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sjplimp 2006-12-13 00:37:25 +00:00
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12
doc/Section_commands.html
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@ -305,14 +305,14 @@ in the command's documentation.
or click on the command itself for a full description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">fix addforce</A></TD><TD ><A HREF = "fix_aveforce.html">fix aveforce</A></TD><TD ><A HREF = "fix_com.html">fix com</A></TD><TD ><A HREF = "fix_drag.html">fix drag</A></TD><TD ><A HREF = "fix_efield.html">fix efield</A></TD><TD ><A HREF = "fix_enforce2d.html">fix enforce2d</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">fix freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">fix gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">fix gravity</A></TD><TD ><A HREF = "fix_gyration.html">fix gyration</A></TD><TD ><A HREF = "fix_indent.html">fix indent</A></TD><TD ><A HREF = "fix_insert.html">fix insert</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">fix addforce</A></TD><TD ><A HREF = "fix_aveforce.html">fix aveforce</A></TD><TD ><A HREF = "fix_com.html">fix com</A></TD><TD ><A HREF = "fix_deposit.html">fix deposit</A></TD><TD ><A HREF = "fix_drag.html">fix drag</A></TD><TD ><A HREF = "fix_efield.html">fix efield</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_enforce2d.html">fix enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">fix freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">fix gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">fix gravity</A></TD><TD ><A HREF = "fix_gyration.html">fix gyration</A></TD><TD ><A HREF = "fix_indent.html">fix indent</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_langevin.html">fix langevin</A></TD><TD ><A HREF = "fix_lineforce.html">fix lineforce</A></TD><TD ><A HREF = "fix_msd.html">fix msd</A></TD><TD ><A HREF = "fix_momentum.html">fix momentum</A></TD><TD ><A HREF = "fix_nph.html">fix nph</A></TD><TD ><A HREF = "fix_npt.html">fix npt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve.html">fix nve</A></TD><TD ><A HREF = "fix_nve_gran.html">fix nve/gran</A></TD><TD ><A HREF = "fix_nvt.html">fix nvt</A></TD><TD ><A HREF = "fix_orient_fcc.html">fix orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">fix planeforce</A></TD><TD ><A HREF = "fix_poems.html">fix poems</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_print.html">fix print</A></TD><TD ><A HREF = "fix_rdf.html">fix rdf</A></TD><TD ><A HREF = "fix_recenter.html">fix recenter</A></TD><TD ><A HREF = "fix_rigid.html">fix rigid</A></TD><TD ><A HREF = "fix_setforce.html">fix setforce</A></TD><TD ><A HREF = "fix_shake.html">fix shake</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_spring.html">fix spring</A></TD><TD ><A HREF = "fix_spring_rg.html">fix spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">fix spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">fix temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">fix tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">fix uniaxial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_vcm.html">fix vcm</A></TD><TD ><A HREF = "fix_viscous.html">fix viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">fix volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">fix wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">fix wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">fix wall/lj126</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_reflect.html">fix wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">fix wiggle</A>
<TR ALIGN="center"><TD ><A HREF = "fix_pour.html">fix pour</A></TD><TD ><A HREF = "fix_print.html">fix print</A></TD><TD ><A HREF = "fix_rdf.html">fix rdf</A></TD><TD ><A HREF = "fix_recenter.html">fix recenter</A></TD><TD ><A HREF = "fix_rigid.html">fix rigid</A></TD><TD ><A HREF = "fix_setforce.html">fix setforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">fix shake</A></TD><TD ><A HREF = "fix_spring.html">fix spring</A></TD><TD ><A HREF = "fix_spring_rg.html">fix spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">fix spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">fix temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">fix tmd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_uniaxial.html">fix uniaxial</A></TD><TD ><A HREF = "fix_vcm.html">fix vcm</A></TD><TD ><A HREF = "fix_viscous.html">fix viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">fix volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">fix wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">fix wall/lj93</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_lj126.html">fix wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">fix wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">fix wiggle</A>
</TD></TR></TABLE></DIV>
<P>Pair styles. See the <A HREF = "pair_style.html">pair_style</A> command for an

3
doc/Section_commands.txt
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@ -361,6 +361,7 @@ or click on the command itself for a full description:
"fix addforce"_fix_addforce.html,
"fix aveforce"_fix_aveforce.html,
"fix com"_fix_com.html,
"fix deposit"_fix_deposit.html,
"fix drag"_fix_drag.html,
"fix efield"_fix_efield.html,
"fix enforce2d"_fix_enforce2d.html,
@ -369,7 +370,6 @@ or click on the command itself for a full description:
"fix gravity"_fix_gravity.html,
"fix gyration"_fix_gyration.html,
"fix indent"_fix_indent.html,
"fix insert"_fix_insert.html,
"fix langevin"_fix_langevin.html,
"fix lineforce"_fix_lineforce.html,
"fix msd"_fix_msd.html,
@ -382,6 +382,7 @@ or click on the command itself for a full description:
"fix orient/fcc"_fix_orient_fcc.html,
"fix planeforce"_fix_planeforce.html,
"fix poems"_fix_poems.html,
"fix pour"_fix_pour.html,
"fix print"_fix_print.html,
"fix rdf"_fix_rdf.html,
"fix recenter"_fix_recenter.html,

2
doc/Section_history.html
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@ -37,7 +37,7 @@ time or interest; others are just a lot of work!
<LI>point dipole force fields
<LI>many-body and bond-order potentials for materials like C, Si, or silica
<LI>modified EAM (MEAM) potentials for metals
<LI>REAXX force field from Bill Goddard's group
<LI>ReaxFF force field from Bill Goddard's group
<LI>Parinello-Rahman non-rectilinear simulation box
</UL>
<HR>

2
doc/Section_howto.html
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@ -328,7 +328,7 @@ the following commands:
</P>
<UL><LI><A HREF = "fix_freeze.html">fix freeze</A>
<LI><A HREF = "fix_gran_diag.html">fix gran/diag</A>
<LI><A HREF = "fix_insert.html">fix insert</A>
<LI><A HREF = "fix_pour.html">fix pour</A>
<LI><A HREF = "fix_viscous.html">fix viscous</A>
<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A>
</UL>

2
doc/Section_howto.txt
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@ -324,7 +324,7 @@ These commands implement fix options specific to granular systems:
"fix freeze"_fix_freeze.html
"fix gran/diag"_fix_gran_diag.html
"fix insert"_fix_insert.html
"fix pour"_fix_pour.html
"fix viscous"_fix_viscous.html
"fix wall/gran"_fix_wall_gran.html :ul

