Inferring ages from velocity dispersions and fitting a GP gyrochronology model.
*ssh into cluster and navigate to aviary_tests/aviary. *Create a new run_.py file and a new pymc3_multi_star.py or edit the get_velocities_general.py. *Change the upper and lower indices in the run file, depending on how many stars you want to run on. *Change the directory and data file in code/get_velocities_general.py *The data file must contain ra, ra_error, dec, dec_error, parallax, parallax_error, pmra, pmra_error, pmdec, pmdec_error. *Create a new .sh file and do module load slurm, sbatch <.sh file>. *To watch progress: tail -f slurm-.out
Training the model: run gp_fit.py
Inferring an age: Currently run Age_posterior in cv_routines.py
gp_fit.py: Fitting Gaussian process model to cluster and kinematic data.
avr.py: Code for applying the Yu and Liu AVR.
dispersion.py: Various tools for calculating the velocity dispersions of stars.
velocities.py: Some basic functions for calculating velocities from gaia data using astropy. Includes definitions of Solar velocity constants.
velocity_pm_conversion.py: Some unit functions for coordinate conversions
pymc3_functions_one_star.py: Functions needed to do coordinate transformations in a pymc3-friendly framework. Calls functions in velocities.
inference.py: Contains the prior and likelihood function for inferring velocities. Calls functions in pymc3_functions_one_star, velocities and velocity_pm_conversion.
code/data.py: Code for assembling data catalogs, used to calculate Kepler velocities and to construct the prior. This catalog is called by aviary/pymc3_functions_one_star: mc_san_gaia_lam.csv.
notebooks/cv_routines.py: code needed for performing cross validation. Contains code for age posteriors and making the main plot, doesn't have code for fitting GP model, that's in aviary/gp_fit.py.
Files used in inference.py to construct a prior: gaia_mc5_velocities.csv
This file is created in ~/projects/old_stuff/aviary///code/calculate_vxyz.py from gaia_mc5.csv which is created in...
Files used in data.py:
kepler_dr2_1arcsec.fits: Megan's crossmatched catalog
santos.csv: Rotation periods from Santos et al.
KeplerRot-LAMOST.csv: Jason Curtis' LAMOST file.
Ruth_McQuillan_Masses_Out.csv: Masses from Travis Berger.
Table_1_Periodic.txt: Rotation periods from McQuillan 2014.
Calibration data:
dbf12.csv: Jason's file of cluster data (modified from original .txt version).
Gyro_Benchmark-Field_Stars.csv: Jason's file of benchmark stars.
mcquillan_kinematic_data.csv: My kinematic ages for Kepler stars.
Gyrokinage2020_Prot.csv: Lucy's kinematic ages.
Add_low_SN: Experimenting with adding in the low S/N rotators.
Cross_Validation: using cross validation to test the quality of the fit.
Get_cluster_scatter: Calculate the scatter in the clusters to estimate errorbars.
GP_fit: a from-scratch version of the GP fit. Currently looks pretty good.
Nice_plots: Making a plot of kinematic data with cluster data for talks.
Comparison_with_Spada: Comparing model with the model of Spada & Lanzafame (2019). Didn't get very far, but has code to load pickled results.
GP_demo_hackszors: mucking around with the GP fit.
GP_demo: Fitting the GP gyro relation.
GP_fit_MEarth: Fitting the GP gyro relation with MEarth data.
Aperiodoc: exploring aperiodic stars.
Are_Asteroseismic_Stars_Aperiodic: More exploration of aperiodic stars.
Better_Prior: Testing the prior.
Bokeh: making main Bokeh plots.
Existing_RVs: Exploring stats of existing RVs.
Full_age_comparison: comparing kinematic ages with benchmark ages.
Multi-dimensional: More extensive work on comparisons.
v_comparison: Generating the velocity comparison figure for the paper.
XD: Applying XD to isochrone data.
Yu_Liu_AVR: Coding up Yu and Liu AVR.