From 08157826ed2ce4cf3bb6bdd5d9cbfd5f9ab84af2 Mon Sep 17 00:00:00 2001 From: sashmish Date: Mon, 18 May 2020 19:47:43 +0530 Subject: [PATCH 1/3] update doc page to a notebook --- docs/physics/physical_quantities.ipynb | 717 +++++++++++++++++++++++++ docs/physics/physical_quantities.rst | 134 ----- 2 files changed, 717 insertions(+), 134 deletions(-) create mode 100644 docs/physics/physical_quantities.ipynb delete mode 100644 docs/physics/physical_quantities.rst diff --git a/docs/physics/physical_quantities.ipynb b/docs/physics/physical_quantities.ipynb new file mode 100644 index 00000000000..133ef67e27c --- /dev/null +++ b/docs/physics/physical_quantities.ipynb @@ -0,0 +1,717 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Accessing Physical Quantities" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "In order to compute the synthetic spectrum, Tardis must either be told\n", + "or must calculate many physical properties of the model. To understand and\n", + "test the code it can be important to look at these values. One\n", + "easy way to do this is to run Tardis in an interactive mode and then\n", + "inspect the model properties." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Runing in interactive Python session" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/Users/sashmish/anaconda3/envs/tardis/lib/python3.6/importlib/_bootstrap.py:219: QAWarning: pyne.data is not yet QA compliant.\n", + " return f(*args, **kwds)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[\u001b[1mtardis.io.atom_data.atom_web_download\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Downloading atomic data from https://media.githubusercontent.com/media/tardis-sn/tardis-refdata/master/atom_data/kurucz_cd23_chianti_H_He.h5 to /Users/sashmish/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5 (\u001b[1matom_web_download.py\u001b[0m:47)\n", + " % Total % Received % Xferd Average Speed Time Time Time Current\n", + " Dload Upload Total Spent Left Speed\n", + "100 980 100 980 0 0 1084 0 --:--:-- --:--:-- --:--:-- 1082\n" + ] + } + ], + "source": [ + "# Download the atomic data\n", + "from tardis.io.atom_data.util import download_atom_data\n", + "download_atom_data('kurucz_cd23_chianti_H_He')\n", + "\n", + "# Download the example configuration file\n", + "!curl -O https://raw.githubusercontent.com/tardis-sn/tardis/master/docs/models/examples/tardis_example.yml" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:74)\n", + "[\u001b[1mtardis.io.atom_data.util\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Atom Data kurucz_cd23_chianti_H_He.h5 not found in local path. Exists in TARDIS Data repo /Users/sashmish/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5 (\u001b[1mutil.py\u001b[0m:29)\n", + "[\u001b[1mtardis.io.atom_data.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Read Atom Data with UUID=6f7b09e887a311e7a06b246e96350010 and MD5=864f1753714343c41f99cb065710cace. (\u001b[1mbase.py\u001b[0m:184)\n", + "[\u001b[1mtardis.io.atom_data.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Non provided atomic data: synpp_refs, photoionization_data (\u001b[1mbase.py\u001b[0m:187)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 7.93730e+42 erg / s Luminosity absorbed = 2.66400e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 9926.501965 10168.422346 0.400392 0.501001\n", + "\t5 9852.611678 10367.510165 0.211205 0.186556\n", + "\t10 9779.813302 10222.882075 0.142695 0.113985\n", + "\t15 9708.082813 9928.649533 0.104556 0.085217\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9933.952 K -- next t_inner 11475.997 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 2/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.41371e+43 erg / s Luminosity absorbed = 4.73752e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 10168.422346 11497.903617 0.501001 0.545136\n", + "\t5 10367.510165 11621.417600 0.186556 0.212874\n", + "\t10 10222.882075 11335.692704 0.113985 0.135635\n", + "\t15 9928.649533 11018.841465 0.085217 0.101203\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11475.997 K -- next t_inner 9933.797 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 3/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.04734e+42 erg / s Luminosity absorbed = 2.55640e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 11497.903617 10477.653343 0.545136 0.439296\n", + "\t5 11621.417600 10856.518852 0.212874 0.159058\n", + "\t10 11335.692704 10635.474976 0.135635 0.100253\n", + "\t15 11018.841465 10290.254692 0.101203 0.075529\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9933.797 K -- next t_inner 11397.084 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 4/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.38199e+43 erg / s Luminosity absorbed = 4.54590e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 10477.653343 11608.211738 0.439296 0.506501\n", + "\t5 10856.518852 11859.259666 0.159058 0.192802\n", + "\t10 10635.474976 11479.604579 0.100253 0.125779\n", + "\t15 10290.254692 11149.192411 0.075529 0.094052\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11397.084 K -- next t_inner 9978.058 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 5/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.16431e+42 erg / s Luminosity absorbed = 2.62454e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 11608.211738 10556.913414 0.506501 0.440229\n", + "\t5 11859.259666 11021.144022 0.192802 0.153136\n", + "\t10 11479.604579 10713.104080 0.125779 0.099268\n", + "\t15 11149.192411 10399.079825 0.094052 0.073482\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9978.058 K -- next t_inner 11365.561 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 6/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.36136e+43 erg / s Luminosity absorbed = 4.54590e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 10556.913414 11562.006340 0.440229 0.509603\n", + "\t5 11021.144022 11799.980145 0.153136 0.194437\n", + "\t10 10713.104080 11482.742597 0.099268 0.124721\n", + "\t15 10399.079825 11124.799749 0.073482 0.093597\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11365.561 K -- next t_inner 10025.564 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 7/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.33278e+42 erg / s Luminosity absorbed = 2.66283e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 11562.006340 10655.549804 0.509603 0.430187\n", + "\t5 11799.980145 11063.665621 0.194437 0.155127\n", + "\t10 11482.742597 10926.058943 0.124721 0.094642\n", + "\t15 11124.799749 10477.041314 0.093597 0.072578\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10025.564 K -- next t_inner 11303.643 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 8/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.34650e+43 erg / s Luminosity absorbed = 4.30670e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 10655.549804 11572.119736 0.430187 0.496558\n", + "\t5 11063.665621 11696.304249 0.155127 0.198228\n", + "\t10 10926.058943 11482.609682 0.094642 0.124382\n", + "\t15 10477.041314 11098.080451 0.072578 0.093537\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11303.643 K -- next t_inner 10025.810 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 9/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.36983e+42 erg / s Luminosity absorbed = 2.63049e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 11572.119736 10590.775937 0.496558 0.439574\n", + "\t5 11696.304249 11060.842307 0.198228 0.154917\n", + "\t10 11482.609682 10761.665022 0.124382 0.099840\n", + "\t15 11098.080451 10436.629671 0.093537 0.074676\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10025.810 K -- next t_inner 11278.874 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 10/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.32624e+43 erg / s Luminosity absorbed = 4.34986e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 10590.775937 11489.769556 0.439574 0.511403\n", + "\t5 11060.842307 11791.517605 0.154917 0.191127\n", + "\t10 10761.665022 11527.732208 0.099840 0.120106\n", + "\t15 10436.629671 11111.114390 0.074676 0.091713\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11278.874 K -- next t_inner 10079.967 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 11/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.51915e+42 erg / s Luminosity absorbed = 2.72009e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 11489.769556 10664.234475 0.511403 0.437272\n", + "\t5 11791.517605 11091.518839 0.191127 0.156638\n", + "\t10 11527.732208 10885.771059 0.120106 0.096973\n", + "\t15 11111.114390 10484.177251 0.091713 0.074261\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10079.967 K -- next t_inner 11239.980 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 12/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.30886e+43 erg / s Luminosity absorbed = 4.28617e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 10664.234475 11510.842068 0.437272 0.495944\n", + "\t5 11091.518839 11716.009425 0.156638 0.189856\n", + "\t10 10885.771059 11479.636914 0.096973 0.120067\n", + "\t15 10484.177251 11117.963837 0.074261 0.090628\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11239.980 K -- next t_inner 10111.668 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 13/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.65047e+42 erg / s Luminosity absorbed = 2.72874e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 11510.842068 10636.025493 0.495944 0.446635\n", + "\t5 11716.009425 11175.711706 0.189856 0.154916\n", + "\t10 11479.636914 10916.188023 0.120067 