fixed import statements in tutorials

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

docs/tutorials/index.rst

@@ -7,7 +7,7 @@ sisl is shipped with these tutorials which introduce the basics.
 All examples are assumed to have this in the header::
 
    import numpy as np
-   from sisl import *
+   import sisl as si
 
 to enable `numpy`_ and sisl.
 

docs/tutorials/tutorial_es_1.ipynb

@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "from sisl import *\n",
+    "import sisl as si\n",
     "from sisl.viz import merge_plots\n",
     "from sisl.viz.processors.math import normalize\n",
     "import matplotlib.pyplot as plt\n",
@@ -35,7 +35,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "graphene = geom.graphene().tile(6, 0).tile(6, 1)"
+    "graphene = si.geom.graphene().tile(6, 0).tile(6, 1)"
    ]
   },
   {
@@ -44,7 +44,7 @@
    "source": [
     "This does *a lot* of things behind the scenes:\n",
     "\n",
-    "1. `geom.graphene`:\n",
+    "1. `si.geom.graphene`:\n",
     "    - create atomic coordinates of pristine graphene with a default bond-length of $1.42\\,\\mathrm{Å}$.\n",
     "    - create pristine graphene unit cell, by default this will create a supercell\n",
     "    with a size `3x3`, i.e. a nearest neighbour unit-cell.\n",
@@ -156,7 +156,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "H = Hamiltonian(system)\n",
+    "H = si.Hamiltonian(system)\n",
     "print(H)"
    ]
   },
@@ -291,7 +291,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "band = BandStructure(\n",
+    "band = si.BandStructure(\n",
     "    H,\n",
     "    [[0, 0, 0], [0, 0.5, 0], [1 / 3, 2 / 3, 0], [0, 0, 0]],\n",
     "    400,\n",
@@ -349,7 +349,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "bz = MonkhorstPack(H, [35, 35, 1])\n",
+    "bz = si.MonkhorstPack(H, [35, 35, 1])\n",
     "bz_average = (\n",
     "    bz.apply.average\n",
     ");  # specify the Brillouin zone to perform an average of subsequent method calls"
@@ -416,7 +416,7 @@
     "print(\"Normalization: {}\".format(f.sum() * (r[1] - r[0])))\n",
     "plt.plot(r, f)\n",
     "plt.ylim([0, None])\n",
-    "orb = SphericalOrbital(1, (r, f));"
+    "orb = si.SphericalOrbital(1, (r, f));"
    ]
   },
   {
@@ -460,7 +460,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "C = Atom(6, orb)\n",
+    "C = si.Atom(6, orb)\n",
     "print(system.atoms)\n",
     "system.atoms.replace(system.atoms[0], C)\n",
     "print(system.atoms)"
@@ -482,7 +482,7 @@
    "outputs": [],
    "source": [
     "es = H.eigenstate(dtype=np.float64).sub([len(H) // 2 + 1])\n",
-    "grid = Grid(0.075, lattice=H.lattice)\n",
+    "grid = si.Grid(0.075, lattice=H.lattice)\n",
     "es.wavefunction(grid)"
    ]
   },
@@ -540,7 +540,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.15"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

docs/tutorials/tutorial_es_2.ipynb

@@ -7,7 +7,8 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "from sisl import *\n",
+    "import sisl as si\n",
+    "from sisl.physics.electron import berry_phase\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "%matplotlib inline"
@@ -32,8 +33,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "graphene = geom.graphene()\n",
-    "H = Hamiltonian(graphene)\n",
+    "graphene = si.geom.graphene()\n",
+    "H = si.Hamiltonian(graphene)\n",
     "H.construct([(0.1, 1.44), (0, -2.7)])"
    ]
   },
@@ -70,7 +71,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "band = BandStructure(\n",
+    "band = si.BandStructure(\n",
     "    H, [[0, 0.5, 0], [1 / 3, 2 / 3, 0], [0.5, 0.5, 0]], 400, [r\"$M$\", r\"$K$\", r\"$M'$\"]\n",
     ")"
    ]
@@ -100,7 +101,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "bz = MonkhorstPack(\n",
+    "bz = si.MonkhorstPack(\n",
     "    H, [41, 41, 1], displacement=[1 / 3, 2 / 3, 0], size=[0.125, 0.125, 1]\n",
     ")\n",
     "bz_average = bz.apply.average  # specify the Brillouin zone to perform an average"
@@ -139,7 +140,7 @@
    "outputs": [],
    "source": [
     "E = np.linspace(-0.5, 0.5, 1000)\n",
-    "dist = get_distribution(\"gaussian\", 0.03)\n",
+    "dist = si.get_distribution(\"gaussian\", 0.03)\n",
     "bz.set_parent(H)\n",
     "plt.plot(\n",
     "    E,\n",
@@ -181,7 +182,7 @@
     "normal = [0, 0, 1]\n",
     "# Origo (in units of reciprocal lattice vectors)\n",
     "origin = [1 / 3, 2 / 3, 0]\n",
-    "circle = BrillouinZone.param_circle(H, N, kR, normal, origin)\n",
+    "circle = si.BrillouinZone.param_circle(H, N, kR, normal, origin)\n",
     "plt.plot(circle.k[:, 0], circle.k[:, 1])\n",
     "plt.xlabel(r\"$k_x$ [$b_x$]\")\n",
     "plt.ylabel(r\"$k_y$ [$b_y$]\")\n",
@@ -224,21 +225,13 @@
    "outputs": [],
    "source": [
     "circle.set_parent(H)\n",
-    "print(\"Pristine graphene (0): {:.5f} rad\".format(electron.berry_phase(circle, sub=0)))\n",
-    "print(\"Pristine graphene (1): {:.5f} rad\".format(electron.berry_phase(circle, sub=1)))\n",
-    "print(\"Pristine graphene (:): {:.5f} rad\".format(electron.berry_phase(circle)))\n",
+    "print(\"Pristine graphene (0): {:.5f} rad\".format(berry_phase(circle, sub=0)))\n",
+    "print(\"Pristine graphene (1): {:.5f} rad\".format(berry_phase(circle, sub=1)))\n",
+    "print(\"Pristine graphene (:): {:.5f} rad\".format(berry_phase(circle)))\n",
     "circle.set_parent(H_bp)\n",
-    "print(\n",
-    "    \"Anti-symmetric graphene (0): {:.5f} rad\".format(\n",
-    "        electron.berry_phase(circle, sub=0)\n",
-    "    )\n",
-    ")\n",
-    "print(\n",
-    "    \"Anti-symmetric graphene (1): {:.5f} rad\".format(\n",
-    "        electron.berry_phase(circle, sub=1)\n",
-    "    )\n",
-    ")\n",
-    "print(\"Anti-symmetric graphene (:): {:.5f} rad\".format(electron.berry_phase(circle)))"
+    "print(\"Anti-symmetric graphene (0): {:.5f} rad\".format(berry_phase(circle, sub=0)))\n",
+    "print(\"Anti-symmetric graphene (1): {:.5f} rad\".format(berry_phase(circle, sub=1)))\n",
+    "print(\"Anti-symmetric graphene (:): {:.5f} rad\".format(berry_phase(circle)))"
    ]
   },
   {
@@ -258,13 +251,13 @@
     "dk = 0.0001\n",
     "bp = np.empty([4, len(kRs)])\n",
     "for i, kR in enumerate(kRs):\n",
-    "    circle = BrillouinZone.param_circle(H_bp, dk, kR, normal, origin)\n",
-    "    bp[0, i] = electron.berry_phase(circle, sub=0)\n",
-    "    circle_other = BrillouinZone.param_circle(\n",
-    "        utils.mathematics.fnorm(H_bp.rcell), dk, kR, normal, origin\n",
+    "    circle = si.BrillouinZone.param_circle(H_bp, dk, kR, normal, origin)\n",
+    "    bp[0, i] = berry_phase(circle, sub=0)\n",
+    "    circle_other = si.BrillouinZone.param_circle(\n",
+    "        si.utils.mathematics.fnorm(H_bp.rcell), dk, kR, normal, origin\n",
     "    )\n",
     "    circle.k[:, :] = circle_other.k[:, :]\n",
-    "    bp[1, i] = electron.berry_phase(circle, sub=0)\n",
+    "    bp[1, i] = berry_phase(circle, sub=0)\n",
     "plt.plot(kRs, bp[0, :] / np.pi, label=r\"1/Ang\")\n",
     "plt.plot(kRs, bp[1, :] / np.pi, label=r\"$b_i$\")\n",
     "plt.legend()\n",
@@ -296,9 +289,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.9"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

