2006-09-22 00:22:34 +08:00
|
|
|
<HTML>
|
|
|
|
<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>
|
|
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
|
2010-05-02 08:59:55 +08:00
|
|
|
<H3>fix rigid command
|
|
|
|
</H3>
|
|
|
|
<H3>fix rigid/nve command
|
|
|
|
</H3>
|
|
|
|
<H3>fix rigid/nvt command
|
2006-09-22 00:22:34 +08:00
|
|
|
</H3>
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<PRE>fix ID group-ID style bodystyle args keyword values ...
|
2006-09-22 00:22:34 +08:00
|
|
|
</PRE>
|
|
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
|
2010-05-02 08:59:55 +08:00
|
|
|
<LI>style = <I>rigid</I> or <I>rigid/nve</I> or <I>rigid/nvt</I>
|
2006-09-22 00:22:34 +08:00
|
|
|
|
2009-01-13 22:38:26 +08:00
|
|
|
<LI>bodystyle = <I>single</I> or <I>molecule</I> or <I>group</I>
|
2006-09-22 00:22:34 +08:00
|
|
|
|
2009-01-13 22:38:26 +08:00
|
|
|
<PRE> <I>single</I> args = none
|
|
|
|
<I>molecule</I> args = none
|
|
|
|
<I>group</I> args = N groupID1 groupID2 ...
|
|
|
|
N = # of groups
|
|
|
|
groupID1, groupID2, ... = list of N group IDs
|
|
|
|
</PRE>
|
|
|
|
<LI>zero or more keyword/value pairs may be appended
|
|
|
|
|
2011-04-30 00:27:56 +08:00
|
|
|
<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>tparam</I> or <I>force</I> or <I>torque</I>
|
2009-01-13 22:38:26 +08:00
|
|
|
|
2011-04-30 00:27:56 +08:00
|
|
|
<PRE> <I>langevin</I> values = Tstart Tstop Tperiod seed
|
|
|
|
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)
|
|
|
|
<I>temp</I> values = Tstart Tstop Tdamp
|
2010-05-02 08:59:55 +08:00
|
|
|
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
|
|
|
|
Tdamp = temperature damping parameter (time units)
|
|
|
|
<I>tparam</I> 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
|
|
|
|
<I>force</I> values = M xflag yflag zflag
|
2009-01-13 22:38:26 +08:00
|
|
|
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
|
|
|
|
<I>torque</I> 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
|
2006-09-22 00:22:34 +08:00
|
|
|
</PRE>
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
</P>
|
|
|
|
<PRE>fix 1 clump rigid single
|
2011-04-30 00:27:56 +08:00
|
|
|
fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
|
2010-05-02 08:59:55 +08:00
|
|
|
fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
|
2009-01-13 22:38:26 +08:00
|
|
|
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 torque * off off off
|
2006-09-22 00:22:34 +08:00
|
|
|
</PRE>
|
|
|
|
<P><B>Description:</B>
|
|
|
|
</P>
|
2009-07-01 01:19:42 +08:00
|
|
|
<P>Treat one or more sets of atoms as independent rigid bodies. This
|
2006-09-22 00:22:34 +08:00
|
|
|
means that each timestep the total force and torque on each rigid body
|
2009-07-01 01:19:42 +08:00
|
|
|
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.
|
|
|
|
</P>
|
|
|
|
<P>Examples of large rigid bodies are a large colloidal particle, or
|
|
|
|
portions of a large biomolecule such as a protein.
|
|
|
|
</P>
|
|
|
|
<P>Example of small rigid bodies are patchy nanoparticles, such as those
|
2009-07-01 01:27:43 +08:00
|
|
|
modeled in <A HREF = "#Zhang">this paper</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, and coarse-grain
|
|
|
|
models of nano or colloidal particles consisting of a small number of
|
|
|
|
constituent particles. Note that the <A HREF = "fix_shake.html">fix shake</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.
|
2009-07-01 01:19:42 +08:00
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<P>These fixes also update the positions and velocities of the atoms in
|
|
|
|
each rigid body via time integration. The <I>rigid</I> and <I>rigid/nve</I>
|
|
|
|
styles do this via constant NVE integration. The only difference is
|
|
|
|
that the <I>rigid</I> style uses an integration technique based on
|
|
|
|
Richardson iterations. The <I>rigid/nve</I> style uses the methods
|
|
|
|
described in the paper by <A HREF = "#Miller">Miller</A>, which are thought to
|
|
|
|
provide better energy conservation than an iterative approach.
