Livecoms reviewer comments

docs/sphinx/requirements.txt

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

docs/sphinx/source/journal-article.bib

@@ -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/source/non-tutorials/prerequisites.rst

@@ -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

docs/sphinx/source/non-tutorials/using-lammps-gui.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/shared/versionLAMMPS.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.