High Performance Computing in Science and Engineering '09 (eBook)

Preface 5
Contents 8
Physics 12
Numerical Models for Emission Line Nebulae in High Redshift Radio Galaxies 13
Introduction 13
Numerical Method 15
Computational and Scientific Results 15
Performance 15
High Redshift Radio Galaxies 15
Summary 24
References 25
The SuperN-Project: Current Advances in Understanding Core Collapse Supernovae 26
Introduction 26
Numerical Models 27
History and Constraints 27
Recent Calculations and the Need for TFlop Simulations 29
The Mathematical Model 30
``Ray-by-Ray Plus'' Variable Eddington Factor Solution of the Neutrino Transport Problem 30
Parallelization 34
Recent Results and Ongoing Work 35
Long-time Simulations of Massive Progenitor Models 35
Explosion Models of Oxygen-neon-magnesium Cores 36
Conclusions and Outlook 38
References 39
Using Computational Steering to Explore the Parameter Space of Stability in a Suspension 42
Introduction 42
Simulation Method 43
Simulation Steering 47
Results 48
Pressure Filtration 48
Observation of Cluster Formation 49
Sedimentation: Hydrodynamic Interaction 52
Summary 53
References 53
Solid State Physics 58
Adsorption of Cysteine on the Au(110)-surface: A Density Functional Theory Study 61
Introduction 61
Computational Methods 62
Results and Discussion 63
Au(110) Surface Energy 63
Au (110)-(1 x 2) Vacancy Formation Energy 64
Cysteine Dimers: The Carboxyl-Carboxyl Hydrogen Bond 66
Outlook 67
References 67
Ab-initio Characterization of Colloidal IV-VI Semiconductor Quantum Dots 69
Introduction 69
Computational Method 70
Theoretical Background 70
Computational Cost 71
Nanocrystal Construction Using Supercells 72
Results and Discussion 73
Structural Properties 73
Electronic Properties 75
Optical Properties 78
Summary and Outlook 79
References 80
Understanding Long-range Indirect Interactions Between Surface Adsorbed Molecules 82
Introduction 82
Computational Method 84
Results 85
Summary 90
References 90
H2 Carrying Capacity by Considering Charging and Discharging Processes -- Case Studies on Small Carbon- and Boron Nitride Nanotubes 92
Introduction 92
Computational Details 94
Results and Discussions 96
Conclusion 109
Publications Associated with the NEC SX-8 Account Under Grant Number WLYIM 114
Performance of VASP on Different Platforms 115
References 115
Molecular Dynamics Study of Plastic Deformation of Nanocrystalline Palladium 117
Introduction 117
Molecular Dynamics Method and Simulation Setup 118
Tensile Straining 120
Compressive Straining 124
Conclusion 126
References 126
Conductance of Correlated Nanostructures 129
Implementation Details 130
Top Level Code 130
Library Code 130
Benchmark of Different Platforms 131
Towards Worker Threads on Graphics Cards 132
Differential Conductance in the Interacting Resonant Level Model 133
Correlations Within the Steady State 137
The Anderson Model with Ferromagnetic Leads 140
Further Projects 140
References 141
Chemistry 142
How do Eigenfunctions of Douglas-Kroll Operators Behave in the Vicinity of Point-like Nuclei? 144
Introduction 144
A Spherical Wave Basis Set 146
Results 148
Hardware and Performance 149
References 150
Distributed Memory Parallelization of the Multi-Configuration Time-Dependent Hartree Method 152
Introduction 152
Equations of Motion and Shared Memory Parallelization of MCTDH 152
Distributed Memory Parallelization of MCTDH 153
Parallelization Scheme 154
Combination of the Shared and Distributed Memory Approach 154
Distributed Memory Parallelization of the Improved Relaxation 155
Efficiency of the Parallel MCTDH Code 156
Benchmark Systems 156
Propagation Runs 156
Improved Relaxation Runs 158
Isotopic Effects in the Infrared Spectrum of the Zundel cation 159
Coordinates and Hamiltonian Operator Setup 160
IR Spectrum of D(D2O)2+, H(D2O)2+ and D(H2O)2+ Isotopologues 163
Conclusions 166
References 167
Development of Models for Large Molecules and Electrolytes in Solution for Process Engineering 169
Introduction 169
Simulation of Electrolyte Solutions 169
Methods 170
Results 170
Conclusions 172
Computational Demands 172
Simulation of Hydrogels 173
Methods and Molecular Models 173
Results 175
Conclusion 176
Computational Demands 177
References 178
Reacting Flows 181
Numerical Characterization of a Gas Turbine Model Combustor 183
Introduction 183
Physical Model 185
Conservation Equations 185
Turbulence Modelling 185
Combustion Modelling 186
Numerical Method 187
Results and Discussion 188
Test Case 188
Numerical Setup 189
