<li><pclass="first">ID, group-ID are documented in <aclass="reference internal"href="fix.html"><spanclass="doc">fix</span></a> command</p>
</li>
<li><pclass="first">style = <em>rigid</em> or <em>rigid/nve</em> or <em>rigid/nvt</em> or <em>rigid/npt</em> or <em>rigid/nph</em> or <em>rigid/small</em> or <em>rigid/nve/small</em> or <em>rigid/nvt/small</em> or <em>rigid/npt/small</em> or <em>rigid/nph/small</em></p>
</li>
<li><pclass="first">bodystyle = <em>single</em> or <em>molecule</em> or <em>group</em></p>
<preclass="literal-block">
<em>single</em> args = none
<em>molecule</em> args = none
<em>group</em> args = N groupID1 groupID2 ...
N = # of groups
groupID1, groupID2, ... = list of N group IDs
</pre>
</li>
<li><pclass="first">zero or more keyword/value pairs may be appended</p>
</li>
<li><pclass="first">keyword = <em>langevin</em> or <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>couple</em> or <em>tparam</em> or <em>pchain</em> or <em>dilate</em> or <em>force</em> or <em>torque</em> or <em>infile</em></p>
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
Tdamp = temperature damping parameter (time units)
seed = random number seed to use for white noise (positive integer)
<em>temp</em> values = Tstart Tstop Tdamp
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
Tdamp = temperature damping parameter (time units)
<em>iso</em> or <em>aniso</em> values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<em>x</em> or <em>y</em> or <em>z</em> values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
<em>couple</em> = <em>none</em> or <em>xyz</em> or <em>xy</em> or <em>yz</em> or <em>xz</em>
<em>tparam</em> values = Tchain Titer Torder
Tchain = length of Nose/Hoover thermostat chain
Titer = number of thermostat iterations performed
Torder = 3 or 5 = Yoshida-Suzuki integration parameters
<em>pchain</em> values = Pchain
Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
<em>dilate</em> value = dilate-group-ID
dilate-group-ID = only dilate atoms in this group due to barostat volume changes
<em>force</em> 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
<em>torque</em> 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
<em>infile</em> filename
filename = file with per-body values of mass, center-of-mass, moments of inertia
<em>mol</em> value = template-ID
template-ID = ID of molecule template specified in a separate <aclass="reference internal"href="molecule.html"><spanclass="doc">molecule</span></a> command
</pre>
</li>
</ul>
</div>
<divclass="section"id="examples">
<h2>Examples</h2>
<preclass="literal-block">
fix 1 clump rigid single
fix 1 clump rigid/small molecule
fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
<p>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. The coordinates, velocities, and orientations of the atoms
in each body are then updated so that the body moves and rotates as a
single entity.</p>
<p>Examples of large rigid bodies are a colloidal particle, or portions
of a biomolecule such as a protein.</p>
<p>Example of small rigid bodies are patchy nanoparticles, such as those
modeled in <aclass="reference internal"href="pair_gran.html#zhang"><spanclass="std std-ref">this paper</span></a> by Sharon Glotzer’s group, clumps of
granular particles, lipid molecules consiting of one or more point
dipoles connected to other spheroids or ellipsoids, irregular
particles built from line segments (2d) or triangles (3d), and
coarse-grain models of nano or colloidal particles consisting of a
small number of constituent particles. Note that the <aclass="reference internal"href="fix_shake.html"><spanclass="doc">fix shake</span></a> 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.</p>
<p>These fixes also update the positions and velocities of the atoms in
each rigid body via time integration, in the NVE, NVT, NPT, or NPH
ensemble, as described below.</p>
<p>There are two main variants of this fix, fix rigid and fix
rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two
variants, as their style names indicate.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">Not all of the <em>bodystyle</em> options and keyword/value options are
available for both the <em>rigid</em> and <em>rigid/small</em> variants. See
details below.</p>
</div>
<p>The <em>rigid</em> styles are typically the best choice for a system with a
small number of large rigid bodies, each of which can extend across
the domain of many processors. It operates by creating a single
global list of rigid bodies, which all processors contribute to.
MPI_Allreduce operations are performed each timestep to sum the
contributions from each processor to the force and torque on all the
bodies. This operation will not scale well in parallel if large
numbers of rigid bodies are simulated.</p>
<p>The <em>rigid/small</em> styles are typically best for a system with a large
number of small rigid bodies. Each body is assigned to the atom
closest to the geometrical center of the body. The fix operates using
local lists of rigid bodies owned by each processor and information is
exchanged and summed via local communication between neighboring
processors when ghost atom info is accumlated.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">To use the <em>rigid/small</em> styles the ghost atom cutoff must be
large enough to span the distance between the atom that owns the body
and every other atom in the body. This distance value is printed out
when the rigid bodies are defined. If the
<aclass="reference internal"href="pair_style.html"><spanclass="doc">pair_style</span></a> cutoff plus neighbor skin does not span
this distance, then you should use the <aclass="reference internal"href="comm_modify.html"><spanclass="doc">comm_modify cutoff</span></a> command with a setting epsilon larger than
the distance.</p>
</div>
<p>Which of the two variants is faster for a particular problem is hard
to predict. The best way to decide is to perform a short test run.
Both variants should give identical numerical answers for short runs.
Long runs should give statistically similar results, but round-off
differences may accumulate to produce divergent trajectories.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">You should not update the atoms in rigid bodies via other
time-integration fixes (e.g. <aclass="reference internal"href="fix_nve.html"><spanclass="doc">fix nve</span></a>, <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix nvt</span></a>, <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix npt</span></a>), or you will be integrating
their motion more than once each timestep. When performing a hybrid
simulation with some atoms in rigid bodies, and some not, a separate
time integration fix like <aclass="reference internal"href="fix_nve.html"><spanclass="doc">fix nve</span></a> or <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix nvt</span></a> should be used for the non-rigid particles.</p>
</div>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">These fixes are 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 <aclass="reference internal"href="velocity.html"><spanclass="doc">velocity</span></a> command),
setting the force on them to 0.0 (via the <aclass="reference internal"href="fix_setforce.html"><spanclass="doc">fix setforce</span></a> command), and integrating them as usual
(e.g. via the <aclass="reference internal"href="fix_nve.html"><spanclass="doc">fix nve</span></a> command).</p>
</div>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">The aggregate properties of each rigid body are calculated one
time at the start of the first simulation run after these fixes are
specified. The properties include the position and velocity of the
center-of-mass of the body, its moments of inertia, and its angular
momentum. This is done using the properties of the constituent atoms
of the body at that point in time (or see the <em>infile</em> keyword
option). Thereafter, changing properties of individual atoms in the
body will have no effect on a rigid body’s dynamics, unless they
affect the <aclass="reference internal"href="pair_style.html"><spanclass="doc">pair_style</span></a> interactions that individual
particles are part of. For example, you might think you could
displace the atoms in a body or add a large velocity to each atom in a
body to make it move in a desired direction before a 2nd run is
performed, using the <aclass="reference internal"href="set.html"><spanclass="doc">set</span></a> or
<aclass="reference internal"href="displace_atoms.html"><spanclass="doc">displace_atoms</span></a> or <aclass="reference internal"href="velocity.html"><spanclass="doc">velocity</span></a>
command. But these commands will not affect the internal attributes
of the body, and the position and velocity of individual atoms in the
body will be reset when time integration starts.</p>
</div>
<hrclass="docutils"/>
<p>Each rigid 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.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">With the <em>rigid/small</em> styles, which require that <em>bodystyle</em> be
specified as <em>molecule</em>, you can define a system that has no rigid
bodies initially. This is useful when you are using the <em>mol</em> keyword
in conjunction with another fix that is adding rigid bodies on-the-fly
as molecules, such as <aclass="reference internal"href="fix_deposit.html"><spanclass="doc">fix deposit</span></a> or <aclass="reference internal"href="fix_pour.html"><spanclass="doc">fix pour</span></a>.</p>
</div>
<p>For bodystyle <em>single</em> the entire fix group of atoms is treated as one
rigid body. This option is only allowed for the <em>rigid</em> styles.</p>
<p>For bodystyle <em>molecule</em>, each set of atoms in the fix group with a
different molecule ID is treated as a rigid body. This option is
allowed for both the <em>rigid</em> and <em>rigid/small</em> styles. Note that
atoms with a molecule ID = 0 will be treated as a single rigid body.
