forked from lijiext/lammps
160 lines
7.3 KiB
Plaintext
160 lines
7.3 KiB
Plaintext
"Previous Section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
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Documentation"_ld - "LAMMPS Commands"_lc - "Next
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Section"_Tools.html :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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Example scripts :h3
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The LAMMPS distribution includes an examples sub-directory with many
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sample problems. Many are 2d models that run quickly and are
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straightforward to visualize, requiring at most a couple of minutes to
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run on a desktop machine. Each problem has an input script (in.*) and
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produces a log file (log.*) when it runs. Some use a data file
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(data.*) of initial coordinates as additional input. A few sample log
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file run on different machines and different numbers of processors are
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included in the directories to compare your answers to. E.g. a log
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file like log.date.crack.foo.P means the "crack" example was run on P
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processors of machine "foo" on that date (i.e. with that version of
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LAMMPS).
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Many of the input files have commented-out lines for creating dump
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files and image files.
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If you uncomment the "dump"_dump.html command in the input script, a
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text dump file will be produced, which can be animated by various
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"visualization programs"_http://lammps.sandia.gov/viz.html.
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If you uncomment the "dump image"_dump.html command in the input
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script, and assuming you have built LAMMPS with a JPG library, JPG
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snapshot images will be produced when the simulation runs. They can
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be quickly post-processed into a movie using commands described on the
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"dump image"_dump_image.html doc page.
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Animations of many of the examples can be viewed on the Movies section
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of the "LAMMPS web site"_lws.
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There are two kinds of sub-directories in the examples dir. Lowercase
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dirs contain one or a few simple, quick-to-run problems. Uppercase
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dirs contain up to several complex scripts that illustrate a
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particular kind of simulation method or model. Some of these run for
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longer times, e.g. to measure a particular quantity.
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Lists of both kinds of directories are given below.
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:line
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Lowercase directories :h4
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accelerate: run with various acceleration options (OpenMP, GPU, Phi)
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airebo: polyethylene with AIREBO potential
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atm: Axilrod-Teller-Muto potential example
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balance: dynamic load balancing, 2d system
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body: body particles, 2d system
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cmap: CMAP 5-body contributions to CHARMM force field
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colloid: big colloid particles in a small particle solvent, 2d system
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comb: models using the COMB potential
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controller: use of fix controller as a thermostat
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coreshell: core/shell model using CORESHELL package
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crack: crack propagation in a 2d solid
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deposit: deposit atoms and molecules on a surface
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dipole: point dipolar particles, 2d system
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dreiding: methanol via Dreiding FF
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eim: NaCl using the EIM potential
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ellipse: ellipsoidal particles in spherical solvent, 2d system
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flow: Couette and Poiseuille flow in a 2d channel
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friction: frictional contact of spherical asperities between 2d surfaces
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gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
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granregion: use of fix wall/region/gran as boundary on granular particles
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hugoniostat: Hugoniostat shock dynamics
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hyper: global and local hyperdynamics of diffusion on Pt surface
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indent: spherical indenter into a 2d solid
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kim: use of potentials from the "OpenKIM Repository"_openkim
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latte: examples for using fix latte for DFTB via the LATTE library
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meam: MEAM test for SiC and shear (same as shear examples)
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melt: rapid melt of 3d LJ system
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message: demos for LAMMPS client/server coupling with the MESSAGE package
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micelle: self-assembly of small lipid-like molecules into 2d bilayers
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min: energy minimization of 2d LJ melt
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mscg: parameterize a multi-scale coarse-graining (MSCG) model
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msst: MSST shock dynamics
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nb3b: use of non-bonded 3-body harmonic pair style
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neb: nudged elastic band (NEB) calculation for barrier finding
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nemd: non-equilibrium MD of 2d sheared system
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obstacle: flow around two voids in a 2d channel
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peptide: dynamics of a small solvated peptide chain (5-mer)
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peri: Peridynamic model of cylinder impacted by indenter
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pour: pouring of granular particles into a 3d box, then chute flow
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prd: parallel replica dynamics of vacancy diffusion in bulk Si
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python: using embedded Python in a LAMMPS input script
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qeq: use of the QEQ package for charge equilibration
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rdf-adf: computing radial and angle distribution functions for water
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reax: RDX and TATB models using the ReaxFF
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rerun: use of rerun and read_dump commands
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rigid: rigid bodies modeled as independent or coupled
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shear: sideways shear applied to 2d solid, with and without a void
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snap: NVE dynamics for BCC tantalum crystal using SNAP potential
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srd: stochastic rotation dynamics (SRD) particles as solvent
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streitz: use of Streitz/Mintmire potential with charge equilibration
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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threebody: regression test input for a variety of manybody potentials
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vashishta: use of the Vashishta potential
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voronoi: Voronoi tesselation via compute voronoi/atom command :tb(s=:)
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Here is how you can run and visualize one of the sample problems:
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cd indent
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cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
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lmp_linux -in in.indent # run the problem :pre
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Running the simulation produces the files {dump.indent} and
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{log.lammps}. You can visualize the dump file of snapshots with a
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variety of 3rd-party tools highlighted on the
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"Visualization"_http://lammps.sandia.gov/viz.html page of the LAMMPS
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web site.
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If you uncomment the "dump image"_dump_image.html line(s) in the input
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script a series of JPG images will be produced by the run (assuming
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you built LAMMPS with JPG support; see the
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"Build_settings"_Build_settings.html doc page for details). These can
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be viewed individually or turned into a movie or animated by tools
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like ImageMagick or QuickTime or various Windows-based tools. See the
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"dump image"_dump_image.html doc page for more details. E.g. this
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Imagemagick command would create a GIF file suitable for viewing in a
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browser.
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% convert -loop 1 *.jpg foo.gif :pre
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:line
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Uppercase directories :h4
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ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc
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COUPLE: examples of how to use LAMMPS as a library
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DIFFUSE: compute diffusion coefficients via several methods
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ELASTIC: compute elastic constants at zero temperature
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ELASTIC_T: compute elastic constants at finite temperature
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HEAT: compute thermal conductivity for LJ and water via fix ehex
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KAPPA: compute thermal conductivity via several methods
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MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
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SPIN: examples for features of the SPIN package
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UNITS: examples that run the same simulation in lj, real, metal units
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USER: examples for USER packages and USER-contributed commands
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VISCOSITY: compute viscosity via several methods :tb(s=:)
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Nearly all of these directories have README files which give more
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details on how to understand and use their contents.
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The USER directory has a large number of sub-directories which
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correspond by name to a USER package. They contain scripts that
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illustrate how to use the command(s) provided in that package. Many
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of the sub-directories have their own README files which give further
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instructions. See the "Packages_details"_Packages_details.html doc
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page for more info on specific USER packages.
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:link(openkim,https://openkim.org)
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