High Performance Computing in Science and Engineering '21: Transactions of the High Performance Computing Center, Stuttgart

Contents
Physics
Ligand-induced protein stabilization and enhanced molecular dynamics sampling techniques
1 Introduction
2 Methods
3 Simulations of p53 cancer mutants and stabilization by ligand binding
3.1 Data reweighting in metadynamics simulations
4 Conclusions
References
Hadronic contributions to the anomalous magnetic moment of the muon from Lattice QCD
1 Introduction
2 Computational setup
3 The hadronic running of the electroweak couplings
4 Hadronic vacuum polarization contribution to αμ
4.1 The intermediate-distance window contribution
4.2 Scattering phase shift and the timelike pion form factor
5 Hadronic light-by-light scattering contribution to
6 Summary and outlook
References
Quantum simulators, phase transitions, resonant tunneling, and variances: A many-body perspective
1 Introduction
2 Theory
3 Quantities of interest
3.1 Oneand two-body densities
3.2 Fragmentation and condensation
3.3 Single-shot measurements
3.3.1 Full distribution functions
4 Quantum simulation of crystallization
5 Dynamics of ultracold bosons in artificial gauge fields: Angular momentum, fragmentation, and the variance of entropy
6 Cavity-induced Mott transition in a Bose–Einstein condensate
7 Interpretable and unsupervised phase classification
8 Longitudinal and transversal many-boson resonant tunneling in two-dimensional Josephson junctions
9 Morphology of a three-dimensional trapped Bose–Einstein condensate from position, momentum, and angular-momentum many-particle
10 Conclusions and outlook
References
Molecules, Interfaces and Solids
Molecular dynamics simulation of selective laser melting
1 Introduction
2 Additive manufacturing by selective laser melting (SLM)
2.1 Description of the method
2.1.1 Defects in manufactured objects
2.1.2 Important parameters and influence of the laser velocity
2.2 Modeling of SLM by molecular dynamics Simulations
2.2.1 Laser absorption
2.2.2 Sample sizes
3 Simulation of SLM
3.1 Preparation of the sample
3.2 Variation of the laser power at fixed laser velocity
3.3 Behavior at reduced laser velocity
4 Summary and outlook
5 Performance of simulation code
5.1 Typical number of applied processors
5.2 Parallelization degree
5.3 Scaling
5.4 Consumed computing resources
References
Molecular dynamics investigations on the influence of solutes on the tensile behavior of Polyamide6
1 Introduction
2 Model
2.1 Model creation
2.2 Equilibration
2.3 Tensile test simulation
3 Results
4 Summary
References
Dynamical properties of the Si(553)-Au nanowire system
1 Introduction
2 Methodology
2.1 Computational details
2.2 Computational performance
3 Results
3.1 Phonon modes at room temperature
3.2 Phonon modes below and above the phase transition
4 Conclusions
References
Reactivity of organic molecules on semiconductor surfaces revealed by density functional theory
1 Introduction
2 Reactivity and selectivity of organic molecules on Si(001) and Ge(001)
2.1 Pyrazine on Ge(001)
2.2 Methyl-substituted benzylazide on Si(001)
2.3 Methyl enol ether functionalized cyclooctyne on Si(001)
3 Interface formation of corroles on Ag(111)
4 Developing accurate and efficient computational models
4.1 The introduction of a hierarchical model system
4.2 Reactivity of a Si(001) dimer vacancy
5 Scaling of computational methods
References
Electro-catalysis for H2O oxidation
1 Introduction
2 Methods
3 Results and discussion
4 Summary
References
Materials Science
Production of defects in two-dimensional materials under ion and electron irradiation: insights from advanced first-principles calculations
1 Introduction
2 Results
2.1 Production of defects in two-dimensional materials under electron irradiation
2.2 Response of supported two-dimensional materials to ion and cluster irradiation
2.3 Influence of defects and impurities on the electronic and chemical properties of two-dimensional materials: insights from density-functional-theory calculations
3 Implementation of the project and technical data
3.1 Codes employed and their scaling
3.1.1 GPAW code
3.1.2 VASP code
3.1.3 LAMMPS code
3.2 CPU time used
3.3 Popular internet articles about our computational research
Conflict of interest
References
High-performance multiphase-field simulations of solid-state phase transformations using Pace3D
1 Introduction
2 Core phase-field model
3 The Pace3D framework: Performance and scaling
