petitRADTRANS.chemistry.core

petitRADTRANS.chemistry.core#

Attributes#

`get_easychem_abundances`
`INVALID_VALUE`
`_ISOTOPE_RATIO_SPECS`

Functions#

`_get_active_abundance_profile_mode`(species_name, ...)	Return the enabled pressure-varying abundance profile mode for a species.
`_build_pressure_varying_mass_fraction_profile`(...)	Build a pressure-varying mass-fraction profile for one species.
`_normalize_parameter_mapping`(parameters)	Convert plain or legacy parameter values to a plain-value mapping.
`_get_parameter_alias_value`(parameters, *names[, default])	Return the first non-`None` parameter value among the provided aliases.
`_get_static_bool_parameter`(→ bool)	Return a Python bool for structural chemistry flags.
`_has_truthy_parameter`(parameters, *names)	Return whether any aliased parameter is explicitly enabled.
`_get_cached_cloud_metadata`(cloud_species)	Return cached `(opacity_name, base_name)` pairs for cloud species.
`_build_cloud_metadata`(cloud_species)	Return `(opacity_name, base_name)` pairs for cloud species.
`_has_explicit_cloud_base`(parameter_keys, cloud_name)
`_resolve_cloud_base_pressure`(cloud_name, *, pressures, ...)
`_resolve_cloud_fsed`(cloud_name, parameters, parameter_keys)
`_resolve_cloud_abundance`(cloud, cloud_name, *, ...)
`resolve_cloud_base_pressures`(pressures, temperatures, ...)	Resolve cloud-base pressures without constructing full cloud profiles.
`_contains_isotope`(→ bool)	Return whether an isotopologue name contains a specific isotope token.
`_replace_isotope`(→ str)	Replace isotope tokens while preserving token separators and element counts.
`_build_isotopologue_ratio_mass_fractions`(*, ...)	Build rare-isotopologue profiles from isotope-ratio parameters.
`_simplify_species_in_original_order`(line_species)	Return simplified species names without reordering the input sequence.
`_resolve_chemistry_mode`(parameters)	Resolve free, precalculated-equilibrium, and full-easyChem chemistry modes.
`_build_easychem_mass_fractions`(pressures, ...)	Build mass fractions from the explicit full easyChem chemistry path.
`calculate_gas_mass_fractions`(pressures[, ...])	Build and normalize per-layer gas mass-fraction profiles.
`calculate_cloud_mass_fractions`(pressures, ...[, ...])	Add cloud abundance profiles and cloud-base metadata to a composition.
`get_abundances`(pressures, temperatures, parameters, ...)	Assemble gas and cloud abundances for a pressure-temperature profile.
`get_abundances_from_legacy_dict`(pressures, ...[, ...])	Legacy wrapper for `get_abundances()`.
`get_abundances_legacy`(pressures, temperatures, ...[, ...])	Legacy abundance pipeline retained for compatibility.

Module Contents#

petitRADTRANS.chemistry.core.get_easychem_abundances = None#

petitRADTRANS.chemistry.core.INVALID_VALUE#

petitRADTRANS.chemistry.core._ISOTOPE_RATIO_SPECS#

petitRADTRANS.chemistry.core._get_active_abundance_profile_mode(species_name, parameters)#

Return the enabled pressure-varying abundance profile mode for a species.

Args:

species_name:: Species name used to look up profile-control parameters.
parameters:: Mapping of model parameters.

Returns:

The first enabled profile mode among "stepped", "linear", and "cubic", or None if no mode is active.

petitRADTRANS.chemistry.core._build_pressure_varying_mass_fraction_profile(pressures, species_name, parameters, profile_mode)#

Build a pressure-varying mass-fraction profile for one species.

Args:

pressures:: Pressure grid on which to evaluate the abundance profile.
species_name:: Species name used to resolve interpolation nodes from parameters.
parameters:: Mapping of model parameters.
profile_mode:: Profile-construction mode understood by build_abundance_profile.

Returns:

A mass-fraction profile sampled on pressures.

petitRADTRANS.chemistry.core._normalize_parameter_mapping(parameters)#: Convert plain or legacy parameter values to a plain-value mapping.

petitRADTRANS.chemistry.core._get_parameter_alias_value(parameters, *names, default=None)#: Return the first non-None parameter value among the provided aliases.

petitRADTRANS.chemistry.core._get_static_bool_parameter(parameter_name, parameter_value) → bool#

Return a Python bool for structural chemistry flags.

Chemistry-mode and profile-selection flags drive Python control flow, so they must remain static scalars when the chemistry path is traced.

petitRADTRANS.chemistry.core._has_truthy_parameter(parameters, *names)#: Return whether any aliased parameter is explicitly enabled.

petitRADTRANS.chemistry.core._get_cached_cloud_metadata(cloud_species)#: Return cached (opacity_name, base_name) pairs for cloud species.

petitRADTRANS.chemistry.core._build_cloud_metadata(cloud_species)#: Return (opacity_name, base_name) pairs for cloud species.

petitRADTRANS.chemistry.core._has_explicit_cloud_base(parameter_keys, cloud_name)#

petitRADTRANS.chemistry.core._resolve_cloud_base_pressure(cloud_name, *, pressures, temperatures, metallicity, co_ratio, parameters, parameter_keys, mean_molar_mass, has_equilibrium_cloud_base)#

petitRADTRANS.chemistry.core._resolve_cloud_fsed(cloud_name, parameters, parameter_keys)#

petitRADTRANS.chemistry.core._resolve_cloud_abundance(cloud, cloud_name, *, metallicity, co_ratio, parameters, parameter_keys, mass_fractions, use_easychem, zero_profile, one_profile)#

petitRADTRANS.chemistry.core.resolve_cloud_base_pressures(pressures: jax.typing.ArrayLike, temperatures: jax.typing.ArrayLike, parameters: dict, line_species: tuple, cloud_species: tuple, filling_species: tuple | dict | None = None, **kwargs)#

Resolve cloud-base pressures without constructing full cloud profiles.

This helper is intended for adaptive pressure-grid setup. When cloud-base pressures are explicitly parameterized, it returns them directly without running chemistry. Otherwise it computes only the gas-composition state needed to derive mean molar masses and then resolves the cloud bases.

petitRADTRANS.chemistry.core._contains_isotope(isotopologue_name: str, isotope: str) → bool#: Return whether an isotopologue name contains a specific isotope token.

petitRADTRANS.chemistry.core._replace_isotope(isotopologue_name: str, from_isotope: str, to_isotope: str) → str#: Replace isotope tokens while preserving token separators and element counts.

petitRADTRANS.chemistry.core._build_isotopologue_ratio_mass_fractions(*, line_species, parameters, mass_fractions_chemical_table)#

Build rare-isotopologue profiles from isotope-ratio parameters.

For each supported isotope ratio, when both a rare isotopologue and its corresponding main isotopologue are present in line_species, this helper defines the rare profile as ratio * main_profile.

petitRADTRANS.chemistry.core._simplify_species_in_original_order(line_species)#: Return simplified species names without reordering the input sequence.

petitRADTRANS.chemistry.core._resolve_chemistry_mode(parameters)#

Resolve free, precalculated-equilibrium, and full-easyChem chemistry modes.

The parameter mapping drives chemistry selection as follows:

use_easychem or use_exoatmos explicitly enables the full easyChem calculation.
Otherwise, a metallicity parameter (metallicity, M/H, or Fe/H) selects the built-in precalculated equilibrium table by default.
If neither signal is present, the caller stays on the free-chemistry path.

petitRADTRANS.chemistry.core._build_easychem_mass_fractions(pressures, temperatures, parameters, line_species, cloud_species, metallicity, co_ratio, carbon_quench_pressure, use_full_easychem, exo_atmos, atomic_mass_fractions, adaptive_mesh_refinement)#: Build mass fractions from the explicit full easyChem chemistry path.

petitRADTRANS.chemistry.core.calculate_gas_mass_fractions(pressures, temperatures=None, imposed_mass_fractions=None, line_species=None, cloud_species=None, filling_species=None, use_equilibrium_chemistry=False, metallicity=None, co_ratio=0.55, carbon_quench_pressure=None, exo_atmos=None, atomic_mass_fractions=None, **kwargs)#

Build and normalize per-layer gas mass-fraction profiles.

The function combines explicitly imposed gas abundances, optional pre-calculated equilibrium chemistry, and background filling species so that each atmospheric layer sums to unity.

Args:

pressures:: Pressure grid for the atmospheric layers.
temperatures:: Temperature profile on the same grid as pressures. Required when interpolating the equilibrium chemistry table.
imposed_mass_fractions:: Mapping of species names to imposed mass fractions. Scalar inputs are broadcast over the pressure grid. Negative values are interpreted as base-10 logarithmic mass fractions.
line_species:: Gas-opacity species names. These are used to reconcile opacity names with chemistry-table names and to discover pressure-varying profile controls.
cloud_species:: Cloud-opacity species names. Accepted for API compatibility with the broader chemistry pipeline; they are not used directly in the active gas-fraction path.
filling_species:: Optional fill-specification for background gases. This may be None, a species name, an iterable of species names, or a mapping of species names to fill weights.
use_equilibrium_chemistry:: If True, use the built-in precalculated equilibrium chemistry table together with metallicity and co_ratio. The explicit full easyChem path is resolved upstream in get_abundances().
metallicity:: Metallicity passed to the pre-calculated equilibrium chemistry table. When provided, equilibrium gas abundances are interpolated.
co_ratio:: Carbon-to-oxygen ratio used with the equilibrium chemistry table.
carbon_quench_pressure:: Optional quench pressure forwarded to the equilibrium chemistry interpolation.
exo_atmos:: Compatibility argument reserved for legacy/easychem callers.
atomic_mass_fractions:: Compatibility argument reserved for legacy/easychem callers.
**kwargs:: Additional keyword arguments. If a parameters mapping is present, it is used to detect pressure-varying abundance-profile controls.

Returns:

A tuple (mass_fractions, m_sum_total) containing the per-species mass-fraction profiles and the total mass-fraction sum in each layer.

petitRADTRANS.chemistry.core.calculate_cloud_mass_fractions(pressures, temperatures, metallicity, co_ratio, cloud_species, parameters, mass_fractions, mean_molar_mass, adaptive_mesh_refinement=False, use_easychem=False)#

Add cloud abundance profiles and cloud-base metadata to a composition.

Args:

pressures:: Pressure grid for the atmospheric layers.
temperatures:: Temperature profile on the same grid as pressures.
metallicity:: Metallicity used when equilibrium cloud abundances or cloud bases are requested.
co_ratio:: Carbon-to-oxygen ratio used with equilibrium cloud calculations.
cloud_species:: Condensate-opacity species names to evaluate.
parameters:: Mapping of plain model parameter values controlling cloud abundances, cloud bases, and sedimentation efficiencies.
mass_fractions:: Existing species mass fractions. This mapping is updated in place with the computed cloud profiles.
mean_molar_mass:: Mean molar-mass profile used when computing cloud-base pressures.
adaptive_mesh_refinement:: Compatibility argument retained for the public API. The current cloud path returns the identity pressure grid.
use_easychem:: If True, copy cloud abundances directly from a full easyChem composition instead of constructing sedimented cloud profiles.

Returns:

A tuple (mass_fractions, p_bases, pressure_indices) containing the updated mass fractions, cloud-base pressures keyed by cloud name, and the pressure-grid indices used by the cloud path.

petitRADTRANS.chemistry.core.get_abundances(pressures: jax.typing.ArrayLike, temperatures: jax.typing.ArrayLike, parameters: dict, line_species: tuple, cloud_species: tuple, filling_species: tuple | dict = None, adaptive_mesh_refinement: bool = False, **kwargs)#

Assemble gas and cloud abundances for a pressure-temperature profile.

