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
PACKAGES directory with its own sub-directories = tests for styles from specific packages

Each is discussed below.

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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 https://www.lammps.org/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
amoeba:   small water and bio models with AMOEBA and HIPPO potentials
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
gjf:      use of fix langevin Gronbech-Jensen/Farago option
granregion: use of fix wall/region/gran as boundary on granular particles
grid      use of commands which overlay grids on the simulation domain
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)
mc:       MC package models: GCMC, Widom, fix mol/swap
mdi:      use of the MDI package and MolSSI MDI code coupling library
meam:     MEAM test for SiC and shear (same as shear examples)
melt:     rapid melt of 3d LJ system
mesh:     create_atoms mesh command
micelle:  self-assembly of small lipid-like molecules into 2d bilayers
min:      energy minimization of 2d LJ melt
mliap:    examples for using several bundled MLIAP potentials
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
numdiff:  numerical difference computation of forces, virial, and Born matrix
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
reaxff:   RDX and TATB and several other models using ReaxFF
replicate: use of replicate command
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
template: examples for using atom_style template and comparing to atom style molecular
tersoff:  regression test input for Tersoff variants
threebody: regression test input for a variety of threebody potentials
triclinic: general triclinic simulation boxes versus orthogonal boxes
ttm:      two-temeperature model examples
vashishta: models using the Vashishta potential
voronoi:  Voronoi tesselation via compute voronoi/atom command
wall:     use of reflective walls with different stochastic models
yaml:     demonstrates use of yaml thermo and dump styles

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

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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
stiffness tensor (elastic constants)
at zero temperature, using an Si example.  See the
ELASTIC/in.elastic file for more info.

The ELASTIC_T directory has example scripts for the computing elastic
stiffness tensor at finite temperature. Two different methods are
demonstrated. DEFORMATION estimates the change in the average
stress tensor between multiple simulations
in which small finite deformations are made to the simulation cell.
BORN_MATRIX runs a single simulation in which the Born matrix and stress
fluctuations are averaged. The second method
is newer in LAMMPS and is generally more efficient and
more reliable.

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-LOOP directory has an example script for using LAMMPS as an
energy-evaluation engine in a iterative Monte Carlo energy-relaxation
loop.

The PACKAGES directory contains subdirectories of example scripts for
individual packages or additional individual styles. Most of those are
contributed by the corresponding package or style developers.
See the README files in those directories (if available) or the
corresponding doc page in the manual for more info.  See the
https://docs.lammps.org/Build_package.html page for more info about
installing and building packages.

The QUANTUM directory has examples of how to use LAMMPS in tandem with
several quantum codes via the MDI code coupling library.

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 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.