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Section"_Section_accelerate.html :c
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:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
4. Packages :h3
This section gives an overview of the add-on optional packages that
extend LAMMPS functionality. 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 by typing "make package" from within the src directory of
the LAMMPS distribution.
Here are links for two tables below, which list standard and user
packages.
4.1 "Standard packages"_#pkg_1
4.2 "User packages"_#pkg_2 :all(b)
"Section 2.3"_Section_start.html#start_3 of the manual describes
the difference between standard packages and user packages. It also
has general details on how to include/exclude specific packages as
part of the LAMMPS build process, and on how to build auxiliary
libraries or modify a machine Makefile if a package requires it.
Following the two tables below, is a sub-section for each package. It
has a summary of what the package contains. It has specific
instructions on how to install it, build or obtain any auxiliary
library it requires, and any Makefile.machine changes it requires. It
also lists pointers to examples of its use or documentation provided
in the LAMMPS distribution. If you want to know the complete list of
commands that a package adds to LAMMPS, simply list the files in its
directory, e.g. "ls src/GRANULAR". Source files with names that start
with compute, fix, pair, bond, etc correspond to command styles with
the same names.
NOTE: The USER package sub-sections below are still being filled in,
as of March 2016.
Unless otherwise noted below, every package is independent of all the
others. I.e. any package can be included or excluded in a LAMMPS
build, independent of all other packages. However, note that some
packages include commands derived from commands in other packages. If
the other package is not installed, the derived command from the new
package will also not be installed when you include the new one.
E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
will not be installed as part of the USER-OMP package if the KSPACE
package is not also installed, since it contains the pair
lj/cut/coul/long command. If you later install the KSPACE package and
the USER-OMP package is already installed, both the pair
lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
:line
4.1 Standard packages :h4,link(pkg_1)
The current list of standard packages is as follows. Each package
name links to a sub-section below with more details.
Package, Description, Author(s), Doc page, Example, Library
"ASPHERE"_#ASPHERE, aspherical particles, -, "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, Kumar (1), "atom_style colloid"_atom_style.html, colloid, -
"COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "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, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu
"GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
"KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5"_accelerate_kokkos.html, kokkos, lib/kokkos
"KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
"MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
"MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
"MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, -
"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
"REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
"RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
"SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
"SNAP"_#SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, -
"SRD"_#SRD, stochastic rotation dynamics, -, "fix srd"_fix_srd.html, srd, -
"VORONOI"_#VORONOI, Voronoi tesselations, Daniel Schwen (LANL), "compute voronoi/atom"_compute_voronoi_atom.html, -, Voro++
:tb(ea=c)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
(1) The COLLOID package includes Fast Lubrication Dynamics pair styles
which were created by Amit Kumar and Michael Bybee from Jonathan
Higdon's group at UIUC.
(2) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).
(4) The KOKKOS package was created primarily by Christian Trott and
Stan Moore (Sandia). It uses the Kokkos library which was developed
by Carter Edwards, Christian Trott, and others at Sandia.
The "Doc page" column links to either a sub-section of the
"Section 6"_Section_howto.html of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided within the package.
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.
The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See details on all of this below for individual packages.
p.s.: are we ever going to get commit messages from you? ;-)
:line
ASPHERE package :link(ASPHERE),h5
Contents: Several computes, time-integration fixes, and pair styles
for aspherical particle models: ellipsoids, 2d lines, 3d triangles.
To install via make or Make.py:
make yes-asphere
make machine :pre
Make.py -p asphere -a machine :pre
To un-install via make or Make.py:
make no-asphere
make machine :pre
Make.py -p ^asphere -a machine :pre
Supporting info: "Section howto 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
:line
BODY package :link(BODY),h5
Contents: Support for body-style particles. Computes,
time-integration fixes, pair styles, as well as the body styles
themselves. See the "body"_body.html doc page for an overview.
To install via make or Make.py:
make yes-body
make machine :pre
Make.py -p body -a machine :pre
To un-install via make or Make.py:
make no-body
make machine :pre
Make.py -p ^body -a machine :pre
Supporting info: "atom_style body"_atom_style.html, "body"_body.html,
"pair_style body"_pair_body.html, examples/body
:line
CLASS2 package :link(CLASS2),h5
Contents: Bond, angle, dihedral, improper, and pair styles for the
COMPASS CLASS2 molecular force field.
To install via make or Make.py:
make yes-class2
make machine :pre
Make.py -p class2 -a machine :pre
To un-install via make or Make.py:
make no-class2
make machine :pre
Make.py -p ^class2 -a machine :pre
Supporting info: "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
:line
COLLOID package :link(COLLOID),h5
Contents: Support for coarse-grained colloidal particles. Wall fix
and pair styles that implement colloidal interaction models for
finite-size particles. This includes the Fast Lubrication Dynamics
method for hydrodynamic interactions, which is a simplified
approximation to Stokesian dynamics.
To install via make or Make.py:
make yes-colloid
make machine :pre
Make.py -p colloid -a machine :pre
To un-install via make or Make.py:
make no-colloid
make machine :pre
Make.py -p ^colloid -a machine :pre
Supporting info: "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
:line
COMPRESS package :link(COMPRESS),h5
Contents: Support for compressed output of dump files via the zlib
compression library, using dump styles with a "gz" in their style
name.
Building with the COMPRESS package assumes you have the zlib
compression library available on your system. The build uses the
lib/compress/Makefile.lammps file in the compile/link process. You
should only need to edit this file if the LAMMPS build cannot find the
zlib info it specifies.
