petitRADTRANS.opacities ======================= .. py:module:: petitRADTRANS.opacities Submodules ---------- .. toctree:: :maxdepth: 1 /autoapi/petitRADTRANS/opacities/opacities/index Classes ------- .. autoapisummary:: petitRADTRANS.opacities.CIAOpacity petitRADTRANS.opacities.CloudOpacity petitRADTRANS.opacities.CorrelatedKOpacity petitRADTRANS.opacities.LineByLineOpacity Package Contents ---------------- .. py:class:: CIAOpacity(species_list, natural_abundance: bool = True, charge: int = 0, source: str = 'unknown', spectral_sampling_type: str = 'R', spectral_sampling: int | float = 830, wavelength_min: float = _default_wavelength_range[0], wavelength_max: float = _default_wavelength_range[1], path_input_data: str = None, species_full_name: str = None, species_base_name: str = None, species_isotopologue_name: str = None, full_extension: str = None, file_name: str = None, sub_path: str = None, absolute_path: str = None) Bases: :py:obj:`Opacity` Class for collision-induced opacity files. Args: species_list: list of str The list of species contributing to the opacity. natural_abundance: bool, optional If True, the species is considered following the Earth's isotopic ratios. Default is True. charge: int, optional The charge of the species (for single-species opacities only). A value of 0 is used for neutral species. Default is 0. source: str, optional The source (i.e., where or how the opacity were obtained) of the opacity. Default is "unknown". spectral_sampling_type: {'DeltaWavelength', 'DeltaWavenumber', 'R'}, optional The opacity spectral sampling type. Default is 'R'. - 'DeltaWavelength': sampling with a constant wavelength step. - 'DeltaWavenumber': sampling with a constant wavenumber step. - 'R': sampling with a constant resolving power (wavelength / wavelength step). spectral_sampling: int or float, optional The opacity spectral sampling value. Default is 830. Units depends on spectral_sampling_type: - 'DeltaWavelength': um - 'DeltaWavenumber': cm-1 - 'R': no units Example: To indicate a spectral sampling with a constant resolving power of 1000. >>> spectral_sampling_type='R' >>> spectral_sampling=1000 wavelength_min: float, optional (um) Lower wavelength bounds of the opacity data. Default is 0.1. wavelength_max: float, optional (um) Upper wavelength bounds of the opacity data. Default is 250. path_input_data: str, optional Absolute path to petitRadtrans "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRadtrans config file. species_full_name: str, optional Override the species full name. The species full name is composed of the species isotopic information, the natural abundance flag (if relevant), and the charge. species_cloud_info: str, optional Override the species cloud information. The species cloud information is composed of the species matter state, and of its solid structure and structure id (if relevant). species_base_name: str, optional Override the species base name. The species base name is the species chemical formula without isotopic information. It may contain cloud information and charge. Examples: "H2O", "H2O(l)", "H2O_+(s)_crystalline_000". species_isotopologue_name: str, optional Override the species isotopologue name. The species isotopologue name is the species name with isotopic information. It may contain cloud information and charge. Examples: "1H2-16O", "H2O-NatAbund(l)", "1H2-18O_+(s)_crystalline_000". extension: str, optional The opacity file type extension. Default is "unknown". Use "petitRADTRANS" for files generated with petitRADTRANS. full_extension: str, optional Override the opacity file full extension. The opacity file full extension is composed of the opacity file type extension, the opacity file generator software extension, and of the file format extension. file_name: str, optional Override the opacity file name. By default, it is generated from the instanciation arguments. sub_path: str, optional Override the opacity sub path. By default, it depends on the selected category. directory: str, optional Override the opacity directory. By default, it is generated from the species full name and from the other path information. absolute_path: str, optional Override the absolute path of the opacity file. By default, it is genrated from the other path information. .. py:attribute:: _default_category :type: str :value: 'cia_opacities' .. py:attribute:: _default_extension :type: str :value: 'ciatable' .. py:attribute:: _default_wavelength_range :type: tuple[float, float] :value: (0.1, 250.0) .. py:attribute:: _default_resolving_power :type: float :value: 831.0 .. py:method:: find(species: str, category: str = None, path_input_data: str = None, find_all: bool = False, search_online: bool = True) -> str :classmethod: Return the absolute filename of a species opacity. The validity of the given species name is checked. Automatically infer the species base and isotopologue directories from the species name. Then, try to match the species name with the files in the folder. If only one file is matched, it is returned. If multiple files match, the configured default file is used if it exists. If not, ask the user to configure a default file. Information given in the species name are decomposed for the match. For example: - "H2O.R120" will match e.g. the file "1H2-16O__HITEMP.R120_0.1-250mu.ktable.petitRADTRANS.h5" - "H2O__POKAZATEL" will match e.g. the file "1H2-16O__POKAZATEL.R1000_0.1-250mu.ktable.petitRADTRANS.h5" If no information on the resolution is given, the default resolution for corr.-k or line-by-line is assumed. If no or partial isotopic information is given: - for line opacities: the main isotope is assumed - for continuum opacities: "NatAbund" (a standard mix of all isotopes) is assumed Args: path_input_data: Path to the input data directory category: Input data category species: Species to get the opacity filename. The species name must be valid. find_all: If True, return all the matched files. If False, raise an error if no file is found, and only one file is returned. search_online: If True, search online for the opacity file Returns: The absolute opacity filename of the species .. py:method:: from_species(species: str, spectral_sampling_type: str = 'R', spectral_sampling: int | float = Opacity._default_line_by_line_resolving_power, wavelength_min: float = _default_wavelength_range[0], wavelength_max: float = _default_wavelength_range[1], path_input_data: str = None, category: str = _default_category) :classmethod: Instantiate an Opacity object from a species name and from spectral sampling information. Args: species: str The species name, containing the species isotopic information, the natural abundance flag (if relevant), and the charge. spectral_sampling_type: {'DeltaWavelength', 'DeltaWavenumber', 'R'}, optional The opacity spectral sampling type. Default is 'R'. - 'DeltaWavelength': sampling with a constant wavelength step. - 'DeltaWavenumber': sampling with a constant wavenumber step. - 'R': sampling with a constant resolving power (wavelength / wavelength step). spectral_sampling: int or float, optional The opacity spectral sampling value. Default is 0. Units depends on spectral_sampling_type: - 'DeltaWavelength': um - 'DeltaWavenumber': cm-1 - 'R': no units wavelength_min: float, optional (um) Lower wavelength bounds of the opacity data. Default is 0. wavelength_max: float, optional (um) Upper wavelength bounds of the opacity data. Default is 0. path_input_data: str, optional Absolute path to petitRADTRANS "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRADTRANS config file. Returns: new_opacity: Opacity A new instance of an Opacity object. .. py:method:: from_species_fullname(species_fullname: str, path_input_data: str = None, category: str = _default_category) :classmethod: Instantiate an Opacity object from a species full name and from spectral sampling information. Args: species_fullname: str The species full name, containing the species isotopic information. May contain the natural abundance flag if relevant and the charge. Absolute path to petitRadtrans' "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRadtrans' config file. category: {'cia_opacities', 'clouds_opacities', 'correlated_k_opacities', 'line_by_line_opacities'}, optional The opacity category. Indicates the input_data subpath. Default is 'unknown'. - 'cia_opacities': for collision-induced absorptions. - 'clouds_opacities': for cloud opacities. - 'correlated_k_opacities': for correlated-k opacities. - 'line_by_line_opacities': for line-by-line opacities. path_input_data: str, optional Absolute path to petitRADTRANS "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRADTRANS config file. Returns: new_opacity: Opacity A new instance of an Opacity object. .. py:method:: write(file: str, colliding_species: tuple[str, Ellipsis], alphas: numpy.typing.NDArray[numpy.floating], wavenumbers: numpy.typing.NDArray[numpy.floating], pressures: numpy.typing.NDArray[numpy.floating], temperatures: numpy.typing.NDArray[numpy.floating], molar_mass: float = None, doi: str = '', contributor: str = '', description: str = '', date_id: str = None, n_g: int = None, wavelength_range: tuple[float] = None) :classmethod: .. py:class:: CloudOpacity(species_list, natural_abundance: bool = True, charge: int = 0, source: str = 'unknown', spectral_sampling_type: str = 'R', spectral_sampling: int | float = Opacity._default_cloud_resolving_power, wavelength_min: float = _default_wavelength_range[0], wavelength_max: float = _default_wavelength_range[1], matter_state: str = Opacity._solid_matter_state, solid_structure: str = 'crystalline', solid_structure_id: str = '000', path_input_data: str = None, species_full_name: str = None, species_cloud_info: str = None, species_base_name: str = None, species_isotopologue_name: str = None, full_extension: str = None, file_name: str = None, sub_path: str = None, absolute_path: str = None) Bases: :py:obj:`Opacity` Class for cloud opacity files. Args: species_list: list of str The list of species contributing to the opacity. For single-species opacities, use [species_name]. Examples: [1H2-17O], [N2, CO2] natural_abundance: bool, optional If True, the species is considered following the Earth's isotopic ratios. Default is True. charge: int, optional The charge of the species (for single-species opacities only). A value of 0 is used for neutral species. Default is 0. source: str, optional The source (i.e., where or how the opacity were obtained) of the opacity. Default is "unknown". spectral_sampling_type: {'DeltaWavelength', 'DeltaWavenumber', 'R'}, optional The opacity spectral sampling type. Default is 'R'. - 'DeltaWavelength': sampling with a constant wavelength step. - 'DeltaWavenumber': sampling with a constant wavenumber step. - 'R': sampling with a constant resolving power (wavelength / wavelength step). spectral_sampling: int or float, optional The opacity spectral sampling value. Default is 39. Units depends on spectral_sampling_type: - 'DeltaWavelength': um - 'DeltaWavenumber': cm-1 - 'R': no units Example: To indicate a spectral sampling with a constant resolving power of 1000. >>> spectral_sampling_type='R' >>> spectral_sampling=1000 wavelength_min: float, optional (um) Lower wavelength bounds of the opacity data. Default is 0. wavelength_max: float, optional (um) Upper wavelength bounds of the opacity data. Default is 0. matter_state: {'(g)', '(l)', '(s)'}, optional The species matter state. Default is '(g)'. - '(g)': gas phase. - '(l)': liquid phase. - '(s)': solid phase. solid_structure: {'amorphous', 'crystalline', 'structureUnclear'}, optional If the species is in solid phase, indicate the solid structure of the species. Default is None. - 'amorphous': the solid has an amorphous internal structure. - 'crystalline': the solid is in a crystal form. - 'structureUnclear': internal structure was not provided by the source. solid_structure_id: str, optional Solid structure identifier. For crystals, this corresponds to the 3-digits space group. See https://en.wikipedia.org/wiki/List_of_space_groups An unknown space group is indicated as '000'. path_input_data: str, optional Absolute path to petitRadtrans' "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRadtrans config file. species_full_name: str, optional Override the species full name. The species full name is composed of the species isotopic information, the natural abundance flag (if relevant), and the charge. species_cloud_info: str, optional Override the species cloud information. The species cloud information is composed of the species matter state, and of its solid structure and structure id (if relevant). species_base_name: str, optional Override the species base name. The species base name is the species chemical formula without isotopic information. It may contain cloud information and charge. Examples: "H2O", "H2O(l)", "H2O_+(s)_crystalline_000". species_isotopologue_name: str, optional Override the species isotopologue name. The species isotopologue name is the species name with isotopic information. It may contain cloud information and charge. Examples: "1H2-16O", "H2O-NatAbund(l)", "1H2-18O_+(s)_crystalline_000". extension: str, optional The opacity file type