lammps/doc/set.txt

"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

set command :h3

[Syntax:]

set style ID keyword values ... :pre

style = {atom} or {type} or {mol} or {group} or {region} :ulb,l
ID = atom ID range or type range or mol ID range or group ID or region ID :l
one or more keyword/value pairs may be appended :l
keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
          {charge} or {dipole} or {dipole/random} or {quat} or \
	  {quat/random} or {diameter} or {shape} or {mass} or \
	  {density} or {volume} or {image} or
	  {bond} or {angle} or {dihedral} or {improper} :l
  {type} value = atom type
  {type/fraction} values = type fraction seed
    type = new atom type
    fraction = fraction of selected atoms to set to new atom type
    seed = random # seed (positive integer)
  {mol} value = molecule ID
  {x},{y},{z} value = atom coordinate (distance units)
  {charge} value = atomic charge (charge units)
  {dipole} values = x y z
    x,y,z = orientation of dipole moment vector
  {dipole/random} value = seed Dlen
    seed = random # seed (positive integer) for dipole moment orientations
    Dlen = magnitude of dipole moment (dipole units)
  {quat} values = a b c theta
    a,b,c = unit vector to rotate particle around via right-hand rule
    theta = rotation angle in degrees
  {quat/random} value = seed
    seed = random # seed (positive integer) for quaternion orientations
  {diameter} value = diameter of spherical particle (distance units)
  {shape} value = Sx Sy Sz
    Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
  {mass} value = per-atom mass (mass units)
  {density} value = particle density for sphere or ellipsoid (mass/distance^3 units)
  {volume} value = particle volume for Peridynamic particle (distance^3 units)
  {image} nx ny nz
    nx,ny,nz = which periodic image of the simulation box the atom is in
  {bond} value = bond type for all bonds between selected atoms
  {angle} value = angle type for all angles between selected atoms
  {dihedral} value = dihedral type for all dihedrals between selected atoms
  {improper} value = improper type for all impropers between selected atoms :pre
:ule

[Examples:]

set group solvent type 2
set group solvent type/fraction 2 0.5 12393
set group edge bond 4
set region half charge 0.5
set type 3 charge 0.5
set type 1*3 charge 0.5
set atom 100*200 x 0.5 y 1.0
set atom 1492 type 3 :pre

[Description:]

Set one or more properties of one or more atoms.  Since atom
properties are initially assigned by the "read_data"_read_data.html,
"read_restart"_read_restart.html or "create_atoms"_create_atoms.html
commands, this command changes those assignments.  This can be useful
for overriding the default values assigned by the
"create_atoms"_create_atoms.html command (e.g. charge = 0.0).  It can
be useful for altering pairwise and molecular force interactions,
since force-field coefficients are defined in terms of types.  It can
be used to change the labeling of atoms by atom type or molecule ID
when they are output in "dump"_dump.html files.  It can be useful for
debugging purposes; i.e. positioning an atom at a precise location to
compute subsequent forces or energy.

The style {atom} selects one or more atoms in a range of atom IDs.
The style {type} selects all the atoms in a range of types.  The style
{mol} selects all the atoms in a range of molecule IDs.

In each of the range cases, a single value can be specified, or a
wildcard asterisk can be used to specify a range of values.  This
takes the form "*" or "*n" or "n*" or "m*n".  For example, for the
style {type}, if N = the number of atom types, then an asterisk with
no numeric values means all types from 1 to N.  A leading asterisk
means all types from 1 to n (inclusive).  A trailing asterisk means
all types from n to N (inclusive).  A middle asterisk means all types
from m to n (inclusive).  Note that the loweest value for the wildcard
is 1, not 0, so you cannot not use this form to select atoms
with molecule ID = 0, for example.

The style {group} selects all the atoms in the specified group.  The
style {region} selects all the atoms in the specified geometric
region.  See the "group"_group.html and "region"_region.html commands
for details of how to specify a group or region.

:line

Keyword {type} sets the atom type for all selected atoms.  The
specified value must be from 1 to ntypes, where ntypes was set by the
"create_box"_create_box.html command or the {atom types} field in the
header of the data file read by the "read_data"_read_data.html
command.

Keyword {type/fraction} sets the atom type for a fraction of the
selected atoms.  The actual number of atoms changed is not guaranteed
to be exactly the requested fraction, but should be statistically
close.  Random numbers are used in such a way that a particular atom
is changed or not changed, regardless of how many processors are being
used.

Keyword {mol} sets the molecule ID for all selected atoms.  The "atom
style"_atom_style.html being used must support the use of molecule
IDs.

Keywords {x}, {y}, {z}, and {charge} set the coordinates or charge of
all selected atoms.  For {charge}, the "atom style"_atom_style.html
being used must support the use of atomic charge.

Keyword {dipole} uses the specified x,y,z values as components of a
vector to set as the orientation of the dipole moment vectors of the
selected atoms.  The magnitude of the dipole moment is set
by the length of this orientation vector.

Keyword {dipole/random} randomizes the orientation of the dipole
moment vectors of the selected atoms and sets the magnitude of each to
the specified {Dlen} value.  For 2d systems, the z component of the
orientation is set to 0.0.  Random numbers are used in such a way that
the orientation of a particular atom is the same, regardless of how
many processors are being used.

Keyword {quat} uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms.
Note that particles defined by "atom_style ellipsoid"_atom_style.html
have 3 shape paraeters whicha are used to specify the aspect ratios of
an ellipsoidal particle, which is oriented by default with its x-axis
along the simulation box's x-axis, and similarly for y and z.  If this
body is rotated (via the right-hand rule) by an angle theta around a
unit rotation vector (a,b,c), then the quaternion that represents its
new orientation is given by (cos(theta/2), a*sin(theta/2),
b*sin(theta/2), c*sin(theta/2)).  The theta and a,b,c values are the
arguments to the {quat} keyword.  LAMMPS normalizes the quaternion in
case (a,b,c) was not specified as a unit vector.  For 2d systems, the
a,b,c values are ignored, since a rotation vector of (0,0,1) is the
only valid choice.

Keyword {quat/random} randomizes the orientation of the quaternion of
the selected atoms.  Random numbers are used in such a way that the
orientation of a particular atom is the same, regardless of how many
processors are being used.  For 2d systems, only orientations in the
xy plane are generated.

Keyword {diameter} sets the size of the selected atoms.  The particles
must be finite-size spheres as defined by the "atom_style
sphere"_atom_style.html command.  The diameter of a particle can be
set to 0.0, which means they will be treated as point particles.  Note
that this command does not adjust the particle mass, even if it was
defined with a density, e.g. via the "read_data"_read_data.html
command.

Keyword {shape} sets the size and shape of the selected atoms.  The
particles must be aspherical ellipsoids as defined by the "atom_style
ellipsoid"_atom_style.html command.  The {Sx}, {Sy}, {Sz} settings are
the 3 diameters of the ellipsoid in each direction.  All 3 can be set
to the same value, which means the ellipsoid is effectively a sphere.
Or then can all be set to 0.0 which means the particle will be treated
as a point particle.  Note that this command does not adjust the
particle mass, even if it was defined with a density, e.g. via the
"read_data"_read_data.html command.

Keyword {mas} sets the mass of all selected particles.  The
particles must have a per-atom mass attribute, as defined by the
"atom_style"_atom_style.html command.  See the "mass" command for how
to set mass values on a per-type basis.

Keyword {density} sets the mass of all selected particles.  The
particles must have a per-atom mass attribute, as defined by the
"atom_style"_atom_style.html command.  See the "mass" command for how
to set mass values on a per-type basis.  If the atom has a radius
attribute (see "atom_style sphere"_atom_style.html) and its radius is
non-zero, its mass is set from the density and particle volume.  The
same is true if the atom has a shape attribute (see "atom_style
ellipsoid"_atom_style.html) and its shape parameters are non-zero.
Otherwise the mass is set to the density value directly.

Keyword {volume} sets the volume of all selected particles.
Currently, only the "atom_style peri"_atom_style.html command defines
particles with a volume attribute.  Note that this command does not
adjust the particle mass.

Keyword {image} sets which image of the simulation box the atom 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 atoms cross periodic boundaries during
the simulation.  The flags can be output with atom snapshots via the
"dump"_dump.html command.  If a value of NULL is specified for any of
nx,ny,nz, then the current image value for that dimension is
unchanged.  For non-periodic dimensions only a value of 0 can be
specified.

This command can be useful after a system has been equilibrated and
atoms have diffused one or more box lengths in various directions.
This command can then reset the image values for atoms so that they
are effectively inside the simulation box, e.g if a diffusion
coefficient is about to be measured via the "compute
msd"_compute_msd.html command.  Care should be taken not to reset the
image flags of two atoms in a bond to the same value if the bond
straddles a periodic boundary (rather they should be different by +/-
1).  This will not affect the dynamics of a simulation, but may mess
up analysis of the trajectories if a LAMMPS diagnostic or your own
analysis relies on the image flags to unwrap a molecule which
straddles the periodic box.

Keywords {bond}, {angle}, {dihedral}, and {improper}, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value from 1 to nbondtypes (nangletypes, etc).  All
atoms in a particular bond (angle, etc) must be selected atoms in
order for the change to be made.  The value of nbondtype (nangletypes,
etc) was set by the {bond types} ({angle types}, etc) field in the
header of the data file read by the "read_data"_read_data.html
command.

[Restrictions:]

You cannot set an atom attribute (e.g. {mol} or {q} or {volume}) if
the "atom_style"_atom_style.html does not have that attribute.

This command requires inter-processor communication to coordinate the
setting of bond types (angle types, etc).  This means that your system
must be ready to perform a simulation before using one of these
keywords (force fields set, atom mass set, etc).  This is not
necessary for other keywords.

Using the {region} style with the bond (angle, etc) keywords can give
unpredictable results if there are bonds (angles, etc) that straddle
periodic boundaries.  This is because the region may only extend up to
the boundary and partner atoms in the bond (angle, etc) may have
coordinates outside the simulation box if they are ghost atoms.

[Related commands:]

"create_box"_create_box.html, "create_atoms"_create_atoms.html,
"read_data"_read_data.html

[Default:] none