2006-09-22 00:22:34 +08:00
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<HTML>
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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 rigid
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</H3>
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<P><B>Syntax:</B>
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</P>
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2009-01-13 22:38:26 +08:00
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<PRE>fix ID group-ID rigid bodystyle args keyword values ...
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2006-09-22 00:22:34 +08:00
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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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2009-01-13 22:38:26 +08:00
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<LI>bodystyle = <I>single</I> or <I>molecule</I> or <I>group</I>
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2006-09-22 00:22:34 +08:00
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2009-01-13 22:38:26 +08:00
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<PRE> <I>single</I> args = none
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<I>molecule</I> args = none
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<I>group</I> args = N groupID1 groupID2 ...
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N = # of groups
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groupID1, groupID2, ... = list of N group IDs
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>force</I> or <I>torque</I>
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<PRE> <I>force</I> values = M xflag yflag zflag
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M = which rigid body from 1-Nbody (see asterisk form below)
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xflag,yflag,zflag = off/on if component of center-of-mass force is active
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<I>torque</I> values = M xflag yflag zflag
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M = which rigid body from 1-Nbody (see asterisk form below)
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xflag,yflag,zflag = off/on if component of center-of-mass torque is active
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2006-09-22 00:22:34 +08:00
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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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2009-01-13 22:38:26 +08:00
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fix 1 clump rigid single force 1 off off on
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2006-09-22 00:22:34 +08:00
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fix 1 polychains rigid molecule
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2009-01-13 22:38:26 +08:00
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fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
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fix 2 fluid rigid group 3 clump1 clump2 clump3
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fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
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2006-09-22 00:22:34 +08:00
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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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2009-03-19 22:34:23 +08:00
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for simulating a system of colloidal particles.
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</P>
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<P>IMPORTANT NOTE: This fix is overkill if you just want to hold group of
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atoms stationary of have them move with a constant velocity. A
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simpler way to hold atoms stationary 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. You can move atoms with a constant velocity by assigning them
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an initial velocity (via the <A HREF = "velocity.html">velocity</A> command),
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setting the force on them to 0.0 (via the <A HREF = "fix_setforce.html">fix
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setforce</A> command), and integrating them as usual
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(e.g. via the <A HREF = "fix_nve.html">fix nve</A> command).
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2006-09-22 00:22:34 +08:00
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</P>
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2009-03-05 01:24:41 +08:00
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<P>IMPORTANT NOTE: This fix updates the positions and velocities of the
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rigid atoms with a constant-energy time integration, so you should not
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update the same 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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2009-01-13 22:38:26 +08:00
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<P>Each body must have two or more atoms. An atom can belong to at most
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one rigid body. Which atoms are in which bodies can be defined via
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several options.
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2006-09-22 00:22:34 +08:00
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</P>
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2009-01-13 22:38:26 +08:00
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<P>For bodystyle <I>single</I> the entire fix group of atoms is treated as one
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rigid body.
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2006-09-22 00:22:34 +08:00
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</P>
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2009-01-13 22:38:26 +08:00
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<P>For bodystyle <I>molecule</I>, each set of atoms in the fix group with a
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different molecule ID is treated as a rigid body.
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2006-09-22 00:22:34 +08:00
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</P>
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2009-01-13 22:38:26 +08:00
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<P>For bodystyle <I>group</I>, each of the listed groups is treated as a
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separate rigid body. Only atoms that are also in the fix group are
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2006-09-22 00:22:34 +08:00
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included in each rigid body.
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</P>
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2009-01-13 22:38:26 +08:00
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<P>By default, each rigid body is acted on by other atoms which induce a
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force and torque on its center of mass, causing it to translate and
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rotate. Components of the center-of-mass force and torque can be
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turned off by the <I>force</I> and <I>torque</I> keywords. This may be useful
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if you wish a body to rotate but not translate, or vice versa. Note
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that if you expect a rigid body not to move or rotate by using these
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keywords, you must insure its initial center-of-mass translational or
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angular velocity is 0.0.
