Alternative translational diffusion calculation which can calculate diffusion in specified regions.

stfcdiffusion mask <mask> [out <file>] [time <time per frame>] [mask2 <mask>] [lower <distance>] [upper <distance>] [nwout <file>]) [avout <file>] [distances] [com] [x|y|z|xy|xz|yz|xyz]

mask <mask> Atoms for which MSDs will be computed.
out <file> Output file: time vs. MSD.
time Time step in the trajectory. (1.0 ps)
mask2 <mask> Compute MSDs only within the lower and upper limit of mask2. IMPORTANT: may be very slow!!!
lower <distance> Smaller distance from reference point(s). (0.01 Å)
upper <distance> Larger distance from reference point(s). (3.5 Å)
nwout <file> Output file containing number of water molecules in the chosen region, see mask2. (off)
avout <file> Output file containing average distances. (off)
x|y|z|xy|xz|yz|xyz Computation of the mean square displacement in the chosen dimension. (xyz) distances Dump un-imaged distances. By default only averages are output. (off)
com Calculate MSD for centre of mass. (off)

Calculate diffusion for selected atoms using code based on the ’diffusion’ routine developed by Hannes Loeffler at STFC (