compute pe/atom command
compute ID group-ID pe/atom keyword ...
ID, group-ID are documented in compute command
pe/atom = style name of this compute command
zero or more keywords may be appended
keyword = pair or bond or angle or dihedral or improper or kspace or fix
compute 1 all pe/atom compute 1 all pe/atom pair compute 1 all pe/atom pair bond
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, kspace (long-range), and fix energy. I.e. it is as if all the keywords were listed. 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 calculation requires 1 extra FFT each timestep that per-atom energy is calculated. This document describes how the long-range per-atom energy calculation is performed.
Various fixes can contribute to the per-atom potential energy of the system if the fix contribution is included. See the doc pages for individual fixes for details of which ones compute a per-atom potential energy.
The fix_modify energy yes command must also be specified if a fix is to contribute per-atom potential energy to this command.
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
The per-atom energy does not include any Lennard-Jones tail corrections to the energy added by the pair_modify tail yes command, since those are contributions to the global system energy.
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 the Howto output doc page for an overview of LAMMPS output options.
The per-atom vector values will be in energy units.
(Heyes) Heyes, Phys Rev B 49, 755 (1994),