lammps/doc/fix_rigid.txt

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)

:line

fix rigid :h3

[Syntax:]

fix ID group-ID rigid bodystyle args keyword values ... :pre

ID, group-ID are documented in "fix"_fix.html command :ulb,l
rigid = style name of this fix command :l
bodystyle = {single} or {molecule} or {group} :l
  {single} args = none
  {molecule} args = none
  {group} args = N groupID1 groupID2 ...
    N = # of groups
    groupID1, groupID2, ... = list of N group IDs :pre

zero or more keyword/value pairs may be appended :l
keyword = {force} or {torque} :l
  {force} values = M xflag yflag zflag
    M = which rigid body from 1-Nbody (see asterisk form below)
    xflag,yflag,zflag = off/on if component of center-of-mass force is active
  {torque} values = M xflag yflag zflag
    M = which rigid body from 1-Nbody (see asterisk form below)
    xflag,yflag,zflag = off/on if component of center-of-mass torque is active :pre
:ule

[Examples:]

fix 1 clump rigid single
fix 1 clump rigid single force 1 off off on
fix 1 polychains rigid molecule
fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
fix 2 fluid rigid group 3 clump1 clump2 clump3
fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off :pre

[Description:]

Treat one or more sets of atoms as independent rigid bodies.  This
means that each timestep the total force and torque on each rigid body
is computed as the sum of the forces and torques on its constituent
particles and the coordinates, velocities, and orientations of the
atoms in each body are updated so that the body moves and rotates as a
single entity.

Examples of large rigid bodies are a large colloidal particle, or
portions of a large biomolecule such as a protein.

Example of small rigid bodies are patchy nanoparticles, such as those
modeled in "this paper"_#Zhang by Sharon Glotzer's group, clumps of
granular particles, lipid molecules consiting of one or more point
dipoles connected to other spheroids or ellipsoids, and coarse-grain
models of nano or colloidal particles consisting of a small number of
constituent particles.  Note that the "fix shake"_fix_shake.html
command can also be used to rigidify small molecules of 2, 3, or 4
atoms, e.g. water molecules.  That fix treats the constituent atoms as
point masses.

The constituent particles within a rigid body can be point particles
(the default in LAMMPS) or finite-size particles, such as spheroids
and ellipsoids.  See the "shape"_shape.html command and "atom_style
granular"_atom_style.html for more details on these kinds of
particles.  Finite-size particles contribute differently to the moment
of inertia of a rigid body than do point particles.  Finite-size
particles can also experience torque (e.g. due to "frictional granular
interactions"_pair_gran.html) and have an orientation.  These
contributions are accounted for by the fix.

Forces between particles within a body do not contribute to the
external force or torque on the body.  Thus for computational
efficiency, you may wish to turn off pairwise and bond interactions
between particles within each rigid body.  The "neigh_modify
exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html
commands are used to do this.  For finite-size particles this also
means the particles can be highly overlapped when creating the rigid
body.

IMPORTANT NOTE: This fix is overkill if you simply want to hold a
collection of atoms stationary or have them move with a constant
velocity.  A simpler way to hold atoms stationary is to not include
those atoms in your time integration fix.  E.g. use "fix 1 mobile nve"
instead of "fix 1 all nve", where "mobile" is the group of atoms that
you want to move.  You can move atoms with a constant velocity by
assigning them an initial velocity (via the "velocity"_velocity.html
command), setting the force on them to 0.0 (via the "fix
setforce"_fix_setforce.html command), and integrating them as usual
(e.g. via the "fix nve"_fix_nve.html command).

IMPORTANT NOTE: This fix updates the positions and velocities of the
rigid atoms with a constant-energy time integration, so you should not
update the same atoms via other fixes (e.g. nve, nvt, npt).

:line

Each body must have two or more atoms.  An atom can belong to at most
one rigid body.  Which atoms are in which bodies can be defined via
several options.

For bodystyle {single} the entire fix group of atoms is treated as one
rigid body.

For bodystyle {molecule}, each set of atoms in the fix group with a
different molecule ID is treated as a rigid body.

For bodystyle {group}, each of the listed groups is treated as a
separate rigid body.  Only atoms that are also in the fix group are
included in each rigid body.

By default, each rigid body is acted on by other atoms which induce an
external force and torque on its center of mass, causing it to
translate and rotate.  Components of the external center-of-mass force
and torque can be turned off by the {force} and {torque} keywords.
This may be useful if you wish a body to rotate but not translate, or
vice versa, or if you wish it to rotate or translate continuously
unaffected by interactions with other particles.  Note that if you
expect a rigid body not to move or rotate by using these keywords, you
must insure its initial center-of-mass translational or angular
velocity is 0.0.  Otherwise the initial translational or angular
momentum the body has will persist.

An xflag, yflag, or zflag set to {off} means turn off the component of
force of torque in that dimension.  A setting of {on} means turn on
the component, which is the default.  Which rigid body(s) the settings
apply to is determined by the first argument of the {force} and
{torque} keywords.  It can be an integer M from 1 to Nbody, where
Nbody is the number of rigid bodies defined.  A wild-card asterisk can
be used in place of, or in conjunction with, the M argument to set the
flags for multiple rigid bodies.  This takes the form "*" or "*n" or
"n*" or "m*n".  If N = the number of rigid bodies, then an asterisk
with no numeric values means all bodies from 1 to N.  A leading
asterisk means all bodies from 1 to n (inclusive).  A trailing
asterisk means all bodies from n to N (inclusive).  A middle asterisk
means all types from m to n (inclusive).  Note that you can use the
{force} or {torque} keywords as many times as you like.  If a
particular rigid body has its component flags set multiple times, the
settings from the final keyword are used.

For computational efficiency, you may wish to turn off pairwise and
bond interactions within each rigid body, as they no longer contribute
to the motion.  The "neigh_modify exclude"_neigh_modify.html and
"delete_bonds"_delete_bonds.html commands are used to do this.

For computational efficiency, you should define one fix rigid which
includes all the desired rigid bodies.  LAMMPS will allow multiple
rigid fixes to be defined, but it is more expensive.

This fix uses constant-energy NVE-style integration, so you may need
to impose additional constraints to control the temperature of an
ensemble of rigid bodies.  You can use "fix
langevin"_fix_langevin.html for this purpose to treat the system as
effectively immersed in an implicit solvent, e.g. a Brownian dynamics
model.  Or you can thermostat only the non-rigid atoms that surround
one or more rigid bodies (i.e. explicit solvent) by appropriate choice
of groups in the compute and fix commands for temperature and
thermostatting.

If you calculate a temperature for particles in the rigid bodies, the
degrees-of-freedom removed by each rigid body are accounted for in the
temperature (and pressure) computation, but only if the temperature
group includes all the particles in a particular rigid body.

A 3d rigid body has 6 degrees of freedom (3 translational, 3
rotational), except for a collection of point particles lying on a
straight line, which has only 5, e.g a dimer.  A 2d rigid body has 3
degrees of freedom (2 translational, 1 rotational).

IMPORTANT NOTE: You may wish to explicitly subtract additional
degrees-of-freedom if you use the {force} and {torque} keywords to
eliminate certain motions of one or more rigid bodies, as LAMMPS does
not do this automatically.

The rigid body contribution to the pressure of the system (virial) is
also accounted for by this fix.

IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
modified when the center-of-mass of the rigid body moves across a
periodic boundary.  They are not incremented/decremented as they would
be for non-rigid atoms.  This change does not affect dynamics, but
means that any diagnostic computation based on the atomic image flag
values must be adjusted accordingly.  For example, the "fix
msd"_fix_msd.html will not compute the expected mean-squared
displacement for such atoms, and the image flag values written to a
"dump file"_dump.html will be different than they would be if the
atoms were not in a rigid body.  It also means that if you have bonds
between a pair of rigid bodies and the bond straddles a periodic
boundary, you cannot use the "replicate"_replicate command to increase
the system size.

[Restart, fix_modify, output, run start/stop, minimize info:]

No information about this fix is written to "binary restart
files"_restart.html.  None of the "fix_modify"_fix_modify.html options
are relevant to this fix.

This fix computes a global array of values which can be accessed by
various "output commands"_Section_howto.html#4_15.  The number of rows
in the array is equal to the number of rigid bodies.  The number of
columns is 12.  Thus for each rigid body, 12 values are stored: the
xyz coords of the center of mass (COM), the xyz components of the COM
velocity, the xyz components of the force acting on the COM, and the
xyz components of the torque acting on the COM.  The force and torque
values in the array are not affected by the {force} and {torque}
keywords in the fix rigid command; they reflect values before any
changes are made by those keywords.

The ordering of the rigid bodies (by row in the array) is as follows.
For the {single} keyword there is just one rigid body.  For the
{molecule} keyword, the bodies are ordered by ascending molecule ID.
For the {group} keyword, the list of group IDs determines the ordering
of bodies.

The array values calculated by this fix are "intensive", meaning they
are independent of the number of atoms in the simulation.

No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.  This fix is not invoked during "energy
minimization"_minimize.html.

[Restrictions:]

This fix performs an MPI_Allreduce each timestep that is proportional
in length to the number of rigid bodies.  Hence it will not scale well
in parallel if large numbers of rigid bodies are simulated.

If the atoms in a single rigid body initially straddle a periodic
boundary, the input data file must define the image flags for each
atom correctly, so that LAMMPS can "unwrap" the atoms into a valid
rigid body.

[Related commands:]

"delete_bonds"_delete_bonds.html, "neigh_modify"_neigh_modify.html
exclude

[Default:]

The option defaults are force * on on on and torque * on on on meaning
all rigid bodies are acted on by center-of-mass force and torque.

:line

:link(Zhang)
[(Zhang)] Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).