updated examples after tutorial

Signed-off-by: Nick Papior <nickpapior@gmail.com>

Author: zerothi

06/run.ipynb

@@ -313,7 +313,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Spectral density of states for all electrodes:"
+    "Spectral density of states for all electrodes:\n",
+    "- As a final exercise you can explore the details of the density of states for single atoms. Take for instance atom 205 (204 in Python index) which is in *both* GNR at the crossing.  \n",
+    "Feel free to play around with different atoms, subset of atoms (pass a `list`) etc.  "
    ]
   },
   {
@@ -331,8 +333,6 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "- As a final exercise you can explore the details of the density of states for single atoms. Take for instance atom 205 (204 in Python index) which is in *both* GNR at the crossing.  \n",
-    "Feel free to play around with different atoms, subset of atoms (pass a `list`) etc.  \n",
     "- For 2D structures one can easily plot the DOS per atom via a scatter plot in `matplotlib`, here is the skeleton code for that, you should select an energy point and figure out how to extract the atom resolved DOS (you will need to look-up the documentation for the `ADOS` method to figure out which flag to use."
    ]
   },

07/run.ipynb

@@ -150,7 +150,6 @@
     "    print(' {}'.format(i+1), end=',')\n",
     "    # Calculate H(Phi)\n",
     "    #dH = ... math.e ** (0.5j ...) ...\n",
-    "    dH = nn * (math.e ** (0.5j * xy / rec_phi) - 1)\n",
     "\n",
     "    with sisl.get_sile('M_{}.dH.nc'.format(rec_phi), mode='w') as fh:\n",
     "        fh.write_delta(dH)"

tutorial.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -47,54 +47,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Help on method tile in module sisl.geometry:\n",
-      "\n",
-      "tile(self, reps, axis) unbound sisl.geometry.Geometry method\n",
-      "    Tile the geometry to create a bigger one\n",
-      "    \n",
-      "    The atomic indices are retained for the base structure.\n",
-      "    \n",
-      "    Parameters\n",
-      "    ----------\n",
-      "    reps  : int\n",
-      "       number of tiles (repetitions)\n",
-      "    axis  : int\n",
-      "       direction of tiling, 0, 1, 2 according to the cell-direction\n",
-      "    \n",
-      "    Examples\n",
-      "    --------\n",
-      "    >>> geom = Geometry([[0, 0, 0], [0.5, 0, 0]], sc=1.)\n",
-      "    >>> g = geom.tile(2,axis=0)\n",
-      "    >>> print(g.xyz)\n",
-      "    [[ 0.   0.   0. ]\n",
-      "     [ 0.5  0.   0. ]\n",
-      "     [ 1.   0.   0. ]\n",
-      "     [ 1.5  0.   0. ]]\n",
-      "    >>> g = geom.tile(2,0).tile(2,axis=1)\n",
-      "    >>> print(g.xyz)\n",
-      "    [[ 0.   0.   0. ]\n",
-      "     [ 0.5  0.   0. ]\n",
-      "     [ 1.   0.   0. ]\n",
-      "     [ 1.5  0.   0. ]\n",
-      "     [ 0.   1.   0. ]\n",
-      "     [ 0.5  1.   0. ]\n",
-      "     [ 1.   1.   0. ]\n",
-      "     [ 1.5  1.   0. ]]\n",
-      "    \n",
-      "    See Also\n",
-      "    --------\n",
-      "    repeat : equivalent but different ordering of final structure\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%pdoc sisl.Geometry.tile\n",
     "help(sisl.Geometry.tile)"
@@ -212,13 +167,6 @@
     "- [Advanced 04](A04/run.ipynb)  \n",
     "  Create a 3rd nearest neighbour graphene model."
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {