The level of flux model is not match with the data #928

kittipongwangnok · 2024-08-24T03:22:30Z

kittipongwangnok
Aug 24, 2024

The shape of light curve look likes the data but the level is not the same, How can we solve this problem?
Thanks

kecnry · 2024-08-26T12:08:57Z

kecnry
Aug 26, 2024
Maintainer

You need to account for the passband luminosity and/or the distance. Please see the following tutorials and let us know if anything isn't clear:

0 replies

kittipongwangnok · 2024-08-26T12:20:58Z

kittipongwangnok
Aug 26, 2024
Author

Thank you for the clarification. However, I got the another problem when I have tried to change the radius of primary and secondary stars with the error likes this: ValueError: Could not lookup ld_coeffs for ***@***.*** @***@***.***@dataset. Try changing ld_coeffs_source to a table that covers a sufficient range of values or set ld_mode to 'manual' and manually provide coefficients via ld_coeffs. Enable 'warning' logger to see out-of-bound arrays. How can we solve this problem? Kittipong

…

On Mon, Aug 26, 2024 at 7:09 PM Kyle Conroy ***@***.***> wrote: You need to account for the passband luminosity and/or the distance. Please see the following tutorials and let us know if anything isn't clear: - passband luminosity <https://phoebe-project.org/docs/latest/tutorials/pblum> - distance <https://phoebe-project.org/docs/latest/tutorials/distance> - third light <https://phoebe-project.org/docs/latest/tutorials/l3> - Inverse problem example <https://phoebe-project.org/docs/latest/examples/inverse_paper_examples> — Reply to this email directly, view it on GitHub <#928 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALO4C3CBQ3CQHCG3S3N2RDTZTMLG5AVCNFSM6AAAAABNBGILP2VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBVGEYDSMA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Kittipong Wangnok +6684 828 6505 School of Physics Institute of Science Suranaree University of Technology

1 reply

kecnry Aug 26, 2024
Maintainer

The error message is telling you what to do (effectively the same as your previous question), and there are also tutorials on these topics on the website that I linked to in the response there. If you try that and are still running into issues, please let us know!

kittipongwangnok · 2024-08-27T12:47:52Z

kittipongwangnok
Aug 27, 2024
Author

I already input this parameter but still get the error with message: ValueError: Could not lookup ld_coeffs for ***@***.*** @***@***.*** Try changing ld_coeffs_source_bol to a table that covers a sufficient range of values or set ld_mode_bol to 'manual' and manually provide coefficients via ld_coeffs_bol. Enable 'warning' logger to see out-of-bound arrays. How can I solve this problem Kittipong

…

On Mon, Aug 26, 2024 at 7:49 PM Kyle Conroy ***@***.***> wrote: The error message is telling you what to do (effectively the same as your previous question <#924 (comment)>), and there are also tutorials on these topics on the website that I linked to in the response there. If you try that and are still running into issues, please let us know! — Reply to this email directly, view it on GitHub <#928 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALO4C3G2VLL3PIP5MNL5EETZTMP5PAVCNFSM6AAAAABNBGILP2VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBVGE2TGNY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Kittipong Wangnok +6684 828 6505 School of Physics Institute of Science Suranaree University of Technology

1 reply

kecnry Aug 27, 2024
Maintainer

What have you tried that is still giving this message?

kittipongwangnok · 2024-08-27T13:05:48Z

kittipongwangnok
Aug 27, 2024
Author

Changing the radius of r1 and r2?

…

On Tue, Aug 27, 2024 at 8:00 PM Kyle Conroy ***@***.***> wrote: What have you tried that is still giving this message? — Reply to this email directly, view it on GitHub <#928 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALO4C3EJM3JWPKTOMMQL7KDZTRZ7BAVCNFSM6AAAAABNBGILP2VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBWGMYTMNI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Kittipong Wangnok +6684 828 6505 School of Physics Institute of Science Suranaree University of Technology

1 reply

kecnry Aug 27, 2024
Maintainer

What are the masses/radii/temperatures? Can you enable the warning logger and paste the output of the message that states the out-of-bounds values?

kittipongwangnok · 2024-08-27T13:11:31Z

kittipongwangnok
Aug 27, 2024
Author

Since there is no reference of parameters for this system, I have tried to change the parameters following the example that I have. Moreover, How can I enable the warning logger? Thanks Kittipong

…

On Tue, Aug 27, 2024 at 8:07 PM Kyle Conroy ***@***.***> wrote: What are the masses/radii/temperatures? Can you enable the warning logger and paste the output of the message that states the out-of-bounds values? — Reply to this email directly, view it on GitHub <#928 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALO4C3CKXENHIRZ4ZNSNWPDZTR2YBAVCNFSM6AAAAABNBGILP2VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBWGMZDGOI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Kittipong Wangnok +6684 828 6505 School of Physics Institute of Science Suranaree University of Technology

1 reply

kecnry Aug 27, 2024
Maintainer

All of your messages sent through email are being censored by GitHub (probably thinking that @ indicates email addresses), can you please go to the page and manually edit the messages so that they are readable?

How can I enable the warning logger?

#924 (comment)

kittipongwangnok · 2024-08-27T13:13:24Z

kittipongwangnok
Aug 27, 2024
Author

This is the set of parameters that I have: b.set_value('incl@binary@component', 85) b.set_value('q@binary@component', 0.5) b.set_value('sma@binary@component', 7) b.set_value('teff@primary@component', 4500) b.set_value('teff@secondary@component', 6000) b.set_value('requiv@primary@component', 35) b.set_value('requiv@secondary@component', 10) b.set_value('distance@system', 3.03) b['ld_coeffs_source_bol@primary'] = 'phoenix' # Or 'ck2004' or 'auto' b['ld_coeffs_source_bol@secondary'] = 'phoenix' # Or 'ck2004' or 'auto' b.set_value('ld_mode', component='primary', dataset='lc01', value='manual') b.set_value('ld_mode', component='secondary', dataset='lc01', value='manual') b.set_value('ld_func', component='primary', dataset='lc01', value='logarithmic') b.set_value('ld_func', component='secondary', dataset='lc01', value='logarithmic') b.set_value_all('ld_mode_bol', value='manual') b.set_value('atm@primary@phoebe01@phoebe@compute', value='blackbody') b.set_value('atm@secondary@phoebe01@phoebe@compute', value='blackbody') b.set_value('mass@primary@star@constraint', 3.00) b.set_value('mass@secondary@star@constraint', 1.5) When I tried to input: b.set_value('period@binary@component', 310) b.set_value('t0_supconj@binary@component', 58667.9) I also get the error. However, PHOEBE has the limitation of the binary period or not because my system is ~300 days.

6 replies

kittipongwangnok Aug 27, 2024
Author

Thank you for your explanation.
The set of parameters is just the guess based on the information that I known.
However, I would like to find the best parameters that match to our real observed data.

kittipongwangnok Aug 27, 2024
Author

This is the example of script and data
r_times.txt

import phoebe
from phoebe import u # units
import numpy as np

logger = phoebe.logger('error')

#phoebe.download_passband('Bolometric:900-40000')
#phoebe.download_passband('Johnson:B')

# Initialize the binary system
b = phoebe.default_binary()
b.set_value('incl@binary@component', 78)
b.set_value('q@binary@component', 0.69)
b.set_value('sma@binary@component', 7.5)
b.set_value('teff@primary@component', 10528)
b.set_value('teff@secondary@component', 7970)
b.set_value('requiv@primary@component', 2.61)
b.set_value('requiv@secondary@component', 1.76)
b.set_value('distance@system', 2.45)
b.set_value('gravb_bol@primary@component', 0.93)
b.set_value('gravb_bol@secondary@component', 0.88)
b.set_value('irrad_frac_refl_bol@primary@component', 0.92)
b.set_value('irrad_frac_refl_bol@secondary@component', 0.84)

# Load light curve data
#InputFile = "binned_data_8314879.dat"
InputFile = "r_times.txt"
Data = np.genfromtxt(InputFile)
time  = np.array(Data[:, 0])
flux = np.array(Data[:, 1])
flux_err = np.array(Data[:, 2])

b = phoebe.default_binary()

b.add_dataset('lc', 
              compute_phases=phoebe.linspace(0,1,201),
              times=time, 
              fluxes=flux, 
              sigmas=flux_err, 
              dataset='lc01')

b.add_compute('ellc', compute='fastcompute')
b.set_value_all('ld_mode', 'lookup')
#b.run_compute(compute='fastcompute')

b.set_value('period@binary@component', 310)
b.set_value('t0_supconj@binary@component', 2458667.9)

b.run_compute(compute='fastcompute', model='orig_model')

kecnry Aug 27, 2024
Maintainer

Ok, thanks. You have a second b = phoebe.default_binary() in there that is going to re-set all the changes you made to the system prior to that line. Removing that and adding a debugging logger exposes the elements that are out-of-bounds:

import phoebe

b = phoebe.default_binary()
b.set_value('incl@binary@component', 78)
b.set_value('q@binary@component', 0.69)
b.set_value('sma@binary@component', 7.5)
b.set_value('teff@primary@component', 10528)
b.set_value('teff@secondary@component', 7970)
b.set_value('requiv@primary@component', 2.61)
b.set_value('requiv@secondary@component', 1.76)
b.set_value('distance@system', 2.45)
b.set_value('gravb_bol@primary@component', 0.93)
b.set_value('gravb_bol@secondary@component', 0.88)
b.set_value('irrad_frac_refl_bol@primary@component', 0.92)
b.set_value('irrad_frac_refl_bol@secondary@component', 0.84)


b.add_dataset('lc', 
              compute_phases=phoebe.linspace(0,1,6),
              dataset='lc01')

b.add_compute('ellc', compute='fastcompute')
b.set_value_all('ld_mode', 'lookup')

b.set_value('period@binary@component', 310)
b.set_value('t0_supconj@binary@component', 2458667.9)

phoebe.logger('debug')
b.run_compute(compute='fastcompute', model='orig_model')

ValueError: Atmosphere parameters out of bounds: ldatm=ck2004, teff=[10528.], logg=[-0.85295305], abun=[0.]

and the following print statement shows that the stellar parameters are entirely unphysical (near zero-mass which is resulting in this logg value):

>>> print(b.filter(qualifier=['teff', 'mass', 'requiv', 'requiv_max'], context='component'))
ParameterSet: 8 parameters
         requiv@primary@component: 2.61 solRad
C    requiv_max@primary@component: 3.0970514659323665 solRad
           teff@primary@component: 10528.0 K
C          mass@primary@component: 3.485461822028102e-05 solMass
       requiv@secondary@component: 1.76 solRad
C  requiv_max@secondary@component: 2.607248025377602 solRad
         teff@secondary@component: 7970.0 K
C        mass@secondary@component: 2.4049686571993898e-05 solMass

My suggestion would be to first work towards understanding the constraints in phoebe (go through the tutorials or examples from past workshops) and ensure that your input parameters are realistic and representative of the type of system you are trying to model. If your system is physical but still falls outside the existing atmosphere tables (which can happen), then follow the advice in the error messages to use a different atmosphere table (or blackbody, if absolutely necessary).

Alternatively, you could start with the default binary and use the estimators in phoebe to try to determine a starting point, but this still requires manually considering if the parameters that you are passing make sense and are physical. At that point, you can use optimizers or samplers to fit around that region of parameter space to determine the best-fit parameters and their uncertainties to explain your observations.

kittipongwangnok Aug 27, 2024
Author

Thank you very much for your clarification.
However, I just wondering, Can we reverse scale of y-axis like from small --> large as large ---> small with this command:

_ = b.plot(dataset='lc01', x='phases',
marker={'dataset': '.'},
model='init_from_model', show=True)

kecnry Aug 27, 2024
Maintainer

There are multiple ways to do that - have you tried anything that isn't working?

