THE DL POLY 3 USER MANUAL I.T. Todorov and W. Smith CCLRC Daresbury Laboratory Daresbury, Warrington WA4 4AD Cheshire, UK Version 3.06, March 2006 °c CCLRC Preface ABOUT DL POLY 3 DL POLY 3 is a parallel molecular dynamics simulation package developed at Daresbury Labo- ratory by W. Smith and I.T. Todorov. The package was developed under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Com- putational Project for the Computer Simulation of Condensed Phases (CCP5), the Computational Chemistry Group at Daresbury Laboratory and the NERC e-Science Project Computational Chem- istry in the Environment, directed by M. Dove. DL POLY 3 is the property of Daresbury Laboratory and is issued free under licence to academic institutions pursuing scienti¯c research of a non-commercial nature. A handling fee is charged for new DL POLY 3 licence for NON-UK users. Commercial organisations may be permitted a licence to use the package after negotiation with the owners. Daresbury Laboratory is the sole centre for distribution of the package. Under no account is it to be redistributed to third parties without consent of the owners. The purpose of the DL POLY 3 package is to provide software for academic research that is inex- pensive, accessible and free of commercial considerations. Users have direct access to source code for modi¯cation and inspection. In the spirit of the enterprise, contributions in the form of working code are welcome, provided the code is compatible with DL POLY 3 in regard to its interfaces and programming style and it is adequately documented. i °c CCLRC Preface DISCLAIMER Neither the CCLRC, EPSRC, NERC, CCP5 nor any of the authors of the DL POLY 3 package or its derivatives guarantee that the package is free from error. Neither do they accept responsibility for any loss or damage that results from its use. ii °c CCLRC Preface ACKNOWLEDGEMENTS DL POLY 3 was developed at the Central Laboratory of the Research Councils, Daresbury Labo- ratory, with support from the Engineering and Physical Sciences Research Council and the Natural Environment Research Council. The package is the property of the Council for the Central Labo- ratory of the Research Councils of the United Kingdom. Advice, assistance and encouragement in the development of DL POLY 3 has been given by many people. We gratefully acknowledge the following: T.R. Forester, Ian Bush, M.F. Guest, M. Leslie, R.J. Allan, D. Tildesley, M. Pinches, D. Ra- paport, the UK's Materials Consortium under C.R.A. Catlow and the NERC e-Science project \Computational Chemistry in the Environment" under M. Dove. iii °c CCLRC Preface Manual Notation In the DL POLY manuals speci¯c fonts are used to convey speci¯c meanings: 1. directories - indicates unix ¯le directories 2. routines - indicates subroutines, functions and programs. 3. macros - indicates a macro (¯le of unix commands) 4. directive - indicates directives or keywords 5. variables - indicates named variables and parameters 6. FILE - indicates ¯lenames. iv Contents Title Page a About DL POLY 3 ....................................... i Disclaimer ............................................. ii Acknowledgements ........................................ iii Manual Notation ......................................... iv Contents v List of Tables x List of Figures xi 1 Introduction 1 1.1 The DL POLY Package .................................. 2 1.2 Functionality ........................................ 2 1.2.1 Molecular Systems ................................. 2 1.2.2 Force Field ..................................... 3 1.2.3 Boundary Conditions ............................... 3 1.2.4 Java Graphical User Interface ........................... 4 1.2.5 Algorithms ..................................... 4 1.3 Programming Style ..................................... 4 1.3.1 Programming Language .............................. 5 1.3.2 Modularisation and Intent ............................. 5 1.3.3 Memory Management ............................... 5 1.3.4 Target Computers ................................. 5 1.3.5 Version Control System (CVS) .......................... 5 1.3.6 Internal Documentation .............................. 6 1.3.7 FORTRAN 90 Parameters and Arithmetic Precision .............. 6 1.3.8 Units ........................................ 6 1.3.9 Error Messages ................................... 7 v °c CCLRC Contents 1.4 The DL POLY 3 Directory Structure ........................... 7 1.4.1 The source Sub-directory ............................. 8 1.4.2 The utility Sub-directory .............................. 8 1.4.3 The data Sub-directory .............................. 8 1.4.4 The bench Sub-directory .............................. 8 1.4.5 The execute Sub-directory ............................. 