QUANTUM ESPRESSO: a Modular and Open-Source Software Project for Quantum Simulations of Materials
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Wannier90 As a Community Code: New
IOP Journal of Physics: Condensed Matter Journal of Physics: Condensed Matter J. Phys.: Condens. Matter J. Phys.: Condens. Matter 32 (2020) 165902 (25pp) https://doi.org/10.1088/1361-648X/ab51ff 32 Wannier90 as a community code: new 2020 features and applications © 2020 IOP Publishing Ltd Giovanni Pizzi1,29,30 , Valerio Vitale2,3,29 , Ryotaro Arita4,5 , Stefan Bl gel6 , Frank Freimuth6 , Guillaume G ranton6 , JCOMEL ü é Marco Gibertini1,7 , Dominik Gresch8 , Charles Johnson9 , Takashi Koretsune10,11 , Julen Ibañez-Azpiroz12 , Hyungjun Lee13,14 , 165902 Jae-Mo Lihm15 , Daniel Marchand16 , Antimo Marrazzo1 , Yuriy Mokrousov6,17 , Jamal I Mustafa18 , Yoshiro Nohara19 , 4 20 21 G Pizzi et al Yusuke Nomura , Lorenzo Paulatto , Samuel Poncé , Thomas Ponweiser22 , Junfeng Qiao23 , Florian Thöle24 , Stepan S Tsirkin12,25 , Małgorzata Wierzbowska26 , Nicola Marzari1,29 , Wannier90 as a community code: new features and applications David Vanderbilt27,29 , Ivo Souza12,28,29 , Arash A Mostofi3,29 and Jonathan R Yates21,29 Printed in the UK 1 Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 CM Lausanne, Switzerland 2 Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom 10.1088/1361-648X/ab51ff 3 Departments of Materials and Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom 4 RIKEN -
Light-Matter Interaction and Optical Spectroscopy from Infrared to X-Rays
24th ETSF Workshop on Electronic Excitations Light-Matter Interaction and Optical Spectroscopy from Infrared to X-Rays Jena, Germany 16 – 20 September 2019 Welcome The workshop series of the European Theoretical Spectroscopy Facility (ETSF) provides a fo- rum for excited states and spectroscopy in condensed-matter physics, chemistry, nanoscience, materials science, and molecular physics attracting theoreticians, code developers, and experi- mentalists alike. Light-matter interaction will be at core of the 2019 edition of the ETSF workshop. Cutting-edge spectroscopy experiments allow to probe electrons, plasmons, excitons, and phonons across different energy and time scales with unprecedented accuracy. A deep physical understanding of the underlying quantum many-body effects is of paramount importance to analyze exper- imental observations and render theoretical simulations predictive. The workshop aims at discussing the most recent advances in the theoretical description of the interaction between light and matter focusing on first-principles methods. This broad subject will be covered in its diverse declinations, from core-level spectroscopy to collective low-energy excitations, dis- cussing also matter under extreme conditions, and systems driven out of equilibrium by strong laser pulses. Exchange between theorists and experimentalists is fostered to open new horizons towards the next generation of novel spectroscopy techniques. The workshop will also face the challenges posed by the formidable complexity of heterogeneous and nanostructured systems such as those of interest for light harvesting and energy generation, prompting to bridge the gap be- tween experimental and in silico spectroscopy. Workshop topics include: Linear and nonlinear optical spectroscopy • Core-level spectroscopies • Ultrafast excitation dynamics • Electron-phonon coupling • Light harvesting in natural and synthetic systems • We are glad to welcome you in Jena, the city of light, and wish you an inspiring workshop with lots of interesting science and fruitful discussions. -
Accelerating Molecular Docking by Parallelized Heterogeneous Computing – a Case Study of Performance, Quality of Results
solis vasquez, leonardo ACCELERATINGMOLECULARDOCKINGBY PARALLELIZEDHETEROGENEOUSCOMPUTING–A CASESTUDYOFPERFORMANCE,QUALITYOF RESULTS,ANDENERGY-EFFICIENCYUSINGCPUS, GPUS,ANDFPGAS Printed and/or published with the support of the German Academic Exchange Service (DAAD). ACCELERATINGMOLECULARDOCKINGBYPARALLELIZED HETEROGENEOUSCOMPUTING–ACASESTUDYOF PERFORMANCE,QUALITYOFRESULTS,AND ENERGY-EFFICIENCYUSINGCPUS,GPUS,ANDFPGAS at the Computer Science Department of the Technische Universität Darmstadt submitted in fulfilment of the requirements for the degree of Doctor of Engineering (Dr.-Ing.) Doctoral thesis by Solis Vasquez, Leonardo from Lima, Peru Reviewers Prof. Dr.-Ing. Andreas Koch Prof. Dr. Christian Plessl Date of the oral exam October 14, 2019 Darmstadt, 2019 D 17 Solis Vasquez, Leonardo: Accelerating Molecular Docking by Parallelized Heterogeneous Computing – A Case Study of Performance, Quality of Re- sults, and Energy-Efficiency using CPUs, GPUs, and FPGAs Darmstadt, Technische Universität Darmstadt Date of the oral exam: October 14, 2019 Please cite this work as: URN: urn:nbn:de:tuda-tuprints-92886 URL: https://tuprints.ulb.tu-darmstadt.de/id/eprint/9288 This document is provided by TUprints, The Publication Service of the Technische Universität Darmstadt https://tuprints.ulb.tu-darmstadt.de This work is licensed under a Creative Commons “Attribution-ShareAlike 4.0 In- ternational” license. ERKLÄRUNGENLAUTPROMOTIONSORDNUNG §8 Abs. 1 lit. c PromO Ich versichere hiermit, dass die elektronische Version meiner Disserta- tion mit der schriftlichen Version übereinstimmt. §8 Abs. 1 lit. d PromO Ich versichere hiermit, dass zu einem vorherigen Zeitpunkt noch keine Promotion versucht wurde. In diesem Fall sind nähere Angaben über Zeitpunkt, Hochschule, Dissertationsthema und Ergebnis dieses Versuchs mitzuteilen. §9 Abs. 1 PromO Ich versichere hiermit, dass die vorliegende Dissertation selbstständig und nur unter Verwendung der angegebenen Quellen verfasst wurde. -
Universid Ade De Sã O Pa
A hardware/software codesign for the chemical reactivity of BRAMS Carlos Alberto Oliveira de Souza Junior Dissertação de Mestrado do Programa de Pós-Graduação em Ciências de Computação e Matemática Computacional (PPG-CCMC) UNIVERSIDADE DE SÃO PAULO DE SÃO UNIVERSIDADE Instituto de Ciências Matemáticas e de Computação Instituto Matemáticas de Ciências SERVIÇO DE PÓS-GRADUAÇÃO DO ICMC-USP Data de Depósito: Assinatura: ______________________ Carlos Alberto Oliveira de Souza Junior A hardware/software codesign for the chemical reactivity of BRAMS Master dissertation submitted to the Instituto de Ciências Matemáticas e de Computação – ICMC- USP, in partial fulfillment of the requirements for the degree of the Master Program in Computer Science and Computational Mathematics. FINAL VERSION Concentration Area: Computer Science and Computational Mathematics Advisor: Prof. Dr. Eduardo Marques USP – São Carlos August 2017 Ficha catalográfica elaborada pela Biblioteca Prof. Achille Bassi e Seção Técnica de Informática, ICMC/USP, com os dados fornecidos pelo(a) autor(a) Souza Junior, Carlos Alberto Oliveira de S684h A hardware/software codesign for the chemical reactivity of BRAMS / Carlos Alberto Oliveira de Souza Junior; orientador Eduardo Marques. -- São Carlos, 2017. 109 p. Dissertação (Mestrado - Programa de Pós-Graduação em Ciências de Computação e Matemática Computacional) -- Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, 2017. 1. Hardware. 2. FPGA. 3. OpenCL. 4. Codesign. 5. Heterogeneous-computing. I. Marques, Eduardo, orient. II. Título. Carlos Alberto Oliveira de Souza Junior Um coprojeto de hardware/software para a reatividade química do BRAMS Dissertação apresentada ao Instituto de Ciências Matemáticas e de Computação – ICMC-USP, como parte dos requisitos para obtenção do título de Mestre em Ciências – Ciências de Computação e Matemática Computacional. -
D7.2 Second Report on the Activity of the High-Level Support Services (Second Year)
Ref. Ares(2020)7219471 - 30/11/2020 HORIZON2020 European Centre of Excellence Deliverable D7.2 Second report on the activity of the High-Level Support services (second year) D7.2 Second report on the activity of the High-Level Support services (second year) Mariella Ippolito, Francisco Ramirez, Giovanni Pizzi, and Elsa Passaro Due date of deliverable: 30/11/2020 Actual submission date: 30/11/2020 Final version: 30/11/2020 Lead beneficiary: CINECA (participant number 8) Dissemination level: PU - Public www.max-centre.eu 1 HORIZON2020 European Centre of Excellence Deliverable D7.2 Second report on the activity of the High-Level Support services (second year) Document information Project acronym: MaX Project full title: Materials Design at the Exascale Research Action Project type: European Centre of Excellence in materials modelling, simulations and design EC Grant agreement no.: 824143 Project starting / end date: 01/12/2018 (month 1) / 30/11/2021 (month 36) Website: www.max-centre.eu Deliverable No.: D7.2 Authors: M. Ippolito, F. Ramirez, G. Pizzi, and E. Passaro To be cited as: M. Ippolito et al., (2020): Second report on the activity of the High-Level Support services (second year). Deliverable D7.2 of the H2020 project MaX (final version as of 30/11/2020). EC grant agreement no: 824143, CINECA, Bologna, Italy. Disclaimer: This document’s contents are not intended to replace consultation of any applicable legal sources or the necessary advice of a legal expert, where appropriate. All information in this document is provided "as is" and no guarantee or warranty is given that the information is fit for any particular purpose. -
Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids
Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Tancogne-Dejean, Nicolas et al. “Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids.” Physical Review Letters 118.8 (2017): n. pag. © 2017 American Physical Society As Published http://dx.doi.org/10.1103/PhysRevLett.118.087403 Publisher American Physical Society Version Final published version Citable link http://hdl.handle.net/1721.1/107908 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. week ending PRL 118, 087403 (2017) PHYSICAL REVIEW LETTERS 24 FEBRUARY 2017 Impact of the Electronic Band Structure in High-Harmonic Generation Spectra of Solids † Nicolas Tancogne-Dejean,1,2,* Oliver D. Mücke,3,4 Franz X. Kärtner,3,4,5,6 and Angel Rubio1,2,3,5, 1Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany 2European Theoretical Spectroscopy Facility (ETSF), Luruper Chaussee 149, 22761 Hamburg, Germany 3Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany 4The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany 5Physics Department, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany 6Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA (Received 29 September 2016; published 24 February 2017) An accurate analytic model describing the microscopic mechanism of high-harmonic generation (HHG) in solids is derived. -
Programming Models for Quantum Many-Body Methods on Multicore and Manycore Processors
Programming models for quantum many-body methods on multicore and manycore processors Jeff Hammond1 and Eugene DePrince2 1 Argonne 2 Georgia Tech 6 February 2011 Jeff Hammond Electronic Structure Calculation Methods on Accelerators Abstract The growing diversity in computer processor architectures poses a serious challenge to the computational chemistry community. This talk considers some of the key issues, including disjoint address spaces, non-standard architectures and execution models, and the different APIs required to use them. Specifically, we will describe our experiences in developing coupled-cluster methods for Intel multicore, Intel MIC, NVIDIA Fermi and Blue Gene/Q in both a clean-sheet implementation and NWChem. Of fundamental interest is the development of codes that scale not only within the node but across thousands of nodes; hence, the interaction between the processor and the network will be analyzed in detail. Jeff Hammond Electronic Structure Calculation Methods on Accelerators Software Automation Jeff Hammond Electronic Structure Calculation Methods on Accelerators The practical TCE { NWChem many-body codes What does it do? 1 GUI input quantum many-body theory e.g. CCSD. 2 Operator specification of theory. 3 Apply Wick's theory to transform operator expressions into array expressions. 4 Transform input array expression to operation tree using many types of optimization. 5 Produce Fortran+Global Arrays+NXTVAL implementation. Developer can intercept at various stages to modify theory, algorithm or implementation. Jeff Hammond Electronic Structure Calculation Methods on Accelerators The practical TCE { Success stories First parallel implementation of many (most) CC methods. First truly generic CC code (not string-based): fRHF,ROHF,UHF}×CCfSD,SDT,SDTQ}×{T /Λ,EOM,LR/QRg Most of the largest calculations of their kind employ TCE: CR-EOMCCSD(T), CCSD-LR α, CCSD-QR β, CCSDT-LR α Reduces implementation time for new methods from years to hours, TCE codes are easy to verify. -
Propriétés Structurales, Opto-Électroniques, Élastiques Et Dynamiques Des Semi-Conducteurs Type II-VI
