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18
doc/compute_chunk_atom.html
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@ -171,7 +171,7 @@ style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>bin/sphere<
</pre>
<ul class="simple">
<li>zero or more keyword/values pairs may be appended</li>
<li>keyword = <em>region</em> or <em>nchunk</em> or <em>static</em> or <em>compress</em> or <em>bound</em> or <em>discard</em> or <em>units</em></li>
<li>keyword = <em>region</em> or <em>nchunk</em> or <em>static</em> or <em>compress</em> or <em>bound</em> or <em>discard</em> or <em>pbc</em> or <em>units</em></li>
</ul>
<pre class="literal-block">
<em>region</em> value = region-ID
@ -198,6 +198,8 @@ style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>bin/sphere<
x/y/z = <em>x</em> or <em>y</em> or <em>z</em> to bound sptial bins in this dimension
lo = <em>lower</em> or coordinate value (distance units)
hi = <em>upper</em> or coordinate value (distance units)
<em>pbc</em> value = <em>no</em> or <em>yes</em>
yes = use periodic distance for bin/sphere and bin/cylinder styles
<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>reduced</em>
</pre>
</div>
@ -616,6 +618,19 @@ value, which is assumed to be inside (or at least near) the simulation
box boundaries, though LAMMPS does not check for this. Note that
using the <em>bound</em> keyword typically reduces the total number of bins
and thus the number of chunks <em>Nchunk</em>.</p>
<p>The <em>pbc</em> keyword only applies to the <em>bin/sphere</em> and <em>bin/cylinder</em>
styles. If set to <em>yes</em>, the distance an atom is from the sphere
origin or cylinder axis is calculated in a minimum image sense with
respect to periodic dimensions, when determining which bin the atom is
in. I.e. if x is a periodic dimension and the distance between the
atom and the sphere center in the x dimension is greater than 0.5 *
simulation box length in x, then a box length is subtracted to give a
distance &lt; 0.5 * simulation box length. This allosws the sphere or
cylinder center to be near a box edge, and atoms on the other side of
the periodic box will still be close to the center point/axis. Note
that with a setting of <em>yes</em>, the outer sphere or cylinder radius must
also be &lt;= 0.5 * simulation box length in any periodic dimension
except for the cylinder axis dimension, or an error is generated.</p>
<p>The <em>units</em> keyword only applies to the <em>binning</em> styles; otherwise it
is ignored. For the <em>bin/1d</em>, <em>bin/2d</em>, <em>bin/3d</em> styles, it
determines the meaning of the distance units used for the bin sizes
@ -683,6 +698,7 @@ the restarted simulation begins.</p>
<li>discard = yes, for all styles except binning</li>
<li>discard = mixed, for binning styles</li>
<li>bound = lower and upper in all dimensions</li>
<li>pbc = no</li>
<li>units = lattice</li>
</ul>
</div>

19
doc/compute_chunk_atom.txt
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@ -48,7 +48,7 @@ style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule}
v_name = per-atom vector calculated by an atom-style variable with name :pre
zero or more keyword/values pairs may be appended :l
keyword = {region} or {nchunk} or {static} or {compress} or {bound} or {discard} or {units} :l
keyword = {region} or {nchunk} or {static} or {compress} or {bound} or {discard} or {pbc} or {units} :l
{region} value = region-ID
region-ID = ID of region atoms must be in to be part of a chunk
{nchunk} value = {once} or {every}
@ -73,6 +73,8 @@ keyword = {region} or {nchunk} or {static} or {compress} or {bound} or {discard}
x/y/z = {x} or {y} or {z} to bound sptial bins in this dimension
lo = {lower} or coordinate value (distance units)
hi = {upper} or coordinate value (distance units)
{pbc} value = {no} or {yes}
yes = use periodic distance for bin/sphere and bin/cylinder styles
{units} value = {box} or {lattice} or {reduced} :pre
:ule
@ -570,6 +572,20 @@ box boundaries, though LAMMPS does not check for this. Note that
using the {bound} keyword typically reduces the total number of bins
and thus the number of chunks {Nchunk}.
