molecular dynamics simulations. At high density we observe the continuous melting to be related to the phase change of the oxygens only, with the hydrogens remaining liquid-like throughout. Moreover, we find an intermediate hexatic phase for the oxygens between the liquid and a triangular solid ice phase, following the Kosterlitz-Thouless-Halperin-Nelson-Young theory for two-dimensional melting. The liquid itself tends to maintain the local structure of the triangular ice, with its two layers being strongly correlated, yet with very slow exchange of matter. The decoupling in the behavior of the oxygens and hydrogens gives rise to a regime in which the complexity of water seems to disappear, resulting in what resembles a simple monoatomic liquid. This intrinsic tendency of our simulated water may be useful for understanding novel behaviors in other confined and interfacial water systems.

A novel kind of crystal order in high-density nanoconfined bilayer ice is proposed from molecular dynamics and density-functional theory simulations. A first-order transition is observed between a low-temperature proton-ordered solid and a high-temperature proton-disordered solid. The latter is shown to possess crystalline order for the oxygen positions, arranged on a close-packed triangular lattice with AA stacking. Uniquely amongst the ice phases, the triangular bilayer is characterized by two levels of disorder (for the bonding network and for the protons) which results in a configurational entropy twice that of bulk ice., Comment: 5 pages, 6 figures

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations., 12 pages, 8 figures

Under the terms of the Creative Commons Attribution License 3.0 (CC-BY)., The direction and impact parameter dependence of electronic stopping power, along with its velocity threshold behavior, is investigated in a prototypical small-band-gap semiconductor. We calculate the electronic stopping power of H in Ge, a semiconductor with relatively low packing density, using time-evolving time-dependent density-functional theory. The calculations are carried out in channeling conditions with different impact parameters and in different crystal directions for projectile velocities ranging from 0.05 to 0.6 atomic units. The satisfactory comparison with available experiments supports the results and conclusions beyond experimental reach. The calculated electronic stopping power is found to differ in different crystal directions; however, strong impact parameter dependence is observed only in one of these directions. The distinct velocity threshold observed in experiments is well reproduced, and its nontrivial relation with the band gap follows a perturbation theory argument surprisingly well. This simple model is also successful in explaining why different density functionals give the same threshold even with substantially different band gaps., The financial support from MINECO-Spain through Plan Nacional Grant No. FIS2012-37549-C05-01, FPI Ph.D. Fellowship Grant No. BES-2013-063728, and Grant No. MAT2013-46593-C6-2-P along with the EU Grant “ElectronStopping” in the Marie Curie CIG Program is duly acknowledged. SGIker (UPV/EHU, MICINN, GV/EJ, ERDF and ESF) support is gratefully acknowledged.

We report on scaling and timing tests of the SIESTA electronic structure code for ab initio molecular dynamics simulations using density-functional theory. The tests are performed on six large-scale supercomputers belonging to the PRACE Tier-0 network with four different architectures: Cray XE6, IBM BlueGene/Q, BullX, and IBM iDataPlex. We employ a systematic strategy for simultaneously testing weak and strong scaling, and propose a measure which is independent of the range of number of cores on which the tests are performed to quantify strong scaling efficiency as a function of simulation size. We find an increase in efficiency with simulation size for all machines, with a qualitatively different curve depending on the supercomputer topology, and discuss the connection of this functional form with weak scaling behaviour. We also analyze the absolute timings obtained in our tests, showing the range of system sizes and cores favourable for different machines. Our results can be employed as a guide both for running SIESTA on parallel architectures, and for executing similar scaling tests of other electronic structure codes., Comment: 9 pages, 9 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., 17 pages, 14 figures

Understanding the interaction between dopants and semiconductor-oxide interfaces is an increasingly important concern in the drive to further miniaturize modern transistors. To this end, using a combination of first-principles density-functional theory and a continuous random network Monte Carlo method, we investigate electrically active arsenic donors at the interface between silicon and its oxide. Using a realistic model of the disordered interface, we find that a small percentage (on the order of ~10%) of the atomic sites in the first few monolayers on the silicon side of the interface are energetically favourable for segregation, and that this is controlled by the local bonding and local strain of the defect centre. We also find that there is a long-range quantum confinement effect due to the interface, which results in an energy barrier for dopant segregation, but that this barrier is small in comparison to the effect of the local environment. Finally, we consider the extent to which the energetics of segregation can be controlled by the application of strain to the interface., Comment: 16 pages, 10 figures

We study by high-resolution transmission electron microscopy the structural response of bilayer graphene to electron irradiation with energies below the knock-on damage threshold of graphene. We observe that one type of divacancy, which we refer to as the butterfly defect, is formed for radiation energies and doses for which no vacancies are formed in clean monolayer graphene. By using first principles calculations based on density-functional theory, we analyze two possible causes related with the presence of a second layer that could explain the observed phenomenon: an increase of the defect stability or a catalytic effect during its creation. For the former, the obtained formation energies of the defect in monolayer and bilayer systems show that the change in stability is negligible. For the latter, ab initio molecular dynamics simulations indicate that the threshold energy for direct expulsion does not decrease in bilayer graphene as compared with monolayer graphene, and we demonstrate the possibility of creating divacancies through catalyzed intermediate states below this threshold energy. The estimated cross section agrees with what is observed experimentally. Therefore, we show the possibility of a catalytic pathway for creating vacancies under electron radiation below the expulsion threshold energy., Comment: 12 pages, 8 figures

We present a comprehensive study of the vacancy in bulk silicon in all its charge states from 2+ to 2-, using a supercell approach within plane-wave density-functional theory, and systematically quantify the various contributions to the well-known finite size errors associated with calculating formation energies and stable charge state transition levels of isolated defects with periodic boundary conditions. Furthermore, we find that transition levels converge faster with respect to supercell size when only the Gamma-point is sampled in the Brillouin zone, as opposed to a dense k-point sampling. This arises from the fact that defect level at the Gamma-point quickly converges to a fixed value which correctly describes the bonding at the defect centre. Our calculated transition levels with 1000-atom supercells and Gamma-point only sampling are in good agreement with available experimental results. We also demonstrate two simple and accurate approaches for calculating the valence band offsets that are required for computing formation energies of charged defects, one based on a potential averaging scheme and the other using maximally-localized Wannier functions (MLWFs). Finally, we show that MLWFs provide a clear description of the nature of the electronic bonding at the defect centre that verifies the canonical Watkins model., Comment: 10 pages, 6 figures

We introduce the construction of a orthogonal wavepacket basis set, using the concept of stroboscopic time propagation, tailored to the efficient description of non-equilibrium extended electronic systems. Thanks to three desirable properties of this basis, significant insight is provided into non-equilibrium processes (both time-dependent and steady-state), and reliable physical estimates of various many-electron quantities such as density, current and spin polarization can be obtained. The use of this novel tool is demonstrated for time-dependent switching-on of the bias in quantum transport, and new results are obtained for current-induced spin accumulation at the edge of a 2D doped semiconductor caused by edge-induced spin-orbit interaction., 4 pages, 2 figures

The isolated substitutional gold impurity in bulk silicon is studied in detail using electronic structure calculations based on density-functional theory. The defect system is found to be a non-spin-polarized negative-U centre, thus providing a simple solution to the long-standing debate over the electron paramagnetic resonance signal for gold in silicon. There is an excellent agreement (within 0.03 eV) between the well-established experimental donor and acceptor levels and the predicted stable charge state transition levels, allowing for the unambiguous assignment of the two experimental levels to the (1+/1-) and (1-/3-) transitions, respectively, in contrast to previously held assumptions about the system., Comment: 6 pages, 5 figures

The following article appeared in Journal of Chemical Physics 139.19 (2013): 194502 and may be found at http://scitation.aip.org/content/aip/journal/jcp/139/19/10.1063/1.4832141, 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, This work was partly funded by Grant Nos. FIS2009- 12721 and FIS2012-37549 from the Spanish Ministry of Science. M.V.F.S. acknowledges a DOE Early Career Award No. DE-SC0003871. SGIker (UPV/EHU, MICINN, GV/EJ, ERDF and ESF) support is gratefully acknowledged