extension. Default is "unknown". Use "petitRADTRANS" for files generated with petitRADTRANS. full_extension: str, optional Override the opacity file full extension. The opacity file full extension is composed of the opacity file type extension, the opacity file generator software extension, and of the file format extension. file_name: str, optional Override the opacity file name. By default, it is generated from the instanciation arguments. sub_path: str, optional Override the opacity sub path. By default, it depends on the selected category. directory: str, optional Override the opacity directory. By default, it is generated from the species full name and from the other path information. absolute_path: str, optional Override the absolute path of the opacity file. By default, it is genrated from the other path information. .. py:attribute:: _default_category :type: str :value: 'clouds_opacities' .. py:attribute:: _default_extension :type: str :value: 'cotable' .. py:attribute:: _default_resolving_power :type: float :value: 39.0 .. py:attribute:: _default_wavelength_range :type: tuple[float, float] :value: (0.1, 250.0) .. py:attribute:: _default_file_names :type: petitRADTRANS.utils.LockedDict .. py:method:: find(species: str, category: str = None, path_input_data: str = None, find_all: bool = False, search_online: bool = True) -> str :classmethod: Return the absolute filename of a species opacity. The validity of the given species name is checked. Automatically infer the species base and isotopologue directories from the species name. Then, try to match the species name with the files in the folder. If only one file is matched, it is returned. If multiple files match, the configured default file is used if it exists. If not, ask the user to configure a default file. Information given in the species name are decomposed for the match. For example: - "H2O.R120" will match e.g. the file "1H2-16O__HITEMP.R120_0.1-250mu.ktable.petitRADTRANS.h5" - "H2O__POKAZATEL" will match e.g. the file "1H2-16O__POKAZATEL.R1000_0.1-250mu.ktable.petitRADTRANS.h5" If no information on the resolution is given, the default resolution for corr.-k or line-by-line is assumed. If no or partial isotopic information is given: - for line opacities: the main isotope is assumed - for continuum opacities: "NatAbund" (a standard mix of all isotopes) is assumed Args: path_input_data: Path to the input data directory category: Input data category species: Species to get the opacity filename. The species name must be valid. find_all: If True, return all the matched files. If False, raise an error if no file is found, and only one file is returned. search_online: If True, search online for the opacity file Returns: The absolute opacity filename of the species .. py:method:: from_species(species: str, spectral_sampling_type: str = 'R', spectral_sampling: int | float = Opacity._default_cloud_resolving_power, wavelength_min: float = _default_wavelength_range[0], wavelength_max: float = _default_wavelength_range[1], path_input_data: str = None, category: str = _default_category) :classmethod: Instantiate an Opacity object from a species name and from spectral sampling information. Args: species: str The species name, containing the species isotopic information, the natural abundance flag (if relevant), and the charge. spectral_sampling_type: {'DeltaWavelength', 'DeltaWavenumber', 'R'}, optional The opacity spectral sampling type. Default is 'R'. - 'DeltaWavelength': sampling with a constant wavelength step. - 'DeltaWavenumber': sampling with a constant wavenumber step. - 'R': sampling with a constant resolving power (wavelength / wavelength step). spectral_sampling: int or float, optional The opacity spectral sampling value. Default is 0. Units depends on spectral_sampling_type: - 'DeltaWavelength': um - 'DeltaWavenumber': cm-1 - 'R': no units wavelength_min: float, optional (um) Lower wavelength bounds of the opacity data. Default is 0. wavelength_max: float, optional (um) Upper wavelength bounds of the opacity data. Default is 0. path_input_data: str, optional Absolute path to petitRADTRANS "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRADTRANS config file. Returns: new_opacity: Opacity A new instance of an Opacity object. .. py:method:: from_species_fullname(species_fullname: str, path_input_data: str = None, category: str = _default_category) :classmethod: Instantiate an Opacity object from a species full name and from spectral sampling information. Args: species_fullname: str The species full name, containing the species isotopic information. May contain the natural abundance flag if relevant and the charge. Absolute path to petitRadtrans' "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRadtrans' config file. category: {'cia_opacities', 'clouds_opacities', 'correlated_k_opacities', 'line_by_line_opacities'}, optional The opacity category. Indicates the input_data subpath. Default is 'unknown'. - 'cia_opacities': for collision-induced absorptions. - 'clouds_opacities': for cloud opacities. - 'correlated_k_opacities': for correlated-k opacities. - 'line_by_line_opacities': for line-by-line opacities. path_input_data: str, optional Absolute path to petitRADTRANS "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRADTRANS config file. Returns: new_opacity: Opacity A new instance of an Opacity object. .. py:method:: get_aliases(name: str) -> str :classmethod: .. py:method:: write(file: str, species_name: str, absorption_opacities: numpy.typing.NDArray[numpy.floating], scattering_opacities: numpy.typing.NDArray[numpy.floating], asymmetry_parameters: numpy.typing.NDArray[numpy.floating], particles_densities: numpy.typing.NDArray[numpy.floating], particles_radius_bin_centers: numpy.typing.NDArray[numpy.floating], particles_radius_bin_edges: numpy.typing.NDArray[numpy.floating], wavenumbers: numpy.typing.NDArray[numpy.floating], doi: str = '', contributor: str = '', description: str = '', date_id: str = None, wavelength_range: tuple[float] = None) :classmethod: .. py:class:: CorrelatedKOpacity(species_list, natural_abundance: bool = False, charge: int = 0, source: str = 'unknown', spectral_sampling_type: str = 'R', spectral_sampling: int | float = Opacity._default_correlated_k_resolving_power, wavelength_min: float = _default_wavelength_range[0], wavelength_max: float = _default_wavelength_range[1], path_input_data: str = None, species_full_name: str = None, species_base_name: str = None, species_isotopologue_name: str = None, full_extension: str = None, file_name: str = None, sub_path: str = None, absolute_path: str = None) Bases: :py:obj:`Opacity` Class for correlated-k opacity files. Args: species_list: list of str The list of species contributing to the opacity. For single-species opacities, use [species_name]. Examples: [1H2-17O], [N2, CO2] natural_abundance: bool, optional If True, the species is considered following the Earth's isotopic ratios. Default is False. charge: int, optional The charge of the species (for single-species opacities only). A value of 0 is used for neutral species. Default is 0. source: str, optional The source (i.e., where or how the opacity were obtained) of the opacity. Default is "unknown". spectral_sampling_type: {'DeltaWavelength', 'DeltaWavenumber', 'R'}, optional The opacity spectral sampling type. Default is 'R'. - 'DeltaWavelength': sampling with a constant wavelength step. - 'DeltaWavenumber': sampling with a constant wavenumber step. - 'R': sampling with a constant resolving power (wavelength / wavelength step). spectral_sampling: int or float, optional The opacity spectral sampling value. Default is 1000. Units depends on spectral_sampling_type: - 'DeltaWavelength': um - 'DeltaWavenumber': cm-1 - 'R': no units Example: To indicate a spectral sampling with a constant resolving power of 1000. >>> spectral_sampling_type='R' >>> spectral_sampling=1000 wavelength_min: float, optional (um) Lower wavelength bounds of the opacity data. Default is 0.1. wavelength_max: float, optional (um) Upper wavelength bounds of the opacity data. Default is 250. species_full_name: str, optional Override the species full name. The species full name is composed of the species isotopic information, the natural abundance flag (if relevant), and the charge. species_cloud_info: str, optional Override the species cloud information. The species cloud information is composed of the species matter state, and of its solid structure and structure id (if relevant). species_base_name: str, optional Override the species base name. The species base name is the species chemical formula without isotopic information. It may contain cloud information and charge. Examples: "H2O", "H2O(l)", "H2O_+(s)_crystalline_000". species_isotopologue_name: str, optional Override the species