6.3. Package details¶
Here is a brief description of all the standard and user packages in LAMMPS. It lists authors (if applicable) and summarizes the package contents. It has specific instructions on how to install the package, including, if necessary, info on how to download or build any extra library it requires. It also gives links to documentation, example scripts, and pictures/movies (if available) that illustrate use of the package.
The majority of packages can be included in a LAMMPS build with a
single setting (
-D PGK_<NAME>=on for CMake) or command
make yes-<name> for make). See the Build package
page for more info. A few packages may require additional steps;
this is indicated in the descriptions below. The Build extras
page gives those details.
To see the complete list of commands a package adds to LAMMPS, you can examine the files in its src directory, e.g. “ls src/GRANULAR”. Files with names that start with fix, compute, atom, pair, bond, angle, etc correspond to commands with the same style name as contained in the file name.
6.3.1. ASPHERE package¶
Computes, time-integration fixes, and pair styles for aspherical particle models including ellipsoids, 2d lines, and 3d triangles.
src/ASPHERE: filenames -> commands
6.3.2. BODY package¶
Body-style particles with internal structure. Computes, time-integration fixes, pair styles, as well as the body styles themselves. See the Howto body page for an overview.
src/BODY filenames -> commands
6.3.3. CLASS2 package¶
Bond, angle, dihedral, improper, and pair styles for the COMPASS CLASS2 molecular force field.
src/CLASS2: filenames -> commands
6.3.4. COLLOID package¶
Coarse-grained finite-size colloidal particles. Pair styles and fix wall styles for colloidal interactions. Includes the Fast Lubrication Dynamics (FLD) method for hydrodynamic interactions, which is a simplified approximation to Stokesian dynamics.
Authors: This package includes Fast Lubrication Dynamics pair styles which were created by Amit Kumar and Michael Bybee from Jonathan Higdon’s group at UIUC.
src/COLLOID: filenames -> commands
6.3.5. COMPRESS package¶
Compressed output of dump files via the zlib compression library, using dump styles with a “gz” in their style name.
To use this package you must have the zlib compression library available on your system.
Author: Axel Kohlmeyer (Temple U).
src/COMPRESS: filenames -> commands
6.3.6. CORESHELL package¶
Compute and pair styles that implement the adiabatic core/shell model for polarizability. The pair styles augment Born, Buckingham, and Lennard-Jones styles with core/shell capabilities. The compute temp/cs command calculates the temperature of a system with core/shell particles. See the Howto coreshell page for an overview of how to use this package.
Author: Hendrik Heenen (Technical U of Munich).
src/CORESHELL: filenames -> commands
6.3.7. DIPOLE package¶
An atom style and several pair styles for point dipole models with short-range or long-range interactions.
src/DIPOLE: filenames -> commands
6.3.8. GPU package¶
Dozens of pair styles and a version of the PPPM long-range Coulombic solver optimized for GPUs. All such styles have a “gpu” as a suffix in their style name. The GPU code can be compiled with either CUDA or OpenCL, however the OpenCL variants are no longer actively maintained and only the CUDA versions are regularly tested. The GPU package page gives details of what hardware and GPU software is required on your system, and details on how to build and use this package. Its styles can be invoked at run time via the “-sf gpu” or “-suffix gpu” command-line switches. See also the KOKKOS package, which has GPU-enabled styles.
Authors: Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen (Northwestern U) while at ORNL and later. AMD HIP support by Evgeny Kuznetsov, Vladimir Stegailov, and Vsevolod Nikolskiy (HSE University).
src/GPU: filenames -> commands
Benchmarks page of web site
6.3.9. GRANULAR package¶
Pair styles and fixes for finite-size granular particles, which interact with each other and boundaries via frictional and dissipative potentials.
src/GRANULAR: filenames -> commands
6.3.10. KIM package¶
This package contains a command with a set of sub-commands that serve as a wrapper on the Open Knowledgebase of Interatomic Models (OpenKIM) repository of interatomic models (IMs) enabling compatible ones to be used in LAMMPS simulations.
This includes kim init, and kim interactions commands to select, initialize and instantiate the IM, a kim query command to perform web queries for material property predictions of OpenKIM IMs, a kim param command to access KIM Model Parameters from LAMMPS, and a kim property command to write material properties computed in LAMMPS to standard KIM property instance format.
The command pair_style kim is called by kim interactions and is not recommended to be directly used in input scripts.