5
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@ -62,6 +62,7 @@ integrators would be in place!
<UL><LI><A HREF = "fix_addforce.html">fix addforce</A> - add a force to each atom
<LI><A HREF = "fix_aveforce.html">fix aveforce</A> - add an averaged force to each atom
<LI><A HREF = "fix_com.html">fix com</A> - compute a center-of-mass
<LI><A HREF = "fix_desosit.html">fix deposit</A> - add new atoms above a surface
<LI><A HREF = "fix_drag.html">fix drag</A> - drag atoms towards a defined coordinate
<LI><A HREF = "fix_efield.html">fix efield</A> - impose electric field on system
<LI><A HREF = "fix_enforce2d.html">fix enforce2d</A> - zero out z-dimension velocity and force
@ -70,7 +71,6 @@ integrators would be in place!
<LI><A HREF = "fix_gravity.html">fix gravity</A> - add gravity to atoms in a granular simulation
<LI><A HREF = "fix_gyration.html">fix gyration</A> - compute radius of gyration
<LI><A HREF = "fix_indent.html">fix indent</A> - impose force due to an indenter
<LI><A HREF = "fix_insert.html">fix insert</A> - add new atoms to a granular simulation
<LI><A HREF = "fix_langevin.html">fix langevin</A> - Langevin temperature control
<LI><A HREF = "fix_lineforce.html">fix lineforce</A> - constrain atoms to move in a line
<LI><A HREF = "fix_msd.html">fix msd</A> - compute mean-squared displacement (i.e. diffusion coefficient)
@ -83,6 +83,7 @@ integrators would be in place!
<LI><A HREF = "fix_orient_fcc.html">fix orient/fcc</A> - add grain boundary migration force
<LI><A HREF = "fix_planeforce.html">fix planeforce</A> - constrain atoms to move in a plane
<LI><A HREF = "fix_poems.html">fix poems</A> - constrain clusters of atoms to move as coupled rigid bodies
<LI><A HREF = "fix_pour.html">fix pour</A> - pour new atoms into a granular simulation domain
<LI><A HREF = "fix_print.html">fix print</A> - print text and variables during a simulation
<LI><A HREF = "fix_rdf.html">fix rdf</A> - compute radial distribution functions
<LI><A HREF = "fix_recenter.html">fix recenter</A> - constrain the center-of-mass position of a group of atoms
@ -109,7 +110,7 @@ integrators would be in place!
if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_2">Making
LAMMPS</A> section for more info.
</P>
<P>The <I>freeze</I>, <I>gran/diag</I>, <I>gravity</I>, <I>insert</I>, <I>nve/gran</I>, and
<P>The <I>freeze</I>, <I>gran/diag</I>, <I>gravity</I>, <I>nve/gran</I>, <I>pour</I>, and
<I>wall/gran</I> styles are part of the "granular" package.
</P>
<P>The <I>poems</I> style is part of the "poems" package.

5
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@ -59,6 +59,7 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
"fix addforce"_fix_addforce.html - add a force to each atom
"fix aveforce"_fix_aveforce.html - add an averaged force to each atom
"fix com"_fix_com.html - compute a center-of-mass
"fix deposit"_fix_desosit.html - add new atoms above a surface
"fix drag"_fix_drag.html - drag atoms towards a defined coordinate
"fix efield"_fix_efield.html - impose electric field on system
"fix enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
@ -67,7 +68,6 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
"fix gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
"fix gyration"_fix_gyration.html - compute radius of gyration
"fix indent"_fix_indent.html - impose force due to an indenter
"fix insert"_fix_insert.html - add new atoms to a granular simulation
"fix langevin"_fix_langevin.html - Langevin temperature control
"fix lineforce"_fix_lineforce.html - constrain atoms to move in a line
"fix msd"_fix_msd.html - compute mean-squared displacement \
@ -84,6 +84,7 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
"fix planeforce"_fix_planeforce.html - constrain atoms to move in a plane
"fix poems"_fix_poems.html - constrain clusters of atoms to move \
as coupled rigid bodies
"fix pour"_fix_pour.html - pour new atoms into a granular simulation domain
"fix print"_fix_print.html - print text and variables during a simulation
"fix rdf"_fix_rdf.html - compute radial distribution functions
"fix recenter"_fix_recenter.html - constrain the center-of-mass position \
@ -117,7 +118,7 @@ Some fix styles are part of specific packages. They are only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_2 section for more info.
The {freeze}, {gran/diag}, {gravity}, {insert}, {nve/gran}, and
The {freeze}, {gran/diag}, {gravity}, {nve/gran}, {pour}, and
{wall/gran} styles are part of the "granular" package.
The {poems} style is part of the "poems" package.

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@ -0,0 +1,145 @@
<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
<LI>seed = random # seed
<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 = "temp_modify.html">temp_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, after which 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>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>

