Initial commit

.gitignore

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+.ipynb_checkpoints/
+*~
+.*.swp

0_Getting_started.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "statewide-honey",
+   "metadata": {},
+   "source": [
+    "#  A mathematical look at electronic structure theory"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "dried-concrete",
+   "metadata": {},
+   "source": [
+    "## About this workshop\n",
+    "\n",
+    "<img src=\"img/dftkfields.png\" width=40% align=\"right\" />\n",
+    "\n",
+    "- Electronic structure theory is a fascinating interdisciplinary field\n",
+    "- Why bother? -> See [my JuliaCon 2020 talk](https://www.youtube.com/watch?v=-RomkxjlIcQ)\n",
+    "\n",
+    "\n",
+    "- Multiple philosophies and general approaches exist\n",
+    "- Focus of this workshop:\n",
+    "    * Solid-state problems (crystals, lattices, ...)\n",
+    "    * Plane-wave discretisations\n",
+    "    * Density functional theory (DFT)\n",
+    "    * Highly successful, but still many open mathematical problems\n",
+    "\n",
+    "\n",
+    "- Topics:\n",
+    "    * Specialities of periodic problems\n",
+    "    * Mathematical formulation of the DFT\n",
+    "    * Numerical solution using the self-consistent field (SCF) procedure\n",
+    "    * Numerical tools for analysis and understanding convergence\n",
+    "    * Opportunities for modern software programming techniques (tracking floating-point error, automatic differentation).\n",
+    "\n",
+    "\n",
+    "- Goals:\n",
+    "    * Allow applied mathematicians to gain access to the topic\n",
+    "    * Allow practitioners to deepen mathematical insight\n",
+    "    * Introduce the [density-functional toolkit](https://dftk.org)\n",
+    "      and its interplay with the Julia package ecosystom."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "several-receipt",
+   "metadata": {},
+   "source": [
+    "## Whoami and whoareyou?\n",
+    "\n",
+    "* Michael F. Herbst\n",
+    "    - Postdoc at Applied and Computational Mathematics departmant at RWTH Aachen University\n",
+    "    - Chemistry background, but worked in maths departments for the past few years\n",
+    "    - Active Julia user since about Julia 0.6\n",
+    "    \n",
+    "    \n",
+    "    - Email: [email protected]\n",
+    "    - Web:   https://michael-herbst.com\n",
+    "    \n",
+    "    \n",
+    "* So who are you?\n",
+    "    - Quick poll: http://etc.ch/rWup"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "representative-employment",
+   "metadata": {},
+   "source": [
+    "## Some general remarks\n",
+    "\n",
+    "- The examples in this notebook were primarily chosen to be quick to run and yield mathematical insight. In particular:\n",
+    "    * Parameters will not give fully converged results\n",
+    "    * Not all examples make physical sense (i.e. it might be better to model things differently in practice)\n",
+    "\n",
+    "\n",
+    "- I have prepared:\n",
+    "    * Some theory\n",
+    "    * Many examples\n",
+    "    * Short exercises \n",
+    "    \n",
+    "    \n",
+    "- This is meant to be interactive:\n",
+    "    * Please ask questions ..."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Julia 1.6.1",
+   "language": "julia",
+   "name": "julia-1.6"
+  },
+  "language_info": {
+   "file_extension": ".jl",
+   "mimetype": "application/julia",
+   "name": "julia",
+   "version": "1.6.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

1_Installation.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "burning-pharmacology",
+   "metadata": {},
+   "source": [
+    "# Installation and setup"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "coated-execution",
+   "metadata": {},
+   "source": [
+    "## Requirements\n",
+    "\n",
+    "- **Julia $\\geq$ 1.6**\n",
+    "- Some working python setup\n",
+    "\n",
+    "These notes have been made targeting DFTK 0.3.9."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "mysterious-snake",
+   "metadata": {},
+   "source": [
+    "## Jupyter notebooks\n",
+    "\n",
+    "To get these notebooks run from a shell as usual:\n",
+    "```shell\n",
+    "$ git clone https://github.com/mfherbst/juliacon_dft_workshop.git\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "permanent-syndication",
+   "metadata": {},
+   "source": [
+    "## 1. Julia dependencies\n",
+    "\n",
+    "Either instantiate the Manifest of this git repository or run the following code to install the packages needed for this workshop:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "automotive-citizen",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "using Pkg\n",
+    "Pkg.add([\n",
+    "\"DFTK\", \"DoubleFloats\", \"FiniteDiff\", \"ForwardDiff\",\n",
+    "\"GenericLinearAlgebra\", \"Infiltrator\", \"IntervalArithmetic\",\n",
+    "\"KrylovKit\", \"LineSearches\", \"NLsolve\", \"Plots\", \"PyCall\",\n",
+    "\"Unitful\", \"UnitfulAtomic\"\n",
+    "])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "baking-young",
+   "metadata": {},
+   "source": [
+    "## 2. Python dependencies\n",
+    "\n",
+    "DFTK has a python dependency, that is unfortunately required for a few tasks. We are [currently working](https://github.com/JuliaMolSim/DFTK.jl/issues/483) on switching to a pure-Julia solution, however.\n",
+    "\n",
+    "But for the moment you need to install `pymatgen`.\n",
+    "\n",
+    "- If you use `Conda.jl`, the DFTK build script has already installed this package to Julia's conda environment.\n",
+    "\n",
+    "- If you use `pip` to manage your packages, run:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "experimental-fifty",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "using PyCall\n",
+    "if !isempty(PyCall.python)\n",
+    "    run(`$(PyCall.python) -m pip install pymatgen`)\n",
+    "end"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "opponent-federal",
+   "metadata": {},
+   "source": [
+    "- If you use an external conda environment then install `pymatgen` from the `conda-forge` channel."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "american-hello",
+   "metadata": {},
+   "source": [
+    "## 3. Verify things are working\n",
+    "\n",
+    "Run this code to see the relevant packages can be found:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "stuffed-motion",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "using PyCall\n",
+    "@show pyimport(\"pymatgen\").__name__  # \"pymatgen\"\n",
+    "\n",
+    "using DFTK\n",
+    "DFTK.setup_threading()  # Prints some threading info"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Julia 1.6.1",
+   "language": "julia",
+   "name": "julia-1.6"
+  },
+  "language_info": {
+   "file_extension": ".jl",
+   "mimetype": "application/julia",
+   "name": "julia",
+   "version": "1.6.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}