The {pbc} keyword only applies to the {bin/sphere} and {bin/cylinder}
styles. If set to {yes}, the distance an atom is from the sphere
origin or cylinder axis is calculated in a minimum image sense with
respect to periodic dimensions, when determining which bin the atom is
in. I.e. if x is a periodic dimension and the distance between the
atom and the sphere center in the x dimension is greater than 0.5 *
simulation box length in x, then a box length is subtracted to give a
distance < 0.5 * simulation box length. This allosws the sphere or
cylinder center to be near a box edge, and atoms on the other side of
the periodic box will still be close to the center point/axis. Note
that with a setting of {yes}, the outer sphere or cylinder radius must
also be <= 0.5 * simulation box length in any periodic dimension
except for the cylinder axis dimension, or an error is generated.
The {units} keyword only applies to the {binning} styles; otherwise it
is ignored. For the {bin/1d}, {bin/2d}, {bin/3d} styles, it
determines the meaning of the distance units used for the bin sizes
@ -645,4 +661,5 @@ compress = no
discard = yes, for all styles except binning
discard = mixed, for binning styles
bound = lower and upper in all dimensions
pbc = no
units = lattice :ul

19
doc/compute_saed.html
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@ -169,7 +169,7 @@ fix saed/vtk 1 1 1 c_2 file Ni_000.saed
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates electron diffraction intensity as
described in <a class="reference internal" href="fix_saed_vtk.html#coleman"><span>(Coleman)</span></a> on a mesh of reciprocal lattice nodes
described in <a class="reference internal" href="compute_xrd.html#coleman"><span>(Coleman)</span></a> on a mesh of reciprocal lattice nodes
defined by the entire simulation domain (or manually) using simulated
radiation of wavelength lambda.</p>
<p>The electron diffraction intensity I at each reciprocal lattice point
@ -212,13 +212,14 @@ the <em>Kmax</em>, <em>Zone</em>, and <em>dR_Ewald</em> parameters. The rectili
created about the origin of reciprocal space is terminated at the
boundary of a sphere of radius <em>Kmax</em> centered at the origin. If
<em>Zone</em> parameters z1=z2=z3=0 are used, diffraction intensities are
computed throughout the entire spherical volume - note this can greatly
increase the cost of computation. Otherwise, <em>Zone</em> parameters will
denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an
intersecting Ewald sphere. Diffraction intensities will only be
computed at the intersection of the reciprocal lattice mesh and a
<em>dR_Ewald</em> thick surface of the Ewald sphere. See the example 3D
intestiety data and the intersection of a [010] zone axis in the below image.</p>
computed throughout the entire spherical volume - note this can
greatly increase the cost of computation. Otherwise, <em>Zone</em>
parameters will denote the z1=h, z2=k, and z3=l (in a global since)
zone axis of an intersecting Ewald sphere. Diffraction intensities
will only be computed at the intersection of the reciprocal lattice
mesh and a <em>dR_Ewald</em> thick surface of the Ewald sphere. See the
example 3D intestiety data and the intersection of a [010] zone axis
in the below image.</p>
<a data-lightbox="group-default"
href="_images/saed_ewald_intersect.jpg"
class=""
@ -279,6 +280,8 @@ options.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-DIFFRACTION package. It is only
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>The compute_saed command does not work for triclinic cells.</p>
</div>
<div class="section" id="related-commands">

29
doc/compute_saed.txt
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@ -82,18 +82,19 @@ it can reduce the likelihood that Bragg reflections will be satisfied
unless small spacing parameters <0.05 Angstrom^(-1) are implemented.
Meshes with manual spacing do not require a periodic boundary.
The limits of the reciprocal lattice mesh are determined by the use of
the {Kmax}, {Zone}, and {dR_Ewald} parameters. The rectilinear mesh
created about the origin of reciprocal space is terminated at the
boundary of a sphere of radius {Kmax} centered at the origin. If
{Zone} parameters z1=z2=z3=0 are used, diffraction intensities are
computed throughout the entire spherical volume - note this can greatly
increase the cost of computation. Otherwise, {Zone} parameters will
denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an
intersecting Ewald sphere. Diffraction intensities will only be
computed at the intersection of the reciprocal lattice mesh and a
{dR_Ewald} thick surface of the Ewald sphere. See the example 3D
intestiety data and the intersection of a \[010\] zone axis in the below image.
