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LAMMPS Users Manual Large-Scale Atomic/Molecular Massively Parallel Simulator

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LAMMPS Users Manual Large-Scale Atomic/Molecular Massively Parallel Simulator 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 Version info:............................................................................................................................................1 1. Introduction.........................................................................................................................................4 1.1 What is LAMMPS......................................................................................................................4 1.2 LAMMPS features......................................................................................................................5 General features................................................................................................................................5 Particle and model types...................................................................................................................5 Force fields........................................................................................................................................5 Atom creation....................................................................................................................................6 Ensembles, constraints, and boundary conditions............................................................................6 Integrators.........................................................................................................................................7 Diagnostics........................................................................................................................................7 Output...............................................................................................................................................7 Multi-replica models.........................................................................................................................7 Pre- and post-processing...................................................................................................................7 Specialized features..........................................................................................................................7 1.3 LAMMPS non-features...............................................................................................................8 1.4 Open source distribution.............................................................................................................9 1.5 Acknowledgments and citations...............................................................................................10 2. Getting Started...................................................................................................................................12 2.1 What's in the LAMMPS distribution........................................................................................12 2.2 Making LAMMPS....................................................................................................................13 2.3 Making LAMMPS with optional packages..............................................................................19 2.4 Building LAMMPS as a library................................................................................................21 2.5 Running LAMMPS...................................................................................................................22 2.6 Command-line options..............................................................................................................23 2.7 LAMMPS screen output...........................................................................................................27 2.8 Tips for users of previous LAMMPS versions.........................................................................28 3. Commands.........................................................................................................................................30 3.1 LAMMPS input script...............................................................................................................30 3.2 Parsing rules..............................................................................................................................31 3.3 Input script structure.................................................................................................................31 3.4 Commands listed by category...................................................................................................33 3.5 Individual commands................................................................................................................33 Fix styles.........................................................................................................................................34 Compute styles................................................................................................................................35 Pair_style potentials........................................................................................................................35 Bond_style potentials......................................................................................................................37 Angle_style potentials.....................................................................................................................37 Dihedral_style potentials................................................................................................................37 Improper_style potentials................................................................................................................38 Kspace solvers................................................................................................................................38 4. Packages............................................................................................................................................39 4.1 Standard packages.....................................................................................................................39 4.2 User packages...........................................................................................................................40 USER-MISC package.....................................................................................................................41 USER-ATC package.......................................................................................................................41 USER-AWPMD package................................................................................................................41 i LAMMPS Users Manual Table of Contents USER-CG-CMM package..............................................................................................................42 USER-CUDA package....................................................................................................................42 USER-EFF package........................................................................................................................43 USER-EWALDN package..............................................................................................................43 USER-OMP package......................................................................................................................44 USER-REAXC package.................................................................................................................44 USER-SPH package........................................................................................................................44 5. Accelerating LAMMPS performance................................................................................................46 5.1 OPT package.............................................................................................................................47 5.2 USER-OMP package................................................................................................................47 5.3 GPU package............................................................................................................................49 5.4 USER-CUDA package..............................................................................................................51 5.5 Comparison of GPU and USER-CUDA packages...................................................................53 6. How-to discussions............................................................................................................................56 6.1 Restarting a simulation.............................................................................................................56 6.2 2d simulations...........................................................................................................................58 6.3 CHARMM, AMBER, and DREIDING force fields.................................................................58 6.4 Running multiple simulations from one input script................................................................59 6.5 Multi-replica simulations..........................................................................................................61
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