compute pe/atom command¶
Syntax¶
compute ID group-ID pe/atom general_keyword general_values keyword ...
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.