THE DL POLY 4 USER MANUAL I.T. Todorov & W. Smith STFC Daresbury Laboratory Daresbury, Warrington WA4 4AD Cheshire, England, United Kingdom Version 4.10.0 { September 2020 ©STFC Preface ABOUT DL POLY 4 DL POLY 4 is a general purpose parallel molecular dynamics simulation package developed at Daresbury Laboratory by I.T. Todorov & W. Smith. The DL POLY project was developed under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computa- tional Project for the Computer Simulation of Condensed Phases (CCP5), the Computational Chemistry & Application Performance Engineering Groups (formerly Molecular Simulation & Advanced Research Com- puting Groups) at Daresbury Laboratory and the Natural Environment Research Council (NERC) for the NERC's eScience project Computational Chemistry in the Environment (eMinerals), directed by M.T. Dove. DL POLY 4 is the property of Daresbury Laboratory and is issued free under licence to academic institu- tions pursuing scientific research of a non-commercial nature. 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 4 package is to provide software for academic research that is inexpensive, accessible and free of commercial considerations. Users have direct access to source code for modification 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 4 in regard to its interfaces and programming style and it is adequately documented. i ©STFC Preface DISCLAIMER Neither the STFC, EPSRC, NERC, CCP5 nor any of the authors of the DL POLY 4 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 ©STFC Preface ACKNOWLEDGEMENTS DL POLY 4 was developed at Daresbury Laboratory (DL - http://www.dl.ac.uk/), the Science & Tech- nology Facilities Council (STFC - http://www.stfc.ac.uk/), UK, with support from the Engineering and Physical Sciences Research Council (EPSRC - http://www.epsrc.ac.uk/) and the Natural Environment Re- search Council (NERC - http://www.nerc.ac.uk/). Advice, assistance and encouragement in the development of DL POLY 4 has been given by many peo- ple. We gratefully acknowledge the following: T.R. Forester, I.J. Bush, M. Leslie, M.F. Guest, R.J. Allan, D. Tildesley, M. Pinches, D. Rapaport, the UK's \Materials Chemistry Consortium" under C.R.A. Catlow and the eMinerals project under M.T. Dove. This document is produced with LATEX & hdvipdfm iii ©STFC Preface Manual Notation In the DL POLY manuals specific fonts are used to convey specific meanings: 1. directories - indicates UNIX file directories 2. routines - indicates subroutines, functions and programs 3. macros - indicates a macro (file of UNIX commands) 4. directive - indicates directives or keywords 5. variables - indicates named variables and parameters 6. FILE - indicates filenames. iv Contents THE DL POLY 4 USER MANUAL a About DL POLY 4 ............................................. i Disclaimer .................................................. ii Acknowledgements ............................................. iii Manual Notation .............................................. iv Contents v List of Tables xiv List of Figures xv 0 Quick Word / INSTALL & RUN 1 1 Introduction 2 1.1 The DL POLY Package ....................................... 3 1.2 Functionality ............................................. 3 1.2.1 Molecular Systems ...................................... 3 1.2.2 Force Field .......................................... 4 1.2.3 Boundary Conditions .................................... 4 1.2.4 Java Graphical User Interface ................................ 4 1.2.5 Algorithms .......................................... 5 1.2.5.1 Parallel Algorithms ................................ 5 1.2.5.2 Molecular Dynamics Algorithms ......................... 5 1.2.6 DL POLY Classic features incompatible or unavalable in DL POLY 4 ......... 5 1.3 Programming Style .......................................... 6 1.3.1 Programming Language ................................... 6 1.3.2 Modularisation and Intent .................................. 6 1.3.3 Memory Management .................................... 6 1.3.4 Target Platforms ....................................... 7 1.3.5 Internal Documentation ................................... 7 1.3.6 FORTRAN90 Parameters and Arithmetic Precision ................... 7 v ©STFC Contents 1.3.7 Units ............................................. 7 1.3.8 Error Messages ........................................ 8 1.4 Directory Structure .......................................... 8 1.4.1 The source Sub-directory .................................. 