forked from lijiext/lammps
169 lines
7.3 KiB
Plaintext
169 lines
7.3 KiB
Plaintext
"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 value ... :pre
|
|
|
|
style = {atom} or {group} or {region} :ulb,l
|
|
ID = atom ID 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 {vx} or {vy} or {vz} or \
|
|
{charge} or {dipole} or {dipole/random} or {quat/random} 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)
|
|
{vx},{vy},{vz} value = velocity component (velocity units)
|
|
{charge} value = atomic charge (charge units)
|
|
{dipole} values = x y z
|
|
x,y,z = orientation of dipole moment vector
|
|
{dipole/random} value = seed
|
|
seed = random # seed (positive integer) for dipole moment orientations
|
|
{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
|
|
{bond} value = bond type for all bonds between selected atoms
|
|
{angle} value = angle type for all angles bewteen 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 atom 100 x 0.5 vx 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 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 a single atom. The style {group} selects the
|
|
entire group of atoms. The style {region} selects all atoms in the
|
|
geometric region. The associated ID for each of these styles is
|
|
either the unique atom ID (typically a number from 1 to N = the number
|
|
of atoms in the simulation), the group ID, or the region ID. 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 statisticaly
|
|
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}, {vx}, {vy}, {vz}, and {charge} set the
|
|
coordinates, velocity, 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 for each atom is
|
|
set by the "dipole"_dipole.html command.
|
|
|
|
Keyword {dipole/random} randomizes the orientation of the dipole
|
|
moment vectors of the selected atoms. The magnitude of the dipole
|
|
moment for each atom is set by the "dipole"_dipole.html command. 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 the "shape"_shape.html command is 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.
|
|
|
|
For the {dipole} and {quat} keywords, the "atom style"_atom_style.html
|
|
being used must support the use of dipoles or quaternions.
|
|
|
|
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}) 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
|