lammps
Link to section 'Description' of 'lammps' Description
LAMMPS is a classical molecular dynamics code with a focus on materials modelling. It’s an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) 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.
Link to section 'Versions' of 'lammps' Versions
- Bell: 20200721, 20201029
- Brown: 7Aug19, 31Mar17
- Scholar: 31Mar17
- Gilbreth: 20190807
- Negishi: 20220623
- Anvil: 20210310, 20210310-kokkos
Link to section 'Module' of 'lammps' Module
You can check available lammps version by:
module spider lammps
You can check how to load the lammps module by the module's full name:
module spider lammps/XXXX
You can load the modules by:
module load lammps # for default version
module load lammps/XXXX # for specific version
Link to section 'Usage' of 'lammps' Usage
LAMMPS reads command lines from an input file like "in.file". The LAMMPS executable is lmp, to run the lammps input file, use the -in command:
lmp -in in.file
For more details about how to run LAMMPS, please check LAMMPS.
Link to section 'Example job' of 'lammps' Example job
#!/bin/bash
# FILENAME: myjobsubmissionfile
#SBATCH --nodes=2 # Total # of nodes
#SBATCH --ntasks=256 # Total # of MPI tasks
#SBATCH --time=1:30:00 # Total run time limit (hh:mm:ss)
#SBATCH -J myjobname # Job name
#SBATCH -o myjob.o%j # Name of stdout output file
#SBATCH -e myjob.e%j # Name of stderr error file
# Manage processing environment, load compilers and applications.
module purge
module load gcc/XXXX openmpi/XXXX # or module load intel/XXXX impi/XXXX | depends on the output of "module spider lammps/XXXX"
module load lammps/XXXX
module list
# Launch MPI code
srun -n $SLURM_NTASKS lmp
Link to section 'Note' of 'lammps' Note
Using mpirun -np $SLURM_NTASKS lmp or mpiexex -np $SLURM_NTASKS lmp may not work for non-exclusive jobs on some clusters. Use srun -n $SLURM_NTASKS lmp or mpirun lmp instead. mpirun lmp without specifying the number of ranks will automatically pick up the number of SLURM_NTASKS and works fine.