Calculate a spectrum from ExoMol¶
Auto-download and compute a SiO spectrum from the ExoMol database ([ExoMol-2020])
from radis import calc_spectrum
s = calc_spectrum(
1080,
1320, # cm-1
species="SiO",
isotope="1",
pressure=1.01325, # bar
Tgas=1000, # K
mole_fraction=0.1,
path_length=1, # cm
databank=(
"exomol",
"EBJT",
), # Or simply use 'exomol' to auto-select the recommended database (if one exists)
)
s.apply_slit(1, "cm-1") # simulate an experimental slit
s.plot("radiance")
--------------------------------------------------------------------------------
SiO - EXOMOL - Fetching 28Si-16O - EBJT
--------------------------------------------------------------------------------
- Local folder: /home/docs/.radisdb/exomol/SiO/28Si-16O/EBJT
Download:
- Total download size: 0.000244 GB
- Downloading 28Si-16O__EBJT.states.bz2
- Total download size: 0.000004 GB
- Total download size: 0.000044 GB
- Downloading 28Si-16O__EBJT.def
- Downloading 28Si-16O__EBJT.pf
28Si-16O__EBJT.def: 0%| | 0.00/4.65k [00:00<?, ?B/s]
28Si-16O__EBJT.def: 100%|██████████| 4.65k/4.65k [00:00<00:00, 34.7MB/s]
28Si-16O__EBJT.states.bz2: 0%| | 0.00/256k [00:00<?, ?B/s]
28Si-16O__EBJT.pf: 0%| | 0.00/45.7k [00:00<?, ?B/s]
28Si-16O__EBJT.pf: 70%|███████ | 32.0k/45.7k [00:00<00:00, 184kB/s]
28Si-16O__EBJT.pf: 100%|██████████| 45.7k/45.7k [00:00<00:00, 262kB/s]
28Si-16O__EBJT.states.bz2: 13%|█▎ | 32.0k/256k [00:00<00:01, 182kB/s]
28Si-16O__EBJT.states.bz2: 47%|████▋ | 120k/256k [00:00<00:00, 369kB/s]
28Si-16O__EBJT.states.bz2: 100%|██████████| 256k/256k [00:00<00:00, 720kB/s]
- Total download size: 0.000016 GB
Broadening:
- Downloading 28Si-16O__H2.broad
- Downloading 28Si-16O__He.broad
- Downloading 28Si-16O__air.broad
- Downloading 28Si-16O__self.broad
28Si-16O__He.broad: 0%| | 0.00/23.0 [00:00<?, ?B/s]
28Si-16O__He.broad: 100%|██████████| 23.0/23.0 [00:00<00:00, 241kB/s]
- Downloading 28Si-16O__Ar.broad
28Si-16O__self.broad: 0%| | 0.00/22.0 [00:00<?, ?B/s]
28Si-16O__self.broad: 100%|██████████| 22.0/22.0 [00:00<00:00, 323kB/s]
- Downloading 28Si-16O__CH4.broad
28Si-16O__air.broad: 0%| | 0.00/16.6k [00:00<?, ?B/s]
28Si-16O__H2.broad: 0%| | 0.00/22.0 [00:00<?, ?B/s]
28Si-16O__H2.broad: 100%|██████████| 22.0/22.0 [00:00<00:00, 326kB/s]
- Downloading 28Si-16O__CO.broad
28Si-16O__air.broad: 100%|██████████| 16.6k/16.6k [00:00<00:00, 188kB/s]
- Downloading 28Si-16O__CO2.broad
28Si-16O__Ar.broad: 0%| | 0.00/23.0 [00:00<?, ?B/s]
28Si-16O__Ar.broad: 100%|██████████| 23.0/23.0 [00:00<00:00, 243kB/s]
- Downloading 28Si-16O__H2.broad
28Si-16O__CH4.broad: 0%| | 0.00/22.0 [00:00<?, ?B/s]
28Si-16O__CH4.broad: 100%|██████████| 22.0/22.0 [00:00<00:00, 309kB/s]
- Downloading 28Si-16O__H2O.broad
28Si-16O__CO.broad: 0%| | 0.00/23.0 [00:00<?, ?B/s]
28Si-16O__CO.broad: 100%|██████████| 23.0/23.0 [00:00<00:00, 295kB/s]
- Downloading 28Si-16O__N2.broad
28Si-16O__CO2.broad: 0%| | 0.00/23.0 [00:00<?, ?B/s]
28Si-16O__CO2.broad: 100%|██████████| 23.0/23.0 [00:00<00:00, 182kB/s]
- Downloading 28Si-16O__NH3.broad
28Si-16O__H2.broad: 0%| | 0.00/22.0 [00:00<?, ?B/s]
28Si-16O__H2.broad: 100%|██████████| 22.0/22.0 [00:00<00:00, 220kB/s]
- Downloading 28Si-16O__NO.broad
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28Si-16O__H2O.broad: 100%|██████████| 23.0/23.0 [00:00<00:00, 319kB/s]
- Downloading 28Si-16O__O2.broad
28Si-16O__N2.broad: 0%| | 0.00/23.0 [00:00<?, ?B/s]
28Si-16O__N2.broad: 100%|██████████| 23.0/23.0 [00:00<00:00, 346kB/s]
- Downloading 28Si-16O__NH3.broad
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28Si-16O__NH3.broad: 100%|██████████| 23.0/23.0 [00:00<00:00, 170kB/s]
- Downloading 28Si-16O__CS.broad
28Si-16O__NO.broad: 0%| | 0.00/23.0 [00:00<?, ?B/s]
28Si-16O__NO.broad: 100%|██████████| 23.0/23.0 [00:00<00:00, 224kB/s]
28Si-16O__O2.broad: 0%| | 0.00/23.0 [00:00<?, ?B/s]
28Si-16O__O2.broad: 100%|██████████| 23.0/23.0 [00:00<00:00, 263kB/s]
28Si-16O__NH3.broad: 0%| | 0.00/23.0 [00:00<?, ?B/s]
28Si-16O__NH3.broad: 100%|██████████| 23.0/23.0 [00:00<00:00, 326kB/s]
Warning: Couldn't download .broad file
- Downloaded 15 broadening file(s): H2, He, air, self, Ar, CH4, CO, CO2, H2, H2O, N2, NH3, NO, O2, NH3
- 1 broadening file(s) not available (using default parameters)
- Caching states data to vaex format. This will be faster on subsequent runs.
Download:
- Total download size: 0.002863 GB
- Downloading 28Si-16O__EBJT.trans.bz2
28Si-16O__EBJT.trans.bz2: 0%| | 0.00/2.93M [00:00<?, ?B/s]
28Si-16O__EBJT.trans.bz2: 1%| | 32.0k/2.93M [00:00<00:16, 183kB/s]
28Si-16O__EBJT.trans.bz2: 6%|▌ | 168k/2.93M [00:00<00:05, 532kB/s]
28Si-16O__EBJT.trans.bz2: 18%|█▊ | 536k/2.93M [00:00<00:02, 1.23MB/s]
28Si-16O__EBJT.trans.bz2: 34%|███▍ | 0.99M/2.93M [00:00<00:01, 1.80MB/s]
28Si-16O__EBJT.trans.bz2: 49%|████▉ | 1.43M/2.93M [00:00<00:00, 2.10MB/s]
28Si-16O__EBJT.trans.bz2: 60%|█████▉ | 1.75M/2.93M [00:01<00:00, 2.38MB/s]
28Si-16O__EBJT.trans.bz2: 68%|██████▊ | 1.99M/2.93M [00:01<00:00, 2.05MB/s]
28Si-16O__EBJT.trans.bz2: 79%|███████▉ | 2.31M/2.93M [00:01<00:00, 2.01MB/s]
28Si-16O__EBJT.trans.bz2: 89%|████████▊ | 2.60M/2.93M [00:01<00:00, 2.22MB/s]
28Si-16O__EBJT.trans.bz2: 98%|█████████▊| 2.88M/2.93M [00:01<00:00, 2.04MB/s]
28Si-16O__EBJT.trans.bz2: 100%|██████████| 2.93M/2.93M [00:01<00:00, 1.89MB/s]
- File 28Si-16O__EBJT.trans
- Caching the *.trans.bz2 file to the vaex (*.h5) format. After the second time, it will become much faster.
