Merge pull request #621 from pfebrer/viz_data_sources

Cleaning tutorial notebooks.

docs/tutorials/tutorial_es_1.ipynb

@@ -10,6 +10,7 @@
     "from sisl import *\n",
     "import sisl.viz\n",
     "from sisl.viz import merge_plots\n",
+    "from sisl.viz.processors.math import normalize\n",
     "import matplotlib.pyplot as plt\n",
     "%matplotlib inline"
    ]
@@ -245,7 +246,7 @@
     "E = np.linspace(-1, -.5, 100)\n",
     "dE = E[1] - E[0]\n",
     "PDOS = es.PDOS(E).sum((0, 2)) * dE # perform integration\n",
-    "system.plot(axes=\"xy\", atoms_style={\"size\": PDOS * 15})\n",
+    "system.plot(axes=\"xy\", atoms_style={\"size\": normalize(PDOS, 0, 1)})\n",
     "#plt.scatter(system.xyz[:, 0], system.xyz[:, 1], 500 * PDOS);\n",
     "#plt.scatter(xyz_remove[0], xyz_remove[1], c='k', marker='*'); # mark the removed atom"
    ]
@@ -370,7 +371,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "system.plot(axes=\"xy\", atoms_style={\"size\": 150 * PDOS})"
+    "system.plot(axes=\"xy\", atoms_style={\"size\": normalize(PDOS, 0, 1)})"
    ]
   },
   {
@@ -519,7 +520,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.8.15"
   }
  },
  "nbformat": 4,

docs/tutorials/tutorial_siesta_1.ipynb

@@ -12,6 +12,7 @@
     "from sisl import *\n",
     "import sisl.viz\n",
     "from sisl.viz import merge_plots\n",
+    "from sisl.viz.processors.math import normalize\n",
     "from functools import partial\n",
     "import matplotlib.pyplot as plt\n",
     "%matplotlib inline"
@@ -237,7 +238,7 @@
     "es = es.sub([idx_lumo - 1, idx_lumo])\n",
     "\n",
     "plots = [\n",
-    "    h2o.plot(axes=\"xy\", atoms_style={\"size\": n * 1.5, \"color\": c})\n",
+    "    h2o.plot(axes=\"xy\", atoms_style={\"size\": normalize(n), \"color\": c})\n",
     "    for n, c in zip(h2o.apply(es.norm2(sum=False),\n",
     "                                           np.sum,\n",
     "                                           mapper=partial(h2o.a2o, all=True),\n",

docs/tutorials/tutorial_siesta_2.ipynb

@@ -148,39 +148,21 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "bz = MonkhorstPack(H, [81, 81, 1])\n",
-    "idx_s = list()\n",
-    "idx_pxy = list()\n",
-    "idx_pz = list()\n",
-    "for i, orb in enumerate(H.geometry.atoms[0]):\n",
-    "    if orb.l == 0:\n",
-    "        idx_s.append(i)\n",
-    "    elif orb.l == 1 and (orb.m in [-1, 1]):\n",
-    "        idx_pxy.append(i)\n",
-    "    elif orb.l == 1 and orb.m == 0:\n",
-    "        idx_pz.append(i)\n",
-    "print('Orbital index of s: {}'.format(idx_s))\n",
-    "print('Orbital index of p_x and p_y: {}'.format(idx_pxy))\n",
-    "print('Orbital index of p_z: {}'.format(idx_pz))\n",
-    "# Get all orbitals\n",
-    "all_s = np.add.outer(H.geometry.a2o([0, 1]), idx_s).ravel()\n",
-    "all_pxy = np.add.outer(H.geometry.a2o([0, 1]), idx_pxy).ravel()\n",
-    "all_pz = np.add.outer(H.geometry.a2o([0, 1]), idx_pz).ravel()\n",
-    "\n",
-    "def wrap(es):\n",
-    "    PDOS = es.PDOS(E)[0]\n",
-    "    pdos_s = PDOS[all_s, :].sum(0)\n",
-    "    pdos_pxy = PDOS[all_pxy, :].sum(0)\n",
-    "    pdos_pz = PDOS[all_pz, :].sum(0)\n",
-    "    return np.stack((pdos_s, pdos_pxy, pdos_pz))\n",
-    "pDOS = bz.apply.average.eigenstate(wrap=wrap)\n",
-    "plt.plot(E, pDOS[0, :], label='$s$');\n",
-    "plt.plot(E, pDOS[1, :], label='$p_x+p_y$');\n",
-    "plt.plot(E, pDOS[2, :], label=r'$p_z$');\n",
-    "plt.xlim(E[0], E[-1]); plt.ylim(0, None)\n",
-    "plt.xlabel(r'$E - E_F$ [eV]')\n",
-    "plt.ylabel(r'DOS [1/eV]')\n",
-    "plt.legend();"
+    "pdos_plot = H.plot.pdos(kgrid=[81, 81, 1], data_Erange=(-6, 4), Erange=[-6, 4], nE=500)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "orb_groups = [\n",
+    "    {\"l\": 0, \"name\": \"s\", \"color\": \"red\"},\n",
+    "    {\"l\": 1, \"m\": [-1, 1], \"name\": \"px + py\", \"color\": \"blue\"},\n",
+    "    {\"l\": 1, \"m\": 0, \"name\": \"pz\", \"color\": \"green\"}\n",
+    "]\n",
+    "pdos_plot.update_inputs(groups=orb_groups)"
    ]
   },
   {
@@ -198,34 +180,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "weight_s = list()\n",
-    "weight_pxy = list()\n",
-    "weight_pz = list()\n",
-    "def wrap_fatbands(eigenstate):\n",
-    "    # The eigenstate object has several features.\n",
-    "    # For now we will simply calculate the <psi_i| S(k) | psi_i> weight for\n",
-    "    # the orbitals we are interested in.\n",
-    "    norm2 = eigenstate.norm2(sum=False)\n",
-    "    weight_s.append(norm2[:, all_s].sum(-1))\n",
-    "    weight_pxy.append(norm2[:, all_pxy].sum(-1))\n",
-    "    weight_pz.append(norm2[:, all_pz].sum(-1))\n",
-    "    return eigenstate.eig\n",
     "# Define the band-structure\n",
     "bz = BandStructure(H, [[0] * 3, [2./3, 1./3, 0], [0.5, 0.5, 0], [1] * 3], 400, \n",
-    "                   names=[r'$\\Gamma$', r'$K$', r'$M$', r'$\\Gamma$'])\n",
-    "\n",
-    "# Calculate all eigenvalues\n",
-    "eig = bz.apply.array.eigenstate(wrap=wrap_fatbands).T\n",
-    "weight_s = np.array(weight_s).T\n",
-    "weight_pxy = np.array(weight_pxy).T\n",
-    "weight_pz = np.array(weight_pz).T"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Finally we plot the fat-bands. Our plots split each of the orbitals contributions into their separate fat band. Thus one can see details on multiple orbital contributions for each band."
+    "                   names=[r'$\\Gamma$', r'$K$', r'$M$', r'$\\Gamma$'])"
    ]
   },
   {
@@ -234,41 +191,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "linear_k, k_tick, k_label = bz.lineark(True)\n",
-    "\n",
-    "Emin, Emax = -21, 10\n",
-    "# This is to determine the width of the fat-bands\n",
-    "# The width of the fat-bands is dependent on the energy range and also on the variety\n",
-    "# of contributions.\n",
-    "dE = (Emax - Emin) / 20.\n",
-    "plt.ylabel(r'$E-E_F$ [eV]')\n",
-    "plt.xlim(linear_k[0], linear_k[-1]);\n",
-    "plt.xticks(k_tick, k_label);\n",
-    "plt.ylim(Emin, Emax);\n",
-    "\n",
-    "# Now plot the bands\n",
-    "for i, e in enumerate(eig):\n",
-    "    s = np.abs(weight_s[i, :] * dE)\n",
-    "    pxy = np.abs(weight_pxy[i, :] * dE)\n",
-    "    pz = np.abs(weight_pz[i, :] * dE)\n",
-    "    plt.plot(linear_k, e, color='k'); # black-line (band-structure)\n",
-    "    # Full fat-band\n",
-    "    plt.fill_between(linear_k, e - dE, e + dE, color='k', alpha=0.1);\n",
-    "    # pz\n",
-    "    plt.fill_between(linear_k, e + (s + pxy), e + (s + pxy + pz), color='g', alpha=0.5);\n",
-    "    plt.fill_between(linear_k, e - (s + pxy + pz), e - (s + pxy), color='g', alpha=0.5);\n",
-    "    # pxy\n",
-    "    plt.fill_between(linear_k, e + (s), e + (s + pxy), color='b', alpha=0.5);\n",
-    "    plt.fill_between(linear_k, e - (s), e - (s + pxy), color='b', alpha=0.5);\n",
-    "    # s\n",
-    "    plt.fill_between(linear_k, e - (s), e + (s), color='r', alpha=0.5);"
+    "bz.plot.fatbands(groups=orb_groups, Erange=[-21, 10])"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "- all, gray\n",
+    "- all, black\n",
     "- $p_z$, green\n",
     "- $s$, red\n",
     "- $p_x+p_y$, blue"
@@ -345,6 +275,13 @@
     "    ax.set_xlabel(r'$x$ [Ang]');\n",
     "    ax.set_ylabel(r'$y$ [Ang]');"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

src/sisl/viz/processors/math.py

@@ -0,0 +1,23 @@
+import numpy as np
+
+def normalize(data, vmin=0, vmax=1):
+    """Normalize data to [vmin, vmax] range.
+
+    Parameters
+    ----------
+    data : array_like
+        Data to normalize.
+    vmin : float, optional
+        Minimum value of normalized data.
+    vmax : float, optional
+        Maximum value of normalized data.
+
+    Returns
+    -------
+    data : array_like
+        Normalized data.
+    """
+    data = np.asarray(data)
+    data_min = np.min(data)
+    data_max = np.max(data)
+    return vmin + (vmax - vmin) * (data - data_min) / (data_max - data_min)

src/sisl/viz/processors/tests/test_math.py

@@ -0,0 +1,12 @@
+import numpy as np
+
+from sisl.viz.processors.math import normalize
+
+def test_normalize():
+
+    data = [0, 1, 2]
+
+    assert np.allclose(normalize(data), [0, 0.5, 1])
+
+    assert np.allclose(normalize(data, vmin=-1, vmax=1), [-1, 0, 1])
+