Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/fix_recenter.html
b704a82dafc5lammm-master

Last Change
Raw File

fix_recenter.html
View Options

<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>
<H3>fix recenter command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID recenter x y z keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>recenter = style name of this fix command
<LI>x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below)
<LI>zero or more keyword/value pairs may be appended to the args
<LI>keyword = <I>shift</I> or <I>units</I>
<PRE> <I>shift</I> value = group-ID
group-ID = group of atoms whose coords are shifted
<I>units</I> value = <I>box</I> or <I>lattice</I> or <I>fraction</I>
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all recenter 0.0 0.5 0.0
fix 1 all recenter INIT INIT NULL
fix 1 all recenter INIT 0.0 0.0 units box
</PRE>
<P><B>Description:</B>
</P>
<P>Constrain the center-of-mass position of a group of atoms by adjusting
the coordinates of the atoms every timestep. This is simply a small
shift that does not alter the dynamics of the system or change the
relative coordinates of any pair of atoms in the group. This can be
used to insure the entire collection of atoms (or a portion of them)
do not drift during the simulation due to random perturbations
(e.g. <A HREF = "fix_langevin.html">fix langevin</A> thermostatting).
</P>
<P>Distance units for the x,y,z values are determined by the setting of
the <I>units</I> keyword, as discussed below. One or more x,y,z values can
also be specified as NULL, which means exclude that dimension from
this operation. Or it can be specified as INIT which means to
constain the center-of-mass to its initial value at the beginning of
the run.
</P>
<P>The center-of-mass (COM) is computed for the group specified by the
fix. If the current COM is different than the specified x,y,z, then a
group of atoms has their coordinates shifted by the difference. By
default the shifted group is also the group specified by the fix. A
different group can be shifted by using the <I>shift</I> keyword. For
example, the COM could be computed on a protein to keep it in the
center of the simulation box. But the entire system (protein + water)
could be shifted.
</P>
<P>If the <I>units</I> keyword is set to <I>box</I>, then the distance units of
x,y,z are defined by the <A HREF = "units.html">units</A> command - e.g. Angstroms
for <I>real</I> units. A <I>lattice</I> value means the distance units are in
lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have been
previously used to define the lattice spacing. A <I>fraction</I> value
means a fractional distance between the lo/hi box boundaries, e.g. 0.5
= middle of the box. The default is to use lattice units.
</P>
<P>Note that the <A HREF = "velocity.html">velocity</A> command can be used to create
velocities with zero aggregate linear and/or angular momentum.
</P>
<P>IMPORTANT NOTE: This fix performs its operations at the same point in
the timestep as other time integration fixes, such as <A HREF = "fix_nve.html">fix
nve</A>, <A HREF = "fix_nvt.html">fix nvt</A>, or <A HREF = "fix_npt.html">fix npt</A>.
Thus fix recenter should normally be the last such fix specified in
the input script, since the adjustments it makes to atom coordinates
should come after the changes made by time integration. LAMMPS will
warn you if your fixes are not ordered this way.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix should not be used with an x,y,z setting that causes a large
shift in the system on the 1st timestep, due to the requested COM
being very different from the initial COM. This could cause atoms to
be lost,especially in parallel. Instead, use the
<A HREF = "displace_atoms.html">displace_atoms</A> command, which can be used to
move atoms a large distance.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_momentum.html">fix momentum</A>, <A HREF = "velocity.html">velocity</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are adjust = fix group-ID, and units = lattice.
</P>
</HTML>
c4science · Help