ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1200 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2007-11-30 23:59:23 +00:00
parent a8184a9e76
commit 8077130fa2
2 changed files with 129 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

67
doc/compute_pe_atom.html Normal file
View File

@ -0,0 +1,67 @@
<HTML>
<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>
</CENTER>
<HR>
<H3>compute pe/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID pe/atom keyword ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>pe/atom = style name of this compute command
<LI>zero or more keywords may be appended
<LI>keyword = <I>pair</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all pe/atom
compute 1 all pe/atom pair
compute 1 all pe/atom pair bond
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that computes the per-atom potential energy for
each atom in a group. See the <A HREF = "compute_pe.html">compute pe</A> command if
you want the potential energy of the entire system. The per-atom
energies can be accessed as scalar values by any command that uses
per-atom computes, e.g. the <A HREF = "dump.html">dump custom</A> command or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command or <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command. See <A HREF = "Section_howto.html#4_15">this
section</A> for an overview.
</P>
<P>The per-atom energy is calulated 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, and improper energy. If any extra keywords are listed, then
only those components are summed to compute the potential energy.
</P>
<P>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.
</P>
<P>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.
</P>
<P>The <A HREF = "dihedral_charmm.html">dihedral_style charmm</A> style calculates
pairwise interactions between 1-4 atoms. The energy contribution of
these terms is included in the pair energy, not the dihedral energy.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_pe.html">compute pe</A>, <A HREF = "compute_stress_atom.html">compute
stress/atom</A>
</P>
<P><B>Default:</B> non
</P>
</HTML>

62
doc/compute_pe_atom.txt Normal file
View File

@ -0,0 +1,62 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute pe/atom command :h3
[Syntax:]
compute ID group-ID pe/atom keyword ... :pre
ID, group-ID are documented in "compute"_compute.html 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} :ul
[Examples:]
compute 1 all pe/atom
compute 1 all pe/atom pair
compute 1 all pe/atom pair bond :pre
[Description:]
Define a computation that computes the per-atom potential energy for
each atom in a group. See the "compute pe"_compute_pe.html command if
you want the potential energy of the entire system. The per-atom
energies can be accessed as scalar values by any command that uses
per-atom computes, e.g. the "dump custom"_dump.html command or "fix
ave/spatial"_fix_ave_spatial.html command or "fix
ave/atom"_fix_ave_atom.html command. See "this
section"_Section_howto.html#4_15 for an overview.
The per-atom energy is calulated 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, and improper 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"_dihedral_charmm.html style calculates
pairwise interactions between 1-4 atoms. The energy contribution of
these terms is included in the pair energy, not the dihedral energy.
[Restrictions:] none
[Related commands:]
"compute pe"_compute_pe.html, "compute
stress/atom"_compute_stress_atom.html
[Default:] none