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 length or tri or theta or theta/random or angmom or omega or mass or density or density/disc or volume or image or bond or angle or dihedral or improper or meso/e or meso/cv or meso/rho or smd/contact/radius or smd/mass/density or dpd/theta or edpd/temp or edpd/cv or cc or i_name or d_name

    type value = atom type
      value can be an atom-style variable (see below)
    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
      value can be an atom-style variable (see below)
    x,y,z value = atom coordinate (distance units)
      value can be an atom-style variable (see below)
    charge value = atomic charge (charge units)
      value can be an atom-style variable (see below)
    dipole values = x y z
      x,y,z = orientation of dipole moment vector
      any of x,y,z can be an atom-style variable (see below)
    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 (degrees)
      any of a,b,c,theta can be an atom-style variable (see below)
    quat/random value = seed
      seed = random # seed (positive integer) for quaternion orientations
    diameter value = diameter of spherical particle (distance units)
      value can be an atom-style variable (see below)
    shape value = Sx Sy Sz
      Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
    length value = len
      len = length of line segment (distance units)
      len can be an atom-style variable (see below)
    tri value = side
      side = side length of equilateral triangle (distance units)
      side can be an atom-style variable (see below)
    theta value = angle (degrees)
      angle = orientation of line segment with respect to x-axis
      angle can be an atom-style variable (see below)
    theta/random value = seed
      seed = random # seed (positive integer) for line segment orienations
    angmom values = Lx Ly Lz
      Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
      any of Lx,Ly,Lz can be an atom-style variable (see below)
    omega values = Wx Wy Wz
      Wx,Wy,Wz = components of angular velocity vector (radians/time units)
      any of wx,wy,wz can be an atom-style variable (see below)
    mass value = per-atom mass (mass units)
      value can be an atom-style variable (see below)
    density value = particle density for a sphere or ellipsoid (mass/distance^3 units), or for a triangle (mass/distance^2 units) or line (mass/distance units) particle
      value can be an atom-style variable (see below)
    density/disc value = particle density for a 2d disc or ellipse (mass/distance^2 units)
      value can be an atom-style variable (see below)
    volume value = particle volume for Peridynamic particle (distance^3 units)
      value can be an atom-style variable (see below)
    image nx ny nz
      nx,ny,nz = which periodic image of the simulation box the atom is in
      any of nx,ny,nz can be an atom-style variable (see below)
    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
    meso/e value = energy of SPH particles (need units)
      value can be an atom-style variable (see below)
    meso/cv value = heat capacity of SPH particles (need units)
      value can be an atom-style variable (see below)
    meso/rho value = density of SPH particles (need units)
      value can be an atom-style variable (see below)
    smd/contact/radius = radius for short range interactions, i.e. contact and friction
      value can be an atom-style variable (see below)
    smd/mass/density = set particle mass based on volume by providing a mass density
      value can be an atom-style variable (see below)
    dpd/theta value = internal temperature of DPD particles (temperature units)
      value can be an atom-style variable (see below)
      value can be NULL which sets internal temp of each particle to KE temp
    edpd/temp value = temperature of eDPD particles (temperature units)
      value can be an atom-style variable (see below)
    edpd/cv value = volumetric heat capacity of eDPD particles (energy/temperature/volume units)
      value can be an atom-style variable (see below)
    cc values = index cc
      index = index of a chemical species (1 to Nspecies)
      cc = chemical concentration of tDPD particles for a species (mole/volume units)
    i_name value = value for custom integer vector with name
    d_name value = value for custom floating-point vector with name
    

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 * charge v_atomfile
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 also be useful for debugging purposes; i.e. positioning an atom at a precise location to compute subsequent forces or energy.

Note that the style and ID arguments determine which atoms have their properties reset. The remaining keywords specify which properties to reset and what the new values are. Some strings like type or mol can be used as a style and/or a keyword.


This section describes how to select which atoms to change the properties of, via the style and ID arguments.

The style atom selects all the 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, the range can be specified as a single numeric value, 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). For all the styles except mol, the lowest value for the wildcard is 1; for mol it is 0.

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.


This section describes the keyword options for which properties to change, for the selected atoms.

Note that except where explicitly prohibited below, all of the keywords allow an atom-style or atomfile-style variable to be used as the specified value(s). 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 resulting per-atom value used to determine the value assigned to each selected atom. Note that the per-atom value from the variable will be ignored for atoms that are not selected via the style and ID settings explained above. A simple way to use per-atom values from the variable to reset a property for all atoms is to use style atom with ID = “*”; this selects all atom IDs.

Atom-style variables can specify formulas with various mathematical functions, and include thermo_style command keywords for the simulation box parameters and timestep and elapsed time. They can also include per-atom values, such as atom coordinates. Thus it is easy to specify a time-dependent or spatially-dependent set of per-atom values. As explained on the variable doc page, atomfile-style variables can be used in place of atom-style variables, and thus as arguments to the set command. Atomfile-style variables read their per-atoms values from a file.

Note

Atom-style and atomfile-style variables return floating point per-atom values. If the values are assigned to an integer variable, such as the molecule ID, then the floating point value is truncated to its integer portion, e.g. a value of 2.6 would become 2.

