Quickstart for TARDIS¶
Every simulation run requires the atomic database (for more info refer to atomic data ) and a configuration file (more info at configuration ).
You can obtain a copy of the atomic database from the
(https://github.com/tardis-sn/tardis-refdata) repository
(atom_data subfolder). We recommended to use the
kurucz_cd23_chianti_H_He.h5 dataset (which is auto-downloaded in the second cell already). The configuration file for this quickstart is tardis_example.yml, which can be downloaded here), though this file is auto-downloaded in the third cell.
After the installation, start a Jupyter server executing jupyter notebook on the command line in a directory that contains this quickstart.
In [1]:
from tardis import run_tardis
from tardis.io.atom_data.util import download_atom_data
/Users/wkerzend/miniconda/envs/tardis/lib/python3.6/importlib/_bootstrap.py:219: QAWarning: pyne.data is not yet QA compliant. return f(*args, **kwds)
Downloading the atomic data¶
In [2]:
# the data is automatically downloaded
download_atom_data('kurucz_cd23_chianti_H_He')
[tardis.io.atom_data.atom_web_download][INFO ] Downloading atomic data from https://media.githubusercontent.com/media/tardis-sn/tardis-refdata/master/atom_data/kurucz_cd23_chianti_H_He.h5 to /Users/wkerzend/projects/tardis/tardis-data/kurucz_cd23_chianti_H_He.h5 (atom_web_download.py:47)
Downloading the example file¶
In [3]:
!curl -O https://raw.githubusercontent.com/tardis-sn/tardis/master/docs/models/examples/tardis_example.yml
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 980 100 980 0 0 4394 0 --:--:-- --:--:-- --:--:-- 4394
Running the simulation (long output)¶
In [4]:
#TARDIS now uses the data in the data repo
sim = run_tardis('tardis_example.yml')
[tardis.plasma.standard_plasmas][INFO ] Reading Atomic Data from kurucz_cd23_chianti_H_He.h5 (standard_plasmas.py:74) [tardis.io.atom_data.util][INFO ] Atom Data kurucz_cd23_chianti_H_He.h5 not found in local path. Exists in TARDIS Data repo /Users/wkerzend/projects/tardis/tardis-data/kurucz_cd23_chianti_H_He.h5 (util.py:29) [tardis.io.atom_data.base][INFO ] Read Atom Data with UUID=6f7b09e887a311e7a06b246e96350010 and MD5=864f1753714343c41f99cb065710cace. (base.py:184) [tardis.io.atom_data.base][INFO ] Non provided atomic data: synpp_refs, photoionization_data (base.py:187) [tardis.simulation.base][INFO ] Starting iteration 1/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 7.93730e+42 erg / s Luminosity absorbed = 2.66400e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 9926.501965 10168.422346 0.400392 0.501001 5 9852.611678 10367.510165 0.211205 0.186556 10 9779.813302 10222.882075 0.142695 0.113985 15 9708.082813 9928.649533 0.104556 0.085217 (base.py:350) [tardis.simulation.base][INFO ] t_inner 9933.952 K -- next t_inner 11475.997 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 2/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 1.41371e+43 erg / s Luminosity absorbed = 4.73752e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 10168.422346 11497.903617 0.501001 0.545136 5 10367.510165 11621.417600 0.186556 0.212874 10 10222.882075 11335.692704 0.113985 0.135635 15 9928.649533 11018.841465 0.085217 0.101203 (base.py:350) [tardis.simulation.base][INFO ] t_inner 11475.997 K -- next t_inner 9933.797 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 3/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 8.04734e+42 erg / s Luminosity absorbed = 2.55640e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 11497.903617 10477.653343 0.545136 0.439296 5 11621.417600 10856.518852 0.212874 0.159058 10 11335.692704 10635.474976 0.135635 0.100253 15 11018.841465 10290.254692 0.101203 0.075529 (base.py:350) [tardis.simulation.base][INFO ] t_inner 9933.797 K -- next t_inner 11397.084 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 4/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 1.38199e+43 erg / s Luminosity absorbed = 4.54590e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 10477.653343 11608.211738 0.439296 0.506501 5 10856.518852 11859.259666 0.159058 0.192802 10 10635.474976 11479.604579 0.100253 0.125779 15 10290.254692 11149.192411 0.075529 0.094052 (base.py:350) [tardis.simulation.base][INFO ] t_inner 