<p>with an additional Urey_Bradley term based on the distance <em>r</em> between

the 1st and 3rd atoms in the angle.  K, theta0, Kub, and Rub are

coefficients defined for each angle type.</p>

<p>See <a class="reference internal" href="dihedral_charmm.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force

<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force

field.</p>

<p>The following coefficients must be defined for each angle type via the

<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a> command as in the example above, or in

<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>

<p>The <em>charmm</em> dihedral style uses the potential</p>

<img alt="_images/dihedral_charmm.jpg" class="align-center" src="_images/dihedral_charmm.jpg" />

<p>See <a class="reference internal" href="#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force

<p>See <a class="reference internal" href="special_bonds.html#mackerell"><span>(MacKerell)</span></a> for a description of the CHARMM force

field.  This dihedral style can also be used for the AMBER force field

(see comment on weighting factors below).  See <a class="reference internal" href="#cornell"><span>(Cornell)</span></a>

(see comment on weighting factors below).  See <a class="reference internal" href="special_bonds.html#cornell"><span>(Cornell)</span></a>

for a description of the AMBER force field.</p>

<p>The following coefficients must be defined for each dihedral type via the

<a class="reference internal" href="dihedral_coeff.html"><em>dihedral_coeff</em></a> command as in the example above, or in

<em>line</em> = color width

  color = <em>type</em>

  width = numeric value for line width (distance units)

<em>tri</em> = color

<em>tri</em> = color tflag width

  color = <em>type</em>

  tflag = 1 for just triangle, 2 for just tri edges, 3 for both

  width = numeric value for tringle edge width (distance units)

<em>body</em> = color bflag1 bflag2

  color = <em>type</em>

  bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn

is in whatever distance <a class="reference internal" href="units.html"><em>units</em></a> the input script defines,

e.g. Angstroms.</p>

<p>The <em>tri</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> is

used to define particles as triangles, and will draw them as

triangles.  If this keyword is not used, such particles will be drawn

as spheres, the same as if they were regular atoms.  The only setting

currently allowed for the <em>color</em> value is <em>type</em>, which will color

the triangles according to the atom type of the particle.  By default

the mapping of types to colors is as follows:</p>

used to define particles as triangles, and will draw them as triangles

or edges (3 lines) or both, depending on the setting for <em>tflag</em>.  If

edges are drawn, the <em>width</em> setting determines the diameters of the

line segments.  If this keyword is not used, triangle particles will

be drawn as spheres, the same as if they were regular atoms.  The only

setting currently allowed for the <em>color</em> value is <em>type</em>, which will

color the triangles according to the atom type of the particle.  By

default the mapping of types to colors is as follows:</p>

<ul class="simple">

<li>type 1 = red</li>

<li>type 2 = green</li>

  {line} = color width

    color = {type}

    width = numeric value for line width (distance units)

  {tri} = color

  {tri} = color tflag width

    color = {type}

    tflag = 1 for just triangle, 2 for just tri edges, 3 for both

    width = numeric value for tringle edge width (distance units)

  {body} = color bflag1 bflag2

    color = {type}

    bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn

e.g. Angstroms.

The {tri} keyword can be used when "atom_style tri"_atom_style.html is

used to define particles as triangles, and will draw them as

triangles.  If this keyword is not used, such particles will be drawn

as spheres, the same as if they were regular atoms.  The only setting

currently allowed for the {color} value is {type}, which will color

the triangles according to the atom type of the particle.  By default

the mapping of types to colors is as follows:

used to define particles as triangles, and will draw them as triangles

or edges (3 lines) or both, depending on the setting for {tflag}.  If

edges are drawn, the {width} setting determines the diameters of the

line segments.  If this keyword is not used, triangle particles will

be drawn as spheres, the same as if they were regular atoms.  The only

setting currently allowed for the {color} value is {type}, which will

color the triangles according to the atom type of the particle.  By

default the mapping of types to colors is as follows:

type 1 = red

type 2 = green

<ul class="simple">

<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>

<li>pour = style name of this fix command</li>

<li>N = # of atoms to insert</li>

<li>type = atom type to assign to inserted atoms (offset for molecule insertion)</li>

<li>N = # of particles to insert</li>

<li>type = atom type to assign to inserted particles (offset for molecule insertion)</li>

<li>seed = random # seed (positive integer)</li>

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

<li>keyword = <em>region</em> or <em>diam</em> or <em>dens</em> or <em>vol</em> or <em>rate</em> or <em>vel</em> or <em>mol</em> or <em>rigid</em> or <em>shake</em></li>

<li>keyword = <em>region</em> or <em>diam</em> or <em>vol</em> or <em>rate</em> or <em>dens</em> or <em>vel</em> or <em>mol</em> or <em>rigid</em> or <em>shake</em> or <em>ignore</em></li>

</ul>

<pre class="literal-block">

<em>region</em> value = region-ID

      Npoly = # of (D,P) pairs

      D1,D2,... = diameter for subset of inserted particles (distance units)

      P1,P2,... = percentage of inserted particles with this diameter (0-1)

<em>id</em> values = idflag

  idflag = <em>max</em> or <em>next</em> = how to choose IDs for inserted particles and molecules

<em>vol</em> values = fraction Nattempt

  fraction = desired volume fraction for filling insertion volume

  Nattempt = max # of insertion attempts per atom

  Nattempt = max # of insertion attempts per particle

<em>rate</em> value = V

  V = z velocity (3d) or y velocity (2d) at which

      insertion volume moves (velocity units)

<em>dens</em> values = Rholo Rhohi

  Rholo,Rhohi = range of densities for inserted particles (mass/volume units)

<em>vel</em> values (3d) = vxlo vxhi vylo vyhi vz

<em>vel</em> values (2d) = vxlo vxhi vy

  vxlo,vxhi = range of x velocities for inserted particles (velocity units)

  fix-ID = ID of <a class="reference internal" href="fix_rigid.html"><em>fix rigid/small</em></a> command

<em>shake</em> value = fix-ID

  fix-ID = ID of <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command

<em>ignore</em> value = none

  skip any line or triangle particles when detecting possible

    overlaps with inserted particles

</pre>

</div>

<div class="section" id="examples">

that the previously inserted particles fall out of the insertion

volume under the influence of gravity.  Insertions continue every so

many timesteps until the desired # of particles has been inserted.</p>

<div class="admonition note">

<p class="first admonition-title">Note</p>

<p class="last">If you are monitoring the temperature of a system where the

particle count is changing due to adding particles, you typically

should use the <a class="reference internal" href="compute_modify.html"><em>compute_modify dynamic yes</em></a>

command for the temperature compute you are using.</p>

</div>

<hr class="docutils" />

<p>All other keywords are optional with defaults as shown below.</p>

<p>The <em>diam</em> option is only used when inserting atoms and specifes the

diameters of inserted particles.  There are 3 styles: <em>one</em>, <em>range</em>,

the molecule can be specified in the file read by the

<a class="reference internal" href="molecule.html"><em>molecule</em></a> command.  If not specified, the diameter of

each atom in the molecule has a default diameter of 1.0.</p>

<p>The <em>dens</em> and <em>vel</em> options enable inserted particles to have a range

of densities or xy velocities.  The specific values for a particular

inserted particle will be chosen randomly and uniformly between the

specified bounds.  The <em>vz</em> or <em>vy</em> value for option <em>vel</em> assigns a

z-velocity (3d) or y-velocity (2d) to each inserted particle.</p>

<p>The <em>id</em> option has two settings which are used to determine the atom

or molecule IDs to assign to inserted particles/molecules.  In both

cases a check is done of the current system to find the maximum

current atom and molecule ID of any existing particle.  Newly inserted

particles and molecules are assigned IDs that increment those max

values.  For the <em>max</em> setting, which is the default, this check is

done at every insertion step, which allows for particles to leave the

system, and their IDs to potentially be re-used.  For the <em>next</em>

setting this check is done only once when the fix is specified, which

can be more efficient if you are sure particles will not be added in

some other way.</p>

<p>The <em>vol</em> option specifies what volume fraction of the insertion

volume will be filled with particles.  For particles with a size

specified by the <em>diam range</em> keyword, they are assumed to all be of

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 <em>dens</em> and <em>vel</em> options enable inserted particles to have a range

of densities or xy velocities.  The specific values for a particular

inserted particle will be chosen randomly and uniformly between the

specified bounds.  Internally, the density value for a particle is

converted to a mass, based on the radius (volume) of the particle.

The <em>vz</em> or <em>vy</em> value for option <em>vel</em> assigns a z-velocity (3d) or

y-velocity (2d) to each inserted particle.</p>

<p>The <em>rate</em> 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>

<div class="admonition note">

<p class="first admonition-title">Note</p>

<p class="last">If you are monitoring the temperature of a system where the

particle count is changing due to adding particles, you typically

should use the <a class="reference internal" href="compute_modify.html"><em>compute_modify dynamic yes</em></a>

command for the temperature compute you are using.</p>

</div>

<p>The <em>ignore</em> option is useful when running a simulation that used line

segment (2d) or triangle (3d) particles, typically to define

boundaries for spherical granular particles to interact with.  See the

<a class="reference internal" href="atom_style.html"><em>atom_style line or tri</em></a> command for details.  Lines

and triangles store their size, and if the size is large it may

overlap (in a spherical sense) with the insertion region, even if the

line/triangle is oriented such that there is no actual overlap.  This

can prevent particles from being inserted.  The <em>ignore</em> keyword

causes the overlap check to skip any line or triangle particles.

Obviously you should only use it if there is in fact no overlap of the

line or triangle particles with the insertion region.</p>

</div>

<hr class="docutils" />

<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">

setting is defined.  If the <em>mol</em> keyword is used, the default for

<em>molfrac</em> is an equal probabilities for all molecules in the template.

Additional option defaults are diam = one 1.0, dens = 1.0 1.0, vol =

0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0.</p>

0.25 50, rate = 0.0, vel = 0.0 0.0 0.0 0.0 0.0 (for 3d), vel = 0.0 0.0 0.0

(for 2d), and id = max.</p>

</div>

</div>