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. This keyword does not allow use of an atom-style variable.

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 for 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. This keyword does not allow use of an atom-style variable.

Keyword quat uses the specified values to create a quaternion (4-vector) that represents the orientation of the selected atoms. The particles must define a quaternion for their orientation (e.g. ellipsoids, triangles, body particles) as defined by the atom_style command. 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 for the selected atoms. The particles must define a quaternion for their orientation (e.g. ellipsoids, triangles, body particles) as defined by the atom_style command. 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, for ellipsoidal particles, the 3 shape values must be non-zero for each particle set by this command. This keyword does not allow use of an atom-style variable.

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 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 length sets the length of selected atoms. The particles must be line segments as defined by the atom_style line command. If the specified value is non-zero the line segment is (re)set to a length = the specified value, centered around the particle position, with an orientation along the x-axis. If the specified value is 0.0, the particle will become 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 tri sets the size of selected atoms. The particles must be triangles as defined by the atom_style tri command. If the specified value is non-zero the triangle is (re)set to be an equilateral triangle in the xy plane with side length = the specified value, with a centroid at the particle position, with its base parallel to the x axis, and the y-axis running from the center of the base to the top point of the triangle. If the specified value is 0.0, the particle will become 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 theta sets the orientation of selected atoms. The particles must be line segments as defined by the atom_style line command. The specified value is used to set the orientation angle of the line segments with respect to the x axis.

Keyword theta/random randomizes the orientation of theta for the selected atoms. The particles must be line segments as defined by the atom_style line command. 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. This keyword does not allow use of an atom-style variable.

Keyword angmom sets the angular momentum of selected atoms. The particles must be ellipsoids as defined by the atom_style ellipsoid command or triangles as defined by the atom_style tri command. The angular momentum vector of the particles is set to the 3 specified components.

Keyword omega sets the angular velocity of selected atoms. The particles must be spheres as defined by the “atom_style sphere”_ atom_style.html command. The angular velocity vector of the particles is set to the 3 specified components.

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 or density/disc also sets the mass of all selected particles, but in a different way. The particles must have a per-atom mass attribute, as defined by the atom_style command. 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 for 3d systems (the input density is assumed to be in mass/distance^3 units). For 2d, the default is for LAMMPS to model particles with a radius attribute as spheres. However, if the density/disc keyword is used, then they can be modeled as 2d discs (circles). Their mass is set from the density and particle area (the input density is assumed to be in mass/distance^2 units).

If the atom has a shape attribute (see atom_style ellipsoid) and its 3 shape parameters are non-zero, then its mass is set from the density and particle volume (the input density is assumed to be in mass/distance^3 units). The density/disc keyword has no effect; it does not (yet) treat 3d ellipsoids as 2d ellipses.

If the atom has a length attribute (see atom_style line) and its length is non-zero, then its mass is set from the density and line segment length (the input density is assumed to be in mass/distance units). If the atom has an area attribute (see atom_style tri) and its area is non-zero, then its mass is set from the density and triangle area (the input density is assumed to be in mass/distance^2 units).

If none of these cases are valid, then the mass is set to the density value directly (the input density is assumed to be in mass units).

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. These keywords do not allow use of an atom-style variable.

Keywords meso/e, meso/cv, and meso/rho set the energy, heat capacity, and density of smoothed particle hydrodynamics (SPH) particles. See this PDF guide to using SPH in LAMMPS.

Keyword smd/mass/density sets the mass of all selected particles, but it is only applicable to the Smooth Mach Dynamics package USER-SMD. It assumes that the particle volume has already been correctly set and calculates particle mass from the provided mass density value.

Keyword smd/contact/radius only applies to simulations with the Smooth Mach Dynamics package USER-SMD. Itsets an interaction radius for computing short-range interactions, e.g. repulsive forces to prevent different individual physical bodies from penetrating each other. Note that the SPH smoothing kernel diameter used for computing long range, nonlocal interactions, is set using the diameter keyword.

Keyword dpd/theta sets the internal temperature of a DPD particle as defined by the USER-DPD package. If the specified value is a number it must be >= 0.0. If the specified value is NULL, then the kinetic temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 m v^2 = 1/2 m (vx*vx+vy*vy+vz*vz). Each particle’s internal temperature is set to Tkin. If the specified value is an atom-style variable, then the variable is evaluated for each particle. If a value >= 0.0, the internal temperature is set to that value. If it is < 0.0, the computation of Tkin is performed and the internal temperature is set to that value.

Keywords edpd/temp and edpd/cv set the temperature and volumetric heat capacity of an eDPD particle as defined by the USER-MESO package. Currently, only atom_style edpd defines particles with these attributes. The values for the temperature and heat capacity must be positive.

Keyword cc sets the chemical concentration of a tDPD particle for a specified species as defined by the USER-MESO package. Currently, only atom_style tdpd defines particles with this attribute. An integer for “index” selects a chemical species (1 to Nspecies) where Nspecies is set by the atom_style command. The value for the chemical concentration must be >= 0.0.

Keywords i_name and d_name refer to custom integer and floating-point properties that have been added to each atom via the fix property/atom command. When that command is used specific names are given to each attribute which are what is specified as the “name” portion of i_name or d_name.

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.