{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# How to run TARDIS with a custom ejecta model\n",
"\n",
"This notebook will go through multiple detailed examples of how to properly run TARDIS with a custom ejecta profile specified by a custom density file and a custom abundance file. "
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import tardis\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Your custom density file\n",
"\n",
"First, let's look at an example of a custom density file."
]
},
{
"cell_type": "raw",
"metadata": {},
"source": [
"80 day\n",
"\n",
"0 9500 9e-16\n",
"1 10500 6e-16\n",
"2 12000 2e-17"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"* The first line specifies the time in days after the explosion\n",
"* After a skipped line, each row corresponds to a shell with index specified by the first column.\n",
"* The second column lists the velocities of the outer boundary of the cell in km/s.\n",
"* The third column lists the density of the cell.\n",
"\n",
"### Important: \n",
"The __default behavior__ of TARDIS is to use the first shell as the inner boundary. This means that v_inner_boundary = 9500, and the corresponding density 9e-16 is ignored because it is within the inner boundary. It can be replaced by an arbitrary number. The outer boundary of the last shell will be used as v_outer_boundary, so the default behavior will set v_outer_boundary = 12000."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Your custom abundance file\n",
"\n",
"Let's look at an example of a custom density file."
]
},
{
"cell_type": "raw",
"metadata": {},
"source": [
"H He\n",
"\n",
"0.0 1.0\n",
"0.4 0.6"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"* The first line indicates which elements (or isotopes) correspond to which columns.\n",
"* After a skipped line, each row specifies the chemical abundance of one shell. Therefore the numbers in a given row should sum to 1.0\n",
"\n",
"### Important: \n",
"Note that there are only 2 shells specified in this abundance file (despite the custom density file having 3 lines). This is because the custom density file specifies the boundaries of the shells, while the abundance file specifies the abundances within each shell."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Running TARDIS with the custom files\n",
"\n",
"Now let's run TARDIS using the example custom files."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/importlib/_bootstrap.py:219: QAWarning: pyne.data is not yet QA compliant.\n",
" return f(*args, **kwds)\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/importlib/_bootstrap.py:219: QAWarning: pyne.material is not yet QA compliant.\n",
" return f(*args, **kwds)\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mtardis.model.base \u001b[0m][\u001b[1;33mWARNING\u001b[0m] Abundances have not been normalized to 1. - normalizing (\u001b[1mbase.py\u001b[0m:367)\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/site-packages/astropy/units/quantity.py:1067: AstropyDeprecationWarning: The truth value of a Quantity is ambiguous. In the future this will raise a ValueError.\n",
" AstropyDeprecationWarning)\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from /home/mew488/Research/TARDIS/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:77)\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/site-packages/IPython/core/interactiveshell.py:3291: PerformanceWarning: indexing past lexsort depth may impact performance.\n",
" exec(code_obj, self.user_global_ns, self.user_ns)\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mtardis.io.atomic \u001b[0m][\u001b[1;37mINFO\u001b[0m ] Read Atom Data with UUID=6f7b09e887a311e7a06b246e96350010 and MD5=864f1753714343c41f99cb065710cace. (\u001b[1matomic.py\u001b[0m:173)\n",
"[\u001b[1mtardis.io.atomic \u001b[0m][\u001b[1;37mINFO\u001b[0m ] Non provided atomic data: synpp_refs, ion_cx_th_data, ion_cx_sp_data (\u001b[1matomic.py\u001b[0m:176)\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/src/dev/tardis/tardis/plasma/properties/ion_population.py:59: FutureWarning: \n",
"Passing list-likes to .loc or [] with any missing label will raise\n",
"KeyError in the future, you can use .reindex() as an alternative.\n",
"\n",
"See the documentation here:\n",
"https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n",
" partition_function.index].dropna())\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/site-packages/astropy/units/equivalencies.py:90: RuntimeWarning: divide by zero encountered in double_scalars\n",
" (si.m, si.Hz, lambda x: _si.c.value / x),\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/site-packages/astropy/units/quantity.py:1067: AstropyDeprecationWarning: The truth value of a Quantity is ambiguous. In the future this will raise a ValueError.\n",
" AstropyDeprecationWarning)\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31327e+42 erg / s Luminosity absorbed = 3.85232e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 1/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6541.006187 6556.13016 0.343875 0.350118\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.915 K -- next t_inner 6482.755 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 2/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21734e+42 erg / s Luminosity absorbed = 2.64889e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 2/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6556.13016 6495.397989 0.350118 0.347789\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.755 K -- next t_inner 6551.611 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 3/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31324e+42 erg / s Luminosity absorbed = 2.21576e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 3/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6495.397989 6558.906259 0.347789 0.348258\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.611 K -- next t_inner 6482.500 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 4/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21685e+42 erg / s Luminosity absorbed = 3.70488e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 4/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6558.906259 6485.545593 0.348258 0.350397\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.500 K -- next t_inner 6552.082 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 5/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31359e+42 erg / s Luminosity absorbed = 2.20402e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 5/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6485.545593 6550.104752 0.350397 0.352096\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6552.082 K -- next t_inner 6482.479 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 6/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21697e+42 erg / s Luminosity absorbed = 2.64706e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 6/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6550.104752 6464.323819 0.352096 0.354247\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.479 K -- next t_inner 6551.873 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 7/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31327e+42 erg / s Luminosity absorbed = 2.76611e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 7/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6464.323819 6586.535643 0.354247 0.344429\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.873 K -- next t_inner 6482.711 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 8/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21723e+42 erg / s Luminosity absorbed = 2.12445e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 8/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6586.535643 6452.0629 0.344429 0.358012\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.711 K -- next t_inner 6551.731 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 9/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31306e+42 erg / s Luminosity absorbed = 3.30756e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 9/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6452.0629 6542.502642 0.358012 0.353289\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.731 K -- next t_inner 6482.870 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 10/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21734e+42 erg / s Luminosity absorbed = 3.17660e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 10/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6542.502642 6474.094395 0.353289 0.353484\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.870 K -- next t_inner 6551.733 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 11/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31318e+42 erg / s Luminosity absorbed = 2.21194e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 11/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6474.094395 6569.860807 0.353484 0.34756\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.733 K -- next t_inner 6482.698 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 12/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21741e+42 erg / s Luminosity absorbed = 1.59417e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 12/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6569.860807 6510.554611 0.34756 0.344308\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.698 K -- next t_inner 6551.446 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 13/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31272e+42 erg / s Luminosity absorbed = 2.20953e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 13/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6510.554611 6546.768598 0.344308 0.352781\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.446 K -- next t_inner 6483.070 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 14/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21777e+42 erg / s Luminosity absorbed = 2.64910e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 14/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6546.768598 6485.552351 0.352781 0.349363\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.070 K -- next t_inner 6551.293 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 15/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31237e+42 erg / s Luminosity absorbed = 2.76461e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 15/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6485.552351 6516.39366 0.349363 0.35982\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.293 K -- next t_inner 6483.402 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 16/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21811e+42 erg / s Luminosity absorbed = 2.64705e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 16/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6516.39366 6487.025434 0.35982 0.350732\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.402 K -- next t_inner 6551.133 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 17/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31225e+42 erg / s Luminosity absorbed = 2.21332e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 17/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6487.025434 6541.53332 0.350732 0.354308\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.133 K -- next t_inner 6483.406 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 18/20 (\u001b[1mbase.py\u001b[0m:266)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21806e+42 erg / s Luminosity absorbed = 3.18123e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 18/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6541.53332 6506.188917 0.354308 0.346155\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.406 K -- next t_inner 6551.206 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 19/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31238e+42 erg / s Luminosity absorbed = 2.76543e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 19/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6506.188917 6589.429688 0.346155 0.342891\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6551.206 K -- next t_inner 6483.296 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 20/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21775e+42 erg / s Luminosity absorbed = 5.09249e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 20 iterations and took 2.68 s (\u001b[1mbase.py\u001b[0m:306)\n"
]
}
],
"source": [
"model = tardis.run_tardis('./test_config.yml')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"You can check to make sure that the model loaded and used by TARDIS during the simulation is consistent with your expectations based on the custom files you provided:"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"v_inner_boundary = 950000000.0 cm / s\n",
