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While the recommended approach for computing viscosity is the Green-Kubo method, the Einstein approach offers convenience both in its ability to ignore inaccuracies in long-time correlations and the convenience in the calculation itself if implemented with the Helfand method. The end goal is still to implement both Green-Kubo and Einstein approaches in this package.
The original plan was to make a utility function that calculates shear viscosity from a NumPy array of the pressure tensor with additional support for GROMACS simulations. The EDRReader in MDAnalysis would obtain pressure tensor components, temperature, and volume directly from EDR files to make the calculation easier on the user. However, after some discussion with Discord user jenclark, @orionarcher, and @hmacdope, we agreed that the Helfand method would be more user-friendly as it does not require any pressure tensors. If the Helfand method turns out to be too difficult to implement, we may return to the utility function idea.
While the recommended approach for computing viscosity is the Green-Kubo method, the Einstein approach offers convenience both in its ability to ignore inaccuracies in long-time correlations and the convenience in the calculation itself if implemented with the Helfand method. The end goal is still to implement both Green-Kubo and Einstein approaches in this package.
Relevant best practices paper: https://livecomsjournal.org/index.php/livecoms/article/view/v1i1e6324
The original plan was to make a utility function that calculates shear viscosity from a NumPy array of the pressure tensor with additional support for GROMACS simulations. The EDRReader in MDAnalysis would obtain pressure tensor components, temperature, and volume directly from EDR files to make the calculation easier on the user. However, after some discussion with Discord user jenclark, @orionarcher, and @hmacdope, we agreed that the Helfand method would be more user-friendly as it does not require any pressure tensors. If the Helfand method turns out to be too difficult to implement, we may return to the utility function idea.
Relevant Helfand method paper: https://doi.org/10.1088/1742-6596/653/1/012106
A more thorough write-up of this can be found on my personal website and blog at https://xhgchen.github.io/posts/gsoc-2023/
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