forked from lijiext/lammps
576 lines
24 KiB
Plaintext
576 lines
24 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 in LAMMPS.
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Below, the packages currently availabe in LAMMPS are listed. For
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standard packages, just a one-line description is given. For user
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packages, more details are provided.
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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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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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(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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: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 (2), "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 (3), "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-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), "fix adapt/fep"_fix_adapt.html, USER/fep, -, -
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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-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-QUIP, QM/MM coupling, Albert Bartok-Partay (U Cambridge), "fix quip"_fix_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-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_USER/sph/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
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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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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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(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
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Jon Zimmerman (Sandia).
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(3) 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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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 witht he 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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More details on each package, from the USER-*/README file is given
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below.
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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
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examples/USER/colvars
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This is a very new interface that does not yet support all
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features in the module and will see future optimizations
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and improvements. The colvars module library is also available
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in NAMD has been thoroughly used and tested there. Bugs and
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problems are likely due to the interface layers code.
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Thus the current version of this package should be considered
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beta quality.
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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-CUDA package :h4
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This package provides acceleration of various LAMMPS pair styles, fix
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styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
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GPUs.
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See this section of the manual to get started:
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"Section_accelerate"_Section_accelerate.html#acc_7
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There are example scripts for using this package in
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examples/USER/cuda.
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This package uses an external library in lib/cuda which must be
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compiled before making LAMMPS. See the lib/cuda/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 Christian Trott at the
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University of Technology Ilmenau, Germany (christian.trott at
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tu-ilmenau.de). Contact him directly if you have questions.
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:line
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USER-EFF package :h4
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This package contains a LAMMPS implementation of the electron Force
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Field (eFF) currently under development at Caltech, as described in
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A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
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2010. The eFF potential was first introduced by Su and Goddard, in
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2007.
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eFF can be viewed as an approximation to QM wave packet dynamics and
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Fermionic molecular dynamics, combining the ability of electronic
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structure methods to describe atomic structure, bonding, and chemistry
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in materials, and of plasma methods to describe nonequilibrium
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dynamics of large systems with a large number of highly excited
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electrons. We classify it as a mixed QM-classical approach rather than
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a conventional force field method, which introduces QM-based terms (a
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spin-dependent repulsion term to account for the Pauli exclusion
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principle and the electron wavefunction kinetic energy associated with
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the Heisenberg principle) that reduce, along with classical
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electrostatic terms between nuclei and electrons, to the sum of a set
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of effective pairwise potentials. This makes eFF uniquely suited to
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simulate materials over a wide range of temperatures and pressures
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where electronically excited and ionized states of matter can occur
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and coexist.
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The necessary customizations to the LAMMPS core are in place to
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enable the correct handling of explicit electron properties during
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minimization and dynamics.
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See the doc page for the pair_style eff/cut command to get started.
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There are example scripts for using this package in
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examples/USER/eff.
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There are auxiliary tools for using this package in tools/eff.
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The person who created this package is Andres Jaramillo-Botero at
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CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
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have questions.
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:line
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USER-FEP package :h4
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This package provides methods for performing free energy perturbation
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simulations with soft-core pair potentials in LAMMPS.
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See these doc pages and their related commands to get started:
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"fix adapt/fep"_fix_adapt_fep.html
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"compute fep"_compute_fep.html
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"soft pair styles"_pair_lj_soft.html :ul
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The person who created this package is Agilio Padua at Universite
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Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
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Contact him directly if you have questions.
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:line
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USER-INTEL package :h4
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This package provides options for performing neighbor list and
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non-bonded force calculations in single, mixed, or double precision
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and also a capability for accelerating calculations with an
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Intel(R) Xeon Phi(TM) coprocessor.
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See this section of the manual to get started:
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"Section_accelerate"_Section_accelerate.html#acc_9
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The person who created this package is W. Michael Brown at Intel
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(michael.w.brown at intel.com). Contact him directly if you have questions.
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:line
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USER-LB package :h4
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This package contains a LAMMPS implementation of a background
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Lattice-Boltzmann fluid, which can be used to model MD particles
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influenced by hydrodynamic forces.
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See this doc page and its related commands to get started:
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"fix lb/fluid"_fix_lb_fluid.html
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The people who created this package are Frances Mackay (fmackay at
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uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
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Western Ontario. Contact them directly if you have questions.
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:line
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USER-MISC package :h4
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The files in this package are a potpourri of (mostly) unrelated
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features contributed to LAMMPS by users. Each feature is a single
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pair of files (*.cpp and *.h).
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More information about each feature can be found by reading its doc
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page in the LAMMPS doc directory. The doc page which lists all LAMMPS
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input script commands is as follows:
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"Section_commands"_Section_commands.html#cmd_5
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User-contributed features are listed at the bottom of the fix,
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compute, pair, etc sections.
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The list of features and author of each is given in the
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src/USER-MISC/README file.
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You should contact the author directly if you have specific questions
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about the feature or its coding.
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:line
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USER-MOLFILE package :h4
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This package contains a dump molfile command which uses molfile
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plugins that are bundled with the
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"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
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analysis program, to enable LAMMPS to dump its information in formats
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compatible with various molecular simulation tools.
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The package only provides the interface code, not the plugins. These
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can be obtained from a VMD installation which has to match the
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platform that you are using to compile LAMMPS for. By adding plugins
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to VMD, support for new file formats can be added to LAMMPS (or VMD or
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other programs that use them) without having to recompile the
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application itself.
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See this doc page to get started:
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"dump molfile"_dump_molfile.html#acc_5
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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-OMP package :h4
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This package provides OpenMP multi-threading support and
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other optimizations of various LAMMPS pair styles, dihedral
|
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styles, and fix styles.
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See this section of the manual to get started:
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"Section_accelerate"_Section_accelerate.html#acc_5
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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-PHONON package :h4
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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.
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See this doc page to get started:
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"fix phonon"_fix_phonon.html
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The person who created this package is Ling-Ti Kong (konglt at
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sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
|
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if you have questions.
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:line
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USER-QMMM package :h4
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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
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|
code from the "Quantum ESPRESSO"_espresso package.
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|
:link(espresso,http://www.quantum-espresso.org)
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|
|
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.
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|
See this doc page to get started:
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"fix qmmm"_fix_qmmm.html
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as well as the lib/qmmm/README file.
|
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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.
|
|
|
|
:line
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|
USER-REAXC package :h4
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|
|
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.
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|
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.
|
|
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|
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:
|
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|
|
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).
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|
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
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|
|
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/USER/sph/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.
|