9 1.4.2 The build Sub-directory ................................... 9 1.4.3 The cmake Sub-directory .................................. 9 1.4.4 The utils Sub-directory ................................... 9 1.4.5 The execute Sub-directory .................................. 9 1.4.6 The data Sub-directory ................................... 9 1.4.7 The bench Sub-directory ................................... 10 1.4.8 The java Sub-directory .................................... 10 1.4.9 The utility Sub-directory ................................... 10 1.5 Obtaining the Source Code ..................................... 10 1.6 OS and Hardware Specific Ports .................................. 10 1.7 Other Information .......................................... 10 2 Force Field Interactions 12 2.1 Introduction to the DL POLY 4 Force Field ............................ 13 2.2 The Intramolecular Potential Functions .............................. 14 2.2.1 Bond Potentials ....................................... 14 2.2.2 Distance Restraints ...................................... 16 2.2.3 Valence Angle Potentials ................................... 17 2.2.4 Angular Restraints ...................................... 19 2.2.5 Dihedral Angle Potentials .................................. 20 2.2.6 Improper Dihedral Angle Potentials ............................ 22 2.2.7 Torsional Restraints ..................................... 23 2.2.8 Inversion Angle Potentials .................................. 24 2.2.9 The Calcite Four-Body Potential .............................. 26 2.2.10 Inversional Restraints .................................... 27 2.2.11 Tethering Forces ....................................... 28 2.3 The Intermolecular Potential Functions .............................. 28 2.3.1 Short Ranged (van der Waals) Potentials ......................... 28 2.3.2 Metal Potentials ....................................... 33 2.3.3 Tersoff Potentials ....................................... 44 2.3.4 Three-Body Potentials .................................... 47 2.3.5 Four-Body Potentials .................................... 48 2.4 Long Ranged Electrostatic (coulombic) Potentials ......................... 49 2.4.1 Default (Point Charges) Electrostatics ........................... 49 2.4.1.1 Direct Coulomb Sum ............................... 49 vi ©STFC Contents 2.4.1.2 Force-Shifted Coulomb Sum ........................... 50 2.4.1.3 Coulomb Sum with Distance Dependent Dielectric ............... 51 2.4.1.4 Reaction Field ................................... 52 2.4.1.5 Smoothed Particle Mesh Ewald .......................... 53 2.4.2 Multipolar Electrostatics .................................. 56 2.4.2.1 Direct Coulomb Sum ............................... 58 2.4.2.2 Force-Shifted Coulomb Sum ........................... 58 2.4.2.3 Coulomb Sum with Distance Dependent Dielectric ............... 59 2.4.2.4 Reaction Field ................................... 59 2.4.2.5 Smoothed Particle Mesh Ewald .......................... 60 2.5 Polarisation Shell Models ...................................... 63 2.5.1 CHARMM Shell Model Self-Induction ........................... 63 2.5.2 Dynamical (Adiabatic Shells) Shell Model ......................... 64 2.5.3 Relaxed (Massless Shells) Model .............................. 65 2.5.4 Breathing Shell Model Extension .............................. 65 2.5.5 Further Notes ......................................... 66 2.6 External Fields ............................................ 66 2.7 Treatment of Frozen Atoms, Rigid Body and Core-Shell Units .................. 68 2.8 Tabulation and interpolation in the treatment of intermolecular interactions .......... 68 2.9 Free Energy Capabilities via the PLUMED plugin ........................ 69 2.10 Open Knowledgebase of Interatomic Models - OpenKIM ..................... 69 3 Integration Algorithms 71 3.1 Introduction .............................................. 72 3.2 Bond Constraints ........................................... 74 3.3 Potential of Mean Force (PMF) Constraints and the Evaluation of Free Energy ........ 76 3.4 Thermostats .............................................. 77 3.4.1 Evans Thermostat (Gaussian Constraints) ......................... 77 3.4.2 Langevin Thermostat .................................... 78 3.4.3 Andersen Thermostat .................................... 80 3.4.4 Berendsen Thermostat .................................... 81 3.4.5 Nos´e-Hoover Thermostat .................................. 81 3.4.6 Gentle Stochastic Thermostat