Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F75488185
compute_pe_atom.html
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Fri, Aug 2, 13:18
Size
3 KB
Mime Type
text/html
Expires
Sun, Aug 4, 13:18 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
19508346
Attached To
rLAMMPS lammps
compute_pe_atom.html
View Options
<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.
</P>
<P>
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, 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>
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:
</P>
<PRE>
compute peratom all pe/atom
compute pe all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_pe
</PRE>
<P>
IMPORTANT NOTE: The per-atom energy does NOT include contributions due
to long-range Coulombic interactions (via the
<A
HREF =
"kspace_style.html"
>
kspace_style
</A>
command). It's not clear this
contribution can easily be computed. It also does not include any
Lennard-Jones tail corrections invoked by the
<A
HREF =
"pair_modify.html"
>
pair_modify tail
yes
</A>
command, since those are global contributions to
the system energy.
</P>
<P><B>
Output info:
</B>
</P>
<P>
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
<A
HREF =
"Section_howto.html#howto_15"
>
this section
</A>
for an overview of LAMMPS
output options.
</P>
<P>
The per-atom vector values will be in energy
<A
HREF =
"units.html"
>
units
</A>
.
</P>
<P><B>
Restrictions:
</B>
</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>
none
</P>
</HTML>
Event Timeline
Log In to Comment