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fix shell info widget
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@wkerzendorf
wkerzendorf committed Jul 27, 2024
1 parent 683e811 commit d381f02
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122 changes: 81 additions & 41 deletions docs/physics/plasma/construction_simple_plasma.ipynb
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Expand Up @@ -9,48 +9,12 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/wkerzend/python/tardis/tardis/__init__.py:20: UserWarning: Astropy is already imported externally. Astropy should be imported after TARDIS.\n",
" warnings.warn(\n"
]
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "a4d91ae0803f463c96fe296874d0bacd",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Iterations: 0/? [00:00<?, ?it/s]"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "ea438710d8a44942820502de430b36ef",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Packets: 0/? [00:00<?, ?it/s]"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"outputs": [],
"source": [
"import numpy as np\n",
"import pandas as pd\n",
"from astropy import units as u\n",
"\n",
"from tardis.io.atom_data import AtomData\n",
Expand Down Expand Up @@ -98,11 +62,87 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"plasma_solver_factory.assemble(d_radfield)"
"base_density = 1e-15 * u.Unit('g/cm^3')\n",
"number_densities = pd.DataFrame(columns=[1], index=[1,2])\n",
"number_densities.loc[1] = 0.5 * (base_density / u.u).to(1/u.cm**3).value\n",
"number_densities.loc[2] = 0.5 * (base_density / u.u).to(1/u.cm**3).value"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"ename": "PlasmaMissingModule",
"evalue": "Module PartitionFunction requires input level_boltzmann_factor which has not been added to this plasma",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mPlasmaMissingModule\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[14], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mplasma_solver_factory\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43massemble\u001b[49m\u001b[43m(\u001b[49m\u001b[43mnumber_densities\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43md_radfield\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m5\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mu\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mday\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/python/tardis/tardis/plasma/assembly/base.py:506\u001b[0m, in \u001b[0;36mPlasmaSolverFactory.assemble\u001b[0;34m(self, number_densities, dilute_planckian_radiation_field, time_explosion, electron_densities)\u001b[0m\n\u001b[1;32m 504\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msetup_electron_densities(electron_densities)\n\u001b[1;32m 505\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mhelium_treatment\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhelium_treatment\n\u001b[0;32m--> 506\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mBasePlasma\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 507\u001b[0m \u001b[43m \u001b[49m\u001b[43mplasma_properties\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mplasma_modules\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 508\u001b[0m \u001b[43m \u001b[49m\u001b[43mproperty_kwargs\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mproperty_kwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 509\u001b[0m \u001b[43m \u001b[49m\u001b[43mplasma_solver_settings\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mplasma_solver_settings\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 510\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 511\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/python/tardis/tardis/io/util.py:195\u001b[0m, in \u001b[0;36mHDFWriterMixin.__new__\u001b[0;34m(cls, *args, **kwargs)\u001b[0m\n\u001b[1;32m 193\u001b[0m instance \u001b[38;5;241m=\u001b[39m \u001b[38;5;28msuper\u001b[39m(HDFWriterMixin, \u001b[38;5;28mcls\u001b[39m)\u001b[38;5;241m.\u001b[39m\u001b[38;5;21m__new__\u001b[39m(\u001b[38;5;28mcls\u001b[39m)\n\u001b[1;32m 194\u001b[0m instance\u001b[38;5;241m.\u001b[39moptional_hdf_properties \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m--> 195\u001b[0m \u001b[43minstance\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[38;5;21;43m__init__\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 196\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m instance\n",
"File \u001b[0;32m~/python/tardis/tardis/plasma/base.py:39\u001b[0m, in \u001b[0;36mBasePlasma.__init__\u001b[0;34m(self, plasma_properties, property_kwargs, plasma_solver_settings, **kwargs)\u001b[0m\n\u001b[1;32m 35\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mplasma_properties \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_init_properties(\n\u001b[1;32m 36\u001b[0m plasma_properties, property_kwargs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs\n\u001b[1;32m 37\u001b[0m )\n\u001b[1;32m 38\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mplasma_solver_settings \u001b[38;5;241m=\u001b[39m plasma_solver_settings\n\u001b[0;32m---> 39\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_build_graph\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 40\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mupdate(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n",
"File \u001b[0;32m~/python/tardis/tardis/plasma/base.py:101\u001b[0m, in \u001b[0;36mBasePlasma._build_graph\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 99\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m \u001b[38;5;28minput\u001b[39m \u001b[38;5;129;01min\u001b[39;00m plasma_property\u001b[38;5;241m.\u001b[39minputs:\n\u001b[1;32m 100\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28minput\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39moutputs_dict:\n\u001b[0;32m--> 101\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m PlasmaMissingModule(\n\u001b[1;32m 102\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mModule \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mplasma_property\u001b[38;5;241m.\u001b[39mname\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m requires input \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 103\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28minput\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m which has not been added\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 104\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m to this plasma\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 105\u001b[0m )\n\u001b[1;32m 106\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 107\u001b[0m position \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39moutputs_dict[\u001b[38;5;28minput\u001b[39m]\u001b[38;5;241m.\u001b[39moutputs\u001b[38;5;241m.\u001b[39mindex(\u001b[38;5;28minput\u001b[39m)\n",
"\u001b[0;31mPlasmaMissingModule\u001b[0m: Module PartitionFunction requires input level_boltzmann_factor which has not been added to this plasma"
]
}
],
"source": [
"plasma_solver_factory.assemble(number_densities, d_radfield, 5 * u.day)"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[tardis.plasma.properties.plasma_input.DilutePlanckianRadField,\n",
" tardis.plasma.properties.plasma_input.DilutePlanckianRadField,\n",
" tardis.plasma.properties.plasma_input.NumberDensity,\n",
" tardis.plasma.properties.plasma_input.TimeExplosion,\n",
" tardis.plasma.properties.plasma_input.AtomicData,\n",
" tardis.plasma.properties.plasma_input.JBlues,\n",
" tardis.plasma.properties.plasma_input.LinkTRadTElectron,\n",
" tardis.plasma.properties.plasma_input.HeliumTreatment,\n",
" tardis.plasma.properties.plasma_input.ContinuumInteractionSpecies,\n",
" tardis.plasma.properties.plasma_input.NLTEIonizationSpecies,\n",
" tardis.plasma.properties.plasma_input.NLTEExcitationSpecies,\n",
" tardis.plasma.properties.plasma_input.TRadiative,\n",
" tardis.plasma.properties.plasma_input.DilutionFactor,\n",
" tardis.plasma.properties.general.BetaRadiation,\n",
" tardis.plasma.properties.atomic.Levels,\n",
" tardis.plasma.properties.atomic.Lines,\n",
" tardis.plasma.properties.partition_function.PartitionFunction,\n",
" tardis.plasma.properties.general.GElectron,\n",
" tardis.plasma.properties.atomic.IonizationData,\n",
" tardis.plasma.properties.atomic.LinesLowerLevelIndex,\n",
" tardis.plasma.properties.atomic.LinesUpperLevelIndex,\n",
" tardis.opacities.tau_sobolev.TauSobolev,\n",
" tardis.plasma.properties.radiative_properties.StimulatedEmissionFactor,\n",
" tardis.plasma.properties.general.SelectedAtoms,\n",
" tardis.plasma.properties.general.ElectronTemperature,\n",
" tardis.plasma.properties.partition_function.LevelBoltzmannFactorLTE,\n",
" tardis.plasma.properties.ion_population.PhiSahaLTE,\n",
" tardis.plasma.properties.level_population.LevelNumberDensity,\n",
" tardis.plasma.properties.ion_population.IonNumberDensity]"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"plasma_solver_factory.plasma_modules"
]
},
{
Expand Down
2 changes: 1 addition & 1 deletion tardis/visualization/widgets/shell_info.py
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Original file line number Diff line number Diff line change
Expand Up @@ -190,7 +190,7 @@ def __init__(self, sim_model):
super().__init__(
sim_model.simulation_state.t_radiative,
sim_model.simulation_state.dilution_factor,
sim_model.plasma.abundance,
sim_model.simulation_state.abundance,
sim_model.plasma.number_density,
sim_model.plasma.ion_number_density,
sim_model.plasma.level_number_density,
Expand Down
8 changes: 5 additions & 3 deletions tardis/visualization/widgets/tests/test_shell_info.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ def base_shell_info(simulation_verysimple):
return BaseShellInfo(
simulation_verysimple.simulation_state.t_radiative,
simulation_verysimple.simulation_state.dilution_factor,
simulation_verysimple.plasma.abundance,
simulation_verysimple.simulation_state.abundance,
simulation_verysimple.plasma.number_density,
simulation_verysimple.plasma.ion_number_density,
simulation_verysimple.plasma.level_number_density,
Expand Down Expand Up @@ -58,12 +58,14 @@ def test_element_count_data(
):
element_count_data = base_shell_info.element_count(1)
assert element_count_data.shape == (
len(simulation_verysimple.plasma.abundance[shell_num - 1]),
len(
simulation_verysimple.simulation_state.abundance[shell_num - 1]
),
2,
)
assert np.allclose(
element_count_data.iloc[:, -1].map(np.float64),
simulation_verysimple.plasma.abundance[shell_num - 1],
simulation_verysimple.simulation_state.abundance[shell_num - 1],
)

@pytest.mark.parametrize(("atomic_num", "shell_num"), [(12, 1), (20, 20)])
Expand Down

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