\(\renewcommand{\AA}{\text{Å}}\)

atom command

Syntax

compute ID group-ID chunk/spread/atom chunkID input1 input2 ...

ID, group-ID are documented in compute command
chunk/spread/atom = style name of this compute command
chunkID = ID of compute chunk/atom command
one or more inputs can be listed

input = c_ID, c_ID[N], f_ID, f_ID[N]

c_ID = global vector calculated by a compute with ID
c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
f_ID = global vector calculated by a fix with ID
f_ID[I] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below)

Examples

compute 1 all chunk/spread/atom mychunk c_com[*] c_gyration

Description

Define a calculation that “spreads” one or more per-chunk values to each atom in the chunk. This can be useful in several scenarios:

For creating a dump file where each atom lists info about the chunk it is in, e.g. for post-processing purposes.
To access chunk value in atom-style variables that need info about the chunk each atom is in.
To use the fix ave/chunk command to spatially average per-chunk values calculated by a per-chunk compute.

Examples are given below.

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.

For inputs that are computes, they must be a compute that calculates per-chunk values. These are computes whose style names end in “/chunk”.

For inputs that are fixes, they should be a fix that calculates per-chunk values. For example, fix ave/chunk or fix ave/time (assuming it is time-averaging per-chunk data).

For each atom, this compute accesses its chunk ID from the specified chunkID compute, then accesses the per-chunk value in each input. Those values are copied to this compute to become the output for that atom.

The values generated by this compute will be 0.0 for atoms not in the specified compute group group-ID. They will also be 0.0 if the atom is not in a chunk, as assigned by the chunkID compute. They will also be 0.0 if the current chunk ID for the atom is out-of-bounds with respect to the number of chunks stored by a particular input compute or fix.

Note

LAMMPS does not check that a compute or fix which calculates per-chunk values uses the same definition of chunks as this compute. It’s up to you to be consistent. Likewise, for a fix input, LAMMPS does not check that it is per-chunk data. It only checks that the fix produces a global vector or array.

Each listed input is operated on independently.

If a bracketed index I is used, it can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the number of columns in the array, then an asterisk with no numeric values means all indices from 1 to N. A leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive).

Using a wildcard is the same as if the individual columns of the array had been listed one by one. E.g. these 2 compute chunk/spread/atom commands are equivalent, since the compute com/chunk command creates a per-atom array with 3 columns:

compute com all com/chunk mychunk
compute 10 all chunk/spread/atom mychunk c_com[*]
compute 10 all chunk/spread/atom mychunk c_com[1] c_com[2] c_com[3]

Here is an example of writing a dump file the with the center-of-mass (COM) for the chunk each atom is in. The commands below can be added to the bench/in.chain script.

compute         cmol all chunk/atom molecule
compute         com all com/chunk cmol
compute         comchunk all chunk/spread/atom cmol c_com[*]
dump            1 all custom 50 tmp.dump id mol type x y z c_comchunk[*]
dump_modify     1 sort id

The same per-chunk data for each atom could be used to define per-atom forces for the fix addforce command. In this example the forces act to pull atoms of an extended polymer chain towards its COM in an attractive manner.

compute         prop all property/atom xu yu zu
variable        k equal 0.1
variable        fx atom v_k*(c_comchunk[1]-c_prop[1])
variable        fy atom v_k*(c_comchunk[2]-c_prop[2])
variable        fz atom v_k*(c_comchunk[3]-c_prop[3])
fix             3 all addforce v_fx v_fy v_fz

Note that compute property/atom is used to generate unwrapped coordinates for use in the per-atom force calculation, so that the effect of periodic boundaries is accounted for properly.

Over time this applied force could shrink each polymer chain’s radius of gyration in a polymer mixture simulation. Here is output from the bench/in.chain script. Thermo output is shown for 1000 steps, where the last column is the average radius of gyration over all 320 chains in the 32000 atom system:

compute         gyr all gyration/chunk cmol
variable        ave equal ave(c_gyr)
thermo_style    custom step etotal press v_ave

       0    22.394765    4.6721833     5.128278
  22.445002    4.8166709    5.0348372
  22.500128    4.8790392    4.9364875
  22.534686    4.9183766    4.8590693
  22.557196    4.9492211    4.7937849
  22.571017    4.9161853    4.7412008
  22.573944    5.0229708    4.6931243
  22.581804    5.0541301    4.6440647
  22.584683    4.9691734    4.6000016
   22.59128    5.0247538    4.5611513
  22.586832      4.94697    4.5238362

Here is an example for using one set of chunks, defined for molecules, to compute the dipole moment vector for each chunk. E.g. for water molecules. Then spreading those values to each atom in each chunk. Then defining a second set of chunks based on spatial bins. And finally, using the fix ave/chunk command to calculate an average dipole moment vector per spatial bin.

compute       cmol all chunk/atom molecule
compute       dipole all dipole/chunk cmol
compute       spread all chunk/spread/atom cmol c_dipole[1] c_dipole[2] c_dipole[3]
compute       cspatial all chunk/atom bin/1d z lower 0.1 units reduced
fix           ave all ave/chunk 100 10 1000 cspatial c_spread[*]

Note that the fix ave/chunk command requires per-atom values as input. That is why the compute chunk/spread/atom command is used to assign per-chunk values to each atom in the chunk. If a molecule straddles bin boundaries, each of its atoms contributes in a weighted manner to the average dipole moment of the spatial bin it is in.

Output info

This compute calculates a per-atom vector or array, which can be accessed by any command that uses per-atom values from a compute as input. See the Howto output page for an overview of LAMMPS output options.

The output is a per-atom vector if a single input value is specified, otherwise a per-atom array is output. The number of columns in the array is the number of inputs provided. The per-atom values for the vector or each column of the array will be in whatever units the corresponding input value is in.

The vector or array values are “intensive”.

Restrictions

none

Default