"v_outer_boundary = 1200000000.0 cm / s\n",
"\n",
"\n",
"velocities of shell boundaries: \n",
"[9.50e+08 1.05e+09 1.20e+09] cm / s\n",
"\n",
"\n",
"densities loaded by TARDIS: (NOTE that the density in the first line of the file was ignored! Densities are also rescaled.)\n",
"[7.5e-14 2.5e-15] g / cm3\n"
]
}
],
"source": [
"print('v_inner_boundary = ',model.model.v_boundary_inner)\n",
"print('v_outer_boundary = ',model.model.v_boundary_outer)\n",
"print('\\n')\n",
"print('velocities of shell boundaries: ')\n",
"print(model.model.velocity)\n",
"print('\\n')\n",
"print('densities loaded by TARDIS: (NOTE that the density in the first line of the file was ignored! Densities are also rescaled.)')\n",
"print(model.model.density)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Specifying boundary velocities in the config file\n",
"\n",
"In addition to specifying custom density and abundance files, the user can set the v_inner_boundary and v_outer_boundary velocities in the YAML config file. This can cause some confusion, so we carefully go through some examples.\n",
"\n",
"### Important: \n",
"Boundary velocities set in the YAML config file must be __within__ the velocity range specified in the custom density file (if one is provided)."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Example 1) v_inner_boundary lower than first velocity in density file\n",
"\n",
"In this example, the first velocity in the density file is 9500 km/s. The user can specify in the config file the velocity of the inner boundary to a lower velocity, say v_inner_boundary = 9000 km/s. This will cause TARDIS to raise an error."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\u001b[1mtardis.model.base \u001b[0m][\u001b[1;33mWARNING\u001b[0m] Abundances have not been normalized to 1. - normalizing (\u001b[1mbase.py\u001b[0m:367)\n"
]
},
{
"ename": "ValueError",
"evalue": "v_boundary_inner is lower than the lowest shell in the model.",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mValueError\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\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_tardis\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'./test_config_ex1.yml'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/src/dev/tardis/tardis/base.py\u001b[0m in \u001b[0;36mrun_tardis\u001b[0;34m(config, atom_data, simulation_callbacks)\u001b[0m\n\u001b[1;32m 35\u001b[0m \u001b[0mtardis_config\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mConfiguration\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 36\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 37\u001b[0;31m \u001b[0msimulation\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSimulation\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtardis_config\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0matom_data\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0matom_data\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 38\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mcb\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msimulation_callbacks\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[0msimulation\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd_callback\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/src/dev/tardis/tardis/simulation/base.py\u001b[0m in \u001b[0;36mfrom_config\u001b[0;34m(cls, config, **kwargs)\u001b[0m\n\u001b[1;32m 430\u001b[0m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'model'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 431\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 432\u001b[0;31m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mRadial1DModel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 433\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m'plasma'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 434\u001b[0m \u001b[0mplasma\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'plasma'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36mfrom_config\u001b[0;34m(cls, config)\u001b[0m\n\u001b[1;32m 383\u001b[0m \u001b[0mv_boundary_inner\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_inner_boundary'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 384\u001b[0m \u001b[0mv_boundary_outer\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_outer_boundary'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\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;32m--> 385\u001b[0;31m electron_densities=electron_densities)\n\u001b[0m",
"\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, velocity, homologous_density, abundance, isotope_abundance, time_explosion, t_inner, luminosity_requested, t_radiative, dilution_factor, v_boundary_inner, v_boundary_outer, electron_densities)\u001b[0m\n\u001b[1;32m 78\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_velocity\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 79\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraw_velocity\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvelocity\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 80\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_boundary_inner\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mv_boundary_inner\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 81\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_boundary_outer\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mv_boundary_outer\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 82\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhomologous_density\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mhomologous_density\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36mv_boundary_inner\u001b[0;34m(self, value)\u001b[0m\n\u001b[1;32m 237\u001b[0m 'the model range.')\n\u001b[1;32m 238\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;34m<\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraw_velocity\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[0;32m--> 239\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_boundary_inner is lower than the lowest shell in the model.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 240\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_v_boundary_inner\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 241\u001b[0m \u001b[0;31m# Invalidate the cached cut-down velocity array\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mValueError\u001b[0m: v_boundary_inner is lower than the lowest shell in the model."
]
}
],
"source": [
"model = tardis.run_tardis('./test_config_ex1.yml')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Example 2) v_outer_boundary larger than last velocity in density file\n",
"\n",
"In this example, the last velocity in the density file is 12000 km/s. The user can specify in the config file the velocity of the outer boundary to a larger velocity, say v_outer_boundary = 13000 km/s. This will cause TARDIS to raise an error."
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\u001b[1mtardis.model.base \u001b[0m][\u001b[1;33mWARNING\u001b[0m] Abundances have not been normalized to 1. - normalizing (\u001b[1mbase.py\u001b[0m:367)\n"
]
},
{
"ename": "ValueError",
"evalue": "v_boundary_outer is larger than the largest shell in the model.",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mValueError\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\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_tardis\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'./test_config_ex2.yml'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/src/dev/tardis/tardis/base.py\u001b[0m in \u001b[0;36mrun_tardis\u001b[0;34m(config, atom_data, simulation_callbacks)\u001b[0m\n\u001b[1;32m 35\u001b[0m \u001b[0mtardis_config\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mConfiguration\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 36\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 37\u001b[0;31m \u001b[0msimulation\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSimulation\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtardis_config\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0matom_data\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0matom_data\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 38\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mcb\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msimulation_callbacks\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[0msimulation\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0madd_callback\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/src/dev/tardis/tardis/simulation/base.py\u001b[0m in \u001b[0;36mfrom_config\u001b[0;34m(cls, config, **kwargs)\u001b[0m\n\u001b[1;32m 430\u001b[0m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'model'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 431\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 432\u001b[0;31m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mRadial1DModel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 433\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m'plasma'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 434\u001b[0m \u001b[0mplasma\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'plasma'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36mfrom_config\u001b[0;34m(cls, config)\u001b[0m\n\u001b[1;32m 383\u001b[0m \u001b[0mv_boundary_inner\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_inner_boundary'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 384\u001b[0m \u001b[0mv_boundary_outer\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mstructure\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_outer_boundary'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\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;32m--> 385\u001b[0;31m electron_densities=electron_densities)\n\u001b[0m",
"\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, velocity, homologous_density, abundance, isotope_abundance, time_explosion, t_inner, luminosity_requested, t_radiative, dilution_factor, v_boundary_inner, v_boundary_outer, electron_densities)\u001b[0m\n\u001b[1;32m 79\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraw_velocity\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvelocity\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 80\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_boundary_inner\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mv_boundary_inner\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 81\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mv_boundary_outer\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mv_boundary_outer\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 82\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhomologous_density\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mhomologous_density\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 83\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_abundance\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mabundance\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/src/dev/tardis/tardis/model/base.py\u001b[0m in \u001b[0;36mv_boundary_outer\u001b[0;34m(self, value)\u001b[0m\n\u001b[1;32m 262\u001b[0m 'the model range.')\n\u001b[1;32m 263\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mvalue\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraw_velocity\u001b[0m\u001b[0;34m[\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[0;32m--> 264\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'v_boundary_outer is larger than the largest shell in the model.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 265\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_v_boundary_outer\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 266\u001b[0m \u001b[0;31m# Invalidate the cached cut-down velocity array\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mValueError\u001b[0m: v_boundary_outer is larger than the largest shell in the model."
