Add ability to remove NPT fluctuations in diffusion calculation#1030
Merged
drroe merged 15 commits intoAmber-MD:masterfrom May 18, 2023
Merged
Add ability to remove NPT fluctuations in diffusion calculation#1030drroe merged 15 commits intoAmber-MD:masterfrom
drroe merged 15 commits intoAmber-MD:masterfrom
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averaging over multiple time origins in parallel. Only want this done if user specifies since it is not as accurate as using the full trajectory.
keyword descriptions. Add aspects created for 'individual' keyword. Add units.
keywords, fixed avgbox command in parallel, and addition of MAT3X3 DataSet read/write to NetCDF data file.
drroe
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Version 6.19.2.
Similar to #1028, add the
avgucellkeyword to thediffusionaction to remove NPT fluctuations during diffusion calculations. Also fixes theavgboxcommand so it works for subsequent commands in parallel, and adds the ability to read/write 3x3 matrix array data from/to NetCDF data files (useful withavgbox). Also adds theallowmultipleoriginskeyword todiffusionto allow calculation of diffusion in parallel when imaging is present by averaging over multiple time origins; disabled by default since this by necessity calculates the MSD out to a shorter time ( <# frames> / # processes) ) and therefore tends to give less accurate diffusion constants compared to using the entire trajectory.Updates docs and adds a test.