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Storing Simulations to HDF¶
You can ask TARDIS to store the state of each iteration of the simulation you are running. We show examples of how this is done:
Initialize the simulation with the tardis_example.yml configuration file.
[1]:
from tardis import run_tardis
from tardis.io.atom_data.util import download_atom_data
# We download the atomic data needed to run the simulation
download_atom_data('kurucz_cd23_chianti_H_He')
# We run the simulation
simulation = run_tardis('tardis_example.yml')
/usr/share/miniconda3/envs/tardis/lib/python3.11/site-packages/setuptools_scm/git.py:162: UserWarning: "/home/runner/work/tardis/tardis" is shallow and may cause errors
warnings.warn(f'"{wd.path}" is shallow and may cause errors')
Atomic Data kurucz_cd23_chianti_H_He already exists in /home/runner/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5. Will not download - override with force_download=True.
[tardis.simulation.base][INFO ]
Reading Atomic Data from kurucz_cd23_chianti_H_He.h5 (base.py:681)
[tardis.io.atom_data.util][INFO ]
Atom Data kurucz_cd23_chianti_H_He.h5 not found in local path.
Exists in TARDIS Data repo /home/runner/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5 (util.py:36)
[tardis.io.atom_data.base][INFO ]
Reading Atom Data with: UUID = 6f7b09e887a311e7a06b246e96350010 MD5 = 864f1753714343c41f99cb065710cace (base.py:258)
[tardis.io.atom_data.base][INFO ]
Non provided Atomic Data: synpp_refs, photoionization_data, yg_data, two_photon_data, linelist (base.py:262)
[tardis.model.parse_input][WARNING]
Number of density points larger than number of shells. Assuming inner point irrelevant (parse_input.py:143)
[tardis.model.matter.decay][INFO ]
Decaying abundances for 1123200.0 seconds (decay.py:101)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 1 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 7.942e+42 erg / s
Luminosity absorbed = 2.659e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 9.93e+03 K | 1.01e+04 K | 0.4 | 0.507 |
| 5 | 9.85e+03 K | 1.02e+04 K | 0.211 | 0.197 |
| 10 | 9.78e+03 K | 1.01e+04 K | 0.143 | 0.117 |
| 15 | 9.71e+03 K | 9.87e+03 K | 0.105 | 0.0869 |
[tardis.simulation.base][INFO ]
Current t_inner = 9933.952 K
Expected t_inner for next iteration = 10703.212 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 2 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.071e+43 erg / s
Luminosity absorbed = 3.576e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.01e+04 K | 1.08e+04 K | 0.507 | 0.525 |
| 5 | 1.02e+04 K | 1.1e+04 K | 0.197 | 0.203 |
| 10 | 1.01e+04 K | 1.08e+04 K | 0.117 | 0.125 |
| 15 | 9.87e+03 K | 1.05e+04 K | 0.0869 | 0.0933 |
[tardis.simulation.base][INFO ]
Current t_inner = 10703.212 K
Expected t_inner for next iteration = 10673.712 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 3 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.074e+43 erg / s
Luminosity absorbed = 3.391e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.08e+04 K | 1.1e+04 K | 0.525 | 0.483 |
| 5 | 1.1e+04 K | 1.12e+04 K | 0.203 | 0.189 |
| 10 | 1.08e+04 K | 1.1e+04 K | 0.125 | 0.118 |
| 15 | 1.05e+04 K | 1.06e+04 K | 0.0933 | 0.0895 |
[tardis.simulation.base][INFO ]
Current t_inner = 10673.712 K
Expected t_inner for next iteration = 10635.953 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 4 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.058e+43 erg / s
Luminosity absorbed = 3.352e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.1e+04 K | 1.1e+04 K | 0.483 | 0.469 |
| 5 | 1.12e+04 K | 1.12e+04 K | 0.189 | 0.182 |
| 10 | 1.1e+04 K | 1.1e+04 K | 0.118 | 0.113 |
| 15 | 1.06e+04 K | 1.07e+04 K | 0.0895 | 0.0861 |
[tardis.simulation.base][INFO ]
Current t_inner = 10635.953 K
Expected t_inner for next iteration = 10638.407 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 5 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.055e+43 erg / s
Luminosity absorbed = 3.399e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 1/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.1e+04 K | 1.1e+04 K | 0.469 | 0.479 |
| 5 | 1.12e+04 K | 1.13e+04 K | 0.182 | 0.178 |
| 10 | 1.1e+04 K | 1.1e+04 K | 0.113 | 0.113 |
| 15 | 1.07e+04 K | 1.07e+04 K | 0.0861 | 0.0839 |
[tardis.simulation.base][INFO ]
