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6
doc/Section_commands.txt
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@ -441,10 +441,10 @@ of each style or click on the style itself for a full description:
"ttm"_fix_ttm.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
"wall/colloid"_fix_wall_colloid.html,
"wall/colloid"_fix_wall.html,
"wall/gran"_fix_wall_gran.html,
"wall/lj126"_fix_wall_lj126.html,
"wall/lj93"_fix_wall_lj93.html,
"wall/lj126"_fix_wall.html,
"wall/lj93"_fix_wall.html,
"wall/reflect"_fix_wall_reflect.html,
"wiggle"_fix_wiggle.html :tb(c=8,ea=c)

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<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 wall/lj93 command
</H3>
<H3>fix wall/lj126 command
</H3>
<H3>fix wall/colloid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID style keyword values ...
</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>
<LI>one or more keyword/value 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</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)
epsilon = strength factor for wall-particle interaction (energy 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</I> values = amplitude period
amplitude = size of oscillation (distance units)
period = time of oscillation (time 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 10.0 1.0 1.0 2.5 vel 1.0
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>
</P>
<P>Bound the simulation domain on one or more of its faces with a flat
wall that interacts with the atoms in the group by generating a force
on the atom in a direction perpendicular to the wall. The energy E of
wall-particle interactions depends on the style.
</P>
<P>For style <I>wall/lj93</I>, the energy is given by the 9/3 potential:
</P>
<CENTER><IMG SRC = "Eqs/fix_wall_lj93.jpg">
</CENTER>
<P>For style <I>wall/lj126</I>, the energy is given by the 12/6 potential:
</P>
<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
</CENTER>
<P>For style <I>wall/colloid</I>, the energy is given by an integrated form of
the <A HREF = "pair_colloid.html">pair_style colloid</A> potential:
</P>
<CENTER><IMG SRC = "Eqs/fix_wall_colloid.jpg">
</CENTER>
<P>In all cases, <I>r</I> is the distance from the particle to the wall
<I>coord</I>, and Rc is the <I>cutoff</I> distance at which the particle and
wall no longer interact, as specified in the command. The energy of
the wall potential is shifted so that the energy of the wall-particle
interaction is 0.0 at the cutoff distance.
</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. Note that this
<I>sigma</I> may be different than any <I>sigma</I> values defined for a pair
style that computes particle-particle interactions.
</P>
<P>The <I>wall/lj93</I> interaction is derived by integrating over a 3d
half-lattice of Lennard-Jones 12/6 particles. The <I>wall/lj126</I>
interaction is effectively a harder, more repulsive wall interaction.
</P>
<P>For the <I>wall/colloid</I> style, <I>epsilon</I> is effectively a Hamaker
constant for the colloid-wall interaction, <I>R</I> is the radius of the
colloid particle, <I>D</I> is the distance from the surface of the colloid
particle to the wall (r-R), and <I>sigma</I> is the size of the constituent
LJ particle inside the colloid particle. Note that the cutoff
distance Rc in this case is the distance from the colloid particle
center to the wall.
</P>
<P>The <I>wall/colloid</I> interaction is derived by integrating over
constituent LJ particles of size <I>sigma</I> within the colloid particle
and a 3d half-lattice of Lennard-Jones 12/6 particles with the same
<I>sigma</I> in the wall.
</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 position (coord), the specified velocity (vel), and the time
elapsed since the beginning of the simulation. See the note below
about making a wall move continuously across multiple runs. 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; 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</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 = pos0 + A sin (omega * delta)
</PRE>
<P>where <I>pos0</I> is the position at the time the beginning of the
simulation, <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 beginning of the simulation.
See the note below about making a wall oscillate continuously across
multiple runs. 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; an <I>xhi</I> wall will move in the -x
direction. A negative velocity means each wall moves initially
outward, away from the center of the box. If you want different walls
to oscillate with different amplitudes or periods, then you need to
use multiple fix wall commands.
</P>
<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
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy of interaction between atoms and each wall to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a scalar energy and a 3-vector of forces (on the
walls), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>. The scalar and vector values
calculated by this fix are "extensive", meaning they scale with the
number of atoms in the simulation. Note that if you define multiple
walls, then the energy and force will be summed over all the walls.
If you want the energy/force on a per-wall basis, you need to use
multiple fix wall commands.
</P>
<P>This fix can change the position of each wall, due to the <I>vel</I> or
<I>wiggle</I> keywords, continuously over multiple runs, using the <I>start</I>
and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. If you do not do
this, the wall position will be reset to <I>coord</I> at the beginning of
each run.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P>IMPORTANT NOTE: If you want the atom/wall interaction energy to be
included in the total potential energy of the system (the quantity
being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
<I>energy</I> option for this fix.
</P>
<P><B>Restrictions:</B>
</P>
<P>Any dimension (xyz) that has a wall must be non-periodic.
</P>
<P>You cannot use both the <I>vel</I> and <I>wiggle</I> keywords together.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_wall_reflect.html<A HREF = "fix_wall_gran.html">>fix wall/reflect</A> wall/gran</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are no velocity and no wiggle.
</P>
</HTML>

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix wall/lj93 command :h3
fix wall/lj126 command :h3
fix wall/colloid command :h3
[Syntax:]
fix ID group-ID style keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
style = {wall/lj93} or {wall/lj126} or {wall/colloid} :l
one or more keyword/value pairs may be appended :l
keyword = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} or {vel} or {wiggle} :l
{xlo}, {xhi}, {ylo}, {yhi}, {zlo}, {zhi} values = coord epsilon sigma cutoff
coord = position of wall (distance units)
epsilon = strength factor for wall-particle interaction (energy units)
sigma = size factor for wall-particle interaction (distance units)
cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
{vel} value = v
v = velocity of wall in perpendicular direction (velocity units)
{wiggle} values = amplitude period
amplitude = size of oscillation (distance units)
period = time of oscillation (time units) :pre
:ule
[Examples:]
fix wallhi all wall/lj93 xhi 10.0 1.0 1.0 2.5
fix wallhi all wall/lj126 xhi 10.0 1.0 1.0 2.5 vel 1.0
fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre
[Description:]
Bound the simulation domain on one or more of its faces with a flat
wall that interacts with the atoms in the group by generating a force
on the atom in a direction perpendicular to the wall. The energy of
wall-particle interactions depends on the style.
For style {wall/lj93}, the energy E is given by the 9/3 potential:
:c,image(Eqs/fix_wall_lj93.jpg)
For style {wall/lj126}, the energy E is given by the 12/6 potential:
:c,image(Eqs/pair_lj.jpg)
For style {wall/colloid}, the energy E is given by an integrated form of
the "pair_style colloid"_pair_colloid.html potential:
:c,image(Eqs/fix_wall_colloid.jpg)
In all cases, {r} is the distance from the particle to the wall at
position {coord}, and Rc is the {cutoff} distance at which the
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.
For the {wall/lj93} and {wall/lj126} styles, {epsilon} and {sigma} are
the usual Lennard-Jones parameters, which determine the strength and
size of the particle as it interacts with the wall. Note that this
{epsilon} and {sigma} may be different than any {epsilon} or {sigma}
values defined for a pair style that computes particle-particle
interactions.
The {wall/lj93} interaction is derived by integrating over a 3d
half-lattice of Lennard-Jones 12/6 particles. The {wall/lj126}
interaction is effectively a harder, more repulsive wall interaction.
For the {wall/colloid} style, {epsilon} is effectively a Hamaker
constant for the colloid-wall interaction, {R} is the radius of the
colloid particle, {D} is the distance from the surface of the colloid
particle to the wall (r-R), and {sigma} is the size of the constituent
LJ particle inside the colloid particle. Note that the cutoff
distance Rc in this case is the distance from the colloid particle
center to the wall.
The {wall/colloid} interaction is derived by integrating over
constituent LJ particles of size {sigma} within the colloid particle
and a 3d half-lattice of Lennard-Jones 12/6 particles of size {sigma}
in the wall.
If the {vel} keyword is specified, the position of all walls will move
during the simulation in a perpendicular direction, based on their
initial {coord} position, the specified velocity {vel}, and the time
elapsed since the beginning of the simulation. See the note below
about making a wall move continuously across multiple runs. A
positive velocity means each wall moves inward, towards the center of
the box. I.e. an {xlo} wall will move in the +x direction and an
{xhi} 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.
If the {wiggle} keyword is specified, the position of all walls will
oscillate sinusoidally during the simulation in the perpendicular
direction, according to the equation:
position = pos0 + A sin (omega * delta) :pre
where {pos0} is the position at the beginning of the simulation, {A}
is the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the
time elapsed since the beginning of the simulation. See the note
below about making a wall oscillate continuously across multiple runs.
A positive amplitude means each wall initially moves inward, towards
the center of the box. I.e. an {xlo} wall will move initially in the
+x direction and an {xhi} wall will move initially in the -x
direction. A negative velocity means each wall moves initially
outward, away from the center of the box. If you want different walls
to oscillate with different amplitudes or periods, then you need to
use multiple fix wall commands.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy of interaction between atoms and each wall to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a scalar energy and a 3-vector of forces (on the
walls), which can be accessed by various "output
commands"_Section_howto.html#4_15. The scalar and vector values
calculated by this fix are "extensive", meaning they scale with the
number of atoms in the simulation. Note that if you define multiple
walls, then the energy and force will be summed over all the walls.
If you want the energy/force on a per-wall basis, you need to use
multiple fix wall commands.
This fix can change the position of each wall, due to the {vel} or
{wiggle} keywords, continuously over multiple runs, using the {start}
and {stop} keywords of the "run"_run.html command. If you do not do
this, the wall position will be reset to {coord} at the beginning of
each run.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
IMPORTANT NOTE: If you want the atom/wall interaction energy to be
included in the total potential energy of the system (the quantity
being minimized), you MUST enable the "fix_modify"_fix_modify.html
{energy} option for this fix.
[Restrictions:]
Any dimension (xyz) that has a wall must be non-periodic.
You cannot use both the {vel} and {wiggle} keywords together.
[Related commands:]
"fix wall/reflect"_fix_wall_reflect.html wall/gran"_fix_wall_gran.html
[Default:]
The option defaults are no velocity and no wiggle.

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@ -1,94 +0,0 @@
<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 wall/colloid command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID wall/colloid style coord A sigma cutoff
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>wall/colloid = style name of this fix command
<LI>style = <I>xlo</I> or <I>xhi</I> or <I>ylo</I> or <I>yhi</I> or <I>zlo</I> or <I>zhi</I>
<LI>coord = position of wall (distance units)
<LI>A = Hamaker constant for colloid-wall interactions (energy units)
<LI>sigma = size of constituent LJ particle that integration is done over (distance units)
<LI>cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix wallhi all wall/colloid xhi 10.0 20.0 1.0 2.5
fix leftwall all wall/colloid zlo 0.0 10.0 1.0 0.858
</PRE>
<P><B>Description:</B>
</P>
<P>Bound the simulation domain on one of its faces with a wall of
Lennard-Jones particles that interacts with finite-size colloidal
particles in the group. The energy E of wall-colloid interactions is
given by an integrated form of the <A HREF = "pair_colloid.html">pair_style
colloid</A> potential
</P>
<CENTER><IMG SRC = "Eqs/fix_wall_colloid.jpg">
</CENTER>
<P>where A is the specified Hamaker constant for the colloid-wall
interaction, <I>r</I> is the distance from the center of the particle to
the wall <I>coord</I>, <I>R</I> is the radius of the colloid particle, <I>D</I> is
the distance from the surface of the colloid particle to the wall
(r-R), sigma is the size of the constituent LJ particle integrated
over as described below, and Rc is the cutoff value specified in the
fix command and is the distance from the particle center to the wall.
