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 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# NIST Atomic Weights and Isotopic Compositions\n",
    "\n",
    "This [database](http://www.nist.gov/pml/data/comp.cfm) provides  atomic weights for elements 1 through 118 and isotopic compositions (abundances). Look [here](http://nist.gov/pml/data/comp-notes.cfm#comp) for the detailed description."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Initialize a database. In this document we'll be using a memory database as an example."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Initializing the database\n",
      "Ingesting basic atomic data\n"
     ]
    }
   ],
   "source": [
    "from carsus import init_db\n",
    "session = init_db(\"sqlite://\")\n",
    "session.commit()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    " Create an ingester"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from carsus.io.nist import NISTWeightsCompIngester\n",
    "ingester = NISTWeightsCompIngester()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use `download()` to download the data from the source. With the default arguments, only the data for the most common isotopes will be downloaded."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Downloading the data from http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl\n"
     ]
    }
   ],
   "source": [
    "ingester.download()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Use `ingest()` to persist the data into the database. Don't forget to commit the session!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Ingesting atomic weights\n"
     ]
    }
   ],
   "source": [
    "ingester.ingest(session)\n",
    "session.commit()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now you have the data in your database. Currently only atomic weights are supported in `carsus`. To get them you can use this query:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "symbol: H, atomic number: 1, weight: 1.007975 u\n",
      "symbol: He, atomic number: 2, weight: 4.002602 u\n",
      "symbol: Li, atomic number: 3, weight: 6.9675 u\n",
      "symbol: Be, atomic number: 4, weight: 9.0121831 u\n",
      "symbol: B, atomic number: 5, weight: 10.8135 u\n"
     ]
    }
   ],
   "source": [
    "from carsus.model import Atom, AtomicWeight\n",
    "q = session.query(Atom, AtomicWeight).join(Atom.quantities.of_type(AtomicWeight))\n",
    "for atom, weight in q[:5]:\n",
    "    print \"symbol: {}, atomic number: {}, weight: {}\".format(atom.symbol, atom.atomic_number, weight.quantity)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You can also convert quanities to different units in queries:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "symbol: H, atomic number: 1, weight: 1.67378149613e-27 kg\n",
      "symbol: He, atomic number: 2, weight: 6.6464755217e-27 kg\n",
      "symbol: Li, atomic number: 3, weight: 1.15698033922e-26 kg\n",
      "symbol: Be, atomic number: 4, weight: 1.4965078809e-26 kg\n",
      "symbol: B, atomic number: 5, weight: 1.79562352324e-26 kg\n"
     ]
    }
   ],
   "source": [
    "from astropy import units as u\n",
    "q = session.query(Atom, AtomicWeight.quantity.to(u.kg).value).\\\n",
    "    join(Atom.quantities.of_type(AtomicWeight))\n",
    "for atom, weight_value in q[:5]:\n",
    "    print \"symbol: {}, atomic number: {}, weight: {}\".format(atom.symbol, atom.atomic_number, weight_value*u.kg)"
   ]
  }
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