2006-09-22 00:22:34 +08:00
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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>fix poems
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</H3>
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<P>Syntax:
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</P>
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<PRE>fix ID group-ID poems keyword values
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>poems = style name of this fix command
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<LI>keyword = <I>group</I> or <I>file</I> or <I>molecule</I>
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<PRE> <I>group</I> values = list of group IDs
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<I>molecule</I> values = none
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<I>file</I> values = filename
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 3 fluid poems group clump1 clump2 clump3
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fix 3 fluid poems file cluster.list
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Treats one or more sets of atoms as coupled rigid bodies. This means
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that each timestep the total force and torque on each rigid body is
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computed and the coordinates and velocities of the atoms are updated
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so that the collection of bodies move as a coupled set. This can be
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useful for treating a large biomolecule as a collection of connected,
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coarse-grained particles.
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</P>
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<P>The coupling, associated motion constraints, and time integration is
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performed by the software package <A HREF = "http://www.rpi.edu/~anderk5/lab">Parallelizable Open source
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Efficient Multibody Software (POEMS)</A> which computes the
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constrained rigid-body motion of articulated (jointed) multibody
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systems <A HREF = "#Anderson">(Anderson)</A>. POEMS was written and is distributed
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by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
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and other members of his group at Rensselaer Polytechnic Institute
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(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For
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copyright information on POEMS and other details, please refer to the
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documents in the poems directory distributed with LAMMPS.
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</P>
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<P>This fix updates the positions and velocities of the rigid atoms with
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a constant-energy time integration, so you should not update the same
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atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
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</P>
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<P>Each body must have a non-degenerate inertia tensor, which means if
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2008-03-19 04:18:54 +08:00
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must contain at least 3 non-collinear atoms. Which atoms are in which
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2006-09-22 00:22:34 +08:00
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bodies can be defined via several options.
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</P>
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<P>For option <I>group</I>, each of the listed groups is treated as a rigid
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body. Note that only atoms that are also in the fix group are
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included in each rigid body.
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</P>
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<P>For option <I>molecule</I>, each set of atoms in the group with a different
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molecule ID is treated as a rigid body.
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</P>
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<P>For option <I>file</I>, sets of atoms are read from the specified file and
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each set is treated as a rigid body. Each line of the file specifies
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a rigid body in the following format:
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</P>
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<P>ID type atom1-ID atom2-ID atom3-ID ...
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</P>
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<P>ID as an integer from 1 to M (the number of rigid bodies). Type is
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any integer; it is not used by the fix poems command. The remaining
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arguments are IDs of atoms in the rigid body, each typically from 1 to
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N (the number of atoms in the system). Only atoms that are also in
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the fix group are included in each rigid body. Blank lines and lines
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that begin with '#' are skipped.
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</P>
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<P>A connection between a pair of rigid bodies is inferred if one atom is
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common to both bodies. The POEMS solver treats that atom as a
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spherical joint with 3 degrees of freedom. Currently, a collection of
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bodies can only be connected by joints as a linear chain. The entire
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collection of rigid bodies can represent one or more chains. Other
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connection topologies (tree, ring) are not allowed, but will be added
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later. Note that if no joints exist, it is more efficient to use the
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<A HREF = "fix_rigid.html">fix rigid</A> command to simulate the system.
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</P>
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<P>When the poems fix is defined, it will print out statistics on the
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total # of clusters, bodies, joints, atoms involved. A cluster in
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this context means a set of rigid bodies connected by joints.
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</P>
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<P>For computational efficiency, you should turn off pairwise and bond
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interactions within each rigid body, as they no longer contribute to
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the motion. The "neigh_modify exclude" and "delete_bonds" commands
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can be used to do this if each rigid body is a group.
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</P>
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<P>For computational efficiency, you should only define one fix poems
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which includes all the desired rigid bodies. LAMMPS will allow
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multiple poems fixes to be defined, but it is more expensive.
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</P>
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<P>The degrees-of-freedom removed by coupled rigid bodies are accounted
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2008-02-20 05:47:37 +08:00
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for in temperature and pressure computations. Similarly, the rigid
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2006-09-22 00:22:34 +08:00
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body contribution to the pressure virial is also accounted for. The
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latter is only correct if forces within the bodies have been turned
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off, and there is only a single fix poems defined.
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</P>
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2007-10-11 06:28:11 +08:00
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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2007-06-26 08:03:39 +08:00
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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2010-04-03 00:51:06 +08:00
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various <A HREF = "Section_howto.html#4_15">output
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2007-10-11 06:28:11 +08:00
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commands</A>. No parameter of this fix can be
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used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
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This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
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2007-06-26 08:03:39 +08:00
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</P>
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2006-09-22 00:22:34 +08:00
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<P><B>Restrictions:</B>
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</P>
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2007-06-26 08:03:39 +08:00
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<P>This fix is part of the "poems" package. It is only enabled if LAMMPS
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was built with that package, which also requires the POEMS library be
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built and linked with LAMMPS. See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info.
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2006-09-22 00:22:34 +08:00
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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 = "fix_rigid.html">fix rigid</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
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<A HREF = "neigh_modify.html">neigh_modify</A> exclude
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Anderson"></A>
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<P><B>(Anderson)</B> Anderson, Mukherjee, Critchley, Ziegler, and Lipton
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"POEMS: Parallelizable Open-source Efficient Multibody Software ",
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Engineering With Computers (2006). (<A HREF = "http://dx.doi.org/10.1007/s00366-006-0026-x">link to
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paper</A>)
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</P>
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</HTML>
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