|
|
|
|
</P>
|
|
|
|
<P>The <I>rigid/nvt</I> style performs constant NVT integration using a
|
|
|
|
Nose/Hoover thermostat with chains as described originally in
|
|
|
|
<A HREF = "#Hoover">(Hoover)</A> and <A HREF = "#Martyna">(Martyna)</A>, which thermostats both
|
|
|
|
the translational and rotational degrees of freedom of the rigid
|
|
|
|
bodies. The rigid-body algorithm used by <I>rigid/nvt</I> is described in
|
|
|
|
the paper by <A HREF = "#Kamberaj">Kamberaj</A>.
|
|
|
|
</P>
|
|
|
|
<P>IMPORTANT NOTE: You should not update the atoms in rigid bodies via
|
|
|
|
other time-integration fixes (e.g. nve, nvt, npt), or you will be
|
|
|
|
integrating their motion more than once each timestep.
|
|
|
|
</P>
|
|
|
|
<P>IMPORTANT NOTE: 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 <A HREF = "velocity.html">velocity</A>
|
|
|
|
command), setting the force on them to 0.0 (via the <A HREF = "fix_setforce.html">fix
|
|
|
|
setforce</A> command), and integrating them as usual
|
|
|
|
(e.g. via the <A HREF = "fix_nve.html">fix nve</A> command).
|
|
|
|
</P>
|
|
|
|
<HR>
|
|
|
|
|
2009-07-01 01:19:42 +08:00
|
|
|
<P>The constituent particles within a rigid body can be point particles
|
2011-04-14 05:39:34 +08:00
|
|
|
(the default in LAMMPS) or finite-size particles, such as spheres and
|
|
|
|
ellipsoids. See the <A HREF = "atom_style.html">atom_style sphere and ellipsoid</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 <A HREF = "pair_gran.html">frictional granular
|
2009-07-01 01:19:42 +08:00
|
|
|
interactions</A>) and have an orientation. These
|
2010-05-02 08:59:55 +08:00
|
|
|
contributions are accounted for by these fixes.
|
2009-07-01 01:19:42 +08:00
|
|
|
</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 <A HREF = "neigh_modify.html">neigh_modify
|
|
|
|
exclude</A> and <A HREF = "delete_bonds.html">delete_bonds</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>
|
|
|
|
<HR>
|
|
|
|
|
2009-01-13 22:38:26 +08:00
|
|
|
<P>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.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2009-01-13 22:38:26 +08:00
|
|
|
<P>For bodystyle <I>single</I> the entire fix group of atoms is treated as one
|
|
|
|
rigid body.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2009-01-13 22:38:26 +08:00
|
|
|
<P>For bodystyle <I>molecule</I>, each set of atoms in the fix group with a
|
|
|
|
different molecule ID is treated as a rigid body.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2009-01-13 22:38:26 +08:00
|
|
|
<P>For bodystyle <I>group</I>, each of the listed groups is treated as a
|
|
|
|
separate rigid body. Only atoms that are also in the fix group are
|
2006-09-22 00:22:34 +08:00
|
|
|
included in each rigid body.
|
|
|
|
</P>
|
2011-02-16 05:14:11 +08:00
|
|
|
<P>IMPORTANT NOTE: 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
|
|
|
|
<A HREF = "set.html">set</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>
|
2009-10-30 00:10:55 +08:00
|
|
|
<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 <I>force</I> and <I>torque</I> 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.
|
2009-01-13 22:38:26 +08:00
|
|
|
</P>
|
|
|
|
<P>An xflag, yflag, or zflag set to <I>off</I> means turn off the component of
|
|
|
|
force of torque in that dimension. A setting of <I>on</I> 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 <I>force</I> and
|
|
|
|
<I>torque</I> 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
|
2009-01-15 08:21:36 +08:00
|
|
|
means all types from m to n (inclusive). Note that you can use the
|
|
|
|
<I>force</I> or <I>torque</I> 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.
|
2009-01-13 22:38:26 +08:00
|
|
|
</P>
|
|
|
|
<P>For computational efficiency, you may wish to turn off pairwise and
|
2006-09-22 00:22:34 +08:00
|
|
|
bond interactions within each rigid body, as they no longer contribute
|
|
|
|
to the motion. The <A HREF = "neigh_modify.html">neigh_modify exclude</A> and
|
|
|
|
<A HREF = "delete_bonds.html">delete_bonds</A> commands are used to do this.
|
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<P>For computational efficiency, you should typically 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.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<HR>
|
|
|
|
|
2011-04-30 00:27:56 +08:00
|
|
|
<P>The keyword/value option pairs are used in the following ways.
|
|
|
|
</P>
|
|
|
|
<P>The <I>langevin</I> and <I>temp</I> and <I>tparam</I> 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 <I>langevin</I> keyword applies a Langevin thermostat to the constant
|
|
|
|
NVE time integration performed by either the <I>rigid</I> or <I>rigid/nve</I>
|
|
|
|
styles. It cannot be used with the <I>rigid/nvt</I> style. The desired
|
|
|
|
temperature at each timestep is a ramped value during the run from
|
|
|
|
<I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> 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
|
|
|
|
<A HREF = "units.html">units</A> command). The random # <I>seed</I> must be a positive
|
|
|
|
integer. The way the Langevin thermostatting operates is explained on
|
|
|
|
the <A HREF = "fix_langevin.html">fix langevin</A> doc page.
