compute vacf/chunk command — LAMMPS documentation

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# compute vacf/chunk command

## Syntax

    compute ID group-ID vacf/chunk chunkID

- ID, group-ID are documented in compute command

- vacf/chunk = style name of this compute command

- chunkID = ID of compute chunk/atom command

## Examples

    compute 1 all vacf/chunk molchunk

## Description

Added in version 2Apr2025.

Define a computation that calculates the velocity auto-correlation function (VACF) 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 product of the initial center of mass velocity (VCM) for each chunk in x, y, and z direction with the current center of mass velocity in the same direction. The fourth component is the total VACF, i.e. the sum of the three components.

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 integral of the VACF versus time is proportional to the diffusion coefficient of the diffusing chunks.

Note

The number of chunks Nchunk calculated by the compute chunk/atom command must remain constant each time this compute is invoked, so that the dot product 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.

Note

This compute stores the original center-of-mass velocities of each chunk. When a VACF 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 command. Note that if this is not the case, the VACF calculation does not have a sensible meaning.

Note

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 vacf/chunk calculation to a file is to use the fix ave/time command, for example:

    compute cc1 all chunk/atom molecule
    compute myChunk all vacf/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 command. The number of columns = 4 for the x, y, z, component and the total VACF. These values can be accessed by any command that uses global array values from a compute as input. See the Howto output page for an overview of LAMMPS output options.

The array values are “intensive”. The array values will be in distance\(^2\) divided by time\(^2\) units.

## Restrictions

> none

## Related commands

compute vacf, compute msd/chunk

## Default

none