High Performance Computing in Science and Engineering ’21. Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2021 PDF
Preview High Performance Computing in Science and Engineering ’21. Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2021
Wolfgang E. Nagel Dietmar H. Kröner Michael M.Resch Editors High Performance Computing in Science and Engineering ’21 1 23 High Performance Computing in Science and Engineering ’21 Wolfgang E. Nagel • Dietmar H. Kröner Michael M. Resch Editors High Performance Computing in Science and Engineering ’21 Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2021 123 Editors Wolfgang E. Nagel Dietmar H. Kröner Zentrum für Informationsdienste Abteilung für Angewandte und Hochleistungsrechnen (ZIH) Mathematik Technische Universität Dresden Universität Freiburg Dresden, Germany Freiburg, Germany Michael M. Resch Höchstleistungsrechenzentrum Stuttgart (HLRS) Universität Stuttgart Stuttgart, Germany ISBN 978-3-031-17936-5 ISBN 978-3-031-17937-2 (eBook) https://doi.org/10.1007/978-3-031-17937-2 Mathematics Subject Classification (2020): 65Cxx, 65C99, 68U20, 90-08, 97M50 © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 This work is subject to copyright. All rights are solely and exclusively licensed by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Cover illustration: The image shows the resulting polycrystalline microstructure of a martensitic phase transformation predicted by a multiphase-field simulation performed with PACE3D. The regions shown in shades of gray represent retained austenite, while the regions depicted in color are martensitic variants. Details can be found in “High-performance multiphase-field simulations of solid-state phase transformations using PACE3D” by E. Schoof, T. Mittnacht, M. Seiz, P. Hoffrogge, H. Hierl, and B. Nestler, Institute of Applied Materials (IAM), Karlsruhe Institute of Technology (KIT), Straße am Forum 7, 76131 Karlsruhe, Germany, on pages 167ff. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Contents Physics ............................................................ 1 Ligand-inducedproteinstabilizationandenhancedmoleculardynamics samplingtechniques ............................................ 3 TimoSchäfer,AndreasC.Joerger,JohnSpencer,FriederikeSchmid,and GiovanniSettanni Hadroniccontributionstotheanomalousmagneticmomentofthemuon fromLatticeQCD .............................................. 19 M. Cè, E.-H. Chao, A. Gérardin, J.R. Green, G. von Hippel, B. Hörz, R.J.Hudspith,H.B.Meyer,K.Miura,D.Mohler,K.Ottnad,S.Paul,A.Risch, T.SanJosé,andH.Wittig Quantum simulators, phase transitions, resonant tunneling, and variances:Amany-bodyperspective ............................... 36 A.U.J.Lode,O.E.Alon,J.Arnold,A.Bhowmik,M.Büttner,L.S.Cederbaum, B.Chatterjee,R.Chitra,S.Dutta,C.Georges,A.Hemmerich,H.Keßler, J.Klinder,C.Lévêque,R. Lin,P.Molignini,F.Schäfer,J.Schmiedmayer,and M.Žonda Molecules,InterfacesandSolids ..................................... 61 Moleculardynamicssimulationofselectivelasermelting .............. 65 FabioOelschläger,DominicKlein,SarahMüller,andJohannesRoth Moleculardynamicsinvestigationsontheinfluenceofsolutesonthe tensilebehaviorofPolyamide6 .................................... 81 Wolfgang Verestek, Johannes Kaiser, Christian Bonten, and Siegfried Schmauder v vi Contents DynamicalpropertiesoftheSi(553)-Aunanowiresystem .............. 97 MikeN.Pionteck,FelixBernhardt,JohannesBilk,ChristofDues,Kevin Eberheim,ChristaFink,KrisHoltgrewe,NiklasJöckel,BrendanMuscutt, FlorianA.Pfeiffer,FerdinandZiese,andSimoneSanna Reactivityoforganicmoleculesonsemiconductorsurfacesrevealedby densityfunctionaltheory ........................................ 113 Fabian Pieck, Jan-Niclas Luy, Florian Kreuter, Badal Mondal, and Ralf Tonner-Zech Electro-catalysisforH2Ooxidation ................................ 