convert to kJ/mol

Part-1-NEB/Part-1-NEB.ipynb

@@ -278,7 +278,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "**Then, view a movie of the minimum energy path alongside the optimized energy profile of the proton transfer (in meV):**"
+    "**Then, view a movie of the minimum energy path alongside the optimized energy profile of the proton transfer (in kJ/mol):**"
    ]
   },
   {
@@ -305,13 +305,13 @@
     "    plt.plot(energies, 'o-')\n",
     "    plt.plot(idx, energies[idx], 'o', markersize=10)\n",
     "    plt.xlabel('NEB image')\n",
-    "    plt.ylabel('Energy (meV)')\n",
+    "    plt.ylabel('Energy (kJ/mol)')\n",
     "    plt.tight_layout()\n",
     "    return plt.show()\n",
     "\n",
-    "# Read the energy of each image, convert to meV and shift IS energy to 0\n",
+    "# Read the energy of each image, convert to kJ/mol and shift IS energy to 0\n",
     "energies = np.loadtxt('energy-pbe.txt')\n",
-    "energies = 27211.38*(energies-energies[0])\n",
+    "energies = 2625.5*(energies-energies[0])\n",
     "\n",
     "# Create a list containing the structure of each optimized NEB image\n",
     "images = []\n",
@@ -331,7 +331,7 @@
    "source": [
     "* Which image number corresponds to the TS?\n",
     "* What can you say based on the reaction barrier height? What about the reaction energy?\n",
-    "    * Hint: The thermal energy at room temperature is about $k_\\mathrm{B}T\\approx25$ meV"
+    "    * Hint: The thermal energy at room temperature is about $k_\\mathrm{B}T\\approx2.5$ kJ/mol"
    ]
   },
   {

Part-3-Hybrid/Part-3-Hybrid.ipynb

@@ -269,7 +269,7 @@
    "id": "dc86be5e-b3cb-46b8-ac8e-0ca21be94c0e",
    "metadata": {},
    "source": [
-    "**Then, plot the PBE0 energy profile together with the PBE profile (in meV):**"
+    "**Then, plot the PBE0 energy profile together with the PBE profile (in kJ/mol):**"
    ]
   },
   {
@@ -282,16 +282,16 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "\n",
-    "# Read the energy of each image, convert to meV and shift IS energy to 0\n",
+    "# Read the energy of each image, convert to kJ/mol and shift IS energy to 0\n",
     "energy_pbe = np.loadtxt('../Part-1-NEB/energy-pbe.txt')\n",
-    "energy_pbe = 27211.38*(energy_pbe-energy_pbe[0])\n",
+    "energy_pbe = 2625.5*(energy_pbe-energy_pbe[0])\n",
     "energy_pbe0 = np.loadtxt('energy-pbe0.txt')\n",
-    "energy_pbe0 = 27211.38*(energy_pbe0-energy_pbe0[0])\n",
+    "energy_pbe0 = 2625.5*(energy_pbe0-energy_pbe0[0])\n",
     "\n",
     "plt.plot(energy_pbe, 'o-', label='PBE')\n",
     "plt.plot(energy_pbe0, 'o-', label='PBE0')\n",
     "plt.xlabel('NEB image')\n",
-    "plt.ylabel('Energy (meV)')\n",
+    "plt.ylabel('Energy (kJ/mol)')\n",
     "plt.legend()\n",
     "plt.tight_layout()\n",
     "plt.show()"
@@ -318,7 +318,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "kT = 25.7  # Boltzmann's constant times 298 K in units of meV\n",
+    "kT = 2.479  # Boltzmann's constant times 298 K in units of kJ/mol\n",
     "K = np.exp(-energy_pbe0[-1]/kT)\n",
     "print(K)"
    ]

Part-4-AIMD/Part-4-AIMD.ipynb

@@ -381,8 +381,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Thermal energy at room temperature in meV\n",
-    "kT = 25.7\n",
+    "# Thermal energy at room temperature in kJ/mol\n",
+    "kT = 2.479\n",
     "\n",
     "# Initialize array for reaction coordinate\n",
     "rc = np.zeros(len(trj))\n",
@@ -418,7 +418,7 @@
     "# Helmholtz free energy profile\n",
     "ax[2].plot(rxn, energy)\n",
     "ax[2].set_xlabel('Reaction coordinate (Å)')\n",
-    "ax[2].set_ylabel('Free energy (meV)')\n",
+    "ax[2].set_ylabel('Free energy (kJ/mol)')\n",
     "\n",
     "plt.tight_layout()\n",
     "plt.show()"