1"""
2
3This file will showcase how you can load collision-induced absorption (CIA)
4data from arts-cat-data into the workspace and do the required setups to
5perform a simple forward calculations using this data
6
7Note that this example presumes that you have set the environment variable
8ARTS_DATA_PATH to contain a path to a local copy of both arts-cat-data and
9arts-xml-data before you import pyarts. Please check that this is the case
10if the example does not work for you. You can easily check if this path is
11set by adding the following two lines at the top of this pyarts-controlfile:
12
13```
14import os
15print(os.environ.get("ARTS_DATA_PATH"))
16```
17
18"""
19
20import pyarts
21import numpy as np
22import matplotlib.pyplot as plt
23
24# Initialize ARTS
25ws = pyarts.workspace.Workspace()
26
27"""
28
29Set ws.abs_species to the species tags that you wish to use. CIA tags are
30structured so that the main and secondary species are separated by the word
31"CIA"
32
33This example sets up self CIA by molecular oxygen
34
35CIA is not just self-induced but can occur between two different molecules. In
36this case you can change the tag to read something like "O2-CIA-N2", though
37you must ensure that there also exists another N2 species in your ws.abs_species
38as this is the only way to pass the volume mixing ratio of the atmosphere into
39ARTS
40
41"""
42ws.absorption_speciesSet(species=["O2-CIA-O2"])
43
44"""
45
46Loads all CIA data from a given folder. This command expects the file
47"cia/O2-CIA-O2.xml" to be found either by relative local path or in the
48user-defined search paths.
49
50"""
51ws.absorption_cia_dataReadSpeciesSplitCatalog(basename="cia/")
52
53
54"""
55
56This example does not deal with line-by-line absorption at all. We must still
57ensure that the line-by-line catalog has the correct size and that it has been
58set so that our automatic agenda routine can do its work
59
60"""
61ws.absorption_bands = []
62
63"""
64
65You should generally always call this after you are done setting up your
66ws.abs_species and ws.abs_lines_per_species. It will deal with the internal
67ARTS setup for you. Note that the flag use_abs_lookup=1 can be passed to this
68method call to set up the agenda for USING the the lookup-table. Without the
69flag, ARTS should be configured correctly to either COMPUTE the lookup-table
70or to compute the absorption on-the-fly
71
72In this case, it turns out that the temparature extrapolation is not enough
73for a tropical atmosphere scenario below, so we extend it a small bit. Play
74with this "T_extrapolfac" value to see the relevant error message
75
76"""
77ws.propagation_matrix_agendaAuto(T_extrapolfac=1)
78
79"""
80
81Compute absorption
82
83Now we can use the propagation_matrix_agenda to compute the absorption of O2-66.
84We can also use this agenda in more complicated setups that might require
85absorption calculations, but that is for other examples
86
87To just execute the agenda we need to still define its both its inputs and the
88inputs required to initialize the propagation matrix
89
90"""
91
92ws.jacobian_targets = pyarts.arts.JacobianTargets()
93ws.frequency_grid = pyarts.arts.convert.wavelen2freq(np.linspace(6900e-9, 5900e-9, 1001))
94ws.atmospheric_point.temperature = 295 # At room temperature
95ws.atmospheric_point.pressure = 1e5 # At 1 bar
96ws.atmospheric_point[ws.absorption_species[0]] = 0.21 # At 21% atmospheric Oxygen
97ws.ray_path_point # No particular POSLOS
98
99# Call the agenda with inputs above
100ws.propagation_matrix_agendaExecute()
101
102# Plot the absorption of this example
103plt.figure(1)
104plt.clf()
105plt.plot(
106 1e9 * pyarts.arts.convert.freq2wavelen(ws.frequency_grid.value),
107 ws.propagation_matrix[:, 0],
108)
109plt.xlabel("Wavelength [nm]")
110plt.ylabel("Absorption [1/m]")
111plt.title("O2-CIA-O2 absorption from examples/arts-cat-data/cia/cia.py")
112
113"""
114That's it! You are done and have reached the end of this example. Everything
115below here is just to ensure that ARTS does not break in the future. It can
116be safely ignored
117
118"""
119# Save test results
120# ws.propagation_matrix.savexml("cia_test_result.xml", type="ascii")
121
122# test that we are still OK
123propagation_matrix_agenda = \
124 pyarts.arts.PropmatVector.fromxml("cia_test_result.xml")
125assert np.allclose(
126 propagation_matrix_agenda, ws.propagation_matrix
127), "O2 Absorption has changed"