fixed notebooks and amended another change

Signed-off-by: Nick Papior <[email protected]>

Author: zerothi

S_01/run.ipynb

@@ -9,6 +9,7 @@
     "import sisl\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "\n",
     "%matplotlib inline"
    ]
   },
@@ -58,7 +59,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Read Hamiltonians using two different methods\n"
+    "# Read Hamiltonians using two different methods"
    ]
   },
   {
@@ -99,12 +100,12 @@
     "\n",
     "# Plot band-structures\n",
     "band.set_parent(<DFT Hamiltonian>)\n",
-    "eigs = band.eigh()\n",
+    "eigs = band.apply.ndarray.eigh()\n",
     "ax.plot(lk, eigs)\n",
     "    \n",
     "# You need to create the TB Hamiltonian, see e.g. TB_01\n",
     "band.set_parent(<TB Hamiltonian>)\n",
-    "eigs = band.eigh()\n",
+    "eigs = band.apply.ndarray.eigh()\n",
     "ax.plot(lk, eigs, '--')"
    ]
   },
@@ -118,7 +119,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -132,7 +133,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

S_02/run.ipynb

@@ -9,6 +9,7 @@
     "import sisl\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "\n",
     "%matplotlib inline"
    ]
   },
@@ -38,8 +39,8 @@
    "outputs": [],
    "source": [
     "graphene = sisl.geom.graphene(1.44)\n",
-    "graphene.write('STRUCT.fdf')\n",
-    "graphene.write('STRUCT.xyz')"
+    "graphene.write(\"STRUCT.fdf\")\n",
+    "graphene.write(\"STRUCT.xyz\")"
    ]
   },
   {
@@ -55,7 +56,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "open('PDOS.fdf', 'w').write(\"\"\"\n",
+    "open(\"PDOS.fdf\", \"w\").write(\n",
+    "    \"\"\"\n",
     "# K-point sampling\n",
     "%block PDOS.kgrid.MonkhorstPack\n",
     "  63  0 0\n",
@@ -70,7 +72,8 @@
     "%block Projected.DensityOfStates\n",
     "-20.00 15.00 0.200 3500 eV\n",
     "%endblock\n",
-    "\"\"\");"
+    "\"\"\"\n",
+    ")"
    ]
   },
   {
@@ -99,7 +102,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "geometry, E, PDOS = sisl.get_sile('siesta.PDOS.xml').read_data()"
+    "geometry, E, PDOS = sisl.get_sile(\"siesta.PDOS.xml\").read_data()"
    ]
   },
   {
@@ -108,7 +111,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Examine output by printing shapes and geometry\n"
+    "# Examine output by printing shapes and geometry"
    ]
   },
   {
@@ -123,16 +126,20 @@
     "3. Figure out which orbital contributes to the Dirac cone by plotting the PDOS for all orbitals\n",
     "4. Read in the Hamiltonian (as done in [S 1](../S_01/run.ipynb)) and create a Monkhorst-Pack grid as the one in Siesta input. Use this snippet to calculate the PDOS using `sisl`\n",
     "\n",
-    "       mp = sisl.MonkhorstPack(H, [nx, ny, 1])\n",
-    "       def wrap_multiple(eigenstate):\n",
-    "           DOS = eigenstate.DOS(E)\n"
-    "           PDOS = eigenstate.PDOS(E)\n"
-    "           return sisl.oplist([DOS, PDOS])\n",
-    "       DOS, PDOS = mp.apply.average.eigenstate(wrap=wrap_multiple, eta=True)\n",
+    "    ```python\n",
+    "    mp = sisl.MonkhorstPack(H, [nx, ny, 1])\n",
+    "    def wrap_multiple(eigenstate):\n",
+    "        DOS = eigenstate.DOS(E)\n",
+    "        PDOS = eigenstate.PDOS(E)\n",
+    "        return sisl.oplist([DOS, PDOS])\n",
+    "    DOS, PDOS = mp.apply.average.eigenstate(wrap=wrap_multiple, eta=True)\n",
+    "    \n",
+    "    ```\n",
     "\n",
     "    Search the API documentation for the `MonkhorstPack.apply.average` method and figure out what it does. Note, there are other `MonkhorstPack.apply.*` methods - these are all extremely useful when calculating many quantities of data in a Brillouin-zone object.\n",
-    "5. Compare the Siesta PDOS with sisl PDOS, why are they different?  \n",
-    "   *HINT*: $\\sigma$. Check the API for the `PDOS` method in the Siesta manual (https://siesta-project.org/SIESTA_MATERIAL/Docs/Manuals/siesta-4.1.5.pdf)."
+    "5. Ensure that the `DOS` and the summed `PDOS` (use Eq. 2) are equivalent.\n",
+    "6. Compare the Siesta PDOS with sisl PDOS, why are they different?  \n",
+    "   *HINT*: $\\sigma$. Check the API for the `PDOS` method in the Siesta manual, provided via this tutorial (`../siesta.pdf`)."
    ]
   },
   {
@@ -141,9 +148,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plt.plot(E, PDOS.sum(0), label='DOS')\n",
-    "plt.xlabel(r'$E - E_F$ [eV]')\n",
-    "plt.ylabel(r'DOS [1/eV]')\n",
+    "plt.plot(E, PDOS.sum(0), label=\"DOS\")\n",
+    "plt.xlabel(r\"$E - E_F$ [eV]\")\n",
+    "plt.ylabel(r\"DOS [1/eV]\")\n",
     "\n",
     "# Add more plots for individual PDOS\n",
     "\n",
@@ -169,7 +176,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

tutorial.ipynb

@@ -233,7 +233,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -247,7 +247,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,