This keyword computes the self-diffusion coefficient (SDC) from the mean-square displacement (MSD) function. If this keyword appears in a run, the MSD function will be computed and the SDC is also calculated as a time derivative of it. The results will be written to msd.out output file.
For this keyword, the command looks like:
compute_msd <sample_interval> <Nc> [<optional_arg>]
with parameters defined as
sample_interval: Sampling interval of the position data
Nc: Maximum number of correlation steps
The optional argument
optional_arg allows an additional special keyword.
The keyword for this function is
The parameters are:
group_methodis the grouping method to use for computation and
groupis the group in the grouping method to use
An example of this function is:
compute_msd 5 200 group 1 1
This means that you
want to calculate the MSD
the position data will be recorded every 5 steps
the maximum number of correlation steps is 200
you would like to compute only over group 1 in group method 1.