Section_packages.txt
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Section_packages.txt
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			4. Packages :h3

			This section gives an overview of the optional packages that extend
			LAMMPS functionality with instructions on how to build LAMMPS with
			each of them. Packages are groups of files that enable a specific set
			of features. For example, force fields for molecular systems or
			granular systems are in packages. You can see the list of all
			packages and "make" commands to manage them by typing "make package"
			from within the src directory of the LAMMPS distribution. "Section
			2.3"_Section_start.html#start_3 gives general info on how to install
			and un-install packages as part of the LAMMPS build process.

			There are two kinds of packages in LAMMPS, standard and user packages:

			"Table of standard packages"_#table_standard
			"Table of user packages"_#table_user :ul

			Either of these kinds of packages may work as is, may require some
			additional code compiled located in the lib folder, or may require
			an external library to be downloaded, compiled, installed, and LAMMPS
			configured to know about its location and additional compiler flags.
			You can often do the build of the internal or external libraries
			in one step by typing "make lib-name args='...'" from the src dir,
			with appropriate arguments included in args='...'. If you just type
			"make lib-name" you should see a help message about supported flags
			and some examples. For more details about this, please study the
			tables below and the sections about the individual packages.

			Standard packages are supported by the LAMMPS developers and are
			written in a syntax and style consistent with the rest of LAMMPS.
			This means the developers will answer questions about them, debug and
			fix them if necessary, and keep them compatible with future changes to
			LAMMPS.

			User packages have been contributed by users, and begin with the
			"user" prefix. If they are a single command (single file), they are
			typically in the user-misc package. User packages don't necessarily
			meet the requirements of the standard packages. This means the
			developers will try to keep things working and usually can answer
			technical questions about compiling the package. If you have problems
			using a feature provided in a user package, you may need to contact
			the contributor directly to get help. Information on how to submit
			additions you make to LAMMPS as single files or as a standard or user
			package are given in "this section"_Section_modify.html#mod_15 of the
			manual.

			Following the next two tables is a sub-section for each package. It
			lists authors (if applicable) and summarizes the package contents. It
			has specific instructions on how to install the package, including (if
			necessary) downloading or building any extra library it requires. It
			also gives links to documentation, example scripts, and
			pictures/movies (if available) that illustrate use of the package.

			NOTE: To see the complete list of commands a package adds to LAMMPS,
			just look at the files in its src directory, e.g. "ls src/GRANULAR".
			Files with names that start with fix, compute, atom, pair, bond,
			angle, etc correspond to commands with the same style names.

			In these two tables, the "Example" column is a sub-directory in the
			examples directory of the distribution which has an input script that
			uses the package. E.g. "peptide" refers to the examples/peptide
			directory; USER/atc refers to the examples/USER/atc directory. The
			"Library" column indicates whether an extra library is needed to build
			and use the package:

			dash = no library
			sys = system library: you likely have it on your machine
			int = internal library: provided with LAMMPS, but you may need to build it
			ext = external library: you will need to download and install it on your machine :ul

			:line
			:line

			[Standard packages] :link(table_standard),p

			Package, Description, Doc page, Example, Library
			"ASPHERE"_#ASPHERE, aspherical particle models, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, -
			"BODY"_#BODY, body-style particles, "body"_body.html, body, -
			"CLASS2"_#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
			"COLLOID"_#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
			"COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
			"CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
			"DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
			"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
			"GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
			"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
			"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
			"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
			"LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
			"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
			"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
			"MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
			"MISC"_#MISC, miscellanous single-file commands, -, -, -
			"MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
			"MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
			"MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
			"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
			"PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
			"POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
			"PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
			"QEQ"_#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
			"REAX"_#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
			"REPLICA"_#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
			"RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
			"SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
			"SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
			"SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
			"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)

			[USER packages] :link(table_user),p

			Package, Description, Doc page, Example, Library
			"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
			"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
			"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
			"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
			"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
			"USER-DIFFRACTION"_#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
			"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
			"USER-DRUDE"_#USER-DRUDE, Drude oscillators, "tutorial"_tutorial_drude.html, USER/drude, -
			"USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
			"USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
			"USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
			"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
			"USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
			"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
			"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
			"USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
			"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
			"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
			"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
			"USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
			"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
			"USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
			"USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
			"USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
			"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
			"USER-REAXC"_#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
			"USER-SMD"_#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
			"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
			"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
			"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
			"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
			"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)

			:line
			:line

			ASPHERE package :link(ASPHERE),h4

			[Contents:]

			Computes, time-integration fixes, and pair styles for aspherical
			particle models including ellipsoids, 2d lines, and 3d triangles.

			[Install or un-install:]

			make yes-asphere
			make machine :pre

			make no-asphere
			make machine :pre

			[Supporting info:]

			src/ASPHERE: filenames -> commands
			"Section 6.14"_Section_howto.html#howto_14
			"pair_style gayberne"_pair_gayberne.html
			"pair_style resquared"_pair_resquared.html
			"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf
			"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf
			examples/ASPHERE
			examples/ellipse
			http://lammps.sandia.gov/movies.html#line
			http://lammps.sandia.gov/movies.html#tri :ul

			:line

			BODY package :link(BODY),h4

			[Contents:]

			Body-style particles with internal structure. Computes,
			time-integration fixes, pair styles, as well as the body styles
			themselves. See the "body"_body.html doc page for an overview.

			[Install or un-install:]

			make yes-body
			make machine :pre

			make no-body
			make machine :pre

			[Supporting info:]

			src/BODY filenames -> commands
			"body"_body.html
			"atom_style body"_atom_style.html
			"fix nve/body"_fix_nve_body.html
			"pair_style body"_pair_body.html
			examples/body :ul

			:line

			CLASS2 package :link(CLASS2),h4

			[Contents:]

			Bond, angle, dihedral, improper, and pair styles for the COMPASS
			CLASS2 molecular force field.

			[Install or un-install:]

			make yes-class2
			make machine :pre

			make no-class2
			make machine :pre

			[Supporting info:]

			src/CLASS2: filenames -> commands
			"bond_style class2"_bond_class2.html
			"angle_style class2"_angle_class2.html
			"dihedral_style class2"_dihedral_class2.html
			"improper_style class2"_improper_class2.html
			"pair_style lj/class2"_pair_class2.html :ul

			:line

			COLLOID package :link(COLLOID),h4

			[Contents:]

			Coarse-grained finite-size colloidal particles. Pair stayle and fix
			wall styles for colloidal interactions. Includes the Fast Lubrication
			Dynamics (FLD) method for hydrodynamic interactions, which is a
			simplified approximation to Stokesian dynamics.

			[Authors:] This package includes Fast Lubrication Dynamics pair styles
			which were created by Amit Kumar and Michael Bybee from Jonathan
			Higdon's group at UIUC.

			[Install or un-install:]

			make yes-colloid
			make machine :pre

			make no-colloid
			make machine :pre

			[Supporting info:]

			src/COLLOID: filenames -> commands
			"fix wall/colloid"_fix_wall.html
			"pair_style colloid"_pair_colloid.html
			"pair_style yukawa/colloid"_pair_yukawa_colloid.html
			"pair_style brownian"_pair_brownian.html
			"pair_style lubricate"_pair_lubricate.html
			"pair_style lubricateU"_pair_lubricateU.html
			examples/colloid
			examples/srd :ul

			:line

			COMPRESS package :link(COMPRESS),h4

			[Contents:]

			Compressed output of dump files via the zlib compression library,
			using dump styles with a "gz" in their style name.

			To use this package you must have the zlib compression library
			available on your system.

			[Author:] Axel Kohlmeyer (Temple U).

			[Install or un-install:]

			Note that building with this package assumes you have the zlib
			compression library available on your system. The LAMMPS build uses
			the settings in the lib/compress/Makefile.lammps file in the
			compile/link process. You should only need to edit this file if the
			LAMMPS build fails on your system.

			make yes-compress
			make machine :pre

			make no-compress
			make machine :pre

			[Supporting info:]

			src/COMPRESS: filenames -> commands
			src/COMPRESS/README
			lib/compress/README
			"dump atom/gz"_dump.html
			"dump cfg/gz"_dump.html
			"dump custom/gz"_dump.html
			"dump xyz/gz"_dump.html :ul

			:line

			CORESHELL package :link(CORESHELL),h4

			[Contents:]

			Compute and pair styles that implement the adiabatic core/shell model
			for polarizability. The pair styles augment Born, Buckingham, and
			Lennard-Jones styles with core/shell capabilities. The "compute
			temp/cs"_compute_temp_cs.html command calculates the temperature of a
			system with core/shell particles. See "Section
			6.26"_Section_howto.html#howto_26 for an overview of how to use this
			package.

			[Author:] Hendrik Heenen (Technical U of Munich).

			[Install or un-install:]

			make yes-coreshell
			make machine :pre

			make no-coreshell
			make machine :pre

			[Supporting info:]

			src/CORESHELL: filenames -> commands
			"Section 6.26"_Section_howto.html#howto_26
			"Section 6.25"_Section_howto.html#howto_25
			"compute temp/cs"_compute_temp_cs.html
			"pair_style born/coul/long/cs"_pair_cs.html
			"pair_style buck/coul/long/cs"_pair_cs.html
			"pair_style lj/cut/coul/long/cs"_pair_lj.html
			examples/coreshell :ul

			:line

			DIPOLE package :link(DIPOLE),h4

			[Contents:]

			An atom style and several pair styles for point dipole models with
			short-range or long-range interactions.

			[Install or un-install:]

			make yes-dipole
			make machine :pre

			make no-dipole
			make machine :pre

			[Supporting info:]

			src/DIPOLE: filenames -> commands
			"atom_style dipole"_atom_style.html
			"pair_style lj/cut/dipole/cut"_pair_dipole.html
			"pair_style lj/cut/dipole/long"_pair_dipole.html
			"pair_style lj/long/dipole/long"_pair_dipole.html
			examples/dipole :ul

			:line

			GPU package :link(GPU),h4

			[Contents:]

			Dozens of pair styles and a version of the PPPM long-range Coulombic
			solver optimized for GPUs. All such styles have a "gpu" as a
			suffix in their style name. The GPU code can be compiled with either
			CUDA or OpenCL, however the OpenCL variants are no longer actively
			maintained and only the CUDA versions are regularly tested.
			"Section 5.3.1"_accelerate_gpu.html gives details of what
			hardware and GPU software is required on your system,
			and details on how to build and use this package. Its styles can be
			invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line
			switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS
			package, which has GPU-enabled styles.

			[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
			(Northwestern U) while at ORNL.

			[Install or un-install:]

			Before building LAMMPS with this package, you must first build the GPU
			library in lib/gpu from a set of provided C and CUDA files. You can
			do this manually if you prefer; follow the instructions in
			lib/gpu/README. Please note, that the GPU library uses MPI calls, so
			you have to make certain to use the same MPI library (or the STUBS
			library) settings as the main LAMMPS code. That same applies to the
			-DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define.

			You can also do it in one step from the lammps/src
			dir, using a command like these, which simply invoke the
			lib/gpu/Install.py script with the specified args:

			make lib-gpu # print help message
			make lib-gpu args="-b" # build GPU library with default Makefile.linux
			make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
			make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre

			Note that this procedure through the '-m machine' flag starts with one of
			the existing Makefile.machine files in lib/gpu. For your convenience,
			machine makefiles for "mpi" and "serial" are provided, which have the
			same settings as the corresponding machine makefiles in the main LAMMPS
			source folder. In addition you can alter 4 important settings in that
			Makefile, via the -h, -a, -p, -e switches, and also save a copy of the
			new Makefile, if desired:

			CUDA_HOME = where NVIDIA CUDA software is installed on your system
			CUDA_ARCH = what GPU hardware you have (see help message for details)
			CUDA_PRECISION = precision (double, mixed, single)
			EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul

			If the library build is successful, at least 3 files should be created:
			lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps.
			The latter has settings that enable LAMMPS to link with CUDA libraries.
			If the settings in Makefile.lammps for your machine are not correct,
			the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to
			be edited.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-gpu
			make machine :pre

			make no-gpu
			make machine :pre

			NOTE: If you re-build the GPU library in lib/gpu, you should always
			un-install the GPU package, then re-install it and re-build LAMMPS.
			This is because the compilation of files in the GPU package use the
			library settings from the lib/gpu/Makefile.machine used to build the
			GPU library.

			[Supporting info:]

			src/GPU: filenames -> commands
			src/GPU/README
			lib/gpu/README
			"Section 5.3"_Section_accelerate.html#acc_3
			"Section 5.3.1"_accelerate_gpu.html
			"Section 2.6 -sf gpu"_Section_start.html#start_6
			"Section 2.6 -pk gpu"_Section_start.html#start_6
			"package gpu"_package.html
			Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g)
			"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul

			:line

			GRANULAR package :link(GRANULAR),h4

			[Contents:]

			Pair styles and fixes for finite-size granular particles, which
			interact with each other and boundaries via frictional and dissipative
			potentials.

			[Install or un-install:]

			make yes-granular
			make machine :pre

			make no-granular
			make machine :pre

			[Supporting info:]

			src/GRANULAR: filenames -> commands
			"Section 6.6"_Section_howto.html#howto_6,
			"fix pour"_fix_pour.html
			"fix wall/gran"_fix_wall_gran.html
			"pair_style gran/hooke"_pair_gran.html
			"pair_style gran/hertz/history"_pair_gran.html
			examples/granregion
			examples/pour
			bench/in.chute
			http://lammps.sandia.gov/pictures.html#jamming
			http://lammps.sandia.gov/movies.html#hopper
			http://lammps.sandia.gov/movies.html#dem
			http://lammps.sandia.gov/movies.html#brazil
			http://lammps.sandia.gov/movies.html#granregion :ul

			:line

			KIM package :link(KIM),h4

			[Contents:]

			A "pair_style kim"_pair_kim.html command which is a wrapper on the
			Knowledge Base for Interatomic Models (KIM) repository of interatomic
			potentials, enabling any of them to be used in LAMMPS simulations.

			To use this package you must have the KIM library available on your
			system.

			Information about the KIM project can be found at its website:
			https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan
			Elliott (U Minnesota) and James Sethna (Cornell U).

			[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
			API which the "pair_style kim"_pair_kim.html command uses. He
			developed the pair style in collaboration with Valeriu Smirichinski (U
			Minnesota).

			[Install or un-install:]

			Before building LAMMPS with this package, you must first download and
			build the KIM library and include the KIM models that you want to
			use. You can do this manually if you prefer; follow the instructions
			in lib/kim/README. You can also do it in one step from the lammps/src
			dir, using a command like these, which simply invoke the
			lib/kim/Install.py script with the specified args.

			make lib-kim # print help message
			make lib-kim args="-b " # (re-)install KIM API lib with only example models
			make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
			make lib-kim args="-b -a everything" # install KIM API lib with all models
			make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
			make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
			make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre

			Note that in LAMMPS lingo, a KIM model driver is a pair style
			(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
			element or alloy and set of parameters, e.g. EAM for Cu with a
			specific EAM potential file. Also note that installing the KIM API
			library with all its models, may take around 30 min to build. Of
			course you only need to do that once.

			See the list of KIM model drivers here:
			https://openkim.org/kim-items/model-drivers/alphabetical

			See the list of all KIM models here:
			https://openkim.org/kim-items/models/by-model-drivers

			See the list of example KIM models included by default here:
			https://openkim.org/kim-api in the "What is in the KIM API source
			package?" section

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-kim
			make machine :pre

			make no-kim
			make machine :pre

			[Supporting info:]

			src/KIM: filenames -> commands
			src/KIM/README
			lib/kim/README
			"pair_style kim"_pair_kim.html
			examples/kim :ul

			:line

			KOKKOS package :link(KOKKOS),h4

			[Contents:]

			Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
			styles adapted to compile using the Kokkos library which can convert
			them to OpenMP or CUDA code so that they run efficiently on multicore
			CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their
			style name. "Section 5.3.3"_accelerate_kokkos.html gives details of
			what hardware and software is required on your system, and how to
			build and use this package. Its styles can be invoked at run time via
			the "-sf kk" or "-suffix kk" "command-line
			switches"_Section_start.html#start_6. Also see the "GPU"_#GPU,
			"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
			packages, which have styles optimized for CPUs, KNLs, and GPUs.

			You must have a C++11 compatible compiler to use this package.

			[Authors:] The KOKKOS package was created primarily by Christian Trott
			and Stan Moore (Sandia), with contributions from other folks as well.
			It uses the open-source "Kokkos library"_https://github.com/kokkos
			which was developed by Carter Edwards, Christian Trott, and others at
			Sandia, and which is included in the LAMMPS distribution in
			lib/kokkos.

			[Install or un-install:]

			For the KOKKOS package, you have 3 choices when building. You can
			build with either CPU or KNL or GPU support. Each choice requires
			additional settings in your Makefile.machine for the KOKKOS_DEVICES
			and KOKKOS_ARCH settings. See the src/MAKE/OPTIONS/Makefile.kokkos*
			files for examples.

			For multicore CPUs using OpenMP:

			KOKKOS_DEVICES = OpenMP
			KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre

			For Intel KNLs using OpenMP:

			KOKKOS_DEVICES = OpenMP
			KOKKOS_ARCH = KNL :pre

			For NVIDIA GPUs using CUDA:

			KOKKOS_DEVICES = Cuda
			KOKKOS_ARCH = Pascal60,Power8 # P100 hosted by an IBM Power8, etc
			KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc :pre

			For GPUs, you also need these 2 lines in your Makefile.machine before
			the CC line is defined, in this case for use with OpenMPI mpicxx. The
			2 lines define a nvcc wrapper compiler, which will use nvcc for
			compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA
			files.

			KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
			export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
			CC = mpicxx :pre

			Once you have an appropriate Makefile.machine, you can
			install/un-install the package and build LAMMPS in the usual manner.
			Note that you cannot build one executable to run on multiple hardware
			targets (CPU or KNL or GPU). You need to build LAMMPS once for each
			hardware target, to produce a separate executable. Also note that we
			do not recommend building with other acceleration packages installed
			(GPU, OPT, USER-INTEL, USER-OMP) when also building with KOKKOS.

			make yes-kokkos
			make machine :pre

			make no-kokkos
			make machine :pre

			[Supporting info:]

			src/KOKKOS: filenames -> commands
			src/KOKKOS/README
			lib/kokkos/README
			"Section 5.3"_Section_accelerate.html#acc_3
			"Section 5.3.3"_accelerate_kokkos.html
			"Section 2.6 -k on ..."_Section_start.html#start_6
			"Section 2.6 -sf kk"_Section_start.html#start_6
			"Section 2.6 -pk kokkos"_Section_start.html#start_6
			"package kokkos"_package.html
			Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k)
			"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul

			:line

			KSPACE package :link(KSPACE),h4

			[Contents:]

			A variety of long-range Coulombic solvers, as well as pair styles
			which compute the corresponding short-range pairwise Coulombic
			interactions. These include Ewald, particle-particle particle-mesh
			(PPPM), and multilevel summation method (MSM) solvers.

			[Install or un-install:]

			Building with this package requires a 1d FFT library be present on
			your system for use by the PPPM solvers. This can be the KISS FFT
			library provided with LAMMPS, 3rd party libraries like FFTW, or a
			vendor-supplied FFT library. See step 6 of "Section
			2.2.2"_Section_start.html#start_2_2 of the manual for details on how
			to select different FFT options in your machine Makefile.

			make yes-kspace
			make machine :pre

			make no-kspace
			make machine :pre

			[Supporting info:]

			src/KSPACE: filenames -> commands
			"kspace_style"_kspace_style.html
			"doc/PDF/kspace.pdf"_PDF/kspace.pdf
			"Section 6.7"_Section_howto.html#howto_7
			"Section 6.8"_Section_howto.html#howto_8
			"Section 6.9"_Section_howto.html#howto_9
			"pair_style coul"_pair_coul.html
			Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 with "long" or "msm" in pair style name
			examples/peptide
			bench/in.rhodo :ul

			:line

			LATTE package :link(LATTE),h4

			[Contents:]

			A fix command which wraps the LATTE DFTB code, so that molecular
			dynamics can be run with LAMMPS using density-functional tight-binding
			quantum forces calculated by LATTE.

			More information on LATTE can be found at this web site:
			"https://github.com/lanl/LATTE"_latte_home. A brief technical
			description is given with the "fix latte"_fix_latte.html command.

			:link(latte_home,https://github.com/lanl/LATTE)

			[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE
			itself is developed at Los Alamos National Laboratory by Marc
			Cawkwell, Anders Niklasson, and Christian Negre.

			[Install or un-install:]

			Before building LAMMPS with this package, you must first download and
			build the LATTE library. You can do this manually if you prefer;
			follow the instructions in lib/latte/README. You can also do it in
			one step from the lammps/src dir, using a command like these, which
			simply invokes the lib/latte/Install.py script with the specified
			args:

			make lib-latte # print help message
			make lib-latte args="-b" # download and build in lib/latte/LATTE-master
			make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
			make lib-latte args="-b -m gfortran" # download and build in lib/latte and
			# copy Makefile.lammps.gfortran to Makefile.lammps
			:pre

			Note that 3 symbolic (soft) links, "includelink" and "liblink" and
			"filelink", are created in lib/latte to point into the LATTE home dir.
			When LAMMPS builds in src it will use these links. You should
			also check that the Makefile.lammps file you create is apporpriate
			for the compiler you use on your system to build LATTE.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-latte
			make machine :pre

			make no-latte
			make machine :pre

			[Supporting info:]

			src/LATTE: filenames -> commands
			src/LATTE/README
			lib/latte/README
			"fix latte"_fix_latte.html
			examples/latte
			"LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul

			:line

			MANYBODY package :link(MANYBODY),h4

			[Contents:]

			A variety of manybody and bond-order potentials. These include
			(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.

			[Install or un-install:]

			make yes-manybody
			make machine :pre

			make no-manybody
			make machine :pre

			[Supporting info:]

			src/MANYBODY: filenames -> commands
			Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
			examples/comb
			examples/eim
			examples/nb3d
			examples/shear
			examples/streitz
			examples/vashishta
			bench/in.eam :ul

			:line

			MC package :link(MC),h4

			[Contents:]

			Several fixes and a pair style that have Monte Carlo (MC) or MC-like
			attributes. These include fixes for creating, breaking, and swapping
			bonds, for performing atomic swaps, and performing grand-canonical MC
			(GCMC) in conjuction with dynamics.

			[Install or un-install:]

			make yes-mc
			make machine :pre

			make no-mc
			make machine :pre

			[Supporting info:]

			src/MC: filenames -> commands
			"fix atom/swap"_fix_atom_swap.html
			"fix bond/break"_fix_bond_break.html
			"fix bond/create"_fix_bond_create.html
			"fix bond/swap"_fix_bond_swap.html
			"fix gcmc"_fix_gcmc.html
			"pair_style dsmc"_pair_dsmc.html
			http://lammps.sandia.gov/movies.html#gcmc :ul

			:line

			MEAM package :link(MEAM),h4

			[Contents:]

			A pair style for the modified embedded atom (MEAM) potential.

			Please note that the MEAM package has been superseded by the
			"USER-MEAMC"_#USER-MEAMC package, which is a direct translation
			of the MEAM package to C++. USER-MEAMC contains additional
			optimizations making it run faster than MEAM on most machines,
			while providing the identical features and USER interface.

			[Author:] Greg Wagner (Northwestern U) while at Sandia.

			[Install or un-install:]

			Before building LAMMPS with this package, you must first build the
			MEAM library in lib/meam. You can do this manually if you prefer;
			follow the instructions in lib/meam/README. You can also do it in one
			step from the lammps/src dir, using a command like these, which simply
			invoke the lib/meam/Install.py script with the specified args:

			make lib-meam # print help message
			make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library
			make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
			make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre

			The build should produce two files: lib/meam/libmeam.a and
			lib/meam/Makefile.lammps. The latter is copied from an existing
			Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
			Fortran (MEAM library). Typically the two compilers used for LAMMPS
			and the MEAM library need to be consistent (e.g. both Intel or both
			GNU compilers). If necessary, you can edit/create a new
			lib/meam/Makefile.machine file for your system, which should define an
			EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
			file.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-meam
			make machine :pre

			make no-meam
			make machine :pre

			NOTE: You should test building the MEAM library with both the Intel
			and GNU compilers to see if a simulation runs faster with one versus
			the other on your system.

			[Supporting info:]

			src/MEAM: filenames -> commands
			src/meam/README
			lib/meam/README
			"pair_style meam"_pair_meam.html
			examples/meam :ul

			:line

			MISC package :link(MISC),h4

			[Contents:]

			A variety of compute, fix, pair, dump styles with specialized
			capabilities that don't align with other packages. Do a directory
			listing, "ls src/MISC", to see the list of commands.

			NOTE: the MISC package contains styles that require using the
			-restrict flag, when compiling with Intel compilers.

			[Install or un-install:]

			make yes-misc
			make machine :pre

			make no-misc
			make machine :pre

			[Supporting info:]

			src/MISC: filenames -> commands
			"compute ti"_compute_ti.html
			"fix evaporate"_fix_evaporate.html
			"fix orient/fcc"_fix_orient.html
			"fix ttm"_fix_ttm.html
			"fix thermal/conductivity"_fix_thermal_conductivity.html
			"fix viscosity"_fix_viscosity.html
			examples/KAPPA
			examples/VISCOSITY
			http://lammps.sandia.gov/pictures.html#ttm
			http://lammps.sandia.gov/movies.html#evaporation :ul

			:line

			MOLECULE package :link(MOLECULE),h4

			[Contents:]

			A large number of atom, pair, bond, angle, dihedral, improper styles
			that are used to model molecular systems with fixed covalent bonds.
			The pair styles include the Dreiding (hydrogen-bonding) and CHARMM
			force fields, and a TIP4P water model.

			[Install or un-install:]

			make yes-molecule
			make machine :pre

			make no-molecule
			make machine :pre

			[Supporting info:]

			src/MOLECULE: filenames -> commands
			"atom_style"_atom_style.html
			"bond_style"_bond_style.html
			"angle_style"_angle_style.html
			"dihedral_style"_dihedral_style.html
			"improper_style"_improper_style.html
			"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html
			"pair_style lj/charmm/coul/charmm"_pair_charmm.html
			"Section 6.3"_Section_howto.html#howto_3
			examples/cmap
			examples/dreiding
			examples/micelle,
			examples/peptide
			bench/in.chain
			bench/in.rhodo :ul

			:line

			MPIIO package :link(MPIIO),h4

			[Contents:]

			Support for parallel output/input of dump and restart files via the
			MPIIO library. It adds "dump styles"_dump.html with a "mpiio" in
			their style name. Restart files with an ".mpiio" suffix are also
			written and read in parallel.

			[Install or un-install:]

			Note that MPIIO is part of the standard message-passing interface
			(MPI) library, so you should not need any additional compiler or link
			settings, beyond what LAMMPS normally uses for MPI on your system.

			make yes-mpiio
			make machine :pre

			make no-mpiio
			make machine :pre

			[Supporting info:]

			src/MPIIO: filenames -> commands
			"dump"_dump.html
			"restart"_restart.html
			"write_restart"_write_restart.html
			"read_restart"_read_restart.html :ul

			:line

			MSCG package :link(mscg),h4

			[Contents:]

			A "fix mscg"_fix_mscg.html command which can parameterize a
			Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
			library"_mscg_home.

			:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)

			To use this package you must have the MS-CG library available on your
			system.

			[Authors:] The fix was written by Lauren Abbott (Sandia). The MS-CG
			library was developed by Jacob Wagner in Greg Voth's group at the
			University of Chicago.

			[Install or un-install:]

			Before building LAMMPS with this package, you must first download and
			build the MS-CG library. Building the MS-CG library and using it from
			LAMMPS requires a C++11 compatible compiler and that the GSL
			(GNU Scientific Library) headers and libraries are installed on your
			machine. See the lib/mscg/README and MSCG/Install files for more details.

			Assuming these libraries are in place, you can do the download and
			build of MS-CG manually if you prefer; follow the instructions in
			lib/mscg/README. You can also do it in one step from the lammps/src
			dir, using a command like these, which simply invoke the
			lib/mscg/Install.py script with the specified args:

			make lib-mscg # print help message
			make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
			# with the settings compatible with "make serial"
			make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
			# with the settings compatible with "make mpi"
			make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre

			Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg
			to point to the MS-CG src/installation dir. When LAMMPS is built in src it will use these links.
			You should not need to edit the lib/mscg/Makefile.lammps file.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-mscg
			make machine :pre

			make no-mscg
			make machine :pre

			[Supporting info:]

			src/MSCG: filenames -> commands
			src/MSCG/README
			lib/mscg/README
			examples/mscg :ul

			:line

			OPT package :link(OPT),h4

			[Contents:]

			A handful of pair styles which are optimized for improved CPU
			performance on single or multiple cores. These include EAM, LJ,
			CHARMM, and Morse potentials. The styles have an "opt" suffix in
			their style name. "Section 5.3.5"_accelerate_opt.html gives details
			of how to build and use this package. Its styles can be invoked at
			run time via the "-sf opt" or "-suffix opt" "command-line
			switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS,
			"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
			have styles optimized for CPU performance.

			[Authors:] James Fischer (High Performance Technologies), David Richie,
			and Vincent Natoli (Stone Ridge Technolgy).

			[Install or un-install:]

			make yes-opt
			make machine :pre

			make no-opt
			make machine :pre

			NOTE: The compile flag "-restrict" must be used to build LAMMPS with
			the OPT package when using Intel compilers. It should be added to
			the CCFLAGS line of your Makefile.machine. See Makefile.opt in
			src/MAKE/OPTIONS for an example.

			CCFLAGS: add -restrict for Intel compilers :ul

			[Supporting info:]

			src/OPT: filenames -> commands
			"Section 5.3"_Section_accelerate.html#acc_3
			"Section 5.3.5"_accelerate_opt.html
			"Section 2.6 -sf opt"_Section_start.html#start_6
			Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)
			"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul

			:line

			PERI package :link(PERI),h4

			[Contents:]

			An atom style, several pair styles which implement different
			Peridynamics materials models, and several computes which calculate
			diagnostics. Peridynamics is a a particle-based meshless continuum
			model.

			[Authors:] The original package was created by Mike Parks (Sandia).
			Additional Peridynamics models were added by Rezwanur Rahman and John
			Foster (UTSA).

			[Install or un-install:]

			make yes-peri
			make machine :pre

			make no-peri
			make machine :pre

			[Supporting info:]

			src/PERI: filenames -> commands
			"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf
			"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf
			"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf
			"atom_style peri"_atom_style.html
			"pair_style peri/*"_pair_peri.html
			"compute damage/atom"_compute_damage_atom.html
			"compute plasticity/atom"_compute_plasticity_atom.html
			examples/peri
			http://lammps.sandia.gov/movies.html#peri :ul

			:line

			POEMS package :link(POEMS),h4

			[Contents:]

			A fix that wraps the Parallelizable Open source Efficient Multibody
			Software (POEMS) library, which is able to simulate the dynamics of
			articulated body systems. These are systems with multiple rigid
			bodies (collections of particles) whose motion is coupled by
			connections at hinge points.

			[Author:] Rudra Mukherjee (JPL) while at RPI.

			[Install or un-install:]

			Before building LAMMPS with this package, you must first build the
			POEMS library in lib/poems. You can do this manually if you prefer;
			follow the instructions in lib/poems/README. You can also do it in
			one step from the lammps/src dir, using a command like these, which
			simply invoke the lib/poems/Install.py script with the specified args:

			make lib-poems # print help message
			make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
			make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
			make lib-poems args="-m icc" # build with Intel icc compiler :pre

			The build should produce two files: lib/poems/libpoems.a and
			lib/poems/Makefile.lammps. The latter is copied from an existing
			Makefile.lammps.* and has settings needed to build LAMMPS with the
			POEMS library (though typically the settings are just blank). If
			necessary, you can edit/create a new lib/poems/Makefile.machine file
			for your system, which should define an EXTRAMAKE variable to specify
			a corresponding Makefile.lammps.machine file.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-poems
			make machine :pre

			make no-meam
			make machine :pre

			[Supporting info:]

			src/POEMS: filenames -> commands
			src/POEMS/README
			lib/poems/README
			"fix poems"_fix_poems.html
			examples/rigid :ul

			:line

			PYTHON package :link(PYTHON),h4

			[Contents:]

			A "python"_python.html command which allow you to execute Python code
			from a LAMMPS input script. The code can be in a separate file or
			embedded in the input script itself. See "Section
			11.2"_Section_python.html#py_2 for an overview of using Python from
			LAMMPS in this manner and the entire section for other ways to use
			LAMMPS and Python together.

			[Install or un-install:]

			make yes-python
			make machine :pre

			make no-python
			make machine :pre

			NOTE: Building with the PYTHON package assumes you have a Python
			shared library available on your system, which needs to be a Python 2
			version, 2.6 or later. Python 3 is not yet supported. See the
			lib/python/README for more details. Note that the build uses the
			lib/python/Makefile.lammps file in the compile/link process. You
			should only need to create a new Makefile.lammps.* file (and copy it
			to Makefile.lammps) if the LAMMPS build fails.

			[Supporting info:]

			src/PYTHON: filenames -> commands
			"Section 11"_Section_python.html
			lib/python/README
			examples/python :ul

			:line

			QEQ package :link(QEQ),h4

			[Contents:]

			Several fixes for performing charge equilibration (QEq) via different
			algorithms. These can be used with pair styles that perform QEq as
			part of their formulation.

			[Install or un-install:]

			make yes-qeq
			make machine :pre

			make no-qeq
			make machine :pre

			[Supporting info:]

			src/QEQ: filenames -> commands
			"fix qeq/*"_fix_qeq.html
			examples/qeq
			examples/streitz :ul

			:line

			REAX package :link(REAX),h4

			[Contents:]

			A pair style which wraps a Fortran library which implements the ReaxFF
			potential, which is a universal reactive force field. See the
			"USER-REAXC package"_#USER-REAXC for an alternate implementation in
			C/C++. Also a "fix reax/bonds"_fix_reax_bonds.html command for
			monitoring molecules as bonds are created and destroyed.

			[Author:] Aidan Thompson (Sandia).

			[Install or un-install:]

			Before building LAMMPS with this package, you must first build the
			REAX library in lib/reax. You can do this manually if you prefer;
			follow the instructions in lib/reax/README. You can also do it in one
			step from the lammps/src dir, using a command like these, which simply
			invoke the lib/reax/Install.py script with the specified args:

			make lib-reax # print help message
			make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
			make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
			make lib-reax args="-m ifort" # build with Intel ifort compiler :pre

			The build should produce two files: lib/reax/libreax.a and
			lib/reax/Makefile.lammps. The latter is copied from an existing
			Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
			Fortran (REAX library). Typically the two compilers used for LAMMPS
			and the REAX library need to be consistent (e.g. both Intel or both
			GNU compilers). If necessary, you can edit/create a new
			lib/reax/Makefile.machine file for your system, which should define an
			EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
			file.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-reax
			make machine :pre

			make no-reax
			make machine :pre

			[Supporting info:]

			src/REAX: filenames -> commands
			lib/reax/README
			"pair_style reax"_pair_reax.html
			"fix reax/bonds"_fix_reax_bonds.html
			examples/reax :ul

			:line

			REPLICA package :link(REPLICA),h4

			[Contents:]

			A collection of multi-replica methods which can be used when running
			multiple LAMMPS simulations (replicas). See "Section
			6.5"_Section_howto.html#howto_5 for an overview of how to run
			multi-replica simulations in LAMMPS. Methods in the package include
			nudged elastic band (NEB), parallel replica dynamics (PRD),
			temperature accelerated dynamics (TAD), parallel tempering, and a
			verlet/split algorithm for performing long-range Coulombics on one set
			of processors, and the remainder of the force field calcalation on
			another set.

			[Install or un-install:]

			make yes-replica
			make machine :pre

			make no-replica
			make machine :pre

			[Supporting info:]

			src/REPLICA: filenames -> commands
			"Section 6.5"_Section_howto.html#howto_5
			"neb"_neb.html
			"prd"_prd.html
			"tad"_tad.html
			"temper"_temper.html,
			"run_style verlet/split"_run_style.html
			examples/neb
			examples/prd
			examples/tad :ul

			:line

			RIGID package :link(RIGID),h4

			[Contents:]

			Fixes which enforce rigid constraints on collections of atoms or
			particles. This includes SHAKE and RATTLE, as well as varous
			rigid-body integrators for a few large bodies or many small bodies.
			Also several computes which calculate properties of rigid bodies.

			To install/build:

			make yes-rigid
			make machine :pre

			To un-install/re-build:

			make no-rigid
			make machine :pre

			[Supporting info:]

			src/RIGID: filenames -> commands
			"compute erotate/rigid"_compute_erotate_rigid.html
			fix shake"_fix_shake.html
			"fix rattle"_fix_shake.html
			"fix rigid/*"_fix_rigid.html
			examples/ASPHERE
			examples/rigid
			bench/in.rhodo
			http://lammps.sandia.gov/movies.html#box
			http://lammps.sandia.gov/movies.html#star :ul

			:line

			SHOCK package :link(SHOCK),h4

			[Contents:]

			Fixes for running impact simulations where a shock-wave passes through
			a material.

			[Install or un-install:]

			make yes-shock
			make machine :pre

			make no-shock
			make machine :pre

			[Supporting info:]

			src/SHOCK: filenames -> commands
			"fix append/atoms"_fix_append_atoms.html
			"fix msst"_fix_msst.html
			"fix nphug"_fix_nphug.html
			"fix wall/piston"_fix_wall_piston.html
			examples/hugoniostat
			examples/msst :ul

			:line

			SNAP package :link(SNAP),h4

			[Contents:]

			A pair style for the spectral neighbor analysis potential (SNAP).
			SNAP is methodology for deriving a highly accurate classical potential
			fit to a large archive of quantum mechanical (DFT) data. Also several
			computes which analyze attributes of the potential.

			[Author:] Aidan Thompson (Sandia).

			[Install or un-install:]

			make yes-snap
			make machine :pre

			make no-snap
			make machine :pre

			[Supporting info:]

			src/SNAP: filenames -> commands
			"pair_style snap"_pair_snap.html
			"compute sna/atom"_compute_sna_atom.html
			"compute snad/atom"_compute_sna_atom.html
			"compute snav/atom"_compute_sna_atom.html
			examples/snap :ul

			:line

			SRD package :link(SRD),h4

			[Contents:]

			A pair of fixes which implement the Stochastic Rotation Dynamics (SRD)
			method for coarse-graining of a solvent, typically around large
			colloidal particles.

			To install/build:

			make yes-srd
			make machine :pre

			To un-install/re-build:

			make no-srd
			make machine :pre

			[Supporting info:]

			src/SRD: filenames -> commands
			"fix srd"_fix_srd.html
			"fix wall/srd"_fix_wall_srd.html
			examples/srd
			examples/ASPHERE
			http://lammps.sandia.gov/movies.html#tri
			http://lammps.sandia.gov/movies.html#line
			http://lammps.sandia.gov/movies.html#poly :ul

			:line

			VORONOI package :link(VORONOI),h4

			[Contents:]

			A compute command which calculates the Voronoi tesselation of a
			collection of atoms by wrapping the "Voro++ library"_voro_home. This
			can be used to calculate the local volume or each atoms or its near
			neighbors.

			:link(voro_home,http://math.lbl.gov/voro++)

			To use this package you must have the Voro++ library available on your
			system.

			[Author:] Daniel Schwen (INL) while at LANL. The open-source Voro++
			library was written by Chris Rycroft (Harvard U) while at UC Berkeley
			and LBNL.

			[Install or un-install:]

			Before building LAMMPS with this package, you must first download and
			build the Voro++ library. You can do this manually if you prefer;
			follow the instructions in lib/voronoi/README. You can also do it in
			one step from the lammps/src dir, using a command like these, which
			simply invoke the lib/voronoi/Install.py script with the specified
			args:

			make lib-voronoi # print help message
			make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
			make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
			make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre

			Note that 2 symbolic (soft) links, "includelink" and "liblink", are
			created in lib/voronoi to point to the Voro++ src dir. When LAMMPS
			builds in src it will use these links. You should not need to edit
			the lib/voronoi/Makefile.lammps file.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-voronoi
			make machine :pre

			make no-voronoi
			make machine :pre

			[Supporting info:]

			src/VORONOI: filenames -> commands
			src/VORONOI/README
			lib/voronoi/README
			"compute voronoi/atom"_compute_voronoi_atom.html
			examples/voronoi :ul

			:line
			:line

			USER-ATC package :link(USER-ATC),h4

			[Contents:]

			ATC stands for atoms-to-continuum. This package implements a "fix
			atc"_fix_atc.html command to either couple molecular dynamics with
			continuum finite element equations or perform on-the-fly conversion of
			atomic information to continuum fields.

			[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).

			[Install or un-install:]

			Before building LAMMPS with this package, you must first build the ATC
			library in lib/atc. You can do this manually if you prefer; follow
			the instructions in lib/atc/README. You can also do it in one step
			from the lammps/src dir, using a command like these, which simply
			invoke the lib/atc/Install.py script with the specified args:

			make lib-atc # print help message
			make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
			make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
			make lib-atc args="-m icc" # build with Intel icc compiler :pre

			The build should produce two files: lib/atc/libatc.a and
			lib/atc/Makefile.lammps. The latter is copied from an existing
			Makefile.lammps.* and has settings needed to build LAMMPS with the ATC
			library. If necessary, you can edit/create a new
			lib/atc/Makefile.machine file for your system, which should define an
			EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
			file.

			Note that the Makefile.lammps file has settings for the BLAS and
			LAPACK linear algebra libraries. As explained in lib/atc/README these
			can either exist on your system, or you can use the files provided in
			lib/linalg. In the latter case you also need to build the library
			in lib/linalg with a command like these:

			make lib-linalg # print help message
			make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
			make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
			make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-user-atc
			make machine :pre

			make no-user-atc
			make machine :pre

			[Supporting info:]

			src/USER-ATC: filenames -> commands
			src/USER-ATC/README
			"fix atc"_fix_atc.html
			examples/USER/atc
			http://lammps.sandia.gov/pictures.html#atc :ul

			:line

			USER-AWPMD package :link(USER-AWPMD),h4

			[Contents:]

			AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This
			package implements an atom, pair, and fix style which allows electrons
			to be treated as explicit particles in a classical molecular dynamics
			model.

			[Author:] Ilya Valuev (JIHT, Russia).

			[Install or un-install:]

			Before building LAMMPS with this package, you must first build the
			AWPMD library in lib/awpmd. You can do this manually if you prefer;
			follow the instructions in lib/awpmd/README. You can also do it in
			one step from the lammps/src dir, using a command like these, which
			simply invoke the lib/awpmd/Install.py script with the specified args:

			make lib-awpmd # print help message
			make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
			make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
			make lib-awpmd args="-m icc" # build with Intel icc compiler :pre

			The build should produce two files: lib/awpmd/libawpmd.a and
			lib/awpmd/Makefile.lammps. The latter is copied from an existing
			Makefile.lammps.* and has settings needed to build LAMMPS with the
			AWPMD library. If necessary, you can edit/create a new
			lib/awpmd/Makefile.machine file for your system, which should define
			an EXTRAMAKE variable to specify a corresponding
			Makefile.lammps.machine file.

			Note that the Makefile.lammps file has settings for the BLAS and
			LAPACK linear algebra libraries. As explained in lib/awpmd/README
			these can either exist on your system, or you can use the files
			provided in lib/linalg. In the latter case you also need to build the
			library in lib/linalg with a command like these:

			make lib-linalg # print help message
			make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
			make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
			make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-user-awpmd
			make machine :pre

			make no-user-awpmd
			make machine :pre

			[Supporting info:]

			src/USER-AWPMD: filenames -> commands
			src/USER-AWPMD/README
			"pair_style awpmd/cut"_pair_awpmd.html
			examples/USER/awpmd :ul

			:line

			USER-CGDNA package :link(USER-CGDNA),h4

			[Contents:]

			Several pair styles, a bond style, and integration fixes for
			coarse-grained models of single- and double-stranded DNA based on the
			oxDNA model of Doye, Louis and Ouldridge at the University of Oxford.
			This includes Langevin-type rigid-body integrators with improved
			stability.

			[Author:] Oliver Henrich (University of Strathclyde, Glasgow).

			[Install or un-install:]

			make yes-user-cgdna
			make machine :pre

			make no-user-cgdna
			make machine :pre

			[Supporting info:]

			src/USER-CGDNA: filenames -> commands
			/src/USER-CGDNA/README
			"pair_style oxdna/*"_pair_oxdna.html
			"pair_style oxdna2/*"_pair_oxdna2.html
			"bond_style oxdna/*"_bond_oxdna.html
			"bond_style oxdna2/*"_bond_oxdna.html
			"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul

			:line

			USER-CGSDK package :link(USER-CGSDK),h4

			[Contents:]

			Several pair styles and an angle style which implement the
			coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
			simulation of ionic liquids, electrolytes, lipids and charged amino
			acids.

			[Author:] Axel Kohlmeyer (Temple U).

			[Install or un-install:]

			make yes-user-cgsdk
			make machine :pre

			make no-user-cgsdk
			make machine :pre

			[Supporting info:]

			src/USER-CGSDK: filenames -> commands
			src/USER-CGSDK/README
			"pair_style lj/sdk/*"_pair_sdk.html
			"angle_style sdk"_angle_sdk.html
			examples/USER/cgsdk
			http://lammps.sandia.gov/pictures.html#cg :ul

			:line

			USER-COLVARS package :link(USER-COLVARS),h4

			[Contents:]

			COLVARS stands for collective variables, which can be used to
			implement various enhanced sampling methods, including Adaptive
			Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and
			Restraints. A "fix colvars"_fix_colvars.html command is implemented
			which wraps a COLVARS library, which implements these methods.
			simulations.

			[Authors:] The COLVARS library is written and maintained by
			Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA)
			and Jerome Henin (LISM, CNRS, Marseille, France), originally for
			the NAMD MD code, but with portability in mind. Axel Kohlmeyer
			(Temple U) provided the interface to LAMMPS.

			[Install or un-install:]

			Before building LAMMPS with this package, you must first build the
			COLVARS library in lib/colvars. You can do this manually if you
			prefer; follow the instructions in lib/colvars/README. You can also
			do it in one step from the lammps/src dir, using a command like these,
			which simply invoke the lib/colvars/Install.py script with the
			specified args:

			make lib-colvars # print help message
			make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
			make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
			make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre

			The build should produce two files: lib/colvars/libcolvars.a and
			lib/colvars/Makefile.lammps. The latter is copied from an existing
			Makefile.lammps.* and has settings needed to build LAMMPS with the
			COLVARS library (though typically the settings are just blank). If
			necessary, you can edit/create a new lib/colvars/Makefile.machine file
			for your system, which should define an EXTRAMAKE variable to specify
			a corresponding Makefile.lammps.machine file.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-user-colvars
			make machine :pre

			make no-user-colvars
			make machine :pre

			[Supporting info:]

			src/USER-COLVARS: filenames -> commands
			"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf
			src/USER-COLVARS/README
			lib/colvars/README
			"fix colvars"_fix_colvars.html
			examples/USER/colvars :ul

			:line

			USER-DIFFRACTION package :link(USER-DIFFRACTION),h4

			[Contents:]

			Two computes and a fix for calculating x-ray and electron diffraction
			intensities based on kinematic diffraction theory.

			[Author:] Shawn Coleman while at the U Arkansas.

			[Install or un-install:]

			make yes-user-diffraction
			make machine :pre

			make no-user-diffraction
			make machine :pre

			[Supporting info:]

			src/USER-DIFFRACTION: filenames -> commands
			"compute saed"_compute_saed.html
			"compute xrd"_compute_xrd.html
			"fix saed/vtk"_fix_saed_vtk.html
			examples/USER/diffraction :ul

			:line

			USER-DPD package :link(USER-DPD),h4

			[Contents:]

			DPD stands for dissipative particle dynamics. This package implements
			coarse-grained DPD-based models for energetic, reactive molecular
			crystalline materials. It includes many pair styles specific to these
			systems, including for reactive DPD, where each particle has internal
			state for multiple species and a coupled set of chemical reaction ODEs
			are integrated each timestep. Highly accurate time intergrators for
			isothermal, isoenergetic, isobaric and isenthalpic conditions are
			included. These enable long timesteps via the Shardlow splitting
			algorithm.

			[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
			Brennan (ARL).

			[Install or un-install:]

			make yes-user-dpd
			make machine :pre

			make no-user-dpd
			make machine :pre

			[Supporting info:]

			src/USER-DPD: filenames -> commands
			/src/USER-DPD/README
			"compute dpd"_compute_dpd.html
			"compute dpd/atom"_compute_dpd_atom.html
			"fix eos/cv"_fix_eos_table.html
			"fix eos/table"_fix_eos_table.html
			"fix eos/table/rx"_fix_eos_table_rx.html
			"fix shardlow"_fix_shardlow.html
			"fix rx"_fix_rx.html
			"pair_style table/rx"_pair_table_rx.html
			"pair_style dpd/fdt"_pair_dpd_fdt.html
			"pair_style dpd/fdt/energy"_pair_dpd_fdt.html
			"pair_style exp6/rx"_pair_exp6_rx.html
			"pair_style multi/lucy"_pair_multi_lucy.html
			"pair_style multi/lucy/rx"_pair_multi_lucy_rx.html
			examples/USER/dpd :ul

			:line

			USER-DRUDE package :link(USER-DRUDE),h4

			[Contents:]

			Fixes, pair styles, and a compute to simulate thermalized Drude
			oscillators as a model of polarization. See "Section
			6.27"_Section_howto.html#howto_27 for an overview of how to use the
			package. There are auxiliary tools for using this package in
			tools/drude.

			[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
			Devemy (CNRS), and Agilio Padua (U Blaise Pascal).

			[Install or un-install:]

			make yes-user-drude
			make machine :pre

			make no-user-drude
			make machine :pre

			[Supporting info:]

			src/USER-DRUDE: filenames -> commands
			"Section 6.27"_Section_howto.html#howto_27
			"Section 6.25"_Section_howto.html#howto_25
			src/USER-DRUDE/README
			"fix drude"_fix_drude.html
			"fix drude/transform/*"_fix_drude_transform.html
			"compute temp/drude"_compute_temp_drude.html
			"pair_style thole"_pair_thole.html
			"pair_style lj/cut/thole/long"_pair_thole.html
			examples/USER/drude
			tools/drude :ul

			:line

			USER-EFF package :link(USER-EFF),h4

			[Contents:]

			EFF stands for electron force field which allows a classical MD code
			to model electrons as particles of variable radius. This package
			contains atom, pair, fix and compute styles which implement the eFF as
			described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
			JCC, 2010. The eFF potential was first introduced by Su and Goddard,
			in 2007. There are auxiliary tools for using this package in
			tools/eff; see its README file.

			[Author:] Andres Jaramillo-Botero (CalTech).

			[Install or un-install:]

			make yes-user-eff
			make machine :pre

			make no-user-eff
			make machine :pre

			[Supporting info:]

			src/USER-EFF: filenames -> commands
			src/USER-EFF/README
			"atom_style electron"_atom_style.html
			"fix nve/eff"_fix_nve_eff.html
			"fix nvt/eff"_fix_nh_eff.html
			"fix npt/eff"_fix_nh_eff.html
			"fix langevin/eff"_fix_langevin_eff.html
			"compute temp/eff"_compute_temp_eff.html
			"pair_style eff/cut"_pair_eff.html
			"pair_style eff/inline"_pair_eff.html
			examples/USER/eff
			tools/eff/README
			tools/eff
			http://lammps.sandia.gov/movies.html#eff :ul

			:line

			USER-FEP package :link(USER-FEP),h4

			[Contents:]

			FEP stands for free energy perturbation. This package provides
			methods for performing FEP simulations by using a "fix
			adapt/fep"_fix_adapt_fep.html command with soft-core pair potentials,
			which have a "soft" in their style name. There are auxiliary tools
			for using this package in tools/fep; see its README file.

			[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)

			[Install or un-install:]

			make yes-user-fep
			make machine :pre

			make no-user-fep
			make machine :pre

			[Supporting info:]

			src/USER-FEP: filenames -> commands
			src/USER-FEP/README
			"fix adapt/fep"_fix_adapt_fep.html
			"compute fep"_compute_fep.html
			"pair_style */soft"_pair_lj_soft.html
			examples/USER/fep
			tools/fep/README
			tools/fep :ul

			:line

			USER-H5MD package :link(USER-H5MD),h4

			[Contents:]

			H5MD stands for HDF5 for MD. "HDF5"_HDF5 is a portable, binary,
			self-describing file format, used by many scientific simulations.
			H5MD is a format for molecular simulations, built on top of HDF5.
			This package implements a "dump h5md"_dump_h5md.html command to output
			LAMMPS snapshots in this format.

			:link(HDF5,http://www.hdfgroup.org/HDF5)

			To use this package you must have the HDF5 library available on your
			system.

			[Author:] Pierre de Buyl (KU Leuven) created both the package and the
			H5MD format.

			[Install or un-install:]

			Note that to follow these steps to compile and link to the CH5MD
			library, you need the standard HDF5 software package installed on your
			system, which should include the h5cc compiler and the HDF5 library.

			Before building LAMMPS with this package, you must first build the
			CH5MD library in lib/h5md. You can do this manually if you prefer;
			follow the instructions in lib/h5md/README. You can also do it in one
			step from the lammps/src dir, using a command like these, which simply
			invoke the lib/h5md/Install.py script with the specified args:

			make lib-h5md # print help message
			make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre

			The build should produce two files: lib/h5md/libch5md.a and
			lib/h5md/Makefile.lammps. The latter is copied from an existing
			Makefile.lammps.* and has settings needed to build LAMMPS with the
			system HDF5 library. If necessary, you can edit/create a new
			lib/h5md/Makefile.machine file for your system, which should define an
			EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
			file.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-user-h5md
			make machine :pre

			make no-user-h5md
			make machine :pre

			[Supporting info:]

			src/USER-H5MD: filenames -> commands
			src/USER-H5MD/README
			lib/h5md/README
			"dump h5md"_dump_h5md.html :ul

			:line

			USER-INTEL package :link(USER-INTEL),h4

			[Contents:]

			Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
			styles which are optimized for Intel CPUs and KNLs (Knights Landing).
			All of them have an "intel" in their style name. "Section
			5.3.2"_accelerate_intel.html gives details of what hardware and
			compilers are required on your system, and how to build and use this
			package. Its styles can be invoked at run time via the "-sf intel" or
			"-suffix intel" "command-line switches"_Section_start.html#start_6.
			Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
			packages, which have styles optimized for CPUs and KNLs.

			You need to have an Intel compiler, version 14 or higher to take full
			advantage of this package. While compilation with GNU compilers is
			supported, performance will be suboptimal.

			NOTE: the USER-INTEL package contains styles that require using the
			-restrict flag, when compiling with Intel compilers.


			[Author:] Mike Brown (Intel).

			[Install or un-install:]

			For the USER-INTEL package, you have 2 choices when building. You can
			build with either CPU or KNL support. Each choice requires additional
			settings in your Makefile.machine for CCFLAGS and LINKFLAGS and
			optimized malloc libraries. See the
			src/MAKE/OPTIONS/Makefile.intel_cpu and src/MAKE/OPTIONS/Makefile.knl
			files for examples.

			For CPUs:

			OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
			CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
			-fno-alias -ansi-alias -restrict $(OPTFLAGS)
			LINKFLAGS = -g -qopenmp $(OPTFLAGS)
			LIB = -ltbbmalloc -ltbbmalloc_proxy :pre

			For KNLs:

			OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
			CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
			-fno-alias -ansi-alias -restrict $(OPTFLAGS)
			LINKFLAGS = -g -qopenmp $(OPTFLAGS)
			LIB = -ltbbmalloc :pre

			Once you have an appropriate Makefile.machine, you can
			install/un-install the package and build LAMMPS in the usual manner.
			Note that you cannot build one executable to run on multiple hardware
			targets (Intel CPUs or KNL). You need to build LAMMPS once for each
			hardware target, to produce a separate executable.

			You should also typically install the USER-OMP package, as it can be
			used in tandem with the USER-INTEL package to good effect, as
			explained in "Section 5.3.2"_accelerate_intel.html.

			make yes-user-intel yes-user-omp
			make machine :pre

			make no-user-intel no-user-omp
			make machine :pre

			[Supporting info:]

			src/USER-INTEL: filenames -> commands
			src/USER-INTEL/README
			"Section 5.3"_Section_accelerate.html#acc_3
			"Section 5.3.2"_accelerate_gpu.html
			"Section 2.6 -sf intel"_Section_start.html#start_6
			"Section 2.6 -pk intel"_Section_start.html#start_6
			"package intel"_package.html
			Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i)
			src/USER-INTEL/TEST
			"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul

			:line

			USER-LB package :link(USER-LB),h4

			[Contents:]

			Fixes which implement a background Lattice-Boltzmann (LB) fluid, which
			can be used to model MD particles influenced by hydrodynamic forces.

			[Authors:] Frances Mackay and Colin Denniston (University of Western
			Ontario).

			[Install or un-install:]

			make yes-user-lb
			make machine :pre

			make no-user-lb
			make machine :pre

			[Supporting info:]

			src/USER-LB: filenames -> commands
			src/USER-LB/README
			"fix lb/fluid"_fix_lb_fluid.html
			"fix lb/momentum"_fix_lb_momentum.html
			"fix lb/viscous"_fix_lb_viscous.html
			examples/USER/lb :ul

			:line

			USER-MGPT package :link(USER-MGPT),h4

			[Contents:]

			A pair style which provides a fast implementation of the quantum-based
			MGPT multi-ion potentials. The MGPT or model GPT method derives from
			first-principles DFT-based generalized pseudopotential theory (GPT)
			through a series of systematic approximations valid for mid-period
			transition metals with nearly half-filled d bands. The MGPT method
			was originally developed by John Moriarty at LLNL. The pair style in
			this package calculates forces and energies using an optimized
			matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.

			[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).

			[Install or un-install:]

			make yes-user-mgpt
			make machine :pre

			make no-user-mgpt
			make machine :pre

			[Supporting info:]

			src/USER-MGPT: filenames -> commands
			src/USER-MGPT/README
			"pair_style mgpt"_pair_mgpt.html
			examples/USER/mgpt :ul

			:line

			USER-MISC package :link(USER-MISC),h4

			[Contents:]

			A potpourri of (mostly) unrelated features contributed to LAMMPS by
			users. Each feature is a single fix, compute, pair, bond, angle,
			dihedral, improper, or command style.

