compute msd/chunk command
compute ID group-ID msd/chunk chunkID
compute 1 all msd/chunk molchunk
Define a computation that calculates the mean-squared displacement (MSD) for multiple chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the compute chunk/atom and Howto chunk doc pages for details of how chunks can be defined and examples of how they can be used to measure properties of a system.
Four quantities are calculated by this compute for each chunk. The first 3 quantities are the squared dx,dy,dz displacements of the center-of-mass. The 4th component is the total squared displacement, i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These calculations include all effects due to atoms passing through periodic boundaries.
Note that only atoms in the specified group contribute to the calculation. The compute chunk/atom command defines its own group; atoms will have a chunk ID = 0 if they are not in that group, signifying they are not assigned to a chunk, and will thus also not contribute to this calculation. You can specify the “all” group for this command if you simply want to include atoms with non-zero chunk IDs.
The slope of the mean-squared displacement (MSD) versus time is proportional to the diffusion coefficient of the diffusing chunks.
The displacement of the center-of-mass of the chunk is from its original center-of-mass position, calculated on the timestep this compute command was first invoked.
The number of chunks Nchunk calculated by the compute chunk/atom command must remain constant each time this compute is invoked, so that the displacement for each chunk from its original position can be computed consistently. If Nchunk does not remain constant, an error will be generated. If needed, you can enforce a constant Nchunk by using the nchunk once or ids once options when specifying the compute chunk/atom command.
This compute stores the original position (of the center-of-mass) of each chunk. When a displacement is calculated on a later timestep, it is assumed that the same atoms are assigned to the same chunk ID. However LAMMPS has no simple way to insure this is the case, though you can use the ids once option when specifying the compute chunk/atom command. Note that if this is not the case, the MSD calculation does not have a sensible meaning.
The initial coordinates of the atoms in each chunk are stored in “unwrapped” form, by using the image flags associated with each atom. See the dump custom command for a discussion of “unwrapped” coordinates. See the Atoms section of the read_data command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.
If you want the quantities calculated by this compute to be continuous when running from a restart file, then you should use the same ID for this compute, as in the original run. This is so that the fix this compute creates to store per-chunk quantities will also have the same ID, and thus be initialized correctly with chunk reference positions from the restart file.
The simplest way to output the results of the compute msd/chunk calculation to a file is to use the fix ave/time command, for example:
compute cc1 all chunk/atom molecule compute myChunk all msd/chunk cc1 fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
This compute calculates a global array where the number of rows = the number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = 4 for dx,dy,dz and the total displacement. These values can be accessed by any command that uses global array values from a compute as input. See the Howto output doc page for an overview of LAMMPS output options.
The array values are “intensive”. The array values will be in distance^2 units.