compute property/atom command

Syntax

compute ID group-ID property/atom input1 input2 ...
  • ID, group-ID are documented in compute command
  • property/atom = style name of this compute command
  • input = one or more atom attributes
possible attributes = id, mol, proc, type, mass,
                   x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
                   vx, vy, vz, fx, fy, fz,
                      q, mux, muy, muz, mu,
                      radius, diameter, omegax, omegay, omegaz,
                   angmomx, angmomy, angmomz,
                   shapex,shapey, shapez,
                   quatw, quati, quatj, quatk, tqx, tqy, tqz,
                   end1x, end1y, end1z, end2x, end2y, end2z,
                   corner1x, corner1y, corner1z,
                   corner2x, corner2y, corner2z,
                   corner3x, corner3y, corner3z,
                   nbonds,
                      vfrac, s0,
                   spin, eradius, ervel, erforce,
                      rho, drho, e, de, cv,
                      i_name, d_name

id = atom ID
mol = molecule ID
proc = ID of processor that owns atom
type = atom type
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
ix,iy,iz = box image that the atom is in
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical or body particles
tqx,tqy,tqz = torque on finite-size particles
end12x, end12y, end12z = end points of line segment
corner123x, corner123y, corner123z = corner points of triangle
nbonds = number of bonds assigned to an atom

PERI package per-atom properties:
vfrac = ???
s0 = ???

USER-EFF and USER-AWPMD package per-atom properties:
spin = electron spin
eradius = electron radius
ervel = electron radial velocity
erforce = electron radial force

USER-SPH package per-atom properties:
rho = ???
drho = ???
e = ???
de = ???
cv = ???

fix property/atom per-atom properties:
i_name = custom integer vector with name
d_name = custom integer vector with name

Examples

compute 1 all property/atom xs vx fx mux
compute 2 all property/atom type
compute 1 all property/atom ix iy iz

Description

Define a computation that simply stores atom attributes for each atom in the group. This is useful so that the values can be used by other output commands that take computes as inputs. See for example, the compute reduce, fix ave/atom, fix ave/histo, fix ave/spatial, and atom-style variable commands.

The list of possible attributes is the same as that used by the dump custom command, which describes their meaning, with some additional quantities that are only defined for certain atom styles. Basically, this augmented list gives an input script access to any per-atom quantity stored by LAMMPS.

The values are stored in a per-atom vector or array as discussed below. Zeroes are stored for atoms not in the specified group or for quantities that are not defined for a particular particle in the group (e.g. shapex if the particle is not an ellipsoid).

The additional quantities only accessible via this command, and not directly via the dump custom command, are as follows.

Shapex, shapey, and shapez are defined for ellipsoidal particles and define the 3d shape of each particle.

Quatw, quati, quatj, and quatk are defined for ellipsoidal particles and body particles and store the 4-vector quaternion representing the orientation of each particle. See the set command for an explanation of the quaternion vector.

End1x, end1y, end1z, end2x, end2y, end2z, are defined for line segment particles and define the end points of each line segment.

Corner1x, corner1y, corner1z, corner2x, corner2y, corner2z, corner3x, corner3y, corner3z, are defined for triangular particles and define the corner points of each triangle.

Nbonds is available for all molecular atom styles and refers to the number of explicit bonds assigned to an atom. Note that if the newton bond command is set to on, which is the default, then every bond in the system is assigned to only one of the two atoms in the bond. Thus a bond between atoms I,J may be tallied for either atom I or atom J. If newton bond off is set, it will be tallied with both atom I and atom J.

The i_name and d_name attributes refer to custom integer and floating-point properties that have been added to each atom via the fix property/atom command. When that command is used specific names are given to each attribute which are what is specified as the “name” portion of i_name or d_name.

Output info:

This compute calculates a per-atom vector or per-atom array depending on the number of input values. If a single input is specified, a per-atom vector is produced. If two or more inputs are specified, a per-atom array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses per-atom values from a compute as input. See this section for an overview of LAMMPS output options.

The vector or array values will be in whatever units the corresponding attribute is in, e.g. velocity units for vx, charge units for q, etc.

Restrictions

none