High Performance Computing in Science and Engineering ’21. Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2021

516 Pages·2023·43.161 MB·English

by  Wolfgang E. Nagel, Dietmar H. Kröner, Michael M. Resch

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
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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:[e-mail]