For a system with atomic solvent (typically this is atoms with
molecule ID = 0) surrounding rigid bodies, this may not be what you
want. Thus you should be careful to use a fix group that only
includes atoms you want to be part of rigid bodies.</p>
<p>For bodystyle <em>group</em>, 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. This option is only allowed for the
<em>rigid</em> styles.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">To compute the initial center-of-mass position and other
properties of each rigid body, the image flags for each atom in the
body are used to “unwrap” the atom coordinates. Thus you must insure
that these image flags are consistent so that the unwrapping creates a
valid rigid body (one where the atoms are close together),
particularly if the atoms in a single rigid body straddle a periodic
boundary. This means the input data file or restart file must define
the image flags for each atom consistently or that you have used the
<aclass="reference internal"href="set.html"><spanclass="doc">set</span></a> command to specify them correctly. If a dimension is
non-periodic then the image flag of each atom must be 0 in that
dimension, else an error is generated.</p>
</div>
<p>The <em>force</em> and <em>torque</em> keywords discussed next are only allowed for
the <em>rigid</em> styles.</p>
<p>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 <em>force</em> and <em>torque</em> 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.</p>
<p>An xflag, yflag, or zflag set to <em>off</em> means turn off the component of
force of torque in that dimension. A setting of <em>on</em> 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 <em>force</em> and
<em>torque</em> 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
<em>force</em> or <em>torque</em> 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.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">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 <aclass="reference internal"href="neigh_modify.html"><spanclass="doc">neigh_modify exclude</span></a> and <aclass="reference internal"href="delete_bonds.html"><spanclass="doc">delete_bonds</span></a>
commands are used to do this. If the rigid bodies have strongly
overalapping atoms, you may need to turn off these interactions to
avoid numerical problems due to large equal/opposite intra-body forces
swamping the contribution of small inter-body forces.</p>
</div>
<p>For computational efficiency, you should typically define one fix
rigid or fix rigid/small command which includes all the desired rigid
bodies. LAMMPS will allow multiple rigid fixes to be defined, but it
is more expensive.</p>
<hrclass="docutils"/>
<p>The constituent particles within a rigid body can be point particles
(the default in LAMMPS) or finite-size particles, such as spheres or
ellipsoids or line segments or triangles. See the <aclass="reference internal"href="atom_style.html"><spanclass="doc">atom_style sphere and ellipsoid and line and tri</span></a> commands 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 <aclass="reference internal"href="pair_gran.html"><spanclass="doc">frictional granular interactions</span></a>) and have an
orientation. These contributions are accounted for by these fixes.</p>
<p>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 <aclass="reference internal"href="neigh_modify.html"><spanclass="doc">neigh_modify exclude</span></a> and <aclass="reference internal"href="delete_bonds.html"><spanclass="doc">delete_bonds</span></a>
commands are used to do this. For finite-size particles this also
means the particles can be highly overlapped when creating the rigid
body.</p>
<hrclass="docutils"/>
<p>The <em>rigid</em>, <em>rigid/nve</em>, <em>rigid/small</em>, and <em>rigid/small/nve</em> styles
perform constant NVE time integration. They are referred to below as
the 4 NVE rigid styles. The only difference is that the <em>rigid</em> and
<em>rigid/small</em> styles use an integration technique based on Richardson
iterations. The <em>rigid/nve</em> and <em>rigid/small/nve</em> styles uses the
methods described in the paper by <aclass="reference internal"href="#miller"><spanclass="std std-ref">Miller</span></a>, which are thought
to provide better energy conservation than an iterative approach.</p>
<p>The <em>rigid/nvt</em> and <em>rigid/nvt/small</em> styles performs constant NVT
integration using a Nose/Hoover thermostat with chains as described
originally in <aclass="reference internal"href="#hoover"><spanclass="std std-ref">(Hoover)</span></a> and <aclass="reference internal"href="#martyna"><spanclass="std std-ref">(Martyna)</span></a>, which
thermostats both the translational and rotational degrees of freedom
of the rigid bodies. They are referred to below as the 2 NVT rigid
styles. The rigid-body algorithm used by <em>rigid/nvt</em> is described in
the paper by <aclass="reference internal"href="#kamberaj"><spanclass="std std-ref">Kamberaj</span></a>.</p>
<p>The <em>rigid/npt</em>, <em>rigid/nph</em>, <em>rigid/npt/small</em>, and <em>rigid/nph/small</em>
styles perform constant NPT or NPH integration using a Nose/Hoover
barostat with chains. They are referred to below as the 4 NPT and NPH
rigid styles. For the NPT case, the same Nose/Hoover thermostat is
also used as with <em>rigid/nvt</em> and <em>rigid/nvt/small</em>.</p>
<p>The barostat parameters are specified using one or more of the <em>iso</em>,
<em>aniso</em>, <em>x</em>, <em>y</em>, <em>z</em> and <em>couple</em> keywords. These keywords give you
the ability to specify 3 diagonal components of the external stress
tensor, and to couple these components together so that the dimensions
they represent are varied together during a constant-pressure
simulation. The effects of these keywords are similar to those
defined in <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix npt/nph</span></a></p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">Currently the <em>rigid/npt</em>, <em>rigid/nph</em>, <em>rigid/npt/small</em>, and
<em>rigid/nph/small</em> styles do not support triclinic (non-orthongonal)
boxes.</p>
</div>
<p>The target pressures for each of the 6 components of the stress tensor
can be specified independently via the <em>x</em>, <em>y</em>, <em>z</em> keywords, which
correspond to the 3 simulation box dimensions. For each component,
the external pressure or tensor component at each timestep is a ramped
value during the run from <em>Pstart</em> to <em>Pstop</em>. If a target pressure is
specified for a component, then the corresponding box dimension will
change during a simulation. For example, if the <em>y</em> keyword is used,
the y-box length will change. A box dimension will not change if that
component is not specified, although you have the option to change
that dimension via the <aclass="reference internal"href="fix_deform.html"><spanclass="doc">fix deform</span></a> command.</p>
<p>For all barostat keywords, the <em>Pdamp</em> parameter operates like the
<em>Tdamp</em> parameter, determining the time scale on which pressure is
relaxed. For example, a value of 10.0 means to relax the pressure in
a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
the <aclass="reference internal"href="units.html"><spanclass="doc">units</span></a> command).</p>
<p>Regardless of what atoms are in the fix group (the only atoms which
are time integrated), a global pressure or stress tensor is computed
for all atoms. Similarly, when the size of the simulation box is
changed, all atoms are re-scaled to new positions, unless the keyword
<em>dilate</em> is specified with a <em>dilate-group-ID</em> for a group that
represents a subset of the atoms. This can be useful, for example, to
leave the coordinates of atoms in a solid substrate unchanged and
controlling the pressure of a surrounding fluid. Another example is a
system consisting of rigid bodies and point particles where the
barostat is only coupled with the rigid bodies. This option should be
used with care, since it can be unphysical to dilate some atoms and
not others, because it can introduce large, instantaneous
displacements between a pair of atoms (one dilated, one not) that are
far from the dilation origin.</p>
<p>The <em>couple</em> keyword allows two or three of the diagonal components of
the pressure tensor to be “coupled” together. The value specified
with the keyword determines which are coupled. For example, <em>xz</em>
means the <em>Pxx</em> and <em>Pzz</em> components of the stress tensor are coupled.
