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Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light-matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).

Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light–matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).

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 lowe

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems., United States. Defense Advanced Research Projects Agency (Grant DE-AR0000180)

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.

First-principles calculations within the framework of real-space time-dependent density functional theory have been performed for the complete chlorophyll (Chl) network of the light-harvesting complex from green plants, LHC-II. A local-dipole analysis method developed for this work has made possible the studies of the optical response of individual Chl molecules subjected to the influence of the remainder of the chromophore network. The spectra calculated using our real-space TDDFT method agree with previous suggestions that weak interaction with the protein microenvironment should produce only minor changes in the absorption spectrum of Chl chromophores in LHC-II. In addition, relative shifting of Chl absorption energies leads the stromal and lumenal sides of LHC-II to absorb in slightly different parts of the visible spectrum providing greater coverage of the available light frequencies. The site-specific alterations in Chl excitation energies support the existence of intrinsic energy transfer pathways within the LHC-II complex.

A systematic study of the optical and magnetic excitations of 12 MSi12 and four MSi10 transition metal encapsulating Si cages has been carried out by employing real time time-dependent density functional theory. Criteria for the choice of transition metals (M) are clusters stability, synthesizability, and diversity. It was found that both the optical absorption and the spin-susceptibility spectra are mainly determined by, in decreasing order of importance, (1) the cage shape, (2) the group in the Periodic Table to which M belongs, and (3) the period of M in the Periodic Table. Cages with similar structures and metal species that are close to each other in the Periodic Table possess spectra sharing many similarities; for example, the optical absorption spectra of the MSi12 (M = V, Nb, Ta, Cr, Mo, and W), which are highly symmetric and belong to groups 4 and 5 of the Periodic Table, all share a very distinctive peak at around 4 eV. In all cases, although some of the observed transitions are located at the Si skeleton of the cages, the transition metal species is always significant for the optical absorption and the spin-susceptibility spectra. Our results provide fingerprint data for identification of gas-phase MSi12 and MSi10 by optical absorption spectroscopy.

We present an analysis of different methods to calculate the classical electrostatic Hartree potential created by charge distributions. Our goal is to provide the reader with an estimation on the performance - in terms of both numerical complexity and accuracy - of popular Poisson solvers, and to give an intuitive idea on the way these solvers operate. Highly parallelizable routines have been implemented in a first-principle simulation code (Octopus) to be used in our tests, so that reliable conclusions about the capability of methods to tackle large systems in cluster computing can be obtained from our work.

We demonstrate the capabilities of time-dependent density functional theory (TDDFT) for strong-field, short wavelength (soft X-ray) physics, as compared to a formalism based on rate equations. We show that TDDFT provides a very good description of the total and individual ionization yields for Ne and Ar atoms exposed to strong laser pulses. We assess the reliability of different adiabatic density functionals and conclude that spatial and temporal non-localities in the exchange and correlation kernel are crucial for obtaining the correct ionization yield over a wide range of intensities (1013–1016 W/cm2 ). Our TDDFT calculations disentangle the contribution from each ionization channel using the Kohn-Sham wavefunction as an approximation to the exact one.

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn–Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn–Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures

Upon ionization, rare-gas (like Ar and Xe) clusters shift their absorptionspectrum from the ultraviolet to the visible. This happens as bonding becomes much stronger due to the removal of an electron from a strongly antibonding orbital. In this article, we study the absorptionspectrum of small cationic xenon clusters (Xe + n , withn=3,…,35 ) by means of time-dependent density functional theory. These calculations include relativistic effects through the use of relativisticj -dependent pseudopotentials in a two-spinor formulation of the Kohn–Sham equations. The peak positions in our calculated spectra are in fairly good agreement with experiment and confirm that absorption is mainly due to a charged linear core composed of 3, 4, or 5 Xe atoms where the positive charge is localized. However, we find large deviations concerning the oscillator strengths, which can be partially explained by the unsatisfactory treatment of exchange in common density functionals. Furthermore, we find that adequate ground-state geometries are necessary for the correct prediction of the qualitative features of the spectra.

ABINIT [http://www.abinit.org] allows one to study, from first-principles, systems made of electrons and nuclei (e.g. periodic solids, molecules, nanostructures, etc.), on the basis of Density-Functional Theory (DFT) and Many-Body Perturbation Theory. Beyond the computation of the total energy, charge density and electronic structure of such systems, ABINIT also implements many dynamical, dielectric, thermodynamical, mechanical, or electronic properties, at different levels of approximation. The present paper provides an exhaustive account of the capabilities of ABINIT. It should be helpful to scientists that are not familiarized with ABINIT, as well as to already regular users. First, we give a broad overview of ABINIT, including the list of the capabilities and how to access them. Then, we present in more details the recent, advanced, developments of ABINIT, with adequate references to the underlying theory, as well as the relevant input variables, tests and, if available, ABINIT tutorials.

[PT]: A caracterizaçao da resposta electronica de nano-estruturas a campos electromagneticos externos e de grande importância, tanto do ponto de vista teorico como do ponto de vista experimental. Em contraste com os elementos leves, novos processos e fenomenos fisicos aparecem nos elementos pesados, onde efeitos relativistas, como o acoplamento de spin-orbita, nao podem ser ignorados. Neste trabalho desenvolvemos um quadro teorico e as ferramentas numericas necessarias para lidar com tais processos no contexto da teoria dos funcionais da densidade dependente do tempo. Em primeiro lugar, aplicamos esta metodologia ao estudo da secçao eficaz da absorçao optica de pequenos agregados cationicos de xenon. No geral, verificamos que o acordo dos nossos resultados com a experiência e bom, excepto na previsao incorrecta da intensidade relativa dos picos. Como segunda aplicaçao, investigamos o efeito do acoplamento de spin-orbita na resposta optica de pequenos agregados de ouro. Verificamos que este efeito nunca e desprezavel, mas que a sua importância depende da dimesionalidade dos agregados (o efeito e mais pronunciado para fios, do que para estruturas 2D e 3D) e do tamanho dos agregados (o efeito e “apagado” com o aumento do tamanho dos agregados). Finalmente, estudamos o papel da nao colinearidade do spin nas propriedades de estado excitado de pequenos agregados de cromio e ferro e a maneira como este se conjuga com o acoplamento de spin-orbita. Em particular, comparamos as respostas dipolar e spin-dipolar de agregados com arranjos colineares e nao colineares de spin. Verificamos em todos os casos que a diferente estrutura electronica das configuraçoes colineares e nao colineares reflecte-se, ate certo ponto, nos espectros. Pelo contrario, nao encontramos nos espectros nenhum efeito directo do acoplamento de spin-orbita., [EN]: The characterization of the electronic response of nanostructures to external electromagnetic fields is of great importance, both from the theoretical and technological points of view. In contrast to light elements, new physical processes and phenomena appear in heavy elements, where relativistic effects, like spin-orbit coupling cannot be ignored. In this work we develop the theoretical framework and the numerical tools needed to address those processes within time-dependent density functional theory (TDDFT). We first apply this methodology to the study of the photoabsorption cross-section of small cationic xenon clusters. Overall, we find our results to be in good agreement with experiment, except for the incorrect prediction of the relative intensities of the peaks. As a second application, we investigate the effect of spin-orbit coupling in the optical response of small gold clusters. We find that this effect is always noticeable, but its importance depends on the dimensionalities of the clusters (the effect is larger for wires than for 2D and 3D structures) and on the size of the clusters (the effect is “quenched” with increasing cluster size). Finally, we study the role of spin noncollinearity in the excited state properties of small chromium and iron clusters and its interplay with spin-orbit coupling. In particular, we compare the dipole and spin-dipole responses of clusters with collinear and noncollinear spin arrangements. We find that, in all cases, the different electronic structure of collinear and noncollinear configurations are reflected to some extent in the spectra. On the contrary, no direct evidence of spin-orbit coupling can be found in the spectra.

By first-principles time-dependent density-functional calculations, we show the relevance of relativistic effects to shape the photoabsorption cross section of small goldclusters (Aun,n <=8, andn = 20 ) and small nanowires(n<=7). The relativistic effects not only dictate the stabilization of planar geometries (as it has already been shown by treating the core electrons relativistically): The spin-orbit coupling also has a strong impact in the absorption spectra (resonances and oscillator strengths). This is especially true for nanowires, where the effect of spin orbit is large and not substantially reduced with the chain length, in contrast to more compact goldclusters where this spin-orbit effect tends to be quenched. These results have far reaching consequences in fields such as electronic transport, where goldnanowires are often used, but where spin-orbit effects are generally disregarded.

The polarizability measures how the system responds to an applied electrical field. Computationally, there are many different ways to evaluate this tensorial quantity, some of which rely on the explicit use of the external perturbation and require several individual calculations to obtain the full tensor. In this work, we present some considerations about symmetry that allow us to take full advantage of Neumann's principle and decrease the number of calculations required by these methods. We illustrate the approach with two examples, the use of the symmetries in real space and in spin space in the calculation of the electrical or the spin response.

We report on the background, current status, and current lines of development of the octopus project. This program materializes the main equations of density-functional theory in the ground state, and of time-dependent density-functional theory for dynamical effects. The focus is nowadays placed on the optical (i.e. electronic) linear response properties of nanostructures and biomolecules, and on the non-linear response to high-intensity fields of finite systems, with particular attention to the coupled ionic-electronic motion (i.e. photo-chemical processes). In addition, we are currently extending the code to the treatment of periodic systems (both to one-dimensional chains, two-dimensional slabs, or fully periodic solids), magnetic properties (ground state properties and excitations), and to the field of quantum-mechanical transport or “molecular electronics.” In this communication, we concentrate on the development of the methodology: we review the essential numerical schemes used in the code, and report on the most recent implementations, with special attention to the introduction of adaptive coordinates, to the extension of our real-space technique to tackle periodic systems, and on large-scale parallelization. More information on the code, as well as the code itself, can be found at http://www.tddft.org/programs/octopus/. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim).