pyROX.line_by_line ================== .. py:module:: pyROX.line_by_line Submodules ---------- .. toctree:: :maxdepth: 1 /autoapi/pyROX/line_by_line/lbl/index /autoapi/pyROX/line_by_line/lbl_exomol/index /autoapi/pyROX/line_by_line/lbl_hitran/index /autoapi/pyROX/line_by_line/lbl_kurucz/index Classes ------- .. autoapisummary:: pyROX.line_by_line.LBL_Kurucz pyROX.line_by_line.LBL_HITRAN pyROX.line_by_line.LBL_ExoMol pyROX.line_by_line.LineByLine Package Contents ---------------- .. py:class:: LBL_Kurucz(config, **kwargs) Bases: :py:obj:`pyROX.line_by_line.lbl.LineByLine` Class for handling line-by-line cross-sections from Kurucz data. .. py:attribute:: parent_dir .. py:attribute:: atoms_info .. py:method:: download_data(config) Download data from Kurucz. :param config: Configuration object containing parameters. :type config: object .. py:method:: _read_configuration_parameters(config) Read parameters specific to Kurucz calculations from the configuration. :param config: Configuration object containing parameters. :type config: object .. py:method:: _read_impact_info(impact_info={}) Read impact width/shift information from the configuration. :param impact_info: Dictionary containing impact information. :type impact_info: dict :returns: Updated impact information. :rtype: dict .. py:method:: _read_partition_function(T_grid=np.arange(1, 7001 + 1e-06, 1)) Read the partition function from the configuration file. :param T_grid: Temperature grid for partition function calculation. :type T_grid: array .. py:method:: _read_kurucz_transitions(input_file) Read transitions from a Kurucz input file. :param input_file: Path to the input file. :type input_file: str :returns: Arrays of transition parameters (nu_0, E_low, A, g_up, gamma_vdW, gamma_N). :rtype: tuple .. py:method:: _read_vald_transitions(input_file) :abstractmethod: Read transitions from a VALD input file. :param input_file: Path to the input file. :type input_file: str :raises NotImplementedError: If the method is not implemented. .. py:method:: compute_vdw_broadening(P, T, E_low, nu_0) Calculate Van der Waals broadening. :param P: Pressure in Pa. :type P: float :param T: Temperature in Kelvin. :type T: float :param E_low: Lower state energies in Joules. :type E_low: array :param nu_0: Transition frequencies in s^-1. :type nu_0: array :returns: Van der Waals broadening in s^-1. :rtype: array .. py:method:: compute_natural_broadening(A) Calculate natural broadening. :param A: Einstein A-coefficient in s^-1. :type A: float :returns: Natural broadening in s^-1. :rtype: float .. py:method:: pressure_shift(P, T, nu_0, delta=None) Apply pressure shift to the transition frequency. :param P: Pressure in Pa. :type P: float :param T: Temperature in Kelvin. :type T: float :param nu_0: Transition frequencies in s^-1. :type nu_0: array :param delta: Pressure shift coefficient. :type delta: float, optional :returns: Pressure-shifted frequencies. :rtype: array .. py:method:: _apply_impact_Allard_ea_2023(P, T, nu_0, gamma=None) Apply impact width/shift (Allard et al. 2023). :param P: Pressure in Pa. :type P: float :param T: Temperature in Kelvin. :type T: float :param nu_0: Transition frequencies in s^-1. :type nu_0: array :param gamma: Line widths. :type gamma: array, optional :returns: Modified transition frequencies or line widths. :rtype: array .. py:method:: process_transitions(input_file, **kwargs) Read transitions from the input file and compute cross-sections. :param input_file: Path to the input file. :type input_file: str :param \*\*kwargs: Additional arguments. .. py:class:: LBL_HITRAN(config, **kwargs) Bases: :py:obj:`pyROX.line_by_line.lbl.LineByLine` Class for handling line-by-line cross-sections from HITRAN data. .. py:method:: download_data(config) Downloads data from HITRAN. :param config: Configuration object containing parameters. :type config: object .. py:method:: _read_configuration_parameters(config) Reads parameters specific to HITRAN calculations from the configuration. :param config: Configuration object containing parameters. :type config: object .. py:method:: process_transitions(input_file, **kwargs) Reads transitions from the input file and computes cross-sections. :param input_file: Path to the input file. :type input_file: str :param \*\*kwargs: Additional arguments. .. py:class:: LBL_ExoMol(config, **kwargs) Bases: :py:obj:`pyROX.line_by_line.lbl.LineByLine` Class for handling line-by-line