2006-09-22 00:22:34 +08:00
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix poems :h3
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Syntax:
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fix ID group-ID poems keyword values :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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poems = style name of this fix command :l
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keyword = {group} or {file} or {molecule} :l
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{group} values = list of group IDs
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{molecule} values = none
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{file} values = filename :pre
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:ule
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[Examples:]
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fix 3 fluid poems group clump1 clump2 clump3
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fix 3 fluid poems file cluster.list :pre
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[Description:]
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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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The coupling, associated motion constraints, and time integration is
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performed by the software package "Parallelizable Open source
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Efficient Multibody Software (POEMS)"_poems which computes the
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constrained rigid-body motion of articulated (jointed) multibody
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systems "(Anderson)"_#Anderson. 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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:link(poems,http://www.rpi.edu/~anderk5/lab)
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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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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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For option {group}, 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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For option {molecule}, 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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For option {file}, 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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ID type atom1-ID atom2-ID atom3-ID ...
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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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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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"fix rigid"_fix_rigid.html command to simulate the system.
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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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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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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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The degrees-of-freedom removed by coupled rigid bodies are accounted
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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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2007-10-11 06:28:11 +08:00
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix. No global scalar or vector or per-atom
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quantities are stored by this fix for access by various "output
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commands"_Section_howto.html#4_15. No parameter of this fix can be
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used with the {start/stop} keywords of the "run"_run.html command.
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This fix is not invoked during "energy minimization"_minimize.html.
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2007-06-26 08:03:39 +08:00
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2006-09-22 00:22:34 +08:00
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[Restrictions:]
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2007-06-26 08:03:39 +08:00
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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 "Making
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LAMMPS"_Section_start.html#2_3 section for more info.
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2006-09-22 00:22:34 +08:00
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[Related commands:]
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"fix rigid"_fix_rigid.html, "delete_bonds"_delete_bonds.html,
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"neigh_modify"_neigh_modify.html exclude
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[Default:] none
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:line
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:link(Anderson)
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[(Anderson)] 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). ("link to
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paper"_http://dx.doi.org/10.1007/s00366-006-0026-x)
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