]
}
],
"source": [
"model = tardis.run_tardis('./test_config_ex2.yml')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Example 3) v_boundaries in config file are within density file velocity range\n",
"\n",
"Here the user sets v_inner_boundary = 9700 and v_outer_boundary = 11500 in the config file. Both values fall within the velocity range specified by the custom density file."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\u001b[1mtardis.model.base \u001b[0m][\u001b[1;33mWARNING\u001b[0m] Abundances have not been normalized to 1. - normalizing (\u001b[1mbase.py\u001b[0m:367)\n",
"[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Reading Atomic Data from /home/mew488/Research/TARDIS/tardis-refdata/atom_data/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:77)\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/site-packages/IPython/core/interactiveshell.py:3291: PerformanceWarning: indexing past lexsort depth may impact performance.\n",
" exec(code_obj, self.user_global_ns, self.user_ns)\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mtardis.io.atomic \u001b[0m][\u001b[1;37mINFO\u001b[0m ] Read Atom Data with UUID=6f7b09e887a311e7a06b246e96350010 and MD5=864f1753714343c41f99cb065710cace. (\u001b[1matomic.py\u001b[0m:173)\n",
"[\u001b[1mtardis.io.atomic \u001b[0m][\u001b[1;37mINFO\u001b[0m ] Non provided atomic data: synpp_refs, ion_cx_th_data, ion_cx_sp_data (\u001b[1matomic.py\u001b[0m:176)\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/src/dev/tardis/tardis/plasma/properties/ion_population.py:59: FutureWarning: \n",
"Passing list-likes to .loc or [] with any missing label will raise\n",
"KeyError in the future, you can use .reindex() as an alternative.\n",
"\n",
"See the documentation here:\n",
"https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n",
" partition_function.index].dropna())\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/site-packages/astropy/units/equivalencies.py:90: RuntimeWarning: divide by zero encountered in double_scalars\n",
" (si.m, si.Hz, lambda x: _si.c.value / x),\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mpy.warnings \u001b[0m][\u001b[1;33mWARNING\u001b[0m] /home/mew488/anaconda2/envs/tardis3/lib/python3.6/site-packages/astropy/units/quantity.py:1067: AstropyDeprecationWarning: The truth value of a Quantity is ambiguous. In the future this will raise a ValueError.\n",
" AstropyDeprecationWarning)\n",
" (\u001b[1mwarnings.py\u001b[0m:99)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 1/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31451e+42 erg / s Luminosity absorbed = 2.20992e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 1/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6475.378267 6488.637521 0.360681 0.366243\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6484.018 K -- next t_inner 6413.863 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 2/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21599e+42 erg / s Luminosity absorbed = 2.64272e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 2/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6488.637521 6427.216436 0.366243 0.363775\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6413.863 K -- next t_inner 6483.959 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 3/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31470e+42 erg / s Luminosity absorbed = 1.66285e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 3/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6427.216436 6492.265498 0.363775 0.364173\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.959 K -- next t_inner 6413.533 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 4/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21561e+42 erg / s Luminosity absorbed = 1.59276e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 4/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6492.265498 6417.052425 0.364173 0.366605\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6413.533 K -- next t_inner 6484.185 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 5/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31470e+42 erg / s Luminosity absorbed = 1.65313e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 5/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6417.052425 6482.377118 0.366605 0.368425\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6484.185 K -- next t_inner 6413.755 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 6/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21602e+42 erg / s Luminosity absorbed = 1.05695e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 6/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6482.377118 6394.506844 0.368425 0.371037\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6413.755 K -- next t_inner 6483.813 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 7/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31410e+42 erg / s Luminosity absorbed = 2.76180e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 7/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6394.506844 6519.309507 0.371037 0.36027\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.813 K -- next t_inner 6414.228 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 8/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21639e+42 erg / s Luminosity absorbed = 2.64764e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 8/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6519.309507 6383.889203 0.36027 0.374686\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6414.228 K -- next t_inner 6483.748 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 9/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31428e+42 erg / s Luminosity absorbed = 5.54016e+37 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 9/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6383.889203 