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 electron or ellipsoid or full or line or mdpd or molecular or oxdna or peri or smd or sph or sphere or spin or tdpd 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 Howto body doc
                    page for details
    sphere arg = 0/1 (optional) for static/dynamic particle radii
    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 or spin/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 spin
atom_style template myMols
atom_style hybrid template twomols charge
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
dielectric	dipole, area, curvature	system with surface polarization
dipole	charge and dipole moment	system with dipolar particles
dpd	internal temperature and internal energies	DPD particles
edpd	temperature and heat capacity	eDPD 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
mdpd	density	mDPD particles
mesont	mass, radius, length, buckling, connections, tube id	mesoscopic nanotubes
molecular	bonds, angles, dihedrals, impropers	uncharged molecules
oxdna	nucleotide polarity	coarse-grained DNA and RNA models
peri	mass, volume	mesoscopic Peridynamic models
smd	volume, kernel diameter, contact radius, mass	solid and fluid SPH particles
sph	rho, esph, cv	SPH particles
sphere	diameter, mass, angular velocity	granular models
spin	magnetic moment	system with magnetic particles
tdpd	chemical concentration	tDPD particles
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 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 the Howto spherical page 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. The sphere style takes an optional 0 or 1 argument. A value of 0 means the radius of each sphere is constant for the duration of the simulation. A value of 1 means the radii may vary dynamically during the simulation, e.g. due to use of the fix adapt 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 dielectric style, each particle can be either a physical particle (e.g. an ion), or an interface particle representing a boundary element. For physical particles, the per-particle properties are the same as atom_style full. For interface particles, in addition to these properties, each particle also has an area, a normal unit vector, a mean local curvature, the mean and difference of the dielectric constants of two sides of the interface, and the local dielectric constant at the boundary element. The distinction between the physical and interface particles is only meaningful when fix polarize commands are applied to the interface particles.

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 oxdna style is for coarse-grained nucleotides and stores the 3’-to-5’ polarity of the nucleotide strand, which is set through the bond topology in the data file. The first (second) atom in a bond definition is understood to point towards the 3’-end (5’-end) of the strand. Note that this style is part of the CG-DNA package.

The dpd style is for dissipative particle dynamics (DPD) particles. Note that it is part of the DPD-REACT 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 sph style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (esph), 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.

For the spin style, a magnetic spin is associated to each atom. Those spins have a norm (their magnetic moment) and a direction.

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. The examples/template directory has a few demo inputs and examples showing the use of the template atom style versus molecular.

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 Howto body 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 on the Howto body doc page.

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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 the Modify doc page.

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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 on the Speed packages doc page. 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, INTEL, OPENMP, 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 Build package page 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 the Speed packages page 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 Build package page 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 oxdna style is part of the CG-DNA package for coarse-grained simulation of DNA and RNA.

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

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

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

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

The mesont style is part of the MESONT package.

The spin style is part of the SPIN package.

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

Related commands

read_data, pair_style

Default

The default atom style is atomic. If atom_style sphere is used its default argument is 0.

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