LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands

#

### LAMMPS Documentation

#### 9 Nov 2016 version

#### Version info:

The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on this page of the WWW site. Every 2-4 months one of the incremental releases is subjected to more thorough testing and labeled as a stable version.

Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of the first page of the manual (this page).

- If you browse the HTML doc pages on the LAMMPS WWW site, they always describe the most current version of LAMMPS.
- If you browse the HTML doc pages included in your tarball, they describe the version you have.
- The PDF file on the WWW site or in the tarball is updated about once per month. This is because it is large, and we don't want it to be part of every patch.
- There is also a Developer.pdf file in the doc directory, which describes the internal structure and algorithms of LAMMPS.

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).

The current core group of LAMMPS developers is at Sandia National Labs and Temple University:

- Steve Plimpton, sjplimp at sandia.gov
- Aidan Thompson, athomps at sandia.gov
- Stan Moore, stamoore at sandia.gov
- Axel Kohlmeyer, akohlmey at gmail.com

Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia. The LAMMPS home page at http://lammps.sandia.gov has more information about the code and its uses. Interaction with external LAMMPS developers, bug reports and feature requests are mainly coordinated through the LAMMPS project on GitHub. The lammps.org domain, currently hosting public continuous integration testing and precompiled Linux RPM and Windows installer packages is located at Temple University and managed by Richard Berger, richard.berger at temple.edu.

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so we can improve the LAMMPS documentation.

Once you are familiar with LAMMPS, you may want to bookmark this page at Section_commands.html#comm since it gives quick access to documentation for all LAMMPS commands.

PDF file of the entire manual, generated by htmldoc

1. Introduction
   1.1 What is LAMMPS
   1.2 LAMMPS features
   1.3 LAMMPS non-features
   1.4 Open source distribution
   1.5 Acknowledgments and citations
2. Getting started
   2.1 What's in the LAMMPS distribution
   2.2 Making LAMMPS
   2.3 Making LAMMPS with optional packages
   2.4 Building LAMMPS via the Make.py script
   2.5 Building LAMMPS as a library
   2.6 Running LAMMPS
   2.7 Command-line options
   2.8 Screen output
   2.9 Tips for users of previous versions
3. Commands
   3.1 LAMMPS input script
   3.2 Parsing rules
   3.3 Input script structure
   3.4 Commands listed by category
   3.5 Commands listed alphabetically
4. Packages
   4.1 Standard packages
   4.2 User packages
5. Accelerating LAMMPS performance
   5.1 Measuring performance
   5.2 Algorithms and code options to boost performace
   5.3 Accelerator packages with optimized styles
   5.3.1 GPU package
   5.3.2 USER-INTEL package
   5.3.3 KOKKOS package
   5.3.4 USER-OMP package
   5.3.5 OPT package
   5.4 Comparison of various accelerator packages
6. How-to discussions
   6.1 Restarting a simulation
   6.2 2d simulations
   6.3 CHARMM and AMBER force fields
   6.4 Running multiple simulations from one input script
   6.5 Multi-replica simulations
   6.6 Granular models
   6.7 TIP3P water model
   6.8 TIP4P water model
   6.9 SPC water model
   6.10 Coupling LAMMPS to other codes
   6.11 Visualizing LAMMPS snapshots
   6.12 Triclinic (non-orthogonal) simulation boxes
   6.13 NEMD simulations
   6.14 Finite-size spherical and aspherical particles
   6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
   6.16 Thermostatting, barostatting, and compute temperature
   6.17 Walls
   6.18 Elastic constants
   6.19 Library interface to LAMMPS
   6.20 Calculating thermal conductivity
   6.21 Calculating viscosity
   6.22 Calculating a diffusion coefficient
   6.23 Using chunks to calculate system properties
   6.24 Setting parameters for pppm/disp
   6.25 Polarizable models
   6.26 Adiabatic core/shell model
   6.27 Drude induced dipoles
7. Example problems
8. Performance & scalability
9. Additional tools
10. Modifying & extending LAMMPS
    10.1 Atom styles
    10.2 Bond, angle, dihedral, improper potentials
    10.3 Compute styles
    10.4 Dump styles
    10.5 Dump custom output options
    10.6 Fix styles
    10.7 Input script commands
    10.8 Kspace computations
    10.9 Minimization styles
    10.10 Pairwise potentials
    10.11 Region styles
    10.12 Body styles
    10.13 Thermodynamic output options
    10.14 Variable options
    10.15 Submitting new features for inclusion in LAMMPS
11. Python interface
    11.1 Overview of running LAMMPS from Python
    11.2 Overview of using Python from a LAMMPS script
    11.3 Building LAMMPS as a shared library
    11.4 Installing the Python wrapper into Python
    11.5 Extending Python with MPI to run in parallel
    11.6 Testing the Python-LAMMPS interface
    11.7 Using LAMMPS from Python
    11.8 Example Python scripts that use LAMMPS
12. Errors
    12.1 Common problems
    12.2 Reporting bugs
    12.3 Error & warning messages
13. Future and history
    13.1 Coming attractions
    13.2 Past versions