forked from lijiext/lammps
185 lines
8.3 KiB
Plaintext
185 lines
8.3 KiB
Plaintext
LAMMPS example problems
|
|
|
|
There are 3 flavors of sub-directories in this file, each with sample
|
|
problems you can run with LAMMPS.
|
|
|
|
lower-case directories = simple test problems for LAMMPS and its packages
|
|
upper-case directories = more complex problems
|
|
USER directory with its own sub-directories = tests for USER packages
|
|
|
|
Each is discussed below.
|
|
|
|
------------------------------------------
|
|
|
|
Lower-case directories
|
|
|
|
Each of these sub-directories contains a sample problem you can run
|
|
with LAMMPS. Most are 2d models so that they run quickly, requiring a
|
|
few seconds to a few minutes to run on a desktop machine. Each
|
|
problem has an input script (in.*) and produces a log file (log.*) and
|
|
(optionally) a dump file (dump.*) or image files (image.*) or movie
|
|
(movie.mpg) when it runs. Some use a data file (data.*) of initial
|
|
coordinates as additional input. Some require that you install one or
|
|
more optional LAMMPS packages.
|
|
|
|
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.date.foo.P means it ran on
|
|
P processors of machine "foo" with the dated version of LAMMPS. Note
|
|
that these problems should get statistically similar answers when run
|
|
on different machines or different numbers of processors, but not
|
|
identical answers to those in the log of dump files included here.
|
|
See the Errors section of the LAMMPS documentation for more
|
|
discussion.
|
|
|
|
Most of the example input scripts have commented-out lines that
|
|
produce dump snapshots of the running simulation in any of 3 formats.
|
|
|
|
If you uncomment the dump command in the input script, a text dump
|
|
file will be produced, which can be animated by various visualization
|
|
programs (see http://lammps.sandia.gov/viz.html) such as Ovito, VMD,
|
|
or AtomEye.
|
|
|
|
If you uncomment the dump image 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
|
|
doc page.
|
|
|
|
If you uncomment the dump movie command in the input script, and
|
|
assuming you have built LAMMPS with the FFMPEG library, an MPG movie
|
|
will be produced when the simulation runs. The movie file can be
|
|
played using various viewers, such as mplayer or QuickTime.
|
|
|
|
Animations of many of these examples can be viewed on the Movies
|
|
section of the LAMMPS WWW Site.
|
|
|
|
These are the sample problems and their output in the various
|
|
sub-directories:
|
|
|
|
accelerate: use of all the various accelerator packages
|
|
airebo: polyethylene with AIREBO potential
|
|
atm: Axilrod-Teller-Muto potential
|
|
balance: dynamic load balancing, 2d system
|
|
body: body particles, 2d system
|
|
cmap: CMAP 5-body contributions to CHARMM force field
|
|
colloid: big colloid particles in a small particle solvent, 2d system
|
|
comb: models using the COMB potential
|
|
coreshell: adiabatic core/shell model
|
|
controller: use of fix controller as a thermostat
|
|
crack: crack propagation in a 2d solid
|
|
deposit: deposition of atoms and molecules onto a 3d substrate
|
|
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
|
|
gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
|
|
gjf: use of fix langevin Gronbech-Jensen/Farago option
|
|
granregion: use of fix wall/region/gran as boundary on granular particles
|
|
hugoniostat: Hugoniostat shock dynamics
|
|
hyper: global and local hyperdynamics of diffusion on Pt surface
|
|
indent: spherical indenter into a 2d solid
|
|
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
|
|
latte: use of LATTE density-functional tight-binding quantum code
|
|
meam: MEAM test for SiC and shear (same as shear examples)
|
|
melt: rapid melt of 3d LJ system
|
|
message: client/server coupling of 2 codes
|
|
micelle: self-assembly of small lipid-like molecules into 2d bilayers
|
|
min: energy minimization of 2d LJ melt
|
|
mscg: parameterize a multi-scale coarse-graining (MSCG) model
|
|
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: use of PYTHON package to invoke Python code from input script
|
|
qeq: use of QEQ package for charge equilibration
|
|
reax: RDX and TATB and several other models using ReaxFF
|
|
rerun: use of rerun and read_dump commands
|
|
rigid: rigid bodies modeled as independent or coupled
|
|
shear: sideways shear applied to 2d solid, with and without a void
|
|
snap: examples for using several bundled SNAP potentials
|
|
srd: stochastic rotation dynamics (SRD) particles as solvent
|
|
steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
|
|
streitz: Streitz-Mintmire potential for Al2O3
|
|
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
|
|
threebody: regression test input for a variety of manybody potentials
|
|
vashishta: models using the Vashishta potential
|
|
voronoi: Voronoi tesselation via compute voronoi/atom command
|
|
|
|
Here is how you might run and visualize one of the sample problems:
|
|
|
|
cd indent
|
|
cp ../../src/lmp_mpi . # copy LAMMPS executable to this dir
|
|
lmp_mpi -in in.indent # run the problem
|
|
|
|
Running the simulation produces the files {dump.indent} and
|
|
{log.lammps}.
|
|
|
|
If you uncomment the dump image 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 dump
|
|
image 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
|
|
|
|
------------------------------------------
|
|
|
|
Upper-case directories
|
|
|
|
The ASPHERE directory has examples of how to model aspherical
|
|
particles with or without solvent, in 3 styles LAMMPS provides.
|
|
Namely point ellipsoids, rigid bodies, and generalized aspherical
|
|
bodies built from line/triangle surface facets in 2d/3d. See the
|
|
ASPHERE/README file to get started.
|
|
|
|
The COUPLE directory has 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.
|
|
|
|
The ELASTIC directory has an example script for computing elastic
|
|
constants at zero temperature, using an Si example. See the
|
|
ELASTIC/in.elastic file for more info.
|
|
|
|
The ELASTIC_T directory has an example script for computing elastic
|
|
constants at finite temperature, using an Si example. See the
|
|
ELASTIC_T/in.elastic file for more info.
|
|
|
|
The HEAT directory has example scripts for heat exchange algorithms
|
|
(e.g. used for establishing a thermal gradient), using two different
|
|
methods. See the HEAT/README file for more info.
|
|
|
|
The KAPPA directory has example scripts for computing the thermal
|
|
conductivity (kappa) of a LJ liquid using 5 different methods. See
|
|
the KAPPA/README file for more info.
|
|
|
|
The MC directory has an example script for using LAMMPS as an
|
|
energy-evaluation engine in a iterative Monte Carlo energy-relaxation
|
|
loop.
|
|
|
|
The TIP4P directory has an example for testing forces computed on a
|
|
GPU.
|
|
|
|
The UNITS directory contains examples of input scripts modeling the
|
|
same Lennard-Jones liquid model, written in 3 different unit systems:
|
|
lj, real, and metal. So that you can see how to scale/unscale input
|
|
and output values read/written by LAMMPS to verify you are performing
|
|
the same simulation in different unit systems.
|
|
|
|
The USER directory contains subdirectories of user-provided example
|
|
scripts for ser packages. See the README files in those directories
|
|
for more info. See the doc/Section_start.html file for more info
|
|
about installing and building user packages.
|
|
|
|
The VISCOSITY directory has example scripts for computing the
|
|
viscosity of a LJ liquid using 4 different methods. See the
|
|
VISCOSITY/README file for more info.
|