LAMMPS Users Manual Large−scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov − Sandia National Laboratories Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License. LAMMPS Users Manual Table of Contents LAMMPS Documentation.............................................................................................................................1 1. Introduction................................................................................................................................................3 1.1 What is LAMMPS.............................................................................................................................3 1.2 LAMMPS features.............................................................................................................................4 Kinds of systems LAMMPS can simulate:.............................................................................................4 Force fields:.............................................................................................................................................4 Creation of atoms:...................................................................................................................................4 Ensembles, constraints, and boundary conditions:..................................................................................5 Integrators:...............................................................................................................................................5 Output:.....................................................................................................................................................5 Pre− and post−processing:.......................................................................................................................5 1.3 LAMMPS non−features....................................................................................................................6 1.4 Open source distribution....................................................................................................................7 1.5 Acknowledgments and citations........................................................................................................8 2. Getting Started.........................................................................................................................................11 2.1 What's in the LAMMPS distribution...............................................................................................11 2.2 Making LAMMPS...........................................................................................................................11 2.3 Making LAMMPS with optional packages.....................................................................................14 2.4 Building LAMMPS as a library......................................................................................................16 2.5 Running LAMMPS.........................................................................................................................17 2.6 Command−line options...................................................................................................................17 2.7 LAMMPS screen output..................................................................................................................19 2.8 Tips for users of previous LAMMPS versions................................................................................20 3. Commands...............................................................................................................................................21 3.1 LAMMPS input script.....................................................................................................................21 3.2 Parsing rules....................................................................................................................................22 3.3 Input script structure........................................................................................................................22 3.4 Commands listed by category.........................................................................................................23 3.5 Individual commands......................................................................................................................24 4. How−to discussions.................................................................................................................................27 4.1 Restarting a simulation....................................................................................................................27 4.2 2d simulations..................................................................................................................................28 4.3 CHARMM and AMBER force fields..............................................................................................29 4.4 Running multiple simulations from one input script.......................................................................29 4.5 Parallel tempering............................................................................................................................31 4.6 Granular models..............................................................................................................................31 4.7 TIP3P water model..........................................................................................................................32 4.8 TIP4P water model..........................................................................................................................33 4.9 SPC water model.............................................................................................................................34 4.10 Coupling LAMMPS to other codes...............................................................................................34 4.11 Visualizing LAMMPS snapshots..................................................................................................35 4.12 Non−orthogonal simulation boxes................................................................................................36 4.13 NEMD simulations........................................................................................................................37 4.14 Aspherical particles.......................................................................................................................37 4.15 Output from LAMMPS.................................................................................................................38 4.16 Thermostatting, barostatting, and computing temperature............................................................41 5. Example problems....................................................................................................................................44 6. Performance &scalability.........................................................................................................................46 i LAMMPS Users Manual Table of Contents 7. Additional tools........................................................................................................................................47 amber2lmp tool......................................................................................................................................47 binary2txt tool.......................................................................................................................................48 ch2lmp tool............................................................................................................................................48 chain tool...............................................................................................................................................48 data2xmovie tool...................................................................................................................................48 eam generate tool...................................................................................................................................48 lmp2arc tool...........................................................................................................................................49 lmp2cfg tool...........................................................................................................................................49 lmp2traj tool..........................................................................................................................................49 lmp2vmd tool.........................................................................................................................................49 matlab tool.............................................................................................................................................49 micelle2d tool........................................................................................................................................50 msi2lmp tool..........................................................................................................................................50 pymol_asphere tool...............................................................................................................................50 python tool.............................................................................................................................................50