Time-Averaged Results 190
Computational Resources 196
Conclusions 196
References 197
Numerical Investigations of NOX-Formation in Scramjet Combustors 200
Introduction 200
NOX-Formation in Scramjet Combustors 201
Governing Equations and Numerical Scheme 202
Geometry and Boundary Conditions 203
Results and Discussion 204
Performance 208
Conclusion 208
References 209
Large-Eddy Simulation of Lean Premixed Flames in a Model Swirl Burner 211
Introduction 211
Numerical Method 212
Computation Set up and Computational Effort 214
Results and Discussion 215
Effect of Thickening-Factor 215
Behaviour of Recirculation Zone 216
Statistics of Velocity 217
Coherent Structures 218
Power Spectrum Analysis 221
Flame Response to Pulsating Flow Rate of Pilot Jet 222
Conclusions and Outlook 223
References 224
Computational Fluid Dynamics 226
Higher Order Adaptive and Parallel Simulations Including Dynamic Load Balancing with the Software Package DUNE 230
Introduction 230
The Dune Interface Library -- Recent Development 231
Applications 232
Poisson's Equation 232
The Euler Equations 235
Free Surface Shallow Water Flow 236
Conclusion 239
References 239
Direct Numerical Simulation of Jet in Crossflow Actuators 241
Introduction 241
Numerical Method 242
General Setup 242
Problem-Specific Extensions 244
Results 246
Vertical Jet 246
Inclined Jet 247
Boundary Layer Control 248
Computational Aspects 251
Conclusions 252
References 252
Laminar Heat Transfer From the Stagnation Region of a Circular Cylinder at Re=140000 254
Introduction 254
Computational Details 256
Numerical Aspects 256
Setup of the Computations 256
Results 258
Study of the Instantaneous Flow 258
Conclusions 261
References 262
Conditional Statistics Along Gradient Trajectories in Fluid Turbulence 264
Introduction and Previous Achievements 264
Dissipation Elements and Gradient Trajectories 265
DNS for Homogeneous Shear Turbulence 265
MPI Parallelization 267
Conditional Statistics Along Gradient Trajectories 268
Theoretical Results and Numerical Verification 269
Computational Performance 271
References 271
Direct Numerical Simulation of Single Gaseous Bubbles in Viscous Liquids 272
Introduction 272
Numerical Method 273
Numerical Setup 274
Discretization 274
Moving Frame of Reference 275
Investigated Cases 276
Results 276
Terminal Rise Velocity 276
Bubble Shape 277
Drag Coefficient 278
Performance 278
Conclusion 283
References 283
Wall Heat Load in Unsteady and Pulsating Combustor Flow 285
Introduction 285
Test Cases and System of Equations 286
Steady Channel Flow with Heat Transfer 287
Results 288
Unsteady Channel Flow with Heat Transfer 291
Low-Reverse Flow Results 292
Wave Dominated Flow 294
Computational Resources 294
Conclusions 295
References 296
Implicit LES of Passive-Scalar Mixing in a Confined Rectangular-Jet Reactor 297
Introduction: Experimental Configuration 297
Implicit LES 298
The ALDM Approach 299
Implicit Subgrid-Scale Modeling for Passive-Scalar Transport 300
Numerical Method and Computational Domain 301
Performance 302
Numerical Results 302
Conclusions 307
References 308
Numerical Simulation of Riblet Controlled Spatial Transition 309
Introduction 309
Governing Equations 311
Boundary Conditions 312
Flow Configuration and Computational Mesh 312
Results and Discussion 313
K-type Transition 314
Oblique Transition 318
Computational Resources 320
Conclusions 321
References 322
Understanding the Dynamics and Control of a Turbulent Impinging Jet via Pulsation and Swirl Using Large Eddy Simulation 323
Introduction 323
Computational Details 326
Numerical Grid 326
Inflow Conditions 326
Outflow Conditions 328
Numerical Code & its Performance
FASTEST 328
Code Performance & Solution Control
Results 330
Conclusions 337
References 337
Stability Analysis of a Coupled Helmholtz Resonator with Large Eddy Simulation 340
Introduction 340
Simulated Configuration 342
Numerical Method 343
Boundary Conditions 344
Results and Discussion 346
Flow Features 346
Comparison of the Calculations with Experiment 346
Computational Efficiency 348
Summary 349
References 350
Diffusers with Three-Dimensional Separation as Test Bed for Hybrid LES/RANS Methods 352
Introduction 352
Test Case Selected and Setup 354
Experiments Simulated 354
Computational Setup 355
Flow Solver Employed 357
Selected Results 358
Simulating Diffuser D1 358
Simulating Diffuser D2 361
Capturing the Geometric Sensitivity 362
Conclusions 364
References 364
Final Report on Project GGT0607: Lattice Boltzmann Direct Numerical Simulations of Grid-Generated Turbulence 366
Problem Formulation 366
Numerical Method 368
Flow Solver 368
Boundary Conditions 370
Physical Results 371
Is Turbulence Self-Similar? 373
Decay Rates 374
Spatial Inhomogeneity 375
Porosity 376
Asymmetry 377
Conclusion and Outlook 378
References 379
Application of FDEM on the Numerical Simulation of Journal Bearings with Turbulence and Inertia Effects 380
Introduction 380
Topic 381
Finite Difference Element Method FDEM 383
Implementation of the Reynolds Equation 384
Numerical Results 387
Concluding Remarks 389
References 391
Numerical Analysis of Transition Effects in 3D Hypersonic Intake Flows 392
Introduction 392
Physical Model 393
Conservation Equations 393
Turbulence Closure 394
Numerical Methods 395
Spatial Discretization and Time Integration 395
Boundary Conditions 396
Results 397
Flow Conditions, Geometrical Description and Numerical Grids 398
Numerical Results 399
Comparison of the Different Intake Configurations 404
Computational Considerations 405
Conclusions 406
References 406
Preinvestigations of a Redesigned HIRENASD Wing Model in Preparation for New Aero-Structural Dynamic Experiments in ETW 407
Introduction 407
Numerical Method and Model Representation 409
CAE Package SOFIA 409
Wind Tunnel Model Specifiactions 411
Structural Model 411
CFD Grid for Flow Simulation 413
Prediction of Aeroelastic Model Behaviour 413
Dynamic Aeroelastic Response Behaviour 414
Conclusions 420
Code Performance 420
References 421
Transport and Climate 422
Modelling Regional Climate Change in Southwest Germany 424
Introduction 424
The CCLM Model 426
Regional Climate Simulations Using the HLRS Facilities 427
Simulation Setup and Downscaling Chain 427
HPC Aspects 427
Results 430
Temperature at 2 m Height 430
Precipitation 431
Added Value of High Resolution and Ensemble Modelling 432
Further Sensitivity Studies 433
Future Work 435
References 435
Modelling Convection over West Africa 437
Introduction 437
Numerical Model 439
Modelled Life Cycle of an MCS over West Africa and Its Sensitivity to Soil Conditions 440
COSMO Model Initialisation and Observed and Simulated Convective Systems on 11 June 2006 441
Investigation of the Different Phases of Convection 444
Summary and Conclusions 448
Comparison of Convection over Land and Ocean 450
COSMO Simulations 451
Structure of the Convective Systems 455
Potential Temperature Budget 457
Outlook 457
References 458
Miscellaneous Topics 461
Molecular Modeling of Hydrogen Bonding Fluids: Vapor-Liquid Coexistence and Interfacial Properties 464
Introduction 464
Fluid Mixtures with Hydrogen Bonding Components 465
Vapor-Liquid Interface Cluster Criteria 467
Contact Angle Dependence on the Fluid-Wall Interaction 469
A Sterically Accurate Generic Benzyl Alcohol Model 471
Computing Performance 471
Conclusion 474
References 475
Towards a Dynamical Model of Mars' Evolution 477
Introduction 477
Chronology of the Early Evolution of Mars 478
General Remarks 478
Accretion and Core Formation 479
The Magma Ocean Solidification of Mars 479
The Generation of the Dichotomy of Mars 480
Observational Constraints 480
Is the Martian Dichotomy Induced by Endogenic Mechanisms? 482
Is the Martian Dichotomy Caused by Impact(s)? 483
Interior Structure Models 483
Tectonic Episodicity 484
Our New Model of Martian Evolution 485
Explaining Introduction 485
Towards a New Structural Model of the Early Mars 486
Numerical Improvements of Terra 491
The Numerical Performance Hitherto Achieved 493
References 494
Computational Considerations for Satellite-Based Geopotential Recovery 503
Introduction 503
Generalized Methodology 505
Problem Dimension 506
Strategies for Solving the Target Function 506
Strategies for Variance-Covariance Estimation 507
Numerical Results 508
``Brute-Force'' Solver 509
LSQR Solver 509
Conclusions 512
References 513
Simulative Analysis of Vehicle-to-X Communication considering Traffic Safety and Efficiency 514
Introduction 514
V2X Simulations 516
Traffic Safety 517
D-FPAV and EMDV 518
Simulation Results 518
Traffic Efficiency 522
Empirical Model 523
Results 525
Conclusion and Outlook 526
References 528
Modelling Structural Failure with Finite Element Analysis of Controlled Demolition of Buildings by Explosives Using LS-DYNA 529
Introduction 529
Aspects of Numerical Simulation 530
General Scope 530
Numerical Algorithms 530
Numerical Examples 535
Academic Example 536
Nine Storey Building 537
Conclusions and Acknowledgments 540
References 540

