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@HajimeKawahara
HajimeKawahara committed Apr 26, 2024
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85 changes: 45 additions & 40 deletions documents/tutorials/reverse_premodit.rst
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Expand Up @@ -45,7 +45,7 @@ In this tutorial, we use ``PreMODIT`` as an opacity calculator.
.. parsed-literal::
/home/exoplanet01/exojax/src/exojax/spec/dtau_mmwl.py:14: FutureWarning: dtau_mmwl might be removed in future.
/home/kawahara/exojax/src/exojax/spec/dtau_mmwl.py:14: FutureWarning: dtau_mmwl might be removed in future.
warnings.warn("dtau_mmwl might be removed in future.", FutureWarning)
Expand Down Expand Up @@ -81,10 +81,18 @@ normlized it, and add Gaussian noise.
flux = dat['flux'].values
wavd = nu2wav(nusd, wavelength_order="ascending")
.. parsed-literal::
/home/kawahara/exojax/src/exojax/spec/unitconvert.py:62: UserWarning: Both input wavelength and output wavenumber are in ascending order.
warnings.warn(
.. code:: ipython3
sigmain = 0.05
norm = 20000
np.random.seed(1)
nflux = flux / norm + np.random.normal(0, sigmain, len(wavd))
We first set the wavenumber grid enough to cover the observed spectrum.
Expand All @@ -104,18 +112,19 @@ We first set the wavenumber grid enough to cover the observed spectrum.
xsmode = premodit
xsmode assumes ESLOG in wavenumber space: mode=premodit
======================================================================
We changed the policy of the order of wavenumber/wavelength grids
wavenumber grid should be in ascending order and now
users can specify the order of the wavelength grid by themselves.
The wavenumber grid should be in ascending order.
The users can specify the order of the wavelength grid by themselves.
Your wavelength grid is in *** ascending *** order
This might causes the bug if you update ExoJAX.
Note that the older ExoJAX assumes ascending order as wavelength grid.
======================================================================
.. parsed-literal::
/home/exoplanet01/exojax/src/exojax/utils/grids.py:145: UserWarning: Resolution may be too small. R=617160.1067701889
/home/kawahara/exojax/src/exojax/spec/unitconvert.py:62: UserWarning: Both input wavelength and output wavenumber are in ascending order.
warnings.warn(
/home/kawahara/exojax/src/exojax/spec/unitconvert.py:62: UserWarning: Both input wavelength and output wavenumber are in ascending order.
warnings.warn(
/home/kawahara/exojax/src/exojax/utils/grids.py:142: UserWarning: Resolution may be too small. R=617160.1067701889
warnings.warn('Resolution may be too small. R=' + str(resolution),
Expand All @@ -133,8 +142,8 @@ We would analyze the emission spectrum. So, we use ``ArtEmisPure`` as
.. parsed-literal::
rtsolver: fbased2st
Flux-based two-stream solver, isothermal layer (ExoJAX1, HELIOS-R1 like)
rtsolver: ibased
Intensity-based n-stream solver, isothermal layer (e.g. NEMESIS, pRT like)
``beta_inst`` is a standard deviation of the instrumental profile.
Expand All @@ -161,31 +170,27 @@ ExoMol website.
nu_grid=nu_grid,
diffmode=diffmode,
auto_trange=[Tlow, Thigh],
dit_grid_resolution=0.2,allow_32bit=True)
dit_grid_resolution=1.0,allow_32bit=True)
.. parsed-literal::
HITRAN exact name= (12C)(1H)4
HITRAN exact name= (12C)(1H)4
.. parsed-literal::
/home/exoplanet01/exojax/src/exojax/utils/molname.py:178: FutureWarning: e2s will be replaced to exact_molname_exomol_to_simple_molname.
/home/kawahara/exojax/src/exojax/utils/molname.py:178: FutureWarning: e2s will be replaced to exact_molname_exomol_to_simple_molname.
warnings.warn(
/home/exoplanet01/exojax/src/exojax/utils/molname.py:65: UserWarning: No isotope number identified.
/home/kawahara/exojax/src/exojax/utils/molname.py:65: UserWarning: No isotope number identified.
warnings.warn("No isotope number identified.", UserWarning)
/home/exoplanet01/exojax/src/exojax/utils/molname.py:65: UserWarning: No isotope number identified.
/home/kawahara/exojax/src/exojax/utils/molname.py:65: UserWarning: No isotope number identified.
warnings.warn("No isotope number identified.", UserWarning)
/home/exoplanet01/exojax/src/exojax/spec/molinfo.py:28: UserWarning: exact molecule name is not Exomol nor HITRAN form.
/home/kawahara/exojax/src/exojax/spec/molinfo.py:28: UserWarning: exact molecule name is not Exomol nor HITRAN form.
warnings.warn("exact molecule name is not Exomol nor HITRAN form.")
