mirror of https://github.com/lammps/lammps.git
110 lines
3.2 KiB
Plaintext
110 lines
3.2 KiB
Plaintext
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.. index:: compute pe/atom
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compute pe/atom command
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=======================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID pe/atom keyword ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* pe/atom = style name of this compute command
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* zero or more keywords may be appended
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* keyword = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace*
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Examples
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""""""""
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.. parsed-literal::
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compute 1 all pe/atom
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compute 1 all pe/atom pair
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compute 1 all pe/atom pair bond
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Description
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"""""""""""
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Define a computation that computes the per-atom potential energy for
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each atom in a group. See the :doc:`compute pe <compute_pe>` command if
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you want the potential energy of the entire system.
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The per-atom energy is calculated by the various pair, bond, etc
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potentials defined for the simulation. If no extra keywords are
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listed, then the potential energy is the sum of pair, bond, angle,
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dihedral,improper, and kspace energy. If any extra keywords are
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listed, then only those components are summed to compute the potential
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energy.
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Note that the energy of each atom is due to its interaction with all
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other atoms in the simulation, not just with other atoms in the group.
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For an energy contribution produced by a small set of atoms (e.g. 4
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atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that
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energy is assigned in equal portions to each atom in the set.
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E.g. 1/4 of the dihedral energy to each of the 4 atoms.
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The :doc:`dihedral_style charmm <dihedral_charmm>` style calculates
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pairwise interactions between 1-4 atoms. The energy contribution of
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these terms is included in the pair energy, not the dihedral energy.
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The KSpace contribution is calculated using the method in
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:ref:`(Heyes) <Heyes>` for the Ewald method and a related method for PPPM,
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as specified by the :doc:`kspace_style pppm <kspace_style>` command.
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For PPPM, the calcluation requires 1 extra FFT each timestep that
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per-atom energy is calculated. Thie `document <PDF/kspace.pdf>`_
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describes how the long-range per-atom energy calculation is performed.
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As an example of per-atom potential energy compared to total potential
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energy, these lines in an input script should yield the same result
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in the last 2 columns of thermo output:
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.. parsed-literal::
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compute peratom all pe/atom
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compute pe all reduce sum c_peratom
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thermo_style custom step temp etotal press pe c_pe
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.. note::
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The per-atom energy does not any Lennard-Jones tail corrections
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invoked by the :doc:`pair_modify tail yes <pair_modify>` command, since
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those are global contributions to the system energy.
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**Output info:**
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This compute calculates a per-atom vector, which can be accessed by
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any command that uses per-atom values from a compute as input. See
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:ref:`Section_howto 15 <howto_15>` for an overview of
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LAMMPS output options.
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The per-atom vector values will be in energy :doc:`units <units>`.
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Restrictions
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""""""""""""
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Related commands
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""""""""""""""""
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:doc:`compute pe <compute_pe>`, :doc:`compute stress/atom <compute_stress_atom>`
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**Default:** none
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----------
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.. _Heyes:
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**(Heyes)** Heyes, Phys Rev B 49, 755 (1994),
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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