133 TravisJones MaterialsScience...................................................149 Productionofdefectsintwo-dimensionalmaterialsunderionandelectron irradiation:insightsfromadvancedfirst-principlescalculations ........ 151 S.Kretschmer,T.Joseph,S.Ghaderzadeh,Y.Wei,M.Ghorbani-Asl,and A.V.Krasheninnikov High-performancemultiphase-fieldsimulationsofsolid-statephase transformationsusingPace3D.................................... 167 E.Schoof,T.Mittnacht,M.Seiz,P.Hoffrogge,H.Hierl,andB.Nestler Bridgingscaleswithvolumecoupling—Scalablesimulationsofmuscle contractionandelectromyography................................. 185 BenjaminMaier,DavidSchneider,MiriamSchulte,andBenjaminUekermann ComputationalFluidDynamics ...................................... 201 Analysisofthehotgasingressintothewheelspaceofanaxialturbinestage207 JannikBorgelt,ThomasHösgen,MatthiasMeinke,andWolfgangSchröder Directnumericalsimulationofbypasstransitionunderfree-stream turbulenceforcompressibleflows ................................. 223 DuncanOhno,BjörnSelent,MarkusJ.Kloker,andUlrichRist Directnumericalsimulationofadisintegratingliquidrivuletatatrailing edge.......................................................... 239 AdrianSchlottke,MatthiasIbach,JonasSteigerwald,andBernhardWeigand NumericalInvestigationoftheFlowandHeatTransferinConvergent SwirlChambers................................................ 259 FlorianSeiboldandBernhardWeigand Contents vii OnthevalidityofthelinearBoussinesqhypothesisforselectedinternal coolingfeaturesofgasturbineblades .............................. 275 PhilippWellingerandBernhardWeigand Development of turbulent inflow methods for the high order HPC frameworkFLEXI.............................................. 289 DanielKempf,MinGao,AndreaBeck,MarcelBlind,PatrickKopper,Thomas Kuhn,MariusKurz,AnnaSchwarz,andClaus-DieterMunz Anarrowband-baseddynamicloadbalancingschemeforthelevel-set ghost-fluidmethod.............................................. 305 DanielAppel,StevenJöns,JensKeim,ChristophMüller,JonasZeifang,and Claus-DieterMunz Numericalsimulationofflakeorientationduringdropletimpacton substratesinspraypaintingprocesses.............................. 321 QiaoyanYeandMartinDreher,andBoShen Alow-passfilterforlinearforcingintheopen-sourcecodeOpenFOAM– Implementationandnumericalperformance ........................ 339 JordanA.Denev,ThorstenZirwes,FeichiZhang,andHenningBockhorn Numericalsimulationofvortexinducedpressurefluctuationsinthe runnerofaFrancisturbineatdeeppartloadconditions .............. 353 JonasWack,MarcoZorn,andStefanRiedelbauch ValidationofACDandACLpropellersimulationusingbladeelement methodbasedonairfoilcharacteristics............................. 367 MichaelSchollenberger,MárioFirnhaberBeckers,andThorstenLutz TransportandClimate.............................................. 381 TheHPCprojectGLOMIR+(GLObalMUSICAIASIRetrievals-plus) . 383 MatthiasSchneider,BenjaminErtl,ChristopherDiekmann,andFarahnaz Khosrawi Globallong-termMIPASdataprocessing........................... 397 MichaelKiefer,BerndFunke,MayaGarcía-Comas,UdoGrabowski,Andrea Linden,AxelMurk,andGeraldE.Nedoluha WRFsimulationstoinvestigateprocessesacrossscales(WRFSCALE)... 411 Hans-StefanBauer,ThomasSchwitalla,OliverBranch,andRohithThundathil viii Contents ComputerScience ..................................................423 Dynamicmoleculardynamicsensemblesformultiscalesimulationcoupling425 PhilippNeumann,NiklasWittmer,VahidJafari,SteffenSeckler,andMatthias Heinen Scalablediscretealgorithmsforbigdataapplications................. 439 DemianHespe,LukasHübner,LorenzHübschle-Schneider,PeterSanders,and DominikSchreiber MiscellaneousTopics ............................................... 451 Largescalesimulationsofpartialdifferentialequationmodelsonthe Hawksupercomputer ........................................... 453 RubenBuijse,MartinParnet,andArneNägel Scalinginthecontextofmoleculardynamicssimulationswithms2andls1 mardyn ....................................................... 467 SimonHomes,RobinFingerhut,GabrielaGuevara-Carrion,MatthiasHeinen, andJadranVrabec Scalablemultigridalgorithmforfluiddynamicshapeoptimization...... 481 JosePinzon,MartinSiebenborn,andAndreasVogel Numericalcalculationofthelean-blow-outinamulti-jetburner........ 497 AlexanderSchwagerus,PeterHabisreuther,andNikolaosZarzalis Data-driven multiscale modeling of self-assembly and hierarchical structuralformationinbiologicalmacro-molecularsystems ........... 513 PhilippNicolasDepta,MaksymDosta,andStefanHeinrich Physics Inthispart,threephysicsprojectsarepresented,whichachievedimportantscientific results in 2020/21 by using Hawk/Hazel Hen at the HLRS and ForHLR II of the SteinbuchCenter. Fascinatingnewresultsarebeingpresentedinthefollowingpagesonsoftmat- ter/biochemicalsystems(ligand-inducedproteinstabilization)andonquantumsys- tems(anomalousmagneticmomentofthemuon,ultracold-bosonquantumsimulators, phasetransitions,resonanttunneling,andvariances). Studiesofthesoftmatter/biochemicalsystemshavefocusedonligand-induced proteinstabilization. T.Schäfer,A.C.Joerger,J.Spencer,F.Schmid,andG.SettannifromMainz(T.S., F.S.,G.S.),Frankfurt(A.C.J.),andSussex(J.S.)presentinterestingnewresultson ligand-inducedproteinstabilizationintheirprojectFlexadfg.Theauthorsshowhow Molecular Dynamics simulations of several cancer mutants of the DNA-binding domainofthetumorsuppressorproteinp53allowedtoestablishthedestabilizingeffect ofthemutationsaswellasthestabilizingeffectsofboundligands.Inaddition,the authorsreportonthedevelopmentofanewreweightingtechniqueformetadynamics simulationsthatspeedsupconvergenceandmayprovideanadvantageinthecaseof simulationsoflargesystems. Studiesofthequantumsystemshavefocusedontheanomalousmagneticmoment ofthemuon,andonultracold-bosonquantumsimulators,phasetransitions,resonant tunneling,andvariances. M.Cè,E.Chao,A.Gérardin,J.R.Green,G.vonHippel,B.Hörz,R.J.Hudspith, H.B.Meyer,K.Miura,D.Mohler,K.Ottnad,S.Paul,A.Risch,T.SanJosé,and H.WittigfromMainz(E.C.,G.v.H.,R.J.H.,H.B.M.,K.M.,K.O.,S.P.,T.S.J.,H.W.), Darmstadt(K.M.,D.M.,T.S.J.),Zeuthen(A.R.),Geneva(M.C.,J.R.G.),Marseille (A.G.),andBerkeley(B.H.)presentinterestingresultsobtainedbytheirlatticeQCD MonteCarlosimulationsonHawk/HazelHenintheirprojectGCS-HQCDonleading hadronic contributions to the anomalous magnetic moment of the muon, on the energydependenceoftheelectromagneticcoupling,ontheelectroweakmixingangle, andonthehadronicvacuumpolarisationandlight-by-lightscatteringcontributions. 1 2 Physics Theauthorsfocuswillturntoincreasingtheoverallprecisionoftheirdetermination ofthehadronicvacuumpolarizationcontributiontothemuonanomalousmagnetic momenttothesub-percentlevel. A.U.J.Lode,O.E.Alon,J.Arnold,A.Bhowmik,M.Büttner,L.S.Cederbaum, B.Chatterjee,R.Chitra,S.Dutta,C.Georges,A.Hemmerich,H.Keßler,J.Klinder, C.Lévêque,R.Lin,P.Molignini,F.Schäfer,J.Schmiedmayer,andM.Žondafrom Freiburg(A.U.J.L.,M.B.),Haifa(O.E.A.,A.B.,S.D.),Basel(J.A.,F.S.),Heidelberg (L.S.C.),Kanpur(B.C.),Zürich(R.C.,R.L.),Hamburg(C.G.,A.H.,H.K.,J.K.),Wien (C.L.,J.S.),Oxford(P.M.),andPrague(M.Z.)presentinterestingresultsobtained intheirprojectMCTDHBwiththeirmulticonfigurationaltime-dependentHartree method for indistinguishable particles (MCTDH-X) on Hazel Hen and Hawk. In the past the authors have implemented their method to solve the many-particle Schrödingerequationfortime-dependentandtime-independentsystemsinvarious softwarepackages.Theauthorspresentinterestingnewresultsoftheirinvestigations onultracoldbosonquantumsimulatorsforcrystallizationandsuperconductorsin amagneticfield,onphasetransitionsofultracoldbosonsinteractingwithacavity, and of charged fermions in lattices described by the Falicov–Kimball model. In addition,theauthorsreportonnewresultsonthemany-bodydynamicsoftunneling andvariances,intwo-andthree-dimensionalultracold-bosonsystems. FachbereichPhysik, PeterNielaba UniversitätKonstanz, 78457Konstanz, Germany, e-mail:[email protected]
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