8 1.4.6 The build Sub-directory .............................. 8 1.4.7 The public Sub-directory .............................. 8 1.4.8 The java Sub-directory ............................... 9 1.5 Obtaining the Source Code ................................ 9 1.6 Other Information ..................................... 10 2 Force Fields 11 2.1 Introduction to DL POLY 3 Force Field ......................... 12 2.2 The Intramolecular Potential Functions ......................... 13 2.2.1 Bond Potentials .................................. 13 2.2.2 Distance Restraints ................................. 15 2.2.3 Valence Angle Potentials .............................. 15 2.2.4 Angular Restraints ................................. 17 2.2.5 Dihedral Angle Potentials ............................. 18 2.2.6 Improper Dihedral Angle Potentials ....................... 20 2.2.7 Inversion Angle Potentials ............................. 21 2.2.8 Tethering Forces .................................. 23 2.2.9 Frozen Atoms .................................... 24 2.3 The Intermolecular Potential Functions ......................... 24 2.3.1 Short Ranged (van der Waals) Potentials .................... 25 2.3.2 Metal Potentials .................................. 27 2.3.3 Terso® Potential .................................. 28 2.3.4 Three Body Potentials ............................... 31 2.3.5 Four Body Potentials ............................... 32 2.4 Long Ranged Electrostatic (coulombic) Potentials .................... 33 2.4.1 Direct Coulomb Sum ................................ 33 2.4.2 Force Shifted Coulomb Sum ............................ 34 2.4.3 Coulomb Sum with Distance Dependent Dielectric ............... 35 2.4.4 Reaction Field ................................... 35 2.4.5 Smoothed Particle Mesh Ewald .......................... 36 2.5 Polarisation Shell Models ................................. 39 vi °c CCLRC Contents 2.5.1 Dynamical (Adiabatic Shells) ........................... 40 2.5.2 Relaxed (Massless Shells) ............................. 40 2.6 External Fields ....................................... 41 3 Integration Algorithms 42 3.1 Introduction ......................................... 43 3.2 Bond Constraints ...................................... 45 3.3 Potential of Mean Force (PMF) Constraints and the Evaluation of Free Energy ... 47 3.4 Thermostats ......................................... 48 3.4.1 Langevin Thermostat ............................... 48 3.4.2 Evans Thermostat (Gaussian Constraints) .................... 50 3.4.3 Berendsen Thermostat ............................... 51 3.4.4 Nos¶e-Hoover Thermostat ............................. 52 3.5 Barostats .......................................... 54 3.5.1 Instantaneous pressure and stress ......................... 55 3.5.2 Berendsen Barostat ................................ 55 3.5.3 The Hoover Barostat ................................ 56 3.5.4 Martyna-Tuckerman-Klein Barostat ....................... 60 4 Construction and Execution 61 4.1 Constructing DL POLY 3 : an Overview ......................... 62 4.1.1 Constructing the Standard Version ........................ 62 4.1.2 Constructing Non-standard Versions ....................... 63 4.2 Compiling and Running DL POLY 3 .......................... 64 4.2.1 Compiling the DL POLY 3 Source Code ..................... 64 4.2.2 Running DL POLY 3 ............................... 66 4.2.3 Restarting DL POLY 3 .............................. 67 4.2.4 Notes on the DL POLY 3 Simulation E±ciency and Performance ....... 67 4.3 A Guide to Preparing Input Files ............................. 68 4.3.1 Inorganic Materials ................................. 69 4.3.2 Macromolecules ................................... 69 4.3.3 Adding Solvent to a Structure .......................... 70 4.3.4 Analysing Results ................................. 70 4.3.5 Choosing Ewald Sum Variables .......................... 70 4.4 DL POLY 3 Warning and Error Processing ....................... 72 4.4.1 The DL POLY 3 Internal Warning Facility ................... 72 4.4.2 The DL POLY 3 Internal Error Facility ..................... 72 vii °c CCLRC Contents 5 Data Files 73 5.1 The INPUT Files ...................................... 74 5.1.1 The CONTROL File ................................ 74 5.1.2 The CONFIG File ................................. 83 5.1.3 The FIELD File .................................. 86 5.1.4 The REFERENCE File .............................. 100 5.1.5 The REVOLD File ................................. 101 5.1.6 The TABLE File .................................. 102 5.2 The OUTPUT Files .................................... 103 5.2.1 The HISTORY File ................................ 104 5.2.2 The DEFECTS File ...............................