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### set command

Syntax:

    set style ID keyword values ...

- style = atom or type or mol or group or region
- ID = atom ID range or type range or mol ID range or group ID or region ID
- one or more keyword/value pairs may be appended
- 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

        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

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

Description:

Set one or more properties of one or more atoms. Since atom properties are initially assigned by the read_data, read_restart or create_atoms commands, this command changes those assignments. This can be useful for overriding the default values assigned by the create_atoms 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 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 and region commands for details of how to specify a group or region.

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 command or the atom types field in the header of the data file read by the read_data 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 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 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 have 3 shape parameters. The 3 values must be non-zero for each particle set by this command. They 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. As with keyword quat, the 3 shape values must be non-zero for each particle set by this command.

Keyword diameter sets the size of the selected atoms. The particles must be finite-size spheres as defined by the atom_style sphere 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 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 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. They can also 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 command.

Keyword mass sets the mass of all selected particles. The particles must have a per-atom mass attribute, as defined by the atom_style 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 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) 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) and its 3 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 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 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 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 command.

Restrictions:

You cannot set an atom attribute (e.g. mol or q or volume) if the atom_style 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_atoms, read_data

Default: none