Skip to content

Instantly share code, notes, and snippets.

@jzuhone

jzuhone/Untitled7.ipynb

Created October 27, 2015 15:28
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save jzuhone/469dad66c640c2fe25e2 to your computer and use it in GitHub Desktop.
Save jzuhone/469dad66c640c2fe25e2 to your computer and use it in GitHub Desktop.
Download ZIP
Display the source blob
Display the rendered blob
Raw
Untitled7.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import yt"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"yt : [INFO ] 2015-10-27 11:27:52,955 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name\n",
"yt : [INFO ] 2015-10-27 11:27:52,956 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name\n",
"yt : [INFO ] 2015-10-27 11:27:52,972 Parameters: current_time = 7.89058001997e+16\n",
"yt : [INFO ] 2015-10-27 11:27:52,972 Parameters: domain_dimensions = [16 16 16]\n",
"yt : [INFO ] 2015-10-27 11:27:52,973 Parameters: domain_left_edge = [ -3.70272000e+24 -3.70272000e+24 -3.70272000e+24]\n",
"yt : [INFO ] 2015-10-27 11:27:52,974 Parameters: domain_right_edge = [ 3.70272000e+24 3.70272000e+24 3.70272000e+24]\n",
"yt : [INFO ] 2015-10-27 11:27:52,974 Parameters: cosmological_simulation = 0.0\n"
]
}
],
"source": [
"ds = yt.load(\"GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0100\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"yt : [INFO ] 2015-10-27 11:27:53,074 Loading field plugins.\n",
"yt : [INFO ] 2015-10-27 11:27:53,074 Loaded angular_momentum (8 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:53,075 Loaded astro (15 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:53,076 Loaded cosmology (22 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:53,077 Loaded fluid (62 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:53,078 Loaded fluid_vector (94 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:53,079 Loaded geometric (110 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:53,080 Loaded local (110 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:53,080 Loaded magnetic_field (118 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:53,081 Loaded my_plugins (118 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:53,082 Loaded species (120 new fields)\n"
]
}
],
"source": [
"sp = ds.sphere(\"c\", (500.,\"kpc\"))"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false,
"scrolled": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"yt : [INFO ] 2015-10-27 11:27:54,933 Saving field data to yt dataset: sloshing_nomag2_hdf5_plt_cnt_0100_sphere.h5.\n"
]
}
],
"source": [
"fn = sp.save_as_dataset(fields=[\"density\",\"kT\",\"velocity_x\",\"velocity_y\",\"velocity_z\"])"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"yt : [INFO ] 2015-10-27 11:27:55,371 Parameters: current_time = 7.89058001997e+16\n",
"yt : [INFO ] 2015-10-27 11:27:55,372 Parameters: domain_dimensions = [2 2 2]\n",
"yt : [INFO ] 2015-10-27 11:27:55,372 Parameters: domain_left_edge = [ -3.70272000e+24 -3.70272000e+24 -3.70272000e+24]\n",
"yt : [INFO ] 2015-10-27 11:27:55,373 Parameters: domain_right_edge = [ 3.70272000e+24 3.70272000e+24 3.70272000e+24]\n",
"yt : [INFO ] 2015-10-27 11:27:55,373 Parameters: cosmological_simulation = 0.0\n"
]
}
],
"source": [
"ds2 = yt.load(fn)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"ad = ds2.all_data()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"yt : [INFO ] 2015-10-27 11:27:55,405 Allocating for 2.450e+06 particles\n",
"yt : [INFO ] 2015-10-27 11:27:55,870 Identified 3.566e+05 octs\n",
"yt : [INFO ] 2015-10-27 11:27:56,041 Loading field plugins.\n",
"yt : [INFO ] 2015-10-27 11:27:56,041 Loaded angular_momentum (8 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:56,042 Loaded astro (15 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:56,042 Loaded cosmology (22 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:56,043 Loaded fluid (63 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:56,044 Loaded fluid_vector (95 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:56,044 Loaded geometric (111 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:56,045 Loaded local (111 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:56,045 Loaded magnetic_field (119 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:56,045 Loaded my_plugins (119 new fields)\n",
"yt : [INFO ] 2015-10-27 11:27:56,046 Loaded species (121 new fields)\n"
]
},
{
"ename": "RuntimeError",
"evalue": "Something has gone terribly wrong, _function is NullFunc for ('all', 'velocity_x')",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-7-dfa2f61eed0f>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mad\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mquantities\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mangular_momentum_vector\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/Users/jzuhone/Source/yt-py2/yt/data_objects/derived_quantities.pyc\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m 66\u001b[0m \u001b[0mstorage\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 67\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0msto\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mds\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mparallel_objects\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mchunks\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstorage\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mstorage\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 68\u001b[0;31m \u001b[0msto\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprocess_chunk\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mds\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 69\u001b[0m \u001b[0;31m# Now storage will have everything, and will be done via pickling, so\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 70\u001b[0m \u001b[0;31m# the units will be preserved. (Credit to Nathan for this\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/jzuhone/Source/yt-py2/yt/data_objects/derived_quantities.pyc\u001b[0m in \u001b[0;36mprocess_chunk\u001b[0;34m(self, data, use_gas, use_particles)\u001b[0m\n\u001b[1;32m 453\u001b[0m rvals.extend([(data[\"gas\", \"specific_angular_momentum_%s\" % axis] *\n\u001b[1;32m 