isotopologue name. The species isotopologue name is the species name with isotopic information. It may contain cloud information and charge. Examples: "1H2-16O", "H2O-NatAbund(l)", "1H2-18O_+(s)_crystalline_000". extension: str, optional The opacity file type extension. Default is "unknown". Use "petitRADTRANS" for files generated with petitRADTRANS. full_extension: str, optional Override the opacity file full extension. The opacity file full extension is composed of the opacity file type extension, the opacity file generator software extension, and of the file format extension. file_name: str, optional Override the opacity file name. By default, it is generated from the instanciation arguments. sub_path: str, optional Override the opacity sub path. By default, it depends on the selected category. directory: str, optional Override the opacity directory. By default, it is generated from the species full name and from the other path information. absolute_path: str, optional Override the absolute path of the opacity file. By default, it is genrated from the other path information. .. py:attribute:: _default_category :type: str :value: 'correlated_k_opacities' .. py:attribute:: _default_extension :type: str :value: 'ktable' .. py:attribute:: _default_rebinning_wavelength_range :type: tuple[float, float] :value: (0.1, 251.0) .. py:attribute:: _default_resolving_power :type: int :value: 1000 .. py:attribute:: _default_wavelength_range :type: tuple[float, float] :value: (0.1, 250.0) .. py:method:: _get_default_rebinning_wavenumber_grid(resolving_power: float) -> numpy.typing.NDArray[numpy.floating] :classmethod: Return the default rebinning wavenumber grid, an equally log-spaced grid from 0.1 to 250 microns. Args: resolving_power: float The resolving power of the grid. Returns: grid: numpy.NDArray The default grid at the given resolving power. .. py:method:: exo_k_multiple_rebin_from_species(species: list[str], resolving_power: float, rewrite: bool = False) :classmethod: This function uses exo-k to bin the c-k table of a multiple species to a desired (lower) spectral resolution. Args: species : string The name of the species resolving_power : int The desired spectral resolving power. rewrite : bool If True, rewrite the rebinned files even if they already exist. .. py:method:: exo_k_multiple_rebin(input_files: list[str], resolving_power: float, rewrite=False) :classmethod: .. py:method:: exo_k_rebin(input_file: str, resolving_power: float, wavenumber_grid: numpy.typing.NDArray[numpy.floating] = None, rewrite: bool = False) -> int :classmethod: .. py:method:: from_species(species: str, spectral_sampling_type: str = 'R', spectral_sampling: int | float = Opacity._default_correlated_k_resolving_power, wavelength_min: float = _default_wavelength_range[0], wavelength_max: float = _default_wavelength_range[1], path_input_data: str = None, category: str = _default_category) :classmethod: Instantiate an Opacity object from a species name and from spectral sampling information. Args: species: str The species name, containing the species isotopic information, the natural abundance flag (if relevant), and the charge. spectral_sampling_type: {'DeltaWavelength', 'DeltaWavenumber', 'R'}, optional The opacity spectral sampling type. Default is 'R'. - 'DeltaWavelength': sampling with a constant wavelength step. - 'DeltaWavenumber': sampling with a constant wavenumber step. - 'R': sampling with a constant resolving power (wavelength / wavelength step). spectral_sampling: int or float, optional The opacity spectral sampling value. Default is 0. Units depends on spectral_sampling_type: - 'DeltaWavelength': um - 'DeltaWavenumber': cm-1 - 'R': no units wavelength_min: float, optional (um) Lower wavelength bounds of the opacity data. Default is 0. wavelength_max: float, optional (um) Upper wavelength bounds of the opacity data. Default is 0. path_input_data: str, optional Absolute path to petitRADTRANS "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRADTRANS config file. Returns: new_opacity: Opacity A new instance of an Opacity object. .. py:method:: from_species_fullname(species_fullname: str, path_input_data: str = None, category: str = _default_category) :classmethod: Instantiate an Opacity object from a species full name and from spectral sampling information. Args: species_fullname: str The species full name, containing the species isotopic information. May