petitRADTRANS.opacities.opacities ================================= .. py:module:: petitRADTRANS.opacities.opacities .. autoapi-nested-parse:: Manage the opacity files. Attributes ---------- .. autoapisummary:: petitRADTRANS.opacities.opacities.comm petitRADTRANS.opacities.opacities.rank petitRADTRANS.opacities.opacities.comm Classes ------- .. autoapisummary:: petitRADTRANS.opacities.opacities.Opacity petitRADTRANS.opacities.opacities.CIAOpacity petitRADTRANS.opacities.opacities.CloudOpacity petitRADTRANS.opacities.opacities.CorrelatedKOpacity petitRADTRANS.opacities.opacities.LineByLineOpacity Module Contents --------------- .. py:data:: comm :value: None .. py:data:: rank :value: 0 .. py:data:: comm .. py:class:: Opacity(species_list: list[str], natural_abundance: bool = False, charge: int = 0, source: str = 'unknown', spectral_sampling_type: str = 'R', spectral_sampling: int | float = 0.0, wavelength_min: float = 0.0, wavelength_max: float = 0.0, matter_state: str = _gas_matter_state, solid_structure: str = None, solid_structure_id: str = None, path_input_data: str = None, category: str = _default_category, species_full_name: str = None, species_cloud_info: str = None, species_base_name: str = None, species_isotopologue_name: str = None, extension: str = _default_extension, full_extension: str = None, file_name: str = None, sub_path: str = None, directory: str = None, absolute_path: str = None) Generic class for opacity files. Opacity files are HDF5 files named by joining information tokens with specific separators. The naming pattern is an extension on the ExoMol https://www.exomol.com/ naming pattern. Species names are formed by joining the atomic element symbols with isotopic information as follows: --... Below is an example for CH3D, monodeuterated methane: 12C-1H3-2H Opacity files ends with the following extensions: ..h5 The naming pattern contains the opacity sampling information ("OSI") as follows: _-mu Neutral species in the gas phase are named with the following pattern (e.g., for CH3D(g)): 12C-1H3-2H__.. Charge information can be added for ions as follows: (e.g., for [CH3D]2+(g)): 12C-1H3-2H_2+__.. Species in the liquid phase are named with the following pattern (e.g., for CH3D(l)): 12C-1H3-2H(l)__.. Species in the solid phase are named with the following pattern (e.g., for CH3D(s)): 12C-1H3-2H(s)____.. Opacities containing a mix of isotopologues following the Earth's "natural" abundances does not display isotopic information and are flagged with the string "NatAbund" (e.g., for CH4): C-H4-NatAbund__.. Opacities originating from multiple species (e.g., collision-induced absorptions, CIAs) are named with this pattern (e.g., for H2-He CIA with the Earth's isotopologue ratios): H2--He-NatAbund__.. 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 0. 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. 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. 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: 'unknown_opacities' .. py:attribute:: _temperature_grid_types :type: set[str] .. py:attribute:: _minus_char :type: str :value: 'm' .. py:attribute:: _plus_char :type: str :value: 'p' .. py:attribute:: _minus_symbol :type: str :value: '-' .. py:attribute:: _plus_symbol :type: str :value: '+' .. py:attribute:: _charges :type: dict[str, str] .. py:attribute:: _charge_symbols :type: set[str] .. py:attribute:: _charge_chars :type: set[str] .. py:attribute:: _gas_matter_state :type: str :value: '(g)' .. py:attribute:: _liquid_matter_state :type: str :value: '(l)' .. py:attribute:: _solid_matter_state :type: str :value: '(s)' .. py:attribute:: _condensed_matter_states :type: set[str] .. py:attribute:: _matter_states .. py:attribute:: _amorphous_structure :type: str :value: 'amorphous' .. py:attribute:: _crystalline_structure :type: str :value: 'crystalline' .. py:attribute:: _unclear_structure :type: str :value: 'structureUnclear' .. py:attribute:: _solid_structures :type: set[str] .. py:attribute:: _constant_delta_wavelength :type: str :value: 'DeltaWavelength' .. py:attribute:: _constant_delta_wavenumber :type: str :value: 'DeltaWavenumber' .. py:attribute:: _constant_resolving_power :type: str :value: 'R' .. py:attribute:: _spectral_sampling_types :type: set[str] .. py:attribute:: _wavelength_units :type: str :value: 'mu' .. py:attribute:: _charge_separator :type: str :value: '_' .. py:attribute:: _default_extension :type: str :value: 'unknown' .. py:attribute:: _extension_opacity :type: str :value: 'petitRADTRANS.h5' .. py:attribute:: _isotope_separator :type: str :value: '-' .. py:attribute:: _colliding_species_separator :type: str :value: '--' .. py:attribute:: _natural_abundance_string :type: str :value: 'NatAbund' .. py:attribute:: _solid_structure_separator :type: str :value: '_' .. py:attribute:: _spectral_information_separator :type: str :value: '.' .. py:attribute:: _source_separator :type: str :value: '__' .. py:attribute:: _wavelength_range_separator :type: str :value: '_' .. py:attribute:: _wavelength_separator :type: str :value: '-' .. py:attribute:: __sl :type: str :value: '\\' .. py:attribute:: _amorphous_structure_id_pattern :type: re.Pattern .. py:attribute:: _charge_pattern :type: re.Pattern .. py:attribute:: _isotope_pattern :type: re.Pattern .. py:attribute:: _space_group_pattern :type: re.Pattern .. py:attribute:: _spectral_sampling_pattern :type: re.Pattern .. py:attribute:: _wavelength_range_pattern :type: re.Pattern .. py:attribute:: _name_pattern .. py:attribute:: _default_cia_resolving_power :type: float :value: 831.0 .. py:attribute:: _default_cloud_resolving_power :type: float :value: 39.0 .. py:attribute:: _default_correlated_k_resolving_power :type: int :value: 1000 .. py:attribute:: _default_line_by_line_resolving_power :type: float :value: 1000000.0 .. py:attribute:: _default_resolving_power :type: int :value: 1000 .. py:attribute:: species_list :type: list[str] .. py:attribute:: natural_abundance :type: bool :value: False .. py:attribute:: charge :type: int :value: 0 .. py:attribute:: source :type: str :value: 'unknown' .. py:attribute:: spectral_sampling_type :type: str :value: 'R' .. py:attribute:: spectral_sampling :type: int | float :value: 0.0 .. py:attribute:: wavelength_min :type: float :value: 0.0 .. py:attribute:: wavelength_max :type: float :value: 0.0 .. py:attribute:: matter_state :type: str :value: '(g)' .. py:attribute:: solid_structure :type: str :value: None .. py:attribute:: solid_structure_id :type: str :value: None .. py:attribute:: category :type: str :value: 'unknown_opacities' .. py:attribute:: extension :type: str :value: 'unknown' .. py:attribute:: path_input_data :type: str :value: None .. py:attribute:: full_extension :type: str :value: None .. py:attribute:: species_full_name :type: str :value: None .. py:attribute:: species_cloud_info :type: str :value: None .. py:attribute:: species_base_name :type: str :value: None .. py:attribute:: species_isotopologue_name :type: str :value: None .. py:attribute:: file_name :type: str :value: None .. py:attribute:: sub_path :type: str :value: None .. py:attribute:: absolute_path :type: str :value: None .. py:property:: has_colliding_species :type: bool .. py:method:: __modify_isotope_string(isotope: str, mode: str, isotope_pattern: str) -> list[str] :staticmethod: Add, remove, or transform isotopic information. .. py:method:: __recursive_merge_contiguous_isotopes(isotope_groups: list[list[str | int]], i: int, index_merge: int | None = None) -> list[list[str | int]] :classmethod: Merge contiguous elements in list of isotope strings. Numbers of contiguous isotopes are converted to int, merged groups numbers are set to 0. Example: >>> [["12C", "2"], ["1H", "2"], ["1H", "2"]] >>> [["12C", 2], ["1H", 4], ["1H", 0]] .. py:method:: _before_write(temperature_grid_type: str, molar_mass: float, species_name: str | tuple[str, Ellipsis], date_id: str) -> tuple[float | numpy.typing.NDArray[numpy.floating], str] :classmethod: Perform operations always done to write an opacity file. .. py:method:: _init_species_name_elements(name: str, species: str, natural_abundance: str, charge: str) -> tuple[str, bool, int] :classmethod: Return the species istopologue name, natural abundance flag, and charge. .. py:method:: _get_sub_path(category: str) -> str :staticmethod: Get the subpath of the opacity file. .. py:method:: _has_isotope(string: str) -> bool :staticmethod: Return True if the string matches an isotopologue name pattern. .. py:method:: _join_spectral_information(spectral_sampling: str, wavelength_range: str) -> str :classmethod: Join the spectral sampling information with the wavelength range. .. py:method:: _match_function(path_input_data: str, sub_path: str, files: str | None = None, filename: str | None = None, expect_default_file_exists: bool = True, find_all: bool = False, display_other_files: bool = False) -> str | list[str] :classmethod: Return the file matching the given file name. If no file name is given, behave as follows depending on the sub path directory content: - 1 file is present: return the found file name. - several files are present: return the default file set in the config file if it is present. Args: path_input_data: str Absolute path to petitRadtrans "input_data" directory, where the opacity files are stored. sub_path: str Sub path to search the files in. files: str, optional Files to be matched with. By default, use te files in the sub path directory. filename: str, optional File name to be matched. expect_default_file_exists: bool, optional If True, raise an error if the default file is not found when looking for it. If False, return the default file even if it was not found. Default is True. find_all: bool, optional If True, return all the files matching with filename rather than only the first one. Default is False. display_other_files: bool, optional If True, print the available files if no matching file are found. Returns: file: str The name of the matched file. .. py:method:: _merge_contiguous_isotopes(species: str, isotope_separator: str) :classmethod: Merge contiguous matches containing the same element, whether they are of the same isotope or not. .. py:method:: check_name(opacity_name: str) :classmethod: Check opacity name, based on the ExoMol format. The name, in this order: - must begin with a number (up to 3 digits) or an uppercase letter - must contains a "valid" chemical formula (N1237He15 is considered valid) - can have isotopes, that should be separated with '-' (e.g. H218O works, but corresponds to 1H218-16O) - can contains '-NatAbund' to signal a mix of isotopes (incompatible with providing isotopic information) - can contains '+', '-', 'p' or 'm', (optionally starting with '_' and a up to 3 digits number) to signal a ion - can contains '(l)' for clouds of liquid particles - can contains '(s)' for clouds of solid particles * must contains 'crystalline' or 'amorphous' for clouds with solid particles - 'crystalline' can be followed by a 3 digit number referring to the crystal space group number - 'amorphous' can be followed by up to 5 characters referring to the amorphous state name - can contains a source or method, starting with '__' - can contains spectral information, starting with '.' * spectral information must start with 'R', 'DeltaWavenumber' or 'DeltaWavelength', indicating respectively opacities evenly spectrally spaced in resolving power, wavenumber or wavelength * spectral spacing must end with a number (integers with or without an exponent format) * can contains the spectral range in micron in the format '_-mu', following spectral spacing Valid examples: - 'H' (simplest) - 'H2O' - '2H2O' (D2O) - '1H2-16O' - '1H-18O-2H+' - 'H2O_m' - 'H2O__HITEMP' - 'H2O.R120' - 'H2O(l)__Mie' - 'H2O(s)_amorphous__Mie' - 'H2O-NatAbund(s)_crystalline_194__DHS.R39_0.1-250mu' - '24Mg2-28Si-16O4(s)_crystalline_068__DHS.R39_0.1-250mu' (most complex) Args: opacity_name: Returns: .. 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:: find_spectral_information(filename: str) -> tuple[str, str] :classmethod: Extract the spectral sampling and wavelength range information from a file name. Args: filename: str The file name to extract information from. Returns: filename_sampling: str The spectral sampling information contained in the file name. This consists in the spectral sampling type key followed by its value. filename_range: str The file wavelength range extracted from the file name. This is the min and max wavelengths of the opacity data, in microns. .. py:method:: from_species(species: str, spectral_sampling_type: str = 'R', spectral_sampling: int | float = 0.0, wavelength_min: float = 0.0, wavelength_max: float = 0.0, path_input_data: str = None) -> Opacity :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_absolute_path() -> str Return the absolute path of this Opacity