cross-sections from ExoMol data. .. py:method:: download_data(config) Downloads data from ExoMol. :param config: Configuration object containing parameters. :type config: object .. py:method:: _read_configuration_parameters(config) Reads parameters specific to ExoMol calculations from the configuration. :param config: Configuration object containing parameters. :type config: object .. py:method:: _read_broadening_per_transition(J_l, J_u, chunk_size=100000) Reads broadening parameters for each transition. :param J_l: Lower state rotational quantum numbers. :type J_l: array :param J_u: Upper state rotational quantum numbers. :type J_u: array :param chunk_size: Size of chunks to process at a time. :type chunk_size: int .. py:method:: _read_states() Reads the states from the states file. .. py:method:: process_transitions(input_file, **kwargs) Reads transitions from the input file and compute cross-sections. :param input_file: Path to the input file. :type input_file: str :param \*\*kwargs: Additional arguments. .. py:class:: LineByLine(config, **kwargs) Bases: :py:obj:`pyROX.CrossSections`, :py:obj:`LineProfileHelper` Base class for line-by-line cross-sections. .. py:method:: _read_configuration_parameters(config) Reads parameters specific to line-by-line calculations from the configuration. :param config: Configuration object containing parameters. :type config: object .. py:method:: _read_equation_of_state() Reads the equation of state for the gas mixture. .. py:method:: _read_mass() Reads the mass of the species from the configuration or database. .. py:method:: _read_pressure_broadening_info() Reads the pressure broadening parameters from the configuration. .. py:method:: _read_partition_function() Reads the partition function from the configuration file. .. py:method:: iterate_over_PT_grid(function, progress_bar=True, **kwargs) Iterate over the pressure-temperature grid in parallel and apply a function. :param function: Function to apply at each grid point. :type function: callable :param progress_bar: Whether to show a progress bar. :type progress_bar: bool :param \*\*kwargs: Additional arguments for the function. .. py:method:: calculate_cross_sections(P, T, nu_0, S_0, E_low, A, delta=None, **kwargs) Computes the cross-sections for given parameters. :param P: Pressure in Pa. :type P: float :param T: Temperature in Kelvin. :type T: float :param nu_0: Transition frequencies in s^-1. :type nu_0: array :param S_0: Line strengths at reference temperature. :type S_0: array :param E_low: Lower state energies in Joules. :type E_low: array :param A: Einstein A-coefficients in s^-1. :type A: array :param delta: Pressure shift coefficients. :type delta: array, optional :param \*\*kwargs: Additional arguments. .. py:method:: calculate_temporary_outputs(overwrite=False, save_in_one_file=False, files_range=None, **kwargs) Calculates temporary outputs for cross-sections. :param overwrite: Whether to overwrite existing files. :type overwrite: bool :param save_in_one_file: Whether to save all outputs in one file. :type save_in_one_file: bool :param files_range: Range of files to process. :type files_range: tuple, optional :param \*\*kwargs: Additional arguments. .. py:method:: save_combined_outputs(**kwargs) Saves the merged outputs to a file. :param \*\*kwargs: Additional arguments for saving. .. py:method:: 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. :param fig: Figure object for plotting. :type fig: matplotlib.figure.Figure :param ax: Axes object for plotting. :type ax: matplotlib.axes.Axes :param return_fig_ax: Whether to return the figure and axes. :type return_fig_ax: bool :param cmaps: List of colormaps for plotting. :type cmaps: list :param xscale: Scale for the x-axis. :type xscale: str :param yscale: Scale for the y-axis. :type yscale: str :param xlim: Limits for the x-axis. :type xlim: tuple, optional :param ylim: Limits for the y-axis. :type ylim: tuple, optional :param ls: Line style for plotting. :type ls: str :param \*\*kwargs: Additional arguments for plotting. .. py:method:: convert_to_pRT3(contributor=None, **kwargs) Converts the cross-sections to petitRADTRANS v3.0 format. :param contributor: Name of the contributor for these data. :type contributor: str :param \*\*kwargs: Additional arguments for conversion. :raises ValueError: If required metadata is missing in the configuration. :raises KeyError: If required keys are missing in the metadata.