deploy: a2cc49f

Author: simongravelle

sphinx/build/doctrees/environment.pickle

@@ -0,0 +1,8 @@
+If you find these tutorials useful for your research or simulations, you can
+cite: A Set of Tutorials for the LAMMPS Simulation Package" by Simon Gravelle,
+Jacob R. Gissinger, and Axel Kohlmeyer (2025) :cite:`gravelle2025tutorials`. You
+can access the full paper on |gravelle2025tutorials_arXiv|.
+
+.. |gravelle2025tutorials_arXiv| raw:: html
+
+    <a href="https://doi.org/10.48550/arXiv.2503.14020" target="_blank">arXiv</a>

sphinx/build/doctrees/non-tutorials/bibliography.doctree

@@ -41,7 +41,7 @@ Pulling on a carbon nanotube
 
 .. include:: ../../non-tutorials/recommand-lj.rst
 
-.. include:: ../../non-tutorials/needhelp.rst
+.. include:: ../../non-tutorials/cite.rst
 
 .. include:: ../../non-tutorials/2Aug2023.rst
 

sphinx/build/doctrees/non-tutorials/cite.doctree

@@ -40,7 +40,7 @@ Lennard-Jones fluid
     simulations, such as system initialization, energy minimization, integration
     of the equations of motion, and trajectory visualization.
 
-.. include:: ../../non-tutorials/needhelp.rst
+.. include:: ../../non-tutorials/cite.rst
 .. include:: ../../non-tutorials/2Aug2023.rst
 
 My first input

sphinx/build/doctrees/tutorials/level1/breaking-a-carbon-nanotube.doctree

@@ -36,7 +36,7 @@ Nanosheared electrolyte
 
 .. include:: ../../non-tutorials/recommand-lj.rst
 
-.. include:: ../../non-tutorials/needhelp.rst
+.. include:: ../../non-tutorials/cite.rst
 
 .. include:: ../../non-tutorials/2Aug2023.rst
 

sphinx/build/doctrees/tutorials/level1/lennard-jones-fluid.doctree

@@ -46,7 +46,7 @@ Polymer in water
 
 .. include:: ../../non-tutorials/recommand-lj.rst
 
-.. include:: ../../non-tutorials/needhelp.rst
+.. include:: ../../non-tutorials/cite.rst
 
 .. include:: ../../non-tutorials/2Aug2023.rst
 

sphinx/build/doctrees/tutorials/level2/nanosheared-electrolyte.doctree

@@ -38,7 +38,7 @@ Free energy calculation
 
 .. include:: ../../non-tutorials/recommand-lj.rst
 
-.. include:: ../../non-tutorials/needhelp.rst
+.. include:: ../../non-tutorials/cite.rst
 
 .. include:: ../../non-tutorials/2Aug2023.rst
 

sphinx/build/doctrees/tutorials/level2/polymer-in-water.doctree

@@ -36,7 +36,7 @@ Reactive silicon dioxide
 
 .. include:: ../../non-tutorials/recommand-lj.rst
 
-.. include:: ../../non-tutorials/needhelp.rst
+.. include:: ../../non-tutorials/cite.rst
 
 .. include:: ../../non-tutorials/2Aug2023.rst
 

sphinx/build/doctrees/tutorials/level3/free-energy-calculation.doctree

@@ -36,7 +36,7 @@ Water adsorption in silica
 
 .. include:: ../../non-tutorials/recommand-lj.rst
 
-.. include:: ../../non-tutorials/needhelp.rst
+.. include:: ../../non-tutorials/cite.rst
 
 .. include:: ../../non-tutorials/2Aug2023.rst
 

sphinx/build/doctrees/tutorials/level3/reactive-silicon-dioxide.doctree

@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="#" /><link rel="search" title="Search" href="search.html" />
 
     <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 --><title>Index - </title>
-<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
+<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=8f2a1f02" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=302659d7" />

sphinx/build/doctrees/tutorials/level3/water-adsorption-in-silica.doctree

@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
         <title>Contact me - </title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=8f2a1f02" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=302659d7" />

sphinx/build/html/_sources/non-tutorials/cite.rst.txt

@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
         <title>&lt;no title&gt; - </title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=8f2a1f02" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=302659d7" />

sphinx/build/html/_sources/tutorials/level1/breaking-a-carbon-nanotube.rst.txt

@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
         <title>&lt;no title&gt; - </title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=8f2a1f02" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=302659d7" />

sphinx/build/html/_sources/tutorials/level1/lennard-jones-fluid.rst.txt

@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
         <title>&lt;no title&gt; - </title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=8f2a1f02" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=302659d7" />

sphinx/build/html/_sources/tutorials/level2/nanosheared-electrolyte.rst.txt

@@ -7,7 +7,7 @@
 
     <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
         <title>Before you start - </title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=8f2a1f02" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../_static/togglebutton.css?v=13237357" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=302659d7" />
@@ -298,7 +298,7 @@ <h2>Required software<a class="headerlink" href="#required-software" title="Link
 <h3>LAMMPS (2Aug2023)<a class="headerlink" href="#lammps-2aug2023" title="Link to this heading">¶</a></h3>
 <div class="justify docutils container">
 <p>Download and install LAMMPS version 2Aug2023 by following the
-instructions of the <a href="https://docs.lammps.org/Install.html" target="_blank">LAMMPS website</a> <span id="id1">[<a class="reference internal" href="bibliography.html#id28" title="Aidan P Thompson, H Metin Aktulga, Richard Berger, Dan S Bolintineanu, W Michael Brown, Paul S Crozier, Pieter J in't Veld, Axel Kohlmeyer, Stan G Moore, Trung Dac Nguyen, and others. LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Computer Physics Communications, 271:108171, 2022.">1</a>]</span>.
+instructions of the <a href="https://docs.lammps.org/Install.html" target="_blank">LAMMPS website</a> <span id="id1">[<a class="reference internal" href="bibliography.html#id29" title="Aidan P Thompson, H Metin Aktulga, Richard Berger, Dan S Bolintineanu, W Michael Brown, Paul S Crozier, Pieter J in't Veld, Axel Kohlmeyer, Stan G Moore, Trung Dac Nguyen, and others. LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Computer Physics Communications, 271:108171, 2022.">1</a>]</span>.
 Depending on your operating system (i.e. Linux, macOS, or Windows),
 the procedure may differ.</p>
 </div>
@@ -324,7 +324,7 @@ <h3>LAMMPS (2Aug2023)<a class="headerlink" href="#lammps-2aug2023" title="Link t
 <h3>VMD (optional)<a class="headerlink" href="#vmd-optional" title="Link to this heading">¶</a></h3>
 <div class="justify docutils container">
 <p>To visualize the simulation, <a href="https://www.ks.uiuc.edu/Research/vmd" target="_blank">VMD</a> version 1.9.3 will
-be used <span id="id2">[<a class="reference internal" href="bibliography.html#id30" title="William Humphrey, Andrew Dalke, and Klaus Schulten. VMD: visual molecular dynamics. Journal of molecular graphics, 14(1):33–38, 1996.">2</a>]</span>. Some basic instructions for VMD are given here in the
+be used <span id="id2">[<a class="reference internal" href="bibliography.html#id31" title="William Humphrey, Andrew Dalke, and Klaus Schulten. VMD: visual molecular dynamics. Journal of molecular graphics, 14(1):33–38, 1996.">2</a>]</span>. Some basic instructions for VMD are given here in the
 <a class="reference internal" href="../tutorials/vmd/vmd-tutorial.html#vmd-label"><span class="std std-ref">VMD tutorial</span></a>. Feel free to use an alternative visualization
 software like <a href="https://www.ovito.org" target="_blank">Ovito</a>.</p>
 </div>
@@ -335,13 +335,13 @@ <h3>Python (optional)<a class="headerlink" href="#python-optional" title="Link t
 <p>To perform post-mortem analysis of the data during the <a class="reference internal" href="../tutorials/mdanalysis/mdanalysis-tutorial.html#mda-label"><span class="std std-ref">MDAnalysis tutorials</span></a>,
 MDAnalysis version 2.6.1 is used
 together with Python version 3.11.4
-<span id="id3">[<a class="reference internal" href="bibliography.html#id29" title="Guido van Rossum and Fred L Drake Jr. Python reference manual. Centrum voor Wiskunde en Informatica Amsterdam, 1995.">3</a>, <a class="reference internal" href="bibliography.html#id32" title="Naveen Michaud-Agrawal, Elizabeth J Denning, Thomas B Woolf, and Oliver Beckstein. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of computational chemistry, 32(10):2319–2327, 2011.">4</a>, <a class="reference internal" href="bibliography.html#id31" title="Richard J Gowers, Max Linke, Jonathan Barnoud, Tyler JE Reddy, Manuel N Melo, Sean L Seyler, Jan Domanski, David L Dotson, Sébastien Buchoux, Ian M Kenney, and others. MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations. In Proceedings of the 15th python in science conference, volume 98, 105. SciPy Austin, TX, 2016.">5</a>]</span>.</p>
+<span id="id3">[<a class="reference internal" href="bibliography.html#id30" title="Guido van Rossum and Fred L Drake Jr. Python reference manual. Centrum voor Wiskunde en Informatica Amsterdam, 1995.">3</a>, <a class="reference internal" href="bibliography.html#id33" title="Naveen Michaud-Agrawal, Elizabeth J Denning, Thomas B Woolf, and Oliver Beckstein. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of computational chemistry, 32(10):2319–2327, 2011.">4</a>, <a class="reference internal" href="bibliography.html#id32" title="Richard J Gowers, Max Linke, Jonathan Barnoud, Tyler JE Reddy, Manuel N Melo, Sean L Seyler, Jan Domanski, David L Dotson, Sébastien Buchoux, Ian M Kenney, and others. MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations. In Proceedings of the 15th python in science conference, volume 98, 105. SciPy Austin, TX, 2016.">5</a>]</span>.</p>
 </div>
 <div class="justify docutils container">
 <p>To plot the results from the simulations,
 <a href="https://matplotlib.org/3.5.3/api/_as_gen/matplotlib.pyplot.html" target="_blank">Matplotlib Pyplot</a> version 3.5.2 is used
 in combination with <a href="https://github.com/henriasv/lammps-logfile" target="_blank">lammps logfile</a>, a library allowing
-one to read the <em>log</em> file produced by LAMMPS <span id="id4">[<a class="reference internal" href="bibliography.html#id34" title="J. D. Hunter. Matplotlib: a 2d graphics environment. Computing in Science &amp; Engineering, 9(3):90–95, 2007.">6</a>, <a class="reference internal" href="bibliography.html#id39" title="Henrik Andersen Sveinsson. LAMMPS logfile reader. https://github.com/henriasv/lammps-logfile, 2021.">7</a>]</span>.</p>
+one to read the <em>log</em> file produced by LAMMPS <span id="id4">[<a class="reference internal" href="bibliography.html#id35" title="J. D. Hunter. Matplotlib: a 2d graphics environment. Computing in Science &amp; Engineering, 9(3):90–95, 2007.">6</a>, <a class="reference internal" href="bibliography.html#id40" title="Henrik Andersen Sveinsson. LAMMPS logfile reader. https://github.com/henriasv/lammps-logfile, 2021.">7</a>]</span>.</p>
 </div>
 </section>
 <section id="text-editing-software">
@@ -366,14 +366,14 @@ <h2>Recommended reading<a class="headerlink" href="#recommended-reading" title="
 <div class="justify docutils container">
 <p>To better understand molecular dynamics simulations, I recommend the reading
 of <em>Understanding molecular simulation</em> by Daan Frenkel and Berend
-Smit <span id="id5">[<a class="reference internal" href="bibliography.html#id40" title="Daan Frenkel and Berend Smit. Understanding molecular simulation: from algorithms to applications. Elsevier, 2023.">8</a>]</span>, as well as
+Smit <span id="id5">[<a class="reference internal" href="bibliography.html#id41" title="Daan Frenkel and Berend Smit. Understanding molecular simulation: from algorithms to applications. Elsevier, 2023.">8</a>]</span>, as well as
 <em>Computer simulation of liquids</em> by Michael Allen and Dominic Tildesley
-<span id="id6">[<a class="reference internal" href="bibliography.html#id26" title="Michael P Allen and Dominic J Tildesley. Computer simulation of liquids. Oxford university press, 2017.">9</a>]</span>. To understand the basic concepts
+<span id="id6">[<a class="reference internal" href="bibliography.html#id27" title="Michael P Allen and Dominic J Tildesley. Computer simulation of liquids. Oxford university press, 2017.">9</a>]</span>. To understand the basic concepts
 of fluid and Soft Matter systems, I recommend reading <em>Basic concepts for
 simple and complex liquids</em> by Jean-Louis Barrat and Jean-Pierre Hansen
 <span id="id7">[<a class="reference internal" href="bibliography.html#id2" title="Jean-Louis Barrat and Jean-Pierre Hansen. Basic concepts for simple and complex liquids. Cambridge University Press, 2003.">10</a>]</span>,
 as well as <em>Theory of simple liquids: with applications to soft matter</em>
-by Jean-Pierre Hansen and Ian Ranald McDonald <span id="id8">[<a class="reference internal" href="bibliography.html#id25" title="Jean-Pierre Hansen and Ian Ranald McDonald. Theory of simple liquids: with applications to soft matter. Academic press, 2013.">11</a>]</span>.</p>
+by Jean-Pierre Hansen and Ian Ranald McDonald <span id="id8">[<a class="reference internal" href="bibliography.html#id26" title="Jean-Pierre Hansen and Ian Ranald McDonald. Theory of simple liquids: with applications to soft matter. Academic press, 2013.">11</a>]</span>.</p>
 </div>
 </section>
 </section>