</P>
<P>This colloid/wall interaction is derived by integrating over both the
constituent LJ particles in the colloid particle and a 3d half-lattice
of Lennard-Jones 12-6 particles in the wall.
</P>
<P>The wall potential is shifted so that the energy of a wall-particle
interaction is 0.0 at the cutoff distance.
</P>
<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
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a scalar energy and a 3-vector of forces (on the
wall), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>. The scalar and vector values
calculated by this fix are "extensive", meaning they scale with the
number of atoms in the simulation.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P>IMPORTANT NOTE: If you want the atom/wall interaction energy to be
included in the total potential energy of the system (the quantity
being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
<I>energy</I> option for this fix.
</P>
<P><B>Restrictions:</B>
</P>
<P>Any dimension (xyz) that has a colloid wall must be non-periodic.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_wall_lj93.html">fix wall/lj93</A>, <A HREF = "pair_colloid.html">pair_style
colloid</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -1,89 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix wall/colloid command :h3
[Syntax:]
fix ID group-ID wall/colloid style coord A sigma cutoff :pre
ID, group-ID are documented in "fix"_fix.html command
wall/colloid = style name of this fix command
style = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi}
coord = position of wall (distance units)
A = Hamaker constant for colloid-wall interactions (energy units)
sigma = size of constituent LJ particle that integration is done over (distance units)
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :ul
[Examples:]
fix wallhi all wall/colloid xhi 10.0 20.0 1.0 2.5
fix leftwall all wall/colloid zlo 0.0 10.0 1.0 0.858 :pre
[Description:]
Bound the simulation domain on one of its faces with a wall of
Lennard-Jones particles that interacts with finite-size colloidal
particles in the group. The energy E of wall-colloid interactions is
given by an integrated form of the "pair_style
colloid"_pair_colloid.html potential
:c,image(Eqs/fix_wall_colloid.jpg)
where A is the specified Hamaker constant for the colloid-wall
interaction, {r} is the distance from the center of the particle to
the wall {coord}, {R} is the radius of the colloid particle, {D} is
the distance from the surface of the colloid particle to the wall
(r-R), sigma is the size of the constituent LJ particle integrated
over as described below, and Rc is the cutoff value specified in the
fix command and is the distance from the particle center to the wall.
This colloid/wall interaction is derived by integrating over both the
constituent LJ particles in the colloid particle and a 3d half-lattice
of Lennard-Jones 12-6 particles in the wall.
The wall potential is shifted so that the energy of a wall-particle
interaction is 0.0 at the cutoff distance.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a scalar energy and a 3-vector of forces (on the
wall), which can be accessed by various "output
commands"_Section_howto.html#4_15. The scalar and vector values
calculated by this fix are "extensive", meaning they scale with the
number of atoms in the simulation.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
IMPORTANT NOTE: If you want the atom/wall interaction energy to be
included in the total potential energy of the system (the quantity
being minimized), you MUST enable the "fix_modify"_fix_modify.html
{energy} option for this fix.
[Restrictions:]
Any dimension (xyz) that has a colloid wall must be non-periodic.
