added choice

Author: simongravelle

.github/workflows/gh-pages.yml

@@ -32,6 +32,7 @@ jobs:
           pip install pygments-lammps
           pip install sphinx-favicon
           pip install sphinxcontrib.bibtex
+          pip install sphinx-tabs
       - name: Build
         run: |
           cd docs/sphinx/

docs/sphinx/source/_static/custom.css

@@ -152,5 +152,12 @@ section {
 }
 
 
+/* Add more specific parent selectors */
+body .sphinx-tabs .tab-button {
+  background-color: red !important;
+}
 
-  
+/* If tabs are inside a specific section or container */
+section div.sphinx-tabs .tab-button {
+  background-color: red !important;
+}

docs/sphinx/source/conf.py

@@ -5,7 +5,8 @@
 
 extensions = ['sphinx_togglebutton',
               'sphinx_favicon',
-              'sphinxcontrib.bibtex']
+              'sphinxcontrib.bibtex',
+              'sphinx_tabs.tabs']
 
 templates_path = ['_templates']
 

docs/sphinx/source/journal-article.bib

@@ -5,6 +5,18 @@ @book{barrat2003basic
   publisher={Cambridge University Press}
 }
 
+@misc{lammps_docs,
+  title = {{LAMMPS} Online Documentation for latest stable version},
+  howpublished = {\url{https://docs.lammps.org/stable}},
+  note = {Accessed: 2024-07-15}
+}
+
+@misc{lammps_run_basics,
+  title = {{LAMMPS} Run Basics Documentation},
+  howpublished = {\url{https://docs.lammps.org/Run_basics.html}},
+  note = {Accessed: 2025-03-22}
+}
+
 @article{gravelle2025tutorials,
   author    = {Simon Gravelle and Jacob R. Gissinger and Axel Kohlmeyer},
   title     = {A Set of Tutorials for the LAMMPS Simulation Package},

docs/sphinx/source/shared/access-the-files.rst

@@ -1,6 +1,9 @@
-You can access the input scripts and data files that
-are used in these tutorials from a dedicated |Github_repository_input_folder|.
-This repository also contains the full solutions to the exercises.
+.. admonition:: Cite
+    :class: non-title-info
+
+    You can access the input scripts and data files that
+    are used in these tutorials from a dedicated |Github_repository_input_folder|.
+    This repository also contains the full solutions to the exercises.
 
 .. |Github_repository_input_folder| raw:: html
 

docs/sphinx/source/tutorial1/tutorial.rst

@@ -9,7 +9,7 @@ Pulling on a carbon nanotube
 
 .. include:: introduction.rst
 .. include:: ../shared/recommend-tutorial1.rst
-.. include:: ../../non-tutorials/needhelp.rst
+.. include:: ../shared/cite.rst
 .. include:: ../shared/versionLAMMPS.rst
 .. include:: tutorial.rst
 .. include:: ../shared/access-the-files.rst

docs/sphinx/source/tutorial2/breaking-a-carbon-nanotube.rst

@@ -10,16 +10,21 @@
     :align: right
     :class: only-light
 
-The objective of this tutorial is to impose the deformation
-of a carbon nanotube (CNT) using LAMMPS.
+In this tutorial, the system of interest is a small, single-walled carbon
+nanotube (CNT) in an empty box.  The CNT is strained
+by imposing a constant velocity on the edge atoms.  To illustrate the
+difference between conventional and reactive force fields, this tutorial
+is divided into two parts: in the first part, a conventional molecular
+force field (called OPLS-AA :cite:`jorgensenDevelopmentTestingOPLS1996`)
+is used and the bonds between the atoms of the CNT are unbreakable.  In
+the second part, a reactive force field (called AIREBO :cite:`stuart2000reactive`)
+is used, which allows chemical bonds to break under large strain.
 
-In this tutorial, a small carbon nanotube (CNT) is simulated
-within an empty box using LAMMPS. An external 
-force is imposed on the CNT, and its deformation is measured over time.
-
-To illustrate the difference between classical and reactive force fields,
-this tutorial is divided into two parts. Within the first part, a classical
-force field is used and the bonds between the atoms of the CNT are
-unbreakable. Within the second part, a reactive force field
-(named AIREBO :cite:`stuart2000reactive`) is used, allowing for the breaking
-of chemical bonds when the CNT undergoes strong deformation.
+To set up this tutorial, select *Start Tutorial 2* from the *Tutorials*
+menu of LAMMPS-GUI and follow the instructions. This will select a folder,
+create one if necessary, and place several files into it.  The initial
+input file, set up for a single-point energy calculation, will also be
+loaded into the editor under the name *unbreakable.lmp*.  Additional files
+are a data file containing the CNT topology and geometry, named
+*unbreakable.data*, a parameters file named *unbreakable.inc*, as well as
+the scripts required for the second part of the tutorial.