REPUBLIQUE ALGERIENNE DEMOCRATIQUE ET POPULAIRE MINISTERE DE L’ENSEIGNEMENT SUPERIEUR ET DE LA RECHERCHE SCIENTIFIQUE UNIVERSITE FERHAT ABBAS – SETIF THESE Présentée à la faculté des Sciences Département de Physique Pour l’obtention du diplôme de DOCTORAT EN SCIENCES Option : physique du solide Par Mr. Benamrani Ammar Thème Propriétés structurales, opto-électroniques, élastiques et dynamiques des Semi-conducteurs type II-VI Soutenue le : 02/06/2012 Devant la commission d’examen : Dr. L. Louail Prof. U. F. A. SETIF Président Dr. K. Kassali Prof. U. F. A. SETIF Rapporteur Dr. Kh. Bouamama Prof. U. F. A. SETIF Co-Encadreur Dr. B. Bennecer Prof. U. Guelma Examinateur Dr. A. El Akrmi Prof. U. Annaba Examinateur Dr. H. Belkhir Prof. U. Annaba Examinateur À la mémoire de mon père, À ma mère, qui m’a enseigné le sens de la patience et de l’espoir, À ma femme, À toute ma famille À toute personne qui explore honnêtement les secrets de ce monde vaste, Je dédie ce modeste travail Remerciements REMERCIEMENTS Ce travail a été réalisé au laboratoire d’optoélectronique et des composants à l’université Ferhat Abbes à Sétif. Je tiens à remercier profondément Pr. Kamel Kassali, mon directeur de thèse pour m’avoir proposé ce thème intéressant et pour sa patience durant toutes les années de préparation de la thèse ainsi que ses conseils précieux et ses réponses à toutes mes questions reliées à mon sujet de thèse. J’exprime également toute ma reconnaissance à Mr. Kh. Bouamama, Professeur à l’université Ferhat Abbes de Sétif, qui m’a grandement fait profiter de ses fructueuses discussions en codes de calcul et dans mon sujet de thèse. -
DFT-Absorption Spectra
2054-9 Structure and Dynamics of Hydrogen-Bonded Systems 26 - 27 October 2009 Effect of Proton Disorder on the Excited State Properties of Ice Olivia PULCI Universita' di Roma II "Tor Vergata" Dipt. di Fisica, Via della Ricerca Scientfica 1, 00133 Rome Italy EffectEffect ofof protonproton disorderdisorder onon thethe excitedexcited statestate propertiesproperties ofof iceice V. Garbuio,Garbuio M. Cascella, R. Del Sole, O. Pulci OUTLINE: •Theoretical approaches •Ice Ic(bulk) • Ice Ih surface Theoretical approaches c MBPT c c EXC W hν hν ωcv hν ωcv ωcv v v v DFT GW BSE 1) 2) 3) Ground state properties Electronic band Optical spectra structure, I, A TDDFT (Step 2) Lars Hedin 1965 Σ = iGW G: single particle Green’s function −1 W: screened Coulomb interaction = ε VW Theoretical approaches c MBPT c c EXC W hν hν ωcv hν ωcv ωcv v v v DFT GW BSE 1) 2) 3) Ground state properties Electronic band Optical spectra structure, I, A TDDFT Step 3: calculation of optical spectra within the Bethe Salpeter Equation c Absorption spectra A photon excites an electron from an occupied state to a conduction state hν e 4 4 4 4 4 PPPP=IQP +IQP Ξ v h Bethe Salpeter Equation (BSE) Kernel: Ξ v= − W e-h exchange bound excitons GWBSE ApplicableApplicable to:to: Ab-initio: (NOT “one puts nothing in, one gets nothing out”!!) •Generality, transferability 0D-3D Biological systems •Detailed physical informations •Complex theory+large comp.cost 3-D 0-D 1-D 2-D Nanowires Surfaces Nanoclusters bulks OUTLINE: •Theoretical approaches •Ic Ice (bulk) • Ice Ih surface HH2OO phasephase diagramdiagram CubicCubic iceice ((IcIc)) • It is a metastable form of ice that can be formed, by condensation of water vapor, at ambient pressure but low temperatures Cubic ice (Ic) – diamond lattice 153 K down to 113 K Studied within DFT and Tight-binding G. -
New Frontiers in Quantum Chemistry Using Supercomputers
New frontiers in quantum chemistry using supercomputers Jeff Hammond Leadership Computing Facility Argonne National Laboratory 4 May 2011 Jeff Hammond NREL Atomistic simulation in chemistry 1 classical molecular dynamics (MD) with empirical potentials 2 ab initio molecular dynamics based upon density-function theory (DFT) 3 quantum chemistry with wavefunctions e.g. perturbation theory (PT), Coupled-Cluster (CC) or Quantum Monte Carlo (QMC). Jeff Hammond NREL Classical molecular dynamics Solves Newton's equations of motion with empirical terms and classical electrostatics. Size: 100K-10M atoms Time: 1-10 ns/day Scaling: ∼ Natoms Data from K. Schulten, et al. \Biomolecular modeling in the era of petascale computing." In D. Bader, ed., Petascale Computing: Algorithms and Applications. Image courtesy of Beno^ıtRoux via ALCF. Jeff Hammond NREL Car-Parrinello molecular dynamics Forces obtained from solving an approximate single-particle