0.097843\n", + "\t15 11117.963837 10431.720831 0.090628 0.077032\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10111.668 K -- next t_inner 11189.420 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 14/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.28712e+43 erg / s Luminosity absorbed = 4.19242e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 10636.025493 11423.118214 0.446635 0.503706\n", + "\t5 11175.711706 11682.224028 0.154916 0.189577\n", + "\t10 10916.188023 11389.994295 0.097843 0.121114\n", + "\t15 10431.720831 11029.450833 0.077032 0.091350\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11189.420 K -- next t_inner 10150.866 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 15/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.76501e+42 erg / s Luminosity absorbed = 2.79433e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 11423.118214 10634.831735 0.503706 0.452948\n", + "\t5 11682.224028 11112.411355 0.189577 0.159316\n", + "\t10 11389.994295 10831.887277 0.121114 0.101805\n", + "\t15 11029.450833 10396.372864 0.091350 0.078776\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10150.866 K -- next t_inner 11159.164 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 16/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.27462e+43 erg / s Luminosity absorbed = 4.13373e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 10634.831735 11415.925493 0.452948 0.501153\n", + "\t5 11112.411355 11688.667754 0.159316 0.188430\n", + "\t10 10831.887277 11397.519913 0.101805 0.120134\n", + "\t15 10396.372864 11045.200458 0.078776 0.090180\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11159.164 K -- next t_inner 10172.913 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 17/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.86785e+42 erg / s Luminosity absorbed = 2.79094e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 11415.925493 10678.510651 0.501153 0.453127\n", + "\t5 11688.667754 11152.822099 0.188430 0.159726\n", + "\t10 11397.519913 10907.112682 0.120134 0.099725\n", + "\t15 11045.200458 10508.816973 0.090180 0.076667\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10172.913 K -- next t_inner 11118.359 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 18/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.24749e+43 erg / s Luminosity absorbed = 4.15445e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 10678.510651 11482.446420 0.453127 0.481917\n", + "\t5 11152.822099 11693.549165 0.159726 0.184456\n", + "\t10 10907.112682 11472.013555 0.099725 0.115208\n", + "\t15 10508.816973 10997.309982 0.076667 0.089730\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11118.359 K -- next t_inner 10245.337 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 19/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 9.09476e+42 erg / s Luminosity absorbed = 2.89713e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", + "\t t_rad next_t_rad w next_w\n", + "\tShell \n", + "\t0 11482.446420 10834.729769 0.481917 0.438322\n", + "\t5 11693.549165 11346.133670 0.184456 0.154204\n", + "\t10 11472.013555 10996.421420 0.115208 0.099677\n", + "\t15 10997.309982 10625.479432 0.089730 0.075531\n", + "\n", + " (\u001b[1mbase.py\u001b[0m:351)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10245.337 K -- next t_inner 11056.949 K (\u001b[1mbase.py\u001b[0m:353)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 20/20 (\u001b[1mbase.py\u001b[0m:269)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.22623e+43 erg / s Luminosity absorbed = 4.00603e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 20 iterations and took 21.97 s (\u001b[1mbase.py\u001b[0m:309)\n" + ] + } + ], + "source": [ + "from tardis import run_tardis\n", + "\n", + "model = run_tardis('tardis_example.yml')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "If all goes well, the simulation should run as usual. Afterwards, the\n", + "information from the simulation will all exist in `Radial1D` and\n", + "can be examined.\n", + "Some examples for useful/interesting quantities are\n", + "given below (but much more information is available: contact us via \n", + "[tardis-sn-users](http://groups.google.com/forum/#!forum/tardis-sn-users) if you need\n", + "further help)." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Examples of finding physical quantities" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "For example, two of our important quantities are the parameters of the\n", + "radiation field model, $T_{\\rm rad}$ and $W$. These exist\n", + "as Astropy [Quantities](http://astropy.readthedocs.org/en/v0.2.1/_generated/astropy.units.quantity.Quantity.html). \n", + "\n", + "Thus `model.t_rad.cgs` will give you a list of the $T_{\\rm rad}$-values for the model zones in cgs units." + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Simulation' object has no attribute 't_rad'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mt_rad\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 't_rad'" + ] + } + ], + "source": [ + "model.t_rad.cgs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "To obtain an array of the values (without units) use `model.t_rad.cgs.value`" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Quantity' object has no 'values' member", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mt_rad\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;32m~/anaconda3/envs/tardis/lib/python3.6/site-packages/astropy/units/quantity.py\u001b[0m in \u001b[0;36m__getattr__\u001b[0;34m(self, attr)\u001b[0m\n\u001b[1;32m 817\u001b[0m \"'{0}' object has no '{1}' member\".format(\n\u001b[1;32m 818\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__name__\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 819\u001b[0;31m attr))\n\u001b[0m\u001b[1;32m 820\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 821\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mget_virtual_unit_attribute\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[0;31mAttributeError\u001b[0m: 'Quantity' object has no 'values' member" + ] + } + ], + "source": [ + "model.model.t_rad.cgs.values" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Similarly, the $W$-values can be accessed using `model.ws.cgs`" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Simulation' object has no attribute 'ws'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mws\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'ws'" + ] + } + ], + "source": [ + "model.ws.cgs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Several important quantities that were setup when the model was defined by the configuration file are located in the `tardis_config` section. For example, the inner and outer velocity boundaries of the zones in the model is given by `model.tardis_config.structure.v_inner.cgs` and `model.tardis_config.structure.v_outer.cgs` respectively." + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Simulation' object has no attribute 'tardis_config'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtardis_config\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_inner\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'tardis_config'" + ] + } + ], + "source": [ + "model.tardis_config.structure.v_inner.cgs" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Simulation' object has no attribute 'tardis_config'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtardis_config\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_inner\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'tardis_config'" + ] + } + ], + "source": [ + "model.tardis_config.structure.v_inner.cgs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The average density in the zones is given by `model.tardis_config.structure.mean_densities.cgs`" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Simulation' object has no attribute 'tardis_config'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtardis_config\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmean_densities\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'tardis_config'" + ] + } + ], + "source": [ + "model.tardis_config.structure.mean_densities.cgs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Many other interesting quantities are stored in the โ€œplasma_arrayโ€.