Merge pull request #107 from lammpstutorials/review-livecoms

Livecoms reviewer comments

Author: simongravelle

.dependencies/.github

@@ -67,6 +67,8 @@ The other pages use the [Sphinx](https://www.sphinx-doc.org/) generator with the
 
 - [Simon Gravelle](https://github.com/simongravelle) (corr. author),
   Université Grenoble Alpes, CNRS, LIPhy, 38000 Grenoble, France.
+- [Cecilia M. S. Alvares](https://github.com/cecimarques),
+  Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
 - [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),

.dependencies/lammpstutorials-inputs

@@ -23,7 +23,7 @@
                             <h1>LAMMPS tutorials</h1> 
                             <h2>
                                 by <a target="_blank" href="https://simongravelle.github.io/"">
-                                Simon Gravelle</a>, Jacob R. Gissinger, and Axel Kohlmeyer                    
+                                Simon Gravelle</a>, Cecilia M. S. Alvares, Jacob R. Gissinger, and Axel Kohlmeyer                    
                             </h2>
                         </center>
                         <br>

README.md

@@ -4,3 +4,5 @@ sphinxcontrib.bibtex
 sphinx-togglebutton
 sphinx-favicon
 pygments-lammps
+furo
+

docs/index.html

@@ -9,6 +9,16 @@ @article{schneider1978molecular
   publisher={APS}
 }
 
+@article{grossfield2009quantifying,
+  title={Quantifying uncertainty and sampling quality in biomolecular simulations},
+  author={Grossfield, Alan and Zuckerman, Daniel M},
+  journal={Annual Reports in Computational Chemistry},
+  volume={5},
+  pages={23--48},
+  year={2009},
+  publisher={Elsevier}
+}
+
 @book{hestenes1952methods,
   title={Methods of conjugate gradients for solving linear systems},
   author={Hestenes, Magnus Rudolph and Stiefel, Eduard and others},

docs/sphinx/requirements.txt

@@ -39,8 +39,8 @@ on statistical mechanics and molecular simulations.
 Software/system requirements
 ============================
 
-The LAMMPS stable release version 29Aug2024 (update2)
-and the matching LAMMPS--GUI software version 1.6.12 are required to
+The LAMMPS stable release version 22Jul2025
+and the matching LAMMPS--GUI software version 1.7.0 are required to
 follow the tutorials, as they include features that were first
 introduced in these versions.  For Linux (x86_64 CPU), macOS (BigSur or
 later), and Windows (10 and 11) you can download a precompiled LAMMPS
@@ -87,18 +87,19 @@ About LAMMPS--GUI
 
 LAMMPS--GUI is a graphical text editor, enhanced for editing LAMMPS
 input files and linked to the LAMMPS library, allowing it to run LAMMPS
-directly.  The text editor functions similarly to other graphical
+directly.  The text editor is similar to other graphical
 editors, such as Notepad or Gedit, but offers the following enhancements
-specifically for LAMMPS:
+specifically for running LAMMPS:
 
 - Wizard dialogs to set up these tutorials
 - Auto-completion of LAMMPS commands and options
 - Context-sensitive online help
 - Syntax highlighting for LAMMPS input files
 - Syntax-aware line indentation
+- Editor switches working directory to that of input file
 - Visualization using LAMMPS' built-in renderer
 - Start and stop simulations via mouse or keyboard
-- Monitoring of simulation progress
+- Monitoring of simulation progress and parallelization
 - Dynamic capture of LAMMPS output in a text window
 - Automatic plotting of thermodynamic data during runs
 - Capture of ``dump image`` outputs for animations

docs/sphinx/source/journal-article.bib

@@ -4,7 +4,11 @@ Scope
 *****
 
 This set of tutorials consists of eight tutorials arranged in order of
-increasing difficulty.  The novelties associated with each tutorial are
+increasing difficulty.  Although each tutorial can be
+read independently, information introduced in earlier tuto-
+rials is generally not repeated in detail in later ones. For this
+reason, we recommend that beginners follow the tutorials in
+order.  The novelties associated with each tutorial are
 briefly described below.
 
 In :ref:`lennard-jones-label`, the structure of LAMMPS
@@ -48,7 +52,8 @@ reactions by dynamically adjusting atomic interactions
 method that allows the partial charges of atoms to adjust according to
 their local environment.
 
-In :ref:`gcmc-silica-label`, a Monte Carlo simulation in
+In :ref:`gcmc-silica-label`, the adsorption of a fluid in silica pores is
+modeled. To do so, a Monte Carlo simulation in
 the grand canonical ensemble is implemented to demonstrate how LAMMPS
 can be used to simulate an open system that exchanges particles with a
 reservoir.

docs/sphinx/source/non-tutorials/prerequisites.rst

@@ -29,7 +29,7 @@ installer package.
 Installing the Linux .tar.gz Package
 ------------------------------------
 
-Download the archive (e.g., LAMMPS-Linux-x86_64-GUI-29Aug2024_update2.tar.gz)
+Download the archive (e.g., LAMMPS-Linux-x86_64-GUI-22Jul2025.tar.gz)
 and unpack it.  This will create a folder named LAMMPS--GUI containing the
 included commands, which can be launched directly using ``./lammps-gui`` or
 ``./lmp``, for example.  Adding this folder to the PATH environment
@@ -41,12 +41,12 @@ Installing the Linux Flatpak Bundle
 
 You have to have Flatpak support installed on Linux machine to be able
 to use the Flatpak bundle.  Download the bundle file
-(e.g., LAMMPS-Linux-x86_64-GUI-29Aug2024_update2.flatpak) and then
+(e.g., LAMMPS-Linux-x86_64-GUI-22Jul2025.flatpak) and then
 install it using the following command:
 
 .. code-block:: bash
 
-    flatpak install --user LAMMPS-Linux-x86_64-GUI-29Aug2024_update2.flatpak
+    flatpak install --user LAMMPS-Linux-x86_64-GUI-22Jul2025.flatpak
 
 This will integrate LAMMPS--GUI into your desktop environment
 (e.g., GNOME, KDE, XFCE) where it should appear in the ``Applications``
@@ -70,7 +70,7 @@ Installing the macOS Application Bundle
 ---------------------------------------
 
 After downloading the macOS app bundle image file
-(e.g., LAMMPS-macOS-multiarch-GUI-29Aug2024_update2.dmg), double-click
+(e.g., LAMMPS-macOS-multiarch-GUI-22Jul2025.dmg), double-click
 on it.  In the dialog that opens drag the LAMMPS--GUI app bundle into
 the Applications folder.  To enable command-line access, follow the
 instructions in the **README.txt** file.  These macOS app-bundles contain
@@ -87,7 +87,7 @@ Installing the Windows package
 ------------------------------
 
 Download the LAMMPS--GUI installer for Windows
-(e.g., LAMMPS-Win10-64bit-GUI-29Aug2024_update2.exe).  Windows may warn
+(e.g., LAMMPS-Win10-64bit-GUI-22Jul2025.exe).  Windows may warn
 you that the file is from an unknown developer and was downloaded from
 the internet.  This happens because neither the installer nor the
 LAMMPS--GUI application (or any other included applications) have been

docs/sphinx/source/non-tutorials/scope.rst

@@ -1,3 +1,3 @@
 .. container:: version
 
-    This tutorial is compatible with the 29Aug2024 (update 2) LAMMPS version.
+    This tutorial is compatible with the 22Jul2025 LAMMPS version.