Current t_inner = 10638.407 K
Expected t_inner for next iteration = 10650.202 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 6 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.061e+43 erg / s
Luminosity absorbed = 3.398e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 2/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.1e+04 K | 1.1e+04 K | 0.479 | 0.47 |
| 5 | 1.13e+04 K | 1.12e+04 K | 0.178 | 0.185 |
| 10 | 1.1e+04 K | 1.11e+04 K | 0.113 | 0.112 |
| 15 | 1.07e+04 K | 1.07e+04 K | 0.0839 | 0.0856 |
[tardis.simulation.base][INFO ]
Current t_inner = 10650.202 K
Expected t_inner for next iteration = 10645.955 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 7 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.061e+43 erg / s
Luminosity absorbed = 3.382e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 3/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.1e+04 K | 1.1e+04 K | 0.47 | 0.47 |
| 5 | 1.12e+04 K | 1.13e+04 K | 0.185 | 0.178 |
| 10 | 1.11e+04 K | 1.11e+04 K | 0.112 | 0.112 |
| 15 | 1.07e+04 K | 1.07e+04 K | 0.0856 | 0.086 |
[tardis.simulation.base][INFO ]
Current t_inner = 10645.955 K
Expected t_inner for next iteration = 10642.050 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 8 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.062e+43 erg / s
Luminosity absorbed = 3.350e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 4/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.1e+04 K | 1.11e+04 K | 0.47 | 0.472 |
| 5 | 1.13e+04 K | 1.14e+04 K | 0.178 | 0.175 |
| 10 | 1.11e+04 K | 1.11e+04 K | 0.112 | 0.111 |
| 15 | 1.07e+04 K | 1.07e+04 K | 0.086 | 0.084 |
[tardis.simulation.base][INFO ]
Current t_inner = 10642.050 K
Expected t_inner for next iteration = 10636.106 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 9 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.052e+43 erg / s
Luminosity absorbed = 3.411e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 5/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.11e+04 K | 1.11e+04 K | 0.472 | 0.469 |
| 5 | 1.14e+04 K | 1.15e+04 K | 0.175 | 0.17 |
| 10 | 1.11e+04 K | 1.11e+04 K | 0.111 | 0.109 |
| 15 | 1.07e+04 K | 1.08e+04 K | 0.084 | 0.0822 |
[tardis.simulation.base][INFO ]
Current t_inner = 10636.106 K
Expected t_inner for next iteration = 10654.313 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 10 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.070e+43 erg / s
Luminosity absorbed = 3.335e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.11e+04 K | 1.1e+04 K | 0.469 | 0.475 |
| 5 | 1.15e+04 K | 1.14e+04 K | 0.17 | 0.177 |
| 10 | 1.11e+04 K | 1.11e+04 K | 0.109 | 0.112 |
| 15 | 1.08e+04 K | 1.06e+04 K | 0.0822 | 0.0878 |
[tardis.simulation.base][INFO ]
Current t_inner = 10654.313 K
Expected t_inner for next iteration = 10628.190 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 11 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.053e+43 erg / s
Luminosity absorbed = 3.363e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 1/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.1e+04 K | 1.1e+04 K | 0.475 | 0.472 |
| 5 | 1.14e+04 K | 1.12e+04 K | 0.177 | 0.184 |
| 10 | 1.11e+04 K | 1.1e+04 K | 0.112 | 0.114 |
| 15 | 1.06e+04 K | 1.06e+04 K | 0.0878 | 0.0859 |
[tardis.simulation.base][INFO ]
Current t_inner = 10628.190 K
Expected t_inner for next iteration = 10644.054 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 12 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.056e+43 erg / s
Luminosity absorbed = 3.420e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.1e+04 K | 1.11e+04 K | 0.472 | 0.467 |
| 5 | 1.12e+04 K | 1.13e+04 K | 0.184 | 0.176 |
| 10 | 1.1e+04 K | 1.11e+04 K | 0.114 | 0.11 |
| 15 | 1.06e+04 K | 1.08e+04 K | 0.0859 | 0.0821 |
[tardis.simulation.base][INFO ]
Current t_inner = 10644.054 K
Expected t_inner for next iteration = 10653.543 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 13 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.062e+43 erg / s
Luminosity absorbed = 3.406e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 1/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.11e+04 K | 1.11e+04 K | 0.467 | 0.466 |
| 5 | 1.13e+04 K | 1.13e+04 K | 0.176 | 0.18 |
| 10 | 1.11e+04 K | 1.11e+04 K | 0.11 | 0.111 |
| 15 | 1.08e+04 K | 1.08e+04 K | 0.0821 | 0.0841 |
[tardis.simulation.base][INFO ]
Current t_inner = 10653.543 K
Expected t_inner for next iteration = 10647.277 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 14 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.063e+43 erg / s
Luminosity absorbed = 3.369e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 2/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.11e+04 K | 1.11e+04 K | 0.466 | 0.469 |
| 5 | 1.13e+04 K | 1.13e+04 K | 0.18 | 0.182 |
| 10 | 1.11e+04 K | 1.1e+04 K | 0.111 | 0.113 |
| 15 | 1.08e+04 K | 1.07e+04 K | 0.0841 | 0.0854 |
[tardis.simulation.base][INFO ]
Current t_inner = 10647.277 K
Expected t_inner for next iteration = 10638.875 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 15 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.053e+43 erg / s
Luminosity absorbed = 3.417e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 3/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.11e+04 K | 1.1e+04 K | 0.469 | 0.484 |
| 5 | 1.13e+04 K | 1.13e+04 K | 0.182 | 0.181 |
| 10 | 1.1e+04 K | 1.1e+04 K | 0.113 | 0.113 |
| 15 | 1.07e+04 K | 1.07e+04 K | 0.0854 | 0.0858 |
[tardis.simulation.base][INFO ]
Current t_inner = 10638.875 K
Expected t_inner for next iteration = 10655.125 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 16 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.059e+43 erg / s
Luminosity absorbed = 3.445e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 4/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.1e+04 K | 1.1e+04 K | 0.484 | 0.472 |
| 5 | 1.13e+04 K | 1.13e+04 K | 0.181 | 0.177 |
| 10 | 1.1e+04 K | 1.1e+04 K | 0.113 | 0.113 |
| 15 | 1.07e+04 K | 1.06e+04 K | 0.0858 | 0.0858 |
[tardis.simulation.base][INFO ]
Current t_inner = 10655.125 K
Expected t_inner for next iteration = 10655.561 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 17 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.067e+43 erg / s
Luminosity absorbed = 3.372e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.1e+04 K | 1.11e+04 K | 0.472 | 0.468 |
| 5 | 1.13e+04 K | 1.14e+04 K | 0.177 | 0.175 |
| 10 | 1.1e+04 K | 1.11e+04 K | 0.113 | 0.11 |
| 15 | 1.06e+04 K | 1.08e+04 K | 0.0858 | 0.0816 |
[tardis.simulation.base][INFO ]
Current t_inner = 10655.561 K
Expected t_inner for next iteration = 10636.536 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 18 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.057e+43 erg / s
Luminosity absorbed = 3.365e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 1/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.11e+04 K | 1.11e+04 K | 0.468 | 0.464 |
| 5 | 1.14e+04 K | 1.13e+04 K | 0.175 | 0.177 |
| 10 | 1.11e+04 K | 1.1e+04 K | 0.11 | 0.113 |
| 15 | 1.08e+04 K | 1.07e+04 K | 0.0816 | 0.0848 |
[tardis.simulation.base][INFO ]
Current t_inner = 10636.536 K
Expected t_inner for next iteration = 10641.692 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Starting iteration 19 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.056e+43 erg / s
Luminosity absorbed = 3.405e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
[tardis.simulation.base][INFO ]
Iteration converged 2/4 consecutive times. (base.py:268)
[tardis.simulation.base][INFO ]
Plasma stratification: (base.py:548)
| Shell No. | t_rad | next_t_rad | w | next_w |
|---|---|---|---|---|
| 0 | 1.11e+04 K | 1.11e+04 K | 0.464 | 0.466 |
| 5 | 1.13e+04 K | 1.13e+04 K | 0.177 | 0.177 |
| 10 | 1.1e+04 K | 1.11e+04 K | 0.113 | 0.111 |
| 15 | 1.07e+04 K | 1.07e+04 K | 0.0848 | 0.0853 |
[tardis.simulation.base][INFO ]
Current t_inner = 10641.692 K
Expected t_inner for next iteration = 10650.463 K
(base.py:575)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/plasma/properties/radiative_properties.py:93: RuntimeWarning: invalid value encountered in divide
(g_lower * n_upper) / (g_upper * n_lower)
(warnings.py:109)
[tardis.simulation.base][INFO ]
Simulation finished in 19 iterations
Simulation took 49.44 s
(base.py:476)
[tardis.simulation.base][INFO ]
Starting iteration 20 of 20 (base.py:398)
[tardis.simulation.base][INFO ]
Luminosity emitted = 1.061e+43 erg / s
Luminosity absorbed = 3.401e+42 erg / s
Luminosity requested = 1.059e+43 erg / s
(base.py:580)
You can now use the to_hdf method, to save properties to a HDF file.
Parameters¶
file_path: Path where the HDF file should be stored. (Required)path: Path inside the HDF store to store the elements. (Optional)name: Name of the group inside HDF store, under which properties will be saved.(Optional) overwrite: If the HDF file already exists, do you overwrite the existing file (Optional, default False)Note
Throughout this notebook, we set overwrite=True so that the notebook can be run repeatedly if needed.
[2]:
simulation.to_hdf('/tmp/full_example.hdf', overwrite=True)
# The commented out code below shows an example of to_hdf with more parameters
#simulation.to_hdf(file_path='/tmp/full_example.hdf', path='/', name='simulation')
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/io/util.py:274: PerformanceWarning:
your performance may suffer as PyTables will pickle object types that it cannot
map directly to c-types [inferred_type->mixed,key->block0_values] [items->Index([0], dtype='int64')]
pd.DataFrame(value).to_hdf(buf, os.path.join(path, key))
(warnings.py:109)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/io/util.py:288: PerformanceWarning:
your performance may suffer as PyTables will pickle object types that it cannot
map directly to c-types [inferred_type->mixed,key->values] [items->None]
pd.Series(scalars).to_hdf(buf, os.path.join(path, "scalars"))
(warnings.py:109)
Open the stored HDF file with pandas and print a list of its entries using the keys() method:
[3]:
import pandas as pd
data = pd.HDFStore('/tmp/full_example.hdf', overwrite=True)
data.keys()
[3]:
['/simulation/iterations_electron_densities',
'/simulation/iterations_t_inner',
'/simulation/iterations_t_rad',
'/simulation/iterations_w',
'/simulation/transport/transport_state/emitted_packet_mask',
'/simulation/transport/transport_state/j_estimator',
'/simulation/transport/transport_state/last_interaction_in_nu',
'/simulation/transport/transport_state/last_interaction_type',
'/simulation/transport/transport_state/last_line_interaction_in_id',
'/simulation/transport/transport_state/last_line_interaction_out_id',
'/simulation/transport/transport_state/last_line_interaction_shell_id',
'/simulation/transport/transport_state/montecarlo_virtual_luminosity',
'/simulation/transport/transport_state/nu_bar_estimator',
'/simulation/transport/transport_state/output_energy',
'/simulation/transport/transport_state/output_nu',
'/simulation/transport/transport_state/packet_luminosity',
'/simulation/transport/transport_state/scalars',
'/simulation/transport/transport_state/spectrum_virtual/_frequency',
'/simulation/transport/transport_state/spectrum_virtual/luminosity',
'/simulation/transport/transport_state/spectrum_virtual/luminosity_density_lambda',
'/simulation/transport/transport_state/spectrum_virtual/scalars',
'/simulation/transport/transport_state/spectrum_virtual/wavelength',
'/simulation/transport/transport_state/spectrum_reabsorbed/_frequency',
'/simulation/transport/transport_state/spectrum_reabsorbed/luminosity',
'/simulation/transport/transport_state/spectrum_reabsorbed/luminosity_density_lambda',
'/simulation/transport/transport_state/spectrum_reabsorbed/scalars',
'/simulation/transport/transport_state/spectrum_reabsorbed/wavelength',
'/simulation/transport/transport_state/spectrum/_frequency',
'/simulation/transport/transport_state/spectrum/luminosity',
'/simulation/transport/transport_state/spectrum/luminosity_density_lambda',
'/simulation/transport/transport_state/spectrum/scalars',
'/simulation/transport/transport_state/spectrum/wavelength',
'/simulation/simulation_state/density',
'/simulation/simulation_state/dilution_factor',
'/simulation/simulation_state/r_inner',
'/simulation/simulation_state/scalars',
'/simulation/simulation_state/t_radiative',
'/simulation/simulation_state/v_inner',
