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The DL-POLY Classic User Manual

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The DL-POLY Classic User Manual The DL POLY Classic User Manual W. Smith, T.R. Forester and I.T. Todorov STFC Daresbury Laboratory Daresbury, Warrington WA4 4AD Cheshire, UK Version 1.9, April 2012 °c STFC Preface About DL POLY Classic DL POLY Classic is a parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC’s Collaborative Computational Project for the Computer Simulation of Condensed Phases (CCP5) and the Computational Science and Engineering Department at Daresbury Laboratory. The package is the copyright of the Science Facilities Research Council (STFC) of the United Kingdom. DL POLY Classic is derived from the DL POLY 2 package, written by W. Smith and T.R. Forester. DL POLY Classic is issued free under a BSD licence, under the terms of which the source code may be freely modified and distributed as long as the copyright statements in the code are retained and proper acknowledgement is made of the authors and Daresbury Laboratory as the place of origin. The purpose of the DL POLY Classic package is to provide software for scientific research that is free, accessible and documented. i °c STFC Preface Disclaimer None of the authors, nor any of the organisations STFC, EPSRC, CCP5 nor any contributor to the DL POLY Classic package or its derivatives guarantee that the software and associated documentation is free from error. Neither do they accept responsibility for any loss or damage that results from its use. The responsibility for ensuring that the software is fit for purpose lies entirely with the user. ii °c STFC Preface DL POLY Classic Acknowledgements DL POLY Classic was developed under the auspices of the Science and Technology Facilities Council, the Engineering and Physical Sciences Research Council, and the former Science and Engineering Research Council, under grants from the Computational Science Initiative and the Science and Materials Computing Committee. Advice, assistance and encouragement in the development of DL POLY Classic has been given by many people. We gratefully acknowledge the comments, feedback and bug reports from the CCP5 community in the United Kingdom and throughout the world. In addition we thank the following people for contributing code to the package. 1. Maurice Leslie contributed the NOSQUISH rotational algorithm at the heart of many of the rigid body routines. 2. The hyperdynamics algorithms in DL POLY Classic were developed in a collaboration with Duncan Harris and John Harding at the University of Sheffield and formerly the University of London. 3. The solvation, free energy and solvent induced spectral shift features were developed in collab- oration with P.-A. Cazade, P. Bordat and R. Brown at the University of Pau. Travel between Pau and Daresbury by the collaborators was enabled by a grant from the Franco-British Alliance fund. 4. The metadynamics features were developed by David Quigley and Mark Rodger at the Uni- versity of Warwick. iii °c STFC Preface Manual Notation In the DL POLY Classic User Manual specific fonts are used to convey specific meanings: 1. directories - itallic font indicate unix file directories 2. routines - small capitals indicate subroutines, functions and programs. 3. macros - sloped text indicates a macro (file of unix commands) 4. directive - bold text indicates directives or keywords 5. variables - typewriter text indicates named variables and parameters 6. FILE - large capitals indicate filenames. iv Contents The DL POLY Classic User Manual a About DL POLY Classic .................................... 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 Classic Package .............................. 3 1.2 Functionality ........................................ 3 1.2.1 Molecular Systems ................................. 3 1.2.2 The DL POLY Classic Force Field ........................ 4 1.2.3 Boundary Conditions ............................... 4 1.2.4 The Java Graphical User Interface ........................ 4 1.2.5 Algorithms ..................................... 5 1.3 Programming Style ..................................... 5 1.3.1 Programming Language .............................. 5 1.3.2 Memory Management ............................... 6 1.3.3 Target Computers ................................. 6 1.3.4 Version Control System (CVS) .......................... 6 1.3.5 Required Program Libraries ............................ 6 1.3.6 Internal Documentation .............................. 6 1.3.7 Subroutine/Function Calling Sequences ..................... 