			[Authors:] The author for each style in the package is listed in the
			src/USER-MISC/README file.

			[Install or un-install:]

			make yes-user-misc
			make machine :pre

			make no-user-misc
			make machine :pre

			[Supporting info:]

			src/USER-MISC: filenames -> commands
			src/USER-MISC/README
			one doc page per individual command listed in src/USER-MISC/README
			examples/USER/misc :ul

			:line

			USER-MANIFOLD package :link(USER-MANIFOLD),h4

			[Contents:]

			Several fixes and a "manifold" class which enable simulations of
			particles constrained to a manifold (a 2D surface within the 3D
			simulation box). This is done by applying the RATTLE constraint
			algorithm to formulate single-particle constraint functions
			g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
			n = grad(g).

			[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The
			Netherlands; since 2017: Brandeis University, Waltham, MA, USA)

			[Install or un-install:]

			make yes-user-manifold
			make machine :pre

			make no-user-manifold
			make machine :pre

			[Supporting info:]

			src/USER-MANIFOLD: filenames -> commands
			src/USER-MANIFOLD/README
			"doc/manifolds"_manifolds.html
			"fix manifoldforce"_fix_manifoldforce.html
			"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
			"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
			examples/USER/manifold
			http://lammps.sandia.gov/movies.html#manifold :ul

			:line

			USER-MEAMC package :link(USER-MEAMC),h4

			[Contents:]

			A pair style for the modified embedded atom (MEAM) potential
			translated from the Fortran version in the "MEAM"_MEAM package
			to plain C++. In contrast to the MEAM package, no library
			needs to be compiled and the pair style can be instantiated
			multiple times.

			[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
			based on the Fortran version of Greg Wagner (Northwestern U) while at
			Sandia.

			[Install or un-install:]

			make yes-user-meamc
			make machine :pre

			make no-user-meamc
			make machine :pre

			[Supporting info:]

			src/USER-MEAMC: filenames -> commands
			src/USER-MEAMC/README
			"pair_style meam/c"_pair_meam.html
			examples/meam :ul

			:line

			USER-MESO package :link(USER-MESO),h4

			[Contents:]

			Several extensions of the the dissipative particle dynamics (DPD)
			method. Specifically, energy-conserving DPD (eDPD) that can model
			non-isothermal processes, many-body DPD (mDPD) for simulating
			vapor-liquid coexistence, and transport DPD (tDPD) for modeling
			advection-diffuion-reaction systems. The equations of motion of these
			DPD extensions are integrated through a modified velocity-Verlet (MVV)
			algorithm.

			[Author:] Zhen Li (Division of Applied Mathematics, Brown University)

			[Install or un-install:]

			make yes-user-meso
			make machine :pre

			make no-user-meso
			make machine :pre

			[Supporting info:]

			src/USER-MESO: filenames -> commands
			src/USER-MESO/README
			"atom_style edpd"_atom_style.html
			"pair_style edpd"_pair_meso.html
			"pair_style mdpd"_pair_meso.html
			"pair_style tdpd"_pair_meso.html
			"fix mvv/dpd"_fix_mvv_dpd.html
			examples/USER/meso
			http://lammps.sandia.gov/movies.html#mesodpd :ul

			:line

			USER-MOLFILE package :link(USER-MOLFILE),h4

			[Contents:]

			A "dump molfile"_dump_molfile.html command which uses molfile plugins
			that are bundled with the "VMD"_vmd_home
			molecular visualization and analysis program, to enable LAMMPS to dump
			snapshots in formats compatible with various molecular simulation
			tools.

			:link(vmd_home,http://www.ks.uiuc.edu/Research/vmd)

			To use this package you must have the desired VMD plugins available on
			your system.

			Note that this package only provides the interface code, not the
			plugins themselves, which will be accessed when requesting a specific
			plugin via the "dump molfile"_dump_molfile.html command. Plugins can
			be obtained from a VMD installation which has to match the platform
			that you are using to compile LAMMPS for. By adding plugins to VMD,
			support for new file formats can be added to LAMMPS (or VMD or other
			programs that use them) without having to recompile the application
			itself. More information about the VMD molfile plugins can be found
			at
			"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.

			[Author:] Axel Kohlmeyer (Temple U).

			[Install or un-install:]

			Note that the lib/molfile/Makefile.lammps file has a setting for a
			dynamic loading library libdl.a that should is typically present on
			all systems, which is required for LAMMPS to link with this package.
			If the setting is not valid for your system, you will need to edit the
			Makefile.lammps file. See lib/molfile/README and
			lib/molfile/Makefile.lammps for details.

			make yes-user-molfile
			make machine :pre

			make no-user-molfile
			make machine :pre

			[Supporting info:]

			src/USER-MOLFILE: filenames -> commands
			src/USER-MOLFILE/README
			lib/molfile/README
			"dump molfile"_dump_molfile.html :ul

			:line

			USER-NETCDF package :link(USER-NETCDF),h4

			[Contents:]

			Dump styles for writing NetCDF formatted dump files. NetCDF is a
			portable, binary, self-describing file format developed on top of
			HDF5. The file contents follow the AMBER NetCDF trajectory conventions
			(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.

			To use this package you must have the NetCDF library available on your
			system.

			Note that NetCDF files can be directly visualized with the following
			tools:

			"Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above)
			"VMD"_vmd_home
			"AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul

			:link(ovito,http://www.ovito.org)
			:link(atomeye,http://www.libatoms.org)

			[Author:] Lars Pastewka (Karlsruhe Institute of Technology).

			[Install or un-install:]

			Note that to follow these steps, you need the standard NetCDF software
			package installed on your system. The lib/netcdf/Makefile.lammps file
			has settings for NetCDF include and library files that LAMMPS needs to
			compile and linkk with this package. If the settings are not valid
			for your system, you will need to edit the Makefile.lammps file. See
			lib/netcdf/README for details.

			make yes-user-netcdf
			make machine :pre

			make no-user-netcdf
			make machine :pre

			[Supporting info:]

			src/USER-NETCDF: filenames -> commands
			src/USER-NETCDF/README
			lib/netcdf/README
			"dump netcdf"_dump_netcdf.html :ul

			:line

			USER-OMP package :link(USER-OMP),h4

			[Contents:]

			Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and
			kspace styles which are altered to enable threading on many-core CPUs
			via OpenMP directives. All of them have an "omp" in their style name.
			"Section 5.3.4"_accelerate_omp.html gives details of what hardware and
			compilers are required on your system, and how to build and use this
			package. Its styles can be invoked at run time via the "-sf omp" or
			"-suffix omp" "command-line switches"_Section_start.html#start_6.
			Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
			"USER-INTEL"_#USER-INTEL packages, which have styles optimized for
			CPUs.

			[Author:] Axel Kohlmeyer (Temple U).

			NOTE: To enable multi-threading support the compile flag "-fopenmp"
			and the link flag "-fopenmp" (for GNU compilers, you have to look up
			the equivalent flags for other compilers) must be used to build LAMMPS.
			When using Intel compilers, also the "-restrict" flag is required.
			The USER-OMP package can be compiled without enabling OpenMP; then
			all code will be compiled as serial and the only improvement over the
			regular styles are some data access optimization. These flags should
			be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine.
			See src/MAKE/OPTIONS/Makefile.omp for an example.

			Once you have an appropriate Makefile.machine, you can
			install/un-install the package and build LAMMPS in the usual manner:

			[Install or un-install:]

			make yes-user-omp
			make machine :pre

			make no-user-omp
			make machine :pre

			CCFLAGS: add -fopenmp (and -restrict when using Intel compilers)
			LINKFLAGS: add -fopenmp :ul

			[Supporting info:]

			src/USER-OMP: filenames -> commands
			src/USER-OMP/README
			"Section 5.3"_Section_accelerate.html#acc_3
			"Section 5.3.4"_accelerate_omp.html
			"Section 2.6 -sf omp"_Section_start.html#start_6
			"Section 2.6 -pk omp"_Section_start.html#start_6
			"package omp"_package.html
			Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o)
			"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul

			:line

			USER-PHONON package :link(USER-PHONON),h4

			[Contents:]

			A "fix phonon"_fix_phonon.html command that calculates dynamical
			matrices, which can then be used to compute phonon dispersion
			relations, directly from molecular dynamics simulations.

			[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).

			[Install or un-install:]

			make yes-user-phonon
			make machine :pre

			make no-user-phonon
			make machine :pre

			[Supporting info:]

			src/USER-PHONON: filenames -> commands
			src/USER-PHONON/README
			"fix phonon"_fix_phonon.html
			examples/USER/phonon :ul

			:line

			USER-QMMM package :link(USER-QMMM),h4

			[Contents:]

			A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
			QM/MM simulation, currently only in combination with the "Quantum
			ESPRESSO"_espresso package.

			:link(espresso,http://www.quantum-espresso.org)

			To use this package you must have Quantum ESPRESSO available on your
			system.

			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.

			[Author:] Axel Kohlmeyer (Temple U).

			[Install or un-install:]

			Before building LAMMPS with this package, you must first build the
			QMMM library in lib/qmmm. You can do this manually if you prefer;
			follow the first two steps explained in lib/qmmm/README. You can
			also do it in one step from the lammps/src dir, using a command like
			these, which simply invoke the lib/qmmm/Install.py script with the
			specified args:

			make lib-qmmm # print help message
			make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
			make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
			make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre

			The build should produce two files: lib/qmmm/libqmmm.a and
			lib/qmmm/Makefile.lammps. The latter is copied from an existing
			Makefile.lammps.* and has settings needed to build LAMMPS with the
			QMMM library (though typically the settings are just blank). If
			necessary, you can edit/create a new lib/qmmm/Makefile.machine file
			for your system, which should define an EXTRAMAKE variable to specify
			a corresponding Makefile.lammps.machine file.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-user-qmmm
			make machine :pre

			make no-user-qmmm
			make machine :pre

			NOTE: The LAMMPS executable these steps produce is not yet functional
			for a QM/MM simulation. You must also build Quantum ESPRESSO and
			create a new executable which links LAMMPS and Quanutm ESPRESSO
			together. These are steps 3 and 4 described in the lib/qmmm/README
			file.

			[Supporting info:]

			src/USER-QMMM: filenames -> commands
			src/USER-QMMM/README
			lib/qmmm/README
			"fix phonon"_fix_phonon.html
			lib/qmmm/example-ec/README
			lib/qmmm/example-mc/README :ul

			:line

			USER-QTB package :link(USER-QTB),h4

			[Contents:]

			Two fixes which provide a self-consistent quantum treatment of
			vibrational modes in a classical molecular dynamics simulation. By
			coupling the MD simulation to a colored thermostat, it introduces zero
			point energy into the system, altering the energy power spectrum and
			the heat capacity to account for their quantum nature. This is useful
			when modeling systems at temperatures lower than their classical
			limits or when temperatures ramp across the classical limits in a
			simulation.

			[Author:] Yuan Shen (Stanford U).

			[Install or un-install:]

			make yes-user-qtb
			make machine :pre

			make no-user-qtb
			make machine :pre

			[Supporting info:]

			src/USER-QTB: filenames -> commands
			src/USER-QTB/README
			"fix qtb"_fix_qtb.html
			"fix qbmsst"_fix_qbmsst.html
			examples/USER/qtb :ul

			:line

			USER-QUIP package :link(USER-QUIP),h4

			[Contents:]

			A "pair_style quip"_pair_quip.html command which wraps the "QUIP
			libAtoms library"_quip, which includes a variety of interatomic
			potentials, including Gaussian Approximation Potential (GAP) models
			developed by the Cambridge University group.

			:link(quip,https://github.com/libAtoms/QUIP)

			To use this package you must have the QUIP libAatoms library available
			on your system.

			[Author:] Albert Bartok (Cambridge University)

			[Install or un-install:]

			Note that to follow these steps to compile and link to the QUIP
			library, you must first download and build QUIP on your systems. It
			can be obtained from GitHub. See step 1 and step 1.1 in the
			lib/quip/README file for details on how to do this. Note that it
			requires setting two environment variables, QUIP_ROOT and QUIP_ARCH,
			which will be accessed by the lib/quip/Makefile.lammps file which is
			used when you compile and link LAMMPS with this package. You should
			only need to edit this file if the LAMMPS build can not use its
			settings to successfully build on your system.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-user-quip
			make machine :pre

			make no-user-quip
			make machine :pre

			[Supporting info:]

			src/USER-QUIP: filenames -> commands
			src/USER-QUIP/README
			"pair_style quip"_pair_quip.html
			examples/USER/quip :ul

			:line

			USER-REAXC package :link(USER-REAXC),h4

			[Contents:]

			A pair style which implements the ReaxFF potential in C/C++ (in
			contrast to the "REAX package"_#REAX and its Fortran library). ReaxFF
			is universal reactive force field. See the src/USER-REAXC/README file
			for more info on differences between the two packages. Also two fixes
			for monitoring molecules as bonds are created and destroyed.

			[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.

			[Install or un-install:]

			make yes-user-reaxc
			make machine :pre

			make no-user-reaxc
			make machine :pre

			[Supporting info:]

			src/USER-REAXC: filenames -> commands
			src/USER-REAXC/README
			"pair_style reax/c"_pair_reaxc.html
			"fix reax/c/bonds"_fix_reax_bonds.html
			"fix reax/c/species"_fix_reaxc_species.html
			examples/reax :ul

			:line

			USER-SMD package :link(USER-SMD),h4

			[Contents:]

			An atom style, fixes, computes, and several pair styles which
			implements smoothed Mach dynamics (SMD) for solids, which is a model
			related to smoothed particle hydrodynamics (SPH) for liquids (see the
			"USER-SPH package"_#USER-SPH).

			This package solves solids mechanics problems via a state of the art
			stabilized meshless method with hourglass control. It can specify
			hydrostatic interactions independently from material strength models,
			i.e. pressure and deviatoric stresses are separated. It provides many
			material models (Johnson-Cook, plasticity with hardening,
			Mie-Grueneisen, Polynomial EOS) and allows new material models to be
			added. It implements rigid boundary conditions (walls) which can be
			specified as surface geometries from *.STL files.

			[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
			Dynamics, Ernst Mach Institute, Germany).

			[Install or un-install:]

			Before building LAMMPS with this package, you must first download the
			Eigen library. Eigen is a template library, so you do not need to
			build it, just download it. You can do this manually if you prefer;
			follow the instructions in lib/smd/README. You can also do it in one
			step from the lammps/src dir, using a command like these, which simply
			invoke the lib/smd/Install.py script with the specified args:

			make lib-smd # print help message
			make lib-smd args="-b" # download and build in default lib/smd/eigen-eigen-...
			make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre

			Note that a symbolic (soft) link named "includelink" is created in
			lib/smd to point to the Eigen dir. When LAMMPS builds it will use
			this link. You should not need to edit the lib/smd/Makefile.lammps file.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-user-smd
			make machine :pre

			make no-user-smd
			make machine :pre

			[Supporting info:]

			src/USER-SMD: filenames -> commands
			src/USER-SMD/README
			doc/PDF/SMD_LAMMPS_userguide.pdf
			examples/USER/smd
			http://lammps.sandia.gov/movies.html#smd :ul

			:line

			USER-SMTBQ package :link(USER-SMTBQ),h4

			[Contents:]

			A pair style which implements a Second Moment Tight Binding model with
			QEq charge equilibration (SMTBQ) potential for the description of
			ionocovalent bonds in oxides.

			[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert
			Tetot (LAAS-CNRS, France).

			[Install or un-install:]

			make yes-user-smtbq
			make machine :pre

			make no-user-smtbq
			make machine :pre

			[Supporting info:]

			src/USER-SMTBQ: filenames -> commands
			src/USER-SMTBQ/README
			"pair_style smtbq"_pair_smtbq.html
			examples/USER/smtbq :ul

			:line

			USER-SPH package :link(USER-SPH),h4

			[Contents:]

			An atom style, fixes, computes, and several pair styles which
			implements smoothed particle hydrodynamics (SPH) for liquids. See the
			related "USER-SMD package"_#USER-SMD package for smooth Mach dynamics
			(SMD) for solids.

			This package contains ideal gas, Lennard-Jones equation of states,
			Tait, and full support for complete (i.e. internal-energy dependent)
			equations of state. It allows for plain or Monaghans XSPH integration
			of the equations of motion. It has options for density continuity or
			density summation to propagate the density field. It has
			"set"_set.html command options to set the internal energy and density
			of particles from the input script and allows the same quantities to
			be output with thermodynamic output or to dump files via the "compute
			property/atom"_compute_property_atom.html command.

			[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
			Dynamics, Ernst Mach Institute, Germany).

			[Install or un-install:]

			make yes-user-sph
			make machine :pre

			make no-user-sph
			make machine :pre

			[Supporting info:]

			src/USER-SPH: filenames -> commands
			src/USER-SPH/README
			doc/PDF/SPH_LAMMPS_userguide.pdf
			examples/USER/sph
			http://lammps.sandia.gov/movies.html#sph :ul

			:line

			USER-TALLY package :link(USER-TALLY),h4

			[Contents:]

			Several compute styles that can be called when pairwise interactions
			are calculated to tally information (forces, heat flux, energy,
			stress, etc) about individual interactions.

			[Author:] Axel Kohlmeyer (Temple U).

			[Install or un-install:]

			make yes-user-tally
			make machine :pre

			make no-user-tally
			make machine :pre

			[Supporting info:]

			src/USER-TALLY: filenames -> commands
			src/USER-TALLY/README
			"compute */tally"_compute_tally.html
			examples/USER/tally :ul

			:line

			USER-UEF package :link(USER-UEF),h4

			[Contents:]

			A fix style for the integration of the equations of motion under
			extensional flow with proper boundary conditions, as well as several
			supporting compute styles and an output option.

			[Author:] David Nicholson (MIT).

			[Install or un-install:]

			make yes-user-uef
			make machine :pre

			make no-user-uef
			make machine :pre

			[Supporting info:]

			src/USER-UEF: filenames -> commands
			src/USER-UEF/README
			"fix nvt/uef"_fix_nh_uef.html
			"fix npt/uef"_fix_nh_uef.html
			"compute pressure/uef"_compute_pressure_uef.html
			"compute temp/uef"_compute_temp_uef.html
			"dump cfg/uef"_dump_cfg_uef.html
			examples/uef :ul

			:line

			USER-VTK package :link(USER-VTK),h4

			[Contents:]

			A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
			"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
			other visuzlization packages.

			:link(vtk,http://www.vtk.org)
			:link(paraview,http://www.paraview.org)

			To use this package you must have VTK library available on your
			system.

			[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).

			[Install or un-install:]

			The lib/vtk/Makefile.lammps file has settings for accessing VTK files
			and its library, which are required for LAMMPS to build and link with
			this package. If the settings are not valid for your system, check if
			one of the other lib/vtk/Makefile.lammps.* files is compatible and
			copy it to Makefile.lammps. If none of the provided files work, you
			will need to edit the Makefile.lammps file.

			You can then install/un-install the package and build LAMMPS in the
			usual manner:

			make yes-user-vtk
			make machine :pre

			make no-user-vtk
			make machine :pre

			[Supporting info:]

			src/USER-VTK: filenames -> commands
			src/USER-VTK/README
			lib/vtk/README
			"dump vtk"_dump_vtk.html :ul

lammps/doc/src/Section_packages.txt281b1dc37571master

Section_packages.txtView Options

lammps/doc/src/Section_packages.txt
281b1dc37571master

Section_packages.txt
View Options