# compute msd/chunk command

## Syntax

``` LAMMPS
compute ID group-ID msd/chunk chunkID
```

-   ID, group-ID are documented in [compute](compute) command
-   msd/chunk = style name of this compute command
-   chunkID = ID of [compute chunk/atom](compute_chunk_atom) command

## Examples

``` LAMMPS
compute 1 all msd/chunk molchunk
```

## Description

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](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](compute_chunk_atom)
and [Howto chunk](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*, and *dz* displacements of the
center-of-mass. The fourth component is the total squared displacement
(i.e., $dx^2 + dy^2 + dz^2$) 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](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.

:::: note
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Note
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The number of chunks *Nchunk* calculated by the [compute
chunk/atom](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](compute_chunk_atom) command.
::::

:::: note
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Note
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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 ensure this is the case, though you can use
the *ids once* option when specifying the [compute
chunk/atom](compute_chunk_atom) command. Note that if this is not the
case, the MSD calculation does not have a sensible meaning.
::::

:::: note
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Note
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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](dump) command for a discussion of \"unwrapped\"
coordinates. See the Atoms section of the [read_data](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](set) command.
::::

:::: note
::: title
Note
:::

If you want the quantities calculated by this compute to be continuous
when running from a [restart file](read_restart), 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](fix_ave_time)
command, for example:

``` LAMMPS
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
```

## Output info

This compute calculates a global array where the number of rows = the
number of chunks *Nchunk* as calculated by the specified [compute
chunk/atom](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](Howto_output) page for an overview of
LAMMPS output options.

The array values are \"intensive\". The array values will be in
distance$^2$ [units](units).

## Restrictions

> none

## Related commands

[compute msd](compute_msd)

## Default

none