deploy: 7d5d8ce

Author: simongravelle

sphinx/build/doctrees/environment.pickle

@@ -982,7 +982,7 @@ Restarting from a saved configuration
 ..  container:: justify
 
     Run *input.md.lammps* using LAMMPS and visualize the trajectory
-    using VMD:
+    using VMD.
 
 .. figure:: ../figures/level1/lennard-jones-fluid/mixing-vmd-light.png
     :alt: LAMMPS VMD tutorial molecular dynamics simulation
@@ -994,7 +994,7 @@ Restarting from a saved configuration
 
 .. container:: figurelegend
 
-    Figure: Evolution of the atom populations during mixing.
+    Figure: Evolution of the system during mixing.
 
 ..  container:: justify
 

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

@@ -1123,7 +1123,7 @@ <h3>Restarting from a saved configuration<a class="headerlink" href="#restarting
 </div>
 <div class="justify docutils container">
 <p>Run <em>input.md.lammps</em> using LAMMPS and visualize the trajectory
-using VMD:</p>
+using VMD.</p>
 </div>
 <figure class="align-default">
 <img alt="LAMMPS VMD tutorial molecular dynamics simulation" class="only-light" src="../../_images/mixing-vmd-light.png" />
@@ -1132,7 +1132,7 @@ <h3>Restarting from a saved configuration<a class="headerlink" href="#restarting
 <img alt="LAMMPS VMD tutorial molecular dynamics simulation" class="only-dark" src="../../_images/mixing-vmd-dark.png" />
 </figure>
 <div class="figurelegend docutils container">
-<p>Figure: Evolution of the atom populations during mixing.</p>
+<p>Figure: Evolution of the system during mixing.</p>
 </div>
 <div class="justify docutils container">
 <p>After running <em>input.md.lammps</em> using LAMMPS, you can observe the number

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

@@ -108,7 +108,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 20,
    "metadata": {},
    "outputs": [
     {
@@ -126,7 +126,7 @@
     "filename = \"mixing-article\"\n",
     "mode = 'light'\n",
     "mygray = colors[\"mylightgray\"]\n",
-    "fig = prepare_figure(mode, transparency = True, desired_figsize=(12,10))\n",
+    "fig = prepare_figure(mode, transparency = False, desired_figsize=(12,10))\n",
     "ax, n, l_tot, c_tot = [], 0, 2, 1\n",
     "n += 1\n",
     "ax.append(plt.subplot(l_tot, c_tot, n))\n",

sphinx/build/html/searchindex.js

@@ -982,7 +982,7 @@ Restarting from a saved configuration
 ..  container:: justify
 
     Run *input.md.lammps* using LAMMPS and visualize the trajectory
-    using VMD:
+    using VMD.
 
 .. figure:: ../figures/level1/lennard-jones-fluid/mixing-vmd-light.png
     :alt: LAMMPS VMD tutorial molecular dynamics simulation
@@ -994,7 +994,7 @@ Restarting from a saved configuration
 
 .. container:: figurelegend
 
-    Figure: Evolution of the atom populations during mixing.
+    Figure: Evolution of the system during mixing.
 
 ..  container:: justify