LAMMPS Users Manual - · PDF fileLAMMPS Users Manual vii. Table of Contents fix addtorque command

LAMMPS Users Manual1 Feb 2014 version

http://lammps.sandia.gov - Sandia National LaboratoriesCopyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.

Table of ContentsLAMMPS Documentation.............................................................................................................................1

1 Feb 2014 version..................................................................................................................................1Version info:.....................................................................................................................................1

1. Introduction.........................................................................................................................................41.1 What is LAMMPS......................................................................................................................41.2 LAMMPS features......................................................................................................................5General features................................................................................................................................5Particle and model types...................................................................................................................5Force fields........................................................................................................................................5Atom creation....................................................................................................................................6Ensembles, constraints, and boundary conditions............................................................................6Integrators.........................................................................................................................................7Diagnostics........................................................................................................................................7Output...............................................................................................................................................7Multi-replica models.........................................................................................................................7Pre- and post-processing...................................................................................................................7Specialized features..........................................................................................................................71.3 LAMMPS non-features...............................................................................................................81.4 Open source distribution.............................................................................................................91.5 Acknowledgments and citations...............................................................................................10

2. Getting Started...................................................................................................................................122.1 What's in the LAMMPS distribution........................................................................................122.2 Making LAMMPS....................................................................................................................132.3 Making LAMMPS with optional packages..............................................................................192.4 Building LAMMPS via the Make.py script..............................................................................222.5 Building LAMMPS as a library................................................................................................232.6 Running LAMMPS...................................................................................................................242.7 Command-line options..............................................................................................................262.8 LAMMPS screen output...........................................................................................................302.9 Tips for users of previous LAMMPS versions.........................................................................31

3. Commands.........................................................................................................................................323.1 LAMMPS input script...............................................................................................................323.2 Parsing rules..............................................................................................................................333.3 Input script structure.................................................................................................................343.4 Commands listed by category...................................................................................................353.5 Individual commands................................................................................................................36Fix styles.........................................................................................................................................37Compute styles................................................................................................................................37Pair_style potentials........................................................................................................................38Bond_style potentials......................................................................................................................40Angle_style potentials.....................................................................................................................40Dihedral_style potentials................................................................................................................41Improper_style potentials................................................................................................................41Kspace solvers................................................................................................................................41

4. Packages............................................................................................................................................434.1 Standard packages.....................................................................................................................434.2 User packages...........................................................................................................................44USER-MISC package.....................................................................................................................45

LAMMPS Users Manual

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Table of ContentsUSER-ATC package.......................................................................................................................46USER-AWPMD package................................................................................................................46USER-COLVARS package............................................................................................................46USER-CG-CMM package..............................................................................................................47USER-CUDA package....................................................................................................................47USER-EFF package........................................................................................................................48USER-OMP package......................................................................................................................48USER-REAXC package.................................................................................................................48USER-SPH package........................................................................................................................49

5. Accelerating LAMMPS performance................................................................................................505.1 Measuring performance............................................................................................................505.2 General strategies......................................................................................................................515.3 Packages with optimized styles................................................................................................525.4 OPT package.............................................................................................................................535.5 USER-OMP package................................................................................................................535.6 GPU package............................................................................................................................555.7 USER-CUDA package..............................................................................................................575.8 Comparison of GPU and USER-CUDA packages...................................................................59

6. How-to discussions............................................................................................................................616.1 Restarting a simulation.............................................................................................................616.2 2d simulations...........................................................................................................................636.3 CHARMM, AMBER, and DREIDING force fields.............................