Commit e1319728 authored by Brandon's avatar Brandon

Merge branch 'bcf/lammps' into 'master'

applications: port LAMMPS page

See merge request !441
parents c61cc2a8 b5051e09
# LAMMPS
[LAMMPS](https://lammps.sandia.gov/) 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.
# How to Access LAMMPS
NERSC uses [modules](../../environment/#nersc-modules-environment) to manage
access to software. To use the default version of LAMMPS, type:
```console
module load lammps
```
# Using LAMMPS on Cori
There are two ways of running LAMMPS on Cori: submitting a batch job, or
running interactively in an interactive batch session.
!!! tip "Sample Batch Script to Run LAMMPS on Cori Haswell"
```console
#!/bin/bash
#SBATCH -J test_lammps
#SBATCH -C haswell
#SBATCH -q debug
#SBATCH -N 2
#SBATCH -t 30:00
#SBATCH -o test_lammps.o%j
module load lammps
# LAMMPS supports 2 different ways of reading inputs files
srun -n 64 -c 2 --cpu-bind=cores lmp_cori < test.in
srun -n 64 -c 2 --cpu-bind=cores lmp_cori -in test.in
```
!!! tip "Sample Batch Script to Run LAMMPS on Cori KNL"
```console
#!/bin/bash
#SBATCH -J test_lammps
#SBATCH -C knl
#SBATCH -q debug
#SBATCH -N 2
#SBATCH -t 30:00
#SBATCH -o test_lammps.o%j
module load lammps
# LAMMPS supports 2 different ways of reading inputs files
srun -n 136 -c 2 --cpu-bind=cores lmp_cori < test.in
srun -n 136 -c 2 --cpu-bind=cores lmp_cori -in test.in
```
These job scripts request two nodes in the debug partition, and run for up to
30 minutes. The first example runs 64 MPI processes across 64 cores on 2 nodes
of Cori Haswell. The second example runs 136 MPI processes across 136 cores on
2 nodes of Cori KNL.
Then submit the job script using the sbatch command, e.g., assuming the job
script name is `test_lammps.slurm`:
```console
sbatch test_lammps.slurm
```
# Official LAMMPS documentation
## Support
* [LAMMPS Online Manual](https://lammps.sandia.gov/doc/Manual.html)
!!! tip
If *after* the checking the above you believe there is an
issue with the NERSC module file a ticket with
our [help desk](https://help.nersc.gov)
......@@ -38,6 +38,7 @@ nav:
- Abinit: applications/abinit/index.md
- BerkeleyGW: applications/berkeleygw/index.md
- CP2K: applications/cp2k/index.md
- LAMMPS: applications/lammps/index.md
- Mathematica : applications/mathematica/index.md
- MATLAB :
- MATLAB Overview: applications/matlab/index.md
......
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