pyROX

pyROX#

Submodules#

Classes#

`LineByLine`	Base class for line-by-line cross-sections.
`LBL_ExoMol`	Class for handling line-by-line cross-sections from ExoMol data.
`LBL_HITRAN`	Class for handling line-by-line cross-sections from HITRAN data.
`LBL_Kurucz`	Class for handling line-by-line cross-sections from Kurucz data.
`CIA`	Base class for Collision-Induced Absorption (CIA) data handling.
`CIA_HITRAN`	Class for handling CIA data from HITRAN.
`CIA_Borysow`	Class for handling Collision-Induced Absorption (CIA) data from Borysow.

Package Contents#

class pyROX.LineByLine(config, **kwargs)#

Bases: pyROX.CrossSections, LineProfileHelper

Base class for line-by-line cross-sections.

_read_configuration_parameters(config)#

Reads parameters specific to line-by-line calculations from the configuration.

Parameters:: config (object) – Configuration object containing parameters.

_read_equation_of_state()#: Reads the equation of state for the gas mixture.

_read_mass()#: Reads the mass of the species from the configuration or database.

_read_pressure_broadening_info()#: Reads the pressure broadening parameters from the configuration.

_read_partition_function()#: Reads the partition function from the configuration file.

iterate_over_PT_grid(function, progress_bar=True, **kwargs)#

Iterates over the pressure-temperature grid and apply a function.

Parameters:

function (callable) – Function to apply at each grid point.
progress_bar (bool) – Whether to show a progress bar.
**kwargs – Additional arguments for the function.

calculate_cross_sections(P, T, nu_0, S_0, E_low, A, delta=None, **kwargs)#

Computes the cross-sections for given parameters.

Parameters:

P (float) – Pressure in Pa.
T (float) – Temperature in Kelvin.
nu_0 (array) – Transition frequencies in s^-1.
S_0 (array) – Line strengths at reference temperature.
E_low (array) – Lower state energies in Joules.
A (array) – Einstein A-coefficients in s^-1.
delta (array, optional) – Pressure shift coefficients.
**kwargs – Additional arguments.

calculate_temporary_outputs(overwrite=False, save_in_one_file=False, files_range=None, **kwargs)#

Calculates temporary outputs for cross-sections.

Parameters:

overwrite (bool) – Whether to overwrite existing files.
save_in_one_file (bool) – Whether to save all outputs in one file.
files_range (tuple, optional) – Range of files to process.
**kwargs – Additional arguments.

save_combined_outputs(**kwargs)#

Saves the merged outputs to a file.

Parameters:: **kwargs – Additional arguments for saving.

plot_combined_outputs(fig=None, ax=None, return_fig_ax=False, cmaps=['coolwarm', 'viridis'], xscale='log', yscale='log', xlim=None, ylim=None, ls='-', lw=0.7, **kwargs)#

Plots the merged outputs.

Parameters:

fig (matplotlib.figure.Figure) – Figure object for plotting.
ax (matplotlib.axes.Axes) – Axes object for plotting.
return_fig_ax (bool) – Whether to return the figure and axes.
cmaps (list) – List of colormaps for plotting.
xscale (str) – Scale for the x-axis.
yscale (str) – Scale for the y-axis.
xlim (tuple, optional) – Limits for the x-axis.
ylim (tuple, optional) – Limits for the y-axis.
ls (str) – Line style for plotting.
**kwargs – Additional arguments for plotting.

convert_to_pRT3(contributor=None, **kwargs)#

Converts the cross-sections to petitRADTRANS v3.0 format.

Parameters:

contributor (str) – Name of the contributor for these data.
**kwargs – Additional arguments for conversion.

Raises:

ValueError – If required metadata is missing in the configuration.
KeyError – If required keys are missing in the metadata.

class pyROX.LBL_ExoMol(config, **kwargs)#

Bases: pyROX.line_by_line.lbl.LineByLine

Class for handling line-by-line cross-sections from ExoMol data.

download_data(config)#

Downloads data from ExoMol.

Parameters:: config (object) – Configuration object containing parameters.

_read_configuration_parameters(config)#

Reads parameters specific to ExoMol calculations from the configuration.

Parameters:: config (object) – Configuration object containing parameters.

_read_broadening_per_transition(J_l, J_u, chunk_size=100000)#

Reads broadening parameters for each transition.

Parameters:

J_l (array) – Lower state rotational quantum numbers.
J_u (array) – Upper state rotational quantum numbers.
chunk_size (int) – Size of chunks to process at a time.

_read_states()#: Reads the states from the states file.

process_transitions(input_file, **kwargs)#

Reads transitions from the input file and compute cross-sections.

Parameters:

input_file (str) – Path to the input file.
**kwargs – Additional arguments.

class pyROX.LBL_HITRAN(config, **kwargs)#

Bases: pyROX.line_by_line.lbl.LineByLine

Class for handling line-by-line cross-sections from HITRAN data.

download_data(config)#

Downloads data from HITRAN.

Parameters:: config (object) – Configuration object containing parameters.

_read_configuration_parameters(config)#

Reads parameters specific to HITRAN calculations from the configuration.

Parameters:: config (object) – Configuration object containing parameters.

process_transitions(input_file, **kwargs)#

Reads transitions from the input file and computes cross-sections.

Parameters:

input_file (str) – Path to the input file.
**kwargs – Additional arguments.

class pyROX.LBL_Kurucz(config, **kwargs)#

Bases: pyROX.line_by_line.lbl.LineByLine

Class for handling line-by-line cross-sections from Kurucz data.

parent_dir#

atoms_info#

download_data(config)#

Download data from Kurucz.

Parameters:: config (object) – Configuration object containing parameters.

_read_configuration_parameters(config)#

Read parameters specific to Kurucz calculations from the configuration.

Parameters:: config (object) – Configuration object containing parameters.

_read_impact_info(impact_info={})#

Read impact width/shift information from the configuration.

Parameters:: impact_info (dict) – Dictionary containing impact information.
Returns:: Updated impact information.
Return type:: dict

_read_partition_function(T_grid=np.arange(1, 7001 + 1e-06, 1))#

Read the partition function from the configuration file.

Parameters:: T_grid (array) – Temperature grid for partition function calculation.

_read_kurucz_transitions(input_file)#

Read transitions from a Kurucz input file.

Parameters:: input_file (str) – Path to the input file.
Returns:: Arrays of transition parameters (nu_0, E_low, A, g_up, gamma_vdW, gamma_N).
Return type:: tuple

abstractmethod _read_vald_transitions(input_file)#

Read transitions from a VALD input file.

Parameters:: input_file (str) – Path to the input file.
Raises:: NotImplementedError – If the method is not implemented.

compute_vdw_broadening(P, T, E_low, nu_0)#

Calculate Van der Waals broadening.

Parameters:

P (float) – Pressure in Pa.
T (float) – Temperature in Kelvin.
E_low (array) – Lower state energies in Joules.
nu_0 (array) – Transition frequencies in s^-1.

Returns:

Van der Waals broadening in s^-1.

Return type:

array

compute_natural_broadening(A)#

Calculate natural broadening.

Parameters:: A (float) – Einstein A-coefficient in s^-1.
Returns:: Natural broadening in s^-1.
Return type:: float

pressure_shift(P, T, nu_0, delta=None)#

Apply pressure shift to the transition frequency.

Parameters:

P (float) – Pressure in Pa.
T (float) – Temperature in Kelvin.
nu_0 (array) – Transition frequencies in s^-1.
delta (float, optional) – Pressure shift coefficient.

Returns:

Pressure-shifted frequencies.

Return type:

array

_apply_impact_Allard_ea_2023(P, T, nu_0, gamma=None)#

Apply impact width/shift (Allard et al. 2023).

Parameters:

P (float) – Pressure in Pa.
T (float) – Temperature in Kelvin.
nu_0 (array) – Transition frequencies in s^-1.
gamma (array, optional) – Line widths.

Returns:

Modified transition frequencies or line widths.

Return type:

array

process_transitions(input_file, **kwargs)#

Read transitions from the input file and compute cross-sections.

Parameters:

input_file (str) – Path to the input file.
**kwargs – Additional arguments.

class pyROX.CIA(config, **kwargs)#

Bases: pyROX.CrossSections

Base class for Collision-Induced Absorption (CIA) data handling.

download_data(config)#

Download CIA data from HITRAN or Borysow.

Parameters:: config (object) – Configuration object containing URLs and input data directory.
Raises:: ValueError – If any file fails to download.

calculate_temporary_outputs(overwrite=False, **kwargs)#

Calculate the CIA coefficients and save temporary outputs.

Parameters:

overwrite (bool) – Whether to overwrite existing temporary files.
**kwargs – Additional arguments for calculation.

save_combined_outputs(**kwargs)#

Save the merged CIA outputs to a file.

Parameters:: **kwargs – Additional arguments for saving.

plot_combined_outputs(return_fig_ax=False, cmap='coolwarm', xscale='log', yscale='log', xlim=None, ylim=None, **kwargs)#

Plot the merged CIA coefficients.

Parameters:

return_fig_ax (bool) – Whether to return the figure and axes objects.
cmap (str) – Colormap for the plot.
xscale (str) – Scale for the x-axis (‘linear’ or ‘log’).
yscale (str) – Scale for the y-axis (‘linear’ or ‘log’).
xlim (tuple, optional) – Limits for the x-axis.
ylim (tuple, optional) – Limits for the y-axis.
**kwargs – Additional arguments for plotting.

convert_to_pRT3(contributor=None, **kwargs)#

Convert the CIA data to petitRADTRANS v3.0 format.

Parameters:

contributor (str) – Name of the contributor for these data.
**kwargs – Additional arguments for conversion.

Raises:

ValueError – If required metadata is missing in the configuration.
KeyError – If required keys are missing in the metadata.

class pyROX.CIA_HITRAN(config, **kwargs)#

Bases: pyROX.collision_induced_absorption.cia.CIA

Class for handling CIA data from HITRAN.

_read_absorption_coefficients(file)#

Reads absorption coefficients from a HITRAN CIA file.

Parameters:: file (str) – Path to the HITRAN CIA file.
Returns:: Temperature grid, absorption coefficients (k), and absorption coefficients (alpha).
Return type:: tuple
Raises:: FileNotFoundError – If the specified file does not exist.

class pyROX.CIA_Borysow(config, **kwargs)#

Bases: pyROX.collision_induced_absorption.cia.CIA

Class for handling Collision-Induced Absorption (CIA) data from Borysow.

_read_absorption_coefficients(file)#

Reads absorption coefficients from a Borysow CIA file.

Parameters:: file (str) – Path to the Borysow CIA file.
Returns:: Temperature grid, absorption coefficients (k), and absorption coefficients (alpha).
Return type:: tuple
Raises:: FileNotFoundError – If the specified file does not exist.