\n", + "For example the calculated ion populations and level populations is given by `model.plasma_array.ion_populations` and `model.plasma_array.level_populations` respectively." + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Simulation' object has no attribute 'plasma_array'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplasma_array\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mion_populations\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'plasma_array'" + ] + } + ], + "source": [ + "model.plasma_array.ion_populations" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Simulation' object has no attribute 'plasma_array'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplasma_array\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlevel_populations\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'plasma_array'" + ] + } + ], + "source": [ + "model.plasma_array.level_populations" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "These are stored as Pandas `DataFrames`. An index can be supplied to obtain the population in a particular zone. E.g., for the ion populations of the innermost zone (index = 0), we will use \n", + "`model.plasma_array.ion_populations[0]`" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Simulation' object has no attribute 'plasma_array'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplasma_array\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mion_populations\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'plasma_array'" + ] + } + ], + "source": [ + "model.plasma_array.ion_populations[0]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Ion populations for a particular ionization stage of a particular element can be accessed by specifying an appropriate tuple (๐‘,๐ถ), which identifies the element (via atomic number ๐‘ ) and the charge (via the ion charge ๐ถ ). Thus, `model.plasma_array.ion_populations.ix[(14,1)]` will identify the ion popuations for Si II (๐‘=14,๐ถ=1) in all the zones. " + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Radial1DModel' object has no attribute 'plasma_array'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplasma_array\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mion_populations\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mix\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m14\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m1\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[0m", + "\u001b[0;31mAttributeError\u001b[0m: 'Radial1DModel' object has no attribute 'plasma_array'" + ] + } + ], + "source": [ + "model.plasma_array.ion_populations.ix[(14,1)]" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "dict_keys(['optional_hdf_properties', '_v_boundary_inner', '_v_boundary_outer', '_velocity', 'raw_velocity', 'homologous_density', '_abundance', 'time_explosion', '_electron_densities', 'raw_abundance', 'raw_isotope_abundance', 't_inner', '_t_radiative', '_dilution_factor'])" + ] + }, + "execution_count": 29, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "model.model.__dict__.keys()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The above examples can be combined to obtain e.g. the Si II population in the innermost zone\n", + "can be obtained by\n", + "`model.plasma_array.ion_populations[0].ix[(14,1)]`" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "model.plasma_array.ion_populations[0].ix[(14,1)]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The level populations are stored (and can be accessed) in a similar way - a third label can be used to pick out a particular atomic level. E.g., to pull out the population of the ground state (index 0) of Si II we can use `model.plasma_array.level_populations.ix[(14,1,0)]`" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "ename": "AttributeError", + "evalue": "'Simulation' object has no attribute 'plasma_array'", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplasma_array\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlevel_populations\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mix\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m14\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m0\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[0m", + "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'plasma_array'" + ] + } + ], + "source": [ + "model.plasma_array.level_populations.ix[(14,1,0)]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Notes\n", + "- If you prefer to work in SI units, all the astropy Quantities may instead by accessed with โ€œxxx.siโ€.\n", + "\n", + "- Information that is not stored as astropy Quantities (e.g. the ion an level populations used in the example above) are usually stored in cgs units (i.e. cmโˆ’3 for the populations)." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.7" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/docs/physics/physical_quantities.rst b/docs/physics/physical_quantities.rst deleted file mode 100644 index b0c4081ce9b..00000000000 --- a/docs/physics/physical_quantities.rst +++ /dev/null @@ -1,134 +0,0 @@ -.. _physical_quantities: - -***************************** -Accessing Physical Quantities -***************************** - -In order to compute the synthetic spectrum, Tardis must either be told -or must calculate many physical properties of the model. To understand and -test the code it can be important to look at these values. One -easy way to do this is to run Tardis in an interactive mode and then -inspect the model properties. - - -Runing in interactive Python session ------------------------------------- - -With iPython installed launch a session using - -.. code-block:: none - - ipython --pylab - -and then run your calculation, which is based on your "my_config.yml" file - -.. code-block:: python - - from tardis import run_tardis - - - model = run_tardis('myconfig.yml') - - -If all goes well, the simulation should run as usual. Afterwards, the -information from the simulation will all exist in "radial1d" and -can be examined. Some examples for useful/interesting quantities are -given below (but much more information is available: contact us via -`tardis-sn-users `_ if you need -further help). - -Examples of finding physical quantities ---------------------------------------- - -For example, two of our important quantities are the parameters of the -radiation field model, :math:`T_{\rm rad}` and :math:`W`. These exist -as Astropy `Quantities `_. Thus - -.. code-block:: python - - model.t_rad.cgs - -will give you a list of the :math:`T_{\rm rad}`-values for the model zones -in cgs units. To obtain an array of the values (without units) use - -.. code-block:: python - - model.t_rad.cgs.value - -Similarly, the :math:`W`-values can be accessed using - -.. code-block:: python - - model.ws.cgs - - -Several important quantities that were setup when the model was defined -by the configuration file are located in the "tardis_config" -section. For example, the inner and outer velocity boundaries of the -zones in the model - -.. code-block:: python - - model.tardis_config.structure.v_inner.cgs - model.tardis_config.structure.v_outer.cgs - -and the average density in the zones - -.. code-block:: python - - model.tardis_config.structure.mean_densities.cgs - -Many other interesting quantities are stored in the -"plasma_array". For example the calculated ion populations or level -populations: - -.. code-block:: python - - model.plasma_array.ion_populations - model.plasma_array.level_populations - -These are stored as Pandas `DataFrames -`_. -An index can be supplied to obtain the population in a particular -zone. E.g., for the ion populations of the innermost zone (index = 0) - -.. code-block:: python - - model.plasma_array.ion_populations[0] - -Ion populations for a particular ionization stage of a particular -element can be accessed by specifying an appropriate tuple :math:`(Z,C)`, which -identifies the element (via atomic number :math:`Z` ) and the charge -(via the ion charge :math:`C` ). Thus, - -.. code-block:: python - - model.plasma_array.ion_populations.ix[(14,1)] - -will identify the ion popuations for Si II (:math:`Z=14, C=1`) in all -the zones. The above examples can be combined to obtain e.g. the Si II -population in the innermost zone - -.. code-block:: python - - model.plasma_array.ion_populations[0].ix[(14,1)] - -The level populations are stored (and can be accessed) in a similar -way - a third label can be used to pick out a particular atomic -level. E.g., to pull out the population of the ground state (index 0) -of Si II - -.. code-block:: python - - model.plasma_array.level_populations.ix[(14,1,0)] - -.. note:: - - If you prefer to work in SI units, all the astropy Quantities may - instead by accessed with "xxx.si". - -.. note:: - - Information that is not stored as astropy Quantities (e.g. the ion - an level populations used in the example above) are usually stored - in cgs units (i.e. :math:`{\rm cm}^{-3}` for the populations). From 6af1e1a5b978231474ba4e73d080fa67d6b13997 Mon Sep 17 00:00:00 2001 From: sashmish Date: Sun, 24 May 2020 01:07:40 +0530 Subject: [PATCH 2/3] fix errors --- docs/physics/physical_quantities.ipynb | 4519 ++++++++++++++++++++++-- 1 file changed, 4269 insertions(+), 250 deletions(-) diff --git a/docs/physics/physical_quantities.ipynb b/docs/physics/physical_quantities.ipynb index 133ef67e27c..3b40f813ebd 100644 --- a/docs/physics/physical_quantities.ipynb +++ b/docs/physics/physical_quantities.ipynb @@ -45,7 +45,7 @@ "[\u001b[1mtardis.io.atom_data.atom_web_download\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Downloading atomic data from https://media.githubusercontent.com/media/tardis-sn/tardis-refdata/master/atom_data/kurucz_cd23_chianti_H_He.h5 to /Users/sashmish/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5 (\u001b[1matom_web_download.py\u001b[0m:47)\n", " % Total % Received % Xferd Average Speed Time Time Time Current\n", " Dload Upload Total Spent Left Speed\n", - "100 980 100 980 0 0 1084 0 --:--:-- --:--:-- --:--:-- 1082\n" + "100 980 100 980 0 0 4600 0 --:--:-- --:--:-- --:--:-- 4600\n" ] } ], @@ -71,8 +71,8 @@ "[\u001b[1mtardis.io.atom_data.util\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Atom Data kurucz_cd23_chianti_H_He.h5 not found in local path. Exists in TARDIS Data repo /Users/sashmish/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5 (\u001b[1mutil.py\u001b[0m:29)\n", "[\u001b[1mtardis.io.atom_data.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Read Atom Data with UUID=6f7b09e887a311e7a06b246e96350010 and MD5=864f1753714343c41f99cb065710cace. (\u001b[1mbase.py\u001b[0m:184)\n", "[\u001b[1mtardis.io.atom_data.