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 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. Published under license by AIP Publishing.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). We also acknowledge Honghui Shang and Xinming Qin for giving us access to the honpas code, where a preliminary version of the hybrid functional support described here was implemented. We are indebted to other contributors to the Siesta project whose names can be seen in the Docs/Contributors.txt file of the Siesta distribution, and we thank those, too many to list, contributing fixes, comments, clarifications, and documentation for the code.Peer reviewe

The CECAM Electronic Structure Library and the modular software development paradigm

First-principles electronic structure calculations are very widely used thanks to the many successful software packages available. Their traditional coding paradigm is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, from the compiler up, with the exception of linear-algebra and message-passing libraries. This model has been quite successful for decades. The rapid progress in methodology, however, has resulted in an ever increasing complexity of those programs, which implies a growing amount of replication in coding and in the recurrent re-engineering needed to adapt to evolving hardware architecture. The Electronic Structure Library (\esl) was initiated by CECAM (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 programs and redesign them as free, open-source libraries. They include ``heavy-duty'' ones with a high degree of parallelisation, and potential for 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 scientists when implementing new ideas. It is a community effort, undertaken by developers of various successful codes, now facing the challenges arising in the new model. This modular paradigm will improve overall coding efficiency and enable specialists (computer scientists or computational scientists) to use their skills more effectively. It will lead to a more sustainable and dynamic evolution of software as well as lower barriers to entry for new developers

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.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-

DFT study on zeolites’ intrinsic Brønsted acidity: The case of BEA

Since Brønsted acidity is a crucial aspect for the applications of zeolitic materials in heterogeneous catalysis, great effort was devolved to characterize the number, strength and location of the potentially active acidic sites. Quantum chemical calculations can turn out essential in estimating the intrinsic acidity by computing deprotonation energy (DPE) values, although each method comes with its own difficulties. In this context, three approaches within density functional theory were employed to study the intrinsic acidity of 30 topologically distinct Brønsted sites in the β-zeolite framework. Advantages and disadvantages of the three methods were outlined and the acidity order between the sites was assessed, being the DPE range 59 kJ mol−1 wide, with the proposed best approach. By dividing the range into three portions, the sites were classified as having high, medium and low acidity. Hydrogen bonds formation was found to be a contributing factor in determining a low Brønsted acidity

ABINIT: Overview and focus on selected capabilities

Paper published as part of the special topic on Electronic Structure SoftwareABINIT is probably the first electronic-structure package to have been released under an open-source license about 20 years ago. It implements density functional theory, density-functional perturbation theory (DFPT), many-body perturbation theory (GW approximation and Bethe–Salpeter equation), and more specific or advanced formalisms, such as dynamical mean-field theory (DMFT) and the “temperaturedependent effective potential” approach for anharmonic effects. Relying on planewaves for the representation of wavefunctions, density, and other space-dependent quantities, with pseudopotentials or projector-augmented waves (PAWs), it is well suited for the study of periodic materials, although nanostructures and molecules can be treated with the supercell technique. The present article starts with a brief description of the project, a summary of the theories upon which ABINIT relies, and a list of the associated capabilities. It then focuses on selected capabilities that might not be present in the majority of electronic structure packages either among planewave codes or, in general, treatment of strongly correlated materials using DMFT; materials under finite electric fields; properties at nuclei (electric field gradient, Mössbauer shifts, and orbital magnetization); positron annihilation; Raman intensities and electro-optic effect; and DFPT calculations of response to strain perturbation (elastic constants and piezoelectricity), spatial dispersion (flexoelectricity), electronic mobility, temperature dependence of the gap, and spin-magnetic-field perturbation. The ABINIT DFPT implementation is very general, including systems with van der Waals interaction or with noncollinear magnetism. Community projects are also described: generation of pseudopotential and PAW datasets, high-throughput calculations (databases of phonon band structure, second-harmonic generation, and GW computations of bandgaps), and the library LIBPAW. ABINIT has strong links with many other software projects that are briefly mentioned.This work (A.H.R.) was supported by the DMREF-NSF Grant No. 1434897, National Science Foundation OAC-1740111, and U.S. Department of Energy DE-SC0016176 and DE-SC0019491 projects. N.A.P. and M.J.V. gratefully acknowledge funding from the Belgian Fonds National de la Recherche Scientifique (FNRS) under Grant No. PDR T.1077.15-1/7. M.J.V. also acknowledges a sabbatical “OUT” grant at ICN2 Barcelona as well as ULiège and the Communauté Française de Belgique (Grant No. ARC AIMED G.A. 15/19-09). X.G. and M.J.V. acknowledge funding from the FNRS under Grant No. T.0103.19-ALPS. X.G. and G.-M. R. acknowledge support from the Communauté française de Belgique through the SURFASCOPE Project (No. ARC 19/24-057). X.G. acknowledges the hospitality of the CEA DAM-DIF during the year 2017. G.H. acknowledges support from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division under Contract No. DE-AC02-05-CH11231 (Materials Project Program No. KC23MP). The Belgian authors acknowledge computational resources from supercomputing facilities of the University of Liège, the Consortium des Equipements de Calcul Intensif (Grant No. FRS-FNRS G.A. 2.5020.11), and Zenobe/CENAERO funded by the Walloon Region under Grant No. G.A. 1117545. M.C. and O.G. acknowledge support from the Fonds de Recherche du Québec Nature et Technologie (FRQ-NT), Canada, and the Natural Sciences and Engineering Research Council of Canada (NSERC) under Grant No. RGPIN-2016-06666. The implementation of the libpaw library (M.T., T.R., and D.C.) was supported by the ANR NEWCASTLE project (Grant No. ANR-2010-COSI-005-01) of the French National Research Agency. M.R. and M.S. acknowledge funding from Ministerio de Economia, Industria y Competitividad (MINECO-Spain) (Grants Nos. MAT2016-77100-C2-2-P and SEV-2015-0496) and Generalitat de Catalunya (Grant No. 2017 SGR1506). This work has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation program (Grant Agreement No. 724529). P.G. acknowledges support from FNRS Belgium through PDR (Grant No. HiT4FiT), ULiège and the Communauté française de Belgique through the ARC project AIMED, the EU and FNRS through M.ERA.NET project SIOX, and the European Funds for Regional Developments (FEDER) and the Walloon Region in the framework of the operational program “Wallonie-2020.EU” through the project Multifunctional thin films/LoCoTED. The Flatiron Institute is a division of the Simons Foundation. A large part of the data presented in this paper is available directly from the Abinit Web page www.abinit.org. Any other data not appearing in this web page can be provided by the corresponding author upon reasonable request.Peer reviewe

How to verify the precision of density-functional-theory implementations via reproducible and universal workflows

In the past decades many density-functional theory methods and codes adopting periodic boundary conditions have been developed and are now extensively used in condensed matter physics and materials science research. Only in 2016, however, their precision (i.e., to which extent properties computed with different codes agree among each other) was systematically assessed on elemental crystals: a first crucial step to evaluate the reliability of such computations. We discuss here general recommendations for verification studies aiming at further testing precision and transferability of density-functional-theory computational approaches and codes. We illustrate such recommendations using a greatly expanded protocol covering the whole periodic table from Z=1 to 96 and characterizing 10 prototypical cubic compounds for each element: 4 unaries and 6 oxides, spanning a wide range of coordination numbers and oxidation states. The primary outcome is a reference dataset of 960 equations of state cross-checked between two all-electron codes, then used to verify and improve nine pseudopotential-based approaches. Such effort is facilitated by deploying AiiDA common workflows that perform automatic input parameter selection, provide identical input/output interfaces across codes, and ensure full reproducibility. Finally, we discuss the extent to which the current results for total energies can be reused for different goals (e.g., obtaining formation energies).Comment: Main text: 23 pages, 4 figures. Supplementary: 68 page

Polar meron-antimeron networks in strained and twisted bilayers

Out-of-plane polar domain structures have recently been discovered in strained and twisted bilayers of inversion symmetry broken systems such as hexagonal boron nitride. Here we show that this symmetry breaking also gives rise to an in-plane component of polarization, and the form of the total polarization is determined purely from symmetry considerations. The in-plane component of the polarization makes the polar domains in strained and twisted bilayers topologically non-trivial, forming a network of merons and antimerons (half-skyrmions and half-antiskyrmions). For twisted systems, the merons are of Bloch type whereas for strained systems they are of N\'eel type. We propose that the polar domains in strained or twisted bilayers may serve as a platform for exploring topological physics in layered materials and discuss how control over topological phases and phase transitions may be achieved in such systems.Comment: Accepted versio

Dielectric function and plasmonic behavior of Ga(II) and Ga(III)

In order to exploit gallium´s (Ga) rich polymorphism in the design of phase-change plasmonic systems, accurate understanding of the dielectric function of the different Ga-phases is crucial. The dielectric dispersion profiles of those phases appearing at atmospheric pressure have been reported in the literature, but there is no information on the dielectric function of the high-pressure Ga-phases. Through first principles calculations we present a comprehensive analysis of the interdependence of the crystal structure, band structure, and dielectric function of two high-pressure Ga phases (Ga(II) and Ga(III)). The plasmonic behavior of these high-pressure Ga-phases is compared to those stable (liquid- and α-Ga) and metastable (β-, γ- and δ-Ga) at atmospherics pressure. This analysis can have important implications in the design of pressure-driven phase-change Ga plasmonic devices and high-pressure SERS substrates.Y.G. and F.M. acknowledges the support by the Army Research Laboratory under Cooperative Agreement Number W911NF-17-2-0023 and by SODERCAN (Sociedad para el Desarrollo de Cantabria) and the Research Vicerrectorate of the University of Cantabria through project 4JU2864661. Y.G. thanks the University of Cantabria for her FPU grant. P.G.-F. and J.J. acknowledge financial support from the Spanish Ministry of Economy and Competitiveness through grant number PGC2018-096955-B-C41

