.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/other/star/plot_flare_spot_lightcurve.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_other_star_plot_flare_spot_lightcurve.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_other_star_plot_flare_spot_lightcurve.py:


Plot the lightcurve of a flaring star with spots
================================================

This example plots the lightcurve caused by a
flaring star when it also has spots.

.. GENERATED FROM PYTHON SOURCE LINES 8-23

.. code-block:: Python


    from astropy import units as u
    import matplotlib.pyplot as plt
    from pathlib import Path
    import numpy as np
    import libpypsg

    from VSPEC import ObservationModel,PhaseAnalyzer
    from VSPEC import params
    from VSPEC import config
    from VSPEC.params.gcm import vspec_to_pygcm

    SEED = 42
    libpypsg.docker.set_url_and_run()





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Saved settings to /home/runner/.libpypsg/settings.json
    Reloading settings...




.. GENERATED FROM PYTHON SOURCE LINES 24-30

Initialize the VSPEC run parameters
-----------------------------------

For this example, we will create the
parameter objects explicitly. This can also
be done using a YAML file.

.. GENERATED FROM PYTHON SOURCE LINES 30-131

.. code-block:: Python


    header = params.Header(
        data_path=Path('.vspec/flare_spot_lightcurve'),
        seed=SEED,verbose=1,
        spec_grid = params.VSPECGridParameters(
            max_teff=3400*u.K,min_teff=2900*u.K,
            impl_bin='rust',impl_interp='scipy',fail_on_missing=False
        )
    )

    star = params.StarParameters(
        psg_star_template='M',
        teff=3300*u.K,
        mass = 0.1*u.M_sun,
        radius=0.15*u.R_sun,
        period = 6*u.day,
        misalignment_dir=0*u.deg,
        misalignment=0*u.deg,
        ld = params.LimbDarkeningParameters.solar(),
        faculae=params.FaculaParameters.none(),
        spots=params.SpotParameters(
            distribution='iso',
            initial_coverage=0.1,
            area_mean=300*config.MSH,
            area_logsigma=0.2,
            teff_umbra=2900*u.K,
            teff_penumbra=3000*u.K,
            equillibrium_coverage=0.1,
            burn_in=0*u.day,
            growth_rate=0/u.day,
            decay_rate=0*config.MSH/u.day,
            initial_area=10*config.MSH
            ),
        flares=params.FlareParameters(
            dist_teff_mean=9000*u.K,
            dist_teff_sigma=500*u.K,
            dist_fwhm_mean=3*u.hr,
            dist_fwhm_logsigma=0.4,
            alpha=-0.829,
            beta=26.87,
            min_energy=1e32*u.erg,
            cluster_size=3
        ),
        granulation=params.GranulationParameters.none(),
        grid_params=(500, 1000),
    )

    planet = params.PlanetParameters.std(init_phase=180*u.deg,init_substellar_lon=0*u.deg)
    system = params.SystemParameters(
        distance=1.3*u.pc,
        inclination=80*u.deg,
        phase_of_periastron=0*u.deg
    )
    observation = params.ObservationParameters(
        observation_time=10*u.day,
        integration_time=4*u.hr
    )
    psg_params = params.psgParameters(
        gcm_binning=200,
        phase_binning=1,
        use_molecular_signatures=True,
        use_continuum_stellar=True,
        nmax=0,
        lmax=0,
        continuum=['Rayleigh', 'Refraction', 'CIA_all'],
    )
    instrument = params.InstrumentParameters.mirecle()

    def gcm_getter():
        return vspec_to_pygcm(
            shape=(30,30,30),
            epsilon=7,
            star_teff=3800*u.K,
            r_star=0.2*u.R_sun,
            r_orbit=0.05*u.AU,
            lat_redistribution=0.0,
            p_surf=1*u.bar,
            p_stop=1e-5*u.bar,
            wind_u=0*u.km/u.s,
            wind_v=0*u.km/u.s,
            albedo=0.3,
            emissivity=1.0,
            gamma=1.4,
            molecules={'CO2':1e-4}
        )
    gcm = params.gcmParameters(
        gcm_getter=gcm_getter,
        mean_molec_weight=28,
        is_static=True
    )
    parameters = params.InternalParameters(
        header = header,
        star = star,
        planet = planet,
        system = system,
        obs=observation,
        psg = psg_params,
        inst=instrument,
        gcm = gcm
    )








.. GENERATED FROM PYTHON SOURCE LINES 132-135

Run the simulation
------------------


.. GENERATED FROM PYTHON SOURCE LINES 135-140

.. code-block:: Python


    model = ObservationModel(params=parameters)
    model.build_planet()
    model.build_spectra()





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Starting at phase 180.0 deg, observe for 10.0 d in 60 steps
    Phases = [180. 186. 192. 198. 204. 210. 216. 222. 228. 234. 240. 246. 252. 258.
     264. 270. 276. 282. 288. 294. 300. 306. 312. 318. 324. 330. 336. 342.
     348. 354.   0.   6.  12.  18.  24.  30.  36.  42.  48.  54.  60.  66.
      72.  78.  84.  90.  96. 102. 108. 114. 120. 126. 132. 138. 144. 150.
     156. 162. 168. 174. 180.] deg

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    Generated 29 mature spots
    Creating interpolators:
    thermal
    thermal, combined
    thermal, combined, stellar
    thermal, combined, stellar, photon noise
    thermal, combined, stellar, photon noise, detector noise
    thermal, combined, stellar, photon noise, detector noise, telescope noise
    thermal, combined, stellar, photon noise, detector noise, telescope noise, background noise
    thermal, combined, stellar, photon noise, detector noise, telescope noise, background noise, transit
    Finished!

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.. GENERATED FROM PYTHON SOURCE LINES 141-146

Load in the data
----------------

We can use VSPEC to read in the synthetic
data we just created.

.. GENERATED FROM PYTHON SOURCE LINES 146-149

.. code-block:: Python


    data = PhaseAnalyzer(model.directories['all_model'])








.. GENERATED FROM PYTHON SOURCE LINES 150-153

Make the figure
---------------


.. GENERATED FROM PYTHON SOURCE LINES 153-174

.. code-block:: Python


    time = (data.time - data.time[0]).to_value(u.day)
    wl = data.wavelength.to_value(u.um)

    emission = (data.thermal/data.total).to_value(u.dimensionless_unscaled)*1e6

    variation = (data.star/data.star[:,0,np.newaxis]-1).to_value(u.dimensionless_unscaled)*100

    fig,ax = plt.subplots(1,2,figsize=(8,4))

    im=ax[0].pcolormesh(time,wl,emission,cmap='cividis')
    fig.colorbar(im,ax=ax[0],label='Planet Thermal Emission (ppm)',location='top')
    # ax[0].set_title('Planet')

    im=ax[1].pcolormesh(time,wl,variation,cmap='cividis')
    fig.colorbar(im,ax=ax[1],label='Stellar Variation (%)',location='top')
    # ax[1].set_title('Star')

    ax[0].set_ylabel('Wavelength (${\\rm \\mu m}$)')
    fig.text(0.5,0.02,'Time (days)',ha='center')




.. image-sg:: /auto_examples/other/star/images/sphx_glr_plot_flare_spot_lightcurve_001.png
   :alt: plot flare spot lightcurve
   :srcset: /auto_examples/other/star/images/sphx_glr_plot_flare_spot_lightcurve_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


    Text(0.5, 0.02, 'Time (days)')




.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (2 minutes 8.537 seconds)


.. _sphx_glr_download_auto_examples_other_star_plot_flare_spot_lightcurve.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_flare_spot_lightcurve.ipynb <plot_flare_spot_lightcurve.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_flare_spot_lightcurve.py <plot_flare_spot_lightcurve.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_flare_spot_lightcurve.zip <plot_flare_spot_lightcurve.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_