deploy: 09a4cc6

sphinx/build/html/_sources/tutorials/level3/free-energy-calculation.rst.txt

@@ -180,11 +180,11 @@ System creation and settings
     The potential and force along the :math:`x`
     axis resembles:
 
-.. figure:: ../figures/level3/free-energy-calculation/potential-light.png
+.. figure:: ../figures/level3/free-energy-calculation/potential.png
    :alt: Imposed potential
    :class: only-light
 
-.. figure:: ../figures/level3/free-energy-calculation/potential-dark.png
+.. figure:: ../figures/level3/free-energy-calculation/potential-dm.png
    :alt: Averaged density profile
    :class: only-dark
 
@@ -295,11 +295,11 @@ Data analysis
     First, let us ensure that the initial equilibration of :math:`1\,\text{ns}`
     is long enough by examining the *density_evolution.dat* file.
 
-.. figure:: ../figures/level3/free-energy-calculation/density_evolution-light.png
+.. figure:: ../figures/level3/free-energy-calculation/density_evolution.png
    :alt: Number of particles in the central region as a function of time
    :class: only-light
 
-.. figure:: ../figures/level3/free-energy-calculation/density_evolution-dark.png
+.. figure:: ../figures/level3/free-energy-calculation/density_evolution-dm.png
    :alt: Number of particles in the central region as a function of time
    :class: only-dark
 
@@ -319,11 +319,11 @@ Data analysis
     center of the box is about two orders of magnitude lower than inside
     the reservoir.
 
-.. figure:: ../figures/level3/free-energy-calculation/density_profile-light.png
+.. figure:: ../figures/level3/free-energy-calculation/density_profile.png
    :alt: Averaged density profile
    :class: only-light
 
-.. figure:: ../figures/level3/free-energy-calculation/density_profile-dark.png
+.. figure:: ../figures/level3/free-energy-calculation/density_profile-dm.png
    :alt: Averaged density profile
    :class: only-dark
 
@@ -624,11 +624,11 @@ WHAM algorithm
     Again, one can compare the result of the PMF with the imposed potential :math:`U`,
     which shows that the agreement is excellent.
 
-.. figure:: ../figures/level3/free-energy-calculation/freeenergy-light.png
+.. figure:: ../figures/level3/free-energy-calculation/freeenergy.png
     :alt: Result of the umbrella sampling
     :class: only-light
 
-.. figure:: ../figures/level3/free-energy-calculation/freeenergy-dark.png
+.. figure:: ../figures/level3/free-energy-calculation/freeenergy-dm.png
     :alt: Result of the umbrella sampling
     :class: only-dark
 

sphinx/build/html/non-tutorials/solutions.html

@@ -865,10 +865,10 @@ <h3>Adsorb water in ZIF-8 nanopores<a class="headerlink" href="#adsorb-water-in-
 with water.</p>
 </div>
 <figure class="align-default">
-<img alt="Water molecule in Zif material with GCMC in LAMMPS" class="only-light" src="tutorials/figures/level3/water-adsorption-in-silica/number_evolution_zif-light.png" />
+<img alt="Water molecule in Zif material with GCMC in LAMMPS" class="only-light" src="../_images/number_evolution_zif-light.png" />
 </figure>
 <figure class="align-default">
-<img alt="Water molecule in Zif material with GCMC in LAMMPS" class="only-dark" src="tutorials/figures/level3/water-adsorption-in-silica/number_evolution_zif-dark.png" />
+<img alt="Water molecule in Zif material with GCMC in LAMMPS" class="only-dark" src="../_images/number_evolution_zif-dark.png" />
 </figure>
 <div class="figurelegend docutils container">
 <p>Figure: Number of water molecules in Zif-8 during the first <span class="math notranslate nohighlight">\(10\,ps\)</span>.</p>

sphinx/build/html/tutorials/level3/free-energy-calculation.html

@@ -438,10 +438,10 @@ <h3>System creation and settings<a class="headerlink" href="#system-creation-and
 axis resembles:</p>
 </div>
 <figure class="align-default">
-<img alt="Imposed potential" class="only-light" src="../../_images/potential-light.png" />
+<img alt="Imposed potential" class="only-light" src="../../_images/potential.png" />
 </figure>
 <figure class="align-default">
-<img alt="Averaged density profile" class="only-dark" src="../../_images/potential-dark.png" />
+<img alt="Averaged density profile" class="only-dark" src="../../_images/potential-dm.png" />
 </figure>
 <div class="figurelegend docutils container">
 <p>Figure: Potential <span class="math notranslate nohighlight">\(U (x)\)</span> (a) and force <span class="math notranslate nohighlight">\(F (x)\)</span> (b) imposed to the atoms as a function of the coordinate <span class="math notranslate nohighlight">\(x\)</span>.</p>
@@ -537,10 +537,10 @@ <h3>Data analysis<a class="headerlink" href="#data-analysis" title="Link to this
 is long enough by examining the <em>density_evolution.dat</em> file.</p>
 </div>
 <figure class="align-default">
-<img alt="Number of particles in the central region as a function of time" class="only-light" src="../../_images/density_evolution-light.png" />
+<img alt="Number of particles in the central region as a function of time" class="only-light" src="../../_images/density_evolution.png" />
 </figure>
 <figure class="align-default">
-<img alt="Number of particles in the central region as a function of time" class="only-dark" src="../../_images/density_evolution-dark.png" />
+<img alt="Number of particles in the central region as a function of time" class="only-dark" src="../../_images/density_evolution-dm.png" />
 </figure>
 <div class="figurelegend docutils container">
 <p>Figure: Evolution of the number of atoms in the central region during equilibration.</p>
@@ -556,10 +556,10 @@ <h3>Data analysis<a class="headerlink" href="#data-analysis" title="Link to this
 the reservoir.</p>
 </div>
 <figure class="align-default">
-<img alt="Averaged density profile" class="only-light" src="../../_images/density_profile-light.png" />
+<img alt="Averaged density profile" class="only-light" src="../../_images/density_profile.png" />
 </figure>
 <figure class="align-default">
-<img alt="Averaged density profile" class="only-dark" src="../../_images/density_profile-dark.png" />
+<img alt="Averaged density profile" class="only-dark" src="../../_images/density_profile-dm.png" />
 </figure>
 <div class="figurelegend docutils container">
 <p>Figure: Fluid density <span class="math notranslate nohighlight">\(\rho\)</span> along the <span class="math notranslate nohighlight">\(x\)</span> direction in the presence
@@ -809,10 +809,10 @@ <h3>WHAM algorithm<a class="headerlink" href="#wham-algorithm" title="Link to th
 which shows that the agreement is excellent.</p>
 </div>
 <figure class="align-default">
-<img alt="Result of the umbrella sampling" class="only-light" src="../../_images/freeenergy-light.png" />
+<img alt="Result of the umbrella sampling" class="only-light" src="../../_images/freeenergy.png" />
 </figure>
 <figure class="align-default">
-<img alt="Result of the umbrella sampling" class="only-dark" src="../../_images/freeenergy-dark.png" />
+<img alt="Result of the umbrella sampling" class="only-dark" src="../../_images/freeenergy-dm.png" />
 </figure>
 <div class="figurelegend docutils container">
 <p>Figure: Calculated potential using umbrella sampling compared to

sphinx/source/tutorials/figures/level3/free-energy-calculation/overlap-pyplot.ipynb

@@ -2,19 +2,20 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "id": "9e485e34",
    "metadata": {},
    "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\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "id": "b599c9db",
    "metadata": {},
    "outputs": [
@@ -35,10 +36,8 @@
     "level = path_in_folder.split(\"/\")[-2]\n",
     "tutorial_name = path_in_folder.split(\"/\")[-1]\n",
     "print(\"level:\" , level, \"& tutorial name:\", tutorial_name)\n",
-    "sys.path.append(git_path + \"/docs/sphinx/source/tutorials/figures/pyplot-perso/\")\n",
-    "from functions import complete_panel, save_figure, set_boundaries, \\\n",
-    "                      add_subplotlabels, set_boundaries\n",
-    "from color_series1 import colors\n",
+    "sys.path.append(git_path + \"/docs/sphinx/source/tutorials/figures/pyplot-perso\")\n",
+    "from plttools import PltTools\n",
     "path_figures = current_path[len(git_path):] + '/'\n",
     "data_path = git_path + \"/docs/lammpstutorials-inputs/\" + level + \"/\" + tutorial_name + \"/BiasedSampling/\"\n",
     "print(\"data path: \", data_path)"
@@ -178,7 +177,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.12.3"
   },
   "vscode": {
    "interpreter": {

sphinx/source/tutorials/level3/free-energy-calculation.rst

@@ -180,11 +180,11 @@ System creation and settings
     The potential and force along the :math:`x`
     axis resembles:
 
-.. figure:: ../figures/level3/free-energy-calculation/potential-light.png
+.. figure:: ../figures/level3/free-energy-calculation/potential.png
    :alt: Imposed potential
    :class: only-light
 
-.. figure:: ../figures/level3/free-energy-calculation/potential-dark.png
+.. figure:: ../figures/level3/free-energy-calculation/potential-dm.png
    :alt: Averaged density profile
    :class: only-dark
 
@@ -295,11 +295,11 @@ Data analysis
     First, let us ensure that the initial equilibration of :math:`1\,\text{ns}`
     is long enough by examining the *density_evolution.dat* file.
 
-.. figure:: ../figures/level3/free-energy-calculation/density_evolution-light.png
+.. figure:: ../figures/level3/free-energy-calculation/density_evolution.png
    :alt: Number of particles in the central region as a function of time
    :class: only-light
 
-.. figure:: ../figures/level3/free-energy-calculation/density_evolution-dark.png
+.. figure:: ../figures/level3/free-energy-calculation/density_evolution-dm.png
    :alt: Number of particles in the central region as a function of time
    :class: only-dark
 
@@ -319,11 +319,11 @@ Data analysis
     center of the box is about two orders of magnitude lower than inside
     the reservoir.
 
-.. figure:: ../figures/level3/free-energy-calculation/density_profile-light.png
+.. figure:: ../figures/level3/free-energy-calculation/density_profile.png
    :alt: Averaged density profile
    :class: only-light
 
-.. figure:: ../figures/level3/free-energy-calculation/density_profile-dark.png
+.. figure:: ../figures/level3/free-energy-calculation/density_profile-dm.png
    :alt: Averaged density profile
    :class: only-dark
 
@@ -624,11 +624,11 @@ WHAM algorithm
     Again, one can compare the result of the PMF with the imposed potential :math:`U`,
     which shows that the agreement is excellent.
 
-.. figure:: ../figures/level3/free-energy-calculation/freeenergy-light.png
+.. figure:: ../figures/level3/free-energy-calculation/freeenergy.png
     :alt: Result of the umbrella sampling
     :class: only-light
 
-.. figure:: ../figures/level3/free-energy-calculation/freeenergy-dark.png
+.. figure:: ../figures/level3/free-energy-calculation/freeenergy-dm.png
     :alt: Result of the umbrella sampling
     :class: only-dark