Single Lined (SB1) Binaries in Allesfitter

[AndreOKovacs]

Hello,
What parameters/settings are needed to fit sigle lined binaries within allesfitter?
Unfortunately, I could only find samples for double lines EBs and exoplanets.
Thanks

[YasminDavis]

Hi,
Generally for single lined binaries you can treat them the same way you would an exoplanet, just adjust the priors to be appropriate for a star rather than a planet.

[MNGuenther]

Hi @andreok thanks for your question(s) and @YasminDavis thanks for your answer!
@andreok I also got a second question from you via email but cannot see this here, so I assume it has already been solved and deleted.
Please let me know if any question remains, otherwise I propose to close this issue soon.

[AndreOKovacs]

Hello @YasminDavis, thank you very much for your answer.

Hello @MNGuenther, I had to delete my previous reply due to an issue that I found just later with my data. Sorry for the inconvenience.

I tried to first fit my phase curve data from TESS, following the settings described on your WASP-18 example for using sines (phase_curve_style=sine_series), and adding the 3 params (b_phase_curve_A1_TESS, b_phase_curve_B1_TESS and b_phase_curve_B2_TESS), but I'm getting the following output:

Filling the Basement


allesfitter version
---------------------
v1.2.10
OrderedDict([('user-given:', ''),
             ('companions_phot', ['B']),
             ('companions_rv', []),
             ('inst_phot', ['TESS']),
             ('inst_rv', []),
             ('multiprocess', True),
             ('multiprocess_cores', '2'),
             ('fast_fit', 'False'),
             ('fast_fit_width', ''),
             ('secondary_eclipse', 'True'),
             ('phase_curve', 'True'),
             ('phase_curve_style', 'sine_series'),
             ('shift_epoch', True),
             ('inst_for_B_epoch', ['TESS']),
             ('mcmc_nwalkers', '100'),
             ('mcmc_total_steps', '2000'),
             ('mcmc_burn_steps', '1000'),
             ('mcmc_thin_by', '1'),
             ('ns_modus', 'dynamic'),
             ('ns_nlive', '500'),
             ('ns_bound', 'single'),
             ('ns_sample', 'rwalk'),
             ('ns_tol', '0.01'),
             ('host_ld_law_TESS', 'quad'),
             ('baseline_flux_TESS', 'sample_offset'),
             ('error_flux_TESS', 'sample'),
             ('t_exp_TESS', ''),
             ('t_exp_n_int_TESS', ''),
             ('host_N_spots_TESS', ''),
             ('N_flares', ''),
             ('fit_ttvs', 'False'),
             ('host_grid_TESS', 'default'),
             ('host_shape_TESS', 'sphere'),
             ('automatically set:', ''),
             ('time_format', 'BJD_TDB'),
             ('inst_rv2', []),
             ('companions_all', ['B']),
             ('inst_all', ['TESS']),
             ('print_progress', True)])
---------------------------------------------------------------------------

ValueError                                Traceback (most recent call last)

<ipython-input-27-bcc7b7648d84> in <cell line: 1>()
      7     np.float = float
      8 
----> 9     fig_list = show_initial_guess(INPUT['datadir'], do_logprint=False, return_figs=True)
     10 
     11     for fig in fig_list:

3 frames

/usr/local/lib/python3.10/dist-packages/allesfitter/general_output.py in show_initial_guess(datadir, quiet, do_logprint, do_plot, return_figs, kwargs_dict)
   1023 def show_initial_guess(datadir, quiet=False, do_logprint=True, do_plot=True, return_figs=False, kwargs_dict=None):
   1024     #::: init
-> 1025     config.init(datadir, quiet=quiet)
   1026 
   1027     #::: show initial guess

/usr/local/lib/python3.10/dist-packages/allesfitter/config.py in init(datadir, quiet)
     25 def init(datadir, quiet=False):
     26     global BASEMENT
---> 27     BASEMENT = Basement(datadir, quiet=quiet)

/usr/local/lib/python3.10/dist-packages/allesfitter/basement.py in __init__(self, datadir, quiet)
     90 
     91         self.load_settings()
---> 92         self.load_params()
     93         self.load_data()
     94 

/usr/local/lib/python3.10/dist-packages/allesfitter/basement.py in load_params(self)
    868                                            (self.params[companion+'_gdc_'+inst] is not None) or (self.settings[companion+'_shape_'+inst]!='sphere'))
    869                     if (phase_curve_model_1 + phase_curve_model_2 + phase_curve_model_3 + phase_curve_model_4 + phase_curve_model_5) > 1:
--> 870                         raise ValueError('You can use either\n'\
    871                                          +'1) the sine_series phase curve model with "*_phase_curve_B1_*",\n'\
    872                                          +'2) the sine_series phase curve model with "*_phase_curve_B1t_*" and "*_phase_curve_B1r_*", or\n'\

ValueError: You can use either
1) the sine_series phase curve model with "*_phase_curve_B1_*",
2) the sine_series phase curve model with "*_phase_curve_B1t_*" and "*_phase_curve_B1r_*", or
3) the sine_physical phase curve model with "*_phase_curve_atmospheric_*",
4) the sine_physical phase curve model with "*_phase_curve_atmospheric_thermal_*" and "*_phase_curve_atmospheric_reflected_*", or
5) the ellc_physical phase curve model with "*_bfac_*", "*_heat_*", "*_gdc_*" etc.
but you shall not pass with a mix&match.

Checking your allesfitter paper, I noticed that in section 4.9.1 there's an additional b_phase_curve_B3_TESS parameter, that might be optional?

Thanks

[MNGuenther]

Hi @andreok - it is hard to tell without seeing your actual files. But I would expect some typos in your files. On a first glance at this log, it seems like you have called the companion "B" (upper case) but typed the parameters as "b_*" (lower case).

[AndreOKovacs]

Hello @MNGuenther,

Sorry for the confusion with the caption of the parameters from my previous message.

Here're the complete settings:

#name,value
###############################################################################,
# General settings,
###############################################################################,
companions_phot,B
companions_rv,
inst_phot,TESS
inst_rv,
###############################################################################,
# Fit performance settings,
###############################################################################,
multiprocess,True
multiprocess_cores,2
fast_fit,False
fast_fit_width,
secondary_eclipse,True
phase_curve,True
#phase_curve_style,GP
phase_curve_style,sine_series
shift_epoch,True
inst_for_B_epoch,all
###############################################################################,
# MCMC settings,
###############################################################################,
mcmc_nwalkers,100
mcmc_total_steps,2000
mcmc_burn_steps,1000
mcmc_thin_by,1
###############################################################################,
# Nested Sampling settings,
###############################################################################,
ns_modus,dynamic
ns_nlive,500
ns_bound,single
ns_sample,rwalk
ns_tol,0.01
###############################################################################,
# Limb darkening law per object and instrument,
# if 'lin' one corresponding parameter called 'ldc_q1_inst' has to be given in params.csv,
# if 'quad' two corresponding parameter called 'ldc_q1_inst' and 'ldc_q2_inst' have to be given in params.csv,
# if 'sing' three corresponding parameter called 'ldc_q1_inst'; 'ldc_q2_inst' and 'ldc_q3_inst' have to be given in params.csv,
###############################################################################,
host_ld_law_TESS,quad
###############################################################################,
# Baseline settings per instrument,
# baseline params per instrument: sample_offset / sample_linear / sample_GP / hybrid_offset / hybrid_poly_1 / hybrid_poly_2 / hybrid_poly_3 / hybrid_pol_4 / hybrid_spline / hybrid_GP,
# if 'sample_offset' one corresponding parameter called 'baseline_offset_key_inst' has to be given in params.csv,
# if 'sample_linear' two corresponding parameters called 'baseline_a_key_inst' and 'baseline_b_key_inst' have to be given in params.csv,
# if 'sample_GP' two corresponding parameters called 'baseline_gp1_key_inst' and 'baseline_gp2_key_inst' have to be given in params.csv,
###############################################################################,
#baseline_flux_TESS,hybrid_offset
baseline_flux_TESS,sample_offset
###############################################################################,
# Error settings per instrument,
# errors (overall scaling) per instrument: sample / hybrid,
# if 'sample' one corresponding parameter called 'ln_err_key_inst' (photometry) or 'ln_jitter_key_inst' (RV) has to be given in params.csv,
###############################################################################,
error_flux_TESS,sample
###############################################################################,
# Exposure times for interpolation,
# needs to be in the same units as the time series,
# if not given the observing times will not be interpolated leading to biased results,
###############################################################################,
t_exp_TESS,
###############################################################################,
# Number of points for exposure interpolation,
# Sample as fine as possible; generally at least with a 2 min sampling for photometry,
# n_int=5 was found to be a good number of interpolation points for any short photometric cadence t_exp;,
# increase to at least n_int=10 for 30 min phot. cadence,
# the impact on RV is not as drastic and generally n_int=5 is fine enough,
###############################################################################,
t_exp_n_int_TESS,
###############################################################################,
# Number of spots per object and instrument,
###############################################################################,
host_N_spots_TESS,
###############################################################################,
# Number of flares (in total),
###############################################################################,
N_flares,
###############################################################################,
# TTVs,
###############################################################################,
fit_ttvs,False
###############################################################################,
# Stellar grid per object and instrument,
###############################################################################,
host_grid_TESS,default
###############################################################################,
# Stellar shape per object and instrument,
###############################################################################,
host_shape_TESS,sphere
###############################################################################,
# Flux weighted RVs per object and instrument,
# ("Yes" for Rossiter-McLaughlin effect),
###############################################################################,