"Numerical Models for Emission Line Nebulae in High Redshift Radio Galaxies (S. 3-4)

Summary. We examine models for line-emitting gas nebulae around powerful radio galaxies in the early universe. The models assume that either the emitting gas clouds are embedded in the shocked ambient gas and driven outwards with it or that they are created and sustained by multi-phase turbulence in the jet cocoon. For this, we perform jet simulations with realistic density contrasts on large scales and on typical activity time scales of several ten million years. The employed magnetohydrodynamics code NIRVANA has been optimized for the NEC SX machines in the previous years and now runs very e?ciently on the SX-6 and SX-8, allowing us simulations both in axisymmetry and full three dimensions. Future simulations on the SX-9 will bene?t signi?cantly from the increased number of shared memory processors per node for the axisymmetric runs, where an MPI-parallelization is generally ine?cient for our setup due to communication overhead.

1 Introduction

Extragalactic jets are amongst the most spectacular phenomena in astrophysics: These collimated beams of dilute but highly energetic plasma are formed in the environs of active black holes, on scales of milliparsecs3 with speeds very close to the speed of light, and propagate far outwards, eventually leaving the galaxy and pushing through the intergalactic gas at hundreds or even thousands of kiloparsecs.

Over these more than seven orders of magnitude in length, they remain collimated and deposit a large fraction of their huge kinetic energies of ∼ 1039 watts on the ambient gas. Yet, due to their low densities relative to the gas in galaxy cluster, they expand only slowly and reach their largest sizes only after several tens of millions of years. While these objects have been discovered already more than 50 years ago as double radio sources, only improving observational techniques made it possible in the 1970s and 1980s to realize the underlying physical mechanism of supersonic beams carrying large amounts of kinetic energy.

Jets do not only occur in the local universe, but also at high redshifts [13], corresponding to a time only some billion years after the big bang, when galaxies were still actively forming. At redshifts z > 0.5, radio galaxies often show luminous emission regions extending far beyond the galaxy itself, which are aligned with the radio source (“alignment e?ect”). These gas nebulae consist of an outer quiescent component, usually outside the radio structures, and an inner component with strongly distorted kinematics and clumpy and irregular structure [15]."