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< title > atom_style command — LAMMPS documentation< / title >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_start.html" > 2. Getting Started< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_commands.html" > 3. Commands< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_packages.html" > 4. Packages< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_accelerate.html" > 5. Accelerating LAMMPS performance< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_howto.html" > 6. How-to discussions< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_perf.html" > 8. Performance & scalability< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_tools.html" > 9. Additional tools< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
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< li > atom_style command< / li >
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< a href = "http://lammps.sandia.gov" > Website< / a >
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< span id = "index-0" > < / span > < h1 > atom_style command< a class = "headerlink" href = "#atom-style-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > atom_style style args
< / pre > < / div >
< / div >
< ul class = "simple" >
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< li > style = < em > angle< / em > or < em > atomic< / em > or < em > body< / em > or < em > bond< / em > or < em > charge< / em > or < em > dipole< / em > or < em > electron< / em > or < em > ellipsoid< / em > or < em > full< / em > or < em > line< / em > or < em > meso< / em > or < em > molecular< / em > or < em > peri< / em > or < em > smd< / em > or < em > sphere< / em > or < em > tri< / em > or < em > template< / em > or < em > hybrid< / em > < / li >
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< / ul >
< pre class = "literal-block" >
args = none for any style except < em > body< / em > and < em > hybrid< / em >
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< em > body< / em > args = bstyle bstyle-args
bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle
see the < a class = "reference internal" href = "body.html" > < em > body< / em > < / a > doc page for details
< em > template< / em > args = template-ID
template-ID = ID of molecule template specified in a separate < a class = "reference internal" href = "molecule.html" > < em > molecule< / em > < / a > command
< em > hybrid< / em > args = list of one or more sub-styles, each with their args
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< / pre >
< ul class = "simple" >
< li > accelerated styles (with same args) = < em > angle/cuda< / em > or < em > angle/kk< / em > or < em > atomic/cuda< / em > or < em > atomic/kk< / em > or < em > bond/kk< / em > or < em > charge/cuda< / em > or < em > charge/kk< / em > or < em > full/cuda< / em > or < em > full/kk< / em > or < em > molecular/kk< / em > < / li >
< / ul >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > atom_style atomic
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atom_style bond
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atom_style full
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atom_style full/cuda
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atom_style body nparticle 2 10
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atom_style hybrid charge bond
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atom_style hybrid charge body nparticle 2 5
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atom_style template myMols
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Define what style of atoms to use in a simulation. This determines
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what attributes are associated with the atoms. This command must be
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used before a simulation is setup via a < a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > ,
< a class = "reference internal" href = "read_restart.html" > < em > read_restart< / em > < / a > , or < a class = "reference internal" href = "create_box.html" > < em > create_box< / em > < / a >
command.< / p >
< p > Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style < em > bond< / em > , angular
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terms cannot be used or added later to the model. It is OK to use a
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style more general than needed, though it may be slightly inefficient.< / p >
< p > The choice of style affects what quantities are stored by each atom,
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what quantities are communicated between processors to enable forces
to be computed, and what quantities are listed in the data file read
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by the < a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > command.< / p >
< p > These are the additional attributes of each style and the typical
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kinds of physical systems they are used to model. All styles store
coordinates, velocities, atom IDs and types. See the
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< a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > , < a class = "reference internal" href = "create_atoms.html" > < em > create_atoms< / em > < / a > , and
< a class = "reference internal" href = "set.html" > < em > set< / em > < / a > commands for info on how to set these various
quantities.< / p >
< table border = "1" class = "docutils" >
< colgroup >
< col width = "13%" / >
< col width = "50%" / >
< col width = "36%" / >
< / colgroup >
< tbody valign = "top" >
< tr class = "row-odd" > < td > < em > angle< / em > < / td >
< td > bonds and angles< / td >
< td > bead-spring polymers with stiffness< / td >
< / tr >
< tr class = "row-even" > < td > < em > atomic< / em > < / td >
< td > only the default values< / td >
< td > coarse-grain liquids, solids, metals< / td >
< / tr >
< tr class = "row-odd" > < td > < em > body< / em > < / td >
< td > mass, inertia moments, quaternion, angular momentum< / td >
< td > arbitrary bodies< / td >
< / tr >
< tr class = "row-even" > < td > < em > bond< / em > < / td >
< td > bonds< / td >
< td > bead-spring polymers< / td >
< / tr >
< tr class = "row-odd" > < td > < em > charge< / em > < / td >
< td > charge< / td >
< td > atomic system with charges< / td >
< / tr >
< tr class = "row-even" > < td > < em > dipole< / em > < / td >
< td > charge and dipole moment< / td >
< td > system with dipolar particles< / td >
< / tr >
< tr class = "row-odd" > < td > < em > electron< / em > < / td >
< td > charge and spin and eradius< / td >
< td > electronic force field< / td >
< / tr >
< tr class = "row-even" > < td > < em > ellipsoid< / em > < / td >
< td > shape, quaternion, angular momentum< / td >
< td > aspherical particles< / td >
< / tr >
< tr class = "row-odd" > < td > < em > full< / em > < / td >
< td > molecular + charge< / td >
< td > bio-molecules< / td >
< / tr >
< tr class = "row-even" > < td > < em > line< / em > < / td >
< td > end points, angular velocity< / td >
< td > rigid bodies< / td >
< / tr >
< tr class = "row-odd" > < td > < em > meso< / em > < / td >
< td > rho, e, cv< / td >
< td > SPH particles< / td >
< / tr >
< tr class = "row-even" > < td > < em > molecular< / em > < / td >
< td > bonds, angles, dihedrals, impropers< / td >
< td > uncharged molecules< / td >
< / tr >
< tr class = "row-odd" > < td > < em > peri< / em > < / td >
< td > mass, volume< / td >
< td > mesocopic Peridynamic models< / td >
< / tr >
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< tr class = "row-even" > < td > < em > smd< / em > < / td >
< td > volume, kernel diameter, contact radius, mass< / td >
< td > solid and fluid SPH particles< / td >
< / tr >
< tr class = "row-odd" > < td > < em > sphere< / em > < / td >
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< td > diameter, mass, angular velocity< / td >
< td > granular models< / td >
< / tr >
