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restructure of geometry #2422

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merged 23 commits into from
Oct 19, 2023
Merged

restructure of geometry #2422

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314cf30
restructure of geometry
wkerzendorf Sep 28, 2023
d353133
add radial1d boundary logic
wkerzendorf Oct 4, 2023
2475551
black format
wkerzendorf Oct 4, 2023
e6d1697
several fixes
wkerzendorf Oct 4, 2023
3c53cda
fix epsilon
wkerzendorf Oct 4, 2023
6dce2b4
add testing of boundaries
wkerzendorf Oct 4, 2023
1fdcea8
change the r_inner_active
wkerzendorf Oct 4, 2023
56e9da5
first integration with `from_config` working
wkerzendorf Oct 7, 2023
f6743d7
hunting down density indexing bug
wkerzendorf Oct 8, 2023
b55b21d
all model tests (without csvy) pass
wkerzendorf Oct 8, 2023
ed978d9
more fixes
wkerzendorf Oct 9, 2023
cae9c19
fix of model to simulation_state
wkerzendorf Oct 9, 2023
d829e73
fix inner boundary packet error
wkerzendorf Oct 9, 2023
9592a97
fix some leftovers
wkerzendorf Oct 10, 2023
4da6869
final fix for csvy
wkerzendorf Oct 10, 2023
f381d2e
blackify
wkerzendorf Oct 10, 2023
e59741d
restructure to readers and remove some leftover code
wkerzendorf Oct 11, 2023
a42dd55
further cleanup
wkerzendorf Oct 11, 2023
3288c6c
first start of the restructure
wkerzendorf Oct 11, 2023
518a8f9
add comment about removing quantitiness
wkerzendorf Oct 11, 2023
c78b6de
add velocity check
wkerzendorf Oct 11, 2023
006ca9d
add new abundance functions
wkerzendorf Oct 12, 2023
9c680a8
remove default units
wkerzendorf Oct 12, 2023
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22 changes: 11 additions & 11 deletions tardis/io/model/model_reader.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ def transport_to_dict(transport):
"input_energy": transport.input_energy,
"input_mu": transport.input_mu,
"input_nu": transport.input_nu,
"input_r_cgs": transport.input_r,
"input_r": transport.input_r,
"j_blue_estimator": transport.j_blue_estimator,
"j_estimator": transport.j_estimator,
"last_interaction_in_nu": transport.last_interaction_in_nu,
Expand Down Expand Up @@ -296,23 +296,23 @@ def model_to_dict(model):
isotope_abundance : dict
"""
model_dict = {
"velocity_cgs": model.velocity,
"velocity_cgs": model.velocity.cgs,
"abundance": model.abundance,
"time_explosion_cgs": model.time_explosion,
"t_inner_cgs": model.t_inner,
"t_radiative_cgs": model.t_radiative,
"time_explosion_cgs": model.time_explosion.cgs,
"t_inner_cgs": model.t_inner.cgs,
"t_radiative_cgs": model.t_radiative.cgs,
"dilution_factor": model.dilution_factor,
"v_boundary_inner_cgs": model.v_boundary_inner,
"v_boundary_outer_cgs": model.v_boundary_outer,
"v_boundary_inner_cgs": model.v_boundary_inner.cgs,
"v_boundary_outer_cgs": model.v_boundary_outer.cgs,
"w": model.w,
"t_rad_cgs": model.t_rad,
"r_inner_cgs": model.r_inner,
"density_cgs": model.density,
"t_rad_cgs": model.t_rad.cgs,
"r_inner_cgs": model.r_inner.cgs,
"density_cgs": model.density.cgs,
}

for key, value in model_dict.items():
if hasattr(value, "unit"):
model_dict[key] = [value.cgs.value, value.unit.to_string()]
model_dict[key] = [value.cgs.value, value.cgs.unit.to_string()]

isotope_abundance = model.raw_isotope_abundance.__dict__

Expand Down
52 changes: 26 additions & 26 deletions tardis/io/tests/test_model_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -138,8 +138,10 @@ def test_model_to_dict(simulation_verysimple):
model_dict, isotope_abundance = model_to_dict(model)

# Check model dictionary
assert np.array_equal(model_dict["velocity_cgs"][0], model.velocity.value)
assert model_dict["velocity_cgs"][1] == model.velocity.unit.to_string()
assert np.array_equal(
model_dict["velocity_cgs"][0], model.velocity.cgs.value
)
assert model_dict["velocity_cgs"][1] == model.velocity.cgs.unit.to_string()
assert np.array_equal(model_dict["abundance"], model.abundance)
assert np.array_equal(
model_dict["time_explosion_cgs"][0], model.time_explosion.value
Expand All @@ -148,36 +150,36 @@ def test_model_to_dict(simulation_verysimple):
model_dict["time_explosion_cgs"][1]
== model.time_explosion.unit.to_string()
)
assert np.array_equal(model_dict["t_inner_cgs"][0], model.t_inner.value)
assert np.array_equal(model_dict["t_inner_cgs"][0], model.t_inner.cgs.value)
assert model_dict["t_inner_cgs"][1] == model.t_inner.unit.to_string()
assert np.array_equal(
model_dict["t_radiative_cgs"][0], model.t_radiative.value
model_dict["t_radiative_cgs"][0], model.t_radiative.cgs.value
)
assert (
model_dict["t_radiative_cgs"][1] == model.t_radiative.unit.to_string()
)
assert np.array_equal(model_dict["dilution_factor"], model.dilution_factor)
assert np.array_equal(
model_dict["v_boundary_inner_cgs"][0], model.v_boundary_inner.value
model_dict["v_boundary_inner_cgs"][0], model.v_boundary_inner.cgs.value
)
assert (
model_dict["v_boundary_inner_cgs"][1]
== model.v_boundary_inner.unit.to_string()
== model.v_boundary_inner.cgs.unit.to_string()
)
assert np.array_equal(
model_dict["v_boundary_outer_cgs"][0], model.v_boundary_outer.value
model_dict["v_boundary_outer_cgs"][0], model.v_boundary_outer.cgs.value
)
assert (
model_dict["v_boundary_outer_cgs"][1]
== model.v_boundary_outer.unit.to_string()
== model.v_boundary_outer.cgs.unit.to_string()
)
assert np.array_equal(model_dict["w"], model.w)
assert np.array_equal(model_dict["t_rad_cgs"][0], model.t_rad.value)
assert model_dict["t_rad_cgs"][1] == model.t_rad.unit.to_string()
assert np.array_equal(model_dict["r_inner_cgs"][0], model.r_inner.value)
assert model_dict["r_inner_cgs"][1] == model.r_inner.unit.to_string()
assert np.array_equal(model_dict["density_cgs"][0], model.density.value)
assert model_dict["density_cgs"][1] == model.density.unit.to_string()
assert np.array_equal(model_dict["t_rad_cgs"][0], model.t_rad.cgs.value)
assert model_dict["t_rad_cgs"][1] == model.t_rad.cgs.unit.to_string()
assert np.array_equal(model_dict["r_inner_cgs"][0], model.r_inner.cgs.value)
assert model_dict["r_inner_cgs"][1] == model.r_inner.cgs.unit.to_string()
assert np.array_equal(model_dict["density_cgs"][0], model.density.cgs.value)
assert model_dict["density_cgs"][1] == model.density.cgs.unit.to_string()


def test_store_model_to_hdf(simulation_verysimple, tmp_path):
Expand All @@ -190,26 +192,26 @@ def test_store_model_to_hdf(simulation_verysimple, tmp_path):

# Check file contents
with h5py.File(fname) as f:
assert np.array_equal(f["model/velocity_cgs"], model.velocity.value)
assert np.array_equal(f["model/velocity_cgs"], model.velocity.cgs.value)
assert np.array_equal(f["model/abundance"], model.abundance)
assert np.array_equal(
f["model/time_explosion_cgs"], model.time_explosion.value
f["model/time_explosion_cgs"], model.time_explosion.cgs.value
)
assert np.array_equal(f["model/t_inner_cgs"], model.t_inner.value)
assert np.array_equal(f["model/t_inner_cgs"], model.t_inner.cgs.value)
assert np.array_equal(
f["model/t_radiative_cgs"], model.t_radiative.value
f["model/t_radiative_cgs"], model.t_radiative.cgs.value
)
assert np.array_equal(f["model/dilution_factor"], model.dilution_factor)
assert np.array_equal(
f["model/v_boundary_inner_cgs"], model.v_boundary_inner.value
f["model/v_boundary_inner_cgs"], model.v_boundary_inner.cgs.value
)
assert np.array_equal(
f["model/v_boundary_outer_cgs"], model.v_boundary_outer.value
f["model/v_boundary_outer_cgs"], model.v_boundary_outer.cgs.value
)
assert np.array_equal(f["model/w"], model.w)
assert np.array_equal(f["model/t_rad_cgs"], model.t_rad.value)
assert np.array_equal(f["model/r_inner_cgs"], model.r_inner.value)
assert np.array_equal(f["model/density_cgs"], model.density.value)
assert np.array_equal(f["model/t_rad_cgs"], model.t_rad.cgs.value)
assert np.array_equal(f["model/r_inner_cgs"], model.r_inner.cgs.value)
assert np.array_equal(f["model/density_cgs"], model.density.cgs.value)


def test_transport_to_dict(simulation_verysimple):
Expand Down Expand Up @@ -289,9 +291,7 @@ def test_store_transport_to_hdf(simulation_verysimple, tmp_path):
assert np.array_equal(
f["transport/input_nu"], transport_data["input_nu"]
)
assert np.array_equal(
f["transport/input_r_cgs"], transport_data["input_r"].value
)
assert np.array_equal(f["transport/input_r"], transport_data["input_r"])
assert np.array_equal(
f["transport/j_blue_estimator"], transport_data["j_blue_estimator"]
)
Expand Down
2 changes: 1 addition & 1 deletion tardis/model/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,4 +6,4 @@
factor of the model used in the simulation.
"""

from tardis.model.base import *
from tardis.model.base import SimulationState
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