To install via make or Make.py:
make yes-compress
make machine :pre
Make.py -p compress -a machine :pre
To un-install via make or Make.py:
make no-compress
make machine :pre
Make.py -p ^compress -a machine :pre
Supporting info: 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
:line
CORESHELL package :link(CORESHELL),h5
Contents: Compute and pair styles that implement the adiabatic
core/shell model for polarizability. The compute temp/cs command
measures the temperature of a system with core/shell particles. The
pair styles augment Born, Buckingham, and Lennard-Jones styles with
core/shell capabilities. See "Section howto
6.26"_Section_howto.html#howto_26 for an overview of how to use the
package.
To install via make or Make.py:
make yes-coreshell
make machine :pre
Make.py -p coreshell -a machine :pre
To un-install via make or Make.py:
make no-coreshell
make machine :pre
Make.py -p ^coreshell -a machine :pre
Supporting info: "Section howto
6.26"_Section_howto.html#howto_26, "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
:line
DIPOLE package :link(DIPOLE),h5
Contents: An atom style and several pair styles to support point
dipole models with short-range or long-range interactions.
To install via make or Make.py:
make yes-dipole
make machine :pre
Make.py -p dipole -a machine :pre
To un-install via make or Make.py:
make no-dipole
make machine :pre
Make.py -p ^dipole -a machine :pre
Supporting info: "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
:line
GPU package :link(GPU),h5
Contents: Dozens of pair styles and a version of the PPPM long-range
Coulombic solver for NVIDIA GPUs. All of them have a "gpu" in their
style name. "Section accelerate gpu"_accelerate_gpu.html gives
details of what hardware and Cuda software is required on your system,
and how to build and use this package. See the KOKKOS package, which
also has GPU-enabled styles.
Building LAMMPS with the GPU package requires first building the GPU
library itself, which is a set of C and Cuda files in lib/gpu.
Details of how to do this are in lib/gpu/README. As illustrated
below, perform a "make" using one of the Makefile.machine files in
lib/gpu which should create a lib/reax/libgpu.a file.
Makefile.linux.* and Makefile.xk7 are examples for different
platforms. There are 3 important settings in the Makefile.machine you
use:
CUDA_HOME = where NVIDIA Cuda software is installed on your system
CUDA_ARCH = appropriate to your GPU hardware
CUDA_PREC = precision (double, mixed, single) you desire :ul
See example Makefile.machine files in lib/gpu for the syntax of these
settings. See lib/gpu/Makefile.linux.double for ARCH settings for
various NVIDIA GPUs. The "make" also creates a
lib/gpu/Makefile.lammps file. This file has settings that enable
LAMMPS to link with Cuda libraries. If the settings in
Makefile.lammps for your machine are not correct, the LAMMPS link will
fail. Note that the Make.py script has a "-gpu" option to allow the
GPU library (with several of its options) and LAMMPS to be built in
one step, with Type "python src/Make.py -h -gpu" to see the details.
To install via make or Make.py:
cd ~/lammps/lib/gpu
make -f Makefile.linux.mixed # for example
cd ~/lammps/src
make yes-gpu
make machine :pre
Make.py -p gpu -gpu mode=mixed arch=35 -a machine :pre
To un-install via make or Make.py:
make no-gpu
make machine :pre
Make.py -p ^gpu -a machine :pre
Supporting info: src/GPU/README, lib/gpu/README, "Section
acclerate"_Section_accelerate.html, "Section accelerate
gpu"_accelerate_gpu.html, Pair Styles section of "Section commands
3.5"_Section_commands.html#cmd_5 for any pair style listed with a (g),
"kspace_style"_kspace_style.html, "package gpu"_package.html,
examples/accelerate, bench/FERMI, bench/KEPLER
:line
GRANULAR package :link(GRANULAR),h5
Contents: Fixes and pair styles that support models of finite-size
granular particles, which interact with each other and boundaries via
frictional and dissipative potentials.
To install via make or Make.py:
make yes-granular
make machine :pre
Make.py -p granular -a machine :pre
To un-install via make or Make.py:
make no-granular
make machine :pre
Make.py -p ^granular -a machine :pre
Supporting info: "Section howto 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/pour, bench/in.chute
:line
KIM package :link(KIM),h5
Contents: A pair style that interfaces to the Knowledge Base for
Interatomic Models (KIM) repository of interatomic potentials, so that
KIM potentials can be used in a LAMMPS simulation.
To build LAMMPS with the KIM package you must have previously
installed the KIM API (library) on your system. The lib/kim/README
file explains how to download and install KIM. Building with the KIM
package also uses the lib/kim/Makefile.lammps file in the compile/link
process. You should not need to edit this file.
To install via make or Make.py:
make yes-kim
make machine :pre
Make.py -p kim -a machine :pre
To un-install via make or Make.py:
make no-kim
make machine :pre
Make.py -p ^kim -a machine :pre
Supporting info: src/KIM/README, lib/kim/README, "pair_style
kim"_pair_kim.html, examples/kim
:line
KOKKOS package :link(KOKKOS),h5
Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
which run with the Kokkos library to provide optimization for
multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in
native mode). All of them have a "kk" in their style name. "Section
accelerate kokkos"_accelerate_kokkos.html gives details of what
hardware and software is required on your system, and how to build and
use this package. See the GPU, OPT, USER-INTEL, USER-OMP packages,
which also provide optimizations for the same range of hardware.
Building with the KOKKOS package requires choosing which of 3 hardware
options you are optimizing for: CPU acceleration via OpenMP, GPU
acceleration, or Intel Xeon Phi. (You can build multiple times to
create LAMMPS executables for different hardware.) It also requires a
C++11 compatible compiler. For GPUs, the NVIDIA "nvcc" compiler is
used, and an appopriate KOKKOS_ARCH setting should be made in your
Makefile.machine for your GPU hardware and NVIDIA software.
The simplest way to do this is to use Makefile.kokkos_cuda or
Makefile.kokkos_omp or Makefile.kokkos_phi in src/MAKE/OPTIONS, via
"make kokkos_cuda" or "make kokkos_omp" or "make kokkos_phi". (Check
the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated
below, you can use the Make.py script with its "-kokkos" option to
choose which hardware to build for. Type "python src/Make.py -h
-kokkos" to see the details. If these methods do not work on your
system, you will need to read the "Section accelerate
kokkos"_accelerate_kokkos.html doc page for details of what
Makefile.machine settings are needed.
To install via make or Make.py for each of 3 hardware options:
make yes-kokkos
make kokkos_omp # for CPUs with OpenMP
make kokkos_cuda # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda
make kokkos_phi # for Xeon Phis :pre
Make.py -p kokkos -kokkos omp -a machine # for CPUs with OpenMP
Make.py -p kokkos -kokkos cuda arch=35 -a machine # for GPUs of style arch
Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis
To un-install via make or Make.py:
make no-kokkos
make machine :pre
Make.py -p ^kokkos -a machine :pre
Supporting info: src/KOKKOS/README, lib/kokkos/README, "Section
acclerate"_Section_accelerate.html, "Section accelerate
kokkos"_accelerate_kokkos.html, Pair Styles section of "Section
commands 3.5"_Section_commands.html#cmd_5 for any pair style listed
with a (k), "package kokkos"_package.html,
examples/accelerate, bench/FERMI, bench/KEPLER
:line
KSPACE package :link(KSPACE),h5
Contents: A variety of long-range Coulombic solvers, and pair styles
which compute the corresponding short-range portion of the pairwise
Coulombic interactions. These include Ewald, particle-particle
particle-mesh (PPPM), and multilevel summation method (MSM) solvers.
Building with the KSPACE 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, or 3rd party libraries like FFTW or a
vendor-supplied FFT library. See step 6 of "Section start
2.2.2"_Section_start.html#start_2_2 of the manual for details of how
to select different FFT options in your machine Makefile. The Make.py
tool has an "-fft" option which can insert these settings into your
machine Makefile automatically. Type "python src/Make.py -h -fft" to
see the details.
To install via make or Make.py:
make yes-kspace
make machine :pre
Make.py -p kspace -a machine :pre
To un-install via make or Make.py:
make no-kspace
make machine :pre
Make.py -p ^kspace -a machine :pre
Supporting info: "kspace_style"_kspace_style.html,
"doc/PDF/kspace.pdf"_PDF/kspace.pdf, "Section howto
6.7"_Section_howto.html#howto_7, "Section howto
6.8"_Section_howto.html#howto_8, "Section howto
6.9"_Section_howto.html#howto_9, "pair_style coul"_pair_coul.html,
other pair style command doc pages which have "long" or "msm" in their
style name, examples/peptide, bench/in.rhodo
:line
MANYBODY package :link(MANYBODY),h5
Contents: A variety of many-body and bond-order potentials. These
include (AI)REBO, EAM, EIM, BOP, Stillinger-Weber, and Tersoff
potentials. Do a directory listing, "ls src/MANYBODY", to see
the full list.
To install via make or Make.py:
make yes-manybody
make machine :pre
Make.py -p manybody -a machine :pre
To un-install via make or Make.py:
make no-manybody
make machine :pre
Make.py -p ^manybody -a machine :pre
Supporting info:
Examples: Pair Styles section of "Section commands
3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,
examples/nb3d, examples/vashishta
:line
MC package :link(MC),h5
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, and for performing atomic swaps and grand-canonical MC
in conjuction with dynamics.
To install via make or Make.py:
make yes-mc
make machine :pre
Make.py -p mc -a machine :pre
To un-install via make or Make.py:
make no-mc
make machine :pre
Make.py -p ^mc -a machine :pre
Supporting info: "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
:line
MEAM package :link(MEAM),h5
Contents: A pair style for the modified embedded atom (MEAM)
potential.
Building LAMMPS with the MEAM package requires first building the MEAM
library itself, which is a set of Fortran 95 files in lib/meam.
Details of how to do this are in lib/meam/README. As illustrated
below, perform a "make" using one of the Makefile.machine files in
lib/meam which should create a lib/meam/libmeam.a file.
Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran
and Intel Fortran compilers. The "make" also copies a
lib/meam/Makefile.lammps.machine file to lib/meam/Makefile.lammps.
This file has settings that enable the C++ compiler used to build
LAMMPS to link with a Fortran library (typically the 2 compilers to be
consistent e.g. both Intel compilers, or both GNU compilers). If the
settings in Makefile.lammps for your compilers and machine are not
correct, the LAMMPS link will fail. Note that the Make.py script has
a "-meam" option to allow the MEAM library and LAMMPS to be built in
one step. Type "python src/Make.py -h -meam" to see the details.
NOTE: The MEAM potential can run dramatically faster if built with the
Intel Fortran compiler, rather than the GNU Fortran compiler.
To install via make or Make.py:
cd ~/lammps/lib/meam
make -f Makefile.gfortran # for example
cd ~/lammps/src
make yes-meam
make machine :pre
Make.py -p meam -meam make=gfortran -a machine :pre
To un-install via make or Make.py:
make no-meam
make machine :pre
Make.py -p ^meam -a machine :pre
Supporting info: lib/meam/README, "pair_style meam"_pair_meam.html,
examples/meam
:line
MISC package :link(MISC),h5
Contents: A variety of computes, fixes, and pair styles that are not
commonly used, but don't align with other packages. Do a directory
listing, "ls src/MISC", to see the list of commands.
To install via make or Make.py:
make yes-misc
make machine :pre
Make.py -p misc -a machine :pre
To un-install via make or Make.py:
make no-misc
make machine :pre
Make.py -p ^misc -a machine :pre
Supporting info: "compute ti"_compute_ti.html, "fix
evaporate"_fix_evaporate.html, "fix tmm"_fix_ttm.html, "fix
viscosity"_fix_viscosity.html, examples/misc
:line
MOLECULE package :link(MOLECULE),h5
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 terms for the Dreiding
(hydrogen-bonding) and CHARMM force fields, and TIP4P water model.
To install via make or Make.py:
make yes-molecule
make machine :pre
Make.py -p molecule -a machine :pre
To un-install via make or Make.py:
make no-molecule
make machine :pre
Make.py -p ^molecule -a machine :pre
Supporting info:"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 howto
6.3"_Section_howto.html#howto_3, examples/micelle, examples/peptide,
bench/in.chain, bench/in.rhodo
:line
MPIIO package :link(MPIIO),h5
Contents: Support for parallel output/input of dump and restart files
via the MPIIO library, which is part of the standard message-passing
interface (MPI) 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.
To install via make or Make.py:
make yes-mpiio
make machine :pre
Make.py -p mpiio -a machine :pre
To un-install via make or Make.py:
make no-mpiio
make machine :pre
Make.py -p ^mpiio -a machine :pre
Supporting info: "dump"_dump.html, "restart"_restart.html,
"write_restart"_write_restart.html, "read_restart"_read_restart.html
:line
OPT package :link(OPT),h5
Contents: A handful of pair styles with an "opt" in their style name
which are optimized for improved CPU performance on single or multiple
cores. These include EAM, LJ, CHARMM, and Morse potentials. "Section
accelerate opt"_accelerate_opt.html gives details of how to build and
use this package. See the KOKKOS, USER-INTEL, and USER-OMP packages,
which also have styles optimized for CPU performance.
Some C++ compilers, like the Intel compiler, require the compile flag
"-restrict" to build LAMMPS with the OPT package. It should be added
to the CCFLAGS line of your Makefile.machine. Or use Makefile.opt in
src/MAKE/OPTIONS, via "make opt". For compilers that use the flag,
the Make.py command adds it automatically to the Makefile.auto file it
creates and uses.
To install via make or Make.py:
make yes-opt
make machine :pre
Make.py -p opt -a machine :pre
To un-install via make or Make.py:
make no-opt
make machine :pre
Make.py -p ^opt -a machine :pre
Supporting info: "Section acclerate"_Section_accelerate.html, "Section
accelerate opt"_accelerate_opt.html, Pair Styles section of "Section
commands 3.5"_Section_commands.html#cmd_5 for any pair style listed
with an (o), examples/accelerate, bench/KEPLER
:line
PERI package :link(PERI),h5
Contents: Support for the Peridynamics method, a particle-based
meshless continuum model. The package includes an atom style, several
computes which calculate diagnostics, and several Peridynamic pair
styles which implement different materials models.
To install via make or Make.py:
make yes-peri
make machine :pre
Make.py -p peri -a machine :pre
To un-install via make or Make.py:
make no-peri
make machine :pre
Make.py -p ^peri -a machine :pre
Supporting info:
"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, "compute damage/atom"_compute_damage_atom.html,
"pair_style peri/pmb"_pair_peri.html, examples/peri
:line
POEMS package :link(POEMS),h5
Contents: A fix that wraps the Parallelizable Open source Efficient
Multibody Software (POEMS) librar, which is able to simulate the
dynamics of articulated body systems. These are systems with multiple
rigid bodies (collections of atoms or particles) whose motion is
coupled by connections at hinge points.
Building LAMMPS with the POEMS package requires first building the
POEMS library itself, which is a set of C++ files in lib/poems.
Details of how to do this are in lib/poems/README. As illustrated
below, perform a "make" using one of the Makefile.machine files in
lib/poems which should create a lib/meam/libpoems.a file.
Makefile.g++ and Makefile.icc are examples for the GNU and Intel C++
compilers. The "make" also creates a lib/poems/Makefile.lammps file
which you should not need to change. Note the Make.py script has a
"-poems" option to allow the POEMS library and LAMMPS to be built in
one step. Type "python src/Make.py -h -poems" to see the details.
To install via make or Make.py:
cd ~/lammps/lib/poems
make -f Makefile.g++ # for example
cd ~/lammps/src
make yes-poems
make machine :pre
Make.py -p poems -poems make=g++ -a machine :pre
To un-install via make or Make.py:
make no-meam
make machine :pre
Make.py -p ^meam -a machine :pre
Supporting info: src/POEMS/README, lib/poems/README,
"fix poems"_fix_poems.html, examples/rigid
:line
PYTHON package :link(PYTHON),h5
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 python
11.2"_Section_python.html" for an overview of using Python from
LAMMPS and for other ways to use LAMMPS and Python together.
Building with the PYTHON package assumes you have a Python shared
library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not supported. The build uses the
contents of the lib/python/Makefile.lammps file to find all the Python
files required in the build/link process. See the lib/python/README
file if the settings in that file do not work on your system. Note
that the Make.py script has a "-python" option to allow an alternate
lib/python/Makefile.lammps file to be specified and LAMMPS to be built
in one step. Type "python src/Make.py -h -python" to see the details.
To install via make or Make.py:
make yes-python
make machine :pre
Make.py -p python -a machine :pre
To un-install via make or Make.py:
make no-python
make machine :pre
Make.py -p ^python -a machine :pre
Supporting info: examples/python
:line
QEQ package :link(QEQ),h5
Contents: Several fixes for performing charge equilibration (QEq) via
severeal different algorithms. These can be used with pair styles
that use QEq as part of their formulation.