This function resolves the requested chemistry mode from parameters, computes gas mass fractions, derives the mean molar mass, and optionally adds condensate abundances and cloud-base information.

Args:

pressures:: Pressure grid for the atmospheric layers.
temperatures:: Temperature profile on the same grid as pressures.
parameters:: Mapping of plain model parameter values. Supported keys depend on the selected chemistry and cloud mode and may include equilibrium-chemistry controls, directly imposed abundances, pressure-varying profile flags, cloud abundance parameters, and cloud-base parameters.
line_species:: Gas-opacity species names.
cloud_species:: Condensate-opacity species names.
filling_species:: Optional background fill-specification forwarded to calculate_gas_mass_fractions. If omitted, a default H2/He fill is used.
adaptive_mesh_refinement:: Forwarded to calculate_cloud_mass_fractions. The current cloud path returns the identity pressure grid.
**kwargs:: Additional keyword arguments forwarded to calculate_gas_mass_fractions.

Returns:

A tuple (mass_fractions, mean_molar_mass, pressure_indices, p_bases) containing the species mass fractions, the mean molar-mass profile, the selected pressure-grid indices, and the cloud-base pressures.

Chemistry-mode selection:

get_abundances distinguishes three chemistry modes from the plain parameter mapping:

free chemistry: no equilibrium selector is present;

precalculated equilibrium chemistry: selected by default when a metallicity parameter such as Fe/H, M/H, or metallicity is present, or when use_equilibrium_chemistry=True;

full easyChem chemistry: selected only when use_easychem or use_exoatmos is explicitly truthy.

An explicit full easyChem request takes precedence over the default precalculated equilibrium-table path.

petitRADTRANS.chemistry.core.get_abundances_from_legacy_dict(pressures: jax.typing.ArrayLike, temperatures: jax.typing.ArrayLike, parameters: dict, line_species: tuple, cloud_species: tuple, filling_species: tuple | dict = None, adaptive_mesh_refinement: bool = False, **kwargs)#

Legacy wrapper for get_abundances().

Converts a legacy parameter dictionary (values accessed via .value) to a plain-value mapping before forwarding to get_abundances().

Args:

pressures:: Pressure grid for the atmospheric layers.
temperatures:: Temperature profile on the same grid as pressures.
parameters:: Legacy parameter mapping whose values expose a .value attribute.
line_species:: Gas-opacity species names.
cloud_species:: Condensate-opacity species names.
filling_species:: Optional background fill-specification forwarded to get_abundances().
adaptive_mesh_refinement:: Forwarded unchanged to get_abundances().
**kwargs:: Additional keyword arguments forwarded to get_abundances().

Returns:

The same tuple returned by get_abundances().

petitRADTRANS.chemistry.core.get_abundances_legacy(pressures, temperatures, line_species, cloud_species, parameters, adaptive_mesh_refinement=False)#

Legacy abundance pipeline retained for compatibility.

This historical implementation supports the older parameter objects whose values are accessed via .value and preserves the original free-chemistry, equilibrium-chemistry, and cloud-handling flow.

Args:

pressures:: Pressure grid for the atmospheric layers.
temperatures:: Temperature profile on the same grid as pressures.
line_species:: Gas-opacity species names.
cloud_species:: Condensate-opacity species names.
parameters:: Legacy parameter mapping whose values are accessed via .value. Supported keys depend on the selected legacy chemistry and cloud mode.
adaptive_mesh_refinement:: Retained for API compatibility. Legacy adaptive pressure-grid expansion has been removed and the input grid is always used.

# Find high resolution pressure grid and indices

Returns:: A tuple (abundances, mmw, pressure_indices, p_bases) containing the species mass fractions, the mean molar-mass profile, the selected pressure-grid indices, and the cloud-base pressures.