kittipongwangnok · 2024-08-27T14:07:05Z

kittipongwangnok
Aug 27, 2024
Author

Ok Kittipong Wangnok +6684 828 6505 School of Physics Institute of Science Suranaree University of Technology

…

On Tue, 27 Aug 2567 BE at 9:03 PM Kyle Conroy ***@***.***> wrote: All of your messages sent through email are being censored by GitHub, can you please go to the page and manually edit the messages so that they are readable? How can I enable the warning logger? #924 (comment) <#924 (comment)> — Reply to this email directly, view it on GitHub <#928 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALO4C3GWMXZ5EHPYTABPILLZTSBLRAVCNFSM6AAAAABNBGILP2VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBWGM4DKNI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

0 replies

kittipongwangnok · 2024-08-27T14:11:02Z

kittipongwangnok
Aug 27, 2024
Author

I already update it Thanks Kittipong

…

On Tue, Aug 27, 2024 at 9:03 PM Kyle Conroy ***@***.***> wrote: All of your messages sent through email are being censored by GitHub, can you please go to the page and manually edit the messages so that they are readable? How can I enable the warning logger? #924 (comment) <#924 (comment)> — Reply to this email directly, view it on GitHub <#928 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALO4C3GWMXZ5EHPYTABPILLZTSBLRAVCNFSM6AAAAABNBGILP2VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBWGM4DKNI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Kittipong Wangnok +6684 828 6505 School of Physics Institute of Science Suranaree University of Technology

0 replies

kittipongwangnok · 2024-09-01T11:13:22Z

kittipongwangnok
Sep 1, 2024
Author

I was just wondering, can phoebe model the system with a period more than 300+ days or not?

…

On Wed, Aug 28, 2024 at 12:01 AM Kyle Conroy ***@***.***> wrote: There are multiple ways to do that - have you tried anything that isn't working? — Reply to this email directly, view it on GitHub <#928 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALO4C3HW4MQUHJGORUZLEOTZTSWHNAVCNFSM6AAAAABNBGILP2VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBWGU4DCMQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Kittipong Wangnok +6684 828 6505 School of Physics Institute of Science Suranaree University of Technology

0 replies

kittipongwangnok · 2024-09-01T11:28:00Z

kittipongwangnok
Sep 1, 2024
Author

After I input:
b.set_value('period@binary@component', 310)

I got this error:
ValueError: Could not lookup ld_coeffs for ld_coeffs_source@primary@lc01@lc@dataset. Try changing ld_coeffs_source to a table that covers a sufficient range of values or set ld_mode to 'manual' and manually provide coefficients via ld_coeffs. Enable 'warning' logger to see out-of-bound arrays.

1 reply

aprsa Sep 1, 2024
Maintainer

The exact same problem as before: you push your atmosphere parameters out of bounds by changing the orbital period. You will need to adjust other parameters accordingly so that Teff/logg/abun are within the supported range, or switch to blackbody.

kittipongwangnok · 2024-09-01T13:24:08Z

kittipongwangnok
Sep 1, 2024
Author

I have tried to check from ck2004 to blackbody, but I still get the error. However, I have used the initial input file from "Time" to "Phase", then I can model and get the model with the good fit but the default period in the model is 1 day (but actually the real period of the model we use to convert from time to phase already). Can I model this way, we can interpret the other parameters?

…

On Sun, Sep 1, 2024 at 7:21 PM Andrej Prsa ***@***.***> wrote: The exact same problem as before: you push your atmosphere parameters out of bounds by changing the orbital period. You will need to adjust other parameters accordingly so that Teff/logg/abun are within the supported range, or switch to blackbody. — Reply to this email directly, view it on GitHub <#928 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALO4C3GNVAKPVAJL3XLHUWLZUMBEVAVCNFSM6AAAAABNBGILP2VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANJRGE4TMMY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Kittipong Wangnok +6684 828 6505 School of Physics Institute of Science Suranaree University of Technology

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The level of flux model is not match with the data #928

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