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2
doc/angle_charmm.html
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@ -155,7 +155,7 @@ angle_coeff 1 300.0 107.0 50.0 3.0
<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

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doc/dihedral_charmm.html
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@ -152,9 +152,9 @@ dihedral_coeff 1 120.0 1 60 0.5
<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

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doc/dump_image.html
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@ -155,8 +155,10 @@
<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
@ -421,12 +423,14 @@ lines will be drawn as cylinders with that diameter, e.g. 1.0, which
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>

18
doc/dump_image.txt
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@ -31,8 +31,10 @@ keyword = {atom} or {adiam} or {bond} or {line} or {tri} or {body} or {size} or
{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
@ -317,12 +319,14 @@ is in whatever distance "units"_units.html the input script defines,
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

67
doc/fix_pour.html
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@ -134,11 +134,11 @@
<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
@ -153,12 +153,16 @@
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)
@ -173,6 +177,9 @@
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">
@ -242,6 +249,14 @@ timestep. Particles are inserted again after enough time has elapsed
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>,
@ -257,11 +272,17 @@ or 1.5. 40% of the particles will be small; 60% will be large.</p>
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
@ -274,16 +295,27 @@ particles are inserted, LAMMPS will make up to a 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 <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">
@ -327,7 +359,8 @@ defined by the <a class="reference internal" href="region.html"><em>region</em><
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>

66
doc/fix_pour.txt
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@ -14,11 +14,11 @@ fix ID group-ID pour N type seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
pour = style name of this fix command :l
N = # of atoms to insert :l
type = atom type to assign to inserted atoms (offset for molecule insertion) :l
N = # of particles to insert :l
type = atom type to assign to inserted particles (offset for molecule insertion) :l
seed = random # seed (positive integer) :l
one or more keyword/value pairs may be appended to args :l
keyword = {region} or {diam} or {dens} or {vol} or {rate} or {vel} or {mol} or {rigid} or {shake} :l
keyword = {region} or {diam} or {vol} or {rate} or {dens} or {vel} or {mol} or {rigid} or {shake} or {ignore} :l
{region} value = region-ID
region-ID = ID of region to use as insertion volume
{diam} values = dstyle args
@ -31,12 +31,16 @@ keyword = {region} or {diam} or {dens} or {vol} or {rate} or {vel} or {mol} or {
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)
{id} values = idflag
idflag = {max} or {next} = how to choose IDs for inserted particles and molecules
{vol} 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
{rate} value = V
V = z velocity (3d) or y velocity (2d) at which
insertion volume moves (velocity units)
{dens} values = Rholo Rhohi
Rholo,Rhohi = range of densities for inserted particles (mass/volume units)
{vel} values (3d) = vxlo vxhi vylo vyhi vz
{vel} values (2d) = vxlo vxhi vy
vxlo,vxhi = range of x velocities for inserted particles (velocity units)
@ -50,7 +54,10 @@ keyword = {region} or {diam} or {dens} or {vol} or {rate} or {vel} or {mol} or {
{rigid} value = fix-ID
fix-ID = ID of "fix rigid/small"_fix_rigid.html command
{shake} value = fix-ID
fix-ID = ID of "fix shake"_fix_shake.html command :pre
fix-ID = ID of "fix shake"_fix_shake.html command
{ignore} value = none
skip any line or triangle particles when detecting possible
overlaps with inserted particles :pre
:ule
[Examples:]
@ -128,6 +135,13 @@ 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.
NOTE: If you are monitoring the temperature of a system where the
particle count is changing due to adding particles, you typically
should use the "compute_modify dynamic yes"_compute_modify.html
command for the temperature compute you are using.
:line
All other keywords are optional with defaults as shown below.
The {diam} option is only used when inserting atoms and specifes the
@ -146,11 +160,17 @@ the molecule can be specified in the file read by the
"molecule"_molecule.html command. If not specified, the diameter of
each atom in the molecule has a default diameter of 1.0.
The {dens} and {vel} 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 {vz} or {vy} value for option {vel} assigns a
z-velocity (3d) or y-velocity (2d) to each inserted particle.
The {id} 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 {max} 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 {next}
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.
The {vol} option specifies what volume fraction of the insertion
volume will be filled with particles. For particles with a size
@ -166,14 +186,29 @@ 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 {dens} and {vel} 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 {vz} or {vy} value for option {vel} assigns a z-velocity (3d) or
y-velocity (2d) to each inserted particle.
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.
NOTE: If you are monitoring the temperature of a system where the
particle count is changing due to adding particles, you typically
should use the "compute_modify dynamic yes"_compute_modify.html
command for the temperature compute you are using.
The {ignore} 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
"atom_style line or tri"_atom_style.html 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 {ignore} 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.
:line
@ -225,4 +260,5 @@ Insertions are performed for individual particles, i.e. no {mol}
setting is defined. If the {mol} keyword is used, the default for
{molfrac} 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.
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.

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doc/searchindex.js
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38
doc/set.html
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@ -135,7 +135,7 @@
<li>style = <em>atom</em> or <em>type</em> or <em>mol</em> or <em>group</em> or <em>region</em></li>
<li>ID = atom ID range or type range or mol ID range or group ID or region ID</li>
<li>one or more keyword/value pairs may be appended</li>
<li>keyword = <em>type</em> or <em>type/fraction</em> or <em>mol</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>charge</em> or <em>dipole</em> or <em>dipole/random</em> or <em>quat</em> or <em>quat/random</em> or <em>diameter</em> or <em>shape</em> or <em>length</em> or <em>tri</em> or <em>theta</em> or <em>theta/random</em> or <em>angmom</em> or <em>omega</em> or <em>mass</em> or <em>density</em> or <em>volume</em> or <em>image</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or <em>meso_e</em> or <em>meso_cv</em> or <em>meso_rho</em> or <em>smd_contact_radius</em> or <em>smd_mass_density</em> or <em>i_name</em> or <em>d_name</em></li>
<li>keyword = <em>type</em> or <em>type/fraction</em> or <em>mol</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>charge</em> or <em>dipole</em> or <em>dipole/random</em> or <em>quat</em> or <em>quat/random</em> or <em>diameter</em> or <em>shape</em> or <em>length</em> or <em>tri</em> or <em>theta</em> or <em>theta/random</em> or <em>angmom</em> or <em>omega</em> or <em>mass</em> or <em>density</em> or <em>volume</em> or <em>image</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or <em>meso/e</em> or <em>meso/cv</em> or <em>meso/rho</em> or <em>smd/contact/radius</em> or <em>smd/mass/density</em> or <em>i_name</em> or <em>d_name</em></li>
</ul>
<pre class="literal-block">
<em>type</em> value = atom type
@ -195,15 +195,15 @@
<em>angle</em> value = angle type for all angles between selected atoms
<em>dihedral</em> value = dihedral type for all dihedrals between selected atoms
<em>improper</em> value = improper type for all impropers between selected atoms
<em>meso_e</em> value = energy of SPH particles (need units)
<em>meso/e</em> value = energy of SPH particles (need units)
value can be an atom-style variable (see below)
<em>meso_cv</em> value = heat capacity of SPH particles (need units)
<em>meso/cv</em> value = heat capacity of SPH particles (need units)
value can be an atom-style variable (see below)
<em>meso_rho</em> value = density of SPH particles (need units)
<em>meso/rho</em> value = density of SPH particles (need units)
value can be an atom-style variable (see below)
<em>smd_contact_radius</em> = radius for short range interactions, i.e. contact and friction
<em>smd/contact/radius</em> = radius for short range interactions, i.e. contact and friction
value can be an atom-style variable (see below)
<em>smd_mass_density</em> = set particle mass based on volume by providing a mass density
<em>smd/mass/density</em> = set particle mass based on volume by providing a mass density
value can be an atom-style variable (see below)
<em>i_name</em> value = value for custom integer vector with name
<em>d_name</em> value = value for custom floating-point vector with name
@ -413,18 +413,6 @@ mass is set from the density and triangle area (the input density is
assumed to be in mass/distance^2 units). If none of these cases are
valid, then the mass is set to the density value directly (the input
density is assumed to be in mass units).</p>
<p>Keyword <em>smd_mass_density</em> also sets the mass of all selected
particles, but it is only applicable to the Smooth Mach Dynamics
package USER-SMD. This command assumes that the particle volume has
already been correctly set and calculates particle mass from the
provided mass density value.</p>
<p>Keyword <em>smd_contact_radius</em> only applies to simulations with the
Smooth Mach Dynamics package USER-SMD. This command sets an
interaction radius for computing short-range interactions,
e.g. repulsive forces to prevent different individual physical bodies
from penetrating each other. Note that the SPH smoothing kernel
diameter used for computing long range, nonlocal interactions, is set
using the <em>diameter</em> keyword.</p>
<p>Keyword <em>volume</em> sets the volume of all selected particles.
Currently, only the <a class="reference internal" href="atom_style.html"><em>atom_style peri</em></a> command defines
particles with a volume attribute. Note that this command does not
@ -458,10 +446,22 @@ order for the change to be made. The value of nbondtype (nangletypes,
etc) was set by the <em>bond types</em> (<em>angle types</em>, etc) field in the
header of the data file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
command. These keywords do not allow use of an atom-style variable.</p>
<p>Keywords <em>meso_e</em>, <em>meso_cv</em>, and <em>meso_rho</em> set the energy, heat
<p>Keywords <em>meso/e</em>, <em>meso/cv</em>, and <em>meso/rho</em> set the energy, heat
capacity, and density of smmothed particle hydrodynamics (SPH)
particles. See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to
using SPH in LAMMPS.</p>
<p>Keyword <em>smd/mass/density</em> sets the mass of all selected particles,
but it is only applicable to the Smooth Mach Dynamics package
USER-SMD. It assumes that the particle volume has already been
correctly set and calculates particle mass from the provided mass
density value.</p>
<p>Keyword <em>smd/contact/radius</em> only applies to simulations with the
Smooth Mach Dynamics package USER-SMD. Itsets an interaction radius
for computing short-range interactions, e.g. repulsive forces to
prevent different individual physical bodies from penetrating each
other. Note that the SPH smoothing kernel diameter used for computing
long range, nonlocal interactions, is set using the <em>diameter</em>
keyword.</p>
<p>Keywords <em>i_name</em> and <em>d_name</em> refer to custom integer and
floating-point properties that have been added to each atom via the
<a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> command. When that command

