compute_msd

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.

Syntax

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 three additional special keyword. The first special keyword is group. The parameters are:

  • group, where group_method is the grouping method to use for computation and group is the group in the grouping method to use

The second special keyword is all_groups. This keyword computes the MSD and SDC for each group in the specified grouping method. Note that group and all_groups cannot be used together. A typical usecase could be to compute the MSD for each molecule in a system. The parameters are:

  • all_groups, where group_method is the grouping method to use for computation

Finally, the third special keyword is save_every. This keyword saves the internal MSD and SDC computed so far during the simulation, which can be helpful during long running simulations. The file will have a name formatted as msd_step[step].out. The parameters are:

  • save_every, where interval is the number of steps between saving a copy. Note that the copy can only be written at most every sample_interval steps. Furthermore, the first msd_step[step].out file will be written after Nc times sample_interval steps. Subsequent files will be written every interval.

Examples

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.

To compute the MSD for all groups in group method 1 and save a copy of the MSD every 100 000 steps, one can write:

compute_msd 5 200 all_groups 1 save_every 100000