LAMMPS
Description
Classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.
License
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of lammps and load default version of lammps as
module avail lammps/ # list available modules module load lammps # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail lammps
and choose explicit version you want to use.
Note 1: Lammps does not work on the oldest clusters. Please specify an option cpu_flag=avx2 in the qsub command. This option will exclude incompatible nodes.
Note 2: There is a significant difference in computing speed of the program between Intel and AMD machine architecture. It runs better on Intel. >> list of MetaVO machines
Notice: This application supports parallel computing (MPI, OpenMP) which can have weird consequences. For more details about parallel computing visit the page Parallelization.
what includes lammps binary
The lammps binary includes many compiled parts. You can get their list by issuing command
lmp -h
If you need more components compiled inside, give us feedback.
Documentation
Documentation is available at https://docs.lammps.org/Manual.html, tutorials are here, description of commands is here.