The CECAM electronic structure library and the modular software development paradigm.

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.

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-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 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, 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.

Structures of Cu n+ ( n = 3-10) Clusters Obtained by Infrared Action Spectroscopy.

Coinage metal clusters are of great importance for a wide range of scientific fields, ranging from microscopy to catalysis. Despite their clear fundamental and technological importance, the experimental structural determination of copper clusters has attracted little attention. We fill this gap by elucidating the structure of cationic copper clusters through infrared (IR) photodissociation spectroscopy of Cu n+-Ar m complexes. Structures of Cu n+ ( n = 3-10) are unambiguously assigned based on the comparison of experimental IR spectra in the 70-280 cm-1 spectral range with spectra calculated using density functional theory. Whereas Cu3+ and Cu4+ are planar, starting from n = 5, Cu n+ clusters adopt 3D structures. Each successive cluster size is composed of its predecessor with a single atom adsorbed onto the face, giving evidence of a stepwise growth.

Shedding Light on the Basis Set Dependence of the Minnesota Functionals: Differences Between Plane Waves, Slater Functions, and Gaussians.

The Minnesota family of exchange-correlation (xc) functionals are among the most popular, accurate, and abundantly used functionals available to date. However, their use in plane-wave based first-principles MD has been limited by their sparse availability. Here, we present an implementation of the M05, M06, and M11 families of xc functionals within a plane wave/pseudopotential framework allowing for a comprehensive analysis of their basis set dependence. While it has been reported that in Gaussian bases some members of the Minnesota family only converge slowly to the basis set limit, (1) we show that converged energies can be conveniently obtained from plane waves if sufficiently dense integration meshes are used. Based on the HC7/11 database, we assess the influence of basis set type on the calculation of reaction enthalpies and show that complete basis set values obtained in plane waves may occasionally differ notably from their atom-centered counterparts. We provide an analysis of the origin of these differences and discuss implications on practical usage.

Roles of Hydration for Inducing Decomposition of 2-Deoxy-d-ribose by Ionization of Oxygen K-Shell Electrons.

To experimentally investigate the role of hydration in the initial process of the decomposition of 2-deoxy-d-ribose (dR), which is a major component of the DNA backbone, we used mass spectrometry to monitor the ions desorbing from hydrated dR films exposed to monochromatic soft X rays (560 eV). The X-ray photons preferentially ionize the K-shell electrons of the oxygen atoms in DNA. Hydrated dR samples were prepared under vacuum by exposing a cooled (∼150 K) dR film deposited on a Si substrate to water vapor. Using a quadrupole mass spectrometer, we observed the desorption of ions such as H+, CH x+, C2H x+, CH xO+, C3H x+ and C2H xO+ ( x = 1, 2, 3 and 4). In addition, the desorption of H2O+ or H3O+ was observed in the mass spectra of hydrated dR films. Except for H+, the yields of these ions decreased when one layer of water molecules was deposited onto the film. These ions are produced by C-C or C-O bond scission. This result suggests that the water molecules act as a quencher, suppressing Coulomb repulsion and thus the extensive molecular decomposition of dR. Ab initio molecular dynamics simulations were performed to rationalize the fragments observed in the experiments. The results of the dynamical process of a hydrated dR molecule after oxygen K-ionization revealed elongation of a C-O bond of dR and the O-H bonds of both dR and water molecules prior to the Auger process, resulting in the ejection of H+ ions. These results strongly suggest that the very early process contributes to reducing the dR fragmentation, producing the H3O+ and H+ detected from the hydrated dR films. These desorbed ions may be involved in the induction of other types of damage, such as oxidatively generated base lesions, concomitantly produced with a strand break when produced in DNA.

Charge migration and charge transfer in molecular systems.

The transfer of charge at the molecular level plays a fundamental role in many areas of chemistry, physics, biology and materials science. Today, more than 60 years after the seminal work of R. A. Marcus, charge transfer is still a very active field of research. An important recent impetus comes from the ability to resolve ever faster temporal events, down to the attosecond time scale. Such a high temporal resolution now offers the possibility to unravel the most elementary quantum dynamics of both electrons and nuclei that participate in the complex process of charge transfer. This review covers recent research that addresses the following questions. Can we reconstruct the migration of charge across a molecule on the atomic length and electronic time scales? Can we use strong laser fields to control charge migration? Can we temporally resolve and understand intramolecular charge transfer in dissociative ionization of small molecules, in transition-metal complexes and in conjugated polymers? Can we tailor molecular systems towards specific charge-transfer processes? What are the time scales of the elementary steps of charge transfer in liquids and nanoparticles? Important new insights into each of these topics, obtained from state-of-the-art ultrafast spectroscopy and/or theoretical methods, are summarized in this review.

Ultrafast Relaxation Dynamics of the Ethylene Cation C(2)H(4)+.

We present a combined experimental and computational study of the relaxation dynamics of the ethylene cation. In the experiment, we apply an extreme-ultraviolet-pump/infrared-probe scheme that permits us to resolve time scales on the order of 10 fs. The photoionization of ethylene followed by an infrared (IR) probe pulse leads to a rich structure in the fragment ion yields reflecting the fast response of the molecule and its nuclei. The temporal resolution of our setup enables us to pinpoint an upper bound of the previously defined ethylene-ethylidene isomerization time to 30 ± 3 fs. Time-dependent density functional based trajectory surface hopping simulations show that internal relaxation between the first excited states and the ground state occurs via three different conical intersections. This relaxation unfolds on femtosecond time scales and can be probed by ultrashort IR pulses. Through this probe mechanism, we demonstrate a route to optical control of the important dissociation pathways leading to separation of H or H2.