forked from lijiext/lammps
207 lines
9.5 KiB
HTML
207 lines
9.5 KiB
HTML
|
<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 move command
|
||
|
|
</H3>
|
||
|
|
<P><B>Syntax:</B>
|
||
|
|
</P>
|
||
|
|
<PRE>fix ID group-ID move style args keyword values ...
|
||
|
|
</PRE>
|
||
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||
|
|
|
||
|
|
<LI>move = style name of this fix command
|
||
|
|
|
||
|
|
<LI>style = <I>linear</I> or <I>wiggle</I> or <I>rotate</I> or <I>variable</I>
|
||
|
|
|
||
|
|
<PRE> <I>linear</I> args = Vx Vy Vz
|
||
|
|
Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
|
||
|
|
<I>wiggle</I> args = Ax Ay Az period
|
||
|
|
Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
|
||
|
|
period = period of oscillation (time units)
|
||
|
|
<I>rotate</I> args = Px Py Pz Rx Ry Rz period
|
||
|
|
Px,Py,Pz = origin point of axis of rotation (distance units)
|
||
|
|
Rx,Ry,Rz = axis of rotation vector
|
||
|
|
period = period of rotation (time units)
|
||
|
|
<I>variable</I> args = v_dx v_dy v_dz v_vx v_vy v_vz
|
||
|
|
v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
|
||
|
|
v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
|
||
|
|
</PRE>
|
||
|
|
<LI>zero or more keyword/value pairs may be appended
|
||
|
|
|
||
|
|
<LI>keyword = <I>units</I>
|
||
|
|
|
||
|
|
<PRE> <I>units</I> value = <I>box</I> or <I>lattice</I>
|
||
|
|
</PRE>
|
||
|
|
|
||
|
|
</UL>
|
||
|
|
<P><B>Examples:</B>
|
||
|
|
</P>
|
||
|
|
<PRE>fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
|
||
|
|
fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
|
||
|
|
fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
|
||
|
|
</PRE>
|
||
|
|
<P><B>Description:</B>
|
||
|
|
</P>
|
||
|
|
<P>Perform updates of position and velocity for atoms in the group each
|
||
|
|
timestep using the specified settings or formulas, without regard to
|
||
|
|
forces on the atoms. This can be useful for boundary or other atoms,
|
||
|
|
whose movement can influence nearby atoms.
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE: The atoms affected by this fix should not normally be
|
||
|
|
time integrated by other fixes (e.g. <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nvt.html">fix
|
||
|
|
nvt</A>), since that will change their positions and
|
||
|
|
velocities twice.
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE: As atoms move due to this fix, they will pass thru
|
||
|
|
periodic boundaries and be remapped to the other side of the
|
||
|
|
simulation box, just as they would during normal time integration
|
||
|
|
(e.g. via the <A HREF = "fix_nve.html">fix nve</A> command). It is up to you to
|
||
|
|
decide whether periodic boundaries are appropriate with the kind of
|
||
|
|
atom motion you are prescribing with this fix.
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE: As dicsussed below, atoms are moved relative to their
|
||
|
|
initial position at the time the fix is specified. These initial
|
||
|
|
coordinates are stored by the fix in "unwrapped" form, by using the
|
||
|
|
image flags associated with each atom. See the <A HREF = "dump.html">dump
|
||
|
|
custom</A> command for a discussion of "unwrapped" coordinates.
|
||
|
|
See the Atoms section of the <A HREF = "read_data.html">read_data</A> command for a
|
||
|
|
discussion of image flags and how they are set for each atom. You can
|
||
|
|
reset the image flags (e.g. to 0) before invoking this fix by using
|
||
|
|
the <A HREF = "set.html">set image</A> command.
|
||
|
|
</P>
|
||
|
|
<HR>
|
||
|
|
|
||
|
|
<P>The <I>linear</I> style moves atoms at a constant velocity, so that their
|
||
|
|
position <I>X</I> = (x,y,z) as a function of time is given in vector
|
||
|
|
notation as
|
||
|
|
</P>
|
||
|
|
<PRE>X(t) = X0 + V * delta
|
||
|
|
</PRE>
|
||
|
|
<P>where <I>X0</I> = (x0,y0,z0) is their position at the time the fix is
|
||
|
|
specified, <I>V</I> is the specified velocity vector with components
|
||
|
|
(Vx,Vy,Vz), and <I>delta</I> is the time elapsed since the beginning of the
|
||
|
|
simulation. This style also sets the velocity of each atom to V =
|
||
|
|
(Vx,Vy,Vz). If any of the velocity components is specified as NULL,
|
||
|
|
then the position and velocity of that component is time integrated
|
||
|
|
the same as the <A HREF = "fix_nve.html">fix nve</A> command would perform, using
|
||
|
|
the corresponding force component on the atom.
|
||
|
|
</P>
|
||
|
|
<P>The <I>wiggle</I> style moves atoms in an oscillatory fashion, so that
|
||
|
|
their position <I>X</I> = (x,y,z) as a function of time is given in vector
|
||
|
|
notation as
|
||
|
|
</P>
|
||
|
|
<PRE>X(t) = X0 + A sin(omega*delta)
|
||
|
|
</PRE>
|
||
|
|
<P>where <I>X0</I> = (x0,y0,z0) is their position at the time the fix is
|
||
|
|
specified, <I>A</I> is the specified amplitude vector with components
|
||
|
|
(Ax,Ay,Az), <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the time
|
||
|
|
elapsed since the beginning of the simulation. This style also sets
|
||
|
|
the velocity of each atom to the time derivative of this expression.
|
||
|
|
If any of the amplitude components is specified as NULL, then the
|
||
|
|
position and velocity of that component is time integrated the same as
|
||
|
|
the <A HREF = "fix_nve.html">fix nve</A> command would perform, using the
|
||
|
|
corresponding force component on the atom.
|
||
|
|
</P>
|
||
|
|
<P>The <I>rotate</I> style rotates atoms around a rotation axis <I>R</I> =
|
||
|
|
(Rx,Ry,Rz) that goes thru a point <I>P</I> = (Px,Py,Pz). The <I>period</I> of
|
||
|
|
the rotation is also specified. This style also sets the velocity of
|
||
|
|
each atom to (omega cross Rperp) where omega is its angular velocity
|
||
|
|
around the rotation axis and Rperp is a perpendicular vector from the
|
||
|
|
rotation axis to the atom. If the defined
|
||
|
|
<A HREF = "atom_style.html">atom_style</A> assigns an angular velocity to each atom,
|
||
|
|
then each atom's angular velocity is also set to omega.
|
||
|
|
</P>
|
||
|
|
<P>The <I>variable</I> style allows the position and velocity components of
|
||
|
|
each atom to be set by formulas specified via the
|
||
|
|
<A HREF = "variable.html">variable</A> command. Each of the 6 variables is
|
||
|
|
specified as an argument to the fix as v_name, where <I>name</I> is the
|
||
|
|
name of the variable that appears elsewhere in the input script.
|
||
|
|
</P>
|
||
|
|
<P>Each variable must be of either the <I>equal</I> or <I>atom</I> style.
|
||
|
|
<I>Equal</I>-style variables compute a single numeric quantity, that can be
|
||
|
|
a function of the timestep as well as of other simulation values.
|
||
|
|
<I>Atom</I>-style variables compute a numeric quantity for each atom, that
|
||
|
|
can be a function per-atom quantities, such as the atom's position, as
|
||
|
|
well as of the timestep and other simulation values. See the
|
||
|
|
<A HREF = "variable.html">variable</A> command for details.
|
||
|
|
</P>
|
||
|
|
<P>The first 3 variables (v_dx,v_dy,v_dz) specified for the <I>variable</I>
|
||
|
|
style are used to calculate a displacement from the atom's original
|
||
|
|
position at the time the fix was specified. The second 3 variables
|
||
|
|
(v_vx,v_vy,v_vz) specified are used to compute a velocity for each
|
||
|
|
atom.
|
||
|
|
</P>
|
||
|
|
<P>Any of the 6 variables can be specified as NULL. If both the
|
||
|
|
displacement and velocity variables for a particular x,y,z component
|
||
|
|
are specified as NULL, then the position and velocity of that
|
||
|
|
component is time integrated the same as the <A HREF = "fix_nve.html">fix nve</A>
|
||
|
|
command would perform, using the corresponding force component on the
|
||
|
|
atom. If only the velocity variable for a component is specified as
|
||
|
|
NULL, then the displacement variable will be used to set the position
|
||
|
|
of the atom, and its velocity component will not be changed. If only
|
||
|
|
the displacement variable for a component is specified as NULL, then
|
||
|
|
the velocity variable will be used to set the velocity of the atom,
|
||
|
|
and the position of the atom will be time integrated using that
|
||
|
|
velocity.
|
||
|
|
</P>
|
||
|
|
<P>The <I>units</I> keyword determines the meaning of the distance units used
|
||
|
|
to define the <I>linear</I> velocity and <I>wiggle</I> amplitude and <I>rotate</I>
|
||
|
|
origin. This setting is ignored for the <I>variable</I> style. A <I>box</I>
|
||
|
|
value selects standard units as defined by the <A HREF = "units.html">units</A>
|
||
|
|
command, e.g. velocity in Angstroms/fmsec and amplitude and position
|
||
|
|
in Angstroms for units = real. A <I>lattice</I> value means the velocity
|
||
|
|
units are in lattice spacings per time and the amplitude and position
|
||
|
|
are in lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have
|
||
|
|
been previously used to define the lattice spacing. Each of these 3
|
||
|
|
quantities may be dependent on the x,y,z dimension, since the lattice
|
||
|
|
spacings can be different in x,y,z.
|
||
|
|
</P>
|
||
|
|
<P>For <A HREF = "run_style.html">rRESPA time integration</A>, this fix adjusts the
|
||
|
|
position and velocity of atoms on the outermost rRESPA level.
|
||
|
|
</P>
|
||
|
|
<HR>
|
||
|
|
|
||
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||
|
|
</P>
|
||
|
|
<P>This fix writes the original coordinates of moving atoms to <A HREF = "restart.html">binary
|
||
|
|
restart files</A>, so that the motion can be continuous in a
|
||
|
|
restarted simulation. 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>
|
||
|
|
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
|
||
|
|
fix.
|
||
|
|
</P>
|
||
|
|
<P>This fix produces a per-atom vector which can be accessed by various
|
||
|
|
<A HREF = "Section_howto.html#4_15">output commands</A>. The length of the vector
|
||
|
|
for each atom is 3, and the components store the original unwrapped
|
||
|
|
x,y,z coords of each atom. The per-atom values be accessed on any
|
||
|
|
timestep.
|
||
|
|
</P>
|
||
|
|
<P>This fix can move atoms continously over multiple runs, using the
|
||
|
|
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
|
||
|
|
<A HREF = "run.html">run</A> command for details of how to do this.
|
||
|
|
</P>
|
||
|
|
<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
||
|
|
</P>
|
||
|
|
<P><B>Restrictions:</B> none
|
||
|
|
</P>
|
||
|
|
<P><B>Related commands:</B>
|
||
|
|
</P>
|
||
|
|
<P><A HREF = "fix_nve.html">fix nve</A>
|
||
|
|
</P>
|
||
|
|
<P><B>Default:</B> none
|
||
|
|
</P>
|
||
|
|
<P>The option default is units = lattice.
|
||
|
|
</P>
|
||
|
|
</HTML>
|