[Related commands:]
"fix wall/lj93"_fix_wall_lj93.html, "pair_style
colloid"_pair_colloid.html
[Default:] none

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@ -1,113 +0,0 @@
<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 wall/lj126 command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID wall/lj126 style coord epsilon sigma cutoff keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>wall/lj126 = style name of this fix command
<LI>style = <I>xlo</I> or <I>xhi</I> or <I>ylo</I> or <I>yhi</I> or <I>zlo</I> or <I>zhi</I>
<LI>coord = position of wall (distance units)
<LI>epsilon = Lennard-Jones epsilon for wall-particle interaction (energy units)
<LI>sigma = Lennard-Jones sigma for wall-particle interaction (distance units)
<LI>cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
<LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>vel</I>
<PRE> <I>vel</I> args = v
v = velocity of wall in perpendicular direction (velocity units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix wallhi all wall/lj126 xhi 10.0 1.0 1.0 1.12
fix leftwall all wall/lj126 zlo 0.0 1.0 1.0 0.858 vel 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Bound the simulation domain on one of its faces with a Lennard-Jones
wall that interacts with the atoms in the group. The energy E of
wall-particle interactions is given by the 12-6 potential
</P>
<CENTER><IMG SRC = "Eqs/pair_lj.jpg">
</CENTER>
<P>where <I>r</I> is the distance from the particle to the wall <I>coord</I>, and
epsilon and sigma are the usual LJ parameters. Rc is the cutoff value
specified in the command. This interaction provides a harder, more
repulsive interaction with the wall than the softer 9-3 potential
provided by the <A HREF = "fix_wall_lj93.html">fix wall/lj93</A> command.
</P>
<P>The wall potential is shifted so that the energy of a wall-particle
interaction is 0.0 at the cutoff distance.
</P>
<P>If the <I>vel</I> keyword is specified, the position of wall will move
during the simulation, based on its initial position (coord), the
specified velocity (vel), and the time elapsed since the beginning of
the simulation. <I>Xlo</I> or <I>xhi</I> walls move in the x direction with
whatever sign you give the <I>v</I> argument. Ditto for <I>y</I> and <I>z</I> walls.
See the note below about making the wall move continuously across
multiple runs.
</P>
<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
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a scalar energy and a 3-vector of forces (on the
wall), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>. The scalar and vector values
calculated by this fix are "extensive", meaning they scale with the
number of atoms in the simulation.
</P>
<P>This fix can change the position of the wall, due to the <I>vel</I>
keyword, continuously over multiple runs, using the <I>start</I> and <I>stop</I>
keywords of the <A HREF = "run.html">run</A> command. If you do not do this, the
wall position will be reset to <I>coord</I> at the beginning of each run.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P>IMPORTANT NOTE: If you want the atom/wall interaction energy to be
included in the total potential energy of the system (the quantity
being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
<I>energy</I> option for this fix.
</P>
<P><B>Restrictions:</B>
</P>
<P>Any dimension (xyz) that has a LJ 12/6 wall must be non-periodic.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_wall_reflect.html">fix wall/reflect</A>, <A HREF = "fix_wall_lj93.html">fix
wall/lj93</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are vel = 0.
</P>
</HTML>

98
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View File

@ -1,98 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix wall/lj126 command :h3
[Syntax:]
fix ID group-ID wall/lj126 style coord epsilon sigma cutoff keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
wall/lj126 = style name of this fix command :l
style = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
coord = position of wall (distance units) :l
epsilon = Lennard-Jones epsilon for wall-particle interaction (energy units) :l
sigma = Lennard-Jones sigma for wall-particle interaction (distance units) :l
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l
one or more keyword/value pairs may be appended :l
keyword = {vel} :l
{vel} args = v
v = velocity of wall in perpendicular direction (velocity units) :pre
:ule
[Examples:]
fix wallhi all wall/lj126 xhi 10.0 1.0 1.0 1.12
fix leftwall all wall/lj126 zlo 0.0 1.0 1.0 0.858 vel 1.0 :pre
[Description:]
Bound the simulation domain on one of its faces with a Lennard-Jones
wall that interacts with the atoms in the group. The energy E of
wall-particle interactions is given by the 12-6 potential
:c,image(Eqs/pair_lj.jpg)
where {r} is the distance from the particle to the wall {coord}, and
epsilon and sigma are the usual LJ parameters. Rc is the cutoff value
specified in the command. This interaction provides a harder, more
repulsive interaction with the wall than the softer 9-3 potential
provided by the "fix wall/lj93"_fix_wall_lj93.html command.
The wall potential is shifted so that the energy of a wall-particle
interaction is 0.0 at the cutoff distance.
If the {vel} keyword is specified, the position of wall will move
during the simulation, based on its initial position (coord), the
specified velocity (vel), and the time elapsed since the beginning of
the simulation. {Xlo} or {xhi} walls move in the x direction with
whatever sign you give the {v} argument. Ditto for {y} and {z} walls.
See the note below about making the wall move continuously across
multiple runs.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a scalar energy and a 3-vector of forces (on the
wall), which can be accessed by various "output
commands"_Section_howto.html#4_15. The scalar and vector values
calculated by this fix are "extensive", meaning they scale with the
number of atoms in the simulation.
This fix can change the position of the wall, due to the {vel}
keyword, continuously over multiple runs, using the {start} and {stop}
keywords of the "run"_run.html command. If you do not do this, the
wall position will be reset to {coord} at the beginning of each run.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
IMPORTANT NOTE: If you want the atom/wall interaction energy to be
included in the total potential energy of the system (the quantity
being minimized), you MUST enable the "fix_modify"_fix_modify.html
{energy} option for this fix.
[Restrictions:]
Any dimension (xyz) that has a LJ 12/6 wall must be non-periodic.
[Related commands:]
"fix wall/reflect"_fix_wall_reflect.html, "fix
wall/lj93"_fix_wall_lj93.html
[Default:]
The option defaults are vel = 0.

114
doc/fix_wall_lj93.html
View File

@ -1,114 +0,0 @@
<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 wall/lj93 command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID wall/lj93 style coord epsilon sigma cutoff keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>wall/lj93 = style name of this fix command
<LI>style = <I>xlo</I> or <I>xhi</I> or <I>ylo</I> or <I>yhi</I> or <I>zlo</I> or <I>zhi</I>
<LI>coord = position of wall (distance units)
<LI>epsilon = Lennard-Jones epsilon for wall-particle interaction (energy units)
<LI>sigma = Lennard-Jones sigma for wall-particle interaction (distance units)
<LI>cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
<LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>vel</I>
<PRE> <I>vel</I> args = v
v = velocity of wall in perpendicular direction (velocity units)
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix wallhi all wall/lj93 xhi 10.0 1.0 1.0 2.5
fix leftwall all wall/lj93 zlo 0.0 1.0 1.0 0.858 vel 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Bound the simulation domain on one of its faces with a Lennard-Jones
wall that interacts with the atoms in the group. The energy E of
wall-particle interactions is given by the 9-3 potential
</P>
<CENTER><IMG SRC = "Eqs/fix_wall_lj93.jpg">
</CENTER>
<P>where <I>r</I> is the distance from the particle to the wall <I>coord</I>, and
epsilon and sigma are the usual LJ parameters. Rc is the cutoff value
specified in the command. This interaction is derived by integrating
over a 3d half-lattice of Lennard-Jones 12-6 particles. A harder,
more repulsive wall interaction can be computed by using the <A HREF = "fix_wall_lj126.html">fix
wall/lj126</A> command.
</P>
<P>The wall potential is shifted so that the energy of a wall-particle
interaction is 0.0 at the cutoff distance.
</P>
<P>If the <I>vel</I> keyword is specified, the position of wall will move
during the simulation, based on its initial position (coord), the
specified velocity (vel), and the time elapsed since the beginning of
the simulation. <I>Xlo</I> or <I>xhi</I> walls move in the x direction with
whatever sign you give the <I>v</I> argument. Ditto for <I>y</I> and <I>z</I> walls.
See the note below about making the wall move continuously across
multiple runs.
</P>
<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
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>.
</P>
<P>This fix computes a scalar energy and a 3-vector of forces (on the
wall), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>. The scalar and vector values
calculated by this fix are "extensive", meaning they scale with the
number of atoms in the simulation.
</P>
<P>This fix can change the position of the wall, due to the <I>vel</I>
keyword, continuously over multiple runs, using the <I>start</I> and <I>stop</I>
keywords of the <A HREF = "run.html">run</A> command. If you do not do this, the
wall position will be reset to <I>coord</I> at the beginning of each run.
</P>
<P>The forces due to this fix are imposed during an energy minimization,
invoked by the <A HREF = "minimize.html">minimize</A> command.
</P>
<P>IMPORTANT NOTE: If you want the atom/wall interaction energy to be
included in the total potential energy of the system (the quantity
being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>
<I>energy</I> option for this fix.
</P>
<P><B>Restrictions:</B>
</P>
<P>Any dimension (xyz) that has a LJ 9/3 wall must be non-periodic.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_wall_reflect.html">fix wall/reflect</A>, <A HREF = "fix_wall_lj126.html">fix
wall/lj126</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are vel = 0.
</P>
</HTML>

99
doc/fix_wall_lj93.txt
View File

@ -1,99 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix wall/lj93 command :h3
[Syntax:]
fix ID group-ID wall/lj93 style coord epsilon sigma cutoff keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
wall/lj93 = style name of this fix command :l
style = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
coord = position of wall (distance units) :l
epsilon = Lennard-Jones epsilon for wall-particle interaction (energy units) :l
sigma = Lennard-Jones sigma for wall-particle interaction (distance units) :l
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :l
one or more keyword/value pairs may be appended :l
keyword = {vel} :l
{vel} args = v
v = velocity of wall in perpendicular direction (velocity units) :pre
:ule
[Examples:]
fix wallhi all wall/lj93 xhi 10.0 1.0 1.0 2.5
fix leftwall all wall/lj93 zlo 0.0 1.0 1.0 0.858 vel 1.0 :pre
[Description:]
Bound the simulation domain on one of its faces with a Lennard-Jones
wall that interacts with the atoms in the group. The energy E of
wall-particle interactions is given by the 9-3 potential
:c,image(Eqs/fix_wall_lj93.jpg)
where {r} is the distance from the particle to the wall {coord}, and
epsilon and sigma are the usual LJ parameters. Rc is the cutoff value
specified in the command. This interaction is derived by integrating
over a 3d half-lattice of Lennard-Jones 12-6 particles. A harder,
more repulsive wall interaction can be computed by using the "fix
wall/lj126"_fix_wall_lj126.html command.
The wall potential is shifted so that the energy of a wall-particle
interaction is 0.0 at the cutoff distance.
If the {vel} keyword is specified, the position of wall will move
during the simulation, based on its initial position (coord), the
specified velocity (vel), and the time elapsed since the beginning of
the simulation. {Xlo} or {xhi} walls move in the x direction with
whatever sign you give the {v} argument. Ditto for {y} and {z} walls.
See the note below about making the wall move continuously across
multiple runs.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html.
The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of "thermodynamic
output"_thermo_style.html.
This fix computes a scalar energy and a 3-vector of forces (on the
wall), which can be accessed by various "output
commands"_Section_howto.html#4_15. The scalar and vector values
calculated by this fix are "extensive", meaning they scale with the
number of atoms in the simulation.
This fix can change the position of the wall, due to the {vel}
keyword, continuously over multiple runs, using the {start} and {stop}
keywords of the "run"_run.html command. If you do not do this, the
wall position will be reset to {coord} at the beginning of each run.
The forces due to this fix are imposed during an energy minimization,
invoked by the "minimize"_minimize.html command.
IMPORTANT NOTE: If you want the atom/wall interaction energy to be
included in the total potential energy of the system (the quantity
being minimized), you MUST enable the "fix_modify"_fix_modify.html
{energy} option for this fix.
[Restrictions:]
Any dimension (xyz) that has a LJ 9/3 wall must be non-periodic.
[Related commands:]
"fix wall/reflect"_fix_wall_reflect.html, "fix
wall/lj126"_fix_wall_lj126.html
[Default:]
The option defaults are vel = 0.