exotr - v1.6.3

[1.6.3] - 2025-08-18

• Added support for retrieving on vmr space; can specify upper bound of mixing ratio with vmr_upper, default is -0.3 (50% upper limit on any non-fill, fitting gas)
• Now possible to define planet temperature prior bounds and planet surface pressure upper bound with Tupper, Tlower, P_upper (defaults to 2000, 100, 8)
• Related: code now automatically cuts opacity files based on T, P bounds defined above
• Support for additional molecules: C4H2, CH3Cl, CH3SH, CS2, DMS, PH3
• Ability to use float32 format for opacity files to cut down on memory usage (usefloat32, default is False)

- Python
Published by MDamiano 6 months ago

exotr - v1.5.0

[1.5.0] - 2024-09-20

• Added the function '__utils.readcross(fname)' to read the cross sections with the '.dat' format.
• Introduced newly calculated cross sections at 200k and 10k spectral resolution.
• New key in the parameter file allow you to choose which cross sections to use. The key is 'opac_data'. The default value is 'mat'. It can be set to '200k' and '10k' to use the relative cross sections.
• If the planetary temperature is not a free parameter, the molecular cross-sections are pre calculated in 'utils.preloadvariables(param)' function. Otherwise, they need to be calculated in 'forward.atmospheric_structure()'.
• The opacities/cross-sections are now tailored in wavelength to the specific problem that is being analyzed, i.e., the wavelength grid is selected based on the minimum and maximum value of the input spectrum.
• The calcmeanmol_mass would in some conditions assign a negative value to the filling gas.
• Added 'hybrid' as possibility for the CLR prior. It is a hybrid between the 'modified' and 'uniform' priors.
• Removed 'modifiedclrprior' as key entry in the parameter file. Replaced by 'clr_prior' that can assume 3 different values: 'uniform', 'modified', and 'hybrid'.
• Introduction of the package 'skbio'. Replaced '_utils.clrto_vmr'.
• Deprecated the 'standardparameters.dat'. Replaced with 'utils.standardparameters()'.
• Many optimizations and bugfixes.
• Fixed Rayleigh scattering calculation that would return NaNs if main gases are not fitted nor gas fill.
• __forward.py hotfix in the total opacity of transit path calculation.

- Python
Published by MDamiano over 1 year ago

exotr - v.1.4.2

[1.4.2] - 2024-08-30

• If in the ExoTR folder it is present the "PHOENIXmodelslight" folder, this will be used to calculate the stellar contribution. The star spectra are pre-calculated to be lighter making the code faster.
• Updated opacity file.
• The best fit model is now saved in a file ("Best_fit.dat") together with 1, 2, and 3 sigmas confidence regions.
• - Rayleigh scattering calculation improved. It is now calculated for H2, N2, H2O, and CO2 and averaged based on the VMR of the aforementioned gases.
• The volume mixing ratio of the gases are now 1D-arrays of the same length of the pressure grid. Previously, they where single values. The change does not affect input parameter files.
• 'takestarspectrum' function moved from 'utils' to 'forward'
• Added support for more gases as free parameters (i.e., OCS).
• Model errorbars can now be plotted in the 'NESTspectrum' plot. Errorbars will automatically plot only if the key 'calclikelihood_data' was set to True in the parameter file.
• Bugfixes.

- Python
Published by MDamiano over 1 year ago

exotr - v1.3.0

[1.3.0] - 2024-07-22

• Added support for more gases as free parameters (i.e., N2O, H2)
• Added the possibility to fit to a delta temperature when using an input P-T profile.
• Added the possibility to input a custom P-T profile. Use the 'TP_profile' key in the parameter file (default is None), provide the path to the files containing the P-T profile. 2 columns: first temperature in K, second pressure in Pa.
• Added the possibility to fit for the planetary mass ('fitMp' in the par file). If True, specify 'Mp' and 'Mperr' to use a gaussian prior distribution, otherwise set 'Mp' to 'None' to select a uniform distribution.
• Dropped 'dynesty' from available optimizers.
• Introduced the 'spectres' python package that substitutes the 'customspectralbinning' util function throughout the ExoTR.
• The chi-squared statistic is also provided together with the Bayesian statistic.
• Added the possibility to calculate the likelihood per single datapoint in post processing. Enabled by the flag 'calclikelihooddata' (default is False), and moderated by the flag 'nlikelihooddata' (default 10000) which specify how many single datapoint likelihood to calculate. This function is MPI compatible. In addition, the calculated spectra are stored.
• Added the possibility to fit the stellar activity using 5 parameters (faculae and spots separated) or 3 parameters (heterogeneity in general). Use the parameter 'stellaractivityparameters' to regulate the behavior.
• Added the possibility to choose the prior functions for the gases. Use 'modifiedclrprior' in the parameter file (default is True, i.e., modified prior). If False, a flat uniform prior between [-25, 25] is instead used.
• Added the possibility to fit more than 6 gases when using the centered-log-ratio. 'definemodifiedclrprior' is the function in '_utils' that calculates the prior for different number of gases.

- Python
Published by MDamiano over 1 year ago

exotr - v1.2.3

[1.2.3]

• Bugfixes (posterior plot)

[1.2.2]

• Added the possibility to fit for a bare rock. Only the planetary radius is fitted. Offsets and stellar heterogeneity are optional.
• Added support for more gases as free parameters (i.e. SO2)

[1.2.1]

• Added 'calcspectra' method in '_multinest'. It calculates 100 transmission spectra extracted from the posterior distribution.

- Python
Published by MDamiano over 1 year ago

exotr - v1.2.0

Initial public release

- Python
Published by MDamiano almost 2 years ago