[yt-svn] commit/yt: ngoldbaum: Merged in ngoldbaum/yt (pull request #1255)
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Tue Oct 21 10:06:01 PDT 2014
1 new commit in yt:
https://bitbucket.org/yt_analysis/yt/commits/f75c6a2bc844/
Changeset: f75c6a2bc844
Branch: yt
User: ngoldbaum
Date: 2014-10-21 17:05:45+00:00
Summary: Merged in ngoldbaum/yt (pull request #1255)
Adding gadget example notebook
Affected #: 4 files
diff -r 297789d102982dc0dd1b6926c7d93dfd60278b9d -r f75c6a2bc84426a9fdc6da2e48d33033143d5d08 doc/source/cookbook/gadget_notebook.rst
--- /dev/null
+++ b/doc/source/cookbook/gadget_notebook.rst
@@ -0,0 +1,7 @@
+.. _gadget-notebook:
+
+Using yt to view and analyze Gadget outputs
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+.. notebook:: yt_gadget_analysis.ipynb
+
diff -r 297789d102982dc0dd1b6926c7d93dfd60278b9d -r f75c6a2bc84426a9fdc6da2e48d33033143d5d08 doc/source/cookbook/tipsy_and_yt.ipynb
--- a/doc/source/cookbook/tipsy_and_yt.ipynb
+++ b/doc/source/cookbook/tipsy_and_yt.ipynb
@@ -1,7 +1,16 @@
{
"metadata": {
+ "kernelspec": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "display_name": "IPython (Python 2)",
+ "language": "python",
+ "name": "python2"
+ },
"name": "",
- "signature": "sha256:2ae8b1599fa35495fa1bb8deb1c67094e3529e70093b30e20354122cd9403d9d"
+ "signature": "sha256:1f6e5cf50123ad75676f035a2a36cd60f4987832462907b9cb78cb25548d8afd"
},
"nbformat": 3,
"nbformat_minor": 0,
@@ -10,14 +19,6 @@
"cells": [
{
"cell_type": "heading",
- "level": 1,
- "metadata": {},
- "source": [
- "Using yt to view and analyze Tipsy outputs from Gasoline"
- ]
- },
- {
- "cell_type": "heading",
"level": 2,
"metadata": {},
"source": [
@@ -193,4 +194,4 @@
"metadata": {}
}
]
-}
+}
\ No newline at end of file
diff -r 297789d102982dc0dd1b6926c7d93dfd60278b9d -r f75c6a2bc84426a9fdc6da2e48d33033143d5d08 doc/source/cookbook/yt_gadget_analysis.ipynb
--- /dev/null
+++ b/doc/source/cookbook/yt_gadget_analysis.ipynb
@@ -0,0 +1,263 @@
+{
+ "metadata": {
+ "kernelspec": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "display_name": "IPython (Python 2)",
+ "language": "python",
+ "name": "python2"
+ },
+ "name": "",
+ "signature": "sha256:42e2b7cc4c70a501432f24bc0d62d0723605d50196399148dd365d28387dd55d"
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": [
+ {
+ "cells": [
+ {
+ "cell_type": "heading",
+ "level": 2,
+ "metadata": {},
+ "source": [
+ "Loading the data"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "First we set up our imports:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "import yt\n",
+ "import numpy as np\n",
+ "import yt.units as units\n",
+ "import pylab"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "First we load the data set, specifying both the unit length/mass/velocity, as well as the size of the bounding box (which should encapsulate all the particles in the data set)\n",
+ "\n",
+ "At the end, we flatten the data into \"ad\" in case we want access to the raw simulation data"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ ">This dataset is available for download at http://yt-project.org/data/GadgetDiskGalaxy.tar.gz (430 MB)."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "fname = 'GadgetDiskGalaxy/snapshot_200.hdf5'\n",
+ "\n",
+ "unit_base = {'UnitLength_in_cm' : 3.08568e+21,\n",
+ " 'UnitMass_in_g' : 1.989e+43,\n",
+ " 'UnitVelocity_in_cm_per_s' : 100000}\n",
+ "\n",
+ "bbox_lim = 1e5 #kpc\n",
+ "\n",
+ "bbox = [[-bbox_lim,bbox_lim],\n",
+ " [-bbox_lim,bbox_lim],\n",
+ " [-bbox_lim,bbox_lim]]\n",
+ " \n",
+ "ds = yt.load(fname,unit_base=unit_base,bounding_box=bbox)\n",
+ "ds.index\n",
+ "ad= ds.all_data()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Let's make a projection plot to look at the entire volume"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "px = yt.ProjectionPlot(ds, 'x', ('gas', 'density'))\n",
+ "px.show()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Let's print some quantities about the domain, as well as the physical properties of the simulation\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "print 'left edge: ',ds.domain_left_edge\n",
+ "print 'right edge: ',ds.domain_right_edge\n",
+ "print 'center: ',ds.domain_center"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "We can also see the fields that are available to query in the dataset"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "sorted(ds.field_list)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Let's create a data object that represents the full simulation domain, and find the total mass in gas and dark matter particles contained in it:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "ad = ds.all_data()\n",
+ "\n",
+ "# total_mass returns a list, representing the total gas and dark matter + stellar mass, respectively\n",
+ "print [tm.in_units('Msun') for tm in ad.quantities.total_mass()]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Now let's say we want to zoom in on the box (since clearly the bounding we chose initially is much larger than the volume containing the gas particles!), and center on wherever the highest gas density peak is. First, let's find this peak:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "density = ad[(\"PartType0\",\"density\")]\n",
+ "wdens = np.where(density == np.max(density))\n",
+ "coordinates = ad[(\"PartType0\",\"Coordinates\")]\n",
+ "center = coordinates[wdens][0]\n",
+ "print 'center = ',center"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Set up the box to zoom into"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "new_box_size = ds.quan(250,'code_length')\n",
+ "\n",
+ "left_edge = center - new_box_size/2\n",
+ "right_edge = center + new_box_size/2\n",
+ "\n",
+ "print new_box_size.in_units('Mpc')\n",
+ "print left_edge.in_units('Mpc')\n",
+ "print right_edge.in_units('Mpc')"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "ad2= ds.region(center=center, left_edge=left_edge, right_edge=right_edge)"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Using this new data object, let's confirm that we're only looking at a subset of the domain by first calculating thte total mass in gas and particles contained in the subvolume:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "print [tm.in_units('Msun') for tm in ad.quantities.total_mass()]"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "And then by visualizing what the new zoomed region looks like"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "collapsed": false,
+ "input": [
+ "px = yt.ProjectionPlot(ds, 'x', ('gas', 'density'), center=center, width=new_box_size)\n",
+ "px.show()"
+ ],
+ "language": "python",
+ "metadata": {},
+ "outputs": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Cool - there's a disk galaxy there!"
+ ]
+ }
+ ],
+ "metadata": {}
+ }
+ ]
+}
\ No newline at end of file
diff -r 297789d102982dc0dd1b6926c7d93dfd60278b9d -r f75c6a2bc84426a9fdc6da2e48d33033143d5d08 doc/source/examining/loading_data.rst
--- a/doc/source/examining/loading_data.rst
+++ b/doc/source/examining/loading_data.rst
@@ -983,6 +983,8 @@
onto the grid, you can also effectively mimic what your data would look like at
lower resolution.
+See :ref:`gadget-notebook` for an example.
+
.. _loading-tipsy-data:
Tipsy Data
Repository URL: https://bitbucket.org/yt_analysis/yt/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
More information about the yt-svn
mailing list