Curadoria em bibliotecas e a prática do bibliotecário como curador

No cenário atual em que o universo informacional é complexo e ao mesmo tempo líquido, definir o que realmente importa ser curado tem sido um grande desafio para bibliotecários. O objetivo do trabalho é descrever a apropriação da curadoria em bibliotecas e a prática do bibliotecário como curador. Por intermédio da pesquisa descritiva demandou-se um esforço para compreender em que contexto os termos curadoria e curador possuem relevância dentro da museologia e arquivologia. Combinando técnicas bibliográficas e bibliométricas, visando apresentar a necessidade de utilização dos termos na biblioteca e sua utilização pela prática bibliotecária, abordou-se o comportamento curatorial à luz dos textos selecionados na base de dados Scopus. Os documentos recuperados para a pesquisa estão distribuídos entre artigos, capítulos de livros, revisões e documentos de conferência. Foram selecionados os resumos de maior pertinência para a pesquisa e submetidos à análise pela utilização das palavras-chave, construindo clusters, tabelas, gráficos e tags. Embora os textos acadêmicos recuperados pela pesquisa evidenciem a preocupação dos bibliotecários com o tratamento e preservação dos dados de pesquisa, observou-se que algumas bibliotecas carecem de diversificar sua atuação, de aprender e ensinar novas e promissoras formas de selecionar, tratar e divulgar o conhecimento. Percebemos que o fazer curadoria já vem sendo praticado por bibliotecas e que o conceito de curador está presente nas práticas comum dos bibliotecários. O que identificamos, porém, a partir dos textos analisados, que a curadoria em bibliotecas carece de infraestrutura tecnológica e a prática do bibliotecário como curador de uma melhor formação profissional que lhes proporcione fortalecer sua missão de recuperar, preservar e disseminar informação.In today's scenario where the informational universe is complex and at the same time liquid, defining what really matters being cured has been a major challenge for librarians. The purpose of this research is to describe the appropriation of curatorship in libraries and the practice of the librarian as a curator. Using a descriptive research, an effort was made to understand in what context the terms curatorship and curator are relevant in the fields of museology and archivology. Combining bibliographical and bibliometric techniques, curatorial behavior was approached in light of the texts selected in the Scopus database, aiming to present the need to use these terms in libraries and in library practice. The documents retrieved for this research are articles, book chapters, reviews, and conference documents. The abstracts of greater relevance for this research were selected and submitted to analysis using keywords, constructing clusters, tables, graphs and tags. Although the academic texts retrieved for this study show the concern of librarians with the treatment and preservation of research data, it was observed that some libraries need to diversify their performance, to learn and teach new and promising ways to select, treat and disseminate knowledge. We realize that curing has already been practiced by libraries and that the concept of curator is present in the common practice of librarians. What we identify, however, from the analyzed texts is that library curation lacks technological infrastructure and the librarian's practice as a curator demands a better professional formation that will strengthen their mission of retrieving, preserving and disseminating information

Simulation of plasmons in gold nanoparticles

RESUMEN: Las nanopartículas metálicas poseen una capacidad extraordinaria para transformar energía electromagnética en calor. Sus buenas propiedades ópticas han atraído el interés de la comunidad científica, incluso originando un nuevo campo: la Termoplasmónica [B, 18]. Dedicamos este trabajo al estudio de los plasmones sobre nanopartículas de oro. Históricamente, la caracterización de las propiedades ópticas de las nanopartículas más pequeñas que 10nm ha sido problemática, debido a la escasez de medidas experimentales precisas y modelos cuánticos consistentes. En este trabajo proponemos simular nanopartículas de oro ab initio, con técnicas de primeros [S, 02] y segundos [GI, 16] principios, respetando la naturaleza cuántica de la interacción luz-materia. Además, revisamos el enfoque clásico al problema: la Teoría de Mie. Dividimos el trabajo en tres secciones: I) teoría clásica, II) simulación de las propiedades ópticas del oro sólido con primeros principios y III) simulación de las propiedades ópticas de nanopartículas de oro con segundos principios.ABSTRACT: Metallic nanoparticles have an extraordinary ability to convert electromagnetic energy into heat. Their fine optical properties have created much interest in the scientific community, leading to a full new topic called Thermoplasmonics [B, 18]. In this document we study the plasmons on gold nanoparticles. Historically, it has been arduous to characterize the optical properties of nanoparticles smaller than 10nm due to the lack of accurate experimental measures and solid quantum models. Here we try to simulate gold nanoparticles ab initio, using first [S, 02] and second [GI, 16] principles methods that take into account the quantum nature of light-matter interactions. Moreover, we revisit the classical take on the problem: Mie’s Theory. We split our work in three sections: I) classical theory, II) simulation of optical properties of bulk gold using first principles and III) simulation of optical properties of gold nanoparticles using second principles.Grado en Físic