Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/src/Section_example.txt
e6ac7757a374efficient_neuronet

Last Change
Raw File

Section_example.txt
View Options

"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_perf.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
7. Example problems :h3
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).
Many of the input files have commented-out lines for creating dump
files and image files.
If you uncomment the "dump"_dump.html command in the input script, a
text dump file will be produced, which can be animated by various
"visualization programs"_http://lammps.sandia.gov/viz.html. It can
also be animated using the xmovie tool described in the "Additional
Tools"_Section_tools.html section of the LAMMPS documentation.
If you uncomment the "dump image"_dump.html 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
"dump image"_dump_image.html doc page.
Animations of many of the examples can be viewed on the Movies section
of the "LAMMPS web site"_lws.
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.
Lists of both kinds of directories are given below.
:line
Lowercase directories :h4
accelerate: run with various acceleration options (OpenMP, GPU, Phi)
balance: dynamic load balancing, 2d system
body: body particles, 2d system
colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential
coreshell: core/shell model using CORESHELL package
crack: crack propagation in a 2d solid
deposit: deposit atoms and molecules on a surface
dipole: point dipolar particles, 2d system
dreiding: methanol via Dreiding FF
eim: NaCl using the EIM potential
ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poiseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces
hugoniostat: Hugoniostat shock dynamics
indent: spherical indenter into a 2d solid
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer)
peri: Peridynamic model of cylinder impacted by indenter
pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: using embedded Python in a LAMMPS input script
qeq: use of the QEQ package for charge equilibration
reax: RDX and TATB models using the ReaxFF
rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void
snap: NVE dynamics for BCC tantalum crystal using SNAP potential
srd: stochastic rotation dynamics (SRD) particles as solvent
streitz: use of Streitz/Mintmire potential with charge equilibration
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
vashishta: use of the Vashishta potential :tb(s=:)
Here is how you can run and visualize one of the sample problems:
cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux -in in.indent # run the problem :pre
Running the simulation produces the files {dump.indent} and
{log.lammps}. You can visualize the dump file of snapshots with a
variety of 3rd-party tools highlighted on the
"Visualization"_http://lammps.sandia.gov/viz.html page of the LAMMPS
web site.
If you uncomment the "dump image"_dump_image.html 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 "Section start
2.2"_Section_start.html 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
"dump image"_dump_image.html doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.
% convert -loop 1 *.jpg foo.gif :pre
:line
Uppercase directories :h4
ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc
COUPLE: examples of how to use LAMMPS as a library
DIFFUSE: compute diffusion coefficients via several methods
ELASTIC: compute elastic constants at zero temperature
ELASTIC_T: compute elastic constants at finite temperature
KAPPA: compute thermal conductivity via several methods
MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
USER: examples for USER packages and USER-contributed commands
VISCOSITY: compute viscosity via several methods :tb(s=:)
Nearly all of these directories have README files which give more
details on how to understand and use their contents.
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 "Section packages"_Section_packages.html doc
page for more info on specific USER packages.
c4science · Help