warrickball/tomso

TOMSO (Tools for Models of Stars and their Oscillations) is a set of Python modules for loading and saving input and output files for and from stellar evolution and oscillation codes.

tomso: Tools for Models of Stars and their Oscillations

tomso is a set of Python modules for loading and saving input and output files for and from stellar evolution and oscillation codes. The functions are bundled together in modules that correspond to a specific stellar evolution code, stellar oscillation code or file format. tomso currently supports the FGONG format and various input/output files for ADIPLS, GYRE, MESA and STARS.

Read the full documentation at tomso.readthedocs.io.

Contributing

Something isn't working

Search the issues on GitHub and, if your problem hasn't been addressed before, open a new issue that describes what you tried to do, what you expected to happen and what happened instead. In case it's helpful, include your operating system, Python version and NumPy version. Also try to include a minimal working example, including the files (or parts thereof) that are causing the problem.

I found a bug and wrote a patch to fix it

If you've found the problem is something in tomso that doesn't work as it should and fixed it yourself, great! Open a pull request that describes what the problem was and how your patch fixes it.

I want tomso to support my favourite file format

Open an issue with links to the specification of the file format or where I can find (or create) examples with which to test new code. I have limited time to extend tomso's features unless it happens to align with research I'm doing but I'll try my best to implement something.

Contributors

• Warrick Ball
• Vincent Vanlaer

tomso's Issues

Mesa history files dont handle retries, backups and restarts

tomso/tomso/mesa.py

Line 38 in 018781b

data = np.genfromtxt(lines[5:], names=True)

Hi,
I noticed you history reading code is missing the ability to remove retries, backups and restarts (from photos) which usually messes up plots when the model number suddenly goes backwards for a bit :)

This chunk of code is adapted from my mesa reading code, its untested with yours but should be a good starting point:

data=data[data['model_number']<=data['model_number'][-1]] # get all model numbers less than the last model    number (fixes issue if last model was from a restart and has a lower number than max(model_number)
mod_rev=data['model_number'][::-1] # Reverse array of elements
mod_uniq,mod_ind=np.unique(mod_rev,return_index=True) # This will return the index of the first unique model number, but as we reversed the array previously this is the last point in the array with this model number
data=data[np.size(data['model_number'])-mod_ind-1] # Flip the reversed index back to "normal" index