forked from lijiext/lammps
85 lines
3.0 KiB
HTML
85 lines
3.0 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>compute pe/atom command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID pe/atom keyword ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>pe/atom = style name of this compute command
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<LI>zero or more keywords may be appended
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<LI>keyword = <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>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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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that computes the per-atom potential energy for
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each atom in a group. See the <A HREF = "compute_pe.html">compute pe</A> command if
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you want the potential energy of the entire system.
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</P>
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<P>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, and improper energy. If any extra keywords are listed, then
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only those components are summed to compute the potential energy.
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</P>
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<P>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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</P>
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<P>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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</P>
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<P>The <A HREF = "dihedral_charmm.html">dihedral_style charmm</A> 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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</P>
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<P>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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</P>
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<PRE>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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</PRE>
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<P>IMPORTANT NOTE: The per-atom energy does NOT include contributions due
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to long-range Coulombic interactions (via the
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<A HREF = "kspace_style.html">kspace_style</A> command). It's not clear this
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contribution can easily be computed.
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</P>
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<P><B>Output info:</B>
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</P>
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<P>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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<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
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output options.
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</P>
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<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_pe.html">compute pe</A>, <A HREF = "compute_stress_atom.html">compute
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stress/atom</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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