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Section_example.html
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<HTML>
<CENTER><A
HREF =
"Section_howto.html"
>
Previous Section
</A>
-
<A
HREF =
"http://lammps.sandia.gov"
>
LAMMPS WWW Site
</A>
-
<A
HREF =
"Manual.html"
>
LAMMPS Documentation
</A>
-
<A
HREF =
"Section_commands.html#comm"
>
LAMMPS Commands
</A>
-
<A
HREF =
"Section_perf.html"
>
Next Section
</A>
</CENTER>
<HR>
<H3>
7. Example problems
</H3>
<P>
The LAMMPS distribution includes an examples sub-directory with
several sample problems. Each problem is in a sub-directory of its
own. Most are 2d models so that they run quickly, 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.*) and dump file
(dump.*) when it runs. Some use a data file (data.*) of initial
coordinates as additional input. A few sample log file outputs 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.crack.foo.P means it ran on P processors of machine "foo".
</P>
<P>
For examples that use input data files, many of them were produced by
<A
HREF =
"http://pizza.sandia.gov"
>
Pizza.py
</A>
or setup tools described in the
<A
HREF =
"Section_tools.html"
>
Additional Tools
</A>
section of the LAMMPS
documentation and provided with the LAMMPS distribution.
</P>
<P>
If you uncomment the
<A
HREF =
"dump.html"
>
dump
</A>
command in the input script, a
text dump file will be produced, which can be animated by various
<A
HREF =
"http://lammps.sandia.gov/viz.html"
>
visualization programs
</A>
. It can
also be animated using the xmovie tool described in the
<A
HREF =
"Section_tools.html"
>
Additional
Tools
</A>
section of the LAMMPS documentation.
</P>
<P>
If you uncomment the
<A
HREF =
"dump.html"
>
dump image
</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
HREF =
"dump_image.html"
>
dump image
</A>
doc page.
</P>
<P>
Animations of many of these examples can be viewed on the Movies
section of the
<A
HREF =
"http://lammps.sandia.gov"
>
LAMMPS WWW Site
</A>
.
</P>
<P>
These are the sample problems in the examples sub-directories:
</P>
<DIV
ALIGN=
center
><TABLE
BORDER=
1
>
<TR><TD
>
balance
</TD><TD
>
dynamic load balancing, 2d system
</TD></TR>
<TR><TD
>
body
</TD><TD
>
body particles, 2d system
</TD></TR>
<TR><TD
>
colloid
</TD><TD
>
big colloid particles in a small particle solvent, 2d system
</TD></TR>
<TR><TD
>
comb
</TD><TD
>
models using the COMB potential
</TD></TR>
<TR><TD
>
crack
</TD><TD
>
crack propagation in a 2d solid
</TD></TR>
<TR><TD
>
cuda
</TD><TD
>
use of the USER-CUDA package for GPU acceleration
</TD></TR>
<TR><TD
>
dipole
</TD><TD
>
point dipolar particles, 2d system
</TD></TR>
<TR><TD
>
dreiding
</TD><TD
>
methanol via Dreiding FF
</TD></TR>
<TR><TD
>
eim
</TD><TD
>
NaCl using the EIM potential
</TD></TR>
<TR><TD
>
ellipse
</TD><TD
>
ellipsoidal particles in spherical solvent, 2d system
</TD></TR>
<TR><TD
>
flow
</TD><TD
>
Couette and Poiseuille flow in a 2d channel
</TD></TR>
<TR><TD
>
friction
</TD><TD
>
frictional contact of spherical asperities between 2d surfaces
</TD></TR>
<TR><TD
>
gpu
</TD><TD
>
use of the GPU package for GPU acceleration
</TD></TR>
<TR><TD
>
hugoniostat
</TD><TD
>
Hugoniostat shock dynamics
</TD></TR>
<TR><TD
>
indent
</TD><TD
>
spherical indenter into a 2d solid
</TD></TR>
<TR><TD
>
intel
</TD><TD
>
use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor
</TD></TR>
<TR><TD
>
kim
</TD><TD
>
use of potentials in Knowledge Base for Interatomic Models (KIM)
</TD></TR>
<TR><TD
>
line
</TD><TD
>
line segment particles in 2d rigid bodies
</TD></TR>
<TR><TD
>
meam
</TD><TD
>
MEAM test for SiC and shear (same as shear examples)
</TD></TR>
<TR><TD
>
melt
</TD><TD
>
rapid melt of 3d LJ system
</TD></TR>
<TR><TD
>
micelle
</TD><TD
>
self-assembly of small lipid-like molecules into 2d bilayers
</TD></TR>
<TR><TD
>
min
</TD><TD
>
energy minimization of 2d LJ melt
</TD></TR>
<TR><TD
>
msst
</TD><TD
>
MSST shock dynamics
</TD></TR>
<TR><TD
>
nb3b
</TD><TD
>
use of nonbonded 3-body harmonic pair style
</TD></TR>
<TR><TD
>
neb
</TD><TD
>
nudged elastic band (NEB) calculation for barrier finding
</TD></TR>
<TR><TD
>
nemd
</TD><TD
>
non-equilibrium MD of 2d sheared system
</TD></TR>
<TR><TD
>
obstacle
</TD><TD
>
flow around two voids in a 2d channel
</TD></TR>
<TR><TD
>
peptide
</TD><TD
>
dynamics of a small solvated peptide chain (5-mer)
</TD></TR>
<TR><TD
>
peri
</TD><TD
>
Peridynamic model of cylinder impacted by indenter
</TD></TR>
<TR><TD
>
pour
</TD><TD
>
pouring of granular particles into a 3d box, then chute flow
</TD></TR>
<TR><TD
>
prd
</TD><TD
>
parallel replica dynamics of vacancy diffusion in bulk Si
</TD></TR>
<TR><TD
>
qeq
</TD><TD
>
use of the QEQ pacakge for charge equilibration
</TD></TR>
<TR><TD
>
reax
</TD><TD
>
RDX and TATB models using the ReaxFF
</TD></TR>
<TR><TD
>
rigid
</TD><TD
>
rigid bodies modeled as independent or coupled
</TD></TR>
<TR><TD
>
shear
</TD><TD
>
sideways shear applied to 2d solid, with and without a void
</TD></TR>
<TR><TD
>
snap
</TD><TD
>
NVE dynamics for BCC tantalum crystal using SNAP potential
</TD></TR>
<TR><TD
>
srd
</TD><TD
>
stochastic rotation dynamics (SRD) particles as solvent
</TD></TR>
<TR><TD
>
tad
</TD><TD
>
temperature-accelerated dynamics of vacancy diffusion in bulk Si
</TD></TR>
<TR><TD
>
tri
</TD><TD
>
triangular particles in rigid bodies
</TD></TR></TABLE></DIV>
<P>
Here is how you might run and visualize one of the sample problems:
</P>
<PRE>
cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux
< in
.
indent
#
run
the
problem
</
PRE
>
<P>
Running the simulation produces the files
<I>
dump.indent
</I>
and
<I>
log.lammps
</I>
. You can visualize the dump file as follows:
</P>
<PRE>
../../tools/xmovie/xmovie -scale dump.indent
</PRE>
<P>
If you uncomment the
<A
HREF =
"dump_image.html"
>
dump image
</A>
line(s) in the input
script a series of JPG images will be produced by the run. 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
HREF =
"dump_image.html"
>
dump image
</A>
doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.
</P>
<PRE>
% convert -loop 1 *.jpg foo.gif
</PRE>
<HR>
<P>
There is also a COUPLE directory with examples of how to use LAMMPS as
a library, either by itself or in tandem with another code or library.
See the COUPLE/README file to get started.
</P>
<P>
There is also an ELASTIC directory with an example script for
computing elastic constants, using a zero temperature Si example. See
the in.elastic file for more info.
</P>
<P>
There is also a USER directory which contains subdirectories of
user-provided examples for user packages. See the README files in
those directories for more info. See the
<A
HREF =
"Section_start.html"
>
Section_start.html
</A>
file for more info about user
packages.
</P>
</HTML>
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