44
doc/set.txt
View File

@ -22,8 +22,8 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{angmom} or {omega} or \
{mass} or {density} or {volume} or {image} or \
{bond} or {angle} or {dihedral} or {improper} or \
{meso_e} or {meso_cv} or {meso_rho} or \
{smd_contact_radius} or {smd_mass_density} or \
{meso/e} or {meso/cv} or {meso/rho} or \
{smd/contact/radius} or {smd/mass/density} or \
{i_name} or {d_name} :l
{type} value = atom type
value can be an atom-style variable (see below)
@ -82,15 +82,15 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{angle} value = angle type for all angles between selected atoms
{dihedral} value = dihedral type for all dihedrals between selected atoms
{improper} value = improper type for all impropers between selected atoms
{meso_e} value = energy of SPH particles (need units)
{meso/e} value = energy of SPH particles (need units)
value can be an atom-style variable (see below)
{meso_cv} value = heat capacity of SPH particles (need units)
{meso/cv} value = heat capacity of SPH particles (need units)
value can be an atom-style variable (see below)
{meso_rho} value = density of SPH particles (need units)
{meso/rho} value = density of SPH particles (need units)
value can be an atom-style variable (see below)
{smd_contact_radius} = radius for short range interactions, i.e. contact and friction
{smd/contact/radius} = radius for short range interactions, i.e. contact and friction
value can be an atom-style variable (see below)
{smd_mass_density} = set particle mass based on volume by providing a mass density
{smd/mass/density} = set particle mass based on volume by providing a mass density
value can be an atom-style variable (see below)
{i_name} value = value for custom integer vector with name
{d_name} value = value for custom floating-point vector with name :pre
@ -333,20 +333,6 @@ assumed to be in mass/distance^2 units). If none of these cases are
valid, then the mass is set to the density value directly (the input
density is assumed to be in mass units).
Keyword {smd_mass_density} also sets the mass of all selected
particles, but it is only applicable to the Smooth Mach Dynamics
package USER-SMD. This command assumes that the particle volume has
already been correctly set and calculates particle mass from the
provided mass density value.
Keyword {smd_contact_radius} only applies to simulations with the
Smooth Mach Dynamics package USER-SMD. This command sets an
interaction radius for computing short-range interactions,
e.g. repulsive forces to prevent different individual physical bodies
from penetrating each other. Note that the SPH smoothing kernel
diameter used for computing long range, nonlocal interactions, is set
using the {diameter} keyword.
Keyword {volume} sets the volume of all selected particles.
Currently, only the "atom_style peri"_atom_style.html command defines
particles with a volume attribute. Note that this command does not
@ -384,11 +370,25 @@ etc) was set by the {bond types} ({angle types}, etc) field in the
header of the data file read by the "read_data"_read_data.html
command. These keywords do not allow use of an atom-style variable.
Keywords {meso_e}, {meso_cv}, and {meso_rho} set the energy, heat
Keywords {meso/e}, {meso/cv}, and {meso/rho} set the energy, heat
capacity, and density of smmothed particle hydrodynamics (SPH)
particles. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to
using SPH in LAMMPS.
Keyword {smd/mass/density} sets the mass of all selected particles,
but it is only applicable to the Smooth Mach Dynamics package
USER-SMD. It assumes that the particle volume has already been
correctly set and calculates particle mass from the provided mass
density value.
Keyword {smd/contact/radius} only applies to simulations with the
Smooth Mach Dynamics package USER-SMD. Itsets an interaction radius
for computing short-range interactions, e.g. repulsive forces to
prevent different individual physical bodies from penetrating each
other. Note that the SPH smoothing kernel diameter used for computing
long range, nonlocal interactions, is set using the {diameter}
keyword.
Keywords {i_name} and {d_name} refer to custom integer and
floating-point properties that have been added to each atom via the
"fix property/atom"_fix_property_atom.html command. When that command