454\u001b[0m data[\"gas\", \"cell_mass\"]).sum(dtype=np.float64) \\\n\u001b[0;32m--> 455\u001b[0;31m for axis in \"xyz\"])\n\u001b[0m\u001b[1;32m 456\u001b[0m \u001b[0mrvals\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"gas\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"cell_mass\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msum\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdtype\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfloat64\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 457\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0muse_particles\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/jzuhone/Source/yt-py2/yt/data_objects/data_containers.pyc\u001b[0m in \u001b[0;36m__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 258\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfield_data\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 259\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 260\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_data\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 261\u001b[0m \u001b[0;31m# fi.units is the unit expression string. We depend on the registry\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 262\u001b[0m \u001b[0;31m# hanging off the dataset to define this unit object.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/jzuhone/Source/yt-py2/yt/data_objects/data_containers.pyc\u001b[0m in \u001b[0;36mget_data\u001b[0;34m(self, fields)\u001b[0m\n\u001b[1;32m 867\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 868\u001b[0m \u001b[0mfields_to_generate\u001b[0m \u001b[0;34m+=\u001b[0m \u001b[0mgen_fluids\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mgen_particles\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 869\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_generate_fields\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfields_to_generate\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 870\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mfield\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfield_data\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mkeys\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 871\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mfield\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mofields\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/jzuhone/Source/yt-py2/yt/data_objects/data_containers.pyc\u001b[0m in \u001b[0;36m_generate_fields\u001b[0;34m(self, fields_to_generate)\u001b[0m\n\u001b[1;32m 887\u001b[0m \u001b[0mfi\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mds\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_field_info\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mfield\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 888\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 889\u001b[0;31m \u001b[0mfd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_generate_field\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfield\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 890\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mfd\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 891\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mRuntimeError\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/jzuhone/Source/yt-py2/yt/data_objects/data_containers.pyc\u001b[0m in \u001b[0;36m_generate_field\u001b[0;34m(self, field)\u001b[0m\n\u001b[1;32m 293\u001b[0m \u001b[0mtr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_generate_container_field\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfield\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 294\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mfinfo\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mparticle_type\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 295\u001b[0;31m \u001b[0mtr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_generate_particle_field\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfield\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 296\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 297\u001b[0m \u001b[0mtr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_generate_fluid_field\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfield\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/jzuhone/Source/yt-py2/yt/data_objects/data_containers.pyc\u001b[0m in \u001b[0;36m_generate_particle_field\u001b[0;34m(self, field)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_field_type_state\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mftype\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfinfo\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgen_obj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0mrv\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mds\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_field_info\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0mfield\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgen_obj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mrv\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/Users/jzuhone/Source/yt-py2/yt/fields/derived_field.pyc\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self, data)\u001b[0m\n\u001b[1;32m 175\u001b[0m raise RuntimeError(\n\u001b[1;32m 176\u001b[0m \u001b[0;34m\"Something has gone terribly wrong, _function is NullFunc \"\u001b[0m \u001b[0;34m+\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 177\u001b[0;31m \"for %s\" % (self.name,))\n\u001b[0m\u001b[1;32m 178\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0munit_registry\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 179\u001b[0m \u001b[0mdd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_function\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mRuntimeError\u001b[0m: Something has gone terribly wrong, _function is NullFunc for ('all', 'velocity_x')"
]
}
],
"source": [
"ad.quantities.angular_momentum_vector()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"language": "python",
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.10"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment