Collision-Induced Absorption#

In this notebook, we’ll explore how pyROX calculates the collision-induced absorption (CIA) coefficients for H\(_2\)-H\(_2\) collisions, using data from HITRAN.

[1]:

from pyROX import utils, cross_sections

Configuration parameters#

The parameters given in the configuration file examples/cia_hitran_h2_h2/cia_hitran_h2_h2.py are similar to those used in the “line-by-line” calculations outlined in the previous notebooks. In the cell below, we’ll define the database, directory-structure, URLs to download, and the wavenumber grid.

[2]:

# Basic information on database and species
database = 'cia_hitran' # Can be ['cia_hitran', 'cia_borysow']
species  = 'h2-h2'      # Species name

# Input/output-directories
input_data_dir  = './examples/cia_hitran_h2_h2/input_data/'
output_data_dir = './examples/cia_hitran_h2_h2/'

# Instructions to download from HITRAN database
urls = [
    'https://hitran.org/data/CIA/H2-H2_2011.cia',
    'https://hitran.org/data/CIA/supplementary/H2-H2_eq_2018.cia', # Extends to lower temperatures
]

# Wavenumber grid
wave_min = 0.3; wave_max = 250.0 # [um]
delta_nu = 10. # [cm^-1] # Can be sparse for CIA calculations

We’ll download two files H2-H2_2011.cia and H2-H2_eq_2018.cia of which the latter extends down to lower temperatures (\(200<T[\mathrm{K}]<3000\) vs. \(40<T[\mathrm{K}]<400\); see the HITRAN documentation). When defining the files to calculate, we can add two callable functions in a tuple like (filename, T_mask(T_grid), nu_mask(nu_grid)).

In the example below, pyROX will crop the temperature-grid that is included in the H2-H2_2011.cia file to \(T\geq 400\ \mathrm{K}\). For the second file, H2-H2_eq_2018.cia, we don’t apply any masks so any CIA coefficients below \(T<400\ \mathrm{K}\) will come from it.

[3]:

# Extents of the CIA data
T_mask_1 = lambda T: (T>=400) & (T<=3000)
nu_mask_1 = lambda nu: (nu>=20) & (nu<=10000) # [cm^-1]

# T_mask_2 = lambda T: (T>=40) & (T<=400)
# nu_mask_2 = lambda nu: (nu>=0) & (nu<=2400) # [cm^-1]

# Input-data files
files = dict(
    cia = [
        (f'{input_data_dir}/H2-H2_2011.cia', T_mask_1, nu_mask_1),
        #(f'{input_data_dir}/H2-H2_eq_2018.cia', T_mask_2, nu_mask_2),
        f'{input_data_dir}/H2-H2_eq_2018.cia',
    ]
)

Calculating CIA coefficients#

We now have all the parameters to download the data and calculate the CIA coefficients. In the next cell, we’ll set up the config object and execute the download, calculations, saving and plotting. This is equivalent to running the command

pyROX examples/cia_hitran_h2_h2/cia_hitran_h2_h2.py -d -c -s -p

[4]:

# Setup a configuration object (done automatically when running pyROX from the command line)
config = utils.update_config_with_args(
    database=database, species=species,
    input_data_dir=input_data_dir, output_data_dir=output_data_dir, urls=urls, files=files,
    wave_min=wave_min, wave_max=wave_max, delta_nu=delta_nu,
)

# Download from the HITRAN database
data = cross_sections.load_data_object(config, download=True)

data.calculate_temporary_outputs(
    #overwrite=False, # If True, answer "yes" to all overwrite prompts
)

data.save_combined_outputs(
    #overwrite=False, # If True, answer "yes" to all overwrite prompts
)

fig, ax = data.plot_combined_outputs(
    T_to_plot=[100,300,500,1000,2000,3000],
    return_fig_ax=True
)
fig.show()


Updating configuration with new parameters
/net/lem/data2/regt/pyROX/pyROX/utils.py:207 UserWarning: Adding parameter "database" as "cia_hitran".
/net/lem/data2/regt/pyROX/pyROX/utils.py:207 UserWarning: Adding parameter "species" as "h2-h2".
/net/lem/data2/regt/pyROX/pyROX/utils.py:207 UserWarning: Adding parameter "input_data_dir" as "./examples/cia_hitran_h2_h2/input_data/".
/net/lem/data2/regt/pyROX/pyROX/utils.py:207 UserWarning: Adding parameter "output_data_dir" as "./examples/cia_hitran_h2_h2/".
/net/lem/data2/regt/pyROX/pyROX/utils.py:207 UserWarning: Adding parameter "urls" as ['https://hitran.org/data/CIA/H2-H2_2011.cia', 'https://hitran.org/data/CIA/supplementary/H2-H2_eq_2018.cia'].
/net/lem/data2/regt/pyROX/pyROX/utils.py:207 UserWarning: Adding parameter "files" as {'cia': [('./examples/cia_hitran_h2_h2/input_data//H2-H2_2011.cia', <function <lambda> at 0x7f994c7befc0>, <function <lambda> at 0x7f994c7bef20>), './examples/cia_hitran_h2_h2/input_data//H2-H2_eq_2018.cia']}.
/net/lem/data2/regt/pyROX/pyROX/utils.py:207 UserWarning: Adding parameter "wave_min" as 0.3.
/net/lem/data2/regt/pyROX/pyROX/utils.py:207 UserWarning: Adding parameter "wave_max" as 250.0.
/net/lem/data2/regt/pyROX/pyROX/utils.py:207 UserWarning: Adding parameter "delta_nu" as 10.0.

------------------------------------------------------------
  Collision-Induced Absorption from HITRAN
------------------------------------------------------------


Downloading CIA data
  Downloading "https://hitran.org/data/CIA/H2-H2_2011.cia"
100% [........................................................................] 24824179 / 24824179
  Downloading "https://hitran.org/data/CIA/supplementary/H2-H2_eq_2018.cia"
100% [..........................................................................] 2113010 / 2113010

Reading parameters from the configuration file
/net/lem/data2/regt/pyROX/pyROX/utils.py:245 UserWarning: Please make sure that the following parameters are given in the expected units:
  - delta_nu [cm^-1]
  - wave_max [um]
  - wave_min [um]


Wavelength-grid:
  Wavelength: 0.30 - 250 um
  Wavenumber: 40 - 33333 cm^-1
  Fixed wavenumber-spacing: 10.001 cm^-1
  Number of grid points: 3330
  Adaptive grid: False

Calculating CIA coefficients
  Reading from "examples/cia_hitran_h2_h2/input_data/H2-H2_2011.cia"
/net/lem/data2/regt/pyROX/pyROX/utils.py:148 RuntimeWarning: divide by zero encountered in log10
  Reading from "examples/cia_hitran_h2_h2/input_data/H2-H2_eq_2018.cia"

Combining temporary files and saving final output
  Merging 2 temporary files into a single grid
  Temporary files:
    - "cia_coeffs_H2-H2_2011.hdf5"
    - "cia_coeffs_H2-H2_eq_2018.hdf5"
  Combining PT-grids of temporary files
  Saving final output to "/net/lem/data2/regt/pyROX/examples/cia_hitran_h2_h2/cia_coeffs.hdf5"

Plotting CIA coefficients

../_images/notebooks_collision_induced_absorption_7_1.png

Important: The final output-file is saved as a compressed hdf5-type. It has 4 datasets:

T_grid: Temperature grid points (in K).
wave: Wavelength grid points (in m).
log10(k): Base-10 logarithm of the \(k\)-coefficient (in log10[m5 molecule-2]) with shape (wave, T_grid).
log10(alpha): Base-10 logarithm of the \(\alpha\)-coefficient (in log10[m-1 molecule-2]) with shape (wave, T_grid).

pyROX saves the k and alpha coefficients, which are scalings of each other (see Eq. 3 of Karman et al. 2019). To convert the \(\alpha\)-coefficient into a cross-section, you can multiply by the number density (\(N_i\), in [\(\mathrm{m^{-3}}\)]) of each collision-component:

\[\sigma[\mathrm{m^2}] = \frac{\alpha}{L_0^2} \cdot \left(\frac{N_1\cdot N_2}{N_\mathrm{tot}}\right) = \frac{\alpha}{L_0^2} \cdot \mathrm{VMR}_1\cdot \mathrm{VMR}_2\cdot N_\mathrm{tot},\]

where \(L_0\) is the Loschmidt constant.

Converting to pRT3-format#

pyROX also offers support to convert the saved alpha into an h5-file that can be read in with petitRADTRANS v3. To generate the right filename and add metadata to the h5-file, we’ll have to add the pRT3_metadata dictionary to the config object. Notice how the molecular mass (in amu) of each collision-component is specified.

[5]:

# Metadata to be stored in pRT3's .h5 file
pRT3_metadata = dict(
    DOI = ['10.1021/jp109441f', '10.3847/1538-4365/aaa07a'],
    mol_mass = [2.0,2.0],
    mol_name = ['H2','H2'],
)

# Update the configuration parameters
config = utils.update_config_with_args(
    config=config,     # Update the previous configuration
    pRT3_metadata=pRT3_metadata, # Add metadata
)
# Re-load the data object
data = cross_sections.load_data_object(config, download=False)

# Convert to the pRT3 format
data.convert_to_pRT3(contributor='Your name!')


Updating configuration with new parameters
/net/lem/data2/regt/pyROX/pyROX/utils.py:207 UserWarning: Adding parameter "pRT3_metadata" as {'DOI': ['10.1021/jp109441f', '10.3847/1538-4365/aaa07a'], 'mol_mass': [2.0, 2.0], 'mol_name': ['H2', 'H2']}.

------------------------------------------------------------
  Collision-Induced Absorption from HITRAN
------------------------------------------------------------


Reading parameters from the configuration file
/net/lem/data2/regt/pyROX/pyROX/utils.py:245 UserWarning: Please make sure that the following parameters are given in the expected units:
  - delta_nu [cm^-1]
  - wave_max [um]
  - wave_min [um]


Wavelength-grid:
  Wavelength: 0.30 - 250 um
  Wavenumber: 40 - 33333 cm^-1
  Fixed wavenumber-spacing: 10.001 cm^-1
  Number of grid points: 3330
  Adaptive grid: False

Converting to petitRADTRANS-v3.0 format
  Saved to "/net/lem/data2/regt/pyROX/examples/cia_hitran_h2_h2/H2--H2-NatAbund__HITRAN.R1000_0.3-250mu.ciatable.petitRADTRANS.h5"

Collision-Induced Absorption

Contents

Collision-Induced Absorption#

Configuration parameters#

Calculating CIA coefficients#

Converting to pRT3-format#