To use this package you must have the KIM API library available on your system. The KIM API is available for download on the OpenKIM website. When installing LAMMPS from binary, the kim-api package is a dependency that is automatically downloaded and installed.
Information about the KIM project can be found at its website: https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota) and is funded by the National Science Foundation.
Authors: Ryan Elliott (U Minnesota) is the main developer for the KIM API and the pair_style kim command. Yaser Afshar (U Minnesota), Axel Kohlmeyer (Temple U), Ellad Tadmor (U Minnesota), and Daniel Karls (U Minnesota) contributed to the kim command interface in close collaboration with Ryan Elliott.
src/KIM: filenames -> commands
6.3.11. KOKKOS package¶
Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute styles adapted to compile using the Kokkos library which can convert them to OpenMP or CUDA code so that they run efficiently on multicore CPUs, KNLs, or GPUs. All the styles have a “kk” as a suffix in their style name. The KOKKOS package page gives details of what hardware and software is required on your system, and how to build and use this package. Its styles can be invoked at run time via the “-sf kk” or “-suffix kk” command-line switches. Also see the GPU, OPT, USER-INTEL, and USER-OMP packages, which have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++14 compatible compiler to use this package. KOKKOS makes extensive use of advanced C++ features, which can expose compiler bugs, especially when compiling for maximum performance at high optimization levels. Please see the file lib/kokkos/README for a list of compilers and their respective platforms, that are known to work.
Authors: The KOKKOS package was created primarily by Christian Trott and Stan Moore (Sandia), with contributions from other folks as well. It uses the open-source Kokkos library which was developed by Carter Edwards, Christian Trott, and others at Sandia, and which is included in the LAMMPS distribution in lib/kokkos.
src/KOKKOS: filenames -> commands
Benchmarks page of web site
6.3.12. KSPACE package¶
A variety of long-range Coulombic solvers, as well as pair styles which compute the corresponding short-range pairwise Coulombic interactions. These include Ewald, particle-particle particle-mesh (PPPM), and multilevel summation method (MSM) solvers.
Building with this package requires a 1d FFT library be present on your system for use by the PPPM solvers. This can be the KISS FFT library provided with LAMMPS, third party libraries like FFTW, or a vendor-supplied FFT library. See the Build settings page for details on how to select different FFT options for your LAMPMS build.
src/KSPACE: filenames -> commands
Search the pair style page for styles with “long” or “msm” in name
6.3.13. LATTE package¶
A fix command which wraps the LATTE DFTB code, so that molecular dynamics can be run with LAMMPS using density-functional tight-binding quantum forces calculated by LATTE.
Authors: Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE itself is developed at Los Alamos National Laboratory by Marc Cawkwell, Anders Niklasson, and Christian Negre.
src/LATTE: filenames -> commands
6.3.14. MANYBODY package¶
A variety of many-body and bond-order potentials. These include (AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
src/MANYBODY: filenames -> commands
Pair style page
6.3.15. MC package¶
Several fixes and a pair style that have Monte Carlo (MC) or MC-like attributes. These include fixes for creating, breaking, and swapping bonds, for performing atomic swaps, and performing grand-canonical MC (GCMC) or similar processes in conjunction with dynamics.
src/MC: filenames -> commands
6.3.16. MESSAGE package¶
Commands to use LAMMPS as either a client or server and couple it to another application.
src/MESSAGE: filenames -> commands
6.3.17. MISC package¶
A variety of compute, fix, pair, dump styles with specialized capabilities that don’t align with other packages. Do a directory listing, “ls src/MISC”, to see the list of commands.
the MISC package contains styles that require using the -restrict flag, when compiling with Intel compilers.
src/MISC: filenames -> commands
6.3.18. MLIAP package¶
A general interface for machine-learning interatomic potentials, including PyTorch.
To use this package, also the SNAP package package needs to be installed. To make the mliappy model available, also the PYTHON package package needs to be installed, the version of Python must be 3.6 or later, and the cython software must be installed.
Author: Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
src/MLIAP: filenames -> commands
examples/mliap (see README)
When built with the mliappy model this package includes an extension for
coupling with Python models, including PyTorch. In this case, the Python
interpreter linked to LAMMPS will need the
installed. The provided examples build models with PyTorch, which would
therefore also needs to be installed to run those examples.
6.3.19. MOLECULE package¶
A large number of atom, pair, bond, angle, dihedral, improper styles that are used to model molecular systems with fixed covalent bonds. The pair styles include the Dreiding (hydrogen-bonding) and CHARMM force fields, and a TIP4P water model.
src/MOLECULE: filenames -> commands
6.3.20. MPIIO package¶
Support for parallel output/input of dump and restart files via the MPIIO library. It adds dump styles with a “mpiio” in their style name. Restart files with an “.mpiio” suffix are also written and read in parallel.
6.3.21. MSCG package¶
To use this package you must have the MS-CG library available on your system.
Authors: The fix was written by Lauren Abbott (Sandia). The MS-CG library was developed by Jacob Wagner in Greg Voth’s group at the University of Chicago.
src/MSCG: filenames -> commands
6.3.22. OPT package¶
A handful of pair styles which are optimized for improved CPU performance on single or multiple cores. These include EAM, LJ, CHARMM, and Morse potentials. The styles have an “opt” suffix in their style name. The OPT package page gives details of how to build and use this package. Its styles can be invoked at run time via the “-sf opt” or “-suffix opt” command-line switches. See also the KOKKOS, USER-INTEL, and USER-OMP packages, which have styles optimized for CPU performance.
Authors: James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge Technology).
src/OPT: filenames -> commands
Search the pair style page for styles followed by (t)
Benchmarks page of web site
6.3.23. PERI package¶
An atom style, several pair styles which implement different Peridynamics materials models, and several computes which calculate diagnostics. Peridynamics is a particle-based meshless continuum model.
Authors: The original package was created by Mike Parks (Sandia). Additional Peridynamics models were added by Rezwanur Rahman and John Foster (UTSA).
src/PERI: filenames -> commands
6.3.24. PLUGIN package¶
A plugin command that can load and unload several kind of styles in LAMMPS from shared object files at runtime without having to recompile and relink LAMMPS.
Authors: Axel Kohlmeyer (Temple U)
6.3.25. POEMS package¶
A fix that wraps the Parallelizable Open source Efficient Multibody Software (POEMS) library, which is able to simulate the dynamics of articulated body systems. These are systems with multiple rigid bodies (collections of particles) whose motion is coupled by connections at hinge points.
Author: Rudra Mukherjee (JPL) while at RPI.
src/POEMS: filenames -> commands
6.3.26. PYTHON package¶
A python command which allow you to execute Python code from a LAMMPS input script. The code can be in a separate file or embedded in the input script itself. See the Python call page for an overview of using Python from LAMMPS in this manner and all the Python manual pages for other ways to use LAMMPS and Python together.
Building with the PYTHON package assumes you have a Python shared library available on your system, which needs to be a Python 2 version, 2.6 or later. Python 3 is not yet supported. See the lib/python/README for more details.
src/PYTHON: filenames -> commands
6.3.27. QEQ package¶
Several fixes for performing charge equilibration (QEq) via different algorithms. These can be used with pair styles that perform QEq as part of their formulation.
src/QEQ: filenames -> commands
6.3.28. REPLICA package¶
A collection of multi-replica methods which can be used when running multiple LAMMPS simulations (replicas). See the Howto replica page for an overview of how to run multi-replica simulations in LAMMPS. Methods in the package include nudged elastic band (NEB), parallel replica dynamics (PRD), temperature accelerated dynamics (TAD), parallel tempering, and a verlet/split algorithm for performing long-range Coulombics on one set of processors, and the remainder of the force field calculation on another set.
src/REPLICA: filenames -> commands
6.3.29. RIGID package¶
Fixes which enforce rigid constraints on collections of atoms or particles. This includes SHAKE and RATTLE, as well as various rigid-body integrators for a few large bodies or many small bodies. Also several computes which calculate properties of rigid bodies.
src/RIGID: filenames -> commands
6.3.30. SHOCK package¶
Fixes for running impact simulations where a shock-wave passes through a material.
src/SHOCK: filenames -> commands
6.3.31. SNAP package¶
A pair style for the spectral neighbor analysis potential (SNAP). SNAP is methodology for deriving a highly accurate classical potential fit to a large archive of quantum mechanical (DFT) data. Also several computes which analyze attributes of the potential.
Author: Aidan Thompson (Sandia).
src/SNAP: filenames -> commands
6.3.32. SPIN package¶
Model atomic magnetic spins classically, coupled to atoms moving in the usual manner via MD. Various pair, fix, and compute styles.
Author: Julien Tranchida (Sandia).
src/SPIN: filenames -> commands
6.3.33. SRD package¶
A pair of fixes which implement the Stochastic Rotation Dynamics (SRD) method for coarse-graining of a solvent, typically around large colloidal particles.
src/SRD: filenames -> commands
6.3.34. VORONOI package¶
A compute command which calculates the Voronoi tesselation of a collection of atoms by wrapping the Voro++ library. This can be used to calculate the local volume or each atoms or its near neighbors.
To use this package you must have the Voro++ library available on your system.
Author: Daniel Schwen (INL) while at LANL. The open-source Voro++ library was written by Chris Rycroft (Harvard U) while at UC Berkeley and LBNL.
src/VORONOI: filenames -> commands
6.3.35. USER-ADIOS package¶
Authors: Norbert Podhorszki (ORNL) from the ADIOS developer team.
src/USER-ADIOS: filenames -> commands
6.3.36. USER-ATC package¶
ATC stands for atoms-to-continuum. This package implements a fix atc command to either couple molecular dynamics with continuum finite element equations or perform on-the-fly conversion of atomic information to continuum fields.
Authors: Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
src/USER-ATC: filenames -> commands
6.3.37. USER-AWPMD package¶
AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This package implements an atom, pair, and fix style which allows electrons to be treated as explicit particles in a classical molecular dynamics model.
Author: Ilya Valuev (JIHT, Russia).
src/USER-AWPMD: filenames -> commands
6.3.38. USER-BOCS package¶
N. J. H. Dunn and W. G. Noid, “Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids,” J. Chem. Phys. 143, 243148 (2015).
Authors: Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
The USER-BOCS user package for LAMMPS is part of the BOCS software package: https://github.com/noid-group/BOCS
See the following reference for information about the entire package:
Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. “BOCS: Bottom-Up Open-Source Coarse-Graining Software.” J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
Example inputs are in the examples/USER/bocs folder.
6.3.39. USER-BROWNIAN package¶
This package provides fix brownian, fix brownian/sphere, and fix brownian/asphere as well as fix propel/self which allow to do Brownian Dynamics time integration of point, spherical and aspherical particles and also support self-propelled particles.
Authors: Sam Cameron (University of Bristol), Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
Example inputs are in the examples/USER/brownian folder.
6.3.40. USER-CGDNA package¶
Several pair styles, bond styles, and integration fixes for coarse-grained modelling of single- and double-stranded DNA and RNA based on the oxDNA and oxRNA model of Doye, Louis and Ouldridge. The package includes Langevin-type rigid-body integrators with improved stability.
Author: Oliver Henrich (University of Strathclyde, Glasgow).
src/USER-CGDNA: filenames -> commands
6.3.41. USER-CGSDK package¶
Several pair styles and an angle style which implement the coarse-grained SDK model of Shinoda, DeVane, and Klein which enables simulation of ionic liquids, electrolytes, lipids and charged amino acids.
Author: Axel Kohlmeyer (Temple U).
src/USER-CGSDK: filenames -> commands
6.3.42. USER-COLVARS package¶
COLVARS stands for collective variables, which can be used to implement various enhanced sampling methods, including Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and Restraints. A fix colvars command is implemented which wraps a COLVARS library, which implements these methods. simulations.
Authors: The COLVARS library is written and maintained by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome Henin (LISM, CNRS, Marseille, France), originally for the NAMD MD code, but with portability in mind. Axel Kohlmeyer (Temple U) provided the interface to LAMMPS.
src/USER-COLVARS: filenames -> commands
6.3.43. USER-PACE package¶
A pair style for the Atomic Cluster Expansion potential (ACE). ACE is a methodology for deriving a highly accurate classical potential fit to a large archive of quantum mechanical (DFT) data. The USER-PACE package provides an efficient implementation for running simulations with ACE potentials.
This package was written by Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
^1: Ruhr-University Bochum, Bochum, Germany
^2: University of Cambridge, Cambridge, United Kingdom
^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
^4: University of British Columbia, Vancouver, BC, Canada
src/USER-PACE: filenames -> commands
6.3.44. USER-PLUMED package¶
The fix plumed command allows you to use the PLUMED free energy plugin for molecular dynamics to analyze and bias your LAMMPS trajectory on the fly. The PLUMED library is called from within the LAMMPS input script by using the fix plumed command.
Authors: The PLUMED library is written and maintained by Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth Tribello.
6.3.45. USER-DIFFRACTION package¶
Two computes and a fix for calculating x-ray and electron diffraction intensities based on kinematic diffraction theory.
Author: Shawn Coleman while at the U Arkansas.
src/USER-DIFFRACTION: filenames -> commands
6.3.46. USER-DPD package¶
DPD stands for dissipative particle dynamics. This package implements coarse-grained DPD-based models for energetic, reactive molecular crystalline materials. It includes many pair styles specific to these systems, including for reactive DPD, where each particle has internal state for multiple species and a coupled set of chemical reaction ODEs are integrated each timestep. Highly accurate time integrators for isothermal, isoenergetic, isobaric and isenthalpic conditions are included. These enable long timesteps via the Shardlow splitting algorithm.
Authors: Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John Brennan (ARL).
src/USER-DPD: filenames -> commands
6.3.47. USER-DRUDE package¶
Fixes, pair styles, and a compute to simulate thermalized Drude oscillators as a model of polarization. See the Howto drude and Howto drude2 pages for an overview of how to use the package. There are auxiliary tools for using this package in tools/drude.
Authors: Alain Dequidt (U Clermont Auvergne), Julien Devemy (CNRS), and Agilio Padua (ENS de Lyon).
src/USER-DRUDE: filenames -> commands
6.3.48. USER-EFF package¶
EFF stands for electron force field which allows a classical MD code to model electrons as particles of variable radius. This package contains atom, pair, fix and compute styles which implement the eFF as described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC, 2010. The eFF potential was first introduced by Su and Goddard, in 2007. There are auxiliary tools for using this package in tools/eff; see its README file.
Author: Andres Jaramillo-Botero (CalTech).
src/USER-EFF: filenames -> commands
6.3.49. USER-FEP package¶
FEP stands for free energy perturbation. This package provides methods for performing FEP simulations by using a fix adapt/fep command with soft-core pair potentials, which have a “soft” in their style name. There are auxiliary tools for using this package in tools/fep; see its README file.
Author: Agilio Padua (ENS de Lyon)
src/USER-FEP: filenames -> commands
6.3.50. USER-H5MD package¶
H5MD stands for HDF5 for MD. HDF5 is a portable, binary, self-describing file format, used by many scientific simulations. H5MD is a format for molecular simulations, built on top of HDF5. This package implements a dump h5md command to output LAMMPS snapshots in this format.
To use this package you must have the HDF5 library available on your system.
Author: Pierre de Buyl (KU Leuven) created both the package and the H5MD format.
src/USER-H5MD: filenames -> commands
6.3.51. USER-HDNNP package¶
A pair_style hdnnp command which allows to use high-dimensional neural network potentials (HDNNPs), a form of machine learning potentials. HDNNPs must be carefully trained prior to their application in a molecular dynamics simulation.
To use this package you must have the n2p2 library installed and compiled on your system.
Author: Andreas Singraber
src/USER-HDNNP: filenames -> commands
6.3.52. USER-INTEL package¶
Dozens of pair, fix, bond, angle, dihedral, improper, and kspace styles which are optimized for Intel CPUs and KNLs (Knights Landing). All of them have an “intel” in their style name. The USER-INTEL package page gives details of what hardware and compilers are required on your system, and how to build and use this package. Its styles can be invoked at run time via the “-sf intel” or “-suffix intel” command-line switches. Also see the KOKKOS, OPT, and USER-OMP packages, which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full advantage of this package. While compilation with GNU compilers is supported, performance will be sub-optimal.
the USER-INTEL package contains styles that require using the -restrict flag, when compiling with Intel compilers.
Author: Mike Brown (Intel).
src/USER-INTEL: filenames -> commands
Benchmarks page of web site
6.3.53. USER-LB package¶
Fixes which implement a background Lattice-Boltzmann (LB) fluid, which can be used to model MD particles influenced by hydrodynamic forces.
Authors: Frances Mackay and Colin Denniston (University of Western Ontario).
src/USER-LB: filenames -> commands
6.3.54. USER-MGPT package¶
A pair style which provides a fast implementation of the quantum-based MGPT multi-ion potentials. The MGPT or model GPT method derives from first-principles DFT-based generalized pseudopotential theory (GPT) through a series of systematic approximations valid for mid-period transition metals with nearly half-filled d bands. The MGPT method was originally developed by John Moriarty at LLNL. The pair style in this package calculates forces and energies using an optimized matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
Authors: Tomas Oppelstrup and John Moriarty (LLNL).
src/USER-MGPT: filenames -> commands
6.3.55. USER-MISC package¶
A potpourri of (mostly) unrelated features contributed to LAMMPS by users. Each feature is a single fix, compute, pair, bond, angle, dihedral, improper, or command style.