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@ -0,0 +1,131 @@
"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 deposit command :h3
[Syntax:]
fix ID group-ID deposit N type M seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
deposit = style name of this fix command :l
N = # of atoms to insert :l
type = atom type to assign to inserted atoms :l
M = insert a single particle every M steps :l
seed = random # seed :l
one or more keyword/value pairs may be appended to args :l
keyword = {region} or {global} or {local} or {near} or {attempt} or {rate} or {vx} or {vy} or {vz} or {units} :l
{region} value = region-ID
region-ID = ID of region to use as insertion volume
{global} values = lo hi
lo,hi = put new particle a distance lo-hi above all other particles (distance units)
{local} 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)
{near} value = R
R = only insert particle if further than R from existing particles (distance units)
{attempt} value = Q
Q = attempt a single insertion up to Q times
{rate} value = V
V = z velocity (y in 2d) at which insertion volume moves (velocity units)
{vx} values = vxlo vxhi
vxlo,vxhi = range of x velocities for inserted particle (velocity units)
{vy} values = vylo vyhi
vylo,vyhi = range of y velocities for inserted particle (velocity units)
{vz} values = vzlo vzhi
vzlo,vzhi = range of z velocities for inserted particle (velocity units)
{units} value = {lattice} or {box}
lattice = the geometry is defined in lattice units
box = the geometry is defined in simulation box units :pre
:ule
[Examples:]
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
[Description:]
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.
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").
If you are computing temperature values which include inserted
particles, you will want to use the "temp_modify"_temp_modify.html
dynamic option, which insures the current number of atoms is used as a
normalizing factor each time temperature is computed.
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
"boundary"_boundary.html 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
"fix wall/reflect"_fix_wall_reflect.html 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.
This command must use the {region} keyword to define an insertion
volume. The specified region must have been previously defined with a
"region"_region.html command. It must be defined with side = {in}.
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 {global} or {local} keyword is used, that
is the trial position. If the {global} 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 {local} 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.
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, after which LAMMPS prints a warning
message.
The {rate} 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 {global} or {local} keywords are used, since those
options choose a z-coordinate for insertion independently.
The vx, vy, and vz components of velocity for the inserted particle
are set using the values specified for the {vx}, {vy}, and {vz}
keywords. Note that normally, new particles should be a assigned a
negative vertical velocity so that they move towards the surface.
The {units} keyword determines the meaning of the distance units used
for the other deposition parameters. 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 spacing.
Note that the units choice affects all the keyword values that have
units of distance or velocity.
[Restrictions:] none
[Related commands:]
"fix_pour"_fix_pour.html, "region"_region.html
[Default:]
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.

2
doc/fix_indent.html
View File

@ -35,7 +35,7 @@
<I>vel</I> args = vx vy vz
vx,vy,vz = velocity of center of indenter (velocity units)
<I>rstart</I> value = R0
R0 = sphere or cylinder radius at start of run
R0 = sphere or cylinder radius at start of run (distance units)
R is value at end of run, so indenter expands/contracts over time
<I>units</I> value = <I>lattice</I> or <I>box</I>
lattice = the geometry is defined in lattice units

2
doc/fix_indent.txt
View File

@ -27,7 +27,7 @@ keyword = {sphere} or {cylinder} or {vel} or {rstart} or {units} :l
{vel} args = vx vy vz
vx,vy,vz = velocity of center of indenter (velocity units)
{rstart} value = R0
R0 = sphere or cylinder radius at start of run
R0 = sphere or cylinder radius at start of run (distance units)
R is value at end of run, so indenter expands/contracts over time
{units} value = {lattice} or {box}
lattice = the geometry is defined in lattice units

24
doc/fix_insert.html → doc/fix_pour.html
View File

@ -9,15 +9,15 @@
<HR>
<H3>fix insert command
<H3>fix pour command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID insert N type seed keyword values ...
<PRE>fix ID group-ID pour N type seed keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>insert = style name of this fix command
<LI>pour = style name of this fix command
<LI>N = # of atoms to insert
@ -52,18 +52,19 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 3 all insert 1000 2 29494 region myblock
fix 2 all insert 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam 0.9 1.1
<PRE>fix 3 all pour 1000 2 29494 region myblock
fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam 0.9 1.1
</PRE>
<P><B>Description:</B>
</P>
<P>Insert particles into a granular run every few timesteps within a
specified region until N particles have been inserted. This is useful
for simulating the pouring of particles into a container.
for simulating the pouring of particles into a container under the
influence of gravity.
</P>
<P>Inserted particles are assigned the specified atom type and are
assigned to two groups: the default group "all" and the group
specified in the fix insert command (which can also be "all").
specified in the fix pour command (which can also be "all").
</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
@ -96,9 +97,9 @@ total of M tries to insert the new particles without overlaps, where M
= # of inserted particles * Nattempt. If LAMMPS is unsuccessful at
completing all insertions, it prints a warning.
</P>
<P>The <I>rate</I> option allows the insertion volume to move in the z
direction (3d) or y direction (2d). This enables pouring particles
from a successively higher height over time.
<P>The <I>rate</I> option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables pouring particles from a
successively higher height over time.
</P>
<P><B>Restrictions:</B>
</P>
@ -111,7 +112,8 @@ must be defined in the -y direction.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_gravity.html">fix_gravity</A>, <A HREF = "region.html">region</A>
<P><A HREF = "fix_deposit.html">fix_deposit</A>, <A HREF = "fix_gravity.html">fix_gravity</A>,
<A HREF = "region.html">region</A>
</P>
<P><B>Default:</B>
</P>

24
doc/fix_insert.txt → doc/fix_pour.txt
View File

@ -6,14 +6,14 @@
:line
fix insert command :h3
fix pour command :h3
[Syntax:]
fix ID group-ID insert N type seed keyword values ... :pre
fix ID group-ID pour N type seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
insert = style name of this fix command :l
pour = style name of this fix command :l
N = # of atoms to insert :l
type = atom type to assign to inserted atoms :l
seed = random # seed :l
@ -41,18 +41,19 @@ keyword = {region} or {diam} or {dens} or {vol} or {rate} or {vel} :l
[Examples:]
fix 3 all insert 1000 2 29494 region myblock
fix 2 all insert 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam 0.9 1.1 :pre
fix 3 all pour 1000 2 29494 region myblock
fix 2 all pour 10000 1 19985583 region disk vol 0.33 100 rate 1.0 diam 0.9 1.1 :pre
[Description:]
Insert particles into a granular run every few timesteps within a
specified region until N particles have been inserted. This is useful
for simulating the pouring of particles into a container.
for simulating the pouring of particles into a container under the
influence of gravity.
Inserted particles are assigned the specified atom type and are
assigned to two groups: the default group "all" and the group
specified in the fix insert command (which can also be "all").
specified in the fix pour command (which can also be "all").
This command must use the {region} keyword to define an insertion
volume. The specified region must have been previously defined with a
@ -85,9 +86,9 @@ total of M tries to insert the new particles without overlaps, where M
= # of inserted particles * Nattempt. If LAMMPS is unsuccessful at
completing all insertions, it prints a warning.
The {rate} option allows the insertion volume to move in the z
direction (3d) or y direction (2d). This enables pouring particles
from a successively higher height over time.
The {rate} option moves the insertion volume in the z direction (3d)
or y direction (2d). This enables pouring particles from a
successively higher height over time.
[Restrictions:]
@ -100,7 +101,8 @@ must be defined in the -y direction.
[Related commands:]
"fix_gravity"_fix_gravity.html, "region"_region.html
"fix_deposit"_fix_deposit.html, "fix_gravity"_fix_gravity.html,
"region"_region.html
[Default:]

19
doc/temp_modify.html
View File

@ -19,16 +19,19 @@
<LI>one or more keyword/value pairs may be listed
<LI>keyword = <I>extra</I>
<LI>keyword = <I>extra</I> or <I>dynamic</I>
<PRE> <I>extra</I> value = N
N = # of extra degrees of freedom to subtract
N = # of extra degrees of freedom to subtract
<I>dynamic</I> value = <I>yes</I> or <I>no</I>
yes/no = do or do not recompute the number of atoms contributing to the temperature
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>temp_modify mine extra 0
<PRE>temp_modify mine extra 0
temp_modify mine dynamic yes
</PRE>
<P><B>Description:</B>
</P>
@ -42,6 +45,14 @@ subtracted (typically from 3N) as a normalizing factor in the
temperature computation. The default is 3 which is a correction
factor for an ensemble of velocities with zero total linear momentum.
</P>
<P>The <I>dynamic</I> keyword determines whether the number of atoms N in the
temperature group is re-computed each time the temperature is
computed. By default, N is assumed to be constant. If you are adding
atoms to the system (see the <A HREF = "fix_pour.html">fix pour</A> or <A HREF = "fix_deposit.html">fix
deposit</A> commands) or expect atoms to be lost
(e.g. due to evaporation), then this option can be used to insure the
temperature is correctly normalized.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
@ -50,6 +61,6 @@ factor for an ensemble of velocities with zero total linear momentum.
</P>
<P><B>Default:</B>
</P>
<P>The option defaults are extra = 3.
<P>The option defaults are extra = 3 and dynamic = no.
</P>
</HTML>

19
doc/temp_modify.txt
View File

@ -14,14 +14,17 @@ temp_modify temp-ID keyword value ... :pre
temp-ID = ID of temperature to modify :ulb,l
one or more keyword/value pairs may be listed :l
keyword = {extra} :l
keyword = {extra} or {dynamic} :l
{extra} value = N
N = # of extra degrees of freedom to subtract :pre
N = # of extra degrees of freedom to subtract
{dynamic} value = {yes} or {no}
yes/no = do or do not recompute the number of atoms contributing to the temperature :pre
:ule
[Examples:]
temp_modify mine extra 0 :pre
temp_modify mine extra 0
temp_modify mine dynamic yes :pre
[Description:]
@ -35,6 +38,14 @@ subtracted (typically from 3N) as a normalizing factor in the
temperature computation. The default is 3 which is a correction
factor for an ensemble of velocities with zero total linear momentum.
The {dynamic} keyword determines whether the number of atoms N in the
temperature group is re-computed each time the temperature is
computed. By default, N is assumed to be constant. If you are adding
atoms to the system (see the "fix pour"_fix_pour.html or "fix
deposit"_fix_deposit.html commands) or expect atoms to be lost
(e.g. due to evaporation), then this option can be used to insure the
temperature is correctly normalized.
[Restrictions:] none
[Related commands:]
@ -43,4 +54,4 @@ factor for an ensemble of velocities with zero total linear momentum.
[Default:]
The option defaults are extra = 3.
The option defaults are extra = 3 and dynamic = no.

5
doc/temperature.html
View File

@ -63,7 +63,10 @@ nvt</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
style means KE = dim/2 N k T, where KE = total kinetic energy of the
group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of
the simulation, N = number of atoms in the group, k = Boltzmann
constant, and T = temperature.
constant, and T = temperature. The number of atoms contributing to
the temperature is assumed to be constant for the duration of the run;
use the <I>dynamic</I> option of the <A HREF = "temp_modify.html">temp_modify</A> command
if this is not the case.
</P>
<P>The <I>partial</I> style uses the same formula as <I>full</I>, except entire
dimensions can be eliminated from the kinetic energy computation.

5
doc/temperature.txt
View File

@ -53,7 +53,10 @@ The style determines how the temperature is computed. The {full}
style means KE = dim/2 N k T, where KE = total kinetic energy of the
group of atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of
the simulation, N = number of atoms in the group, k = Boltzmann
constant, and T = temperature.
constant, and T = temperature. The number of atoms contributing to
the temperature is assumed to be constant for the duration of the run;
use the {dynamic} option of the "temp_modify"_temp_modify.html command
if this is not the case.
The {partial} style uses the same formula as {full}, except entire
dimensions can be eliminated from the kinetic energy computation.

2
examples/pour/in.pour
View File

@ -23,7 +23,7 @@ fix 2 all gravity spherical 0.0 -180.0
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all insert 3000 1 300719 vol 0.13 50 region slab
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
thermo_style granular
thermo 1000

2
examples/pour/in.pour.2d
View File

@ -25,7 +25,7 @@ fix xwalls all wall/gran xplane 0 100 50 0
fix ywalls all wall/gran yplane 0 NULL 50 0
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all insert 1000 1 4767548 vol 0.4 10 &
fix ins all pour 1000 1 4767548 vol 0.4 10 &
diam 0.5 1.0 region slab
fix 3 all enforce2d