forked from lijiext/lammps
859 lines
33 KiB
Plaintext
859 lines
33 KiB
Plaintext
"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
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"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
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Section"_Section_accelerate.html :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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4. Packages :h3
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This section gives a quick overview of the add-on packages that extend
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LAMMPS functionality.
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4.1 "Standard packages"_#pkg_1
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4.2 "User packages"_#pkg_2 :all(b)
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LAMMPS includes many optional packages, which are groups of files that
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enable a specific set of features. For example, force fields for
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molecular systems or granular systems are in packages. You can see
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the list of all packages by typing "make package" from within the src
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directory of the LAMMPS distribution.
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See "Section_start 3"_Section_start.html#start_3 of the manual for
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details on how to include/exclude specific packages as part of the
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LAMMPS build process, and for more details about the differences
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between standard packages and user packages.
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Unless otherwise noted below, every package is independent of all the
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others. I.e. any package can be included or excluded in a LAMMPS
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build, independent of all other packages. However, note that some
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packages include commands derived from commands in other packages. If
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the other package is not installed, the derived command from the new
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package will also not be installed when you include the new one.
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E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
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will not be installed as part of the USER-OMP package if the KSPACE
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package is not also installed, since it contains the pair
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lj/cut/coul/long command. If you later install the KSPACE pacakge and
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the USER-OMP package is already installed, both the pair
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lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
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The two tables below list currently available packages in LAMMPS, with
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a one-line descriptions of each. The sections below give a few more
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details, including instructions for building LAMMPS with the package,
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either via the make command or the Make.py tool described in "Section
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2.4"_Section_start.html#start_4.
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:line
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:line
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4.1 Standard packages :h4,link(pkg_1)
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The current list of standard packages is as follows.
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Package, Description, Author(s), Doc page, Example, Library
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ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, -
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BODY, body-style particles, -, "body"_body.html, body, -
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CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
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COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, -
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COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
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CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section_howto 6.25"_Section_howto.html#howto_25, coreshell, -
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DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
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FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, -
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GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu
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GRANULAR, granular systems, -, "Section_howto 6.6"_Section_howto.html#howto_6, pour, -
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KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
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KOKKOS, Kokkos-enabled styles, Trott & Edwards (4), "Section_accelerate"_accelerate_kokkos.html, kokkos, lib/kokkos
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KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
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MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
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MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
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MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
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MOLECULE, molecular system force fields, -, "Section_howto 6.3"_Section_howto.html#howto_3, peptide, -
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OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, -
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PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
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POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
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PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
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REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
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REPLICA, multi-replica methods, -, "Section_howto 6.5"_Section_howto.html#howto_5, tad, -
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RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
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SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
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SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, -
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SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
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VORONOI, Voronoi tesselations, Daniel Schwen (LANL), "compute voronoi/atom"_compute_voronoi_atom.html, -, Voro++
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XTC, dumps in XTC format, -, "dump"_dump.html, -, -
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:tb(ea=c)
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The "Authors" column lists a name(s) if a specific person is
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responible for creating and maintaining the package.
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More details on
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multiple authors are give below.
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(1) The FLD package was created by Amit Kumar and Michael Bybee from
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Jonathan Higdon's group at UIUC.
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(2) The OPT package was created by James Fischer (High Performance
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Technologies), David Richie, and Vincent Natoli (Stone Ridge
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Technolgy).
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(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
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and Ellad Tadmor (U Minn).
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(4) The KOKKOS package was created primarily by Christian Trott
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(Sandia). It uses the Kokkos library which was developed by Carter
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Edwards, Christian, and collaborators at Sandia.
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The "Doc page" column links to either a portion of the
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"Section_howto"_Section_howto.html of the manual, or an input script
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command implemented as part of the package.
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The "Example" column is a sub-directory in the examples directory of
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the distribution which has an input script that uses the package.
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E.g. "peptide" refers to the examples/peptide directory.