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Non provided atomic data: synpp_refs, photoionization_data (\u001b[1mbase.py\u001b[0m:187)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 7.93730e+42 erg / s Luminosity absorbed = 2.66400e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 7.93730e+42 erg / s Luminosity absorbed = 2.66400e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -81,10 +81,10 @@ "\t10 9779.813302 10222.882075 0.142695 0.113985\n", "\t15 9708.082813 9928.649533 0.104556 0.085217\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9933.952 K -- next t_inner 11475.997 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 2/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.41371e+43 erg / s Luminosity absorbed = 4.73752e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9933.952 K -- next t_inner 11475.997 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 2/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.41371e+43 erg / s Luminosity absorbed = 4.73752e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -93,10 +93,10 @@ "\t10 10222.882075 11335.692704 0.113985 0.135635\n", "\t15 9928.649533 11018.841465 0.085217 0.101203\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11475.997 K -- next t_inner 9933.797 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 3/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.04734e+42 erg / s Luminosity absorbed = 2.55640e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11475.997 K -- next t_inner 9933.797 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 3/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.04734e+42 erg / s Luminosity absorbed = 2.55640e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -105,10 +105,10 @@ "\t10 11335.692704 10635.474976 0.135635 0.100253\n", "\t15 11018.841465 10290.254692 0.101203 0.075529\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9933.797 K -- next t_inner 11397.084 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 4/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.38199e+43 erg / s Luminosity absorbed = 4.54590e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9933.797 K -- next t_inner 11397.084 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 4/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.38199e+43 erg / s Luminosity absorbed = 4.54590e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -117,10 +117,10 @@ "\t10 10635.474976 11479.604579 0.100253 0.125779\n", "\t15 10290.254692 11149.192411 0.075529 0.094052\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11397.084 K -- next t_inner 9978.058 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 5/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.16431e+42 erg / s Luminosity absorbed = 2.62454e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11397.084 K -- next t_inner 9978.058 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 5/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.16431e+42 erg / s Luminosity absorbed = 2.62454e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -129,10 +129,10 @@ "\t10 11479.604579 10713.104080 0.125779 0.099268\n", "\t15 11149.192411 10399.079825 0.094052 0.073482\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9978.058 K -- next t_inner 11365.561 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 6/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.36136e+43 erg / s Luminosity absorbed = 4.54590e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 9978.058 K -- next t_inner 11365.561 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 6/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.36136e+43 erg / s Luminosity absorbed = 4.54590e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -141,10 +141,10 @@ "\t10 10713.104080 11482.742597 0.099268 0.124721\n", "\t15 10399.079825 11124.799749 0.073482 0.093597\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11365.561 K -- next t_inner 10025.564 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 7/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.33278e+42 erg / s Luminosity absorbed = 2.66283e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11365.561 K -- next t_inner 10025.564 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 7/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.33278e+42 erg / s Luminosity absorbed = 2.66283e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -153,10 +153,10 @@ "\t10 11482.742597 10926.058943 0.124721 0.094642\n", "\t15 11124.799749 10477.041314 0.093597 0.072578\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10025.564 K -- next t_inner 11303.643 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 8/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.34650e+43 erg / s Luminosity absorbed = 4.30670e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10025.564 K -- next t_inner 11303.643 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 8/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.34650e+43 erg / s Luminosity absorbed = 4.30670e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -165,10 +165,10 @@ "\t10 10926.058943 11482.609682 0.094642 0.124382\n", "\t15 10477.041314 11098.080451 0.072578 0.093537\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11303.643 K -- next t_inner 10025.810 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 9/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.36983e+42 erg / s Luminosity absorbed = 2.63049e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11303.643 K -- next t_inner 10025.810 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 9/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.36983e+42 erg / s Luminosity absorbed = 2.63049e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -177,16 +177,16 @@ "\t10 11482.609682 10761.665022 0.124382 0.099840\n", "\t15 11098.080451 10436.629671 0.093537 0.074676\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n" + " (\u001b[1mbase.py\u001b[0m:350)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10025.810 K -- next t_inner 11278.874 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 10/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.32624e+43 erg / s Luminosity absorbed = 4.34986e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10025.810 K -- next t_inner 11278.874 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 10/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.32624e+43 erg / s Luminosity absorbed = 4.34986e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -195,10 +195,10 @@ "\t10 10761.665022 11527.732208 0.099840 0.120106\n", "\t15 10436.629671 11111.114390 0.074676 0.091713\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11278.874 K -- next t_inner 10079.967 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 11/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.51915e+42 erg / s Luminosity absorbed = 2.72009e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11278.874 K -- next t_inner 10079.967 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 11/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.51915e+42 erg / s Luminosity absorbed = 2.72009e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -207,10 +207,10 @@ "\t10 11527.732208 10885.771059 0.120106 0.096973\n", "\t15 11111.114390 10484.177251 0.091713 0.074261\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10079.967 K -- next t_inner 11239.980 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 12/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.30886e+43 erg / s Luminosity absorbed = 4.28617e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10079.967 K -- next t_inner 11239.980 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 12/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.30886e+43 erg / s Luminosity absorbed = 4.28617e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -219,10 +219,10 @@ "\t10 10885.771059 11479.636914 0.096973 0.120067\n", "\t15 10484.177251 11117.963837 0.074261 0.090628\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11239.980 K -- next t_inner 10111.668 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 13/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.65047e+42 erg / s Luminosity absorbed = 2.72874e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11239.980 K -- next t_inner 10111.668 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 13/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.65047e+42 erg / s Luminosity absorbed = 2.72874e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -231,10 +231,10 @@ "\t10 11479.636914 10916.188023 0.120067 0.097843\n", "\t15 11117.963837 10431.720831 0.090628 0.077032\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10111.668 K -- next t_inner 11189.420 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 14/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.28712e+43 erg / s Luminosity absorbed = 4.19242e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10111.668 K -- next t_inner 11189.420 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 14/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.28712e+43 erg / s Luminosity absorbed = 4.19242e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -243,10 +243,10 @@ "\t10 10916.188023 11389.994295 0.097843 0.121114\n", "\t15 10431.720831 11029.450833 0.077032 0.091350\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11189.420 K -- next t_inner 10150.866 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 15/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.76501e+42 erg / s Luminosity absorbed = 2.79433e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11189.420 K -- next t_inner 10150.866 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 15/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.76501e+42 erg / s Luminosity absorbed = 2.79433e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -255,10 +255,10 @@ "\t10 11389.994295 10831.887277 0.121114 0.101805\n", "\t15 11029.450833 10396.372864 0.091350 0.078776\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10150.866 K -- next t_inner 11159.164 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 16/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.27462e+43 erg / s Luminosity absorbed = 4.13373e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10150.866 K -- next t_inner 11159.164 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 16/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.27462e+43 erg / s Luminosity absorbed = 4.13373e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -267,10 +267,10 @@ "\t10 10831.887277 11397.519913 0.101805 0.120134\n", "\t15 10396.372864 11045.200458 0.078776 0.090180\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11159.164 K -- next t_inner 10172.913 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 17/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.86785e+42 erg / s Luminosity absorbed = 2.79094e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11159.164 K -- next t_inner 10172.913 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 17/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 8.86785e+42 erg / s Luminosity absorbed = 2.79094e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -279,10 +279,10 @@ "\t10 11397.519913 10907.112682 0.120134 0.099725\n", "\t15 11045.200458 10508.816973 0.090180 0.076667\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10172.913 K -- next t_inner 11118.359 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 18/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.24749e+43 erg / s Luminosity absorbed = 4.15445e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10172.913 K -- next t_inner 11118.359 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 18/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.24749e+43 erg / s Luminosity absorbed = 4.15445e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -291,10 +291,10 @@ "\t10 10907.112682 11472.013555 0.099725 0.115208\n", "\t15 10508.816973 10997.309982 0.076667 0.089730\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11118.359 K -- next t_inner 10245.337 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 19/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 9.09476e+42 erg / s Luminosity absorbed = 2.89713e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", + " (\u001b[1mbase.py\u001b[0m:350)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 11118.359 K -- next t_inner 10245.337 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 19/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 9.09476e+42 erg / s Luminosity absorbed = 2.89713e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Plasma stratification:\n", "\t t_rad next_t_rad w next_w\n", "\tShell \n", @@ -303,24 +303,24 @@ "\t10 11472.013555 10996.421420 0.115208 0.099677\n", "\t15 10997.309982 10625.479432 0.089730 0.075531\n", "\n", - " (\u001b[1mbase.py\u001b[0m:351)\n" + " (\u001b[1mbase.py\u001b[0m:350)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10245.337 K -- next t_inner 11056.949 K (\u001b[1mbase.py\u001b[0m:353)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 20/20 (\u001b[1mbase.py\u001b[0m:269)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.22623e+43 erg / s Luminosity absorbed = 4.00603e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:360)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 20 iterations and took 21.97 s (\u001b[1mbase.py\u001b[0m:309)\n" + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10245.337 K -- next t_inner 11056.949 K (\u001b[1mbase.py\u001b[0m:352)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 20/20 (\u001b[1mbase.py\u001b[0m:268)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.22623e+43 erg / s Luminosity absorbed = 4.00603e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 20 iterations and took 27.14 s (\u001b[1mbase.py\u001b[0m:308)\n" ] } ], "source": [ "from tardis import run_tardis\n", "\n", - "model = run_tardis('tardis_example.yml')" + "simulation = run_tardis('tardis_example.yml')" ] }, { @@ -328,7 +328,7 @@ "metadata": {}, "source": [ "If all goes well, the simulation should run as usual. Afterwards, the\n", - "information from the simulation will all exist in `Radial1D` and\n", + "information from the simulation will all exist in `Simulation` and\n", "can be examined.\n", "Some examples for useful/interesting quantities are\n", "given below (but much more information is available: contact us via \n", @@ -348,215 +348,4140 @@ "metadata": {}, "source": [ "For example, two of our important quantities are the parameters of the\n", - "radiation field model, $T_{\\rm rad}$ and $W$. These exist\n", - "as Astropy [Quantities](http://astropy.readthedocs.org/en/v0.2.1/_generated/astropy.units.quantity.Quantity.html). \n", + "radiation field model, $T_{\\rm rad}$ and $W$. These exist as `numpy.ndarray`\n", "\n", - "Thus `model.t_rad.cgs` will give you a list of the $T_{\\rm rad}$-values for the model zones in cgs units." + "Thus `simulation.plasma.t_rad` will give you a list of the $T_{\\rm rad}$-values for the model zones in cgs units." ] }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 3, "metadata": {}, "outputs": [ { - "ename": "AttributeError", - "evalue": "'Simulation' object has no attribute 't_rad'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mt_rad\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 't_rad'" - ] - } - ], - "source": [ - "model.t_rad.cgs" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "To obtain an array of the values (without units) use `model.t_rad.cgs.value`" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": {}, - "outputs": [ - { - "ename": "AttributeError", - "evalue": "'Quantity' object has no 'values' member", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mt_rad\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m~/anaconda3/envs/tardis/lib/python3.6/site-packages/astropy/units/quantity.py\u001b[0m in \u001b[0;36m__getattr__\u001b[0;34m(self, attr)\u001b[0m\n\u001b[1;32m 817\u001b[0m \"'{0}' object has no '{1}' member\".format(\n\u001b[1;32m 818\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__name__\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 819\u001b[0;31m attr))\n\u001b[0m\u001b[1;32m 820\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 821\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mget_virtual_unit_attribute\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[0;31mAttributeError\u001b[0m: 'Quantity' object has no 'values' member" - ] + "data": { + "text/plain": [ + "array([10834.7297692 , 11024.52012206, 11134.85912792, 11299.31893687,\n", + " 11304.06901637, 11346.13367044, 11273.8729839 , 11201.3282228 ,\n", + " 11080.35051086, 11053.1815164 , 10996.42142 , 10906.50207322,\n", + " 10852.60134857, 10768.23991178, 10701.07288864, 10625.47943241,\n", + " 10578.25968193, 10462.71630881, 10328.2464022 , 10198.53837217])" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "model.model.t_rad.cgs.values" + "simulation.plasma.t_rad" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "Similarly, the $W$-values can be accessed using `model.ws.cgs`" + "Similarly, the $W$-values can be accessed using `simulation.plasma.w`" ] }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 4, "metadata": {}, "outputs": [ { - "ename": "AttributeError", - "evalue": "'Simulation' object has no attribute 'ws'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mws\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'ws'" - ] + "data": { + "text/plain": [ + "array([0.43832195, 0.32677702, 0.26128919, 0.20770296, 0.17725587,\n", + " 0.15420374, 0.1387194 , 0.1264399 , 0.11830376, 0.10744254,\n", + " 0.09967675, 0.09360326, 0.08756804, 0.08325674, 0.07930315,\n", + " 0.07553141, 0.07138798, 0.06935054, 0.06784402, 0.06650938])" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "model.ws.cgs" + "simulation.plasma.w" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "Several important quantities that were setup when the model was defined by the configuration file are located in the `tardis_config` section. For example, the inner and outer velocity boundaries of the zones in the model is given by `model.tardis_config.structure.v_inner.cgs` and `model.tardis_config.structure.v_outer.cgs` respectively." + "Several important quantities that were setup when the model was defined by the configuration file are located in the `model` section of the simulation. For example, the inner and outer velocity boundaries of the zones in the model is given by `simulation.model.v_inner.cgs` and `simulation.model.v_outer.cgs` respectively." ] }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 5, "metadata": {}, "outputs": [ { - "ename": "AttributeError", - "evalue": "'Simulation' object has no attribute 'tardis_config'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtardis_config\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_inner\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'tardis_config'" - ] + "data": { + "text/latex": [ + "$[1.1 \\times 10^{9},~1.145 \\times 10^{9},~1.19 \\times 10^{9},~1.235 \\times 10^{9},~1.28 \\times 10^{9},~1.325 \\times 10^{9},~1.37 \\times 10^{9},~1.415 \\times 10^{9},~1.46 \\times 10^{9},~1.505 \\times 10^{9},~1.55 \\times 10^{9},~1.595 \\times 10^{9},~1.64 \\times 10^{9},~1.685 \\times 10^{9},~1.73 \\times 