Merge pull request #8 from mishinma/nist-atomic-weights-notebook

Notebook for the NIST Atomic Weights and Isotopic Compositions

docs/index.rst

@@ -4,6 +4,11 @@ Carsus is a TARDIS support package for creating and working with atomic datasets
 
 See the :ref:`notebooks/quickstart.ipynb` for a short introduction.
 
+Supported data sources:
+-----------------------
+
+    - :ref:`notebooks/nist_weights_comp.ipynb`
+
 For more information about how to use this package, see the :ref:`api`.
 
 
@@ -13,10 +18,6 @@ Contents:
     :maxdepth: 1
 
     notebooks/quickstart.ipynb
+    notebooks/nist_weights_comp.ipynb
     api
-
-
-
-
-
-
+

docs/notebooks/nist_weights_comp.ipynb

@@ -0,0 +1,202 @@
+{
+ "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)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 2",
+   "language": "python",
+   "name": "python2"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2.0
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}