forked from lijiext/lammps
147 lines
6.0 KiB
HTML
147 lines
6.0 KiB
HTML
<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>fix poems
|
|
</H3>
|
|
<P>Syntax:
|
|
</P>
|
|
<PRE>fix ID group-ID poems keyword values
|
|
</PRE>
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
<LI>poems = style name of this fix command
|
|
|
|
<LI>keyword = <I>group</I> or <I>file</I> or <I>molecule</I>
|
|
|
|
<PRE> <I>group</I> values = list of group IDs
|
|
<I>molecule</I> values = none
|
|
<I>file</I> values = filename
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>fix 3 fluid poems group clump1 clump2 clump3
|
|
fix 3 fluid poems file cluster.list
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Treats one or more sets of atoms as coupled rigid bodies. This means
|
|
that each timestep the total force and torque on each rigid body is
|
|
computed and the coordinates and velocities of the atoms are updated
|
|
so that the collection of bodies move as a coupled set. This can be
|
|
useful for treating a large biomolecule as a collection of connected,
|
|
coarse-grained particles.
|
|
</P>
|
|
<P>The coupling, associated motion constraints, and time integration is
|
|
performed by the software package <A HREF = "http://www.rpi.edu/~anderk5/lab">Parallelizable Open source
|
|
Efficient Multibody Software (POEMS)</A> which computes the
|
|
constrained rigid-body motion of articulated (jointed) multibody
|
|
systems <A HREF = "#Anderson">(Anderson)</A>. POEMS was written and is distributed
|
|
by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
|
|
and other members of his group at Rensselaer Polytechnic Institute
|
|
(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For
|
|
copyright information on POEMS and other details, please refer to the
|
|
documents in the poems directory distributed with LAMMPS.
|
|
</P>
|
|
|
|
|
|
<P>This fix updates the positions and velocities of the rigid atoms with
|
|
a constant-energy time integration, so you should not update the same
|
|
atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
|
|
</P>
|
|
<P>Each body must have a non-degenerate inertia tensor, which means if
|
|
must contain at least 3 non-collinear atoms. Which atoms are in which
|
|
bodies can be defined via several options.
|
|
</P>
|
|
<P>For option <I>group</I>, each of the listed groups is treated as a rigid
|
|
body. Note that only atoms that are also in the fix group are
|
|
included in each rigid body.
|
|
</P>
|
|
<P>For option <I>molecule</I>, each set of atoms in the group with a different
|
|
molecule ID is treated as a rigid body.
|
|
</P>
|
|
<P>For option <I>file</I>, sets of atoms are read from the specified file and
|
|
each set is treated as a rigid body. Each line of the file specifies
|
|
a rigid body in the following format:
|
|
</P>
|
|
<P>ID type atom1-ID atom2-ID atom3-ID ...
|
|
</P>
|
|
<P>ID as an integer from 1 to M (the number of rigid bodies). Type is
|
|
any integer; it is not used by the fix poems command. The remaining
|
|
arguments are IDs of atoms in the rigid body, each typically from 1 to
|
|
N (the number of atoms in the system). Only atoms that are also in
|
|
the fix group are included in each rigid body. Blank lines and lines
|
|
that begin with '#' are skipped.
|
|
</P>
|
|
<P>A connection between a pair of rigid bodies is inferred if one atom is
|
|
common to both bodies. The POEMS solver treats that atom as a
|
|
spherical joint with 3 degrees of freedom. Currently, a collection of
|
|
bodies can only be connected by joints as a linear chain. The entire
|
|
collection of rigid bodies can represent one or more chains. Other
|
|
connection topologies (tree, ring) are not allowed, but will be added
|
|
later. Note that if no joints exist, it is more efficient to use the
|
|
<A HREF = "fix_rigid.html">fix rigid</A> command to simulate the system.
|
|
</P>
|
|
<P>When the poems fix is defined, it will print out statistics on the
|
|
total # of clusters, bodies, joints, atoms involved. A cluster in
|
|
this context means a set of rigid bodies connected by joints.
|
|
</P>
|
|
<P>For computational efficiency, you should turn off pairwise and bond
|
|
interactions within each rigid body, as they no longer contribute to
|
|
the motion. The "neigh_modify exclude" and "delete_bonds" commands
|
|
can be used to do this if each rigid body is a group.
|
|
</P>
|
|
<P>For computational efficiency, you should only define one fix poems
|
|
which includes all the desired rigid bodies. LAMMPS will allow
|
|
multiple poems fixes to be defined, but it is more expensive.
|
|
</P>
|
|
<P>The degrees-of-freedom removed by coupled rigid bodies are accounted
|
|
for in temperature and pressure computations. Similarly, the rigid
|
|
body contribution to the pressure virial is also accounted for. The
|
|
latter is only correct if forces within the bodies have been turned
|
|
off, and there is only a single fix poems defined.
|
|
</P>
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
|
</P>
|
|
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
|
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
|
are relevant to this fix. No global or per-atom quantities are stored
|
|
by this fix for access by various <A HREF = "Section_howto.html#4_15">output
|
|
commands</A>. No parameter of this fix can be
|
|
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
|
|
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
|
</P>
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>This fix is part of the "poems" package. It is only enabled if LAMMPS
|
|
was built with that package, which also requires the POEMS library be
|
|
built and linked with LAMMPS. See the <A HREF = "Section_start.html#2_3">Making
|
|
LAMMPS</A> section for more info.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "fix_rigid.html">fix rigid</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
|
|
<A HREF = "neigh_modify.html">neigh_modify</A> exclude
|
|
</P>
|
|
<P><B>Default:</B> none
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "Anderson"></A>
|
|
|
|
<P><B>(Anderson)</B> Anderson, Mukherjee, Critchley, Ziegler, and Lipton
|
|
"POEMS: Parallelizable Open-source Efficient Multibody Software ",
|
|
Engineering With Computers (2006). (<A HREF = "http://dx.doi.org/10.1007/s00366-006-0026-x">link to
|
|
paper</A>)
|
|
</P>
|
|
</HTML>
|