compute ave/sphere/atom command — LAMMPS documentation

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# compute ave/sphere/atom command

Accelerator Variants: ave/sphere/atom/kk

## Syntax

    compute ID group-ID ave/sphere/atom keyword values ...

- ID, group-ID are documented in compute command

- ave/sphere/atom = style name of this compute command

- one or more keyword/value pairs may be appended

      keyword = cutoff
        cutoff value = distance cutoff

## Examples

    compute 1 all ave/sphere/atom

    compute 1 all ave/sphere/atom cutoff 5.0
    comm_modify cutoff 5.0

## Description

Added in version 7Jan2022.

Define a computation that calculates the local mass density and temperature for each atom based on its neighbors inside a spherical cutoff. If an atom has \(M\) neighbors, then its local mass density is calculated as the sum of its mass and its \(M\) neighbor masses, divided by the volume of the cutoff sphere (or circle in 2d). The local temperature of the atom is calculated as the temperature of the collection of \(M+1\) atoms, after subtracting the center-of-mass velocity of the \(M+1\) atoms from each of the \(M+1\) atom’s velocities. This is effectively the thermal velocity of the neighborhood of the central atom, similar to compute temp/com.

The optional keyword cutoff defines the distance cutoff used when searching for neighbors. The default value is the cutoff specified by the pair style. If no pair style is defined, then a cutoff must be defined using this keyword. If the specified cutoff is larger than that of the pair_style plus neighbor skin (or no pair style is defined), the comm_modify cutoff option must also be set to match that of the cutoff keyword.

The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms is dumped). Thus it can be inefficient to compute/dump this quantity too frequently.

Note

If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the special_bonds command, and means those pairwise interactions do not appear in the neighbor list. Because this compute uses the neighbor list, it also means those pairs will not be included in the order parameter. This difficulty can be circumvented by writing a dump file, and using the rerun command to compute the order parameter for snapshots in the dump file. The rerun script can use a special_bonds command that includes all pairs in the neighbor list.

Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Accelerator packages page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP, and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package page for more info.

You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

See the Accelerator packages page for more instructions on how to use the accelerated styles effectively.

## Output info

This compute calculates a per-atom array with two columns: mass density in density units and temperature in temperature units.

These values can be accessed by any command that uses per-atom values from a compute as input. See the Howto output doc page for an overview of LAMMPS output options.

## Restrictions

This compute is part of the EXTRA-COMPUTE package. It is only enabled if LAMMPS was built with that package. See the Build package page for more info.

This compute requires neighbor styles ‘bin’ or ‘nsq’.

## Related commands

comm_modify

## Default

The option defaults are cutoff = pair style cutoff.