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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<H3>fix rigid
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID rigid 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>rigid = style name of this fix command
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<LI>keyword = <I>single</I> or <I>molecule</I> or <I>group</I>
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<PRE> <I>single</I> values = none
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<I>molecule</I> values = none
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<I>group</I> values = list of group IDs
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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 1 clump rigid single
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fix 1 polychains rigid molecule
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fix 2 fluid rigid group clump1 clump2 clump3
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Treat one or more sets of atoms as an independent rigid body. This
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means that each timestep the total force and torque on each rigid body
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is computed and the coordinates and velocities of the atoms in each
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body are updated so that they move as a rigid body. This can be
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useful for freezing one or more portions of a large biomolecule, or
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for simulating a system of colloidal particles.
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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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2007-03-16 22:57:02 +08:00
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atoms via other fixes (e.g. nve, nvt, npt).
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2006-09-22 00:22:34 +08:00
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</P>
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<P>Each body must have two or more atoms. Which atoms are in which
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bodies can be defined via several options.
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</P>
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<P>For option <I>single</I> the entire group of atoms is treated as one rigid
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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>group</I>, each of the listed groups is treated as a separate
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rigid 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 computational efficiency, you should also turn off pairwise and
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bond interactions within each rigid body, as they no longer contribute
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to the motion. The <A HREF = "neigh_modify.html">neigh_modify exclude</A> and
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<A HREF = "delete_bonds.html">delete_bonds</A> commands are used to do this.
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</P>
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<P>For computational efficiency, you should define one fix rigid which
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includes all the desired rigid bodies. LAMMPS will allow multiple
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rigid 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 rigid bodies are accounted for in
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2007-04-13 23:43:08 +08:00
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temperature and pressure computations. Similary, the rigid body
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contribution to the pressure virial is also accounted for. The latter
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2006-09-22 00:22:34 +08:00
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is only correct if forces within the bodies have been turned off, and
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2006-12-14 00:50:24 +08:00
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there is only a single fix rigid defined. For each linear rigid body
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2007-04-13 23:43:08 +08:00
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of three or more atoms, one degree-of-freedom must be subtracted using
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2007-04-13 23:46:45 +08:00
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a <A HREF = "compute_modify.html">compute_modify</A> command (i.e. for a simulation
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of 10 such rigid bodies, use "compute_modify thermo_temp extra 13",
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after the thermo_style command, where 3 is the default setting and
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an additional 10 degrees-of-freedom are subtracted).
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2006-09-22 00:22:34 +08:00
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</P>
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2007-03-16 22:57:02 +08:00
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<P>Note that this fix uses constant-energy integration, so you may need
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to impose additional constraints to control the temperature of an
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2006-09-22 00:22:34 +08:00
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ensemble of rigid bodies. You can use <A HREF = "fix_langevin.html">fix
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langevin</A> for this purpose to treat the system as
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effectively immersed in an implicit solvent, i.e. a Brownian dynamics
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2007-03-16 22:57:02 +08:00
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model. Or you can thermostat additional atoms of an explicit solvent
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2006-09-22 00:22:34 +08:00
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directly.
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</P>
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2007-08-29 22:13:51 +08:00
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<P>IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
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modified when the center-of-mass of the rigid body moves across a
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periodic boundary. They are not incremented/decremented as they would
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be for non-rigid atoms. This change does not affect dynamics, but
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means that any diagnostic computation based on the atomic image flag
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values must be adjusted accordingly. For example, the <A HREF = "fix_msd.html">fix
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msd</A> will not compute the expected mean-squared
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displacement for such atoms, and the image flag values written to a
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<A HREF = "dump.html">dump file</A> will be different than they would be if the
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atoms were not in a rigid body.
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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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2007-10-11 06:28:11 +08:00
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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 <A HREF = "Section_howto.html#4_15">output
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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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<P>This fix performs an MPI_Allreduce each timestep that is proportional
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in length to the number of rigid bodies. Hence it will not scale well
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in parallel if large numbers of rigid bodies are simulated.
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</P>
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<P>If the atoms in a single rigid body initially straddle a periodic
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boundary, the input data file must define the image flags for each
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atom correctly, so that LAMMPS can "unwrap" the atoms into a valid
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rigid body.
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</P>
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2007-02-10 05:42:49 +08:00
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<P>You should not use this fix if you just want to hold group of atoms
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stationary. A better way to do this is to not include those atoms in
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your time integration fix. E.g. use "fix 1 mobile nve" instead of
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"fix 1 all nve", where "mobile" is the group of atoms that you want to
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move.
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2007-02-08 01:52:15 +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>Related commands:</B>
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</P>
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<P><A HREF = "delete_bonds.html">delete_bonds</A>, <A HREF = "neigh_modify.html">neigh_modify</A>
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exclude
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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