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diff --git a/sphinx/build/doctrees/environment.pickle b/sphinx/build/doctrees/environment.pickle
diff --git a/sphinx/build/doctrees/tutorials/level2/nanosheared-electrolyte.doctree b/sphinx/build/doctrees/tutorials/level2/nanosheared-electrolyte.doctree
diff --git a/sphinx/build/html/_images/density-dark.png b/sphinx/build/html/_images/density-dark.png
diff --git a/sphinx/build/html/_images/density-dm.png b/sphinx/build/html/_images/density-dm.png
diff --git a/sphinx/build/html/_images/density-light.png b/sphinx/build/html/_images/density-light.png
diff --git a/sphinx/build/html/_images/density.png b/sphinx/build/html/_images/density.png
diff --git a/sphinx/build/html/_images/equilibration-dark.png b/sphinx/build/html/_images/equilibration-dark.png
diff --git a/sphinx/build/html/_images/equilibration-dm.png b/sphinx/build/html/_images/equilibration-dm.png
diff --git a/sphinx/build/html/_images/equilibration-light.png b/sphinx/build/html/_images/equilibration-light.png
diff --git a/sphinx/build/html/_images/equilibration.png b/sphinx/build/html/_images/equilibration.png
diff --git a/sphinx/build/html/_images/minimization-dark.png b/sphinx/build/html/_images/minimization-dark.png
diff --git a/sphinx/build/html/_images/minimization-dm.png b/sphinx/build/html/_images/minimization-dm.png
diff --git a/sphinx/build/html/_images/minimization-light.png b/sphinx/build/html/_images/minimization-light.png
diff --git a/sphinx/build/html/_images/minimization.png b/sphinx/build/html/_images/minimization.png
diff --git a/sphinx/build/html/_images/shearing-dark.png b/sphinx/build/html/_images/shearing-dark.png
diff --git a/sphinx/build/html/_images/shearing-dm.png b/sphinx/build/html/_images/shearing-dm.png
diff --git a/sphinx/build/html/_images/shearing-light.png b/sphinx/build/html/_images/shearing-light.png
diff --git a/sphinx/build/html/_images/shearing.png b/sphinx/build/html/_images/shearing.png
diff --git a/sphinx/build/html/_sources/tutorials/level2/nanosheared-electrolyte.rst.txt b/sphinx/build/html/_sources/tutorials/level2/nanosheared-electrolyte.rst.txt
@@ -563,11 +563,11 @@ Energy minimization
     of the 3 steps, before re-increasing a little after the 
     temperature is increased from 1 to :math:`300\,\text{K}`.
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/minimization-light.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/minimization.png
     :alt: Energy minimisation of the confined water and salt
     :class: only-light
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/minimization-dark.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/minimization-dm.png
     :alt: Energy minimisation of the confined water and salt
     :class: only-dark
 
@@ -665,11 +665,11 @@ System equilibration
     the distance between the two walls
     reduces until it reaches an equilibrium value.
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/equilibration-light.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/equilibration.png
     :alt: Plot showing the distance between the walls as a function of time.
     :class: only-light
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/equilibration-dark.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/equilibration-dm.png
     :alt: Plot showing the distance between the walls as a function of time.
     :class: only-dark
 
@@ -814,11 +814,11 @@ Imposed shearing
     can be plotted. As expected for such Couette flow geometry, the velocity
     of the fluid is found to increase linearly along :math:`z`.
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/shearing-light.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/shearing.png
     :alt: Velocity of the nanosheared fluid
     :class: only-light
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/shearing-dark.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/shearing-dm.png
     :alt: Velocity of the nanosheared fluid
     :class: only-dark
 
@@ -828,11 +828,11 @@ Imposed shearing
     along the *z* axis. The line is a linear fit assuming that 
     the pore size is :math:`h = 1.8\,\text{nm}`.
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/density-light.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/density.png
     :alt: density of the nanosheared fluid
     :class: only-light
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/density-dark.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/density-dm.png
     :alt: density of the nanosheared fluid
     :class: only-dark
 

diff --git a/sphinx/build/html/tutorials/level2/nanosheared-electrolyte.html b/sphinx/build/html/tutorials/level2/nanosheared-electrolyte.html
@@ -758,10 +758,10 @@ <h3>Energy minimization<a class="headerlink" href="#energy-minimization" title="
 temperature is increased from 1 to <span class="math notranslate nohighlight">\(300\,\text{K}\)</span>.</p>
 </div>
 <figure class="align-default">
-<img alt="Energy minimisation of the confined water and salt" class="only-light" src="../../_images/minimization-light.png" />
+<img alt="Energy minimisation of the confined water and salt" class="only-light" src="../../_images/minimization.png" />
 </figure>
 <figure class="align-default">
-<img alt="Energy minimisation of the confined water and salt" class="only-dark" src="../../_images/minimization-dark.png" />
+<img alt="Energy minimisation of the confined water and salt" class="only-dark" src="../../_images/minimization-dm.png" />
 </figure>
 <div class="figurelegend docutils container">
 <p>Figure: Total energy of the system <span class="math notranslate nohighlight">\(E_\text{tot}\)</span> as a function of
@@ -845,10 +845,10 @@ <h3>System equilibration<a class="headerlink" href="#system-equilibration" title
 reduces until it reaches an equilibrium value.</p>
 </div>
 <figure class="align-default">
-<img alt="Plot showing the distance between the walls as a function of time." class="only-light" src="../../_images/equilibration-light.png" />
+<img alt="Plot showing the distance between the walls as a function of time." class="only-light" src="../../_images/equilibration.png" />
 </figure>
 <figure class="align-default">
-<img alt="Plot showing the distance between the walls as a function of time." class="only-dark" src="../../_images/equilibration-dark.png" />
+<img alt="Plot showing the distance between the walls as a function of time." class="only-dark" src="../../_images/equilibration-dm.png" />
 </figure>
 <div class="figurelegend docutils container">
 <p>Figure: Distance between the walls as a function of time.
@@ -977,21 +977,21 @@ <h2>Imposed shearing<a class="headerlink" href="#imposed-shearing" title="Link t
 of the fluid is found to increase linearly along <span class="math notranslate nohighlight">\(z\)</span>.</p>
 </div>
 <figure class="align-default">
-<img alt="Velocity of the nanosheared fluid" class="only-light" src="../../_images/shearing-light.png" />
+<img alt="Velocity of the nanosheared fluid" class="only-light" src="../../_images/shearing.png" />
 </figure>
 <figure class="align-default">
-<img alt="Velocity of the nanosheared fluid" class="only-dark" src="../../_images/shearing-dark.png" />
+<img alt="Velocity of the nanosheared fluid" class="only-dark" src="../../_images/shearing-dm.png" />
 </figure>
 <div class="figurelegend docutils container">
 <p>Figure: Velocity profiles for water molecules, ions and walls
 along the <em>z</em> axis. The line is a linear fit assuming that
 the pore size is <span class="math notranslate nohighlight">\(h = 1.8\,\text{nm}\)</span>.</p>
 </div>
 <figure class="align-default">
-<img alt="density of the nanosheared fluid" class="only-light" src="../../_images/density-light.png" />
+<img alt="density of the nanosheared fluid" class="only-light" src="../../_images/density.png" />
 </figure>
 <figure class="align-default">
-<img alt="density of the nanosheared fluid" class="only-dark" src="../../_images/density-dark.png" />
+<img alt="density of the nanosheared fluid" class="only-dark" src="../../_images/density-dm.png" />
 </figure>
 <div class="figurelegend docutils container">
 <p>Figure: Water density <span class="math notranslate nohighlight">\(\rho\)</span> profile

diff --git a/...urce/tutorials/figures/level2/nanosheared-electrolyte/density-article-light.png b/...urce/tutorials/figures/level2/nanosheared-electrolyte/density-article-light.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/density-article.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/density-article.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/density-dark.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/density-dark.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/density-dm.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/density-dm.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/density-light.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/density-light.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/density.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/density.png
diff --git a/...utorials/figures/level2/nanosheared-electrolyte/equilibration-article-light.png b/...utorials/figures/level2/nanosheared-electrolyte/equilibration-article-light.png
diff --git a/...urce/tutorials/figures/level2/nanosheared-electrolyte/equilibration-article.png b/...urce/tutorials/figures/level2/nanosheared-electrolyte/equilibration-article.png
diff --git a/.../source/tutorials/figures/level2/nanosheared-electrolyte/equilibration-dark.png b/.../source/tutorials/figures/level2/nanosheared-electrolyte/equilibration-dark.png
diff --git a/...nx/source/tutorials/figures/level2/nanosheared-electrolyte/equilibration-dm.png b/...nx/source/tutorials/figures/level2/nanosheared-electrolyte/equilibration-dm.png
diff --git a/...source/tutorials/figures/level2/nanosheared-electrolyte/equilibration-light.png b/...source/tutorials/figures/level2/nanosheared-electrolyte/equilibration-light.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/equilibration-pyplot.ipynb b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/equilibration-pyplot.ipynb
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/equilibration.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/equilibration.png
diff --git a/...tutorials/figures/level2/nanosheared-electrolyte/minimization-article-light.png b/...tutorials/figures/level2/nanosheared-electrolyte/minimization-article-light.png
diff --git a/...ource/tutorials/figures/level2/nanosheared-electrolyte/minimization-article.png b/...ource/tutorials/figures/level2/nanosheared-electrolyte/minimization-article.png
diff --git a/...x/source/tutorials/figures/level2/nanosheared-electrolyte/minimization-dark.png b/...x/source/tutorials/figures/level2/nanosheared-electrolyte/minimization-dark.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/minimization-dm.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/minimization-dm.png
diff --git a/.../source/tutorials/figures/level2/nanosheared-electrolyte/minimization-light.png b/.../source/tutorials/figures/level2/nanosheared-electrolyte/minimization-light.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/minimization-pyplot.ipynb b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/minimization-pyplot.ipynb
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/minimization.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/minimization.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/shearing-dark.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/shearing-dark.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/shearing-dm.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/shearing-dm.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/shearing-light.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/shearing-light.png
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/shearing-pyplot.ipynb b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/shearing-pyplot.ipynb
diff --git a/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/shearing.png b/sphinx/source/tutorials/figures/level2/nanosheared-electrolyte/shearing.png
diff --git a/...rce/tutorials/figures/level2/nanosheared-electrolyte/velocity-article-light.png b/...rce/tutorials/figures/level2/nanosheared-electrolyte/velocity-article-light.png
diff --git a/...nx/source/tutorials/figures/level2/nanosheared-electrolyte/velocity-article.png b/...nx/source/tutorials/figures/level2/nanosheared-electrolyte/velocity-article.png
diff --git a/sphinx/source/tutorials/figures/level2/polymer-in-water/distance-pyplot.ipynb b/sphinx/source/tutorials/figures/level2/polymer-in-water/distance-pyplot.ipynb
@@ -7,8 +7,9 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import sys, os, git\n",
-    "from matplotlib import pyplot as plt"
+    "import sys, os, git, lammps_logfile\n",
+    "import warnings\n",
+    "warnings.filterwarnings(\"ignore\")"
    ]
   },
   {

diff --git a/sphinx/source/tutorials/level2/nanosheared-electrolyte.rst b/sphinx/source/tutorials/level2/nanosheared-electrolyte.rst
@@ -563,11 +563,11 @@ Energy minimization
     of the 3 steps, before re-increasing a little after the 
     temperature is increased from 1 to :math:`300\,\text{K}`.
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/minimization-light.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/minimization.png
     :alt: Energy minimisation of the confined water and salt
     :class: only-light
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/minimization-dark.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/minimization-dm.png
     :alt: Energy minimisation of the confined water and salt
     :class: only-dark
 
@@ -665,11 +665,11 @@ System equilibration
     the distance between the two walls
     reduces until it reaches an equilibrium value.
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/equilibration-light.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/equilibration.png
     :alt: Plot showing the distance between the walls as a function of time.
     :class: only-light
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/equilibration-dark.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/equilibration-dm.png
     :alt: Plot showing the distance between the walls as a function of time.
     :class: only-dark
 
@@ -814,11 +814,11 @@ Imposed shearing
     can be plotted. As expected for such Couette flow geometry, the velocity
     of the fluid is found to increase linearly along :math:`z`.
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/shearing-light.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/shearing.png
     :alt: Velocity of the nanosheared fluid
     :class: only-light
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/shearing-dark.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/shearing-dm.png
     :alt: Velocity of the nanosheared fluid
     :class: only-dark
 
@@ -828,11 +828,11 @@ Imposed shearing
     along the *z* axis. The line is a linear fit assuming that 
     the pore size is :math:`h = 1.8\,\text{nm}`.
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/density-light.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/density.png
     :alt: density of the nanosheared fluid
     :class: only-light
 
-.. figure:: ../figures/level2/nanosheared-electrolyte/density-dark.png
+.. figure:: ../figures/level2/nanosheared-electrolyte/density-dm.png
     :alt: density of the nanosheared fluid
     :class: only-dark