compute rigid/local command

Syntax

compute ID group-ID rigid/local rigidID input1 input2 ...
  • ID, group-ID are documented in compute command

  • rigid/local = style name of this compute command

  • rigidID = ID of fix rigid/small command or one of its variants

  • input = one or more rigid body attributes

    possible attributes = id, mol, mass,
                          x, y, z, xu, yu, zu, ix, iy, iz
                          vx, vy, vz, fx, fy, fz,
                          omegax, omegay, omegaz,
                          angmomx, angmomy, angmomz,
                          quatw, quati, quatj, quatk,
                          tqx, tqy, tqz,
                          inertiax, inertiay, inertiaz
        id = atom ID of atom within body which owns body properties
        mol = molecule ID used to define body in fix rigid/small command
        mass = total mass of body
        x,y,z = center of mass coords of body
        xu,yu,zu = unwrapped center of mass coords of body
        ix,iy,iz = box image that the center of mass is in
        vx,vy,vz = center of mass velocities
        fx,fy,fz = force of center of mass
        omegax,omegay,omegaz = angular velocity of body
        angmomx,angmomy,angmomz = angular momentum of body
        quatw,quati,quatj,quatk = quaternion components for body
        tqx,tqy,tqz = torque on body
        inertiax,inertiay,inertiaz = diagonalized moments of inertia of body
    

Examples

compute 1 all rigid/local myRigid mol x y z

Description

Define a computation that simply stores rigid body attributes for rigid bodies defined by the fix rigid/small command or one of its NVE, NVT, NPT, NPH variants. The data is stored as local data so it can be accessed by other output commands that process local data, such as the compute reduce or dump local commands.

Note that this command only works with the fix rigid/small command or its variants, not the fix rigid command and its variants. The ID of the fix rigid/small command used to define rigid bodies must be specified as rigidID. The fix rigid command is typically used to define a handful of (potentially very large) rigid bodies. It outputs similar per-body information as this command directly from the fix as global data; see the fix rigid doc page for details

The local data stored by this command is generated by looping over all the atoms owned on a processor. If the atom is not in the specified group-ID or is not part of a rigid body it is skipped. If it is not the atom within a body that is assigned to store the body information it is skipped (only one atom per body is so assigned). If it is the assigned atom, then the info for that body is output. This means that information for N bodies is generated. N may be less than the # of bodies defined by the fix rigid command, if the atoms in some bodies are not in the group-ID.

Note

Which atom in a body owns the body info is determined internal to LAMMPS; it’s the one nearest the geometric center of the body. Typically you should avoid this complication, by defining the group associated with this fix to include/exclude entire bodies.

Note that as atoms and bodies migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next.

Here is an example of how to use this compute to dump rigid body info to a file:

compute 1 all rigid/local myRigid mol x y z fx fy fz
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]

This section explains the rigid body attributes that can be specified.

The id attribute is the atomID of the atom which owns the rigid body, which is assigned by the fix rigid/small command.

The mol attribute is the molecule ID of the rigid body. It should be the molecule ID which all of the atoms in the body belong to, since that is how the fix rigid/small command defines its rigid bodies.

The mass attribute is the total mass of the rigid body.

There are two options for outputting the coordinates of the center of mass (COM) of the body. The x, y, z attributes write the COM “unscaled”, in the appropriate distance units (Angstroms, sigma, etc). Use xu, yu, zu if you want the COM “unwrapped” by the image flags for each atobody. Unwrapped means that if the body COM has passed thru a periodic boundary one or more times, the value is generated what the COM coordinate would be if it had not been wrapped back into the periodic box.

The image flags for the body can be generated directly using the ix, iy, iz attributes. For periodic dimensions, they specify which image of the simulation box the COM is considered to be in. An image of 0 means it is inside the box as defined. A value of 2 means add 2 box lengths to get the true value. A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as the rigid body COMs cross periodic boundaries during the simulation.

The vx, vy, vz, fx, fy, fz attributes are components of the COM velocity and force on the COM of the body.

The omegax, omegay, and omegaz attributes are the angular velocity components of the body around its COM.

The angmomx, angmomy, and angmomz attributes are the angular momentum components of the body around its COM.

The quatw, quati, quatj, and quatk attributes are the components of the 4-vector quaternion representing the orientation of the rigid body. See the set command for an explanation of the quaternion vector.

The angmomx, angmomy, and angmomz attributes are the angular momentum components of the body around its COM.

The tqx, tqy, tqz attributes are components of the torque acting on the body around its COM.

The inertiax, inertiay, inertiaz attributes are components of diagonalized inertia tensor for the body, i.e the 3 moments of inertia for the body around its principal axes, as computed internally by LAMMPS.


Output info:

This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the array is the number of rigid bodies. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local 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:

  • id,mol = unitless
  • mass = mass units
  • x,y,z and xy,yu,zu = distance units
  • vx,vy,vz = velocity units
  • fx,fy,fz = force units
  • omegax,omegay,omegaz = radians/time units
  • angmomx,angmomy,angmomz = mass*distance^2/time units
  • quatw,quati,quatj,quatk = unitless
  • tqx,tqy,tqz = torque units
  • inertiax,inertiay,inertiaz = mass*distance^2 units

Restrictions

This compute is part of the RIGID package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.