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345 lines
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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 command
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</H3>
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<H3>fix rigid/nve command
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</H3>
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<H3>fix rigid/nvt command
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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 style bodystyle args 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>style = <I>rigid</I> or <I>rigid/nve</I> or <I>rigid/nvt</I>
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<LI>bodystyle = <I>single</I> or <I>molecule</I> or <I>group</I>
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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>temp</I> or <I>press</I> or <I>tparam</I> or <I>pparam</I> or <I>force</I> or <I>torque</I>
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<PRE> <I>temp</I> values = Tstart Tstop Tperiod
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Tstart,Tstop = desired temperature at start/stop of run (temperature units)
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Tdamp = temperature damping parameter (time units)
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<I>tparam</I> values = Tchain Titer Torder
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Tchain = length of Nose/Hoover thermostat chain
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Titer = number of thermostat iterations performed
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Torder = 3 or 5 = Yoshida-Suzuki integration parameters
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<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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</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 clump rigid single force 1 off off on
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fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
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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 torque * off off off
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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 independent rigid bodies. This
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means that each timestep the total force and torque on each rigid body
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is computed as the sum of the forces and torques on its constituent
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particles and the coordinates, velocities, and orientations of the
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atoms in each body are updated so that the body moves and rotates as a
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single entity.
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</P>
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<P>Examples of large rigid bodies are a large colloidal particle, or
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portions of a large biomolecule such as a protein.
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</P>
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<P>Example of small rigid bodies are patchy nanoparticles, such as those
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modeled in <A HREF = "#Zhang">this paper</A> by Sharon Glotzer's group, clumps of
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granular particles, lipid molecules consiting of one or more point
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dipoles connected to other spheroids or ellipsoids, and coarse-grain
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models of nano or colloidal particles consisting of a small number of
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constituent particles. Note that the <A HREF = "fix_shake.html">fix shake</A>
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command can also be used to rigidify small molecules of 2, 3, or 4
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atoms, e.g. water molecules. That fix treats the constituent atoms as
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point masses.
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</P>
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<P>These fixes also update the positions and velocities of the atoms in
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each rigid body via time integration. The <I>rigid</I> and <I>rigid/nve</I>
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styles do this via constant NVE integration. The only difference is
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that the <I>rigid</I> style uses an integration technique based on
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Richardson iterations. The <I>rigid/nve</I> style uses the methods
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described in the paper by <A HREF = "#Miller">Miller</A>, which are thought to
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provide better energy conservation than an iterative approach.
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</P>
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<P>The <I>rigid/nvt</I> style performs constant NVT integration using a
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Nose/Hoover thermostat with chains as described originally in
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<A HREF = "#Hoover">(Hoover)</A> and <A HREF = "#Martyna">(Martyna)</A>, which thermostats both
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the translational and rotational degrees of freedom of the rigid
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bodies. The rigid-body algorithm used by <I>rigid/nvt</I> is described in
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the paper by <A HREF = "#Kamberaj">Kamberaj</A>.
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</P>
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<P>IMPORTANT NOTE: You should not update the atoms in rigid bodies via
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other time-integration fixes (e.g. nve, nvt, npt), or you will be
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integrating their motion more than once each timestep.
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</P>
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<P>IMPORTANT NOTE: These fixes are overkill if you simply want to hold a
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collection of atoms stationary or have them move with a constant
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velocity. A simpler way to hold atoms stationary is to not include
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those atoms in your time integration fix. E.g. use "fix 1 mobile nve"
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instead of "fix 1 all nve", where "mobile" is the group of atoms that
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you want to move. You can move atoms with a constant velocity by
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assigning them an initial velocity (via the <A HREF = "velocity.html">velocity</A>
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command), 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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</P>
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<HR>
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<P>The constituent particles within a rigid body can be point particles
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(the default in LAMMPS) or finite-size particles, such as spheroids
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and ellipsoids. See the <A HREF = "shape.html">shape</A> command and <A HREF = "atom_style.html">atom_style
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granular</A> for more details on these kinds of
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particles. Finite-size particles contribute differently to the moment
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of inertia of a rigid body than do point particles. Finite-size
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particles can also experience torque (e.g. due to <A HREF = "pair_gran.html">frictional granular
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interactions</A>) and have an orientation. These
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contributions are accounted for by these fixes.
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</P>
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<P>Forces between particles within a body do not contribute to the
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external force or torque on the body. Thus for computational
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efficiency, you may wish to turn off pairwise and bond interactions
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between particles within each rigid body. The <A HREF = "neigh_modify.html">neigh_modify
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exclude</A> and <A HREF = "delete_bonds.html">delete_bonds</A>
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commands are used to do this. For finite-size particles this also
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means the particles can be highly overlapped when creating the rigid
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body.
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</P>
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<HR>
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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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</P>
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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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</P>
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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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</P>
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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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included in each rigid body.
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</P>
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<P>By default, each rigid body is acted on by other atoms which induce an
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external force and torque on its center of mass, causing it to
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translate and rotate. Components of the external center-of-mass force
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and torque can be turned off by the <I>force</I> and <I>torque</I> keywords.
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This may be useful if you wish a body to rotate but not translate, or
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vice versa, or if you wish it to rotate or translate continuously
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unaffected by interactions with other particles. Note that if you
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expect a rigid body not to move or rotate by using these keywords, you
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must insure its initial center-of-mass translational or angular
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velocity is 0.0. Otherwise the initial translational or angular
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momentum the body has will persist.
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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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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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</P>
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<P>For computational efficiency, you may wish to 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 typically define one fix
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rigid which includes all the desired rigid bodies. LAMMPS will allow
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multiple rigid fixes to be defined, but it is more expensive.
