The DL_POLY Tutorial

4/7/2003


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Table of Contents

The DL_POLY Tutorial

Programme

Part 1

DL_POLY Background

DL_POLY Versions

The DL_POLY Force Field

DL_POLY Force Field

DL_POLY Force Field

Boundary Conditions

Algorithms and Ensembles

DL_POLY_2&3 Differences

DL_POLY_2 Spin-Offs

The DL_POLY Java GUI

The DL_POLY Java GUI

DL_POLY People

Information

Part 2

Criteria for Assessing Parallel Strategies

Scaling in Parallel Computing

Performance Parameters

Performance Parameters

Key Stages in MD Simulation

Basic MD Parallelization Strategies

Replicated Data

Replicated Data MD Algorithm

PPT Slide

PPT Slide

Replicated Data MD Algorithm

Replicated Data MD Algorithm

Link Cell Algorithm

Domain Decomposition MD

Domain Decomposition MD

PPT Slide

PPT Slide

Domain Decomposition MD

Domain Decomposition MD

Part 3

Itinerary

Parallel Force Calculation

Scheme for Distributing Bond Forces

DL_POLY_3 and Bond Forces

Nonbonded Forces: RD Verlet List

The SHAKE Algorithm

Parallel SHAKE

Parallel SHAKE

Parallel SHAKE

Parallel SHAKE

Parallel SHAKE

The Ewald Summation

Parallel Ewald Summation

PPT Slide

Smoothed Particle-Mesh Ewald

SPME: Spline Scheme

SPME: Building the Arrays

SPME: Comments

Part 4

HPCx Miscellanea

Compiling DL_POLY on HPCx

Running DL_POLY on HPCx

Running DL_POLY on HPCx

DL_POLY Directories

DL_POLY I/O Files

DL_POLY_3 on HPCx

DL_POLY_3 on HPCx

DL_POLY_3 on HPCx

DL_POLY_3 on HPCx

DL_POLY_3 on HPCx

DL_POLY_3 on HPCx

DL_POLY_3 on HPCx

Part 5

GUI Overview

GUI Appearance

Invoking the GUI

Compiling/Editing the GUI

Menus Available

Using the Menus

A Typical GUI Panel

Part 6

“Hands-On Session”

Hands-on Session Info

Author: Bill Smith

Email: w.smith@dl.ac.uk