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.
angle atomic body bond charge dipole electron ellipsoid full line meso molecular peri sphere template tri wavepacket bonds and angles only the default values mass, inertia moments, quaternion, angular momentum bonds charge charge and dipole moment charge and spin and eradius shape, quaternion, angular momentum molecular + charge end points, angular velocity rho, e, cv bonds, angles, dihedrals, impropers mass, volume diameter, mass, angular velocity template index, template atom corner points, angular momentum charge, spin, eradius, etag, cs_re, cs_im bead-spring polymers with stiffness coarse-grain liquids, solids, metals arbitrary bodies bead-spring polymers atomic system with charges system with dipolar particles electronic force field aspherical particles bio-molecules rigid bodies SPH particles uncharged molecules mesocopic Peridynamic models granular models small molecules with fixed topology rigid bodies AWPMD IMPORTANT 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_howto 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.
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 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 meso style is for smoothed particle hydrodynamics (SPH) particles which store a density (rho), energy (e), and heat capacity (cv).
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 topolgy (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 thetemplate 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.
IMPORTANT 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 \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 descibes 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 thebond 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 \hybrid sphere dipole\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.
Restrictions:
This command cannot be used after the simulation box is defined by a read_data or create_box command.
The angle, bond, full, molecular, and template styles are part of the MOLECULAR package. The line and tri styles are part of the ASPHERE pacakge. The body style is part of the BODY package. Thedipole 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 mesostyle is part of the USER-SPH package for smoothed particle hydrodyanmics (SPH). See this PDF guide to using SPH in LAMMPS. The wavepacket style is part of the USER-AWPMD package for
theantisymmetrized wave packet MD method. They are only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info. Related commands: read_data, pair_style Default:
atom_style atomic
(Grime) Grime and Voth, to appear in J Chem Theory & Computation (2014).
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boundary command Syntax: boundary x y z
x,y,z = p or s or f or m, one or two letters ? p is periodic
? f is non-periodic and fixed
? s is non-periodic and shrink-wrapped
? m is non-periodic and shrink-wrapped with a minimum value Examples:
?
boundary p p f boundary p fs p boundary s f fm Description:
Set the style of boundaries for the global simulation box in each dimension. A single letter assigns the same style to both the lower and upper face of the box. Two letters assigns the first style to the lower face and the second style to the upper face. The initial size of the simulation box is set by the read_data, read_restart, or create_box commands.
The style p means the box is periodic, so that particles interact across the boundary, and they can exit one end of the box and re-enter the other end. A periodic dimension can change in size due to constant pressure boundary conditions or box deformation (see the fix npt and fix deform commands). The p style must be applied to both faces of a dimension. The styles f, s, and m mean the box is non-periodic, so that particles do not interact across the boundary and do not
move from one side of the box to the other. For style f, the position of the face is fixed. If an atom moves outside the face it may be lost. For style s, the position of the face is set so as to encompass the atoms in that dimension (shrink-wrapping), no matter how far they move. For style m, shrink-wrapping occurs, but is bounded by the value specified in the data or restart file or set by the create_box command. For example, if the upper z face has a value of 50.0 in the data
file, the face will always be positioned at 50.0 or above, even if the maximum z-extent of all the atoms becomes less than 50.0.
For triclinic (non-orthogonal) simulation boxes, if the 2nd dimension of a tilt factor (e.g. y for xy) is periodic, then the periodicity is enforced with the tilt factor offset. If the 1st dimension is shrink-wrapped, then the shrink wrapping is applied to the tilted box face, to encompass the atoms. E.g. for a positive xy tilt, the xlo and xhi faces of the box are planes tilting in the +y direction as y increases. These tilted planes are shrink-wrapped around the atoms to determine the x extent of the box.
See Section_howto 12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. Restrictions:
This command cannot be used after the simulation box is defined by a read_data or create_box command or read_restart command. See the change_box command for how to change the simulation box boundaries after it has been defined. For 2d simulations, the z dimension must be periodic. Related commands:
See the thermo_modify command for a discussion of lost atoms. Default: boundary p p p
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neighbor command Syntax:
neighbor skin style
skin = extra distance beyond force cutoff (distance units) ? style = bin or nsq or multi Examples:
?
neighbor 0.3 bin neighbor 2.0 nsq Description:
This command sets parameters that affect the building of pairwise neighbor lists. All atom pairs within a neighbor cutoff distance equal to the their force cutoff plus the skin distance are stored in the list. Typically, the larger the skin distance, the less often neighbor lists need to be built, but more pairs must be checked for possible force interactions every timestep. The default value for skin depends on the choice of units for the simulation; see the default values below. The skin distance is also used to determine how often atoms migrate to new processors if the check option of the
neigh_modify command is set to yes. Atoms are migrated (communicated) to new processors on the same timestep that neighbor lists are re-built.
The style value selects what algorithm is used to build the list. The bin style creates the list by binning which is an operation that scales linearly with N/P, the number of atoms per processor where N = total number of atoms and P = number of processors. It is almost always faster than the nsq style which scales as (N/P)^2. For unsolvated small molecules in a non-periodic box, the nsq choice can sometimes be faster. Either style should give the same answers.
The multi style is a modified binning algorithm that is useful for systems with a wide range of cutoff distances, e.g. due to different size particles. For the bin style, the bin size is set to 1/2 of the largest cutoff distance between any pair of atom types and a single set of bins is defined to search over for all atom types. This can be inefficient if one pair of types has a very long cutoff, but other type pairs have a much shorter cutoff. For style multi the bin size is set to 1/2 of the shortest cutoff distance and multiple sets of bins are defined to search over for different atom types. This imposes some extra setup overhead, but the searches themselves may be much faster for the short-cutoff cases. See the communicate multi command for a communication option option that may also be beneficial for simulations of this kind.
The neigh_modify command has additional options that control how often neighbor lists are built and which pairs are stored in the list.
When a run is finished, counts of the number of neighbors stored in the pairwise list and the number of times neighbor lists were built are printed to the screen and log file. See this section for details. Restrictions: none Related commands:
neigh_modify, units, communicate Default:
0.3 bin for units = lj, skin = 0.3 sigma
2.0 bin for units = real or metal, skin = 2.0 Angstroms 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm
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lattice command Syntax:
lattice style scale keyword values ...
style = none or sc or bcc or fcc or hcp or diamond or sq or sq2 or hex or custom ? scale = scale factor between lattice and simulation box ? scale = reduced density rho* (for LJ units)
? scale = lattice constant in distance units (for all other units) ? zero or more keyword/value pairs may be appended
? keyword = origin or orient or spacing or a1 or a2 or a3 or basis ? origin values = x y z
? x,y,z = fractions of a unit cell (0 <= x,y,z < 1) ? orient values = dim i j k ? dim = x or y or z
? i,j,k = integer lattice directions ? spacing values = dx dy dz
? dx,dy,dz = lattice spacings in the x,y,z box directions ? a1,a2,a3 values = x y z
? x,y,z = primitive vector components that define unit cell ? basis values = x y z
? x,y,z = fractional coords of a basis atom (0 <= x,y,z < 1) Examples:
?
lattice fcc 3.52