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</P>
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<P>An xflag, yflag, or zflag set to <I>off</I> means turn off the component of
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force of torque in that dimension. A setting of <I>on</I> means turn on
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the component, which is the default. Which rigid body(s) the settings
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apply to is determined by the first argument of the <I>force</I> and
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<I>torque</I> keywords. It can be an integer M from 1 to Nbody, where
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Nbody is the number of rigid bodies defined. A wild-card asterisk can
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be used in place of, or in conjunction with, the M argument to set the
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flags for multiple rigid bodies. This takes the form "*" or "*n" or
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"n*" or "m*n". If N = the number of rigid bodies, then an asterisk
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with no numeric values means all bodies from 1 to N. A leading
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asterisk means all bodies from 1 to n (inclusive). A trailing
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asterisk means all bodies from n to N (inclusive). A middle asterisk
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2009-01-15 08:21:36 +08:00
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means all types from m to n (inclusive). Note that you can use the
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<I>force</I> or <I>torque</I> keywords as many times as you like. If a
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particular rigid body has its component flags set multiple times, the
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settings from the final keyword are used.
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2009-01-13 22:38:26 +08:00
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</P>
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<P>For computational efficiency, you may wish to turn off pairwise and
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2006-09-22 00:22:34 +08:00
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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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2008-01-10 07:22:14 +08:00
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<P>This fix uses constant-energy integration, so you may need to impose
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additional constraints to control the temperature of an ensemble of
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rigid bodies. You can use <A HREF = "fix_langevin.html">fix langevin</A> for this
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purpose to treat the system as effectively immersed in an implicit
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2009-01-23 02:56:18 +08:00
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solvent, e.g. a Brownian dynamics model. Or you can thermostat only
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the non-rigid atoms that surround one or more rigid bodies
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(i.e. explicit solvent) by appropriate choice of groups in the compute
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and fix commands for temperature and thermostatting.
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</P>
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<P>If you do calculate a temperature for the rigid bodies, the
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degrees-of-freedom removed by each rigid body are accounted for in the
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temperature (and pressure) computation, but only if the temperature
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group includes the entire rigid body. Rigid bodies in 3d have 6
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degrees of freedom (3 translational, 3 rotational), except for dimers
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which only have 5. Rigid bodies in 2d have 3 degrees of freedom.
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Note that linear rigid bodies in 3d of three or more atoms also have 5
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degrees of freedom instead of 6, but LAMMPS will not detect this. So
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you should use the <A HREF = "compute_modify.html">compute_modify</A> command to
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subtract an additional degree of freedom per rigid body. You may also
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wish to explicitly subtract additional degrees-of-freedom if you use
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the <I>force</I> and <I>torque</I> keywords to eliminate certain motions of the
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rigid body, as LAMMPS does not do this automatically.
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</P>
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<P>The rigid body contribution to the pressure of the system (virial) is
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also accounted for by this fix.
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2006-09-22 00:22:34 +08:00
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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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2008-10-08 23:02:35 +08:00
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atoms were not in a rigid body. It also means that if you have bonds
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between a pair of rigid bodies and the bond straddles a periodic
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boundary, you cannot use the <A HREF = "replicate">replicate</A> command to increase
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the system size.
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2007-08-29 22:13:51 +08:00
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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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2009-01-13 22:38:26 +08:00
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are relevant to this fix.
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</P>
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<P>This fix computes a global vector of quantities which can be accessed
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by various <A HREF = "Section_howto.html#4_15">output commands</A>. For each rigid
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body, 12 values are stored: the xyz coords of the center of mass
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(COM), the xyz components of the COM velocity, the xyz components of
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the force acting on the COM, and the xyz components of the torque
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acting on the COM. The force and torque values in the vector are not
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affected by the <I>force</I> and <I>torque</I> keywords in the fix rigid
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command; they reflect values before any changes are made by those
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keywords.
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</P>
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<P>The total length of the vector is 12*Nbody where Nbody is the number
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of rigid bodies defined by the fix. Thus the 15th value in the vector
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would be the z-coord of the COM of the 2nd rigid body. LAMMPS chooses
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the ordering of the rigid bodies internally. The ordering of the
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rigid bodies is as follows. For the <I>single</I> keyword there is just
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one rigid body. For the <I>molecule</I> keyword, the bodies are ordered by
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ascending molecule ID. For the <I>group</I> keyword, the list of group IDs
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determines the ordering of bodies. The vector values calculated by
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this fix are "intensive", meaning they are independent of the number
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of atoms in the simulation.
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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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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<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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2009-01-13 22:38:26 +08:00
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<P><B>Default:</B>
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</P>
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2009-05-19 22:43:06 +08:00
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<P>The option defaults are force * on on on and torque * on on on meaning
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2009-01-13 22:38:26 +08:00
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all rigid bodies are acted on by center-of-mass force and torque.
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2006-09-22 00:22:34 +08:00
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</P>
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</HTML>
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