docs/tutorials/tutorial_siesta_1.ipynb

@@ -10,7 +10,7 @@
     "\n",
     "os.chdir(\"siesta_1\")\n",
     "import numpy as np\n",
-    "from sisl import *\n",
+    "import sisl as si\n",
     "from sisl.viz import merge_plots\n",
     "from sisl.viz.processors.math import normalize\n",
     "from functools import partial\n",
@@ -39,10 +39,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "h2o = Geometry(\n",
+    "h2o = si.Geometry(\n",
     "    [[0, 0, 0], [0.8, 0.6, 0], [-0.8, 0.6, 0.0]],\n",
-    "    [Atom(\"O\"), Atom(\"H\"), Atom(\"H\")],\n",
-    "    lattice=Lattice(10, origin=[-5] * 3),\n",
+    "    [si.Atom(\"O\"), si.Atom(\"H\"), si.Atom(\"H\")],\n",
+    "    lattice=si.Lattice(10, origin=[-5] * 3),\n",
     ")"
    ]
   },
@@ -144,7 +144,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fdf = get_sile(\"RUN.fdf\")\n",
+    "fdf = si.get_sile(\"RUN.fdf\")\n",
     "H = fdf.read_hamiltonian()\n",
     "# Create a short-hand to handle the geometry\n",
     "h2o = H.geometry\n",
@@ -285,7 +285,7 @@
     "    )\n",
     "\n",
     "\n",
-    "g = Grid(0.2, lattice=h2o.lattice)\n",
+    "g = si.Grid(0.2, lattice=h2o.lattice)\n",
     "es.sub(0).wavefunction(g)\n",
     "integrate(g)\n",
     "# g.write('HOMO.cube')\n",
@@ -314,7 +314,7 @@
    "outputs": [],
    "source": [
     "DM = fdf.read_density_matrix()\n",
-    "rho = get_sile(\"siesta_1.nc\").read_grid(\"Rho\")"
+    "rho = si.get_sile(\"siesta_1.nc\").read_grid(\"Rho\")"
    ]
   },
   {
@@ -363,7 +363,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.15"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

docs/tutorials/tutorial_siesta_2.ipynb

@@ -10,7 +10,7 @@
     "\n",
     "os.chdir(\"siesta_2\")\n",
     "import numpy as np\n",
-    "from sisl import *\n",
+    "import sisl as si\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "%matplotlib inline"
@@ -37,7 +37,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "graphene = geom.graphene(1.44)"
+    "graphene = si.geom.graphene(1.44)"
    ]
   },
   {
@@ -106,7 +106,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fdf = get_sile(\"RUN.fdf\")\n",
+    "fdf = si.get_sile(\"RUN.fdf\")\n",
     "H = fdf.read_hamiltonian()\n",
     "print(H)"
    ]
@@ -128,7 +128,7 @@
    "source": [
     "E = np.linspace(-6, 4, 500)\n",
     "for nk in [21, 41, 61, 81]:\n",
-    "    bz = MonkhorstPack(H, [nk, nk, 1])\n",
+    "    bz = si.MonkhorstPack(H, [nk, nk, 1])\n",
     "    plt.plot(\n",
     "        E,\n",
     "        bz.apply.average.eigenvalue(wrap=lambda ev: ev.DOS(E)),\n",
@@ -189,7 +189,7 @@
    "outputs": [],
    "source": [
     "# Define the band-structure\n",
-    "bz = BandStructure(\n",
+    "bz = si.BandStructure(\n",
     "    H,\n",
     "    [[0] * 3, [2.0 / 3, 1.0 / 3, 0], [0.5, 0.5, 0], [1] * 3],\n",
     "    400,\n",
@@ -239,7 +239,7 @@
     "es = es.sub(idx_valence)\n",
     "\n",
     "# Generate a grid encompassing a 2x2 graphene unit-cell\n",
-    "g = Grid(0.2, lattice=H.geometry.lattice.tile(2, 0).tile(2, 1))\n",
+    "g = si.Grid(0.2, lattice=H.geometry.lattice.tile(2, 0).tile(2, 1))\n",
     "# Calculate the real-space wavefunctions\n",
     "es.wavefunction(g)\n",
     "\n",
@@ -275,7 +275,7 @@
     "es = H.eigenstate([1.0 / 2, 0, 0])\n",
     "idx_valence = (es.eig > 0).nonzero()[0][0] - 1\n",
     "es = es.sub(idx_valence)\n",
-    "g = Grid(0.2, dtype=np.complex128, lattice=H.geometry.lattice.tile(4, 0).tile(4, 1))\n",
+    "g = si.Grid(0.2, dtype=np.complex128, lattice=H.geometry.lattice.tile(4, 0).tile(4, 1))\n",
     "es.wavefunction(g)\n",
     "x, y = np.mgrid[: g.shape[0], : g.shape[1]]\n",
     "x, y = x * g.dcell[0, 0] + y * g.dcell[1, 0], x * g.dcell[0, 1] + y * g.dcell[1, 1]\n",
@@ -312,7 +312,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.15"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

docs/tutorials/tutorial_siesta_2_ahc.ipynb

@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "from sisl import *\n",
+    "import sisl as si\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "%matplotlib inline"
@@ -32,7 +32,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "H = get_sile(\"siesta_2/RUN.fdf\").read_hamiltonian()"
+    "H = si.get_sile(\"siesta_2/RUN.fdf\").read_hamiltonian()"
    ]
   },
   {