bug: fixed TB_01

TB_01/run.ipynb

@@ -179,6 +179,23 @@
     "We find 8 non-zero elements, as there should be. Remark, even though we set the on-site terms to $0$, they are interpreted as non-zero elements due to explicitly setting them."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "After having setup the Hamilton, we may easily calculate the eigenvalues at any $\\mathbf k$ (in reduced coordinates $\\mathbf k\\in]-0.5:0.5]$)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(\"Gamma:\", H.eigh())\n",
+    "print(\"K:\", H.eigh(k=[2./3,1./3,0]))"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -204,7 +221,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "for ia, io in H:\n",
+    "for ia, io in H.geometry.iter_orbitals(local=False):\n",
     "    # This loops over all atoms and the orbitals\n",
     "    # corresponding to the atom.\n",
     "    # In this case the geometry has one orbital per atom, hence\n",
@@ -217,7 +234,7 @@
     "    # Hamiltonian (H.geom)\n",
     "    # and use a function called `close` which returns ALL \n",
     "    # atomic indices within certain ranges of a given point or atom\n",
-    "    idx = H.geom.close(ia, R = [0.1, 1.43])\n",
+    "    idx = H.geometry.close(ia, R = [0.1, 1.43])\n",
     "    # the argument R has two entries:\n",
     "    #   0.1 and 1.43\n",
     "    # Each value represents a radii of a sphere.\n",
@@ -295,7 +312,7 @@
     "band = sisl.BandStructure(H, [[0., 0.], [2./3, 1./3],\n",
     "                              [1./2, 1./2], [1., 1.]], 301,\n",
     "                              [r'$\\Gamma$', 'K', 'M', r'$\\Gamma$'])\n",
-    "eigs = band.eigh()"
+    "eigs = band.apply.array.eigh()"
    ]
   },
   {