diff --git a/doc/fix_wall_lj126.html b/doc/fix_wall_lj126.html index ac718c8b3..e70816500 100644 --- a/doc/fix_wall_lj126.html +++ b/doc/fix_wall_lj126.html @@ -1,111 +1,113 @@ <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 <LI>epsilon = Lennard-Jones epsilon for wall-particle interaction <LI>sigma = Lennard-Jones sigma for wall-particle interaction <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) and the -specified velocity (vel). <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. Note that if you do multiple runs, the initial -position of the wall does not change, so it will continue to move at -the specified velocity. +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>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>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> diff --git a/doc/fix_wall_lj126.txt b/doc/fix_wall_lj126.txt index 13512b9ac..caa809e24 100644 --- a/doc/fix_wall_lj126.txt +++ b/doc/fix_wall_lj126.txt @@ -1,96 +1,98 @@ "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 :l epsilon = Lennard-Jones epsilon for wall-particle interaction :l sigma = Lennard-Jones sigma for wall-particle interaction :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) and the -specified velocity (vel). {Xlo} or {xhi} walls move in the x -direction with whatever sign you give the {v} argument. Ditto for {y} -and {z} walls. Note that if you do multiple runs, the initial -position of the wall does not change, so it will continue to move at -the specified velocity. +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. -No parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. +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.