10^{9},~1.775 \\times 10^{9},~1.82 \\times 10^{9},~1.865 \\times 10^{9},~1.91 \\times 10^{9},~1.955 \\times 10^{9}] \\; \\mathrm{\\frac{cm}{s}}$" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "model.tardis_config.structure.v_inner.cgs" + "simulation.model.v_inner.cgs" ] }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 6, "metadata": {}, "outputs": [ { - "ename": "AttributeError", - "evalue": "'Simulation' object has no attribute 'tardis_config'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtardis_config\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_inner\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'tardis_config'" - ] + "data": { + "text/latex": [ + "$[1.145 \\times 10^{9},~1.19 \\times 10^{9},~1.235 \\times 10^{9},~1.28 \\times 10^{9},~1.325 \\times 10^{9},~1.37 \\times 10^{9},~1.415 \\times 10^{9},~1.46 \\times 10^{9},~1.505 \\times 10^{9},~1.55 \\times 10^{9},~1.595 \\times 10^{9},~1.64 \\times 10^{9},~1.685 \\times 10^{9},~1.73 \\times 10^{9},~1.775 \\times 10^{9},~1.82 \\times 10^{9},~1.865 \\times 10^{9},~1.91 \\times 10^{9},~1.955 \\times 10^{9},~2 \\times 10^{9}] \\; \\mathrm{\\frac{cm}{s}}$" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "model.tardis_config.structure.v_inner.cgs" + "simulation.model.v_outer.cgs" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "The average density in the zones is given by `model.tardis_config.structure.mean_densities.cgs`" + "The average density in the zones is given by `simulation.model.density.cgs`" ] }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 7, "metadata": {}, "outputs": [ { - "ename": "AttributeError", - "evalue": "'Simulation' object has no attribute 'tardis_config'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtardis_config\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmean_densities\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcgs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'tardis_config'" - ] + "data": { + "text/latex": [ + "$[7.5428036 \\times 10^{-14},~5.728475 \\times 10^{-14},~4.3960742 \\times 10^{-14},~3.4062874 \\times 10^{-14},~2.6631346 \\times 10^{-14},~2.0995965 \\times 10^{-14},~1.6682872 \\times 10^{-14},~1.3353105 \\times 10^{-14},~1.0761538 \\times 10^{-14},~8.7290848 \\times 10^{-15},~7.1236516 \\times 10^{-15},~5.8469209 \\times 10^{-15},~4.8250928 \\times 10^{-15},~4.0023242 \\times 10^{-15},~3.3360386 \\times 10^{-15},~2.7935404 \\times 10^{-15},~2.3495504 \\times 10^{-15},~1.9843968 \\times 10^{-15},~1.6826769 \\times 10^{-15},~1.4322598 \\times 10^{-15}] \\; \\mathrm{\\frac{g}{cm^{3}}}$" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "model.tardis_config.structure.mean_densities.cgs" + "simulation.model.density.cgs" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "Many other interesting quantities are stored in the โ€œplasma_arrayโ€.\n", - "For example the calculated ion populations and level populations is given by `model.plasma_array.ion_populations` and `model.plasma_array.level_populations` respectively." + "Many other interesting quantities are stored in the `plasma`.\n", + "For example the calculated ion populations and level populations is given by `simulation.plasma.ion_number_density` and `simulation.plasma.level_number_density` respectively." ] }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 8, "metadata": {}, "outputs": [ { - "ename": "AttributeError", - "evalue": "'Simulation' object has no attribute 'plasma_array'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplasma_array\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mion_populations\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'plasma_array'" - ] + "data": { + "text/html": [ + "
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atomic_numberion_numberlevel_number
800724.299083316.384041159.21835975.95554446.16808627.10340518.92781713.43399610.3725977.1026245.1401433.9544882.9198232.282355e+001.757802e+001.385998e+001.056041e+009.050186e-018.094569e-017.275697e-01
1425.541419185.94975193.59724544.66410827.14843115.93892911.1296107.8981956.0969664.1746793.0208792.3236691.7155191.340759e+001.032475e+008.139671e-016.201311e-015.313209e-014.750836e-014.269029e-01
2140.55874661.42990730.92330514.7583448.9706795.2668853.6774802.6095982.0142701.3791690.9979470.7675670.5666544.428354e-013.409936e-012.688096e-012.047875e-011.754414e-011.568526e-011.409282e-01
388.06386839.88856920.48986710.0708456.1265653.6236882.4981951.7499891.3214570.9002950.6446310.4875200.3562412.739129e-012.081708e-011.616668e-011.220039e-011.020938e-018.875591e-027.756551e-02
41.6296180.7690110.4042880.2055220.1251480.0746510.0507200.0350070.0257780.0174620.0123540.0091640.0066184.994795e-033.739352e-032.854639e-032.131074e-031.735927e-031.461477e-031.237289e-03
50.0403280.0208520.0115440.0063270.0038610.0023470.0015440.0010310.0007180.0004800.0003310.0002350.0001651.196208e-048.660153e-056.363173e-054.636896e-053.556994e-052.787792e-052.198773e-05
60.0161880.0084280.0046840.0025820.0015760.0009590.0006290.0004190.0002910.0001940.0001330.0000950.0000664.789850e-053.458903e-052.534132e-051.843267e-051.407569e-051.097219e-058.607646e-06
70.0043880.0023360.0013150.0007380.0004510.0002760.0001790.0001190.0000810.0000540.0000370.0000260.0000181.287856e-059.223661e-066.694378e-064.840483e-063.642144e-062.789568e-062.150620e-06
80.0073110.0038930.0021910.0012300.0007510.0004590.0002990.0001980.0001350.0000900.0000610.0000430.0000302.145848e-051.536859e-051.115424e-058.065254e-066.068553e-064.647971e-063.583345e-06
90.0102310.0054480.0030660.0017220.0010510.0006430.0004180.0002770.0001890.0001260.0000860.0000600.0000423.002712e-052.150540e-051.560817e-051.128571e-058.491681e-066.503828e-065.014082e-06
100.0033620.0017990.0010150.0005720.0003490.0002140.0001390.0000920.0000630.0000420.0000280.0000200.0000149.852180e-067.044304e-065.102842e-063.685227e-062.764553e-062.109822e-061.620802e-06
110.0056030.0029970.0016920.0009530.0005820.0003560.0002320.0001530.0001040.0000690.0000470.0000330.0000231.641907e-051.173962e-058.504093e-066.141578e-064.607234e-063.516097e-062.701124e-06
120.0011210.0005990.0003380.0001910.0001160.0000710.0000460.0000310.0000210.0000140.0000090.0000070.0000053.283746e-062.347875e-061.700782e-061.228289e-069.214269e-077.032039e-075.402128e-07
130.0022580.0012270.0006980.0003990.0002440.0001500.0000970.0000630.0000430.0000280.0000190.0000130.0000096.578356e-064.676593e-063.365578e-062.420553e-061.797254e-061.354899e-061.028308e-06
140.0012260.0006680.0003800.0002180.0001330.0000820.0000530.0000350.0000230.0000150.0000110.0000070.0000053.571458e-062.537378e-061.824754e-061.311786e-069.729029e-077.324624e-075.551699e-07
150.0031390.0017130.0009780.0005600.0003420.0002100.0001360.0000890.0000600.0000400.0000270.0000190.0000139.132513e-066.481784e-064.656043e-063.344735e-062.476215e-061.860264e-061.407004e-06
160.0024420.0013330.0007610.0004360.0002660.0001640.0001060.0000690.0000470.0000310.0000210.0000150.0000107.102984e-065.041329e-063.621325e-062.601430e-061.925923e-061.446855e-061.094323e-06
170.0017440.0009520.0005430.0003110.0001900.0001170.0000750.0000490.0000330.0000220.0000150.0000100.0000075.073477e-063.600890e-062.586618e-061.858133e-061.375636e-061.033450e-067.816457e-07
180.0010460.0005710.0003260.0001870.0001140.0000700.0000450.0000300.0000200.0000130.0000090.0000060.0000043.044044e-062.160504e-061.551949e-061.114864e-068.253697e-076.200611e-074.689806e-07
190.0003490.0001900.0001090.0000620.0000380.0000230.0000150.0000100.0000070.0000040.0000030.0000020.0000011.014675e-067.201632e-075.173129e-073.716190e-072.751214e-072.066856e-071.563258e-07
200.0010370.0005660.0003230.0001850.0001130.0000700.0000450.0000290.0000200.0000130.0000090.0000060.0000043.016739e-062.141003e-061.537842e-061.104685e-068.177511e-076.142634e-074.645400e-07
210.0017280.0009430.0005390.0003090.0001890.0001160.0000750.0000490.0000330.0000220.0000150.0000100.0000075.027852e-063.568305e-062.563046e-061.841125e-061.362905e-061.023762e-067.742258e-07
220.0024200.0013210.0007540.0004320.0002640.0001620.0001050.0000690.0000460.0000310.0000210.0000140.0000107.038908e-064.995567e-063.588220e-062.577543e-061.908044e-061.433249e-061.083902e-06
230.0008380.0004590.0002630.0001510.0000920.0000570.0000370.0000240.0000160.0000110.0000070.0000050.0000032.434600e-061.725531e-061.237515e-068.880885e-076.558311e-074.912221e-073.704348e-07
240.0013970.0007650.0004380.0002520.0001540.0000950.0000610.0000400.0000270.0000180.0000120.0000080.0000064.057302e-062.875625e-062.062337e-061.480012e-061.092951e-068.186267e-076.173327e-07
250.0019550.0010710.0006130.0003520.0002150.0001320.0000850.0000560.0000370.0000250.0000170.0000120.0000085.679315e-064.025227e-062.886805e-062.071680e-061.529879e-061.145886e-068.641199e-07
260.0007750.0004250.0002430.0001400.0000860.0000530.0000340.0000220.0000150.0000100.0000070.0000050.0000032.250648e-061.594368e-061.142805e-068.198292e-076.048888e-074.525892e-073.409460e-07
270.0012920.0007090.0004060.0002330.0001430.0000880.0000570.0000370.0000250.0000160.0000110.0000080.0000053.751039e-062.657251e-061.904654e-061.366367e-061.008137e-067.543069e-075.682369e-07
280.0002580.0001420.0000810.0000470.0000290.0000180.0000110.0000070.0000050.0000030.0000020.0000020.0000017.501817e-075.314315e-073.809173e-072.732637e-072.016202e-071.508559e-071.136432e-07
290.0014910.0008210.0004710.0002720.0001660.0001020.0000660.0000430.0000290.0000190.0000130.0000090.0000064.324013e-063.059414e-062.189866e-061.569593e-061.155555e-068.623594e-076.479636e-07
.....................................................................
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640.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+00
650.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+00
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670.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+00
680.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.0000000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+000.000000e+00
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4435 rows ร— 20 columns

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1.028308e-06 \n", + " 14 5.551699e-07 \n", + " 15 1.407004e-06 \n", + " 16 1.094323e-06 \n", + " 17 7.816457e-07 \n", + " 18 4.689806e-07 \n", + " 19 1.563258e-07 \n", + " 20 4.645400e-07 \n", + " 21 7.742258e-07 \n", + " 22 1.083902e-06 \n", + " 23 3.704348e-07 \n", + " 24 6.173327e-07 \n", + " 25 8.641199e-07 \n", + " 26 3.409460e-07 \n", + " 27 5.682369e-07 \n", + " 28 1.136432e-07 \n", + " 29 6.479636e-07 \n", + "... ... \n", + "20 8 53 0.000000e+00 \n", + " 54 0.000000e+00 \n", + " 55 0.000000e+00 \n", + " 56 0.000000e+00 \n", + " 57 0.000000e+00 \n", + " 58 0.000000e+00 \n", + " 59 0.000000e+00 \n", + " 60 0.000000e+00 \n", + " 61 0.000000e+00 \n", + " 62 0.000000e+00 \n", + " 63 0.000000e+00 \n", + " 64 0.000000e+00 \n", + " 65 0.000000e+00 \n", + " 66 0.000000e+00 \n", + " 67 0.000000e+00 \n", + " 68 0.000000e+00 \n", + " 69 0.000000e+00 \n", + " 70 0.000000e+00 \n", + " 9 0 0.000000e+00 \n", + " 10 0 0.000000e+00 \n", + " 11 0 0.000000e+00 \n", + " 12 0 0.000000e+00 \n", + " 13 0 0.000000e+00 \n", + " 14 0 0.000000e+00 \n", + " 15 0 0.000000e+00 \n", + " 16 0 0.000000e+00 \n", + " 17 0 0.000000e+00 \n", + " 18 0 0.000000e+00 \n", + " 19 0 0.000000e+00 \n", + " 20 0 0.000000e+00 \n", + "\n", + "[4435 rows x 20 columns]" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "model.plasma_array.level_populations" + "simulation.plasma.level_number_density" ] }, { @@ -564,76 +4489,136 @@ "metadata": {}, "source": [ "These are stored as Pandas `DataFrames`. An index can be supplied to obtain the population in a particular zone. E.g., for the ion populations of the innermost zone (index = 0), we will use \n", - "`model.plasma_array.ion_populations[0]`" + "`simulation.plasma.ion_number_density[0]`" ] }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 10, "metadata": {}, "outputs": [ { - "ename": "AttributeError", - "evalue": "'Simulation' object has no attribute 'plasma_array'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplasma_array\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mion_populations\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'plasma_array'" - ] + "data": { + "text/plain": [ + "atomic_number ion_number\n", + "8 0 1.380280e+03\n", + " 1 5.393290e+08\n", + " 2 9.780989e+04\n", + " 3 3.252281e-09\n", + " 4 0.000000e+00\n", + " 5 0.000000e+00\n", + " 6 0.000000e+00\n", + " 7 0.000000e+00\n", + " 8 0.000000e+00\n", + "12 0 1.346333e-06\n", + " 1 6.084662e+02\n", + " 2 5.606550e+07\n", + " 3 4.120107e-17\n", + " 4 0.000000e+00\n", + " 5 0.000000e+00\n", + " 6 0.000000e+00\n", + " 7 0.000000e+00\n", + " 8 0.000000e+00\n", + " 9 0.000000e+00\n", + " 10 0.000000e+00\n", + " 11 0.000000e+00\n", + " 12 0.000000e+00\n", + "14 0 7.121410e-04\n", + " 1 1.057234e+05\n", + " 2 8.401073e+08\n", + " 3 8.192553e+05\n", + " 4 7.678176e-04\n", + " 5 0.000000e+00\n", + " 6 0.000000e+00\n", + " 7 0.000000e+00\n", + " ... \n", + "18 10 0.000000e+00\n", + " 11 0.000000e+00\n", + " 12 0.000000e+00\n", + " 13 0.000000e+00\n", + " 14 0.000000e+00\n", + " 15 0.000000e+00\n", + " 16 0.000000e+00\n", + " 17 0.000000e+00\n", + " 18 0.000000e+00\n", + "20 0 1.332681e-08\n", + " 1 2.335159e+01\n", + " 2 3.400155e+07\n", + " 3 7.014243e-04\n", + " 4 0.000000e+00\n", + " 5 0.000000e+00\n", + " 6 0.000000e+00\n", + " 7 0.000000e+00\n", + " 8 0.000000e+00\n", + " 9 0.000000e+00\n", + " 10 0.000000e+00\n", + " 11 0.000000e+00\n", + " 12 0.000000e+00\n", + " 13 0.000000e+00\n", + " 14 0.000000e+00\n", + " 15 0.000000e+00\n", + " 16 0.000000e+00\n", + " 17 0.000000e+00\n", + " 18 0.000000e+00\n", + " 19 0.000000e+00\n", + " 20 0.000000e+00\n", + "Name: 0, Length: 94, dtype: float64" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "model.plasma_array.ion_populations[0]" + "simulation.plasma.ion_number_density[0]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "Ion populations for a particular ionization stage of a particular element can be accessed by specifying an appropriate tuple (๐‘,๐ถ), which identifies the element (via atomic number ๐‘ ) and the charge (via the ion charge ๐ถ ). Thus, `model.plasma_array.ion_populations.ix[(14,1)]` will identify the ion popuations for Si II (๐‘=14,๐ถ=1) in all the zones. " - ] - }, - { - "cell_type": "code", - "execution_count": 28, - "metadata": {}, - "outputs": [ - { - "ename": "AttributeError", - "evalue": "'Radial1DModel' object has no attribute 'plasma_array'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplasma_array\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mion_populations\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mix\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m14\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m1\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[0m", - "\u001b[0;31mAttributeError\u001b[0m: 'Radial1DModel' object has no attribute 'plasma_array'" - ] - } - ], - "source": [ - "model.plasma_array.ion_populations.ix[(14,1)]" + "Ion populations for a particular ionization stage of a particular element can be accessed by specifying an appropriate tuple (๐‘,๐ถ), which identifies the element (via atomic number ๐‘ ) and the charge (via the ion charge ๐ถ ). Thus, `simulation.plasma.ion_number_density.loc[14,1]` will identify the ion popuations for Si II (๐‘=14,๐ถ=1) in all the zones. " ] }, { "cell_type": "code", - "execution_count": 29, + "execution_count": 11, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "dict_keys(['optional_hdf_properties', '_v_boundary_inner', '_v_boundary_outer', '_velocity', 'raw_velocity', 'homologous_density', '_abundance', 'time_explosion', '_electron_densities', 'raw_abundance', 'raw_isotope_abundance', 't_inner', '_t_radiative', '_dilution_factor'])" + "0 105723.411638\n", + "1 44090.436208\n", + "2 21594.422001\n", + "3 9886.848793\n", + "4 5989.365036\n", + "5 3468.313242\n", + "6 2460.782422\n", + "7 1775.244868\n", + "8 1412.252955\n", + "9 971.631213\n", + "10 712.387551\n", + "11 560.635175\n", + "12 419.305282\n", + "13 335.000930\n", + "14 262.499557\n", + "15 211.157774\n", + "16 162.834905\n", + "17 144.128751\n", + "18 133.932017\n", + "19 124.963505\n", + "Name: (14, 1), dtype: float64" ] }, - "execution_count": 29, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "model.model.