tutorials: Fix typos

espressomd · Apr 10, 2024 · 180e342 · 180e342
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diff --git a/doc/tutorials/electrodes/electrodes_part1.ipynb b/doc/tutorials/electrodes/electrodes_part1.ipynb
@@ -296,7 +296,7 @@
    "id": "20957c03",
    "metadata": {},
    "source": [
-    "### Task\n",
+    "**Task**\n",
     "\n",
     "* Set up [ELC](https://espressomd.github.io/doc/espressomd.html#espressomd.electrostatics.ELC) with ``p3m`` as its actor."
    ]
@@ -345,7 +345,7 @@
    "id": "23398839",
    "metadata": {},
    "source": [
-    "### TASK\n",
+    "**Task**\n",
     "\n",
     "* Using the (area) density of ICC particles defined in the cell above, calculate the x/y positions of the particles for a uniform, quadratic grid. \n",
     "* Add fixed particles on the electrodes. Make sure to use the correct ``type``. Give the top (bottom) plate a total charge of $+1$ ($-1$). \n",
@@ -390,12 +390,12 @@
    "id": "5326e038",
    "metadata": {},
    "source": [
-    "### Task\n",
+    "**Task**\n",
     "\n",
     "* Set ``elc`` as ``system.electrostatics.solver``\n",
     "* Create an [ICC object]((https://espressomd.github.io/doc/espressomd.html#espressomd.electrostatic_extensions.ICC) and set it as ``system.electrostatics.extension``\n",
     "\n",
-    "### Hints\n",
+    "**Hints**\n",
     "\n",
     "* ICC variables are defined in the second code cell from the top.\n",
     "* Make sure to not mark our test particles ``p1`` and ``p2`` (with ids 0 and 1) as ICC particles."

diff --git a/doc/tutorials/electrodes/electrodes_part2.ipynb b/doc/tutorials/electrodes/electrodes_part2.ipynb
@@ -5,7 +5,7 @@
    "id": "357a65e2",
    "metadata": {},
    "source": [
-    "# Basic simulation of electrodes in ESPResSo part II: Electrolyte capacitor and Poisson–Boltzmann theory"
+    "# Basic simulation of electrodes in ESPResSo part II: Electrolytic capacitor and Poisson–Boltzmann theory"
    ]
   },
   {
@@ -306,7 +306,7 @@
    "id": "867de4db",
    "metadata": {},
    "source": [
-    "### Task\n",
+    "**Task**\n",
     "\n",
     "* write a function \n",
     "`get_box_dimension(concentration, distance, n_ionpairs=N_IONPAIRS)`\n",
@@ -413,7 +413,8 @@
    "id": "48abb259",
    "metadata": {},
    "source": [
-    "### Task\n",
+    "**Task**\n",
+    "\n",
     "* add two wall constraints at $z=0$ and $z=L_z$ to stop particles from\n",
     "crossing the boundaries and model the electrodes.\n",
     "Refer to \n",
@@ -458,7 +459,7 @@
    "source": [
     "#### 1.2.2 Add particles for the ions\n",
     "\n",
-    "### Task\n",
+    "**Task**\n",
     "\n",
     "* place ion pairs at random positions between the electrodes.\n",
     "\n",
@@ -507,7 +508,7 @@
    "source": [
     "#### 1.2.3 Add interactions:\n",
     "\n",
-    "### Task\n",
+    "**Task**\n",
     "\n",
     "* For excluded volume interactions, add a WCA potential. \n",
     "\n",
@@ -556,7 +557,7 @@
     "This function will take care of tuning the P3M and ELC parameters.\n",
     "For our purposes, an accuracy of $10^{-3}$ is sufficient.\n",
     "\n",
-    "### Task\n",
+    "**Task**\n",
     "\n",
     "* Write a function `setup_electrostatic_solver(potential_diff)` that\n",
     "returns the ELC instance."
@@ -719,7 +720,7 @@
     "The time average is obtained through a\n",
     "[espressomd.accumulators.MeanVarianceCalculator](espressomd.accumulators.MeanVarianceCalculator).\n",
     "\n",
-    "### Task\n",
+    "**Task**\n",
     "\n",
     "* Write a function `setup_densityprofile_accumulators(bin_width)` that returns the\n",
     "`bin_centers` and the accumulators for both ion species in the $z$-range $[0,d]$.\n",

diff --git a/doc/tutorials/error_analysis/error_analysis_part2.ipynb b/doc/tutorials/error_analysis/error_analysis_part2.ipynb
@@ -210,7 +210,7 @@
     "fig = plt.figure(figsize=(10, 6))\n",
     "plt.plot(autocov)\n",
     "plt.xlabel(\"lag time $j$\")\n",
-    "plt.ylabel(\"$\\hat{K}^{XX}_j$\")\n",
+    "plt.ylabel(r\"$\\hat{K}^{XX}_j$\")\n",
     "plt.show()"
    ]
   },
@@ -251,7 +251,7 @@
     "plt.gca().axhline(0, color=\"gray\", linewidth=1)\n",
     "plt.plot(autocov)\n",
     "plt.xlabel(\"lag time $j$\")\n",
-    "plt.ylabel(\"$\\hat{K}^{XX}_j$\")\n",
+    "plt.ylabel(r\"$\\hat{K}^{XX}_j$\")\n",
     "plt.show()"
    ]
   },
@@ -304,7 +304,7 @@
     "plt.xlim((1, N_MAX))\n",
     "plt.xscale(\"log\")\n",
     "plt.xlabel(\"lag time $j$\")\n",
-    "plt.ylabel(\"$\\hat{K}^{XX}_j$\")\n",
+    "plt.ylabel(r\"$\\hat{K}^{XX}_j$\")\n",
     "plt.legend()\n",
     "plt.show()\n",
     "\n",
@@ -498,7 +498,7 @@
     "    plt.gca().axhline(0, color=\"gray\",linewidth=1)\n",
     "    plt.plot(acf)\n",
     "    plt.xlabel(\"lag time $j$\")\n",
-    "    plt.ylabel(\"$\\hat{K}^{XX}_j$\")\n",
+    "    plt.ylabel(r\"$\\hat{K}^{XX}_j$\")\n",
     "    plt.show()\n",
     "\n",
     "    # create integrated ACF plot\n",

diff --git a/doc/tutorials/langevin_dynamics/langevin_dynamics.ipynb b/doc/tutorials/langevin_dynamics/langevin_dynamics.ipynb
@@ -489,7 +489,7 @@
     "# SOLUTION CELL\n",
     "plt.figure(figsize=(10, 6))\n",
     "plt.xlabel(r'$\\gamma$')\n",
-    "plt.ylabel('Diffusion coefficient [$\\sigma^2/t$]')\n",
+    "plt.ylabel(r'Diffusion coefficient [$\\sigma^2/t$]')\n",
     "x = np.linspace(0.9 * min(gammas), 1.1 * max(gammas), 50)\n",
     "y = KT / x\n",
     "plt.plot(x, y, '-', label=r'$k_\\mathrm{B}T\\gamma^{-1}$')\n",

diff --git a/doc/tutorials/lennard_jones/lennard_jones.ipynb b/doc/tutorials/lennard_jones/lennard_jones.ipynb
@@ -120,8 +120,8 @@
     "plt.plot(xs, ys_lj, label='LJ')\n",
     "plt.plot(xs, ys_WCA, label='WCA')\n",
     "plt.axhline(y=0, color='grey')\n",
-    "plt.xlabel(\"$r/\\sigma$\")\n",
-    "plt.ylabel(\"$V(r)/(k_{\\mathrm{B}}T)$\")\n",
+    "plt.xlabel(r\"$r/\\sigma$\")\n",
+    "plt.ylabel(r\"$V(r)/(k_{\\mathrm{B}}T)$\")\n",
     "plt.legend()\n",
     "plt.ylim(-1.5, 2.5)\n",
     "plt.show()"

diff --git a/doc/tutorials/polymers/polymers.ipynb b/doc/tutorials/polymers/polymers.ipynb
@@ -651,7 +651,7 @@
     "             ls='', marker='o', capsize=5, capthick=1,\n",
     "             label=r'$R_g^{\\mathrm{simulation}}$')\n",
     "plt.xlabel('Number of monomers $N$')\n",
-    "plt.ylabel('Radius of gyration [$\\sigma$]')\n",
+    "plt.ylabel(r'Radius of gyration [$\\sigma$]')\n",
     "plt.legend()\n",
     "plt.show()"
    ]
@@ -717,7 +717,7 @@
     "             ls='', marker='o', capsize=5, capthick=1,\n",
     "             label=r'$R_h^{\\mathrm{simulation}}$')\n",
     "plt.xlabel('Number of monomers $N$')\n",
-    "plt.ylabel('Hydrodynamic radius [$\\sigma$]')\n",
+    "plt.ylabel(r'Hydrodynamic radius [$\\sigma$]')\n",
     "plt.legend()\n",
     "plt.show()"
    ]