7 1.3.8 FORTRAN Parameters .............................. 7 1.3.9 Arithmetic Precision ................................ 7 1.3.10 Units ........................................ 7 1.3.11 Error Messages ................................... 8 1.4 The DL POLY Classic Directory Structure ....................... 8 1.4.1 The source Sub-directory ............................. 8 1.4.2 The utility Sub-directory .............................. 8 1.4.3 The data Sub-directory .............................. 9 1.4.4 The bench Sub-directory .............................. 9 1.4.5 The execute Sub-directory ............................. 9 1.4.6 The build Sub-directory .............................. 9 v °c STFC Contents 1.4.7 The java Sub-directory ............................... 9 1.5 Obtaining the Source Code ................................ 9 1.6 Other Information ..................................... 10 2 Force Fields and Algorithms 11 2.1 The DL POLY Classic Force Field ............................ 13 2.2 The Intramolecular Potential Functions ......................... 15 2.2.1 Bond Potentials .................................. 15 2.2.2 Distance Restraints ................................. 17 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 Inversion Angle Potentials ............................. 23 2.2.8 The Calcite Four-Body Potential ......................... 25 2.2.9 Tethering Forces .................................. 26 2.2.10 Frozen Atoms .................................... 27 2.3 The Intermolecular Potential Functions ......................... 28 2.3.1 Short Ranged (van der Waals) Potentials .................... 28 2.3.2 Three Body Potentials ............................... 30 2.3.3 The Tersoff Covalent Potential .......................... 31 2.3.4 Four Body Potentials ............................... 34 2.3.5 Metal Potentials .................................. 34 2.3.6 External Fields ................................... 41 2.4 Long Ranged Electrostatic (Coulombic) Potentials ................... 42 2.4.1 Atomistic and Charge Group Implementation .................. 43 2.4.2 Direct Coulomb Sum ................................ 43 2.4.3 Truncated and Shifted Coulomb Sum ...................... 44 2.4.4 Damped Shifted Force Coulomb sum ....................... 44 2.4.5 Coulomb Sum with Distance Dependent Dielectric ............... 45 2.4.6 Ewald Sum ..................................... 46 2.4.7 Smoothed Particle Mesh Ewald .......................... 48 2.4.8 Hautman Klein Ewald (HKE) ........................... 50 2.4.9 Reaction Field ................................... 52 2.4.10 Dynamical Shell Model .............................. 53 2.4.11 Relaxed Shell Model ................................ 54 2.5 Integration algorithms ................................... 54 2.5.1 The Verlet Algorithms ............................... 54 2.5.2 Bond Constraints .................................. 57 2.5.3 Potential of Mean Force (PMF) Constraints and the Evaluation of Free Energy 59 2.5.4 Thermostats .................................... 59 2.5.5 Gaussian Constraints ............................... 62 2.5.6 Barostats ...................................... 63 2.5.7 Rigid Bodies and Rotational Integration Algorithms .............. 67 2.5.8 The DL POLY Classic Multiple Timestep Algorithm .............. 74 2.6 DL POLY Parallelisation ................................. 74 2.6.1 The Replicated Data Strategy ........................... 75 2.6.2 Distributing the Intramolecular Bonded Terms ................. 76 2.6.3 Distributing the Nonbonded Terms ........................ 76 vi °c STFC Contents 2.6.4 Modifications for the Ewald Sum ......................... 77 2.6.5 Modifications for SPME .............................. 78 2.6.6 Three and Four Body Forces ........................... 78 2.6.7 Metal Potentials .................................. 78 2.6.8 Summing the Atomic Forces ............................ 78 2.6.9 The SHAKE, RATTLE and Parallel QSHAKE Algorithms .......... 79 3 Construction and Execution 81 3.1 Constructing DL POLY Classic .............................. 83 3.1.1 Overview ...................................... 83 3.2 Compiling and Running DL POLY Classic ........................ 83 3.2.1 Compiling the Source Code ............................ 83 3.2.2 Running DL POLY Classic ............................ 86 3.2.3 Restarting DL POLY Classic ........................... 87 3.2.4 Optimising the Starting Structure ........................ 88 3.2.5 Choosing Ewald Sum Variables .........................
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