/home/exoplanet01/exojax/src/exojax/spec/molinfo.py:29: UserWarning: No molmass available
/home/kawahara/exojax/src/exojax/spec/molinfo.py:29: UserWarning: No molmass available
warnings.warn("No molmass available", UserWarning)
.. parsed-literal::
HITRAN exact name= (12C)(1H)4
HITRAN exact name= (12C)(1H)4
Molecule: CH4
Isotopologue: 12C-1H4
Background atmosphere: H2
Expand All @@ -211,48 +216,49 @@ ExoMol website.
.. parsed-literal::
/home/exoplanet01/anaconda3/lib/python3.10/site-packages/radis-0.15-py3.10-linux-x86_64.egg/radis/api/exomolapi.py:607: AccuracyWarning: The default broadening parameter (alpha = 0.0488 cm^-1 and n = 0.4) are used for J'' > 16 up to J'' = 40
/home/kawahara/exojax/src/radis/radis/api/exomolapi.py:607: AccuracyWarning: The default broadening parameter (alpha = 0.0488 cm^-1 and n = 0.4) are used for J'' > 16 up to J'' = 40
warnings.warn(
.. parsed-literal::
N= 80505310
OpaPremodit: params automatically set.
Robust range: 397.77407283130566 - 1689.7679243628259 K
Tref changed: 296.0K->1153.6267095763965K
default elower grid trange (degt) file version: 2
Robust range: 393.5569458240504 - 1647.2060977798956 K
Tref changed: 296.0K->1108.1485374361412K
.. parsed-literal::
/home/exoplanet01/exojax/src/exojax/utils/jaxstatus.py:19: UserWarning: JAX is 32bit mode. We recommend to use 64bit mode.
/home/kawahara/exojax/src/exojax/utils/jaxstatus.py:19: UserWarning: JAX is 32bit mode. We recommend to use 64bit mode.
You can change to 64bit mode by writing
from jax import config
config.update("jax_enable_x64", True)
warnings.warn(msg+how_change_msg)
/home/exoplanet01/exojax/src/exojax/spec/opacalc.py:169: UserWarning: dit_grid_resolution is not None. Ignoring broadening_parameter_resolution.
/home/kawahara/exojax/src/exojax/spec/opacalc.py:171: UserWarning: dit_grid_resolution is not None. Ignoring broadening_parameter_resolution.
warnings.warn(
/home/exoplanet01/exojax/src/exojax/spec/api.py:390: RuntimeWarning: divide by zero encountered in log
/home/kawahara/exojax/src/exojax/spec/api.py:326: RuntimeWarning: divide by zero encountered in log
self.logsij0 = np.log(self.line_strength_ref)
.. parsed-literal::
OpaPremodit: Tref_broadening is set to 774.5966692414833 K
# of reference width grid : 3
# of reference width grid : 2
# of temperature exponent grid : 2
.. parsed-literal::
uniqidx: 100%|██████████| 1/1 [00:01<00:00, 1.68s/it]
uniqidx: 0it [00:00, ?it/s]
.. parsed-literal::
Premodit: Twt= 461.3329793405918 K Tref= 1153.6267095763965 K
Premodit: Twt= 457.65619999186345 K Tref= 1108.1485374361412 K
Making LSD:|####################| 100%
Expand Down Expand Up @@ -374,8 +380,7 @@ The following is the numpyro model, i.e. prior and sample.
kernel = NUTS(model_c, forward_mode_differentiation=False)
Let’s run the HMC-NUTS. In my environment, it took ~2 hours using A4500.
We observed here the number of divergences of 179. If you use FP64,
maybe no divergence.
We observed here the number of divergences of 2.

.. code:: ipython3
Expand All @@ -386,21 +391,21 @@ maybe no divergence.
.. parsed-literal::
sample: 100%|██████████| 1500/1500 [2:18:31<00:00, 5.54s/it, 511 steps of size 4.79e-03. acc. prob=0.69]
sample: 100%|██████████| 1500/1500 [2:25:22<00:00, 5.81s/it, 1023 steps of size 4.53e-03. acc. prob=0.94]
.. parsed-literal::
mean std median 5.0% 95.0% n_eff r_hat
MMR_CH4 0.01 0.00 0.01 0.01 0.01 196.80 1.02
RV 9.40 0.38 9.38 8.80 10.07 231.02 1.00
Rp 0.57 0.10 0.56 0.42 0.70 196.13 1.02
T0 1221.15 17.40 1220.48 1192.18 1246.90 270.27 1.00
alpha 0.11 0.01 0.11 0.10 0.12 153.76 1.00
vsini 19.68 0.70 19.66 18.48 20.82 203.31 1.00
MMR_CH4 0.01 0.00 0.01 0.00 0.01 459.21 1.00
RV 9.32 0.40 9.33 8.69 9.99 547.61 1.00
Rp 0.67 0.19 0.62 0.40 0.98 448.36 1.00
T0 1204.92 17.17 1204.94 1174.23 1229.56 635.51 1.00
alpha 0.10 0.01 0.10 0.10 0.11 497.56 1.00
vsini 19.50 0.67 19.47 18.47 20.67 648.31 1.00
Number of divergences: 179
Number of divergences: 2
.. code:: ipython3
Expand Down

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