7. Example problemsΒΆ
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”.
For examples that use input data files, many of them were produced by Pizza.py or setup tools described in the Additional Tools section of the LAMMPS documentation and provided with the LAMMPS distribution.
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. It can also be animated using the xmovie tool described in the Additional Tools section of the LAMMPS documentation.
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.
Animations of many of these examples can be viewed on the Movies section of the LAMMPS WWW Site.
These are the sample problems in the examples sub-directories:
| 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 |
| crack | crack propagation in a 2d solid |
| cuda | use of the USER-CUDA package for GPU acceleration |
| 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 |
| gpu | use of the GPU package for GPU acceleration |
| hugoniostat | Hugoniostat shock dynamics |
| indent | spherical indenter into a 2d solid |
| intel | use of the USER-INTEL package for CPU or Intel(R) Xeon Phi(TM) coprocessor |
| kim | use of potentials in Knowledge Base for Interatomic Models (KIM) |
| line | line segment particles in 2d rigid bodies |
| 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 |
| qeq | use of the QEQ pacakge 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 |
| tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
| tri | triangular particles in rigid bodies |
vashishta: models using the Vashishta potential
Here is how you might 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
Running the simulation produces the files dump.indent and log.lammps. You can visualize the dump file as follows:
../../tools/xmovie/xmovie -scale dump.indent
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
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.
There is also an ELASTIC directory with an example script for computing elastic constants at zero temperature, using an Si example. See the ELASTIC/in.elastic file for more info.
There is also an ELASTIC_T directory with an example script for computing elastic constants at finite temperature, using an Si example. See the ELASTIC_T/in.elastic file for more info.
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 Section_start.html file for more info about user packages.