116 lines
3.6 KiB
ReStructuredText
116 lines
3.6 KiB
ReStructuredText
.. 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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.. code-block:: LAMMPS
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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* or *fix*
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Examples
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""""""""
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.. code-block:: LAMMPS
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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, :math:`k`-space (long-range), and fix energy (i.e., it is as
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though all the keywords were listed). If any extra keywords are listed,
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then only those components are summed to compute the potential 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 (e.g., 1/4 of the
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dihedral energy to each of the four 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) <Heyes1>` 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 calculation requires 1 extra FFT each timestep that
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per-atom energy is calculated. This `document <PDF/kspace.pdf>`_
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describes how the long-range per-atom energy calculation is performed.
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Various fixes can contribute to the per-atom potential energy of the
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system if the *fix* contribution is included. See the doc pages for
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:doc:`individual fixes <fix>` for details of which ones compute a
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per-atom potential energy.
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.. note::
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The :doc:`fix_modify energy yes <fix_modify>` command must also be
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specified if a fix is to contribute per-atom potential energy to this
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command.
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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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.. code-block:: LAMMPS
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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 include any Lennard-Jones tail
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corrections to the energy added by the
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:doc:`pair_modify tail yes <pair_modify>` command, since those are
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contributions to the global system energy.
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Output info
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"""""""""""
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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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the :doc:`Howto output <Howto_output>` page 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
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"""""""
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none
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----------
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.. _Heyes1:
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**(Heyes)** Heyes, Phys Rev B 49, 755 (1994),
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