LAMMPS
A general-purpose open-source application for classical molecular dynamics simulation, distributed under the GPL license. This package can perform molecular dynamics calculation of various systems such as soft matters, solids, and mesoscopic systems. It can be used as a simulator of classical dynamics of realistic atoms as well as general model particles. It supports parallel computing through spatial divisions. Its codes are designed so that their modification and extension are easy.
Websites
Official home Page: http://lammps.sandia.gov/
Official Document: http://lammps.sandia.gov/doc/Manual.html
LAMMPS on MateriApps: https://ma.issp.u-tokyo.ac.jp/en/app/613
Installed versions (2023-05-22)
20220623_update4
How to use LAMMPS on ISSP Supercomputer
Hereafter, replace $MA_ROOT with the following:
System B: /home/issp/materiapps/oneapi_compiler_classic-2023.0.0--openmpi-4.1.5
System C: /home/issp/materiapps/PrgEnv-intel_8.3.3
Preparation
LAMMPS is installed under
$MA_ROOT/intel/lammps/The following command
$ source $MA_ROOT/lammps/lammpsvars.shsets the value of the environment variable LAMMPS_ROOT the root directory of LAMMPS, and adds the directory including the executable files, $LAMMPS_ROOT/bin , to PATH and the directory including the libraries, $LAMMPS_ROOT/lib, to LD_LIBRARY_PATH .
The default version may be updated without an announcement. To specify the version to be used, source the configuration file with the desired version number instead of lammpsvars.sh .
Executable binary
The executable binary file is lammps . Please invoke lammps via srun (ohtaka) or mpiexec (kugui) even for a single process.
Sample input files
LAMMPS’s official sample files are available from
$LAMMPS_ROOT/share/lammps/examplesCopy them to your directory
$ cp -r $LAMMPS_ROOT/share/lammps/examples .How to submit job
A sample job script lammps.sh is available from
$MA_ROOT/lammps/sample_jobscript/Copy it to the current directory, and then edit lammps.sh (e.g., rename in.param ), and finally submit a job:
$ cp $MA_ROOT/lammps/sample_jobscript/lammps.sh .
# System B
$ sbatch lammps.sh
# System C
$ qsub lammps.sh