User:Stuekero/LAMMPS

Example of input file

The input file below can be used with either of the example job scripts.

INPUTSerial jobMPI jobMPI job - Whole node (Graham)

File : lammps.in

# 3d Lennard-Jones melt

units           lj
atom_style      atomic

lattice         fcc 0.8442
region          box block 0 15 0 15 0 15
create_box      1 box
create_atoms    1 box
mass            1 1.0

velocity        all create 1.44 87287 loop geom

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0 2.5
neighbor        0.3 bin
neigh_modify    delay 5 every 1

fix             1 all nve
thermo          5
run             10000
write_data     config.end_sim

# End of the Input file.

File : run_lmp_serial.sh

#!/bin/bash
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=2500M      # memory; default unit is megabytes.
#SBATCH --time=0-00:30           # time (DD-HH:MM).

# Load the module:
module load lammps-omp/20170811

echo "Starting run at: `date`"

lmp_exec=lmp_icc_openmpi
lmp_input="lammps.in"
lmp_output="lammps_lj_output.txt"

${lmp_exec} < ${lmp_input} > ${lmp_output}

echo "Program finished with exit code $? at: `date`"

File : run_lmp_mpi.sh

#!/bin/bash
#SBATCH --ntasks=4               # number of MPI processes.
#SBATCH --mem-per-cpu=2500M      # memory; default unit is megabytes.
#SBATCH --time=0-00:30           # time (DD-HH:MM).

# Load the module:
module load lammps-omp/20170811

echo "Starting run at: `date`"

lmp_exec=lmp_icc_openmpi
lmp_input="lammps.in"
lmp_output="lammps_lj_output.txt"

srun ${lmp_exec} < ${lmp_input} > ${lmp_output}

echo "Program finished with exit code $? at: `date`"

File : run_lmp_mpi.sh

#!/bin/bash
#SBATCH --nodes=1                # number of nodes
#SBATCH --ntasks-per-node=32     # MPI processes per node
#SBATCH --mem=0                  # request all memory on node
#SBATCH --time=0-00:30           # time (DD-HH:MM).

# Load the module:
module load lammps-omp/20170811

echo "Starting run at: `date`"

lmp_exec=lmp_icc_openmpi
lmp_input="lammps.in"
lmp_output="lammps_lj_output.txt"

srun ${lmp_exec} < ${lmp_input} > ${lmp_output}

echo "Program finished with exit code $? at: `date`"

Message Passing Interface