'/simulation/simulation_state/v_outer',
'/simulation/plasma/abundance',
'/simulation/plasma/atomic_mass',
'/simulation/plasma/beta_rad',
'/simulation/plasma/beta_sobolev',
'/simulation/plasma/continuum_interaction_species',
'/simulation/plasma/density',
'/simulation/plasma/electron_densities',
'/simulation/plasma/excitation_energy',
'/simulation/plasma/f_lu',
'/simulation/plasma/g',
'/simulation/plasma/g_electron',
'/simulation/plasma/general_level_boltzmann_factor',
'/simulation/plasma/ion_number_density',
'/simulation/plasma/ionization_data',
'/simulation/plasma/j_blues',
'/simulation/plasma/level_boltzmann_factor',
'/simulation/plasma/level_number_density',
'/simulation/plasma/levels',
'/simulation/plasma/lines',
'/simulation/plasma/lines_lower_level_index',
'/simulation/plasma/lines_upper_level_index',
'/simulation/plasma/macro_atom_data',
'/simulation/plasma/metastability',
'/simulation/plasma/nlte_excitation_species',
'/simulation/plasma/nlte_ionization_species',
'/simulation/plasma/nu',
'/simulation/plasma/number_density',
'/simulation/plasma/partition_function',
'/simulation/plasma/phi',
'/simulation/plasma/scalars',
'/simulation/plasma/selected_atoms',
'/simulation/plasma/stimulated_emission_factor',
'/simulation/plasma/t_electrons',
'/simulation/plasma/t_rad',
'/simulation/plasma/tau_sobolevs',
'/simulation/plasma/transition_probabilities',
'/simulation/plasma/w',
'/simulation/plasma/wavelength_cm']
Access model.density under simulation, which is a one-dimensional array
[4]:
print(data['/simulation/simulation_state/density'])
0 7.542804e-14
1 5.728475e-14
2 4.396074e-14
3 3.406287e-14
4 2.663135e-14
5 2.099596e-14
6 1.668287e-14
7 1.335311e-14
8 1.076154e-14
9 8.729085e-15
10 7.123652e-15
11 5.846921e-15
12 4.825093e-15
13 4.002324e-15
14 3.336039e-15
15 2.793540e-15
16 2.349550e-15
17 1.984397e-15
18 1.682677e-15
19 1.432260e-15
dtype: float64
Scalars are stored in a scalars pandas.Series for every module. For example to access model.t_inner under simulation, one would need to do the following.
[5]:
print(data['/simulation/simulation_state/scalars']['t_inner'])
10650.463255529794
Breakdown of the various to_hdf methods¶
Every module in TARDIS has its own to_hdf method responsible to store its own data to an HDF file.
Plasma¶
The following call will store every plasma property to /tmp/plasma_output.hdf under /parent/plasma
[6]:
simulation.plasma.to_hdf('/tmp/plasma_output.hdf', path='parent', overwrite=True)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/io/util.py:274: PerformanceWarning:
your performance may suffer as PyTables will pickle object types that it cannot
map directly to c-types [inferred_type->mixed,key->block0_values] [items->Index([0], dtype='int64')]
pd.DataFrame(value).to_hdf(buf, os.path.join(path, key))
(warnings.py:109)
[py.warnings ][WARNING]
/home/runner/work/tardis/tardis/tardis/io/util.py:288: PerformanceWarning:
your performance may suffer as PyTables will pickle object types that it cannot
map directly to c-types [inferred_type->mixed,key->values] [items->None]
pd.Series(scalars).to_hdf(buf, os.path.join(path, "scalars"))
(warnings.py:109)
[7]:
import pandas
plasma_data = pandas.HDFStore('/tmp/plasma_output.hdf')
plasma_data.keys()
[7]:
['/parent/plasma/abundance',
'/parent/plasma/atomic_mass',
'/parent/plasma/beta_rad',
'/parent/plasma/beta_sobolev',
'/parent/plasma/continuum_interaction_species',
'/parent/plasma/density',
'/parent/plasma/electron_densities',
'/parent/plasma/excitation_energy',
'/parent/plasma/f_lu',
'/parent/plasma/g',
'/parent/plasma/g_electron',
'/parent/plasma/general_level_boltzmann_factor',
'/parent/plasma/ion_number_density',
'/parent/plasma/ionization_data',
'/parent/plasma/j_blues',
'/parent/plasma/level_boltzmann_factor',
'/parent/plasma/level_number_density',
'/parent/plasma/levels',
'/parent/plasma/lines',
'/parent/plasma/lines_lower_level_index',
'/parent/plasma/lines_upper_level_index',
'/parent/plasma/macro_atom_data',
'/parent/plasma/metastability',
'/parent/plasma/nlte_excitation_species',
'/parent/plasma/nlte_ionization_species',
'/parent/plasma/nu',
'/parent/plasma/number_density',
'/parent/plasma/partition_function',
'/parent/plasma/phi',
'/parent/plasma/scalars',
'/parent/plasma/selected_atoms',
'/parent/plasma/stimulated_emission_factor',
'/parent/plasma/t_electrons',
'/parent/plasma/t_rad',
'/parent/plasma/tau_sobolevs',
'/parent/plasma/transition_probabilities',
'/parent/plasma/w',
'/parent/plasma/wavelength_cm']
Plasma’s to_hdf method can also accept a collection parameter which can specify which types of plasma properties will be stored. For example if we wanted to only store Input plasma properties, we would do the following:
[8]:
from tardis.plasma.properties.base import Input
simulation.plasma.to_hdf('/tmp/plasma_input_output.hdf', collection=[Input], overwrite=True)
[9]:
import pandas
plasma_input_data = pandas.HDFStore('/tmp/plasma_input_output.hdf')
plasma_input_data.keys()
[9]:
['/plasma/abundance',
'/plasma/continuum_interaction_species',
'/plasma/density',
'/plasma/nlte_excitation_species',
'/plasma/nlte_ionization_species',
'/plasma/scalars',
'/plasma/t_rad',
'/plasma/w']
Model¶
The following call will store properties of the SimulationState to /tmp/model_output.hdf under /simulation_state.
[10]:
simulation.simulation_state.to_hdf('/tmp/model_output.hdf', overwrite=True)
[11]:
import pandas
model_data = pandas.HDFStore('/tmp/model_output.hdf')
model_data.keys()
[11]:
['/simulation_state/density',
'/simulation_state/dilution_factor',
'/simulation_state/r_inner',
'/simulation_state/scalars',
'/simulation_state/t_radiative',
'/simulation_state/v_inner',
'/simulation_state/v_outer']
MontecarloTransport¶
The following call will store properties of the MontecarloTransport to /tmp/transport_output.hdf under /transport.
[12]:
simulation.transport.to_hdf('/tmp/transport_output.hdf', overwrite=True)
[13]:
import pandas
transport_data = pandas.HDFStore('/tmp/transport_output.hdf')
transport_data.keys()
[13]:
['/transport/transport_state/emitted_packet_mask',
'/transport/transport_state/j_estimator',
'/transport/transport_state/last_interaction_in_nu',
'/transport/transport_state/last_interaction_type',
'/transport/transport_state/last_line_interaction_in_id',
'/transport/transport_state/last_line_interaction_out_id',
'/transport/transport_state/last_line_interaction_shell_id',
'/transport/transport_state/montecarlo_virtual_luminosity',
'/transport/transport_state/nu_bar_estimator',
'/transport/transport_state/output_energy',
'/transport/transport_state/output_nu',
'/transport/transport_state/packet_luminosity',
'/transport/transport_state/scalars',
'/transport/transport_state/spectrum_virtual/_frequency',
'/transport/transport_state/spectrum_virtual/luminosity',
'/transport/transport_state/spectrum_virtual/luminosity_density_lambda',
'/transport/transport_state/spectrum_virtual/scalars',
'/transport/transport_state/spectrum_virtual/wavelength',
'/transport/transport_state/spectrum_reabsorbed/_frequency',
'/transport/transport_state/spectrum_reabsorbed/luminosity',
'/transport/transport_state/spectrum_reabsorbed/luminosity_density_lambda',
'/transport/transport_state/spectrum_reabsorbed/scalars',
'/transport/transport_state/spectrum_reabsorbed/wavelength',
'/transport/transport_state/spectrum/_frequency',
'/transport/transport_state/spectrum/luminosity',
'/transport/transport_state/spectrum/luminosity_density_lambda',
'/transport/transport_state/spectrum/scalars',
'/transport/transport_state/spectrum/wavelength']