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Commit c0cface3 authored by athomps's avatar athomps
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Added doc for fix wall/piston and fix append/atoms 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7229 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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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 append_atoms command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID append_atoms face arg ... keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>append_atoms = style name of this fix command
<LI>one face/arg pairs must be appended
<LI>face = <I>zhi</I>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>size</I> or <I>freq</I> or <I>temp</I> or <I>random</I> or <I>units</I>
<PRE> <I>size</I> args = Lz
Lz = z size of lattice region appended in a single event(distance units)
<I>freq</I> args = freq
freq = the number of timesteps between append events
<I>temp</I> args = target damp seed extent
target = target velocity for region immediately ahead of the piston
damp = damping parameter (time units)
seed = random number seed for langevin kicks
extent = extent of thermostated region (distance units)
<I>random</I> args = xmax ymax zmax seed
<I>xmax</I>, <I>ymax</I>, <I>zmax</I> = maximum displacement in particular direction (distance units)
<I>seed</I> = random number seed for random displacement
<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 1 all append_atoms zhi size 5.0 freq 295 units lattice
fix 4 all append_atoms zhi size 15.0 freq 5 units box
fix A all append_atoms zhi size 1.0 freq 1000 units lattice
</PRE>
<P><B>Description:</B>
</P>
<P>This fix creates atoms on a lattice, appended on the zhi edge of the system box.
This can be useful when a shock or wave is propagating from zlo. This allows
the system to grow with time to accommodate an expanding wave. A simulation
box must already exist, which is typically created via the
<A HREF = "create_box.html">create_box</A> command. Before using this command, a
lattice must also be defined using the <A HREF = "lattice.html">lattice</A> command.
</P>
<P>This fix will automatically freeze atoms on the zhi edge of the system, so that
overlaps are avoided when new atoms are appended.
</P>
<P>The <I>size</I> keyword defines the size in z of the chunk of material to be added.
</P>
<P>The <I>random</I> keyword will give the atoms random displacements around their
lattice points to simulate some initial temperature.
</P>
<P>The <I>temp</I> keyword will cause a region to be thermostated with a Langevin
thermostat on the zhi boundary. The size of the region is measured from zhi and
is set with the <I>extent</I> argument.
</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.
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><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. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. 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>The zhi boundary on which atoms are added with append_atoms must be shrink-wrapped.
The zlo boundary may be any boundary type other than periodic.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_wall_piston.html">fix wall/piston</A> command
</P>
<P><B>Default:</B> <I>size</I> = 0.0, <I>freq</I> = 0, <I>units</I> = lattice.
</P>
<HR>
</HTML>
doc/fix_append_atoms.txt 0 → 100644
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− 0
View file @ c0cface3
"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 append_atoms command :h3
[Syntax:]
fix ID group-ID append_atoms face arg ... keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
append_atoms = style name of this fix command :l
one face/arg pairs must be appended :l
face = {zhi} :l
zero or more keyword/value pairs may be appended :l
keyword = {size} or {freq} or {temp} or {random} or {units} :l
{size} args = Lz
Lz = z size of lattice region appended in a single event(distance units)
{freq} args = freq
freq = the number of timesteps between append events
{temp} args = target damp seed extent
target = target velocity for region immediately ahead of the piston
damp = damping parameter (time units)
seed = random number seed for langevin kicks
extent = extent of thermostated region (distance units)
{random} args = xmax ymax zmax seed
{xmax}, {ymax}, {zmax} = maximum displacement in particular direction (distance units)
{seed} = random number seed for random displacement
{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 1 all append_atoms zhi size 5.0 freq 295 units lattice
fix 4 all append_atoms zhi size 15.0 freq 5 units box
fix A all append_atoms zhi size 1.0 freq 1000 units lattice :pre
[Description:]
This fix creates atoms on a lattice, appended on the zhi edge of the system box.
This can be useful when a shock or wave is propagating from zlo. This allows
the system to grow with time to accommodate an expanding wave. A simulation
box must already exist, which is typically created via the
"create_box"_create_box.html command. Before using this command, a
lattice must also be defined using the "lattice"_lattice.html command.
This fix will automatically freeze atoms on the zhi edge of the system, so that
overlaps are avoided when new atoms are appended.
The {size} keyword defines the size in z of the chunk of material to be added.
The {random} keyword will give the atoms random displacements around their
lattice points to simulate some initial temperature.
The {temp} keyword will cause a region to be thermostated with a Langevin
thermostat on the zhi boundary. The size of the region is measured from zhi and
is set with the {extent} argument.
The {units} keyword determines the meaning of the distance units used
to define a wall position, but only when a numeric constant is used.
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
[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. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#4_15. 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:]
The zhi boundary on which atoms are added with append_atoms must be shrink-wrapped.
The zlo boundary may be any boundary type other than periodic.
[Related commands:]
"fix wall/piston"_fix_wall_piston.html command
[Default:] {size} = 0.0, {freq} = 0, {units} = lattice.
:line
doc/fix_nphug.html
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− 2
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...@@ -153,10 +153,10 @@ operation of the fix continues in an uninterrupted fashion. ...@@ -153,10 +153,10 @@ operation of the fix continues in an uninterrupted fashion.
</P> </P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>e0</I>, <I>v0</I> and <I>p0</I> keywords <P>The <A HREF = "fix_modify.html">fix_modify</A> <I>e0</I>, <I>v0</I> and <I>p0</I> keywords
can be used to define the values of E0, V0, and P0. Note the can be used to define the values of E0, V0, and P0. Note the
the values for <I>e0</I> and <I>p0</I> are extensive, and so must correspond the values for <I>e0</I> and <I>v0</I> are extensive, and so must correspond
to the total energy and volume of the entire system, not energy and to the total energy and volume of the entire system, not energy and
volume per atom. If any of these quantities are not specified, then the volume per atom. If any of these quantities are not specified, then the
instanteous value in the system at the start of the simulation is used. instantaneous value in the system at the start of the simulation is used.
</P> </P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are <P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
supported by these fixes. You can use them to assign a supported by these fixes. You can use them to assign a
......
doc/fix_nphug.txt
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− 2
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...@@ -148,10 +148,10 @@ operation of the fix continues in an uninterrupted fashion. ...@@ -148,10 +148,10 @@ operation of the fix continues in an uninterrupted fashion.
The "fix_modify"_fix_modify.html {e0}, {v0} and {p0} keywords The "fix_modify"_fix_modify.html {e0}, {v0} and {p0} keywords
can be used to define the values of E0, V0, and P0. Note the can be used to define the values of E0, V0, and P0. Note the
the values for {e0} and {p0} are extensive, and so must correspond the values for {e0} and {v0} are extensive, and so must correspond
to the total energy and volume of the entire system, not energy and to the total energy and volume of the entire system, not energy and
volume per atom. If any of these quantities are not specified, then the volume per atom. If any of these quantities are not specified, then the
instanteous value in the system at the start of the simulation is used. instantaneous value in the system at the start of the simulation is used.
The "fix_modify"_fix_modify.html {temp} and {press} options are The "fix_modify"_fix_modify.html {temp} and {press} options are
supported by these fixes. You can use them to assign a supported by these fixes. You can use them to assign a
......
doc/fix_wall_piston.html 0 → 100644
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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/piston command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID wall/piston face arg ... keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>wall/piston = style name of this fix command
<LI>one face/arg pair must be appended
<LI>face = <I>zlo</I>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>pos</I> or <I>vel</I> or <I>ramp</I> or <I>units</I>
<PRE> <I>pos</I> args = z
z = z coordinate at which the piston begins (distance units)
<I>vel</I> args = vz
vz = final velocity of the piston (velocity units)
<I>ramp</I> = use a linear velocity ramp from 0 to vz
<I>temp</I> args = target damp seed extent
target = target velocity for region immediately ahead of the piston
damp = damping paramter (time units)
seed = random number seed for langevin kicks
extent = extent of thermostated region (distance units)
<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/piston zlo
fix walls all wall/piston zlo pos 1.0 0.0 0.0 vel 0.0 0.0 10.0 units box
fix top all wall/piston zlo vel 0.0 0.0 10.0 ramp
</PRE>
<P><B>Description:</B>
</P>
<P>Bound the simulation with a moving wall which reflect particles
in the specified group and drive the system with an effective infinite-mass
piston capable of driving shock waves.
</P>
<P>A momentum mirror technique is used, which means that if an atom (or the wall)
moves such that an atom is outside the wall on a timestep
by a distance delta (e.g. due to <A HREF = "fix_nve.html">fix nve</A>), then it is
put back inside the face by the same delta, and the velocity relative to
the moving wall is flipped in z. For instance, a stationary particle hit with a
piston wall with velocity vz, will end the timestep with a velocity of 2*vz.
</P>
<P>Currently only face <I>zlo</I> may be specified.
This creates a piston moving in the positive z direction.
Particles with z coordinate less than the wall position
are reflected to a z coordinate
greater than the wall position.
If the piston velocity is vpz and the particle velocity
before reflection is vzi, the particle velocity after
reflection is -vzi + 2*vpz.
</P>
<P>The initial position of the wall can be specified by the <I>pos</I> keyword.
</P>
<P>The final velocity of the wall can be specified by the <I>vel</I> keyword
</P>
<P>The <I>ramp</I> keyword will cause the wall/piston to adjust the velocity linearly
from zero velocity to <I>vel</I> over the course of the run. If the <I>ramp</I> keyword is omitted
then the wall/piston moves at a constant velocity defined by <I>vel</I>.
</P>
<P>The <I>temp</I> keyword will cause the region immediately in front of the wall/piston
to be thermostated with a Langevin thermostat. This region moves with the piston.
The damping and kicking are measured in the reference frame of the piston.
So, a temperature of zero would mean all particles were moving at exactly the speed
of the wall/piston.
</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.
</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><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. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#4_15">output
commands</A>. 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>The face that has the wall/piston must be boundary type 'm' (shrink-wrapped
with minimum a minimum value). The opposing face can be
any boundary type other than periodic.
</P>
<P>A wall/piston should not be used with rigid bodies such as those
defined by a "fix rigid" command. This is because the wall/piston
displaces atoms directly rather than exerting a force on them.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_wall.html">fix wall/reflect</A> command
</P>
<P><A HREF = "fix_append_atoms.html">fix append/atoms</A> command
</P>
<P><B>Default:</B> <I>pos</I> = 0, <I>vel</I> = 0, <I>units</I> = lattice.
</P>
<HR>
</HTML>
doc/fix_wall_piston.txt 0 → 100644
+ 117
− 0
View file @ c0cface3
"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/piston command :h3
[Syntax:]
fix ID group-ID wall/piston face arg ... keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
wall/piston = style name of this fix command :l
one face/arg pair must be appended :l
face = {zlo} :l
zero or more keyword/value pairs may be appended :l
keyword = {pos} or {vel} or {ramp} or {units} :l
{pos} args = z
z = z coordinate at which the piston begins (distance units)
{vel} args = vz
vz = final velocity of the piston (velocity units)
{ramp} = use a linear velocity ramp from 0 to vz
{temp} args = target damp seed extent
target = target velocity for region immediately ahead of the piston
damp = damping paramter (time units)
seed = random number seed for langevin kicks
extent = extent of thermostated region (distance units)
{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/piston zlo
fix walls all wall/piston zlo pos 1.0 0.0 0.0 vel 0.0 0.0 10.0 units box
fix top all wall/piston zlo vel 0.0 0.0 10.0 ramp :pre
[Description:]
Bound the simulation with a moving wall which reflect particles
in the specified group and drive the system with an effective infinite-mass
piston capable of driving shock waves.
A momentum mirror technique is used, which means that if an atom (or the wall)
moves such that an atom is outside the wall on a timestep
by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is
put back inside the face by the same delta, and the velocity relative to
the moving wall is flipped in z. For instance, a stationary particle hit with a
piston wall with velocity vz, will end the timestep with a velocity of 2*vz.
Currently only face {zlo} may be specified.
This creates a piston moving in the positive z direction.
Particles with z coordinate less than the wall position
are reflected to a z coordinate
greater than the wall position.
If the piston velocity is vpz and the particle velocity
before reflection is vzi, the particle velocity after
reflection is -vzi + 2*vpz.
The initial position of the wall can be specified by the {pos} keyword.
The final velocity of the wall can be specified by the {vel} keyword
The {ramp} keyword will cause the wall/piston to adjust the velocity linearly
from zero velocity to {vel} over the course of the run. If the {ramp} keyword is omitted
then the wall/piston moves at a constant velocity defined by {vel}.
The {temp} keyword will cause the region immediately in front of the wall/piston
to be thermostated with a Langevin thermostat. This region moves with the piston.
The damping and kicking are measured in the reference frame of the piston.
So, a temperature of zero would mean all particles were moving at exactly the speed
of the wall/piston.
The {units} keyword determines the meaning of the distance units used
to define a wall position, but only when a numeric constant is used.
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
[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. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#4_15. 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:]
The face that has the wall/piston must be boundary type 'm' (shrink-wrapped
with minimum a minimum value). The opposing face can be
any boundary type other than periodic.
A wall/piston should not be used with rigid bodies such as those
defined by a "fix rigid" command. This is because the wall/piston
displaces atoms directly rather than exerting a force on them.
[Related commands:]
"fix wall/reflect"_fix_wall.html command
"fix append/atoms"_fix_append_atoms.html command
[Default:] {pos} = 0, {vel} = 0, {units} = lattice.
:line
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