2006-09-22 00:22:34 +08:00
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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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<HR>
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<H3>fix recenter 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 recenter x y z keyword value ...
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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>recenter = style name of this fix command
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<LI>x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below)
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2007-07-03 04:04:44 +08:00
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<LI>zero or more keyword/value pairs may be appended
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2006-09-22 00:22:34 +08:00
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<LI>keyword = <I>shift</I> or <I>units</I>
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<PRE> <I>shift</I> value = group-ID
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group-ID = group of atoms whose coords are shifted
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<I>units</I> value = <I>box</I> or <I>lattice</I> or <I>fraction</I>
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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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2006-10-03 04:53:54 +08:00
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<PRE>fix 1 all recenter 0.0 0.5 0.0
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fix 1 all recenter INIT INIT NULL
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2006-10-03 04:21:36 +08:00
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fix 1 all recenter INIT 0.0 0.0 units box
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2006-09-22 00:22:34 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Constrain the center-of-mass position of a group of atoms by adjusting
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the coordinates of the atoms every timestep. This is simply a small
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shift that does not alter the dynamics of the system or change the
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relative coordinates of any pair of atoms in the group. This can be
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used to insure the entire collection of atoms (or a portion of them)
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do not drift during the simulation due to random perturbations
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(e.g. <A HREF = "fix_langevin.html">fix langevin</A> thermostatting).
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</P>
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<P>Distance units for the x,y,z values are determined by the setting of
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the <I>units</I> keyword, as discussed below. One or more x,y,z values can
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also be specified as NULL, which means exclude that dimension from
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this operation. Or it can be specified as INIT which means to
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constain the center-of-mass to its initial value at the beginning of
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the run.
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</P>
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<P>The center-of-mass (COM) is computed for the group specified by the
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fix. If the current COM is different than the specified x,y,z, then a
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group of atoms has their coordinates shifted by the difference. By
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default the shifted group is also the group specified by the fix. A
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different group can be shifted by using the <I>shift</I> keyword. For
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example, the COM could be computed on a protein to keep it in the
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center of the simulation box. But the entire system (protein + water)
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could be shifted.
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</P>
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<P>If the <I>units</I> keyword is set to <I>box</I>, then the distance units of
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x,y,z are defined by the <A HREF = "units.html">units</A> command - e.g. Angstroms
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2006-11-14 06:18:34 +08:00
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for <I>real</I> units. A <I>lattice</I> value means the distance units are in
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lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have been
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previously used to define the lattice spacing. A <I>fraction</I> value
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means a fractional distance between the lo/hi box boundaries, e.g. 0.5
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= middle of the box. The default is to use lattice units.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>Note that the <A HREF = "velocity.html">velocity</A> command can be used to create
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velocities with zero aggregate linear and/or angular momentum.
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</P>
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2007-02-20 02:03:15 +08:00
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<P>IMPORTANT NOTE: This fix performs its operations at the same point in
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the timestep as other time integration fixes, such as <A HREF = "fix_nve.html">fix
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nve</A>, <A HREF = "fix_nvt.html">fix nvt</A>, or <A HREF = "fix_npt.html">fix npt</A>.
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Thus fix recenter should normally be the last such fix specified in
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the input script, since the adjustments it makes to atom coordinates
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should come after the changes made by time integration. LAMMPS will
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warn you if your fixes are not ordered this way.
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</P>
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2007-09-28 07:25:52 +08:00
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<P>IMPORTANT NOTE: If you use this fix on a small group of atoms (e.g. a
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molecule in solvent) without using the <I>shift</I> keyword to adjust the
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positions of all atoms in the system, then the results can be
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unpredictable. For example, if the molecule is pushed in one
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direction by the solvent, its velocity will increase. But its
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coordinates will be recentered, meaning it is pushed back towards the
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force. Thus over time, the velocity and temperature of the molecule
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could become very large (though it won't appear to be moving due to
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the recentering). If you are thermostatting the entire system, then
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the solvent would be cooled to compensate. A better solution for this
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simulation scenario is to use the <A HREF = "fix_spring.html">fix spring</A> command
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to tether the molecule in place.
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</P>
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2007-10-11 06:28:11 +08:00
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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2007-06-26 08:03:39 +08:00
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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2007-10-11 06:28:11 +08:00
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are relevant to this fix. No global scalar or vector or per-atom
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quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
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commands</A>. No parameter of this fix can be
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used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
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This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
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2007-06-26 08:03:39 +08:00
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</P>
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2006-09-22 00:22:34 +08:00
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<P><B>Restrictions:</B>
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</P>
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<P>This fix should not be used with an x,y,z setting that causes a large
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shift in the system on the 1st timestep, due to the requested COM
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being very different from the initial COM. This could cause atoms to
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be lost,especially in parallel. Instead, use the
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2007-04-02 22:26:01 +08:00
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<A HREF = "displace_atoms.html">displace_atoms</A> command, which can be used to
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move atoms a large distance.
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2006-09-22 00:22:34 +08:00
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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 = "fix_momentum.html">fix momentum</A>, <A HREF = "velocity.html">velocity</A>
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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 adjust = fix group-ID, and units = lattice.
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</P>
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</HTML>
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