and the complete parameters:

#name,value,fit,bounds,label,unit
#companion B astrophysical params,,,,,
B_rr,0.358106,1,uniform 0.05810599999999999 0.758106,$R_B / R_\star$,
B_rsuma,0.1447849125635028,1,uniform 0.07538651525737243 0.3978751912448472,$(R_\star + R_B) / a_B$,
B_cosi,0.06627074535270697,1,trunc_normal 0 1 0.06627074535270697 0.0017371972034756905,$\cos{i_B}$,
B_epoch,2458867.7506,0,trunc_normal -1000000000000.0 1000000000000.0 2458867.7506 0.0,$T_{0;B}$,$\mathrm{BJD}$
B_period,4.241822,0,trunc_normal -1000000000000.0 1000000000000.0 4.241822 0.0,$P_B$,$\mathrm{d}$
B_f_c,0.0,0,trunc_normal -1 1 0.0 0.0,$\sqrt{e_B} \cos{\omega_B}$,
B_f_s,0.0,0,trunc_normal -1 1 0.0 0.0,$\sqrt{e_B} \sin{\omega_B}$,
#dilution per instrument,,,,,
dil_TESS,0.0,0,trunc_normal 0 1 0.0 0.0,$D_\mathrm{0; TESS}$,
#limb darkening coefficients per instrument,,,,,
host_ldc_q1_TESS,0.327947,1,uniform 0.317947 1.0,$q_{1; \mathrm{TESS}}$,
host_ldc_q2_TESS,0.339773,1,uniform 0.329773 1.0,$q_{2; \mathrm{TESS}}$,
#surface brightness per instrument and companion,,,,,
B_sbratio_TESS,0.0,0,trunc_normal 0 1 0.0 0.0,$J_{B; \mathrm{TESS}}$,
#phase curve per instrument and companion,,,,,
B_phase_curve_A1_TESS,0.021,1,uniform 0 1,phase curve: $A_\mathrm{1; B; TESS}$,
B_phase_curve_B1_TESS,-0.1744,1,uniform -1 0,phase curve: $B_\mathrm{1; B; TESS}$,
B_phase_curve_B2_TESS,-0.1905,1,uniform -1 0,phase curve: $B_\mathrm{2; B; TESS}$,
#albedo per instrument and companion,,,,,
host_geom_albedo_TESS,0.0,0,trunc_normal 0 1 0.0 0.0,$A_{\mathrm{geom}; host; \mathrm{TESS}}$,
B_geom_albedo_TESS,0.0,0,trunc_normal 0 1 0.0 0.0,$A_{\mathrm{geom}; B; \mathrm{TESS}}$,
#gravity darkening per instrument and companion,,,,,
host_gdc_TESS,0.0,0,trunc_normal 0 1 0.0 0.0,$Grav. dark._{B; \mathrm{TESS}}$,
#spots per instrument and companion,,,,,
#baseline per instrument,,,,,
baseline_offset_flux_TESS,0.0001,1,uniform -0.01 0.01,$\Delta F_\mathrm{TESS}$,
#errors per instrument,
ln_err_flux_TESS,-7.0,1,uniform -15.0 0.0,$\ln{\sigma_\mathrm{TESS}}$,$\ln{ \mathrm{rel. flux.} }$

I had to remove a few extra columns at the end of the phase_curve_* parameters, when I copied them from your WASP-18 example.

Thanks

[MNGuenther]

Hi @andreok - a few things going on here:

• your files seem to mix various phase curve modii, which results in the shown error message. The settings.csv indicates the code to use "sine_series". But then the params.csv gives the code various free parameters that relate to other modii. For example, the geometric albedos and gravity darkening. If you compare this with the actual WASP-18 example, you can see that these parameters are not in there. See also the description for the different sets of parameters in the documentation: https://www.allesfitter.com/setup/parameters

• the surface brightness ratio parameter should probably be freed up; I would assume it will not be zero in a binary star system.

• several of the parameters listed in the file are not actually used for the fits (e.g. eccentricity and dilution); feel free to delete unused rows from the file to clean it up

Hope this helps! Please let me know if we can close this issue.

[AndreOKovacs]

Hello @MNGuenther,

I managed to get the fit to work following your recommendations.
However, I'm getting the following error when I try to generate the outputs:

Filling the Basement


allesfitter version
---------------------
v1.2.10
OrderedDict([('user-given:', ''),
             ('companions_phot', ['B']),
             ('companions_rv', []),
             ('inst_phot', ['TESS']),
             ('inst_rv', []),
             ('multiprocess', True),
             ('multiprocess_cores', '2'),
             ('fast_fit', 'False'),
             ('secondary_eclipse', 'True'),
             ('phase_curve', 'True'),
             ('phase_curve_style', 'sine_series'),
             ('shift_epoch', True),
             ('inst_for_B_epoch', ['TESS']),
             ('mcmc_nwalkers', '500'),
             ('mcmc_total_steps', '5000'),
             ('mcmc_burn_steps', '1000'),
             ('mcmc_thin_by', '50'),
             ('mcmc_pre_run_loops', '0'),
             ('mcmc_pre_run_steps', '0'),
             ('ns_modus', 'dynamic'),
             ('ns_nlive', '500'),
             ('ns_bound', 'single'),
             ('ns_sample', 'rwalk'),
             ('ns_tol', '0.01'),
             ('host_ld_law_TESS', 'quad'),
             ('baseline_flux_TESS', 'sample_offset'),
             ('error_flux_TESS', 'sample'),
             ('host_grid_TESS', 'very_sparse'),
             ('b_grid_TESS', 'very_sparse'),
             ('automatically set:', ''),
             ('time_format', 'BJD_TDB'),
             ('inst_rv2', []),
             ('companions_all', ['B']),
             ('inst_all', ['TESS']),
             ('print_progress', True)])

Shifting epochs into the data center
------------------------------------
Companion B
	input epoch: 2458867.7506


! WARNING:
 You are pushing your luck: you want to run on 2 cores, but your computer has only 2. I will let you go through with it this time...
type: <class 'UserWarning'>, file: /usr/local/lib/python3.10/dist-packages/allesfitter/basement.py, line: 260

Plotting collage for companion B...

100%|██████████| 6/6 [00:03<00:00,  1.65it/s]

! WARNING:
 color is redundantly defined by the 'color' keyword argument and the fmt string "b." (-> color='b'). The keyword argument will take precedence.
type: <class 'UserWarning'>, file: /usr/local/lib/python3.10/dist-packages/allesfitter/general_output.py, line: 720

Plotting individual transits for companion B and instrument TESS...

100%|██████████| 1/1 [00:00<00:00,  1.67it/s]


Results:
----------
log(Z) = -53777.52925478203 +- 0.26211579394622214
Nr. of posterior samples: 46996

---------------------------------------------------------------------------

AttributeError                            Traceback (most recent call last)

[<ipython-input-5-ab5cccf0cb2a>](https://localhost:8080/#) in <cell line: 1>()
----> 1 allesfitter.ns_output('/content/TESS')

[/usr/local/lib/python3.10/dist-packages/allesfitter/nested_sampling_output.py](https://localhost:8080/#) in ns_output(datadir)
    235                         caxes[i,j].yaxis.set_major_formatter(fmt)
    236 
--> 237                     for tick in caxes[i,j].xaxis.get_major_ticks(): tick.label.set_fontsize(24)
    238                     for tick in caxes[i,j].yaxis.get_major_ticks(): tick.label.set_fontsize(24)
    239         else:

AttributeError: 'XTick' object has no attribute 'label'

But the outputs seems to be ok!? :-O
Should I just ignore it?

Thank you very much for your support.