LAMMPS

LAMMPS is a large scale classical molecular dynamics code, and stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers), solid-state materials (metals, semiconductors) 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.

Availability¶

Wulver

Software	Version	Dependent Toolchain	Module Load Command
LAMMPS	23Jun2022-kokkos-CUDA-11.4.1	foss/2021b	`module load foss/2021b LAMMPS/23Jun2022-kokkos-CUDA-11.4.1`
LAMMPS	23Jun2022-kokkos	foss/2021b	`module load foss/2021b LAMMPS/23Jun2022-kokkos`

Note

To know the deatils about dependent toolchain please go to Toolchains

Application Information, Documentation and Support¶

The official LAMMPS is available at LAMMPS Online Manual. LAMMPS has a large user base and a good user support. Question related to using LAMMPS can be posted to the LAMMPS User forum. Archived user mailing list are also useful to resolve some of the common user issues.

Tip

If after checking the above forum, if you believe that there is an issue with the module, please file a ticket with Service Now

Using LAMMPS¶

Sample Batch Script to Run LAMMPS

Wulver

#!/bin/bash
#SBATCH -J test_lammps
#SBATCH --output=%x.%j.out # %x.%j expands to slurm JobName.JobID
#SBATCH --error=%x.%j.err # prints the error message
#SBATCH --partition=general 
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=128
#SBATCH --mem-per-cpu=4000M # Maximum allowable memory per CPU 4G
#SBATCH --qos=standard
#SBATCH --account=PI_ucid # Replace PI_ucid which the NJIT UCID of PI
#SBATCH --time=71:59:59  # D-HH:MM:SS

###############################################
#
# Purge and load modules needed for run
#
################################################
module purge
module load wulver # Load slurm, easybuild
module load foss/2021b LAMMPS

srun lmp -in test.in

Then submit the job script using the sbatch command, e.g., assuming the job script name is test_lammps.slurm:

sbatch test_lammps.slurm

Building LAMMPS from source¶

Some users may be interested in building LAMMPS from source to enable more specific LAMMPS packages. The source files for LAMMPS can be downloaded as either a tar file or from the LAMMPS Github repository.

Building on Cluster

The following procedure was used to build LAMMPS on Wulver. In the terminal:

WulverLochness

module purge
module load wulver
module load foss
module load CMake

git clone https://github.com/lammps/lammps.git
cd lammps
mkdir build
cd build

cmake -DCMAKE_INSTALL_PREFIX=$PWD/../install_hsw -DCMAKE_CXX_COMPILER=mpicxx \
            -DCMAKE_BUILD_TYPE=Release -D BUILD_MPI=yes -DKokkos_ENABLE_OPENMP=ON \
            -DKokkos_ARCH_HSW=ON -DCMAKE_CXX_STANDARD=17 -D PKG_MANYBODY=ON \
            -D PKG_MOLECULE=ON -D PKG_KSPACE=ON -D PKG_REPLICA=ON -D PKG_ASPHERE=ON \
            -D PKG_RIGID=ON -D PKG_KOKKOS=ON -D DOWNLOAD_KOKKOS=ON \
            -D CMAKE_POSITION_INDEPENDENT_CODE=ON -D CMAKE_EXE_FLAGS="-dynamic" ../cmake
make -j16
make install

module purge
module load foss
module load CMake

git clone https://github.com/lammps/lammps.git
cd lammps
mkdir build
cd build

cmake -DCMAKE_INSTALL_PREFIX=$PWD/../install_hsw -DCMAKE_CXX_COMPILER=mpicxx \
            -DCMAKE_BUILD_TYPE=Release -D BUILD_MPI=yes -DKokkos_ENABLE_OPENMP=ON \
            -DKokkos_ARCH_HSW=ON -DCMAKE_CXX_STANDARD=17 -D PKG_MANYBODY=ON \
            -D PKG_MOLECULE=ON -D PKG_KSPACE=ON -D PKG_REPLICA=ON -D PKG_ASPHERE=ON \
            -D PKG_RIGID=ON -D PKG_KOKKOS=ON -D DOWNLOAD_KOKKOS=ON \
            -D CMAKE_POSITION_INDEPENDENT_CODE=ON -D CMAKE_EXE_FLAGS="-dynamic" ../cmake
make -j16
make install

GROMACS

User Contributed Information¶

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