The remap keyword only applies to the single style. If it is set to yes, then if the specified position is outside the simulation box, it will mapped back into the box, assuming the relevant dimensions are periodic. If it is set to no, no remapping is done and no particle is created if its position is outside the box.
The units keyword determines the meaning of the distance units used to specify the coordinates of the one particle created by the single style. A box value selects standard distance units as defined by the units command, e.g. Angstroms for units = real or metal. A lattice value means the distance units are in lattice spacings.
Atom IDs are assigned to created atoms in the following way. The collection of created atoms are assigned consecutive IDs that start immediately following the largest atom ID existing before the create_atoms command was invoked. When a simulation is performed on different numbers of processors, there is no guarantee a particular created atom will be
assigned the same ID. If molecules are being created, molecule IDs are assigned to created molecules in a similar fashion. Aside from their ID, atom type, and xyz position, other properties of created atoms are set to default values, depending on which quantities are defined by the chosen atom style. See the atom stylecommand for more details. See the set and velocity commands for info on how to change these values.
charge = 0.0
? dipole moment magnitude = 0.0 ? diameter = 1.0 ? shape = 0.0 0.0 0.0 ? density = 1.0 ? volume = 1.0
? velocity = 0.0 0.0 0.0
? angular velocity = 0.0 0.0 0.0 ? angular momentum = 0.0 0.0 0.0 ? quaternion = (1,0,0,0)
? bonds, angles, dihedrals, impropers = none
If molecules are being created, these defaults can be overridden by values specified in the file read by
the molecule command. E.g. the file typically defines bonds (angles,etc) between atoms in the molecule, and can optionally define charges on each atom.
?
Note that the sphere atom style sets the default particle diameter to 1.0 as well as the density. This means the mass for the particle is not 1.0, but is PI/6 * diameter^3 = 0.5236.
Note that the ellipsoid atom style sets the default particle shape to (0.0 0.0 0.0) and the density to 1.0 which means it is a point particle, not an ellipsoid, and has a mass of 1.0.
Note that the peri style sets the default volume and density to 1.0 and thus also set the mass for the particle to 1.0. The set command can be used to override many of these default settings. Restrictions:
An atom_style must be previously defined to use this command. Related commands:
lattice, region, create_box, read_data, read_restart Default:
The default for the basis keyword is that all created atoms are assigned the argument type as their atom type (when single atoms are being created). The other defaults are remap = no and units = lattice.
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
displace_atoms command Syntax:
displace_atoms group-ID style args keyword value ...
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
group-ID = ID of group of atoms to displace style = move or ramp or random or rotate move args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units) ramp args = ddim dlo dhi dim clo chi ddim = x or y or z
dlo,dhi = displacement distance between dlo and dhi (distance units) dim = x or y or z
clo,chi = lower and upper bound of domain to displace (distance units) random args = dx dy dz seed
dx,dy,dz = random displacement magnitude in each dimension (distance units) seed = random # seed (positive integer) rotate args = Px Py Pz Rx Ry Rz theta
Px,Py,Pz = origin point of axis of rotation (distance units) Rx,Ry,Rz = axis of rotation vector theta = angle of rotation (degrees)
zero or more keyword/value pairs may be appended keyword = units
value = box or lattice
Examples:
displace_atoms top move 0 -5 0 units box displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 Description:
Displace a group of atoms. This can be used to move atoms a large distance before beginning a simulation or to
randomize atoms initially on a lattice. For example, in a shear simulation, an initial strain can be imposed on the system. Or two groups of atoms can be brought into closer proximity.
The move style displaces the group of atoms by the specified 3d distance.
The ramp style displaces atoms a variable amount in one dimension depending on the atom's coordinate in a (possibly) different dimension. For example, the second example command displaces atoms in the x-direction an amount between 0.0 and 5.0 distance units. Each atom's displacement depends on the fractional distance its y coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside those bounds will be moved the minimum (0.0) or maximum (5.0) amount. The random style independently moves each atom in the group by a random displacement, uniformly sampled from a value between -dx and +dx in the x dimension, and similarly for y and z. Random numbers are used in such a way that the displacement of a particular atom is the same, regardless of how many processors are being used.
The rotate style rotates each atom in the group by the angle theta around a rotation axis R = (Rx,Ry,Rz) that goes thru a point P = (Px,Py,Pz). The direction of rotation for the atoms around the rotation axis is consistent with the right-hand rule: if your right-hand's thumb points along R, then your fingers wrap around the axis in the direction of positive theta. Distance units for displacements and the origin point of the rotate style are determined by the setting of box or lattice for the units keyword. Box means distance units as defined by the unitscommand - e.g. Angstroms
for real units. Lattice means distance units are in lattice spacings. The lattice command must have been previously used to define the lattice spacing.
