compute pe/atom command — LIGGGHTS v3.X documentation

# compute pe/atom command

## Syntax

    compute ID group-ID pe/atom general_keyword general_values keyword ...

- ID, group-ID are documented in compute command
- pe/atom = style name of this compute command
- general_keywords general_values are documented in compute
- zero or more keywords may be appended
- keyword = pair or bond or angle or dihedral or improper or kspace

## Examples

    compute 1 all pe/atom
    compute 1 all pe/atom pair
    compute 1 all pe/atom pair bond

## Description

Define a computation that computes the per-atom potential energy for each atom in a group. See the compute pe command if you want the potential energy of the entire system.

The per-atom energy is calculated by the various pair, bond, etc potentials defined for the simulation. If no extra keywords are listed, then the potential energy is the sum of pair, bond, angle, dihedral,improper, and kspace energy. If any extra keywords are listed, then only those components are summed to compute the potential energy.

Note that the energy of each atom is due to its interaction with all other atoms in the simulation, not just with other atoms in the group.

For an energy contribution produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that energy is assigned in equal portions to each atom in the set. E.g. 1/4 of the dihedral energy to each of the 4 atoms.

The `dihedral_style charmm` style calculates pairwise interactions between 1-4 atoms. The energy contribution of these terms is included in the pair energy, not the dihedral energy.

The KSpace contribution is calculated using the method in (Heyes) for the Ewald method and a related method for PPPM, as specified by the `kspace_style pppm` command. For PPPM, the calcluation requires 1 extra FFT each timestep that per-atom energy is calculated. Thie document describes how the long-range per-atom energy calculation is performed.

As an example of per-atom potential energy compared to total potential energy, these lines in an input script should yield the same result in the last 2 columns of thermo output:

    compute              peratom all pe/atom
    compute              pe all reduce sum c_peratom
    thermo_style custom step temp etotal press pe c_pe

Warning

The per-atom energy does not any Lennard-Jones tail corrections invoked by the `pair_modify tail yes` command, since those are global contributions to the system energy.

Output info:

This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LIGGGHTS(R)-PUBLIC output options.

The per-atom vector values will be in energy units.

## Restrictions

This compute does not include the potential energy due to the overlap of granular particles.

## Related commands

compute pe, compute stress/atom

Default: none

(Heyes) Heyes, Phys Rev B 49, 755 (1994),