Authors: The author for each style in the package is listed in the src/USER-MISC/README file.
src/USER-MISC: filenames -> commands
one page per individual command listed in src/USER-MISC/README
6.3.56. USER-MANIFOLD package¶
Several fixes and a “manifold” class which enable simulations of particles constrained to a manifold (a 2D surface within the 3D simulation box). This is done by applying the RATTLE constraint algorithm to formulate single-particle constraint functions g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) n = grad(g).
Author: Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
src/USER-MANIFOLD: filenames -> commands
6.3.57. USER-MDI package¶
A LAMMPS command and fix to allow client-server coupling of LAMMPS to other atomic or molecular simulation codes via the MolSSI Driver Interface (MDI) library.
Author: Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
6.3.58. USER-MEAMC package¶
A pair style for the modified embedded atom (MEAM) potential translated from the Fortran version in the (obsolete) MEAM package to plain C++. The USER-MEAMC fully replaces the MEAM package, which has been removed from LAMMPS after the 12 December 2018 version.
Author: Sebastian Huetter, (Otto-von-Guericke University Magdeburg) based on the Fortran version of Greg Wagner (Northwestern U) while at Sandia.
src/USER-MEAMC: filenames -> commands
6.3.59. USER-MESODPD package¶
Several extensions of the dissipative particle dynamics (DPD) method. Specifically, energy-conserving DPD (eDPD) that can model non-isothermal processes, many-body DPD (mDPD) for simulating vapor-liquid coexistence, and transport DPD (tDPD) for modeling advection-diffusion-reaction systems. The equations of motion of these DPD extensions are integrated through a modified velocity-Verlet (MVV) algorithm.
Author: Zhen Li (Division of Applied Mathematics, Brown University)
src/USER-MESODPD: filenames -> commands
6.3.60. USER-MESONT package¶
USER-MESONT is a LAMMPS package for simulation of nanomechanics of
nanotubes (NTs). The model is based on a coarse-grained representation
of NTs as “flexible cylinders” consisting of a variable number of
segments. Internal interactions within a NT and the van der Waals
interaction between the tubes are described by a mesoscopic force field
designed and parameterized based on the results of atomic-level
molecular dynamics simulations. The description of the force field is
provided in the papers listed below. This package contains two
independent implementations of this model: pair_style mesocnt is a (minimal) C++ implementation, and pair_style
mesont/tpm is a more general and feature rich
implementation based on a Fortran library in the
Download of potential files:
The potential files for these pair styles are very large and thus are not included in the regular downloaded packages of LAMMPS or the git repositories. Instead, they will be automatically downloaded from a web server when the package is installed for the first time.
Authors of the *mesont* styles:
Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia)
Author of the *mesocnt* pair style: Philipp Kloza (U Cambridge)
src/USER-MESONT: filenames -> commands
6.3.61. USER-MOFFF package¶
Pair, angle and improper styles needed to employ the MOF-FF force field by Schmid and coworkers with LAMMPS. MOF-FF is a first principles derived force field with the primary aim to simulate MOFs and related porous framework materials, using spherical Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B 2013, 250, 1128-1141. For the usage of MOF-FF see the example in the example directory as well as the MOF+ website.
Author: Hendrik Heenen (Technical U of Munich), Rochus Schmid (Ruhr-University Bochum).
src/USER-MOFFF: filenames -> commands
6.3.62. USER-MOLFILE package¶
A dump molfile command which uses molfile plugins that are bundled with the VMD molecular visualization and analysis program, to enable LAMMPS to dump snapshots in formats compatible with various molecular simulation tools.
To use this package you must have the desired VMD plugins available on your system.
Note that this package only provides the interface code, not the plugins themselves, which will be accessed when requesting a specific plugin via the dump molfile command. Plugins can be obtained from a VMD installation which has to match the platform that you are using to compile LAMMPS for. By adding plugins to VMD, support for new file formats can be added to LAMMPS (or VMD or other programs that use them) without having to re-compile the application itself. More information about the VMD molfile plugins can be found at http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
Author: Axel Kohlmeyer (Temple U).
src/USER-MOLFILE: filenames -> commands
6.3.63. USER-NETCDF package¶
Dump styles for writing NetCDF formatted dump files. NetCDF is a portable, binary, self-describing file format developed on top of HDF5. The file contents follow the AMBER NetCDF trajectory conventions (http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
To use this package you must have the NetCDF library available on your system.
Note that NetCDF files can be directly visualized with the following tools:
Author: Lars Pastewka (Karlsruhe Institute of Technology).
src/USER-NETCDF: filenames -> commands
6.3.64. USER-OMP package¶
Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and kspace styles which are altered to enable threading on many-core CPUs via OpenMP directives. All of them have an “omp” in their style name. The USER-OMP package page gives details of what hardware and compilers are required on your system, and how to build and use this package. Its styles can be invoked at run time via the “-sf omp” or “-suffix omp” command-line switches. Also see the KOKKOS, OPT, and USER-INTEL packages, which have styles optimized for CPUs.
Author: Axel Kohlmeyer (Temple U).
To enable multi-threading support the compile flag “-fopenmp” and the link flag “-fopenmp” (for GNU compilers, you have to look up the equivalent flags for other compilers) must be used to build LAMMPS. When using Intel compilers, also the “-restrict” flag is required. The USER-OMP package can be compiled without enabling OpenMP; then all code will be compiled as serial and the only improvement over the regular styles are some data access optimization. These flags should be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.omp for an example.
Once you have an appropriate Makefile.machine, you can install/un-install the package and build LAMMPS in the usual manner:
src/USER-OMP: filenames -> commands
Benchmarks page of web site
6.3.65. USER-PHONON package¶
A fix phonon command that calculates dynamical matrices, which can then be used to compute phonon dispersion relations, directly from molecular dynamics simulations. And a dynamical_matrix as well as a third_order command to compute the dynamical matrix and third order tensor from finite differences.
Authors: Ling-Ti Kong (Shanghai Jiao Tong University) for “fix phonon” and Charlie Sievers (UC Davis) for “dynamical_matrix” and “third_order”
src/USER-PHONON: filenames -> commands
6.3.66. USER-PTM package¶
A compute ptm/atom command that calculates local structure characterization using the Polyhedral Template Matching methodology.
Author: Peter Mahler Larsen (MIT).
src/USER-PTM: filenames not starting with ptm_ -> commands
src/USER-PTM: filenames starting with ptm_ -> supporting code
6.3.67. USER-QMMM package¶
To use this package you must have Quantum ESPRESSO (QE) available on your system and include its coupling library in the compilation and then compile LAMMPS as a library. For QM/MM calculations you then build a custom binary with MPI support, that sets up 3 partitions with MPI sub-communicators (for inter- and intra-partition communication) and then calls the corresponding library interfaces on each partition (2x LAMMPS and 1x QE).
The current implementation supports an ONIOM style mechanical coupling and a multi-pole based electrostatic coupling to the Quantum ESPRESSO plane wave DFT package. The QM/MM interface has been written in a manner that coupling to other QM codes should be possible without changes to LAMMPS itself.
Authors: Axel Kohlmeyer (Temple U). Mariella Ippolito and Carlo Cavazzoni (CINECA, Italy)
src/USER-QMMM: filenames -> commands
6.3.68. USER-QTB package¶
Two fixes which provide a self-consistent quantum treatment of vibrational modes in a classical molecular dynamics simulation. By coupling the MD simulation to a colored thermostat, it introduces zero point energy into the system, altering the energy power spectrum and the heat capacity to account for their quantum nature. This is useful when modeling systems at temperatures lower than their classical limits or when temperatures ramp across the classical limits in a simulation.
Author: Yuan Shen (Stanford U).
6.3.69. USER-QUIP package¶
A pair_style quip command which wraps the QUIP libAtoms library, which includes a variety of interatomic potentials, including Gaussian Approximation Potential (GAP) models developed by the Cambridge University group.
To use this package you must have the QUIP libAtoms library available on your system.
Author: Albert Bartok (Cambridge University)
src/USER-QUIP: filenames -> commands
6.3.70. USER-RANN package¶
A pair style for using rapid atomistic neural network (RANN) potentials. These neural network potentials work by first generating a series of symmetry functions from the neighbor list and then using these values as the input layer of a neural network.
This package was written by Christopher Barrett with contributions by Doyl Dickel, Mississippi State University.
src/USER-RANN: filenames -> commands
6.3.71. USER-REACTION package¶
This package allows for complex bond topology changes (reactions) during a running MD simulation, when using classical force fields. Topology changes are defined in pre- and post-reaction molecule templates and can include creation and deletion of bonds, angles, dihedrals, impropers, atom types, bond types, angle types, dihedral types, improper types, and/or atomic charges. Other options currently available include reaction constraints (e.g. angle and Arrhenius constraints), deletion of reaction byproducts or other small molecules, and chiral-sensitive reactions.
Author: Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center.
src/USER-REACTION: filenames -> commands
6.3.72. USER-REAXC package¶
A pair style which implements the ReaxFF potential in C/C++. ReaxFF is a universal reactive force field. See the src/USER-REAXC/README file for more info on differences between the two packages. Also two fixes for monitoring molecules as bonds are created and destroyed.
Author: Hasan Metin Aktulga (MSU) while at Purdue University.
src/USER-REAXC: filenames -> commands
6.3.73. USER-SCAFACOS package¶
A KSpace style which wraps the ScaFaCoS Coulomb solver library to compute long-range Coulombic interactions.
To use this package you must have the ScaFaCoS library available on your system.
Author: Rene Halver (JSC) wrote the scafacos LAMMPS command.
ScaFaCoS itself was developed by a consortium of German research facilities with a BMBF (German Ministry of Science and Education) funded project in 2009-2012. Participants of the consortium were the Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the Forschungszentrum Juelich.
src/USER-SCAFACOS: filenames -> commands
6.3.74. USER-SDPD package¶
A pair style for smoothed dissipative particle dynamics (SDPD), which is an extension of smoothed particle hydrodynamics (SPH) to mesoscale where thermal fluctuations are important (see the USER-SPH package). Also two fixes for moving and rigid body integration of SPH/SDPD particles (particles of atom_style meso).
Author: Morteza Jalalvand (Institute for Advanced Studies in Basic Sciences, Iran).
src/USER-SDPD: filenames -> commands
6.3.75. USER-SMD package¶
An atom style, fixes, computes, and several pair styles which implements smoothed Mach dynamics (SMD) for solids, which is a model related to smoothed particle hydrodynamics (SPH) for liquids (see the USER-SPH package).
This package solves solids mechanics problems via a state of the art stabilized meshless method with hourglass control. It can specify hydrostatic interactions independently from material strength models, i.e. pressure and deviatoric stresses are separated. It provides many material models (Johnson-Cook, plasticity with hardening, Mie-Grueneisen, Polynomial EOS) and allows new material models to be added. It implements rigid boundary conditions (walls) which can be specified as surface geometries from *.STL files.
Author: Georg Ganzenmuller (Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute, Germany).
src/USER-SMD: filenames -> commands
6.3.76. USER-SMTBQ package¶
A pair style which implements a Second Moment Tight Binding model with QEq charge equilibration (SMTBQ) potential for the description of ionocovalent bonds in oxides.
Authors: Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
src/USER-SMTBQ: filenames -> commands
6.3.77. USER-SPH package¶
An atom style, fixes, computes, and several pair styles which implements smoothed particle hydrodynamics (SPH) for liquids. See the related USER-SMD package package for smooth Mach dynamics (SMD) for solids.
This package contains ideal gas, Lennard-Jones equation of states, Tait, and full support for complete (i.e. internal-energy dependent) equations of state. It allows for plain or Monaghans XSPH integration of the equations of motion. It has options for density continuity or density summation to propagate the density field. It has set command options to set the internal energy and density of particles from the input script and allows the same quantities to be output with thermodynamic output or to dump files via the compute property/atom command.
Author: Georg Ganzenmuller (Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute, Germany).
src/USER-SPH: filenames -> commands
6.3.78. USER-TALLY package¶
Several compute styles that can be called when pairwise interactions are calculated to tally information (forces, heat flux, energy, stress, etc) about individual interactions.
Author: Axel Kohlmeyer (Temple U).
src/USER-TALLY: filenames -> commands
6.3.79. USER-UEF package¶
A fix style for the integration of the equations of motion under extensional flow with proper boundary conditions, as well as several supporting compute styles and an output option.
Author: David Nicholson (MIT).
src/USER-UEF: filenames -> commands
6.3.80. USER-VTK package¶
To use this package you must have VTK library available on your system.
Authors: Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
src/USER-VTK: filenames -> commands
6.3.81. USER-YAFF package¶
Some potentials that are also implemented in the Yet Another Force Field (YAFF) code. The expressions and their use are discussed in the following papers
Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) link
Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) link
which discuss the QuickFF methodology.
Author: Steven Vandenbrande.