atom_style command

Syntax

atom_style style args
  • style = bond or charge or ellipsoid or full or line or molecular or tri or hybrid or sphere or granular or bond/gran or superquadric or convexhull or sph
args = none for any style except body and hybrid
body args = bstyle bstyle-args
  bstyle = style of body particles
  bstyle-args = additional arguments specific to the bstyle
                see the body doc page for details
hybrid args = list of one or more sub-styles, each with their args

Examples

atom_style bond
atom_style sphere
atom_style superquadric (not available yet in the PUBLIC version)
atom_style hybrid sphere bond

Description

Define what style of atoms to use in a simulation. This determines what attributes are associated with the atoms. This command must be used before a simulation is setup via a read_data, read_restart, or create_box command.

Once a style is assigned, it cannot be changed, so use a style general enough to encompass all attributes. E.g. with style bond, angular terms cannot be used or added later to the model. It is OK to use a style more general than needed, though it may be slightly inefficient.

The choice of style affects what quantities are stored by each atom, what quantities are communicated between processors to enable forces to be computed, and what quantities are listed in the data file read by the read_data command.

These are the additional attributes of each style and the typical kinds of physical systems they are used to model. All styles store coordinates, velocities, atom IDs and types. See the read_data, create_atoms, and set commands for info on how to set these various quantities.

bond bonds bead-spring polymers
bond/gran number of bonds and bond information granular bond models
charge charge atomic system with charges
convexhull mass, angular velocity, quaternion granular models
ellipsoid shape, quaternion, angular momentum aspherical particles
line end points, angular velocity rigid bodies
molecular bonds, angles, dihedrals, impropers uncharged molecules
sph q(pressure), density SPH particles
sphere or granular diameter, mass, angular velocity granular models
superquadric semi-axes, blockiness parameters, mass, angular velocity, quaternion granular models
tri corner points, angular momentum rigid bodies AWPMD

Warning

It is possible to add some attributes, such as a molecule ID, to atom styles that do not have them via the fix property/atom command. This command also allows new custom attributes consisting of extra integer or floating-point values to be added to atoms. See the fix property/atom doc page for examples of cases where this is useful and details on how to initialize, access, and output the custom values.

All of the styles assign mass to particles on a per-type basis, using the mass command, except for sphere or granular styles. They assign mass to individual particles on a per-particle basis.

For the sphere style, the particles are spheres and each stores a per-particle diameter and mass. If the diameter > 0.0, the particle is a finite-size sphere. If the diameter = 0.0, it is a point particle. This is typically used for granular models. Instead of sphere, keyword granular can be used.

For the bond/gran style, the number of granular bonds per atom is stored, and the information associated to it: the type of each bond, the ID of the bonded partner atom and the so-called bond history. The bond history is similar to the contact history for granular interaction, it stores the internal state of the bond. What exactly is stored in this internal state is defined by the granular bond style used. There are 2 parameters: The number of bond types, and the maximum number of bonds that each atom can have. For each bond type, the parameters have to be specified via the bond_coeff command (see example here ) Note that bond/gran is an experimental code which is may not be available in your release of LIGGGHTS. An example for the sytnax is given below:

atom_style bond/gran n_bondtypes 1 bonds_per_atom 6

For the ellipsoid style, the particles are ellipsoids and each stores a flag which indicates whether it is a finite-size ellipsoid or a point particle. If it is an ellipsoid, it also stores a shape vector with the 3 diamters of the ellipsoid and a quaternion 4-vector with its orientation.

For the line style, the particles are idealized line segments and each stores a per-particle mass and length and orientation (i.e. the end points of the line segment).

For the tri style, the particles are planar triangles and each stores a per-particle mass and size and orientation (i.e. the corner points of the triangle).

Typically, simulations require only a single (non-hybrid) atom style. If some atoms in the simulation do not have all the properties defined by a particular style, use the simplest style that defines all the needed properties by any atom. For example, if some atoms in a simulation are charged, but others are not, use the charge style. If some atoms have bonds, but others do not, use the bond style.

The only scenario where the hybrid style is needed is if there is no single style which defines all needed properties of all atoms. For example, if you want dipolar particles which will rotate due to torque, you would need to use “atom_style hybrid sphere dipole”. When a hybrid style is used, atoms store and communicate the union of all quantities implied by the individual styles.

LIGGGHTS(R)-PUBLIC can be extended with new atom styles as well as new body styles; see this section.

Restrictions

This command cannot be used after the simulation box is defined by a read_data or create_box command.

The superquadric style is not yet available in the PUBLIC version The convexhull style is not yet available in the PUBLIC version

The bond, molecular styles are part of the MOLECULAR package. The line and tri styles are part of the ASPHERE package. They are only enabled if LIGGGHTS(R)-PUBLIC was built with that package. See the Making LIGGGHTS(R)-PUBLIC section for more info.