Similar to #1028, add the avgucell keyword to the diffusion action to remove NPT fluctuations during diffusion calculations. Also fixes the avgbox command 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 with avgbox). Also adds the allowmultipleorigins keyword to diffusion to 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.
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.