westpy_100.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This tutorial can be downloaded [link](http://greatfire.uchicago.edu/west-public/westpy/raw/master/doc/tutorials/westpy_100.ipynb)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 1.0 Getting Started: Ground State"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We are going to generate an input file for the [QuantumEspresso](https://www.quantum-espresso.org/) code or [Qbox](http://qboxcode.org/). Each code will compute the ground state electronic stucture for the methane molecule using Density Functional Theory. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 1: Load westpy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " \n",
      " _    _ _____ _____ _____            \n",
      "| |  | |  ___/  ___|_   _|           \n",
      "| |  | | |__ \\ `--.  | |_ __  _   _  \n",
      "| |/\\| |  __| `--. \\ | | '_ \\| | | | \n",
      "\\  /\\  / |___/\\__/ / | | |_) | |_| | \n",
      " \\/  \\/\\____/\\____/  \\_/ .__/ \\__, | \n",
      "                       | |     __/ | \n",
      "                       |_|    |___/  \n",
      " \n",
      "WEST version     :  3.1.1\n",
      "Today            :  2018-09-19 15:21:13.244247\n"
     ]
    }
   ],
   "source": [
    "from westpy import *"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 2: Geometry"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "geom = Geometry()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's define a cubic cell of edge 25 Bohr."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "geom.setCell((25,0,0),(0,25,0),(0,0,25))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We load the atomic positions from a XYZ file, available online. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "geom.addAtomsFromOnlineXYZ( \"http://www.west-code.org/doc/training/methane/CH4.xyz\" )"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We associate pseudopotential files to each species."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "geom.addSpecies( \"C\", \"http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf\")\n",
    "geom.addSpecies( \"H\", \"http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 3.1: Ground State"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The ground state calculation is defined by the geometry, a choice of the exchange-correlation functional, and by setting an energy cutoff for the wavefunctions. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "gs = GroundState(geom,xc=\"PBE\",ecut=40.0)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We are now able to generate the input file for QuantumEspresso."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Generated file:  pw.in\n"
     ]
    }
   ],
   "source": [
    "gs.generateInputPW()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can inspect the file pw.in"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "&CONTROL\n",
      "calculation       = 'scf'\n",
      "restart_mode      = 'from_scratch'\n",
      "pseudo_dir        = './'\n",
      "outdir            = './'\n",
      "prefix            = 'calc'\n",
      "wf_collect        = .TRUE.\n",
      "/\n",
      "&SYSTEM\n",
      "ibrav             = 0\n",
      "nat               = 5\n",
      "ntyp              = 2\n",
      "ecutwfc           = 40.0\n",
      "nbnd              = 8\n",
      "input_dft         = 'PBE'\n",
      "nosym             = .TRUE.\n",
      "noinv             = .TRUE.\n",
      "/\n",
      "&ELECTRONS\n",
      "diago_full_acc = .TRUE.\n",
      "conv_thr       = 1.d-8\n",
      "/\n",
      "ATOMIC_SPECIES\n",
      "C 12.011 C_ONCV_PBE-1.0.upf\n",
      "H 1.008 H_ONCV_PBE-1.0.upf\n",
      "ATOMIC_POSITIONS {bohr}\n",
      "C 0.0 0.0 0.0\n",
      "H 1.185992116575257 -1.185803143962673 1.185992116575257\n",
      "H -1.185992116575257 1.185992116575257 1.185992116575257\n",
      "H -1.185992116575257 -1.185992116575257 -1.185992116575257\n",
      "H 1.185992116575257 1.185992116575257 -1.185992116575257\n",
      "K_POINTS {gamma}\n",
      "CELL_PARAMETERS {bohr}\n",
      "25.0 0.0 0.0\n",
      "0.0 25.0 0.0\n",
      "0.0 0.0 25.0\n",
      "\n"
     ]
    }
   ],
   "source": [
    "with open(\"pw.in\",\"r\") as file :\n",
    "    data = file.read()\n",
    "    print(data)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can optionally also download the pseudopotentials files. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Downloaded file:  C_ONCV_PBE-1.0.upf , from url:  http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf\n",
      "Downloaded file:  H_ONCV_PBE-1.0.upf , from url:  http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf\n"
     ]
    }
   ],
   "source": [
    "gs.downloadPseudopotentials()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Step 3.2: Ground State with Qbox"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To generate the input for Qbox we can simply update Species to use the xml formats."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "gs.updateSpecies(\"C\", \"http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml\")\n",
    "gs.updateSpecies(\"H\", \"http://www.quantum-simulation.org/potentials/sg15_oncv/xml/H_ONCV_PBE-1.0.xml\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We are now able to generate the input file for QuantumEspresso."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "Generated file:  qbox.in\n"
     ]
    }
   ],
   "source": [
    "gs.generateInputQbox()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can inspect the file qbox.in"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "set cell 25.0 0.0 0.0 0.0 25.0 0.0 0.0 0.0 25.0\n",
      "species Carbon http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml\n",
      "species Hydrogen http://www.quantum-simulation.org/potentials/sg15_oncv/xml/H_ONCV_PBE-1.0.xml\n",
      "atom C1 Carbon 0.0 0.0 0.0\n",
      "atom H2 Hydrogen 1.185992116575257 -1.185803143962673 1.185992116575257\n",
      "atom H3 Hydrogen -1.185992116575257 1.185992116575257 1.185992116575257\n",
      "atom H4 Hydrogen -1.185992116575257 -1.185992116575257 -1.185992116575257\n",
      "atom H5 Hydrogen 1.185992116575257 1.185992116575257 -1.185992116575257\n",
      "set ecut 40.0\n",
      "set wf_dyn JD\n",
      "set xc PBE\n",
      "set scf_tol 1.e-8\n",
      "randomize_wf\n",
      "run -atomic_density 0 100 5\n",
      "save gs.xml\n",
      "\n"
     ]
    }
   ],
   "source": [
    "with open(\"qbox.in\",\"r\") as file :\n",
    "    data = file.read()\n",
    "    print(data)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can optionally also download the pseudopotentials files. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Downloaded file:  C_ONCV_PBE-1.0.xml , from url:  http://www.quantum-simulation.org/potentials/sg15_oncv/xml/C_ONCV_PBE-1.0.xml\n",
      "Downloaded file:  H_ONCV_PBE-1.0.xml , from url:  http://www.quantum-simulation.org/potentials/sg15_oncv/xml/H_ONCV_PBE-1.0.xml\n"
     ]
    }
   ],
   "source": [
    "gs.downloadPseudopotentials()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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