lammps/doc/displace_atoms.txt

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displace_atoms command :h3

[Syntax:]

displace_atoms group-ID style args keyword value ... :pre

group-ID = ID of group of atoms to displace :ulb,l
style = {move} or {ramp} or {random} or {rotate} :l
  {move} args = delx dely delz
    delx,dely,delz = distance to displace in each dimension (distance units)
    any of delx,dely,delz can be a variable (see below)
  {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)
  {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) :pre

zero or more keyword/value pairs may be appended :l
  keyword = {units}
    value = {box} or {lattice} :pre
:ule

[Examples:]

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

[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
displacement vector.  Any of the 3 quantities defining the vector
components can be specified as an equal-style or atom-style
"variable"_variable.html.  If the value is a variable, it should be
specified as v_name, where name is the variable name.  In this case,
the variable will be evaluated, and its value(s) used for the
displacement(s).  The scale factor implied by the {units} keyword will
also be applied to the variable result.

Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed
time.  Atom-style variables can specify the same formulas as
equal-style variables but can also include per-atom values, such as
atom coordinates or per-atom values read from a file.  Note that if
the variable references other "compute"_compute.html or "fix"_fix.html
commands, those values must be up-to-date for the current timestep.
See the "Variable Accuracy" section of the "variable"_variable.html
doc page for more details.

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 thumb points along {R}, then your fingers wrap around the
axis in the direction of positive theta.

If the defined "atom_style"_atom_style.html assigns an orientation to
each atom ("atom styles"_atom_style.html ellipsoid, line, tri, body),
then that property is also updated appropriately to correspond to the
atom's rotation.

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"_units.html command - e.g. Angstroms for {real} units.
{Lattice} means distance units are in lattice spacings.  The
"lattice"_lattice.html command must have been previously used to
define the lattice spacing.

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NOTE: 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"_boundary.html 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"_change_box.html command if that effect is desired.

NOTE: Atoms can be moved arbitrarily long distances by this command.
If the simulation box is non-periodic and shrink-wrapped (see the
"boundary"_boundary.html 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"_processors.html 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.

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[Restrictions:]

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

[Related commands:]

"lattice"_lattice.html, "change_box"_change_box.html,
"fix_move"_fix_move.html

[Default:]

The option defaults are units = lattice.