Merge pull request #3 from lammpstutorials/restructure

Restructure the folder, update the inputs

Author: simongravelle

.DESCRIPTION.md

@@ -0,0 +1,16 @@
+## Input files for LAMMPS tutorials [![DOI](https://zenodo.org/badge/739720878.svg)](https://zenodo.org/doi/10.5281/zenodo.13341091)
+
+LAMMPS and Python input files corresponding
+associated with [lammps tutorials](https://lammpstutorials.github.io/).
+
+The files include:
+
+- LAMMPS data files, input files, and parameter files,
+- the detailed solutions to the exercises,
+- Python scripts for generating structures and analyzing data.
+
+### Main repository
+
+Find [here](https://github.com/lammpstutorials/lammpstutorials.github.io)
+the main repository for LAMMPS tutorial.
+

.dependencies/.github

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

.files.txt

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

.generateREADME.sh

@@ -13,7 +13,7 @@ inputs/freeenergy/BiasedSampling/wham-release-2.0.11
 docs/sphinx/build
 
 # force the upload of certain dump and log files
-!vmd/dump.lammpstrj
+# tofix
 !level1/lennard-jones-fluid/my-first-input/log.lammps
 !level1/breaking-a-carbon-nanotube/breakable-bonds/dump.lammpstrj
 !level1/breaking-a-carbon-nanotube/breakable-bonds/log.lammps

.gitignore

@@ -0,0 +1,6 @@
+[submodule "dependencies/.github"]
+	path = dependencies/.github
+	url = git@github.com:lammpstutorials/.github.git
+[submodule ".dependencies/.github"]
+	path = .dependencies/.github
+	url = git@github.com:lammpstutorials/.github.git

.gitmodules

@@ -1,4 +1,13 @@
-## Input files for LAMMPS tutorials
+<!--
+WARNING: DO NOT MODIFY DIRECTLY THE README.md!
+This README.md file was assembled using the sed command from the files listed in
+"files.txt". See the script in "generateREADME.sh". To modify the content of 
+the  README.md, modify the files listed in "files.txt", or add a new file to the
+list in "files.txt".
+-->
+
+
+## Input files for LAMMPS tutorials [![DOI](https://zenodo.org/badge/739720878.svg)](https://zenodo.org/doi/10.5281/zenodo.13341091)
 
 LAMMPS and Python input files corresponding
 associated with [lammps tutorials](https://lammpstutorials.github.io/).
@@ -14,21 +23,26 @@ The files include:
 Find [here](https://github.com/lammpstutorials/lammpstutorials.github.io)
 the main repository for LAMMPS tutorial.
 
-### About me & Contact
 
-I am a computer physicist in soft matter and fluids at interfaces. You can 
-find more information on my [personal webpage](https://simongravelle.github.io/).
 
-See the [contact page](https://lammpstutorials.github.io/sphinx/build/html/non-tutorials/contact-me.html). 
-You can report issues here on Github, or send me an [email](https://simongravelle.github.io/). Your feedback is always appreciated.
+## Authors
+
+- [Simon Gravelle](https://github.com/simongravelle) (corr. author),
+  Université Grenoble Alpes, CNRS, LIPhy, 38000 Grenoble, France.
+- [Jacob R. Gissinger](https://www.stevens.edu/profile/jgissing),
+  Stevens Institute of Technology, Hoboken, NJ 07030, USA.
+- [Axel Kohlmeyer](https://sites.google.com/site/akohlmey),
+  Institute for Computational Molecular Science, Temple University, Philadelphia,
+  PA 19122, USA.
+
+
 
-### License & Acknowledgments
+## Acknowledgements
 
-All the LAMMPS inputs/data/parameter files and Python scripts are released under the 
-GNU general public license v3.0.
+- Simon Gravelle acknowledges funding from the European Union's Horizon 2020
+  research and innovation programme under the Marie Skłodowska-Curie grant
+  agreement N°101065060.
+- Axel Kohlmeyer acknowledges financial support from Sandia National Laboratories
+  under POs 2149742 and 2407526.
 
-This project has received funding from the European
-Union's Horizon 2020 research and innovation programme
-under the Marie Skłodowska-Curie grant agreement No 101065060.
 
-![Acknowledgments-logos](https://raw.githubusercontent.com/simongravelle/credits/1c44b5ae76a33c5bbbd33a54243365c6abdc24b2/cnrs-uga-liphy-msca.png)