2.3. Synthesis

This is the simplest use of the code because it should always work once the input and configuration files are correctly defined. A typical configuration file for the synthesis mode follows:

# Hazel configuration File

[Working mode]
Output file = output.h5


[Spectral regions]
    [[Region 1]]
    Name = spec1
    Wavelength = 10826, 10833, 150
    Topology = ph1 -> ch1 -> te1 -> st1
    Stokes weights = 1.0, 1.0, 1.0, 1.0
    LOS = 0.0, 0.0, 90.0
    Boundary condition = 1.0, 0.0, 0.0, 0.0       # I/Ic(mu=1), Q/Ic(mu=1), U/Ic(mu=1), V/Ic(mu=1)
    Wavelength file = 'observations/10830.wavelength'
    Wavelength weight file = 'observations/10830.weights'

[Atmospheres]

    [[Photosphere 1]]
    Name = ph1
    Reference atmospheric model = 'photospheres/model_photosphere.1d'
    Spectral region = spec1
    Wavelength = 10826, 10833
    Spectral lines = 300,

    [[Chromosphere 1]]
    Name = ch1                                              # Name of the atmosphere component
    Spectral region = spec1                                 # Spectral region to be used for synthesis
    Height = 3.0                                            # Height of the slab
    Line = 10830                                            # 10830, 5876
    Wavelength = 10826, 10833                         # Wavelength range used for synthesis
    Reference atmospheric model = 'chromospheres/model_chromosphere.1d'    # File with model parameters

    [[Parametric 1]]
    Name = te1
    Spectral region = spec1
    Wavelength = 10826, 10833
    Reference atmospheric model = 'telluric/model_telluric.1d'    # File with model parameters
    Type = Gaussian           # Gaussian, Voigt, MoGaussian, MoVoigt

    [[Straylight 1]]
    Name = st1
    Spectral region = spec1
    Wavelength = 10826, 10833
    Reference atmospheric model = 'straylight/model_stray.1d'    # File with model parameters

This configuration file defines a spectral region in the near infrared that contains four different atmospheres, one after the other. The first one is a photosphere, with the physical conditions been read from the photospheres/model_photosphere.1d file. Note that all files in this example are 1D so the result is just a single synthesis. But you might as well use 3D files (as described in input) and the output would be the synthesis for many pixels. The second component is a chromosphere, the third is used to add a telluric component and the fourth one is a straylight contamination.

In the case of a 1D model, you can easily do the synthesis by invoking, assuming that the configuration file is saved on conf.ini:

mod = hazel.Model('conf.ini', working_mode='synthesis')
mod.open_output()
mod.synthesize()
mod.write_output()
mod.close_output()

The output is described in Output files. For 3D cases, we recommend the user to use iterators. Otherwise, one needs to manually read the observations at every pixel. For instance, one can do the synthesis for many pixels using 3D atmospheres in serial model by invoking:

iterator = hazel.Iterator(use_mpi=False)
mod = hazel.Model('conf.ini', working_mode='synthesis')
iterator.use_model(model=mod)
iterator.run_all_pixels()

or the following piece of code if many cores are to be used. Remember that this piece of code needs to be called with a call to the MPI mpiexec

mpiexec -n n_nodes python inversion.py

where inversion.py contains the following piece of code:

iterator = hazel.Iterator(use_mpi=True)
rank = iterator.get_rank()
mod = hazel.Model('conf_mpi_invh5.ini', rank=rank)
iterator.use_model(model=mod)
iterator.run_all_pixels()