The limits of the reciprocal lattice mesh are determined by the use of
the {Kmax}, {Zone}, and {dR_Ewald} parameters. The rectilinear mesh
created about the origin of reciprocal space is terminated at the
boundary of a sphere of radius {Kmax} centered at the origin. If
{Zone} parameters z1=z2=z3=0 are used, diffraction intensities are
computed throughout the entire spherical volume - note this can
greatly increase the cost of computation. Otherwise, {Zone}
parameters will denote the z1=h, z2=k, and z3=l (in a global since)
zone axis of an intersecting Ewald sphere. Diffraction intensities
will only be computed at the intersection of the reciprocal lattice
mesh and a {dR_Ewald} thick surface of the Ewald sphere. See the
example 3D intestiety data and the intersection of a \[010\] zone axis
in the below image.
:c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg)
@ -151,6 +152,10 @@ All array values calculated by this compute are "intensive".
[Restrictions:]
This compute is part of the USER-DIFFRACTION package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
The compute_saed command does not work for triclinic cells.
[Related commands:]

10
doc/compute_xrd.html
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@ -167,7 +167,7 @@ fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2T
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Define a computation that calculates x-ray diffraction intensity as described
in <a class="reference internal" href="fix_saed_vtk.html#coleman"><span>(Coleman)</span></a> on a mesh of reciprocal lattice nodes defined
in <a class="reference internal" href="#coleman"><span>(Coleman)</span></a> on a mesh of reciprocal lattice nodes defined
by the entire simulation domain (or manually) using a simulated radiation
of wavelength lambda.</p>
<p>The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
@ -297,13 +297,15 @@ which by the mesh. The global array has 2 columns.</p>
<p>The first column contains the diffraction angle in the units (radians
or degrees) provided with the <em>2Theta</em> values. The second column contains
the computed diffraction intensities as described above.</p>
<p>The array can be accessed by any command that uses global values
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The array can be accessed by any command that uses global values from
a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a>
for an overview of LAMMPS output options.</p>
<p>All array values calculated by this compute are &#8220;intensive&#8221;.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This compute is part of the USER-DIFFRACTION package. It is only
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>The compute_xrd command does not work for triclinic cells.</p>
</div>
<div class="section" id="related-commands">

10
doc/compute_xrd.txt
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@ -163,14 +163,18 @@ The first column contains the diffraction angle in the units (radians
or degrees) provided with the {2Theta} values. The second column contains
the computed diffraction intensities as described above.
The array can be accessed by any command that uses global values
from a compute as input. See "this section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The array can be accessed by any command that uses global values from
a compute as input. See "this section"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
All array values calculated by this compute are "intensive".
[Restrictions:]
This compute is part of the USER-DIFFRACTION package. It is only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
The compute_xrd command does not work for triclinic cells.
[Related commands:]

34
doc/fix_store_state.html
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@ -138,10 +138,10 @@
<li>input = one or more atom attributes</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre>possible attributes = id, mol, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
radius, omegax, omegay, omegaz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
c_ID, c_ID[N], f_ID, f_ID[N], v_name,
d_name, i_name
@ -154,12 +154,14 @@ mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
xsu,ysu,zsu = scaled unwrapped atom coordinates
ix,iy,iz = box image that the atom is in
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
radius = radius of spherical particle
mu = magnitued of dipole moment of atom
radius,diameter = radius.diameter of spherical particle
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
@ -195,25 +197,23 @@ time the fix is defined. If <em>N</em> is 0, then the values are never
updated, so this is a way of archiving an atom attribute at a given
time for future use in a calculation or output. See the discussion of
<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a> that take fixes as
inputs. And see for example, the <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a>, <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a>, <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>,
