LAMMPS

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 (2025-01-17)

20240829_update1

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 (CPU): /home/issp/materiapps/PrgEnv-intel_8.3.3
System C (GPU): /home/issp/materiapps/nvhpc-nompi_24.7__openmpi_nvhpc_4.1.2

Preparation

LAMMPS is installed under

$MA_ROOT/lammps/

The following command

$ source $MA_ROOT/lammps/lammpsvars.sh

sets 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.

Packages

The following packages of Lammps (https://docs.lammps.org/Packages_list.html), which do not require extra libraries are installed.

AMOEBA ASPHERE BOCS BODY BPM BROWNIAN CG-DNA CG-SPICA CLASS2 COLLOID COLVARS CORESHELL DIELECTRIC DIFFRACTION DIPOLE DPD-BASIC DPD-MESO DPD-REACT DPD-SMOOTH DRUDE EFF EXTRA-COMMAND EXTRA-COMPUTE EXTRA-DUMP EXTRA-FIX EXTRA-MOLECULE EXTRA-PAIR FEP GRANULAR INTEL INTERLAYER KSPACE MANIFOLD MANYBODY MC MEAM MESONT MGPT MISC ML-IAP ML-POD ML-RANN ML-SNAP ML-UF3 MOFFF MOLECULE OPENMP OPT ORIENT PERI PHONON PLUGIN POEMS PTM QEQ QTB REACTION REAXFF REPLICA RHEO RIGID SHOCK SMTBQ SPH SPIN SRD TALLY UEF YAFF

(Technically, all_on.cmake and nolib.cmake are used for building Lammps.)

Sample input files

LAMMPS’s official sample files are available from

$LAMMPS_ROOT/share/lammps/examples

Copy 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