<em>Xyz</em> means all 3 diagonal components are coupled. Coupling means two
things: the instantaneous stress will be computed as an average of the
corresponding diagonal components, and the coupled box dimensions will
be changed together in lockstep, meaning coupled dimensions will be
dilated or contracted by the same percentage every timestep. The
<em>Pstart</em>, <em>Pstop</em>, <em>Pdamp</em> parameters for any coupled dimensions must
be identical. <em>Couple xyz</em> can be used for a 2d simulation; the <em>z</em>
dimension is simply ignored.</p>
<p>The <em>iso</em> and <em>aniso</em> keywords are simply shortcuts that are
equivalent to specifying several other keywords together.</p>
<p>The keyword <em>iso</em> means couple all 3 diagonal components together when
pressure is computed (hydrostatic pressure), and dilate/contract the
dimensions together. Using “iso Pstart Pstop Pdamp” is the same as
<p>The keyword/value option pairs are used in the following ways.</p>
<p>The <em>langevin</em> and <em>temp</em> and <em>tparam</em> keywords perform thermostatting
of the rigid bodies, altering both their translational and rotational
degrees of freedom. What is meant by “temperature” of a collection of
rigid bodies and how it can be monitored via the fix output is
discussed below.</p>
<p>The <em>langevin</em> keyword applies a Langevin thermostat to the constant
NVE time integration performed by any of the 4 NVE rigid styles:
<em>rigid</em>, <em>rigid/nve</em>, <em>rigid/small</em>, <em>rigid/small/nve</em>. It cannot be
used with the 2 NVT rigid styles: <em>rigid/nvt</em>, <em>rigid/small/nvt</em>. The
desired temperature at each timestep is a ramped value during the run
from <em>Tstart</em> to <em>Tstop</em>. The <em>Tdamp</em> parameter is specified in time
units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<aclass="reference internal"href="units.html"><spanclass="doc">units</span></a> command). The random # <em>seed</em> must be a positive
integer.</p>
<p>The way that Langevin thermostatting operates is explained on the <aclass="reference internal"href="fix_langevin.html"><spanclass="doc">fix langevin</span></a> doc page. If you wish to simply viscously
damp the rotational motion without thermostatting, you can set
<em>Tstart</em> and <em>Tstop</em> to 0.0, which means only the viscous drag term in
the Langevin thermostat will be applied. See the discussion on the
<aclass="reference internal"href="fix_viscous.html"><spanclass="doc">fix viscous</span></a> doc page for details.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">When the <em>langevin</em> keyword is used with fix rigid versus fix
rigid/small, different dynamics will result for parallel runs. This
is because of the way random numbers are used in the two cases. The
dynamics for the two cases should be statistically similar, but will
not be identical, even for a single timestep.</p>
</div>
<p>The <em>temp</em> and <em>tparam</em> keywords apply a Nose/Hoover thermostat to the
NVT time integration performed by the 2 NVT rigid styles. They cannot
be used with the 4 NVE rigid styles. The desired temperature at each
timestep is a ramped value during the run from <em>Tstart</em> to <em>Tstop</em>.
The <em>Tdamp</em> parameter is specified in time units and determines how
rapidly the temperature is relaxed. For example, a value of 100.0
means to relax the temperature in a timespan of (roughly) 100 time
units (tau or fmsec or psec - see the <aclass="reference internal"href="units.html"><spanclass="doc">units</span></a> command).</p>
<p>Nose/Hoover chains are used in conjunction with this thermostat. The
<em>tparam</em> keyword can optionally be used to change the chain settings
used. <em>Tchain</em> is the number of thermostats in the Nose Hoover chain.
This value, along with <em>Tdamp</em> can be varied to dampen undesirable
oscillations in temperature that can occur in a simulation. As a rule
of thumb, increasing the chain length should lead to smaller
oscillations. The keyword <em>pchain</em> specifies the number of
thermostats in the chain thermostatting the barostat degrees of
freedom.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">There are alternate ways to thermostat a system of rigid bodies.
You can use <aclass="reference internal"href="fix_langevin.html"><spanclass="doc">fix langevin</span></a> to treat the individual
particles in the rigid bodies as effectively immersed in an implicit
solvent, e.g. a Brownian dynamics model. For hybrid systems with both
rigid bodies and solvent particles, you can thermostat only the
solvent particles that surround one or more rigid bodies by
appropriate choice of groups in the compute and fix commands for
temperature and thermostatting. The solvent interactions with the
rigid bodies should then effectively thermostat the rigid body
temperature as well without use of the Langevin or Nose/Hoover options
associated with the fix rigid commands.</p>
</div>
<hrclass="docutils"/>
<p>The <em>mol</em> keyword can only be used with the <em>rigid/small</em> styles. It
must be used when other commands, such as <aclass="reference internal"href="fix_deposit.html"><spanclass="doc">fix deposit</span></a> or <aclass="reference internal"href="fix_pour.html"><spanclass="doc">fix pour</span></a>, add rigid
bodies on-the-fly during a simulation. You specify a <em>template-ID</em>
previously defined using the <aclass="reference internal"href="molecule.html"><spanclass="doc">molecule</span></a> command, which
reads a file that defines the molecule. You must use the same
<em>template-ID</em> that the other fix which is adding rigid bodies uses.
