LAMMPS is an open source molecular dynamics application, and OCTOPUS enables the use of LAMMPS by batch request.
Basic use
The execution of LAMMPS is permitted only by processing by batch request. The example of the job script and the job execution method for LAMMPS(22-Jul-25) are described below.
* Please refer to the official website for the manual about LAMMPS.
Writing a job script file
The following example is a job script when LAMMPS is executed with 512 processes (2 nodes are used, 256 processes per node). Although there is no particular specification for the file name, we named "lammps.sh" in this section.
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#!/bin/bash #PBS -q OCT #PBS -l cpunum_job=256 #PBS --group=[group name] #PBS -l elapstim_req=01:00:00 #PBS -b 2 #PBS -T intmpi #PBS -v OMP_NUM_THREADS=1 module load BaseApp module load lammps/22Jul2025 cd $PBS_O_WORKDIR mpirun ${NQSV_MPIOPTS} -np 512 lmp < input_file |
For various input files of LAMMPS, please see official HP.
About other lines of job script, please see here.
Packages
The packages already installed are as follows.
ASPHERE, ATC, AWPMD, BOCS, BODY, CG-DNA, CG-SPICA, CLASS2, COLLOID, COLVARS, COMPRESS, CORESHELL, DIFFRACTION, DIPOLE, DPD-MESO, DRUDE, EFF, ELECTRODE, EXTRA-COMPUTE, EXTRA-DUMP, EXTRA-FIX, EXTRA-MOLECULE, EXTRA-PAIR, FEP, GRANULAR, INTEL, INTERLAYER, KSPACE, LATBOLTZ, MANIFOLD, MANYBODY, MC, MDI, MGPT, MISC, MOFFF, MOLECULE, NETCDF, OPENMP, OPT, ORIENT, PERI, PHONON, POEMS, PYTHON, QEQ, QTB, REAXFF, REPLICA, RIGID, SHOCK, SMTBQ, SPH, SPIN, SRD, TALLY, UEF, VORONOI
How to execute
Submit the job script you created.
$ qsub lammps.sh
How to check the status of the submitted job is here. When the execution is finished, the calculation result is output to the result file.