contain the natural abundance flag if relevant and the charge. Absolute path to petitRadtrans' "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRadtrans' config file. category: {'cia_opacities', 'clouds_opacities', 'correlated_k_opacities', 'line_by_line_opacities'}, optional The opacity category. Indicates the input_data subpath. Default is 'unknown'. - 'cia_opacities': for collision-induced absorptions. - 'clouds_opacities': for cloud opacities. - 'correlated_k_opacities': for correlated-k opacities. - 'line_by_line_opacities': for line-by-line opacities. path_input_data: str, optional Absolute path to petitRADTRANS "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRADTRANS config file. Returns: new_opacity: Opacity A new instance of an Opacity object. .. py:method:: get_default_resolving_power() -> int :classmethod: Return the Opacity object species default resolving power. .. py:method:: write(file: str, species_name: str, k_coefficients: numpy.typing.NDArray[numpy.floating], wavenumber_bin_centers: numpy.typing.NDArray[numpy.floating], wavenumber_bin_edges: numpy.typing.NDArray[numpy.floating], pressures: numpy.typing.NDArray[numpy.floating], temperatures: numpy.typing.NDArray[numpy.floating], temperature_grid_type: str, g_weights: numpy.typing.NDArray[numpy.floating], g_samples: numpy.typing.NDArray[numpy.floating], molar_mass: float = None, doi: str = '', contributor: str = '', description: str = '', date_id: str = None, wavelength_range: tuple[float] = None) :classmethod: .. py:class:: LineByLineOpacity(species_list, natural_abundance: bool = False, charge: int = 0, source: str = 'unknown', spectral_sampling_type: str = 'R', spectral_sampling: int | float = Opacity._default_line_by_line_resolving_power, wavelength_min: float = _default_wavelength_range[0], wavelength_max: float = _default_wavelength_range[1], path_input_data: str = None, species_full_name: str = None, species_base_name: str = None, species_isotopologue_name: str = None, full_extension: str = None, file_name: str = None, sub_path: str = None, absolute_path: str = None) Bases: :py:obj:`Opacity` Class for line-by-line opacity files. Args: species_list: list of str The list of species contributing to the opacity. For single-species opacities, use [species_name]. Examples: [1H2-17O], [N2, CO2] natural_abundance: bool, optional If True, the species is considered following the Earth's isotopic ratios. Default is False. charge: int, optional The charge of the species (for single-species opacities only). A value of 0 is used for neutral species. Default is 0. source: str, optional The source (i.e., where or how the opacity were obtained) of the opacity. Default is "unknown". spectral_sampling_type: {'DeltaWavelength', 'DeltaWavenumber', 'R'}, optional The opacity spectral sampling type. Default is 'R'. - 'DeltaWavelength': sampling with a constant wavelength step. - 'DeltaWavenumber': sampling with a constant wavenumber step. - 'R': sampling with a constant resolving power (wavelength / wavelength step). spectral_sampling: int or float, optional The opacity spectral sampling value. Default is 1e6. Units depends on spectral_sampling_type: - 'DeltaWavelength': um - 'DeltaWavenumber': cm-1 - 'R': no units Example: To indicate a spectral sampling with a constant resolving power of 1000. >>> spectral_sampling_type='R' >>> spectral_sampling=1000 wavelength_min: float, optional (um) Lower wavelength bounds of the opacity data. Default is 0.1. wavelength_max: float, optional (um) Upper wavelength bounds of the opacity data. Default is 250. species_full_name: str, optional Override the species full name. The species full name is composed of the species isotopic information, the natural abundance flag (if relevant), and the charge. species_cloud_info: str, optional Override the species cloud information. The species cloud information is composed of the species matter state, and of its solid structure and structure id (if relevant). species_base_name: str, optional Override the species base name. The species base name is the species chemical formula without isotopic information. It may contain cloud information and charge. Examples: "H2O", "H2O(l)", "H2O_+(s)_crystalline_000". species_isotopologue_name: str, optional Override the species isotopologue name. The species isotopologue name is the species name with isotopic information. It may contain cloud information