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created a notebook for nist atomic weights and isotop comp source
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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)" | ||
] | ||
} | ||
], | ||
"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 | ||
} |