The coordinates, atom types, atom diameters, center-of-mass, and
moments of inertia can be specified in the molecule file. See the
<aclass="reference internal"href="molecule.html"><spanclass="doc">molecule</span></a> command for details. The only settings
required to be in this file are the coordinates and types of atoms in
the molecule, in which case the molecule command calculates the other
quantities itself.</p>
<p>Note that these other fixes create new rigid bodies, in addition to
those defined initially by this fix via the <em>bodystyle</em> setting.</p>
<p>Also note that when using the <em>mol</em> keyword, extra restart information
about all rigid bodies is written out whenever a restart file is
written out. See the NOTE in the next section for details.</p>
<hrclass="docutils"/>
<p>The <em>infile</em> keyword allows a file of rigid body attributes to be read
in from a file, rather then having LAMMPS compute them. There are 5
such attributes: the total mass of the rigid body, its center-of-mass
position, its 6 moments of inertia, its center-of-mass velocity, and
the 3 image flags of the center-of-mass position. For rigid bodies
consisting of point particles or non-overlapping finite-size
particles, LAMMPS can compute these values accurately. However, for
rigid bodies consisting of finite-size particles which overlap each
other, LAMMPS will ignore the overlaps when computing these 4
attributes. The amount of error this induces depends on the amount of
overlap. To avoid this issue, the values can be pre-computed
(e.g. using Monte Carlo integration).</p>
<p>The format of the file is as follows. Note that the file does not
have to list attributes for every rigid body integrated by fix rigid.
Only bodies which the file specifies will have their computed
attributes overridden. The file can contain initial blank lines or
comment lines starting with “#” which are ignored. The first
non-blank, non-comment line should list N = the number of lines to
follow. The N successive lines contain the following information:</p>
<p>The rigid body IDs are all positive integers. For the <em>single</em>
bodystyle, only an ID of 1 can be used. For the <em>group</em> bodystyle,
IDs from 1 to Ng can be used where Ng is the number of specified
groups. For the <em>molecule</em> bodystyle, use the molecule ID for the
atoms in a specific rigid body as the rigid body ID.</p>
<p>The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are
self-explanatory. The center-of-mass should be consistent with what
is calculated for the position of the rigid body with all its atoms
unwrapped by their respective image flags. If this produces a
center-of-mass that is outside the simulation box, LAMMPS wraps it
back into the box.</p>
<p>The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
values consistent with the current orientation of the rigid body
around its center of mass. The values are with respect to the
simulation box XYZ axes, not with respect to the prinicpal axes of the
rigid body itself. LAMMPS performs the latter calculation internally.</p>
<p>The (vxcm,vycm,vzcm) values are the velocity of the center of mass.
The (lx,ly,lz) values are the angular momentum of the body. The
(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you
wish the body to have no initial motion.</p>
<p>The (ixcm,iycm,izcm) values are the image flags of the center of mass
of the body. For periodic dimensions, they specify which image of the
simulation box the body is considered to be in. An image of 0 means
it is inside the box as defined. A value of 2 means add 2 box lengths
to get the true value. A value of -1 means subtract 1 box length to
get the true value. LAMMPS updates these flags as the rigid bodies
cross periodic boundaries during the simulation.</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">If you use the <em>infile</em> or <em>mol</em> keywords and write restart
files during a simulation, then each time a restart file is written,
the fix also write an auxiliary restart file with the name
rfile.rigid, where “rfile” is the name of the restart file,
e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
file is in the same format described above. Thus it can be used in a
new input script that restarts the run and re-specifies a rigid fix
using an <em>infile</em> keyword and the appropriate filename. Note that the
auxiliary file will contain one line for every rigid body, even if the
original file only listed a subset of the rigid bodies.</p>
</div>
<hrclass="docutils"/>
<p>If you use a <aclass="reference internal"href="compute.html"><spanclass="doc">temperature compute</span></a> with a group that
includes particles in 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.</p>
<p>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).</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">You may wish to explicitly subtract additional
degrees-of-freedom if you use the <em>force</em> and <em>torque</em> keywords to
eliminate certain motions of one or more rigid bodies. LAMMPS does
not do this automatically.</p>
</div>
<p>The rigid body contribution to the pressure of the system (virial) is
also accounted for by this fix.</p>
<hrclass="docutils"/>
<p>If your simlulation is a hybrid model with a mixture of rigid bodies
and non-rigid particles (e.g. solvent) there are several ways these
rigid fixes can be used in tandem with <aclass="reference internal"href="fix_nve.html"><spanclass="doc">fix nve</span></a>, <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix nvt</span></a>, <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix npt</span></a>, and <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix nph</span></a>.</p>
<p>If you wish to perform NVE dynamics (no thermostatting or
barostatting), use one of 4 NVE rigid styles to integrate the rigid
bodies, and <aclass="reference internal"href="fix_nve.html"><spanclass="doc">fix nve</span></a> to integrate the non-rigid
particles.</p>
<p>If you wish to perform NVT dynamics (thermostatting, but no
barostatting), you can use one of the 2 NVT rigid styles for the rigid
bodies, and any thermostatting fix for the non-rigid particles (<aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix nvt</span></a>, <aclass="reference internal"href="fix_langevin.html"><spanclass="doc">fix langevin</span></a>, <aclass="reference internal"href="fix_temp_berendsen.html"><spanclass="doc">fix temp/berendsen</span></a>). You can also use one of the
4 NVE rigid styles for the rigid bodies and thermostat them using <aclass="reference internal"href="fix_langevin.html"><spanclass="doc">fix langevin</span></a> on the group that contains all the
particles in the rigid bodies. The net force added by <aclass="reference internal"href="fix_langevin.html"><spanclass="doc">fix langevin</span></a> to each rigid body effectively thermostats
its translational center-of-mass motion. Not sure how well it does at
thermostatting its rotational motion.</p>
<p>If you with to perform NPT or NPH dynamics (barostatting), you cannot
use both <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix npt</span></a> and the NPT or NPH rigid styles. This
is because there can only be one fix which monitors the global
pressure and changes the simulation box dimensions. So you have 3
choices:</p>
<ulclass="simple">
<li>Use one of the 4 NPT or NPH styles for the rigid bodies. Use the
<em>dilate</em> all option so that it will dilate the positions of the
non-rigid particles as well. Use <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix nvt</span></a> (or any other
thermostat) for the non-rigid particles.</li>
<li>Use <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix npt</span></a> for the group of non-rigid particles. Use
the <em>dilate</em> all option so that it will dilate the center-of-mass
positions of the rigid bodies as well. Use one of the 4 NVE or 2 NVT
rigid styles for the rigid bodies.</li>
<li>Use <aclass="reference internal"href="fix_press_berendsen.html"><spanclass="doc">fix press/berendsen</span></a> to compute the
pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT
rigid styles for the rigid bodies. Use <aclass="reference external"href="fix_nh.thml">fix nvt</a> (or any
other thermostat) for the non-rigid particles.</li>
</ul>
<p>In all case, the rigid bodies and non-rigid particles both contribute
to the global pressure and the box is scaled the same by any of the
barostatting fixes.</p>
<p>You could even use the 2nd and 3rd options for a non-hybrid simulation
consisting of only rigid bodies, assuming you give <aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix npt</span></a> an empty group, though it’s an odd thing to do. The
barostatting fixes (<aclass="reference internal"href="fix_nh.html"><spanclass="doc">fix npt</span></a> and <aclass="reference internal"href="fix_press_berendsen.html"><spanclass="doc">fix press/berensen</span></a>) will monitor the pressure
and change the box dimensions, but not time integrate any particles.
