Multiple paths #258
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Multiple paths #258
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Add multiple paths finding Update tests according to correct F
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I have added this notebook to showcase the multiple path functionality. |
stefsmeets
reviewed
Feb 8, 2024
stefsmeets
reviewed
Feb 8, 2024
stefsmeets
approved these changes
Feb 8, 2024
Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>
Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>
Refactor nested loop
stefsmeets
reviewed
Feb 12, 2024
stefsmeets
reviewed
Feb 12, 2024
stefsmeets
approved these changes
Feb 12, 2024
Co-authored-by: Stef Smeets <stefsmeets@users.noreply.github.com>
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This PR has the following two main objectives
(1) Fix a small bug in the definition of the free energy graph:
Instead of weighting the graph edge between
iandjasweight = F[j]we now do instead
weight = 0.5*(F[i] + F[j]).This guarantees that the graph is well balanced and the optimal path is calculated corrected in all edge cases.
The tests have been update according to this new definition.
(2) Address #204
I have added the function
paths.multiple_pathsthat returns a list ofPathwayobject, corresponding to the desired number of optimal paths between two selected sites.The multiple paths are collected according to this algorithm (implemented in networkx ) , while discarding all the ones that are too similar.
I have updated
energy_along_pathandpath_on_landscapeto accept lists of paths as input and produce plots like this one: