Add diffusion calculation from multiple time origins and toroidal-view scheme #1032
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original diffusion calc
… scheme keyword for unwrap.
consistent with previous behavior
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Jenkins failure is yet another python error I cannot reproduce locally. I am not a fan of python. |
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@swails @hainm if you get a chance can you see if you can reproduce this pytraj error: https://jenkins.jasonswails.com/blue/organizations/jenkins/amber-github%2Fpytraj/detail/pytraj/599/pipeline |
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Version 6.19.3. Adds new commands and keywords related to the calculation of diffusion constants.
calcdiffusionAnalysis command.tordiffAction command.schemekeyword to theunwrapAction command.The
calcdiffusionanalysis command will calculate diffusion from multiple time origins.This command does not perform imaging, so coordinate need to be unwrapped prior. This is the first Analysis command to be MPI parallelized (and is also OpenMP parallelized).
The
tordiffaction command calculate diffusion using the toroidal-view-preserving scheme (https://arxiv.org/abs/2303.09418), which is an alternate way of unwrapping NPT trajectories. It only works for orthogonal cells currently.The
schemekeyword for theunwrapAction ([scheme {frac|tor}]) will optionally use the toroidal-view-preserving scheme for unwrapping instead of the default of fractional coordinates. This currently only works by molecule and for orthogonal unit cells.Updates the manual and also adds tests.