During the past decades, quantum mechanical methods have undergone an amazing transition from pioneering investigations of experts into a wide range of practical applications, made by a vast community of researchers. First principles calculations of systems containing up to a few hundred atoms have become a standard in many branches of science. The sizes of the systems which can be simulated have increased even further during recent years, and quantum-mechanical calculations of systems up to many thousands of atoms are nowadays possible. This opens up new appealing possibilities, in particular for interdisciplinary work, bridging together communities of different needs and sensibilities. In this review we will present the current status of this topic, and will also give an outlook on the vast multitude of applications, challenges, and opportunities stimulated by electronic structure calculations, making this field an important working tool and bringing together researchers of many different domains. ; We would like to thank Modesto Orozco and Hansel Gómez for fruitful discussions and Fátima Lucas for providing various test systems and helping with some visualizations. This work was supported by the EXTMOS project, grant agreement number 646176, and the Energy oriented Centre of Excellence (EoCoE), grant agreement number 676629, funded both within the Horizon2020 framework of the European Union. This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-06CH11357. ; Peer Reviewed ; Postprint (author's final draft)
During the past decades, quantum mechanical methods have undergone an amazing transition from pioneering investigations of experts into a wide range of practical applications, made by a vast community of researchers. First principles calculations of systems containing up to a few hundred atoms have become a standard in many branches of science. The sizes of the systems which can be simulated have increased even further during recent years, and quantum-mechanical calculations of systems up to many thousands of atoms are nowadays possible. This opens up new appealing possibilities, in particular for interdisciplinary work, bridging together communities of different needs and sensibilities. In this review we will present the current status of this topic, and will also give an outlook on the vast multitude of applications, challenges, and opportunities stimulated by electronic structure calculations, making this field an important working tool and bringing together researchers of many different domains. ; We would like to thank Modesto Orozco and Hansel Gómez for fruitful discussions and Fátima Lucas for providing various test systems and helping with some visualizations. This work was supported by the EXTMOS project, grant agreement number 646176, and the Energy oriented Centre of Excellence (EoCoE), grant agreement number 676629, funded both within the Horizon2020 framework of the European Union. This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-06CH11357. ; Peer Reviewed ; Postprint (author's final draft)
With big-data driven materials research, the new paradigm of materials science, sharing and wide accessibility of data are becoming crucial aspects. Obviously, a prerequisite for data exchange and big-data analytics is standardization, which means using consistent and unique conventions for, e.g., units, zero base lines, and file formats. There are two main strategies to achieve this goal. One accepts the heterogeneous nature of the community, which comprises scientists from physics, chemistry, bio-physics, and materials science, by complying with the diverse ecosystem of computer codes and thus develops "converters" for the input and output files of all important codes. These converters then translate the data of each code into a standardized, code-independent format. The other strategy is to provide standardized open libraries that code developers can adopt for shaping their inputs, outputs, and restart files, directly into the same code-independent format. In this perspective paper, we present both strategies and argue that they can and should be regarded as complementary, if not even synergetic. The represented appropriate format and conventions were agreed upon by two teams, the Electronic Structure Library (ESL) of the European Center for Atomic and Molecular Computations (CECAM) and the NOvel MAterials Discovery (NOMAD) Laboratory, a European Centre of Excellence (CoE). A key element of this work is the definition of hierarchical metadata describing state-of-the-art electronic-structure calculations. ; We thank James Kermode and Saulius Gražulis for their contribution to the discussion on the metadata, and Pasquale Pavone for precious suggestions on the metadata structure and names. We thank Patrick Rinke and Ghanshyam Pilania for carefully reading the manuscript. We thank Claudia Draxl and Kristian Thygesen for their contribution to the discussions on the necessary information to be stored for excitedstate calculations and on the error bars and uncertainties. We gratefully acknowledge Damien Caliste, Fabiano Corsetti, Hubert Ebert, Jan Minar, Yann Pouillon, Thomas Ruh, David Strubbe, and Marc Torrent for their contributions to the ESCDF specifications. We acknowledge Benjamin Regler for the development of the graphical interface for the query on the NOMAD Archive. We acknowledge inspiring discussions with Georg Kresse, Peter Blaha, Xavier Gonze, Bernard Delley, and Jörg Hutter on the energy-zero definition and scalar-field representation. We thank Ole Andersen, Evert Jan Baerends, Peter Blaha, Lambert Colin, Bernard Delley, Thierry Deutsch, Claudia Draxl, John Kay Dewhurst, Roberto Dovesi, Paolo Giannozzi, Mike Gillan, Xavier Gonze, Michael Frisch, Martin Head-Gordon, Juerg Hutter, Klaus Koepernik, Georg Kresse, Roland Lindh, Hans Lischka, Andrea Marini, Todd Martinez, Jens Jørgen Mortensen, Frank Neese, Richard Needs, Taisuke Ozaki, Mike Payne, Angel Rubio, Trond Saue, Chris Skylaris, Jose Soler, John Stanton, James Stewart, Marat Valiev for checking the information provided in Table 1 and for useful suggestions. This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 676580, The NOMAD Laboratory, a European Center of Excellence, and the BBDC (contract 01IS14013E). ; Peer Reviewed ; Postprint (published version)
With big-data driven materials research, the new paradigm of materials science, sharing and wide accessibility of data are becoming crucial aspects. Obviously, a prerequisite for data exchange and big-data analytics is standardization, which means using consistent and unique conventions for, e.g., units, zero base lines, and file formats. There are two main strategies to achieve this goal. One accepts the heterogeneous nature of the community, which comprises scientists from physics, chemistry, bio-physics, and materials science, by complying with the diverse ecosystem of computer codes and thus develops "converters" for the input and output files of all important codes. These converters then translate the data of each code into a standardized, code-independent format. The other strategy is to provide standardized open libraries that code developers can adopt for shaping their inputs, outputs, and restart files, directly into the same code-independent format. In this perspective paper, we present both strategies and argue that they can and should be regarded as complementary, if not even synergetic. The represented appropriate format and conventions were agreed upon by two teams, the Electronic Structure Library (ESL) of the European Center for Atomic and Molecular Computations (CECAM) and the NOvel MAterials Discovery (NOMAD) Laboratory, a European Centre of Excellence (CoE). A key element of this work is the definition of hierarchical metadata describing state-of-the-art electronic-structure calculations. ; We thank James Kermode and Saulius Gražulis for their contribution to the discussion on the metadata, and Pasquale Pavone for precious suggestions on the metadata structure and names. We thank Patrick Rinke and Ghanshyam Pilania for carefully reading the manuscript. We thank Claudia Draxl and Kristian Thygesen for their contribution to the discussions on the necessary information to be stored for excitedstate calculations and on the error bars and uncertainties. We gratefully acknowledge Damien Caliste, Fabiano Corsetti, Hubert Ebert, Jan Minar, Yann Pouillon, Thomas Ruh, David Strubbe, and Marc Torrent for their contributions to the ESCDF specifications. We acknowledge Benjamin Regler for the development of the graphical interface for the query on the NOMAD Archive. We acknowledge inspiring discussions with Georg Kresse, Peter Blaha, Xavier Gonze, Bernard Delley, and Jörg Hutter on the energy-zero definition and scalar-field representation. We thank Ole Andersen, Evert Jan Baerends, Peter Blaha, Lambert Colin, Bernard Delley, Thierry Deutsch, Claudia Draxl, John Kay Dewhurst, Roberto Dovesi, Paolo Giannozzi, Mike Gillan, Xavier Gonze, Michael Frisch, Martin Head-Gordon, Juerg Hutter, Klaus Koepernik, Georg Kresse, Roland Lindh, Hans Lischka, Andrea Marini, Todd Martinez, Jens Jørgen Mortensen, Frank Neese, Richard Needs, Taisuke Ozaki, Mike Payne, Angel Rubio, Trond Saue, Chris Skylaris, Jose Soler, John Stanton, James Stewart, Marat Valiev for checking the information provided in Table 1 and for useful suggestions. This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 676580, The NOMAD Laboratory, a European Center of Excellence, and the BBDC (contract 01IS14013E). ; Peer Reviewed ; Postprint (published version)
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 has been historically supported by different Spanish National Plan projects: MEC-DGESPB95-0202, 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. Currently, we thank financial support from the Spanish Ministry of Science, Innovation and Universities through the grant No. PGC2018-096955-B. We acknowledge the Severo Ochoa Centers of Excellence Program under Grants No. 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 RTI2018-097895-B-C41. R.C. acknowledges to the European Union's Horizon 2020 research and innovation program under the Marie Skłodoswka–Curie grant agreement no. 665919. D.S.P, P.K, and P.B acknowledge MAT2016-78293-C6, FET-Open No. 863098, and UPV-EHU Grant IT1246-19. V. Yu was supported by a MolSSI fellowship (U.S. NSF award 1547580), and the ELSI development (V.B.,V.Yu) by NSF award 1450280. We also acknowledge Honghui Shang and Xinming Qin for giving us access to the HONPAS code, where a preliminary version of the hybrid functionals support described here was implemented. We are indebted to other contributors to the SIESTA project, whose names can be seen in the file 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. The data that support the findings of this study are available from the corresponding author upon reasonable request. ; Peer Reviewed ; Postprint (author's final draft)
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 like to thank CECAM for launching and pushing the ESL, as well as hosting part of its infrastructure, and partly funding the extended workshops where most of the coding was done, both in the Lausanne headquarters and in the Dublin, Trieste, and Zaragoza nodes. Within CECAM, the authors particularly thank Sara Bonella, Bogdan Nichita, and Ignacio Pagonabarraga. The authors also acknowledge all the people who have supported and contributed to the ESL in different ways, including Luis Agapito, Xavier Andrade, Balint Aradi, Emanuele Bosoni, Lori A. Burns, Christian Carbogno, Ivan Carnimeo, Abel Carreras Conill, Alberto Castro, Michele Ceriotti, Anoop Chandran, Wibe de Jong, Pietro Delugas, Thierry Deutsch, Hubert Ebert, Aleksandr Fonari, Luca Ghiringhelli, Paolo Giannozzi, Matteo Giantomassi, Judit Gimenez, Ivan Girotto, Xavier Gonze, Benjamin Hourahine, Jürg Hutter, Thomas Keal, Jan Kloppenburg, Hyungjun Lee, Liang Liang, Lin Lin, Jianfeng Lu, Nicola Marzari, Donal MacKernan, Layla Martin-Samos, Paolo Medeiros, Fawzi Mohamed, Jens Jørgen Mortensen, Sebastian Ohlmann, David O'Regan, Charles Patterson, Etienne Plésiat, Markus Rampp, Laura Ratcliff, Stefano Sanvito, Paul Saxe, Matthias Scheffler, Didier Sebilleau, Søren Smidstrup, James Spencer, Atsushi Togo, Joost Vandevondele, Matthieu Verstraete, and Brian Wylie. 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. ACI-1547580). 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. RTC-2016-5681-7). 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 ; Peer Reviewed ; Postprint (author's final draft)
