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+

compute dipole/chunk command

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Syntax

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compute ID group-ID dipole/chunk chunkID charge-correction
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  • ID, group-ID are documented in compute command
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  • dipole/chunk = style name of this compute command
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  • chunkID = ID of compute chunk/atom command
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  • charge-correction = mass or geometry, use COM or geometric center for charged chunk correction (optional)
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Examples

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compute 1 fluid dipole/chunk molchunk
+compute dw water dipole/chunk 1 geometry
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Description

+

Define a computation that calculates the dipole vector and total dipole +for multiple chunks of atoms.

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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 doc page and “Section_howto 23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system.

+

This compute calculates the x,y,z coordinates of the dipole vector +and the total dipole moment for each chunk, which includes all effects +due to atoms passing thru periodic boundaries. For chunks with a net +charge the resulting dipole is made position independent by subtracting +the position vector of the center of mass or geometric center times the +net charge from the computed dipole vector.

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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.

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Note

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The coordinates of an atom contribute to the chunk’s +dipole 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.

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The simplest way to output the results of the compute com/chunk +calculation to a file is to use the fix ave/time +command, for example:

+
compute cc1 all chunk/atom molecule
+compute myChunk all dipole/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
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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 dipole vector components and the total dipole of each +chunk. These values can be accessed by any command that uses global +array values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +options.

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The array values are “intensive”. The array values will be in +dipole units, i.e. charge units times distance units.

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Restrictions

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none
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