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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

[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)

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

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

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

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