2016-05-10 01:33:12 +08:00
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< h1 > 7. Example problems< / h1 >
< p > The LAMMPS distribution includes an examples sub-directory with many
sample problems. Many are 2d models that run quickly are are
straightforward to visualize, requiring at most a couple of minutes to
run on a desktop machine. Each problem has an input script (in.*) and
produces a log file (log.*) when it runs. Some use a data file
(data.*) of initial coordinates as additional input. A few sample log
file run on different machines and different numbers of processors are
included in the directories to compare your answers to. E.g. a log
file like log.date.crack.foo.P means the “ crack” example was run on P
processors of machine “ foo” on that date (i.e. with that version of
LAMMPS).< / p >
< p > Many of the input files have commented-out lines for creating dump
files and image files.< / p >
< p > If you uncomment the < a class = "reference internal" href = "dump.html" > < span class = "doc" > dump< / span > < / a > command in the input script, a
text dump file will be produced, which can be animated by various
< a class = "reference external" href = "http://lammps.sandia.gov/viz.html" > visualization programs< / a > . It can
also be animated using the xmovie tool described in the < a class = "reference internal" href = "Section_tools.html" > < span class = "doc" > Additional Tools< / span > < / a > section of the LAMMPS documentation.< / p >
< p > If you uncomment the < a class = "reference internal" href = "dump.html" > < span class = "doc" > dump image< / span > < / a > command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG
snapshot images will be produced when the simulation runs. They can
be quickly post-processed into a movie using commands described on the
< a class = "reference internal" href = "dump_image.html" > < span class = "doc" > dump image< / span > < / a > doc page.< / p >
< p > Animations of many of the examples can be viewed on the Movies section
of the < a class = "reference external" href = "http://lammps.sandia.gov" > LAMMPS web site< / a > .< / p >
< p > There are two kinds of sub-directories in the examples dir. Lowercase
dirs contain one or a few simple, quick-to-run problems. Uppercase
dirs contain up to several complex scripts that illustrate a
particular kind of simulation method or model. Some of these run for
longer times, e.g. to measure a particular quantity.< / p >
< p > Lists of both kinds of directories are given below.< / p >
< hr class = "docutils" / >
< div class = "section" id = "lowercase-directories" >
< h2 > 7.1. Lowercase directories< / h2 >
< table border = "1" class = "docutils" >
< colgroup >
< col width = "16%" / >
< col width = "84%" / >
< / colgroup >
< tbody valign = "top" >
< tr class = "row-odd" > < td > accelerate< / td >
< td > run with various acceleration options (OpenMP, GPU, Phi)< / td >
< / tr >
< tr class = "row-even" > < td > balance< / td >
< td > dynamic load balancing, 2d system< / td >
< / tr >
< tr class = "row-odd" > < td > body< / td >
< td > body particles, 2d system< / td >
< / tr >
< tr class = "row-even" > < td > colloid< / td >
< td > big colloid particles in a small particle solvent, 2d system< / td >
< / tr >
< tr class = "row-odd" > < td > comb< / td >
< td > models using the COMB potential< / td >
< / tr >
< tr class = "row-even" > < td > coreshell< / td >
< td > core/shell model using CORESHELL package< / td >
< / tr >
< tr class = "row-odd" > < td > crack< / td >
< td > crack propagation in a 2d solid< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > deposit< / td >
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< td > deposit atoms and molecules on a surface< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > dipole< / td >
2016-05-10 01:33:12 +08:00
< td > point dipolar particles, 2d system< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > dreiding< / td >
2016-05-10 01:33:12 +08:00
< td > methanol via Dreiding FF< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > eim< / td >
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< td > NaCl using the EIM potential< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > ellipse< / td >
2016-05-10 01:33:12 +08:00
< td > ellipsoidal particles in spherical solvent, 2d system< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > flow< / td >
2016-05-10 01:33:12 +08:00
< td > Couette and Poiseuille flow in a 2d channel< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > friction< / td >
2016-05-10 01:33:12 +08:00
< td > frictional contact of spherical asperities between 2d surfaces< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > hugoniostat< / td >
2016-05-10 01:33:12 +08:00
< td > Hugoniostat shock dynamics< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > indent< / td >
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< td > spherical indenter into a 2d solid< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > kim< / td >
2016-05-10 01:33:12 +08:00
< td > use of potentials in Knowledge Base for Interatomic Models (KIM)< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > meam< / td >
2016-05-10 01:33:12 +08:00
< td > MEAM test for SiC and shear (same as shear examples)< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > melt< / td >
2016-05-10 01:33:12 +08:00
< td > rapid melt of 3d LJ system< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > micelle< / td >
2016-05-10 01:33:12 +08:00
< td > self-assembly of small lipid-like molecules into 2d bilayers< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > min< / td >
2016-05-10 01:33:12 +08:00
< td > energy minimization of 2d LJ melt< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > msst< / td >
2016-05-10 01:33:12 +08:00
< td > MSST shock dynamics< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > nb3b< / td >
2016-05-10 01:33:12 +08:00
< td > use of nonbonded 3-body harmonic pair style< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > neb< / td >
2016-05-10 01:33:12 +08:00
< td > nudged elastic band (NEB) calculation for barrier finding< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > nemd< / td >
2016-05-10 01:33:12 +08:00
< td > non-equilibrium MD of 2d sheared system< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > obstacle< / td >
2016-05-10 01:33:12 +08:00
< td > flow around two voids in a 2d channel< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > peptide< / td >
2016-05-10 01:33:12 +08:00
< td > dynamics of a small solvated peptide chain (5-mer)< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > peri< / td >
2016-05-10 01:33:12 +08:00
< td > Peridynamic model of cylinder impacted by indenter< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > pour< / td >
2016-05-10 01:33:12 +08:00
< td > pouring of granular particles into a 3d box, then chute flow< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > prd< / td >
2016-05-10 01:33:12 +08:00
< td > parallel replica dynamics of vacancy diffusion in bulk Si< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > python< / td >
2016-05-10 01:33:12 +08:00
< td > using embedded Python in a LAMMPS input script< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > qeq< / td >
2016-05-10 01:33:12 +08:00
< td > use of the QEQ package for charge equilibration< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > reax< / td >
2016-05-10 01:33:12 +08:00
< td > RDX and TATB models using the ReaxFF< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > rigid< / td >
2016-05-10 01:33:12 +08:00
< td > rigid bodies modeled as independent or coupled< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > shear< / td >
2016-05-10 01:33:12 +08:00
< td > sideways shear applied to 2d solid, with and without a void< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > snap< / td >
2016-05-10 01:33:12 +08:00
< td > NVE dynamics for BCC tantalum crystal using SNAP potential< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > srd< / td >
2016-05-10 01:33:12 +08:00
< td > stochastic rotation dynamics (SRD) particles as solvent< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > streitz< / td >
2016-05-10 01:33:12 +08:00
< td > use of Streitz/Mintmire potential with charge equilibration< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-odd" > < td > tad< / td >
2016-05-10 01:33:12 +08:00
< td > temperature-accelerated dynamics of vacancy diffusion in bulk Si< / td >
< / tr >
2016-06-01 00:07:15 +08:00
< tr class = "row-even" > < td > vashishta< / td >
2016-05-10 01:33:12 +08:00
< td > use of the Vashishta potential< / td >
< / tr >
< / tbody >
< / table >
< p > Here is how you can run and visualize one of the sample problems:< / p >
2016-09-07 22:09:53 +08:00
< pre class = "literal-block" >
cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux -in in.indent # run the problem
< / pre >
2016-05-10 01:33:12 +08:00
< p > Running the simulation produces the files < em > dump.indent< / em > and
< em > log.lammps< / em > . You can visualize the dump file of snapshots with a
variety of 3rd-party tools highlighted on the
< a class = "reference external" href = "http://lammps.sandia.gov/viz.html" > Visualization< / a > page of the LAMMPS
web site.< / p >
< p > If you uncomment the < a class = "reference internal" href = "dump_image.html" > < span class = "doc" > dump image< / span > < / a > line(s) in the input
script a series of JPG images will be produced by the run (assuming
you built LAMMPS with JPG support; see < a class = "reference internal" href = "Section_start.html" > < span class = "doc" > Section start 2.2< / span > < / a > for details). These can be viewed
individually or turned into a movie or animated by tools like
ImageMagick or QuickTime or various Windows-based tools. See the
< a class = "reference internal" href = "dump_image.html" > < span class = "doc" > dump image< / span > < / a > doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.< / p >
2016-09-07 22:09:53 +08:00
< pre class = "literal-block" >
% convert -loop 1 *.jpg foo.gif
< / pre >
2016-05-10 01:33:12 +08:00
< / div >
< hr class = "docutils" / >
< div class = "section" id = "uppercase-directories" >
< h2 > 7.2. Uppercase directories< / h2 >
< table border = "1" class = "docutils" >
< colgroup >
2016-09-07 22:09:53 +08:00
< col width = "11%" / >
< col width = "89%" / >
2016-05-10 01:33:12 +08:00
< / colgroup >
< tbody valign = "top" >
< tr class = "row-odd" > < td > ASPHERE< / td >
< td > various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc< / td >
< / tr >
< tr class = "row-even" > < td > COUPLE< / td >
< td > examples of how to use LAMMPS as a library< / td >
< / tr >
< tr class = "row-odd" > < td > DIFFUSE< / td >
< td > compute diffusion coefficients via several methods< / td >
< / tr >
< tr class = "row-even" > < td > ELASTIC< / td >
< td > compute elastic constants at zero temperature< / td >
< / tr >
< tr class = "row-odd" > < td > ELASTIC_T< / td >
< td > compute elastic constants at finite temperature< / td >
< / tr >
< tr class = "row-even" > < td > KAPPA< / td >
< td > compute thermal conductivity via several methods< / td >
< / tr >
< tr class = "row-odd" > < td > MC< / td >
< td > using LAMMPS in a Monte Carlo mode to relax the energy of a system< / td >
< / tr >
< tr class = "row-even" > < td > USER< / td >
< td > examples for USER packages and USER-contributed commands< / td >
< / tr >
< tr class = "row-odd" > < td > VISCOSITY< / td >
< td > compute viscosity via several methods< / td >
< / tr >
< / tbody >
< / table >
< p > Nearly all of these directories have README files which give more
details on how to understand and use their contents.< / p >
< p > The USER directory has a large number of sub-directories which
correspond by name to a USER package. They contain scripts that
illustrate how to use the command(s) provided in that package. Many
of the sub-directories have their own README files which give further
instructions. See the < a class = "reference internal" href = "Section_packages.html" > < span class = "doc" > Section packages< / span > < / a > doc
page for more info on specific USER packages.< / p >
< / div >
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