Merge pull request #88 from lammpstutorials/restructure

Restructure the folders, simplify the website, prepare for GUI

Author: simongravelle

.DESCRIPTION.md

@@ -0,0 +1,54 @@
+# LAMMPS tutorials
+
+This is the repository of the [LAMMPS tutorials](https://lammpstutorials.github.io/)
+webpage. All the LAMMPS input scripts and data files can be found in a separate
+repository named [lammpstutorials-inputs](https://github.com/lammpstutorials/lammpstutorials-inputs).
+
+The tutorials are compatible with the XXXX2024 release of LAMMPS.
+
+## About LAMMPS tutorials
+
+The LAMMPStutorials website is made of seven tutorials that are ordered by increasing difficulty.
+[Lennard-Jones fluid](https://lammpstutorials.github.io/sphinx/build/html/tutorials/level1/lennard-jones-fluid.html)
+is meant for absolute LAMMPS and molecular dynamics beginners, and the complexity of the simulation is
+progressively increased for [Pulling on a carbon nanotube](https://lammpstutorials.github.io/sphinx/build/html/tutorials/level1/breaking-a-carbon-nanotube.html), 
+[Polymer in water](https://lammpstutorials.github.io/sphinx/build/html/tutorials/level2/polymer-in-water.html), 
+[Nanosheared electrolyte](https://lammpstutorials.github.io/sphinx/build/html/tutorials/level2/nanosheared-electrolyte.html),
+and [Reactive silicon dioxide](https://lammpstutorials.github.io/sphinx/build/html/tutorials/level3/reactive-silicon-dioxide.html). 
+Finally, [Water adsorption in silica](https://lammpstutorials.github.io/sphinx/build/html/tutorials/level3/water-adsorption-in-silica.html) and
+[Free energy calculation](https://lammpstutorials.github.io/sphinx/build/html/tutorials/level3/free-energy-calculation.html) use some more advanced simulation methods that are commonly used when studying soft matter systems, respectively grand canonical Monte Carlo simulations and a free energy method named umbrella sampling.
+
+<p float="left">
+    <a href="https://lammpstutorials.github.io/sphinx/build/html/tutorials/level1/lennard-jones-fluid.html">
+        <img src="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials.github.io/2Aug2023/docs/avatars/level1/lennard-jones-fluid/avatar-Lennard-Jones-LAMMPS.png" width="32%" />
+    </a>
+    <a href="https://lammpstutorials.github.io/sphinx/build/html/tutorials/level1/breaking-a-carbon-nanotube.html">
+        <img src="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials.github.io/2Aug2023/docs/avatars/level1/breaking-a-carbon-nanotube/CNT.png" width="32%" />
+    </a>
+    <a href="https://lammpstutorials.github.io/sphinx/build/html/tutorials/level3/water-adsorption-in-silica.html">
+        <img src="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials.github.io/2Aug2023/docs/avatars/level3/water-adsorption-in-silica/water-adsorption.png" width="32%" />
+    </a>
+</p>
+
+## Access the files
+
+You can access all the files by cloning this repository with its submodules:
+
+```
+git clone https://github.com/lammpstutorials/lammpstutorials.github.io.git --recurse-submodule
+```
+
+Alternatively, you can download the [inputs](https://github.com/lammpstutorials/lammpstutorials-inputs) only:
+
+```
+git clone https://github.com/lammpstutorials/lammpstutorials.github.io.git
+```
+
+The Matplotlib Pyplot functions for the figures are shared [here](https://github.com/simongravelle/pyplot-perso).
+
+### Template ###
+
+The template from the first page has been adapted from [HTML5 UP](https://html5up.net/).
+The other pages use the [Sphinx](https://www.sphinx-doc.org/) generator with the
+[furo style](https://github.com/pradyunsg/furo).
+

.dependencies/.github

@@ -0,0 +1,4 @@
+.dependencies/.github/COMMENT.md
+.DESCRIPTION.md
+.dependencies/.github/AUTHORS.md
+.dependencies/.github/ACKNOWLEDGEMENTS.md

.dependencies/lammpstutorials-inputs

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+.dependencies/.github/generateREADME.sh

.dependencies/pyplot-perso

@@ -35,6 +35,7 @@ jobs:
           pip install pygments-lammps
           pip install sphinx-favicon
           pip install sphinxcontrib.bibtex
+          pip install sphinx-tabs
       - name: Build
         run: |
           cd docs/sphinx/

.files.txt

@@ -11,10 +11,6 @@
 inputs/freeenergy/BiasedSampling/wham-release-2.0.11
 docs/sphinx/build
 
-# force the upload of certain dump files
-!docs/inputs/vmd/dump.lammpstrj
-!docs/inputs/level1/breaking-a-carbon-nanotube/breakable-bonds/dump.lammpstrj
-
 # latex
 ebook/**/*.aux
 ebook/**/*.log
@@ -28,3 +24,4 @@ ebook/tutorials/*
 ebook/non-tutorials/*
 
 **/untitled.*.ppm
+**/untitled.*.ppn

.generateREADME.sh

@@ -1,6 +1,11 @@
-[submodule "docs/lammpstutorials-inputs"]
-	path = docs/lammpstutorials-inputs
-	url = git@github.com:lammpstutorials/lammpstutorials-inputs.git
-[submodule "docs/sphinx/source/tutorials/figures/pyplot-perso"]
-	path = docs/sphinx/source/tutorials/figures/pyplot-perso
+[submodule ".dependencies/.github"]
+	path = .dependencies/.github
+	url = git@github.com:lammpstutorials/.github.git
+[submodule ".dependencies/pyplot-perso"]
+	path = .dependencies/pyplot-perso
 	url = git@github.com:simongravelle/pyplot-perso.git
+	branch = LAMMPS-livecom
+[submodule ".dependencies/lammpstutorials-inputs"]
+	path = .dependencies/lammpstutorials-inputs
+	url = git@github.com:lammpstutorials/lammpstutorials-inputs.git
+	branch = main