The integration of the rigid bodies will be performed by fix
rigid/nvt.</p>
<hrclass="docutils"/>
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">Section 5</span></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <aclass="reference internal"href="Section_start.html#start-3"><spanclass="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <aclass="reference internal"href="Section_start.html#start-7"><spanclass="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <aclass="reference internal"href="suffix.html"><spanclass="doc">suffix</span></a> command in your input script.</p>
<p>See <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">Section 5</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hrclass="docutils"/>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<p>No information about the 4 NVE rigid styles is written to <aclass="reference internal"href="restart.html"><spanclass="doc">binary restart files</span></a>. The exception is if the <em>infile</em> or
<em>mol</em> keyword is used, in which case an auxiliary file is written out
with rigid body information each time a restart file is written, as
explained above for the <em>infile</em> keyword. For the 2 NVT rigid styles,
the state of the Nose/Hoover thermostat is written to <aclass="reference internal"href="restart.html"><spanclass="doc">binary restart files</span></a>. Ditto for the 4 NPT and NPH rigid styles, and
the state of the Nose/Hoover barostat. See the
<aclass="reference internal"href="read_restart.html"><spanclass="doc">read_restart</span></a> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.</p>
<p>The <aclass="reference internal"href="fix_modify.html"><spanclass="doc">fix_modify</span></a><em>energy</em> option is supported by the 6
NVT, NPT, NPH rigid styles to add the energy change induced by the
thermostatting to the system’s potential energy as part of
<p>The <aclass="reference internal"href="fix_modify.html"><spanclass="doc">fix_modify</span></a><em>temp</em> and <em>press</em> options are
supported by the 4 NPT and NPH rigid styles to change the computes
used to calculate the instantaneous pressure tensor. Note that the 2
NVT rigid fixes do not use any external compute to compute
instantaneous temperature.</p>
<p>The 2 NVE rigid fixes compute a global scalar which can be accessed by
various <aclass="reference internal"href="Section_howto.html#howto-15"><spanclass="std std-ref">output commands</span></a>. The scalar
value calculated by these fixes is “intensive”. The scalar is the
current temperature of the collection of rigid bodies. This is
averaged over all rigid bodies and their translational and rotational
degrees of freedom. The translational energy of a rigid body is 1/2 m
v^2, where m = total mass of the body and v = the velocity of its
center of mass. The rotational energy of a rigid body is 1/2 I w^2,
where I = the moment of inertia tensor of the body and w = its angular
velocity. Degrees of freedom constrained by the <em>force</em> and <em>torque</em>
keywords are removed from this calculation, but only for the <em>rigid</em>
and <em>rigid/nve</em> fixes.</p>
<p>The 6 NVT, NPT, NPH rigid fixes compute a global scalar which can be
accessed by various <aclass="reference internal"href="Section_howto.html#howto-15"><spanclass="std std-ref">output commands</span></a>.
The scalar value calculated by these fixes is “extensive”. The scalar
is the cumulative energy change due to the thermostatting and
barostatting the fix performs.</p>
<p>All of the <em>rigid</em> styles (not the <em>rigid/small</em> styles) compute a
global array of values which can be accessed by various <aclass="reference internal"href="Section_howto.html#howto-15"><spanclass="std std-ref">output commands</span></a>. Similar information about the
bodies defined by the <em>rigid/small</em> styles can be accessed via the
<p>These fixes are all part of the RIGID package. It is only enabled if
LAMMPS was built with that package. See the <aclass="reference internal"href="Section_start.html#start-3"><spanclass="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>Assigning a temperature via the <aclass="reference internal"href="velocity.html"><spanclass="doc">velocity create</span></a>
command to a system with <aclass="reference internal"href="#"><spanclass="doc">rigid bodies</span></a> may not have
the desired outcome for two reasons. First, the velocity command can
be invoked before the rigid-body fix is invoked or initialized and the
number of adjusted degrees of freedom (DOFs) is known. Thus it is not
possible to compute the target temperature correctly. Second, the
assigned velocities may be partially canceled when constraints are
first enforced, leading to a different temperature than desired. A
workaround for this is to perform a <aclass="reference internal"href="run.html"><spanclass="doc">run 0</span></a> command, which
insures all DOFs are accounted for properly, and then rescale the
temperature to the desired value before performing a simulation. For
<spanclass="n">run</span><spanclass="mi">0</span><spanclass="c1"># temperature may not be 300K</span>
<spanclass="n">velocity</span><spanclass="nb">all</span><spanclass="n">scale</span><spanclass="mf">300.0</span><spanclass="c1"># now it should be</span>
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