Cleaning up promolecule nci notebook

website/examples/promolecule_nci.ipynb

@@ -26,7 +26,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# # Install packages in Google Colab. \n",
+    "# # Install packages in Google Colab.\n",
     "# # Don't run this cell if packages/data is already in your environment\n",
     "# ! pip install git+https://github.com/theochem/iodata.git\n",
     "# ! pip install git+https://github.com/theochem/grid.git\n",
@@ -91,7 +91,7 @@
     "from importlib_resources import files\n",
     "\n",
     "# Load the H2O dimer from a .xyz file\n",
-    "data_file= 'data/h2o_dimer.xyz'\n",
+    "data_file = files(atomdb).joinpath(\"../docs/notebooks/data/h2o_dimer.xyz\")\n",
     "mol_data = iodata.load_one(data_file)\n",
     "\n",
     "atnums = mol_data.atcorenums\n",
@@ -104,8 +104,7 @@
     "print(\"Atomic coordinates dimer:\\n\", atcoords)\n",
     "\n",
     "print(\"Atomic numbers monomer:\\n\", atnums_mono)\n",
-    "print(\"Atomic coordinates monomer:\\n\", atcoords_mono)\n",
-    "\n"
+    "print(\"Atomic coordinates monomer:\\n\", atcoords_mono)"
    ]
   },
   {
@@ -174,8 +173,8 @@
    "source": [
     "import numpy as np\n",
     "\n",
-    "dimer_promol = atomdb.make_promolecule(atnums=atnums, coords=atcoords, dataset='slater')\n",
-    "mono_promol = atomdb.make_promolecule(atnums=atnums_mono, coords=atcoords_mono, dataset='slater')\n",
+    "dimer_promol = atomdb.make_promolecule(atnums=atnums, coords=atcoords, dataset=\"slater\")\n",
+    "mono_promol = atomdb.make_promolecule(atnums=atnums_mono, coords=atcoords_mono, dataset=\"slater\")\n",
     "\n",
     "# compute the density and gradient of the density at the grid points\n",
     "dimer_rho = dimer_promol.density(cubgrid.points, log=True)\n",
@@ -233,7 +232,7 @@
     "import matplotlib.pyplot as plt\n",
     "\n",
     "# compute the reduced density gradient for the dimer\n",
-    "coeff = 2 * (3 * np.pi ** 2) ** (1 / 3)\n",
+    "coeff = 2 * (3 * np.pi**2) ** (1 / 3)\n",
     "dimer_grad_norm = np.linalg.norm(dimer_grad_rho, axis=1)\n",
     "dimer_rdg = dimer_grad_norm / (coeff * dimer_rho ** (4 / 3))\n",
     "\n",
@@ -244,10 +243,10 @@
     "import matplotlib.pyplot as plt\n",
     "\n",
     "# Plot the reduced gradient as a function of the density\n",
-    "plt.scatter(dimer_rho, dimer_rdg, label='Water dimer')\n",
-    "plt.scatter(mono_rho, mono_rdg, label='Water monomer')\n",
-    "plt.xlabel(r'$\\rho(R)$')\n",
-    "plt.ylabel(r'Reduced gradient')\n",
+    "plt.scatter(dimer_rho, dimer_rdg, label=\"Water dimer\")\n",
+    "plt.scatter(mono_rho, mono_rdg, label=\"Water monomer\")\n",
+    "plt.xlabel(r\"$\\rho(R)$\")\n",
+    "plt.ylabel(r\"Reduced gradient\")\n",
     "\n",
     "# Set y-axis limits from 0 to 1\n",
     "plt.ylim(0, 2)\n",