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</P>
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<HR>
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<P>As stated above, the <I>rigid</I> and <I>rigid/nve</I> styles perform constant
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NVE time integration. Thus the <I>temp</I>, <I>press</I>, and <I>tparam</I> keywords
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cannot be used with these styles.
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</P>
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<P>The <I>rigid/nvt</I> style performs constant NVT time integration, using a
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temperature it computes for the rigid bodies which includes their
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translational and rotational motion. The <I>temp</I> keyword must be used
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with this style. The desired temperature at each timestep is a ramped
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value during the run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter
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is specified in time units and determines how rapidly the temperature
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is relaxed. For example, a value of 100.0 means to relax the
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temperature in a timespan of (roughly) 100 time units (tau or fmsec or
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psec - see the <A HREF = "units.html">units</A> command).
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</P>
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<P>Nose/Hoover chains are used in conjunction with this thermostat. The
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<I>tparam</I> keyword can optionally be used to change the chain settings
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used. <I>Tchain</I> is the number of thermostats in the Nose Hoover chain.
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This value, along with <I>Tdamp</I> can be varied to dampen undesirable
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oscillations in temperature that can occur in a simulation. As a rule
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of thumb, increasing the chain length should lead to smaller
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oscillations.
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</P>
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<P>There are alternate ways to thermostat a system of rigid bodies. You
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can use <A HREF = "fix_langevin.html">fix langevin</A> to treat the system as
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effectively immersed in an implicit solvent, e.g. a Brownian dynamics
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model. For hybrid systems with both rigid bodies and solvent
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particles, you can thermostat only the solvent particles that surround
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one or more rigid bodies by appropriate choice of groups in the
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compute and fix commands for temperature and thermostatting. The
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solvent interactions with the rigid bodies should then effectively
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thermostat the rigid body temperature as well.
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</P>
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<HR>
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<P>If you use a <A HREF = "compute.html">temperature compute</A> with a group that
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includes particles in rigid bodies, the degrees-of-freedom removed by
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each rigid body are accounted for in the temperature (and pressure)
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computation, but only if the temperature group includes all the
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particles in a particular rigid body.
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</P>
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<P>A 3d rigid body has 6 degrees of freedom (3 translational, 3
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rotational), except for a collection of point particles lying on a
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straight line, which has only 5, e.g a dimer. A 2d rigid body has 3
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degrees of freedom (2 translational, 1 rotational).
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</P>
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<P>IMPORTANT NOTE: You may wish to explicitly subtract additional
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degrees-of-freedom if you use the <I>force</I> and <I>torque</I> keywords to
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eliminate certain motions of one or more rigid bodies. LAMMPS does
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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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</P>
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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 = "compute_msd.html">compute
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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. 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.html">replicate</A> command to
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increase the system size.
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</P>
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<HR>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about the <I>rigid</I> and <I>rigid/nve</I> fixes are written to
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<A HREF = "restart.html">binary restart files</A>. For style <I>rigid/nvt</I> the state
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of the Nose/Hoover thermostat is written to <A HREF = "restart.html">binary restart
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files</A>. See the <A HREF = "read_restart.html">read_restart</A> command
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for info on how to re-specify a fix in an input script that reads a
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restart file, so that the operation of the fix continues in an
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uninterrupted fashion.
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</P>
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<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to these
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fixes.
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</P>
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<P>These fixes compute a global array of values which can be accessed by
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various <A HREF = "Section_howto.html#4_15">output commands</A>. The number of rows
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in the array is equal to the number of rigid bodies. The number of
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columns is 12. Thus for each rigid body, 12 values are stored: the
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xyz coords of the center of mass (COM), the xyz components of the COM
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velocity, the xyz components of the force acting on the COM, and the
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xyz components of the torque acting on the COM. The force and torque
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values in the array are not affected by the <I>force</I> and <I>torque</I>
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keywords in the fix rigid command; they reflect values before any
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changes are made by those keywords.
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</P>
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<P>The ordering of the rigid bodies (by row in the array) is as follows.
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For the <I>single</I> keyword there is just one rigid body. For the
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<I>molecule</I> keyword, the bodies are ordered by ascending molecule ID.
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For the <I>group</I> keyword, the list of group IDs determines the ordering
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of bodies.
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</P>
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<P>The array values calculated by these fixes are "intensive", meaning
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they are independent of the number of atoms in the simulation.
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</P>
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<P>No parameter of these fixes can be used with the <I>start/stop</I> keywords
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of the <A HREF = "run.html">run</A> command. These fixes are not invoked during
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<A HREF = "minimize.html">energy minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>These fixes performs an MPI_Allreduce each timestep that is
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proportional in length to the number of rigid bodies. Hence they will
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not scale well in parallel if large numbers of rigid bodies are
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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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<P><B>Default:</B>
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</P>
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<P>The option defaults are force * on on on and torque * on on on,
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meaning all rigid bodies are acted on by center-of-mass force and
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torque. Also Tchain = 10, Titer = 1, Torder = 3.
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</P>
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<HR>
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<A NAME = "Hoover"></A>
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<P><B>(Hoover)</B> Hoover, Phys Rev A, 31, 1695 (1985).
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</P>
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<A NAME = "Kamberaj"></A>
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<P><B>(Kamberaj)</B> Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).
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</P>
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<A NAME = "Martyna"></A>
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<P><B>(Martyna)</B> Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
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Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
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</P>
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<A NAME = "Miller"></A>
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<P><B>(Miller)</B> Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
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J Chem Phys, 116, 8649 (2002).
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</P>
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<A NAME = "Zhang"></A>
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<P><B>(Zhang)</B> Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).
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</P>
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</HTML>
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