|
|
|
|
</P>
|
|
|
|
<P>The <I>temp</I> and <I>tparam</I> keywords apply a Nose/Hoover thermostat to the
|
|
|
|
NVT time integration performed by the <I>rigid/nvt</I> style. They cannot
|
|
|
|
be used with the <I>rigid</I> or <I>rigid/nve</I> styles. The desired
|
|
|
|
temperature at each timestep is a ramped value during the run from
|
|
|
|
<I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> 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
|
|
|
|
<A HREF = "units.html">units</A> command).
|
2010-05-02 08:59:55 +08:00
|
|
|
</P>
|
|
|
|
<P>Nose/Hoover chains are used in conjunction with this thermostat. The
|
|
|
|
<I>tparam</I> keyword can optionally be used to change the chain settings
|
|
|
|
used. <I>Tchain</I> is the number of thermostats in the Nose Hoover chain.
|
|
|
|
This value, along with <I>Tdamp</I> 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.
|
|
|
|
</P>
|
2011-04-30 00:27:56 +08:00
|
|
|
<P>IMPORTANT NOTE: There are alternate ways to thermostat a system of
|
|
|
|
rigid bodies. You can use <A HREF = "fix_langevin.html">fix langevin</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.
|
2009-07-02 22:39:37 +08:00
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<HR>
|
|
|
|
|
2011-04-30 00:27:56 +08:00
|
|
|
<P>The keyword/value option pairs are used in the following ways.
|
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<P>If you use a <A HREF = "compute.html">temperature compute</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.
|
2009-07-02 22:39:37 +08:00
|
|
|
</P>
|
2009-07-02 23:09:14 +08:00
|
|
|
<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>
|
|
|
|
<P>IMPORTANT NOTE: You may wish to explicitly subtract additional
|
|
|
|
degrees-of-freedom if you use the <I>force</I> and <I>torque</I> keywords to
|
2010-05-02 08:59:55 +08:00
|
|
|
eliminate certain motions of one or more rigid bodies. LAMMPS does
|
2009-07-02 23:09:14 +08:00
|
|
|
not do this automatically.
|
2009-01-23 02:56:18 +08:00
|
|
|
</P>
|
|
|
|
<P>The rigid body contribution to the pressure of the system (virial) is
|
|
|
|
also accounted for by this fix.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2007-08-29 22:13:51 +08:00
|
|
|
<P>IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
|
2010-10-07 22:59:11 +08:00
|
|
|
altered so that the rigid body can be reconstructed correctly when it
|
|
|
|
straddles periodic boundaries. The atom image flags are not
|
2010-10-07 23:10:14 +08:00
|
|
|
incremented/decremented as they would be for non-rigid atoms as the
|
|
|
|
rigid body crosses periodic boundaries. This means you cannot
|
|
|
|
interpret them as you normally would. For example, the image flag
|
|
|
|
values written to a <A HREF = "dump.html">dump file</A> will be different than they
|
|
|
|
would be if the atoms were not in a rigid body. Likewise the <A HREF = "compute_msd.html">compute
|
|
|
|
msd</A> will not compute the expected mean-squared
|
|
|
|
displacement for such atoms if the body moves across periodic
|
|
|
|
boundaries. 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 <A HREF = "replicate.html">replicate</A> command to increase the system
|
|
|
|
size. Note that this fix does define image flags for each rigid body,
|
|
|
|
which are incremented when the rigid body crosses a periodic boundary
|
|
|
|
in the usual way. These image flags have the same meaning as atom
|
|
|
|
images (see the "dump" command) and can be accessed and output as
|
|
|
|
described below.
|
2007-08-29 22:13:51 +08:00
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<HR>
|
|
|
|
|
2007-10-11 06:28:11 +08:00
|
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
2007-06-26 08:03:39 +08:00
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<P>No information about the <I>rigid</I> and <I>rigid/nve</I> fixes are written to
|
|
|
|
<A HREF = "restart.html">binary restart files</A>. For style <I>rigid/nvt</I> the state
|
|
|
|
of the Nose/Hoover thermostat is written to <A HREF = "restart.html">binary restart
|
|
|
|
files</A>. See the <A HREF = "read_restart.html">read_restart</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>
|
2010-11-24 23:04:48 +08:00
|
|
|
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by the
|
|
|
|
rigid/nvt fix to add the energy change induced by the thermostatting
|
|
|
|
to the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
|
|
|
|
output</A>.
