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Thursday, April 16, 2015

pair potential style and LAMMPS (pairwise interactions and many-body effects)

In a script we have:

pair_style eam
pair_coeff * * Au_u3.eam

The command "pair_style" is very important.

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 "pairwise" potentials because the set of interacting atoms changes with time (unlike molecular bonds) and thus a neighbor list is used to find nearby interacting atoms.

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:

-∂E/∂r is a force

If the pair_style command has a cutoff argument, it sets global cutoffs for all pairs of atom types.

There are also additional accelerated pair styles (not listed on the pair_style doc page) 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.

The list of pair_style (LAMMPS 2015 january):

• 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
• pair_style meam - modified embedded atom method (MEAM)
• pair_style mie/cut - Mie potential
• pair_style morse - Morse potential
• pair_style nb3b/harmonic - nonbonded 3-body harmonic potential
• pair_style nm/cut - N-M potential
• pair_style nm/cut/coul/cut - N-M potential with cutoff Coulomb
• pair_style nm/cut/coul/long - N-M potential with long-range Coulombics
• pair_style peri/eps - peridynamic EPS potential
• pair_style peri/lps - peridynamic LPS potential
• pair_style peri/pmb - peridynamic PMB potential
• pair_style peri/ves - peridynamic VES potential
• pair_style reax - ReaxFF potential
• pair_style rebo - 2nd generation REBO potential of Brenner
• pair_style resquared - Everaers RE-Squared ellipsoidal potential
• pair_style snap - SNAP quantum-accurate potential • pair_style soft - Soft (cosine) potential
• pair_style sw - Stillinger-Weber 3-body potential
• pair_style table - tabulated pair potential
• pair_style tersoff - Tersoff 3-body potential
• pair_style tersoff/mod - modified Tersoff 3-body potential
• pair_style tersoff/zbl - Tersoff/ZBL 3-body potential
• pair_style tip4p/cut - Coulomb for TIP4P water w/out LJ
• pair_style tip4p/long - long-range Coulombics for TIP4P water w/out LJ
• pair_style tri/lj - LJ potential between triangles
• pair_style yukawa - Yukawa potential
• pair_style yukawa/colloid - screened Yukawa potential for finite-size particles
• pair_style zbl - Ziegler-Biersack-Littmark potential

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