__dict__.keys()" + "simulation.plasma.ion_number_density.loc[14,1]" ] }, { @@ -642,44 +4627,74 @@ "source": [ "The above examples can be combined to obtain e.g. the Si II population in the innermost zone\n", "can be obtained by\n", - "`model.plasma_array.ion_populations[0].ix[(14,1)]`" + "`simulation.plasma.ion_number_density[0].loc[14,1]`" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "105723.41163844905" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "model.plasma_array.ion_populations[0].ix[(14,1)]" + "simulation.plasma.ion_number_density[0].loc[14,1]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "The level populations are stored (and can be accessed) in a similar way - a third label can be used to pick out a particular atomic level. E.g., to pull out the population of the ground state (index 0) of Si II we can use `model.plasma_array.level_populations.ix[(14,1,0)]`" + "The level populations are stored (and can be accessed) in a similar way - a third label can be used to pick out a particular atomic level. E.g., to pull out the population of the ground state (index 0) of Si II we can use `simulation.plasma.level_number_density.loc[14,1,0]`" ] }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 13, "metadata": {}, "outputs": [ { - "ename": "AttributeError", - "evalue": "'Simulation' object has no attribute 'plasma_array'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplasma_array\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlevel_populations\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mix\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m14\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m0\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[0m", - "\u001b[0;31mAttributeError\u001b[0m: 'Simulation' object has no attribute 'plasma_array'" - ] + "data": { + "text/plain": [ + "0 35851.432649\n", + "1 14931.643658\n", + "2 7307.391148\n", + "3 3341.597977\n", + "4 2024.238524\n", + "5 1171.823393\n", + "6 831.862975\n", + "7 600.439318\n", + "8 478.083068\n", + "9 328.985257\n", + "10 241.304587\n", + "11 190.021082\n", + "12 142.171548\n", + "13 113.651958\n", + "14 89.095253\n", + "15 71.705046\n", + "16 55.312585\n", + "17 48.994766\n", + "18 45.567026\n", + "19 42.549623\n", + "Name: (14, 1, 0), dtype: float64" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ - "model.plasma_array.level_populations.ix[(14,1,0)]" + "simulation.plasma.level_number_density.loc[14,1,0]" ] }, { @@ -710,6 +4725,10 @@ "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.7" + }, + "nbsphinx": { + "execute": "always", + "timeout": -1 } }, "nbformat": 4, From 00c7a80fe7ccfd9f9ac193a5861c41f7779ccd0a Mon Sep 17 00:00:00 2001 From: sashmish Date: Tue, 2 Jun 2020 00:14:21 +0530 Subject: [PATCH 3/3] mention units as Astropy Quantities wherever present --- docs/physics/physical_quantities.ipynb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/physics/physical_quantities.ipynb b/docs/physics/physical_quantities.ipynb index 3b40f813ebd..f136aef7d87 100644 --- a/docs/physics/physical_quantities.ipynb +++ b/docs/physics/physical_quantities.ipynb @@ -45,7 +45,7 @@ "[\u001b[1mtardis.io.atom_data.atom_web_download\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Downloading atomic data from https://media.githubusercontent.com/media/tardis-sn/tardis-refdata/master/atom_data/kurucz_cd23_chianti_H_He.h5 to /Users/sashmish/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5 (\u001b[1matom_web_download.py\u001b[0m:47)\n", " % Total % Received % Xferd Average Speed Time Time Time Current\n", " Dload Upload Total Spent Left Speed\n", - "100 980 100 980 0 0 4600 0 --:--:-- --:--:-- --:--:-- 4600\n" + "100 980 100 980 0 0 2222 0 --:--:-- --:--:-- --:--:-- 2222\n" ] } ], @@ -313,7 +313,7 @@ "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 10245.337 K -- next t_inner 11056.949 K (\u001b[1mbase.py\u001b[0m:352)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 20/20 (\u001b[1mbase.py\u001b[0m:268)\n", "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 1.22623e+43 erg / s Luminosity absorbed = 4.00603e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:359)\n", - "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 20 iterations and took 27.14 s (\u001b[1mbase.py\u001b[0m:308)\n" + "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 20 iterations and took 23.27 s (\u001b[1mbase.py\u001b[0m:308)\n" ] } ], @@ -411,7 +411,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Several important quantities that were setup when the model was defined by the configuration file are located in the `model` section of the simulation. For example, the inner and outer velocity boundaries of the zones in the model is given by `simulation.model.v_inner.cgs` and `simulation.model.v_outer.cgs` respectively." + "Several important quantities that were setup when the model was defined by the configuration file are located in the `model` section of the simulation. For example, the inner and outer velocity boundaries of the zones in the model is given by `simulation.model.v_inner.cgs` and `simulation.model.v_outer.cgs` respectively. These exist as Astropy [Quantities](http://astropy.readthedocs.org/en/v0.2.1/_generated/astropy.units.quantity.Quantity.html)." ] }, { @@ -470,7 +470,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The average density in the zones is given by `simulation.model.density.cgs`" + "The average density in the zones is given by `simulation.model.density.cgs`. These also exist as Astropy [Quantities](http://astropy.readthedocs.org/en/v0.2.1/_generated/astropy.units.quantity.Quantity.html)." ] }, { @@ -4702,9 +4702,9 @@ "metadata": {}, "source": [ "### Notes\n", - "- If you prefer to work in SI units, all the astropy Quantities may instead by accessed with โ€œxxx.siโ€.\n", + "- If you prefer to work in SI units, all the Astropy Quantities may instead by accessed with โ€œxxx.siโ€.\n", "\n", - "- Information that is not stored as astropy Quantities (e.g. the ion an level populations used in the example above) are usually stored in cgs units (i.e. cmโˆ’3 for the populations)." + "- Information that is not stored as Astropy Quantities (e.g. the ion and level populations used in the example above) are usually stored in cgs units (i.e. cmโˆ’3 for the populations)." ] } ],