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Transport Properties using Onsager Formalism #56

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Transport Properties using Onsager Formalism #56

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rohithsrinivaas
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Fixes #44 #45 #18

Changes made in this Pull Request:

  • Added code to compute diffusion coefficient(Einstein Approach aka Slope fitting) based on the Onsager formalism with the FFT approach. The standard deviation of the Onsager coefficients are also computed with respect to time. If the linear fitting regime is not provided, weighted linear regression is performed using the inverse of the standard deviation as the weights. This solves the manual intervention for the identifying the suitable fitting region.
  • Added code to compute the conductivity, true transference number(Einstein Approach aka Slope fitting) based on the Onsager formalism with the FFT approach. The standard deviation of the Onsager coefficients are also computed with respect to time. If the linear fitting regime is not provided, weighted linear regression is performed using the inverse of the standard deviation as the weights. This solves the manual intervention for the identifying the suitable fitting region.
  • Added code to compute the conductivity, true transference number(Green Kubo Approach aka Integration) based on the Onsager formalism. The velocity autocorrelations are computed with FFT

References:
https://github.com/kdfong/transport-coefficients-MSD
https://github.com/kdfong/transport-coefficients
https://pubs.acs.org/doi/10.1021/acs.macromol.0c02001
https://arxiv.org/abs/2006.16164

PR Checklist

  • Tests?
  • Docs?
  • CHANGELOG updated?
  • Issue raised/referenced?

@pep8speaks
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pep8speaks commented Nov 25, 2024 •
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Hello @rohithsrinivaas! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

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Comment last updated at 2024-12-02 05:30:19 UTC

@rohithsrinivaas rohithsrinivaas changed the title Diffusion coeff Transport Properties using Onsager Formalism Nov 25, 2024
@orionarcher
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Would you mind linting this with something like black before I review?

@rohithsrinivaas
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@orionarcher I have used black to lint as suggested. Kindly review the code and provide your comments

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Add conductivity impementation
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@rohithsrinivaas @pep8speaks @orionarcher