and charge. Examples: "1H2-16O", "H2O-NatAbund(l)", "1H2-18O_+(s)_crystalline_000". extension: str, optional The opacity file type extension. Default is "unknown". Use "petitRADTRANS" for files generated with petitRADTRANS. full_extension: str, optional Override the opacity file full extension. The opacity file full extension is composed of the opacity file type extension, the opacity file generator software extension, and of the file format extension. file_name: str, optional Override the opacity file name. By default, it is generated from the instanciation arguments. sub_path: str, optional Override the opacity sub path. By default, it depends on the selected category. directory: str, optional Override the opacity directory. By default, it is generated from the species full name and from the other path information. absolute_path: str, optional Override the absolute path of the opacity file. By default, it is genrated from the other path information. .. py:attribute:: _default_category :type: str :value: 'line_by_line_opacities' .. py:attribute:: _default_extension :type: str :value: 'xsec' .. py:attribute:: _default_resolving_power :type: float :value: 1000000.0 .. py:attribute:: _default_wavelength_range :type: tuple[float, float] :value: (0.3, 28) .. py:method:: from_species(species: str, spectral_sampling_type: str = 'R', spectral_sampling: int | float = Opacity._default_line_by_line_resolving_power, wavelength_min: float = _default_wavelength_range[0], wavelength_max: float = _default_wavelength_range[1], path_input_data: str = None, category: str = _default_category) :classmethod: Instantiate an Opacity object from a species name and from spectral sampling information. Args: species: str The species name, containing the species isotopic information, the natural abundance flag (if relevant), and the charge. spectral_sampling_type: {'DeltaWavelength', 'DeltaWavenumber', 'R'}, optional The opacity spectral sampling type. Default is 'R'. - 'DeltaWavelength': sampling with a constant wavelength step. - 'DeltaWavenumber': sampling with a constant wavenumber step. - 'R': sampling with a constant resolving power (wavelength / wavelength step). spectral_sampling: int or float, optional The opacity spectral sampling value. Default is 0. Units depends on spectral_sampling_type: - 'DeltaWavelength': um - 'DeltaWavenumber': cm-1 - 'R': no units wavelength_min: float, optional (um) Lower wavelength bounds of the opacity data. Default is 0. wavelength_max: float, optional (um) Upper wavelength bounds of the opacity data. Default is 0. path_input_data: str, optional Absolute path to petitRADTRANS "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRADTRANS config file. Returns: new_opacity: Opacity A new instance of an Opacity object. .. py:method:: from_species_fullname(species_fullname: str, path_input_data: str = None, category: str = _default_category) :classmethod: Instantiate an Opacity object from a species full name and from spectral sampling information. Args: species_fullname: str The species full name, containing the species isotopic information. May contain the natural abundance flag if relevant and the charge. Absolute path to petitRadtrans' "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRadtrans' config file. category: {'cia_opacities', 'clouds_opacities', 'correlated_k_opacities', 'line_by_line_opacities'}, optional The opacity category. Indicates the input_data subpath. Default is 'unknown'. - 'cia_opacities': for collision-induced absorptions. - 'clouds_opacities': for cloud opacities. - 'correlated_k_opacities': for correlated-k opacities. - 'line_by_line_opacities': for line-by-line opacities. path_input_data: str, optional Absolute path to petitRADTRANS "input_data" directory, where the opacity files are stored. By default, use the path provided in petitRADTRANS config file. Returns: new_opacity: Opacity A new instance of an Opacity object. .. py:method:: write(file: str, species_name: str, cross_sections: numpy.typing.NDArray[numpy.floating], wavenumber_bin_edges: numpy.typing.NDArray[numpy.floating], pressures: numpy.typing.NDArray[numpy.floating], temperatures: numpy.typing.NDArray[numpy.floating], temperature_grid_type: str, molar_mass: float = None, doi: str = '', contributor: str = '', description: str = '', date_id: str = None, n_g: int = None, wavelength_range: tuple[float] = None) :classmethod: