displace_atoms command

Syntax

displace_atoms group-ID style args keyword value ...
  • group-ID = ID of group of atoms to displace
  • style = move or ramp or random or rotate
move args = delx dely delz
  delx,dely,delz = distance to displace in each dimension (distance units)
ramp args = ddim dlo dhi dim clo chi
  ddim = x or y or z
  dlo,dhi = displacement distance between dlo and dhi (distance units)
  dim = x or y or z
  clo,chi = lower and upper bound of domain to displace (distance units)
random args = dx dy dz seed
  dx,dy,dz = random displacement magnitude in each dimension (distance units)
  seed = random # seed (prime number greater 10000)
rotate args = Px Py Pz Rx Ry Rz theta
  Px,Py,Pz = origin point of axis of rotation (distance units)
  Rx,Ry,Rz = axis of rotation vector
  theta = angle of rotation (degrees)
  • zero or more keyword/value pairs may be appended
keyword = units
  value = box or lattice

Examples

displace_atoms top move 0 -5 0 units box
displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5

Description

Displace a group of atoms. This can be used to move atoms a large distance before beginning a simulation or to randomize atoms initially on a lattice. For example, in a shear simulation, an initial strain can be imposed on the system. Or two groups of atoms can be brought into closer proximity.

The move style displaces the group of atoms by the specified 3d distance.

The ramp style displaces atoms a variable amount in one dimension depending on the atom’s coordinate in a (possibly) different dimension. For example, the second example command displaces atoms in the x-direction an amount between 0.0 and 5.0 distance units. Each atom’s displacement depends on the fractional distance its y coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside those bounds will be moved the minimum (0.0) or maximum (5.0) amount.

The random style independently moves each atom in the group by a random displacement, uniformly sampled from a value between -dx and +dx in the x dimension, and similarly for y and z. Random numbers are used in such a way that the displacement of a particular atom is the same, regardless of how many processors are being used.

The rotate style rotates each atom in the group by the angle theta around a rotation axis R = (Rx,Ry,Rz) that goes thru a point P = (Px,Py,Pz). The direction of rotation for the atoms around the rotation axis is consistent with the right-hand rule: if your right-hand’s thumb points along R, then your fingers wrap around the axis in the direction of positive theta.

Distance units for displacements and the origin point of the rotate style are determined by the setting of box or lattice for the units keyword. Box means distance units as defined by the units command - e.g. Angstroms for real units. Lattice means distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing.

Warning

Care should be taken not to move atoms on top of other atoms. After the move, atoms are remapped into the periodic simulation box if needed, and any shrink-wrap boundary conditions (see the boundary command) are enforced which may change the box size. Other than this effect, this command does not change the size or shape of the simulation box. See the change_box command if that effect is desired.

Warning

Atoms can be moved arbitrarily long distances by this command. If the simulation box is non-periodic and shrink-wrapped (see the boundary command), this can change its size or shape. This is not a problem, except that the mapping of processors to the simulation box is not changed by this command from its initial 3d configuration; see the processors command. Thus, if the box size/shape changes dramatically, the mapping of processors to the simulation box may not end up as optimal as the initial mapping attempted to be.

Restrictions

You cannot rotate around any rotation vector except the z-axis for a 2d simulation.

Default

The option defaults are units = lattice.