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The "Library" column lists an external library which must be built
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first and which LAMMPS links to when it is built. If it is listed as
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lib/package, then the code for the library is under the lib directory
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of the LAMMPS distribution. See the lib/package/README file for info
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on how to build the library. If it is not listed as lib/package, then
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it is a third-party library not included in the LAMMPS distribution.
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See the src/package/README or src/package/Makefile.lammps file for
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info on where to download the library. "Section
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start"_Section_start.html#start_3_3 of the manual also gives details
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on how to build LAMMPS with both kinds of auxiliary libraries.
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Except where explained below, all of these packages can be installed,
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and LAMMPS re-built, by issuing these commands from the src dir.
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make yes-package
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make machine
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or
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Make.py -p package -a machine :pre
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To un-install the package and re-build LAMMPS without it:
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make no-package
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make machine
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or
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Make.py -p ^package -a machine :pre
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"Package" is the name of the package in lower-case letters,
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e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or
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serial.
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:line
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:line
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Build instructions for COMPRESS package :h4
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:line
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Build instructions for GPU package :h4
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:line
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Build instructions for KIM package :h4
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:line
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Build instructions for KOKKOS package :h4
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:line
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Build instructions for KSPACE package :h4
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:line
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Build instructions for MEAM package :h4
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:line
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Build instructions for POEMS package :h4
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:line
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Build instructions for PYTHON package :h4
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:line
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Build instructions for REAX package :h4
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:line
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Build instructions for VORONOI package :h4
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:line
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Build instructions for XTC package :h4
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:line
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:line
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4.2 User packages :h4,link(pkg_2)
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The current list of user-contributed packages is as follows:
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Package, Description, Author(s), Doc page, Example, Pic/movie, Library
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USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
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USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
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USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
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USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
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USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
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USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
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USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
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USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
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USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
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USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
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USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
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USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
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USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -
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USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
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USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
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USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -
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USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
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USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
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USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix_qbmsst"_fix_qbmsst.html, qtb, -, -
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USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip
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USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
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USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, -
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USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, -
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USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
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USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, -
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:tb(ea=c)
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:link(atc,http://lammps.sandia.gov/pictures.html#atc)
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:link(cg,http://lammps.sandia.gov/pictures.html#cg)
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:link(eff,http://lammps.sandia.gov/movies.html#eff)
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:link(sph,http://lammps.sandia.gov/movies.html#sph)
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:link(VMD,http://www.ks.uiuc.edu/Research/vmd)
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The "Authors" column lists a name(s) if a specific person is
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responible for creating and maintaining the package.
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(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
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Jon Zimmerman (Sandia).
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(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
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the colvars module library written by Giacomo Fiorin (Temple U) and
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Jerome Henin (LISM, Marseille, France).
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(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
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Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
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(U Blaise Pascal).
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(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
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Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
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If the Library is not listed as lib/package, then it is a third-party
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library not included in the LAMMPS distribution. See the
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src/package/Makefile.lammps file for info on where to download the
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library from.
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The "Doc page" column links to either a portion of the
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"Section_howto"_Section_howto.html of the manual, or an input script
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command implemented as part of the package, or to additional
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documentation provided within the package.
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The "Example" column is a sub-directory in the examples directory of
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the distribution which has an input script that uses the package.
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E.g. "peptide" refers to the examples/peptide directory. USER/cuda
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refers to the examples/USER/cuda directory.
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The "Library" column lists an external library which must be built
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first and which LAMMPS links to when it is built. If it is listed as
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lib/package, then the code for the library is under the lib directory
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of the LAMMPS distribution. See the lib/package/README file for info
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on how to build the library. If it is not listed as lib/package, then
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it is a third-party library not included in the LAMMPS distribution.
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See the src/package/Makefile.lammps file for info on where to download
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the library. "Section start"_Section_start.html#start_3_3 of the
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manual also gives details on how to build LAMMPS with both kinds of
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auxiliary libraries.
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Except where explained below, all of these packages can be installed,
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and LAMMPS re-built, by issuing these commands from the src dir.
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make yes-user-package
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make machine
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or
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Make.py -p package -a machine :pre
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To un-install the package and re-build LAMMPS without it:
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make no-user-package
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make machine
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or
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Make.py -p ^package -a machine :pre
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"Package" is the name of the package (in this case without the user
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prefix) in lower-case letters, e.g. drude or phonon, and "machine" is
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the build target, e.g. mpi or serial.
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:line
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:line
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USER-ATC package :h4
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This package implements a "fix atc" command which can be used in a
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LAMMPS input script. This fix can be employed to either do concurrent
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coupling of MD with FE-based physics surrogates or on-the-fly
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post-processing of atomic information to continuum fields.
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See the doc page for the fix atc command to get started. At the
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bottom of the doc page are many links to additional documentation
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contained in the doc/USER/atc directory.
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There are example scripts for using this package in examples/USER/atc.
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This package uses an external library in lib/atc which must be
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compiled before making LAMMPS. See the lib/atc/README file and the
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LAMMPS manual for information on building LAMMPS with external
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libraries.
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The primary people who created this package are Reese Jones (rjones at
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sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
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Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
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you have questions.
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:line
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USER-AWPMD package :h4
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This package contains a LAMMPS implementation of the Antisymmetrized
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Wave Packet Molecular Dynamics (AWPMD) method.
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See the doc page for the pair_style awpmd/cut command to get started.
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There are example scripts for using this package in examples/USER/awpmd.
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This package uses an external library in lib/awpmd which must be
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compiled before making LAMMPS. See the lib/awpmd/README file and the
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LAMMPS manual for information on building LAMMPS with external
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libraries.
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The person who created this package is Ilya Valuev at the JIHT in
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Russia (valuev at physik.hu-berlin.de). Contact him directly if you
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have questions.
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:line
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USER-CG-CMM package :h4
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This package implements 3 commands which can be used in a LAMMPS input
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script:
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pair_style lj/sdk
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pair_style lj/sdk/coul/long
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angle_style sdk :ul
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These styles allow coarse grained MD simulations with the
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parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
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(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
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and charged amino acids.
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See the doc pages for these commands for details.
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There are example scripts for using this package in
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examples/USER/cg-cmm.
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This is the second generation implementation reducing the the clutter
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of the previous version. For many systems with electrostatics, it will
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be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
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instead of the combined lj/sdk/coul/long style. since the number of
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charged atom types is usually small. For any other coulomb
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interactions this is now required. To exploit this property, the use
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of the kspace_style pppm/cg is recommended over regular pppm. For all
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new styles, input file backward compatibility is provided. The old
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implementation is still available through appending the /old
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suffix. These will be discontinued and removed after the new
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implementation has been fully validated.
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The current version of this package should be considered beta
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quality. The CG potentials work correctly for "normal" situations, but
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have not been testing with all kinds of potential parameters and
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simulation systems.
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The person who created this package is Axel Kohlmeyer at Temple U
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(akohlmey at gmail.com). Contact him directly if you have questions.
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:line
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USER-COLVARS package :h4
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This package implements the "fix colvars" command which can be
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used in a LAMMPS input script.
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This fix allows to use "collective variables" to implement
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Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
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Sampling and Restraints. This code consists of two parts:
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A portable collective variable module library written and maintained
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by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
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Jerome Henin (LISM, CNRS, Marseille, France). This code is located in
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the directory lib/colvars and needs to be compiled first. The colvars
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fix and an interface layer, exchanges information between LAMMPS and
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the collective variable module. :ul
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See the doc page of "fix colvars"_fix_colvars.html for more details.
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There are example scripts for using this package in
|
|
examples/USER/colvars
|
|
|
|
This is a very new interface that does not yet support all
|
|
features in the module and will see future optimizations
|
|
and improvements. The colvars module library is also available
|
|
in NAMD has been thoroughly used and tested there. Bugs and
|
|
problems are likely due to the interface layers code.
|
|
Thus the current version of this package should be considered
|
|
beta quality.
|
|
|
|
The person who created this package is Axel Kohlmeyer at Temple U
|
|
(akohlmey at gmail.com). Contact him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-CUDA package :h4
|
|
|
|
This package provides acceleration of various LAMMPS pair styles, fix
|
|
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
|
|
GPUs.
|
|
|
|
See this section of the manual to get started:
|
|
|
|
"Section_accelerate"_Section_accelerate.html#acc_7
|
|
|
|
There are example scripts for using this package in
|
|
examples/USER/cuda.
|
|
|
|
This package uses an external library in lib/cuda which must be
|
|
compiled before making LAMMPS. See the lib/cuda/README file and the
|
|
LAMMPS manual for information on building LAMMPS with external
|
|
libraries.
|
|
|
|
The person who created this package is Christian Trott at the
|
|
University of Technology Ilmenau, Germany (christian.trott at
|
|
tu-ilmenau.de). Contact him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-DIFFRACTION package :h4
|
|
|
|
This package contains the commands neeed to calculate x-ray and
|
|
electron diffraction intensities based on kinematic diffraction
|
|
theory.
|
|
|
|
See these doc pages and their related commands to get started:
|
|
|
|
"compute xrd"_compute_xrd.html
|
|
"compute saed"_compute_saed.html
|
|
"fix saed/vtk"_fix_saed_vtk.html :ul
|
|
|
|
The person who created this package is Shawn P. Coleman
|
|
(shawn.p.coleman8.ctr at mail.mil) while at the University of
|
|
Arkansas. Contact him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-DRUDE package :h4
|
|
|
|
This package implements methods for simulating polarizable systems
|
|
in LAMMPS using thermalized Drude oscillators.
|
|
|
|
See these doc pages and their related commands to get started:
|
|
|
|
"Drude tutorial"_tutorial_drude.html
|
|
"fix drude"_fix_drude.html
|
|
"compute temp/drude"_compute_temp_drude.html
|
|
"fix langevin/drude"_fix_langevin_drude.html
|
|
"fix drude/transform/..."_fix_drude_transform.html
|
|
"pair thole"_pair_thole.html :ul
|
|
|
|
There are auxiliary tools for using this package in tools/drude.
|
|
|
|
The person who created this package is Alain Dequidt at Universite
|
|
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
|
|
Contact him directly if you have questions. Co-authors: Julien Devemy,
|
|
Agilio Padua.
|
|
|
|
:line
|
|
|
|
USER-EFF package :h4
|
|
|
|
This package contains a LAMMPS implementation of the electron Force
|
|
Field (eFF) currently under development at Caltech, 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.
|
|
|
|
eFF can be viewed as an approximation to QM wave packet dynamics and
|
|
Fermionic molecular dynamics, combining the ability of electronic
|
|
structure methods to describe atomic structure, bonding, and chemistry
|
|
in materials, and of plasma methods to describe nonequilibrium
|
|
dynamics of large systems with a large number of highly excited
|
|
electrons. We classify it as a mixed QM-classical approach rather than
|
|
a conventional force field method, which introduces QM-based terms (a
|
|
spin-dependent repulsion term to account for the Pauli exclusion
|
|
principle and the electron wavefunction kinetic energy associated with
|
|
the Heisenberg principle) that reduce, along with classical
|
|
electrostatic terms between nuclei and electrons, to the sum of a set
|
|
of effective pairwise potentials. This makes eFF uniquely suited to
|
|
simulate materials over a wide range of temperatures and pressures
|
|
where electronically excited and ionized states of matter can occur
|
|
and coexist.
|
|
|
|
The necessary customizations to the LAMMPS core are in place to
|
|
enable the correct handling of explicit electron properties during
|
|
minimization and dynamics.
|
|
|
|
See the doc page for the pair_style eff/cut command to get started.
|
|
|
|
There are example scripts for using this package in
|
|
examples/USER/eff.
|
|
|
|
There are auxiliary tools for using this package in tools/eff.
|
|
|
|
The person who created this package is Andres Jaramillo-Botero at
|
|
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
|
|
have questions.
|
|
|
|
:line
|
|
|
|
USER-FEP package :h4
|
|
|
|
This package provides methods for performing free energy perturbation
|
|
simulations with soft-core pair potentials in LAMMPS.
|
|
|
|
See these doc pages and their related commands to get started:
|
|
|
|
"fix adapt/fep"_fix_adapt_fep.html
|
|
"compute fep"_compute_fep.html
|
|
"soft pair styles"_pair_lj_soft.html :ul
|
|
|
|
The person who created this package is Agilio Padua at Universite
|
|
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
|
|
Contact him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-H5MD package :h4
|
|
|
|
This package contains a "dump h5md"_dump_h5md.html command for
|
|
performing a dump of atom properties in HDF5 format. "HDF5
|
|
files"_HDF5 are binary, portable and self-describing and can be
|
|
examined and used by a variety of auxiliary tools. The output HDF5
|
|
files are structured in a format called H5MD, which was designed to
|
|
store molecular data, and can be used and produced by various MD and
|
|
MD-related codes. The "dump h5md"_doc/dump_h5md.html command gives a
|
|
citation to a paper describing the format.
|
|
|
|
:link(HDF5,http://www.hdfgroup.org/HDF5/)
|
|
|
|
The person who created this package and the underlying H5MD format is
|
|
Pierre de Buyl at KU Leuven (see http://pdebuyl.be). Contact him
|
|
directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-INTEL package :h4
|
|
|
|
This package provides options for performing neighbor list and
|
|
non-bonded force calculations in single, mixed, or double precision
|
|
and also a capability for accelerating calculations with an
|
|
Intel(R) Xeon Phi(TM) coprocessor.
|
|
|
|
See this section of the manual to get started:
|
|
|
|
"Section_accelerate"_Section_accelerate.html#acc_9
|
|
|
|
The person who created this package is W. Michael Brown at Intel
|
|
(michael.w.brown at intel.com). Contact him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-LB package :h4
|
|
|
|
This package contains a LAMMPS implementation of a background
|
|
Lattice-Boltzmann fluid, which can be used to model MD particles
|
|
influenced by hydrodynamic forces.
|
|
|
|
See this doc page and its related commands to get started:
|
|
|
|
"fix lb/fluid"_fix_lb_fluid.html
|
|
|
|
The people who created this package are Frances Mackay (fmackay at
|
|
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
|
|
Western Ontario. Contact them directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-MGPT package :h4
|
|
|
|
This package contains a fast implementation for LAMMPS of
|
|
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 Lawrence
|
|
Livermore National Lab (LLNL).
|
|
|
|
In the general matrix representation of MGPT, which can also be
|
|
applied to f-band actinide metals, the multi-ion potentials are
|
|
evaluated on the fly during a simulation through d- or f-state matrix
|
|
multiplication, and the forces that move the ions are determined
|
|
analytically. The {mgpt} pair style in this package calculates forces
|
|
and energies using an optimized matrix-MGPT algorithm due to Tomas
|
|
Oppelstrup at LLNL.
|
|
|
|
See this doc page to get started:
|
|
|
|
"pair_style mgpt"_pair_mgpt.html
|
|
|
|
The persons who created the USER-MGPT package are Tomas Oppelstrup
|
|
(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov)
|
|
Contact them directly if you have any questions.
|
|
|
|
:line
|
|
|
|
USER-MISC package :h4
|
|
|
|
The files in this package are a potpourri of (mostly) unrelated
|
|
features contributed to LAMMPS by users. Each feature is a single
|
|
pair of files (*.cpp and *.h).