6473.974678 0.374686 0.369973\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.748 K -- next t_inner 6413.915 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 10/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21596e+42 erg / s Luminosity absorbed = 2.63810e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 10/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6473.974678 6406.611113 0.369973 0.369657\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6413.915 K -- next t_inner 6484.063 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 11/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31457e+42 erg / s Luminosity absorbed = 2.20714e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 11/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6406.611113 6501.97906 0.369657 0.363763\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6484.063 K -- next t_inner 6413.825 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 12/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21609e+42 erg / s Luminosity absorbed = 1.59204e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 12/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6501.97906 6442.380908 0.363763 0.360018\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6413.825 K -- next t_inner 6483.774 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 13/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31415e+42 erg / s Luminosity absorbed = 1.64927e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 13/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6442.380908 6479.130222 0.360018 0.369277\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.774 K -- next t_inner 6414.121 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 14/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21646e+42 erg / s Luminosity absorbed = 1.59283e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 14/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6479.130222 6416.085322 0.369277 0.365588\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6414.121 K -- next t_inner 6483.538 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 15/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31368e+42 erg / s Luminosity absorbed = 2.20875e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 15/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6416.085322 6449.419113 0.365588 0.376548\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.538 K -- next t_inner 6414.538 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 16/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21696e+42 erg / s Luminosity absorbed = 1.05743e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 16/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6449.419113 6417.878262 0.376548 0.367147\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6414.538 K -- next t_inner 6483.218 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 17/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31321e+42 erg / s Luminosity absorbed = 2.75526e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 17/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6417.878262 6473.045585 0.367147 0.371157\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6483.218 K -- next t_inner 6414.863 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 18/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21737e+42 erg / s Luminosity absorbed = 1.58484e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 18/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6473.045585 6436.504989 0.371157 0.362441\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6414.863 K -- next t_inner 6482.959 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 19/20 (\u001b[1mbase.py\u001b[0m:266)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.31299e+42 erg / s Luminosity absorbed = 2.20411e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Iteration converged 19/4 consecutive times. (\u001b[1mbase.py\u001b[0m:194)\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 6436.504989 6520.140466 0.362441 0.358913\n",
"\n",
" (\u001b[1mbase.py\u001b[0m:348)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] t_inner 6482.959 K -- next t_inner 6414.912 K (\u001b[1mbase.py\u001b[0m:350)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Starting iteration 20/20 (\u001b[1mbase.py\u001b[0m:266)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Luminosity emitted = 2.21744e+42 erg / s Luminosity absorbed = 1.90600e+38 erg / s Luminosity requested = 2.26469e+42 erg / s (\u001b[1mbase.py\u001b[0m:357)\n",
"[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m ] Simulation finished in 20 iterations and took 2.44 s (\u001b[1mbase.py\u001b[0m:306)\n"
]
}
],
"source": [
"model = tardis.run_tardis('./test_config_ex3.yml')"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"v_inner_boundary = 970000000.0 cm / s\n",
"v_outer_boundary = 1150000000.0 cm / s\n",
"\n",
"\n",
"velocities of shell boundaries: \n",
"[9.70e+08 1.05e+09 1.15e+09] cm / s\n",
"\n",
"\n",
"densities loaded by TARDIS: (NOTE that the density in the first line of the file was ignored! Densities are also rescaled.)\n",
"[7.5e-14 2.5e-15] g / cm3\n"
]
}
],
"source": [
"print('v_inner_boundary = ',model.model.v_boundary_inner)\n",
"print('v_outer_boundary = ',model.model.v_boundary_outer)\n",
"print('\\n')\n",
"print('velocities of shell boundaries: ')\n",
"print(model.model.velocity)\n",
"print('\\n')\n",
"print('densities loaded by TARDIS: (NOTE that the density in the first line of the file was ignored! Densities are also rescaled.)')\n",
"print(model.model.density)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Important: \n",
"Notice that the inner and outer boundary velocities are the ones specifically set by the user."
]
}
],
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