object. .. py:method:: get_base_name(join: bool = False) -> str Return the base name of this Opacity object. The species base name is the species chemical formula without isotopic information. It may contain cloud information and charge. Example: >>> Opacity.from_species_fullname("24Mg2-28Si-16O4(s)_crystalline_000__DHS") >>> Opacity.get_base_name() >>> "Mg2SiO4" Args: join: bool # TODO remove in 4.0.0 Has no effect here. Returns: species_base_name: str The species base name. .. py:method:: get_cloud_info() -> str Return the cloud information of this Opacity object. Cloud information consists in the species matter state, and, if relevant, its solid internal structure and internal structure ID. Example: >>> Opacity.from_species_fullname("24Mg2-28Si-16O4(s)_crystalline_000__DHS") >>> Opacity.get_cloud_info() >>> "(s)_crystalline_000" Returns: The Opacity object cloud information. .. py:method:: get_charge_string(replace_symbol_with_char=True) -> str Return the charge of the Opacity object species in string format. Example: >>> Opacity.from_species_fullname("24Mg2-28Si-16O4_2+(s)_crystalline_000__DHS") >>> Opacity.get_charge_string() >>> "2p" >>> Opacity.get_charge_string(replace_symbol_with_char=False) >>> "2+" Args: replace_symbol_with_char: bool, optional # TODO replace with "replace_charge_symbol_with_char" in 4.0.0. If True, replace the "+" or "-" of the charge string with "p" or "m", respectively. Default is True. Returns: charge_string: str The charge of the Opacity object species. .. py:method:: get_default_category() -> str :classmethod: Return the Opacity object default category. Used to obtain the Opacity file sub path. .. py:method:: get_default_extension() -> str :classmethod: Return the Opacity object file default extension. .. py:method:: get_default_resolving_power() :classmethod: Return the Opacity object species default resolving power. .. py:method:: get_directory() -> str Return the Opacity object file directory. .. py:method:: get_file_name() -> str Return the Opacity object file name. .. py:method:: get_file_name_elements(isotope_separator: str = None, isotope_pattern: str = None, natural_abundance_string: str = None, colliding_species_separator: str = None) -> tuple[str, str, str, str] :classmethod: Return the isotope separator, isotope pattern, natural abundance string, and colliding species separator of Opacity objects. Args: isotope_separator: str, optional Override the default isotope separator ("-"). isotope_pattern: str, optional Override the default isotope regex pattern. natural_abundance_string: str, optional Override the default natural abundance string ("NatAbund"). colliding_species_separator: str, optional Override the default colliding species separator ("--"). Returns: isotope_separator: str The isotope separator. isotope_pattern: str The isotope regex pattern. natural_abundance_string: str The natural abundance string. colliding_species_separator: str The colliding species separator. .. py:method:: get_full_extension() -> str Return this Opacity object file full extension, i.e. the opacity type and the generator software. .. py:method:: get_full_name() -> str Return this Opacity object species full name, containing the species isotopic information, the natural abundance flag (if relevant), and the charge. Example: >>> Opacity.from_species_fullname("24Mg2-28Si-16O4_2+(s)_crystalline_000__DHS") >>> Opacity.get_full_name() >>> "24Mg2-28Si-16O4_2p" .. py:method:: get_isotopologue_name(join: bool = False) -> str Return this Opacity object species isotopologye name, containing the species isotopic information, the natural abundance flag (if relevant), and the charge. Args: join: bool, optional # TODO remove in 4.0.0 If True, add the charge information to the isotopologue_name. Default is False. Example: >>> Opacity.from_species_fullname("24Mg2-28Si-16O4_2+(s)_crystalline_000__DHS") >>> Opacity.get_isotopologue_name() >>> "24Mg2-28Si-16O4" >>> Opacity.get_isotopologue_name(join=False) >>> "24Mg2-28Si-16O4_2p" .. py:method:: get_resolving_power_from_string(string: str) -> int :classmethod: Return resolving power information from a string following the petitRADTRANS Opacity format. Args: string: str The string to extract resolving power information from. Returns: resolving_power: str The resolving