Homec4science
Diffusion lammps (master) Browse

lammps/doc/html/_sources/compute_pe_atom.txt
53ebd8cfeb5amaster

Last Change
Raw File

compute_pe_atom.txt
View Options

.. index:: compute pe/atom
compute pe/atom command
=======================
Syntax
""""""
.. parsed-literal::
compute ID group-ID pe/atom keyword ...
* ID, group-ID are documented in :doc:`compute <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*
Examples
""""""""
.. parsed-literal::
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 :doc:`compute pe <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 :doc:`dihedral_style charmm <dihedral_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
:ref:`(Heyes) <Heyes>` for the Ewald method and a related method for PPPM,
as specified by the :doc:`kspace_style pppm <kspace_style>` command.
For PPPM, the calcluation requires 1 extra FFT each timestep that
per-atom energy is calculated. Thie `document <PDF/kspace.pdf>`_
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
:doc:`individual fixes <fix>` for details of which ones compute a
per-atom potential energy.
.. note::
The :doc:`fix_modify energy yes <fix_modify>` 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:
.. parsed-literal::
compute peratom all pe/atom
compute pe all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_pe
.. note::
The per-atom energy does not any Lennard-Jones tail corrections
invoked by the :doc:`pair_modify tail yes <pair_modify>` 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
:ref:`Section_howto 15 <howto_15>` for an overview of
LAMMPS output options.
The per-atom vector values will be in energy :doc:`units <units>`.
Restrictions
""""""""""""
Related commands
""""""""""""""""
:doc:`compute pe <compute_pe>`, :doc:`compute stress/atom <compute_stress_atom>`
**Default:** none
----------
.. _Heyes:
**(Heyes)** Heyes, Phys Rev B 49, 755 (1994),
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help