Schr¨odingerequation; time-propagation via Lagrangian approach. Size: 100-1000 atoms Time: 0.01-1 ps/day x Scaling: ∼ Nel (x=1-3) F. Gygi, IBM J. Res. Dev. 52, 137 (2008); E. J. Bylaska et al. J. Phys.: Conf. Ser. 180, 012028 (2009). Image courtesy of Giulia Galli via ALCF. Jeff Hammond NREL Wavefunction theory MP2 is second-order PT and is accurate via magical cancellation of error. CC is infinite-order solution to many-body Schr¨odingerequation truncated via clusters. QMC is Monte Carlo integration applied to the Schr¨odingerequation. Size: 10-100 atoms, maybe 100-1000 atoms with MP2. Time: N/A x Scaling: ∼ Nbf (x=2-7) Image courtesy of Karol Kowalski and Niri Govind. Jeff Hammond NREL Quantum chemistry | standard model 1 Separate molecule(s) from environment (closed to both matter and energy) 2 Ignore relativity, QED, spin-orbit coupling 3 Separate electronic and nuclear degrees of freedom −! non-relativistic electronic Schr¨odingerequation in a vacuum at zero temperature. -
Package Name Software Description Project
A S T 1 Package Name Software Description Project URL 2 Autoconf An extensible package of M4 macros that produce shell scripts to automatically configure software source code packages https://www.gnu.org/software/autoconf/ 3 Automake www.gnu.org/software/automake 4 Libtool www.gnu.org/software/libtool 5 bamtools BamTools: a C++ API for reading/writing BAM files. https://github.com/pezmaster31/bamtools 6 Biopython (Python module) Biopython is a set of freely available tools for biological computation written in Python by an international team of developers www.biopython.org/ 7 blas The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations. http://www.netlib.org/blas/ 8 boost Boost provides free peer-reviewed portable C++ source libraries. http://www.boost.org 9 CMake Cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software http://www.cmake.org/ 10 Cython (Python module) The Cython compiler for writing C extensions for the Python language https://www.python.org/ 11 Doxygen http://www.doxygen.org/ FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created. It supports the most obscure ancient formats up to the cutting edge. No matter if they were designed by some standards 12 ffmpeg committee, the community or a corporation. https://www.ffmpeg.org FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and 13 fftw complex data (as well as of even/odd data, i.e. -
Virt&L-Comm.3.2012.1
Virt&l-Comm.3.2012.1 A MODERN APPROACH TO AB INITIO COMPUTING IN CHEMISTRY, MOLECULAR AND MATERIALS SCIENCE AND TECHNOLOGIES ANTONIO LAGANA’, DEPARTMENT OF CHEMISTRY, UNIVERSITY OF PERUGIA, PERUGIA (IT)* ABSTRACT In this document we examine the present situation of Ab initio computing in Chemistry and Molecular and Materials Science and Technologies applications. To this end we give a short survey of the most popular quantum chemistry and quantum (as well as classical and semiclassical) molecular dynamics programs and packages. We then examine the need to move to higher complexity multiscale computational applications and the related need to adopt for them on the platform side cloud and grid computing. On this ground we examine also the need for reorganizing. The design of a possible roadmap to establishing a Chemistry Virtual Research Community is then sketched and some examples of Chemistry and Molecular and Materials Science and Technologies prototype applications exploiting the synergy between competences and distributed platforms are illustrated for these applications the middleware and work habits into cooperative schemes and virtual research communities (part of the first draft of this paper has been incorporated in the white paper issued by the Computational Chemistry Division of EUCHEMS in August 2012) INTRODUCTION The computational chemistry (CC) community is made of individuals (academics, affiliated to research institutions and operators of chemistry related companies) carrying out computational research in Chemistry, Molecular and Materials Science and Technology (CMMST). It is to a large extent registered into the CC division (DCC) of the European Chemistry and Molecular Science (EUCHEMS) Society and is connected to other chemistry related organizations operating in Chemical Engineering, Biochemistry, Chemometrics, Omics-sciences, Medicinal chemistry, Forensic chemistry, Food chemistry, etc.