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Add a Green-Kubo viscosity implementation #10

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xhgchen opened this issue Jun 9, 2023 · 0 comments
Open

Add a Green-Kubo viscosity implementation #10

xhgchen opened this issue Jun 9, 2023 · 0 comments
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enhancement New feature or request

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@xhgchen
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xhgchen commented Jun 9, 2023

The recommended approach for computing viscosity is the Green-Kubo method, making it quite desirable to have in this package. The plan is to provide a utility function to calculate shear viscosity from a NumPy array of the pressure tensor, as explained in Issue #9. Again, for GROMACS simulations, the EDRReader in MDAnalysis can obtain pressure tensor components, temperature, and volume directly from EDR files. For simulations from other MD packages, the user would input this information in the utility function.

Relevant best practices paper: https://livecomsjournal.org/index.php/livecoms/article/view/v1i1e6324

A more thorough write-up of this can be found on my personal website and blog at https://xhgchen.github.io/posts/gsoc-2023/

@xhgchen xhgchen added the enhancement New feature or request label Jun 9, 2023
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