power information. .. py:method:: get_resolving_power_string(resolving_power: int | float | str) -> str :classmethod: Return resolving power in the petitRADTRANS Opacity format from a number. Args: resolving_power: int, float, or str The resolving power to convert into string. Returns: resolving_power: str The resolving power in petitRADTRANS Opacity format. .. py:method:: get_species_base_name(species_full_name: str, join: bool = False) -> str :classmethod: Return the base name of a species. The species base name is the species chemical formula without isotopic information. It may contain cloud information and charge. Example: >>> Opacity.get_species_base_name("24Mg2-28Si-16O4(s)_crystalline_000__DHS") >>> "Mg2SiO4" Args: species_full_name: str The species full name, containing the species isotopic information. May contain the natural abundance flag if relevant and the charge. join: bool, optional If True, add the species charge, matter state, and solid structure information (if relevant) to the base name. Default is False. Returns: species_base_name: str The species base name. .. py:method:: get_species_directory(species: str, category: str = None, path_input_data: str = None, base_name: str = None, isotopologue_name: str = None, sub_path: str = None) -> str :classmethod: Return the petitRADTRANS absolute path for the given species. Args: species: str The species name. May contain the species isotopic information, the natural abundance flag if relevant and the charge. 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. base_name: str, optional Override the species base name. By default, it is extracted from the value of the "species" argument. isotopologue_name: str, optional Override the species isotopologue name. By default, it is extracted from the value of the "species" argument. sub_path: str, optional Override the species sub path. By default, it is extracted from the value of the "species" argument. Returns: species_directory: str The absolute path of the Opacity object species. .. py:method:: get_species_isotopologue_name(species_name: str, join: bool = False) -> str :classmethod: Return the isotopologue name of a species. The species isotopologue name is the species chemical formula with separated isotopes. It may contain cloud information and charge. Example: >>> Opacity.get_species_isotopologue_name("24Mg2-28Si-16O4(s)_crystalline_000__DHS") >>> "24Mg2-28Si-16O4" >>> Opacity.get_species_isotopologue_name("24Mg2-28Si-16O4(s)_crystalline_000__DHS", join=True) >>> "24Mg2-28Si-16O4_2+(s)_crystalline_000" Args: species_name: str The species name. May contain the species isotopic information, the natural abundance flag if relevant and the charge. join: bool, optional If True, add the species charge, matter state, and solid structure information (if relevant) to the base name. Default is False. Returns: species_base_name: str The species base name. .. py:method:: get_species_scientific_name(species: str) -> str :classmethod: Return the name of a species in LaTeX format. The species scientific name is the species chemical full formula with isotopes. It does not contain charges. Example: >>> Opacity.get_species_scientific_name("24Mg2-28Si-16O4(s)_crystalline_000__DHS") >>> "24Mg2-28Si-16O4" >>> Opacity.get_species_isotopologue_name("24Mg2-28Si-16O4(s)_crystalline_000__DHS", join=True) >>> "24Mg2-28Si-16O4_2+(s)_crystalline_000" Args: species: str The species name. May contain the species isotopic information, the natural abundance flag if relevant and the charge. Returns: species_base_name: str The species base name. .. py:method:: get_spectral_info() -> str Return this Opacity object spectral information. Spectral information contains the opacity spectral sampling type, its value, and the opacity wavelength range boundaries in microns. Example: >>> Opacity.from_species_fullname("24Mg2-28Si-16O4_2+(s)_crystalline_000__DHS.R39_0.1-250mu") >>> Opacity.get_spectral_info() >>> "R39_0.1-250" .. py:method:: join_species_all_info(species_name: str, natural_abundance: str = '', charge: str = '', cloud_info: str = '', source: str = '', spectral_info: str = '', spectral_sampling: str = None, wavelength_range: str = None) -> str :classmethod: Join together species information, using the petitRADTRANS Opacity