improved figures tutorial 1

Author: simongravelle

docs/sphinx/source/tutorials/figures/level1/breaking-a-carbon-nanotube/energy-breakable-pyplot.ipynb

@@ -5,16 +5,7 @@
    "execution_count": 1,
    "id": "7c8c9669",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/simon/.local/lib/python3.12/site-packages/matplotlib/projections/__init__.py:63: UserWarning: Unable to import Axes3D. This may be due to multiple versions of Matplotlib being installed (e.g. as a system package and as a pip package). As a result, the 3D projection is not available.\n",
-      "  warnings.warn(\"Unable to import Axes3D. This may be due to multiple versions of \"\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import numpy as np\n",
     "import sys, os, git, lammps_logfile\n",
@@ -62,17 +53,16 @@
     "log = lammps_logfile.File(data_path + \"log.lammps\")\n",
     "timestep = 0.005\n",
     "Time_EM = log.get(\"Step\", run_num = 0)*timestep\n",
-    "PotEng_EM = log.get(\"PotEng\", run_num = 0)\n",
-    "KinEng_EM = log.get(\"KinEng\", run_num = 0)\n",
+    "PotEng_EM = log.get(\"TotEng\", run_num = 0) # its the same if Kin En = 0\n",
     "Time_MD = log.get(\"Step\", run_num = 1)*timestep\n",
     "PotEng_MD = log.get(\"PotEng\", run_num = 1)\n",
     "KinEng_MD = log.get(\"KinEng\", run_num = 1)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "id": "90ba3a69",
+   "execution_count": 7,
+   "id": "5b2dc55f",
    "metadata": {},
    "outputs": [
     {
@@ -103,7 +93,7 @@
     "    myplt.prepare_figure(fig_size = (18,10), dark_mode = dark_mode,\n",
     "                        transparency = True, use_serif=True, n_line=2)\n",
     "    myplt.add_panel()\n",
-    "    myplt.add_plot(x = Time_EM, y = PotEng_EM, type = \"plot\", linewidth_data = 3,\n",
+    "    myplt.add_plot(x = Time_EM, y = PotEng_EM, linewidth_data = 3,\n",
     "                   marker = \"-\", data_color = 1, markersize = 12,\n",
     "                   data_label = r'$E_{12}$')\n",
     "    myplt.add_plot(x = Time_MD, y = PotEng_MD, type = \"plot\", linewidth_data = 3,\n",
@@ -114,7 +104,7 @@
     "    myplt.set_boundaries(x_ticks=np.arange(0, 25, 5), x_boundaries=(-0.5, 20.5),\n",
     "                         y_ticks=np.arange(-1, 0.2, 0.2), y_boundaries=(-1, 0.1))\n",
     "    myplt.add_panel()\n",
-    "    myplt.add_plot(x = Time_EM, y = KinEng_EM, type = \"plot\", linewidth_data = 3,\n",
+    "    myplt.add_plot(x = Time_EM, y = PotEng_EM*0, type = \"plot\", linewidth_data = 3,\n",
     "                   marker = \"-\", data_color = 1, markersize = 12,\n",
     "                   data_label = r'$\\mathrm{Energy~Minimization}$')\n",
     "    myplt.add_plot(x = Time_MD, y = KinEng_MD, type = \"plot\", linewidth_data = 3,\n",