|
|
|
|
More information about each feature can be found by reading its doc
|
|
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
|
|
input script commands is as follows:
|
|
|
|
"Section_commands"_Section_commands.html#cmd_5
|
|
|
|
User-contributed features are listed at the bottom of the fix,
|
|
compute, pair, etc sections.
|
|
|
|
The list of features and author of each is given in the
|
|
src/USER-MISC/README file.
|
|
|
|
You should contact the author directly if you have specific questions
|
|
about the feature or its coding.
|
|
|
|
:line
|
|
|
|
USER-MOLFILE package :h4
|
|
|
|
This package contains a dump molfile command which uses molfile
|
|
plugins that are bundled with the
|
|
"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
|
|
analysis program, to enable LAMMPS to dump its information in formats
|
|
compatible with various molecular simulation tools.
|
|
|
|
The package only provides the interface code, not the plugins. These
|
|
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 recompile the
|
|
application itself.
|
|
|
|
See this doc page to get started:
|
|
|
|
"dump molfile"_dump_molfile.html#acc_5
|
|
|
|
The person who created this package is Axel Kohlmeyer at Temple U
|
|
(akohlmey at gmail.com). Contact him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-OMP package :h4
|
|
|
|
This package provides OpenMP multi-threading support and
|
|
other optimizations of various LAMMPS pair styles, dihedral
|
|
styles, and fix styles.
|
|
|
|
See this section of the manual to get started:
|
|
|
|
"Section_accelerate"_Section_accelerate.html#acc_5
|
|
|
|
The person who created this package is Axel Kohlmeyer at Temple U
|
|
(akohlmey at gmail.com). Contact him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-PHONON package :h4
|
|
|
|
This package contains a fix phonon command that calculates dynamical
|
|
matrices, which can then be used to compute phonon dispersion
|
|
relations, directly from molecular dynamics simulations.
|
|
|
|
See this doc page to get started:
|
|
|
|
"fix phonon"_fix_phonon.html
|
|
|
|
The person who created this package is Ling-Ti Kong (konglt at
|
|
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
|
|
if you have questions.
|
|
|
|
:line
|
|
|
|
USER-QMMM package :h4
|
|
|
|
This package provides a fix qmmm command which allows LAMMPS to be
|
|
used in a QM/MM simulation, currently only in combination with pw.x
|
|
code from the "Quantum ESPRESSO"_espresso package.
|
|
|
|
:link(espresso,http://www.quantum-espresso.org)
|
|
|
|
The current implementation only supports an ONIOM style mechanical
|
|
coupling to the Quantum ESPRESSO plane wave DFT package.
|
|
Electrostatic coupling is in preparation and the interface has been
|
|
written in a manner that coupling to other QM codes should be possible
|
|
without changes to LAMMPS itself.
|
|
|
|
See this doc page to get started:
|
|
|
|
"fix qmmm"_fix_qmmm.html
|
|
|
|
as well as the lib/qmmm/README file.
|
|
|
|
The person who created this package is Axel Kohlmeyer at Temple U
|
|
(akohlmey at gmail.com). Contact him directly if you have questions.
|
|
|
|
:line
|
|
|
|
USER-QTB package :h4
|
|
|
|
This package provides a self-consistent quantum treatment of the
|
|
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, alter the energy power spectrum and the
|
|
heat capacity towards their quantum nature. This package could be of
|
|
interest if one wants to model systems at temperatures lower than
|
|
their classical limits or when temperatures ramp up across the
|
|
classical limits in the simulation.
|
|
|
|
See these two doc pages to get started:
|
|
|
|
"fix qtb"_fix_qtb.html provides quantum nulcear correction through a
|
|
colored thermostat and can be used with other time integration schemes
|
|
like "fix nve"_fix_nve.html or "fix nph"_fix_nh.html.
|
|
|
|
"fix qbmsst"_fix_qbmsst.html enables quantum nuclear correction of a
|
|
multi-scale shock technique simulation by coupling the quantum thermal
|
|
bath with the shocked system.
|
|
|
|
The person who created this package is Yuan Shen (sy0302 at
|
|
stanford.edu) at Stanford University. Contact him directly if you
|
|
have questions.
|
|
|
|
:line
|
|
|
|
USER-REAXC package :h4
|
|
|
|
This package contains a implementation for LAMMPS of the ReaxFF force
|
|
field. ReaxFF uses distance-dependent bond-order functions to
|
|
represent the contributions of chemical bonding to the potential
|
|
energy. It was originally developed by Adri van Duin and the Goddard
|
|
group at CalTech.
|
|
|
|
The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
|
|
C, should give identical or very similar results to pair_style reax,
|
|
which is a ReaxFF implementation on top of a Fortran library, a
|
|
version of which library was originally authored by Adri van Duin.
|
|
|
|
The reax/c version should be somewhat faster and more scalable,
|
|
particularly with respect to the charge equilibration calculation. It
|
|
should also be easier to build and use since there are no complicating
|
|
issues with Fortran memory allocation or linking to a Fortran library.
|
|
|
|
For technical details about this implemention of ReaxFF, see
|
|
this paper:
|
|
|
|
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
|
|
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
|
|
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
|
|
|
|
See the doc page for the pair_style reax/c command for details
|
|
of how to use it in LAMMPS.
|
|
|
|
The person who created this package is Hasan Metin Aktulga (hmaktulga
|
|
at lbl.gov), while at Purdue University. Contact him directly, or
|
|
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
|
|
questions.
|
|
|
|
:line
|
|
|
|
USER-SMD package :h4
|
|
|
|
This package implements smoothed Mach dynamics (SMD) in
|
|
LAMMPS. Currently, the package has the following features:
|
|
|
|
* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
|
|
|
|
* Also solves solids mechanics problems via a state of the art
|
|
stabilized meshless method with hourglass control.
|
|
|
|
* Can specify hydrostatic interactions independently from material
|
|
strength models, i.e. pressure and deviatoric stresses are separated.
|
|
|
|
* Many material models available (Johnson-Cook, plasticity with
|
|
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
|
|
material models.
|
|
|
|
* Rigid boundary conditions (walls) can be loaded as surface geometries
|
|
from *.STL files.
|
|
|
|
See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.
|
|
|
|
There are example scripts for using this package in examples/USER/smd.
|
|
|
|
The person who created this package is Georg Ganzenmuller at the
|
|
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
|
|
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
|
|
you have questions.
|
|
|
|
:line
|
|
|
|
USER-SMTBQ package :h4
|
|
|
|
This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
|
|
potential for the description of ionocovalent bonds in oxides.
|
|
|
|
There are example scripts for using this package in
|
|
examples/USER/smtbq.
|
|
|
|
See this doc page to get started:
|
|
|
|
"pair_style smtbq"_pair_smtbq.html
|
|
|
|
The persons who created the USER-SMTBQ package are Nicolas Salles,
|
|
Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
|
|
these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact
|
|
them directly if you have any questions.
|
|
|
|
:line
|
|
|
|
USER-SPH package :h4
|
|
|
|
This package implements smoothed particle hydrodynamics (SPH) in
|
|
LAMMPS. Currently, the package has the following features:
|
|
|
|
* Tait, ideal gas, Lennard-Jones equation of states, full support for
|
|
complete (i.e. internal-energy dependent) equations of state
|
|
|
|
* Plain or Monaghans XSPH integration of the equations of motion
|
|
|
|
* Density continuity or density summation to propagate the density field
|
|
|
|
* Commands to set internal energy and density of particles from the
|
|
input script
|
|
|
|
* Output commands to access internal energy and density for dumping and
|
|
thermo output
|
|
|
|
See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.
|
|
|
|
There are example scripts for using this package in examples/USER/sph.
|
|
|
|
The person who created this package is Georg Ganzenmuller at the
|
|
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
|
|
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
|
|
you have questions.
|