USER-ATOMS

USER-ATOMS is a LAMMPS user package developed at ATOMS/UFRJ

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Installation

1. Download and install LAMMPS from their website.

2. Go to the LAMMPS source directory (src) and run the following commands:

    git clone https://github.com/atoms-ufrj/USER-ATOMS
    make yes-USER-ATOMS

3. Proceed with normal LAMMPS compilation.

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Included features

1) Pair style lj/sf/coul/sf

Syntax:

    pair_style lj/sf/coul/sf cutoff (cutoff2)

• cutoff = global cutoff for Lennard-Jones interactions (distance units)
• cutoff2 = global cutoff for Coulombic interactions (optional) (distance units)

Examples:

    pair_style lj/sf/coul/sf 10.0
    pair_style lj/sf/coul/sf  8.0 10.0

Description:

The pair style lj/sf/coul/sf computes the shifted-force version of a combined Lennard-Jones/Coulombic pair potential.

2) Compute style ke/com

Syntax:

    compute ID group ke/com

Example:

    compute KinEngCoM all ke/com
    thermo_style custom step temp pe ke c_KinEngCoM

Description:

The compute style ke/com computes the translational part (that is, based on the center-of-mass velocities) of the kinetic energy. The center of mass of each molecule is computed considering only those atoms that belong to the specified group.

3) Fix style msd/chunk

Syntax:

    fix ID group msd/chunk chunkID nEvery blockSize file nUpdate

• chunkID =
• nEvery =
• blockSize =
• file =
• nUpdate =

Example:

    compute mols all chunk/atom molecule
    fix     msd all msd/chunk mols 20 10 msd.dat 10000

Description: