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.

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.

Mechanically interlocked single-wall carbon nanotubes.

Extensive research has been devoted to the chemical manipulation of carbon nanotubes. The attachment of molecular fragments through covalent-bond formation produces kinetically stable products, but implies the saturation of some of the C-C double bonds of the nanotubes. Supramolecular modification maintains the structure of the SWNTs but yields labile species. Herein, we present a strategy for the synthesis of mechanically interlocked derivatives of SWNTs (MINTs). In the key rotaxane-forming step, we employed macrocycle precursors equipped with two π-extended tetrathiafulvalene SWNT recognition units and terminated with bisalkenes that were closed around the nanotubes through ring-closing metathesis (RCM). The mechanically interlocked nature of the derivatives was probed by analytical, spectroscopic, and microscopic techniques, as well as by appropriate control experiments. Individual macrocycles were observed by HR STEM to circumscribe the nanotubes.

Bimodal supramolecular functionalization of carbon nanotubes triggered by covalent bond formation.

Many applications of carbon nanotubes require their chemical functionalization. Both covalent and supramolecular approaches have been extensively investigated. A less trodden path is the combination of both covalent and noncovalent chemistries, where the formation of covalent bonds triggers a particularly stable noncovalent interaction with the nanotubes. We describe a series of naphthalene diimide (NDI) bisalkene molecules that, upon mixing with single-walled carbon nanotubes (SWNTs) and Grubbs' catalyst, undergo two different reaction pathways. On one hand, they ring-close around the SWNTs to form rotaxane-like mechanically interlocked derivatives of SWNTs (MINTs). Alternatively, they oligomerize and then wrap around the SWNTs. The balance of MINTs to oligomer-wrapped SWNTs depends on the affinity of the NDI molecules for the SWNTs and the kinetics of the metathesis reactions, which can be controlled by varying the solvent. Thorough characterization of the products (TGA, TEM, AFM, Raman, UV-vis-NIR, PLE, XPS and UPS) confirms their structure and shows that each type of functionalization affects the electronic properties of the SWNTs differently.

The mechanical bond on carbon nanotubes: diameter-selective functionalization and effects on physical properties.

We describe the functionalization of SWNTs enriched in (6,5) chirality with electron donating macrocycles to yield rotaxane-type mechanically interlocked carbon nanotubes (MINTs). Investigations by means of electron microscopy and control experiments corroborated the interlocked nature of the MINTs. A comprehensive characterization of the MINTs through UV-vis-NIR, Raman, fluorescence, transient absorption spectroscopy, cyclic voltammetry, and chronoamperometry was carried out. Analyses of the spectroscopic data reveal that the MINT-forming reaction proceeds with diameter selectivity, favoring functionalization of (6,5) SWNTs rather than larger (7,6) SWNTs. In the ground state, we found a lack of significant charge-transfer interactions between the electron donor exTTF and the SWNTs. Upon photoexcitation, efficient charge-transfer between the electron donating exTTF macrocycles and SWNTs was demonstrated. As a complement, we established significantly different charge-transfer rate constants and diffusion coefficients for MINTs and the supramolecular models, which confirms the fundamentally different type of interactions between exTTF and SWNTs in the presence or absence of the mechanical bond. Molecular mechanics and DFT calculations support the experimental findings.