4 Modeling and simulating solid-state phase transformations using Pace3D
4.1 Martensitic transformation
4.2 Shape-instabilities of finite three-dimensional rods
4.3 Coarsening and grain growth in SOFC anodes
5 Conclusion
References
Bridging scales with volume coupling— Scalable simulations of muscle contraction and electromyography
1 Introduction
1.1 Related work
1.2 Research targets
1.3 Main contributions of this work
2 Models and solvers
2.1 Continuum mechanics model (3D)
2.2 Model of the electric potential (3D)
2.3 Model of muscle fiber activation (1D)
2.4 Subcellular force generation model (0D)
2.5 Discretization and solution
3 Partitioning methods
4 Performance results
4.1 Weak scaling of the electrophysiology solver
4.2 Performance evaluation of the full multi-scale solver
4.3 Simulation results of the full multi-scale model
5 Conclusion and outlook
References
Computational Fluid Dynamics
Analysis of the hot gas ingress into the wheel space of an axial turbine stage
1 Introduction
2 Numerical method
2.1 Governing equations
2.2 Numerical method
2.3 Zonal RANS/LES method
2.3.1 Synthetic turbulence generation (STG)
2.3.2 Reconstruction of the eddy viscosity (RTV)
3 Computing resources
4 One-stage axial turbine
4.1 Computational setup
4.1.1 Reduced computational setup for zonal RANS/LES method
4.2 Results
4.3 Reduced setup
5 Conclusion
References
Direct numerical simulation of bypass transition under free-stream turbulence for compressible flows
1 Introduction
2 Numerical methods
Direct numerical simulation
Generation of free-stream turbulence
Modified boundary conditions
3 Numerical simulations
Setup
Single free-stream disturbances
Bypass transition
4 Performance analysis
Single node performance
Multi node performance
5 Conclusions
References
Direct numerical simulation of a disintegrating liquid rivulet at a trailing edge
1 Introduction
2 Mathematical description and numerical approach
3 Computational setup
4 Results and discussion
5 Computational performance
5.1 Benchmark case and performance analysis
5.1.1 Strong scaling
5.1.2 Weak scaling
6 Conclusions
References
Numerical Investigation of the Flow and Heat Transfer in Convergent Swirl Chambers
1 Introduction
2 Geometry
3 Numerical setup
4 Results
4.1 Flow field
4.2 Heat transfer
5 Usage of computational resources
6 Summary and conclusion
Conflict of interest
References
On the validity of the linear Boussinesq hypothesis for selected internal cooling features of gas turbine blades
1 Introduction
2 Numerical setup
3 Results
3.1 Reference case: planar channel
3.2 Validation of the flow field prediction
3.3 Validity of the linear Boussinesq hypothesis for the selected test cases
4 Computational performance
5 Conclusion
References
Development of turbulent inflow methods for the high order HPC framework FLEXI
1 Introduction
2 Methods
2.1 Recycling-rescaling anisotropic linear forcing
2.2 Synthetic eddy method
3 Performance
3.1 FLEXI on HAWK
3.2 Parallel implementation of SEM
4 Results
4.1 Subsonic turbulent flat plate
4.2 Supersonic turbulent flat plate
5 Summary and outlook
References
A narrow band-based dynamic load balancing scheme for the level-set ghost-fluid method
1 Introduction
2 Governing equations
3 Numerical method
3.1 Fluid solver
3.2 Interface capturing
3.3 The level-set ghost-fluid method
4 Load balancing
4.1 Characterization of load imbalance
4.2 Domain decomposition and repartitioning
4.3 Code instrumentation and algorithmic details
5 Numerical results
5.1 Strong scaling behavior
5.2 Shock-droplet interaction
6 Conclusion
References
Numerical simulation of flake orientation during droplet impact on substrates in spray painting processes
1 Introduction
2 Basic numerical methods
2.1 Simulation of viscous droplet impact on dry solid surfaces
2.2 Simulation of viscous droplet impact on wet solid surfaces
2.3 Simulation of flake orientation
3 Results and discussion
3.1 Evolution of interface of gas-liquid by droplet impact on wet solid surface without flake
3.2 Validation of simulation of droplet impact on dry solid surface without flake
3.3 Flake orientation by droplet impact on dry solid surfaces
3.4 Flake orientation by droplet impact on wet solid surfaces
4 Computational performance
5 Conclusions
References
A low-pass filter for linear forcing in the open-source code OpenFOAM – Implementation and numerical performance
1 Introduction
2 Mathematical description
3 DNS results with the proposed filter for linear forcing
4 Parallel performance
5 Conclusions
References
Numerical simulation of vortex induced pressure fluctuations in the runner of a Francis turbine at deep part load conditions
1 Introduction
2 Numerical setup
3 Experimental setup
4 Results
4.1 Vortex movement
4.2 Pressure fluctuations on the runner blade
5 Computational resources
6 Conclusion and outlook
References
Validation of ACD and ACL propeller simulation using blade element method based on airfoil characteristics
1 Introduction
2 Simulation methods and numerical setup
2.1 Propeller Simulation
2.1.1 Fully resolved propeller (full)
2.1.2 Actuator Disk (ACD)
2.1.3 Actuator Line (ACL)
2.2 Single blade simulation
2.3 Grids and numerical setup
3 Results
3.1 Airfoil characteristics
3.2 Isolated propeller
3.2.1 Propeller slipstream
3.2.2 Propeller blade flow
3.3 Installed propeller
3.3.1 Propeller wing interaction
3.3.2 Wing propeller interaction
4 Scaling test
5 Conclusion
References
Transport and Climate
The HPC project GLOMIR+ (GLObal MUSICA IASI Retrievals - plus)
1 Introduction
2 Data processing
2.1 Computations, parallelism, and scaling
2.2 Summary of used computation resources
3 Scientific results
3.1 Data set dissemination and presentation
3.2 Research of the atmospheric water cycle
3.3 Research on atmospheric methane emissions
3.4 Validation of satellite data
References
Global long-term MIPAS data processing
1 The MIPAS/Envisat mission
2 L1b data delivery and L2 data generation
2.1 L1b data processing and delivery by ESA
2.2 L2 Data generation
3 Computational considerations
4 First results
4.1 Water vapour
4.2 Nitrogen oxide and nitrogen dioxide
4.3 Carbon monoxide
5 Summary and conclusions
References
WRF simulations to investigate processes across scales (WRFSCALE)
1 Introduction and motivation
2 Work done since March 2020
2.1 Cases and model setup
2.2 Optimization of the model setup on Hawk
2.3 Results of the simulations
3 Used resources
References
Computer Science
Dynamic molecular dynamics ensembles for multiscale simulation coupling
1 Introduction
2 Molecular-continuum coupling
2.1 Short-range Molecular Dynamics
2.2 Computational fluid dynamics
2.3 Molecular-continuum algorithm in a nutshell
2.4 MaMiCo
2.5 Related work
3 Implementation of dynamic MD ensemble handling
4 Results
4.1 Validation
4.2 Scalability
5 Summary and outlook
References
Scalable discrete algorithms for big data applications
1 Introduction
2 Scientific work accomplished and results obtained
2.1 High-Performance SAT Solving
2.1.1 Usage statistics
2.2 Malleable job scheduling and load balancing
2.3 Fault-tolerance for massively parallel phylogenetic inference
2.3.1 Usage statistics
3 Publications with project results
4 Ongoing theses within the project
4.1 Low overhead fault-tolerant MapReduce for HPC clusters
5 Theses completed within the project
6 Project retrospective
References
Miscellaneous Topics
Large scale simulations of partial differential equation models on the Hawk supercomputer
1 Introduction
2 Methods
2.1 Multilevel solvers
2.2 Time integration
2.3 Hawk Apollo supercomputer
3 Results
3.1 Weak scaling for Poisson’s equation
3.1.1 Standard process assignment
3.1.2 Topology aware process assignment
3.1.3 Summary
3.2 Strong scaling for the heat equation
3.3 Thermohaline transport
Conclusion
References
Scaling in the context of molecular dynamics simulations with ms2 and ls1 mardyn
1 Finite size effects of multicomponent diffusion coefficients
2 Strong scaling of ms2 when sampling the structure
3 Droplet coalescence on Hawk and Hazel Hen
4 Scaling of energy flux implementation in ls1 mardyn
References
Scalable multigrid algorithm for fluid dynamic shape optimization
1 Introduction
2 Mathematical background
3 Numerical results
3.1 2d results
3.2 2d grid study
3.3 3d results
4 Scalability results
5 Conclusion and outlook
References
Numerical calculation of the lean-blow-out in a multi-jet burner
1 Introduction
2 Numerical setup
3 General description of the flame
4 LBO results
5 Calculation of an industrial burner
6 Performance and required resources
7 Conclusion
References
Data-driven multiscale modeling of self-assembly and hierarchical structural formation in biological macro-molecular systems
1 Introduction
2 Methods
2.1 Modeling framework
2.2 Molecular dynamics setup
2.3 Iterative multivariant interpolation using Universal Kriging
2.4 MDEM: Molecular Discrete Element Method
2.5 Parallelism and scaling
3 Results
3.1 HBcAg interaction potential
3.2 VLP assembly
3.3 Computational resources
4 Conclusion
Appendix
References