atom_style command

Syntax

atom_style style args

• style = angle or atomic or body or bond or charge or dipole or dpd or edpd or mdpd or tdpd or electron or ellipsoid or full or line or meso or molecular or peri or smd or sphere or tri or template or hybrid

args = none for any style except the following
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
tdpd arg = Nspecies
Nspecies = # of chemical species
template arg = template-ID
template-ID = ID of molecule template specified in a separate molecule command
hybrid args = list of one or more sub-styles, each with their args

• accelerated styles (with same args) = angle/kk or atomic/kk or bond/kk or charge/kk or full/kk or molecular/kk

Examples

atom_style atomic
atom_style bond
atom_style full
atom_style body nparticle 2 10
atom_style hybrid charge bond
atom_style hybrid charge body nparticle 2 5
atom_style template myMols
atom_style tdpd 2


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.

Note

Many of the atom styles discussed here are only enabled if LAMMPS was built with a specific package, as listed below in the Restrictions section.

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.

 angle bonds and angles bead-spring polymers with stiffness atomic only the default values coarse-grain liquids, solids, metals body mass, inertia moments, quaternion, angular momentum arbitrary bodies bond bonds bead-spring polymers charge charge atomic system with charges dipole charge and dipole moment system with dipolar particles dpd internal temperature and internal energies DPD particles edpd temperature and heat capacity eDPD particles mdpd density mDPD particles tdpd chemical concentration tDPD particles electron charge and spin and eradius electronic force field ellipsoid shape, quaternion, angular momentum aspherical particles full molecular + charge bio-molecules line end points, angular velocity rigid bodies meso rho, e, cv SPH particles molecular bonds, angles, dihedrals, impropers uncharged molecules peri mass, volume mesocopic Peridynamic models smd volume, kernel diameter, contact radius, mass solid and fluid SPH particles sphere diameter, mass, angular velocity granular models template template index, template atom small molecules with fixed topology tri corner points, angular momentum rigid bodies wavepacket charge, spin, eradius, etag, cs_re, cs_im AWPMD

Note

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 above styles define point particles, except the sphere, ellipsoid, electron, peri, wavepacket, line, tri, and body styles, which define finite-size particles. See Section 6.14 for an overview of using finite-size particle models with LAMMPS.

All of the point-particle styles assign mass to particles on a per-type basis, using the mass command, The finite-size particle styles 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. Note that by use of the disc keyword with the fix nve/sphere, fix nvt/sphere, fix nph/sphere, fix npt/sphere commands, spheres can be effectively treated as 2d discs for a 2d simulation if desired. See also the set density/disc command.

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 diameters of the ellipsoid and a quaternion 4-vector with its orientation.

For the dipole style, a point dipole is defined for each point particle. Note that if you wish the particles to be finite-size spheres as in a Stockmayer potential for a dipolar fluid, so that the particles can rotate due to dipole-dipole interactions, then you need to use atom_style hybrid sphere dipole, which will assign both a diameter and dipole moment to each particle.

For the electron style, the particles representing electrons are 3d Gaussians with a specified position and bandwidth or uncertainty in position, which is represented by the eradius = electron size.

For the peri style, the particles are spherical and each stores a per-particle mass and volume.

The dpd style is for dissipative particle dynamics (DPD) particles. Note that it is part of the USER-DPD package, and is not for use with the pair_style dpd or dpd/stat commands, which can simply use atom_style atomic. Atom_style dpd extends DPD particle properties with internal temperature (dpdTheta), internal conductive energy (uCond), internal mechanical energy (uMech), and internal chemical energy (uChem).

The edpd style is for energy-conserving dissipative particle dynamics (eDPD) particles which store a temperature (edpd_temp), and heat capacity(edpd_cv).

The mdpd style is for many-body dissipative particle dynamics (mDPD) particles which store a density (rho) for considering density-dependent many-body interactions.

The tdpd style is for transport dissipative particle dynamics (tDPD) particles which store a set of chemical concentration. An integer “cc_species” is required to specify the number of chemical species involved in a tDPD system.

The meso style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity (cv).

The smd style is for a general formulation of Smooth Particle Hydrodynamics. Both fluids and solids can be modeled. Particles store the mass and volume of an integration point, a kernel diameter used for calculating the field variables (e.g. stress and deformation) and a contact radius for calculating repulsive forces which prevent individual physical bodies from penetrating each other.

The wavepacket style is similar to electron, but the electrons may consist of several Gaussian wave packets, summed up with coefficients cs= (cs_re,cs_im). Each of the wave packets is treated as a separate particle in LAMMPS, wave packets belonging to the same electron must have identical etag values.

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).

The template style allows molecular topology (bonds,angles,etc) to be defined via a molecule template using the molecule command. The template stores one or more molecules with a single copy of the topology info (bonds,angles,etc) of each. Individual atoms only store a template index and template atom to identify which molecule and which atom-within-the-molecule they represent. Using the template style instead of the bond, angle, molecular styles can save memory for systems comprised of a large number of small molecules, all of a single type (or small number of types). See the paper by Grime and Voth, in (Grime), for examples of how this can be advantageous for large-scale coarse-grained systems.

Note

When using the template style with a molecule template that contains multiple molecules, you should insure the atom types, bond types, angle_types, etc in all the molecules are consistent. E.g. if one molecule represents H2O and another CO2, then you probably do not want each molecule file to define 2 atom types and a single bond type, because they will conflict with each other when a mixture system of H2O and CO2 molecules is defined, e.g. by the read_data command. Rather the H2O molecule should define atom types 1 and 2, and bond type 1. And the CO2 molecule should define atom types 3 and 4 (or atom types 3 and 2 if a single oxygen type is desired), and bond type 2.

For the body style, the particles are arbitrary bodies with internal attributes defined by the “style” of the bodies, which is specified by the bstyle argument. Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc.

The body doc page describes the body styles LAMMPS currently supports, and provides more details as to the kind of body particles they represent. For all styles, each body particle stores moments of inertia and a quaternion 4-vector, so that its orientation and position can be time integrated due to forces and torques.

Note that there may be additional arguments required along with the bstyle specification, in the atom_style body command. These arguments are described in the body doc page.

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, as mentioned above, if you want dipolar particles which will rotate due to torque, you 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.

When using the hybrid style, you cannot combine the template style with another molecular style that stores bond,angle,etc info on a per-atom basis.

LAMMPS can be extended with new atom styles as well as new body styles; see this section.

Styles with a kk suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in Section 5 of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

Note that other acceleration packages in LAMMPS, specifically the GPU, USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom styles.

The accelerated styles are part of the KOKKOS package. They are only enabled if LAMMPS was built with those packages. See the Making LAMMPS section for more info.

You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

See Section 5 of the manual for more instructions on how to use the accelerated styles effectively.

Restrictions

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

Many of the styles listed above are only enabled if LAMMPS was built with a specific package, as listed below. See the Making LAMMPS section for more info.

The angle, bond, full, molecular, and template styles are part of the MOLECULE package.

The line and tri styles are part of the ASPHERE package.

The body style is part of the BODY package.

The dipole style is part of the DIPOLE package.

The peri style is part of the PERI package for Peridynamics.

The electron style is part of the USER-EFF package for electronic force fields.

The dpd style is part of the USER-DPD package for dissipative particle dynamics (DPD).

The edpd, mdpd, and tdpd styles are part of the USER-MESO package for energy-conserving dissipative particle dynamics (eDPD), many-body dissipative particle dynamics (mDPD), and transport dissipative particle dynamics (tDPD), respectively.

The meso style is part of the USER-SPH package for smoothed particle hydrodynamics (SPH). See this PDF guide to using SPH in LAMMPS.

The wavepacket style is part of the USER-AWPMD package for the antisymmetrized wave packet MD method.

Default

atom_style atomic

(Grime) Grime and Voth, to appear in J Chem Theory & Computation (2014).