/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/io/exomol.py:263: AccuracyWarning: ExoMol cache file /home/docs/.radisdb/exomol/SiO/28Si-16O/EBJT/28Si-16O__EBJT.trans.hdf5 is missing columns ['gupper', 'glower']. This may be from an older version of RADIS. Regenerate the cache with `cache='regen'` to fix this.
warnings.warn(
Cleaned up downloaded file: 28Si-16O__EBJT.trans.bz2
Broadening code level: m0
Broadening code level: a0
/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/exomolapi.py:728: AccuracyWarning: The default broadening parameter (alpha = 0.07 cm^-1 and n = 0.5) are used for J'' > 0 up to J'' = 396
warnings.warn(
ExoMol database loading complete
9.39s - Loaded database
/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/misc/warning.py:443: MissingPressureShiftWarning: Pressure-shift coefficient not given in database: assumed 0 pressure shift
warnings.warn(WarningType(message))
Calculating Equilibrium Spectrum
Physical Conditions
----------------------------------------
Tgas 1000 K
isotope 1
medium air
mole_fraction 0.1
path_length 1 cm
pressure 1.01325 bar
self_absorption True
species SiO
state X
wavenum_max 1320.0000 cm-1
wavenum_min 1080.0000 cm-1
Computation Parameters
----------------------------------------
Tref 296 K
add_at_used numpy
broadening_method voigt_poly
cutoff 1e-27 cm-1/(#.cm-2)
dbformat exomol-radisdb
dbpath /home/docs/.radisdb/exomol/SiO/28Si-16O/EBJT
diluent air
folding_thresh 1e-06
include_neighbouring_lines True
isatom False
isneutral None
lbfunc None
memory_mapping_engine auto
neighbour_lines 0 cm-1
optimization simple
parsum_mode full summation
pfsource default
potential_lowering None
pseudo_continuum_threshold 0
sparse_ldm True
truncation 50 cm-1
waveunit cm-1
wstep 0.01 cm-1
zero_padding 24001
----------------------------------------
0.03s - Spectrum calculated
Slice 1/1
"""ExoMol lines can be downloaded and accessed separately using
:py:func:`~radis.io.exomol.fetch_exomol`
"""
# See line data:
from radis.io.exomol import fetch_exomol
df = fetch_exomol("SiO", database="EBJT", isotope=1, load_wavenum_max=5000)
print(df)
/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/io/exomol.py:263: AccuracyWarning: ExoMol cache file /home/docs/.radisdb/exomol/SiO/28Si-16O/EBJT/28Si-16O__EBJT.trans.hdf5 is missing columns ['gupper', 'glower']. This may be from an older version of RADIS. Regenerate the cache with `cache='regen'` to fix this.
warnings.warn(
Broadening code level: m0
Broadening code level: a0
/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/exomolapi.py:728: AccuracyWarning: The default broadening parameter (alpha = 0.07 cm^-1 and n = 0.5) are used for J'' > 0 up to J'' = 408
warnings.warn(
i_upper i_lower A ... Tdpair selbrd selbrd_Tdpair
0 24300 24299 1.926600e-12 ... 0.5 0.082 0.5
1 4698 5073 3.431600e-10 ... NaN 0.070 0.5
2 24273 24272 1.652000e-10 ... 0.5 0.082 0.5
3 24301 24300 1.725200e-11 ... 0.5 0.070 0.5
4 24232 24231 7.675700e-10 ... 0.5 0.082 0.5
... ... ... ... ... ... ... ...
249599 3769 1818 2.429700e-04 ... 0.5 0.070 0.5
249600 8052 6269 1.481800e-02 ... 0.5 0.070 0.5
249601 8693 6938 1.601100e-02 ... 0.5 0.070 0.5
249602 8659 6904 1.166600e-02 ... 0.5 0.070 0.5
249603 7665 5871 3.160000e-03 ... 0.5 0.070 0.5
[249604 rows x 15 columns]
See the list of recommended databases for the 1st isotope of SiO :
from radis.io.exomol import get_exomol_database_list, get_exomol_full_isotope_name
databases, recommended = get_exomol_database_list(
"SiO", get_exomol_full_isotope_name("SiO", 1)
)
print("Databases for SiO: ", databases)
print("Database recommended by ExoMol: ", recommended)
Databases for SiO: [np.str_('EBJT'), np.str_('Kurucz-SiO'), np.str_('SiOUVenIR'), np.str_('xsec-SiOUVenIR')]
Database recommended by ExoMol: SiOUVenIR
Total running time of the script: (0 minutes 11.614 seconds)