added 3 siesta tutorials

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

S_01/RUN.fdf

@@ -0,0 +1,31 @@
+Diag.ParallelOverK true
+%block kgrid.MonkhorstPack
+    21  0  0 0.
+    0 21  0 0.
+    0  0  1 0.
+%endblock kgrid.MonkhorstPack
+
+# This is the remaining default SIESTA options
+PAO.BasisSize         SZP
+
+XC.functional     GGA
+XC.authors        PBE
+MeshCutoff        250.000000 Ry
+FilterCutoff      150.000000 Ry
+
+ElectronicTemperature   300 K
+
+MinSCFIterations       3
+SCF.DM.Tolerance       0.0001
+# Mixing parameters:
+SCF.Mixer.Weight       0.10
+SCF.Mixer.History      12
+SCF.Mix.First          true
+DM.UseSaveDM           true
+
+MD.NumCGSteps 0
+
+SaveHS     true
+TS.HS.Save true
+
+%include STRUCT.fdf

S_01/run.ipynb

@@ -0,0 +1,152 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from __future__ import print_function\n",
+    "import sisl\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "%matplotlib inline"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "First Siesta example for analyzing output.\n",
+    "\n",
+    "This example will calculate the electronic structure of graphene using Siesta and we will post-process the data to calculate band-structures etc.\n",
+    "\n",
+    "We remark that settings during the Siesta/TranSiesta tutorials are not necessarily converged or proper settings. Users need to invest time in understanding the intrinsics of Siesta before performing real calculations!"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "graphene = sisl.geom.graphene(1.44)\n",
+    "graphene.write('STRUCT.fdf')\n",
+    "graphene.write('STRUCT.xyz')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Exercises\n",
+    "\n",
+    "As this is your first example of running Siesta there are a few things you should know:\n",
+    "\n",
+    "1. Start by calculating the electronic structure using Siesta\n",
+    "\n",
+    "       siesta RUN.fdf > RUN.out\n",
+    "\n",
+    "  - Go through the output of Siesta to get used to it, also to assert that it has runned without errors (always do this!) ((always, **always** do THIS!))\n",
+    "  - Ensure the SCF has indeed converged, Siesta will, by default, die if it hasn't converged the SCF.\n",
+    "  \n",
+    "2. Use `sisl` to read in the electronic structure (the Hamiltonian), there are several ways of doing this, for now you should try these two methods:\n",
+    "\n",
+    "         H_fdf = sisl.Hamiltonian.read('RUN.fdf')\n",
+    "         H_TSHS = sisl.Hamiltonian.read('siesta.TSHS')\n",
+    "         \n",
+    "    print the objects and note the difference between the two objects.\n",
+    "    What do you think these differences mean?\n",
+    "    \n",
+    "3. Calculate the $\\Gamma$-point eigen spectrum using both above Hamiltonians (search the sisl documentation for `eigh`), are they different? If so, why, if not, why not? Once answered, you should know which of the two above methods is the *best* way to read the electronic structure. \n",
+    "\n",
+    "4. Calculate the band-structure using the DFT electronic structure using `sisl`. Also calculate the band-structure using the tight-binding Hamiltonian ([TB 1](../TB_01/run.ipynb)) and compare the two.  \n",
+    "HINT: zoom in on an energy-range from $-3$ eV to $3$ eV and plot both the DFT bands and the TB bands in the same plot.  "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Read Hamiltonians using two different methods\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Calculate eigenspectrum at the \\Gamma-point\n",
+    "eig_fdf = H_fdf.<>\n",
+    "eig_TSHS = H_TSHS.<>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Calculate band-structure from DFT Hamiltonian and TB Hamiltonian\n",
+    "band = sisl.BandStructure(graphene, <fill-in correct points and labels>)\n",
+    "xtick, xtick_label = band.lineartick()\n",
+    "lk = band.lineark()\n",
+    "\n",
+    "ax = plt.gca()\n",
+    "ax.xaxis.set_ticks(xtick)\n",
+    "ax.set_xticklabels(xtick_label)\n",
+    "\n",
+    "# Define limits of the y-axis (Energy!)\n",
+    "# Play with this if you want! :)\n",
+    "ax.set_ylim(-3, 3)\n",
+    "ax.set_ylabel('Eigenspectrum [eV]')\n",
+    "\n",
+    "# Plot x-major lines at the ticks\n",
+    "ymin, ymax = ax.get_ylim()\n",
+    "for tick in xtick:\n",
+    "    ax.plot([tick,tick], [ymin, ymax], 'k')\n",
+    "\n",
+    "# Plot band-structures\n",
+    "band.set_parent(<DFT Hamiltonian>)\n",
+    "eigs = band.eigh()\n",
+    "ax.plot(lk, eigs)\n",
+    "    \n",
+    "# You need to create the TB Hamiltonian, see e.g. example TB 1\n",
+    "band.set_parent(<TB Hamiltonian>)\n",
+    "eigs = band.eigh()\n",
+    "ax.plot(lk, eigs, '--')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}