Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/src/displace_atoms.txt
3b8ecd5c0634lammps-icms

Last Change
Raw File

displace_atoms.txt
View Options

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
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.
:line
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.
:line
[Restrictions:]
For a 2d simulation, only rotations around the a vector parallel to
the z-axis are allowed.
[Related commands:]
"lattice"_lattice.html, "change_box"_change_box.html,
"fix move"_fix_move.html
[Default:]
The option defaults are units = lattice.
c4science · Help