11397.084 K -- next t_inner 9978.058 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 5/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 8.16431e+42 erg / s Luminosity absorbed = 2.62454e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 11608.211738 10556.913414 0.506501 0.440229 5 11859.259666 11021.144022 0.192802 0.153136 10 11479.604579 10713.104080 0.125779 0.099268 15 11149.192411 10399.079825 0.094052 0.073482 (base.py:350) [tardis.simulation.base][INFO ] t_inner 9978.058 K -- next t_inner 11365.561 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 6/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 1.36136e+43 erg / s Luminosity absorbed = 4.54590e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 10556.913414 11562.006340 0.440229 0.509603 5 11021.144022 11799.980145 0.153136 0.194437 10 10713.104080 11482.742597 0.099268 0.124721 15 10399.079825 11124.799749 0.073482 0.093597 (base.py:350) [tardis.simulation.base][INFO ] t_inner 11365.561 K -- next t_inner 10025.564 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 7/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 8.33278e+42 erg / s Luminosity absorbed = 2.66283e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 11562.006340 10655.549804 0.509603 0.430187 5 11799.980145 11063.665621 0.194437 0.155127 10 11482.742597 10926.058943 0.124721 0.094642 15 11124.799749 10477.041314 0.093597 0.072578 (base.py:350) [tardis.simulation.base][INFO ] t_inner 10025.564 K -- next t_inner 11303.643 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 8/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 1.34650e+43 erg / s Luminosity absorbed = 4.30670e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 10655.549804 11572.119736 0.430187 0.496558 5 11063.665621 11696.304249 0.155127 0.198228 10 10926.058943 11482.609682 0.094642 0.124382 15 10477.041314 11098.080451 0.072578 0.093537 (base.py:350) [tardis.simulation.base][INFO ] t_inner 11303.643 K -- next t_inner 10025.810 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 9/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 8.36983e+42 erg / s Luminosity absorbed = 2.63049e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 11572.119736 10590.775937 0.496558 0.439574 5 11696.304249 11060.842307 0.198228 0.154917 10 11482.609682 10761.665022 0.124382 0.099840 15 11098.080451 10436.629671 0.093537 0.074676 (base.py:350) [tardis.simulation.base][INFO ] t_inner 10025.810 K -- next t_inner 11278.874 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 10/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 1.32624e+43 erg / s Luminosity absorbed = 4.34986e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 10590.775937 11489.769556 0.439574 0.511403 5 11060.842307 11791.517605 0.154917 0.191127 10 10761.665022 11527.732208 0.099840 0.120106 15 10436.629671 11111.114390 0.074676 0.091713 (base.py:350) [tardis.simulation.base][INFO ] t_inner 11278.874 K -- next t_inner 10079.967 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 11/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 8.51915e+42 erg / s Luminosity absorbed = 2.72009e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 11489.769556 10664.234475 0.511403 0.437272 5 11791.517605 11091.518839 0.191127 0.156638 10 11527.732208 10885.771059 0.120106 0.096973 15 11111.114390 10484.177251 0.091713 0.074261 (base.py:350) [tardis.simulation.base][INFO ] t_inner 10079.967 K -- next t_inner 11239.980 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 12/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 1.30886e+43 erg / s Luminosity absorbed = 4.28617e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 10664.234475 11510.842068 0.437272 0.495944 5 11091.518839 11716.009425 0.156638 0.189856 10 10885.771059 11479.636914 0.096973 0.120067 15 10484.177251 11117.963837 0.074261 0.090628 (base.py:350) [tardis.simulation.base][INFO ] t_inner 11239.980 K -- next t_inner 10111.668 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 13/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 8.65047e+42 erg / s Luminosity absorbed = 2.72874e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 11510.842068 10636.025493 0.495944 0.446635 5 11716.009425 11175.711706 0.189856 0.154916 10 11479.636914 10916.188023 0.120067 0.097843 15 11117.963837 10431.720831 0.090628 0.077032 (base.py:350) [tardis.simulation.base][INFO ] t_inner 10111.668 K -- next t_inner 11189.420 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 14/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 1.28712e+43 erg / s Luminosity absorbed = 4.19242e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 10636.025493 11423.118214 0.446635 0.503706 5 11175.711706 11682.224028 0.154916 0.189577 10 10916.188023 11389.994295 0.097843 0.121114 15 10431.720831 11029.450833 0.077032 0.091350 (base.py:350) [tardis.simulation.base][INFO ] t_inner 11189.420 K -- next t_inner 10150.866 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 15/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 8.76501e+42 erg / s Luminosity absorbed = 2.79433e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 11423.118214 10634.831735 0.503706 0.452948 5 11682.224028 11112.411355 0.189577 0.159316 10 11389.994295 10831.887277 0.121114 0.101805 15 11029.450833 10396.372864 0.091350 0.078776 (base.py:350) [tardis.simulation.base][INFO ] t_inner 10150.866 K -- next t_inner 11159.164 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 16/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 1.27462e+43 erg / s Luminosity absorbed = 4.13373e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 10634.831735 11415.925493 0.452948 0.501153 5 11112.411355 11688.667754 0.159316 0.188430 10 10831.887277 11397.519913 0.101805 0.120134 15 10396.372864 11045.200458 0.078776 0.090180 (base.py:350) [tardis.simulation.base][INFO ] t_inner 11159.164 K -- next t_inner 10172.913 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 17/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 8.86785e+42 erg / s Luminosity absorbed = 2.79094e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 11415.925493 10678.510651 0.501153 0.453127 5 11688.667754 11152.822099 0.188430 0.159726 10 11397.519913 10907.112682 0.120134 0.099725 15 11045.200458 10508.816973 0.090180 0.076667 (base.py:350) [tardis.simulation.base][INFO ] t_inner 10172.913 K -- next t_inner 11118.359 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 18/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 1.24749e+43 erg / s Luminosity absorbed = 4.15445e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 10678.510651 11482.446420 0.453127 0.481917 5 11152.822099 11693.549165 0.159726 0.184456 10 10907.112682 11472.013555 0.099725 0.115208 15 10508.816973 10997.309982 0.076667 0.089730 (base.py:350) [tardis.simulation.base][INFO ] t_inner 11118.359 K -- next t_inner 10245.337 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 19/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 9.09476e+42 erg / s Luminosity absorbed = 2.89713e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Plasma stratification: t_rad next_t_rad w next_w Shell 0 11482.446420 10834.729769 0.481917 0.438322 5 11693.549165 11346.133670 0.184456 0.154204 10 11472.013555 10996.421420 0.115208 0.099677 15 10997.309982 10625.479432 0.089730 0.075531 (base.py:350) [tardis.simulation.base][INFO ] t_inner 10245.337 K -- next t_inner 11056.949 K (base.py:352) [tardis.simulation.base][INFO ] Starting iteration 20/20 (base.py:268) [tardis.simulation.base][INFO ] Luminosity emitted = 1.22623e+43 erg / s Luminosity absorbed = 4.00603e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (base.py:359) [tardis.simulation.base][INFO ] Simulation finished in 20 iterations and took 23.52 s (base.py:308)
Plotting the Spectrum¶
In [5]:
%pylab inline
spectrum = sim.runner.spectrum
spectrum_virtual = sim.runner.spectrum_virtual
spectrum_integrated = sim.runner.spectrum_integrated
figure(figsize=(10,6))
plot(spectrum.wavelength, spectrum.luminosity_density_lambda, label='normal packets')
plot(spectrum.wavelength, spectrum_virtual.luminosity_density_lambda, label='virtual packets')
plot(spectrum.wavelength, spectrum_integrated.luminosity_density_lambda, label='formal integral')
xlabel('Wavelength [$\AA$]')
ylabel('Luminosity [erg/s/$\AA$]')
legend()
xlim(3000, 9000)
Populating the interactive namespace from numpy and matplotlib
Out[5]:
(3000, 9000)
In [ ]: