Syntax:
displace_atoms group-ID style args keyword value ...
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 (positive integer)
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.
Distance units for displacement 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.
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.
Atoms can be moved arbitrarily long distances by this command. If the simulation box is non-periodic, 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 or shape changes dramatically, the simulation may not be as well load-balanced (atoms per processor) as the initial mapping tried to achieve.
Restrictions:
This command requires inter-processor communication to migrate atoms once they have been displaced. This means that your system must be ready to perform a simulation before using this command (force fields are setup, atom masses are set, etc).
Related commands:
Default:
The option defaults are units = lattice.