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,
                          spx, spy, spz, sp, fmx, fmy, fmz,
                          nbonds,
                          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,
                          i_name, d_name, i2_name[I], d2_name[I],
                          vfrac, s0, espin, eradius, ervel, erforce,
                          rho, drho, e, de, cv, buckling,
    
    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
    spx, spy, spz = direction of the atomic magnetic spin
    sp = magintude of atomic magnetic spin moment
    fmx, fmy, fmz = magnetic force
    nbonds = number of bonds assigned to an 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
    i_name = custom integer vector with name
    d_name = custom floating point vector with name
    i2_name[I] = Ith column of custom integer array with name
    d2_name[I] = Ith column of custom floating-point array with name
    PERI package per-atom properties:
    vfrac = volume fraction
    s0 = max stretch of any bond a particle is part of
    
    EFF and AWPMD package per-atom properties:
    espin = electron spin
    eradius = electron radius
    ervel = electron radial velocity
    erforce = electron radial force
    
    SPH package per-atom properties:
    rho = density of SPH particles
    drho = change in density
    e = energy
    de = change in thermal energy
    cv = heat capacity
    
    MESONT package per-atom properties:
    buckling = buckling flag used in mesoscopic simulation of nanotubes
    

Examples

compute 1 all property/atom xs vx fx mux
compute 2 all property/atom type
compute 1 all property/atom ix iy iz
compute 3 all property/atom sp spx spy spz
compute 1 all property/atom i_myFlag d_Sxyz[1] d_Sxyz[3]

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/chunk, and atom-style variable commands.

The list of possible attributes is essentially 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. The goal of 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).

Attributes i_name, d_name, i2_name, d2_name refer to custom per-atom integer and floating-point vectors or arrays that have been added via the fix property/atom command. When that command is used specific names are given to each attribute which are the “name” portion of these attributes. For arrays i2_name and d2_name, the column of the array must also be included following the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).

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

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 \(I\) and \(J\) 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 quantities shapex, shapey, and shapez are defined for ellipsoidal particles and define the 3d shape of each particle.

The quantities 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.

In addition, the various per-atom quantities listed above for specific packages are only accessible by this command.

Changed in version 15Sep2022: The espin property was previously called spin.

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 the Howto output page 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).

For the spin quantities, sp is in the units of the Bohr magneton; spx, spy, and spz are unitless quantities; and fmx, fmy, and fmz are given in rad/THz.

Restrictions

none

Default

none