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doc/fix_wall.html
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@ -19,39 +19,40 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID style keyword values ...
<PRE>fix ID group-ID style face args ... keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>style = <I>wall/lj93</I> or <I>wall/lj126</I> or <I>wall/colloid</I> or <I>wall/harmonic</I>
<LI>one or more keyword/value pairs may be appended
<LI>one or more face/arg pairs may be appended
<LI>keyword = <I>xlo</I> or <I>xhi</I> or <I>ylo</I> or <I>yhi</I> or <I>zlo</I> or <I>zhi</I> or <I>vel</I> or <I>wiggle/sin</I> or <I>wiggle/cos</I> or <I>units</I>
<LI>face = <I>xlo</I> or <I>xhi</I> or <I>ylo</I> or <I>yhi</I> or <I>zlo</I> or <I>zhi</I>
<PRE> <I>xlo</I>, <I>xhi</I>, <I>ylo</I>, <I>yhi</I>, <I>zlo</I>, <I>zhi</I> values = coord epsilon sigma cutoff
coord = position of wall (distance units)
<PRE> args = coord epsilon sigma cutoff
coord = position of wall = EDGE or constant or variable
EDGE = current lo or hi edge of simulation box
constant = number like 0.0 or -30.0 (distance units)
variable = <A HREF = "variable.html">equal-style variable</A> like v_x or v_wiggle
epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
sigma = size factor for wall-particle interaction (distance units)
cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
<I>vel</I> value = v
v = velocity of wall in perpendicular direction (velocity units)
<I>wiggle/sin</I> values = amplitude period
amplitude = size of oscillation (distance units)
period = time of oscillation (time units)
<I>wiggle/cos</I> values = amplitude period
amplitude = size of oscillation (distance units)
period = time of oscillation (time units)
<I>units</I> value = <I>lattice</I> or <I>box</I>
lattice = the wall is defined in lattice units
box = the wall is defined in simulation box units
cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>units</I>
<PRE> <I>units</I> value = <I>lattice</I> or <I>box</I>
<I>lattice</I> = the wall position is defined in lattice units
<I>box</I> = the wall position is defined in simulation box units
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix wallhi all wall/lj93 xhi 10.0 1.0 1.0 2.5
fix wallhi all wall/lj126 xhi 23.2 1.0 1.0 2.5 vel 1.0 units box
<PRE>fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
</PRE>
<P><B>Description:</B>
@ -85,6 +86,27 @@ particle and wall no longer interact. The energy of the wall
potential is shifted so that the wall-particle interaction energy is
0.0 at the cutoff distance.
</P>
<P>Up to 6 walls or faces can be specified in a single command: <I>xlo</I>,
<I>xhi</I>, <I>ylo</I>, <I>yhi</I>, <I>zlo</I>, <I>zhi</I>. A <I>lo</I> face interacts with
particles near the lower side of the simulation box in that dimension.
A <I>hi</I> face interacts with particles near the upper side of the
simulation box in that dimension.
</P>
<P>The position of each wall can be specified in one of 3 ways: as the
EDGE of the simulation box, as a constant value, or as a variable. If
EDGE is used, then the corresponding boundary of the current
simulation box is used. If a numeric constant is specified then the
wall is placed at that position in the appropriate dimension (x, y, or
z). In both the EDGE and constant cases, the wall will never move.
If the wall position is a variable, it should be specified as v_name,
where name is an <A HREF = "variable.html">equal-style variable</A> name. In this
case the variable is evaluated each timestep and the result becomes
the current position of the reflecting wall. Equal-style variables
can specify formulas with various mathematical functions, and include
<A HREF = "thermo_style.html">thermo_style</A> command keywords for the simulation
box parameters and timestep and elapsed time. Thus it is easy to
specify a time-dependent wall position. See examples below.
</P>
<P>For the <I>wall/lj93</I> and <I>wall/lj126</I> styles, <I>epsilon</I> and <I>sigma</I> are
the usual Lennard-Jones parameters, which determine the strength and
size of the particle as it interacts with the wall. Epsilon has
@ -129,56 +151,55 @@ potential and does not blow up as r -> 0, but you must use a large
enough <I>epsilon</I> that particles always reamin on the correct side of
the wall (r > 0).
</P>
<P>If the <I>vel</I> keyword is specified, the position of all walls will move
during the simulation in a perpendicular direction, based on their
initial <I>coord</I> position, the specified velocity <I>vel</I>, and the time
elapsed since the fix was specified. A positive velocity means each
wall moves inward, towards the center of the box. I.e. an <I>xlo</I> wall
will move in the +x direction and an <I>xhi</I> wall will move in the -x
direction. A negative velocity means each wall moves outward, away
from the center of the box. If you want different walls to move with
different velocities, then you need to use multiple fix wall commands.
</P>
<P>If the <I>wiggle/sin</I> keyword is specified, the position of all walls
will oscillate sinusoidally during the simulation in the perpendicular
direction, according to the equation:
</P>
<PRE>position = coord + A sin(omega*delta)
</PRE>
<P>If the <I>wiggle/cos</I> keyword is specified, the position of all walls
will oscillate sinusoidally during the simulation in the perpendicular
direction, according to the equation:
</P>
<PRE>position = coord + A (1 - cos(omega*delta))
</PRE>
<P>In both cases, <I>coord</I> is the specified initial position of the wall,
<I>A</I> is the <I>amplitude</I>, <I>omega</I> is 2 PI / <I>period</I>, and <I>delta</I> is the
time elapsed since the fix was specified. A positive amplitude means
each wall initially moves inward, towards the center of the box.
I.e. an <I>xlo</I> wall will move initially in the +x direction and an
<I>xhi</I> wall will move initially in the -x direction. A negative
velocity means each wall moves initially outward, away from the center
of the box. Note that the <I>wiggle/sin</I> option oscillates with
amplitude <I>A</I> around the pos0 position and the velocity of the wall is
a maximum at time 0. By contrast, for the <I>wiggle/cos</I> option the
wall moves up to <I>2A</I> away from pos0 in one direction and the velocity
of the wall is 0 at time 0. If you want different walls to oscillate
with different amplitudes or periods, then you need to use multiple
fix wall commands.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
to define the position of the wall and its velocity and wiggle
amplitude. A <I>box</I> value selects standard distance units as defined
by the <A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or
metal. 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. Note that with the
<I>lattice</I> option, the wall's position is specified in lattice
spacings, the wall's velocity is specified in lattice spacings per
time, and the wall's oscillation amplitude is specified in lattice
spacings. 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.
to define a wall position, but only when a numeric constant is used.
It is not relevant when EDGE or a variable is used to specify a face
position.
</P>
<P>A <I>box</I> value selects standard distance units as defined by the
<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
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 spacings.
</P>
<HR>
<P>Here are examples of variable definitions that move the wall position
in a time-dependent fashion using equal-style
<A HREF = "variable.html">variables</A>.
</P>
<PRE>variable ramp equal ramp(0,10)
fix 1 all wall xlo v_ramp 1.0 1.0 2.5
</PRE>
<PRE>variable linear equal vlinear(0,20)
fix 1 all wall xlo v_linear 1.0 1.0 2.5
</PRE>
<PRE>variable wiggle equal swiggle(0.0,5.0,3.0)
fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
</PRE>
<PRE>variable wiggle equal cwiggle(0.0,5.0,3.0)
fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
</PRE>
<P>The ramp(lo,hi) function adjusts the wall position linearly from lo to
hi over the course of a run. The linear(c0,velocity) function does
something similar using the equation position = c0 + velocity*delta,
where delta is the elapsed time.
</P>
<P>The swiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, where omega = 2 PI
/ period:
</P>
<PRE>position = c0 + A sin(omega*delta)
</PRE>
<P>The cwiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, which will have an
initial wall velocity of 0.0, and thus may impose a gentler
perturbation on the particles:
</P>
<PRE>position = c0 + A (1 - cos(omega*delta))
</PRE>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart