compute dipole/chunk command
compute dipole/tip4p/chunk command
compute ID group-ID style chunkID arg
compute 1 fluid dipole/chunk molchunk
compute dw water dipole/chunk 1 geometry
Define a computation that calculates the dipole vector and total dipole 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.
These computes calculate 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 through 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. Both per-atom charges and per-atom dipole moments, if present, contribute to the computed dipole.
New in version 28Mar2023.
Compute dipole/tip4p/chunk includes adjustments for the charge carrying point M in molecules with TIP4P water geometry. The corresponding parameters are extracted from the pair style.
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 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.
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
These computes calculate 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 is 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 the Howto output page for an overview of LAMMPS output options.
Compute style dipole/tip4p/chunk 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.
Compute style dipole/tip4p/chunk can only be used with tip4p pair styles.
Using the center of mass is the default setting for the net charge correction.