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LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator.
LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of interatomic potentials (force fields) and boundary conditions. It can model 2d or 3d systems with sizes ranging from only a few particles up to billions.
LAMMPS can be built and run on single laptop or desktop machines, but is designed for parallel computers. It will run in serial and on any parallel machine that supports the MPI message-passing library. This includes shared-memory multicore, multi-CPU servers and distributed-memory clusters and supercomputers. Parts of LAMMPS also support OpenMP multi-threading, vectorization, and GPU acceleration.
LAMMPS is written in C++ and requires a compiler that is at least compatible with the C++-11 standard. Earlier versions were written in F77, F90, and C++-98. See the History page of the website for details. All versions can be downloaded as source code from the LAMMPS website.
LAMMPS is designed to be easy to modify or extend with new capabilities, such as new force fields, atom types, boundary conditions, or diagnostics. See the Modifying & extending LAMMPS section of for more details.
In the most general sense, LAMMPS integrates Newton’s equations of motion for a collection of interacting particles. A single particle can be an atom or molecule or electron, a coarse-grained cluster of atoms, or a mesoscopic or macroscopic clump of material. The interaction models that LAMMPS includes are mostly short-ranged in nature; some long-range models are included as well.
LAMMPS uses neighbor lists to keep track of nearby particles. The lists are optimized for systems with particles that are repulsive at short distances, so that the local density of particles never becomes too large. This is in contrast to methods used for modeling plasma or gravitational bodies (like galaxy formation).
On parallel machines, LAMMPS uses spatial-decomposition techniques with MPI parallelization to partition the simulation domain into subdomains of equal computational cost, one of which is assigned to each processor. Processors communicate and store “ghost” atom information for atoms that border their subdomain. Multi-threading parallelization and GPU acceleration with particle-decomposition can be used in addition.
https://docs.lammps.org/Manual.html
Binary Location:
/data/apps/lammps/IntelMPI/src/lmp_mpi
Version:
Job Script:
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/bin/bash
SBATCH --partition=large ##sinfo --all ##medium 128 core-1 week and high_mem 256 core and 2 weeks
#SBATCH --ntasks=128
#SBATCH --job-name=lammps
##SBATCH --mail-user=
#SBATCH --output lammps.%J.out
#SBATCH --error lammps.%J.err###Inputs###
### modify the appropriate version of the executable
export exec_name=/data/apps/lammps/IntelMPI/src/lmp_mpi
export INP= ## mention the path of your input file## keep the input file on the local directory where this job is launchedulimit -s unlimited
module purge
module load compiler/2022.0.2 mkl/2022.0.2 mpi/2021.2.0export I_MPI_FABRICS=shm:ofi
export UCX_TLS=sm,udexport UCX_NET_DEVICES=mlx5_0:1
export FI_PROVIDER=mlx
export UCX_UNIFIED_MODE=y
export UCX_USE_MT_MUTEX=yexport OMP_NUM_THREADS=1
#export I_MPI_PIN_ORDER=bunch
#export I_MPI_PIN_DOMAIN=core##Application Execution###
{ time mpiexec.hydra -np $SLURM_NPROCS ${exec_name} -in ${INP}; } > lammps_${SLURM_JOB_ID}.std.out 2>&1
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