git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5175 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
203
doc/fix_wall_srd.html
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203
doc/fix_wall_srd.html
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@ -0,0 +1,203 @@
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<HTML>
|
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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>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>fix wall/srd command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID wall/srd face arg ... keyword value ...
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
|
||||
<LI>wall/srd = style name of this fix command
|
||||
|
||||
<LI>one or more face/arg pairs may be appended
|
||||
|
||||
<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>ylo</I>,<I>zlo</I> arg = EDGE or constant or variable
|
||||
EDGE = current lo 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
|
||||
<I>xhi</I>,<I>yhi</I>,<I>zhi</I> arg = EDGE or constant or variable
|
||||
EDGE = current hi edge of simulation box
|
||||
constant = number like 50.0 or 100.3 (distance units)
|
||||
variable = <A HREF = "variable.html">equal-style variable</A> like v_x or v_wiggle
|
||||
</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 xwalls all wall/srd xlo EDGE xhi EDGE
|
||||
fix walls all wall/srd xlo 0.0 ylo 10.0 units box
|
||||
fix top all wall/srd zhi v_pressdown
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Bound the simulation with one or more walls which interact with
|
||||
stochastic reaction dynamics (SRD) particles as slip (smooth) or
|
||||
no-slip (rough) flat surfaces. The wall interaction is actually
|
||||
invoked via the <A HREF = "fix_srd.html">fix srd</A> command, only on the group of
|
||||
SRD particles it defines, so the group setting for the fix wall/srd
|
||||
command is ignored.
|
||||
</P>
|
||||
<P>A particle/wall collision occurs if an SRD particle moves outside the
|
||||
wall on a timestep. This alters the position and velocity of the SRD
|
||||
particle and imparts a force to the wall.
|
||||
</P>
|
||||
<P>The <I>collision</I> and <I>Tsrd</I> settings specified via the <A HREF = "fix_srd.html">fix
|
||||
srd</A> command affect the SRD/wall collisions. A <I>slip</I>
|
||||
setting for the <I>collision</I> keyword means that the tangential
|
||||
component of the SRD particle momentum is preserved. Thus only a
|
||||
normal force is imparted to the wall. The normal component of the new
|
||||
SRD velocity is sampled from a Gaussian distribution at temperature
|
||||
<I>Tsrd</I>.
|
||||
</P>
|
||||
<P>For a <I>noslip</I> setting of the <I>collision</I> keyword, both the normal and
|
||||
tangential components of the new SRD velocity are sampled from a
|
||||
Gaussian distribution at temperature <I>Tsrd</I>. Additionally, a new
|
||||
tangential direction for the SRD velocity is chosen randomly. This
|
||||
collision style imparts both a normal and tangential force to the
|
||||
wall.
|
||||
</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 reflects particles
|
||||
that move to a coordinate less than the wall position, back in the
|
||||
<I>hi</I> direction. A <I>hi</I> face reflects particles that move to a
|
||||
coordinate higher than the wall position, back in the <I>lo</I> direction.
|
||||
</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.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Because the trajectory of the SRD particle is tracked
|
||||
as it collides with the wall, you must insure that r = distance of the
|
||||
particle from the wall, is always > 0 for SRD particles, or LAMMPS
|
||||
will generate an error. This means you cannot start your simulation
|
||||
with SRD particles at the wall position <I>coord</I> (r = 0) or with
|
||||
particles on the wrong side of the wall (r < 0).
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: If you have 2 or more walls that come together at an
|
||||
edge or corner (e.g. walls in the x and y dimensions), then be sure to
|
||||
set the <I>overlap</I> keyword to <I>yes</I> in the <A HREF = "fix_srd.html">fix srd</A>
|
||||
command, since the walls effectively overlap when SRD particles
|
||||
collide with them. LAMMPS will issue a warning if you do not do this.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: The walls of this fix only interact with SRD
|
||||
particles, as defined by the <A HREF = "fix_srd.html">fix srd</A> command. If you
|
||||
are simulating a mixture containing other kinds of particles, then you
|
||||
should typically use <A HREF = "fix_wall.html">another wall command</A> to act on
|
||||
the other particles. Since SRD particles will be colliding both with
|
||||
the walls and the other particles, it is important to insure that the
|
||||
other particle's finite extent does not overlap an SRD wall. If you
|
||||
do not do this, you may generate errors when SRD particles end up
|
||||
"inside" another particle or a wall at the beginning of a collision
|
||||
step.
|
||||
</P>
|
||||
<P>The <I>units</I> keyword determines the meaning of the distance units used
|
||||
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
|
||||
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
||||
are relevant to this fix.
|
||||
</P>
|
||||
<P>This fix computes a global array of values which can be accessed by
|
||||
various <A HREF = "Section_howto.html#4_15">output commands</A>. The number of rows
|
||||
in the array is equal to the number of walls defined by the fix. The
|
||||
number of columns is 3, for the x,y,z components of force on each
|
||||
wall.
|
||||
</P>
|
||||
<P>Note that an outward normal force on a wall will be a negative value
|
||||
for <I>lo</I> walls and a positive value for <I>hi</I> walls. The array values
|
||||
calculated by this fix are "extensive".
|
||||
</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. This fix is not invoked during <A HREF = "minimize.html">energy
|
||||
minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>Any dimension (xyz) that has an SRD wall must be non-periodic.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_wall_reflect.html">fix wall/reflect</A> command
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
190
doc/fix_wall_srd.txt
Normal file
190
doc/fix_wall_srd.txt
Normal file
@ -0,0 +1,190 @@
|
||||
"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/srd command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID wall/srd face arg ... keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
wall/srd = style name of this fix command :l
|
||||
one or more face/arg pairs may be appended :l
|
||||
face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :l
|
||||
{xlo},{ylo},{zlo} arg = EDGE or constant or variable
|
||||
EDGE = current lo edge of simulation box
|
||||
constant = number like 0.0 or -30.0 (distance units)
|
||||
variable = "equal-style variable"_variable.html like v_x or v_wiggle
|
||||
{xhi},{yhi},{zhi} arg = EDGE or constant or variable
|
||||
EDGE = current hi edge of simulation box
|
||||
constant = number like 50.0 or 100.3 (distance units)
|
||||
variable = "equal-style variable"_variable.html like v_x or v_wiggle :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {units} :l
|
||||
{units} value = {lattice} or {box}
|
||||
{lattice} = the wall position is defined in lattice units
|
||||
{box} = the wall position is defined in simulation box units :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix xwalls all wall/srd xlo EDGE xhi EDGE
|
||||
fix walls all wall/srd xlo 0.0 ylo 10.0 units box
|
||||
fix top all wall/srd zhi v_pressdown :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Bound the simulation with one or more walls which interact with
|
||||
stochastic reaction dynamics (SRD) particles as slip (smooth) or
|
||||
no-slip (rough) flat surfaces. The wall interaction is actually
|
||||
invoked via the "fix srd"_fix_srd.html command, only on the group of
|
||||
SRD particles it defines, so the group setting for the fix wall/srd
|
||||
command is ignored.
|
||||
|
||||
A particle/wall collision occurs if an SRD particle moves outside the
|
||||
wall on a timestep. This alters the position and velocity of the SRD
|
||||
particle and imparts a force to the wall.
|
||||
|
||||
The {collision} and {Tsrd} settings specified via the "fix
|
||||
srd"_fix_srd.html command affect the SRD/wall collisions. A {slip}
|
||||
setting for the {collision} keyword means that the tangential
|
||||
component of the SRD particle momentum is preserved. Thus only a
|
||||
normal force is imparted to the wall. The normal component of the new
|
||||
SRD velocity is sampled from a Gaussian distribution at temperature
|
||||
{Tsrd}.
|
||||
|
||||
For a {noslip} setting of the {collision} keyword, both the normal and
|
||||
tangential components of the new SRD velocity are sampled from a
|
||||
Gaussian distribution at temperature {Tsrd}. Additionally, a new
|
||||
tangential direction for the SRD velocity is chosen randomly. This
|
||||
collision style imparts both a normal and tangential force to the
|
||||
wall.
|
||||
|
||||
Up to 6 walls or faces can be specified in a single command: {xlo},
|
||||
{xhi}, {ylo}, {yhi}, {zlo}, {zhi}. A {lo} face reflects particles
|
||||
that move to a coordinate less than the wall position, back in the
|
||||
{hi} direction. A {hi} face reflects particles that move to a
|
||||
coordinate higher than the wall position, back in the {lo} direction.
|
||||
|
||||
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 "equal-style variable"_variable.html 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
|
||||
"thermo_style"_thermo_style.html command keywords for the simulation
|
||||
box parameters and timestep and elapsed time. Thus it is easy to
|
||||
specify a time-dependent wall position.
|
||||
|
||||
IMPORTANT NOTE: Because the trajectory of the SRD particle is tracked
|
||||
as it collides with the wall, you must insure that r = distance of the
|
||||
particle from the wall, is always > 0 for SRD particles, or LAMMPS
|
||||
will generate an error. This means you cannot start your simulation
|
||||
with SRD particles at the wall position {coord} (r = 0) or with
|
||||
particles on the wrong side of the wall (r < 0).
|
||||
|
||||
IMPORTANT NOTE: If you have 2 or more walls that come together at an
|
||||
edge or corner (e.g. walls in the x and y dimensions), then be sure to
|
||||
set the {overlap} keyword to {yes} in the "fix srd"_fix_srd.html
|
||||
command, since the walls effectively overlap when SRD particles
|
||||
collide with them. LAMMPS will issue a warning if you do not do this.
|
||||
|
||||
IMPORTANT NOTE: The walls of this fix only interact with SRD
|
||||
particles, as defined by the "fix srd"_fix_srd.html command. If you
|
||||
are simulating a mixture containing other kinds of particles, then you
|
||||
should typically use "another wall command"_fix_wall.html to act on
|
||||
the other particles. Since SRD particles will be colliding both with
|
||||
the walls and the other particles, it is important to insure that the
|
||||
other particle's finite extent does not overlap an SRD wall. If you
|
||||
do not do this, you may generate errors when SRD particles end up
|
||||
"inside" another particle or a wall at the beginning of a collision
|
||||
step.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
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.
|
||||
|
||||
A {box} value selects standard distance units as defined by the
|
||||
"units"_units.html command, e.g. Angstroms for units = real or metal.
|
||||
A {lattice} value means the distance units are in lattice spacings.
|
||||
The "lattice"_lattice.html command must have been previously used to
|
||||
define the lattice spacings.
|
||||
|
||||
:line
|
||||
|
||||
Here are examples of variable definitions that move the wall position
|
||||
in a time-dependent fashion using equal-style
|
||||
"variables"_variable.html.
|
||||
|
||||
variable ramp equal ramp(0,10)
|
||||
fix 1 all wall xlo v_ramp 1.0 1.0 2.5 :pre
|
||||
|
||||
variable linear equal vlinear(0,20)
|
||||
fix 1 all wall xlo v_linear 1.0 1.0 2.5 :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
|
||||
|
||||
variable wiggle equal cwiggle(0.0,5.0,3.0)
|
||||
fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 :pre
|
||||
|
||||
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.
|
||||
|
||||
The swiggle(c0,A,period) function causes the wall position to
|
||||
oscillate sinusoidally according to this equation, where omega = 2 PI
|
||||
/ period:
|
||||
|
||||
position = c0 + A sin(omega*delta) :pre
|
||||
|
||||
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:
|
||||
|
||||
position = c0 + A (1 - cos(omega*delta)) :pre
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix.
|
||||
|
||||
This fix computes a global array of values which can be accessed by
|
||||
various "output commands"_Section_howto.html#4_15. The number of rows
|
||||
in the array is equal to the number of walls defined by the fix. The
|
||||
number of columns is 3, for the x,y,z components of force on each
|
||||
wall.
|
||||
|
||||
Note that an outward normal force on a wall will be a negative value
|
||||
for {lo} walls and a positive value for {hi} walls. The array values
|
||||
calculated by this fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Any dimension (xyz) that has an SRD wall must be non-periodic.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix wall/reflect"_fix_wall_reflect.html command
|
||||
|
||||
[Default:] none
|
||||
Reference in New Issue
Block a user