separators. The results may not be a valid petitRADTRANS Opacity name. Args: species_name: str The species chemical formula. natural_abundance: str, optional The natural abundance flag. Empty by default. charge: str, optional The charge in string format. Empty by default. cloud_info: str, optional The matter state, solid structure and solid structure ID. Empty by default. source: str, optional The opacity source. Empty by default. spectral_info: str, optional The opacity sampling type, its value, and the opacity wavenumber boundaries in microns. Empty by default. spectral_sampling: str, optional The opacity sampling type and its value. Activated if "spectral_info" is empty. wavelength_range: str, optional The opacity wavenumber boundaries in microns. Activated if "spectral_info" is empty. Returns: species_name: str The species name, using the petitRADTRANS Opacity separators. .. py:method:: load(file: str) .. py:method:: modify_isotope_numbers(species: str, mode: str, isotope_separator: str = None, isotope_pattern: str = None, natural_abundance_string: str = None, colliding_species_separator: str = None) -> str :classmethod: Add or remove isotope numbers from a species. Note that using improper isotope separation can lead to incorrect results (e.g. H218O -> 1H218-16O). Args: species: Species name. Can also be a species collision (e.g. H2--He). mode: Can be 'add', 'remove', or 'scientific'. In 'add' mode, add the isotope number of each of the species will be added to the species name, and each isotope is separated with a '-'. By default, the main isotope number is used. If partial isotope information is provided (e.g. 13C2H2, H2-18O, ...), use the main isotope number on the isotopes for which no information is given (e.g. 13C2-1H2, 1H2-18O, ...). In 'remove' mode, remove all isotope numbers (e.g. 13C2-1H2 -> C2H2). In 'scientific' mode, convert the species into scientific notation using LaTeX formatting. isotope_separator: Isotope separator. If None, use the default value. isotope_pattern: Regex pattern string to detect isotopes in a species name. If None, use the default value. natural_abundance_string: Natural abundance string. If None, use the default value. colliding_species_separator: Colliding species separator. If None, use the default value. Returns: The species name with added or removed isotope information. .. py:method:: save(file: str) .. py:method:: split_cloud_info(cloud_info: str) -> tuple[str, str, str] :classmethod: Split the matter state, solid structure and solid structure ID from a string in petitRADTRANS format. Example: >>> Opacity.split_cloud_info("(s)_crystalline_000") >>> ('(s)', 'crystalline', '000') Args: cloud_info: str A string in petitRADTRANS format. Returns: matter_state: str The matter state. solid_structure: str The solid structure. solid_structure_id: str The solid structure ID. .. py:method:: split_species_all_info(species: str, replace_charge_symbol_with_char: bool = False, full: bool = False) -> tuple[str, Ellipsis] :classmethod: Split a species name in the petitRADTRANS Opacity format into its components. Examples: >>> Opacity.split_species_all_info("24Mg2-28Si-16O4_2+(s)_crystalline_000__DHS.R39_0.1-250mu") >>> ('24Mg2-28Si-16O4', '', '2+', '(s)_crystalline_000', 'DHS', 'R39_0.1-250mu') >>> Opacity.split_species_all_info("H-NatAbund_2-__X.R100_0.1-250mu", replace_charge_symbol_with_char=True) >>> ('H_2-', 'NatAbund', '2m', '', 'X', 'R100_0.1-250mu') >>> Opacity.split_species_all_info("24Mg2-28Si-16O4_2+(s)_crystalline_000__DHS.R39_0.1-250mu", full=True) >>> ('24Mg2-28Si-16O4', '', '2+', '(s)', 'crystalline', '000', 'DHS', 'R', '39', '0.1', '250') Args: species: str The species name, in the petitRADTRANS Opacity format. replace_charge_symbol_with_char: bool, optional If True, replace the "+" or "-" of the charge string with "p" or "m", respectively. Default is False. full: bool, optional If True, return the complete decomposition of the species name. Default is False. Returns: name: str The species name. natural_abundance: str The natural abundance flag. charge: str The charge in string format. cloud_info: str If full is False only. The matter state, solid structure, and solid structure ID. matter_state: str If full is True only. solid_structure: str If full is True only. solid_structure_id: str If full is True only. source: str The source. spectral_info: str If full is False only. The spectral sampling type, its value, and the opacity wavelength boundaries. spectral_sampling_type: str If full is True only. spectral_sampling_value: str If full is True only. wavelength_min: str If full is True only. wavelength_max: str If full is True only. .. py:method:: split_species_charge(species: str, replace_symbol_with_char: bool = False) -> tuple[str, str] :classmethod: Separate the charge from a species name in the petitRADTRANS Opacity format. Examples: >>> Opacity.split_species_charge("24Mg2-28Si-16O4_2+") >>> ('24Mg2-28Si-16O4', '2+') >>> Opacity.split_species_charge("24Mg2-28Si-16O4_2+", replace_symbol_with_char=True) >>> ('24Mg2-28Si-16O4', '2p') Args: species: str The species name, containing only the spectral formula and the charge. replace_symbol_with_char: # TODO replace with "replace_charge_symbol_with_char" in 4.0.0. If True, replace the "+" or "-" of the charge string with "p" or "m", respectively. Default is True. Returns: name: str The species chemical formula. charge: str The species charge in string format. .. py:method:: split_species_cloud_info(species: str) -> tuple[str, str] :staticmethod: Separate the cloud information from a species name in the petitRADTRANS Opacity format. Example: >>> Opacity.split_species_cloud_info("24Mg2-28Si-16O4_2+(s)_crystalline_000") >>> ('24Mg2-28Si-16O4_2+', '(s)_crystalline_000') Args: species: str The species name, containing the cloud information. Returns: name: str The species name, minus the cloud information. cloud_info: str The species cloud information. .. py:method:: split_species_source(species: str) -> tuple[str, str] :classmethod: Separate the species source from a species name in the petitRADTRANS Opacity format. Example: >>> Opacity.split_species_source("24Mg2-28Si-16O4_2+(s)_crystalline_000__DHS") >>> ('24Mg2-28Si-16O4_2+(s)_crystalline_000', 'DHS') Args: species: str The species name, containing the source. Returns: name: str The species name, minus the source. source: str The species opacity source. .. py:method:: split_species_spectral_info(species: str) -> tuple[str, str] :classmethod: Separate the spectral information from a species name in the petitRADTRANS Opacity format. Example: >>> Opacity.split_species_spectral_info("24Mg2-28Si-16O4_2+(s)_crystalline_000__DHS.R39_0.1-250mu") >>> ('24Mg2-28Si-16O4_2+(s)_crystalline_000__DHS', 'R39_0.1-250mu') Args: species: str The species name, containing the spectral information. Returns: name: str The species name, minus the spectral information. cloud_info: str The species spectral information. .. py:method:: split_spectral_sampling_info(spectral_sampling_info: str) -> tuple[str, str] :classmethod: Split spectral sampling information into its sampling type and its value. Example: >>> Opacity.split_spectral_sampling_info("R39") >>> ('R', '39') Args: spectral_sampling_info: str The spectral sampling information to split, containing the sampling type and its value. Returns: spectral_sampling_type: str The spectral sampling type. spectral_sampling_value: str The spectral sampling value. .. py:method:: split_spectral_info(spectral_info: str) -> tuple[str, str] :classmethod: Split spectral information into the spectral sampling information and the opacity wavelength boundaries. Example: >>> Opacity.split_spectral_sampling_info("R39_0.1-250mu") >>> ('R39', '0.1-250mu') Args: spectral_info: str The spectral information to split, containing only the spectral sampling information and the opacity wavelength boundaries. Returns: spectral_sampling_info: str The spectral type information. wavelength_range_info: str The opacity wavelength boundaries. .. py:method:: split_wavelength_range_info(wavelength_range_info: str) -> tuple[str, str] :classmethod: Split wavelenght range information into the opacity lower and upper boundaries. Example: >>> Opacity.split_spectral_sampling_info("0.1-250mu") >>> ('0.1', '250') Args: wavelength_range_info: str The wavelength range to split. Returns: wavelength_min: str The lower opacity wavelength boundary. wavelength_max: str The upper opacity wavelength boundary. .. py:method:: write(**kwargs) :staticmethod: .. 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: