lammps/doc/fix_deposit.html

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</CENTER>


<HR>

<H3>fix deposit command 
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID deposit N type M seed keyword values ... 
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command 

<LI>deposit = style name of this fix command 

<LI>N = # of atoms to insert 

<LI>type = atom type to assign to inserted atoms 

<LI>M = insert a single particle every M steps 

<LI>seed = random # seed (positive integer) 

<LI>one or more keyword/value pairs may be appended to args 

<LI>keyword = <I>region</I> or <I>global</I> or <I>local</I> or <I>near</I> or <I>attempt</I> or <I>rate</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>units</I> 

<PRE>  <I>region</I> value = region-ID
    region-ID = ID of region to use as insertion volume
  <I>global</I> values = lo hi
    lo,hi = put new particle a distance lo-hi above all other particles (distance units)
  <I>local</I> values = lo hi delta
    lo,hi = put new particle a distance lo-hi above any nearby particle beneath it (distance units)
    delta = lateral distance within which a neighbor is considered "nearby" (distance units)
  <I>near</I> value = R
    R = only insert particle if further than R from existing particles (distance units)
  <I>attempt</I> value = Q
    Q = attempt a single insertion up to Q times
  <I>rate</I> value = V
    V = z velocity (y in 2d) at which insertion volume moves (velocity units)
  <I>vx</I> values = vxlo vxhi
    vxlo,vxhi = range of x velocities for inserted particle (velocity units)
  <I>vy</I> values = vylo vyhi
    vylo,vyhi = range of y velocities for inserted particle (velocity units)
  <I>vz</I> values = vzlo vzhi
    vzlo,vzhi = range of z velocities for inserted particle (velocity units)
  <I>units</I> value = <I>lattice</I> or <I>box</I>
    lattice = the geometry is defined in lattice units
    box = the geometry is defined in simulation box units 
</PRE>

</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8 
</PRE>
<P><B>Description:</B>
</P>
<P>Insert a single particle into the simulation domain every M timesteps
until N particles have been inserted.  This is useful for simulating
the deposition of particles onto a surface.
</P>
<P>Inserted particles have the specified atom type and are assigned to
two groups: the default group "all" and the group specified in the fix
deposit command (which can also be "all").
</P>
<P>If you are computing temperature values which include inserted
particles, you will want to use the <A HREF = "compute_modify.html">compute_modify</A>
dynamic option, which insures the current number of atoms is used as a
normalizing factor each time temperature is computed.
</P>
<P>Care must be taken that inserted particles are not too near existing
particles, using the options described below.  When inserting
particles above a surface in a non-perioidic box (see the
<A HREF = "boundary.html">boundary</A> command), the possibility of a particle
escaping the surface and flying upward should be considered, since the
particle may be lost or the box size may grow infinitely large.  A
<A HREF = "fix_wall_reflect.html">fix wall/reflect</A> command can be used to
prevent this behavior.  Note that if a shrink-wrap boundary is used,
it is OK to insert the new particle outside the box, however the box
will immediately be expanded to include the new particle.
</P>
<P>This command must use the <I>region</I> keyword to define an insertion
volume.  The specified region must have been previously defined with a
<A HREF = "region.html">region</A> command.  It must be defined with side = <I>in</I>.
</P>
<P>Each timestep a particle is to be inserted, its coordinates are chosen
as follows.  A random position within the insertion volume is
generated.  If neither the <I>global</I> or <I>local</I> keyword is used, that
is the trial position.  If the <I>global</I> keyword is used, the random
x,y values are used, but the z position of the new particle is set
above the highest current atom in the simulation by a distance
randomly chosen between lo/hi.  (For a 2d simulation, this is done for
the y position.)  If the <I>local</I> keyword is used, the z position is
set a distance between lo/hi above the highest current atom in the
simulation that is "nearby" the chosen x,y position.  In this context,
"nearby" means the lateral distance (in x,y) between the new and old
particles is less than the delta parameter.
</P>
<P>Once a trial x,y,z location has been computed, the insertion is only
performed if no current particle in the simulation is within a
distance R of the new particle.  If this test fails, a new random
position within the insertion volume is chosen and another trial is
made.  Up to Q attempts are made.  If an atom is not successfully
deposited, LAMMPS prints a warning message.
</P>
<P>The <I>rate</I> option moves the insertion volume in the z direction (3d)
or y direction (2d).  This enables particles to be inserted from a
successively higher height over time.  Note that this parameter is
ignored if the <I>global</I> or <I>local</I> keywords are used, since those
options choose a z-coordinate for insertion independently.
</P>
<P>The vx, vy, and vz components of velocity for the inserted particle
are set using the values specified for the <I>vx</I>, <I>vy</I>, and <I>vz</I>
keywords.  Note that normally, new particles should be a assigned a
negative vertical velocity so that they move towards the surface.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
for the other deposition parameters.  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 the units choice affects all the keyword values that have
units of distance or velocity.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the deposition to <A HREF = "restart.html">binary restart
files</A>.  This includes information about how many atoms
have been depositied, the random number generator seed, the next
timestep for deposition, etc.  See the
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
</P>
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
fix.  No global scalar or vector 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> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_pour.html">fix_pour</A>, <A HREF = "region.html">region</A>
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are delta = 0.0, near = 0.0, attempt = 10, rate =
0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0, and units = lattice.
</P>
</HTML>
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@188 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2006-12-13 08:37:25 +08:00			`<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 deposit command`
			`</H3>`
			`<P><B>Syntax:</B>`
			`</P>`
			`<PRE>fix ID group-ID deposit N type M seed keyword values ...`
			`</PRE>`
			`<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command`

			`<LI>deposit = style name of this fix command`

			`<LI>N = # of atoms to insert`

			`<LI>type = atom type to assign to inserted atoms`

			`<LI>M = insert a single particle every M steps`

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@996 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2007-10-10 07:40:45 +08:00			`<LI>seed = random # seed (positive integer)`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@188 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2006-12-13 08:37:25 +08:00
			`<LI>one or more keyword/value pairs may be appended to args`

			`<LI>keyword = <I>region</I> or <I>global</I> or <I>local</I> or <I>near</I> or <I>attempt</I> or <I>rate</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>units</I>`

			`<PRE> <I>region</I> value = region-ID`
			`region-ID = ID of region to use as insertion volume`
			`<I>global</I> values = lo hi`
			`lo,hi = put new particle a distance lo-hi above all other particles (distance units)`
			`<I>local</I> values = lo hi delta`
			`lo,hi = put new particle a distance lo-hi above any nearby particle beneath it (distance units)`
			`delta = lateral distance within which a neighbor is considered "nearby" (distance units)`
			`<I>near</I> value = R`
			`R = only insert particle if further than R from existing particles (distance units)`
			`<I>attempt</I> value = Q`
			`Q = attempt a single insertion up to Q times`
			`<I>rate</I> value = V`
			`V = z velocity (y in 2d) at which insertion volume moves (velocity units)`
			`<I>vx</I> values = vxlo vxhi`
			`vxlo,vxhi = range of x velocities for inserted particle (velocity units)`
			`<I>vy</I> values = vylo vyhi`
			`vylo,vyhi = range of y velocities for inserted particle (velocity units)`
			`<I>vz</I> values = vzlo vzhi`
			`vzlo,vzhi = range of z velocities for inserted particle (velocity units)`
			`<I>units</I> value = <I>lattice</I> or <I>box</I>`
			`lattice = the geometry is defined in lattice units`
			`box = the geometry is defined in simulation box units`
			`</PRE>`

			`</UL>`
			`<P><B>Examples:</B>`
			`</P>`
			`<PRE>fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box`
			`fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8`
			`</PRE>`
			`<P><B>Description:</B>`
			`</P>`
			`<P>Insert a single particle into the simulation domain every M timesteps`
			`until N particles have been inserted. This is useful for simulating`
			`the deposition of particles onto a surface.`
			`</P>`
			`<P>Inserted particles have the specified atom type and are assigned to`
			`two groups: the default group "all" and the group specified in the fix`
			`deposit command (which can also be "all").`
			`</P>`
			`<P>If you are computing temperature values which include inserted`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@474 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2007-04-12 03:46:48 +08:00			`particles, you will want to use the <A HREF = "compute_modify.html">compute_modify</A>`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@188 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2006-12-13 08:37:25 +08:00			`dynamic option, which insures the current number of atoms is used as a`
			`normalizing factor each time temperature is computed.`
			`</P>`
			`<P>Care must be taken that inserted particles are not too near existing`
			`particles, using the options described below. When inserting`
			`particles above a surface in a non-perioidic box (see the`
			`<A HREF = "boundary.html">boundary</A> command), the possibility of a particle`
			`escaping the surface and flying upward should be considered, since the`
			`particle may be lost or the box size may grow infinitely large. A`
			`<A HREF = "fix_wall_reflect.html">fix wall/reflect</A> command can be used to`
			`prevent this behavior. Note that if a shrink-wrap boundary is used,`
			`it is OK to insert the new particle outside the box, however the box`
			`will immediately be expanded to include the new particle.`
			`</P>`
			`<P>This command must use the <I>region</I> keyword to define an insertion`
			`volume. The specified region must have been previously defined with a`
			`<A HREF = "region.html">region</A> command. It must be defined with side = <I>in</I>.`
			`</P>`
			`<P>Each timestep a particle is to be inserted, its coordinates are chosen`
			`as follows. A random position within the insertion volume is`
			`generated. If neither the <I>global</I> or <I>local</I> keyword is used, that`
			`is the trial position. If the <I>global</I> keyword is used, the random`
			`x,y values are used, but the z position of the new particle is set`
			`above the highest current atom in the simulation by a distance`
			`randomly chosen between lo/hi. (For a 2d simulation, this is done for`
			`the y position.) If the <I>local</I> keyword is used, the z position is`
			`set a distance between lo/hi above the highest current atom in the`
			`simulation that is "nearby" the chosen x,y position. In this context,`
			`"nearby" means the lateral distance (in x,y) between the new and old`
			`particles is less than the delta parameter.`
			`</P>`
			`<P>Once a trial x,y,z location has been computed, the insertion is only`
			`performed if no current particle in the simulation is within a`
			`distance R of the new particle. If this test fails, a new random`
			`position within the insertion volume is chosen and another trial is`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@892 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2007-09-20 05:36:00 +08:00			`made. Up to Q attempts are made. If an atom is not successfully`
			`deposited, LAMMPS prints a warning message.`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@188 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2006-12-13 08:37:25 +08:00			`</P>`
			`<P>The <I>rate</I> option moves the insertion volume in the z direction (3d)`
			`or y direction (2d). This enables particles to be inserted from a`
			`successively higher height over time. Note that this parameter is`
			`ignored if the <I>global</I> or <I>local</I> keywords are used, since those`
			`options choose a z-coordinate for insertion independently.`
			`</P>`
			`<P>The vx, vy, and vz components of velocity for the inserted particle`
			`are set using the values specified for the <I>vx</I>, <I>vy</I>, and <I>vz</I>`
			`keywords. Note that normally, new particles should be a assigned a`
			`negative vertical velocity so that they move towards the surface.`
			`</P>`
			`<P>The <I>units</I> keyword determines the meaning of the distance units used`
			`for the other deposition parameters. 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 the units choice affects all the keyword values that have`
			`units of distance or velocity.`
			`</P>`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1001 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2007-10-11 06:28:11 +08:00			`<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@673 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2007-06-26 08:03:39 +08:00			`</P>`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1035 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2007-10-13 01:37:26 +08:00			`<P>This fix writes the state of the deposition to <A HREF = "restart.html">binary restart`
			`files</A>. This includes information about how many atoms`
			`have been depositied, the random number generator seed, the next`
			`timestep for deposition, etc. See the`
			`<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify`
			`a fix in an input script that reads a restart file, so that the`
			`operation of the fix continues in an uninterrupted fashion.`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@673 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2007-06-26 08:03:39 +08:00			`</P>`
			`<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1001 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2007-10-11 06:28:11 +08:00			`fix. No global scalar or vector 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>.`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@673 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2007-06-26 08:03:39 +08:00			`</P>`
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@188 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2006-12-13 08:37:25 +08:00			`<P><B>Restrictions:</B> none`
			`</P>`
			`<P><B>Related commands:</B>`
			`</P>`
			`<P><A HREF = "fix_pour.html">fix_pour</A>, <A HREF = "region.html">region</A>`
			`</P>`
			`<P><B>Default:</B>`
			`</P>`
			`<P>The option defaults are delta = 0.0, near = 0.0, attempt = 10, rate =`
			`0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0, and units = lattice.`
			`</P>`
			`</HTML>`