and <a class="reference internal" href="variable.html"><em>atom-style variable</em></a> commands.</p>
inputs.</p>
<p>If <em>N</em> is not zero, then the attributes will be updated every <em>N</em>
steps.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Actually, only atom attributes specified by keywords like <em>xu</em>
or <em>vy</em> are initially stored immediately at the point in your input
script when the fix is defined. Attributes specified by a compute,
fix, or variable are not initially stored until the first run
following the fix definition begins. This is because calculating
those attributes may require quantities that are not defined in
between runs.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Actually, only atom attributes specified by keywords
like <em>xu</em> or <em>vy</em> or <em>radius</em> are initially stored immediately at the
point in your input script when the fix is defined. Attributes
specified by a compute, fix, or variable are not initially stored
until the first run following the fix definition begins. This is
because calculating those attributes may require quantities that are
not defined in between runs.</p>
</div>
<p>The list of possible attributes is the same as that used by the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command, which describes their meaning.</p>
<p>If the <em>com</em> keyword is set to <em>yes</em> then the <em>xu</em>, <em>yu</em>, and <em>zu</em>
inputs store the position of each atom relative to the center-of-mass
of the group of atoms, instead of storing the absolute position. This
option is used by the <a class="reference internal" href="compute_msd.html"><em>compute msd</em></a> command.</p>
of the group of atoms, instead of storing the absolute position.</p>
<p>The requested values are stored in a per-atom vector or array as
discussed below. Zeroes are stored for atoms not in the specified
group.</p>

32
doc/fix_store_state.txt
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@ -17,10 +17,10 @@ store/state = style name of this fix command :l
N = store atom attributes every N steps, N = 0 for initial store only :l
input = one or more atom attributes :l
possible attributes = id, mol, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
radius, omegax, omegay, omegaz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name,
d_name, i_name :pre
@ -32,12 +32,14 @@ input = one or more atom attributes :l
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
xu,yu,zu = unwrapped atom coordinates
xsu,ysu,zsu = scaled unwrapped atom coordinates
ix,iy,iz = box image that the atom is in
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
radius = radius of spherical particle
mu = magnitued of dipole moment of atom
radius,diameter = radius.diameter of spherical particle
omegax,omegay,omegaz = angular velocity of spherical particle
angmomx,angmomy,angmomz = angular momentum of aspherical particle
tqx,tqy,tqz = torque on finite-size particles
@ -67,29 +69,25 @@ time the fix is defined. If {N} is 0, then the values are never
updated, so this is a way of archiving an atom attribute at a given
time for future use in a calculation or output. See the discussion of
"output commands"_Section_howto.html#howto_15 that take fixes as
inputs. And see for example, the "compute
reduce"_compute_reduce.html, "fix ave/atom"_fix_ave_atom.html, "fix
ave/histo"_fix_ave_histo.html, "fix ave/spatial"_fix_ave_spatial.html,
and "atom-style variable"_variable.html commands.
inputs.
If {N} is not zero, then the attributes will be updated every {N}
steps.
NOTE: Actually, only atom attributes specified by keywords like {xu}
or {vy} are initially stored immediately at the point in your input
script when the fix is defined. Attributes specified by a compute,
fix, or variable are not initially stored until the first run
following the fix definition begins. This is because calculating
those attributes may require quantities that are not defined in
between runs.
IMPORTANT NOTE: Actually, only atom attributes specified by keywords
like {xu} or {vy} or {radius} are initially stored immediately at the
point in your input script when the fix is defined. Attributes
specified by a compute, fix, or variable are not initially stored
until the first run following the fix definition begins. This is
because calculating those attributes may require quantities that are
not defined in between runs.
The list of possible attributes is the same as that used by the "dump
custom"_dump.html command, which describes their meaning.
If the {com} keyword is set to {yes} then the {xu}, {yu}, and {zu}
inputs store the position of each atom relative to the center-of-mass
of the group of atoms, instead of storing the absolute position. This
option is used by the "compute msd"_compute_msd.html command.
of the group of atoms, instead of storing the absolute position.
The requested values are stored in a per-atom vector or array as
discussed below. Zeroes are stored for atoms not in the specified

2
doc/searchindex.js
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45
doc/set.html
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@ -139,7 +139,7 @@
<li><p class="first">one or more keyword/value pairs may be appended</p>
</li>
<li><dl class="first docutils">
<dt>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>angmom</em> or <em>omega</em> or <em>mass</em> or <em>density</em> or <em>volume</em> or <em>image</em> or</dt>
<dt>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</dt>
<dd><p class="first last"><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></p>
</dd>
@ -184,6 +184,8 @@
<em>theta</em> value = angle (degrees)
angle = orientation of line segment with respect to x-axis
angle can be an atom-style variable (see below)
<em>theta/random</em> value = seed
seed = random # seed (positive integer) for line segment orienations
<em>angmom</em> values = Lx Ly Lz
Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
any of Lx,Ly,Lz can be an atom-style variable (see below)
@ -318,19 +320,20 @@ vector to set as the orientation of the dipole moment vectors of the
selected atoms. The magnitude of the dipole moment is set
by the length of this orientation vector.</p>
<p>Keyword <em>dipole/random</em> randomizes the orientation of the dipole
moment vectors of the selected atoms and sets the magnitude of each to
the specified <em>Dlen</em> value. For 2d systems, the z component of the
moment vectors for the selected atoms and sets the magnitude of each
to the specified <em>Dlen</em> value. For 2d systems, the z component of the
orientation is set to 0.0. Random numbers are used in such a way that
the orientation of a particular atom is the same, regardless of how
many processors are being used. This keyword does not allow use of an
atom-style variable.</p>
<p>Keyword <em>quat</em> uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms. The
particles must be ellipsoids as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> command or triangles as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> command. Note that particles defined
by <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> have 3 shape parameters.
The 3 values must be non-zero for each particle set by this command.
They are used to specify the aspect ratios of an ellipsoidal particle,
particles must define a quaternion for their orientation
(e.g. ellipsoids, triangles, body particles) as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a> command. Note that particles defined by
<a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> have 3 shape parameters. The 3
values must be non-zero for each particle set by this command. They
are used to specify the aspect ratios of an ellipsoidal particle,
which is oriented by default with its x-axis along the simulation
box&#8217;s x-axis, and similarly for y and z. If this body is rotated (via
the right-hand rule) by an angle theta around a unit rotation vector
@ -340,16 +343,16 @@ c*sin(theta/2)). The theta and a,b,c values are the arguments to the
<em>quat</em> keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
not specified as a unit vector. For 2d systems, the a,b,c values are
ignored, since a rotation vector of (0,0,1) is the only valid choice.</p>
<p>Keyword <em>quat/random</em> randomizes the orientation of the quaternion of
the selected atoms. The particles must be ellipsoids as defined by
the <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> command or triangles as
defined by the <a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> command. Random
numbers are used in such a way that the orientation of a particular
atom is the same, regardless of how many processors are being used.
For 2d systems, only orientations in the xy plane are generated. As
with keyword <em>quat</em>, for ellipsoidal particles, the 3 shape values
must be non-zero for each particle set by this command. This keyword
does not allow use of an atom-style variable.</p>
<p>Keyword <em>quat/random</em> randomizes the orientation of the quaternion for
the selected atoms. The particles must define a quaternion for their
orientation (e.g. ellipsoids, triangles, body particles) as defined by
the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> command. Random numbers are used in
such a way that the orientation of a particular atom is the same,
regardless of how many processors are being used. For 2d systems,
only orientations in the xy plane are generated. As with keyword
<em>quat</em>, for ellipsoidal particles, the 3 shape values must be non-zero
for each particle set by this command. This keyword does not allow
use of an atom-style variable.</p>
<p>Keyword <em>diameter</em> sets the size of the selected atoms. The particles
must be finite-size spheres as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a> command. The diameter of a particle can be
set to 0.0, which means they will be treated as point particles. Note
@ -385,6 +388,12 @@ density, e.g. via the <a class="reference internal" href="read_data.html"><em>re
<p>Keyword <em>theta</em> sets the orientation of selected atoms. The particles
must be line segments as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style line</em></a> command. The specified value is used to set the
orientation angle of the line segments with respect to the x axis.</p>
<p>Keyword <em>theta/random</em> randomizes the orientation of theta for the
selected atoms. The particles must be line segments as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style line</em></a> command. Random numbers are used in
such a way that the orientation of a particular atom is the same,
regardless of how many processors are being used. This keyword does
not allow use of an atom-style variable.</p>
<p>Keyword <em>angmom</em> sets the angular momentum of selected atoms. The
particles must be ellipsoids as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> command or triangles as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> command. The angular momentum vector

47
doc/set.txt
View File

@ -18,7 +18,7 @@ one or more keyword/value pairs may be appended :l
keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{charge} or {dipole} or {dipole/random} or {quat} or \
{quat/random} or {diameter} or {shape} or \
{length} or {tri} or {theta} or {angmom} or {omega} or \
{length} or {tri} or {theta} or {theta/random} 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 \
@ -61,6 +61,8 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{theta} value = angle (degrees)
angle = orientation of line segment with respect to x-axis
angle can be an atom-style variable (see below)
{theta/random} value = seed
seed = random # seed (positive integer) for line segment orienations
{angmom} values = Lx Ly Lz
Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
any of Lx,Ly,Lz can be an atom-style variable (see below)
@ -209,8 +211,8 @@ selected atoms. The magnitude of the dipole moment is set
by the length of this orientation vector.
Keyword {dipole/random} randomizes the orientation of the dipole
moment vectors of the selected atoms and sets the magnitude of each to
the specified {Dlen} value. For 2d systems, the z component of the
moment vectors for the selected atoms and sets the magnitude of each
to the specified {Dlen} value. For 2d systems, the z component of the
orientation is set to 0.0. Random numbers are used in such a way that
the orientation of a particular atom is the same, regardless of how
many processors are being used. This keyword does not allow use of an
@ -218,12 +220,12 @@ atom-style variable.
Keyword {quat} uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms. The
particles must be ellipsoids as defined by the "atom_style
ellipsoid"_atom_style.html command or triangles as defined by the
"atom_style tri"_atom_style.html command. Note that particles defined
by "atom_style ellipsoid"_atom_style.html have 3 shape parameters.
The 3 values must be non-zero for each particle set by this command.
They are used to specify the aspect ratios of an ellipsoidal particle,
particles must define a quaternion for their orientation
(e.g. ellipsoids, triangles, body particles) as defined by the
"atom_style"_atom_style.html command. Note that particles defined by
"atom_style ellipsoid"_atom_style.html have 3 shape parameters. The 3
values must be non-zero for each particle set by this command. They
are used to specify the aspect ratios of an ellipsoidal particle,
which is oriented by default with its x-axis along the simulation
box's x-axis, and similarly for y and z. If this body is rotated (via
the right-hand rule) by an angle theta around a unit rotation vector
@ -234,16 +236,16 @@ c*sin(theta/2)). The theta and a,b,c values are the arguments to the
not specified as a unit vector. For 2d systems, the a,b,c values are
ignored, since a rotation vector of (0,0,1) is the only valid choice.
Keyword {quat/random} randomizes the orientation of the quaternion of
the selected atoms. The particles must be ellipsoids as defined by
the "atom_style ellipsoid"_atom_style.html command or triangles as
defined by the "atom_style tri"_atom_style.html command. Random
numbers are used in such a way that the orientation of a particular
atom is the same, regardless of how many processors are being used.
For 2d systems, only orientations in the xy plane are generated. As
with keyword {quat}, for ellipsoidal particles, the 3 shape values
must be non-zero for each particle set by this command. This keyword
does not allow use of an atom-style variable.
Keyword {quat/random} randomizes the orientation of the quaternion for
the selected atoms. The particles must define a quaternion for their
orientation (e.g. ellipsoids, triangles, body particles) as defined by
the "atom_style"_atom_style.html command. Random numbers are used in
such a way that the orientation of a particular atom is the same,
regardless of how many processors are being used. For 2d systems,
only orientations in the xy plane are generated. As with keyword
{quat}, for ellipsoidal particles, the 3 shape values must be non-zero
for each particle set by this command. This keyword does not allow
use of an atom-style variable.
Keyword {diameter} sets the size of the selected atoms. The particles
must be finite-size spheres as defined by the "atom_style
@ -288,6 +290,13 @@ Keyword {theta} sets the orientation of selected atoms. The particles
must be line segments as defined by the "atom_style
line"_atom_style.html command. The specified value is used to set the
orientation angle of the line segments with respect to the x axis.
Keyword {theta/random} randomizes the orientation of theta for the
selected atoms. The particles must be line segments as defined by the
"atom_style line"_atom_style.html command. Random numbers are used in
such a way that the orientation of a particular atom is the same,
regardless of how many processors are being used. This keyword does
not allow use of an atom-style variable.
Keyword {angmom} sets the angular momentum of selected atoms. The
particles must be ellipsoids as defined by the "atom_style