Report on Computational Science and Engineering Support Activities at Daresbury Laboratory 2000/2001 icon

Report on Computational Science and Engineering Support Activities at Daresbury Laboratory 2000/2001


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Report on Computational Science and Engineering Support Activities at Daresbury Laboratory 2000/2001


Richard Blake


Version 1.0


99226.doc

Contents

Introduction 7

Hardware, Operations and Computing Infrastructure 7

Hardware Resources 7

Operational Support for the IBM RS6000-SP System 8

Technical Support for the Beowulf Systems 8

Computing Infrastructure 10

CCP Support 11

CCP Steering Panel 12

Reporting 12

CCP1 - Electronic Structure of Molecules 14

CCP2 - Continuum States of Atoms and Molecules 17

CCP3 – Computational Studies of Surfaces 20

CCP5 - Computer Simulation of Condensed Phases 24

CCP6 - Heavy Particle Dynamics 28

CCP9 - Electronic Structure of Solids 29

CCP12 - High Performance Computational Engineering 31

HPC Development 34

Evaluation and Development of Hardware and Software Technologies 35

High End Applications Development 37

Distributed Computing Support (DisCo) 41

Finance 45

Original Program Estimates 2000/2001 45

Outturn 2000/2001 46

Annex 1 - Report on IBM /SP Operations 2000/2001 47

Annex 2 - CCP Steering Panel Minutes 53

Annex 3 - Quantum Chemistry 62

CCP1 - Electronic Structure of Molecules 62

The GAMESS-UK Electronic Structure Code 63

CCP1 GUI Development – a Prototype Based on Python 65

Integration of GAMESS-UK and CHARMM 68

The ChemShell Package 69

2nd Derivatives of the Electronic Energy in Density Functional Theory 70

A Repository for Density Functionals 71

The QUASI Project 73

Geometric Derivatives of Excited State Energies within the Random Phase Approximation 75

Annex 4 - Atomic and Molecular Physics 77

Resonance Enhanced Harmonic Generation in Argon 77

Atomic Rearrangement Collisions 80

Electron Collisions with Ions in the Iron-peak Region of the Periodic Table 81

Whittaker Functions 84

Annex 5 - Materials Simulation 85

CCP3 - Computational Studies of Surfaces 85

CRYSTAL-2001 – First Principles Simulations 87

DL Visualize 88

The Synchrotron Radiation Research Theory Network - SRRTNet 89

A New Modular Low Energy Electron Diffraction Package - DL_LEED 90

A Systematic Investigation of Al2O3(0001) and its Interactions with Palladium 91

^ On the Prediction of Band Gaps from Hybrid Functional Theory 93

The Stability of Polar Oxide Surfaces: Ab Initio Studies of the ZnO(0001) and (000-1) Surfaces 95

Ab Initio Studies of the ZnO(10-10) and (11-20) Surfaces 97

High End Applications in Materials Science 99

Annex 6 - Molecular Simulation 101

CCP5: Computer Simulation of Condensed Phases 101

Democritus: Molecular Dynamics Teaching Software 104

DL_POLY: The Parallel Molecular Dynamics Simulation Package 105

DL_MULTI - A Package for DL_POLY to Simulate Rigid Molecules with Multipoles 107

The DL_POLY Java GUI 107

Daresbury Laboratory and UCL Collaboration in Polymorph Prediction 108

POWMOD: Molecular Dynamics Simulations of Surface Contact Studies 109

^ Daresbury Laboratory and RIKEN Collaboration in Molecular Dynamics 113

Annex 7 - Band Theory 115

The Relationship Between Interlayer Spacing and Magnetic Ordering in Gadolinium 115

Nonlocal Effects in the Electron-Positron Interaction in Metals 115

^ Doping Dependence of the Superconducting Gap in YBa2Cu3O7- δ 116

First Principles Relativistic Theory of Photoemision from Magnetic Surfaces 116

Self-Interaction-Corrected Description of the Electronic Properties of Americium Monochalcogenides and Monopnictides 117

Cu Valency Change Induced by O Doping in YBCO 117

^ Annex 8 - Computational Engineering 119

High Performance Computing in Engineering: CCP12 119

Computational Combustion for Engineering 120

UK Turbulence Consortium (UKTC) 121

Modelling Low Reynolds Number Rarefied Gas Flows in Micro-channels 122

Numerical Modelling of Low Reynolds Number Rarefied Gas Flow Past a Confined Microsphere 125

^ A North West Microfluidic Analytical & Screening Technology Centre 129

Annex 9 - HPC Development 131

UK High-End Computing Collaboration (UKHEC) 131

Performance Analysis of GA-based Applications using the Vampir Tool 133

CLIPS - CLRC Library of Parallel Subroutines 136

GRID-based High Performance Computing 137

The HPCGrid Services Portal and Related Work 139

Performance Comparison of Java with Fortran 90 and C 142

Adopting Quantum Chemistry Applications for Metacomputing: Density Functional Calculations with GAMESS-UK 143

Annex 10 – Distributed Computing and Applications Performance 147

^ DisCo: the Distributed Computing Support Programme 147

DisCo Workshops 150

Daresbury Laboratory Beowulf Projects 152

SPEC Benchmarks 154

Computational Chemistry Benchmarks 158

Communications Performance Benchmarks 162

Metrics used in the Performance Evaluation of Beowulf Clusters 165

Performance Analysis Tools 167

Applications Performance: NWChem 169

Applications Performance: GAMESS-UK DFT, MP2 and 2nd Derivatives 171

Applications Performance: GAMESS-UK DFT Coulomb Module 175

Applications Performance: DL_POLY 185

Applications Performance: CHARMM 189

Applications Performance: CASTEP, CPMD and CRYSTAL 189

Applications Performance: ANGUS 193

Applications Performance: FLITE3D 196

Applications Performance: SUMMARY 197








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