To install via make or Make.py:
make yes-qeq
make machine :pre
Make.py -p qeq -a machine :pre
To un-install via make or Make.py:
make no-qeq
make machine :pre
Make.py -p ^qeq -a machine :pre
Supporting info: "fix qeq/*"_fix_qeq.html, examples/qeq
:line
REAX package :link(REAX),h5
Contents: A pair style for the ReaxFF potential, a universal reactive
force field, as well as a "fix reax/bonds"_fix_reax_bonds.html command
for monitoring molecules as bonds are created and destroyed.
Building LAMMPS with the REAX package requires first building the REAX
library itself, which is a set of Fortran 95 files in lib/reax.
Details of how to do this are in lib/reax/README. As illustrated
below, perform a "make" using one of the Makefile.machine files in
lib/reax which should create a lib/reax/libreax.a file.
Makefile.gfortran and Makefile.ifort are examples for the GNU Fortran
and Intel Fortran compilers. The "make" also copies a
lib/reax/Makefile.lammps.machine file to lib/reax/Makefile.lammps.
This file has settings that enable the C++ compiler used to build
LAMMPS to link with a Fortran library (typically the 2 compilers to be
consistent e.g. both Intel compilers, or both GNU compilers). If the
settings in Makefile.lammps for your compilers and machine are not
correct, the LAMMPS link will fail. Note that the Make.py script has
a "-reax" option to allow the REAX library and LAMMPS to be built in
one step. Type "python src/Make.py -h -reax" to see the details.
To install via make or Make.py:
cd ~/lammps/lib/reax
make -f Makefile.gfortran # for example
cd ~/lammps/src
make yes-reax
make machine :pre
Make.py -p reax -reax make=gfortran -a machine :pre
To un-install via make or Make.py:
make no-reax
make machine :pre
Make.py -p ^reax -a machine :pre
Supporting info: lib/reax/README, "pair_style reax"_pair_reax.html,
"fix reax/bonds"_fix_reax_bonds.html, examples/reax
:line
REPLICA package :link(REPLICA),h5
Contents: A collection of multi-replica methods that are used by
invoking multiple instances (replicas) of LAMMPS
simulations. Communication between individual replicas is performed in
different ways by the different methods. See "Section howto
6.5"_Section_howto.html#howto_5 for an overview of how to run
multi-replica simulations in LAMMPS. Multi-replica methods included
in the package are 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 remainded of the force
field calcalation on another set.
To install via make or Make.py:
make yes-replica
make machine :pre
Make.py -p replica -a machine :pre
To un-install via make or Make.py:
make no-replica
make machine :pre
Make.py -p ^replica -a machine :pre
Supporting info: "Section howto 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
:line
RIGID package :link(RIGID),h5
Contents: A collection of computes and fixes which enforce rigid
constraints on collections of atoms or particles. This includes SHAKE
and RATTLE, as well as variants of rigid-body time integrators for a
few large bodies or many small bodies.
To install via make or Make.py:
make yes-rigid
make machine :pre
Make.py -p rigid -a machine :pre
To un-install via make or Make.py:
make no-rigid
make machine :pre
Make.py -p ^rigid -a machine :pre
Supporting info: "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
:line
SHOCK package :link(SHOCK),h5
Contents: A small number of fixes useful for running impact
simulations where a shock-wave passes through a material.
To install via make or Make.py:
make yes-shock
make machine :pre
Make.py -p shock -a machine :pre
To un-install via make or Make.py:
make no-shock
make machine :pre
Make.py -p ^shock -a machine :pre
Supporting info: "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
:line
SNAP package :link(SNAP),h5
Contents: A pair style for the spectral neighbor analysis potential
(SNAP), which is an empirical potential which can be quantum accurate
when fit to an archive of DFT data. Computes useful for analyzing
properties of the potential are also included.
To install via make or Make.py:
make yes-snap
make machine :pre
Make.py -p snap -a machine :pre
To un-install via make or Make.py:
make no-snap
make machine :pre
Make.py -p ^snap -a machine :pre
Supporting info: "pair 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
:line
SRD package :link(SRD),h5
Contents: Two fixes which implement the Stochastic Rotation Dynamics
(SRD) method for coarse-graining of a solvent, typically around large
colloidal-scale particles.
To install via make or Make.py:
make yes-srd
make machine :pre
Make.py -p srd -a machine :pre
To un-install via make or Make.py:
make no-srd
make machine :pre
Make.py -p ^srd -a machine :pre
Supporting info: "fix srd"_fix_srd.html, "fix
wall/srd"_fix_wall_srd.html, examples/srd, examples/ASPHERE
:line
VORONOI package :link(VORONOI),h5
Contents: A "compute voronoi/atom"_compute_voronoi_atom.html command
which computes the Voronoi tesselation of a collection of atoms or
particles by wrapping the Voro++ lib
To build LAMMPS with the KIM package you must have previously
installed the KIM API (library) on your system. The lib/kim/README
file explains how to download and install KIM. Building with the KIM
package also uses the lib/kim/Makefile.lammps file in the compile/link
process. You should not need to edit this file.
To build LAMMPS with the VORONOI package you must have previously
installed the Voro++ library on your system. The lib/voronoi/README
file explains how to download and install Voro++. There is a
lib/voronoi/install.py script which automates the process. Type
"python install.py" to see instructions. The final step is to create
soft links in the lib/voronoi directory for "includelink" and
"liblink" which point to installed Voro++ directories. Building with
the VORONOI package uses the contents of the
lib/voronoi/Makefile.lammps file in the compile/link process. You
should not need to edit this file. Note that the Make.py script has a
"-voronoi" option to allow the Voro++ library to be downloaded and/or
installed and LAMMPS to be built in one step. Type "python
src/Make.py -h -voronoi" to see the details.
To install via make or Make.py:
cd ~/lammps/lib/voronoi
python install.py -g -b -l # download Voro++, build in lib/voronoi, create links
cd ~/lammps/src
make yes-voronoi
make machine :pre
Make.py -p voronoi -voronoi install="-g -b -l" -a machine :pre
To un-install via make or Make.py:
make no-voronoi
make machine :pre
Make.py -p ^voronoi -a machine :pre
Supporting info: src/VORONOI/README, lib/voronoi/README, "compute
voronoi/atom"_compute_voronoi_atom.html, examples/voronoi
:line
4.2 User packages :h4,link(pkg_2)
The current list of user-contributed packages is as follows:
Package, Description, Author(s), Doc page, Example, Pic/movie, Library
"USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
"USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
"USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
"USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
"USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
"USER-DRUDE"_#USER-DRUDE, Drude oscillators, Dequidt & Devemy & Padua (3), "tutorial"_tutorial_drude.html, USER/drude, -, -
"USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
"USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
"USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
"USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
"USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -
"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
"USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -
"USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
"USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
"USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, -
"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip
"USER-REAXC"_#USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
"USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, -
"USER-SMTBQ"_#USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, -
"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
"USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute XXX/tally"_compute_tally.html, USER/tally, -, -
"USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_dump_custom_vtk.html, -, -, lib/vtk
:tb(ea=c)
:link(atc,http://lammps.sandia.gov/pictures.html#atc)
:link(cg,http://lammps.sandia.gov/pictures.html#cg)
:link(eff,http://lammps.sandia.gov/movies.html#eff)
:link(manifold,http://lammps.sandia.gov/movies.html#manifold)
:link(sph,http://lammps.sandia.gov/movies.html#sph)
:link(VMD,http://www.ks.uiuc.edu/Research/vmd)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).
(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
the colvars module library written by Giacomo Fiorin (Temple U) and
Jerome Henin (LISM, Marseille, France).
(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(U Blaise Pascal).
(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
(5) The USER-DPD package was created by James Larentzos (ARL), Timothy
Mattox (Engility), and John Brennan (ARL).
(6) The USER-VTK package was created by Richard Berger (JKU) and
Daniel Queteschiner (DCS Computing).
The "Doc page" column links to either a sub-section of the
"Section 6"_Section_howto.html of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided within the package.
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.
The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See details on all of this below for individual packages.
:line
USER-ATC package :link(USER-ATC),h5
Contents: ATC stands for atoms-to-continuum. This package implements
a "fix atc"_fix_atc.html command to either couple MD with continuum
finite element equations or perform on-the-fly post-processing of
atomic information to continuum fields. See src/USER-ATC/README for
more details.
To build LAMMPS with this package ...
To install via make or Make.py:
make yes-user-atc
make machine :pre
Make.py -p atc -a machine :pre
To un-install via make or Make.py:
make no-user-atc
make machine :pre
Make.py -p ^atc -a machine :pre
Supporting info:src/USER-ATC/README, "fix atc"_fix_atc.html,
examples/USER/atc
Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl
at sandia.gov) and Jon Zimmerman (jzimmer at sandia.gov) at Sandia.
Contact them directly if you have questions.
:line
USER-AWPMD package :link(USER-AWPMD),h5
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 an MD
calculation. See src/USER-AWPMD/README for more details.
To build LAMMPS with this package ...
Supporting info: src/USER-AWPMD/README, "fix
awpmd/cut"_pair_awpmd.html, examples/USER/awpmd
Author: Ilya Valuev at the JIHT in Russia (valuev at
physik.hu-berlin.de). Contact him directly if you have questions.
:line
USER-CG-CMM package :link(USER-CG-CMM),h5
Contents: CG-CMM stands for coarse-grained ??. This package
implements several pair styles and an angle style using the coarse
grained parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27
(2007) (SDK), with extensions to simulate ionic liquids, electrolytes,
lipids and charged amino acids. See src/USER-CG-CMM/README for more
details.
Supporting info: src/USER-CG-CMM/README, "pair lj/sdk"_pair_sdk.html,
"pair lj/sdk/coul/long"_pair_sdk.html, "angle sdk"_angle_sdk.html,
examples/USER/cg-cmm
Author: Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact
him directly if you have questions.
:line
USER-COLVARS package :link(USER-COLVARS),h5
Contents: COLVARS stands for collective variables which can be used to
implement Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This package implements a "fix
colvars"_fix_colvars.html command which wraps a COLVARS library which
can perform those kinds of simulations. See src/USER-COLVARS/README
for more details.
Supporting info:
"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
Authors: Axel Kohlmeyer at Temple U (akohlmey at gmail.com) wrote the
fix. The COLVARS library itself is written and maintained by Giacomo
Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome
Henin (LISM, CNRS, Marseille, France). Contact them directly if you
have questions.
:line
USER-DIFFRACTION package :link(USER-DIFFRACTION),h5
Contents: This packages implements two computes and a fix for
calculating x-ray and electron diffraction intensities based on
kinematic diffraction theory. See src/USER-DIFFRACTION/README for
more details.
Supporting info: "compute saed"_compute_saed.html, "compute
xrd"_compute_xrd.html, "fix saed/vtk"_fix_saed_vtk.html,
examples/USER/diffraction
Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at
the University of Arkansas. Contact him directly if you have
questions.
:line
USER-DPD package :link(USER-DPD),h5
Contents: DPD stands for dissipative particle dynamics, This package
implements DPD for isothermal, isoenergetic, isobaric and isenthalpic
conditions. It also has extensions for performing reactive DPD, where
each particle has internal state for multiple species and a coupled
set of chemical reaction ODEs are integrated each timestep. The DPD
equations of motion are integrated efficiently through the Shardlow
splitting algorithm. See src/USER-DPD/README for more details.
Supporting info: /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 table/rx"_pair_table_rx.html
"pair dpd/fdt"_pair_dpd_fdt.html "pair dpd/fdt/energy"_pair_dpd_fdt.html
"pair exp6/rx"_pair_exp6_rx.html "pair multi/lucy"_pair_multi_lucy.html
"pair multi/lucy/rx"_pair_multi_lucy_rx.html, examples/USER/dpd
Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),
Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com)
and John Brennan (ARL) (john.k.brennan.civ at mail.mil). Contact them
directly if you have questions.
:line
USER-DRUDE package :link(USER-DRUDE),h5
Contents: This package contains methods for simulating polarizable
systems using thermalized Drude oscillators. It has computes, fixes,
and pair styles for this purpose. See "Section howto
6.27"_Section_howto.html#howto_27 for an overview of how to use the
package. See src/USER-DRUDE/README for additional details. There are
auxiliary tools for using this package in tools/drude.
Supporting info: "Section howto 6.27"_Section_howto.html#howto_27,
src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix
drude/transform/*"_fix_drude_transform.html, "compute
temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html,
"pair lj/cut/thole/long"_pair_thole.html, examples/USER/drude,
tools/drude
Authors: Alain Dequidt at Universite Blaise Pascal Clermont-Ferrand
(alain.dequidt at univ-bpclermont.fr); co-authors: Julien Devemy,
Agilio Padua. Contact them directly if you have questions.
:line
USER-EFF package :link(USER-EFF),h5
Contents: EFF stands for electron force field. 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. See src/USER-EFF/README for more details. There are
auxiliary tools for using this package in tools/eff; see its README
file.
Supporting info:
Author: Andres Jaramillo-Botero at CalTech (ajaramil at
wag.caltech.edu). Contact him directly if you have questions.
:line
USER-FEP package :link(USER-FEP),h5
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. See src/USER-FEP/README for
more details. There are auxiliary tools for using this package in
tools/fep; see its README file.
Supporting info: 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
Author: Agilio Padua at Universite Blaise Pascal Clermont-Ferrand
(agilio.padua at univ-bpclermont.fr). Contact him directly if you have
questions.
:line
USER-H5MD package :link(USER-H5MD),h5
Contents: H5MD stands for HDF5 for MD. "HDF5"_HDF5 is a binary,
portable, 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. See src/USER-H5MD/README
for more details.
:link(HDF5,http://www.hdfgroup.org/HDF5/)
Supporting info: src/USER-H5MD/README, lib/h5md/README, "dump
h5md"_dump_h5md.html
Author: Pierre de Buyl at KU Leuven (see http://pdebuyl.be) created
this package as well as the H5MD format and library. Contact him
directly if you have questions.
:line
USER-INTEL package :link(USER-INTEL),h5
Contents: Dozens of pair, bond, angle, dihedral, and improper styles
that are optimized for Intel CPUs and the Intel Xeon Phi (in offload
mode). All of them have an "intel" in their style name. "Section
accelerate intel"_accelerate_intel.html gives details of what hardware
and compilers are required on your system, and how to build and use
this package. Also see src/USER-INTEL/README for more details. See
the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
Phi-enabled styles.
Supporting info: examples/accelerate, src/USER-INTEL/TEST
"Section 5"_Section_accelerate.html#acc_3
Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact
him directly if you have questions.
For the USER-INTEL package, you have 2 choices when building. You can
build with CPU or Phi support. The latter uses Xeon Phi chips in
"offload" mode. Each of these modes requires additional settings in
your Makefile.machine for CCFLAGS and LINKFLAGS.
For CPU mode (if using an Intel compiler):
CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
LINKFLAGS: add -fopenmp :ul
For Phi mode add the following in addition to the CPU mode flags:
CCFLAGS: add -DLMP_INTEL_OFFLOAD and
LINKFLAGS: add -offload :ul
And also add this to CCFLAGS:
-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" :pre
Examples:
:line
USER-LB package :link(USER-LB),h5
Supporting info:
This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.
See this doc page and its related commands to get started:
"fix lb/fluid"_fix_lb_fluid.html
The people who created this package are Frances Mackay (fmackay at
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
Western Ontario. Contact them directly if you have questions.
Examples: examples/USER/lb
:line
USER-MGPT package :link(USER-MGPT),h5
Supporting info:
This package contains a fast implementation for LAMMPS of
quantum-based MGPT multi-ion potentials. The MGPT or model GPT method
derives from first-principles DFT-based generalized pseudopotential
theory (GPT) through a series of systematic approximations valid for
mid-period transition metals with nearly half-filled d bands. The
MGPT method was originally developed by John Moriarty at Lawrence
Livermore National Lab (LLNL).
In the general matrix representation of MGPT, which can also be
applied to f-band actinide metals, the multi-ion potentials are
evaluated on the fly during a simulation through d- or f-state matrix
multiplication, and the forces that move the ions are determined
analytically. The {mgpt} pair style in this package calculates forces
and energies using an optimized matrix-MGPT algorithm due to Tomas
Oppelstrup at LLNL.
See this doc page to get started:
"pair_style mgpt"_pair_mgpt.html
The persons who created the USER-MGPT package are Tomas Oppelstrup
(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov)
Contact them directly if you have any questions.
Examples: examples/USER/mgpt
:line
USER-MISC package :link(USER-MISC),h5
Supporting info:
The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
pair of files (*.cpp and *.h).
More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:
"Section 3"_Section_commands.html#cmd_5
User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
The list of features and author of each is given in the
src/USER-MISC/README file.
You should contact the author directly if you have specific questions
about the feature or its coding.
Examples: examples/USER/misc
:line
USER-MANIFOLD package :link(USER-MANIFOLD),h5
Supporting info:
This package contains a dump molfile command which uses molfile
plugins that are bundled with the
"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
analysis program, to enable LAMMPS to dump its information in formats
compatible with various molecular simulation tools.
This package allows LAMMPS to perform MD simulations of particles
constrained on a manifold (i.e., a 2D subspace of the 3D simulation
box). It achieves this using the RATTLE constraint algorithm applied
to single-particle constraint functions g(xi,yi,zi) = 0 and their
derivative (i.e. the normal of the manifold) n = grad(g).
See this doc page to get started:
"fix manifoldforce"_fix_manifoldforce.html
The person who created this package is Stefan Paquay, at the Eindhoven
University of Technology (TU/e), The Netherlands (s.paquay at tue.nl).
Contact him directly if you have questions.
:line
USER-MOLFILE package :link(USER-MOLFILE),h5
Supporting info:
This package contains a dump molfile command which uses molfile
plugins that are bundled with the
"VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
analysis program, to enable LAMMPS to dump its information in formats
compatible with various molecular simulation tools.
The package only provides the interface code, not the plugins. These
can be obtained from a VMD installation which has to match the
platform that you are using to compile LAMMPS for. By adding plugins
to VMD, support for new file formats can be added to LAMMPS (or VMD or
other programs that use them) without having to recompile the
application itself.
See this doc page to get started:
"dump molfile"_dump_molfile.html
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
:line
USER-OMP package :link(USER-OMP),h5
Supporting info:
This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.
See this section of the manual to get started:
"Section 5"_Section_accelerate.html#acc_3
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
For the USER-OMP package, your Makefile.machine needs additional
settings for CCFLAGS and LINKFLAGS.
CCFLAGS: add -fopenmp and -restrict
LINKFLAGS: add -fopenmp :ul
Examples: examples/accelerate, bench/KEPLER
:line
USER-PHONON package :link(USER-PHONON),h5
This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.
See this doc page to get started:
"fix phonon"_fix_phonon.html
The person who created this package is Ling-Ti Kong (konglt at
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
if you have questions.
Examples: examples/USER/phonon
:line
USER-QMMM package :link(USER-QMMM),h5
Supporting info:
This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the "Quantum ESPRESSO"_espresso package.
:link(espresso,http://www.quantum-espresso.org)
The current implementation only supports an ONIOM style mechanical
coupling to the Quantum ESPRESSO plane wave DFT package.
Electrostatic coupling is in preparation and the interface has been
written in a manner that coupling to other QM codes should be possible
without changes to LAMMPS itself.
See this doc page to get started:
"fix qmmm"_fix_qmmm.html
as well as the lib/qmmm/README file.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
:line
USER-QTB package :link(USER-QTB),h5
Supporting info:
This package provides a self-consistent quantum treatment of the
vibrational modes in a classical molecular dynamics simulation. By
coupling the MD simulation to a colored thermostat, it introduces zero
point energy into the system, alter the energy power spectrum and the
heat capacity towards their quantum nature. This package could be of
interest if one wants to model systems at temperatures lower than
their classical limits or when temperatures ramp up across the
classical limits in the simulation.
See these two doc pages to get started:
"fix qtb"_fix_qtb.html provides quantum nulcear correction through a
colored thermostat and can be used with other time integration schemes
like "fix nve"_fix_nve.html or "fix nph"_fix_nh.html.
"fix qbmsst"_fix_qbmsst.html enables quantum nuclear correction of a
multi-scale shock technique simulation by coupling the quantum thermal
bath with the shocked system.
The person who created this package is Yuan Shen (sy0302 at
stanford.edu) at Stanford University. Contact him directly if you
have questions.
Examples: examples/USER/qtb
:line
USER-QUIP package :link(USER-QUIP),h5
Supporting info:
Examples: examples/USER/quip
:line
USER-REAXC package :link(USER-REAXC),h5
Supporting info:
This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. It was originally developed by Adri van Duin and the Goddard
group at CalTech.
The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
C, should give identical or very similar results to pair_style reax,
which is a ReaxFF implementation on top of a Fortran library, a
version of which library was originally authored by Adri van Duin.
The reax/c version should be somewhat faster and more scalable,
particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
For technical details about this implemention of ReaxFF, see
this paper:
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.
The person who created this package is Hasan Metin Aktulga (hmaktulga
at lbl.gov), while at Purdue University. Contact him directly, or
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.
Examples: examples/reax
:line
USER-SMD package :link(USER-SMD),h5
Supporting info:
This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:
* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
* Also solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control.
* Can specify hydrostatic interactions independently from material
strength models, i.e. pressure and deviatoric stresses are separated.
* Many material models available (Johnson-Cook, plasticity with
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
material models.
* Rigid boundary conditions (walls) can be loaded as surface geometries
from *.STL files.
See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.
There are example scripts for using this package in examples/USER/smd.
The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
Examples: examples/USER/smd
:line
USER-SMTBQ package :link(USER-SMTBQ),h5
Supporting info:
This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
potential for the description of ionocovalent bonds in oxides.
There are example scripts for using this package in
examples/USER/smtbq.
See this doc page to get started:
"pair_style smtbq"_pair_smtbq.html
The persons who created the USER-SMTBQ package are Nicolas Salles,
Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact
them directly if you have any questions.
Examples: examples/USER/smtbq
:line
USER-SPH package :link(USER-SPH),h5
Supporting info:
This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:
* Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state
* Plain or Monaghans XSPH integration of the equations of motion
* Density continuity or density summation to propagate the density field
* Commands to set internal energy and density of particles from the
input script
* Output commands to access internal energy and density for dumping and
thermo output
See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.
There are example scripts for using this package in examples/USER/sph.
The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
Examples: examples/USER/sph
:line
USER-TALLY package :link(USER-TALLY),h5
Supporting info:
Examples: examples/USER/tally
:line
USER-VTK package :link(USER-VTK),h5
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