.. _usermodel: =========== ``[Model]`` =========== This header defines the type of forward model (FM) that will be computed by TauREx3. There are several built-in forward ``model_type`` values: - ``transmission`` - Transmission forward model - ``emission`` - Emission forward model - ``directimage`` - Direct-image forward model - ``multi_transit`` - Composite transmission model combining multiple 1D regions - ``multi_eclipse`` - Composite emission model combining multiple 1D regions - ``multi_directimage`` - Composite direct-imaging model combining multiple 1D regions - ``custom`` - User-type forward model, See :ref:`customtypes` Both emission and direct image also include an optional keyword ``ngauss`` which dictates the number of Gaussian quadrate points used in the integration. By default this is set to ``ngauss=4``. Composite Forward Models ======================== TauREx also includes built-in composite forward models for stitching together multiple 1D atmospheric regions into a single weighted spectrum. These were previously distributed through the ``taurex-multimodel`` plugin and are now available directly in the main package. The parameter-file-driven entry points are: +-------------------------+-------------------------------------------------------+ | ``model_type`` | Description | +-------------------------+-------------------------------------------------------+ | ``multi_transit`` | Weighted combination of multiple transmission regions | +-------------------------+-------------------------------------------------------+ | ``multi_eclipse`` | Weighted combination of multiple emission regions | +-------------------------+-------------------------------------------------------+ | ``multi_directimage`` | Weighted combination of multiple direct-image regions | +-------------------------+-------------------------------------------------------+ Each region is defined through a separate parameter file listed in ``parfiles``. TauREx reads the temperature, chemistry, pressure, and contribution sections from each file and combines the resulting spectra with the optional ``fractions`` list. For retrievals, provide ``N-1`` fractions rather than ``N`` if you want TauREx to adapt the last region automatically. In that case the final fraction is inferred from the remaining weight so that the total remains unity. For a complete worked setup, see the multimodel notebook example in :ref:`Examples`. Example composite transmission setup:: [Model] model_type = multi_transit parfiles = day.par, night.par fractions = 0.7 The same pattern applies to ``multi_eclipse`` and ``multi_directimage``. Two internal helper models are also exposed for advanced use: - ``emission_radscale`` or ``eclipse_radscale`` for radius-scaled emission regions. - ``direct_radscale`` or ``directimage_radscale`` for radius-scaled direct-image regions. --------------------------- Contributions ============= Contributions define what processes in the atmosphere contribute to the optical depth. These contributions are defined as *subheaders* with the name of the header being the contribution to add into the forward model.Any forward model type can be augmented with these contributions. -------- Examples -------- Transmission spectrum with molecular absorption and CIA from ``H2-He`` and ``H2-H2``:: [Model] model_type = transmission [[Absorption]] [[CIA]] cia_pairs = H2-He,He-He Emission spectrum with molecular absorption, CIA and Rayleigh scattering:: [Model] model_type = emission ngauss = 4 [[Absorption]] [[CIA]] cia_pairs = H2-He,He-He [[Rayleigh]] The following sections give a list of available contributions ----------------------------- Molecular Absorption ==================== ``[[Absorption]]`` Adds molecular absorption to the forward model. Here the *active* molecules contribute to absorption. No other keywords are needed. No fitting parameters. --------------------- Collisionally Induced Absorption ================================ ``[[CIA]]`` Adds collisionally induced absorption to the forward model. Requires ``cia_path`` to be set. Both *active* and *inactive* molecules can contribute. No fitting parameters -------- Keywords -------- +---------------+-------------+------------------------------------------------+ | Variable | Type | Description | +---------------+-------------+------------------------------------------------+ | ``cia_pairs`` | :obj:`list` | List of molecular pairs. e.g. ``H2-He, H2-H2`` | +---------------+-------------+------------------------------------------------+ --------------------- Rayleigh Scattering =================== ``[[Rayleigh]]`` Adds Rayleigh scattering to the forward model. Both *active* and *inactive* molecules can contribute. No keywords or fitting parameters. --------------------- Optically thick clouds ====================== ``[[SimpleClouds]]`` or ``[[ThickClouds]]`` A simple cloud model that puts a infinitely absorping cloud deck in the atmosphere. -------- Keywords -------- +---------------------+--------------+-------------------------------------+ | Variable | Type | Description | +---------------------+--------------+-------------------------------------+ | ``clouds_pressure`` | :obj:`float` | Pressure of top of cloud-deck in Pa | +---------------------+--------------+-------------------------------------+ ------------------ Fitting Parameters ------------------ +---------------------+--------------+-------------------------------------+ | Variable | Type | Description | +---------------------+--------------+-------------------------------------+ | ``clouds_pressure`` | :obj:`float` | Pressure of top of cloud-deck in Pa | +---------------------+--------------+-------------------------------------+ --------------------------- Mie scattering (Lee) ====================== ``[[LeeMie]]`` Computes Mie scattering contribution to optical depth Formalism taken from: Lee et al. 2013, ApJ, 778, 97 -------- Keywords -------- +-----------------------+--------------+----------------------------+ | Variable | Type | Description | +-----------------------+--------------+----------------------------+ | ``lee_mie_radius`` | :obj:`float` | Particle radius in um | +-----------------------+--------------+----------------------------+ | ``lee_mie_q`` | :obj:`float` | Extinction coefficient | +-----------------------+--------------+----------------------------+ | ``lee_mie_mix_ratio`` | :obj:`float` | Mixing ratio in atmosphere | +-----------------------+--------------+----------------------------+ | ``lee_mie_bottomP`` | :obj:`float` | Bottom of cloud deck in Pa | +-----------------------+--------------+----------------------------+ | ``lee_mie_topP`` | :obj:`float` | Top of cloud deck in Pa | +-----------------------+--------------+----------------------------+ ------------------ Fitting Parameters ------------------ +-----------------------+--------------+----------------------------+ | Parameter | Type | Description | +-----------------------+--------------+----------------------------+ | ``lee_mie_radius`` | :obj:`float` | Particle radius in um | +-----------------------+--------------+----------------------------+ | ``lee_mie_q`` | :obj:`float` | Extinction coefficient | +-----------------------+--------------+----------------------------+ | ``lee_mie_mix_ratio`` | :obj:`float` | Mixing ratio in atmosphere | +-----------------------+--------------+----------------------------+ | ``lee_mie_bottomP`` | :obj:`float` | Bottom of cloud deck in Pa | +-----------------------+--------------+----------------------------+ | ``lee_mie_topP`` | :obj:`float` | Top of cloud deck in Pa | +-----------------------+--------------+----------------------------+ --------------------------- Mie scattering (BH) ====================== ``[[BHMie]]`` Computes a Mie scattering contribution using method given by Bohren & Huffman 2007 -------- Keywords -------- +------------------------+-----------------------+----------------------------------------+ | Variable | Type | Description | +------------------------+-----------------------+----------------------------------------+ | ``bh_particle_radius`` | :obj:`float` | Particle radius in um | +------------------------+-----------------------+----------------------------------------+ | ``bh_cloud_mix`` | :obj:`float` | Mixing ratio in atmosphere | +------------------------+-----------------------+----------------------------------------+ | ``bh_clouds_bottomP`` | :obj:`float` | Bottom of cloud deck in Pa | +------------------------+-----------------------+----------------------------------------+ | ``bh_clouds_topP`` | :obj:`float` | Top of cloud deck in Pa | +------------------------+-----------------------+----------------------------------------+ | ``mie_path`` | :obj:`str` | Path to molecule scattering parameters | +------------------------+-----------------------+----------------------------------------+ | ``mie_type`` | ``cloud`` or ``haze`` | Type of mie cloud | +------------------------+-----------------------+----------------------------------------+ ------------------ Fitting Parameters ------------------ +------------------------+-----------------------+----------------------------------------+ | Parameter | Type | Description | +------------------------+-----------------------+----------------------------------------+ | ``bh_particle_radius`` | :obj:`float` | Particle radius in um | +------------------------+-----------------------+----------------------------------------+ | ``bh_cloud_mix`` | :obj:`float` | Mixing ratio in atmosphere | +------------------------+-----------------------+----------------------------------------+ | ``bh_clouds_bottomP`` | :obj:`float` | Bottom of cloud deck in Pa | +------------------------+-----------------------+----------------------------------------+ | ``bh_clouds_topP`` | :obj:`float` | Top of cloud deck in Pa | +------------------------+-----------------------+----------------------------------------+ --------------------------- Mie scattering (Flat) ====================== ``[[FlatMie]]`` Computes a flat absorbing region of the atmosphere across all wavelengths -------- Keywords -------- +--------------------+--------------+----------------------------------+ | Variable | Type | Description | +--------------------+--------------+----------------------------------+ | ``flat_mix_ratio`` | :obj:`float` | Opacity value | +--------------------+--------------+----------------------------------+ | ``flat_bottomP`` | :obj:`float` | Bottom of absorbing region in Pa | +--------------------+--------------+----------------------------------+ | ``flat_topP`` | :obj:`float` | Top of absorbing region in Pa | +--------------------+--------------+----------------------------------+ ------------------ Fitting Parameters ------------------ +--------------------+--------------+----------------------------------+ | Parameter | Type | Description | +--------------------+--------------+----------------------------------+ | ``flat_mix_ratio`` | :obj:`float` | Opacity value | +--------------------+--------------+----------------------------------+ | ``flat_bottomP`` | :obj:`float` | Bottom of absorbing region in Pa | +--------------------+--------------+----------------------------------+ | ``flat_topP`` | :obj:`float` | Top of absorbing region in Pa | +--------------------+--------------+----------------------------------+