IMPORTANT NOTE: Care should be taken not to move atoms on top of other atoms. After the move, atoms are remapped into the periodic simulation box if needed, and any shrink-wrap boundary conditions (see the boundary command) are enforced which may change the box size. Other than this effect, this command does not change the size or shape of the simulation box. See the change_box command if that effect is desired.
IMPORTANT NOTE: Atoms can be moved arbitrarily long distances by this command. If the simulation box is non-periodic and shrink-wrapped (see the boundary command), this can change its size or shape. This is not a problem, except that the mapping of processors to the simulation box is not changed by this command from its initial 3d configuration; see the processors command. Thus, if the box size/shape changes dramatically, the mapping of processors to the simulation box may not end up as optimal as the initial mapping attempted to be.
Restrictions:
You cannot rotate around any rotation vector except the z-axis for a 2d simulation. Related commands: lattice, change_box, fix_move Default:
The option defaults are units = lattice.
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
pair_style command Syntax:
pair_style style args
style = one of the styles from the list below ? args = arguments used by a particular style Examples:
?
pair_style lj/cut 2.5 pair_style eam/alloy
pair_style hybrid lj/charmm/coul/long 10.0 eam pair_style table linear 1000 pair_style none Description:
Set the formula(s) LAMMPS uses to compute pairwise interactions. In LAMMPS, pair potentials are defined between pairs of atoms that are within a cutoff distance and the set of active interactions typically changes over time. See the bond_style command to define potentials between pairs of bonded atoms, which typically remain in place for the duration of a simulation.
In LAMMPS, pairwise force fields encompass a variety of interactions, some of which include many-body effects, e.g. EAM, Stillinger-Weber, Tersoff, REBO potentials. They are still classified as \atoms changes with time (unlike molecular bonds) and thus a neighbor list is used to find nearby interacting atoms. Hybrid models where specified pairs of atom types interact via different pair potentials can be setup using the hybrid pair style.
The coefficients associated with a pair style are typically set for each pair of atom types, and are specified by the pair_coeff command or read from a file by the read_data or read_restart commands.
The pair_modify command sets options for mixing of type I-J interaction coefficients and adding energy offsets or tail corrections to Lennard-Jones potentials. Details on these options as they pertain to individual potentials are described on the doc page for the potential. Likewise, info on whether the potential information is stored in a restart file is listed on the potential doc page.
In the formulas listed for each pair style, E is the energy of a pairwise interaction between two atoms separated by a distance r. The force between the atoms is the negative derivative of this expression.
If the pair_style command has a cutoff argument, it sets global cutoffs for all pairs of atom types. The distance(s) can be smaller or larger than the dimensions of the simulation box.
Typically, the global cutoff value can be overridden for a specific pair of atom types by the pair_coeff command. The pair style settings (including global cutoffs) can be changed by a subsequent pair_style command using the same style. This will reset the cutoffs for all atom type pairs, including those previously set explicitly by a pair_coeff command. The exceptions to this are that pair_style table and hybrid settings cannot be reset. A new pair_style command for these styles will wipe out all previously specified pair_coeff values.
Here is an alphabetic list of pair styles defined in LAMMPS. They are also given in more compact form in the pair section of this page.
Click on the style to display the formula it computes, arguments specified in the pair_style command, and coefficients specified by the associated pair_coeff command.
There are also additional pair styles (not listed here) submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the pair section of this page.
There are also additional accelerated pair styles (not listed here) included in the LAMMPS distribution for faster
performance on CPUs and GPUs. The list of these with links to the individual styles are given in the pair section of this page.
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
pair_style none - turn off pairwise interactions
pair_style hybrid - multiple styles of pairwise interactions
pair_style hybrid/overlay - multiple styles of superposed pairwise interactions pair_style adp - angular dependent potential (ADP) of Mishin pair_style airebo - AIREBO potential of Stuart pair_style beck - Beck potential
pair_style body - interactions between body particles pair_style bop - BOP potential of Pettifor
pair_style born - Born-Mayer-Huggins potential
pair_style born/coul/long - Born-Mayer-Huggins with long-range Coulombics
pair_style born/coul/msm - Born-Mayer-Huggins with long-range MSM Coulombics pair_style born/coul/wolf - Born-Mayer-Huggins with Coulombics via Wolf potential pair_style brownian - Brownian potential for Fast Lubrication Dynamics
pair_style brownian/poly - Brownian potential for Fast Lubrication Dynamics with polydispersity pair_style buck - Buckingham potential
pair_style buck/coul/cut - Buckingham with cutoff Coulomb
pair_style buck/coul/long - Buckingham with long-range Coulombics pair_style buck/coul/msm - Buckingham long-range MSM Coulombics
pair_style buck/long/coul/long - long-range Buckingham with long-range Coulombics pair_style colloid - integrated colloidal potential
pair_style comb - charge-optimized many-body (COMB) potential pair_style comb3 - charge-optimized many-body (COMB3) potential pair_style coul/cut - cutoff Coulombic potential
pair_style coul/debye - cutoff Coulombic potential with Debye screening
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? pair_style coul/dsf - Coulombics via damped shifted forces pair_style coul/long - long-range Coulombic potential pair_style coul/msm - long-range MSM Coulombics pair_style coul/wolf - Coulombics via Wolf potential pair_style dpd - dissipative particle dynamics (DPD) pair_style dpd/tstat - DPD thermostatting
pair_style dsmc - Direct Simulation Monte Carlo (DSMC) pair_style eam - embedded atom method (EAM) pair_style eam/alloy - alloy EAM
pair_style eam/fs - Finnis-Sinclair EAM
pair_style eim - embedded ion method (EIM) pair_style gauss - Gaussian potential
pair_style gayberne - Gay-Berne ellipsoidal potential
pair_style gran/hertz/history - granular potential with Hertzian interactions pair_style gran/hooke - granular potential with history effects
pair_style gran/hooke/history - granular potential without history effects pair_style hbond/dreiding/lj - DREIDING hydrogen bonding LJ potential
pair_style hbond/dreiding/morse - DREIDING hydrogen bonding Morse potential pair_style kim - interface to potentials provided by KIM project pair_style lcbop - long-range bond-order potential (LCBOP) pair_style line/lj - LJ potential between line segments
pair_style lj/charmm/coul/charmm - CHARMM potential with cutoff Coulomb pair_style lj/charmm/coul/charmm/implicit - CHARMM for implicit solvent pair_style lj/charmm/coul/long - CHARMM with long-range Coulomb
pair_style lj/charmm/coul/msm - CHARMM with long-range MSM Coulombics pair_style lj/class2 - COMPASS (class 2) force field with no Coulomb pair_style lj/class2/coul/cut - COMPASS with cutoff Coulomb
pair_style lj/class2/coul/long - COMPASS with long-range Coulomb pair_style lj/cut - cutoff Lennard-Jones potential with no Coulomb pair_style lj/cut/coul/cut - LJ with cutoff Coulomb
pair_style lj/cut/coul/debye - LJ with Debye screening added to Coulomb pair_style lj/cut/coul/dsf - LJ with Coulombics via damped shifted forces pair_style lj/cut/coul/long - LJ with long-range Coulombics
pair_style lj/cut/coul/msm - LJ with long-range MSM Coulombics pair_style dipole/cut - point dipoles with cutoff
pair_style dipole/long - point dipoles with long-range Ewald
pair_style lj/cut/tip4p/cut - LJ with cutoff Coulomb for TIP4P water
pair_style lj/cut/tip4p/long - LJ with long-range Coulomb for TIP4P water pair_style lj/expand - Lennard-Jones for variable size particles pair_style lj/gromacs - GROMACS-style Lennard-Jones potential
pair_style lj/gromacs/coul/gromacs - GROMACS-style LJ and Coulombic potential pair_style lj/long/coul/long - long-range LJ and long-range Coulombics pair_style lj/long/dipole/long - long-range LJ and long-range point dipoles
pair_style lj/long/tip4p/long - long-range LJ and long-range Coulomb for TIP4P water pair_style lj/smooth - smoothed Lennard-Jones potential
pair_style lj/smooth/linear - linear smoothed Lennard-Jones potential pair_style lj96/cut - Lennard-Jones 9/6 potential
pair_style lubricate - hydrodynamic lubrication forces
pair_style lubricate/poly - hydrodynamic lubrication forces with polydispersity
pair_style lubricateU - hydrodynamic lubrication forces for Fast Lubrication Dynamics
pair_style lubricateU/poly - hydrodynamic lubrication forces for Fast Lubrication with polydispersity