From 6deec536932a4c83fb2d76a4512cfd636193fae0 Mon Sep 17 00:00:00 2001
From: Simon Gravelle <simon.gravelle@live.fr>
Date: Wed, 11 Sep 2024 17:46:31 +0200
Subject: [PATCH] added LAMMPS page

---
 docs/source/index.rst  |  5 +--
 docs/source/lammps.rst | 77 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 80 insertions(+), 2 deletions(-)
 create mode 100644 docs/source/lammps.rst

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 3a8e138..6ad1d7f 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -10,14 +10,15 @@ start a discussion on |GitHub_discussion|.
     <a href="https://github.com/orgs/psm-compute/discussions" target="_blank">GitHub</a>
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Contents:
 
    oar
+   lammps
    git
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Contributors:
 
    sphinx
diff --git a/docs/source/lammps.rst b/docs/source/lammps.rst
new file mode 100644
index 0000000..6cb82ec
--- /dev/null
+++ b/docs/source/lammps.rst
@@ -0,0 +1,77 @@
+LAMMPS tips
+===========
+
+Choose where to compile LAMMPS
+------------------------------
+
+If the code must be accessed only by you, you can save it in your ``/home/`` folder on
+Dahu/Bigfoot. If you want the code to be available to all the member from
+your group, you can use ``/bettik/PROJECTS/``. For instance, for the members of `tamtam`:
+
+.. code-block:: bash
+
+    /bettik/PROJECTS/pr-tamtam/
+
+Download LAMMPS 
+---------------
+
+From the |LAMMPS| webpage, download the version of your choice.
+For instance, from the terminal, download the last stable release:
+
+.. code-block:: bash
+
+    wget https://download.lammps.org/tars/lammps.tar.gz
+    tar -xzvf lammps.tar.gz
+
+.. |LAMMPS| raw:: html
+
+    <a href="https://www.lammps.org/download.html" target="_blank">LAMMPS</a>
+
+
+Compile LAMMPS
+--------------
+
+For compiling in serial, simply navidate to the ``src/`` folder, and type:
+
+.. code-block:: bash
+
+    make serial
+
+For compilling in parallel, you will need to load manually openmpi and gcc using NIX:
+
+.. code-block:: bash
+
+    source /applis/site/nix.sh
+    nix-shell -p openmpi -p gcc
+
+Then, from the ``src/`` folder, type:
+
+.. code-block:: bash
+
+    make mpi
+
+Run LAMMPS
+----------
+
+Create a bash (``.sh``) file with the following content:
+
+.. code-block:: bash
+
+    #!/bin/bash
+    #OAR -n test
+    #OAR -l /nodes=1/cpu=1/core=4,walltime=12:00:00
+    #OAR --stdout log.out
+    #OAR --stderr log.err
+    #OAR --project tamtam
+
+    mpirun -np 4 /PATH-TO-LAMMPS/lmp_mpi -in input.lmp
+
+where ``input.lmp`` is your LAMMPS input file, and there the project was assumed
+to be `tamtam` (to adapt to your case). Here, 4 CPU cores are requested,
+as well as a total duration of 12 hours. Then, make the file file executable with
+chmod and launch it using:
+
+.. code-block:: bash
+
+    chmod +x ./myfile.sh
+    oarsub -S ./myfile.sh