|
|
|
|
</P>
|
2011-04-30 00:27:56 +08:00
|
|
|
<P>The rigid and rigid/nve fixes computes a global scalar which can be
|
2011-08-26 01:01:01 +08:00
|
|
|
accessed by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
|
|
|
|
The scalar value calculated by these fixes is "intensive". The scalar
|
|
|
|
is the current temperature of the collection of rigid bodies. This is
|
2011-04-30 00:27:56 +08:00
|
|
|
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 <I>force</I> and <I>torque</I>
|
|
|
|
keywords are removed from this calculation.
|
|
|
|
</P>
|
2010-11-24 23:04:48 +08:00
|
|
|
<P>The rigid/nvt fix computes a global scalar which can be accessed by
|
2011-08-26 01:01:01 +08:00
|
|
|
various <A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar
|
|
|
|
value calculated by the rigid/nvt fix is "extensive". The scalar is
|
|
|
|
the cumulative energy change due to the thermostatting the fix
|
|
|
|
performs.
|
2010-11-24 23:04:48 +08:00
|
|
|
</P>
|
|
|
|
<P>All of these fixes compute a global array of values which can be
|
2011-08-26 01:01:01 +08:00
|
|
|
accessed by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
|
|
|
|
The number of rows in the array is equal to the number of rigid
|
|
|
|
bodies. The number of columns is 15. Thus for each rigid body, 15
|
|
|
|
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, the xyz components of the torque acting on the COM, and
|
|
|
|
the xyz image flags of the COM, which have the same meaning as image
|
|
|
|
flags for atom positions (see the "dump" command). The force and
|
|
|
|
torque values in the array are not affected by the <I>force</I> and
|
|
|
|
<I>torque</I> keywords in the fix rigid command; they reflect values before
|
|
|
|
any changes are made by those keywords.
|
2009-12-19 01:25:39 +08:00
|
|
|
</P>
|
|
|
|
<P>The ordering of the rigid bodies (by row in the array) is as follows.
|
|
|
|
For the <I>single</I> keyword there is just one rigid body. For the
|
|
|
|
<I>molecule</I> keyword, the bodies are ordered by ascending molecule ID.
|
|
|
|
For the <I>group</I> keyword, the list of group IDs determines the ordering
|
|
|
|
of bodies.
|
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<P>The array values calculated by these fixes are "intensive", meaning
|
|
|
|
they are independent of the number of atoms in the simulation.
|
2009-01-13 22:38:26 +08:00
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<P>No parameter of these fixes can be used with the <I>start/stop</I> keywords
|
|
|
|
of the <A HREF = "run.html">run</A> command. These fixes are not invoked during
|
|
|
|
<A HREF = "minimize.html">energy minimization</A>.
|
2007-06-26 08:03:39 +08:00
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<P>These fixes performs an MPI_Allreduce each timestep that is
|
|
|
|
proportional in length to the number of rigid bodies. Hence they will
|
|
|
|
not scale well in parallel if large numbers of rigid bodies are
|
|
|
|
simulated.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
</P>
|
|
|
|
<P><A HREF = "delete_bonds.html">delete_bonds</A>, <A HREF = "neigh_modify.html">neigh_modify</A>
|
|
|
|
exclude
|
|
|
|
</P>
|
2009-01-13 22:38:26 +08:00
|
|
|
<P><B>Default:</B>
|
|
|
|
</P>
|
2010-05-02 08:59:55 +08:00
|
|
|
<P>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. Also Tchain = 10, Titer = 1, Torder = 3.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2009-07-01 01:19:42 +08:00
|
|
|
<HR>
|
|
|
|
|
2010-05-02 08:59:55 +08:00
|
|
|
<A NAME = "Hoover"></A>
|
|
|
|
|
|
|
|
<P><B>(Hoover)</B> Hoover, Phys Rev A, 31, 1695 (1985).
|
|
|
|
</P>
|
|
|
|
<A NAME = "Kamberaj"></A>
|
|
|
|
|
|
|
|
<P><B>(Kamberaj)</B> Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).
|
|
|
|
</P>
|
|
|
|
<A NAME = "Martyna"></A>
|
|
|
|
|
|
|
|
<P><B>(Martyna)</B> Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
|
|
|
|
Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
|
|
|
|
</P>
|
|
|
|
<A NAME = "Miller"></A>
|
|
|
|
|
|
|
|
<P><B>(Miller)</B> Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
|
|
|
|
J Chem Phys, 116, 8649 (2002).
|
|
|
|
</P>
|
2009-07-01 01:27:43 +08:00
|
|
|
<A NAME = "Zhang"></A>
|
2009-07-01 01:19:42 +08:00
|
|
|
|
|
|
|
<P><B>(Zhang)</B> Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).
|
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
</HTML>
|