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< tr class = "row-even" > < td > < em > template< / em > < / td >
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< td > template index, template atom< / td >
< td > small molecules with fixed topology< / td >
< / tr >
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< tr class = "row-odd" > < td > < em > tri< / em > < / td >
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< td > corner points, angular momentum< / td >
< td > rigid bodies< / td >
< / tr >
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< tr class = "row-even" > < td > < em > wavepacket< / em > < / td >
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< td > charge, spin, eradius, etag, cs_re, cs_im< / td >
< td > AWPMD< / td >
< / tr >
< / tbody >
< / table >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the < a class = "reference internal" href = "fix_property_atom.html" > < em > fix property/atom< / em > < / a > command. This command also
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allows new custom attributes consisting of extra integer or
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floating-point values to be added to atoms. See the < a class = "reference internal" href = "fix_property_atom.html" > < em > fix property/atom< / em > < / a > doc page for examples of cases
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where this is useful and details on how to initialize, access, and
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output the custom values.< / p >
< / div >
< p > All of the above styles define point particles, except the < em > sphere< / em > ,
< em > ellipsoid< / em > , < em > electron< / em > , < em > peri< / em > , < em > wavepacket< / em > , < em > line< / em > , < em > tri< / em > , and
< em > body< / em > styles, which define finite-size particles. See < a class = "reference internal" href = "Section_howto.html#howto-14" > < span > Section_howto 14< / span > < / a > for an overview of using finite-size
particle models with LAMMPS.< / p >
< p > All of the point-particle styles assign mass to particles on a
per-type basis, using the < a class = "reference internal" href = "mass.html" > < em > mass< / em > < / a > command, The finite-size
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particle styles assign mass to individual particles on a per-particle
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basis.< / p >
< p > For the < em > sphere< / em > style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
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is a finite-size sphere. If the diameter = 0.0, it is a point
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particle.< / p >
< p > For the < em > ellipsoid< / em > style, the particles are ellipsoids and each
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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
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with its orientation.< / p >
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< p > For the < em > dipole< / em > 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.< / p >
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< p > For the < em > electron< / em > style, the particles representing electrons are 3d
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Gaussians with a specified position and bandwidth or uncertainty in
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position, which is represented by the eradius = electron size.< / p >
< p > For the < em > peri< / em > style, the particles are spherical and each stores a
per-particle mass and volume.< / p >
< p > The < em > meso< / em > style is for smoothed particle hydrodynamics (SPH)
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particles which store a density (rho), energy (e), and heat capacity
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(cv).< / p >
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< p > The < em > smd< / em > 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 penetretating each other.< / p >
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< p > The < em > wavepacket< / em > style is similar to < em > electron< / em > , but the electrons may
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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
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have identical < em > etag< / em > values.< / p >
< p > For the < em > line< / em > style, the particles are idealized line segments and
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each stores a per-particle mass and length and orientation (i.e. the
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end points of the line segment).< / p >
< p > For the < em > tri< / em > style, the particles are planar triangles and each
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stores a per-particle mass and size and orientation (i.e. the corner
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points of the triangle).< / p >
< p > The < em > template< / em > style allows molecular topolgy (bonds,angles,etc) to be
defined via a molecule template using the < a class = "reference external" href = "molecule.txt" > molecule< / a >
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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
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< em > template< / em > style instead of the < em > bond< / em > , < em > angle< / em > , < em > molecular< / em > styles
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can save memory for systems comprised of a large number of small
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molecules, all of a single type (or small number of types). See the
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paper by Grime and Voth, in < a class = "reference internal" href = "#grime" > < span > (Grime)< / span > < / a > , for examples of how this
can be advantageous for large-scale coarse-grained systems.< / p >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
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< p class = "last" > When using the < em > template< / em > style with a < a class = "reference internal" href = "molecule.html" > < em > molecule template< / em > < / a > that contains multiple molecules, you should
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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
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defined, e.g. by the < a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > command. Rather the
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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
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2 if a single oxygen type is desired), and bond type 2.< / p >
< / div >
< p > For the < em > body< / em > style, the particles are arbitrary bodies with internal
attributes defined by the “ style” of the bodies, which is specified by
the < em > bstyle< / em > argument. Body particles can represent complex entities,
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such as surface meshes of discrete points, collections of
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sub-particles, deformable objects, etc.< / p >
< p > The < a class = "reference internal" href = "body.html" > < em > body< / em > < / a > doc page descibes the body styles LAMMPS
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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
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and position can be time integrated due to forces and torques.< / p >
< p > Note that there may be additional arguments required along with the
< em > bstyle< / em > specification, in the atom_style body command. These
arguments are described in the < a class = "reference internal" href = "body.html" > < em > body< / em > < / a > doc page.< / p >
< hr class = "docutils" / >
< p > Typically, simulations require only a single (non-hybrid) atom style.
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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
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simulation are charged, but others are not, use the < em > charge< / em > style.
If some atoms have bonds, but others do not, use the < em > bond< / em > style.< / p >
< p > The only scenario where the < em > hybrid< / em > style is needed is if there is no
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single style which defines all needed properties of all atoms. For
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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.< / p >
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< p > When using the < em > hybrid< / em > style, you cannot combine the < em > template< / em > style
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with another molecular style that stores bond,angle,etc info on a
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per-atom basis.< / p >
< p > LAMMPS can be extended with new atom styles as well as new body
styles; see < a class = "reference internal" href = "Section_modify.html" > < em > this section< / em > < / a > .< / p >
< hr class = "docutils" / >
< p > Styles with a < em > cuda< / em > or < em > kk< / em > suffix are functionally the same as the
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corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
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< a class = "reference internal" href = "Section_accelerate.html" > < em > Section_accelerate< / em > < / a > of the manual. The
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accelerated styles take the same arguments and should produce the same
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results, except for round-off and precision issues.< / p >
< p > Note that other acceleration packages in LAMMPS, specifically the GPU,
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USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
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styles.< / p >
< p > The accelerated styles are part of the USER-CUDA and KOKKOS packages
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respectively. They are only enabled if LAMMPS was built with those
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packages. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section
for more info.< / p >
< p > You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the < a class = "reference internal" href = "Section_start.html#start-7" > < span > -suffix command-line switch< / span > < / a > when you invoke LAMMPS, or you can
use the < a class = "reference internal" href = "suffix.html" > < em > suffix< / em > < / a > command in your input script.< / p >
< p > See < a class = "reference internal" href = "Section_accelerate.html" > < em > Section_accelerate< / em > < / a > of the manual for
more instructions on how to use the accelerated styles effectively.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This command cannot be used after the simulation box is defined by a
< a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > or < a class = "reference internal" href = "create_box.html" > < em > create_box< / em > < / a > command.< / p >
< p > The < em > angle< / em > , < em > bond< / em > , < em > full< / em > , < em > molecular< / em > , and < em > template< / em > styles are
part of the MOLECULE package. The < em > line< / em > and < em > tri< / em > styles are part
of the ASPHERE pacakge. The < em > body< / em > style is part of the BODY package.
The < em > dipole< / em > style is part of the DIPOLE package. The < em > peri< / em > style is
part of the PERI package for Peridynamics. The < em > electron< / em > style is
part of the USER-EFF package for < a class = "reference internal" href = "pair_eff.html" > < em > electronic force fields< / em > < / a > . The < em > meso< / em > style is part of the USER-SPH
package for smoothed particle hydrodyanmics (SPH). See < a class = "reference external" href = "USER/sph/SPH_LAMMPS_userguide.pdf" > this PDF guide< / a > to using SPH in LAMMPS. The
< em > wavepacket< / em > style is part of the USER-AWPMD package for the
< a class = "reference internal" href = "pair_awpmd.html" > < em > antisymmetrized wave packet MD method< / em > < / a > . They are
only enabled if LAMMPS was built with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > , < a class = "reference internal" href = "pair_style.html" > < em > pair_style< / em > < / a > < / p >
< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > atom_style atomic< / p >
< hr class = "docutils" / >
< p id = "grime" > < strong > (Grime)< / strong > Grime and Voth, to appear in J Chem Theory & Computation
(2014).< / p >
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